Starting phenix.real_space_refine on Tue Jun 17 10:34:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tkg_25968/06_2025/7tkg_25968.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tkg_25968/06_2025/7tkg_25968.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7tkg_25968/06_2025/7tkg_25968.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tkg_25968/06_2025/7tkg_25968.map" model { file = "/net/cci-nas-00/data/ceres_data/7tkg_25968/06_2025/7tkg_25968.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tkg_25968/06_2025/7tkg_25968.cif" } resolution = 4.5 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= 0.002 sd= 0.114 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 3 Type Number sf(0) Gaussians C 10112 2.51 5 N 5056 2.21 5 O 5060 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 20228 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: 2004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 501, 2004 Classifications: {'peptide': 501} Incomplete info: {'backbone_only': 454} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 18, 'TRANS': 480} Unresolved chain link angles: 19 Unresolved non-hydrogen bonds: 1862 Unresolved non-hydrogen angles: 2709 Unresolved non-hydrogen dihedrals: 1130 Unresolved non-hydrogen chiralities: 607 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': 37, 'ARG:plan': 29} Unresolved non-hydrogen planarities: 811 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: 1984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 1984 Classifications: {'peptide': 496} Incomplete info: {'backbone_only': 450} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 18, 'TRANS': 475} Chain breaks: 1 Unresolved chain link angles: 19 Unresolved non-hydrogen bonds: 1844 Unresolved non-hydrogen angles: 2683 Unresolved non-hydrogen dihedrals: 1118 Unresolved non-hydrogen chiralities: 602 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': 36, 'ARG:plan': 29} Unresolved non-hydrogen planarities: 800 Chain: "D" 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: "E" Number of atoms: 1880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 1880 Classifications: {'peptide': 470} Incomplete info: {'backbone_only': 424} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 446} Unresolved chain link angles: 23 Unresolved non-hydrogen bonds: 1726 Unresolved non-hydrogen angles: 2519 Unresolved non-hydrogen dihedrals: 1034 Unresolved non-hydrogen chiralities: 580 Planarities with less than four sites: {'GLN:plan1': 18, 'ARG:plan': 22, 'TYR:plan': 10, 'ASN:plan1': 10, 'HIS:plan': 7, 'PHE:plan': 17, 'GLU:plan': 37, 'ASP:plan': 25} Unresolved non-hydrogen planarities: 711 Chain: "F" 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: "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: 16.56, per 1000 atoms: 0.82 Number of scatterers: 20228 At special positions: 0 Unit cell: (126.665, 148.225, 234.465, 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 5060 8.00 N 5056 7.00 C 10112 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.82 Conformation dependent library (CDL) restraints added in 4.6 seconds 9968 Ramachandran restraints generated. 4984 Oldfield, 0 Emsley, 4984 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 0 Finding SS restraints... Secondary structure from input PDB file: 195 helices and 25 sheets defined 59.5% alpha, 10.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.40 Creating SS restraints... Processing helix chain '0' and resid 1 through 17 removed outlier: 3.514A pdb=" N GLY 0 13 " --> pdb=" O TYR 0 9 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ILE 0 17 " --> pdb=" O GLY 0 13 " (cutoff:3.500A) Processing helix chain '0' and resid 18 through 40 removed outlier: 4.231A 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: 3.625A pdb=" N THR 0 61 " --> pdb=" O LEU 0 57 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLY 0 62 " --> pdb=" O SER 0 58 " (cutoff:3.500A) Processing helix chain '1' and resid 2 through 17 removed outlier: 3.785A pdb=" N ILE 1 17 " --> pdb=" O GLY 1 13 " (cutoff:3.500A) Processing helix chain '1' and resid 18 through 40 removed outlier: 4.470A pdb=" N ALA 1 22 " --> pdb=" O GLY 1 18 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA 1 27 " --> pdb=" O GLY 1 23 " (cutoff:3.500A) Processing helix chain '1' and resid 43 through 74 Proline residue: 1 49 - end of helix removed outlier: 3.577A pdb=" N THR 1 61 " --> pdb=" O LEU 1 57 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLY 1 62 " --> pdb=" O SER 1 58 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N CYS 1 65 " --> pdb=" O THR 1 61 " (cutoff:3.500A) Processing helix chain '2' and resid 2 through 17 removed outlier: 3.856A pdb=" N ILE 2 17 " --> pdb=" O GLY 2 13 " (cutoff:3.500A) Processing helix chain '2' and resid 18 through 40 removed outlier: 4.430A pdb=" N ALA 2 22 " --> pdb=" O GLY 2 18 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ALA 2 27 " --> pdb=" O GLY 2 23 " (cutoff:3.500A) Processing helix chain '2' and resid 43 through 74 Proline residue: 2 49 - end of helix removed outlier: 3.858A pdb=" N THR 2 61 " --> pdb=" O LEU 2 57 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N GLY 2 62 " --> pdb=" O SER 2 58 " (cutoff:3.500A) Processing helix chain '3' and resid 3 through 17 removed outlier: 3.885A pdb=" N ILE 3 17 " --> pdb=" O GLY 3 13 " (cutoff:3.500A) Processing helix chain '3' and resid 19 through 40 removed outlier: 3.951A 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: 3.610A pdb=" N GLY 3 62 " --> pdb=" O SER 3 58 " (cutoff:3.500A) Processing helix chain '4' and resid 2 through 17 removed outlier: 3.677A pdb=" N ILE 4 17 " --> pdb=" O GLY 4 13 " (cutoff:3.500A) Processing helix chain '4' and resid 18 through 40 removed outlier: 4.065A pdb=" N ALA 4 22 " --> pdb=" O GLY 4 18 " (cutoff:3.500A) Processing helix chain '4' and resid 43 through 75 Proline residue: 4 49 - end of helix removed outlier: 3.881A pdb=" N THR 4 61 " --> pdb=" O LEU 4 57 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N GLY 4 62 " --> pdb=" O SER 4 58 " (cutoff:3.500A) Processing helix chain '5' and resid 2 through 17 removed outlier: 3.776A pdb=" N ILE 5 17 " --> pdb=" O GLY 5 13 " (cutoff:3.500A) Processing helix chain '5' and resid 18 through 40 removed outlier: 4.353A pdb=" N ALA 5 22 " --> pdb=" O GLY 5 18 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA 5 27 " --> pdb=" O GLY 5 23 " (cutoff:3.500A) Processing helix chain '5' and resid 43 through 75 Proline residue: 5 49 - end of helix removed outlier: 3.501A pdb=" N THR 5 61 " --> pdb=" O LEU 5 57 " (cutoff:3.500A) removed outlier: 4.035A 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: 4.451A pdb=" N ALA 6 22 " --> pdb=" O GLY 6 18 " (cutoff:3.500A) Processing helix chain '6' and resid 43 through 75 Proline residue: 6 49 - end of helix removed outlier: 3.600A pdb=" N THR 6 61 " --> pdb=" O LEU 6 57 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLY 6 62 " --> pdb=" O SER 6 58 " (cutoff:3.500A) Processing helix chain '7' and resid 2 through 40 removed outlier: 3.683A pdb=" N THR 7 16 " --> pdb=" O ALA 7 12 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ILE 7 17 " --> pdb=" O GLY 7 13 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N GLY 7 18 " --> pdb=" O ILE 7 14 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LEU 7 19 " --> pdb=" O SER 7 15 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU 7 20 " --> pdb=" O THR 7 16 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N GLY 7 21 " --> pdb=" O ILE 7 17 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ALA 7 22 " --> pdb=" O GLY 7 18 " (cutoff:3.500A) removed outlier: 3.803A 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: 3.550A pdb=" N THR 7 61 " --> pdb=" O LEU 7 57 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLY 7 62 " --> pdb=" O SER 7 58 " (cutoff:3.500A) Processing helix chain '8' and resid 2 through 17 removed outlier: 3.711A pdb=" N ILE 8 17 " --> pdb=" O GLY 8 13 " (cutoff:3.500A) Processing helix chain '8' and resid 18 through 40 removed outlier: 4.277A pdb=" N ALA 8 22 " --> pdb=" O GLY 8 18 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA 8 27 " --> pdb=" O GLY 8 23 " (cutoff:3.500A) Processing helix chain '8' and resid 43 through 74 Proline residue: 8 49 - end of helix removed outlier: 3.832A pdb=" N THR 8 61 " --> pdb=" O LEU 8 57 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N GLY 8 62 " --> pdb=" O SER 8 58 " (cutoff:3.500A) Processing helix chain '9' and resid 3 through 17 removed outlier: 3.769A pdb=" N ILE 9 17 " --> pdb=" O GLY 9 13 " (cutoff:3.500A) Processing helix chain '9' and resid 18 through 40 removed outlier: 4.293A pdb=" N ALA 9 22 " --> pdb=" O GLY 9 18 " (cutoff:3.500A) Processing helix chain '9' and resid 43 through 75 Proline residue: 9 49 - end of helix removed outlier: 3.542A pdb=" N THR 9 61 " --> pdb=" O LEU 9 57 " (cutoff:3.500A) removed outlier: 3.686A 