Starting phenix.refine on Fri Aug 9 09:31:39 2024 by nigel =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, 4phenix_1w60.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/1w60/1w60.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_1w60.prmtop amber.coordinate_file_name=4amber_1w60.rst7 amber.order_file_name=4amber_1w60.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_1w60.order 4amber_1w60.rst7 4amber_1w60.prmtop Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/1w60/1w60.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/1w60/1w60.mtz" model { file = "4phenix_1w60.pdb" } default_model = "4phenix_1w60.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_1w60.prmtop coordinate_file_name = 4amber_1w60.rst7 order_file_name = 4amber_1w60.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: 7874 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 3937 Classifications: {'peptide': 255} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 7, 'TRANS': 247} Chain: "B" Number of atoms: 3937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 3937 Classifications: {'peptide': 255} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 7, 'TRANS': 247} Time building chain proxies: 0.87, per 1000 atoms: 0.11 Number of scatterers: 7874 At special positions: 0 Unit cell: (82.892, 82.892, 70.859, 90, 90, 120) Space group: P 3 (No. 143) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 32 16.00 O 786 8.00 N 644 7.00 C 2466 6.00 H 3946 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: 1.34 Conformation dependent library (CDL) restraints added in 168.4 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 968 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 8 helices and 6 sheets defined 16.1% alpha, 33.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 9 through 16 Processing helix chain 'A' and resid 72 through 79 Processing helix chain 'A' and resid 141 through 152 Processing helix chain 'A' and resid 209 through 218 removed outlier: 4.053A pdb=" N LYS A 217 " --> pdb=" O ASN A 213 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N ALA A 218 " --> pdb=" O PHE A 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 19 removed outlier: 3.714A pdb=" N ALA B 18 " --> pdb=" O LYS B 14 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU B 19 " --> pdb=" O VAL B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 79 Processing helix chain 'B' and resid 141 through 152 Processing helix chain 'B' and resid 209 through 221 removed outlier: 4.138A pdb=" N LYS B 217 " --> pdb=" O ASN B 213 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N ALA B 218 " --> pdb=" O PHE B 214 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N THR B 219 " --> pdb=" O PHE B 215 " (cutoff:3.500A) Proline residue: B 220 - end of helix Processing sheet with id= A, first strand: chain 'A' and resid 59 through 62 Processing sheet with id= B, first strand: chain 'A' and resid 66 through 71 removed outlier: 3.624A pdb=" N ALA A 26 " --> pdb=" O VAL A 70 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N GLU A 25 " --> pdb=" O MET A 40 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N MET A 40 " --> pdb=" O GLU A 25 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N CYS A 27 " --> pdb=" O GLN A 38 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N GLN A 38 " --> pdb=" O CYS A 27 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 204 through 208 removed outlier: 5.816A pdb=" N ALA A 157 " --> pdb=" O SER A 172 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N SER A 172 " --> pdb=" O ALA A 157 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 59 through 62 Processing sheet with id= E, first strand: chain 'B' and resid 66 through 71 removed outlier: 3.620A pdb=" N ALA B 26 " --> pdb=" O VAL B 70 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N GLU B 25 " --> pdb=" O MET B 40 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N MET B 40 " --> pdb=" O GLU B 25 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N CYS B 27 " --> pdb=" O GLN B 38 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N GLN B 38 " --> pdb=" O CYS B 27 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 203 through 208 removed outlier: 5.650A pdb=" N ALA B 157 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N SER B 172 " --> pdb=" O ALA B 157 " (cutoff:3.500A) 187 hydrogen bonds defined for protein. 