Starting phenix.real_space_refine on Sat Dec 28 05:25:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uin_42300/12_2024/8uin_42300.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uin_42300/12_2024/8uin_42300.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/8uin_42300/12_2024/8uin_42300.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uin_42300/12_2024/8uin_42300.map" model { file = "/net/cci-nas-00/data/ceres_data/8uin_42300/12_2024/8uin_42300.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uin_42300/12_2024/8uin_42300.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= 0.001 sd= 0.023 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 28184 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: 4 Type Number sf(0) Gaussians S 121 5.16 5 C 17972 2.51 5 N 4785 2.21 5 O 5371 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 28249 Number of models: 1 Model: "" Number of chains: 12 Chain: "C" Number of atoms: 944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 944 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 3, 'TRANS': 112} Chain: "D" Number of atoms: 944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 944 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 3, 'TRANS': 112} Chain: "J" Number of atoms: 1513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1513 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 65} Link IDs: {'PTRANS': 6, 'TRANS': 213} Chain breaks: 1 Unresolved non-hydrogen bonds: 244 Unresolved non-hydrogen angles: 298 Unresolved non-hydrogen dihedrals: 208 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 3, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 9, 'PHE:plan': 1, 'GLU:plan': 9, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 133 Chain: "A" Number of atoms: 4987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 641, 4987 Classifications: {'peptide': 641} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 2, 'PTRANS': 35, 'TRANS': 603} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 6695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 895, 6695 Classifications: {'peptide': 895} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 115} Link IDs: {'PCIS': 1, 'PTRANS': 38, 'TRANS': 855} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 461 Unresolved non-hydrogen angles: 565 Unresolved non-hydrogen dihedrals: 376 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 13, 'ASP:plan': 18, 'TYR:plan': 2, 'ASN:plan1': 6, 'HIS:plan': 2, 'PHE:plan': 4, 'GLU:plan': 26, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 336 Chain: "G" Number of atoms: 4946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 640, 4946 Classifications: {'peptide': 640} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PCIS': 2, 'PTRANS': 34, 'TRANS': 603} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "H" Number of atoms: 6578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 897, 6578 Classifications: {'peptide': 897} Incomplete info: {'truncation_to_alanine': 147} Link IDs: {'PCIS': 1, 'PTRANS': 38, 'TRANS': 857} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 608 Unresolved non-hydrogen angles: 760 Unresolved non-hydrogen dihedrals: 517 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'GLN:plan1': 11, 'ASP:plan': 13, 'TYR:plan': 8, 'ASN:plan1': 10, 'TRP:plan': 2, 'HIS:plan': 3, 'PHE:plan': 8, 'GLU:plan': 30, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 415 Chain: "X" Number of atoms: 1572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1572 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PTRANS': 6, 'TRANS': 214} Chain breaks: 1 Unresolved non-hydrogen bonds: 186 Unresolved non-hydrogen angles: 227 Unresolved non-hydrogen dihedrals: 154 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 3, 'ASN:plan1': 4, 'ASP:plan': 7, 'GLU:plan': 9, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 122 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 12.36, per 1000 atoms: 0.44 Number of scatterers: 28249 At special positions: 0 Unit cell: (113.52, 191.84, 170.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 121 16.00 O 5371 8.00 N 4785 7.00 C 17972 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS C 58 " - pdb=" SG CYS C 113 " distance=2.03 Simple disulfide: pdb=" SG CYS C 81 " - pdb=" SG CYS C 91 " distance=2.03 Simple disulfide: pdb=" SG CYS D 58 " - pdb=" SG CYS D 113 " distance=2.03 Simple disulfide: pdb=" SG CYS D 81 " - pdb=" SG CYS D 91 " distance=2.03 Simple disulfide: pdb=" SG CYS A 537 " - pdb=" SG CYS B 794 " distance=2.03 Simple disulfide: pdb=" SG CYS A 605 " - pdb=" SG CYS A 640 " distance=2.03 Simple disulfide: pdb=" SG CYS B 851 " - pdb=" SG CYS B1491 " distance=2.03 Simple disulfide: pdb=" SG CYS B1079 " - pdb=" SG CYS B1136 " distance=2.03 Simple disulfide: pdb=" SG CYS B1336 " - pdb=" SG CYS B1467 " distance=2.03 Simple disulfide: pdb=" SG CYS B1367 " - pdb=" SG CYS B1436 " distance=2.03 Simple disulfide: pdb=" SG CYS B1484 " - pdb=" SG CYS B1489 " distance=2.03 Simple disulfide: pdb=" SG CYS B1496 " - pdb=" SG CYS B1568 " distance=2.03 Simple disulfide: pdb=" SG CYS B1515 " - pdb=" SG CYS B1639 " distance=2.03 Simple disulfide: pdb=" SG CYS B1615 " - pdb=" SG CYS B1624 " distance=2.03 Simple disulfide: pdb=" SG CYS G 537 " - pdb=" SG CYS H 794 " distance=2.03 Simple disulfide: pdb=" SG CYS G 605 " - pdb=" SG CYS G 640 " distance=2.03 Simple disulfide: pdb=" SG CYS H 851 " - pdb=" SG CYS H1491 " distance=2.03 Simple disulfide: pdb=" SG CYS H1079 " - pdb=" SG CYS H1136 " distance=2.03 Simple disulfide: pdb=" SG CYS H1336 " - pdb=" SG CYS H1467 " distance=2.03 Simple disulfide: pdb=" SG CYS H1367 " - pdb=" SG CYS H1436 " distance=2.03 Simple disulfide: pdb=" SG CYS H1484 " - pdb=" SG CYS H1489 " distance=2.03 Simple disulfide: pdb=" SG CYS H1496 " - pdb=" SG CYS H1568 " distance=2.03 Simple disulfide: pdb=" SG CYS H1515 " - pdb=" SG CYS H1639 " distance=2.03 Simple disulfide: pdb=" SG CYS H1615 " - pdb=" SG CYS H1624 " distance=2.03 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 Links applied BETA1-4 " NAG M 1 " - " NAG M 2 " NAG-ASN " NAG B1701 " - " ASN B 917 " " NAG G 701 " - " ASN G 63 " " NAG H1701 " - " ASN H 917 " " NAG M 1 " - " ASN A 63 " Time building additional restraints: 5.26 Conformation dependent library (CDL) restraints added in 2.8 seconds 7436 Ramachandran restraints generated. 3718 Oldfield, 0 Emsley, 3718 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7050 Finding SS restraints... Secondary structure from input PDB file: 93 helices and 51 sheets defined 27.2% alpha, 26.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.05 Creating SS restraints... Processing helix chain 'C' and resid 2 through 13 Processing helix chain 'C' and resid 22 through 38 removed outlier: 3.580A pdb=" N ARG C 38 " --> pdb=" O GLN C 34 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 46 Processing helix chain 'C' and resid 55 through 79 removed outlier: 3.908A pdb=" N VAL C 59 " --> pdb=" O SER C 55 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER C 78 " --> pdb=" O TYR C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 111 removed outlier: 4.230A pdb=" N ASP C 97 " --> pdb=" O GLU C 93 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N ASP C 98 " --> pdb=" O ASP C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 114 No H-bonds generated for 'chain 'C' and resid 112 through 114' Processing helix chain 'D' and resid 2 through 13 Processing helix chain 'D' and resid 22 through 38 removed outlier: 3.512A pdb=" N ARG D 38 " --> pdb=" O GLN D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 47 removed outlier: 3.784A pdb=" N GLY D 47 " --> pdb=" O ARG D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 79 Processing helix chain 'D' and resid 88 through 111 removed outlier: 3.962A pdb=" N ASP D 97 " --> pdb=" O GLU D 93 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N ASP D 98 " --> pdb=" O ASP D 94 " (cutoff:3.500A) Processing helix chain 'J' and resid 256 through 277 removed outlier: 4.313A pdb=" N ASN J 260 " --> pdb=" O ILE J 256 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLY J 263 " --> pdb=" O SER J 259 " (cutoff:3.500A) Processing helix chain 'J' and resid 301 through 305 removed outlier: 4.096A pdb=" N SER J 305 " --> pdb=" O ALA J 302 " (cutoff:3.500A) Processing helix chain 'J' and resid 306 through 315 removed outlier: 3.579A pdb=" N VAL J 310 " --> pdb=" O ASN J 306 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ASN J 315 " --> pdb=" O THR J 311 " (cutoff:3.500A) Processing helix chain 'J' and resid 318 through 322 removed outlier: 4.052A pdb=" N HIS J 322 " --> pdb=" O TYR J 319 " (cutoff:3.500A) Processing helix chain 'J' and resid 329 through 342 Processing helix chain 'J' and resid 373 through 384 Processing helix chain 'J' and resid 410 through 418 removed outlier: 3.767A pdb=" N ILE J 414 " --> pdb=" O ASN J 410 " (cutoff:3.500A) Processing helix chain 'J' and resid 431 through 433 No H-bonds generated for 'chain 'J' and resid 431 through 433' Processing helix chain 'J' and resid 436 through 444 removed outlier: 3.837A pdb=" N GLN J 442 " --> pdb=" O ASP J 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 59 Processing helix chain 'A' and resid 71 through 77 removed outlier: 4.065A pdb=" N GLU A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 266 removed outlier: 3.740A pdb=" N LEU A 266 " --> pdb=" O PRO A 263 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 263 through 266' Processing helix chain 'A' and resid 281 through 289 removed outlier: 3.720A pdb=" N VAL A 289 " --> pdb=" O LEU A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 298 Processing helix chain 'A' and resid 458 through 462 removed outlier: 3.606A pdb=" N GLU A 462 " --> pdb=" O ARG A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 504 removed outlier: 3.682A pdb=" N PHE A 503 " --> pdb=" O THR A 500 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ILE A 504 " --> pdb=" O THR A 501 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 500 through 504' Processing helix chain 'A' and resid 578 through 584 Processing helix chain 'A' and resid 590 through 601 Processing helix chain 'A' and resid 612 through 621 Processing helix chain 'B' and resid 978 through 982 removed outlier: 3.524A pdb=" N ILE B 982 " --> pdb=" O LYS B 979 " (cutoff:3.500A) Processing helix chain 'B' and resid 988 through 1010 Proline residue: B 998 - end of helix Processing helix chain 'B' and resid 1011 through 1016 Processing helix chain 'B' and resid 1018 through 1035 removed outlier: 4.056A pdb=" N GLY B1022 " --> pdb=" O GLU B1018 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU B1035 " --> pdb=" O TYR B1031 " (cutoff:3.500A) Processing helix chain 'B' and resid 1036 through 1038 No H-bonds generated for 'chain 'B' and resid 1036 through 1038' Processing helix chain 'B' and resid 1053 through 1068 Processing helix chain 'B' and resid 1074 through 1089 removed outlier: 3.628A pdb=" N GLU B1088 " --> pdb=" O TRP B1084 " (cutoff:3.500A) Processing helix chain 'B' and resid 1109 through 1113 removed outlier: 3.791A pdb=" N ASN B1113 " --> pdb=" O GLY B1110 " (cutoff:3.500A) Processing helix chain 'B' and resid 1116 through 1131 Processing helix chain 'B' and resid 1142 through 1157 removed outlier: 3.522A pdb=" N ASN B1157 " --> pdb=" O PHE B1153 " (cutoff:3.500A) Processing helix chain 'B' and resid 1163 through 1178 removed outlier: 3.931A pdb=" N MET B1177 " --> pdb=" O ALA B1173 " (cutoff:3.500A) Processing helix chain 'B' and resid 1182 through 1192 removed outlier: 3.858A pdb=" N ALA B1192 " --> pdb=" O PHE B1188 " (cutoff:3.500A) Processing helix chain 'B' and resid 1203 through 1222 removed outlier: 4.036A pdb=" N ASN B1207 " --> pdb=" O LYS B1203 " (cutoff:3.500A) Processing helix chain 'B' and resid 1226 through 1238 removed outlier: 3.676A pdb=" N VAL B1230 " --> pdb=" O PHE B1226 " (cutoff:3.500A) Processing helix chain 'B' and resid 1246 through 1261 Processing helix chain 'B' and resid 1392 through 1401 Processing helix chain 'B' and resid 1409 through 1414 removed outlier: 4.565A pdb=" N LYS B1414 " --> pdb=" O TYR B1410 " (cutoff:3.500A) Processing helix chain 'B' and resid 1507 through 1514 Processing helix chain 'B' and resid 1567 through 1570 removed outlier: 4.281A pdb=" N GLU B1570 " --> pdb=" O LYS B1567 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1567 through 1570' Processing helix chain 'B' and resid 1613 through 1616 Processing helix chain 'B' and resid 1617 through 1637 removed outlier: 4.010A pdb=" N LYS B1622 " --> pdb=" O GLU B1618 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N GLN B1623 " --> pdb=" O GLU B1619 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 59 Processing helix chain 'G' and resid 71 through 77 removed outlier: 4.202A pdb=" N GLU G 77 " --> pdb=" O GLU G 73 " (cutoff:3.500A) Processing helix chain 'G' and resid 263 through 266 removed outlier: 3.598A pdb=" N LEU G 266 " --> pdb=" O PRO G 263 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 263 through 266' Processing helix chain 'G' and resid 281 through 289 removed outlier: 3.869A pdb=" N VAL G 289 " --> pdb=" O LEU G 285 " (cutoff:3.500A) Processing helix chain 'G' and resid 294 through 298 Processing helix chain 'G' and resid 458 through 463 removed outlier: 4.592A pdb=" N ALA G 463 " --> pdb=" O ARG G 459 " (cutoff:3.500A) Processing helix chain 'G' and resid 500 through 504 removed outlier: 3.769A pdb=" N PHE G 503 " --> pdb=" O THR G 500 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ILE G 504 " --> pdb=" O THR G 501 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 500 through 504' Processing helix chain 'G' and resid 578 through 584 Processing helix chain 'G' and resid 590 through 601 Processing helix chain 'G' and resid 612 through 621 Processing helix chain 'H' and resid 988 through 1010 Proline residue: H 998 - end of helix removed outlier: 3.665A pdb=" N ILE H1001 " --> pdb=" O THR H 997 " (cutoff:3.500A) Processing helix chain 'H' and resid 1011 through 1015 Processing helix chain 