Starting phenix.real_space_refine on Tue Jun 17 10:39:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tk8_25960/06_2025/7tk8_25960.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tk8_25960/06_2025/7tk8_25960.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7tk8_25960/06_2025/7tk8_25960.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tk8_25960/06_2025/7tk8_25960.map" model { file = "/net/cci-nas-00/data/ceres_data/7tk8_25960/06_2025/7tk8_25960.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tk8_25960/06_2025/7tk8_25960.cif" } resolution = 4.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.118 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 3 Type Number sf(0) Gaussians C 10112 2.51 5 N 5056 2.21 5 O 5059 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 20227 Number of models: 1 Model: "" Number of chains: 27 Chain: "0" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 300 Classifications: {'peptide': 75} Incomplete info: {'backbone_only': 65} Link IDs: {'PTRANS': 2, 'TRANS': 72} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 246 Unresolved non-hydrogen angles: 363 Unresolved non-hydrogen dihedrals: 146 Unresolved non-hydrogen chiralities: 94 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1, 'PHE:plan': 6, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 75 Chain: "1" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 300 Classifications: {'peptide': 75} Incomplete info: {'backbone_only': 65} Link IDs: {'PTRANS': 2, 'TRANS': 72} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 246 Unresolved non-hydrogen angles: 363 Unresolved non-hydrogen dihedrals: 146 Unresolved non-hydrogen chiralities: 94 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1, 'PHE:plan': 6, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 75 Chain: "2" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 300 Classifications: {'peptide': 75} Incomplete info: {'backbone_only': 65} Link IDs: {'PTRANS': 2, 'TRANS': 72} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 246 Unresolved non-hydrogen angles: 363 Unresolved non-hydrogen dihedrals: 146 Unresolved non-hydrogen chiralities: 94 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1, 'PHE:plan': 6, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 75 Chain: "3" Number of atoms: 296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 296 Classifications: {'peptide': 74} Incomplete info: {'backbone_only': 64} Link IDs: {'PTRANS': 2, 'TRANS': 71} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 242 Unresolved non-hydrogen angles: 358 Unresolved non-hydrogen dihedrals: 143 Unresolved non-hydrogen chiralities: 93 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1, 'PHE:plan': 6, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 75 Chain: "4" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 300 Classifications: {'peptide': 75} Incomplete info: {'backbone_only': 65} Link IDs: {'PTRANS': 2, 'TRANS': 72} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 246 Unresolved non-hydrogen angles: 363 Unresolved non-hydrogen dihedrals: 146 Unresolved non-hydrogen chiralities: 94 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1, 'PHE:plan': 6, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 75 Chain: "5" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 300 Classifications: {'peptide': 75} Incomplete info: {'backbone_only': 65} Link IDs: {'PTRANS': 2, 'TRANS': 72} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 246 Unresolved non-hydrogen angles: 363 Unresolved non-hydrogen dihedrals: 146 Unresolved non-hydrogen chiralities: 94 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1, 'PHE:plan': 6, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 75 Chain: "6" Number of atoms: 296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 296 Classifications: {'peptide': 74} Incomplete info: {'backbone_only': 64} Link IDs: {'PTRANS': 2, 'TRANS': 71} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 242 Unresolved non-hydrogen angles: 358 Unresolved non-hydrogen dihedrals: 143 Unresolved non-hydrogen chiralities: 93 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1, 'PHE:plan': 6, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 75 Chain: "7" Number of atoms: 292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 292 Classifications: {'peptide': 73} Incomplete info: {'backbone_only': 64} Link IDs: {'PTRANS': 2, 'TRANS': 70} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 238 Unresolved non-hydrogen angles: 352 Unresolved non-hydrogen dihedrals: 139 Unresolved non-hydrogen chiralities: 93 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1, 'PHE:plan': 5, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 68 Chain: "8" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 300 Classifications: {'peptide': 75} Incomplete info: {'backbone_only': 65} Link IDs: {'PTRANS': 2, 'TRANS': 72} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 246 Unresolved non-hydrogen angles: 363 Unresolved non-hydrogen dihedrals: 146 Unresolved non-hydrogen chiralities: 94 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1, 'PHE:plan': 6, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 75 Chain: "9" Number of atoms: 296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 296 Classifications: {'peptide': 74} Incomplete info: {'backbone_only': 64} Link IDs: {'PTRANS': 2, 'TRANS': 71} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 242 Unresolved non-hydrogen angles: 358 Unresolved non-hydrogen dihedrals: 143 Unresolved non-hydrogen chiralities: 93 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1, 'PHE:plan': 6, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 75 Chain: "A" Number of atoms: 1996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 499, 1996 Classifications: {'peptide': 499} Incomplete info: {'backbone_only': 453} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 18, 'TRANS': 478} Chain breaks: 1 Unresolved chain link angles: 19 Unresolved non-hydrogen bonds: 1854 Unresolved non-hydrogen angles: 2698 Unresolved non-hydrogen dihedrals: 1123 Unresolved non-hydrogen chiralities: 606 Planarities with less than four sites: {'GLN:plan1': 25, 'HIS:plan': 6, 'TYR:plan': 14, 'ASN:plan1': 17, 'TRP:plan': 2, 'ASP:plan': 21, 'PHE:plan': 13, 'GLU:plan': 37, 'ARG:plan': 29} Unresolved non-hydrogen planarities: 804 Chain: "B" Number of atoms: 2020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 505, 2020 Classifications: {'peptide': 505} Incomplete info: {'backbone_only': 459} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 483} Chain breaks: 1 Unresolved chain link angles: 20 Unresolved non-hydrogen bonds: 1875 Unresolved non-hydrogen angles: 2729 Unresolved non-hydrogen dihedrals: 1135 Unresolved non-hydrogen chiralities: 614 Planarities with less than four sites: {'GLN:plan1': 26, 'HIS:plan': 6, 'TYR:plan': 14, 'ASN:plan1': 17, 'TRP:plan': 2, 'ASP:plan': 21, 'PHE:plan': 13, 'GLU:plan': 37, 'ARG:plan': 29} Unresolved non-hydrogen planarities: 808 Chain: "C" Number of atoms: 1992 Number of conformers: 1 Conformer: "" Number of residues, atoms: 498, 1992 Classifications: {'peptide': 498} Incomplete info: {'backbone_only': 451} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 18, 'TRANS': 477} Unresolved chain link angles: 19 Unresolved non-hydrogen bonds: 1852 Unresolved non-hydrogen angles: 2694 Unresolved non-hydrogen dihedrals: 1125 Unresolved non-hydrogen chiralities: 603 Planarities with less than four sites: {'GLN:plan1': 25, 'HIS:plan': 6, 'TYR:plan': 14, 'ASN:plan1': 17, 'TRP:plan': 2, 'ASP:plan': 21, 'PHE:plan': 14, 'GLU:plan': 36, 'ARG:plan': 29} Unresolved non-hydrogen planarities: 807 Chain: "D" Number of atoms: 1880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 1880 Classifications: {'peptide': 470} Incomplete info: {'backbone_only': 424} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 446} Unresolved chain link angles: 23 Unresolved non-hydrogen bonds: 1726 Unresolved non-hydrogen angles: 2519 Unresolved non-hydrogen dihedrals: 1034 Unresolved non-hydrogen chiralities: 580 Planarities with less than four sites: {'GLN:plan1': 18, 'ARG:plan': 22, 'TYR:plan': 10, 'ASN:plan1': 10, 'HIS:plan': 7, 'PHE:plan': 17, 'GLU:plan': 37, 'ASP:plan': 25} Unresolved non-hydrogen planarities: 711 Chain: "E" Number of atoms: 1872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 1872 Classifications: {'peptide': 468} Incomplete info: {'backbone_only': 422} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 445} Unresolved chain link angles: 22 Unresolved non-hydrogen bonds: 1721 Unresolved non-hydrogen angles: 2511 Unresolved non-hydrogen dihedrals: 1032 Unresolved non-hydrogen chiralities: 577 Planarities with less than four sites: {'GLN:plan1': 18, 'ARG:plan': 22, 'TYR:plan': 10, 'ASN:plan1': 10, 'HIS:plan': 7, 'PHE:plan': 17, 'GLU:plan': 37, 'ASP:plan': 25} Unresolved non-hydrogen planarities: 711 Chain: "F" Number of atoms: 1876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 1876 Classifications: {'peptide': 469} Incomplete info: {'backbone_only': 423} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 444} Unresolved chain link angles: 23 Unresolved non-hydrogen bonds: 1724 Unresolved non-hydrogen angles: 2516 Unresolved non-hydrogen dihedrals: 1033 Unresolved non-hydrogen chiralities: 579 Planarities with less than four sites: {'GLN:plan1': 18, 'ARG:plan': 22, 'TYR:plan': 10, 'ASN:plan1': 10, 'HIS:plan': 7, 'PHE:plan': 17, 'GLU:plan': 37, 'ASP:plan': 25} Unresolved non-hydrogen planarities: 711 Chain: "G" Number of atoms: 1060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 1060 Classifications: {'peptide': 265} Incomplete info: {'backbone_only': 255} Link IDs: {'PTRANS': 9, 'TRANS': 255} Chain breaks: 1 Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 1024 Unresolved non-hydrogen angles: 1472 Unresolved non-hydrogen dihedrals: 628 Unresolved non-hydrogen chiralities: 328 Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 3, 'TYR:plan': 7, 'ASN:plan1': 18, 'ASP:plan': 14, 'PHE:plan': 8, 'GLU:plan': 16, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 413 Chain: "H" Number of atoms: 479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 479 Classifications: {'peptide': 120} Incomplete info: {'backbone_only': 113, 'n_c_alpha_c_only': 1} Link IDs: {'PTRANS': 6, 'TRANS': 113} Chain breaks: 4 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 440 Unresolved non-hydrogen angles: 644 Unresolved non-hydrogen dihedrals: 258 Unresolved non-hydrogen chiralities: 151 Planarities with less than four sites: {'GLN:plan1': 7, 'ASP:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 7, 'HIS:plan': 2, 'PHE:plan': 5, 