Starting phenix.refine on Mon May 20 17:15:26 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/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 strategy=individual_sites+individual_adp+individual_sites_real_space ramachandran_plot_restraints.enabled=True secondary_structure.enabled=True main.nqh_flips=True 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 = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/1w60.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/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 { max_number_of_iterations = 100 nproc = 20 } modify_start_model { modify { selection = element H occupancies { set = 1 } } } pdb_interpretation { secondary_structure { enabled = True } ramachandran_plot_restraints { enabled = True } nonbonded_weight = 100 } target_weights { optimize_xyz_weight = true optimize_adp_weight = true } } Starting job =============================================================================== Symmetric amino acids flipped None Time to flip residues: 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/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: 1.35, per 1000 atoms: 0.17 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: 1.85 Conformation dependent library (CDL) restraints added in 250.2 milliseconds 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. 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: 0.55 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: 1.70 Time building geometry restraints manager: 2.14 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=" N SER A 112 " pdb=" H SER A 112 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.46e+01 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 ... (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: 2837 126.92 - 134.18: 20 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 - 17.84: 3107 17.84 - 35.68: 335 35.68 - 53.52: 181 53.52 - 71.37: 70 71.37 - 89.21: 19 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 HIS A 246 " 0.034 2.00e-02 2.50e+03 1.68e-02 6.34e+00 pdb=" CG HIS A 246 " -0.015 2.00e-02 2.50e+03 pdb=" ND1 HIS A 246 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 HIS A 246 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 HIS A 246 " 0.006 2.00e-02 2.50e+03 pdb=" NE2 HIS A 246 " 0.009 2.00e-02 2.50e+03 pdb=" HD1 HIS A 246 " -0.021 2.00e-02 2.50e+03 pdb=" HD2 HIS A 246 " -0.012 2.00e-02 2.50e+03 pdb=" HE1 HIS A 246 " 0.017 2.00e-02 2.50e+03 ... (remaining 1183 not shown) Histogram of nonbonded interaction distances: 0.94 - 1.67: 57 1.67 - 2.40: 2974 2.40 - 3.13: 23916 3.13 - 3.87: 33489 3.87 - 4.60: 51667 Warning: very small nonbonded interaction distances. Nonbonded interactions: 112103 Sorted by model distance: nonbonded pdb=" O LEU B 182 " pdb=" HG SER B 183 " model vdw 0.936 1.850 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="HG13 VAL B 195 " pdb=" H THR B 196 " model vdw 1.203 2.270 nonbonded pdb=" HG2 PRO B 140 " pdb=" HG3 GLU B 193 " model vdw 1.204 2.440 ... (remaining 112098 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. ============================== 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 { 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 } ramachandran_plot_restraints { enabled = True } nonbonded_weight = 100 } target_weights { optimize_xyz_weight = True optimize_adp_weight = True } } output { prefix = "1w60_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Total: count: 3946 occupancy sum: 3946.00 (% of total atoms 50.11) Rotatable: count: 1214 occupancy sum: 1214.00 (% of total atoms 15.42) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 3.14 - 25.21 A, n_refl.