Starting phenix.refine on Mon May 20 17:17:37 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 ramachandran_plot_restraints.enabled=False secondary_structure.enabled=True main.nqh_flips=False 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 { 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 } } Starting job =============================================================================== Symmetric amino acids flipped None Time to flip residues: 0.01s 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: 2.69, per 1000 atoms: 0.34 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: 5.73 Conformation dependent library (CDL) restraints added in 968.8 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: 2.12 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: 6.28 Time building geometry restraints manager: 3.88 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 { 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 } } 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 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 15.536715 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.207977 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 0.2324 0.2782 0.0458 0.003 0.6 2.7 2.0 15.2 0 0.125 0.2273 0.2755 0.0482 0.003 0.5 2.4 2.0 15.0 0 0.250 0.2196 0.2718 0.0522 0.003 0.6 2.3 2.2 14.8 0 0.500 0.2092 0.2718 0.0626 0.004 0.6 3.3 2.8 15.0 0 1.000 0.1991 0.2726 0.0735 0.005 0.7 4.8 3.0 16.1 0 2.000 0.1932 0.2739 0.0807 0.006 0.8 6.5 2.8 17.7 0 3.000 0.1894 0.2747 0.0853 0.008 0.9 6.9 2.8 19.1 0 4.000 0.1861 0.2730 0.0869 0.009 1.0 8.9 3.2 19.5 0 5.000 0.1844 0.2703 0.0859 0.010 1.1 9.9 3.2 20.2 0 6.000 0.1821 0.2727 0.0907 0.011 1.2 12.1 3.2 20.9 0 7.000 0.1804 0.2714 0.0910 0.012 1.3 12.7 3.4 21.3 0 8.000 0.1788 0.2712 0.0924 0.013 1.3 13.3 3.4 21.5 0 9.000 0.1774 0.2700 0.0926 0.014 1.4 13.5 3.4 22.4 0 10.000 0.1808 0.2710 0.0901 0.012 1.2 11.9 3.4 21.3 0 7.768 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2196 0.2718 0.0522 0.003 0.6 2.3 2.2 14.8 0 0.500 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 21.96 27.18 5.22 6.626 55.231 0.208 0.057 22.97 27.89 4.92 6.173 55.923 0.006 0.061 22.71 27.83 5.12 6.102 55.882 0.026 0.060 21.86 27.62 5.76 6.323 55.835 0.104 0.056 21.12 27.49 6.38 7.141 55.888 0.208 0.052 20.66 27.49 6.83 8.005 56.012 0.312 0.050 20.37 27.48 7.11 8.748 56.145 0.416 0.049 20.09 27.49 7.41 9.750 56.455 0.520 0.047 19.92 27.50 7.58 10.361 56.589 0.624 0.047 19.80 27.50 7.71 10.862 56.701 0.728 0.046 19.70 27.52 7.82 11.309 56.807 0.832 0.046 19.61 27.53 7.92 11.723 56.908 0.936 0.045 19.49 27.54 8.05 12.415 57.134 1.040 0.045 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: 21.86 27.62 5.76 6.323 55.835 0.104 0.056 Individual atomic B min max mean iso aniso Overall: 22.42 154.13 57.65 6.22 3928 0 Protein: 22.42 154.13 57.65 6.22 3928 0 Chain A: 23.51 154.13 57.62 N/A 1964 0 Chain B: 22.42 152.09 57.67 N/A 1964 0 Histogram: Values Number of atoms 22.42 - 35.59 307 35.59 - 48.76 1308 48.76 - 61.94 1076 61.94 - 75.11 561 75.11 - 88.28 332 88.28 - 101.45 197 101.45 - 114.62 62 114.62 - 127.79 20 127.79 - 140.96 24 140.96 - 154.13 41 =========================== Idealize ADP of riding H ========================== r_work=0.2186 r_free=0.2762 r_work=0.2180 r_free=0.2755 *********************** REFINEMENT MACRO_CYCLE 2 OF 3 ************************* |--(resolution: 3.14 - 25.21 A, n_refl.