'GLU:plan': 13, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 177 Chain: "I" Number of atoms: 193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 193 Classifications: {'peptide': 48} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 47} Link IDs: {'PTRANS': 2, 'TRANS': 45} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 188 Unresolved non-hydrogen angles: 278 Unresolved non-hydrogen dihedrals: 114 Unresolved non-hydrogen chiralities: 62 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 4, 'ASN:plan1': 3, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 89 Chain: "O" Number of atoms: 748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 748 Classifications: {'peptide': 187} Incomplete info: {'backbone_only': 174} Link IDs: {'PTRANS': 7, 'TRANS': 179} Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 691 Unresolved non-hydrogen angles: 1001 Unresolved non-hydrogen dihedrals: 414 Unresolved non-hydrogen chiralities: 235 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 3, 'TYR:plan': 3, 'ASN:plan1': 12, 'ASP:plan': 10, 'PHE:plan': 5, 'GLU:plan': 11, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 249 Chain: "T" Number of atoms: 897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 897 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 207} Link IDs: {'PTRANS': 7, 'TRANS': 216} Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 925 Unresolved non-hydrogen angles: 1359 Unresolved non-hydrogen dihedrals: 607 Unresolved non-hydrogen chiralities: 306 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 3, 'TYR:plan': 10, 'ASN:plan1': 11, 'TRP:plan': 5, 'ASP:plan': 2, 'PHE:plan': 18, 'GLU:plan': 3, 'ARG:plan': 3, 'HIS%COO:plan': 1} Unresolved non-hydrogen planarities: 371 Chain: "U" Number of atoms: 620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 620 Classifications: {'peptide': 155} Incomplete info: {'backbone_only': 152} Link IDs: {'PTRANS': 2, 'TRANS': 152} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 631 Unresolved non-hydrogen angles: 908 Unresolved non-hydrogen dihedrals: 388 Unresolved non-hydrogen chiralities: 198 Planarities with less than four sites: {'GLN:plan1': 11, 'HIS:plan': 2, 'TYR:plan': 3, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 8, 'PHE:plan': 6, 'GLU:plan': 16, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 283 Chain: "V" Number of atoms: 685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 685 Classifications: {'peptide': 171} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 166} Link IDs: {'PTRANS': 5, 'TRANS': 165} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 705 Unresolved non-hydrogen angles: 1009 Unresolved non-hydrogen dihedrals: 446 Unresolved non-hydrogen chiralities: 214 Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 2, 'TYR:plan': 4, 'ASN:plan1': 7, 'TRP:plan': 2, 'ASP:plan': 13, 'PHE:plan': 5, 'GLU:plan': 13, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 302 Chain: "W" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 340 Classifications: {'peptide': 85} Incomplete info: {'backbone_only': 79} Link IDs: {'PTRANS': 7, 'TRANS': 77} Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 348 Unresolved non-hydrogen angles: 503 Unresolved non-hydrogen dihedrals: 241 Unresolved non-hydrogen chiralities: 97 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 2, 'TYR:plan': 6, 'ASN:plan1': 5, 'TRP:plan': 1, 'HIS:plan': 3, 'PHE:plan': 5, 'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 162 Chain: "X" Number of atoms: 248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 248 Classifications: {'peptide': 62} Incomplete info: {'backbone_only': 60} Link IDs: {'PTRANS': 7, 'TRANS': 54} Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 257 Unresolved non-hydrogen angles: 375 Unresolved non-hydrogen dihedrals: 161 Unresolved non-hydrogen chiralities: 77 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 3, 'GLU:plan': 7, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 117 Chain: "Y" Number of atoms: 148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 148 Classifications: {'peptide': 37} Incomplete info: {'backbone_only': 35} Link IDs: {'PTRANS': 3, 'TRANS': 33} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 155 Unresolved non-hydrogen angles: 225 Unresolved non-hydrogen dihedrals: 110 Unresolved non-hydrogen chiralities: 44 Planarities with less than four sites: {'TYR:plan': 3, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 68 Chain: "Z" Number of atoms: 193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 193 Classifications: {'peptide': 48} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 46} Link IDs: {'PTRANS': 3, 'TRANS': 44} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 231 Unresolved non-hydrogen angles: 330 Unresolved non-hydrogen dihedrals: 158 Unresolved non-hydrogen chiralities: 67 Planarities with less than four sites: {'GLN:plan1': 3, 'PHE:plan': 7, 'ASN:plan1': 1, 'ARG:plan': 2, 'TYR:plan': 3} Unresolved non-hydrogen planarities: 99 Time building chain proxies: 13.83, per 1000 atoms: 0.68 Number of scatterers: 20227 At special positions: 0 Unit cell: (126.665, 150.92, 235.812, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 5059 8.00 N 5056 7.00 C 10112 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.96 Conformation dependent library (CDL) restraints added in 4.1 seconds 9968 Ramachandran restraints generated. 4984 Oldfield, 0 Emsley, 4984 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 0 Finding SS restraints... Secondary structure from input PDB file: 208 helices and 29 sheets defined 60.7% alpha, 11.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.39 Creating SS restraints... Processing helix chain '0' and resid 1 through 17 removed outlier: 3.824A pdb=" N ILE 0 17 " --> pdb=" O GLY 0 13 " (cutoff:3.500A) Processing helix chain '0' and resid 18 through 40 removed outlier: 4.332A pdb=" N ALA 0 22 " --> pdb=" O GLY 0 18 " (cutoff:3.500A) Processing helix chain '0' and resid 43 through 75 Proline residue: 0 49 - end of helix removed outlier: 3.510A pdb=" N THR 0 61 " --> pdb=" O LEU 0 57 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLY 0 62 " --> pdb=" O SER 0 58 " (cutoff:3.500A) Processing helix chain '1' and resid 2 through 17 removed outlier: 3.815A pdb=" N GLY 1 13 " --> pdb=" O TYR 1 9 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ILE 1 17 " --> pdb=" O GLY 1 13 " (cutoff:3.500A) Processing helix chain '1' and resid 18 through 40 removed outlier: 4.311A pdb=" N ALA 1 22 " --> pdb=" O GLY 1 18 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ALA 1 27 " --> pdb=" O GLY 1 23 " (cutoff:3.500A) Processing helix chain '1' and resid 43 through 74 Proline residue: 1 49 - end of helix removed outlier: 3.556A pdb=" N CYS 1 65 " --> pdb=" O THR 1 61 " (cutoff:3.500A) Processing helix chain '2' and resid 2 through 16 Processing helix chain '2' and resid 18 through 39 removed outlier: 4.303A pdb=" N ALA 2 22 " --> pdb=" O GLY 2 18 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ALA 2 27 " --> pdb=" O GLY 2 23 " (cutoff:3.500A) Processing helix chain '2' and resid 43 through 74 Proline residue: 2 49 - end of helix removed outlier: 4.107A pdb=" N THR 2 61 " --> pdb=" O LEU 2 57 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N GLY 2 62 " --> pdb=" O SER 2 58 " (cutoff:3.500A) Processing helix chain '3' and resid 3 through 17 removed outlier: 3.987A pdb=" N ILE 3 17 " --> pdb=" O GLY 3 13 " (cutoff:3.500A) Processing helix chain '3' and resid 18 through 40 removed outlier: 4.105A pdb=" N ALA 3 22 " --> pdb=" O GLY 3 18 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA 3 27 " --> pdb=" O GLY 3 23 " (cutoff:3.500A) Processing helix chain '3' and resid 43 through 74 Proline residue: 3 49 - end of helix removed outlier: 3.891A pdb=" N GLY 3 62 " --> pdb=" O SER 3 58 " (cutoff:3.500A) Processing helix chain '4' and resid 2 through 16 removed outlier: 3.517A pdb=" N TYR 4 9 " --> pdb=" O LEU 4 5 " (cutoff:3.500A) Processing helix chain '4' and resid 18 through 40 removed outlier: 4.289A pdb=" N ALA 4 22 " --> pdb=" O GLY 4 18 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA 4 27 " --> pdb=" O GLY 4 23 " (cutoff:3.500A) Processing helix chain '4' and resid 43 through 74 Proline residue: 4 49 - end of helix removed outlier: 3.933A pdb=" N THR 4 61 " --> pdb=" O LEU 4 57 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N GLY 4 62 " --> pdb=" O SER 4 58 " (cutoff:3.500A) Processing helix chain '5' and resid 2 through 17 removed outlier: 3.643A pdb=" N ILE 5 17 " --> pdb=" O GLY 5 13 " (cutoff:3.500A) Processing helix chain '5' and resid 18 through 40 removed outlier: 4.070A pdb=" N ALA 5 22 " --> pdb=" O GLY 5 18 " (cutoff:3.500A) Processing helix chain '5' and resid 43 through 75 Proline residue: 5 49 - end of helix removed outlier: 3.517A pdb=" N LEU 5 57 " --> pdb=" O LEU 5 53 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLY 5 62 " --> pdb=" O SER 5 58 " (cutoff:3.500A) Processing helix chain '6' and resid 3 through 16 removed outlier: 3.557A pdb=" N THR 6 16 " --> pdb=" O ALA 6 12 " (cutoff:3.500A) Processing helix chain '6' and resid 18 through 40 removed outlier: 4.494A pdb=" N ALA 6 22 " --> pdb=" O GLY 6 18 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA 6 27 " --> pdb=" O GLY 6 23 " (cutoff:3.500A) Processing helix chain '6' and resid 43 through 75 Proline residue: 6 49 - end of helix removed outlier: 3.540A pdb=" N THR 6 61 " --> pdb=" O LEU 6 57 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLY 6 62 " --> pdb=" O SER 6 58 " (cutoff:3.500A) Processing helix chain '7' and resid 2 through 40 removed outlier: 3.558A pdb=" N THR 7 16 " --> pdb=" O ALA 7 12 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N ILE 7 17 " --> pdb=" O GLY 7 13 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N GLY 7 18 " --> pdb=" O ILE 7 14 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N LEU 7 19 " --> pdb=" O SER 7 15 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU 7 20 " --> pdb=" O THR 7 16 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N GLY 7 21 " --> pdb=" O ILE 7 17 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ALA 7 22 " --> pdb=" O GLY 7 18 " (cutoff:3.500A) Processing helix chain '7' and resid 43 through 73 Proline residue: 7 49 - end of helix removed outlier: 3.800A pdb=" N GLY 7 62 " --> pdb=" O SER 7 58 " (cutoff:3.500A) Processing helix chain '8' and resid 2 through 17 removed outlier: 3.516A pdb=" N THR 8 16 " --> pdb=" O ALA 8 12 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ILE 8 17 " --> pdb=" O GLY 8 13 " (cutoff:3.500A) Processing helix chain '8' and resid 18 through 40 removed outlier: 4.282A pdb=" N ALA 8 