Starting phenix.real_space_refine on Mon Dec 30 14:41:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ml0_23904/12_2024/7ml0_23904.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ml0_23904/12_2024/7ml0_23904.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ml0_23904/12_2024/7ml0_23904.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ml0_23904/12_2024/7ml0_23904.map" model { file = "/net/cci-nas-00/data/ceres_data/7ml0_23904/12_2024/7ml0_23904.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ml0_23904/12_2024/7ml0_23904.cif" } resolution = 3.0 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 17 6.06 5 P 132 5.49 5 Mg 1 5.21 5 S 354 5.16 5 C 40068 2.51 5 N 11287 2.21 5 O 12351 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 113 residue(s): 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 64214 Number of models: 1 Model: "" Number of chains: 52 Chain: "A" Number of atoms: 10996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1398, 10996 Classifications: {'peptide': 1398} Link IDs: {'PCIS': 2, 'PTRANS': 62, 'TRANS': 1333} Chain breaks: 5 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 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: "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: "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: "T" Number of atoms: 1345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 1345 Classifications: {'DNA': 66} Link IDs: {'rna3p': 65} Chain: "N" Number of atoms: 1361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 1361 Classifications: {'DNA': 66} Link IDs: {'rna3p': 65} Chain: "0" Number of atoms: 6099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 753, 6099 Classifications: {'peptide': 753} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 720} Chain breaks: 1 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: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 102 Classifications: {'peptide': 14} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 12} 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: "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: {'PCIS': 1, 'PTRANS': 18, '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: 3020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 461, 3020 Classifications: {'peptide': 461} Incomplete info: {'backbone_only': 154, 'truncation_to_alanine': 14} Link IDs: {'CIS': 2, 'PTRANS': 17, 'TRANS': 441} 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: "3" Number of atoms: 890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 890 Classifications: {'peptide': 137} Incomplete info: {'truncation_to_alanine': 68} Link IDs: {'PTRANS': 5, 'TRANS': 131} Unresolved non-hydrogen bonds: 257 Unresolved non-hydrogen angles: 328 Unresolved non-hydrogen dihedrals: 206 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'TYR:plan': 4, 'ASN:plan1': 5, 'ASP:plan': 8, 'PHE:plan': 3, 'GLU:plan': 11, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 153 Chain: "7" Number of atoms: 4478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 638, 4478 Classifications: {'peptide': 638} Incomplete info: {'backbone_only': 162} Link IDs: {'PTRANS': 26, 'TRANS': 611} 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: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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: "0" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} 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: "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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 812 SG CYS A 107 86.929 122.076 129.030 1.00 0.00 S ATOM 836 SG CYS A 110 85.408 120.929 132.177 1.00 0.00 S ATOM 1141 SG CYS A 148 88.983 122.484 131.866 1.00 0.00 S ATOM 1210 SG CYS A 167 87.715 118.987 130.006 1.00 0.00 S ATOM 507 SG CYS A 67 43.024 135.295 116.911 1.00 0.00 S ATOM 529 SG CYS A 70 42.781 136.307 120.842 1.00 0.00 S ATOM 582 SG CYS A 77 44.380 138.594 117.920 1.00 0.00 S ATOM 19646 SG CYS B1163 51.099 133.916 133.459 1.00 0.00 S ATOM 19664 SG CYS B1166 53.739 133.428 130.738 1.00 0.00 S ATOM 19789 SG CYS B1182 50.405 131.918 130.379 1.00 0.00 S ATOM 19808 SG CYS B1185 53.062 130.589 132.705 1.00 0.00 S ATOM 20775 SG CYS C 86 11.666 193.004 95.361 1.00 0.00 S ATOM 20792 SG CYS C 88 12.850 189.542 94.463 1.00 0.00 S ATOM 20825 SG CYS C 92 11.285 192.291 92.074 1.00 0.00 S ATOM 20848 SG CYS C 95 14.952 192.330 93.550 1.00 0.00 S ATOM 28338 SG CYS I 7 131.916 157.685 89.452 1.00 0.00 S ATOM 28363 SG CYS I 10 129.335 154.563 90.066 1.00 0.00 S ATOM 28529 SG CYS I 29 130.780 155.727 92.766 1.00 0.00 S ATOM 28553 SG CYS I 32 133.062 154.341 89.936 1.00 0.00 S ATOM 28880 SG CYS I 75 119.372 199.643 91.844 1.00 0.00 S ATOM 28902 SG CYS I 78 117.814 201.524 89.071 1.00 0.00 S ATOM 29118 SG CYS I 103 117.341 197.493 89.271 1.00 0.00 S ATOM 29138 SG CYS I 106 119.789 198.957 87.809 1.00 0.00 S ATOM 29283 SG CYS J 7 44.075 203.717 92.221 1.00 0.00 S ATOM 29306 SG CYS J 10 41.899 207.117 93.280 1.00 0.00 S ATOM 29586 SG CYS J 45 45.711 206.706 93.683 1.00 0.00 S ATOM 29592 SG CYS J 46 44.211 207.199 90.624 1.00 0.00 S ATOM 30715 SG CYS L 31 41.860 167.530 67.080 1.00 0.00 S ATOM 30735 SG CYS L 34 39.563 168.141 63.716 1.00 0.00 S ATOM 30839 SG CYS L 48 39.825 165.082 65.628 1.00 0.00 S ATOM 30862 SG CYS L 51 42.747 165.996 63.635 1.00 0.00 S ATOM 31090 SG CYS M 24 21.250 150.660 115.457 1.00 0.00 S ATOM 31112 SG CYS M 27 18.082 152.195 114.179 1.00 0.00 S ATOM 31256 SG CYS M 45 21.271 153.065 112.292 1.00 0.00 S ATOM 31275 SG CYS M 48 21.059 154.210 115.662 1.00 0.00 S ATOM 36546 SG CYS W 124 32.814 121.264 115.166 1.00 0.00 S ATOM 36567 SG CYS W 127 36.037 122.636 115.899 1.00 0.00 S ATOM 36752 SG CYS W 149 33.328 124.016 117.809 1.00 0.00 S ATOM 36772 SG CYS W 152 33.386 124.726 113.887 1.00 0.00 S ATOM 43158 SG CYS 0 115 79.418 48.500 145.584 1.00117.61 S ATOM 43300 SG CYS 0 133 75.364 48.789 149.293 1.00 46.59 S ATOM 43786 SG CYS 0 191 77.614 42.995 149.268 1.00115.32 S ATOM 52570 SG CYS 4 289 143.775 25.361 147.277 1.00 0.00 S ATOM 52589 SG CYS 4 292 144.945 24.961 150.914 1.00 0.00 S ATOM 52674 SG CYS 4 305 144.412 22.238 149.175 1.00 0.00 S ATOM 52690 SG CYS 4 308 141.514 24.002 150.641 1.00 0.00 S ATOM 54988 SG CYS 6 403 160.271 45.760 171.697 1.00 0.00 S ATOM 55010 SG CYS 6 406 161.969 48.514 170.431 1.00 0.00 S ATOM 55178 SG CYS 6 437 158.522 49.502 171.113 1.00 0.00 S ATOM 55194 SG CYS 6 440 158.998 46.824 168.442 1.00 0.00 S ATOM 55136 SG CYS 6 429 151.471 37.087 170.157 1.00 0.00 S ATOM 55152 SG CYS 6 432 154.573 35.851 171.352 1.00 0.00 S ATOM 55272 SG CYS 6 451 154.312 36.553 167.439 1.00 0.00 S ATOM 55287 SG CYS 6 454 152.641 33.688 168.840 1.00 0.00 S ATOM 54633 SG CYS 6 349 153.687 28.479 129.172 1.00 0.00 S ATOM 54654 SG CYS 6 352 154.272 30.079 125.907 1.00 0.00 S ATOM 54723 SG CYS 6 363 151.345 31.339 127.755 1.00 0.00 S ATOM 54741 SG CYS 6 366 150.791 28.054 127.005 1.00 0.00 S ATOM 54550 SG CYS 6 336 156.768 40.814 123.576 1.00 30.00 S ATOM 54561 SG CYS 6 338 154.232 40.625 126.420 1.00 30.00 S ATOM 54688 SG CYS 6 357 157.088 42.783 126.845 1.00 30.00 S ATOM 58859 SG CYS 3 13 52.260 93.067 132.503 1.00163.05 S ATOM 58880 SG CYS 3 16 53.516 95.846 130.154 1.00164.11 S ATOM 59075 SG CYS 3 39 53.361 96.376 133.787 1.00156.98 S ATOM 59096 SG CYS 3 42 50.145 96.338 131.846 1.00154.76 S ATOM 59028 SG CYS 3 34 42.850 87.804 138.504 1.00151.96 S ATOM 59186 SG CYS 3 54 43.523 90.024 135.473 1.00157.81 S ATOM 59224 SG CYS 3 59 40.489 87.768 135.276 1.00157.50 S Residues with excluded nonbonded symmetry interactions: 11 residue: pdb=" P DT T 100 " occ=0.00 ... (18 atoms not shown) pdb=" C6 DT T 100 " occ=0.00 residue: pdb=" P DT T 102 " occ=0.00 ... (18 atoms not shown) pdb=" C6 DT T 102 " occ=0.00 residue: pdb=" P DA T 109 " occ=0.00 ... (19 atoms not shown) pdb=" C4 DA T 109 " occ=0.00 residue: pdb=" P DT T 114 " occ=0.00 ... (18 atoms not shown) pdb=" C6 DT T 114 " occ=0.00 residue: pdb=" P DT T 121 " occ=0.00 ... (18 atoms not shown) pdb=" C6 DT T 121 " occ=0.00 residue: pdb=" P DA N 45 " occ=0.00 ... (19 atoms not shown) pdb=" C4 DA N 45 " occ=0.00 residue: pdb=" P DA N 52 " occ=0.00 ... (19 atoms not shown) pdb=" C4 DA N 52 " occ=0.00 residue: pdb=" P DT N 55 " occ=0.00 ... (18 atoms not shown) pdb=" C6 DT N 55 " occ=0.00 residue: pdb=" P DT N 57 " occ=0.00 ... (18 atoms not shown) pdb=" C6 DT N 57 " occ=0.00 residue: pdb=" P DA N 64 " occ=0.00 ... (19 atoms not shown) pdb=" C4 DA N 64 " occ=0.00 residue: pdb=" P DA N 66 " occ=0.00 ... (19 atoms not shown) pdb=" C4 DA N 66 " occ=0.00 Time building chain proxies: 25.57, per 1000 atoms: 0.40 Number of scatterers: 64214 At special positions: 0 Unit cell: (218.36, 246.98, 200.34, 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 17 29.99 Fe 4 26.01 S 354 16.00 P 132 15.00 Mg 1 11.99 O 12351 8.00 N 11287 7.00 C 40068 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 1 352 " - " 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: 12.97 Conformation dependent library (CDL) restraints added in 5.9 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 0 801 " pdb="FE4 SF4 0 801 " - pdb=" SG CYS 0 191 " 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=" SD MET 0 136 " pdb="FE4 SF4 0 801 " - pdb=" SG CYS 0 156 " Number of angles added : 15 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 16 " pdb="ZN ZN 3 401 " - pdb=" SG CYS 3 42 " pdb="ZN ZN 3 401 " - pdb=" SG CYS 3 13 " pdb=" ZN 3 402 " pdb="ZN ZN 3 402 " - pdb=" ND1 HIS 3 36 " pdb="ZN ZN 3 402 " - pdb=" SG CYS 3 54 " pdb="ZN ZN 3 402 " - pdb=" SG CYS 3 59 " pdb="ZN ZN 3 402 " - pdb=" SG CYS 3 34 " pdb=" ZN 4 401 " pdb="ZN ZN 4 401 " - pdb=" SG CYS 4 292 " 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 4 289 " pdb=" ZN 6 501 " pdb="ZN ZN 6 501 " - pdb=" SG CYS 6 406 " pdb="ZN ZN 6 501 " - pdb=" SG CYS 6 440 " pdb="ZN ZN 6 501 " - pdb=" SG CYS 6 403 " pdb="ZN ZN 6 501 " - pdb=" SG CYS 6 437 " pdb=" ZN 6 502 " pdb="ZN ZN 6 502 " - pdb=" SG CYS 6 454 " pdb="ZN ZN 6 502 " - pdb=" SG CYS 6 432 " pdb="ZN ZN 6 502 " - pdb=" SG CYS 6 429 " pdb="ZN ZN 6 502 " - pdb=" SG CYS 6 451 " pdb=" ZN 6 503 " pdb="ZN ZN 6 503 " - pdb=" SG CYS 6 349 " pdb="ZN ZN 6 503 " - pdb=" SG CYS 6 366 " pdb="ZN ZN 6 503 " - pdb=" SG CYS 6 363 " 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 6 338 " pdb="ZN ZN 6 504 " - pdb=" SG CYS 6 357 " pdb="ZN ZN 6 504 " - pdb=" SG CYS 6 336 " pdb=" ZN A1801 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 107 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 110 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 167 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 148 " pdb=" ZN A1802 " pdb="ZN ZN A1802 " - pdb=" NE2 HIS A 80 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 67 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 70 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 77 " pdb=" ZN B1301 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1166 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1182 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1163 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1185 " pdb=" ZN C 401 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 88 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 92 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 86 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 95 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 32 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 29 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 7 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 10 " pdb=" ZN I 202 " 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 ZN I 202 " - pdb=" SG CYS I 103 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 46 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " 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 34 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 31 " pdb=" ZN M 401 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 48 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 45 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 24 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 27 " pdb=" ZN W 501 " 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 149 " pdb="ZN ZN W 501 " - pdb=" SG CYS W 152 " Number of angles added : 93 15688 Ramachandran restraints generated. 7844 Oldfield, 0 Emsley, 7844 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14770 Finding SS restraints... Secondary structure from input PDB file: 331 helices and 73 sheets defined 45.2% alpha, 11.8% beta 58 base pairs and 107 stacking pairs defined. Time for finding SS restraints: 17.83 Creating SS restraints... Processing helix chain 'A' and resid 23 through 31 Processing helix chain 'A' and resid 95 through 104 removed outlier: 3.876A pdb=" N VAL A 102 " --> pdb=" O LYS A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 126 Processing helix chain 'A' and resid 130 through 143 removed outlier: 3.530A pdb=" N ARG A 134 " --> pdb=" O ASP A 130 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA A 136 " --> pdb=" O LYS A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 213 removed outlier: 3.863A pdb=" N ILE A 207 " --> pdb=" O SER A 203 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N HIS A 213 " --> pdb=" O ASN A 209 " (cutoff:3.500A) 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: 3.689A pdb=" N LEU A 276 " --> pdb=" O ALA A 272 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR A 278 " --> pdb=" O ILE A 274 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLU A 280 " --> pdb=" O LEU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 305 removed outlier: 3.682A pdb=" N SER A 294 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE A 298 " --> pdb=" O SER A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 330 removed outlier: 3.656A pdb=" N LEU A 329 " --> pdb=" O ILE A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 340 Processing helix chain 'A' and resid 368 through 372 Processing helix chain 'A' and resid 384 through 395 Processing helix chain 'A' and resid 451 through 453 No H-bonds generated for 'chain 'A' and resid 451 through 453' Processing helix chain 'A' and resid 474 through 479 removed outlier: 3.575A pdb=" N TYR A 478 " --> pdb=" O VAL A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 505 Processing helix chain 'A' and resid 507 through 510 Processing helix chain 'A' and resid 525 through 536 Processing helix chain 'A' and resid 542 through 553 removed outlier: 3.713A pdb=" N VAL A 553 " --> pdb=" O MET A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 582 removed outlier: 4.058A pdb=" N ALA A 581 " --> pdb=" O ILE A 577 " (cutoff:3.500A) removed outlier: 3.812A 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 638 Processing helix chain 'A' and resid 638 through 661 removed outlier: 3.672A pdb=" N GLY A 647 " --> pdb=" O ALA A 643 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N PHE A 655 " --> pdb=" O LYS A 651 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 670 removed outlier: 3.682A pdb=" N ILE A 670 " --> pdb=" O GLY A 667 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 699 removed outlier: 3.551A pdb=" N ALA A 686 " --> pdb=" O THR A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 737 removed outlier: 3.676A pdb=" N ASN A 736 " --> pdb=" O LEU A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 743 through 749 Processing helix chain 'A' and resid 754 through 763 Processing helix chain 'A' and resid 793 through 798 Processing helix chain 'A' and resid 809 through 845 removed outlier: 3.534A pdb=" N GLU A 822 " --> pdb=" O MET A 818 " (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: 5.904A pdb=" N GLU A 914 " --> pdb=" O SER A 911 " (cutoff:3.500A) Processing helix chain 'A' and resid 915 through 920 removed outlier: 3.586A pdb=" N LEU A 920 " --> pdb=" O GLY A 916 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 947 removed outlier: 3.805A pdb=" N LEU A 928 " --> pdb=" O LYS A 924 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ASP A 930 " --> pdb=" O GLN A 926 " (cutoff:3.500A) Processing helix chain 'A' and resid 960 through 972 Processing helix chain 'A' and resid 982 through 994 Processing helix chain 'A' and resid 995 through 997 No H-bonds generated for 'chain 'A' and resid 995 through 997' Processing helix chain 'A' and resid 1004 through 1015 removed outlier: 3.681A 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 removed outlier: 3.625A pdb=" N ASP A1043 " --> pdb=" O LYS A1039 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TRP A1044 " --> pdb=" O GLN A1040 " (cutoff:3.500A) Processing helix chain 'A' and resid 1063 through 1074 Processing helix chain 'A' and resid 1075 through 1078 Processing helix chain 'A' and resid 1096 through 1106 removed outlier: 3.698A pdb=" N ARG A1100 " --> pdb=" O SER A1096 " (cutoff:3.500A) Processing helix chain 'A' and resid 1127 through 1139 Processing helix chain 'A' and resid 1163 through 1175 removed outlier: 3.936A pdb=" N GLU A1167 " --> pdb=" O ILE A1163 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLU A1168 " --> pdb=" O PRO A1164 " (cutoff:3.500A) removed outlier: 4.168A 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 1220 Processing helix chain 'A' and resid 1256 through 1270 removed outlier: 3.565A pdb=" N ASN A1265 " --> pdb=" O LYS A1261 " (cutoff:3.500A) Processing helix chain 'A' and resid 1312 through 1319 removed outlier: 3.821A pdb=" N THR A1318 " --> pdb=" O SER A1314 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL A1319 " --> pdb=" O GLU A1315 " (cutoff:3.500A) Processing helix chain 'A' and resid 1331 through 1359 removed outlier: 3.585A pdb=" N ILE A1335 " --> pdb=" O SER A1331 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N ILE A1341 " --> pdb=" O GLU A1337 " (cutoff:3.500A) removed outlier: 9.288A pdb=" N GLU A1342 " --> pdb=" O VAL A1338 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ALA A1343 " --> pdb=" O LEU A1339 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ASP A1359 " --> pdb=" O VAL A1355 " (cutoff:3.500A) Processing helix chain 'A' and resid 1364 through 1375 removed outlier: 3.858A pdb=" N MET A1368 " --> pdb=" O ASN A1364 " (cutoff:3.500A) Processing helix chain 'A' and resid 1388 through 1392 removed outlier: 3.678A pdb=" N ARG A1391 " --> pdb=" O GLY A1388 " (cutoff:3.500A) Processing helix chain 'A' and resid 1395 through 1400 Processing helix chain 'A' and resid 1404 through 1416 Processing helix chain 'A' and resid 1423 through 1430 Processing helix chain 'A' and resid 1436 through 1440 Processing helix chain 'A' and resid 1447 through 1452 removed outlier: 4.137A 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 42 removed outlier: 3.625A pdb=" N VAL B 33 " --> pdb=" O ASP B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 57 removed outlier: 3.671A pdb=" N PHE B 51 " --> pdb=" O GLN B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 65 Processing helix chain 'B' and resid 113 through 121 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 298 Processing helix chain 'B' and resid 299 through 301 No H-bonds generated for 'chain 'B' and resid 299 through 301' Processing helix chain 'B' and resid 307 through 319 removed outlier: 3.818A pdb=" N LEU B 311 " --> pdb=" O ASP B 307 " (cutoff:3.500A) Proline residue: B 316 - end of helix Processing helix chain 'B' and resid 320 through 322 No H-bonds generated for 'chain 'B' and resid 320 through 322' Processing helix chain 'B' and resid 326 through 336 Processing helix chain 'B' and resid 344 through 360 removed outlier: 3.614A pdb=" N GLN B 350 " --> pdb=" O GLU B 346 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLN B 357 " --> pdb=" O LYS B 353 " (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 438 removed outlier: 3.599A pdb=" N THR B 419 " --> pdb=" O GLN B 415 " (cutoff:3.500A) 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 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 removed outlier: 3.642A pdb=" N GLU B 560 " --> pdb=" O THR B 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 565 through 569 Processing helix chain 'B' and resid 592 through 606 Processing helix chain 'B' and resid 619 through 621 No H-bonds generated for 'chain 'B' and resid 619 through 621' Processing helix chain 'B' and resid 654 through 666 removed outlier: 3.665A pdb=" N THR B 664 " --> pdb=" O LYS B 660 " (cutoff:3.500A) Processing helix chain 'B' and resid 680 through 687 removed outlier: 3.506A pdb=" N LEU B 684 " --> pdb=" O THR B 680 " (cutoff:3.500A) Processing helix chain 'B' and resid 696 through 701 removed outlier: 3.711A pdb=" N ILE B 701 " --> pdb=" O GLU B 698 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 711 Processing helix chain 'B' and resid 744 through 749 removed outlier: 3.709A pdb=" N LEU B 749 " --> pdb=" O SER B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 751 through 755 Processing helix chain 'B' and resid 758 through 762 removed outlier: 3.623A pdb=" N ASN B 762 " --> pdb=" O PRO B 759 " (cutoff:3.500A) Processing helix chain 'B' and resid 763 through 774 removed outlier: 3.511A 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 784 through 788 Processing helix chain 'B' and resid 806 through 811 Processing helix chain 'B' and resid 843 through 848 Processing helix chain 'B' and resid 927 through 932 removed outlier: 4.085A pdb=" N TYR B 931 " --> pdb=" O GLN B 927 " (cutoff:3.500A) Processing helix chain 'B' and resid 995 through 999 Processing helix chain 'B' and resid 1013 through 1015 No H-bonds generated for 'chain 'B' and resid 1013 through 1015' Processing helix chain 'B' and resid 1016 through 1021 removed outlier: 3.837A pdb=" N ARG B1020 " --> pdb=" O ALA B1016 " (cutoff:3.500A) Processing helix chain 'B' and resid 1022 through 1039 removed outlier: 4.054A pdb=" N LEU B1026 " --> pdb=" O THR B1022 " (cutoff:3.500A) Processing helix chain 'B' and resid 1051 through 1062 Processing helix chain 'B' and resid 1098 through 1102 Processing helix chain 'B' and resid 1121 through 1125 Processing helix chain 'B' and resid 1131 through 1142 Processing helix chain 'B' and resid 1143 through 1152 Processing helix chain 'B' and resid 1198 through 1209 removed outlier: 3.635A pdb=" N ALA B1209 " --> pdb=" O GLN B1205 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 40 Processing helix chain 'C' and resid 59 through 69 removed outlier: 3.663A pdb=" N LEU C 69 " --> pdb=" O HIS C 65 " (cutoff:3.500A) 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 163 through 171 removed outlier: 6.650A pdb=" N ALA C 168 " --> pdb=" O LYS C 165 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N LYS C 169 " --> pdb=" O GLU C 166 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLY C 171 " --> pdb=" O ALA C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 201 Processing helix chain 'C' and resid 205 through 209 Processing helix chain 'C' and resid 239 through 263 removed outlier: 3.611A pdb=" N THR C 263 " --> pdb=" O LEU C 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 34 Processing helix chain 'D' and resid 53 through 76 removed outlier: 3.532A pdb=" N LYS D 60 " --> pdb=" O ARG D 56 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS D 71 " --> pdb=" O ARG D 67 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LYS D 76 " --> pdb=" O ARG D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 134 removed outlier: 4.605A pdb=" N GLU D 124 " --> pdb=" O GLU D 120 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N SER D 125 " --> pdb=" O LYS D 121 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N THR D 133 " --> pdb=" O LEU D 129 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 151 removed outlier: 3.508A pdb=" N TYR D 147 " --> pdb=" O ASN D 143 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 168 Processing helix chain 'D' and resid 173 through 183 Processing helix chain 'D' and resid 188 through 195 removed outlier: 4.002A pdb=" N LYS D 192 " --> pdb=" O ALA D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 218 removed outlier: 3.572A pdb=" N ILE D 210 " --> pdb=" O GLU D 206 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASN D 216 " --> pdb=" O LYS D 212 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 26 Processing helix chain 'E' and resid 31 through 35 Processing helix chain 'E' and resid 38 through 47 Processing helix chain 'E' and resid 54 through 59 removed outlier: 3.529A pdb=" N SER E 59 " --> pdb=" O ARG E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 72 removed outlier: 3.565A pdb=" N ILE E 69 " --> pdb=" O THR E 65 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER E 70 " --> pdb=" O GLU E 66 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 104 removed outlier: 3.522A pdb=" N ILE E 98 " --> pdb=" O LYS E 94 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 124 removed outlier: 3.509A pdb=" N VAL E 124 " --> pdb=" O ALA E 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 142 removed outlier: 4.151A pdb=" N VAL E 142 " --> pdb=" O ALA E 139 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 147 Processing helix chain 'E' and resid 157 through 168 removed outlier: 3.732A pdb=" N LYS E 166 " --> pdb=" O ARG E 162 " (cutoff:3.500A) Processing helix chain 'E' and resid 171 through 175 Processing helix chain 'E' and resid 182 through 189 Processing helix chain 'F' and resid 86 through 102 Processing helix chain 'F' and resid 116 through 127 Processing helix chain 'G' and resid 14 through 18 Processing helix chain 'G' and resid 21 through 35 removed outlier: 3.788A pdb=" N TYR G 25 " --> pdb=" O ARG G 21 " (cutoff:3.500A) Processing helix chain 'G' and resid 63 through 66 removed outlier: 3.991A pdb=" N GLY G 66 " --> pdb=" O PRO G 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 63 through 66' Processing helix chain 'G' and resid 113 through 115 No H-bonds generated for 'chain 'G' and resid 113 through 115' Processing helix chain 'H' and resid 129 through 133 Processing helix chain 'I' and resid 61 through 65 removed outlier: 3.539A pdb=" N ASP I 65 " --> pdb=" O ILE I 62 " (cutoff:3.500A) Processing helix chain 'J' and resid 17 through 28 removed outlier: 3.607A pdb=" N ASP J 28 " --> pdb=" O LEU J 24 " (cutoff:3.500A) Processing helix chain 'J' and resid 31 through 39 removed outlier: 4.148A pdb=" N SER J 37 " --> pdb=" O GLY J 33 " (cutoff:3.500A) Processing helix chain 'J' and resid 43 through 53 removed outlier: 3.825A pdb=" N MET J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE J 50 " --> pdb=" O CYS J 46 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 63 removed outlier: 3.568A pdb=" N ARG J 62 " --> pdb=" O GLU J 58 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N TYR J 63 " --> pdb=" O LYS J 59 " (cutoff:3.500A) Processing helix chain 'K' and resid 39 through 51 removed outlier: 3.865A pdb=" N LEU K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 110 removed outlier: 3.712A pdb=" N LYS K 88 " --> pdb=" O LYS K 84 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLU K 108 " --> pdb=" O ASN K 104 " (cutoff:3.500A) Processing helix chain 'M' and resid 38 through 40 No H-bonds generated for 'chain 'M' and resid 38 through 40' Processing helix chain 'M' and resid 60 through 65 Processing helix chain 'M' and resid 85 through 89 Processing helix chain 'M' and resid 103 through 114 removed outlier: 5.248A pdb=" N GLU M 109 " --> pdb=" O ARG M 105 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLN M 114 " --> pdb=" O LEU M 110 " (cutoff:3.500A) Processing helix chain 'M' and resid 115 through 117 No H-bonds generated for 'chain 'M' and resid 115 through 117' Processing helix chain 'M' and resid 122 through 140 removed outlier: 3.610A pdb=" N ALA M 129 " --> pdb=" O GLU M 125 " (cutoff:3.500A) Processing helix chain 'M' and resid 143 through 158 removed outlier: 3.641A pdb=" N LYS M 147 " --> pdb=" O PRO M 143 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ASP M 148 " --> pdb=" O LYS M 144 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LYS M 155 " --> pdb=" O LYS M 151 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N CYS M 157 " --> pdb=" O ALA M 153 " (cutoff:3.500A) Processing helix chain 'M' and resid 168 through 183 removed outlier: 4.169A pdb=" N MET M 172 " --> pdb=" O MET M 168 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ILE M 176 " --> pdb=" O MET M 172 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU M 177 " --> pdb=" O ALA M 173 " (cutoff:3.500A) Processing helix chain 'M' and resid 188 through 196 Processing helix chain 'M' and resid 201 through 218 removed outlier: 3.550A pdb=" N ILE M 209 " --> pdb=" O LYS M 205 " (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 246 removed outlier: 4.290A pdb=" N ARG M 241 " --> pdb=" O THR M 237 " (cutoff:3.500A) Processing helix chain 'M' and resid 249 through 267 removed outlier: 3.792A pdb=" N THR M 253 " --> pdb=" O PRO M 249 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA M 256 " --> pdb=" O VAL M 252 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU M 257 " --> pdb=" O THR M 253 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N TYR M 258 " --> pdb=" O THR M 254 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE M 266 " --> pdb=" O LYS M 262 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N LYS M 267 " --> pdb=" O CYS M 263 " (cutoff:3.500A) Processing helix chain 'M' and resid 274 through 289 removed outlier: 3.877A pdb=" N SER M 281 " --> pdb=" O ILE M 277 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE M 282 " --> pdb=" O ALA M 278 " (cutoff:3.500A) Processing helix chain 'M' and resid 294 through 303 removed outlier: 3.909A pdb=" N GLN M 300 " --> pdb=" O ALA M 296 " (cutoff:3.500A) Processing helix chain 'M' and resid 306 through 318 removed outlier: 3.615A pdb=" N ILE M 315 " --> pdb=" O SER M 311 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU M 316 " --> pdb=" O GLY M 312 " (cutoff:3.500A) Processing helix chain 'Q' and resid 26 through 35 removed outlier: 4.224A pdb=" N ASN Q 30 " --> pdb=" O ARG Q 26 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU Q 32 " --> pdb=" O ARG Q 28 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ARG Q 35 " --> pdb=" O PHE Q 31 " (cutoff:3.500A) Processing helix chain 'Q' and resid 108 through 114 Processing helix chain 'Q' and resid 129 through 133 Processing helix chain 'Q' and resid 337 through 345 Processing helix chain 'Q' and resid 407 through 413 removed outlier: 4.065A pdb=" N LYS Q 411 " --> pdb=" O ASP Q 407 " (cutoff:3.500A) Processing helix chain 'R' and resid 74 through 80 Processing helix chain 'R' and resid 234 through 242 Processing helix chain 'R' and resid 243 through 246 Processing helix chain 'R' and resid 258 through 265 removed outlier: 3.912A pdb=" N THR R 262 " --> pdb=" O THR R 258 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N MET R 263 " --> pdb=" O VAL R 259 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER R 264 " --> pdb=" O GLY R 260 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N HIS R 265 " --> pdb=" O VAL R 261 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 258 through 265' Processing helix chain 'R' and resid 295 through 310 Processing helix chain 'R' and resid 314 through 323 removed outlier: 3.512A pdb=" N ARG R 321 " --> pdb=" O GLY R 317 " (cutoff:3.500A) Processing helix chain 'R' and resid 325 through 333 removed outlier: 4.013A pdb=" N LEU R 329 " --> pdb=" O PRO R 325 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU R 333 " --> pdb=" O LEU R 329 " (cutoff:3.500A) Processing helix chain 'W' and resid 5 through 20 Processing helix chain 'W' and resid 24 through 34 removed outlier: 3.868A pdb=" N VAL W 28 " --> pdb=" O SER W 24 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU W 29 " --> pdb=" O PHE W 25 " (cutoff:3.500A) Processing helix chain 'W' and resid 39 through 48 removed outlier: 4.053A pdb=" N LEU W 43 " --> pdb=" O ALA W 39 " (cutoff:3.500A) Processing helix chain 'W' and resid 54 through 64 removed outlier: 3.573A pdb=" N ARG W 60 " --> pdb=" O PRO W 56 " (cutoff:3.500A) Processing helix chain 'W' and resid 90 through 111 Processing helix chain 'W' and resid 112 through 115 Processing helix chain 'W' and resid 132 through 140 Processing helix chain 'W' and resid 161 through 177 removed outlier: 4.090A pdb=" N ASN W 165 " --> pdb=" O SER W 161 " (cutoff:3.500A) Processing helix chain 'W' and resid 181 through 191 removed outlier: 3.830A pdb=" N SER W 185 " --> pdb=" O PRO W 181 " (cutoff:3.500A) Processing helix chain 'X' and resid 124 through 139 Processing helix chain 'X' and resid 143 through 151 removed outlier: 3.935A pdb=" N LEU X 151 " --> pdb=" O LEU X 147 " (cutoff:3.500A) Processing helix chain 'X' and resid 156 through 166 removed outlier: 3.842A 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 removed outlier: 3.787A pdb=" N ASP X 212 " --> pdb=" O LYS X 208 " (cutoff:3.500A) Processing helix chain 'X' and resid 216 through 224 removed outlier: 3.621A pdb=" N THR X 220 " --> pdb=" O GLN X 216 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASN X 222 " --> pdb=" O ASP X 218 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LEU X 224 " --> pdb=" O THR X 220 " (cutoff:3.500A) Processing helix chain 'X' and resid 256 through 266 Processing helix chain 'X' and resid 272 through 282 removed outlier: 3.574A pdb=" N GLN X 279 " --> pdb=" O PRO X 275 " (cutoff:3.500A) Processing helix chain 'O' and resid 81 through 89 Processing helix chain 'O' and resid 128 through 147 Processing helix chain 'O' and resid 171 through 179 Processing helix chain 'O' and resid 219 through 237 removed outlier: 3.790A pdb=" N ILE O 223 " --> pdb=" O GLN O 219 " (cutoff:3.500A) Proline residue: O 232 - end of helix Processing helix chain '0' and resid 18 through 34 removed outlier: 3.621A pdb=" N TYR 0 22 " --> pdb=" O TYR 0 18 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL 0 34 " --> pdb=" O LYS 0 30 " (cutoff:3.500A) Processing helix chain '0' and resid 47 through 63 removed outlier: 3.668A pdb=" N LEU 0 55 " --> pdb=" O SER 0 51 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA 0 58 " --> pdb=" O SER 0 54 " (cutoff:3.500A) Processing helix chain '0' and resid 75 through 97 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 Processing helix chain '0' and resid 157 through 166 Processing helix chain '0' and resid 177 through 188 removed outlier: 3.977A pdb=" N LYS 0 183 " --> pdb=" O GLU 0 179 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS 0 188 " --> pdb=" O TYR 0 184 " (cutoff:3.500A) Processing helix chain '0' and resid 191 through 200 removed outlier: 3.837A pdb=" N ILE 0 195 " --> pdb=" O CYS 0 191 " (cutoff:3.500A) Processing helix chain '0' and resid 210 through 215 Processing helix chain '0' and resid 223 through 228 Processing helix chain '0' and resid 239 through 245 removed outlier: 3.612A pdb=" N VAL 0 243 " --> pdb=" O ASN 0 239 " (cutoff:3.500A) Processing helix chain '0' and resid 247 through 249 No H-bonds generated for 'chain '0' and resid 247 through 249' Processing helix chain '0' and resid 253 through 278 Processing helix chain '0' and resid 279 through 291 Processing helix chain '0' and resid 294 through 299 removed outlier: 3.722A pdb=" N LEU 0 299 " --> pdb=" O SER 0 295 " (cutoff:3.500A) Processing helix chain '0' and resid 322 through 326 Processing helix chain '0' and resid 327 through 347 removed outlier: 4.180A pdb=" N LYS 0 347 " --> pdb=" O LYS 0 343 " (cutoff:3.500A) Processing helix chain '0' and resid 355 through 367 removed outlier: 3.719A pdb=" N HIS 0 362 " --> pdb=" O SER 0 358 " (cutoff:3.500A) Processing helix chain '0' and resid 370 through 387 removed outlier: 3.968A pdb=" N PHE 0 376 " --> pdb=" O LYS 0 372 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N SER 0 378 " --> pdb=" O LEU 0 374 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N GLU 0 379 " --> pdb=" O ARG 0 375 " (cutoff:3.500A) Processing helix chain '0' and resid 393 through 412 removed outlier: 3.737A pdb=" N ALA 0 398 " --> pdb=" O GLU 0 394 " (cutoff:3.500A) Processing helix chain '0' and resid 424 through 428 Processing helix chain '0' and resid 441 through 453 removed outlier: 4.344A pdb=" N ALA 0 445 " --> pdb=" O ASP 0 441 " (cutoff:3.500A) Proline residue: 0 448 - end of helix removed outlier: 3.728A 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: 3.867A pdb=" N VAL 0 519 " --> pdb=" O ASP 0 515 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER 0 524 " --> pdb=" O ARG 0 520 " (cutoff:3.500A) Processing helix chain '0' and resid 543 through 557 Processing helix chain '0' and resid 558 through 567 removed outlier: 4.087A pdb=" N GLU 0 562 " --> pdb=" O GLY 0 558 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL 0 563 " --> pdb=" O ILE 0 559 " (cutoff:3.500A) Processing helix chain '0' and resid 575 through 592 removed outlier: 3.629A pdb=" N THR 0 579 " --> pdb=" O ASP 0 575 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLU 0 584 " --> pdb=" O SER 0 580 " (cutoff:3.500A) Processing helix chain '0' and resid 604 through 610 Processing helix chain '0' and resid 632 through 646 removed outlier: 3.939A pdb=" N LYS 0 636 " --> pdb=" O SER 0 632 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N PHE 0 641 " --> pdb=" O ALA 0 637 " (cutoff:3.500A) Processing helix chain '0' and resid 649 through 667 removed outlier: 3.581A pdb=" N MET 0 659 " --> pdb=" O SER 0 655 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLN 0 664 " --> pdb=" O ARG 0 660 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LEU 0 666 " --> pdb=" O ALA 0 662 " (cutoff:3.500A) 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 693 removed outlier: 3.511A pdb=" N ARG 0 690 " --> pdb=" O SER 0 687 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N SER 0 691 " --> pdb=" O ARG 0 688 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU 0 693 " --> pdb=" O ARG 0 690 " (cutoff:3.500A) Processing helix chain '0' and resid 694 through 701 Processing helix chain '0' and resid 709 through 726 removed outlier: 3.529A pdb=" N SER 0 715 " --> pdb=" O ASP 0 711 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ASN 0 716 " --> pdb=" O MET 0 712 " (cutoff:3.500A) Processing helix chain '0' and resid 733 through 739 removed outlier: 3.849A pdb=" N SER 0 737 " --> pdb=" O GLN 0 733 " (cutoff:3.500A) Processing helix chain '0' and resid 743 through 752 Processing helix chain '1' and resid 170 through 175 Processing helix chain '1' and resid 177 through 186 Processing helix chain '1' and resid 188 through 200 removed outlier: 4.615A pdb=" N THR 1 198 " --> pdb=" O VAL 1 194 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL 1 199 " --> pdb=" O PHE 1 195 " (cutoff:3.500A) Processing helix chain '1' and resid 205 through 211 removed outlier: 3.764A pdb=" N SER 1 211 " --> pdb=" O SER 1 207 " (cutoff:3.500A) Processing helix chain '1' and resid 213 through 225 Processing helix chain '1' and resid 230 through 235 No H-bonds generated for 'chain '1' and resid 230 through 235' Processing helix chain '1' and resid 251 through 263 Processing helix chain '1' and resid 263 through 273 Processing helix chain '1' and resid 282 through 295 removed outlier: 3.637A pdb=" N SER 1 289 " --> pdb=" O ALA 1 285 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER 1 290 " --> pdb=" O ARG 1 286 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LYS 1 291 " --> pdb=" O PHE 1 287 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N LEU 1 292 " --> pdb=" O PHE 1 288 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N PHE 1 293 " --> pdb=" O SER 1 289 " (cutoff:3.500A) Processing helix chain '1' and resid 308 through 310 No H-bonds generated for 'chain '1' and resid 308 through 310' Processing helix chain '1' and resid 311 through 330 removed outlier: 4.294A pdb=" N LEU 1 315 " --> pdb=" O UNK 1 311 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N UNK 1 316 " --> pdb=" O UNK 1 312 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N UNK 1 319 " --> pdb=" O LEU 1 315 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N UNK 1 320 " --> pdb=" O UNK 1 316 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N PHE 1 321 " --> pdb=" O UNK 1 317 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N UNK 1 326 " --> pdb=" O UNK 1 322 " (cutoff:3.500A) Processing helix chain '1' and resid 338 through 345 Processing helix chain '1' and resid 371 through 391 Processing helix chain '1' and resid 468 through 483 Processing helix chain '1' and resid 496 through 516 removed outlier: 3.615A pdb=" N ILE 1 509 " --> pdb=" O THR 1 505 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ASN 1 510 " --> pdb=" O UNK 1 506 " (cutoff:3.500A) Processing helix chain '1' and resid 540 through 567 removed outlier: 3.874A pdb=" N LEU 1 547 " --> pdb=" O PRO 1 543 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU 1 548 " --> pdb=" O ILE 1 544 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ILE 1 566 " --> pdb=" O LYS 1 562 " (cutoff:3.500A) Processing helix chain '1' and resid 575 through 605 removed outlier: 4.235A pdb=" N VAL 1 579 " --> pdb=" O GLN 1 575 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS 1 580 " --> pdb=" O ALA 1 576 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU 1 601 " --> pdb=" O PHE 1 597 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ASN 1 602 " --> pdb=" O GLN 1 598 " (cutoff:3.500A) Processing helix chain '1' and resid 606 through 616 removed outlier: 3.580A pdb=" N ALA 1 614 " --> pdb=" O ASN 1 610 " (cutoff:3.500A) Processing helix chain '1' and resid 616 through 639 removed outlier: 4.020A pdb=" N LEU 1 620 " --> pdb=" O LEU 1 616 " (cutoff:3.500A) Processing helix chain '4' and resid 33 through 43 Processing helix chain '4' and resid 49 through 68 removed outlier: 3.847A pdb=" N VAL 4 53 " --> pdb=" O SER 4 49 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU 4 55 " --> pdb=" O ILE 4 51 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ASN 4 62 " --> pdb=" O ILE 4 58 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASN 4 68 " --> pdb=" O HIS 4 64 " (cutoff:3.500A) Processing helix chain '4' and resid 117 through 135 removed outlier: 3.661A pdb=" N VAL 4 121 " --> pdb=" O ARG 4 117 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLU 4 128 " --> pdb=" O THR 4 124 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU 4 135 " --> pdb=" O LYS 4 131 " (cutoff:3.500A) Processing helix chain '4' and resid 137 through 143 removed outlier: 3.752A pdb=" N ASN 4 143 " --> pdb=" O GLN 4 139 " (cutoff:3.500A) Processing helix chain '4' and resid 148 through 167 Processing helix chain '4' and resid 192 through 207 Processing helix chain '4' and resid 221 through 232 Processing helix chain '4' and resid 244 through 252 removed outlier: 3.507A pdb=" N THR 4 250 " --> pdb=" O GLN 4 246 " (cutoff:3.500A) Processing helix chain '4' and resid 313 through 320 Processing helix chain '4' and resid 321 through 323 No H-bonds generated for 'chain '4' and resid 321 through 323' Processing helix chain '6' and resid 133 through 138 Processing helix chain '6' and resid 144 through 164 removed outlier: 3.509A pdb=" N MET 6 148 " --> pdb=" O ASN 6 144 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ASP 6 155 " --> pdb=" O GLN 6 151 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE 6 156 " --> pdb=" O TYR 6 152 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N HIS 6 158 " --> pdb=" O ILE 6 154 " (cutoff:3.500A) Processing helix chain '6' and resid 188 through 202 removed outlier: 4.123A pdb=" N HIS 6 192 " --> pdb=" O ASN 6 188 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LYS 6 197 " --> pdb=" O ILE 6 193 " (cutoff:3.500A) Processing helix chain '6' and resid 209 through 221 removed outlier: 3.507A pdb=" N GLU 6 215 " --> pdb=" O GLN 6 211 " (cutoff:3.500A) Processing helix chain '6' and resid 247 through 257 Processing helix chain '6' and resid 270 through 281 Processing helix chain '6' and resid 293 through 306 removed outlier: 3.820A pdb=" N GLU 6 299 " --> pdb=" O THR 6 295 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N THR 6 306 " --> pdb=" O ASN 6 302 " (cutoff:3.500A) Processing helix chain '6' and resid 373 through 380 removed outlier: 3.627A pdb=" N SER 6 379 " --> pdb=" O HIS 6 375 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N TYR 6 380 " --> pdb=" O LEU 6 376 " (cutoff:3.500A) Processing helix chain '6' and resid 437 through 445 Processing helix chain '6' and resid 451 through 456 Processing helix chain '2' and resid 10 through 16 Processing helix chain '2' and resid 18 through 26 Processing helix chain '2' and resid 28 through 39 Processing helix chain '2' and resid 40 through 52 removed outlier: 3.847A pdb=" N PHE 2 52 " --> pdb=" O MET 2 48 " (cutoff:3.500A) Processing helix chain '2' and resid 59 through 64 Processing helix chain '2' and resid 70 through 84 removed outlier: 3.772A pdb=" N PHE 2 74 " --> pdb=" O GLY 2 70 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N GLN 2 75 " --> pdb=" O LYS 2 71 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER 2 80 " --> pdb=" O ASN 2 76 " (cutoff:3.500A) Processing helix chain '2' and resid 101 through 113 removed outlier: 3.588A pdb=" N ALA 2 111 " --> pdb=" O SER 2 107 " (cutoff:3.500A) Processing helix chain '2' and resid 137 through 152 removed outlier: 4.128A pdb=" N LYS 2 142 " --> pdb=" O TYR 2 138 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N LEU 2 147 " --> pdb=" O TRP 2 143 " (cutoff:3.500A) 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 removed outlier: 4.491A pdb=" N GLN 2 206 " --> pdb=" O THR 2 202 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N TYR 2 207 " --> pdb=" O LEU 2 203 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU 2 208 " --> pdb=" O LEU 2 204 " (cutoff:3.500A) Processing helix chain '2' and resid 217 through 231 removed outlier: 3.673A pdb=" N PHE 2 224 " --> pdb=" O ASP 2 220 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU 2 228 " --> pdb=" O PHE 2 224 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU 2 231 " --> pdb=" O MET 2 227 " (cutoff:3.500A) Processing helix chain '2' and resid 243 through 257 Processing helix chain '2' and resid 272 through 279 removed outlier: 3.988A pdb=" N LEU 2 276 " --> pdb=" O THR 2 272 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N THR 2 279 " --> pdb=" O ALA 2 275 " (cutoff:3.500A) Processing helix chain '2' and resid 355 through 362 Processing helix chain '2' and resid 379 through 390 removed outlier: 3.874A pdb=" N ARG 2 384 " --> pdb=" O ARG 2 380 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ARG 2 385 " --> pdb=" O GLU 2 381 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ALA 2 386 " --> pdb=" O SER 2 382 " (cutoff:3.500A) Processing helix chain '2' and resid 393 through 403 removed outlier: 3.641A pdb=" N ILE 2 397 " --> pdb=" O ALA 2 393 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ALA 2 398 " --> pdb=" O ASP 2 394 " (cutoff:3.500A) Processing helix chain '2' and resid 404 through 409 removed outlier: 4.135A pdb=" N ARG 2 409 " --> pdb=" O PRO 2 406 " (cutoff:3.500A) Processing helix chain '2' and resid 410 through 415 Processing helix chain '2' and resid 435 through 450 Processing helix chain '2' and resid 485 through 489 removed outlier: 3.521A pdb=" N LYS 2 489 " --> pdb=" O ASP 2 486 " (cutoff:3.500A) Processing helix chain '5' and resid 13 through 28 Processing helix chain '5' and resid 46 through 62 Processing helix chain '3' and resid 39 through 48 Processing helix chain '3' and resid 64 through 68 Processing helix chain '3' and resid 75 through 92 Processing helix chain '3' and resid 93 through 95 No H-bonds generated for 'chain '3' and resid 93 through 95' Processing helix chain '3' and resid 102 through 123 Processing helix chain '3' and resid 127 through 143 Processing helix chain '7' and resid 124 through 129 removed outlier: 4.069A pdb=" N ALA 7 128 " --> pdb=" O ARG 7 124 " (cutoff:3.500A) Processing helix chain '7' and resid 150 through 152 No H-bonds generated for 'chain '7' and resid 150 through 152' Processing helix chain '7' and resid 153 through 159 Processing helix chain '7' and resid 176 through 184 removed outlier: 3.718A pdb=" N LEU 7 180 " --> pdb=" O THR 7 176 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N TYR 7 181 " --> pdb=" O ALA 7 177 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL 7 184 " --> pdb=" O LEU 7 180 " (cutoff:3.500A) Processing helix chain '7' and resid 189 through 200 removed outlier: 3.877A pdb=" N ILE 7 193 " --> pdb=" O GLU 7 189 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ILE 7 194 " --> pdb=" O THR 7 190 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ARG 7 199 " --> pdb=" O SER 7 195 " (cutoff:3.500A) Processing helix chain '7' and resid 206 through 217 Processing helix chain '7' and resid 241 through 245 Processing helix chain '7' and resid 304 through 308 removed outlier: 4.391A pdb=" N ASP 7 307 " --> pdb=" O GLU 7 304 " (cutoff:3.500A) Processing helix chain '7' and resid 325 through 333 removed outlier: 4.546A pdb=" N GLN 7 331 " --> pdb=" O LYS 7 327 " (cutoff:3.500A) Processing helix chain '7' and resid 366 through 372 Processing helix chain '7' and resid 391 through 402 removed outlier: 3.727A pdb=" N VAL 7 395 " --> pdb=" O GLY 7 391 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ALA 7 399 " --> pdb=" O VAL 7 395 " (cutoff:3.500A) Processing helix chain '7' and resid 416 through 420 Processing helix chain '7' and resid 456 through 461 removed outlier: 3.594A pdb=" N VAL 7 460 " --> pdb=" O THR 7 456 " (cutoff:3.500A) Processing helix chain '7' and resid 468 through 480 removed outlier: 3.849A pdb=" N ASP 7 475 " --> pdb=" O GLN 7 471 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N PHE 7 476 " --> pdb=" O LYS 7 472 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU 7 477 " --> pdb=" O VAL 7 473 " (cutoff:3.500A) Processing helix chain '7' and resid 494 through 503 removed outlier: 6.312A pdb=" N ARG 7 500 " --> pdb=" O ALA 7 496 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N VAL 7 501 " --> pdb=" O MET 7 497 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL 7 502 " --> pdb=" O PHE 7 498 " (cutoff:3.500A) Processing helix chain '7' and resid 526 through 530 removed outlier: 3.805A pdb=" N PHE 7 529 " --> pdb=" O ASP 7 526 " (cutoff:3.500A) Processing helix chain '7' and resid 562 through 570 removed outlier: 4.364A pdb=" N GLU 7 568 " --> pdb=" O GLU 7 564 " (cutoff:3.500A) Processing helix chain '7' and resid 575 through 583 removed outlier: 3.899A pdb=" N LEU 7 579 " --> pdb=" O ARG 7 575 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N LEU 7 580 " --> pdb=" O LYS 7 576 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N TYR 7 581 " --> pdb=" O ARG 7 577 " (cutoff:3.500A) Processing helix chain '7' and resid 585 through 601 removed outlier: 3.933A pdb=" N GLN 7 589 " --> pdb=" O PRO 7 585 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N PHE 7 593 " --> pdb=" O GLN 7 589 " (cutoff:3.500A) Processing helix chain '7' and resid 611 through 620 removed outlier: 4.610A pdb=" N GLU 7 617 " --> pdb=" O TYR 7 613 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU 7 620 " --> pdb=" O GLN 7 616 " (cutoff:3.500A) Processing helix chain '7' and resid 633 through 640 removed outlier: 3.897A pdb=" N ILE 7 639 " --> pdb=" O ARG 7 636 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU 7 640 " --> pdb=" O MET 7 637 " (cutoff:3.500A) Processing helix chain '7' and resid 657 through 661 Processing helix chain '7' and resid 679 through 687 Processing helix chain '7' and resid 687 through 692 removed outlier: 4.387A pdb=" N LEU 7 691 " --> pdb=" O LEU 7 687 " (cutoff:3.500A) Processing helix chain '7' and resid 715 through 724 Processing helix chain '7' and resid 725 through 730 removed outlier: 3.556A pdb=" N ASP 7 728 " --> pdb=" O PHE 7 725 " (cutoff:3.500A) Processing helix chain '7' and resid 752 through 770 removed outlier: 3.747A pdb=" N ARG 7 756 " --> pdb=" O SER 7 752 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN 7 761 " --> pdb=" O ARG 7 757 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N LEU 7 765 " --> pdb=" O GLN 7 761 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N LYS 7 766 " --> pdb=" O GLU 7 762 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ASN 7 767 " --> pdb=" O VAL 7 763 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1418 through 1419 Processing sheet with id=AA2, first strand: chain 'A' and resid 82 through 91 removed outlier: 7.080A pdb=" N THR A 237 " --> pdb=" O LEU A 86 " (cutoff:3.500A) removed outlier: 10.273A pdb=" N LYS A 88 " --> pdb=" O ILE A 235 " (cutoff:3.500A) removed outlier: 10.157A pdb=" N ILE A 235 " --> pdb=" O LYS A 88 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 173 through 176 Processing sheet with id=AA4, first strand: chain 'A' and resid 250 through 252 Processing sheet with id=AA5, first strand: chain 'A' and resid 343 through 345 removed outlier: 3.902A pdb=" N LEU B1128 " --> pdb=" O VAL A 345 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 1104 through 1106 removed outlier: 3.573A pdb=" N THR A 351 " --> pdb=" O MET A 487 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 375 through 379 removed outlier: 4.008A pdb=" N TYR A 404 " --> pdb=" O GLU A 433 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N HIS A 435 " --> pdb=" O ALA A 402 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N ALA A 402 " --> pdb=" O HIS A 435 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 512 through 513 removed outlier: 3.630A pdb=" N LYS A 518 " --> pdb=" O SER A 513 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 540 through 541 Processing sheet with id=AB1, first strand: chain 'A' and resid 587 through 590 removed outlier: 6.644A pdb=" N LEU A 606 " --> pdb=" O ILE A 613 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 766 through 767 Processing sheet with id=AB3, first strand: chain 'A' and resid 849 through 850 removed outlier: 6.681A pdb=" N THR A 856 " --> pdb=" O ILE A 864 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 879 through 882 Processing sheet with id=AB5, first strand: chain 'A' and resid 1284 through 1288 Processing sheet with id=AB6, first strand: chain 'A' and resid 1141 through 1142 removed outlier: 6.757A pdb=" N THR A1141 " --> pdb=" O LEU A1273 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1226 through 1228 removed outlier: 7.020A pdb=" N ARG A1194 " --> pdb=" O SER A1150 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N SER A1150 " --> pdb=" O ARG A1194 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N GLU A1196 " --> pdb=" O ILE A1148 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N SER A1150 " --> pdb=" O ARG I 45 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ARG I 45 " --> pdb=" O SER A1150 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ILE A1152 " --> pdb=" O VAL I 43 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1291 through 1292 Processing sheet with id=AB9, first strand: chain 'D' and resid 48 through 49 removed outlier: 4.447A pdb=" N ILE D 48 " --> pdb=" O ILE G 4 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE G 4 " --> pdb=" O ILE D 48 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N GLY G 59 " --> pdb=" O ILE A1445 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N VAL A1443 " --> pdb=" O ILE G 61 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 48 through 49 removed outlier: 4.447A pdb=" N ILE D 48 " --> pdb=" O ILE G 4 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE G 4 " --> pdb=" O ILE D 48 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N ARG G 75 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N VAL G 48 " --> pdb=" O ARG G 75 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N VAL G 77 " --> pdb=" O LEU G 46 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 69 through 73 Processing sheet with id=AC3, first strand: chain 'B' and resid 95 through 97 removed outlier: 4.035A pdb=" N GLY B 168 " --> pdb=" O LEU B 128 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N VAL B 130 " --> pdb=" O PHE B 166 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N PHE B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 101 through 103 Processing sheet with id=AC5, first strand: chain 'B' and resid 203 through 205 Processing sheet with id=AC6, first strand: chain 'B' and resid 404 through 407 removed outlier: 6.412A pdb=" N ALA B 214 " --> pdb=" O ASN B 499 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 223 through 227 removed outlier: 4.101A pdb=" N HIS B 236 " --> pdb=" O LEU B 258 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU B 254 " --> pdb=" O ILE B 240 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 544 through 545 Processing sheet with id=AC9, first strand: chain 'B' and resid 650 through 651 Processing sheet with id=AD1, first strand: chain 'B' and resid 586 through 590 removed outlier: 6.736A pdb=" N VAL B 580 " --> pdb=" O HIS B 587 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N VAL B 589 " --> pdb=" O THR B 578 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N THR B 578 " --> pdb=" O VAL B 589 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 793 through 796 removed outlier: 6.722A pdb=" N PHE B 963 " --> pdb=" O VAL B 954 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N VAL B 954 " --> pdb=" O PHE B 963 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N LYS B 965 " --> pdb=" O VAL B 952 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N VAL B 952 " --> pdb=" O LYS B 965 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ARG B 967 " --> pdb=" O ASP B 950 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 804 through 805 Processing sheet with id=AD4, first strand: chain 'B' and resid 1069 through 1070 removed outlier: 6.793A pdb=" N MET B 839 " --> pdb=" O GLY B 991 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N THR B 993 " --> pdb=" O MET B 839 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N MET B 841 " --> pdb=" O