Starting phenix.real_space_refine on Thu Sep 18 20:15:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tjz_25947/09_2025/7tjz_25947.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tjz_25947/09_2025/7tjz_25947.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/7tjz_25947/09_2025/7tjz_25947.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tjz_25947/09_2025/7tjz_25947.map" model { file = "/net/cci-nas-00/data/ceres_data/7tjz_25947/09_2025/7tjz_25947.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tjz_25947/09_2025/7tjz_25947.cif" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.104 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 3 Type Number sf(0) Gaussians C 10112 2.51 5 N 5056 2.21 5 O 5060 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20228 Number of models: 1 Model: "" Number of chains: 27 Chain: "0" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 300 Classifications: {'peptide': 75} Incomplete info: {'backbone_only': 65} Link IDs: {'PTRANS': 2, 'TRANS': 72} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 246 Unresolved non-hydrogen angles: 363 Unresolved non-hydrogen dihedrals: 146 Unresolved non-hydrogen chiralities: 94 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'PHE:plan': 6, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 75 Chain: "1" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 300 Classifications: {'peptide': 75} Incomplete info: {'backbone_only': 65} Link IDs: {'PTRANS': 2, 'TRANS': 72} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 246 Unresolved non-hydrogen angles: 363 Unresolved non-hydrogen dihedrals: 146 Unresolved non-hydrogen chiralities: 94 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'PHE:plan': 6, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 75 Chain: "2" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 300 Classifications: {'peptide': 75} Incomplete info: {'backbone_only': 65} Link IDs: {'PTRANS': 2, 'TRANS': 72} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 246 Unresolved non-hydrogen angles: 363 Unresolved non-hydrogen dihedrals: 146 Unresolved non-hydrogen chiralities: 94 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'PHE:plan': 6, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 75 Chain: "3" Number of atoms: 296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 296 Classifications: {'peptide': 74} Incomplete info: {'backbone_only': 64} Link IDs: {'PTRANS': 2, 'TRANS': 71} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 242 Unresolved non-hydrogen angles: 358 Unresolved non-hydrogen dihedrals: 143 Unresolved non-hydrogen chiralities: 93 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'PHE:plan': 6, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 75 Chain: "4" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 300 Classifications: {'peptide': 75} Incomplete info: {'backbone_only': 65} Link IDs: {'PTRANS': 2, 'TRANS': 72} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 246 Unresolved non-hydrogen angles: 363 Unresolved non-hydrogen dihedrals: 146 Unresolved non-hydrogen chiralities: 94 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'PHE:plan': 6, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 75 Chain: "5" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 300 Classifications: {'peptide': 75} Incomplete info: {'backbone_only': 65} Link IDs: {'PTRANS': 2, 'TRANS': 72} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 246 Unresolved non-hydrogen angles: 363 Unresolved non-hydrogen dihedrals: 146 Unresolved non-hydrogen chiralities: 94 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'PHE:plan': 6, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 75 Chain: "6" Number of atoms: 296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 296 Classifications: {'peptide': 74} Incomplete info: {'backbone_only': 64} Link IDs: {'PTRANS': 2, 'TRANS': 71} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 242 Unresolved non-hydrogen angles: 358 Unresolved non-hydrogen dihedrals: 143 Unresolved non-hydrogen chiralities: 93 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'PHE:plan': 6, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 75 Chain: "7" Number of atoms: 292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 292 Classifications: {'peptide': 73} Incomplete info: {'backbone_only': 64} Link IDs: {'PTRANS': 2, 'TRANS': 70} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 238 Unresolved non-hydrogen angles: 352 Unresolved non-hydrogen dihedrals: 139 Unresolved non-hydrogen chiralities: 93 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'PHE:plan': 5, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 68 Chain: "8" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 300 Classifications: {'peptide': 75} Incomplete info: {'backbone_only': 65} Link IDs: {'PTRANS': 2, 'TRANS': 72} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 246 Unresolved non-hydrogen angles: 363 Unresolved non-hydrogen dihedrals: 146 Unresolved non-hydrogen chiralities: 94 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'PHE:plan': 6, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 75 Chain: "9" Number of atoms: 296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 296 Classifications: {'peptide': 74} Incomplete info: {'backbone_only': 64} Link IDs: {'PTRANS': 2, 'TRANS': 71} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 242 Unresolved non-hydrogen angles: 358 Unresolved non-hydrogen dihedrals: 143 Unresolved non-hydrogen chiralities: 93 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'PHE:plan': 6, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 75 Chain: "A" Number of atoms: 1996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 499, 1996 Classifications: {'peptide': 499} Incomplete info: {'backbone_only': 453} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 18, 'TRANS': 478} Chain breaks: 1 Unresolved chain link angles: 19 Unresolved non-hydrogen bonds: 1854 Unresolved non-hydrogen angles: 2698 Unresolved non-hydrogen