Starting phenix.real_space_refine on Sat Jun 21 05:53:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xl4_33272/06_2025/7xl4_33272.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xl4_33272/06_2025/7xl4_33272.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xl4_33272/06_2025/7xl4_33272.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xl4_33272/06_2025/7xl4_33272.map" model { file = "/net/cci-nas-00/data/ceres_data/7xl4_33272/06_2025/7xl4_33272.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xl4_33272/06_2025/7xl4_33272.cif" } resolution = 3.86 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 24 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 Mg 1 5.21 5 S 82 5.16 5 C 15397 2.51 5 N 4497 2.21 5 O 4581 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 93 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 24560 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1700 Classifications: {'peptide': 225} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 6, 'TRANS': 218} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 23 Chain: "B" Number of atoms: 1568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1568 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 6, 'TRANS': 205} Chain breaks: 2 Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'HIS:plan': 1, 'ARG:plan': 4, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 53 Chain: "C" Number of atoms: 9297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1324, 9297 Classifications: {'peptide': 1324} Incomplete info: {'truncation_to_alanine': 254} Link IDs: {'PTRANS': 53, 'TRANS': 1270} Chain breaks: 1 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 1073 Unresolved non-hydrogen angles: 1385 Unresolved non-hydrogen dihedrals: 842 Unresolved non-hydrogen chiralities: 110 Planarities with less than four sites: {'GLN:plan1': 12, 'HIS:plan': 7, 'TYR:plan': 10, 'ASN:plan1': 16, 'TRP:plan': 1, 'ASP:plan': 31, 'PHE:plan': 12, 'GLU:plan': 45, 'ARG:plan': 20} Unresolved non-hydrogen planarities: 633 Chain: "D" Number of atoms: 9403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1339, 9403 Classifications: {'peptide': 1339} Incomplete info: {'truncation_to_alanine': 221} Link IDs: {'PTRANS': 60, 'TRANS': 1278} Chain breaks: 2 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 1022 Unresolved non-hydrogen angles: 1309 Unresolved non-hydrogen dihedrals: 805 Unresolved non-hydrogen chiralities: 82 Planarities with less than four sites: {'GLN:plan1': 11, 'HIS:plan': 6, 'TYR:plan': 5, 'ASN:plan1': 16, 'TRP:plan': 2, 'ASP:plan': 43, 'PHE:plan': 10, 'GLU:plan': 48, 'ARG:plan': 23} Unresolved non-hydrogen planarities: 630 Chain: "E" Number of atoms: 500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 500 Classifications: {'peptide': 70} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 2, 'TRANS': 67} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 31 Chain: "G" Number of atoms: 194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 194 Classifications: {'peptide': 31} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 1, 'TRANS': 29} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 36 Chain: "F" Number of atoms: 1895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 1895 Classifications: {'peptide': 278} Incomplete info: {'truncation_to_alanine': 81} Link IDs: {'PTRANS': 11, 'TRANS': 266} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 371 Unresolved non-hydrogen angles: 478 Unresolved non-hydrogen dihedrals: 292 Unresolved non-hydrogen chiralities: 37 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 11, 'ASN:plan1': 3, 'TRP:plan': 1, 'HIS:plan': 3, 'PHE:plan': 5, 'GLU:plan': 16, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 213 Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 13014 SG CYS D 72 114.989 48.653 64.498 1.00 53.33 S ATOM 13114 SG CYS D 85 117.378 48.252 67.785 1.00 53.73 S ATOM 19078 SG CYS D 898 79.659 69.095 122.992 1.00 17.60 S Time building chain proxies: 15.30, per 1000 atoms: 0.62 Number of scatterers: 24560 At special positions: 0 Unit cell: (141.9, 155.1, 155.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 82 16.00 Mg 1 11.99 O 4581 8.00 N 4497 7.00 C 15397 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.36 Conformation dependent library (CDL) restraints added in 3.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1501 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 72 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 85 " pdb=" ZN D1502 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 898 " 6910 Ramachandran restraints generated. 3455 Oldfield, 0 Emsley, 3455 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6428 Finding SS restraints... Secondary structure from input PDB file: 114 helices and 46 sheets defined 37.7% alpha, 12.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.17 Creating SS restraints... Processing helix chain 'A' and resid 35 through 50 removed outlier: 3.580A pdb=" N ARG A 45 " --> pdb=" O ASN A 41 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE A 46 " --> pdb=" O ALA A 42 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU A 48 " --> pdb=" O ARG A 44 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER A 50 " --> pdb=" O ILE A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 85 Processing helix chain 'A' and resid 113 through 115 No H-bonds generated for 'chain 'A' and resid 113 through 115' Processing helix chain 'A' and resid 211 through 232 removed outlier: 3.828A pdb=" N ILE A 216 " --> pdb=" O PRO A 212 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ARG A 217 " --> pdb=" O GLU A 213 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ILE A 222 " --> pdb=" O ARG A 218 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU A 223 " --> pdb=" O ALA A 219 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ALA A 229 " --> pdb=" O GLN A 225 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N PHE A 230 " --> pdb=" O GLN A 226 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N VAL A 231 " --> pdb=" O LEU A 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 49 removed outlier: 3.702A pdb=" N ILE B 46 " --> pdb=" O ALA B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 87 removed outlier: 3.613A pdb=" N ILE B 81 " --> pdb=" O ASP B 77 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU B 82 " --> pdb=" O VAL B 78 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS B 86 " --> pdb=" O LEU B 82 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N GLY B 87 " --> pdb=" O LEU B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 115 No H-bonds generated for 'chain 'B' and resid 113 through 115' Processing helix chain 'B' and resid 211 through 226 removed outlier: 3.866A pdb=" N ILE B 216 " --> pdb=" O PRO B 212 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ARG B 217 " --> pdb=" O GLU B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 231 removed outlier: 3.561A pdb=" N VAL B 231 " --> pdb=" O ALA B 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 40 removed outlier: 3.674A pdb=" N SER C 34 " --> pdb=" O ILE C 30 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TYR C 35 " --> pdb=" O GLN C 31 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLU C 37 " --> pdb=" O ASP C 33 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N PHE C 38 " --> pdb=" O SER C 34 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 58 Processing helix chain 'C' and resid 87 through 92 removed outlier: 3.656A pdb=" N LEU C 91 " --> pdb=" O LYS C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 217 removed outlier: 3.586A pdb=" N ALA C 216 " --> pdb=" O VAL C 212 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LEU C 217 " --> pdb=" O LEU C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 228 removed outlier: 4.000A pdb=" N PHE C 228 " --> pdb=" O ILE C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 284 removed outlier: 3.855A pdb=" N GLU C 283 " --> pdb=" O ILE C 279 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS C 284 " --> pdb=" O ASN C 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 279 through 284' Processing helix chain 'C' and resid 295 through 299 removed outlier: 3.893A pdb=" N ILE C 298 " --> pdb=" O ASP C 295 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N GLY C 299 " --> pdb=" O TYR C 296 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 295 through 299' Processing helix chain 'C' and resid 323 through 333 removed outlier: 3.589A pdb=" N ALA C 328 " --> pdb=" O LEU C 324 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LYS C 329 " --> pdb=" O ASP C 325 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS C 332 " --> pdb=" O ALA C 328 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 356 removed outlier: 3.777A pdb=" N THR C 355 " --> pdb=" O PHE C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 363 through 376 removed outlier: 3.782A pdb=" N ALA C 367 " --> pdb=" O ASN C 363 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N VAL C 369 " --> pdb=" O LEU C 365 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU C 370 " --> pdb=" O GLU C 366 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N TYR C 372 " --> pdb=" O LEU C 368 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ARG C 373 " --> pdb=" O VAL C 369 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N MET C 374 " --> pdb=" O GLU C 370 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N MET C 375 " --> pdb=" O ILE C 371 " (cutoff:3.500A) Processing helix chain 'C' and resid 382 through 391 removed outlier: 3.659A pdb=" N GLU C 387 " --> pdb=" O LYS C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 415 removed outlier: 3.766A pdb=" N ARG C 407 " --> pdb=" O SER C 403 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N MET C 408 " --> pdb=" O ALA C 404 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ARG C 413 " --> pdb=" O LYS C 409 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ILE C 414 " --> pdb=" O PHE C 410 " (cutoff:3.500A) Processing helix chain 'C' and resid 431 through 443 removed outlier: 3.651A pdb=" N LEU C 437 " --> pdb=" O VAL C 433 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N VAL C 438 " --> pdb=" O LEU C 434 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ASP C 439 " --> pdb=" O LYS C 435 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE C 440 " --> pdb=" O THR C 436 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY C 443 " --> pdb=" O ASP C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 452 through 454 No H-bonds generated for 'chain 'C' and resid 452 through 454' Processing helix chain 'C' and resid 460 through 475 removed outlier: 3.626A pdb=" N ASN C 467 " --> pdb=" O GLU C 463 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLN C 468 " --> pdb=" O MET C 464 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLY C 472 " --> pdb=" O GLN C 468 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG C 475 " --> pdb=" O VAL C 471 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 487 removed outlier: 3.818A pdb=" N ALA C 479 " --> pdb=" O ARG C 475 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL C 480 " --> pdb=" O VAL C 476 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N SER C 485 " --> pdb=" O LYS C 481 " (cutoff:3.500A) Processing helix chain 'C' and resid 493 through 498 Processing helix chain 'C' and resid 500 through 509 Processing helix chain 'C' and resid 524 through 533 removed outlier: 3.526A pdb=" N ILE C 529 " --> pdb=" O PRO C 525 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYS C 532 " --> pdb=" O GLU C 528 " (cutoff:3.500A) Processing helix chain 'C' and resid 556 through 560 removed outlier: 3.532A pdb=" N TYR C 560 " --> pdb=" O PRO C 557 " (cutoff:3.500A) Processing helix chain 'C' and resid 613 through 617 removed outlier: 3.685A pdb=" N GLU C 616 " --> pdb=" O ALA C 613 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ALA C 617 " --> pdb=" O ILE C 614 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 613 through 617' Processing helix chain 'C' and resid 661 through 665 removed outlier: 3.953A pdb=" N VAL C 665 " --> pdb=" O PRO C 662 " (cutoff:3.500A) Processing helix chain 'C' and resid 667 through 672 removed outlier: 3.890A pdb=" N LEU C 672 " --> pdb=" O VAL C 668 " (cutoff:3.500A) Processing helix chain 'C' and resid 675 through 679 Processing helix chain 'C' and resid 680 through 691 removed outlier: 3.521A pdb=" N MET C 686 " --> pdb=" O ASN C 682 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER C 688 " --> pdb=" O ALA C 684 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ASN C 689 " --> pdb=" O LEU C 685 " (cutoff:3.500A) Processing helix chain 'C' and resid 710 through 715 removed outlier: 3.698A pdb=" N ALA C 714 " --> pdb=" O GLU C 710 " (cutoff:3.500A) Processing helix chain 'C' and resid 825 through 830 removed outlier: 3.689A pdb=" N GLU C 830 " --> pdb=" O ARG C 826 " (cutoff:3.500A) Processing helix chain 'C' and resid 901 through 911 removed outlier: 3.823A pdb=" N LEU C 907 " --> pdb=" O GLU C 903 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ALA C 909 " --> pdb=" O LYS C 905 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILE C 910 " --> pdb=" O LEU C 906 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N PHE C 911 " --> pdb=" O LEU C 907 " (cutoff:3.500A) Processing helix chain 'C' and resid 947 through 981 removed outlier: 3.666A pdb=" N LEU C 951 " --> pdb=" O ASP C 947 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N SER C 952 " --> pdb=" O SER C 948 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE C 953 " --> pdb=" O ARG C 949 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LEU C 965 " --> pdb=" O ILE C 961 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ARG C 970 " --> pdb=" O ASN C 966 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE C 971 " --> pdb=" O GLU C 967 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL C 972 " --> pdb=" O GLU C 968 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ARG C 979 " --> pdb=" O ALA C 975 " (cutoff:3.500A) Processing helix chain 'C' and resid 1021 through 1055 removed outlier: 3.695A pdb=" N ASN C1025 " --> pdb=" O ASP C1021 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLN C1040 " --> pdb=" O SER C1036 " (cutoff:3.500A) Processing helix chain 'C' and resid 1118 through 1123 removed outlier: 3.934A pdb=" N SER C1122 " --> pdb=" O LEU C1118 " (cutoff:3.500A) Processing helix chain 'C' and resid 1126 through 1150 Processing helix chain 'C' and resid 1154 through 1167 removed outlier: 3.704A pdb=" N LEU C1158 " --> pdb=" O LYS C1154 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS C1160 " --> pdb=" O ALA C1156 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N PHE C1161 " --> pdb=" O GLU C1157 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ILE C1165 " --> pdb=" O PHE C1161 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASN C1167 " --> pdb=" O HIS C1163 " (cutoff:3.500A) Processing helix chain 'C' and resid 1181 through 1189 removed outlier: 3.890A pdb=" N LEU C1185 " --> pdb=" O ASP C1181 " (cutoff:3.500A) Processing helix chain 'C' and resid 1206 through 1217 removed outlier: 4.007A pdb=" N MET C1213 " --> pdb=" O GLU C1209 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU C1214 " --> pdb=" O ILE C1210 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LYS C1215 " --> pdb=" O LYS C1211 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU C1216 " --> pdb=" O ALA C1212 " (cutoff:3.500A) Processing helix chain 'C' and resid 1253 through 1257 removed outlier: 3.605A pdb=" N ASP C1256 " --> pdb=" O LEU C1253 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS C1257 " --> pdb=" O VAL C1254 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1253 through 1257' Processing helix chain 'C' and resid 1286 through 1296 removed outlier: 3.548A pdb=" N VAL C1290 " --> pdb=" O GLY C1286 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA C1292 " --> pdb=" O MET C1288 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N TYR C1296 " --> pdb=" O ALA C1292 " (cutoff:3.500A) Processing helix chain 'C' and resid 1299 through 1308 removed outlier: 3.551A pdb=" N LEU C1306 " --> pdb=" O LEU C1302 " (cutoff:3.500A) Processing helix chain 'C' and resid 1313 through 1326 removed outlier: 4.022A pdb=" N THR C1317 " --> pdb=" O VAL C1313 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS C1321 " --> pdb=" O THR C1317 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASN C1322 " --> pdb=" O LYS C1318 " (cutoff:3.500A) Processing helix chain 'C' and resid 1335 through 1347 removed outlier: 3.584A pdb=" N ASN C1339 " --> pdb=" O PRO C1335 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL C1340 " --> pdb=" O GLU C1336 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LEU C1341 " --> pdb=" O SER C1337 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 33 removed outlier: 3.817A pdb=" N ARG D 31 " --> pdb=" O PRO D 27 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N SER D 32 " --> pdb=" O GLU D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 100 Processing helix chain 'D' and resid 131 through 140 removed outlier: 3.663A pdb=" N ILE D 135 " --> pdb=" O THR D 131 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N GLU D 136 " --> pdb=" O LEU D 132 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 172 removed outlier: 3.825A pdb=" N PHE D 166 " --> pdb=" O ASP D 162 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLU D 170 " --> pdb=" O PHE D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 191 removed outlier: 3.998A pdb=" N VAL D 185 " --> pdb=" O GLY D 181 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA D 191 " --> pdb=" O GLU D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 204 removed outlier: 3.599A pdb=" N ILE D 198 " --> pdb=" O LEU D 194 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N GLY D 199 " --> pdb=" O GLU D 195 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ARG D 200 " --> pdb=" O HIS D 196 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU D 201 " --> pdb=" O GLU D 197 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU D 203 " --> pdb=" O GLY D 199 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU D 204 " --> pdb=" O ARG D 200 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 225 removed outlier: 3.639A pdb=" N LYS D 216 " --> pdb=" O THR D 212 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG D 220 " --> pdb=" O LYS D 216 " (cutoff:3.500A) Processing helix chain 'D' and resid 225 through 230 Processing helix chain 'D' and resid 233 through 237 removed outlier: 3.540A pdb=" N MET D 237 " --> pdb=" O PRO D 234 " (cutoff:3.500A) Processing helix chain 'D' and resid 263 through 283 removed outlier: 3.894A pdb=" N ASP D 267 " --> pdb=" O SER D 263 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU D 268 " --> pdb=" O ASP D 264 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL D 272 " --> pdb=" O LEU D 268 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ARG D 278 " --> pdb=" O ASN D 274 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 308 removed outlier: 3.772A pdb=" N ASN D 294 " --> pdb=" O ILE D 290 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU D 295 " --> pdb=" O ILE D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 333 Processing helix chain 'D' and resid 370 through 377 removed outlier: 3.886A pdb=" N GLU D 375 " --> pdb=" O LYS D 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 389 removed outlier: 3.545A pdb=" N PHE D 382 " --> pdb=" O LYS D 378 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLY D 383 " --> pdb=" O PRO D 379 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU D 386 " --> pdb=" O PHE D 382 " (cutoff:3.500A) Processing helix chain 'D' and resid 393 through 402 removed outlier: 3.524A pdb=" N ALA D 397 " --> pdb=" O THR D 393 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LYS D 399 " --> pdb=" O LYS D 395 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N MET D 400 " --> pdb=" O ALA D 396 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL D 401 " --> pdb=" O ALA D 397 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU D 402 " --> pdb=" O LYS D 398 " (cutoff:3.500A) Processing helix chain 'D' and resid 407 through 417 removed outlier: 3.738A pdb=" N VAL D 411 " --> pdb=" O GLU D 407 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N GLU D 414 " --> pdb=" O ASP D 410 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N VAL D 415 " --> pdb=" O VAL D 411 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE D 416 " --> pdb=" O LEU D 412 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ARG D 417 " --> pdb=" O ALA D 413 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 432 No H-bonds generated for 'chain 'D' and resid 430 through 432' Processing helix chain 'D' and resid 453 through 458 removed outlier: 3.537A pdb=" N TYR D 457 " --> pdb=" O VAL D 453 " (cutoff:3.500A) Processing helix chain 'D' and resid 473 through 483 removed outlier: 3.591A pdb=" N GLU D 479 " --> pdb=" O GLU D 475 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU D 483 " --> pdb=" O GLU D 479 " (cutoff:3.500A) Processing helix chain 'D' and resid 503 through 514 removed outlier: 3.856A pdb=" N GLY D 509 " --> pdb=" O ASP D 505 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 539 removed outlier: 3.641A pdb=" N VAL D 533 " --> pdb=" O ASP D 529 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASP D 534 " --> pdb=" O LEU D 530 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG D 535 " --> pdb=" O GLN D 531 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 580 removed outlier: 3.645A pdb=" N ALA D 577 " --> pdb=" O THR D 573 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE D 580 " --> pdb=" O ARG D 576 " (cutoff:3.500A) Processing helix chain 'D' and resid 589 through 593 Processing helix chain 'D' and resid 597 through 612 removed outlier: 3.923A pdb=" N LYS D 603 " --> pdb=" O LYS D 599 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N LEU D 604 " --> pdb=" O ALA D 600 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASN D 606 " --> pdb=" O SER D 602 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ARG D 610 " --> pdb=" O ASN D 606 " (cutoff:3.500A) Processing helix chain 'D' and resid 614 through 635 removed outlier: 3.761A pdb=" N ILE D 619 " --> pdb=" O LYS D 615 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N TYR D 631 " --> pdb=" O THR D 627 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR D 633 " --> pdb=" O PHE D 629 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE D 634 " --> pdb=" O ALA D 630 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER D 635 " --> pdb=" O TYR D 631 " (cutoff:3.500A) Processing helix chain 'D' and resid 649 through 669 removed outlier: 3.562A pdb=" N ILE D 653 " --> pdb=" O GLU D 649 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASP D 659 " --> pdb=" O ASN D 655 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS D 662 " --> pdb=" O THR D 658 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU D 663 " --> pdb=" O ASP D 659 " (cutoff:3.500A) Processing helix chain 'D' and resid 674 through 703 removed outlier: 3.947A pdb=" N ASN D 680 " --> pdb=" O GLY D 676 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASP D 684 " --> pdb=" O ASN D 680 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N LEU D 685 " --> pdb=" O LYS D 681 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N TRP D 686 " --> pdb=" O VAL D 682 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER D 687 " --> pdb=" O ILE D 683 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ASP D 691 " --> pdb=" O SER D 687 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLU D 692 " --> pdb=" O LYS D 688 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LYS D 703 " --> pdb=" O ALA D 699 " (cutoff:3.500A) Processing helix chain 'D' and resid 720 through 728 removed outlier: 3.604A pdb=" N SER D 728 " --> pdb=" O MET D 724 " (cutoff:3.500A) Processing helix chain 'D' and resid 733 through 738 removed outlier: 3.661A pdb=" N ILE D 737 " --> pdb=" O SER D 733 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ARG D 738 " --> pdb=" O ALA D 734 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 733 through 738' Processing helix chain 'D' and resid 768 through 804 removed outlier: 3.675A pdb=" N SER D 775 " --> pdb=" O GLN D 771 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N HIS D 777 " --> pdb=" O PHE D 773 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N GLY D 778 " --> pdb=" O ILE D 774 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU D 788 " --> pdb=" O ALA D 784 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N THR D 790 " --> pdb=" O THR D 786 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ALA D 791 " --> pdb=" O ALA D 787 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG D 799 " --> pdb=" O TYR D 795 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL D 801 " --> pdb=" O THR D 797 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ASP D 802 " --> pdb=" O ARG D 798 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL D 803 " --> pdb=" O ARG D 799 " (cutoff:3.500A) Processing helix chain 'D' and resid 834 through 839 removed outlier: 3.768A pdb=" N ARG D 838 " --> pdb=" O PRO D 834 " (cutoff:3.500A) Processing helix chain 'D' and resid 865 through 875 removed outlier: 4.028A pdb=" N ASP D 870 " --> pdb=" O GLU D 866 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLU D 873 " --> pdb=" O VAL D 869 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL D 874 " --> pdb=" O ASP D 870 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N MET D 875 " --> pdb=" O PHE D 871 " (cutoff:3.500A) Processing helix chain 'D' and resid 884 through 888 removed outlier: 3.756A pdb=" N CYS D 888 " --> pdb=" O PRO D 885 " (cutoff:3.500A) Processing helix chain 'D' and resid 914 through 925 removed outlier: 3.773A pdb=" N ILE D 918 " --> pdb=" O ALA D 914 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA D 919 " --> pdb=" O VAL D 915 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA D 920 " --> pdb=" O GLY D 916 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER D 922 " --> pdb=" O ILE D 918 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ILE D 923 " --> pdb=" O ALA D 919 " (cutoff:3.500A) Processing