Starting phenix.real_space_refine on Wed Apr 17 18:53:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sr1_40717/04_2024/8sr1_40717_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sr1_40717/04_2024/8sr1_40717.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sr1_40717/04_2024/8sr1_40717_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sr1_40717/04_2024/8sr1_40717_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sr1_40717/04_2024/8sr1_40717_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sr1_40717/04_2024/8sr1_40717.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sr1_40717/04_2024/8sr1_40717.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sr1_40717/04_2024/8sr1_40717_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sr1_40717/04_2024/8sr1_40717_trim_updated.pdb" } resolution = 2.18 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.036 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 20898 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Cu 9 5.60 5 P 36 5.49 5 S 93 5.16 5 C 15042 2.51 5 N 3417 2.21 5 O 4248 1.98 5 F 9 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 406": "OD1" <-> "OD2" Residue "C ARG 165": "NH1" <-> "NH2" Residue "C PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 406": "OD1" <-> "OD2" Residue "I PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 406": "OD1" <-> "OD2" Residue "G ARG 165": "NH1" <-> "NH2" Residue "G PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 165": "NH1" <-> "NH2" Residue "K PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 22854 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 3017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 3017 Classifications: {'peptide': 382} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 356} Chain: "B" Number of atoms: 1977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1977 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 12, 'TRANS': 228} Chain: "C" Number of atoms: 1972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1972 Classifications: {'peptide': 236} Link IDs: {'CIS': 1, 'PTRANS': 9, 'TRANS': 225} Chain: "E" Number of atoms: 3017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 3017 Classifications: {'peptide': 382} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 356} Chain: "F" Number of atoms: 1977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1977 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 12, 'TRANS': 228} Chain: "I" Number of atoms: 3017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 3017 Classifications: {'peptide': 382} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 356} Chain: "J" Number of atoms: 1977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1977 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 12, 'TRANS': 228} Chain: "G" Number of atoms: 1972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1972 Classifications: {'peptide': 236} Link IDs: {'CIS': 1, 'PTRANS': 9, 'TRANS': 225} Chain: "K" Number of atoms: 1972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1972 Classifications: {'peptide': 236} Link IDs: {'CIS': 1, 'PTRANS': 9, 'TRANS': 225} Chain: "A" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 12 Unusual residues: {' CU': 2, 'D10': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 200 Unusual residues: {'D10': 4, 'P1O': 2, 'PLC': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "C" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 323 Unusual residues: {' CU': 1, 'D10': 1, 'HXG': 2, 'P1O': 2, 'PLC': 4, 'WIY': 1} Classifications: {'undetermined': 11} Link IDs: {None: 10} Chain: "E" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 12 Unusual residues: {' CU': 2, 'D10': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 200 Unusual residues: {'D10': 4, 'P1O': 2, 'PLC': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "I" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 12 Unusual residues: {' CU': 2, 'D10': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "J" Number of atoms: 200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 200 Unusual residues: {'D10': 4, 'P1O': 2, 'PLC': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "G" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 323 Unusual residues: {' CU': 1, 'D10': 