Starting phenix.real_space_refine on Sun Dec 10 16:53:47 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ljv_4062/12_2023/5ljv_4062_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ljv_4062/12_2023/5ljv_4062.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ljv_4062/12_2023/5ljv_4062.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ljv_4062/12_2023/5ljv_4062.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ljv_4062/12_2023/5ljv_4062_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ljv_4062/12_2023/5ljv_4062_updated.pdb" } resolution = 3.64 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= -0.000 sd= 0.023 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs 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: 6 Type Number sf(0) Gaussians P 12 5.49 5 Mg 6 5.21 5 S 72 5.16 5 C 9474 2.51 5 N 2580 2.21 5 O 2856 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 15000 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2472 Classifications: {'peptide': 325} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 306} Chain: "B" Number of atoms: 2472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2472 Classifications: {'peptide': 325} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 306} Chain: "C" Number of atoms: 2472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2472 Classifications: {'peptide': 325} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 306} Chain: "D" Number of atoms: 2472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2472 Classifications: {'peptide': 325} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 306} Chain: "E" Number of atoms: 2472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2472 Classifications: {'peptide': 325} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 306} Chain: "F" Number of atoms: 2472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2472 Classifications: {'peptide': 325} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 306} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.92, per 1000 atoms: 0.53 Number of scatterers: 15000 At special positions: 0 Unit cell: (97.82, 92.46, 187.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 72 16.00 P 12 15.00 Mg 6 11.99 O 2856 8.00 N 2580 7.00 C 9474 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: 6.54 Conformation dependent library (CDL) restraints added in 3.0 seconds 3876 Ramachandran restraints generated. 1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3588 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 78 helices and 24 sheets defined 42.5% alpha, 17.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.15 Creating SS restraints... Processing helix chain 'A' and resid 45 through 51 removed outlier: 3.541A pdb=" N LYS A 49 " --> pdb=" O VAL A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 66 removed outlier: 5.450A pdb=" N SER A 66 " --> pdb=" O PHE A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 101 Processing helix chain 'A' and resid 121 through 132 Processing helix chain 'A' and resid 143 through 151 Processing helix chain 'A' and resid 189 through 201 Processing helix chain 'A' and resid 211 through 221 removed outlier: 3.551A pdb=" N ALA A 216 " --> pdb=" O ASN A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 256 Processing helix chain 'A' and resid 258 through 271 removed outlier: 3.644A pdb=" N SER A 271 " --> pdb=" O THR A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 283 removed outlier: 4.718A pdb=" N ALA A 278 " --> pdb=" O PRO A 274 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N THR A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASN A 283 " --> pdb=" O THR A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 292 Processing helix chain 'A' and resid 296 through 307 Proline residue: A 306 - end of helix Processing helix chain 'A' and resid 321 through 330 Processing helix chain 'B' and resid 45 through 51 removed outlier: 3.528A pdb=" N LYS B 49 " --> pdb=" O VAL B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 66 removed outlier: 5.444A pdb=" N SER B 66 " --> pdb=" O PHE B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 101 removed outlier: 3.906A pdb=" N GLU B 88 " --> pdb=" O ASP