Starting phenix.refine on Fri Aug 9 09:31:39 2024 by nigel =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, 4phenix_1fp9.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/1fp9/1fp9.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_1fp9.prmtop amber.coordinate_file_name=4amber_1fp9.rst7 amber.order_file_name=4amber_1fp9.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_1fp9.order 4amber_1fp9.prmtop 4amber_1fp9.rst7 Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/1fp9/1fp9.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/1fp9/1fp9.mtz" model { file = "4phenix_1fp9.pdb" } default_model = "4phenix_1fp9.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_1fp9.prmtop coordinate_file_name = 4amber_1fp9.rst7 order_file_name = 4amber_1fp9.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: 7980 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 7980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 500, 7980 Classifications: {'peptide': 500} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 38, 'TRANS': 461} Time building chain proxies: 0.87, per 1000 atoms: 0.11 Number of scatterers: 7980 At special positions: 0 Unit cell: (104.913, 52.445, 104.908, 90, 96.42, 90) Space group: C 1 2 1 (No. 5) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 11 16.00 O 707 8.00 N 703 7.00 C 2641 6.00 H 3918 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 1.47 Conformation dependent library (CDL) restraints added in 235.9 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 910 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 26 helices and 3 sheets defined 45.2% alpha, 6.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.23 Creating SS restraints... Processing helix chain 'A' and resid 13 through 15 No H-bonds generated for 'chain 'A' and resid 13 through 15' Processing helix chain 'A' and resid 27 through 38 Processing helix chain 'A' and resid 69 through 71 No H-bonds generated for 'chain 'A' and resid 69 through 71' Processing helix chain 'A' and resid 75 through 80 removed outlier: 3.994A pdb=" N ARG A 80 " --> pdb=" O PRO A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 118 removed outlier: 3.803A pdb=" N TRP A 105 " --> pdb=" O TYR A 101 " (cutoff:3.500A) Proline residue: A 106 - end of helix removed outlier: 3.572A pdb=" N GLU A 117 " --> pdb=" O ARG A 113 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LYS A 118 " --> pdb=" O GLY A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 133 Processing helix chain 'A' and resid 135 through 150 removed outlier: 4.644A pdb=" N ASP A 140 " --> pdb=" O TRP A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 158 No H-bonds generated for 'chain 'A' and resid 156 through 158' Processing helix chain 'A' and resid 161 through 164 No H-bonds generated for 'chain 'A' and resid 161 through 164' Processing helix chain 'A' and resid 168 through 177 Processing helix chain 'A' and resid 179 through 205 Processing helix chain 'A' and resid 223 through 227 Processing helix chain 'A' and resid 229 through 231 No H-bonds generated for 'chain 'A' and resid 229 through 231' Processing helix chain 'A' and resid 265 through 270 Processing helix chain 'A' and resid 274 through 286 Processing helix chain 'A' and resid 295 through 298 Processing helix chain 'A' and resid 321 through 332 Processing helix chain 'A' and resid 347 through 356 Processing helix chain 'A' and resid 364 through 366 No H-bonds generated for 'chain 'A' and resid 364 through 366' Processing helix chain 'A' and resid 378 through 380 No H-bonds generated for 'chain 'A' and resid 378 through 380' Processing helix chain 'A' and resid 399 through 403 Processing helix chain 'A' and resid 408 through 421 removed outlier: 3.814A pdb=" N ASP A 420 " --> pdb=" O ARG A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 441 Processing helix chain 'A' and resid 451 through 454 No H-bonds generated for 'chain 'A' and resid 451 through 454' Processing helix chain 'A' and resid 459 through 461 No H-bonds generated for 'chain 'A' and resid 459 through 461' Processing helix chain 'A' and resid 484 through 496 removed outlier: 3.687A pdb=" N MET A 493 " --> pdb=" O ARG A 489 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 446 through 450 removed outlier: 7.402A pdb=" N ALA A 6 " --> pdb=" O ALA A 447 " (cutoff:3.500A) removed outlier: 8.223A pdb=" N TYR A 449 " --> pdb=" O ALA A 6 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N GLY A 8 " --> pdb=" O TYR A 449 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N TYR A 43 " --> pdb=" O LEU A 9 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ARG A 209 " --> pdb=" O TRP A 44 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N LEU A 289 " --> pdb=" O GLY A 212 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N MET A 214 " --> pdb=" O LEU A 289 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N ARG A 291 " --> pdb=" O MET A 214 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 300 through 303 Processing sheet with id= C, first strand: chain 'A' and resid 360 through 363 129 hydrogen bonds defined for protein. 381 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: 1.26 Time building geometry restraints manager: 1.67 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: 3917 1.15 - 1.32: 661 1.32 - 1.48: 1834 1.48 - 1.65: 1688 1.65 - 1.82: 21 Bond restraints: 8121 Sorted by residual: bond pdb=" NH1 ARG A 84 " pdb="HH11 ARG A 84 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.46e+01 bond pdb=" NH2 ARG A 279 " pdb="HH22 ARG A 279 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" NE1 TRP A 159 " pdb=" HE1 TRP A 159 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N GLN A 256 " pdb=" H GLN A 256 " 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 416 " pdb="HH22 ARG A 416 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 ... (remaining 8116 not shown) Histogram of bond angle deviations from ideal: 100.21 - 106.96: 414 106.96 - 113.72: 8839 113.72 - 120.48: 2790 120.48 - 127.23: 2534 127.23 - 133.99: 74 Bond angle restraints: 14651 Sorted by residual: angle pdb=" OE1 GLN A 27 " pdb=" CD GLN A 27 " pdb=" NE2 GLN A 27 " ideal model delta sigma weight residual 122.60 112.79 9.81 1.00e+00 1.00e+00 9.63e+01 angle pdb=" N THR A 391 " pdb=" CA THR A 391 " pdb=" C THR A 391 " ideal model delta sigma weight residual 111.36 102.64 8.72 1.09e+00 8.42e-01 6.40e+01 angle pdb=" CG GLN A 27 " pdb=" CD GLN A 27 " pdb=" NE2 GLN A 27 " ideal model delta sigma weight residual 116.40 126.40 -10.00 1.50e+00 4.44e-01 4.44e+01 angle pdb=" N GLY A 21 " pdb=" CA GLY A 21 " pdb=" C GLY A 21 " ideal model delta sigma weight residual 114.90 124.70 -9.80 1.54e+00 4.22e-01 4.05e+01 angle pdb=" N GLY A 114 " pdb=" CA GLY A 114 " pdb=" C GLY A 114 " ideal model delta sigma weight residual 114.67 108.55 6.12 1.10e+00 8.26e-01 3.10e+01 ... (remaining 14646 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.79: 3458 15.79 - 31.58: 183 31.58 - 47.38: 94 47.38 - 63.17: 90 63.17 - 78.96: 12 Dihedral angle restraints: 3837 sinusoidal: 2018 harmonic: 1819 Sorted by residual: dihedral pdb=" CG ARG A 84 " pdb=" CD ARG A 84 " pdb=" NE ARG A 84 " pdb=" CZ ARG A 84 " ideal model delta sinusoidal sigma weight residual 180.00 136.22 43.78 2 1.50e+01 4.44e-03 1.02e+01 dihedral pdb=" N GLU A 180 " pdb=" CA GLU A 180 " pdb=" CB GLU A 180 " pdb=" CG GLU A 180 " ideal model delta sinusoidal sigma weight residual 180.00 -129.53 -50.47 3 1.50e+01 4.44e-03 8.90e+00 dihedral pdb=" CA CYS A 308 " pdb=" CB CYS A 308 " pdb=" SG CYS A 308 " pdb=" HG CYS A 308 " ideal model delta sinusoidal sigma weight residual 180.00 130.05 49.95 3 1.50e+01 4.44e-03 8.84e+00 ... (remaining 3834 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 255 0.056 - 0.112: 233 0.112 - 0.168: 47 0.168 - 0.224: 23 0.224 - 0.280: 6 Chirality restraints: 564 Sorted by residual: chirality pdb=" CA PRO A 469 " pdb=" N PRO A 469 " pdb=" C PRO A 469 " pdb=" CB PRO A 469 " both_signs ideal model delta sigma weight residual False 2.72 2.44 0.28 2.00e-01 2.50e+01 1.97e+00 chirality pdb=" CA VAL A 349 " pdb=" N VAL A 349 " pdb=" C VAL A 349 " pdb=" CB VAL A 349 " both_signs ideal model delta sigma weight residual False 2.44 2.69 -0.25 2.00e-01 2.50e+01 1.50e+00 chirality pdb=" CA VAL A 182 " pdb=" N VAL A 182 " pdb=" C VAL A 182 " pdb=" CB VAL A 182 " both_signs ideal model delta sigma weight residual False 2.44 2.68 -0.24 2.00e-01 2.50e+01 1.40e+00 ... (remaining 561 not shown) Planarity restraints: 1211 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 141 " 0.051 2.00e-02 2.50e+03 2.06e-02 1.27e+01 pdb=" CG TYR A 141 " -0.010 2.00e-02 2.50e+03 pdb=" CD1 TYR A 141 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 TYR A 141 " -0.012 2.00e-02 