Starting phenix.real_space_refine on Thu Sep 18 20:14:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tko_25976/09_2025/7tko_25976.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tko_25976/09_2025/7tko_25976.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7tko_25976/09_2025/7tko_25976.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tko_25976/09_2025/7tko_25976.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7tko_25976/09_2025/7tko_25976.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tko_25976/09_2025/7tko_25976.map" } resolution = 4.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.120 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 3 Type Number sf(0) Gaussians C 10112 2.51 5 N 5056 2.21 5 O 5061 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20229 Number of models: 1 Model: "" Number of chains: 27 Chain: "0" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 300 Classifications: {'peptide': 75} Incomplete info: {'backbone_only': 65} Link IDs: {'PTRANS': 2, 'TRANS': 72} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 246 Unresolved non-hydrogen angles: 363 Unresolved non-hydrogen dihedrals: 146 Unresolved non-hydrogen chiralities: 94 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'PHE:plan': 6, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 75 Chain: "1" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 300 Classifications: {'peptide': 75} Incomplete info: {'backbone_only': 65} Link IDs: {'PTRANS': 2, 'TRANS': 72} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 246 Unresolved non-hydrogen angles: 363 Unresolved non-hydrogen dihedrals: 146 Unresolved non-hydrogen chiralities: 94 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'PHE:plan': 6, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 75 Chain: "2" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 300 Classifications: {'peptide': 75} Incomplete info: {'backbone_only': 65} Link IDs: {'PTRANS': 2, 'TRANS': 72} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 246 Unresolved non-hydrogen angles: 363 Unresolved non-hydrogen dihedrals: 146 Unresolved non-hydrogen chiralities: 94 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'PHE:plan': 6, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 75 Chain: "3" Number of atoms: 296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 296 Classifications: {'peptide': 74} Incomplete info: {'backbone_only': 64} Link IDs: {'PTRANS': 2, 'TRANS': 71} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 242 Unresolved non-hydrogen angles: 358 Unresolved non-hydrogen dihedrals: 143 Unresolved non-hydrogen chiralities: 93 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'PHE:plan': 6, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 75 Chain: "4" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 300 Classifications: {'peptide': 75} Incomplete info: {'backbone_only': 65} Link IDs: {'PTRANS': 2, 'TRANS': 72} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 246 Unresolved non-hydrogen angles: 363 Unresolved non-hydrogen dihedrals: 146 Unresolved non-hydrogen chiralities: 94 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'PHE:plan': 6, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 75 Chain: "5" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 300 Classifications: {'peptide': 75} Incomplete info: {'backbone_only': 65} Link IDs: {'PTRANS': 2, 'TRANS': 72} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 246 Unresolved non-hydrogen angles: 363 Unresolved non-hydrogen dihedrals: 146 Unresolved non-hydrogen chiralities: 94 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'PHE:plan': 6, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 75 Chain: "6" Number of atoms: 296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 296 Classifications: {'peptide': 74} Incomplete info: {'backbone_only': 64} Link IDs: {'PTRANS': 2, 'TRANS': 71} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 242 Unresolved non-hydrogen angles: 358 Unresolved non-hydrogen dihedrals: 143 Unresolved non-hydrogen chiralities: 93 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'PHE:plan': 6, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 75 Chain: "7" Number of atoms: 292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 292 Classifications: {'peptide': 73} Incomplete info: {'backbone_only': 64} Link IDs: {'PTRANS': 2, 'TRANS': 70} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 238 Unresolved non-hydrogen angles: 352 Unresolved non-hydrogen dihedrals: 139 Unresolved non-hydrogen chiralities: 93 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'PHE:plan': 5, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 68 Chain: "8" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 300 Classifications: {'peptide': 75} Incomplete info: {'backbone_only': 65} Link IDs: {'PTRANS': 2, 'TRANS': 72} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 246 Unresolved non-hydrogen angles: 363 Unresolved non-hydrogen dihedrals: 146 Unresolved non-hydrogen chiralities: 94 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'PHE:plan': 6, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 75 Chain: "9" Number of atoms: 296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 296 Classifications: {'peptide': 74} Incomplete info: {'backbone_only': 64} Link IDs: {'PTRANS': 2, 'TRANS': 71} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 242 Unresolved non-hydrogen angles: 358 Unresolved non-hydrogen dihedrals: 143 Unresolved non-hydrogen chiralities: 93 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'PHE:plan': 6, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 75 Chain: "A" Number of atoms: 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: {'GLU:plan': 37, 'ARG:plan': 29, 'ASP:plan': 21, 'ASN:plan1': 17, 'PHE:plan': 13, 'GLN:plan1': 25, 'HIS:plan': 6, 'TRP:plan': 2, 'TYR:plan': 14} Unresolved non-hydrogen planarities: 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, 'GLU:plan': 37, 'ARG:plan': 29, 'ASP:plan': 21, 'ASN:plan1': 17, 'PHE:plan': 14, 'HIS:plan': 6, 'TRP:plan': 2, 'TYR:plan': 14} 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: {'GLU:plan': 36, 'ARG:plan': 29, 'ASP:plan': 21, 'ASN:plan1': 17, 'PHE:plan': 13, 'GLN:plan1': 25, 'HIS:plan': 6, 'TRP:plan': 2, 'TYR:plan': 14} Unresolved non-hydrogen planarities: 800 Chain: "D" Number of atoms: 1872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 1872 Classifications: {'peptide': 468} Incomplete info: {'backbone_only': 422} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 445} Unresolved chain link angles: 22 Unresolved non-hydrogen bonds: 1721 Unresolved non-hydrogen angles: 2511 Unresolved non-hydrogen dihedrals: 1032 Unresolved non-hydrogen chiralities: 577 Planarities with less than four sites: {'ASP:plan': 25, 'HIS:plan': 7, 'PHE:plan': 17, 'GLU:plan': 37, 'GLN:plan1': 18, 'ASN:plan1': 10, 'ARG:plan': 22, 'TYR:plan': 10} Unresolved non-hydrogen planarities: 711 Chain: "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: {'ASP:plan': 25, 'HIS:plan': 7, 'PHE:plan': 17, 'GLU:plan': 37, 'GLN:plan1': 18, 'ASN:plan1': 10, 'ARG:plan': 22, 'TYR:plan': 10} Unresolved non-hydrogen planarities: 711 Chain: "F" Number of atoms: 1880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 1880 Classifications: {'peptide': 470} Incomplete info: {'backbone_only': 424} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 446} Unresolved chain link angles: 23 Unresolved non-hydrogen bonds: 1726 Unresolved non-hydrogen angles: 2519 Unresolved non-hydrogen dihedrals: 1034 Unresolved non-hydrogen chiralities: 580 Planarities with less than four sites: {'ASP:plan': 25, 'HIS:plan': 7, 'PHE:plan': 17, 'GLU:plan': 37, 'GLN:plan1': 18, 'ASN:plan1': 10, 'ARG:plan': 22, 'TYR:plan': 10} Unresolved non-hydrogen planarities: 711 Chain: "G" Number of atoms: 1060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 1060 Classifications: {'peptide': 265} Incomplete info: {'backbone_only': 255} Link IDs: {'PTRANS': 9, 'TRANS': 255} Chain breaks: 1 Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 1024 Unresolved non-hydrogen angles: 1472 Unresolved non-hydrogen dihedrals: 628 Unresolved non-hydrogen chiralities: 328 Planarities with less than four sites: {'GLU:plan': 16, 'ARG:plan': 11, 'ASN:plan1': 18, 'ASP:plan': 14, 'GLN:plan1': 9, 'PHE:plan': 8, 'TYR:plan': 7, 'HIS:plan': 3} Unresolved non-hydrogen planarities: 413 Chain: "H" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 480 Classifications: {'peptide': 120} Incomplete info: {'backbone_only': 114} Link IDs: {'PTRANS': 6, 'TRANS': 113} Chain breaks: 4 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 439 Unresolved non-hydrogen angles: 643 Unresolved non-hydrogen dihedrals: 258 Unresolved non-hydrogen chiralities: 151 Planarities with less than four sites: {'GLN:plan1': 7, 'PHE:plan': 5, 'HIS:plan': 2, 'GLU:plan': 13, 'TYR:plan': 1, 'ASN:plan1': 7, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 177 Chain: "I" Number of atoms: 193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 193 Classifications: {'peptide': 48} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 47} Link IDs: {'PTRANS': 2, 'TRANS': 45} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 188 Unresolved non-hydrogen angles: 278 Unresolved non-hydrogen dihedrals: 114 Unresolved non-hydrogen chiralities: 62 Planarities with less than four sites: {'TYR:plan': 4, 'ASN:plan1': 3, 'GLN:plan1': 4, 'ARG:plan': 2, 'GLU:plan': 2, 'ASP:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 89 Chain: "O" Number of atoms: 748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 748 Classifications: {'peptide': 187} Incomplete info: {'backbone_only': 174} Link IDs: {'PTRANS': 7, 'TRANS': 179} Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 691 Unresolved non-hydrogen angles: 1001 Unresolved non-hydrogen dihedrals: 414 Unresolved non-hydrogen chiralities: 235 Planarities with less than four sites: {'ARG:plan': 4, 'PHE:plan': 5, 'GLU:plan': 11, 'TYR:plan': 3, 'GLN:plan1': 5, 'ASN:plan1': 12, 'ASP:plan': 10, 'HIS:plan': 3} Unresolved non-hydrogen