Starting phenix.real_space_refine on Sun Mar 17 01:02:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rwa_24712/03_2024/7rwa_24712.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rwa_24712/03_2024/7rwa_24712.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rwa_24712/03_2024/7rwa_24712.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rwa_24712/03_2024/7rwa_24712.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rwa_24712/03_2024/7rwa_24712.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rwa_24712/03_2024/7rwa_24712.pdb" } resolution = 4.7 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= 0.002 sd= 0.049 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: 3 Type Number sf(0) Gaussians C 9654 2.51 5 N 3252 2.21 5 O 3252 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 16158 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 2978 Classifications: {'peptide': 600} Incomplete info: {'truncation_to_alanine': 526} Link IDs: {'PTRANS': 22, 'TRANS': 577} Unresolved chain link angles: 22 Unresolved non-hydrogen bonds: 1845 Unresolved non-hydrogen angles: 2366 Unresolved non-hydrogen dihedrals: 1508 Unresolved non-hydrogen chiralities: 193 Planarities with less than four sites: {'GLN:plan1': 22, 'HIS:plan': 14, 'TYR:plan': 22, 'ASN:plan1': 29, 'TRP:plan': 4, 'ASP:plan': 29, 'PHE:plan': 20, 'GLU:plan': 39, 'ARG:plan': 33} Unresolved non-hydrogen planarities: 963 Chain: "B" Number of atoms: 2471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 2471 Classifications: {'peptide': 496} Incomplete info: {'truncation_to_alanine': 447} Link IDs: {'PTRANS': 24, 'TRANS': 471} Unresolved chain link angles: 24 Unresolved non-hydrogen bonds: 1523 Unresolved non-hydrogen angles: 1953 Unresolved non-hydrogen dihedrals: 1222 Unresolved non-hydrogen chiralities: 165 Planarities with less than four sites: {'GLN:plan1': 19, 'HIS:plan': 6, 'TYR:plan': 16, 'ASN:plan1': 25, 'TRP:plan': 3, 'ASP:plan': 35, 'PHE:plan': 12, 'GLU:plan': 40, 'ARG:plan': 23} Unresolved non-hydrogen planarities: 772 Chain: "M" Number of atoms: 1875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 1875 Classifications: {'peptide': 379} Incomplete info: {'truncation_to_alanine': 339} Link IDs: {'PTRANS': 17, 'TRANS': 361} Chain breaks: 3 Unresolved chain link angles: 17 Unresolved non-hydrogen bonds: 1259 Unresolved non-hydrogen angles: 1596 Unresolved non-hydrogen dihedrals: 1066 Unresolved non-hydrogen chiralities: 107 Planarities with less than four sites: {'GLN:plan1': 11, 'ASP:plan': 15, 'TYR:plan': 14, 'ASN:plan1': 20, 'TRP:plan': 5, 'HIS:plan': 6, 'PHE:plan': 19, 'GLU:plan': 23, 'ARG:plan': 27} Unresolved non-hydrogen planarities: 663 Chain: "S" Number of atoms: 707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 707 Classifications: {'peptide': 142} Incomplete info: {'truncation_to_alanine': 131} Link IDs: {'TRANS': 141} Unresolved non-hydrogen bonds: 517 Unresolved non-hydrogen angles: 665 Unresolved non-hydrogen dihedrals: 430 Unresolved non-hydrogen chiralities: 45 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 4, 'TYR:plan': 8, 'ASN:plan1': 10, 'TRP:plan': 1, 'ASP:plan': 8, 'PHE:plan': 11, 'GLU:plan': 12, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 317 Chain: "Y" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 48 Classifications: {'peptide': 5} Link IDs: {'TRANS': 4} Chain: "a" Number of atoms: 2978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 2978 Classifications: {'peptide': 600} Incomplete info: {'truncation_to_alanine': 526} Link IDs: {'PTRANS': 22, 'TRANS': 577} Unresolved chain link angles: 22 Unresolved non-hydrogen bonds: 1845 Unresolved non-hydrogen angles: 2366 Unresolved non-hydrogen dihedrals: 1508 Unresolved non-hydrogen chiralities: 193 Planarities with less than four sites: {'GLN:plan1': 22, 'HIS:plan': 14, 'TYR:plan': 22, 'ASN:plan1': 29, 'TRP:plan': 4, 'ASP:plan': 29, 'PHE:plan': 20, 'GLU:plan': 39, 'ARG:plan': 33} Unresolved non-hydrogen planarities: 963 Chain: "b" Number of atoms: 2471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 2471 Classifications: {'peptide': 496} Incomplete info: {'truncation_to_alanine': 447} Link IDs: {'PTRANS': 24, 'TRANS': 471} Unresolved chain link angles: 24 Unresolved non-hydrogen bonds: 1523 Unresolved non-hydrogen angles: 1953 Unresolved non-hydrogen dihedrals: 1222 Unresolved non-hydrogen chiralities: 165 Planarities with less than four sites: {'GLN:plan1': 19, 'HIS:plan': 6, 'TYR:plan': 16, 'ASN:plan1': 25, 'TRP:plan': 3, 'ASP:plan': 35, 'PHE:plan': 12, 'GLU:plan': 40, 'ARG:plan': 23} Unresolved non-hydrogen planarities: 772 Chain: "m" Number of atoms: 1875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 1875 Classifications: {'peptide': 379} Incomplete info: {'truncation_to_alanine': 339} Link IDs: {'PTRANS': 17, 'TRANS': 361} Chain breaks: 3 Unresolved chain link angles: 17 Unresolved non-hydrogen bonds: 1259 Unresolved non-hydrogen angles: 1596 Unresolved non-hydrogen dihedrals: 1066 Unresolved non-hydrogen chiralities: 107 Planarities with less than four sites: {'GLN:plan1': 11, 'ASP:plan': 15, 'TYR:plan': 14, 'ASN:plan1': 20, 'TRP:plan': 5, 'HIS:plan': 6, 'PHE:plan': 19, 'GLU:plan': 23, 'ARG:plan': 27} Unresolved non-hydrogen planarities: 663 Chain: "s" Number of atoms: 707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 707 Classifications: {'peptide': 142} Incomplete info: {'truncation_to_alanine': 131} Link IDs: {'TRANS': 141} Unresolved non-hydrogen bonds: 517 Unresolved non-hydrogen angles: 665 Unresolved non-hydrogen dihedrals: 430 Unresolved non-hydrogen chiralities: 45 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 4, 'TYR:plan': 8, 'ASN:plan1': 10, 'TRP:plan': 1, 'ASP:plan': 8, 'PHE:plan': 11, 'GLU:plan': 12, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 317 Chain: "y" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 48 Classifications: {'peptide': 5} Link IDs: {'TRANS': 4} Time building chain proxies: 10.01, per 1000 atoms: 0.62 Number of scatterers: 16158 At special positions: 0 Unit cell: (199.815, 158.235, 103.95, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 3252 8.00 N 3252 7.00 C 9654 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: 7.23 Conformation dependent library (CDL) restraints added in 4.6 seconds 6424 Ramachandran restraints generated. 