22 " --> pdb=" O GLY 8 18 " (cutoff:3.500A) Processing helix chain '8' and resid 43 through 75 Proline residue: 8 49 - end of helix removed outlier: 3.947A pdb=" N THR 8 61 " --> pdb=" O LEU 8 57 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLY 8 62 " --> pdb=" O SER 8 58 " (cutoff:3.500A) Processing helix chain '9' and resid 3 through 17 removed outlier: 3.732A pdb=" N ILE 9 17 " --> pdb=" O GLY 9 13 " (cutoff:3.500A) Processing helix chain '9' and resid 18 through 40 removed outlier: 4.406A pdb=" N ALA 9 22 " --> pdb=" O GLY 9 18 " (cutoff:3.500A) Processing helix chain '9' and resid 43 through 75 Proline residue: 9 49 - end of helix removed outlier: 3.558A pdb=" N GLY 9 62 " --> pdb=" O SER 9 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 20 Processing helix chain 'A' and resid 80 through 84 Processing helix chain 'A' and resid 102 through 106 removed outlier: 4.043A pdb=" N LEU A 105 " --> pdb=" O GLY A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 159 removed outlier: 3.545A pdb=" N ALA A 157 " --> pdb=" O LYS A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 194 removed outlier: 3.820A pdb=" N THR A 184 " --> pdb=" O VAL A 180 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE A 185 " --> pdb=" O ALA A 181 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYS A 189 " --> pdb=" O ILE A 185 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ARG A 190 " --> pdb=" O LEU A 186 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N TRP A 191 " --> pdb=" O ASN A 187 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLY A 194 " --> pdb=" O ARG A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 200 Processing helix chain 'A' and resid 211 through 225 Processing helix chain 'A' and resid 241 through 262 Proline residue: A 249 - end of helix removed outlier: 4.061A pdb=" N PHE A 259 " --> pdb=" O ILE A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 287 removed outlier: 3.534A pdb=" N VAL A 278 " --> pdb=" O SER A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 296 Processing helix chain 'A' and resid 297 through 298 No H-bonds generated for 'chain 'A' and resid 297 through 298' Processing helix chain 'A' and resid 299 through 309 Processing helix chain 'A' and resid 338 through 348 Processing helix chain 'A' and resid 355 through 361 Processing helix chain 'A' and resid 376 through 381 Processing helix chain 'A' and resid 382 through 388 Processing helix chain 'A' and resid 389 through 402 removed outlier: 3.756A pdb=" N LYS A 393 " --> pdb=" O ALA A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 407 removed outlier: 3.717A pdb=" N GLN A 407 " --> pdb=" O ALA A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 430 Processing helix chain 'A' and resid 439 through 452 Proline residue: A 445 - end of helix Processing helix chain 'A' and resid 453 through 458 removed outlier: 4.090A pdb=" N GLY A 457 " --> pdb=" O GLY A 453 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE A 458 " --> pdb=" O HIS A 454 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 453 through 458' Processing helix chain 'A' and resid 459 through 478 removed outlier: 4.331A pdb=" N GLY A 464 " --> pdb=" O LEU A 460 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N GLU A 465 " --> pdb=" O SER A 461 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N SER A 468 " --> pdb=" O GLY A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 489 Processing helix chain 'A' and resid 492 through 509 Processing helix chain 'B' and resid 10 through 19 Processing helix chain 'B' and resid 24 through 28 Processing helix chain 'B' and resid 80 through 84 removed outlier: 4.147A pdb=" N LEU B 83 " --> pdb=" O SER B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 157 removed outlier: 3.525A pdb=" N ALA B 157 " --> pdb=" O ALA B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 188 removed outlier: 3.529A pdb=" N VAL B 180 " --> pdb=" O GLY B 176 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ALA B 181 " --> pdb=" O LYS B 177 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N THR B 184 " --> pdb=" O VAL B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 193 Processing helix chain 'B' and resid 211 through 225 Processing helix chain 'B' and resid 227 through 229 No H-bonds generated for 'chain 'B' and resid 227 through 229' Processing helix chain 'B' and resid 241 through 261 Proline residue: B 249 - end of helix removed outlier: 3.931A pdb=" N PHE B 259 " --> pdb=" O ILE B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 287 Processing helix chain 'B' and resid 292 through 296 Processing helix chain 'B' and resid 299 through 309 Processing helix chain 'B' and resid 315 through 319 Processing helix chain 'B' and resid 338 through 348 Processing helix chain 'B' and resid 355 through 361 Processing helix chain 'B' and resid 376 through 380 Processing helix chain 'B' and resid 383 through 388 Processing helix chain 'B' and resid 391 through 407 removed outlier: 4.147A pdb=" N GLU B 401 " --> pdb=" O ALA B 397 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLN B 407 " --> pdb=" O ALA B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 431 removed outlier: 3.598A pdb=" N LYS B 431 " --> pdb=" O THR B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 452 Proline residue: B 445 - end of helix Processing helix chain 'B' and resid 453 through 457 removed outlier: 3.653A pdb=" N ASP B 456 " --> pdb=" O GLY B 453 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLY B 457 " --> pdb=" O HIS B 454 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 453 through 457' Processing helix chain 'B' and resid 459 through 461 No H-bonds generated for 'chain 'B' and resid 459 through 461' Processing helix chain 'B' and resid 462 through 478 Processing helix chain 'B' and resid 479 through 488 Processing helix chain 'B' and resid 492 through 509 Processing helix chain 'C' and resid 13 through 21 Processing helix chain 'C' and resid 102 through 106 removed outlier: 3.808A pdb=" N LEU C 105 " --> pdb=" O GLY C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 159 Processing helix chain 'C' and resid 176 through 188 removed outlier: 4.103A pdb=" N ALA C 181 " --> pdb=" O LYS C 177 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N THR C 184 " --> pdb=" O VAL C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 188 through 194 removed outlier: 3.642A pdb=" N GLY C 194 " --> pdb=" O ARG C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 200 Processing helix chain 'C' and resid 211 through 225 Processing helix chain 'C' and resid 241 through 263 Proline residue: C 249 - end of helix removed outlier: 3.862A pdb=" N PHE C 259 " --> pdb=" O ILE C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 286 removed outlier: 3.502A pdb=" N VAL C 278 " --> pdb=" O SER C 274 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 296 Processing helix chain 'C' and resid 299 through 309 Processing helix chain 'C' and resid 332 through 335 Processing helix chain 'C' and resid 338 through 348 Processing helix chain 'C' and resid 355 through 361 Processing helix chain 'C' and resid 376 through 380 removed outlier: 3.958A pdb=" N ALA C 379 " --> pdb=" O VAL C 376 " (cutoff:3.500A) Processing helix chain 'C' and resid 382 through 389 Processing helix chain 'C' and resid 391 through 408 removed outlier: 3.694A pdb=" N PHE C 408 " --> pdb=" O ALA C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 431 Processing helix chain 'C' and resid 439 through 442 Processing helix chain 'C' and resid 443 through 452 Processing helix chain 'C' and resid 453 through 458 Processing helix chain 'C' and resid 459 through 461 No H-bonds generated for 'chain 'C' and resid 459 through 461' Processing helix chain 'C' and resid 462 through 477 Processing helix chain 'C' and resid 478 through 489 Processing helix chain 'C' and resid 492 through 508 removed outlier: 3.895A pdb=" N ALA C 508 " --> pdb=" O GLU C 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 145 Processing helix chain 'D' and resid 162 through 178 removed outlier: 4.395A pdb=" N LYS D 176 " --> pdb=" O ASN D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 204 Processing helix chain 'D' and resid 225 through 231 Processing helix chain 'D' and resid 231 through 245 removed outlier: 3.953A pdb=" N THR D 235 " --> pdb=" O ARG D 231 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 273 removed outlier: 3.729A pdb=" N PHE D 261 " --> pdb=" O ASN D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 277 through 281 Processing helix chain 'D' and resid 284 through 296 removed outlier: 3.714A pdb=" N ILE D 296 " --> pdb=" O LEU D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 313 through 316 Processing helix chain 'D' and resid 319 through 329 removed outlier: 3.714A pdb=" N ALA D 327 " --> pdb=" O ALA D 323 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N HIS D 328 " --> pdb=" O THR D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 336 through 342 Processing helix chain 'D' and resid 359 through 364 Processing helix chain 'D' and resid 364 through 391 removed outlier: 4.016A pdb=" N ASP D 386 " --> pdb=" O LYS D 382 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ILE D 387 " --> pdb=" O SER D 383 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ILE D 390 " --> pdb=" O ASP D 386 " (cutoff:3.500A) Processing helix chain 'D' and resid 397 through 414 Processing helix chain 'D' and resid 418 through 422 Processing helix chain 'D' and resid 433 through 447 Processing helix chain 'D' and resid 453 through 457 Processing helix chain 'D' and resid 462 through 475 Processing helix chain 'E' and resid 138 through 145 Processing helix chain 'E' and resid 162 through 178 Processing helix chain 'E' and resid 190 through 204 Processing helix chain 'E' and resid 225 through 248 removed outlier: 4.705A pdb=" N ALA E 233 " --> pdb=" O ARG E 229 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N LEU E 234 " --> pdb=" O ALA E 230 " (cutoff:3.500A) Processing helix chain 'E' and resid 258 through 273 Processing helix chain 'E' and resid 284 through 296 removed outlier: 3.531A pdb=" N ILE E 296 " --> pdb=" O LEU E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 319 through 329 removed outlier: 3.530A pdb=" N ALA E 323 " --> pdb=" O ASP E 319 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N HIS E 328 " --> pdb=" O THR E 324 " (cutoff:3.500A) Processing helix chain 'E' and resid 336 through 342 Processing helix chain 'E' and resid 359 through 364 Processing helix chain 'E' and resid 364 through 392 removed outlier: 3.996A pdb=" N ILE E 387 " --> pdb=" O SER E 383 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ILE