Starting phenix.real_space_refine on Tue Jun 17 10:43:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tkp_25977/06_2025/7tkp_25977.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tkp_25977/06_2025/7tkp_25977.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7tkp_25977/06_2025/7tkp_25977.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tkp_25977/06_2025/7tkp_25977.map" model { file = "/net/cci-nas-00/data/ceres_data/7tkp_25977/06_2025/7tkp_25977.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tkp_25977/06_2025/7tkp_25977.cif" } resolution = 4.6 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= 0.120 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: 1996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 499, 1996 Classifications: {'peptide': 499} Incomplete info: {'backbone_only': 453} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 18, 'TRANS': 478} Chain breaks: 1 Unresolved chain link angles: 19 Unresolved non-hydrogen bonds: 1854 Unresolved non-hydrogen angles: 2698 Unresolved non-hydrogen dihedrals: 1123 Unresolved non-hydrogen chiralities: 606 Planarities with less than four sites: {'GLN:plan1': 25, 'HIS:plan': 6, 'TYR:plan': 14, 'ASN:plan1': 17, 'TRP:plan': 2, 'ASP:plan': 21, 'PHE:plan': 13, 'GLU:plan': 37, 'ARG:plan': 29} Unresolved non-hydrogen planarities: 804 Chain: "B" Number of atoms: 2028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 2028 Classifications: {'peptide': 507} Incomplete info: {'backbone_only': 460} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 485} Unresolved chain link angles: 20 Unresolved non-hydrogen bonds: 1883 Unresolved non-hydrogen angles: 2740 Unresolved non-hydrogen dihedrals: 1142 Unresolved non-hydrogen chiralities: 615 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': 14, 'GLU:plan': 37, 'ARG:plan': 29} Unresolved non-hydrogen planarities: 815 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': 2, 'PCIS': 1, 'PTRANS': 18, 'TRANS': 474} 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: 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: "E" 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: "F" 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: "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: 13.80, per 1000 atoms: 0.68 Number of scatterers: 20228 At special positions: 0 Unit cell: (122.622, 146.877, 235.812, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 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: 5.88 Conformation dependent library (CDL) restraints added in 3.9 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: 204 helices and 30 sheets defined 60.3% alpha, 11.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.62 Creating SS restraints... Processing helix chain '0' and resid 1 through 17 removed outlier: 3.512A pdb=" N GLY 0 13 " --> pdb=" O TYR 0 9 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ILE 0 17 " --> pdb=" O GLY 0 13 " (cutoff:3.500A) Processing helix chain '0' and resid 18 through 40 removed outlier: 4.197A pdb=" N ALA 0 22 " --> pdb=" O GLY 0 18 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA 0 27 " --> pdb=" O GLY 0 23 " (cutoff:3.500A) Processing helix chain '0' and resid 43 through 75 Proline residue: 0 49 - end of helix removed outlier: 3.531A pdb=" N THR 0 61 " --> pdb=" O LEU 0 57 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLY 0 62 " --> pdb=" O SER 0 58 " (cutoff:3.500A) Processing helix chain '1' and resid 2 through 17 removed outlier: 3.929A pdb=" N GLY 1 13 " --> pdb=" O TYR 1 9 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ILE 1 17 " --> pdb=" O GLY 1 13 " (cutoff:3.500A) Processing helix chain '1' and resid 18 through 40 removed outlier: 4.463A pdb=" N ALA 1 22 " --> pdb=" O GLY 1 18 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA 1 27 " --> pdb=" O GLY 1 23 " (cutoff:3.500A) Processing helix chain '1' and resid 43 through 75 Proline residue: 1 49 - end of helix removed outlier: 3.500A pdb=" N GLY 1 62 " --> pdb=" O SER 1 58 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N CYS 1 65 " --> pdb=" O THR 1 61 " (cutoff:3.500A) Processing helix chain '2' and resid 2 through 16 Processing helix chain '2' and resid 18 through 40 removed outlier: 4.318A pdb=" N ALA 2 22 " --> pdb=" O GLY 2 18 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ALA 2 27 " --> pdb=" O GLY 2 23 " (cutoff:3.500A) Processing helix chain '2' and resid 43 through 75 Proline residue: 2 49 - end of helix removed outlier: 3.978A pdb=" N THR 2 61 " --> pdb=" O LEU 2 57 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N GLY 2 62 " --> pdb=" O SER 2 58 " (cutoff:3.500A) Processing helix chain '3' and resid 3 through 17 removed outlier: 3.807A pdb=" N ILE 3 17 " --> pdb=" O GLY 3 13 " (cutoff:3.500A) Processing helix chain '3' and resid 19 through 40 removed outlier: 3.885A 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: 3.880A pdb=" N GLY 3 62 " --> pdb=" O SER 3 58 " (cutoff:3.500A) Processing helix chain '4' and resid 2 through 16 Processing helix chain '4' and resid 18 through 40 removed outlier: 4.088A 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: 3.891A pdb=" N THR 4 61 " --> pdb=" O LEU 4 57 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N GLY 4 62 " --> pdb=" O SER 4 58 " (cutoff:3.500A) Processing helix chain '5' and resid 2 through 16 Processing helix chain '5' and resid 18 through 40 removed outlier: 4.189A pdb=" N ALA 5 22 " --> pdb=" O GLY 5 18 " (cutoff:3.500A) Processing helix chain '5' and resid 43 through 75 Proline residue: 5 49 - end of helix removed outlier: 3.739A pdb=" N GLY 5 62 " --> pdb=" O SER 5 58 " (cutoff:3.500A) Processing helix chain '6' and resid 3 through 40 removed outlier: 3.690A pdb=" N THR 6 16 " --> pdb=" O ALA 6 12 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ILE 6 17 " --> pdb=" O GLY 6 13 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N GLY 6 18 " --> pdb=" O ILE 6 14 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N LEU 6 19 " --> pdb=" O SER 6 15 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU 6 20 " --> pdb=" O THR 6 16 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N GLY 6 21 " --> pdb=" O ILE 6 17 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N ALA 6 22 " --> pdb=" O GLY 6 18 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA 6 27 " --> pdb=" O GLY 6 23 " (cutoff:3.500A) Processing helix chain '6' and resid 43 through 75 Proline residue: 6 49 - end of helix removed outlier: 3.646A pdb=" N THR 6 61 " --> pdb=" O LEU 6 57 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLY 6 62 " --> pdb=" O SER 6 58 " (cutoff:3.500A) Processing helix chain '7' and resid 2 through 40 removed outlier: 4.197A pdb=" N ILE 7 17 " --> pdb=" O GLY 7 13 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N GLY 7 18 " --> pdb=" O ILE 7 14 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N LEU 7 19 " --> pdb=" O SER 7 15 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU 7 20 " --> pdb=" O THR 7 16 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N GLY 7 21 " --> pdb=" O ILE 7 17 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ALA 7 22 " --> pdb=" O GLY 7 18 " (cutoff:3.500A) removed outlier: 3.632A 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: 3.790A pdb=" N GLY 7 62 " --> pdb=" O SER 7 58 " (cutoff:3.500A) Processing helix chain '8' and resid 2 through 17 removed outlier: 3.804A pdb=" N ILE 8 17 " --> pdb=" O GLY 8 13 " (cutoff:3.500A) Processing helix chain '8' and resid 18 through 40 removed outlier: 4.119A pdb=" N ALA 8 22 " --> pdb=" O GLY 8 18 " (cutoff:3.500A) Processing helix chain '8' and resid 43 through 75 Proline residue: 8 49 - end of helix removed outlier: 3.793A pdb=" N THR 8 61 " --> pdb=" O LEU 8 57 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLY 8 62 " --> pdb=" O SER 8 58 " (cutoff:3.500A) Processing helix chain '9' and resid 3 through 17 removed outlier: 3.826A pdb=" N ILE 9 17 " --> pdb=" O GLY 9 13 " (cutoff:3.500A) Processing helix chain '9' and resid 18 through 40 removed outlier: 4.289A 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: 3.585A pdb=" N THR 9 61 " --> pdb=" O LEU 9 57 " (cutoff:3.500A) removed outlier: 3.928A 