510 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: 1.27 Time building geometry restraints manager: 1.55 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: 3934 1.15 - 1.32: 712 1.32 - 1.49: 1460 1.49 - 1.66: 1768 1.66 - 1.83: 52 Bond restraints: 7926 Sorted by residual: bond pdb=" NE1 TRP B 28 " pdb=" CE2 TRP B 28 " ideal model delta sigma weight residual 1.370 1.483 -0.113 1.10e-02 8.26e+03 1.06e+02 bond pdb=" ND2 ASN B 107 " pdb="HD22 ASN B 107 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.46e+01 bond pdb=" N GLN B 131 " pdb=" H GLN B 131 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N LEU B 6 " pdb=" H LEU B 6 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" NE2 GLN A 8 " pdb="HE22 GLN A 8 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 ... (remaining 7921 not shown) Histogram of bond angle deviations from ideal: 97.88 - 105.14: 87 105.14 - 112.40: 9571 112.40 - 119.66: 1859 119.66 - 126.92: 2839 126.92 - 134.18: 18 Bond angle restraints: 14374 Sorted by residual: angle pdb=" N ASP B 232 " pdb=" CA ASP B 232 " pdb=" CB ASP B 232 " ideal model delta sigma weight residual 114.17 108.16 6.01 1.14e+00 7.69e-01 2.78e+01 angle pdb=" CD ARG A 64 " pdb=" NE ARG A 64 " pdb=" CZ ARG A 64 " ideal model delta sigma weight residual 124.40 117.23 7.17 1.40e+00 5.10e-01 2.62e+01 angle pdb=" N PRO B 234 " pdb=" CA PRO B 234 " pdb=" CB PRO B 234 " ideal model delta sigma weight residual 103.31 107.82 -4.51 8.90e-01 1.26e+00 2.57e+01 angle pdb=" CD ARG A 61 " pdb=" NE ARG A 61 " pdb=" CZ ARG A 61 " ideal model delta sigma weight residual 124.40 117.32 7.08 1.40e+00 5.10e-01 2.56e+01 angle pdb=" N PRO B 202 " pdb=" CA PRO B 202 " pdb=" CB PRO B 202 " ideal model delta sigma weight residual 103.19 107.64 -4.45 9.00e-01 1.23e+00 2.45e+01 ... (remaining 14369 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.52: 3113 17.52 - 35.05: 331 35.05 - 52.57: 169 52.57 - 70.10: 79 70.10 - 87.62: 20 Dihedral angle restraints: 3712 sinusoidal: 2056 harmonic: 1656 Sorted by residual: dihedral pdb=" CA ASP A 122 " pdb=" C ASP A 122 " pdb=" N VAL A 123 " pdb=" CA VAL A 123 " ideal model delta harmonic sigma weight residual -180.00 -162.23 -17.77 0 5.00e+00 4.00e-02 1.26e+01 dihedral pdb=" CA ASN A 95 " pdb=" C ASN A 95 " pdb=" N ALA A 96 " pdb=" CA ALA A 96 " ideal model delta harmonic sigma weight residual -180.00 -162.99 -17.01 0 5.00e+00 4.00e-02 1.16e+01 dihedral pdb=" CA ASP B 122 " pdb=" C ASP B 122 " pdb=" N VAL B 123 " pdb=" CA VAL B 123 " ideal model delta harmonic sigma weight residual -180.00 -163.34 -16.66 0 5.00e+00 4.00e-02 1.11e+01 ... (remaining 3709 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 402 0.037 - 0.075: 108 0.075 - 0.112: 81 0.112 - 0.149: 23 0.149 - 0.187: 22 Chirality restraints: 636 Sorted by residual: chirality pdb=" CB THR B 219 " pdb=" CA THR B 219 " pdb=" OG1 THR B 219 " pdb=" CG2 THR B 219 " both_signs ideal model delta sigma weight residual False 2.55 2.74 -0.19 2.00e-01 2.50e+01 8.73e-01 chirality pdb=" CB THR A 219 " pdb=" CA THR A 219 " pdb=" OG1 THR A 219 " pdb=" CG2 THR A 219 " both_signs ideal model delta sigma weight residual False 2.55 2.73 -0.18 2.00e-01 2.50e+01 8.13e-01 chirality pdb=" CB THR B 73 " pdb=" CA THR B 73 " pdb=" OG1 THR B 73 " pdb=" CG2 THR B 73 " both_signs ideal model delta sigma weight residual False 2.55 2.73 -0.18 2.00e-01 2.50e+01 7.95e-01 ... (remaining 633 not shown) Planarity restraints: 1186 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 239 " -0.113 2.00e-02 2.50e+03 4.19e-02 5.26e+01 pdb=" CG TYR B 239 " 0.027 2.00e-02 2.50e+03 pdb=" CD1 TYR B 239 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 TYR B 239 " 0.029 2.00e-02 2.50e+03 pdb=" CE1 TYR B 239 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR B 239 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR B 239 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR B 239 " -0.043 2.00e-02 2.50e+03 pdb=" HD1 TYR B 239 " 0.037 2.00e-02 2.50e+03 pdb=" HD2 TYR B 239 " 0.052 2.00e-02 2.50e+03 pdb=" HE1 TYR B 239 " -0.002 2.00e-02 2.50e+03 pdb=" HE2 TYR B 239 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS B 246 " -0.035 2.00e-02 2.50e+03 1.72e-02 6.67e+00 pdb=" CG HIS B 246 " 0.015 2.00e-02 2.50e+03 pdb=" ND1 HIS B 246 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 HIS B 246 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 HIS B 246 " -0.006 2.00e-02 2.50e+03 pdb=" NE2 HIS B 246 " -0.009 2.00e-02 2.50e+03 pdb=" HD1 HIS B 246 " 0.022 2.00e-02 2.50e+03 pdb=" HD2 HIS B 246 " 0.013 2.00e-02 2.50e+03 pdb=" HE1 HIS B 246 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 60 " -0.034 2.00e-02 2.50e+03 1.38e-02 5.71e+00 pdb=" CG TYR A 60 " 0.007 2.00e-02 2.50e+03 pdb=" CD1 TYR A 60 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 TYR A 60 " 0.011 