=9255 (all), 4.80 % free)-------------| | | | r_work= 0.2180 r_free= 0.2755 coordinate error (max.-lik. estimate): 0.51 A | | | | normalized target function (ls_wunit_k1) (work): 0.055452 | | target function (ls_wunit_k1) not normalized (work): 488.583971 | | target function (ls_wunit_k1) not normalized (free): 42.940063 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2208 0.2180 0.2755 n_refl.: 9255 re-set all scales: r(all,work,free)=0.3300 0.3274 0.3773 n_refl.: 9255 remove outliers: r(all,work,free)=0.3300 0.3274 0.3773 n_refl.: 9255 overall B=0.00 to atoms: r(all,work,free)=0.3300 0.3274 0.3773 n_refl.: 9255 bulk-solvent and scaling: r(all,work,free)=0.2206 0.2179 0.2738 n_refl.: 9255 remove outliers: r(all,work,free)=0.2206 0.2179 0.2738 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 0.2134 535.979 518.506 1.575 1.018 0.390 13.182-10.771 91.67 92 7 0.2119 541.666 506.166 1.292 1.019 0.360 10.742-8.763 94.15 183 10 0.1581 480.687 462.842 1.204 1.016 0.360 8.709-7.139 97.85 350 14 0.1710 421.512 410.854 1.204 1.013 0.358 7.120-5.819 98.85 652 33 0.2081 293.391 281.330 1.069 1.006 0.350 5.810-4.742 98.41 1191 49 0.1814 355.110 340.053 0.988 0.997 0.310 4.737-3.861 98.48 2221 114 0.1992 319.240 306.693 1.033 0.983 0.220 3.860-3.143 97.34 4027 214 0.2768 184.263 172.369 1.052 0.960 0.050 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.1000 b_overall=4.2733 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 3.480523 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.055691 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 0.2118 0.2725 0.0607 0.003 0.5 3.0 2.4 10.8 0 0.125 0.2035 0.2757 0.0721 0.003 0.6 5.2 2.4 11.7 0 0.250 0.1973 0.2751 0.0778 0.005 0.7 7.1 2.8 13.7 0 0.500 0.1894 0.2773 0.0879 0.009 1.0 8.4 2.8 16.4 0 1.000 0.1827 0.2751 0.0924 0.015 1.3 12.3 2.8 20.2 0 2.000 0.1780 0.2754 0.0974 0.021 1.7 16.8 3.4 21.1 0 3.000 0.1750 0.2735 0.0985 0.025 2.0 19.8 3.6 22.0 0 4.000 0.1720 0.2738 0.1017 0.030 2.2 22.0 4.9 24.0 0 5.000 0.1700 0.2742 0.1042 0.033 2.5 23.1 5.7 25.1 0 6.000 0.1683 0.2752 0.1069 0.037 2.7 25.4 6.3 25.6 0 7.000 0.1667 0.2762 0.1095 0.041 2.9 27.4 6.5 25.6 0 8.000 0.1655 0.2773 0.1117 0.043 3.1 27.1 6.3 26.5 0 9.000 0.1646 0.2796 0.1149 0.046 3.3 29.7 6.9 26.9 1 10.000 0.1841 0.2767 0.0926 0.014 1.2 11.3 2.8 19.1 0 1.740 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2118 0.2725 0.0607 0.003 0.5 3.0 2.4 10.8 0 0.125 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 21.18 27.25 6.07 9.511 62.665 0.056 5.643 23.90 29.14 5.24 9.152 65.929 0.002 5.721 22.74 28.46 5.72 9.683 63.824 0.007 5.686 20.97 27.40 6.43 9.789 62.413 0.028 