Starting phenix.real_space_refine on Thu Sep 18 20:12:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tkg_25968/09_2025/7tkg_25968.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tkg_25968/09_2025/7tkg_25968.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7tkg_25968/09_2025/7tkg_25968.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tkg_25968/09_2025/7tkg_25968.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7tkg_25968/09_2025/7tkg_25968.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tkg_25968/09_2025/7tkg_25968.map" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.114 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 3 Type Number sf(0) Gaussians C 10112 2.51 5 N 5056 2.21 5 O 5060 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20228 Number of models: 1 Model: "" Number of chains: 27 Chain: "0" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 300 Classifications: {'peptide': 75} Incomplete info: {'backbone_only': 65} Link IDs: {'PTRANS': 2, 'TRANS': 72} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 246 Unresolved non-hydrogen angles: 363 Unresolved non-hydrogen dihedrals: 146 Unresolved non-hydrogen chiralities: 94 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'PHE:plan': 6, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 1, 'GLU: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, 'PHE:plan': 6, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 1, 'GLU: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, 'PHE:plan': 6, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 1, 'GLU: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, 'PHE:plan': 6, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 1, 'GLU: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, 'PHE:plan': 6, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 1, 'GLU: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, 'PHE:plan': 6, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 1, 'GLU: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, 'PHE:plan': 6, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 1, 'GLU: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, 'PHE:plan': 5, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 1, 'GLU: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, 'PHE:plan': 6, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 1, 'GLU: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, 'PHE:plan': 6, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 75 Chain: "A" Number of atoms: 2004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 501, 2004 Classifications: {'peptide': 501} Incomplete info: {'backbone_only': 454} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 18, 'TRANS': 480} Unresolved chain link angles: 19 Unresolved non-hydrogen bonds: 1862 Unresolved non-hydrogen angles: 2709 Unresolved non-hydrogen dihedrals: 1130 Unresolved non-hydrogen chiralities: 607 Planarities with less than four sites: {'GLU:plan': 37, 'ARG:plan': 29, 'ASP:plan': 21, 'ASN:plan1': 17, 'PHE:plan': 14, 'GLN:plan1': 25, 'HIS:plan': 6, 'TRP:plan': 2, 'TYR:plan': 14} Unresolved non-hydrogen planarities: 811 Chain: "B" Number of atoms: 2020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 505, 2020 Classifications: {'peptide': 505} Incomplete info: {'backbone_only': 459} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 483} Chain breaks: 1 Unresolved chain link angles: 20 Unresolved non-hydrogen bonds: 1875 Unresolved non-hydrogen angles: 2729 Unresolved non-hydrogen dihedrals: 1135 Unresolved non-hydrogen chiralities: 614 Planarities with less than four sites: {'GLN:plan1': 26, 'GLU:plan': 37, 'ARG:plan': 29, 'ASP:plan': 21, 'ASN:plan1': 17, 'PHE:plan': 13, 'HIS:plan': 6, 'TRP:plan': 2, 'TYR:plan': 14} Unresolved non-hydrogen planarities: 808 Chain: "C" Number of atoms: 1984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 1984 Classifications: {'peptide': 496} Incomplete info: {'backbone_only': 450} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 18, 'TRANS': 475} Chain breaks: 1 Unresolved chain link angles: 19 Unresolved non-hydrogen bonds: 1844 Unresolved non-hydrogen angles: 2683 Unresolved non-hydrogen dihedrals: 1118 Unresolved non-hydrogen chiralities: 602 Planarities with less than four sites: {'GLU:plan': 36, 'ARG:plan': 29, 'ASP:plan': 21, 'ASN:plan1': 17, 'PHE:plan': 13, 'GLN:plan1': 25, 'HIS:plan': 6, 'TRP:plan': 2, 'TYR:plan': 14} Unresolved non-hydrogen planarities: 800 Chain: "D" Number of atoms: 1876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 1876 Classifications: {'peptide': 469} Incomplete info: {'backbone_only': 423} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 444} Unresolved chain link angles: 23 Unresolved non-hydrogen bonds: 1724 Unresolved non-hydrogen angles: 2516 Unresolved non-hydrogen dihedrals: 1033 Unresolved non-hydrogen chiralities: 579 Planarities with less than four sites: {'ASP:plan': 25, 'HIS:plan': 7, 'PHE:plan': 17, 'GLU:plan': 37, 'GLN:plan1': 18, 'ASN:plan1': 10, 'ARG:plan': 22, 'TYR:plan': 10} Unresolved non-hydrogen planarities: 711 Chain: "E" Number of atoms: 1880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 1880 Classifications: {'peptide': 470} Incomplete info: {'backbone_only': 424} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 446} Unresolved chain link angles: 23 Unresolved non-hydrogen bonds: 1726 Unresolved non-hydrogen angles: 2519 Unresolved non-hydrogen dihedrals: 1034 Unresolved non-hydrogen chiralities: 580 Planarities with less than four sites: {'ASP:plan': 25, 'HIS:plan': 7, 'PHE:plan': 17, 'GLU:plan': 37, 'GLN:plan1': 18, 'ASN:plan1': 10, 'ARG:plan': 22, 'TYR:plan': 10} Unresolved non-hydrogen planarities: 711 Chain: "F" Number of atoms: 1872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 1872 Classifications: {'peptide': 468} Incomplete info: {'backbone_only': 422} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 445} Unresolved chain link angles: 22 Unresolved non-hydrogen bonds: 1721 Unresolved non-hydrogen angles: 2511 Unresolved non-hydrogen dihedrals: 1032 Unresolved non-hydrogen chiralities: 577 Planarities with less than four sites: {'ASP:plan': 25, 'HIS:plan': 7, 'PHE:plan': 17, 'GLU:plan': 37, 'GLN:plan1': 18, 'ASN:plan1': 10, 'ARG:plan': 22, 'TYR:plan': 10} Unresolved non-hydrogen planarities: 711 Chain: "G" Number of atoms: 1060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 1060 Classifications: {'peptide': 265} Incomplete info: {'backbone_only': 255} Link IDs: {'PTRANS': 9, 'TRANS': 255} Chain breaks: 1 Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 1024 Unresolved non-hydrogen angles: 1472 Unresolved non-hydrogen dihedrals: 628 Unresolved non-hydrogen chiralities: 328 Planarities with less than four sites: {'GLU:plan': 16, 'ARG:plan': 11, 'ASN:plan1': 18, 'ASP:plan': 14, 'GLN:plan1': 9, 'PHE:plan': 8, 'TYR:plan': 7, 'HIS:plan': 3} 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, 'PHE:plan': 5, 'HIS:plan': 2, 'GLU:plan': 13, 'TYR:plan': 1, 'ASN:plan1': 7, 'ARG:plan': 2, 'ASP:plan': 1} 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: {'TYR:plan': 4, 'ASN:plan1': 3, 'GLN:plan1': 4, 'ARG:plan': 2, 'GLU:plan': 2, 'ASP:plan': 1, 'PHE:plan': 1} 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: {'ARG:plan': 4, 'PHE:plan': 5, 'GLU:plan': 11, 'TYR:plan': 3, 'GLN:plan1': 5, 'ASN:plan1': 12, 'ASP:plan': 10, 'HIS:plan': 3} 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: {'PHE:plan': 18, 'TYR:plan': 10, 'ASN:plan1': 11, 'ARG:plan': 3, 'TRP:plan': 5, 'GLN:plan1': 3, 'GLU:plan': 3, 'ASP:plan': 2, 'HIS: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: {'ASN:plan1': 5, 'ASP:plan': 8, 'GLU:plan': 16, 'PHE:plan': 6, 'TYR:plan': 3, 'ARG:plan': 7, 'HIS:plan': 2, 'GLN:plan1': 11, 'TRP:plan': 1} 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: {'ASN:plan1': 7, 'ASP:plan': 13, 'TRP:plan': 2, 'ARG:plan': 7, 'GLN:plan1': 9, 'PHE:plan': 5, 'GLU:plan': 13, 'HIS:plan': 2, 'TYR:plan': 4} 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: {'ASN:plan1': 5, 'ARG:plan': 3, 'HIS:plan': 3, 'PHE:plan': 5, 'TYR:plan': 6, 'GLN:plan1': 1, 'ASP:plan': 2, 'TRP:plan': 1, 'GLU:plan': 1} 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: {'ASN:plan1': 5, 'GLN:plan1': 5, 'ASP:plan': 3, 'TYR:plan': 2, 'ARG:plan': 1, 'GLU:plan': 7, 'TRP:plan': 1, 'HIS: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: {'ARG:plan': 1, 'PHE:plan': 3, 'TYR:plan': 3, 'TRP:plan': 1, 'ASP:plan': 1, 'ASN:plan1': 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, 'TYR:plan': 3, 'ASN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 99 Time building chain proxies: 5.96, per 1000 atoms: 0.29 Number of scatterers: 20228 At special positions: 0 Unit cell: (126.665, 148.225, 234.465, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 5060 8.00 N 5056 7.00 C 10112 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.20 Conformation dependent library (CDL) restraints added in 1.5 seconds Enol-peptide restraints added in 1.2 microseconds 9968 Ramachandran restraints generated. 4984 Oldfield, 0 Emsley, 4984 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 0 Finding SS restraints... Secondary structure from input PDB file: 195 helices and 25 sheets defined 59.5% alpha, 10.