dihedrals: 1123 Unresolved non-hydrogen chiralities: 606 Planarities with less than four sites: {'GLU:plan': 37, 'ARG:plan': 29, 'ASP:plan': 21, 'ASN:plan1': 17, 'PHE:plan': 13, 'GLN:plan1': 25, 'HIS:plan': 6, 'TRP:plan': 2, 'TYR:plan': 14} Unresolved non-hydrogen planarities: 804 Chain: "B" Number of atoms: 2020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 505, 2020 Classifications: {'peptide': 505} Incomplete info: {'backbone_only': 459} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 483} Chain breaks: 1 Unresolved chain link angles: 20 Unresolved non-hydrogen bonds: 1875 Unresolved non-hydrogen angles: 2729 Unresolved non-hydrogen dihedrals: 1135 Unresolved non-hydrogen chiralities: 614 Planarities with less than four sites: {'GLN:plan1': 26, 'GLU:plan': 37, 'ARG:plan': 29, 'ASP:plan': 21, 'ASN:plan1': 17, 'PHE:plan': 13, 'HIS:plan': 6, 'TRP:plan': 2, 'TYR:plan': 14} Unresolved non-hydrogen planarities: 808 Chain: "C" Number of atoms: 1992 Number of conformers: 1 Conformer: "" Number of residues, atoms: 498, 1992 Classifications: {'peptide': 498} Incomplete info: {'backbone_only': 451} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 18, 'TRANS': 477} Unresolved chain link angles: 19 Unresolved non-hydrogen bonds: 1852 Unresolved non-hydrogen angles: 2694 Unresolved non-hydrogen dihedrals: 1125 Unresolved non-hydrogen chiralities: 603 Planarities with less than four sites: {'GLU:plan': 36, 'ARG:plan': 29, 'ASP:plan': 21, 'ASN:plan1': 17, 'PHE:plan': 14, 'GLN:plan1': 25, 'HIS:plan': 6, 'TRP:plan': 2, 'TYR:plan': 14} Unresolved non-hydrogen planarities: 807 Chain: "D" Number of atoms: 1880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 1880 Classifications: {'peptide': 470} Incomplete info: {'backbone_only': 424} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 446} Unresolved chain link angles: 23 Unresolved non-hydrogen bonds: 1726 Unresolved non-hydrogen angles: 2519 Unresolved non-hydrogen dihedrals: 1034 Unresolved non-hydrogen chiralities: 580 Planarities with less than four sites: {'ASP:plan': 25, 'HIS:plan': 7, 'PHE:plan': 17, 'GLU:plan': 37, 'GLN:plan1': 18, 'ASN:plan1': 10, 'ARG:plan': 22, 'TYR:plan': 10} Unresolved non-hydrogen planarities: 711 Chain: "E" Number of atoms: 1872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 1872 Classifications: {'peptide': 468} Incomplete info: {'backbone_only': 422} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 445} Unresolved chain link angles: 22 Unresolved non-hydrogen bonds: 1721 Unresolved non-hydrogen angles: 2511 Unresolved non-hydrogen dihedrals: 1032 Unresolved non-hydrogen chiralities: 577 Planarities with less than four sites: {'ASP:plan': 25, 'HIS:plan': 7, 'PHE:plan': 17, 'GLU:plan': 37, 'GLN:plan1': 18, 'ASN:plan1': 10, 'ARG:plan': 22, 'TYR:plan': 10} Unresolved non-hydrogen planarities: 711 Chain: "F" Number of atoms: 1876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 1876 Classifications: {'peptide': 469} Incomplete info: {'backbone_only': 423} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 444} Unresolved chain link angles: 23 Unresolved non-hydrogen bonds: 1724 Unresolved non-hydrogen angles: 2516 Unresolved non-hydrogen dihedrals: 1033 Unresolved non-hydrogen chiralities: 579 Planarities with less than four sites: {'ASP:plan': 25, 'HIS:plan': 7, 'PHE:plan': 17, 'GLU:plan': 37, 'GLN:plan1': 18, 'ASN:plan1': 10, 'ARG:plan': 22, 'TYR:plan': 10} Unresolved non-hydrogen planarities: 711 Chain: "G" Number of atoms: 1060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 1060 Classifications: {'peptide': 265} Incomplete info: {'backbone_only': 255} Link IDs: {'PTRANS': 9, 'TRANS': 255} Chain breaks: 1 Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 1024 Unresolved non-hydrogen angles: 1472 Unresolved non-hydrogen dihedrals: 628 Unresolved non-hydrogen chiralities: 328 Planarities with less than four sites: {'GLU:plan': 16, 'ARG:plan': 11, 'ASN:plan1': 18, 'ASP:plan': 14, 'GLN:plan1': 9, 'PHE:plan': 8, 'TYR:plan': 7, 'HIS:plan': 3} Unresolved non-hydrogen planarities: 413 Chain: "H" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 480 Classifications: {'peptide': 120} Incomplete info: {'backbone_only': 114} Link IDs: {'PTRANS': 6, 'TRANS': 113} Chain breaks: 4 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 439 Unresolved non-hydrogen angles: 643 Unresolved non-hydrogen dihedrals: 258 Unresolved non-hydrogen chiralities: 151 Planarities with less than four sites: {'GLN:plan1': 7, 'PHE:plan': 5, 'HIS:plan': 2, 'GLU:plan': 13, 'TYR:plan': 1, 'ASN:plan1': 7, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 177 Chain: "I" Number of atoms: 193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 193 Classifications: {'peptide': 48} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 47} Link IDs: {'PTRANS': 2, 'TRANS': 45} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 188 Unresolved non-hydrogen angles: 278 Unresolved non-hydrogen dihedrals: 114 Unresolved non-hydrogen chiralities: 62 Planarities with less than four sites: {'TYR:plan': 4, 'ASN:plan1': 3, 'GLN:plan1': 4, 'ARG:plan': 2, 'GLU:plan': 2, 'ASP:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 89 Chain: "O" Number of atoms: 748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 748 Classifications: {'peptide': 187} Incomplete info: {'backbone_only': 174} Link IDs: {'PTRANS': 7, 'TRANS': 179} Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 691 Unresolved non-hydrogen angles: 1001 Unresolved non-hydrogen dihedrals: 414 Unresolved non-hydrogen chiralities: 235 Planarities with less than four sites: {'ARG:plan': 4, 'PHE:plan': 5, 'GLU:plan': 11, 'TYR:plan': 3, 'GLN:plan1': 5, 'ASN:plan1': 12, 'ASP:plan': 10, 'HIS:plan': 3} Unresolved non-hydrogen planarities: 249 Chain: "T" Number of atoms: 897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 897 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 207} Link IDs: {'PTRANS': 7, 'TRANS': 216} Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 925 Unresolved