Starting phenix.real_space_refine on Mon Jun 23 07:06:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7v4h_31711/06_2025/7v4h_31711.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v4h_31711/06_2025/7v4h_31711.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7v4h_31711/06_2025/7v4h_31711.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v4h_31711/06_2025/7v4h_31711.map" model { file = "/net/cci-nas-00/data/ceres_data/7v4h_31711/06_2025/7v4h_31711.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v4h_31711/06_2025/7v4h_31711.cif" } resolution = 2.9 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= 0.018 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: 4 Type Number sf(0) Gaussians S 80 5.16 5 C 17300 2.51 5 N 4750 2.21 5 O 5210 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 27340 Number of models: 1 Model: "" Number of chains: 10 Chain: "J" Number of atoms: 2734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2734 Classifications: {'peptide': 352} Link IDs: {'PTRANS': 22, 'TRANS': 329} Chain: "A" Number of atoms: 2734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2734 Classifications: {'peptide': 352} Link IDs: {'PTRANS': 22, 'TRANS': 329} Chain: "B" Number of atoms: 2734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2734 Classifications: {'peptide': 352} Link IDs: {'PTRANS': 22, 'TRANS': 329} Chain: "C" Number of atoms: 2734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2734 Classifications: {'peptide': 352} Link IDs: {'PTRANS': 22, 'TRANS': 329} Chain: "D" Number of atoms: 2734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2734 Classifications: {'peptide': 352} Link IDs: {'PTRANS': 22, 'TRANS': 329} Chain: "E" Number of atoms: 2734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2734 Classifications: {'peptide': 352} Link IDs: {'PTRANS': 22, 'TRANS': 329} Chain: "F" Number of atoms: 2734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2734 Classifications: {'peptide': 352} Link IDs: {'PTRANS': 22, 'TRANS': 329} Chain: "G" Number of atoms: 2734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2734 Classifications: {'peptide': 352} Link IDs: {'PTRANS': 22, 'TRANS': 329} Chain: "H" Number of atoms: 2734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2734 Classifications: {'peptide': 352} Link IDs: {'PTRANS': 22, 'TRANS': 329} Chain: "I" Number of atoms: 2734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2734 Classifications: {'peptide': 352} Link IDs: {'PTRANS': 22, 'TRANS': 329} Time building chain proxies: 18.34, per 1000 atoms: 0.67 Number of scatterers: 27340 At special positions: 0 Unit cell: (134.33, 136.35, 107.06, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 80 16.00 O 5210 8.00 N 4750 7.00 C 17300 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 - 3.00 Amino acid : True - 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: 6.14 Conformation dependent library (CDL) restraints added in 3.4 seconds 7000 Ramachandran restraints generated. 3500 Oldfield, 0 Emsley, 3500 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6240 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 26 sheets defined 32.6% alpha, 26.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.23 Creating SS restraints... Processing helix chain 'J' and resid 46 through 50 removed outlier: 3.529A pdb=" N LEU J 50 " --> pdb=" O PRO J 47 " (cutoff:3.500A) Processing helix chain 'J' and resid 106 through 115 removed outlier: 3.591A pdb=" N ALA J 110 " --> pdb=" O LYS J 106 " (cutoff:3.500A) Processing helix chain 'J' and resid 116 through 123 Processing helix chain 'J' and resid 168 through 183 removed outlier: 3.567A pdb=" N VAL J 172 " --> pdb=" O GLY J 168 " (cutoff:3.500A) Processing helix chain 'J' and resid 208 through 229 removed outlier: 3.902A pdb=" N TYR J 219 " --> pdb=" O TRP J 215 " (cutoff:3.500A) Processing helix chain 'J' and resid 262 through 274 Processing helix chain 'J' and resid 276 through 284 Processing helix chain 'J' and resid 294 through 298 removed outlier: 3.579A pdb=" N GLU J 297 " --> pdb=" O GLY J 294 " (cutoff:3.500A) Processing helix chain 'J' and resid 319 through 324 Processing helix chain 'J' and resid 339 through 349 Processing helix chain 'A' and resid 46 through 50 Processing helix chain 'A' and resid 106 through 115 removed outlier: 3.698A pdb=" N ALA A 110 " --> pdb=" O LYS A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 122 Processing helix chain 'A' and resid 168 through 183 removed outlier: 3.682A pdb=" N VAL A 172 " --> pdb=" O GLY A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 229 removed outlier: 3.640A pdb=" N TYR A 219 " --> pdb=" O TRP A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 274 Processing helix chain 'A' and resid 276 through 284 Processing helix chain 'A' and resid 294 through 298 removed outlier: 3.535A pdb=" N GLU A 297 " --> pdb=" O GLY A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 324 Processing helix chain 'A' and resid 339 through 352 Processing helix chain 'B' and resid 46 through 50 Processing helix chain 'B' and resid 106 through 115 removed outlier: 3.661A pdb=" N ALA B 110 " --> pdb=" O LYS B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 123 removed outlier: 3.773A pdb=" N GLU B 123 " --> pdb=" O VAL B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 183 removed outlier: 3.545A pdb=" N VAL B 172 " --> pdb=" O GLY B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 229 removed outlier: 3.632A pdb=" N TYR B 219 " --> pdb=" O TRP B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 259 Processing helix chain 'B' and resid 262 through 274 Processing helix chain 'B' and resid 276 through 284 Processing helix chain 'B' and resid 294 through 298 removed outlier: 3.508A pdb=" N GLU B 297 " --> pdb=" O GLY B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 325 Processing helix chain 'B' and resid 339 through 353 Processing helix chain 'C' and resid 46 through 50 Processing helix chain 'C' and resid 106 through 115 removed outlier: 3.747A pdb=" N ALA C 110 " --> pdb=" O LYS C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 123 Processing helix chain 'C' and resid 168 through 183 removed outlier: 3.711A pdb=" N VAL C 172 " --> pdb=" O GLY C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 229 Processing helix chain 'C' and resid 254 through 259 Processing helix chain 'C' and resid 262 through 274 Processing helix chain 'C' and resid 276 through 284 Processing helix chain 'C' and resid 294 through 298 Processing helix chain 'C' and resid 319 through 324 Processing helix chain 'C' and resid 339 through 353 removed outlier: 3.688A pdb=" N THR C 351 " --> pdb=" O ILE C 347 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU C 353 " --> pdb=" O ASP C 349 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 50 Processing helix chain 'D' and resid 106 through 115 removed outlier: 3.691A pdb=" N ALA D 110 " --> pdb=" O LYS D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 116 through 123 removed outlier: 3.772A pdb=" N GLU D 123 " --> pdb=" O VAL D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 183 removed outlier: 3.544A pdb=" N VAL D 172 " --> pdb=" O GLY D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 229 removed outlier: 4.317A pdb=" N GLY D 211 " --> pdb=" O GLY D 207 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N TYR D 219 " --> pdb=" O TRP D 215 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 259 removed outlier: 3.600A pdb=" N ASN D 259 " --> pdb=" O SER D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 262 through 274 Processing helix chain 'D' and resid 276 