2.50e+03 pdb=" CE1 TYR A 141 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR A 141 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR A 141 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR A 141 " 0.037 2.00e-02 2.50e+03 pdb=" HD1 TYR A 141 " -0.015 2.00e-02 2.50e+03 pdb=" HD2 TYR A 141 " -0.018 2.00e-02 2.50e+03 pdb=" HE1 TYR A 141 " -0.008 2.00e-02 2.50e+03 pdb=" HE2 TYR A 141 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 59 " -0.051 2.00e-02 2.50e+03 1.96e-02 1.15e+01 pdb=" CG TYR A 59 " 0.012 2.00e-02 2.50e+03 pdb=" CD1 TYR A 59 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 TYR A 59 " 0.011 2.00e-02 2.50e+03 pdb=" CE1 TYR A 59 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR A 59 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR A 59 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 59 " -0.032 2.00e-02 2.50e+03 pdb=" HD1 TYR A 59 " 0.017 2.00e-02 2.50e+03 pdb=" HD2 TYR A 59 " 0.016 2.00e-02 2.50e+03 pdb=" HE1 TYR A 59 " 0.004 2.00e-02 2.50e+03 pdb=" HE2 TYR A 59 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 192 " 0.052 2.00e-02 2.50e+03 1.93e-02 1.11e+01 pdb=" CG PHE A 192 " -0.016 2.00e-02 2.50e+03 pdb=" CD1 PHE A 192 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE A 192 " -0.013 2.00e-02 2.50e+03 pdb=" CE1 PHE A 192 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 192 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE A 192 " 0.007 2.00e-02 2.50e+03 pdb=" HD1 PHE A 192 " -0.018 2.00e-02 2.50e+03 pdb=" HD2 PHE A 192 " -0.022 2.00e-02 2.50e+03 pdb=" HE1 PHE A 192 " 0.002 2.00e-02 2.50e+03 pdb=" HE2 PHE A 192 " 0.005 2.00e-02 2.50e+03 pdb=" HZ PHE A 192 " 0.017 2.00e-02 2.50e+03 ... (remaining 1208 not shown) Histogram of nonbonded interaction distances: 0.67 - 1.45: 18 1.45 - 2.24: 1320 2.24 - 3.03: 24272 3.03 - 3.81: 37998 3.81 - 4.60: 60529 Warning: very small nonbonded interaction distances. Nonbonded interactions: 124137 Sorted by model distance: nonbonded pdb=" HD1 HIS A 379 " pdb=" HH TYR A 417 " model vdw 0.668 2.100 nonbonded pdb=" HG1 THR A 407 " pdb=" HG3 GLU A 410 " model vdw 1.041 2.270 nonbonded pdb=" HD2 HIS A 12 " pdb=" HG1 THR A 14 " model vdw 1.214 2.100 nonbonded pdb=" HG SER A 61 " pdb=" H SER A 63 " model vdw 1.247 2.100 nonbonded pdb=" HG1 THR A 346 " pdb=" HD2 PRO A 347 " model vdw 1.271 2.270 ... (remaining 124132 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. ============================== Initializing Amber ============================= topology : 4amber_1fp9.prmtop atom order : 4amber_1fp9.order coordinates : 4amber_1fp9.rst7 ===================================== ... ===================================== ============================== Scattering factors ============================= ----------X-ray scattering dictionary---------- Number of scattering types: 5 Type Number sf(0) Gaussians S 11 15.96 2 O 707 7.97 1 N 703 6.97 1 C 2641 5.97 2 H 3918 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: 3918 of 7980 ******************************************************************************* Automatic adjustment: hydrogens.refine=riding ******************************************************************************* n_use = 7980 n_use_u_iso = 7980 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 = 7980 ================== Extract refinement strategy and selections ================= Refinement flags and selection counts: individual_sites = True (7980 atoms) torsion_angles = False (0 atoms) rigid_body = False (0 atoms in 0 groups) individual_adp = True (iso = 7980 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 13 through 15 helix_type = alpha pi *3_10 unknown } helix { serial_number = "2" helix_identifier = "2" selection = chain 'A' and resid 27 through 38 } helix { serial_number = "3" helix_identifier = "3" selection = chain 'A' and resid 69 through 71 helix_type = alpha pi *3_10 unknown } helix { serial_number = "4" helix_identifier = "4" selection = chain 'A' and resid 75 through 80 } helix { serial_number = "5" helix_identifier = "5" selection = chain 'A' and resid 97 through 118 } helix { serial_number = "6" helix_identifier = "6" selection = chain 'A' and resid 123 through 133 } helix { serial_number = "7" helix_identifier = "7" selection = chain 'A' and resid 135 through 150 } helix { serial_number = "8" helix_identifier = "8" selection = chain 'A' and resid 156 through 158 