non-hydrogen angles: 1359 Unresolved non-hydrogen dihedrals: 607 Unresolved non-hydrogen chiralities: 306 Planarities with less than four sites: {'PHE:plan': 18, 'TYR:plan': 10, 'ASN:plan1': 11, 'ARG:plan': 3, 'TRP:plan': 5, 'GLN:plan1': 3, 'GLU:plan': 3, 'ASP:plan': 2, 'HIS:plan': 3, 'HIS%COO:plan': 1} Unresolved non-hydrogen planarities: 371 Chain: "U" Number of atoms: 620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 620 Classifications: {'peptide': 155} Incomplete info: {'backbone_only': 152} Link IDs: {'PTRANS': 2, 'TRANS': 152} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 631 Unresolved non-hydrogen angles: 908 Unresolved non-hydrogen dihedrals: 388 Unresolved non-hydrogen chiralities: 198 Planarities with less than four sites: {'ASN:plan1': 5, 'ASP:plan': 8, 'GLU:plan': 16, 'PHE:plan': 6, 'TYR:plan': 3, 'ARG:plan': 7, 'HIS:plan': 2, 'GLN:plan1': 11, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 283 Chain: "V" Number of atoms: 685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 685 Classifications: {'peptide': 171} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 166} Link IDs: {'PTRANS': 5, 'TRANS': 165} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 705 Unresolved non-hydrogen angles: 1009 Unresolved non-hydrogen dihedrals: 446 Unresolved non-hydrogen chiralities: 214 Planarities with less than four sites: {'ASN:plan1': 7, 'ASP:plan': 13, 'TRP:plan': 2, 'ARG:plan': 7, 'GLN:plan1': 9, 'PHE:plan': 5, 'GLU:plan': 13, 'HIS:plan': 2, 'TYR:plan': 4} Unresolved non-hydrogen planarities: 302 Chain: "W" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 340 Classifications: {'peptide': 85} Incomplete info: {'backbone_only': 79} Link IDs: {'PTRANS': 7, 'TRANS': 77} Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 348 Unresolved non-hydrogen angles: 503 Unresolved non-hydrogen dihedrals: 241 Unresolved non-hydrogen chiralities: 97 Planarities with less than four sites: {'ASN:plan1': 5, 'ARG:plan': 3, 'HIS:plan': 3, 'PHE:plan': 5, 'TYR:plan': 6, 'GLN:plan1': 1, 'ASP:plan': 2, 'TRP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 162 Chain: "X" Number of atoms: 248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 248 Classifications: {'peptide': 62} Incomplete info: {'backbone_only': 60} Link IDs: {'PTRANS': 7, 'TRANS': 54} Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 257 Unresolved non-hydrogen angles: 375 Unresolved non-hydrogen dihedrals: 161 Unresolved non-hydrogen chiralities: 77 Planarities with less than four sites: {'ASN:plan1': 5, 'GLN:plan1': 5, 'ASP:plan': 3, 'TYR:plan': 2, 'ARG:plan': 1, 'GLU:plan': 7, 'TRP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 117 Chain: "Y" Number of atoms: 148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 148 Classifications: {'peptide': 37} Incomplete info: {'backbone_only': 35} Link IDs: {'PTRANS': 3, 'TRANS': 33} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 155 Unresolved non-hydrogen angles: 225 Unresolved non-hydrogen dihedrals: 110 Unresolved non-hydrogen chiralities: 44 Planarities with less than four sites: {'ARG:plan': 1, 'PHE:plan': 3, 'TYR:plan': 3, 'TRP:plan': 1, 'ASP:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 68 Chain: "Z" Number of atoms: 193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 193 Classifications: {'peptide': 48} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 46} Link IDs: {'PTRANS': 3, 'TRANS': 44} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 231 Unresolved non-hydrogen angles: 330 Unresolved non-hydrogen dihedrals: 158 Unresolved non-hydrogen chiralities: 67 Planarities with less than four sites: {'GLN:plan1': 3, 'PHE:plan': 7, 'TYR:plan': 3, 'ASN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 99 Time building chain proxies: 5.52, per 1000 atoms: 0.27 Number of scatterers: 20228 At special positions: 0 Unit cell: (123.97, 148.225, 235.812, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 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: 1.65 Conformation dependent library (CDL) restraints added in 1.4 seconds Enol-peptide restraints added in 476.8 nanoseconds 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: 191 helices and 28 sheets defined 59.3% alpha, 11.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.60 Creating SS restraints... Processing helix chain '0' and resid 1 through 17 removed outlier: 3.581A pdb=" N GLY 0 13 " --> pdb=" O TYR 0 9 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE 0 17 " --> pdb=" O GLY 0 13 " (cutoff:3.500A) Processing helix chain '0' and resid 18 through 40 removed outlier: 3.980A pdb=" N ALA 0 22 " --> pdb=" O GLY 0 18 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA 0 27 " --> pdb=" O GLY 0 23 " (cutoff:3.500A) Processing helix chain '0' and resid 43 through 75 Proline residue: 0 49 - end of helix removed outlier: 3.501A pdb=" N THR 0 61 " --> pdb=" O LEU 0 57 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY 0 62 " --> pdb=" O SER 0 58 " (cutoff:3.500A) Processing helix chain '1' and resid 2 through 17 removed outlier: 3.557A pdb=" N GLY 1 13 " --> pdb=" O TYR 1 9 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ILE 1 17 " --> pdb=" O GLY 1 13 " (cutoff:3.500A) Processing helix chain '1' and resid 18 through 40 removed outlier: 4.442A pdb=" N ALA 1 22 " --> pdb=" O GLY 1 18 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ALA 1 27 " --> pdb=" O GLY 1 23 " (cutoff:3.500A) Processing helix chain '1' and resid 43 through 74 Proline residue: 1 49 - end of helix Processing helix chain '2' and resid 2 through 16 Processing helix chain '2' and resid 18 through 40 removed outlier: 4.171A pdb=" N ALA 2 22 " --> pdb=" O GLY 2 18 " (cutoff:3.500A) removed outlier: 3.702A 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: 4.363A pdb=" N THR 2 61 " --> pdb=" O LEU 2 57 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N GLY 2 62 " --> pdb=" O SER 2 58 " (cutoff:3.500A) Processing helix chain '3' and resid 3 through 17 removed outlier: 3.815A pdb=" N ILE 3 17 " --> pdb=" O GLY 3 13 " (cutoff:3.500A) Processing helix chain '3' and resid 18 through 40 removed outlier: 4.237A pdb=" N ALA 3 22 " --> pdb=" O GLY 3 18 " (cutoff:3.500A) removed outlier: 3.782A 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: 3.660A 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: 4.267A 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: 3.905A pdb=" N THR 4 61 " --> pdb=" O LEU 4 57 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N GLY 4 62 " --> pdb=" O SER 4 58 " (cutoff:3.500A) Processing helix chain '5' and resid 2 through 17 removed outlier: 3.845A pdb=" N ILE 5 17 " --> pdb=" O GLY 5 13 " (cutoff:3.500A) Processing helix chain '5' and resid 19 through 40 removed outlier: 3.522A 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: 3.860A pdb=" N GLY 5 62 " --> pdb=" O SER 5 58 " (cutoff:3.500A) Processing helix chain '6' and resid 3 through 16 Processing helix chain '6' and resid 19 through 40 removed outlier: 3.687A pdb=" N ALA 6 27 " --> pdb=" O GLY 6 23 " (cutoff:3.500A) Processing helix chain '6' and resid 43 through 75 Proline residue: 6 49 - end of helix removed outlier: 3.837A pdb=" N THR 6 61 " --> pdb=" O LEU 6 57 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLY 6 62 " --> pdb=" O SER 6 58 " (cutoff:3.500A) Processing helix chain '7' and resid 2 through 40 removed outlier: 3.641A pdb=" N THR 7 16 " --> pdb=" O ALA 7 12 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N ILE 7 17 " --> pdb=" O GLY 7 13 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N GLY 7 18 " --> pdb=" O ILE 7 14 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N LEU 7 19 " --> pdb=" O SER 7 15 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU 7 20 " --> pdb=" O THR 7 16 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLY 7 21 " --> pdb=" O ILE 7 17 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ALA 7 22 " --> pdb=" O GLY 7 18 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ALA 7 27 " --> pdb=" O GLY 7 23 " (cutoff:3.500A) Processing helix chain '7' and resid 43 through 73 Proline residue: 7 49 - end of helix removed outlier: 3.832A pdb=" N GLY 7 62 " --> pdb=" O SER 7 58 " (cutoff:3.500A) Processing helix chain '8' and resid 2 through 16 removed outlier: 3.827A pdb=" N THR 8 16 " --> pdb=" O ALA 8 12 " (cutoff:3.500A) Processing helix chain '8' and resid 16 through 40 removed outlier: 3.975A pdb=" N LEU 8 20 " --> pdb=" O THR 8 16 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N GLY 8 21 " --> pdb=" O ILE 8 17 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ALA 8 22 " --> pdb=" O GLY 8 18 " (cutoff:3.500A) Processing helix chain '8' and resid 43 through 75 Proline residue: 8 49 - end of helix removed outlier: 3.546A pdb=" N THR 8 61 " --> pdb=" O LEU 8 57 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLY 8 62 " --> pdb=" O SER 8 58 " (cutoff:3.500A) Processing helix chain '9' and resid 3 through 18 removed outlier: 3.600A pdb=" N ILE 9 17 " --> pdb=" O GLY 9 13 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLY 9 18 " --> pdb=" O ILE 9 14 " (cutoff:3.500A) Processing helix chain '9' and resid 18 through 40 removed outlier: 4.201A pdb=" N ALA 9 22 " --> pdb=" O GLY 9 18 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA 9 27 " --> pdb=" O GLY 9 23 " (cutoff:3.500A) Processing helix chain '9' and resid 43 through 75 Proline residue: 9 49 - end of helix Processing helix chain 'A' and resid 10 through 20 Processing helix chain 'A' and resid 152 through 159 Processing helix chain 'A' and resid 176 through 194 removed outlier: 3.890A pdb=" N THR A 184 " --> pdb=" O VAL A 180 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE A 185 " --> pdb=" O ALA A 181 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LYS A 189 " --> pdb=" O ILE A 185 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N ARG A 190 " --> pdb=" O LEU A 186 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N TRP A 191 " --> pdb=" O ASN A 187 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLY A 194 " --> pdb=" O ARG A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 225 Processing helix chain 'A' and resid 241 through 262 Proline residue: A 249 - end of helix removed outlier: 3.712A pdb=" N PHE A 259 " --> pdb=" O ILE A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 288 Processing helix chain 'A' and resid 292 through 296 Processing helix chain 'A' and resid 299 through 309 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 381 Processing helix chain 'A' and resid 382 through 388 Processing helix chain 'A' and resid 389 through 402 removed outlier: 3.711A pdb=" N LYS A 393 " --> pdb=" O ALA A 389 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU A 394 " --> pdb=" O GLY A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 407 removed outlier: 3.737A pdb=" N GLN A 407 " --> pdb=" O ALA A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 430 Processing helix chain 'A' and resid 439 through 452 Proline residue: A 445 - end of helix Processing helix chain 'A' and resid 453 through 457 removed outlier: 3.561A pdb=" N GLY A 457 " --> pdb=" O HIS A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 478 removed outlier: 3.642A pdb=" N SER A 468 " --> pdb=" O GLY A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 489 removed outlier: 3.784A pdb=" N LEU A 482 " --> pdb=" O HIS A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 509 Processing helix chain 'B' and resid 10 through 19 Processing helix chain 'B' and resid 80 through 84 Processing helix chain 'B' and resid 102 through 106 removed outlier: 3.638A pdb=" N LEU B 105 " --> pdb=" O GLY B 102 " (cutoff:3.500A) removed outlier: 3.795A 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 176 through 188 removed outlier: 4.071A pdb=" N VAL B 180 " --> pdb=" O GLY B 176 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ALA B 181 " --> pdb=" O LYS B 177 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N THR B 184 " --> pdb=" O VAL B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 225 Processing