Starting phenix.real_space_refine on Mon Dec 30 20:11:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ml1_23905/12_2024/7ml1_23905.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ml1_23905/12_2024/7ml1_23905.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ml1_23905/12_2024/7ml1_23905.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ml1_23905/12_2024/7ml1_23905.map" model { file = "/net/cci-nas-00/data/ceres_data/7ml1_23905/12_2024/7ml1_23905.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ml1_23905/12_2024/7ml1_23905.cif" } resolution = 4.0 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Fe 4 7.16 5 Zn 19 6.06 5 P 114 5.49 5 Mg 1 5.21 5 S 359 5.16 5 C 40326 2.51 5 N 11344 2.21 5 O 12371 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 100 residue(s): 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 64538 Number of models: 1 Model: "" Number of chains: 56 Chain: "1" Number of atoms: 380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 380 Classifications: {'peptide': 51} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 3, 'TRANS': 47} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "1" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 29 Classifications: {'peptide': 4} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'UNK:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "1" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 34 Classifications: {'peptide': 5} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'UNK:plan-1': 2} Unresolved non-hydrogen planarities: 2 Chain: "1" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 16 Classifications: {'peptide': 3} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'UNK:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "1" Number of atoms: 489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 489 Classifications: {'peptide': 66} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 4, 'TRANS': 61} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 36 Planarities with less than four sites: {'PHE:plan': 1, 'UNK:plan-1': 17, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "1" Number of atoms: 247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 247 Classifications: {'peptide': 41} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 1, 'TRANS': 39} Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'UNK:plan-1': 29} Unresolved non-hydrogen planarities: 29 Chain: "1" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 41 Classifications: {'peptide': 6} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 5} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'UNK:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "1" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 57 Classifications: {'peptide': 8} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 6} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'UNK:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "1" Number of atoms: 167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 167 Classifications: {'peptide': 24} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'TRANS': 23} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'UNK:plan-1': 8} Unresolved non-hydrogen planarities: 8 Chain: "1" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 22 Classifications: {'peptide': 3} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'UNK:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "1" Number of atoms: 299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 299 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'TRANS': 52} Chain breaks: 1 Unresolved non-hydrogen bonds: 82 Unresolved non-hydrogen angles: 123 Unresolved non-hydrogen dihedrals: 41 Planarities with less than four sites: {'UNK:plan-1': 41} Unresolved non-hydrogen planarities: 41 Chain: "1" Number of atoms: 630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 630 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 63} Link IDs: {'PTRANS': 2, 'TRANS': 100} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 209 Unresolved non-hydrogen angles: 268 Unresolved non-hydrogen dihedrals: 168 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 7, 'TYR:plan': 3, 'UNK:plan-1': 4, 'HIS:plan': 3, 'PHE:plan': 1, 'GLU:plan': 6, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 118 Chain: "4" Number of atoms: 506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 506 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 3, 'TRANS': 69} Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 36 Chain: "4" Number of atoms: 1535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1535 Classifications: {'peptide': 211} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 8, 'TRANS': 202} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 104 Unresolved non-hydrogen angles: 130 Unresolved non-hydrogen dihedrals: 84 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'ASN:plan1': 1, 'TYR:plan': 1, 'UNK:plan-1': 2, 'ASP:plan': 3, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 48 Chain: "0" Number of atoms: 6108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 754, 6108 Classifications: {'peptide': 754} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 721} Chain: "6" Number of atoms: 2264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2264 Classifications: {'peptide': 305} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 19, 'TRANS': 285} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 143 Unresolved non-hydrogen angles: 180 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'PHE:plan': 5, 'GLU:plan': 4, 'ARG:plan': 3, 'TYR:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 77 Chain: "6" Number of atoms: 263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 263 Classifications: {'peptide': 46} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 1, 'TRANS': 44} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 99 Unresolved non-hydrogen angles: 131 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'TYR:plan': 1, 'UNK:plan-1': 13, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 63 Chain: "2" Number of atoms: 3011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3011 Classifications: {'peptide': 460} Incomplete info: {'backbone_only': 154, 'truncation_to_alanine': 14} Link IDs: {'CIS': 2, 'PTRANS': 17, 'TRANS': 440} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 727 Unresolved non-hydrogen angles: 1042 Unresolved non-hydrogen dihedrals: 468 Unresolved non-hydrogen chiralities: 210 Planarities with less than four sites: {'GLN:plan1': 11, 'ARG:plan': 3, 'TYR:plan': 5, 'ASN:plan1': 11, 'TRP:plan': 2, 'ASP:plan': 12, 'PHE:plan': 8, 'GLU:plan': 16, 'HIS:plan': 4} Unresolved non-hydrogen planarities: 352 Chain: "5" Number of atoms: 498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 498 Classifications: {'peptide': 66} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 3, 'TRANS': 62} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "7" Number of atoms: 4447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 634, 4447 Classifications: {'peptide': 634} Incomplete info: {'backbone_only': 162} Link IDs: {'CIS': 3, 'PTRANS': 26, 'TRANS': 604} Chain breaks: 1 Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 688 Unresolved non-hydrogen angles: 1003 Unresolved non-hydrogen dihedrals: 436 Unresolved non-hydrogen chiralities: 214 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 14, 'TYR:plan': 6, 'ASN:plan1': 3, 'TRP:plan': 1, 'HIS:plan': 6, 'PHE:plan': 7, 'GLU:plan': 8, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 312 Chain: "3" Number of atoms: 860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 860 Classifications: {'peptide': 138} Incomplete info: {'truncation_to_alanine': 79} Link IDs: {'PTRANS': 5, 'TRANS': 132} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 298 Unresolved non-hydrogen angles: 379 Unresolved non-hydrogen dihedrals: 241 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'TYR:plan': 5, 'ASN:plan1': 6, 'ASP:plan': 10, 'PHE:plan': 3, 'GLU:plan': 12, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 178 Chain: "O" Number of atoms: 1416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1416 Classifications: {'peptide': 180} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 171} Chain: "N" Number of atoms: 1178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 1178 Classifications: {'DNA': 57} Link IDs: {'rna3p': 56} Chain: "T" Number of atoms: 1159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 1159 Classifications: {'DNA': 57} Link IDs: {'rna3p': 56} Chain: "A" Number of atoms: 10997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1398, 10997 Classifications: {'peptide': 1398} Link IDs: {'PCIS': 2, 'PTRANS': 62, 'TRANS': 1333} Chain breaks: 5 Chain: "B" Number of atoms: 9132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1147, 9132 Classifications: {'peptide': 1147} Link IDs: {'PTRANS': 51, 'TRANS': 1095} Chain breaks: 6 Chain: "C" Number of atoms: 2061 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2061 Classifications: {'peptide': 262} Link IDs: {'PTRANS': 11, 'TRANS': 250} Chain: "D" Number of atoms: 1253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1253 Classifications: {'peptide': 157} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Chain breaks: 1 Chain: "E" Number of atoms: 1744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1744 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 200} Chain: "F" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 670 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 6, 'TRANS': 76} Chain: "G" Number of atoms: 1340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1340 Classifications: {'peptide': 171} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 162} Chain: "H" Number of atoms: 1089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1089 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 131} Chain breaks: 1 Chain: "I" Number of atoms: 944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 944 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 5, 'TRANS': 110} Chain: "J" Number of atoms: 532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 532 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "K" Number of atoms: 904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 904 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 5, 'TRANS': 106} Chain: "L" Number of atoms: 358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 358 Classifications: {'peptide': 45} Link IDs: {'TRANS': 44} Chain: "M" Number of atoms: 2175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2175 Classifications: {'peptide': 279} Link IDs: {'PTRANS': 10, 'TRANS': 268} Chain breaks: 2 Chain: "Q" Number of atoms: 1144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1144 Classifications: {'peptide': 148} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 141} Chain breaks: 3 Unresolved non-hydrogen bonds: 126 Unresolved non-hydrogen angles: 151 Unresolved non-hydrogen dihedrals: 105 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 9, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 77 Chain: "R" Number of atoms: 1303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1303 Classifications: {'peptide': 190} Incomplete info: {'truncation_to_alanine': 72} Link IDs: {'PTRANS': 7, 'TRANS': 182} Chain breaks: 6 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 293 Unresolved non-hydrogen angles: 371 Unresolved non-hydrogen dihedrals: 253 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 6, 'TYR:plan': 6, 'ASN:plan1': 3, 'TRP:plan': 1, 'HIS:plan': 2, 'PHE:plan': 3, 'GLU:plan': 6, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 158 Chain: "U" Number of atoms: 366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 366 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'TRANS': 43} Chain: "V" Number of atoms: 389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 389 Classifications: {'peptide': 50} Link IDs: {'TRANS': 49} Chain breaks: 1 Chain: "W" Number of atoms: 1469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1469 Classifications: {'peptide': 191} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 8, 'TRANS': 182} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 97 Unresolved non-hydrogen angles: 125 Unresolved non-hydrogen dihedrals: 85 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 4, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 58 Chain: "X" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 984 Classifications: {'peptide': 156} Incomplete info: {'truncation_to_alanine': 85} Link IDs: {'PTRANS': 7, 'TRANS': 148} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 321 Unresolved non-hydrogen angles: 405 Unresolved non-hydrogen dihedrals: 277 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 3, 'TYR:plan': 5, 'ASN:plan1': 2, 'TRP:plan': 2, 'ASP:plan': 8, 'PHE:plan': 2, 'GLU:plan': 6, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 148 Chain: "4" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "0" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "6" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' ZN': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "3" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 1, ' ZN': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "X" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4247 SG CYS 4 289 203.914 22.560 97.653 1.00 0.00 S ATOM 4266 SG CYS 4 292 206.052 23.878 100.475 1.00 0.00 S ATOM 4351 SG CYS 4 305 206.346 20.223 99.044 1.00 0.00 S ATOM 4367 SG CYS 4 308 203.623 21.387 101.429 1.00 0.00 S ATOM 5390 SG CYS 0 115 139.705 24.410 122.969 1.00117.61 S ATOM 5717 SG CYS 0 156 136.566 20.494 124.186 1.00 90.79 S ATOM 5532 SG CYS 0 133 136.955 22.844 127.098 1.00 46.59 S ATOM 5717 SG CYS 0 156 136.566 20.494 124.186 1.00 90.79 S ATOM 12773 SG CYS 6 403 218.660 48.410 117.176 1.00 0.00 S ATOM 12795 SG CYS 6 406 219.511 51.724 115.721 1.00 0.00 S ATOM 12963 SG CYS 6 437 215.876 50.959 116.774 1.00 0.00 S ATOM 12979 SG CYS 6 440 217.128 49.445 113.712 1.00 0.00 S ATOM 12921 SG CYS 6 429 213.099 37.214 116.773 1.00 0.00 S ATOM 12937 SG CYS 6 432 216.763 37.702 117.597 1.00 0.00 S ATOM 13057 SG CYS 6 451 215.474 38.843 114.307 1.00 0.00 S ATOM 13072 SG CYS 6 454 215.563 35.112 114.869 1.00 0.00 S ATOM 12418 SG CYS 6 349 202.700 31.849 77.560 1.00 0.00 S ATOM 12439 SG CYS 6 352 201.597 32.634 74.246 1.00 0.00 S ATOM 12508 SG CYS 6 363 198.927 32.568 77.077 1.00 0.00 S ATOM 12526 SG CYS 6 366 200.197 29.396 76.039 1.00 0.00 S ATOM 12335 SG CYS 6 336 200.122 44.164 72.433 1.00 30.00 S ATOM 12346 SG CYS 6 338 199.583 42.077 75.577 1.00 30.00 S ATOM 12473 SG CYS 6 357 202.238 44.926 75.601 1.00 30.00 S ATOM 21074 SG CYS 3 13 101.915 61.143 124.785 1.00 0.00 S ATOM 21268 SG CYS 3 39 102.005 62.574 125.879 1.00 0.00 S ATOM 21221 SG CYS 3 34 95.428 53.443 131.002 1.00 0.00 S ATOM 21417 SG CYS 3 59 94.875 50.891 126.832 1.00 0.00 S ATOM 26469 SG CYS A 107 117.277 105.265 120.803 1.00 0.00 S ATOM 26493 SG CYS A 110 116.761 102.957 123.731 1.00 0.00 S ATOM 26798 SG CYS A 148 119.107 105.858 124.067 1.00 0.00 S ATOM 26867 SG CYS A 167 120.027 102.815 121.914 1.00 0.00 S ATOM 26164 SG CYS A 67 69.735 98.271 119.173 1.00 0.00 S ATOM 26186 SG CYS A 70 69.608 99.443 122.722 1.00 0.00 S ATOM 26239 SG CYS A 77 69.268 101.924 120.003 1.00 0.00 S ATOM 45303 SG CYS B1163 81.304 100.442 133.481 1.00 0.00 S ATOM 45321 SG CYS B1166 83.152 101.642 130.101 1.00 0.00 S ATOM 45446 SG CYS B1182 80.874 98.665 130.298 1.00 0.00 S ATOM 45465 SG CYS B1185 84.263 98.610 131.955 1.00 0.00 S ATOM 46432 SG CYS C 86 14.977 138.418 109.162 1.00 0.00 S ATOM 46449 SG CYS C 88 16.354 135.086 107.664 1.00 0.00 S ATOM 46482 SG CYS C 92 13.439 136.878 106.162 1.00 0.00 S ATOM 46505 SG CYS C 95 17.085 138.266 105.924 1.00 0.00 S ATOM 53995 SG CYS I 7 134.144 153.045 74.636 1.00 0.00 S ATOM 54020 SG CYS I 10 133.195 149.129 74.468 1.00 0.00 S ATOM 54186 SG CYS I 29 134.112 150.784 77.758 1.00 0.00 S ATOM 54210 SG CYS I 32 136.574 150.526 74.685 1.00 0.00 S ATOM 54537 SG CYS I 75 105.791 186.129 82.266 1.00 0.00 S ATOM 54559 SG CYS I 78 104.551 188.807 79.835 1.00 0.00 S ATOM 54775 SG CYS I 103 104.341 185.193 78.884 1.00 0.00 S ATOM 54795 SG CYS I 106 107.731 186.813 79.068 1.00 0.00 S ATOM 54940 SG CYS J 7 37.005 160.225 99.257 1.00 0.00 S ATOM 54963 SG CYS J 10 33.648 161.980 100.169 1.00 0.00 S ATOM 55243 SG CYS J 45 36.780 164.023 100.356 1.00 0.00 S ATOM 55249 SG CYS J 46 35.287 162.891 97.131 1.00 0.00 S ATOM 56372 SG CYS L 31 43.151 125.472 72.632 1.00 0.00 S ATOM 56392 SG CYS L 34 39.762 125.914 70.097 1.00 0.00 S ATOM 56496 SG CYS L 48 41.145 122.742 71.359 1.00 0.00 S ATOM 56519 SG CYS L 51 43.092 124.829 68.920 1.00 0.00 S ATOM 56747 SG CYS M 24 44.409 102.570 122.965 1.00 0.00 S ATOM 56769 SG CYS M 27 40.773 102.281 122.884 1.00 0.00 S ATOM 56913 SG CYS M 45 42.397 104.793 120.535 1.00 0.00 S ATOM 56932 SG CYS M 48 42.672 105.599 124.160 1.00 0.00 S ATOM 62958 SG CYS W 124 66.174 80.590 118.931 1.00 0.00 S ATOM 62979 SG CYS W 127 69.097 82.856 118.694 1.00 0.00 S ATOM 63164 SG CYS W 149 66.893 83.212 121.642 1.00 0.00 S ATOM 63184 SG CYS W 152 65.509 84.365 118.360 1.00 0.00 S Residues with excluded nonbonded symmetry interactions: 8 residue: pdb=" P DA N 52 " occ=0.00 ... (19 atoms not shown) pdb=" C4 DA N 52 " occ=0.00 residue: pdb=" P DA N 54 " occ=0.00 ... (19 atoms not shown) pdb=" C4 DA N 54 " occ=0.00 residue: pdb=" P DA N 56 " occ=0.00 ... (19 atoms not shown) pdb=" C4 DA N 56 " occ=0.00 residue: pdb=" P DA N 58 " occ=0.00 ... (19 atoms not shown) pdb=" C4 DA N 58 " occ=0.00 residue: pdb=" P DT T 108 " occ=0.00 ... (18 atoms not shown) pdb=" C6 DT T 108 " occ=0.00 residue: pdb=" P DT T 110 " occ=0.00 ... (18 atoms not shown) pdb=" C6 DT T 110 " occ=0.00 residue: pdb=" P DT T 112 " occ=0.00 ... (18 atoms not shown) pdb=" C6 DT T 112 " occ=0.00 residue: pdb=" P DT T 114 " occ=0.00 ... (18 atoms not shown) pdb=" C6 DT T 114 " occ=0.00 Time building chain proxies: 24.78, per 1000 atoms: 0.38 Number of scatterers: 64538 At special positions: 0 Unit cell: (259.7, 209.88, 188.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 19 29.99 Fe 4 26.01 S 359 16.00 P 114 15.00 Mg 1 11.99 O 12371 8.00 N 11344 7.00 C 40326 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied TRANS " UNK 1 219 " - " ARG 1 218 " " UNK 1 223 " - " LEU 1 222 " " UNK 1 228 " - " LYS 1 227 " " UNK 1 231 " - " PRO 1 230 " " UNK 1 297 " - " LEU 1 296 " " UNK 1 338 " - " ILE 1 337 " " UNK 1 344 " - " ILE 1 343 " " UNK 1 352 " - " GLY 1 351 " " UNK 1 388 " - " MET 1 387 " " UNK 1 391 " - " LYS 1 390 " " UNK 1 515 " - " ALA 1 514 " " UNK 6 412 " - " PRO 6 411 " Time building additional restraints: 12.41 Conformation dependent library (CDL) restraints added in 6.2 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 0 801 " pdb="FE3 SF4 0 801 " - pdb=" SG CYS 0 133 " pdb="FE1 SF4 0 801 " - pdb=" SG CYS 0 115 " pdb="FE2 SF4 0 801 " - pdb=" SG CYS 0 156 " Number of angles added : 9 Zn2+ tetrahedral coordination pdb=" ZN 3 401 " pdb="ZN ZN 3 401 " - pdb=" SG CYS 3 39 " pdb="ZN ZN 3 401 " - pdb=" SG CYS 3 13 " pdb=" ZN 3 402 " pdb="ZN ZN 3 402 " - pdb=" SG CYS 3 34 " pdb="ZN ZN 3 402 " - pdb=" NE2 HIS 3 36 " pdb="ZN ZN 3 402 " - pdb=" SG CYS 3 59 " pdb=" ZN 4 401 " pdb="ZN ZN 4 401 " - pdb=" SG CYS 4 305 " pdb="ZN ZN 4 401 " - pdb=" SG CYS 4 308 " pdb="ZN ZN 4 401 " - pdb=" SG CYS 4 292 " pdb="ZN ZN 4 401 " - pdb=" SG CYS 4 289 " pdb=" ZN 6 501 " pdb="ZN ZN 6 501 " - pdb=" SG CYS 6 437 " pdb="ZN ZN 6 501 " - pdb=" SG CYS 6 406 " pdb="ZN ZN 6 501 " - pdb=" SG CYS 6 403 " pdb="ZN ZN 6 501 " - pdb=" SG CYS 6 440 " pdb=" ZN 6 502 " pdb="ZN ZN 6 502 " - pdb=" SG CYS 6 451 " pdb="ZN ZN 6 502 " - pdb=" SG CYS 6 429 " pdb="ZN ZN 6 502 " - pdb=" SG CYS 6 432 " pdb="ZN ZN 6 502 " - pdb=" SG CYS 6 454 " pdb=" ZN 6 503 " pdb="ZN ZN 6 503 " - pdb=" SG CYS 6 349 " pdb="ZN ZN 6 503 " - pdb=" SG CYS 6 363 " pdb="ZN ZN 6 503 " - pdb=" SG CYS 6 366 " pdb="ZN ZN 6 503 " - pdb=" SG CYS 6 352 " pdb=" ZN 6 504 " pdb="ZN ZN 6 504 " - pdb=" ND1 HIS 6 339 " pdb="ZN ZN 6 504 " - pdb=" SG CYS 6 336 " pdb="ZN ZN 6 504 " - pdb=" SG CYS 6 338 " pdb="ZN ZN 6 504 " - pdb=" SG CYS 6 357 " pdb=" ZN A1801 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 110 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 107 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 148 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 167 " pdb=" ZN A1802 " pdb="ZN ZN A1802 " - pdb=" NE2 HIS A 80 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 70 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 67 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 77 " pdb=" ZN B1301 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1182 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1185 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1163 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1166 " pdb=" ZN C 401 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 92 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 88 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 95 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 86 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 32 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 7 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 10 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 29 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 103 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 106 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 78 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 75 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 46 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 48 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 51 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 31 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 34 " pdb=" ZN M 401 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 24 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 45 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 48 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 27 " pdb=" ZN W 501 " pdb="ZN ZN W 501 " - pdb=" SG CYS W 149 " pdb="ZN ZN W 501 " - pdb=" SG CYS W 127 " pdb="ZN ZN W 501 " - pdb=" SG CYS W 124 " pdb="ZN ZN W 501 " - pdb=" SG CYS W 152 " Number of angles added : 84 15856 Ramachandran restraints generated. 7928 Oldfield, 0 Emsley, 7928 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14946 Finding SS restraints... Secondary structure from input PDB file: 327 helices and 83 sheets defined 45.7% alpha, 12.9% beta 38 base pairs and 76 stacking pairs defined. Time for finding SS restraints: 18.75 Creating SS restraints... Processing helix chain '1' and resid 170 through 177 Processing helix chain '1' and resid 177 through 188 Processing helix chain '1' and resid 188 through 199 removed outlier: 3.538A pdb=" N MET 1 192 " --> pdb=" O ASN 1 188 " (cutoff:3.500A) Processing helix chain '1' and resid 205 through 225 removed outlier: 3.702A pdb=" N ARG 1 213 " --> pdb=" O PHE 1 209 " (cutoff:3.500A) Proline residue: 1 215 - end of helix Processing helix chain '1' and resid 231 through 236 Processing helix chain '1' and resid 251 through 263 Processing helix chain '1' and resid 263 through 273 Processing helix chain '1' and resid 279 through 295 removed outlier: 3.789A pdb=" N ALA 1 285 " --> pdb=" O PRO 1 281 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N SER 1 289 " --> pdb=" O ALA 1 285 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU 1 292 " --> pdb=" O PHE 1 288 " (cutoff:3.500A) Processing helix chain '1' and resid 309 through 329 removed outlier: 3.746A pdb=" N UNK 1 320 " --> pdb=" O UNK 1 316 " (cutoff:3.500A) Processing helix chain '1' and resid 338 through 343 removed outlier: 3.522A pdb=" N ASN 1 342 " --> pdb=" O UNK 1 338 " (cutoff:3.500A) Processing helix chain '1' and resid 371 through 388 Processing helix chain '1' and resid 467 through 483 Processing helix chain '1' and resid 496 through 516 removed outlier: 3.804A pdb=" N ILE 1 509 " --> pdb=" O THR 1 505 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N ASN 1 510 " --> pdb=" O UNK 1 506 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA 1 514 " --> pdb=" O ASN 1 510 " (cutoff:3.500A) Processing helix chain '1' and resid 540 through 567 removed outlier: 3.621A pdb=" N THR 1 556 " --> pdb=" O MET 1 552 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU 1 561 " --> pdb=" O CYS 1 557 " (cutoff:3.500A) Processing helix chain '1' and resid 575 through 604 Processing helix chain '1' and resid 606 through 639 removed outlier: 3.559A pdb=" N TYR 1 615 " --> pdb=" O THR 1 611 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU 1 616 " --> pdb=" O CYS 1 612 " (cutoff:3.500A) Proline residue: 1 618 - end of helix Processing helix chain '4' and resid 33 through 43 Processing helix chain '4' and resid 49 through 68 removed outlier: 3.598A pdb=" N VAL 4 53 " --> pdb=" O SER 4 49 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N VAL 4 59 " --> pdb=" O GLU 4 55 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N HIS 4 64 " --> pdb=" O PHE 4 60 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N LEU 4 65 " --> pdb=" O LEU 4 61 " (cutoff:3.500A) Processing helix chain '4' and resid 116 through 135 removed outlier: 4.033A pdb=" N ASN 4 120 " --> pdb=" O ARG 4 116 " (cutoff:3.500A) Processing helix chain '4' and resid 137 through 143 removed outlier: 3.820A pdb=" N ASN 4 143 " --> pdb=" O GLN 4 139 " (cutoff:3.500A) Processing helix chain '4' and resid 148 through 167 removed outlier: 3.646A pdb=" N SER 4 154 " --> pdb=" O ALA 4 150 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N LEU 4 157 " --> pdb=" O MET 4 153 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N THR 4 158 " --> pdb=" O SER 4 154 " (cutoff:3.500A) Processing helix chain '4' and resid 192 through 207 removed outlier: 3.537A pdb=" N ASN 4 198 " --> pdb=" O ILE 4 194 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N PHE 4 201 " --> pdb=" O MET 4 197 " (cutoff:3.500A) Processing helix chain '4' and resid 221 through 231 Processing helix chain '4' and resid 244 through 252 Processing helix chain '4' and resid 313 through 321 Processing helix chain '0' and resid 18 through 34 Processing helix chain '0' and resid 47 through 63 removed outlier: 3.837A pdb=" N SER 0 51 " --> pdb=" O GLY 0 47 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LEU 0 55 " --> pdb=" O SER 0 51 " (cutoff:3.500A) Processing helix chain '0' and resid 75 through 98 Processing helix chain '0' and resid 117 through 123 Processing helix chain '0' and resid 125 through 137 Processing helix chain '0' and resid 138 through 147 removed outlier: 3.783A pdb=" N ARG 0 143 " --> pdb=" O GLY 0 139 " (cutoff:3.500A) Processing helix chain '0' and resid 157 through 165 Processing helix chain '0' and resid 177 through 188 Processing helix chain '0' and resid 191 through 199 Processing helix chain '0' and resid 200 through 202 No H-bonds generated for 'chain '0' and resid 200 through 202' Processing helix chain '0' and resid 210 through 215 Processing helix chain '0' and resid 223 through 228 Processing helix chain '0' and resid 237 through 239 No H-bonds generated for 'chain '0' and resid 237 through 239' Processing helix chain '0' and resid 240 through 248 Processing helix chain '0' and resid 253 through 279 Processing helix chain '0' and resid 279 through 292 removed outlier: 3.665A pdb=" N GLY 0 292 " --> pdb=" O LYS 0 288 " (cutoff:3.500A) Processing helix chain '0' and resid 294 through 299 removed outlier: 3.660A pdb=" N LEU 0 299 " --> pdb=" O SER 0 295 " (cutoff:3.500A) Processing helix chain '0' and resid 322 through 326 removed outlier: 3.864A pdb=" N ARG 0 326 " --> pdb=" O GLY 0 323 " (cutoff:3.500A) Processing helix chain '0' and resid 327 through 347 removed outlier: 3.507A pdb=" N GLU 0 340 " --> pdb=" O LYS 0 336 " (cutoff:3.500A) Processing helix chain '0' and resid 355 through 367 Processing helix chain '0' and resid 370 through 375 Processing helix chain '0' and resid 375 through 389 removed outlier: 4.565A pdb=" N GLU 0 379 " --> pdb=" O ARG 0 375 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG 0 386 " --> pdb=" O SER 0 382 " (cutoff:3.500A) Processing helix chain '0' and resid 393 through 412 removed outlier: 4.450A pdb=" N ALA 0 398 " --> pdb=" O GLU 0 394 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N LEU 0 399 " --> pdb=" O ASP 0 395 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASP 0 401 " --> pdb=" O THR 0 397 " (cutoff:3.500A) Processing helix chain '0' and resid 424 through 428 Processing helix chain '0' and resid 442 through 453 Proline residue: 0 448 - end of helix removed outlier: 3.618A pdb=" N PHE 0 453 " --> pdb=" O VAL 0 449 " (cutoff:3.500A) Processing helix chain '0' and resid 467 through 474 Processing helix chain '0' and resid 515 through 533 removed outlier: 3.970A pdb=" N ASN 0 521 " --> pdb=" O SER 0 517 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLU 0 528 " --> pdb=" O SER 0 524 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N PHE 0 529 " --> pdb=" O MET 0 525 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA 0 530 " --> pdb=" O LEU 0 526 " (cutoff:3.500A) Processing helix chain '0' and resid 543 through 557 removed outlier: 4.264A pdb=" N MET 0 553 " --> pdb=" O SER 0 549 " (cutoff:3.500A) Processing helix chain '0' and resid 558 through 567 removed outlier: 4.307A pdb=" N GLU 0 562 " --> pdb=" O GLY 0 558 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N VAL 0 563 " --> pdb=" O ILE 0 559 " (cutoff:3.500A) Processing helix chain '0' and resid 575 through 592 Processing helix chain '0' and resid 605 through 610 removed outlier: 3.517A pdb=" N GLY 0 609 " --> pdb=" O LYS 0 605 " (cutoff:3.500A) Processing helix chain '0' and resid 633 through 646 Processing helix chain '0' and resid 649 through 667 Processing helix chain '0' and resid 668 through 670 No H-bonds generated for 'chain '0' and resid 668 through 670' Processing helix chain '0' and resid 683 through 691 removed outlier: 3.533A pdb=" N SER 0 687 " --> pdb=" O ARG 0 684 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG 0 690 " --> pdb=" O SER 0 687 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N SER 0 691 " --> pdb=" O ARG 0 688 " (cutoff:3.500A) Processing helix chain '0' and resid 694 through 701 Processing helix chain '0' and resid 702 through 706 Processing helix chain '0' and resid 709 through 726 removed outlier: 3.795A pdb=" N ARG 0 722 " --> pdb=" O LYS 0 718 " (cutoff:3.500A) Processing helix chain '0' and resid 733 through 739 removed outlier: 3.725A pdb=" N SER 0 737 " --> pdb=" O GLN 0 733 " (cutoff:3.500A) Processing helix chain '0' and resid 743 through 752 removed outlier: 3.504A pdb=" N SER 0 750 " --> pdb=" O LYS 0 746 " (cutoff:3.500A) Processing helix chain '6' and resid 133 through 138 removed outlier: 3.524A pdb=" N GLU 6 138 " --> pdb=" O GLU 6 134 " (cutoff:3.500A) Processing helix chain '6' and resid 144 through 164 removed outlier: 3.578A pdb=" N MET 6 148 " --> pdb=" O ASN 6 144 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASP 6 155 " --> pdb=" O GLN 6 151 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N PHE 6 156 " --> pdb=" O TYR 6 152 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL 6 157 " --> pdb=" O ALA 6 153 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N HIS 6 158 " --> pdb=" O ILE 6 154 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU 6 159 " --> pdb=" O ASP 6 155 " (cutoff:3.500A) Processing helix chain '6' and resid 188 through 202 removed outlier: 4.067A pdb=" N HIS 6 192 " --> pdb=" O ASN 6 188 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS 6 197 " --> pdb=" O ILE 6 193 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N SER 6 198 " --> pdb=" O ASP 6 194 " (cutoff:3.500A) Processing helix chain '6' and resid 209 through 221 Processing helix chain '6' and resid 246 through 257 Processing helix chain '6' and resid 270 through 281 Processing helix chain '6' and resid 293 through 305 removed outlier: 3.815A pdb=" N LEU 6 300 " --> pdb=" O HIS 6 296 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE 6 301 " --> pdb=" O LEU 6 297 " (cutoff:3.500A) Processing helix chain '6' and resid 373 through 384 removed outlier: 3.672A pdb=" N ALA 6 377 " --> pdb=" O SER 6 373 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N SER 6 379 " --> pdb=" O HIS 6 375 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N TYR 6 380 " --> pdb=" O LEU 6 376 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N HIS 6 381 " --> pdb=" O ALA 6 377 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N HIS 6 382 " --> pdb=" O ARG 6 378 " (cutoff:3.500A) Processing helix chain '6' and resid 418 through 423 removed outlier: 4.449A pdb=" N UNK 6 423 " --> pdb=" O UNK 6 419 " (cutoff:3.500A) Processing helix chain '6' and resid 437 through 447 Processing helix chain '6' and resid 451 through 456 Processing helix chain '2' and resid 9 through 17 removed outlier: 3.600A pdb=" N TYR 2 13 " --> pdb=" O SER 2 9 " (cutoff:3.500A) Processing helix chain '2' and resid 18 through 27 Processing helix chain '2' and resid 28 through 37 removed outlier: 3.690A pdb=" N TYR 2 36 " --> pdb=" O CYS 2 32 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ARG 2 37 " --> pdb=" O LEU 2 33 " (cutoff:3.500A) Processing helix chain '2' and resid 40 through 53 removed outlier: 3.612A pdb=" N MET 2 50 " --> pdb=" O PHE 2 46 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N PHE 2 52 " --> pdb=" O MET 2 48 " (cutoff:3.500A) Processing helix chain '2' and resid 59 through 66 removed outlier: 3.569A pdb=" N VAL 2 66 " --> pdb=" O LEU 2 62 " (cutoff:3.500A) Processing helix chain '2' and resid 70 through 85 removed outlier: 3.918A pdb=" N PHE 2 74 " --> pdb=" O GLY 2 70 " (cutoff:3.500A) Processing helix chain '2' and resid 101 through 113 removed outlier: 3.978A pdb=" N ALA 2 111 " --> pdb=" O SER 2 107 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N THR 2 113 " --> pdb=" O ARG 2 109 " (cutoff:3.500A) Processing helix chain '2' and resid 117 through 122 Processing helix chain '2' and resid 136 through 152 Processing helix chain '2' and resid 160 through 171 Processing helix chain '2' and resid 185 through 194 Processing helix chain '2' and resid 196 through 211 Processing helix chain '2' and resid 217 through 231 removed outlier: 3.791A pdb=" N LEU 2 231 " --> pdb=" O MET 2 227 " (cutoff:3.500A) Processing helix chain '2' and resid 243 through 256 Processing helix chain '2' and resid 262 through 266 removed outlier: 3.797A pdb=" N ASP 2 266 " --> pdb=" O HIS 2 263 " (cutoff:3.500A) Processing helix chain '2' and resid 272 through 281 removed outlier: 4.382A pdb=" N LEU 2 276 " --> pdb=" O THR 2 272 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU 2 278 " --> pdb=" O LEU 2 274 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N THR 2 279 " --> pdb=" O ALA 2 275 " (cutoff:3.500A) Processing helix chain '2' and resid 353 through 361 removed outlier: 3.623A pdb=" N VAL 2 359 " --> pdb=" O LEU 2 355 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N LEU 2 360 " --> pdb=" O GLN 2 356 " (cutoff:3.500A) Processing helix chain '2' and resid 362 through 364 No H-bonds generated for 'chain '2' and resid 362 through 364' Processing helix chain '2' and resid 383 through 389 Processing helix chain '2' and resid 394 through 403 removed outlier: 4.200A pdb=" N ALA 2 398 " --> pdb=" O ASP 2 394 " (cutoff:3.500A) Processing helix chain '2' and resid 404 through 407 Processing helix chain '2' and resid 408 through 417 Processing helix chain '2' and resid 434 through 443 Processing helix chain '2' and resid 444 through 448 removed outlier: 3.598A pdb=" N GLU 2 447 " --> pdb=" O TRP 2 444 " (cutoff:3.500A) Processing helix chain '2' and resid 464 through 479 Processing helix chain '2' and resid 495 through 503 removed outlier: 4.047A pdb=" N SER 2 499 " --> pdb=" O LYS 2 495 " (cutoff:3.500A) Processing helix chain '5' and resid 14 through 27 removed outlier: 4.266A pdb=" N GLN 5 22 " --> pdb=" O ALA 5 18 " (cutoff:3.500A) Processing helix chain '5' and resid 43 through 46 Processing helix chain '5' and resid 47 through 60 removed outlier: 4.333A pdb=" N LYS 5 51 " --> pdb=" O VAL 5 47 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLU 5 53 " --> pdb=" O PHE 5 49 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASN 5 55 " --> pdb=" O LYS 5 51 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU 5 58 " --> pdb=" O LEU 5 54 " (cutoff:3.500A) Processing helix chain '7' and resid 124 through 128 removed outlier: 3.655A pdb=" N HIS 7 127 " --> pdb=" O ARG 7 124 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ALA 7 128 " --> pdb=" O PRO 7 125 " (cutoff:3.500A) No H-bonds generated for 'chain '7' and resid 124 through 128' Processing helix chain '7' and resid 149 through 161 removed outlier: 3.637A pdb=" N THR 7 159 " --> pdb=" O ASP 7 155 " (cutoff:3.500A) Processing helix chain '7' and resid 176 through 187 Processing helix chain '7' and resid 189 through 201 removed outlier: 3.887A pdb=" N ILE 7 193 " --> pdb=" O GLU 7 189 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LEU 7 197 " --> pdb=" O ILE 7 193 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASP 7 198 " --> pdb=" O ILE 7 194 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N LEU 7 200 " --> pdb=" O VAL 7 196 " (cutoff:3.500A) Processing helix chain '7' and resid 206 through 218 Processing helix chain '7' and resid 238 through 247 Processing helix chain '7' and resid 251 through 255 removed outlier: 3.773A pdb=" N LEU 7 254 " --> pdb=" O ILE 7 251 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ARG 7 255 " --> pdb=" O GLY 7 252 " (cutoff:3.500A) No H-bonds generated for 'chain '7' and resid 251 through 255' Processing helix chain '7' and resid 262 through 268 Processing helix chain '7' and resid 322 through 334 removed outlier: 4.219A pdb=" N VAL 7 326 " --> pdb=" O SER 7 322 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG 7 329 " --> pdb=" O VAL 7 325 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N CYS 7 330 " --> pdb=" O VAL 7 326 " (cutoff:3.500A) Processing helix chain '7' and resid 342 through 346 Processing helix chain '7' and resid 365 through 375 removed outlier: 3.786A pdb=" N SER 7 371 " --> pdb=" O GLU 7 367 " (cutoff:3.500A) Processing helix chain '7' and resid 391 through 404 Processing helix chain '7' and resid 413 through 426 removed outlier: 4.025A pdb=" N GLN 7 419 " --> pdb=" O VAL 7 415 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLN 7 423 " --> pdb=" O GLN 7 419 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N PHE 7 424 " --> pdb=" O TRP 7 420 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LEU 7 425 " --> pdb=" O ARG 7 421 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N GLN 7 426 " --> pdb=" O GLN 7 422 " (cutoff:3.500A) Processing helix chain '7' and resid 457 through 461 Processing helix chain '7' and resid 470 through 480 removed outlier: 3.687A pdb=" N MET 7 474 " --> pdb=" O SER 7 470 " (cutoff:3.500A) Processing helix chain '7' and resid 490 through 493 Processing helix chain '7' and resid 494 through 502 removed outlier: 3.535A pdb=" N PHE 7 498 " --> pdb=" O PRO 7 494 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG 7 500 " --> pdb=" O ALA 7 496 " (cutoff:3.500A) Processing helix chain '7' and resid 526 through 530 removed outlier: 3.612A pdb=" N LEU 7 530 " --> pdb=" O LEU 7 527 " (cutoff:3.500A) Processing helix chain '7' and resid 562 through 572 Processing helix chain '7' and resid 576 through 582 removed outlier: 3.527A pdb=" N LEU 7 580 " --> pdb=" O LYS 7 576 " (cutoff:3.500A) Processing helix chain '7' and resid 584 through 602 Processing helix chain '7' and resid 612 through 623 removed outlier: 4.088A pdb=" N LYS 7 621 " --> pdb=" O GLU 7 617 " (cutoff:3.500A) Processing helix chain '7' and resid 632 through 642 removed outlier: 3.904A pdb=" N ARG 7 636 " --> pdb=" O PRO 7 632 " (cutoff:3.500A) Processing helix chain '7' and resid 679 through 691 removed outlier: 4.466A pdb=" N GLY 7 688 " --> pdb=" O ALA 7 684 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG 7 689 " --> pdb=" O GLN 7 685 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N LEU 7 691 " --> pdb=" O LEU 7 687 " (cutoff:3.500A) Processing helix chain '7' and resid 713 through 729 removed outlier: 4.307A pdb=" N TYR 7 717 " --> pdb=" O THR 7 713 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N TYR 7 718 " --> pdb=" O GLN 7 714 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLN 7 729 " --> pdb=" O PHE 7 725 " (cutoff:3.500A) Processing helix chain '7' and resid 754 through 759 Processing helix chain '7' and resid 759 through 764 removed outlier: 4.037A pdb=" N VAL 7 763 " --> pdb=" O LEU 7 759 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU 7 764 " --> pdb=" O LEU 7 760 " (cutoff:3.500A) No H-bonds generated for 'chain '7' and resid 759 through 764' Processing helix chain '3' and resid 39 through 48 removed outlier: 4.493A pdb=" N ARG 3 45 " --> pdb=" O SER 3 41 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N SER 3 48 " --> pdb=" O ASP 3 44 " (cutoff:3.500A) Processing helix chain '3' and resid 75 through 92 Processing helix chain '3' and resid 102 through 123 removed outlier: 4.138A pdb=" N GLY 3 123 " --> pdb=" O LYS 3 119 " (cutoff:3.500A) Processing helix chain '3' and resid 127 through 145 Processing helix chain 'O' and resid 81 through 89 Processing helix chain 'O' and resid 128 through 147 removed outlier: 3.668A pdb=" N ILE O 146 " --> pdb=" O ILE O 142 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLY O 147 " --> pdb=" O ILE O 143 " (cutoff:3.500A) Processing helix chain 'O' and resid 171 through 179 Processing helix chain 'O' and resid 219 through 237 Proline residue: O 232 - end of helix Processing helix chain 'A' and resid 23 through 31 Processing helix chain 'A' and resid 92 through 104 removed outlier: 4.155A pdb=" N ALA A 97 " --> pdb=" O VAL A 93 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N LYS A 98 " --> pdb=" O GLY A 94 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLU A 104 " --> pdb=" O LYS A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 127 removed outlier: 3.768A pdb=" N ARG A 123 " --> pdb=" O ASN A 119 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA A 125 " --> pdb=" O LEU A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 144 removed outlier: 3.805A pdb=" N ALA A 137 " --> pdb=" O LYS A 133 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N THR A 144 " --> pdb=" O THR A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 213 Processing helix chain 'A' and resid 215 through 223 Processing helix chain 'A' and resid 230 through 233 Processing helix chain 'A' and resid 243 through 247 Processing helix chain 'A' and resid 260 through 282 removed outlier: 3.604A pdb=" N LEU A 276 " --> pdb=" O ALA A 272 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU A 280 " --> pdb=" O LEU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 305 Processing helix chain 'A' and resid 324 through 329 Processing helix chain 'A' and resid 334 through 340 Processing helix chain 'A' and resid 368 through 374 Processing helix chain 'A' and resid 384 through 395 Processing helix chain 'A' and resid 471 through 476 removed outlier: 3.759A pdb=" N SER A 476 " --> pdb=" O SER A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 505 removed outlier: 3.589A pdb=" N LEU A 504 " --> pdb=" O GLU A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 511 Processing helix chain 'A' and resid 525 through 535 removed outlier: 3.595A pdb=" N LYS A 533 " --> pdb=" O CYS A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 553 removed outlier: 4.186A pdb=" N ASN A 548 " --> pdb=" O ASP A 544 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL A 553 " --> pdb=" O MET A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 582 removed outlier: 4.128A pdb=" N ALA A 581 " --> pdb=" O ILE A 577 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ILE A 582 " --> pdb=" O LEU A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 623 Processing helix chain 'A' and resid 628 through 659 Proline residue: A 639 - end of helix removed outlier: 3.754A pdb=" N CYS A 642 " --> pdb=" O GLY A 638 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LYS A 644 " --> pdb=" O GLN A 640 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N LYS A 651 " --> pdb=" O GLY A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 670 Processing helix chain 'A' and resid 672 through 699 Processing helix chain 'A' and resid 709 through 737 Processing helix chain 'A' and resid 741 through 750 Processing helix chain 'A' and resid 754 through 763 removed outlier: 3.773A pdb=" N ILE A 758 " --> pdb=" O SER A 754 " (cutoff:3.500A) Processing helix chain 'A' and resid 793 through 798 Processing helix chain 'A' and resid 803 through 807 removed outlier: 3.630A pdb=" N GLY A 807 " --> pdb=" O TYR A 804 " (cutoff:3.500A) Processing helix chain 'A' and resid 809 through 845 removed outlier: 3.806A pdb=" N GLY A 823 " --> pdb=" O GLY A 819 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU A 824 " --> pdb=" O GLY A 820 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLY A 835 " --> pdb=" O THR A 831 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TYR A 836 " --> pdb=" O ALA A 832 " (cutoff:3.500A) Processing helix chain 'A' and resid 867 through 871 Processing helix chain 'A' and resid 874 through 878 Processing helix chain 'A' and resid 889 through 898 Processing helix chain 'A' and resid 909 through 914 removed outlier: 5.381A pdb=" N GLU A 914 " --> pdb=" O SER A 911 " (cutoff:3.500A) Processing helix chain 'A' and resid 915 through 920 removed outlier: 3.763A pdb=" N LEU A 920 " --> pdb=" O GLY A 916 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 947 removed outlier: 3.716A pdb=" N LEU A 928 " --> pdb=" O LYS A 924 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU A 929 " --> pdb=" O LEU A 925 " (cutoff:3.500A) Processing helix chain 'A' and resid 959 through 972 removed outlier: 3.834A pdb=" N ILE A 963 " --> pdb=" O ASN A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 994 Processing helix chain 'A' and resid 1004 through 1015 removed outlier: 3.631A pdb=" N VAL A1015 " --> pdb=" O GLN A1011 " (cutoff:3.500A) Processing helix chain 'A' and resid 1015 through 1026 Processing helix chain 'A' and resid 1027 through 1034 Processing helix chain 'A' and resid 1038 through 1056 Processing helix chain 'A' and resid 1063 through 1078 removed outlier: 3.558A pdb=" N LEU A1067 " --> pdb=" O MET A1063 " (cutoff:3.500A) Proline residue: A1075 - end of helix removed outlier: 3.817A pdb=" N GLN A1078 " --> pdb=" O GLU A1074 " (cutoff:3.500A) Processing helix chain 'A' and resid 1096 through 1106 removed outlier: 3.772A pdb=" N ARG A1100 " --> pdb=" O SER A1096 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU A1101 " --> pdb=" O GLY A1097 " (cutoff:3.500A) Processing helix chain 'A' and resid 1127 through 1139 removed outlier: 3.512A pdb=" N ILE A1134 " --> pdb=" O GLN A1130 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N SER A1136 " --> pdb=" O LYS A1132 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ALA A1137 " --> pdb=" O LEU A1133 " (cutoff:3.500A) Processing helix chain 'A' and resid 1142 through 1145 Processing helix chain 'A' and resid 1163 through 1175 removed outlier: 4.094A pdb=" N GLU A1167 " --> pdb=" O ILE A1163 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLU A1168 " --> pdb=" O PRO A1164 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N ILE A1169 " --> pdb=" O GLU A1165 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ILE A1170 " --> pdb=" O ASP A1166 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLN A1171 " --> pdb=" O GLU A1167 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU A1172 " --> pdb=" O GLU A1168 " (cutoff:3.500A) Processing helix chain 'A' and resid 1198 through 1203 Processing helix chain 'A' and resid 1208 through 1221 Processing helix chain 'A' and resid 1255 through 1269 removed outlier: 4.487A pdb=" N MET A1259 " --> pdb=" O GLU A1255 " (cutoff:3.500A) Processing helix chain 'A' and resid 1312 through 1318 removed outlier: 3.590A pdb=" N THR A1318 " --> pdb=" O SER A1314 " (cutoff:3.500A) Processing helix chain 'A' and resid 1332 through 1339 Processing helix chain 'A' and resid 1339 through 1357 removed outlier: 4.122A pdb=" N ALA A1343 " --> pdb=" O LEU A1339 " (cutoff:3.500A) Processing helix chain 'A' and resid 1358 through 1360 No H-bonds generated for 'chain 'A' and resid 1358 through 1360' Processing helix chain 'A' and resid 1364 through 1376 removed outlier: 3.883A pdb=" N MET A1368 " --> pdb=" O ASN A1364 " (cutoff:3.500A) Processing helix chain 'A' and resid 1395 through 1403 removed outlier: 3.603A pdb=" N ARG A1399 " --> pdb=" O GLY A1395 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N PHE A1402 " --> pdb=" O MET A1398 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N GLU A1403 " --> pdb=" O ARG A1399 " (cutoff:3.500A) Processing helix chain 'A' and resid 1404 through 1415 Processing helix chain 'A' and resid 1423 through 1431 removed outlier: 3.541A pdb=" N ASN A1427 " --> pdb=" O GLY A1423 " (cutoff:3.500A) Processing helix chain 'A' and resid 1436 through 1439 Processing helix chain 'A' and resid 1448 through 1452 removed outlier: 3.932A pdb=" N LYS A1452 " --> pdb=" O SER A1449 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 28 No H-bonds generated for 'chain 'B' and resid 26 through 28' Processing helix chain 'B' and resid 29 through 41 removed outlier: 3.636A pdb=" N VAL B 33 " --> pdb=" O ASP B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 57 Processing helix chain 'B' and resid 57 through 66 removed outlier: 3.708A pdb=" N ASP B 61 " --> pdb=" O TYR B 57 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ILE B 63 " --> pdb=" O LEU B 59 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ASP B 66 " --> pdb=" O ILE B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 120 Processing helix chain 'B' and resid 185 through 192 Processing helix chain 'B' and resid 282 through 290 Processing helix chain 'B' and resid 293 through 300 Processing helix chain 'B' and resid 308 through 321 Proline residue: B 316 - end of helix Processing helix chain 'B' and resid 326 through 338 Processing helix chain 'B' and resid 344 through 358 removed outlier: 4.246A pdb=" N GLN B 350 " --> pdb=" O GLU B 346 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ALA B 352 " --> pdb=" O ARG B 348 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LYS B 353 " --> pdb=" O ILE B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 390 Processing helix chain 'B' and resid 400 through 402 No H-bonds generated for 'chain 'B' and resid 400 through 402' Processing helix chain 'B' and resid 408 through 439 Processing helix chain 'B' and resid 443 through 448 Processing helix chain 'B' and resid 449 through 451 No H-bonds generated for 'chain 'B' and resid 449 through 451' Processing helix chain 'B' and resid 452 through 463 removed outlier: 3.629A pdb=" N TYR B 459 " --> pdb=" O SER B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 496 Processing helix chain 'B' and resid 515 through 519 Processing helix chain 'B' and resid 551 through 560 Processing helix chain 'B' and resid 565 through 569 Processing helix chain 'B' and resid 592 through 606 removed outlier: 3.648A pdb=" N GLU B 598 " --> pdb=" O ALA B 594 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR B 599 " --> pdb=" O ARG B 595 " (cutoff:3.500A) Processing helix chain 'B' and resid 654 through 666 Processing helix chain 'B' and resid 680 through 688 removed outlier: 3.750A pdb=" N LEU B 684 " --> pdb=" O THR B 680 " (cutoff:3.500A) Processing helix chain 'B' and resid 695 through 699 removed outlier: 3.586A pdb=" N GLU B 699 " --> pdb=" O ALA B 695 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 695 through 699' Processing helix chain 'B' and resid 706 through 711 Processing helix chain 'B' and resid 744 through 749 removed outlier: 3.715A pdb=" N LEU B 749 " --> pdb=" O SER B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 750 through 755 removed outlier: 4.226A pdb=" N ILE B 755 " --> pdb=" O VAL B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 762 Processing helix chain 'B' and resid 763 through 774 removed outlier: 3.714A pdb=" N ASN B 767 " --> pdb=" O GLN B 763 " (cutoff:3.500A) Processing helix chain 'B' and resid 775 through 777 No H-bonds generated for 'chain 'B' and resid 775 through 777' Processing helix chain 'B' and resid 807 through 813 removed outlier: 3.623A pdb=" N GLU B 810 " --> pdb=" O ARG B 807 " (cutoff:3.500A) Processing helix chain 'B' and resid 843 through 848 Processing helix chain 'B' and resid 927 through 932 removed outlier: 4.182A pdb=" N TYR B 931 " --> pdb=" O GLN B 927 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N HIS B 932 " --> pdb=" O ARG B 928 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 927 through 932' Processing helix chain 'B' and resid 1015 through 1021 removed outlier: 4.248A pdb=" N SER B1019 " --> pdb=" O HIS B1015 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG B1020 " --> pdb=" O ALA B1016 " (cutoff:3.500A) Processing helix chain 'B' and resid 1022 through 1039 removed outlier: 3.872A pdb=" N LEU B1026 " --> pdb=" O THR B1022 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N CYS B1029 " --> pdb=" O HIS B1025 " (cutoff:3.500A) Processing helix chain 'B' and resid 1051 through 1062 removed outlier: 3.687A pdb=" N ILE B1055 " --> pdb=" O THR B1051 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU B1061 " --> pdb=" O LYS B1057 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N HIS B1062 " --> pdb=" O LEU B1058 " (cutoff:3.500A) Processing helix chain 'B' and resid 1098 through 1102 Processing helix chain 'B' and resid 1131 through 1142 Processing helix chain 'B' and resid 1143 through 1152 Processing helix chain 'B' and resid 1197 through 1210 Processing helix chain 'C' and resid 26 through 39 Processing helix chain 'C' and resid 59 through 69 Processing helix chain 'C' and resid 76 through 80 Processing helix chain 'C' and resid 116 through 118 No H-bonds generated for 'chain 'C' and resid 116 through 118' Processing helix chain 'C' and resid 167 through 171 Processing helix chain 'C' and resid 196 through 201 Processing helix chain 'C' and resid 206 through 210 Processing helix chain 'C' and resid 239 through 263 Processing helix chain 'D' and resid 30 through 34 removed outlier: 3.528A pdb=" N GLN D 34 " --> pdb=" O GLN D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 75 removed outlier: 3.818A pdb=" N LYS D 60 " --> pdb=" O ARG D 56 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLU D 61 " --> pdb=" O LEU D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 134 removed outlier: 3.559A pdb=" N GLU D 124 " --> pdb=" O GLU D 120 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N SER D 125 " --> pdb=" O LYS D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 150 removed outlier: 3.780A pdb=" N LYS D 142 " --> pdb=" O ASN D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 168 Processing helix chain 'D' and resid 169 through 171 No H-bonds generated for 'chain 'D' and resid 169 through 171' Processing helix chain 'D' and resid 173 through 183 Processing helix chain 'D' and resid 187 through 195 Processing helix chain 'D' and resid 203 through 217 removed outlier: 3.661A pdb=" N LEU D 207 " --> pdb=" O SER D 203 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 26 removed outlier: 4.370A pdb=" N ASN E 8 " --> pdb=" O GLU E 4 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE E 9 " --> pdb=" O ASN E 5 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 36 Processing helix chain 'E' and resid 38 through 47 Processing helix chain 'E' and resid 54 through 59 removed outlier: 4.017A pdb=" N SER E 59 " --> pdb=" O ARG E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 72 Processing helix chain 'E' and resid 89 through 104 Processing helix chain 'E' and resid 117 through 123 Processing helix chain 'E' and resid 138 through 142 removed outlier: 3.843A pdb=" N VAL E 141 " --> pdb=" O ALA E 138 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N VAL E 142 " --> pdb=" O ALA E 139 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 138 through 142' Processing helix chain 'E' and resid 157 through 169 Processing helix chain 'E' and resid 171 through 175 removed outlier: 3.717A pdb=" N LEU E 175 " --> pdb=" O GLU E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 189 Processing helix chain 'F' and resid 75 through 79 Processing helix chain 'F' and resid 86 through 103 Processing helix chain 'F' and resid 116 through 128 Processing helix chain 'F' and resid 149 through 151 No H-bonds generated for 'chain 'F' and resid 149 through 151' Processing helix chain 'G' and resid 14 through 18 Processing helix chain 'G' and resid 19 through 20 No H-bonds generated for 'chain 'G' and resid 19 through 20' Processing helix chain 'G' and resid 21 through 35 removed outlier: 3.589A pdb=" N LEU G 31 " --> pdb=" O LYS G 27 " (cutoff:3.500A) Processing helix chain 'H' and resid 128 through 133 removed outlier: 3.594A pdb=" N LEU H 132 " --> pdb=" O ASN H 128 " (cutoff:3.500A) Processing helix chain 'I' and resid 61 through 65 Processing helix chain 'J' and resid 16 through 29 removed outlier: 4.422A pdb=" N SER J 20 " --> pdb=" O ASP J 16 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU J 25 " --> pdb=" O TYR J 21 " (cutoff:3.500A) Processing helix chain 'J' and resid 31 through 40 removed outlier: 3.725A pdb=" N SER J 37 " --> pdb=" O GLY J 33 " (cutoff:3.500A) Processing helix chain 'J' and resid 46 through 53 removed outlier: 3.588A pdb=" N ILE J 50 " --> pdb=" O CYS J 46 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU J 51 " --> pdb=" O ARG J 47 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 61 removed outlier: 4.281A pdb=" N LYS J 59 " --> pdb=" O ASP J 55 " (cutoff:3.500A) Processing helix chain 'K' and resid 6 through 11 removed outlier: 3.619A pdb=" N PHE K 10 " --> pdb=" O ARG K 6 " (cutoff:3.500A) Processing helix chain 'K' and resid 39 through 53 removed outlier: 4.350A pdb=" N LEU K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU K 49 " --> pdb=" O LEU K 45 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ASN K 52 " --> pdb=" O ALA K 48 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ASP K 53 " --> pdb=" O GLU K 49 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 111 removed outlier: 3.690A pdb=" N ALA K 90 " --> pdb=" O ALA K 86 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASN K 92 " --> pdb=" O LYS K 88 " (cutoff:3.500A) Processing helix chain 'M' and resid 103 through 114 removed outlier: 3.754A pdb=" N GLU M 109 " --> pdb=" O ARG M 105 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU M 110 " --> pdb=" O PHE M 106 " (cutoff:3.500A) Processing helix chain 'M' and resid 115 through 116 No H-bonds generated for 'chain 'M' and resid 115 through 116' Processing helix chain 'M' and resid 117 through 121 removed outlier: 3.838A pdb=" N LYS M 121 " --> pdb=" O VAL M 118 " (cutoff:3.500A) Processing helix chain 'M' and resid 122 through 140 removed outlier: 4.426A pdb=" N VAL M 126 " --> pdb=" O LYS M 122 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA M 131 " --> pdb=" O GLN M 127 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASP M 138 " --> pdb=" O THR M 134 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA M 140 " --> pdb=" O LEU M 136 " (cutoff:3.500A) Processing helix chain 'M' and resid 143 through 158 removed outlier: 3.732A pdb=" N LYS M 147 " --> pdb=" O PRO M 143 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASP M 148 " --> pdb=" O LYS M 144 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N CYS M 157 " --> pdb=" O ALA M 153 " (cutoff:3.500A) Processing helix chain 'M' and resid 169 through 183 removed outlier: 4.108A pdb=" N SER M 175 " --> pdb=" O ILE M 171 " (cutoff:3.500A) Processing helix chain 'M' and resid 188 through 194 Processing helix chain 'M' and resid 200 through 218 removed outlier: 3.640A pdb=" N GLY M 204 " --> pdb=" O THR M 200 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ILE M 209 " --> pdb=" O LYS M 205 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LYS M 211 " --> pdb=" O LEU M 207 " (cutoff:3.500A) Processing helix chain 'M' and resid 234 through 236 No H-bonds generated for 'chain 'M' and resid 234 through 236' Processing helix chain 'M' and resid 237 through 245 removed outlier: 4.751A pdb=" N ARG M 241 " --> pdb=" O THR M 237 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N CYS M 243 " --> pdb=" O ILE M 239 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N HIS M 245 " --> pdb=" O ARG M 241 " (cutoff:3.500A) Processing helix chain 'M' and resid 251 through 267 removed outlier: 3.520A pdb=" N SER M 255 " --> pdb=" O GLN M 251 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N CYS M 263 " --> pdb=" O THR M 259 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N LYS M 264 " --> pdb=" O ALA M 260 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N GLU M 265 " --> pdb=" O LYS M 261 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ILE M 266 " --> pdb=" O LYS M 262 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LYS M 267 " --> pdb=" O CYS M 263 " (cutoff:3.500A) Processing helix chain 'M' and resid 275 through 287 removed outlier: 4.367A pdb=" N VAL M 279 " --> pdb=" O ILE M 275 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N VAL M 280 " --> pdb=" O THR M 276 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE M 282 " --> pdb=" O ALA M 278 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU M 284 " --> pdb=" O VAL M 280 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ASN M 285 " --> pdb=" O SER M 281 " (cutoff:3.500A) Processing helix chain 'M' and resid 294 through 302 Processing helix chain 'M' and resid 305 through 319 removed outlier: 4.115A pdb=" N HIS M 319 " --> pdb=" O ILE M 315 " (cutoff:3.500A) Processing helix chain 'M' and resid 320 through 323 Processing helix chain 'Q' and resid 28 through 35 removed outlier: 3.816A pdb=" N LEU Q 32 " --> pdb=" O ARG Q 28 " (cutoff:3.500A) Processing helix chain 'Q' and resid 108 through 114 Processing helix chain 'Q' and resid 129 through 134 removed outlier: 3.966A pdb=" N HIS Q 134 " --> pdb=" O VAL Q 130 " (cutoff:3.500A) Processing helix chain 'Q' and resid 337 through 346 Processing helix chain 'Q' and resid 408 through 413 Processing helix chain 'R' and resid 74 through 80 removed outlier: 3.555A pdb=" N LYS R 80 " --> pdb=" O PHE R 76 " (cutoff:3.500A) Processing helix chain 'R' and resid 234 through 245 removed outlier: 3.525A pdb=" N LYS R 245 " --> pdb=" O ARG R 241 " (cutoff:3.500A) Processing helix chain 'R' and resid 258 through 265 removed outlier: 4.166A pdb=" N HIS R 265 " --> pdb=" O VAL R 261 " (cutoff:3.500A) Processing helix chain 'R' and resid 295 through 310 removed outlier: 3.666A pdb=" N ILE R 299 " --> pdb=" O PRO R 295 " (cutoff:3.500A) Processing helix chain 'R' and resid 314 through 322 Processing helix chain 'R' and resid 325 through 337 removed outlier: 3.677A pdb=" N ASP R 334 " --> pdb=" O LYS R 330 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N LYS R 335 " --> pdb=" O GLU R 331 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N VAL R 336 " --> pdb=" O CYS R 332 " (cutoff:3.500A) Processing helix chain 'W' and resid 5 through 20 Processing helix chain 'W' and resid 23 through 35 removed outlier: 3.843A pdb=" N LEU W 27 " --> pdb=" O GLY W 23 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N VAL W 28 " --> pdb=" O SER W 24 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU W 29 " --> pdb=" O PHE W 25 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N HIS W 35 " --> pdb=" O ALA W 31 " (cutoff:3.500A) Processing helix chain 'W' and resid 39 through 48 removed outlier: 3.516A pdb=" N LEU W 43 " --> pdb=" O ALA W 39 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU W 47 " --> pdb=" O LEU W 43 " (cutoff:3.500A) Processing helix chain 'W' and resid 50 through 53 removed outlier: 3.555A pdb=" N GLU W 53 " --> pdb=" O ASN W 50 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 50 through 53' Processing helix chain 'W' and resid 54 through 64 Processing helix chain 'W' and resid 90 through 116 removed outlier: 3.596A pdb=" N ILE W 95 " --> pdb=" O TYR W 91 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASP W 96 " --> pdb=" O PRO W 92 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LYS W 99 " --> pdb=" O ILE W 95 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N TRP W 100 " --> pdb=" O ASP W 96 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASP W 114 " --> pdb=" O LYS W 110 " (cutoff:3.500A) Processing helix chain 'W' and resid 132 through 140 removed outlier: 3.511A pdb=" N GLN W 138 " --> pdb=" O LEU W 134 " (cutoff:3.500A) Processing helix chain 'W' and resid 161 through 188 removed outlier: 4.125A pdb=" N ASN W 165 " --> pdb=" O SER W 161 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LYS W 166 " --> pdb=" O GLY W 162 " (cutoff:3.500A) Proline residue: W 181 - end of helix Processing helix chain 'X' and resid 124 through 139 Processing helix chain 'X' and resid 143 through 152 removed outlier: 3.606A pdb=" N ASP X 149 " --> pdb=" O ASN X 145 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LEU X 151 " --> pdb=" O LEU X 147 " (cutoff:3.500A) Processing helix chain 'X' and resid 156 through 166 removed outlier: 3.975A pdb=" N ILE X 160 " --> pdb=" O ASP X 156 " (cutoff:3.500A) Processing helix chain 'X' and resid 188 through 198 Processing helix chain 'X' and resid 207 through 214 Processing helix chain 'X' and resid 216 through 224 removed outlier: 3.763A pdb=" N THR X 220 " --> pdb=" O GLN X 216 " (cutoff:3.500A) Processing helix chain 'X' and resid 256 through 266 Processing helix chain 'X' and resid 272 through 281 removed outlier: 4.166A pdb=" N ARG X 276 " --> pdb=" O ALA X 272 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain '4' and resid 82 through 85 removed outlier: 6.354A pdb=" N LEU 4 26 " --> pdb=" O ALA 4 74 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N ILE 4 76 " --> pdb=" O LEU 4 26 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N VAL 4 28 " --> pdb=" O ILE 4 76 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N ALA 4 78 " --> pdb=" O VAL 4 28 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N ILE 4 30 " --> pdb=" O ALA 4 78 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU 4 179 " --> pdb=" O ILE 4 29 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU 4 31 " --> pdb=" O LEU 4 179 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N CYS 4 181 " --> pdb=" O GLU 4 31 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N LEU 4 176 " --> pdb=" O ASP 4 211 " (cutoff:3.500A) removed outlier: 8.699A pdb=" N VAL 4 213 " --> pdb=" O LEU 4 176 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N VAL 4 178 " --> pdb=" O VAL 4 213 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N ILE 4 215 " --> pdb=" O VAL 4 178 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N THR 4 180 " --> pdb=" O ILE 4 215 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain '4' and resid 287 through 288 removed outlier: 3.570A pdb=" N VAL 6 320 " --> pdb=" O ILE 4 288 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '0' and resid 2 through 4 Processing sheet with id=AA4, first strand: chain '0' and resid 105 through 108 removed outlier: 6.706A pdb=" N LEU 0 106 " --> pdb=" O ILE 0 207 " (cutoff:3.500A) removed outlier: 9.075A pdb=" N SER 0 209 " --> pdb=" O LEU 0 106 " (cutoff:3.500A) removed outlier: 8.229A pdb=" N LEU 0 108 " --> pdb=" O SER 0 209 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ASP 0 235 " --> pdb=" O CYS 0 72 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N VAL 0 232 " --> pdb=" O ILE 0 457 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N THR 0 459 " --> pdb=" O VAL 0 232 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N PHE 0 234 " --> pdb=" O THR 0 459 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain '0' and resid 352 through 354 Processing sheet with id=AA6, first strand: chain '0' and resid 494 through 496 removed outlier: 5.805A pdb=" N VAL 0 620 " --> pdb=" O VAL 0 680 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N ALA 0 682 " --> pdb=" O VAL 0 620 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N MET 0 622 " --> pdb=" O ALA 0 682 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain '0' and resid 568 through 570 removed outlier: 5.972A pdb=" N LEU 0 568 " --> pdb=" O ILE 0 597 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain '6' and resid 178 through 186 removed outlier: 5.787A pdb=" N ILE 6 171 " --> pdb=" O VAL 6 182 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N GLN 6 184 " --> pdb=" O MET 6 169 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N MET 6 169 " --> pdb=" O GLN 6 184 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ARG 6 124 " --> pdb=" O GLN 6 168 " (cutoff:3.500A) removed outlier: 8.421A pdb=" N GLY 6 170 " --> pdb=" O ARG 6 124 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N LEU 6 126 " --> pdb=" O GLY 6 170 " (cutoff:3.500A) removed outlier: 8.222A pdb=" N ILE 6 172 " --> pdb=" O LEU 6 126 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N LEU 6 128 " --> pdb=" O ILE 6 172 " (cutoff:3.500A) removed outlier: 8.456A pdb=" N MET 6 174 " --> pdb=" O LEU 6 128 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE 6 127 " --> pdb=" O GLU 6 231 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain '6' and resid 326 through 327 Processing sheet with id=AB1, first strand: chain '6' and resid 390 through 391 Processing sheet with id=AB2, first strand: chain '2' and resid 57 through 58 Processing sheet with id=AB3, first strand: chain '2' and resid 365 through 369 removed outlier: 4.367A pdb=" N HIS 2 365 " --> pdb=" O GLN 2 377 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLN 2 377 " --> pdb=" O HIS 2 365 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N LEU 2 375 " --> pdb=" O LYS 2 367 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain '2' and resid 457 through 458 removed outlier: 3.645A pdb=" N ILE 2 493 " --> pdb=" O SER 2 457 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain '5' and resid 10 through 11 Processing sheet with id=AB6, first strand: chain '7' and resid 133 through 135 Processing sheet with id=AB7, first strand: chain '7' and resid 226 through 227 Processing sheet with id=AB8, first strand: chain '7' and resid 383 through 384 removed outlier: 7.231A pdb=" N ILE 7 383 " --> pdb=" O LEU 7 535 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain '7' and resid 453 through 456 Processing sheet with id=AC1, first strand: chain '7' and resid 487 through 488 removed outlier: 6.134A pdb=" N LEU 7 487 " --> pdb=" O LEU 7 513 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain '7' and resid 554 through 555 removed outlier: 6.388A pdb=" N CYS 7 554 " --> pdb=" O LYS 7 734 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain '7' and resid 558 through 559 Processing sheet with id=AC4, first strand: chain '7' and resid 605 through 608 Processing sheet with id=AC5, first strand: chain '3' and resid 52 through 53 Processing sheet with id=AC6, first strand: chain 'O' and resid 92 through 95 removed outlier: 4.884A pdb=" N ASN O 95 " --> pdb=" O ALA O 101 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N ALA O 101 " --> pdb=" O ASN O 95 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N MET O 104 " --> pdb=" O ALA O 113 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE O 106 " --> pdb=" O THR O 111 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N LYS O 120 " --> pdb=" O PHE O 116 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N VAL O 161 " --> pdb=" O GLN O 68 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ILE O 70 " --> pdb=" O ASN O 159 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ASN O 159 " --> pdb=" O ILE O 70 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ALA O 72 " --> pdb=" O ILE O 157 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ILE O 157 " --> pdb=" O ALA O 72 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N VAL O 74 " --> pdb=" O PHE O 155 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N PHE O 155 " --> pdb=" O VAL O 74 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N GLY O 192 " --> pdb=" O GLU O 186 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N GLU O 186 " --> pdb=" O GLY O 192 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 1418 through 1419 Processing sheet with id=AC8, first strand: chain 'A' and resid 82 through 91 removed outlier: 6.332A pdb=" N THR A 237 " --> pdb=" O LEU A 86 " (cutoff:3.500A) removed outlier: 10.554A pdb=" N LYS A 88 " --> pdb=" O ILE A 235 " (cutoff:3.500A) removed outlier: 10.557A pdb=" N ILE A 235 " --> pdb=" O LYS A 88 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 176 through 177 Processing sheet with id=AD1, first strand: chain 'A' and resid 249 through 252 Processing sheet with id=AD2, first strand: chain 'A' and resid 343 through 345 removed outlier: 3.747A pdb=" N LEU B1128 " --> pdb=" O VAL A 345 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1104 through 1106 removed outlier: 3.621A pdb=" N SER A 348 " --> pdb=" O ARG B1106 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N THR A 351 " --> pdb=" O MET A 487 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N VAL A 364 " --> pdb=" O LYS A 461 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ILE A 463 " --> pdb=" O VAL A 364 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N VAL A 366 " --> pdb=" O ILE A 463 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N PHE A 468 " --> pdb=" O ARG A 350 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N VAL A 352 " --> pdb=" O PHE A 468 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N LEU A 470 " --> pdb=" O VAL A 352 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N SER A 354 " --> pdb=" O LEU A 470 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'A' and resid 375 through 379 removed outlier: 3.590A pdb=" N ARG A 434 " --> pdb=" O TYR A 376 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N TYR A 404 " --> pdb=" O GLU A 433 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N HIS A 435 " --> pdb=" O ALA A 402 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ALA A 402 " --> pdb=" O HIS A 435 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'A' and resid 541 through 542 Processing sheet with id=AD6, first strand: chain 'A' and resid 565 through 566 removed outlier: 3.673A pdb=" N ARG H 145 " --> pdb=" O THR H 56 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR H 56 " --> pdb=" O ARG H 145 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N VAL H 12 " --> pdb=" O ALA H 29 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ALA H 29 " --> pdb=" O VAL H 12 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'A' and resid 565 through 566 removed outlier: 3.673A pdb=" N ARG H 145 " --> pdb=" O THR H 56 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR H 56 " --> pdb=" O ARG H 145 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N VAL H 12 " --> pdb=" O ALA H 29 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ALA H 29 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS H 37 " --> pdb=" O GLU H 126 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LYS H 103 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N SER H 117 " --> pdb=" O ALA H 101 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N ALA H 101 " --> pdb=" O SER H 117 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'A' and resid 587 through 590 removed outlier: 3.556A pdb=" N LEU A 588 " --> pdb=" O ILE A 607 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N LEU A 606 " --> pdb=" O ILE A 613 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'A' and resid 766 through 767 Processing sheet with id=AE1, first strand: chain 'A' and resid 849 through 850 removed outlier: 3.856A pdb=" N MET A 849 " --> pdb=" O ARG A 857 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG A 857 " --> pdb=" O MET A 849 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N THR A 856 " --> pdb=" O ILE A 864 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'A' and resid 879 through 882 Processing sheet with id=AE3, first strand: chain 'A' and resid 1115 through 1118 Processing sheet with id=AE4, first strand: chain 'A' and resid 1225 through 1228 removed outlier: 3.564A pdb=" N ILE A1238 " --> pdb=" O LEU A1195 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LEU A1192 " --> pdb=" O ILE A1152 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ILE A1152 " --> pdb=" O LEU A1192 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ARG A1194 " --> pdb=" O SER A1150 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N SER A1150 " --> pdb=" O ARG A1194 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N GLU A1196 " --> pdb=" O ILE A1148 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N TYR A1154 " --> pdb=" O LEU I 42 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N LEU I 42 " --> pdb=" O TYR A1154 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'A' and resid 1290 through 1292 Processing sheet with id=AE6, first strand: chain 'F' and resid 143 through 147 removed outlier: 4.590A pdb=" N GLY G 59 " --> pdb=" O ILE A1445 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'F' and resid 143 through 147 removed outlier: 4.590A pdb=" N GLY G 59 " --> pdb=" O ILE A1445 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N ARG G 75 " --> pdb=" O LEU G 49 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N CYS G 47 " --> pdb=" O VAL G 77 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N PHE G 79 " --> pdb=" O ILE G 45 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N ILE G 45 " --> pdb=" O PHE G 79 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B' and resid 69 through 73 removed outlier: 4.981A pdb=" N ASP B 131 " --> pdb=" O GLY B 93 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N ILE B 95 " --> pdb=" O PHE B 129 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N PHE B 129 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N VAL B 97 " --> pdb=" O GLY B 127 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N GLY B 127 " --> pdb=" O VAL B 97 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLY B 168 " --> pdb=" O LEU B 128 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N VAL B 130 " --> pdb=" O PHE B 166 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N PHE B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N VAL B 132 " --> pdb=" O LYS B 164 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N LYS B 164 " --> pdb=" O VAL B 132 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B' and resid 101 through 103 Processing sheet with id=AF1, first strand: chain 'B' and resid 203 through 205 Processing sheet with id=AF2, first strand: chain 'B' and resid 404 through 407 removed outlier: 6.591A pdb=" N ALA B 214 " --> pdb=" O ASN B 499 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'B' and resid 226 through 227 Processing sheet with id=AF4, first strand: chain 'B' and resid 255 through 258 removed outlier: 4.288A pdb=" N GLN B 255 " --> pdb=" O THR B 272 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'B' and resid 544 through 547 removed outlier: 4.218A pdb=" N ARG B 632 " --> pdb=" O SER B 546 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'B' and resid 586 through 590 removed outlier: 5.364A pdb=" N TRP B 586 " --> pdb=" O VAL B 582 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N VAL B 582 " --> pdb=" O TRP B 586 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLY B 588 " --> pdb=" O VAL B 580 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N ARG B 579 " --> pdb=" O LEU B 624 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N ILE B 626 " --> pdb=" O ARG B 579 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N PHE B 581 " --> pdb=" O ILE B 626 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'B' and resid 640 through 641 Processing sheet with id=AF8, first strand: chain 'B' and resid 703 through 704 Processing sheet with id=AF9, first strand: chain 'B' and resid 793 through 796 removed outlier: 3.723A pdb=" N SER B 853 " --> pdb=" O LYS B 972 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N ARG B 969 " --> pdb=" O VAL B 949 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N VAL B 949 " --> pdb=" O ARG B 969 " (cutoff:3.500A) removed outlier: 8.535A pdb=" N THR B 971 " --> pdb=" O GLY B 947 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N GLY B 947 " --> pdb=" O THR B 971 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'B' and resid 1069 through 1070 removed outlier: 6.744A pdb=" N MET B 839 " --> pdb=" O GLY B 991 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N THR B 993 " --> pdb=" O MET B 839 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N MET B 841 " --> pdb=" O THR B 993 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N PHE B1086 " --> pdb=" O ILE B 827 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'B' and resid 873 through 874 Processing sheet with id=AG3, first strand: chain 'B' and resid 910 through 912 removed outlier: 3.600A pdb=" N ILE B 912 " --> pdb=" O THR B 939 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'B' and resid 1001 through 1002 Processing sheet with id=AG5, first strand: chain 'B' and resid 1159 through 1163 Processing sheet with id=AG6, first strand: chain 'C' and resid 10 through 13 removed outlier: 3.544A pdb=" N GLU C 12 " --> pdb=" O ASP C 19 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'C' and resid 119 through 120 removed outlier: 6.025A pdb=" N GLU C 152 " --> pdb=" O THR C 53 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N THR C 53 " --> pdb=" O GLU C 152 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N LYS C 154 " --> pdb=" O VAL C 51 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N VAL C 51 " --> pdb=" O LYS C 154 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N THR C 156 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N VAL C 49 " --> pdb=" O THR C 156 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N VAL C 158 " --> pdb=" O ASP C 47 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'C' and resid 72 through 74 removed outlier: 4.191A pdb=" N HIS C 131 " --> pdb=" O GLN C 73 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'C' and resid 111 through 114 Processing sheet with id=AH1, first strand: chain 'D' and resid 37 through 38 Processing sheet with id=AH2, first strand: chain 'E' and resid 60 through 62 removed outlier: 6.023A pdb=" N TRP E 79 " --> pdb=" O ILE E 109 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N VAL E 111 " --> pdb=" O TRP E 79 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N GLU E 81 " --> pdb=" O VAL E 111 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'E' and resid 87 through 88 Processing sheet with id=AH4, first strand: chain 'E' and resid 177 through 178 Processing sheet with id=AH5, first strand: chain 'F' and resid 84 through 85 Processing sheet with id=AH6, first strand: chain 'G' and resid 169 through 171 removed outlier: 4.113A pdb=" N GLY G 169 " --> pdb=" O ARG G 144 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG G 144 " --> pdb=" O GLY G 169 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ARG G 142 " --> pdb=" O ILE G 171 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N ILE G 147 " --> pdb=" O SER G 162 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N SER G 162 " --> pdb=" O ILE G 147 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N LYS G 107 " --> pdb=" O ILE G 157 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N ALA G 159 " --> pdb=" O LYS G 107 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N THR G 111 " --> pdb=" O GLY G 161 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N GLY G 98 " --> pdb=" O CYS G 94 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N CYS G 94 " --> pdb=" O GLY G 98 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N GLU G 100 " --> pdb=" O VAL G 92 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLU G 85 " --> pdb=" O ILE G 147 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'G' and resid 120 through 122 removed outlier: 3.916A pdb=" N SER G 129 " --> pdb=" O ASN G 122 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'I' and resid 15 through 19 Processing sheet with id=AH9, first strand: chain 'I' and resid 70 through 71 removed outlier: 4.114A pdb=" N ASN I 83 " --> pdb=" O SER I 71 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'K' and resid 19 through 23 Processing sheet with id=AI2, first strand: chain 'L' and resid 30 through 31 removed outlier: 3.543A pdb=" N ILE L 30 " --> pdb=" O LEU L 57 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'M' and resid 34 through 35 removed outlier: 6.770A pdb=" N VAL M 43 " --> pdb=" O LEU M 52 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'Q' and resid 138 through 141 removed outlier: 3.630A pdb=" N TRP Q 361 " --> pdb=" O MET Q 352 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N THR Q 360 " --> pdb=" O ARG Q 398 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N THR Q 116 " --> pdb=" O LYS Q 391 " (cutoff:3.500A) removed outlier: 8.471A pdb=" N TYR Q 393 " --> pdb=" O THR Q 116 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N LEU Q 118 " --> pdb=" O TYR Q 393 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N PHE Q 395 " --> pdb=" O LEU Q 118 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N LYS Q 120 " --> pdb=" O PHE Q 395 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N ALA Q 397 " --> pdb=" O LYS Q 120 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N PHE R 135 " --> pdb=" O HIS Q 117 " (cutoff:3.500A) removed outlier: 8.177A pdb=" N GLU R 132 " --> pdb=" O THR R 217 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N THR R 217 " --> pdb=" O GLU R 132 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N VAL R 134 " --> pdb=" O VAL R 215 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LYS R 211 " --> pdb=" O GLN R 138 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLU R 62 " --> pdb=" O ILE R 214 " (cutoff:3.500A) removed outlier: 8.481A pdb=" N GLY R 216 " --> pdb=" O GLU R 62 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N SER R 64 " --> pdb=" O GLY R 216 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N VAL R 218 " --> pdb=" O SER R 64 " (cutoff:3.500A) removed outlier: 9.112A pdb=" N ARG R 66 " --> pdb=" O VAL R 218 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'Q' and resid 374 through 378 removed outlier: 3.603A pdb=" N THR Q 385 " --> pdb=" O SER Q 377 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'R' and resid 71 through 72 removed outlier: 7.333A pdb=" N ARG R 72 " --> pdb=" O VAL R 224 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N GLU R 221 " --> pdb=" O THR R 125 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN R 223 " --> pdb=" O GLU R 123 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'R' and resid 93 through 94 Processing sheet with id=AI8, first strand: chain 'V' and resid 71 through 72 removed outlier: 6.277A pdb=" N ASP V 109 " --> pdb=" O ASN V 82 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N GLN V 84 " --> pdb=" O SER V 107 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N SER V 107 " --> pdb=" O GLN V 84 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N THR V 86 " --> pdb=" O VAL V 105 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N VAL V 105 " --> pdb=" O THR V 86 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N LEU U 245 " --> pdb=" O GLY U 265 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N GLY U 265 " --> pdb=" O LEU U 245 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU U 247 " --> pdb=" O LYS U 263 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N SER U 261 " --> pdb=" O ASP U 249 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N VAL U 251 " --> pdb=" O LYS U 259 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N LYS U 259 " --> pdb=" O VAL U 251 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ARG U 257 " --> pdb=" O GLU U 284 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N GLU U 284 " --> pdb=" O ARG U 257 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N LYS U 259 " --> pdb=" O GLU U 282 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N GLU U 282 " --> pdb=" O LYS U 259 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N SER U 261 " --> pdb=" O GLN U 280 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N GLN U 280 " --> pdb=" O SER U 261 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N LYS U 263 " --> pdb=" O LYS U 278 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N LYS U 278 " --> pdb=" O LYS U 263 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLY U 265 " --> pdb=" O PHE U 276 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE U 276 " --> pdb=" O GLY U 265 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N SER V 58 " --> pdb=" O TYR U 274 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N PHE U 276 " --> pdb=" O SER V 58 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N LEU V 60 " --> pdb=" O PHE U 276 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N LYS U 278 " --> pdb=" O LEU V 60 " (cutoff:3.500A) removed outlier: 8.331A pdb=" N VAL V 62 " --> pdb=" O LYS U 278 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N GLN U 280 " --> pdb=" O VAL V 62 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N GLY V 64 " --> pdb=" O GLN U 280 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N GLU U 282 " --> pdb=" O GLY V 64 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N LEU V 66 " --> pdb=" O GLU U 282 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N GLU U 284 " --> pdb=" O LEU V 66 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N THR V 68 " --> pdb=" O GLU U 284 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ASN V 65 " --> pdb=" O ASN V 82 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N ASN V 82 " --> pdb=" O ASN V 65 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N ASP V 67 " --> pdb=" O VAL V 80 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N VAL V 80 " --> pdb=" O ASP V 67 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'W' and resid 68 through 72 removed outlier: 3.864A pdb=" N TYR W 86 " --> pdb=" O HIS W 70 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLN W 72 " --> pdb=" O ARG W 84 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'W' and resid 129 through 130 Processing sheet with id=AJ2, first strand: chain 'W' and resid 148 through 149 2665 hydrogen bonds defined for protein. 