THR B 993 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N PHE B1086 " --> pdb=" O ILE B 827 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 873 through 874 Processing sheet with id=AD6, first strand: chain 'B' and resid 910 through 912 Processing sheet with id=AD7, first strand: chain 'B' and resid 1001 through 1002 Processing sheet with id=AD8, first strand: chain 'B' and resid 1157 through 1163 Processing sheet with id=AD9, first strand: chain 'C' and resid 7 through 13 removed outlier: 6.235A pdb=" N ASP C 19 " --> pdb=" O ARG C 11 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ALA C 13 " --> pdb=" O ASN C 17 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N ASN C 17 " --> pdb=" O ALA C 13 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N ASN C 231 " --> pdb=" O ILE C 176 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N ILE C 176 " --> pdb=" O ASN C 231 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N GLU C 233 " --> pdb=" O ALA C 174 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 119 through 120 removed outlier: 6.724A pdb=" N GLU C 152 " --> pdb=" O THR C 53 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N THR C 53 " --> pdb=" O GLU C 152 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N LYS C 154 " --> pdb=" O VAL C 51 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N VAL C 51 " --> pdb=" O LYS C 154 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N THR C 156 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N VAL C 49 " --> pdb=" O THR C 156 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N VAL C 158 " --> pdb=" O ASP C 47 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 111 through 114 removed outlier: 3.605A pdb=" N CYS C 145 " --> pdb=" O VAL C 113 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 36 through 38 removed outlier: 3.827A pdb=" N GLN D 37 " --> pdb=" O GLU D 45 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 60 through 62 removed outlier: 6.513A pdb=" N TRP E 79 " --> pdb=" O ILE E 109 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N VAL E 111 " --> pdb=" O TRP E 79 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N GLU E 81 " --> pdb=" O VAL E 111 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 152 through 155 removed outlier: 3.672A pdb=" N LYS E 152 " --> pdb=" O ILE E 199 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N ILE E 178 " --> pdb=" O MET E 215 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 83 through 90 removed outlier: 5.476A pdb=" N LYS G 83 " --> pdb=" O GLY G 149 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N GLY G 149 " --> pdb=" O LYS G 83 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N GLU G 85 " --> pdb=" O ILE G 147 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N ILE G 147 " --> pdb=" O SER G 162 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N SER G 162 " --> pdb=" O ILE G 147 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 83 through 90 removed outlier: 5.476A pdb=" N LYS G 83 " --> pdb=" O GLY G 149 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N GLY G 149 " --> pdb=" O LYS G 83 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N GLU G 85 " --> pdb=" O ILE G 147 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ARG G 142 " --> pdb=" O ILE G 171 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLY G 169 " --> pdb=" O ARG G 144 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 98 through 103 removed outlier: 3.556A pdb=" N PHE G 99 " --> pdb=" O VAL G 110 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL G 110 " --> pdb=" O PHE G 99 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'G' and resid 130 through 131 Processing sheet with id=AF1, first strand: chain 'H' and resid 7 through 16 removed outlier: 6.626A pdb=" N GLU H 27 " --> pdb=" O SER H 13 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N VAL H 15 " --> pdb=" O ARG H 25 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ARG H 25 " --> pdb=" O VAL H 15 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU H 126 " --> pdb=" O LYS H 37 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N LEU H 122 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LYS H 103 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N SER H 117 " --> pdb=" O ALA H 101 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N ALA H 101 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG H 145 " --> pdb=" O THR H 56 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N THR H 56 " --> pdb=" O ARG H 145 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASP H 8 " --> pdb=" O VAL H 57 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'I' and resid 16 through 19 Processing sheet with id=AF3, first strand: chain 'I' and resid 70 through 71 Processing sheet with id=AF4, first strand: chain 'K' and resid 19 through 22 removed outlier: 6.552A pdb=" N LYS K 72 " --> pdb=" O TYR K 61 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N TYR K 61 " --> pdb=" O LYS K 72 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ARG K 74 " --> pdb=" O ALA K 59 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ALA K 59 " --> pdb=" O ARG K 74 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N GLN K 76 " --> pdb=" O LEU K 57 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'L' and resid 30 through 31 removed outlier: 3.605A pdb=" N ILE L 30 " --> pdb=" O LEU L 57 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'M' and resid 34 through 37 removed outlier: 6.560A pdb=" N VAL M 43 " --> pdb=" O LEU M 52 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'Q' and resid 140 through 141 removed outlier: 7.174A pdb=" N PHE Q 395 " --> pdb=" O LEU Q 118 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N LYS Q 120 " --> pdb=" O PHE Q 395 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N ALA Q 397 " --> pdb=" O LYS Q 120 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'Q' and resid 387 through 388 removed outlier: 4.047A pdb=" N VAL Q 374 " --> pdb=" O VAL R 71 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N VAL R 71 " --> pdb=" O VAL Q 374 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LEU Q 376 " --> pdb=" O TRP R 69 " (cutoff:3.500A) removed outlier: 8.422A pdb=" N ARG R 66 " --> pdb=" O VAL R 218 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N HIS R 220 " --> pdb=" O ARG R 66 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N VAL R 68 " --> pdb=" O HIS R 220 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N CYS R 222 " --> pdb=" O VAL R 68 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N LEU R 70 " --> pdb=" O CYS R 222 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'R' and resid 93 through 94 Processing sheet with id=AG1, first strand: chain 'W' and resid 69 through 71 Processing sheet with id=AG2, first strand: chain 'W' and resid 129 through 131 Processing sheet with id=AG3, first strand: chain 'O' and resid 92 through 93 removed outlier: 4.120A pdb=" N LYS O 120 " --> pdb=" O PHE O 116 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N LEU O 67 " --> pdb=" O GLY O 162 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N GLY O 162 " --> pdb=" O LEU O 67 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ASN O 69 " --> pdb=" O ILE O 160 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N ILE O 160 " --> pdb=" O ASN O 69 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N VAL O 71 " --> pdb=" O GLN O 158 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N THR O 75 " --> pdb=" O ASP O 154 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N ASP O 154 " --> pdb=" O THR O 75 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain '0' and resid 2 through 4 Processing sheet with id=AG5, first strand: chain '0' and resid 40 through 41 Processing sheet with id=AG6, first strand: chain '0' and resid 105 through 106 removed outlier: 6.872A pdb=" N LEU 0 106 " --> pdb=" O ILE 0 207 " (cutoff:3.500A) removed outlier: 9.380A pdb=" N SER 0 209 " --> pdb=" O LEU 0 106 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N TYR 0 208 " --> pdb=" O TYR 0 71 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N VAL 0 232 " --> pdb=" O ILE 0 457 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N THR 0 459 " --> pdb=" O VAL 0 232 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N PHE 0 234 " --> pdb=" O THR 0 459 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain '0' and resid 352 through 354 removed outlier: 3.557A pdb=" N GLU 0 421 " --> pdb=" O ILE 0 434 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain '0' and resid 493 through 494 removed outlier: 6.522A pdb=" N LEU 0 493 " --> pdb=" O MET 0 679 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N LEU 0 681 " --> pdb=" O LEU 0 493 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N MET 0 622 " --> pdb=" O VAL 0 680 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N MET 0 537 " --> pdb=" O LEU 0 598 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N SER 0 600 " --> pdb=" O MET 0 537 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N VAL 0 539 " --> pdb=" O SER 0 600 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N LEU 0 570 " --> pdb=" O LEU 0 599 " (cutoff:3.500A) removed outlier: 8.891A pdb=" N VAL 0 601 " --> pdb=" O LEU 0 570 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain '4' and resid 83 through 85 removed outlier: 3.648A pdb=" N GLU 4 31 " --> pdb=" O LEU 4 179 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N CYS 4 181 " --> pdb=" O GLU 4 31 " (cutoff:3.500A) removed outlier: 8.443A pdb=" N VAL 4 213 " --> pdb=" O LEU 4 176 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N VAL 4 178 " --> pdb=" O VAL 4 213 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N ILE 4 215 " --> pdb=" O VAL 4 178 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N THR 4 180 " --> pdb=" O ILE 4 215 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain '4' and resid 287 through 288 Processing sheet with id=AH2, first strand: chain '6' and resid 178 through 186 removed outlier: 6.404A pdb=" N GLN 6 180 " --> pdb=" O ARG 6 175 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ARG 6 175 " --> pdb=" O GLN 6 180 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N VAL 6 182 " --> pdb=" O ILE 6 173 " (cutoff:3.500A) removed outlier: 8.053A pdb=" N ILE 6 173 " --> pdb=" O VAL 6 182 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N GLN 6 184 " --> pdb=" O ILE 6 171 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N ILE 6 171 " --> pdb=" O GLN 6 184 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N SER 6 125 " --> pdb=" O GLU 6 231 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N LEU 6 233 " --> pdb=" O SER 6 125 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N ILE 6 127 " --> pdb=" O LEU 6 233 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N VAL 6 235 " --> pdb=" O ILE 6 127 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N THR 6 129 " --> pdb=" O VAL 6 235 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain '6' and resid 347 through 348 removed outlier: 3.699A pdb=" N TYR 6 347 " --> pdb=" O VAL 6 356 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain '2' and resid 87 through 90 removed outlier: 3.556A pdb=" N ASN 2 99 " --> pdb=" O ILE 2 88 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain '2' and resid 365 through 369 removed outlier: 6.608A pdb=" N LEU 2 366 " --> pdb=" O GLN 2 377 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N GLN 2 377 " --> pdb=" O LEU 2 366 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain '2' and resid 452 through 453 removed outlier: 3.680A pdb=" N ILE 2 452 " --> pdb=" O GLN 5 11 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N LEU 5 41 " --> pdb=" O GLU 5 34 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N GLU 5 34 " --> pdb=" O LEU 5 41 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain '2' and resid 458 through 459 removed outlier: 3.590A pdb=" N ARG 5 5 " --> pdb=" O LEU 2 458 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain '3' and resid 52 through 53 removed outlier: 3.539A pdb=" N ALA 3 52 " --> pdb=" O LEU 3 63 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain '7' and resid 382 through 385 removed outlier: 4.483A pdb=" N GLY 7 382 " --> pdb=" O LYS 7 510 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N THR 7 514 " --> pdb=" O ILE 7 384 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N ILE 7 485 " --> pdb=" O LEU 7 511 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N LEU 7 513 " --> pdb=" O ILE 7 485 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N LEU 7 487 " --> pdb=" O LEU 7 513 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ILE 7 408 " --> pdb=" O ILE 7 486 " (cutoff:3.500A) removed outlier: 8.447A pdb=" N ASP 7 488 " --> pdb=" O ILE 7 408 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain '7' and resid 605 through 608 removed outlier: 5.855A pdb=" N LEU 7 670 " --> pdb=" O TYR 7 706 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N LEU 7 708 " --> pdb=" O LEU 7 670 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N GLN 7 672 " --> pdb=" O LEU 7 708 " (cutoff:3.500A) removed outlier: 8.155A pdb=" N SER 7 710 " --> pdb=" O GLN 7 672 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N CYS 7 554 " --> pdb=" O LYS 7 734 " (cutoff:3.500A) 2570 hydrogen bonds defined for protein. 7191 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 127 hydrogen bonds 246 hydrogen bond angles 0 basepair planarities 58 basepair parallelities 107 stacking parallelities Total time for adding SS restraints: 33.75 Time building geometry restraints manager: 15.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.40: 26354 1.40 - 1.62: 38647 1.62 - 1.84: 544 1.84 - 2.06: 0 2.06 - 2.28: 12 Bond restraints: 65557 Sorted by residual: bond pdb=" C SER A 354 " pdb=" N GLY A 355 " ideal model delta sigma weight residual 1.332 1.228 0.105 1.91e-02 2.74e+03 3.00e+01 bond pdb=" C LYS A 569 " pdb=" N PRO A 570 " ideal model delta sigma weight residual 1.330 1.269 0.062 1.19e-02 7.06e+03 2.68e+01 bond pdb=" CA GLU A1404 " pdb=" CB GLU A1404 " ideal model delta sigma weight residual 1.531 1.374 0.157 3.12e-02 1.03e+03 2.53e+01 bond pdb=" C CYS I 32 " pdb=" N SER I 33 " ideal model delta sigma weight residual 1.332 1.266 0.066 1.40e-02 5.10e+03 2.23e+01 bond pdb=" C ASN 6 188 " pdb=" N PRO 6 189 " ideal model delta sigma weight residual 1.336 1.283 0.053 1.20e-02 6.94e+03 1.94e+01 ... (remaining 65552 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.74: 87782 3.74 - 7.49: 1151 7.49 - 11.23: 111 11.23 - 14.97: 2 14.97 - 18.72: 2 Bond angle restraints: 89048 Sorted by residual: angle pdb=" C ASN B1013 " pdb=" N PRO B1014 " pdb=" CA PRO B1014 " ideal model delta sigma weight residual 119.56 129.73 -10.17 1.02e+00 9.61e-01 9.94e+01 angle pdb=" C UNK 1 506 " pdb=" N ILE 1 507 " pdb=" CA ILE 1 507 " ideal model delta sigma weight residual 121.70 109.86 11.84 1.80e+00 3.09e-01 4.33e+01 angle pdb=" N ASN W 116 " pdb=" CA ASN W 116 " pdb=" C ASN W 116 " ideal model delta sigma weight residual 108.07 116.83 -8.76 1.38e+00 5.25e-01 4.03e+01 angle pdb=" N ILE 7 333 " pdb=" CA ILE 7 333 " pdb=" C ILE 7 333 " ideal model delta sigma weight residual 112.29 106.67 5.62 9.40e-01 1.13e+00 3.57e+01 angle pdb=" N GLN A 71 " pdb=" CA GLN A 71 " pdb=" C GLN A 71 " ideal model delta sigma weight residual 109.86 118.54 -8.68 1.55e+00 4.16e-01 3.13e+01 ... (remaining 89043 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 33082 17.99 - 35.98: 4003 35.98 - 53.98: 1694 53.98 - 71.97: 503 71.97 - 89.96: 113 Dihedral angle restraints: 39395 sinusoidal: 16354 harmonic: 23041 Sorted by residual: dihedral pdb=" CA GLN A 71 " pdb=" C GLN A 71 " pdb=" N GLU A 72 " pdb=" CA GLU A 72 " ideal model delta harmonic sigma weight residual -180.00 -125.54 -54.46 0 5.00e+00 4.00e-02 1.19e+02 dihedral pdb=" CA TYR M 30 " pdb=" C TYR M 30 " pdb=" N PRO M 31 " pdb=" CA PRO M 31 " ideal model delta harmonic sigma weight residual 180.00 127.38 52.62 0 5.00e+00 4.00e-02 1.11e+02 dihedral pdb=" CA ASP 4 255 " pdb=" C ASP 4 255 " pdb=" N PRO 4 256 " pdb=" CA PRO 4 256 " ideal model delta harmonic sigma weight residual 180.00 -131.72 -48.28 0 5.00e+00 4.00e-02 9.32e+01 ... (remaining 39392 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 7497 0.068 - 0.135: 2210 0.135 - 0.203: 286 0.203 - 0.270: 22 0.270 - 0.338: 6 Chirality restraints: 10021 Sorted by residual: chirality pdb=" CB VAL J 14 " pdb=" CA VAL J 14 " pdb=" CG1 VAL J 14 " pdb=" CG2 VAL J 14 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.34 2.00e-01 2.50e+01 2.85e+00 chirality pdb=" CB VAL B 211 " pdb=" CA VAL B 211 " pdb=" CG1 VAL B 211 " pdb=" CG2 VAL B 211 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.25e+00 chirality pdb=" CB VAL A 622 " pdb=" CA VAL A 622 " pdb=" CG1 VAL A 622 " pdb=" CG2 VAL A 622 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.19e+00 ... (remaining 10018 not shown) Planarity restraints: 11132 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 756 " -0.051 5.00e-02 4.00e+02 7.63e-02 9.32e+00 pdb=" N PRO B 757 " 0.132 5.00e-02 4.00e+02 pdb=" CA PRO B 757 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO B 757 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN 7 431 " -0.046 5.00e-02 4.00e+02 6.97e-02 7.77e+00 pdb=" N PRO 7 432 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO 7 432 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO 7 432 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP 4 255 " 0.046 5.00e-02 4.00e+02 6.96e-02 7.75e+00 pdb=" N PRO 4 256 " -0.120 5.00e-02 4.00e+02 pdb=" CA PRO 4 256 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO 4 256 " 0.039 5.00e-02 4.00e+02 ... (remaining 11129 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 1379 2.51 - 3.11: 58880 3.11 - 3.70: 109863 3.70 - 4.30: 154165 4.30 - 4.90: 235260 Nonbonded interactions: 559547 Sorted by model distance: nonbonded pdb=" O GLN 2 466 " pdb=" N LEU 2 470 " model vdw 1.912 3.120 nonbonded pdb=" OH TYR 2 350 " pdb=" O TRP 7 133 " model vdw 1.930 3.040 nonbonded pdb=" OD1 ASN 5 43 " pdb=" OG SER 5 45 " model vdw 1.951 3.040 nonbonded pdb=" N2 DG T 119 " pdb=" O2 DC N 47 " model vdw 1.957 2.496 nonbonded pdb=" CB CYS 0 156 " pdb=" S1 SF4 0 801 " model vdw 1.968 3.040 ... (remaining 559542 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 individual isotropic 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: 5.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.080 Extract box with map and model: 1.850 Check model and map are aligned: 0.370 Set scattering table: 0.430 Process input model: 151.110 Find NCS groups from input model: 0.720 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:11.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 171.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6152 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 : 0.018 0.157 65557 Z= 1.205 Angle : 1.120 18.715 89048 Z= 0.603 Chirality : 0.061 0.338 10021 Planarity : 0.006 0.076 11121 Dihedral : 19.838 89.962 24592 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 37.28 Ramachandran Plot: Outliers : 0.27 % Allowed : 15.57 % Favored : 84.17 % Rotamer: Outliers : 20.13 % Allowed : 14.64 % Favored : 65.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.03 % Twisted Proline : 1.47 % Twisted General : 0.29 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.87 (0.08), residues: 7844 helix: -2.54 (0.08), residues: 2659 sheet: -1.98 (0.16), residues: 896 loop : -2.77 (0.09), residues: 4289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.004 TRP C 192 HIS 0.017 0.002 HIS B 363 PHE 0.038 0.003 PHE Q 347 TYR 0.039 0.003 TYR E 187 ARG 0.020 0.001 ARG J 6 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15688 Ramachandran restraints generated. 7844 Oldfield, 0 Emsley, 7844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15688 Ramachandran restraints generated. 7844 Oldfield, 0 Emsley, 7844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1549 residues out of total 7137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1279 poor density : 270 time to evaluate : 5.589 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: A 446 ARG cc_start: 0.8341 (OUTLIER) cc_final: 0.7983 (ttt-90) REVERT: A 510 GLN cc_start: 0.8025 (OUTLIER) cc_final: 0.7709 (mm-40) REVERT: A 839 ARG cc_start: 0.7765 (OUTLIER) cc_final: 0.7437 (ttm-80) REVERT: A 845 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8372 (mp) REVERT: A 1187 GLN cc_start: 0.7401 (OUTLIER) cc_final: 0.6726 (pt0) REVERT: A 1327 ILE cc_start: 0.8172 (OUTLIER) cc_final: 0.7823 (tt) REVERT: B 587 HIS cc_start: 0.7722 (OUTLIER) cc_final: 0.6901 (m90) REVERT: B 1108 ARG cc_start: 0.8657 (OUTLIER) cc_final: 0.7882 (mtm110) REVERT: C 106 GLU cc_start: 0.6266 (OUTLIER) cc_final: 0.6016 (mt-10) REVERT: J 17 LYS cc_start: 0.8149 (OUTLIER) cc_final: 0.7859 (mptt) REVERT: J 59 LYS cc_start: 0.8061 (OUTLIER) cc_final: 0.7814 (mttt) REVERT: M 96 ILE cc_start: 0.2955 (OUTLIER) cc_final: 0.2507 (pp) REVERT: M 104 MET cc_start: 0.2460 (OUTLIER) cc_final: -0.0647 (mpt) REVERT: M 236 LEU cc_start: 0.5377 (OUTLIER) cc_final: 0.4859 (mp) REVERT: Q 347 PHE cc_start: 0.6074 (OUTLIER) cc_final: 0.5679 (p90) REVERT: 0 37 ASN cc_start: 0.5120 (OUTLIER) cc_final: 0.4540 (m-40) REVERT: 0 346 MET cc_start: 0.5168 (tpp) cc_final: 0.4867 (tpp) REVERT: 0 347 LYS cc_start: 0.6879 (OUTLIER) cc_final: 0.6603 (mmtp) REVERT: 0 413 GLU cc_start: 0.7537 (OUTLIER) cc_final: 0.7315 (pm20) REVERT: 0 605 LYS cc_start: 0.8808 (OUTLIER) cc_final: 0.8601 (pmtt) REVERT: 0 632 SER cc_start: 0.6362 (OUTLIER) cc_final: 0.6122 (t) REVERT: 1 209 PHE cc_start: 0.5682 (OUTLIER) cc_final: 0.5462 (t80) REVERT: 1 287 PHE cc_start: 0.4279 (OUTLIER) cc_final: 0.3706 (t80) REVERT: 6 118 TYR cc_start: 0.5864 (OUTLIER) cc_final: 0.5038 (m-80) REVERT: 6 139 LYS cc_start: 0.8051 (OUTLIER) cc_final: 0.7694 (mmmt) REVERT: 6 193 ILE cc_start: 0.7852 (OUTLIER) cc_final: 0.7597 (mm) REVERT: 6 239 LEU cc_start: 0.9110 (OUTLIER) cc_final: 0.8899 (tm) REVERT: 2 13 TYR cc_start: 0.8662 (t80) cc_final: 0.8402 (OUTLIER) REVERT: 2 14 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8589 (mt) REVERT: 2 17 ILE cc_start: 0.9161 (OUTLIER) cc_final: 0.8846 (tp) REVERT: 2 55 ASN cc_start: 0.8171 (OUTLIER) cc_final: 0.7879 (p0) REVERT: 2 373 MET cc_start: 0.6633 (tpt) cc_final: 0.5662 (tpt) REVERT: 3 25 ASP cc_start: 0.6393 (OUTLIER) cc_final: 0.6029 (p0) REVERT: 3 73 PHE cc_start: 0.6983 (OUTLIER) cc_final: 0.6710 (m-80) REVERT: 7 311 ASP cc_start: 0.8802 (p0) cc_final: 0.8431 (m-30) REVERT: 7 365 TYR cc_start: 0.0254 (OUTLIER) cc_final: -0.1807 (m-80) REVERT: 7 447 GLN cc_start: 0.2424 (OUTLIER) cc_final: 0.1211 (mp10) outliers start: 1279 outliers final: 580 residues processed: 1501 average time/residue: 1.2291 time to fit residues: 2472.8345 Evaluate side-chains 863 residues out of total 7137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 612 poor density : 251 time to evaluate : 5.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 55 ASP Chi-restraints excluded: chain A residue 57 ARG Chi-restraints excluded: chain A residue 62 ASP Chi-restraints excluded: chain A residue 63 ARG Chi-restraints excluded: chain A residue 75 ASN Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 92 HIS Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 107 CYS Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 177 ASP Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 209 ASN Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 249 SER Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 305 ASP Chi-restraints excluded: chain A residue 316 GLN Chi-restraints excluded: chain A residue 344 ARG Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 389 THR Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 409 SER Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 418 SER Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 465 TYR Chi-restraints excluded: chain A residue 466 SER Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 502 SER Chi-restraints excluded: chain A residue 510 GLN Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 624 SER Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 666 ILE Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 743 VAL Chi-restraints excluded: chain A residue 758 ILE Chi-restraints excluded: chain A residue 764 CYS Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 839 ARG Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 862 ASN Chi-restraints excluded: chain A residue 867 ILE Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 890 ASP Chi-restraints excluded: chain A residue 907 THR Chi-restraints excluded: chain A residue 909 ASP Chi-restraints excluded: chain A residue 930 ASP Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 979 SER Chi-restraints excluded: chain A residue 980 ASP Chi-restraints excluded: chain A residue 982 THR Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 1022 LEU Chi-restraints excluded: chain A residue 1028 THR Chi-restraints excluded: chain A residue 1038 THR Chi-restraints excluded: chain A residue 1095 THR Chi-restraints excluded: chain A residue 1098 VAL Chi-restraints excluded: chain A residue 1102 LYS Chi-restraints excluded: chain A residue 1120 LEU Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain A residue 1130 GLN Chi-restraints excluded: chain A residue 1146 VAL Chi-restraints excluded: chain A residue 1163 ILE Chi-restraints excluded: chain A residue 1187 GLN Chi-restraints excluded: chain A residue 1197 LEU Chi-restraints excluded: chain A residue 1204 ASP Chi-restraints excluded: chain A residue 1205 LYS Chi-restraints excluded: chain A residue 1208 THR Chi-restraints excluded: chain A residue 1209 MET Chi-restraints excluded: chain A residue 1211 GLN Chi-restraints excluded: chain A residue 1230 GLU Chi-restraints excluded: chain A residue 1239 ARG Chi-restraints excluded: chain A residue 1243 VAL Chi-restraints excluded: chain A residue 1255 GLU Chi-restraints excluded: chain A residue 1266 THR Chi-restraints excluded: chain A residue 1269 GLU Chi-restraints excluded: chain A residue 1272 THR Chi-restraints excluded: chain A residue 1308 THR Chi-restraints excluded: chain A residue 1318 THR Chi-restraints excluded: chain A residue 1325 THR Chi-restraints excluded: chain A residue 1327 ILE Chi-restraints excluded: chain A residue 1335 ILE Chi-restraints excluded: chain A residue 1350 LYS Chi-restraints excluded: chain A residue 1361 SER Chi-restraints excluded: chain A residue 1372 VAL Chi-restraints excluded: chain A residue 1417 GLU Chi-restraints excluded: chain A residue 1424 VAL Chi-restraints excluded: chain A residue 1436 ILE Chi-restraints excluded: chain A residue 1445 ILE Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 137 TYR Chi-restraints excluded: chain B residue 178 ASN Chi-restraints excluded: chain B residue 199 MET Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 326 ASP Chi-restraints excluded: chain B residue 345 LYS Chi-restraints excluded: chain B residue 349 ILE Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 398 ARG Chi-restraints excluded: chain B residue 452 THR Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 493 SER Chi-restraints excluded: chain B residue 502 ILE Chi-restraints excluded: chain B residue 510 LYS Chi-restraints excluded: chain B residue 540 SER Chi-restraints excluded: chain B residue 544 CYS Chi-restraints excluded: chain B residue 556 THR Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 568 ASP Chi-restraints excluded: chain B residue 587 HIS Chi-restraints excluded: chain B residue 591 ARG Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 608 ASP Chi-restraints excluded: chain B residue 619 ILE Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain B residue 649 LYS Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 705 MET Chi-restraints excluded: chain B residue 737 THR Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 755 ILE Chi-restraints excluded: chain B residue 771 SER Chi-restraints excluded: chain B residue 827 ILE Chi-restraints excluded: chain B residue 845 SER Chi-restraints excluded: chain B residue 858 SER Chi-restraints excluded: chain B residue 873 THR Chi-restraints excluded: chain B residue 881 ASN Chi-restraints excluded: chain B residue 887 HIS Chi-restraints excluded: chain B residue 889 THR Chi-restraints excluded: chain B residue 895 ASP Chi-restraints excluded: chain B residue 899 ILE Chi-restraints excluded: chain B residue 906 SER Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 938 SER Chi-restraints excluded: chain B residue 943 SER Chi-restraints excluded: chain B residue 944 THR Chi-restraints excluded: chain B residue 959 ASP Chi-restraints excluded: chain B residue 963 PHE Chi-restraints excluded: chain B residue 976 ILE Chi-restraints excluded: chain B residue 986 GLN Chi-restraints excluded: chain B residue 987 LYS Chi-restraints excluded: chain B residue 1049 ASP