helix chain 'B' and resid 227 through 229 No H-bonds generated for 'chain 'B' and resid 227 through 229' Processing helix chain 'B' and resid 241 through 261 Proline residue: B 249 - end of helix removed outlier: 3.646A pdb=" N PHE B 259 " --> pdb=" O ILE B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 287 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 383 through 388 Processing helix chain 'B' and resid 391 through 407 removed outlier: 3.590A pdb=" N ARG B 400 " --> pdb=" O LEU B 396 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLU B 401 " --> pdb=" O ALA B 397 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLN B 407 " --> pdb=" O ALA B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 431 removed outlier: 3.627A pdb=" N LYS B 431 " --> pdb=" O THR B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 452 Proline residue: B 445 - end of helix 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 489 removed outlier: 7.599A pdb=" N GLU B 480 " --> pdb=" O SER B 476 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N LEU B 481 " --> pdb=" O ASN B 477 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N LEU B 482 " --> pdb=" O HIS B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 509 Processing helix chain 'C' and resid 13 through 22 Processing helix chain 'C' and resid 102 through 106 removed outlier: 3.904A pdb=" N LEU C 105 " --> pdb=" O GLY C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 159 Processing helix chain 'C' and resid 176 through 188 removed outlier: 4.176A pdb=" N ALA C 181 " --> pdb=" O LYS C 177 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR C 184 " --> pdb=" O VAL C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 188 through 194 removed outlier: 3.846A pdb=" N GLY C 194 " --> pdb=" O ARG C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 225 Processing helix chain 'C' and resid 241 through 263 Proline residue: C 249 - end of helix removed outlier: 3.888A pdb=" N PHE C 259 " --> pdb=" O ILE C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 286 removed outlier: 3.642A pdb=" N GLN C 276 " --> pdb=" O ASP C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 297 Proline residue: C 297 - end of helix Processing helix chain 'C' and resid 298 through 309 removed outlier: 4.336A pdb=" N TYR C 302 " --> pdb=" O GLY C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 348 Processing helix chain 'C' and resid 355 through 362 Processing helix chain 'C' and resid 382 through 389 Processing helix chain 'C' and resid 391 through 408 Processing helix chain 'C' and resid 413 through 431 Processing helix chain 'C' and resid 439 through 442 Processing helix chain 'C' and resid 443 through 452 Processing helix chain 'C' and resid 453 through 458 removed outlier: 4.381A pdb=" N GLY C 457 " --> pdb=" O GLY C 453 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N ILE C 458 " --> pdb=" O HIS C 454 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 453 through 458' Processing helix chain 'C' and resid 459 through 461 No H-bonds generated for 'chain 'C' and resid 459 through 461' Processing helix chain 'C' and resid 462 through 477 Processing helix chain 'C' and resid 478 through 489 Processing helix chain 'C' and resid 492 through 506 Processing helix chain 'D' and resid 138 through 145 Processing helix chain 'D' and resid 162 through 178 removed outlier: 4.267A pdb=" N LYS D 176 " --> pdb=" O ASN D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 204 Processing helix chain 'D' and resid 225 through 246 removed outlier: 4.591A pdb=" N ALA D 233 " --> pdb=" O ARG D 229 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N LEU D 234 " --> pdb=" O ALA D 230 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE D 239 " --> pdb=" O THR D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 273 removed outlier: 3.683A pdb=" N PHE D 261 " --> pdb=" O ASN D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 277 through 281 Processing helix chain 'D' and resid 284 through 296 Processing helix chain 'D' and resid 313 through 316 Processing helix chain 'D' and resid 319 through 329 removed outlier: 3.622A pdb=" N ALA D 327 " --> pdb=" O ALA D 323 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N HIS D 328 " --> pdb=" O THR D 324 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU D 329 " --> pdb=" O THR D 325 " (cutoff:3.500A) Processing helix chain 'D' and resid 336 through 343 Processing helix chain 'D' and resid 359 through 364 Processing helix chain 'D' and resid 364 through 391 removed outlier: 4.501A pdb=" N ASP D 386 " --> pdb=" O LYS D 382 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N ILE D 387 " --> pdb=" O SER D 383 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ILE D 390 " --> pdb=" O ASP D 386 " (cutoff:3.500A) Processing helix chain 'D' and resid 397 through 412 Processing helix chain 'D' and resid 420 through 425 removed outlier: 4.028A pdb=" N PHE D 424 " --> pdb=" O VAL D 420 " (cutoff:3.500A) Processing helix chain 'D' and resid 433 through 447 removed outlier: 3.775A pdb=" N VAL D 444 " --> pdb=" O SER D 440 " (cutoff:3.500A) Processing helix chain 'D' and resid 453 through 457 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 Processing helix chain 'E' and resid 190 through 204 Processing helix chain 'E' and resid 225 through 247 removed outlier: 4.866A pdb=" N ALA E 233 " --> pdb=" O ARG E 229 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N LEU E 234 " --> pdb=" O ALA E 230 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE E 239 " --> pdb=" O THR E 235 " (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 removed outlier: 3.527A pdb=" N ARG E 295 " --> pdb=" O LEU E 291 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ILE E 296 " --> pdb=" O LEU E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 312 through 316 removed outlier: 3.844A pdb=" N ASP E 315 " --> pdb=" O VAL E 312 " (cutoff:3.500A) Processing helix chain 'E' and resid 319 through 329 Processing helix chain 'E' and resid 336 through 