7521 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 87 hydrogen bonds 170 hydrogen bond angles 0 basepair planarities 38 basepair parallelities 76 stacking parallelities Total time for adding SS restraints: 34.24 Time building geometry restraints manager: 14.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.42: 27024 1.42 - 1.64: 38256 1.64 - 1.85: 549 1.85 - 2.07: 0 2.07 - 2.28: 12 Bond restraints: 65841 Sorted by residual: bond pdb=" C PHE B 758 " pdb=" O PHE B 758 " ideal model delta sigma weight residual 1.233 1.218 0.015 4.80e-03 4.34e+04 9.92e+00 bond pdb=" CA VAL A1098 " pdb=" CB VAL A1098 " ideal model delta sigma weight residual 1.537 1.522 0.015 5.00e-03 4.00e+04 9.35e+00 bond pdb=" CA LYS B 451 " pdb=" C LYS B 451 " ideal model delta sigma weight residual 1.523 1.477 0.046 1.80e-02 3.09e+03 6.54e+00 bond pdb=" SD MET Q 114 " pdb=" CE MET Q 114 " ideal model delta sigma weight residual 1.791 1.849 -0.058 2.50e-02 1.60e+03 5.34e+00 bond pdb=" CA GLU B 560 " pdb=" C GLU B 560 " ideal model delta sigma weight residual 1.523 1.486 0.038 1.80e-02 3.09e+03 4.35e+00 ... (remaining 65836 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.93: 87556 1.93 - 3.87: 1579 3.87 - 5.80: 191 5.80 - 7.74: 24 7.74 - 9.67: 5 Bond angle restraints: 89355 Sorted by residual: angle pdb=" C ILE 4 298 " pdb=" N ILE 4 299 " pdb=" CA ILE 4 299 " ideal model delta sigma weight residual 120.24 125.55 -5.31 6.30e-01 2.52e+00 7.11e+01 angle pdb=" N ILE 1 336 " pdb=" CA ILE 1 336 " pdb=" C ILE 1 336 " ideal model delta sigma weight residual 111.62 107.45 4.17 7.90e-01 1.60e+00 2.79e+01 angle pdb=" C ILE 4 299 " pdb=" CA ILE 4 299 " pdb=" CB ILE 4 299 " ideal model delta sigma weight residual 114.35 108.90 5.45 1.06e+00 8.90e-01 2.65e+01 angle pdb=" N SER 7 322 " pdb=" CA SER 7 322 " pdb=" C SER 7 322 " ideal model delta sigma weight residual 109.56 117.03 -7.47 1.84e+00 2.95e-01 1.65e+01 angle pdb=" N SER A 466 " pdb=" CA SER A 466 " pdb=" C SER A 466 " ideal model delta sigma weight residual 108.58 115.46 -6.88 1.82e+00 3.02e-01 1.43e+01 ... (remaining 89350 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.29: 35076 18.29 - 36.58: 2990 36.58 - 54.88: 1159 54.88 - 73.17: 312 73.17 - 91.46: 52 Dihedral angle restraints: 39589 sinusoidal: 16281 harmonic: 23308 Sorted by residual: dihedral pdb=" CA HIS B 363 " pdb=" C HIS B 363 " pdb=" N ILE B 364 " pdb=" CA ILE B 364 " ideal model delta harmonic sigma weight residual -180.00 -131.31 -48.69 0 5.00e+00 4.00e-02 9.48e+01 dihedral pdb=" CA THR 6 116 " pdb=" C THR 6 116 " pdb=" N PRO 6 117 " pdb=" CA PRO 6 117 " ideal model delta harmonic sigma weight residual -180.00 -135.23 -44.77 0 5.00e+00 4.00e-02 8.02e+01 dihedral pdb=" CA LYS M 272 " pdb=" C LYS M 272 " pdb=" N SER M 273 " pdb=" CA SER M 273 " ideal model delta harmonic sigma weight residual 180.00 -135.63 -44.37 0 5.00e+00 4.00e-02 7.87e+01 ... (remaining 39586 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 7171 0.039 - 0.078: 2071 0.078 - 0.117: 734 0.117 - 0.157: 90 0.157 - 0.196: 3 Chirality restraints: 10069 Sorted by residual: chirality pdb=" CB VAL 7 323 " pdb=" CA VAL 7 323 " pdb=" CG1 VAL 7 323 " pdb=" CG2 VAL 7 323 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 9.57e-01 chirality pdb=" CG LEU 6 448 " pdb=" CB LEU 6 448 " pdb=" CD1 LEU 6 448 " pdb=" CD2 LEU 6 448 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 6.93e-01 chirality pdb=" CA ARG 2 450 " pdb=" N ARG 2 450 " pdb=" C ARG 2 450 " pdb=" CB ARG 2 450 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.49e-01 ... (remaining 10066 not shown) Planarity restraints: 11228 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DA N 11 " -0.040 2.00e-02 2.50e+03 1.69e-02 7.88e+00 pdb=" N9 DA N 11 " 0.026 2.00e-02 2.50e+03 pdb=" C8 DA N 11 " 0.013 2.00e-02 2.50e+03 pdb=" N7 DA N 11 " 0.009 2.00e-02 2.50e+03 pdb=" C5 DA N 11 " -0.005 2.00e-02 2.50e+03 pdb=" C6 DA N 11 " 0.003 2.00e-02 2.50e+03 pdb=" N6 DA N 11 " -0.022 2.00e-02 2.50e+03 pdb=" N1 DA N 11 " -0.001 2.00e-02 2.50e+03 pdb=" C2 DA N 11 " 0.006 2.00e-02 2.50e+03 pdb=" N3 DA N 11 " 0.012 2.00e-02 2.50e+03 pdb=" C4 DA N 11 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 463 " -0.044 5.00e-02 4.00e+02 6.71e-02 7.19e+00 pdb=" N PRO A 464 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO A 464 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 464 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR 6 116 " -0.041 5.00e-02 4.00e+02 6.27e-02 6.29e+00 pdb=" N PRO 6 117 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO 6 117 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO 6 117 " -0.035 5.00e-02 4.00e+02 ... (remaining 11225 not shown) Histogram of nonbonded interaction distances: 1.77 - 2.39: 589 2.39 - 3.02: 42691 3.02 - 3.65: 108066 3.65 - 4.27: 156394 4.27 - 4.90: 242972 Nonbonded interactions: 550712 Sorted by model distance: nonbonded pdb=" CB CYS 0 156 " pdb=" S1 SF4 0 801 " model vdw 1.767 3.040 nonbonded pdb=" OD2 ASP A 483 " pdb="MG MG A1803 " model vdw 1.961 2.170 nonbonded pdb=" OD2 ASP A 485 " pdb="MG MG A1803 " model vdw 1.963 2.170 nonbonded pdb=" OD1 ASP A 483 " pdb="MG MG A1803 " model vdw 2.042 2.170 nonbonded pdb=" O ILE Q 127 " pdb=" OH TYR R 133 " model vdw 2.044 3.040 ... (remaining 550707 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.00 max=1.00 mean=0.99 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: 4.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.070 Extract box with map and model: 1.910 Check model and map are aligned: 0.360 Set scattering table: 0.440 Process input model: 151.910 Find NCS groups from input model: 0.960 Set up NCS constraints: 0.230 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: 0.020 Load rotamer database and sin/cos tables:2.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 162.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5813 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 : 0.005 0.065 65841 Z= 0.300 Angle : 0.658 9.673 89355 Z= 0.378 Chirality : 0.042 0.196 10069 Planarity : 0.004 0.067 11216 Dihedral : 16.747 91.460 24607 Min Nonbonded Distance : 1.767 Molprobity Statistics. All-atom Clashscore : 25.40 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.80 % Favored : 91.12 % Rotamer: Outliers : 12.14 % Allowed : 12.70 % Favored : 75.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % Cis-general : 0.07 % Twisted Proline : 0.59 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.89 (0.09), residues: 7928 helix: -0.27 (0.10), residues: 2696 sheet: -1.72 (0.16), residues: 990 loop : -1.80 (0.09), residues: 4242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP 7 482 HIS 0.006 0.001 HIS 6 375 PHE 0.015 0.001 PHE K 7 TYR 0.019 0.002 TYR 7 581 ARG 0.007 0.001 ARG 7 689 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15856 Ramachandran restraints generated. 7928 Oldfield, 0 Emsley, 7928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15856 Ramachandran restraints generated. 7928 Oldfield, 0 Emsley, 7928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1094 residues out of total 7221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 780 poor density : 314 time to evaluate : 6.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 1 MET cc_start: 0.5270 (mtp) cc_final: 0.4678 (mtp) REVERT: 0 351 VAL cc_start: 0.5881 (OUTLIER) cc_final: 0.3974 (p) REVERT: 6 158 HIS cc_start: 0.7167 (OUTLIER) cc_final: 0.6897 (p90) REVERT: 2 22 GLN cc_start: 0.9117 (OUTLIER) cc_final: 0.8843 (mt0) REVERT: 2 25 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.6954 (mm) REVERT: 2 55 ASN cc_start: 0.4234 (OUTLIER) cc_final: 0.3901 (p0) REVERT: 2 450 ARG cc_start: -0.0274 (OUTLIER) cc_final: -0.0807 (mtt180) REVERT: 7 343 PHE cc_start: 0.6230 (OUTLIER) cc_final: 0.5788 (p90) REVERT: 7 349 ASN cc_start: 0.6891 (OUTLIER) cc_final: 0.6608 (m-40) REVERT: 7 475 ASP cc_start: 0.8286 (OUTLIER) cc_final: 0.7359 (m-30) REVERT: 7 534 LYS cc_start: -0.0697 (OUTLIER) cc_final: -0.1981 (mmtt) REVERT: 7 583 MET cc_start: 0.3960 (ptt) cc_final: 0.3692 (ptt) REVERT: O 153 THR cc_start: 0.1661 (OUTLIER) cc_final: 0.1441 (m) REVERT: A 167 CYS cc_start: 0.6842 (OUTLIER) cc_final: 0.6603 (p) REVERT: A 708 MET cc_start: 0.5631 (ptp) cc_final: 0.5316 (ptp) REVERT: A 1220 PHE cc_start: 0.4680 (OUTLIER) cc_final: 0.4171 (m-80) REVERT: A 1336 MET cc_start: 0.7510 (tmm) cc_final: 0.7155 (tmm) REVERT: A 1393 ASN cc_start: 0.7298 (OUTLIER) cc_final: 0.6657 (p0) REVERT: A 1400 CYS cc_start: 0.7609 (OUTLIER) cc_final: 0.7399 (t) REVERT: A 1450 LEU cc_start: 0.5682 (OUTLIER) cc_final: 0.5473 (tp) REVERT: B 364 ILE cc_start: 0.7495 (OUTLIER) cc_final: 0.7162 (pt) REVERT: B 747 MET cc_start: 0.7402 (mmm) cc_final: 0.7161 (mmp) REVERT: B 996 ARG cc_start: 0.8148 (OUTLIER) cc_final: 0.7755 (ttt-90) REVERT: B 1049 ASP cc_start: 0.7717 (OUTLIER) cc_final: 0.7325 (p0) REVERT: B 1192 TYR cc_start: 0.6365 (OUTLIER) cc_final: 0.5817 (m-80) REVERT: C 82 TYR cc_start: 0.7407 (OUTLIER) cc_final: 0.7203 (m-10) REVERT: C 91 HIS cc_start: 0.5943 (OUTLIER) cc_final: 0.5387 (p-80) REVERT: C 165 LYS cc_start: 0.8601 (OUTLIER) cc_final: 0.8018 (ttmp) REVERT: C 219 PHE cc_start: 0.8056 (OUTLIER) cc_final: 0.7636 (p90) REVERT: E 57 MET cc_start: 0.6837 (ppp) cc_final: 0.6451 (ppp) REVERT: F 86 THR cc_start: 0.7575 (OUTLIER) cc_final: 0.7276 (p) REVERT: H 10 PHE cc_start: 0.6492 (OUTLIER) cc_final: 0.5549 (m-80) REVERT: Q 386 MET cc_start: 0.0884 (mpp) cc_final: 0.0430 (mpp) REVERT: R 270 MET cc_start: 0.2786 (mpp) cc_final: 0.2451 (mmp) REVERT: U 255 LYS cc_start: -0.1435 (OUTLIER) cc_final: -0.2021 (mptt) REVERT: X 262 MET cc_start: 0.4549 (ptt) cc_final: 0.4347 (ppp) outliers start: 780 outliers final: 332 residues processed: 1061 average time/residue: 0.5878 time to fit residues: 1058.4741 Evaluate side-chains 613 residues out of total 7221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 359 poor density : 254 time to evaluate : 5.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 180 LEU Chi-restraints excluded: chain 1 residue 263 TYR Chi-restraints excluded: chain 1 residue 276 LYS Chi-restraints excluded: chain 1 residue 287 PHE Chi-restraints excluded: chain 1 residue 553 LEU Chi-restraints excluded: chain 1 residue 556 THR Chi-restraints excluded: chain 1 residue 563 HIS Chi-restraints excluded: chain 1 residue 585 HIS Chi-restraints excluded: chain 1 residue 593 LEU Chi-restraints excluded: chain 4 residue 43 GLU Chi-restraints excluded: chain 4 residue 61 LEU Chi-restraints excluded: chain 4 residue 129 ILE Chi-restraints excluded: chain 4 residue 137 LYS Chi-restraints excluded: chain 4 residue 161 ASN Chi-restraints excluded: chain 4 residue 162 ARG Chi-restraints excluded: chain 4 residue 175 ARG Chi-restraints excluded: chain 4 residue 180 THR Chi-restraints excluded: chain 4 residue 229 ASP Chi-restraints excluded: chain 4 residue 239 GLU Chi-restraints excluded: chain 4 residue 258 LEU Chi-restraints excluded: chain 4 residue 259 ARG Chi-restraints excluded: chain 4 residue 288 ILE Chi-restraints excluded: chain 0 residue 14 TYR Chi-restraints excluded: chain 0 residue 34 VAL Chi-restraints excluded: chain 0 residue 48 LYS Chi-restraints excluded: chain 0 residue 54 SER Chi-restraints excluded: chain 0 residue 85 GLU Chi-restraints excluded: chain 0 residue 111 ARG Chi-restraints excluded: chain 0 residue 113 ASN Chi-restraints excluded: chain 0 residue 133 CYS Chi-restraints excluded: chain 0 residue 138 ASN Chi-restraints excluded: chain 0 residue 165 ILE Chi-restraints excluded: chain 0 residue 207 ILE Chi-restraints excluded: chain 0 residue 213 LEU Chi-restraints excluded: chain 0 residue 222 VAL Chi-restraints excluded: chain 0 residue 226 VAL Chi-restraints excluded: chain 0 residue 232 VAL Chi-restraints excluded: chain 0 residue 284 ASP Chi-restraints excluded: chain 0 residue 351 VAL Chi-restraints excluded: chain 0 residue 355 THR Chi-restraints excluded: chain 0 residue 383 LEU Chi-restraints excluded: chain 0 residue 411 THR Chi-restraints excluded: chain 0 residue 430 VAL Chi-restraints excluded: chain 0 residue 447 LYS Chi-restraints excluded: chain 0 residue 453 PHE Chi-restraints excluded: chain 0 residue 458 ILE Chi-restraints excluded: chain 0 residue 477 THR Chi-restraints excluded: chain 0 residue 487 LEU Chi-restraints excluded: chain 0 residue 506 ILE Chi-restraints excluded: chain 0 residue 520 ARG Chi-restraints excluded: chain 0 residue 539 VAL Chi-restraints excluded: chain 0 residue 599 LEU Chi-restraints excluded: chain 0 residue 614 HIS Chi-restraints excluded: chain 0 residue 627 PHE Chi-restraints excluded: chain 0 residue 639 LEU Chi-restraints excluded: chain 0 residue 649 ARG Chi-restraints excluded: chain 0 residue 705 ASP Chi-restraints excluded: chain 0 residue 711 ASP Chi-restraints excluded: chain 6 residue 119 GLN Chi-restraints excluded: chain 6 residue 120 ARG Chi-restraints excluded: chain 6 residue 138 GLU Chi-restraints excluded: chain 6 residue 158 HIS Chi-restraints excluded: chain 6 residue 164 ASN Chi-restraints excluded: chain 6 residue 227 HIS Chi-restraints excluded: chain 6 residue 241 THR Chi-restraints excluded: chain 6 residue 263 VAL Chi-restraints excluded: chain 6 residue 291 LEU Chi-restraints excluded: chain 6 residue 293 ASP Chi-restraints excluded: chain 6 residue 297 LEU Chi-restraints excluded: chain 6 residue 305 VAL Chi-restraints excluded: chain 6 residue 308 LEU Chi-restraints excluded: chain 6 residue 320 VAL Chi-restraints excluded: chain 6 residue 363 CYS Chi-restraints excluded: chain 6 residue 372 LEU Chi-restraints excluded: chain 6 residue 375 HIS Chi-restraints excluded: chain 6 residue 386 LEU Chi-restraints excluded: chain 6 residue 448 LEU Chi-restraints excluded: chain 6 residue 449 HIS Chi-restraints excluded: chain 2 residue 16 GLU Chi-restraints excluded: chain 2 residue 22 GLN Chi-restraints excluded: chain 2 residue 25 LEU Chi-restraints excluded: chain 2 residue 55 ASN Chi-restraints excluded: chain 2 residue 56 GLU Chi-restraints excluded: chain 2 residue 61 ASP Chi-restraints excluded: chain 2 residue 74 PHE Chi-restraints excluded: chain 2 residue 99 ASN Chi-restraints excluded: chain 2 residue 208 LEU Chi-restraints excluded: chain 2 residue 286 ARG Chi-restraints excluded: chain 2 residue 348 TYR Chi-restraints excluded: chain 2 residue 352 ASN Chi-restraints excluded: chain 2 residue 371 VAL Chi-restraints excluded: chain 2 residue 380 ARG Chi-restraints excluded: chain 2 residue 413 GLU Chi-restraints excluded: chain 2 residue 450 ARG Chi-restraints excluded: chain 2 residue 457 SER Chi-restraints excluded: chain 2 residue 484 LYS Chi-restraints excluded: chain 2 residue 487 LYS Chi-restraints excluded: chain 2 residue 491 PHE Chi-restraints excluded: chain 5 residue 26 LYS Chi-restraints excluded: chain 5 residue 42 VAL Chi-restraints excluded: chain 5 residue 50 VAL Chi-restraints excluded: chain 5 residue 54 LEU Chi-restraints excluded: chain 5 residue 58 LEU Chi-restraints excluded: chain 7 residue 343 PHE Chi-restraints excluded: chain 7 residue 348 ARG Chi-restraints excluded: chain 7 residue 349 ASN Chi-restraints excluded: chain 7 residue 362 ILE Chi-restraints excluded: chain 7 residue 363 ARG Chi-restraints excluded: chain 7 residue 385 VAL Chi-restraints excluded: chain 7 residue 393 THR Chi-restraints excluded: chain 7 residue 411 CYS Chi-restraints excluded: chain 7 residue 419 GLN Chi-restraints excluded: chain 7 residue 428 CYS Chi-restraints excluded: chain 7 residue 433 GLU Chi-restraints excluded: chain 7 residue 453 VAL Chi-restraints excluded: chain 7 residue 456 THR Chi-restraints excluded: chain 7 residue 464 ARG Chi-restraints excluded: chain 7 residue 469 ASP Chi-restraints excluded: chain 7 residue 475 ASP Chi-restraints excluded: chain 7 residue 491 HIS Chi-restraints excluded: chain 7 residue 510 LYS Chi-restraints excluded: chain 7 residue 514 THR Chi-restraints excluded: chain 7 residue 524 ILE Chi-restraints excluded: chain 7 residue 534 LYS Chi-restraints excluded: chain 7 residue 552 VAL Chi-restraints excluded: chain 7 residue 566 TYR Chi-restraints excluded: chain 7 residue 571 ARG Chi-restraints excluded: chain 7 residue 576 LYS Chi-restraints excluded: chain 7 residue 579 LEU Chi-restraints excluded: chain 7 residue 626 PHE Chi-restraints excluded: chain 7 residue 637 MET Chi-restraints excluded: chain 7 residue 638 ASN Chi-restraints excluded: chain 7 residue 663 ASP Chi-restraints excluded: chain 7 residue 666 GLU Chi-restraints excluded: chain 7 residue 712 ASP Chi-restraints excluded: chain 7 residue 722 ARG Chi-restraints excluded: chain 7 residue 723 GLN Chi-restraints excluded: chain 3 residue 34 CYS Chi-restraints excluded: chain O residue 153 THR Chi-restraints excluded: chain O residue 159 ASN Chi-restraints excluded: chain O residue 214 LEU Chi-restraints excluded: chain O residue 234 LEU Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 47 ARG Chi-restraints excluded: chain A residue 54 ASN Chi-restraints excluded: chain A residue 55 ASP Chi-restraints excluded: chain A residue 62 ASP Chi-restraints excluded: chain A residue 81 PHE Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 91 PHE Chi-restraints excluded: chain A residue 124 GLN Chi-restraints excluded: chain A residue 167 CYS Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 177 ASP Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 232 GLU Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 299 HIS Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 346 ASP Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 438 ASP Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 525 GLN Chi-restraints excluded: chain A residue 526 ASP Chi-restraints excluded: chain A residue 529 CYS Chi-restraints excluded: chain A residue 538 ASP Chi-restraints excluded: chain A residue 544 ASP Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 592 ASP Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 666 ILE Chi-restraints excluded: chain A residue 672 ASP Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 694 THR Chi-restraints excluded: chain A residue 712 GLU Chi-restraints excluded: chain A residue 717 ASN Chi-restraints excluded: chain A residue 765 VAL Chi-restraints excluded: chain A residue 770 VAL Chi-restraints excluded: chain A residue 801 GLU Chi-restraints excluded: chain A residue 862 ASN Chi-restraints excluded: chain A residue 889 SER Chi-restraints excluded: chain A residue 909 ASP Chi-restraints excluded: chain A residue 931 GLU Chi-restraints excluded: chain A residue 949 ASP Chi-restraints excluded: chain A residue 953 ASN Chi-restraints excluded: chain A residue 979 SER Chi-restraints excluded: chain A residue 982 THR Chi-restraints excluded: chain A residue 1038 THR Chi-restraints excluded: chain A residue 1113 THR Chi-restraints excluded: chain A residue 1128 GLN Chi-restraints excluded: chain A residue 1138 ILE Chi-restraints excluded: chain A residue 1144 LYS Chi-restraints excluded: chain A residue 1197 LEU Chi-restraints excluded: chain A residue 1206 ASP Chi-restraints excluded: chain A residue 1209 MET Chi-restraints excluded: chain A residue 1211 GLN Chi-restraints excluded: chain A residue 1220 PHE Chi-restraints excluded: chain A residue 1231 ASP Chi-restraints excluded: chain A residue 1266 THR Chi-restraints excluded: chain A residue 1295 THR Chi-restraints excluded: chain A residue 1305 VAL Chi-restraints excluded: chain A residue 1327 ILE Chi-restraints excluded: chain A residue 1330 ASN Chi-restraints excluded: chain A residue 1334 ASP Chi-restraints excluded: chain A residue 1359 ASP Chi-restraints excluded: chain A residue 1393 ASN Chi-restraints excluded: chain A residue 1400 CYS Chi-restraints excluded: chain A residue 1404 GLU Chi-restraints excluded: chain A residue 1424 VAL Chi-restraints excluded: chain A residue 1450 LEU Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 61 ASP Chi-restraints excluded: chain B residue 86 ARG Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 333 PHE Chi-restraints excluded: chain B residue 363 HIS Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 391 ASP Chi-restraints excluded: chain B residue 399 ASP Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 502 ILE Chi-restraints excluded: chain B residue 527 THR Chi-restraints excluded: chain B residue 595 ARG Chi-restraints excluded: chain B residue 612 GLU Chi-restraints excluded: chain B residue 644 GLU Chi-restraints excluded: chain B residue 657 HIS Chi-restraints excluded: chain B residue 680 THR Chi-restraints excluded: chain B residue 690 VAL Chi-restraints excluded: chain B residue 697 GLU Chi-restraints excluded: chain B residue 734 HIS Chi-restraints excluded: chain B residue 805 THR Chi-restraints excluded: chain B residue 806 THR Chi-restraints excluded: chain B residue 889 THR Chi-restraints excluded: chain B residue 916 THR Chi-restraints excluded: chain B residue 918 ILE Chi-restraints excluded: chain B residue 955 THR Chi-restraints excluded: chain B residue 956 THR Chi-restraints excluded: chain B residue 959 ASP Chi-restraints excluded: chain B residue 967 ARG Chi-restraints excluded: chain B residue 982 SER Chi-restraints excluded: chain B residue 989 THR Chi-restraints excluded: chain B residue 993 THR Chi-restraints excluded: chain B residue 996 ARG Chi-restraints excluded: chain B residue 1002 THR Chi-restraints excluded: chain B residue 1049 ASP Chi-restraints excluded: chain B residue 1051 THR Chi-restraints excluded: chain B residue 1058 LEU Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain B residue 1080 LYS Chi-restraints excluded: chain B residue 1081 LEU Chi-restraints excluded: chain B residue 1093 GLN Chi-restraints excluded: chain B residue 1115 THR Chi-restraints excluded: chain B residue 1145 SER Chi-restraints excluded: chain B residue 1149 GLU Chi-restraints excluded: chain B residue 1163 CYS Chi-restraints excluded: chain B residue 1177 HIS Chi-restraints excluded: chain B residue 1192 TYR Chi-restraints excluded: chain C residue 10 ILE Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 82 TYR Chi-restraints excluded: chain C residue 91 HIS Chi-restraints excluded: chain C residue 95 CYS Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 165 LYS Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain C residue 219 PHE Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 173 HIS Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 34 GLU Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 81 GLU Chi-restraints excluded: chain E residue 84 ASP Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 182 ASP Chi-restraints excluded: chain E residue 213 ILE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain G residue 17 PHE Chi-restraints excluded: chain G residue 33 GLU Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain H residue 10 PHE Chi-restraints excluded: chain H residue 13 SER Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 41 ASP Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 110 ASP Chi-restraints excluded: chain H residue 112 ILE Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain I residue 4 PHE Chi-restraints excluded: chain I residue 5 ARG Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain I residue 108 HIS Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 10 CYS Chi-restraints excluded: chain J residue 57 ILE Chi-restraints excluded: chain K residue 10 PHE Chi-restraints excluded: chain K residue 19 LEU Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 75 ILE Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain K residue 92 ASN Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 53 HIS Chi-restraints excluded: chain L residue 60 ARG Chi-restraints excluded: chain M residue 23 THR Chi-restraints excluded: chain M residue 51 VAL Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 54 ASP Chi-restraints excluded: chain M residue 101 THR Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain M residue 125 GLU Chi-restraints excluded: chain M residue 152 GLU Chi-restraints excluded: chain M residue 197 HIS Chi-restraints excluded: chain M residue 234 GLN Chi-restraints excluded: chain M residue 236 LEU Chi-restraints excluded: chain M residue 243 CYS Chi-restraints excluded: chain M residue 287 LEU Chi-restraints excluded: chain M residue 289 PHE Chi-restraints excluded: chain M residue 319 HIS Chi-restraints excluded: chain Q residue 116 THR Chi-restraints excluded: chain Q residue 346 GLU Chi-restraints excluded: chain Q residue 359 ASN Chi-restraints excluded: chain R residue 118 HIS Chi-restraints excluded: chain R residue 123 GLU Chi-restraints excluded: chain R residue 225 MET Chi-restraints excluded: chain U residue 255 LYS Chi-restraints excluded: chain V residue 74 ASP Chi-restraints excluded: chain V residue 108 VAL Chi-restraints excluded: chain W residue 133 GLN Chi-restraints excluded: chain W residue 141 ASN Chi-restraints excluded: chain W residue 143 ASP Chi-restraints excluded: chain W residue 152 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 792 random chunks: chunk 668 optimal weight: 0.8980 chunk 600 optimal weight: 10.0000 chunk 333 optimal weight: 40.0000 chunk 205 optimal weight: 4.9990 chunk 404 optimal weight: 1.9990 chunk 320 optimal weight: 1.9990 chunk 620 optimal weight: 1.9990 chunk 240 optimal weight: 0.0980 chunk 377 optimal weight: 0.9980 chunk 462 optimal weight: 7.9990 chunk 719 optimal weight: 8.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 62 ASN ** 0 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 716 ASN 6 192 HIS 2 23 ASN ** 2 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 425 ASN 2 469 ASN ** 7 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 682 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 91 ASN O 158 GLN A 109 HIS A 525 GLN A 545 GLN ** A 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 736 ASN A 742 ASN A1009 ASN ** A1364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1427 ASN B 215 GLN ** B 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 794 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1062 HIS E 113 GLN F 100 GLN ** H 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 89 GLN J 26 GLN ** L 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 114 GLN ** M 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 212 ASN R 65 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5661 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 65841 Z= 0.219 Angle : 0.718 12.804 89355 Z= 0.379 Chirality : 0.046 0.265 10069 Planarity : 0.005 0.068 11216 Dihedral : 15.129 89.263 10780 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 16.30 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.07 % Favored : 91.86 % Rotamer: Outliers : 6.49 % Allowed : 15.90 % Favored : 77.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % Cis-general : 0.07 % Twisted Proline : 0.59 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.09), residues: 7928 helix: -0.04 (0.09), residues: 3123 sheet: -1.52 (0.16), residues: 943 loop : -1.82 (0.10), residues: 3862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP Q 361 HIS 0.009 0.001 HIS 0 294 PHE 0.034 0.002 PHE 3 47 TYR 0.028 0.002 TYR 1 583 ARG 0.008 0.001 ARG 7 380 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15856 Ramachandran restraints generated. 7928 Oldfield, 0 Emsley, 7928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15856 Ramachandran restraints generated. 7928 Oldfield, 0 Emsley, 7928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 697 residues out of total 7221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 417 poor density : 280 time to evaluate : 5.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 1 MET cc_start: 0.5241 (mtp) cc_final: 0.4933 (mtp) REVERT: 0 346 MET cc_start: 0.4159 (tpp) cc_final: 0.3606 (tpp) REVERT: 6 146 HIS cc_start: 0.6172 (OUTLIER) cc_final: 0.5711 (p-80) REVERT: 5 50 VAL cc_start: 0.4472 (OUTLIER) cc_final: 0.3984 (m) REVERT: 7 343 PHE cc_start: 0.5993 (OUTLIER) cc_final: 0.5471 (p90) REVERT: 7 393 THR cc_start: 0.5380 (OUTLIER) cc_final: 0.5089 (m) REVERT: 7 403 ILE cc_start: 0.1575 (OUTLIER) cc_final: 0.0967 (pt) REVERT: 7 534 LYS cc_start: 0.0674 (OUTLIER) cc_final: -0.0463 (mmtt) REVERT: 7 549 ILE cc_start: 0.6138 (OUTLIER) cc_final: 0.5908 (mt) REVERT: 7 583 MET cc_start: 0.3873 (ptt) cc_final: 0.3662 (ptt) REVERT: O 153 THR cc_start: 0.1665 (OUTLIER) cc_final: 0.1453 (m) REVERT: A 76 GLU cc_start: 0.6044 (OUTLIER) cc_final: 0.5779 (tp30) REVERT: A 167 CYS cc_start: 0.7225 (OUTLIER) cc_final: 0.6673 (p) REVERT: A 420 ARG cc_start: 0.6256 (OUTLIER) cc_final: 0.5542 (ttm170) REVERT: A 465 TYR cc_start: 0.7297 (OUTLIER) cc_final: 0.6905 (p90) REVERT: A 708 MET cc_start: 0.5419 (ptp) cc_final: 0.5173 (ptp) REVERT: A 873 MET cc_start: 0.7668 (mmm) cc_final: 0.7004 (mmm) REVERT: A 1113 THR cc_start: 0.7520 (OUTLIER) cc_final: 0.7315 (p) REVERT: A 1336 MET cc_start: 0.7230 (tmm) cc_final: 0.7016 (tmm) REVERT: B 764 SER cc_start: 0.8189 (OUTLIER) cc_final: 0.7858 (t) REVERT: B 967 ARG cc_start: 0.8290 (OUTLIER) cc_final: 0.7698 (ttt-90) REVERT: C 91 HIS cc_start: 0.5816 (OUTLIER) cc_final: 0.5218 (p-80) REVERT: C 165 LYS cc_start: 0.8802 (OUTLIER) cc_final: 0.8453 (ttmp) REVERT: C 219 PHE cc_start: 0.8044 (OUTLIER) cc_final: 0.7708 (p90) REVERT: E 182 ASP cc_start: 0.6687 (OUTLIER) cc_final: 0.6461 (t0) REVERT: H 10 PHE cc_start: 0.5697 (OUTLIER) cc_final: 0.4717 (m-80) REVERT: R 268 MET cc_start: 0.1820 (mmt) cc_final: 0.1457 (mtp) REVERT: X 262 MET cc_start: 0.4350 (ptt) cc_final: 0.4029 (ppp) outliers start: 417 outliers final: 227 residues processed: 678 average time/residue: 0.5959 time to fit residues: 689.5371 Evaluate side-chains 504 residues out of total 7221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 247 poor density : 257 time to evaluate : 5.