Starting phenix.real_space_refine on Sat Jun 14 15:09:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rwa_24712/06_2025/7rwa_24712.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rwa_24712/06_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_24712/06_2025/7rwa_24712.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rwa_24712/06_2025/7rwa_24712.map" model { file = "/net/cci-nas-00/data/ceres_data/7rwa_24712/06_2025/7rwa_24712.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rwa_24712/06_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-5710/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: 11.54, per 1000 atoms: 0.71 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: 4.97 Conformation dependent library (CDL) restraints added in 3.2 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: 2.41 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: 6.30 Time building geometry restraints manager: 5.66 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: 0.12 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: 1.230 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: 0.670 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 44.130 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.060 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:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.380 ------------------------------------------------------------------------------- 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 : 0.008 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 1 average time/residue: 0.1637 time to fit residues: 0.1764 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 : 0.283 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 10 average time/residue: 0.0520 time to fit residues: 1.5652 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 : 0.371 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 : 0.225 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0207 time to fit residues: 0.8069 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 : 0.203 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 : 0.081 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.0100 time to fit residues: 0.1971 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 : 0.078 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 : 0.274 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 7 average time/residue: 0.0256 time to fit residues: 0.7148 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 : 0.305 ------------------------------------------------------------------------------- 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 = 0.062749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 21)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.056660 restraints weight = 565.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.057957 restraints weight = 396.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.058931 restraints weight = 283.230| |-----------------------------------------------------------------------------| r_work (final): 0.2891 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.053737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.037180 restraints weight = 22338.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.036912 restraints weight = 24456.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.036699 restraints weight = 26345.600| |-----------------------------------------------------------------------------| r_work (final): 0.2882 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.038645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.033621 restraints weight = 61807.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.033129 restraints weight = 81828.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.032771 restraints weight = 100245.328| |-----------------------------------------------------------------------------| r_work (final): 0.2682 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.041105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2767 r_free = 0.2767 target = 0.035291 restraints weight = 9850.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.035780 restraints weight = 7846.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.036163 restraints weight = 6522.739| |-----------------------------------------------------------------------------| r_work (final): 0.2781 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.048527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.038783 restraints weight = 35837.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.039208 restraints weight = 29862.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.039515 restraints weight = 25927.405| |-----------------------------------------------------------------------------| r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6560 moved from start: 0.1443 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= 0.127 Angle : 0.463 7.224 22506 Z= 0.290 Chirality : 0.042 0.137 3138 Planarity : 0.002 0.013 3236 Dihedral : 4.603 28.089 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 0.03728 ( 1528) hydrogen bonds : angle 4.56279 ( 4590) covalent geometry : bond 0.00163 (16144) covalent geometry : angle 0.46307 (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 : 0.007 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 1 average time/residue: 0.0516 time to fit residues: 0.0634 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 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 : 0.309 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 10 average time/residue: 0.0286 time to fit residues: 1.0285 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 : 0.353 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 : 0.211 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0212 time to fit residues: 0.7842 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 : 0.201 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 : 0.087 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.0101 time to fit residues: 0.1827 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 : 0.276 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 7 average time/residue: 0.0252 time to fit residues: 0.7189 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 : 0.278 ------------------------------------------------------------------------------- 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: 20.0000 chunk 30 optimal weight: 3.9990 chunk 57 optimal weight: 20.0000 chunk 279 optimal weight: 9.9990 chunk 60 optimal weight: 50.0000 chunk 143 optimal weight: 0.0270 chunk 52 optimal weight: 0.7980 chunk 215 optimal weight: 9.9990 chunk 59 optimal weight: 0.0970 chunk 255 optimal weight: 0.9990 chunk 17 optimal weight: 0.0970 overall best weight: 0.4036 ------------------------------------------------------------------------------- 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 = 0.3100 r_free = 0.3100 target = 0.063229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.059892 restraints weight = 436.