342 removed outlier: 3.612A pdb=" N SER E 340 " --> pdb=" O SER E 336 " (cutoff:3.500A) Processing helix chain 'E' and resid 359 through 364 Processing helix chain 'E' and resid 364 through 392 removed outlier: 3.641A pdb=" N ILE E 387 " --> pdb=" O SER E 383 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE E 390 " --> pdb=" O ASP E 386 " (cutoff:3.500A) Processing helix chain 'E' and resid 397 through 414 removed outlier: 3.522A pdb=" N LYS E 409 " --> pdb=" O GLU E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 421 through 426 Processing helix chain 'E' and resid 433 through 446 Processing helix chain 'E' and resid 453 through 457 Processing helix chain 'E' and resid 462 through 475 removed outlier: 3.689A pdb=" N ALA E 468 " --> pdb=" O GLU E 464 " (cutoff:3.500A) Processing helix chain 'F' and resid 138 through 145 Processing helix chain 'F' and resid 162 through 178 removed outlier: 4.333A pdb=" N LYS F 176 " --> pdb=" O ASN F 172 " (cutoff:3.500A) Processing helix chain 'F' and resid 190 through 204 Processing helix chain 'F' and resid 225 through 231 removed outlier: 3.540A pdb=" N ARG F 231 " --> pdb=" O GLY F 227 " (cutoff:3.500A) Processing helix chain 'F' and resid 231 through 245 removed outlier: 3.517A pdb=" N PHE F 243 " --> pdb=" O ILE F 239 " (cutoff:3.500A) Processing helix chain 'F' and resid 258 through 273 removed outlier: 4.185A pdb=" N ALA F 270 " --> pdb=" O SER F 266 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N LEU F 271 " --> pdb=" O GLU F 267 " (cutoff:3.500A) Processing helix chain 'F' and resid 277 through 281 Processing helix chain 'F' and resid 284 through 295 Processing helix chain 'F' and resid 313 through 316 Processing helix chain 'F' and resid 319 through 327 removed outlier: 3.589A pdb=" N THR F 325 " --> pdb=" O ALA F 321 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ALA F 327 " --> pdb=" O ALA F 323 " (cutoff:3.500A) Processing helix chain 'F' and resid 336 through 342 Processing helix chain 'F' and resid 364 through 384 Processing helix chain 'F' and resid 384 through 391 Processing helix chain 'F' and resid 392 through 396 Processing helix chain 'F' and resid 397 through 414 Processing helix chain 'F' and resid 421 through 426 Processing helix chain 'F' and resid 433 through 446 removed outlier: 3.535A pdb=" N ALA F 439 " --> pdb=" O LYS F 435 " (cutoff:3.500A) Processing helix chain 'F' and resid 453 through 458 Processing helix chain 'F' and resid 462 through 475 Processing helix chain 'G' and resid 2 through 55 removed outlier: 3.646A pdb=" N LYS G 33 " --> pdb=" O THR G 29 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N SER G 40 " --> pdb=" O LYS G 36 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE G 51 " --> pdb=" O ALA G 47 " (cutoff:3.500A) Processing helix chain 'G' and resid 86 through 102 removed outlier: 3.814A pdb=" N ASP G 101 " --> pdb=" O ARG G 97 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLN G 102 " --> pdb=" O HIS G 98 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 122 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: 3.558A pdb=" N GLN G 190 " --> pdb=" O LYS G 186 " (cutoff:3.500A) Processing helix chain 'G' and resid 204 through 276 removed outlier: 4.180A pdb=" N GLU G 211 " --> pdb=" O ARG G 207 " (cutoff:3.500A) Processing helix chain 'H' and resid 100 through 115 removed outlier: 3.613A pdb=" N SER H 114 " --> pdb=" O LYS H 110 " (cutoff:3.500A) Processing helix chain 'H' and resid 119 through 136 removed outlier: 3.860A 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 39 Processing helix chain 'O' and resid 16 through 29 Processing helix chain 'O' and resid 32 through 49 removed outlier: 3.698A pdb=" N ALA O 36 " --> pdb=" O SER O 32 " (cutoff:3.500A) Processing helix chain 'O' and resid 63 through 77 Processing helix chain 'O' and resid 83 through 95 Processing helix chain 'O' and resid 101 through 117 Processing helix chain 'O' and resid 130 through 144 Processing helix chain 'O' and resid 179 through 191 removed outlier: 3.610A pdb=" N LYS O 183 " --> pdb=" O SER O 179 " (cutoff:3.500A) Processing helix chain 'T' and resid 27 through 43 Processing helix chain 'T' and resid 58 through 77 removed outlier: 3.847A pdb=" N GLN T 62 " --> pdb=" O TRP T 58 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N TYR T 66 " --> pdb=" O GLN T 62 " (cutoff:3.500A) Processing helix chain 'T' and resid 85 through 100 removed outlier: 3.510A pdb=" N PHE T 95 " --> pdb=" O THR T 91 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ILE T 96 " --> pdb=" O LEU T 92 " (cutoff:3.500A) Processing helix chain 'T' and resid 114 through 137 removed outlier: 3.758A pdb=" N ILE T 118 " --> pdb=" O HIS T 114 " (cutoff:3.500A) Processing helix chain 'T' and resid 138 through 146 Processing helix chain 'T' and resid 151 through 155 Processing helix chain 'T' and resid 156 through 167 removed outlier: 3.745A pdb=" N GLU T 162 " --> pdb=" O LEU T 158 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N SER T 165 " --> pdb=" O ILE T 161 " (cutoff:3.500A) Processing helix chain 'T' and resid 168 through 199 removed outlier: 3.924A pdb=" N LEU T 173 " --> pdb=" O ARG T 169 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N GLY T 174 " --> pdb=" O ALA T 170 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU T 177 " --> pdb=" O LEU T 173 " (cutoff:3.500A) Processing helix chain 'T' and resid 202 through 207 Processing helix chain 'T' and resid 210 through 247 removed outlier: 3.721A pdb=" N MET T 215 " --> pdb=" O VAL T 211 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE T 228 " --> pdb=" O PHE T 224 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ALA T 235 " --> pdb=" O GLY T 231 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA T 239 " --> pdb=" O ALA T 235 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LEU T 242 " --> pdb=" O THR T 238 " (cutoff:3.500A) Processing helix chain 'U' and resid 54 through 184 removed outlier: 3.662A pdb=" N LEU U 58 " --> pdb=" O ASP U 54 