1, 'HXG': 2, 'P1O': 2, 'PLC': 4, 'WIY': 1} Classifications: {'undetermined': 11} Link IDs: {None: 10} Chain: "K" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 323 Unusual residues: {' CU': 1, 'D10': 1, 'HXG': 2, 'P1O': 2, 'PLC': 4, 'WIY': 1} Classifications: {'undetermined': 11} Link IDs: {None: 10} Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 70 Classifications: {'water': 70} Link IDs: {None: 69} Chain: "B" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 36 Classifications: {'water': 36} Link IDs: {None: 35} Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "E" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 70 Classifications: {'water': 70} Link IDs: {None: 69} Chain: "F" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 34 Classifications: {'water': 34} Link IDs: {None: 33} Chain: "I" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 69 Classifications: {'water': 69} Link IDs: {None: 68} Chain: "J" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 37 Classifications: {'water': 37} Link IDs: {None: 36} Chain: "G" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "K" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Time building chain proxies: 12.04, per 1000 atoms: 0.53 Number of scatterers: 22854 At special positions: 0 Unit cell: (107.936, 107.936, 120.635, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Cu 9 28.99 S 93 16.00 P 36 15.00 F 9 9.00 O 4248 8.00 N 3417 7.00 C 15042 6.00 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: 11.00 Conformation dependent library (CDL) restraints added in 3.8 seconds 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4758 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 81 helices and 24 sheets defined 47.3% alpha, 14.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.08 Creating SS restraints... Processing helix chain 'A' and resid 40 through 44 Processing helix chain 'A' and resid 163 through 165 No H-bonds generated for 'chain 'A' and resid 163 through 165' Processing helix chain 'A' and resid 185 through 207 Processing helix chain 'A' and resid 213 through 220 Processing helix chain 'A' and resid 232 through 256 Processing helix chain 'A' and resid 338 through 340 No H-bonds generated for 'chain 'A' and resid 338 through 340' Processing helix chain 'A' and resid 369 through 373 Processing helix chain 'A' and resid 377 through 381 removed outlier: 3.630A pdb=" N ILE A 380 " --> pdb=" O SER A 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 44 Processing helix chain 'B' and resid 46 through 50 Processing helix chain 'B' and resid 59 through 83 Proline residue: B 65 - end of helix removed outlier: 4.441A pdb=" N THR B 70 " --> pdb=" O ILE B 66 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N PHE B 71 " --> pdb=" O VAL B 67 " (cutoff:3.500A) Proline residue: B 72 - end of helix removed outlier: 3.958A pdb=" N GLU B 81 " --> pdb=" O SER B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 106 Processing helix chain 'B' and resid 116 through 119 No H-bonds generated for 'chain 'B' and resid 116 through 119' Processing helix chain 'B' and resid 125 through 136 Processing helix chain 'B' and resid 141 through 168 removed outlier: 4.110A pdb=" N ALA B 149 " --> pdb=" O ALA B 145 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N PHE B 156 " --> pdb=" O TRP B 152 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N TYR B 157 " --> pdb=" O GLY B 153 " (cutoff:3.500A) Proline residue: B 158 - end of helix Proline residue: B 162 - end of helix Proline residue: B 166 - end of helix Processing helix chain 'B' and resid 180 through 187 Processing helix chain 'B' and resid 195 through 197 No H-bonds generated for 'chain 'B' and resid 195 through 197' Processing helix chain 'B' and resid 212 through 238 removed outlier: 3.764A pdb=" N PHE B 233 " --> pdb=" O PHE B 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 50 through 72 removed outlier: 3.906A pdb=" N TYR C 58 " --> pdb=" O ALA C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 88 Processing helix chain 'C' and resid 90 through 113 Processing helix chain 'C' and resid 124 through 149 Processing helix chain 'C' and resid 151 through 160 Processing helix chain 'C' and resid 171 through 175 Processing helix chain 'C' and resid 180 through 198 