=9258 (all), 4.80 % free)-------------| | | | r_work= 0.3127 r_free= 0.3555 coordinate error (max.-lik. estimate): 0.43 A | | | | normalized target function (ml) (work): 6.213664 | | target function (ml) not normalized (work): 54767.234476 | | target function (ml) not normalized (free): 2756.138780 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3221 0.3675 6.7019 6.6358| | 2: 4.52 - 3.60 0.98 2955 140 0.3038 0.3318 6.2193 6.2826| | 3: 3.60 - 3.14 0.97 2898 173 0.3059 0.3697 5.709 5.8225| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 40.73 0.91 0.65 115062.26| | 2: 4.52 - 3.60 2955 140 0.68 38.46 1.23 0.87 57473.34| | 3: 3.60 - 3.14 2898 173 0.73 34.32 1.19 0.95 19014.54| |alpha: min = 0.65 max = 0.95 mean = 0.83| |beta: min = 19014.54 max = 115062.26 mean = 64174.86| |figures of merit: min = 0.00 max = 0.99 mean = 0.68| |phase err.(work): min = 0.00 max = 89.90 mean = 37.86| |phase err.(test): min = 0.00 max = 88.83 mean = 37.54| |-----------------------------------------------------------------------------| ----------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 : 15.37 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= 0.3127 r_free= 0.3555 coordinate error (max.-lik. estimate): 0.43 A | | | | normalized target function (ml) (work): 6.213664 | | target function (ml) not normalized (work): 54767.234476 | | target function (ml) not normalized (free): 2756.138780 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.3149 0.3127 0.3555 n_refl.: 9258 re-set all scales: r(all,work,free)=0.3149 0.3127 0.3555 n_refl.: 9258 remove outliers: r(all,work,free)=0.3148 0.3126 0.3555 n_refl.: 9255 overall B=5.77 to atoms: r(all,work,free)=0.3305 0.3283 0.3719 n_refl.: 9255 bulk-solvent and scaling: r(all,work,free)=0.2347 0.2324 0.2782 n_refl.: 9255 remove outliers: r(all,work,free)=0.2347 0.2324 0.2782 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 0.2240 720.927 692.011 1.575 1.004 0.382 13.182-10.771 92.52 92 7 0.2328 728.577 659.686 1.354 1.009 0.372 10.742-8.763 94.15 183 10 0.1786 646.556 624.296 1.235 1.006 0.367 8.709-7.139 97.85 350 14 0.1955 566.962 549.169 1.218 1.006 0.361 7.120-5.819 98.85 652 33 0.2417 394.630 369.156 1.076 1.002 0.357 5.810-4.742 98.41 1191 49 0.2078 477.646 452.627 0.970 0.997 0.284 4.737-3.861 98.48 2221 114 0.2121 429.398 408.632 1.018 0.988 0.203 3.860-3.143 97.34 4027 214 0.2781 247.845 230.388 1.027 0.974 0.071 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.1000 b_overall=4.8102 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update phi&psi targets =========================== 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ================================== NQH flips ================================== r_work=0.2324 r_free=0.2782 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.2324 r_free=0.2782 ========================= Local real-space refinement ========================= Before: r_work=0.2324 r_free=0.2782 227 residues out of total 446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 121 time to evaluate : 0.329 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 106 outliers final: 51 residues processed: 106 average time/residue: 0.2705 time to fit residues: 35.2345 After: r_work=0.2382 r_free=0.2897 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 15.343131 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.208013 