'H' and resid 1016 through 1017 No H-bonds generated for 'chain 'H' and resid 1016 through 1017' Processing helix chain 'H' and resid 1018 through 1037 removed outlier: 4.127A pdb=" N GLY H1022 " --> pdb=" O GLU H1018 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLN H1033 " --> pdb=" O LYS H1029 " (cutoff:3.500A) Processing helix chain 'H' and resid 1053 through 1068 removed outlier: 3.783A pdb=" N LEU H1066 " --> pdb=" O LYS H1062 " (cutoff:3.500A) Processing helix chain 'H' and resid 1074 through 1088 Processing helix chain 'H' and resid 1108 through 1113 removed outlier: 3.703A pdb=" N ASN H1113 " --> pdb=" O GLY H1110 " (cutoff:3.500A) Processing helix chain 'H' and resid 1116 through 1132 Processing helix chain 'H' and resid 1133 through 1137 removed outlier: 3.697A pdb=" N GLU H1137 " --> pdb=" O ASP H1134 " (cutoff:3.500A) Processing helix chain 'H' and resid 1142 through 1157 Processing helix chain 'H' and resid 1163 through 1178 removed outlier: 3.677A pdb=" N MET H1177 " --> pdb=" O ALA H1173 " (cutoff:3.500A) Processing helix chain 'H' and resid 1182 through 1192 removed outlier: 4.212A pdb=" N ASN H1186 " --> pdb=" O GLY H1182 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA H1192 " --> pdb=" O PHE H1188 " (cutoff:3.500A) Processing helix chain 'H' and resid 1193 through 1196 Processing helix chain 'H' and resid 1203 through 1222 removed outlier: 3.938A pdb=" N ASN H1207 " --> pdb=" O LYS H1203 " (cutoff:3.500A) Processing helix chain 'H' and resid 1226 through 1238 removed outlier: 3.739A pdb=" N VAL H1230 " --> pdb=" O PHE H1226 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG H1238 " --> pdb=" O LEU H1234 " (cutoff:3.500A) Processing helix chain 'H' and resid 1246 through 1263 Processing helix chain 'H' and resid 1392 through 1402 removed outlier: 3.745A pdb=" N ASN H1401 " --> pdb=" O LYS H1397 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY H1402 " --> pdb=" O GLN H1398 " (cutoff:3.500A) Processing helix chain 'H' and resid 1408 through 1413 Processing helix chain 'H' and resid 1507 through 1515 Processing helix chain 'H' and resid 1567 through 1572 removed outlier: 3.925A pdb=" N ALA H1571 " --> pdb=" O LYS H1567 " (cutoff:3.500A) Processing helix chain 'H' and resid 1613 through 1616 removed outlier: 3.741A pdb=" N GLN H1616 " --> pdb=" O ASP H1613 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 1613 through 1616' Processing helix chain 'H' and resid 1617 through 1638 removed outlier: 3.789A pdb=" N VAL H1636 " --> pdb=" O GLU H1632 " (cutoff:3.500A) Processing helix chain 'X' and resid 257 through 277 removed outlier: 3.582A pdb=" N THR X 262 " --> pdb=" O ALA X 258 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N GLY X 263 " --> pdb=" O SER X 259 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA X 264 " --> pdb=" O ASN X 260 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N LYS X 265 " --> pdb=" O PHE X 261 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LYS X 266 " --> pdb=" O THR X 262 " (cutoff:3.500A) Processing helix chain 'X' and resid 301 through 305 removed outlier: 3.878A pdb=" N SER X 305 " --> pdb=" O ALA X 302 " (cutoff:3.500A) Processing helix chain 'X' and resid 306 through 317 removed outlier: 3.752A pdb=" N ASN X 315 " --> pdb=" O THR X 311 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE X 317 " --> pdb=" O GLN X 313 " (cutoff:3.500A) Processing helix chain 'X' and resid 318 through 322 removed outlier: 3.987A pdb=" N HIS X 322 " --> pdb=" O TYR X 319 " (cutoff:3.500A) Processing helix chain 'X' and resid 329 through 341 removed outlier: 3.718A pdb=" N VAL X 337 " --> pdb=" O ALA X 333 " (cutoff:3.500A) Processing helix chain 'X' and resid 351 through 355 Processing helix chain 'X' and resid 373 through 384 removed outlier: 3.712A pdb=" N LEU X 384 " --> pdb=" O ILE X 380 " (cutoff:3.500A) Processing helix chain 'X' and resid 410 through 418 removed outlier: 3.504A pdb=" N ILE X 414 " --> pdb=" O ASN X 410 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ASN X 415 " --> pdb=" O GLN X 411 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALA X 416 " --> pdb=" O VAL X 412 " (cutoff:3.500A) Processing helix chain 'X' and resid 431 through 434 removed outlier: 3.710A pdb=" N GLU X 434 " --> pdb=" O LYS X 431 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 431 through 434' Processing helix chain 'X' and resid 436 through 444 removed outlier: 3.521A pdb=" N PHE X 440 " --> pdb=" O LEU X 436 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N GLN X 442 " --> pdb=" O ASP X 438 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'J' and resid 294 through 297 removed outlier: 6.169A pdb=" N LEU J 286 " --> pdb=" O TRP J 296 " (cutoff:3.500A) removed outlier: 8.481A pdb=" N VAL J 287 " --> pdb=" O ILE J 246 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N LEU J 248 " --> pdb=" O VAL J 287 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N TYR J 289 " --> pdb=" O LEU J 248 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N LEU J 250 " --> pdb=" O TYR J 289 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N ASN J 245 " --> pdb=" O VAL J 358 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N ILE J 360 " --> pdb=" O ASN J 245 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N TYR J 247 " --> pdb=" O ILE J 360 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N MET J 362 " --> pdb=" O TYR J 247 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N VAL J 249 " --> pdb=" O MET J 362 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N HIS J 357 " --> pdb=" O ASP J 399 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N TYR J 401 " --> pdb=" O HIS J 357 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N ILE J 359 " --> pdb=" O TYR J 401 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N PHE J 403 " --> pdb=" O ILE J 359 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N LEU J 361 " --> pdb=" O PHE J 403 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 61 through 66 removed outlier: 3.939A pdb=" N PHE A 66 " --> pdb=" O GLU A 18 " (cutoff:3.500A) removed outlier: 8.456A pdb=" N THR A 19 " --> pdb=" O PRO A 9 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 11 through 12 removed outlier: 4.689A pdb=" N LYS A 82 " --> pdb=" O VAL A 101 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N PHE A 83 " --> pdb=" O PHE A 40 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N THR A 34 " --> pdb=" O THR A 89 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 107 through 112 Processing sheet with id=AA5, first strand: chain 'A' and resid 116 through 117 removed outlier: 3.616A pdb=" N GLY A 180 " --> pdb=" O VAL A 202 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N VAL A 141 " --> pdb=" O SER A 157 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N SER A 157 " --> pdb=" O VAL A 141 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N VAL A 143 " --> pdb=" O GLN A 155 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N GLN A 155 " --> pdb=" O VAL A 143 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N ILE A 145 " --> pdb=" O VAL A 153 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 210 through 216 removed outlier: 3.506A pdb=" N ILE A 213 " --> pdb=" O THR A 234 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR A 232 " --> pdb=" O GLU A 215 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU A 229 " --> pdb=" O LEU A 280 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL A 231 " --> pdb=" O VAL A 278 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 245 through 248 Processing sheet with id=AA8, first strand: chain 'A' and resid 245 through 248 removed outlier: 6.011A pdb=" N LEU A 302 " --> pdb=" O GLY A 323 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 341 through 342 removed outlier: 3.735A pdb=" N LEU A 398 " --> pdb=" O ALA A 421 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 348 through 349 Processing sheet with id=AB2, first strand: chain 'A' and resid 352 through 353 removed outlier: 3.630A pdb=" N VAL A 352 " --> pdb=" O ALA A 385 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 433 through 437 removed outlier: 3.508A pdb=" N TYR A 433 " --> pdb=" O ARG A 456 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG A 456 " --> pdb=" O TYR A 433 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL A 451 " --> pdb=" O LEU A 495 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL A 493 " --> pdb=" O PHE A 453 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 477 through 485 removed outlier: 6.985A pdb=" N ILE A 472 " --> pdb=" O LEU A 479 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N ALA A 481 " --> pdb=" O TYR A 470 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N TYR A 470 " --> pdb=" O ALA A 481 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ARG A 483 " --> pdb=" O TYR A 468 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N TYR A 468 " --> pdb=" O ARG A 483 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N TYR A 467 " --> pdb=" O THR A 514 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N THR A 514 " --> pdb=" O TYR A 467 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N VAL A 525 " --> pdb=" O TYR A 513 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU A 515 " --> pdb=" O GLU A 523 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU A 523 " --> pdb=" O LEU A 515 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLY A 517 " --> pdb=" O GLN A 521 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 542 through 545 Processing sheet with id=AB6, first strand: chain 'A' and resid 542 through 545 removed outlier: 3.530A pdb=" N MET A 559 " --> pdb=" O ILE B 771 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE B 771 " --> pdb=" O MET A 559 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU A 561 " --> pdb=" O MET B 769 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N MET B 769 " --> pdb=" O LEU A 561 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 748 through 749 Processing sheet with id=AB8, first strand: chain 'B' and resid 748 through 749 Processing sheet with id=AB9, first strand: chain 'B' and resid 807 through 812 removed outlier: 4.008A pdb=" N PHE B 808 " --> pdb=" O TYR B 830 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL B 828 " --> pdb=" O ASP B 810 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ARG B 826 " --> pdb=" O ARG B 812 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 816 through 818 removed outlier: 3.530A pdb=" N GLN B 886 " --> pdb=" O LEU B 907 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N VAL B 909 " --> pdb=" O GLY B 884 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLY B 884 " --> pdb=" O VAL B 909 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N HIS B 860 " --> pdb=" O LEU B 844 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 914 through 916 removed outlier: 3.848A pdb=" N ILE B 914 " --> pdb=" O ALA B1328 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ALA B1328 " --> pdb=" O ILE B 914 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N MET B 916 " --> pdb=" O TYR B1326 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N TYR B1326 " --> pdb=" O MET B 916 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ALA B 921 " --> pdb=" O VAL B1322 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N THR B1324 " --> pdb=" O THR B 919 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N THR B 919 " --> pdb=" O THR B1324 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 914 through 916 removed outlier: 3.848A pdb=" N ILE B 914 " --> pdb=" O ALA B1328 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ALA B1328 " --> pdb=" O ILE B 914 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N MET B 916 " --> pdb=" O TYR B1326 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N TYR B1326 " --> pdb=" O MET B 916 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 935 through 940 removed outlier: 3.697A pdb=" N PHE B1308 " --> pdb=" O ILE B 940 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 1339 through 1347 removed outlier: 3.674A pdb=" N LYS B1346 " --> pdb=" O ILE B1363 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA B1390 " --> pdb=" O HIS B1442 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 1405 through 1406 removed outlier: 3.571A pdb=" N TYR B1458 " --> pdb=" O ILE B1380 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLY B1453 " --> pdb=" O TYR B1471 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 1589 through 1590 removed outlier: 7.068A pdb=" N PHE B1536 " --> pdb=" O LEU B1532 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N LEU B1532 " --> pdb=" O PHE B1536 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N GLU B1538 " --> pdb=" O VAL B1530 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N VAL B1530 " --> pdb=" O GLU B1538 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N ILE B1540 " --> pdb=" O VAL B1528 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N LYS B1524 " --> pdb=" O GLU B1544 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N THR B1546 " --> pdb=" O VAL B1522 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N VAL B1522 " --> pdb=" O THR B1546 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N TYR B1521 " --> pdb=" O GLY B1584 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N MET B1582 " --> pdb=" O TYR B1523 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N HIS B1579 " --> pdb=" O TRP B1609 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N TRP B1583 " --> pdb=" O TRP B1605 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N TRP B1605 " --> pdb=" O TRP B1583 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 61 through 64 Processing sheet with id=AC9, first strand: chain 'G' and resid 11 through 12 removed outlier: 3.585A pdb=" N VAL G 31 " --> pdb=" O LEU G 54 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 107 through 112 Processing sheet with id=AD2, first strand: chain 'G' and resid 116 through 117 removed outlier: 3.701A pdb=" N