Starting phenix.real_space_refine on Mon Mar 18 08:12:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tkq_25978/03_2024/7tkq_25978.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tkq_25978/03_2024/7tkq_25978.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tkq_25978/03_2024/7tkq_25978.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tkq_25978/03_2024/7tkq_25978.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tkq_25978/03_2024/7tkq_25978.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tkq_25978/03_2024/7tkq_25978.pdb" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.115 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 Symmetric amino acids flipped None Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 20228 Number of models: 1 Model: "" Number of chains: 27 Chain: "0" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 300 Classifications: {'peptide': 75} Incomplete info: {'backbone_only': 65} Link IDs: {'PTRANS': 2, 'TRANS': 72} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 246 Unresolved non-hydrogen angles: 363 Unresolved non-hydrogen dihedrals: 146 Unresolved non-hydrogen chiralities: 94 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1, 'PHE:plan': 6, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 75 Chain: "1" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 300 Classifications: {'peptide': 75} Incomplete info: {'backbone_only': 65} Link IDs: {'PTRANS': 2, 'TRANS': 72} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 246 Unresolved non-hydrogen angles: 363 Unresolved non-hydrogen dihedrals: 146 Unresolved non-hydrogen chiralities: 94 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1, 'PHE:plan': 6, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 75 Chain: "2" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 300 Classifications: {'peptide': 75} Incomplete info: {'backbone_only': 65} Link IDs: {'PTRANS': 2, 'TRANS': 72} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 246 Unresolved non-hydrogen angles: 363 Unresolved non-hydrogen dihedrals: 146 Unresolved non-hydrogen chiralities: 94 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1, 'PHE:plan': 6, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 75 Chain: "3" Number of atoms: 296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 296 Classifications: {'peptide': 74} Incomplete info: {'backbone_only': 64} Link IDs: {'PTRANS': 2, 'TRANS': 71} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 242 Unresolved non-hydrogen angles: 358 Unresolved non-hydrogen dihedrals: 143 Unresolved non-hydrogen chiralities: 93 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1, 'PHE:plan': 6, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 75 Chain: "4" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 300 Classifications: {'peptide': 75} Incomplete info: {'backbone_only': 65} Link IDs: {'PTRANS': 2, 'TRANS': 72} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 246 Unresolved non-hydrogen angles: 363 Unresolved non-hydrogen dihedrals: 146 Unresolved non-hydrogen chiralities: 94 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1, 'PHE:plan': 6, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 75 Chain: "5" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 300 Classifications: {'peptide': 75} Incomplete info: {'backbone_only': 65} Link IDs: {'PTRANS': 2, 'TRANS': 72} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 246 Unresolved non-hydrogen angles: 363 Unresolved non-hydrogen dihedrals: 146 Unresolved non-hydrogen chiralities: 94 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1, 'PHE:plan': 6, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 75 Chain: "6" Number of atoms: 296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 296 Classifications: {'peptide': 74} Incomplete info: {'backbone_only': 64} Link IDs: {'PTRANS': 2, 'TRANS': 71} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 242 Unresolved non-hydrogen angles: 358 Unresolved non-hydrogen dihedrals: 143 Unresolved non-hydrogen chiralities: 93 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1, 'PHE:plan': 6, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 75 Chain: "7" Number of atoms: 292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 292 Classifications: {'peptide': 73} Incomplete info: {'backbone_only': 64} Link IDs: {'PTRANS': 2, 'TRANS': 70} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 238 Unresolved non-hydrogen angles: 352 Unresolved non-hydrogen dihedrals: 139 Unresolved non-hydrogen chiralities: 93 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1, 'PHE:plan': 5, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 68 Chain: "8" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 300 Classifications: {'peptide': 75} Incomplete info: {'backbone_only': 65} Link IDs: {'PTRANS': 2, 'TRANS': 72} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 246 Unresolved non-hydrogen angles: 363 Unresolved non-hydrogen dihedrals: 146 Unresolved non-hydrogen chiralities: 94 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1, 'PHE:plan': 6, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 75 Chain: "9" Number of atoms: 296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 296 Classifications: {'peptide': 74} Incomplete info: {'backbone_only': 64} Link IDs: {'PTRANS': 2, 'TRANS': 71} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 242 Unresolved non-hydrogen angles: 358 Unresolved non-hydrogen dihedrals: 143 Unresolved non-hydrogen chiralities: 93 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1, 'PHE:plan': 6, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 75 Chain: "A" Number of atoms: 1996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 499, 1996 Classifications: {'peptide': 499} Incomplete info: {'backbone_only': 453} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 18, 'TRANS': 478} Chain breaks: 1 Unresolved chain link angles: 19 Unresolved non-hydrogen bonds: 1854 Unresolved non-hydrogen angles: 2698 Unresolved non-hydrogen dihedrals: 1123 Unresolved non-hydrogen chiralities: 606 Planarities with less than four sites: {'GLN:plan1': 25, 'HIS:plan': 6, 'TYR:plan': 14, 'ASN:plan1': 17, 'TRP:plan': 2, 'ASP:plan': 21, 'PHE:plan': 13, 'GLU:plan': 37, 'ARG:plan': 29} Unresolved non-hydrogen planarities: 804 Chain: "B" Number of atoms: 2028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 2028 Classifications: {'peptide': 507} Incomplete info: {'backbone_only': 460} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 485} Unresolved chain link angles: 20 Unresolved non-hydrogen bonds: 1883 Unresolved non-hydrogen angles: 2740 Unresolved non-hydrogen dihedrals: 1142 Unresolved non-hydrogen chiralities: 615 Planarities with less than four sites: {'GLN:plan1': 26, 'HIS:plan': 6, 'TYR:plan': 14, 'ASN:plan1': 17, 'TRP:plan': 2, 'ASP:plan': 21, 'PHE:plan': 14, 'GLU:plan': 37, 'ARG:plan': 29} Unresolved non-hydrogen planarities: 815 Chain: "C" Number of atoms: 1984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 1984 Classifications: {'peptide': 496} Incomplete info: {'backbone_only': 450} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 18, 'TRANS': 474} Chain breaks: 1 Unresolved chain link angles: 19 Unresolved non-hydrogen bonds: 1844 Unresolved non-hydrogen angles: 2683 Unresolved non-hydrogen dihedrals: 1118 Unresolved non-hydrogen chiralities: 602 Planarities with less than four sites: {'GLN:plan1': 25, 'HIS:plan': 6, 'TYR:plan': 14, 'ASN:plan1': 17, 'TRP:plan': 2, 'ASP:plan': 21, 'PHE:plan': 13, 'GLU:plan': 36, 'ARG:plan': 29} Unresolved non-hydrogen planarities: 800 Chain: "D" Number of atoms: 1872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 1872 Classifications: {'peptide': 468} Incomplete info: {'backbone_only': 422} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 445} Unresolved chain link angles: 22 Unresolved non-hydrogen bonds: 1721 Unresolved non-hydrogen angles: 2511 Unresolved non-hydrogen dihedrals: 1032 Unresolved non-hydrogen chiralities: 577 Planarities with less than four sites: {'GLN:plan1': 18, 'ARG:plan': 22, 'TYR:plan': 10, 'ASN:plan1': 10, 'HIS:plan': 7, 'PHE:plan': 17, 'GLU:plan': 37, 'ASP:plan': 25} Unresolved non-hydrogen planarities: 711 Chain: "E" Number of atoms: 1876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 1876 Classifications: {'peptide': 469} Incomplete info: {'backbone_only': 423} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 444} Unresolved chain link angles: 23 Unresolved non-hydrogen bonds: 1724 Unresolved non-hydrogen angles: 2516 Unresolved non-hydrogen dihedrals: 1033 Unresolved non-hydrogen chiralities: 579 Planarities with less than four sites: {'GLN:plan1': 18, 'ARG:plan': 22, 'TYR:plan': 10, 'ASN:plan1': 10, 'HIS:plan': 7, 'PHE:plan': 17, 'GLU:plan': 37, 'ASP:plan': 25} Unresolved non-hydrogen