# Date 2011-01-13 Time 17:48:55 EST -0500 (1294958935.99 s) #phil __OFF__ Command line arguments: "/Users/nick/k94e_208/.phenix/project_data/refine_48.eff" "--overwrite" USER = nick PID = 4769 ------------------------------------------------------------------------------- PHENIX: Python-based Hierarchical ENvironment for Integrated Xtallography Version: 1.7 Release tag: 637 Platform: mac-intel-osx-x86_64 osx-10.6.6 User: nick ------------------------------------------------------------------------------- phenix.refine: Macromolecular Structure Refinement ------------------------------------------------------------------------------- Phenix developers include: Paul Adams, Pavel Afonine, Vincent Chen, Ian Davis, Nathaniel Echols, Kreshna Gopal, Ralf Grosse-Kunstleve, Jeffrey Headd, Li-Wei Hung, Robert Immormino, Tom Ioerger, Airlie McCoy, Erik McKee, Nigel Moriarty, Reetal Pai, Randy Read, Jane Richardson, David Richardson, Tod Romo, Jim Sacchettini, Nicholas Sauter, Jacob Smith, Laurent Storoni, Tom Terwilliger, Peter Zwart Phenix home page: http://www.phenix-online.org/ ------------------------------------------------------------------------------- ------------------------------------------------------------------------------- Phenix components are copyrighted by: - Lawrence Berkeley National Laboratory - Los Alamos National Laboratory - University of Cambridge - Duke University - Texas Agricultural Experiment Station & Texas Engineering Experiment Station ------------------------------------------------------------------------------- ------------------------------------------------------------------------------- Major third-party components of Phenix include: Python, wxWidgets, wxPython, Boost, SCons, Clipper, CCP4 Monomer Library, CCP4 I/O libraries, PyCifRW, FFTPACK, L-BFGS, MUSCLE, KSDSSP, PULCHRA, ANTLRv3 Enter phenix.acknowledgments for details. ------------------------------------------------------------------------------- Processing inputs. This may take a minute or two. Working crystal symmetry after inspecting all inputs: Unit cell: (88.66, 151.07, 88.74, 90, 107.01, 90) Space group: P 1 21 1 (No. 4) Monomer Library directory: "/usr/local/phenix-1.7-637/chem_data/mon_lib" Total number of atoms: 14331 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 3384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3384 Unusual residues: {'UPG': 1} Classifications: {'undetermined': 1, 'peptide': 430} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 414, None: 1, 'PCIS': 1} Not linked: pdbres="VAL A 466 " pdbres="UPG A 501 " Chain breaks: 3 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "B" Number of atoms: 3409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3409 Unusual residues: {'UPG': 1} Classifications: {'undetermined': 1, 'peptide': 432} Link IDs: {'PTRANS': 14, 'TRANS': 416, None: 1, 'PCIS': 1} Not linked: pdbres="LYS B 465 " pdbres="UPG B 501 " Chain breaks: 3 Chain: "C" Number of atoms: 3324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3324 Classifications: {'peptide': 428} Link IDs: {'PTRANS': 14, 'TRANS': 412, 'PCIS': 1} Chain breaks: 4 Chain: "C" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'UPG': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 3338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3338 Classifications: {'peptide': 430} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 413, 'PCIS': 1} Chain breaks: 4 Chain: "D" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'UPG': 1} Classifications: {'undetermined': 1} Chain: "S" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 804, 804 Classifications: {'water': 804} Link IDs: {None: 803} Time building chain proxies: 8.05, per 1000 atoms: 0.56 Number of scatterers: 14331 At special positions: 0 Unit cell: (88.66, 151.07, 88.74, 90, 107.01, 90) Space group: P 1 21 1 (No. 4) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 73 16.00 P 8 15.00 O 3389 8.00 N 2315 7.00 C 8546 6.00 sf(0) = scattering factor at diffraction angle 0. ================================== X-ray data ================================= F-obs: /Users/nick/k94e_208/Refine_30M/k94e_2_refine_data.mtz:F-obs,SIGF-obs R-free flags: /Users/nick/k94e_208/Refine_30M/k94e_2_refine_data.mtz:R-free-flags Miller array info: /Users/nick/k94e_208/Refine_30M/k94e_2_refine_data.mtz:F-obs,SIGF-obs Observation type: xray.amplitude Type of data: double, size=131093 Type of sigmas: double, size=131093 Number of Miller indices: 131093 Anomalous flag: False Unit cell: (88.66, 151.07, 88.74, 90, 107.01, 90) Space group: P 1 21 1 (No. 4) Systematic absences: 0 Centric reflections: 2068 Resolution range: 43.3056 2.08007 Completeness in resolution range: 0.980963 Completeness with d_max=infinity: 0.980861 Number of F-obs in resolution range: 131093 Number of F-obs<0 (these reflections will be rejected): 0 Number of F-obs=0 (these reflections will be used in refinement): 0 Refinement resolution range: d_max = 43.3056 d_min = 2.0801 Miller array info: /Users/nick/k94e_208/Refine_30M/k94e_2_refine_data.mtz:R-free-flags Observation type: None Type of data: int, size=133637 Type of sigmas: None Number of Miller indices: 133637 Anomalous flag: False Unit cell: (88.66, 151.07, 88.74, 90, 107.01, 90) Space group: P 1 21 1 (No. 4) Systematic absences: 0 Centric reflections: 2727 Resolution range: 43.3056 2.08007 Completeness in resolution range: 1 Completeness with d_max=infinity: 0.999895 Test (R-free flags) flag value: 0 Number of work/free reflections by resolution: work free %free bin 1: 43.3150 - 4.4799 [13279/13507] 12596 683 5.1% bin 2: 4.4799 - 3.5563 [13101/13398] 12409 692 5.3% bin 3: 3.5563 - 3.1069 [13118/13380] 12458 660 5.0% bin 4: 3.1069 - 2.8229 [13190/13380] 12553 637 4.8% bin 5: 2.8229 - 2.6206 [13122/13311] 12438 684 5.2% bin 6: 2.6206 - 2.4661 [13113/13323] 12477 636 4.9% bin 7: 2.4661 - 2.3426 [13126/13313] 12457 669 5.1% bin 8: 2.3426 - 2.2407 [13150/13351] 12490 660 5.0% bin 9: 2.2407 - 2.1544 [13085/13296] 12420 665 5.1% bin 10: 2.1544 - 2.0801 [12809/13378] 12177 632 4.9% overall 124475 6618 5.0% Writing MTZ file: /Users/nick/k94e_208/Refine_48/k94e_2_refine_data.mtz ============================== Scattering factors ============================= ----------X-ray scattering dictionary---------- Number of scattering types: 5 Type Number sf(0) Gaussians S 73 15.96 2 P 8 14.95 2 O 3389 7.97 2 N 2315 6.97 2 C 8546 5.97 2 sf(0) = scattering factor at diffraction angle 0. ========================== Anomalous scatterer groups ========================= All atoms refined with f_prime=0 and f_double_prime=0. ======================== Summary of geometry restraints ======================= Number of disulfides: simple=0, symmetry=0 Time building geometry restraints manager: 0.49 seconds NOTE: a complete listing of the restaints can be found in the .geo file. Histogram of bond lengths: 0.75 - 0.97: 2 0.97 - 1.20: 2 1.20 - 1.42: 5536 1.42 - 1.64: 8125 1.64 - 1.86: 100 Bond restraints: 13765 Sorted by residual: bond pdb=" C ALA D 138 " pdb=" N SER D 139 " ideal model delta sigma weight residual 1.329 0.751 0.578 1.40e-02 5.10e+03 1.71e+03 bond pdb=" C GLU C 138 " pdb=" N SER C 139 " ideal model delta sigma weight residual 1.329 0.896 0.433 1.40e-02 5.10e+03 9.56e+02 bond pdb=" CE1 PHE D 144 " pdb=" CZ PHE D 144 " ideal model delta sigma weight residual 1.382 1.274 0.108 3.00e-02 1.11e+03 1.30e+01 bond pdb=" CD ARG C 65 " pdb=" NE ARG C 65 " ideal model delta sigma weight residual 1.460 1.410 0.050 1.80e-02 3.09e+03 7.61e+00 bond pdb=" CA ILE C 140 " pdb=" C ILE C 140 " ideal model delta sigma weight residual 1.525 1.582 -0.057 2.10e-02 2.27e+03 7.48e+00 ... (remaining 13760 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.21: 18279 3.21 - 6.41: 331 6.41 - 9.62: 24 9.62 - 12.82: 6 12.82 - 16.03: 3 Bond angle restraints: 18643 Sorted by residual: angle pdb=" C ALA D 138 " pdb=" N SER D 139 " pdb=" CA SER D 139 " ideal model delta sigma weight residual 121.70 137.73 -16.03 1.80e+00 3.09e-01 7.93e+01 angle pdb=" O ALA D 138 " pdb=" C ALA D 138 " pdb=" N SER D 139 " ideal model delta sigma weight residual 123.00 109.12 13.88 1.60e+00 3.91e-01 7.52e+01 angle pdb=" CD ARG C 65 " pdb=" NE ARG C 65 " pdb=" CZ ARG C 65 " ideal model delta sigma weight residual 124.20 136.43 -12.23 1.50e+00 4.44e-01 6.65e+01 angle pdb=" O GLU C 138 " pdb=" C GLU C 138 " pdb=" N SER C 139 " ideal model delta sigma weight residual 123.00 112.62 10.38 1.60e+00 3.91e-01 4.21e+01 angle pdb=" C ILE D 143 " pdb=" CA ILE D 143 " pdb=" CB ILE D 143 " ideal model delta sigma weight residual 109.10 95.33 13.77 2.20e+00 2.07e-01 3.92e+01 ... (remaining 18638 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.63: 4886 35.63 - 71.26: 197 71.26 - 106.89: 11 106.89 - 142.52: 0 142.52 - 178.16: 4 Dihedral angle restraints: 5098 sinusoidal: 3348 harmonic: 1750 Sorted by residual: dihedral pdb=" C2 UPG C 501 " pdb=" N1 UPG C 501 " pdb=" C1* UPG C 501 " pdb=" C2* UPG C 501 " ideal model delta sinusoidal sigma weight residual -55.88 122.28 -178.16 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C2 UPG B 501 " pdb=" N1 UPG B 501 " pdb=" C1* UPG B 501 " pdb=" C2* UPG B 501 " ideal model delta sinusoidal sigma weight residual -55.88 121.03 -176.91 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C2 UPG D 501 " pdb=" N1 UPG D 501 " pdb=" C1* UPG D 501 " pdb=" C2* UPG D 501 " ideal model delta sinusoidal sigma weight residual -55.88 117.40 -173.27 1 2.00e+01 2.50e-03 4.78e+01 ... (remaining 5095 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 1841 0.097 - 0.194: 269 0.194 - 0.291: 38 0.291 - 0.388: 2 0.388 - 0.486: 2 Chirality restraints: 2152 Sorted by residual: chirality pdb=" CA ASP D 145 " pdb=" N ASP D 145 " pdb=" C ASP D 145 " pdb=" CB ASP D 145 " both_signs ideal model delta sigma weight residual False 2.50 2.02 0.49 2.00e-01 2.50e+01 5.89e+00 chirality pdb=" CA ASN A 147 " pdb=" N ASN A 147 " pdb=" C ASN A 147 " pdb=" CB ASN A 147 " both_signs ideal model delta sigma weight residual False 2.47 2.06 0.41 2.00e-01 2.50e+01 4.12e+00 chirality pdb=" CA CYS B 276 " pdb=" N CYS B 276 " pdb=" C CYS B 276 " pdb=" CB CYS B 276 " both_signs ideal model delta sigma weight residual False 2.50 2.14 0.36 2.00e-01 2.50e+01 3.22e+00 ... (remaining 2149 not shown) Planarity restraints: 2368 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" O GLU C 138 " -0.045 2.00e-02 2.50e+03 8.49e-02 7.20e+01 pdb=" CA GLU C 138 " -0.038 2.00e-02 2.50e+03 pdb=" C GLU C 138 " 0.146 2.00e-02 2.50e+03 pdb=" N SER C 139 " -0.063 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA D 138 " 0.021 2.00e-02 2.50e+03 4.81e-02 2.31e+01 pdb=" C ALA D 138 " -0.082 2.00e-02 2.50e+03 pdb=" O ALA D 138 " 0.022 2.00e-02 2.50e+03 pdb=" N SER D 139 " 0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP D 145 " 0.017 2.00e-02 2.50e+03 3.50e-02 1.22e+01 pdb=" C ASP D 145 " -0.060 2.00e-02 2.50e+03 pdb=" O ASP D 145 " 0.023 2.00e-02 2.50e+03 pdb=" N ALA D 146 " 0.020 2.00e-02 2.50e+03 ... (remaining 2365 not shown) Histogram of nonbonded interaction distances: 1.26 - 1.98: 13 1.98 - 2.71: 1025 2.71 - 3.44: 22381 3.44 - 4.17: 41664 4.17 - 4.90: 66638 Nonbonded interactions: 131721 Sorted by model distance: nonbonded pdb=" O ALA D 146 " pdb=" O HOH S 428 " model vdw 1.256 3.040 nonbonded pdb=" C ALA D 146 " pdb=" O HOH S 428 " model vdw 1.807 3.270 nonbonded pdb=" ND2 ASN C 147 " pdb=" O HOH S 642 " model vdw 1.831 3.120 nonbonded pdb=" NZ LYS D 220 " pdb=" O HOH S 145 " model vdw 1.845 3.120 nonbonded pdb=" OG1 THR C 33 " pdb=" O HOH S 508 " model vdw 1.850 3.040 ... (remaining 131716 not shown) NOTE: a complete listing of the restaints can be found in the .geo file. ==================== Fixing bad ADP in input model (if any) =================== ====================== Modifying start model if requested ===================== ================== Extract refinement strategy and selections ================= Refinement flags and selection counts: individual_sites = True (14331 atoms) torsion_angles = False (0 atoms) rigid_body = False (0 atoms in 0 groups) individual_adp = True (iso = 14331 aniso = 0) group_adp = False (0 atoms in 0 groups) tls = False (0 atoms in 0 groups) occupancies = False (0 atoms) group_anomalous = False n_use = 14331 n_use_u_iso = 14331 n_use_u_aniso = 0 n_grad_site = 0 n_grad_u_iso = 0 n_grad_u_aniso = 0 n_grad_occupancy = 0 n_grad_fp = 0 n_grad_fdp = 0 total number of scatterers = 14331 ==================== Process input NCS or/and find new NCS ==================== NCS groups found in parameter file: 0 Automatic NCS search: # simple_ncs_from_pdb # # Find ncs among chains in a PDB file # type phenix.doc for help Updated/new NCS groups: refinement.ncs.restraint_group { reference = chain 'A' and (resseq 2:76 or resseq 78:88 or resseq 110:131 or \ resseq 143:279 or resseq 281:297 or resseq 299:382 or resseq \ 389:465 ) selection = chain 'B' and (resseq 2:76 or resseq 78:88 or resseq 110:131 or \ resseq 143:279 or resseq 281:297 or resseq 299:382 or resseq \ 389:465 ) selection = chain 'C' and (resseq 2:76 or resseq 78:88 or resseq 110:131 or \ resseq 143:279 or resseq 281:297 or resseq 299:382 or resseq \ 389:465 ) selection = chain 'D' and (resseq 2:76 or resseq 78:88 or resseq 110:131 or \ resseq 143:279 or resseq 281:297 or resseq 299:382 or resseq \ 389:465 ) } ----------Building NCS restraints---------- NCS restraint group 1: NCS operator 1: Reference selection: "chain A and (resseq 2:76 or resseq 78:88 or resseq 110:131 or resseq 143:279 or resseq 281:297 or resseq 299:382 or resseq 389:465 )" Other selection: "chain B and (resseq 2:76 or resseq 78:88 or resseq 110:131 or resseq 143:279 or resseq 281:297 or resseq 299:382 or resseq 389:465 )" Number of atom pairs: 3297 Rotation={{0.305444, 0.0460409, -0.951096}, {0.036737, -0.998657, -0.0365451}, {-0.951501, -0.023778, -0.306725}} Translation={{61.3852}, {12.5407}, {84.5987}} Histogram of differences: 0.001645 - 0.320555: 3254 0.320555 - 0.639465: 11 0.639465 - 0.958374: 11 0.958374 - 1.277284: 11 1.277284 - 1.596194: 4 1.596194 - 1.915103: 6 RMS difference with respect to the reference: 0.133315 NCS operator 2: Reference selection: "chain A and (resseq 2:76 or resseq 78:88 or resseq 110:131 or resseq 143:279 or resseq 281:297 or resseq 299:382 or resseq 389:465 )" Other selection: "chain C and (resseq 2:76 or resseq 78:88 or resseq 110:131 or resseq 143:279 or resseq 281:297 or resseq 299:382 or resseq 389:465 )" Number of atom pairs: 3233 Rotation={{-0.70499, -0.590687, 0.392528}, {-0.614404, 0.232211, -0.754047}, {0.354256, -0.772766, -0.526627}} Translation={{85.8449}, {48.0462}, {34.0077}} Histogram of differences: 0.002268 - 0.366983: 3193 0.366983 - 0.731698: 24 0.731698 - 1.096413: 10 1.096413 - 1.461128: 1 1.461128 - 1.825843: 3 1.825843 - 2.190558: 2 RMS difference with respect to the reference: 0.120397 NCS operator 3: Reference selection: "chain A and (resseq 2:76 or resseq 78:88 or resseq 110:131 or resseq 143:279 or resseq 281:297 or resseq 299:382 or resseq 389:465 )" Other selection: "chain D and (resseq 2:76 or resseq 78:88 or resseq 110:131 or resseq 143:279 or resseq 281:297 or resseq 299:382 or resseq 389:465 )" Number of atom pairs: 3219 Rotation={{-0.626613, 0.538132, 0.563711}, {0.535072, -0.228831, 0.813225}, {0.566617, 0.811203, -0.144551}} Translation={{69.4979}, {-50.59}, {2.15679}} Histogram of differences: 0.002913 - 0.345679: 3168 0.345679 - 0.688444: 10 0.688444 - 1.031210: 14 1.031210 - 1.373975: 17 1.373975 - 1.716741: 5 1.716741 - 2.059507: 5 RMS difference with respect to the reference: 0.156000 =================== Write initial parameters into .eff file =================== Writing effective parameters to file: /Users/nick/k94e_208/Refine_48/k94e_2_refine_48.eff Writing geometry restraints to file: /Users/nick/k94e_208/Refine_48/k94e_2_refine_48.geo CPU time processing inputs: 39.56 ============================ Non-default parameters =========================== A complete record of all parameters was written to the .eff file above. Below are only the non-defaults. #phil __ON__ refinement { crystal_symmetry { unit_cell = 88.66 151.07 88.74 90 107.01 90 space_group = "P 1 21 1" } input { pdb { file_name = "/Users/nick/k94e_208/Refine_30M/ligand_revised2-coot-0.pdb" } neutron_data { r_free_flags { generate = True } } xray_data { file_name = "/Users/nick/k94e_208/Refine_30M/k94e_2_refine_data.mtz" labels = "F-obs,SIGF-obs" r_free_flags { file_name = "/Users/nick/k94e_208/Refine_30M/k94e_2_refine_data.mtz" label = "R-free-flags" test_flag_value = 0 } } monomers { file_name = "/Users/nick/Desktop/UPG_2.cif" } } output { prefix = "k94e_2_refine" serial = 48 serial_format = "%d" write_def_file = False } electron_density_maps { map_coefficients { map_type = "2mFo-DFc" mtz_label_amplitudes = "2FOFCWT" mtz_label_phases = "PH2FOFCWT" fill_missing_f_obs = True } map_coefficients { map_type = "2mFo-DFc" mtz_label_amplitudes = "2FOFCWT_no_fill" mtz_label_phases = "PH2FOFCWT_no_fill" } map_coefficients { map_type = "mFo-DFc" mtz_label_amplitudes = "FOFCWT" mtz_label_phases = "PHFOFCWT" } map_coefficients { map_type = "anomalous" mtz_label_amplitudes = "ANOM" mtz_label_phases = "PANOM" } map { map_type = "2mFo-DFc" fill_missing_f_obs = True } map { map_type = "2mFo-DFc" } map { map_type = "mFo-DFc" } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls occupancies group_anomalous } main { nqh_flips = False ordered_solvent = True ncs = True use_experimental_phases = False } ncs { excessive_distance_limit = None restraint_group { reference = "chain A and (resseq 2:76 or resseq 78:88 or resseq 110:131 or resseq 143:279 or resseq 281:297 or resseq 299:382 or resseq 389:465 )" selection = "chain B and (resseq 2:76 or resseq 78:88 or resseq 110:131 or resseq 143:279 or resseq 281:297 or resseq 299:382 or resseq 389:465 )" selection = "chain C and (resseq 2:76 or resseq 78:88 or resseq 110:131 or resseq 143:279 or resseq 281:297 or resseq 299:382 or resseq 389:465 )" selection = "chain D and (resseq 2:76 or resseq 78:88 or resseq 110:131 or resseq 143:279 or resseq 281:297 or resseq 299:382 or resseq 389:465 )" } } target_weights { bonds_rmsd_max = 0.0225 angles_rmsd_max = 2.5 } twinning { twin_law = "l,-k,h" detwin { map_types { aniso_correct = True } } } secondary_structure { h_bond_restraints { substitute_n_for_h = True } } gui { base_output_dir = "/Users/nick/k94e_208" tmp_dir = "/Users/nick/k94e_208/.phenix/tmp" notify_email = "nsennett@gmail.com" } } #phil __OFF__ =============================== refinement start ============================== ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 2.08 - 43.31 A; n_refl. = 131093)-----------------------------| | | | r_work= 0.2392 r_free= 0.2713 ksol= 0.34 Bsol= 41.03 scale= 1.042 | | | | overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):| | (0.48,0.01,-0.50,-0.00,-0.07,-0.00); trace/3= 0.00 | | | | maximum likelihood estimate for coordinate error: 0.35 A | | x-ray target function (ml) for work reflections: 5.596641 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 43.3150 - 6.4563 0.99 4259 244 0.2176 0.2239 6.6263 6.6328| | 2: 6.4563 - 5.1272 0.98 4171 229 0.2364 0.2559 6.4177 6.4404| | 3: 5.1272 - 4.4799 0.98 