E 390 " --> pdb=" O ASP E 386 " (cutoff:3.500A) Processing helix chain 'E' and resid 393 through 396 Processing helix chain 'E' and resid 397 through 414 Processing helix chain 'E' and resid 421 through 426 Processing helix chain 'E' and resid 433 through 446 removed outlier: 3.556A pdb=" N PHE E 441 " --> pdb=" O THR E 437 " (cutoff:3.500A) Processing helix chain 'E' and resid 453 through 458 Processing helix chain 'E' and resid 462 through 475 removed outlier: 3.771A pdb=" N ALA E 468 " --> pdb=" O GLU E 464 " (cutoff:3.500A) Processing helix chain 'F' and resid 138 through 145 Processing helix chain 'F' and resid 162 through 179 removed outlier: 4.751A pdb=" N LYS F 176 " --> pdb=" O ASN F 172 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ALA F 177 " --> pdb=" O ASN F 173 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLY F 179 " --> pdb=" O ALA F 175 " (cutoff:3.500A) Processing helix chain 'F' and resid 190 through 204 Processing helix chain 'F' and resid 225 through 245 removed outlier: 3.523A pdb=" N ARG F 231 " --> pdb=" O GLY F 227 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ALA F 233 " --> pdb=" O ARG F 229 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N LEU F 234 " --> pdb=" O ALA F 230 " (cutoff:3.500A) Processing helix chain 'F' and resid 258 through 273 removed outlier: 3.899A pdb=" N ALA F 270 " --> pdb=" O SER F 266 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU F 271 " --> pdb=" O GLU F 267 " (cutoff:3.500A) Processing helix chain 'F' and resid 277 through 281 removed outlier: 3.602A pdb=" N TYR F 281 " --> pdb=" O ALA F 278 " (cutoff:3.500A) Processing helix chain 'F' and resid 282 through 283 No H-bonds generated for 'chain 'F' and resid 282 through 283' Processing helix chain 'F' and resid 284 through 296 Processing helix chain 'F' and resid 313 through 316 Processing helix chain 'F' and resid 319 through 327 removed outlier: 3.799A pdb=" N ALA F 327 " --> pdb=" O ALA F 323 " (cutoff:3.500A) Processing helix chain 'F' and resid 336 through 342 Processing helix chain 'F' and resid 364 through 384 Processing helix chain 'F' and resid 384 through 391 Processing helix chain 'F' and resid 392 through 396 removed outlier: 3.540A pdb=" N LEU F 396 " --> pdb=" O MET F 393 " (cutoff:3.500A) Processing helix chain 'F' and resid 397 through 414 Processing helix chain 'F' and resid 421 through 426 Processing helix chain 'F' and resid 433 through 446 removed outlier: 3.509A pdb=" N ALA F 439 " --> pdb=" O LYS F 435 " (cutoff:3.500A) Processing helix chain 'F' and resid 453 through 458 removed outlier: 3.599A pdb=" N PHE F 457 " --> pdb=" O PRO F 453 " (cutoff:3.500A) Processing helix chain 'F' and resid 462 through 475 Processing helix chain 'G' and resid 2 through 56 removed outlier: 3.890A pdb=" N LYS G 33 " --> pdb=" O THR G 29 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N SER G 40 " --> pdb=" O LYS G 36 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU G 48 " --> pdb=" O MET G 44 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N PHE G 51 " --> pdb=" O ALA G 47 " (cutoff:3.500A) Processing helix chain 'G' and resid 86 through 99 removed outlier: 3.568A pdb=" N HIS G 98 " --> pdb=" O ALA G 94 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 122 removed outlier: 3.766A pdb=" N LYS G 115 " --> pdb=" O GLY G 111 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLN G 117 " --> pdb=" O LYS G 113 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG G 120 " --> pdb=" O MET G 116 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N THR G 121 " --> pdb=" O GLN G 117 " (cutoff:3.500A) Processing helix chain 'G' and resid 139 through 153 Processing helix chain 'G' and resid 155 through 159 Processing helix chain 'G' and resid 184 through 191 Processing helix chain 'G' and resid 204 through 276 removed outlier: 4.194A pdb=" N GLU G 211 " --> pdb=" O ARG G 207 " (cutoff:3.500A) Processing helix chain 'H' and resid 93 through 97 Processing helix chain 'H' and resid 100 through 115 removed outlier: 4.120A pdb=" N SER H 113 " --> pdb=" O LYS H 109 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N SER H 114 " --> pdb=" O LYS H 110 " (cutoff:3.500A) Processing helix chain 'H' and resid 119 through 136 removed outlier: 3.535A pdb=" N VAL H 136 " --> pdb=" O ASN H 132 " (cutoff:3.500A) Processing helix chain 'I' and resid 9 through 22 Processing helix chain 'I' and resid 31 through 37 Processing helix chain 'O' and resid 16 through 29 removed outlier: 3.843A pdb=" N ALA O 20 " --> pdb=" O GLU O 16 " (cutoff:3.500A) Processing helix chain 'O' and resid 33 through 49 Processing helix chain 'O' and resid 63 through 78 removed outlier: 3.750A pdb=" N HIS O 78 " --> pdb=" O ILE O 74 " (cutoff:3.500A) Processing helix chain 'O' and resid 83 through 95 Processing helix chain 'O' and resid 101 through 117 Processing helix chain 'O' and resid 130 through 144 Processing helix chain 'O' and resid 180 through 191 Processing helix chain 'T' and resid 27 through 43 removed outlier: 3.628A pdb=" N SER T 42 " --> pdb=" O LEU T 38 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU T 43 " --> pdb=" O VAL T 39 " (cutoff:3.500A) Processing helix chain 'T' and resid 58 through 77 removed outlier: 4.192A pdb=" N GLN T 62 " --> pdb=" O TRP T 58 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N TYR T 66 " --> pdb=" O GLN T 62 " (cutoff:3.500A) Processing helix chain 'T' and resid 82 through 84 No H-bonds generated for 'chain 'T' and resid 82 through 84' Processing helix chain 'T' and resid 85 through 103 removed outlier: 3.726A pdb=" N ILE T 96 " --> pdb=" O LEU T 92 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N LEU T 101 " --> pdb=" O PHE T 97 " (cutoff:3.500A) Processing helix chain 'T' and resid 114 through 137 removed outlier: 3.773A pdb=" N ILE T 118 " --> pdb=" O HIS T 114 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU T 132 " --> pdb=" O GLY T 128 " (cutoff:3.500A) Processing helix chain 'T' and resid 139 through 145 removed outlier: 3.535A pdb=" N PHE T 142 " --> pdb=" O TRP T 139 " (cutoff:3.500A) Processing helix chain 'T' and resid 151 through 155 Processing helix chain 'T' and resid 156 through 167 removed outlier: 3.988A pdb=" N GLU T 162 " --> pdb=" O LEU T 158 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N SER T 165 " --> pdb=" O ILE T 161 " (cutoff:3.500A) Processing helix chain 'T' and resid 168 through 199 removed outlier: 4.083A pdb=" N LEU T 173 " --> pdb=" O ARG T 169 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N GLY T 174 " --> pdb=" O ALA T 170 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU T 177 " --> pdb=" O LEU T 173 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N MET T 199 " --> pdb=" O THR T 195 " (cutoff:3.500A) Processing helix chain 'T' and resid 202 through 207 removed outlier: 3.561A pdb=" N LEU T 206 " --> pdb=" O ASN T 202 " (cutoff:3.500A) Processing helix chain 'T' and resid 210 through 247 removed outlier: 3.529A pdb=" N MET T 215 " --> pdb=" O VAL T 211 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA T 239 " --> pdb=" O ALA T 235 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU T 242 " --> pdb=" O THR T 238 " (cutoff:3.500A) Processing helix chain 'U' and resid 54 through 186 removed outlier: 3.682A pdb=" N LEU U 58 " --> pdb=" O ASP U 54 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ALA U 74 " --> pdb=" O ALA U 70 " (cutoff:3.500A) Proline residue: U 75 - end of helix removed outlier: 3.510A pdb=" N GLN U 112 " --> pdb=" O ASP U 108 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU U 113 " --> pdb=" O SER U 109 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASN U 115 " --> pdb=" O SER U 111 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLU U 118 " --> pdb=" O GLN U 114 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N LYS U 121 " --> pdb=" O ALA U 117 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N VAL U 122 " --> pdb=" O GLU U 118 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLU U 139 " --> pdb=" O SER U 135 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER U 175 " --> pdb=" O GLN U 171 " (cutoff:3.500A) Processing helix chain 'U' and resid 187 through 206 removed outlier: 3.927A pdb=" N VAL U 193 " --> pdb=" O PHE U 189 " (cutoff:3.500A) Processing helix chain 'V' and resid 4 through 19 Processing helix chain 'V' and resid 26 through 48 Processing helix chain 'V' and resid 57 through 62 Processing helix chain 'V' and resid 67 through 78 Processing helix chain 'V' and resid 90 through 126 removed outlier: 3.573A pdb=" N SER V 94 " --> pdb=" O GLN V 90 " (cutoff:3.500A) Processing helix chain 'V' and resid 134 through 142 removed outlier: 3.787A pdb=" N LEU V 138 " --> pdb=" O THR V 134 " (cutoff:3.500A) Processing helix chain 'V' and resid 143 through 156 removed outlier: 3.520A pdb=" N GLY V 156 " --> pdb=" O MET V 152 " (cutoff:3.500A) Processing helix chain 'V' and resid 162 through 166 Processing helix chain 'W' and resid 5 through 9 removed outlier: 3.944A pdb=" N LYS W 8 " --> pdb=" O ILE W 5 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL W 9 " --> pdb=" O PRO W 6 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 5 through 9' Processing helix chain 'W' and resid 12 through 17 removed outlier: 3.856A pdb=" N SER W 17 " --> pdb=" O LYS W 13 " (cutoff:3.500A) Processing helix chain 'W' and resid 18 through 30 removed outlier: 4.338A pdb=" N LYS W 22 " --> pdb=" O ALA W 18 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N VAL W 28 " --> pdb=" O ILE W 24 " (cutoff:3.500A) Processing helix chain 'W' and resid 48 through 56 Processing helix chain 'W' and resid 63 through 85 removed outlier: 3.916A pdb=" N ILE W 73 " --> pdb=" O PHE W 69 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE W 76 " --> pdb=" O GLY W 72 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY W 77 " --> pdb=" O ILE W 73 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER W 79 " --> pdb=" O ALA W 75 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N TYR W 82 " --> pdb=" O TYR W 78 " (cutoff:3.500A) Processing helix chain 'X' and resid 2 through 14 Processing helix chain 'X' and resid 20 through 27 removed outlier: 3.533A pdb=" N ASN X 27 " --> pdb=" O ASP X 23 " (cutoff:3.500A) Processing helix chain 'X' and resid 45 through 57 removed outlier: 4.042A pdb=" N ALA X 49 " --> pdb=" O GLN X 45 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LEU X 50 " --> pdb=" O GLY X 46 " (cutoff:3.500A) Processing helix chain 'Y' and resid 13 through 35 Processing helix chain 'Z' and resid 1 through 5 Processing helix chain 'Z' and resid 8 through 30 Processing helix chain 'Z' and resid 30 through 48 removed