Starting phenix.real_space_refine on Wed Apr 10 19:39:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tk0_25948/04_2024/7tk0_25948.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tk0_25948/04_2024/7tk0_25948.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tk0_25948/04_2024/7tk0_25948.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tk0_25948/04_2024/7tk0_25948.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tk0_25948/04_2024/7tk0_25948.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tk0_25948/04_2024/7tk0_25948.pdb" } resolution = 4.4 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= 0.106 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 10108 2.51 5 N 5054 2.21 5 O 5058 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 20220 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: 1872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 1872 Classifications: {'peptide': 468} Incomplete info: {'backbone_only': 422} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 21, 'TRANS': 444} 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: "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: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 480 Classifications: {'peptide': 120} Incomplete info: {'backbone_only': 114} Link IDs: {'PTRANS': 6, 'TRANS': 113} Chain breaks: 4 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 439 Unresolved non-hydrogen angles: 643 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: 12.53, per 1000 atoms: 0.62 Number of scatterers: 20220 At special positions: 0 Unit cell: (125.317, 150.92, 237.16, 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 5058 8.00 N 5054 7.00 C 10108 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 - 3.50 Amino acid : False - 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: 9.50 Conformation dependent library (CDL) restraints added in 5.8 seconds 9964 Ramachandran restraints generated. 4982 Oldfield, 0 Emsley, 4982 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: 202 helices and 24 sheets defined 60.5% alpha, 8.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.89 Creating SS restraints... Processing helix chain '0' and resid 1 through 17 removed outlier: 3.753A pdb=" N GLY 0 13 " --> pdb=" O TYR 0 9 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ILE 0 17 " --> pdb=" O GLY 0 13 " (cutoff:3.500A) Processing helix chain '0' and resid 18 through 40 removed outlier: 4.040A 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: 3.573A pdb=" N THR 0 61 " --> pdb=" O LEU 0 57 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLY 0 62 " --> pdb=" O SER 0 58 " (cutoff:3.500A) Processing helix chain '1' and resid 2 through 17 removed outlier: 3.504A pdb=" N GLY 1 13 " --> pdb=" O TYR 1 9 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ILE 1 17 " --> pdb=" O GLY 1 13 " (cutoff:3.500A) Processing helix chain '1' and resid 18 through 40 removed outlier: 4.485A pdb=" N ALA 1 22 " --> pdb=" O GLY 1 18 " (cutoff:3.500A) removed outlier: 3.696A 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 Processing helix chain '2' and resid 2 through 16 Processing helix chain '2' and resid 18 through 40 removed outlier: 4.138A pdb=" N ALA 2 22 " --> pdb=" O GLY 2 18 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA 2 27 " --> pdb=" O GLY 2 23 " (cutoff:3.500A) Processing helix chain '2' and resid 43 through 75 Proline residue: 2 49 - end of helix removed outlier: 4.282A pdb=" N THR 2 61 " --> pdb=" O LEU 2 57 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N GLY 2 62 " --> pdb=" O SER 2 58 " (cutoff:3.500A) Processing helix chain '3' and resid 3 through 17 removed outlier: 3.837A pdb=" N ILE 3 17 " --> pdb=" O GLY 3 13 " (cutoff:3.500A) Processing helix chain '3' and resid 19 through 40 removed outlier: 3.779A 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: 3.865A pdb=" N GLY 3 62 " --> pdb=" O SER 3 58 " (cutoff:3.500A) Processing helix chain '4' and resid 2 through 16 Processing helix chain '4' and resid 18 through 40 removed outlier: 4.133A pdb=" N ALA 4 22 " --> pdb=" O GLY 4 18 " (cutoff:3.500A) removed outlier: 3.589A 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: 3.790A pdb=" N THR 4 61 " --> pdb=" O LEU 4 57 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLY 4 62 " --> pdb=" O SER 4 58 " (cutoff:3.500A) Processing helix chain '5' and resid 2 through 17 removed outlier: 3.838A pdb=" N ILE 5 17 " --> pdb=" O GLY 5 13 " (cutoff:3.500A) Processing helix chain '5' and resid 18 through 40 removed outlier: 4.264A 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: 3.714A pdb=" N GLY 5 62 " --> pdb=" O SER 5 58 " (cutoff:3.500A) Processing helix chain '6' and resid 3 through 16 Processing helix chain '6' and resid 18 through 40 removed outlier: 4.483A pdb=" N ALA 6 22 " --> pdb=" O GLY 6 18 " (cutoff:3.500A) removed outlier: 3.870A 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: 3.567A pdb=" N THR 6 61 " --> pdb=" O LEU 6 57 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLY 6 62 " --> pdb=" O SER 6 58 " (cutoff:3.500A) Processing helix chain '7' and resid 2 through 40 removed outlier: 3.741A pdb=" N THR 7 16 " --> pdb=" O ALA 7 12 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ILE 7 17 " --> pdb=" O GLY 7 13 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N GLY 7 18 " --> pdb=" O ILE 7 14 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N LEU 7 19 " --> pdb=" O SER 7 15 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU 7 20 " --> pdb=" O THR 7 16 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLY 7 21 " --> pdb=" O ILE 7 17 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ALA 7 22 " --> pdb=" O GLY 7 18 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA 7 27 " --> pdb=" O GLY 7 23 " (cutoff:3.500A) Processing helix chain '7' and resid 43 through 73 Proline residue: 7 49 - end of helix removed outlier: 3.643A pdb=" N GLY 7 62 " --> pdb=" O SER 7 58 " (cutoff:3.500A) Processing helix chain '8' and resid 2 through 40 removed outlier: 3.686A pdb=" N THR 8 16 " --> pdb=" O ALA 8 12 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ILE 8 17 " --> pdb=" O GLY 8 13 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N GLY 8 18 " --> pdb=" O ILE 8 14 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N LEU 8 19 " --> pdb=" O SER 8 15 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU 8 20 " --> pdb=" O THR 8 16 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N GLY 8 21 " --> pdb=" O ILE 8 17 " (cutoff:3.500A) removed outlier: 3.944A 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: 3.855A pdb=" N THR 8 61 " --> pdb=" O LEU 8 57 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLY 8 62 " --> pdb=" O SER 8 58 " (cutoff:3.500A) Processing helix chain '9' and resid 3 through 17 removed outlier: 3.892A pdb=" N ILE 9 17 " --> pdb=" O GLY 9 13 " (cutoff:3.500A) Processing helix chain '9' and resid 18 through 40 removed outlier: 4.206A pdb=" N ALA 9 22 " --> pdb=" O GLY 9 18 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA 9 27 " --> pdb=" O GLY 9 23 " (cutoff:3.500A) Processing helix chain '9' and resid 43 through 75 Proline residue: 9 49 - end of helix removed outlier: 3.540A 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 