helix chain 'D' and resid 926 through 930 Processing helix chain 'D' and resid 1137 through 1147 removed outlier: 3.729A pdb=" N ASP D1143 " --> pdb=" O PRO D1139 " (cutoff:3.500A) Processing helix chain 'D' and resid 1216 through 1224 removed outlier: 3.841A pdb=" N ILE D1220 " --> pdb=" O ASN D1216 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU D1221 " --> pdb=" O PRO D1217 " (cutoff:3.500A) Processing helix chain 'D' and resid 1226 through 1243 removed outlier: 3.840A pdb=" N ALA D1230 " --> pdb=" O VAL D1226 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LYS D1231 " --> pdb=" O SER D1227 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N ASP D1239 " --> pdb=" O ASN D1235 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N VAL D1240 " --> pdb=" O GLU D1236 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N TYR D1241 " --> pdb=" O ILE D1237 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU D1243 " --> pdb=" O ASP D1239 " (cutoff:3.500A) Processing helix chain 'D' and resid 1249 through 1261 removed outlier: 4.113A pdb=" N ILE D1253 " --> pdb=" O ASN D1249 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE D1256 " --> pdb=" O HIS D1252 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLN D1259 " --> pdb=" O THR D1255 " (cutoff:3.500A) Processing helix chain 'D' and resid 1280 through 1291 removed outlier: 3.686A pdb=" N VAL D1285 " --> pdb=" O GLU D1281 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU D1286 " --> pdb=" O LEU D1282 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ASN D1289 " --> pdb=" O VAL D1285 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLN D1291 " --> pdb=" O GLU D1287 " (cutoff:3.500A) Processing helix chain 'D' and resid 1311 through 1315 removed outlier: 3.700A pdb=" N SER D1315 " --> pdb=" O ALA D1312 " (cutoff:3.500A) Processing helix chain 'D' and resid 1327 through 1339 removed outlier: 3.618A pdb=" N THR D1333 " --> pdb=" O THR D1329 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLU D1334 " --> pdb=" O ARG D1330 " (cutoff:3.500A) Processing helix chain 'D' and resid 1347 through 1354 removed outlier: 3.832A pdb=" N VAL D1351 " --> pdb=" O LEU D1347 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N VAL D1352 " --> pdb=" O LYS D1348 " (cutoff:3.500A) Processing helix chain 'D' and resid 1362 through 1372 Processing helix chain 'E' and resid 9 through 14 removed outlier: 3.923A pdb=" N VAL E 13 " --> pdb=" O CYS E 9 " (cutoff:3.500A) Processing helix chain 'E' and resid 17 through 32 removed outlier: 3.861A pdb=" N GLN E 29 " --> pdb=" O LYS E 25 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU E 30 " --> pdb=" O ARG E 26 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 56 removed outlier: 3.762A pdb=" N ALA E 50 " --> pdb=" O PRO E 46 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LEU E 51 " --> pdb=" O THR E 47 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ARG E 52 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLU E 53 " --> pdb=" O VAL E 49 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ILE E 54 " --> pdb=" O ALA E 50 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA E 55 " --> pdb=" O LEU E 51 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER E 56 " --> pdb=" O ARG E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 70 removed outlier: 3.580A pdb=" N VAL E 64 " --> pdb=" O ASP E 60 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLN E 65 " --> pdb=" O GLU E 61 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASP E 68 " --> pdb=" O VAL E 64 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ILE E 69 " --> pdb=" O GLN E 65 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL E 70 " --> pdb=" O GLN E 66 " (cutoff:3.500A) Processing helix chain 'G' and resid 59 through 78 removed outlier: 3.527A pdb=" N PHE G 74 " --> pdb=" O ALA G 70 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU G 75 " --> pdb=" O MET G 71 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N SER G 76 " --> pdb=" O GLU G 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 62 through 70 removed outlier: 3.588A pdb=" N TYR F 66 " --> pdb=" O ALA F 62 " (cutoff:3.500A) Processing helix chain 'F' and resid 77 through 91 removed outlier: 4.001A pdb=" N VAL F 82 " --> pdb=" O PRO F 78 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N HIS F 83 " --> pdb=" O GLU F 79 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LYS F 90 " --> pdb=" O ARG F 86 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLY F 91 " --> pdb=" O LEU F 87 " (cutoff:3.500A) Processing helix chain 'F' and resid 92 through 103 removed outlier: 3.995A pdb=" N ARG F 96 " --> pdb=" O ASP F 92 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LYS F 97 " --> pdb=" O PRO F 93 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ASN F 103 " --> pdb=" O MET F 99 " (cutoff:3.500A) Processing helix chain 'F' and resid 103 through 112 removed outlier: 4.108A pdb=" N VAL F 107 " --> pdb=" O ASN F 103 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N VAL F 108 " --> pdb=" O LEU F 104 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N LYS F 109 " --> pdb=" O ARG F 105 " (cutoff:3.500A) Processing helix chain 'F' and resid 120 through 138 removed outlier: 3.804A pdb=" N LEU F 130 " --> pdb=" O GLU F 126 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLY F 131 " --> pdb=" O GLU F 127 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU F 132 " --> pdb=" O GLY F 128 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU F 137 " --> pdb=" O ILE F 133 " (cutoff:3.500A) Processing helix chain 'F' and resid 140 through 144 removed outlier: 3.639A pdb=" N GLY F 144 " --> pdb=" O PRO F 141 " (cutoff:3.500A) Processing helix chain 'F' and resid 146 through 167 removed outlier: 3.947A pdb=" N TRP F 153 " --> pdb=" O THR F 149 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N TRP F 154 " --> pdb=" O TYR F 150 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE F 159 " --> pdb=" O ILE F 155 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N MET F 164 " --> pdb=" O GLU F 160 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR F 167 " --> pdb=" O ILE F 163 " (cutoff:3.500A) Processing helix chain 'F' and resid 173 through 195 removed outlier: 3.578A pdb=" N LYS F 178 " --> pdb=" O ILE F 174 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N GLU F 179 " --> pdb=" O HIS F 175 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LEU F 180 " --> pdb=" O VAL F 176 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASN F 181 " --> pdb=" O VAL F 177 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N VAL F 182 " --> pdb=" O LYS F 178 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TYR F 183 " --> pdb=" O GLU F 179 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N HIS F 192 " --> pdb=" O ARG F 188 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU F 194 " --> pdb=" O LEU F 190 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASP F 195 " --> pdb=" O THR F 191 " (cutoff:3.500A) Processing helix chain 'F' and resid 199 through 207 removed outlier: 3.712A pdb=" N ILE F 203 " --> pdb=" O SER F 199 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ALA F 204 " --> pdb=" O PRO F 200 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASN F 205 " --> pdb=" O GLU F 201 " (cutoff:3.500A) Processing helix chain 'F' and resid 210 through 219 removed outlier: 3.788A pdb=" N ARG F 216 " --> pdb=" O ALA F 212 " (cutoff:3.500A) Processing helix chain 'F' and resid 238 through 242 removed outlier: 3.826A pdb=" N ASP F 241 " --> pdb=" O THR F 238 " (cutoff:3.500A) Processing helix chain 'F' and resid 250 through 272 removed outlier: 3.665A pdb=" N ASP F 257 " --> pdb=" O GLU F 253 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASP F 258 " --> pdb=" O LEU F 254 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASP F 265 " --> pdb=" O SER F 261 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLN F 266 " --> pdb=" O GLU F 262 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N THR F 272 " --> pdb=" O LEU F 268 " (cutoff:3.500A) Processing helix chain 'F' and resid 275 through 283 removed outlier: 3.537A pdb=" N VAL F 279 " --> pdb=" O GLN F 275 " (cutoff:3.500A) Processing helix chain 'F' and resid 292 through 298 Processing helix chain 'F' and resid 305 through 326 removed outlier: 3.763A pdb=" N ILE F 310 " --> pdb=" O ARG F 306 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLN F 311 " --> pdb=" O VAL F 307 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU F 323 " --> pdb=" O ARG F 319 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLY F 326 " --> pdb=" O LEU F 322 " (cutoff:3.500A) Processing helix chain 'F' and resid 328 through 333 Processing sheet with id=AA1, first strand: chain 'A' and resid 15 through 17 removed outlier: 4.797A pdb=" N ARG A 23 " --> pdb=" O THR A 206 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N THR A 206 " --> pdb=" O ARG A 23 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N LYS A 25 " --> pdb=" O LEU A 204 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N LEU A 204 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N THR A 27 " --> pdb=" O LEU A 202 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N LEU A 202 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N GLU A 29 " --> pdb=" O LEU A 200 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LEU A 200 " --> pdb=" O GLU A 29 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ARG A 181 " --> pdb=" O GLU A 205 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 98 through 105 removed outlier: 3.594A pdb=" N VAL A 98 " --> pdb=" O VAL A 145 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ALA A 146 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N VAL A 56 " --> pdb=" O ALA A 146 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N GLY A 148 " --> pdb=" O CYS A 54 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N CYS A 54 " --> pdb=" O GLY A 148 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 92 Processing sheet with id=AA4, first strand: chain 'A' and resid 110 through 111 removed outlier: 7.169A pdb=" N VAL A 110 " --> pdb=" O ILE A 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 16 through 18 removed outlier: 4.177A pdb=" N LEU B 197 " --> pdb=" O ALA B 189 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASP B 203 " --> pdb=" O SER B 183 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N SER B 183 " --> pdb=" O ASP B 203 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 50 through 61 removed outlier: 8.242A pdb=" N GLY B 150 " --> pdb=" O PRO B 52 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N CYS B 54 " --> pdb=" O GLY B 148 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N GLY B 148 " --> pdb=" O CYS B 54 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N VAL B 56 " --> pdb=" O ALA B 146 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ALA B 146 " --> pdb=" O VAL B 56 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N MET B 141 " --> pdb=" O LEU B 102 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LEU B 102 " --> pdb=" O MET B 141 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU B 143 " --> pdb=" O LEU B 100 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL B 98 " --> pdb=" O VAL B 145 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 90 through 92 Processing sheet with id=AA8, first strand: chain 'B' and resid 110 through 111 removed outlier: 7.466A pdb=" N VAL B 110 " --> pdb=" O ILE B 130 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 13 through 14 removed outlier: 6.280A pdb=" N LYS C 13 " --> pdb=" O ALA C1198 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 70 through 79 removed outlier: 3.627A pdb=" N VAL C 75 " --> pdb=" O LYS C 103 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N LYS C 103 " --> pdb=" O VAL C 75 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N TYR C 77 " --> pdb=" O ARG C 101 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ARG C 101 " --> pdb=" O TYR C 77 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N LEU C 79 " --> pdb=" O PRO C 99 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N VAL C 98 " --> pdb=" O GLY C 129 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N GLY C 129 " --> pdb=" O VAL C 98 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N LEU C 100 " --> pdb=" O TYR C 127 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N TYR C 127 " --> pdb=" O LEU C 100 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N VAL C 102 " --> pdb=" O GLU C 125 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N GLU C 123 " --> pdb=" O VAL C 104 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 140 through 142 removed outlier: 3.567A pdb=" N PHE C 140 " --> pdb=" O ARG C 147 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL C 148 " --> pdb=" O GLN C 518 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 456 through 458 removed outlier: 6.030A pdb=" N SER C 151 " --> pdb=" O SER C 536 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 189 through 193 removed outlier: 3.676A pdb=" N CYS C 197 " --> pdb=" O ASP C 193 