Chi-restraints excluded: chain B residue 1056 SER Chi-restraints excluded: chain B residue 1082 MET Chi-restraints excluded: chain B residue 1093 GLN Chi-restraints excluded: chain B residue 1108 ARG Chi-restraints excluded: chain B residue 1113 VAL Chi-restraints excluded: chain B residue 1115 THR Chi-restraints excluded: chain B residue 1120 GLU Chi-restraints excluded: chain B residue 1145 SER Chi-restraints excluded: chain B residue 1152 MET Chi-restraints excluded: chain B residue 1163 CYS Chi-restraints excluded: chain B residue 1170 THR Chi-restraints excluded: chain B residue 1201 LYS Chi-restraints excluded: chain B residue 1215 ARG Chi-restraints excluded: chain C residue 4 GLU Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 48 SER Chi-restraints excluded: chain C residue 50 GLU Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 86 CYS Chi-restraints excluded: chain C residue 106 GLU Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 136 ASP Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 215 GLU Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 237 SER Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 264 GLN Chi-restraints excluded: chain D residue 75 LYS Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 131 GLU Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 147 TYR Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain D residue 202 ILE Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 41 ASP Chi-restraints excluded: chain E residue 58 MET Chi-restraints excluded: chain E residue 67 GLU Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 83 CYS Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 113 GLN Chi-restraints excluded: chain E residue 126 SER Chi-restraints excluded: chain E residue 156 LEU Chi-restraints excluded: chain E residue 157 SER Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 204 THR Chi-restraints excluded: chain F residue 72 LYS Chi-restraints excluded: chain F residue 77 ASP Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 85 MET Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 148 VAL Chi-restraints excluded: chain F residue 150 GLU Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 53 ASN Chi-restraints excluded: chain G residue 54 ILE Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 69 GLU Chi-restraints excluded: chain G residue 74 TYR Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 122 ASN Chi-restraints excluded: chain G residue 148 GLU Chi-restraints excluded: chain G residue 151 ILE Chi-restraints excluded: chain G residue 160 ILE Chi-restraints excluded: chain G residue 163 ILE Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 33 GLN Chi-restraints excluded: chain H residue 53 ASP Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 92 ASP Chi-restraints excluded: chain H residue 94 ASP Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 108 SER Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain H residue 123 MET Chi-restraints excluded: chain H residue 131 ASN Chi-restraints excluded: chain H residue 134 ASN Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain H residue 146 ARG Chi-restraints excluded: chain I residue 3 THR Chi-restraints excluded: chain I residue 8 ARG Chi-restraints excluded: chain I residue 19 ASP Chi-restraints excluded: chain I residue 37 GLU Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain I residue 62 ILE Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain I residue 106 CYS Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 6 ARG Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 17 LYS Chi-restraints excluded: chain J residue 28 ASP Chi-restraints excluded: chain J residue 59 LYS Chi-restraints excluded: chain K residue 10 PHE Chi-restraints excluded: chain K residue 26 LYS Chi-restraints excluded: chain K residue 70 ARG Chi-restraints excluded: chain K residue 103 THR Chi-restraints excluded: chain L residue 33 GLU Chi-restraints excluded: chain L residue 34 CYS Chi-restraints excluded: chain L residue 35 SER Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 40 LEU Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 50 ASP Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain M residue 29 VAL Chi-restraints excluded: chain M residue 44 VAL Chi-restraints excluded: chain M residue 51 VAL Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 62 GLU Chi-restraints excluded: chain M residue 94 THR Chi-restraints excluded: chain M residue 96 ILE Chi-restraints excluded: chain M residue 100 GLU Chi-restraints excluded: chain M residue 104 MET Chi-restraints excluded: chain M residue 118 VAL Chi-restraints excluded: chain M residue 142 LEU Chi-restraints excluded: chain M residue 171 ILE Chi-restraints excluded: chain M residue 176 ILE Chi-restraints excluded: chain M residue 195 LEU Chi-restraints excluded: chain M residue 200 THR Chi-restraints excluded: chain M residue 209 ILE Chi-restraints excluded: chain M residue 214 LEU Chi-restraints excluded: chain M residue 234 GLN Chi-restraints excluded: chain M residue 236 LEU Chi-restraints excluded: chain M residue 237 THR Chi-restraints excluded: chain M residue 252 VAL Chi-restraints excluded: chain M residue 276 THR Chi-restraints excluded: chain M residue 284 LEU Chi-restraints excluded: chain M residue 304 VAL Chi-restraints excluded: chain M residue 308 THR Chi-restraints excluded: chain M residue 315 ILE Chi-restraints excluded: chain M residue 323 LEU Chi-restraints excluded: chain Q residue 27 MET Chi-restraints excluded: chain Q residue 104 ARG Chi-restraints excluded: chain Q residue 116 THR Chi-restraints excluded: chain Q residue 118 LEU Chi-restraints excluded: chain Q residue 119 LEU Chi-restraints excluded: chain Q residue 332 LEU Chi-restraints excluded: chain Q residue 336 ASP Chi-restraints excluded: chain Q residue 347 PHE Chi-restraints excluded: chain Q residue 358 TYR Chi-restraints excluded: chain Q residue 385 THR Chi-restraints excluded: chain Q residue 392 VAL Chi-restraints excluded: chain Q residue 396 THR Chi-restraints excluded: chain R residue 62 GLU Chi-restraints excluded: chain R residue 96 ARG Chi-restraints excluded: chain R residue 108 LEU Chi-restraints excluded: chain R residue 207 THR Chi-restraints excluded: chain R residue 212 THR Chi-restraints excluded: chain R residue 224 VAL Chi-restraints excluded: chain R residue 253 THR Chi-restraints excluded: chain R residue 254 THR Chi-restraints excluded: chain R residue 259 VAL Chi-restraints excluded: chain R residue 262 THR Chi-restraints excluded: chain R residue 269 SER Chi-restraints excluded: chain R residue 275 SER Chi-restraints excluded: chain W residue 5 ILE Chi-restraints excluded: chain W residue 6 ASP Chi-restraints excluded: chain W residue 16 VAL Chi-restraints excluded: chain W residue 91 TYR Chi-restraints excluded: chain W residue 111 ASP Chi-restraints excluded: chain W residue 120 ASN Chi-restraints excluded: chain W residue 137 VAL Chi-restraints excluded: chain W residue 141 ASN Chi-restraints excluded: chain W residue 149 CYS Chi-restraints excluded: chain W residue 169 GLN Chi-restraints excluded: chain X residue 192 LEU Chi-restraints excluded: chain X residue 209 ASP Chi-restraints excluded: chain X residue 256 ASP Chi-restraints excluded: chain O residue 64 VAL Chi-restraints excluded: chain O residue 122 VAL Chi-restraints excluded: chain O residue 178 SER Chi-restraints excluded: chain 0 residue 6 ASP Chi-restraints excluded: chain 0 residue 17 ILE Chi-restraints excluded: chain 0 residue 28 ILE Chi-restraints excluded: chain 0 residue 34 VAL Chi-restraints excluded: chain 0 residue 37 ASN Chi-restraints excluded: chain 0 residue 50 VAL Chi-restraints excluded: chain 0 residue 73 SER Chi-restraints excluded: chain 0 residue 78 GLU Chi-restraints excluded: chain 0 residue 80 GLU Chi-restraints excluded: chain 0 residue 94 THR Chi-restraints excluded: chain 0 residue 120 VAL Chi-restraints excluded: chain 0 residue 130 ASP Chi-restraints excluded: chain 0 residue 131 GLU Chi-restraints excluded: chain 0 residue 137 THR Chi-restraints excluded: chain 0 residue 150 GLU Chi-restraints excluded: chain 0 residue 155 LEU Chi-restraints excluded: chain 0 residue 201 SER Chi-restraints excluded: chain 0 residue 204 ASN Chi-restraints excluded: chain 0 residue 209 SER Chi-restraints excluded: chain 0 residue 221 ARG Chi-restraints excluded: chain 0 residue 240 ILE Chi-restraints excluded: chain 0 residue 245 ILE Chi-restraints excluded: chain 0 residue 255 ASP Chi-restraints excluded: chain 0 residue 257 LEU Chi-restraints excluded: chain 0 residue 284 ASP Chi-restraints excluded: chain 0 residue 321 ILE Chi-restraints excluded: chain 0 residue 339 ILE Chi-restraints excluded: chain 0 residue 347 LYS Chi-restraints excluded: chain 0 residue 351 VAL Chi-restraints excluded: chain 0 residue 354 GLU Chi-restraints excluded: chain 0 residue 360 LEU Chi-restraints excluded: chain 0 residue 407 THR Chi-restraints excluded: chain 0 residue 413 GLU Chi-restraints excluded: chain 0 residue 416 PHE Chi-restraints excluded: chain 0 residue 418 LEU Chi-restraints excluded: chain 0 residue 423 TYR Chi-restraints excluded: chain 0 residue 438 THR Chi-restraints excluded: chain 0 residue 453 PHE Chi-restraints excluded: chain 0 residue 487 LEU Chi-restraints excluded: chain 0 residue 498 THR Chi-restraints excluded: chain 0 residue 533 THR Chi-restraints excluded: chain 0 residue 559 ILE Chi-restraints excluded: chain 0 residue 563 VAL Chi-restraints excluded: chain 0 residue 573 THR Chi-restraints excluded: chain 0 residue 591 SER Chi-restraints excluded: chain 0 residue 594 ARG Chi-restraints excluded: chain 0 residue 605 LYS Chi-restraints excluded: chain 0 residue 614 HIS Chi-restraints excluded: chain 0 residue 632 SER Chi-restraints excluded: chain 0 residue 649 ARG Chi-restraints excluded: chain 0 residue 651 ASN Chi-restraints excluded: chain 0 residue 655 SER Chi-restraints excluded: chain 0 residue 657 ASP Chi-restraints excluded: chain 0 residue 673 LYS Chi-restraints excluded: chain 0 residue 674 ASP Chi-restraints excluded: chain 0 residue 678 VAL Chi-restraints excluded: chain 0 residue 683 ASP Chi-restraints excluded: chain 0 residue 689 LYS Chi-restraints excluded: chain 0 residue 706 LEU Chi-restraints excluded: chain 0 residue 716 ASN Chi-restraints excluded: chain 0 residue 717 THR Chi-restraints excluded: chain 0 residue 739 TRP Chi-restraints excluded: chain 0 residue 741 TYR Chi-restraints excluded: chain 0 residue 743 ASP Chi-restraints excluded: chain 1 residue 185 LEU Chi-restraints excluded: chain 1 residue 209 PHE Chi-restraints excluded: chain 1 residue 210 TRP Chi-restraints excluded: chain 1 residue 211 SER Chi-restraints excluded: chain 1 residue 213 ARG Chi-restraints excluded: chain 1 residue 214 ILE Chi-restraints excluded: chain 1 residue 233 VAL Chi-restraints excluded: chain 1 residue 271 THR Chi-restraints excluded: chain 1 residue 287 PHE Chi-restraints excluded: chain 1 residue 374 ILE Chi-restraints excluded: chain 1 residue 381 LEU Chi-restraints excluded: chain 1 residue 561 LEU Chi-restraints excluded: chain 1 residue 621 ASN Chi-restraints excluded: chain 4 residue 22 SER Chi-restraints excluded: chain 4 residue 27 THR Chi-restraints excluded: chain 4 residue 43 GLU Chi-restraints excluded: chain 4 residue 122 ASP Chi-restraints excluded: chain 4 residue 133 PHE Chi-restraints excluded: chain 4 residue 137 LYS Chi-restraints excluded: chain 4 residue 179 LEU Chi-restraints excluded: chain 4 residue 180 THR Chi-restraints excluded: chain 4 residue 194 ILE Chi-restraints excluded: chain 4 residue 200 ILE Chi-restraints excluded: chain 4 residue 202 SER Chi-restraints excluded: chain 4 residue 212 VAL Chi-restraints excluded: chain 4 residue 222 THR Chi-restraints excluded: chain 4 residue 227 THR Chi-restraints excluded: chain 4 residue 228 THR Chi-restraints excluded: chain 4 residue 236 LEU Chi-restraints excluded: chain 4 residue 253 PHE Chi-restraints excluded: chain 4 residue 260 PRO Chi-restraints excluded: chain 4 residue 269 SER Chi-restraints excluded: chain 4 residue 270 VAL Chi-restraints excluded: chain 4 residue 274 THR Chi-restraints excluded: chain 4 residue 276 CYS Chi-restraints excluded: chain 4 residue 288 ILE Chi-restraints excluded: chain 6 residue 114 ASN Chi-restraints excluded: chain 6 residue 116 THR Chi-restraints excluded: chain 6 residue 118 TYR Chi-restraints excluded: chain 6 residue 119 GLN Chi-restraints excluded: chain 6 residue 139 LYS Chi-restraints excluded: chain 6 residue 146 HIS Chi-restraints excluded: chain 6 residue 155 ASP Chi-restraints excluded: chain 6 residue 158 HIS Chi-restraints excluded: chain 6 residue 182 VAL Chi-restraints excluded: chain 6 residue 193 ILE Chi-restraints excluded: chain 6 residue 222 LEU Chi-restraints excluded: chain 6 residue 238 SER Chi-restraints excluded: chain 6 residue 239 LEU Chi-restraints excluded: chain 6 residue 243 ASP Chi-restraints excluded: chain 6 residue 261 VAL Chi-restraints excluded: chain 6 residue 280 THR Chi-restraints excluded: chain 6 residue 282 TYR Chi-restraints excluded: chain 6 residue 289 LYS Chi-restraints excluded: chain 6 residue 291 LEU Chi-restraints excluded: chain 6 residue 293 ASP Chi-restraints excluded: chain 6 residue 306 THR Chi-restraints excluded: chain 6 residue 310 VAL Chi-restraints excluded: chain 6 residue 317 PHE Chi-restraints excluded: chain 6 residue 318 THR Chi-restraints excluded: chain 6 residue 319 LEU Chi-restraints excluded: chain 6 residue 326 THR Chi-restraints excluded: chain 6 residue 406 CYS Chi-restraints excluded: chain 6 residue 448 LEU Chi-restraints excluded: chain 2 residue 11 THR Chi-restraints excluded: chain 2 residue 14 LEU Chi-restraints excluded: chain 2 residue 17 ILE Chi-restraints excluded: chain 2 residue 21 VAL Chi-restraints excluded: chain 2 residue 28 SER Chi-restraints excluded: chain 2 residue 53 ASN Chi-restraints excluded: chain 2 residue 55 ASN Chi-restraints excluded: chain 2 residue 60 LEU Chi-restraints excluded: chain 2 residue 61 ASP Chi-restraints excluded: chain 2 residue 80 SER Chi-restraints excluded: chain 2 residue 95 THR Chi-restraints excluded: chain 2 residue 208 LEU Chi-restraints excluded: chain 2 residue 284 THR Chi-restraints excluded: chain 2 residue 348 TYR Chi-restraints excluded: chain 2 residue 350 TYR Chi-restraints excluded: chain 2 residue 353 SER Chi-restraints excluded: chain 2 residue 356 GLN Chi-restraints excluded: chain 2 residue 370 PHE Chi-restraints excluded: chain 2 residue 372 ASN Chi-restraints excluded: chain 2 residue 379 THR Chi-restraints excluded: chain 2 residue 389 ASN Chi-restraints excluded: chain 2 residue 391 ILE Chi-restraints excluded: chain 2 residue 395 GLN Chi-restraints excluded: chain 2 residue 408 MET Chi-restraints excluded: chain 2 residue 411 LEU Chi-restraints excluded: chain 2 residue 450 ARG Chi-restraints excluded: chain 2 residue 457 SER Chi-restraints excluded: chain 2 residue 462 PHE Chi-restraints excluded: chain 2 residue 470 LEU Chi-restraints excluded: chain 2 residue 486 ASP Chi-restraints excluded: chain 2 residue 489 LYS Chi-restraints excluded: chain 2 residue 495 LYS Chi-restraints excluded: chain 2 residue 508 LYS Chi-restraints excluded: chain 5 residue 9 LEU Chi-restraints excluded: chain 5 residue 13 ASP Chi-restraints excluded: chain 5 residue 26 LYS Chi-restraints excluded: chain 5 residue 33 GLU Chi-restraints excluded: chain 5 residue 42 VAL Chi-restraints excluded: chain 5 residue 46 LYS Chi-restraints excluded: chain 5 residue 47 VAL Chi-restraints excluded: chain 3 residue 25 ASP Chi-restraints excluded: chain 3 residue 44 ASP Chi-restraints excluded: chain 3 residue 49 LEU Chi-restraints excluded: chain 3 residue 73 PHE Chi-restraints excluded: chain 7 residue 302 GLU Chi-restraints excluded: chain 7 residue 309 ASP Chi-restraints excluded: chain 7 residue 315 SER Chi-restraints excluded: chain 7 residue 316 PHE Chi-restraints excluded: chain 7 residue 320 ASN Chi-restraints excluded: chain 7 residue 331 GLN Chi-restraints excluded: chain 7 residue 360 THR Chi-restraints excluded: chain 7 residue 365 TYR Chi-restraints excluded: chain 7 residue 378 ARG Chi-restraints excluded: chain 7 residue 398 THR Chi-restraints excluded: chain 7 residue 402 THR Chi-restraints excluded: chain 7 residue 412 THR Chi-restraints excluded: chain 7 residue 419 GLN Chi-restraints excluded: chain 7 residue 428 CYS Chi-restraints excluded: chain 7 residue 431 GLN Chi-restraints excluded: chain 7 residue 439 THR Chi-restraints excluded: chain 7 residue 442 ASN Chi-restraints excluded: chain 7 residue 447 GLN Chi-restraints excluded: chain 7 residue 454 VAL Chi-restraints excluded: chain 7 residue 456 THR Chi-restraints excluded: chain 7 residue 473 VAL Chi-restraints excluded: chain 7 residue 475 ASP Chi-restraints excluded: chain 7 residue 490 VAL Chi-restraints excluded: chain 7 residue 498 PHE Chi-restraints excluded: chain 7 residue 499 ARG Chi-restraints excluded: chain 7 residue 500 ARG Chi-restraints excluded: chain 7 residue 501 VAL Chi-restraints excluded: chain 7 residue 505 ILE Chi-restraints excluded: chain 7 residue 518 VAL Chi-restraints excluded: chain 7 residue 527 LEU Chi-restraints excluded: chain 7 residue 541 MET Chi-restraints excluded: chain 7 residue 545 GLN Chi-restraints excluded: chain 7 residue 549 ILE Chi-restraints excluded: chain 7 residue 562 THR Chi-restraints excluded: chain 7 residue 565 PHE 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 656 LYS Chi-restraints excluded: chain 7 residue 676 HIS Chi-restraints excluded: chain 7 residue 695 ARG Chi-restraints excluded: chain 7 residue 697 ASN Chi-restraints excluded: chain 7 residue 712 ASP Chi-restraints excluded: chain 7 residue 717 TYR Chi-restraints excluded: chain 7 residue 719 SER Chi-restraints excluded: chain 7 residue 735 VAL Chi-restraints excluded: chain 7 residue 761 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 786 random chunks: chunk 663 optimal weight: 1.9990 chunk 595 optimal weight: 6.9990 chunk 330 optimal weight: 2.9990 chunk 203 optimal weight: 2.9990 chunk 401 optimal weight: 7.9990 chunk 318 optimal weight: 1.9990 chunk 616 optimal weight: 9.9990 chunk 238 optimal weight: 0.8980 chunk 374 optimal weight: 0.9980 chunk 458 optimal weight: 20.0000 chunk 713 optimal weight: 10.0000 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 363 GLN A 451 HIS A 742 ASN A 757 ASN A 865 GLN A1040 GLN A1048 ASN ** A1171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 667 GLN B 794 ASN ** D 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 114 ASN F 104 ASN G 117 GLN I 23 ASN I 46 HIS I 83 ASN I 89 GLN I 90 GLN L 66 GLN M 212 ASN M 234 GLN ** Q 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 158 GLN ** 0 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0 164 ASN ** 0 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 164 ASN 6 227 HIS 6 249 GLN ** 6 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 76 ASN 2 403 HIS ** 2 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 9 ASN ** 3 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 331 GLN 7 345 ASN 7 431 GLN ** 7 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 508 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 528 ASN 7 545 GLN ** 7 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 714 GLN 7 729 GLN 7 761 GLN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5894 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 65557 Z= 0.289 Angle : 0.840 15.801 89048 Z= 0.440 Chirality : 0.048 0.374 10021 Planarity : 0.006 0.073 11121 Dihedral : 17.530 95.682 11333 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 17.10 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.76 % Favored : 91.10 % Rotamer: Outliers : 10.22 % Allowed : 20.68 % Favored : 69.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.03 % Twisted Proline : 1.18 % Twisted General : 0.28 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.62 (0.09), residues: 7844 helix: -1.00 (0.09), residues: 3044 sheet: -1.82 (0.16), residues: 918 loop : -2.33 (0.10), residues: 3882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 954 HIS 0.013 0.002 HIS W 103 PHE 0.035 0.002 PHE 1 564 TYR 0.047 0.002 TYR 1 630 ARG 0.009 0.001 ARG E 162 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15688 Ramachandran restraints generated. 7844 Oldfield, 0 Emsley, 7844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15688 Ramachandran restraints generated. 7844 Oldfield, 0 Emsley, 7844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 915 residues out of total 7137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 649 poor density : 266 time to evaluate : 5.683 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: A 77 CYS cc_start: 0.6928 (OUTLIER) cc_final: 0.6604 (t) REVERT: A 605 MET cc_start: 0.7413 (tpp) cc_final: 0.7150 (tpt) REVERT: A 1022 LEU cc_start: 0.7730 (OUTLIER) cc_final: 0.7508 (tp) REVERT: A 1187 GLN cc_start: 0.6953 (OUTLIER) cc_final: 0.6436 (pt0) REVERT: D 187 THR cc_start: 0.3254 (OUTLIER) cc_final: 0.2995 (t) REVERT: G 69 GLU cc_start: 0.6400 (OUTLIER) cc_final: 0.6077 (tt0) REVERT: M 96 ILE cc_start: 0.3029 (OUTLIER) cc_final: 0.2690 (pp) REVERT: M 236 LEU cc_start: 0.5290 (OUTLIER) cc_final: 0.4823 (mp) REVERT: 0 605 LYS cc_start: 0.8388 (OUTLIER) cc_final: 0.8119 (pmtt) REVERT: 0 614 HIS cc_start: 0.7406 (OUTLIER) cc_final: 0.7200 (m-70) REVERT: 0 674 ASP cc_start: 0.8532 (OUTLIER) cc_final: 0.8124 (p0) REVERT: 0 683 ASP cc_start: 0.5802 (OUTLIER) cc_final: 0.5525 (t0) REVERT: 6 118 TYR cc_start: 0.4989 (OUTLIER) cc_final: 0.4259 (m-80) REVERT: 2 81 MET cc_start: 0.9230 (ptp) cc_final: 0.9019 (mpp) REVERT: 7 309 ASP cc_start: 0.4513 (OUTLIER) cc_final: 0.4248 (m-30) REVERT: 7 365 TYR cc_start: 0.0802 (OUTLIER) cc_final: -0.0681 (m-80) REVERT: 7 442 ASN cc_start: 0.6838 (OUTLIER) cc_final: 0.6516 (m110) REVERT: 7 454 VAL cc_start: 0.7212 (OUTLIER) cc_final: 0.6826 (m) REVERT: 7 456 THR cc_start: 0.4941 (OUTLIER) cc_final: 0.4684 (t) outliers start: 649 outliers final: 292 residues processed: 887 average time/residue: 1.1597 time to fit residues: 1407.2919 Evaluate side-chains 555 residues out of total 7137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 309 poor density : 246 time to evaluate : 5.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 55 ASP Chi-restraints excluded: chain A residue 77 CYS Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 177 ASP Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 209 ASN Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 316 GLN Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 409 SER Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 465 TYR Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 625 SER Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 743 VAL Chi-restraints excluded: chain A residue 758 ILE Chi-restraints excluded: chain A residue 764 CYS Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 839 ARG Chi-restraints excluded: chain A residue 865 GLN Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 979 SER Chi-restraints excluded: chain A residue 982 THR Chi-restraints excluded: chain A residue 1022 LEU Chi-restraints excluded: chain A residue 1038 THR Chi-restraints excluded: chain A residue 1095 THR Chi-restraints excluded: chain A residue 1120 LEU Chi-restraints excluded: chain A residue 1130 GLN Chi-restraints excluded: chain A residue 1146 VAL Chi-restraints excluded: chain A residue 1169 ILE Chi-restraints excluded: chain A residue 1187 GLN Chi-restraints excluded: chain A residue 1204 ASP Chi-restraints excluded: chain A residue 1208 THR Chi-restraints excluded: chain A residue 1239 ARG Chi-restraints excluded: chain A residue 1240 CYS Chi-restraints excluded: chain A residue 1260 LEU Chi-restraints excluded: chain A residue 1272 THR Chi-restraints excluded: chain A residue 1318 THR Chi-restraints excluded: chain A residue 1335 ILE Chi-restraints excluded: chain A residue 1361 SER Chi-restraints excluded: chain A residue 1372 VAL Chi-restraints excluded: chain A residue 1417 GLU Chi-restraints excluded: chain A residue 1424 VAL Chi-restraints excluded: chain A residue 1436 ILE Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 137 TYR Chi-restraints excluded: chain B residue 193 LYS Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 480 SER Chi-restraints excluded: chain B residue 493 SER Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 540 SER Chi-restraints excluded: chain B residue 544 CYS Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 675 ASP Chi-restraints excluded: chain B residue 737 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 895 ASP Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 944 THR Chi-restraints excluded: chain B residue 963 PHE Chi-restraints excluded: chain B residue 976 ILE Chi-restraints excluded: chain B residue 1093 GLN Chi-restraints excluded: chain B residue 1120 GLU Chi-restraints excluded: chain B residue 1201 LYS Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 48 SER Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 86 CYS Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain D residue 75 LYS Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 72 PHE Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain F residue 72 LYS Chi-restraints excluded: chain F residue 148 VAL Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 69 GLU Chi-restraints excluded: chain G residue 74 TYR Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 122 ASN Chi-restraints excluded: chain G residue 148 GLU Chi-restraints excluded: chain G residue 151 ILE Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 53 ASP Chi-restraints excluded: chain H residue 92 ASP Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain H residue 131 ASN Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain I residue 3 THR Chi-restraints excluded: chain I residue 8 ARG Chi-restraints excluded: chain I residue 19 ASP Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain I residue 62 ILE Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 6 ARG Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 52 THR Chi-restraints excluded: chain K residue 10 PHE Chi-restraints excluded: chain K residue 70 ARG Chi-restraints excluded: chain L residue 34 CYS Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 50 ASP Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain M residue 29 VAL Chi-restraints excluded: chain M residue 44 VAL Chi-restraints excluded: chain M residue 51 VAL Chi-restraints excluded: chain M residue 96 ILE Chi-restraints excluded: chain M residue 100 GLU Chi-restraints excluded: chain M residue 118 VAL Chi-restraints excluded: chain M residue 119 MET Chi-restraints excluded: chain M residue 142 LEU Chi-restraints excluded: chain M residue 176 ILE Chi-restraints excluded: chain M residue 181 ARG Chi-restraints excluded: chain M residue 195 LEU Chi-restraints excluded: chain M residue 200 THR Chi-restraints excluded: chain M residue 234 GLN Chi-restraints excluded: chain M residue 236 LEU Chi-restraints excluded: chain M residue 237 THR Chi-restraints excluded: chain M residue 252 VAL Chi-restraints excluded: chain M residue 276 THR Chi-restraints excluded: chain M residue 308 THR Chi-restraints excluded: chain M residue 317 TYR Chi-restraints excluded: chain Q residue 104 ARG Chi-restraints excluded: chain Q residue 116 THR Chi-restraints excluded: chain Q residue 119 LEU Chi-restraints excluded: chain Q residue 132 ASP Chi-restraints excluded: chain Q residue 332 LEU Chi-restraints excluded: chain Q residue 358 TYR Chi-restraints excluded: chain Q residue 392 VAL Chi-restraints excluded: chain R residue 108 LEU Chi-restraints excluded: chain R residue 212 THR Chi-restraints excluded: chain R residue 253 THR Chi-restraints excluded: chain R residue 254 THR Chi-restraints excluded: chain R residue 262 THR Chi-restraints excluded: chain R residue 269 SER Chi-restraints excluded: chain R residue 275 SER Chi-restraints excluded: chain W residue 91 TYR Chi-restraints excluded: chain W residue 105 VAL Chi-restraints excluded: chain W residue 143 ASP Chi-restraints excluded: chain W residue 149 CYS Chi-restraints excluded: chain X residue 220 THR Chi-restraints excluded: chain O residue 64 VAL Chi-restraints excluded: chain O residue 122 VAL Chi-restraints excluded: chain 0 residue 17 ILE Chi-restraints excluded: chain 0 residue 34 VAL Chi-restraints excluded: chain 0 residue 120 VAL Chi-restraints excluded: chain 0 residue 130 ASP Chi-restraints excluded: chain 0 residue 131 GLU Chi-restraints excluded: chain 0 residue 137 THR Chi-restraints excluded: chain 0 residue 142 LYS Chi-restraints excluded: chain 0 residue 155 LEU Chi-restraints excluded: chain 0 residue 190 LEU Chi-restraints excluded: chain 0 residue 204 ASN Chi-restraints excluded: chain 0 residue 221 ARG Chi-restraints excluded: chain 0 residue 240 ILE Chi-restraints excluded: chain 0 residue 249 SER Chi-restraints