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 180 LEU Chi-restraints excluded: chain 1 residue 214 ILE Chi-restraints excluded: chain 1 residue 276 LYS Chi-restraints excluded: chain 1 residue 287 PHE Chi-restraints excluded: chain 1 residue 553 LEU Chi-restraints excluded: chain 1 residue 556 THR Chi-restraints excluded: chain 4 residue 30 ILE Chi-restraints excluded: chain 4 residue 43 GLU Chi-restraints excluded: chain 4 residue 129 ILE Chi-restraints excluded: chain 4 residue 162 ARG Chi-restraints excluded: chain 4 residue 175 ARG Chi-restraints excluded: chain 4 residue 180 THR Chi-restraints excluded: chain 4 residue 239 GLU Chi-restraints excluded: chain 4 residue 258 LEU Chi-restraints excluded: chain 4 residue 259 ARG Chi-restraints excluded: chain 4 residue 288 ILE Chi-restraints excluded: chain 0 residue 14 TYR Chi-restraints excluded: chain 0 residue 85 GLU Chi-restraints excluded: chain 0 residue 111 ARG Chi-restraints excluded: chain 0 residue 207 ILE Chi-restraints excluded: chain 0 residue 213 LEU Chi-restraints excluded: chain 0 residue 226 VAL Chi-restraints excluded: chain 0 residue 232 VAL Chi-restraints excluded: chain 0 residue 284 ASP Chi-restraints excluded: chain 0 residue 285 GLU Chi-restraints excluded: chain 0 residue 355 THR Chi-restraints excluded: chain 0 residue 456 VAL Chi-restraints excluded: chain 0 residue 462 THR Chi-restraints excluded: chain 0 residue 477 THR Chi-restraints excluded: chain 0 residue 487 LEU Chi-restraints excluded: chain 0 residue 506 ILE Chi-restraints excluded: chain 0 residue 539 VAL Chi-restraints excluded: chain 0 residue 614 HIS Chi-restraints excluded: chain 0 residue 664 GLN Chi-restraints excluded: chain 0 residue 710 THR Chi-restraints excluded: chain 0 residue 741 TYR Chi-restraints excluded: chain 0 residue 745 ILE Chi-restraints excluded: chain 6 residue 119 GLN Chi-restraints excluded: chain 6 residue 120 ARG Chi-restraints excluded: chain 6 residue 129 THR Chi-restraints excluded: chain 6 residue 146 HIS Chi-restraints excluded: chain 6 residue 155 ASP Chi-restraints excluded: chain 6 residue 164 ASN Chi-restraints excluded: chain 6 residue 227 HIS Chi-restraints excluded: chain 6 residue 263 VAL Chi-restraints excluded: chain 6 residue 291 LEU Chi-restraints excluded: chain 6 residue 293 ASP Chi-restraints excluded: chain 6 residue 297 LEU Chi-restraints excluded: chain 6 residue 305 VAL Chi-restraints excluded: chain 6 residue 308 LEU Chi-restraints excluded: chain 6 residue 320 VAL Chi-restraints excluded: chain 6 residue 336 CYS Chi-restraints excluded: chain 6 residue 363 CYS Chi-restraints excluded: chain 6 residue 366 CYS Chi-restraints excluded: chain 6 residue 372 LEU Chi-restraints excluded: chain 6 residue 375 HIS Chi-restraints excluded: chain 6 residue 448 LEU Chi-restraints excluded: chain 2 residue 22 GLN Chi-restraints excluded: chain 2 residue 56 GLU Chi-restraints excluded: chain 2 residue 74 PHE Chi-restraints excluded: chain 2 residue 99 ASN Chi-restraints excluded: chain 2 residue 286 ARG Chi-restraints excluded: chain 2 residue 343 THR Chi-restraints excluded: chain 2 residue 371 VAL Chi-restraints excluded: chain 2 residue 380 ARG Chi-restraints excluded: chain 2 residue 413 GLU Chi-restraints excluded: chain 2 residue 474 TYR Chi-restraints excluded: chain 2 residue 481 LEU Chi-restraints excluded: chain 2 residue 484 LYS Chi-restraints excluded: chain 2 residue 487 LYS Chi-restraints excluded: chain 2 residue 491 PHE Chi-restraints excluded: chain 5 residue 26 LYS Chi-restraints excluded: chain 5 residue 42 VAL Chi-restraints excluded: chain 5 residue 50 VAL Chi-restraints excluded: chain 5 residue 54 LEU Chi-restraints excluded: chain 5 residue 58 LEU Chi-restraints excluded: chain 7 residue 343 PHE Chi-restraints excluded: chain 7 residue 362 ILE Chi-restraints excluded: chain 7 residue 363 ARG Chi-restraints excluded: chain 7 residue 365 TYR Chi-restraints excluded: chain 7 residue 393 THR Chi-restraints excluded: chain 7 residue 403 ILE Chi-restraints excluded: chain 7 residue 433 GLU Chi-restraints excluded: chain 7 residue 440 SER Chi-restraints excluded: chain 7 residue 456 THR Chi-restraints excluded: chain 7 residue 464 ARG Chi-restraints excluded: chain 7 residue 491 HIS Chi-restraints excluded: chain 7 residue 501 VAL Chi-restraints excluded: chain 7 residue 510 LYS Chi-restraints excluded: chain 7 residue 514 THR Chi-restraints excluded: chain 7 residue 524 ILE Chi-restraints excluded: chain 7 residue 534 LYS Chi-restraints excluded: chain 7 residue 549 ILE Chi-restraints excluded: chain 7 residue 552 VAL Chi-restraints excluded: chain 7 residue 566 TYR Chi-restraints excluded: chain 7 residue 579 LEU Chi-restraints excluded: chain 7 residue 599 GLU Chi-restraints excluded: chain 7 residue 605 ILE Chi-restraints excluded: chain 7 residue 626 PHE Chi-restraints excluded: chain 7 residue 638 ASN Chi-restraints excluded: chain 7 residue 663 ASP Chi-restraints excluded: chain 7 residue 666 GLU Chi-restraints excluded: chain 7 residue 722 ARG Chi-restraints excluded: chain 7 residue 723 GLN Chi-restraints excluded: chain 7 residue 745 ILE Chi-restraints excluded: chain 3 residue 30 VAL Chi-restraints excluded: chain 3 residue 72 ILE Chi-restraints excluded: chain O residue 153 THR Chi-restraints excluded: chain O residue 159 ASN Chi-restraints excluded: chain O residue 164 CYS Chi-restraints excluded: chain O residue 214 LEU Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 47 ARG Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 167 CYS Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 177 ASP Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain A residue 299 HIS Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 420 ARG Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 465 TYR Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 525 GLN Chi-restraints excluded: chain A residue 544 ASP Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 666 ILE Chi-restraints excluded: chain A residue 694 THR Chi-restraints excluded: chain A residue 909 ASP Chi-restraints excluded: chain A residue 949 ASP Chi-restraints excluded: chain A residue 979 SER Chi-restraints excluded: chain A residue 982 THR Chi-restraints excluded: chain A residue 1038 THR Chi-restraints excluded: chain A residue 1113 THR Chi-restraints excluded: chain A residue 1197 LEU Chi-restraints excluded: chain A residue 1231 ASP Chi-restraints excluded: chain A residue 1243 VAL Chi-restraints excluded: chain A residue 1295 THR Chi-restraints excluded: chain A residue 1305 VAL Chi-restraints excluded: chain A residue 1327 ILE Chi-restraints excluded: chain A residue 1400 CYS Chi-restraints excluded: chain A residue 1424 VAL Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 86 ARG Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 333 PHE Chi-restraints excluded: chain B residue 363 HIS Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 399 ASP Chi-restraints excluded: chain B residue 502 ILE Chi-restraints excluded: chain B residue 527 THR Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 680 THR Chi-restraints excluded: chain B residue 690 VAL Chi-restraints excluded: chain B residue 734 HIS Chi-restraints excluded: chain B residue 764 SER Chi-restraints excluded: chain B residue 805 THR Chi-restraints excluded: chain B residue 916 THR Chi-restraints excluded: chain B residue 918 ILE Chi-restraints excluded: chain B residue 956 THR Chi-restraints excluded: chain B residue 967 ARG Chi-restraints excluded: chain B residue 971 THR Chi-restraints excluded: chain B residue 989 THR Chi-restraints excluded: chain B residue 993 THR Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain B residue 1115 THR Chi-restraints excluded: chain B residue 1163 CYS Chi-restraints excluded: chain B residue 1169 MET Chi-restraints excluded: chain B residue 1177 HIS Chi-restraints excluded: chain B residue 1215 ARG Chi-restraints excluded: chain C residue 23 SER Chi-restraints excluded: chain C residue 91 HIS Chi-restraints excluded: chain C residue 95 CYS Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 135 GLN Chi-restraints excluded: chain C residue 165 LYS Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain C residue 219 PHE Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 173 HIS Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 182 ASP Chi-restraints excluded: chain E residue 213 ILE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain G residue 33 GLU Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain H residue 10 PHE Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 112 ILE Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain I residue 4 PHE Chi-restraints excluded: chain I residue 5 ARG Chi-restraints excluded: chain I residue 29 CYS Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain J residue 10 CYS Chi-restraints excluded: chain J residue 57 ILE Chi-restraints excluded: chain K residue 10 PHE Chi-restraints excluded: chain K residue 19 LEU Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain L residue 53 HIS Chi-restraints excluded: chain L residue 60 ARG Chi-restraints excluded: chain M residue 23 THR Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain M residue 125 GLU Chi-restraints excluded: chain M residue 152 GLU Chi-restraints excluded: chain M residue 197 HIS Chi-restraints excluded: chain M residue 234 GLN Chi-restraints excluded: chain M residue 236 LEU Chi-restraints excluded: chain M residue 287 LEU Chi-restraints excluded: chain M residue 289 PHE Chi-restraints excluded: chain M residue 319 HIS Chi-restraints excluded: chain Q residue 27 MET Chi-restraints excluded: chain Q residue 343 ARG Chi-restraints excluded: chain Q residue 346 GLU Chi-restraints excluded: chain Q residue 359 ASN Chi-restraints excluded: chain R residue 63 ARG Chi-restraints excluded: chain R residue 118 HIS Chi-restraints excluded: chain U residue 244 MET Chi-restraints excluded: chain V residue 108 VAL Chi-restraints excluded: chain W residue 12 LEU Chi-restraints excluded: chain W residue 133 GLN Chi-restraints excluded: chain W residue 141 ASN Chi-restraints excluded: chain W residue 152 CYS Chi-restraints excluded: chain X residue 218 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 792 random chunks: chunk 399 optimal weight: 20.0000 chunk 223 optimal weight: 0.0020 chunk 598 optimal weight: 10.0000 chunk 489 optimal weight: 8.9990 chunk 198 optimal weight: 5.9990 chunk 720 optimal weight: 0.9980 chunk 778 optimal weight: 30.0000 chunk 641 optimal weight: 5.9990 chunk 714 optimal weight: 4.9990 chunk 245 optimal weight: 10.0000 chunk 578 optimal weight: 6.9990 overall best weight: 3.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 62 ASN ** 0 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0 242 ASN ** 0 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 555 GLN ** 0 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 269 GLN ** 2 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 634 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 682 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 31 ASN A 525 GLN ** A 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5708 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 65841 Z= 0.244 Angle : 0.665 13.062 89355 Z= 0.347 Chirality : 0.044 0.311 10069 Planarity : 0.005 0.070 11216 Dihedral : 14.474 89.730 10440 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 16.32 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.17 % Favored : 91.75 % Rotamer: Outliers : 5.76 % Allowed : 16.85 % Favored : 77.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % Cis-general : 0.07 % Twisted Proline : 0.29 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.09), residues: 7928 helix: 0.10 (0.09), residues: 3124 sheet: -1.49 (0.16), residues: 946 loop : -1.77 (0.10), residues: 3858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP 7 482 HIS 0.009 0.001 HIS 7 508 PHE 0.031 0.001 PHE K 7 TYR 0.027 0.001 TYR 1 583 ARG 0.015 0.000 ARG 7 577 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15856 Ramachandran restraints generated. 7928 Oldfield, 0 Emsley, 7928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15856 Ramachandran restraints generated. 7928 Oldfield, 0 Emsley, 7928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 636 residues out of total 7221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 370 poor density : 266 time to evaluate : 6.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 1 MET cc_start: 0.5247 (mtp) cc_final: 0.4711 (mtp) REVERT: 0 136 MET cc_start: 0.4390 (ptm) cc_final: 0.4143 (ptt) REVERT: 0 221 ARG cc_start: 0.7553 (OUTLIER) cc_final: 0.6583 (pmt-80) REVERT: 0 346 MET cc_start: 0.4292 (tpp) cc_final: 0.3145 (tpt) REVERT: 0 389 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.8030 (pm20) REVERT: 6 146 HIS cc_start: 0.6256 (OUTLIER) cc_final: 0.5570 (p-80) REVERT: 5 50 VAL cc_start: 0.4583 (OUTLIER) cc_final: 0.4162 (m) REVERT: 7 343 PHE cc_start: 0.5834 (OUTLIER) cc_final: 0.5473 (p90) REVERT: 7 534 LYS cc_start: 0.0730 (OUTLIER) cc_final: -0.0238 (mmtt) REVERT: 7 663 ASP cc_start: 0.2269 (OUTLIER) cc_final: 0.2057 (m-30) REVERT: A 76 GLU cc_start: 0.6184 (OUTLIER) cc_final: 0.5902 (tp30) REVERT: A 81 PHE cc_start: 0.7988 (OUTLIER) cc_final: 0.7398 (m-80) REVERT: A 167 CYS cc_start: 0.7183 (OUTLIER) cc_final: 0.6793 (p) REVERT: A 215 SER cc_start: 0.7430 (OUTLIER) cc_final: 0.7072 (p) REVERT: A 420 ARG cc_start: 0.6178 (OUTLIER) cc_final: 0.5433 (ttm170) REVERT: A 465 TYR cc_start: 0.7395 (OUTLIER) cc_final: 0.6906 (p90) REVERT: A 873 MET cc_start: 0.7712 (mmm) cc_final: 0.6877 (mmm) REVERT: A 1336 MET cc_start: 0.7336 (tmm) cc_final: 0.7118 (tmm) REVERT: B 364 ILE cc_start: 0.7313 (OUTLIER) cc_final: 0.7008 (pt) REVERT: B 597 MET cc_start: 0.6502 (tpt) cc_final: 0.6288 (tpp) REVERT: B 764 SER cc_start: 0.8307 (OUTLIER) cc_final: 0.8067 (t) REVERT: B 967 ARG cc_start: 0.8260 (OUTLIER) cc_final: 0.7775 (ttt-90) REVERT: B 1152 MET cc_start: 0.8041 (mmm) cc_final: 0.7759 (mmm) REVERT: C 91 HIS cc_start: 0.5760 (OUTLIER) cc_final: 0.5071 (p-80) REVERT: C 165 LYS cc_start: 0.8821 (OUTLIER) cc_final: 0.8373 (ttmp) REVERT: C 219 PHE cc_start: 0.7976 (OUTLIER) cc_final: 0.7666 (p90) REVERT: E 57 MET cc_start: 0.6431 (ppp) cc_final: 0.5519 (ppp) REVERT: X 262 MET cc_start: 0.4312 (ptt) cc_final: 0.3553 (ppp) outliers start: 370 outliers final: 234 residues processed: 624 average time/residue: 0.5980 time to fit residues: 639.2726 Evaluate side-chains 506 residues out of total 7221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 253 poor density : 253 time to evaluate : 5.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 180 LEU Chi-restraints excluded: chain 1 residue 214 ILE Chi-restraints excluded: chain 1 residue 276 LYS Chi-restraints excluded: chain 1 residue 287 PHE Chi-restraints excluded: chain 1 residue 553 LEU Chi-restraints excluded: chain 1 residue 556 THR Chi-restraints excluded: chain 4 residue 129 ILE Chi-restraints excluded: chain 4 residue 162 ARG Chi-restraints excluded: chain 4 residue 175 ARG Chi-restraints excluded: chain 4 residue 258 LEU Chi-restraints excluded: chain 4 residue 259 ARG Chi-restraints excluded: chain 4 residue 288 ILE Chi-restraints excluded: chain 0 residue 14 TYR Chi-restraints excluded: chain 0 residue 34 VAL Chi-restraints excluded: chain 0 residue 120 VAL Chi-restraints excluded: chain 0 residue 165 ILE Chi-restraints excluded: chain 0 residue 213 LEU Chi-restraints excluded: chain 0 residue 221 ARG Chi-restraints excluded: chain 0 residue 222 VAL Chi-restraints excluded: chain 0 residue 226 VAL Chi-restraints excluded: chain 0 residue 232 VAL Chi-restraints excluded: chain 0 residue 284 ASP Chi-restraints excluded: chain 0 residue 285 GLU Chi-restraints excluded: chain 0 residue 321 ILE Chi-restraints excluded: chain 0 residue 355 THR Chi-restraints excluded: chain 0 residue 389 GLU Chi-restraints excluded: chain 0 residue 430 VAL Chi-restraints excluded: chain 0 residue 447 LYS Chi-restraints excluded: chain 0 residue 453 PHE Chi-restraints excluded: chain 0 residue 456 VAL Chi-restraints excluded: chain 0 residue 462 THR Chi-restraints excluded: chain 0 residue 477 THR Chi-restraints excluded: chain 0 residue 487 LEU Chi-restraints excluded: chain 0 residue 506 ILE Chi-restraints excluded: chain 0 residue 539 VAL Chi-restraints excluded: chain 0 residue 557 MET Chi-restraints excluded: chain 0 residue 614 HIS Chi-restraints excluded: chain 0 residue 664 GLN Chi-restraints excluded: chain 0 residue 711 ASP Chi-restraints excluded: chain 0 residue 718 LYS Chi-restraints excluded: chain 0 residue 745 ILE Chi-restraints excluded: chain 6 residue 119 GLN Chi-restraints excluded: chain 6 residue 120 ARG Chi-restraints excluded: chain 6 residue 146 HIS Chi-restraints excluded: chain 6 residue 155 ASP Chi-restraints excluded: chain 6 residue 164 ASN Chi-restraints excluded: chain 6 residue 210 LEU Chi-restraints excluded: chain 6 residue 227 HIS Chi-restraints excluded: chain 6 residue 263 VAL Chi-restraints excluded: chain 6 residue 291 LEU Chi-restraints excluded: chain 6 residue 293 ASP Chi-restraints excluded: chain 6 residue 297 LEU Chi-restraints excluded: chain 6 residue 305 VAL Chi-restraints excluded: chain 6 residue 308 LEU Chi-restraints excluded: chain 6 residue 320 VAL Chi-restraints excluded: chain 6 residue 336 CYS Chi-restraints excluded: chain 6 residue 363 CYS Chi-restraints excluded: chain 6 residue 366 CYS Chi-restraints excluded: chain 6 residue 372 LEU Chi-restraints excluded: chain 6 residue 375 HIS Chi-restraints excluded: chain 6 residue 406 CYS Chi-restraints excluded: chain 6 residue 448 LEU Chi-restraints excluded: chain 2 residue 55 ASN Chi-restraints excluded: chain 2 residue 56 GLU Chi-restraints excluded: chain 2 residue 74 PHE Chi-restraints excluded: chain 2 residue 99 ASN Chi-restraints excluded: chain 2 residue 286 ARG Chi-restraints excluded: chain 2 residue 343 THR Chi-restraints excluded: chain 2 residue 348 TYR Chi-restraints excluded: chain 2 residue 359 VAL Chi-restraints excluded: chain 2 residue 371 VAL Chi-restraints excluded: chain 2 residue 380 ARG Chi-restraints excluded: chain 2 residue 413 GLU Chi-restraints excluded: chain 2 residue 474 TYR Chi-restraints excluded: chain 2 residue 481 LEU Chi-restraints excluded: chain 2 residue 484 LYS Chi-restraints excluded: chain 2 residue 487 LYS Chi-restraints excluded: chain 2 residue 491 PHE Chi-restraints excluded: chain 5 residue 26 LYS Chi-restraints excluded: chain 5 residue 42 VAL Chi-restraints excluded: chain 5 residue 50 VAL Chi-restraints excluded: chain 5 residue 54 LEU Chi-restraints excluded: chain 5 residue 58 LEU Chi-restraints excluded: chain 7 residue 343 PHE Chi-restraints excluded: chain 7 residue 348 ARG Chi-restraints excluded: chain 7 residue 362 ILE Chi-restraints excluded: chain 7 residue 363 ARG Chi-restraints excluded: chain 7 residue 365 TYR Chi-restraints excluded: chain 7 residue 440 SER Chi-restraints excluded: chain 7 residue 456 THR Chi-restraints excluded: chain 7 residue 464 ARG Chi-restraints excluded: chain 7 residue 491 HIS Chi-restraints excluded: chain 7 residue 501 VAL Chi-restraints excluded: chain 7 residue 510 LYS Chi-restraints excluded: chain 7 residue 514 THR Chi-restraints excluded: chain 7 residue 524 ILE Chi-restraints excluded: chain 7 residue 534 LYS Chi-restraints excluded: chain 7 residue 552 VAL Chi-restraints excluded: chain 7 residue 566 TYR Chi-restraints excluded: chain 7 residue 579 LEU Chi-restraints excluded: chain 7 residue 605 ILE Chi-restraints excluded: chain 7 residue 626 PHE Chi-restraints excluded: chain 7 residue 638 ASN Chi-restraints excluded: chain 7 residue 663 ASP Chi-restraints excluded: chain 7 residue 722 ARG Chi-restraints excluded: chain 7 residue 723 GLN Chi-restraints excluded: chain 7 residue 745 ILE Chi-restraints excluded: chain O residue 159 ASN Chi-restraints excluded: chain O residue 164 CYS Chi-restraints excluded: chain O residue 214 LEU Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 47 ARG Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 81 PHE Chi-restraints excluded: chain A residue 167 CYS Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 177 ASP Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain A residue 299 HIS Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 420 ARG Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 465 TYR Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 525 GLN Chi-restraints excluded: chain A residue 544 ASP Chi-restraints excluded: chain A residue 549 MET Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 694 THR Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 889 SER Chi-restraints excluded: chain A residue 909 ASP Chi-restraints excluded: chain A residue 949 ASP Chi-restraints excluded: chain A residue 982 THR Chi-restraints excluded: chain A residue 1038 THR Chi-restraints excluded: chain A residue 1144 LYS Chi-restraints excluded: chain A residue 1197 LEU Chi-restraints excluded: chain A residue 1231 ASP Chi-restraints excluded: chain A residue 1295 THR Chi-restraints excluded: chain A residue 1305 VAL Chi-restraints excluded: chain A residue 1327 ILE Chi-restraints excluded: chain A residue 1400 CYS Chi-restraints excluded: chain A residue 1424 VAL Chi-restraints excluded: chain A residue 1450 LEU Chi-restraints excluded: chain A residue 1452 LYS Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 86 ARG Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 363 HIS Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 527 THR Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 690 VAL Chi-restraints excluded: chain B residue 734 HIS Chi-restraints excluded: chain B residue 764 SER Chi-restraints excluded: chain B residue 805 THR Chi-restraints excluded: chain B residue 916 THR Chi-restraints excluded: chain B residue 918 ILE Chi-restraints excluded: chain B residue 956 THR Chi-restraints excluded: chain B residue 967 ARG Chi-restraints excluded: chain B residue 971 THR Chi-restraints excluded: chain B residue 989 THR Chi-restraints excluded: chain B residue 993 THR Chi-restraints excluded: chain B residue 1007 VAL Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain B residue 1115 THR Chi-restraints excluded: chain B residue 1177 HIS Chi-restraints excluded: chain B residue 1215 ARG Chi-restraints excluded: chain C residue 23 SER Chi-restraints excluded: chain C residue 91 HIS Chi-restraints excluded: chain C residue 95 CYS Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 135 GLN Chi-restraints excluded: chain C residue 165 LYS Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain C residue 219 PHE Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 173 HIS Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain D residue 221 TYR Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 213 ILE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain G residue 33 GLU Chi-restraints excluded: chain G residue 54 ILE Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 112 ILE Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain I residue 4 PHE Chi-restraints excluded: chain I residue 5 ARG Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 10 CYS Chi-restraints excluded: chain J residue 57 ILE Chi-restraints excluded: chain K residue 19 LEU Chi-restraints excluded: chain K residue 51 LEU Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 53 HIS Chi-restraints excluded: chain L residue 60 ARG Chi-restraints excluded: chain M residue 23 THR Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 101 THR Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain M residue 125 GLU Chi-restraints excluded: chain M residue 152 GLU Chi-restraints excluded: chain M residue 176 ILE Chi-restraints excluded: chain M residue 197 HIS Chi-restraints excluded: chain M residue 234 GLN Chi-restraints excluded: chain M residue 236 LEU Chi-restraints excluded: chain M residue 289 PHE Chi-restraints excluded: chain M residue 319 HIS Chi-restraints excluded: chain Q residue 127 ILE Chi-restraints excluded: chain Q residue 343 ARG Chi-restraints excluded: chain Q residue 346 GLU Chi-restraints excluded: chain Q residue 359 ASN Chi-restraints excluded: chain R residue 63 ARG Chi-restraints excluded: chain R residue 118 HIS Chi-restraints excluded: chain R residue 224 VAL Chi-restraints excluded: chain R residue 253 THR Chi-restraints excluded: chain U residue 244 MET Chi-restraints excluded: chain U residue 257 ARG Chi-restraints excluded: chain V residue 108 VAL Chi-restraints excluded: chain V residue 114 VAL Chi-restraints excluded: chain W residue 12 LEU Chi-restraints excluded: chain W residue 133 GLN Chi-restraints excluded: chain W residue 137 VAL Chi-restraints excluded: chain W residue 152 CYS Chi-restraints excluded: chain X residue 270 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 792 random chunks: chunk 711 optimal weight: 0.0670 chunk 541 optimal weight: 5.9990 chunk 373 optimal weight: 2.9990 chunk 79 optimal weight: 8.9990 chunk 343 optimal weight: 20.0000 chunk 483 optimal weight: 3.9990 chunk 723 optimal weight: 5.9990 chunk 765 optimal weight: 40.0000 chunk 377 optimal weight: 0.9990 chunk 685 optimal weight: 5.9990 chunk 206 optimal weight: 0.7980 overall best weight: 1.7724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 151 GLN 6 269 GLN ** 2 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 592 GLN ** 7 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 634 GLN ** 7 682 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 659 HIS ** A1128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 465 ASN B 513 GLN B1093 GLN ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 102 GLN ** H 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 12 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5650 moved from start: 0.2939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 65841 Z= 0.181 Angle : 0.641 13.485 89355 Z= 0.332 Chirality : 0.043 0.239 10069 Planarity : 0.004 0.070 11216 Dihedral : 14.161 88.538 10390 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 14.09 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.54 % Favored : 92.39 % Rotamer: Outliers : 4.90 % Allowed : 17.68 % Favored : 77.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % Cis-general : 0.07 % Twisted Proline : 0.29 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.09), residues: 7928 helix: 0.25 (0.09), residues: 3151 sheet: -1.31 (0.16), residues: 929 loop : -1.74 (0.10), residues: 3848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP W 100 HIS 0.005 0.001 HIS 0 294 PHE 0.034 0.001 PHE K 10 TYR 0.024 0.001 TYR 0 208 ARG 0.017 0.000 ARG K 6 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15856 Ramachandran restraints generated. 7928 Oldfield, 0 Emsley, 7928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15856 Ramachandran restraints generated. 7928 Oldfield, 0 Emsley, 7928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 576 residues out of total 7221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 315 poor density : 261 time to evaluate : 5.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 136 MET cc_start: 0.5126 (ptm) cc_final: 0.4712 (ptm) REVERT: 0 221 ARG cc_start: 0.7542 (OUTLIER) cc_final: 0.6573 (pmt-80) REVERT: 0 389 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.8036 (pm20) REVERT: 6 146 HIS cc_start: 0.5999 (OUTLIER) cc_final: 0.5457 (p-80) REVERT: 2 374 VAL cc_start: 0.5678 (OUTLIER) cc_final: 0.5430 (m) REVERT: 5 50 VAL cc_start: 0.5009 (OUTLIER) cc_final: 0.4808 (m) REVERT: 7 534 LYS cc_start: 0.0865 (OUTLIER) cc_final: -0.0062 (mmtt) REVERT: 7 663 ASP cc_start: 0.1947 (OUTLIER) cc_final: 0.1645 (m-30) REVERT: A 76 GLU cc_start: 0.5965 (OUTLIER) cc_final: 0.5706 (tp30) REVERT: A 167 CYS cc_start: 0.7214 (OUTLIER) cc_final: 0.6776 (p) REVERT: A 215 SER cc_start: 0.7309 (OUTLIER) cc_final: 0.6979 (p) REVERT: A 304 MET cc_start: 0.6336 (mmt) cc_final: 0.6058 (mmm) REVERT: A 420 ARG cc_start: 0.6087 (OUTLIER) cc_final: 0.5343 (ttm170) REVERT: A 465 TYR cc_start: 0.7327 (OUTLIER) cc_final: 0.6969 (p90) REVERT: A 873 MET cc_start: 0.7709 (mmm) cc_final: 0.6942 (mmm) REVERT: A 900 ASP cc_start: 0.6830 (OUTLIER) cc_final: 0.6592 (p0) REVERT: B 364 ILE cc_start: 0.7137 (OUTLIER) cc_final: 0.6881 (pt) REVERT: B 764 SER cc_start: 0.8140 (OUTLIER) cc_final: 0.7932 (t) REVERT: B 948 ILE cc_start: 0.8864 (OUTLIER) cc_final: 0.8563 (mp) REVERT: C 91 HIS cc_start: 0.5863 (OUTLIER) cc_final: 0.5127 (p-80) REVERT: C 219 PHE cc_start: 0.7992 (OUTLIER) cc_final: 0.7637 (p90) REVERT: G 102 GLN cc_start: 0.6306 (OUTLIER) cc_final: 0.6007 (tt0) REVERT: X 262 MET cc_start: 0.4378 (ptt) cc_final: 0.3861 (ppp) outliers start: 315 outliers final: 197 residues processed: 567 average time/residue: 0.6028 time to fit residues: 587.9693 Evaluate side-chains 463 residues out of total 7221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 216 poor density : 247 time to evaluate : 5.