planarities: 249 Chain: "T" Number of atoms: 897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 897 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 207} Link IDs: {'PTRANS': 7, 'TRANS': 216} Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 925 Unresolved non-hydrogen angles: 1359 Unresolved non-hydrogen dihedrals: 607 Unresolved non-hydrogen chiralities: 306 Planarities with less than four sites: {'PHE:plan': 18, 'TYR:plan': 10, 'ASN:plan1': 11, 'ARG:plan': 3, 'TRP:plan': 5, 'GLN:plan1': 3, 'GLU:plan': 3, 'ASP:plan': 2, 'HIS:plan': 3, 'HIS%COO:plan': 1} Unresolved non-hydrogen planarities: 371 Chain: "U" Number of atoms: 621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 621 Classifications: {'peptide': 155} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 151} Link IDs: {'PTRANS': 2, 'TRANS': 152} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 631 Unresolved non-hydrogen angles: 908 Unresolved non-hydrogen dihedrals: 388 Unresolved non-hydrogen chiralities: 198 Planarities with less than four sites: {'ASN:plan1': 5, 'ASP:plan': 8, 'GLU:plan': 16, 'PHE:plan': 6, 'TYR:plan': 3, 'ARG:plan': 7, 'HIS:plan': 2, 'GLN:plan1': 11, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 283 Chain: "V" Number of atoms: 685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 685 Classifications: {'peptide': 171} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 166} Link IDs: {'PTRANS': 5, 'TRANS': 165} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 705 Unresolved non-hydrogen angles: 1009 Unresolved non-hydrogen dihedrals: 446 Unresolved non-hydrogen chiralities: 214 Planarities with less than four sites: {'ASN:plan1': 7, 'ASP:plan': 13, 'TRP:plan': 2, 'ARG:plan': 7, 'GLN:plan1': 9, 'PHE:plan': 5, 'GLU:plan': 13, 'HIS:plan': 2, 'TYR:plan': 4} Unresolved non-hydrogen planarities: 302 Chain: "W" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 340 Classifications: {'peptide': 85} Incomplete info: {'backbone_only': 79} Link IDs: {'PTRANS': 7, 'TRANS': 77} Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 348 Unresolved non-hydrogen angles: 503 Unresolved non-hydrogen dihedrals: 241 Unresolved non-hydrogen chiralities: 97 Planarities with less than four sites: {'ASN:plan1': 5, 'ARG:plan': 3, 'HIS:plan': 3, 'PHE:plan': 5, 'TYR:plan': 6, 'GLN:plan1': 1, 'ASP:plan': 2, 'TRP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 162 Chain: "X" Number of atoms: 248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 248 Classifications: {'peptide': 62} Incomplete info: {'backbone_only': 60} Link IDs: {'PTRANS': 7, 'TRANS': 54} Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 257 Unresolved non-hydrogen angles: 375 Unresolved non-hydrogen dihedrals: 161 Unresolved non-hydrogen chiralities: 77 Planarities with less than four sites: {'ASN:plan1': 5, 'GLN:plan1': 5, 'ASP:plan': 3, 'TYR:plan': 2, 'ARG:plan': 1, 'GLU:plan': 7, 'TRP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 117 Chain: "Y" Number of atoms: 148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 148 Classifications: {'peptide': 37} Incomplete info: {'backbone_only': 35} Link IDs: {'PTRANS': 3, 'TRANS': 33} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 155 Unresolved non-hydrogen angles: 225 Unresolved non-hydrogen dihedrals: 110 Unresolved non-hydrogen chiralities: 44 Planarities with less than four sites: {'ARG:plan': 1, 'PHE:plan': 3, 'TYR:plan': 3, 'TRP:plan': 1, 'ASP:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 68 Chain: "Z" Number of atoms: 193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 193 Classifications: {'peptide': 48} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 46} Link IDs: {'PTRANS': 3, 'TRANS': 44} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 231 Unresolved non-hydrogen angles: 330 Unresolved non-hydrogen dihedrals: 158 Unresolved non-hydrogen chiralities: 67 Planarities with less than four sites: {'GLN:plan1': 3, 'PHE:plan': 7, 'TYR:plan': 3, 'ASN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 99 Time building chain proxies: 5.68, per 1000 atoms: 0.28 Number of scatterers: 20229 At special positions: 0 Unit cell: (118.58, 145.53, 235.812, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 5061 8.00 N 5056 7.00 C 10112 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.80 Conformation dependent library (CDL) restraints added in 1.6 seconds Enol-peptide restraints added in 1.2 microseconds 9968 Ramachandran restraints generated. 4984 Oldfield, 0 Emsley, 4984 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 0 Finding SS restraints... Secondary structure from input PDB file: 198 helices and 28 sheets defined 59.8% alpha, 10.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain '0' and resid 1 through 18 removed outlier: 3.631A pdb=" N ILE 0 17 " --> pdb=" O GLY 0 13 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N GLY 0 18 " --> pdb=" O ILE 0 14 " (cutoff:3.500A) Processing helix chain '0' and resid 18 through 40 removed outlier: 4.185A pdb=" N ALA 0 22 " --> pdb=" O GLY 0 18 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ALA 0 27 " --> pdb=" O GLY 0 23 " (cutoff:3.500A) Processing helix chain '0' and resid 43 through 75 Proline residue: 0 49 - end of helix removed outlier: 3.578A pdb=" N GLY 0 62 " --> pdb=" O SER 0 58 " (cutoff:3.500A) Processing helix chain '1' and resid 2 through 17 removed outlier: 3.514A pdb=" N GLY 1 13 " --> pdb=" O TYR 1 9 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE 1 17 " --> pdb=" O GLY 1 13 " (cutoff:3.500A) Processing helix chain '1' and resid 18 through 40 removed outlier: 4.547A pdb=" N ALA 1 22 " --> pdb=" O GLY 1 18 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALA 1 27 " --> pdb=" O GLY 1 23 " (cutoff:3.500A) Processing helix chain '1' and resid 43 through 74 Proline residue: 1 49 - end of helix removed outlier: 3.518A pdb=" N THR 1 61 " --> pdb=" O LEU 1 57 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLY 1 62 " --> pdb=" O SER 1 58 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N CYS 1 65 " --> pdb=" O THR 1 61 " (cutoff:3.500A) Processing helix chain '2' and resid 2 through 16 Processing helix chain '2' and resid 18 through 40 removed outlier: 4.251A pdb=" N ALA 2 22 " --> pdb=" O GLY 2 18 " (cutoff:3.500A) Processing helix chain '2' and resid 43 through 74 Proline residue: 2 49 - end of helix removed outlier: 3.850A pdb=" N THR 2 61 " --> pdb=" O LEU 2 57 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N GLY 2 62 " --> pdb=" O SER 2 58 " (cutoff:3.500A) Processing helix chain '3' and resid 3 through 17 removed outlier: 3.504A pdb=" N THR 3 16 " --> pdb=" O ALA 3 12 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ILE 3 17 " --> pdb=" O GLY 3 13 " (cutoff:3.500A) Processing helix chain '3' and resid 18 through 40 removed outlier: 4.462A pdb=" N ALA 3 22 " --> pdb=" O GLY 3 18 " (cutoff:3.500A) removed outlier: 4.055A 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: 3.588A pdb=" N THR 3 61 " --> pdb=" O LEU 3 57 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLY 3 62 " --> pdb=" O SER 3 58 " (cutoff:3.500A) Processing helix chain '4' and resid 2 through 17 removed outlier: 3.805A pdb=" N ILE 4 17 " --> pdb=" O GLY 4 13 " (cutoff:3.500A) Processing helix chain '4' and resid 18 through 40 removed outlier: 4.173A pdb=" N ALA 4 22 " --> pdb=" O GLY 4 18 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA 4 27 " --> pdb=" O GLY 4 23 " (cutoff:3.500A) Processing helix chain '4' and resid 43 through 74 Proline residue: 4 49 - end of helix removed outlier: 4.051A pdb=" N THR 4 61 " --> pdb=" O LEU 4 57 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N GLY 4 62 " --> pdb=" O SER 4 58 " (cutoff:3.500A) Processing helix chain '5' and resid 2 through 17 removed outlier: 3.677A pdb=" N ILE 5 17 " --> pdb=" O GLY 5 13 " (cutoff:3.500A) Processing helix chain '5' and resid 18 through 40 removed outlier: 4.310A pdb=" N ALA 5 22 " --> pdb=" O GLY 5 18 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA 5 27 " --> pdb=" O GLY 5 23 " (cutoff:3.500A) Processing helix chain '5' and resid 43 through 75 Proline residue: 5 49 - end of helix removed outlier: 3.642A pdb=" N GLY 5 62 " --> pdb=" O SER 5 58 " (cutoff:3.500A) Processing helix chain '6' and resid 3 through 18 removed outlier: 3.850A pdb=" N ILE 6 17 " --> pdb=" O GLY 6 13 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N GLY 6 18 " --> pdb=" O ILE 6 14 " (cutoff:3.500A) Processing helix chain '6' and resid 18 through 40 removed outlier: 4.426A pdb=" N ALA 6 22 " --> pdb=" O GLY 6 18 " (cutoff:3.500A) removed outlier: 3.615A 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: 3.913A pdb=" N GLY 6 62 " --> pdb=" O SER 6 58 " (cutoff:3.500A) Processing helix chain '7' and resid 2 through 40 removed outlier: 3.645A pdb=" N THR 7 16 " --> pdb=" O ALA 7 12 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ILE 7 17 " --> pdb=" O GLY 7 13 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N GLY 7 18 " --> pdb=" O ILE 7 14 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N LEU 7 19 " --> pdb=" O SER 7 15 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU 7 20 " --> pdb=" O THR 7 16 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N GLY 7 21 " --> pdb=" O ILE 7 17 " (cutoff:3.500A) removed outlier: 4.258A 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: 3.536A pdb=" N THR 7 61 " --> pdb=" O LEU 7 57 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLY 7 62 " --> pdb=" O SER 7 58 " (cutoff:3.500A) Processing helix chain '8' and resid 2 through 17 removed outlier: 3.842A pdb=" N ILE 8 17 " --> pdb=" O GLY 8 13 " (cutoff:3.500A) Processing helix chain '8' and resid 19 through 40 removed outlier: 3.852A 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: 3.714A pdb=" N THR 8 61 " --> pdb=" O LEU 8 57 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLY 8 62 " --> pdb=" O SER 8 58 " (cutoff:3.500A) Processing helix chain '9' and resid 3 through 17 removed outlier: 3.979A pdb=" N ILE 9 17 " --> pdb=" O GLY 9 13 " (cutoff:3.500A) Processing helix chain '9' and resid 18 through 40 removed outlier: 