2.00e-02 2.50e+03 pdb=" CE1 TYR A 60 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR A 60 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR A 60 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR A 60 " -0.013 2.00e-02 2.50e+03 pdb=" HD1 TYR A 60 " 0.006 2.00e-02 2.50e+03 pdb=" HD2 TYR A 60 " 0.023 2.00e-02 2.50e+03 pdb=" HE1 TYR A 60 " 0.002 2.00e-02 2.50e+03 pdb=" HE2 TYR A 60 " -0.015 2.00e-02 2.50e+03 ... (remaining 1183 not shown) Histogram of nonbonded interaction distances: 0.73 - 1.50: 30 1.50 - 2.28: 1530 2.28 - 3.05: 22631 3.05 - 3.83: 33787 3.83 - 4.60: 54038 Warning: very small nonbonded interaction distances. Nonbonded interactions: 112016 Sorted by model distance: nonbonded pdb=" O LEU B 182 " pdb=" HG SER B 183 " model vdw 0.726 2.450 nonbonded pdb=" HG CYS B 135 " pdb=" HB2 MET B 199 " model vdw 0.785 2.440 nonbonded pdb=" HB2 GLN B 184 " pdb="HG11 VAL B 195 " model vdw 1.002 2.440 nonbonded pdb="HG13 VAL A 188 " pdb=" HB2 ALA B 252 " model vdw sym.op. 1.043 2.440 -x+y+1,-x+1,z nonbonded pdb=" HG SER A 152 " pdb="HD21 ASN A 213 " model vdw 1.073 2.100 ... (remaining 112011 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. ============================== Initializing Amber ============================= topology : 4amber_1w60.prmtop atom order : 4amber_1w60.order coordinates : 4amber_1w60.rst7 ===================================== ... ===================================== ============================== Scattering factors ============================= ----------X-ray scattering dictionary---------- Number of scattering types: 5 Type Number sf(0) Gaussians S 32 15.96 2 O 786 7.97 1 N 644 6.97 1 C 2466 5.97 2 H 3946 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: 3946 of 7874 ******************************************************************************* Automatic adjustment: hydrogens.refine=riding ******************************************************************************* n_use = 7874 n_use_u_iso = 7874 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 = 7874 ================== Extract refinement strategy and selections ================= Refinement flags and selection counts: individual_sites = True (7874 atoms) torsion_angles = False (0 atoms) rigid_body = False (0 atoms in 0 groups) individual_adp = True (iso = 7874 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 9 through 16 } helix { serial_number = "2" helix_identifier = "2" selection = chain 'A' and resid 72 through 79 } helix { serial_number = "3" helix_identifier = "3" selection = chain 'A' and resid 141 through 152 } helix { serial_number = "4" helix_identifier = "4" selection = chain 'A' and resid 209 through 218 } helix { serial_number = "5" helix_identifier = "5" selection = chain 'B' and resid 9 through 19 } helix { serial_number = "6" helix_identifier = "6" selection = chain 'B' and resid 72 through 79 } helix { serial_number = "7" helix_identifier = "7" selection = chain 'B' and resid 141 through 152 } helix { serial_number = "8" helix_identifier = "8" selection = chain 'B' and resid 209 through 221 } sheet { first_strand = chain 'A' and resid 59 through 62 sheet_id = " A" strand { selection = chain 'A' and resid 2 through 6 sense = parallel *antiparallel unknown bond_start_current = chain 'A' and resid 5 and name N bond_start_previous = chain 'A' and resid 59 and name O } strand { selection = chain 'A' and resid 87 through 92 sense = parallel *antiparallel unknown bond_start_current = chain 'A' and resid 92 and name N bond_start_previous = chain 'A' and resid 2 and name O } strand { selection = chain 'A' and resid 98 through 104 sense = parallel *antiparallel unknown bond_start_current = chain 'A' and resid 104 and name N bond_start_previous = chain 'A' and resid 87 and name O } strand { selection = chain 'A' and resid 111 through 117 sense = parallel *antiparallel unknown bond_start_current = chain 'A' and resid 116 and name N bond_start_previous = chain 'A' and resid 99 and name O } } sheet { first_strand = chain 'A' and resid 66 through 71 sheet_id = " B" strand { selection = chain 'A' and resid 25 through 31 sense = parallel *antiparallel unknown bond_start_current = chain 'A' and resid 30 and name N bond_start_previous = chain 'A' and resid 66 and name O } strand { selection = chain 'A' and resid 34 through 40 sense = parallel *antiparallel unknown bond_start_current = chain 'A' and resid 36 and name N bond_start_previous = chain 'A' and resid 29 and name O } strand { selection = chain 'A' and resid 46 through 53 sense = parallel *antiparallel unknown bond_start_current = chain 'A' and resid 52 and