3212 Oldfield, 0 Emsley, 3212 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6272 Finding SS restraints... Secondary structure from input PDB file: 154 helices and 20 sheets defined 62.4% alpha, 14.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.99 Creating SS restraints... Processing helix chain 'A' and resid 11 through 22 Processing helix chain 'A' and resid 25 through 45 removed outlier: 3.755A pdb=" N GLU A 29 " --> pdb=" O SER A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 69 Processing helix chain 'A' and resid 76 through 84 removed outlier: 4.241A pdb=" N LEU A 82 " --> pdb=" O GLU A 78 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU A 83 " --> pdb=" O ALA A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 101 Processing helix chain 'A' and resid 106 through 121 removed outlier: 3.863A pdb=" N ALA A 121 " --> pdb=" O LYS A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 138 removed outlier: 3.829A pdb=" N MET A 128 " --> pdb=" O ASN A 124 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL A 138 " --> pdb=" O CYS A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 146 removed outlier: 3.511A pdb=" N ALA A 144 " --> pdb=" O SER A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 156 Processing helix chain 'A' and resid 161 through 179 Processing helix chain 'A' and resid 188 through 193 removed outlier: 3.672A pdb=" N VAL A 192 " --> pdb=" O TRP A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 198 removed outlier: 3.692A pdb=" N ASN A 197 " --> pdb=" O HIS A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 218 Processing helix chain 'A' and resid 219 through 223 removed outlier: 3.517A pdb=" N PHE A 222 " --> pdb=" O PRO A 219 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LYS A 223 " --> pdb=" O GLU A 220 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 219 through 223' Processing helix chain 'A' and resid 224 through 238 removed outlier: 4.740A pdb=" N LEU A 228 " --> pdb=" O THR A 224 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N THR A 238 " --> pdb=" O SER A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 246 No H-bonds generated for 'chain 'A' and resid 244 through 246' Processing helix chain 'A' and resid 254 through 266 removed outlier: 3.694A pdb=" N SER A 258 " --> pdb=" O ALA A 254 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLN A 266 " --> pdb=" O LEU A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 293 removed outlier: 3.521A pdb=" N GLU A 293 " --> pdb=" O ASN A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 321 removed outlier: 4.318A pdb=" N SER A 303 " --> pdb=" O LYS A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 339 removed outlier: 3.883A pdb=" N GLN A 339 " --> pdb=" O GLY A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 357 Processing helix chain 'A' and resid 359 through 369 removed outlier: 4.316A pdb=" N GLU A 364 " --> pdb=" O GLU A 360 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N ALA A 365 " --> pdb=" O PHE A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 380 Processing helix chain 'A' and resid 383 through 396 removed outlier: 3.653A pdb=" N GLN A 387 " --> pdb=" O VAL A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 415 Processing helix chain 'A' and resid 419 through 435 Processing helix chain 'A' and resid 438 through 453 Processing helix chain 'A' and resid 460 through 473 removed outlier: 3.562A pdb=" N ASP A 473 " --> pdb=" O VAL A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 488 removed outlier: 4.579A pdb=" N TYR A 478 " --> pdb=" O ASP A 474 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLN A 488 " --> pdb=" O PHE A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 512 removed outlier: 6.620A pdb=" N ASN A 509 " --> pdb=" O GLY A 505 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N LEU A 510 " --> pdb=" O GLU A 506 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ILE A 511 " --> pdb=" O PHE A 507 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 517 Processing helix chain 'A' and resid 518 through 530 Processing helix chain 'A' and resid 534 through 552 Processing helix chain 'A' and resid 555 through 563 Processing helix chain 'A' and resid 565 through 570 Processing helix chain 'A' and resid 573 through 590 Processing helix chain 'A' and resid 593 through 599 removed outlier: 3.544A pdb=" N LEU A 599 " --> pdb=" O LEU A 595 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 96 Processing helix chain 'B' and resid 99 through 113 removed outlier: 3.584A pdb=" N CYS B 112 " --> pdb=" O ARG B 108 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ILE B 113 " --> pdb=" O THR B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 131 removed outlier: 4.534A pdb=" N GLU B 124 " --> pdb=" O GLU B 120 " (cutoff:3.500A) Proline residue: B 125 - end of helix removed outlier: 4.250A pdb=" N LYS B 128 " --> pdb=" O GLU B 124 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N CYS B 129 " --> pdb=" O PRO B 125 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS B 131 " --> pdb=" O ARG B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 150 removed outlier: 3.638A pdb=" N ASP B 150 " --> pdb=" O ALA B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 168 Processing helix chain 'B' and resid 173 through 188 Processing helix chain 'B' and resid 200 through 214 Processing helix chain 'B' and resid 215 through 226 Processing helix chain 'B' and resid 227 through 229 No H-bonds generated for 'chain 'B' and resid 227 through 229' Processing helix chain 'B' and resid 233 through 245 removed outlier: 3.771A pdb=" N ALA B 237 " --> pdb=" O ASP B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 266 Processing helix chain 'B' and resid 275 through 291 removed outlier: 3.695A pdb=" N MET B 279 " --> pdb=" O ASP B 275 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ALA B 285 " --> pdb=" O LEU B 281 " (cutoff:3.500A) Proline residue: B 286 - end of helix removed outlier: 3.563A pdb=" N LEU B 291 " --> pdb=" O PRO B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 294 No H-bonds