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain '0' and resid 1 through 17 removed outlier: 3.514A pdb=" N GLY 0 13 " --> pdb=" O TYR 0 9 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ILE 0 17 " --> pdb=" O GLY 0 13 " (cutoff:3.500A) Processing helix chain '0' and resid 18 through 40 removed outlier: 4.231A pdb=" N ALA 0 22 " --> pdb=" O GLY 0 18 " (cutoff:3.500A) Processing helix chain '0' and resid 43 through 75 Proline residue: 0 49 - end of helix removed outlier: 3.625A pdb=" N THR 0 61 " --> pdb=" O LEU 0 57 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLY 0 62 " --> pdb=" O SER 0 58 " (cutoff:3.500A) Processing helix chain '1' and resid 2 through 17 removed outlier: 3.785A pdb=" N ILE 1 17 " --> pdb=" O GLY 1 13 " (cutoff:3.500A) Processing helix chain '1' and resid 18 through 40 removed outlier: 4.470A pdb=" N ALA 1 22 " --> pdb=" O GLY 1 18 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA 1 27 " --> pdb=" O GLY 1 23 " (cutoff:3.500A) Processing helix chain '1' and resid 43 through 74 Proline residue: 1 49 - end of helix removed outlier: 3.577A pdb=" N THR 1 61 " --> pdb=" O LEU 1 57 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLY 1 62 " --> pdb=" O SER 1 58 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N CYS 1 65 " --> pdb=" O THR 1 61 " (cutoff:3.500A) Processing helix chain '2' and resid 2 through 17 removed outlier: 3.856A pdb=" N ILE 2 17 " --> pdb=" O GLY 2 13 " (cutoff:3.500A) Processing helix chain '2' and resid 18 through 40 removed outlier: 4.430A pdb=" N ALA 2 22 " --> pdb=" O GLY 2 18 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ALA 2 27 " --> pdb=" O GLY 2 23 " (cutoff:3.500A) Processing helix chain '2' and resid 43 through 74 Proline residue: 2 49 - end of helix removed outlier: 3.858A pdb=" N THR 2 61 " --> pdb=" O LEU 2 57 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N GLY 2 62 " --> pdb=" O SER 2 58 " (cutoff:3.500A) Processing helix chain '3' and resid 3 through 17 removed outlier: 3.885A pdb=" N ILE 3 17 " --> pdb=" O GLY 3 13 " (cutoff:3.500A) Processing helix chain '3' and resid 19 through 40 removed outlier: 3.951A pdb=" N ALA 3 27 " --> pdb=" O GLY 3 23 " (cutoff:3.500A) Processing helix chain '3' and resid 43 through 74 Proline residue: 3 49 - end of helix removed outlier: 3.610A pdb=" N GLY 3 62 " --> pdb=" O SER 3 58 " (cutoff:3.500A) Processing helix chain '4' and resid 2 through 17 removed outlier: 3.677A pdb=" N ILE 4 17 " --> pdb=" O GLY 4 13 " (cutoff:3.500A) Processing helix chain '4' and resid 18 through 40 removed outlier: 4.065A pdb=" N ALA 4 22 " --> pdb=" O GLY 4 18 " (cutoff:3.500A) Processing helix chain '4' and resid 43 through 75 Proline residue: 4 49 - end of helix removed outlier: 3.881A pdb=" N THR 4 61 " --> pdb=" O LEU 4 57 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N GLY 4 62 " --> pdb=" O SER 4 58 " (cutoff:3.500A) Processing helix chain '5' and resid 2 through 17 removed outlier: 3.776A pdb=" N ILE 5 17 " --> pdb=" O GLY 5 13 " (cutoff:3.500A) Processing helix chain '5' and resid 18 through 40 removed outlier: 4.353A pdb=" N ALA 5 22 " --> pdb=" O GLY 5 18 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA 5 27 " --> pdb=" O GLY 5 23 " (cutoff:3.500A) Processing helix chain '5' and resid 43 through 75 Proline residue: 5 49 - end of helix removed outlier: 3.501A pdb=" N THR 5 61 " --> pdb=" O LEU 5 57 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLY 5 62 " --> pdb=" O SER 5 58 " (cutoff:3.500A) Processing helix chain '6' and resid 3 through 16 Processing helix chain '6' and resid 18 through 40 removed outlier: 4.451A pdb=" N ALA 6 22 " --> pdb=" O GLY 6 18 " (cutoff:3.500A) Processing helix chain '6' and resid 43 through 75 Proline residue: 6 49 - end of helix removed outlier: 3.600A pdb=" N THR 6 61 " --> pdb=" O LEU 6 57 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLY 6 62 " --> pdb=" O SER 6 58 " (cutoff:3.500A) Processing helix chain '7' and resid 2 through 40 removed outlier: 3.683A pdb=" N THR 7 16 " --> pdb=" O ALA 7 12 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ILE 7 17 " --> pdb=" O GLY 7 13 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N GLY 7 18 " --> pdb=" O ILE 7 14 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LEU 7 19 " --> pdb=" O SER 7 15 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU 7 20 " --> pdb=" O THR 7 16 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N GLY 7 21 " --> pdb=" O ILE 7 17 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ALA 7 22 " --> pdb=" O GLY 7 18 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ALA 7 27 " --> pdb=" O GLY 7 23 " (cutoff:3.500A) Processing helix chain '7' and resid 43 through 73 Proline residue: 7 49 - end of helix removed outlier: 3.550A pdb=" N THR 7 61 " --> pdb=" O LEU 7 57 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLY 7 62 " --> pdb=" O SER 7 58 " (cutoff:3.500A) Processing helix chain '8' and resid 2 through 17 removed outlier: 3.711A pdb=" N ILE 8 17 " --> pdb=" O GLY 8 13 " (cutoff:3.500A) Processing helix chain '8' and resid 18 through 40 removed outlier: 4.277A pdb=" N ALA 8 22 " --> pdb=" O GLY 8 18 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA 8 27 " --> pdb=" O GLY 8 23 " (cutoff:3.500A) Processing helix chain '8' and resid 43 through 74 Proline residue: 8 49 - end of helix removed outlier: 3.832A pdb=" N THR 8 61 " --> pdb=" O LEU 8 57 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N GLY 8 62 " --> pdb=" O SER 8 58 " (cutoff:3.500A) Processing helix chain '9' and resid 3 through 17 removed outlier: 3.769A pdb=" N ILE 9 17 " --> pdb=" O GLY 9 13 " (cutoff:3.500A) Processing helix chain '9' and resid 18 through 40 removed outlier: 4.293A pdb=" N ALA 9 22 " --> pdb=" O GLY 9 18 " (cutoff:3.500A) Processing helix chain '9' and resid 43 through 75 Proline residue: 9 49 - end of helix removed outlier: 3.542A pdb=" N THR 9 61 " --> pdb=" O LEU 9 57 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLY 9 62 " --> pdb=" O SER 9 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 20 Processing helix chain 'A' and resid 152 through 159 Processing helix chain 'A' and resid 176 through 194 removed outlier: 3.863A pdb=" N ALA A 181 " --> pdb=" O LYS A 177 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N THR A 184 " --> pdb=" O VAL A 180 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ARG A 190 " --> pdb=" O LEU A 186 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N TRP A 191 " --> pdb=" O ASN A 187 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY A 194 " --> pdb=" O ARG A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 199 Processing helix chain 'A' and resid 211 through 225 Processing helix chain 'A' and resid 241 through 263 Proline residue: A 249 - end of helix removed outlier: 3.625A pdb=" N ILE A 255 " --> pdb=" O THR A 251 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N PHE A 259 " --> pdb=" O ILE A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 286 removed outlier: 3.780A pdb=" N GLN A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 296 Processing helix chain 'A' and resid 297 through 298 No H-bonds generated for 'chain 'A' and resid 297 through 298' Processing helix chain 'A' and resid 299 through 309 Processing helix chain 'A' and resid 332 through 335 removed outlier: 3.807A pdb=" N ASP A 335 " --> pdb=" O GLN A 332 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 332 through 335' Processing helix chain 'A' and resid 338 through 348 Processing helix chain 'A' and resid 355 through 362 Processing helix chain 'A' and resid 382 through 389 Processing helix chain 'A' and resid 391 through 407 removed outlier: 3.609A pdb=" N GLN A 407 " --> pdb=" O ALA A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 431 removed outlier: 3.503A pdb=" N THR A 419 " --> pdb=" O SER A 415 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ARG A 425 " --> pdb=" O VAL A 421 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS A 431 " --> pdb=" O THR A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 442 Processing helix chain 'A' and resid 443 through 452 Processing helix chain 'A' and resid 459 through 461 No H-bonds generated for 'chain 'A' and resid 459 through 461' Processing helix chain 'A' and resid 462 through 477 Processing helix chain 'A' and resid 478 through 489 removed outlier: 3.510A pdb=" N LEU A 482 " --> pdb=" O HIS A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 508 removed outlier: 4.573A pdb=" N ALA A 508 " --> pdb=" O GLU A 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 19 Processing helix chain 'B' and resid 102 through 106 removed outlier: 3.860A pdb=" N LEU B 105 " --> pdb=" O GLY B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 159 Processing helix chain 'B' and resid 176 through 194 removed outlier: 4.048A pdb=" N THR B 184 " --> pdb=" O VAL B 180 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ILE B 185 " --> pdb=" O ALA B 181 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N LYS B 189 " --> pdb=" O ILE B 185 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N ARG B 190 " --> pdb=" O LEU B 186 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N TRP B 191 " --> pdb=" O ASN B 187 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N GLY B 194 " --> pdb=" O ARG B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 225 Processing helix chain 'B' and resid 241 through 262 Proline residue: B 249 - end of helix removed outlier: 3.506A pdb=" N ILE B 255 " --> pdb=" O THR B 251 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N PHE B 259 " --> pdb=" O ILE B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 287 removed outlier: 3.506A pdb=" N GLN B 276 " --> pdb=" O ASP B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 296 Processing helix chain 'B' and resid 299 through 309 Processing helix chain 'B' and resid 338 through 348 Processing helix chain 'B' and resid 355 through 361 removed outlier: 3.582A pdb=" N PHE B 359 " --> pdb=" O GLU B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 381 Processing helix chain 'B' and resid 382 through 