name N bond_start_previous = chain 'A' and resid 35 and name O } strand { selection = chain 'A' and resid 245 through 251 sense = parallel *antiparallel unknown bond_start_current = chain 'A' and resid 250 and name N bond_start_previous = chain 'A' and resid 47 and name O } strand { selection = chain 'A' and resid 235 through 239 sense = parallel *antiparallel unknown bond_start_current = chain 'A' and resid 239 and name N bond_start_previous = chain 'A' and resid 247 and name O } strand { selection = chain 'A' and resid 224 through 229 sense = parallel *antiparallel unknown bond_start_current = chain 'A' and resid 228 and name N bond_start_previous = chain 'A' and resid 236 and name O } strand { selection = chain 'A' and resid 135 through 140 sense = parallel *antiparallel unknown bond_start_current = chain 'A' and resid 139 and name N bond_start_previous = chain 'A' and resid 225 and name O } } sheet { first_strand = chain 'A' and resid 204 through 208 sheet_id = " C" strand { selection = chain 'A' and resid 157 through 162 sense = parallel *antiparallel unknown bond_start_current = chain 'A' and resid 160 and name N bond_start_previous = chain 'A' and resid 205 and name O } strand { selection = chain 'A' and resid 167 through 172 sense = parallel *antiparallel unknown bond_start_current = chain 'A' and resid 170 and name N bond_start_previous = chain 'A' and resid 159 and name O } strand { selection = chain 'A' and resid 177 through 182 sense = parallel *antiparallel unknown bond_start_current = chain 'A' and resid 182 and name N bond_start_previous = chain 'A' and resid 167 and name O } } sheet { first_strand = chain 'B' and resid 59 through 62 sheet_id = " D" strand { selection = chain 'B' and resid 2 through 6 sense = parallel *antiparallel unknown bond_start_current = chain 'B' and resid 5 and name N bond_start_previous = chain 'B' and resid 59 and name O } strand { selection = chain 'B' and resid 87 through 92 sense = parallel *antiparallel unknown bond_start_current = chain 'B' and resid 92 and name N bond_start_previous = chain 'B' and resid 2 and name O } strand { selection = chain 'B' and resid 98 through 104 sense = parallel *antiparallel unknown bond_start_current = chain 'B' and resid 104 and name N bond_start_previous = chain 'B' and resid 87 and name O } strand { selection = chain 'B' and resid 112 through 117 sense = parallel *antiparallel unknown bond_start_current = chain 'B' and resid 116 and name N bond_start_previous = chain 'B' and resid 99 and name O } } sheet { first_strand = chain 'B' and resid 66 through 71 sheet_id = " E" strand { selection = chain 'B' and resid 25 through 31 sense = parallel *antiparallel unknown bond_start_current = chain 'B' and resid 30 and name N bond_start_previous = chain 'B' and resid 66 and name O } strand { selection = chain 'B' and resid 34 through 40 sense = parallel *antiparallel unknown bond_start_current = chain 'B' and resid 36 and name N bond_start_previous = chain 'B' and resid 29 and name O } strand { selection = chain 'B' and resid 46 through 53 sense = parallel *antiparallel unknown bond_start_current = chain 'B' and resid 52 and name N bond_start_previous = chain 'B' and resid 35 and name O } strand { selection = chain 'B' and resid 245 through 251 sense = parallel *antiparallel unknown bond_start_current = chain 'B' and resid 250 and name N bond_start_previous = chain 'B' and resid 47 and name O } strand { selection = chain 'B' and resid 235 through 239 sense = parallel *antiparallel unknown bond_start_current = chain 'B' and resid 239 and name N bond_start_previous = chain 'B' and resid 247 and name O } strand { selection = chain 'B' and resid 224 through 229 sense = parallel *antiparallel unknown bond_start_current = chain 'B' and resid 228 and name N bond_start_previous = chain 'B' and resid 236 and name O } strand { selection = chain 'B' and resid 135 through 140 sense = parallel *antiparallel unknown bond_start_current = chain 'B' and resid 139 and name N bond_start_previous = chain 'B' and resid 225 and name O } } sheet { first_strand = chain 'B' and resid 203 through 208 sheet_id = " F" strand { selection = chain 'B' and resid 157 through 162 sense = parallel *antiparallel unknown bond_start_current = chain 'B' and resid 162 and name N bond_start_previous = chain 'B' and resid 203 and name O } strand { selection = chain 'B' and resid 167 through 172 sense = parallel *antiparallel unknown bond_start_current = chain 'B' and resid 170 and name N bond_start_previous = chain 'B' and resid 159 and name O } strand { selection = chain 'B' and resid 177 through 181 sense = parallel *antiparallel unknown bond_start_current = chain 'B' and resid 180 and name N bond_start_previous = chain 'B' and resid 169 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_1w60.prmtop" coordinate_file_name = "4amber_1w60.rst7" order_file_name = "4amber_1w60.order" } } output { prefix = "4phenix_1w60_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: 3.14 - 25.21 A, n_refl.