excluded: chain 0 residue 284 ASP Chi-restraints excluded: chain 0 residue 321 ILE Chi-restraints excluded: chain 0 residue 355 THR Chi-restraints excluded: chain 0 residue 416 PHE Chi-restraints excluded: chain 0 residue 418 LEU Chi-restraints excluded: chain 0 residue 421 GLU Chi-restraints excluded: chain 0 residue 438 THR Chi-restraints excluded: chain 0 residue 453 PHE Chi-restraints excluded: chain 0 residue 487 LEU Chi-restraints excluded: chain 0 residue 498 THR Chi-restraints excluded: chain 0 residue 559 ILE Chi-restraints excluded: chain 0 residue 563 VAL Chi-restraints excluded: chain 0 residue 573 THR Chi-restraints excluded: chain 0 residue 594 ARG Chi-restraints excluded: chain 0 residue 597 ILE Chi-restraints excluded: chain 0 residue 605 LYS Chi-restraints excluded: chain 0 residue 614 HIS Chi-restraints excluded: chain 0 residue 649 ARG Chi-restraints excluded: chain 0 residue 674 ASP Chi-restraints excluded: chain 0 residue 683 ASP Chi-restraints excluded: chain 0 residue 706 LEU Chi-restraints excluded: chain 0 residue 717 THR Chi-restraints excluded: chain 0 residue 739 TRP Chi-restraints excluded: chain 0 residue 741 TYR Chi-restraints excluded: chain 0 residue 743 ASP Chi-restraints excluded: chain 1 residue 210 TRP Chi-restraints excluded: chain 1 residue 213 ARG Chi-restraints excluded: chain 1 residue 214 ILE Chi-restraints excluded: chain 1 residue 233 VAL Chi-restraints excluded: chain 1 residue 382 SER Chi-restraints excluded: chain 4 residue 22 SER Chi-restraints excluded: chain 4 residue 27 THR Chi-restraints excluded: chain 4 residue 194 ILE Chi-restraints excluded: chain 4 residue 212 VAL Chi-restraints excluded: chain 4 residue 222 THR Chi-restraints excluded: chain 4 residue 228 THR Chi-restraints excluded: chain 4 residue 236 LEU Chi-restraints excluded: chain 4 residue 245 ILE Chi-restraints excluded: chain 4 residue 253 PHE Chi-restraints excluded: chain 4 residue 267 HIS Chi-restraints excluded: chain 4 residue 270 VAL Chi-restraints excluded: chain 4 residue 276 CYS Chi-restraints excluded: chain 6 residue 116 THR Chi-restraints excluded: chain 6 residue 118 TYR Chi-restraints excluded: chain 6 residue 145 ARG Chi-restraints excluded: chain 6 residue 166 ILE Chi-restraints excluded: chain 6 residue 182 VAL Chi-restraints excluded: chain 6 residue 222 LEU Chi-restraints excluded: chain 6 residue 261 VAL Chi-restraints excluded: chain 6 residue 282 TYR Chi-restraints excluded: chain 6 residue 291 LEU Chi-restraints excluded: chain 6 residue 306 THR Chi-restraints excluded: chain 6 residue 317 PHE Chi-restraints excluded: chain 6 residue 326 THR Chi-restraints excluded: chain 6 residue 448 LEU Chi-restraints excluded: chain 2 residue 11 THR Chi-restraints excluded: chain 2 residue 16 GLU Chi-restraints excluded: chain 2 residue 21 VAL Chi-restraints excluded: chain 2 residue 28 SER Chi-restraints excluded: chain 2 residue 53 ASN Chi-restraints excluded: chain 2 residue 284 THR Chi-restraints excluded: chain 2 residue 348 TYR Chi-restraints excluded: chain 2 residue 353 SER Chi-restraints excluded: chain 2 residue 356 GLN Chi-restraints excluded: chain 2 residue 389 ASN Chi-restraints excluded: chain 2 residue 391 ILE Chi-restraints excluded: chain 2 residue 411 LEU Chi-restraints excluded: chain 2 residue 457 SER Chi-restraints excluded: chain 2 residue 462 PHE Chi-restraints excluded: chain 2 residue 470 LEU Chi-restraints excluded: chain 2 residue 486 ASP Chi-restraints excluded: chain 5 residue 13 ASP Chi-restraints excluded: chain 5 residue 47 VAL Chi-restraints excluded: chain 5 residue 52 HIS Chi-restraints excluded: chain 3 residue 49 LEU Chi-restraints excluded: chain 7 residue 309 ASP Chi-restraints excluded: chain 7 residue 316 PHE Chi-restraints excluded: chain 7 residue 361 GLN Chi-restraints excluded: chain 7 residue 365 TYR Chi-restraints excluded: chain 7 residue 398 THR Chi-restraints excluded: chain 7 residue 412 THR Chi-restraints excluded: chain 7 residue 439 THR Chi-restraints excluded: chain 7 residue 442 ASN Chi-restraints excluded: chain 7 residue 446 PHE Chi-restraints excluded: chain 7 residue 454 VAL Chi-restraints excluded: chain 7 residue 456 THR Chi-restraints excluded: chain 7 residue 498 PHE Chi-restraints excluded: chain 7 residue 500 ARG Chi-restraints excluded: chain 7 residue 505 ILE Chi-restraints excluded: chain 7 residue 518 VAL Chi-restraints excluded: chain 7 residue 527 LEU Chi-restraints excluded: chain 7 residue 531 ILE Chi-restraints excluded: chain 7 residue 534 LYS Chi-restraints excluded: chain 7 residue 549 ILE Chi-restraints excluded: chain 7 residue 565 PHE Chi-restraints excluded: chain 7 residue 572 GLU Chi-restraints excluded: chain 7 residue 573 THR Chi-restraints excluded: chain 7 residue 579 LEU Chi-restraints excluded: chain 7 residue 656 LYS Chi-restraints excluded: chain 7 residue 676 HIS Chi-restraints excluded: chain 7 residue 681 ARG Chi-restraints excluded: chain 7 residue 695 ARG Chi-restraints excluded: chain 7 residue 712 ASP Chi-restraints excluded: chain 7 residue 717 TYR Chi-restraints excluded: chain 7 residue 735 VAL Chi-restraints excluded: chain 7 residue 736 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 786 random chunks: chunk 396 optimal weight: 2.9990 chunk 221 optimal weight: 6.9990 chunk 594 optimal weight: 10.0000 chunk 486 optimal weight: 30.0000 chunk 196 optimal weight: 2.9990 chunk 715 optimal weight: 10.0000 chunk 772 optimal weight: 40.0000 chunk 636 optimal weight: 20.0000 chunk 709 optimal weight: 9.9990 chunk 243 optimal weight: 2.9990 chunk 573 optimal weight: 4.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 865 GLN A1048 ASN ** A1171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1211 GLN ** B 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 887 HIS C 203 GLN ** D 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 113 GLN F 104 ASN I 23 ASN ** I 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 165 ASN ** 0 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 291 GLN ** 0 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0 555 GLN ** 1 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 164 ASN 6 168 GLN ** 6 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 407 GLN ** 2 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 320 ASN 7 345 ASN ** 7 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 508 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 767 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5930 moved from start: 0.2735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 65557 Z= 0.405 Angle : 0.794 13.900 89048 Z= 0.409 Chirality : 0.048 0.377 10021 Planarity : 0.005 0.082 11121 Dihedral : 16.101 87.617 10635 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 16.68 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.14 % Favored : 90.69 % Rotamer: Outliers : 8.12 % Allowed : 22.07 % Favored : 69.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.03 % Twisted Proline : 1.18 % Twisted General : 0.24 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.22 (0.09), residues: 7844 helix: -0.59 (0.09), residues: 3069 sheet: -1.57 (0.16), residues: 929 loop : -2.19 (0.10), residues: 3846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 954 HIS 0.014 0.001 HIS W 103 PHE 0.022 0.002 PHE A 219 TYR 0.036 0.002 TYR 2 13 ARG 0.006 0.001 ARG 2 450 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15688 Ramachandran restraints generated. 7844 Oldfield, 0 Emsley, 7844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15688 Ramachandran restraints generated. 7844 Oldfield, 0 Emsley, 7844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 772 residues out of total 7137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 516 poor density : 256 time to evaluate : 5.654 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: A 77 CYS cc_start: 0.6720 (OUTLIER) cc_final: 0.6486 (t) REVERT: A 465 TYR cc_start: 0.7693 (OUTLIER) cc_final: 0.6273 (p90) REVERT: A 605 MET cc_start: 0.7406 (tpp) cc_final: 0.7137 (tpt) REVERT: A 619 LYS cc_start: 0.7752 (OUTLIER) cc_final: 0.7485 (ttpt) REVERT: A 839 ARG cc_start: 0.7753 (OUTLIER) cc_final: 0.7403 (ttm-80) REVERT: A 1187 GLN cc_start: 0.6934 (OUTLIER) cc_final: 0.6468 (pt0) REVERT: B 1098 MET cc_start: 0.7958 (mpp) cc_final: 0.7757 (mtp) REVERT: D 187 THR cc_start: 0.2949 (OUTLIER) cc_final: 0.2677 (t) REVERT: J 6 ARG cc_start: 0.8006 (OUTLIER) cc_final: 0.7101 (ptt180) REVERT: J 49 MET cc_start: 0.7714 (OUTLIER) cc_final: 0.6737 (mmm) REVERT: M 96 ILE cc_start: 0.3313 (OUTLIER) cc_final: 0.2803 (pp) REVERT: M 236 LEU cc_start: 0.5199 (OUTLIER) cc_final: 0.4746 (mp) REVERT: 0 485 MET cc_start: 0.7521 (tpp) cc_final: 0.7072 (tpp) REVERT: 0 605 LYS cc_start: 0.8527 (OUTLIER) cc_final: 0.8287 (pmtt) REVERT: 0 614 HIS cc_start: 0.7426 (OUTLIER) cc_final: 0.7171 (m-70) REVERT: 0 674 ASP cc_start: 0.8431 (OUTLIER) cc_final: 0.8155 (OUTLIER) REVERT: 0 683 ASP cc_start: 0.5840 (OUTLIER) cc_final: 0.5601 (t0) REVERT: 6 118 TYR cc_start: 0.5023 (OUTLIER) cc_final: 0.4166 (m-80) REVERT: 7 309 ASP cc_start: 0.3930 (OUTLIER) cc_final: 0.2314 (m-30) REVERT: 7 311 ASP cc_start: 0.8354 (p0) cc_final: 0.8053 (m-30) REVERT: 7 365 TYR cc_start: 0.0898 (OUTLIER) cc_final: -0.0349 (m-80) REVERT: 7 445 MET cc_start: 0.1725 (ptt) cc_final: 0.1399 (ppp) REVERT: 7 446 PHE cc_start: -0.0990 (OUTLIER) cc_final: -0.1434 (t80) REVERT: 7 695 ARG cc_start: 0.1163 (OUTLIER) cc_final: -0.0234 (ppt170) outliers start: 516 outliers final: 303 residues processed: 745 average time/residue: 1.1403 time to fit residues: 1167.2965 Evaluate side-chains 564 residues out of total 7137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 321 poor density : 243 time to evaluate : 5.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 55 ASP Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 77 CYS Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 177 ASP Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 209 ASN Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 299 HIS Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 409 SER Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 465 TYR Chi-restraints excluded: chain A residue 466 SER Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 619 LYS Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 724 GLU Chi-restraints excluded: chain A residue 743 VAL Chi-restraints excluded: chain A residue 758 ILE Chi-restraints excluded: chain A residue 764 CYS Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 839 ARG Chi-restraints excluded: chain A residue 867 ILE 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 1095 THR Chi-restraints excluded: chain A residue 1102 LYS Chi-restraints excluded: chain A residue 1120 LEU Chi-restraints excluded: chain A residue 1130 GLN Chi-restraints excluded: chain A residue 1146 VAL Chi-restraints excluded: chain A residue 1187 GLN Chi-restraints excluded: chain A residue 1197 LEU Chi-restraints excluded: chain A residue 1204 ASP Chi-restraints excluded: chain A residue 1208 THR Chi-restraints excluded: chain A residue 1211 GLN Chi-restraints excluded: chain A residue 1239 ARG Chi-restraints excluded: chain A residue 1240 CYS Chi-restraints excluded: chain A residue 1260 LEU Chi-restraints excluded: chain A residue 1272 THR Chi-restraints excluded: chain A residue 1317 MET Chi-restraints excluded: chain A residue 1318 THR Chi-restraints excluded: chain A residue 1327 ILE Chi-restraints excluded: chain A residue 1335 ILE Chi-restraints excluded: chain A residue 1361 SER Chi-restraints excluded: chain A residue 1417 GLU Chi-restraints excluded: chain A residue 1424 VAL Chi-restraints excluded: chain A residue 1445 ILE Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 178 ASN Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 489 SER Chi-restraints excluded: chain B residue 493 SER Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 502 ILE Chi-restraints excluded: chain B residue 544 CYS Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 675 ASP Chi-restraints excluded: chain B residue 737 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 895 ASP Chi-restraints excluded: chain B residue 929 THR Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 944 THR Chi-restraints excluded: chain B residue 963 PHE Chi-restraints excluded: chain B residue 976 ILE Chi-restraints excluded: chain B residue 1093 GLN Chi-restraints excluded: chain B residue 1113 VAL Chi-restraints excluded: chain B residue 1120 GLU Chi-restraints excluded: chain B residue 1201 LYS Chi-restraints excluded: chain C residue 4 GLU Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 48 SER Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 86 CYS Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain D residue 75 LYS Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 144 THR Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain D residue 202 ILE Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 156 LEU Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain F residue 72 LYS Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 148 VAL Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 54 ILE Chi-restraints excluded: chain G residue 73 LYS Chi-restraints excluded: chain G residue 74 TYR Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 122 ASN Chi-restraints excluded: chain G residue 151 ILE Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 53 ASP Chi-restraints excluded: chain H residue 92 ASP Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain H residue 131 ASN Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain I residue 3 THR Chi-restraints excluded: chain I residue 7 CYS Chi-restraints excluded: chain I residue 8 ARG Chi-restraints excluded: chain I residue 23 ASN Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain I residue 62 ILE Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 6 ARG Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 49 MET Chi-restraints excluded: chain J residue 52 THR Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 10 PHE Chi-restraints excluded: chain K residue 103 THR Chi-restraints excluded: chain L residue 34 CYS Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 40 LEU Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 50 ASP Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain M residue 29 VAL Chi-restraints excluded: chain M residue 44 VAL Chi-restraints excluded: chain M residue 51 VAL Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 96 ILE Chi-restraints excluded: chain M residue 100 GLU Chi-restraints excluded: chain M residue 118 VAL Chi-restraints excluded: chain M residue 119 MET Chi-restraints excluded: chain M residue 142 LEU Chi-restraints excluded: chain M residue 176 ILE Chi-restraints excluded: chain M residue 195 LEU Chi-restraints excluded: chain M residue 200 THR Chi-restraints excluded: chain M residue 234 GLN Chi-restraints excluded: chain M residue 236 LEU Chi-restraints excluded: chain M residue 237 THR Chi-restraints excluded: chain M residue 252 VAL Chi-restraints excluded: chain M residue 276 THR Chi-restraints excluded: chain M residue 298 VAL Chi-restraints excluded: chain M residue 304 VAL Chi-restraints excluded: chain M residue 317 TYR Chi-restraints excluded: chain Q residue 116 THR Chi-restraints excluded: chain Q residue 119 LEU Chi-restraints excluded: chain Q residue 332 LEU Chi-restraints excluded: chain Q residue 336 ASP Chi-restraints excluded: chain Q residue 358 TYR Chi-restraints excluded: chain Q residue 392 VAL Chi-restraints excluded: chain R residue 108 LEU Chi-restraints excluded: chain R residue 118 HIS Chi-restraints excluded: chain R residue 212 THR Chi-restraints excluded: chain R residue 222 CYS Chi-restraints excluded: chain R residue 253 THR Chi-restraints excluded: chain R residue 254 THR Chi-restraints excluded: chain R residue 262 THR Chi-restraints excluded: chain R residue 269 SER Chi-restraints excluded: chain W residue 105 VAL Chi-restraints excluded: chain W residue 120 ASN Chi-restraints excluded: chain W residue 149 CYS Chi-restraints excluded: chain X residue 220 THR Chi-restraints excluded: chain X residue 251 ASN Chi-restraints excluded: chain O residue 64 VAL Chi-restraints excluded: chain O residue 122 VAL Chi-restraints excluded: chain 0 residue 6 ASP Chi-restraints excluded: chain 0 residue 17 ILE Chi-restraints excluded: chain 0 residue 34 VAL Chi-restraints excluded: chain 0 residue 50 VAL Chi-restraints excluded: chain 0 residue 110 SER Chi-restraints excluded: chain 0 residue 120 VAL Chi-restraints excluded: chain 0 residue 130 ASP Chi-restraints excluded: chain 0 residue 137 THR Chi-restraints excluded: chain 0 residue 142 LYS Chi-restraints excluded: chain 0 residue 155 LEU Chi-restraints excluded: chain 0 residue 190 LEU Chi-restraints excluded: chain 0 residue 204 ASN Chi-restraints excluded: chain 0 residue 221 ARG Chi-restraints excluded: chain 0 residue 240 ILE Chi-restraints excluded: chain 0 residue 284 ASP Chi-restraints excluded: chain 0 residue 321 ILE Chi-restraints excluded: chain 0 residue 355 THR Chi-restraints excluded: chain 0 residue 407 THR Chi-restraints excluded: chain 0 residue 416 PHE Chi-restraints excluded: chain 0 residue 418 LEU Chi-restraints excluded: chain 0 residue 438 THR Chi-restraints excluded: chain 0 residue 453 PHE Chi-restraints excluded: chain 0 residue 459 THR Chi-restraints excluded: chain 0 residue 487 LEU Chi-restraints excluded: chain 0 residue 498 THR Chi-restraints excluded: chain 0 residue 515 ASP Chi-restraints excluded: chain 0 residue 559 ILE Chi-restraints excluded: chain 0 residue 573 THR Chi-restraints excluded: chain 0 residue 594 ARG Chi-restraints excluded: chain 0 residue 597 ILE Chi-restraints excluded: chain 0 residue 605 LYS Chi-restraints excluded: chain 0 residue 614 HIS Chi-restraints excluded: chain 0 residue 673 LYS Chi-restraints excluded: chain 0 residue 674 ASP Chi-restraints excluded: chain 0 residue 683 ASP Chi-restraints excluded: chain 0 residue 706 LEU Chi-restraints excluded: chain 0 residue 717 THR Chi-restraints excluded: chain 1 residue 213 ARG Chi-restraints excluded: chain 1 residue 214 ILE Chi-restraints excluded: chain 1 residue 233 VAL Chi-restraints excluded: chain 1 residue 345 ASP Chi-restraints excluded: chain 4 residue 27 THR Chi-restraints excluded: chain 4 residue 153 MET Chi-restraints excluded: chain 4 residue 194 ILE Chi-restraints excluded: chain 4 residue 212 VAL Chi-restraints excluded: chain 4 residue 222 THR Chi-restraints excluded: chain 4 residue 236 LEU Chi-restraints excluded: chain 4 residue 253 PHE Chi-restraints excluded: chain 4 residue 270 VAL Chi-restraints excluded: chain 4 residue 276 CYS Chi-restraints excluded: chain 6 residue 116 THR Chi-restraints excluded: chain 6 residue 118 TYR Chi-restraints excluded: chain 6 residue 128 LEU Chi-restraints excluded: chain 6 residue 145 ARG Chi-restraints excluded: chain 6 residue 166 ILE Chi-restraints excluded: chain 6 residue 182 VAL Chi-restraints excluded: chain 6 residue 222 LEU Chi-restraints excluded: chain 6 residue 239 LEU Chi-restraints excluded: chain 6 residue 261 VAL Chi-restraints excluded: chain 6 residue 282 TYR Chi-restraints excluded: chain 6 residue 291 LEU Chi-restraints excluded: chain 6 residue 306 THR Chi-restraints excluded: chain 6 residue 317 PHE Chi-restraints excluded: chain 6 residue 318 THR Chi-restraints excluded: chain 6 residue 326 THR Chi-restraints excluded: chain 6 residue 448 LEU Chi-restraints excluded: chain 2 residue 11 THR Chi-restraints excluded: chain 2 residue 16 GLU Chi-restraints excluded: chain 2 residue 28 SER Chi-restraints excluded: chain 2 residue 53 ASN Chi-restraints excluded: chain 2 residue 284 THR Chi-restraints excluded: chain 2 residue 343 THR Chi-restraints excluded: chain 2 residue 348 TYR Chi-restraints excluded: chain 2 residue 353 SER Chi-restraints excluded: chain 2 residue 366 LEU Chi-restraints excluded: chain 2 residue 389 ASN Chi-restraints excluded: chain 2 residue 391 ILE Chi-restraints excluded: chain 2 residue 411 LEU Chi-restraints excluded: chain 2 residue 462 PHE Chi-restraints excluded: chain 2 residue 470 LEU Chi-restraints excluded: chain 2 residue 486 ASP Chi-restraints excluded: chain 5 residue 40 LEU Chi-restraints excluded: chain 5 residue 47 VAL Chi-restraints excluded: chain 5 residue 52 HIS Chi-restraints excluded: chain 3 residue 49 LEU Chi-restraints excluded: chain 3 residue 60 ASP Chi-restraints excluded: chain 7 residue 309 ASP Chi-restraints excluded: chain 7 residue 316 PHE Chi-restraints excluded: chain 7 residue 365 TYR Chi-restraints excluded: chain 7 residue 372 LYS Chi-restraints excluded: chain 7 residue 412 THR Chi-restraints excluded: chain 7 residue 439 THR Chi-restraints excluded: chain 7 residue 442 ASN Chi-restraints excluded: chain 7 residue 446 PHE Chi-restraints excluded: chain 7 residue 500 ARG Chi-restraints excluded: chain 7 residue 505 ILE Chi-restraints excluded: chain 7 residue 518 VAL Chi-restraints excluded: chain 7 residue 527 LEU Chi-restraints excluded: chain 7 residue 531 ILE Chi-restraints excluded: chain 7 residue 534 LYS Chi-restraints excluded: chain 7 residue 571 ARG Chi-restraints excluded: chain 7 residue 572 GLU Chi-restraints excluded: chain 7 residue 613 TYR Chi-restraints excluded: chain 7 residue 656 LYS Chi-restraints excluded: chain 7 residue 676 HIS Chi-restraints excluded: chain 7 residue 681 ARG Chi-restraints excluded: chain 7 residue 695 ARG Chi-restraints excluded: chain 7 residue 697 ASN Chi-restraints excluded: chain 7 residue 712 ASP Chi-restraints excluded: chain 7 residue 717 TYR Chi-restraints excluded: chain 7 residue 735 VAL Chi-restraints excluded: chain 7 residue 736 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 786 random chunks: chunk 706 optimal weight: 0.9990 chunk 537 optimal weight: 8.9990 chunk 371 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 341 optimal weight: 7.9990 chunk 480 optimal weight: 50.0000 chunk 717 optimal weight: 40.0000 chunk 759 optimal weight: 7.9990 chunk 374 optimal weight: 0.9990 chunk 680 optimal weight: 10.0000 chunk 204 optimal weight: 20.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1048 ASN ** A1171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 887 HIS C 203 GLN ** D 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 104 ASN ** I 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 98 ASN W 133 GLN ** 0 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 164 ASN ** 6 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 471 GLN ** 7 508 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 729 GLN 7 767 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5901 moved from start: 0.3114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 65557 Z= 0.335 Angle : 0.745 14.586 89048 Z= 0.383 Chirality : 0.046 0.304 10021 Planarity : 0.005 0.073 11121 Dihedral : 15.669 87.850 10558 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 15.51 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.52 % Favored : 91.34 % Rotamer: Outliers : 7.22 % Allowed : 22.46 % Favored : 70.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.03 % Twisted Proline : 1.47 % Twisted General : 0.21 % 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: -1.94 (0.09), residues: 7844 helix: -0.33 (0.09), residues: 3077 sheet: -1.44 (0.17), residues: 913 loop : -2.07 (0.10), residues: 3854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP X 263 HIS 0.011 0.001 HIS B 363 PHE 0.021 0.002 PHE A 219 TYR 0.029 0.002 TYR G 25 ARG 0.007 0.000 ARG 4 259 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15688 Ramachandran restraints generated. 7844 Oldfield, 0 Emsley, 7844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15688 Ramachandran restraints generated. 7844 Oldfield, 0 Emsley, 7844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 714 residues out of total 7137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 459 poor density : 255 time to evaluate : 5.750 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: A 465 TYR cc_start: 0.7609 (OUTLIER) cc_final: 0.6327 (p90) REVERT: A 605 MET cc_start: 0.7425 (tpp) cc_final: 0.7104 (tpt) REVERT: A 839 ARG cc_start: 0.7735 (OUTLIER) cc_final: 0.7390 (ttm-80) REVERT: A 1187 GLN cc_start: 0.6877 (OUTLIER) cc_final: 0.6442 (pt0) REVERT: D 187 THR cc_start: 0.2627 (OUTLIER) cc_final: 0.2350 (t) REVERT: G 122 ASN cc_start: 0.2644 (OUTLIER) cc_final: 0.2260 (m110) REVERT: J 49 MET cc_start: 0.7697 (OUTLIER) cc_final: 0.6696 (mmm) REVERT: K 70 ARG cc_start: 0.7925 (OUTLIER) cc_final: 0.6714 (ttp80) REVERT: M 96 ILE cc_start: 0.3369 (OUTLIER) cc_final: 0.2899 (pp) REVERT: M 236 LEU cc_start: 0.5037 (OUTLIER) cc_final: 0.4610 (mp) REVERT: 0 594 ARG cc_start: 0.5553 (OUTLIER) cc_final: 0.5133 (ptp-110) REVERT: 0 614 HIS cc_start: 0.7160 (OUTLIER) cc_final: 0.6959 (m-70) REVERT: 6 118 TYR cc_start: 0.5087 (OUTLIER) cc_final: 0.4226 (m-80) REVERT: 2 81 MET cc_start: 0.9217 (ptp) cc_final: 0.8959 (mpp) REVERT: 7 309 ASP cc_start: 0.3870 (OUTLIER) cc_final: 0.2261 (m-30) REVERT: 7 311 ASP cc_start: 0.8361 (p0) cc_final: 0.8115 (m-30) REVERT: 7 365 TYR cc_start: 0.0960 (OUTLIER) cc_final: -0.0754 (m-80) REVERT: 7 445 MET cc_start: 0.1673 (ptt) cc_final: 0.1407 (ptt) REVERT: 7 676 HIS cc_start: 0.1758 (OUTLIER) cc_final: 0.0706 (p-80) REVERT: 7 695 ARG cc_start: 0.1225 (OUTLIER) cc_final: -0.0553 (ppt170) outliers start: 459 outliers final: 265 residues processed: 690 average time/residue: 1.1735 time to fit residues: 1109.7539 Evaluate side-chains 531 residues out of total 7137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 281 poor density : 250 time to evaluate : 5.