generated for 'chain 'B' and resid 292 through 294' Processing helix chain 'B' and resid 295 through 313 Processing helix chain 'B' and resid 331 through 346 Processing helix chain 'B' and resid 350 through 363 removed outlier: 3.786A pdb=" N THR B 363 " --> pdb=" O LYS B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 384 Processing helix chain 'B' and resid 384 through 400 Processing helix chain 'B' and resid 403 through 421 Processing helix chain 'B' and resid 427 through 435 removed outlier: 4.273A pdb=" N THR B 431 " --> pdb=" O SER B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 455 Processing helix chain 'B' and resid 461 through 470 Processing helix chain 'B' and resid 477 through 495 Processing helix chain 'B' and resid 496 through 498 No H-bonds generated for 'chain 'B' and resid 496 through 498' Processing helix chain 'B' and resid 499 through 514 Processing helix chain 'B' and resid 516 through 531 Processing helix chain 'B' and resid 533 through 541 removed outlier: 3.628A pdb=" N GLU B 539 " --> pdb=" O VAL B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 564 Processing helix chain 'B' and resid 569 through 575 removed outlier: 4.124A pdb=" N VAL B 573 " --> pdb=" O SER B 569 " (cutoff:3.500A) Processing helix chain 'B' and resid 577 through 581 Processing helix chain 'M' and resid 25 through 37 removed outlier: 3.889A pdb=" N VAL M 29 " --> pdb=" O GLY M 25 " (cutoff:3.500A) Processing helix chain 'M' and resid 74 through 94 removed outlier: 3.913A pdb=" N VAL M 78 " --> pdb=" O ASN M 74 " (cutoff:3.500A) Processing helix chain 'M' and resid 97 through 103 Processing helix chain 'M' and resid 104 through 115 Processing helix chain 'M' and resid 414 through 416 No H-bonds generated for 'chain 'M' and resid 414 through 416' Processing helix chain 'S' and resid 24 through 41 removed outlier: 3.719A pdb=" N VAL S 41 " --> pdb=" O ALA S 37 " (cutoff:3.500A) Processing helix chain 'S' and resid 76 through 96 removed outlier: 3.540A pdb=" N PHE S 95 " --> pdb=" O LEU S 91 " (cutoff:3.500A) Processing helix chain 'S' and resid 99 through 106 removed outlier: 3.535A pdb=" N LEU S 103 " --> pdb=" O CYS S 99 " (cutoff:3.500A) Processing helix chain 'S' and resid 106 through 117 Processing helix chain 'S' and resid 127 through 141 removed outlier: 3.899A pdb=" N LEU S 141 " --> pdb=" O MET S 137 " (cutoff:3.500A) Processing helix chain 'a' and resid 11 through 22 Processing helix chain 'a' and resid 25 through 45 removed outlier: 3.755A pdb=" N GLU a 29 " --> pdb=" O SER a 25 " (cutoff:3.500A) Processing helix chain 'a' and resid 52 through 69 Processing helix chain 'a' and resid 76 through 84 removed outlier: 4.242A pdb=" N LEU a 82 " --> pdb=" O GLU a 78 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU a 83 " --> pdb=" O ALA a 79 " (cutoff:3.500A) Processing helix chain 'a' and resid 87 through 101 Processing helix chain 'a' and resid 106 through 121 removed outlier: 3.862A pdb=" N ALA a 121 " --> pdb=" O LYS a 117 " (cutoff:3.500A) Processing helix chain 'a' and resid 124 through 138 removed outlier: 3.829A pdb=" N MET a 128 " --> pdb=" O ASN a 124 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL a 138 " --> pdb=" O CYS a 134 " (cutoff:3.500A) Processing helix chain 'a' and resid 140 through 146 removed outlier: 3.511A pdb=" N ALA a 144 " --> pdb=" O SER a 140 " (cutoff:3.500A) Processing helix chain 'a' and resid 149 through 156 Processing helix chain 'a' and resid 161 through 179 Processing helix chain 'a' and resid 188 through 193 removed outlier: 3.672A pdb=" N VAL a 192 " --> pdb=" O TRP a 188 " (cutoff:3.500A) Processing helix chain 'a' and resid 194 through 198 removed outlier: 3.691A pdb=" N ASN a 197 " --> pdb=" O HIS a 194 " (cutoff:3.500A) Processing helix chain 'a' and resid 200 through 218 Processing helix chain 'a' and resid 219 through 223 removed outlier: 3.516A pdb=" N PHE a 222 " --> pdb=" O PRO a 219 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LYS a 223 " --> pdb=" O GLU a 220 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 219 through 223' Processing helix chain 'a' and resid 224 through 238 removed outlier: 4.740A pdb=" N LEU a 228 " --> pdb=" O THR a 224 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N THR a 238 " --> pdb=" O SER a 234 " (cutoff:3.500A) Processing helix chain 'a' and resid 244 through 246 No H-bonds generated for 'chain 'a' and resid 244 through 246' Processing helix chain 'a' and resid 254 through 266 removed outlier: 3.694A pdb=" N SER a 258 " --> pdb=" O ALA a 254 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLN a 266 " --> pdb=" O LEU a 262 " (cutoff:3.500A) Processing helix chain 'a' and resid 273 through 293 removed outlier: 3.520A pdb=" N GLU a 293 " --> pdb=" O ASN a 289 " (cutoff:3.500A) Processing helix chain 'a' and resid 299 through 321 removed outlier: 4.318A pdb=" N SER a 303 " --> pdb=" O LYS a 299 " (cutoff:3.500A) Processing helix chain 'a' and resid 323 through 339 removed outlier: 3.884A pdb=" N GLN a 339 " --> pdb=" O GLY a 335 " (cutoff:3.500A) Processing helix chain 'a' and resid 342 through 357 Processing helix chain 'a' and resid 359 through 369 removed outlier: 4.315A pdb=" N GLU a 364 " --> pdb=" O GLU a 360 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N ALA a 365 " --> pdb=" O PHE a 361 " (cutoff:3.500A) Processing helix chain 'a' and resid 369 through 380 Processing helix chain 'a' and resid 383 through 396 removed outlier: 3.654A pdb=" N GLN a 387 " --> pdb=" O VAL a 383 " (cutoff:3.500A) Processing helix chain 'a' and resid 398 through 415 Processing helix chain 'a' and resid 419 through 435 Processing helix chain 'a' and resid 438 through 453 Processing helix chain 'a' and resid 460 through 473 removed outlier: 3.561A pdb=" N ASP a 473 " --> pdb=" O VAL a 469 " (cutoff:3.500A) Processing helix chain 'a' and resid 474 through 488 removed outlier: 4.579A pdb=" N TYR a 478 " --> pdb=" O ASP a 474 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLN a 488 " --> pdb=" O PHE a 484 " (cutoff:3.500A) Processing helix chain 'a' and resid 493 through 512 removed outlier: 6.619A pdb=" N ASN a 509 " --> pdb=" O GLY a 505 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N