Starting phenix.real_space_refine on Tue Jun 17 10:43:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tkh_25969/06_2025/7tkh_25969.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tkh_25969/06_2025/7tkh_25969.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7tkh_25969/06_2025/7tkh_25969.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tkh_25969/06_2025/7tkh_25969.map" model { file = "/net/cci-nas-00/data/ceres_data/7tkh_25969/06_2025/7tkh_25969.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tkh_25969/06_2025/7tkh_25969.cif" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.119 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 3 Type Number sf(0) Gaussians C 10112 2.51 5 N 5056 2.21 5 O 5060 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 20228 Number of models: 1 Model: "" Number of chains: 27 Chain: "0" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 300 Classifications: {'peptide': 75} Incomplete info: {'backbone_only': 65} Link IDs: {'PTRANS': 2, 'TRANS': 72} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 246 Unresolved non-hydrogen angles: 363 Unresolved non-hydrogen dihedrals: 146 Unresolved non-hydrogen chiralities: 94 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1, 'PHE:plan': 6, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 75 Chain: "1" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 300 Classifications: {'peptide': 75} Incomplete info: {'backbone_only': 65} Link IDs: {'PTRANS': 2, 'TRANS': 72} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 246 Unresolved non-hydrogen angles: 363 Unresolved non-hydrogen dihedrals: 146 Unresolved non-hydrogen chiralities: 94 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1, 'PHE:plan': 6, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 75 Chain: "2" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 300 Classifications: {'peptide': 75} Incomplete info: {'backbone_only': 65} Link IDs: {'PTRANS': 2, 'TRANS': 72} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 246 Unresolved non-hydrogen angles: 363 Unresolved non-hydrogen dihedrals: 146 Unresolved non-hydrogen chiralities: 94 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1, 'PHE:plan': 6, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 75 Chain: "3" Number of atoms: 296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 296 Classifications: {'peptide': 74} Incomplete info: {'backbone_only': 64} Link IDs: {'PTRANS': 2, 'TRANS': 71} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 242 Unresolved non-hydrogen angles: 358 Unresolved non-hydrogen dihedrals: 143 Unresolved non-hydrogen chiralities: 93 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1, 'PHE:plan': 6, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 75 Chain: "4" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 300 Classifications: {'peptide': 75} Incomplete info: {'backbone_only': 65} Link IDs: {'PTRANS': 2, 'TRANS': 72} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 246 Unresolved non-hydrogen angles: 363 Unresolved non-hydrogen dihedrals: 146 Unresolved non-hydrogen chiralities: 94 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1, 'PHE:plan': 6, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 75 Chain: "5" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 300 Classifications: {'peptide': 75} Incomplete info: {'backbone_only': 65} Link IDs: {'PTRANS': 2, 'TRANS': 72} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 246 Unresolved non-hydrogen angles: 363 Unresolved non-hydrogen dihedrals: 146 Unresolved non-hydrogen chiralities: 94 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1, 'PHE:plan': 6, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 75 Chain: "6" Number of atoms: 296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 296 Classifications: {'peptide': 74} Incomplete info: {'backbone_only': 64} Link IDs: {'PTRANS': 2, 'TRANS': 71} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 242 Unresolved non-hydrogen angles: 358 Unresolved non-hydrogen dihedrals: 143 Unresolved non-hydrogen chiralities: 93 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1, 'PHE:plan': 6, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 75 Chain: "7" Number of atoms: 292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 292 Classifications: {'peptide': 73} Incomplete info: {'backbone_only': 64} Link IDs: {'PTRANS': 2, 'TRANS': 70} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 238 Unresolved non-hydrogen angles: 352 Unresolved non-hydrogen dihedrals: 139 Unresolved non-hydrogen chiralities: 93 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1, 'PHE:plan': 5, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 68 Chain: "8" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 300 Classifications: {'peptide': 75} Incomplete info: {'backbone_only': 65} Link IDs: {'PTRANS': 2, 'TRANS': 72} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 246 Unresolved non-hydrogen angles: 363 Unresolved non-hydrogen dihedrals: 146 Unresolved non-hydrogen chiralities: 94 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1, 'PHE:plan': 6, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 75 Chain: "9" Number of atoms: 296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 296 Classifications: {'peptide': 74} Incomplete info: {'backbone_only': 64} Link IDs: {'PTRANS': 2, 'TRANS': 71} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 242 Unresolved non-hydrogen angles: 358 Unresolved non-hydrogen dihedrals: 143 Unresolved non-hydrogen chiralities: 93 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1, 'PHE:plan': 6, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 75 Chain: "A" Number of atoms: 2004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 501, 2004 Classifications: {'peptide': 501} Incomplete info: {'backbone_only': 454} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 18, 'TRANS': 480} Unresolved chain link angles: 19 Unresolved non-hydrogen bonds: 1862 Unresolved non-hydrogen angles: 2709 Unresolved non-hydrogen dihedrals: 1130 Unresolved non-hydrogen chiralities: 607 Planarities with less than four sites: {'GLN:plan1': 25, 'HIS:plan': 6, 'TYR:plan': 14, 'ASN:plan1': 17, 'TRP:plan': 2, 'ASP:plan': 21, 'PHE:plan': 14, 'GLU:plan': 37, 'ARG:plan': 29} Unresolved non-hydrogen planarities: 811 Chain: "B" Number of atoms: 2020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 505, 2020 Classifications: {'peptide': 505} Incomplete info: {'backbone_only': 459} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 483} Chain breaks: 1 Unresolved chain link angles: 20 Unresolved non-hydrogen bonds: 1875 Unresolved non-hydrogen angles: 2729 Unresolved non-hydrogen dihedrals: 1135 Unresolved non-hydrogen chiralities: 614 Planarities with less than four sites: {'GLN:plan1': 26, 'HIS:plan': 6, 'TYR:plan': 14, 'ASN:plan1': 17, 'TRP:plan': 2, 'ASP:plan': 21, 'PHE:plan': 13, 'GLU:plan': 37, 'ARG:plan': 29} Unresolved non-hydrogen planarities: 808 Chain: "C" Number of atoms: 1984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 1984 Classifications: {'peptide': 496} Incomplete info: {'backbone_only': 450} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 18, 'TRANS': 475} Chain breaks: 1 Unresolved chain link angles: 19 Unresolved non-hydrogen bonds: 1844 Unresolved non-hydrogen angles: 2683 Unresolved non-hydrogen dihedrals: 1118 Unresolved non-hydrogen chiralities: 602 Planarities with less than four sites: {'GLN:plan1': 25, 'HIS:plan': 6, 'TYR:plan': 14, 'ASN:plan1': 17, 'TRP:plan': 2, 'ASP:plan': 21, 'PHE:plan': 13, 'GLU:plan': 36, 'ARG:plan': 29} Unresolved non-hydrogen planarities: 800 Chain: "D" Number of atoms: 1876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 1876 Classifications: {'peptide': 469} Incomplete info: {'backbone_only': 423} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 444} Unresolved chain link angles: 23 Unresolved non-hydrogen bonds: 1724 Unresolved non-hydrogen angles: 2516 Unresolved non-hydrogen dihedrals: 1033 Unresolved non-hydrogen chiralities: 579 Planarities with less than four sites: {'GLN:plan1': 18, 'ARG:plan': 22, 'TYR:plan': 10, 'ASN:plan1': 10, 'HIS:plan': 7, 'PHE:plan': 17, 'GLU:plan': 37, 'ASP:plan': 25} Unresolved non-hydrogen planarities: 711 Chain: "E" Number of atoms: 1880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 1880 Classifications: {'peptide': 470} Incomplete info: {'backbone_only': 424} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 446} Unresolved chain link angles: 23 Unresolved non-hydrogen bonds: 1726 Unresolved non-hydrogen angles: 2519 Unresolved non-hydrogen dihedrals: 1034 Unresolved non-hydrogen chiralities: 580 Planarities with less than four sites: {'GLN:plan1': 18, 'ARG:plan': 22, 'TYR:plan': 10, 'ASN:plan1': 10, 'HIS:plan': 7, 'PHE:plan': 17, 'GLU:plan': 37, 'ASP:plan': 25} Unresolved non-hydrogen planarities: 711 Chain: "F" Number of atoms: 1872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 1872 Classifications: {'peptide': 468} Incomplete info: {'backbone_only': 422} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 445} Unresolved chain link angles: 22 Unresolved non-hydrogen bonds: 1721 Unresolved non-hydrogen angles: 2511 Unresolved non-hydrogen dihedrals: 1032 Unresolved non-hydrogen chiralities: 577 Planarities with less than four sites: {'GLN:plan1': 18, 'ARG:plan': 22, 'TYR:plan': 10, 'ASN:plan1': 10, 'HIS:plan': 7, 'PHE:plan': 17, 'GLU:plan': 37, 'ASP:plan': 25} Unresolved non-hydrogen planarities: 711 Chain: "G" Number of atoms: 1060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 1060 Classifications: {'peptide': 265} Incomplete info: {'backbone_only': 255} Link IDs: {'PTRANS': 9, 'TRANS': 255} Chain breaks: 1 Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 1024 Unresolved non-hydrogen angles: 1472 Unresolved non-hydrogen dihedrals: 628 Unresolved non-hydrogen chiralities: 328 Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 3, 'TYR:plan': 7, 'ASN:plan1': 18, 'ASP:plan': 14, 'PHE:plan': 8, 'GLU:plan': 16, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 413 Chain: "H" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 480 Classifications: {'peptide': 120} Incomplete info: {'backbone_only': 114} Link IDs: {'PTRANS': 6, 'TRANS': 113} Chain breaks: 4 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 439 Unresolved non-hydrogen angles: 643 Unresolved non-hydrogen dihedrals: 258 