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 55 ASP Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 177 ASP Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 209 ASN Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 299 HIS Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 444 PHE Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 465 TYR Chi-restraints excluded: chain A residue 466 SER Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 724 GLU Chi-restraints excluded: chain A residue 743 VAL Chi-restraints excluded: chain A residue 758 ILE Chi-restraints excluded: chain A residue 764 CYS Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 839 ARG Chi-restraints excluded: chain A residue 865 GLN Chi-restraints excluded: chain A residue 867 ILE Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 1095 THR Chi-restraints excluded: chain A residue 1102 LYS Chi-restraints excluded: chain A residue 1120 LEU Chi-restraints excluded: chain A residue 1146 VAL Chi-restraints excluded: chain A residue 1187 GLN Chi-restraints excluded: chain A residue 1197 LEU Chi-restraints excluded: chain A residue 1208 THR Chi-restraints excluded: chain A residue 1239 ARG Chi-restraints excluded: chain A residue 1240 CYS Chi-restraints excluded: chain A residue 1260 LEU Chi-restraints excluded: chain A residue 1272 THR Chi-restraints excluded: chain A residue 1285 MET Chi-restraints excluded: chain A residue 1317 MET Chi-restraints excluded: chain A residue 1335 ILE Chi-restraints excluded: chain A residue 1361 SER Chi-restraints excluded: chain A residue 1417 GLU Chi-restraints excluded: chain A residue 1424 VAL Chi-restraints excluded: chain A residue 1445 ILE Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 178 ASN Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 337 ARG Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 489 SER Chi-restraints excluded: chain B residue 493 SER Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 502 ILE Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 675 ASP Chi-restraints excluded: chain B residue 737 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 873 THR Chi-restraints excluded: chain B residue 895 ASP Chi-restraints excluded: chain B residue 929 THR Chi-restraints excluded: chain B residue 933 SER Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 944 THR Chi-restraints excluded: chain B residue 976 ILE Chi-restraints excluded: chain B residue 1093 GLN Chi-restraints excluded: chain B residue 1113 VAL Chi-restraints excluded: chain B residue 1120 GLU Chi-restraints excluded: chain B residue 1201 LYS Chi-restraints excluded: chain C residue 4 GLU Chi-restraints excluded: chain C residue 48 SER Chi-restraints excluded: chain C residue 86 CYS Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain D residue 75 LYS Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 144 THR Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 156 LEU Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain F residue 72 LYS Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 148 VAL Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 47 CYS Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 54 ILE Chi-restraints excluded: chain G residue 74 TYR Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 122 ASN Chi-restraints excluded: chain G residue 151 ILE Chi-restraints excluded: chain H residue 53 ASP Chi-restraints excluded: chain H residue 92 ASP Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 131 ASN Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain I residue 3 THR Chi-restraints excluded: chain I residue 7 CYS Chi-restraints excluded: chain I residue 8 ARG Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain I residue 62 ILE Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 49 MET Chi-restraints excluded: chain J residue 52 THR Chi-restraints excluded: chain K residue 10 PHE Chi-restraints excluded: chain K residue 70 ARG Chi-restraints excluded: chain K residue 103 THR Chi-restraints excluded: chain L residue 34 CYS Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 40 LEU Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain M residue 29 VAL Chi-restraints excluded: chain M residue 44 VAL Chi-restraints excluded: chain M residue 51 VAL Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 96 ILE Chi-restraints excluded: chain M residue 100 GLU Chi-restraints excluded: chain M residue 118 VAL Chi-restraints excluded: chain M residue 119 MET Chi-restraints excluded: chain M residue 176 ILE Chi-restraints excluded: chain M residue 181 ARG Chi-restraints excluded: chain M residue 195 LEU Chi-restraints excluded: chain M residue 200 THR Chi-restraints excluded: chain M residue 236 LEU Chi-restraints excluded: chain M residue 237 THR Chi-restraints excluded: chain M residue 252 VAL Chi-restraints excluded: chain M residue 276 THR Chi-restraints excluded: chain M residue 298 VAL Chi-restraints excluded: chain M residue 317 TYR Chi-restraints excluded: chain Q residue 116 THR Chi-restraints excluded: chain Q residue 119 LEU Chi-restraints excluded: chain Q residue 332 LEU Chi-restraints excluded: chain Q residue 358 TYR Chi-restraints excluded: chain Q residue 392 VAL Chi-restraints excluded: chain R residue 118 HIS Chi-restraints excluded: chain R residue 212 THR Chi-restraints excluded: chain R residue 222 CYS Chi-restraints excluded: chain R residue 253 THR Chi-restraints excluded: chain R residue 254 THR Chi-restraints excluded: chain R residue 262 THR Chi-restraints excluded: chain W residue 105 VAL Chi-restraints excluded: chain W residue 120 ASN Chi-restraints excluded: chain X residue 193 LEU Chi-restraints excluded: chain X residue 220 THR Chi-restraints excluded: chain X residue 251 ASN Chi-restraints excluded: chain O residue 64 VAL Chi-restraints excluded: chain O residue 122 VAL Chi-restraints excluded: chain 0 residue 6 ASP Chi-restraints excluded: chain 0 residue 17 ILE Chi-restraints excluded: chain 0 residue 34 VAL Chi-restraints excluded: chain 0 residue 50 VAL Chi-restraints excluded: chain 0 residue 109 THR Chi-restraints excluded: chain 0 residue 110 SER Chi-restraints excluded: chain 0 residue 120 VAL Chi-restraints excluded: chain 0 residue 130 ASP Chi-restraints excluded: chain 0 residue 137 THR Chi-restraints excluded: chain 0 residue 142 LYS Chi-restraints excluded: chain 0 residue 190 LEU Chi-restraints excluded: chain 0 residue 204 ASN Chi-restraints excluded: chain 0 residue 221 ARG Chi-restraints excluded: chain 0 residue 284 ASP Chi-restraints excluded: chain 0 residue 298 ILE Chi-restraints excluded: chain 0 residue 321 ILE Chi-restraints excluded: chain 0 residue 407 THR Chi-restraints excluded: chain 0 residue 416 PHE Chi-restraints excluded: chain 0 residue 438 THR Chi-restraints excluded: chain 0 residue 453 PHE Chi-restraints excluded: chain 0 residue 487 LEU Chi-restraints excluded: chain 0 residue 498 THR Chi-restraints excluded: chain 0 residue 515 ASP Chi-restraints excluded: chain 0 residue 559 ILE Chi-restraints excluded: chain 0 residue 573 THR Chi-restraints excluded: chain 0 residue 594 ARG Chi-restraints excluded: chain 0 residue 597 ILE Chi-restraints excluded: chain 0 residue 614 HIS Chi-restraints excluded: chain 0 residue 673 LYS Chi-restraints excluded: chain 0 residue 674 ASP Chi-restraints excluded: chain 0 residue 706 LEU Chi-restraints excluded: chain 0 residue 741 TYR Chi-restraints excluded: chain 1 residue 213 ARG Chi-restraints excluded: chain 1 residue 214 ILE Chi-restraints excluded: chain 1 residue 233 VAL Chi-restraints excluded: chain 1 residue 345 ASP Chi-restraints excluded: chain 4 residue 27 THR Chi-restraints excluded: chain 4 residue 194 ILE Chi-restraints excluded: chain 4 residue 222 THR Chi-restraints excluded: chain 4 residue 236 LEU Chi-restraints excluded: chain 4 residue 253 PHE Chi-restraints excluded: chain 4 residue 270 VAL Chi-restraints excluded: chain 4 residue 274 THR Chi-restraints excluded: chain 4 residue 276 CYS Chi-restraints excluded: chain 6 residue 116 THR Chi-restraints excluded: chain 6 residue 118 TYR Chi-restraints excluded: chain 6 residue 128 LEU Chi-restraints excluded: chain 6 residue 145 ARG Chi-restraints excluded: chain 6 residue 146 HIS Chi-restraints excluded: chain 6 residue 166 ILE Chi-restraints excluded: chain 6 residue 182 VAL Chi-restraints excluded: chain 6 residue 222 LEU Chi-restraints excluded: chain 6 residue 261 VAL Chi-restraints excluded: chain 6 residue 282 TYR Chi-restraints excluded: chain 6 residue 291 LEU Chi-restraints excluded: chain 6 residue 306 THR Chi-restraints excluded: chain 6 residue 317 PHE Chi-restraints excluded: chain 6 residue 318 THR Chi-restraints excluded: chain 6 residue 326 THR Chi-restraints excluded: chain 6 residue 448 LEU Chi-restraints excluded: chain 2 residue 11 THR Chi-restraints excluded: chain 2 residue 16 GLU Chi-restraints excluded: chain 2 residue 28 SER Chi-restraints excluded: chain 2 residue 284 THR Chi-restraints excluded: chain 2 residue 348 TYR Chi-restraints excluded: chain 2 residue 353 SER Chi-restraints excluded: chain 2 residue 389 ASN Chi-restraints excluded: chain 2 residue 391 ILE Chi-restraints excluded: chain 2 residue 411 LEU Chi-restraints excluded: chain 2 residue 462 PHE Chi-restraints excluded: chain 2 residue 470 LEU Chi-restraints excluded: chain 2 residue 486 ASP Chi-restraints excluded: chain 5 residue 40 LEU Chi-restraints excluded: chain 5 residue 47 VAL Chi-restraints excluded: chain 3 residue 30 VAL Chi-restraints excluded: chain 7 residue 309 ASP Chi-restraints excluded: chain 7 residue 313 VAL Chi-restraints excluded: chain 7 residue 316 PHE Chi-restraints excluded: chain 7 residue 361 GLN Chi-restraints excluded: chain 7 residue 365 TYR Chi-restraints excluded: chain 7 residue 372 LYS Chi-restraints excluded: chain 7 residue 412 THR Chi-restraints excluded: chain 7 residue 439 THR Chi-restraints excluded: chain 7 residue 442 ASN Chi-restraints excluded: chain 7 residue 500 ARG Chi-restraints excluded: chain 7 residue 518 VAL Chi-restraints excluded: chain 7 residue 527 LEU Chi-restraints excluded: chain 7 residue 531 ILE Chi-restraints excluded: chain 7 residue 571 ARG Chi-restraints excluded: chain 7 residue 572 GLU Chi-restraints excluded: chain 7 residue 656 LYS Chi-restraints excluded: chain 7 residue 676 HIS Chi-restraints excluded: chain 7 residue 681 ARG Chi-restraints excluded: chain 7 residue 695 ARG Chi-restraints excluded: chain 7 residue 712 ASP Chi-restraints excluded: chain 7 residue 717 TYR Chi-restraints excluded: chain 7 residue 735 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 786 random chunks: chunk 632 optimal weight: 0.9980 chunk 431 optimal weight: 20.0000 chunk 11 optimal weight: 6.9990 chunk 565 optimal weight: 10.0000 chunk 313 optimal weight: 2.9990 chunk 648 optimal weight: 6.9990 chunk 525 optimal weight: 30.0000 chunk 0 optimal weight: 8.9990 chunk 387 optimal weight: 6.9990 chunk 681 optimal weight: 30.0000 chunk 191 optimal weight: 3.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 316 GLN ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 757 ASN A1048 ASN A1130 GLN ** A1171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 667 GLN B 887 HIS C 203 GLN ** D 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 63 ASN F 104 ASN I 23 ASN I 83 ASN ** Q 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 164 ASN ** 6 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 508 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 729 GLN 7 767 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5921 moved from start: 0.3254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 65557 Z= 0.406 Angle : 0.757 14.301 89048 Z= 0.388 Chirality : 0.047 0.273 10021 Planarity : 0.005 0.075 11121 Dihedral : 15.428 92.410 10497 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 15.66 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.98 % Favored : 90.86 % Rotamer: Outliers : 7.27 % Allowed : 22.81 % Favored : 69.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.03 % Twisted Proline : 1.47 % Twisted General : 0.17 % 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: -1.83 (0.09), residues: 7844 helix: -0.23 (0.09), residues: 3092 sheet: -1.39 (0.16), residues: 937 loop : -2.01 (0.10), residues: 3815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP X 263 HIS 0.013 0.001 HIS B 363 PHE 0.022 0.002 PHE A 219 TYR 0.036 0.002 TYR 2 13 ARG 0.008 0.000 ARG 4 259 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15688 Ramachandran restraints generated. 7844 Oldfield, 0 Emsley, 7844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15688 Ramachandran restraints generated. 7844 Oldfield, 0 Emsley, 7844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 714 residues out of total 7137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 462 poor density : 252 time to evaluate : 5.751 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: A 465 TYR cc_start: 0.7741 (OUTLIER) cc_final: 0.6496 (p90) REVERT: A 605 MET cc_start: 0.7491 (tpp) cc_final: 0.7170 (tpt) REVERT: A 839 ARG cc_start: 0.7700 (OUTLIER) cc_final: 0.7449 (ttm-80) REVERT: A 845 LEU cc_start: 0.8425 (OUTLIER) cc_final: 0.8187 (mp) REVERT: D 187 THR cc_start: 0.2592 (OUTLIER) cc_final: 0.2330 (t) REVERT: J 49 MET cc_start: 0.7720 (OUTLIER) cc_final: 0.6722 (mmm) REVERT: K 70 ARG cc_start: 0.7933 (OUTLIER) cc_final: 0.6829 (ttp80) REVERT: M 96 ILE cc_start: 0.3552 (OUTLIER) cc_final: 0.3043 (pp) REVERT: M 236 LEU cc_start: 0.5052 (OUTLIER) cc_final: 0.4585 (mp) REVERT: 0 485 MET cc_start: 0.7450 (tpp) cc_final: 0.6991 (tpp) REVERT: 0 594 ARG cc_start: 0.5590 (OUTLIER) cc_final: 0.5131 (ptp-110) REVERT: 6 118 TYR cc_start: 0.5156 (OUTLIER) cc_final: 0.4297 (m-80) REVERT: 2 51 VAL cc_start: 0.8927 (OUTLIER) cc_final: 0.8608 (t) REVERT: 7 365 TYR cc_start: 0.1101 (OUTLIER) cc_final: -0.0818 (m-80) REVERT: 7 445 MET cc_start: 0.1734 (ptt) cc_final: 0.1378 (ptt) REVERT: 7 676 HIS cc_start: 0.1784 (OUTLIER) cc_final: 0.0964 (p-80) REVERT: 7 695 ARG cc_start: 0.1253 (OUTLIER) cc_final: -0.0561 (ppt170) outliers start: 462 outliers final: 286 residues processed: 690 average time/residue: 1.1333 time to fit residues: 1080.5326 Evaluate side-chains 549 residues out of total 7137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 300 poor density : 249 time to evaluate : 5.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 55 ASP Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 177 ASP Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 209 ASN Chi-restraints excluded: chain A residue 234 MET Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 444 PHE Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 465 TYR Chi-restraints excluded: chain A residue 466 SER Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 724 GLU Chi-restraints excluded: chain A residue 743 VAL Chi-restraints excluded: chain A residue 758 ILE Chi-restraints excluded: chain A residue 764 CYS Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 839 ARG Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 867 ILE Chi-restraints excluded: chain A residue 948 VAL 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 1095 THR Chi-restraints excluded: chain A residue 1107 VAL Chi-restraints excluded: chain A residue 1120 LEU Chi-restraints excluded: chain A residue 1146 VAL Chi-restraints excluded: chain A residue 1169 ILE Chi-restraints excluded: chain A residue 1197 LEU Chi-restraints excluded: chain A residue 1208 THR Chi-restraints excluded: chain A residue 1240 CYS Chi-restraints excluded: chain A residue 1260 LEU Chi-restraints excluded: chain A residue 1272 THR Chi-restraints excluded: chain A residue 1285 MET Chi-restraints excluded: chain A residue 1317 MET Chi-restraints excluded: chain A residue 1335 ILE Chi-restraints excluded: chain A residue 1417 GLU Chi-restraints excluded: chain A residue 1424 VAL Chi-restraints excluded: chain A residue 1436 ILE Chi-restraints excluded: chain A residue 1445 ILE Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 178 ASN Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 310 MET Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 398 ARG Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 489 SER Chi-restraints excluded: chain B residue 493 SER Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 502 ILE Chi-restraints excluded: chain B residue 544 CYS Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 675 ASP Chi-restraints excluded: chain B residue 737 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 873 THR Chi-restraints excluded: chain B residue 895 ASP Chi-restraints excluded: chain B residue 929 THR Chi-restraints excluded: chain B residue 933 SER Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 944 THR Chi-restraints excluded: chain B residue 976 ILE Chi-restraints excluded: chain B residue 1093 GLN Chi-restraints excluded: chain B residue 1113 VAL Chi-restraints excluded: chain B residue 1152 MET Chi-restraints excluded: chain B residue 1201 LYS Chi-restraints excluded: chain C residue 4 GLU Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 86 CYS Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain D residue 75 LYS Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 144 THR Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain D residue 202 ILE Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 156 LEU Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain F residue 72 LYS Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 148 VAL Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 47 CYS Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 54 ILE Chi-restraints excluded: chain G residue 73 LYS Chi-restraints excluded: chain G residue 74 TYR Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 122 ASN Chi-restraints excluded: chain G residue 145 VAL Chi-restraints excluded: chain G residue 151 ILE Chi-restraints excluded: chain H residue 13 SER Chi-restraints excluded: chain H residue 53 ASP Chi-restraints excluded: chain H residue 92 ASP Chi-restraints excluded: chain H residue 131 ASN Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain I residue 7 CYS Chi-restraints excluded: chain I residue 8 ARG Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain I residue 62 ILE Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 49 MET Chi-restraints excluded: chain J residue 52 THR Chi-restraints excluded: chain K residue 10 PHE Chi-restraints excluded: chain K residue 70 ARG Chi-restraints excluded: chain K residue 103 THR Chi-restraints excluded: chain L residue 34 CYS Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 40 LEU Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 50 ASP Chi-restraints excluded: chain M residue 29 VAL Chi-restraints excluded: chain M residue 44 VAL Chi-restraints excluded: chain M residue 51 VAL Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 96 ILE Chi-restraints excluded: chain M residue 100 GLU Chi-restraints excluded: chain M residue 118 VAL Chi-restraints excluded: chain M residue 119 MET Chi-restraints excluded: chain M residue 156 LEU Chi-restraints excluded: chain M residue 171 ILE Chi-restraints excluded: chain M residue 176 ILE Chi-restraints excluded: chain M residue 181 ARG Chi-restraints excluded: chain M residue 195 LEU Chi-restraints excluded: chain M residue 200 THR Chi-restraints excluded: chain M residue 234 GLN Chi-restraints excluded: chain M residue 236 LEU Chi-restraints excluded: chain M residue 237 THR Chi-restraints excluded: chain M residue 252 VAL Chi-restraints excluded: chain M residue 276 THR Chi-restraints excluded: chain M residue 298 VAL Chi-restraints excluded: chain M residue 304 VAL Chi-restraints excluded: chain M residue 317 TYR Chi-restraints excluded: chain Q residue 116 THR Chi-restraints excluded: chain Q residue 119 LEU Chi-restraints excluded: chain Q residue 130 VAL Chi-restraints excluded: chain Q residue 332 LEU Chi-restraints excluded: chain Q residue 336 ASP Chi-restraints excluded: chain Q residue 358 TYR Chi-restraints excluded: chain Q residue 392 VAL Chi-restraints excluded: chain R residue 68 VAL Chi-restraints excluded: chain R residue 98 ASN Chi-restraints excluded: chain R residue 118 HIS Chi-restraints excluded: chain R residue 212 THR Chi-restraints excluded: chain R residue 222 CYS Chi-restraints excluded: chain R residue 254 THR Chi-restraints excluded: chain R residue 262 THR Chi-restraints excluded: chain W residue 105 VAL Chi-restraints excluded: chain W residue 120 ASN Chi-restraints excluded: chain X residue 220 THR Chi-restraints excluded: chain X residue 251 ASN Chi-restraints excluded: chain O residue 64 VAL Chi-restraints excluded: chain O residue 122 VAL Chi-restraints excluded: chain 0 residue 6 ASP Chi-restraints excluded: chain 0 residue 34 VAL Chi-restraints excluded: chain 0 residue 50 VAL Chi-restraints excluded: chain 0 residue 109 THR Chi-restraints excluded: chain 0 residue 110 SER Chi-restraints excluded: chain 0 residue 120 VAL Chi-restraints excluded: chain 0 residue 130 ASP Chi-restraints excluded: chain 0 residue 137 THR Chi-restraints excluded: chain 0 residue 142 LYS Chi-restraints excluded: chain 0 residue 204 ASN Chi-restraints excluded: chain 0 residue 221 ARG Chi-restraints excluded: chain 0 residue 284 ASP Chi-restraints excluded: chain 0 residue 298 ILE Chi-restraints excluded: chain 0 residue 318 THR Chi-restraints excluded: chain 0 residue 321 ILE Chi-restraints excluded: chain 0 residue 355 THR Chi-restraints excluded: chain 0 residue 416 PHE Chi-restraints excluded: chain 0 residue 418 LEU Chi-restraints excluded: chain 0 residue 435 MET Chi-restraints excluded: chain 0 residue 453 PHE Chi-restraints excluded: chain 0 residue 487 LEU Chi-restraints excluded: chain 0 residue 498 THR Chi-restraints excluded: chain 0 residue 515 ASP Chi-restraints excluded: chain 0 residue 559 ILE Chi-restraints excluded: chain 0 residue 573 THR Chi-restraints excluded: chain 0 residue 594 ARG Chi-restraints excluded: chain 0 residue 597 ILE Chi-restraints excluded: chain 0 residue 673 LYS Chi-restraints excluded: chain 0 residue 674 ASP Chi-restraints excluded: chain 0 residue 706 LEU Chi-restraints excluded: chain 0 residue 729 ASP Chi-restraints excluded: chain 0 residue 741 TYR Chi-restraints excluded: chain 1 residue 213 ARG Chi-restraints excluded: chain 1 residue 214 ILE Chi-restraints excluded: chain 1 residue 233 VAL Chi-restraints excluded: chain 1 residue 345 ASP Chi-restraints excluded: chain 4 residue 27 THR Chi-restraints excluded: chain 4 residue 180 THR Chi-restraints excluded: chain 4 residue 194 ILE Chi-restraints excluded: chain 4 residue 222 THR Chi-restraints excluded: chain 4 residue 236 LEU Chi-restraints excluded: chain 4 residue 253 PHE Chi-restraints excluded: chain 4 residue 270 VAL Chi-restraints excluded: chain 4 residue 274 THR Chi-restraints excluded: chain 4 residue 276 CYS Chi-restraints excluded: chain 6 residue 116 THR Chi-restraints excluded: chain 6 residue 118 TYR Chi-restraints excluded: chain 6 residue 128 LEU Chi-restraints excluded: chain 6 residue 145 ARG Chi-restraints excluded: chain 6 residue 146 HIS Chi-restraints excluded: chain 6 residue 164 ASN Chi-restraints excluded: chain 6 residue 166 ILE Chi-restraints excluded: chain 6 residue 182 VAL Chi-restraints excluded: chain 6 residue 222 LEU Chi-restraints excluded: chain 6 residue 261 VAL Chi-restraints excluded: chain 6 residue 266 LEU Chi-restraints excluded: chain 6 residue 282 TYR Chi-restraints excluded: chain 6 residue 291 LEU Chi-restraints excluded: chain 6 residue 306 THR Chi-restraints excluded: chain 6 residue 317 PHE Chi-restraints excluded: chain 6 residue 326 THR Chi-restraints excluded: chain 6 residue 448 LEU Chi-restraints excluded: chain 2 residue 11 THR Chi-restraints excluded: chain 2 residue 16 GLU Chi-restraints excluded: chain 2 residue 28 SER Chi-restraints excluded: chain 2 residue 51 VAL Chi-restraints excluded: chain 2 residue 284 THR Chi-restraints excluded: chain 2 residue 348 TYR Chi-restraints excluded: chain 2 residue 389 ASN Chi-restraints excluded: chain 2 residue 391 ILE Chi-restraints excluded: chain 2 residue 411 LEU Chi-restraints excluded: chain 2 residue 462 PHE Chi-restraints excluded: chain 2 residue 470 LEU Chi-restraints excluded: chain 2 residue 486 ASP Chi-restraints excluded: chain 2 residue 488 LYS Chi-restraints excluded: chain 5 residue 40 LEU Chi-restraints excluded: chain 5 residue 47 VAL Chi-restraints excluded: chain 3 residue 30 VAL Chi-restraints excluded: chain 3 residue 60 ASP Chi-restraints excluded: chain 7 residue 313 VAL Chi-restraints excluded: chain 7 residue 316 PHE Chi-restraints excluded: chain 7 residue 361 GLN Chi-restraints excluded: chain 7 residue 365 TYR Chi-restraints excluded: chain 7 residue 372 LYS Chi-restraints excluded: chain 7 residue 412 THR Chi-restraints excluded: chain 7 residue 439 THR Chi-restraints excluded: chain 7 residue 442 ASN Chi-restraints excluded: chain 7 residue 500 ARG Chi-restraints excluded: chain 7 residue 518 VAL Chi-restraints excluded: chain 7 residue 527 LEU Chi-restraints excluded: chain 7 residue 531 ILE Chi-restraints excluded: chain 7 residue 572 GLU Chi-restraints excluded: chain 7 residue 613 TYR Chi-restraints excluded: chain 7 residue 656 LYS Chi-restraints excluded: chain 7 residue 676 HIS Chi-restraints excluded: chain 7 residue 681 ARG Chi-restraints excluded: chain 7 residue 695 ARG Chi-restraints excluded: chain 7 residue 697 ASN Chi-restraints excluded: chain 7 residue 717 TYR Chi-restraints excluded: chain 7 residue 735 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 786 random chunks: chunk 255 optimal weight: 2.9990 chunk 684 optimal weight: 20.0000 chunk 150 optimal weight: 6.9990 chunk 446 optimal weight: 7.9990 chunk 187 optimal weight: 1.9990 chunk 760 optimal weight: 10.0000 chunk 631 optimal weight: 1.9990 chunk 352 optimal weight: 8.9990 chunk 63 optimal weight: 0.6980 chunk 251 optimal weight: 0.7980 chunk 399 optimal weight: 6.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 451 HIS A 587 HIS A1048 ASN A1130 GLN A1187 GLN ** A1364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 887 HIS C 203 GLN ** D 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 104 ASN ** I 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 234 GLN ** Q 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 251 ASN ** O 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 291 GLN ** 0 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 188 ASN 6 164 ASN ** 6 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 500 GLN ** 5 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 508 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 644 GLN 7 729 GLN 7 767 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5846 moved from start: 0.3667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 65557 Z= 0.221 Angle : 0.716 14.970 89048 Z= 0.362 Chirality : 0.045 0.346 10021 Planarity : 0.005 0.076 11121 Dihedral : 15.150 102.510 10469 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.94 % Favored : 91.93 % Rotamer: Outliers : 5.78 % Allowed : 24.11 % Favored : 70.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.03 % Twisted Proline : 1.18 % Twisted General : 0.12 % 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: -1.56 (0.09), residues: 7844 helix: 0.00 (0.09), residues: 3112 sheet: -1.28 (0.16), residues: 948 loop : -1.87 (0.10), residues: 3784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP X 263 HIS 0.014 0.001 HIS B 363 PHE 0.021 0.001 PHE A 219 TYR 0.034 0.001 TYR 2 13 ARG 0.011 0.000 ARG 7 571 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15688 Ramachandran restraints generated. 7844 Oldfield, 0 Emsley, 7844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15688 Ramachandran restraints generated. 7844 Oldfield, 0 Emsley, 7844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 623 residues out of total 7137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 367 poor density : 256 time to evaluate : 5.659 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: A 465 TYR cc_start: 0.7522 (OUTLIER) cc_final: 0.6444 (p90) REVERT: A 839 ARG cc_start: 0.7725 (OUTLIER) cc_final: 0.7417 (ttm-80) REVERT: D 187 THR cc_start: 0.2289 (OUTLIER) cc_final: 0.2043 (t) REVERT: G 122 ASN cc_start: 0.2690 (OUTLIER) cc_final: 0.2215 (m-40) REVERT: J 49 MET cc_start: 0.7622 (OUTLIER) cc_final: 0.6606 (mmm) REVERT: M 96 ILE cc_start: 0.3632 (OUTLIER) cc_final: 0.3177 (pp) REVERT: M 236 LEU cc_start: 0.5031 (OUTLIER) cc_final: 0.4582 (mp) REVERT: 0 498 THR cc_start: 0.7831 (OUTLIER) cc_final: 0.7015 (p) REVERT: 0 594 ARG cc_start: 0.5424 (OUTLIER) cc_final: 0.4941 (ptp-110) REVERT: 6 118 TYR cc_start: 0.5080 (OUTLIER) cc_final: 0.4211 (m-80) REVERT: 2 47 ILE cc_start: 0.9239 (OUTLIER) cc_final: 0.9030 (mp) REVERT: 7 303 ARG cc_start: 0.0583 (OUTLIER) cc_final: 0.0365 (tmm-80) REVERT: 7 365 TYR cc_start: 0.1113 (OUTLIER) cc_final: -0.0855 (m-80) REVERT: 7 445 MET cc_start: 0.1509 (ptt) cc_final: 0.1099 (ptt) REVERT: 7 676 HIS cc_start: 0.1537 (OUTLIER) cc_final: 0.0824 (p-80) outliers start: 367 outliers final: 220 residues processed: 607 average time/residue: 1.3087 time to fit residues: 1112.4065 Evaluate side-chains 482 residues out of total 7137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 234 poor density : 248 time to evaluate : 5.