LEU a 510 " --> pdb=" O GLU a 506 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ILE a 511 " --> pdb=" O PHE a 507 " (cutoff:3.500A) Processing helix chain 'a' and resid 514 through 517 Processing helix chain 'a' and resid 518 through 530 Processing helix chain 'a' and resid 534 through 552 Processing helix chain 'a' and resid 555 through 563 Processing helix chain 'a' and resid 565 through 570 Processing helix chain 'a' and resid 573 through 590 Processing helix chain 'a' and resid 593 through 599 removed outlier: 3.544A pdb=" N LEU a 599 " --> pdb=" O LEU a 595 " (cutoff:3.500A) Processing helix chain 'b' and resid 88 through 96 Processing helix chain 'b' and resid 99 through 113 removed outlier: 3.584A pdb=" N CYS b 112 " --> pdb=" O ARG b 108 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ILE b 113 " --> pdb=" O THR b 109 " (cutoff:3.500A) Processing helix chain 'b' and resid 117 through 131 removed outlier: 4.534A pdb=" N GLU b 124 " --> pdb=" O GLU b 120 " (cutoff:3.500A) Proline residue: b 125 - end of helix removed outlier: 4.249A pdb=" N LYS b 128 " --> pdb=" O GLU b 124 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N CYS b 129 " --> pdb=" O PRO b 125 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS b 131 " --> pdb=" O ARG b 127 " (cutoff:3.500A) Processing helix chain 'b' and resid 134 through 150 removed outlier: 3.638A pdb=" N ASP b 150 " --> pdb=" O ALA b 146 " (cutoff:3.500A) Processing helix chain 'b' and resid 155 through 168 Processing helix chain 'b' and resid 173 through 188 Processing helix chain 'b' and resid 200 through 214 Processing helix chain 'b' and resid 215 through 226 Processing helix chain 'b' and resid 227 through 229 No H-bonds generated for 'chain 'b' and resid 227 through 229' Processing helix chain 'b' and resid 233 through 245 removed outlier: 3.771A pdb=" N ALA b 237 " --> pdb=" O ASP b 233 " (cutoff:3.500A) Processing helix chain 'b' and resid 252 through 266 Processing helix chain 'b' and resid 275 through 291 removed outlier: 3.695A pdb=" N MET b 279 " --> pdb=" O ASP b 275 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ALA b 285 " --> pdb=" O LEU b 281 " (cutoff:3.500A) Proline residue: b 286 - end of helix removed outlier: 3.563A pdb=" N LEU b 291 " --> pdb=" O PRO b 287 " (cutoff:3.500A) Processing helix chain 'b' and resid 292 through 294 No H-bonds generated for 'chain 'b' and resid 292 through 294' Processing helix chain 'b' and resid 295 through 313 Processing helix chain 'b' and resid 331 through 346 Processing helix chain 'b' and resid 350 through 363 removed outlier: 3.787A pdb=" N THR b 363 " --> pdb=" O LYS b 359 " (cutoff:3.500A) Processing helix chain 'b' and resid 366 through 384 Processing helix chain 'b' and resid 384 through 400 Processing helix chain 'b' and resid 403 through 421 Processing helix chain 'b' and resid 427 through 435 removed outlier: 4.273A pdb=" N THR b 431 " --> pdb=" O SER b 427 " (cutoff:3.500A) Processing helix chain 'b' and resid 441 through 455 Processing helix chain 'b' and resid 461 through 470 Processing helix chain 'b' and resid 477 through 495 Processing helix chain 'b' and resid 496 through 498 No H-bonds generated for 'chain 'b' and resid 496 through 498' Processing helix chain 'b' and resid 499 through 514 Processing helix chain 'b' and resid 516 through 531 Processing helix chain 'b' and resid 533 through 541 removed outlier: 3.629A pdb=" N GLU b 539 " --> pdb=" O VAL b 535 " (cutoff:3.500A) Processing helix chain 'b' and resid 556 through 564 Processing helix chain 'b' and resid 569 through 575 removed outlier: 4.123A pdb=" N VAL b 573 " --> pdb=" O SER b 569 " (cutoff:3.500A) Processing helix chain 'b' and resid 577 through 581 Processing helix chain 'm' and resid 25 through 37 removed outlier: 3.890A pdb=" N VAL m 29 " --> pdb=" O GLY m 25 " (cutoff:3.500A) Processing helix chain 'm' and resid 74 through 94 removed outlier: 3.911A pdb=" N VAL m 78 " --> pdb=" O ASN m 74 " (cutoff:3.500A) Processing helix chain 'm' and resid 97 through 103 Processing helix chain 'm' and resid 104 through 115 Processing helix chain 'm' and resid 414 through 416 No H-bonds generated for 'chain 'm' and resid 414 through 416' Processing helix chain 's' and resid 24 through 41 removed outlier: 3.719A pdb=" N VAL s 41 " --> pdb=" O ALA s 37 " (cutoff:3.500A) Processing helix chain 's' and resid 76 through 96 removed outlier: 3.540A pdb=" N PHE s 95 " --> pdb=" O LEU s 91 " (cutoff:3.500A) Processing helix chain 's' and resid 99 through 106 removed outlier: 3.535A pdb=" N LEU s 103 " --> pdb=" O CYS s 99 " (cutoff:3.500A) Processing helix chain 's' and resid 106 through 117 Processing helix chain 's' and resid 127 through 141 removed outlier: 3.899A pdb=" N LEU s 141 " --> pdb=" O MET s 137 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 248 through 249 Processing sheet with id=AA2, first strand: chain 'M' and resid 14 through 19 removed outlier: 7.117A pdb=" N ILE M 7 " --> pdb=" O LEU M 15 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N SER M 17 " --> pdb=" O LEU M 5 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N LEU M 5 " --> pdb=" O SER M 17 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N GLY M 4 " --> pdb=" O VAL M 68 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL M 68 " --> pdb=" O GLY M 4 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL M 58 " --> pdb=" O LEU M 65 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N THR M 69 " --> pdb=" O SER M 54 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER M 54 " --> pdb=" O THR M 69 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'M' and resid 116 through 117 Processing sheet with id=AA4, first strand: chain 'M' and resid 245 through 248 removed outlier: 3.587A pdb=" N ASP M 245 " --> pdb=" O ARG M 278 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N MET M 275 " --> pdb=" O VAL M 200 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL M 200 " --> pdb=" O MET M 275 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU M 178 " --> pdb=" O ARG M 199 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ASN M 171 " --> pdb=" O ILE M 419 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N