Unresolved non-hydrogen chiralities: 151 Planarities with less than four sites: {'GLN:plan1': 7, 'ASP:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 7, 'HIS:plan': 2, 'PHE:plan': 5, 'GLU:plan': 13, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 177 Chain: "I" Number of atoms: 193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 193 Classifications: {'peptide': 48} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 47} Link IDs: {'PTRANS': 2, 'TRANS': 45} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 188 Unresolved non-hydrogen angles: 278 Unresolved non-hydrogen dihedrals: 114 Unresolved non-hydrogen chiralities: 62 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 4, 'ASN:plan1': 3, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 89 Chain: "O" Number of atoms: 748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 748 Classifications: {'peptide': 187} Incomplete info: {'backbone_only': 174} Link IDs: {'PTRANS': 7, 'TRANS': 179} Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 691 Unresolved non-hydrogen angles: 1001 Unresolved non-hydrogen dihedrals: 414 Unresolved non-hydrogen chiralities: 235 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 3, 'TYR:plan': 3, 'ASN:plan1': 12, 'ASP:plan': 10, 'PHE:plan': 5, 'GLU:plan': 11, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 249 Chain: "T" Number of atoms: 897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 897 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 207} Link IDs: {'PTRANS': 7, 'TRANS': 216} Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 925 Unresolved non-hydrogen angles: 1359 Unresolved non-hydrogen dihedrals: 607 Unresolved non-hydrogen chiralities: 306 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 3, 'TYR:plan': 10, 'ASN:plan1': 11, 'TRP:plan': 5, 'ASP:plan': 2, 'PHE:plan': 18, 'GLU:plan': 3, 'ARG:plan': 3, 'HIS%COO:plan': 1} Unresolved non-hydrogen planarities: 371 Chain: "U" Number of atoms: 620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 620 Classifications: {'peptide': 155} Incomplete info: {'backbone_only': 152} Link IDs: {'PTRANS': 2, 'TRANS': 152} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 631 Unresolved non-hydrogen angles: 908 Unresolved non-hydrogen dihedrals: 388 Unresolved non-hydrogen chiralities: 198 Planarities with less than four sites: {'GLN:plan1': 11, 'HIS:plan': 2, 'TYR:plan': 3, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 8, 'PHE:plan': 6, 'GLU:plan': 16, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 283 Chain: "V" Number of atoms: 685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 685 Classifications: {'peptide': 171} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 166} Link IDs: {'PTRANS': 5, 'TRANS': 165} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 705 Unresolved non-hydrogen angles: 1009 Unresolved non-hydrogen dihedrals: 446 Unresolved non-hydrogen chiralities: 214 Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 2, 'TYR:plan': 4, 'ASN:plan1': 7, 'TRP:plan': 2, 'ASP:plan': 13, 'PHE:plan': 5, 'GLU:plan': 13, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 302 Chain: "W" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 340 Classifications: {'peptide': 85} Incomplete info: {'backbone_only': 79} Link IDs: {'PTRANS': 7, 'TRANS': 77} Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 348 Unresolved non-hydrogen angles: 503 Unresolved non-hydrogen dihedrals: 241 Unresolved non-hydrogen chiralities: 97 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 2, 'TYR:plan': 6, 'ASN:plan1': 5, 'TRP:plan': 1, 'HIS:plan': 3, 'PHE:plan': 5, 'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 162 Chain: "X" Number of atoms: 248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 248 Classifications: {'peptide': 62} Incomplete info: {'backbone_only': 60} Link IDs: {'PTRANS': 7, 'TRANS': 54} Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 257 Unresolved non-hydrogen angles: 375 Unresolved non-hydrogen dihedrals: 161 Unresolved non-hydrogen chiralities: 77 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 3, 'GLU:plan': 7, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 117 Chain: "Y" Number of atoms: 148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 148 Classifications: {'peptide': 37} Incomplete info: {'backbone_only': 35} Link IDs: {'PTRANS': 3, 'TRANS': 33} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 155 Unresolved non-hydrogen angles: 225 Unresolved non-hydrogen dihedrals: 110 Unresolved non-hydrogen chiralities: 44 Planarities with less than four sites: {'TYR:plan': 3, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 68 Chain: "Z" Number of atoms: 193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 193 Classifications: {'peptide': 48} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 46} Link IDs: {'PTRANS': 3, 'TRANS': 44} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 231 Unresolved non-hydrogen angles: 330 Unresolved non-hydrogen dihedrals: 158 Unresolved non-hydrogen chiralities: 67 Planarities with less than four sites: {'GLN:plan1': 3, 'PHE:plan': 7, 'ASN:plan1': 1, 'ARG:plan': 2, 'TYR:plan': 3} Unresolved non-hydrogen planarities: 99 Time building chain proxies: 14.28, per 1000 atoms: 0.71 Number of scatterers: 20228 At special positions: 0 Unit cell: (132.055, 148.225, 234.465, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 5060 8.00 N 5056 7.00 C 10112 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.73 Conformation dependent library (CDL) restraints added in 4.5 seconds 9968 Ramachandran restraints generated. 4984 Oldfield, 0 Emsley, 4984 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 0 Finding SS restraints... Secondary structure from input PDB file: 207 helices and 26 sheets defined 60.5% alpha, 11.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.49 Creating SS restraints... Processing helix chain '0' and resid 1 through 17 removed outlier: 3.559A pdb=" N GLY 0 13 " --> pdb=" O TYR 0 9 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ILE 0 17 " --> pdb=" O GLY 0 13 " (cutoff:3.500A) Processing helix chain '0' and resid 18 through 40 removed outlier: 4.285A pdb=" N ALA 0 22 " --> pdb=" O GLY 0 18 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ALA 0 27 " --> pdb=" O GLY 0 23 " (cutoff:3.500A) Processing helix chain '0' and resid 43 through 74 Proline residue: 0 49 - end of helix removed outlier: 3.504A pdb=" N THR 0 61 " --> pdb=" O LEU 0 57 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLY 0 62 " --> pdb=" O SER 0 58 " (cutoff:3.500A) Processing helix chain '1' and resid 2 through 17 removed outlier: 3.782A pdb=" N GLY 1 13 " --> pdb=" O TYR 1 9 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE 1 17 " --> pdb=" O GLY 1 13 " (cutoff:3.500A) Processing helix chain '1' and resid 18 through 40 removed outlier: 4.284A pdb=" N ALA 1 22 " --> pdb=" O GLY 1 18 " (cutoff:3.500A) removed outlier: 3.762A 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: 3.512A pdb=" N THR 1 61 " --> pdb=" O LEU 1 57 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N CYS 1 65 " --> pdb=" O THR 1 61 " (cutoff:3.500A) Processing helix chain '2' and resid 2 through 17 removed outlier: 3.802A pdb=" N ILE 2 17 " --> pdb=" O GLY 2 13 " (cutoff:3.500A) Processing helix chain '2' and resid 18 through 40 removed outlier: 4.298A pdb=" N ALA 2 22 " --> pdb=" O GLY 2 18 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA 2 27 " --> pdb=" O GLY 2 23 " (cutoff:3.500A) Processing helix chain '2' and resid 43 through 75 Proline residue: 2 49 - end of helix removed outlier: 3.935A pdb=" N THR 2 61 " --> pdb=" O LEU 2 57 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N GLY 2 62 " --> pdb=" O SER 2 58 " (cutoff:3.500A) Processing helix chain '3' and resid 3 through 17 removed outlier: 3.974A pdb=" N ILE 3 17 " --> pdb=" O GLY 3 13 " (cutoff:3.500A) Processing helix chain '3' and resid 18 through 40 removed outlier: 4.313A pdb=" N ALA 3 22 " --> pdb=" O GLY 3 18 " (cutoff:3.500A) removed outlier: 4.066A 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: 3.866A pdb=" N GLY 3 62 " --> pdb=" O SER 3 58 " (cutoff:3.500A) Processing helix chain '4' and resid 2 through 16 Processing helix chain '4' and resid 18 through 40 removed outlier: 4.295A pdb=" N ALA 4 22 " --> pdb=" O GLY 4 18 " (cutoff:3.500A) Processing helix chain '4' and resid 43 through 75 Proline residue: 4 49 - end of helix removed outlier: 3.641A pdb=" N THR 4 61 " --> pdb=" O LEU 4 57 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLY 4 62 " --> pdb=" O SER 4 58 " (cutoff:3.500A) Processing helix chain '5' and resid 2 through 17 removed outlier: 3.827A pdb=" N ILE 5 17 " --> pdb=" O GLY 5 13 " (cutoff:3.500A) Processing helix chain '5' and resid 18 through 40 removed outlier: 4.322A pdb=" N ALA 5 22 " --> pdb=" O GLY 5 18 " (cutoff:3.500A) removed outlier: 3.508A 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: 3.673A pdb=" N GLY 5 62 " --> pdb=" O SER 5 58 " (cutoff:3.500A) Processing helix chain '6' and resid 3 through 40 removed outlier: 3.615A pdb=" N THR 6 16 " --> pdb=" O ALA 6 12 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N ILE 6 17 " --> pdb=" O GLY 6 13 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N GLY 6 18 " --> pdb=" O ILE 6 14 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LEU 6 19 " --> pdb=" O SER 6 15 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU 6 20 " --> pdb=" O THR 6 16 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N GLY 6 21 " --> pdb=" O ILE 6 17 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ALA 6 22 " --> pdb=" O GLY 6 18 " (cutoff:3.500A) removed outlier: 3.594A 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: 3.844A pdb=" N THR 6 61 " --> pdb=" O LEU 6 57 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLY 6 62 " --> pdb=" O SER 6 58 " (cutoff:3.500A) Processing helix chain '7' and resid 2 through 40 removed outlier: 4.109A pdb=" N ILE 7 17 " --> pdb=" O GLY 7 13 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLY 7 18 " --> pdb=" O ILE 7 14 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LEU 7 19 " --> pdb=" O SER 7 15 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU 7 20 " --> pdb=" O THR 7 16 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N GLY 7 21 " --> pdb=" O ILE 7 17 " (cutoff:3.500A) removed outlier: 4.163A 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: 