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 55 ASP Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 177 ASP Chi-restraints excluded: chain A residue 209 ASN Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 299 HIS Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 444 PHE Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 465 TYR Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 724 GLU Chi-restraints excluded: chain A residue 743 VAL Chi-restraints excluded: chain A residue 758 ILE Chi-restraints excluded: chain A residue 839 ARG Chi-restraints excluded: chain A residue 1038 THR Chi-restraints excluded: chain A residue 1120 LEU Chi-restraints excluded: chain A residue 1197 LEU Chi-restraints excluded: chain A residue 1208 THR Chi-restraints excluded: chain A residue 1240 CYS Chi-restraints excluded: chain A residue 1260 LEU Chi-restraints excluded: chain A residue 1272 THR Chi-restraints excluded: chain A residue 1327 ILE Chi-restraints excluded: chain A residue 1335 ILE Chi-restraints excluded: chain A residue 1417 GLU Chi-restraints excluded: chain A residue 1424 VAL Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 337 ARG Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 493 SER Chi-restraints excluded: chain B residue 502 ILE Chi-restraints excluded: chain B residue 544 CYS Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 675 ASP Chi-restraints excluded: chain B residue 737 THR Chi-restraints excluded: chain B residue 895 ASP Chi-restraints excluded: chain B residue 933 SER Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 944 THR Chi-restraints excluded: chain B residue 976 ILE Chi-restraints excluded: chain B residue 1093 GLN Chi-restraints excluded: chain B residue 1113 VAL Chi-restraints excluded: chain B residue 1201 LYS Chi-restraints excluded: chain C residue 4 GLU Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 86 CYS Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 75 LYS Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 144 THR Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain E residue 34 GLU Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain F residue 72 LYS Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 148 VAL Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 54 ILE Chi-restraints excluded: chain G residue 74 TYR Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 122 ASN Chi-restraints excluded: chain G residue 151 ILE Chi-restraints excluded: chain H residue 53 ASP Chi-restraints excluded: chain H residue 92 ASP Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 131 ASN Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain I residue 3 THR Chi-restraints excluded: chain I residue 7 CYS Chi-restraints excluded: chain I residue 8 ARG Chi-restraints excluded: chain I residue 23 ASN Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain I residue 62 ILE Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 49 MET Chi-restraints excluded: chain J residue 52 THR Chi-restraints excluded: chain K residue 10 PHE Chi-restraints excluded: chain L residue 34 CYS Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 40 LEU Chi-restraints excluded: chain M residue 44 VAL Chi-restraints excluded: chain M residue 51 VAL Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 96 ILE Chi-restraints excluded: chain M residue 100 GLU Chi-restraints excluded: chain M residue 118 VAL Chi-restraints excluded: chain M residue 119 MET Chi-restraints excluded: chain M residue 170 SER Chi-restraints excluded: chain M residue 195 LEU Chi-restraints excluded: chain M residue 200 THR Chi-restraints excluded: chain M residue 236 LEU Chi-restraints excluded: chain M residue 237 THR Chi-restraints excluded: chain M residue 252 VAL Chi-restraints excluded: chain M residue 287 LEU Chi-restraints excluded: chain M residue 298 VAL Chi-restraints excluded: chain M residue 304 VAL Chi-restraints excluded: chain M residue 317 TYR Chi-restraints excluded: chain Q residue 103 LEU Chi-restraints excluded: chain Q residue 104 ARG Chi-restraints excluded: chain Q residue 116 THR Chi-restraints excluded: chain Q residue 119 LEU Chi-restraints excluded: chain Q residue 130 VAL Chi-restraints excluded: chain Q residue 332 LEU Chi-restraints excluded: chain Q residue 358 TYR Chi-restraints excluded: chain Q residue 392 VAL Chi-restraints excluded: chain R residue 68 VAL Chi-restraints excluded: chain R residue 118 HIS Chi-restraints excluded: chain R residue 212 THR Chi-restraints excluded: chain R residue 222 CYS Chi-restraints excluded: chain R residue 254 THR Chi-restraints excluded: chain W residue 32 ILE Chi-restraints excluded: chain W residue 105 VAL Chi-restraints excluded: chain W residue 115 LYS Chi-restraints excluded: chain W residue 120 ASN Chi-restraints excluded: chain X residue 220 THR Chi-restraints excluded: chain O residue 64 VAL Chi-restraints excluded: chain O residue 122 VAL Chi-restraints excluded: chain 0 residue 34 VAL Chi-restraints excluded: chain 0 residue 50 VAL Chi-restraints excluded: chain 0 residue 110 SER Chi-restraints excluded: chain 0 residue 120 VAL Chi-restraints excluded: chain 0 residue 130 ASP Chi-restraints excluded: chain 0 residue 137 THR Chi-restraints excluded: chain 0 residue 142 LYS Chi-restraints excluded: chain 0 residue 204 ASN Chi-restraints excluded: chain 0 residue 221 ARG Chi-restraints excluded: chain 0 residue 284 ASP Chi-restraints excluded: chain 0 residue 298 ILE Chi-restraints excluded: chain 0 residue 318 THR Chi-restraints excluded: chain 0 residue 321 ILE Chi-restraints excluded: chain 0 residue 355 THR Chi-restraints excluded: chain 0 residue 407 THR Chi-restraints excluded: chain 0 residue 416 PHE Chi-restraints excluded: chain 0 residue 435 MET Chi-restraints excluded: chain 0 residue 453 PHE Chi-restraints excluded: chain 0 residue 487 LEU Chi-restraints excluded: chain 0 residue 498 THR Chi-restraints excluded: chain 0 residue 515 ASP Chi-restraints excluded: chain 0 residue 573 THR Chi-restraints excluded: chain 0 residue 594 ARG Chi-restraints excluded: chain 0 residue 597 ILE Chi-restraints excluded: chain 0 residue 673 LYS Chi-restraints excluded: chain 0 residue 674 ASP Chi-restraints excluded: chain 0 residue 706 LEU Chi-restraints excluded: chain 0 residue 741 TYR Chi-restraints excluded: chain 1 residue 213 ARG Chi-restraints excluded: chain 1 residue 214 ILE Chi-restraints excluded: chain 1 residue 233 VAL Chi-restraints excluded: chain 1 residue 345 ASP Chi-restraints excluded: chain 4 residue 194 ILE Chi-restraints excluded: chain 4 residue 222 THR Chi-restraints excluded: chain 4 residue 236 LEU Chi-restraints excluded: chain 4 residue 245 ILE Chi-restraints excluded: chain 4 residue 253 PHE Chi-restraints excluded: chain 4 residue 270 VAL Chi-restraints excluded: chain 4 residue 276 CYS Chi-restraints excluded: chain 6 residue 116 THR Chi-restraints excluded: chain 6 residue 118 TYR Chi-restraints excluded: chain 6 residue 128 LEU Chi-restraints excluded: chain 6 residue 145 ARG Chi-restraints excluded: chain 6 residue 146 HIS Chi-restraints excluded: chain 6 residue 164 ASN Chi-restraints excluded: chain 6 residue 166 ILE Chi-restraints excluded: chain 6 residue 182 VAL Chi-restraints excluded: chain 6 residue 222 LEU Chi-restraints excluded: chain 6 residue 266 LEU Chi-restraints excluded: chain 6 residue 282 TYR Chi-restraints excluded: chain 6 residue 291 LEU Chi-restraints excluded: chain 6 residue 306 THR Chi-restraints excluded: chain 6 residue 448 LEU Chi-restraints excluded: chain 2 residue 16 GLU Chi-restraints excluded: chain 2 residue 28 SER Chi-restraints excluded: chain 2 residue 47 ILE Chi-restraints excluded: chain 2 residue 51 VAL Chi-restraints excluded: chain 2 residue 348 TYR Chi-restraints excluded: chain 2 residue 389 ASN Chi-restraints excluded: chain 2 residue 391 ILE Chi-restraints excluded: chain 2 residue 411 LEU Chi-restraints excluded: chain 2 residue 470 LEU Chi-restraints excluded: chain 2 residue 486 ASP Chi-restraints excluded: chain 5 residue 40 LEU Chi-restraints excluded: chain 5 residue 49 PHE Chi-restraints excluded: chain 3 residue 25 ASP Chi-restraints excluded: chain 3 residue 60 ASP Chi-restraints excluded: chain 7 residue 303 ARG Chi-restraints excluded: chain 7 residue 313 VAL Chi-restraints excluded: chain 7 residue 316 PHE Chi-restraints excluded: chain 7 residue 361 GLN Chi-restraints excluded: chain 7 residue 365 TYR Chi-restraints excluded: chain 7 residue 412 THR Chi-restraints excluded: chain 7 residue 439 THR Chi-restraints excluded: chain 7 residue 442 ASN Chi-restraints excluded: chain 7 residue 446 PHE Chi-restraints excluded: chain 7 residue 500 ARG Chi-restraints excluded: chain 7 residue 527 LEU Chi-restraints excluded: chain 7 residue 531 ILE Chi-restraints excluded: chain 7 residue 572 GLU Chi-restraints excluded: chain 7 residue 613 TYR Chi-restraints excluded: chain 7 residue 656 LYS Chi-restraints excluded: chain 7 residue 676 HIS Chi-restraints excluded: chain 7 residue 735 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 786 random chunks: chunk 733 optimal weight: 20.0000 chunk 85 optimal weight: 6.9990 chunk 433 optimal weight: 40.0000 chunk 555 optimal weight: 6.9990 chunk 430 optimal weight: 30.0000 chunk 640 optimal weight: 6.9990 chunk 424 optimal weight: 20.0000 chunk 757 optimal weight: 7.9990 chunk 474 optimal weight: 50.0000 chunk 461 optimal weight: 8.9990 chunk 349 optimal weight: 0.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 339 ASN A1048 ASN A1130 GLN A1432 GLN B 887 HIS C 203 GLN ** D 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 251 ASN ** O 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 164 ASN ** 6 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 508 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 729 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5942 moved from start: 0.3492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.083 65557 Z= 0.522 Angle : 0.802 17.755 89048 Z= 0.407 Chirality : 0.048 0.443 10021 Planarity : 0.005 0.078 11121 Dihedral : 15.134 105.048 10431 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 15.86 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.86 % Favored : 90.96 % Rotamer: Outliers : 5.82 % Allowed : 24.33 % Favored : 69.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.03 % Twisted Proline : 1.47 % Twisted General : 0.11 % 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: -1.66 (0.09), residues: 7844 helix: -0.08 (0.09), residues: 3094 sheet: -1.33 (0.16), residues: 958 loop : -1.92 (0.10), residues: 3792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP X 263 HIS 0.015 0.001 HIS W 103 PHE 0.025 0.002 PHE Q 347 TYR 0.036 0.002 TYR 1 630 ARG 0.009 0.001 ARG 4 259 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15688 Ramachandran restraints generated. 7844 Oldfield, 0 Emsley, 7844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15688 Ramachandran restraints generated. 7844 Oldfield, 0 Emsley, 7844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 621 residues out of total 7137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 370 poor density : 251 time to evaluate : 5.679 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: A 465 TYR cc_start: 0.7868 (OUTLIER) cc_final: 0.6692 (p90) REVERT: A 839 ARG cc_start: 0.7714 (OUTLIER) cc_final: 0.7430 (ttm-80) REVERT: D 187 THR cc_start: 0.2353 (OUTLIER) cc_final: 0.2047 (t) REVERT: J 49 MET cc_start: 0.7759 (OUTLIER) cc_final: 0.6772 (mmm) REVERT: M 96 ILE cc_start: 0.3598 (OUTLIER) cc_final: 0.3121 (pp) REVERT: M 236 LEU cc_start: 0.5109 (OUTLIER) cc_final: 0.4645 (mp) REVERT: 0 498 THR cc_start: 0.7772 (OUTLIER) cc_final: 0.6921 (p) REVERT: 6 118 TYR cc_start: 0.5209 (OUTLIER) cc_final: 0.4357 (m-80) REVERT: 7 365 TYR cc_start: 0.1072 (OUTLIER) cc_final: -0.0870 (m-80) REVERT: 7 445 MET cc_start: 0.1785 (ptt) cc_final: 0.1341 (ptt) REVERT: 7 676 HIS cc_start: 0.1851 (OUTLIER) cc_final: 0.1105 (p-80) REVERT: 7 695 ARG cc_start: 0.1214 (OUTLIER) cc_final: -0.0530 (ppt170) outliers start: 370 outliers final: 256 residues processed: 597 average time/residue: 1.1577 time to fit residues: 949.5115 Evaluate side-chains 513 residues out of total 7137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 267 poor density : 246 time to evaluate : 5.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 55 ASP Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 177 ASP Chi-restraints excluded: chain A residue 209 ASN Chi-restraints excluded: chain A residue 234 MET Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 444 PHE Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 465 TYR Chi-restraints excluded: chain A residue 466 SER Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 521 MET Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 724 GLU Chi-restraints excluded: chain A residue 743 VAL Chi-restraints excluded: chain A residue 758 ILE Chi-restraints excluded: chain A residue 839 ARG 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 1095 THR Chi-restraints excluded: chain A residue 1098 VAL Chi-restraints excluded: chain A residue 1107 VAL Chi-restraints excluded: chain A residue 1120 LEU Chi-restraints excluded: chain A residue 1146 VAL Chi-restraints excluded: chain A residue 1208 THR Chi-restraints excluded: chain A residue 1240 CYS Chi-restraints excluded: chain A residue 1260 LEU Chi-restraints excluded: chain A residue 1272 THR Chi-restraints excluded: chain A residue 1335 ILE Chi-restraints excluded: chain A residue 1417 GLU Chi-restraints excluded: chain A residue 1424 VAL Chi-restraints excluded: chain A residue 1445 ILE Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 310 MET Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 489 SER Chi-restraints excluded: chain B residue 493 SER Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 502 ILE Chi-restraints excluded: chain B residue 544 CYS Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 675 ASP Chi-restraints excluded: chain B residue 737 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 873 THR Chi-restraints excluded: chain B residue 895 ASP Chi-restraints excluded: chain B residue 929 THR Chi-restraints excluded: chain B residue 933 SER Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 944 THR Chi-restraints excluded: chain B residue 970 THR Chi-restraints excluded: chain B residue 976 ILE Chi-restraints excluded: chain B residue 1093 GLN Chi-restraints excluded: chain B residue 1113 VAL Chi-restraints excluded: chain B residue 1120 GLU Chi-restraints excluded: chain B residue 1152 MET Chi-restraints excluded: chain B residue 1201 LYS Chi-restraints excluded: chain C residue 4 GLU Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 86 CYS Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 75 LYS Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 144 THR Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain D residue 206 GLU Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 156 LEU Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain F residue 72 LYS Chi-restraints excluded: chain F residue 148 VAL Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 47 CYS Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 54 ILE Chi-restraints excluded: chain G residue 74 TYR Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 106 MET Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 122 ASN Chi-restraints excluded: chain G residue 151 ILE Chi-restraints excluded: chain H residue 13 SER Chi-restraints excluded: chain H residue 53 ASP Chi-restraints excluded: chain H residue 92 ASP Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 131 ASN Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain I residue 3 THR Chi-restraints excluded: chain I residue 7 CYS Chi-restraints excluded: chain I residue 8 ARG Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain I residue 62 ILE Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 49 MET Chi-restraints excluded: chain J residue 52 THR Chi-restraints excluded: chain K residue 10 PHE Chi-restraints excluded: chain L residue 34 CYS Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 40 LEU Chi-restraints excluded: chain L residue 50 ASP Chi-restraints excluded: chain M residue 44 VAL Chi-restraints excluded: chain M residue 51 VAL Chi-restraints excluded: chain M residue 96 ILE Chi-restraints excluded: chain M residue 100 GLU Chi-restraints excluded: chain M residue 118 VAL Chi-restraints excluded: chain M residue 119 MET Chi-restraints excluded: chain M residue 156 LEU Chi-restraints excluded: chain M residue 170 SER Chi-restraints excluded: chain M residue 176 ILE Chi-restraints excluded: chain M residue 195 LEU Chi-restraints excluded: chain M residue 197 HIS Chi-restraints excluded: chain M residue 200 THR Chi-restraints excluded: chain M residue 234 GLN Chi-restraints excluded: chain M residue 236 LEU Chi-restraints excluded: chain M residue 237 THR Chi-restraints excluded: chain M residue 252 VAL Chi-restraints excluded: chain M residue 287 LEU Chi-restraints excluded: chain M residue 304 VAL Chi-restraints excluded: chain M residue 317 TYR Chi-restraints excluded: chain Q residue 103 LEU Chi-restraints excluded: chain Q residue 104 ARG Chi-restraints excluded: chain Q residue 116 THR Chi-restraints excluded: chain Q residue 119 LEU Chi-restraints excluded: chain Q residue 130 VAL Chi-restraints excluded: chain Q residue 332 LEU Chi-restraints excluded: chain Q residue 358 TYR Chi-restraints excluded: chain Q residue 386 MET Chi-restraints excluded: chain Q residue 392 VAL Chi-restraints excluded: chain R residue 68 VAL Chi-restraints excluded: chain R residue 118 HIS Chi-restraints excluded: chain R residue 212 THR Chi-restraints excluded: chain R residue 222 CYS Chi-restraints excluded: chain R residue 254 THR Chi-restraints excluded: chain R residue 262 THR Chi-restraints excluded: chain W residue 32 ILE Chi-restraints excluded: chain W residue 105 VAL Chi-restraints excluded: chain W residue 115 LYS Chi-restraints excluded: chain W residue 120 ASN Chi-restraints excluded: chain X residue 220 THR Chi-restraints excluded: chain O residue 64 VAL Chi-restraints excluded: chain O residue 122 VAL Chi-restraints excluded: chain 0 residue 6 ASP Chi-restraints excluded: chain 0 residue 34 VAL Chi-restraints excluded: chain 0 residue 50 VAL Chi-restraints excluded: chain 0 residue 109 THR Chi-restraints excluded: chain 0 residue 110 SER Chi-restraints excluded: chain 0 residue 120 VAL Chi-restraints excluded: chain 0 residue 130 ASP Chi-restraints excluded: chain 0 residue 137 THR Chi-restraints excluded: chain 0 residue 142 LYS Chi-restraints excluded: chain 0 residue 162 LEU Chi-restraints excluded: chain 0 residue 204 ASN Chi-restraints excluded: chain 0 residue 221 ARG Chi-restraints excluded: chain 0 residue 284 ASP Chi-restraints excluded: chain 0 residue 298 ILE Chi-restraints excluded: chain 0 residue 318 THR Chi-restraints excluded: chain 0 residue 321 ILE Chi-restraints excluded: chain 0 residue 355 THR Chi-restraints excluded: chain 0 residue 407 THR Chi-restraints excluded: chain 0 residue 416 PHE Chi-restraints excluded: chain 0 residue 453 PHE Chi-restraints excluded: chain 0 residue 487 LEU Chi-restraints excluded: chain 0 residue 498 THR Chi-restraints excluded: chain 0 residue 515 ASP Chi-restraints excluded: chain 0 residue 573 THR Chi-restraints excluded: chain 0 residue 597 ILE Chi-restraints excluded: chain 0 residue 673 LYS Chi-restraints excluded: chain 0 residue 674 ASP Chi-restraints excluded: chain 0 residue 706 LEU Chi-restraints excluded: chain 0 residue 729 ASP Chi-restraints excluded: chain 0 residue 741 TYR Chi-restraints excluded: chain 1 residue 213 ARG Chi-restraints excluded: chain 1 residue 214 ILE Chi-restraints excluded: chain 1 residue 233 VAL Chi-restraints excluded: chain 1 residue 345 ASP Chi-restraints excluded: chain 4 residue 194 ILE Chi-restraints excluded: chain 4 residue 222 THR Chi-restraints excluded: chain 4 residue 236 LEU Chi-restraints excluded: chain 4 residue 245 ILE Chi-restraints excluded: chain 4 residue 253 PHE Chi-restraints excluded: chain 4 residue 270 VAL Chi-restraints excluded: chain 4 residue 274 THR Chi-restraints excluded: chain 4 residue 276 CYS Chi-restraints excluded: chain 6 residue 116 THR Chi-restraints excluded: chain 6 residue 118 TYR Chi-restraints excluded: chain 6 residue 128 LEU Chi-restraints excluded: chain 6 residue 145 ARG Chi-restraints excluded: chain 6 residue 164 ASN Chi-restraints excluded: chain 6 residue 166 ILE Chi-restraints excluded: chain 6 residue 175 ARG Chi-restraints excluded: chain 6 residue 182 VAL Chi-restraints excluded: chain 6 residue 222 LEU Chi-restraints excluded: chain 6 residue 266 LEU Chi-restraints excluded: chain 6 residue 282 TYR Chi-restraints excluded: chain 6 residue 291 LEU Chi-restraints excluded: chain 6 residue 306 THR Chi-restraints excluded: chain 6 residue 448 LEU Chi-restraints excluded: chain 2 residue 11 THR Chi-restraints excluded: chain 2 residue 28 SER Chi-restraints excluded: chain 2 residue 51 VAL Chi-restraints excluded: chain 2 residue 95 THR Chi-restraints excluded: chain 2 residue 348 TYR Chi-restraints excluded: chain 2 residue 353 SER Chi-restraints excluded: chain 2 residue 389 ASN Chi-restraints excluded: chain 2 residue 391 ILE Chi-restraints excluded: chain 2 residue 411 LEU Chi-restraints excluded: chain 2 residue 457 SER Chi-restraints excluded: chain 2 residue 470 LEU Chi-restraints excluded: chain 2 residue 486 ASP Chi-restraints excluded: chain 5 residue 40 LEU Chi-restraints excluded: chain 3 residue 30 VAL Chi-restraints excluded: chain 3 residue 60 ASP Chi-restraints excluded: chain 7 residue 313 VAL Chi-restraints excluded: chain 7 residue 316 PHE Chi-restraints excluded: chain 7 residue 361 GLN Chi-restraints excluded: chain 7 residue 365 TYR Chi-restraints excluded: chain 7 residue 412 THR Chi-restraints excluded: chain 7 residue 442 ASN Chi-restraints excluded: chain 7 residue 446 PHE Chi-restraints excluded: chain 7 residue 500 ARG Chi-restraints excluded: chain 7 residue 527 LEU Chi-restraints excluded: chain 7 residue 531 ILE Chi-restraints excluded: chain 7 residue 572 GLU Chi-restraints excluded: chain 7 residue 583 MET Chi-restraints excluded: chain 7 residue 613 TYR Chi-restraints excluded: chain 7 residue 656 LYS Chi-restraints excluded: chain 7 residue 676 HIS Chi-restraints excluded: chain 7 residue 695 ARG Chi-restraints excluded: chain 7 residue 735 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 786 random chunks: chunk 468 optimal weight: 20.0000 chunk 302 optimal weight: 7.9990 chunk 452 optimal weight: 20.0000 chunk 228 optimal weight: 3.9990 chunk 148 optimal weight: 0.7980 chunk 146 optimal weight: 0.9980 chunk 481 optimal weight: 6.9990 chunk 516 optimal weight: 6.9990 chunk 374 optimal weight: 0.8980 chunk 70 optimal weight: 0.8980 chunk 595 optimal weight: 6.9990 overall best weight: 1.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1048 ASN ** A1364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 887 HIS ** D 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 104 ASN ** I 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 87 GLN ** Q 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 251 ASN ** O 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 88 ASN ** 0 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 164 ASN ** 6 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 22 GLN ** 2 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 22 GLN ** 5 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 508 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5841 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 0.050 65557 Z= 0.215 Angle : 0.732 14.946 89048 Z= 0.369 Chirality : 0.045 0.505 10021 Planarity : 0.005 0.077 11121 Dihedral : 14.945 104.086 10426 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.80 % Favored : 92.08 % Rotamer: Outliers : 4.79 % Allowed : 25.55 % Favored : 69.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.03 % Twisted Proline : 1.18 % Twisted General : 0.13 % 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: -1.43 (0.09), residues: 7844 helix: 0.12 (0.09), residues: 3114 sheet: -1.15 (0.17), residues: 946 loop : -1.82 (0.10), residues: 3784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP X 263 HIS 0.013 0.001 HIS B 363 PHE 0.021 0.001 PHE 1 287 TYR 0.049 0.001 TYR 1 630 ARG 0.022 0.000 ARG 5 56 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15688 Ramachandran restraints generated. 7844 Oldfield, 0 Emsley, 7844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15688 Ramachandran restraints generated. 7844 Oldfield, 0 Emsley, 7844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 555 residues out of total 7137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 304 poor density : 251 time to evaluate : 5.679 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: A 465 TYR cc_start: 0.7589 (OUTLIER) cc_final: 0.6560 (p90) REVERT: A 839 ARG cc_start: 0.7709 (OUTLIER) cc_final: 0.7401 (ttm-80) REVERT: D 187 THR cc_start: 0.2237 (OUTLIER) cc_final: 0.1965 (t) REVERT: E 50 MET cc_start: 0.4091 (ppp) cc_final: 0.3629 (pp-130) REVERT: F 148 VAL cc_start: 0.8132 (OUTLIER) cc_final: 0.7920 (m) REVERT: G 122 ASN cc_start: 0.2969 (OUTLIER) cc_final: 0.2550 (m-40) REVERT: J 49 MET cc_start: 0.7572 (OUTLIER) cc_final: 0.6559 (mmm) REVERT: M 96 ILE cc_start: 0.3650 (OUTLIER) cc_final: 0.3176 (pp) REVERT: M 236 LEU cc_start: 0.4875 (OUTLIER) cc_final: 0.4571 (mp) REVERT: 0 221 ARG cc_start: 0.7969 (OUTLIER) cc_final: 0.7685 (pmt-80) REVERT: 0 498 THR cc_start: 0.7765 (OUTLIER) cc_final: 0.6965 (p) REVERT: 6 118 TYR cc_start: 0.5261 (OUTLIER) cc_final: 0.4384 (m-80) REVERT: 7 445 MET cc_start: 0.1588 (ptt) cc_final: 0.1083 (ptt) REVERT: 7 676 HIS cc_start: 0.1373 (OUTLIER) cc_final: 0.0751 (p-80) REVERT: 7 695 ARG cc_start: 0.0929 (OUTLIER) cc_final: -0.0544 (ppt170) outliers start: 304 outliers final: 212 residues processed: 536 average time/residue: 1.1919 time to fit residues: 876.6562 Evaluate side-chains 471 residues out of total 7137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 225 poor density : 246 time to evaluate : 5.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 55 ASP Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 177 ASP Chi-restraints excluded: chain A residue 209 ASN Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 444 PHE Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 465 TYR Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 521 MET Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 724 GLU Chi-restraints excluded: chain A residue 743 VAL Chi-restraints excluded: chain A residue 758 ILE Chi-restraints excluded: chain A residue 764 CYS Chi-restraints excluded: chain A residue 839 ARG Chi-restraints excluded: chain A residue 948 VAL 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 1095 THR Chi-restraints excluded: chain A residue 1120 LEU Chi-restraints excluded: chain A residue 1208 THR Chi-restraints excluded: chain A residue 1240 CYS Chi-restraints excluded: chain A residue 1260 LEU Chi-restraints excluded: chain A residue 1272 THR Chi-restraints excluded: chain A residue 1327 ILE Chi-restraints excluded: chain A residue 1335 ILE Chi-restraints excluded: chain A residue 1417 GLU Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 310 MET Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 489 SER Chi-restraints excluded: chain B residue 493 SER Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 502 ILE Chi-restraints excluded: chain B residue 544 CYS Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 675 ASP Chi-restraints excluded: chain B residue 895 ASP Chi-restraints excluded: chain B residue 933 SER Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 944 THR Chi-restraints excluded: chain B residue 970 THR Chi-restraints excluded: chain B residue 976 ILE Chi-restraints excluded: chain B residue 1093 GLN Chi-restraints excluded: chain B residue 1113 VAL Chi-restraints excluded: chain B residue 1201 LYS Chi-restraints excluded: chain C residue 4 GLU Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 86 CYS Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 75 LYS Chi-restraints excluded: chain D residue 144 THR Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain E residue 34 GLU Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain F residue 72 LYS Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 148 VAL Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 47 CYS Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 54 ILE Chi-restraints excluded: chain G residue 74 TYR Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 106 MET Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 122 ASN Chi-restraints excluded: chain G residue 151 ILE Chi-restraints excluded: chain H residue 53 ASP Chi-restraints excluded: chain H residue 92 ASP Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 131 ASN Chi-restraints excluded: chain I residue 7 CYS Chi-restraints excluded: chain I residue 8 ARG Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 49 MET Chi-restraints excluded: chain J residue 52 THR Chi-restraints excluded: chain K residue 10 PHE Chi-restraints excluded: chain L residue 34 CYS Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 40 LEU Chi-restraints excluded: chain L residue 50 ASP Chi-restraints excluded: chain M residue 51 VAL Chi-restraints excluded: chain M residue 96 ILE Chi-restraints excluded: chain M residue 100 GLU Chi-restraints excluded: chain M residue 119 MET Chi-restraints excluded: chain M residue 156 LEU Chi-restraints excluded: chain M residue 176 ILE Chi-restraints excluded: chain M residue 195 LEU Chi-restraints excluded: chain M residue 197 HIS Chi-restraints excluded: chain M residue 200 THR Chi-restraints excluded: chain M residue 234 GLN Chi-restraints excluded: chain M residue 236 LEU Chi-restraints excluded: chain M residue 252 VAL Chi-restraints excluded: chain M residue 298 VAL Chi-restraints excluded: chain M residue 304 VAL Chi-restraints excluded: chain M residue 317 TYR Chi-restraints excluded: chain Q residue 103 LEU Chi-restraints excluded: chain Q residue 104 ARG Chi-restraints excluded: chain Q residue 116 THR Chi-restraints excluded: chain Q residue 119 LEU Chi-restraints excluded: chain Q residue 130 VAL Chi-restraints excluded: chain Q residue 332 LEU Chi-restraints excluded: chain Q residue 358 TYR Chi-restraints excluded: chain Q residue 386 MET Chi-restraints excluded: chain Q residue 392 VAL Chi-restraints excluded: chain R residue 118 HIS Chi-restraints excluded: chain R residue 212 THR Chi-restraints excluded: chain R residue 222 CYS Chi-restraints excluded: chain R residue 254 THR Chi-restraints excluded: chain W residue 32 ILE Chi-restraints excluded: chain W residue 105 VAL Chi-restraints excluded: chain W residue 115 LYS Chi-restraints excluded: chain W residue 120 ASN Chi-restraints excluded: chain X residue 220 THR Chi-restraints excluded: chain O residue 64 VAL Chi-restraints excluded: chain O residue 122 VAL Chi-restraints excluded: chain 0 residue 34 VAL Chi-restraints excluded: chain 0 residue 50 VAL Chi-restraints excluded: chain 0 residue 109 THR Chi-restraints excluded: chain 0 residue 110 SER Chi-restraints excluded: chain 0 residue 120 VAL Chi-restraints excluded: chain 0 residue 130 ASP Chi-restraints excluded: chain 0 residue 137 THR Chi-restraints excluded: chain 0 residue 142 LYS Chi-restraints excluded: chain 0 residue 162 LEU Chi-restraints excluded: chain 0 residue 204 ASN Chi-restraints excluded: chain 0 residue 221 ARG Chi-restraints excluded: chain 0 residue 284 ASP Chi-restraints excluded: chain 0 residue 298 ILE Chi-restraints excluded: chain 0 residue 318 THR Chi-restraints excluded: chain 0 residue 321 ILE Chi-restraints excluded: chain 0 residue 407 THR Chi-restraints excluded: chain 0 residue 453 PHE Chi-restraints excluded: chain 0 residue 487 LEU Chi-restraints excluded: chain 0 residue 498 THR Chi-restraints excluded: chain 0 residue 515 ASP Chi-restraints excluded: chain 0 residue 573 THR Chi-restraints excluded: chain 0 residue 597 ILE Chi-restraints excluded: chain 0 residue 673 LYS Chi-restraints excluded: chain 0 residue 706 LEU Chi-restraints excluded: chain 0 residue 741 TYR Chi-restraints excluded: chain 1 residue 213 ARG Chi-restraints excluded: chain 1 residue 214 ILE Chi-restraints excluded: chain 1 residue 233 VAL Chi-restraints excluded: chain 1 residue 345 ASP Chi-restraints excluded: chain 1 residue 600 VAL Chi-restraints excluded: chain 4 residue 194 ILE Chi-restraints excluded: chain 4 residue 222 THR Chi-restraints excluded: chain 4 residue 234 VAL Chi-restraints excluded: chain 4 residue 236 LEU Chi-restraints excluded: chain 4 residue 245 ILE Chi-restraints excluded: chain 4 residue 258 LEU Chi-restraints excluded: chain 4 residue 270 VAL Chi-restraints excluded: chain 4 residue 276 CYS Chi-restraints excluded: chain 6 residue 116 THR Chi-restraints excluded: chain 6 residue 118 TYR Chi-restraints excluded: chain 6 residue 128 LEU Chi-restraints excluded: chain 6 residue 146 HIS Chi-restraints excluded: chain 6 residue 164 ASN Chi-restraints excluded: chain 6 residue 166 ILE Chi-restraints excluded: chain 6 residue 182 VAL Chi-restraints excluded: chain 6 residue 222 LEU Chi-restraints excluded: chain 6 residue 282 TYR Chi-restraints excluded: chain 6 residue 291 LEU Chi-restraints excluded: chain 6 residue 306 THR Chi-restraints excluded: chain 6 residue 448 LEU Chi-restraints excluded: chain 2 residue 11 THR Chi-restraints excluded: chain 2 residue 28 SER Chi-restraints excluded: chain 2 residue 51 VAL Chi-restraints excluded: chain 2 residue 348 TYR Chi-restraints excluded: chain 2 residue 389 ASN Chi-restraints excluded: chain 2 residue 391 ILE Chi-restraints excluded: chain 2 residue 411 LEU Chi-restraints excluded: chain 2 residue 470 LEU Chi-restraints excluded: chain 2 residue 486 ASP Chi-restraints excluded: chain 5 residue 40 LEU Chi-restraints excluded: chain 5 residue 52 HIS Chi-restraints excluded: chain 3 residue 30 VAL Chi-restraints excluded: chain 3 residue 60 ASP Chi-restraints excluded: chain 7 residue 313 VAL Chi-restraints excluded: chain 7 residue 361 GLN Chi-restraints excluded: chain 7 residue 365 TYR Chi-restraints excluded: chain 7 residue 412 THR Chi-restraints excluded: chain 7 residue 500 ARG Chi-restraints excluded: chain 7 residue 527 LEU Chi-restraints excluded: chain 7 residue 531 ILE Chi-restraints excluded: chain 7 residue 572 GLU Chi-restraints excluded: chain 7 residue 583 MET Chi-restraints excluded: chain 7 residue 613 TYR Chi-restraints excluded: chain 7 residue 656 LYS Chi-restraints excluded: chain 7 residue 676 HIS Chi-restraints excluded: chain 7 residue 695 ARG Chi-restraints excluded: chain 7 residue 717 TYR Chi-restraints excluded: chain 7 residue 735 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 786 random chunks: chunk 689 optimal weight: 3.9990 chunk 725 optimal weight: 0.4980 chunk 662 optimal weight: 8.9990 chunk 705 optimal weight: 20.0000 chunk 424 optimal weight: 5.9990 chunk 307 optimal weight: 2.9990 chunk 554 optimal weight: 8.9990 chunk 216 optimal weight: 0.6980 chunk 637 optimal weight: 6.9990 chunk 667 optimal weight: 5.9990 chunk 703 optimal weight: 0.0570 overall best weight: 1.6502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1048 ASN A1130 GLN ** A1364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 887 HIS C 203 GLN ** D 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 83 ASN ** Q 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 251 ASN ** O 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 60 GLN ** 0 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 164 ASN 6 351 ASN ** 6 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 508 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 616 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5837 moved from start: 0.4066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 65557 Z= 0.222 Angle : 0.738 15.275 89048 Z= 0.369 Chirality : 0.045 0.482 10021 Planarity : 0.005 0.076 11121 Dihedral : 14.718 89.033 10401 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.84 % Favored : 92.06 % Rotamer: Outliers : 4.33 % Allowed : 26.03 % Favored : 69.