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.060783 restraints weight = 245.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.061419 restraints weight = 158.428| |-----------------------------------------------------------------------------| r_work (final): 0.3044 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.041579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.032064 restraints weight = 57184.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.032064 restraints weight = 59240.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.032064 restraints weight = 59240.531| |-----------------------------------------------------------------------------| r_work (final): 0.2718 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.043510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.036455 restraints weight = 29831.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.036581 restraints weight = 28320.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.036647 restraints weight = 27200.856| |-----------------------------------------------------------------------------| r_work (final): 0.2967 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.041134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.035430 restraints weight = 9861.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.035898 restraints weight = 7730.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.036316 restraints weight = 6425.233| |-----------------------------------------------------------------------------| r_work (final): 0.2788 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.048938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.038962 restraints weight = 35014.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.039371 restraints weight = 29237.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.039635 restraints weight = 25197.714| |-----------------------------------------------------------------------------| r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6612 moved from start: 0.1563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.121 16144 Z= 0.144 Angle : 0.557 7.983 22506 Z= 0.347 Chirality : 0.046 0.199 3138 Planarity : 0.003 0.046 3236 Dihedral : 4.672 26.049 3232 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 1.11 Ramachandran Plot: Outliers : 0.37 % Allowed : 4.73 % Favored : 94.89 % 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: 0.28 (0.14), residues: 3212 helix: 1.19 (0.11), residues: 1918 sheet: 0.28 (0.28), residues: 328 loop : -1.92 (0.19), residues: 966 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 0.003 0.000 TYR y 350 ARG 0.000 0.000 ARG y 352 Details of bonding type rmsd hydrogen bonds : bond 0.03761 ( 1528) hydrogen bonds : angle 4.58431 ( 4590) covalent geometry : bond 0.00239 (16144) covalent geometry : angle 0.55660 (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 : 0.007 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0105 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 : 0.328 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 10 average time/residue: 0.0286 time to fit residues: 1.0255 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 : 0.332 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 : 0.203 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0201 time to fit residues: 0.7798 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 : 0.218 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 : 0.079 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.0099 time to fit residues: 0.1866 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 : 0.078 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 : 0.269 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 7 average time/residue: 0.0249 time to fit residues: 0.7354 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 : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 9 optimal weight: 3.9990 chunk 132 optimal weight: 0.2980 chunk 224 optimal weight: 9.9990 chunk 69 optimal weight: 0.0010 chunk 177 optimal weight: 30.0000 chunk 199 optimal weight: 8.9990 chunk 6 optimal weight: 7.9990 chunk 104 optimal weight: 0.0170 chunk 196 optimal weight: 50.0000 chunk 251 optimal weight: 0.0470 chunk 272 optimal weight: 10.0000 overall best weight: 0.8724 ------------------------------------------------------------------------------- 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 = 0.3190 r_free = 0.3190 target = 0.067068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 20)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.062199 restraints weight = 570.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.063376 restraints weight = 328.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.064225 restraints weight = 210.947| |-----------------------------------------------------------------------------| r_work (final): 0.3113 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.041218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2755 r_free = 0.2755 target = 0.031630 restraints weight = 57165.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2755 r_free = 0.2755 target = 0.031630 restraints weight = 58813.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2755 r_free = 0.2755 target = 0.031630 restraints weight = 58813.738| |-----------------------------------------------------------------------------| r_work (final): 0.2694 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.043510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.036481 restraints weight = 29411.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.036544 restraints weight = 27989.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.036544 restraints weight = 27348.524| |-----------------------------------------------------------------------------| r_work (final): 0.2962 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.041134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.035430 restraints weight = 9858.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 17)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.035899 restraints weight = 7728.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.036316 restraints weight = 6423.233| |-----------------------------------------------------------------------------| r_work (final): 0.2788 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.048949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.038995 restraints weight = 34724.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.039414 restraints weight = 29051.