388 Processing helix chain 'B' and resid 389 through 402 removed outlier: 3.676A pdb=" N LYS B 393 " --> pdb=" O ALA B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 407 Processing helix chain 'B' and resid 413 through 430 Processing helix chain 'B' and resid 439 through 452 Proline residue: B 445 - end of helix removed outlier: 3.527A pdb=" N GLY B 450 " --> pdb=" O LEU B 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 489 removed outlier: 4.414A pdb=" N GLY B 464 " --> pdb=" O LEU B 460 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N GLU B 465 " --> pdb=" O SER B 461 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N SER B 468 " --> pdb=" O GLY B 464 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASN B 479 " --> pdb=" O LYS B 475 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N GLU B 480 " --> pdb=" O SER B 476 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N LEU B 481 " --> pdb=" O ASN B 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 509 Processing helix chain 'C' and resid 13 through 21 Processing helix chain 'C' and resid 80 through 84 Processing helix chain 'C' and resid 153 through 157 Processing helix chain 'C' and resid 176 through 188 removed outlier: 3.570A pdb=" N VAL C 180 " --> pdb=" O GLY C 176 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ALA C 181 " --> pdb=" O LYS C 177 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR C 184 " --> pdb=" O VAL C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 225 Processing helix chain 'C' and resid 227 through 229 No H-bonds generated for 'chain 'C' and resid 227 through 229' Processing helix chain 'C' and resid 241 through 247 Processing helix chain 'C' and resid 247 through 261 removed outlier: 3.675A pdb=" N PHE C 259 " --> pdb=" O ILE C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 287 removed outlier: 3.517A pdb=" N GLN C 276 " --> pdb=" O ASP C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 296 Processing helix chain 'C' and resid 299 through 309 Processing helix chain 'C' and resid 338 through 348 Processing helix chain 'C' and resid 355 through 361 Processing helix chain 'C' and resid 376 through 380 removed outlier: 3.589A pdb=" N ALA C 379 " --> pdb=" O VAL C 376 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 388 Processing helix chain 'C' and resid 391 through 407 removed outlier: 3.972A pdb=" N GLU C 401 " --> pdb=" O ALA C 397 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N PHE C 405 " --> pdb=" O GLU C 401 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLN C 407 " --> pdb=" O ALA C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 431 removed outlier: 3.710A pdb=" N LYS C 431 " --> pdb=" O THR C 427 " (cutoff:3.500A) Processing helix chain 'C' and resid 439 through 452 Proline residue: C 445 - end of helix Processing helix chain 'C' and resid 459 through 461 No H-bonds generated for 'chain 'C' and resid 459 through 461' Processing helix chain 'C' and resid 462 through 478 removed outlier: 3.562A pdb=" N SER C 468 " --> pdb=" O GLY C 464 " (cutoff:3.500A) Processing helix chain 'C' and resid 479 through 489 Processing helix chain 'C' and resid 492 through 509 Processing helix chain 'D' and resid 88 through 92 removed outlier: 3.503A pdb=" N THR D 91 " --> pdb=" O GLY D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 145 Processing helix chain 'D' and resid 162 through 175 Processing helix chain 'D' and resid 190 through 204 Processing helix chain 'D' and resid 225 through 231 Processing helix chain 'D' and resid 231 through 245 Processing helix chain 'D' and resid 258 through 273 removed outlier: 4.324A pdb=" N ALA D 270 " --> pdb=" O SER D 266 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N LEU D 271 " --> pdb=" O GLU D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 277 through 281 Processing helix chain 'D' and resid 284 through 295 Processing helix chain 'D' and resid 312 through 316 removed outlier: 3.636A pdb=" N ASP D 315 " --> pdb=" O VAL D 312 " (cutoff:3.500A) Processing helix chain 'D' and resid 319 through 327 removed outlier: 3.509A pdb=" N THR D 325 " --> pdb=" O ALA D 321 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA D 327 " --> pdb=" O ALA D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 336 through 342 Processing helix chain 'D' and resid 363 through 384 removed outlier: 3.977A pdb=" N HIS D 367 " --> pdb=" O VAL D 363 " (cutoff:3.500A) Processing helix chain 'D' and resid 384 through 391 Processing helix chain 'D' and resid 397 through 415 removed outlier: 4.099A pdb=" N SER D 415 " --> pdb=" O GLN D 411 " (cutoff:3.500A) Processing helix chain 'D' and resid 420 through 426 removed outlier: 4.330A pdb=" N PHE D 424 " --> pdb=" O VAL D 420 " (cutoff:3.500A) Processing helix chain 'D' and resid 433 through 446 removed outlier: 3.602A pdb=" N ALA D 439 " --> pdb=" O LYS D 435 " (cutoff:3.500A) Processing helix chain 'D' and resid 453 through 458 Processing helix chain 'D' and resid 462 through 475 Processing helix chain 'E' and resid 138 through 145 Processing helix chain 'E' and resid 162 through 178 removed outlier: 4.417A pdb=" N LYS E 176 " --> pdb=" O ASN E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 204 Processing helix chain 'E' and resid 225 through 245 removed outlier: 3.569A pdb=" N ARG E 231 " --> pdb=" O GLY E 227 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ALA E 233 " --> pdb=" O ARG E 229 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N LEU E 234 " --> pdb=" O ALA E 230 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N THR E 235 " --> pdb=" O ARG E 231 " (cutoff:3.500A) Processing helix chain 'E' and resid 257 through 273 removed outlier: 3.663A pdb=" N PHE E 261 " --> pdb=" O ASN E 257 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA E 270 " --> pdb=" O SER E 266 " (cutoff:3.500A) Processing helix chain 'E' and resid 277 through 281 Processing helix chain 'E' and resid 284 through 296 removed outlier: 3.521A pdb=" N ILE E 296 " --> pdb=" O LEU E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 313 through 316 Processing helix chain 'E' and resid 319 through 329 removed outlier: 3.802A pdb=" N ALA E 327 " --> pdb=" O ALA E 323 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N HIS E 328 " --> pdb=" O THR E 324 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU E 329 " --> pdb=" O THR E 325 " (cutoff:3.500A) Processing helix chain 'E' and resid 336 through 342 Processing helix chain 'E' and resid 363 through 391 removed outlier: 4.136A pdb=" N HIS E 367 " --> pdb=" O VAL E 363 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ASP E 386 " --> pdb=" O LYS E 382 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N ILE E 387 " --> pdb=" O SER E 383 " (cutoff:3.500A) Processing helix chain 'E' and resid 397 through 414 Processing helix chain 'E' and resid 418 through 422 Processing helix chain 'E' and resid 433 through 447 Processing helix chain 'E' and resid 453 through 457 Processing helix chain 'E' and resid 462 through 475 Processing helix chain 'F' and resid 88 through 92 Processing helix chain 'F' and resid 138 through 145 Processing helix chain 'F' and resid 162 through 178 Processing helix chain 'F' and resid 190 through 204 Processing helix chain 'F' and resid 225 through 248 removed outlier: 4.853A pdb=" N ALA F 233 " --> pdb=" O ARG F 229 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N LEU F 234 " --> pdb=" O ALA F 230 " (cutoff:3.500A) Processing helix chain 'F' and resid 258 through 273 Processing helix chain 'F' and resid 277 through 281 Processing helix chain 'F' and resid 284 through 296 removed outlier: 3.566A pdb=" N ILE F 296 " --> pdb=" O LEU F 292 " (cutoff:3.500A) Processing helix chain 'F' and resid 312 through 316 Processing helix chain 'F' and resid 319 through 329 Processing helix chain 'F' and resid 336 through 341 Processing helix chain 'F' and resid 363 through 392 removed outlier: 4.140A pdb=" N HIS F 367 " --> pdb=" O VAL F 363 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ILE F 387 " --> pdb=" O SER F 383 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE F 390 " --> pdb=" O ASP F 386 " (cutoff:3.500A) Processing helix chain 'F' and resid 397 through 415 removed outlier: 3.592A pdb=" N SER F 415 " --> pdb=" O GLN F 411 " (cutoff:3.500A) Processing helix chain 'F' and resid 418 through 420 No H-bonds generated for 'chain 'F' and resid 418 through 420' Processing helix chain 'F' and resid 421 through 426 Processing helix chain 'F' and resid 433 through 446 Processing helix chain 'F' and resid 453 through 457 Processing helix chain 'F' and resid 462 through 475 Processing helix chain 'G' and resid 2 through 56 removed outlier: 3.931A pdb=" N LYS G 33 " --> pdb=" O THR G 29 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER G 40 " --> pdb=" O LYS G 36 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA G 47 " --> pdb=" O LYS G 43 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLU G 48 " --> pdb=" O MET G 44 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE G 51 " --> pdb=" O ALA G 47 " (cutoff:3.500A) Processing helix chain 'G' and resid 86 through 98 Processing helix chain 'G' and resid 111 through 122 removed outlier: 3.814A pdb=" N GLN G 117 " --> pdb=" O LYS G 113 " (cutoff:3.500A) Processing helix chain 'G' and resid 139 through 155 Processing helix chain 'G' and resid 156 through 159 Processing helix chain 'G' and resid 184 through 191 removed outlier: 3.600A pdb=" N GLN G 190 " --> pdb=" O LYS G 186 " (cutoff:3.500A) Processing helix chain 'G' and resid 204 through 276 removed outlier: 4.291A pdb=" N GLU G 211 " --> pdb=" O ARG G 207 " (cutoff:3.500A) Processing