outlier: 3.825A pdb=" N LEU Z 38 " --> pdb=" O MET Z 34 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 37 removed outlier: 6.997A pdb=" N ARG A 42 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N VAL A 36 " --> pdb=" O ILE A 40 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ILE A 40 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N GLY A 74 " --> pdb=" O LEU A 66 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LEU A 66 " --> pdb=" O GLY A 74 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 10 through 17 current: chain 'A' and resid 90 through 96 Processing sheet with id=AA2, first strand: chain 'A' and resid 31 through 37 removed outlier: 6.997A pdb=" N ARG A 42 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N VAL A 36 " --> pdb=" O ILE A 40 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ILE A 40 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N GLY A 74 " --> pdb=" O LEU A 66 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LEU A 66 " --> pdb=" O GLY A 74 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 62 through 68 current: chain 'E' and resid 36 through 41 removed outlier: 6.159A pdb=" N ARG E 60 " --> pdb=" O ALA E 51 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N VAL E 23 " --> pdb=" O VAL E 59 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL E 21 " --> pdb=" O THR E 61 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ILE E 20 " --> pdb=" O VAL E 16 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N VAL E 16 " --> pdb=" O ILE E 20 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N ASP E 22 " --> pdb=" O THR E 14 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 10 through 17 current: chain 'A' and resid 90 through 96 Processing sheet with id=AA3, first strand: chain 'A' and resid 98 through 101 Processing sheet with id=AA4, first strand: chain 'A' and resid 108 through 111 removed outlier: 3.564A pdb=" N ILE A 233 " --> pdb=" O ARG A 108 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N TYR A 205 " --> pdb=" O VAL A 234 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N ALA A 236 " --> pdb=" O TYR A 205 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N ALA A 207 " --> pdb=" O ALA A 236 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 172 removed outlier: 5.952A pdb=" N ILE A 169 " --> pdb=" O ILE A 329 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N THR A 331 " --> pdb=" O ILE A 169 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N GLY A 171 " --> pdb=" O THR A 331 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 350 through 354 removed outlier: 4.712A pdb=" N PHE A 353 " --> pdb=" O LEU A 371 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N LEU A 371 " --> pdb=" O PHE A 353 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 77 through 78 removed outlier: 6.743A pdb=" N ARG F 60 " --> pdb=" O ALA F 51 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ILE F 17 " --> pdb=" O ILE F 20 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N HIS F 24 " --> pdb=" O VAL F 13 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N VAL F 13 " --> pdb=" O HIS F 24 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N GLY B 63 " --> pdb=" O PHE B 78 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N PHE B 78 " --> pdb=" O GLY B 63 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N ALA B 65 " --> pdb=" O VAL B 76 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N VAL B 76 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N ILE B 40 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N VAL B 36 " --> pdb=" O ILE B 40 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N ARG B 42 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N LEU B 54 " --> pdb=" O THR B 93 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N GLU B 53 " --> pdb=" O ALA B 65 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 98 through 101 Processing sheet with id=AA9, first strand: chain 'B' and resid 109 through 111 removed outlier: 6.171A pdb=" N CYS B 203 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N VAL B 234 " --> pdb=" O CYS B 203 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N TYR B 205 " --> pdb=" O VAL B 234 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N ALA B 236 " --> pdb=" O TYR B 205 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N ALA B 207 " --> pdb=" O ALA B 236 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ALA B 266 " --> pdb=" O THR B 324 " (cutoff:3.500A) removed outlier: 8.367A pdb=" N LEU B 326 " --> pdb=" O ALA B 266 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ILE B 268 " --> pdb=" O LEU B 326 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N VAL B 328 " --> pdb=" O ILE B 268 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N TYR B 270 " --> pdb=" O VAL B 328 " (cutoff:3.500A) removed outlier: 8.177A pdb=" N GLU B 330 " --> pdb=" O TYR B 270 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N PHE B 353 " --> pdb=" O LEU B 371 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N LEU B 371 " --> pdb=" O PHE B 353 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 147 through 148 removed outlier: 4.441A pdb=" N ILE B 161 " --> pdb=" O VAL B 148 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 30 through 33 removed outlier: 3.502A pdb=" N ASN C 67 " --> pdb=" O GLY C 74 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N VAL C 76 " --> pdb=" O ALA C 65 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N ALA C 65 " --> pdb=" O VAL C 76 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N GLU C 53 " --> pdb=" O ALA C 65 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N LEU C 54 " --> pdb=" O THR C 93 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 98 through 101 Processing sheet with id=AB4, first strand: chain 'C' and resid 108 through 110 removed outlier: 3.891A pdb=" N ARG C 108 " --> pdb=" O SER C 231 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N VAL C 204 " --> pdb=" O VAL C 269 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N ASP C 271 " --> pdb=" O VAL C 204 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N VAL C 206 " --> pdb=" O ASP C 271 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLY C 171 " --> pdb=" O ILE C 329 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N LEU C 168 " --> pdb=" O ILE C 352 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N LEU C 354 " --> pdb=" O LEU C 168 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ILE C 170 " --> pdb=" O LEU C 354 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N PHE C 353 " --> pdb=" O LEU C 371 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N LEU C 371 " --> pdb=" O PHE C 353 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 147 through 148 removed outlier: 4.453A pdb=" N ILE C 161 " --> pdb=" O VAL C 148 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 11 through 17 removed outlier: 6.511A pdb=" N ASP D 22 " --> pdb=" O THR D 14 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N VAL D 16 " --> pdb=" O ILE D 20 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N ILE D 20 " --> pdb=" O VAL D 16 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N THR D 58 " --> pdb=" O HIS D 53 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N HIS D 53 " --> pdb=" O THR D 58 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ARG D 60 " --> pdb=" O ALA D 51 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 84 through 87 removed outlier: 3.775A pdb=" N LEU D 113 " --> pdb=" O VAL D 87 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 216 through 221 removed outlier: 6.308A pdb=" N PHE D 184 " --> pdb=" O VAL D 218 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N GLY D 220 " --> pdb=" O PHE D 184 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N GLY D 186 " --> pdb=" O GLY D 220 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N LEU D 253 " --> pdb=" O VAL D 307 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N ALA D 309 " --> pdb=" O LEU D 253 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ILE D 255 " --> pdb=" O ALA D 309 " (cutoff:3.500A) removed outlier: 8.736A pdb=" N TYR D 311 " --> pdb=" O ILE D 255 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ILE D 153 " --> pdb=" O GLN D 308 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N VAL D 310 " --> pdb=" O ILE D 153 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N LEU D 155 " --> pdb=" O VAL D 310 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA D 331 " --> pdb=" O LYS D 152 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 84 through 87 removed outlier: 3.667A pdb=" N LEU E 113 " --> pdb=" O VAL E 87 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 95 through 96 removed outlier: 4.123A pdb=" N PHE E 219 " --> pdb=" O ILE E 96 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N ALA E 216 " --> pdb=" O VAL E 183 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N THR E 185 " --> pdb=" O ALA E 216 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N VAL E 218 " --> pdb=" O THR E 185 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N VAL E 187 " --> pdb=" O VAL E 218 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N GLY E 220 " --> pdb=" O VAL E 187 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N PHE E 181 " --> pdb=" O LEU E 252 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N PHE E 254 " --> pdb=" O PHE E 181 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N VAL E 183 " --> pdb=" O PHE E 254 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N ASP E 256 " --> pdb=" O VAL E 183 " (cutoff:3.500A) removed outlier: 8.277A pdb=" N THR E 185 " --> pdb=" O ASP E 256 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ASN E 257 " --> pdb=" O ALA E 309 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 133 through 134 removed outlier: 3.544A pdb=" N TYR E 147 " --> pdb=" O LEU E 134 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 84 through 87 removed outlier: 3.736A pdb=" N LEU F 113 " --> pdb=" O VAL F 87 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 95 through 96 removed outlier: 5.562A pdb=" N ILE F 96 " --> pdb=" O PHE F 219 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N GLN F 221 " --> pdb=" O ILE F 96 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N SER F 182 " --> pdb=" O ALA F 216 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N VAL F 218 " --> pdb=" O SER F 182 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N PHE F 184 " --> pdb=" O VAL F 218 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N GLY F 220 " --> pdb=" O PHE F 184 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N GLY F 186 " --> pdb=" O GLY F 220 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASP F 256 " --> pdb=" O THR F 185 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N THR F 305 " --> pdb=" O VAL F 251 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ILE F 153 " --> pdb=" O GLN F 308 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N VAL F 310 " --> pdb=" O ILE F 153 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N LEU F 155 " --> pdb=" O VAL F 310 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N PHE F 156 " --> pdb=" O THR F 333 " (cutoff:3.500A) removed outlier: 10.844A pdb=" N THR F 332 " --> pdb=" O LEU F 351 " (cutoff:3.500A) removed outlier: 9.276A pdb=" N LEU F 351 " --> pdb=" O THR F 332 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N VAL F 334 " --> pdb=" O ASP F 349 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 133 through 134 Processing sheet with id=AC6, first strand: chain 'G' and resid 126 through 129 removed outlier: 5.683A pdb=" N ILE G 107 " --> pdb=" O LEU G 128 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N GLU G 72 " --> pdb=" O ASP G 106 " (cutoff:3.500A) removed outlier: 8.671A pdb=" N VAL G 108 " --> pdb=" O GLU G 72 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ILE G 74 " --> pdb=" O VAL G 108 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N ILE G 110 " --> pdb=" O ILE G 74 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N ALA G 76 " --> pdb=" O ILE G 110 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N LEU G 73 " --> pdb=" O SER G 163 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N PHE G 165 " --> pdb=" O LEU G 73 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N VAL G 75 " --> pdb=" O PHE G 165 " (cutoff:3.500A) removed outlier: 8.761A pdb=" N ASN G 167 " --> pdb=" O VAL G 75 " (cutoff:3.500A) removed outlier: 8.804A pdb=" N ILE G 77 " --> pdb=" O ASN G 167 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ILE G 162 " --> pdb=" O ILE G 182 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N SER G 174 " --> pdb=" O VAL G 170 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 12 through 15 removed outlier: 5.732A pdb=" N GLN H 13 " --> pdb=" O VAL H 85 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N ALA H 87 " --> pdb=" O GLN H 13 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N ALA H 15 " --> pdb=" O ALA H 87 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 37 through 42 removed outlier: 6.590A pdb=" N VAL H 56 " --> pdb=" O PRO H 33 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 43 through 44 Processing sheet with id=AD1, first strand: chain 'O' and resid 118 through 119 Processing sheet with id=AD2, first strand: chain 'O' and resid 156 through 159 2320 hydrogen bonds defined for protein. 6702 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.91 Time building geometry restraints manager: 6.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.27: 5059 1.27 - 1.34: 670 1.34 - 1.41: 4350 1.41 - 1.48: 5218 1.48 - 1.55: 4894 Bond restraints: 20191 Sorted by residual: bond pdb=" CA LEU B 34 " pdb=" C LEU B 34 " ideal model delta sigma weight residual 1.531 1.491 0.040 5.40e-03 3.43e+04 5.49e+01 bond pdb=" CA LYS O 174 " pdb=" C LYS O 174 " ideal model delta sigma weight residual 1.520 1.459 0.062 1.21e-02 6.83e+03 2.59e+01 bond pdb=" CA ALA A 157 " pdb=" C ALA A 157 " ideal model delta sigma weight residual 1.521 1.471 0.049 9.90e-03 1.02e+04 2.49e+01 bond pdb=" CA GLY D 55 " pdb=" C GLY D 55 " ideal model delta sigma weight residual 1.516 1.481 0.034 6.90e-03 2.10e+04 2.47e+01 bond pdb=" CA GLY D 11 " pdb=" C GLY D 11 " ideal model delta sigma weight residual 1.514 1.472 0.041 8.60e-03 1.35e+04 2.33e+01 ... (remaining 20186 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.83: 20977 2.83 - 5.65: 3396 5.65 - 8.48: 692 8.48 - 11.31: 99 11.31 - 14.13: 15 Bond angle restraints: 25179 Sorted by residual: angle pdb=" N ILE T 54 " pdb=" CA ILE T 54 " pdb=" C ILE T 54 " ideal model delta sigma weight residual 112.12 102.52 9.60 8.40e-01 1.42e+00 1.31e+02 angle pdb=" CA VAL G 205 " pdb=" C VAL G 205 " pdb=" N PRO G 206 " ideal model delta sigma weight residual 121.00 129.35 -8.35 8.30e-01 1.45e+00 1.01e+02 angle pdb=" N VAL O 176 " pdb=" CA VAL O 176 " pdb=" C VAL O 176 " ideal model delta sigma weight residual 108.12 93.99 14.13 1.44e+00 4.82e-01 9.63e+01 angle pdb=" N GLN V 90 " pdb=" CA GLN V 90 " pdb=" C GLN V 90 " ideal model delta sigma weight residual 113.88 101.81 12.07 1.23e+00 6.61e-01 9.63e+01 angle pdb=" CA PRO D 225 " pdb=" C PRO D 225 " pdb=" O PRO D 225 " ideal model delta sigma weight residual 120.90 114.41 6.49 7.20e-01 1.93e+00 8.11e+01 ... (remaining 25174 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.83: 4996 21.83 - 43.65: 24 43.65 - 65.48: 2 65.48 - 87.30: 0 87.30 - 109.12: 2 Dihedral angle restraints: 5024 sinusoidal: 4 harmonic: 5020 Sorted by residual: dihedral pdb=" CA ASP D 256 " pdb=" C ASP D 256 " pdb=" N ASN D 257 " pdb=" CA ASN D 257 " ideal model delta harmonic sigma weight residual -180.00 -70.88 -109.12 0 5.00e+00 4.00e-02 4.76e+02 dihedral pdb=" CA ASN 7 40 " pdb=" C ASN 7 40 " pdb=" N PRO 7 41 " pdb=" CA PRO 7 41 " ideal model delta harmonic sigma weight residual -180.00 -136.73 -43.27 0 5.00e+00 4.00e-02 7.49e+01 dihedral pdb=" CA ASN 6 40 " pdb=" C ASN 6 40 " pdb=" N PRO 6 41 " pdb=" CA PRO 6 41 " ideal model delta harmonic sigma weight residual -180.00 -138.63 -41.37 0 5.00e+00 4.00e-02 6.85e+01 ... (remaining 5021 not shown) Chirality restraints: 0 Planarity restraints: 5024 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU X 8 " -0.021 2.00e-02 2.50e+03 4.24e-02 1.80e+01 pdb=" C LEU X 8 " 0.073 2.00e-02 2.50e+03 pdb=" O LEU X 8 " -0.028 2.00e-02 2.50e+03 pdb=" N ARG X 9 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL D 206 " -0.020 2.00e-02 2.50e+03 4.07e-02 1.66e+01 pdb=" C VAL D 206 " 0.070 2.00e-02 2.50e+03 pdb=" O VAL D 206 " -0.027 2.00e-02 2.50e+03 pdb=" N ILE D 207 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU E 422 " -0.020 2.00e-02 2.50e+03 3.94e-02 1.55e+01 pdb=" C GLU E 422 " 0.068 2.00e-02 2.50e+03 pdb=" O GLU E 422 " -0.026 2.00e-02 2.50e+03 pdb=" N VAL E 423 " -0.023 2.00e-02 2.50e+03 ... (remaining 5021 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.89: 9897 2.89 - 3.39: 17523 3.39 - 3.90: 26530 3.90 - 4.40: 27601 4.40 - 4.90: 40515 Nonbonded interactions: 122066 Sorted by model distance: nonbonded pdb=" N LEU F 252 " pdb=" O LEU F 252 " model vdw 2.390 2.496 nonbonded pdb=" N SER G 171 " pdb=" O SER G 171 " model vdw 2.406 2.496 nonbonded pdb=" N MET A 64 " pdb=" O MET A 64 " model vdw 2.410 2.496 nonbonded pdb=" N SER C 129 " pdb=" O SER C 129 " model vdw 2.414 2.496 nonbonded pdb=" N SER O 179 " pdb=" O SER O 179 " model vdw 2.415 2.496 ... (remaining 122061 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain '0' and resid 2 through 73) selection = (chain '1' and resid 2 through 73) selection = (chain '2' and resid 2 through 73) selection = (chain '3' and resid 2 through 73) selection = (chain '4' and resid 2 through 73) selection = (chain '5' and resid 2 through 73) selection = (chain '6' and resid 2 through 73) selection = (chain '7' and resid 2 through 73) selection = (chain '8' and resid 2 through 73) selection = (chain '9' and resid 2 through 73) } ncs_group { reference = (chain 'A' and resid 12 through 509) selection = (chain 'B' and resid 12 through 509) selection = (chain 'C' and (resid 12 through 407 or resid 410 through 509)) } ncs_group { reference = (chain 'D' and resid 8 through 475) selection = chain 'E' selection = (chain 'F' and resid 8 through 475) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.730 Check model and map are aligned: 0.150 Set scattering table: 0.160 Process input model: 54.360 Find NCS groups from input model: 1.130 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6243 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 : 0.019 0.062 20191 Z= 1.474 Angle : 2.213 14.132 25179 Z= 1.599 Chirality : 0.000 0.000 0 Planarity : 0.010 0.042 5024 Dihedral : 6.676 109.125 5024 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 0.08 Ramachandran Plot: Outliers : 1.50 % Allowed : 4.09 % Favored : 94.40 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.96 % Cis-general : 0.08 % Twisted Proline : 3.94 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.11), residues: 4984 helix: 0.85 (0.09), residues: 2826 sheet: -1.43 (0.22), residues: 515 loop : -1.93 (0.13), residues: 1643 Details of bonding type rmsd hydrogen bonds : bond 0.22000 ( 2311) hydrogen bonds : angle 8.06355 ( 6702) covalent geometry : bond 0.01880 (20191) covalent geometry : angle 2.21314 (25179) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9968 Ramachandran restraints generated. 4984 Oldfield, 0 Emsley, 4984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9968 Ramachandran restraints generated. 4984 Oldfield, 0 Emsley, 4984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 4114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 2.126 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.1721 time to fit residues: 29.9874 Evaluate side-chains 82 residues out of total 4114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 2.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 415 optimal weight: 6.9990 chunk 372 optimal weight: 5.9990 chunk 206 optimal weight: 7.9990 chunk 127 optimal weight: 9.9990 chunk 251 optimal weight: 4.9990 chunk 199 optimal weight: 7.9990 chunk 385 optimal weight: 7.9990 chunk 149 optimal weight: 9.9990 chunk 234 optimal weight: 5.9990 chunk 287 optimal weight: 6.9990 chunk 446 optimal weight: 40.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2509 r_free = 0.2509 target = 0.031922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2277 r_free = 0.2277 target = 0.024116 restraints weight = 286200.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2282 r_free = 0.2282 target = 0.024181 restraints weight = 268408.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2282 r_free = 0.2282 target = 0.024197 restraints weight = 251426.379| |-----------------------------------------------------------------------------| r_work (final): 0.2108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.1975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 20191 Z= 0.176 Angle : 0.504 6.757 25179 Z= 0.324 Chirality : 0.000 0.000 0 Planarity : 0.003 0.024 5024 Dihedral : 5.015 88.239 5024 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 0.39 Ramachandran Plot: Outliers : 0.30 % Allowed : 2.83 % Favored : 96.87 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.96 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 1.32 (0.12), residues: 4984 helix: 2.27 (0.10), residues: 2835 sheet: -1.06 (0.21), residues: 566 loop : -0.97 (0.15), residues: 1583 Details of bonding type rmsd hydrogen bonds : bond 0.04865 ( 2311) hydrogen bonds : angle 4.61644 ( 6702) covalent geometry : bond 0.00234 (20191) covalent geometry : angle 0.50398 (25179) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9968 Ramachandran restraints generated. 