TRP M 421 " --> pdb=" O ASN M 171 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N LEU M 173 " --> pdb=" O TRP M 421 " (cutoff:3.500A) removed outlier: 8.198A pdb=" N ARG M 423 " --> pdb=" O LEU M 173 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N LEU M 175 " --> pdb=" O ARG M 423 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N ILE M 425 " --> pdb=" O LEU M 175 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N VAL M 177 " --> pdb=" O ILE M 425 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ARG M 427 " --> pdb=" O VAL M 177 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N GLU M 179 " --> pdb=" O ARG M 427 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N GLY M 429 " --> pdb=" O GLU M 179 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N VAL M 181 " --> pdb=" O GLY M 429 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N TYR M 431 " --> pdb=" O VAL M 181 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N LEU M 183 " --> pdb=" O TYR M 431 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N THR M 433 " --> pdb=" O LEU M 183 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N MET M 185 " --> pdb=" O THR M 433 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N ARG M 427 " --> pdb=" O VAL M 392 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N VAL M 392 " --> pdb=" O ARG M 427 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N GLY M 429 " --> pdb=" O PHE M 390 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N PHE M 390 " --> pdb=" O GLY M 429 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N TYR M 431 " --> pdb=" O MET M 388 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER M 387 " --> pdb=" O ARG M 323 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N GLU M 391 " --> pdb=" O LYS M 319 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N LYS M 319 " --> pdb=" O GLU M 391 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL M 322 " --> pdb=" O TRP M 353 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N TRP M 353 " --> pdb=" O VAL M 322 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ILE M 324 " --> pdb=" O ILE M 351 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE M 351 " --> pdb=" O ILE M 324 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'M' and resid 270 through 272 removed outlier: 3.535A pdb=" N LEU M 178 " --> pdb=" O ARG M 199 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ASN M 171 " --> pdb=" O ILE M 419 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N TRP M 421 " --> pdb=" O ASN M 171 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N LEU M 173 " --> pdb=" O TRP M 421 " (cutoff:3.500A) removed outlier: 8.198A pdb=" N ARG M 423 " --> pdb=" O LEU M 173 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N LEU M 175 " --> pdb=" O ARG M 423 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N ILE M 425 " --> pdb=" O LEU M 175 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N VAL M 177 " --> pdb=" O ILE M 425 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ARG M 427 " --> pdb=" O VAL M 177 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N GLU M 179 " --> pdb=" O ARG M 427 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N GLY M 429 " --> pdb=" O GLU M 179 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N VAL M 181 " --> pdb=" O GLY M 429 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N TYR M 431 " --> pdb=" O VAL M 181 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N LEU M 183 " --> pdb=" O TYR M 431 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N THR M 433 " --> pdb=" O LEU M 183 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N MET M 185 " --> pdb=" O THR M 433 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'M' and resid 263 through 265 removed outlier: 4.239A pdb=" N ILE M 263 " --> pdb=" O PHE M 214 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'M' and resid 287 through 290 Processing sheet with id=AA8, first strand: chain 'M' and resid 287 through 290 removed outlier: 3.525A pdb=" N VAL M 303 " --> pdb=" O ALA M 368 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 14 through 19 removed outlier: 7.760A pdb=" N THR S 14 " --> pdb=" O ASN S 9 " (cutoff:3.500A) removed outlier: 8.244A pdb=" N ASN S 9 " --> pdb=" O THR S 14 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LEU S 16 " --> pdb=" O ILE S 7 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE S 7 " --> pdb=" O LEU S 16 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LYS S 56 " --> pdb=" O VAL S 71 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N VAL S 50 " --> pdb=" O ILE S 57 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 118 through 119 Processing sheet with id=AB2, first strand: chain 'a' and resid 248 through 249 Processing sheet with id=AB3, first strand: chain 'm' and resid 14 through 19 removed outlier: 7.117A pdb=" N ILE m 7 " --> pdb=" O LEU m 15 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N SER m 17 " --> pdb=" O LEU m 5 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N LEU m 5 " --> pdb=" O SER m 17 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N GLY m 4 " --> pdb=" O VAL m 68 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL m 68 " --> pdb=" O GLY m 4 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL m 58 " --> pdb=" O LEU m 65 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N THR m 69 " --> pdb=" O SER m 54 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER m 54 " --> pdb=" O THR m 69 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'm' and resid 116 through 117 Processing sheet with id=AB5, first strand: chain 'm' and resid 245 through 248 removed outlier: 3.587A pdb=" N ASP m 245 " --> pdb=" O ARG m 278 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N MET m 275 " --> pdb=" O VAL m 200 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL m 200 " --> pdb=" O MET m 275 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU m 178 " --> pdb=" O ARG m 199 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ASN m 171 " --> pdb=" O ILE m 419 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N TRP m 421 " --> pdb=" O ASN m 