helix chain 'H' and resid 93 through 97 Processing helix chain 'H' and resid 100 through 115 removed outlier: 3.847A pdb=" N SER H 113 " --> pdb=" O LYS H 109 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N SER H 114 " --> pdb=" O LYS H 110 " (cutoff:3.500A) Processing helix chain 'H' and resid 119 through 136 removed outlier: 3.650A pdb=" N VAL H 136 " --> pdb=" O ASN H 132 " (cutoff:3.500A) Processing helix chain 'I' and resid 9 through 22 Processing helix chain 'I' and resid 31 through 37 Processing helix chain 'O' and resid 16 through 29 Processing helix chain 'O' and resid 33 through 49 Processing helix chain 'O' and resid 63 through 78 removed outlier: 4.014A pdb=" N HIS O 78 " --> pdb=" O ILE O 74 " (cutoff:3.500A) Processing helix chain 'O' and resid 83 through 95 Processing helix chain 'O' and resid 101 through 117 Processing helix chain 'O' and resid 130 through 144 Processing helix chain 'O' and resid 179 through 191 removed outlier: 3.736A pdb=" N LYS O 183 " --> pdb=" O SER O 179 " (cutoff:3.500A) Processing helix chain 'T' and resid 27 through 46 removed outlier: 4.076A pdb=" N TYR T 44 " --> pdb=" O ILE T 40 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU T 46 " --> pdb=" O SER T 42 " (cutoff:3.500A) Processing helix chain 'T' and resid 58 through 74 removed outlier: 3.961A pdb=" N GLN T 62 " --> pdb=" O TRP T 58 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N MET T 72 " --> pdb=" O THR T 68 " (cutoff:3.500A) Processing helix chain 'T' and resid 82 through 84 No H-bonds generated for 'chain 'T' and resid 82 through 84' Processing helix chain 'T' and resid 85 through 100 removed outlier: 4.096A pdb=" N ILE T 96 " --> pdb=" O LEU T 92 " (cutoff:3.500A) Processing helix chain 'T' and resid 101 through 105 Processing helix chain 'T' and resid 114 through 138 removed outlier: 4.171A pdb=" N ILE T 118 " --> pdb=" O HIS T 114 " (cutoff:3.500A) Processing helix chain 'T' and resid 139 through 146 removed outlier: 3.828A pdb=" N PHE T 142 " --> pdb=" O TRP T 139 " (cutoff:3.500A) Processing helix chain 'T' and resid 151 through 155 Processing helix chain 'T' and resid 156 through 167 removed outlier: 3.867A pdb=" N GLU T 162 " --> pdb=" O LEU T 158 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N SER T 165 " --> pdb=" O ILE T 161 " (cutoff:3.500A) Processing helix chain 'T' and resid 168 through 199 removed outlier: 4.043A pdb=" N LEU T 173 " --> pdb=" O ARG T 169 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N GLY T 174 " --> pdb=" O ALA T 170 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LEU T 177 " --> pdb=" O LEU T 173 " (cutoff:3.500A) Processing helix chain 'T' and resid 202 through 206 Processing helix chain 'T' and resid 209 through 247 removed outlier: 3.954A pdb=" N LEU T 213 " --> pdb=" O GLY T 209 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N PHE T 224 " --> pdb=" O MET T 220 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA T 225 " --> pdb=" O MET T 221 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ALA T 235 " --> pdb=" O GLY T 231 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA T 239 " --> pdb=" O ALA T 235 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU T 242 " --> pdb=" O THR T 238 " (cutoff:3.500A) Processing helix chain 'U' and resid 55 through 184 removed outlier: 4.965A pdb=" N ALA U 74 " --> pdb=" O ALA U 70 " (cutoff:3.500A) Proline residue: U 75 - end of helix removed outlier: 3.933A pdb=" N GLU U 118 " --> pdb=" O GLN U 114 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR U 119 " --> pdb=" O ASN U 115 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N LYS U 121 " --> pdb=" O ALA U 117 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N VAL U 122 " --> pdb=" O GLU U 118 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU U 123 " --> pdb=" O THR U 119 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS U 128 " --> pdb=" O PHE U 124 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU U 136 " --> pdb=" O GLU U 132 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLU U 139 " --> pdb=" O SER U 135 " (cutoff:3.500A) Processing helix chain 'U' and resid 187 through 206 removed outlier: 4.306A pdb=" N VAL U 193 " --> pdb=" O PHE U 189 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU U 194 " --> pdb=" O GLN U 190 " (cutoff:3.500A) Processing helix chain 'V' and resid 4 through 19 Processing helix chain 'V' and resid 26 through 48 Processing helix chain 'V' and resid 56 through 62 removed outlier: 3.809A pdb=" N SER V 60 " --> pdb=" O SER V 56 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEU V 62 " --> pdb=" O TYR V 58 " (cutoff:3.500A) Processing helix chain 'V' and resid 67 through 78 Processing helix chain 'V' and resid 90 through 127 Processing helix chain 'V' and resid 134 through 142 Processing helix chain 'V' and resid 143 through 156 Processing helix chain 'W' and resid 12 through 17 removed outlier: 4.115A pdb=" N SER W 17 " --> pdb=" O LYS W 13 " (cutoff:3.500A) Processing helix chain 'W' and resid 18 through 30 removed outlier: 3.776A pdb=" N LYS W 22 " --> pdb=" O ALA W 18 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N VAL W 28 " --> pdb=" O ILE W 24 " (cutoff:3.500A) Processing helix chain 'W' and resid 48 through 56 Processing helix chain 'W' and resid 63 through 85 removed outlier: 4.004A pdb=" N GLY W 72 " --> pdb=" O HIS W 68 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ILE W 73 " --> pdb=" O PHE W 69 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TYR W 78 " --> pdb=" O ILE W 74 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N TYR W 82 " --> pdb=" O TYR W 78 " (cutoff:3.500A) Processing helix chain 'X' and resid 2 through 14 Processing helix chain 'X' and resid 20 through 27 Processing helix chain 'X' and resid 46 through 57 removed outlier: 4.095A pdb=" N LEU X 50 " --> pdb=" O GLY X 46 " (cutoff:3.500A) Processing helix chain 'Y' and resid 13 through 35 Processing helix chain 'Z' and resid 8 through 30 Processing helix chain 'Z' and resid 30 through 48 removed outlier: 3.517A pdb=" N MET Z 34 " --> pdb=" O PHE Z 30 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU Z 38 " --> pdb=" O MET Z 34 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 28 removed outlier: 3.521A pdb=" N LEU O 167 " --> pdb=" O LEU O 178 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 31 through 37 removed outlier: 6.495A pdb=" N ARG A 42 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N VAL A 36 " --> pdb=" O ILE A 40 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N ILE A 40 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N VAL A 76 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N ALA A 65 " --> pdb=" O VAL A 76 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N GLU A 53 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N LEU A 54 " --> pdb=" O THR A 93 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 98 through 101 Processing sheet with id=AA4, first strand: chain 'A' and resid 108 through 110 removed outlier: 3.684A pdb=" N ARG A 108 " --> pdb=" O SER A 231 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N TYR A 202 " --> pdb=" O LEU A 267 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N VAL A 269 " --> pdb=" O TYR A 202 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N VAL A 204 " --> pdb=" O VAL A 269 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N ASP A 271 " --> pdb=" O VAL A 204 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N VAL A 206 " --> pdb=" O ASP A 271 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N LEU A 168 " --> pdb=" O ILE A 352 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 31 through 37 removed outlier: 6.970A pdb=" N ARG B 42 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N VAL B 36 " --> pdb=" O ILE B 40 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ILE B 40 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N GLY B 74 " --> pdb=" O LEU B 66 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N LEU B 66 " --> pdb=" O GLY B 74 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 10 through 17 current: chain 'B' and resid 90 through 92 Processing sheet with id=AA6, first strand: chain 'B' and resid 31 through 37 removed outlier: 6.970A pdb=" N ARG B 42 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N VAL B 36 " --> pdb=" O ILE B 40 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ILE B 40 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N GLY B 74 " --> pdb=" O LEU B 66 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N LEU B 66 " --> pdb=" O GLY B 74 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 62 through 68 current: chain 'F' and resid 36 through 40 removed outlier: 6.093A pdb=" N ARG F 60 " --> pdb=" O ALA F 51 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N VAL F 23 " --> pdb=" O VAL F 59 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ILE F 20 " --> pdb=" O VAL F 16 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N VAL F 16 " --> pdb=" O ILE F 20 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N ASP F 22 " --> pdb=" O THR F 14 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 10 through 17 current: chain 'B' and resid 90 through 92 Processing sheet with id=AA7, first strand: chain 'B' and resid 98 through 101 Processing sheet with id=AA8, first strand: chain 'B' and resid 109 through 110 removed outlier: 6.116A pdb=" N VAL B 110 " --> pdb=" O ALA B 235 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N THR B 237 " --> pdb=" O VAL B 110 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N TYR B 205 " --> pdb=" O VAL B 234 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N