through 284 Processing helix chain 'D' and resid 294 through 298 removed outlier: 3.600A pdb=" N GLU D 297 " --> pdb=" O GLY D 294 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 325 removed outlier: 3.565A pdb=" N GLU D 322 " --> pdb=" O GLY D 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 339 through 352 Processing helix chain 'E' and resid 11 through 15 removed outlier: 3.941A pdb=" N ASP E 14 " --> pdb=" O ASN E 11 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 50 removed outlier: 3.673A pdb=" N LEU E 50 " --> pdb=" O PRO E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 106 through 115 Processing helix chain 'E' and resid 116 through 123 Processing helix chain 'E' and resid 168 through 183 removed outlier: 3.508A pdb=" N VAL E 172 " --> pdb=" O GLY E 168 " (cutoff:3.500A) Processing helix chain 'E' and resid 207 through 229 removed outlier: 4.138A pdb=" N GLY E 211 " --> pdb=" O GLY E 207 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE E 227 " --> pdb=" O ARG E 223 " (cutoff:3.500A) Processing helix chain 'E' and resid 261 through 274 removed outlier: 4.082A pdb=" N VAL E 265 " --> pdb=" O GLY E 261 " (cutoff:3.500A) Processing helix chain 'E' and resid 276 through 284 Processing helix chain 'E' and resid 318 through 325 Processing helix chain 'E' and resid 339 through 352 Processing helix chain 'F' and resid 11 through 15 removed outlier: 3.889A pdb=" N ASP F 14 " --> pdb=" O ASN F 11 " (cutoff:3.500A) Processing helix chain 'F' and resid 46 through 50 removed outlier: 3.634A pdb=" N LEU F 50 " --> pdb=" O PRO F 47 " (cutoff:3.500A) Processing helix chain 'F' and resid 106 through 115 Processing helix chain 'F' and resid 116 through 123 Processing helix chain 'F' and resid 168 through 183 Processing helix chain 'F' and resid 207 through 229 removed outlier: 4.177A pdb=" N GLY F 211 " --> pdb=" O GLY F 207 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N TRP F 215 " --> pdb=" O GLY F 211 " (cutoff:3.500A) Processing helix chain 'F' and resid 254 through 259 Processing helix chain 'F' and resid 261 through 274 removed outlier: 4.137A pdb=" N VAL F 265 " --> pdb=" O GLY F 261 " (cutoff:3.500A) Processing helix chain 'F' and resid 276 through 283 Processing helix chain 'F' and resid 287 through 292 removed outlier: 3.525A pdb=" N ARG F 291 " --> pdb=" O GLY F 287 " (cutoff:3.500A) Processing helix chain 'F' and resid 318 through 325 Processing helix chain 'F' and resid 339 through 352 Processing helix chain 'G' and resid 11 through 15 removed outlier: 3.896A pdb=" N ASP G 14 " --> pdb=" O ASN G 11 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 50 removed outlier: 3.569A pdb=" N LEU G 50 " --> pdb=" O PRO G 47 " (cutoff:3.500A) Processing helix chain 'G' and resid 106 through 115 Processing helix chain 'G' and resid 116 through 123 Processing helix chain 'G' and resid 168 through 183 Processing helix chain 'G' and resid 207 through 229 removed outlier: 4.134A pdb=" N GLY G 211 " --> pdb=" O GLY G 207 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLU G 226 " --> pdb=" O GLU G 222 " (cutoff:3.500A) Processing helix chain 'G' and resid 254 through 259 Processing helix chain 'G' and resid 261 through 274 removed outlier: 4.127A pdb=" N VAL G 265 " --> pdb=" O GLY G 261 " (cutoff:3.500A) Processing helix chain 'G' and resid 276 through 283 Processing helix chain 'G' and resid 287 through 292 removed outlier: 3.639A pdb=" N ARG G 291 " --> pdb=" O GLY G 287 " (cutoff:3.500A) Processing helix chain 'G' and resid 318 through 325 Processing helix chain 'G' and resid 339 through 352 Processing helix chain 'H' and resid 11 through 15 removed outlier: 3.887A pdb=" N ASP H 14 " --> pdb=" O ASN H 11 " (cutoff:3.500A) Processing helix chain 'H' and resid 46 through 50 removed outlier: 3.688A pdb=" N LEU H 50 " --> pdb=" O PRO H 47 " (cutoff:3.500A) Processing helix chain 'H' and resid 106 through 115 Processing helix chain 'H' and resid 116 through 122 Processing helix chain 'H' and resid 168 through 183 removed outlier: 3.532A pdb=" N VAL H 172 " --> pdb=" O GLY H 168 " (cutoff:3.500A) Processing helix chain 'H' and resid 207 through 229 removed outlier: 4.082A pdb=" N GLY H 211 " --> pdb=" O GLY H 207 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N TRP H 215 " --> pdb=" O GLY H 211 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE H 227 " --> pdb=" O ARG H 223 " (cutoff:3.500A) Processing helix chain 'H' and resid 261 through 274 removed outlier: 3.991A pdb=" N VAL H 265 " --> pdb=" O GLY H 261 " (cutoff:3.500A) Processing helix chain 'H' and resid 276 through 284 Processing helix chain 'H' and resid 318 through 325 removed outlier: 3.658A pdb=" N GLU H 322 " --> pdb=" O GLY H 318 " (cutoff:3.500A) Processing helix chain 'H' and resid 339 through 352 Processing helix chain 'I' and resid 46 through 50 removed outlier: 3.664A pdb=" N LEU I 50 " --> pdb=" O PRO I 47 " (cutoff:3.500A) Processing helix chain 'I' and resid 106 through 115 Processing helix chain 'I' and resid 116 through 123 Processing helix chain 'I' and resid 168 through 183 removed outlier: 3.526A pdb=" N VAL I 172 " --> pdb=" O GLY I 168 " (cutoff:3.500A) Processing helix chain 'I' and resid 207 through 229 removed outlier: 4.134A pdb=" N GLY I 211 " --> pdb=" O GLY I 207 " (cutoff:3.500A) Processing helix chain 'I' and resid 254 through 259 Processing helix chain 'I' and resid 262 through 274 removed outlier: 3.888A pdb=" N ILE I 266 " --> pdb=" O GLY I 262 " (cutoff:3.500A) Processing helix chain 'I' and resid 276 through 283 Processing helix chain 'I' and resid 287 through 292 removed outlier: 3.641A pdb=" N ARG I 291 " --> pdb=" O GLY I 287 " (cutoff:3.500A) Processing helix chain 'I' and resid 318 through 325 Processing helix chain 'I' and resid 339 through 352 Processing sheet with id=AA1, first strand: chain 'J' and resid 33 through 40 removed outlier: 6.445A pdb=" N ILE J 20 " --> pdb=" O ILE J 88 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N VAL J 90 " --> pdb=" O ILE J 20 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N GLU J 22 " --> pdb=" O VAL J 90 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N CYS J 92 " --> pdb=" O GLU J 22 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ILE J 24 " --> pdb=" O CYS J 92 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N THR J 94 " --> pdb=" O ILE J 24 " (cutoff:3.500A) removed outlier: 8.762A pdb=" N ILE J 26 " --> pdb=" O THR J 94 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N LEU J 89 " --> pdb=" O ILE J 77 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ILE J 77 " --> pdb=" O LEU J 89 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ILE J 91 " --> pdb=" O GLN J 75 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N TRP J 53 " --> pdb=" O ILE J 72 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'J' and resid 186 through 191 removed outlier: 5.684A pdb=" N GLN J 201 " --> pdb=" O SER J 187 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N ILE J 189 " --> pdb=" O GLU J 199 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N GLU J 199 " --> pdb=" O ILE J 189 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N GLY J 191 " --> pdb=" O GLN J 197 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N GLN J 197 " --> pdb=" O GLY J 191 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N TYR J 126 " --> pdb=" O PRO J 204 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'J' and resid 186 through 191 removed outlier: 5.684A pdb=" N GLN J 201 " --> pdb=" O SER J 187 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N ILE J 189 " --> pdb=" O GLU J 199 