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 102 through 106 removed outlier: 4.064A pdb=" N LEU A 105 " --> pdb=" O GLY A 102 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU A 106 " --> pdb=" O PRO A 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 102 through 106' Processing helix chain 'A' and resid 153 through 157 Processing helix chain 'A' and resid 176 through 188 removed outlier: 3.704A pdb=" N VAL A 180 " --> pdb=" O GLY A 176 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ALA A 181 " --> pdb=" O LYS A 177 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR A 184 " --> pdb=" O VAL A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 193 Processing helix chain 'A' and resid 196 through 200 Processing helix chain 'A' and resid 211 through 225 Processing helix chain 'A' and resid 227 through 229 No H-bonds generated for 'chain 'A' and resid 227 through 229' Processing helix chain 'A' and resid 241 through 247 Processing helix chain 'A' and resid 247 through 261 removed outlier: 3.582A pdb=" N PHE A 259 " --> pdb=" O ILE A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 287 Processing helix chain 'A' and resid 292 through 296 Processing helix chain 'A' and resid 299 through 309 Processing helix chain 'A' and resid 338 through 348 removed outlier: 3.525A pdb=" N ILE A 347 " --> pdb=" O ASN A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 361 Processing helix chain 'A' and resid 376 through 381 removed outlier: 4.360A pdb=" N ALA A 380 " --> pdb=" O VAL A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 388 Processing helix chain 'A' and resid 391 through 407 removed outlier: 3.799A pdb=" N GLU A 401 " --> pdb=" O ALA A 397 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE A 405 " --> pdb=" O GLU A 401 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N GLN A 407 " --> pdb=" O ALA A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 431 removed outlier: 3.506A pdb=" N LYS A 431 " --> pdb=" O THR A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 452 Proline residue: A 445 - end of helix 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 479 removed outlier: 3.559A pdb=" N SER A 468 " --> pdb=" O GLY A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 489 Processing helix chain 'A' and resid 492 through 509 Processing helix chain 'B' and resid 10 through 19 Processing helix chain 'B' and resid 25 through 28 Processing helix chain 'B' and resid 152 through 159 Processing helix chain 'B' and resid 176 through 188 removed outlier: 3.830A pdb=" N VAL B 180 " --> pdb=" O GLY B 176 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ALA B 181 " --> pdb=" O LYS B 177 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N THR B 184 " --> pdb=" O VAL B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 194 removed outlier: 3.530A pdb=" N GLY B 194 " --> pdb=" O ARG B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 199 Processing helix chain 'B' and resid 211 through 225 Processing helix chain 'B' and resid 241 through 263 Proline residue: B 249 - end of helix removed outlier: 3.938A pdb=" N PHE B 259 " --> pdb=" O ILE B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 286 removed outlier: 3.615A 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 332 through 335 Processing helix chain 'B' and resid 338 through 348 Processing helix chain 'B' and resid 355 through 362 removed outlier: 3.650A pdb=" N PHE B 359 " --> pdb=" O GLU B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 380 removed outlier: 3.696A pdb=" N ALA B 379 " --> pdb=" O VAL B 376 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA B 380 " --> pdb=" O GLY B 377 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 376 through 380' Processing helix chain 'B' and resid 382 through 389 Processing helix chain 'B' and resid 391 through 407 removed outlier: 3.708A pdb=" N GLN B 407 " --> pdb=" O ALA B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 431 removed outlier: 3.507A pdb=" N ARG B 425 " --> pdb=" O VAL B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 442 Processing helix chain 'B' and resid 443 through 452 Processing helix chain 'B' and resid 453 through 458 removed outlier: 4.348A pdb=" N GLY B 457 " --> pdb=" O GLY B 453 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE B 458 " --> pdb=" O HIS B 454 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 453 through 458' Processing helix chain 'B' and resid 459 through 461 No H-bonds generated for 'chain 'B' and resid 459 through 461' Processing helix chain 'B' and resid 462 through 477 Processing helix chain 'B' and resid 478 through 489 Processing helix chain 'B' and resid 492 through 508 Processing helix chain 'C' and resid 13 through 22 Processing helix chain 'C' and resid 80 through 84 Processing helix chain 'C' and resid 102 through 106 removed outlier: 3.631A pdb=" N LEU C 105 " --> pdb=" O GLY C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 159 Processing helix chain 'C' and resid 176 through 194 removed outlier: 4.007A pdb=" N THR C 184 " --> pdb=" O VAL C 180 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE C 185 " --> pdb=" O ALA C 181 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LYS C 189 " --> pdb=" O ILE C 185 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N ARG C 190 " --> pdb=" O LEU C 186 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N TRP C 191 " --> pdb=" O ASN C 187 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLY C 194 " --> pdb=" O ARG C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 225 Processing helix chain 'C' and resid 241 through 262 Proline residue: C 249 - end of helix removed outlier: 3.685A pdb=" N ILE C 255 " --> pdb=" O THR C 251 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N PHE C 259 " --> pdb=" O ILE C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 287 removed outlier: 3.567A 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 297 through 298 No H-bonds generated for 'chain 'C' and resid 297 through 298' 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 368 through 372 Processing helix chain 'C' and resid 376 through 381 Processing helix chain 'C' and resid 382 through 388 Processing helix chain 'C' and resid 389 through 402 removed outlier: 3.501A pdb=" N LYS C 393 " --> pdb=" O ALA C 389 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 407 Processing helix chain 'C' and resid 413 through 430 Processing helix chain 'C' and resid 439 through 452 Proline residue: C 445 - end of helix Processing helix chain 'C' and resid 459 through 478 removed outlier: 4.293A pdb=" N GLY C 464 " --> pdb=" O LEU C 460 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N GLU C 465 " --> pdb=" O SER C 461 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N SER C 468 " --> pdb=" O GLY C 464 " (cutoff:3.500A) Processing helix chain 'C' and resid 478 through 489 Processing helix chain 'C' and resid 492 through 509 Processing helix chain 'D' and resid 138 through 145 Processing helix chain 'D' and resid 162 through 178 Processing helix chain 'D' and resid 190 through 204 Processing helix chain 'D' and resid 225 through 248 removed outlier: 4.467A pdb=" N ALA D 233 " --> pdb=" O ARG D 229 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N LEU D 234 " --> pdb=" O ALA D 230 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 273 Processing helix chain 'D' and resid 277 through 281 Processing helix chain 'D' and resid 284 through 293 Processing helix chain 'D' and resid 319 through 329 removed outlier: 3.531A pdb=" N HIS D 328 " --> pdb=" O THR D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 336 through 341 Processing helix chain 'D' and resid 359 through 364 Processing helix chain 'D' and resid 364 through 392 removed outlier: 3.861A pdb=" N ILE D 387 " --> pdb=" O SER D 383 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ILE D 390 " --> pdb=" O ASP D 386 " (cutoff:3.500A) Processing helix chain 'D' and resid 393 through 396 Processing helix chain 'D' and resid 397 through 415 removed outlier: 4.050A pdb=" N SER D 415 " --> pdb=" O GLN D 411 " (cutoff:3.500A) Processing helix chain 'D' and resid 418 through 420 No H-bonds generated for 'chain 'D' and resid 418 through 