B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 132 Processing helix chain 'B' and resid 143 through 151 Processing helix chain 'B' and resid 189 through 201 Processing helix chain 'B' and resid 211 through 221 removed outlier: 3.584A pdb=" N ALA B 216 " --> pdb=" O ASN B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 256 Processing helix chain 'B' and resid 258 through 271 removed outlier: 3.616A pdb=" N SER B 271 " --> pdb=" O THR B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 283 removed outlier: 4.707A pdb=" N ALA B 278 " --> pdb=" O PRO B 274 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N THR B 279 " --> pdb=" O GLU B 275 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASN B 283 " --> pdb=" O THR B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 292 Processing helix chain 'B' and resid 296 through 307 Proline residue: B 306 - end of helix Processing helix chain 'B' and resid 321 through 330 Processing helix chain 'C' and resid 45 through 51 removed outlier: 3.530A pdb=" N LYS C 49 " --> pdb=" O VAL C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 66 removed outlier: 5.437A pdb=" N SER C 66 " --> pdb=" O PHE C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 101 Processing helix chain 'C' and resid 121 through 132 Processing helix chain 'C' and resid 143 through 151 Processing helix chain 'C' and resid 189 through 203 removed outlier: 3.884A pdb=" N ARG C 203 " --> pdb=" O ALA C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 221 removed outlier: 3.563A pdb=" N ALA C 216 " --> pdb=" O ASN C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 256 Processing helix chain 'C' and resid 258 through 271 removed outlier: 3.624A pdb=" N SER C 271 " --> pdb=" O THR C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 283 removed outlier: 4.715A pdb=" N ALA C 278 " --> pdb=" O PRO C 274 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N THR C 279 " --> pdb=" O GLU C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 292 Processing helix chain 'C' and resid 296 through 307 Proline residue: C 306 - end of helix Processing helix chain 'C' and resid 321 through 330 Processing helix chain 'D' and resid 45 through 51 removed outlier: 3.537A pdb=" N LYS D 49 " --> pdb=" O VAL D 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 59 through 66 removed outlier: 5.439A pdb=" N SER D 66 " --> pdb=" O PHE D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 101 Processing helix chain 'D' and resid 121 through 132 Processing helix chain 'D' and resid 143 through 151 Processing helix chain 'D' and resid 189 through 203 removed outlier: 3.891A pdb=" N ARG D 203 " --> pdb=" O ALA D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 211 through 221 removed outlier: 3.575A pdb=" N ALA D 216 " --> pdb=" O ASN D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 256 Processing helix chain 'D' and resid 258 through 271 removed outlier: 3.633A pdb=" N SER D 271 " --> pdb=" O THR D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 283 removed outlier: 4.716A pdb=" N ALA D 278 " --> pdb=" O PRO D 274 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N THR D 279 " --> pdb=" O GLU D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 289 through 292 Processing helix chain 'D' and resid 296 through 307 Proline residue: D 306 - end of helix Processing helix chain 'D' and resid 321 through 330 Processing helix chain 'E' and resid 45 through 51 removed outlier: 3.537A pdb=" N LYS E 49 " --> pdb=" O VAL E 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 59 through 66 removed outlier: 5.438A pdb=" N SER E 66 " --> pdb=" O PHE E 62 " (cutoff:3.500A) Processing helix chain 'E' and resid 84 through 101 removed outlier: 3.912A pdb=" N GLU E 88 " --> pdb=" O ASP E 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 132 Processing helix chain 'E' and resid 143 through 151 Processing helix chain 'E' and resid 189 through 201 Processing helix chain 'E' and resid 211 through 221 removed outlier: 3.595A pdb=" N ALA E 216 " --> pdb=" O ASN E 212 " (cutoff:3.500A) Processing helix chain 'E' and resid 247 through 256 Processing helix chain 'E' and resid 258 through 271 removed outlier: 3.630A pdb=" N SER E 271 " --> pdb=" O THR E 267 " (cutoff:3.500A) Processing helix chain 'E' and resid 274 through 283 removed outlier: 4.709A pdb=" N ALA E 278 " --> pdb=" O PRO E 274 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N THR E 279 " --> pdb=" O GLU E 275 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASN E 283 " --> pdb=" O THR E 279 " (cutoff:3.500A) Processing helix chain 'E' and resid 289 through 292 Processing helix chain 'E' and resid 296 through 307 Proline residue: E 306 - end of helix Processing helix chain 'E' and resid 321 through 330 Processing helix chain 'F' and resid 45 through 51 removed outlier: 3.549A pdb=" N LYS F 49 " --> pdb=" O VAL F 45 " (cutoff:3.500A) Processing helix chain 'F' and resid 59 through 66 removed outlier: 5.443A pdb=" N SER F 66 " --> pdb=" O PHE F 62 " (cutoff:3.500A) Processing helix chain 'F' and resid 85 through 101 Processing helix chain 'F' and resid 121 through 132 Processing helix chain 'F' and resid 143 through 151 Processing helix chain 'F' and resid 189 through 201 Processing helix chain 'F' and resid 211 through 221 removed outlier: 3.569A pdb=" N ALA F 216 " --> pdb=" O ASN F 212 " (cutoff:3.500A) Processing helix chain 'F' and resid 247 through 256 Processing helix chain 'F' and resid 258 through 271 removed outlier: 3.648A pdb=" N SER F 271 " --> pdb=" O THR F 267 " (cutoff:3.500A) Processing helix chain 'F' and resid 274 through 283 removed outlier: 5.039A pdb=" N ALA F 278 " --> pdb=" O GLU F 275 " (cutoff:3.500A) Processing helix chain 'F' and resid 289 through 292 Processing helix chain 'F' and resid 296 through 307 Proline residue: F 306 - end of helix Processing helix chain 'F' and resid 321 through 330 Processing sheet with id= A, first strand: chain 'A' and resid 32 through 36 removed outlier: 5.677A pdb=" N GLU A 108 " --> pdb=" O LEU A 12 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N LEU A 14 " --> pdb=" O GLU A 108 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N CYS A 110 " --> pdb=" O LEU A 14 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N VAL A 16 " --> pdb=" O CYS A 110 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N VAL A 112 " --> pdb=" O VAL A 16 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N THR A 137 " --> pdb=" O ALA A 111 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N ILE A 113 " --> pdb=" O THR A 137 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N LEU A 139 " --> pdb=" O ILE A 113 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N VAL A 115 " --> pdb=" O LEU A 139 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N VAL A 141 " --> pdb=" O VAL A 115 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 39 through 42 Processing sheet with id= C, first strand: chain 'A' and resid 285 through 287 Processing sheet with id= D, first strand: chain 'A' and resid 232 through 237 Processing sheet with id= E, first strand: chain 'B' and resid 32 through 36 removed outlier: 5.701A pdb=" N GLU B 108 " --> pdb=" O LEU B 12 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N LEU B 14 " --> pdb=" O GLU B 108 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N CYS B 110 " --> pdb=" O LEU B 14 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N VAL B 16 " --> pdb=" O CYS B 110 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N VAL B 112 " --> pdb=" O VAL B 16 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N THR B 137 " --> pdb=" O ALA B 111 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N ILE B 113 " --> pdb=" O THR B 137 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N LEU B 139 " --> pdb=" O ILE B 113 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N VAL B 115 " --> pdb=" O LEU B 139 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N VAL B 141 " --> pdb=" O VAL B 115 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 39 through 42 Processing sheet with id= G, first strand: chain 'B' and resid 285 through 287 removed outlier: 3.922A pdb=" N THR B 157 " --> pdb=" O LEU B 172 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 232 through 237 Processing sheet with id= I, first strand: chain 'C' and resid 32 through 36 removed outlier: 5.718A pdb=" N GLU C 108 " --> pdb=" O LEU C 12 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N