Starting phenix.refine on Fri Aug 9 09:31:39 2024 by nigel =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, 4phenix_2a8z.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/2a8z/2a8z.mtz Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- optimize_xyz=true optimize_adp=true main.number_of_mac=3 main.max_number_of_iterations=100 main.nproc=20 nonbonded_weight=100 modify_start_model.modify.selection=element H modify_start_model.modify.occupancies.set=1 amber.topology_file_name=4amber_2a8z.prmtop amber.coordinate_file_name=4amber_2a8z.rst7 amber.order_file_name=4amber_2a8z.order use_amber=True strategy=individual_sites+individual_adp ramachandran_plot_restraints.enabled=False secondary_structure.enabled=True main.nqh_flips=False Processing files from PHIL: ------------------------------------------------------------------------------- Files not used by program: -------------------------- 4amber_2a8z.rst7 4amber_2a8z.order 4amber_2a8z.prmtop Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/2a8z/2a8z.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/2a8z/2a8z.mtz" model { file = "4phenix_2a8z.pdb" } default_model = "4phenix_2a8z.pdb" } refinement { 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 \ den } main { nqh_flips = False max_number_of_iterations = 100 nproc = 20 } modify_start_model { modify { selection = element H occupancies { set = 1 } } } pdb_interpretation { secondary_structure { enabled = True } nonbonded_weight = 100 } target_weights { optimize_xyz_weight = true optimize_adp_weight = true } amber { use_amber = True topology_file_name = 4amber_2a8z.prmtop coordinate_file_name = 4amber_2a8z.rst7 order_file_name = 4amber_2a8z.order } } Starting job =============================================================================== Symmetric amino acids flipped None Time to flip residues: 0.00s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/bootstrap/modules/chem_data/mon_lib" Total number of atoms: 6280 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 6280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 6280 Classifications: {'peptide': 404} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 388} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N THR A 217 " occ=0.50 ... (12 atoms not shown) pdb="HG23 THR A 217 " occ=0.50 residue: pdb=" N TYR A 381 " occ=0.60 ... (19 atoms not shown) pdb=" HH TYR A 381 " occ=0.60 Time building chain proxies: 0.73, per 1000 atoms: 0.12 Number of scatterers: 6280 At special positions: 0 Unit cell: (77.779, 77.779, 149.634, 90, 90, 120) Space group: P 31 2 1 (No. 152) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 12 16.00 O 612 8.00 N 555 7.00 C 2066 6.00 H 3035 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 324 " - pdb=" SG CYS A 339 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.17 Conformation dependent library (CDL) restraints added in 137.5 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 746 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 16 helices and 2 sheets defined 48.0% alpha, 4.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.09 Creating SS restraints... Processing helix chain 'A' and resid 11 through 14 No H-bonds generated for 'chain 'A' and resid 11 through 14' Processing helix chain 'A' and resid 20 through 23 No H-bonds generated for 'chain 'A' and resid 20 through 23' Processing helix chain 'A' and resid 29 through 41 Processing helix chain 'A' and resid 77 through 90 Processing helix chain 'A' and resid 93 through 106 Processing helix chain 'A' and resid 116 through 118 No H-bonds generated for 'chain 'A' and resid 116 through 118' Processing helix chain 'A' and resid 143 through 160 Processing helix chain 'A' and resid 168 through 182 Processing helix chain 'A' and resid 201 through 203 No H-bonds generated for 'chain 'A' and resid 201 through 203' Processing helix chain 'A' and resid 206 through 215 Processing helix chain 'A' and resid 219 through 243 removed outlier: 3.558A pdb=" N ASN A 223 " --> pdb=" O GLN A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 295 removed outlier: 4.545A pdb=" N ILE A 286 " --> pdb=" O TRP A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 318 removed outlier: 3.835A pdb=" N THR A 318 " --> pdb=" O SER A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 353 removed outlier: 3.532A pdb=" N LEU A 352 " --> pdb=" O ASN A 348 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N LEU