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 233 through 235 Processing sheet with id=AB6, first strand: chain 'C' and resid 243 through 244 removed outlier: 3.918A pdb=" N LEU C 243 " --> pdb=" O LEU C 290 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU C 290 " --> pdb=" O LEU C 243 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'C' and resid 254 through 255 removed outlier: 3.817A pdb=" N ALA C 255 " --> pdb=" O ARG C 272 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ARG C 272 " --> pdb=" O ALA C 255 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'C' and resid 585 through 586 Processing sheet with id=AB9, first strand: chain 'C' and resid 585 through 586 Processing sheet with id=AC1, first strand: chain 'C' and resid 639 through 642 removed outlier: 3.541A pdb=" N VAL C 639 " --> pdb=" O LYS C 650 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 721 through 722 removed outlier: 6.437A pdb=" N VAL C 721 " --> pdb=" O LEU C 788 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 755 through 757 removed outlier: 3.890A pdb=" N SER C 731 " --> pdb=" O VAL C 738 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 762 through 763 removed outlier: 3.713A pdb=" N ILE C 770 " --> pdb=" O THR C 762 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 794 through 795 Processing sheet with id=AC6, first strand: chain 'C' and resid 1224 through 1225 removed outlier: 7.910A pdb=" N ILE C 821 " --> pdb=" O SER C1094 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ILE C1096 " --> pdb=" O ILE C 821 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N LEU C 823 " --> pdb=" O ILE C1096 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N CYS C 822 " --> pdb=" O VAL C1114 " (cutoff:3.500A) removed outlier: 8.933A pdb=" N ILE C1113 " --> pdb=" O ASN C 804 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ARG C 806 " --> pdb=" O ILE C1113 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N LEU C1115 " --> pdb=" O ARG C 806 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ALA C 808 " --> pdb=" O LEU C1115 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N MET C1247 " --> pdb=" O GLN C 803 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N MET C 805 " --> pdb=" O MET C1245 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N THR C1241 " --> pdb=" O PHE C 809 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 835 through 843 removed outlier: 3.666A pdb=" N THR C 835 " --> pdb=" O ARG C1075 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ASP C 935 " --> pdb=" O TYR C1070 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ALA C1072 " --> pdb=" O VAL C 933 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N VAL C 933 " --> pdb=" O ALA C1072 " (cutoff:3.500A) removed outlier: 8.167A pdb=" N LYS C1074 " --> pdb=" O GLY C 931 " (cutoff:3.500A) removed outlier: 8.443A pdb=" N GLY C 931 " --> pdb=" O LYS C1074 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLY C 931 " --> pdb=" O VAL C 882 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 847 through 848 removed outlier: 4.050A pdb=" N THR C 848 " --> pdb=" O GLY C 851 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 854 through 855 removed outlier: 4.294A pdb=" N GLU C 854 " --> pdb=" O VAL C 892 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N VAL C 892 " --> pdb=" O GLU C 854 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 887 through 889 removed outlier: 7.190A pdb=" N LEU C 923 " --> pdb=" O LEU C 888 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 1259 through 1261 removed outlier: 3.575A pdb=" N HIS C1259 " --> pdb=" O ARG D 352 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ARG D 352 " --> pdb=" O HIS C1259 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG C1261 " --> pdb=" O SER D 350 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N SER D 350 " --> pdb=" O ARG C1261 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLY D 351 " --> pdb=" O VAL D 468 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N SER D 353 " --> pdb=" O MET D 466 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N CYS D 366 " --> pdb=" O VAL D 440 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N ILE D 442 " --> pdb=" O CYS D 366 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N LEU D 368 " --> pdb=" O ILE D 442 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 1259 through 1261 removed outlier: 3.575A pdb=" N HIS C1259 " --> pdb=" O ARG D 352 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ARG D 352 " --> pdb=" O HIS C1259 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG C1261 " --> pdb=" O SER D 350 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N SER D 350 " --> pdb=" O ARG C1261 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N ILE D 447 " --> pdb=" O ARG D 352 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N VAL D 354 " --> pdb=" O ILE D 447 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N LEU D 449 " --> pdb=" O VAL D 354 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N THR D 356 " --> pdb=" O LEU D 449 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'C' and resid 1284 through 1285 Processing sheet with id=AD5, first strand: chain 'C' and resid 1350 through 1354 Processing sheet with id=AD6, first strand: chain 'D' and resid 34 through 37 removed outlier: 7.894A pdb=" N HIS D 104 " --> pdb=" O PHE D 35 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N GLU D 37 " --> pdb=" O HIS D 104 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N GLU D 106 " --> pdb=" O GLU D 37 " (cutoff:3.500A) removed outlier: 10.266A pdb=" N LEU D 107 " --> pdb=" O PRO D 243 " (cutoff:3.500A) removed outlier: 10.727A pdb=" N SER D 109 " --> pdb=" O VAL D 241 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N VAL D 241 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 145 through 147 removed outlier: 3.892A pdb=" N ASP D 177 " --> pdb=" O ILE D 147 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 526 through 527 removed outlier: 4.108A pdb=" N ARG D 551 " --> pdb=" O PHE D 527 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 706 through 707 Processing sheet with id=AE1, first strand: chain 'D' and resid 809 through 811 removed outlier: 3.742A pdb=" N THR D 810 " --> pdb=" O ILE D 894 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'D' and resid 821 through 822 removed outlier: 3.653A pdb=" N VAL D 880 " --> pdb=" O MET D 822 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 949 through 951 removed outlier: 3.576A pdb=" N VAL D 950 " --> pdb=" O ALA D1018 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ALA D1018 " --> pdb=" O VAL D 950 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'D' and resid 957 through 961 removed outlier: 3.981A pdb=" N HIS D 961 " --> pdb=" O GLU D 981 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N GLU D 981 " --> pdb=" O HIS D 961 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N GLU D 993 " --> pdb=" O VAL D 984 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 965 through 967 removed outlier: 3.687A pdb=" N VAL D 974 " --> pdb=" O VAL D 966 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 1024 through 1025 removed outlier: 3.623A pdb=" N ILE D1124 " --> pdb=" O HIS D1025 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 1035 through 1038 removed outlier: 3.522A pdb=" N VAL D1038 " --> pdb=" O ALA D1077 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 1059 through 1060 removed outlier: 3.940A pdb=" N ILE D1059 " --> pdb=" O VAL D1107 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 1188 through 1190 Processing sheet with id=AF1, first strand: chain 'D' and resid 1278 through 1279 786 hydrogen bonds defined for protein. 2220 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: 11.59 Time building geometry restraints manager: 7.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 8597 1.34 - 1.46: 4231 1.46 - 1.58: 11897 1.58 - 1.69: 0 1.69 - 1.81: 142 Bond restraints: 24867 Sorted by residual: bond pdb=" C PHE C 61 " pdb=" N PRO C 62 " ideal model delta sigma weight residual 1.334 1.351 -0.017 2.34e-02 1.83e+03 5.28e-01 bond pdb=" CA VAL B 64 " pdb=" CB VAL B 64 " ideal model delta sigma weight residual 1.527 1.536 -0.009 1.31e-02 5.83e+03 4.99e-01 bond pdb=" N ILE C 131 " pdb=" CA ILE C 131 " ideal model delta sigma weight residual 1.468 1.461 0.007 1.05e-02 9.07e+03 4.89e-01 bond pdb=" C ALA D 426 " pdb=" N PRO D 427 " ideal model delta sigma weight residual 1.334 1.350 -0.016 2.34e-02 1.83e+03 4.88e-01 bond pdb=" C GLU B 29 " pdb=" N PRO B 30 " ideal model delta sigma weight residual 1.334 1.350 -0.016 2.34e-02 1.83e+03 4.83e-01 ... (remaining 24862 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.13: 33167 1.13 - 2.26: 428 2.26 - 3.39: 126 3.39 - 4.52: 15 4.52 - 5.65: 6 Bond angle restraints: 33742 Sorted by residual: angle pdb=" CA LEU D1138 " pdb=" C LEU D1138 " pdb=" N PRO D1139 " ideal model delta sigma weight residual 118.44 121.62 -3.18 1.59e+00 3.96e-01 4.00e+00 angle pdb=" N LEU D1138 " pdb=" CA LEU D1138 " pdb=" C LEU D1138 " ideal model delta sigma weight residual 109.81 113.56 -3.75 2.21e+00 2.05e-01 2.88e+00 angle pdb=" CA LEU D 221 " pdb=" CB LEU D 221 " pdb=" CG LEU D 221 " ideal model delta sigma weight residual 116.30 121.95 -5.65 3.50e+00 8.16e-02 2.61e+00 angle pdb=" CA LEU D1138 " pdb=" C LEU D1138 " pdb=" O LEU D1138 " ideal model delta sigma weight residual 120.16 117.95 2.21 1.37e+00 5.33e-01 2.60e+00 angle pdb=" NE ARG C 715 " pdb=" CZ ARG C 715 " pdb=" NH1 ARG C 715 " ideal model delta sigma weight residual 121.50 120.01 1.49 1.00e+00 1.00e+00 2.21e+00 ... (remaining 33737 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 14555 17.82 - 35.65: 559 35.65 - 53.47: 65 53.47 - 71.30: 6 71.30 - 89.12: 9 Dihedral angle restraints: 15194 sinusoidal: 5243 harmonic: 9951 Sorted by residual: dihedral pdb=" CB GLU D 443 " pdb=" CG GLU D 443 " pdb=" CD GLU D 443 " pdb=" OE1 GLU D 443 " ideal model delta sinusoidal sigma weight residual 0.00 89.12 -89.12 1 3.00e+01 1.11e-03 1.05e+01 dihedral pdb=" CB GLU C 291 " pdb=" CG GLU C 291 " pdb=" CD GLU C 291 " pdb=" OE1 GLU C 291 " ideal model delta sinusoidal sigma weight residual 0.00 -86.79 86.79 1 3.00e+01 1.11e-03 1.01e+01 dihedral pdb=" CB GLU F 126 " pdb=" CG GLU F 126 " pdb=" CD GLU F 126 " pdb=" OE1 GLU F 126 " ideal model delta sinusoidal sigma weight residual 0.00 -84.53 84.53 1 3.00e+01 1.11e-03 9.65e+00 ... (remaining 15191 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 2275 0.026 - 0.053: 1204 0.053 - 0.079: 252 0.079 - 0.106: 217 0.106 - 0.132: 80 Chirality restraints: 4028 Sorted by residual: chirality pdb=" CA VAL D 583 " pdb=" N VAL D 583 " pdb=" C VAL D 583 " pdb=" CB VAL D 583 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.35e-01 chirality pdb=" CA ILE D1190 " pdb=" N ILE D1190 " pdb=" C ILE D1190 " pdb=" CB ILE D1190 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.11e-01 chirality pdb=" CA ILE D1159 " pdb=" N ILE D1159 " pdb=" C ILE D1159 " pdb=" CB ILE D1159 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.10e-01 ... (remaining 4025 not shown) Planarity restraints: 4459 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL D 501 " -0.024 5.00e-02 4.00e+02 3.64e-02 2.12e+00 pdb=" N PRO D 502 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO D 502 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO D 502 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 29 " 0.021 5.00e-02 4.00e+02 3.26e-02 1.70e+00 pdb=" N PRO A 30 " -0.056 5.00e-02 4.00e+02 pdb=" CA PRO A 30 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 30 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS D 850 " -0.021 5.00e-02 4.00e+02 3.13e-02 1.57e+00 pdb=" N PRO D 851 " 0.054 5.00e-02 4.00e+02 pdb=" CA PRO D 851 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO D 851 " -0.017 5.00e-02 4.00e+02 ... (remaining 4456 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 6729 2.80 - 3.32: 20400 3.32 - 3.85: 35952 3.85 - 4.37: 40216 4.37 - 4.90: 71137 Nonbonded interactions: 174434 Sorted by model distance: nonbonded pdb=" O LYS D1251 " pdb=" OG1 THR D1255 " model vdw 2.274 3.040 nonbonded pdb=" OD1 ASP D 464 " pdb="MG MG D1503 " model vdw 2.292 2.170 nonbonded pdb=" O GLY D 613 " pdb=" OG1 THR D 617 " model vdw 2.301 3.040 nonbonded pdb=" O SER C 59 " pdb=" OG SER C 59 " model vdw 2.312 3.040 nonbonded pdb=" O SER D 319 " pdb=" OG SER D 319 " model vdw 2.329 3.040 ... (remaining 174429 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 8 through 13 or (resid 14 through 15 and (name N or name C \ A or name C or name O or name CB )) or resid 16 through 59 or (resid 60 through \ 62 and (name N or name CA or name C or name O or name CB )) or resid 63 through \ 74 or (resid 75 and (name N or name CA or name C or name O or name CB )) or resi \ d 76 through 79 or (resid 80 and (name N or name CA or name C or name O or name \ CB )) or resid 81 through 89 or (resid 90 and (name N or name CA or name C or na \ me O or name CB or name CG1 or name CG2)) or resid 91 through 94 or (resid 95 an \ d (name N or name CA or name C or name O or name CB or name CG )) or resid 96 th \ rough 104 or (resid 105 and (name N or name CA or