Starting phenix.real_space_refine on Sat May 17 23:30:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rwa_24712/05_2025/7rwa_24712.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rwa_24712/05_2025/7rwa_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/cci-nas-00/data/ceres_data/7rwa_24712/05_2025/7rwa_24712.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rwa_24712/05_2025/7rwa_24712.map" model { file = "/net/cci-nas-00/data/ceres_data/7rwa_24712/05_2025/7rwa_24712.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rwa_24712/05_2025/7rwa_24712.cif" } 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 Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 16158 Number of models: 1 Model: "" Number of chains: 5 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} Restraints were copied for chains: Y, a, M, S, b Time building chain proxies: 11.89, per 1000 atoms: 0.74 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 - 3.00 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: 4.93 Conformation dependent library (CDL) restraints added in 3.1 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: 2.52 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: 6.79 Time building geometry restraints manager: 5.52 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: 0.00 - 2.06: 21728 2.06 - 4.12: 686 4.12 - 6.18: 64 6.18 - 8.24: 15 8.24 - 10.30: 13 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 3.120 nonbonded pdb=" O THR m 299 " pdb=" N LEU m 372 " model vdw 2.260 3.120 nonbonded pdb=" O SER b 274 " pdb=" N TYR b 276 " model vdw 2.350 3.120 nonbonded pdb=" O SER B 274 " pdb=" N TYR B 276 " model vdw 2.351 3.120 nonbonded pdb=" O SER A 419 " pdb=" N GLU A 422 " model vdw 2.353 3.120 ... (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 Time spend for trying shortcut: 0.13 Found NCS groups: ncs_group { reference = chain 'y' selection = chain 'Y' } ncs_group { reference = chain 'A' selection = chain 'a' } ncs_group { reference = chain 'm' selection = chain 'M' } ncs_group { reference = chain 's' selection = chain 'S' } ncs_group { reference = chain 'B' selection = chain 'b' } Set up NCS constraints Number of NCS constrained groups: 5 pdb_interpretation.ncs_group { reference = chain 'y' selection = chain 'Y' } pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'a' } 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 'B' selection = chain 'b' } 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: 2.270 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: 0.020 Extract box with map and model: 0.630 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 44.290 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.050 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.670 ------------------------------------------------------------------------------- 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= 0.201 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 Details of bonding type rmsd hydrogen bonds : bond 0.17051 ( 1528) hydrogen bonds : angle 7.17457 ( 4590) covalent geometry : bond 0.00278 (16144) covalent geometry : angle 0.88643 (22506) *********************** 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 1 residues out of total 5 (non-[ALA,GLY,PRO]) need to be fit. 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: 0.1481 time to fit residues: 0.1592 Evaluate side-chains 0 residues out of total 5 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.006 Evaluate side-chains 10 residues out of total 526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.317 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 10 average time/residue: 0.0332 time to fit residues: 1.0146 Evaluate side-chains 10 residues out of total 526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.303 Evaluate side-chains 13 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.190 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0197 time to fit residues: 0.7302 Evaluate side-chains 13 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.194 Evaluate side-chains 4 residues out of total 131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.073 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.0097 time to fit residues: 0.1719 Evaluate side-chains 4 residues out of total 131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.074 Evaluate side-chains 7 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 7 time to evaluate : 0.256 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 7 average time/residue: 0.0238 time to fit residues: 0.6797 Evaluate side-chains 7 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 7 time to evaluate : 0.250 ------------------------------------------------------------------------------- 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: 0.8980 chunk 242 optimal weight: 8.9990 chunk 134 optimal weight: 3.9990 chunk 82 optimal weight: 10.0000 chunk 163 optimal weight: 0.8980 chunk 129 optimal weight: 0.8980 chunk 250 optimal weight: 6.9990 chunk 97 optimal weight: 30.0000 chunk 152 optimal weight: 30.0000 chunk 186 optimal weight: 5.9990 chunk 290 optimal weight: 50.0000 overall best weight: 2.5384 ------------------------------------------------------------------------------- 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 ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.062748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.056664 restraints weight = 565.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.057922 restraints weight = 396.