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.03 % Twisted Proline : 1.18 % Twisted General : 0.11 % 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: -1.30 (0.10), residues: 7844 helix: 0.21 (0.09), residues: 3115 sheet: -1.00 (0.17), residues: 930 loop : -1.75 (0.10), residues: 3799 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP X 263 HIS 0.013 0.001 HIS B 363 PHE 0.021 0.001 PHE A 219 TYR 0.022 0.001 TYR 1 583 ARG 0.012 0.000 ARG 5 56 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15688 Ramachandran restraints generated. 7844 Oldfield, 0 Emsley, 7844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15688 Ramachandran restraints generated. 7844 Oldfield, 0 Emsley, 7844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 526 residues out of total 7137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 275 poor density : 251 time to evaluate : 5.538 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: A 465 TYR cc_start: 0.7536 (OUTLIER) cc_final: 0.6532 (p90) REVERT: D 187 THR cc_start: 0.2310 (OUTLIER) cc_final: 0.2053 (t) REVERT: G 122 ASN cc_start: 0.2704 (OUTLIER) cc_final: 0.2476 (m-40) REVERT: J 49 MET cc_start: 0.7602 (OUTLIER) cc_final: 0.6555 (mmm) REVERT: K 10 PHE cc_start: 0.4467 (OUTLIER) cc_final: 0.4162 (m-80) REVERT: M 96 ILE cc_start: 0.3663 (OUTLIER) cc_final: 0.3223 (pp) REVERT: M 236 LEU cc_start: 0.4946 (OUTLIER) cc_final: 0.4603 (mp) REVERT: 0 60 GLN cc_start: 0.6576 (OUTLIER) cc_final: 0.6161 (tp-100) REVERT: 0 221 ARG cc_start: 0.7868 (OUTLIER) cc_final: 0.7622 (pmt-80) REVERT: 6 118 TYR cc_start: 0.5310 (OUTLIER) cc_final: 0.4429 (m-80) REVERT: 3 73 PHE cc_start: 0.6090 (m-80) cc_final: 0.5845 (m-80) REVERT: 7 316 PHE cc_start: 0.7405 (OUTLIER) cc_final: 0.7054 (p90) REVERT: 7 365 TYR cc_start: 0.1467 (OUTLIER) cc_final: -0.0534 (m-80) REVERT: 7 445 MET cc_start: 0.1727 (ptt) cc_final: 0.1182 (ptt) REVERT: 7 459 MET cc_start: 0.6878 (pmm) cc_final: 0.6635 (pmm) REVERT: 7 676 HIS cc_start: 0.1398 (OUTLIER) cc_final: 0.0836 (p-80) REVERT: 7 695 ARG cc_start: 0.0987 (OUTLIER) cc_final: -0.0489 (ppt170) outliers start: 275 outliers final: 196 residues processed: 509 average time/residue: 1.1998 time to fit residues: 834.0978 Evaluate side-chains 457 residues out of total 7137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 210 poor density : 247 time to evaluate : 5.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 177 ASP Chi-restraints excluded: chain A residue 209 ASN Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 444 PHE Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 465 TYR Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 521 MET Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 724 GLU Chi-restraints excluded: chain A residue 743 VAL Chi-restraints excluded: chain A residue 758 ILE Chi-restraints excluded: chain A residue 761 MET Chi-restraints excluded: chain A residue 764 CYS Chi-restraints excluded: chain A residue 886 ILE 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 1095 THR Chi-restraints excluded: chain A residue 1102 LYS Chi-restraints excluded: chain A residue 1120 LEU Chi-restraints excluded: chain A residue 1208 THR Chi-restraints excluded: chain A residue 1240 CYS Chi-restraints excluded: chain A residue 1260 LEU Chi-restraints excluded: chain A residue 1272 THR Chi-restraints excluded: chain A residue 1327 ILE Chi-restraints excluded: chain A residue 1335 ILE Chi-restraints excluded: chain A residue 1417 GLU Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 310 MET Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 489 SER Chi-restraints excluded: chain B residue 493 SER Chi-restraints excluded: chain B residue 502 ILE Chi-restraints excluded: chain B residue 544 CYS Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 675 ASP Chi-restraints excluded: chain B residue 873 THR Chi-restraints excluded: chain B residue 895 ASP Chi-restraints excluded: chain B residue 933 SER Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 970 THR Chi-restraints excluded: chain B residue 976 ILE Chi-restraints excluded: chain B residue 1093 GLN Chi-restraints excluded: chain B residue 1113 VAL Chi-restraints excluded: chain B residue 1201 LYS Chi-restraints excluded: chain C residue 4 GLU Chi-restraints excluded: chain C residue 86 CYS Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 75 LYS Chi-restraints excluded: chain D residue 144 THR Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain D residue 206 GLU Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain E residue 34 GLU Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 47 CYS Chi-restraints excluded: chain G residue 54 ILE Chi-restraints excluded: chain G residue 73 LYS Chi-restraints excluded: chain G residue 74 TYR Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 122 ASN Chi-restraints excluded: chain H residue 53 ASP Chi-restraints excluded: chain H residue 92 ASP Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 131 ASN Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain I residue 7 CYS Chi-restraints excluded: chain I residue 8 ARG Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 49 MET Chi-restraints excluded: chain J residue 52 THR Chi-restraints excluded: chain K residue 10 PHE Chi-restraints excluded: chain L residue 34 CYS Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 40 LEU Chi-restraints excluded: chain M residue 51 VAL Chi-restraints excluded: chain M residue 96 ILE Chi-restraints excluded: chain M residue 100 GLU Chi-restraints excluded: chain M residue 119 MET Chi-restraints excluded: chain M residue 170 SER Chi-restraints excluded: chain M residue 195 LEU Chi-restraints excluded: chain M residue 197 HIS Chi-restraints excluded: chain M residue 200 THR Chi-restraints excluded: chain M residue 234 GLN Chi-restraints excluded: chain M residue 236 LEU Chi-restraints excluded: chain M residue 252 VAL Chi-restraints excluded: chain M residue 287 LEU Chi-restraints excluded: chain M residue 298 VAL Chi-restraints excluded: chain M residue 304 VAL Chi-restraints excluded: chain M residue 317 TYR Chi-restraints excluded: chain Q residue 116 THR Chi-restraints excluded: chain Q residue 119 LEU Chi-restraints excluded: chain Q residue 130 VAL Chi-restraints excluded: chain Q residue 332 LEU Chi-restraints excluded: chain Q residue 358 TYR Chi-restraints excluded: chain Q residue 386 MET Chi-restraints excluded: chain R residue 118 HIS Chi-restraints excluded: chain R residue 212 THR Chi-restraints excluded: chain R residue 222 CYS Chi-restraints excluded: chain R residue 254 THR Chi-restraints excluded: chain R residue 262 THR Chi-restraints excluded: chain W residue 32 ILE Chi-restraints excluded: chain W residue 105 VAL Chi-restraints excluded: chain W residue 120 ASN Chi-restraints excluded: chain X residue 220 THR Chi-restraints excluded: chain O residue 122 VAL Chi-restraints excluded: chain 0 residue 50 VAL Chi-restraints excluded: chain 0 residue 60 GLN Chi-restraints excluded: chain 0 residue 109 THR Chi-restraints excluded: chain 0 residue 110 SER Chi-restraints excluded: chain 0 residue 120 VAL Chi-restraints excluded: chain 0 residue 130 ASP Chi-restraints excluded: chain 0 residue 137 THR Chi-restraints excluded: chain 0 residue 162 LEU Chi-restraints excluded: chain 0 residue 204 ASN Chi-restraints excluded: chain 0 residue 221 ARG Chi-restraints excluded: chain 0 residue 284 ASP Chi-restraints excluded: chain 0 residue 298 ILE Chi-restraints excluded: chain 0 residue 318 THR Chi-restraints excluded: chain 0 residue 355 THR Chi-restraints excluded: chain 0 residue 407 THR Chi-restraints excluded: chain 0 residue 453 PHE Chi-restraints excluded: chain 0 residue 487 LEU Chi-restraints excluded: chain 0 residue 515 ASP Chi-restraints excluded: chain 0 residue 573 THR Chi-restraints excluded: chain 0 residue 597 ILE Chi-restraints excluded: chain 0 residue 673 LYS Chi-restraints excluded: chain 0 residue 706 LEU Chi-restraints excluded: chain 0 residue 741 TYR Chi-restraints excluded: chain 1 residue 213 ARG Chi-restraints excluded: chain 1 residue 214 ILE Chi-restraints excluded: chain 1 residue 345 ASP Chi-restraints excluded: chain 1 residue 600 VAL Chi-restraints excluded: chain 4 residue 32 ILE Chi-restraints excluded: chain 4 residue 153 MET Chi-restraints excluded: chain 4 residue 222 THR Chi-restraints excluded: chain 4 residue 234 VAL Chi-restraints excluded: chain 4 residue 236 LEU Chi-restraints excluded: chain 4 residue 245 ILE Chi-restraints excluded: chain 6 residue 116 THR Chi-restraints excluded: chain 6 residue 118 TYR Chi-restraints excluded: chain 6 residue 128 LEU Chi-restraints excluded: chain 6 residue 164 ASN Chi-restraints excluded: chain 6 residue 166 ILE Chi-restraints excluded: chain 6 residue 182 VAL Chi-restraints excluded: chain 6 residue 222 LEU Chi-restraints excluded: chain 6 residue 291 LEU Chi-restraints excluded: chain 6 residue 306 THR Chi-restraints excluded: chain 6 residue 448 LEU Chi-restraints excluded: chain 2 residue 11 THR Chi-restraints excluded: chain 2 residue 28 SER Chi-restraints excluded: chain 2 residue 348 TYR Chi-restraints excluded: chain 2 residue 389 ASN Chi-restraints excluded: chain 2 residue 391 ILE Chi-restraints excluded: chain 2 residue 411 LEU Chi-restraints excluded: chain 2 residue 470 LEU Chi-restraints excluded: chain 2 residue 486 ASP Chi-restraints excluded: chain 5 residue 40 LEU Chi-restraints excluded: chain 3 residue 30 VAL Chi-restraints excluded: chain 3 residue 60 ASP Chi-restraints excluded: chain 7 residue 313 VAL Chi-restraints excluded: chain 7 residue 316 PHE Chi-restraints excluded: chain 7 residue 361 GLN Chi-restraints excluded: chain 7 residue 365 TYR Chi-restraints excluded: chain 7 residue 412 THR Chi-restraints excluded: chain 7 residue 500 ARG Chi-restraints excluded: chain 7 residue 505 ILE Chi-restraints excluded: chain 7 residue 527 LEU Chi-restraints excluded: chain 7 residue 531 ILE Chi-restraints excluded: chain 7 residue 572 GLU Chi-restraints excluded: chain 7 residue 613 TYR Chi-restraints excluded: chain 7 residue 656 LYS Chi-restraints excluded: chain 7 residue 676 HIS Chi-restraints excluded: chain 7 residue 695 ARG Chi-restraints excluded: chain 7 residue 735 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 786 random chunks: chunk 463 optimal weight: 6.9990 chunk 746 optimal weight: 2.9990 chunk 455 optimal weight: 10.0000 chunk 354 optimal weight: 8.9990 chunk 518 optimal weight: 7.9990 chunk 783 optimal weight: 7.9990 chunk 720 optimal weight: 40.0000 chunk 623 optimal weight: 7.9990 chunk 64 optimal weight: 0.9980 chunk 481 optimal weight: 40.0000 chunk 382 optimal weight: 10.0000 overall best weight: 5.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1048 ASN B 887 HIS C 203 GLN ** D 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 251 ASN ** O 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 60 GLN ** 0 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 164 ASN ** 6 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 419 GLN ** 7 508 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5921 moved from start: 0.3865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.076 65557 Z= 0.474 Angle : 0.814 16.839 89048 Z= 0.410 Chirality : 0.048 0.475 10021 Planarity : 0.005 0.076 11121 Dihedral : 14.765 88.916 10374 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 15.82 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.72 % Favored : 91.13 % Rotamer: Outliers : 3.90 % Allowed : 26.62 % Favored : 69.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.03 % Twisted Proline : 1.18 % Twisted General : 0.09 % 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: -1.47 (0.09), residues: 7844 helix: 0.07 (0.09), residues: 3121 sheet: -1.19 (0.16), residues: 965 loop : -1.82 (0.10), residues: 3758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP X 263 HIS 0.012 0.001 HIS A 786 PHE 0.027 0.002 PHE 6 160 TYR 0.052 0.002 TYR 1 630 ARG 0.012 0.001 ARG B 337 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15688 Ramachandran restraints generated. 7844 Oldfield, 0 Emsley, 7844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15688 Ramachandran restraints generated. 7844 Oldfield, 0 Emsley, 7844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 500 residues out of total 7137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 248 poor density : 252 time to evaluate : 5.598 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: A 465 TYR cc_start: 0.7803 (OUTLIER) cc_final: 0.6654 (p90) REVERT: D 187 THR cc_start: 0.2019 (OUTLIER) cc_final: 0.1784 (t) REVERT: E 50 MET cc_start: 0.4178 (ppp) cc_final: 0.3560 (pp-130) REVERT: J 49 MET cc_start: 0.7761 (OUTLIER) cc_final: 0.6777 (mmm) REVERT: M 96 ILE cc_start: 0.3739 (OUTLIER) cc_final: 0.3282 (pp) REVERT: M 236 LEU cc_start: 0.5046 (OUTLIER) cc_final: 0.4762 (mp) REVERT: Q 114 MET cc_start: 0.3716 (ppp) cc_final: 0.3444 (ppp) REVERT: 0 60 GLN cc_start: 0.6496 (OUTLIER) cc_final: 0.6201 (tp-100) REVERT: 0 221 ARG cc_start: 0.7905 (OUTLIER) cc_final: 0.7637 (pmt-80) REVERT: 6 118 TYR cc_start: 0.5283 (OUTLIER) cc_final: 0.4421 (m-80) REVERT: 3 73 PHE cc_start: 0.6094 (m-80) cc_final: 0.5845 (m-80) REVERT: 7 316 PHE cc_start: 0.7628 (OUTLIER) cc_final: 0.7162 (p90) REVERT: 7 365 TYR cc_start: 0.1144 (OUTLIER) cc_final: -0.0879 (m-80) REVERT: 7 445 MET cc_start: 0.1936 (ptt) cc_final: 0.1046 (ptt) REVERT: 7 531 ILE cc_start: 0.4653 (OUTLIER) cc_final: 0.4434 (mp) REVERT: 7 676 HIS cc_start: 0.1764 (OUTLIER) cc_final: 0.1116 (p-80) REVERT: 7 695 ARG cc_start: 0.1247 (OUTLIER) cc_final: -0.0300 (ppt170) outliers start: 248 outliers final: 204 residues processed: 486 average time/residue: 1.1819 time to fit residues: 788.9477 Evaluate side-chains 463 residues out of total 7137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 217 poor density : 246 time to evaluate : 6.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 177 ASP Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 209 ASN Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 299 HIS Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 444 PHE Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 465 TYR Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 521 MET Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 724 GLU Chi-restraints excluded: chain A residue 743 VAL Chi-restraints excluded: chain A residue 758 ILE Chi-restraints excluded: chain A residue 764 CYS Chi-restraints excluded: chain A residue 886 ILE 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 1095 THR Chi-restraints excluded: chain A residue 1102 LYS Chi-restraints excluded: chain A residue 1120 LEU Chi-restraints excluded: chain A residue 1208 THR Chi-restraints excluded: chain A residue 1240 CYS Chi-restraints excluded: chain A residue 1260 LEU Chi-restraints excluded: chain A residue 1263 ILE Chi-restraints excluded: chain A residue 1272 THR Chi-restraints excluded: chain A residue 1335 ILE Chi-restraints excluded: chain A residue 1417 GLU Chi-restraints excluded: chain A residue 1445 ILE Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 64 CYS Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 310 MET Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 489 SER Chi-restraints excluded: chain B residue 493 SER Chi-restraints excluded: chain B residue 502 ILE Chi-restraints excluded: chain B residue 544 CYS Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 675 ASP Chi-restraints excluded: chain B residue 873 THR Chi-restraints excluded: chain B residue 895 ASP Chi-restraints excluded: chain B residue 933 SER Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 970 THR Chi-restraints excluded: chain B residue 976 ILE Chi-restraints excluded: chain B residue 1093 GLN Chi-restraints excluded: chain B residue 1113 VAL Chi-restraints excluded: chain B residue 1201 LYS Chi-restraints excluded: chain C residue 4 GLU Chi-restraints excluded: chain C residue 86 CYS Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 75 LYS Chi-restraints excluded: chain D residue 144 THR Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain D residue 206 GLU Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain G residue 33 GLU Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 47 CYS Chi-restraints excluded: chain G residue 54 ILE Chi-restraints excluded: chain G residue 73 LYS Chi-restraints excluded: chain G residue 74 TYR Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 145 VAL Chi-restraints excluded: chain H residue 53 ASP Chi-restraints excluded: chain H residue 92 ASP Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 131 ASN Chi-restraints excluded: chain I residue 7 CYS Chi-restraints excluded: chain I residue 8 ARG Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 49 MET Chi-restraints excluded: chain J residue 52 THR Chi-restraints excluded: chain K residue 10 PHE Chi-restraints excluded: chain L residue 34 CYS Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 40 LEU Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain M residue 47 LEU Chi-restraints excluded: chain M residue 51 VAL Chi-restraints excluded: chain M residue 96 ILE Chi-restraints excluded: chain M residue 100 GLU Chi-restraints excluded: chain M residue 119 MET Chi-restraints excluded: chain M residue 156 LEU Chi-restraints excluded: chain M residue 170 SER Chi-restraints excluded: chain M residue 195 LEU Chi-restraints excluded: chain M residue 197 HIS Chi-restraints excluded: chain M residue 200 THR Chi-restraints excluded: chain M residue 234 GLN Chi-restraints excluded: chain M residue 236 LEU Chi-restraints excluded: chain M residue 252 VAL Chi-restraints excluded: chain M residue 287 LEU Chi-restraints excluded: chain M residue 298 VAL Chi-restraints excluded: chain M residue 304 VAL Chi-restraints excluded: chain M residue 317 TYR Chi-restraints excluded: chain Q residue 116 THR Chi-restraints excluded: chain Q residue 119 LEU Chi-restraints excluded: chain Q residue 130 VAL Chi-restraints excluded: chain Q residue 332 LEU Chi-restraints excluded: chain Q residue 358 TYR Chi-restraints excluded: chain Q residue 386 MET Chi-restraints excluded: chain R residue 118 HIS Chi-restraints excluded: chain R residue 212 THR Chi-restraints excluded: chain R residue 222 CYS Chi-restraints excluded: chain R residue 254 THR Chi-restraints excluded: chain R residue 262 THR Chi-restraints excluded: chain W residue 32 ILE Chi-restraints excluded: chain W residue 105 VAL Chi-restraints excluded: chain W residue 120 ASN Chi-restraints excluded: chain X residue 220 THR Chi-restraints excluded: chain O residue 122 VAL Chi-restraints excluded: chain 0 residue 50 VAL Chi-restraints excluded: chain 0 residue 60 GLN Chi-restraints excluded: chain 0 residue 109 THR Chi-restraints excluded: chain 0 residue 110 SER Chi-restraints excluded: chain 0 residue 120 VAL Chi-restraints excluded: chain 0 residue 130 ASP Chi-restraints excluded: chain 0 residue 137 THR Chi-restraints excluded: chain 0 residue 162 LEU Chi-restraints excluded: chain 0 residue 204 ASN Chi-restraints excluded: chain 0 residue 221 ARG Chi-restraints excluded: chain 0 residue 284 ASP Chi-restraints excluded: chain 0 residue 298 ILE Chi-restraints excluded: chain 0 residue 318 THR Chi-restraints excluded: chain 0 residue 355 THR Chi-restraints excluded: chain 0 residue 407 THR Chi-restraints excluded: chain 0 residue 453 PHE Chi-restraints excluded: chain 0 residue 487 LEU Chi-restraints excluded: chain 0 residue 515 ASP Chi-restraints excluded: chain 0 residue 573 THR Chi-restraints excluded: chain 0 residue 597 ILE Chi-restraints excluded: chain 0 residue 673 LYS Chi-restraints excluded: chain 0 residue 706 LEU Chi-restraints excluded: chain 0 residue 741 TYR Chi-restraints excluded: chain 1 residue 213 ARG Chi-restraints excluded: chain 1 residue 214 ILE Chi-restraints excluded: chain 1 residue 600 VAL Chi-restraints excluded: chain 1 residue 630 TYR Chi-restraints excluded: chain 4 residue 32 ILE Chi-restraints excluded: chain 4 residue 153 MET Chi-restraints excluded: chain 4 residue 222 THR Chi-restraints excluded: chain 4 residue 234 VAL Chi-restraints excluded: chain 4 residue 236 LEU Chi-restraints excluded: chain 4 residue 245 ILE Chi-restraints excluded: chain 4 residue 276 CYS Chi-restraints excluded: chain 6 residue 116 THR Chi-restraints excluded: chain 6 residue 118 TYR Chi-restraints excluded: chain 6 residue 128 LEU Chi-restraints excluded: chain 6 residue 164 ASN Chi-restraints excluded: chain 6 residue 166 ILE Chi-restraints excluded: chain 6 residue 182 VAL Chi-restraints excluded: chain 6 residue 222 LEU Chi-restraints excluded: chain 6 residue 291 LEU Chi-restraints excluded: chain 6 residue 306 THR Chi-restraints excluded: chain 6 residue 448 LEU Chi-restraints excluded: chain 2 residue 11 THR Chi-restraints excluded: chain 2 residue 28 SER Chi-restraints excluded: chain 2 residue 348 TYR Chi-restraints excluded: chain 2 residue 353 SER Chi-restraints excluded: chain 2 residue 389 ASN Chi-restraints excluded: chain 2 residue 391 ILE Chi-restraints excluded: chain 2 residue 411 LEU Chi-restraints excluded: chain 2 residue 470 LEU Chi-restraints excluded: chain 2 residue 486 ASP Chi-restraints excluded: chain 5 residue 40 LEU Chi-restraints excluded: chain 3 residue 30 VAL Chi-restraints excluded: chain 3 residue 60 ASP Chi-restraints excluded: chain 7 residue 316 PHE Chi-restraints excluded: chain 7 residue 361 GLN Chi-restraints excluded: chain 7 residue 365 TYR Chi-restraints excluded: chain 7 residue 412 THR Chi-restraints excluded: chain 7 residue 500 ARG Chi-restraints excluded: chain 7 residue 505 ILE Chi-restraints excluded: chain 7 residue 527 LEU Chi-restraints excluded: chain 7 residue 531 ILE Chi-restraints excluded: chain 7 residue 572 GLU Chi-restraints excluded: chain 7 residue 613 TYR Chi-restraints excluded: chain 7 residue 656 LYS Chi-restraints excluded: chain 7 residue 676 HIS Chi-restraints excluded: chain 7 residue 695 ARG Chi-restraints excluded: chain 7 residue 735 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 786 random chunks: chunk 495 optimal weight: 20.0000 chunk 664 optimal weight: 10.0000 chunk 191 optimal weight: 3.9990 chunk 574 optimal weight: 6.9990 chunk 92 optimal weight: 0.9990 chunk 173 optimal weight: 7.9990 chunk 624 optimal weight: 6.9990 chunk 261 optimal weight: 3.9990 chunk 641 optimal weight: 0.9990 chunk 79 optimal weight: 0.8980 chunk 115 optimal weight: 7.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1048 ASN ** A1364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 706 GLN B 887 HIS C 203 GLN ** D 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 216 ASN F 104 ASN ** I 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 265 HIS X 251 ASN ** O 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 291 GLN ** 0 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 188 ASN 6 164 ASN 6 188 ASN ** 6 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 508 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.070430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.049720 restraints weight = 470824.122| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 3.68 r_work: 0.3064 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3048 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3048 r_free = 0.3048 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 633 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3048 r_free = 0.3048 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 634 | |-----------------------------------------------------------------------------| r_final: 0.3048 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.4112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.103 65557 Z= 0.250 Angle : 0.768 19.026 89048 Z= 0.385 Chirality : 0.046 0.450 10021 Planarity : 0.005 0.076 11121 Dihedral : 14.674 88.843 10372 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.89 % Favored : 91.98 % Rotamer: Outliers : 3.78 % Allowed : 26.76 % Favored : 69.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.03 % Twisted Proline : 1.18 % Twisted General : 0.09 % 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: -1.30 (0.10), residues: 7844 helix: 0.21 (0.09), residues: 3116 sheet: -1.01 (0.17), residues: 933 loop : -1.75 (0.10), residues: 3795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP X 263 HIS 0.013 0.001 HIS A 786 PHE 0.022 0.001 PHE A 219 TYR 0.046 0.001 TYR 1 630 ARG 0.011 0.000 ARG 7 681 =============================================================================== Job complete usr+sys time: 19700.75 seconds wall clock time: 343 minutes 22.64 seconds (20602.64 seconds total)