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 152 through 159 Processing helix chain 'A' and resid 176 through 194 removed outlier: 3.863A pdb=" N ALA A 181 " --> pdb=" O LYS A 177 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N THR A 184 " --> pdb=" O VAL A 180 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ARG A 190 " --> pdb=" O LEU A 186 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N TRP A 191 " --> pdb=" O ASN A 187 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY A 194 " --> pdb=" O ARG A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 199 Processing helix chain 'A' and resid 211 through 225 Processing helix chain 'A' and resid 241 through 263 Proline residue: A 249 - end of helix removed outlier: 3.625A pdb=" N ILE A 255 " --> pdb=" O THR A 251 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N PHE A 259 " --> pdb=" O ILE A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 286 removed outlier: 3.780A 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 297 through 298 No H-bonds generated for 'chain 'A' and resid 297 through 298' Processing helix chain 'A' and resid 299 through 309 Processing helix chain 'A' and resid 332 through 335 removed outlier: 3.807A pdb=" N ASP A 335 " --> pdb=" O GLN A 332 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 332 through 335' Processing helix chain 'A' and resid 338 through 348 Processing helix chain 'A' and resid 355 through 362 Processing helix chain 'A' and resid 382 through 389 Processing helix chain 'A' and resid 391 through 407 removed outlier: 3.609A pdb=" N GLN A 407 " --> pdb=" O ALA A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 431 removed outlier: 3.503A pdb=" N THR A 419 " --> pdb=" O SER A 415 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ARG A 425 " --> pdb=" O VAL A 421 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS A 431 " --> pdb=" O THR A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 442 Processing helix chain 'A' and resid 443 through 452 Processing helix chain 'A' and resid 459 through 461 No H-bonds generated for 'chain 'A' and resid 459 through 461' Processing helix chain 'A' and resid 462 through 477 Processing helix chain 'A' and resid 478 through 489 removed outlier: 3.510A pdb=" N LEU A 482 " --> pdb=" O HIS A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 508 removed outlier: 4.573A pdb=" N ALA A 508 " --> pdb=" O GLU A 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 19 Processing helix chain 'B' and resid 102 through 106 removed outlier: 3.860A pdb=" N LEU B 105 " --> pdb=" O GLY B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 159 Processing helix chain 'B' and resid 176 through 194 removed outlier: 4.048A pdb=" N THR B 184 " --> pdb=" O VAL B 180 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ILE B 185 " --> pdb=" O ALA B 181 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N LYS B 189 " --> pdb=" O ILE B 185 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N ARG B 190 " --> pdb=" O LEU B 186 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N TRP B 191 " --> pdb=" O ASN B 187 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N GLY B 194 " --> pdb=" O ARG B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 225 Processing helix chain 'B' and resid 241 through 262 Proline residue: B 249 - end of helix removed outlier: 3.506A pdb=" N ILE B 255 " --> pdb=" O THR B 251 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N PHE B 259 " --> pdb=" O ILE B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 287 removed outlier: 3.506A pdb=" N GLN B 276 " --> pdb=" O ASP B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 296 Processing helix chain 'B' and resid 299 through 309 Processing helix chain 'B' and resid 338 through 348 Processing helix chain 'B' and resid 355 through 361 removed outlier: 3.582A pdb=" N PHE B 359 " --> pdb=" O GLU B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 381 Processing helix chain 'B' and resid 382 through 388 Processing helix chain 'B' and resid 389 through 402 removed outlier: 3.676A pdb=" N LYS B 393 " --> pdb=" O ALA B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 407 Processing helix chain 'B' and resid 413 through 430 Processing helix chain 'B' and resid 439 through 452 Proline residue: B 445 - end of helix removed outlier: 3.527A pdb=" N GLY B 450 " --> pdb=" O LEU B 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 489 removed outlier: 4.414A pdb=" N GLY B 464 " --> pdb=" O LEU B 460 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N GLU B 465 " --> pdb=" O SER B 461 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N SER B 468 " --> pdb=" O GLY B 464 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASN B 479 " --> pdb=" O LYS B 475 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N GLU B 480 " --> pdb=" O SER B 476 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N LEU B 481 " --> pdb=" O ASN B 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 509 Processing helix chain 'C' and resid 13 through 21 Processing helix chain 'C' and resid 80 through 84 Processing helix chain 'C' and resid 153 through 157 Processing helix chain 'C' and resid 176 through 188 removed outlier: 3.570A pdb=" N VAL C 180 " --> pdb=" O GLY C 176 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ALA C 181 " --> pdb=" O LYS C 177 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR C 184 " --> pdb=" O VAL C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 225 Processing helix chain 'C' and resid 227 through 229 No H-bonds generated for 'chain 'C' and resid 227 through 229' Processing helix chain 'C' and resid 241 through 247 Processing helix chain 'C' and resid 247 through 261 removed outlier: 3.675A pdb=" N PHE C 259 " --> pdb=" O ILE C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 287 removed outlier: 3.517A pdb=" N GLN C 276 " --> pdb=" O ASP C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 296 Processing helix chain 'C' and resid 299 through 309 Processing helix chain 'C' and resid 338 through 348 Processing helix chain 'C' and resid 355 through 361 Processing helix chain 'C' and resid 376 through 380 removed outlier: 3.589A pdb=" N ALA C 379 " --> pdb=" O VAL C 376 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 388 Processing helix chain 'C' and resid 391 through 407 removed outlier: 3.972A pdb=" N GLU C 401 " --> pdb=" O ALA C 397 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N PHE C 405 " --> pdb=" O GLU C 401 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLN C 407 " --> pdb=" O ALA C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 431 removed outlier: 3.710A pdb=" N LYS C 431 " --> pdb=" O THR C 427 " (cutoff:3.500A) Processing helix chain 'C' and resid 439 through 452 Proline residue: C 445 - end of helix 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 478 removed outlier: 3.562A pdb=" N SER C 468 " --> pdb=" O GLY C 464 " (cutoff:3.500A) Processing helix chain 'C' and resid 479 through 489 Processing helix chain 'C' and resid 492 through 509 Processing helix chain 'D' and resid 88 through 92 removed outlier: 3.503A pdb=" N THR D 91 " --> pdb=" O GLY D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 145 Processing helix chain 'D' and resid 162 through 175 Processing helix chain 'D' and resid 190 through 204 Processing helix chain 'D' and resid 225 through 231 Processing helix chain 'D' and resid 231 through 245 Processing helix chain 'D' and resid 258 through 273 removed outlier: 4.324A pdb=" N ALA D 270 " --> pdb=" O SER D 266 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N LEU D 271 " --> pdb=" O GLU D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 277 through 281 Processing helix chain 'D' and resid 284 through 295 Processing helix chain 'D' and resid 312 through 316 removed outlier: 3.636A pdb=" N ASP D 315 " --> pdb=" O VAL D 312 " (cutoff:3.500A) Processing helix chain 'D' and resid 319 through 327 removed outlier: 3.509A pdb=" N THR D 325 " --> pdb=" O ALA D 321 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA D 327 " --> pdb=" O ALA D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 336 through 342 Processing helix chain 'D' and resid 363 through 384 removed outlier: 3.977A pdb=" N HIS D 367 " --> pdb=" O VAL D 363 " (cutoff:3.500A) Processing helix chain 'D' and resid 384 through 391 Processing helix chain 'D' and resid 397 through 415 removed outlier: 4.099A pdb=" N SER D 415 " --> pdb=" O GLN D 411 " (cutoff:3.500A) Processing helix chain 'D' and resid 420 through 426 removed outlier: 4.330A pdb=" N PHE D 424 " --> pdb=" O VAL D 420 " (cutoff:3.500A) Processing helix chain 'D' and resid 433 through 446 removed outlier: 3.602A pdb=" N ALA D 439 " --> pdb=" O LYS D 435 " (cutoff:3.500A) Processing helix chain 'D' and resid 453 through 458 Processing helix chain 'D' and resid 462 through 475 Processing helix chain 'E' and resid 138 through 