A 353 " --> pdb=" O ALA A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 369 removed outlier: 3.547A pdb=" N GLU A 367 " --> pdb=" O GLU A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 392 Processing sheet with id= A, first strand: chain 'A' and resid 50 through 55 removed outlier: 5.865A pdb=" N GLU A 55 " --> pdb=" O TYR A 59 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N TYR A 59 " --> pdb=" O GLU A 55 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 125 through 128 removed outlier: 6.158A pdb=" N LYS A 127 " --> pdb=" O LYS A 136 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N LYS A 136 " --> pdb=" O LYS A 127 " (cutoff:3.500A) 133 hydrogen bonds defined for protein. 366 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.32 Time building geometry restraints manager: 1.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.98 - 1.15: 3035 1.15 - 1.32: 568 1.32 - 1.49: 1477 1.49 - 1.66: 1273 1.66 - 1.84: 22 Bond restraints: 6375 Sorted by residual: bond pdb=" N THR A 403 " pdb=" H THR A 403 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N MET A 89 " pdb=" H MET A 89 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N VAL A 216 " pdb=" H VAL A 216 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" NH2 ARG A 190 " pdb="HH21 ARG A 190 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" NH1 ARG A 379 " pdb="HH12 ARG A 379 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.44e+01 ... (remaining 6370 not shown) Histogram of bond angle deviations from ideal: 98.94 - 106.02: 217 106.02 - 113.10: 6605 113.10 - 120.19: 2340 120.19 - 127.27: 2193 127.27 - 134.35: 34 Bond angle restraints: 11389 Sorted by residual: angle pdb=" N ASP A 73 " pdb=" CA ASP A 73 " pdb=" C ASP A 73 " ideal model delta sigma weight residual 110.35 119.54 -9.19 1.40e+00 5.10e-01 4.31e+01 angle pdb=" N LEU A 49 " pdb=" CA LEU A 49 " pdb=" C LEU A 49 " ideal model delta sigma weight residual 114.75 107.29 7.46 1.26e+00 6.30e-01 3.50e+01 angle pdb=" N GLN A 47 " pdb=" CA GLN A 47 " pdb=" C GLN A 47 " ideal model delta sigma weight residual 113.50 107.61 5.89 1.23e+00 6.61e-01 2.30e+01 angle pdb=" N ASN A 320 " pdb=" CA ASN A 320 " pdb=" C ASN A 320 " ideal model delta sigma weight residual 108.69 116.64 -7.95 1.77e+00 3.19e-01 2.02e+01 angle pdb=" CA PHE A 404 " pdb=" C PHE A 404 " pdb=" O PHE A 404 " ideal model delta sigma weight residual 121.00 134.22 -13.22 3.00e+00 1.11e-01 1.94e+01 ... (remaining 11384 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.49: 2695 17.49 - 34.99: 228 34.99 - 52.48: 108 52.48 - 69.97: 30 69.97 - 87.46: 9 Dihedral angle restraints: 3070 sinusoidal: 1572 harmonic: 1498 Sorted by residual: dihedral pdb=" CA PRO A 141 " pdb=" C PRO A 141 " pdb=" N ALA A 142 " pdb=" CA ALA A 142 " ideal model delta harmonic sigma weight residual 180.00 158.17 21.83 0 5.00e+00 4.00e-02 1.91e+01 dihedral pdb=" CA ALA A 142 " pdb=" C ALA A 142 " pdb=" N PRO A 143 " pdb=" CA PRO A 143 " ideal model delta harmonic sigma weight residual 180.00 -161.65 -18.35 0 5.00e+00 4.00e-02 1.35e+01 dihedral pdb=" CA TRP A 277 " pdb=" C TRP A 277 " pdb=" N TYR A 278 " pdb=" CA TYR A 278 " ideal model delta harmonic sigma weight residual 180.00 162.47 17.53 0 5.00e+00 4.00e-02 1.23e+01 ... (remaining 3067 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 273 0.066 - 0.133: 106 0.133 - 0.199: 54 0.199 - 0.265: 12 0.265 - 0.332: 3 Chirality restraints: 448 Sorted by residual: chirality pdb=" CA TRP A 124 " pdb=" N TRP A 124 " pdb=" C TRP A 124 " pdb=" CB TRP A 124 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.75e+00 chirality pdb=" CA TRP A 249 " pdb=" N TRP A 249 " pdb=" C TRP A 249 " pdb=" CB TRP A 249 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" CA PHE A 364 " pdb=" N PHE A 364 " pdb=" C PHE A 364 " pdb=" CB PHE A 364 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.79e+00 ... (remaining 445 not shown) Planarity restraints: 990 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 37 " -0.002 2.00e-02 2.50e+03 1.04e-02 3.24e+00 pdb=" CG PHE A 37 " 0.025 2.00e-02 2.50e+03 pdb=" CD1 PHE A 37 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE A 37 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE A 37 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE A 37 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 37 " 0.003 2.00e-02 2.50e+03 pdb=" HD1 PHE A 37 " -0.004 2.00e-02 2.50e+03 pdb=" HD2 PHE A 37 " -0.018 