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.039765 restraints weight = 25088.037| |-----------------------------------------------------------------------------| r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6598 moved from start: 0.1563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.121 16144 Z= 0.144 Angle : 0.557 7.983 22506 Z= 0.347 Chirality : 0.046 0.199 3138 Planarity : 0.003 0.046 3236 Dihedral : 4.672 26.049 3232 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 1.11 Ramachandran Plot: Outliers : 0.37 % Allowed : 4.73 % Favored : 94.89 % 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: 0.28 (0.14), residues: 3212 helix: 1.19 (0.11), residues: 1918 sheet: 0.28 (0.28), residues: 328 loop : -1.92 (0.19), residues: 966 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 0.003 0.000 TYR Y 350 ARG 0.000 0.000 ARG Y 352 Details of bonding type rmsd hydrogen bonds : bond 0.03761 ( 1528) hydrogen bonds : angle 4.58432 ( 4590) covalent geometry : bond 0.00239 (16144) covalent geometry : angle 0.55659 (22506) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3786 Ramachandran restraints generated. 1893 Oldfield, 0 Emsley, 1893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3786 Ramachandran restraints generated. 1893 Oldfield, 0 Emsley, 1893 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 : 0.007 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0123 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 : 0.008 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 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 10 average time/residue: 0.0316 time to fit residues: 1.1441 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 : 0.242 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0215 time to fit residues: 0.8789 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 : 0.208 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 : 0.086 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.0107 time to fit residues: 0.1924 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 : 0.088 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 : 0.272 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 7 average time/residue: 0.0263 time to fit residues: 0.7879 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 : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 164 optimal weight: 0.0970 chunk 60 optimal weight: 50.0000 chunk 20 optimal weight: 7.9990 chunk 16 optimal weight: 2.9990 chunk 49 optimal weight: 20.0000 chunk 225 optimal weight: 8.9990 chunk 77 optimal weight: 0.4980 chunk 24 optimal weight: 0.9990 chunk 46 optimal weight: 6.9990 chunk 165 optimal weight: 0.0270 chunk 198 optimal weight: 30.0000 overall best weight: 0.9240 ------------------------------------------------------------------------------- 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 = 0.3190 r_free = 0.3190 target = 0.067068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.062497 restraints weight = 509.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.063560 restraints weight = 299.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.064350 restraints weight = 197.112| |-----------------------------------------------------------------------------| r_work (final): 0.3116 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.041219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.031632 restraints weight = 56691.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.031594 restraints weight = 58712.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.031550 restraints weight = 59789.826| |-----------------------------------------------------------------------------| r_work (final): 0.2692 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.043510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.036486 restraints weight = 29429.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.036537 restraints weight = 27992.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.036543 restraints weight = 27369.253| |-----------------------------------------------------------------------------| r_work (final): 0.2962 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.041134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.035463 restraints weight = 9618.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.035979 restraints weight = 7650.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.036361 restraints weight = 6297.559| |-----------------------------------------------------------------------------| r_work (final): 0.2790 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.048949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.039017 restraints weight = 34783.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.039457 restraints weight = 28826.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.039772 restraints weight = 24865.542| |-----------------------------------------------------------------------------| r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6599 moved from start: 0.1563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.121 16144 Z= 0.142 Angle : 0.556 7.975 22506 Z= 0.347 Chirality : 0.046 0.198 3138 Planarity : 0.003 0.046 3236 Dihedral : 4.672 26.051 3232 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 1.11 Ramachandran Plot: Outliers : 0.37 % Allowed : 4.73 % Favored : 94.89 % 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: 0.28 (0.14), residues: 3212 helix: 1.19 (0.11), residues: 1918 sheet: 0.28 (0.28), residues: 328 loop : -1.92 (0.19), residues: 966 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 0.003 0.000 TYR Y 350 ARG 0.000 0.000 ARG Y 352 Details of bonding type rmsd hydrogen bonds : bond 0.03761 ( 1528) hydrogen bonds : angle 4.58447 ( 4590) covalent geometry : bond 0.00238 (16144) covalent geometry : angle 0.55638 (22506) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3786 Ramachandran restraints generated. 1893 Oldfield, 0 Emsley, 1893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3786 Ramachandran restraints generated. 1893 Oldfield, 0 Emsley, 1893 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 : 0.008 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0120 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 : 0.008 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 : 0.369 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 10 average time/residue: 0.0324 time to fit residues: 1.1482 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 : 0.318 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 : 0.204 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0216 time to fit residues: 0.7828 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 : 0.206 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 : 0.094 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.0137 time to fit residues: 0.2417 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 : 0.069 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 : 0.233 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 7 average time/residue: 0.0214 time to fit residues: 0.6126 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 : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 49 optimal weight: 20.0000 chunk 291 optimal weight: 40.0000 chunk 39 optimal weight: 2.9990 chunk 141 optimal weight: 4.9990 chunk 193 optimal weight: 50.0000 chunk 27 optimal weight: 6.9990 chunk 151 optimal weight: 10.0000 chunk 183 optimal weight: 10.0000 chunk 281 optimal weight: 10.0000 chunk 305 optimal weight: 5.9990 chunk 212 optimal weight: 6.