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N GLU J 199 " --> pdb=" O ILE J 189 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N GLY J 191 " --> pdb=" O GLN J 197 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N GLN J 197 " --> pdb=" O GLY J 191 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N TYR J 126 " --> pdb=" O PRO J 204 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLY J 307 " --> pdb=" O VAL J 315 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 33 through 40 removed outlier: 6.543A pdb=" N ILE A 20 " --> pdb=" O ILE A 88 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N VAL A 90 " --> pdb=" O ILE A 20 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N GLU A 22 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N CYS A 92 " --> pdb=" O GLU A 22 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ILE A 24 " --> pdb=" O CYS A 92 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N THR A 94 " --> pdb=" O ILE A 24 " (cutoff:3.500A) removed outlier: 8.787A pdb=" N ILE A 26 " --> pdb=" O THR A 94 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N LEU A 89 " --> pdb=" O ILE A 77 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ILE A 77 " --> pdb=" O LEU A 89 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ILE A 91 " --> pdb=" O GLN A 75 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 186 through 191 removed outlier: 5.919A pdb=" N GLN A 201 " --> pdb=" O SER A 187 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N ILE A 189 " --> pdb=" O GLU A 199 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N GLU A 199 " --> pdb=" O ILE A 189 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N GLY A 191 " --> pdb=" O GLN A 197 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N GLN A 197 " --> pdb=" O GLY A 191 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N TYR A 126 " --> pdb=" O PRO A 204 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N VAL A 206 " --> pdb=" O THR A 124 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N THR A 124 " --> pdb=" O VAL A 206 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 186 through 191 removed outlier: 5.919A pdb=" N GLN A 201 " --> pdb=" O SER A 187 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N ILE A 189 " --> pdb=" O GLU A 199 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N GLU A 199 " --> pdb=" O ILE A 189 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N GLY A 191 " --> pdb=" O GLN A 197 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N GLN A 197 " --> pdb=" O GLY A 191 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N TYR A 126 " --> pdb=" O PRO A 204 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N VAL A 206 " --> pdb=" O THR A 124 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N THR A 124 " --> pdb=" O VAL A 206 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLY A 307 " --> pdb=" O VAL A 315 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 33 through 40 removed outlier: 6.458A pdb=" N ILE B 20 " --> pdb=" O ILE B 88 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N VAL B 90 " --> pdb=" O ILE B 20 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N GLU B 22 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N CYS B 92 " --> pdb=" O GLU B 22 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ILE B 24 " --> pdb=" O CYS B 92 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N THR B 94 " --> pdb=" O ILE B 24 " (cutoff:3.500A) removed outlier: 8.773A pdb=" N ILE B 26 " --> pdb=" O THR B 94 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N LEU B 89 " --> pdb=" O ILE B 77 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N ILE B 77 " --> pdb=" O LEU B 89 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ILE B 91 " --> pdb=" O GLN B 75 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 186 through 191 removed outlier: 5.800A pdb=" N GLN B 201 " --> pdb=" O SER B 187 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N ILE B 189 " --> pdb=" O GLU B 199 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N GLU B 199 " --> pdb=" O ILE B 189 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N GLY B 191 " --> pdb=" O GLN B 197 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N GLN B 197 " --> pdb=" O GLY B 191 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N TYR B 126 " --> pdb=" O PRO B 204 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 186 through 191 removed outlier: 5.800A pdb=" N GLN B 201 " --> pdb=" O SER B 187 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N ILE B 189 " --> pdb=" O GLU B 199 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N GLU B 199 " --> pdb=" O ILE B 189 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N GLY B 191 " --> pdb=" O GLN B 197 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N GLN B 197 " --> pdb=" O GLY B 191 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N TYR B 126 " --> pdb=" O PRO B 204 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY B 307 " --> pdb=" O VAL B 315 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 33 through 40 removed outlier: 6.456A pdb=" N ILE C 20 " --> pdb=" O ILE C 88 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N VAL C 90 " --> pdb=" O ILE C 20 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N GLU C 22 " --> pdb=" O VAL C 90 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N CYS C 92 " --> pdb=" O GLU C 22 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ILE C 24 " --> pdb=" O CYS C 92 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N THR C 94 " --> pdb=" O ILE C 24 " (cutoff:3.500A) removed outlier: 8.799A pdb=" N ILE C 26 " --> pdb=" O THR C 94 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N LEU C 89 " --> pdb=" O ILE C 77 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ILE C 77 " --> pdb=" O LEU C 89 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ILE C 91 " --> pdb=" O GLN C 75 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 186 through 191 removed outlier: 5.688A pdb=" N GLN C 201 " --> pdb=" O SER C 187 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N ILE C 189 " --> pdb=" O GLU C 199 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N GLU C 199 " --> pdb=" O ILE C 189 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N GLY C 191 " --> pdb=" O GLN C 197 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N GLN C 197 " --> pdb=" O GLY C 191 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N TYR C 126 " --> pdb=" O PRO C 204 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 186 through 191 removed outlier: 5.688A pdb=" N GLN C 201 " --> pdb=" O SER C 187 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N ILE C 189 " --> pdb=" O GLU C 199 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N GLU C 199 " --> pdb=" O ILE C 189 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N GLY C 191 " --> pdb=" O GLN C 197 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N GLN C 197 " --> pdb=" O GLY C 191 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N TYR C 126 " --> pdb=" O PRO C 204 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY C 307 " --> pdb=" O VAL C 315 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 33 through 40 removed outlier: 6.497A pdb=" N ILE D 20 " --> pdb=" O ILE D 88 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N VAL D 90 " --> pdb=" O ILE D 20 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N GLU D 22 " --> pdb=" O VAL D 90 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N CYS D 92 " --> pdb=" O GLU D 22 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ILE