helix_type = alpha pi *3_10 unknown } helix { serial_number = "9" helix_identifier = "9" selection = chain 'A' and resid 161 through 164 } helix { serial_number = "10" helix_identifier = "10" selection = chain 'A' and resid 168 through 177 } helix { serial_number = "11" helix_identifier = "11" selection = chain 'A' and resid 179 through 205 } helix { serial_number = "12" helix_identifier = "12" selection = chain 'A' and resid 223 through 227 } helix { serial_number = "13" helix_identifier = "13" selection = chain 'A' and resid 229 through 231 helix_type = alpha pi *3_10 unknown } helix { serial_number = "14" helix_identifier = "14" selection = chain 'A' and resid 265 through 270 } helix { serial_number = "15" helix_identifier = "15" selection = chain 'A' and resid 274 through 286 } helix { serial_number = "16" helix_identifier = "16" selection = chain 'A' and resid 295 through 298 helix_type = alpha pi *3_10 unknown } helix { serial_number = "17" helix_identifier = "17" selection = chain 'A' and resid 321 through 332 } helix { serial_number = "18" helix_identifier = "18" selection = chain 'A' and resid 347 through 356 } helix { serial_number = "19" helix_identifier = "19" selection = chain 'A' and resid 364 through 366 helix_type = alpha pi *3_10 unknown } helix { serial_number = "20" helix_identifier = "20" selection = chain 'A' and resid 378 through 380 helix_type = alpha pi *3_10 unknown } helix { serial_number = "21" helix_identifier = "21" selection = chain 'A' and resid 399 through 403 } helix { serial_number = "22" helix_identifier = "22" selection = chain 'A' and resid 408 through 421 } helix { serial_number = "23" helix_identifier = "23" selection = chain 'A' and resid 431 through 441 } helix { serial_number = "24" helix_identifier = "24" selection = chain 'A' and resid 451 through 454 } helix { serial_number = "25" helix_identifier = "25" selection = chain 'A' and resid 459 through 461 helix_type = alpha pi *3_10 unknown } helix { serial_number = "26" helix_identifier = "26" selection = chain 'A' and resid 484 through 496 } sheet { first_strand = chain 'A' and resid 446 through 450 sheet_id = " A" strand { selection = chain 'A' and resid 6 through 10 sense = *parallel antiparallel unknown bond_start_current = chain 'A' and resid 6 and name N bond_start_previous = chain 'A' and resid 447 and name O } strand { selection = chain 'A' and resid 43 through 45 sense = *parallel antiparallel unknown bond_start_current = chain 'A' and resid 43 and name N bond_start_previous = chain 'A' and resid 9 and name O } strand { selection = chain 'A' and resid 209 through 215 sense = *parallel antiparallel unknown bond_start_current = chain 'A' and resid 209 and name N bond_start_previous = chain 'A' and resid 44 and name O } strand { selection = chain 'A' and resid 289 through 293 sense = *parallel antiparallel unknown bond_start_current = chain 'A' and resid 289 and name N bond_start_previous = chain 'A' and resid 212 and name O } strand { selection = chain 'A' and resid 337 through 339 sense = *parallel antiparallel unknown bond_start_current = chain 'A' and resid 338 and name N bond_start_previous = chain 'A' and resid 290 and name O } } sheet { first_strand = chain 'A' and resid 300 through 303 sheet_id = " B" strand { selection = chain 'A' and resid 315 through 318 sense = parallel *antiparallel unknown bond_start_current = chain 'A' and resid 317 and name N bond_start_previous = chain 'A' and resid 301 and name O } } sheet { first_strand = chain 'A' and resid 360 through 363 sheet_id = " C" strand { selection = chain 'A' and resid 387 through 390 sense = *parallel antiparallel unknown bond_start_current = chain 'A' and resid 388 and name N bond_start_previous = chain 'A' and resid 360 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_1fp9.prmtop" coordinate_file_name = "4amber_1fp9.rst7" order_file_name = "4amber_1fp9.order" } } output { prefix = "4phenix_1fp9_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: 3.10 - 52.13 A, n_refl.=10132 (all), 10.01 % free)------------| | | | r_work= 0.4295 r_free= 0.5328 coordinate error (max.