planarities: 711 Chain: "F" Number of atoms: 1880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 1880 Classifications: {'peptide': 470} Incomplete info: {'backbone_only': 424} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 446} Unresolved chain link angles: 23 Unresolved non-hydrogen bonds: 1726 Unresolved non-hydrogen angles: 2519 Unresolved non-hydrogen dihedrals: 1034 Unresolved non-hydrogen chiralities: 580 Planarities with less than four sites: {'GLN:plan1': 18, 'ARG:plan': 22, 'TYR:plan': 10, 'ASN:plan1': 10, 'HIS:plan': 7, 'PHE:plan': 17, 'GLU:plan': 37, 'ASP:plan': 25} Unresolved non-hydrogen planarities: 711 Chain: "G" Number of atoms: 1060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 1060 Classifications: {'peptide': 265} Incomplete info: {'backbone_only': 255} Link IDs: {'PTRANS': 9, 'TRANS': 255} Chain breaks: 1 Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 1024 Unresolved non-hydrogen angles: 1472 Unresolved non-hydrogen dihedrals: 628 Unresolved non-hydrogen chiralities: 328 Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 3, 'TYR:plan': 7, 'ASN:plan1': 18, 'ASP:plan': 14, 'PHE:plan': 8, 'GLU:plan': 16, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 413 Chain: "H" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 480 Classifications: {'peptide': 120} Incomplete info: {'backbone_only': 114} Link IDs: {'PTRANS': 6, 'TRANS': 113} Chain breaks: 4 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 439 Unresolved non-hydrogen angles: 643 Unresolved non-hydrogen dihedrals: 258 Unresolved non-hydrogen chiralities: 151 Planarities with less than four sites: {'GLN:plan1': 7, 'ASP:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 7, 'HIS:plan': 2, 'PHE:plan': 5, 'GLU:plan': 13, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 177 Chain: "I" Number of atoms: 193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 193 Classifications: {'peptide': 48} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 47} Link IDs: {'PTRANS': 2, 'TRANS': 45} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 188 Unresolved non-hydrogen angles: 278 Unresolved non-hydrogen dihedrals: 114 Unresolved non-hydrogen chiralities: 62 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 4, 'ASN:plan1': 3, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 89 Chain: "O" Number of atoms: 748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 748 Classifications: {'peptide': 187} Incomplete info: {'backbone_only': 174} Link IDs: {'PTRANS': 7, 'TRANS': 179} Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 691 Unresolved non-hydrogen angles: 1001 Unresolved non-hydrogen dihedrals: 414 Unresolved non-hydrogen chiralities: 235 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 3, 'TYR:plan': 3, 'ASN:plan1': 12, 'ASP:plan': 10, 'PHE:plan': 5, 'GLU:plan': 11, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 249 Chain: "T" Number of atoms: 897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 897 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 207} Link IDs: {'PTRANS': 7, 'TRANS': 216} Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 925 Unresolved non-hydrogen angles: 1359 Unresolved non-hydrogen dihedrals: 607 Unresolved non-hydrogen chiralities: 306 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 3, 'TYR:plan': 10, 'ASN:plan1': 11, 'TRP:plan': 5, 'ASP:plan': 2, 'PHE:plan': 18, 'GLU:plan': 3, 'ARG:plan': 3, 'HIS%COO:plan': 1} Unresolved non-hydrogen planarities: 371 Chain: "U" Number of atoms: 620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 620 Classifications: {'peptide': 155} Incomplete info: {'backbone_only': 152} Link IDs: {'PTRANS': 2, 'TRANS': 152} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 631 Unresolved non-hydrogen angles: 908 Unresolved non-hydrogen dihedrals: 388 Unresolved non-hydrogen chiralities: 198 Planarities with less than four sites: {'GLN:plan1': 11, 'HIS:plan': 2, 'TYR:plan': 3, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 8, 'PHE:plan': 6, 'GLU:plan': 16, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 283 Chain: "V" Number of atoms: 685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 685 Classifications: {'peptide': 171} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 166} Link IDs: {'PTRANS': 5, 'TRANS': 165} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 705 Unresolved non-hydrogen angles: 1009 Unresolved non-hydrogen dihedrals: 446 Unresolved non-hydrogen chiralities: 214 Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 2, 'TYR:plan': 4, 'ASN:plan1': 7, 'TRP:plan': 2, 'ASP:plan': 13, 'PHE:plan': 5, 'GLU:plan': 13, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 302 Chain: "W" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 340 Classifications: {'peptide': 85} Incomplete info: {'backbone_only': 79} Link IDs: {'PTRANS': 7, 'TRANS': 77} Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 348 Unresolved non-hydrogen angles: 503 Unresolved non-hydrogen dihedrals: 241 Unresolved non-hydrogen chiralities: 97 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 2, 'TYR:plan': 6, 'ASN:plan1': 5, 'TRP:plan': 1, 'HIS:plan': 3, 'PHE:plan': 5, 'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 162 Chain: "X" Number of atoms: 248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 248 Classifications: {'peptide': 62} Incomplete info: {'backbone_only': 60} Link IDs: {'PTRANS': 7, 'TRANS': 54} Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 257 Unresolved non-hydrogen angles: 375 Unresolved non-hydrogen dihedrals: 161 Unresolved non-hydrogen chiralities: 77 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 3, 'GLU:plan': 7, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 117 Chain: "Y" Number of atoms: 148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 148 Classifications: {'peptide': 37} Incomplete info: {'backbone_only': 35} Link IDs: {'PTRANS': 3, 'TRANS': 33} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 155 Unresolved non-hydrogen angles: 225 Unresolved non-hydrogen dihedrals: 110 Unresolved non-hydrogen chiralities: 44 Planarities with less than four sites: {'TYR:plan': 3, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 68 Chain: "Z" Number of atoms: 193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 193 Classifications: {'peptide': 48} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 46} Link IDs: {'PTRANS': 3, 'TRANS': 44} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 231 Unresolved non-hydrogen angles: 330 Unresolved non-hydrogen dihedrals: 158 Unresolved non-hydrogen chiralities: 67 Planarities with less than four sites: {'GLN:plan1': 3, 'PHE:plan': 7, 'ASN:plan1': 1, 'ARG:plan': 2, 'TYR:plan': 3} Unresolved non-hydrogen planarities: 99 Time building chain proxies: 12.36, per 1000 atoms: 0.61 Number of scatterers: 20228 At special positions: 0 Unit cell: (126.665, 145.53, 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.69 Conformation dependent library (CDL) restraints added in 6.1 seconds 9968 Ramachandran restraints generated. 4984 Oldfield, 0 Emsley, 4984 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 0 Finding SS restraints... Secondary structure from input PDB file: 190 helices and 26 sheets defined 59.0% alpha, 9.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.74 Creating SS restraints... Processing helix chain '0' and resid 1 through 17 removed outlier: 3.778A pdb=" N GLY 0 13 " --> pdb=" O TYR 0 9 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ILE 0 17 " --> pdb=" O GLY 0 13 " (cutoff:3.500A) Processing helix chain '0' and resid 18 through 40 removed outlier: 4.393A 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: 3.576A pdb=" N THR 0 61 " --> pdb=" O LEU 0 57 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLY 0 62 " --> pdb=" O SER 0 58 " (cutoff:3.500A) Processing helix chain '1' and resid 2 through 17 removed outlier: 3.509A pdb=" N GLY 1 13 " --> pdb=" O TYR 1 9 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ILE 1 17 " --> pdb=" O GLY 1 13 " (cutoff:3.500A) Processing helix chain '1' and resid 18 through 40 removed outlier: 4.343A pdb=" N ALA 1 22 " --> pdb=" O GLY 1 18 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA 1 27 " --> pdb=" O GLY 1 23 " (cutoff:3.500A) Processing helix chain '1' and resid 43 through 74 Proline residue: 1 49 - end of helix Processing helix chain '2' and resid 2 through 17 removed outlier: 3.912A pdb=" N ILE 2 17 " --> pdb=" O GLY 2 13 " (cutoff:3.500A) Processing helix chain '2' and resid 18 through 40 removed outlier: 4.186A pdb=" N ALA 2 22 " --> pdb=" O GLY 2 18 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ALA 2 27 " --> pdb=" O GLY 2 23 " (cutoff:3.500A) Processing helix chain '2' and resid 43 through 75 Proline residue: 2 49 - end of helix removed outlier: 3.873A pdb=" N THR 2 