4.305A pdb=" N ALA 9 22 " --> pdb=" O GLY 9 18 " (cutoff:3.500A) Processing helix chain '9' and resid 43 through 75 Proline residue: 9 49 - end of helix removed outlier: 3.552A pdb=" N THR 9 61 " --> pdb=" O LEU 9 57 " (cutoff:3.500A) removed outlier: 3.575A 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 176 through 188 removed outlier: 3.996A pdb=" N VAL A 180 " --> pdb=" O GLY A 176 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N ALA A 181 " --> pdb=" O LYS A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 193 Processing helix chain 'A' and resid 196 through 200 Processing helix chain 'A' and resid 211 through 225 Processing helix chain 'A' and resid 227 through 229 No H-bonds generated for 'chain 'A' and resid 227 through 229' Processing helix chain 'A' and resid 241 through 261 Proline residue: A 249 - end of helix removed outlier: 3.717A 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 338 through 348 Processing helix chain 'A' and resid 355 through 361 Processing helix chain 'A' and resid 376 through 380 removed outlier: 3.879A 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: 3.677A pdb=" N GLU A 401 " --> pdb=" O ALA A 397 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N GLN A 407 " --> pdb=" O ALA A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 431 removed outlier: 3.705A pdb=" N LYS A 431 " --> pdb=" O THR A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 452 removed outlier: 3.510A pdb=" N VAL A 444 " --> pdb=" O THR A 440 " (cutoff:3.500A) 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: 7.727A pdb=" N GLU A 480 " --> pdb=" O SER A 476 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N LEU A 481 " --> pdb=" O ASN A 477 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N LEU A 482 " --> pdb=" O HIS A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 509 Processing helix chain 'B' and resid 6 through 9 Processing helix chain 'B' and resid 10 through 19 Processing helix chain 'B' and resid 25 through 28 Processing helix chain 'B' and resid 152 through 159 Processing helix chain 'B' and resid 176 through 194 removed outlier: 3.616A pdb=" N VAL B 180 " --> pdb=" O GLY B 176 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ALA B 181 " --> pdb=" O LYS B 177 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N THR B 184 " --> pdb=" O VAL B 180 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ARG B 190 " --> pdb=" O LEU B 186 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N TRP B 191 " --> pdb=" O ASN B 187 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLY B 194 " --> pdb=" O ARG B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 199 Processing helix chain 'B' and resid 211 through 225 Processing helix chain 'B' and resid 241 through 263 Proline residue: B 249 - end of helix removed outlier: 3.765A pdb=" N PHE B 259 " --> pdb=" O ILE B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 286 removed outlier: 3.809A pdb=" N GLN B 276 " --> pdb=" O ASP B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 296 Processing helix chain 'B' and resid 299 through 309 Processing helix chain 'B' and resid 338 through 348 Processing helix chain 'B' and resid 355 through 362 removed outlier: 3.581A pdb=" N PHE B 359 " --> pdb=" O GLU B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 381 removed outlier: 4.053A pdb=" N ALA B 379 " --> pdb=" O VAL B 376 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ALA B 380 " --> pdb=" O GLY B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 389 Processing helix chain 'B' and resid 391 through 408 removed outlier: 4.056A pdb=" N PHE B 408 " --> pdb=" O ALA B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 431 Processing helix chain 'B' and resid 439 through 442 Processing helix chain 'B' and resid 443 through 452 Processing helix chain 'B' and resid 454 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 506 Processing helix chain 'C' and resid 13 through 21 Processing helix chain 'C' and resid 152 through 159 Processing helix chain 'C' and resid 176 through 194 removed outlier: 3.695A pdb=" N VAL C 180 " --> pdb=" O GLY C 176 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA C 181 " --> pdb=" O LYS C 177 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N THR C 184 " --> pdb=" O VAL C 180 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE C 185 " --> pdb=" O ALA C 181 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ARG C 190 " --> pdb=" O LEU C 186 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N TRP C 191 " --> pdb=" O ASN C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 200 Processing helix chain 'C' and resid 211 through 225 Processing helix chain 'C' and resid 241 through 262 Proline residue: C 249 - end of helix removed outlier: 3.750A pdb=" N PHE C 259 " --> pdb=" O ILE C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 287 removed outlier: 3.552A pdb=" N VAL C 278 " --> pdb=" O SER C 274 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 296 Processing helix chain 'C' and resid 299 through 310 removed outlier: 3.900A pdb=" N ARG C 310 " --> pdb=" O ARG C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 348 Processing helix chain 'C' and resid 355 through 361 Processing helix chain 'C' and resid 376 through 381 Processing helix chain 'C' and resid 382 through 388 Processing helix chain 'C' and resid 389 through 402 Processing helix chain 'C' and resid 403 through 406 Processing helix chain 'C' and resid 413 through 430 Processing helix chain 'C' and resid 439 through 452 Proline residue: C 445 - end of helix Processing helix chain 'C' and resid 459 through 461 No H-bonds generated for 'chain 'C' and resid 459 through 461' Processing helix chain 'C' and resid 462 through 489 removed outlier: 3.630A pdb=" N SER C 468 " --> pdb=" O GLY C 464 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ASN C 479 " --> pdb=" O LYS C 475 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N GLU C 480 " --> pdb=" O SER C 476 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N LEU C 481 " --> pdb=" O ASN C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 492 through 509 Processing helix chain 'D' and resid 88 through 92 Processing helix chain 'D' and resid 138 through 145 Processing helix chain 'D' and resid 162 through 178 Processing helix chain 'D' and resid 190 through 204 Processing helix chain 'D' and resid 225 through 247 removed outlier: 4.698A pdb=" N ALA D 233 " --> pdb=" O ARG D 229 " (cutoff:3.500A) removed outlier: 4.511A 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 319 through 329 removed outlier: 3.561A pdb=" N HIS D 328 " --> pdb=" O THR D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 336 through 342 Processing helix chain 'D' and resid 359 through 364 Processing helix chain 'D' and resid 364 through 392 removed outlier: 3.821A pdb=" N ILE D 387 " --> pdb=" O SER D 383 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE D 390 " --> pdb=" O ASP D 386 " (cutoff:3.500A) Processing helix chain 'D' and resid 393 through 396 removed outlier: 3.500A pdb=" N LEU D 396 " --> pdb=" O MET D 393 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 393 through 396' Processing helix chain 'D' and resid 397 through 415 removed outlier: 3.803A pdb=" N SER D 415 " --> pdb=" O GLN D 411 " (cutoff:3.500A) Processing helix chain 'D' and resid 418 through 420 No H-bonds generated for 'chain 'D' and resid 418 through 420' Processing helix chain 'D' and resid 421 through 426 Processing helix chain 'D' and resid 433 through 446 removed outlier: 3.544A pdb=" N PHE D 441 " --> pdb=" O THR D 437 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 452 removed outlier: 3.505A pdb=" N ASN D 451 " --> pdb=" O LYS D 448 " (cutoff:3.500A) Processing helix chain 'D' and resid 453 through 457 Processing helix chain 'D' and resid 462 through 475 removed outlier: 3.573A pdb=" N ALA D 468 " --> pdb=" O GLU D 464 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU D 471 " --> pdb=" O VAL D 467 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 92 Processing helix chain 'E' and resid 138 through 145 Processing helix chain 'E' and resid 162 through 175 Processing helix chain 'E' and resid 190 through 204 Processing helix chain 'E' and resid 225 through 231 removed outlier: 3.813A pdb=" N ARG E 231 " --> pdb=" O GLY E 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 231 through 245 Processing helix chain 'E' and resid 258 through 273 removed outlier: 3.909A pdb=" N ALA E 270 " --> pdb=" O SER E 266 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU E 271 " --> pdb=" O GLU E 267 " (cutoff:3.500A) Processing helix chain 'E' and resid 284 through 294 Processing helix chain 'E' and resid 313 through 316 Processing helix chain 'E' and resid 319 through 327 removed outlier: 3.773A pdb=" N ALA E 327 " --> pdb=" O ALA E 323 " (cutoff:3.500A) Processing helix chain 'E' and resid 336 through 342 Processing helix chain 'E' and resid 357 through 359 No H-bonds generated for 'chain 'E' and resid 357 through 359' Processing helix chain 'E' and resid 363 through 391 removed outlier: 3.994A pdb=" N HIS E 367 " --> pdb=" O VAL E 363 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ASP E 386 " --> pdb=" O LYS E 382 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N ILE E 387 " --> pdb=" O SER E 383 " (cutoff:3.500A) Processing helix chain 'E' and resid 397 through 414 Processing helix chain 'E' and resid 421 through 426 Processing helix chain 'E' and resid 433 through 446 Processing helix chain 'E' and resid 453 through 458 Processing helix chain 'E' and resid 462 through 475 Processing helix chain 'F' and resid 88 through 92 Processing helix chain 'F' and resid 138 through 145 Processing helix chain 'F' and resid 162 through 178 removed outlier: 4.273A 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: 4.105A pdb=" N ALA F 233 " --> pdb=" O ARG F 229 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N LEU F 234 " --> pdb=" O ALA F 230 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR F 235 " --> pdb=" O ARG F 231 " (cutoff:3.500A) Processing helix