Processing helix chain 'C' and resid 208 through 231 Proline residue: C 217 - end of helix removed outlier: 3.579A pdb=" N ILE C 220 " --> pdb=" O GLY C 216 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N LEU C 221 " --> pdb=" O PRO C 217 " (cutoff:3.500A) Proline residue: C 222 - end of helix removed outlier: 4.662A pdb=" N GLY C 225 " --> pdb=" O LEU C 221 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N LEU C 226 " --> pdb=" O PRO C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 269 removed outlier: 4.535A pdb=" N GLY C 247 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE C 248 " --> pdb=" O HIS C 245 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE C 250 " --> pdb=" O GLY C 247 " (cutoff:3.500A) Processing helix chain 'E' and resid 40 through 44 Processing helix chain 'E' and resid 163 through 165 No H-bonds generated for 'chain 'E' and resid 163 through 165' Processing helix chain 'E' and resid 185 through 207 Processing helix chain 'E' and resid 213 through 220 Processing helix chain 'E' and resid 232 through 256 Processing helix chain 'E' and resid 338 through 340 No H-bonds generated for 'chain 'E' and resid 338 through 340' Processing helix chain 'E' and resid 369 through 373 Processing helix chain 'E' and resid 377 through 381 removed outlier: 3.630A pdb=" N ILE E 380 " --> pdb=" O SER E 377 " (cutoff:3.500A) Processing helix chain 'F' and resid 11 through 44 Processing helix chain 'F' and resid 46 through 50 Processing helix chain 'F' and resid 59 through 83 Proline residue: F 65 - end of helix removed outlier: 4.440A pdb=" N THR F 70 " --> pdb=" O ILE F 66 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N PHE F 71 " --> pdb=" O VAL F 67 " (cutoff:3.500A) Proline residue: F 72 - end of helix removed outlier: 3.958A pdb=" N GLU F 81 " --> pdb=" O SER F 77 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 106 Processing helix chain 'F' and resid 116 through 119 No H-bonds generated for 'chain 'F' and resid 116 through 119' Processing helix chain 'F' and resid 125 through 136 Processing helix chain 'F' and resid 141 through 168 removed outlier: 4.110A pdb=" N ALA F 149 " --> pdb=" O ALA F 145 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N PHE F 156 " --> pdb=" O TRP F 152 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N TYR F 157 " --> pdb=" O GLY F 153 " (cutoff:3.500A) Proline residue: F 158 - end of helix Proline residue: F 162 - end of helix Proline residue: F 166 - end of helix Processing helix chain 'F' and resid 180 through 187 Processing helix chain 'F' and resid 195 through 197 No H-bonds generated for 'chain 'F' and resid 195 through 197' Processing helix chain 'F' and resid 212 through 238 removed outlier: 3.766A pdb=" N PHE F 233 " --> pdb=" O PHE F 229 " (cutoff:3.500A) Processing helix chain 'I' and resid 40 through 44 Processing helix chain 'I' and resid 163 through 165 No H-bonds generated for 'chain 'I' and resid 163 through 165' Processing helix chain 'I' and resid 185 through 207 Processing helix chain 'I' and resid 213 through 220 Processing helix chain 'I' and resid 232 through 256 Processing helix chain 'I' and resid 338 through 340 No H-bonds generated for 'chain 'I' and resid 338 through 340' Processing helix chain 'I' and resid 369 through 373 Processing helix chain 'I' and resid 377 through 381 removed outlier: 3.630A pdb=" N ILE I 380 " --> pdb=" O SER I 377 " (cutoff:3.500A) Processing helix chain 'J' and resid 11 through 44 Processing helix chain 'J' and resid 46 through 50 Processing helix chain 'J' and resid 59 through 83 Proline residue: J 65 - end of helix removed outlier: 4.441A pdb=" N THR J 70 " --> pdb=" O ILE J 66 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N PHE J 71 " --> pdb=" O VAL J 67 " (cutoff:3.500A) Proline residue: J 72 - end of helix removed outlier: 3.957A pdb=" N GLU J 81 " --> pdb=" O SER J 77 " (cutoff:3.500A) Processing helix chain 'J' and resid 88 through 106 Processing helix chain 'J' and resid 116 through 119 No H-bonds generated for 'chain 'J' and resid 116 through 119' Processing helix chain 'J' and resid 125 through 136 Processing helix chain 'J' and resid 141 through 168 removed outlier: 4.108A pdb=" N ALA J 149 " --> pdb=" O ALA J 145 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N