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 0.2327 0.2822 0.0495 0.003 0.6 4.7 1.8 11.0 0 0.125 0.2302 0.2815 0.0512 0.004 0.7 4.7 1.8 11.0 0 0.250 0.2262 0.2792 0.0530 0.004 0.7 4.7 1.8 10.8 0 0.500 0.2204 0.2791 0.0587 0.005 0.8 5.6 1.8 11.2 0 1.000 0.2043 0.2765 0.0722 0.005 0.8 7.6 1.8 11.7 0 2.000 0.1988 0.2758 0.0770 0.007 0.9 8.1 1.8 12.8 0 3.000 0.1949 0.2755 0.0806 0.008 0.9 8.9 2.0 13.0 0 4.000 0.1914 0.2760 0.0846 0.009 1.0 9.8 2.0 13.0 0 5.000 0.1890 0.2766 0.0876 0.010 1.1 10.7 2.2 13.7 0 6.000 0.1867 0.2788 0.0921 0.011 1.2 12.7 2.0 15.5 0 7.000 0.1848 0.2802 0.0954 0.012 1.2 13.6 2.0 15.9 0 8.000 0.1830 0.2797 0.0967 0.013 1.3 14.1 2.2 15.9 0 9.000 0.1816 0.2797 0.0981 0.014 1.4 14.4 2.2 17.5 0 10.000 0.1855 0.2789 0.0934 0.012 1.2 12.8 2.0 15.9 0 7.672 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2262 0.2792 0.0530 0.004 0.7 4.7 1.8 10.8 0 0.500 ===================== Post-minimization rotamer correction ==================== Before: r_work=0.2262 r_free=0.2792 171 residues out of total 446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 123 time to evaluate : 1.238 revert: symmetry clash outliers start: 48 outliers final: 1 residues processed: 48 average time/residue: 0.4556 time to fit residues: 31.7036 After: r_work=0.2319 r_free=0.2762 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 23.19 27.62 4.43 6.626 55.231 0.208 0.063 24.07 28.20 4.13 6.196 55.928 0.006 0.067 23.79 28.22 4.43 6.137 55.890 0.026 0.066 22.89 28.25 5.36 6.454 55.856 0.104 0.061 22.11 28.28 6.17 7.385 55.945 0.208 0.057 21.63 28.28 6.66 8.367 56.118 0.312 0.055 21.30 28.27 6.97 9.265 56.324 0.416 0.053 21.03 28.28 7.25 10.237 56.602 0.520 0.052 20.86 28.30 7.44 10.882 56.749 0.624 0.051 20.74 28.35 7.61 11.417 56.871 0.728 0.051 20.57 28.41 7.84 12.279 57.150 0.832 0.050 20.47 28.44 7.97 12.807 57.289 0.936 0.050 20.40 28.47 8.07 13.199 57.379 1.040 0.049 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.006 Accepted refinement result: 24.07 28.20 4.13 6.196 55.928 0.006 0.067 Individual atomic B min max mean iso aniso Overall: 24.64 153.21 57.83 5.36 3928 0 Protein: 24.64 153.21 57.83 5.36 3928 0 Chain A: 24.64 153.21 57.83 N/A 1964 0 Chain B: 24.67 151.85 57.84 N/A 1964 0 Histogram: Values Number of atoms 24.64 - 37.50 353 37.50 - 50.36 1389 50.36 - 63.21 1060 63.21 - 76.07 499 76.07 - 88.93 300 88.93 - 101.78 191 101.78 - 114.64 49 114.64 - 127.50 30 127.50 - 140.35 21 140.35 - 153.21 36 =========================== Idealize ADP of riding H ========================== r_work=0.2407 r_free=0.2820 r_work=0.2411 r_free=0.2805 *********************** REFINEMENT MACRO_CYCLE 2 OF 3 ************************* |--(resolution: 3.14 - 25.21 A, n_refl.=9255 (all), 4.80 % free)-------------| | | | r_work= 0.2411 r_free= 0.2805 coordinate error (max.-lik. estimate): 0.45 A | | | | normalized target function (ls_wunit_k1) (work): 0.067676 | | target function (ls_wunit_k1) not normalized (work): 596.291483 | | target function (ls_wunit_k1) not normalized (free): 43.216086 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2430 0.2411 0.2805 n_refl.: 9255 re-set all scales: r(all,work,free)=0.3413 0.3390 0.3851 n_refl.: 9255 remove outliers: r(all,work,free)=0.3413 0.3390 0.3851 n_refl.: 9255 overall B=0.00 to atoms: r(all,work,free)=0.3413 0.3390 0.3851 n_refl.: 9255 bulk-solvent and scaling: r(all,work,free)=0.2429 0.2409 0.2818 n_refl.: 9255 remove outliers: r(all,work,free)=0.2429 0.2409 0.2818 