3.903A pdb=" N GLY 7 62 " --> pdb=" O SER 7 58 " (cutoff:3.500A) Processing helix chain '8' and resid 2 through 17 removed outlier: 3.870A pdb=" N ILE 8 17 " --> pdb=" O GLY 8 13 " (cutoff:3.500A) Processing helix chain '8' and resid 18 through 40 removed outlier: 4.411A pdb=" N ALA 8 22 " --> pdb=" O GLY 8 18 " (cutoff:3.500A) removed outlier: 3.528A 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: 3.546A pdb=" N THR 8 61 " --> pdb=" O LEU 8 57 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLY 8 62 " --> pdb=" O SER 8 58 " (cutoff:3.500A) Processing helix chain '9' and resid 3 through 17 removed outlier: 3.765A pdb=" N ILE 9 17 " --> pdb=" O GLY 9 13 " (cutoff:3.500A) Processing helix chain '9' and resid 18 through 40 removed outlier: 4.312A 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: 3.521A pdb=" N THR 9 61 " --> pdb=" O LEU 9 57 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLY 9 62 " --> pdb=" O SER 9 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 20 Processing helix chain 'A' and resid 102 through 106 removed outlier: 3.869A pdb=" N LEU A 105 " --> pdb=" O GLY A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 159 Processing helix chain 'A' and resid 176 through 188 removed outlier: 3.831A pdb=" N ALA A 181 " --> pdb=" O LYS A 177 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N THR A 184 " --> pdb=" O VAL A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 194 removed outlier: 3.672A pdb=" N GLY A 194 " --> pdb=" O ARG A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 199 Processing helix chain 'A' and resid 211 through 225 Processing helix chain 'A' and resid 241 through 263 Proline residue: A 249 - end of helix removed outlier: 4.062A pdb=" N PHE A 259 " --> pdb=" O ILE A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 286 Processing helix chain 'A' and resid 292 through 296 Processing helix chain 'A' and resid 299 through 309 Processing helix chain 'A' and resid 332 through 335 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: 4.103A pdb=" N ALA A 379 " --> pdb=" O VAL A 376 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA A 380 " --> pdb=" O GLY A 377 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 376 through 380' Processing helix chain 'A' and resid 382 through 389 Processing helix chain 'A' and resid 391 through 409 removed outlier: 4.106A pdb=" N PHE A 408 " --> pdb=" O ALA A 404 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLY A 409 " --> pdb=" O PHE A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 431 removed outlier: 3.544A pdb=" N LYS A 431 " --> pdb=" O THR A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 442 Processing helix chain 'A' and resid 443 through 452 Processing helix chain 'A' and resid 453 through 458 removed outlier: 3.950A pdb=" N GLY A 457 " --> pdb=" O GLY A 453 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ILE A 458 " --> pdb=" O HIS A 454 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 453 through 458' Processing helix chain 'A' and resid 459 through 461 No H-bonds generated for 'chain 'A' and resid 459 through 461' Processing helix chain 'A' and resid 462 through 477 Processing helix chain 'A' and resid 478 through 489 Processing helix chain 'A' and resid 492 through 506 Processing helix chain 'B' and resid 10 through 19 Processing helix chain 'B' and resid 80 through 84 removed outlier: 3.612A pdb=" N LEU B 83 " --> pdb=" O SER B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 106 removed outlier: 4.074A pdb=" N LEU B 105 " --> pdb=" O GLY B 102 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU B 106 " --> pdb=" O PRO B 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 102 through 106' Processing helix chain 'B' and resid 152 through 159 Processing helix chain 'B' and resid 176 through 194 removed outlier: 3.591A pdb=" N VAL B 180 " --> pdb=" O GLY B 176 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N THR B 184 " --> pdb=" O VAL B 180 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE B 185 " --> pdb=" O ALA B 181 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LYS B 189 " --> pdb=" O ILE B 185 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N ARG B 190 " --> pdb=" O LEU B 186 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N TRP B 191 " --> pdb=" O ASN B 187 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N GLY B 194 " --> pdb=" O ARG B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 200 Processing helix chain 'B' and resid 211 through 225 Processing helix chain 'B' and resid 227 through 231 Processing helix chain 'B' and resid 241 through 262 Proline residue: B 249 - end of helix removed outlier: 3.700A pdb=" N TRP B 258 " --> pdb=" O SER B 254 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N PHE B 259 " --> pdb=" O ILE B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 287 removed outlier: 3.504A pdb=" N VAL B 278 " --> pdb=" O SER B 274 " (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 315 through 319 Processing helix chain 'B' and resid 338 through 348 Processing helix chain 'B' and resid 355 through 361 Processing helix chain 'B' and resid 376 through 380 Processing helix chain 'B' and resid 382 through 388 Processing helix chain 'B' and resid 389 through 402 removed outlier: 3.654A pdb=" N LYS B 393 " --> pdb=" O ALA B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 407 removed outlier: 4.006A pdb=" N GLN B 407 " --> pdb=" O ALA B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 430 Processing helix chain 'B' and resid 439 through 452 Proline residue: B 445 - end of helix Processing helix chain 'B' and resid 453 through 457 removed outlier: 3.912A pdb=" N GLY B 457 " --> pdb=" O HIS B 454 " (cutoff:3.500A) 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 478 Processing helix chain 'B' and resid 478 through 489 Processing helix chain 'B' and resid 492 through 509 Processing helix chain 'C' and resid 13 through 22 Processing helix chain 'C' and resid 80 through 84 Processing helix chain 'C' and resid 102 through 106 removed outlier: 4.070A pdb=" N LEU C 105 " --> pdb=" O GLY C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 159 Processing helix chain 'C' and resid 178 through 188 removed outlier: 3.531A pdb=" N THR C 184 " --> pdb=" O VAL C 180 " (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 227 through 229 No H-bonds generated for 'chain 'C' and resid 227 through 229' Processing helix chain 'C' and resid 241 through 247 Processing helix chain 'C' and resid 247 through 261 removed outlier: 3.848A pdb=" N PHE C 259 " --> pdb=" O ILE C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 287 removed outlier: 3.509A pdb=" N GLN C 276 " --> pdb=" O ASP C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 296 Processing helix chain 'C' and resid 299 through 309 Processing helix chain 'C' and resid 315 through 319 Processing helix chain 'C' and resid 332 through 335 Processing helix chain 'C' and resid 338 through 348 Processing helix chain 'C' and resid 355 through 361 Processing helix chain 'C' and resid 383 through 388 Processing helix chain 'C' and resid 391 through 407 removed outlier: 4.183A pdb=" N GLU C 401 " --> pdb=" O ALA C 397 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLN C 407 " --> pdb=" O ALA C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 431 removed outlier: 3.910A pdb=" N LYS C 431 " --> pdb=" O THR C 427 " (cutoff:3.500A) Processing helix chain 'C' and resid 439 through 452 Proline residue: C 445 - end of helix Processing helix chain 'C' and resid 459 through 461 No H-bonds generated for 'chain 'C' and resid 459 through 461' Processing helix chain 'C' and resid 462 through 479 removed outlier: 3.627A pdb=" N SER C 468 " --> pdb=" O GLY C 464 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASN C 479 " --> pdb=" O LYS C 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 479 through 489 Processing helix chain 'C' and resid 492 through 509 removed outlier: 3.575A pdb=" N THR C 509 " --> pdb=" O SER C 505 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 145 Processing helix chain 'D' and resid 162 through 179 removed outlier: 4.915A pdb=" N LYS D 176 " --> pdb=" O ASN D 172 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ALA D 177 " --> pdb=" O ASN D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 204 Processing helix chain 'D' and resid 225 through 231 removed outlier: 3.738A pdb=" N ARG D 231 " --> pdb=" O GLY D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 245 Processing helix chain 'D' and resid 258 through 273 removed outlier: 3.746A pdb=" N ALA D 270 " --> pdb=" O SER D 266 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LEU D 271 " --> pdb=" O GLU D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 277 through 281 Processing helix chain 'D' and resid 282 through 283 No H-bonds generated for 'chain 'D' and resid 282 through 283' Processing helix chain 'D' and resid 284 through 295 Processing helix chain 'D' and resid 313 through 316 Processing helix chain 'D' and resid 319 through 329 removed outlier: 3.509A pdb=" N ALA D 327 " --> pdb=" O ALA D 323 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N HIS D 328 " --> pdb=" O THR D 324 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU D 329 " --> pdb=" O THR D 325 " (cutoff:3.500A) Processing helix chain 'D' and resid 336 through 342 Processing helix chain 'D' and resid 363 through 384 removed outlier: 4.056A pdb=" N HIS D 367 " --> pdb=" O VAL D 363 " (cutoff:3.500A) Processing helix chain 'D' and resid 384 through 391 Processing helix chain 'D' and resid 392 through 396 Processing helix chain 'D' and resid 397 through 414 Processing helix chain 'D' and resid 421 through 426 Processing helix chain 'D' and resid 433 through 446 Processing helix chain 'D' and resid 453 through 458 removed outlier: 3.629A pdb=" N PHE D 457 " --> pdb=" O PRO D 453 " (cutoff:3.500A) Processing helix chain 'D' and resid 462 through 475 Processing helix chain 'E' and resid 138 through 145 Processing helix chain 'E' and resid 162 through 178 removed outlier: 4.210A pdb=" N LYS E 176 " --> pdb=" O ASN E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 204 Processing helix chain 'E' and resid 225 through 231 removed outlier: 3.588A pdb=" N ARG E 231 " --> pdb=" O GLY E 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 231 through 245 removed outlier: 3.599A pdb=" N THR E 235 " --> pdb=" O