VAL G 202 " --> pdb=" O GLY G 180 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY G 180 " --> pdb=" O VAL G 202 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N VAL G 141 " --> pdb=" O SER G 157 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N SER G 157 " --> pdb=" O VAL G 141 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N VAL G 143 " --> pdb=" O GLN G 155 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N GLN G 155 " --> pdb=" O VAL G 143 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N ILE G 145 " --> pdb=" O VAL G 153 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 210 through 216 removed outlier: 3.684A pdb=" N THR G 232 " --> pdb=" O GLU G 215 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 258 through 261 removed outlier: 3.557A pdb=" N GLY G 245 " --> pdb=" O ILE G 271 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 258 through 261 removed outlier: 5.940A pdb=" N LEU G 302 " --> pdb=" O GLY G 323 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 332 through 334 removed outlier: 3.746A pdb=" N VAL G 352 " --> pdb=" O ALA G 385 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 341 through 342 Processing sheet with id=AD8, first strand: chain 'G' and resid 366 through 368 Processing sheet with id=AD9, first strand: chain 'G' and resid 433 through 438 removed outlier: 3.707A pdb=" N ARG G 456 " --> pdb=" O TYR G 433 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N VAL G 451 " --> pdb=" O LEU G 495 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL G 493 " --> pdb=" O PHE G 453 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 478 through 485 removed outlier: 6.731A pdb=" N ILE G 472 " --> pdb=" O LEU G 479 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N ALA G 481 " --> pdb=" O TYR G 470 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N TYR G 470 " --> pdb=" O ALA G 481 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ARG G 483 " --> pdb=" O TYR G 468 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N TYR G 468 " --> pdb=" O ARG G 483 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N TYR G 467 " --> pdb=" O THR G 514 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N THR G 514 " --> pdb=" O TYR G 467 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VAL G 525 " --> pdb=" O TYR G 513 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 506 through 507 Processing sheet with id=AE3, first strand: chain 'G' and resid 542 through 545 removed outlier: 3.501A pdb=" N LEU G 561 " --> pdb=" O MET H 769 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N MET H 769 " --> pdb=" O LEU G 561 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 748 through 749 Processing sheet with id=AE5, first strand: chain 'H' and resid 753 through 755 Processing sheet with id=AE6, first strand: chain 'H' and resid 809 through 811 removed outlier: 3.934A pdb=" N VAL H 828 " --> pdb=" O ASP H 810 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE H 878 " --> pdb=" O VAL H 823 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'H' and resid 816 through 818 removed outlier: 3.666A pdb=" N VAL H 910 " --> pdb=" O VAL H 817 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL H 909 " --> pdb=" O GLY H 884 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLY H 884 " --> pdb=" O VAL H 909 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N HIS H 860 " --> pdb=" O LEU H 844 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'H' and resid 914 through 925 removed outlier: 3.718A pdb=" N LYS H 918 " --> pdb=" O THR H1324 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR H1324 " --> pdb=" O LYS H 918 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL H 920 " --> pdb=" O VAL H1322 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N VAL H1322 " --> pdb=" O VAL H 920 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N VAL H 922 " --> pdb=" O LEU H1320 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N LEU H1320 " --> pdb=" O VAL H 922 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N THR H 924 " --> pdb=" O GLY H1318 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N GLY H1318 " --> pdb=" O THR H 924 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'H' and resid 935 through 940 removed outlier: 3.685A pdb=" N GLN H 936 " --> pdb=" O ALA H1312 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE H1308 " --> pdb=" O ILE H 940 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'H' and resid 1038 through 1039 removed outlier: 3.688A pdb=" N ALA H1043 " --> pdb=" O GLN H1039 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'H' and resid 1339 through 1347 Processing sheet with id=AF3, first strand: chain 'H' and resid 1405 through 1406 removed outlier: 3.551A pdb=" N TYR H1458 " --> pdb=" O ILE H1380 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY H1453 " --> pdb=" O TYR H1471 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'H' and resid 1482 through 1484 Processing sheet with id=AF5, first strand: chain 'H' and resid 1589 through 1590 removed outlier: 3.702A pdb=" N TYR H1539 " --> pdb=" O PHE H1562 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER H1564 " --> pdb=" O ASP H1537 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N LYS H1529 " --> pdb=" O ILE H1540 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N ALA H1542 " --> pdb=" O LEU H1527 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N LEU H1527 " --> pdb=" O ALA H1542 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N GLU H1544 " --> pdb=" O THR H1525 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N THR H1525 " --> pdb=" O GLU H1544 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N THR H1546 " --> pdb=" O TYR H1523 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N TYR H1523 " --> pdb=" O THR H1546 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'X' and resid 294 through 297 removed outlier: 6.235A pdb=" N LEU X 286 " --> pdb=" O TRP X 296 " (cutoff:3.500A) removed outlier: 8.496A pdb=" N VAL X 287 " --> pdb=" O ILE X 246 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LEU X 248 " --> pdb=" O VAL X 287 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N TYR X 289 " --> pdb=" O LEU X 248 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N LEU X 250 " --> pdb=" O TYR X 289 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N ASN X 245 " --> pdb=" O VAL X 358 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N ILE X 360 " --> pdb=" O ASN X 245 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N TYR X 247 " --> pdb=" O ILE X 360 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N MET X 362 " --> pdb=" O TYR X 247 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N VAL X 249 " --> pdb=" O MET X 362 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N HIS X 357 " --> pdb=" O ASP X 399 " (cutoff:3.500A) removed outlier: 8.220A pdb=" N TYR X 401 " --> pdb=" O HIS X 357 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N ILE X 359 " --> pdb=" O TYR X 401 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N PHE X 403 " --> pdb=" O ILE X 359 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N LEU X 361 " --> pdb=" O PHE X 403 " (cutoff:3.500A) 1147 hydrogen bonds defined for protein. 3192 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.62 Time building geometry restraints manager: 6.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9275 1.34 - 1.46: 5465 1.46 - 1.58: 13865 1.58 - 1.70: 2 1.70 - 1.82: 189 Bond restraints: 28796 Sorted by residual: bond pdb=" N ASN G 63 " pdb=" CA ASN G 63 " ideal model delta sigma weight residual 1.456 1.489 -0.032 1.21e-02 6.83e+03 7.08e+00 bond pdb=" N VAL G 64 " pdb=" CA VAL G 64 " ideal model delta sigma weight residual 1.453 1.494 -0.042 1.63e-02 3.76e+03 6.56e+00 bond pdb=" N PHE A 40 " pdb=" CA PHE A 40 " ideal model delta sigma weight residual 1.462 1.487 -0.025 1.05e-02 9.07e+03 5.69e+00 bond pdb=" N GLY G 62 " pdb=" CA GLY G 62 " ideal model delta sigma weight residual 1.449 1.477 -0.028 1.45e-02 4.76e+03 3.67e+00 bond pdb=" CB PRO J 393 " pdb=" CG PRO J 393 " ideal model delta sigma weight residual 1.492 1.585 -0.093 5.00e-02 4.00e+02 3.43e+00 ... (remaining 28791 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.48: 38269 1.48 - 2.95: 756 2.95 - 4.43: 147 4.43 - 5.90: 30 5.90 - 7.38: 4 Bond angle restraints: 39206 Sorted by residual: angle pdb=" C GLN B 967 " pdb=" CA GLN B 967 " pdb=" CB GLN B 967 " ideal model delta sigma weight residual 116.63 110.49 6.14 1.16e+00 7.43e-01 2.80e+01 angle pdb=" CA GLN B 967 " pdb=" C GLN B 967 " pdb=" N MET B 968 " ideal model delta sigma weight residual 119.63 116.73 2.90 8.10e-01 1.52e+00 1.28e+01 angle pdb=" CA VAL G 64 " pdb=" C VAL G 64 " pdb=" O VAL G 64 " ideal model delta sigma weight residual 121.93 118.14 3.79 1.12e+00 7.97e-01 1.15e+01 angle pdb=" CA PRO X 407 " pdb=" N PRO X 407 " pdb=" CD PRO X 407 " ideal model delta sigma weight residual 112.00 107.86 4.14 1.40e+00 5.10e-01 8.76e+00 angle pdb=" CA PRO J 393 " pdb=" N PRO J 393 " pdb=" CD PRO J 393 " ideal model delta sigma weight residual 112.00 107.90 4.10 1.40e+00 5.10e-01 8.56e+00 ... (remaining 39201 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.98: 16307 21.98 - 43.96: 981 43.96 - 65.94: 118 65.94 - 87.92: 58 87.92 - 109.90: 12 Dihedral angle restraints: 17476 sinusoidal: 6562 harmonic: 10914 Sorted by residual: dihedral pdb=" CB CYS G 605 " pdb=" SG CYS G 605 " pdb=" SG CYS G 640 " pdb=" CB CYS G 640 " ideal model delta sinusoidal sigma weight residual 93.00 179.44 -86.44 1 1.00e+01 1.00e-02 9.00e+01 dihedral pdb=" CB CYS D 58 " pdb=" SG CYS D 58 " pdb=" SG CYS D 113 " pdb=" CB CYS D 113 " ideal model delta sinusoidal sigma weight residual -86.00 -163.42 77.42 1 1.00e+01 1.00e-02 7.51e+01 dihedral pdb=" CB CYS C 81 " pdb=" SG CYS C 81 " pdb=" SG CYS C 91 " pdb=" CB CYS C 91 " ideal model delta sinusoidal sigma weight residual 93.00 162.27 -69.27 1 1.00e+01 1.00e-02 6.20e+01 ... (remaining 17473 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 3807 0.055 - 0.109: 717 0.109 - 0.164: 92 0.164 - 0.219: 1 0.219 - 0.274: 2 Chirality restraints: 4619 Sorted by residual: chirality pdb=" C1 NAG M 1 " pdb=" ND2 ASN A 63 " pdb=" C2 NAG M 1 " pdb=" O5 NAG M 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" C1 NAG G 701 " pdb=" ND2 ASN G 63 " pdb=" C2 NAG G 701 " pdb=" O5 NAG G 701 " both_signs ideal model delta sigma weight residual False -2.40 -2.17 -0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" CA PRO X 407 " pdb=" N PRO X 407 " pdb=" C PRO X 407 " pdb=" CB PRO X 407 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.18 2.00e-01 2.50e+01 7.80e-01 ... (remaining 4616 not shown) Planarity restraints: 5039 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN J 392 " -0.059 5.00e-02 4.00e+02 8.76e-02 1.23e+01 pdb=" N PRO J 393 " 0.151 5.00e-02 4.00e+02 pdb=" CA PRO J 393 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO J 393 " -0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY J 406 " 0.056 5.00e-02 4.00e+02 8.38e-02 1.12e+01 pdb=" N PRO J 407 " -0.145 5.00e-02 4.00e+02 pdb=" CA PRO J 407 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO J 407 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY X 406 " -0.055 5.00e-02 4.00e+02 8.18e-02 1.07e+01 pdb=" N PRO X 407 " 0.141 5.00e-02 4.00e+02 pdb=" CA PRO X 407 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO X 407 " -0.045 5.00e-02 4.00e+02 ... (remaining 5036 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 1220 2.72 - 3.27: 28391 3.27 - 3.81: 44876 3.81 - 4.36: 50986 4.36 - 4.90: 88536 Nonbonded interactions: 214009 Sorted by model distance: nonbonded pdb=" OD1 ASP A 527 " pdb=" N SER A 528 " model vdw 2.178 3.120 nonbonded pdb=" OH TYR J 289 " pdb=" OG1 THR J 363 " model vdw 2.202 3.040 nonbonded pdb=" O VAL B 949 " pdb=" OG1 THR B 952 " model vdw 2.215 3.040 nonbonded pdb=" OD1 ASP H1007 " pdb=" NE1 TRP H1012 " model vdw 2.222 3.120 nonbonded pdb=" OG1 THR B1344 " pdb=" O GLU B1365 " model vdw 2.228 3.040 ... (remaining 214004 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 1 through 71 or (resid 72 and (name N or name CA or name C \ or name O or name CB )) or resid 73 through 74 or (resid 75 and (name N or name \ CA or name C or name O or name CB )) or resid 76 or (resid 77 through 78 and (n \ ame N or name CA or name C or name O or name CB )) or resid 79 or (resid 80 and \ (name N or name CA or name C or name O or name CB )) or resid 81 through 100 or \ (resid 101 and (name N or name CA or name C or name O or name CB )) or resid 102 \ through 145 or (resid 146 and (name N or name CA or name C or name O or name CB \ )) or resid 147 through 381 or (resid 382 and (name N or name CA or name C or n \ ame O or name CB )) or resid 383 through 441 or (resid 442 and (name N or name C \ A or name C or name O or name CB )) or resid 443 through 548 or (resid 549 and ( \ name N or name CA or name C or name O or name CB )) or resid 550 through 598 or \ (resid 599 and (name N or name CA or name C or name O or name CB )) or resid 600 \ through 640)) selection = (chain 'G' and (resid 1 through 372 or (resid 373 and (name N or name CA or name \ C or name O or name CB )) or resid 374 through 395 or (resid 396 and (name N or \ name CA or name C or name O or name CB )) or resid 397 through 410 or (resid 41 \ 1 through 412 and (name N or name CA or name C or name O or name CB )) or resid \ 413 through 640)) } ncs_group { reference = (chain 'B' and (resid 731 through 915 or (resid 916 and (name N or name CA or na \ me C or name O or name CB )) or resid 917 through 927 or (resid 928 through 930 \ and (name N or name CA or name C or name O or name CB )) or resid 931 through 96 \ 9 or (resid 970 through 972 and (name N or name CA or name C or name O or name C \ B )) or resid 973 through 978 or (resid 979 through 980 and (name N or name CA o \ r name C or name O or name CB )) or resid 981 through 983 or (resid 984 and (nam \ e N or name CA or name C or name O or name CB )) or resid 985 or (resid 986 and \ (name N