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 0.2024 536.469 521.676 1.512 1.013 0.380 13.182-10.771 91.67 92 7 0.2286 542.162 499.640 1.319 1.017 0.373 10.742-8.763 94.15 183 10 0.1940 481.127 457.244 1.174 1.014 0.361 8.709-7.139 97.85 350 14 0.1918 421.898 408.118 1.161 1.012 0.357 7.120-5.819 98.85 652 33 0.2435 293.660 276.743 1.018 1.005 0.350 5.810-4.742 98.41 1191 49 0.2003 355.435 338.660 0.953 0.997 0.300 4.737-3.861 98.48 2221 114 0.2226 319.532 304.024 1.000 0.983 0.190 3.860-3.143 97.34 4027 214 0.3001 184.431 169.920 1.020 0.961 0.050 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0577 b_overall=3.8535 ============================ Set refinement target ============================ using refinement target ml ============================ Update phi&psi targets =========================== 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.2409 r_free=0.2818 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 71 ASN B 108 GLN Total number of N/Q/H flips: 2 r_work=0.2408 r_free=0.2820 ========================= Local real-space refinement ========================= Before: r_work=0.2408 r_free=0.2820 125 residues out of total 446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 124 time to evaluate : 1.863 outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.4677 time to fit residues: 2.8438 After: r_work=0.2409 r_free=0.2823 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 3.193629 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.053358 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 0.2278 0.2750 0.0472 0.003 0.6 5.5 1.2 1.1 0 0.125 0.2174 0.2737 0.0563 0.004 0.6 7.4 1.4 2.0 0 0.250 0.2090 0.2750 0.0660 0.006 0.8 9.1 1.4 3.4 0 0.500 0.2000 0.2818 0.0817 0.010 1.0 10.7 1.4 7.0 0 1.000 0.1906 0.2867 0.0961 0.016 1.4 15.2 1.6 14.3 0 2.000 0.1850 0.2857 0.1006 0.021 1.8 17.9 2.0 17.5 0 3.000 0.1809 0.2842 0.1033 0.026 2.0 20.2 2.4 18.8 0 4.000 0.1779 0.2827 0.1049 0.030 2.3 22.7 2.6 21.1 0 5.000 0.1752 0.2833 0.1082 0.034 2.6 25.4 3.0 23.1 0 6.000 0.1729 0.2834 0.1105 0.038 2.8 27.8 3.2 23.3 0 7.000 0.1711 0.2844 0.1133 0.041 3.0 27.9 3.8 23.1 0 8.000 0.1692 0.2870 0.1178 0.045 3.2 30.7 4.2 25.8 0 9.000 0.1678 0.2867 0.1189 0.048 3.3 31.6 4.2 25.3 1 10.000 0.1937 0.2860 0.0923 0.014 1.3 13.2 1.6 12.3 0 1.597 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2278 0.2750 0.0472 0.003 0.6 5.5 1.2 1.1 0 0.125 ===================== Post-minimization rotamer correction ==================== Before: r_work=0.2278 r_free=0.2750 125 residues out of total 446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 120 time to evaluate : 1.313 outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2759 time to fit residues: 3.8764 After: r_work=0.2281 r_free=0.2757 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 22.81 27.57 4.76 9.213 62.728 0.053 5.687 24.42 28.82 4.40 9.356 65.926 0.002 5.734 22.96 28.63 5.67 9.421 64.294 0.007 5.694 22.10 27.72 5.62 9.574 62.458 0.027 5.664 21.08 27.64 6.56 11.032 62.763 0.053 5.632 20.82 27.54 6.72 11.631 63.067 0.080 5.624 20.67 27.51 6.84 12.112 63.290 0.107 5.620 20.53 27.51 6.98 12.657 63.530 0.133 5.616 20.43 27.49 7.07 13.146 63.731 0.160 5.613 20.35 27.48 7.13 13.575 63.896 0.187 5.611 20.29 27.50 7.21 13.948 64.036 0.213 5.610 20.25 27.51 7.26 14.280 64.155 0.240 5.608 20.21 27.53 7.32 14.577 64.261 0.267 5.608 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.027 Accepted refinement result: 22.10 27.72 5.62 9.574 62.458 0.027 5.664 Individual atomic B min max