-lik. estimate): 0.35 A | | | | normalized target function (ml) (work): 5.558989 | | target function (ml) not normalized (work): 50686.864796 | | target function (ml) not normalized (free): 5602.271093 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 52.13 - 5.93 0.97 1355 151 0.4602 0.4874 6.2068 6.1555| | 2: 5.93 - 4.71 0.96 1323 147 0.3544 0.4795 5.7545 5.7031| | 3: 4.71 - 4.11 0.96 1288 144 0.4082 0.5276 5.5702 5.4467| | 4: 4.11 - 3.74 0.96 1288 143 0.4547 0.5635 5.5131 5.6228| | 5: 3.74 - 3.47 0.96 1281 142 0.4750 0.5963 5.4715 5.2668| | 6: 3.47 - 3.26 0.97 1282 142 0.4415 0.5861 5.2548 5.3944| | 7: 3.26 - 3.10 0.97 1301 145 0.4199 0.5255 5.1058 5.0494| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 52.13 - 5.93 1355 151 0.16 77.68 0.60 0.03 59901.83| | 2: 5.93 - 4.71 1323 147 0.58 46.12 1.30 0.17 26677.67| | 3: 4.71 - 4.11 1288 144 0.83 24.33 1.53 0.26 9229.97| | 4: 4.11 - 3.74 1288 143 0.81 25.76 1.67 0.28 8210.22| | 5: 3.74 - 3.47 1281 142 0.80 27.33 1.71 0.29 7263.69| | 6: 3.47 - 3.26 1282 142 0.77 30.42 1.60 0.27 6275.54| | 7: 3.26 - 3.10 1301 145 0.73 33.59 1.45 0.23 4594.24| |alpha: min = 0.03 max = 0.29 mean = 0.22| |beta: min = 4594.24 max = 59901.83 mean = 17794.65| |figures of merit: min = 0.00 max = 1.00 mean = 0.66| |phase err.(work): min = 0.00 max = 89.98 mean = 38.22| |phase err.(test): min = 0.00 max = 89.98 mean = 38.63| |-----------------------------------------------------------------------------| ----------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 : 0.005 0.046 4203 Z= 0.337 Angle : 1.249 9.998 5718 Z= 0.861 Chirality : 0.082 0.280 564 Planarity : 0.005 0.040 750 Dihedral : 14.688 74.118 1524 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 28.95 Ramachandran Plot: Outliers : 1.81 % Allowed : 12.25 % Favored : 85.94 % Rotamer: Outliers : 2.24 % Allowed : 2.24 % Favored : 95.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -5.15 (0.30), residues: 498 helix: -4.21 (0.20), residues: 229 sheet: -1.62 (0.66), residues: 60 loop : -2.83 (0.38), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 279 TYR 0.043 0.007 TYR A 141 PHE 0.032 0.005 PHE A 192 TRP 0.033 0.006 TRP A 159 HIS 0.002 0.000 HIS A 384 Individual atomic B min max mean iso aniso Overall: 12.70 77.70 33.40 2.74 4062 0 Protein: 12.70 77.70 33.40 2.74 4062 0 Chain A: 12.70 77.70 33.40 N/A 4062 0 Histogram: Values Number of atoms 12.70 - 19.20 560 19.20 - 25.70 851 25.70 - 32.20 919 32.20 - 38.70 595 38.70 - 45.20 378 45.20 - 51.70 244 51.70 - 58.20 183 58.20 - 64.70 129 64.70 - 71.20 85 71.20 - 77.70 118 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 3 ************************* |--(resolution: 3.10 - 52.13 A, n_refl.=10132 (all), 10.01 % free)------------| | | | r_work= 0.4295 r_free= 0.5328 coordinate error (max.-lik. estimate): 0.35 A | | | | normalized target function (ml) (work): 5.558989 | | target function (ml) not normalized (work): 50686.864796 | | target function (ml) not normalized (free): 5602.271093 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.4404 0.4295 0.5328 n_refl.: 10132 re-set all scales: r(all,work,free)=0.4404 0.4295 0.5328 n_refl.: 10132 remove outliers: r(all,work,free)=0.4157 0.4025 0.5328 n_refl.: 10127 overall B=3.26 to atoms: r(all,work,free)=0.4305 0.4163 0.5509 n_refl.: 10127 bulk-solvent and scaling: r(all,work,free)=0.2404 0.2401 0.2431 n_refl.: 10127 remove outliers: r(all,work,free)=0.2402 0.2401 0.2416 n_refl.: 10126 ======================== 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 52.125-14.829 89.91 87 11 0.2454 1487.424 1450.339 1.092 1.233 0.404 14.763-11.705 97.09 91 9 0.1774 1550.330 1543.477 0.964 1.219 0.398 11.688-9.266 96.82 191 22 0.1309 1811.722 1783.418 0.960 1.198 0.395 9.245-7.329 97.77 355 40 0.1752 1351.053 1329.221 0.936 1.167 0.392 7.324-5.801 97.35 727 80 0.2314 959.259 925.839 0.864 1.120 0.389 5.796-4.593 96.03 1414 157 0.2080 1149.592 1113.942 0.922 1.043 0.352 4.593-3.637 95.93 2819 313 0.2376 1063.635 1016.292 1.114 0.918 0.295 3.636-3.100 96.41 3429 381 0.2969 729.268 668.087 1.241 0.769 0.121 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0577 b_overall=4.7458 ============================ 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 = 3.540979 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.301448 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 0.2140 0.2486 0.0346 0.022 2.5 11.0 0.4 2.2 0 1.770 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 21.40 24.86 3.46 1.968 36.447 0.301 0.055 21.78 25.14 3.36 4.017 36.992 0.009 0.057 21.29 25.13 3.84 3.988 36.958 0.038 0.055 20.15 25.12 4.98 4.610 36.929 0.151 0.049 19.45 25.29 5.84 5.968 37.148 