4166 210 0.2092 0.2436 6.5547 6.7087| | 4: 4.4799 - 4.0706 0.98 4121 241 0.2221 0.2541 6.565 6.6447| | 5: 4.0706 - 3.7790 0.98 4145 248 0.2250 0.2658 6.4426 6.5376| | 6: 3.7790 - 3.5563 0.98 4143 203 0.2312 0.2342 6.3834 6.4325| | 7: 3.5563 - 3.3783 0.98 4139 225 0.2406 0.2655 6.2733 6.273| | 8: 3.3783 - 3.2313 0.98 4163 231 0.2354 0.2611 6.1008 6.1447| | 9: 3.2313 - 3.1069 0.98 4156 204 0.2404 0.2759 6.0001 6.0345| | 10: 3.1069 - 2.9998 0.98 4188 211 0.2496 0.2829 5.922 5.9632| | 11: 2.9998 - 2.9060 0.98 4163 216 0.2564 0.3155 5.8481 5.9527| | 12: 2.9060 - 2.8229 0.99 4202 210 0.2517 0.3049 5.7304 5.8102| | 13: 2.8229 - 2.7486 0.98 4162 211 0.2392 0.2670 5.6118 5.6867| | 14: 2.7486 - 2.6816 0.99 4156 229 0.2478 0.2769 5.5258 5.6057| | 15: 2.6816 - 2.6206 0.99 4120 244 0.2475 0.2835 5.4595 5.5852| | 16: 2.6206 - 2.5649 0.98 4192 195 0.2491 0.2813 5.3963 5.4675| | 17: 2.5649 - 2.5136 0.98 4149 217 0.2567 0.3075 5.3566 5.4726| | 18: 2.5136 - 2.4661 0.99 4136 224 0.2584 0.2996 5.3176 5.4144| | 19: 2.4661 - 2.4221 0.98 4141 235 0.2522 0.3195 5.2594 5.3849| | 20: 2.4221 - 2.3810 0.98 4186 214 0.2568 0.3102 5.2263 5.3307| | 21: 2.3810 - 2.3426 0.99 4130 220 0.2690 0.2938 5.1687 5.2581| | 22: 2.3426 - 2.3066 0.98 4188 215 0.2484 0.3055 5.1017 5.1942| | 23: 2.3066 - 2.2727 0.99 4160 214 0.2457 0.2919 5.0396 5.1391| | 24: 2.2727 - 2.2407 0.98 4142 231 0.2520 0.2988 5.0136 5.1122| | 25: 2.2407 - 2.2104 0.98 4162 215 0.2600 0.3234 4.9781 5.1215| | 26: 2.2104 - 2.1817 0.98 4219 209 0.2743 0.3052 4.943 5.0426| | 27: 2.1817 - 2.1544 0.98 4039 241 0.2813 0.3246 4.9261 5.0519| | 28: 2.1544 - 2.1284 0.98 4211 217 0.2911 0.3460 4.8969 4.9755| | 29: 2.1284 - 2.1037 0.98 4137 225 0.2863 0.3437 4.8626 4.9423| | 30: 2.1037 - 2.0801 0.90 3829 190 0.3093 0.3553 4.8715 4.9361| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 43.3150 - 6.4563 4259 244 0.86 21.42 0.97 0.99 94167.90| | 2: 6.4563 - 5.1272 4171 229 0.84 23.80 0.94 0.95 75846.26| | 3: 5.1272 - 4.4799 4166 210 0.88 20.08 1.02 1.02 88889.26| | 4: 4.4799 - 4.0706 4121 241 0.87 21.74 1.05 1.06 94537.14| | 5: 4.0706 - 3.7790 4145 248 0.85 23.34 1.04 1.03 79952.84| | 6: 3.7790 - 3.5563 4143 203 0.86 22.43 1.04 1.01 63409.13| | 7: 3.5563 - 3.3783 4139 225 0.85 23.58 1.04 1.01 51361.41| | 8: 3.3783 - 3.2313 4163 231 0.84 24.16 1.03 0.99 38412.66| | 9: 3.2313 - 3.1069 4156 204 0.84 24.40 1.01 0.98 31003.27| | 10: 3.1069 - 2.9998 4188 211 0.82 26.20 1.01 0.96 27109.96| | 11: 2.9998 - 2.9060 4163 216 0.80 28.28 0.98 0.92 25662.14| | 12: 2.9060 - 2.8229 4202 210 0.79 28.89 0.96 0.90 21416.71| | 13: 2.8229 - 2.7486 4162 211 0.82 26.24 0.96 0.92 15844.89| | 14: 2.7486 - 2.6816 4156 229 0.82 26.10 0.96 0.93 12788.16| | 15: 2.6816 - 2.6206 4120 244 0.82 26.57 0.96 0.93 11331.77| | 16: 2.6206 - 2.5649 4192 195 0.81 27.46 0.95 0.92 10598.38| | 17: 2.5649 - 2.5136 4149 217 0.80 28.42 0.93 0.89 9823.03| | 18: 2.5136 - 2.4661 4136 224 0.79 28.73 0.93 0.87 9280.00| | 19: 2.4661 - 2.4221 4141 235 0.79 29.34 0.93 0.87 8637.53| | 20: 2.4221 - 2.3810 4186 214 0.79 29.28 0.94 0.87 7891.57| | 21: 2.3810 - 2.3426 4130 220 0.79 29.38 0.91 0.86 6958.63| | 22: 2.3426 - 2.3066 4188 215 0.80 27.73 0.94 0.88 5856.09| | 23: 2.3066 - 2.2727 4160 214 0.82 26.73 0.94 0.89 5177.06| | 24: 2.2727 - 2.2407 4142 231 0.81 27.23 0.93 0.86 4865.86| | 25: 2.2407 - 2.2104 4162 215 0.79 29.04 0.93 0.84 4792.24| | 26: 2.2104 - 2.1817 4219 209 0.77 30.52 0.92 0.85 4700.66| | 27: 2.1817 - 2.1544 4039 241 0.76 31.42 0.92 0.86 4619.88| | 28: 2.1544 - 2.1284 4211 217 0.75 32.70 0.91 0.85 4464.62| | 29: 2.1284 - 2.1037 4137 225 0.74 33.28 0.92 0.83 4219.53| | 30: 2.1037 - 2.0801 3829 190 0.74 33.43 0.91 0.79 3892.31| |alpha: min = 0.77 max = 1.07 mean = 0.92| |beta: min = 3772.27 max = 102400.65 mean = 27682.94| |figures of merit: min = 0.00 max = 1.00 mean = 0.81| |phase err.(work): min = 0.00 max = 89.88 mean = 27.04| |phase err.(test): min = 0.00 max = 89.35 mean = 27.42| |-----------------------------------------------------------------------------| ============================== Outliers rejection ============================= Distribution of F-obs values before outliers rejection: 15.308 - 318.007 : 91358 318.007 - 620.707 : 25817 620.707 - 923.407 : 10044 923.407 - 1226.107 : 2920 1226.107 - 1528.807 : 685 1528.807 - 1831.507 : 196 1831.507 - 2134.207 : 51 2134.207 - 2436.906 : 13 2436.906 - 2739.606 : 1 2739.606 - 3042.306 : 8 basic_wilson_outliers = 0 extreme_wilson_outliers = 0 beamstop_shadow_outliers = 3 model_based_outliers = 1 total = 3 Distribution of F-obs values after outliers rejection: 22.681 - 324.643 : 92305 324.643 - 626.606 : 25169 626.606 - 928.569 : 9834 928.569 - 1230.531 : 2850 1230.531 - 1532.494 : 668 1532.494 - 1834.456 : 192 1834.456 - 2136.419 : 50 2136.419 - 2438.381 : 13 2438.381 - 2740.344 : 1 2740.344 - 3042.306 : 8 ----------Initial model statistics (before refinement)---------- |-Geometry statistics: start--------------------------------------------------| | Histogram of deviations from ideal values for | | Bonds | Angles | Nonbonded contacts | | 0.000 - 0.058: 13759 | 0.000 - 1.603: 16829 | 1.256 - 1.620: 1 | | 0.058 - 0.116: 4 | 1.603 - 3.206: 1450 | 1.620 - 1.985: 12 | | 0.116 - 0.174: 0 | 3.206 - 4.808: 277 | 1.985 - 2.349: 112 | | 0.174 - 0.231: 0 | 4.808 - 6.411: 54 | 2.349 - 2.714: 913 | | 0.231 - 0.289: 0 | 6.411 - 8.014: 15 | 2.714 - 3.078: 10502 | | 0.289 - 0.347: 0 | 8.014 - 9.616: 9 | 3.078 - 3.442: 11879 | | 0.347 - 0.405: 0 | 9.616 - 11.219: 4 | 3.442 - 3.807: 19713 | | 0.405 - 0.463: 1 | 11.219 - 12.822: 2 | 3.807 - 4.171: 21951 | | 0.463 - 0.521: 0 | 12.822 - 14.425: 2 | 4.171 - 4.536: 29815 | | 0.521 - 0.578: 1 | 14.425 - 16.027: 1 | 4.536 - 4.900: 36823 | |-----------------------------------------------------------------------------| |-Geometry statistics: start--------------------------------------------------| | Type | Count | Deviation from ideal | Targets | Target (sum) | | | | rmsd max min | | | | bond | 13765 | 0.010 0.578 0.000 | 0.319 | | | angle | 18643 | 1.084 16.027 0.000 | 0.247 | | | chirality | 2152 | 0.071 0.486 0.000 | 0.126 | 0.109 | | planarity | 2368 | 0.005 0.085 0.000 | 0.189 | | | dihedral | 5098 | 15.286 178.156 0.001 | 1.100 | | | nonbonded | 13765 | 4.108 4.900 1.256 | 0.256 | | |-----------------------------------------------------------------------------| |-ADP statistics (Wilson B = 33.949)------------------------------------------| | Atom | Number of | Isotropic or equivalent| Anisotropy lmin/max | | type |iso aniso | min max mean | min max mean | | - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - - | | all : 14331 0 12.45 98.47 39.94 None None None | | all(noH): 14331 0 12.45 98.47 39.94 None None None | | Sol. : 804 0 16.91 70.68 40.84 None None None | | Mac. : 13527 0 12.45 98.47 39.89 None None None | | Hyd. : 0 0 None None None None None None | | - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - | | Distribution of isotropic (or equivalent) ADP for non-H atoms: | | Bin# value range #atoms | Bin# value range #atoms | | 0: 12.450 - 21.052: 898 | 5: 55.460 - 64.062: 1012 | | 1: 21.052 - 29.654: 3165 | 6: 64.062 - 72.664: 555 | | 2: 29.654 - 38.256: 3429 | 7: 72.664 - 81.266: 238 | | 3: 38.256 - 46.858: 2868 | 8: 81.266 - 89.868: 207 | | 4: 46.858 - 55.460: 1875 | 9: 89.868 - 98.470: 84 | | =>continue=> | |-----------------------------------------------------------------------------| |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 1 OF 3 ************************* |--(resolution: 2.08 - 43.31 A; n_refl. = 131090)-----------------------------| | | | r_work= 0.2392 r_free= 0.2713 ksol= 0.34 Bsol= 41.03 scale= 1.043 | | | | overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):| | (0.48,0.01,-0.50,-0.00,-0.07,-0.00); trace/3= 0.00 | | | | maximum likelihood estimate for coordinate error: 0.35 A | | x-ray target function (ml) for work reflections: 5.596226 | |-----------------------------------------------------------------------------| ====================== bulk solvent modeling and scaling ====================== |-Mask optimization: start----------------------------------------------------| | Solvent (probe) radius= 1.11 Shrink truncation radius= 0.90 | | all data: 500 lowest resolution reflections: | | r_work= 0.2392 r_free= 0.2713 r_work= 0.2992 (resolution: 43.31-13.14 A)| |-----------------------------------------------------------------------------| r_solv= 0.00 r_shrink= 0.00 r_work=0.2702 r_free=0.3002 r_work_low=0.8181 r_solv= 0.10 r_shrink= 0.00 r_work=0.2657 r_free=0.2955 r_work_low=0.6642 r_solv= 0.20 r_shrink= 0.00 r_work=0.2608 r_free=0.2908 r_work_low=0.5259 r_solv= 0.30 r_shrink= 0.00 r_work=0.2555 r_free=0.2853 r_work_low=0.4236 r_solv= 0.40 r_shrink= 0.04 r_work=0.2502 r_free=0.2807 r_work_low=0.3662 r_solv= 0.50 r_shrink= 0.16 r_work=0.2457 r_free=0.2772 r_work_low=0.3458 r_solv= 0.60 r_shrink= 0.27 r_work=0.2428 r_free=0.2750 r_work_low=0.3560 r_solv= 0.70 r_shrink= 0.38 r_work=0.2416 r_free=0.2741 r_work_low=0.3816 r_solv= 0.80 r_shrink= 0.49 r_work=0.2425 r_free=0.2747 r_work_low=0.3150 r_solv= 0.90 r_shrink= 0.61 r_work=0.2412 r_free=0.2728 r_work_low=0.3065 r_solv= 1.00 r_shrink= 0.72 r_work=0.2406 r_free=0.2726 r_work_low=0.2923 r_solv= 1.10 r_shrink= 0.83 r_work=0.2394 r_free=0.2714 r_work_low=0.2963 r_solv= 1.20 r_shrink= 0.95 r_work=0.2388 r_free=0.2714 r_work_low=0.3098 r_solv= 1.30 r_shrink= 1.06 r_work=0.2387 r_free=0.2710 r_work_low=0.3047 r_solv= 1.40 r_shrink= 1.17 r_work=0.2388 r_free=0.2712 r_work_low=0.2909 |-Mask optimization: final----------------------------------------------------| | Solvent (probe) radius= 