mean iso aniso Overall: 25.22 153.07 57.29 5.45 3928 0 Protein: 25.22 153.07 57.29 5.45 3928 0 Chain A: 25.71 153.07 57.27 N/A 1964 0 Chain B: 25.22 151.17 57.32 N/A 1964 0 Histogram: Values Number of atoms 25.22 - 38.01 482 38.01 - 50.79 1346 50.79 - 63.58 988 63.58 - 76.36 504 76.36 - 89.15 304 89.15 - 101.93 179 101.93 - 114.72 44 114.72 - 127.50 23 127.50 - 140.29 27 140.29 - 153.07 31 =========================== Idealize ADP of riding H ========================== r_work=0.2210 r_free=0.2772 r_work=0.2205 r_free=0.2775 *********************** REFINEMENT MACRO_CYCLE 3 OF 3 ************************* |--(resolution: 3.14 - 25.21 A, n_refl.=9255 (all), 4.80 % free)-------------| | | | r_work= 0.2205 r_free= 0.2775 coordinate error (max.-lik. estimate): 0.47 A | | | | normalized target function (ml) (work): 5.662379 | | target function (ml) not normalized (work): 49891.217112 | | target function (ml) not normalized (free): 2566.581017 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2231 0.2205 0.2775 n_refl.: 9255 re-set all scales: r(all,work,free)=0.3295 0.3268 0.3815 n_refl.: 9255 remove outliers: r(all,work,free)=0.3295 0.3268 0.3815 n_refl.: 9255 overall B=0.00 to atoms: r(all,work,free)=0.3295 0.3268 0.3815 n_refl.: 9255 bulk-solvent and scaling: r(all,work,free)=0.2229 0.2203 0.2763 n_refl.: 9255 remove outliers: r(all,work,free)=0.2229 0.2203 0.2763 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 0.2163 536.469 511.577 1.527 1.021 0.384 13.182-10.771 91.67 92 7 0.1980 542.162 508.985 1.349 1.021 0.376 10.742-8.763 94.15 183 10 0.1646 481.127 462.178 1.201 1.017 0.370 8.709-7.139 97.85 350 14 0.1768 421.898 409.144 1.201 1.015 0.367 7.120-5.819 98.85 652 33 0.2219 293.660 278.894 1.062 1.008 0.360 5.810-4.742 98.41 1191 49 0.1902 355.435 338.408 0.982 0.999 0.310 4.737-3.861 98.48 2221 114 0.2041 319.532 305.258 1.016 0.984 0.200 3.860-3.143 97.34 4027 214 0.2699 184.431 171.882 1.033 0.962 0.050 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.1000 b_overall=5.0654 ============================ Set refinement target ============================ using refinement target ml ============================ Update phi&psi targets =========================== 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.2203 r_free=0.2763 After: r_work=0.2203 r_free=0.2763 ================================== NQH flips ================================== r_work=0.2203 r_free=0.2763 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 ASN B 108 GLN Total number of N/Q/H flips: 2 r_work=0.2203 r_free=0.2764 ========================= Local real-space refinement ========================= Before: r_work=0.2203 r_free=0.2764 121 residues out of total 446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 0.838 outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8632 After: r_work=0.2203 r_free=0.2764 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 3.488685 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.054568 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 0.2198 0.2763 0.0565 0.003 0.6 5.8 1.2 0.2 0 0.125 0.2188 0.2768 0.0580 0.003 0.6 6.0 1.2 0.2 0 0.250 0.2136 0.2773 0.0638 0.007 0.7 7.0 1.2 0.4 0 0.500 0.1993 0.2763 0.0771 0.013 1.4 11.6 1.4 0.9 0 1.000 0.1914 0.2783 0.0868 0.018 1.8 21.8 1.4 7.2 0 2.000 0.1873 0.2788 0.0915 0.021 2.1 23.5 1.6 7.0 0 3.000 0.1830 0.2799 0.0969 0.025 2.7 26.9 1.8 9.2 0 4.000 0.1802 0.2806 0.1004 0.030 2.9 33.1 2.8 15.5 0 5.000 0.1781 0.2770 0.0989 0.033 2.9 30.4 2.2 13.7 0 6.000 0.1751 