ALA B 236 " --> pdb=" O TYR B 205 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N ALA B 207 " --> pdb=" O ALA B 236 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N VAL B 204 " --> pdb=" O VAL B 269 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N ASP B 271 " --> pdb=" O VAL B 204 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N VAL B 206 " --> pdb=" O ASP B 271 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 328 through 331 removed outlier: 6.078A pdb=" N ILE B 169 " --> pdb=" O ILE B 329 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N THR B 331 " --> pdb=" O ILE B 169 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N GLY B 171 " --> pdb=" O THR B 331 " (cutoff:3.500A) removed outlier: 9.171A pdb=" N GLN B 351 " --> pdb=" O GLY B 370 " (cutoff:3.500A) removed outlier: 8.490A pdb=" N GLY B 370 " --> pdb=" O GLN B 351 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N PHE B 353 " --> pdb=" O ASN B 368 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 77 through 78 removed outlier: 6.744A pdb=" N ARG D 60 " --> pdb=" O ALA D 51 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N HIS D 53 " --> pdb=" O THR D 58 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N THR D 58 " --> pdb=" O HIS D 53 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE D 17 " --> pdb=" O ILE D 20 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N HIS D 24 " --> pdb=" O VAL D 13 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N VAL D 13 " --> pdb=" O HIS D 24 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N GLY C 63 " --> pdb=" O PHE C 78 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N PHE C 78 " --> pdb=" O GLY C 63 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N ALA C 65 " --> pdb=" O VAL C 76 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N VAL C 76 " --> pdb=" O ALA C 65 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N ILE C 40 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N VAL C 36 " --> pdb=" O ILE C 40 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N ARG C 42 " --> pdb=" O LEU C 34 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N LEU C 54 " --> pdb=" O THR C 93 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N GLU C 53 " --> pdb=" O ALA C 65 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 98 through 101 Processing sheet with id=AB3, first strand: chain 'C' and resid 109 through 111 removed outlier: 6.191A pdb=" N CYS C 203 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N VAL C 234 " --> pdb=" O CYS C 203 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N TYR C 205 " --> pdb=" O VAL C 234 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N ALA C 236 " --> pdb=" O TYR C 205 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N ALA C 207 " --> pdb=" O ALA C 236 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N TYR C 202 " --> pdb=" O HIS C 265 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N TYR C 270 " --> pdb=" O LEU C 326 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N GLU C 167 " --> pdb=" O PRO C 327 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N ILE C 329 " --> pdb=" O GLU C 167 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N ILE C 169 " --> pdb=" O ILE C 329 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N THR C 331 " --> pdb=" O ILE C 169 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N GLY C 171 " --> pdb=" O THR C 331 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N LEU C 168 " --> pdb=" O ILE C 352 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N LEU C 354 " --> pdb=" O LEU C 168 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ILE C 170 " --> pdb=" O LEU C 354 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 84 through 87 removed outlier: 4.056A pdb=" N LEU D 113 " --> pdb=" O VAL D 87 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 95 through 96 removed outlier: 5.750A pdb=" N ILE D 96 " --> pdb=" O PHE D 219 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N GLN D 221 " --> pdb=" O ILE D 96 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ALA D 216 " --> pdb=" O VAL D 183 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N THR D 185 " --> pdb=" O ALA D 216 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N VAL D 218 " --> pdb=" O THR D 185 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N VAL D 187 " --> pdb=" O VAL D 218 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N GLY D 220 " --> pdb=" O VAL D 187 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR D 305 " --> pdb=" O VAL D 251 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 133 through 134 removed outlier: 3.807A pdb=" N TYR D 147 " --> pdb=" O LEU D 134 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 331 through 335 removed outlier: 10.567A pdb=" N THR D 332 " --> pdb=" O LEU D 351 " (cutoff:3.500A) removed outlier: 9.230A pdb=" N LEU D 351 " --> pdb=" O THR D 332 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N VAL D 334 " --> pdb=" O ASP D 349 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 11 through 17 removed outlier: 6.600A pdb=" N ASP E 22 " --> pdb=" O THR E 14 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N VAL E 16 " --> pdb=" O ILE E 20 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N ILE E 20 " --> pdb=" O VAL E 16 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N THR E 58 " --> pdb=" O HIS E 53 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N HIS E 53 " --> pdb=" O THR E 58 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ARG E 60 " --> pdb=" O ALA E 51 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N LYS E 40 " --> pdb=" O LYS E 75 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N LYS E 75 " --> pdb=" O LYS E 40 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 84 through 87 removed outlier: 3.973A pdb=" N LEU E 113 " --> pdb=" O VAL E 87 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 95 through 96 removed outlier: 6.385A pdb=" N PHE E 184 " --> pdb=" O VAL E 218 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N GLY E 220 " --> pdb=" O PHE E 184 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N GLY E 186 " --> pdb=" O GLY E 220 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N VAL E 183 " --> pdb=" O PHE E 254 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N ASP E 256 " --> pdb=" O VAL E 183 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N THR E 185 " --> pdb=" O ASP E 256 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA E 331 " --> pdb=" O LYS E 152 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N GLY E 158 " --> pdb=" O LEU E 335 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 84 through 87 removed outlier: 3.858A pdb=" N LEU F 113 " --> pdb=" O VAL F 87 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 95 through 96 removed outlier: 3.710A pdb=" N PHE F 219 " --> pdb=" O ILE F 96 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N ALA F 216 " --> pdb=" O VAL F 183 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N THR F 185 " --> pdb=" O ALA F 216 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N VAL F 218 " --> pdb=" O THR F 185 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N VAL F 187 " --> pdb=" O VAL F 218 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N GLY F 220 " --> pdb=" O VAL F 187 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N PHE F 181 " --> pdb=" O LEU F 252 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N PHE F 254 " --> pdb=" O PHE F 181 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N VAL F 183 " --> pdb=" O PHE F 254 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N ASP F 256 " --> pdb=" O VAL F 183 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N THR F 185 " --> pdb=" O ASP F 256 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N VAL F 307 " --> pdb=" O LEU F 252 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N PHE F 254 " --> pdb=" O VAL F 307 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N ALA F 309 " --> pdb=" O PHE F 254 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N ASP F 256 " --> pdb=" O ALA F 309 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS F 354 " --> pdb=" O THR F 332 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 133 through 134 removed outlier: 3.632A pdb=" N TYR F 147 " --> pdb=" O LEU F 134 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 176 through 182 removed outlier: 3.897A pdb=" N ILE G 162 " --> pdb=" O ILE G 182 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N ASN G 167 " --> pdb=" O ILE G 77 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N GLU G 72 " --> pdb=" O ASP G 106 " (cutoff:3.500A) removed outlier: 8.391A pdb=" N VAL G 108 " --> pdb=" O GLU G 72 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ILE G 74 " --> pdb=" O VAL G 108 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N ILE G 110 " --> pdb=" O ILE G 74 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N ALA G 76 " --> pdb=" O ILE G 110 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ILE G 107 " --> pdb=" O ILE G 126 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N LEU G 128 " --> pdb=" O ILE G 107 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 12 through 15 removed outlier: 6.032A pdb=" N GLN H 13 " --> pdb=" O VAL H 85 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N ALA H 87 " --> pdb=" O GLN H 13 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N ALA H 15 " --> pdb=" O ALA H 87 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 37 through 42 removed outlier: 6.517A pdb=" N VAL H 56 " --> pdb=" O PRO H 33 " (cutoff:3.500A) 2292 hydrogen bonds defined for protein. 