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 180 LEU Chi-restraints excluded: chain 1 residue 214 ILE Chi-restraints excluded: chain 1 residue 276 LYS Chi-restraints excluded: chain 1 residue 287 PHE Chi-restraints excluded: chain 1 residue 553 LEU Chi-restraints excluded: chain 1 residue 556 THR Chi-restraints excluded: chain 1 residue 600 VAL Chi-restraints excluded: chain 4 residue 30 ILE Chi-restraints excluded: chain 4 residue 162 ARG Chi-restraints excluded: chain 4 residue 175 ARG Chi-restraints excluded: chain 4 residue 180 THR Chi-restraints excluded: chain 4 residue 258 LEU Chi-restraints excluded: chain 4 residue 273 ARG Chi-restraints excluded: chain 4 residue 288 ILE Chi-restraints excluded: chain 0 residue 14 TYR Chi-restraints excluded: chain 0 residue 34 VAL Chi-restraints excluded: chain 0 residue 120 VAL Chi-restraints excluded: chain 0 residue 213 LEU Chi-restraints excluded: chain 0 residue 221 ARG Chi-restraints excluded: chain 0 residue 355 THR Chi-restraints excluded: chain 0 residue 389 GLU Chi-restraints excluded: chain 0 residue 430 VAL Chi-restraints excluded: chain 0 residue 453 PHE Chi-restraints excluded: chain 0 residue 462 THR Chi-restraints excluded: chain 0 residue 477 THR Chi-restraints excluded: chain 0 residue 487 LEU Chi-restraints excluded: chain 0 residue 506 ILE Chi-restraints excluded: chain 0 residue 539 VAL Chi-restraints excluded: chain 0 residue 557 MET Chi-restraints excluded: chain 0 residue 614 HIS Chi-restraints excluded: chain 0 residue 664 GLN Chi-restraints excluded: chain 0 residue 711 ASP Chi-restraints excluded: chain 0 residue 718 LYS Chi-restraints excluded: chain 0 residue 745 ILE Chi-restraints excluded: chain 6 residue 119 GLN Chi-restraints excluded: chain 6 residue 146 HIS Chi-restraints excluded: chain 6 residue 155 ASP Chi-restraints excluded: chain 6 residue 210 LEU Chi-restraints excluded: chain 6 residue 227 HIS Chi-restraints excluded: chain 6 residue 263 VAL Chi-restraints excluded: chain 6 residue 291 LEU Chi-restraints excluded: chain 6 residue 293 ASP Chi-restraints excluded: chain 6 residue 305 VAL Chi-restraints excluded: chain 6 residue 320 VAL Chi-restraints excluded: chain 6 residue 336 CYS Chi-restraints excluded: chain 6 residue 363 CYS Chi-restraints excluded: chain 6 residue 366 CYS Chi-restraints excluded: chain 6 residue 372 LEU Chi-restraints excluded: chain 6 residue 375 HIS Chi-restraints excluded: chain 6 residue 448 LEU Chi-restraints excluded: chain 2 residue 55 ASN Chi-restraints excluded: chain 2 residue 56 GLU Chi-restraints excluded: chain 2 residue 74 PHE Chi-restraints excluded: chain 2 residue 88 ILE Chi-restraints excluded: chain 2 residue 99 ASN Chi-restraints excluded: chain 2 residue 343 THR Chi-restraints excluded: chain 2 residue 348 TYR Chi-restraints excluded: chain 2 residue 359 VAL Chi-restraints excluded: chain 2 residue 371 VAL Chi-restraints excluded: chain 2 residue 374 VAL Chi-restraints excluded: chain 2 residue 380 ARG Chi-restraints excluded: chain 2 residue 474 TYR Chi-restraints excluded: chain 2 residue 481 LEU Chi-restraints excluded: chain 2 residue 484 LYS Chi-restraints excluded: chain 2 residue 487 LYS Chi-restraints excluded: chain 2 residue 491 PHE Chi-restraints excluded: chain 5 residue 26 LYS Chi-restraints excluded: chain 5 residue 42 VAL Chi-restraints excluded: chain 5 residue 50 VAL Chi-restraints excluded: chain 5 residue 54 LEU Chi-restraints excluded: chain 7 residue 362 ILE Chi-restraints excluded: chain 7 residue 365 TYR Chi-restraints excluded: chain 7 residue 440 SER Chi-restraints excluded: chain 7 residue 456 THR Chi-restraints excluded: chain 7 residue 464 ARG Chi-restraints excluded: chain 7 residue 491 HIS Chi-restraints excluded: chain 7 residue 510 LYS Chi-restraints excluded: chain 7 residue 514 THR Chi-restraints excluded: chain 7 residue 524 ILE Chi-restraints excluded: chain 7 residue 534 LYS Chi-restraints excluded: chain 7 residue 552 VAL Chi-restraints excluded: chain 7 residue 566 TYR Chi-restraints excluded: chain 7 residue 579 LEU Chi-restraints excluded: chain 7 residue 626 PHE Chi-restraints excluded: chain 7 residue 634 GLN Chi-restraints excluded: chain 7 residue 638 ASN Chi-restraints excluded: chain 7 residue 663 ASP Chi-restraints excluded: chain 7 residue 666 GLU Chi-restraints excluded: chain 7 residue 722 ARG Chi-restraints excluded: chain 7 residue 723 GLN Chi-restraints excluded: chain 7 residue 745 ILE Chi-restraints excluded: chain 3 residue 72 ILE Chi-restraints excluded: chain O residue 164 CYS Chi-restraints excluded: chain O residue 214 LEU Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 47 ARG Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 167 CYS Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 177 ASP Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 299 HIS Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 420 ARG Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 465 TYR Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 525 GLN Chi-restraints excluded: chain A residue 544 ASP Chi-restraints excluded: chain A residue 549 MET Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 694 THR Chi-restraints excluded: chain A residue 724 GLU Chi-restraints excluded: chain A residue 900 ASP Chi-restraints excluded: chain A residue 909 ASP Chi-restraints excluded: chain A residue 949 ASP Chi-restraints excluded: chain A residue 1038 THR Chi-restraints excluded: chain A residue 1101 LEU Chi-restraints excluded: chain A residue 1197 LEU Chi-restraints excluded: chain A residue 1305 VAL Chi-restraints excluded: chain A residue 1327 ILE Chi-restraints excluded: chain A residue 1400 CYS Chi-restraints excluded: chain A residue 1452 LYS Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 363 HIS Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 527 THR Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 690 VAL Chi-restraints excluded: chain B residue 734 HIS Chi-restraints excluded: chain B residue 764 SER Chi-restraints excluded: chain B residue 805 THR Chi-restraints excluded: chain B residue 916 THR Chi-restraints excluded: chain B residue 918 ILE Chi-restraints excluded: chain B residue 948 ILE Chi-restraints excluded: chain B residue 956 THR Chi-restraints excluded: chain B residue 971 THR Chi-restraints excluded: chain B residue 989 THR Chi-restraints excluded: chain B residue 993 THR Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain B residue 1093 GLN Chi-restraints excluded: chain B residue 1115 THR Chi-restraints excluded: chain B residue 1163 CYS Chi-restraints excluded: chain B residue 1177 HIS Chi-restraints excluded: chain C residue 23 SER Chi-restraints excluded: chain C residue 82 TYR Chi-restraints excluded: chain C residue 91 HIS Chi-restraints excluded: chain C residue 95 CYS Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 135 GLN Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain C residue 219 PHE Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain D residue 221 TYR Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 213 ILE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain G residue 33 GLU Chi-restraints excluded: chain G residue 102 GLN Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 112 ILE Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain I residue 4 PHE Chi-restraints excluded: chain I residue 5 ARG Chi-restraints excluded: chain I residue 12 ASN Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 10 CYS Chi-restraints excluded: chain J residue 57 ILE Chi-restraints excluded: chain K residue 19 LEU Chi-restraints excluded: chain K residue 51 LEU Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain L residue 53 HIS Chi-restraints excluded: chain L residue 60 ARG Chi-restraints excluded: chain M residue 23 THR Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain M residue 125 GLU Chi-restraints excluded: chain M residue 152 GLU Chi-restraints excluded: chain M residue 197 HIS Chi-restraints excluded: chain M residue 234 GLN Chi-restraints excluded: chain M residue 236 LEU Chi-restraints excluded: chain M residue 289 PHE Chi-restraints excluded: chain M residue 319 HIS Chi-restraints excluded: chain Q residue 27 MET Chi-restraints excluded: chain Q residue 127 ILE Chi-restraints excluded: chain Q residue 343 ARG Chi-restraints excluded: chain Q residue 359 ASN Chi-restraints excluded: chain Q residue 396 THR Chi-restraints excluded: chain R residue 118 HIS Chi-restraints excluded: chain R residue 224 VAL Chi-restraints excluded: chain R residue 253 THR Chi-restraints excluded: chain U residue 257 ARG Chi-restraints excluded: chain V residue 108 VAL Chi-restraints excluded: chain W residue 12 LEU Chi-restraints excluded: chain W residue 133 GLN Chi-restraints excluded: chain W residue 152 CYS Chi-restraints excluded: chain X residue 270 GLN Chi-restraints excluded: chain X residue 276 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 792 random chunks: chunk 637 optimal weight: 6.9990 chunk 434 optimal weight: 3.9990 chunk 11 optimal weight: 9.9990 chunk 570 optimal weight: 6.9990 chunk 315 optimal weight: 7.9990 chunk 653 optimal weight: 10.0000 chunk 529 optimal weight: 6.9990 chunk 0 optimal weight: 70.0000 chunk 390 optimal weight: 0.0470 chunk 687 optimal weight: 0.9990 chunk 193 optimal weight: 10.0000 overall best weight: 3.8086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 682 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 576 GLN ** A1128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1093 GLN D 179 GLN ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 102 GLN ** H 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5699 moved from start: 0.3103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 65841 Z= 0.236 Angle : 0.642 12.424 89355 Z= 0.332 Chirality : 0.043 0.281 10069 Planarity : 0.004 0.071 11216 Dihedral : 13.950 88.451 10320 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 15.06 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.07 % Favored : 91.86 % Rotamer: Outliers : 4.84 % Allowed : 18.22 % Favored : 76.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % Cis-general : 0.07 % Twisted Proline : 0.29 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.09), residues: 7928 helix: 0.37 (0.09), residues: 3154 sheet: -1.33 (0.17), residues: 921 loop : -1.75 (0.10), residues: 3853 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP 7 482 HIS 0.006 0.001 HIS A 399 PHE 0.028 0.001 PHE J 8 TYR 0.016 0.001 TYR 7 613 ARG 0.010 0.000 ARG B1135 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15856 Ramachandran restraints generated. 7928 Oldfield, 0 Emsley, 7928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15856 Ramachandran restraints generated. 7928 Oldfield, 0 Emsley, 7928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 566 residues out of total 7221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 311 poor density : 255 time to evaluate : 5.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 136 MET cc_start: 0.5211 (ptm) cc_final: 0.4734 (ptm) REVERT: 0 221 ARG cc_start: 0.7483 (OUTLIER) cc_final: 0.6523 (pmt-80) REVERT: 0 389 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.8018 (pm20) REVERT: 6 146 HIS cc_start: 0.5930 (OUTLIER) cc_final: 0.5284 (p-80) REVERT: 7 534 LYS cc_start: 0.1333 (OUTLIER) cc_final: 0.0411 (mmtt) REVERT: 7 663 ASP cc_start: 0.1619 (OUTLIER) cc_final: 0.1411 (m-30) REVERT: 3 49 LEU cc_start: 0.2571 (OUTLIER) cc_final: 0.2136 (mt) REVERT: A 167 CYS cc_start: 0.7277 (OUTLIER) cc_final: 0.6839 (p) REVERT: A 215 SER cc_start: 0.7379 (OUTLIER) cc_final: 0.7108 (p) REVERT: A 420 ARG cc_start: 0.6331 (OUTLIER) cc_final: 0.5518 (ttm170) REVERT: A 465 TYR cc_start: 0.7359 (OUTLIER) cc_final: 0.7051 (p90) REVERT: A 900 ASP cc_start: 0.6907 (OUTLIER) cc_final: 0.6608 (p0) REVERT: A 1375 MET cc_start: 0.6524 (mtp) cc_final: 0.6249 (ttp) REVERT: B 364 ILE cc_start: 0.7297 (OUTLIER) cc_final: 0.7041 (pt) REVERT: B 764 SER cc_start: 0.8168 (OUTLIER) cc_final: 0.7946 (t) REVERT: B 923 GLU cc_start: 0.2593 (OUTLIER) cc_final: 0.1081 (mt-10) REVERT: B 948 ILE cc_start: 0.8826 (OUTLIER) cc_final: 0.8497 (mp) REVERT: C 91 HIS cc_start: 0.5721 (OUTLIER) cc_final: 0.4986 (p-80) REVERT: C 219 PHE cc_start: 0.7985 (OUTLIER) cc_final: 0.7632 (p90) REVERT: E 57 MET cc_start: 0.6504 (ppp) cc_final: 0.6116 (ppp) REVERT: E 75 MET cc_start: 0.5195 (tpt) cc_final: 0.4915 (tpt) REVERT: E 215 MET cc_start: 0.7591 (pmm) cc_final: 0.7218 (pmm) REVERT: X 262 MET cc_start: 0.4261 (ptt) cc_final: 0.3822 (ppp) outliers start: 311 outliers final: 221 residues processed: 559 average time/residue: 0.5919 time to fit residues: 573.1101 Evaluate side-chains 483 residues out of total 7221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 238 poor density : 245 time to evaluate : 5.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 180 LEU Chi-restraints excluded: chain 1 residue 214 ILE Chi-restraints excluded: chain 1 residue 276 LYS Chi-restraints excluded: chain 1 residue 287 PHE Chi-restraints excluded: chain 1 residue 553 LEU Chi-restraints excluded: chain 1 residue 556 THR Chi-restraints excluded: chain 4 residue 162 ARG Chi-restraints excluded: chain 4 residue 175 ARG Chi-restraints excluded: chain 4 residue 180 THR Chi-restraints excluded: chain 4 residue 245 ILE Chi-restraints excluded: chain 4 residue 258 LEU Chi-restraints excluded: chain 4 residue 273 ARG Chi-restraints excluded: chain 4 residue 288 ILE Chi-restraints excluded: chain 0 residue 14 TYR Chi-restraints excluded: chain 0 residue 34 VAL Chi-restraints excluded: chain 0 residue 115 CYS Chi-restraints excluded: chain 0 residue 120 VAL Chi-restraints excluded: chain 0 residue 213 LEU Chi-restraints excluded: chain 0 residue 221 ARG Chi-restraints excluded: chain 0 residue 222 VAL Chi-restraints excluded: chain 0 residue 226 VAL Chi-restraints excluded: chain 0 residue 321 ILE Chi-restraints excluded: chain 0 residue 355 THR Chi-restraints excluded: chain 0 residue 389 GLU Chi-restraints excluded: chain 0 residue 430 VAL Chi-restraints excluded: chain 0 residue 447 LYS Chi-restraints excluded: chain 0 residue 453 PHE Chi-restraints excluded: chain 0 residue 456 VAL Chi-restraints excluded: chain 0 residue 462 THR Chi-restraints excluded: chain 0 residue 477 THR Chi-restraints excluded: chain 0 residue 487 LEU Chi-restraints excluded: chain 0 residue 506 ILE Chi-restraints excluded: chain 0 residue 539 VAL Chi-restraints excluded: chain 0 residue 614 HIS Chi-restraints excluded: chain 0 residue 664 GLN Chi-restraints excluded: chain 0 residue 711 ASP Chi-restraints excluded: chain 0 residue 718 LYS Chi-restraints excluded: chain 0 residue 745 ILE Chi-restraints excluded: chain 6 residue 119 GLN Chi-restraints excluded: chain 6 residue 128 LEU Chi-restraints excluded: chain 6 residue 146 HIS Chi-restraints excluded: chain 6 residue 155 ASP Chi-restraints excluded: chain 6 residue 210 LEU Chi-restraints excluded: chain 6 residue 227 HIS Chi-restraints excluded: chain 6 residue 293 ASP Chi-restraints excluded: chain 6 residue 305 VAL Chi-restraints excluded: chain 6 residue 320 VAL Chi-restraints excluded: chain 6 residue 336 CYS Chi-restraints excluded: chain 6 residue 363 CYS Chi-restraints excluded: chain 6 residue 366 CYS Chi-restraints excluded: chain 6 residue 372 LEU Chi-restraints excluded: chain 6 residue 375 HIS Chi-restraints excluded: chain 6 residue 448 LEU Chi-restraints excluded: chain 2 residue 55 ASN Chi-restraints excluded: chain 2 residue 56 GLU Chi-restraints excluded: chain 2 residue 74 PHE Chi-restraints excluded: chain 2 residue 88 ILE Chi-restraints excluded: chain 2 residue 99 ASN Chi-restraints excluded: chain 2 residue 208 LEU Chi-restraints excluded: chain 2 residue 343 THR Chi-restraints excluded: chain 2 residue 348 TYR Chi-restraints excluded: chain 2 residue 359 VAL Chi-restraints excluded: chain 2 residue 371 VAL Chi-restraints excluded: chain 2 residue 380 ARG Chi-restraints excluded: chain 2 residue 474 TYR Chi-restraints excluded: chain 2 residue 481 LEU Chi-restraints excluded: chain 2 residue 484 LYS Chi-restraints excluded: chain 2 residue 487 LYS Chi-restraints excluded: chain 2 residue 491 PHE Chi-restraints excluded: chain 5 residue 42 VAL Chi-restraints excluded: chain 5 residue 54 LEU Chi-restraints excluded: chain 7 residue 362 ILE Chi-restraints excluded: chain 7 residue 365 TYR Chi-restraints excluded: chain 7 residue 440 SER Chi-restraints excluded: chain 7 residue 456 THR Chi-restraints excluded: chain 7 residue 464 ARG Chi-restraints excluded: chain 7 residue 491 HIS Chi-restraints excluded: chain 7 residue 501 VAL Chi-restraints excluded: chain 7 residue 510 LYS Chi-restraints excluded: chain 7 residue 514 THR Chi-restraints excluded: chain 7 residue 524 ILE Chi-restraints excluded: chain 7 residue 534 LYS Chi-restraints excluded: chain 7 residue 552 VAL Chi-restraints excluded: chain 7 residue 566 TYR Chi-restraints excluded: chain 7 residue 579 LEU Chi-restraints excluded: chain 7 residue 626 PHE Chi-restraints excluded: chain 7 residue 634 GLN Chi-restraints excluded: chain 7 residue 638 ASN Chi-restraints excluded: chain 7 residue 663 ASP Chi-restraints excluded: chain 7 residue 666 GLU Chi-restraints excluded: chain 7 residue 722 ARG Chi-restraints excluded: chain 7 residue 745 ILE Chi-restraints excluded: chain 7 residue 760 LEU Chi-restraints excluded: chain 3 residue 49 LEU Chi-restraints excluded: chain 3 residue 72 ILE Chi-restraints excluded: chain O residue 164 CYS Chi-restraints excluded: chain O residue 214 LEU Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 47 ARG Chi-restraints excluded: chain A residue 167 CYS Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 177 ASP Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 299 HIS Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 420 ARG Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 453 MET Chi-restraints excluded: chain A residue 465 TYR Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 525 GLN Chi-restraints excluded: chain A residue 544 ASP Chi-restraints excluded: chain A residue 549 MET Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 694 THR Chi-restraints excluded: chain A residue 724 GLU Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 889 SER Chi-restraints excluded: chain A residue 900 ASP Chi-restraints excluded: chain A residue 909 ASP Chi-restraints excluded: chain A residue 914 GLU Chi-restraints excluded: chain A residue 949 ASP Chi-restraints excluded: chain A residue 1169 ILE Chi-restraints excluded: chain A residue 1197 LEU Chi-restraints excluded: chain A residue 1295 THR Chi-restraints excluded: chain A residue 1305 VAL Chi-restraints excluded: chain A residue 1327 ILE Chi-restraints excluded: chain A residue 1400 CYS Chi-restraints excluded: chain A residue 1450 LEU Chi-restraints excluded: chain A residue 1452 LYS Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 134 LYS Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 363 HIS Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 527 THR Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 690 VAL Chi-restraints excluded: chain B residue 734 HIS Chi-restraints excluded: chain B residue 764 SER Chi-restraints excluded: chain B residue 805 THR Chi-restraints excluded: chain B residue 916 THR Chi-restraints excluded: chain B residue 918 ILE Chi-restraints excluded: chain B residue 923 GLU Chi-restraints excluded: chain B residue 948 ILE Chi-restraints excluded: chain B residue 956 THR Chi-restraints excluded: chain B residue 971 THR Chi-restraints excluded: chain B residue 989 THR Chi-restraints excluded: chain B residue 993 THR Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain B residue 1115 THR Chi-restraints excluded: chain B residue 1163 CYS Chi-restraints excluded: chain B residue 1177 HIS Chi-restraints excluded: chain C residue 23 SER Chi-restraints excluded: chain C residue 82 TYR Chi-restraints excluded: chain C residue 91 HIS Chi-restraints excluded: chain C residue 95 CYS Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 135 GLN Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain C residue 219 PHE Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 221 TYR Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 213 ILE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain G residue 33 GLU Chi-restraints excluded: chain G residue 54 ILE Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 112 ILE Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain I residue 4 PHE Chi-restraints excluded: chain I residue 5 ARG Chi-restraints excluded: chain I residue 13 MET Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 10 CYS Chi-restraints excluded: chain J residue 57 ILE Chi-restraints excluded: chain K residue 19 LEU Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 51 LEU Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 53 HIS Chi-restraints excluded: chain L residue 57 LEU Chi-restraints excluded: chain L residue 60 ARG Chi-restraints excluded: chain M residue 23 THR Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 101 THR Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain M residue 125 GLU Chi-restraints excluded: chain M residue 152 GLU Chi-restraints excluded: chain M residue 176 ILE Chi-restraints excluded: chain M residue 197 HIS Chi-restraints excluded: chain M residue 236 LEU Chi-restraints excluded: chain M residue 243 CYS Chi-restraints excluded: chain M residue 248 LEU Chi-restraints excluded: chain M residue 289 PHE Chi-restraints excluded: chain M residue 319 HIS Chi-restraints excluded: chain Q residue 127 ILE Chi-restraints excluded: chain Q residue 343 ARG Chi-restraints excluded: chain Q residue 346 GLU Chi-restraints excluded: chain Q residue 359 ASN Chi-restraints excluded: chain Q residue 396 THR Chi-restraints excluded: chain R residue 63 ARG Chi-restraints excluded: chain R residue 118 HIS Chi-restraints excluded: chain R residue 224 VAL Chi-restraints excluded: chain R residue 253 THR Chi-restraints excluded: chain U residue 257 ARG Chi-restraints excluded: chain V residue 108 VAL Chi-restraints excluded: chain W residue 12 LEU Chi-restraints excluded: chain W residue 133 GLN Chi-restraints excluded: chain W residue 152 CYS Chi-restraints excluded: chain X residue 270 GLN Chi-restraints excluded: chain X residue 276 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 792 random chunks: chunk 257 optimal weight: 40.0000 chunk 689 optimal weight: 10.0000 chunk 151 optimal weight: 3.9990 chunk 449 optimal weight: 10.0000 chunk 188 optimal weight: 20.0000 chunk 766 optimal weight: 8.9990 chunk 636 optimal weight: 0.9980 chunk 354 optimal weight: 2.9990 chunk 63 optimal weight: 20.0000 chunk 253 optimal weight: 6.9990 chunk 402 optimal weight: 0.9980 overall best weight: 3.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 431 GLN ** 7 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 596 GLN ** 7 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 634 GLN ** 7 682 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5689 moved from start: 0.3338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 65841 Z= 0.209 Angle : 0.636 12.320 89355 Z= 0.329 Chirality : 0.043 0.269 10069 Planarity : 0.004 0.070 11216 Dihedral : 13.843 89.208 10301 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 14.55 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.82 % Favored : 92.12 % Rotamer: Outliers : 4.62 % Allowed : 18.63 % Favored : 76.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % Cis-general : 0.07 % Twisted Proline : 0.29 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.09), residues: 7928 helix: 0.46 (0.09), residues: 3163 sheet: -1.30 (0.16), residues: 926 loop : -1.71 (0.10), residues: 3839 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP 7 420 HIS 0.007 0.001 HIS A 80 PHE 0.026 0.001 PHE 7 593 TYR 0.027 0.001 TYR O 231 ARG 0.008 0.000 ARG J 48 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15856 Ramachandran restraints generated. 7928 Oldfield, 0 Emsley, 7928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15856 Ramachandran restraints generated. 7928 Oldfield, 0 Emsley, 7928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 545 residues out of total 7221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 297 poor density : 248 time to evaluate : 5.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 221 ARG cc_start: 0.7496 (OUTLIER) cc_final: 0.6530 (pmt-80) REVERT: 0 285 GLU cc_start: 0.6034 (OUTLIER) cc_final: 0.5469 (tm-30) REVERT: 0 346 MET cc_start: 0.3079 (tpt) cc_final: 0.0987 (tpt) REVERT: 0 389 GLU cc_start: 0.8460 (OUTLIER) cc_final: 0.8146 (pm20) REVERT: 6 146 HIS cc_start: 0.5787 (OUTLIER) cc_final: 0.5131 (p-80) REVERT: 5 27 MET cc_start: 0.3247 (ppp) cc_final: 0.2942 (ppp) REVERT: 7 534 LYS cc_start: 0.1089 (OUTLIER) cc_final: 0.0599 (mmtt) REVERT: 3 49 LEU cc_start: 0.2575 (OUTLIER) cc_final: 0.2115 (mt) REVERT: A 167 CYS cc_start: 0.7241 (OUTLIER) cc_final: 0.6826 (p) REVERT: A 215 SER cc_start: 0.7506 (OUTLIER) cc_final: 0.7215 (p) REVERT: A 420 ARG cc_start: 0.6254 (OUTLIER) cc_final: 0.5452 (ttm170) REVERT: A 873 MET cc_start: 0.7638 (mmm) cc_final: 0.7127 (mmm) REVERT: A 900 ASP cc_start: 0.6893 (OUTLIER) cc_final: 0.6640 (p0) REVERT: A 1375 MET cc_start: 0.6614 (mtp) cc_final: 0.6307 (ttp) REVERT: B 364 ILE cc_start: 0.7234 (OUTLIER) cc_final: 0.6966 (pt) REVERT: B 662 MET cc_start: 0.5931 (mtp) cc_final: 0.5658 (mmm) REVERT: B 764 SER cc_start: 0.8084 (OUTLIER) cc_final: 0.7862 (t) REVERT: B 923 GLU cc_start: 0.2527 (OUTLIER) cc_final: 0.1052 (mt-10) REVERT: B 948 ILE cc_start: 0.8828 (OUTLIER) cc_final: 0.8475 (mp) REVERT: C 91 HIS cc_start: 0.5746 (OUTLIER) cc_final: 0.4994 (p-80) REVERT: C 219 PHE cc_start: 0.7966 (OUTLIER) cc_final: 0.7633 (p90) REVERT: E 57 MET cc_start: 0.6488 (ppp) cc_final: 0.6025 (ppp) REVERT: K 16 GLU cc_start: 0.1854 (OUTLIER) cc_final: 0.1645 (pm20) REVERT: X 262 MET cc_start: 0.4176 (ptt) cc_final: 0.3779 (ppp) outliers start: 297 outliers final: 225 residues processed: 539 average time/residue: 0.5816 time to fit residues: 544.3529 Evaluate side-chains 484 residues out of total 7221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 242 poor density : 242 time to evaluate : 5.