0.2811 0.1060 0.038 3.3 35.1 3.0 16.6 0 7.000 0.1720 0.2818 0.1098 0.045 3.8 38.2 3.2 18.2 1 8.000 0.1724 0.2802 0.1078 0.043 3.8 34.0 3.2 14.6 0 9.000 0.1693 0.2832 0.1139 0.050 4.1 40.0 3.6 19.7 2 10.000 0.1929 0.2774 0.0844 0.015 1.7 19.1 1.4 4.9 0 1.744 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2198 0.2763 0.0565 0.003 0.6 5.8 1.2 0.2 0 0.125 ===================== Post-minimization rotamer correction ==================== Before: r_work=0.2198 r_free=0.2763 121 residues out of total 446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 120 time to evaluate : 0.811 outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1749 time to fit residues: 0.9969 After: r_work=0.2199 r_free=0.2767 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 21.99 27.67 5.68 9.197 62.222 0.055 5.661 24.47 28.70 4.23 8.873 65.298 0.002 5.738 23.29 28.43 5.14 9.388 63.523 0.007 5.705 21.99 27.67 5.68 9.197 62.222 0.027 5.661 21.52 27.78 6.26 9.719 61.944 0.055 5.647 20.48 27.68 7.20 11.726 62.184 0.082 5.617 20.34 27.63 7.29 12.096 62.396 0.109 5.613 20.19 27.62 7.43 12.609 62.657 0.136 5.609 20.14 27.62 7.48 12.852 62.777 0.164 5.607 20.07 27.63 7.55 13.190 62.933 0.191 5.605 20.02 27.64 7.62 13.490 63.064 0.218 5.604 19.98 27.65 7.67 13.755 63.175 0.246 5.603 19.94 27.66 7.71 13.991 63.272 0.273 5.602 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.027 Accepted refinement result: 21.99 27.67 5.68 9.197 62.222 0.027 5.661 Individual atomic B min max mean iso aniso Overall: 25.22 153.07 57.29 5.45 3928 0 Protein: 25.22 153.07 57.29 5.45 3928 0 Chain A: 25.71 153.07 57.27 N/A 1964 0 Chain B: 25.22 151.17 57.32 N/A 1964 0 Histogram: Values Number of atoms 25.22 - 38.01 482 38.01 - 50.79 1346 50.79 - 63.58 988 63.58 - 76.36 504 76.36 - 89.15 304 89.15 - 101.93 179 101.93 - 114.72 44 114.72 - 127.50 23 127.50 - 140.29 27 140.29 - 153.07 31 =========================== Idealize ADP of riding H ========================== r_work=0.2199 r_free=0.2767 r_work=0.2199 r_free=0.2767 ----------X-ray data---------- |--(resolution: 3.14 - 25.21 A, n_refl.=9255 (all), 4.80 % free)-------------| | | | r_work= 0.2199 r_free= 0.2767 coordinate error (max.-lik. estimate): 0.47 A | | | | normalized target function (ml) (work): 5.661197 | | target function (ml) not normalized (work): 49880.807559 | | target function (ml) not normalized (free): 2566.414666 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1895 0.2503 5.8904 6.0064| | 2: 4.52 - 3.60 0.98 2955 140 0.2310 0.2651 5.7165 5.8782| | 3: 3.60 - 3.14 0.97 2898 173 0.2717 0.3350 5.3709 5.5296| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 0.85 23.07 1.00 0.93 25623.00| | 2: 4.52 - 3.60 2955 140 0.82 26.27 1.02 0.91 16843.78| | 3: 3.60 - 3.14 2898 173 0.77 30.92 0.97 0.87 9130.73| |alpha: min = 0.87 max = 0.93 mean = 0.90| |beta: min = 9130.73 max = 25623.00 mean = 17254.24| |figures of merit: min = 0.01 max = 1.00 mean = 0.81| |phase err.(work): min = 0.00 max = 89.37 mean = 26.72| |phase err.