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.058864 restraints weight = 286.388| |-----------------------------------------------------------------------------| r_work (final): 0.2890 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.053749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.037163 restraints weight = 22342.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.036909 restraints weight = 24410.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.036689 restraints weight = 26230.843| |-----------------------------------------------------------------------------| r_work (final): 0.2884 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.038647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.033301 restraints weight = 62110.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.032569 restraints weight = 112699.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2749 r_free = 0.2749 target = 0.032266 restraints weight = 144693.489| |-----------------------------------------------------------------------------| r_work (final): 0.2651 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.041104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.035262 restraints weight = 9850.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.035774 restraints weight = 7943.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.036101 restraints weight = 6565.027| |-----------------------------------------------------------------------------| r_work (final): 0.2778 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.048526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.038779 restraints weight = 35836.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.039202 restraints weight = 29902.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.039444 restraints weight = 25941.309| |-----------------------------------------------------------------------------| r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6574 moved from start: 0.1444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 16144 Z= 0.128 Angle : 0.463 7.224 22506 Z= 0.291 Chirality : 0.042 0.137 3138 Planarity : 0.002 0.013 3236 Dihedral : 4.603 28.084 3232 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 0.60 Ramachandran Plot: Outliers : 0.37 % Allowed : 3.99 % Favored : 95.64 % 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: 1.05 (0.15), residues: 3212 helix: 1.84 (0.12), residues: 1892 sheet: 0.47 (0.28), residues: 330 loop : -1.54 (0.20), residues: 990 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 0.008 0.000 TYR y 350 ARG 0.002 0.001 ARG y 352 Details of bonding type rmsd hydrogen bonds : bond 0.03727 ( 1528) hydrogen bonds : angle 4.56246 ( 4590) covalent geometry : bond 0.00163 (16144) covalent geometry : angle 0.46310 (22506) *********************** 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 1 residues out of total 5 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1 time to evaluate : 0.012 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 1 average time/residue: 0.0579 time to fit residues: 0.0708 Evaluate side-chains 1 residues out of total 5 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1 time to evaluate : 0.009 Evaluate side-chains 10 residues out of total 526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.363 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 10 average time/residue: 0.0305 time to fit residues: 1.0994 Evaluate side-chains 10 residues out of total 526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.357 Evaluate side-chains 13 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.232 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0211 time to fit residues: 0.8189 Evaluate side-chains 13 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.214 Evaluate side-chains 4 residues out of total 131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.085 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.0107 time to fit residues: 0.1983 Evaluate side-chains 4 residues out of total 131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.085 Evaluate side-chains 7 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 7 time to evaluate : 0.289 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 7 average time/residue: 0.0263 time to fit residues: 0.7639 Evaluate side-chains 7 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 7 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 107 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 57 optimal weight: 20.0000 chunk 279 optimal weight: 5.9990 chunk 60 optimal weight: 50.0000 chunk 143 optimal weight: 0.2980 chunk 52 optimal weight: 0.0980 chunk 215 optimal weight: 8.9990 chunk 59 optimal weight: 0.7980 chunk 255 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.065691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.061914 restraints weight = 477.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.063179 restraints weight = 287.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.063843 restraints weight = 188.061| |-----------------------------------------------------------------------------| r_work (final): 0.3058 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.042170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.032687 restraints weight = 56599.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.032687 restraints weight = 59144.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.032687 restraints weight = 59145.776| |-----------------------------------------------------------------------------| r_work (final): 0.3117 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.038827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.033775 restraints weight = 66094.