ARG E 231 " (cutoff:3.500A) Processing helix chain 'E' and resid 258 through 273 Processing helix chain 'E' and resid 277 through 281 Processing helix chain 'E' and resid 284 through 296 Processing helix chain 'E' and resid 313 through 316 Processing helix chain 'E' and resid 319 through 329 removed outlier: 3.723A pdb=" N ALA E 327 " --> pdb=" O ALA E 323 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N HIS E 328 " --> pdb=" O THR E 324 " (cutoff:3.500A) Processing helix chain 'E' and resid 336 through 342 Processing helix chain 'E' and resid 359 through 364 Processing helix chain 'E' and resid 364 through 391 removed outlier: 4.107A pdb=" N ASP E 386 " --> pdb=" O LYS E 382 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ILE E 387 " --> pdb=" O SER E 383 " (cutoff:3.500A) Processing helix chain 'E' and resid 397 through 414 Processing helix chain 'E' and resid 418 through 422 Processing helix chain 'E' and resid 433 through 447 Processing helix chain 'E' and resid 453 through 457 Processing helix chain 'E' and resid 462 through 475 Processing helix chain 'F' and resid 138 through 145 Processing helix chain 'F' and resid 162 through 178 Processing helix chain 'F' and resid 190 through 204 Processing helix chain 'F' and resid 225 through 248 removed outlier: 4.490A pdb=" N ALA F 233 " --> pdb=" O ARG F 229 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N LEU F 234 " --> pdb=" O ALA F 230 " (cutoff:3.500A) Processing helix chain 'F' and resid 258 through 273 Processing helix chain 'F' and resid 284 through 296 removed outlier: 3.783A pdb=" N ILE F 296 " --> pdb=" O LEU F 292 " (cutoff:3.500A) Processing helix chain 'F' and resid 319 through 329 Processing helix chain 'F' and resid 336 through 341 Processing helix chain 'F' and resid 359 through 364 Processing helix chain 'F' and resid 364 through 392 removed outlier: 3.881A pdb=" N ILE F 387 " --> pdb=" O SER F 383 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ILE F 390 " --> pdb=" O ASP F 386 " (cutoff:3.500A) Processing helix chain 'F' and resid 393 through 396 Processing helix chain 'F' and resid 397 through 415 removed outlier: 3.854A pdb=" N SER F 415 " --> pdb=" O GLN F 411 " (cutoff:3.500A) Processing helix chain 'F' and resid 421 through 426 Processing helix chain 'F' and resid 433 through 446 Processing helix chain 'F' and resid 462 through 475 removed outlier: 3.625A pdb=" N ALA F 468 " --> pdb=" O GLU F 464 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 55 removed outlier: 3.839A pdb=" N LYS G 33 " --> pdb=" O THR G 29 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA G 47 " --> pdb=" O LYS G 43 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLU G 48 " --> pdb=" O MET G 44 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE G 51 " --> pdb=" O ALA G 47 " (cutoff:3.500A) Processing helix chain 'G' and resid 86 through 102 removed outlier: 3.599A pdb=" N HIS G 98 " --> pdb=" O ALA G 94 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASP G 101 " --> pdb=" O ARG G 97 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 122 removed outlier: 3.685A pdb=" N LYS G 115 " --> pdb=" O GLY G 111 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLN G 117 " --> pdb=" O LYS G 113 " (cutoff:3.500A) Processing helix chain 'G' and resid 139 through 155 Processing helix chain 'G' and resid 156 through 159 Processing helix chain 'G' and resid 184 through 191 removed outlier: 3.501A pdb=" N ILE G 188 " --> pdb=" O ASN G 184 " (cutoff:3.500A) Processing helix chain 'G' and resid 204 through 276 removed outlier: 4.047A pdb=" N GLU G 211 " --> pdb=" O ARG G 207 " (cutoff:3.500A) Processing helix chain 'H' and resid 93 through 97 Processing helix chain 'H' and resid 100 through 112 Processing helix chain 'H' and resid 119 through 136 removed outlier: 3.573A pdb=" N VAL H 136 " --> pdb=" O ASN H 132 " (cutoff:3.500A) Processing helix chain 'I' and resid 9 through 22 Processing helix chain 'I' and resid 31 through 37 Processing helix chain 'O' and resid 16 through 29 Processing helix chain 'O' and resid 33 through 49 Processing helix chain 'O' and resid 63 through 78 Processing helix chain 'O' and resid 83 through 95 Processing helix chain 'O' and resid 101 through 117 Processing helix chain 'O' and resid 130 through 144 Processing helix chain 'O' and resid 180 through 191 Processing helix chain 'T' and resid 27 through 46 removed outlier: 3.571A pdb=" N LEU T 43 " --> pdb=" O VAL T 39 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N TYR T 44 " --> pdb=" O ILE T 40 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU T 46 " --> pdb=" O SER T 42 " (cutoff:3.500A) Processing helix chain 'T' and resid 58 through 74 removed outlier: 4.162A pdb=" N GLN T 62 " --> pdb=" O TRP T 58 " (cutoff:3.500A) Processing helix chain 'T' and resid 82 through 84 No H-bonds generated for 'chain 'T' and resid 82 through 84' Processing helix chain 'T' and resid 85 through 100 removed outlier: 3.822A pdb=" N ILE T 96 " --> pdb=" O LEU T 92 " (cutoff:3.500A) Processing helix chain 'T' and resid 114 through 138 removed outlier: 3.854A pdb=" N ILE T 118 " --> pdb=" O HIS T 114 " (cutoff:3.500A) Processing helix chain 'T' and resid 139 through 146 Processing helix chain 'T' and resid 151 through 155 Processing helix chain 'T' and resid 156 through 167 removed outlier: 3.701A pdb=" N GLU T 162 " --> pdb=" O LEU T 158 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N SER T 165 " --> pdb=" O ILE T 161 " (cutoff:3.500A) Processing helix chain 'T' and resid 168 through 200 removed outlier: 3.579A pdb=" N LEU T 173 " --> pdb=" O ARG T 169 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N GLY T 174 " --> pdb=" O ALA T 170 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N LEU T 177 " --> pdb=" O LEU T 173 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ASN T 197 " --> pdb=" O GLY T 193 " (cutoff:3.500A) Processing helix chain 'T' and resid 202 through 207 removed outlier: 3.648A pdb=" N LEU T 206 " --> pdb=" O ASN T 202 " (cutoff:3.500A) Processing helix chain 'T' and resid 210 through 247 removed outlier: 3.606A pdb=" N ALA T 235 " --> pdb=" O GLY T 231 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU T 242 " --> pdb=" O THR T 238 " (cutoff:3.500A) Processing helix chain 'U' and resid 54 through 186 removed outlier: 4.124A pdb=" N LEU U 58 " --> pdb=" O ASP U 54 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N ALA U 74 " --> pdb=" O ALA U 70 " (cutoff:3.500A) Proline residue: U 75 - end of helix removed outlier: 3.510A pdb=" N GLN U 112 " --> pdb=" O ASP U 108 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU U 113 " --> pdb=" O SER U 109 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLU U 118 " --> pdb=" O GLN U 114 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N LYS U 121 " --> pdb=" O ALA U 117 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N VAL U 122 " --> pdb=" O GLU U 118 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LEU U 123 " --> pdb=" O THR U 119 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS U 128 " --> pdb=" O PHE U 124 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SER U 135 " --> pdb=" O VAL U 131 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU U 136 " --> pdb=" O GLU U 132 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLU U 139 " --> pdb=" O SER U 135 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU U 140 " --> pdb=" O GLU U 136 " (cutoff:3.500A) Processing helix chain 'U' and resid 187 through 206 removed outlier: 4.202A pdb=" N VAL U 193 " --> pdb=" O PHE U 189 " (cutoff:3.500A) Processing helix chain 'V' and resid 4 through 19 Processing helix chain 'V' and resid 26 through 48 Processing helix chain 'V' and resid 56 through 62 removed outlier: 3.624A pdb=" N SER V 60 " --> pdb=" O SER V 56 " (cutoff:3.500A) Processing helix chain 'V' and resid 67 through 78 Processing helix chain 'V' and resid 90 through 127 removed outlier: 3.558A pdb=" N ALA V 127 " --> pdb=" O ASN V 123 " (cutoff:3.500A) Processing helix chain 'V' and resid 134 through 142 removed outlier: 3.607A pdb=" N LEU V 138 " --> pdb=" O THR V 134 " (cutoff:3.500A) Processing helix chain 'V' and resid 143 through 156 Processing helix chain 'V' and resid 162 through 166 removed outlier: 3.533A pdb=" N ARG V 166 " --> pdb=" O TYR V 163 " (cutoff:3.500A) Processing helix chain 'W' and resid 18 through 30 removed outlier: 4.244A pdb=" N LYS W 22 " --> pdb=" O ALA W 18 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA W 25 " --> pdb=" O ALA W 21 " (cutoff:3.500A) removed outlier: 4.161A 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: 3.655A pdb=" N ILE W 73 " --> pdb=" O PHE W 69 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N SER W 79 " --> pdb=" O ALA W 75 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N TYR W 82 " --> pdb=" O TYR W 78 " (cutoff:3.500A) Processing helix chain 'X' and resid 2 through 14 Processing helix chain 'X' and resid 20 through 27 removed outlier: 3.586A pdb=" N ASN X 27 " --> pdb=" O ASP X 23 " (cutoff:3.500A) Processing helix chain 'X' and resid 46 through 57 removed outlier: 4.521A 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 1 through 5 removed outlier: 3.679A pdb=" N LEU Z 4 " --> pdb=" O MET Z 1 " (cutoff:3.500A) Processing helix chain 'Z' and resid 8 through 30 Processing helix chain 'Z' and resid 30 through 48 removed outlier: 3.759A pdb=" N LEU Z 38 " --> pdb=" O MET Z 34 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 90 through 96 removed outlier: 7.398A pdb=" N LEU A 54 " --> pdb=" O THR A 93 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLU A 53 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N ALA A 65 " --> pdb=" O VAL A 76 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N VAL A 76 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ILE A 40 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N VAL A 36 " --> pdb=" O ILE A 40 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ARG A 42 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ARG D 60 " --> pdb=" O ALA D 51 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N HIS D 53 " --> pdb=" O THR D 58 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N THR D 58 " --> pdb=" O HIS D 53 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ILE D 17 " --> pdb=" O ILE D 20 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N HIS D 24 " --> pdb=" O VAL D 13 