1.30 Shrink truncation radius= 1.06 | | all data: 500 lowest resolution reflections: | | r_work= 0.2387 r_free= 0.2710 r_work= 0.3047 (resolution: 43.31-13.14 A)| |-----------------------------------------------------------------------------| |--(resolution: 2.08 - 43.31 A; n_refl. = 131090)-----------------------------| | | | r_work= 0.2387 r_free= 0.2710 ksol= 0.34 Bsol= 41.03 scale= 1.032 | | | | overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):| | (0.48,0.01,-0.50,-0.00,-0.07,-0.00); trace/3= 0.00 | | | | maximum likelihood estimate for coordinate error: 0.34 A | | x-ray target function (ml) for work reflections: 5.595405 | |-----------------------------------------------------------------------------| ========================== Target weights: x-ray data ========================= |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 9.597673 wxc_scale = 0.500 wc = 1.000 | | angle between x-ray and geometry gradient vectors: 113.238 (deg) | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.179638 wxu_scale = 1.000 wu = 1.000 | | angle between Xray and ADP gradient vectors: 157.654 (deg) | |-----------------------------------------------------------------------------| ================================ xyz refinement =============================== |-LBFGS minimization----------------------------------------------------------| | start r-factor (work) = 0.2387 final r-factor (work) = 0.2373 | | start r-factor (free) = 0.2710 final r-factor (free) = 0.2731 | |-----------------------------------------------------------------------------| | T_start = wxc * wxc_scale * Exray + wc * Echem | | 27.1463 = 9.60 * 0.50 * 5.5966 + 1.00 * 0.2890 | | | | T_final = wxc * wxc_scale * Exray + wc * Echem | | 26.9487 = 9.60 * 0.50 * 5.5906 + 1.00 * 0.1204 | |-----------------------------------------------------------------------------| | number of iterations = 25 | number of function evaluations = 26 | |-----------------------------------------------------------------------------| ================================ ADP refinement =============================== ----------Individual ADP refinement---------- |-LBFGS minimization----------------------------------------------------------| | start r-factor (work) = 0.2373 final r-factor (work) = 0.2375 | | start r-factor (free) = 0.2731 final r-factor (free) = 0.2737 | |-----------------------------------------------------------------------------| | T_start = wxu * wxu_scale * Exray + wu * Eadp | | 1.0077 = 0.18 * 1.00 * 5.5906 + 1.00 * 0.0034 | | | | T_final = wxu * wxu_scale * Exray + wu * Eadp | | 1.0080 = 0.18 * 1.00 * 5.5926 + 1.00 * 0.0033 | |-----------------------------------------------------------------------------| | number of iterations = 24 | number of function evaluations = 28 | |-----------------------------------------------------------------------------| |-ADP statistics (Wilson B = 33.949)------------------------------------------| | Atom | Number of | Isotropic or equivalent| Anisotropy lmin/max | | type |iso aniso | min max mean | min max mean | | - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - - | | all : 14331 0 11.86 100.08 39.58 None None None | | all(noH): 14331 0 11.86 100.08 39.58 None None None | | Sol. : 804 0 16.99 74.55 40.51 None None None | | Mac. : 13527 0 11.86 100.08 39.53 None None None | | Hyd. : 0 0 None None None None None None | | - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - | | Distribution of isotropic (or equivalent) ADP for non-H atoms: | | Bin# value range #atoms | Bin# value range #atoms | | 0: 11.859 - 20.681: 874 | 5: 55.968 - 64.790: 962 | | 1: 20.681 - 29.503: 3266 | 6: 64.790 - 73.611: 487 | | 2: 29.503 - 38.325: 3531 | 7: 73.611 - 82.433: 235 | | 3: 38.325 - 47.146: 2878 | 8: 82.433 - 91.255: 197 | | 4: 47.146 - 55.968: 1839 | 9: 91.255 - 100.077: 62 | | =>continue=> | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 3 ************************* |--(resolution: 2.08 - 43.31 A; n_refl. = 131090)-----------------------------| | | | r_work= 0.2375 r_free= 0.2737 ksol= 0.34 Bsol= 41.03 scale= 1.027 | | | | overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):| | (0.48,0.01,-0.50,-0.00,-0.07,-0.00); trace/3= 0.00 | | | | maximum likelihood estimate for coordinate error: 0.35 A | | x-ray target function (ml) for work reflections: 5.593272 | |-----------------------------------------------------------------------------| ====================== bulk solvent modeling and scaling ====================== |-Mask optimization: start----------------------------------------------------| | Solvent (probe) radius= 1.30 Shrink truncation radius= 1.06 | | all data: 500 lowest resolution reflections: | | r_work= 0.2375 r_free= 0.2737 r_work= 0.3040 (resolution: 43.31-13.14 A)| |-----------------------------------------------------------------------------| r_solv= 0.00 r_shrink= 0.00 r_work=0.2697 r_free=0.3030 r_work_low=0.8094 r_solv= 0.10 r_shrink= 0.00 r_work=0.2653 r_free=0.2984 r_work_low=0.6572 r_solv= 0.20 r_shrink= 0.00 r_work=0.2605 r_free=0.2939 r_work_low=0.5204 r_solv= 0.30 r_shrink= 0.00 r_work=0.2551 r_free=0.2884 r_work_low=0.4189 r_solv= 0.40 r_shrink= 0.04 r_work=0.2496 r_free=0.2839 r_work_low=0.3632 r_solv= 0.50 r_shrink= 0.16 r_work=0.2449 r_free=0.2801 r_work_low=0.3452 r_solv= 0.60 r_shrink= 0.27 r_work=0.2418 r_free=0.2776 r_work_low=0.3555 r_solv= 0.70 r_shrink= 0.38 r_work=0.2404 r_free=0.2763 r_work_low=0.3814 r_solv= 0.80 r_shrink= 0.49 r_work=0.2415 r_free=0.2778 r_work_low=0.3154 r_solv= 0.90 r_shrink= 0.61 r_work=0.2402 r_free=0.2757 r_work_low=0.3077 r_solv= 1.00 r_shrink= 0.72 r_work=0.2396 r_free=0.2753 r_work_low=0.2925 r_solv= 1.10 r_shrink= 0.83 r_work=0.2381 r_free=0.2739 r_work_low=0.2952 r_solv= 1.20 r_shrink= 0.95 r_work=0.2376 r_free=0.2740 r_work_low=0.3081 r_solv= 1.30 r_shrink= 1.06 r_work=0.2374 r_free=0.2729 r_work_low=0.3052 r_solv= 1.40 r_shrink= 1.17 r_work=0.2375 r_free=0.2730 r_work_low=0.2913 |-Mask optimization: final----------------------------------------------------| | Solvent (probe) radius= 1.30 Shrink truncation radius= 1.06 | | all data: 500 lowest resolution reflections: | | r_work= 0.2374 r_free= 0.2729 r_work= 0.3052 (resolution: 43.31-13.14 A)| |-----------------------------------------------------------------------------| |--(resolution: 2.08 - 43.31 A; n_refl. = 131090)-----------------------------| | | | r_work= 0.2370 r_free= 0.2725 ksol= 0.34 Bsol= 41.35 scale= 1.032 | | | | overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):| | (0.48,0.02,-0.50,0.00,-0.07,0.00); trace/3= 0.00 | | | | maximum likelihood estimate for coordinate error: 0.35 A | | x-ray target function (ml) for work reflections: 5.592894 | |-----------------------------------------------------------------------------| ================== ordered solvent: location/analysis/update ================== Start model: number = 804 b_iso_min = 17.30 (limit = 1.00) b_iso_max = 74.86 (limit = 80.00) b_iso_mean = 40.82 anisotropy_min = 1.00 (limit = 0.10) occupancy_min = 1.00 (limit = 0.10) occupancy_max = 1.00 (limit = 1.00) dist_sol_mol_min = -1.00 (limit = 1.80) dist_sol_mol_max = 5.99 (limit = 6.00) Filtered: number = 796 b_iso_min = 17.30 (limit = 1.00) b_iso_max = 74.86 (limit = 80.00) b_iso_mean = 40.77 anisotropy_min = 1.00 (limit = 0.10) occupancy_min = 1.00 (limit = 0.10) occupancy_max = 1.00 (limit = 1.00) dist_sol_mol_min = -1.00 (limit = 1.80) dist_sol_mol_max = 5.99 (limit = 6.00) Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 993 Filter by distance & map next to the model: mapped sites are within: 0.383 - 5.994 number of sites selected in [dist_min= 1.80, dist_max= 6.00]: 501 from: 993 mapped sites are within: 1.801 - 5.994 Just added new: number = 1297 b_iso_min = 17.30 (limit = 1.00) b_iso_max = 74.86 (limit = 80.00) b_iso_mean = 40.41 anisotropy_min = 1.00 (limit = 0.10) occupancy_min = 1.00 (limit = 0.10) occupancy_max = 1.00 (limit = 1.00) dist_sol_mol_min = -1.00 (limit = 1.80) dist_sol_mol_max = 5.99 (limit = 6.00) Filtered: number = 998 b_iso_min = 17.30 (limit = 1.00) b_iso_max = 74.86 (limit = 80.00) b_iso_mean = 40.58 anisotropy_min = 1.00 (limit = 0.10) occupancy_min = 1.00 (limit = 0.10) occupancy_max = 1.00 (limit = 1.00) dist_sol_mol_min = -1.00 (limit = 1.80) dist_sol_mol_max = 5.99 (limit = 6.00) Number of peaks found at 2mFobs-DFmodel map (map cutoff=1.00 sigma)= 9932 Filter by distance & map next to the model: mapped sites are within: 0.010 - 0.500 number of sites selected in [dist_min= 0.01, dist_max= 0.50]: 4314 from: 9932 mapped sites are within: 0.010 - 0.500 ADP refinement (water only), start r_work=0.2353 r_free=0.2648 ADP refinement (water only), final r_work=0.2342 r_free=0.2656 Before filtering: number = 998 b_iso_min = 16.53 (limit = 1.00) b_iso_max = 80.37 (limit = 80.00) b_iso_mean = 43.50 anisotropy_min = 1.00 (limit = 0.10) occupancy_min = 1.00 (limit = 0.10) occupancy_max = 1.00 (limit = 1.00) dist_sol_mol_min = -1.00 (limit = 1.80) dist_sol_mol_max = 5.99 (limit = 6.00) Before RSCC filtering: 940 After RSCC filtering: 880 2mFo-DFmodel map selection: number = 880 b_iso_min = 16.53 (limit = 1.00) b_iso_max = 71.38 (limit = 80.00) b_iso_mean = 41.55 anisotropy_min = 1.00 (limit = 0.10) occupancy_min = 1.00 (limit = 0.10) occupancy_max = 1.00 (limit = 1.00) dist_sol_mol_min = -1.00 (limit = 1.80) dist_sol_mol_max = 5.99 (limit = 6.00) Final: number = 880 b_iso_min = 16.53 (limit = 1.00) b_iso_max = 71.38 (limit = 80.00) b_iso_mean = 41.55 anisotropy_min = 1.00 (limit = 0.10) occupancy_min = 1.00 (limit = 0.10) occupancy_max = 1.00 (limit = 