61 " --> pdb=" O LEU 2 57 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N GLY 2 62 " --> pdb=" O SER 2 58 " (cutoff:3.500A) Processing helix chain '3' and resid 3 through 17 removed outlier: 3.790A pdb=" N ILE 3 17 " --> pdb=" O GLY 3 13 " (cutoff:3.500A) Processing helix chain '3' and resid 18 through 40 removed outlier: 4.322A pdb=" N ALA 3 22 " --> pdb=" O GLY 3 18 " (cutoff:3.500A) removed outlier: 3.635A 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: 3.550A pdb=" N THR 3 61 " --> pdb=" O LEU 3 57 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLY 3 62 " --> pdb=" O SER 3 58 " (cutoff:3.500A) Processing helix chain '4' and resid 2 through 16 Processing helix chain '4' and resid 18 through 40 removed outlier: 4.160A pdb=" N ALA 4 22 " --> pdb=" O GLY 4 18 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA 4 27 " --> pdb=" O GLY 4 23 " (cutoff:3.500A) Processing helix chain '4' and resid 43 through 75 Proline residue: 4 49 - end of helix removed outlier: 3.805A pdb=" N THR 4 61 " --> pdb=" O LEU 4 57 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLY 4 62 " --> pdb=" O SER 4 58 " (cutoff:3.500A) Processing helix chain '5' and resid 2 through 17 removed outlier: 3.755A pdb=" N ILE 5 17 " --> pdb=" O GLY 5 13 " (cutoff:3.500A) Processing helix chain '5' and resid 18 through 40 removed outlier: 4.186A pdb=" N ALA 5 22 " --> pdb=" O GLY 5 18 " (cutoff:3.500A) Processing helix chain '5' and resid 43 through 75 Proline residue: 5 49 - end of helix removed outlier: 3.526A pdb=" N GLY 5 62 " --> pdb=" O SER 5 58 " (cutoff:3.500A) Processing helix chain '6' and resid 3 through 17 removed outlier: 3.695A pdb=" N ILE 6 17 " --> pdb=" O GLY 6 13 " (cutoff:3.500A) Processing helix chain '6' and resid 18 through 40 removed outlier: 4.201A pdb=" N ALA 6 22 " --> pdb=" O GLY 6 18 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA 6 27 " --> pdb=" O GLY 6 23 " (cutoff:3.500A) Processing helix chain '6' and resid 43 through 75 Proline residue: 6 49 - end of helix removed outlier: 3.666A pdb=" N THR 6 61 " --> pdb=" O LEU 6 57 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLY 6 62 " --> pdb=" O SER 6 58 " (cutoff:3.500A) Processing helix chain '7' and resid 2 through 16 Processing helix chain '7' and resid 18 through 40 removed outlier: 4.286A pdb=" N ALA 7 22 " --> pdb=" O GLY 7 18 " (cutoff:3.500A) Processing helix chain '7' and resid 43 through 73 Proline residue: 7 49 - end of helix removed outlier: 3.556A pdb=" N THR 7 61 " --> pdb=" O LEU 7 57 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLY 7 62 " --> pdb=" O SER 7 58 " (cutoff:3.500A) Processing helix chain '8' and resid 2 through 18 removed outlier: 3.779A pdb=" N ILE 8 17 " --> pdb=" O GLY 8 13 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N GLY 8 18 " --> pdb=" O ILE 8 14 " (cutoff:3.500A) Processing helix chain '8' and resid 19 through 40 removed outlier: 3.502A pdb=" N ALA 8 27 " --> pdb=" O GLY 8 23 " (cutoff:3.500A) Processing helix chain '8' and resid 43 through 75 Proline residue: 8 49 - end of helix removed outlier: 3.524A pdb=" N THR 8 61 " --> pdb=" O LEU 8 57 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLY 8 62 " --> pdb=" O SER 8 58 " (cutoff:3.500A) Processing helix chain '9' and resid 3 through 16 removed outlier: 3.539A pdb=" N THR 9 16 " --> pdb=" O ALA 9 12 " (cutoff:3.500A) Processing helix chain '9' and resid 18 through 40 removed outlier: 4.230A pdb=" N ALA 9 22 " --> pdb=" O GLY 9 18 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ALA 9 27 " --> pdb=" O GLY 9 23 " (cutoff:3.500A) Processing helix chain '9' and resid 43 through 75 Proline residue: 9 49 - end of helix removed outlier: 3.654A pdb=" N THR 9 61 " --> pdb=" O LEU 9 57 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLY 9 62 " --> pdb=" O SER 9 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 20 Processing helix chain 'A' and resid 102 through 106 removed outlier: 3.700A pdb=" N LEU A 105 " --> pdb=" O GLY A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 188 removed outlier: 3.815A pdb=" N VAL A 180 " --> pdb=" O GLY A 176 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ALA A 181 " --> pdb=" O LYS A 177 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N THR A 184 " --> pdb=" O VAL A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 225 Processing helix chain 'A' and resid 227 through 229 No H-bonds generated for 'chain 'A' and resid 227 through 229' Processing helix chain 'A' and resid 241 through 261 Proline residue: A 249 - end of helix removed outlier: 4.061A pdb=" N PHE A 259 " --> pdb=" O ILE A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 287 Processing helix chain 'A' and resid 292 through 296 Processing helix chain 'A' and resid 299 through 309 Processing helix chain 'A' and resid 315 through 319 Processing helix chain 'A' and resid 332 through 335 Processing helix chain 'A' and resid 338 through 348 Processing helix chain 'A' and resid 355 through 361 Processing helix chain 'A' and resid 376 through 380 removed outlier: 3.530A pdb=" N ALA A 379 " --> pdb=" O VAL A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 388 Processing helix chain 'A' and resid 391 through 407 removed outlier: 4.030A pdb=" N GLU A 401 " --> pdb=" O ALA A 397 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N GLN A 407 " --> pdb=" O ALA A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 431 removed outlier: 3.558A pdb=" N LYS A 431 " --> pdb=" O THR A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 452 Proline residue: A 445 - end of helix Processing helix chain 'A' and resid 459 through 461 No H-bonds generated for 'chain 'A' and resid 459 through 461' Processing helix chain 'A' and resid 462 through 489 removed outlier: 7.718A pdb=" N GLU A 480 " --> pdb=" O SER A 476 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N LEU A 481 " --> pdb=" O ASN A 477 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N LEU A 482 " --> pdb=" O HIS A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 509 removed outlier: 3.551A pdb=" N THR A 509 " --> pdb=" O SER A 505 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 9 Processing helix chain 'B' and resid 10 through 19 Processing helix chain 'B' and resid 152 through 159 Processing helix chain 'B' and resid 176 through 188 removed outlier: 3.696A pdb=" N VAL B 180 " --> pdb=" O GLY B 176 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ALA B 181 " --> pdb=" O LYS B 177 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N THR B 184 " --> pdb=" O VAL B 180 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE B 185 " --> pdb=" O ALA B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 194 removed outlier: 4.049A pdb=" N GLY B 194 " --> pdb=" O ARG B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 199 Processing helix chain 'B' and resid 211 through 225 Processing helix chain 'B' and resid 241 through 263 Proline residue: B 249 - end of helix removed outlier: 4.034A pdb=" N PHE B 259 " --> pdb=" O ILE B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 286 removed outlier: 3.943A pdb=" N GLN B 276 " --> pdb=" O ASP B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 296 removed outlier: 3.546A pdb=" N TYR B 296 " --> pdb=" O ARG B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 309 Processing helix chain 'B' and resid 315 through 319 Processing helix chain 'B' and resid 338 through 348 Processing helix chain 'B' and resid 355 through 362 Processing helix chain 'B' and resid 382 through 389 Processing helix chain 'B' and resid 391 through 408 removed outlier: 3.632A pdb=" N GLN B 407 " --> pdb=" O ALA B 403 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N PHE B 408 " --> pdb=" O ALA B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 431 removed outlier: 3.537A pdb=" N ARG B 425 " --> pdb=" O VAL B 421 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LYS B 431 " --> pdb=" O THR B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 442 Processing helix chain 'B' and resid 443 through 452 Processing helix chain 'B' and resid 453 through 458 removed outlier: 3.996A pdb=" N GLY B 457 " --> pdb=" O GLY B 453 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ILE B 458 " --> pdb=" O HIS B 454 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 453 through 458' Processing helix chain 'B' and resid 459 through 461 No H-bonds generated for 'chain 'B' and resid 459 through 461' Processing helix chain 'B' and resid 462 through 477 Processing helix chain 'B' and resid 478 through 489 Processing helix chain 'B' and resid 492 through 508 removed outlier: 4.047A pdb=" N ALA B 508 " --> pdb=" O GLU B 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 22 Processing helix chain 'C' and resid 80 through 84 Processing helix chain 'C' and resid 152 through 158 Processing helix chain 