145 Processing helix chain 'E' and resid 162 through 178 removed outlier: 4.417A pdb=" N LYS E 176 " --> pdb=" O ASN E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 204 Processing helix chain 'E' and resid 225 through 245 removed outlier: 3.569A pdb=" N ARG E 231 " --> pdb=" O GLY E 227 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ALA E 233 " --> pdb=" O ARG E 229 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N LEU E 234 " --> pdb=" O ALA E 230 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N THR E 235 " --> pdb=" O ARG E 231 " (cutoff:3.500A) Processing helix chain 'E' and resid 257 through 273 removed outlier: 3.663A pdb=" N PHE E 261 " --> pdb=" O ASN E 257 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA E 270 " --> pdb=" O SER E 266 " (cutoff:3.500A) Processing helix chain 'E' and resid 277 through 281 Processing helix chain 'E' and resid 284 through 296 removed outlier: 3.521A pdb=" N ILE E 296 " --> pdb=" O LEU E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 313 through 316 Processing helix chain 'E' and resid 319 through 329 removed outlier: 3.802A pdb=" N ALA E 327 " --> pdb=" O ALA E 323 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N HIS E 328 " --> pdb=" O THR E 324 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU E 329 " --> pdb=" O THR E 325 " (cutoff:3.500A) Processing helix chain 'E' and resid 336 through 342 Processing helix chain 'E' and resid 363 through 391 removed outlier: 4.136A pdb=" N HIS E 367 " --> pdb=" O VAL E 363 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ASP E 386 " --> pdb=" O LYS E 382 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N ILE E 387 " --> pdb=" O SER E 383 " (cutoff:3.500A) Processing helix chain 'E' and resid 397 through 414 Processing helix chain 'E' and resid 418 through 422 Processing helix chain 'E' and resid 433 through 447 Processing helix chain 'E' and resid 453 through 457 Processing helix chain 'E' and resid 462 through 475 Processing helix chain 'F' and resid 88 through 92 Processing helix chain 'F' and resid 138 through 145 Processing helix chain 'F' and resid 162 through 178 Processing helix chain 'F' and resid 190 through 204 Processing helix chain 'F' and resid 225 through 248 removed outlier: 4.853A pdb=" N ALA F 233 " --> pdb=" O ARG F 229 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N LEU F 234 " --> pdb=" O ALA F 230 " (cutoff:3.500A) Processing helix chain 'F' and resid 258 through 273 Processing helix chain 'F' and resid 277 through 281 Processing helix chain 'F' and resid 284 through 296 removed outlier: 3.566A pdb=" N ILE F 296 " --> pdb=" O LEU F 292 " (cutoff:3.500A) Processing helix chain 'F' and resid 312 through 316 Processing helix chain 'F' and resid 319 through 329 Processing helix chain 'F' and resid 336 through 341 Processing helix chain 'F' and resid 363 through 392 removed outlier: 4.140A pdb=" N HIS F 367 " --> pdb=" O VAL F 363 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ILE F 387 " --> pdb=" O SER F 383 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE F 390 " --> pdb=" O ASP F 386 " (cutoff:3.500A) Processing helix chain 'F' and resid 397 through 415 removed outlier: 3.592A pdb=" N SER F 415 " --> pdb=" O GLN F 411 " (cutoff:3.500A) Processing helix chain 'F' and resid 418 through 420 No H-bonds generated for 'chain 'F' and resid 418 through 420' 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 457 Processing helix chain 'F' and resid 462 through 475 Processing helix chain 'G' and resid 2 through 56 removed outlier: 3.931A pdb=" N LYS G 33 " --> pdb=" O THR G 29 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER G 40 " --> pdb=" O LYS G 36 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA G 47 " --> pdb=" O LYS G 43 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLU G 48 " --> pdb=" O MET G 44 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE G 51 " --> pdb=" O ALA G 47 " (cutoff:3.500A) Processing helix chain 'G' and resid 86 through 98 Processing helix chain 'G' and resid 111 through 122 removed outlier: 3.814A pdb=" N GLN G 117 " --> pdb=" O LYS G 113 " (cutoff:3.500A) 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 removed outlier: 3.600A pdb=" N GLN G 190 " --> pdb=" O LYS G 186 " (cutoff:3.500A) Processing helix chain 'G' and resid 204 through 276 removed outlier: 4.291A pdb=" N GLU G 211 " --> pdb=" O ARG G 207 " (cutoff:3.500A) Processing helix chain 'H' and resid 93 through 97 Processing helix chain 'H' and resid 100 through 115 removed outlier: 3.847A pdb=" N SER H 113 " --> pdb=" O LYS H 109 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N SER H 114 " --> pdb=" O LYS H 110 " (cutoff:3.500A) Processing helix chain 'H' and resid 119 through 136 removed outlier: 3.650A pdb=" N VAL H 136 " --> pdb=" O ASN H 132 " (cutoff:3.500A) Processing helix chain 'I' and resid 9 through 22 Processing helix chain 'I' and resid 31 through 37 Processing helix chain 'O' and resid 16 through 29 Processing helix chain 'O' and resid 33 through 49 Processing helix chain 'O' and resid 63 through 78 removed outlier: 4.014A pdb=" N HIS O 78 " --> pdb=" O ILE O 74 " (cutoff:3.500A) Processing helix chain 'O' and resid 83 through 95 Processing helix chain 'O' and resid 101 through 117 Processing helix chain 'O' and resid 130 through 144 Processing helix chain 'O' and resid 179 through 191 removed outlier: 3.736A pdb=" N LYS O 183 " --> pdb=" O SER O 179 " (cutoff:3.500A) Processing helix chain 'T' and resid 27 through 46 removed outlier: 4.076A pdb=" N TYR T 44 " --> pdb=" O ILE T 40 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU T 46 " --> pdb=" O SER T 42 " (cutoff:3.500A) Processing helix chain 'T' and resid 58 through 74 removed outlier: 3.961A pdb=" N GLN T 62 " --> pdb=" O TRP T 58 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N MET T 72 " --> pdb=" O THR T 68 " (cutoff:3.500A) Processing helix chain 'T' and resid 82 through 84 No H-bonds generated for 'chain 'T' and resid 82 through 84' Processing helix chain 'T' and resid 85 through 100 removed outlier: 4.096A pdb=" N ILE T 96 " --> pdb=" O LEU T 92 " (cutoff:3.500A) Processing helix chain 'T' and resid 101 through 105 Processing helix chain 'T' and resid 114 through 138 removed outlier: 4.171A pdb=" N ILE T 118 " --> pdb=" O HIS T 114 " (cutoff:3.500A) Processing helix chain 'T' and resid 139 through 146 removed outlier: 3.828A pdb=" N PHE T 142 " --> pdb=" O TRP T 139 " (cutoff:3.500A) Processing helix chain 'T' and resid 151 through 155 Processing helix chain 'T' and resid 156 through 167 removed outlier: 3.867A pdb=" N GLU T 162 " --> pdb=" O LEU T 158 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N SER T 165 " --> pdb=" O ILE T 161 " (cutoff:3.500A) Processing helix chain 'T' and resid 168 through 199 removed outlier: 4.043A pdb=" N LEU T 173 " --> pdb=" O ARG T 169 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N GLY T 174 " --> pdb=" O ALA T 170 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LEU T 177 " --> pdb=" O LEU T 173 " (cutoff:3.500A) Processing helix chain 'T' and resid 202 through 206 Processing helix chain 'T' and resid 209 through 247 removed outlier: 3.954A pdb=" N LEU T 213 " --> pdb=" O GLY T 209 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N PHE T 224 " --> pdb=" O MET T 220 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA T 225 " --> pdb=" O MET T 221 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ALA T 235 " --> pdb=" O GLY T 231 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA T 239 " --> pdb=" O ALA T 235 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU T 242 " --> pdb=" O THR T 238 " (cutoff:3.500A) Processing helix chain 'U' and resid 55 through 184 removed outlier: 4.965A pdb=" N ALA U 74 " --> pdb=" O ALA U 70 " (cutoff:3.500A) Proline residue: U 75 - end of helix removed outlier: 3.933A pdb=" N GLU U 118 " --> pdb=" O GLN U 114 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR U 119 " --> pdb=" O ASN U 115 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N LYS U 121 " --> pdb=" O ALA U 117 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N VAL U 122 " --> pdb=" O GLU U 118 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU U 123 " --> pdb=" O THR U 119 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS U 128 " --> pdb=" O PHE U 124 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU U 136 " --> pdb=" O GLU U 132 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLU U 139 " --> pdb=" O SER U 135 " (cutoff:3.500A) Processing helix chain 'U' and resid 187 through 206 removed outlier: 4.306A pdb=" N VAL U 193 " --> pdb=" O PHE U 189 " (cutoff:3.500A) removed outlier: 3.526A 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: 3.809A pdb=" N SER V 60 " --> pdb=" O SER V 56 " (cutoff:3.500A) removed outlier: 3.829A 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 Processing helix chain 'V' and resid 