5.635 20.60 27.39 6.79 10.327 62.198 0.056 5.623 19.89 27.44 7.55 11.873 62.436 0.084 5.602 19.72 27.46 7.74 12.237 62.678 0.111 5.597 19.65 27.46 7.80 12.412 62.790 0.139 5.595 19.57 27.47 7.91 12.702 62.953 0.167 5.593 19.50 27.50 8.00 12.964 63.085 0.195 5.591 19.45 27.50 8.05 13.190 63.196 0.223 5.590 19.37 27.54 8.17 13.637 63.395 0.251 5.588 19.35 27.55 8.20 13.744 63.444 0.278 5.588 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.007 Accepted refinement result: 22.74 28.46 5.72 9.683 63.824 0.007 5.686 Individual atomic B min max mean iso aniso Overall: 31.16 149.13 59.97 4.69 3928 0 Protein: 31.16 149.13 59.97 4.69 3928 0 Chain A: 31.16 149.13 59.89 N/A 1964 0 Chain B: 31.56 147.09 60.05 N/A 1964 0 Histogram: Values Number of atoms 31.16 - 42.95 587 42.95 - 54.75 1313 54.75 - 66.55 967 66.55 - 78.35 500 78.35 - 90.14 271 90.14 - 101.94 149 101.94 - 113.74 43 113.74 - 125.54 35 125.54 - 137.34 26 137.34 - 149.13 37 =========================== Idealize ADP of riding H ========================== r_work=0.2274 r_free=0.2846 r_work=0.2290 r_free=0.2852 *********************** REFINEMENT MACRO_CYCLE 3 OF 3 ************************* |--(resolution: 3.14 - 25.21 A, n_refl.=9255 (all), 4.80 % free)-------------| | | | r_work= 0.2290 r_free= 0.2852 coordinate error (max.-lik. estimate): 0.48 A | | | | normalized target function (ml) (work): 5.690594 | | target function (ml) not normalized (work): 50139.826649 | | target function (ml) not normalized (free): 2574.897036 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2316 0.2290 0.2852 n_refl.: 9255 re-set all scales: r(all,work,free)=0.3459 0.3434 0.3938 n_refl.: 9255 remove outliers: r(all,work,free)=0.3459 0.3434 0.3938 n_refl.: 9255 overall B=0.00 to atoms: r(all,work,free)=0.3459 0.3434 0.3938 n_refl.: 9255 bulk-solvent and scaling: r(all,work,free)=0.2320 0.2294 0.2844 n_refl.: 9255 remove outliers: r(all,work,free)=0.2320 0.2294 0.2844 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 0.2005 535.979 523.854 1.552 1.008 0.400 13.182-10.771 91.67 92 7 0.1906 541.666 515.439 1.260 1.009 0.368 10.742-8.763 94.15 183 10 0.1562 480.687 455.838 1.139 1.007 0.363 8.709-7.139 97.85 350 14 0.1730 421.512 418.962 1.185 1.005 0.360 7.120-5.819 98.85 652 33 0.2323 293.391 276.875 1.022 1.001 0.350 5.810-4.742 98.41 1191 49 0.2015 355.110 335.051 0.976 0.996 0.330 4.737-3.861 98.48 2221 114 0.2109 319.240 303.984 1.000 0.987 0.220 3.860-3.143 97.34 4027 214 0.2872 184.263 170.689 1.014 0.974 0.050 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0577 b_overall=3.4040 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.2294 r_free=0.2844 After: r_work=0.2294 r_free=0.2844 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 3.540454 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.053102 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 0.2294 0.2850 0.0556 0.002 0.5 3.4 2.4 10.5 0 0.125 0.2286 0.2851 0.0565 0.003 0.5 3.7 2.4 10.5 0 0.250 0.2229 0.2852 0.0622 0.008 0.7 5.3 2.4 10.5 0 0.500 