'C' and resid 176 through 194 removed outlier: 3.771A pdb=" N VAL C 180 " --> pdb=" O GLY C 176 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N THR C 184 " --> pdb=" O VAL C 180 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ILE C 185 " --> pdb=" O ALA C 181 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ARG C 190 " --> pdb=" O LEU C 186 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N TRP C 191 " --> pdb=" O ASN C 187 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLY C 194 " --> pdb=" O ARG C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 225 Processing helix chain 'C' and resid 241 through 262 Proline residue: C 249 - end of helix removed outlier: 3.626A pdb=" N TRP C 258 " --> pdb=" O SER C 254 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N PHE C 259 " --> pdb=" O ILE C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 287 Processing helix chain 'C' and resid 292 through 296 Processing helix chain 'C' and resid 299 through 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 Processing helix chain 'C' and resid 382 through 402 removed outlier: 4.662A pdb=" N SER C 391 " --> pdb=" O GLN C 387 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N LEU C 392 " --> pdb=" O VAL C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 430 Processing helix chain 'C' and resid 439 through 452 Proline residue: C 445 - end of helix Processing helix chain 'C' and resid 453 through 458 removed outlier: 4.139A pdb=" N GLY C 457 " --> pdb=" O GLY C 453 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ILE C 458 " --> pdb=" O HIS C 454 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 453 through 458' Processing helix chain 'C' and resid 460 through 489 removed outlier: 4.446A pdb=" N GLY C 464 " --> pdb=" O LEU C 460 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N GLU C 465 " --> pdb=" O SER C 461 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASN C 479 " --> pdb=" O LYS C 475 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N GLU C 480 " --> pdb=" O SER C 476 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N LEU C 481 " --> pdb=" O ASN C 477 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU C 482 " --> pdb=" O HIS C 478 " (cutoff:3.500A) Processing helix chain 'C' and resid 492 through 509 Processing helix chain 'D' and resid 138 through 145 Processing helix chain 'D' and resid 162 through 178 Processing helix chain 'D' and resid 190 through 204 removed outlier: 3.560A pdb=" N ASP D 196 " --> pdb=" O ARG D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 225 through 248 removed outlier: 4.614A pdb=" N ALA D 233 " --> pdb=" O ARG D 229 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N LEU D 234 " --> pdb=" O ALA D 230 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 273 Processing helix chain 'D' and resid 284 through 293 Processing helix chain 'D' and resid 312 through 316 Processing helix chain 'D' and resid 319 through 329 Processing helix chain 'D' and resid 336 through 341 Processing helix chain 'D' and resid 359 through 392 removed outlier: 5.502A pdb=" N GLN D 365 " --> pdb=" O ALA D 361 " (cutoff:3.500A) removed outlier: 8.975A pdb=" N GLU D 366 " --> pdb=" O VAL D 362 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N HIS D 367 " --> pdb=" O VAL D 363 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ILE D 387 " --> pdb=" O SER D 383 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ILE D 390 " --> pdb=" O ASP D 386 " (cutoff:3.500A) Processing helix chain 'D' and resid 393 through 396 Processing helix chain 'D' and resid 397 through 415 removed outlier: 4.106A pdb=" N SER D 415 " --> pdb=" O GLN D 411 " (cutoff:3.500A) Processing helix chain 'D' and resid 421 through 426 Processing helix chain 'D' and resid 433 through 446 Processing helix chain 'D' and resid 462 through 475 removed outlier: 3.944A pdb=" N ALA D 468 " --> pdb=" O GLU D 464 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 145 Processing helix chain 'E' and resid 162 through 179 removed outlier: 4.442A pdb=" N LYS E 176 " --> pdb=" O ASN E 172 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N GLY E 179 " --> pdb=" O ALA E 175 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 204 Processing helix chain 'E' and resid 225 through 245 removed outlier: 3.807A pdb=" N ARG E 231 " --> pdb=" O GLY E 227 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ALA E 233 " --> pdb=" O ARG E 229 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N LEU E 234 " --> pdb=" O ALA E 230 " (cutoff:3.500A) Processing helix chain 'E' and resid 257 through 273 removed outlier: 3.776A pdb=" N PHE E 261 " --> pdb=" O ASN E 257 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ALA E 270 " --> pdb=" O SER E 266 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N LEU E 271 " --> pdb=" O GLU E 267 " (cutoff:3.500A) Processing helix chain 'E' and resid 284 through 296 Processing helix chain 'E' and resid 313 through 316 Processing helix chain 'E' and resid 319 through 328 removed outlier: 3.944A pdb=" N ALA E 327 " --> pdb=" O ALA E 323 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N HIS E 328 " --> pdb=" O THR E 324 " (cutoff:3.500A) Processing helix chain 'E' and resid 336 through 342 Processing helix chain 'E' and resid 359 through 364 Processing helix chain 'E' and resid 364 through 384 Processing helix chain 'E' and resid 384 through 391 Processing helix chain 'E' and resid 397 through 415 removed outlier: 3.802A pdb=" N SER E 415 " --> pdb=" O GLN E 411 " (cutoff:3.500A) Processing helix chain 'E' and resid 421 through 426 Processing helix chain 'E' and resid 433 through 446 Processing helix chain 'E' and resid 453 through 458 removed outlier: 3.588A pdb=" N PHE E 457 " --> pdb=" O PRO E 453 " (cutoff:3.500A) Processing helix chain 'E' and resid 462 through 475 Processing helix chain 'F' and resid 138 through 145 Processing helix chain 'F' and resid 162 through 178 removed outlier: 4.729A pdb=" N LYS F 176 " --> pdb=" O ASN F 172 " (cutoff:3.500A) Processing helix chain 'F' and resid 190 through 204 Processing helix chain 'F' and resid 225 through 245 removed outlier: 4.494A pdb=" N ALA F 233 " --> pdb=" O ARG F 229 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N LEU F 234 " --> pdb=" O ALA F 230 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR F 235 " --> pdb=" O ARG F 231 " (cutoff:3.500A) Processing helix chain 'F' and resid 258 through 273 removed outlier: 3.564A pdb=" N ALA F 270 " --> pdb=" O SER F 266 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU F 271 " --> pdb=" O GLU F 267 " (cutoff:3.500A) Processing helix chain 'F' and resid 277 through 281 Processing helix chain 'F' and resid 284 through 296 Processing helix chain 'F' and resid 313 through 316 Processing helix chain 'F' and resid 319 through 329 Processing helix chain 'F' and resid 336 through 343 Processing helix chain 'F' and resid 363 through 391 removed outlier: 4.256A pdb=" N HIS F 367 " --> pdb=" O VAL F 363 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ASP F 386 " --> pdb=" O LYS F 382 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ILE F 387 " --> pdb=" O SER F 383 " (cutoff:3.500A) Processing helix chain 'F' and resid 397 through 414 Processing helix chain 'F' and resid 418 through 422 Processing helix chain 'F' and resid 433 through 447 removed outlier: 3.509A pdb=" N VAL F 444 " --> pdb=" O SER F 440 " (cutoff:3.500A) 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 55 removed outlier: 3.996A pdb=" N LYS G 33 " --> pdb=" O THR G 29 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER G 40 " --> pdb=" O LYS G 36 " (cutoff:3.500A) removed outlier: 3.516A 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: 3.528A pdb=" N LYS G 115 " --> pdb=" O GLY G 111 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLN G 117 " --> pdb=" O LYS G 113 " (cutoff:3.500A) Processing helix chain 'G' and resid 139 through 155 Processing helix chain 'G' and resid 156 through 159 Processing helix chain 'G' and resid 184 through 191 Processing helix chain 'G' and resid 192 through 195 Processing helix chain 'G' and resid 204 through 276 removed outlier: 4.037A pdb=" N GLU G 211 " --> pdb=" O ARG G 207 " (cutoff:3.500A) Processing helix chain 'H' and resid 93 through 97 Processing helix chain 'H' and resid 100 through 115 removed outlier: 4.125A pdb=" N SER H 113 " --> pdb=" O LYS H 109 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N SER H 114 " --> pdb=" O LYS H 110 " (cutoff:3.500A) Processing helix chain 'H' and resid 119 through 136 Processing helix chain 'I' and resid 9 through 22 Processing helix chain 'I' and resid 31 through 37 Processing helix chain 'O' and resid 16 through 29 removed outlier: 3.961A pdb=" N ALA O 20 " --> pdb=" O GLU O 16 " (cutoff:3.500A) Processing helix chain 'O' and resid 