D 24 " --> pdb=" O CYS D 92 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N THR D 94 " --> pdb=" O ILE D 24 " (cutoff:3.500A) removed outlier: 8.784A pdb=" N ILE D 26 " --> pdb=" O THR D 94 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N LEU D 89 " --> pdb=" O ILE D 77 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ILE D 77 " --> pdb=" O LEU D 89 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ILE D 91 " --> pdb=" O GLN D 75 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 186 through 191 removed outlier: 5.865A pdb=" N GLN D 201 " --> pdb=" O SER D 187 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N ILE D 189 " --> pdb=" O GLU D 199 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N GLU D 199 " --> pdb=" O ILE D 189 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N GLY D 191 " --> pdb=" O GLN D 197 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N GLN D 197 " --> pdb=" O GLY D 191 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N TYR D 126 " --> pdb=" O PRO D 204 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 186 through 191 removed outlier: 5.865A pdb=" N GLN D 201 " --> pdb=" O SER D 187 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N ILE D 189 " --> pdb=" O GLU D 199 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N GLU D 199 " --> pdb=" O ILE D 189 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N GLY D 191 " --> pdb=" O GLN D 197 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N GLN D 197 " --> pdb=" O GLY D 191 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N TYR D 126 " --> pdb=" O PRO D 204 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 33 through 40 removed outlier: 6.333A pdb=" N ILE E 20 " --> pdb=" O ILE E 88 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N VAL E 90 " --> pdb=" O ILE E 20 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N GLU E 22 " --> pdb=" O VAL E 90 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N CYS E 92 " --> pdb=" O GLU E 22 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N ILE E 24 " --> pdb=" O CYS E 92 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N THR E 94 " --> pdb=" O ILE E 24 " (cutoff:3.500A) removed outlier: 8.445A pdb=" N ILE E 26 " --> pdb=" O THR E 94 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N LEU E 89 " --> pdb=" O ILE E 77 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ILE E 77 " --> pdb=" O LEU E 89 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ILE E 91 " --> pdb=" O GLN E 75 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 230 through 233 Processing sheet with id=AB9, first strand: chain 'E' and resid 230 through 233 removed outlier: 6.391A pdb=" N TYR E 126 " --> pdb=" O PRO E 204 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N GLN E 197 " --> pdb=" O GLY E 191 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N GLY E 191 " --> pdb=" O GLN E 197 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N GLU E 199 " --> pdb=" O ILE E 189 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N ILE E 189 " --> pdb=" O GLU E 199 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N GLN E 201 " --> pdb=" O SER E 187 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N SER E 187 " --> pdb=" O THR G 39 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N THR G 39 " --> pdb=" O SER E 187 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N GLY E 191 " --> pdb=" O SER G 35 " (cutoff:3.500A) removed outlier: 8.201A pdb=" N SER G 35 " --> pdb=" O GLY E 191 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ILE G 20 " --> pdb=" O ILE G 88 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N VAL G 90 " --> pdb=" O ILE G 20 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N GLU G 22 " --> pdb=" O VAL G 90 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N CYS G 92 " --> pdb=" O GLU G 22 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N ILE G 24 " --> pdb=" O CYS G 92 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N THR G 94 " --> pdb=" O ILE G 24 " (cutoff:3.500A) removed outlier: 8.526A pdb=" N ILE G 26 " --> pdb=" O THR G 94 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N LEU G 89 " --> pdb=" O ILE G 77 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ILE G 77 " --> pdb=" O LEU G 89 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ILE G 91 " --> pdb=" O GLN G 75 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 53 through 56 removed outlier: 6.526A pdb=" N ILE F 91 " --> pdb=" O GLN F 75 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N ILE F 77 " --> pdb=" O LEU F 89 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LEU F 89 " --> pdb=" O ILE F 77 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ILE F 20 " --> pdb=" O ILE F 88 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N VAL F 90 " --> pdb=" O ILE F 20 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N GLU F 22 " --> pdb=" O VAL F 90 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N CYS F 92 " --> pdb=" O GLU F 22 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N ILE F 24 " --> pdb=" O CYS F 92 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N THR F 94 " --> pdb=" O ILE F 24 " (cutoff:3.500A) removed outlier: 8.424A pdb=" N ILE F 26 " --> pdb=" O THR F 94 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N SER F 35 " --> pdb=" O GLY G 191 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N GLY G 191 " --> pdb=" O SER F 35 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLY G 188 " --> pdb=" O GLN G 201 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N TYR G 126 " --> pdb=" O PRO G 204 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 53 through 56 removed outlier: 6.526A pdb=" N ILE F 91 " --> pdb=" O GLN F 75 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N ILE F 77 " --> pdb=" O LEU F 89 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LEU F 89 " --> pdb=" O ILE F 77 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ILE F 20 " --> pdb=" O ILE F 88 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N VAL F 90 " --> pdb=" O ILE F 20 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N GLU F 22 " --> pdb=" O VAL F 90 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N CYS F 92 " --> pdb=" O GLU F 22 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N ILE F 24 " --> pdb=" O CYS F 92 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N THR F 94 " --> pdb=" O ILE F 24 " (cutoff:3.500A) removed outlier: 8.424A pdb=" N ILE F 26 " --> pdb=" O THR F 94 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N SER F 35 " --> pdb=" O GLY G 191 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N GLY G 191 " --> pdb=" O SER F 35 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLY G 188 " --> pdb=" O GLN G 201 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N TYR G 126 " --> pdb=" O PRO G 204 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 230 through 233 Processing sheet with id=AC4, first strand: chain 'F' and resid 230 through 233 removed outlier: 6.288A pdb=" N TYR F 126 " --> pdb=" O PRO F 204 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N GLY F 188 " --> pdb=" O GLN F 201 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N GLY F 191 " --> pdb=" O SER H 35 " (cutoff:3.500A) removed outlier: 8.230A pdb=" N SER H 35 " --> pdb=" O GLY F 191 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ILE H 20 " --> pdb=" O ILE H 88 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N VAL H 90 " --> pdb=" O ILE H 20 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N GLU H 22 " --> pdb=" O VAL H 90 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N CYS H 92 " --> pdb=" O GLU H 22 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ILE H 24 " --> pdb=" O CYS H 92 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N THR H 94 " --> pdb=" O ILE H 24 " (cutoff:3.500A) removed outlier: 8.577A pdb=" N ILE H 26 " --> pdb=" O THR H 94 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N LEU H 89 " --> pdb=" O ILE H 77 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ILE H 77 " --> pdb=" O LEU H 89 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ILE H 91 " --> pdb=" O GLN H 75 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 231 through 233 Processing sheet with id=AC6, first strand: chain 'H' and resid 231 through 233 removed outlier: 6.277A pdb=" N TYR H 126 " --> pdb=" O PRO H 204 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLY H 188 " --> pdb=" O GLN H 201 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N GLY H 191 " --> pdb=" O SER I 35 " (cutoff:3.500A) removed outlier: 8.221A pdb=" N SER I 35 " --> pdb=" O GLY H 191 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N ILE I 20 " --> pdb=" O ILE I 88 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N VAL I 90 " --> pdb=" O ILE I 20 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N GLU I 22 " --> pdb=" O VAL I 90 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N CYS I 92 " --> pdb=" O GLU I 22 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N ILE I 24 " --> pdb=" O CYS I 92 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N THR I 94 " --> pdb=" O ILE I 24 " (cutoff:3.500A) removed outlier: 8.462A pdb=" N ILE I 26 " --> pdb=" O THR I 94 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N LEU I 89 " --> pdb=" O ILE I 77 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ILE I 77 " --> pdb=" O LEU I 89 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ILE I 91 " --> pdb=" O GLN I 75 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 186 through 191 removed outlier: 5.922A pdb=" N GLN I 201 " --> pdb=" O SER I 187 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N ILE I 189 " --> pdb=" O GLU I 199 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N GLU I 199 " --> pdb=" O ILE I 189 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N GLY I 191 " --> pdb=" O GLN I 197 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N GLN I 197 " --> pdb=" O GLY I 191 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N TYR I 126 " --> pdb=" O PRO I 204 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 186 through 191 removed outlier: 5.922A pdb=" N GLN I 201 " --> pdb=" O SER I 187 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N ILE I 189 " --> pdb=" O GLU I 199 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N GLU I 199 " --> pdb=" O ILE I 189 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N GLY I 191 " --> pdb=" O GLN I 197 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N GLN I 197 " --> pdb=" O GLY I 191 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N TYR I 126 " --> pdb=" O PRO I 204 " (cutoff:3.500A) 1180 hydrogen bonds defined for protein. 3303 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: 10.79 Time building geometry restraints manager: 7.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9053 1.34 - 1.45: 4195 1.45 - 1.57: 14692 1.57 - 1.69: 0 1.69 - 1.81: 130 Bond restraints: 28070 Sorted by residual: bond pdb=" CB TRP J 53 " pdb=" CG TRP J 53 " ideal model delta sigma weight residual 1.498 1.440 0.058 3.10e-02 1.04e+03 3.54e+00 bond pdb=" C GLY D 99 " pdb=" N GLU D 100 " ideal model delta sigma weight residual 1.331 1.295 0.036 2.07e-02 2.33e+03 2.97e+00 bond pdb=" CB TRP I 53 " pdb=" CG TRP I 53 " ideal model delta sigma weight residual 1.498 1.448 0.050 3.10e-02 1.04e+03 2.58e+00 bond pdb=" CB GLU E 199 " pdb=" CG GLU E 199 " ideal model delta sigma weight residual 1.520 1.473 0.047 3.00e-02 1.11e+03 2.41e+00 bond pdb=" CB TRP F 53 " pdb=" CG TRP F 53 " ideal model delta sigma weight residual 1.498 1.451 0.047 3.10e-02 1.04e+03 2.34e+00 ... (remaining 28065 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.62: 37237 1.62 - 3.23: 769 3.23 - 4.85: 153 4.85 - 6.46: 17 6.46 - 8.08: 4 Bond angle restraints: 38180 Sorted by residual: angle pdb=" CA TRP D 53 " pdb=" CB TRP D 53 " pdb=" CG TRP D 53 " ideal model delta sigma weight residual 113.60 120.31 -6.71 1.90e+00 2.77e-01 1.25e+01 angle pdb=" CA TRP C 53 " pdb=" CB TRP C 53 " pdb=" CG TRP C 53 " ideal model delta sigma weight residual 113.60 120.30 -6.70 1.90e+00 2.77e-01 1.24e+01 angle pdb=" N GLY E 188 " pdb=" CA GLY E 188 " pdb=" C GLY E 188 " ideal model delta sigma weight residual 110.96 114.97 -4.01 1.19e+00 7.06e-01 1.13e+01 angle pdb=" N TRP H 53 " pdb=" CA TRP H 53 " pdb=" C TRP H 53 " ideal model delta sigma weight residual 109.18 113.84 -4.66 1.42e+00 4.96e-01 1.08e+01 angle pdb=" N TRP I 53 " pdb=" CA TRP I 53 " pdb=" C TRP I 53 " ideal model delta sigma weight residual 109.18 113.74 -4.56 1.42e+00 4.96e-01 1.03e+01 ... (remaining 38175 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.48: 14934 17.48 - 34.97: 1213 34.97 - 52.45: 238 52.45 - 69.93: 37 69.93 - 87.42: 28 Dihedral angle restraints: 16450 sinusoidal: 6540 harmonic: 9910 Sorted by residual: dihedral pdb=" CA MET C 338 " pdb=" C MET C 338 " pdb=" N ASP C 339 " pdb=" CA ASP C 339 " ideal model delta harmonic sigma weight residual 180.00 158.28 21.72 0 5.00e+00 4.00e-02 1.89e+01 dihedral pdb=" CA MET J 338 " pdb=" C MET J 338 " pdb=" N ASP J 339 " pdb=" CA ASP J 339 " ideal model delta harmonic sigma weight residual 180.00 158.32 21.68 0 5.00e+00 4.00e-02 1.88e+01 dihedral pdb=" CA GLU E 199 " pdb=" C GLU E 199 " pdb=" N PHE E 200 " pdb=" CA PHE E 200 " ideal model delta harmonic sigma weight residual 180.00 158.32 21.68 0 5.00e+00 4.00e-02 1.88e+01 ... (remaining 16447 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 2347 0.034 - 0.067: 1109 0.067 - 0.101: 327 0.101 - 0.135: 190 0.135 - 0.169: 17 Chirality restraints: 3990 Sorted by residual: chirality pdb=" CA ILE H 139 " pdb=" N ILE H 139 " pdb=" C ILE H 139 " pdb=" CB ILE H 139 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.11e-01 chirality pdb=" CA TRP I 53 " pdb=" N TRP I 53 " pdb=" C TRP I 53 " pdb=" CB TRP I 53 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.14e-01 chirality pdb=" CA VAL B 230 " pdb=" N VAL B 230 " pdb=" C VAL B 230 " pdb=" CB VAL B 230 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.49e-01 ... (remaining 3987 not shown) Planarity restraints: 5030 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 53 " -0.043 2.00e-02 2.50e+03 2.99e-02 2.23e+01 pdb=" CG TRP D 53 " 0.079 2.00e-02 2.50e+03 pdb=" CD1 TRP D 53 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP D 53 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP D 53 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP D 53 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP D 53 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 53 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 53 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP D 53 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP I 53 " -0.033 2.00e-02 2.50e+03 1.84e-02 8.47e+00 pdb=" CG TRP I 53 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 TRP I 53 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TRP I 53 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP I 53 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP I 53 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP I 53 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP I 53 " -0.010 2.00e-02 2.50e+03 pdb=" CZ3 TRP I 53 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP I 53 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP H 53 " 0.031 2.00e-02 2.50e+03 1.74e-02 7.58e+00 pdb=" CG TRP H 53 " -0.043 2.00e-02 2.50e+03 pdb=" CD1 TRP H 53 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TRP H 53 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP H 53 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP H 53 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP H 53 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 53 " 0.009 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 53 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP H 53 " 0.002 2.00e-02 2.50e+03 ... (remaining 5027 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 291 2.65 - 3.21: 24342 3.21 - 3.77: 41309 3.77 - 4.34: 60277 4.34 - 4.90: 100624 Nonbonded interactions: 226843 Sorted by model distance: nonbonded pdb=" ND2 ASN A 190 " pdb=" OE2 GLU A 199 " model vdw 2.083 3.120 nonbonded pdb=" OD2 ASP C 46 " pdb=" OG SER C 48 " model vdw 2.149 3.040 nonbonded pdb=" NH2 ARG E 84 " pdb=" O ASP G 6 " model vdw 2.168 3.120 nonbonded pdb=" O GLY H 318 " pdb=" OG1 THR H 321 " model vdw 2.169 3.040 nonbonded pdb=" O THR I 293 " pdb=" OG1 THR I 298 " model vdw 2.170 3.040 ... (remaining 226838 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } 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: 11.920 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: 0.030 Extract box with map and model: 1.420 Check model and map are aligned: 0.200 Set scattering table: 0.250 Process input model: 63.470 Find NCS groups from input model: 1.030 Set up NCS constraints: 0.190 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:14.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 93.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 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 : 0.004 0.058 28070 Z= 0.161 Angle : 0.589 8.080 38180 Z= 0.316 Chirality : 0.046 0.169 3990 Planarity : 0.005 0.063 5030 Dihedral : 13.651 87.417 10210 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % 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: -1.11 (0.14), residues: 3500 helix: -0.42 (0.15), residues: 1110 sheet: -0.56 (0.19), residues: 790 loop : -0.92 (0.16), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.079 0.002 TRP D 53 HIS 0.003 0.001 HIS E 280 PHE 0.016 0.001 PHE G 200 TYR 0.024 0.002 TYR A 176 ARG 0.006 0.000 ARG H 38 Details of bonding type rmsd hydrogen bonds : bond 0.16142 ( 1098) hydrogen bonds : angle 7.32515 ( 3303) covalent geometry : bond 0.00383 (28070) covalent geometry : angle 0.58856 (38180) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7000 Ramachandran restraints generated. 3500 Oldfield, 0 Emsley, 3500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7000 Ramachandran restraints generated. 3500 Oldfield, 0 Emsley, 3500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 268 time to evaluate : 2.989 Fit side-chains REVERT: D 56 ASP cc_start: 0.7882 (t70) cc_final: 0.7617 (t70) REVERT: I 199 GLU cc_start: 0.7787 (tt0) cc_final: 0.7511 (tt0) outliers start: 0 outliers final: 1 residues processed: 268 average time/residue: 1.3778 time to fit residues: 432.6088 Evaluate side-chains 193 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 192 time to evaluate : 3.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 338 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 295 optimal weight: 0.6980 chunk 265 optimal weight: 10.0000 chunk 147 optimal weight: 1.9990 chunk 90 optimal weight: 6.9990 chunk 178 optimal weight: 3.9990 chunk 141 optimal weight: 7.9990 chunk 274 optimal weight: 0.6980 chunk 106 optimal weight: 6.9990 chunk 166 optimal weight: 6.9990 chunk 204 optimal weight: 30.0000 chunk 317 optimal weight: 3.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 75 GLN ** J 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 87 ASN ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 ASN ** C 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 185 ASN ** D 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 9 ASN E 140 GLN F 9 ASN F 140 GLN G 9 ASN G 140 GLN H 9 ASN H 136 GLN I 9 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.184527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.125837 restraints weight = 29379.203| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 2.19 r_work: 0.3249 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.0905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 28070 Z= 0.169 Angle : 0.590 8.706 38180 Z= 0.310 Chirality : 0.047 0.156 3990 Planarity : 0.005 0.063 5030 Dihedral : 4.738 28.611 3863 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 1.51 % Allowed : 6.69 % Favored : 91.80 % 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: -0.69 (0.14), residues: 3500 helix: 0.41 (0.15), residues: 1130 sheet: -0.44 (0.19), residues: 720 loop : -1.01 (0.15), residues: 1650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP D 53 HIS 0.003 0.001 HIS I 280 PHE 0.017 0.001 PHE G 200 TYR 0.026 0.002 TYR A 176 ARG 0.005 0.000 ARG H 316 Details of bonding type rmsd hydrogen bonds : bond 0.04967 ( 1098) hydrogen bonds : angle 5.16604 ( 3303) covalent geometry : bond 0.00416 (28070) covalent geometry : angle 0.58986 (38180) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7000 Ramachandran restraints generated. 3500 Oldfield, 0 Emsley, 3500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7000 Ramachandran restraints generated. 3500 Oldfield, 0 Emsley, 3500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 215 time to evaluate : 2.981 Fit side-chains REVERT: J 22 GLU cc_start: 0.8347 (tp30) cc_final: 0.8139 (tp30) REVERT: J 53 TRP cc_start: 0.8560 (OUTLIER) cc_final: 0.6902 (m-10) REVERT: J 136 GLN cc_start: 0.8910 (OUTLIER) cc_final: 0.7979 (mt0) REVERT: B 136 GLN cc_start: 0.9003 (OUTLIER) cc_final: 0.8302 (mt0) REVERT: C 129 GLU cc_start: 0.8358 (mt-10) cc_final: 0.8120 (mt-10) REVERT: F 49 LYS cc_start: 0.7683 (pttm) cc_final: 0.7395 (pttp) REVERT: G 49 LYS cc_start: 0.7631 (pttm) cc_final: 0.7263 (pttp) REVERT: H 54 ASN cc_start: 0.8020 (p0) cc_final: 0.7669 (p0) REVERT: H 140 GLN cc_start: 0.8632 (mm-40) cc_final: 0.8422 (mm110) REVERT: I 84 ARG cc_start: 0.8382 (OUTLIER) cc_final: 0.7113 (mpt-90) outliers start: 43 outliers final: 22 residues processed: 239 average time/residue: 1.2941 time to fit residues: 363.7225 Evaluate side-chains 213 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 187 time to evaluate : 2.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 53 TRP Chi-restraints excluded: chain J residue 136 GLN Chi-restraints excluded: chain J residue 170 ASP Chi-restraints excluded: chain A residue 53 TRP Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain B residue 53 TRP Chi-restraints excluded: chain B residue 136 GLN Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 350 THR Chi-restraints excluded: chain C residue 170 ASP Chi-restraints excluded: chain C residue 338 MET Chi-restraints excluded: chain D residue 170 ASP Chi-restraints excluded: chain D residue 338 MET Chi-restraints excluded: chain E residue 84 ARG Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain E residue 233 SER Chi-restraints excluded: chain F residue 100 GLU Chi-restraints excluded: chain F residue 104 THR Chi-restraints excluded: chain F residue 233 SER Chi-restraints excluded: chain G residue 104 THR Chi-restraints excluded: chain H residue 84 ARG Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain H residue 233 SER Chi-restraints excluded: chain I residue 84 ARG Chi-restraints excluded: chain I residue 104 THR Chi-restraints excluded: chain I residue 314 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 103 optimal weight: 8.9990 chunk 249 optimal weight: 4.9990 chunk 263 optimal weight: 0.7980 chunk 278 optimal weight: 9.9990 chunk 19 optimal weight: 5.9990 chunk 93 optimal weight: 0.9980 chunk 192 optimal weight: 1.9990 chunk 66 optimal weight: 20.0000 chunk 61 optimal weight: 5.9990 chunk 95 optimal weight: 8.9990 chunk 153 optimal weight: 4.