chain 'F' and resid 257 through 273 removed outlier: 3.601A pdb=" N PHE F 261 " --> pdb=" O ASN F 257 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA F 270 " --> pdb=" O SER F 266 " (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 removed outlier: 3.549A pdb=" N ALA F 327 " --> pdb=" O ALA F 323 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N HIS F 328 " --> pdb=" O THR F 324 " (cutoff:3.500A) Processing helix chain 'F' and resid 336 through 343 Processing helix chain 'F' and resid 359 through 363 removed outlier: 3.729A pdb=" N VAL F 363 " --> pdb=" O ALA F 360 " (cutoff:3.500A) Processing helix chain 'F' and resid 364 through 391 removed outlier: 4.326A pdb=" N ASP F 386 " --> pdb=" O LYS F 382 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N ILE F 387 " --> pdb=" O SER F 383 " (cutoff:3.500A) Processing helix chain 'F' and resid 392 through 396 Processing helix chain 'F' and resid 397 through 414 Processing helix chain 'F' and resid 418 through 422 Processing helix chain 'F' and resid 433 through 447 Processing helix chain 'F' and resid 453 through 457 Processing helix chain 'F' and resid 462 through 475 Processing helix chain 'G' and resid 2 through 56 removed outlier: 3.887A pdb=" N LYS G 33 " --> pdb=" O THR G 29 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER G 40 " --> pdb=" O LYS G 36 " (cutoff:3.500A) Processing helix chain 'G' and resid 86 through 102 removed outlier: 3.504A pdb=" N GLN G 102 " --> pdb=" O HIS G 98 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 122 removed outlier: 3.673A pdb=" N ARG G 120 " --> pdb=" O MET G 116 " (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: 4.298A pdb=" N GLU G 211 " --> pdb=" O ARG G 207 " (cutoff:3.500A) Processing helix chain 'H' and resid 100 through 115 removed outlier: 4.174A pdb=" N SER H 113 " --> pdb=" O LYS H 109 " (cutoff:3.500A) removed outlier: 4.336A 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 38 Processing helix chain 'O' and resid 16 through 29 removed outlier: 3.508A pdb=" N ALA O 20 " --> pdb=" O GLU O 16 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS O 29 " --> pdb=" O GLN O 25 " (cutoff:3.500A) Processing helix chain 'O' and resid 32 through 49 Processing helix chain 'O' and resid 64 through 78 removed outlier: 3.811A pdb=" N HIS O 78 " --> pdb=" O ILE O 74 " (cutoff:3.500A) Processing helix chain 'O' and resid 83 through 96 Processing helix chain 'O' and resid 101 through 117 Processing helix chain 'O' and resid 130 through 144 Processing helix chain 'O' and resid 179 through 191 removed outlier: 3.623A pdb=" N LYS O 183 " --> pdb=" O SER O 179 " (cutoff:3.500A) Processing helix chain 'T' and resid 27 through 43 Processing helix chain 'T' and resid 56 through 74 removed outlier: 3.647A pdb=" N ILE T 60 " --> pdb=" O SER T 56 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N SER T 61 " --> pdb=" O ARG T 57 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLN T 62 " --> pdb=" O TRP T 58 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N MET T 72 " --> pdb=" O THR T 68 " (cutoff:3.500A) Processing helix chain 'T' and resid 80 through 85 Processing helix chain 'T' and resid 85 through 100 removed outlier: 3.765A pdb=" N ILE T 96 " --> pdb=" O LEU T 92 " (cutoff:3.500A) Processing helix chain 'T' and resid 114 through 138 removed outlier: 4.031A pdb=" N ILE T 118 " --> pdb=" O HIS T 114 " (cutoff:3.500A) Processing helix chain 'T' and resid 139 through 146 removed outlier: 3.522A 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 164 removed outlier: 4.013A pdb=" N GLU T 162 " --> pdb=" O LEU T 158 " (cutoff:3.500A) Processing helix chain 'T' and resid 168 through 199 removed outlier: 4.022A pdb=" N LEU T 173 " --> pdb=" O ARG T 169 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N GLY T 174 " --> pdb=" O ALA T 170 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N LEU T 177 " --> pdb=" O LEU T 173 " (cutoff:3.500A) Processing helix chain 'T' and resid 209 through 247 removed outlier: 3.731A pdb=" N LEU T 213 " --> pdb=" O GLY T 209 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N PHE T 224 " --> pdb=" O MET T 220 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA T 225 " --> pdb=" O MET T 221 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ALA T 239 " --> pdb=" O ALA T 235 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LEU T 242 " --> pdb=" O THR T 238 " (cutoff:3.500A) Processing helix chain 'U' and resid 55 through 184 removed outlier: 4.421A pdb=" N ALA U 74 " --> pdb=" O ALA U 70 " (cutoff:3.500A) Proline residue: U 75 - end of helix removed outlier: 3.563A pdb=" N LYS U 104 " --> pdb=" O VAL U 100 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLN U 112 " --> pdb=" O ASP U 108 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASN U 115 " --> pdb=" O SER U 111 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N GLU U 118 " --> pdb=" O GLN U 114 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LYS U 121 " --> pdb=" O ALA U 117 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL U 122 " --> pdb=" O GLU U 118 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LYS U 128 " --> pdb=" O PHE U 124 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N PHE U 138 " --> pdb=" O GLU U 134 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N GLU U 139 " --> pdb=" O SER U 135 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU U 140 " --> pdb=" O GLU U 136 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA U 147 " --> pdb=" O LYS U 143 " (cutoff:3.500A) Processing helix chain 'U' and resid 187 through 206 removed outlier: 4.309A pdb=" N VAL U 193 " --> pdb=" O PHE U 189 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LEU U 194 " --> pdb=" O GLN U 190 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLN U 195 " --> pdb=" O GLU U 191 " (cutoff:3.500A) Processing helix chain 'V' and resid 4 through 19 Processing helix chain 'V' and resid 26 through 48 Processing helix chain 'V' and resid 54 through 59 Processing helix chain 'V' and resid 67 through 78 Processing helix chain 'V' and resid 90 through 127 Processing helix chain 'V' and resid 134 through 142 Processing helix chain 'V' and resid 143 through 156 Processing helix chain 'V' and resid 162 through 166 removed outlier: 3.759A pdb=" N ARG V 166 " --> pdb=" O TYR V 163 " (cutoff:3.500A) Processing helix chain 'W' and resid 18 through 30 removed outlier: 3.929A pdb=" N LYS W 22 " --> pdb=" O ALA W 18 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N VAL W 28 " --> pdb=" O ILE W 24 " (cutoff:3.500A) Processing helix chain 'W' and resid 48 through 56 Processing helix chain 'W' and resid 63 through 85 removed outlier: 4.338A pdb=" N TYR W 78 " --> pdb=" O ILE W 74 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N SER W 79 " --> pdb=" O ALA W 75 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N TYR W 82 " --> pdb=" O TYR W 78 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N TYR W 83 " --> pdb=" O SER W 79 " (cutoff:3.500A) Processing helix chain 'X' and resid 2 through 14 Processing helix chain 'X' and resid 20 through 27 removed outlier: 4.087A pdb=" N GLY X 26 " --> pdb=" O GLN X 22 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ASN X 27 " --> pdb=" O ASP X 23 " (cutoff:3.500A) Processing helix chain 'X' and resid 46 through 57 removed outlier: 3.942A pdb=" N LEU X 50 " --> pdb=" O GLY X 46 " (cutoff:3.500A) Processing helix chain 'Y' and resid 13 through 35 Processing helix chain 'Z' and resid 8 through 30 Processing helix chain 'Z' and resid 30 through 48 removed outlier: 3.651A pdb=" N MET Z 34 " --> pdb=" O PHE Z 30 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ILE Z 35 " --> pdb=" O PHE Z 31 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 28 removed outlier: 3.939A pdb=" N LEU A 27 " --> pdb=" O THR O 175 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR O 175 " --> pdb=" O LEU A 27 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL O 158 " --> pdb=" O VAL O 123 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 31 through 36 removed outlier: 6.011A pdb=" N ARG A 42 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N VAL A 36 " --> pdb=" O ILE A 40 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ILE A 40 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASN A 67 " --> pdb=" O GLY A 74 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N VAL A 76 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N ALA A 65 " --> pdb=" O VAL A 76 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N PHE A 78 " --> pdb=" O GLY A 63 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N GLY A 63 " --> pdb=" O PHE A 78 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL A 61 " --> pdb=" O PHE A 57 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N GLU A 53 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ASN A 95 " --> pdb=" O LEU A 54 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N GLU A 56 " --> pdb=" O THR A 93 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N THR A 93 " --> pdb=" O GLU A 56 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 98 through 101 Processing sheet with id=AA4, first strand: chain 'A' and resid 109 through 111 removed outlier: 6.690A pdb=" N ILE A 169 " --> pdb=" O ILE A 329 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N THR A 331 " --> pdb=" O ILE A 169 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N GLY A 171 " --> pdb=" O THR A 331 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 351 through 352 Processing sheet with id=AA6, first strand: chain 'B' and resid 30 through 33 removed outlier: 6.450A pdb=" N VAL B 76 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N ALA B 65 " --> pdb=" O VAL B 76 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N GLU B 53 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N LEU B 54 " --> pdb=" O THR B 93 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 98 through 101 Processing sheet with id=AA8, first strand: chain 'B' and resid 109 through 110 removed outlier: 6.060A pdb=" N VAL B 110 " --> pdb=" O ALA B 235 