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 179 LYS Chi-restraints excluded: chain 1 residue 212 THR Chi-restraints excluded: chain 1 residue 214 ILE Chi-restraints excluded: chain 1 residue 276 LYS Chi-restraints excluded: chain 1 residue 287 PHE Chi-restraints excluded: chain 1 residue 553 LEU Chi-restraints excluded: chain 1 residue 556 THR Chi-restraints excluded: chain 4 residue 162 ARG Chi-restraints excluded: chain 4 residue 175 ARG Chi-restraints excluded: chain 4 residue 180 THR Chi-restraints excluded: chain 4 residue 245 ILE Chi-restraints excluded: chain 4 residue 258 LEU Chi-restraints excluded: chain 4 residue 273 ARG Chi-restraints excluded: chain 4 residue 288 ILE Chi-restraints excluded: chain 0 residue 14 TYR Chi-restraints excluded: chain 0 residue 34 VAL Chi-restraints excluded: chain 0 residue 115 CYS Chi-restraints excluded: chain 0 residue 120 VAL Chi-restraints excluded: chain 0 residue 165 ILE Chi-restraints excluded: chain 0 residue 213 LEU Chi-restraints excluded: chain 0 residue 217 LYS Chi-restraints excluded: chain 0 residue 221 ARG Chi-restraints excluded: chain 0 residue 222 VAL Chi-restraints excluded: chain 0 residue 226 VAL Chi-restraints excluded: chain 0 residue 285 GLU Chi-restraints excluded: chain 0 residue 321 ILE Chi-restraints excluded: chain 0 residue 355 THR Chi-restraints excluded: chain 0 residue 389 GLU Chi-restraints excluded: chain 0 residue 430 VAL Chi-restraints excluded: chain 0 residue 447 LYS Chi-restraints excluded: chain 0 residue 453 PHE Chi-restraints excluded: chain 0 residue 456 VAL Chi-restraints excluded: chain 0 residue 462 THR Chi-restraints excluded: chain 0 residue 477 THR Chi-restraints excluded: chain 0 residue 487 LEU Chi-restraints excluded: chain 0 residue 506 ILE Chi-restraints excluded: chain 0 residue 507 SER Chi-restraints excluded: chain 0 residue 539 VAL Chi-restraints excluded: chain 0 residue 614 HIS Chi-restraints excluded: chain 0 residue 664 GLN Chi-restraints excluded: chain 0 residue 711 ASP Chi-restraints excluded: chain 0 residue 745 ILE Chi-restraints excluded: chain 6 residue 119 GLN Chi-restraints excluded: chain 6 residue 128 LEU Chi-restraints excluded: chain 6 residue 146 HIS Chi-restraints excluded: chain 6 residue 155 ASP Chi-restraints excluded: chain 6 residue 210 LEU Chi-restraints excluded: chain 6 residue 227 HIS Chi-restraints excluded: chain 6 residue 293 ASP Chi-restraints excluded: chain 6 residue 305 VAL Chi-restraints excluded: chain 6 residue 310 VAL Chi-restraints excluded: chain 6 residue 320 VAL Chi-restraints excluded: chain 6 residue 336 CYS Chi-restraints excluded: chain 6 residue 363 CYS Chi-restraints excluded: chain 6 residue 366 CYS Chi-restraints excluded: chain 6 residue 372 LEU Chi-restraints excluded: chain 6 residue 375 HIS Chi-restraints excluded: chain 6 residue 448 LEU Chi-restraints excluded: chain 2 residue 12 GLN Chi-restraints excluded: chain 2 residue 56 GLU Chi-restraints excluded: chain 2 residue 74 PHE Chi-restraints excluded: chain 2 residue 88 ILE Chi-restraints excluded: chain 2 residue 99 ASN Chi-restraints excluded: chain 2 residue 208 LEU Chi-restraints excluded: chain 2 residue 343 THR Chi-restraints excluded: chain 2 residue 348 TYR Chi-restraints excluded: chain 2 residue 359 VAL Chi-restraints excluded: chain 2 residue 371 VAL Chi-restraints excluded: chain 2 residue 380 ARG Chi-restraints excluded: chain 2 residue 474 TYR Chi-restraints excluded: chain 2 residue 481 LEU Chi-restraints excluded: chain 2 residue 484 LYS Chi-restraints excluded: chain 2 residue 487 LYS Chi-restraints excluded: chain 2 residue 491 PHE Chi-restraints excluded: chain 5 residue 42 VAL Chi-restraints excluded: chain 5 residue 54 LEU Chi-restraints excluded: chain 7 residue 362 ILE Chi-restraints excluded: chain 7 residue 365 TYR Chi-restraints excluded: chain 7 residue 440 SER Chi-restraints excluded: chain 7 residue 456 THR Chi-restraints excluded: chain 7 residue 464 ARG Chi-restraints excluded: chain 7 residue 491 HIS Chi-restraints excluded: chain 7 residue 510 LYS Chi-restraints excluded: chain 7 residue 514 THR Chi-restraints excluded: chain 7 residue 524 ILE Chi-restraints excluded: chain 7 residue 534 LYS Chi-restraints excluded: chain 7 residue 545 GLN Chi-restraints excluded: chain 7 residue 552 VAL Chi-restraints excluded: chain 7 residue 579 LEU Chi-restraints excluded: chain 7 residue 626 PHE Chi-restraints excluded: chain 7 residue 634 GLN Chi-restraints excluded: chain 7 residue 638 ASN Chi-restraints excluded: chain 7 residue 666 GLU Chi-restraints excluded: chain 7 residue 722 ARG Chi-restraints excluded: chain 7 residue 745 ILE Chi-restraints excluded: chain 3 residue 49 LEU Chi-restraints excluded: chain 3 residue 72 ILE Chi-restraints excluded: chain O residue 164 CYS Chi-restraints excluded: chain O residue 214 LEU Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 47 ARG Chi-restraints excluded: chain A residue 124 GLN Chi-restraints excluded: chain A residue 167 CYS Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 177 ASP Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 299 HIS Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 420 ARG Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 453 MET Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 511 ILE Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 525 GLN Chi-restraints excluded: chain A residue 544 ASP Chi-restraints excluded: chain A residue 549 MET Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 724 GLU Chi-restraints excluded: chain A residue 889 SER Chi-restraints excluded: chain A residue 900 ASP Chi-restraints excluded: chain A residue 909 ASP Chi-restraints excluded: chain A residue 914 GLU Chi-restraints excluded: chain A residue 949 ASP Chi-restraints excluded: chain A residue 982 THR Chi-restraints excluded: chain A residue 1169 ILE Chi-restraints excluded: chain A residue 1197 LEU Chi-restraints excluded: chain A residue 1327 ILE Chi-restraints excluded: chain A residue 1400 CYS Chi-restraints excluded: chain A residue 1452 LYS Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 86 ARG Chi-restraints excluded: chain B residue 134 LYS Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 363 HIS Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain B residue 527 THR Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 690 VAL Chi-restraints excluded: chain B residue 734 HIS Chi-restraints excluded: chain B residue 764 SER Chi-restraints excluded: chain B residue 805 THR Chi-restraints excluded: chain B residue 916 THR Chi-restraints excluded: chain B residue 918 ILE Chi-restraints excluded: chain B residue 923 GLU Chi-restraints excluded: chain B residue 948 ILE Chi-restraints excluded: chain B residue 971 THR Chi-restraints excluded: chain B residue 989 THR Chi-restraints excluded: chain B residue 993 THR Chi-restraints excluded: chain B residue 1007 VAL Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain B residue 1115 THR Chi-restraints excluded: chain B residue 1163 CYS Chi-restraints excluded: chain B residue 1177 HIS Chi-restraints excluded: chain C residue 4 GLU Chi-restraints excluded: chain C residue 23 SER Chi-restraints excluded: chain C residue 91 HIS Chi-restraints excluded: chain C residue 95 CYS Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 135 GLN Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain C residue 219 PHE Chi-restraints excluded: chain C residue 234 SER Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain D residue 221 TYR Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 84 ASP Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 213 ILE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain G residue 33 GLU Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 163 ILE Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 112 ILE Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain I residue 4 PHE Chi-restraints excluded: chain I residue 5 ARG Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 10 CYS Chi-restraints excluded: chain J residue 57 ILE Chi-restraints excluded: chain K residue 16 GLU Chi-restraints excluded: chain K residue 19 LEU Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 51 LEU Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 47 ARG Chi-restraints excluded: chain L residue 53 HIS Chi-restraints excluded: chain L residue 57 LEU Chi-restraints excluded: chain M residue 23 THR Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 101 THR Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain M residue 125 GLU Chi-restraints excluded: chain M residue 152 GLU Chi-restraints excluded: chain M residue 176 ILE Chi-restraints excluded: chain M residue 197 HIS Chi-restraints excluded: chain M residue 236 LEU Chi-restraints excluded: chain M residue 243 CYS Chi-restraints excluded: chain M residue 248 LEU Chi-restraints excluded: chain M residue 289 PHE Chi-restraints excluded: chain Q residue 127 ILE Chi-restraints excluded: chain Q residue 343 ARG Chi-restraints excluded: chain Q residue 359 ASN Chi-restraints excluded: chain Q residue 396 THR Chi-restraints excluded: chain R residue 63 ARG Chi-restraints excluded: chain R residue 118 HIS Chi-restraints excluded: chain R residue 253 THR Chi-restraints excluded: chain U residue 257 ARG Chi-restraints excluded: chain V residue 108 VAL Chi-restraints excluded: chain V residue 114 VAL Chi-restraints excluded: chain W residue 12 LEU Chi-restraints excluded: chain W residue 133 GLN Chi-restraints excluded: chain W residue 141 ASN Chi-restraints excluded: chain W residue 152 CYS Chi-restraints excluded: chain X residue 270 GLN Chi-restraints excluded: chain X residue 276 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 792 random chunks: chunk 738 optimal weight: 7.9990 chunk 86 optimal weight: 7.9990 chunk 436 optimal weight: 6.9990 chunk 559 optimal weight: 0.5980 chunk 433 optimal weight: 0.9980 chunk 645 optimal weight: 6.9990 chunk 427 optimal weight: 0.7980 chunk 763 optimal weight: 7.9990 chunk 477 optimal weight: 5.9990 chunk 465 optimal weight: 10.0000 chunk 352 optimal weight: 0.0370 overall best weight: 1.6860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 682 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5647 moved from start: 0.3594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 65841 Z= 0.171 Angle : 0.631 17.403 89355 Z= 0.323 Chirality : 0.043 0.215 10069 Planarity : 0.004 0.069 11216 Dihedral : 13.711 89.403 10286 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.53 % Favored : 92.41 % Rotamer: Outliers : 4.30 % Allowed : 19.55 % Favored : 76.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % Cis-general : 0.07 % Twisted Proline : 0.29 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.10), residues: 7928 helix: 0.58 (0.09), residues: 3168 sheet: -1.23 (0.16), residues: 937 loop : -1.69 (0.10), residues: 3823 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP 7 420 HIS 0.005 0.001 HIS 4 64 PHE 0.025 0.001 PHE K 7 TYR 0.034 0.001 TYR O 231 ARG 0.007 0.000 ARG B1135 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15856 Ramachandran restraints generated. 7928 Oldfield, 0 Emsley, 7928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15856 Ramachandran restraints generated. 7928 Oldfield, 0 Emsley, 7928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 7221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 276 poor density : 254 time to evaluate : 5.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 1 MET cc_start: 0.3270 (mtp) cc_final: 0.3045 (mtm) REVERT: 0 221 ARG cc_start: 0.7355 (OUTLIER) cc_final: 0.6388 (pmt-80) REVERT: 0 285 GLU cc_start: 0.5088 (OUTLIER) cc_final: 0.4719 (tm-30) REVERT: 0 389 GLU cc_start: 0.8446 (OUTLIER) cc_final: 0.8127 (pm20) REVERT: 0 521 ASN cc_start: 0.6770 (OUTLIER) cc_final: 0.6318 (t0) REVERT: 6 146 HIS cc_start: 0.5698 (OUTLIER) cc_final: 0.5046 (p-80) REVERT: 7 583 MET cc_start: 0.3706 (ptt) cc_final: 0.3486 (tpt) REVERT: 7 622 MET cc_start: 0.4538 (ppp) cc_final: 0.4167 (ppp) REVERT: 3 49 LEU cc_start: 0.2370 (OUTLIER) cc_final: 0.2020 (mt) REVERT: A 76 GLU cc_start: 0.5948 (OUTLIER) cc_final: 0.5622 (tp30) REVERT: A 167 CYS cc_start: 0.7223 (OUTLIER) cc_final: 0.6786 (p) REVERT: A 215 SER cc_start: 0.7464 (OUTLIER) cc_final: 0.7173 (p) REVERT: A 420 ARG cc_start: 0.6182 (OUTLIER) cc_final: 0.5365 (ttm170) REVERT: A 873 MET cc_start: 0.7514 (mmm) cc_final: 0.6980 (mmm) REVERT: A 900 ASP cc_start: 0.6824 (OUTLIER) cc_final: 0.6596 (p0) REVERT: A 1375 MET cc_start: 0.6544 (mtp) cc_final: 0.6231 (ttp) REVERT: B 364 ILE cc_start: 0.7189 (OUTLIER) cc_final: 0.6903 (pt) REVERT: B 948 ILE cc_start: 0.8783 (OUTLIER) cc_final: 0.8437 (mp) REVERT: C 91 HIS cc_start: 0.5642 (OUTLIER) cc_final: 0.4851 (p-80) REVERT: C 219 PHE cc_start: 0.7870 (OUTLIER) cc_final: 0.7573 (p90) REVERT: E 215 MET cc_start: 0.7244 (pmm) cc_final: 0.6835 (mpp) REVERT: R 270 MET cc_start: 0.0949 (mmt) cc_final: -0.0095 (mmt) REVERT: X 262 MET cc_start: 0.4074 (ptt) cc_final: 0.3697 (ppp) outliers start: 276 outliers final: 216 residues processed: 522 average time/residue: 0.5809 time to fit residues: 525.2641 Evaluate side-chains 479 residues out of total 7221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 231 poor density : 248 time to evaluate : 5.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 179 LYS Chi-restraints excluded: chain 1 residue 200 ILE Chi-restraints excluded: chain 1 residue 212 THR Chi-restraints excluded: chain 1 residue 214 ILE Chi-restraints excluded: chain 1 residue 276 LYS Chi-restraints excluded: chain 1 residue 287 PHE Chi-restraints excluded: chain 1 residue 553 LEU Chi-restraints excluded: chain 1 residue 556 THR Chi-restraints excluded: chain 4 residue 162 ARG Chi-restraints excluded: chain 4 residue 175 ARG Chi-restraints excluded: chain 4 residue 180 THR Chi-restraints excluded: chain 4 residue 245 ILE Chi-restraints excluded: chain 4 residue 258 LEU Chi-restraints excluded: chain 4 residue 273 ARG Chi-restraints excluded: chain 4 residue 288 ILE Chi-restraints excluded: chain 0 residue 14 TYR Chi-restraints excluded: chain 0 residue 34 VAL Chi-restraints excluded: chain 0 residue 120 VAL Chi-restraints excluded: chain 0 residue 165 ILE Chi-restraints excluded: chain 0 residue 213 LEU Chi-restraints excluded: chain 0 residue 217 LYS Chi-restraints excluded: chain 0 residue 221 ARG Chi-restraints excluded: chain 0 residue 222 VAL Chi-restraints excluded: chain 0 residue 226 VAL Chi-restraints excluded: chain 0 residue 285 GLU Chi-restraints excluded: chain 0 residue 355 THR Chi-restraints excluded: chain 0 residue 389 GLU Chi-restraints excluded: chain 0 residue 430 VAL Chi-restraints excluded: chain 0 residue 447 LYS Chi-restraints excluded: chain 0 residue 453 PHE Chi-restraints excluded: chain 0 residue 456 VAL Chi-restraints excluded: chain 0 residue 462 THR Chi-restraints excluded: chain 0 residue 477 THR Chi-restraints excluded: chain 0 residue 487 LEU Chi-restraints excluded: chain 0 residue 506 ILE Chi-restraints excluded: chain 0 residue 521 ASN Chi-restraints excluded: chain 0 residue 539 VAL Chi-restraints excluded: chain 0 residue 594 ARG Chi-restraints excluded: chain 0 residue 614 HIS Chi-restraints excluded: chain 0 residue 619 THR Chi-restraints excluded: chain 0 residue 664 GLN Chi-restraints excluded: chain 0 residue 711 ASP Chi-restraints excluded: chain 0 residue 745 ILE Chi-restraints excluded: chain 6 residue 119 GLN Chi-restraints excluded: chain 6 residue 128 LEU Chi-restraints excluded: chain 6 residue 146 HIS Chi-restraints excluded: chain 6 residue 155 ASP Chi-restraints excluded: chain 6 residue 210 LEU Chi-restraints excluded: chain 6 residue 227 HIS Chi-restraints excluded: chain 6 residue 305 VAL Chi-restraints excluded: chain 6 residue 310 VAL Chi-restraints excluded: chain 6 residue 320 VAL Chi-restraints excluded: chain 6 residue 336 CYS Chi-restraints excluded: chain 6 residue 363 CYS Chi-restraints excluded: chain 6 residue 371 ILE Chi-restraints excluded: chain 6 residue 372 LEU Chi-restraints excluded: chain 6 residue 375 HIS Chi-restraints excluded: chain 6 residue 448 LEU Chi-restraints excluded: chain 2 residue 12 GLN Chi-restraints excluded: chain 2 residue 55 ASN Chi-restraints excluded: chain 2 residue 74 PHE Chi-restraints excluded: chain 2 residue 88 ILE Chi-restraints excluded: chain 2 residue 99 ASN Chi-restraints excluded: chain 2 residue 208 LEU Chi-restraints excluded: chain 2 residue 348 TYR Chi-restraints excluded: chain 2 residue 359 VAL Chi-restraints excluded: chain 2 residue 371 VAL Chi-restraints excluded: chain 2 residue 380 ARG Chi-restraints excluded: chain 2 residue 474 TYR Chi-restraints excluded: chain 2 residue 481 LEU Chi-restraints excluded: chain 2 residue 484 LYS Chi-restraints excluded: chain 2 residue 487 LYS Chi-restraints excluded: chain 2 residue 491 PHE Chi-restraints excluded: chain 5 residue 42 VAL Chi-restraints excluded: chain 7 residue 362 ILE Chi-restraints excluded: chain 7 residue 365 TYR Chi-restraints excluded: chain 7 residue 440 SER Chi-restraints excluded: chain 7 residue 456 THR Chi-restraints excluded: chain 7 residue 464 ARG Chi-restraints excluded: chain 7 residue 491 HIS Chi-restraints excluded: chain 7 residue 510 LYS Chi-restraints excluded: chain 7 residue 514 THR Chi-restraints excluded: chain 7 residue 524 ILE Chi-restraints excluded: chain 7 residue 534 LYS Chi-restraints excluded: chain 7 residue 545 GLN Chi-restraints excluded: chain 7 residue 552 VAL Chi-restraints excluded: chain 7 residue 579 LEU Chi-restraints excluded: chain 7 residue 626 PHE Chi-restraints excluded: chain 7 residue 634 GLN Chi-restraints excluded: chain 7 residue 638 ASN Chi-restraints excluded: chain 7 residue 666 GLU Chi-restraints excluded: chain 7 residue 722 ARG Chi-restraints excluded: chain 7 residue 745 ILE Chi-restraints excluded: chain 3 residue 49 LEU Chi-restraints excluded: chain 3 residue 72 ILE Chi-restraints excluded: chain O residue 164 CYS Chi-restraints excluded: chain O residue 214 LEU Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 47 ARG Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 124 GLN Chi-restraints excluded: chain A residue 167 CYS Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 177 ASP Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 281 HIS Chi-restraints excluded: chain A residue 299 HIS Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 420 ARG Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 453 MET Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 525 GLN Chi-restraints excluded: chain A residue 544 ASP Chi-restraints excluded: chain A residue 549 MET Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 889 SER Chi-restraints excluded: chain A residue 900 ASP Chi-restraints excluded: chain A residue 909 ASP Chi-restraints excluded: chain A residue 949 ASP Chi-restraints excluded: chain A residue 1101 LEU Chi-restraints excluded: chain A residue 1169 ILE Chi-restraints excluded: chain A residue 1197 LEU Chi-restraints excluded: chain A residue 1295 THR Chi-restraints excluded: chain A residue 1327 ILE Chi-restraints excluded: chain A residue 1400 CYS Chi-restraints excluded: chain A residue 1452 LYS Chi-restraints excluded: chain B residue 86 ARG Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 319 GLU Chi-restraints excluded: chain B residue 363 HIS Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain B residue 527 THR Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 690 VAL Chi-restraints excluded: chain B residue 734 HIS Chi-restraints excluded: chain B residue 805 THR Chi-restraints excluded: chain B residue 916 THR Chi-restraints excluded: chain B residue 918 ILE Chi-restraints excluded: chain B residue 948 ILE Chi-restraints excluded: chain B residue 971 THR Chi-restraints excluded: chain B residue 989 THR Chi-restraints excluded: chain B residue 993 THR Chi-restraints excluded: chain B residue 1007 VAL Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain B residue 1115 THR Chi-restraints excluded: chain B residue 1163 CYS Chi-restraints excluded: chain B residue 1177 HIS Chi-restraints excluded: chain C residue 4 GLU Chi-restraints excluded: chain C residue 23 SER Chi-restraints excluded: chain C residue 91 HIS Chi-restraints excluded: chain C residue 95 CYS Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain C residue 219 PHE Chi-restraints excluded: chain C residue 234 SER Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain D residue 221 TYR Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 84 ASP Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 213 ILE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 100 GLN Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 147 SER Chi-restraints excluded: chain G residue 33 GLU Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 112 ILE Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain I residue 5 ARG Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 10 CYS Chi-restraints excluded: chain J residue 57 ILE Chi-restraints excluded: chain K residue 19 LEU Chi-restraints excluded: chain K residue 51 LEU Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 47 ARG Chi-restraints excluded: chain L residue 50 ASP Chi-restraints excluded: chain L residue 53 HIS Chi-restraints excluded: chain M residue 23 THR Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 101 THR Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain M residue 125 GLU Chi-restraints excluded: chain M residue 152 GLU Chi-restraints excluded: chain M residue 176 ILE Chi-restraints excluded: chain M residue 197 HIS Chi-restraints excluded: chain M residue 236 LEU Chi-restraints excluded: chain M residue 243 CYS Chi-restraints excluded: chain M residue 248 LEU Chi-restraints excluded: chain M residue 289 PHE Chi-restraints excluded: chain Q residue 127 ILE Chi-restraints excluded: chain Q residue 343 ARG Chi-restraints excluded: chain Q residue 359 ASN Chi-restraints excluded: chain Q residue 396 THR Chi-restraints excluded: chain R residue 118 HIS Chi-restraints excluded: chain R residue 253 THR Chi-restraints excluded: chain U residue 257 ARG Chi-restraints excluded: chain V residue 108 VAL Chi-restraints excluded: chain V residue 114 VAL Chi-restraints excluded: chain W residue 12 LEU Chi-restraints excluded: chain W residue 133 GLN Chi-restraints excluded: chain W residue 141 ASN Chi-restraints excluded: chain W residue 152 CYS Chi-restraints excluded: chain X residue 270 GLN Chi-restraints excluded: chain X residue 276 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 792 random chunks: chunk 472 optimal weight: 30.0000 chunk 304 optimal weight: 10.0000 chunk 455 optimal weight: 5.9990 chunk 229 optimal weight: 0.9990 chunk 149 optimal weight: 4.9990 chunk 147 optimal weight: 40.0000 chunk 485 optimal weight: 6.9990 chunk 520 optimal weight: 8.9990 chunk 377 optimal weight: 0.9980 chunk 71 optimal weight: 9.9990 chunk 600 optimal weight: 9.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 633 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 634 GLN ** 7 682 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 HIS ** B 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 587 HIS ** H 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5705 moved from start: 0.3659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 65841 Z= 0.239 Angle : 0.655 17.043 89355 Z= 0.334 Chirality : 0.043 0.227 10069 Planarity : 0.004 0.070 11216 Dihedral : 13.665 89.654 10275 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 15.12 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.01 % Favored : 91.93 % Rotamer: Outliers : 4.34 % Allowed : 19.59 % Favored : 76.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % Cis-general : 0.07 % Twisted Proline : 0.29 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.10), residues: 7928 helix: 0.61 (0.09), residues: 3177 sheet: -1.24 (0.16), residues: 970 loop : -1.67 (0.10), residues: 3781 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP 7 420 HIS 0.012 0.001 HIS 1 585 PHE 0.024 0.001 PHE 7 593 TYR 0.028 0.001 TYR O 231 ARG 0.019 0.000 ARG H 146 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15856 Ramachandran restraints generated. 7928 Oldfield, 0 Emsley, 7928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15856 Ramachandran restraints generated. 7928 Oldfield, 0 Emsley, 7928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 525 residues out of total 7221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 279 poor density : 246 time to evaluate : 5.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 1 MET cc_start: 0.3841 (mtp) cc_final: 0.3218 (mtm) REVERT: 0 221 ARG cc_start: 0.7455 (OUTLIER) cc_final: 0.6503 (pmt-80) REVERT: 0 285 GLU cc_start: 0.5051 (OUTLIER) cc_final: 0.4767 (tm-30) REVERT: 0 389 GLU cc_start: 0.8483 (OUTLIER) cc_final: 0.8138 (pm20) REVERT: 0 521 ASN cc_start: 0.6764 (OUTLIER) cc_final: 0.6544 (t0) REVERT: 0 547 MET cc_start: 0.6148 (mtt) cc_final: 0.5598 (mtt) REVERT: 6 146 HIS cc_start: 0.5736 (OUTLIER) cc_final: 0.5030 (p-80) REVERT: 7 534 LYS cc_start: 0.1383 (OUTLIER) cc_final: 0.1152 (mmtt) REVERT: 7 622 MET cc_start: 0.4511 (ppp) cc_final: 0.4168 (ppp) REVERT: 3 49 LEU cc_start: 0.2489 (OUTLIER) cc_final: 0.2100 (mt) REVERT: A 76 GLU cc_start: 0.5982 (OUTLIER) cc_final: 0.5638 (tp30) REVERT: A 81 PHE cc_start: 0.7895 (OUTLIER) cc_final: 0.7448 (m-80) REVERT: A 167 CYS cc_start: 0.7253 (OUTLIER) cc_final: 0.6862 (p) REVERT: A 215 SER cc_start: 0.7459 (OUTLIER) cc_final: 0.7097 (p) REVERT: A 420 ARG cc_start: 0.6205 (OUTLIER) cc_final: 0.5374 (ttm170) REVERT: A 873 MET cc_start: 0.7709 (mmm) cc_final: 0.7066 (mmm) REVERT: A 900 ASP cc_start: 0.6995 (OUTLIER) cc_final: 0.6685 (p0) REVERT: B 948 ILE cc_start: 0.8760 (OUTLIER) cc_final: 0.8405 (mp) REVERT: C 91 HIS cc_start: 0.5768 (OUTLIER) cc_final: 0.5001 (p-80) REVERT: C 219 PHE cc_start: 0.7886 (OUTLIER) cc_final: 0.7605 (p90) REVERT: H 112 ILE cc_start: 0.7978 (OUTLIER) cc_final: 0.7518 (tt) REVERT: Q 358 TYR cc_start: 0.1576 (OUTLIER) cc_final: 0.0035 (p90) REVERT: Q 386 MET cc_start: 0.1062 (mpp) cc_final: 0.0706 (mmp) REVERT: X 262 MET cc_start: 0.4045 (ptt) cc_final: 0.3623 (ppp) outliers start: 279 outliers final: 219 residues processed: 514 average time/residue: 0.6114 time to fit residues: 541.9211 Evaluate side-chains 478 residues out of total 7221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 237 poor density : 241 time to evaluate : 6.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 179 LYS Chi-restraints excluded: chain 1 residue 212 THR Chi-restraints excluded: chain 1 residue 214 ILE Chi-restraints excluded: chain 1 residue 276 LYS Chi-restraints excluded: chain 1 residue 287 PHE Chi-restraints excluded: chain 1 residue 553 LEU Chi-restraints excluded: chain 1 residue 556 THR Chi-restraints excluded: chain 1 residue 563 HIS Chi-restraints excluded: chain 4 residue 162 ARG Chi-restraints excluded: chain 4 residue 180 THR Chi-restraints excluded: chain 4 residue 258 LEU Chi-restraints excluded: chain 4 residue 273 ARG Chi-restraints excluded: chain 4 residue 288 ILE Chi-restraints excluded: chain 0 residue 14 TYR Chi-restraints excluded: chain 0 residue 34 VAL Chi-restraints excluded: chain 0 residue 115 CYS Chi-restraints excluded: chain 0 residue 120 VAL Chi-restraints excluded: chain 0 residue 165 ILE Chi-restraints excluded: chain 0 residue 213 LEU Chi-restraints excluded: chain 0 residue 217 LYS Chi-restraints excluded: chain 0 residue 221 ARG Chi-restraints excluded: chain 0 residue 222 VAL Chi-restraints excluded: chain 0 residue 226 VAL Chi-restraints excluded: chain 0 residue 285 GLU Chi-restraints excluded: chain 0 residue 355 THR Chi-restraints excluded: chain 0 residue 389 GLU Chi-restraints excluded: chain 0 residue 430 VAL Chi-restraints excluded: chain 0 residue 447 LYS Chi-restraints excluded: chain 0 residue 453 PHE Chi-restraints excluded: chain 0 residue 456 VAL Chi-restraints excluded: chain 0 residue 462 THR Chi-restraints excluded: chain 0 residue 477 THR Chi-restraints excluded: chain 0 residue 487 LEU Chi-restraints excluded: chain 0 residue 506 ILE Chi-restraints excluded: chain 0 residue 521 ASN Chi-restraints excluded: chain 0 residue 539 VAL Chi-restraints excluded: chain 0 residue 594 ARG Chi-restraints excluded: chain 0 residue 614 HIS Chi-restraints excluded: chain 0 residue 664 GLN Chi-restraints excluded: chain 0 residue 711 ASP Chi-restraints excluded: chain 0 residue 745 ILE Chi-restraints excluded: chain 6 residue 119 GLN Chi-restraints excluded: chain 6 residue 128 LEU Chi-restraints excluded: chain 6 residue 146 HIS Chi-restraints excluded: chain 6 residue 155 ASP Chi-restraints excluded: chain 6 residue 210 LEU Chi-restraints excluded: chain 6 residue 227 HIS Chi-restraints excluded: chain 6 residue 305 VAL Chi-restraints excluded: chain 6 residue 310 VAL Chi-restraints excluded: chain 6 residue 320 VAL Chi-restraints excluded: chain 6 residue 336 CYS Chi-restraints excluded: chain 6 residue 363 CYS Chi-restraints excluded: chain 6 residue 366 CYS Chi-restraints excluded: chain 6 residue 371 ILE Chi-restraints excluded: chain 6 residue 372 LEU Chi-restraints excluded: chain 6 residue 375 HIS Chi-restraints excluded: chain 6 residue 448 LEU Chi-restraints excluded: chain 2 residue 12 GLN Chi-restraints excluded: chain 2 residue 55 ASN Chi-restraints excluded: chain 2 residue 74 PHE Chi-restraints excluded: chain 2 residue 88 ILE Chi-restraints excluded: chain 2 residue 208 LEU Chi-restraints excluded: chain 2 residue 348 TYR Chi-restraints excluded: chain 2 residue 359 VAL Chi-restraints excluded: chain 2 residue 371 VAL Chi-restraints excluded: chain 2 residue 380 ARG Chi-restraints excluded: chain 2 residue 474 TYR Chi-restraints excluded: chain 2 residue 481 LEU Chi-restraints excluded: chain 2 residue 484 LYS Chi-restraints excluded: chain 2 residue 487 LYS Chi-restraints excluded: chain 2 residue 491 PHE Chi-restraints excluded: chain 5 residue 42 VAL Chi-restraints excluded: chain 7 residue 362 ILE Chi-restraints excluded: chain 7 residue 365 TYR Chi-restraints excluded: chain 7 residue 385 VAL Chi-restraints excluded: chain 7 residue 440 SER Chi-restraints excluded: chain 7 residue 456 THR Chi-restraints excluded: chain 7 residue 464 ARG Chi-restraints excluded: chain 7 residue 491 HIS Chi-restraints excluded: chain 7 residue 510 LYS Chi-restraints excluded: chain 7 residue 514 THR Chi-restraints excluded: chain 7 residue 524 ILE Chi-restraints excluded: chain 7 residue 534 LYS Chi-restraints excluded: chain 7 residue 545 GLN Chi-restraints excluded: chain 7 residue 552 VAL Chi-restraints excluded: chain 7 residue 579 LEU Chi-restraints excluded: chain 7 residue 626 PHE Chi-restraints excluded: chain 7 residue 634 GLN Chi-restraints excluded: chain 7 residue 638 ASN Chi-restraints excluded: chain 7 residue 722 ARG Chi-restraints excluded: chain 7 residue 745 ILE Chi-restraints excluded: chain 3 residue 49 LEU Chi-restraints excluded: chain 3 residue 72 ILE Chi-restraints excluded: chain O residue 159 ASN Chi-restraints excluded: chain O residue 164 CYS Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 47 ARG Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 81 PHE Chi-restraints excluded: chain A residue 167 CYS Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 177 ASP Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 281 HIS Chi-restraints excluded: chain A residue 299 HIS Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 420 ARG Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 453 MET Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 525 GLN Chi-restraints excluded: chain A residue 549 MET Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 724 GLU Chi-restraints excluded: chain A residue 889 SER Chi-restraints excluded: chain A residue 900 ASP Chi-restraints excluded: chain A residue 909 ASP Chi-restraints excluded: chain A residue 949 ASP Chi-restraints excluded: chain A residue 982 THR Chi-restraints excluded: chain A residue 1169 ILE Chi-restraints excluded: chain A residue 1295 THR Chi-restraints excluded: chain A residue 1327 ILE Chi-restraints excluded: chain A residue 1400 CYS Chi-restraints excluded: chain A residue 1452 LYS Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 134 LYS Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 319 GLU Chi-restraints excluded: chain B residue 363 HIS Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain B residue 527 THR Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 690 VAL Chi-restraints excluded: chain B residue 734 HIS Chi-restraints excluded: chain B residue 792 MET Chi-restraints excluded: chain B residue 805 THR Chi-restraints excluded: chain B residue 916 THR Chi-restraints excluded: chain B residue 918 ILE Chi-restraints excluded: chain B residue 948 ILE Chi-restraints excluded: chain B residue 971 THR Chi-restraints excluded: chain B residue 989 THR Chi-restraints excluded: chain B residue 993 THR Chi-restraints excluded: chain B residue 1007 VAL Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain B residue 1115 THR Chi-restraints excluded: chain B residue 1163 CYS Chi-restraints excluded: chain B residue 1177 HIS Chi-restraints excluded: chain C residue 4 GLU Chi-restraints excluded: chain C residue 23 SER Chi-restraints excluded: chain C residue 91 HIS Chi-restraints excluded: chain C residue 95 CYS Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 135 GLN Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain C residue 219 PHE Chi-restraints excluded: chain C residue 234 SER Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 221 TYR Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 84 ASP Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 213 ILE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 100 GLN Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 147 SER Chi-restraints excluded: chain G residue 33 GLU Chi-restraints excluded: chain G residue 54 ILE Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 112 ILE Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain I residue 4 PHE Chi-restraints excluded: chain I residue 5 ARG Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 10 CYS Chi-restraints excluded: chain J residue 57 ILE Chi-restraints excluded: chain K residue 19 LEU Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 51 LEU Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 47 ARG Chi-restraints excluded: chain L residue 50 ASP Chi-restraints excluded: chain L residue 53 HIS Chi-restraints excluded: chain L residue 57 LEU Chi-restraints excluded: chain M residue 23 THR Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 101 THR Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain M residue 125 GLU Chi-restraints excluded: chain M residue 152 GLU Chi-restraints excluded: chain M residue 176 ILE Chi-restraints excluded: chain M residue 197 HIS Chi-restraints excluded: chain M residue 236 LEU Chi-restraints excluded: chain M residue 243 CYS Chi-restraints excluded: chain M residue 248 LEU Chi-restraints excluded: chain M residue 289 PHE Chi-restraints excluded: chain Q residue 127 ILE Chi-restraints excluded: chain Q residue 343 ARG Chi-restraints excluded: chain Q residue 346 GLU Chi-restraints excluded: chain Q residue 358 TYR Chi-restraints excluded: chain Q residue 359 ASN Chi-restraints excluded: chain Q residue 396 THR Chi-restraints excluded: chain R residue 118 HIS Chi-restraints excluded: chain R residue 253 THR Chi-restraints excluded: chain U residue 257 ARG Chi-restraints excluded: chain V residue 114 VAL Chi-restraints excluded: chain W residue 12 LEU Chi-restraints excluded: chain W residue 133 GLN Chi-restraints excluded: chain W residue 141 ASN Chi-restraints excluded: chain W residue 152 CYS Chi-restraints excluded: chain X residue 270 GLN Chi-restraints excluded: chain X residue 276 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 792 random chunks: chunk 694 optimal weight: 0.1980 chunk 731 optimal weight: 0.5980 chunk 667 optimal weight: 6.9990 chunk 711 optimal weight: 2.9990 chunk 428 optimal weight: 6.9990 chunk 309 optimal weight: 9.9990 chunk 558 optimal weight: 6.9990 chunk 218 optimal weight: 8.9990 chunk 642 optimal weight: 0.9980 chunk 672 optimal weight: 0.8980 chunk 708 optimal weight: 20.0000 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 164 ASN ** 0 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 716 ASN ** 2 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 52 HIS ** 7 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 633 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 682 GLN ** 7 702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 451 HIS ** A 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 285 ASN ** U 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5636 moved from start: 0.3916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 65841 Z= 0.162 Angle : 0.647 15.366 89355 Z= 0.328 Chirality : 0.043 0.295 10069 Planarity : 0.004 0.070 11216 Dihedral : 13.533 89.809 10262 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.21 % Favored : 92.75 % Rotamer: Outliers : 3.83 % Allowed : 20.17 % Favored : 76.