2.00e-02 2.50e+03 pdb=" HE1 PHE A 37 " -0.015 2.00e-02 2.50e+03 pdb=" HE2 PHE A 37 " -0.002 2.00e-02 2.50e+03 pdb=" HZ PHE A 37 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 312 " -0.011 2.00e-02 2.50e+03 9.92e-03 2.95e+00 pdb=" CG PHE A 312 " 0.025 2.00e-02 2.50e+03 pdb=" CD1 PHE A 312 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE A 312 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE A 312 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A 312 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE A 312 " -0.000 2.00e-02 2.50e+03 pdb=" HD1 PHE A 312 " -0.001 2.00e-02 2.50e+03 pdb=" HD2 PHE A 312 " -0.015 2.00e-02 2.50e+03 pdb=" HE1 PHE A 312 " -0.011 2.00e-02 2.50e+03 pdb=" HE2 PHE A 312 " 0.004 2.00e-02 2.50e+03 pdb=" HZ PHE A 312 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 124 " 0.013 2.00e-02 2.50e+03 7.84e-03 2.46e+00 pdb=" CG TRP A 124 " -0.024 2.00e-02 2.50e+03 pdb=" CD1 TRP A 124 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 TRP A 124 " -0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP A 124 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 124 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 124 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 124 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 124 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A 124 " -0.000 2.00e-02 2.50e+03 pdb=" HD1 TRP A 124 " 0.012 2.00e-02 2.50e+03 pdb=" HE1 TRP A 124 " -0.002 2.00e-02 2.50e+03 pdb=" HE3 TRP A 124 " -0.002 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 124 " 0.005 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 124 " 0.007 2.00e-02 2.50e+03 pdb=" HH2 TRP A 124 " -0.004 2.00e-02 2.50e+03 ... (remaining 987 not shown) Histogram of nonbonded interaction distances: 0.66 - 1.45: 20 1.45 - 2.24: 1004 2.24 - 3.02: 18556 3.02 - 3.81: 30493 3.81 - 4.60: 48762 Warning: very small nonbonded interaction distances. Nonbonded interactions: 98835 Sorted by model distance: nonbonded pdb="HH11 ARG A 284 " pdb=" HH TYR A 381 " model vdw 0.662 2.100 nonbonded pdb=" HG1 THR A 217 " pdb="HD22 ASN A 28 " model vdw sym.op. 0.943 2.100 -x+1,-x+y,-z+1/3 nonbonded pdb="HD22 ASN A 28 " pdb=" HG1 THR A 217 " model vdw sym.op. 0.943 2.100 -x+1,-x+y+1,-z+1/3 nonbonded pdb=" HH TYR A 50 " pdb="HD22 ASN A 98 " model vdw 0.983 2.100 nonbonded pdb=" HH TYR A 17 " pdb=" H PHE A 399 " model vdw 0.991 2.100 ... (remaining 98830 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. ============================== Initializing Amber ============================= topology : 4amber_2a8z.prmtop atom order : 4amber_2a8z.order coordinates : 4amber_2a8z.rst7 ===================================== ... ===================================== ============================== Scattering factors ============================= ----------X-ray scattering dictionary---------- Number of scattering types: 5 Type Number sf(0) Gaussians S 12 15.96 2 O 612 7.97 1 N 555 6.97 1 C 2066 5.97 2 H 3035 1.00 1 sf(0) = scattering factor at diffraction angle 0. =========================== Regularize ADP if needed ========================== ========================== Anomalous scatterer groups ========================= All atoms refined with f_prime=0 and f_double_prime=0. ====================== Modifying start model if requested ===================== Setting occupancies to: 1.000: selected atoms: 3035 of 6280 ******************************************************************************* Automatic adjustment: hydrogens.refine=riding ******************************************************************************* n_use = 6280 n_use_u_iso = 6280 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 = 6280 ================== Extract refinement strategy and selections ================= Refinement flags and selection counts: individual_sites = True (6280 atoms) torsion_angles = False (0 atoms) rigid_body = False (0 atoms in 0 groups) individual_adp = True (iso = 6280 aniso = 0) group_adp = False (0 atoms in 0 groups) tls = False (0 atoms in 0 groups) occupancies = False (0 atoms) group_anomalous = False ============================ 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 { 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 den } main { nqh_flips = False max_number_of_iterations = 100 nproc = 20 } modify_start_model { modify { selection = element H occupancies { set = 1 } } } hydrogens { refine = individual *riding Auto } pdb_interpretation { secondary_structure { protein { helix { serial_number = "1" helix_identifier = "1" selection = chain 'A' and resid 11 through 14 } helix { serial_number = "2" helix_identifier = "2" selection = chain 'A' and resid 20 through 23 } helix { serial_number = "3" helix_identifier = "3" selection = chain 'A' and resid 29 through 41 } helix { serial_number = "4" helix_identifier = "4" selection = chain 'A' and resid 77 through 90 } helix { serial_number = "5" helix_identifier = "5" selection = chain 'A' and resid 93 through 106 } helix { serial_number = "6" helix_identifier = "6" selection = chain 'A' and resid 116 through 118 helix_type = alpha pi *3_10 unknown } helix { serial_number = "7" helix_identifier = "7" selection = chain 'A' and resid 143 through 160 } helix { serial_number = "8" helix_identifier = "8" selection = chain 'A' and resid 168 through 182 } helix { serial_number = "9" helix_identifier = "9" selection = chain 'A' and resid 201 through 203 helix_type = alpha pi *3_10 unknown } helix { serial_number = "10" helix_identifier = "10" selection = chain 'A' and resid 206 through 215 } helix { serial_number = "11" helix_identifier = "11" selection = chain 'A' and resid 219 through 243 } helix { serial_number = "12" helix_identifier = "12" selection = chain 'A' and resid 282 through 295 helix_type = alpha pi *3_10 unknown } helix { serial_number = "13" helix_identifier = "13" selection = chain 'A' and resid 300 through 318 } helix { serial_number = "14" helix_identifier = "14" selection = chain 'A' and resid 342 through 353 } helix { serial_number = "15" helix_identifier = "15" selection = chain 'A' and resid 358 through 369 } helix { serial_number = "16" helix_identifier = "16" selection = chain 'A' and resid 379 through 392 } sheet { first_strand = chain 'A' and resid 50 through 55 sheet_id = " A" strand { selection = chain 'A' and resid 58 through 64 sense = parallel *antiparallel unknown bond_start_current = chain 'A' and resid 63 and name N bond_start_previous = chain 'A' and resid 51 and name O } } sheet { first_strand = chain 'A' and resid 125 through 128 sheet_id = " B" strand { selection = chain 'A' and resid 134 through 138 sense = parallel *antiparallel unknown bond_start_current = chain 'A' and resid 138 and name N bond_start_previous = chain 'A' and resid 125 and name O } } } enabled = True } nonbonded_weight = 100 } target_weights { optimize_xyz_weight = True optimize_adp_weight = True } amber { use_amber = True topology_file_name = "4amber_2a8z.prmtop" coordinate_file_name = "4amber_2a8z.rst7" order_file_name = "4amber_2a8z.order" } } output { prefix = "4phenix_2a8z_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== WARNING: failed to analyze molecule topology. Atomic model may be wrong. ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 3.20 - 12.00 A, n_refl.=8335 (all), 4.73 % free)-------------| | | | r_work= 0.3129 r_free= 0.3544 coordinate error (max.-lik. estimate): 0.39 A | | | | normalized target function (ml) (work): 5.774468 | | target function (ml) not normalized (work): 45855.053064 | | target function (ml) not normalized (free): 2284.420541 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 12.00 - 4.56 0.92 2698 109 0.3334 0.3788 5.9904 6.0301| | 2: 4.56 - 3.65 0.94 2624 139 0.2857 0.3228 5.8247 5.8383| | 3: 3.65 - 3.20 0.95 2619 146 0.3196 0.3667 5.5017 5.5864| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 12.00 - 4.56 2698 109 0.66 38.44 0.93 0.31 29588.62| | 2: 4.56 - 3.65 2624 139 0.72 33.79 1.09 0.35 19246.12| | 3: 3.65 - 3.20 2619 146 0.70 35.80 1.05 0.38 11572.46| |alpha: min = 0.31 max = 0.38 mean = 0.35| |beta: min = 11572.46 max = 29588.62 mean = 20229.22| |figures of merit: min = 0.00 max = 1.00 mean = 0.69| |phase err.(work): min = 0.00 max = 89.98 mean = 36.03| |phase err.(test): min = 0.00 max = 88.17 mean = 36.03| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.100 3340 Z= 0.544 Angle : 1.367 13.217 4535 Z= 0.896 Chirality : 0.089 0.332 448 Planarity : 0.003 0.010 602 Dihedral : 17.613 81.511 1181 Min Nonbonded Distance : 1.756 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.75 % Allowed : 7.71 % Favored : 91.54 % Rotamer: Outliers : 7.81 % Allowed : 9.31 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.93 (0.33), residues: 402 helix: -2.91 (0.26), residues: 192 sheet: -2.64 (0.92), residues: 22 loop : -2.13 (0.39), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 337 TYR 0.020 0.003 TYR A 148 PHE 0.022 0.003 PHE A 312 TRP 0.021 0.003 TRP A 124 HIS 0.007 0.001 HIS A 302 Individual atomic B min max mean iso aniso Overall: 3.85 57.10 26.96 0.66 3245 0 Protein: 3.85 57.10 26.96 0.66 3245 0 Chain A: 3.85 57.10 26.96 N/A 3245 0 Histogram: Values Number of atoms 3.85 - 9.18 8 9.18 - 14.50 371 14.50 - 19.83 524 19.83 - 25.15 498 25.15 - 30.48 647 30.48 - 35.80 648 35.80 - 41.12 295 41.12 - 46.45 151 46.45 - 51.78 45 51.78 - 57.10 58 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 3 ************************* |--(resolution: 3.20 - 12.00 A, n_refl.