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N TYR B 202 " --> pdb=" O HIS B 265 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU B 267 " --> pdb=" O TYR B 202 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N ILE B 169 " --> pdb=" O ILE B 329 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N LEU B 168 " --> pdb=" O ILE B 352 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 147 through 148 removed outlier: 4.174A pdb=" N ILE B 161 " --> pdb=" O VAL B 148 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 31 through 37 removed outlier: 6.896A pdb=" N ARG C 42 " --> pdb=" O LEU C 34 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N VAL C 36 " --> pdb=" O ILE C 40 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ILE C 40 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N GLY C 74 " --> pdb=" O LEU C 66 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU C 66 " --> pdb=" O GLY C 74 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ALA C 65 " --> pdb=" O GLU C 53 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N GLU C 53 " --> pdb=" O ALA C 65 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N LEU C 54 " --> pdb=" O THR C 93 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 31 through 37 removed outlier: 6.896A pdb=" N ARG C 42 " --> pdb=" O LEU C 34 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N VAL C 36 " --> pdb=" O ILE C 40 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ILE C 40 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N GLY C 74 " --> pdb=" O LEU C 66 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU C 66 " --> pdb=" O GLY C 74 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N ASP D 22 " --> pdb=" O THR D 14 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N VAL D 16 " --> pdb=" O ILE D 20 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N ILE D 20 " --> pdb=" O VAL D 16 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL D 21 " --> pdb=" O THR D 61 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL D 23 " --> pdb=" O VAL D 59 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N THR D 58 " --> pdb=" O HIS D 53 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N HIS D 53 " --> pdb=" O THR D 58 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ARG D 60 " --> pdb=" O ALA D 51 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 98 through 101 Processing sheet with id=AB4, first strand: chain 'C' and resid 108 through 111 Processing sheet with id=AB5, first strand: chain 'C' and resid 147 through 148 removed outlier: 4.511A pdb=" N ILE C 161 " --> pdb=" O VAL C 148 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 328 through 331 removed outlier: 5.822A pdb=" N ILE C 169 " --> pdb=" O ILE C 329 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N THR C 331 " --> pdb=" O ILE C 169 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N GLY C 171 " --> pdb=" O THR C 331 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU C 354 " --> pdb=" O ILE C 170 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ASP C 172 " --> pdb=" O LEU C 354 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE C 353 " --> pdb=" O LEU C 371 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N LEU C 371 " --> pdb=" O PHE C 353 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 84 through 87 removed outlier: 3.689A pdb=" N LEU D 113 " --> pdb=" O VAL D 87 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 95 through 96 removed outlier: 3.882A pdb=" N PHE D 219 " --> pdb=" O ILE D 96 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ALA D 216 " --> pdb=" O VAL D 183 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N THR D 185 " --> pdb=" O ALA D 216 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N VAL D 218 " --> pdb=" O THR D 185 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N VAL D 187 " --> pdb=" O VAL D 218 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N GLY D 220 " --> pdb=" O VAL D 187 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N PHE D 181 " --> pdb=" O LEU D 252 " (cutoff:3.500A) removed outlier: 8.274A pdb=" N PHE D 254 " --> pdb=" O PHE D 181 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N VAL D 183 " --> pdb=" O PHE D 254 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N ASP D 256 " --> pdb=" O VAL D 183 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N THR D 185 " --> pdb=" O ASP D 256 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N VAL D 307 " --> pdb=" O VAL D 251 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N LEU D 253 " --> pdb=" O VAL D 307 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N ALA D 309 " --> pdb=" O LEU D 253 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ILE D 255 " --> pdb=" O ALA D 309 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 133 through 134 removed outlier: 3.743A pdb=" N TYR D 147 " --> pdb=" O LEU D 134 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 11 through 17 removed outlier: 6.606A pdb=" N ASP E 22 " --> pdb=" O THR E 14 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N VAL E 16 " --> pdb=" O ILE E 20 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ILE E 20 " --> pdb=" O VAL E 16 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ARG E 60 " --> pdb=" O ALA E 51 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 84 through 87 removed outlier: 4.017A pdb=" N LEU E 113 " --> pdb=" O VAL E 87 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 95 through 96 removed outlier: 5.746A pdb=" N ILE E 96 " --> pdb=" O PHE E 219 " (cutoff:3.500A) removed outlier: 8.180A pdb=" N GLN E 221 " --> pdb=" O ILE E 96 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N PHE E 184 " --> pdb=" O VAL E 218 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N GLY E 220 " --> pdb=" O PHE E 184 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N GLY E 186 " --> pdb=" O GLY E 220 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N THR E 305 " --> pdb=" O VAL E 251 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N LYS E 152 " --> pdb=" O ALA E 331 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N THR E 333 " --> pdb=" O LYS E 152 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N GLY E 154 " --> pdb=" O THR E 333 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N LEU E 335 " --> pdb=" O GLY E 154 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N PHE E 156 " --> pdb=" O LEU E 335 " (cutoff:3.500A) removed outlier: 10.762A pdb=" N THR E 332 " --> pdb=" O LEU E 351 " (cutoff:3.500A) removed outlier: 9.376A pdb=" N LEU E 351 " --> pdb=" O THR E 332 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N VAL E 334 " --> pdb=" O ASP E 349 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 11 through 17 removed outlier: 6.627A pdb=" N ASP F 22 " --> pdb=" O THR F 14 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N VAL F 16 " --> pdb=" O ILE F 20 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N ILE F 20 " --> pdb=" O VAL F 16 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N THR F 58 " --> pdb=" O HIS F 53 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N HIS F 53 " --> pdb=" O THR F 58 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ARG F 60 " --> pdb=" O ALA F 51 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 84 through 87 Processing sheet with id=AC6, first strand: chain 'F' and resid 216 through 221 removed outlier: 6.386A pdb=" N PHE F 184 " --> pdb=" O VAL F 218 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N GLY F 220 " --> pdb=" O PHE F 184 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N GLY F 186 " --> pdb=" O GLY F 220 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N LEU F 253 " --> pdb=" O VAL F 307 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N ALA F 309 " --> pdb=" O LEU F 253 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ILE F 255 " --> pdb=" O ALA F 309 " (cutoff:3.500A) removed outlier: 8.865A pdb=" N TYR F 311 " --> pdb=" O ILE F 255 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ILE F 153 " --> pdb=" O GLN F 308 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N VAL F 310 " --> pdb=" O ILE F 153 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N LEU F 155 " --> pdb=" O VAL F 310 " (cutoff:3.500A) removed outlier: 11.558A pdb=" N THR F 332 " --> pdb=" O LEU F 351 " (cutoff:3.500A) removed outlier: 9.929A pdb=" N LEU F 351 " --> pdb=" O THR F 332 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N VAL F 334 " --> pdb=" O ASP F 349 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 73 through 77 removed outlier: 6.544A pdb=" N ILE G 107 " --> pdb=" O ILE G 126 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N LEU G 128 " --> pdb=" O ILE G 107 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 164 through 171 removed outlier: 6.389A pdb=" N SER G 174 " --> pdb=" O VAL G 170 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 12 through 15 removed outlier: 6.305A pdb=" N GLN H 13 " --> pdb=" O VAL H 85 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N ALA H 87 " --> pdb=" O GLN H 13 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N ALA H 15 " --> pdb=" O ALA H 87 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLN H 82 " --> pdb=" O GLN H 78 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 37 through 42 removed outlier: 6.344A pdb=" N VAL H 56 " --> pdb=" O PRO H 33 " (cutoff:3.500A) 2327 hydrogen bonds defined for protein. 