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.033263 restraints weight = 87089.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.033184 restraints weight = 106057.027| |-----------------------------------------------------------------------------| r_work (final): 0.2708 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.041109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.036274 restraints weight = 10066.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.036530 restraints weight = 8413.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.036872 restraints weight = 7380.599| |-----------------------------------------------------------------------------| r_work (final): 0.2808 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.048930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.039002 restraints weight = 35321.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.039473 restraints weight = 29567.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.039716 restraints weight = 25304.360| |-----------------------------------------------------------------------------| r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6750 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 16144 Z= 0.116 Angle : 0.504 7.901 22506 Z= 0.316 Chirality : 0.045 0.190 3138 Planarity : 0.004 0.044 3236 Dihedral : 4.514 25.758 3232 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 0.68 Ramachandran Plot: Outliers : 0.37 % Allowed : 5.17 % Favored : 94.46 % Rotamer: Outliers : 0.00 % Allowed : 20.00 % Favored : 80.00 % 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: 0.23 (0.15), residues: 3212 helix: 1.25 (0.12), residues: 1898 sheet: 0.23 (0.28), residues: 328 loop : -2.09 (0.18), residues: 986 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 0.001 0.000 TYR Y 350 ARG 0.001 0.001 ARG Y 352 Details of bonding type rmsd hydrogen bonds : bond 0.03475 ( 1528) hydrogen bonds : angle 4.40620 ( 4590) covalent geometry : bond 0.00168 (16144) covalent geometry : angle 0.50420 (22506) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 0 residues out of total 5 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.009 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0141 Evaluate side-chains 0 residues out of total 5 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.007 Evaluate side-chains 10 residues out of total 526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.317 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 10 average time/residue: 0.0282 time to fit residues: 0.9827 Evaluate side-chains 10 residues out of total 526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.331 Evaluate side-chains 13 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.213 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0206 time to fit residues: 0.7819 Evaluate side-chains 13 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.191 Evaluate side-chains 4 residues out of total 131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.073 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.0099 time to fit residues: 0.1752 Evaluate side-chains 4 residues out of total 131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.077 Evaluate side-chains 7 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 7 time to evaluate : 0.247 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 7 average time/residue: 0.0244 time to fit residues: 0.6843 Evaluate side-chains 7 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 7 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 704, in refine_xyz self.minimization_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 801, in minimization_ncs ncs_groups = ncs_groups) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/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-5687/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-5687/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-5687/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-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/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-5687/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-5687/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-5687/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-5687/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-5687/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: 71.1308 > 50: distance: 0 - 1: 58.104 distance: 1 - 2: 44.310 distance: 1 - 4: 56.614 distance: 2 - 3: 5.774 distance: 2 - 5: 69.917 distance: 5 - 6: 40.259 distance: 6 - 7: 55.602 distance: 6 - 9: 68.338 distance: 7 - 8: 57.752 distance: 7 - 10: 55.607 distance: 10 - 11: 40.338 distance: 11 - 14: 25.847 distance: 12 - 13: 40.488 distance: 12 - 15: 24.491 distance: 15 - 16: 61.848 distance: 16 - 17: 41.012 distance: 16 - 19: 69.390 distance: 17 - 18: 56.516 distance: 17 - 20: 57.545 distance: 20 - 21: 39.643 distance: 21 - 22: 56.649 distance: 21 - 24: 56.359 distance: 22 - 23: 38.996 distance: 22 - 25: 40.649 distance: 25 - 26: 40.764 distance: 26 - 29: 56.820 distance: 27 - 28: 43.416 distance: 27 - 30: 56.378 distance: 31 - 32: 41.054 distance: 31 - 34: 64.007 distance: 32 - 33: 39.964 distance: 32 - 35: 50.590 distance: 35 - 36: 36.741 distance: 36 - 37: 32.796 distance: 36 - 39: 5.904 distance: 37 - 38: 41.004 distance: 37 - 40: 24.883 distance: 40 - 41: 41.260 distance: 41 - 42: 57.449 distance: 41 - 44: 49.363 distance: 42 - 43: 45.201 distance: 42 - 45: 46.922 distance: 45 - 46: 52.200 distance: 46 - 47: 66.637 distance: 46 - 49: 55.884 distance: 47 - 48: 55.336