LEU C 14 " --> pdb=" O GLU C 108 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N CYS C 110 " --> pdb=" O LEU C 14 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N VAL C 16 " --> pdb=" O CYS C 110 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N VAL C 112 " --> pdb=" O VAL C 16 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N LEU C 18 " --> pdb=" O VAL C 112 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N GLY C 114 " --> pdb=" O LEU C 18 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N THR C 137 " --> pdb=" O ALA C 111 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N ILE C 113 " --> pdb=" O THR C 137 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N LEU C 139 " --> pdb=" O ILE C 113 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N VAL C 115 " --> pdb=" O LEU C 139 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N VAL C 141 " --> pdb=" O VAL C 115 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 39 through 42 Processing sheet with id= K, first strand: chain 'C' and resid 285 through 287 Processing sheet with id= L, first strand: chain 'C' and resid 232 through 237 Processing sheet with id= M, first strand: chain 'D' and resid 32 through 36 removed outlier: 5.707A pdb=" N GLU D 108 " --> pdb=" O LEU D 12 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N LEU D 14 " --> pdb=" O GLU D 108 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N CYS D 110 " --> pdb=" O LEU D 14 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N VAL D 16 " --> pdb=" O CYS D 110 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N VAL D 112 " --> pdb=" O VAL D 16 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N LEU D 18 " --> pdb=" O VAL D 112 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N GLY D 114 " --> pdb=" O LEU D 18 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N THR D 137 " --> pdb=" O ALA D 111 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N ILE D 113 " --> pdb=" O THR D 137 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N LEU D 139 " --> pdb=" O ILE D 113 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N VAL D 115 " --> pdb=" O LEU D 139 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N VAL D 141 " --> pdb=" O VAL D 115 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 39 through 42 Processing sheet with id= O, first strand: chain 'D' and resid 285 through 287 Processing sheet with id= P, first strand: chain 'D' and resid 232 through 237 Processing sheet with id= Q, first strand: chain 'E' and resid 32 through 36 removed outlier: 5.694A pdb=" N GLU E 108 " --> pdb=" O LEU E 12 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N LEU E 14 " --> pdb=" O GLU E 108 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N CYS E 110 " --> pdb=" O LEU E 14 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N VAL E 16 " --> pdb=" O CYS E 110 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N VAL E 112 " --> pdb=" O VAL E 16 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N LEU E 18 " --> pdb=" O VAL E 112 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N GLY E 114 " --> pdb=" O LEU E 18 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N THR E 137 " --> pdb=" O ALA E 111 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N ILE E 113 " --> pdb=" O THR E 137 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N LEU E 139 " --> pdb=" O ILE E 113 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N VAL E 115 " --> pdb=" O LEU E 139 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N VAL E 141 " --> pdb=" O VAL E 115 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 39 through 42 Processing sheet with id= S, first strand: chain 'E' and resid 285 through 287 Processing sheet with id= T, first strand: chain 'E' and resid 232 through 237 Processing sheet with id= U, first strand: chain 'F' and resid 32 through 36 removed outlier: 5.666A pdb=" N GLU F 108 " --> pdb=" O LEU F 12 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N LEU F 14 " --> pdb=" O GLU F 108 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N CYS F 110 " --> pdb=" O LEU F 14 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N VAL F 16 " --> pdb=" O CYS