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ALA U 74 " --> pdb=" O ALA U 70 " (cutoff:3.500A) Proline residue: U 75 - end of helix removed outlier: 3.511A pdb=" N LYS U 104 " --> pdb=" O VAL U 100 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLN U 112 " --> pdb=" O ASP U 108 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LEU U 113 " --> pdb=" O SER U 109 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASN U 115 " --> pdb=" O SER U 111 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLU U 118 " --> pdb=" O GLN U 114 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR U 119 " --> pdb=" O ASN U 115 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LYS U 121 " --> pdb=" O ALA U 117 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL U 122 " --> pdb=" O GLU U 118 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS U 128 " --> pdb=" O PHE U 124 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU U 136 " --> pdb=" O GLU U 132 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLU U 139 " --> pdb=" O SER U 135 " (cutoff:3.500A) Processing helix chain 'U' and resid 187 through 206 removed outlier: 4.244A pdb=" N VAL U 193 " --> pdb=" O PHE U 189 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU U 194 " --> pdb=" O GLN U 190 " (cutoff:3.500A) Processing helix chain 'V' and resid 4 through 19 Processing helix chain 'V' and resid 26 through 48 removed outlier: 3.518A pdb=" N GLN V 42 " --> pdb=" O GLU V 38 " (cutoff:3.500A) Processing helix chain 'V' and resid 57 through 62 removed outlier: 3.848A pdb=" N LEU V 62 " --> pdb=" O TYR V 58 " (cutoff:3.500A) Processing helix chain 'V' and resid 67 through 78 Processing helix chain 'V' and resid 90 through 127 removed outlier: 3.572A pdb=" N ALA V 127 " --> pdb=" O ASN V 123 " (cutoff:3.500A) Processing helix chain 'V' and resid 134 through 142 Processing helix chain 'V' and resid 143 through 156 Processing helix chain 'W' and resid 5 through 9 removed outlier: 3.659A pdb=" N LYS W 8 " --> pdb=" O ILE W 5 " (cutoff:3.500A) Processing helix chain 'W' and resid 18 through 30 removed outlier: 3.735A pdb=" N LYS W 22 " --> pdb=" O ALA W 18 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N VAL W 28 " --> pdb=" O ILE W 24 " (cutoff:3.500A) Processing helix chain 'W' and resid 48 through 56 Processing helix chain 'W' and resid 63 through 82 removed outlier: 3.790A pdb=" N ILE W 73 " --> pdb=" O PHE W 69 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER W 79 " --> pdb=" O ALA W 75 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N TYR W 82 " --> pdb=" O TYR W 78 " (cutoff:3.500A) Processing helix chain 'X' and resid 2 through 14 removed outlier: 3.648A pdb=" N THR X 14 " --> pdb=" O GLU X 10 " (cutoff:3.500A) Processing helix chain 'X' and resid 20 through 27 removed outlier: 3.712A pdb=" N ALA X 24 " --> pdb=" O THR X 20 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU X 25 " --> pdb=" O LEU X 21 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N GLY X 26 " --> pdb=" O GLN X 22 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ASN X 27 " --> pdb=" O ASP X 23 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 20 through 27' Processing helix chain 'X' and resid 47 through 57 Processing helix chain 'Y' and resid 13 through 35 Processing helix chain 'Z' and resid 8 through 30 Processing helix chain 'Z' and resid 30 through 48 removed outlier: 3.663A pdb=" N ILE Z 35 " --> pdb=" O PHE Z 31 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU Z 38 " --> pdb=" O MET Z 34 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 37 removed outlier: 6.747A pdb=" N ARG A 42 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N VAL A 36 " --> pdb=" O ILE A 40 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ILE A 40 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N GLY A 74 " --> pdb=" O LEU A 66 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU A 66 " --> pdb=" O GLY A 74 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 10 through 17 current: chain 'A' and resid 90 through 96 Processing sheet with id=AA2, first strand: chain 'A' and resid 31 through 37 removed outlier: 6.747A pdb=" N ARG A 42 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N VAL A 36 " --> pdb=" O ILE A 40 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ILE A 40 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N GLY A 74 " --> pdb=" O LEU A 66 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU A 66 " --> pdb=" O GLY A 74 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 62 through 68 current: chain 'E' and resid 36 through 41 removed outlier: 6.370A pdb=" N ARG E 60 " --> pdb=" O ALA E 51 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N HIS E 53 " --> pdb=" O THR E 58 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N THR E 58 " --> pdb=" O HIS E 53 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL E 23 " --> pdb=" O VAL E 59 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ILE E 20 " --> pdb=" O VAL E 16 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N VAL E 16 " --> pdb=" O ILE E 20 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N ASP E 22 " --> pdb=" O THR E 14 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 10 through 17 current: chain 'A' and resid 90 through 96 Processing sheet with id=AA3, first strand: chain 'A' and resid 98 through 101 Processing sheet with id=AA4, first strand: chain 'A' and resid 109 through 110 removed outlier: 6.385A pdb=" N VAL A 110 " --> pdb=" O ALA A 235 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N THR A 237 " --> pdb=" O VAL A 110 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 328 through 331 removed outlier: 5.855A pdb=" N ILE A 169 " --> pdb=" O ILE A 329 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N THR A 331 " --> pdb=" O ILE A 169 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N GLY A 171 " --> pdb=" O THR A 331 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ILE A 170 " --> pdb=" O LEU A 354 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 