=9258 (all), 4.80 % free)-------------| | | | r_work= 0.3126 r_free= 0.3547 coordinate error (max.-lik. estimate): 0.43 A | | | | normalized target function (ml) (work): 6.213131 | | target function (ml) not normalized (work): 54762.537623 | | target function (ml) not normalized (free): 2755.544572 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 25.21 - 4.53 0.98 2961 131 0.3220 0.3667 6.702 6.6336| | 2: 4.52 - 3.60 0.98 2955 140 0.3037 0.3313 6.2183 6.2834| | 3: 3.60 - 3.14 0.97 2898 173 0.3056 0.3684 5.7083 5.82| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 25.21 - 4.53 2961 131 0.65 40.60 0.91 0.65 114503.06| | 2: 4.52 - 3.60 2955 140 0.68 38.37 1.23 0.88 57181.31| | 3: 3.60 - 3.14 2898 173 0.73 34.21 1.19 0.95 18918.11| |alpha: min = 0.65 max = 0.95 mean = 0.83| |beta: min = 18918.11 max = 114503.06 mean = 63857.39| |figures of merit: min = 0.00 max = 0.99 mean = 0.69| |phase err.(work): min = 0.00 max = 89.89 mean = 37.75| |phase err.(test): min = 0.00 max = 88.86 mean = 37.39| |-----------------------------------------------------------------------------| ----------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 : 0.007 0.113 3980 Z= 0.441 Angle : 1.399 7.165 5378 Z= 0.912 Chirality : 0.058 0.187 636 Planarity : 0.003 0.044 692 Dihedral : 23.356 87.623 1492 Min Nonbonded Distance : 1.684 Molprobity Statistics. All-atom Clashscore : 15.62 Ramachandran Plot: Outliers : 2.96 % Allowed : 6.32 % Favored : 90.71 % Rotamer: Outliers : 23.77 % Allowed : 18.39 % Favored : 57.85 % 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: -3.75 (0.31), residues: 506 helix: -2.40 (0.42), residues: 82 sheet: -1.98 (0.30), residues: 252 loop : -2.98 (0.35), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 61 TYR 0.086 0.005 TYR B 239 PHE 0.018 0.001 PHE B 103 TRP 0.020 0.004 TRP B 28 HIS 0.002 0.001 HIS B 246 Individual atomic B min max mean iso aniso Overall: 2.00 149.48 50.67 9.35 3928 0 Protein: 2.00 149.48 50.67 9.35 3928 0 Chain A: 2.00 149.40 50.68 N/A 1964 0 Chain B: 3.06 149.48 50.65 N/A 1964 0 Histogram: Values Number of atoms 2.00 - 16.75 88 16.75 - 31.50 624 31.50 - 46.24 1249 46.24 - 60.99 942 60.99 - 75.74 488 75.74 - 90.49 299 90.49 - 105.24 135 105.24 - 119.98 34 119.98 - 134.73 25 134.73 - 149.48 44 |-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: 3.14 - 25.21 A, n_refl.=9258 (all), 4.80 % free)-------------| | | | r_work= 0.3126 r_free= 0.3547 coordinate error (max.-lik. estimate): 0.43 A | | | | normalized target function (ml) (work): 6.213131 | | target function (ml) not normalized (work): 54762.537623 | | target function (ml) not normalized (free): 2755.544572 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.3147 0.3126 0.3547 n_refl.: 9258 re-set all scales: r(all,work,free)=0.3147 0.3126 0.3547 n_refl.: 9258 remove outliers: r(all,work,free)=0.3147 0.3125 0.3547 n_refl.: 9255 overall B=5.75 to atoms: r(all,work,free)=0.3302 0.3281 0.3710 n_refl.: 9255 bulk-solvent and scaling: r(all,work,free)=0.2347 0.2325 0.2781 n_refl.: 9255 remove outliers: r(all,work,free)=0.2347 0.2325 0.2781 n_refl.: 9255 ======================== 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 25.215-13.182 84.48 95 3 0.2239 720.927 691.451 1.578 1.004 0.382 13.182-10.771 92.52 92 7 0.2356 728.577 668.757 1.392 1.009 0.376 10.742-8.763 94.15 183 10 0.1795 646.556 619.652 1.239 1.006 0.374 8.709-7.139 97.85 350 14 0.1959 566.962 549.301 1.222 1.006 0.361 7.120-5.819 98.85 652 33 0.2408 394.630 369.352 1.066 1.002 0.347 5.810-4.742 98.41 1191 49 0.2078 477.646 452.624 0.971 0.997 0.284 4.737-3.861 98.48 2221 114 0.2122 429.398 408.551 1.019 0.988 0.203 3.860-3.143 97.34 4027 214 0.2781 247.845 230.509 1.028 0.974 0.071 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.1000 b_overall=4.7898 ============================ 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 = 4.074555 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.208065 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 0.2333 0.2945 0.0612 0.013 2.0 1.1 2.2 10.8 0 0.125 0.2164 0.2897 0.0733 0.013 2.0 1.1 1.8 11.7 1 0.250 0.2009 0.2820 0.0811 0.014 2.1 1.0 1.6 12.3 1 0.500 0.1859 0.2758 0.0900 0.016 2.4 2.2 2.4 13.9 1 1.000 0.1716 0.2725 0.1008 0.019 2.8 5.6 2.0 17.0 3 2.000 0.1647 0.2743 0.1097 0.023 3.2 8.5 2.4 20.2 6 3.000 0.1600 0.2775 0.1175 0.026 3.6 11.4 3.6 22.6 9 4.000 0.1562 0.2779 0.1216 0.029 3.9 13.2 4.2 23.5 15 5.000 0.1529 0.2816 0.1287 0.032 4.2 14.4 4.7 24.9 17 6.000 0.1504 0.2820 0.1316 0.034 4.5 17.3 5.1 25.3 18 7.000 0.1486 0.2835 0.1350 0.037 4.7 19.6 5.5 27.1 22 8.000 0.1464 0.2873 0.1409 0.039 5.0 23.4 6.7 27.8 25 9.000 0.1449 0.2882 0.1434 0.041 5.2 23.0 7.1 28.7 26 10.000 0.1715 0.2731 0.1016 0.019 2.9 6.4 2.6 16.6 4 2.037 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1716 0.2725 0.1008 0.019 2.8 5.6 2.0 17.0 3 2.