=8335 (all), 4.73 % free)-------------| | | | r_work= 0.3129 r_free= 0.3544 coordinate error (max.-lik. estimate): 0.39 A | | | | normalized target function (ml) (work): 5.774468 | | target function (ml) not normalized (work): 45855.053064 | | target function (ml) not normalized (free): 2284.420541 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.3148 0.3129 0.3544 n_refl.: 8335 re-set all scales: r(all,work,free)=0.3148 0.3129 0.3544 n_refl.: 8335 remove outliers: r(all,work,free)=0.3148 0.3129 0.3544 n_refl.: 8334 overall B=20.20 to atoms: r(all,work,free)=0.3415 0.3393 0.3871 n_refl.: 8334 bulk-solvent and scaling: r(all,work,free)=0.2141 0.2122 0.2538 n_refl.: 8334 remove outliers: r(all,work,free)=0.2141 0.2122 0.2538 n_refl.: 8334 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 11.998-10.364 91.74 96 4 0.2070 1018.425 980.586 1.014 0.997 0.326 10.272-9.295 90.91 94 6 0.2063 877.802 846.999 1.054 0.991 0.356 9.288-8.400 90.37 120 2 0.1819 902.982 893.417 1.033 0.995 0.353 8.393-7.595 91.10 165 9 0.1966 807.789 781.439 1.078 0.999 0.362 7.592-6.868 91.57 220 8 0.2409 650.451 625.343 1.015 0.994 0.373 6.866-6.210 91.74 299 12 0.2722 553.993 521.405 1.012 0.996 0.372 6.206-5.619 92.63 386 16 0.2376 540.519 514.087 0.988 0.997 0.354 5.613-5.076 92.87 551 22 0.2132 562.932 548.116 0.991 0.996 0.335 5.075-4.591 93.18 709 29 0.1929 622.531 607.939 0.996 0.999 0.306 4.589-4.150 93.71 986 42 0.1841 661.890 646.037 1.033 0.998 0.260 4.148-3.753 93.94 1277 72 0.2026 564.671 549.496 1.068 1.005 0.186 3.750-3.393 94.50 1743 97 0.2139 460.408 441.935 1.128 1.008 0.141 3.392-3.201 94.81 1294 75 0.2534 357.507 336.116 1.119 1.009 0.069 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-5.6976 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ==================== Compute data/restraints target weights =================== Setting wxc_scale using amber.wxc_factor : 0.500 * 1.000 = 0.500 |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 3.287420 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.237704 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2334 0.2703 0.0369 0.013 1.8 0.6 0.5 2.4 0 0.125 0.2207 0.2611 0.0404 0.013 1.8 1.0 0.5 3.6 0 0.250 0.2067 0.2614 0.0546 0.014 1.9 1.1 0.5 2.4 0 0.500 0.1947 0.2545 0.0598 0.016 2.2 2.1 0.5 6.6 0 1.000 0.1827 0.2638 0.0811 0.021 2.8 4.5 1.0 8.1 3 2.000 0.1749 0.2678 0.0929 0.025 3.3 6.2 1.7 8.4 8 3.000 0.1807 0.2552 0.0744 0.028 2.8 8.3 0.2 9.0 2 4.000 0.1822 0.2539 0.0718 0.029 2.7 9.6 0.2 8.7 1 5.000 0.1804 0.2536 0.0732 0.032 2.8 10.2 0.2 8.7 1 6.000 0.1810 0.2533 0.0723 0.033 2.8 10.7 0.2 8.7 1 7.000 0.1768 0.2546 0.0778 0.037 3.1 12.1 0.5 9.0 2 8.000 0.1777 0.2535 0.0759 0.038 3.1 12.1 0.5 9.3 1 9.000 0.1756 0.2544 0.0788 0.041 3.3 12.7 0.5 9.3 2 10.000 0.1862 0.2631 0.0769 0.019 2.6 3.3 0.7 7.8 2 1.644 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2067 0.2614 0.0546 0.014 1.9 1.1 0.5 2.4 0 0.500 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 20.67 26.14 5.46 0.478 47.112 0.238 0.049 20.70 26.06 5.36 1.389 47.167 0.007 0.049 20.26 25.92 5.66 1.583 47.206 0.030 0.047 19.55 25.79 6.24 2.505 47.280 0.119 0.044 18.66 25.68 7.01 4.975 47.666 0.238 0.040 18.42 25.70 7.29 5.919 47.883 0.357 0.039 18.26 25.72 7.45 6.630 48.065 0.475 0.039 18.18 25.72 7.55 7.106 48.186 0.594 0.038 18.07 25.75 7.68 7.727 48.367 0.713 0.038 18.02 25.77 7.75 8.058 48.457 0.832 0.038 17.84 25.81 7.98 9.267 48.846 0.951 0.037 17.74 25.89 8.15 9.931 49.062 1.070 0.036 17.71 25.93 8.22 10.240 49.152 1.189 0.036 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.030 Accepted refinement result: 20.26 25.92 5.66 1.583 47.206 0.030 0.047 Individual atomic B min max mean iso aniso Overall: 28.12 76.32 47.34 1.35 3245 0 Protein: 28.12 76.32 47.34 1.35 3245 0 Chain A: 28.12 76.32 47.34 N/A 3245 0 Histogram: Values Number of atoms 28.12 - 32.94 143 32.94 - 37.76 398 37.76 - 42.58 581 42.58 - 47.40 518 47.40 - 52.22 654 52.22 - 57.04 487 57.04 - 61.86 244 61.86 - 66.68 119 66.68 - 71.50 46 71.50 - 76.32 55 =========================== Idealize ADP of riding H ========================== r_work=0.2026 r_free=0.2592 r_work=0.2021 r_free=0.2581 *********************** REFINEMENT MACRO_CYCLE 2 OF 3 ************************* |--(resolution: 3.20 - 12.00 A, n_refl.