6726 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.34 Time building geometry restraints manager: 2.25 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: 5061 1.28 - 1.35: 1363 1.35 - 1.41: 3657 1.41 - 1.48: 5125 1.48 - 1.55: 4987 Bond restraints: 20193 Sorted by residual: bond pdb=" CA HIS C 478 " pdb=" C HIS C 478 " ideal model delta sigma weight residual 1.531 1.472 0.059 1.15e-02 7.56e+03 2.62e+01 bond pdb=" CA VAL F 312 " pdb=" C VAL F 312 " ideal model delta sigma weight residual 1.528 1.485 0.042 8.50e-03 1.38e+04 2.49e+01 bond pdb=" CA GLY F 11 " pdb=" C GLY F 11 " ideal model delta sigma weight residual 1.514 1.471 0.042 8.60e-03 1.35e+04 2.43e+01 bond pdb=" CA HIS E 24 " pdb=" C HIS E 24 " ideal model delta sigma weight residual 1.522 1.466 0.056 1.18e-02 7.18e+03 2.29e+01 bond pdb=" CA ALA C 157 " pdb=" C ALA C 157 " ideal model delta sigma weight residual 1.521 1.474 0.046 9.90e-03 1.02e+04 2.20e+01 ... (remaining 20188 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.15: 21666 3.15 - 6.30: 2968 6.30 - 9.45: 477 9.45 - 12.60: 65 12.60 - 15.75: 6 Bond angle restraints: 25182 Sorted by residual: angle pdb=" C ASN G 204 " pdb=" N VAL G 205 " pdb=" CA VAL G 205 " ideal model delta sigma weight residual 120.24 126.99 -6.75 6.30e-01 2.52e+00 1.15e+02 angle pdb=" N GLN A 398 " pdb=" CA GLN A 398 " pdb=" C GLN A 398 " ideal model delta sigma weight residual 113.41 101.25 12.16 1.22e+00 6.72e-01 9.94e+01 angle pdb=" N VAL W 9 " pdb=" CA VAL W 9 " pdb=" C VAL W 9 " ideal model delta sigma weight residual 112.90 103.87 9.03 9.60e-01 1.09e+00 8.85e+01 angle pdb=" N GLY A 31 " pdb=" CA GLY A 31 " pdb=" C GLY A 31 " ideal model delta sigma weight residual 111.14 97.41 13.73 1.46e+00 4.69e-01 8.84e+01 angle pdb=" CA PRO E 225 " pdb=" C PRO E 225 " pdb=" O PRO E 225 " ideal model delta sigma weight residual 120.90 114.25 6.65 7.20e-01 1.93e+00 8.53e+01 ... (remaining 25177 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.11: 4993 22.11 - 44.21: 28 44.21 - 66.31: 2 66.31 - 88.41: 1 88.41 - 110.52: 1 Dihedral angle restraints: 5025 sinusoidal: 5 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 -69.48 -110.52 0 5.00e+00 4.00e-02 4.89e+02 dihedral pdb=" CA ASN 7 40 " pdb=" C ASN 7 40 " pdb=" N PRO 7 41 " pdb=" CA PRO 7 41 " ideal model delta harmonic sigma weight residual -180.00 -137.53 -42.47 0 5.00e+00 4.00e-02 7.22e+01 dihedral pdb=" CA ASN 6 40 " pdb=" C ASN 6 40 " pdb=" N PRO 6 41 " pdb=" CA PRO 6 41 " ideal model delta harmonic sigma weight residual 180.00 -138.44 -41.56 0 5.00e+00 4.00e-02 6.91e+01 ... (remaining 5022 not shown) Chirality restraints: 0 Planarity restraints: 5025 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN B 193 " -0.020 2.00e-02 2.50e+03 4.03e-02 1.63e+01 pdb=" C ASN B 193 " 0.070 2.00e-02 2.50e+03 pdb=" O ASN B 193 " -0.027 2.00e-02 2.50e+03 pdb=" N GLY B 194 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 32 " -0.020 2.00e-02 2.50e+03 3.98e-02 1.59e+01 pdb=" C ARG A 32 " 0.069 2.00e-02 2.50e+03 pdb=" O ARG A 32 " -0.026 2.00e-02 2.50e+03 pdb=" N VAL A 33 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS C 265 " -0.019 2.00e-02 2.50e+03 3.74e-02 1.40e+01 pdb=" C HIS C 265 " 0.065 2.00e-02 2.50e+03 pdb=" O HIS C 265 " -0.025 2.00e-02 2.50e+03 pdb=" N ALA C 266 " -0.021 2.00e-02 2.50e+03 ... (remaining 5022 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 8002 2.83 - 3.35: 17513 3.35 - 3.87: 27340 3.87 - 4.38: 27591 4.38 - 4.90: 41792 Nonbonded interactions: 122238 Sorted by model distance: nonbonded pdb=" N GLY A 31 " pdb=" O GLY A 31 " model vdw 2.314 2.496 nonbonded pdb=" N PRO X 33 " pdb=" O PRO X 33 " model vdw 2.370 2.496 nonbonded pdb=" N LEU E 252 " pdb=" O LEU E 252 " model vdw 2.373 2.496 nonbonded pdb=" N VAL A 61 " pdb=" O VAL A 61 " model vdw 2.387 2.496 nonbonded pdb=" N THR D 305 " pdb=" O THR D 305 " model vdw 2.392 2.496 ... (remaining 122233 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain '0' and resid 2 through 73) selection = (chain '1' and resid 2 through 73) selection = (chain '2' and resid 2 through 73) selection = (chain '3' and resid 2 through 73) selection = (chain '4' and resid 2 through 73) selection = (chain '5' and resid 2 through 73) selection = (chain '6' and resid 2 through 73) selection = (chain '7' and resid 2 through 73) selection = (chain '8' and resid 2 through 73) selection = (chain '9' and resid 2 through 73) } ncs_group { reference = (chain 'A' and resid 12 through 509) selection = (chain 'B' and (resid 12 through 407 or resid 410 through 509)) selection = chain 'C' } ncs_group { reference = chain 'D' selection = (chain 'E' and resid 8 through 475) selection = (chain 'F' and resid 8 through 475) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.120 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: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 21.510 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6563 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 20193 Z= 1.506 Angle : 2.227 15.755 25182 Z= 1.597 Chirality : 0.000 0.000 0 Planarity : 0.010 0.040 5025 Dihedral : 6.740 110.516 5025 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 0.12 Ramachandran Plot: Outliers : 1.38 % Allowed : 4.76 % Favored : 93.86 % 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 : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.54 (0.11), residues: 4984 helix: 0.85 (0.09), residues: 2757 sheet: -1.59 (0.21), residues: 570 loop : -1.93 (0.13), residues: 1657 Details of bonding type rmsd covalent geometry : bond 0.01922 (20193) covalent geometry : angle 2.22717 (25182) hydrogen bonds : bond 0.21011 ( 2318) hydrogen bonds : angle 7.98849 ( 6726) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9968 Ramachandran restraints generated. 4984 Oldfield, 0 Emsley, 4984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9968 Ramachandran restraints generated. 4984 Oldfield, 0 Emsley, 4984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 4114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.514 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.0742 time to fit residues: 12.3802 Evaluate side-chains 82 residues out of total 4114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 432 optimal weight: 5.9990 chunk 197 optimal weight: 7.9990 chunk 388 optimal weight: 6.9990 chunk 455 optimal weight: 9.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 5.9990 chunk 470 optimal weight: 40.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2411 r_free = 0.2411 target = 0.030461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2164 r_free = 0.2164 target = 0.022733 restraints weight = 294638.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2170 r_free = 0.2170 target = 0.022837 restraints weight = 274255.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 17)----------------| | r_work = 0.2173 r_free = 0.2173 target = 0.022892 restraints weight = 255844.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2173 r_free = 0.2173 target = 0.022892 restraints weight = 243385.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.2173 r_free = 0.2173 target = 0.022892 restraints weight = 243379.765| |-----------------------------------------------------------------------------| r_work (final): 0.1989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 20193 Z= 0.177 Angle : 0.538 8.563 25182 Z= 0.333 Chirality : 0.000 0.000 0 Planarity : 0.003 0.022 5025 Dihedral : 5.040 67.812 5025 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 0.54 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 : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.40 (0.12), residues: 4984 helix: 2.45 (0.10), residues: 2801 sheet: -1.16 (0.21), residues: 560 loop : -1.05 (0.15), residues: 1623 Details of bonding type rmsd covalent geometry : bond 0.00237 (20193) covalent geometry : angle 0.53794 (25182) hydrogen bonds : bond 0.04560 ( 2318) hydrogen bonds : angle 4.71485 ( 6726) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9968 Ramachandran restraints generated. 4984 Oldfield, 0 Emsley, 4984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9968 Ramachandran restraints generated. 4984 Oldfield, 0 Emsley, 4984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 4114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.694 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.0804 time to fit residues: 13.6151 Evaluate side-chains 82 residues out of total 4114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 149 optimal weight: 40.0000 chunk 38 optimal weight: 60.0000 chunk 234 optimal weight: 30.0000 chunk 169 optimal weight: 50.0000 chunk 77 optimal weight: 50.0000 chunk 454 optimal weight: 30.0000 chunk 352 optimal weight: 30.0000 chunk 275 optimal weight: 1.9990 chunk 389 optimal weight: 40.0000 chunk 56 optimal weight: 50.0000 chunk 141 optimal weight: 20.0000 overall best weight: 22.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2317 r_free = 0.2317 target = 0.028065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2075 r_free = 0.2075 target = 0.020891 restraints weight = 317225.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2076 r_free = 0.2076 target = 0.020909 restraints weight = 283053.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2077 r_free = 0.2077 target = 0.020932 restraints weight = 262134.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2078 r_free = 0.2078 target = 0.020963 restraints weight = 256947.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2079 r_free = 0.2079 target = 0.020965 restraints weight = 251745.788| |-----------------------------------------------------------------------------| r_work (final): 0.1897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.3798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 20193 Z= 0.427 Angle : 0.899 18.517 25182 Z= 0.570 Chirality : 0.000 0.000 0 Planarity : 0.005 0.021 5025 Dihedral : 6.279 54.351 5025 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.10 % Favored : 93.56 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.96 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.71 (0.12), residues: 4984 helix: 1.80 (0.10), residues: 2781 sheet: -1.23 (0.22), residues: 500 loop : -1.24 (0.15), residues: 1703 Details of bonding type rmsd covalent geometry : bond 0.00576 (20193) covalent geometry : angle 0.89949 (25182) hydrogen bonds : bond 0.06495 ( 2318) hydrogen bonds : angle 6.25557 ( 6726) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9968 Ramachandran restraints generated. 4984 Oldfield, 0 Emsley, 4984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9968 Ramachandran restraints generated. 