134 through 142 Processing helix chain 'V' and resid 143 through 156 Processing helix chain 'W' and resid 12 through 17 removed outlier: 4.115A pdb=" N SER W 17 " --> pdb=" O LYS W 13 " (cutoff:3.500A) Processing helix chain 'W' and resid 18 through 30 removed outlier: 3.776A pdb=" N LYS W 22 " --> pdb=" O ALA W 18 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N VAL W 28 " --> pdb=" O ILE W 24 " (cutoff:3.500A) Processing helix chain 'W' and resid 48 through 56 Processing helix chain 'W' and resid 63 through 85 removed outlier: 4.004A pdb=" N GLY W 72 " --> pdb=" O HIS W 68 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ILE W 73 " --> pdb=" O PHE W 69 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TYR W 78 " --> pdb=" O ILE W 74 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N TYR W 82 " --> pdb=" O TYR W 78 " (cutoff:3.500A) Processing helix chain 'X' and resid 2 through 14 Processing helix chain 'X' and resid 20 through 27 Processing helix chain 'X' and resid 46 through 57 removed outlier: 4.095A pdb=" N LEU X 50 " --> pdb=" O GLY X 46 " (cutoff:3.500A) Processing helix chain 'Y' and resid 13 through 35 Processing helix chain 'Z' and resid 8 through 30 Processing helix chain 'Z' and resid 30 through 48 removed outlier: 3.517A pdb=" N MET Z 34 " --> pdb=" O PHE Z 30 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU Z 38 " --> pdb=" O MET Z 34 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 28 removed outlier: 3.521A pdb=" N LEU O 167 " --> pdb=" O LEU O 178 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 31 through 37 removed outlier: 6.495A pdb=" N ARG A 42 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N VAL A 36 " --> pdb=" O ILE A 40 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N ILE A 40 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N VAL A 76 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N ALA A 65 " --> pdb=" O VAL A 76 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N GLU A 53 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N LEU A 54 " --> pdb=" O THR A 93 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 98 through 101 Processing sheet with id=AA4, first strand: chain 'A' and resid 108 through 110 removed outlier: 3.684A pdb=" N ARG A 108 " --> pdb=" O SER A 231 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N TYR A 202 " --> pdb=" O LEU A 267 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N VAL A 269 " --> pdb=" O TYR A 202 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N VAL A 204 " --> pdb=" O VAL A 269 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N ASP A 271 " --> pdb=" O VAL A 204 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N VAL A 206 " --> pdb=" O ASP A 271 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N LEU A 168 " --> pdb=" O ILE A 352 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 31 through 37 removed outlier: 6.970A pdb=" N ARG B 42 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N VAL B 36 " --> pdb=" O ILE B 40 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ILE B 40 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N GLY B 74 " --> pdb=" O LEU B 66 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N LEU B 66 " --> pdb=" O GLY B 74 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 10 through 17 current: chain 'B' and resid 90 through 92 Processing sheet with id=AA6, first strand: chain 'B' and resid 31 through 37 removed outlier: 6.970A pdb=" N ARG B 42 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N VAL B 36 " --> pdb=" O ILE B 40 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ILE B 40 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N GLY B 74 " --> pdb=" O LEU B 66 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N LEU B 66 " --> pdb=" O GLY B 74 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 62 through 68 current: chain 'F' and resid 36 through 40 removed outlier: 6.093A pdb=" N ARG F 60 " --> pdb=" O ALA F 51 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N VAL F 23 " --> pdb=" O VAL F 59 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ILE F 20 " --> pdb=" O VAL F 16 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N VAL F 16 " --> pdb=" O ILE F 20 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N ASP F 22 " --> pdb=" O THR F 14 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 10 through 17 current: chain 'B' and resid 90 through 92 Processing sheet with id=AA7, first strand: chain 'B' and resid 98 through 101 Processing sheet with id=AA8, first strand: chain 'B' and resid 109 through 110 removed outlier: 6.116A pdb=" N VAL B 110 " --> pdb=" O ALA B 235 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N THR B 237 " --> pdb=" O VAL B 110 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N TYR B 205 " --> pdb=" O VAL B 234 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N ALA B 236 " --> pdb=" O TYR B 205 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N ALA B 207 " --> pdb=" O ALA B 236 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N VAL B 204 " --> pdb=" O VAL B 269 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N ASP B 271 " --> pdb=" O VAL B 204 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N VAL B 206 " --> pdb=" O ASP B 271 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 328 through 331 removed outlier: 6.078A pdb=" N ILE B 169 " --> pdb=" O ILE B 329 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N THR B 331 " --> pdb=" O ILE B 169 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N GLY B 171 " --> pdb=" O THR B 331 " (cutoff:3.500A) removed outlier: 9.171A pdb=" N GLN B 351 " --> pdb=" O GLY B 370 " (cutoff:3.500A) removed outlier: 8.490A pdb=" N GLY B 370 " --> pdb=" O GLN B 351 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N PHE B 353 " --> pdb=" O ASN B 368 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 77 through 78 removed outlier: 6.744A pdb=" N ARG D 60 " --> pdb=" O ALA D 51 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N HIS D 53 " --> pdb=" O THR D 58 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N THR D 58 " --> pdb=" O HIS D 53 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE D 17 " --> pdb=" O ILE D 20 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N HIS D 24 " --> pdb=" O VAL D 13 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N VAL D 13 " --> pdb=" O HIS D 24 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N GLY C 63 " --> pdb=" O PHE C 78 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N PHE C 78 " --> pdb=" O GLY C 63 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N ALA C 65 " --> pdb=" O VAL C 76 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N VAL C 76 " --> pdb=" O ALA C 65 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N ILE C 40 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N VAL C 36 " --> pdb=" O ILE C 40 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N ARG C 42 " --> pdb=" O LEU C 34 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N LEU C 54 " --> pdb=" O THR C 93 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N GLU C 53 " --> pdb=" O ALA C 65 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 98 through 101 Processing sheet with id=AB3, first strand: chain 'C' and resid 109 through 111 removed outlier: 6.191A pdb=" N CYS C 203 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N VAL C 234 " --> pdb=" O CYS C 203 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N TYR C 205 " --> pdb=" O VAL C 234 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N ALA C 236 " --> pdb=" O TYR C 205 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N ALA C 207 " --> pdb=" O ALA C 236 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N TYR C 202 " --> pdb=" O HIS C 265 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N TYR C 270 " --> pdb=" O LEU C 326 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N GLU C 167 " --> pdb=" O PRO C 327 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N ILE C 329 " --> pdb=" O GLU C 167 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N ILE C 169 " --> pdb=" O ILE C 329 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N THR C 331 " --> pdb=" O ILE C 169 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N GLY C 171 " --> pdb=" O THR C 331 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N LEU C 168 " --> pdb=" O ILE C 352 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N LEU C 354 " --> pdb=" O LEU C 168 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ILE C 170 " --> pdb=" O LEU C 354 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 84 through 87 removed outlier: 4.056A pdb=" N LEU D 113 " --> pdb=" O VAL D 87 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 95 through 96 removed outlier: 5.750A pdb=" N ILE D 96 " --> pdb=" O PHE D 219 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N