0.301 0.046 19.12 25.42 6.30 6.992 37.351 0.452 0.044 18.88 25.51 6.63 7.996 37.625 0.603 0.043 18.71 25.58 6.87 8.826 37.852 0.754 0.042 18.64 25.65 7.01 9.270 37.943 0.904 0.042 18.56 25.71 7.15 9.769 38.073 1.055 0.041 18.50 25.74 7.24 10.187 38.179 1.206 0.041 18.21 25.92 7.71 12.281 38.865 1.357 0.040 18.16 25.98 7.82 12.727 38.981 1.507 0.040 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.151 Accepted refinement result: 20.15 25.12 4.98 4.610 36.929 0.151 0.049 Individual atomic B min max mean iso aniso Overall: 14.40 87.59 37.61 4.23 4062 0 Protein: 14.40 87.59 37.61 4.23 4062 0 Chain A: 14.40 87.59 37.61 N/A 4062 0 Histogram: Values Number of atoms 14.40 - 21.72 208 21.72 - 29.04 972 29.04 - 36.36 1147 36.36 - 43.67 697 43.67 - 50.99 423 50.99 - 58.31 242 58.31 - 65.63 158 65.63 - 72.95 99 72.95 - 80.27 84 80.27 - 87.59 32 =========================== Idealize ADP of riding H ========================== r_work=0.2015 r_free=0.2512 r_work=0.2002 r_free=0.2507 *********************** REFINEMENT MACRO_CYCLE 2 OF 3 ************************* |--(resolution: 3.10 - 52.13 A, n_refl.=10126 (all), 10.00 % free)------------| | | | r_work= 0.2002 r_free= 0.2507 coordinate error (max.-lik. estimate): 0.42 A | | | | normalized target function (ls_wunit_k1) (work): 0.048265 | | target function (ls_wunit_k1) not normalized (work): 439.835419 | | target function (ls_wunit_k1) not normalized (free): 77.955714 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2052 0.2002 0.2507 n_refl.: 10126 re-set all scales: r(all,work,free)=0.4229 0.4061 0.5565 n_refl.: 10126 remove outliers: r(all,work,free)=0.4229 0.4061 0.5565 n_refl.: 10126 overall B=0.00 to atoms: r(all,work,free)=0.4229 0.4061 0.5565 n_refl.: 10126 bulk-solvent and scaling: r(all,work,free)=0.2053 0.2002 0.2518 n_refl.: 10126 remove outliers: r(all,work,free)=0.2053 0.2002 0.2518 n_refl.: 10126 ======================== 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 52.125-14.829 89.91 87 11 0.2298 807.954 792.874 1.120 1.209 0.404 14.763-11.705 97.09 91 9 0.1588 842.124 841.200 0.997 1.197 0.400 11.688-9.266 96.82 191 22 0.1176 984.110 971.980 0.983 1.178 0.400 9.245-7.329 97.77 355 40 0.1474 733.879 727.562 0.962 1.150 0.400 7.324-5.801 97.35 727 80 0.1960 521.060 510.539 0.884 1.106 0.380 5.796-4.593 96.03 1414 157 0.1733 624.447 613.504 0.944 1.034 0.380 4.593-3.637 95.93 2819 313 0.1933 577.756 563.952 1.117 0.919 0.300 3.636-3.100 96.41 3429 381 0.2493 396.131 373.556 1.252 0.781 0.090 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0577 b_overall=3.8162 ============================ 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 = 0.831317 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.068300 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 0.2219 0.2546 0.0327 0.016 2.0 2.6 0.0 2.2 0 0.042 0.2056 0.2569 0.0513 0.015 2.3 3.9 0.2 2.5 0 0.125 0.1937 0.2611 0.0674 0.019 2.7 5.5 0.4 2.7 1 0.249 0.1846 0.2655 0.0808 0.022 3.2 9.0 1.0 3.5 2 0.374 0.1863 0.2591 0.0728 0.026 3.0 12.9 0.8 3.0 1 0.499 0.1852 0.2578 0.0726 0.028 3.0 13.2 1.0 3.0 1 0.623 0.1834 0.2588 0.0754 0.030 3.2 13.4 1.2 3.0 1 0.748 0.1992 0.2516 0.0524 0.023 2.5 11.4 0.4 2.2 0 0.873 0.1858 0.2629 0.0772 0.024 3.1 9.6 1.0 3.5 2 0.416 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1992 0.2516 0.0524 0.023 2.5 11.4 0.4 2.2 0 0.873 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 19.92 25.16 5.24 6.323 41.353 0.068 6.289 22.72 25.98 3.27 7.144 43.974 0.002 6.367 20.99 25.30 4.30 6.700 41.262 0.009 6.314 19.77 25.33 5.56 6.692 41.139 0.034 6.280 19.41 25.47 6.06 7.217 41.019 0.068 6.270 18.86 25.85 6.99 8.986 41.226 0.102 6.255 18.71 25.92 7.22 9.535 41.457 0.137 6.252 18.60 25.99 7.39 10.032 41.651 0.171 6.251 18.53 26.06 7.53 10.461 41.808 0.205 6.250 18.48 26.12 7.63 10.840 41.940 0.239 6.249 18.44 26.16 7.73 11.196 42.059 0.273 6.249 18.40 26.21 7.81 11.501 42.160 0.307 6.249 18.38 26.25 7.87 11.767 42.247 0.341 6.249 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.009 Accepted refinement result: 20.99 25.30 4.30 6.700 41.262 0.009 6.314 Individual atomic B min max mean iso aniso Overall: 17.09 88.98 37.43 2.57 4062 0 Protein: 17.09 88.98 37.43 2.57 4062 0 Chain A: 17.09 88.98 37.43 N/A 4062 0 Histogram: Values Number of atoms 17.09 - 24.28 274 24.28 - 31.46 1171 31.46 - 38.65 1221 38.65 - 45.84 605 45.84 - 53.03 346 53.03 - 60.22 190 60.22 - 67.41 123 67.41 - 74.60 71 74.60 - 81.79 52 81.79 - 88.98 9 =========================== Idealize ADP of riding H ========================== r_work=0.2099 r_free=0.2530 r_work=0.2108 r_free=0.2530 *********************** REFINEMENT MACRO_CYCLE 3 OF 3 ************************* |--(resolution: 3.10 - 52.13 A, n_refl.