removed outlier: 3.695A pdb=" N LEU A 83 " --> pdb=" O SER A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 106 removed outlier: 3.779A pdb=" N LEU A 105 " --> pdb=" O GLY A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 159 Processing helix chain 'A' and resid 176 through 194 removed outlier: 3.668A pdb=" N THR A 184 " --> pdb=" O VAL A 180 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE A 185 " --> pdb=" O ALA A 181 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LYS A 189 " --> pdb=" O ILE A 185 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ARG A 190 " --> pdb=" O LEU A 186 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N TRP A 191 " --> pdb=" O ASN A 187 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLY A 194 " --> pdb=" O ARG A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 200 removed outlier: 3.643A pdb=" N LYS A 200 " --> pdb=" O GLU A 197 " (cutoff:3.500A) 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: 3.926A pdb=" N PHE A 259 " --> pdb=" O ILE A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 287 removed outlier: 3.547A pdb=" N GLN A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 296 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 380 Processing helix chain 'A' and resid 382 through 388 Processing helix chain 'A' and resid 389 through 402 removed outlier: 3.712A pdb=" N LYS A 393 " --> pdb=" O ALA A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 407 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: 4.278A pdb=" N GLY A 457 " --> pdb=" O GLY A 453 " (cutoff:3.500A) removed outlier: 4.035A 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 460 through 489 removed outlier: 4.335A pdb=" N GLY A 464 " --> pdb=" O LEU A 460 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N GLU A 465 " --> pdb=" O SER A 461 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N SER A 468 " --> pdb=" O GLY A 464 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N GLU A 480 " --> pdb=" O SER A 476 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N LEU A 481 " --> pdb=" O ASN A 477 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU A 482 " --> pdb=" O HIS A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 509 Processing helix chain 'B' and resid 6 through 9 Processing helix chain 'B' and resid 10 through 19 Processing helix chain 'B' and resid 80 through 84 removed outlier: 3.502A pdb=" N LEU B 83 " --> pdb=" O SER B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 106 removed outlier: 3.763A pdb=" N LEU B 105 " --> pdb=" O GLY B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 188 removed outlier: 4.027A pdb=" N VAL B 180 " --> pdb=" O GLY B 176 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ALA B 181 " --> pdb=" O LYS B 177 " (cutoff:3.500A) removed outlier: 3.699A 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 247 Processing helix chain 'B' and resid 247 through 261 removed outlier: 3.754A 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 383 through 388 Processing helix chain 'B' and resid 391 through 407 removed outlier: 3.519A pdb=" N ARG B 400 " --> pdb=" O LEU B 396 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N GLU B 401 " --> pdb=" O ALA B 397 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLN B 407 " --> pdb=" O ALA B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 431 removed outlier: 3.743A 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 459 through 461 No H-bonds generated for 'chain 'B' and resid 459 through 461' Processing helix chain 'B' and resid 462 through 479 removed outlier: 3.530A pdb=" N SER B 468 " --> pdb=" O GLY B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 489 Processing helix chain 'B' and resid 492 through 509 removed outlier: 3.986A pdb=" N THR B 509 " --> pdb=" O SER B 505 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 21 Processing helix chain 'C' and resid 80 through 84 Processing helix chain 'C' and resid 152 through 159 Processing helix chain 'C' and resid 176 through 188 removed outlier: 3.602A pdb=" N VAL C 180 " --> pdb=" O GLY C 176 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ALA C 181 " --> pdb=" O LYS C 177 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N THR C 184 " --> pdb=" O VAL C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 188 through 193 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: 3.911A pdb=" N PHE C 259 " --> pdb=" O ILE C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 286 removed outlier: 3.589A pdb=" N GLN C 276 " --> pdb=" O ASP C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 297 Proline residue: C 297 - end of helix Processing helix chain 'C' and resid 298 through 309 removed outlier: 4.261A pdb=" N TYR C 302 " --> pdb=" O GLY C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 348 Processing helix chain 'C' and resid 355 through 362 Processing helix chain 'C' and resid 382 through 389 Processing helix chain 'C' and resid 391 through 407 Processing helix chain 'C' and resid 413 through 431 removed outlier: 3.550A pdb=" N LYS C 431 " --> pdb=" O THR C 427 " (cutoff:3.500A) Processing helix chain 'C' and resid 439 through 442 Processing helix chain 'C' and resid 443 through 452 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 506 Processing helix chain 'D' and resid 88 through 92 Processing helix chain 'D' and resid 138 through 145 Processing helix chain 'D' and resid 162 through 178 Processing helix chain 'D' and resid 190 through 205 Processing helix chain 'D' and resid 225 through 246 removed outlier: 4.776A pdb=" N ALA D 233 " --> pdb=" O ARG D 229 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N LEU D 234 " --> pdb=" O ALA D 230 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 272 removed outlier: 3.686A 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 294 Processing helix chain 'D' and resid 312 through 316 Processing helix chain 'D' and resid 319 through 327 Processing helix chain 'D' and resid 336 through 343 Processing helix chain 'D' and resid 359 through 364 Processing helix chain 'D' and resid 364 through 396 removed outlier: 3.603A pdb=" N TYR D 381 " --> pdb=" O THR D 377 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N ASP D 386 " --> pdb=" O LYS D 382 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ILE D 387 " --> pdb=" O SER D 383 " (cutoff:3.500A) removed outlier: 8.301A pdb=" N MET D 393 " --> pdb=" O ALA D 389 " (cutoff:3.500A) removed outlier: 9.558A pdb=" N ASP D 394 " --> pdb=" O ILE D 390 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLU D 395 " --> pdb=" O LEU D 391 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LEU D 396 " --> pdb=" O GLY D 392 " (cutoff:3.500A) Processing helix chain 'D' and resid 397 through 414 Processing helix chain 'D' and resid 419 through 424 removed outlier: 4.264A pdb=" N VAL D 423 " --> pdb=" O ALA D 419 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N PHE D 424 " --> pdb=" O VAL D 420 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 419 through 424' Processing helix chain 'D' and resid 433 through 446 Processing helix chain 'D' and resid 453 through 457 Processing helix chain 'D' and resid 462 through 475 Processing helix chain 'E' and resid 88 through 92 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: 