=8334 (all), 4.73 % free)-------------| | | | r_work= 0.2021 r_free= 0.2581 coordinate error (max.-lik. estimate): 0.37 A | | | | normalized target function (ls_wunit_k1) (work): 0.046790 | | target function (ls_wunit_k1) not normalized (work): 371.510950 | | target function (ls_wunit_k1) not normalized (free): 31.147494 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2047 0.2021 0.2581 n_refl.: 8334 re-set all scales: r(all,work,free)=0.3445 0.3421 0.3950 n_refl.: 8334 remove outliers: r(all,work,free)=0.3445 0.3421 0.3950 n_refl.: 8334 overall B=-5.03 to atoms: r(all,work,free)=0.3350 0.3326 0.3841 n_refl.: 8334 bulk-solvent and scaling: r(all,work,free)=0.2041 0.2016 0.2555 n_refl.: 8334 remove outliers: r(all,work,free)=0.2041 0.2016 0.2555 n_refl.: 8334 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 11.998-10.364 92.59 96 4 0.1890 695.577 677.862 1.131 0.993 0.344 10.272-9.295 91.74 94 6 0.1894 599.532 583.404 1.158 0.986 0.370 9.288-8.400 91.04 120 2 0.1637 616.730 612.510 1.144 0.990 0.376 8.393-7.595 91.58 165 9 0.1770 551.714 541.461 1.164 0.995 0.378 7.592-6.868 92.31 220 8 0.2156 444.253 433.787 1.083 0.990 0.378 6.866-6.210 92.28 299 12 0.2244 378.373 366.799 1.061 0.992 0.378 6.206-5.619 93.06 386 16 0.2148 369.171 359.482 1.041 0.994 0.370 5.613-5.076 93.02 551 22 0.2005 384.478 380.617 1.027 0.993 0.350 5.075-4.591 93.42 709 29 0.1757 425.184 420.322 1.026 0.996 0.338 4.589-4.150 93.88 986 42 0.1717 452.066 445.264 1.044 0.995 0.299 4.148-3.753 94.07 1277 72 0.1951 385.666 380.991 1.054 1.003 0.239 3.750-3.393 94.60 1743 97 0.2152 314.455 305.433 1.092 1.006 0.155 3.392-3.201 94.94 1294 75 0.2582 244.174 234.021 1.044 1.007 0.056 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0610 b_overall=1.5823 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ==================== Compute data/restraints target weights =================== Setting wxc_scale using amber.wxc_factor : 0.500 * 1.000 = 0.500 |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 0.747477 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.046989 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2196 0.2622 0.0426 0.014 1.8 0.5 0.5 3.0 0 0.037 0.2016 0.2556 0.0540 0.014 1.9 1.1 0.5 2.4 0 0.112 0.2016 0.2555 0.0539 0.014 1.9 1.1 0.5 2.4 0 0.224 0.2016 0.2555 0.0539 0.014 1.9 1.1 0.5 2.4 0 0.336 0.2012 0.2554 0.0542 0.014 1.9 1.1 0.5 2.4 0 0.448 0.2005 0.2556 0.0551 0.014 1.9 1.0 0.5 2.7 0 0.561 0.1994 0.2556 0.0561 0.015 2.0 1.0 0.5 3.0 0 0.673 0.1989 0.2560 0.0571 0.015 2.0 1.1 0.5 3.0 0 0.785 0.2015 0.2555 0.0539 0.014 1.9 1.1 0.5 2.4 0 0.374 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2196 0.2622 0.0426 0.014 1.8 0.5 0.5 3.0 0 0.037 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 21.96 26.22 4.26 6.726 46.867 0.047 5.996 22.41 26.43 4.02 6.855 46.861 0.001 6.010 21.96 26.22 4.26 6.726 46.867 0.006 5.996 21.39 26.15 4.76 7.102 46.740 0.023 5.977 20.28 26.25 5.97 8.622 46.819 0.047 5.947 20.05 26.31 6.26 9.131 47.084 0.070 5.942 19.88 26.36 6.48 9.664 47.328 0.094 5.938 19.78 26.42 6.64 10.150 47.526 0.117 5.936 19.72 26.48 6.76 10.532 47.670 0.141 5.935 19.67 26.53 6.85 10.849 47.785 0.164 5.935 19.66 26.58 6.92 11.026 47.847 0.188 5.935 19.62 26.62 7.00 11.402 47.976 0.211 5.934 19.59 26.65 7.06 11.663 48.064 0.235 5.934 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.023 Accepted refinement result: 21.39 26.15 4.76 7.102 46.740 0.023 5.977 Individual atomic B min max mean iso aniso Overall: 18.09 73.54 42.06 2.52 3245 0 Protein: 18.09 73.54 42.06 2.52 3245 0 Chain A: 18.09 73.54 42.06 N/A 3245 0 Histogram: Values Number of atoms 18.09 - 23.63 22 23.63 - 29.18 252 29.18 - 34.72 559 34.72 - 40.27 608 40.27 - 45.82 681 45.82 - 51.36 609 51.36 - 56.91 289 56.91 - 62.45 133 62.45 - 68.00 47 68.00 - 73.54 45 =========================== Idealize ADP of riding H ========================== r_work=0.2139 r_free=0.2615 r_work=0.2135 r_free=0.2616 *********************** REFINEMENT MACRO_CYCLE 3 OF 3 ************************* |--(resolution: 3.20 - 12.00 A, n_refl.