171 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N LEU m 173 " --> pdb=" O TRP m 421 " (cutoff:3.500A) removed outlier: 8.199A pdb=" N ARG m 423 " --> pdb=" O LEU m 173 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N LEU m 175 " --> pdb=" O ARG m 423 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N ILE m 425 " --> pdb=" O LEU m 175 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N VAL m 177 " --> pdb=" O ILE m 425 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ARG m 427 " --> pdb=" O VAL m 177 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N GLU m 179 " --> pdb=" O ARG m 427 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N GLY m 429 " --> pdb=" O GLU m 179 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N VAL m 181 " --> pdb=" O GLY m 429 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N TYR m 431 " --> pdb=" O VAL m 181 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N LEU m 183 " --> pdb=" O TYR m 431 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N THR m 433 " --> pdb=" O LEU m 183 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N MET m 185 " --> pdb=" O THR m 433 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N ARG m 427 " --> pdb=" O VAL m 392 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N VAL m 392 " --> pdb=" O ARG m 427 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N GLY m 429 " --> pdb=" O PHE m 390 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N PHE m 390 " --> pdb=" O GLY m 429 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N TYR m 431 " --> pdb=" O MET m 388 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER m 387 " --> pdb=" O ARG m 323 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N GLU m 391 " --> pdb=" O LYS m 319 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N LYS m 319 " --> pdb=" O GLU m 391 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL m 322 " --> pdb=" O TRP m 353 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N TRP m 353 " --> pdb=" O VAL m 322 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ILE m 324 " --> pdb=" O ILE m 351 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE m 351 " --> pdb=" O ILE m 324 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'm' and resid 270 through 272 removed outlier: 3.535A pdb=" N LEU m 178 " --> pdb=" O ARG m 199 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ASN m 171 " --> pdb=" O ILE m 419 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N TRP m 421 " --> pdb=" O ASN m 171 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N LEU m 173 " --> pdb=" O TRP m 421 " (cutoff:3.500A) removed outlier: 8.199A pdb=" N ARG m 423 " --> pdb=" O LEU m 173 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N LEU m 175 " --> pdb=" O ARG m 423 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N ILE m 425 " --> pdb=" O LEU m 175 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N VAL m 177 " --> pdb=" O ILE m 425 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ARG m 427 " --> pdb=" O VAL m 177 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N GLU m 179 " --> pdb=" O ARG m 427 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N GLY m 429 " --> pdb=" O GLU m 179 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N VAL m 181 " --> pdb=" O GLY m 429 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N TYR m 431 " --> pdb=" O VAL m 181 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N LEU m 183 " --> pdb=" O TYR m 431 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N THR m 433 " --> pdb=" O LEU m 183 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N MET m 185 " --> pdb=" O THR m 433 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'm' and resid 263 through 265 removed outlier: 4.239A pdb=" N ILE m 263 " --> pdb=" O PHE m 214 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'm' and resid 287 through 290 Processing sheet with id=AB9, first strand: chain 'm' and resid 287 through 290 removed outlier: 3.525A pdb=" N VAL m 303 " --> pdb=" O ALA m 368 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 's' and resid 14 through 19 removed outlier: 7.759A pdb=" N THR s 14 " --> pdb=" O ASN s 9 " (cutoff:3.500A) removed outlier: 8.246A pdb=" N ASN s 9 " --> pdb=" O THR s 14 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LEU s 16 " --> pdb=" O ILE s 7 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE s 7 " --> pdb=" O LEU s 16 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LYS s 56 " --> pdb=" O VAL s 71 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N VAL s 50 " --> pdb=" O ILE s 57 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 's' and resid 118 through 119 1562 hydrogen bonds defined for protein. 4590 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.82 Time building geometry restraints manager: 7.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.29: 3250 1.29 - 1.36: 3228 1.36 - 1.42: 22 1.42 - 1.49: 3248 1.49 - 1.55: 6396 Bond restraints: 16144 Sorted by residual: bond pdb=" C VAL a 535 " pdb=" N PRO a 536 " ideal model delta sigma weight residual 1.335 1.368 -0.033 1.28e-02 6.10e+03 6.76e+00 bond pdb=" C VAL A 535 " pdb=" N PRO A 536 " ideal model delta sigma weight residual 1.335 1.368 -0.033 1.28e-02 6.10e+03 6.74e+00 bond pdb=" C THR b 245 " pdb=" N PRO b 246 " ideal model delta sigma weight residual 1.336 1.357 -0.021 1.08e-02 8.57e+03 3.91e+00 bond pdb=" C THR B 245 " pdb=" N PRO B 246 " ideal model delta sigma weight residual 1.336 1.357 -0.021 1.08e-02 8.57e+03 3.91e+00 bond pdb=" C GLU b 124 " pdb=" N PRO b 125 " ideal model delta sigma weight residual 1.335 1.361 -0.026 1.36e-02 5.41e+03 3.67e+00 ... (remaining 16139 not shown) Histogram of bond angle deviations from ideal: 102.46 - 108.16: 285 108.16 - 113.85: 9097 113.85 - 119.55: 3871 119.55 - 125.24: 9223 125.24 - 130.94: 30 Bond angle restraints: 22506 Sorted by residual: angle pdb=" C GLU a 323 " pdb=" N PRO a 324 " pdb=" CA PRO a 324 " ideal model delta sigma weight residual 118.85 127.24 -8.39 1.09e+00 8.42e-01 5.92e+01 angle pdb=" C GLU A 323 " pdb=" N PRO A 324 " pdb=" CA PRO A 324 " ideal model delta sigma weight residual 118.85 127.08 -8.23 1.09e+00 