name C or name O or name CB )) \ or resid 106 through 113 or (resid 114 and (name N or name CA or name C or name \ O or name CB )) or resid 115 through 118 or (resid 119 and (name N or name CA o \ r name C or name O or name CB )) or resid 120 through 134 or resid 139 through 1 \ 54 or (resid 155 through 157 and (name N or name CA or name C or name O or name \ CB )) or (resid 169 and (name N or name CA or name C or name O or name CB )) or \ resid 170 through 182 or (resid 183 and (name N or name CA or name C or name O o \ r name CB )) or resid 184 through 189 or (resid 190 and (name N or name CA or na \ me C or name O or name CB )) or resid 191 or (resid 192 and (name N or name CA o \ r name C or name O or name CB )) or resid 193 through 230 or (resid 231 through \ 232 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'B' and (resid 8 through 14 or (resid 15 and (name N or name CA or name C \ or name O or name CB )) or resid 16 through 25 or (resid 26 and (name N or name \ CA or name C or name O or name CB or name CG1 or name CG2)) or (resid 27 and (n \ ame N or name CA or name C or name O or name CB )) or resid 28 through 126 or (r \ esid 127 and (name N or name CA or name C or name O or name CB or name CG )) or \ resid 128 through 139 or (resid 140 and (name N or name CA or name C or name O o \ r name CB or name CG )) or resid 141 through 151 or (resid 152 and (name N or na \ me CA or name C or name O or name CB )) or resid 153 through 193 or (resid 194 t \ hrough 196 and (name N or name CA or name C or name O or name CB )) or resid 197 \ through 224 or (resid 225 and (name N or name CA or name C or name O or name CB \ )) or resid 226 through 232)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.130 Construct map_model_manager: 0.020 Extract box with map and model: 0.840 Check model and map are aligned: 0.160 Set scattering table: 0.240 Process input model: 64.870 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.604 24870 Z= 0.157 Angle : 0.361 5.653 33742 Z= 0.215 Chirality : 0.039 0.132 4028 Planarity : 0.002 0.036 4459 Dihedral : 9.417 89.122 8766 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % 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: -4.82 (0.10), residues: 3455 helix: -4.72 (0.05), residues: 1093 sheet: -1.97 (0.26), residues: 327 loop : -2.58 (0.11), residues: 2035 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP D 115 HIS 0.001 0.000 HIS F 175 PHE 0.004 0.000 PHE D1319 TYR 0.003 0.000 TYR C1296 ARG 0.001 0.000 ARG C1316 Details of bonding type rmsd hydrogen bonds : bond 0.34683 ( 784) hydrogen bonds : angle 9.69554 ( 2220) metal coordination : bond 0.38657 ( 3) covalent geometry : bond 0.00127 (24867) covalent geometry : angle 0.36145 (33742) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6910 Ramachandran restraints generated. 3455 Oldfield, 0 Emsley, 3455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6910 Ramachandran restraints generated. 3455 Oldfield, 0 Emsley, 3455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 584 residues out of total 2935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 583 time to evaluate : 4.800 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash Corrupt residue: chain: F residue: PRO 248 >>> skipping revert: symmetry clash revert: symmetry clash REVERT: B 41 ASN cc_start: 0.8938 (t0) cc_final: 0.8738 (t0) REVERT: B 218 ARG cc_start: 0.8078 (tpt170) cc_final: 0.7833 (tpp-160) REVERT: B 226 GLN cc_start: 0.7222 (mt0) cc_final: 0.6856 (mm-40) REVERT: B 227 LEU cc_start: 0.7054 (tp) cc_final: 0.6594 (tp) REVERT: C 709 MET cc_start: 0.7673 (mmm) cc_final: 0.7425 (tpp) REVERT: C 958 LEU cc_start: 0.9080 (tp) cc_final: 0.8742 (tt) REVERT: C 963 LYS cc_start: 0.8563 (tmtt) cc_final: 0.8268 (ptmt) REVERT: C 1120 VAL cc_start: 0.8368 (t) cc_final: 0.8089 (t) REVERT: C 1259 HIS cc_start: 0.7542 (p-80) cc_final: 0.7291 (p-80) REVERT: D 297 ARG cc_start: 0.7797 (mtm180) cc_final: 0.7418 (mtm-85) REVERT: D 485 MET cc_start: 0.9153 (tpt) cc_final: 0.8659 (tpt) REVERT: F 309 GLN cc_start: 0.7642 (tt0) cc_final: 0.6900 (mt0) outliers start: 1 outliers final: 1 residues processed: 584 average time/residue: 0.5018 time to fit residues: 422.0955 Evaluate side-chains 345 residues out of total 2935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 344 time to evaluate : 2.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 248 PRO Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 291 optimal weight: 20.0000 chunk 261 optimal weight: 6.9990 chunk 145 optimal weight: 10.0000 chunk 89 optimal weight: 10.0000 chunk 176 optimal weight: 0.5980 chunk 139 optimal weight: 9.9990 chunk 270 optimal weight: 9.9990 chunk 104 optimal weight: 20.0000 chunk 164 optimal weight: 0.6980 chunk 201 optimal weight: 4.9990 chunk 313 optimal weight: 2.9990 overall best weight: 3.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 HIS ** A 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 132 ASN A 171 GLN B 37 HIS B 224 GLN C 40 GLN C 137 ASN C 154 HIS ** C 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 693 GLN ** C 813 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 816 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 837 HIS C 839 GLN ** C1128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1133 HIS C1163 HIS C1252 HIS C1259 HIS C1279 GLN D 300 GLN D 335 GLN D 419 HIS D 465 GLN D 477 GLN D 519 ASN ** D 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 594 GLN D 642 ASN D 929 GLN D1235 ASN ** D1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 64 GLN F 116 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.147839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.120228 restraints weight = 44982.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.119477 restraints weight = 42181.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.120924 restraints weight = 35244.100| |-----------------------------------------------------------------------------| r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.2903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 24870 Z= 0.256 Angle : 0.645 8.088 33742 Z= 0.337 Chirality : 0.046 0.254 4028 Planarity : 0.005 0.054 4459 Dihedral : 3.501 19.763 3723 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.40 % Allowed : 11.63 % Favored : 85.96 % 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: -3.39 (0.12), residues: 3455 helix: -2.68 (0.12), residues: 1135 sheet: -1.43 (0.26), residues: 372 loop : -2.15 (0.12), residues: 1948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 41 HIS 0.007 0.001 HIS D 545 PHE 0.018 0.002 PHE A 35 TYR 0.017 0.002 TYR A 151 ARG 0.021 0.001 ARG B 181 Details of bonding type rmsd hydrogen bonds : bond 0.05426 ( 784) hydrogen bonds : angle 5.57500 ( 2220) metal coordination : bond 0.01006 ( 3) covalent geometry : bond 0.00589 (24867) covalent geometry : angle 0.64506 (33742) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6910 Ramachandran restraints generated. 3455 Oldfield, 0 Emsley, 3455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6910 Ramachandran restraints generated. 3455 Oldfield, 0 Emsley, 3455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 2935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 345 time to evaluate : 2.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash Corrupt residue: chain: F residue: PRO 248 >>> skipping revert: symmetry clash REVERT: A 135 ASP cc_start: 0.7217 (p0) cc_final: 0.6910 (p0) REVERT: A 222 ILE cc_start: 0.9155 (tt) cc_final: 0.8566 (mt) REVERT: B 27 THR cc_start: 0.8904 (m) cc_final: 0.8665 (p) REVERT: B 171 GLN cc_start: 0.7124 (mm-40) cc_final: 0.6875 (mm-40) REVERT: C 520 MET cc_start: 0.8533 (tmm) cc_final: 0.7810 (ttt) REVERT: C 690 MET cc_start: 0.8377 (mpp) cc_final: 0.7950 (mmt) REVERT: C 709 MET cc_start: 0.8256 (mmm) cc_final: 0.7887 (tpp) REVERT: C 946 ARG cc_start: 0.4614 (ptm160) cc_final: 0.3596 (mtp85) REVERT: C 963 LYS cc_start: 0.8991 (tmtt) cc_final: 0.8478 (ptmt) REVERT: C 1148 MET cc_start: 0.8509 (ttm) cc_final: 0.8200 (ttm) REVERT: D 237 MET cc_start: 0.8098 (mtm) cc_final: 0.7892 (mtm) REVERT: D 276 ASN cc_start: 0.8718 (t0) cc_final: 0.8484 (t0) REVERT: D 330 MET cc_start: 0.5677 (mtp) cc_final: 0.5435 (mtp) REVERT: F 320 GLU cc_start: 0.7663 (OUTLIER) cc_final: 0.7362 (mp0) outliers start: 53 outliers final: 30 residues processed: 380 average time/residue: 0.4200 time to fit residues: 250.4608 Evaluate side-chains 317 residues out of total 2935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 286 time to evaluate : 2.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 438 VAL Chi-restraints excluded: chain C residue 769 CYS Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 807 VAL Chi-restraints excluded: chain C residue 844 VAL Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1350 ILE Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 129 ASP Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 808 VAL Chi-restraints excluded: chain D residue 810 THR Chi-restraints excluded: chain D residue 895 CYS Chi-restraints excluded: chain D residue 1226 VAL Chi-restraints excluded: chain D residue 1243 LEU Chi-restraints excluded: chain F residue 168 ARG Chi-restraints excluded: chain F residue 214 VAL Chi-restraints excluded: chain F residue 218 LEU Chi-restraints excluded: chain F residue 226 SER Chi-restraints excluded: chain F residue 248 PRO Chi-restraints excluded: chain F residue 320 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 2 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 chunk 89 optimal weight: 6.9990 chunk 320 optimal weight: 8.9990 chunk 244 optimal weight: 6.9990 chunk 219 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 339 optimal weight: 5.9990 chunk 268 optimal weight: 8.9990 chunk 237 optimal weight: 2.9990 chunk 64 optimal weight: 30.0000 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 GLN B 37 HIS B 224 GLN ** C 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 813 ASN ** C 816 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1133 HIS C1314 ASN D 300 GLN ** D1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 181 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.143321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.117027 restraints weight = 45094.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.116429 restraints weight = 48887.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.117694 restraints weight = 42760.816| |-----------------------------------------------------------------------------| r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.3774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 24870 Z= 0.252 Angle : 0.628 7.660 33742 Z= 0.325 Chirality : 0.046 0.166 4028 Planarity : 0.004 0.058 4459 Dihedral : 4.055 21.020 3723 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 3.69 % Allowed : 14.45 % Favored : 81.86 % 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: -2.74 (0.13), residues: 3455 helix: -1.72 (0.14), residues: 1174 sheet: -1.34 (0.26), residues: 369 loop : -1.98 (0.13), residues: 1912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 41 HIS 0.036 0.002 HIS B 37 PHE 0.020 0.002 PHE D 437 TYR 0.015 0.002 TYR C 77 ARG 0.008 0.001 ARG A 95 Details of bonding type rmsd hydrogen bonds : bond 0.04726 ( 784) hydrogen bonds : angle 5.24833 ( 2220) metal coordination : bond 0.00714 ( 3) covalent geometry : bond 0.00589 (24867) covalent geometry : angle 0.62795 (33742) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6910 Ramachandran restraints generated. 3455 Oldfield, 0 Emsley, 3455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6910 Ramachandran restraints generated. 3455 Oldfield, 0 Emsley, 3455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 2935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 316 time to evaluate : 3.126 Fit side-chains revert: symmetry clash revert: symmetry clash Corrupt residue: chain: C residue: PRO 309 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash Corrupt residue: chain: F residue: PRO 248 >>> skipping revert: symmetry clash REVERT: A 222 ILE cc_start: 0.9154 (tt) cc_final: 0.8633 (mt) REVERT: A 224 GLN cc_start: 0.8446 (tm-30) cc_final: 0.8185 (tp40) REVERT: B 27 THR cc_start: 0.8917 (m) cc_final: 0.8648 (p) REVERT: B 37 HIS cc_start: 0.8862 (OUTLIER) cc_final: 0.8226 (t70) REVERT: C 520 MET cc_start: 0.8595 (tmm) cc_final: 0.7920 (ttt) REVERT: C 690 MET cc_start: 0.8474 (mpp) cc_final: 0.8170 (mmm) REVERT: C 709 MET cc_start: 0.8410 (mmm) cc_final: 0.7902 (tpp) REVERT: C 946 ARG cc_start: 0.4086 (ptm160) cc_final: 0.3452 (mtp85) REVERT: C 963 LYS cc_start: 0.8886 (tmtt) cc_final: 0.8430 (ptmt) REVERT: C 1148 MET cc_start: 0.8502 (ttm) cc_final: 0.8168 (ttm) REVERT: D 34 SER cc_start: 0.8409 (OUTLIER) cc_final: 0.7930 (p) REVERT: D 276 ASN cc_start: 0.8768 (t0) cc_final: 0.8439 (t0) REVERT: D 297 ARG cc_start: 0.8323 (mtm180) cc_final: 0.7725 (mtm-85) REVERT: D 508 MET cc_start: 0.8817 (mmm) cc_final: 0.8343 (tpp) REVERT: D 820 LEU cc_start: 0.9079 (OUTLIER) cc_final: 0.8763 (pp) REVERT: F 185 ARG cc_start: 0.6505 (OUTLIER) cc_final: 0.6124 (tpp-160) REVERT: F 240 LEU cc_start: 0.8770 (mm) cc_final: 0.8540 (mp) outliers start: 82 outliers final: 53 residues processed: 376 average time/residue: 0.5061 time to fit residues: 304.1003 Evaluate side-chains 328 residues out of total 2935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 271 time to evaluate : 5.