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N VAL D 13 " --> pdb=" O HIS D 24 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 90 through 96 removed outlier: 7.398A pdb=" N LEU A 54 " --> pdb=" O THR A 93 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLU A 53 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N ALA A 65 " --> pdb=" O VAL A 76 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N VAL A 76 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ILE A 40 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N VAL A 36 " --> pdb=" O ILE A 40 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ARG A 42 " --> pdb=" O LEU A 34 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 98 through 101 Processing sheet with id=AA4, first strand: chain 'A' and resid 108 through 110 removed outlier: 6.127A pdb=" N ARG A 108 " --> pdb=" O ILE A 233 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N ALA A 235 " --> pdb=" O ARG A 108 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N VAL A 110 " --> pdb=" O ALA A 235 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N THR A 237 " --> pdb=" O VAL A 110 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N TYR A 202 " --> pdb=" O LEU A 267 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N VAL A 269 " --> pdb=" O TYR A 202 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N VAL A 204 " --> pdb=" O VAL A 269 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N ASP A 271 " --> pdb=" O VAL A 204 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N VAL A 206 " --> pdb=" O ASP A 271 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N ILE A 169 " --> pdb=" O ILE A 329 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N LEU A 168 " --> pdb=" O ILE A 352 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 62 through 69 removed outlier: 3.558A pdb=" N ALA B 65 " --> pdb=" O GLU B 53 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N GLU B 53 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N LEU B 54 " --> pdb=" O THR B 93 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ARG B 42 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N VAL B 36 " --> pdb=" O ILE B 40 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ILE B 40 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N GLN B 72 " --> pdb=" O LEU B 68 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N LEU B 68 " --> pdb=" O GLN B 72 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N GLY B 74 " --> pdb=" O LEU B 66 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU B 66 " --> pdb=" O GLY B 74 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N LYS F 75 " --> pdb=" O LYS F 40 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N LYS F 40 " --> pdb=" O LYS F 75 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ARG F 60 " --> pdb=" O ALA F 51 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N HIS F 53 " --> pdb=" O THR F 58 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N THR F 58 " --> pdb=" O HIS F 53 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL F 23 " --> pdb=" O VAL F 59 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL F 21 " --> pdb=" O THR F 61 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ILE F 20 " --> pdb=" O VAL F 16 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N VAL F 16 " --> pdb=" O ILE F 20 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N ASP F 22 " --> pdb=" O THR F 14 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 98 through 101 Processing sheet with id=AA7, first strand: chain 'B' and resid 109 through 111 removed outlier: 6.166A pdb=" N VAL B 110 " --> pdb=" O ALA B 235 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N THR B 237 " --> pdb=" O VAL B 110 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N TYR B 205 " --> pdb=" O VAL B 234 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N ALA B 236 " --> pdb=" O TYR B 205 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N ALA B 207 " --> pdb=" O ALA B 236 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 147 through 148 removed outlier: 4.437A pdb=" N ILE B 161 " --> pdb=" O VAL B 148 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 169 through 172 removed outlier: 6.234A pdb=" N ILE B 169 " --> pdb=" O ILE B 329 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N THR B 331 " --> pdb=" O ILE B 169 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N GLY B 171 " --> pdb=" O THR B 331 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 351 through 354 removed outlier: 9.370A pdb=" N GLN B 351 " --> pdb=" O GLY B 370 " (cutoff:3.500A) removed outlier: 8.714A pdb=" N GLY B 370 " --> pdb=" O GLN B 351 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N PHE B 353 " --> pdb=" O ASN B 368 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 30 through 37 removed outlier: 5.309A pdb=" N ARG C 42 " --> pdb=" O LEU C 34 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N VAL C 36 " --> pdb=" O ILE C 40 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N ILE C 40 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N VAL C 76 " --> pdb=" O ALA C 65 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N ALA C 65 " --> pdb=" O VAL C 76 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N PHE C 78 " --> pdb=" O GLY C 63 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N GLY C 63 " --> pdb=" O PHE C 78 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N GLU C 53 " --> pdb=" O ALA C 65 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N LEU C 54 " --> pdb=" O THR C 93 " (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 109 through 111 removed outlier: 6.227A pdb=" N VAL C 110 " --> pdb=" O ALA C 235 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N CYS C 203 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N VAL C 234 " --> pdb=" O CYS C 203 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N TYR C 205 " --> pdb=" O VAL C 234 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N ALA C 236 " --> pdb=" O TYR C 205 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N ALA C 207 " --> pdb=" O ALA C 236 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ILE C 169 " --> pdb=" O ILE C 329 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N THR C 331 " --> pdb=" O ILE C 169 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N GLY C 171 " --> pdb=" O THR C 331 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N ILE C 170 " --> pdb=" O LEU C 354 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE C 353 " --> pdb=" O LEU C 371 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N LEU C 371 " --> pdb=" O PHE C 353 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 147 through 148 removed outlier: 4.376A pdb=" N ILE C 161 " --> pdb=" O VAL C 148 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 84 through 87 removed outlier: 3.849A pdb=" N LEU D 113 " --> pdb=" O VAL D 87 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 95 through 96 removed outlier: 5.620A pdb=" N ILE D 96 " --> pdb=" O PHE D 219 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N GLN D 221 " --> pdb=" O ILE D 96 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N SER D 182 " --> pdb=" O ALA D 216 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N VAL D 218 " --> pdb=" O SER D 182 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N PHE D 184 " --> pdb=" O VAL D 218 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N GLY D 220 " --> pdb=" O PHE D 184 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N GLY D 186 " --> pdb=" O GLY D 220 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N THR D 305 " --> pdb=" O VAL D 251 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N LYS D 152 " --> pdb=" O ALA D 331 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N THR D 333 " --> pdb=" O LYS D 152 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N GLY D 154 " --> pdb=" O THR D 333 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N LEU D 335 " --> pdb=" O GLY D 154 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N PHE D 156 " --> pdb=" O LEU D 335 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N ASP D 352 " --> pdb=" O VAL D 334 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 11 through 16 removed outlier: 6.611A pdb=" N ASP E 22 " --> pdb=" O THR E 14 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N VAL E 16 " --> pdb=" O ILE E 20 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N ILE E 20 " --> pdb=" O VAL E 16 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N THR E 58 " --> pdb=" O HIS E 53 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N HIS E 53 " --> pdb=" O THR E 58 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ARG E 60 " --> pdb=" O ALA E 51 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 84 through 87 removed outlier: 3.682A pdb=" N LEU E 113 " --> pdb=" O VAL E 87 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 216 through 221 removed outlier: 6.393A pdb=" N PHE E 184 " --> pdb=" O VAL E 218 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N GLY E 220 " --> pdb=" O PHE E 184 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N GLY E 186 " --> pdb=" O GLY E 220 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 84 through 87 removed outlier: 4.221A pdb=" N LEU F 113 " --> pdb=" O VAL F 87 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 95 through 96 removed outlier: 3.970A pdb=" N PHE F 219 " --> pdb=" O ILE F 96 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N SER F 182 " --> pdb=" O ALA F 216 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N VAL F 218 " --> pdb=" O SER F 182 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N PHE F 184 " --> pdb=" O VAL F 218 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N GLY F 220 " --> pdb=" O PHE F 184 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N GLY F 186 " --> pdb=" O GLY F 220 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N VAL F 183 " --> pdb=" O PHE F 254 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N ASP F 256 " --> pdb=" O VAL F 183 " (cutoff:3.500A) removed outlier: 8.084A pdb=" N THR F 185 " --> pdb=" O ASP F 256 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA F 309 " --> pdb=" O ILE F 255 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ASN F 257 " --> pdb=" O ALA F 309 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 73 through 77 removed outlier: 6.553A pdb=" N ILE G 74 " --> pdb=" O VAL G 108 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N ILE G 110 " --> pdb=" O ILE G 74 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ALA G 76 " --> pdb=" O ILE G 110 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N ILE G 107 " --> pdb=" O LYS G 127 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N SER G 129 " --> pdb=" O ILE G 107 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N THR G 109 " --> pdb=" O SER G 129 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 162 through 171 removed outlier: 3.672A pdb=" N ILE G 162 " --> pdb=" O ILE G 182 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N SER G 174 " --> pdb=" O VAL G 170 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 12 through 15 removed outlier: 6.005A pdb=" N GLN H 13 " --> pdb=" O VAL H 85 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N ALA H 87 " --> pdb=" O GLN H 13 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N ALA H 15 " --> pdb=" O ALA H 87 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 37 through 42 removed outlier: 6.641A pdb=" N VAL H 56 " --> pdb=" O PRO H 33 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'O' and resid 157 through 159 removed outlier: 3.881A pdb=" N VAL O 158 " --> pdb=" O VAL O 123 " (cutoff:3.500A) 2332 hydrogen bonds defined for protein. 