8.42e-01 5.70e+01 angle pdb=" OE1 GLN Y 351 " pdb=" CD GLN Y 351 " pdb=" NE2 GLN Y 351 " ideal model delta sigma weight residual 122.60 115.68 6.92 1.00e+00 1.00e+00 4.78e+01 angle pdb=" OE1 GLN y 351 " pdb=" CD GLN y 351 " pdb=" NE2 GLN y 351 " ideal model delta sigma weight residual 122.60 115.73 6.87 1.00e+00 1.00e+00 4.73e+01 angle pdb=" N ASP a 321 " pdb=" CA ASP a 321 " pdb=" C ASP a 321 " ideal model delta sigma weight residual 111.74 120.45 -8.71 1.35e+00 5.49e-01 4.17e+01 ... (remaining 22501 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 6.50: 8849 6.50 - 13.00: 557 13.00 - 19.51: 96 19.51 - 26.01: 22 26.01 - 32.51: 6 Dihedral angle restraints: 9530 sinusoidal: 28 harmonic: 9502 Sorted by residual: dihedral pdb=" CA SER B 274 " pdb=" C SER B 274 " pdb=" N ASP B 275 " pdb=" CA ASP B 275 " ideal model delta harmonic sigma weight residual -180.00 -149.88 -30.12 0 5.00e+00 4.00e-02 3.63e+01 dihedral pdb=" CA SER b 274 " pdb=" C SER b 274 " pdb=" N ASP b 275 " pdb=" CA ASP b 275 " ideal model delta harmonic sigma weight residual -180.00 -149.91 -30.09 0 5.00e+00 4.00e-02 3.62e+01 dihedral pdb=" CA SER a 458 " pdb=" C SER a 458 " pdb=" N GLU a 459 " pdb=" CA GLU a 459 " ideal model delta harmonic sigma weight residual 180.00 154.18 25.82 0 5.00e+00 4.00e-02 2.67e+01 ... (remaining 9527 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 2440 0.056 - 0.112: 630 0.112 - 0.169: 60 0.169 - 0.225: 6 0.225 - 0.281: 2 Chirality restraints: 3138 Sorted by residual: chirality pdb=" CA ASP A 321 " pdb=" N ASP A 321 " pdb=" C ASP A 321 " pdb=" CB ASP A 321 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.97e+00 chirality pdb=" CA ASP a 321 " pdb=" N ASP a 321 " pdb=" C ASP a 321 " pdb=" CB ASP a 321 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.97e+00 chirality pdb=" CA GLU a 423 " pdb=" N GLU a 423 " pdb=" C GLU a 423 " pdb=" CB GLU a 423 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.99e-01 ... (remaining 3135 not shown) Planarity restraints: 3236 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN a 401 " 0.011 2.00e-02 2.50e+03 2.18e-02 4.73e+00 pdb=" C ASN a 401 " -0.038 2.00e-02 2.50e+03 pdb=" O ASN a 401 " 0.014 2.00e-02 2.50e+03 pdb=" N ALA a 402 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 401 " -0.011 2.00e-02 2.50e+03 2.14e-02 4.59e+00 pdb=" C ASN A 401 " 0.037 2.00e-02 2.50e+03 pdb=" O ASN A 401 " -0.014 2.00e-02 2.50e+03 pdb=" N ALA A 402 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE a 420 " -0.009 2.00e-02 2.50e+03 1.81e-02 3.26e+00 pdb=" C ILE a 420 " 0.031 2.00e-02 2.50e+03 pdb=" O ILE a 420 " -0.012 2.00e-02 2.50e+03 pdb=" N ARG a 421 " -0.010 2.00e-02 2.50e+03 ... (remaining 3233 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 4064 2.79 - 3.32: 16056 3.32 - 3.84: 24955 3.84 - 4.37: 22143 4.37 - 4.90: 38483 Nonbonded interactions: 105701 Sorted by model distance: nonbonded pdb=" O THR M 299 " pdb=" N LEU M 372 " model vdw 2.260 2.520 nonbonded pdb=" O THR m 299 " pdb=" N LEU m 372 " model vdw 2.260 2.520 nonbonded pdb=" O SER b 274 " pdb=" N TYR b 276 " model vdw 2.350 2.520 nonbonded pdb=" O SER B 274 " pdb=" N TYR B 276 " model vdw 2.351 2.520 nonbonded pdb=" O SER A 419 " pdb=" N GLU A 422 " model vdw 2.353 2.520 ... (remaining 105696 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 'a' } ncs_group { reference = chain 'B' selection = chain 'b' } ncs_group { reference = chain 'M' selection = chain 'm' } ncs_group { reference = chain 'S' selection = chain 's' } ncs_group { reference = chain 'Y' selection = chain 'y' } Set up NCS constraints Number of NCS constrained groups: 5 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'a' } pdb_interpretation.ncs_group { reference = chain 'B' selection = chain 'b' } pdb_interpretation.ncs_group { reference = chain 'M' selection = chain 'm' } pdb_interpretation.ncs_group { reference = chain 'S' selection = chain 's' } pdb_interpretation.ncs_group { reference = chain 'Y' selection = chain 'y' } Set refine NCS operators NCS operators will be refined. 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: 1.270 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: 6.660 Check model and map are aligned: 0.220 Set scattering table: 0.140 Process input model: 50.460 Find NCS groups from input model: 1.040 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: 0.000 Load rotamer database and sin/cos tables:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 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 : 0.003 0.038 16144 Z= 0.203 Angle : 0.886 10.299 22506 Z= 0.619 Chirality : 0.047 0.281 3138 Planarity : 0.002 0.022 3236 Dihedral : 5.837 32.509 3258 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.50 % Allowed : 5.79 % Favored : 93.71 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.12 (0.15), residues: 3212 helix: 0.74 (0.12), residues: 1822 sheet: 0.33 (0.28), residues: 340 loop : -1.63 (0.19), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 188 PHE 0.000 0.000 PHE A 16 TYR 0.004 0.000 TYR y 350 ARG 0.002 0.001 ARG Y 352 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6424 Ramachandran restraints generated. 3212 Oldfield, 0 Emsley, 3212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6424 Ramachandran restraints generated. 3212 Oldfield, 0 Emsley, 3212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 10 residues out of total 526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 10 time to evaluate : 0.368 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 10 average time/residue: 0.0382 time to fit residues: 1.2252 Evaluate side-chains 10 residues out of total 526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 10 time to evaluate : 0.321 Evaluate side-chains 7 residues out of total 447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 7 time to evaluate : 0.266 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 7 average time/residue: 0.0263 time to fit residues: 0.7744 Evaluate side-chains 7 residues out of total 447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 7 time to evaluate : 0.311 Evaluate side-chains 13 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.229 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0219 