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 17.16 27.25 10.08 6.626 55.219 0.208 0.035 18.41 28.27 9.86 6.211 55.931 0.006 0.039 18.18 28.25 10.08 6.088 55.878 0.026 0.038 17.46 28.18 10.72 6.032 55.786 0.104 0.036 16.85 28.09 11.24 6.446 55.790 0.208 0.033 16.46 28.09 11.62 7.000 55.857 0.312 0.032 16.20 28.07 11.87 7.484 55.903 0.416 0.031 16.02 28.05 12.03 7.916 55.950 0.520 0.030 15.88 28.06 12.17 8.327 56.014 0.624 0.030 15.77 28.06 12.29 8.731 56.101 0.728 0.029 15.69 28.07 12.38 9.029 56.146 0.832 0.029 15.63 28.07 12.45 9.304 56.196 0.936 0.029 15.56 28.09 12.53 9.613 56.268 1.040 0.029 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.104 Accepted refinement result: 17.46 28.18 10.72 6.032 55.786 0.104 0.036 Individual atomic B min max mean iso aniso Overall: 22.25 152.79 57.55 5.97 3928 0 Protein: 22.25 152.79 57.55 5.97 3928 0 Chain A: 22.25 152.79 57.53 N/A 1964 0 Chain B: 23.00 151.49 57.57 N/A 1964 0 Histogram: Values Number of atoms 22.25 - 35.30 257 35.30 - 48.35 1325 48.35 - 61.41 1109 61.41 - 74.46 557 74.46 - 87.52 319 87.52 - 100.57 212 100.57 - 113.62 59 113.62 - 126.68 26 126.68 - 139.73 23 139.73 - 152.79 41 =========================== Idealize ADP of riding H ========================== r_work=0.1746 r_free=0.2818 r_work=0.1762 r_free=0.2809 *********************** REFINEMENT MACRO_CYCLE 2 OF 3 ************************* |--(resolution: 3.14 - 25.21 A, n_refl.=9255 (all), 4.80 % free)-------------| | | | r_work= 0.1762 r_free= 0.2809 coordinate error (max.-lik. estimate): 0.50 A | | | | normalized target function (ls_wunit_k1) (work): 0.036038 | | target function (ls_wunit_k1) not normalized (work): 317.531788 | | target function (ls_wunit_k1) not normalized (free): 43.734644 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1810 0.1762 0.2809 n_refl.: 9255 re-set all scales: r(all,work,free)=0.3065 0.3022 0.3832 n_refl.: 9255 remove outliers: r(all,work,free)=0.3065 0.3022 0.3832 n_refl.: 9255 overall B=0.00 to atoms: r(all,work,free)=0.3065 0.3022 0.3832 n_refl.: 9255 bulk-solvent and scaling: r(all,work,free)=0.1798 0.1749 0.2819 n_refl.: 9255 remove outliers: r(all,work,free)=0.1798 0.1749 0.2819 n_refl.: 9255 ======================== 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 25.215-13.182 84.48 95 3 0.2049 514.743 501.142 1.398 1.039 0.374 13.182-10.771 91.67 92 7 0.1690 520.206 492.718 1.309 1.042 0.370 10.742-8.763 94.15 183 10 0.1278 461.642 446.701 1.151 1.035 0.353 8.709-7.139 97.85 350 14 0.1419 404.812 395.804 1.133 1.031 0.347 7.120-5.819 98.85 652 33 0.1775 281.767 272.540 0.998 1.019 0.330 5.810-4.742 98.41 1191 49 0.1403 341.041 333.397 0.953 1.003 0.280 4.737-3.861 98.48 2221 114 0.1520 306.591 300.469 1.010 0.977 0.180 3.860-3.143 97.34 4027 214 0.2262 176.962 170.765 1.050 0.938 0.040 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0577 b_overall=3.6563 ============================ 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 = 0.981131 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.055850 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 0.2179 0.2963 0.0785 0.013 2.1 0.5 2.0 9.6 0 0.049 0.1906 0.2856 0.0950 0.014 2.3 1.3 1.6 13.2 1 0.147 0.1771 0.2824 0.1052 0.017 2.8 4.1 2.4 14.8 1 0.294 0.1695 0.2804 0.1109 0.021 3.1 6.0 2.6 16.8 4 0.442 0.1652 0.2786 0.1134 0.024 3.5 6.7 1.8 17.0 7 0.589 0.1681 0.2815 0.1134 0.024 3.2 6.7 2.0 17.5 4 0.736 0.1629 0.2823 0.1194 0.030 3.6 7.1 2.2 17.7 7 0.883 0.1635 0.2816 0.1181 0.031 3.6 7.4 2.2 17.9 7 1.030 0.1680 0.2793 0.1113 0.021 3.2 6.0 2.2 17.3 5 0.491 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1652 0.2786 0.1134 0.024 3.5 6.7 1.8 17.0 7 0.589 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 16.52 27.86 11.34 9.383 62.407 0.056 5.472 19.38 29.43 10.05 9.264 65.514 0.002 5.556 18.30 28.97 10.67 9.425 64.076 0.007 5.530 16.40 27.96 11.56 9.620 62.180 0.028 5.469 16.19 27.90 11.71 9.869 62.107 0.056 5.463 15.82 28.01 12.19 10.737 61.842 