6765 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: 10.54 Time building geometry restraints manager: 7.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.28: 5060 1.28 - 1.35: 1202 1.35 - 1.41: 3819 1.41 - 1.48: 5103 1.48 - 1.54: 5008 Bond restraints: 20192 Sorted by residual: bond pdb=" CA GLY F 220 " pdb=" C GLY F 220 " ideal model delta sigma weight residual 1.518 1.476 0.043 7.30e-03 1.88e+04 3.44e+01 bond pdb=" CA GLY E 11 " pdb=" C GLY E 11 " ideal model delta sigma weight residual 1.514 1.468 0.046 8.60e-03 1.35e+04 2.84e+01 bond pdb=" CA ILE B 40 " pdb=" C ILE B 40 " ideal model delta sigma weight residual 1.527 1.483 0.044 8.50e-03 1.38e+04 2.71e+01 bond pdb=" CA ALA A 236 " pdb=" C ALA A 236 " ideal model delta sigma weight residual 1.530 1.478 0.052 1.08e-02 8.57e+03 2.36e+01 bond pdb=" N LEU B 27 " pdb=" CA LEU B 27 " ideal model delta sigma weight residual 1.458 1.414 0.044 9.00e-03 1.23e+04 2.36e+01 ... (remaining 20187 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.95: 21298 2.95 - 5.89: 3228 5.89 - 8.84: 558 8.84 - 11.78: 90 11.78 - 14.73: 6 Bond angle restraints: 25180 Sorted by residual: angle pdb=" N VAL V 67 " pdb=" CA VAL V 67 " pdb=" C VAL V 67 " ideal model delta sigma weight residual 113.71 102.42 11.29 9.50e-01 1.11e+00 1.41e+02 angle pdb=" N VAL D 161 " pdb=" CA VAL D 161 " pdb=" C VAL D 161 " ideal model delta sigma weight residual 112.17 101.95 10.22 9.50e-01 1.11e+00 1.16e+02 angle pdb=" CA PRO D 225 " pdb=" C PRO D 225 " pdb=" O PRO D 225 " ideal model delta sigma weight residual 120.90 114.18 6.72 7.20e-01 1.93e+00 8.71e+01 angle pdb=" N ILE O 33 " pdb=" CA ILE O 33 " pdb=" C ILE O 33 " ideal model delta sigma weight residual 111.90 104.55 7.35 8.10e-01 1.52e+00 8.24e+01 angle pdb=" CA PRO E 225 " pdb=" C PRO E 225 " pdb=" O PRO E 225 " ideal model delta sigma weight residual 120.90 114.46 6.44 7.20e-01 1.93e+00 7.99e+01 ... (remaining 25175 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.57: 4999 23.57 - 47.14: 21 47.14 - 70.71: 1 70.71 - 94.28: 2 94.28 - 117.85: 1 Dihedral angle restraints: 5024 sinusoidal: 4 harmonic: 5020 Sorted by residual: dihedral pdb=" CA ASP E 256 " pdb=" C ASP E 256 " pdb=" N ASN E 257 " pdb=" CA ASN E 257 " ideal model delta harmonic sigma weight residual -180.00 -62.15 -117.85 0 5.00e+00 4.00e-02 5.56e+02 dihedral pdb=" CA GLU B 29 " pdb=" C GLU B 29 " pdb=" N THR B 30 " pdb=" CA THR B 30 " ideal model delta harmonic sigma weight residual 180.00 88.23 91.77 0 5.00e+00 4.00e-02 3.37e+02 dihedral pdb=" CA ASN 5 40 " pdb=" C ASN 5 40 " pdb=" N PRO 5 41 " pdb=" CA PRO 5 41 " ideal model delta harmonic sigma weight residual -180.00 -137.32 -42.68 0 5.00e+00 4.00e-02 7.29e+01 ... (remaining 5021 not shown) Chirality restraints: 0 Planarity restraints: 5024 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN A 193 " -0.019 2.00e-02 2.50e+03 3.86e-02 1.49e+01 pdb=" C ASN A 193 " 0.067 2.00e-02 2.50e+03 pdb=" O ASN A 193 " -0.026 2.00e-02 2.50e+03 pdb=" N GLY A 194 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY B 176 " -0.018 2.00e-02 2.50e+03 3.56e-02 1.26e+01 pdb=" C GLY B 176 " 0.061 2.00e-02 2.50e+03 pdb=" O GLY B 176 " -0.024 2.00e-02 2.50e+03 pdb=" N LYS B 177 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU F 422 " 0.018 2.00e-02 2.50e+03 3.53e-02 1.24e+01 pdb=" C GLU F 422 " -0.061 2.00e-02 2.50e+03 pdb=" O GLU F 422 " 0.023 2.00e-02 2.50e+03 pdb=" N VAL F 423 " 0.020 2.00e-02 2.50e+03 ... (remaining 5021 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.89: 9910 2.89 - 3.39: 17486 3.39 - 3.89: 26463 3.89 - 4.40: 27450 4.40 - 4.90: 40225 Nonbonded interactions: 121534 Sorted by model distance: nonbonded pdb=" N ASN B 26 " pdb=" N LEU B 27 " model vdw 2.385 2.560 nonbonded pdb=" N SER G 171 " pdb=" O SER G 171 " model vdw 2.386 2.496 nonbonded pdb=" N LEU D 252 " pdb=" O LEU D 252 " model vdw 2.396 2.496 nonbonded pdb=" N VAL D 161 " pdb=" N GLY D 162 " model vdw 2.398 2.560 nonbonded pdb=" N LYS D 12 " pdb=" O LYS D 12 " model vdw 2.400 2.496 ... (remaining 121529 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain '0' and resid 2 through 73) selection = (chain '1' and resid 2 through 73) selection = (chain '2' and resid 2 through 73) selection = (chain '3' and resid 2 through 73) selection = (chain '4' and resid 2 through 73) selection = (chain '5' and resid 2 through 73) selection = (chain '6' and resid 2 through 73) selection = (chain '7' and resid 2 through 73) selection = (chain '8' and resid 2 through 73) selection = (chain '9' and resid 2 through 73) } ncs_group { reference = (chain 'A' and (resid 12 through 407 or resid 410 through 509)) selection = (chain 'B' and resid 12 through 509) selection = chain 'C' } ncs_group { reference = (chain 'D' and resid 8 through 475) selection = (chain 'E' and resid 8 through 475) selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.790 Check model and map are aligned: 0.140 Set scattering table: 0.180 Process input model: 60.120 Find NCS groups from input model: 1.240 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6356 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 0.056 20192 Z= 1.502 Angle : 2.189 14.730 25180 Z= 1.579 Chirality : 0.000 0.000 0 Planarity : 0.010 0.039 5024 Dihedral : 6.809 117.855 5024 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 0.08 Ramachandran Plot: Outliers : 1.40 % Allowed : 3.87 % Favored : 94.72 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.46 % Cis-general : 0.08 % Twisted Proline : 4.43 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.11), residues: 4984 helix: 0.93 (0.09), residues: 2796 sheet: -1.30 (0.21), residues: 524 loop : -1.86 (0.13), residues: 1664 Details of bonding type rmsd hydrogen bonds : bond 0.21109 ( 2315) hydrogen bonds : angle 8.06499 ( 6765) covalent geometry : bond 0.01913 (20192) covalent geometry : angle 2.18864 (25180) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9968 Ramachandran restraints generated. 4984 Oldfield, 0 Emsley, 4984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9968 Ramachandran restraints generated. 4984 Oldfield, 0 Emsley, 4984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 4114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 2.348 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.1708 time to fit residues: 30.0923 Evaluate side-chains 82 residues out of total 4114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 2.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 416 optimal weight: 5.9990 chunk 373 optimal weight: 6.9990 chunk 207 optimal weight: 6.9990 chunk 127 optimal weight: 30.0000 chunk 252 optimal weight: 5.9990 chunk 199 optimal weight: 5.9990 chunk 386 optimal weight: 20.0000 chunk 149 optimal weight: 10.0000 chunk 234 optimal weight: 5.9990 chunk 287 optimal weight: 0.0170 chunk 447 optimal weight: 50.0000 overall best weight: 4.8026 ------------------------------------------------------------------------------- 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 = 0.2631 r_free = 0.2631 target = 0.032031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2389 r_free = 0.2389 target = 0.024478 restraints weight = 280987.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2378 r_free = 0.2378 target = 0.024338 restraints weight = 265156.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2377 r_free = 0.2377 target = 0.024310 restraints weight = 267183.853| |-----------------------------------------------------------------------------| r_work (final): 0.2194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 20192 Z= 0.170 Angle : 0.506 8.328 25180 Z= 0.323 Chirality : 0.000 0.000 0 Planarity : 0.003 0.031 5024 Dihedral : 4.800 79.213 5024 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 0.23 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.67 % Favored : 97.07 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.96 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.12), residues: 4984 helix: 2.35 (0.10), residues: 2833 sheet: -0.96 (0.21), residues: 571 loop : -0.99 (0.15), residues: 1580 Details of bonding type rmsd hydrogen bonds : bond 0.04354 ( 2315) hydrogen bonds : angle 4.54744 ( 6765) covalent geometry : bond 0.00224 (20192) covalent geometry : angle 0.50636 (25180) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9968 Ramachandran restraints generated. 4984 Oldfield, 0 Emsley, 4984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9968 Ramachandran restraints generated. 4984 Oldfield, 0 Emsley, 4984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 4114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 2.285 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.1723 time to fit residues: 30.4958 Evaluate side-chains 82 residues out of total 4114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 2.