=10126 (all), 10.00 % free)------------| | | | r_work= 0.2108 r_free= 0.2530 coordinate error (max.-lik. estimate): 0.42 A | | | | normalized target function (ml) (work): 6.316458 | | target function (ml) not normalized (work): 57561.884054 | | target function (ml) not normalized (free): 6503.310003 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2149 0.2108 0.2530 n_refl.: 10126 re-set all scales: r(all,work,free)=0.4282 0.4117 0.5595 n_refl.: 10126 remove outliers: r(all,work,free)=0.4282 0.4117 0.5595 n_refl.: 10126 overall B=0.00 to atoms: r(all,work,free)=0.4282 0.4117 0.5595 n_refl.: 10126 bulk-solvent and scaling: r(all,work,free)=0.2147 0.2106 0.2525 n_refl.: 10126 remove outliers: r(all,work,free)=0.2147 0.2106 0.2525 n_refl.: 10126 ======================== 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 52.125-14.829 89.91 87 11 0.2277 807.954 792.987 1.106 1.221 0.404 14.763-11.705 97.09 91 9 0.1563 842.124 842.136 0.983 1.208 0.399 11.688-9.266 96.82 191 22 0.1159 984.110 973.233 0.971 1.189 0.399 9.245-7.329 97.77 355 40 0.1471 733.879 726.838 0.953 1.158 0.396 7.324-5.801 97.35 727 80 0.1981 521.060 509.967 0.885 1.113 0.390 5.796-4.593 96.03 1414 157 0.1802 624.447 611.765 0.938 1.037 0.380 4.593-3.637 95.93 2819 313 0.2065 577.756 560.271 1.114 0.916 0.300 3.636-3.100 96.41 3429 381 0.2659 396.131 369.383 1.266 0.771 0.090 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0577 b_overall=4.0199 ============================ 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 = 0.779125 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.072183 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 0.2325 0.2549 0.0224 0.014 2.1 2.4 0.0 2.2 0 0.039 0.2159 0.2576 0.0417 0.015 2.3 3.4 0.2 2.5 0 0.117 0.2041 0.2619 0.0578 0.019 2.7 5.6 0.2 2.5 1 0.234 0.1938 0.2679 0.0741 0.024 3.3 8.9 0.8 3.2 4 0.351 0.1949 0.2603 0.0654 0.026 3.1 12.8 1.0 2.7 3 0.467 0.1947 0.2590 0.0643 0.028 3.1 13.4 0.8 2.7 1 0.584 0.1937 0.2584 0.0647 0.031 3.2 13.5 1.0 3.0 1 0.701 0.1934 0.2582 0.0648 0.033 3.2 14.2 1.0 3.2 1 0.818 0.1984 0.2593 0.0609 0.023 2.9 11.5 0.4 2.5 0 0.390 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2325 0.2549 0.0224 0.014 2.1 2.4 0.0 2.2 0 0.039 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 23.25 25.49 2.24 5.750 41.101 0.072 6.378 24.33 26.07 1.74 6.124 42.551 0.002 6.422 23.03 25.81 2.78 6.271 41.058 0.009 6.373 22.41 25.67 3.25 6.331 40.983 0.036 6.349 21.11 26.15 5.04 8.650 41.547 0.072 6.311 20.79 26.33 5.55 9.860 41.996 0.108 6.302 20.70 26.48 5.77 10.289 42.143 0.144 6.302 20.57 26.59 6.01 11.014 42.387 0.180 6.300 20.48 26.69 6.21 11.621 42.584 0.217 6.299 20.41 26.76 6.35 12.141 42.750 0.253 6.298 20.36 26.83 6.47 12.589 42.890 0.289 6.298 20.32 26.88 6.56 12.969 43.009 0.325 6.298 20.29 26.93 6.64 13.304 43.113 0.361 6.298 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.036 Accepted refinement result: 22.41 25.67 3.25 6.331 40.983 0.036 6.349 Individual atomic B min max mean iso aniso Overall: 13.43 91.48 37.20 3.93 4062 0 Protein: 13.43 91.48 37.20 3.93 4062 0 Chain A: 13.43 91.48 37.20 N/A 4062 0 Histogram: Values Number of atoms 13.43 - 21.24 149 21.24 - 29.04 942 29.04 - 36.85 1338 36.85 - 44.65 730 44.65 - 52.45 436 52.45 - 60.26 209 60.26 - 68.06 127 68.06 - 75.87 79 75.87 - 83.67 44 83.67 - 91.48 8 =========================== Idealize ADP of riding H ========================== r_work=0.2241 r_free=0.2567 r_work=0.2235 r_free=0.2568 ----------X-ray data---------- |--(resolution: 3.10 - 52.13 A, n_refl.=10126 (all), 10.00 % free)------------| | | | r_work= 0.2235 r_free= 0.2568 coordinate error (max.