time to fit residues: 0.8399 Evaluate side-chains 13 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.208 Evaluate side-chains 4 residues out of total 131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 4 time to evaluate : 0.078 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.0101 time to fit residues: 0.1821 Evaluate side-chains 4 residues out of total 131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 4 time to evaluate : 0.091 Evaluate side-chains 1 residues out of total 5 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1 time to evaluate : 0.007 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 1 average time/residue: 0.1406 time to fit residues: 0.1519 Evaluate side-chains 0 residues out of total 5 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 270 optimal weight: 0.0370 chunk 242 optimal weight: 0.7980 chunk 134 optimal weight: 40.0000 chunk 82 optimal weight: 5.9990 chunk 163 optimal weight: 5.9990 chunk 129 optimal weight: 8.9990 chunk 250 optimal weight: 1.9990 chunk 97 optimal weight: 20.0000 chunk 152 optimal weight: 30.0000 chunk 186 optimal weight: 30.0000 chunk 290 optimal weight: 20.0000 overall best weight: 2.9664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.1394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 16144 Z= 0.119 Angle : 0.458 7.230 22506 Z= 0.289 Chirality : 0.042 0.139 3138 Planarity : 0.002 0.018 3236 Dihedral : 4.659 28.205 3232 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 1.32 Ramachandran Plot: Outliers : 0.37 % Allowed : 4.42 % Favored : 95.21 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 1.04 (0.15), residues: 3212 helix: 1.82 (0.12), residues: 1886 sheet: 0.62 (0.28), residues: 326 loop : -1.54 (0.20), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 188 PHE 0.000 0.000 PHE A 16 TYR 0.006 0.000 TYR Y 350 ARG 0.005 0.002 ARG Y 352 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4534 Ramachandran restraints generated. 2267 Oldfield, 0 Emsley, 2267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4534 Ramachandran restraints generated. 2267 Oldfield, 0 Emsley, 2267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 10 residues out of total 526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 10 time to evaluate : 0.380 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 10 average time/residue: 0.0321 time to fit residues: 1.1518 Evaluate side-chains 10 residues out of total 526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 10 time to evaluate : 0.383 Evaluate side-chains 7 residues out of total 447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 7 time to evaluate : 0.234 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 7 average time/residue: 0.0214 time to fit residues: 0.6241 Evaluate side-chains 7 residues out of total 447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 7 time to evaluate : 0.338 Evaluate side-chains 13 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.234 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0217 time to fit residues: 0.8460 Evaluate side-chains 13 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.237 Evaluate side-chains 4 residues out of total 131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 4 time to evaluate : 0.090 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.0111 time to fit residues: 0.2090 Evaluate side-chains 4 residues out of total 131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 4 time to evaluate : 0.094 Evaluate side-chains 1 residues out of total 5 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1 time to evaluate : 0.008 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 1 average time/residue: 0.0587 time to fit residues: 0.0716 Evaluate side-chains 1 residues out of total 5 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1 time to evaluate : 0.007 ------------------------------------------------------------------------------- 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-dev-5265/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-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 798, in minimization_ncs ncs_groups = ncs_groups) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 400, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 133, in refine refine_sites = True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 434, in __init__ ignore_line_search_failed_maxfev=True)) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 459, in compute_functional_and_gradients x=self.x) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 248, in target_and_gradients grad = g_data) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 112, in restraints_target_and_grads compute_gradients = True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-dev-5265/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-dev-5265/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: 66.3188 > 50: distance: 0 - 1: 5.451 distance: 1 - 2: 5.558 distance: 1 - 4: 6.337 distance: 2 - 3: 4.075 distance: 2 - 5: 17.876 distance: 3 - 20: 29.152 distance: 5 - 6: 9.318 distance: 6 - 7: 23.020 distance: 6 - 9: 14.543 distance: 7 - 8: 14.632 distance: 7 - 10: 32.021 distance: 10 - 11: 19.288 distance: 11 - 12: 23.907 distance: 11 - 14: 19.287 distance: 12 - 13: 5.828 distance: 12 - 15: 44.441 distance: 15 - 16: 66.319 distance: 16 - 17: 38.234 distance: 16 - 19: 43.215 distance: 17 - 18: 21.119 distance: 17 - 20: 42.365 distance: 20 - 21: 56.074 distance: 21 - 22: 37.053 distance: 21 - 24: 37.644 distance: 22 - 23: 16.587 distance: 22 - 25: 26.482 distance: 25 - 26: 26.755 distance: 26 - 27: 51.926 distance: 26 - 29: 45.997 distance: 27 - 28: 60.524 distance: 27 - 30: 51.826 distance: 30 - 31: 56.592 distance: 31 - 32: 9.061 distance: 31 - 34: 56.604 distance: 32 - 33: 49.858 distance: 32 - 35: 40.227 distance: 35 - 36: 14.028 distance: 36 - 37: 49.954 distance: 36 - 39: 40.226 distance: 37 - 38: 50.759 distance: 37 - 40: 50.653 distance: 40 - 41: 48.280 distance: 41 - 42: 40.287 distance: 41 - 44: 49.421 distance: 42 - 43: 45.880 distance: 42 - 45: 39.005 distance: 45 - 46: 16.446 distance: 46 - 47: 7.611 distance: 46 - 49: 7.945 distance: 47 - 48: 4.737