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 9 ASN E 140 GLN E 280 HIS F 9 ASN F 105 ASN F 140 GLN G 9 ASN G 105 ASN G 108 HIS G 140 GLN H 9 ASN H 105 ASN I 9 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.182837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.123246 restraints weight = 29499.988| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 2.22 r_work: 0.3248 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.1150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 28070 Z= 0.187 Angle : 0.592 9.243 38180 Z= 0.309 Chirality : 0.047 0.156 3990 Planarity : 0.005 0.066 5030 Dihedral : 4.759 24.200 3860 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 1.73 % Allowed : 9.82 % Favored : 88.45 % 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: -0.67 (0.14), residues: 3500 helix: 0.53 (0.15), residues: 1130 sheet: -0.51 (0.19), residues: 720 loop : -1.04 (0.15), residues: 1650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP D 53 HIS 0.004 0.001 HIS E 280 PHE 0.018 0.002 PHE G 200 TYR 0.027 0.002 TYR A 176 ARG 0.005 0.000 ARG H 316 Details of bonding type rmsd hydrogen bonds : bond 0.04961 ( 1098) hydrogen bonds : angle 4.98297 ( 3303) covalent geometry : bond 0.00468 (28070) covalent geometry : angle 0.59198 (38180) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7000 Ramachandran restraints generated. 3500 Oldfield, 0 Emsley, 3500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7000 Ramachandran restraints generated. 3500 Oldfield, 0 Emsley, 3500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 205 time to evaluate : 3.304 Fit side-chains revert: symmetry clash REVERT: J 22 GLU cc_start: 0.8249 (tp30) cc_final: 0.8048 (tp30) REVERT: B 136 GLN cc_start: 0.9034 (OUTLIER) cc_final: 0.8297 (mt0) REVERT: D 22 GLU cc_start: 0.8328 (tp30) cc_final: 0.8118 (tp30) REVERT: F 49 LYS cc_start: 0.7777 (pttm) cc_final: 0.7488 (pttp) REVERT: G 49 LYS cc_start: 0.7739 (pttm) cc_final: 0.7369 (pttp) REVERT: H 140 GLN cc_start: 0.8647 (mm-40) cc_final: 0.8432 (mm110) outliers start: 49 outliers final: 36 residues processed: 234 average time/residue: 1.4309 time to fit residues: 391.0284 Evaluate side-chains 228 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 191 time to evaluate : 3.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 44 VAL Chi-restraints excluded: chain J residue 53 TRP Chi-restraints excluded: chain J residue 170 ASP Chi-restraints excluded: chain A residue 53 TRP Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 53 TRP Chi-restraints excluded: chain B residue 136 GLN Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 350 THR Chi-restraints excluded: chain C residue 53 TRP Chi-restraints excluded: chain C residue 170 ASP Chi-restraints excluded: chain C residue 199 GLU Chi-restraints excluded: chain D residue 170 ASP Chi-restraints excluded: chain D residue 338 MET Chi-restraints excluded: chain D residue 350 THR Chi-restraints excluded: chain E residue 84 ARG Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain E residue 164 ASP Chi-restraints excluded: chain E residue 233 SER Chi-restraints excluded: chain F residue 100 GLU Chi-restraints excluded: chain F residue 104 THR Chi-restraints excluded: chain F residue 164 ASP Chi-restraints excluded: chain F residue 233 SER Chi-restraints excluded: chain G residue 112 LYS Chi-restraints excluded: chain G residue 164 ASP Chi-restraints excluded: chain G residue 199 GLU Chi-restraints excluded: chain G residue 314 SER Chi-restraints excluded: chain H residue 84 ARG Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain H residue 164 ASP Chi-restraints excluded: chain H residue 233 SER Chi-restraints excluded: chain I residue 22 GLU Chi-restraints excluded: chain I residue 84 ARG Chi-restraints excluded: chain I residue 104 THR Chi-restraints excluded: chain I residue 314 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 104 optimal weight: 8.9990 chunk 257 optimal weight: 4.9990 chunk 283 optimal weight: 8.9990 chunk 164 optimal weight: 8.9990 chunk 281 optimal weight: 0.0980 chunk 90 optimal weight: 3.9990 chunk 151 optimal weight: 0.9990 chunk 140 optimal weight: 6.9990 chunk 134 optimal weight: 9.9990 chunk 235 optimal weight: 30.0000 chunk 299 optimal weight: 4.9990 overall best weight: 3.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 9 ASN E 140 GLN F 9 ASN F 140 GLN G 9 ASN G 140 GLN H 9 ASN I 9 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.182183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.122507 restraints weight = 29706.640| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 2.22 r_work: 0.3224 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.1277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 28070 Z= 0.200 Angle : 0.598 9.411 38180 Z= 0.312 Chirality : 0.047 0.158 3990 Planarity : 0.005 0.067 5030 Dihedral : 4.813 24.527 3860 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.61 % Allowed : 11.09 % Favored : 86.30 % 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: -0.74 (0.14), residues: 3500 helix: 0.50 (0.15), residues: 1130 sheet: -0.41 (0.19), residues: 730 loop : -1.19 (0.15), residues: 1640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP J 53 HIS 0.003 0.001 HIS H 280 PHE 0.018 0.002 PHE G 200 TYR 0.029 0.002 TYR A 176 ARG 0.003 0.000 ARG H 316 Details of bonding type rmsd hydrogen bonds : bond 0.04973 ( 1098) hydrogen bonds : angle 4.94997 ( 3303) covalent geometry : bond 0.00503 (28070) covalent geometry : angle 0.59816 (38180) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7000 Ramachandran restraints generated. 3500 Oldfield, 0 Emsley, 3500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7000 Ramachandran restraints generated. 3500 Oldfield, 0 Emsley, 3500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 198 time to evaluate : 3.101 Fit side-chains revert: symmetry clash REVERT: J 136 GLN cc_start: 0.8942 (OUTLIER) cc_final: 0.7999 (mt0) REVERT: B 136 GLN cc_start: 0.9041 (OUTLIER) cc_final: 0.8301 (mt0) REVERT: C 136 GLN cc_start: 0.8956 (OUTLIER) cc_final: 0.8318 (mt0) REVERT: D 22 GLU cc_start: 0.8266 (tp30) cc_final: 0.8024 (tp30) REVERT: D 136 GLN cc_start: 0.9006 (OUTLIER) cc_final: 0.8324 (mt0) REVERT: F 49 LYS cc_start: 0.7812 (pttm) cc_final: 0.7498 (pttp) REVERT: G 49 LYS cc_start: 0.7759 (pttm) cc_final: 0.7389 (pttp) REVERT: H 140 GLN cc_start: 0.8635 (mm-40) cc_final: 0.8423 (mm110) outliers start: 74 outliers final: 42 residues processed: 252 average time/residue: 1.5234 time to fit residues: 452.7356 Evaluate side-chains 236 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 190 time to evaluate : 3.