4984 Oldfield, 0 Emsley, 4984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 4114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.661 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.0770 time to fit residues: 12.9464 Evaluate side-chains 82 residues out of total 4114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 315 optimal weight: 50.0000 chunk 476 optimal weight: 50.0000 chunk 379 optimal weight: 40.0000 chunk 281 optimal weight: 30.0000 chunk 405 optimal weight: 10.0000 chunk 1 optimal weight: 50.0000 chunk 475 optimal weight: 0.5980 chunk 453 optimal weight: 30.0000 chunk 346 optimal weight: 50.0000 chunk 329 optimal weight: 50.0000 chunk 395 optimal weight: 10.0000 overall best weight: 16.1196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2326 r_free = 0.2326 target = 0.028285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2071 r_free = 0.2071 target = 0.020887 restraints weight = 311506.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.2076 r_free = 0.2076 target = 0.020970 restraints weight = 283002.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2080 r_free = 0.2080 target = 0.021054 restraints weight = 262369.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2080 r_free = 0.2080 target = 0.021054 restraints weight = 250836.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2080 r_free = 0.2080 target = 0.021054 restraints weight = 250836.905| |-----------------------------------------------------------------------------| r_work (final): 0.1902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.4419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 20193 Z= 0.297 Angle : 0.649 13.800 25182 Z= 0.412 Chirality : 0.000 0.000 0 Planarity : 0.003 0.023 5025 Dihedral : 5.431 51.908 5025 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 2.08 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.22 % Favored : 93.52 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.96 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.99 (0.12), residues: 4984 helix: 2.11 (0.10), residues: 2819 sheet: -1.44 (0.24), residues: 458 loop : -1.26 (0.15), residues: 1707 Details of bonding type rmsd covalent geometry : bond 0.00400 (20193) covalent geometry : angle 0.64903 (25182) hydrogen bonds : bond 0.04936 ( 2318) hydrogen bonds : angle 5.44065 ( 6726) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9968 Ramachandran restraints generated. 4984 Oldfield, 0 Emsley, 4984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9968 Ramachandran restraints generated. 4984 Oldfield, 0 Emsley, 4984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 4114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.807 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.0765 time to fit residues: 12.9541 Evaluate side-chains 82 residues out of total 4114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 442 optimal weight: 50.0000 chunk 310 optimal weight: 20.0000 chunk 251 optimal weight: 50.0000 chunk 286 optimal weight: 20.0000 chunk 109 optimal weight: 30.0000 chunk 441 optimal weight: 40.0000 chunk 111 optimal weight: 30.0000 chunk 49 optimal weight: 40.0000 chunk 39 optimal weight: 50.0000 chunk 408 optimal weight: 30.0000 chunk 137 optimal weight: 50.0000 overall best weight: 26.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2294 r_free = 0.2294 target = 0.027465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2044 r_free = 0.2044 target = 0.020390 restraints weight = 324229.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 18)----------------| | r_work = 0.2050 r_free = 0.2050 target = 0.020503 restraints weight = 293403.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2055 r_free = 0.2055 target = 0.020589 restraints weight = 266718.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2056 r_free = 0.2056 target = 0.020608 restraints weight = 249915.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.2057 r_free = 0.2057 target = 0.020610 restraints weight = 245270.854| |-----------------------------------------------------------------------------| r_work (final): 0.1877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.5604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 20193 Z= 0.449 Angle : 0.899 19.019 25182 Z= 0.573 Chirality : 0.000 0.000 0 Planarity : 0.005 0.027 5025 Dihedral : 6.712 48.207 5025 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.28 % Allowed : 9.37 % Favored : 90.35 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.96 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.51 (0.12), residues: 4984 helix: 0.87 (0.09), residues: 2787 sheet: -2.02 (0.25), residues: 405 loop : -1.84 (0.15), residues: 1792 Details of bonding type rmsd covalent geometry : bond 0.00601 (20193) covalent geometry : angle 0.89927 (25182) hydrogen bonds : bond 0.06953 ( 2318) hydrogen bonds : angle 7.14630 ( 6726) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9968 Ramachandran restraints generated. 4984 Oldfield, 0 Emsley, 4984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9968 Ramachandran restraints generated. 4984 Oldfield, 0 Emsley, 4984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 4114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.795 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.0811 time to fit residues: 13.5832 Evaluate side-chains 82 residues out of total 4114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 444 optimal weight: 50.0000 chunk 414 optimal weight: 7.9990 chunk 357 optimal weight: 30.0000 chunk 375 optimal weight: 30.0000 chunk 62 optimal weight: 7.9990 chunk 373 optimal weight: 6.9990 chunk 99 optimal weight: 7.9990 chunk 82 optimal weight: 40.0000 chunk 312 optimal weight: 7.9990 chunk 1 optimal weight: 50.0000 chunk 377 optimal weight: 5.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2405 r_free = 0.2405 target = 0.029218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2125 r_free = 0.2125 target = 0.021745 restraints weight = 297872.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.2132 r_free = 0.2132 target = 0.021849 restraints weight = 277507.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2138 r_free = 0.2138 target = 0.021948 restraints weight = 251920.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2140 r_free = 0.2140 target = 0.021989 restraints weight = 240942.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.2142 r_free = 0.2142 target = 0.022026 restraints weight = 232537.045| |-----------------------------------------------------------------------------| r_work (final): 0.2113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.5404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 20193 Z= 0.161 Angle : 0.464 12.745 25182 Z= 0.290 Chirality : 0.000 0.000 0 Planarity : 0.002 0.017 5025 Dihedral : 4.979 58.015 5025 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 1.23 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.90 % Favored : 93.86 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.96 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.98 (0.13), residues: 4984 helix: 2.25 (0.10), residues: 2835 sheet: -1.98 (0.24), residues: 436 loop : -1.44 (0.16), residues: 1713 Details of bonding type rmsd covalent geometry : bond 0.00214 (20193) covalent geometry : angle 0.46379 (25182) hydrogen bonds : bond 0.04050 ( 2318) hydrogen bonds : angle 5.12303 ( 6726) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9968 Ramachandran restraints generated. 4984 Oldfield, 0 Emsley, 4984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9968 Ramachandran restraints generated. 4984 Oldfield, 0 Emsley, 4984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 4114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.809 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.0769 time to fit residues: 13.0353 Evaluate side-chains 82 residues out of total 4114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 111 optimal weight: 30.0000 chunk 134 optimal weight: 10.0000 chunk 31 optimal weight: 50.0000 chunk 430 optimal weight: 50.0000 chunk 267 optimal weight: 50.0000 chunk 65 optimal weight: 120.0000 chunk 478 optimal weight: 90.0000 chunk 197 optimal weight: 7.9990 chunk 27 optimal weight: 9.9990 chunk 448 optimal weight: 120.0000 chunk 488 optimal weight: 50.0000 overall best weight: 21.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2296 r_free = 0.2296 target = 0.027504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2049 r_free = 0.2049 target = 0.020448 restraints weight = 321106.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2050 r_free = 0.2050 target = 0.020464 restraints weight = 292639.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2057 r_free = 0.2057 target = 0.020586 restraints weight = 280741.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2061 r_free = 0.2061 target = 0.020691 restraints weight = 255223.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.2061 r_free = 0.2061 target = 0.020687 restraints weight = 236470.167| |-----------------------------------------------------------------------------| r_work (final): 0.1882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.5993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 20193 Z= 0.377 Angle : 0.728 13.795 25182 Z= 0.472 Chirality : 0.000 0.000 0 Planarity : 0.004 0.021 5025 Dihedral : 5.859 50.221 5025 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.26 % Allowed : 10.17 % Favored : 89.57 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.96 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.17 (0.12), residues: 4984 helix: 1.60 (0.10), residues: 2812 sheet: -2.23 (0.25), residues: 409 loop : -1.80 (0.15), residues: 1763 Details of bonding type rmsd covalent geometry : bond 0.00507 (20193) covalent geometry : angle 0.72765 (25182) hydrogen bonds : bond 0.05965 ( 2318) hydrogen bonds : angle 6.40129 ( 6726) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9968 Ramachandran restraints generated. 4984 Oldfield, 0 Emsley, 4984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9968 Ramachandran restraints generated. 