6657 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.88 Time building geometry restraints manager: 2.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.28: 5060 1.28 - 1.35: 3069 1.35 - 1.42: 1965 1.42 - 1.49: 5837 1.49 - 1.56: 4261 Bond restraints: 20192 Sorted by residual: bond pdb=" CA GLY E 11 " pdb=" C GLY E 11 " ideal model delta sigma weight residual 1.516 1.466 0.050 8.20e-03 1.49e+04 3.71e+01 bond pdb=" CA VAL E 312 " pdb=" C VAL E 312 " ideal model delta sigma weight residual 1.528 1.487 0.041 8.50e-03 1.38e+04 2.32e+01 bond pdb=" CA ILE B 40 " pdb=" C ILE B 40 " ideal model delta sigma weight residual 1.527 1.486 0.041 8.50e-03 1.38e+04 2.32e+01 bond pdb=" CA SER A 374 " pdb=" C SER A 374 " ideal model delta sigma weight residual 1.526 1.475 0.051 1.08e-02 8.57e+03 2.22e+01 bond pdb=" CA GLY H 40 " pdb=" C GLY H 40 " ideal model delta sigma weight residual 1.514 1.473 0.040 8.60e-03 1.35e+04 2.22e+01 ... (remaining 20187 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.86: 21200 2.86 - 5.72: 3199 5.72 - 8.58: 673 8.58 - 11.44: 100 11.44 - 14.29: 8 Bond angle restraints: 25180 Sorted by residual: angle pdb=" N VAL V 67 " pdb=" CA VAL V 67 " pdb=" C VAL V 67 " ideal model delta sigma weight residual 113.71 100.50 13.21 9.50e-01 1.11e+00 1.93e+02 angle pdb=" C ASN G 204 " pdb=" N VAL G 205 " pdb=" CA VAL G 205 " ideal model delta sigma weight residual 120.24 126.47 -6.23 6.30e-01 2.52e+00 9.78e+01 angle pdb=" N THR B 175 " pdb=" CA THR B 175 " pdb=" C THR B 175 " ideal model delta sigma weight residual 112.57 102.94 9.63 1.13e+00 7.83e-01 7.26e+01 angle pdb=" CA PRO W 6 " pdb=" C PRO W 6 " pdb=" N PRO W 7 " ideal model delta sigma weight residual 117.93 128.10 -10.17 1.20e+00 6.94e-01 7.18e+01 angle pdb=" CA PRO D 225 " pdb=" C PRO D 225 " pdb=" O PRO D 225 " ideal model delta sigma weight residual 120.90 115.07 5.83 7.20e-01 1.93e+00 6.56e+01 ... (remaining 25175 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.40: 5003 24.40 - 48.79: 18 48.79 - 73.19: 0 73.19 - 97.59: 1 97.59 - 121.98: 2 Dihedral angle restraints: 5024 sinusoidal: 4 harmonic: 5020 Sorted by residual: dihedral pdb=" CA ASP E 256 " pdb=" C ASP E 256 " pdb=" N ASN E 257 " pdb=" CA ASN E 257 " ideal model delta harmonic sigma weight residual -180.00 -58.02 -121.98 0 5.00e+00 4.00e-02 5.95e+02 dihedral pdb=" CA GLU B 29 " pdb=" C GLU B 29 " pdb=" N THR B 30 " pdb=" CA THR B 30 " ideal model delta harmonic sigma weight residual 180.00 80.88 99.12 0 5.00e+00 4.00e-02 3.93e+02 dihedral pdb=" CA ASN 7 40 " pdb=" C ASN 7 40 " pdb=" N PRO 7 41 " pdb=" CA PRO 7 41 " ideal model delta harmonic sigma weight residual -180.00 -137.31 -42.69 0 5.00e+00 4.00e-02 7.29e+01 ... (remaining 5021 not shown) Chirality restraints: 0 Planarity restraints: 5024 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY A 321 " 0.025 2.00e-02 2.50e+03 5.08e-02 2.58e+01 pdb=" C GLY A 321 " -0.088 2.00e-02 2.50e+03 pdb=" O GLY A 321 " 0.034 2.00e-02 2.50e+03 pdb=" N SER A 322 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR C 93 " -0.019 2.00e-02 2.50e+03 3.89e-02 1.52e+01 pdb=" C THR C 93 " 0.067 2.00e-02 2.50e+03 pdb=" O THR C 93 " -0.026 2.00e-02 2.50e+03 pdb=" N GLY C 94 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL E 206 " 0.019 2.00e-02 2.50e+03 3.85e-02 1.48e+01 pdb=" C VAL E 206 " -0.067 2.00e-02 2.50e+03 pdb=" O VAL E 206 " 0.026 2.00e-02 2.50e+03 pdb=" N ILE E 207 " 0.022 2.00e-02 2.50e+03 ... (remaining 5021 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.87: 9438 2.87 - 3.38: 17295 3.38 - 3.88: 26879 3.88 - 4.39: 27378 4.39 - 4.90: 40921 Nonbonded interactions: 121911 Sorted by model distance: nonbonded pdb=" N LEU D 252 " pdb=" O LEU D 252 " model vdw 2.361 2.496 nonbonded pdb=" N GLN B 6 " pdb=" O GLN B 6 " model vdw 2.375 2.496 nonbonded pdb=" N ARG F 114 " pdb=" O ARG F 114 " model vdw 2.378 2.496 nonbonded pdb=" N VAL V 67 " pdb=" N ILE V 68 " model vdw 2.389 2.560 nonbonded pdb=" N SER G 171 " pdb=" O SER G 171 " model vdw 2.398 2.496 ... (remaining 121906 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain '0' and resid 2 through 73) selection = (chain '1' and resid 2 through 73) selection = (chain '2' and resid 2 through 73) selection = (chain '3' and resid 2 through 73) selection = (chain '4' and resid 2 through 73) selection = (chain '5' and resid 2 through 73) selection = (chain '6' and resid 2 through 73) selection = (chain '7' and resid 2 through 73) selection = (chain '8' and resid 2 through 73) selection = (chain '9' and resid 2 through 73) } ncs_group { reference = (chain 'A' and (resid 12 through 407 or resid 410 through 509)) selection = (chain 'B' and resid 12 through 509) selection = chain 'C' } ncs_group { reference = (chain 'D' and resid 8 through 475) selection = (chain 'E' and resid 8 through 475) selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.090 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: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 22.810 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.060 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:1.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6196 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.019 0.061 20192 Z= 1.489 Angle : 2.199 14.294 25180 Z= 1.581 Chirality : 0.000 0.000 0 Planarity : 0.010 0.051 5024 Dihedral : 6.948 121.984 5024 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 0.08 Ramachandran Plot: Outliers : 1.46 % Allowed : 4.29 % Favored : 94.24 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.96 % Cis-general : 0.08 % Twisted Proline : 3.45 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.60 (0.11), residues: 4984 helix: 0.75 (0.09), residues: 2831 sheet: -1.38 (0.21), residues: 587 loop : -2.09 (0.13), residues: 1566 Details of bonding type rmsd covalent geometry : bond 0.01897 (20192) covalent geometry : angle 2.19913 (25180) hydrogen bonds : bond 0.20878 ( 2283) hydrogen bonds : angle 8.05741 ( 6657) *********************** 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 : 0.748 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.0828 time to fit residues: 14.0506 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 : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 432 optimal weight: 6.9990 chunk 197 optimal weight: 8.9990 chunk 388 optimal weight: 6.9990 chunk 455 optimal weight: 20.0000 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 40.0000 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 30.0000 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 9.9990 chunk 470 optimal weight: 7.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2614 r_free = 0.2614 target = 0.030822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2380 r_free = 0.2380 target = 0.024346 restraints weight = 299932.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2388 r_free = 0.2388 target = 0.024502 restraints weight = 271166.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2393 r_free = 0.2393 target = 0.024589 restraints weight = 246536.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2397 r_free = 0.2397 target = 0.024669 restraints weight = 230577.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.2400 r_free = 0.2400 target = 0.024720 restraints weight = 219290.610| |-----------------------------------------------------------------------------| r_work (final): 0.2388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 20192 Z= 0.191 Angle : 0.558 9.426 25180 Z= 0.349 Chirality : 0.000 0.000 0 Planarity : 0.003 0.022 5024 Dihedral : 5.011 76.612 5024 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 0.46 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.13 % Favored : 96.63 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.96 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.14 (0.12), residues: 4984 helix: 2.22 (0.10), residues: 2854 sheet: -1.11 (0.20), residues: 614 loop : -1.30 (0.15), residues: 1516 Details of bonding type rmsd covalent geometry : bond 0.00253 (20192) covalent geometry : angle 0.55766 (25180) hydrogen bonds : bond 0.04437 ( 2283) hydrogen bonds : angle 4.68512 ( 6657) *********************** 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 : 0.750 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.0867 time to fit residues: 14.5931 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 : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 217 optimal weight: 40.0000 chunk 149 optimal weight: 7.9990 chunk 38 optimal weight: 50.0000 chunk 234 optimal weight: 30.0000 chunk 169 optimal weight: 40.0000 chunk 77 optimal weight: 40.0000 chunk 454 optimal weight: 50.0000 chunk 352 optimal weight: 50.0000 chunk 275 optimal weight: 0.2980 chunk 389 optimal weight: 40.0000 chunk 56 optimal weight: 50.0000 overall best weight: 23.6594 ------------------------------------------------------------------------------- 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 = 0.2471 r_free = 0.2471 target = 0.035563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2409 r_free = 0.2409 target = 0.031356 restraints weight = 322312.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2392 r_free = 0.2392 target = 0.030172 restraints weight = 745257.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2394 r_free = 0.2394 target = 0.030033 restraints weight = 1210461.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2395 r_free = 0.2395 target = 0.029957 restraints weight = 1135863.