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 141 MET Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 224 GLN Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 309 PRO Chi-restraints excluded: chain C residue 438 VAL Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 574 ILE Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain C residue 769 CYS Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 807 VAL Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1155 VAL Chi-restraints excluded: chain C residue 1269 VAL Chi-restraints excluded: chain C residue 1304 GLU Chi-restraints excluded: chain C residue 1350 ILE Chi-restraints excluded: chain D residue 34 SER Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 129 ASP Chi-restraints excluded: chain D residue 215 LYS Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 300 GLN Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 353 SER Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 808 VAL Chi-restraints excluded: chain D residue 820 LEU Chi-restraints excluded: chain D residue 895 CYS Chi-restraints excluded: chain D residue 1226 VAL Chi-restraints excluded: chain D residue 1243 LEU Chi-restraints excluded: chain D residue 1260 MET Chi-restraints excluded: chain D residue 1280 VAL Chi-restraints excluded: chain D residue 1309 ILE Chi-restraints excluded: chain D residue 1340 LYS Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain F residue 82 VAL Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 185 ARG Chi-restraints excluded: chain F residue 214 VAL Chi-restraints excluded: chain F residue 248 PRO Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 328 optimal weight: 0.9980 chunk 177 optimal weight: 0.0000 chunk 90 optimal weight: 6.9990 chunk 223 optimal weight: 0.4980 chunk 136 optimal weight: 4.9990 chunk 80 optimal weight: 0.8980 chunk 147 optimal weight: 0.7980 chunk 261 optimal weight: 8.9990 chunk 318 optimal weight: 6.9990 chunk 337 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 overall best weight: 0.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 GLN B 226 GLN ** C 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 678 HIS ** C1128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1133 HIS C1283 GLN D 300 GLN D 469 HIS D 642 ASN ** D1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.147492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.121079 restraints weight = 44708.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.120678 restraints weight = 49769.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.122020 restraints weight = 41620.397| |-----------------------------------------------------------------------------| r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.3783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 24870 Z= 0.093 Angle : 0.465 6.912 33742 Z= 0.239 Chirality : 0.041 0.143 4028 Planarity : 0.003 0.051 4459 Dihedral : 3.405 17.287 3723 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.72 % Allowed : 16.44 % Favored : 80.84 % 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: -2.04 (0.13), residues: 3455 helix: -0.94 (0.15), residues: 1160 sheet: -1.11 (0.27), residues: 373 loop : -1.67 (0.13), residues: 1922 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 41 HIS 0.006 0.001 HIS B 37 PHE 0.008 0.001 PHE D 377 TYR 0.011 0.001 TYR A 68 ARG 0.007 0.000 ARG A 180 Details of bonding type rmsd hydrogen bonds : bond 0.03358 ( 784) hydrogen bonds : angle 4.63274 ( 2220) metal coordination : bond 0.00100 ( 3) covalent geometry : bond 0.00209 (24867) covalent geometry : angle 0.46550 (33742) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6910 Ramachandran restraints generated. 3455 Oldfield, 0 Emsley, 3455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6910 Ramachandran restraints generated. 3455 Oldfield, 0 Emsley, 3455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 2935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 313 time to evaluate : 3.423 Fit side-chains Corrupt residue: chain: C residue: PRO 309 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash Corrupt residue: chain: F residue: PRO 248 >>> skipping revert: symmetry clash REVERT: A 222 ILE cc_start: 0.9021 (tt) cc_final: 0.8386 (mt) REVERT: B 27 THR cc_start: 0.8791 (m) cc_final: 0.8501 (p) REVERT: B 184 TYR cc_start: 0.8855 (p90) cc_final: 0.8437 (p90) REVERT: C 520 MET cc_start: 0.8446 (tmm) cc_final: 0.7705 (ttt) REVERT: C 690 MET cc_start: 0.8366 (mpp) cc_final: 0.8083 (mmm) REVERT: C 709 MET cc_start: 0.8189 (mmm) cc_final: 0.7755 (tpp) REVERT: C 946 ARG cc_start: 0.4157 (ptm160) cc_final: 0.3325 (mtt-85) REVERT: C 963 LYS cc_start: 0.8844 (tmtt) cc_final: 0.8287 (ptmt) REVERT: D 34 SER cc_start: 0.8434 (t) cc_final: 0.7942 (p) REVERT: D 237 MET cc_start: 0.8059 (mtm) cc_final: 0.7834 (mtm) REVERT: D 508 MET cc_start: 0.8548 (mmm) cc_final: 0.8184 (tpp) REVERT: D 820 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8655 (pp) REVERT: D 1183 SER cc_start: 0.8045 (t) cc_final: 0.7818 (p) REVERT: D 1329 THR cc_start: 0.8870 (OUTLIER) cc_final: 0.8610 (m) outliers start: 61 outliers final: 39 residues processed: 356 average time/residue: 0.4867 time to fit residues: 285.2695 Evaluate side-chains 317 residues out of total 2935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 276 time to evaluate : 3.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 141 MET Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 309 PRO Chi-restraints excluded: chain C residue 577 ILE Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 719 VAL Chi-restraints excluded: chain C residue 769 CYS Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 805 MET Chi-restraints excluded: chain C residue 1269 VAL Chi-restraints excluded: chain C residue 1283 GLN Chi-restraints excluded: chain C residue 1304 GLU Chi-restraints excluded: chain C residue 1350 ILE Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 129 ASP Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 215 LYS Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 743 MET Chi-restraints excluded: chain D residue 818 HIS Chi-restraints excluded: chain D residue 820 LEU Chi-restraints excluded: chain D residue 895 CYS Chi-restraints excluded: chain D residue 1226 VAL Chi-restraints excluded: chain D residue 1243 LEU Chi-restraints excluded: chain D residue 1329 THR Chi-restraints excluded: chain D residue 1340 LYS Chi-restraints excluded: chain D residue 1366 HIS Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 168 ARG Chi-restraints excluded: chain F residue 248 PRO Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 114 optimal weight: 6.9990 chunk 79 optimal weight: 0.9990 chunk 236 optimal weight: 4.9990 chunk 266 optimal weight: 1.9990 chunk 204 optimal weight: 0.6980 chunk 296 optimal weight: 0.9990 chunk 166 optimal weight: 2.9990 chunk 49 optimal weight: 9.9990 chunk 113 optimal weight: 0.6980 chunk 185 optimal weight: 0.8980 chunk 171 optimal weight: 5.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 GLN ** B 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.147655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.120132 restraints weight = 44988.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.119498 restraints weight = 42580.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.121268 restraints weight = 35524.975| |-----------------------------------------------------------------------------| r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.3883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 24870 Z= 0.098 Angle : 0.465 7.389 33742 Z= 0.237 Chirality : 0.041 0.140 4028 Planarity : 0.003 0.050 4459 Dihedral : 3.236 15.817 3723 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.82 % Allowed : 17.41 % Favored : 79.78 % 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: -1.62 (0.14), residues: 3455 helix: -0.46 (0.16), residues: 1147 sheet: -1.06 (0.27), residues: 383 loop : -1.47 (0.13), residues: 1925 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 41 HIS 0.003 0.001 HIS D 777 PHE 0.015 0.001 PHE B 230 TYR 0.026 0.001 TYR F 150 ARG 0.008 0.000 ARG C 962 Details of bonding type rmsd hydrogen bonds : bond 0.03125 ( 784) hydrogen bonds : angle 4.36634 ( 2220) metal coordination : bond 0.00185 ( 3) covalent geometry : bond 0.00228 (24867) covalent geometry : angle 0.46482 (33742) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6910 Ramachandran restraints generated. 3455 Oldfield, 0 Emsley, 3455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6910 Ramachandran restraints generated. 3455 Oldfield, 0 Emsley, 3455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 2935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 300 time to evaluate : 4.616 Fit side-chains Corrupt residue: chain: C residue: PRO 309 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash Corrupt residue: chain: E residue: PRO 46 >>> skipping Corrupt residue: chain: F residue: PRO 248 >>> skipping revert: symmetry clash REVERT: A 104 LYS cc_start: 0.7749 (tptt) cc_final: 0.7457 (mmtt) REVERT: A 222 ILE cc_start: 0.9089 (tt) cc_final: 0.8405 (mt) REVERT: B 184 TYR cc_start: 0.8829 (p90) cc_final: 0.8315 (p90) REVERT: C 520 MET cc_start: 0.8461 (tmm) cc_final: 0.7747 (ttt) REVERT: C 690 MET cc_start: 0.8457 (mpp) cc_final: 0.8092 (mmm) REVERT: C 709 MET cc_start: 0.8201 (mmm) cc_final: 0.7741 (tpp) REVERT: C 946 ARG cc_start: 0.4365 (ptm160) cc_final: 0.3054 (mtt180) REVERT: C 963 LYS cc_start: 0.8995 (tmtt) cc_final: 0.8464 (ptmt) REVERT: C 1206 LYS cc_start: 0.7684 (OUTLIER) cc_final: 0.7462 (ttpp) REVERT: C 1218 ASP cc_start: 0.8021 (t0) cc_final: 0.7797 (t0) REVERT: D 34 SER cc_start: 0.8484 (t) cc_final: 0.8001 (p) REVERT: D 130 MET cc_start: 0.6767 (mmt) cc_final: 0.6482 (mmt) REVERT: D 227 PHE cc_start: 0.8412 (m-80) cc_final: 0.8085 (m-10) REVERT: D 363 LEU cc_start: 0.9215 (OUTLIER) cc_final: 0.8937 (tt) REVERT: D 508 MET cc_start: 0.8478 (mmm) cc_final: 0.8073 (tpp) REVERT: D 820 LEU cc_start: 0.8996 (OUTLIER) cc_final: 0.8709 (pp) REVERT: D 1183 SER cc_start: 0.8134 (t) cc_final: 0.7882 (p) REVERT: D 1329 THR cc_start: 0.8873 (OUTLIER) cc_final: 0.8639 (m) outliers start: 64 outliers final: 48 residues processed: 345 average time/residue: 0.3739 time to fit residues: 209.4163 Evaluate side-chains 329 residues out of total 2935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 277 time to evaluate : 2.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 141 MET Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 309 PRO Chi-restraints excluded: chain C residue 577 ILE Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 719 VAL Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain C residue 769 CYS Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 805 MET Chi-restraints excluded: chain C residue 827 VAL Chi-restraints excluded: chain C residue 1206 LYS Chi-restraints excluded: chain C residue 1269 VAL Chi-restraints excluded: chain C residue 1350 ILE Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 215 LYS Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 743 MET Chi-restraints excluded: chain D residue 818 HIS Chi-restraints excluded: chain D residue 820 LEU Chi-restraints excluded: chain D residue 826 ILE Chi-restraints excluded: chain D residue 895 CYS Chi-restraints excluded: chain D residue 1144 LEU Chi-restraints excluded: chain D residue 1226 VAL Chi-restraints excluded: chain D residue 1243 LEU Chi-restraints excluded: chain D residue 1329 THR Chi-restraints excluded: chain D residue 1340 LYS Chi-restraints excluded: chain D residue 1342 ASP Chi-restraints excluded: chain D residue 1366 HIS Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 46 PRO Chi-restraints excluded: chain F residue 82 VAL Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 168 ARG Chi-restraints excluded: chain F residue 248 PRO Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 91 optimal weight: 6.9990 chunk 130 optimal weight: 6.9990 chunk 259 optimal weight: 0.9990 chunk 323 optimal weight: 9.9990 chunk 247 optimal weight: 4.9990 chunk 138 optimal weight: 8.9990 chunk 162 optimal weight: 5.9990 chunk 1 optimal weight: 7.9990 chunk 340 optimal weight: 7.9990 chunk 133 optimal weight: 2.9990 chunk 161 optimal weight: 0.6980 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 GLN B 224 GLN B 226 GLN ** C 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1133 HIS D 642 ASN ** D1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 256 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.142065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.114072 restraints weight = 45402.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.112944 restraints weight = 43906.