F 110 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N VAL F 112 " --> pdb=" O VAL F 16 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N THR F 137 " --> pdb=" O ALA F 111 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N ILE F 113 " --> pdb=" O THR F 137 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N LEU F 139 " --> pdb=" O ILE F 113 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N VAL F 115 " --> pdb=" O LEU F 139 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N VAL F 141 " --> pdb=" O VAL F 115 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'F' and resid 39 through 42 Processing sheet with id= W, first strand: chain 'F' and resid 285 through 287 Processing sheet with id= X, first strand: chain 'F' and resid 232 through 237 650 hydrogen bonds defined for protein. 1842 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: 4.61 Time building geometry restraints manager: 6.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.11 - 1.26: 2365 1.26 - 1.42: 3797 1.42 - 1.57: 8777 1.57 - 1.72: 211 1.72 - 1.87: 108 Bond restraints: 15258 Sorted by residual: bond pdb=" CA HIS A 22 " pdb=" C HIS A 22 " ideal model delta sigma weight residual 1.520 1.374 0.146 1.21e-02 6.83e+03 1.46e+02 bond pdb=" CA VAL C 160 " pdb=" C VAL C 160 " ideal model delta sigma weight residual 1.527 1.426 0.101 8.50e-03 1.38e+04 1.41e+02 bond pdb=" CA HIS F 22 " pdb=" C HIS F 22 " ideal model delta sigma weight residual 1.520 1.377 0.144 1.21e-02 6.83e+03 1.41e+02 bond pdb=" CA VAL D 160 " pdb=" C VAL D 160 " ideal model delta sigma weight residual 1.527 1.429 0.097 8.50e-03 1.38e+04 1.31e+02 bond pdb=" CA VAL D 183 " pdb=" CB VAL D 183 " ideal model delta sigma weight residual 1.550 1.435 0.115 1.03e-02 9.43e+03 1.25e+02 ... (remaining 15253 not shown) Histogram of bond angle deviations from ideal: 91.91 - 100.40: 133 100.40 - 108.90: 3029 108.90 - 117.39: 8684 117.39 - 125.89: 8661 125.89 - 134.38: 229 Bond angle restraints: 20736 Sorted by residual: angle pdb=" C VAL E 147 " pdb=" CA VAL E 147 " pdb=" CB VAL E 147 " ideal model delta sigma weight residual 111.97 98.86 13.11 1.28e+00 6.10e-01 1.05e+02 angle pdb=" C VAL B 147 " pdb=" CA VAL B 147 " pdb=" CB VAL B 147 " ideal model delta sigma weight residual 111.97 99.07 12.90 1.28e+00 6.10e-01 1.01e+02 angle pdb=" C VAL D 147 " pdb=" CA VAL D 147 " pdb=" CB VAL D 147 " ideal model delta sigma weight residual 111.97 99.35 12.62 1.28e+00 6.10e-01 9.73e+01 angle pdb=" C VAL C 147 " pdb=" CA VAL C 147 " pdb=" CB VAL C 147 " ideal model delta sigma weight residual 111.81 99.72 12.09 1.25e+00 6.40e-01 9.35e+01 angle pdb=" C VAL F 147 " pdb=" CA VAL F 147 " pdb=" CB VAL F 147 " ideal model delta sigma weight residual 111.97 100.08 11.89 1.28e+00 6.10e-01 8.63e+01 ... (remaining 20731 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.13: 7969 20.13 - 40.27: 1016 40.27 - 60.40: 269 60.40 - 80.53: 20 80.53 - 100.67: 14 Dihedral angle restraints: 9288 sinusoidal: 3708 harmonic: 5580 Sorted by residual: dihedral pdb=" C MET D 258 " pdb=" N MET D 258 " pdb=" CA MET D 258 " pdb=" CB MET D 258 " ideal model delta harmonic sigma weight residual -122.60 -142.76 20.16 0 2.50e+00 1.60e-01 6.50e+01 dihedral pdb=" C MET C 258 " pdb=" N MET C 258 " pdb=" CA MET C 258 " pdb=" CB MET C 258 " ideal model delta harmonic sigma weight residual -122.60 -142.34 19.74 0 2.50e+00 1.60e-01 6.23e+01 dihedral pdb=" C MET E 258 " pdb=" N MET E 258 " pdb=" CA MET E 258 " pdb=" CB MET E 258 " ideal model delta harmonic sigma weight residual -122.60 -142.24 19.64 0 2.50e+00 1.60e-01 6.17e+01 ... (remaining 9285 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.192: 2035 0.192 - 0.384: 340 0.384 - 0.576: 49 0.576 - 0.768: 6 0.768 - 0.960: 6 Chirality restraints: 2436 Sorted by residual: chirality pdb=" CA MET F 258 " pdb=" N MET F 258 " pdb=" C MET F 258 " pdb=" CB MET F 258 " both_signs ideal model delta sigma weight residual False 2.51 1.55 0.96 2.00e-01 2.50e+01 2.30e+01 chirality pdb=" CA MET E 258 " pdb=" N MET E 258 " pdb=" C MET E 258 " pdb=" CB MET E 258 " both_signs ideal model delta sigma weight residual False 2.51 1.55 0.96 2.00e-01 2.50e+01 2.28e+01 chirality pdb=" CA MET A 258 " pdb=" N MET A 258 " pdb=" C