=8334 (all), 4.73 % free)-------------| | | | r_work= 0.2135 r_free= 0.2616 coordinate error (max.-lik. estimate): 0.39 A | | | | normalized target function (ml) (work): 5.975950 | | target function (ml) not normalized (work): 47449.044386 | | target function (ml) not normalized (free): 2399.460279 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2157 0.2135 0.2616 n_refl.: 8334 re-set all scales: r(all,work,free)=0.3419 0.3396 0.3876 n_refl.: 8334 remove outliers: r(all,work,free)=0.3419 0.3396 0.3876 n_refl.: 8334 overall B=0.00 to atoms: r(all,work,free)=0.3419 0.3396 0.3876 n_refl.: 8334 bulk-solvent and scaling: r(all,work,free)=0.2148 0.2126 0.2600 n_refl.: 8334 remove outliers: r(all,work,free)=0.2148 0.2126 0.2600 n_refl.: 8334 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 11.998-10.364 92.59 96 4 0.2085 695.577 669.053 1.142 0.996 0.350 10.272-9.295 91.74 94 6 0.1966 599.532 583.416 1.147 0.990 0.371 9.288-8.400 91.04 120 2 0.1807 616.730 610.322 1.133 0.994 0.380 8.393-7.595 91.58 165 9 0.1877 551.714 542.529 1.175 0.998 0.383 7.592-6.868 92.31 220 8 0.2309 444.253 428.336 1.080 0.992 0.386 6.866-6.210 92.28 299 12 0.2390 378.373 365.650 1.060 0.994 0.386 6.206-5.619 93.06 386 16 0.2398 369.171 354.958 1.024 0.995 0.383 5.613-5.076 93.02 551 22 0.2181 384.478 376.647 1.022 0.993 0.370 5.075-4.591 93.42 709 29 0.1939 425.184 416.466 1.012 0.995 0.370 4.589-4.150 93.88 986 42 0.1774 452.066 442.414 1.017 0.993 0.305 4.148-3.753 94.07 1277 72 0.2055 385.666 377.412 1.024 0.998 0.290 3.750-3.393 94.60 1743 97 0.2267 314.455 301.704 1.061 0.999 0.160 3.392-3.201 94.94 1294 75 0.2543 244.174 231.846 1.029 0.998 0.040 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0610 b_overall=2.9842 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ==================== Compute data/restraints target weights =================== Setting wxc_scale using amber.wxc_factor : 0.500 * 1.000 = 0.500 |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 0.768119 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.050597 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2173 0.2647 0.0474 0.013 1.8 0.5 0.5 3.0 0 0.038 0.2126 0.2600 0.0474 0.014 1.8 0.5 0.5 3.0 0 0.115 0.2126 0.2600 0.0474 0.014 1.8 0.5 0.5 3.0 0 0.230 0.2122 0.2597 0.0475 0.014 1.8 0.5 0.5 3.0 0 0.346 0.2106 0.2593 0.0486 0.014 1.8 0.5 0.5 3.0 0 0.461 0.2100 0.2594 0.0494 0.014 1.8 0.5 0.5 3.0 0 0.576 0.2094 0.2597 0.0502 0.014 1.8 0.5 0.5 3.0 0 0.691 0.2063 0.2591 0.0528 0.016 1.9 0.6 0.5 3.0 0 0.807 0.2116 0.2596 0.0481 0.014 1.8 0.5 0.5 3.0 0 0.384 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2106 0.2593 0.0486 0.014 1.8 0.5 0.5 3.0 0 0.461 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 21.06 25.93 4.86 6.221 46.103 0.051 5.968 21.92 26.16 4.24 6.224 46.108 0.002 5.996 21.55 26.09 4.54 6.275 46.015 0.006 5.983 21.06 25.93 4.87 6.223 46.102 0.025 5.968 20.32 25.90 5.58 7.157 45.825 0.051 5.946 19.57 26.06 6.49 8.805 46.074 0.076 5.929 19.44 26.10 6.66 9.272 46.284 0.101 5.927 19.35 26.17 6.82 9.668 46.455 0.126 5.926 19.29 26.22 6.93 10.041 46.604 0.152 5.925 19.26 26.27 7.02 10.330 46.715 0.177 5.925 19.24 26.33 7.08 10.499 46.782 0.202 5.925 19.20 26.36 7.16 10.807 46.893 0.228 5.925 19.18 26.40 7.22 11.035 46.975 0.253 5.925 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.051 Accepted refinement result: 20.32 25.90 5.58 7.157 45.825 0.051 5.946 Individual atomic B min max mean iso aniso Overall: 13.09 79.16 41.53 4.45 3245 0 Protein: 13.09 79.16 41.53 4.45 3245 0 Chain A: 13.09 79.16 41.53 N/A 3245 0 Histogram: Values Number of atoms 13.09 - 19.70 11 19.70 - 26.30 171 26.30 - 32.91 544 32.91 - 39.52 737 39.52 - 46.12 748 46.12 - 52.73 592 52.73 - 59.34 267 59.34 - 65.94 114 65.94 - 72.55 43 72.55 - 79.16 18 =========================== Idealize ADP of riding H ========================== r_work=0.2032 r_free=0.2590 r_work=0.2026 r_free=0.2592 ----------X-ray data---------- |--(resolution: 3.20 - 12.00 A, n_refl.=8334 (all), 4.73 % free)-------------| | | | r_work= 0.2026 r_free= 0.2592 coordinate error (max.