4984 Oldfield, 0 Emsley, 4984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 4114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.768 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.0766 time to fit residues: 13.0118 Evaluate side-chains 82 residues out of total 4114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 288 optimal weight: 50.0000 chunk 319 optimal weight: 30.0000 chunk 376 optimal weight: 50.0000 chunk 420 optimal weight: 40.0000 chunk 213 optimal weight: 30.0000 chunk 348 optimal weight: 50.0000 chunk 272 optimal weight: 30.0000 chunk 359 optimal weight: 40.0000 chunk 90 optimal weight: 30.0000 chunk 64 optimal weight: 30.0000 chunk 491 optimal weight: 40.0000 overall best weight: 30.0000 ------------------------------------------------------------------------------- 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 = 0.2280 r_free = 0.2280 target = 0.027080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2043 r_free = 0.2043 target = 0.020270 restraints weight = 329051.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.2051 r_free = 0.2051 target = 0.020395 restraints weight = 294063.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2049 r_free = 0.2049 target = 0.020430 restraints weight = 255134.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2051 r_free = 0.2051 target = 0.020453 restraints weight = 253191.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2053 r_free = 0.2053 target = 0.020478 restraints weight = 242007.565| |-----------------------------------------------------------------------------| r_work (final): 0.1876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.6762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.095 20193 Z= 0.505 Angle : 0.918 16.776 25182 Z= 0.599 Chirality : 0.000 0.000 0 Planarity : 0.006 0.027 5025 Dihedral : 6.832 57.855 5025 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.26 % Allowed : 12.46 % Favored : 87.28 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.96 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.32 (0.12), residues: 4984 helix: 0.22 (0.09), residues: 2766 sheet: -2.39 (0.26), residues: 356 loop : -2.21 (0.14), residues: 1862 Details of bonding type rmsd covalent geometry : bond 0.00680 (20193) covalent geometry : angle 0.91777 (25182) hydrogen bonds : bond 0.07521 ( 2318) hydrogen bonds : angle 7.72193 ( 6726) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9968 Ramachandran restraints generated. 4984 Oldfield, 0 Emsley, 4984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9968 Ramachandran restraints generated. 4984 Oldfield, 0 Emsley, 4984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 4114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.796 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.0782 time to fit residues: 13.2394 Evaluate side-chains 82 residues out of total 4114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 11 optimal weight: 20.0000 chunk 21 optimal weight: 70.0000 chunk 427 optimal weight: 50.0000 chunk 214 optimal weight: 30.0000 chunk 453 optimal weight: 20.0000 chunk 273 optimal weight: 0.0370 chunk 166 optimal weight: 50.0000 chunk 213 optimal weight: 0.0050 chunk 141 optimal weight: 20.0000 chunk 457 optimal weight: 40.0000 chunk 438 optimal weight: 30.0000 overall best weight: 12.0084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2311 r_free = 0.2311 target = 0.027824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2059 r_free = 0.2059 target = 0.020634 restraints weight = 314902.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 19)----------------| | r_work = 0.2065 r_free = 0.2065 target = 0.020733 restraints weight = 291159.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2065 r_free = 0.2065 target = 0.020733 restraints weight = 265106.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2065 r_free = 0.2065 target = 0.020733 restraints weight = 264969.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2065 r_free = 0.2065 target = 0.020733 restraints weight = 264969.897| |-----------------------------------------------------------------------------| r_work (final): 0.1882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.6597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 20193 Z= 0.222 Angle : 0.543 13.320 25182 Z= 0.344 Chirality : 0.000 0.000 0 Planarity : 0.003 0.021 5025 Dihedral : 5.546 55.423 5025 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.26 % Allowed : 9.53 % Favored : 90.21 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.96 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.04 (0.12), residues: 4984 helix: 1.44 (0.10), residues: 2833 sheet: -2.44 (0.25), residues: 391 loop : -1.92 (0.15), residues: 1760 Details of bonding type rmsd covalent geometry : bond 0.00299 (20193) covalent geometry : angle 0.54262 (25182) hydrogen bonds : bond 0.04672 ( 2318) hydrogen bonds : angle 5.98489 ( 6726) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9968 Ramachandran restraints generated. 4984 Oldfield, 0 Emsley, 4984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9968 Ramachandran restraints generated. 4984 Oldfield, 0 Emsley, 4984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 4114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.831 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.0858 time to fit residues: 14.2856 Evaluate side-chains 82 residues out of total 4114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 228 optimal weight: 50.0000 chunk 291 optimal weight: 3.9990 chunk 391 optimal weight: 20.0000 chunk 427 optimal weight: 50.0000 chunk 410 optimal weight: 40.0000 chunk 414 optimal weight: 20.0000 chunk 318 optimal weight: 0.6980 chunk 306 optimal weight: 50.0000 chunk 23 optimal weight: 120.0000 chunk 6 optimal weight: 50.0000 chunk 203 optimal weight: 6.9990 overall best weight: 10.3392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2316 r_free = 0.2316 target = 0.028042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2071 r_free = 0.2071 target = 0.020868 restraints weight = 315281.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2078 r_free = 0.2078 target = 0.020967 restraints weight = 282114.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2078 r_free = 0.2078 target = 0.021030 restraints weight = 253096.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2081 r_free = 0.2081 target = 0.021061 restraints weight = 246321.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2081 r_free = 0.2081 target = 0.021064 restraints weight = 236826.788| |-----------------------------------------------------------------------------| r_work (final): 0.1897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.6663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 20193 Z= 0.197 Angle : 0.476 12.727 25182 Z= 0.302 Chirality : 0.000 0.000 0 Planarity : 0.002 0.018 5025 Dihedral : 4.814 48.313 5025 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 2.23 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.87 % Favored : 90.89 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.96 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.94 (0.13), residues: 4984 helix: 2.34 (0.10), residues: 2838 sheet: -2.35 (0.25), residues: 401 loop : -1.64 (0.16), residues: 1745 Details of bonding type rmsd covalent geometry : bond 0.00266 (20193) covalent geometry : angle 0.47589 (25182) hydrogen bonds : bond 0.04064 ( 2318) hydrogen bonds : angle 5.20691 ( 6726) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9968 Ramachandran restraints generated. 4984 Oldfield, 0 Emsley, 4984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9968 Ramachandran restraints generated. 4984 Oldfield, 0 Emsley, 4984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 4114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.753 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.0774 time to fit residues: 13.1362 Evaluate side-chains 82 residues out of total 4114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 369 optimal weight: 40.0000 chunk 30 optimal weight: 110.0000 chunk 356 optimal weight: 50.0000 chunk 252 optimal weight: 5.9990 chunk 460 optimal weight: 20.0000 chunk 77 optimal weight: 50.0000 chunk 396 optimal weight: 2.9990 chunk 206 optimal weight: 0.6980 chunk 141 optimal weight: 30.0000 chunk 142 optimal weight: 6.9990 chunk 147 optimal weight: 0.5980 overall best weight: 3.4586 ------------------------------------------------------------------------------- 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 = 0.2419 r_free = 0.2419 target = 0.029531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2149 r_free = 0.2149 target = 0.022178 restraints weight = 298665.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2150 r_free = 0.2150 target = 0.022257 restraints weight = 270897.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2150 r_free = 0.2150 target = 0.022268 restraints weight = 249879.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2151 r_free = 0.2151 target = 0.022286 restraints weight = 244789.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2151 r_free = 0.2151 target = 0.022286 restraints weight = 239045.606| |-----------------------------------------------------------------------------| r_work (final): 0.2116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.6593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.017 20193 Z= 0.096 Angle : 0.337 9.196 25182 Z= 0.211 Chirality : 0.000 0.000 0 Planarity : 0.002 0.015 5025 Dihedral : 4.042 47.886 5025 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 0.54 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.36 % Favored : 94.42 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.96 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.86 (0.13), residues: 4984 helix: 3.11 (0.10), residues: 2862 sheet: -2.21 (0.25), residues: 417 loop : -1.27 (0.16), residues: 1705 Details of bonding type rmsd covalent geometry : bond 0.00125 (20193) covalent geometry : angle 0.33659 (25182) hydrogen bonds : bond 0.03103 ( 2318) hydrogen bonds : angle 4.22926 ( 6726) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2124.68 seconds wall clock time: 37 minutes 4.79 seconds (2224.79 seconds total)