MET A 258 " pdb=" CB MET A 258 " both_signs ideal model delta sigma weight residual False 2.51 1.56 0.95 2.00e-01 2.50e+01 2.25e+01 ... (remaining 2433 not shown) Planarity restraints: 2676 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR F 67 " 0.069 2.00e-02 2.50e+03 4.21e-02 3.55e+01 pdb=" CG TYR F 67 " -0.083 2.00e-02 2.50e+03 pdb=" CD1 TYR F 67 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR F 67 " -0.026 2.00e-02 2.50e+03 pdb=" CE1 TYR F 67 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 TYR F 67 " 0.020 2.00e-02 2.50e+03 pdb=" CZ TYR F 67 " 0.032 2.00e-02 2.50e+03 pdb=" OH TYR F 67 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE E 286 " -0.063 2.00e-02 2.50e+03 4.45e-02 3.47e+01 pdb=" CG PHE E 286 " 0.093 2.00e-02 2.50e+03 pdb=" CD1 PHE E 286 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE E 286 " 0.015 2.00e-02 2.50e+03 pdb=" CE1 PHE E 286 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE E 286 " -0.026 2.00e-02 2.50e+03 pdb=" CZ PHE E 286 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 67 " 0.064 2.00e-02 2.50e+03 3.90e-02 3.04e+01 pdb=" CG TYR A 67 " -0.078 2.00e-02 2.50e+03 pdb=" CD1 TYR A 67 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR A 67 " -0.023 2.00e-02 2.50e+03 pdb=" CE1 TYR A 67 " 0.011 2.00e-02 2.50e+03 pdb=" CE2 TYR A 67 " 0.018 2.00e-02 2.50e+03 pdb=" CZ TYR A 67 " 0.028 2.00e-02 2.50e+03 pdb=" OH TYR A 67 " -0.005 2.00e-02 2.50e+03 ... (remaining 2673 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 833 2.64 - 3.20: 15441 3.20 - 3.77: 25332 3.77 - 4.33: 35597 4.33 - 4.90: 55144 Nonbonded interactions: 132347 Sorted by model distance: nonbonded pdb=" NZ LYS A 49 " pdb=" OH TYR C 149 " model vdw 2.070 2.520 nonbonded pdb=" OH TYR D 149 " pdb=" NZ LYS F 49 " model vdw 2.075 2.520 nonbonded pdb=" OH TYR A 149 " pdb=" NZ LYS B 49 " model vdw 2.106 2.520 nonbonded pdb=" NZ LYS E 49 " pdb=" OH TYR F 149 " model vdw 2.132 2.520 nonbonded pdb=" O THR D 20 " pdb=" OG1 THR D 20 " model vdw 2.181 2.440 ... (remaining 132342 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 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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 group one per residue 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: 1.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 5.510 Check model and map are aligned: 0.220 Set scattering table: 0.130 Process input model: 42.780 Find NCS groups from input model: 1.140 Set up NCS constraints: 0.110 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: 0.010 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.030 0.189 15258 Z= 1.992 Angle : 2.849 21.364 20736 Z= 1.714 Chirality : 0.155 0.960 2436 Planarity : 0.016 0.126 2676 Dihedral : 18.809 100.668 5700 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 21.28 Ramachandran Plot: Outliers : 2.89 % Allowed : 7.38 % Favored : 89.73 % Rotamer: Outliers : 11.82 % Allowed : 13.25 % Favored : 74.94 % Cbeta Deviations : 4.74 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 5.56 % Twisted General : 0.82 % 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: -4.53 (0.15), residues: 1938 helix: -3.57 (0.11), residues: 870 sheet: -0.64 (0.27), residues: 306 loop : -3.16 (0.18), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.016 0.006 HIS E 22 PHE 0.093 0.013 PHE E 286 TYR 0.083 0.015 TYR F 67 ARG 0.010 0.002 ARG C 203 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3876 Ramachandran restraints generated. 1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3876 Ramachandran restraints generated. 1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 697 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 190 poor density : 507 time to evaluate : 1.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 190 outliers final: 37 residues processed: 627 average time/residue: 0.2732 time to fit residues: 247.1463 Evaluate side-chains 293 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 256 time to evaluate : 1.826 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 4 residues processed: 37 average time/residue: 0.1365 time to fit residues: 11.8962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 0.8980 chunk 145 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 98 optimal weight: 0.9980 chunk 77 optimal weight: 0.7980 chunk 150 optimal weight: 0.8980 chunk 58 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 chunk 112 optimal weight: 0.9990 chunk 174 optimal weight: 0.