4.589A pdb=" N ALA E 233 " --> pdb=" O ARG E 229 " (cutoff:3.500A) removed outlier: 4.665A 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 277 through 281 Processing helix chain 'E' and resid 284 through 293 Processing helix chain 'E' and resid 312 through 316 removed outlier: 3.577A pdb=" N ASP E 315 " --> pdb=" O VAL E 312 " (cutoff:3.500A) Processing helix chain 'E' and resid 319 through 329 Processing helix chain 'E' and resid 336 through 342 removed outlier: 3.524A pdb=" N SER E 340 " --> pdb=" O SER E 336 " (cutoff:3.500A) Processing helix chain 'E' and resid 364 through 392 removed outlier: 3.645A pdb=" N ASP E 386 " --> pdb=" O LYS E 382 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ILE E 387 " --> pdb=" O SER E 383 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE E 390 " --> pdb=" O ASP E 386 " (cutoff:3.500A) Processing helix chain 'E' and resid 397 through 415 removed outlier: 4.175A pdb=" N SER E 415 " --> pdb=" O GLN E 411 " (cutoff:3.500A) Processing helix chain 'E' and resid 421 through 426 Processing helix chain 'E' and resid 433 through 446 Processing helix chain 'E' and resid 453 through 457 Processing helix chain 'E' and resid 462 through 475 removed outlier: 3.629A pdb=" N ALA E 468 " --> pdb=" O GLU E 464 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 92 removed outlier: 3.543A pdb=" N THR F 91 " --> pdb=" O GLY F 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 123 through 127 Processing helix chain 'F' and resid 138 through 145 Processing helix chain 'F' and resid 162 through 178 removed outlier: 4.413A pdb=" N LYS F 176 " --> pdb=" O ASN F 172 " (cutoff:3.500A) Processing helix chain 'F' and resid 190 through 204 Processing helix chain 'F' and resid 225 through 231 removed outlier: 3.530A pdb=" N ARG F 231 " --> pdb=" O GLY F 227 " (cutoff:3.500A) Processing helix chain 'F' and resid 231 through 245 Processing helix chain 'F' and resid 258 through 273 removed outlier: 3.949A pdb=" N ALA F 270 " --> pdb=" O SER F 266 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N LEU F 271 " --> pdb=" O GLU F 267 " (cutoff:3.500A) Processing helix chain 'F' and resid 277 through 281 removed outlier: 3.706A pdb=" N TYR F 281 " --> pdb=" O ALA F 278 " (cutoff:3.500A) Processing helix chain 'F' and resid 284 through 295 Processing helix chain 'F' and resid 312 through 316 removed outlier: 3.540A pdb=" N ASP F 316 " --> pdb=" O PRO F 313 " (cutoff:3.500A) Processing helix chain 'F' and resid 319 through 327 removed outlier: 3.562A pdb=" N THR F 325 " --> pdb=" O ALA F 321 " (cutoff:3.500A) removed outlier: 3.830A 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 359 through 364 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 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 Processing helix chain 'F' and resid 453 through 458 removed outlier: 3.627A 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 55 removed outlier: 4.059A pdb=" N LYS G 33 " --> pdb=" O THR G 29 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N SER G 40 " --> pdb=" O LYS G 36 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ALA G 47 " --> pdb=" O LYS G 43 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU G 48 " --> pdb=" O MET G 44 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE G 51 " --> pdb=" O ALA G 47 " (cutoff:3.500A) Processing helix chain 'G' and resid 86 through 102 removed outlier: 3.809A pdb=" N ASP G 101 " --> pdb=" O ARG G 97 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLN G 102 " --> pdb=" O HIS G 98 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 122 Processing helix chain 'G' and resid 139 through 155 Processing helix chain 'G' and resid 156 through 159 Processing helix chain 'G' and resid 184 through 191 Processing helix chain 'G' and resid 204 through 276 removed outlier: 4.173A pdb=" N GLU G 211 " --> pdb=" O ARG G 207 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N SER G 276 " --> pdb=" O THR G 272 " (cutoff:3.500A) Processing helix chain 'H' and resid 93 through 97 Processing helix chain 'H' and resid 100 through 115 removed outlier: 3.540A pdb=" N SER H 114 " --> pdb=" O LYS H 110 " (cutoff:3.500A) Processing helix chain 'H' and resid 119 through 136 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: 3.659A 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: 4.180A pdb=" N HIS O 78 " --> pdb=" O ILE O 74 " (cutoff:3.500A) Processing helix chain 'O' and resid 82 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 179 through 191 removed outlier: 3.565A pdb=" N LYS O 183 " --> pdb=" O SER O 179 " (cutoff:3.500A) Processing helix chain 'T' and resid 27 through 43 removed outlier: 3.509A pdb=" N LEU T 43 " --> pdb=" O VAL T 39 " (cutoff:3.500A) Processing helix chain 'T' and resid 58 through 77 removed outlier: 3.994A pdb=" N GLN T 62 " --> pdb=" O TRP T 58 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TYR T 66 " --> pdb=" O GLN T 62 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLY T 75 " --> pdb=" O ASN T 71 " (cutoff:3.500A) Processing helix chain 'T' and resid 85 through 103 removed outlier: 3.808A pdb=" N ILE T 96 " --> pdb=" O LEU T 92 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N LEU T 101 " --> pdb=" O PHE T 97 " (cutoff:3.500A) Processing helix chain 'T' and resid 114 through 137 removed outlier: 3.881A pdb=" N ILE T 118 " --> pdb=" O HIS T 114 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU T 132 " --> pdb=" O GLY T 128 " (cutoff:3.500A) Processing helix chain 'T' and resid 138 through 146 Processing helix chain 'T' and resid 151 through 155 Processing helix chain 'T' and resid 156 through 167 removed outlier: 3.715A pdb=" N GLU T 162 " --> pdb=" O LEU T 158 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N SER T 165 " --> pdb=" O ILE T 161 " (cutoff:3.500A) Processing helix chain 'T' and resid 168 through 199 removed outlier: 3.817A pdb=" N LEU T 173 " --> pdb=" O ARG T 169 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N GLY T 174 " --> pdb=" O ALA T 170 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N LEU T 177 " --> pdb=" O LEU T 173 " (cutoff:3.500A) Processing helix chain 'T' and resid 202 through 207 Processing helix chain 'T' and resid 209 through 247 removed outlier: 3.716A pdb=" N LEU T 213 " --> pdb=" O GLY T 209 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N MET T 215 " --> pdb=" O VAL T 211 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ILE T 228 " --> pdb=" O PHE T 224 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA T 235 " --> pdb=" O GLY T 231 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LEU T 242 " --> pdb=" O THR T 238 " (cutoff:3.500A) Processing helix chain 'U' and resid 54 through 186 removed outlier: 3.780A pdb=" N LEU U 58 " --> pdb=" O ASP U 54 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ALA U 74 " --> pdb=" O ALA U 70 " (cutoff:3.500A) Proline residue: U 75 - end of helix removed outlier: 3.629A pdb=" N GLN U 112 " --> pdb=" O ASP U 108 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU U 113 " --> pdb=" O SER U 109 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASN U 115 " --> pdb=" O SER U 111 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLU U 118 " --> pdb=" O GLN U 114 