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 282 optimal weight: 50.0000 chunk 87 optimal weight: 30.0000 chunk 349 optimal weight: 30.0000 chunk 439 optimal weight: 40.0000 chunk 341 optimal weight: 40.0000 chunk 130 optimal weight: 20.0000 chunk 450 optimal weight: 120.0000 chunk 117 optimal weight: 30.0000 chunk 48 optimal weight: 50.0000 chunk 350 optimal weight: 30.0000 chunk 326 optimal weight: 0.8980 overall best weight: 22.1796 ------------------------------------------------------------------------------- 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 = 0.2570 r_free = 0.2570 target = 0.030128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2333 r_free = 0.2333 target = 0.023117 restraints weight = 298871.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2326 r_free = 0.2326 target = 0.023040 restraints weight = 287925.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2324 r_free = 0.2324 target = 0.023003 restraints weight = 285227.366| |-----------------------------------------------------------------------------| r_work (final): 0.2129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.3296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 20192 Z= 0.417 Angle : 0.850 17.564 25180 Z= 0.551 Chirality : 0.000 0.000 0 Planarity : 0.005 0.029 5024 Dihedral : 5.783 77.276 5024 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.96 % Favored : 94.72 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.96 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.12), residues: 4984 helix: 1.96 (0.10), residues: 2780 sheet: -1.13 (0.23), residues: 506 loop : -1.08 (0.15), residues: 1698 Details of bonding type rmsd hydrogen bonds : bond 0.06086 ( 2315) hydrogen bonds : angle 5.85709 ( 6765) covalent geometry : bond 0.00556 (20192) covalent geometry : angle 0.84962 (25180) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9968 Ramachandran restraints generated. 4984 Oldfield, 0 Emsley, 4984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9968 Ramachandran restraints generated. 4984 Oldfield, 0 Emsley, 4984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 4114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 2.459 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.1694 time to fit residues: 29.8533 Evaluate side-chains 82 residues out of total 4114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 2.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 108 optimal weight: 20.0000 chunk 470 optimal weight: 50.0000 chunk 66 optimal weight: 50.0000 chunk 19 optimal weight: 8.9990 chunk 189 optimal weight: 10.0000 chunk 184 optimal weight: 20.0000 chunk 107 optimal weight: 50.0000 chunk 262 optimal weight: 30.0000 chunk 361 optimal weight: 50.0000 chunk 233 optimal weight: 50.0000 chunk 204 optimal weight: 50.0000 overall best weight: 17.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2565 r_free = 0.2565 target = 0.029970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2317 r_free = 0.2317 target = 0.022915 restraints weight = 302590.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2315 r_free = 0.2315 target = 0.022899 restraints weight = 289563.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2311 r_free = 0.2311 target = 0.022847 restraints weight = 279888.775| |-----------------------------------------------------------------------------| r_work (final): 0.2116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.4344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 20192 Z= 0.344 Angle : 0.674 14.555 25180 Z= 0.441 Chirality : 0.000 0.000 0 Planarity : 0.004 0.026 5024 Dihedral : 5.398 89.858 5024 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 2.04 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.00 % Favored : 93.68 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.96 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.12), residues: 4984 helix: 2.01 (0.10), residues: 2792 sheet: -1.46 (0.23), residues: 514 loop : -1.02 (0.16), residues: 1678 Details of bonding type rmsd hydrogen bonds : bond 0.04977 ( 2315) hydrogen bonds : angle 5.39653 ( 6765) covalent geometry : bond 0.00458 (20192) covalent geometry : angle 0.67403 (25180) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9968 Ramachandran restraints generated. 4984 Oldfield, 0 Emsley, 4984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9968 Ramachandran restraints generated. 4984 Oldfield, 0 Emsley, 4984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 4114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 2.330 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.1655 time to fit residues: 29.1098 Evaluate side-chains 82 residues out of total 4114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 2.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 197 optimal weight: 0.1980 chunk 70 optimal weight: 50.0000 chunk 19 optimal weight: 6.9990 chunk 150 optimal weight: 30.0000 chunk 99 optimal weight: 30.0000 chunk 431 optimal weight: 20.0000 chunk 318 optimal weight: 20.0000 chunk 30 optimal weight: 6.9990 chunk 433 optimal weight: 50.0000 chunk 280 optimal weight: 30.0000 chunk 293 optimal weight: 5.9990 overall best weight: 8.0390 ------------------------------------------------------------------------------- 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 = 0.2574 r_free = 0.2574 target = 0.030246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2332 r_free = 0.2332 target = 0.023133 restraints weight = 298985.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2311 r_free = 0.2311 target = 0.022882 restraints weight = 291632.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2311 r_free = 0.2311 target = 0.022889 restraints weight = 294262.011| |-----------------------------------------------------------------------------| r_work (final): 0.2118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.4407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 20192 Z= 0.171 Angle : 0.426 8.751 25180 Z= 0.274 Chirality : 0.000 0.000 0 Planarity : 0.002 0.027 5024 Dihedral : 4.552 88.994 5024 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 0.77 Ramachandran Plot: Outliers : 0.30 % Allowed : 4.78 % Favored : 94.92 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.96 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.83 (0.13), residues: 4984 helix: 2.82 (0.10), residues: 2787 sheet: -1.44 (0.22), residues: 538 loop : -0.71 (0.17), residues: 1659 Details of bonding type rmsd hydrogen bonds : bond 0.03769 ( 2315) hydrogen bonds : angle 4.42003 ( 6765) covalent geometry : bond 0.00227 (20192) covalent geometry : angle 0.42599 (25180) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9968 Ramachandran restraints generated. 4984 Oldfield, 0 Emsley, 4984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9968 Ramachandran restraints generated. 4984 Oldfield, 0 Emsley, 4984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 4114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 2.299 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.1640 time to fit residues: 28.8501 Evaluate side-chains 82 residues out of total 4114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 2.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 164 optimal weight: 0.2980 chunk 484 optimal weight: 20.0000 chunk 277 optimal weight: 50.0000 chunk 362 optimal weight: 50.0000 chunk 489 optimal weight: 20.0000 chunk 335 optimal weight: 30.0000 chunk 345 optimal weight: 50.0000 chunk 61 optimal weight: 6.9990 chunk 123 optimal weight: 40.0000 chunk 180 optimal weight: 50.0000 chunk 248 optimal weight: 50.0000 overall best weight: 15.4594 ------------------------------------------------------------------------------- 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 = 0.2587 r_free = 0.2587 target = 0.030196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2328 r_free = 0.2328 target = 0.023184 restraints weight = 296210.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2337 r_free = 0.2337 target = 0.023333 restraints weight = 253516.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2342 r_free = 0.2342 target = 0.023472 restraints weight = 223322.397| |-----------------------------------------------------------------------------| r_work (final): 0.2108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.4868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 20192 Z= 0.299 Angle : 0.590 13.225 25180 Z= 0.387 Chirality : 0.000 0.000 0 Planarity : 0.003 0.027 5024 Dihedral : 5.068 82.340 5024 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 1.93 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.16 % Favored : 92.58 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.96 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.13), residues: 4984 helix: 2.45 (0.10), residues: 2805 sheet: -1.70 (0.23), residues: 514 loop : -0.86 (0.17), residues: 1665 Details of bonding type rmsd hydrogen bonds : bond 0.04741 ( 2315) hydrogen bonds : angle 5.14069 ( 6765) covalent geometry : bond 0.00396 (20192) covalent geometry : angle 0.59047 (25180) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9968 Ramachandran restraints generated. 4984 Oldfield, 0 Emsley, 4984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9968 Ramachandran restraints generated. 4984 Oldfield, 0 Emsley, 4984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 4114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 2.256 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.1597 time to fit residues: 28.1360 Evaluate side-chains 82 residues out of total 4114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 2.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 381 optimal weight: 6.9990 chunk 215 optimal weight: 50.0000 chunk 85 optimal weight: 50.0000 chunk 354 optimal weight: 50.0000 chunk 34 optimal weight: 50.0000 chunk 308 optimal weight: 30.0000 chunk 145 optimal weight: 40.0000 chunk 122 optimal weight: 40.0000 chunk 320 optimal weight: 30.0000 chunk 311 optimal weight: 50.0000 chunk 433 optimal weight: 50.0000 overall best weight: 29.3998 ------------------------------------------------------------------------------- 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 = 0.2524 r_free = 0.2524 target = 0.028902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2292 r_free = 0.2292 target = 0.022389 restraints weight = 317411.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2283 r_free = 0.2283 target = 0.022283 restraints weight = 310245.