or name CA or name C or name O or name CB )) or resid 987 or (resid 988 \ and (name N or name CA or name C or name O or name CB )) or resid 989 or (resid \ 990 through 991 and (name N or name CA or name C or name O or name CB )) or resi \ d 992 through 993 or (resid 994 and (name N or name CA or name C or name O or na \ me CB )) or resid 995 through 998 or (resid 999 through 1000 and (name N or name \ CA or name C or name O or name CB )) or resid 1001 through 1002 or (resid 1003 \ and (name N or name CA or name C or name O or name CB )) or resid 1004 through 1 \ 017 or (resid 1018 and (name N or name CA or name C or name O or name CB )) or r \ esid 1019 through 1023 or (resid 1024 through 1025 and (name N or name CA or nam \ e C or name O or name CB )) or resid 1026 through 1027 or (resid 1028 through 10 \ 29 and (name N or name CA or name C or name O or name CB )) or resid 1030 or (re \ sid 1031 through 1032 and (name N or name CA or name C or name O or name CB )) o \ r resid 1033 through 1036 or (resid 1037 and (name N or name CA or name C or nam \ e O or name CB )) or resid 1038 or (resid 1039 and (name N or name CA or name C \ or name O or name CB )) or resid 1040 or (resid 1041 and (name N or name CA or n \ ame C or name O or name CB )) or resid 1042 through 1058 or (resid 1059 and (nam \ e N or name CA or name C or name O or name CB )) or resid 1060 through 1063 or ( \ resid 1064 and (name N or name CA or name C or name O or name CB )) or resid 106 \ 5 or (resid 1066 through 1067 and (name N or name CA or name C or name O or name \ CB )) or resid 1068 or (resid 1069 and (name N or name CA or name C or name O o \ r name CB )) or resid 1070 through 1073 or (resid 1074 through 1076 and (name N \ or name CA or name C or name O or name CB )) or resid 1077 or (resid 1078 and (n \ ame N or name CA or name C or name O or name CB )) or resid 1079 through 1082 or \ (resid 1083 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 084 through 1086 or (resid 1087 through 1088 and (name N or name CA or name C or \ name O or name CB )) or resid 1089 through 1098 or (resid 1099 through 1100 and \ (name N or name CA or name C or name O or name CB )) or resid 1101 through 1106 \ or (resid 1107 and (name N or name CA or name C or name O or name CB )) or resi \ d 1108 through 1110 or (resid 1111 through 1112 and (name N or name CA or name C \ or name O or name CB )) or resid 1113 through 1115 or (resid 1116 through 1118 \ and (name N or name CA or name C or name O or name CB )) or resid 1119 through 1 \ 120 or (resid 1121 and (name N or name CA or name C or name O or name CB )) or r \ esid 1122 through 1123 or (resid 1124 and (name N or name CA or name C or name O \ or name CB )) or resid 1125 or (resid 1126 and (name N or name CA or name C or \ name O or name CB )) or resid 1127 through 1128 or (resid 1129 and (name N or na \ me CA or name C or name O or name CB )) or resid 1130 or (resid 1131 through 113 \ 4 and (name N or name CA or name C or name O or name CB )) or resid 1135 through \ 1142 or (resid 1143 and (name N or name CA or name C or name O or name CB )) or \ resid 1144 through 1152 or (resid 1153 and (name N or name CA or name C or name \ O or name CB )) or resid 1154 through 1156 or (resid 1157 through 1160 and (nam \ e N or name CA or name C or name O or name CB )) or resid 1161 through 1171 or ( \ resid 1172 through 1173 and (name N or name CA or name C or name O or name CB )) \ or resid 1174 through 1176 or (resid 1177 and (name N or name CA or name C or n \ ame O or name CB )) or resid 1178 or (resid 1179 and (name N or name CA or name \ C or name O or name CB )) or resid 1180 through 1192 or (resid 1193 through 1195 \ and (name N or name CA or name C or name O or name CB )) or resid 1196 through \ 1204 or (resid 1205 through 1207 and (name N or name CA or name C or name O or n \ ame CB )) or resid 1208 or (resid 1209 through 1210 and (name N or name CA or na \ me C or name O or name CB )) or resid 1211 or (resid 1212 through 1214 and (name \ N or name CA or name C or name O or name CB )) or resid 1215 or (resid 1216 thr \ ough 1217 and (name N or name CA or name C or name O or name CB )) or resid 1218 \ through 1232 or (resid 1233 and (name N or name CA or name C or name O or name \ CB )) or resid 1234 through 1250 or (resid 1251 through 1252 and (name N or name \ CA or name C or name O or name CB )) or resid 1253 or (resid 1254 and (name N o \ r name CA or name C or name O or name CB )) or resid 1255 through 1261 or (resid \ 1262 and (name N or name CA or name C or name O or name CB )) or resid 1263 thr \ ough 1290 or (resid 1291 and (name N or name CA or name C or name O or name CB ) \ ) or resid 1292 through 1302 or (resid 1303 through 1304 and (name N or name CA \ or name C or name O or name CB )) or resid 1305 through 1349 or resid 1360 throu \ gh 1475 or (resid 1476 and (name N or name CA or name C or name O or name CB )) \ or resid 1477 through 1485 or (resid 1486 through 1487 and (name N or name CA or \ name C or name O or name CB )) or resid 1488 through 1516 or (resid 1517 and (n \ ame N or name CA or name C or name O or name CB )) or resid 1518 through 1530 or \ (resid 1531 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 532 through 1553 or (resid 1554 through 1555 and (name N or name CA or name C or \ name O or name CB )) or resid 1556 through 1592 or (resid 1593 and (name N or n \ ame CA or name C or name O or name CB )) or resid 1594 or (resid 1595 and (name \ N or name CA or name C or name O or name CB )) or resid 1596 through 1640 or (re \ sid 1641 and (name N or name CA or name C or name O or name CB )) or resid 1701) \ ) selection = (chain 'H' and (resid 731 through 856 or (resid 857 and (name N or name CA or na \ me C or name O or name CB )) or resid 858 through 917 or (resid 918 and (name N \ or name CA or name C or name O or name CB )) or resid 919 through 922 or (resid \ 923 and (name N or name CA or name C or name O or name CB )) or resid 924 throug \ h 936 or (resid 937 and (name N or name CA or name C or name O or name CB )) or \ resid 938 or (resid 939 and (name N or name CA or name C or name O or name CB )) \ or resid 940 through 950 or (resid 951 and (name N or name CA or name C or name \ O or name CB )) or resid 952 through 968 or (resid 969 through 972 and (name N \ or name CA or name C or name O or name CB )) or resid 973 through 1047 or (resid \ 1048 through 1051 and (name N or name CA or name C or name O or name CB )) or r \ esid 1052 through 1151 or (resid 1152 through 1153 and (name N or name CA or nam \ e C or name O or name CB )) or resid 1154 through 1180 or (resid 1181 and (name \ N or name CA or name C or name O or name CB )) or resid 1182 through 1185 or (re \ sid 1186 through 1187 and (name N or name CA or name C or name O or name CB )) o \ r resid 1188 through 1200 or (resid 1201 and (name N or name CA or name C or nam \ e O or name CB )) or resid 1202 through 1222 or (resid 1223 and (name N or name \ CA or name C or name O or name CB )) or resid 1224 or (resid 1225 and (name N or \ name CA or name C or name O or name CB )) or resid 1226 through 1231 or (resid \ 1232 through 1233 and (name N or name CA or name C or name O or name CB )) or re \ sid 1234 through 1268 or (resid 1269 and (name N or name CA or name C or name O \ or name CB )) or resid 1270 through 1276 or (resid 1277 and (name N or name CA o \ r name C or name O or name CB )) or resid 1278 through 1294 or (resid 1295 and ( \ name N or name CA or name C or name O or name CB )) or resid 1296 through 1310 o \ r (resid 1311 through 1313 and (name N or name CA or name C or name O or name CB \ )) or resid 1314 or (resid 1315 and (name N or name CA or name C or name O or n \ ame CB )) or resid 1316 or (resid 1317 and (name N or name CA or name C or name \ O or name CB )) or resid 1318 through 1330 or (resid 1331 through 1332 and (name \ N or name CA or name C or name O or name CB )) or resid 1333 or (resid 1334 and \ (name N or name CA or name C or name O or name CB )) or resid 1335 through 1349 \ or resid 1360 through 1496 or (resid 1497 and (name N or name CA or name C or n \ ame O or name CB )) or resid 1498 or (resid 1506 and (name N or name CA or name \ C or name O or name CB )) or resid 1507 or (resid 1508 through 1510 and (name N \ or name CA or name C or name O or name CB )) or resid 1511 or (resid 1512 throug \ h 1514 and (name N or name CA or name C or name O or name CB )) or resid 1515 th \ rough 1535 or (resid 1536 and (name N or name CA or name C or name O or name CB \ )) or resid 1537 through 1551 or (resid 1552 through 1555 and (name N or name CA \ or name C or name O or name CB )) or resid 1556 through 1568 or (resid 1569 thr \ ough 1571 and (name N or name CA or name C or name O or name CB )) or resid 1572 \ through 1576 or (resid 1577 and (name N or name CA or name C or name O or name \ CB )) or resid 1578 through 1619 or (resid 1620 through 1621 and (name N or name \ CA or name C or name O or name CB )) or resid 1622 through 1624 or (resid 1625 \ and (name N or name CA or name C or name O or name CB )) or resid 1626 through 1 \ 630 or (resid 1631 through 1632 and (name N or name CA or name C or name O or na \ me CB )) or resid 1633 through 1641 or resid 1701)) } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = (chain 'J' and (resid 235 through 242 or (resid 243 through 244 and (name N or n \ ame CA or name C or name O or name CB )) or resid 245 through 249 or (resid 250 \ and (name N or name CA or name C or name O or name CB )) or resid 251 through 25 \ 8 or (resid 259 and (name N or name CA or name C or name O or name CB )) or resi \ d 260 through 316 or (resid 317 and (name N or name CA or name C or name O or na \ me CB )) or resid 318 through 352 or (resid 353 through 354 and (name N or name \ CA or name C or name O or name CB )) or resid 355 through 391 or (resid 392 and \ (name N or name CA or name C or name O or name CB )) or resid 393 or (resid 394 \ through 397 and (name N or name CA or name C or name O or name CB )) or resid 39 \ 8 through 410 or (resid 411 through 412 and (name N or name CA or name C or name \ O or name CB )) or resid 413 through 423 or (resid 424 and (name N or name CA o \ r name C or name O or name CB )) or resid 425 through 430 or (resid 431 through \ 434 and (name N or name CA or name C or name O or name CB )) or resid 435 throug \ h 446 or (resid 447 through 448 and (name N or name CA or name C or name O or na \ me CB )) or resid 449 through 450 or (resid 451 through 452 and (name N or name \ CA or name C or name O or name CB )) or resid 453 through 462)) selection = (chain 'X' and ((resid 235 and (name N or name CA or name C or name O or name CB \ )) or resid 236 or (resid 237 through 238 and (name N or name CA or name C or n \ ame O or name CB )) or resid 239 through 240 or (resid 241 and (name N or name C \ A or name C or name O or name CB )) or (resid 242 through 244 and (name N or nam \ e CA or name C or name O or name CB )) or resid 245 through 253 or (resid 254 an \ d (name N or name CA or name C or name O or name CB )) or resid 255 through 260 \ or (resid 261 and (name N or name CA or name C or name O or name CB )) or resid \ 262 through 264 or (resid 265 through 266 and (name N or name CA or name C or na \ me O or name CB )) or resid 267 or (resid 268 and (name N or name CA or name C o \ r name O or name CB )) or resid 269 through 279 or (resid 280 through 281 and (n \ ame N or name CA or name C or name O or name CB )) or resid 282 through 300 or ( \ resid 301 through 302 and (name N or name CA or name C or name O or name CB )) o \ r resid 303 through 323 or (resid 324 through 326 and (name N or name CA or name \ C or name O or name CB )) or resid 327 through 330 or (resid 331 through 333 an \ d (name N or name CA or name C or name O or name CB )) or resid 334 through 336 \ or (resid 337 and (name N or name CA or name C or name O or name CB )) or resid \ 338 or (resid 339 through 343 and (name N or name CA or name C or name O or name \ CB )) or resid 352 through 355 or (resid 356 and (name N or name CA or name C o \ r name O or name CB )) or resid 357 through 365 or (resid 366 and (name N or nam \ e CA or name C or name O or name CB )) or resid 367 through 371 or (resid 372 an \ d (name N or name CA or name C or name O or name CB )) or resid 373 through 379 \ or (resid 380 and (name N or name CA or name C or name O or name CB )) or resid \ 381 through 388 or (resid 389 through 392 and (name N or name CA or name C or na \ me O or name CB )) or resid 393 through 435 or (resid 436 through 437 and (name \ N or name CA or name C or name O or name CB )) or resid 438 through 449 or (resi \ d 450 through 452 and (name N or name CA or name C or name O or name CB )) or re \ sid 453 through 462)) } 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: 1.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.250 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: 0.190 Process input model: 50.930 Find NCS groups from input model: 1.050 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.093 28796 Z= 0.228 Angle : 0.534 7.381 39206 Z= 0.280 Chirality : 0.043 0.274 4619 Planarity : 0.004 0.088 5035 Dihedral : 14.528 109.899 10354 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.68 % Favored : 96.23 % Rotamer: Outliers : 0.07 % Allowed : 0.24 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.55 % 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: 0.38 (0.14), residues: 3718 helix: 1.21 (0.19), residues: 858 sheet: 0.48 (0.17), residues: 1118 loop : -0.31 (0.15), residues: 1742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP H1055 HIS 0.011 0.001 HIS B1442 PHE 0.020 0.001 PHE B1416 TYR 0.016 0.001 TYR C 25 ARG 0.013 0.000 ARG J 460 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7436 Ramachandran restraints generated. 3718 Oldfield, 0 Emsley, 3718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7436 Ramachandran restraints generated. 3718 Oldfield, 0 Emsley, 3718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 3313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 337 time to evaluate : 2.