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N LYS U 121 " --> pdb=" O ALA U 117 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL U 122 " --> pdb=" O GLU U 118 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS U 128 " --> pdb=" O PHE U 124 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N GLU U 139 " --> pdb=" O SER U 135 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY U 185 " --> pdb=" O GLN U 181 " (cutoff:3.500A) Processing helix chain 'U' and resid 187 through 206 removed outlier: 3.970A pdb=" N VAL U 193 " --> pdb=" O PHE U 189 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU U 194 " --> pdb=" O GLN U 190 " (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 56 through 62 removed outlier: 3.978A pdb=" N SER V 60 " --> pdb=" O SER V 56 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU V 62 " --> pdb=" O TYR V 58 " (cutoff:3.500A) Processing helix chain 'V' and resid 67 through 78 Processing helix chain 'V' and resid 90 through 127 removed outlier: 3.829A pdb=" N SER V 94 " --> pdb=" O GLN V 90 " (cutoff:3.500A) Processing helix chain 'V' and resid 134 through 142 Processing helix chain 'V' and resid 143 through 156 Processing helix chain 'W' and resid 5 through 9 Processing helix chain 'W' and resid 18 through 30 removed outlier: 4.151A pdb=" N LYS W 22 " --> pdb=" O ALA W 18 " (cutoff:3.500A) removed outlier: 3.933A 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 84 Processing helix chain 'X' and resid 2 through 14 Processing helix chain 'X' and resid 20 through 27 removed outlier: 3.613A pdb=" N ALA X 24 " --> pdb=" O THR X 20 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLY X 26 " --> pdb=" O GLN X 22 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ASN X 27 " --> pdb=" O ASP X 23 " (cutoff:3.500A) Processing helix chain 'X' and resid 47 through 57 Processing helix chain 'Y' and resid 7 through 11 removed outlier: 3.921A pdb=" N LEU Y 10 " --> pdb=" O THR Y 7 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LYS Y 11 " --> pdb=" O PRO Y 8 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 7 through 11' Processing helix chain 'Y' and resid 13 through 35 Processing helix chain 'Z' and resid 8 through 30 Processing helix chain 'Z' and resid 30 through 48 removed outlier: 3.541A pdb=" N MET Z 34 " --> pdb=" O PHE Z 30 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ILE Z 35 " --> pdb=" O PHE Z 31 " (cutoff:3.500A) removed outlier: 3.536A 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: 6.720A pdb=" N ARG A 42 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N VAL A 36 " --> pdb=" O ILE A 40 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ILE A 40 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N GLY A 74 " --> pdb=" O LEU A 66 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LEU A 66 " --> pdb=" O GLY A 74 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N GLU A 53 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N LEU A 54 " --> pdb=" O THR A 93 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 98 through 101 Processing sheet with id=AA3, first strand: chain 'A' and resid 108 through 110 removed outlier: 6.700A pdb=" N ARG A 108 " --> pdb=" O ILE A 233 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N ALA A 235 " --> pdb=" O ARG A 108 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N VAL A 110 " --> pdb=" O ALA A 235 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N THR A 237 " --> pdb=" O VAL A 110 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N TYR A 205 " --> pdb=" O VAL A 234 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N ALA A 236 " --> pdb=" O TYR A 205 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N ALA A 207 " --> pdb=" O ALA A 236 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 169 through 172 removed outlier: 5.970A pdb=" N ILE A 169 " --> pdb=" O ILE A 329 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N THR A 331 " --> pdb=" O ILE A 169 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N GLY A 171 " --> pdb=" O THR A 331 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 30 through 37 removed outlier: 5.812A pdb=" N ARG B 42 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N VAL B 36 " --> pdb=" O ILE B 40 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N ILE B 40 " --> pdb=" O VAL B 36 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 40 through 45 current: chain 'B' and resid 62 through 69 removed outlier: 5.823A pdb=" N GLY B 63 " --> pdb=" O PHE B 78 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N PHE B 78 " --> pdb=" O GLY B 63 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N ALA B 65 " --> pdb=" O VAL B 76 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N VAL B 76 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASN B 67 " --> pdb=" O GLY B 74 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 72 through 78 current: chain 'C' and resid 40 through 45 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 40 through 45 current: chain 'C' and resid 62 through 68 removed outlier: 5.628A pdb=" N ALA C 65 " --> pdb=" O VAL C 76 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N VAL C 76 " --> pdb=" O ALA C 65 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 72 through 77 current: chain 'D' and resid 20 through 25 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 20 through 25 current: chain 'D' and resid 44 through 55 removed outlier: 6.704A pdb=" N ARG D 60 " --> pdb=" O ALA D 51 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N HIS D 53 " --> pdb=" O THR D 58 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N THR D 58 " --> pdb=" O HIS D 53 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 58 through 63 current: chain 'F' and resid 20 through 25 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 20 through 25 current: chain 'F' and resid 44 through 53 removed outlier: 6.473A pdb=" N ARG F 60 " --> pdb=" O ALA F 51 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N HIS F 53 " --> pdb=" O THR F 58 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N THR F 58 " --> pdb=" O HIS F 53 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 98 through 101 Processing sheet with id=AA7, first strand: chain 'B' and resid 109 through 111 removed outlier: 6.427A pdb=" N CYS B 203 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N VAL B 234 " --> pdb=" O CYS B 203 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N TYR B 205 " --> pdb=" O VAL B 234 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N ALA B 236 " --> pdb=" O TYR B 205 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ALA B 207 " --> pdb=" O ALA B 236 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ILE B 268 " --> pdb=" O LEU B 326 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N VAL B 328 " --> pdb=" O ILE B 268 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N TYR B 270 " --> pdb=" O VAL B 328 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N GLU B 330 " --> pdb=" O TYR B 270 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ILE B 169 " --> pdb=" O ILE B 329 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N THR B 331 " --> pdb=" O ILE B 169 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N GLY B 171 " --> pdb=" O