-lik. estimate): 0.39 A | | | | normalized target function (ml) (work): 5.945137 | | target function (ml) not normalized (work): 47204.385887 | | target function (ml) not normalized (free): 2397.015517 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 12.00 - 4.56 0.92 2697 109 0.2041 0.2547 6.1181 6.2837| | 2: 4.56 - 3.65 0.94 2624 139 0.1843 0.2368 5.9615 6.1099| | 3: 3.65 - 3.20 0.95 2619 146 0.2275 0.2952 5.7506 5.9097| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 12.00 - 4.56 2697 109 0.82 23.42 1.00 0.88 34942.01| | 2: 4.56 - 3.65 2624 139 0.84 22.60 1.00 0.87 28471.61| | 3: 3.65 - 3.20 2619 146 0.76 29.99 0.99 0.84 22744.65| |alpha: min = 0.84 max = 0.88 mean = 0.87| |beta: min = 22744.65 max = 34942.01 mean = 28780.39| |figures of merit: min = 0.00 max = 1.00 mean = 0.81| |phase err.(work): min = 0.00 max = 89.82 mean = 25.31| |phase err.(test): min = 0.00 max = 87.13 mean = 24.90| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.2052 0.2026 0.2592 n_refl.: 8334 re-set all scales: r(all,work,free)=0.3343 0.3318 0.3851 n_refl.: 8334 remove outliers: r(all,work,free)=0.3343 0.3318 0.3851 n_refl.: 8334 overall B=0.00 to atoms: r(all,work,free)=0.3343 0.3318 0.3851 n_refl.: 8334 bulk-solvent and scaling: r(all,work,free)=0.2051 0.2026 0.2591 n_refl.: 8334 remove outliers: r(all,work,free)=0.2051 0.2026 0.2591 n_refl.: 8334 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 11.998-10.364 92.59 96 4 0.2055 695.577 670.638 1.130 0.996 0.340 10.272-9.295 91.74 94 6 0.1964 599.532 583.066 1.157 0.989 0.375 9.288-8.400 91.04 120 2 0.1781 616.730 611.171 1.135 0.993 0.380 8.393-7.595 91.58 165 9 0.1825 551.714 542.605 1.175 0.997 0.382 7.592-6.868 92.31 220 8 0.2280 444.253 429.071 1.079 0.992 0.383 6.866-6.210 92.28 299 12 0.2336 378.373 366.458 1.059 0.993 0.383 6.206-5.619 93.06 386 16 0.2340 369.171 355.160 1.024 0.993 0.383 5.613-5.076 93.02 551 22 0.2111 384.478 377.067 1.021 0.992 0.370 5.075-4.591 93.42 709 29 0.1853 425.184 416.620 1.008 0.993 0.370 4.589-4.150 93.88 986 42 0.1676 452.066 442.483 1.013 0.991 0.310 4.148-3.753 94.07 1277 72 0.1940 385.666 377.935 1.020 0.996 0.290 3.750-3.393 94.60 1743 97 0.2121 314.455 302.252 1.057 0.996 0.160 3.392-3.201 94.94 1294 75 0.2382 244.174 232.945 1.030 0.995 0.020 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0577 b_overall=3.0404 ================= 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) ------------------------------------------------------------------------ stage r-work r-free bonds angles b_min b_max b_ave n_water shift 0 : 0.3129 0.3544 0.008 1.367 3.9 57.1 27.0 0 0.000 1_bss: 0.2122 0.2538 0.008 1.367 24.0 77.3 47.2 0 0.000 1_settarget: 0.2122 0.2538 0.008 1.367 24.0 77.3 47.2 0 0.000 1_weight: 0.2122 0.2538 0.008 1.367 24.0 77.3 47.2 0 0.000 1_xyzrec: 0.2067 0.2614 0.014 1.922 24.0 77.3 47.2 0 0.281 1_adp: 0.2026 0.2592 0.014 1.922 28.1 76.3 47.3 0 0.281 1_regHadp: 0.2021 0.2581 0.014 1.922 28.1 76.3 47.3 0 0.281 2_bss: 0.2016 0.2555 0.014 1.922 23.1 71.3 42.3 0 0.281 2_settarget: 0.2016 0.2555 0.014 1.922 23.1 71.3 42.3 0 0.281 2_updatecdl: 0.2016 0.2555 0.014 1.919 23.1 71.3 42.3 0 0.281 2_weight: 0.2016 0.2555 0.014 1.919 23.1 71.3 42.3 0 0.281 2_xyzrec: 0.2196 0.2622 0.014 1.805 23.1 71.3 42.3 0 0.343 2_adp: 0.2139 0.2615 0.014 1.805 18.1 73.5 42.1 0 0.343 2_regHadp: 0.2135 0.2616 0.014 1.805 18.1 73.5 42.1 0 0.343 3_bss: 0.2126 0.2600 0.014 1.805 18.1 73.5 42.1 0 0.343 3_settarget: 0.2126 0.2600 0.014 1.805 18.1 73.5 42.1 0 0.343 3_updatecdl: 0.2126 0.2600 0.014 1.801 18.1 73.5 42.1 0 0.343 3_setrh: 0.2126 0.2600 0.014 1.801 18.1 73.5 42.1 0 0.343 3_weight: 0.2126 0.2600 0.014 1.801 18.1 73.5 42.1 0 0.343 3_xyzrec: 0.2106 0.2593 0.014 1.822 18.1 73.5 42.1 0 0.343 3_adp: 0.2032 0.2590 0.014 1.822 13.1 79.2 41.5 0 0.343 3_regHadp: 0.2026 0.2592 0.014 1.822 13.1 79.2 41.5 0 0.343 end: 0.2026 0.2591 0.014 1.822 13.1 79.2 41.5 0 0.343 ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/cci-filer3/home/nigel/work/ANI/result/xray/pairs/4phenix_2a8z_refine_001.cif Writing default parameters for subsequent refinement: /net/cci-filer3/home/nigel/work/ANI/result/xray/pairs/4phenix_2a8z_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 4.2400 Refinement macro-cycles (run) : 184.4400 Write final files (write_after_run_outputs) : 9.8400 Total : 198.5200 Total CPU time: 3.87 minutes =========================== phenix.refine: finished =========================== # Date 2024-08-09 Time 09:39:33 PDT -0700 (1723221573.77 s) Start R-work = 0.2122, R-free = 0.2538 Final R-work = 0.2026, R-free = 0.2591 =============================================================================== Job complete usr+sys time: 239.90 seconds wall clock time: 8 minutes 4.96 seconds (484.96 seconds total)