0.084 5.457 15.58 28.09 12.51 11.521 62.019 0.112 5.453 15.51 28.10 12.59 11.722 62.143 0.140 5.453 15.47 28.10 12.64 11.872 62.233 0.168 5.453 15.43 28.11 12.68 12.013 62.315 0.195 5.453 15.41 28.12 12.71 12.137 62.384 0.223 5.453 15.39 28.13 12.74 12.275 62.456 0.251 5.453 15.37 28.14 12.76 12.347 62.496 0.279 5.453 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.002 Accepted refinement result: 19.38 29.43 10.05 9.264 65.514 0.002 5.556 Individual atomic B min max mean iso aniso Overall: 37.77 147.79 63.78 3.96 3928 0 Protein: 37.77 147.79 63.78 3.96 3928 0 Chain A: 37.77 147.79 63.75 N/A 1964 0 Chain B: 39.02 146.49 63.81 N/A 1964 0 Histogram: Values Number of atoms 37.77 - 48.77 422 48.77 - 59.77 1606 59.77 - 70.78 970 70.78 - 81.78 468 81.78 - 92.78 218 92.78 - 103.78 123 103.78 - 114.78 30 114.78 - 125.78 31 125.78 - 136.78 25 136.78 - 147.79 35 =========================== Idealize ADP of riding H ========================== r_work=0.1938 r_free=0.2943 r_work=0.1963 r_free=0.2928 *********************** REFINEMENT MACRO_CYCLE 3 OF 3 ************************* |--(resolution: 3.14 - 25.21 A, n_refl.=9255 (all), 4.80 % free)-------------| | | | r_work= 0.1963 r_free= 0.2928 coordinate error (max.-lik. estimate): 0.34 A | | | | normalized target function (ml) (work): 5.561383 | | target function (ml) not normalized (work): 49001.342594 | | target function (ml) not normalized (free): 2555.764075 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2006 0.1963 0.2928 n_refl.: 9255 re-set all scales: r(all,work,free)=0.3454 0.3413 0.4237 n_refl.: 9255 remove outliers: r(all,work,free)=0.3454 0.3413 0.4237 n_refl.: 9255 overall B=-5.41 to atoms: r(all,work,free)=0.3252 0.3209 0.4060 n_refl.: 9255 bulk-solvent and scaling: r(all,work,free)=0.1968 0.1925 0.2868 n_refl.: 9255 remove outliers: r(all,work,free)=0.1968 0.1925 0.2868 n_refl.: 9255 ======================== 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 25.215-13.182 84.48 95 3 0.1890 514.743 502.776 1.322 1.049 0.370 13.182-10.771 91.67 92 7 0.1459 520.206 503.860 1.250 1.051 0.364 10.742-8.763 94.15 183 10 0.1225 461.642 446.262 1.131 1.043 0.352 8.709-7.139 97.85 350 14 0.1369 404.812 397.157 1.127 1.038 0.350 7.120-5.819 98.85 652 33 0.2001 281.767 267.158 1.009 1.023 0.341 5.810-4.742 98.41 1191 49 0.1642 341.041 328.512 0.985 1.003 0.305 4.737-3.861 98.48 2221 114 0.1790 306.591 295.539 1.034 0.972 0.183 3.860-3.143 97.34 4027 214 0.2424 176.962 166.692 1.095 0.925 0.045 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0610 b_overall=2.4448 ============================ 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 = 1.006266 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.056672 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 0.2315 0.3029 0.0714 0.013 2.1 0.6 1.6 12.1 0 0.050 0.2079 0.2960 0.0881 0.015 2.4 1.9 1.8 15.0 1 0.151 0.1930 0.2917 0.0987 0.019 2.9 4.7 2.4 16.4 3 0.302 0.1837 0.2954 0.1117 0.023 3.5 7.0 3.6 20.0 7 0.453 0.1918 0.2869 0.0951 0.024 3.5 6.7 1.8 17.0 7 0.604 0.1925 0.2868 0.0943 0.024 3.5 6.7 1.8 17.0 7 0.755 0.1925 0.2868 0.0943 0.024 3.5 6.7 1.8 17.0 7 0.906 0.1917 0.2870 0.0953 0.025 3.5 6.6 1.8 17.0 8 1.057 0.1828 0.2900 0.1072 0.024 3.6 7.5 3.4 18.8 8 0.503 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1925 0.2868 0.0943 0.024 3.5 6.7 1.8 17.0 7 0.755 0.1925 0.2868 0.0943 0.024 3.5 6.7 1.8 17.0 7 0.906 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 19.25 28.68 9.43 9.556 64.150 0.057 5.560 20.88 30.66 9.78 8.623 69.925 0.002 5.601 18.66 28.69 10.03 9.668 64.054 0.007 5.544 18.12 28.54 10.42 10.126 63.834 0.028 5.527 17.02 28.35 11.33 11.153 64.376 0.057 5.495 16.82 28.37 11.55 11.578 64.657 0.085 5.490 16.70 28.41 11.71 11.953 64.861 0.113 5.487 16.62 28.45 11.82 12.272 65.020 0.142 5.486 16.57 28.49 11.92 12.541 65.140 0.170 5.485 16.53 28.50 11.97 12.772 65.240 0.198 5.485 16.50 28.52 12.02 12.968 65.322 0.227 5.484 16.47 28.53 12.06 13.138 65.391 0.255 5.483 16.45 28.56 12.10 13.284 65.450 0.283 5.484 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.002 Accepted refinement result: 20.88 30.66 9.78 8.623 69.925 0.002 5.601 Individual atomic B min max mean iso aniso Overall: 46.34 137.37 69.95 2.65 3928 0 Protein: 46.34 137.37 69.95 2.65 3928 0 Chain A: 46.36 137.37 70.01 N/A 1964 0 Chain B: 46.34 136.08 69.88 N/A 1964 0 Histogram: Values Number of atoms 46.34 - 55.44 99 55.44 - 64.55 1304 64.55 - 73.65 1528 73.65 - 82.75 558 82.75 - 91.86 248 91.86 - 100.96 71 100.96 - 110.06 39 110.06 - 119.17 21 119.17 - 128.27 28 128.27 - 137.37 32 =========================== Idealize ADP of riding H ========================== r_work=0.2088 r_free=0.3066 r_work=0.2092 r_free=0.3052 ----------X-ray data---------- |--(resolution: 3.14 - 25.21 A, n_refl.