4984 Oldfield, 0 Emsley, 4984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9968 Ramachandran restraints generated. 4984 Oldfield, 0 Emsley, 4984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 4114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 2.460 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.1710 time to fit residues: 30.2267 Evaluate side-chains 82 residues out of total 4114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 2.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 217 optimal weight: 50.0000 chunk 282 optimal weight: 20.0000 chunk 87 optimal weight: 30.0000 chunk 348 optimal weight: 30.0000 chunk 438 optimal weight: 50.0000 chunk 340 optimal weight: 0.0040 chunk 130 optimal weight: 50.0000 chunk 449 optimal weight: 50.0000 chunk 117 optimal weight: 50.0000 chunk 48 optimal weight: 50.0000 chunk 350 optimal weight: 40.0000 overall best weight: 24.0008 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2499 r_free = 0.2499 target = 0.030477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2241 r_free = 0.2241 target = 0.023143 restraints weight = 300043.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2243 r_free = 0.2243 target = 0.023214 restraints weight = 276580.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2242 r_free = 0.2242 target = 0.023189 restraints weight = 265708.088| |-----------------------------------------------------------------------------| r_work (final): 0.2049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.3554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.117 20191 Z= 0.440 Angle : 0.851 14.813 25179 Z= 0.557 Chirality : 0.000 0.000 0 Planarity : 0.005 0.032 5024 Dihedral : 5.943 86.934 5024 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.34 % Favored : 94.36 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.96 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.12), residues: 4984 helix: 1.60 (0.09), residues: 2789 sheet: -1.26 (0.23), residues: 484 loop : -1.20 (0.15), residues: 1711 Details of bonding type rmsd hydrogen bonds : bond 0.06840 ( 2311) hydrogen bonds : angle 6.01142 ( 6702) covalent geometry : bond 0.00594 (20191) covalent geometry : angle 0.85061 (25179) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9968 Ramachandran restraints generated. 4984 Oldfield, 0 Emsley, 4984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9968 Ramachandran restraints generated. 4984 Oldfield, 0 Emsley, 4984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 4114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 2.026 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.1582 time to fit residues: 27.8640 Evaluate side-chains 82 residues out of total 4114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 2.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 95 optimal weight: 50.0000 chunk 210 optimal weight: 50.0000 chunk 108 optimal weight: 20.0000 chunk 469 optimal weight: 50.0000 chunk 66 optimal weight: 20.0000 chunk 19 optimal weight: 6.9990 chunk 188 optimal weight: 4.9990 chunk 183 optimal weight: 30.0000 chunk 107 optimal weight: 30.0000 chunk 262 optimal weight: 40.0000 chunk 360 optimal weight: 7.9990 overall best weight: 11.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2447 r_free = 0.2447 target = 0.041745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2370 r_free = 0.2370 target = 0.036131 restraints weight = 322122.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2353 r_free = 0.2353 target = 0.035747 restraints weight = 398993.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2349 r_free = 0.2349 target = 0.035655 restraints weight = 506200.033| |-----------------------------------------------------------------------------| r_work (final): 0.2233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.3965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 20191 Z= 0.218 Angle : 0.508 8.027 25179 Z= 0.328 Chirality : 0.000 0.000 0 Planarity : 0.003 0.024 5024 Dihedral : 4.911 85.517 5024 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 1.31 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.94 % Favored : 94.78 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.96 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.12), residues: 4984 helix: 2.30 (0.10), residues: 2815 sheet: -1.21 (0.22), residues: 498 loop : -1.08 (0.15), residues: 1671 Details of bonding type rmsd hydrogen bonds : bond 0.04407 ( 2311) hydrogen bonds : angle 4.81537 ( 6702) covalent geometry : bond 0.00293 (20191) covalent geometry : angle 0.50766 (25179) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9968 Ramachandran restraints generated. 4984 Oldfield, 0 Emsley, 4984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9968 Ramachandran restraints generated. 4984 Oldfield, 0 Emsley, 4984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 4114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 2.250 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.1719 time to fit residues: 30.2447 Evaluate side-chains 82 residues out of total 4114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 2.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 166 optimal weight: 70.0000 chunk 380 optimal weight: 6.9990 chunk 347 optimal weight: 30.0000 chunk 196 optimal weight: 20.0000 chunk 70 optimal weight: 50.0000 chunk 19 optimal weight: 50.0000 chunk 150 optimal weight: 50.0000 chunk 98 optimal weight: 30.0000 chunk 431 optimal weight: 50.0000 chunk 317 optimal weight: 20.0000 chunk 30 optimal weight: 8.9990 overall best weight: 17.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2490 r_free = 0.2490 target = 0.030183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2234 r_free = 0.2234 target = 0.022812 restraints weight = 303630.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2232 r_free = 0.2232 target = 0.022817 restraints weight = 285855.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2230 r_free = 0.2230 target = 0.022788 restraints weight = 272337.559| |-----------------------------------------------------------------------------| r_work (final): 0.2030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.5017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 20191 Z= 0.309 Angle : 0.660 11.439 25179 Z= 0.422 Chirality : 0.000 0.000 0 Planarity : 0.004 0.029 5024 Dihedral : 5.602 88.505 5024 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.30 % Allowed : 7.56 % Favored : 92.13 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.96 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.12), residues: 4984 helix: 1.92 (0.10), residues: 2798 sheet: -1.52 (0.24), residues: 427 loop : -1.40 (0.15), residues: 1759 Details of bonding type rmsd hydrogen bonds : bond 0.05504 ( 2311) hydrogen bonds : angle 5.62787 ( 6702) covalent geometry : bond 0.00416 (20191) covalent geometry : angle 0.65977 (25179) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9968 Ramachandran restraints generated. 4984 Oldfield, 0 Emsley, 4984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9968 Ramachandran restraints generated. 4984 Oldfield, 0 Emsley, 4984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 4114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 2.241 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.1619 time to fit residues: 28.6404 Evaluate side-chains 82 residues out of total 4114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 2.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 238 optimal weight: 50.0000 chunk 247 optimal weight: 50.0000 chunk 393 optimal weight: 50.0000 chunk 54 optimal weight: 20.0000 chunk 164 optimal weight: 20.0000 chunk 483 optimal weight: 50.0000 chunk 277 optimal weight: 0.0070 chunk 361 optimal weight: 50.0000 chunk 488 optimal weight: 40.0000 chunk 334 optimal weight: 20.0000 chunk 345 optimal weight: 40.0000 overall best weight: 20.0014 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2260 r_free = 0.2260 target = 0.026439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2160 r_free = 0.2160 target = 0.021701 restraints weight = 333149.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2136 r_free = 0.2136 target = 0.021162 restraints weight = 668477.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2131 r_free = 0.2131 target = 0.021023 restraints weight = 989696.990| |-----------------------------------------------------------------------------| r_work (final): 0.2292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.5886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.103 20191 Z= 0.350 Angle : 0.677 10.426 25179 Z= 0.448 Chirality : 0.000 0.000 0 Planarity : 0.004 0.029 5024 Dihedral : 5.705 82.409 5024 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.83 % Favored : 91.91 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.96 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.12), residues: 4984 helix: 1.46 (0.10), residues: 2808 sheet: -1.81 (0.24), residues: 421 loop : -1.71 (0.15), residues: 1755 Details of bonding type rmsd hydrogen bonds : bond 0.05769 ( 2311) hydrogen bonds : angle 6.03462 ( 6702) covalent geometry : bond 0.00473 (20191) covalent geometry : angle 0.67683 (25179) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9968 Ramachandran restraints generated. 4984 Oldfield, 0 Emsley, 4984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9968 Ramachandran restraints generated. 4984 Oldfield, 0 Emsley, 4984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 4114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 2.365 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.1636 time to fit residues: 28.9464 Evaluate side-chains 82 residues out of total 4114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 2.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 387 optimal weight: 9.9990 chunk 126 optimal weight: 20.0000 chunk 316 optimal weight: 6.9990 chunk 96 optimal weight: 40.0000 chunk 410 optimal weight: 50.0000 chunk 380 optimal weight: 90.0000 chunk 214 optimal weight: 30.0000 chunk 84 optimal weight: 30.0000 chunk 354 optimal weight: 30.0000 chunk 34 optimal weight: 50.0000 chunk 307 optimal weight: 3.9990 overall best weight: 14.