PHE J 156 " --> pdb=" O TRP J 152 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N TYR J 157 " --> pdb=" O GLY J 153 " (cutoff:3.500A) Proline residue: J 158 - end of helix Proline residue: J 162 - end of helix Proline residue: J 166 - end of helix Processing helix chain 'J' and resid 180 through 187 Processing helix chain 'J' and resid 195 through 197 No H-bonds generated for 'chain 'J' and resid 195 through 197' Processing helix chain 'J' and resid 212 through 238 removed outlier: 3.765A pdb=" N PHE J 233 " --> pdb=" O PHE J 229 " (cutoff:3.500A) Processing helix chain 'G' and resid 50 through 72 removed outlier: 3.906A pdb=" N TYR G 58 " --> pdb=" O ALA G 54 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 88 Processing helix chain 'G' and resid 90 through 113 Processing helix chain 'G' and resid 124 through 149 Processing helix chain 'G' and resid 151 through 160 Processing helix chain 'G' and resid 171 through 175 Processing helix chain 'G' and resid 180 through 198 Processing helix chain 'G' and resid 208 through 231 Proline residue: G 217 - end of helix removed outlier: 3.578A pdb=" N ILE G 220 " --> pdb=" O GLY G 216 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N LEU G 221 " --> pdb=" O PRO G 217 " (cutoff:3.500A) Proline residue: G 222 - end of helix removed outlier: 4.661A pdb=" N GLY G 225 " --> pdb=" O LEU G 221 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N LEU G 226 " --> pdb=" O PRO G 222 " (cutoff:3.500A) Processing helix chain 'G' and resid 243 through 269 removed outlier: 4.535A pdb=" N GLY G 247 " --> pdb=" O LEU G 244 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE G 248 " --> pdb=" O HIS G 245 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE G 250 " --> pdb=" O GLY G 247 " (cutoff:3.500A) Processing helix chain 'K' and resid 50 through 72 removed outlier: 3.906A pdb=" N TYR K 58 " --> pdb=" O ALA K 54 " (cutoff:3.500A) Processing helix chain 'K' and resid 83 through 88 Processing helix chain 'K' and resid 90 through 113 Processing helix chain 'K' and resid 124 through 149 Processing helix chain 'K' and resid 151 through 160 Processing helix chain 'K' and resid 171 through 175 Processing helix chain 'K' and resid 180 through 198 Processing helix chain 'K' and resid 208 through 231 Proline residue: K 217 - end of helix removed outlier: 3.579A pdb=" N ILE K 220 " --> pdb=" O GLY K 216 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N LEU K 221 " --> pdb=" O PRO K 217 " (cutoff:3.500A) Proline residue: K 222 - end of helix removed outlier: 4.662A pdb=" N GLY K 225 " --> pdb=" O LEU K 221 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N LEU K 226 " --> pdb=" O PRO K 222 " (cutoff:3.500A) Processing helix chain 'K' and resid 243 through 269 removed outlier: 4.535A pdb=" N GLY K 247 " --> pdb=" O LEU K 244 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE K 248 " --> pdb=" O HIS K 245 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE K 250 " --> pdb=" O GLY K 247 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 47 through 50 removed outlier: 6.729A pdb=" N LYS A 129 " --> pdb=" O ARG A 100 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N ARG A 100 " --> pdb=" O LYS A 129 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 58 through 60 removed outlier: 8.377A pdb=" N VAL A 59 " --> pdb=" O TRP A 156 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N THR A 158 " --> pdb=" O VAL A 59 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 141 through 144 Processing sheet with id= D, first strand: chain 'A' and resid 169 through 171 Processing sheet with id= E, first strand: chain 'A' and resid 282 through 286 Processing sheet with id= F, first strand: chain 'A' and resid 298 through 300 removed outlier: 6.453A pdb=" N ILE A 410 " --> pdb=" O TYR A 291 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 323 through 325 removed outlier: 6.555A pdb=" N PHE A 392 " --> pdb=" O GLY A 315 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N PHE A 317 " --> pdb=" O LEU A 390 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N LEU A 390 " --> pdb=" O PHE A 317 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 170 through 173 Processing sheet with id= I, first strand: chain 'E' and resid 47 through 50 removed