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2395 r_free = 0.2395 target = 0.029941 restraints weight = 1125579.059| |-----------------------------------------------------------------------------| r_work (final): 0.2252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.4363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 20192 Z= 0.429 Angle : 0.904 16.484 25180 Z= 0.587 Chirality : 0.000 0.000 0 Planarity : 0.005 0.035 5024 Dihedral : 6.528 86.102 5024 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.36 % Favored : 93.40 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.96 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.01 (0.12), residues: 4984 helix: 1.28 (0.10), residues: 2780 sheet: -1.53 (0.22), residues: 475 loop : -1.64 (0.14), residues: 1729 Details of bonding type rmsd covalent geometry : bond 0.00576 (20192) covalent geometry : angle 0.90370 (25180) hydrogen bonds : bond 0.06726 ( 2283) hydrogen bonds : angle 6.38404 ( 6657) *********************** 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 : 0.856 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.0838 time to fit residues: 14.2313 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 : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 353 optimal weight: 50.0000 chunk 408 optimal weight: 10.0000 chunk 299 optimal weight: 30.0000 chunk 315 optimal weight: 50.0000 chunk 476 optimal weight: 2.9990 chunk 379 optimal weight: 50.0000 chunk 281 optimal weight: 20.0000 chunk 405 optimal weight: 8.9990 chunk 1 optimal weight: 50.0000 chunk 475 optimal weight: 0.0980 chunk 453 optimal weight: 30.0000 overall best weight: 8.4192 ------------------------------------------------------------------------------- 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 = 0.2563 r_free = 0.2563 target = 0.044200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2532 r_free = 0.2532 target = 0.039014 restraints weight = 288415.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2507 r_free = 0.2507 target = 0.038140 restraints weight = 616809.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2506 r_free = 0.2506 target = 0.037714 restraints weight = 912345.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2504 r_free = 0.2504 target = 0.037558 restraints weight = 1010334.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2504 r_free = 0.2504 target = 0.037489 restraints weight = 1001305.203| |-----------------------------------------------------------------------------| r_work (final): 0.2289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.4329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 20192 Z= 0.186 Angle : 0.492 10.362 25180 Z= 0.314 Chirality : 0.000 0.000 0 Planarity : 0.002 0.017 5024 Dihedral : 4.951 89.610 5024 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 0.96 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.18 % Favored : 94.60 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.96 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.04 (0.12), residues: 4984 helix: 2.19 (0.10), residues: 2849 sheet: -1.47 (0.22), residues: 513 loop : -1.34 (0.15), residues: 1622 Details of bonding type rmsd covalent geometry : bond 0.00247 (20192) covalent geometry : angle 0.49178 (25180) hydrogen bonds : bond 0.04061 ( 2283) hydrogen bonds : angle 4.73847 ( 6657) *********************** 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 : 0.727 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.0722 time to fit residues: 12.2894 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 : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 267 optimal weight: 40.0000 chunk 167 optimal weight: 1.9990 chunk 58 optimal weight: 120.0000 chunk 442 optimal weight: 10.0000 chunk 310 optimal weight: 50.0000 chunk 251 optimal weight: 0.0870 chunk 286 optimal weight: 20.0000 chunk 109 optimal weight: 30.0000 chunk 441 optimal weight: 50.0000 chunk 111 optimal weight: 50.0000 chunk 49 optimal weight: 50.0000 overall best weight: 12.4172 ------------------------------------------------------------------------------- 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 = 0.2533 r_free = 0.2533 target = 0.043369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2493 r_free = 0.2493 target = 0.038560 restraints weight = 285600.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2475 r_free = 0.2475 target = 0.037864 restraints weight = 584638.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2477 r_free = 0.2477 target = 0.037076 restraints weight = 870728.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2472 r_free = 0.2472 target = 0.036857 restraints weight = 1115706.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2472 r_free = 0.2472 target = 0.036825 restraints weight = 1189879.154| |-----------------------------------------------------------------------------| r_work (final): 0.2286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.4989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20192 Z= 0.233 Angle : 0.544 10.895 25180 Z= 0.347 Chirality : 0.000 0.000 0 Planarity : 0.003 0.017 5024 Dihedral : 4.927 88.563 5024 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 1.50 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.58 % Favored : 93.20 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.96 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.23 (0.13), residues: 4984 helix: 2.36 (0.10), residues: 2853 sheet: -1.46 (0.23), residues: 472 loop : -1.29 (0.16), residues: 1659 Details of bonding type rmsd covalent geometry : bond 0.00311 (20192) covalent geometry : angle 0.54375 (25180) hydrogen bonds : bond 0.04326 ( 2283) hydrogen bonds : angle 4.79007 ( 6657) *********************** 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 : 0.647 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.0749 time to fit residues: 12.5283 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 : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 240 optimal weight: 50.0000 chunk 446 optimal weight: 50.0000 chunk 223 optimal weight: 30.0000 chunk 338 optimal weight: 30.0000 chunk 9 optimal weight: 9.9990 chunk 444 optimal weight: 120.0000 chunk 414 optimal weight: 8.9990 chunk 357 optimal weight: 50.0000 chunk 375 optimal weight: 20.0000 chunk 62 optimal weight: 100.0000 chunk 373 optimal weight: 9.9990 overall best weight: 15.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2567 r_free = 0.2567 target = 0.030358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2332 r_free = 0.2332 target = 0.022859 restraints weight = 221567.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2342 r_free = 0.2342 target = 0.023070 restraints weight = 189471.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2350 r_free = 0.2350 target = 0.023242 restraints weight = 164652.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.2350 r_free = 0.2350 target = 0.023251 restraints weight = 148262.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 15)----------------| | r_work = 0.2361 r_free = 0.2361 target = 0.023469 restraints weight = 147657.296| |-----------------------------------------------------------------------------| r_work (final): 0.2354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.5743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 20192 Z= 0.284 Angle : 0.608 12.788 25180 Z= 0.392 Chirality : 0.000 0.000 0 Planarity : 0.003 0.018 5024 Dihedral : 5.305 83.308 5024 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.48 % Favored : 92.28 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.96 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.72 (0.12), residues: 4984 helix: 1.96 (0.10), residues: 2835 sheet: -1.65 (0.24), residues: 450 loop : -1.52 (0.15), residues: 1699 Details of bonding type rmsd covalent geometry : bond 0.00378 (20192) covalent geometry : angle 0.60798 (25180) hydrogen bonds : bond 0.04929 ( 2283) hydrogen bonds : angle 5.34960 ( 6657) *********************** 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 : 0.691 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.0794 time to fit residues: 13.3237 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 : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 154 optimal weight: 40.0000 chunk 259 optimal weight: 50.0000 chunk 235 optimal weight: 20.0000 chunk 313 optimal weight: 0.0030 chunk 490 optimal weight: 50.0000 chunk 43 optimal weight: 50.0000 chunk 212 optimal weight: 50.0000 chunk 111 optimal weight: 40.0000 chunk 134 optimal weight: 50.0000 chunk 31 optimal weight: 80.0000 chunk 430 optimal weight: 50.0000 overall best weight: 30.0006 ------------------------------------------------------------------------------- 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 = 0.2377 r_free = 0.2377 target = 0.030661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2318 r_free = 0.2318 target = 0.026748 restraints weight = 337800.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2295 r_free = 0.2295 target = 0.025957 restraints weight = 695689.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2299 r_free = 0.2299 target = 0.025801 restraints weight = 1050252.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2298 r_free = 0.2298 target = 0.025721 restraints weight = 1089493.