0.2094 0.2844 0.0751 0.012 1.4 12.3 2.0 11.7 0 1.000 0.2025 0.2831 0.0805 0.018 1.6 20.4 2.4 15.2 0 2.000 0.1958 0.2830 0.0873 0.024 2.4 24.3 2.6 15.9 0 3.000 0.1921 0.2811 0.0890 0.029 2.6 29.1 3.6 20.0 0 4.000 0.1897 0.2824 0.0927 0.031 3.0 34.9 3.6 20.6 0 5.000 0.1878 0.2806 0.0927 0.033 3.1 31.5 5.3 23.3 0 6.000 0.1847 0.2818 0.0971 0.038 3.7 31.4 3.6 20.9 0 7.000 0.1806 0.2826 0.1020 0.047 4.0 39.5 4.3 23.3 1 8.000 0.1791 0.2833 0.1042 0.050 4.2 40.6 4.7 24.0 1 9.000 0.1789 0.2832 0.1043 0.052 4.5 42.4 5.3 24.9 2 10.000 0.2015 0.2823 0.0808 0.018 2.0 18.9 2.2 14.1 0 1.770 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2294 0.2850 0.0556 0.002 0.5 3.4 2.4 10.5 0 0.125 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 22.94 28.50 5.56 9.315 65.350 0.053 5.692 24.34 29.68 5.35 8.567 68.904 0.002 5.739 22.72 28.44 5.72 9.378 65.220 0.007 5.688 22.44 28.41 5.97 9.556 65.154 0.027 5.677 21.09 28.14 7.06 11.259 65.292 0.053 5.637 20.75 28.21 7.45 12.005 65.756 0.080 5.628 20.53 28.26 7.73 12.780 66.144 0.106 5.623 20.39 28.31 7.93 13.496 66.458 0.133 5.619 20.28 28.36 8.08 14.148 66.718 0.159 5.617 20.32 28.39 8.07 14.013 66.687 0.186 5.618 20.40 28.32 7.91 13.682 66.577 0.212 5.618 20.41 28.30 7.89 13.713 66.600 0.239 5.618 20.39 28.32 7.93 13.931 66.691 0.266 5.617 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: 22.44 28.41 5.97 9.556 65.154 0.027 5.677 Individual atomic B min max mean iso aniso Overall: 27.35 149.16 59.58 4.72 3928 0 Protein: 27.35 149.16 59.58 4.72 3928 0 Chain A: 27.35 149.16 59.49 N/A 1964 0 Chain B: 29.12 146.81 59.67 N/A 1964 0 Histogram: Values Number of atoms 27.35 - 39.53 379 39.53 - 51.71 1238 51.71 - 63.89 1110 63.89 - 76.07 576 76.07 - 88.25 308 88.25 - 100.43 165 100.43 - 112.61 54 112.61 - 124.80 30 124.80 - 136.98 32 136.98 - 149.16 36 =========================== Idealize ADP of riding H ========================== r_work=0.2244 r_free=0.2841 r_work=0.2240 r_free=0.2840 ----------X-ray data---------- |--(resolution: 3.14 - 25.21 A, n_refl.=9255 (all), 4.80 % free)-------------| | | | r_work= 0.2240 r_free= 0.2840 coordinate error (max.-lik. estimate): 0.50 A | | | | normalized target function (ml) (work): 5.676115 | | target function (ml) not normalized (work): 50012.247048 | | target function (ml) not normalized (free): 2575.680674 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1934 0.2525 5.9 6.0153| | 2: 4.52 - 3.60 0.98 2955 140 0.2339 0.2791 5.7349 5.9225| | 3: 3.60 - 3.14 0.97 2898 173 0.2778 0.3411 5.3876 5.5406| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 23.36 1.00 0.98 25887.94| | 2: 4.52 - 3.60 2955 140 0.81 26.88 1.02 0.95 17471.04| | 3: 3.60 - 3.14 2898 173 0.75 32.49 0.96 0.89 9748.55| |alpha: min = 0.89 max = 0.98 mean = 0.94| |beta: min = 9748.55 max = 25887.94 mean = 17756.76| |figures of merit: min = 0.01 max = 1.00 mean = 0.80| |phase err.(work): min = 0.00 max = 89.07 mean = 27.54| |phase err.