outlier: 6.728A pdb=" N LYS E 129 " --> pdb=" O ARG E 100 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N ARG E 100 " --> pdb=" O LYS E 129 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 58 through 60 removed outlier: 8.376A pdb=" N VAL E 59 " --> pdb=" O TRP E 156 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N THR E 158 " --> pdb=" O VAL E 59 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 141 through 144 Processing sheet with id= L, first strand: chain 'E' and resid 169 through 171 Processing sheet with id= M, first strand: chain 'E' and resid 282 through 286 Processing sheet with id= N, first strand: chain 'E' and resid 298 through 300 removed outlier: 6.453A pdb=" N ILE E 410 " --> pdb=" O TYR E 291 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 323 through 325 removed outlier: 6.555A pdb=" N PHE E 392 " --> pdb=" O GLY E 315 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N PHE E 317 " --> pdb=" O LEU E 390 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N LEU E 390 " --> pdb=" O PHE E 317 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'F' and resid 170 through 173 Processing sheet with id= Q, first strand: chain 'I' and resid 47 through 50 removed outlier: 6.728A pdb=" N LYS I 129 " --> pdb=" O ARG I 100 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N ARG I 100 " --> pdb=" O LYS I 129 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'I' and resid 58 through 60 removed outlier: 8.377A pdb=" N VAL I 59 " --> pdb=" O TRP I 156 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N THR I 158 " --> pdb=" O VAL I 59 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'I' and resid 141 through 144 Processing sheet with id= T, first strand: chain 'I' and resid 169 through 171 Processing sheet with id= U, first strand: chain 'I' and resid 282 through 286 Processing sheet with id= V, first strand: chain 'I' and resid 298 through 300 removed outlier: 6.454A pdb=" N ILE I 410 " --> pdb=" O TYR I 291 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'I' and resid 323 through 325 removed outlier: 6.556A pdb=" N PHE I 392 " --> pdb=" O GLY I 315 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N PHE I 317 " --> pdb=" O LEU I 390 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N LEU I 390 " --> pdb=" O PHE I 317 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'J' and resid 170 through 173 1002 hydrogen bonds defined for protein. 2763 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: 6.94 Time building geometry restraints manager: 11.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3312 1.32 - 1.44: 6811 1.44 - 1.57: 12712 1.57 - 1.69: 133 1.69 - 1.81: 180 Bond restraints: 23148 Sorted by residual: bond pdb=" CE1 HIS C 231 " pdb=" NE2 HIS C 231 " ideal model delta sigma weight residual 1.321 1.393 -0.072 1.00e-02 1.00e+04 5.20e+01 bond pdb=" CE1 HIS G 231 " pdb=" NE2 HIS G 231 " ideal model delta sigma weight residual 1.321 1.393 -0.072 1.00e-02 1.00e+04 5.17e+01 bond pdb=" CE1 HIS K 231 " pdb=" NE2 HIS K 231 " ideal model delta sigma weight residual 1.321 1.392 -0.071 1.00e-02 1.00e+04 5.10e+01 bond pdb=" CG HIS G 245 " pdb=" ND1 HIS G 245 " ideal model delta sigma weight residual 1.378 1.455 -0.077 1.10e-02 8.26e+03 4.95e+01 bond pdb=" CG HIS C 245 " pdb=" ND1 HIS C 245 " ideal model delta sigma weight residual 1.378 1.455 -0.077 1.10e-02 8.26e+03 4.91e+01 ... (remaining 23143 not shown) Histogram of bond angle deviations from ideal: 98.72 - 105.83: 574 105.83 - 112.94: 12360 112.94 - 120.05: 8401 120.05 - 127.16: 9567 127.16 - 134.27: 418 Bond angle restraints: 31320 Sorted by residual: angle pdb=" CA HIS K 160 " pdb=" CB HIS K 160 " pdb=" CG HIS K 160 " ideal model delta sigma weight residual 113.80 105.68 8.12 1.00e+00 1.00e+00 6.59e+01 angle pdb=" CA HIS G 160 " pdb=" CB HIS G 160 " pdb=" CG HIS G 160 " ideal model delta sigma weight residual 113.80 105.69 8.11 1.00e+00 1.00e+00 6.58e+01 angle pdb=" CA HIS C 160 " pdb=" CB HIS C 160 " pdb=" CG HIS C 160 " ideal model delta sigma weight residual 113.80 105.71 8.09 1.00e+00 1.00e+00 6.55e+01 angle pdb=" CB HIS K 173 " pdb=" CG HIS K 173 " pdb=" CD2 HIS K 173 " ideal model delta sigma weight residual 131.20 121.90 9.30 1.30e+00 5.92e-01 5.12e+01 angle pdb=" CB HIS G 173 " pdb=" CG