GLN D 221 " --> pdb=" O ILE D 96 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ALA D 216 " --> pdb=" O VAL D 183 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N THR D 185 " --> pdb=" O ALA D 216 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N VAL D 218 " --> pdb=" O THR D 185 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N VAL D 187 " --> pdb=" O VAL D 218 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N GLY D 220 " --> pdb=" O VAL D 187 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR D 305 " --> pdb=" O VAL D 251 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 133 through 134 removed outlier: 3.807A pdb=" N TYR D 147 " --> pdb=" O LEU D 134 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 331 through 335 removed outlier: 10.567A pdb=" N THR D 332 " --> pdb=" O LEU D 351 " (cutoff:3.500A) removed outlier: 9.230A pdb=" N LEU D 351 " --> pdb=" O THR D 332 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N VAL D 334 " --> pdb=" O ASP D 349 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 11 through 17 removed outlier: 6.600A pdb=" N ASP E 22 " --> pdb=" O THR E 14 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N VAL E 16 " --> pdb=" O ILE E 20 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N ILE E 20 " --> pdb=" O VAL E 16 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N THR E 58 " --> pdb=" O HIS E 53 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N HIS E 53 " --> pdb=" O THR E 58 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ARG E 60 " --> pdb=" O ALA E 51 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N LYS E 40 " --> pdb=" O LYS E 75 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N LYS E 75 " --> pdb=" O LYS E 40 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 84 through 87 removed outlier: 3.973A pdb=" N LEU E 113 " --> pdb=" O VAL E 87 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 95 through 96 removed outlier: 6.385A pdb=" N PHE E 184 " --> pdb=" O VAL E 218 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N GLY E 220 " --> pdb=" O PHE E 184 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N GLY E 186 " --> pdb=" O GLY E 220 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N VAL E 183 " --> pdb=" O PHE E 254 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N ASP E 256 " --> pdb=" O VAL E 183 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N THR E 185 " --> pdb=" O ASP E 256 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA E 331 " --> pdb=" O LYS E 152 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N GLY E 158 " --> pdb=" O LEU E 335 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 84 through 87 removed outlier: 3.858A pdb=" N LEU F 113 " --> pdb=" O VAL F 87 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 95 through 96 removed outlier: 3.710A pdb=" N PHE F 219 " --> pdb=" O ILE F 96 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N ALA F 216 " --> pdb=" O VAL F 183 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N THR F 185 " --> pdb=" O ALA F 216 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N VAL F 218 " --> pdb=" O THR F 185 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N VAL F 187 " --> pdb=" O VAL F 218 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N GLY F 220 " --> pdb=" O VAL F 187 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N PHE F 181 " --> pdb=" O LEU F 252 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N PHE F 254 " --> pdb=" O PHE F 181 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N VAL F 183 " --> pdb=" O PHE F 254 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N ASP F 256 " --> pdb=" O VAL F 183 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N THR F 185 " --> pdb=" O ASP F 256 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N VAL F 307 " --> pdb=" O LEU F 252 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N PHE F 254 " --> pdb=" O VAL F 307 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N ALA F 309 " --> pdb=" O PHE F 254 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N ASP F 256 " --> pdb=" O ALA F 309 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS F 354 " --> pdb=" O THR F 332 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 133 through 134 removed outlier: 3.632A pdb=" N TYR F 147 " --> pdb=" O LEU F 134 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 176 through 182 removed outlier: 3.897A pdb=" N ILE G 162 " --> pdb=" O ILE G 182 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N ASN G 167 " --> pdb=" O ILE G 77 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N GLU G 72 " --> pdb=" O ASP G 106 " (cutoff:3.500A) removed outlier: 8.391A pdb=" N VAL G 108 " --> pdb=" O GLU G 72 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ILE G 74 " --> pdb=" O VAL G 108 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N ILE G 110 " --> pdb=" O ILE G 74 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N ALA G 76 " --> pdb=" O ILE G 110 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ILE G 107 " --> pdb=" O ILE G 126 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N LEU G 128 " --> pdb=" O ILE G 107 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 12 through 15 removed outlier: 6.032A pdb=" N GLN H 13 " --> pdb=" O VAL H 85 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N ALA H 87 " --> pdb=" O GLN H 13 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N ALA H 15 " --> pdb=" O ALA H 87 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 37 through 42 removed outlier: 6.517A pdb=" N VAL H 56 " --> pdb=" O PRO H 33 " (cutoff:3.500A) 2292 hydrogen bonds defined for protein. 6657 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: 9.57 Time building geometry restraints manager: 6.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.28: 5060 1.28 - 1.35: 3069 1.35 - 1.42: 1965 1.42 - 1.49: 5837 1.49 - 1.56: 4261 Bond restraints: 20192 Sorted by residual: bond pdb=" CA GLY E 11 " pdb=" C GLY E 11 " ideal model delta sigma weight residual 1.516 1.466 0.050 8.20e-03 1.49e+04 3.71e+01 bond pdb=" CA VAL E 312 " pdb=" C VAL E 312 " ideal model delta sigma weight residual 1.528 1.487 0.041 8.50e-03 1.38e+04 2.32e+01 bond pdb=" CA ILE B 40 " pdb=" C ILE B 40 " ideal model delta sigma weight residual 1.527 1.486 0.041 8.50e-03 1.38e+04 2.32e+01 bond pdb=" CA SER A 374 " pdb=" C SER A 374 " ideal model delta sigma weight residual 1.526 1.475 0.051 1.08e-02 8.57e+03 2.22e+01 bond pdb=" CA GLY H 40 " pdb=" C GLY H 40 " ideal model delta sigma weight residual 1.514 1.473 0.040 8.60e-03 1.35e+04 2.22e+01 ... (remaining 20187 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.86: 21200 2.86 - 5.72: 3199 5.72 - 8.58: 673 8.58 - 11.44: 100 11.44 - 14.29: 8 Bond angle restraints: 25180 Sorted by residual: angle pdb=" N VAL V 67 " pdb=" CA VAL V 67 " pdb=" C VAL V 67 " ideal model delta sigma weight residual 113.71 100.50 13.21 9.50e-01 1.11e+00 1.93e+02 angle pdb=" C ASN G 204 " pdb=" N VAL G 205 " pdb=" CA VAL G 205 " ideal model delta sigma weight residual 120.24 126.47 -6.23 6.30e-01 2.52e+00 9.78e+01 angle pdb=" N THR B 175 " pdb=" CA THR B 175 " pdb=" C THR B 175 " ideal model delta sigma weight residual 112.57 102.94 9.63 1.13e+00 7.83e-01 7.26e+01 angle pdb=" CA PRO W 6 " pdb=" C PRO W 6 " pdb=" N PRO W 7 " ideal model delta sigma weight residual 117.93 128.10 -10.17 1.20e+00 6.94e-01 7.18e+01 angle pdb=" CA PRO D 225 " pdb=" C PRO D 225 " pdb=" O PRO D 225 " ideal model delta sigma weight residual 120.90 115.07 5.83 7.20e-01 1.93e+00 6.56e+01 ... (remaining 25175 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.40: 5003 24.40 - 48.79: 18 48.79 - 73.19: 0 73.19 - 97.59: 1 97.59 - 121.98: 2 Dihedral angle restraints: 5024 sinusoidal: 4 harmonic: 5020 Sorted by residual: dihedral pdb=" CA ASP E 256 " pdb=" C ASP E 256 " pdb=" N ASN E 257 " pdb=" CA ASN E 257 " ideal model delta harmonic sigma weight residual -180.00 -58.02 -121.98 0 5.00e+00 4.00e-02 5.95e+02 dihedral pdb=" CA GLU B 29 " pdb=" C GLU B 29 " pdb=" N THR B 30 " pdb=" CA THR B 30 " ideal model delta harmonic sigma weight residual 180.00 80.88 99.12 0 5.00e+00 4.00e-02 3.93e+02 dihedral pdb=" CA ASN 7 40 " pdb=" C ASN 7 40 " pdb=" N PRO 7 41 " pdb=" CA PRO 7 41 " ideal model delta harmonic sigma weight residual -180.00 -137.31 -42.69 0 5.00e+00 4.00e-02 7.29e+01 ... (remaining 5021 not shown) Chirality restraints: 0 Planarity restraints: 5024 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY A 321 " 0.025 2.00e-02 2.50e+03 5.08e-02 2.58e+01 pdb=" C GLY A 321 " -0.088 2.00e-02 2.50e+03 pdb=" O GLY A 321 " 0.034 2.00e-02 2.50e+03 pdb=" N SER A 322 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR C 93 " -0.019 2.00e-02 2.50e+03 3.89e-02 1.52e+01 pdb=" C THR C 93 " 0.067 2.00e-02 2.50e+03 pdb=" O THR C 93 " -0.026 2.00e-02 2.50e+03 pdb=" N GLY C 94 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL E 206 " 0.019 2.00e-02 2.50e+03 3.85e-02 1.48e+01 pdb=" C VAL E 206 " -0.067 2.00e-02 2.50e+03 pdb=" O VAL E 206 " 0.026 2.00e-02 2.50e+03 pdb=" N ILE E 207 " 0.022 2.00e-02 2.50e+03 ... (remaining 5021 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.87: 9438 2.87 - 3.38: 17295 3.38 - 3.88: 26879 3.88 - 4.39: 27378 4.39 - 4.90: 40921 Nonbonded interactions: 121911 Sorted by model distance: nonbonded pdb=" N LEU D 252 " pdb=" O LEU D 252 " model vdw 2.361 2.496 nonbonded pdb=" N GLN B 6 " pdb=" O GLN B 6 " model vdw 2.375 2.496 nonbonded pdb=" N ARG F 114 " pdb=" O ARG F 114 " model vdw 2.378 2.496 nonbonded pdb=" N VAL V 67 " pdb=" N ILE V 68 " model vdw 2.389 2.560 nonbonded pdb=" N SER G 171 " pdb=" O SER G 171 " model vdw 2.398 2.496 ... (remaining 121906 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain '0' and resid 2 through 73) selection = (chain '1' and resid 2 through 73) selection = (chain '2' and resid 2 through 73) selection = (chain '3' and resid 2 through 73) selection = (chain '4' and resid 2 through 73) selection = (chain '5' and resid 2 through 73) selection = (chain '6' and resid 2 through 73) selection = (chain '7' and resid 2 through 73) selection = (chain '8' and resid 2 through 73) selection = (chain '9' and resid 2 through 73) } ncs_group { reference = (chain 'A' and (resid 12 through 407 or resid 410 through 509)) selection = (chain 'B' and resid 12 through 509) selection = chain 'C' } ncs_group { reference = (chain 'D' and resid 8 through 475) selection = (chain 'E' and resid 8 through 475) selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.830 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: 0.020 Extract box with map and model: 0.790 Check model and map are aligned: 0.160 Set scattering table: 0.190 Process input model: 58.640 Find NCS groups from input model: 1.060 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:3.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6196 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 0.061 20192 Z= 1.489 Angle : 2.199 14.294 25180 Z= 1.581 Chirality : 0.000 0.000 0 Planarity : 0.010 0.051 5024 Dihedral : 6.948 121.984 5024 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 0.08 Ramachandran Plot: Outliers : 1.46 % Allowed : 4.29 % Favored : 94.24 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.96 % Cis-general : 0.08 % Twisted Proline : 3.45 % 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: -0.60 (0.11), residues: 4984 helix: 0.75 (0.09), residues: 2831 sheet: -1.38 (0.21), residues: 587 loop : -2.09 (0.13), residues: 1566 Details of bonding type rmsd hydrogen bonds : bond 0.20878 ( 2283) hydrogen bonds : angle 8.05741 ( 6657) covalent geometry : bond 0.01897 (20192) covalent geometry : angle 2.19913 (25180) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9968 Ramachandran restraints generated. 4984 Oldfield, 0 Emsley, 4984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9968 Ramachandran restraints generated. 4984 Oldfield, 0 Emsley, 4984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 4114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 2.335 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.1731 time to fit residues: 30.2870 Evaluate side-chains 82 residues out of total 4114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 2.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 416 optimal weight: 6.9990 chunk 373 optimal weight: 8.9990 chunk 207 optimal weight: 9.9990 chunk 127 optimal weight: 5.9990 chunk 252 optimal weight: 8.9990 chunk 199 optimal weight: 0.5980 chunk 386 optimal weight: 5.9990 chunk 149 optimal weight: 20.0000 chunk 234 optimal weight: 6.9990 chunk 287 optimal weight: 5.9990 chunk 447 optimal weight: 20.0000 overall best weight: 5.1188 ------------------------------------------------------------------------------- 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 = 0.2624 r_free = 0.2624 target = 0.031106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2391 r_free = 0.2391 target = 0.024576 restraints weight = 297715.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2397 r_free = 0.2397 target = 0.024687 restraints weight = 267957.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 15)----------------| | r_work = 0.2402 r_free = 0.2402 target = 0.024786 restraints weight = 248453.913| |-----------------------------------------------------------------------------| r_work (final): 0.2389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 20192 Z= 0.164 Angle : 0.524 9.249 25180 Z= 0.328 Chirality : 0.000 0.000 0 Planarity : 0.003 0.020 5024 Dihedral : 4.880 76.398 5024 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 0.23 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.93 % Favored : 96.83 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.96 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.12), residues: 4984 helix: 2.28 (0.10), residues: 2843 sheet: -1.10 (0.20), residues: 602 loop : -1.27 (0.15), residues: 1539 Details of bonding type rmsd hydrogen bonds : bond 0.04242 ( 2283) hydrogen bonds : angle 4.56272 ( 6657) covalent geometry : bond 0.00217 (20192) covalent geometry : angle 0.52360 (25180) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9968 Ramachandran restraints generated. 4984 Oldfield, 0 Emsley, 4984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9968 Ramachandran restraints generated. 4984 Oldfield, 0 Emsley, 4984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 4114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 2.372 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.1654 time to fit residues: 28.9861 Evaluate side-chains 82 residues out of total 4114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 2.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 282 optimal weight: 9.9990 chunk 87 optimal weight: 20.0000 chunk 349 optimal weight: 40.0000 chunk 439 optimal weight: 30.0000 chunk 341 optimal weight: 50.0000 chunk 130 optimal weight: 40.0000 chunk 450 optimal weight: 120.0000 chunk 117 optimal weight: 50.0000 chunk 48 optimal weight: 50.0000 chunk 350 optimal weight: 50.0000 chunk 326 optimal weight: 50.0000 overall best weight: 27.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2485 r_free = 0.2485 target = 0.038439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2433 r_free = 0.2433 target = 0.034446 restraints weight = 332145.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2420 r_free = 0.2420 target = 0.033940 restraints weight = 782480.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2419 r_free = 0.2419 target = 0.033757 restraints weight = 1039899.573| |-----------------------------------------------------------------------------| r_work (final): 0.2265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.4547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.072 20192 Z= 0.495 Angle : 0.992 17.759 25180 Z= 0.641 Chirality : 0.000 0.000 0 Planarity : 0.006 0.033 5024 Dihedral : 7.020 87.024 5024 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.80 % Favored : 92.96 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.96 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.11), residues: 4984 helix: 0.84 (0.09), residues: 2767 sheet: -1.61 (0.23), residues: 434 loop : -1.80 (0.14), residues: 1783 Details of bonding type rmsd hydrogen bonds : bond 0.07580 ( 2283) hydrogen bonds : angle 7.00993 ( 6657) covalent geometry : bond 0.00659 (20192) covalent geometry : angle 0.99194 (25180) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9968 Ramachandran restraints generated. 4984 Oldfield, 0 Emsley, 4984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9968 Ramachandran restraints generated. 4984 Oldfield, 0 Emsley, 4984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 4114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 2.389 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.1691 time to fit residues: 29.8295 Evaluate side-chains 82 residues out of total 4114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 2.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 108 optimal weight: 20.0000 chunk 470 optimal weight: 50.0000 chunk 66 optimal weight: 50.0000 chunk 19 optimal weight: 50.0000 chunk 189 optimal weight: 30.0000 chunk 184 optimal weight: 30.0000 chunk 107 optimal weight: 30.0000 chunk 262 optimal weight: 30.0000 chunk 361 optimal weight: 50.0000 chunk 233 optimal weight: 50.0000 chunk 204 optimal weight: 0.0670 overall best weight: 22.0134 ------------------------------------------------------------------------------- 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 = 0.2475 r_free = 0.2475 target = 0.039799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2453 r_free = 0.2453 target = 0.035395 restraints weight = 323427.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2418 r_free = 0.2418 target = 0.034421 restraints weight = 559911.