33 through 49 Processing helix chain 'O' and resid 64 through 78 removed outlier: 3.882A pdb=" N HIS O 78 " --> pdb=" O ILE O 74 " (cutoff:3.500A) Processing helix chain 'O' and resid 83 through 95 removed outlier: 3.583A pdb=" N LYS O 90 " --> pdb=" O VAL O 86 " (cutoff:3.500A) Processing helix chain 'O' and resid 101 through 117 Processing helix chain 'O' and resid 130 through 144 Processing helix chain 'O' and resid 180 through 191 Processing helix chain 'T' and resid 27 through 43 Processing helix chain 'T' and resid 58 through 74 removed outlier: 4.106A pdb=" N GLN T 62 " --> pdb=" O TRP T 58 " (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 99 removed outlier: 3.879A pdb=" N ILE T 96 " --> pdb=" O LEU T 92 " (cutoff:3.500A) Processing helix chain 'T' and resid 114 through 137 removed outlier: 3.925A pdb=" N ILE T 118 " --> pdb=" O HIS T 114 " (cutoff:3.500A) Processing helix chain 'T' and resid 139 through 146 removed outlier: 4.008A 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: 3.550A pdb=" N GLU T 162 " --> pdb=" O LEU T 158 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N SER T 165 " --> pdb=" O ILE T 161 " (cutoff:3.500A) Processing helix chain 'T' and resid 168 through 199 removed outlier: 4.004A pdb=" N LEU T 173 " --> pdb=" O ARG T 169 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N GLY T 174 " --> pdb=" O ALA T 170 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LEU T 177 " --> pdb=" O LEU T 173 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASN T 197 " --> pdb=" O GLY T 193 " (cutoff:3.500A) Processing helix chain 'T' and resid 202 through 207 removed outlier: 3.576A pdb=" N LEU T 206 " --> pdb=" O ASN T 202 " (cutoff:3.500A) Processing helix chain 'T' and resid 210 through 247 removed outlier: 3.509A pdb=" N ALA T 225 " --> pdb=" O MET T 221 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA T 239 " --> pdb=" O ALA T 235 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU T 242 " --> pdb=" O THR T 238 " (cutoff:3.500A) Processing helix chain 'U' and resid 54 through 184 removed outlier: 3.903A pdb=" N LEU U 58 " --> pdb=" O ASP U 54 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N ALA U 74 " --> pdb=" O ALA U 70 " (cutoff:3.500A) Proline residue: U 75 - end of helix removed outlier: 3.504A pdb=" N LEU U 113 " --> pdb=" O SER U 109 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLU U 118 " --> pdb=" O GLN U 114 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N LYS U 121 " --> pdb=" O ALA U 117 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N VAL U 122 " --> pdb=" O GLU U 118 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU U 123 " --> pdb=" O THR U 119 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS U 128 " --> pdb=" O PHE U 124 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU U 136 " --> pdb=" O GLU U 132 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLU U 139 " --> pdb=" O SER U 135 " (cutoff:3.500A) Processing helix chain 'U' and resid 187 through 206 removed outlier: 3.952A pdb=" N VAL U 193 " --> pdb=" O PHE U 189 " (cutoff:3.500A) Processing helix chain 'V' and resid 4 through 19 Processing helix chain 'V' and resid 26 through 48 removed outlier: 3.637A pdb=" N LEU V 43 " --> pdb=" O ALA V 39 " (cutoff:3.500A) Processing helix chain 'V' and resid 57 through 62 removed outlier: 3.926A 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 removed outlier: 3.729A pdb=" N LEU V 138 " --> pdb=" O THR V 134 " (cutoff:3.500A) Processing helix chain 'V' and resid 143 through 156 Processing helix chain 'W' and resid 18 through 30 removed outlier: 4.138A pdb=" N LYS W 22 " --> pdb=" O ALA W 18 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N VAL W 28 " --> pdb=" O ILE W 24 " (cutoff:3.500A) Processing helix chain 'W' and resid 48 through 56 Processing helix chain 'W' and resid 63 through 82 removed outlier: 3.689A pdb=" N ILE W 73 " --> pdb=" O PHE W 69 " (cutoff:3.500A) removed outlier: 3.694A 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: 4.232A 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 32 through 48 removed outlier: 3.541A pdb=" N LEU Z 38 " --> pdb=" O MET Z 34 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 37 removed outlier: 6.802A pdb=" N ARG A 42 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N VAL A 36 " --> pdb=" O ILE A 40 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ILE A 40 " --> pdb=" O VAL A 36 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 40 through 45 current: chain 'A' and resid 62 through 68 removed outlier: 5.462A pdb=" N ALA A 65 " --> pdb=" O VAL A 76 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N VAL A 76 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASN A 67 " --> pdb=" O GLY A 74 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 73 through 77 current: chain 'B' and resid 40 through 45 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 40 through 45 current: chain 'B' and resid 62 through 68 removed outlier: 5.340A pdb=" N ALA B 65 " --> pdb=" O VAL B 76 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N VAL B 76 " --> pdb=" O ALA B 65 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 72 through 77 current: chain 'E' and resid 20 through 25 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 20 through 25 current: chain 'E' and resid 46 through 53 removed outlier: 6.513A pdb=" N ARG E 60 " --> pdb=" O ALA E 51 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N HIS E 53 " --> pdb=" O THR E 58 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N THR E 58 " --> pdb=" O HIS E 53 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 98 through 101 Processing sheet with id=AA3, first strand: chain 'A' and resid 109 through 110 removed outlier: 6.013A pdb=" N VAL A 110 " --> pdb=" O ALA A 235 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N CYS A 203 " --> pdb=" O ILE A 232 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N VAL A 234 " --> pdb=" O CYS A 203 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N TYR A 205 " --> pdb=" O VAL A 234 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N ALA A 236 " --> pdb=" O TYR A 205 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N ALA A 207 " --> pdb=" O ALA A 236 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ILE A 169 " --> pdb=" O ILE A 329 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N THR A 331 " --> pdb=" O ILE A 169 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N GLY A 171 " --> pdb=" O THR A 331 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 351 through 352 Processing sheet with id=AA5, first strand: chain 'B' and resid 98 through 101 Processing sheet with id=AA6, first strand: chain 'B' and resid 108 through 110 removed outlier: 6.109A pdb=" N ARG B 108 " --> pdb=" O ILE B 233 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N ALA B 235 " --> pdb=" O ARG B 108 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N VAL B 110 " --> pdb=" O ALA B 235 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N THR B 237 " --> pdb=" O VAL B 110 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N LEU B 168 " --> pdb=" O ILE B 352 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 147 through 148 removed outlier: 4.177A pdb=" N ILE B 161 " --> pdb=" O VAL B 148 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 16 through 17 removed outlier: 3.959A pdb=" N LEU C 66 " --> pdb=" O GLY C 74 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N GLY C 74 " --> pdb=" O LEU C 66 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ILE C 40 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N VAL C 36 " --> pdb=" O ILE C 40 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ARG C 42 " --> pdb=" O LEU C 34 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N LEU C 54 " --> pdb=" O THR C 93 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N GLU C 53 " --> pdb=" O ALA C 65 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA C 65 " --> pdb=" O GLU C 53 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 98 through 101 Processing sheet with id=AB1, first strand: chain 'C' and resid 108 through 111 removed outlier: 6.054A pdb=" N TYR C 205 " --> pdb=" O VAL C 234 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N ALA C 236 " --> pdb=" O TYR C 205 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N ALA C 207 " --> pdb=" O ALA C 236 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 169 through 172 removed outlier: 6.041A pdb=" N ILE C 169 " --> pdb=" O ILE C 329 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N THR C 331 " --> pdb=" O ILE C 169 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N GLY C 171 " --> pdb=" O THR C 331 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 351 through 353 removed outlier: 9.800A pdb=" N GLN C 351 " --> pdb=" O GLY C 370 " (cutoff:3.500A) removed outlier: 8.720A pdb=" N GLY C 370 " --> pdb=" O GLN C 351 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N PHE C 353 " --> pdb=" O ASN C 368 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 10 through 13 removed outlier: 7.424A pdb=" N THR D 58 " --> pdb=" O HIS D 53 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N HIS D 53 " --> pdb=" O THR D 58 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N ARG D 60 " --> pdb=" O ALA D 51 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N LYS D 40 " --> pdb=" O LYS D 75 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N LYS D 75 " --> pdb=" O LYS D 40 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 84 through 87 removed outlier: 3.739A pdb=" N LEU D 113 " --> pdb=" O VAL D 87 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 95 through 96 removed outlier: 3.803A pdb=" N PHE D 219 " --> pdb=" O ILE D 96 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N ALA D 216 " --> pdb=" O VAL D 183 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N THR D 185 " --> pdb=" O ALA D 216 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N VAL D 218 " --> pdb=" O THR D 185 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N VAL D 187 " --> pdb=" O VAL D 218 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N GLY D 220 " --> pdb=" O VAL D 187 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N VAL D 183 " --> pdb=" O PHE D 254 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N ASP D 256 " --> pdb=" O VAL D 183 " (cutoff:3.500A) removed outlier: 8.344A pdb=" N THR D 185 " --> pdb=" O ASP D 256 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N LEU D 253 " --> pdb=" O VAL D 307 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N ALA D 309 " --> pdb=" O LEU D 253 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N ILE D 255 " --> pdb=" O ALA D 309 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLN D 308 " --> pdb=" O ILE D 153 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA D 331 " --> pdb=" O LYS D 152 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 132 through 133 removed outlier: 4.686A pdb=" N GLU D 132 " --> pdb=" O ARG D 149 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 84 through 87 removed outlier: 3.858A pdb=" N LEU E 113 " --> pdb=" O VAL E 87 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 95 through 96 removed outlier: 5.736A pdb=" N ILE E 96 " --> pdb=" O PHE E 219 " (cutoff:3.500A) removed outlier: 8.148A pdb=" N GLN E 221 " --> pdb=" O ILE E 96 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N SER E 182 " --> pdb=" O ALA E 216 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N VAL E 218 " --> pdb=" O SER E 182 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N PHE E 184 " --> pdb=" O VAL E 218 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N GLY E 220 " --> pdb=" O PHE E 184 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N GLY E 186 " --> pdb=" O GLY E 220 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N LYS E 152 " --> pdb=" O ALA E 331 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N THR E 333 " --> pdb=" O LYS E 152 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLY E 154 " --> pdb=" O THR E 333 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N LEU E 335 " --> pdb=" O GLY E 154 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N PHE E 156 " --> pdb=" O LEU E 335 " (cutoff:3.500A) removed outlier: 11.227A pdb=" N THR E 332 " --> pdb=" O LEU E 351 " (cutoff:3.500A) removed outlier: 9.536A pdb=" N LEU E 351 " --> pdb=" O THR E 332 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N VAL E 334 " --> pdb=" O ASP E 349 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 11 through 17 removed outlier: 3.540A pdb=" N LYS F 12 " --> pdb=" O HIS F 24 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ASP F 22 " --> pdb=" O THR F 14 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N VAL F 16 " --> pdb=" O ILE F 20 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N ILE F 20 " --> pdb=" O VAL F 16 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N THR F 58 " --> pdb=" O HIS F 53 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N HIS F 53 " --> pdb=" O THR F 58 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ARG F 60 " --> pdb=" O ALA F 51 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 84 through 87 removed outlier: 3.534A pdb=" N LYS F 115 " --> pdb=" O VAL F 85 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU F 113 " --> pdb=" O VAL F 87 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 216 through 221 removed outlier: 3.833A pdb=" N VAL F 183 " --> pdb=" O LEU F 252 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N LYS F 152 " --> pdb=" O ALA F 331 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N THR F 333 " --> pdb=" O LYS F 152 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N GLY F 154 " --> pdb=" O THR F 333 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N LEU F 335 " --> pdb=" O GLY F 154 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N PHE F 156 " --> pdb=" O LEU F 335 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 73 through 77 removed outlier: 6.413A pdb=" N ILE G 74 " --> pdb=" O VAL G 108 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N ILE G 110 " --> pdb=" O ILE G 74 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ALA G 76 " --> pdb=" O ILE G 110 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ILE G 107 " --> pdb=" O ILE G 126 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LEU G 128 " --> pdb=" O ILE G 107 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 162 through 171 removed outlier: 4.255A pdb=" N ILE G 162 " --> pdb=" O ILE G 182 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N SER G 174 " --> pdb=" O VAL G 170 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 13 through 15 Processing sheet with id=AC7, first strand: chain 'H' and resid 37 through 42 removed outlier: 6.403A pdb=" N VAL H 56 " --> pdb=" O PRO H 33 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'O' and resid 156 through 159 removed outlier: 3.536A pdb=" N VAL O 158 " --> pdb=" O VAL O 123 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU O 167 " --> pdb=" O LEU O 178 " (cutoff:3.500A) 2265 hydrogen bonds defined for protein. 6609 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: 7.65 Time building geometry restraints manager: 9.44 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: 998 1.35 - 1.41: 4022 1.41 - 1.48: 5116 1.48 - 1.54: 4996 Bond restraints: 20192 Sorted by residual: bond pdb=" CA GLY F 11 " pdb=" C GLY F 11 " ideal model delta sigma weight residual 1.516 1.476 0.040 8.20e-03 1.49e+04 2.43e+01 bond pdb=" CA LYS D 112 " pdb=" C LYS D 112 " ideal model delta sigma weight residual 1.524 1.490 0.034 7.00e-03 2.04e+04 2.36e+01 bond pdb=" N VAL F 312 " pdb=" CA VAL F 312 " ideal model delta sigma weight residual 1.458 1.421 0.037 7.70e-03 1.69e+04 2.29e+01 bond pdb=" CA SER E 84 " pdb=" C SER E 84 " ideal model delta sigma weight residual 1.523 1.464 0.059 1.23e-02 6.61e+03 2.28e+01 bond pdb=" CA ALA C 157 " pdb=" C ALA C 157 " ideal model delta sigma weight residual 1.523 1.484 0.040 8.40e-03 1.42e+04 2.22e+01 ... (remaining 20187 not shown) Histogram of bond angle deviations from ideal: 95.58 - 103.99: 451 103.99 - 112.40: 3793 112.40 - 120.82: 9950 120.82 - 129.23: 10970 129.23 - 137.64: 16 Bond angle restraints: 25180 Sorted by residual: angle pdb=" CA PRO W 6 " pdb=" C PRO W 6 " pdb=" N PRO W 7 " ideal model delta sigma weight residual 117.93 129.92 -11.99 1.20e+00 6.94e-01 9.98e+01 angle pdb=" N VAL V 172 " pdb=" CA VAL V 172 " pdb=" C VAL V 172 " ideal model delta sigma weight residual 113.71 104.62 9.09 9.50e-01 1.11e+00 9.15e+01 angle pdb=" N VAL C 99 " pdb=" CA VAL C 99 " pdb=" C VAL C 99 " ideal model delta sigma weight residual 109.19 101.41 7.78 8.20e-01 1.49e+00 9.00e+01 angle pdb=" N VAL T 146 " pdb=" CA VAL T 146 " pdb=" C VAL T 146 " ideal model delta sigma weight residual 107.60 97.46 10.14 1.07e+00 8.73e-01 8.97e+01 angle pdb=" N ILE O 33 " pdb=" CA ILE O 33 " pdb=" C ILE O 33 " ideal model delta sigma weight residual 111.81 103.78 8.03 8.60e-01 1.35e+00 8.71e+01 ... (remaining 25175 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.58: 5001 23.58 - 47.15: 21 47.15 - 70.73: 0 70.73 - 94.31: 1 94.31 - 117.88: 1 Dihedral angle restraints: 5024 sinusoidal: 4 harmonic: 5020 Sorted by residual: dihedral pdb=" CA ASP F 256 " pdb=" C ASP F 256 " pdb=" N ASN F 257 " pdb=" CA ASN F 257 " ideal model delta harmonic sigma weight residual -180.00 -62.12 -117.88 0 5.00e+00 4.00e-02 5.56e+02 dihedral pdb=" CA ASN 6 40 " pdb=" C ASN 6 40 " pdb=" N PRO 6 41 " pdb=" CA PRO 6 41 " ideal model delta harmonic sigma weight residual 180.00 -133.96 -46.04 0 5.00e+00 4.00e-02 8.48e+01 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 -135.30 -44.70 0 5.00e+00 4.00e-02 7.99e+01 ... (remaining 5021 not shown) Chirality restraints: 0 Planarity restraints: 5024 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU X 8 " -0.024 2.00e-02 2.50e+03 4.89e-02 2.39e+01 pdb=" C LEU X 8 " 0.084 2.00e-02 2.50e+03 pdb=" O LEU X 8 " -0.033 2.00e-02 2.50e+03 pdb=" N ARG X 9 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY B 176 " -0.023 2.00e-02 2.50e+03 4.55e-02 2.07e+01 pdb=" C GLY B 176 " 0.079 2.00e-02 2.50e+03 pdb=" O GLY B 176 " -0.030 2.00e-02 2.50e+03 pdb=" N LYS B 177 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER B 322 " 0.020 2.00e-02 2.50e+03 3.91e-02 1.53e+01 pdb=" C SER B 322 " -0.068 2.00e-02 2.50e+03 pdb=" O SER B 322 " 0.026 2.00e-02 2.50e+03 pdb=" N LEU B 323 " 0.022 2.00e-02 2.50e+03 ... (remaining 5021 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.88: 9663 2.88 - 3.38: 17490 3.38 - 3.89: 26691 3.89 - 4.39: 27761 4.39 - 4.90: 40471 Nonbonded interactions: 122076 Sorted by model distance: nonbonded pdb=" N GLN V 49 " pdb=" O GLN V 49 " model vdw 2.371 2.496 nonbonded pdb=" N THR B 30 " pdb=" O THR B 30 " model vdw 2.375 2.496 nonbonded pdb=" N ARG D 114 " pdb=" O ARG D 114 " model vdw 2.388 2.496 nonbonded pdb=" N SER B 129 " pdb=" O SER B 129 " model vdw 2.389 2.496 nonbonded pdb=" N THR D 305 " pdb=" O THR D 305 " model vdw 2.391 2.496 ... (remaining 122071 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain '0' and resid 2 through 73) selection = (chain '1' and resid 2 through 73) selection = (chain '2' and resid 2 through 73) selection = (chain '3' and resid 2 through 73) selection = (chain '4' and resid 2 through 73) selection = (chain '5' and resid 2 through 73) selection = (chain '6' and resid 2 through 73) selection = (chain '7' and resid 2 through 73) selection = (chain '8' and resid 2 through 73) selection = (chain '9' and resid 2 through 73) } ncs_group { reference = (chain 'A' and resid 12 through 509) selection = (chain 'B' and (resid 12 through 407 or resid 410 through 509)) selection = chain 'C' } ncs_group { reference = chain 'D' selection = (chain 'E' and resid 8 through 475) selection = (chain 'F' and resid 8 through 475) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.930 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: 4.540 Check model and map are aligned: 0.320 Set scattering table: 0.190 Process input model: 60.770 Find NCS groups from input model: 1.840 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6213 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.019 0.059 20192 Z= 1.450 Angle : 2.211 15.941 25180 Z= 1.594 Chirality : 0.000 0.000 0 Planarity : 0.010 0.049 5024 Dihedral : 6.724 117.882 5024 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 0.08 Ramachandran Plot: Outliers : 1.50 % Allowed : 3.95 % Favored : 94.54 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.46 % Cis-general : 0.10 % Twisted Proline : 4.43 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.11), residues: 4984 helix: 0.87 (0.09), residues: 2769 sheet: -1.58 (0.20), residues: 560 loop : -1.87 (0.13), residues: 1655 *********************** 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 fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 2.112 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.1668 time to fit residues: 29.1538 Evaluate side-chains 82 residues out of total 4114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 2.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 415 optimal weight: 20.0000 chunk 372 optimal weight: 50.0000 chunk 206 optimal weight: 3.9990 chunk 127 optimal weight: 10.0000 chunk 251 optimal weight: 8.9990 chunk 199 optimal weight: 10.0000 chunk 385 optimal weight: 9.9990 chunk 149 optimal weight: 10.0000 chunk 234 optimal weight: 5.9990 chunk 287 optimal weight: 10.0000 chunk 446 optimal weight: 50.0000 overall best weight: 7.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6274 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20192 Z= 0.199 Angle : 0.541 8.123 25180 Z= 0.346 Chirality : 0.000 0.000 0 Planarity : 0.003 0.028 5024 Dihedral : 5.025 79.977 5024 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 1.66 Ramachandran Plot: Outliers : 0.32 % Allowed : 2.89 % Favored : 96.79 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.96 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.12), residues: 4984 helix: 2.29 (0.10), residues: 2826 sheet: -1.06 (0.21), residues: 570 loop : -1.14 (0.15), residues: 1588 *********************** 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 fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 2.534 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.1785 time to fit residues: 31.3731 Evaluate side-chains 82 residues out of total 4114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 2.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 248 optimal weight: 50.0000 chunk 138 optimal weight: 20.0000 chunk 371 optimal weight: 20.0000 chunk 304 optimal weight: 30.0000 chunk 123 optimal weight: 40.0000 chunk 447 optimal weight: 5.9990 chunk 483 optimal weight: 40.0000 chunk 398 optimal weight: 50.0000 chunk 443 optimal weight: 120.0000 chunk 152 optimal weight: 10.0000 chunk 359 optimal weight: 50.0000 overall best weight: 17.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6591 moved from start: 0.3604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 20192 Z= 0.343 Angle : 0.747 12.597 25180 Z= 0.484 Chirality : 0.000 0.000 0 Planarity : 0.004 0.024 5024 Dihedral : 5.814 61.975 5024 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.32 % Favored : 94.38 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.96 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.12), residues: 4984 helix: 2.17 (0.10), residues: 2801 sheet: -1.13 (0.23), residues: 481 loop : -1.02 (0.15), residues: 1702 *********************** 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 fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 2.550 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.1627 time to fit residues: 28.6108 Evaluate side-chains 82 residues out of total 4114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 2.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 442 optimal weight: 100.0000 chunk 336 optimal weight: 8.9990 chunk 232 optimal weight: 20.0000 chunk 49 optimal weight: 90.0000 chunk 213 optimal weight: 0.4980 chunk 300 optimal weight: 30.0000 chunk 449 optimal weight: 90.0000 chunk 475 optimal weight: 1.9990 chunk 234 optimal weight: 30.0000 chunk 425 optimal weight: 50.0000 chunk 128 optimal weight: 40.0000 overall best weight: 12.2992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6550 moved from start: 0.4059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 20192 Z= 0.229 Angle : 0.523 12.241 25180 Z= 0.339 Chirality : 0.000 0.000 0 Planarity : 0.003 0.023 5024 Dihedral : 4.823 38.335 5024 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.82 % Favored : 94.90 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.96 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.13), residues: 4984 helix: 2.64 (0.10), residues: 2796 sheet: -1.18 (0.23), residues: 499 loop : -0.88 (0.16), residues: 1689 *********************** 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 fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 2.577 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.1780 time to fit residues: 31.3415 Evaluate side-chains 82 residues out of total 4114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 2.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 396 optimal weight: 60.0000 chunk 269 optimal weight: 7.9990 chunk 6 optimal weight: 6.9990 chunk 354 optimal weight: 40.0000 chunk 196 optimal weight: 20.0000 chunk 405 optimal weight: 40.0000 chunk 328 optimal weight: 50.0000 chunk 0 optimal weight: 90.0000 chunk 242 optimal weight: 30.0000 chunk 426 optimal weight: 50.0000 chunk 120 optimal weight: 50.0000 overall best weight: 20.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6739 moved from start: 0.5053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 20192 Z= 0.380 Angle : 0.740 14.501 25180 Z= 0.487 Chirality : 0.000 0.000 0 Planarity : 0.004 0.026 5024 Dihedral : 5.984 57.152 5024 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.38 % Allowed : 8.09 % Favored : 91.53 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.96 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.12), residues: 4984 helix: 1.72 (0.10), residues: 2793 sheet: -1.44 (0.25), residues: 397 loop : -1.30 (0.15), residues: 1794 *********************** 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 fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 2.406 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.1687 time to fit residues: 29.6696 Evaluate side-chains 82 residues out of total 4114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 2.