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 HIS A 123 ASN A 136 HIS A 198 ASN B 92 HIS B 123 ASN B 132 GLN B 198 ASN B 212 ASN C 92 HIS C 198 ASN C 212 ASN D 92 HIS D 132 GLN D 182 GLN D 212 ASN E 92 HIS E 123 ASN E 132 GLN E 136 HIS E 198 ASN E 212 ASN F 92 HIS F 123 ASN ** F 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 198 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.3897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 15258 Z= 0.316 Angle : 0.895 8.524 20736 Z= 0.437 Chirality : 0.051 0.191 2436 Planarity : 0.007 0.068 2676 Dihedral : 9.649 101.149 2166 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 5.10 % Allowed : 20.27 % Favored : 74.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -2.22 (0.17), residues: 1938 helix: -1.28 (0.16), residues: 900 sheet: -0.62 (0.25), residues: 324 loop : -1.94 (0.21), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.002 HIS E 136 PHE 0.018 0.002 PHE D 221 TYR 0.015 0.002 TYR A 191 ARG 0.006 0.001 ARG F 118 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3876 Ramachandran restraints generated. 1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3876 Ramachandran restraints generated. 1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 357 time to evaluate : 1.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 82 outliers final: 33 residues processed: 414 average time/residue: 0.2457 time to fit residues: 157.7819 Evaluate side-chains 304 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 271 time to evaluate : 1.666 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 0 residues processed: 33 average time/residue: 0.1507 time to fit residues: 11.6706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 71.6085 > 50: distance: 20 - 38: 36.643 distance: 28 - 50: 25.813 distance: 32 - 54: 34.164 distance: 36 - 38: 34.200 distance: 38 - 39: 40.592 distance: 39 - 40: 68.421 distance: 39 - 42: 40.383 distance: 40 - 41: 59.318 distance: 40 - 50: 17.859 distance: 42 - 43: 43.542 distance: 43 - 44: 38.404 distance: 43 - 45: 40.739 distance: 44 - 46: 15.007 distance: 45 - 47: 12.902 distance: 46 - 48: 4.024 distance: 47 - 48: 3.260 distance: 48 - 49: 45.954 distance: 50 - 51: 45.205 distance: 51 - 52: 57.442 distance: 52 - 53: 68.810 distance: 52 - 54: 40.548 distance: 54 - 55: 60.239 distance: 55 - 56: 42.799 distance: 55 - 58: 42.102 distance: 56 - 57: 50.935 distance: 56 - 62: 18.570 distance: 58 - 59: 45.389 distance: 59 - 60: 59.313 distance: 59 - 61: 41.474 distance: 62 - 63: 42.462 distance: 63 - 64: 56.920 distance: 63 - 66: 56.007 distance: 64 - 65: 56.579 distance: 64 - 70: 69.955 distance: 66 - 67: 38.619 distance: 67 - 68: 68.622 distance: 67 - 69: 54.299 distance: 70 - 71: 39.644 distance: 71 - 72: 55.809 distance: 71 - 74: 39.219 distance: 72 - 73: 57.037 distance: 72 - 79: 57.388 distance: 74 - 75: 58.049 distance: 75 - 76: 39.017 distance: 77 - 78: 45.400 distance: 79 - 80: 48.343 distance: 80 - 81: 56.780 distance: 80 - 83: 30.732 distance: 81 - 82: 28.209 distance: 81 - 87: 40.441 distance: 83 - 84: 63.543 distance: 84 - 85: 70.404 distance: 84 - 86: 44.234 distance: 87 - 88: 51.737 distance: 88 - 89: 40.696 distance: 88 - 91: 50.896 distance: 89 - 90: 46.607 distance: 89 - 95: 44.048 distance: 91 - 92: 55.529 distance: 91 - 93: 44.969 distance: 92 - 94: 3.998 distance: 95 - 96: 39.434 distance: 96 - 97: 44.096 distance: 96 - 99: 43.259 distance: 97 - 98: 36.865 distance: 97 - 103: 7.437 distance: 99 - 100: 14.220 distance: 100 - 101: 58.909 distance: 100 - 102: 30.566 distance: 103 - 104: 50.656 distance: 104 - 105: 40.283 distance: 104 - 107: 38.961 distance: 105 - 106: 61.780 distance: 105 - 110: 57.463 distance: 107 - 108: 55.546 distance: 107 - 109: 68.686 distance: 110 - 111: 69.201 distance: 111 - 112: 54.066 distance: 111 - 114: 51.363 distance: 112 - 113: 41.044 distance: 112 - 118: 32.424 distance: 113 - 207: 31.818 distance: 114 - 115: 27.651 distance: 114 - 116: 8.050 distance: 115 - 117: 42.600