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2415 r_free = 0.2415 target = 0.034277 restraints weight = 870680.467| |-----------------------------------------------------------------------------| r_work (final): 0.2229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.5257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 20192 Z= 0.369 Angle : 0.751 13.702 25180 Z= 0.487 Chirality : 0.000 0.000 0 Planarity : 0.004 0.021 5024 Dihedral : 5.935 72.026 5024 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.46 % Favored : 92.30 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.96 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.12), residues: 4984 helix: 0.89 (0.10), residues: 2809 sheet: -1.83 (0.23), residues: 465 loop : -1.78 (0.15), residues: 1710 Details of bonding type rmsd hydrogen bonds : bond 0.05477 ( 2283) hydrogen bonds : angle 6.05482 ( 6657) covalent geometry : bond 0.00492 (20192) covalent geometry : angle 0.75108 (25180) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9968 Ramachandran restraints generated. 4984 Oldfield, 0 Emsley, 4984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9968 Ramachandran restraints generated. 4984 Oldfield, 0 Emsley, 4984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 4114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 2.335 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.1626 time to fit residues: 28.7749 Evaluate side-chains 82 residues out of total 4114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 2.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 197 optimal weight: 8.9990 chunk 70 optimal weight: 40.0000 chunk 19 optimal weight: 50.0000 chunk 150 optimal weight: 40.0000 chunk 99 optimal weight: 30.0000 chunk 431 optimal weight: 50.0000 chunk 318 optimal weight: 30.0000 chunk 30 optimal weight: 50.0000 chunk 433 optimal weight: 100.0000 chunk 280 optimal weight: 40.0000 chunk 293 optimal weight: 10.0000 overall best weight: 23.7998 ------------------------------------------------------------------------------- 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 = 0.2486 r_free = 0.2486 target = 0.034007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2447 r_free = 0.2447 target = 0.030416 restraints weight = 342929.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2425 r_free = 0.2425 target = 0.029431 restraints weight = 663935.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2424 r_free = 0.2424 target = 0.029291 restraints weight = 896030.219| |-----------------------------------------------------------------------------| r_work (final): 0.2219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.6142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 20192 Z= 0.413 Angle : 0.819 16.516 25180 Z= 0.532 Chirality : 0.000 0.000 0 Planarity : 0.005 0.027 5024 Dihedral : 6.447 70.771 5024 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.24 % Allowed : 10.01 % Favored : 89.75 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.96 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.04 (0.12), residues: 4984 helix: 0.50 (0.10), residues: 2760 sheet: -1.95 (0.24), residues: 416 loop : -2.23 (0.14), residues: 1808 Details of bonding type rmsd hydrogen bonds : bond 0.06437 ( 2283) hydrogen bonds : angle 6.76221 ( 6657) covalent geometry : bond 0.00547 (20192) covalent geometry : angle 0.81929 (25180) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9968 Ramachandran restraints generated. 4984 Oldfield, 0 Emsley, 4984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9968 Ramachandran restraints generated. 4984 Oldfield, 0 Emsley, 4984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 4114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 2.175 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.1665 time to fit residues: 29.1193 Evaluate side-chains 82 residues out of total 4114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 2.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 164 optimal weight: 40.0000 chunk 484 optimal weight: 40.0000 chunk 277 optimal weight: 50.0000 chunk 362 optimal weight: 9.9990 chunk 489 optimal weight: 50.0000 chunk 335 optimal weight: 40.0000 chunk 345 optimal weight: 50.0000 chunk 61 optimal weight: 100.0000 chunk 123 optimal weight: 40.0000 chunk 180 optimal weight: 50.0000 chunk 248 optimal weight: 50.0000 overall best weight: 33.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2289 r_free = 0.2289 target = 0.025308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2234 r_free = 0.2234 target = 0.022086 restraints weight = 374317.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2217 r_free = 0.2217 target = 0.021702 restraints weight = 632424.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2214 r_free = 0.2214 target = 0.021638 restraints weight = 876851.011| |-----------------------------------------------------------------------------| r_work (final): 0.2198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.7225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.098 20192 Z= 0.551 Angle : 1.024 19.456 25180 Z= 0.672 Chirality : 0.000 0.000 0 Planarity : 0.006 0.034 5024 Dihedral : 7.511 64.996 5024 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.28 % Allowed : 13.96 % Favored : 85.75 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.96 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.54 (0.11), residues: 4984 helix: -0.84 (0.09), residues: 2702 sheet: -2.56 (0.23), residues: 399 loop : -2.64 (0.14), residues: 1883 Details of bonding type rmsd hydrogen bonds : bond 0.07821 ( 2283) hydrogen bonds : angle 8.25173 ( 6657) covalent geometry : bond 0.00734 (20192) covalent geometry : angle 1.02350 (25180) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9968 Ramachandran restraints generated. 4984 Oldfield, 0 Emsley, 4984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9968 Ramachandran restraints generated. 4984 Oldfield, 0 Emsley, 4984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 4114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 2.476 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.1727 time to fit residues: 30.5341 Evaluate side-chains 82 residues out of total 4114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 2.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 381 optimal weight: 5.9990 chunk 215 optimal weight: 50.0000 chunk 85 optimal weight: 50.0000 chunk 354 optimal weight: 50.0000 chunk 34 optimal weight: 10.0000 chunk 308 optimal weight: 50.0000 chunk 145 optimal weight: 30.0000 chunk 122 optimal weight: 40.0000 chunk 320 optimal weight: 40.0000 chunk 311 optimal weight: 40.0000 chunk 433 optimal weight: 70.0000 overall best weight: 25.1998 ------------------------------------------------------------------------------- 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 = 0.2452 r_free = 0.2452 target = 0.031590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2416 r_free = 0.2416 target = 0.027852 restraints weight = 346260.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2394 r_free = 0.2394 target = 0.027292 restraints weight = 507173.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2394 r_free = 0.2394 target = 0.027292 restraints weight = 706644.727| |-----------------------------------------------------------------------------| r_work (final): 0.2181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.7291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 20192 Z= 0.409 Angle : 0.803 16.840 25180 Z= 0.527 Chirality : 0.000 0.000 0 Planarity : 0.005 0.027 5024 Dihedral : 6.628 67.526 5024 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.24 % Allowed : 13.20 % Favored : 86.56 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.96 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.22 (0.11), residues: 4984 helix: -0.49 (0.09), residues: 2728 sheet: -2.58 (0.23), residues: 419 loop : -2.64 (0.14), residues: 1837 Details of bonding type rmsd hydrogen bonds : bond 0.06236 ( 2283) hydrogen bonds : angle 7.23688 ( 6657) covalent geometry : bond 0.00546 (20192) covalent geometry : angle 0.80299 (25180) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9968 Ramachandran restraints generated. 4984 Oldfield, 0 Emsley, 4984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9968 Ramachandran restraints generated. 4984 Oldfield, 0 Emsley, 4984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 4114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 2.160 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.1625 time to fit residues: 28.3939 Evaluate side-chains 82 residues out of total 4114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 2.