1.00) dist_sol_mol_min = -1.00 (limit = 1.80) dist_sol_mol_max = 5.99 (limit = 6.00) ========================== Target weights: x-ray data ========================= |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 8.746330 wxc_scale = 0.500 wc = 1.000 | | angle between x-ray and geometry gradient vectors: 150.893 (deg) | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.176996 wxu_scale = 1.000 wu = 1.000 | | angle between Xray and ADP gradient vectors: 157.311 (deg) | |-----------------------------------------------------------------------------| ================================ xyz refinement =============================== |-LBFGS minimization----------------------------------------------------------| | start r-factor (work) = 0.2360 final r-factor (work) = 0.2361 | | start r-factor (free) = 0.2686 final r-factor (free) = 0.2721 | |-----------------------------------------------------------------------------| | T_start = wxc * wxc_scale * Exray + wc * Echem | | 24.5652 = 8.75 * 0.50 * 5.5860 + 1.00 * 0.1365 | | | | T_final = wxc * wxc_scale * Exray + wc * Echem | | 24.5464 = 8.75 * 0.50 * 5.5871 + 1.00 * 0.1131 | |-----------------------------------------------------------------------------| | number of iterations = 25 | number of function evaluations = 27 | |-----------------------------------------------------------------------------| ================================ ADP refinement =============================== ----------Individual ADP refinement---------- |-LBFGS minimization----------------------------------------------------------| | start r-factor (work) = 0.2361 final r-factor (work) = 0.2364 | | start r-factor (free) = 0.2721 final r-factor (free) = 0.2724 | |-----------------------------------------------------------------------------| | T_start = wxu * wxu_scale * Exray + wu * Eadp | | 0.9923 = 0.18 * 1.00 * 5.5871 + 1.00 * 0.0034 | | | | T_final = wxu * wxu_scale * Exray + wu * Eadp | | 0.9927 = 0.18 * 1.00 * 5.5898 + 1.00 * 0.0034 | |-----------------------------------------------------------------------------| | number of iterations = 15 | number of function evaluations = 16 | |-----------------------------------------------------------------------------| |-ADP statistics--------------------------------------------------------------| | Atom | Number of | Isotropic or equivalent| Anisotropy lmin/max | | type |iso aniso | min max mean | min max mean | | - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - - | | all : 14407 0 11.85 100.01 39.64 None None None | | all(noH): 14407 0 11.85 100.01 39.64 None None None | | Sol. : 880 0 17.21 76.71 41.13 None None None | | Mac. : 13527 0 11.85 100.01 39.54 None None None | | Hyd. : 0 0 None None None None None None | | - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - | | Distribution of isotropic (or equivalent) ADP for non-H atoms: | | Bin# value range #atoms | Bin# value range #atoms | | 0: 11.847 - 20.663: 880 | 5: 55.930 - 64.746: 977 | | 1: 20.663 - 29.480: 3263 | 6: 64.746 - 73.563: 496 | | 2: 29.480 - 38.297: 3523 | 7: 73.563 - 82.380: 240 | | 3: 38.297 - 47.113: 2893 | 8: 82.380 - 91.196: 197 | | 4: 47.113 - 55.930: 1877 | 9: 91.196 - 100.013: 61 | | =>continue=> | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 3 ************************* |--(resolution: 2.08 - 43.31 A; n_refl. = 131090)-----------------------------| | | | r_work= 0.2364 r_free= 0.2724 ksol= 0.34 Bsol= 41.35 scale= 1.026 | | | | overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):| | (0.48,0.02,-0.50,0.00,-0.07,0.00); trace/3= 0.00 | | | | maximum likelihood estimate for coordinate error: 0.35 A | | x-ray target function (ml) for work reflections: 5.590053 | |-----------------------------------------------------------------------------| ====================== bulk solvent modeling and scaling ====================== |-Mask optimization: start----------------------------------------------------| | Solvent (probe) radius= 1.30 Shrink truncation radius= 1.06 | | all data: 500 lowest resolution reflections: | | r_work= 0.2364 r_free= 0.2724 r_work= 0.3082 (resolution: 43.31-13.14 A)| |-----------------------------------------------------------------------------| r_solv= 0.00 r_shrink= 0.00 r_work=0.2683 r_free=0.3019 r_work_low=0.8049 r_solv= 0.10 r_shrink= 0.00 r_work=0.2640 r_free=0.2978 r_work_low=0.6540 r_solv= 0.20 r_shrink= 0.00 r_work=0.2593 r_free=0.2934 r_work_low=0.5184 r_solv= 0.30 r_shrink= 0.00 r_work=0.2539 r_free=0.2880 r_work_low=0.4196 r_solv= 0.40 r_shrink= 0.04 r_work=0.2484 r_free=0.2832 r_work_low=0.3640 r_solv= 0.50 r_shrink= 0.16 r_work=0.2438 r_free=0.2794 r_work_low=0.3488 r_solv= 0.60 r_shrink= 0.27 r_work=0.2406 r_free=0.2769 r_work_low=0.3609 r_solv= 0.70 r_shrink= 0.38 r_work=0.2392 r_free=0.2754 r_work_low=0.3872 r_solv= 0.80 r_shrink= 0.49 r_work=0.2404 r_free=0.2766 r_work_low=0.3161 r_solv= 0.90 r_shrink= 0.61 r_work=0.2390 r_free=0.2749 r_work_low=0.3084 r_solv= 1.00 r_shrink= 0.72 r_work=0.2384 r_free=0.2742 r_work_low=0.2953 r_solv= 1.10 r_shrink= 0.83 r_work=0.2371 r_free=0.2728 r_work_low=0.2996 r_solv= 1.20 r_shrink= 0.95 r_work=0.2365 r_free=0.2725 r_work_low=0.3110 r_solv= 1.30 r_shrink= 1.06 r_work=0.2364 r_free=0.2718 r_work_low=0.3106 r_solv= 1.40 r_shrink= 1.17 r_work=0.2365 r_free=0.2720 r_work_low=0.2991 |-Mask optimization: final----------------------------------------------------| | Solvent (probe) radius= 1.30 Shrink truncation radius= 1.06 | | all data: 500 lowest resolution reflections: | | r_work= 0.2364 r_free= 0.2718 r_work= 0.3106 (resolution: 43.31-13.14 A)| |-----------------------------------------------------------------------------| |--(resolution: 2.08 - 43.31 A; n_refl. = 131090)-----------------------------| | | | r_work= 0.2360 r_free= 0.2714 ksol= 0.34 Bsol= 41.67 scale= 1.031 | | | | overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):| | (0.48,0.02,-0.51,0.00,-0.08,0.00); trace/3= 0.00 | | | | maximum likelihood estimate for coordinate error: 0.35 A | | x-ray target function (ml) for work reflections: 5.589912 | |-----------------------------------------------------------------------------| ================== ordered solvent: location/analysis/update ================== Start model: number = 880 b_iso_min = 17.53 (limit = 1.00) b_iso_max = 77.03 (limit = 80.00) b_iso_mean = 41.45 anisotropy_min = 1.00 (limit = 0.10) occupancy_min = 1.00 (limit = 0.10) occupancy_max = 1.00 (limit = 1.00) dist_sol_mol_min = -1.00 (limit = 1.80) dist_sol_mol_max = 5.99 (limit = 6.00) Filtered: number = 861 b_iso_min = 17.53 (limit = 1.00) b_iso_max = 77.03 (limit = 80.00) b_iso_mean = 41.36 anisotropy_min = 1.00 (limit = 0.10) occupancy_min = 1.00 (limit = 0.10) occupancy_max = 1.00 (limit = 1.00) dist_sol_mol_min = -1.00 (limit = 1.80) dist_sol_mol_max = 5.99 (limit = 6.00) Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 983 Filter by distance & map next to the model: mapped sites are within: 0.349 - 5.999 number of sites selected in [dist_min= 1.80, dist_max= 6.00]: 459 from: 983 mapped sites are within: 1.800 - 5.999 Just added new: number = 1320 b_iso_min = 17.53 (limit = 1.00) b_iso_max = 77.03 (limit = 80.00) b_iso_mean = 40.84 anisotropy_min = 1.00 (limit = 0.10) occupancy_min = 1.00 (limit = 0.10) occupancy_max = 1.00 (limit = 1.00) dist_sol_mol_min = -1.00 (limit = 1.80) dist_sol_mol_max = 6.00 (limit = 6.00) Filtered: number = 1019 b_iso_min = 17.53 (limit = 1.00) b_iso_max = 77.03 (limit = 80.00) b_iso_mean = 41.13 anisotropy_min = 1.00 (limit = 0.10) occupancy_min = 1.00 (limit = 0.10) occupancy_max = 1.00 (limit = 1.00) dist_sol_mol_min = -1.00 (limit = 1.80) dist_sol_mol_max = 5.99 (limit = 6.00) Number of peaks found at 2mFobs-DFmodel map (map cutoff=1.00 sigma)= 9888 Filter by distance & map next to the model: mapped sites are within: 0.013 - 0.500 number of sites selected in [dist_min= 0.01, dist_max= 0.50]: 4360 from: 9888 mapped sites are within: 0.013 - 0.500 ADP refinement (water only), start r_work=0.2348 r_free=0.2641 ADP refinement (water only), final r_work=0.2339 r_free=0.2652 Before filtering: number = 1019 b_iso_min = 16.25 (limit = 1.00) b_iso_max = 82.86 (limit = 80.00) b_iso_mean = 43.73 anisotropy_min = 1.00 (limit = 0.10) occupancy_min = 1.00 (limit = 0.10) occupancy_max = 1.00 (limit = 1.00) dist_sol_mol_min = -1.00 (limit = 1.80) dist_sol_mol_max = 5.97 (limit = 6.00) Before RSCC filtering: 961 After RSCC filtering: 880 2mFo-DFmodel map selection: number = 880 b_iso_min = 16.25 (limit = 1.00) b_iso_max = 76.19 (limit = 80.00) b_iso_mean = 41.17 anisotropy_min = 1.00 (limit = 0.10) occupancy_min = 1.00 (limit = 0.10) occupancy_max = 1.00 (limit = 1.00) dist_sol_mol_min = -1.00 (limit = 1.80) dist_sol_mol_max = 5.95 (limit = 6.00) Final: number = 880 b_iso_min = 16.25 (limit = 1.00) b_iso_max = 76.19 (limit = 80.00) b_iso_mean = 41.17 anisotropy_min = 1.00 (limit = 0.10) occupancy_min = 1.00 (limit = 0.10) occupancy_max = 1.00 (limit = 1.00) dist_sol_mol_min = -1.00 (limit = 1.80) dist_sol_mol_max = 5.95 (limit = 6.00) ========================== Target weights: x-ray data ========================= |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 8.738837 wxc_scale = 0.500 wc = 1.000 | | angle between x-ray and geometry gradient vectors: 159.321 (deg) | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.176522 wxu_scale = 1.000 wu = 1.000 | | angle between Xray and ADP gradient vectors: 157.728 (deg) | |-----------------------------------------------------------------------------| ================================ xyz refinement =============================== |-LBFGS minimization----------------------------------------------------------| | start r-factor (work) = 0.2361 final r-factor (work) = 0.2360 | | start r-factor (free) = 0.2687 final r-factor (free) = 0.2723 | |-----------------------------------------------------------------------------| | T_start = wxc * wxc_scale * Exray + wc * Echem | | 24.5274 = 8.74 * 0.50 * 5.5854 + 1.00 * 0.1225 | | | | T_final = wxc * wxc_scale * Exray + wc * Echem | | 24.5212 = 8.74 * 0.50 * 5.5866 + 1.00 * 0.1109 | |-----------------------------------------------------------------------------| | number of iterations = 25 | number of function evaluations = 28 | |-----------------------------------------------------------------------------| ================================ ADP refinement =============================== ----------Individual ADP refinement---------- |-LBFGS minimization----------------------------------------------------------| | start r-factor (work) = 0.2360 final r-factor (work) = 0.2363 | | start r-factor (free) = 0.2723 final r-factor (free) = 0.2727 | |-----------------------------------------------------------------------------| | T_start = wxu * wxu_scale * Exray + wu * Eadp | | 0.9896 = 0.18 * 1.00 * 5.5866 + 1.00 * 0.0034 | | | | T_final = wxu * wxu_scale * Exray + wu * Eadp | | 0.9900 = 0.18 * 1.00 * 5.5894 + 1.00 * 0.0033 | |-----------------------------------------------------------------------------| | number of iterations = 19 | number of function evaluations = 20 | |-----------------------------------------------------------------------------| |-ADP statistics--------------------------------------------------------------| | Atom | Number of | Isotropic or equivalent| Anisotropy lmin/max | | type |iso aniso | min max mean | min max mean | | - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - - | | all : 14407 0 11.74 97.98 39.53 None None None | | all(noH): 14407 0 11.74 97.98 39.53 None None None | | Sol. : 880 0 16.96 79.73 40.79 None None None | | Mac. : 13527 0 11.74 97.98 39.45 None None None | | Hyd. : 0 0 None None None None None None | | - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - | | Distribution of isotropic (or equivalent) ADP for non-H atoms: | | Bin# value range #atoms | Bin# value range #atoms | | 0: 11.736 - 20.360: 808 | 5: 54.859 - 63.484: 1019 | | 1: 20.360 - 28.985: 3105 | 6: 63.484 - 72.109: 555 | | 2: 28.985 - 37.610: 3521 | 7: 72.109 - 80.733: 232 | | 3: 37.610 - 46.235: 2936 | 8: 80.733 - 89.358: 208 | | 4: 46.235 - 54.859: 1935 | 9: 89.358 - 97.983: 88 | | =>continue=> | |-----------------------------------------------------------------------------| ======================= ordered solvent: final clean up ======================= Start model: number = 880 b_iso_min = 16.96 (limit = 1.00) b_iso_max = 79.73 (limit = 80.00) b_iso_mean = 40.79 anisotropy_min = 1.00 (limit = 0.10) occupancy_min = 1.00 (limit = 0.10) occupancy_max = 1.00 (limit = 1.00) dist_sol_mol_min = -1.00 (limit = 1.80) dist_sol_mol_max = 5.99 (limit = 6.00) Filtered: number = 865 b_iso_min = 16.96 (limit = 1.00) b_iso_max = 79.73 (limit = 80.00) b_iso_mean = 40.67 anisotropy_min = 1.00 (limit = 0.10) occupancy_min = 1.00 (limit = 0.10) occupancy_max = 1.00 (limit = 1.00) dist_sol_mol_min = -1.00 (limit = 1.80) dist_sol_mol_max = 5.99 (limit = 6.00) Number of peaks found at 2mFobs-DFmodel map (map cutoff=1.00 sigma)= 9921 Filter by distance & map next to the model: mapped sites are within: 0.004 - 0.500 number of sites selected in [dist_min= 0.01, dist_max= 0.50]: 4297 from: 9921 mapped sites are within: 0.012 - 0.500 Before filtering: number = 865 b_iso_min = 16.96 (limit = 1.00) b_iso_max = 79.73 (limit = 80.00) b_iso_mean = 40.67 anisotropy_min = 1.00 (limit = 0.10) occupancy_min = 1.00 (limit = 0.10) occupancy_max = 1.00 (limit = 1.00) dist_sol_mol_min = -1.00 (limit = 1.80) dist_sol_mol_max = 5.99 (limit = 6.00) Before RSCC filtering: 860 After RSCC filtering: 854 2mFo-DFmodel map selection: number = 854 b_iso_min = 16.96 (limit = 1.00) b_iso_max = 79.73 (limit = 80.00) b_iso_mean = 40.50 anisotropy_min = 1.00 (limit = 0.10) occupancy_min = 1.00 (limit = 0.10) occupancy_max = 1.00 (limit = 1.00) dist_sol_mol_min = -1.00 (limit = 1.80) dist_sol_mol_max = 5.99 (limit = 6.00) Final: number = 854 b_iso_min = 16.96 (limit = 1.00) b_iso_max = 79.73 (limit = 80.00) b_iso_mean = 40.50 anisotropy_min = 1.00 (limit = 0.10) occupancy_min = 1.00 (limit = 0.10) occupancy_max = 1.00 (limit = 1.00) dist_sol_mol_min = -1.00 (limit = 1.80) dist_sol_mol_max = 5.99 (limit = 6.00) ----------X-ray data---------- |--(resolution: 2.08 - 43.31 A; n_refl. = 131090)-----------------------------| | | | r_work= 0.2367 r_free= 0.2696 ksol= 0.34 Bsol= 41.67 scale= 1.024 | | | | overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):| | (0.48,0.02,-0.51,0.00,-0.08,0.00); trace/3= 0.00 | | | | maximum likelihood estimate for coordinate error: 0.35 A | | x-ray target function (ml) for work reflections: 5.589332 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 43.3150 - 6.4563 0.99 4256 244 0.2162 0.2281 6.6057 6.6387| | 2: 6.4563 - 5.1272 0.98 4171 229 0.2361 0.2590 6.4028 6.4378| | 3: 5.1272 - 4.4799 0.98 4166 210 0.2071 0.2389 6.5562 6.6997| | 4: 4.4799 - 4.0706 0.98 4121 241 0.2197 0.2443 6.5552 6.6219| | 5: 4.0706 - 3.7790 0.98 4145 248 0.2228 0.2567 6.4323 6.515| | 6: 3.7790 - 3.5563 0.98 4143 203 0.2292 0.2347 6.372 6.4256| | 7: 3.5563 - 3.3783 0.98 4139 225 0.2392 0.2585 6.2617 6.2646| | 8: 3.3783 - 3.2313 0.98 4163 231 0.2320 0.2632 6.0907 6.155| | 9: 3.2313 - 3.1069 0.98 4156 204 0.2357 0.2758 5.9904 6.0407| | 10: 3.1069 - 2.9998 0.98 4188 211 0.2451 0.2885 5.9097 5.9724| | 11: 2.9998 - 2.9060 0.98 4163 216 0.2505 0.3181 5.8462 5.958| | 12: 2.9060 - 2.8229 0.99 4202 210 0.2486 0.2993 5.7165 5.7804| | 13: 2.8229 - 2.7486 0.98 4162 211 0.2360 0.2662 5.5977 5.6695| | 14: 2.7486 - 2.6816 0.99 4156 229 0.2475 0.2791 5.5237 5.6128| | 15: 2.6816 - 2.6206 0.99 4120 244 0.2455 0.2863 5.4629 5.6065| | 16: 2.6206 - 2.5649 0.98 4192 195 0.2481 0.2899 5.4016 5.479| | 17: 2.5649 - 2.5136 0.98 4149 217 0.2525 0.3117 5.3541 5.4836| | 18: 2.5136 - 2.4661 0.99 4136 224 0.2517 0.2970 5.3075 5.4093| | 19: 2.4661 - 2.4221 0.98 4141 235 0.2490 0.3114 5.2504 5.3726| | 20: 2.4221 - 2.3810 0.98 4186 214 0.2529 0.3012 5.2182 5.3413| | 21: 2.3810 - 2.3426 0.99 4130 220 0.2658 0.2783 5.164 5.2476| | 22: 2.3426 - 2.3066 0.98 4188 215 0.2445 0.3053 5.0897 5.2025| | 23: 2.3066 - 2.2727 0.99 4160 214 0.2425 0.2966 5.0263 5.1434| | 24: 2.2727 - 2.2407 0.98 4142 231 0.2488 0.2906 5.0052 5.09| | 25: 2.2407 - 2.2104 0.98 4162 215 0.2563 0.3296 4.9756 5.1295| | 26: 2.2104 - 2.1817 0.98 4219 209 0.2734 0.3063 4.9415 5.0437| | 27: 2.1817 - 2.1544 0.98 4039 241 0.2799 0.3199 4.9287 5.0505| | 28: 2.1544 - 2.1284 0.98 4211 217 0.2895 0.3533 4.8925 4.9778| | 29: 2.1284 - 2.1037 0.98 4137 225 0.2843 0.3410 4.8627 4.9225| | 30: 2.1037 - 2.0801 0.90 3829 190 0.3038 0.3547 4.8595 4.9336| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 43.3150 - 6.4563 4256 244 0.87 21.08 0.96 0.96 93456.18| | 2: 6.4563 - 5.1272 4171 229 0.85 22.96 0.93 0.89 68539.99| | 3: 5.1272 - 4.4799 4166 210 0.88 20.13 1.02 1.01 90956.14| | 4: 4.4799 - 4.0706 4121 241 0.87 21.25 1.05 1.05 91738.22| | 5: 4.0706 - 3.7790 4145 248 0.86 22.44 1.05 1.01 74475.56| | 6: 3.7790 - 3.5563 4143 203 0.86 22.28 1.05 1.01 63715.65| | 7: 3.5563 - 3.3783 4139 225 0.85 23.09 1.05 0.99 49006.54| | 8: 3.3783 - 3.2313 4163 231 0.85 23.76 1.04 0.99 37615.21| | 9: 3.2313 - 3.1069 4156 204 0.84 24.56 1.02 0.97 31460.28| | 10: 3.1069 - 2.9998 4188 211 0.82 26.49 1.02 0.96 27854.97| | 11: 2.9998 - 2.9060 4163 216 0.79 29.17 0.99 0.89 26824.84| | 12: 2.9060 - 2.8229 4202 210 0.80 28.23 0.97 0.89 20517.79| | 13: 2.8229 - 2.7486 4162 211 0.83 25.42 0.96 0.91 14889.30| | 14: 2.7486 - 2.6816 4156 229 0.82 26.41 0.96 0.91 12827.98| | 15: 2.6816 - 2.6206 4120 244 0.81 27.23 0.97 0.92 11851.26| | 16: 2.6206 - 2.5649 4192 195 0.80 28.23 0.96 0.91 11139.15| | 17: 2.5649 - 2.5136 4149 217 0.79 28.90 0.94 0.86 9922.74| | 18: 2.5136 - 2.4661 4136 224 0.80 28.44 0.94 0.87 9188.26| | 19: 2.4661 - 2.4221 4141 235 0.79 28.95 0.94 0.86 8391.35| | 20: 2.4221 - 2.3810 4186 214 0.79 29.10 0.94 0.87 7882.68| | 21: 2.3810 - 2.3426 4130 220 0.78 29.54 0.92 0.84 6916.53| | 22: 2.3426 - 2.3066 4188 215 0.81 27.12 0.94 0.88 5739.64| | 23: 2.3066 - 2.2727 4160 214 0.82 26.02 0.94 0.89 5005.45| | 24: 2.2727 - 2.2407 4142 231 0.82 26.83 0.93 0.84 4737.21| | 25: 2.2407 - 2.2104 4162 215 0.79 29.38 0.93 0.82 4888.45| | 26: 2.2104 - 2.1817 4219 209 0.77 30.63 0.92 0.83 4674.87| | 27: 2.1817 - 2.1544 4039 241 0.76 31.78 0.92 0.85 4767.39| | 28: 2.1544 - 2.1284 4211 217 0.75 32.75 0.91 0.82 4387.84| | 29: 2.1284 - 2.1037 4137 225 0.75 32.76 0.92 0.84 4229.56| | 30: 2.1037 - 2.0801 3829 190 0.76 31.95 0.91 0.77 3617.11| |alpha: min = 0.77 max = 1.06 mean = 0.90| |beta: min = 3467.31 max = 106498.25 mean = 27138.02| |figures of merit: min = 0.00 max = 1.00 mean = 0.81| |phase err.(work): min = 0.00 max = 89.82 mean = 26.88| |phase err.(test): min = 0.00 max = 89.08 mean = 27.28| |-----------------------------------------------------------------------------| ====================== bulk solvent modeling and scaling ====================== |-Mask optimization: start----------------------------------------------------| | Solvent (probe) radius= 1.30 Shrink truncation radius= 1.06 | | all data: 500 lowest resolution reflections: | | r_work= 0.2367 r_free= 0.2696 r_work= 0.3089 (resolution: 43.31-13.14 A)| |-----------------------------------------------------------------------------| r_solv= 0.00 r_shrink= 0.00 r_work=0.2690 r_free=0.2995 r_work_low=0.8031 r_solv= 0.10 r_shrink= 0.00 r_work=0.2646 r_free=0.2953 r_work_low=0.6526 r_solv= 0.20 r_shrink= 0.00 r_work=0.2598 r_free=0.2907 r_work_low=0.5161 r_solv= 0.30 r_shrink= 0.00 r_work=0.2545 r_free=0.2854 r_work_low=0.4171 r_solv= 0.40 r_shrink= 0.04 r_work=0.2490 r_free=0.2807 r_work_low=0.3623 r_solv= 0.50 r_shrink= 0.16 r_work=0.2443 r_free=0.2772 r_work_low=0.3464 r_solv= 0.60 r_shrink= 0.27 r_work=0.2411 r_free=0.2747 r_work_low=0.3553 r_solv= 0.70 r_shrink= 0.38 r_work=0.2397 r_free=0.2731 r_work_low=0.3816 r_solv= 0.80 r_shrink= 0.49 r_work=0.2409 r_free=0.2744 r_work_low=0.3143 r_solv= 0.90 r_shrink= 0.61 r_work=0.2395 r_free=0.2720 r_work_low=0.3069 r_solv= 1.00 r_shrink= 0.72 r_work=0.2388 r_free=0.2717 r_work_low=0.2924 r_solv= 1.10 r_shrink= 0.83 r_work=0.2375 r_free=0.2704 r_work_low=0.2983 r_solv= 1.20 r_shrink= 0.95 r_work=0.2369 r_free=0.2703 r_work_low=0.3093 r_solv= 1.30 r_shrink= 1.06 r_work=0.2367 r_free=0.2696 r_work_low=0.3089 r_solv= 1.40 r_shrink= 1.17 r_work=0.2368 r_free=0.2693 r_work_low=0.2964 |-Mask optimization: final----------------------------------------------------| | Solvent (probe) radius= 1.30 Shrink truncation radius= 1.06 | | all data: 500 lowest resolution reflections: | | r_work= 0.2367 r_free= 0.2696 r_work= 0.3089 (resolution: 43.31-13.14 A)| |-----------------------------------------------------------------------------| |--(resolution: 2.08 - 43.31 A; n_refl. = 131090)-----------------------------| | | | r_work= 0.2362 r_free= 0.2691 ksol= 0.34 Bsol= 42.02 scale= 1.031 | | | | overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):| | (0.48,0.03,-0.50,0.00,-0.08,0.00); trace/3= 0.00 | | | | maximum likelihood estimate for coordinate error: 0.34 A | | x-ray target function (ml) for work reflections: 5.589341 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 2.08 - 43.31 A; n_refl. = 131090)-----------------------------| | | | r_work= 0.2362 r_free= 0.2691 ksol= 0.34 Bsol= 42.02 scale= 1.031 | | | | overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):| | (0.48,0.03,-0.50,0.00,-0.08,0.00); trace/3= 0.00 | | | | maximum likelihood estimate for coordinate error: 0.34 A | | x-ray target function (ml) for work reflections: 5.589341 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 43.3150 - 6.4563 0.99 4256 244 0.2168 0.2285 6.6057 6.6386| | 2: 6.4563 - 5.1272 0.98 4171 229 0.2368 0.2599 6.4028 6.4378| | 3: 5.1272 - 4.4799 0.98 4166 210 0.2070 0.2388 6.5563 6.6997| | 4: 4.4799 - 4.0706 0.98 4121 241 0.2196 0.2441 6.5551 6.6218| | 5: 4.0706 - 3.7790 0.98 4145 248 0.2227 0.2567 6.4323 6.515| | 6: 3.7790 - 3.5563 0.98 4143 203 0.2293 0.2347 6.372 6.4256| | 7: 3.5563 - 3.3783 0.98 4139 225 0.2394 0.2586 6.2617 6.2645| | 8: 3.3783 - 3.2313 0.98 4163 231 0.2322 0.2633 6.0907 6.155| | 9: 3.2313 - 3.1069 0.98 4156 204 0.2359 0.2757 5.9904 6.0407| | 10: 3.1069 - 2.9998 0.98 4188 211 0.2453 0.2886 5.9098 5.9724| | 11: 2.9998 - 2.9060 0.98 4163 216 0.2503 0.3174 5.8462 5.958| | 12: 2.9060 - 2.8229 0.99 4202 210 0.2481 0.2987 5.7165 5.7804| | 13: 2.8229 - 2.7486 0.98 4162 211 0.2353 0.2652 5.5977 5.6695| | 14: 2.7486 - 2.6816 0.99 4156 229 0.2467 0.2784 5.5237 5.6128| | 15: 2.6816 - 2.6206 0.99 4120 244 0.2446 0.2860 5.4629 5.6065| | 16: 2.6206 - 2.5649 0.98 4192 195 0.2471 0.2889 5.4016 5.479| | 17: 2.5649 - 2.5136 0.98 4149 217 0.2510 0.3102 5.3542 5.4836| | 18: 2.5136 - 2.4661 0.99 4136 224 0.2501 0.2962 5.3075 5.4093| | 19: 2.4661 - 2.4221 0.98 4141 235 0.2474 0.3095 5.2504 5.3726| | 20: 2.4221 - 2.3810 0.98 4186 214 0.2513 0.3000 5.2182 5.3413| | 21: 2.3810 - 2.3426 0.99 4130 220 0.2633 0.2764 5.164 5.2476| | 22: 2.3426 - 2.3066 0.98 4188 215 0.2428 0.3028 5.0897 5.2024| | 23: 2.3066 - 2.2727 0.99 4160 214 0.2407 0.2947 5.0263 5.1434| | 24: 2.2727 - 2.2407 0.98 4142 231 0.2465 0.2883 5.0052 5.09| | 25: 2.2407 - 2.2104 0.98 4162 215 0.2540 0.3261 4.9757 5.1295| | 26: 2.2104 - 2.1817 0.98 4219 209 0.2706 0.3038 4.9415 5.0438| | 27: 2.1817 - 2.1544 0.98 4039 241 0.2772 0.3184 4.9287 5.0506| | 28: 2.1544 - 2.1284 0.98 4211 217 0.2868 0.3497 4.8925 4.9778| | 29: 2.1284 - 2.1037 0.98 4137 225 0.2817 0.3385 4.8627 4.9225| | 30: 2.1037 - 2.0801 0.90 3829 190 0.3011 0.3515 4.8595 4.9337| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 43.3150 - 6.4563 4256 244 0.87 21.08 0.96 0.96 93451.17| | 2: 6.4563 - 5.1272 4171 229 0.85 22.96 0.93 0.90 68546.00| | 3: 5.1272 - 4.4799 4166 210 0.88 20.14 1.01 1.01 90962.92| | 4: 4.4799 - 4.0706 4121 241 0.87 21.25 1.05 1.06 91736.84| | 5: 4.0706 - 3.7790 4145 248 0.86 22.44 1.05 1.01 74466.49| | 6: 3.7790 - 3.5563 4143 203 0.86 22.28 1.05 1.02 63707.21| | 7: 3.5563 - 3.3783 4139 225 0.85 23.09 1.05 1.00 49000.96| | 8: 3.3783 - 3.2313 4163 231 0.85 23.77 1.04 0.99 37614.31| | 9: 3.2313 - 3.1069 4156 204 0.84 24.56 1.03 0.98 31459.61| | 10: 3.1069 - 2.9998 4188 211 0.82 26.50 1.03 0.97 27856.53| | 11: 2.9998 - 2.9060 4163 216 0.79 29.17 0.99 0.90 26825.84| | 12: 2.9060 - 2.8229 4202 210 0.80 28.23 0.97 0.90 20515.94| | 13: 2.8229 - 2.7486 4162 211 0.83 25.42 0.97 0.92 14888.66| | 14: 2.7486 - 2.6816 4156 229 0.82 26.41 0.97 0.92 12828.59| | 15: 2.6816 - 2.6206 4120 244 0.81 27.23 0.98 0.94 11851.62| | 16: 2.6206 - 2.5649 4192 195 0.80 28.23 0.96 0.92 11139.15| | 17: 2.5649 - 2.5136 4149 217 0.79 28.90 0.95 0.87 9922.66| | 18: 2.5136 - 2.4661 4136 224 0.80 28.44 0.95 0.88 9187.96| | 19: 2.4661 - 2.4221 4141 235 0.79 28.95 0.95 0.87 8390.70| | 20: 2.4221 - 2.3810 4186 214 0.79 29.10 0.95 0.88 7882.77| | 21: 2.3810 - 2.3426 4130 220 0.78 29.54 0.93 0.85 6917.05| | 22: 2.3426 - 2.3066 4188 215 0.81 27.13 0.95 0.89 5739.67| | 23: 2.3066 - 2.2727 4160 214 0.82 26.02 0.95 0.90 5005.43| | 24: 2.2727 - 2.2407 4142 231 0.82 26.83 0.94 0.86 4737.04| | 25: 2.2407 - 2.2104 4162 215 0.79 29.38 0.94 0.84 4888.37| | 26: 2.2104 - 2.1817 4219 209 0.77 30.63 0.93 0.84 4675.19| | 27: 2.1817 - 2.1544 4039 241 0.76 31.78 0.93 0.87 4767.80| | 28: 2.1544 - 2.1284 4211 217 0.75 32.75 0.92 0.83 4387.99| | 29: 2.1284 - 2.1037 4137 225 0.75 32.77 0.93 0.85 4229.81| | 30: 2.1037 - 2.0801 3829 190 0.76 31.95 0.93 0.79 3616.95| |alpha: min = 0.79 max = 1.07 mean = 0.92| |beta: min = 3467.01 max = 106495.00 mean = 27137.45| |figures of merit: min = 0.00 max = 1.00 mean = 0.81| |phase err.(work): min = 0.00 max = 89.82 mean = 26.88| |phase err.(test): min = 0.00 max = 89.08 mean = 27.28| |-----------------------------------------------------------------------------| |-ADP statistics--------------------------------------------------------------| | Atom | Number of | Isotropic or equivalent| Anisotropy lmin/max | | type |iso aniso | min max mean | min max mean | | - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - - | | all : 14381 0 12.09 98.33 39.87 None None None | | all(noH): 14381 0 12.09 98.33 39.87 None None None | | Sol. : 854 0 17.31 80.08 40.85 None None None | | Mac. : 13527 0 12.09 98.33 39.80 None None None | | Hyd. : 0 0 None None None None None None | | - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - | | Distribution of isotropic (or equivalent) ADP for non-H atoms: | | Bin# value range #atoms | Bin# value range #atoms | | 0: 12.086 - 20.711: 808 | 5: 55.209 - 63.834: 1013 | | 1: 20.711 - 29.335: 3105 | 6: 63.834 - 72.459: 553 | | 2: 29.335 - 37.960: 3519 | 7: 72.459 - 81.083: 232 | | 3: 37.960 - 46.585: 2928 | 8: 81.083 - 89.708: 208 | | 4: 46.585 - 55.209: 1927 | 9: 89.708 - 98.333: 88 | | =>continue=> | |-----------------------------------------------------------------------------| ================= overall refinement statistics: step by step ================= ****************** REFINEMENT STATISTICS STEP BY STEP ****************** leading digit, like 1_, means number of macro-cycle 0 : statistics at the very beginning when nothing is done yet 1_bss: bulk solvent correction and/or (anisotropic) scaling 1_xyz: refinement of coordinates 1_adp: refinement of ADPs (Atomic Displacement Parameters) 1_wat: ordered solvent update (add / remove) ------------------------------------------------------------------------ R-factors, x-ray target values and norm of gradient of x-ray target stage r-work r-free xray_target_w xray_target_t 0 : 0.2392 0.2713 5.596226e+00 5.686326e+00 1_bss: 0.2387 0.2710 5.595405e+00 5.684586e+00 1_xyz: 0.2373 0.2731 5.593305e+00 5.691945e+00 1_adp: 0.2375 0.2737 5.593272e+00 5.692512e+00 2_bss: 0.2370 0.2725 5.592894e+00 5.691145e+00 2_xyz: 0.2361 0.2721 5.590557e+00 5.689720e+00 2_adp: 0.2364 0.2724 5.590053e+00 5.689032e+00 3_bss: 0.2360 0.2714 5.589912e+00 5.688044e+00 3_xyz: 0.2360 0.2723 5.590028e+00 5.691465e+00 3_adp: 0.2363 0.2727 5.589848e+00 5.691361e+00 3_bss: 0.2362 0.2691 5.589341e+00 5.683836e+00 ------------------------------------------------------------------------ stage k_sol b_sol b11 b22 b33 b12 b13 b23 0 : 0.341 41.035 0.484 0.013 -0.497 -0.000 -0.071 -0.000 1_bss: 0.341 41.035 0.484 0.013 -0.497 -0.000 -0.071 -0.000 1_xyz: 0.341 41.035 0.484 0.013 -0.497 -0.000 -0.071 -0.000 1_adp: 0.341 41.035 0.484 0.013 -0.497 -0.000 -0.071 -0.000 2_bss: 0.341 41.347 0.479 0.022 -0.501 0.000 -0.073 0.000 2_xyz: 0.341 41.347 0.479 0.022 -0.501 0.000 -0.073 0.000 2_adp: 0.341 41.347 0.479 0.022 -0.501 0.000 -0.073 0.000 3_bss: 0.341 41.665 0.483 0.023 -0.506 0.000 -0.076 0.000 3_xyz: 0.341 41.665 0.483 0.023 -0.506 0.000 -0.076 0.000 3_adp: 0.341 41.665 0.483 0.023 -0.506 0.000 -0.076 0.000 3_bss: 0.341 42.016 0.475 0.026 -0.501 0.000 -0.079 0.000 ------------------------------------------------------------------------ stage fom alpha beta 0 : 27.062 0.8104 0.9177 