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2276 r_free = 0.2276 target = 0.026776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2163 r_free = 0.2163 target = 0.021910 restraints weight = 306012.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2139 r_free = 0.2139 target = 0.021149 restraints weight = 714599.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2141 r_free = 0.2141 target = 0.020998 restraints weight = 1019531.134| |-----------------------------------------------------------------------------| r_work (final): 0.2312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.6100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 20191 Z= 0.245 Angle : 0.524 8.329 25179 Z= 0.343 Chirality : 0.000 0.000 0 Planarity : 0.003 0.024 5024 Dihedral : 5.072 83.212 5024 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.50 % Favored : 92.24 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.96 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.12), residues: 4984 helix: 1.92 (0.10), residues: 2813 sheet: -1.77 (0.26), residues: 397 loop : -1.68 (0.15), residues: 1774 Details of bonding type rmsd hydrogen bonds : bond 0.04581 ( 2311) hydrogen bonds : angle 5.30731 ( 6702) covalent geometry : bond 0.00331 (20191) covalent geometry : angle 0.52383 (25179) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9968 Ramachandran restraints generated. 4984 Oldfield, 0 Emsley, 4984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9968 Ramachandran restraints generated. 4984 Oldfield, 0 Emsley, 4984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 4114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 2.757 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.1761 time to fit residues: 31.2754 Evaluate side-chains 82 residues out of total 4114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 2.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 283 optimal weight: 50.0000 chunk 334 optimal weight: 50.0000 chunk 490 optimal weight: 50.0000 chunk 367 optimal weight: 50.0000 chunk 31 optimal weight: 90.0000 chunk 285 optimal weight: 10.0000 chunk 167 optimal weight: 40.0000 chunk 239 optimal weight: 0.0470 chunk 330 optimal weight: 20.0000 chunk 245 optimal weight: 40.0000 chunk 249 optimal weight: 50.0000 overall best weight: 22.0094 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2252 r_free = 0.2252 target = 0.026090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2162 r_free = 0.2162 target = 0.021322 restraints weight = 310877.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2140 r_free = 0.2140 target = 0.020831 restraints weight = 587485.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2134 r_free = 0.2134 target = 0.020682 restraints weight = 827284.317| |-----------------------------------------------------------------------------| r_work (final): 0.2110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.6708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.096 20191 Z= 0.382 Angle : 0.712 10.986 25179 Z= 0.475 Chirality : 0.000 0.000 0 Planarity : 0.004 0.030 5024 Dihedral : 5.855 89.941 5024 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.26 % Allowed : 9.73 % Favored : 90.01 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.96 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.12), residues: 4984 helix: 1.29 (0.10), residues: 2792 sheet: -2.00 (0.27), residues: 364 loop : -1.91 (0.14), residues: 1828 Details of bonding type rmsd hydrogen bonds : bond 0.06090 ( 2311) hydrogen bonds : angle 6.34153 ( 6702) covalent geometry : bond 0.00514 (20191) covalent geometry : angle 0.71187 (25179) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9968 Ramachandran restraints generated. 4984 Oldfield, 0 Emsley, 4984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9968 Ramachandran restraints generated. 4984 Oldfield, 0 Emsley, 4984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 4114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 2.548 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.1687 time to fit residues: 29.8735 Evaluate side-chains 82 residues out of total 4114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 2.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 148 optimal weight: 40.0000 chunk 31 optimal weight: 90.0000 chunk 439 optimal weight: 80.0000 chunk 455 optimal weight: 50.0000 chunk 309 optimal weight: 50.0000 chunk 301 optimal weight: 5.9990 chunk 303 optimal weight: 0.0980 chunk 490 optimal weight: 50.0000 chunk 436 optimal weight: 100.0000 chunk 179 optimal weight: 3.9990 chunk 435 optimal weight: 9.9990 overall best weight: 12.0190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2275 r_free = 0.2275 target = 0.026663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2169 r_free = 0.2169 target = 0.022019 restraints weight = 292622.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2147 r_free = 0.2147 target = 0.021186 restraints weight = 747513.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2148 r_free = 0.2148 target = 0.021022 restraints weight = 1147216.324| |-----------------------------------------------------------------------------| r_work (final): 0.2327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.6702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 20191 Z= 0.219 Angle : 0.488 7.657 25179 Z= 0.322 Chirality : 0.000 0.000 0 Planarity : 0.003 0.023 5024 Dihedral : 5.054 89.109 5024 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 2.16 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.80 % Favored : 91.93 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.96 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.12), residues: 4984 helix: 1.89 (0.10), residues: 2804 sheet: -2.00 (0.26), residues: 373 loop : -1.81 (0.15), residues: 1807 Details of bonding type rmsd hydrogen bonds : bond 0.04413 ( 2311) hydrogen bonds : angle 5.33664 ( 6702) covalent geometry : bond 0.00296 (20191) covalent geometry : angle 0.48808 (25179) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9968 Ramachandran restraints generated. 4984 Oldfield, 0 Emsley, 4984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9968 Ramachandran restraints generated. 4984 Oldfield, 0 Emsley, 4984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 4114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 2.460 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.1716 time to fit residues: 30.2227 Evaluate side-chains 82 residues out of total 4114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 2.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 302 optimal weight: 30.0000 chunk 162 optimal weight: 0.2980 chunk 259 optimal weight: 20.0000 chunk 143 optimal weight: 30.0000 chunk 443 optimal weight: 120.0000 chunk 293 optimal weight: 40.0000 chunk 409 optimal weight: 60.0000 chunk 396 optimal weight: 50.0000 chunk 374 optimal weight: 50.0000 chunk 169 optimal weight: 60.0000 chunk 380 optimal weight: 40.0000 overall best weight: 24.0596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2244 r_free = 0.2244 target = 0.025896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2158 r_free = 0.2158 target = 0.021318 restraints weight = 308170.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2128 r_free = 0.2128 target = 0.020678 restraints weight = 602755.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2124 r_free = 0.2124 target = 0.020519 restraints weight = 941410.491| |-----------------------------------------------------------------------------| r_work (final): 0.2100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.7234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.106 20191 Z= 0.398 Angle : 0.727 11.254 25179 Z= 0.487 Chirality : 0.000 0.000 0 Planarity : 0.004 0.029 5024 Dihedral : 5.931 83.684 5024 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.24 % Allowed : 10.89 % Favored : 88.86 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.96 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.12), residues: 4984 helix: 1.05 (0.10), residues: 2793 sheet: -2.28 (0.26), residues: 365 loop : -2.13 (0.14), residues: 1826 Details of bonding type rmsd hydrogen bonds : bond 0.06379 ( 2311) hydrogen bonds : angle 6.53612 ( 6702) covalent geometry : bond 0.00538 (20191) covalent geometry : angle 0.72745 (25179) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9968 Ramachandran restraints generated. 4984 Oldfield, 0 Emsley, 4984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9968 Ramachandran restraints generated. 4984 Oldfield, 0 Emsley, 4984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 4114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 2.335 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.1644 time to fit residues: 29.1620 Evaluate side-chains 82 residues out of total 4114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 2.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 120 optimal weight: 9.9990 chunk 310 optimal weight: 50.0000 chunk 335 optimal weight: 20.0000 chunk 486 optimal weight: 50.0000 chunk 334 optimal weight: 40.0000 chunk 178 optimal weight: 40.0000 chunk 363 optimal weight: 30.0000 chunk 158 optimal weight: 50.0000 chunk 196 optimal weight: 20.0000 chunk 176 optimal weight: 20.0000 chunk 430 optimal weight: 50.0000 overall best weight: 19.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2255 r_free = 0.2255 target = 0.026064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2172 r_free = 0.2172 target = 0.021484 restraints weight = 300377.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2149 r_free = 0.2149 target = 0.020998 restraints weight = 544281.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2146 r_free = 0.2146 target = 0.020873 restraints weight = 817972.082| |-----------------------------------------------------------------------------| r_work (final): 0.2119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.7405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 20191 Z= 0.332 Angle : 0.639 9.931 25179 Z= 0.427 Chirality : 0.000 0.000 0 Planarity : 0.004 0.026 5024 Dihedral : 5.674 84.221 5024 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.24 % Allowed : 10.01 % Favored : 89.75 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.96 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.12), residues: 4984 helix: 1.10 (0.10), residues: 2781 sheet: -2.42 (0.26), residues: 349 loop : -2.18 (0.14), residues: 1854 Details of bonding type rmsd hydrogen bonds : bond 0.05486 ( 2311) hydrogen bonds : angle 6.19517 ( 6702) covalent geometry : bond 0.00449 (20191) covalent geometry : angle 0.63941 (25179) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4482.95 seconds wall clock time: 77 minutes 37.79 seconds (4657.79 seconds total)