420' Processing helix chain 'D' and resid 421 through 426 Processing helix chain 'D' and resid 433 through 446 Processing helix chain 'D' and resid 453 through 457 Processing helix chain 'D' and resid 462 through 475 removed outlier: 3.698A pdb=" N ALA D 468 " --> pdb=" O GLU D 464 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 92 Processing helix chain 'E' and resid 138 through 145 Processing helix chain 'E' and resid 162 through 178 removed outlier: 3.617A pdb=" N PHE E 166 " --> pdb=" O GLY E 162 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE E 167 " --> pdb=" O LYS E 163 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N LYS E 176 " --> pdb=" O ASN E 172 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALA E 177 " --> pdb=" O ASN E 173 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 204 Processing helix chain 'E' and resid 225 through 231 removed outlier: 3.622A pdb=" N ARG E 231 " --> pdb=" O GLY E 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 231 through 245 Processing helix chain 'E' and resid 257 through 273 removed outlier: 3.557A pdb=" N PHE E 261 " --> pdb=" O ASN E 257 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ALA E 270 " --> pdb=" O SER E 266 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N LEU E 271 " --> pdb=" O GLU E 267 " (cutoff:3.500A) Processing helix chain 'E' and resid 284 through 294 Processing helix chain 'E' and resid 312 through 316 Processing helix chain 'E' and resid 319 through 327 removed outlier: 4.045A pdb=" N ALA E 327 " --> pdb=" O ALA E 323 " (cutoff:3.500A) Processing helix chain 'E' and resid 336 through 342 Processing helix chain 'E' and resid 357 through 359 No H-bonds generated for 'chain 'E' and resid 357 through 359' Processing helix chain 'E' and resid 364 through 384 Processing helix chain 'E' and resid 384 through 391 Processing helix chain 'E' and resid 392 through 396 Processing helix chain 'E' and resid 397 through 415 removed outlier: 3.514A pdb=" N LEU E 402 " --> pdb=" O GLU E 398 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N SER E 415 " --> pdb=" O GLN E 411 " (cutoff:3.500A) Processing helix chain 'E' and resid 421 through 426 Processing helix chain 'E' and resid 433 through 446 Processing helix chain 'E' and resid 453 through 458 removed outlier: 3.626A pdb=" N PHE E 457 " --> pdb=" O PRO E 453 " (cutoff:3.500A) Processing helix chain 'E' and resid 462 through 475 Processing helix chain 'F' and resid 138 through 145 Processing helix chain 'F' and resid 162 through 178 removed outlier: 4.266A pdb=" N LYS F 176 " --> pdb=" O ASN F 172 " (cutoff:3.500A) Processing helix chain 'F' and resid 190 through 204 Processing helix chain 'F' and resid 225 through 245 removed outlier: 4.361A pdb=" N ALA F 233 " --> pdb=" O ARG F 229 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N LEU F 234 " --> pdb=" O ALA F 230 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR F 235 " --> pdb=" O ARG F 231 " (cutoff:3.500A) Processing helix chain 'F' and resid 257 through 273 removed outlier: 3.701A pdb=" N PHE F 261 " --> pdb=" O ASN F 257 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ALA F 270 " --> pdb=" O SER F 266 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LEU F 271 " --> pdb=" O GLU F 267 " (cutoff:3.500A) Processing helix chain 'F' and resid 277 through 281 Processing helix chain 'F' and resid 284 through 296 Processing helix chain 'F' and resid 313 through 316 Processing helix chain 'F' and resid 319 through 329 Processing helix chain 'F' and resid 336 through 342 removed outlier: 3.566A pdb=" N SER F 340 " --> pdb=" O SER F 336 " (cutoff:3.500A) Processing helix chain 'F' and resid 363 through 391 removed outlier: 3.924A pdb=" N HIS F 367 " --> pdb=" O VAL F 363 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ASP F 386 " --> pdb=" O LYS F 382 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ILE F 387 " --> pdb=" O SER F 383 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE F 390 " --> pdb=" O ASP F 386 " (cutoff:3.500A) Processing helix chain 'F' and resid 397 through 414 Processing helix chain 'F' and resid 418 through 422 Processing helix chain 'F' and resid 433 through 447 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: 4.015A pdb=" N LYS G 33 " --> pdb=" O THR G 29 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N SER G 40 " --> pdb=" O LYS G 36 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU G 48 " --> pdb=" O MET G 44 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N PHE G 51 " --> pdb=" O ALA G 47 " (cutoff:3.500A) Processing helix chain 'G' and resid 86 through 102 removed outlier: 3.779A pdb=" N ASP G 101 " --> pdb=" O ARG G 97 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLN G 102 " --> pdb=" O HIS G 98 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 122 removed outlier: 3.677A 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 Processing helix chain 'G' and resid 192 through 197 removed outlier: 3.962A pdb=" N GLY G 195 " --> pdb=" O PRO G 192 " (cutoff:3.500A) Processing helix chain 'G' and resid 204 through 276 removed outlier: 4.111A pdb=" N GLU G 211 " --> pdb=" O ARG G 207 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER G 276 " --> pdb=" O THR G 272 " (cutoff:3.500A) Processing helix chain 'H' and resid 93 through 97 Processing helix chain 'H' and resid 100 through 115 Processing helix chain 'H' and resid 119 through 136 removed outlier: 3.826A pdb=" N VAL H 136 " --> pdb=" O ASN H 132 " (cutoff:3.500A) Processing helix chain 'I' and resid 9 through 23 Processing helix chain 'I' and resid 31 through 37 removed outlier: 3.942A pdb=" N LEU I 35 " --> pdb=" O THR I 31 " (cutoff:3.500A) Processing helix chain 'O' and resid 17 through 29 Processing helix chain 'O' and resid 33 through 49 Processing helix chain 'O' and resid 64 through 77 Processing helix chain 'O' and resid 83 through 95 Processing helix chain 'O' and resid 101 through 117 Processing helix chain 'O' and resid 130 through 144 Processing helix chain 'O' and resid 180 through 191 Processing helix chain 'T' and resid 27 through 43 removed outlier: 3.539A pdb=" N SER T 42 " --> pdb=" O LEU T 38 " (cutoff:3.500A) Processing helix chain 'T' and resid 58 through 74 removed outlier: 3.894A pdb=" N GLN T 62 " --> pdb=" O TRP T 58 " (cutoff:3.500A) removed outlier: 3.694A 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 103 removed outlier: 3.954A pdb=" N ILE T 96 " --> pdb=" O LEU T 92 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LEU T 101 " --> pdb=" O PHE T 97 " (cutoff:3.500A) Processing helix chain 'T' and resid 114 through 138 removed outlier: 3.990A pdb=" N ILE T 118 " --> pdb=" O HIS T 114 " (cutoff:3.500A) Processing helix chain 'T' and resid 140 through 146 Processing helix chain 'T' and resid 151 through 155 Processing helix chain 'T' and resid 156 through 167 removed outlier: 4.019A pdb=" N GLU T 162 " --> pdb=" O LEU T 158 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N SER T 165 " --> pdb=" O ILE T 161 " (cutoff:3.500A) Processing helix chain 'T' and resid 168 through 199 removed outlier: 4.056A pdb=" N LEU T 173 " --> pdb=" O ARG T 169 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N GLY T 174 " --> pdb=" O ALA T 170 " (cutoff:3.500A) removed outlier: 4.211A 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 210 through 247 removed outlier: 3.679A pdb=" N PHE T 224 " --> pdb=" O MET T 220 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA T 225 " --> pdb=" O MET T 221 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA T 239 " --> pdb=" O ALA T 235 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LEU T 242 " --> pdb=" O THR T 238 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N TYR T 247 " --> pdb=" O LYS T 243 " (cutoff:3.500A) Processing helix chain 'U' and resid 54 through 186 removed outlier: 4.099A pdb=" N LEU U 58 " --> pdb=" O ASP U 54 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ALA U 74 " --> pdb=" O ALA U 70 " (cutoff:3.500A) Proline residue: U 75 - end of helix removed outlier: 3.681A pdb=" N GLU U 118 " --> pdb=" O GLN U 114 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N LYS U 121 " --> pdb=" O ALA U 117 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N VAL U 122 " --> pdb=" O GLU U 118 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLU U 139 " --> pdb=" O SER U 135 " (cutoff:3.500A) Processing helix chain 'U' and resid 187 through 206 removed outlier: 4.026A pdb=" N VAL U 193 " --> pdb=" O PHE U 189 " (cutoff:3.500A) Processing helix chain 'V' and resid 4 through 19 Processing helix chain 'V' and resid 26 through 48 removed outlier: 3.703A pdb=" N LEU V 43 " --> pdb=" O ALA V 39 " (cutoff:3.500A) Processing helix chain 'V' and resid 56 through 62 removed outlier: 3.808A pdb=" N SER V 60 " --> pdb=" O SER V 56 " (cutoff:3.500A) Processing helix chain 'V' and resid 67 through 78 Processing helix chain 'V' and resid 90 through 127 removed outlier: 3.566A pdb=" N SER V 94 " --> pdb=" O GLN V 90 " (cutoff:3.500A) Processing helix chain 'V' and resid 134 through 142 Processing helix chain 'V' and resid 143 through 156 Processing helix chain 'V' and resid 162 through 166 Processing helix chain 'W' and resid 17 through 30 removed outlier: 4.236A pdb=" N ALA W 21 " --> pdb=" O SER W 17 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LYS W 22 " --> pdb=" O ALA W 18 " (cutoff:3.500A) removed outlier: 4.228A 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 82 removed outlier: 3.533A pdb=" N ILE W 73 " --> pdb=" O PHE W 69 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N TYR W 78 " --> pdb=" O ILE W 74 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N SER W 79 " --> pdb=" O ALA W 75 " (cutoff:3.500A) Processing helix chain 'X' and resid 2 through 14 Processing helix chain 'X' and resid 20 through 28 removed outlier: 3.969A pdb=" N GLY X 26 " --> pdb=" O GLN X 22 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ASN X 27 " --> pdb=" O ASP X 23 " (cutoff:3.500A) Processing helix chain 'X' and resid 46 through 57 removed outlier: 4.261A 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: 3.632A pdb=" N MET Z 34 " --> pdb=" O PHE Z 30 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE Z 35 " --> pdb=" O PHE Z 31 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 62 through 69 removed outlier: 4.586A pdb=" N GLU A 53 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N ASN A 95 " --> pdb=" O LEU A 54 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N GLU A 56 " --> pdb=" O THR A 93 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N THR A 93 " --> pdb=" O GLU A 56 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG A 32 " --> pdb=" O PHE A 44 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N ARG A 42 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N VAL A 36 " --> pdb=" O ILE A 40 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N ILE A 40 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASN A 67 " --> pdb=" O GLY A 74 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N VAL A 76 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N ALA A 65 " --> pdb=" O VAL A 76 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N PHE A 78 " --> pdb=" O GLY A 63 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N GLY A 63 " --> pdb=" O PHE A 78 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ARG E 60 " --> pdb=" O ALA E 51 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ILE E 17 " --> pdb=" O ILE E 20 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N HIS E 24 " --> pdb=" O VAL E 13 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N VAL E 13 " --> pdb=" O HIS E 24 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 98 through 101 Processing sheet with id=AA3, first strand: chain 'A' and resid 109 through 111 removed outlier: 6.148A pdb=" N CYS A 203 " --> pdb=" O ILE A 232 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N VAL A 234 " --> pdb=" O CYS A 203 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N TYR A 205 " --> pdb=" O VAL A 234 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N ALA A 236 " --> pdb=" O TYR A 205 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ALA A 207 " --> pdb=" O ALA A 236 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ALA A 266 " --> pdb=" O THR A 324 " (cutoff:3.500A) removed outlier: 8.387A pdb=" N LEU A 326 " --> pdb=" O ALA A 266 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ILE A 268 " --> pdb=" O LEU A 326 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N VAL A 328 " --> pdb=" O ILE A 268 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N TYR A 270 " --> pdb=" O VAL A 328 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N GLU A 330 " --> pdb=" O TYR A 270 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ILE A 169 " --> pdb=" O ILE A 329 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N THR A 331 " --> pdb=" O ILE A 169 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N GLY A 171 " --> pdb=" O THR A 331 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 147 through 148 removed outlier: 4.322A pdb=" N ILE A 161 " --> pdb=" O VAL A 148 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 351 through 354 removed outlier: 3.530A pdb=" N PHE A 353 " --> pdb=" O LEU A 371 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N LEU A 371 " --> pdb=" O PHE A 353 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 30 through 37 removed outlier: 6.975A pdb=" N ARG B 42 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N VAL B 36 " --> pdb=" O ILE B 40 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ILE B 40 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N VAL B 76 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N ALA B 65 " --> pdb=" O VAL B 76 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLU B 53 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N LEU B 54 " --> pdb=" O THR B 93 " (cutoff:3.500A) 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: 6.016A pdb=" N VAL B 110 " --> pdb=" O ALA B 235 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N THR B 237 " --> pdb=" O VAL B 110 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N TYR B 202 " --> pdb=" O LEU B 267 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N VAL B 269 " --> pdb=" O TYR B 202 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N VAL B 204 " --> pdb=" O VAL B 269 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N ASP B 271 " --> pdb=" O VAL B 204 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N VAL B 206 " --> pdb=" O ASP B 271 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLY B 171 " --> pdb=" O ILE B 329 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N LEU B 168 " --> pdb=" O ILE B 352 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 147 through 148 removed outlier: 3.780A pdb=" N ILE B 161 " --> pdb=" O VAL B 148 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 31 through 37 removed outlier: 6.751A pdb=" N ARG C 42 " --> pdb=" O LEU C 34 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N VAL C 36 " --> pdb=" O ILE C 40 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ILE C 40 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N GLY C 74 " --> pdb=" O LEU C 66 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LEU C 66 " --> pdb=" O GLY C 74 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 10 through 17 current: chain 'C' and resid 90 through 96 Processing sheet with id=AB2, first strand: chain 'C' and resid 31 through 37 removed outlier: 6.751A pdb=" N ARG C 42 " --> pdb=" O LEU C 34 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N VAL C 36 " --> pdb=" O ILE C 40 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ILE C 40 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N GLY C 74 " --> pdb=" O LEU C 66 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LEU C 66 " --> pdb=" O GLY C 74 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 62 through 68 current: chain 'D' and resid 36 through 41 removed outlier: 6.114A pdb=" N ARG D 60 " --> pdb=" O ALA D 51 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N HIS D 53 " --> pdb=" O THR D 58 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N THR D 58 " --> pdb=" O HIS D 53 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N VAL D 23 " --> pdb=" O VAL D 59 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ILE D 20 " --> pdb=" O VAL D 16 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N VAL D 16 " --> pdb=" O ILE D 20 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N ASP D 22 " --> pdb=" O THR D 14 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 10 through 17 current: chain 'C' and resid 90 through 96 Processing sheet with id=AB3, first strand: chain 'C' and resid 98 through 101 Processing sheet with id=AB4, first strand: chain 'C' and resid 109 through 110 removed outlier: 6.204A pdb=" N VAL C 110 " --> pdb=" O ALA C 235 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N THR C 237 " --> pdb=" O VAL C 110 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N TYR C 205 " --> pdb=" O VAL C 234 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N ALA C 236 " --> pdb=" O TYR C 205 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N ALA C 207 " --> pdb=" O ALA C 236 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 147 through 148 removed outlier: 4.577A pdb=" N ILE C 161 " --> pdb=" O VAL C 148 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 328 through 331 removed outlier: 7.395A pdb=" N ILE C 170 " --> pdb=" O LEU C 354 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 84 through 87 removed outlier: 4.383A pdb=" N LEU D 113 " --> pdb=" O VAL D 87 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 95 through 96 removed outlier: 3.640A pdb=" N PHE D 219 " --> pdb=" O ILE D 96 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N VAL D 183 " --> pdb=" O PHE D 254 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N ASP D 256 " --> pdb=" O VAL D 183 " (cutoff:3.500A) removed outlier: 8.306A pdb=" N THR D 185 " --> pdb=" O ASP D 256 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N PHE D 254 " --> pdb=" O VAL D 307 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N ALA D 309 " --> pdb=" O PHE D 254 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N ASP D 256 " --> pdb=" O ALA D 309 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 84 through 87 removed outlier: 4.222A 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: 5.848A pdb=" N ILE E 96 " --> pdb=" O PHE E 219 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N GLN E 221 " --> pdb=" O ILE E 96 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ALA E 216 " --> pdb=" O VAL E 183 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N THR E 185 " --> pdb=" O ALA E 216 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N VAL E 218 " --> pdb=" O THR E 185 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N VAL E 187 " --> pdb=" O VAL E 218 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N GLY E 220 " --> pdb=" O VAL E 187 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL E 251 " --> pdb=" O THR E 305 " (cutoff:3.500A) removed outlier: 8.612A pdb=" N VAL E 307 " --> pdb=" O VAL E 251 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N LEU E 253 " --> pdb=" O VAL E 307 " (cutoff:3.500A) removed outlier: 8.467A pdb=" N ALA E 309 " --> pdb=" O LEU E 253 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N ILE E 255 " --> pdb=" O ALA E 309 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 133 through 134 Processing sheet with id=AC3, first strand: chain 'E' and resid 331 through 335 removed outlier: 5.656A pdb=" N ASP E 352 " --> pdb=" O VAL E 334 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 13 through 17 removed outlier: 3.765A pdb=" N ALA F 15 " --> pdb=" O ASP F 22 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ARG F 60 " --> pdb=" O ALA F 51 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 84 through 87 Processing sheet with id=AC6, first strand: chain 'F' and resid 216 through 221 removed outlier: 6.762A pdb=" N ILE F 153 " --> pdb=" O GLN F 308 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N VAL F 310 " --> pdb=" O ILE F 153 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N LEU F 155 " --> pdb=" O VAL F 310 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LYS F 152 " --> pdb=" O ALA F 331 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N THR F 333 " --> pdb=" O LYS F 152 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N GLY F 154 " --> pdb=" O THR F 333 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N LEU F 335 " --> pdb=" O GLY F 154 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N PHE F 156 " --> pdb=" O LEU F 335 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 126 through 130 removed outlier: 7.089A pdb=" N ILE G 107 " --> pdb=" O LYS G 127 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N SER G 129 " --> pdb=" O ILE G 107 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N THR G 109 " --> pdb=" O SER G 129 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N GLU G 72 " --> pdb=" O ASP G 106 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N VAL G 108 " --> pdb=" O GLU G 72 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N ILE G 74 " --> pdb=" O VAL G 108 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N ILE G 110 " --> pdb=" O ILE G 74 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N ALA G 76 " --> pdb=" O ILE G 110 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N LEU G 73 " --> pdb=" O SER G 163 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N PHE G 165 " --> pdb=" O LEU G 73 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N VAL G 75 " --> pdb=" O PHE G 165 " (cutoff:3.500A) removed outlier: 8.904A pdb=" N ASN G 167 " --> pdb=" O VAL G 75 " (cutoff:3.500A) removed outlier: 9.004A pdb=" N ILE G 77 " --> pdb=" O ASN G 167 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N SER G 174 " --> pdb=" O VAL G 170 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 20 through 22 removed outlier: 5.633A pdb=" N GLN H 13 " --> pdb=" O VAL H 85 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N ALA H 87 " --> pdb=" O GLN H 13 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N ALA H 15 " --> pdb=" O ALA H 87 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 37 through 42 removed outlier: 6.372A pdb=" N VAL H 56 " --> pdb=" O PRO H 33 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 43 through 45 Processing sheet with id=AD2, first strand: chain 'O' and resid 118 through 119 Processing sheet with id=AD3, first strand: chain 'O' and resid 157 through 159 removed outlier: 3.520A pdb=" N VAL O 158 " --> pdb=" O VAL O 123 " (cutoff:3.500A) 2313 hydrogen bonds defined for protein. 6681 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: 9.08 Time building geometry restraints manager: 6.67 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: 1503 1.35 - 1.41: 3518 1.41 - 1.48: 5111 1.48 - 1.54: 5000 Bond restraints: 20192 Sorted by residual: bond pdb=" CA ALA A 157 " pdb=" C ALA A 157 " ideal model delta sigma weight residual 1.523 1.465 0.059 8.20e-03 1.49e+04 5.11e+01 bond pdb=" CA ALA C 157 " pdb=" C ALA C 157 " ideal model delta sigma weight residual 1.523 1.473 0.050 8.40e-03 1.42e+04 3.61e+01 bond pdb=" CA GLY F 220 " pdb=" C GLY F 220 " ideal model delta sigma weight residual 1.520 1.480 0.041 7.30e-03 1.88e+04 3.09e+01 bond pdb=" CA GLY F 11 " pdb=" C GLY F 11 " ideal model delta sigma weight residual 1.514 1.472 0.042 8.60e-03 1.35e+04 2.38e+01 bond pdb=" CA ALA F 148 " pdb=" C ALA F 148 " ideal model delta sigma weight residual 1.522 1.465 0.057 1.21e-02 6.83e+03 2.20e+01 ... (remaining 20187 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.03: 21475 3.03 - 6.06: 3095 6.06 - 9.09: 523 9.09 - 12.12: 82 12.12 - 15.14: 5 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 113.71 102.41 11.30 9.50e-01 1.11e+00 1.41e+02 angle pdb=" N VAL T 146 " pdb=" CA VAL T 146 " pdb=" C VAL T 146 " ideal model delta sigma weight residual 108.15 98.75 9.40 9.90e-01 1.02e+00 9.02e+01 angle pdb=" N VAL C 376 " pdb=" CA VAL C 376 " pdb=" C VAL C 376 " ideal model delta sigma weight residual 111.81 103.76 8.05 8.60e-01 1.35e+00 8.76e+01 angle pdb=" N GLN A 398 " pdb=" CA GLN A 398 " pdb=" C GLN A 398 " ideal model delta sigma weight residual 113.41 102.08 11.33 1.22e+00 6.72e-01 8.62e+01 angle pdb=" C ASN G 204 " pdb=" N VAL G 205 " pdb=" CA VAL G 205 " ideal model delta sigma weight residual 120.24 125.96 -5.72 6.30e-01 2.52e+00 8.24e+01 ... (remaining 25175 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.18: 5005 24.18 - 48.36: 17 48.36 - 72.54: 0 72.54 - 96.72: 1 96.72 - 120.90: 1 Dihedral angle restraints: 5024 sinusoidal: 4 harmonic: 5020 Sorted by residual: dihedral pdb=" CA ASP F 256 " pdb=" C ASP F 256 " pdb=" N ASN F 257 " pdb=" CA ASN F 257 " ideal model delta harmonic sigma weight residual -180.00 -59.10 -120.90 0 5.00e+00 4.00e-02 5.85e+02 dihedral pdb=" CA ASN 7 40 " pdb=" C ASN 7 40 " pdb=" N PRO 7 41 " pdb=" CA PRO 7 41 " ideal model delta harmonic sigma weight residual -180.00 -136.35 -43.65 0 5.00e+00 4.00e-02 7.62e+01 dihedral pdb=" CA ASN 9 40 " pdb=" C ASN 9 40 " pdb=" N PRO 9 41 " pdb=" CA PRO 9 41 " ideal model delta harmonic sigma weight residual -180.00 -139.25 -40.75 0 5.00e+00 4.00e-02 6.64e+01 ... (remaining 5021 not shown) Chirality restraints: 0 Planarity restraints: 5024 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR G 2 " -0.020 2.00e-02 2.50e+03 4.02e-02 1.62e+01 pdb=" C THR G 2 " 0.070 2.00e-02 2.50e+03 pdb=" O THR G 2 " -0.026 2.00e-02 2.50e+03 pdb=" N LEU G 3 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY B 321 " -0.020 2.00e-02 2.50e+03 4.01e-02 1.61e+01 pdb=" C GLY B 321 " 0.069 2.00e-02 2.50e+03 pdb=" O GLY B 321 " -0.026 2.00e-02 2.50e+03 pdb=" N SER B 322 " -0.023 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 3.85e-02 1.49e+01 pdb=" C THR C 93 " 0.067 2.00e-02 2.50e+03 pdb=" O THR C 93 " -0.025 2.00e-02 2.50e+03 pdb=" N GLY C 94 " -0.022 2.00e-02 2.50e+03 ... (remaining 5021 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 9286 2.86 - 3.37: 17245 3.37 - 3.88: 26971 3.88 - 4.39: 27447 4.39 - 4.90: 40984 Nonbonded interactions: 121933 Sorted by model distance: nonbonded pdb=" N THR T 150 " pdb=" O THR T 150 " model vdw 2.352 2.496 nonbonded pdb=" N LEU H 16 " pdb=" O LEU H 16 " model vdw 2.365 2.496 nonbonded pdb=" N GLU A 167 " pdb=" O GLU A 167 " model vdw 2.388 2.496 nonbonded pdb=" N THR D 305 " pdb=" O THR D 305 " model vdw 2.389 2.496 nonbonded pdb=" N ASP F 256 " pdb=" O ASP F 256 " model vdw 2.400 2.496 ... (remaining 121928 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain '0' and resid 2 through 73) selection = (chain '1' and resid 2 through 73) selection = (chain '2' and resid 2 through 73) selection = (chain '3' and resid 2 through 73) selection = (chain '4' and resid 2 through 73) selection = (chain '5' and resid 2 through 73) selection = (chain '6' and resid 2 through 73) selection = (chain '7' and resid 2 through 73) selection = (chain '8' and resid 2 through 73) selection = (chain '9' and resid 2 through 73) } ncs_group { reference = (chain 'A' and resid 12 through 509) selection = (chain 'B' and (resid 12 through 407 or resid 410 through 509)) selection = chain 'C' } ncs_group { reference = chain 'D' selection = (chain 'E' and resid 8 through 475) selection = (chain 'F' and resid 8 through 475) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.710 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: 0.690 Check model and map are aligned: 0.140 Set scattering table: 0.170 Process input model: 54.400 Find NCS groups from input model: 1.080 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6413 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 0.059 20192 Z= 1.503 Angle : 2.202 15.144 25180 Z= 1.587 Chirality : 0.000 0.000 0 Planarity : 0.010 0.040 5024 Dihedral : 6.684 120.900 5024 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 0.12 Ramachandran Plot: Outliers : 1.28 % Allowed : 4.17 % Favored : 94.54 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.46 % Cis-general : 0.08 % Twisted Proline : 4.43 % 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: -0.50 (0.11), residues: 4984 helix: 0.82 (0.09), residues: 2800 sheet: -1.39 (0.20), residues: 575 loop : -1.92 (0.13), residues: 1609 Details of bonding type rmsd hydrogen bonds : bond 0.20955 ( 2304) hydrogen bonds : angle 8.00638 ( 6681) covalent geometry : bond 0.01914 (20192) covalent geometry : angle 2.20171 (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 : 2.258 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.1714 time to fit residues: 30.0092 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 : 2.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 415 optimal weight: 6.9990 chunk 372 optimal weight: 6.9990 chunk 206 optimal weight: 8.9990 chunk 127 optimal weight: 7.9990 chunk 251 optimal weight: 6.9990 chunk 199 optimal weight: 8.9990 chunk 385 optimal weight: 5.9990 chunk 149 optimal weight: 8.9990 chunk 234 optimal weight: 20.0000 chunk 287 optimal weight: 10.0000 chunk 446 optimal weight: 10.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- 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 = 0.2562 r_free = 0.2562 target = 0.031718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2307 r_free = 0.2307 target = 0.024059 restraints weight = 287540.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2304 r_free = 0.2304 target = 0.024094 restraints weight = 253686.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2306 r_free = 0.2306 target = 0.024171 restraints weight = 237077.221| |-----------------------------------------------------------------------------| r_work (final): 0.2292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.1955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 20192 Z= 0.202 Angle : 0.541 8.789 25180 Z= 0.345 Chirality : 0.000 0.000 0 Planarity : 0.003 0.021 5024 Dihedral : 4.880 67.086 5024 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 0.27 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.83 % Favored : 96.95 % 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: 1.47 (0.12), residues: 4984 helix: 2.40 (0.10), residues: 2841 sheet: -0.90 (0.21), residues: 552 loop : -0.98 (0.15), residues: 1591 Details of bonding type rmsd hydrogen bonds : bond 0.04629 ( 2304) hydrogen bonds : angle 4.59852 ( 6681) covalent geometry : bond 0.00267 (20192) covalent geometry : angle 0.54074 (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 : 2.213 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.1706 time to fit residues: 29.8028 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 : 2.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 282 optimal weight: 40.0000 chunk 87 optimal weight: 20.0000 chunk 348 optimal weight: 50.0000 chunk 438 optimal weight: 40.0000 chunk 340 optimal weight: 3.9990 chunk 130 optimal weight: 2.9990 chunk 449 optimal weight: 110.0000 chunk 117 optimal weight: 30.0000 chunk 48 optimal weight: 50.0000 chunk 350 optimal weight: 40.0000 chunk 325 optimal weight: 20.0000 overall best weight: 15.3996 ------------------------------------------------------------------------------- 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 = 0.2346 r_free = 0.2346 target = 0.029668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2251 r_free = 0.2251 target = 0.024662 restraints weight = 340551.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 19)----------------| | r_work = 0.2246 r_free = 0.2246 target = 0.024577 restraints weight = 444230.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 13)----------------| | r_work = 0.2246 r_free = 0.2246 target = 0.024576 restraints weight = 460936.134| |-----------------------------------------------------------------------------| r_work (final): 0.2367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.3535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 20192 Z= 0.318 Angle : 0.705 13.040 25180 Z= 0.452 Chirality : 0.000 0.000 0 Planarity : 0.004 0.024 5024 Dihedral : 5.345 59.895 5024 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 1.46 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.12 % Favored : 94.64 % 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: 1.52 (0.12), residues: 4984 helix: 2.46 (0.10), residues: 2815 sheet: -1.05 (0.22), residues: 506 loop : -0.89 (0.16), residues: 1663 Details of bonding type rmsd hydrogen bonds : bond 0.05371 ( 2304) hydrogen bonds : angle 5.21392 ( 6681) covalent geometry : bond 0.00426 (20192) covalent geometry : angle 0.70458 (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 : 2.294 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.1652 time to fit residues: 29.1066 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 : 2.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 108 optimal weight: 40.0000 chunk 469 optimal weight: 50.0000 chunk 66 optimal weight: 20.0000 chunk 19 optimal weight: 50.0000 chunk 188 optimal weight: 50.0000 chunk 183 optimal weight: 30.0000 chunk 107 optimal weight: 30.0000 chunk 262 optimal weight: 30.0000 chunk 360 optimal weight: 50.0000 chunk 233 optimal weight: 40.0000 chunk 204 optimal weight: 6.9990 overall best weight: 23.3998 ------------------------------------------------------------------------------- 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 = 0.2474 r_free = 0.2474 target = 0.029199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2197 r_free = 0.2197 target = 0.021865 restraints weight = 314383.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2204 r_free = 0.2204 target = 0.021961 restraints weight = 286528.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2212 r_free = 0.2212 target = 0.022096 restraints weight = 262769.640| |-----------------------------------------------------------------------------| r_work (final): 0.2214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.5114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 20192 Z= 0.446 Angle : 0.826 17.571 25180 Z= 0.538 Chirality : 0.000 0.000 0 Planarity : 0.005 0.027 5024 Dihedral : 6.306 49.178 5024 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.92 % Favored : 92.84 % 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 : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.12), residues: 4984 helix: 1.30 (0.09), residues: 2783 sheet: -1.53 (0.25), residues: 407 loop : -1.50 (0.15), residues: 1794 Details of bonding type rmsd hydrogen bonds : bond 0.06652 ( 2304) hydrogen bonds : angle 6.48357 ( 6681) covalent geometry : bond 0.00592 (20192) covalent geometry : angle 0.82586 (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 : 2.250 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.1702 time to fit residues: 29.9499 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 : 2.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 196 optimal weight: 8.9990 chunk 70 optimal weight: 50.0000 chunk 19 optimal weight: 50.0000 chunk 150 optimal weight: 10.0000 chunk 98 optimal weight: 50.0000 chunk 431 optimal weight: 50.0000 chunk 317 optimal weight: 7.9990 chunk 30 optimal weight: 40.0000 chunk 432 optimal weight: 50.0000 chunk 279 optimal weight: 20.0000 chunk 293 optimal weight: 30.0000 overall best weight: 15.3996 ------------------------------------------------------------------------------- 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 = 0.2414 r_free = 0.2414 target = 0.031417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2340 r_free = 0.2340 target = 0.026727 restraints weight = 337228.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2327 r_free = 0.2327 target = 0.026451 restraints weight = 398047.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2325 r_free = 0.2325 target = 0.026409 restraints weight = 500291.064| |-----------------------------------------------------------------------------| r_work (final): 0.2347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.5271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 20192 Z= 0.279 Angle : 0.596 12.888 25180 Z= 0.386 Chirality : 0.000 0.000 0 Planarity : 0.003 0.016 5024 Dihedral : 5.359 49.418 5024 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 2.04 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.84 % Favored : 92.94 % 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 : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.12), residues: 4984 helix: 1.83 (0.10), residues: 2814 sheet: -1.62 (0.24), residues: 437 loop : -1.54 (0.15), residues: 1733 Details of bonding type rmsd hydrogen bonds : bond 0.04800 ( 2304) hydrogen bonds : angle 5.38565 ( 6681) covalent geometry : bond 0.00373 (20192) covalent geometry : angle 0.59630 (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 : 2.196 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.1712 time to fit residues: 29.9179 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 : 2.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 164 optimal weight: 20.0000 chunk 483 optimal weight: 20.0000 chunk 277 optimal weight: 20.0000 chunk 361 optimal weight: 6.9990 chunk 488 optimal weight: 0.8980 chunk 334 optimal weight: 40.0000 chunk 345 optimal weight: 30.0000 chunk 61 optimal weight: 5.9990 chunk 123 optimal weight: 9.9990 chunk 179 optimal weight: 20.0000 chunk 247 optimal weight: 50.0000 overall best weight: 8.7790 ------------------------------------------------------------------------------- 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 = 0.2493 r_free = 0.2493 target = 0.029803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2216 r_free = 0.2216 target = 0.022259 restraints weight = 300315.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2222 r_free = 0.2222 target = 0.022368 restraints weight = 273209.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2222 r_free = 0.2222 target = 0.022368 restraints weight = 251249.292| |-----------------------------------------------------------------------------| r_work (final): 0.2219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.5372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 20192 Z= 0.170 Angle : 0.428 9.540 25180 Z= 0.275 Chirality : 0.000 0.000 0 Planarity : 0.002 0.013 5024 Dihedral : 4.519 46.262 5024 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 0.92 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.80 % Favored : 93.98 % 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 : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.13), residues: 4984 helix: 2.65 (0.10), residues: 2831 sheet: -1.64 (0.23), residues: 489 loop : -1.21 (0.16), residues: 1664 Details of bonding type rmsd hydrogen bonds : bond 0.03812 ( 2304) hydrogen bonds : angle 4.51874 ( 6681) covalent geometry : bond 0.00226 (20192) covalent geometry : angle 0.42839 (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 : 2.175 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.1618 time to fit residues: 28.2877 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 380 optimal weight: 40.0000 chunk 214 optimal weight: 30.0000 chunk 84 optimal weight: 20.0000 chunk 354 optimal weight: 50.0000 chunk 34 optimal weight: 50.0000 chunk 307 optimal weight: 30.0000 chunk 145 optimal weight: 9.9990 chunk 122 optimal weight: 50.0000 chunk 319 optimal weight: 0.0020 chunk 311 optimal weight: 10.0000 chunk 432 optimal weight: 100.0000 overall best weight: 14.0002 ------------------------------------------------------------------------------- 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 = 0.2400 r_free = 0.2400 target = 0.029381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2309 r_free = 0.2309 target = 0.024525 restraints weight = 342986.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2301 r_free = 0.2301 target = 0.024349 restraints weight = 414932.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2301 r_free = 0.2301 target = 0.024347 restraints weight = 473933.935| |-----------------------------------------------------------------------------| r_work (final): 0.2345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.5774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 20192 Z= 0.265 Angle : 0.554 13.164 25180 Z= 0.359 Chirality : 0.000 0.000 0 Planarity : 0.003 0.020 5024 Dihedral : 4.954 51.820 5024 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 2.12 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.85 % Favored : 91.95 % 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: 1.25 (0.13), residues: 4984 helix: 2.46 (0.10), residues: 2833 sheet: -1.79 (0.24), residues: 449 loop : -1.33 (0.16), residues: 1702 Details of bonding type rmsd hydrogen bonds : bond 0.04644 ( 2304) hydrogen bonds : angle 5.12167 ( 6681) covalent geometry : bond 0.00354 (20192) covalent geometry : angle 0.55398 (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 : 2.361 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.1738 time to fit residues: 30.6451 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 : 2.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 167 optimal weight: 50.0000 chunk 239 optimal weight: 50.0000 chunk 330 optimal weight: 50.0000 chunk 245 optimal weight: 0.4980 chunk 249 optimal weight: 10.0000 chunk 9 optimal weight: 20.0000 chunk 447 optimal weight: 10.0000 chunk 420 optimal weight: 50.0000 chunk 181 optimal weight: 40.0000 chunk 72 optimal weight: 20.0000 chunk 209 optimal weight: 20.0000 overall best weight: 12.0996 ------------------------------------------------------------------------------- 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 = 0.2418 r_free = 0.2418 target = 0.030985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2341 r_free = 0.2341 target = 0.026004 restraints weight = 326682.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2327 r_free = 0.2327 target = 0.025736 restraints weight = 411233.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2327 r_free = 0.2327 target = 0.025736 restraints weight = 495400.732| |-----------------------------------------------------------------------------| r_work (final): 0.2350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.5998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20192 Z= 0.218 Angle : 0.481 10.488 25180 Z= 0.312 Chirality : 0.000 0.000 0 Planarity : 0.003 0.015 5024 Dihedral : 4.623 49.818 5024 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 1.43 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.68 % Favored : 93.12 % 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 : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.13), residues: 4984 helix: 2.58 (0.10), residues: 2842 sheet: -1.84 (0.24), residues: 442 loop : -1.35 (0.16), residues: 1700 Details of bonding type rmsd hydrogen bonds : bond 0.03988 ( 2304) hydrogen bonds : angle 4.73850 ( 6681) covalent geometry : bond 0.00291 (20192) covalent geometry : angle 0.48089 (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 : 2.329 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.1698 time to fit residues: 29.8866 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 : 2.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 436 optimal weight: 50.0000 chunk 179 optimal weight: 20.0000 chunk 435 optimal weight: 30.0000 chunk 487 optimal weight: 50.0000 chunk 362 optimal weight: 40.0000 chunk 65 optimal weight: 50.0000 chunk 47 optimal weight: 50.0000 chunk 468 optimal weight: 9.9990 chunk 366 optimal weight: 50.0000 chunk 112 optimal weight: 50.0000 chunk 383 optimal weight: 50.0000 overall best weight: 29.9998 ------------------------------------------------------------------------------- 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 = 0.2461 r_free = 0.2461 target = 0.028733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2191 r_free = 0.2191 target = 0.021625 restraints weight = 320679.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2197 r_free = 0.2197 target = 0.021722 restraints weight = 288809.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2197 r_free = 0.2197 target = 0.021722 restraints weight = 265762.698| |-----------------------------------------------------------------------------| r_work (final): 0.1994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.6666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.087 20192 Z= 0.496 Angle : 0.859 15.730 25180 Z= 0.580 Chirality : 0.000 0.000 0 Planarity : 0.006 0.024 5024 Dihedral : 6.243 57.374 5024 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.26 % Allowed : 10.31 % Favored : 89.43 % 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 : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.12), residues: 4984 helix: 0.95 (0.10), residues: 2785 sheet: -2.14 (0.26), residues: 367 loop : -2.08 (0.14), residues: 1832 Details of bonding type rmsd hydrogen bonds : bond 0.06936 ( 2304) hydrogen bonds : angle 6.88692 ( 6681) covalent geometry : bond 0.00660 (20192) covalent geometry : angle 0.85949 (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 : 2.326 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.1666 time to fit residues: 29.4259 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 : 2.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 169 optimal weight: 50.0000 chunk 380 optimal weight: 20.0000 chunk 386 optimal weight: 50.0000 chunk 98 optimal weight: 8.9990 chunk 147 optimal weight: 8.9990 chunk 226 optimal weight: 30.0000 chunk 284 optimal weight: 30.0000 chunk 7 optimal weight: 7.9990 chunk 489 optimal weight: 70.0000 chunk 233 optimal weight: 30.0000 chunk 490 optimal weight: 50.0000 overall best weight: 15.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2421 r_free = 0.2421 target = 0.031698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2351 r_free = 0.2351 target = 0.026547 restraints weight = 327064.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2351 r_free = 0.2351 target = 0.026547 restraints weight = 384740.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2351 r_free = 0.2351 target = 0.026547 restraints weight = 384740.191| |-----------------------------------------------------------------------------| r_work (final): 0.2358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.6635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 20192 Z= 0.268 Angle : 0.563 11.612 25180 Z= 0.369 Chirality : 0.000 0.000 0 Planarity : 0.003 0.021 5024 Dihedral : 5.393 57.497 5024 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 2.23 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.99 % Favored : 91.81 % 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 : 0.10 % 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: 0.15 (0.12), residues: 4984 helix: 1.62 (0.10), residues: 2833 sheet: -2.28 (0.24), residues: 392 loop : -1.91 (0.15), residues: 1759 Details of bonding type rmsd hydrogen bonds : bond 0.04780 ( 2304) hydrogen bonds : angle 5.63729 ( 6681) covalent geometry : bond 0.00357 (20192) covalent geometry : angle 0.56281 (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 : 2.149 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.1736 time to fit residues: 30.4342 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 : 2.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 430 optimal weight: 60.0000 chunk 423 optimal weight: 7.9990 chunk 207 optimal weight: 50.0000 chunk 54 optimal weight: 6.9990 chunk 82 optimal weight: 40.0000 chunk 242 optimal weight: 50.0000 chunk 344 optimal weight: 6.9990 chunk 221 optimal weight: 30.0000 chunk 7 optimal weight: 1.9990 chunk 286 optimal weight: 9.9990 chunk 426 optimal weight: 50.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- 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 = 0.030848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2353 r_free = 0.2353 target = 0.026054 restraints weight = 331309.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 18)----------------| | r_work = 0.2353 r_free = 0.2353 target = 0.026054 restraints weight = 389435.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2353 r_free = 0.2353 target = 0.026053 restraints weight = 389470.628| |-----------------------------------------------------------------------------| r_work (final): 0.2364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.6568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 20192 Z= 0.142 Angle : 0.388 8.164 25180 Z= 0.251 Chirality : 0.000 0.000 0 Planarity : 0.002 0.020 5024 Dihedral : 4.381 50.110 5024 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 0.96 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.52 % Favored : 93.28 % 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: 1.36 (0.13), residues: 4984 helix: 2.73 (0.10), residues: 2840 sheet: -2.12 (0.24), residues: 443 loop : -1.53 (0.16), residues: 1701 Details of bonding type rmsd hydrogen bonds : bond 0.03519 ( 2304) hydrogen bonds : angle 4.53114 ( 6681) covalent geometry : bond 0.00188 (20192) covalent geometry : angle 0.38759 (25180) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4558.34 seconds wall clock time: 79 minutes 4.46 seconds (4744.46 seconds total)