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2280 r_free = 0.2280 target = 0.022236 restraints weight = 304058.452| |-----------------------------------------------------------------------------| r_work (final): 0.2095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.5734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.089 20192 Z= 0.525 Angle : 0.895 17.589 25180 Z= 0.593 Chirality : 0.000 0.000 0 Planarity : 0.006 0.027 5024 Dihedral : 6.503 77.614 5024 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 5.59 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 : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.12), residues: 4984 helix: 0.71 (0.10), residues: 2768 sheet: -2.19 (0.24), residues: 427 loop : -1.57 (0.15), residues: 1789 Details of bonding type rmsd hydrogen bonds : bond 0.07051 ( 2315) hydrogen bonds : angle 7.06112 ( 6765) covalent geometry : bond 0.00698 (20192) covalent geometry : angle 0.89539 (25180) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9968 Ramachandran restraints generated. 4984 Oldfield, 0 Emsley, 4984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9968 Ramachandran restraints generated. 4984 Oldfield, 0 Emsley, 4984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 4114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 2.305 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.1677 time to fit residues: 29.8028 Evaluate side-chains 82 residues out of total 4114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 2.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 167 optimal weight: 30.0000 chunk 240 optimal weight: 40.0000 chunk 331 optimal weight: 20.0000 chunk 246 optimal weight: 10.0000 chunk 249 optimal weight: 50.0000 chunk 9 optimal weight: 9.9990 chunk 447 optimal weight: 50.0000 chunk 448 optimal weight: 40.0000 chunk 421 optimal weight: 50.0000 chunk 181 optimal weight: 40.0000 chunk 72 optimal weight: 5.9990 overall best weight: 15.1996 ------------------------------------------------------------------------------- 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 = 0.2575 r_free = 0.2575 target = 0.029776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2317 r_free = 0.2317 target = 0.022849 restraints weight = 306118.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2329 r_free = 0.2329 target = 0.023042 restraints weight = 267977.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2332 r_free = 0.2332 target = 0.023148 restraints weight = 226108.959| |-----------------------------------------------------------------------------| r_work (final): 0.2099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.5712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 20192 Z= 0.282 Angle : 0.571 12.648 25180 Z= 0.372 Chirality : 0.000 0.000 0 Planarity : 0.003 0.028 5024 Dihedral : 5.374 82.608 5024 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 2.12 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.85 % Favored : 91.89 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.12), residues: 4984 helix: 1.51 (0.10), residues: 2792 sheet: -2.32 (0.24), residues: 429 loop : -1.42 (0.15), residues: 1763 Details of bonding type rmsd hydrogen bonds : bond 0.04808 ( 2315) hydrogen bonds : angle 5.60145 ( 6765) covalent geometry : bond 0.00376 (20192) covalent geometry : angle 0.57069 (25180) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9968 Ramachandran restraints generated. 4984 Oldfield, 0 Emsley, 4984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9968 Ramachandran restraints generated. 4984 Oldfield, 0 Emsley, 4984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 4114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 2.460 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.1736 time to fit residues: 30.6781 Evaluate side-chains 82 residues out of total 4114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 2.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 491 optimal weight: 50.0000 chunk 437 optimal weight: 50.0000 chunk 180 optimal weight: 40.0000 chunk 435 optimal weight: 7.9990 chunk 488 optimal weight: 50.0000 chunk 363 optimal weight: 40.0000 chunk 65 optimal weight: 50.0000 chunk 47 optimal weight: 50.0000 chunk 468 optimal weight: 50.0000 chunk 367 optimal weight: 50.0000 chunk 112 optimal weight: 50.0000 overall best weight: 37.5998 ------------------------------------------------------------------------------- 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 = 0.2515 r_free = 0.2515 target = 0.028602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2272 r_free = 0.2272 target = 0.021997 restraints weight = 324307.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2274 r_free = 0.2274 target = 0.022092 restraints weight = 302271.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2274 r_free = 0.2274 target = 0.022081 restraints weight = 282759.091| |-----------------------------------------------------------------------------| r_work (final): 0.2093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.6588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.109 20192 Z= 0.644 Angle : 1.055 19.717 25180 Z= 0.710 Chirality : 0.000 0.000 0 Planarity : 0.007 0.031 5024 Dihedral : 7.236 72.368 5024 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.34 % Allowed : 12.90 % Favored : 86.76 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.96 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.08 (0.11), residues: 4984 helix: -0.57 (0.09), residues: 2756 sheet: -2.74 (0.25), residues: 336 loop : -2.25 (0.14), residues: 1892 Details of bonding type rmsd hydrogen bonds : bond 0.08238 ( 2315) hydrogen bonds : angle 8.18451 ( 6765) covalent geometry : bond 0.00855 (20192) covalent geometry : angle 1.05451 (25180) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9968 Ramachandran restraints generated. 4984 Oldfield, 0 Emsley, 4984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9968 Ramachandran restraints generated. 4984 Oldfield, 0 Emsley, 4984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 4114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 2.329 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.1678 time to fit residues: 29.6161 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 : 3.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 375 optimal weight: 30.0000 chunk 169 optimal weight: 20.0000 chunk 381 optimal weight: 5.9990 chunk 386 optimal weight: 50.0000 chunk 98 optimal weight: 6.9990 chunk 147 optimal weight: 7.9990 chunk 227 optimal weight: 30.0000 chunk 285 optimal weight: 10.0000 chunk 7 optimal weight: 6.9990 chunk 490 optimal weight: 8.9990 chunk 233 optimal weight: 40.0000 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 = 0.2578 r_free = 0.2578 target = 0.029873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2320 r_free = 0.2320 target = 0.022860 restraints weight = 298841.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2330 r_free = 0.2330 target = 0.023053 restraints weight = 259765.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2336 r_free = 0.2336 target = 0.023183 restraints weight = 221703.065| |-----------------------------------------------------------------------------| r_work (final): 0.2096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.6208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 20192 Z= 0.172 Angle : 0.446 8.273 25180 Z= 0.291 Chirality : 0.000 0.000 0 Planarity : 0.003 0.030 5024 Dihedral : 5.159 83.518 5024 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 1.19 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.34 % Favored : 93.42 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.12), residues: 4984 helix: 1.50 (0.10), residues: 2778 sheet: -2.50 (0.24), residues: 412 loop : -1.47 (0.15), residues: 1794 Details of bonding type rmsd hydrogen bonds : bond 0.04347 ( 2315) hydrogen bonds : angle 5.36706 ( 6765) covalent geometry : bond 0.00227 (20192) covalent geometry : angle 0.44559 (25180) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9968 Ramachandran restraints generated. 4984 Oldfield, 0 Emsley, 4984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9968 Ramachandran restraints generated. 4984 Oldfield, 0 Emsley, 4984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 4114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 2.420 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.1651 time to fit residues: 29.2433 Evaluate side-chains 82 residues out of total 4114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 2.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 176 optimal weight: 20.0000 chunk 431 optimal weight: 40.0000 chunk 424 optimal weight: 5.9990 chunk 208 optimal weight: 9.9990 chunk 54 optimal weight: 60.0000 chunk 82 optimal weight: 2.9990 chunk 243 optimal weight: 50.0000 chunk 345 optimal weight: 30.0000 chunk 222 optimal weight: 3.9990 chunk 7 optimal weight: 70.0000 chunk 286 optimal weight: 30.0000 overall best weight: 8.5992 ------------------------------------------------------------------------------- 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 = 0.2584 r_free = 0.2584 target = 0.029987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2326 r_free = 0.2326 target = 0.022950 restraints weight = 301412.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2335 r_free = 0.2335 target = 0.023145 restraints weight = 260833.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2341 r_free = 0.2341 target = 0.023270 restraints weight = 223072.878| |-----------------------------------------------------------------------------| r_work (final): 0.2100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.6236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 20192 Z= 0.172 Angle : 0.419 8.021 25180 Z= 0.270 Chirality : 0.000 0.000 0 Planarity : 0.002 0.028 5024 Dihedral : 4.584 77.430 5024 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 1.31 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.93 % Favored : 91.83 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.96 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.13), residues: 4984 helix: 2.38 (0.10), residues: 2786 sheet: -2.50 (0.23), residues: 450 loop : -1.20 (0.16), residues: 1748 Details of bonding type rmsd hydrogen bonds : bond 0.03749 ( 2315) hydrogen bonds : angle 4.77192 ( 6765) covalent geometry : bond 0.00230 (20192) covalent geometry : angle 0.41862 (25180) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4722.18 seconds wall clock time: 81 minutes 50.98 seconds (4910.98 seconds total)