=9255 (all), 4.80 % free)-------------| | | | r_work= 0.2092 r_free= 0.3052 coordinate error (max.-lik. estimate): 0.32 A | | | | normalized target function (ml) (work): 5.602879 | | target function (ml) not normalized (work): 49366.967832 | | target function (ml) not normalized (free): 2569.529247 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 25.21 - 4.53 0.98 2958 131 0.1762 0.2545 5.8088 5.9924| | 2: 4.52 - 3.60 0.98 2955 140 0.2185 0.3018 5.6467 5.9016| | 3: 3.60 - 3.14 0.97 2898 173 0.2699 0.3907 5.348 5.5393| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 25.21 - 4.53 2958 131 0.84 23.38 0.96 1.04 24422.23| | 2: 4.52 - 3.60 2955 140 0.80 27.72 1.06 1.10 17780.79| | 3: 3.60 - 3.14 2898 173 0.70 36.27 1.12 1.13 11435.33| |alpha: min = 1.04 max = 1.13 mean = 1.09| |beta: min = 11435.33 max = 24422.23 mean = 17923.36| |figures of merit: min = 0.00 max = 1.00 mean = 0.78| |phase err.(work): min = 0.00 max = 89.66 mean = 29.08| |phase err.(test): min = 5.97 max = 85.22 mean = 30.98| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.2136 0.2092 0.3052 n_refl.: 9255 re-set all scales: r(all,work,free)=0.3822 0.3781 0.4606 n_refl.: 9255 remove outliers: r(all,work,free)=0.3822 0.3781 0.4606 n_refl.: 9255 overall B=-13.09 to atoms: r(all,work,free)=0.3327 0.3283 0.4176 n_refl.: 9255 bulk-solvent and scaling: r(all,work,free)=0.2053 0.2008 0.2992 n_refl.: 9255 remove outliers: r(all,work,free)=0.2053 0.2008 0.2992 n_refl.: 9255 ======================== 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 25.215-13.182 84.48 95 3 0.1877 439.566 428.871 1.364 1.021 0.374 13.182-10.771 92.52 92 7 0.1437 444.230 428.293 1.275 1.026 0.364 10.742-8.763 94.15 183 10 0.1189 394.220 382.104 1.166 1.020 0.363 8.709-7.139 97.85 350 14 0.1351 345.690 339.665 1.156 1.019 0.369 7.120-5.819 98.85 652 33 0.1994 240.615 229.016 1.034 1.011 0.369 5.810-4.742 98.41 1191 49 0.1751 291.232 280.608 0.981 1.000 0.316 4.737-3.861 98.48 2221 114 0.1902 261.814 252.117 1.005 0.983 0.192 3.860-3.143 97.34 4027 214 0.2538 151.117 141.887 1.043 0.956 0.035 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0610 b_overall=3.2221 ================= 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 : 0.3126 0.3547 0.007 1.399 2.0 149.5 50.7 0 0.000 1_bss: 0.2325 0.2781 0.007 1.399 7.7 155.2 56.4 0 0.000 1_settarget: 0.2325 0.2781 0.007 1.399 7.7 155.2 56.4 0 0.000 1_weight: 0.2325 0.2781 0.007 1.399 7.7 155.2 56.4 0 0.000 1_xyzrec: 0.1716 0.2725 0.019 2.849 7.7 155.2 56.4 0 0.450 1_adp: 0.1746 0.2818 0.019 2.849 22.2 152.8 57.6 0 0.450 1_regHadp: 0.1762 0.2809 0.019 2.849 22.2 152.8 57.6 0 0.450 2_bss: 0.1749 0.2819 0.019 2.849 22.2 152.8 57.6 0 0.450 2_settarget: 0.1749 0.2819 0.019 2.849 22.2 152.8 57.6 0 0.450 2_updatecdl: 0.1749 0.2819 0.019 2.858 22.2 152.8 57.6 0 0.450 2_weight: 0.1749 0.2819 0.019 2.858 22.2 152.8 57.6 0 0.450 2_xyzrec: 0.1652 0.2786 0.024 3.503 22.2 152.8 57.6 0 0.478 2_adp: 0.1938 0.2943 0.024 3.503 37.8 147.8 63.8 0 0.478 2_regHadp: 0.1963 0.2928 0.024 3.503 37.8 147.8 63.8 0 0.478 3_bss: 0.1925 0.2868 0.024 3.503 32.4 142.4 58.4 0 0.478 3_settarget: 0.1925 0.2868 0.024 3.503 32.4 142.4 58.4 0 0.478 3_updatecdl: 0.1925 0.2868 0.024 3.502 32.4 142.4 58.4 0 0.478 3_setrh: 0.1925 0.2868 0.024 3.502 32.4 142.4 58.4 0 0.478 3_weight: 0.1925 0.2868 0.024 3.502 32.4 142.4 58.4 0 0.478 3_xyzrec: 0.1925 0.2868 0.024 3.502 32.4 142.4 58.4 0 0.478 3_adp: 0.2088 0.3066 0.024 3.502 46.3 137.4 69.9 0 0.478 3_regHadp: 0.2092 0.3052 0.024 3.502 46.3 137.4 69.9 0 0.478 end: 0.2008 0.2992 0.024 3.502 33.3 124.3 56.9 0 0.478 ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/cci-filer3/home/nigel/work/ANI/result/xray/pairs/4phenix_1w60_refine_001.cif Writing default parameters for subsequent refinement: /net/cci-filer3/home/nigel/work/ANI/result/xray/pairs/4phenix_1w60_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 4.9500 Refinement macro-cycles (run) : 176.2800 Write final files (write_after_run_outputs) : 12.3000 Total : 193.5300 Total CPU time: 3.69 minutes =========================== phenix.refine: finished =========================== # Date 2024-08-09 Time 09:38:19 PDT -0700 (1723221499.31 s) Start R-work = 0.2325, R-free = 0.2781 Final R-work = 0.2008, R-free = 0.2992 =============================================================================== Job complete usr+sys time: 230.08 seconds wall clock time: 6 minutes 51.12 seconds (411.12 seconds total)