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2298 r_free = 0.2298 target = 0.025716 restraints weight = 1099351.226| |-----------------------------------------------------------------------------| r_work (final): 0.2208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.6756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 20192 Z= 0.483 Angle : 0.919 16.947 25180 Z= 0.602 Chirality : 0.000 0.000 0 Planarity : 0.006 0.031 5024 Dihedral : 6.794 70.643 5024 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.34 % Allowed : 11.16 % Favored : 88.50 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.32 (0.11), residues: 4984 helix: 0.24 (0.09), residues: 2762 sheet: -2.20 (0.24), residues: 384 loop : -2.28 (0.14), residues: 1838 Details of bonding type rmsd covalent geometry : bond 0.00643 (20192) covalent geometry : angle 0.91930 (25180) hydrogen bonds : bond 0.07134 ( 2283) hydrogen bonds : angle 7.32571 ( 6657) *********************** 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 : 0.798 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.0830 time to fit residues: 14.0268 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 : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 63 optimal weight: 90.0000 chunk 409 optimal weight: 4.9990 chunk 355 optimal weight: 50.0000 chunk 56 optimal weight: 50.0000 chunk 171 optimal weight: 7.9990 chunk 290 optimal weight: 20.0000 chunk 97 optimal weight: 20.0000 chunk 288 optimal weight: 20.0000 chunk 319 optimal weight: 40.0000 chunk 376 optimal weight: 50.0000 chunk 420 optimal weight: 50.0000 overall best weight: 14.5996 ------------------------------------------------------------------------------- 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 = 0.2545 r_free = 0.2545 target = 0.040755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2523 r_free = 0.2523 target = 0.037050 restraints weight = 322671.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2503 r_free = 0.2503 target = 0.036495 restraints weight = 599420.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2499 r_free = 0.2499 target = 0.036298 restraints weight = 862114.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2498 r_free = 0.2498 target = 0.036237 restraints weight = 913881.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2498 r_free = 0.2498 target = 0.036237 restraints weight = 906241.678| |-----------------------------------------------------------------------------| r_work (final): 0.2249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.6642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 20192 Z= 0.253 Angle : 0.572 13.316 25180 Z= 0.368 Chirality : 0.000 0.000 0 Planarity : 0.003 0.019 5024 Dihedral : 5.435 70.734 5024 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 2.16 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.35 % Favored : 91.41 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.96 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.37 (0.12), residues: 4984 helix: 1.10 (0.10), residues: 2827 sheet: -2.17 (0.23), residues: 446 loop : -1.98 (0.15), residues: 1711 Details of bonding type rmsd covalent geometry : bond 0.00338 (20192) covalent geometry : angle 0.57195 (25180) hydrogen bonds : bond 0.04675 ( 2283) hydrogen bonds : angle 5.71248 ( 6657) *********************** 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 : 0.787 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.0815 time to fit residues: 13.9028 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 : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 131 optimal weight: 0.8980 chunk 489 optimal weight: 40.0000 chunk 146 optimal weight: 0.7980 chunk 84 optimal weight: 40.0000 chunk 365 optimal weight: 50.0000 chunk 316 optimal weight: 50.0000 chunk 449 optimal weight: 50.0000 chunk 42 optimal weight: 90.0000 chunk 457 optimal weight: 50.0000 chunk 144 optimal weight: 30.0000 chunk 11 optimal weight: 50.0000 overall best weight: 22.3392 ------------------------------------------------------------------------------- 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 = 0.2378 r_free = 0.2378 target = 0.030269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2330 r_free = 0.2330 target = 0.026666 restraints weight = 338249.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2310 r_free = 0.2310 target = 0.026155 restraints weight = 599649.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2310 r_free = 0.2310 target = 0.026147 restraints weight = 865897.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2306 r_free = 0.2306 target = 0.025852 restraints weight = 856839.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2303 r_free = 0.2303 target = 0.025739 restraints weight = 952176.466| |-----------------------------------------------------------------------------| r_work (final): 0.2208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.7079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 20192 Z= 0.368 Angle : 0.730 14.996 25180 Z= 0.478 Chirality : 0.000 0.000 0 Planarity : 0.004 0.026 5024 Dihedral : 5.995 70.379 5024 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.24 % Allowed : 11.74 % Favored : 88.02 % 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 : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.92 (0.12), residues: 4984 helix: 0.71 (0.10), residues: 2788 sheet: -2.31 (0.24), residues: 407 loop : -2.32 (0.14), residues: 1789 Details of bonding type rmsd covalent geometry : bond 0.00489 (20192) covalent geometry : angle 0.72961 (25180) hydrogen bonds : bond 0.05813 ( 2283) hydrogen bonds : angle 6.50221 ( 6657) *********************** 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 : 0.850 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.0842 time to fit residues: 14.2552 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 : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 288 optimal weight: 20.0000 chunk 126 optimal weight: 30.0000 chunk 403 optimal weight: 60.0000 chunk 233 optimal weight: 50.0000 chunk 2 optimal weight: 50.0000 chunk 140 optimal weight: 40.0000 chunk 316 optimal weight: 40.0000 chunk 8 optimal weight: 0.0050 chunk 228 optimal weight: 0.0050 chunk 291 optimal weight: 0.0370 chunk 391 optimal weight: 10.0000 overall best weight: 6.0094 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2545 r_free = 0.2545 target = 0.038867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2495 r_free = 0.2495 target = 0.035616 restraints weight = 313449.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2483 r_free = 0.2483 target = 0.034538 restraints weight = 684756.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2482 r_free = 0.2482 target = 0.034337 restraints weight = 1178533.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2482 r_free = 0.2482 target = 0.034239 restraints weight = 1115316.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2482 r_free = 0.2482 target = 0.034188 restraints weight = 1163365.074| |-----------------------------------------------------------------------------| r_work (final): 0.2271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.6874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 20192 Z= 0.133 Angle : 0.413 10.271 25180 Z= 0.262 Chirality : 0.000 0.000 0 Planarity : 0.002 0.018 5024 Dihedral : 4.700 70.515 5024 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 1.04 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.42 % Favored : 93.34 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.96 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.57 (0.13), residues: 4984 helix: 2.06 (0.10), residues: 2827 sheet: -2.27 (0.24), residues: 431 loop : -1.84 (0.15), residues: 1726 Details of bonding type rmsd covalent geometry : bond 0.00177 (20192) covalent geometry : angle 0.41303 (25180) hydrogen bonds : bond 0.03634 ( 2283) hydrogen bonds : angle 4.80709 ( 6657) ********************** 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 : 0.726 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.0836 time to fit residues: 14.1590 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 : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 340 optimal weight: 9.9990 chunk 107 optimal weight: 50.0000 chunk 3 optimal weight: 50.0000 chunk 91 optimal weight: 20.0000 chunk 112 optimal weight: 50.0000 chunk 369 optimal weight: 50.0000 chunk 30 optimal weight: 90.0000 chunk 356 optimal weight: 30.0000 chunk 252 optimal weight: 50.0000 chunk 460 optimal weight: 50.0000 chunk 77 optimal weight: 30.0000 overall best weight: 27.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2374 r_free = 0.2374 target = 0.026997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2331 r_free = 0.2331 target = 0.023843 restraints weight = 353561.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2314 r_free = 0.2314 target = 0.023514 restraints weight = 630504.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2312 r_free = 0.2312 target = 0.023416 restraints weight = 908493.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2311 r_free = 0.2311 target = 0.023412 restraints weight = 869348.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2311 r_free = 0.2311 target = 0.023408 restraints weight = 866050.689| |-----------------------------------------------------------------------------| r_work (final): 0.2212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.7464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 20192 Z= 0.456 Angle : 0.821 16.754 25180 Z= 0.547 Chirality : 0.000 0.000 0 Planarity : 0.005 0.028 5024 Dihedral : 6.161 72.489 5024 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.28 % Allowed : 12.00 % Favored : 87.72 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.99 (0.12), residues: 4984 helix: 0.66 (0.10), residues: 2795 sheet: -2.52 (0.24), residues: 395 loop : -2.33 (0.15), residues: 1794 Details of bonding type rmsd covalent geometry : bond 0.00605 (20192) covalent geometry : angle 0.82079 (25180) hydrogen bonds : bond 0.06545 ( 2283) hydrogen bonds : angle 6.83568 ( 6657) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2266.69 seconds wall clock time: 39 minutes 32.20 seconds (2372.20 seconds total)