27709.777 1_bss: 26.944 0.8117 0.9167 27517.316 1_xyz: 27.324 0.8075 0.9134 28154.189 1_adp: 27.355 0.8071 0.9032 28198.710 2_bss: 27.313 0.8076 0.9130 27905.812 2_xyz: 27.225 0.8086 0.9120 27828.051 2_adp: 27.184 0.8090 0.9030 27771.129 3_bss: 27.152 0.8093 0.9129 27534.477 3_xyz: 27.271 0.8080 0.9110 27915.861 3_adp: 27.256 0.8082 0.9010 27915.529 3_bss: 26.901 0.8121 0.9151 27163.233 ------------------------------------------------------------------------ stage angl bond chir dihe plan repu geom_target 0 : 1.084 0.010 0.071 15.286 0.005 4.108 1.0851e-01 1_bss: 1.084 0.010 0.071 15.286 0.005 4.108 1.0851e-01 1_xyz: 1.072 0.009 0.070 15.179 0.005 4.109 8.4430e-02 1_adp: 1.072 0.009 0.070 15.179 0.005 4.109 8.4430e-02 2_bss: 1.072 0.009 0.070 15.179 0.005 4.109 8.4430e-02 2_xyz: 1.034 0.008 0.068 15.058 0.004 4.108 8.0891e-02 2_adp: 1.034 0.008 0.068 15.058 0.004 4.108 8.0891e-02 3_bss: 1.034 0.008 0.068 15.058 0.004 4.108 8.0891e-02 3_xyz: 1.033 0.008 0.068 14.945 0.004 4.108 7.9237e-02 3_adp: 1.033 0.008 0.068 14.945 0.004 4.108 7.9237e-02 3_bss: 1.033 0.008 0.068 14.945 0.004 4.108 8.5537e-02 ------------------------------------------------------------------------ Maximal deviations: stage angl bond chir dihe plan repu |grad| 0 : 16.027 0.578 0.486178.156 0.085 1.256 7.6550e-02 1_bss: 16.027 0.578 0.486178.156 0.085 1.256 7.6550e-02 1_xyz: 12.016 0.081 0.362177.973 0.040 1.999 3.7068e-02 1_adp: 12.016 0.081 0.362177.973 0.040 1.999 3.7068e-02 2_bss: 12.016 0.081 0.362177.973 0.040 1.999 3.7068e-02 2_xyz: 12.052 0.068 0.344177.588 0.038 1.977 3.2512e-02 2_adp: 12.052 0.068 0.344177.588 0.038 1.977 3.2512e-02 3_bss: 12.052 0.068 0.344177.588 0.038 1.977 3.2512e-02 3_xyz: 12.020 0.071 0.342177.732 0.039 1.975 3.2467e-02 3_adp: 12.020 0.071 0.342177.732 0.039 1.975 3.2467e-02 3_bss: 12.020 0.071 0.342177.732 0.039 1.813 3.2794e-02 ------------------------------------------------------------------------ |-----overall-----|---macromolecule----|------solvent-------| stage b_max b_min b_ave b_max b_min b_ave b_max b_min b_ave 0 : 98.47 12.45 39.94 98.47 12.45 39.89 70.68 16.91 40.84 1_bss: 98.47 12.45 39.94 98.47 12.45 39.89 70.68 16.91 40.84 1_xyz: 98.47 12.45 39.94 98.47 12.45 39.89 70.68 16.91 40.84 1_adp: 100.08 11.86 39.58 100.08 11.86 39.53 74.55 16.99 40.51 2_bss: 100.39 12.17 39.89 100.39 12.17 39.84 74.86 17.30 40.82 2_xyz: 100.39 12.17 39.94 100.39 12.17 39.84 71.38 16.53 41.55 2_adp: 100.01 11.85 39.64 100.01 11.85 39.54 76.71 17.21 41.13 3_bss: 100.33 12.17 39.96 100.33 12.17 39.86 77.03 17.53 41.45 3_xyz: 100.33 12.17 39.94 100.33 12.17 39.86 76.19 16.25 41.17 3_adp: 97.98 11.74 39.53 97.98 11.74 39.45 79.73 16.96 40.79 3_bss: 98.33 12.09 39.87 98.33 12.09 39.80 80.08 17.31 40.85 ------------------------------------------------------------------------ stage Deviation of refined model from start model max min mean 0 : 0.000 0.000 0.000 1_bss: 0.000 0.000 0.000 1_xyz: 2.134 0.000 0.028 1_adp: 2.134 0.000 0.028 2_bss: 2.134 0.000 0.028 2_xyz: 2.060 0.000 0.030 2_adp: 2.060 0.000 0.030 3_bss: 2.060 0.000 0.030 3_xyz: 2.086 0.001 0.038 3_adp: 2.086 0.001 0.038 3_bss: 2.086 0.001 0.038 ------------------------------------------------------------------------ stage number of ordered solvent 0 : 804 1_bss: 804 1_xyz: 804 1_adp: 804 2_bss: 804 2_xyz: 880 2_adp: 880 3_bss: 880 3_xyz: 880 3_adp: 880 3_bss: 854 ------------------------------------------------------------------------ ===================== NCS restraints at end of refinement ===================== NCS restraint group 1: NCS operator 1: Reference selection: "chain A and (resseq 2:76 or resseq 78:88 or resseq 110:131 or resseq 143:279 or resseq 281:297 or resseq 299:382 or resseq 389:465 )" Other selection: "chain B and (resseq 2:76 or resseq 78:88 or resseq 110:131 or resseq 143:279 or resseq 281:297 or resseq 299:382 or resseq 389:465 )" Number of atom pairs: 3297 Rotation={{0.305524, 0.0458086, -0.951082}, {0.0364952, -0.998672, -0.0363771}, {-0.951485, -0.0235959, -0.30679}} Translation={{61.3788}, {12.5496}, {84.6039}} Histogram of differences: 0.002945 - 0.038894: 1932 0.038894 - 0.074844: 1064 0.074844 - 0.110793: 235 0.110793 - 0.146742: 52 0.146742 - 0.182692: 7 0.182692 - 0.218641: 7 RMS difference with respect to the reference: 0.047453 NCS operator 2: Reference selection: "chain A and (resseq 2:76 or resseq 78:88 or resseq 110:131 or resseq 143:279 or resseq 281:297 or resseq 299:382 or resseq 389:465 )" Other selection: "chain C and (resseq 2:76 or resseq 78:88 or resseq 110:131 or resseq 143:279 or resseq 281:297 or resseq 299:382 or resseq 389:465 )" Number of atom pairs: 3233 Rotation={{-0.705187, -0.590347, 0.392685}, {-0.61445, 0.232488, -0.753923}, {0.353782, -0.772942, -0.526686}} Translation={{85.8394}, {48.033}, {34.0495}} Histogram of differences: 0.004075 - 0.152705: 3176 0.152705 - 0.301336: 49 0.301336 - 0.449966: 4 0.449966 - 0.598596: 1 0.598596 - 0.747226: 0 0.747226 - 0.895857: 3 RMS difference with respect to the reference: 0.070576 NCS operator 3: Reference selection: "chain A and (resseq 2:76 or resseq 78:88 or resseq 110:131 or resseq 143:279 or resseq 281:297 or resseq 299:382 or resseq 389:465 )" Other selection: "chain D and (resseq 2:76 or resseq 78:88 or resseq 110:131 or resseq 143:279 or resseq 281:297 or resseq 299:382 or resseq 389:465 )" Number of atom pairs: 3219 Rotation={{-0.626588, 0.538039, 0.563827}, {0.534894, -0.22927, 0.813218}, {0.566812, 0.811141, -0.144136}} Translation={{69.4889}, {-50.5923}, {2.14066}} Histogram of differences: 0.003555 - 0.139093: 3166 0.139093 - 0.274631: 49 0.274631 - 0.410169: 2 0.410169 - 0.545707: 0 0.545707 - 0.681245: 0 0.681245 - 0.816783: 2 RMS difference with respect to the reference: 0.060626 CPU time actual refinement: 1148.92 ============================== Exporting results ============================== Writing refined structure to PDB file: /Users/nick/k94e_208/Refine_48/k94e_2_refine_48.pdb n_use = 14381 n_use_u_iso = 14381 n_use_u_aniso = 0 n_grad_site = 0 n_grad_u_iso = 14381 n_grad_u_aniso = 0 n_grad_occupancy = 0 n_grad_fp = 0 n_grad_fdp = 0 total number of scatterers = 14381 =============================== Detailed timings ============================== Pure refinement (no I/O, processing, etc)= 1148.65 Macro-tasks: bulk solvent and scale = 227.43 weights calculation = 53.89 collect and process = 25.13 model show statistics = 2.82 TOTAL for macro-tasks = 309.27 Micro-tasks: mask = 103.96 f_calc = 212.99 alpha_beta = 40.49 target = 5.88 gradients_wrt_atomic_parameters = 207.79 fmodel = 0.00 r_factors = 0.31 phase_errors = 74.07 foms = 1.08 TOTAL for micro-tasks = 646.57 NUMBER OF MASK CALCS= 0 Time per interpreted Python bytecode instruction: 1.737 micro seconds Total CPU time: 20.28 minutes from_scatterers_fft: 378 calls, 211.67 s gradients_fft: 289 calls, 186.03 s =========================== phenix.refine: finished =========================== # Date 2011-01-13 Time 18:09:13 EST -0500 (1294960153.09 s) wall clock time: 1217.10 s Start R-work = 0.2392, R-free = 0.2713 (no bulk solvent and anisotropic scale) Final R-work = 0.3273, R-free = 0.3620 (no bulk solvent and anisotropic scale) Start R-work = 0.2387, R-free = 0.2710 Final R-work = 0.2362, R-free = 0.2691 ======================== Running MolProbity validation ======================== ============= Adding hydrogens and flipping sidechains with REDUCE ============ recommend flipping A 363 HIS recommend flipping B 43 ASN recommend flipping B 365 HIS recommend flipping C 43 ASN recommend flipping D 43 ASN recommend flipping D 292 ASN recommend flipping D 409 HIS ============================ Ramachandran analysis ============================ residue:score%:phi:psi:evaluation:type A 151 ALA:0.00:157.09:10.65:OUTLIER:General B 151 ALA:0.00:156.15:10.51:OUTLIER:General C 151 ALA:0.00:156.93:11.26:OUTLIER:General D 151 ASN:0.00:147.13:37.86:OUTLIER:General SUMMARY: 0.24% outliers (Goal: < 0.2%) SUMMARY: 97.57% favored (Goal: > 98%) =============================== Rotamer analysis ============================== residue:score%:chi1:chi2:chi3:chi4:rotamer A 40 SER:0.5:344.8::::OUTLIER A 177 ARG:0.0:77.4:284.9:203.1:225.6:OUTLIER A 249 GLU:0.8:201.6:239.3:325.8::OUTLIER B 40 SER:0.4:346.0::::OUTLIER B 148 THR:0.9:33.0::::OUTLIER B 177 ARG:0.0:77.1:284.2:203.3:225.0:OUTLIER B 249 GLU:1.0:199.2:240.0:325.2::OUTLIER C 40 SER:0.4:345.7::::OUTLIER C 141 ARG:0.9:254.1:138.6:212.0:198.4:OUTLIER C 177 ARG:0.1:78.3:285.9:204.4:221.6:OUTLIER D 40 SER:0.5:344.5::::OUTLIER D 148 THR:1.0:33.6::::OUTLIER D 177 ARG:0.1:79.3:287.9:205.1:218.8:OUTLIER D 249 GLU:0.9:200.4:240.3:325.3::OUTLIER SUMMARY: 0.96% outliers (Goal: < 1%) ========================= Checking for C-beta outliers ======================== filename /Users/nick/k94e_208/Refine_48/k94e_2_refine_48.pdb ======================== Finding bad clashes with PROBE ======================= Determining coordinates for all bad overlaps ============================ Finding missing atoms ============================ =========================== Generating kinemage file ========================== apply_default_filter: found data points dmin->higher = 500 found data points dmin->lower = 500 used data points dmin->higher = 500 used data points dmin->lower = 500 =========================== Checking final geometry =========================== ======================= Extracting refinement statistics ====================== ====================== Calculating real-space correlation ===================== Saving data for Coot GUI done =================================== Complete ==================================