-lik. estimate): 0.45 A | | | | normalized target function (ml) (work): 6.347068 | | target function (ml) not normalized (work): 57840.829076 | | target function (ml) not normalized (free): 6514.720933 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 52.13 - 5.93 0.97 1352 151 0.1780 0.2033 6.3911 6.4924| | 2: 5.93 - 4.71 0.96 1323 147 0.1948 0.2263 6.3864 6.4327| | 3: 4.71 - 4.11 0.96 1288 144 0.2066 0.2151 6.4654 6.4802| | 4: 4.11 - 3.74 0.96 1287 142 0.2279 0.2863 6.4405 6.6305| | 5: 3.74 - 3.47 0.96 1281 142 0.2637 0.2757 6.4273 6.3965| | 6: 3.47 - 3.26 0.97 1281 142 0.2552 0.3213 6.2307 6.4644| | 7: 3.26 - 3.10 0.97 1301 145 0.3019 0.3551 6.0874 6.123| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 52.13 - 5.93 1352 151 0.88 17.53 1.03 1.02 53124.23| | 2: 5.93 - 4.71 1323 147 0.87 19.80 1.01 0.96 56630.01| | 3: 4.71 - 4.11 1288 144 0.87 19.78 0.98 0.92 59311.48| | 4: 4.11 - 3.74 1287 142 0.84 23.33 0.99 0.93 64255.32| | 5: 3.74 - 3.47 1281 142 0.81 26.42 1.03 0.94 62567.69| | 6: 3.47 - 3.26 1281 142 0.77 30.15 0.99 0.90 55345.73| | 7: 3.26 - 3.10 1301 145 0.74 32.53 0.89 0.77 39502.80| |alpha: min = 0.77 max = 1.02 mean = 0.92| |beta: min = 39502.80 max = 64255.32 mean = 55774.77| |figures of merit: min = 0.00 max = 1.00 mean = 0.83| |phase err.(work): min = 0.00 max = 89.75 mean = 24.16| |phase err.(test): min = 0.00 max = 87.51 mean = 24.60| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.2268 0.2235 0.2568 n_refl.: 10126 re-set all scales: r(all,work,free)=0.4293 0.4132 0.5601 n_refl.: 10126 remove outliers: r(all,work,free)=0.4293 0.4132 0.5601 n_refl.: 10126 overall B=2.50 to atoms: r(all,work,free)=0.4413 0.4247 0.5738 n_refl.: 10126 bulk-solvent and scaling: r(all,work,free)=0.2256 0.2223 0.2562 n_refl.: 10126 remove outliers: r(all,work,free)=0.2256 0.2223 0.2562 n_refl.: 10126 ======================== 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 52.125-14.829 89.91 87 11 0.2397 807.954 785.756 1.081 1.226 0.399 14.763-11.705 97.09 91 9 0.1640 842.124 837.494 1.002 1.214 0.400 11.688-9.266 96.82 191 22 0.1219 984.110 974.083 1.010 1.194 0.402 9.245-7.329 97.77 355 40 0.1563 733.879 726.185 0.986 1.163 0.401 7.324-5.801 97.35 727 80 0.2136 521.060 506.134 0.916 1.116 0.396 5.796-4.593 96.03 1414 157 0.1910 624.447 608.255 0.953 1.038 0.380 4.593-3.637 95.93 2819 313 0.2219 577.756 555.597 1.128 0.913 0.337 3.636-3.100 96.41 3429 381 0.2742 396.131 366.363 1.290 0.763 0.104 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0913 b_overall=5.1369 ================= 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 : 0.4295 0.5328 0.005 1.249 12.7 77.7 33.4 0 0.000 1_bss: 0.2401 0.2416 0.005 1.249 16.0 81.0 36.7 0 0.000 1_settarget: 0.2401 0.2416 0.005 1.249 16.0 81.0 36.7 0 0.000 1_weight: 0.2401 0.2416 0.005 1.249 16.0 81.0 36.7 0 0.000 1_xyzrec: 0.2140 0.2486 0.022 2.459 16.0 81.0 36.7 0 0.062 1_adp: 0.2015 0.2512 0.022 2.459 14.4 87.6 37.6 0 0.062 1_regHadp: 0.2002 0.2507 0.022 2.459 14.4 87.6 37.6 0 0.062 2_bss: 0.2002 0.2518 0.022 2.459 14.4 87.6 37.6 0 0.062 2_settarget: 0.2002 0.2518 0.022 2.459 14.4 87.6 37.6 0 0.062 2_updatecdl: 0.2002 0.2518 0.022 2.452 14.4 87.6 37.6 0 0.062 2_weight: 0.2002 0.2518 0.022 2.452 14.4 87.6 37.6 0 0.062 2_xyzrec: 0.1992 0.2516 0.023 2.466 14.4 87.6 37.6 0 0.063 2_adp: 0.2099 0.2530 0.023 2.466 17.1 89.0 37.4 0 0.063 2_regHadp: 0.2108 0.2530 0.023 2.466 17.1 89.0 37.4 0 0.063 3_bss: 0.2106 0.2525 0.023 2.466 17.1 89.0 37.4 0 0.063 3_settarget: 0.2106 0.2525 0.023 2.466 17.1 89.0 37.4 0 0.063 3_updatecdl: 0.2106 0.2525 0.023 2.466 17.1 89.0 37.4 0 0.063 3_setrh: 0.2106 0.2525 0.023 2.466 17.1 89.0 37.4 0 0.063 3_weight: 0.2106 0.2525 0.023 2.466 17.1 89.0 37.4 0 0.063 3_xyzrec: 0.2325 0.2549 0.014 2.077 17.1 89.0 37.4 0 0.136 3_adp: 0.2241 0.2567 0.014 2.077 13.4 91.5 37.2 0 0.136 3_regHadp: 0.2235 0.2568 0.014 2.077 13.4 91.5 37.2 0 0.136 end: 0.2223 0.2562 0.014 2.077 15.9 94.0 39.7 0 0.136 ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/cci-filer3/home/nigel/work/ANI/result/xray/pairs/4phenix_1fp9_refine_001.cif Writing default parameters for subsequent refinement: /net/cci-filer3/home/nigel/work/ANI/result/xray/pairs/4phenix_1fp9_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 5.4300 Refinement macro-cycles (run) : 202.0000 Write final files (write_after_run_outputs) : 11.8400 Total : 219.2700 Total CPU time: 4.21 minutes =========================== phenix.refine: finished =========================== # Date 2024-08-09 Time 09:36:59 PDT -0700 (1723221419.55 s) Start R-work = 0.2401, R-free = 0.2416 Final R-work = 0.2223, R-free = 0.2562 =============================================================================== Job complete usr+sys time: 263.13 seconds wall clock time: 5 minutes 33.44 seconds (333.44 seconds total)