(test): min = 0.00 max = 86.62 mean = 28.51| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.2268 0.2240 0.2840 n_refl.: 9255 re-set all scales: r(all,work,free)=0.3416 0.3389 0.3928 n_refl.: 9255 remove outliers: r(all,work,free)=0.3416 0.3389 0.3928 n_refl.: 9255 overall B=0.00 to atoms: r(all,work,free)=0.3416 0.3389 0.3928 n_refl.: 9255 bulk-solvent and scaling: r(all,work,free)=0.2268 0.2240 0.2843 n_refl.: 9255 remove outliers: r(all,work,free)=0.2268 0.2240 0.2843 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 0.2014 535.979 522.696 1.556 1.008 0.400 13.182-10.771 91.67 92 7 0.1893 541.666 515.129 1.264 1.009 0.368 10.742-8.763 94.15 183 10 0.1548 480.687 455.649 1.141 1.006 0.363 8.709-7.139 97.85 350 14 0.1729 421.512 418.751 1.187 1.005 0.360 7.120-5.819 98.85 652 33 0.2285 293.391 277.239 1.024 1.001 0.350 5.810-4.742 98.41 1191 49 0.1978 355.110 335.477 0.975 0.996 0.330 4.737-3.861 98.48 2221 114 0.2051 319.240 304.590 0.998 0.988 0.220 3.860-3.143 97.34 4027 214 0.2784 184.263 171.337 1.014 0.975 0.040 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0577 b_overall=3.4140 ================= 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_weight: 0.2324 0.2782 0.007 1.399 7.8 155.3 56.4 0 0.000 1_xyzrec: 0.2196 0.2718 0.003 0.560 7.8 155.3 56.4 0 0.186 1_adp: 0.2186 0.2762 0.003 0.560 22.4 154.1 57.6 0 0.186 1_regHadp: 0.2180 0.2755 0.003 0.560 22.4 154.1 57.6 0 0.186 2_bss: 0.2179 0.2738 0.003 0.560 22.4 154.1 57.6 0 0.186 2_settarget: 0.2179 0.2738 0.003 0.560 22.4 154.1 57.6 0 0.186 2_updatecdl: 0.2179 0.2738 0.003 0.623 22.4 154.1 57.6 0 0.186 2_weight: 0.2179 0.2738 0.003 0.623 22.4 154.1 57.6 0 0.186 2_xyzrec: 0.2118 0.2725 0.003 0.510 22.4 154.1 57.6 0 0.271 2_adp: 0.2274 0.2846 0.003 0.510 31.2 149.1 60.0 0 0.271 2_regHadp: 0.2290 0.2852 0.003 0.510 31.2 149.1 60.0 0 0.271 3_bss: 0.2294 0.2844 0.003 0.510 31.2 149.1 60.0 0 0.271 3_settarget: 0.2294 0.2844 0.003 0.510 31.2 149.1 60.0 0 0.271 3_updatecdl: 0.2294 0.2844 0.003 0.556 31.2 149.1 60.0 0 0.271 3_setrh: 0.2294 0.2844 0.003 0.556 31.2 149.1 60.0 0 0.271 3_weight: 0.2294 0.2844 0.003 0.556 31.2 149.1 60.0 0 0.271 3_xyzrec: 0.2294 0.2850 0.002 0.515 31.2 149.1 60.0 0 0.272 3_adp: 0.2244 0.2841 0.002 0.515 27.3 149.2 59.6 0 0.272 3_regHadp: 0.2240 0.2840 0.002 0.515 27.3 149.2 59.6 0 0.272 end: 0.2240 0.2843 0.002 0.515 27.3 149.2 59.6 0 0.272 ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V3/1w60_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V3/1w60_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 11.7400 Refinement macro-cycles (run) : 253.8500 Write final files (write_after_run_outputs) : 21.3300 Total : 286.9200 Total CPU time: 5.56 minutes =========================== phenix.refine: finished =========================== # Date 2024-05-20 Time 17:35:01 PDT -0700 (1716251701.94 s) Start R-work = 0.2324, R-free = 0.2782 Final R-work = 0.2240, R-free = 0.2843 =============================================================================== Job complete usr+sys time: 350.26 seconds wall clock time: 17 minutes 46.07 seconds (1066.07 seconds total)