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 239 ASP cc_start: 0.5929 (t70) cc_final: 0.5143 (t70) REVERT: J 364 ASP cc_start: 0.8263 (p0) cc_final: 0.7871 (p0) REVERT: B 996 MET cc_start: 0.7641 (ppp) cc_final: 0.6304 (mmt) REVERT: H 806 ASP cc_start: 0.8435 (t0) cc_final: 0.8203 (t0) REVERT: H 1239 TYR cc_start: 0.8138 (t80) cc_final: 0.7813 (t80) REVERT: H 1382 ASP cc_start: 0.8326 (t70) cc_final: 0.8105 (t0) REVERT: H 1582 MET cc_start: 0.7739 (ptm) cc_final: 0.7229 (pmm) REVERT: X 239 ASP cc_start: 0.6722 (t0) cc_final: 0.5315 (p0) REVERT: X 329 ASN cc_start: 0.8315 (t0) cc_final: 0.7981 (t0) REVERT: X 364 ASP cc_start: 0.8028 (p0) cc_final: 0.7567 (p0) outliers start: 2 outliers final: 0 residues processed: 339 average time/residue: 0.2877 time to fit residues: 161.3690 Evaluate side-chains 270 residues out of total 3313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 270 time to evaluate : 2.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 314 optimal weight: 20.0000 chunk 281 optimal weight: 20.0000 chunk 156 optimal weight: 40.0000 chunk 96 optimal weight: 10.0000 chunk 190 optimal weight: 8.9990 chunk 150 optimal weight: 50.0000 chunk 291 optimal weight: 20.0000 chunk 112 optimal weight: 6.9990 chunk 177 optimal weight: 0.9990 chunk 217 optimal weight: 5.9990 chunk 337 optimal weight: 7.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 435 ASN A 38 HIS A 144 ASN ** A 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 639 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 805 GLN ** B 835 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1004 HIS B1248 GLN B1259 GLN H 992 ASN H1033 GLN H1034 GLN ** H1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H1545 GLN X 245 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.101 28796 Z= 0.584 Angle : 0.766 16.823 39206 Z= 0.398 Chirality : 0.049 0.246 4619 Planarity : 0.005 0.053 5035 Dihedral : 6.460 89.876 4097 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.43 % Favored : 94.49 % Rotamer: Outliers : 1.61 % Allowed : 10.06 % Favored : 88.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.55 % 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: -0.15 (0.14), residues: 3718 helix: 0.75 (0.18), residues: 884 sheet: 0.12 (0.16), residues: 1100 loop : -0.61 (0.15), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP H1012 HIS 0.010 0.002 HIS B1442 PHE 0.029 0.003 PHE B1226 TYR 0.028 0.002 TYR G 424 ARG 0.006 0.001 ARG A 403 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7436 Ramachandran restraints generated. 3718 Oldfield, 0 Emsley, 3718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7436 Ramachandran restraints generated. 3718 Oldfield, 0 Emsley, 3718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 3313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 276 time to evaluate : 3.085 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 84 HIS cc_start: 0.7476 (m90) cc_final: 0.7038 (m90) REVERT: J 239 ASP cc_start: 0.6012 (t70) cc_final: 0.5451 (t70) REVERT: J 364 ASP cc_start: 0.8086 (p0) cc_final: 0.7713 (p0) REVERT: J 402 VAL cc_start: 0.9233 (m) cc_final: 0.9019 (p) REVERT: A 346 MET cc_start: 0.8182 (tpp) cc_final: 0.7807 (mmm) REVERT: A 515 LEU cc_start: 0.8979 (pt) cc_final: 0.8740 (pp) REVERT: A 551 ARG cc_start: 0.8031 (mmt-90) cc_final: 0.7755 (mmt-90) REVERT: B 800 GLU cc_start: 0.8600 (mm-30) cc_final: 0.8317 (mm-30) REVERT: B 996 MET cc_start: 0.7774 (ppp) cc_final: 0.6914 (tpp) REVERT: B 1033 GLN cc_start: 0.7255 (tm-30) cc_final: 0.7049 (pt0) REVERT: B 1239 TYR cc_start: 0.7265 (t80) cc_final: 0.6998 (t80) REVERT: G 61 MET cc_start: 0.8339 (tmm) cc_final: 0.7386 (tmm) REVERT: G 142 MET cc_start: 0.8175 (mmm) cc_final: 0.7973 (mmm) REVERT: H 806 ASP cc_start: 0.8591 (t0) cc_final: 0.8242 (t0) REVERT: H 1226 PHE cc_start: 0.6502 (t80) cc_final: 0.6274 (t80) REVERT: H 1239 TYR cc_start: 0.8091 (t80) cc_final: 0.7740 (t80) REVERT: H 1382 ASP cc_start: 0.8500 (t70) cc_final: 0.8191 (t70) REVERT: H 1545 GLN cc_start: 0.6745 (OUTLIER) cc_final: 0.6045 (pp30) REVERT: X 239 ASP cc_start: 0.6677 (t0) cc_final: 0.5210 (p0) REVERT: X 364 ASP cc_start: 0.8093 (p0) cc_final: 0.7650 (p0) outliers start: 47 outliers final: 33 residues processed: 310 average time/residue: 0.2888 time to fit residues: 148.7430 Evaluate side-chains 295 residues out of total 3313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 261 time to evaluate : 2.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 14 THR Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain J residue 363 THR Chi-restraints excluded: chain J residue 442 GLN Chi-restraints excluded: chain A residue 23 GLU Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 178 ASN Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 559 MET Chi-restraints excluded: chain B residue 753 VAL Chi-restraints excluded: chain B residue 775 ASP Chi-restraints excluded: chain B residue 878 ILE Chi-restraints excluded: chain B residue 1368 THR Chi-restraints excluded: chain B residue 1404 ASP Chi-restraints excluded: chain B residue 1563 ILE Chi-restraints excluded: chain G residue 58 THR Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 176 LEU Chi-restraints excluded: chain G residue 278 VAL Chi-restraints excluded: chain G residue 427 VAL Chi-restraints excluded: chain H residue 775 ASP Chi-restraints excluded: chain H residue 1017 LEU Chi-restraints excluded: chain H residue 1387 THR Chi-restraints excluded: chain H residue 1545 GLN Chi-restraints excluded: chain H residue 1596 LEU Chi-restraints excluded: chain H residue 1599 ILE Chi-restraints excluded: chain X residue 358 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 187 optimal weight: 9.9990 chunk 104 optimal weight: 0.2980 chunk 281 optimal weight: 50.0000 chunk 230 optimal weight: 5.9990 chunk 93 optimal weight: 0.9990 chunk 338 optimal weight: 8.9990 chunk 365 optimal weight: 0.0570 chunk 301 optimal weight: 40.0000 chunk 335 optimal weight: 0.9990 chunk 115 optimal weight: 0.9990 chunk 271 optimal weight: 1.9990 overall best weight: 0.6704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 313 GLN J 415 ASN A 552 GLN ** A 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 639 GLN ** B 835 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1011 GLN G 111 GLN G 490 GLN ** H1033 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 245 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.1571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 28796 Z= 0.164 Angle : 0.553 15.571 39206 Z= 0.284 Chirality : 0.044 0.189 4619 Planarity : 0.004 0.055 5035 Dihedral : 5.461 69.403 4097 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.85 % Favored : 97.07 % Rotamer: Outliers : 1.44 % Allowed : 13.00 % Favored : 85.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.55 % 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: 0.13 (0.14), residues: 3718 helix: 1.03 (0.18), residues: 882 sheet: 0.27 (0.16), residues: 1104 loop : -0.45 (0.15), residues: 1732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B1233 HIS 0.007 0.001 HIS B1442 PHE 0.017 0.001 PHE B1015 TYR 0.023 0.001 TYR G 512 ARG 0.004 0.000 ARG G 268 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7436 Ramachandran restraints generated. 3718 Oldfield, 0 Emsley, 3718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7436 Ramachandran restraints generated. 3718 Oldfield, 0 Emsley, 3718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 3313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 303 time to evaluate : 2.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 90 GLU cc_start: 0.6868 (tt0) cc_final: 0.6635 (tt0) REVERT: D 83 ASP cc_start: 0.8092 (p0) cc_final: 0.7710 (p0) REVERT: J 239 ASP cc_start: 0.6022 (t70) cc_final: 0.5220 (t70) REVERT: J 364 ASP cc_start: 0.8115 (p0) cc_final: 0.7604 (p0) REVERT: J 373 PRO cc_start: 0.8982 (Cg_endo) cc_final: 0.8727 (Cg_exo) REVERT: J 442 GLN cc_start: 0.7897 (OUTLIER) cc_final: 0.6699 (mp-120) REVERT: A 346 MET cc_start: 0.7998 (tpp) cc_final: 0.7634 (mmm) REVERT: A 451 VAL cc_start: 0.8879 (OUTLIER) cc_final: 0.8677 (m) REVERT: A 551 ARG cc_start: 0.7916 (mmt-90) cc_final: 0.7560 (mmt-90) REVERT: B 800 GLU cc_start: 0.8630 (mm-30) cc_final: 0.8352 (mm-30) REVERT: B 1033 GLN cc_start: 0.7227 (tm-30) cc_final: 0.6953 (pt0) REVERT: B 1226 PHE cc_start: 0.7741 (OUTLIER) cc_final: 0.7415 (t80) REVERT: B 1239 TYR cc_start: 0.7166 (t80) cc_final: 0.6869 (t80) REVERT: B 1562 PHE cc_start: 0.7777 (m-80) cc_final: 0.7250 (m-10) REVERT: B 1582 MET cc_start: 0.7281 (ptt) cc_final: 0.7066 (pmm) REVERT: B 1634 MET cc_start: 0.7686 (tpp) cc_final: 0.7368 (tpp) REVERT: G 61 MET cc_start: 0.8267 (tmm) cc_final: 0.7414 (tmm) REVERT: G 351 MET cc_start: 0.8227 (mmp) cc_final: 0.7951 (mmp) REVERT: H 800 GLU cc_start: 0.8469 (mm-30) cc_final: 0.8003 (mm-30) REVERT: H 806 ASP cc_start: 0.8632 (t0) cc_final: 0.8308 (t0) REVERT: H 1239 TYR cc_start: 0.8070 (t80) cc_final: 0.7723 (t80) REVERT: H 1378 MET cc_start: 0.8397 (ttm) cc_final: 0.8121 (ttm) REVERT: H 1382 ASP cc_start: 0.8400 (t70) cc_final: 0.8167 (t70) REVERT: X 239 ASP cc_start: 0.6720 (t0) cc_final: 0.6096 (t70) REVERT: X 364 ASP cc_start: 0.8105 (p0) cc_final: 0.7624 (p0) REVERT: X 426 HIS cc_start: 0.8012 (m-70) cc_final: 0.7724 (m-70) REVERT: X 458 GLU cc_start: 0.8387 (mp0) cc_final: 0.8149 (mp0) outliers start: 42 outliers final: 27 residues processed: 333 average time/residue: 0.2940 time to fit residues: 163.1084 Evaluate side-chains 299 residues out of total 3313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 269 time to evaluate : 2.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 19 ASP Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain J residue 363 THR Chi-restraints excluded: chain J residue 442 GLN Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 178 ASN Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 559 MET Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain B residue 793 ILE Chi-restraints excluded: chain B residue 878 ILE Chi-restraints excluded: chain B residue 1226 PHE Chi-restraints excluded: chain B residue 1563 ILE Chi-restraints excluded: chain G residue 23 GLU Chi-restraints excluded: chain G residue 137 VAL Chi-restraints excluded: chain G residue 176 LEU Chi-restraints excluded: chain G residue 284 VAL Chi-restraints excluded: chain H residue 793 ILE Chi-restraints excluded: chain H residue 1387 THR Chi-restraints excluded: chain H residue 1445 PHE Chi-restraints excluded: chain H residue 1546 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 334 optimal weight: 2.9990 chunk 254 optimal weight: 0.9980 chunk 175 optimal weight: 5.9990 chunk 37 optimal weight: 10.0000 chunk 161 optimal weight: 20.0000 chunk 227 optimal weight: 4.9990 chunk 339 optimal weight: 9.9990 chunk 359 optimal weight: 20.0000 chunk 177 optimal weight: 0.0060 chunk 321 optimal weight: 3.9990 chunk 96 optimal weight: 7.9990 overall best weight: 2.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 835 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1033 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 357 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.1787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 28796 Z= 0.283 Angle : 0.584 16.327 39206 Z= 0.298 Chirality : 0.044 0.186 4619 Planarity : 0.004 0.056 5035 Dihedral : 5.190 57.743 4097 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.28 % Favored : 95.64 % Rotamer: Outliers : 2.46 % Allowed : 14.68 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.55 % 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: 0.12 (0.14), residues: 3718 helix: 1.04 (0.18), residues: 879 sheet: 0.24 (0.16), residues: 1097 loop : -0.45 (0.15), residues: 1742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP J 296 HIS 0.005 0.001 HIS B1442 PHE 0.021 0.002 PHE H1226 TYR 0.020 0.001 TYR G 512 ARG 0.005 0.000 ARG H1232 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7436 Ramachandran restraints generated. 3718 Oldfield, 0 Emsley, 3718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7436 Ramachandran restraints generated. 3718 Oldfield, 0 Emsley, 3718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 3313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 278 time to evaluate : 2.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 239 ASP cc_start: 0.6068 (t70) cc_final: 0.5284 (t70) REVERT: J 364 ASP cc_start: 0.8023 (p0) cc_final: 0.7534 (p0) REVERT: J 373 PRO cc_start: 0.9017 (Cg_endo) cc_final: 0.8749 (Cg_exo) REVERT: J 402 VAL cc_start: 0.9133 (m) cc_final: 0.8888 (p) REVERT: J 442 GLN cc_start: 0.7872 (OUTLIER) cc_final: 0.6690 (mp-120) REVERT: A 346 MET cc_start: 0.8110 (tpp) cc_final: 0.7767 (mmm) REVERT: A 451 VAL cc_start: 0.8890 (OUTLIER) cc_final: 0.8649 (m) REVERT: A 551 ARG cc_start: 0.7996 (mmt-90) cc_final: 0.7587 (mmt-90) REVERT: B 800 GLU cc_start: 0.8614 (mm-30) cc_final: 0.8350 (mm-30) REVERT: B 834 GLN cc_start: 0.1363 (OUTLIER) cc_final: -0.1239 (mt0) REVERT: B 996 MET cc_start: 0.6914 (ppp) cc_final: 0.6044 (ppp) REVERT: B 1226 PHE cc_start: 0.7804 (OUTLIER) cc_final: 0.7417 (t80) REVERT: B 1239 TYR cc_start: 0.7142 (t80) cc_final: 0.6852 (t80) REVERT: B 1252 MET cc_start: 0.8744 (ttt) cc_final: 0.8473 (ttt) REVERT: B 1562 PHE cc_start: 0.7850 (m-80) cc_final: 0.7333 (m-80) REVERT: B 1582 MET cc_start: 0.7578 (ptt) cc_final: 0.7139 (pmm) REVERT: G 61 MET cc_start: 0.8282 (tmm) cc_final: 0.7379 (tmm) REVERT: G 201 GLU cc_start: 0.7752 (OUTLIER) cc_final: 0.7386 (pm20) REVERT: G 419 MET cc_start: 0.8604 (tmm) cc_final: 0.8353 (tmm) REVERT: H 800 GLU cc_start: 0.8483 (mm-30) cc_final: 0.8022 (mm-30) REVERT: H 806 ASP cc_start: 0.8624 (t0) cc_final: 0.8235 (t0) REVERT: H 1239 TYR cc_start: 0.8060 (t80) cc_final: 0.7710 (t80) REVERT: H 1382 ASP cc_start: 0.8419 (t70) cc_final: 0.8218 (t70) REVERT: H 1385 MET cc_start: 0.8026 (mtm) cc_final: 0.7585 (mtm) REVERT: X 239 ASP cc_start: 0.6685 (t0) cc_final: 0.5276 (p0) REVERT: X 364 ASP cc_start: 0.8075 (p0) cc_final: 0.7599 (p0) outliers start: 72 outliers final: 56 residues processed: 332 average time/residue: 0.2956 time to fit residues: 165.9539 Evaluate side-chains 325 residues out of total 3313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 264 time to evaluate : 2.