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 160 optimal weight: 40.0000 chunk 428 optimal weight: 50.0000 chunk 94 optimal weight: 40.0000 chunk 279 optimal weight: 8.9990 chunk 117 optimal weight: 40.0000 chunk 476 optimal weight: 50.0000 chunk 395 optimal weight: 20.0000 chunk 220 optimal weight: 50.0000 chunk 39 optimal weight: 50.0000 chunk 157 optimal weight: 40.0000 chunk 249 optimal weight: 40.0000 overall best weight: 29.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6877 moved from start: 0.6102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 20192 Z= 0.512 Angle : 0.924 17.304 25180 Z= 0.619 Chirality : 0.000 0.000 0 Planarity : 0.006 0.031 5024 Dihedral : 7.052 60.057 5024 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 21.92 Ramachandran Plot: Outliers : 0.34 % Allowed : 10.83 % Favored : 88.82 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.96 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.11), residues: 4984 helix: 0.12 (0.09), residues: 2770 sheet: -1.85 (0.27), residues: 349 loop : -2.04 (0.14), residues: 1865 *********************** 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 fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 2.302 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.1602 time to fit residues: 28.1778 Evaluate side-chains 82 residues out of total 4114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 2.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 458 optimal weight: 0.0970 chunk 53 optimal weight: 50.0000 chunk 271 optimal weight: 0.9990 chunk 347 optimal weight: 5.9990 chunk 269 optimal weight: 10.0000 chunk 400 optimal weight: 40.0000 chunk 265 optimal weight: 9.9990 chunk 474 optimal weight: 40.0000 chunk 296 optimal weight: 20.0000 chunk 289 optimal weight: 30.0000 chunk 218 optimal weight: 30.0000 overall best weight: 5.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6618 moved from start: 0.5741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 20192 Z= 0.129 Angle : 0.415 11.083 25180 Z= 0.269 Chirality : 0.000 0.000 0 Planarity : 0.002 0.021 5024 Dihedral : 4.944 53.745 5024 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.80 % Favored : 93.92 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.96 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.13), residues: 4984 helix: 2.09 (0.10), residues: 2810 sheet: -1.94 (0.25), residues: 401 loop : -1.45 (0.15), residues: 1773 *********************** 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 fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 2.233 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.1674 time to fit residues: 29.3580 Evaluate side-chains 82 residues out of total 4114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 2.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 293 optimal weight: 50.0000 chunk 189 optimal weight: 40.0000 chunk 283 optimal weight: 20.0000 chunk 142 optimal weight: 50.0000 chunk 93 optimal weight: 9.9990 chunk 91 optimal weight: 50.0000 chunk 301 optimal weight: 30.0000 chunk 323 optimal weight: 30.0000 chunk 234 optimal weight: 30.0000 chunk 44 optimal weight: 50.0000 chunk 372 optimal weight: 2.9990 overall best weight: 18.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6758 moved from start: 0.6077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 20192 Z= 0.317 Angle : 0.608 13.469 25180 Z= 0.405 Chirality : 0.000 0.000 0 Planarity : 0.003 0.024 5024 Dihedral : 5.455 60.257 5024 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.30 % Allowed : 9.93 % Favored : 89.77 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.96 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.12), residues: 4984 helix: 1.85 (0.10), residues: 2786 sheet: -1.90 (0.26), residues: 351 loop : -1.67 (0.15), residues: 1847 *********************** 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 fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 2.359 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.1591 time to fit residues: 27.9423 Evaluate side-chains 82 residues out of total 4114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 2.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 431 optimal weight: 40.0000 chunk 454 optimal weight: 60.0000 chunk 414 optimal weight: 7.9990 chunk 441 optimal weight: 50.0000 chunk 265 optimal weight: 0.3980 chunk 192 optimal weight: 0.4980 chunk 346 optimal weight: 5.9990 chunk 135 optimal weight: 50.0000 chunk 399 optimal weight: 1.9990 chunk 417 optimal weight: 50.0000 chunk 440 optimal weight: 9.9990 overall best weight: 3.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6560 moved from start: 0.5931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.014 20192 Z= 0.098 Angle : 0.350 10.068 25180 Z= 0.225 Chirality : 0.000 0.000 0 Planarity : 0.002 0.019 5024 Dihedral : 4.294 49.902 5024 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.82 % Favored : 94.92 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.96 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.13), residues: 4984 helix: 2.87 (0.10), residues: 2818 sheet: -1.85 (0.25), residues: 404 loop : -1.24 (0.16), residues: 1762 *********************** 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 fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 2.273 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.1647 time to fit residues: 28.8280 Evaluate side-chains 82 residues out of total 4114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 2.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 290 optimal weight: 20.0000 chunk 467 optimal weight: 50.0000 chunk 285 optimal weight: 50.0000 chunk 221 optimal weight: 30.0000 chunk 324 optimal weight: 50.0000 chunk 490 optimal weight: 40.0000 chunk 451 optimal weight: 40.0000 chunk 390 optimal weight: 7.9990 chunk 40 optimal weight: 50.0000 chunk 301 optimal weight: 9.9990 chunk 239 optimal weight: 4.9990 overall best weight: 14.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6707 moved from start: 0.6186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 20192 Z= 0.259 Angle : 0.524 12.475 25180 Z= 0.348 Chirality : 0.000 0.000 0 Planarity : 0.003 0.023 5024 Dihedral : 4.827 59.585 5024 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.28 % Allowed : 8.73 % Favored : 90.99 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.96 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.13), residues: 4984 helix: 2.68 (0.10), residues: 2811 sheet: -1.87 (0.25), residues: 376 loop : -1.43 (0.15), residues: 1797 ********************** 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 fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 3.337 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.1695 time to fit residues: 29.5924 Evaluate side-chains 82 residues out of total 4114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 2.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 310 optimal weight: 50.0000 chunk 415 optimal weight: 50.0000 chunk 119 optimal weight: 50.0000 chunk 359 optimal weight: 40.0000 chunk 57 optimal weight: 50.0000 chunk 108 optimal weight: 40.0000 chunk 390 optimal weight: 50.0000 chunk 163 optimal weight: 30.0000 chunk 401 optimal weight: 40.0000 chunk 49 optimal weight: 120.0000 chunk 72 optimal weight: 50.0000 overall best weight: 40.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2497 r_free = 0.2497 target = 0.029736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2274 r_free = 0.2274 target = 0.023300 restraints weight = 326147.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2278 r_free = 0.2278 target = 0.023358 restraints weight = 302578.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2273 r_free = 0.2273 target = 0.023290 restraints weight = 292615.937| |-----------------------------------------------------------------------------| r_work (final): 0.2112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.7180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.078 20192 Z= 0.630 Angle : 1.080 16.167 25180 Z= 0.733 Chirality : 0.000 0.000 0 Planarity : 0.008 0.037 5024 Dihedral : 7.521 59.944 5024 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 34.86 Ramachandran Plot: Outliers : 0.48 % Allowed : 13.64 % Favored : 85.87 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.96 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.20 (0.11), residues: 4984 helix: -0.54 (0.09), residues: 2737 sheet: -2.34 (0.27), residues: 318 loop : -2.61 (0.13), residues: 1929 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2406.83 seconds wall clock time: 43 minutes 56.12 seconds (2636.12 seconds total)