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- 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 = 0.3174 r_free = 0.3174 target = 0.065893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.060643 restraints weight = 484.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.062487 restraints weight = 303.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.063457 restraints weight = 201.921| |-----------------------------------------------------------------------------| r_work (final): 0.3096 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.039166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2676 r_free = 0.2676 target = 0.030665 restraints weight = 85799.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2672 r_free = 0.2672 target = 0.030533 restraints weight = 91539.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2668 r_free = 0.2668 target = 0.030431 restraints weight = 96451.967| |-----------------------------------------------------------------------------| r_work (final): 0.2659 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.037526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.032119 restraints weight = 66010.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2719 r_free = 0.2719 target = 0.031354 restraints weight = 91322.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2710 r_free = 0.2710 target = 0.031099 restraints weight = 127565.934| |-----------------------------------------------------------------------------| r_work (final): 0.2600 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.039067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2736 r_free = 0.2736 target = 0.033741 restraints weight = 10584.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.034180 restraints weight = 8408.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.034569 restraints weight = 7033.555| |-----------------------------------------------------------------------------| r_work (final): 0.2753 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.045018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.033847 restraints weight = 38343.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.033886 restraints weight = 38000.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.033927 restraints weight = 37339.344| |-----------------------------------------------------------------------------| r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5374 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 16144 Z= 0.170 Angle : 0.515 6.615 22506 Z= 0.331 Chirality : 0.043 0.149 3138 Planarity : 0.004 0.042 3236 Dihedral : 4.844 31.734 3232 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 1.71 Ramachandran Plot: Outliers : 0.37 % Allowed : 7.29 % Favored : 92.34 % Rotamer: Outliers : 0.00 % Allowed : 40.00 % Favored : 60.00 % 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: -0.96 (0.14), residues: 3212 helix: 0.38 (0.11), residues: 1892 sheet: -0.77 (0.27), residues: 330 loop : -2.54 (0.18), 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 0.006 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 4.68369 ( 4590) covalent geometry : bond 0.00235 (16144) covalent geometry : angle 0.51474 (22506) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3786 Ramachandran restraints generated. 1893 Oldfield, 0 Emsley, 1893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3786 Ramachandran restraints generated. 1893 Oldfield, 0 Emsley, 1893 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 : 0.007 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0112 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 : 0.008 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 : 0.330 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 10 average time/residue: 0.0311 time to fit residues: 1.1076 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 : 0.382 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 : 0.205 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0217 time to fit residues: 0.8043 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 : 0.226 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 : 0.099 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.0124 time to fit residues: 0.2440 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 : 0.082 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 : 0.272 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 7 average time/residue: 0.0262 time to fit residues: 0.7718 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 : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 704, in refine_xyz self.minimization_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 400, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 133, in refine refine_sites = True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/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-5710/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-5710/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-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 72.5838 > 50: distance: 2 - 3: 25.741 distance: 3 - 4: 42.284 distance: 3 - 6: 29.562 distance: 4 - 5: 45.179 distance: 4 - 7: 19.854 distance: 7 - 8: 49.480 distance: 8 - 9: 28.229 distance: 8 - 11: 39.060 distance: 9 - 10: 39.672 distance: 9 - 12: 55.913 distance: 12 - 13: 7.741 distance: 13 - 14: 28.604 distance: 13 - 16: 53.062 distance: 14 - 15: 48.688 distance: 14 - 17: 53.547 distance: 15 - 32: 38.915 distance: 17 - 18: 36.401 distance: 18 - 19: 52.198 distance: 18 - 21: 55.866 distance: 19 - 20: 57.701 distance: 19 - 22: 37.213 distance: 20 - 37: 53.747 distance: 22 - 23: 30.332 distance: 23 - 24: 55.224 distance: 23 - 26: 48.294 distance: 24 - 25: 39.692 distance: 24 - 27: 43.148 distance: 25 - 42: 54.389 distance: 27 - 28: 33.114 distance: 28 - 29: 43.438 distance: 28 - 31: 62.480 distance: 29 - 30: 32.129 distance: 29 - 32: 40.373 distance: 30 - 47: 35.416 distance: 32 - 33: 40.917 distance: 33 - 34: 41.173 distance: 33 - 36: 68.963 distance: 34 - 35: 55.843 distance: 34 - 37: 40.020 distance: 37 - 38: 40.090 distance: 38 - 39: 55.746 distance: 38 - 41: 53.531 distance: 39 - 40: 40.095 distance: 39 - 42: 41.184 distance: 42 - 43: 39.454 distance: 43 - 44: 29.159 distance: 43 - 46: 55.124 distance: 44 - 45: 49.461 distance: 44 - 47: 36.243 distance: 47 - 48: 19.943 distance: 48 - 49: 44.556