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.113811 restraints weight = 41103.114| |-----------------------------------------------------------------------------| r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.4399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 24870 Z= 0.228 Angle : 0.590 8.589 33742 Z= 0.304 Chirality : 0.044 0.143 4028 Planarity : 0.004 0.052 4459 Dihedral : 3.986 20.231 3723 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 4.20 % Allowed : 17.45 % Favored : 78.35 % 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: -1.74 (0.14), residues: 3455 helix: -0.58 (0.15), residues: 1166 sheet: -1.12 (0.27), residues: 375 loop : -1.53 (0.13), residues: 1914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 41 HIS 0.008 0.001 HIS C 678 PHE 0.017 0.002 PHE D 437 TYR 0.025 0.002 TYR F 150 ARG 0.005 0.001 ARG A 95 Details of bonding type rmsd hydrogen bonds : bond 0.03969 ( 784) hydrogen bonds : angle 4.71968 ( 2220) metal coordination : bond 0.00718 ( 3) covalent geometry : bond 0.00538 (24867) covalent geometry : angle 0.59018 (33742) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6910 Ramachandran restraints generated. 3455 Oldfield, 0 Emsley, 3455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6910 Ramachandran restraints generated. 3455 Oldfield, 0 Emsley, 3455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 2935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 282 time to evaluate : 2.582 Fit side-chains revert: symmetry clash Corrupt residue: chain: C residue: PRO 309 >>> skipping revert: symmetry clash Corrupt residue: chain: F residue: PRO 248 >>> skipping revert: symmetry clash REVERT: A 222 ILE cc_start: 0.9222 (tt) cc_final: 0.8673 (mt) REVERT: B 184 TYR cc_start: 0.8973 (p90) cc_final: 0.8540 (p90) REVERT: B 199 LYS cc_start: 0.8982 (ptmt) cc_final: 0.8567 (ptpt) REVERT: C 520 MET cc_start: 0.8523 (tmm) cc_final: 0.7831 (ttt) REVERT: C 709 MET cc_start: 0.8457 (mmm) cc_final: 0.8098 (tpp) REVERT: C 864 GLU cc_start: 0.7515 (tp30) cc_final: 0.7211 (tp30) REVERT: C 946 ARG cc_start: 0.4514 (ptm160) cc_final: 0.3178 (mtt180) REVERT: C 963 LYS cc_start: 0.8981 (tmtt) cc_final: 0.8340 (ptmt) REVERT: D 34 SER cc_start: 0.8519 (t) cc_final: 0.8050 (p) REVERT: D 118 LYS cc_start: 0.6710 (mtpt) cc_final: 0.6419 (mtmt) REVERT: D 297 ARG cc_start: 0.8404 (mtm180) cc_final: 0.7720 (mtm-85) REVERT: D 363 LEU cc_start: 0.9286 (OUTLIER) cc_final: 0.8982 (tt) REVERT: D 508 MET cc_start: 0.8758 (mmm) cc_final: 0.8267 (tpp) REVERT: D 820 LEU cc_start: 0.9151 (OUTLIER) cc_final: 0.8751 (pp) REVERT: D 913 GLU cc_start: 0.7624 (tt0) cc_final: 0.7411 (tt0) REVERT: F 185 ARG cc_start: 0.6620 (OUTLIER) cc_final: 0.6360 (tpp-160) outliers start: 93 outliers final: 69 residues processed: 356 average time/residue: 0.3608 time to fit residues: 207.2077 Evaluate side-chains 340 residues out of total 2935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 268 time to evaluate : 2.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 224 GLN Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 309 PRO Chi-restraints excluded: chain C residue 438 VAL Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 574 ILE Chi-restraints excluded: chain C residue 577 ILE Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 805 MET Chi-restraints excluded: chain C residue 807 VAL Chi-restraints excluded: chain C residue 827 VAL Chi-restraints excluded: chain C residue 1050 LYS Chi-restraints excluded: chain C residue 1269 VAL Chi-restraints excluded: chain C residue 1304 GLU Chi-restraints excluded: chain C residue 1350 ILE Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 129 ASP Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 215 LYS Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 353 SER Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 570 VAL Chi-restraints excluded: chain D residue 673 VAL Chi-restraints excluded: chain D residue 743 MET Chi-restraints excluded: chain D residue 818 HIS Chi-restraints excluded: chain D residue 820 LEU Chi-restraints excluded: chain D residue 826 ILE Chi-restraints excluded: chain D residue 895 CYS Chi-restraints excluded: chain D residue 1035 VAL Chi-restraints excluded: chain D residue 1144 LEU Chi-restraints excluded: chain D residue 1226 VAL Chi-restraints excluded: chain D residue 1243 LEU Chi-restraints excluded: chain D residue 1309 ILE Chi-restraints excluded: chain D residue 1342 ASP Chi-restraints excluded: chain D residue 1366 HIS Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain F residue 82 VAL Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 185 ARG Chi-restraints excluded: chain F residue 242 THR Chi-restraints excluded: chain F residue 248 PRO Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 328 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 260 optimal weight: 0.7980 chunk 121 optimal weight: 8.9990 chunk 314 optimal weight: 1.9990 chunk 254 optimal weight: 0.4980 chunk 208 optimal weight: 0.8980 chunk 192 optimal weight: 0.4980 chunk 150 optimal weight: 1.9990 chunk 70 optimal weight: 8.9990 chunk 226 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 278 HIS ** C1128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 642 ASN D 667 GLN D 910 ASN ** D1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.145953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.118579 restraints weight = 44918.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.117810 restraints weight = 40897.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.118882 restraints weight = 37670.478| |-----------------------------------------------------------------------------| r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.4340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 24870 Z= 0.096 Angle : 0.475 9.415 33742 Z= 0.242 Chirality : 0.041 0.139 4028 Planarity : 0.003 0.056 4459 Dihedral : 3.458 17.372 3723 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.72 % Allowed : 19.25 % Favored : 78.02 % 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: -1.40 (0.14), residues: 3455 helix: -0.18 (0.16), residues: 1177 sheet: -1.06 (0.27), residues: 380 loop : -1.38 (0.13), residues: 1898 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 41 HIS 0.003 0.001 HIS D 777 PHE 0.010 0.001 PHE C 161 TYR 0.022 0.001 TYR F 150 ARG 0.008 0.000 ARG C 962 Details of bonding type rmsd hydrogen bonds : bond 0.03075 ( 784) hydrogen bonds : angle 4.26643 ( 2220) metal coordination : bond 0.00142 ( 3) covalent geometry : bond 0.00222 (24867) covalent geometry : angle 0.47457 (33742) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6910 Ramachandran restraints generated. 3455 Oldfield, 0 Emsley, 3455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6910 Ramachandran restraints generated. 3455 Oldfield, 0 Emsley, 3455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 2935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 294 time to evaluate : 2.717 Fit side-chains Corrupt residue: chain: C residue: PRO 309 >>> skipping revert: symmetry clash revert: symmetry clash Corrupt residue: chain: E residue: PRO 46 >>> skipping Corrupt residue: chain: F residue: PRO 248 >>> skipping revert: symmetry clash REVERT: A 222 ILE cc_start: 0.9115 (tt) cc_final: 0.8454 (mt) REVERT: B 184 TYR cc_start: 0.8822 (p90) cc_final: 0.8238 (p90) REVERT: C 520 MET cc_start: 0.8462 (tmm) cc_final: 0.7737 (ttt) REVERT: C 690 MET cc_start: 0.8531 (mpp) cc_final: 0.8217 (mmm) REVERT: C 709 MET cc_start: 0.8223 (mmm) cc_final: 0.7866 (tpp) REVERT: C 864 GLU cc_start: 0.7462 (tp30) cc_final: 0.7246 (tp30) REVERT: C 946 ARG cc_start: 0.4508 (ptm160) cc_final: 0.3116 (mtt180) REVERT: C 962 ARG cc_start: 0.8015 (ttp80) cc_final: 0.7667 (tmm160) REVERT: C 963 LYS cc_start: 0.8987 (tmtt) cc_final: 0.8275 (ptmt) REVERT: D 34 SER cc_start: 0.8504 (t) cc_final: 0.7988 (p) REVERT: D 180 MET cc_start: 0.6786 (ttt) cc_final: 0.6541 (tpp) REVERT: D 363 LEU cc_start: 0.9183 (OUTLIER) cc_final: 0.8911 (tt) REVERT: D 508 MET cc_start: 0.8498 (mmm) cc_final: 0.8256 (tpp) REVERT: D 697 MET cc_start: 0.8703 (ttp) cc_final: 0.8467 (ttp) REVERT: D 820 LEU cc_start: 0.9120 (OUTLIER) cc_final: 0.8842 (pp) REVERT: D 913 GLU cc_start: 0.7482 (tt0) cc_final: 0.7252 (tt0) REVERT: D 1183 SER cc_start: 0.8127 (t) cc_final: 0.7886 (p) outliers start: 62 outliers final: 48 residues processed: 342 average time/residue: 0.4027 time to fit residues: 226.6482 Evaluate side-chains 328 residues out of total 2935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 278 time to evaluate : 2.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 309 PRO Chi-restraints excluded: chain C residue 577 ILE Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 805 MET Chi-restraints excluded: chain C residue 807 VAL Chi-restraints excluded: chain C residue 827 VAL Chi-restraints excluded: chain C residue 1050 LYS Chi-restraints excluded: chain C residue 1304 GLU Chi-restraints excluded: chain C residue 1350 ILE Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 215 LYS Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 570 VAL Chi-restraints excluded: chain D residue 743 MET Chi-restraints excluded: chain D residue 820 LEU Chi-restraints excluded: chain D residue 895 CYS Chi-restraints excluded: chain D residue 1035 VAL Chi-restraints excluded: chain D residue 1144 LEU Chi-restraints excluded: chain D residue 1226 VAL Chi-restraints excluded: chain D residue 1243 LEU Chi-restraints excluded: chain D residue 1342 ASP Chi-restraints excluded: chain D residue 1366 HIS Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 46 PRO Chi-restraints excluded: chain F residue 82 VAL Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 168 ARG Chi-restraints excluded: chain F residue 242 THR Chi-restraints excluded: chain F residue 248 PRO Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 328 optimal weight: 1.9990 chunk 114 optimal weight: 4.9990 chunk 306 optimal weight: 5.9990 chunk 115 optimal weight: 0.0570 chunk 238 optimal weight: 0.9980 chunk 203 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 chunk 216 optimal weight: 0.0870 chunk 124 optimal weight: 0.4980 chunk 228 optimal weight: 6.9990 chunk 208 optimal weight: 2.9990 overall best weight: 0.7278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 224 GLN B 226 GLN ** C 804 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1133 HIS ** D 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.146649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.118844 restraints weight = 44765.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.117936 restraints weight = 44632.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.118864 restraints weight = 35932.243| |-----------------------------------------------------------------------------| r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.4368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 24870 Z= 0.092 Angle : 0.475 8.912 33742 Z= 0.240 Chirality : 0.041 0.151 4028 Planarity : 0.003 0.054 4459 Dihedral : 3.250 15.741 3723 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 3.00 % Allowed : 19.34 % Favored : 77.65 % 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: -1.10 (0.14), residues: 3455 helix: 0.16 (0.16), residues: 1166 sheet: -0.80 (0.27), residues: 380 loop : -1.28 (0.14), residues: 1909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 41 HIS 0.003 0.001 HIS C 54 PHE 0.020 0.001 PHE D1319 TYR 0.023 0.001 TYR F 150 ARG 0.007 0.000 ARG C 962 Details of bonding type rmsd hydrogen bonds : bond 0.02854 ( 784) hydrogen bonds : angle 4.08120 ( 2220) metal coordination : bond 0.00156 ( 3) covalent geometry : bond 0.00216 (24867) covalent geometry : angle 0.47459 (33742) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6910 Ramachandran restraints generated. 3455 Oldfield, 0 Emsley, 3455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6910 Ramachandran restraints generated. 3455 Oldfield, 0 Emsley, 3455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 2935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 292 time to evaluate : 2.741 Fit side-chains Corrupt residue: chain: C residue: PRO 309 >>> skipping revert: symmetry clash revert: symmetry clash Corrupt residue: chain: E residue: PRO 46 >>> skipping Corrupt residue: chain: F residue: PRO 248 >>> skipping revert: symmetry clash REVERT: A 104 LYS cc_start: 0.7720 (tptt) cc_final: 0.7416 (mmtt) REVERT: A 222 ILE cc_start: 0.9086 (tt) cc_final: 0.8418 (mt) REVERT: B 184 TYR cc_start: 0.8707 (p90) cc_final: 0.8105 (p90) REVERT: C 520 MET cc_start: 0.8461 (tmm) cc_final: 0.7729 (ttt) REVERT: C 690 MET cc_start: 0.8498 (mpp) cc_final: 0.8170 (mmm) REVERT: C 709 MET cc_start: 0.8192 (mmm) cc_final: 0.7849 (tpp) REVERT: C 946 ARG cc_start: 0.4355 (ptm160) cc_final: 0.2976 (mtt180) REVERT: C 962 ARG cc_start: 0.8110 (ttp80) cc_final: 0.7689 (tmm160) REVERT: C 963 LYS cc_start: 0.9014 (tmtt) cc_final: 0.8350 (ptmt) REVERT: D 34 SER cc_start: 0.8492 (t) cc_final: 0.7976 (p) REVERT: D 118 LYS cc_start: 0.6953 (mtmt) cc_final: 0.6587 (mtmt) REVERT: D 363 LEU cc_start: 0.9262 (OUTLIER) cc_final: 0.8976 (tt) REVERT: D 508 MET cc_start: 0.8369 (mmm) cc_final: 0.8150 (tpp) REVERT: D 697 MET cc_start: 0.8742 (ttp) cc_final: 0.8397 (ttp) REVERT: D 820 LEU cc_start: 0.9104 (OUTLIER) cc_final: 0.8841 (pp) REVERT: D 1183 SER cc_start: 0.8178 (t) cc_final: 0.7903 (p) outliers start: 68 outliers final: 56 residues processed: 350 average time/residue: 0.3685 time to fit residues: 210.1980 Evaluate side-chains 344 residues out of total 2935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 286 time to evaluate : 2.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 224 GLN Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 309 PRO Chi-restraints excluded: chain C residue 577 ILE Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 805 MET Chi-restraints excluded: chain C residue 807 VAL Chi-restraints excluded: chain C residue 827 VAL Chi-restraints excluded: chain C residue 1050 LYS Chi-restraints excluded: chain C residue 1304 GLU Chi-restraints excluded: chain C residue 1350 ILE Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 353 SER Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 570 VAL Chi-restraints excluded: chain D residue 673 VAL Chi-restraints excluded: chain D residue 743 MET Chi-restraints excluded: chain D residue 818 HIS Chi-restraints excluded: chain D residue 820 LEU Chi-restraints excluded: chain D residue 895 CYS Chi-restraints excluded: chain D residue 1035 VAL Chi-restraints excluded: chain D residue 1144 LEU Chi-restraints excluded: chain D residue 1226 VAL Chi-restraints excluded: chain D residue 1243 LEU Chi-restraints excluded: chain D residue 1342 ASP Chi-restraints excluded: chain D residue 1366 HIS Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 46 PRO Chi-restraints excluded: chain F residue 82 VAL Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 168 ARG Chi-restraints excluded: chain F residue 218 LEU Chi-restraints excluded: chain F residue 242 THR Chi-restraints excluded: chain F residue 248 PRO Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 126 optimal weight: 5.9990 chunk 239 optimal weight: 0.7980 chunk 150 optimal weight: 0.9980 chunk 208 optimal weight: 0.9980 chunk 211 optimal weight: 0.0980 chunk 216 optimal weight: 0.1980 chunk 201 optimal weight: 6.9990 chunk 233 optimal weight: 0.5980 chunk 196 optimal weight: 0.0170 chunk 72 optimal weight: 6.9990 chunk 322 optimal weight: 9.9990 overall best weight: 0.3418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 37 HIS ** B 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 GLN C 804 ASN ** C1128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 181 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.148340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.121015 restraints weight = 44789.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.120572 restraints weight = 41789.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.121708 restraints weight = 37798.610| |-----------------------------------------------------------------------------| r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.4368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 24870 Z= 0.084 Angle : 0.467 10.471 33742 Z= 0.234 Chirality : 0.041 0.146 4028 Planarity : 0.003 0.052 4459 Dihedral : 3.066 15.307 3723 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.22 % Allowed : 20.50 % Favored : 77.29 % 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: -0.81 (0.14), residues: 3455 helix: 0.43 (0.16), residues: 1153 sheet: -0.58 (0.28), residues: 367 loop : -1.13 (0.14), residues: 1935 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 41 HIS 0.003 0.000 HIS D 777 PHE 0.017 0.001 PHE A 176 TYR 0.025 0.001 TYR F 150 ARG 0.006 0.000 ARG C 962 Details of bonding type rmsd hydrogen bonds : bond 0.02604 ( 784) hydrogen bonds : angle 3.89388 ( 2220) metal coordination : bond 0.00064 ( 3) covalent geometry : bond 0.00190 (24867) covalent geometry : angle 0.46680 (33742) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6910 Ramachandran restraints generated. 3455 Oldfield, 0 Emsley, 3455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6910 Ramachandran restraints generated. 3455 Oldfield, 0 Emsley, 3455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 2935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 303 time to evaluate : 2.825 Fit side-chains Corrupt residue: chain: C residue: PRO 309 >>> skipping revert: symmetry clash revert: symmetry clash Corrupt residue: chain: E residue: PRO 46 >>> skipping Corrupt residue: chain: F residue: PRO 248 >>> skipping revert: symmetry clash REVERT: A 97 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.7490 (pp20) REVERT: A 104 LYS cc_start: 0.7735 (tptt) cc_final: 0.7486 (mmtt) REVERT: B 184 TYR cc_start: 0.8678 (p90) cc_final: 0.8092 (p90) REVERT: C 520 MET cc_start: 0.8417 (tmm) cc_final: 0.7720 (ttt) REVERT: C 690 MET cc_start: 0.8470 (mpp) cc_final: 0.8136 (mmm) REVERT: C 709 MET cc_start: 0.8127 (mmm) cc_final: 0.7733 (tpp) REVERT: C 946 ARG cc_start: 0.4189 (ptm160) cc_final: 0.2947 (mtt180) REVERT: C 962 ARG cc_start: 0.7992 (ttp80) cc_final: 0.7572 (tmm160) REVERT: C 963 LYS cc_start: 0.9018 (tmtt) cc_final: 0.8362 (ptmt) REVERT: D 34 SER cc_start: 0.8447 (t) cc_final: 0.7870 (p) REVERT: D 118 LYS cc_start: 0.6823 (mtmt) cc_final: 0.6440 (mtmt) REVERT: D 363 LEU cc_start: 0.9249 (OUTLIER) cc_final: 0.8978 (tt) REVERT: D 820 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8810 (pp) REVERT: D 1183 SER cc_start: 0.8162 (t) cc_final: 0.7871 (p) outliers start: 51 outliers final: 40 residues processed: 345 average time/residue: 0.3545 time to fit residues: 199.8605 Evaluate side-chains 331 residues out of total 2935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 288 time to evaluate : 2.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 309 PRO Chi-restraints excluded: chain C residue 577 ILE Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 805 MET Chi-restraints excluded: chain C residue 1050 LYS Chi-restraints excluded: chain C residue 1350 ILE Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 570 VAL Chi-restraints excluded: chain D residue 743 MET Chi-restraints excluded: chain D residue 820 LEU Chi-restraints excluded: chain D residue 895 CYS Chi-restraints excluded: chain D residue 1035 VAL Chi-restraints excluded: chain D residue 1144 LEU Chi-restraints excluded: chain D residue 1226 VAL Chi-restraints excluded: chain D residue 1243 LEU Chi-restraints excluded: chain D residue 1342 ASP Chi-restraints excluded: chain D residue 1366 HIS Chi-restraints excluded: chain E residue 46 PRO Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 168 ARG Chi-restraints excluded: chain F residue 218 LEU Chi-restraints excluded: chain F residue 248 PRO Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 196 optimal weight: 0.7980 chunk 137 optimal weight: 0.2980 chunk 286 optimal weight: 9.9990 chunk 74 optimal weight: 20.0000 chunk 2 optimal weight: 3.9990 chunk 223 optimal weight: 6.9990 chunk 139 optimal weight: 9.9990 chunk 189 optimal weight: 0.7980 chunk 122 optimal weight: 0.1980 chunk 193 optimal weight: 10.0000 chunk 186 optimal weight: 3.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 ASN A 171 GLN B 37 HIS B 226 GLN C 522 GLN ** C1128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.146437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.119115 restraints weight = 44772.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.118816 restraints weight = 40871.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.119817 restraints weight = 36372.275| |-----------------------------------------------------------------------------| r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.4450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 24870 Z= 0.113 Angle : 0.485 9.774 33742 Z= 0.244 Chirality : 0.041 0.148 4028 Planarity : 0.003 0.051 4459 Dihedral : 3.159 16.447 3723 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.54 % Allowed : 20.08 % Favored : 77.38 % 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: -0.76 (0.14), residues: 3455 helix: 0.47 (0.16), residues: 1159 sheet: -0.52 (0.27), residues: 387 loop : -1.12 (0.14), residues: 1909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 41 HIS 0.011 0.001 HIS B 37 PHE 0.035 0.001 PHE D1319 TYR 0.025 0.001 TYR F 150 ARG 0.006 0.000 ARG C 962 Details of bonding type rmsd hydrogen bonds : bond 0.02808 ( 784) hydrogen bonds : angle 3.94293 ( 2220) metal coordination : bond 0.00260 ( 3) covalent geometry : bond 0.00270 (24867) covalent geometry : angle 0.48527 (33742) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6910 Ramachandran restraints generated. 3455 Oldfield, 0 Emsley, 3455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6910 Ramachandran restraints generated. 3455 Oldfield, 0 Emsley, 3455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 284 time to evaluate : 3.037 Fit side-chains Corrupt residue: chain: C residue: PRO 309 >>> skipping revert: symmetry clash revert: symmetry clash Corrupt residue: chain: E residue: PRO 46 >>> skipping Corrupt residue: chain: F residue: PRO 248 >>> skipping revert: symmetry clash REVERT: A 97 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.7522 (pp20) REVERT: A 222 ILE cc_start: 0.9101 (tt) cc_final: 0.8430 (mt) REVERT: B 184 TYR cc_start: 0.8721 (p90) cc_final: 0.8104 (p90) REVERT: C 520 MET cc_start: 0.8384 (tmm) cc_final: 0.7626 (ttt) REVERT: C 709 MET cc_start: 0.8170 (mmm) cc_final: 0.7825 (tpp) REVERT: C 946 ARG cc_start: 0.4302 (ptm160) cc_final: 0.3006 (mtt180) REVERT: C 962 ARG cc_start: 0.8043 (ttp80) cc_final: 0.7664 (tmm160) REVERT: C 963 LYS cc_start: 0.8984 (tmtt) cc_final: 0.8347 (ptmt) REVERT: D 34 SER cc_start: 0.8453 (t) cc_final: 0.7906 (p) REVERT: D 118 LYS cc_start: 0.6893 (mtmt) cc_final: 0.6486 (mtmt) REVERT: D 363 LEU cc_start: 0.9255 (OUTLIER) cc_final: 0.8974 (tt) REVERT: D 820 LEU cc_start: 0.9100 (OUTLIER) cc_final: 0.8814 (pp) outliers start: 58 outliers final: 52 residues processed: 330 average time/residue: 0.3475 time to fit residues: 186.9754 Evaluate side-chains 338 residues out of total 2935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 283 time to evaluate : 2.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 309 PRO Chi-restraints excluded: chain C residue 577 ILE Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 805 MET Chi-restraints excluded: chain C residue 1050 LYS Chi-restraints excluded: chain C residue 1304 GLU Chi-restraints excluded: chain C residue 1350 ILE Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 353 SER Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 411 VAL Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 570 VAL Chi-restraints excluded: chain D residue 743 MET Chi-restraints excluded: chain D residue 820 LEU Chi-restraints excluded: chain D residue 826 ILE Chi-restraints excluded: chain D residue 895 CYS Chi-restraints excluded: chain D residue 1035 VAL Chi-restraints excluded: chain D residue 1144 LEU Chi-restraints excluded: chain D residue 1226 VAL Chi-restraints excluded: chain D residue 1243 LEU Chi-restraints excluded: chain D residue 1342 ASP Chi-restraints excluded: chain D residue 1366 HIS Chi-restraints excluded: chain E residue 46 PRO Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 168 ARG Chi-restraints excluded: chain F residue 218 LEU Chi-restraints excluded: chain F residue 242 THR Chi-restraints excluded: chain F residue 248 PRO Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 327 optimal weight: 0.2980 chunk 336 optimal weight: 8.9990 chunk 85 optimal weight: 30.0000 chunk 186 optimal weight: 6.9990 chunk 254 optimal weight: 0.0970 chunk 25 optimal weight: 4.9990 chunk 158 optimal weight: 4.9990 chunk 197 optimal weight: 0.9990 chunk 5 optimal weight: 10.0000 chunk 145 optimal weight: 0.6980 chunk 121 optimal weight: 7.9990 overall best weight: 1.4182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 GLN ** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 224 GLN B 226 GLN ** C1128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.145544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.118339 restraints weight = 44699.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.118047 restraints weight = 40248.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.119253 restraints weight = 34335.966| |-----------------------------------------------------------------------------| r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.4550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 24870 Z= 0.122 Angle : 0.491 9.494 33742 Z= 0.248 Chirality : 0.042 0.148 4028 Planarity : 0.003 0.052 4459 Dihedral : 3.272 16.634 3723 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.49 % Allowed : 20.08 % Favored : 77.42 % 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: -0.75 (0.14), residues: 3455 helix: 0.50 (0.16), residues: 1155 sheet: -0.47 (0.27), residues: 382 loop : -1.13 (0.14), residues: 1918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 41 HIS 0.009 0.001 HIS B 37 PHE 0.034 0.001 PHE D1319 TYR 0.024 0.001 TYR F 150 ARG 0.006 0.000 ARG C 962 Details of bonding type rmsd hydrogen bonds : bond 0.02916 ( 784) hydrogen bonds : angle 4.00481 ( 2220) metal coordination : bond 0.00276 ( 3) covalent geometry : bond 0.00291 (24867) covalent geometry : angle 0.49149 (33742) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8498.38 seconds wall clock time: 154 minutes 14.58 seconds (9254.58 seconds total)