THR B 331 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N ILE B 170 " --> pdb=" O LEU B 354 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N PHE B 353 " --> pdb=" O LEU B 371 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N LEU B 371 " --> pdb=" O PHE B 353 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 100 through 101 Processing sheet with id=AA9, first strand: chain 'C' and resid 109 through 110 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 109 through 110 current: chain 'C' and resid 231 through 237 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 231 through 237 current: chain 'C' and resid 322 through 331 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 322 through 331 current: chain 'C' and resid 373 through 374 No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'C' and resid 147 through 148 removed outlier: 4.614A pdb=" N ILE C 161 " --> pdb=" O VAL C 148 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 84 through 86 Processing sheet with id=AB3, first strand: chain 'D' and resid 95 through 96 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 95 through 96 current: chain 'D' and resid 215 through 221 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 215 through 221 current: chain 'D' and resid 302 through 310 No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'E' and resid 10 through 17 removed outlier: 5.984A pdb=" N ASP E 22 " --> pdb=" O THR E 14 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N VAL E 16 " --> pdb=" O ILE E 20 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ILE E 20 " --> pdb=" O VAL E 16 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL E 21 " --> pdb=" O THR E 61 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL E 23 " --> pdb=" O VAL E 59 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N THR E 58 " --> pdb=" O HIS E 53 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N HIS E 53 " --> pdb=" O THR E 58 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ARG E 60 " --> pdb=" O ALA E 51 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N LYS E 40 " --> pdb=" O LYS E 75 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N LYS E 75 " --> pdb=" O LYS E 40 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 84 through 87 removed outlier: 3.863A pdb=" N LEU E 113 " --> pdb=" O VAL E 87 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 95 through 96 removed outlier: 3.720A pdb=" N PHE E 219 " --> pdb=" O ILE E 96 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N SER E 182 " --> pdb=" O ALA E 216 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N VAL E 218 " --> pdb=" O SER E 182 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N PHE E 184 " --> pdb=" O VAL E 218 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N GLY E 220 " --> pdb=" O PHE E 184 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N GLY E 186 " --> pdb=" O GLY E 220 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N VAL E 183 " --> pdb=" O PHE E 254 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N ASP E 256 " --> pdb=" O VAL E 183 " (cutoff:3.500A) removed outlier: 8.115A pdb=" N THR E 185 " --> pdb=" O ASP E 256 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA E 309 " --> pdb=" O ILE E 255 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ASN E 257 " --> pdb=" O ALA E 309 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 133 through 134 removed outlier: 3.962A pdb=" N TYR E 147 " --> pdb=" O LEU E 134 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 84 through 87 removed outlier: 4.147A pdb=" N LEU F 113 " --> pdb=" O VAL F 87 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 95 through 96 removed outlier: 6.051A pdb=" N ILE F 96 " --> pdb=" O PHE F 219 " (cutoff:3.500A) removed outlier: 8.373A pdb=" N GLN F 221 " --> pdb=" O ILE F 96 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ALA F 216 " --> pdb=" O VAL F 183 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N THR F 185 " --> pdb=" O ALA F 216 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N VAL F 218 " --> pdb=" O THR F 185 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N VAL F 187 " --> pdb=" O VAL F 218 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N GLY F 220 " --> pdb=" O VAL F 187 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N THR F 305 " --> pdb=" O VAL F 251 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N LYS F 152 " --> pdb=" O ALA F 331 " (cutoff:3.500A) removed outlier: 8.216A pdb=" N THR F 333 " --> pdb=" O LYS F 152 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N GLY F 154 " --> pdb=" O THR F 333 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N LEU F 335 " --> pdb=" O GLY F 154 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N PHE F 156 " --> pdb=" O LEU F 335 " (cutoff:3.500A) removed outlier: 10.962A pdb=" N THR F 332 " --> pdb=" O LEU F 351 " (cutoff:3.500A) removed outlier: 9.440A pdb=" N LEU F 351 " --> pdb=" O THR F 332 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N VAL F 334 " --> pdb=" O ASP F 349 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 133 through 134 removed outlier: 3.664A pdb=" N TYR F 147 " --> pdb=" O LEU F 134 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 174 through 182 removed outlier: 6.320A pdb=" N SER G 174 " --> pdb=" O VAL G 170 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL G 170 " --> pdb=" O SER G 174 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ILE G 162 " --> pdb=" O ILE G 182 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N LEU G 73 " --> pdb=" O SER G 163 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N PHE G 165 " --> pdb=" O LEU G 73 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N VAL G 75 " --> pdb=" O PHE G 165 " (cutoff:3.500A) removed outlier: 8.969A pdb=" N ASN G 167 " --> pdb=" O VAL G 75 " (cutoff:3.500A) removed outlier: 8.954A pdb=" N ILE G 77 " --> pdb=" O ASN G 167 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ILE G 74 " --> pdb=" O VAL G 108 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N ILE G 110 " --> pdb=" O ILE G 74 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N ALA G 76 " --> pdb=" O ILE G 110 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N ILE G 107 " --> pdb=" O LEU G 128 " (cutoff:3.500A) removed outlier: 8.150A pdb=" N ILE G 130 " --> pdb=" O ILE G 107 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N THR G 109 " --> pdb=" O ILE G 130 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 12 through 15 Processing sheet with id=AC4, first strand: chain 'H' and resid 37 through 42 removed outlier: 6.658A pdb=" N VAL H 56 " --> pdb=" O PRO H 33 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'O' and resid 119 through 120 removed outlier: 6.622A pdb=" N LEU O 119 " --> pdb=" O LYS O 154 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'O' and resid 157 through 159 2227 hydrogen bonds defined for protein. 6456 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: 8.96 Time building geometry restraints manager: 10.