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % Cis-general : 0.07 % Twisted Proline : 0.29 % Twisted General : 0.07 % 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: -0.93 (0.10), residues: 7928 helix: 0.69 (0.09), residues: 3178 sheet: -1.19 (0.16), residues: 969 loop : -1.62 (0.10), residues: 3781 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP 7 420 HIS 0.005 0.001 HIS 4 64 PHE 0.024 0.001 PHE K 7 TYR 0.023 0.001 TYR O 231 ARG 0.009 0.000 ARG H 146 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15856 Ramachandran restraints generated. 7928 Oldfield, 0 Emsley, 7928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15856 Ramachandran restraints generated. 7928 Oldfield, 0 Emsley, 7928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 7221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 246 poor density : 250 time to evaluate : 5.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 1 MET cc_start: 0.3540 (mtp) cc_final: 0.2840 (mtm) REVERT: 0 221 ARG cc_start: 0.7306 (OUTLIER) cc_final: 0.6364 (pmt-80) REVERT: 0 389 GLU cc_start: 0.8446 (OUTLIER) cc_final: 0.8124 (pm20) REVERT: 0 485 MET cc_start: 0.1784 (mmm) cc_final: 0.0194 (mpp) REVERT: 0 547 MET cc_start: 0.6143 (mtt) cc_final: 0.5715 (mtt) REVERT: 0 642 MET cc_start: 0.7502 (ppp) cc_final: 0.7290 (ppp) REVERT: 6 146 HIS cc_start: 0.5595 (OUTLIER) cc_final: 0.4930 (p-80) REVERT: 7 534 LYS cc_start: 0.1981 (OUTLIER) cc_final: 0.1778 (mmtt) REVERT: 3 49 LEU cc_start: 0.2395 (OUTLIER) cc_final: 0.2008 (mt) REVERT: A 76 GLU cc_start: 0.5795 (OUTLIER) cc_final: 0.5489 (tp30) REVERT: A 81 PHE cc_start: 0.7770 (OUTLIER) cc_final: 0.7504 (m-80) REVERT: A 167 CYS cc_start: 0.7251 (OUTLIER) cc_final: 0.6796 (p) REVERT: A 215 SER cc_start: 0.7479 (OUTLIER) cc_final: 0.7133 (p) REVERT: A 420 ARG cc_start: 0.6053 (OUTLIER) cc_final: 0.5275 (ttm170) REVERT: A 873 MET cc_start: 0.7500 (mmm) cc_final: 0.6949 (mmm) REVERT: A 900 ASP cc_start: 0.6855 (OUTLIER) cc_final: 0.6599 (p0) REVERT: B 364 ILE cc_start: 0.7032 (OUTLIER) cc_final: 0.6762 (pt) REVERT: B 948 ILE cc_start: 0.8686 (OUTLIER) cc_final: 0.8344 (mp) REVERT: C 91 HIS cc_start: 0.5493 (OUTLIER) cc_final: 0.4715 (p-80) REVERT: C 219 PHE cc_start: 0.7868 (OUTLIER) cc_final: 0.7566 (p90) REVERT: D 145 MET cc_start: 0.3484 (mmm) cc_final: 0.3257 (tpp) REVERT: Q 358 TYR cc_start: 0.1536 (OUTLIER) cc_final: -0.0243 (p90) REVERT: Q 386 MET cc_start: 0.0800 (mpp) cc_final: 0.0578 (mmp) REVERT: R 270 MET cc_start: 0.0745 (mmt) cc_final: -0.0077 (mmt) REVERT: X 262 MET cc_start: 0.3966 (ptt) cc_final: 0.3566 (ppp) outliers start: 246 outliers final: 206 residues processed: 487 average time/residue: 0.5926 time to fit residues: 500.4324 Evaluate side-chains 464 residues out of total 7221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 222 poor density : 242 time to evaluate : 5.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 179 LYS Chi-restraints excluded: chain 1 residue 212 THR Chi-restraints excluded: chain 1 residue 214 ILE Chi-restraints excluded: chain 1 residue 276 LYS Chi-restraints excluded: chain 1 residue 287 PHE Chi-restraints excluded: chain 1 residue 553 LEU Chi-restraints excluded: chain 1 residue 556 THR Chi-restraints excluded: chain 1 residue 563 HIS Chi-restraints excluded: chain 4 residue 162 ARG Chi-restraints excluded: chain 4 residue 180 THR Chi-restraints excluded: chain 4 residue 258 LEU Chi-restraints excluded: chain 4 residue 273 ARG Chi-restraints excluded: chain 4 residue 288 ILE Chi-restraints excluded: chain 0 residue 14 TYR Chi-restraints excluded: chain 0 residue 34 VAL Chi-restraints excluded: chain 0 residue 120 VAL Chi-restraints excluded: chain 0 residue 165 ILE Chi-restraints excluded: chain 0 residue 213 LEU Chi-restraints excluded: chain 0 residue 217 LYS Chi-restraints excluded: chain 0 residue 221 ARG Chi-restraints excluded: chain 0 residue 222 VAL Chi-restraints excluded: chain 0 residue 226 VAL Chi-restraints excluded: chain 0 residue 355 THR Chi-restraints excluded: chain 0 residue 389 GLU Chi-restraints excluded: chain 0 residue 430 VAL Chi-restraints excluded: chain 0 residue 447 LYS Chi-restraints excluded: chain 0 residue 453 PHE Chi-restraints excluded: chain 0 residue 456 VAL Chi-restraints excluded: chain 0 residue 462 THR Chi-restraints excluded: chain 0 residue 477 THR Chi-restraints excluded: chain 0 residue 487 LEU Chi-restraints excluded: chain 0 residue 506 ILE Chi-restraints excluded: chain 0 residue 539 VAL Chi-restraints excluded: chain 0 residue 594 ARG Chi-restraints excluded: chain 0 residue 614 HIS Chi-restraints excluded: chain 0 residue 664 GLN Chi-restraints excluded: chain 0 residue 711 ASP Chi-restraints excluded: chain 0 residue 745 ILE Chi-restraints excluded: chain 6 residue 119 GLN Chi-restraints excluded: chain 6 residue 146 HIS Chi-restraints excluded: chain 6 residue 155 ASP Chi-restraints excluded: chain 6 residue 210 LEU Chi-restraints excluded: chain 6 residue 227 HIS Chi-restraints excluded: chain 6 residue 292 LEU Chi-restraints excluded: chain 6 residue 305 VAL Chi-restraints excluded: chain 6 residue 310 VAL Chi-restraints excluded: chain 6 residue 320 VAL Chi-restraints excluded: chain 6 residue 336 CYS Chi-restraints excluded: chain 6 residue 363 CYS Chi-restraints excluded: chain 6 residue 366 CYS Chi-restraints excluded: chain 6 residue 371 ILE Chi-restraints excluded: chain 6 residue 372 LEU Chi-restraints excluded: chain 6 residue 375 HIS Chi-restraints excluded: chain 6 residue 448 LEU Chi-restraints excluded: chain 2 residue 12 GLN Chi-restraints excluded: chain 2 residue 55 ASN Chi-restraints excluded: chain 2 residue 74 PHE Chi-restraints excluded: chain 2 residue 88 ILE Chi-restraints excluded: chain 2 residue 348 TYR Chi-restraints excluded: chain 2 residue 359 VAL Chi-restraints excluded: chain 2 residue 371 VAL Chi-restraints excluded: chain 2 residue 380 ARG Chi-restraints excluded: chain 2 residue 474 TYR Chi-restraints excluded: chain 2 residue 481 LEU Chi-restraints excluded: chain 2 residue 484 LYS Chi-restraints excluded: chain 2 residue 487 LYS Chi-restraints excluded: chain 2 residue 491 PHE Chi-restraints excluded: chain 5 residue 42 VAL Chi-restraints excluded: chain 7 residue 362 ILE Chi-restraints excluded: chain 7 residue 365 TYR Chi-restraints excluded: chain 7 residue 385 VAL Chi-restraints excluded: chain 7 residue 440 SER Chi-restraints excluded: chain 7 residue 456 THR Chi-restraints excluded: chain 7 residue 464 ARG Chi-restraints excluded: chain 7 residue 491 HIS Chi-restraints excluded: chain 7 residue 510 LYS Chi-restraints excluded: chain 7 residue 514 THR Chi-restraints excluded: chain 7 residue 524 ILE Chi-restraints excluded: chain 7 residue 534 LYS Chi-restraints excluded: chain 7 residue 545 GLN Chi-restraints excluded: chain 7 residue 552 VAL Chi-restraints excluded: chain 7 residue 579 LEU Chi-restraints excluded: chain 7 residue 583 MET Chi-restraints excluded: chain 7 residue 626 PHE Chi-restraints excluded: chain 7 residue 634 GLN Chi-restraints excluded: chain 7 residue 638 ASN Chi-restraints excluded: chain 7 residue 722 ARG Chi-restraints excluded: chain 7 residue 745 ILE Chi-restraints excluded: chain 3 residue 49 LEU Chi-restraints excluded: chain 3 residue 72 ILE Chi-restraints excluded: chain O residue 159 ASN Chi-restraints excluded: chain O residue 164 CYS Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 47 ARG Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 81 PHE Chi-restraints excluded: chain A residue 167 CYS Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 177 ASP Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 281 HIS Chi-restraints excluded: chain A residue 299 HIS Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 420 ARG Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 451 HIS Chi-restraints excluded: chain A residue 453 MET Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 525 GLN Chi-restraints excluded: chain A residue 549 MET Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 889 SER Chi-restraints excluded: chain A residue 900 ASP Chi-restraints excluded: chain A residue 909 ASP Chi-restraints excluded: chain A residue 949 ASP Chi-restraints excluded: chain A residue 982 THR Chi-restraints excluded: chain A residue 1169 ILE Chi-restraints excluded: chain A residue 1295 THR Chi-restraints excluded: chain A residue 1327 ILE Chi-restraints excluded: chain A residue 1400 CYS Chi-restraints excluded: chain A residue 1452 LYS Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 319 GLU Chi-restraints excluded: chain B residue 363 HIS Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain B residue 527 THR Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 690 VAL Chi-restraints excluded: chain B residue 734 HIS Chi-restraints excluded: chain B residue 805 THR Chi-restraints excluded: chain B residue 916 THR Chi-restraints excluded: chain B residue 918 ILE Chi-restraints excluded: chain B residue 948 ILE Chi-restraints excluded: chain B residue 971 THR Chi-restraints excluded: chain B residue 989 THR Chi-restraints excluded: chain B residue 993 THR Chi-restraints excluded: chain B residue 1007 VAL Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain B residue 1115 THR Chi-restraints excluded: chain B residue 1124 ARG Chi-restraints excluded: chain B residue 1163 CYS Chi-restraints excluded: chain B residue 1177 HIS Chi-restraints excluded: chain C residue 4 GLU Chi-restraints excluded: chain C residue 23 SER Chi-restraints excluded: chain C residue 91 HIS Chi-restraints excluded: chain C residue 95 CYS Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 135 GLN Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain C residue 219 PHE Chi-restraints excluded: chain C residue 234 SER Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 221 TYR Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 84 ASP Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 213 ILE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 100 GLN Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 147 SER Chi-restraints excluded: chain G residue 18 PHE Chi-restraints excluded: chain G residue 33 GLU Chi-restraints excluded: chain G residue 54 ILE Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain I residue 5 ARG Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 10 CYS Chi-restraints excluded: chain J residue 57 ILE Chi-restraints excluded: chain K residue 19 LEU Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 51 LEU Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain L residue 47 ARG Chi-restraints excluded: chain L residue 53 HIS Chi-restraints excluded: chain M residue 23 THR Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 101 THR Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain M residue 125 GLU Chi-restraints excluded: chain M residue 152 GLU Chi-restraints excluded: chain M residue 176 ILE Chi-restraints excluded: chain M residue 197 HIS Chi-restraints excluded: chain M residue 236 LEU Chi-restraints excluded: chain M residue 289 PHE Chi-restraints excluded: chain Q residue 127 ILE Chi-restraints excluded: chain Q residue 343 ARG Chi-restraints excluded: chain Q residue 346 GLU Chi-restraints excluded: chain Q residue 358 TYR Chi-restraints excluded: chain Q residue 396 THR Chi-restraints excluded: chain R residue 118 HIS Chi-restraints excluded: chain R residue 253 THR Chi-restraints excluded: chain R residue 263 MET Chi-restraints excluded: chain U residue 257 ARG Chi-restraints excluded: chain V residue 114 VAL Chi-restraints excluded: chain V residue 119 LYS Chi-restraints excluded: chain W residue 12 LEU Chi-restraints excluded: chain W residue 133 GLN Chi-restraints excluded: chain W residue 141 ASN Chi-restraints excluded: chain W residue 152 CYS Chi-restraints excluded: chain X residue 270 GLN Chi-restraints excluded: chain X residue 276 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 792 random chunks: chunk 467 optimal weight: 0.9980 chunk 752 optimal weight: 9.9990 chunk 459 optimal weight: 6.9990 chunk 356 optimal weight: 8.9990 chunk 522 optimal weight: 0.3980 chunk 789 optimal weight: 50.0000 chunk 726 optimal weight: 9.9990 chunk 628 optimal weight: 0.9990 chunk 65 optimal weight: 7.9990 chunk 485 optimal weight: 6.9990 chunk 385 optimal weight: 6.9990 overall best weight: 3.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 749 ASN ** 2 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 633 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 634 GLN ** A 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5685 moved from start: 0.3979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 65841 Z= 0.212 Angle : 0.665 18.771 89355 Z= 0.336 Chirality : 0.043 0.328 10069 Planarity : 0.004 0.070 11216 Dihedral : 13.483 89.778 10257 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 15.01 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.76 % Favored : 92.18 % Rotamer: Outliers : 3.67 % Allowed : 20.48 % Favored : 75.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % Cis-general : 0.07 % Twisted Proline : 0.29 % Twisted General : 0.07 % 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: -0.91 (0.10), residues: 7928 helix: 0.72 (0.09), residues: 3179 sheet: -1.21 (0.16), residues: 988 loop : -1.61 (0.10), residues: 3761 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP 7 558 HIS 0.021 0.001 HIS A 451 PHE 0.024 0.001 PHE K 7 TYR 0.023 0.001 TYR O 231 ARG 0.011 0.000 ARG B1135 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15856 Ramachandran restraints generated. 7928 Oldfield, 0 Emsley, 7928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15856 Ramachandran restraints generated. 7928 Oldfield, 0 Emsley, 7928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 7221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 236 poor density : 244 time to evaluate : 5.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 1 MET cc_start: 0.3658 (mtp) cc_final: 0.2944 (mtm) REVERT: 0 221 ARG cc_start: 0.7425 (OUTLIER) cc_final: 0.6486 (pmt-80) REVERT: 6 146 HIS cc_start: 0.5677 (OUTLIER) cc_final: 0.4991 (p-80) REVERT: 3 49 LEU cc_start: 0.2696 (OUTLIER) cc_final: 0.2284 (mt) REVERT: A 76 GLU cc_start: 0.5896 (OUTLIER) cc_final: 0.5589 (tp30) REVERT: A 81 PHE cc_start: 0.7907 (OUTLIER) cc_final: 0.7457 (m-80) REVERT: A 108 MET cc_start: 0.6439 (pmm) cc_final: 0.6154 (pmm) REVERT: A 167 CYS cc_start: 0.7233 (OUTLIER) cc_final: 0.6847 (p) REVERT: A 215 SER cc_start: 0.7453 (OUTLIER) cc_final: 0.7154 (p) REVERT: A 420 ARG cc_start: 0.6075 (OUTLIER) cc_final: 0.5280 (ttm170) REVERT: A 873 MET cc_start: 0.7696 (mmm) cc_final: 0.7043 (mmm) REVERT: A 900 ASP cc_start: 0.6990 (OUTLIER) cc_final: 0.6686 (p0) REVERT: B 364 ILE cc_start: 0.7061 (OUTLIER) cc_final: 0.6808 (pt) REVERT: C 91 HIS cc_start: 0.5717 (OUTLIER) cc_final: 0.4955 (p-80) REVERT: C 219 PHE cc_start: 0.7902 (OUTLIER) cc_final: 0.7637 (p90) REVERT: D 145 MET cc_start: 0.3597 (mmm) cc_final: 0.3373 (tpp) REVERT: E 75 MET cc_start: 0.5234 (tpt) cc_final: 0.4782 (tpt) REVERT: F 85 MET cc_start: 0.7895 (tmm) cc_final: 0.7338 (ttt) REVERT: H 123 MET cc_start: 0.6962 (ppp) cc_final: 0.6761 (ppp) REVERT: Q 358 TYR cc_start: 0.1250 (OUTLIER) cc_final: -0.0409 (p90) REVERT: Q 386 MET cc_start: 0.0979 (mpp) cc_final: 0.0743 (mmp) REVERT: R 270 MET cc_start: 0.1076 (mmt) cc_final: -0.0054 (mmt) REVERT: X 262 MET cc_start: 0.3979 (ptt) cc_final: 0.3577 (ppp) outliers start: 236 outliers final: 204 residues processed: 469 average time/residue: 0.6005 time to fit residues: 488.4668 Evaluate side-chains 459 residues out of total 7221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 217 poor density : 242 time to evaluate : 5.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 179 LYS Chi-restraints excluded: chain 1 residue 212 THR Chi-restraints excluded: chain 1 residue 214 ILE Chi-restraints excluded: chain 1 residue 276 LYS Chi-restraints excluded: chain 1 residue 287 PHE Chi-restraints excluded: chain 1 residue 553 LEU Chi-restraints excluded: chain 1 residue 556 THR Chi-restraints excluded: chain 1 residue 563 HIS Chi-restraints excluded: chain 4 residue 59 VAL Chi-restraints excluded: chain 4 residue 162 ARG Chi-restraints excluded: chain 4 residue 180 THR Chi-restraints excluded: chain 4 residue 258 LEU Chi-restraints excluded: chain 4 residue 273 ARG Chi-restraints excluded: chain 4 residue 288 ILE Chi-restraints excluded: chain 0 residue 14 TYR Chi-restraints excluded: chain 0 residue 34 VAL Chi-restraints excluded: chain 0 residue 115 CYS Chi-restraints excluded: chain 0 residue 120 VAL Chi-restraints excluded: chain 0 residue 163 TYR Chi-restraints excluded: chain 0 residue 165 ILE Chi-restraints excluded: chain 0 residue 213 LEU Chi-restraints excluded: chain 0 residue 217 LYS Chi-restraints excluded: chain 0 residue 221 ARG Chi-restraints excluded: chain 0 residue 222 VAL Chi-restraints excluded: chain 0 residue 226 VAL Chi-restraints excluded: chain 0 residue 355 THR Chi-restraints excluded: chain 0 residue 430 VAL Chi-restraints excluded: chain 0 residue 447 LYS Chi-restraints excluded: chain 0 residue 453 PHE Chi-restraints excluded: chain 0 residue 456 VAL Chi-restraints excluded: chain 0 residue 462 THR Chi-restraints excluded: chain 0 residue 477 THR Chi-restraints excluded: chain 0 residue 487 LEU Chi-restraints excluded: chain 0 residue 506 ILE Chi-restraints excluded: chain 0 residue 539 VAL Chi-restraints excluded: chain 0 residue 594 ARG Chi-restraints excluded: chain 0 residue 614 HIS Chi-restraints excluded: chain 0 residue 664 GLN Chi-restraints excluded: chain 0 residue 745 ILE Chi-restraints excluded: chain 6 residue 119 GLN Chi-restraints excluded: chain 6 residue 146 HIS Chi-restraints excluded: chain 6 residue 155 ASP Chi-restraints excluded: chain 6 residue 210 LEU Chi-restraints excluded: chain 6 residue 227 HIS Chi-restraints excluded: chain 6 residue 292 LEU Chi-restraints excluded: chain 6 residue 310 VAL Chi-restraints excluded: chain 6 residue 320 VAL Chi-restraints excluded: chain 6 residue 336 CYS Chi-restraints excluded: chain 6 residue 363 CYS Chi-restraints excluded: chain 6 residue 366 CYS Chi-restraints excluded: chain 6 residue 371 ILE Chi-restraints excluded: chain 6 residue 372 LEU Chi-restraints excluded: chain 6 residue 375 HIS Chi-restraints excluded: chain 6 residue 448 LEU Chi-restraints excluded: chain 2 residue 12 GLN Chi-restraints excluded: chain 2 residue 55 ASN Chi-restraints excluded: chain 2 residue 74 PHE Chi-restraints excluded: chain 2 residue 88 ILE Chi-restraints excluded: chain 2 residue 348 TYR Chi-restraints excluded: chain 2 residue 359 VAL Chi-restraints excluded: chain 2 residue 371 VAL Chi-restraints excluded: chain 2 residue 380 ARG Chi-restraints excluded: chain 2 residue 474 TYR Chi-restraints excluded: chain 2 residue 481 LEU Chi-restraints excluded: chain 2 residue 484 LYS Chi-restraints excluded: chain 2 residue 487 LYS Chi-restraints excluded: chain 2 residue 491 PHE Chi-restraints excluded: chain 5 residue 42 VAL Chi-restraints excluded: chain 7 residue 362 ILE Chi-restraints excluded: chain 7 residue 365 TYR Chi-restraints excluded: chain 7 residue 385 VAL Chi-restraints excluded: chain 7 residue 440 SER Chi-restraints excluded: chain 7 residue 456 THR Chi-restraints excluded: chain 7 residue 464 ARG Chi-restraints excluded: chain 7 residue 491 HIS Chi-restraints excluded: chain 7 residue 510 LYS Chi-restraints excluded: chain 7 residue 514 THR Chi-restraints excluded: chain 7 residue 524 ILE Chi-restraints excluded: chain 7 residue 545 GLN Chi-restraints excluded: chain 7 residue 552 VAL Chi-restraints excluded: chain 7 residue 579 LEU Chi-restraints excluded: chain 7 residue 626 PHE Chi-restraints excluded: chain 7 residue 634 GLN Chi-restraints excluded: chain 7 residue 638 ASN Chi-restraints excluded: chain 7 residue 660 THR Chi-restraints excluded: chain 7 residue 722 ARG Chi-restraints excluded: chain 7 residue 745 ILE Chi-restraints excluded: chain 3 residue 49 LEU Chi-restraints excluded: chain 3 residue 72 ILE Chi-restraints excluded: chain O residue 159 ASN Chi-restraints excluded: chain O residue 164 CYS Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 47 ARG Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 81 PHE Chi-restraints excluded: chain A residue 167 CYS Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 177 ASP Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 281 HIS Chi-restraints excluded: chain A residue 299 HIS Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 420 ARG Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 549 MET Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 849 MET Chi-restraints excluded: chain A residue 889 SER Chi-restraints excluded: chain A residue 900 ASP Chi-restraints excluded: chain A residue 909 ASP Chi-restraints excluded: chain A residue 949 ASP Chi-restraints excluded: chain A residue 982 THR Chi-restraints excluded: chain A residue 1169 ILE Chi-restraints excluded: chain A residue 1295 THR Chi-restraints excluded: chain A residue 1327 ILE Chi-restraints excluded: chain A residue 1400 CYS Chi-restraints excluded: chain A residue 1452 LYS Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 363 HIS Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain B residue 527 THR Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 690 VAL Chi-restraints excluded: chain B residue 734 HIS Chi-restraints excluded: chain B residue 805 THR Chi-restraints excluded: chain B residue 916 THR Chi-restraints excluded: chain B residue 918 ILE Chi-restraints excluded: chain B residue 971 THR Chi-restraints excluded: chain B residue 989 THR Chi-restraints excluded: chain B residue 993 THR Chi-restraints excluded: chain B residue 1007 VAL Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain B residue 1115 THR Chi-restraints excluded: chain B residue 1124 ARG Chi-restraints excluded: chain B residue 1163 CYS Chi-restraints excluded: chain B residue 1177 HIS Chi-restraints excluded: chain C residue 4 GLU Chi-restraints excluded: chain C residue 23 SER Chi-restraints excluded: chain C residue 91 HIS Chi-restraints excluded: chain C residue 95 CYS Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 135 GLN Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain C residue 219 PHE Chi-restraints excluded: chain C residue 234 SER Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 221 TYR Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 84 ASP Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 213 ILE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 100 GLN Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 147 SER Chi-restraints excluded: chain G residue 18 PHE Chi-restraints excluded: chain G residue 33 GLU Chi-restraints excluded: chain G residue 54 ILE Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain I residue 4 PHE Chi-restraints excluded: chain I residue 5 ARG Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 10 CYS Chi-restraints excluded: chain J residue 57 ILE Chi-restraints excluded: chain K residue 19 LEU Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 51 LEU Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain L residue 47 ARG Chi-restraints excluded: chain L residue 53 HIS Chi-restraints excluded: chain M residue 23 THR Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 101 THR Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain M residue 125 GLU Chi-restraints excluded: chain M residue 152 GLU Chi-restraints excluded: chain M residue 176 ILE Chi-restraints excluded: chain M residue 197 HIS Chi-restraints excluded: chain M residue 289 PHE Chi-restraints excluded: chain Q residue 127 ILE Chi-restraints excluded: chain Q residue 343 ARG Chi-restraints excluded: chain Q residue 346 GLU Chi-restraints excluded: chain Q residue 358 TYR Chi-restraints excluded: chain Q residue 396 THR Chi-restraints excluded: chain R residue 118 HIS Chi-restraints excluded: chain R residue 253 THR Chi-restraints excluded: chain R residue 263 MET Chi-restraints excluded: chain U residue 257 ARG Chi-restraints excluded: chain V residue 108 VAL Chi-restraints excluded: chain V residue 114 VAL Chi-restraints excluded: chain W residue 12 LEU Chi-restraints excluded: chain W residue 133 GLN Chi-restraints excluded: chain W residue 141 ASN Chi-restraints excluded: chain W residue 152 CYS Chi-restraints excluded: chain X residue 270 GLN Chi-restraints excluded: chain X residue 276 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 792 random chunks: chunk 499 optimal weight: 0.8980 chunk 669 optimal weight: 6.9990 chunk 192 optimal weight: 0.7980 chunk 579 optimal weight: 7.9990 chunk 92 optimal weight: 0.3980 chunk 174 optimal weight: 0.8980 chunk 629 optimal weight: 9.9990 chunk 263 optimal weight: 50.0000 chunk 646 optimal weight: 8.9990 chunk 79 optimal weight: 20.0000 chunk 115 optimal weight: 5.9990 overall best weight: 1.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 633 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 525 GLN ** A 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1188 GLN ** A1211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.061008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.039421 restraints weight = 645359.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.040469 restraints weight = 424354.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.040436 restraints weight = 259205.882| |-----------------------------------------------------------------------------| r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3139 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3139 r_free = 0.3139 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 363 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3139 r_free = 0.3139 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 364 | |-----------------------------------------------------------------------------| r_final: 0.3139 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.4141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 65841 Z= 0.171 Angle : 0.651 14.951 89355 Z= 0.329 Chirality : 0.043 0.335 10069 Planarity : 0.004 0.070 11216 Dihedral : 13.359 89.930 10245 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 14.06 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.30 % Favored : 92.65 % Rotamer: Outliers : 3.45 % Allowed : 20.68 % Favored : 75.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % Cis-general : 0.07 % Twisted Proline : 0.29 % Twisted General : 0.07 % 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: -0.86 (0.10), residues: 7928 helix: 0.76 (0.09), residues: 3181 sheet: -1.19 (0.16), residues: 1004 loop : -1.58 (0.10), residues: 3743 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP 7 558 HIS 0.005 0.001 HIS 4 64 PHE 0.026 0.001 PHE K 7 TYR 0.020 0.001 TYR O 231 ARG 0.009 0.000 ARG B1135 =============================================================================== Job complete usr+sys time: 11770.35 seconds wall clock time: 209 minutes 56.76 seconds (12596.76 seconds total)