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 44 VAL Chi-restraints excluded: chain J residue 53 TRP Chi-restraints excluded: chain J residue 136 GLN Chi-restraints excluded: chain J residue 170 ASP Chi-restraints excluded: chain A residue 53 TRP Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 53 TRP Chi-restraints excluded: chain B residue 136 GLN Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 350 THR Chi-restraints excluded: chain C residue 53 TRP Chi-restraints excluded: chain C residue 136 GLN Chi-restraints excluded: chain C residue 170 ASP Chi-restraints excluded: chain C residue 199 GLU Chi-restraints excluded: chain D residue 136 GLN Chi-restraints excluded: chain D residue 170 ASP Chi-restraints excluded: chain D residue 199 GLU Chi-restraints excluded: chain D residue 350 THR Chi-restraints excluded: chain E residue 84 ARG Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain E residue 164 ASP Chi-restraints excluded: chain E residue 233 SER Chi-restraints excluded: chain F residue 100 GLU Chi-restraints excluded: chain F residue 104 THR Chi-restraints excluded: chain F residue 164 ASP Chi-restraints excluded: chain F residue 233 SER Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain G residue 112 LYS Chi-restraints excluded: chain G residue 164 ASP Chi-restraints excluded: chain G residue 199 GLU Chi-restraints excluded: chain G residue 314 SER Chi-restraints excluded: chain H residue 84 ARG Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain H residue 139 ILE Chi-restraints excluded: chain H residue 141 TRP Chi-restraints excluded: chain H residue 164 ASP Chi-restraints excluded: chain H residue 233 SER Chi-restraints excluded: chain I residue 22 GLU Chi-restraints excluded: chain I residue 84 ARG Chi-restraints excluded: chain I residue 96 THR Chi-restraints excluded: chain I residue 104 THR Chi-restraints excluded: chain I residue 314 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 339 optimal weight: 20.0000 chunk 296 optimal weight: 0.9980 chunk 277 optimal weight: 10.0000 chunk 145 optimal weight: 0.9990 chunk 249 optimal weight: 2.9990 chunk 233 optimal weight: 1.9990 chunk 132 optimal weight: 9.9990 chunk 97 optimal weight: 20.0000 chunk 297 optimal weight: 0.7980 chunk 140 optimal weight: 6.9990 chunk 321 optimal weight: 0.0270 overall best weight: 0.9642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 9 ASN E 140 GLN F 9 ASN F 140 GLN G 9 ASN G 140 GLN G 302 ASN H 9 ASN I 9 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.186781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.127637 restraints weight = 29394.848| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 2.23 r_work: 0.3273 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.1436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 28070 Z= 0.103 Angle : 0.505 8.207 38180 Z= 0.263 Chirality : 0.044 0.154 3990 Planarity : 0.005 0.060 5030 Dihedral : 4.308 19.096 3860 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.18 % Allowed : 12.15 % Favored : 85.67 % 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: -0.44 (0.14), residues: 3500 helix: 0.82 (0.15), residues: 1130 sheet: -0.32 (0.19), residues: 730 loop : -1.03 (0.15), residues: 1640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP J 53 HIS 0.002 0.000 HIS H 280 PHE 0.016 0.001 PHE G 200 TYR 0.014 0.001 TYR A 176 ARG 0.004 0.000 ARG H 316 Details of bonding type rmsd hydrogen bonds : bond 0.03643 ( 1098) hydrogen bonds : angle 4.65194 ( 3303) covalent geometry : bond 0.00238 (28070) covalent geometry : angle 0.50470 (38180) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7000 Ramachandran restraints generated. 3500 Oldfield, 0 Emsley, 3500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7000 Ramachandran restraints generated. 3500 Oldfield, 0 Emsley, 3500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 233 time to evaluate : 3.278 Fit side-chains REVERT: J 136 GLN cc_start: 0.8906 (OUTLIER) cc_final: 0.8570 (mp10) REVERT: E 271 GLU cc_start: 0.3922 (OUTLIER) cc_final: 0.3508 (mp0) REVERT: F 49 LYS cc_start: 0.7677 (pttm) cc_final: 0.7390 (pttp) REVERT: G 31 MET cc_start: 0.7436 (OUTLIER) cc_final: 0.6590 (mtm) REVERT: G 49 LYS cc_start: 0.7625 (pttm) cc_final: 0.7275 (pttp) REVERT: G 199 GLU cc_start: 0.8531 (OUTLIER) cc_final: 0.8229 (tt0) outliers start: 62 outliers final: 36 residues processed: 276 average time/residue: 1.3104 time to fit residues: 430.9085 Evaluate side-chains 245 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 205 time to evaluate : 3.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 44 VAL Chi-restraints excluded: chain J residue 53 TRP Chi-restraints excluded: chain J residue 72 ILE Chi-restraints excluded: chain J residue 136 GLN Chi-restraints excluded: chain J residue 170 ASP Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 199 GLU Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain C residue 53 TRP Chi-restraints excluded: chain C residue 170 ASP Chi-restraints excluded: chain D residue 170 ASP Chi-restraints excluded: chain E residue 84 ARG Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain E residue 164 ASP Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 233 SER Chi-restraints excluded: chain E residue 271 GLU Chi-restraints excluded: chain F residue 100 GLU Chi-restraints excluded: chain F residue 104 THR Chi-restraints excluded: chain F residue 164 ASP Chi-restraints excluded: chain F residue 233 SER Chi-restraints excluded: chain G residue 31 MET Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain G residue 199 GLU Chi-restraints excluded: chain G residue 222 GLU Chi-restraints excluded: chain G residue 314 SER Chi-restraints excluded: chain H residue 84 ARG Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain H residue 139 ILE Chi-restraints excluded: chain H residue 164 ASP Chi-restraints excluded: chain H residue 233 SER Chi-restraints excluded: chain I residue 96 THR Chi-restraints excluded: chain I residue 104 THR Chi-restraints excluded: chain I residue 141 TRP Chi-restraints excluded: chain I residue 314 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-dev-5710/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-dev-5710/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-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-dev-5710/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-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-dev-5710/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-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 71.4789 > 50: distance: 20 - 22: 33.920 distance: 22 - 23: 40.282 distance: 22 - 28: 69.267 distance: 23 - 24: 38.580 distance: 23 - 26: 40.561 distance: 24 - 25: 40.279 distance: 24 - 29: 57.489 distance: 26 - 27: 39.564 distance: 30 - 31: 38.946 distance: 30 - 33: 40.526 distance: 31 - 32: 57.461 distance: 31 - 36: 57.173 distance: 33 - 34: 57.459 distance: 33 - 35: 38.147 distance: 37 - 38: 40.004 distance: 38 - 39: 40.801 distance: 38 - 42: 40.180 distance: 40 - 41: 56.892 distance: 42 - 43: 38.242 distance: 44 - 45: 13.998 distance: 45 - 63: 13.058 distance: 47 - 49: 39.163 distance: 50 - 51: 69.002 distance: 50 - 56: 41.457 distance: 51 - 52: 39.673 distance: 52 - 53: 69.552 distance: 55 - 56: 56.704 distance: 57 - 58: 69.690 distance: 58 - 59: 55.343 distance: 58 - 61: 69.628 distance: 59 - 60: 40.403 distance: 59 - 63: 39.986 distance: 64 - 65: 38.554 distance: 64 - 67: 57.557 distance: 65 - 66: 57.268 distance: 65 - 72: 38.641 distance: 67 - 68: 39.491 distance: 72 - 73: 43.032 distance: 73 - 74: 39.218 distance: 73 - 76: 50.242 distance: 74 - 75: 31.386 distance: 74 - 80: 42.007 distance: 76 - 77: 55.896 distance: 77 - 78: 40.545 distance: 77 - 79: 57.313 distance: 80 - 81: 56.267 distance: 80 - 86: 40.888 distance: 81 - 82: 39.784 distance: 81 - 84: 40.050 distance: 82 - 87: 40.839 distance: 84 - 85: 39.555 distance: 85 - 86: 40.009 distance: 88 - 91: 40.617 distance: 89 - 90: 56.677 distance: 89 - 96: 33.835 distance: 92 - 93: 39.210 distance: 93 - 94: 56.790 distance: 94 - 95: 56.380