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 167 optimal weight: 6.9990 chunk 240 optimal weight: 40.0000 chunk 331 optimal weight: 20.0000 chunk 246 optimal weight: 50.0000 chunk 249 optimal weight: 9.9990 chunk 9 optimal weight: 120.0000 chunk 447 optimal weight: 50.0000 chunk 448 optimal weight: 50.0000 chunk 421 optimal weight: 50.0000 chunk 181 optimal weight: 20.0000 chunk 72 optimal weight: 30.0000 overall best weight: 17.3996 ------------------------------------------------------------------------------- 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 = 0.2438 r_free = 0.2438 target = 0.030437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2413 r_free = 0.2413 target = 0.027206 restraints weight = 347986.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2389 r_free = 0.2389 target = 0.026535 restraints weight = 591174.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.2385 r_free = 0.2385 target = 0.026442 restraints weight = 962513.304| |-----------------------------------------------------------------------------| r_work (final): 0.2234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.7326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 20192 Z= 0.291 Angle : 0.634 15.315 25180 Z= 0.409 Chirality : 0.000 0.000 0 Planarity : 0.004 0.023 5024 Dihedral : 5.846 68.902 5024 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.24 % Allowed : 11.66 % Favored : 88.10 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.96 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.43 (0.12), residues: 4984 helix: 0.28 (0.10), residues: 2746 sheet: -2.39 (0.24), residues: 394 loop : -2.50 (0.14), residues: 1844 Details of bonding type rmsd hydrogen bonds : bond 0.05047 ( 2283) hydrogen bonds : angle 6.31083 ( 6657) covalent geometry : bond 0.00390 (20192) covalent geometry : angle 0.63359 (25180) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9968 Ramachandran restraints generated. 4984 Oldfield, 0 Emsley, 4984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9968 Ramachandran restraints generated. 4984 Oldfield, 0 Emsley, 4984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 4114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 2.191 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.1645 time to fit residues: 28.8631 Evaluate side-chains 82 residues out of total 4114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 2.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 491 optimal weight: 30.0000 chunk 437 optimal weight: 50.0000 chunk 180 optimal weight: 9.9990 chunk 435 optimal weight: 50.0000 chunk 488 optimal weight: 120.0000 chunk 363 optimal weight: 50.0000 chunk 65 optimal weight: 50.0000 chunk 47 optimal weight: 50.0000 chunk 468 optimal weight: 50.0000 chunk 367 optimal weight: 30.0000 chunk 112 optimal weight: 50.0000 overall best weight: 33.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2285 r_free = 0.2285 target = 0.025546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2222 r_free = 0.2222 target = 0.022196 restraints weight = 364965.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2208 r_free = 0.2208 target = 0.021894 restraints weight = 561435.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2206 r_free = 0.2206 target = 0.021809 restraints weight = 726585.470| |-----------------------------------------------------------------------------| r_work (final): 0.2146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.7980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.098 20192 Z= 0.533 Angle : 0.960 19.450 25180 Z= 0.635 Chirality : 0.000 0.000 0 Planarity : 0.006 0.035 5024 Dihedral : 7.207 66.212 5024 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.24 % Allowed : 16.75 % Favored : 83.01 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.96 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.74 (0.11), residues: 4984 helix: -0.88 (0.09), residues: 2679 sheet: -2.65 (0.26), residues: 351 loop : -2.95 (0.13), residues: 1954 Details of bonding type rmsd hydrogen bonds : bond 0.07648 ( 2283) hydrogen bonds : angle 8.11309 ( 6657) covalent geometry : bond 0.00709 (20192) covalent geometry : angle 0.96043 (25180) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9968 Ramachandran restraints generated. 4984 Oldfield, 0 Emsley, 4984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9968 Ramachandran restraints generated. 4984 Oldfield, 0 Emsley, 4984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 4114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 2.377 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.1916 time to fit residues: 33.2435 Evaluate side-chains 82 residues out of total 4114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 2.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 375 optimal weight: 0.4980 chunk 169 optimal weight: 30.0000 chunk 381 optimal weight: 5.9990 chunk 386 optimal weight: 30.0000 chunk 98 optimal weight: 20.0000 chunk 147 optimal weight: 5.9990 chunk 227 optimal weight: 50.0000 chunk 285 optimal weight: 0.8980 chunk 7 optimal weight: 6.9990 chunk 490 optimal weight: 50.0000 chunk 233 optimal weight: 5.9990 overall best weight: 3.8786 ------------------------------------------------------------------------------- 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 = 0.2535 r_free = 0.2535 target = 0.036119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2492 r_free = 0.2492 target = 0.032204 restraints weight = 310365.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2470 r_free = 0.2470 target = 0.031516 restraints weight = 751596.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2470 r_free = 0.2470 target = 0.031255 restraints weight = 1041679.145| |-----------------------------------------------------------------------------| r_work (final): 0.2266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.7468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 20192 Z= 0.128 Angle : 0.431 10.171 25180 Z= 0.275 Chirality : 0.000 0.000 0 Planarity : 0.002 0.018 5024 Dihedral : 4.871 65.409 5024 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 0.69 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.94 % Favored : 93.82 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.96 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.12), residues: 4984 helix: 1.35 (0.10), residues: 2813 sheet: -2.37 (0.25), residues: 382 loop : -2.28 (0.15), residues: 1789 Details of bonding type rmsd hydrogen bonds : bond 0.03694 ( 2283) hydrogen bonds : angle 5.06125 ( 6657) covalent geometry : bond 0.00167 (20192) covalent geometry : angle 0.43093 (25180) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9968 Ramachandran restraints generated. 4984 Oldfield, 0 Emsley, 4984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9968 Ramachandran restraints generated. 4984 Oldfield, 0 Emsley, 4984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 4114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 2.225 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.1648 time to fit residues: 28.9895 Evaluate side-chains 82 residues out of total 4114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 2.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 176 optimal weight: 8.9990 chunk 431 optimal weight: 50.0000 chunk 424 optimal weight: 50.0000 chunk 208 optimal weight: 50.0000 chunk 54 optimal weight: 6.9990 chunk 82 optimal weight: 7.9990 chunk 243 optimal weight: 50.0000 chunk 345 optimal weight: 50.0000 chunk 222 optimal weight: 50.0000 chunk 7 optimal weight: 60.0000 chunk 286 optimal weight: 50.0000 overall best weight: 24.7994 ------------------------------------------------------------------------------- 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 = 0.2424 r_free = 0.2424 target = 0.030962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2382 r_free = 0.2382 target = 0.027414 restraints weight = 335666.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2360 r_free = 0.2360 target = 0.026939 restraints weight = 569246.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2359 r_free = 0.2359 target = 0.026879 restraints weight = 855699.504| |-----------------------------------------------------------------------------| r_work (final): 0.2190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.7872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 20192 Z= 0.412 Angle : 0.763 16.537 25180 Z= 0.505 Chirality : 0.000 0.000 0 Planarity : 0.005 0.029 5024 Dihedral : 5.995 68.281 5024 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.26 % Allowed : 13.34 % Favored : 86.40 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.96 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.12), residues: 4984 helix: 0.57 (0.10), residues: 2740 sheet: -2.53 (0.25), residues: 374 loop : -2.53 (0.14), residues: 1870 Details of bonding type rmsd hydrogen bonds : bond 0.06055 ( 2283) hydrogen bonds : angle 6.71290 ( 6657) covalent geometry : bond 0.00546 (20192) covalent geometry : angle 0.76277 (25180) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4455.62 seconds wall clock time: 77 minutes 21.36 seconds (4641.36 seconds total)