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.28: 5058 1.28 - 1.35: 2342 1.35 - 1.42: 2676 1.42 - 1.48: 5358 1.48 - 1.55: 4750 Bond restraints: 20184 Sorted by residual: bond pdb=" CA HIS A 478 " pdb=" C HIS A 478 " ideal model delta sigma weight residual 1.533 1.479 0.054 9.60e-03 1.09e+04 3.19e+01 bond pdb=" CA LEU T 111 " pdb=" C LEU T 111 " ideal model delta sigma weight residual 1.524 1.489 0.035 7.00e-03 2.04e+04 2.55e+01 bond pdb=" CA SER E 306 " pdb=" C SER E 306 " ideal model delta sigma weight residual 1.520 1.462 0.058 1.20e-02 6.94e+03 2.34e+01 bond pdb=" CA ASP B 156 " pdb=" C ASP B 156 " ideal model delta sigma weight residual 1.523 1.459 0.064 1.34e-02 5.57e+03 2.28e+01 bond pdb=" CA PHE F 156 " pdb=" C PHE F 156 " ideal model delta sigma weight residual 1.530 1.472 0.059 1.23e-02 6.61e+03 2.28e+01 ... (remaining 20179 not shown) Histogram of bond angle deviations from ideal: 95.91 - 102.97: 325 102.97 - 110.03: 1957 110.03 - 117.09: 5046 117.09 - 124.15: 16279 124.15 - 131.21: 1563 Bond angle restraints: 25170 Sorted by residual: angle pdb=" N VAL A 376 " pdb=" CA VAL A 376 " pdb=" C VAL A 376 " ideal model delta sigma weight residual 111.62 103.02 8.60 7.90e-01 1.60e+00 1.19e+02 angle pdb=" N GLN B 398 " pdb=" CA GLN B 398 " pdb=" C GLN B 398 " ideal model delta sigma weight residual 113.41 101.89 11.52 1.22e+00 6.72e-01 8.92e+01 angle pdb=" N ILE O 180 " pdb=" CA ILE O 180 " pdb=" C ILE O 180 " ideal model delta sigma weight residual 111.58 102.08 9.50 1.06e+00 8.90e-01 8.03e+01 angle pdb=" N ILE F 95 " pdb=" CA ILE F 95 " pdb=" C ILE F 95 " ideal model delta sigma weight residual 108.11 95.91 12.20 1.40e+00 5.10e-01 7.60e+01 angle pdb=" N ILE E 258 " pdb=" CA ILE E 258 " pdb=" C ILE E 258 " ideal model delta sigma weight residual 113.22 102.70 10.52 1.23e+00 6.61e-01 7.32e+01 ... (remaining 25165 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.60: 4935 17.60 - 35.21: 81 35.21 - 52.81: 4 52.81 - 70.41: 1 70.41 - 88.02: 1 Dihedral angle restraints: 5022 sinusoidal: 4 harmonic: 5018 Sorted by residual: 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 -138.88 -41.12 0 5.00e+00 4.00e-02 6.76e+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 -139.31 -40.69 0 5.00e+00 4.00e-02 6.62e+01 dihedral pdb=" CA ASN 3 40 " pdb=" C ASN 3 40 " pdb=" N PRO 3 41 " pdb=" CA PRO 3 41 " ideal model delta harmonic sigma weight residual -180.00 -142.07 -37.93 0 5.00e+00 4.00e-02 5.75e+01 ... (remaining 5019 not shown) Chirality restraints: 0 Planarity restraints: 5022 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL V 67 " 0.020 2.00e-02 2.50e+03 3.91e-02 1.53e+01 pdb=" C VAL V 67 " -0.068 2.00e-02 2.50e+03 pdb=" O VAL V 67 " 0.025 2.00e-02 2.50e+03 pdb=" N ILE V 68 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR X 7 " -0.019 2.00e-02 2.50e+03 3.80e-02 1.45e+01 pdb=" C TYR X 7 " 0.066 2.00e-02 2.50e+03 pdb=" O TYR X 7 " -0.025 2.00e-02 2.50e+03 pdb=" N LEU X 8 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU O 76 " -0.018 2.00e-02 2.50e+03 3.67e-02 1.34e+01 pdb=" C GLU O 76 " 0.063 2.00e-02 2.50e+03 pdb=" O GLU O 76 " -0.024 2.00e-02 2.50e+03 pdb=" N THR O 77 " -0.021 2.00e-02 2.50e+03 ... (remaining 5019 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.90: 9969 2.90 - 3.40: 17544 3.40 - 3.90: 26394 3.90 - 4.40: 27402 4.40 - 4.90: 39981 Nonbonded interactions: 121290 Sorted by model distance: nonbonded pdb=" N GLN B 6 " pdb=" O GLN B 6 " model vdw 2.394 2.496 nonbonded pdb=" N LEU H 16 " pdb=" O LEU H 16 " model vdw 2.396 2.496 nonbonded pdb=" N PHE E 181 " pdb=" O PHE E 181 " model vdw 2.397 2.496 nonbonded pdb=" N SER V 66 " pdb=" N VAL V 67 " model vdw 2.398 2.560 nonbonded pdb=" N THR E 305 " pdb=" O THR E 305 " model vdw 2.399 2.496 ... (remaining 121285 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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' 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=0.00 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: 1.220 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: 4.820 Check model and map are aligned: 0.310 Set scattering table: 0.190 Process input model: 62.270 Find NCS groups from input model: 1.900 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6274 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 0.064 20184 Z= 1.443 Angle : 2.214 12.819 25170 Z= 1.593 Chirality : 0.000 0.000 0 Planarity : 0.009 0.039 5022 Dihedral : 6.549 88.015 5022 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 0.08 Ramachandran Plot: Outliers : 1.55 % Allowed : 3.93 % Favored : 94.52 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.97 % Cis-general : 0.10 % Twisted Proline : 3.96 % 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: -0.40 (0.11), residues: 4982 helix: 0.81 (0.09), residues: 2764 sheet: -1.04 (0.22), residues: 545 loop : -1.77 (0.13), residues: 1673 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9964 Ramachandran restraints generated. 4982 Oldfield, 0 Emsley, 4982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9964 Ramachandran restraints generated. 4982 Oldfield, 0 Emsley, 4982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 4112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 2.266 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.1668 time to fit residues: 29.3315 Evaluate side-chains 82 residues out of total 4112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 2.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 491 random chunks: chunk 414 optimal weight: 5.9990 chunk 372 optimal weight: 7.9990 chunk 206 optimal weight: 5.9990 chunk 127 optimal weight: 20.0000 chunk 251 optimal weight: 10.0000 chunk 198 optimal weight: 9.9990 chunk 384 optimal weight: 6.9990 chunk 148 optimal weight: 3.9990 chunk 234 optimal weight: 5.9990 chunk 286 optimal weight: 8.9990 chunk 445 optimal weight: 9.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6284 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 20184 Z= 0.181 Angle : 0.514 6.995 25170 Z= 0.327 Chirality : 0.000 0.000 0 Planarity : 0.003 0.021 5022 Dihedral : 4.787 80.608 5022 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 0.69 Ramachandran Plot: Outliers : 0.32 % Allowed : 2.65 % Favored : 97.03 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.97 % Cis-general : 0.10 % 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: 1.48 (0.12), residues: 4982 helix: 2.44 (0.10), residues: 2794 sheet: -0.83 (0.21), residues: 562 loop : -0.97 (0.15), residues: 1626 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9964 Ramachandran restraints generated. 4982 Oldfield, 0 Emsley, 4982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9964 Ramachandran restraints generated. 4982 Oldfield, 0 Emsley, 4982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 4112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 2.454 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.1729 time to fit residues: 30.3934 Evaluate side-chains 82 residues out of total 4112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 2.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 491 random chunks: chunk 247 optimal weight: 50.0000 chunk 138 optimal weight: 30.0000 chunk 371 optimal weight: 50.0000 chunk 303 optimal weight: 20.0000 chunk 122 optimal weight: 30.0000 chunk 446 optimal weight: 50.0000 chunk 482 optimal weight: 0.4980 chunk 397 optimal weight: 0.9990 chunk 442 optimal weight: 120.0000 chunk 152 optimal weight: 20.0000 chunk 358 optimal weight: 50.0000 overall best weight: 14.2994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6584 moved from start: 0.3387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 20184 Z= 0.301 Angle : 0.657 9.910 25170 Z= 0.419 Chirality : 0.000 0.000 0 Planarity : 0.004 0.026 5022 Dihedral : 5.282 69.820 5022 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.36 % Allowed : 4.90 % Favored : 94.74 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.97 % Cis-general : 0.10 % 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: 1.52 (0.12), residues: 4982 helix: 2.53 (0.10), residues: 2773 sheet: -0.90 (0.21), residues: 553 loop : -0.99 (0.15), residues: 1656 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9964 Ramachandran restraints generated. 4982 Oldfield, 0 Emsley, 4982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9964 Ramachandran restraints generated. 4982 Oldfield, 0 Emsley, 4982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 4112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 2.609 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.1792 time to fit residues: 31.3370 Evaluate side-chains 82 residues out of total 4112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 2.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 491 random chunks: chunk 441 optimal weight: 80.0000 chunk 335 optimal weight: 30.0000 chunk 231 optimal weight: 10.0000 chunk 49 optimal weight: 110.0000 chunk 213 optimal weight: 30.0000 chunk 299 optimal weight: 20.0000 chunk 448 optimal weight: 90.0000 chunk 474 optimal weight: 50.0000 chunk 234 optimal weight: 30.0000 chunk 424 optimal weight: 0.0470 chunk 127 optimal weight: 6.9990 overall best weight: 13.4092 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6600 moved from start: 0.4087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20184 Z= 0.252 Angle : 0.544 8.368 25170 Z= 0.347 Chirality : 0.000 0.000 0 Planarity : 0.003 0.020 5022 Dihedral : 4.748 62.581 5022 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.58 % Favored : 95.10 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.97 % Cis-general : 0.10 % 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: 1.53 (0.12), residues: 4982 helix: 2.60 (0.10), residues: 2813 sheet: -1.24 (0.22), residues: 529 loop : -1.09 (0.15), residues: 1640 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9964 Ramachandran restraints generated. 4982 Oldfield, 0 Emsley, 4982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9964 Ramachandran restraints generated. 4982 Oldfield, 0 Emsley, 4982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 4112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 2.723 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.1714 time to fit residues: 30.4063 Evaluate side-chains 82 residues out of total 4112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 2.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 491 random chunks: chunk 395 optimal weight: 50.0000 chunk 269 optimal weight: 50.0000 chunk 6 optimal weight: 9.9990 chunk 353 optimal weight: 30.0000 chunk 195 optimal weight: 9.9990 chunk 404 optimal weight: 8.9990 chunk 328 optimal weight: 20.0000 chunk 0 optimal weight: 70.0000 chunk 242 optimal weight: 8.9990 chunk 425 optimal weight: 40.0000 chunk 119 optimal weight: 50.0000 overall best weight: 11.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6629 moved from start: 0.4538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20184 Z= 0.224 Angle : 0.496 9.158 25170 Z= 0.316 Chirality : 0.000 0.000 0 Planarity : 0.003 0.021 5022 Dihedral : 4.530 50.321 5022 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.56 % Favored : 94.16 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.97 % Cis-general : 0.10 % 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: 1.64 (0.13), residues: 4982 helix: 2.77 (0.10), residues: 2803 sheet: -1.28 (0.23), residues: 493 loop : -1.16 (0.15), residues: 1686 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9964 Ramachandran restraints generated. 4982 Oldfield, 0 Emsley, 4982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9964 Ramachandran restraints generated. 4982 Oldfield, 0 Emsley, 4982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 4112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 2.497 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.1802 time to fit residues: 34.5434 Evaluate side-chains 82 residues out of total 4112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 2.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 491 random chunks: chunk 159 optimal weight: 40.0000 chunk 427 optimal weight: 50.0000 chunk 93 optimal weight: 10.0000 chunk 278 optimal weight: 50.0000 chunk 117 optimal weight: 50.0000 chunk 475 optimal weight: 50.0000 chunk 394 optimal weight: 50.0000 chunk 219 optimal weight: 30.0000 chunk 39 optimal weight: 50.0000 chunk 157 optimal weight: 0.0470 chunk 249 optimal weight: 0.5980 overall best weight: 16.1290 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6728 moved from start: 0.5164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 20184 Z= 0.290 Angle : 0.603 10.355 25170 Z= 0.387 Chirality : 0.000 0.000 0 Planarity : 0.003 0.020 5022 Dihedral : 5.111 49.012 5022 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.30 % Allowed : 6.68 % Favored : 93.01 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.97 % Cis-general : 0.10 % 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: 0.95 (0.12), residues: 4982 helix: 2.21 (0.10), residues: 2795 sheet: -1.57 (0.26), residues: 383 loop : -1.47 (0.15), residues: 1804 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9964 Ramachandran restraints generated. 4982 Oldfield, 0 Emsley, 4982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9964 Ramachandran restraints generated. 4982 Oldfield, 0 Emsley, 4982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 4112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 2.568 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.1722 time to fit residues: 30.3400 Evaluate side-chains 82 residues out of total 4112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 2.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 491 random chunks: chunk 458 optimal weight: 40.0000 chunk 53 optimal weight: 50.0000 chunk 270 optimal weight: 30.0000 chunk 346 optimal weight: 50.0000 chunk 268 optimal weight: 50.0000 chunk 399 optimal weight: 40.0000 chunk 265 optimal weight: 20.0000 chunk 473 optimal weight: 50.0000 chunk 296 optimal weight: 6.9990 chunk 288 optimal weight: 50.0000 chunk 218 optimal weight: 50.0000 overall best weight: 27.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6887 moved from start: 0.6038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 20184 Z= 0.463 Angle : 0.840 13.541 25170 Z= 0.551 Chirality : 0.000 0.000 0 Planarity : 0.005 0.025 5022 Dihedral : 6.385 50.403 5022 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 16.46 Ramachandran Plot: Outliers : 0.34 % Allowed : 9.63 % Favored : 90.02 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.97 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.97 (0.12), residues: 4982 helix: 0.49 (0.09), residues: 2758 sheet: -2.00 (0.28), residues: 342 loop : -2.08 (0.14), residues: 1882 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9964 Ramachandran restraints generated. 4982 Oldfield, 0 Emsley, 4982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9964 Ramachandran restraints generated. 4982 Oldfield, 0 Emsley, 4982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 4112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 2.459 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.1692 time to fit residues: 30.1463 Evaluate side-chains 82 residues out of total 4112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 2.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 491 random chunks: chunk 292 optimal weight: 30.0000 chunk 188 optimal weight: 30.0000 chunk 282 optimal weight: 30.0000 chunk 142 optimal weight: 50.0000 chunk 92 optimal weight: 40.0000 chunk 91 optimal weight: 5.9990 chunk 300 optimal weight: 20.0000 chunk 322 optimal weight: 30.0000 chunk 233 optimal weight: 40.0000 chunk 44 optimal weight: 50.0000 chunk 371 optimal weight: 9.9990 overall best weight: 19.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6829 moved from start: 0.6135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 20184 Z= 0.329 Angle : 0.655 11.494 25170 Z= 0.427 Chirality : 0.000 0.000 0 Planarity : 0.004 0.021 5022 Dihedral : 5.685 47.413 5022 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.28 % Allowed : 10.06 % Favored : 89.66 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.97 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.69 (0.12), residues: 4982 helix: 0.80 (0.10), residues: 2773 sheet: -2.15 (0.26), residues: 361 loop : -2.07 (0.14), residues: 1848 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9964 Ramachandran restraints generated. 4982 Oldfield, 0 Emsley, 4982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9964 Ramachandran restraints generated. 4982 Oldfield, 0 Emsley, 4982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 4112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 2.412 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.1677 time to fit residues: 29.6023 Evaluate side-chains 82 residues out of total 4112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 2.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 491 random chunks: chunk 430 optimal weight: 20.0000 chunk 453 optimal weight: 50.0000 chunk 413 optimal weight: 20.0000 chunk 441 optimal weight: 50.0000 chunk 265 optimal weight: 20.0000 chunk 192 optimal weight: 30.0000 chunk 346 optimal weight: 50.0000 chunk 135 optimal weight: 50.0000 chunk 398 optimal weight: 0.0040 chunk 417 optimal weight: 50.0000 chunk 439 optimal weight: 110.0000 overall best weight: 18.0008 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6820 moved from start: 0.6437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 20184 Z= 0.309 Angle : 0.620 11.454 25170 Z= 0.402 Chirality : 0.000 0.000 0 Planarity : 0.003 0.020 5022 Dihedral : 5.436 44.290 5022 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.26 % Allowed : 10.94 % Favored : 88.80 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.97 % Cis-general : 0.10 % 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: -0.45 (0.12), residues: 4982 helix: 1.08 (0.10), residues: 2764 sheet: -2.15 (0.28), residues: 328 loop : -2.09 (0.14), residues: 1890 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9964 Ramachandran restraints generated. 4982 Oldfield, 0 Emsley, 4982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9964 Ramachandran restraints generated. 4982 Oldfield, 0 Emsley, 4982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 4112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 2.534 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.1816 time to fit residues: 32.0794 Evaluate side-chains 82 residues out of total 4112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 2.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 491 random chunks: chunk 289 optimal weight: 40.0000 chunk 466 optimal weight: 50.0000 chunk 284 optimal weight: 20.0000 chunk 221 optimal weight: 40.0000 chunk 324 optimal weight: 40.0000 chunk 489 optimal weight: 60.0000 chunk 450 optimal weight: 50.0000 chunk 389 optimal weight: 30.0000 chunk 40 optimal weight: 220.0000 chunk 300 optimal weight: 30.0000 chunk 238 optimal weight: 30.0000 overall best weight: 30.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6959 moved from start: 0.7061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 20184 Z= 0.495 Angle : 0.885 14.328 25170 Z= 0.587 Chirality : 0.000 0.000 0 Planarity : 0.006 0.024 5022 Dihedral : 6.749 50.030 5022 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 20.73 Ramachandran Plot: Outliers : 0.36 % Allowed : 13.53 % Favored : 86.11 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.97 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.88 (0.11), residues: 4982 helix: -0.20 (0.09), residues: 2698 sheet: -2.01 (0.32), residues: 273 loop : -2.60 (0.13), residues: 2011 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9964 Ramachandran restraints generated. 4982 Oldfield, 0 Emsley, 4982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9964 Ramachandran restraints generated. 4982 Oldfield, 0 Emsley, 4982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 4112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 2.653 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.1823 time to fit residues: 32.0218 Evaluate side-chains 82 residues out of total 4112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 2.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 491 random chunks: chunk 309 optimal weight: 9.9990 chunk 414 optimal weight: 20.0000 chunk 119 optimal weight: 50.0000 chunk 359 optimal weight: 50.0000 chunk 57 optimal weight: 50.0000 chunk 108 optimal weight: 20.0000 chunk 390 optimal weight: 0.0970 chunk 163 optimal weight: 40.0000 chunk 400 optimal weight: 30.0000 chunk 49 optimal weight: 9.9990 chunk 71 optimal weight: 20.0000 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 = 0.2408 r_free = 0.2408 target = 0.028234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2288 r_free = 0.2288 target = 0.023185 restraints weight = 338304.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2283 r_free = 0.2283 target = 0.023070 restraints weight = 389662.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2283 r_free = 0.2283 target = 0.023070 restraints weight = 420947.142| |-----------------------------------------------------------------------------| r_work (final): 0.2241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.6843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 20184 Z= 0.219 Angle : 0.513 10.282 25170 Z= 0.325 Chirality : 0.000 0.000 0 Planarity : 0.003 0.017 5022 Dihedral : 5.243 44.492 5022 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.28 % Allowed : 8.89 % Favored : 90.83 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.97 % Cis-general : 0.10 % 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: -0.45 (0.12), residues: 4982 helix: 1.16 (0.10), residues: 2752 sheet: -2.11 (0.29), residues: 320 loop : -2.22 (0.14), residues: 1910 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2500.19 seconds wall clock time: 46 minutes 17.44 seconds (2777.44 seconds total)