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 19 ASP Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain J residue 362 MET Chi-restraints excluded: chain J residue 363 THR Chi-restraints excluded: chain J residue 409 VAL Chi-restraints excluded: chain J residue 442 GLN Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 178 ASN Chi-restraints excluded: chain A residue 201 GLU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 559 MET Chi-restraints excluded: chain A residue 563 ILE Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain B residue 753 VAL Chi-restraints excluded: chain B residue 793 ILE Chi-restraints excluded: chain B residue 834 GLN Chi-restraints excluded: chain B residue 878 ILE Chi-restraints excluded: chain B residue 1226 PHE Chi-restraints excluded: chain B residue 1404 ASP Chi-restraints excluded: chain B residue 1563 ILE Chi-restraints excluded: chain B residue 1599 ILE Chi-restraints excluded: chain G residue 58 THR Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain G residue 137 VAL Chi-restraints excluded: chain G residue 176 LEU Chi-restraints excluded: chain G residue 201 GLU Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 280 LEU Chi-restraints excluded: chain G residue 284 VAL Chi-restraints excluded: chain G residue 478 LEU Chi-restraints excluded: chain G residue 492 LEU Chi-restraints excluded: chain G residue 529 VAL Chi-restraints excluded: chain H residue 775 ASP Chi-restraints excluded: chain H residue 793 ILE Chi-restraints excluded: chain H residue 922 VAL Chi-restraints excluded: chain H residue 1368 THR Chi-restraints excluded: chain H residue 1384 SER Chi-restraints excluded: chain H residue 1387 THR Chi-restraints excluded: chain H residue 1445 PHE Chi-restraints excluded: chain H residue 1546 THR Chi-restraints excluded: chain H residue 1596 LEU Chi-restraints excluded: chain X residue 359 ILE Chi-restraints excluded: chain X residue 362 MET Chi-restraints excluded: chain X residue 376 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 299 optimal weight: 40.0000 chunk 204 optimal weight: 6.9990 chunk 5 optimal weight: 0.0470 chunk 267 optimal weight: 6.9990 chunk 148 optimal weight: 3.9990 chunk 306 optimal weight: 50.0000 chunk 248 optimal weight: 0.9990 chunk 0 optimal weight: 0.6980 chunk 183 optimal weight: 0.0370 chunk 322 optimal weight: 0.0770 chunk 90 optimal weight: 7.9990 overall best weight: 0.3716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 835 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1034 GLN ** H1033 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H1186 ASN X 245 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 28796 Z= 0.149 Angle : 0.531 14.984 39206 Z= 0.271 Chirality : 0.043 0.185 4619 Planarity : 0.004 0.056 5035 Dihedral : 4.775 57.474 4097 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.07 % Favored : 96.85 % Rotamer: Outliers : 1.95 % Allowed : 16.39 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.55 % 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: 0.30 (0.14), residues: 3718 helix: 1.13 (0.18), residues: 885 sheet: 0.43 (0.16), residues: 1076 loop : -0.34 (0.15), residues: 1757 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP J 296 HIS 0.004 0.001 HIS B1442 PHE 0.013 0.001 PHE B1188 TYR 0.027 0.001 TYR B1031 ARG 0.002 0.000 ARG C 38 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7436 Ramachandran restraints generated. 3718 Oldfield, 0 Emsley, 3718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7436 Ramachandran restraints generated. 3718 Oldfield, 0 Emsley, 3718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 3313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 301 time to evaluate : 2.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 42 ILE cc_start: 0.7295 (OUTLIER) cc_final: 0.7090 (tt) REVERT: C 90 GLU cc_start: 0.6851 (tt0) cc_final: 0.6649 (tt0) REVERT: J 364 ASP cc_start: 0.7967 (p0) cc_final: 0.7496 (p0) REVERT: J 373 PRO cc_start: 0.8894 (Cg_endo) cc_final: 0.8643 (Cg_exo) REVERT: J 384 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.8310 (mm) REVERT: A 179 MET cc_start: 0.8458 (mpp) cc_final: 0.8252 (mpp) REVERT: A 346 MET cc_start: 0.7936 (tpp) cc_final: 0.7593 (mmm) REVERT: A 451 VAL cc_start: 0.8646 (OUTLIER) cc_final: 0.8437 (p) REVERT: A 551 ARG cc_start: 0.7916 (mmt-90) cc_final: 0.7421 (mmt-90) REVERT: B 800 GLU cc_start: 0.8610 (mm-30) cc_final: 0.8335 (mm-30) REVERT: B 1226 PHE cc_start: 0.7703 (OUTLIER) cc_final: 0.7302 (t80) REVERT: B 1239 TYR cc_start: 0.7110 (t80) cc_final: 0.6803 (t80) REVERT: B 1562 PHE cc_start: 0.7679 (m-80) cc_final: 0.7179 (m-80) REVERT: B 1582 MET cc_start: 0.7470 (ptt) cc_final: 0.7020 (pmm) REVERT: G 61 MET cc_start: 0.8234 (tmm) cc_final: 0.7373 (tmm) REVERT: G 142 MET cc_start: 0.8105 (mmm) cc_final: 0.7762 (mmm) REVERT: G 201 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.7381 (pm20) REVERT: H 806 ASP cc_start: 0.8609 (t0) cc_final: 0.8222 (t0) REVERT: H 881 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8415 (mm) REVERT: H 1239 TYR cc_start: 0.8038 (t80) cc_final: 0.7703 (t80) REVERT: H 1382 ASP cc_start: 0.8396 (t70) cc_final: 0.8194 (t70) REVERT: H 1385 MET cc_start: 0.7989 (mtm) cc_final: 0.7549 (mtm) REVERT: X 239 ASP cc_start: 0.6696 (t0) cc_final: 0.6067 (t70) REVERT: X 364 ASP cc_start: 0.8071 (p0) cc_final: 0.7334 (t0) REVERT: X 426 HIS cc_start: 0.7913 (m-70) cc_final: 0.7631 (m-70) REVERT: X 458 GLU cc_start: 0.8424 (mp0) cc_final: 0.8181 (mp0) outliers start: 57 outliers final: 40 residues processed: 341 average time/residue: 0.2936 time to fit residues: 166.7257 Evaluate side-chains 322 residues out of total 3313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 276 time to evaluate : 2.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 19 ASP Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 113 CYS Chi-restraints excluded: chain J residue 362 MET Chi-restraints excluded: chain J residue 363 THR Chi-restraints excluded: chain J residue 384 LEU Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 201 GLU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 559 MET Chi-restraints excluded: chain B residue 769 MET Chi-restraints excluded: chain B residue 878 ILE Chi-restraints excluded: chain B residue 922 VAL Chi-restraints excluded: chain B residue 1226 PHE Chi-restraints excluded: chain B residue 1563 ILE Chi-restraints excluded: chain B residue 1596 LEU Chi-restraints excluded: chain G residue 23 GLU Chi-restraints excluded: chain G residue 137 VAL Chi-restraints excluded: chain G residue 201 GLU Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 284 VAL Chi-restraints excluded: chain G residue 354 VAL Chi-restraints excluded: chain G residue 529 VAL Chi-restraints excluded: chain H residue 793 ILE Chi-restraints excluded: chain H residue 881 LEU Chi-restraints excluded: chain H residue 922 VAL Chi-restraints excluded: chain H residue 1378 MET Chi-restraints excluded: chain H residue 1384 SER Chi-restraints excluded: chain H residue 1387 THR Chi-restraints excluded: chain H residue 1445 PHE Chi-restraints excluded: chain H residue 1589 PHE Chi-restraints excluded: chain H residue 1596 LEU Chi-restraints excluded: chain X residue 362 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 120 optimal weight: 0.9980 chunk 323 optimal weight: 1.9990 chunk 71 optimal weight: 6.9990 chunk 211 optimal weight: 3.9990 chunk 88 optimal weight: 6.9990 chunk 359 optimal weight: 8.9990 chunk 298 optimal weight: 10.0000 chunk 166 optimal weight: 30.0000 chunk 29 optimal weight: 10.0000 chunk 119 optimal weight: 0.9980 chunk 188 optimal weight: 20.0000 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 835 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1033 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.2033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 28796 Z= 0.307 Angle : 0.585 15.473 39206 Z= 0.299 Chirality : 0.044 0.187 4619 Planarity : 0.004 0.059 5035 Dihedral : 4.808 56.480 4097 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.25 % Favored : 95.67 % Rotamer: Outliers : 3.22 % Allowed : 16.94 % Favored : 79.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.55 % 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: 0.25 (0.14), residues: 3718 helix: 1.17 (0.18), residues: 883 sheet: 0.30 (0.16), residues: 1092 loop : -0.35 (0.15), residues: 1743 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP J 296 HIS 0.004 0.001 HIS B1442 PHE 0.021 0.002 PHE B1015 TYR 0.017 0.002 TYR G 512 ARG 0.004 0.000 ARG B1298 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7436 Ramachandran restraints generated. 3718 Oldfield, 0 Emsley, 3718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7436 Ramachandran restraints generated. 3718 Oldfield, 0 Emsley, 3718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 3313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 278 time to evaluate : 2.460 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: C 84 HIS cc_start: 0.7956 (m170) cc_final: 0.7728 (m170) REVERT: C 90 GLU cc_start: 0.7222 (tt0) cc_final: 0.6848 (tt0) REVERT: J 364 ASP cc_start: 0.7920 (p0) cc_final: 0.7467 (p0) REVERT: J 373 PRO cc_start: 0.8997 (Cg_endo) cc_final: 0.8727 (Cg_exo) REVERT: J 384 LEU cc_start: 0.8588 (OUTLIER) cc_final: 0.8307 (mm) REVERT: J 442 GLN cc_start: 0.7910 (OUTLIER) cc_final: 0.6666 (mp-120) REVERT: A 54 LEU cc_start: 0.8217 (OUTLIER) cc_final: 0.7925 (mt) REVERT: A 242 LYS cc_start: 0.8296 (mmtt) cc_final: 0.8081 (mmtt) REVERT: A 346 MET cc_start: 0.8119 (tpp) cc_final: 0.7773 (mmm) REVERT: A 400 ILE cc_start: 0.9033 (mm) cc_final: 0.8673 (tp) REVERT: A 451 VAL cc_start: 0.8717 (OUTLIER) cc_final: 0.8502 (p) REVERT: A 551 ARG cc_start: 0.7999 (mmt-90) cc_final: 0.7475 (mmt-90) REVERT: B 800 GLU cc_start: 0.8597 (mm-30) cc_final: 0.8322 (mm-30) REVERT: B 834 GLN cc_start: 0.1244 (OUTLIER) cc_final: -0.1321 (mt0) REVERT: B 1239 TYR cc_start: 0.7106 (t80) cc_final: 0.6844 (t80) REVERT: B 1252 MET cc_start: 0.8877 (OUTLIER) cc_final: 0.8619 (ttt) REVERT: B 1562 PHE cc_start: 0.7828 (m-80) cc_final: 0.7300 (m-10) REVERT: B 1582 MET cc_start: 0.7591 (ptt) cc_final: 0.7079 (pmm) REVERT: G 61 MET cc_start: 0.8286 (tmm) cc_final: 0.7375 (tmm) REVERT: G 201 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.7447 (pm20) REVERT: G 351 MET cc_start: 0.8363 (mmp) cc_final: 0.7977 (mmp) REVERT: G 419 MET cc_start: 0.8598 (tmm) cc_final: 0.8339 (tmm) REVERT: H 806 ASP cc_start: 0.8626 (t0) cc_final: 0.8292 (t0) REVERT: H 881 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8472 (mm) REVERT: H 1239 TYR cc_start: 0.7977 (t80) cc_final: 0.7709 (t80) REVERT: H 1325 MET cc_start: 0.7486 (tpp) cc_final: 0.6493 (mpp) REVERT: H 1385 MET cc_start: 0.8139 (mtm) cc_final: 0.7732 (mtm) REVERT: X 239 ASP cc_start: 0.6752 (t0) cc_final: 0.5322 (p0) REVERT: X 364 ASP cc_start: 0.8049 (p0) cc_final: 0.7336 (t0) REVERT: X 458 GLU cc_start: 0.8453 (mp0) cc_final: 0.8197 (mp0) outliers start: 94 outliers final: 67 residues processed: 349 average time/residue: 0.2864 time to fit residues: 167.8248 Evaluate side-chains 340 residues out of total 3313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 265 time to evaluate : 2.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 41 ILE Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 19 ASP Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 113 CYS Chi-restraints excluded: chain J residue 363 THR Chi-restraints excluded: chain J residue 384 LEU Chi-restraints excluded: chain J residue 409 VAL Chi-restraints excluded: chain J residue 442 GLN Chi-restraints excluded: chain A residue 23 GLU Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 201 GLU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 559 MET Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain B residue 773 LEU Chi-restraints excluded: chain B residue 793 ILE Chi-restraints excluded: chain B residue 834 GLN Chi-restraints excluded: chain B residue 878 ILE Chi-restraints excluded: chain B residue 922 VAL Chi-restraints excluded: chain B residue 1226 PHE Chi-restraints excluded: chain B residue 1252 MET Chi-restraints excluded: chain B residue 1404 ASP Chi-restraints excluded: chain B residue 1563 ILE Chi-restraints excluded: chain B residue 1599 ILE Chi-restraints excluded: chain G residue 58 THR Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain G residue 137 VAL Chi-restraints excluded: chain G residue 176 LEU Chi-restraints excluded: chain G residue 201 GLU Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 280 LEU Chi-restraints excluded: chain G residue 284 VAL Chi-restraints excluded: chain G residue 401 THR Chi-restraints excluded: chain G residue 492 LEU Chi-restraints excluded: chain G residue 524 VAL Chi-restraints excluded: chain G residue 529 VAL Chi-restraints excluded: chain H residue 775 ASP Chi-restraints excluded: chain H residue 793 ILE Chi-restraints excluded: chain H residue 881 LEU Chi-restraints excluded: chain H residue 922 VAL Chi-restraints excluded: chain H residue 1167 VAL Chi-restraints excluded: chain H residue 1368 THR Chi-restraints excluded: chain H residue 1378 MET Chi-restraints excluded: chain H residue 1384 SER Chi-restraints excluded: chain H residue 1387 THR Chi-restraints excluded: chain H residue 1396 LEU Chi-restraints excluded: chain H residue 1445 PHE Chi-restraints excluded: chain H residue 1546 THR Chi-restraints excluded: chain H residue 1589 PHE Chi-restraints excluded: chain H residue 1596 LEU Chi-restraints excluded: chain H residue 1599 ILE Chi-restraints excluded: chain X residue 328 THR Chi-restraints excluded: chain X residue 362 MET Chi-restraints excluded: chain X residue 376 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 347 optimal weight: 5.9990 chunk 40 optimal weight: 5.9990 chunk 205 optimal weight: 7.9990 chunk 262 optimal weight: 0.9990 chunk 203 optimal weight: 6.9990 chunk 302 optimal weight: 7.9990 chunk 200 optimal weight: 7.9990 chunk 358 optimal weight: 40.0000 chunk 224 optimal weight: 1.9990 chunk 218 optimal weight: 0.4980 chunk 165 optimal weight: 6.9990 overall best weight: 3.