HIS G 173 " pdb=" CD2 HIS G 173 " ideal model delta sigma weight residual 131.20 121.93 9.27 1.30e+00 5.92e-01 5.09e+01 ... (remaining 31315 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.45: 12578 34.45 - 68.89: 823 68.89 - 103.34: 104 103.34 - 137.79: 37 137.79 - 172.24: 12 Dihedral angle restraints: 13554 sinusoidal: 6102 harmonic: 7452 Sorted by residual: dihedral pdb=" CD ARG G 165 " pdb=" NE ARG G 165 " pdb=" CZ ARG G 165 " pdb=" NH1 ARG G 165 " ideal model delta sinusoidal sigma weight residual 0.00 68.33 -68.33 1 1.00e+01 1.00e-02 6.06e+01 dihedral pdb=" CD ARG C 165 " pdb=" NE ARG C 165 " pdb=" CZ ARG C 165 " pdb=" NH1 ARG C 165 " ideal model delta sinusoidal sigma weight residual 0.00 68.33 -68.33 1 1.00e+01 1.00e-02 6.05e+01 dihedral pdb=" CD ARG K 165 " pdb=" NE ARG K 165 " pdb=" CZ ARG K 165 " pdb=" NH1 ARG K 165 " ideal model delta sinusoidal sigma weight residual 0.00 68.29 -68.29 1 1.00e+01 1.00e-02 6.05e+01 ... (remaining 13551 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 2337 0.049 - 0.097: 635 0.097 - 0.146: 178 0.146 - 0.194: 38 0.194 - 0.243: 19 Chirality restraints: 3207 Sorted by residual: chirality pdb=" C2 PLC G 308 " pdb=" C1 PLC G 308 " pdb=" C3 PLC G 308 " pdb=" O2 PLC G 308 " both_signs ideal model delta sigma weight residual False -2.31 -2.56 0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" C2 PLC C 307 " pdb=" C1 PLC C 307 " pdb=" C3 PLC C 307 " pdb=" O2 PLC C 307 " both_signs ideal model delta sigma weight residual False -2.31 -2.55 0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" C2 PLC K 308 " pdb=" C1 PLC K 308 " pdb=" C3 PLC K 308 " pdb=" O2 PLC K 308 " both_signs ideal model delta sigma weight residual False -2.31 -2.55 0.24 2.00e-01 2.50e+01 1.45e+00 ... (remaining 3204 not shown) Planarity restraints: 3732 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG G 165 " -0.939 9.50e-02 1.11e+02 4.21e-01 1.09e+02 pdb=" NE ARG G 165 " 0.066 2.00e-02 2.50e+03 pdb=" CZ ARG G 165 " -0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG G 165 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG G 165 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 165 " -0.938 9.50e-02 1.11e+02 4.21e-01 1.09e+02 pdb=" NE ARG C 165 " 0.065 2.00e-02 2.50e+03 pdb=" CZ ARG C 165 " -0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG C 165 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG C 165 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG K 165 " -0.938 9.50e-02 1.11e+02 4.21e-01 1.09e+02 pdb=" NE ARG K 165 " 0.065 2.00e-02 2.50e+03 pdb=" CZ ARG K 165 " -0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG K 165 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG K 165 " -0.015 2.00e-02 2.50e+03 ... (remaining 3729 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.42: 149 2.42 - 3.04: 14614 3.04 - 3.66: 37938 3.66 - 4.28: 62140 4.28 - 4.90: 98901 Nonbonded interactions: 213742 Sorted by model distance: nonbonded pdb=" CA GLU K 238 " pdb=" F1 WIY K 311 " model vdw 1.795 3.420 nonbonded pdb=" CA GLU G 238 " pdb=" F1 WIY G 311 " model vdw 1.795 3.420 nonbonded pdb=" CA GLU C 238 " pdb=" F1 WIY C 310 " model vdw 1.795 3.420 nonbonded pdb=" NH2 ARG K 165 " pdb=" F2 WIY K 311 " model vdw 1.836 2.470 nonbonded pdb=" NH2 ARG C 165 " pdb=" F2 WIY C 310 " model vdw 1.836 2.470 ... (remaining 213737 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'I' } ncs_group { reference = (chain 'B' and (resid 7 through 247 or resid 304 through 306)) selection = (chain 'F' and (resid 7 through 247 or resid 304 through 306)) selection = (chain 'J' and (resid 7 through 247 or resid 304 through 306)) } ncs_group { reference = (chain 'C' and (resid 45 through 280 or resid 309)) selection = (chain 'G' and (resid 45 through 280 or resid 309)) selection = (chain 'K' and (resid 45 through 280 or resid 309)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.250 Construct map_model_manager: 0.020 Extract box with map and model: 4.710 Check model and map are aligned: 0.310 Set scattering table: 0.200 Process input model: 63.070 Find NCS groups from input model: 1.490 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 82.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6418 moved from start: 0.0000 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: