Starting phenix.real_space_refine on Tue Jun 17 10:09:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tkm_25974/06_2025/7tkm_25974.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tkm_25974/06_2025/7tkm_25974.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7tkm_25974/06_2025/7tkm_25974.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tkm_25974/06_2025/7tkm_25974.map" model { file = "/net/cci-nas-00/data/ceres_data/7tkm_25974/06_2025/7tkm_25974.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tkm_25974/06_2025/7tkm_25974.cif" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.117 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 3 Type Number sf(0) Gaussians C 10112 2.51 5 N 5056 2.21 5 O 5059 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 20227 Number of models: 1 Model: "" Number of chains: 27 Chain: "0" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 300 Classifications: {'peptide': 75} Incomplete info: {'backbone_only': 65} Link IDs: {'PTRANS': 2, 'TRANS': 72} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 246 Unresolved non-hydrogen angles: 363 Unresolved non-hydrogen dihedrals: 146 Unresolved non-hydrogen chiralities: 94 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1, 'PHE:plan': 6, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 75 Chain: "1" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 300 Classifications: {'peptide': 75} Incomplete info: {'backbone_only': 65} Link IDs: {'PTRANS': 2, 'TRANS': 72} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 246 Unresolved non-hydrogen angles: 363 Unresolved non-hydrogen dihedrals: 146 Unresolved non-hydrogen chiralities: 94 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1, 'PHE:plan': 6, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 75 Chain: "2" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 300 Classifications: {'peptide': 75} Incomplete info: {'backbone_only': 65} Link IDs: {'PTRANS': 2, 'TRANS': 72} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 246 Unresolved non-hydrogen angles: 363 Unresolved non-hydrogen dihedrals: 146 Unresolved non-hydrogen chiralities: 94 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1, 'PHE:plan': 6, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 75 Chain: "3" Number of atoms: 296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 296 Classifications: {'peptide': 74} Incomplete info: {'backbone_only': 64} Link IDs: {'PTRANS': 2, 'TRANS': 71} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 242 Unresolved non-hydrogen angles: 358 Unresolved non-hydrogen dihedrals: 143 Unresolved non-hydrogen chiralities: 93 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1, 'PHE:plan': 6, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 75 Chain: "4" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 300 Classifications: {'peptide': 75} Incomplete info: {'backbone_only': 65} Link IDs: {'PTRANS': 2, 'TRANS': 72} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 246 Unresolved non-hydrogen angles: 363 Unresolved non-hydrogen dihedrals: 146 Unresolved non-hydrogen chiralities: 94 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1, 'PHE:plan': 6, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 75 Chain: "5" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 300 Classifications: {'peptide': 75} Incomplete info: {'backbone_only': 65} Link IDs: {'PTRANS': 2, 'TRANS': 72} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 246 Unresolved non-hydrogen angles: 363 Unresolved non-hydrogen dihedrals: 146 Unresolved non-hydrogen chiralities: 94 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1, 'PHE:plan': 6, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 75 Chain: "6" Number of atoms: 296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 296 Classifications: {'peptide': 74} Incomplete info: {'backbone_only': 64} Link IDs: {'PTRANS': 2, 'TRANS': 71} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 242 Unresolved non-hydrogen angles: 358 Unresolved non-hydrogen dihedrals: 143 Unresolved non-hydrogen chiralities: 93 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1, 'PHE:plan': 6, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 75 Chain: "7" Number of atoms: 292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 292 Classifications: {'peptide': 73} Incomplete info: {'backbone_only': 64} Link IDs: {'PTRANS': 2, 'TRANS': 70} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 238 Unresolved non-hydrogen angles: 352 Unresolved non-hydrogen dihedrals: 139 Unresolved non-hydrogen chiralities: 93 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1, 'PHE:plan': 5, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 68 Chain: "8" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 300 Classifications: {'peptide': 75} Incomplete info: {'backbone_only': 65} Link IDs: {'PTRANS': 2, 'TRANS': 72} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 246 Unresolved non-hydrogen angles: 363 Unresolved non-hydrogen dihedrals: 146 Unresolved non-hydrogen chiralities: 94 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1, 'PHE:plan': 6, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 75 Chain: "9" Number of atoms: 296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 296 Classifications: {'peptide': 74} Incomplete info: {'backbone_only': 64} Link IDs: {'PTRANS': 2, 'TRANS': 71} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 242 Unresolved non-hydrogen angles: 358 Unresolved non-hydrogen dihedrals: 143 Unresolved non-hydrogen chiralities: 93 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1, 'PHE:plan': 6, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 75 Chain: "A" Number of atoms: 1996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 499, 1996 Classifications: {'peptide': 499} Incomplete info: {'backbone_only': 453} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 18, 'TRANS': 478} Chain breaks: 1 Unresolved chain link angles: 19 Unresolved non-hydrogen bonds: 1854 Unresolved non-hydrogen angles: 2698 Unresolved non-hydrogen dihedrals: 1123 Unresolved non-hydrogen chiralities: 606 Planarities with less than four sites: {'GLN:plan1': 25, 'HIS:plan': 6, 'TYR:plan': 14, 'ASN:plan1': 17, 'TRP:plan': 2, 'ASP:plan': 21, 'PHE:plan': 13, 'GLU:plan': 37, 'ARG:plan': 29} Unresolved non-hydrogen planarities: 804 Chain: "B" Number of atoms: 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: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 1059 Classifications: {'peptide': 265} Incomplete info: {'backbone_only': 254, 'n_c_alpha_c_only': 1} Link IDs: {'PTRANS': 9, 'TRANS': 255} Chain breaks: 1 Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 1025 Unresolved non-hydrogen angles: 1473 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: 14.75, per 1000 atoms: 0.73 Number of scatterers: 20227 At special positions: 0 Unit cell: (129.36, 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 5059 8.00 N 5056 7.00 C 10112 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.97 Conformation dependent library (CDL) restraints added in 4.2 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: 199 helices and 27 sheets defined 59.8% alpha, 8.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.53 Creating SS restraints... Processing helix chain '0' and resid 1 through 17 removed outlier: 3.553A pdb=" N GLY 0 13 " --> pdb=" O TYR 0 9 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ILE 0 17 " --> pdb=" O GLY 0 13 " (cutoff:3.500A) Processing helix chain '0' and resid 18 through 40 removed outlier: 4.324A pdb=" N ALA 0 22 " --> pdb=" O GLY 0 18 " (cutoff:3.500A) removed outlier: 3.629A 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: 3.994A pdb=" N THR 0 61 " --> pdb=" O LEU 0 57 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLY 0 62 " --> pdb=" O SER 0 58 " (cutoff:3.500A) Processing helix chain '1' and resid 2 through 17 removed outlier: 3.678A pdb=" N GLY 1 13 " --> pdb=" O TYR 1 9 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ILE 1 17 " --> pdb=" O GLY 1 13 " (cutoff:3.500A) Processing helix chain '1' and resid 18 through 40 removed outlier: 4.388A pdb=" N ALA 1 22 " --> pdb=" O GLY 1 18 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ALA 1 27 " --> pdb=" O GLY 1 23 " (cutoff:3.500A) Processing helix chain '1' and resid 43 through 74 Proline residue: 1 49 - end of helix removed outlier: 3.662A pdb=" N CYS 1 65 " --> pdb=" O THR 1 61 " (cutoff:3.500A) Processing helix chain '2' and resid 2 through 17 removed outlier: 3.829A pdb=" N ILE 2 17 " --> pdb=" O GLY 2 13 " (cutoff:3.500A) Processing helix chain '2' and resid 18 through 40 removed outlier: 4.359A pdb=" N ALA 2 22 " --> pdb=" O GLY 2 18 " (cutoff:3.500A) removed outlier: 3.653A 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: 3.934A pdb=" N THR 2 61 " --> pdb=" O LEU 2 57 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLY 2 62 " --> pdb=" O SER 2 58 " (cutoff:3.500A) Processing helix chain '3' and resid 3 through 17 removed outlier: 3.842A pdb=" N ILE 3 17 " --> pdb=" O GLY 3 13 " (cutoff:3.500A) Processing helix chain '3' and resid 18 through 40 removed outlier: 4.243A pdb=" N ALA 3 22 " --> pdb=" O GLY 3 18 " (cutoff:3.500A) removed outlier: 3.671A 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: 3.803A 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: 4.271A pdb=" N ALA 4 22 " --> pdb=" O GLY 4 18 " (cutoff:3.500A) Processing helix chain '4' and resid 43 through 74 Proline residue: 4 49 - end of helix removed outlier: 4.118A pdb=" N THR 4 61 " --> pdb=" O LEU 4 57 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N GLY 4 62 " --> pdb=" O SER 4 58 " (cutoff:3.500A) Processing helix chain '5' and resid 2 through 17 removed outlier: 3.824A pdb=" N ILE 5 17 " --> pdb=" O GLY 5 13 " (cutoff:3.500A) Processing helix chain '5' and resid 18 through 40 removed outlier: 4.070A pdb=" N ALA 5 22 " --> pdb=" O GLY 5 18 " (cutoff:3.500A) Processing helix chain '5' and resid 43 through 75 Proline residue: 5 49 - end of helix removed outlier: 3.689A pdb=" N GLY 5 62 " --> pdb=" O SER 5 58 " (cutoff:3.500A) Processing helix chain '6' and resid 3 through 16 removed outlier: 3.564A pdb=" N THR 6 16 " --> pdb=" O ALA 6 12 " (cutoff:3.500A) Processing helix chain '6' and resid 18 through 40 removed outlier: 4.317A pdb=" N ALA 6 22 " --> pdb=" O GLY 6 18 " (cutoff:3.500A) Processing helix chain '6' and resid 43 through 75 Proline residue: 6 49 - end of helix removed outlier: 3.644A pdb=" N THR 6 61 " --> pdb=" O LEU 6 57 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLY 6 62 " --> pdb=" O SER 6 58 " (cutoff:3.500A) Processing helix chain '7' and resid 2 through 16 removed outlier: 3.545A pdb=" N THR 7 16 " --> pdb=" O ALA 7 12 " (cutoff:3.500A) Processing helix chain '7' and resid 16 through 40 removed outlier: 3.895A pdb=" N LEU 7 20 " --> pdb=" O THR 7 16 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N GLY 7 21 " --> pdb=" O ILE 7 17 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ALA 7 22 " --> pdb=" O GLY 7 18 " (cutoff:3.500A) removed outlier: 3.719A 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: 3.732A pdb=" N GLY 7 62 " --> pdb=" O SER 7 58 " (cutoff:3.500A) Processing helix chain '8' and resid 2 through 17 removed outlier: 3.888A pdb=" N ILE 8 17 " --> pdb=" O GLY 8 13 " (cutoff:3.500A) Processing helix chain '8' and resid 18 through 40 removed outlier: 4.507A 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: 3.810A pdb=" N THR 8 61 " --> pdb=" O LEU 8 57 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N GLY 8 62 " --> pdb=" O SER 8 58 " (cutoff:3.500A) Processing helix chain '9' and resid 3 through 17 removed outlier: 3.900A pdb=" N ILE 9 17 " --> pdb=" O GLY 9 13 " (cutoff:3.500A) Processing helix chain '9' and resid 18 through 40 removed outlier: 4.434A pdb=" N ALA 9 22 " --> pdb=" O GLY 9 18 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA 9 27 " --> pdb=" O GLY 9 23 " (cutoff:3.500A) Processing helix chain '9' and resid 43 through 75 Proline residue: 9 49 - end of helix removed outlier: 3.539A pdb=" N THR 9 61 " --> pdb=" O LEU 9 57 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLY 9 62 " --> pdb=" O SER 9 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 20 Processing helix chain 'A' and resid 80 through 84 Processing helix chain 'A' and resid 102 through 106 removed outlier: 3.890A pdb=" N LEU A 105 " --> pdb=" O GLY A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 188 removed outlier: 4.282A pdb=" N VAL A 180 " --> pdb=" O GLY A 176 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ALA A 181 " --> pdb=" O LYS A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 193 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 261 Proline residue: A 249 - end of helix removed outlier: 3.577A 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 332 through 335 removed outlier: 3.573A pdb=" N ASP A 335 " --> pdb=" O GLN A 332 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 332 through 335' Processing helix chain 'A' and resid 338 through 348 Processing helix chain 'A' and resid 355 through 361 Processing helix chain 'A' and resid 375 through 380 removed outlier: 3.549A pdb=" N SER A 378 " --> pdb=" O ARG A 375 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA A 379 " --> 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: 4.019A pdb=" N GLU A 401 " --> pdb=" O ALA A 397 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE A 405 " --> pdb=" O GLU A 401 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN A 407 " --> pdb=" O ALA A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 431 removed outlier: 3.593A 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 removed outlier: 3.521A pdb=" N GLY A 450 " --> pdb=" O LEU A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 458 removed outlier: 3.531A pdb=" N ASP A 456 " --> pdb=" O GLY A 453 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE A 458 " --> pdb=" O LEU A 455 " (cutoff:3.500A) 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 478 Processing helix chain 'A' and resid 479 through 488 Processing helix chain 'A' and resid 492 through 509 removed outlier: 3.542A pdb=" N THR A 509 " --> pdb=" O SER A 505 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 19 Processing helix chain 'B' and resid 102 through 106 removed outlier: 3.799A pdb=" N LEU B 105 " --> pdb=" O GLY B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 159 Processing helix chain 'B' and resid 176 through 194 removed outlier: 3.604A pdb=" N ALA B 181 " --> pdb=" O LYS B 177 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N THR B 184 " --> pdb=" O VAL B 180 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LYS B 189 " --> pdb=" O ILE B 185 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N ARG B 190 " --> pdb=" O LEU B 186 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N TRP B 191 " --> pdb=" O ASN B 187 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLY B 194 " --> pdb=" O ARG B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 225 Processing helix chain 'B' and resid 227 through 229 No H-bonds generated for 'chain 'B' and resid 227 through 229' Processing helix chain 'B' and resid 241 through 263 Proline residue: B 249 - end of helix removed outlier: 3.666A pdb=" N PHE B 259 " --> pdb=" O ILE B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 287 Processing helix chain 'B' and resid 299 through 309 Processing helix chain 'B' and resid 315 through 319 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 Processing helix chain 'B' and resid 382 through 389 Processing helix chain 'B' and resid 391 through 407 Processing helix chain 'B' and resid 413 through 431 Processing helix chain 'B' and resid 439 through 442 Processing helix chain 'B' and resid 443 through 452 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 removed outlier: 3.755A pdb=" N SER B 468 " --> pdb=" O GLY B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 489 Processing helix chain 'B' and resid 492 through 508 removed outlier: 4.299A pdb=" N ALA B 508 " --> pdb=" O GLU B 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 22 Processing helix chain 'C' and resid 152 through 159 Processing helix chain 'C' and resid 176 through 194 removed outlier: 3.532A pdb=" N VAL C 180 " --> pdb=" O GLY C 176 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA C 181 " --> pdb=" O LYS C 177 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N THR C 184 " --> pdb=" O VAL C 180 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE C 185 " --> pdb=" O ALA C 181 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ARG C 190 " --> pdb=" O LEU C 186 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N TRP C 191 " --> pdb=" O ASN C 187 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLY C 194 " --> pdb=" O ARG C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 200 Processing helix chain 'C' and resid 211 through 225 Processing helix chain 'C' and resid 241 through 262 Proline residue: C 249 - end of helix removed outlier: 3.567A pdb=" N TRP C 258 " --> pdb=" O SER C 254 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N PHE C 259 " --> pdb=" O ILE C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 287 Processing helix chain 'C' and resid 292 through 296 Processing helix chain 'C' and resid 299 through 310 Processing helix chain 'C' and resid 338 through 348 Processing helix chain 'C' and resid 355 through 361 Processing helix chain 'C' and resid 376 through 381 Processing helix chain 'C' and resid 382 through 388 Processing helix chain 'C' and resid 389 through 402 removed outlier: 3.813A pdb=" N LYS C 393 " --> pdb=" O ALA C 389 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU C 394 " --> pdb=" O GLY C 390 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 406 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 453 through 457 removed outlier: 3.811A pdb=" N GLY C 457 " --> pdb=" O HIS C 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 461 through 478 removed outlier: 4.509A pdb=" N GLU C 465 " --> pdb=" O SER C 461 " (cutoff:3.500A) Processing helix chain 'C' and resid 478 through 489 removed outlier: 3.542A pdb=" N LEU C 482 " --> pdb=" O HIS C 478 " (cutoff:3.500A) Processing helix chain 'C' and resid 492 through 509 Processing helix chain 'D' and resid 88 through 92 Processing helix chain 'D' and resid 138 through 145 Processing helix chain 'D' and resid 162 through 178 Processing helix chain 'D' and resid 190 through 204 Processing helix chain 'D' and resid 225 through 247 removed outlier: 4.607A pdb=" N ALA D 233 " --> pdb=" O ARG D 229 " (cutoff:3.500A) removed outlier: 4.464A 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 Processing helix chain 'D' and resid 336 through 342 removed outlier: 3.766A pdb=" N SER D 340 " --> pdb=" O SER D 336 " (cutoff:3.500A) Processing helix chain 'D' and resid 364 through 392 removed outlier: 3.952A pdb=" N ILE D 387 " --> pdb=" O SER D 383 " (cutoff:3.500A) removed outlier: 3.957A 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: 3.831A pdb=" N SER D 415 " --> pdb=" O GLN D 411 " (cutoff:3.500A) 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 Processing helix chain 'E' and resid 88 through 92 removed outlier: 3.548A pdb=" N THR E 91 " --> pdb=" O GLY E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 145 Processing helix chain 'E' and resid 159 through 178 removed outlier: 3.783A pdb=" N VAL E 165 " --> pdb=" O VAL E 161 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N LYS E 176 " --> pdb=" O ASN E 172 " (cutoff:3.500A) removed outlier: 3.574A 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 245 removed outlier: 3.525A pdb=" N ARG E 231 " --> pdb=" O GLY E 227 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ALA E 233 " --> pdb=" O ARG E 229 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N LEU E 234 " --> pdb=" O ALA E 230 " (cutoff:3.500A) Processing helix chain 'E' and resid 258 through 273 removed outlier: 4.284A pdb=" N ALA E 270 " --> pdb=" O SER E 266 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N LEU E 271 " --> pdb=" O GLU E 267 " (cutoff:3.500A) Processing helix chain 'E' and resid 284 through 295 Processing helix chain 'E' and resid 312 through 316 Processing helix chain 'E' and resid 319 through 327 removed outlier: 3.608A 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 359 through 364 Processing helix chain 'E' and resid 364 through 384 Processing helix chain 'E' and resid 384 through 391 Processing helix chain 'E' and resid 397 through 414 Processing helix chain 'E' and resid 421 through 426 Processing helix chain 'E' and resid 433 through 446 Processing helix chain 'E' and resid 453 through 458 removed outlier: 3.806A pdb=" N PHE E 457 " --> pdb=" O PRO E 453 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N TYR E 458 " --> pdb=" O GLU E 454 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 453 through 458' 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: 4.255A pdb=" N LYS F 176 " --> pdb=" O ASN F 172 " (cutoff:3.500A) Processing helix chain 'F' and resid 190 through 204 Processing helix chain 'F' and resid 225 through 231 Processing helix chain 'F' and resid 231 through 245 removed outlier: 3.625A pdb=" N THR F 235 " --> pdb=" O ARG F 231 " (cutoff:3.500A) Processing helix chain 'F' and resid 257 through 273 removed outlier: 3.617A pdb=" N PHE F 261 " --> pdb=" O ASN F 257 " (cutoff:3.500A) Processing helix chain 'F' and resid 277 through 281 Processing helix chain 'F' and resid 284 through 296 removed outlier: 3.530A pdb=" N ILE F 296 " --> pdb=" O LEU F 292 " (cutoff:3.500A) Processing helix chain 'F' and resid 313 through 316 Processing helix chain 'F' and resid 319 through 329 removed outlier: 3.580A pdb=" N ALA F 327 " --> pdb=" O ALA F 323 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N HIS F 328 " --> pdb=" O THR F 324 " (cutoff:3.500A) Processing helix chain 'F' and resid 336 through 343 Processing helix chain 'F' and resid 359 through 364 Processing helix chain 'F' and resid 364 through 390 removed outlier: 4.149A pdb=" N ASP F 386 " --> pdb=" O LYS F 382 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ILE F 387 " --> pdb=" O SER F 383 " (cutoff:3.500A) Processing helix chain 'F' and resid 397 through 415 removed outlier: 3.882A pdb=" N SER F 415 " --> pdb=" O GLN F 411 " (cutoff:3.500A) 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: 4.041A pdb=" N LYS G 33 " --> pdb=" O THR G 29 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER G 40 " --> pdb=" O LYS G 36 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA G 47 " --> pdb=" O LYS G 43 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLU G 48 " --> pdb=" O MET G 44 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N PHE G 51 " --> pdb=" O ALA G 47 " (cutoff:3.500A) Processing helix chain 'G' and resid 86 through 98 removed outlier: 3.696A pdb=" N HIS G 98 " --> pdb=" O ALA G 94 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 122 removed outlier: 4.017A pdb=" N LYS G 115 " --> pdb=" O GLY G 111 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N MET G 116 " --> pdb=" O ASP G 112 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLN G 117 " --> pdb=" O LYS G 113 " (cutoff:3.500A) Processing helix chain 'G' and resid 139 through 155 Processing helix chain 'G' and resid 156 through 159 Processing helix chain 'G' and resid 184 through 191 removed outlier: 3.515A pdb=" N GLN G 190 " --> pdb=" O LYS G 186 " (cutoff:3.500A) Processing helix chain 'G' and resid 192 through 197 removed outlier: 3.621A pdb=" N LYS G 196 " --> pdb=" O SER G 193 " (cutoff:3.500A) Processing helix chain 'G' and resid 204 through 276 removed outlier: 4.367A pdb=" N GLU G 211 " --> pdb=" O ARG G 207 " (cutoff:3.500A) Processing helix chain 'H' and resid 93 through 97 Processing helix chain 'H' and resid 100 through 115 removed outlier: 4.275A pdb=" N SER H 114 " --> pdb=" O LYS H 110 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N SER H 115 " --> pdb=" O ASN H 111 " (cutoff:3.500A) Processing helix chain 'H' and resid 119 through 136 removed outlier: 3.555A pdb=" N VAL H 136 " --> pdb=" O ASN H 132 " (cutoff:3.500A) Processing helix chain 'I' and resid 9 through 22 Processing helix chain 'I' and resid 31 through 38 Processing helix chain 'O' and resid 16 through 29 Processing helix chain 'O' and resid 32 through 49 removed outlier: 3.754A pdb=" N ALA O 36 " --> pdb=" O SER O 32 " (cutoff:3.500A) Processing helix chain 'O' and resid 64 through 78 removed outlier: 3.812A pdb=" N HIS O 78 " --> pdb=" O ILE O 74 " (cutoff:3.500A) Processing helix chain 'O' and resid 83 through 95 Processing helix chain 'O' and resid 101 through 117 Processing helix chain 'O' and resid 130 through 143 Processing helix chain 'O' and resid 180 through 191 Processing helix chain 'T' and resid 27 through 43 removed outlier: 3.592A pdb=" N LEU T 43 " --> pdb=" O VAL T 39 " (cutoff:3.500A) Processing helix chain 'T' and resid 58 through 77 removed outlier: 4.238A pdb=" N GLN T 62 " --> pdb=" O TRP T 58 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N MET T 72 " --> pdb=" O THR T 68 " (cutoff:3.500A) Processing helix chain 'T' and resid 82 through 84 No H-bonds generated for 'chain 'T' and resid 82 through 84' Processing helix chain 'T' and resid 85 through 100 removed outlier: 3.613A pdb=" N ILE T 96 " --> pdb=" O LEU T 92 " (cutoff:3.500A) Processing helix chain 'T' and resid 101 through 105 Processing helix chain 'T' and resid 114 through 137 removed outlier: 3.651A pdb=" N ILE T 118 " --> pdb=" O HIS T 114 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU T 132 " --> pdb=" O GLY T 128 " (cutoff:3.500A) Processing helix chain 'T' and resid 138 through 146 removed outlier: 3.622A pdb=" N PHE T 141 " --> pdb=" O GLY T 138 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N PHE T 142 " --> pdb=" O TRP T 139 " (cutoff:3.500A) Processing helix chain 'T' and resid 151 through 155 Processing helix chain 'T' and resid 156 through 167 removed outlier: 3.647A pdb=" N GLU T 162 " --> pdb=" O LEU T 158 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N SER T 165 " --> pdb=" O ILE T 161 " (cutoff:3.500A) Processing helix chain 'T' and resid 168 through 199 removed outlier: 3.639A pdb=" N LEU T 173 " --> pdb=" O ARG T 169 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N GLY T 174 " --> pdb=" O ALA T 170 " (cutoff:3.500A) removed outlier: 4.258A 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: 3.691A pdb=" N ALA T 235 " --> pdb=" O GLY T 231 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ALA T 239 " --> pdb=" O ALA T 235 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU T 242 " --> pdb=" O THR T 238 " (cutoff:3.500A) Processing helix chain 'U' and resid 54 through 184 removed outlier: 4.258A pdb=" N LEU U 58 " --> pdb=" O ASP U 54 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N ALA U 74 " --> pdb=" O ALA U 70 " (cutoff:3.500A) Proline residue: U 75 - end of helix removed outlier: 3.574A pdb=" N VAL U 103 " --> pdb=" O HIS U 99 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LYS U 104 " --> pdb=" O VAL U 100 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU U 113 " --> pdb=" O SER U 109 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ASN U 115 " --> pdb=" O SER U 111 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL U 116 " --> pdb=" O GLN U 112 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU U 118 " --> pdb=" O GLN U 114 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N LYS U 121 " --> pdb=" O ALA U 117 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N VAL U 122 " --> pdb=" O GLU U 118 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE U 138 " --> pdb=" O GLU U 134 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLU U 139 " --> pdb=" O SER U 135 " (cutoff:3.500A) Processing helix chain 'U' and resid 187 through 207 removed outlier: 3.648A pdb=" N VAL U 193 " --> pdb=" O PHE U 189 " (cutoff:3.500A) Processing helix chain 'V' and resid 4 through 19 Processing helix chain 'V' and resid 26 through 48 Processing helix chain 'V' and resid 67 through 78 Processing helix chain 'V' and resid 90 through 127 Processing helix chain 'V' and resid 134 through 142 Processing helix chain 'V' and resid 143 through 156 Processing helix chain 'W' and resid 17 through 30 removed outlier: 3.901A pdb=" N ALA W 21 " --> pdb=" O SER W 17 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N VAL W 28 " --> pdb=" O ILE W 24 " (cutoff:3.500A) Processing helix chain 'W' and resid 48 through 56 Processing helix chain 'W' and resid 63 through 84 removed outlier: 3.898A pdb=" N GLY W 72 " --> pdb=" O HIS W 68 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ILE W 73 " --> pdb=" O PHE W 69 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N TYR W 78 " --> pdb=" O ILE W 74 " (cutoff:3.500A) Processing helix chain 'X' and resid 2 through 14 Processing helix chain 'X' and resid 20 through 27 removed outlier: 3.525A pdb=" N GLY X 26 " --> pdb=" O GLN X 22 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASN X 27 " --> pdb=" O ASP X 23 " (cutoff:3.500A) Processing helix chain 'X' and resid 45 through 57 removed outlier: 3.942A pdb=" N ALA X 49 " --> pdb=" O GLN X 45 " (cutoff:3.500A) removed outlier: 3.754A 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 removed outlier: 3.543A pdb=" N TYR Z 15 " --> pdb=" O ASN Z 11 " (cutoff:3.500A) Processing helix chain 'Z' and resid 30 through 48 removed outlier: 3.704A pdb=" N MET Z 34 " --> pdb=" O PHE Z 30 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE Z 35 " --> pdb=" O PHE Z 31 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU Z 38 " --> pdb=" O MET Z 34 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 37 removed outlier: 6.198A pdb=" N ARG A 42 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N VAL A 36 " --> pdb=" O ILE A 40 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ILE A 40 " --> pdb=" O VAL A 36 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 40 through 45 current: chain 'A' and resid 62 through 69 removed outlier: 5.812A pdb=" N GLY A 63 " --> pdb=" O PHE A 78 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N PHE A 78 " --> pdb=" O GLY A 63 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N ALA A 65 " --> pdb=" O VAL A 76 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N VAL A 76 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASN A 67 " --> pdb=" O GLY A 74 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 72 through 78 current: chain 'B' and resid 40 through 45 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 40 through 45 current: chain 'B' and resid 62 through 67 removed outlier: 5.516A pdb=" N ALA B 65 " --> pdb=" O VAL B 76 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N VAL B 76 " --> pdb=" O ALA B 65 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 72 through 77 current: chain 'E' and resid 20 through 25 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 20 through 25 current: chain 'E' and resid 44 through 53 removed outlier: 6.556A pdb=" N ARG E 60 " --> pdb=" O ALA E 51 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N HIS E 53 " --> pdb=" O THR E 58 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N THR E 58 " --> pdb=" O HIS E 53 " (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 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 109 through 111 current: chain 'A' and resid 231 through 236 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 231 through 236 current: chain 'A' and resid 322 through 331 No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 147 through 148 removed outlier: 4.671A 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: 3.684A pdb=" N PHE A 353 " --> pdb=" O LEU A 371 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N LEU A 371 " --> pdb=" O PHE A 353 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 98 through 101 Processing sheet with id=AA7, first strand: chain 'B' and resid 109 through 110 removed outlier: 5.901A pdb=" N VAL B 110 " --> pdb=" O ALA B 235 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N THR B 237 " --> pdb=" O VAL B 110 " (cutoff:3.500A) removed outlier: 8.472A pdb=" N ILE B 232 " --> pdb=" O LEU B 201 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N CYS B 203 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N VAL B 234 " --> pdb=" O CYS B 203 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N TYR B 205 " --> pdb=" O VAL B 234 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N ALA B 236 " --> pdb=" O TYR B 205 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N ALA B 207 " --> pdb=" O ALA B 236 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N TYR B 202 " --> pdb=" O LEU B 267 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N VAL B 269 " --> pdb=" O TYR B 202 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N VAL B 204 " --> pdb=" O VAL B 269 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N ASP B 271 " --> pdb=" O VAL B 204 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N VAL B 206 " --> pdb=" O ASP B 271 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N LEU B 168 " --> pdb=" O ILE B 352 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 147 through 148 removed outlier: 4.096A pdb=" N ILE B 161 " --> pdb=" O VAL B 148 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 31 through 37 removed outlier: 6.992A pdb=" N ARG C 42 " --> pdb=" O LEU C 34 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N VAL C 36 " --> pdb=" O ILE C 40 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ILE C 40 " --> pdb=" O VAL C 36 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 40 through 45 current: chain 'C' and resid 62 through 68 removed outlier: 4.129A pdb=" N LEU C 66 " --> pdb=" O GLY C 74 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N GLY C 74 " --> pdb=" O LEU C 66 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 73 through 77 current: chain 'D' and resid 20 through 25 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 20 through 25 current: chain 'D' and resid 44 through 53 removed outlier: 6.330A pdb=" N ARG D 60 " --> pdb=" O ALA D 51 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 98 through 101 Processing sheet with id=AB2, first strand: chain 'C' and resid 108 through 111 Processing sheet with id=AB3, first strand: chain 'C' and resid 169 through 172 removed outlier: 5.872A pdb=" N ILE C 169 " --> pdb=" O ILE C 329 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N THR C 331 " --> pdb=" O ILE C 169 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N GLY C 171 " --> pdb=" O THR C 331 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'C' and resid 350 through 354 removed outlier: 3.619A pdb=" N PHE C 353 " --> pdb=" O LEU C 371 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N LEU C 371 " --> pdb=" O PHE C 353 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 84 through 87 removed outlier: 4.093A pdb=" N LEU D 113 " --> pdb=" O VAL D 87 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 133 through 134 removed outlier: 4.087A pdb=" N TYR D 147 " --> pdb=" O LEU D 134 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 215 through 219 removed outlier: 6.422A pdb=" N VAL D 183 " --> pdb=" O PHE D 254 " (cutoff:3.500A) removed outlier: 8.195A pdb=" N ASP D 256 " --> pdb=" O VAL D 183 " (cutoff:3.500A) removed outlier: 8.398A pdb=" N THR D 185 " --> pdb=" O ASP D 256 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N PHE D 254 " --> pdb=" O VAL D 307 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N ALA D 309 " --> pdb=" O PHE D 254 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N ASP D 256 " --> pdb=" O ALA D 309 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 84 through 87 removed outlier: 3.547A pdb=" N LEU E 113 " --> pdb=" O VAL E 87 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 95 through 96 removed outlier: 5.713A pdb=" N ILE E 96 " --> pdb=" O PHE E 219 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N GLN E 221 " --> pdb=" O ILE E 96 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N SER E 182 " --> pdb=" O ALA E 216 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N VAL E 218 " --> pdb=" O SER E 182 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N PHE E 184 " --> pdb=" O VAL E 218 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N GLY E 220 " --> pdb=" O PHE E 184 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N GLY E 186 " --> pdb=" O GLY E 220 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N THR E 305 " --> pdb=" O VAL E 251 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 133 through 134 removed outlier: 3.886A pdb=" N TYR E 147 " --> pdb=" O LEU E 134 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 331 through 335 removed outlier: 10.839A pdb=" N THR E 332 " --> pdb=" O LEU E 351 " (cutoff:3.500A) removed outlier: 9.318A pdb=" N LEU E 351 " --> pdb=" O THR E 332 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N VAL E 334 " --> pdb=" O ASP E 349 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 13 through 17 removed outlier: 6.638A pdb=" N ASP F 22 " --> pdb=" O THR F 14 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N VAL F 16 " --> pdb=" O ILE F 20 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N ILE F 20 " --> pdb=" O VAL F 16 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N THR F 58 " --> pdb=" O HIS F 53 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N HIS F 53 " --> pdb=" O THR F 58 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ARG F 60 " --> pdb=" O ALA F 51 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 84 through 87 removed outlier: 3.515A pdb=" N LYS F 115 " --> pdb=" O VAL F 85 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N LEU F 113 " --> pdb=" O VAL F 87 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 95 through 96 removed outlier: 3.782A pdb=" N ILE F 96 " --> pdb=" O LEU F 217 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N PHE F 219 " --> pdb=" O ILE F 96 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N PHE F 184 " --> pdb=" O VAL F 218 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N VAL F 183 " --> pdb=" O PHE F 254 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 133 through 134 removed outlier: 4.251A pdb=" N TYR F 147 " --> pdb=" O LEU F 134 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 174 through 182 removed outlier: 6.464A pdb=" N SER G 174 " --> pdb=" O VAL G 170 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL G 170 " --> pdb=" O SER G 174 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ILE G 162 " --> pdb=" O ILE G 182 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N ASN G 167 " --> pdb=" O ILE G 77 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ILE G 74 " --> pdb=" O VAL G 108 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N ILE G 110 " --> pdb=" O ILE G 74 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N ALA G 76 " --> pdb=" O ILE G 110 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N ILE G 107 " --> pdb=" O LEU G 128 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N ILE G 130 " --> pdb=" O ILE G 107 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N THR G 109 " --> pdb=" O ILE G 130 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 19 through 22 removed outlier: 4.434A pdb=" N THR H 20 " --> pdb=" O LEU H 16 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N LEU H 16 " --> pdb=" O THR H 20 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N GLN H 13 " --> pdb=" O VAL H 85 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N ALA H 87 " --> pdb=" O GLN H 13 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N ALA H 15 " --> pdb=" O ALA H 87 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLN H 82 " --> pdb=" O GLN H 78 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLY H 72 " --> pdb=" O LEU H 53 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N LEU H 53 " --> pdb=" O GLY H 72 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N PHE H 74 " --> pdb=" O GLN H 51 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N GLN H 51 " --> pdb=" O PHE H 74 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N THR H 76 " --> pdb=" O VAL H 49 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N VAL H 49 " --> pdb=" O THR H 76 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N VAL H 56 " --> pdb=" O PRO H 33 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'O' and resid 156 through 159 2229 hydrogen bonds defined for protein. 6477 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.76 Time building geometry restraints manager: 7.80 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: 5059 1.28 - 1.35: 1321 1.35 - 1.41: 3699 1.41 - 1.48: 5130 1.48 - 1.55: 4982 Bond restraints: 20191 Sorted by residual: bond pdb=" CA HIS O 78 " pdb=" C HIS O 78 " ideal model delta sigma weight residual 1.533 1.475 0.058 9.60e-03 1.09e+04 3.69e+01 bond pdb=" CA ALA C 157 " pdb=" C ALA C 157 " ideal model delta sigma weight residual 1.523 1.477 0.046 8.40e-03 1.42e+04 3.00e+01 bond pdb=" N ASN C 28 " pdb=" CA ASN C 28 " ideal model delta sigma weight residual 1.467 1.419 0.047 8.70e-03 1.32e+04 2.96e+01 bond pdb=" CA LYS D 214 " pdb=" C LYS D 214 " ideal model delta sigma weight residual 1.524 1.487 0.037 7.00e-03 2.04e+04 2.86e+01 bond pdb=" N VAL F 312 " pdb=" CA VAL F 312 " ideal model delta sigma weight residual 1.458 1.417 0.041 7.70e-03 1.69e+04 2.84e+01 ... (remaining 20186 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.22: 21743 3.22 - 6.44: 2937 6.44 - 9.65: 441 9.65 - 12.87: 56 12.87 - 16.09: 2 Bond angle restraints: 25179 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 113.71 102.34 11.37 9.50e-01 1.11e+00 1.43e+02 angle pdb=" N ARG V 59 " pdb=" CA ARG V 59 " pdb=" C ARG V 59 " ideal model delta sigma weight residual 114.62 103.28 11.34 1.14e+00 7.69e-01 9.89e+01 angle pdb=" N ILE O 33 " pdb=" CA ILE O 33 " pdb=" C ILE O 33 " ideal model delta sigma weight residual 111.81 103.49 8.32 8.60e-01 1.35e+00 9.36e+01 angle pdb=" N GLN A 398 " pdb=" CA GLN A 398 " pdb=" C GLN A 398 " ideal model delta sigma weight residual 113.41 102.17 11.24 1.22e+00 6.72e-01 8.49e+01 angle pdb=" N VAL V 172 " pdb=" CA VAL V 172 " pdb=" C VAL V 172 " ideal model delta sigma weight residual 111.58 101.82 9.76 1.06e+00 8.90e-01 8.47e+01 ... (remaining 25174 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.48: 5000 23.48 - 46.95: 21 46.95 - 70.42: 0 70.42 - 93.90: 2 93.90 - 117.37: 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 -62.63 -117.37 0 5.00e+00 4.00e-02 5.51e+02 dihedral pdb=" CA ASN 5 40 " pdb=" C ASN 5 40 " pdb=" N PRO 5 41 " pdb=" CA PRO 5 41 " ideal model delta harmonic sigma weight residual 180.00 -137.95 -42.05 0 5.00e+00 4.00e-02 7.07e+01 dihedral pdb=" CA ASN 6 40 " pdb=" C ASN 6 40 " pdb=" N PRO 6 41 " pdb=" CA PRO 6 41 " ideal model delta harmonic sigma weight residual 180.00 -137.97 -42.03 0 5.00e+00 4.00e-02 7.07e+01 ... (remaining 5021 not shown) Chirality restraints: 0 Planarity restraints: 5024 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS D 448 " -0.019 2.00e-02 2.50e+03 3.90e-02 1.52e+01 pdb=" C LYS D 448 " 0.067 2.00e-02 2.50e+03 pdb=" O LYS D 448 " -0.026 2.00e-02 2.50e+03 pdb=" N TYR D 449 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL F 206 " -0.019 2.00e-02 2.50e+03 3.84e-02 1.48e+01 pdb=" C VAL F 206 " 0.066 2.00e-02 2.50e+03 pdb=" O VAL F 206 " -0.026 2.00e-02 2.50e+03 pdb=" N ILE F 207 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER D 182 " 0.019 2.00e-02 2.50e+03 3.84e-02 1.47e+01 pdb=" C SER D 182 " -0.066 2.00e-02 2.50e+03 pdb=" O SER D 182 " 0.025 2.00e-02 2.50e+03 pdb=" N VAL D 183 " 0.022 2.00e-02 2.50e+03 ... (remaining 5021 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.89: 9858 2.89 - 3.39: 17387 3.39 - 3.89: 26670 3.89 - 4.40: 27405 4.40 - 4.90: 40452 Nonbonded interactions: 121772 Sorted by model distance: nonbonded pdb=" N LEU E 252 " pdb=" O LEU E 252 " model vdw 2.385 2.496 nonbonded pdb=" N THR D 305 " pdb=" O THR D 305 " model vdw 2.389 2.496 nonbonded pdb=" N PRO X 33 " pdb=" O PRO X 33 " model vdw 2.401 2.496 nonbonded pdb=" N ARG D 114 " pdb=" O ARG D 114 " model vdw 2.407 2.496 nonbonded pdb=" N ILE F 255 " pdb=" O ILE F 255 " model vdw 2.418 2.496 ... (remaining 121767 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: 1.070 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: 0.870 Check model and map are aligned: 0.160 Set scattering table: 0.210 Process input model: 57.260 Find NCS groups from input model: 1.220 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: 0.000 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6078 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 0.058 20191 Z= 1.486 Angle : 2.223 16.087 25179 Z= 1.598 Chirality : 0.000 0.000 0 Planarity : 0.010 0.039 5024 Dihedral : 6.776 117.369 5024 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 0.12 Ramachandran Plot: Outliers : 1.52 % Allowed : 4.31 % Favored : 94.16 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.46 % Cis-general : 0.10 % Twisted Proline : 4.43 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.11), residues: 4984 helix: 0.92 (0.09), residues: 2794 sheet: -1.33 (0.21), residues: 581 loop : -2.02 (0.13), residues: 1609 Details of bonding type rmsd hydrogen bonds : bond 0.21527 ( 2229) hydrogen bonds : angle 7.74371 ( 6477) covalent geometry : bond 0.01893 (20191) covalent geometry : angle 2.22273 (25179) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9968 Ramachandran restraints generated. 4984 Oldfield, 0 Emsley, 4984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9968 Ramachandran restraints generated. 4984 Oldfield, 0 Emsley, 4984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 4114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 2.566 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.1663 time to fit residues: 29.3701 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 : 2.224 ------------------------------------------------------------------------------- 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: 5.9990 chunk 372 optimal weight: 6.9990 chunk 206 optimal weight: 6.9990 chunk 127 optimal weight: 20.0000 chunk 251 optimal weight: 5.9990 chunk 199 optimal weight: 8.9990 chunk 385 optimal weight: 20.0000 chunk 149 optimal weight: 8.9990 chunk 234 optimal weight: 5.9990 chunk 287 optimal weight: 9.9990 chunk 446 optimal weight: 20.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- 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 = 0.2666 r_free = 0.2666 target = 0.035124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2429 r_free = 0.2429 target = 0.026564 restraints weight = 278384.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2401 r_free = 0.2401 target = 0.026263 restraints weight = 277579.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2398 r_free = 0.2398 target = 0.026183 restraints weight = 297791.715| |-----------------------------------------------------------------------------| r_work (final): 0.2219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 20191 Z= 0.193 Angle : 0.543 8.589 25179 Z= 0.347 Chirality : 0.000 0.000 0 Planarity : 0.003 0.020 5024 Dihedral : 5.018 81.816 5024 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 0.23 Ramachandran Plot: Outliers : 0.28 % Allowed : 2.73 % Favored : 96.99 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.96 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.12), residues: 4984 helix: 2.38 (0.10), residues: 2827 sheet: -1.00 (0.21), residues: 604 loop : -1.28 (0.15), residues: 1553 Details of bonding type rmsd hydrogen bonds : bond 0.04793 ( 2229) hydrogen bonds : angle 4.47303 ( 6477) covalent geometry : bond 0.00252 (20191) covalent geometry : angle 0.54337 (25179) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9968 Ramachandran restraints generated. 4984 Oldfield, 0 Emsley, 4984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9968 Ramachandran restraints generated. 4984 Oldfield, 0 Emsley, 4984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 4114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 2.403 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.1653 time to fit residues: 29.2672 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 : 2.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 217 optimal weight: 60.0000 chunk 282 optimal weight: 40.0000 chunk 87 optimal weight: 20.0000 chunk 348 optimal weight: 0.0980 chunk 438 optimal weight: 40.0000 chunk 340 optimal weight: 6.9990 chunk 130 optimal weight: 50.0000 chunk 449 optimal weight: 90.0000 chunk 117 optimal weight: 40.0000 chunk 48 optimal weight: 120.0000 chunk 350 optimal weight: 40.0000 overall best weight: 21.4194 ------------------------------------------------------------------------------- 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 = 0.2576 r_free = 0.2576 target = 0.032337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2339 r_free = 0.2339 target = 0.024493 restraints weight = 296829.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2314 r_free = 0.2314 target = 0.024213 restraints weight = 299129.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2312 r_free = 0.2312 target = 0.024178 restraints weight = 313112.055| |-----------------------------------------------------------------------------| r_work (final): 0.2138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.3934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.105 20191 Z= 0.413 Angle : 0.833 14.547 25179 Z= 0.537 Chirality : 0.000 0.000 0 Planarity : 0.005 0.024 5024 Dihedral : 6.166 88.973 5024 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 2.20 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.96 % Favored : 93.74 % 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: 0.59 (0.12), residues: 4984 helix: 1.65 (0.09), residues: 2829 sheet: -1.35 (0.23), residues: 491 loop : -1.25 (0.15), residues: 1664 Details of bonding type rmsd hydrogen bonds : bond 0.06662 ( 2229) hydrogen bonds : angle 5.87490 ( 6477) covalent geometry : bond 0.00560 (20191) covalent geometry : angle 0.83313 (25179) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9968 Ramachandran restraints generated. 4984 Oldfield, 0 Emsley, 4984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9968 Ramachandran restraints generated. 4984 Oldfield, 0 Emsley, 4984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 4114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 2.701 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.1727 time to fit residues: 30.5534 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 : 2.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 95 optimal weight: 40.0000 chunk 210 optimal weight: 20.0000 chunk 108 optimal weight: 40.0000 chunk 469 optimal weight: 2.9990 chunk 66 optimal weight: 50.0000 chunk 19 optimal weight: 50.0000 chunk 188 optimal weight: 8.9990 chunk 183 optimal weight: 30.0000 chunk 107 optimal weight: 30.0000 chunk 262 optimal weight: 0.8980 chunk 360 optimal weight: 50.0000 overall best weight: 12.5792 ------------------------------------------------------------------------------- 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 = 0.2401 r_free = 0.2401 target = 0.029450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2286 r_free = 0.2286 target = 0.023891 restraints weight = 331764.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2250 r_free = 0.2250 target = 0.023183 restraints weight = 677689.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2250 r_free = 0.2250 target = 0.023013 restraints weight = 992169.967| |-----------------------------------------------------------------------------| r_work (final): 0.2367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.4375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 20191 Z= 0.247 Angle : 0.547 12.274 25179 Z= 0.354 Chirality : 0.000 0.000 0 Planarity : 0.003 0.016 5024 Dihedral : 4.903 86.680 5024 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 0.96 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.78 % Favored : 94.94 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.96 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.12), residues: 4984 helix: 2.25 (0.10), residues: 2861 sheet: -1.29 (0.23), residues: 513 loop : -1.10 (0.16), residues: 1610 Details of bonding type rmsd hydrogen bonds : bond 0.04473 ( 2229) hydrogen bonds : angle 4.62328 ( 6477) covalent geometry : bond 0.00332 (20191) covalent geometry : angle 0.54726 (25179) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9968 Ramachandran restraints generated. 4984 Oldfield, 0 Emsley, 4984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9968 Ramachandran restraints generated. 4984 Oldfield, 0 Emsley, 4984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 4114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 2.442 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.1727 time to fit residues: 30.4969 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 : 2.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 166 optimal weight: 50.0000 chunk 380 optimal weight: 50.0000 chunk 347 optimal weight: 50.0000 chunk 196 optimal weight: 30.0000 chunk 70 optimal weight: 40.0000 chunk 19 optimal weight: 50.0000 chunk 150 optimal weight: 50.0000 chunk 98 optimal weight: 0.7980 chunk 431 optimal weight: 50.0000 chunk 317 optimal weight: 30.0000 chunk 30 optimal weight: 50.0000 overall best weight: 30.1596 ------------------------------------------------------------------------------- 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 = 0.2326 r_free = 0.2326 target = 0.027303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2217 r_free = 0.2217 target = 0.021897 restraints weight = 328148.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2177 r_free = 0.2177 target = 0.021168 restraints weight = 590585.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2177 r_free = 0.2177 target = 0.021021 restraints weight = 881265.603| |-----------------------------------------------------------------------------| r_work (final): 0.2103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.6044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.118 20191 Z= 0.514 Angle : 0.962 15.071 25179 Z= 0.635 Chirality : 0.000 0.000 0 Planarity : 0.006 0.027 5024 Dihedral : 6.999 81.595 5024 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.32 % Allowed : 10.01 % Favored : 89.67 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.96 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.11), residues: 4984 helix: 0.30 (0.09), residues: 2779 sheet: -2.00 (0.24), residues: 400 loop : -1.97 (0.14), residues: 1805 Details of bonding type rmsd hydrogen bonds : bond 0.07902 ( 2229) hydrogen bonds : angle 7.17495 ( 6477) covalent geometry : bond 0.00691 (20191) covalent geometry : angle 0.96231 (25179) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9968 Ramachandran restraints generated. 4984 Oldfield, 0 Emsley, 4984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9968 Ramachandran restraints generated. 4984 Oldfield, 0 Emsley, 4984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 4114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 2.349 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.1715 time to fit residues: 30.3490 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 : 2.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 238 optimal weight: 20.0000 chunk 247 optimal weight: 40.0000 chunk 393 optimal weight: 50.0000 chunk 54 optimal weight: 50.0000 chunk 164 optimal weight: 8.9990 chunk 483 optimal weight: 0.7980 chunk 277 optimal weight: 8.9990 chunk 361 optimal weight: 9.9990 chunk 488 optimal weight: 10.0000 chunk 334 optimal weight: 40.0000 chunk 345 optimal weight: 8.9990 overall best weight: 7.5588 ------------------------------------------------------------------------------- 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 = 0.2381 r_free = 0.2381 target = 0.028823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2257 r_free = 0.2257 target = 0.023144 restraints weight = 306484.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2225 r_free = 0.2225 target = 0.022225 restraints weight = 667507.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2225 r_free = 0.2225 target = 0.022015 restraints weight = 906009.981| |-----------------------------------------------------------------------------| r_work (final): 0.2125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.5799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 20191 Z= 0.165 Angle : 0.464 12.677 25179 Z= 0.292 Chirality : 0.000 0.000 0 Planarity : 0.002 0.018 5024 Dihedral : 5.023 78.741 5024 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 1.04 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.78 % Favored : 93.92 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.96 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.12), residues: 4984 helix: 1.81 (0.10), residues: 2854 sheet: -1.81 (0.23), residues: 467 loop : -1.49 (0.16), residues: 1663 Details of bonding type rmsd hydrogen bonds : bond 0.04230 ( 2229) hydrogen bonds : angle 4.81953 ( 6477) covalent geometry : bond 0.00220 (20191) covalent geometry : angle 0.46401 (25179) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9968 Ramachandran restraints generated. 4984 Oldfield, 0 Emsley, 4984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9968 Ramachandran restraints generated. 4984 Oldfield, 0 Emsley, 4984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 4114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 2.298 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.1768 time to fit residues: 31.2627 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 : 2.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 387 optimal weight: 50.0000 chunk 126 optimal weight: 20.0000 chunk 316 optimal weight: 50.0000 chunk 96 optimal weight: 20.0000 chunk 410 optimal weight: 50.0000 chunk 380 optimal weight: 50.0000 chunk 214 optimal weight: 50.0000 chunk 84 optimal weight: 50.0000 chunk 354 optimal weight: 50.0000 chunk 34 optimal weight: 20.0000 chunk 307 optimal weight: 20.0000 overall best weight: 26.0000 ------------------------------------------------------------------------------- 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 = 0.2318 r_free = 0.2318 target = 0.027430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2236 r_free = 0.2236 target = 0.022299 restraints weight = 325202.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2197 r_free = 0.2197 target = 0.021685 restraints weight = 457808.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2195 r_free = 0.2195 target = 0.021643 restraints weight = 664477.366| |-----------------------------------------------------------------------------| r_work (final): 0.2110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.6489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.107 20191 Z= 0.430 Angle : 0.767 12.953 25179 Z= 0.509 Chirality : 0.000 0.000 0 Planarity : 0.005 0.024 5024 Dihedral : 6.013 78.245 5024 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.34 % Allowed : 10.63 % Favored : 89.02 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.96 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.12), residues: 4984 helix: 0.87 (0.10), residues: 2807 sheet: -2.08 (0.25), residues: 408 loop : -1.95 (0.15), residues: 1769 Details of bonding type rmsd hydrogen bonds : bond 0.06582 ( 2229) hydrogen bonds : angle 6.30486 ( 6477) covalent geometry : bond 0.00577 (20191) covalent geometry : angle 0.76673 (25179) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9968 Ramachandran restraints generated. 4984 Oldfield, 0 Emsley, 4984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9968 Ramachandran restraints generated. 4984 Oldfield, 0 Emsley, 4984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 4114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 2.415 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.1744 time to fit residues: 30.6812 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 : 2.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 283 optimal weight: 20.0000 chunk 334 optimal weight: 40.0000 chunk 490 optimal weight: 120.0000 chunk 367 optimal weight: 50.0000 chunk 31 optimal weight: 50.0000 chunk 285 optimal weight: 30.0000 chunk 167 optimal weight: 40.0000 chunk 239 optimal weight: 30.0000 chunk 330 optimal weight: 0.0010 chunk 245 optimal weight: 0.0870 chunk 249 optimal weight: 20.0000 overall best weight: 14.0176 ------------------------------------------------------------------------------- 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 = 0.2335 r_free = 0.2335 target = 0.027953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2239 r_free = 0.2239 target = 0.022250 restraints weight = 310612.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2208 r_free = 0.2208 target = 0.021820 restraints weight = 394979.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2206 r_free = 0.2206 target = 0.021715 restraints weight = 536908.444| |-----------------------------------------------------------------------------| r_work (final): 0.2180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.6555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 20191 Z= 0.253 Angle : 0.549 12.719 25179 Z= 0.355 Chirality : 0.000 0.000 0 Planarity : 0.003 0.018 5024 Dihedral : 5.239 75.448 5024 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 2.00 Ramachandran Plot: Outliers : 0.30 % Allowed : 8.53 % Favored : 91.17 % 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: 0.03 (0.12), residues: 4984 helix: 1.42 (0.10), residues: 2845 sheet: -2.02 (0.24), residues: 435 loop : -1.86 (0.15), residues: 1704 Details of bonding type rmsd hydrogen bonds : bond 0.04811 ( 2229) hydrogen bonds : angle 5.28193 ( 6477) covalent geometry : bond 0.00342 (20191) covalent geometry : angle 0.54916 (25179) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9968 Ramachandran restraints generated. 4984 Oldfield, 0 Emsley, 4984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9968 Ramachandran restraints generated. 4984 Oldfield, 0 Emsley, 4984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 4114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 2.678 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.1744 time to fit residues: 30.8304 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 : 2.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 148 optimal weight: 8.9990 chunk 31 optimal weight: 50.0000 chunk 439 optimal weight: 50.0000 chunk 455 optimal weight: 50.0000 chunk 309 optimal weight: 40.0000 chunk 301 optimal weight: 30.0000 chunk 303 optimal weight: 40.0000 chunk 490 optimal weight: 50.0000 chunk 436 optimal weight: 50.0000 chunk 179 optimal weight: 40.0000 chunk 435 optimal weight: 50.0000 overall best weight: 31.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2302 r_free = 0.2302 target = 0.026856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2220 r_free = 0.2220 target = 0.021805 restraints weight = 324921.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2187 r_free = 0.2187 target = 0.021356 restraints weight = 442061.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2183 r_free = 0.2183 target = 0.021205 restraints weight = 621094.073| |-----------------------------------------------------------------------------| r_work (final): 0.2095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.7293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.114 20191 Z= 0.519 Angle : 0.911 14.155 25179 Z= 0.610 Chirality : 0.000 0.000 0 Planarity : 0.006 0.029 5024 Dihedral : 6.644 78.084 5024 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.32 % Allowed : 12.72 % Favored : 86.96 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.96 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.62 (0.11), residues: 4984 helix: 0.08 (0.09), residues: 2727 sheet: -2.32 (0.25), residues: 368 loop : -2.52 (0.14), residues: 1889 Details of bonding type rmsd hydrogen bonds : bond 0.07512 ( 2229) hydrogen bonds : angle 7.10612 ( 6477) covalent geometry : bond 0.00700 (20191) covalent geometry : angle 0.91067 (25179) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9968 Ramachandran restraints generated. 4984 Oldfield, 0 Emsley, 4984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9968 Ramachandran restraints generated. 4984 Oldfield, 0 Emsley, 4984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 4114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 2.454 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.1700 time to fit residues: 29.8929 Evaluate side-chains 82 residues out of total 4114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 2.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 302 optimal weight: 10.0000 chunk 162 optimal weight: 50.0000 chunk 259 optimal weight: 50.0000 chunk 143 optimal weight: 30.0000 chunk 443 optimal weight: 120.0000 chunk 293 optimal weight: 50.0000 chunk 409 optimal weight: 30.0000 chunk 396 optimal weight: 50.0000 chunk 374 optimal weight: 0.1980 chunk 169 optimal weight: 50.0000 chunk 380 optimal weight: 40.0000 overall best weight: 22.0396 ------------------------------------------------------------------------------- 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 = 0.2311 r_free = 0.2311 target = 0.027202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2232 r_free = 0.2232 target = 0.022002 restraints weight = 313276.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2207 r_free = 0.2207 target = 0.021602 restraints weight = 412899.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2202 r_free = 0.2202 target = 0.021465 restraints weight = 517583.609| |-----------------------------------------------------------------------------| r_work (final): 0.2097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.7438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.103 20191 Z= 0.368 Angle : 0.709 14.237 25179 Z= 0.466 Chirality : 0.000 0.000 0 Planarity : 0.004 0.022 5024 Dihedral : 6.057 75.736 5024 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.30 % Allowed : 11.64 % Favored : 88.06 % 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: -1.36 (0.12), residues: 4984 helix: 0.35 (0.09), residues: 2759 sheet: -2.44 (0.25), residues: 391 loop : -2.49 (0.14), residues: 1834 Details of bonding type rmsd hydrogen bonds : bond 0.05913 ( 2229) hydrogen bonds : angle 6.31132 ( 6477) covalent geometry : bond 0.00502 (20191) covalent geometry : angle 0.70866 (25179) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9968 Ramachandran restraints generated. 4984 Oldfield, 0 Emsley, 4984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9968 Ramachandran restraints generated. 4984 Oldfield, 0 Emsley, 4984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 4114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 2.327 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.1686 time to fit residues: 29.8104 Evaluate side-chains 82 residues out of total 4114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 2.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 120 optimal weight: 9.9990 chunk 310 optimal weight: 50.0000 chunk 335 optimal weight: 50.0000 chunk 486 optimal weight: 30.0000 chunk 334 optimal weight: 40.0000 chunk 178 optimal weight: 20.0000 chunk 363 optimal weight: 1.9990 chunk 158 optimal weight: 30.0000 chunk 196 optimal weight: 10.0000 chunk 176 optimal weight: 50.0000 chunk 430 optimal weight: 50.0000 overall best weight: 14.3996 ------------------------------------------------------------------------------- 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 = 0.2328 r_free = 0.2328 target = 0.027689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2244 r_free = 0.2244 target = 0.022235 restraints weight = 309196.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2213 r_free = 0.2213 target = 0.021773 restraints weight = 423574.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2211 r_free = 0.2211 target = 0.021709 restraints weight = 576078.668| |-----------------------------------------------------------------------------| r_work (final): 0.2104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.7485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 20191 Z= 0.250 Angle : 0.552 13.564 25179 Z= 0.357 Chirality : 0.000 0.000 0 Planarity : 0.003 0.019 5024 Dihedral : 5.408 75.873 5024 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.30 % Allowed : 10.93 % Favored : 88.76 % 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: -0.54 (0.12), residues: 4984 helix: 1.10 (0.10), residues: 2806 sheet: -2.46 (0.25), residues: 397 loop : -2.25 (0.15), residues: 1781 Details of bonding type rmsd hydrogen bonds : bond 0.04798 ( 2229) hydrogen bonds : angle 5.49912 ( 6477) covalent geometry : bond 0.00343 (20191) covalent geometry : angle 0.55236 (25179) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4941.21 seconds wall clock time: 85 minutes 24.82 seconds (5124.82 seconds total)