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1237 GLN ** H1033 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H1398 GLN H1545 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.2183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 28796 Z= 0.315 Angle : 0.606 16.061 39206 Z= 0.309 Chirality : 0.044 0.210 4619 Planarity : 0.004 0.062 5035 Dihedral : 4.864 57.468 4097 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.28 % Favored : 95.64 % Rotamer: Outliers : 3.52 % Allowed : 17.69 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.55 % 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: 0.19 (0.14), residues: 3718 helix: 1.11 (0.18), residues: 883 sheet: 0.25 (0.16), residues: 1103 loop : -0.39 (0.15), residues: 1732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B1233 HIS 0.005 0.001 HIS B1442 PHE 0.016 0.002 PHE G 507 TYR 0.022 0.002 TYR B1031 ARG 0.007 0.000 ARG H1232 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7436 Ramachandran restraints generated. 3718 Oldfield, 0 Emsley, 3718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7436 Ramachandran restraints generated. 3718 Oldfield, 0 Emsley, 3718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 3313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 280 time to evaluate : 2.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 84 HIS cc_start: 0.7983 (m170) cc_final: 0.6472 (m170) REVERT: C 90 GLU cc_start: 0.7187 (tt0) cc_final: 0.6094 (tt0) REVERT: C 94 ASP cc_start: 0.8546 (t0) cc_final: 0.8319 (m-30) REVERT: J 364 ASP cc_start: 0.7846 (p0) cc_final: 0.7434 (p0) REVERT: J 373 PRO cc_start: 0.9019 (Cg_endo) cc_final: 0.8736 (Cg_exo) REVERT: J 384 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8330 (mm) REVERT: J 442 GLN cc_start: 0.7880 (OUTLIER) cc_final: 0.6703 (mp-120) REVERT: A 54 LEU cc_start: 0.8247 (OUTLIER) cc_final: 0.7948 (mt) REVERT: A 346 MET cc_start: 0.8134 (tpp) cc_final: 0.7808 (mmm) REVERT: A 451 VAL cc_start: 0.8761 (OUTLIER) cc_final: 0.8560 (p) REVERT: A 551 ARG cc_start: 0.8020 (mmt-90) cc_final: 0.7673 (mmt-90) REVERT: B 800 GLU cc_start: 0.8567 (mm-30) cc_final: 0.8298 (mm-30) REVERT: B 834 GLN cc_start: 0.1243 (OUTLIER) cc_final: -0.1169 (pt0) REVERT: B 1239 TYR cc_start: 0.7203 (t80) cc_final: 0.6916 (t80) REVERT: B 1325 MET cc_start: 0.6681 (tpt) cc_final: 0.6393 (tpt) REVERT: B 1341 LEU cc_start: 0.8530 (OUTLIER) cc_final: 0.8261 (mp) REVERT: B 1562 PHE cc_start: 0.7879 (m-80) cc_final: 0.7300 (m-10) REVERT: B 1582 MET cc_start: 0.7575 (ptt) cc_final: 0.7084 (pmm) REVERT: G 61 MET cc_start: 0.8309 (tmm) cc_final: 0.7388 (tmm) REVERT: G 89 THR cc_start: 0.8954 (OUTLIER) cc_final: 0.8688 (p) REVERT: G 201 GLU cc_start: 0.7742 (OUTLIER) cc_final: 0.7429 (pm20) REVERT: H 806 ASP cc_start: 0.8625 (t0) cc_final: 0.8208 (t0) REVERT: H 879 VAL cc_start: 0.8784 (OUTLIER) cc_final: 0.8432 (m) REVERT: H 881 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8401 (mm) REVERT: H 1239 TYR cc_start: 0.7906 (t80) cc_final: 0.7582 (t80) REVERT: H 1385 MET cc_start: 0.8231 (mtm) cc_final: 0.7843 (mtm) REVERT: H 1545 GLN cc_start: 0.6429 (OUTLIER) cc_final: 0.5701 (pp30) REVERT: X 239 ASP cc_start: 0.6714 (t0) cc_final: 0.5210 (p0) REVERT: X 364 ASP cc_start: 0.8018 (p0) cc_final: 0.7591 (p0) outliers start: 103 outliers final: 74 residues processed: 357 average time/residue: 0.2944 time to fit residues: 176.7518 Evaluate side-chains 349 residues out of total 3313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 264 time to evaluate : 2.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 41 ILE Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 19 ASP Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 113 CYS Chi-restraints excluded: chain J residue 384 LEU Chi-restraints excluded: chain J residue 409 VAL Chi-restraints excluded: chain J residue 442 GLN Chi-restraints excluded: chain A residue 23 GLU Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 178 ASN Chi-restraints excluded: chain A residue 201 GLU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 559 MET Chi-restraints excluded: chain A residue 563 ILE Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain B residue 753 VAL Chi-restraints excluded: chain B residue 773 LEU Chi-restraints excluded: chain B residue 793 ILE Chi-restraints excluded: chain B residue 834 GLN Chi-restraints excluded: chain B residue 878 ILE Chi-restraints excluded: chain B residue 922 VAL Chi-restraints excluded: chain B residue 1226 PHE Chi-restraints excluded: chain B residue 1237 GLN Chi-restraints excluded: chain B residue 1341 LEU Chi-restraints excluded: chain B residue 1404 ASP Chi-restraints excluded: chain B residue 1563 ILE Chi-restraints excluded: chain B residue 1599 ILE Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain G residue 58 THR Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain G residue 137 VAL Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain G residue 176 LEU Chi-restraints excluded: chain G residue 201 GLU Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 278 VAL Chi-restraints excluded: chain G residue 280 LEU Chi-restraints excluded: chain G residue 284 VAL Chi-restraints excluded: chain G residue 401 THR Chi-restraints excluded: chain G residue 524 VAL Chi-restraints excluded: chain G residue 529 VAL Chi-restraints excluded: chain H residue 754 GLU Chi-restraints excluded: chain H residue 775 ASP Chi-restraints excluded: chain H residue 793 ILE Chi-restraints excluded: chain H residue 879 VAL Chi-restraints excluded: chain H residue 881 LEU Chi-restraints excluded: chain H residue 922 VAL Chi-restraints excluded: chain H residue 1167 VAL Chi-restraints excluded: chain H residue 1368 THR Chi-restraints excluded: chain H residue 1378 MET Chi-restraints excluded: chain H residue 1384 SER Chi-restraints excluded: chain H residue 1387 THR Chi-restraints excluded: chain H residue 1396 LEU Chi-restraints excluded: chain H residue 1419 ARG Chi-restraints excluded: chain H residue 1445 PHE Chi-restraints excluded: chain H residue 1545 GLN Chi-restraints excluded: chain H residue 1546 THR Chi-restraints excluded: chain H residue 1589 PHE Chi-restraints excluded: chain H residue 1596 LEU Chi-restraints excluded: chain H residue 1599 ILE Chi-restraints excluded: chain X residue 328 THR Chi-restraints excluded: chain X residue 362 MET Chi-restraints excluded: chain X residue 376 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 221 optimal weight: 0.7980 chunk 143 optimal weight: 40.0000 chunk 214 optimal weight: 5.9990 chunk 108 optimal weight: 0.3980 chunk 70 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 227 optimal weight: 2.9990 chunk 244 optimal weight: 2.9990 chunk 177 optimal weight: 3.9990 chunk 33 optimal weight: 6.9990 chunk 281 optimal weight: 3.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 435 ASN ** A 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1033 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 28796 Z= 0.202 Angle : 0.572 15.056 39206 Z= 0.289 Chirality : 0.044 0.182 4619 Planarity : 0.004 0.061 5035 Dihedral : 4.728 56.919 4097 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.50 % Favored : 96.42 % Rotamer: Outliers : 3.01 % Allowed : 18.45 % Favored : 78.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.55 % 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: 0.26 (0.14), residues: 3718 helix: 1.12 (0.18), residues: 883 sheet: 0.35 (0.16), residues: 1094 loop : -0.36 (0.15), residues: 1741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B1233 HIS 0.004 0.001 HIS B1442 PHE 0.023 0.001 PHE B1015 TYR 0.023 0.001 TYR H 815 ARG 0.004 0.000 ARG J 460 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7436 Ramachandran restraints generated. 3718 Oldfield, 0 Emsley, 3718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7436 Ramachandran restraints generated. 3718 Oldfield, 0 Emsley, 3718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 3313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 289 time to evaluate : 2.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 84 HIS cc_start: 0.7972 (m170) cc_final: 0.6516 (m170) REVERT: C 90 GLU cc_start: 0.7144 (tt0) cc_final: 0.5987 (tt0) REVERT: C 94 ASP cc_start: 0.8477 (t0) cc_final: 0.8272 (m-30) REVERT: J 364 ASP cc_start: 0.7815 (p0) cc_final: 0.7407 (p0) REVERT: J 373 PRO cc_start: 0.8977 (Cg_endo) cc_final: 0.8707 (Cg_exo) REVERT: J 384 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.8310 (mm) REVERT: J 442 GLN cc_start: 0.7833 (OUTLIER) cc_final: 0.6471 (mp-120) REVERT: A 54 LEU cc_start: 0.8257 (OUTLIER) cc_final: 0.7984 (mt) REVERT: A 346 MET cc_start: 0.8129 (tpp) cc_final: 0.7770 (mmm) REVERT: A 451 VAL cc_start: 0.8796 (OUTLIER) cc_final: 0.8536 (p) REVERT: A 551 ARG cc_start: 0.7982 (mmt-90) cc_final: 0.7635 (mmt-90) REVERT: B 800 GLU cc_start: 0.8555 (mm-30) cc_final: 0.8292 (mm-30) REVERT: B 996 MET cc_start: 0.6942 (tmm) cc_final: 0.5248 (mtm) REVERT: B 1107 MET cc_start: 0.7151 (ptt) cc_final: 0.6491 (mmp) REVERT: B 1239 TYR cc_start: 0.7143 (t80) cc_final: 0.6849 (t80) REVERT: B 1252 MET cc_start: 0.8917 (ttp) cc_final: 0.8561 (ttt) REVERT: B 1325 MET cc_start: 0.6662 (tpt) cc_final: 0.6423 (tpt) REVERT: B 1562 PHE cc_start: 0.7849 (m-80) cc_final: 0.7333 (m-80) REVERT: B 1582 MET cc_start: 0.7534 (ptt) cc_final: 0.7065 (pmm) REVERT: G 61 MET cc_start: 0.8287 (tmm) cc_final: 0.7408 (tmm) REVERT: G 201 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.7371 (pm20) REVERT: H 806 ASP cc_start: 0.8653 (t0) cc_final: 0.8259 (t0) REVERT: H 879 VAL cc_start: 0.8781 (OUTLIER) cc_final: 0.8414 (m) REVERT: H 881 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8388 (mm) REVERT: H 1239 TYR cc_start: 0.7910 (t80) cc_final: 0.7598 (t80) REVERT: H 1385 MET cc_start: 0.8204 (mtm) cc_final: 0.7865 (mtm) REVERT: X 239 ASP cc_start: 0.6687 (t0) cc_final: 0.5967 (t70) REVERT: X 364 ASP cc_start: 0.7991 (p0) cc_final: 0.7343 (t0) REVERT: X 443 MET cc_start: 0.7202 (mmm) cc_final: 0.6778 (tpt) REVERT: X 458 GLU cc_start: 0.8533 (mp0) cc_final: 0.8256 (mp0) REVERT: X 460 ARG cc_start: 0.8805 (mtm-85) cc_final: 0.8227 (mtm-85) outliers start: 88 outliers final: 68 residues processed: 355 average time/residue: 0.2938 time to fit residues: 177.3767 Evaluate side-chains 346 residues out of total 3313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 271 time to evaluate : 2.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 19 ASP Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 113 CYS Chi-restraints excluded: chain J residue 384 LEU Chi-restraints excluded: chain J residue 409 VAL Chi-restraints excluded: chain J residue 442 GLN Chi-restraints excluded: chain A residue 23 GLU Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 178 ASN Chi-restraints excluded: chain A residue 201 GLU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 563 ILE Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain B residue 753 VAL Chi-restraints excluded: chain B residue 775 ASP Chi-restraints excluded: chain B residue 793 ILE Chi-restraints excluded: chain B residue 878 ILE Chi-restraints excluded: chain B residue 922 VAL Chi-restraints excluded: chain B residue 1226 PHE Chi-restraints excluded: chain B residue 1368 THR Chi-restraints excluded: chain B residue 1404 ASP Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain G residue 58 THR Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain G residue 137 VAL Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain G residue 176 LEU Chi-restraints excluded: chain G residue 201 GLU Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 278 VAL Chi-restraints excluded: chain G residue 284 VAL Chi-restraints excluded: chain G residue 401 THR Chi-restraints excluded: chain G residue 492 LEU Chi-restraints excluded: chain G residue 494 VAL Chi-restraints excluded: chain G residue 524 VAL Chi-restraints excluded: chain G residue 529 VAL Chi-restraints excluded: chain H residue 754 GLU Chi-restraints excluded: chain H residue 793 ILE Chi-restraints excluded: chain H residue 879 VAL Chi-restraints excluded: chain H residue 881 LEU Chi-restraints excluded: chain H residue 922 VAL Chi-restraints excluded: chain H residue 1167 VAL Chi-restraints excluded: chain H residue 1188 PHE Chi-restraints excluded: chain H residue 1368 THR Chi-restraints excluded: chain H residue 1378 MET Chi-restraints excluded: chain H residue 1384 SER Chi-restraints excluded: chain H residue 1387 THR Chi-restraints excluded: chain H residue 1396 LEU Chi-restraints excluded: chain H residue 1445 PHE Chi-restraints excluded: chain H residue 1546 THR Chi-restraints excluded: chain H residue 1589 PHE Chi-restraints excluded: chain H residue 1596 LEU Chi-restraints excluded: chain X residue 328 THR Chi-restraints excluded: chain X residue 362 MET Chi-restraints excluded: chain X residue 376 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 326 optimal weight: 0.7980 chunk 343 optimal weight: 20.0000 chunk 313 optimal weight: 20.0000 chunk 334 optimal weight: 0.7980 chunk 201 optimal weight: 8.9990 chunk 145 optimal weight: 0.6980 chunk 262 optimal weight: 0.6980 chunk 102 optimal weight: 0.5980 chunk 301 optimal weight: 50.0000 chunk 316 optimal weight: 6.9990 chunk 332 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 ASN ** B1237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1033 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.2339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 28796 Z= 0.166 Angle : 0.562 13.595 39206 Z= 0.283 Chirality : 0.043 0.177 4619 Planarity : 0.004 0.058 5035 Dihedral : 4.500 57.613 4097 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.20 % Favored : 96.72 % Rotamer: Outliers : 2.77 % Allowed : 19.03 % Favored : 78.