(test): min = 0.00 max = 89.01 mean = 27.76| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.2225 0.2199 0.2766 n_refl.: 9255 re-set all scales: r(all,work,free)=0.3296 0.3270 0.3815 n_refl.: 9255 remove outliers: r(all,work,free)=0.3296 0.3270 0.3815 n_refl.: 9255 overall B=0.00 to atoms: r(all,work,free)=0.3296 0.3270 0.3815 n_refl.: 9255 bulk-solvent and scaling: r(all,work,free)=0.2223 0.2196 0.2764 n_refl.: 9255 remove outliers: r(all,work,free)=0.2223 0.2196 0.2764 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 0.2154 536.469 512.283 1.506 1.034 0.384 13.182-10.771 91.67 92 7 0.1955 542.162 508.676 1.331 1.033 0.376 10.742-8.763 94.15 183 10 0.1619 481.127 461.898 1.183 1.028 0.370 8.709-7.139 97.85 350 14 0.1763 421.898 408.988 1.188 1.024 0.367 7.120-5.819 98.85 652 33 0.2223 293.660 278.761 1.055 1.014 0.360 5.810-4.742 98.41 1191 49 0.1891 355.435 338.664 0.978 1.001 0.310 4.737-3.861 98.48 2221 114 0.2037 319.532 305.245 1.018 0.980 0.200 3.860-3.143 97.34 4027 214 0.2693 184.431 171.946 1.045 0.949 0.050 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.1000 b_overall=5.1817 ================= 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 : 0.3127 0.3555 0.007 1.399 2.0 149.5 50.7 0 0.000 1_bss: 0.2324 0.2782 0.007 1.399 7.8 155.3 56.4 0 0.000 1_settarget: 0.2324 0.2782 0.007 1.399 7.8 155.3 56.4 0 0.000 1_updatephipsi: 0.2324 0.2782 0.007 1.399 7.8 155.3 56.4 0 0.000 1_nqh: 0.2324 0.2782 0.007 1.399 7.8 155.3 56.4 0 0.000 1_realsrl: 0.2382 0.2897 0.007 1.399 7.8 155.3 56.4 0 0.084 1_weight: 0.2382 0.2897 0.007 1.399 7.8 155.3 56.4 0 0.084 1_xyzrec: 0.2262 0.2792 0.004 0.687 7.8 155.3 56.4 0 0.215 1_realsrl2: 0.2319 0.2762 0.004 0.687 7.8 155.3 56.4 0 0.251 1_adp: 0.2407 0.2820 0.004 0.687 24.6 153.2 57.8 0 0.251 1_regHadp: 0.2411 0.2805 0.004 0.687 24.6 153.2 57.8 0 0.251 2_bss: 0.2409 0.2818 0.004 0.687 24.6 153.2 57.8 0 0.251 2_settarget: 0.2409 0.2818 0.004 0.687 24.6 153.2 57.8 0 0.251 2_updatephipsi: 0.2409 0.2818 0.004 0.687 24.6 153.2 57.8 0 0.251 2_updatecdl: 0.2409 0.2818 0.004 0.730 24.6 153.2 57.8 0 0.251 2_nqh: 0.2408 0.2820 0.004 0.730 24.6 153.2 57.8 0 0.253 2_realsrl: 0.2409 0.2823 0.004 0.730 24.6 153.2 57.8 0 0.254 2_weight: 0.2409 0.2823 0.004 0.730 24.6 153.2 57.8 0 0.254 2_xyzrec: 0.2278 0.2750 0.003 0.571 24.6 153.2 57.8 0 0.321 2_realsrl2: 0.2281 0.2757 0.003 0.571 24.6 153.2 57.8 0 0.323 2_adp: 0.2210 0.2772 0.003 0.571 25.2 153.1 57.3 0 0.323 2_regHadp: 0.2205 0.2775 0.003 0.571 25.2 153.1 57.3 0 0.323 3_bss: 0.2203 0.2763 0.003 0.571 25.2 153.1 57.3 0 0.323 3_settarget: 0.2203 0.2763 0.003 0.571 25.2 153.1 57.3 0 0.323 3_updatephipsi: 0.2203 0.2763 0.003 0.571 25.2 153.1 57.3 0 0.323 3_updatecdl: 0.2203 0.2763 0.003 0.592 25.2 153.1 57.3 0 0.323 3_setrh: 0.2203 0.2763 0.003 0.592 25.2 153.1 57.3 0 0.323 3_nqh: 0.2203 0.2764 0.003 0.592 25.2 153.1 57.3 0 0.323 3_realsrl: 0.2203 0.2764 0.003 0.592 25.2 153.1 57.3 0 0.323 3_weight: 0.2203 0.2764 0.003 0.592 25.2 153.1 57.3 0 0.323 3_xyzrec: 0.2198 0.2763 0.003 0.579 25.2 153.1 57.3 0 0.324 3_realsrl2: 0.2199 0.2767 0.003 0.579 25.2 153.1 57.3 0 0.324 3_adp: 0.2199 0.2767 0.003 0.579 25.2 153.1 57.3 0 0.324 3_regHadp: 0.2199 0.2767 0.003 0.579 25.2 153.1 57.3 0 0.324 end: 0.2196 0.2764 0.003 0.579 25.2 153.1 57.3 0 0.324 ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V0/1w60_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V0/1w60_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 5.9400 Refinement macro-cycles (run) : 380.8900 Write final files (write_after_run_outputs) : 22.5300 Total : 409.3600 Total CPU time: 7.26 minutes =========================== phenix.refine: finished =========================== # Date 2024-05-20 Time 17:34:45 PDT -0700 (1716251685.38 s) Start R-work = 0.2324, R-free = 0.2782 Final R-work = 0.2196, R-free = 0.2764 =============================================================================== Job complete usr+sys time: 457.91 seconds wall clock time: 19 minutes 42.83 seconds (1182.83 seconds total)