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.55 % 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: 0.36 (0.14), residues: 3718 helix: 1.16 (0.18), residues: 891 sheet: 0.46 (0.16), residues: 1088 loop : -0.30 (0.16), residues: 1739 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP B1233 HIS 0.006 0.001 HIS D 84 PHE 0.020 0.001 PHE B1188 TYR 0.021 0.001 TYR B1031 ARG 0.004 0.000 ARG J 460 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7436 Ramachandran restraints generated. 3718 Oldfield, 0 Emsley, 3718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7436 Ramachandran restraints generated. 3718 Oldfield, 0 Emsley, 3718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 3313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 295 time to evaluate : 2.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 72 ASP cc_start: 0.8450 (t0) cc_final: 0.8163 (t0) REVERT: C 90 GLU cc_start: 0.7100 (tt0) cc_final: 0.6379 (tt0) REVERT: J 364 ASP cc_start: 0.7751 (p0) cc_final: 0.7343 (p0) REVERT: J 373 PRO cc_start: 0.8910 (Cg_endo) cc_final: 0.8675 (Cg_exo) REVERT: J 384 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8283 (mm) REVERT: J 442 GLN cc_start: 0.7663 (OUTLIER) cc_final: 0.5960 (mp-120) REVERT: A 54 LEU cc_start: 0.8214 (OUTLIER) cc_final: 0.7950 (mt) REVERT: A 346 MET cc_start: 0.8041 (tpp) cc_final: 0.7701 (mmm) REVERT: A 400 ILE cc_start: 0.9038 (mm) cc_final: 0.8567 (tp) REVERT: A 451 VAL cc_start: 0.8605 (OUTLIER) cc_final: 0.8337 (m) REVERT: A 551 ARG cc_start: 0.7931 (mmt-90) cc_final: 0.7449 (mmt-90) REVERT: B 800 GLU cc_start: 0.8553 (mm-30) cc_final: 0.8275 (mm-30) REVERT: B 996 MET cc_start: 0.6918 (tmm) cc_final: 0.5256 (mtm) REVERT: B 1107 MET cc_start: 0.7047 (ptt) cc_final: 0.6406 (mmp) REVERT: B 1239 TYR cc_start: 0.7089 (t80) cc_final: 0.6807 (t80) REVERT: B 1252 MET cc_start: 0.8926 (OUTLIER) cc_final: 0.8725 (ttt) REVERT: B 1562 PHE cc_start: 0.7784 (m-80) cc_final: 0.7265 (m-80) REVERT: B 1582 MET cc_start: 0.7436 (ptt) cc_final: 0.7010 (pmm) REVERT: B 1589 PHE cc_start: 0.7239 (p90) cc_final: 0.6803 (p90) REVERT: G 61 MET cc_start: 0.8267 (tmm) cc_final: 0.7389 (tmm) REVERT: G 201 GLU cc_start: 0.7683 (OUTLIER) cc_final: 0.7385 (pm20) REVERT: G 454 LEU cc_start: 0.8653 (mm) cc_final: 0.8342 (mm) REVERT: H 806 ASP cc_start: 0.8578 (t0) cc_final: 0.8203 (t0) REVERT: H 879 VAL cc_start: 0.8764 (OUTLIER) cc_final: 0.8397 (m) REVERT: H 881 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8343 (mm) REVERT: H 996 MET cc_start: 0.4746 (ppp) cc_final: 0.3433 (mtt) REVERT: H 1239 TYR cc_start: 0.7898 (t80) cc_final: 0.7595 (t80) REVERT: H 1325 MET cc_start: 0.7513 (tpp) cc_final: 0.6446 (mpp) REVERT: H 1344 THR cc_start: 0.6825 (m) cc_final: 0.6599 (p) REVERT: H 1385 MET cc_start: 0.8174 (mtm) cc_final: 0.7817 (mtm) REVERT: X 239 ASP cc_start: 0.6760 (t0) cc_final: 0.6055 (t70) REVERT: X 364 ASP cc_start: 0.7997 (p0) cc_final: 0.7429 (t0) REVERT: X 443 MET cc_start: 0.7255 (mmm) cc_final: 0.6796 (tpt) REVERT: X 458 GLU cc_start: 0.8510 (mp0) cc_final: 0.8270 (mp0) REVERT: X 460 ARG cc_start: 0.8820 (mtm-85) cc_final: 0.8259 (mtm-85) outliers start: 81 outliers final: 65 residues processed: 353 average time/residue: 0.2837 time to fit residues: 168.3488 Evaluate side-chains 350 residues out of total 3313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 277 time to evaluate : 2.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 19 ASP Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 113 CYS Chi-restraints excluded: chain J residue 362 MET Chi-restraints excluded: chain J residue 384 LEU Chi-restraints excluded: chain J residue 409 VAL Chi-restraints excluded: chain J residue 442 GLN Chi-restraints excluded: chain A residue 23 GLU Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 201 GLU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 563 ILE Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain B residue 753 VAL Chi-restraints excluded: chain B residue 775 ASP Chi-restraints excluded: chain B residue 793 ILE Chi-restraints excluded: chain B residue 922 VAL Chi-restraints excluded: chain B residue 1226 PHE Chi-restraints excluded: chain B residue 1252 MET Chi-restraints excluded: chain B residue 1404 ASP Chi-restraints excluded: chain B residue 1599 ILE Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain G residue 58 THR Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain G residue 137 VAL Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain G residue 176 LEU Chi-restraints excluded: chain G residue 201 GLU Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 249 VAL Chi-restraints excluded: chain G residue 278 VAL Chi-restraints excluded: chain G residue 280 LEU Chi-restraints excluded: chain G residue 284 VAL Chi-restraints excluded: chain G residue 401 THR Chi-restraints excluded: chain G residue 492 LEU Chi-restraints excluded: chain G residue 494 VAL Chi-restraints excluded: chain G residue 529 VAL Chi-restraints excluded: chain G residue 623 THR Chi-restraints excluded: chain H residue 754 GLU Chi-restraints excluded: chain H residue 775 ASP Chi-restraints excluded: chain H residue 793 ILE Chi-restraints excluded: chain H residue 879 VAL Chi-restraints excluded: chain H residue 881 LEU Chi-restraints excluded: chain H residue 922 VAL Chi-restraints excluded: chain H residue 1167 VAL Chi-restraints excluded: chain H residue 1188 PHE Chi-restraints excluded: chain H residue 1368 THR Chi-restraints excluded: chain H residue 1387 THR Chi-restraints excluded: chain H residue 1396 LEU Chi-restraints excluded: chain H residue 1445 PHE Chi-restraints excluded: chain H residue 1447 VAL Chi-restraints excluded: chain H residue 1546 THR Chi-restraints excluded: chain H residue 1589 PHE Chi-restraints excluded: chain H residue 1596 LEU Chi-restraints excluded: chain X residue 328 THR Chi-restraints excluded: chain X residue 362 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 219 optimal weight: 9.9990 chunk 353 optimal weight: 7.9990 chunk 215 optimal weight: 5.9990 chunk 167 optimal weight: 20.0000 chunk 245 optimal weight: 3.9990 chunk 370 optimal weight: 20.0000 chunk 341 optimal weight: 30.0000 chunk 295 optimal weight: 5.9990 chunk 30 optimal weight: 30.0000 chunk 227 optimal weight: 4.9990 chunk 180 optimal weight: 5.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 102 GLN ** D 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 435 ASN ** A 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 ASN ** B1237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1033 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H1130 GLN H1545 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.2519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.080 28796 Z= 0.527 Angle : 0.730 15.119 39206 Z= 0.372 Chirality : 0.048 0.341 4619 Planarity : 0.005 0.069 5035 Dihedral : 5.002 57.134 4097 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.27 % Favored : 94.65 % Rotamer: Outliers : 2.84 % Allowed : 18.99 % Favored : 78.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.55 % 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: 0.05 (0.14), residues: 3718 helix: 1.03 (0.18), residues: 866 sheet: 0.15 (0.16), residues: 1092 loop : -0.46 (0.15), residues: 1760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B1233 HIS 0.007 0.001 HIS B 897 PHE 0.038 0.002 PHE H1226 TYR 0.029 0.002 TYR H 815 ARG 0.006 0.001 ARG G 268 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7436 Ramachandran restraints generated. 3718 Oldfield, 0 Emsley, 3718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7436 Ramachandran restraints generated. 3718 Oldfield, 0 Emsley, 3718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 3313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 264 time to evaluate : 2.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 72 ASP cc_start: 0.8558 (t0) cc_final: 0.8128 (t0) REVERT: J 373 PRO cc_start: 0.9094 (Cg_endo) cc_final: 0.8816 (Cg_exo) REVERT: J 442 GLN cc_start: 0.7927 (OUTLIER) cc_final: 0.6937 (mp-120) REVERT: A 54 LEU cc_start: 0.8285 (OUTLIER) cc_final: 0.7974 (mt) REVERT: A 346 MET cc_start: 0.8241 (tpp) cc_final: 0.7872 (mmm) REVERT: A 451 VAL cc_start: 0.8934 (OUTLIER) cc_final: 0.8728 (p) REVERT: A 551 ARG cc_start: 0.8048 (mmt-90) cc_final: 0.7562 (mmt-90) REVERT: B 800 GLU cc_start: 0.8531 (mm-30) cc_final: 0.8288 (mm-30) REVERT: B 834 GLN cc_start: 0.1288 (OUTLIER) cc_final: -0.1301 (mt0) REVERT: B 996 MET cc_start: 0.6904 (tmm) cc_final: 0.5215 (mtm) REVERT: B 1107 MET cc_start: 0.7119 (ptt) cc_final: 0.6491 (mmp) REVERT: B 1239 TYR cc_start: 0.7243 (t80) cc_final: 0.6960 (t80) REVERT: B 1582 MET cc_start: 0.7729 (ptt) cc_final: 0.7228 (pmm) REVERT: G 61 MET cc_start: 0.8366 (tmm) cc_final: 0.7379 (tmm) REVERT: G 89 THR cc_start: 0.9007 (OUTLIER) cc_final: 0.8754 (p) REVERT: G 201 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.7485 (pm20) REVERT: H 806 ASP cc_start: 0.8658 (t0) cc_final: 0.8163 (t0) REVERT: H 881 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8509 (mm) REVERT: H 1090 GLN cc_start: 0.5429 (OUTLIER) cc_final: 0.5117 (pt0) REVERT: H 1239 TYR cc_start: 0.7955 (t80) cc_final: 0.7611 (t80) REVERT: H 1385 MET cc_start: 0.8366 (mtm) cc_final: 0.8015 (mtm) REVERT: X 239 ASP cc_start: 0.6766 (t0) cc_final: 0.5142 (p0) REVERT: X 364 ASP cc_start: 0.7958 (p0) cc_final: 0.7546 (p0) REVERT: X 443 MET cc_start: 0.7038 (mmm) cc_final: 0.6620 (tpt) REVERT: X 458 GLU cc_start: 0.8574 (mp0) cc_final: 0.8297 (mp0) REVERT: X 460 ARG cc_start: 0.8765 (mtm-85) cc_final: 0.8193 (mtm-85) outliers start: 83 outliers final: 64 residues processed: 328 average time/residue: 0.2980 time to fit residues: 163.8283 Evaluate side-chains 331 residues out of total 3313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 259 time to evaluate : 2.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 19 ASP Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 113 CYS Chi-restraints excluded: chain J residue 328 THR Chi-restraints excluded: chain J residue 362 MET Chi-restraints excluded: chain J residue 384 LEU Chi-restraints excluded: chain J residue 409 VAL Chi-restraints excluded: chain J residue 442 GLN Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 201 GLU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain B residue 753 VAL Chi-restraints excluded: chain B residue 775 ASP Chi-restraints excluded: chain B residue 793 ILE Chi-restraints excluded: chain B residue 834 GLN Chi-restraints excluded: chain B residue 878 ILE Chi-restraints excluded: chain B residue 922 VAL Chi-restraints excluded: chain B residue 1226 PHE Chi-restraints excluded: chain B residue 1404 ASP Chi-restraints excluded: chain G residue 58 THR Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain G residue 137 VAL Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain G residue 176 LEU Chi-restraints excluded: chain G residue 201 GLU Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 278 VAL Chi-restraints excluded: chain G residue 280 LEU Chi-restraints excluded: chain G residue 284 VAL Chi-restraints excluded: chain G residue 401 THR Chi-restraints excluded: chain G residue 492 LEU Chi-restraints excluded: chain G residue 524 VAL Chi-restraints excluded: chain G residue 529 VAL Chi-restraints excluded: chain G residue 623 THR Chi-restraints excluded: chain H residue 754 GLU Chi-restraints excluded: chain H residue 775 ASP Chi-restraints excluded: chain H residue 793 ILE Chi-restraints excluded: chain H residue 881 LEU Chi-restraints excluded: chain H residue 922 VAL Chi-restraints excluded: chain H residue 1090 GLN Chi-restraints excluded: chain H residue 1167 VAL Chi-restraints excluded: chain H residue 1188 PHE Chi-restraints excluded: chain H residue 1368 THR Chi-restraints excluded: chain H residue 1387 THR Chi-restraints excluded: chain H residue 1396 LEU Chi-restraints excluded: chain H residue 1445 PHE Chi-restraints excluded: chain H residue 1447 VAL Chi-restraints excluded: chain H residue 1546 THR Chi-restraints excluded: chain H residue 1589 PHE Chi-restraints excluded: chain H residue 1596 LEU Chi-restraints excluded: chain X residue 328 THR Chi-restraints excluded: chain X residue 362 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 234 optimal weight: 3.9990 chunk 314 optimal weight: 5.9990 chunk 90 optimal weight: 2.9990 chunk 272 optimal weight: 1.9990 chunk 43 optimal weight: 7.9990 chunk 82 optimal weight: 7.9990 chunk 295 optimal weight: 9.9990 chunk 123 optimal weight: 4.9990 chunk 303 optimal weight: 20.0000 chunk 37 optimal weight: 8.9990 chunk 54 optimal weight: 0.8980 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1033 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.139692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.101415 restraints weight = 59808.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.097636 restraints weight = 40403.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.098918 restraints weight = 38745.332| |-----------------------------------------------------------------------------| r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.2549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 28796 Z= 0.314 Angle : 0.641 14.464 39206 Z= 0.322 Chirality : 0.045 0.179 4619 Planarity : 0.004 0.065 5035 Dihedral : 4.877 57.695 4097 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.71 % Favored : 96.21 % Rotamer: Outliers : 2.77 % Allowed : 19.13 % Favored : 78.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.55 % 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: 0.09 (0.14), residues: 3718 helix: 1.03 (0.18), residues: 880 sheet: 0.14 (0.16), residues: 1101 loop : -0.41 (0.16), residues: 1737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B1233 HIS 0.007 0.001 HIS C 84 PHE 0.018 0.002 PHE B1188 TYR 0.028 0.002 TYR H1260 ARG 0.004 0.000 ARG B1298 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4196.05 seconds wall clock time: 75 minutes 27.70 seconds (4527.70 seconds total)