350 through 351 Processing sheet with id=AA7, first strand: chain 'F' and resid 77 through 78 removed outlier: 6.587A pdb=" N ARG F 60 " --> pdb=" O ALA F 51 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N HIS F 53 " --> pdb=" O THR F 58 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N THR F 58 " --> pdb=" O HIS F 53 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE F 17 " --> pdb=" O ILE F 20 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N HIS F 24 " --> pdb=" O VAL F 13 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N VAL F 13 " --> pdb=" O HIS F 24 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N GLY B 63 " --> pdb=" O PHE B 78 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N PHE B 78 " --> pdb=" O GLY B 63 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N ALA B 65 " --> pdb=" O VAL B 76 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N VAL B 76 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASN B 67 " --> pdb=" O GLY B 74 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N ILE B 40 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N VAL B 36 " --> pdb=" O ILE B 40 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N ARG B 42 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N LEU B 54 " --> pdb=" O THR B 93 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N GLU B 53 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL B 61 " --> pdb=" O PHE B 57 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 98 through 101 Processing sheet with id=AA9, first strand: chain 'B' and resid 109 through 111 removed outlier: 6.394A pdb=" N CYS B 203 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N VAL B 234 " --> pdb=" O CYS B 203 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N TYR B 205 " --> pdb=" O VAL B 234 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N ALA B 236 " --> pdb=" O TYR B 205 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N ALA B 207 " --> pdb=" O ALA B 236 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N TYR B 202 " --> pdb=" O LEU B 267 " (cutoff:3.500A) removed outlier: 8.136A pdb=" N VAL B 269 " --> pdb=" O TYR B 202 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N VAL B 204 " --> pdb=" O VAL B 269 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N ASP B 271 " --> pdb=" O VAL B 204 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N VAL B 206 " --> pdb=" O ASP B 271 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ALA B 266 " --> pdb=" O THR B 324 " (cutoff:3.500A) removed outlier: 8.439A pdb=" N LEU B 326 " --> pdb=" O ALA B 266 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ILE B 268 " --> pdb=" O LEU B 326 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N VAL B 328 " --> pdb=" O ILE B 268 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N TYR B 270 " --> pdb=" O VAL B 328 " (cutoff:3.500A) removed outlier: 8.085A pdb=" N GLU B 330 " --> pdb=" O TYR B 270 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ILE B 169 " --> pdb=" O ILE B 329 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N THR B 331 " --> pdb=" O ILE B 169 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N GLY B 171 " --> pdb=" O THR B 331 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N ILE B 170 " --> pdb=" O LEU B 354 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N PHE B 353 " --> pdb=" O LEU B 371 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N LEU B 371 " --> pdb=" O PHE B 353 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 30 through 35 removed outlier: 7.004A pdb=" N ARG C 42 " --> pdb=" O LEU C 34 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLU C 53 " --> pdb=" O ALA C 65 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N LEU C 54 " --> pdb=" O THR C 93 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 98 through 101 Processing sheet with id=AB3, first strand: chain 'C' and resid 109 through 110 removed outlier: 6.169A pdb=" N VAL C 110 " --> pdb=" O ALA C 235 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 109 through 110 removed outlier: 6.169A pdb=" N VAL C 110 " --> pdb=" O ALA C 235 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLY C 171 " --> pdb=" O ILE C 329 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N LEU C 168 " --> pdb=" O ILE C 352 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 147 through 148 removed outlier: 3.971A pdb=" N ILE C 161 " --> pdb=" O VAL C 148 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 11 through 16 removed outlier: 6.804A pdb=" N ASP D 22 " --> pdb=" O THR D 14 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ARG D 60 " --> pdb=" O ALA D 51 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 84 through 87 removed outlier: 3.508A pdb=" N LYS D 115 " --> pdb=" O VAL D 85 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 217 through 221 Processing sheet with id=AB9, first strand: chain 'E' and resid 84 through 87 removed outlier: 4.504A pdb=" N LEU E 113 " --> pdb=" O VAL E 87 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 95 through 96 removed outlier: 3.745A pdb=" N PHE E 219 " --> pdb=" O ILE E 96 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N SER E 182 " --> pdb=" O ALA E 216 " (cutoff:3.500A) removed outlier: 8.142A pdb=" N VAL E 218 " --> pdb=" O SER E 182 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N PHE E 184 " --> pdb=" O VAL E 218 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N GLY E 220 " --> pdb=" O PHE E 184 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N GLY E 186 " --> pdb=" O GLY E 220 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N PHE E 181 " --> pdb=" O LEU E 252 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N PHE E 254 " --> pdb=" O PHE E 181 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N VAL E 183 " --> pdb=" O PHE E 254 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N ASP E 256 " --> pdb=" O VAL E 183 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N THR E 185 " --> pdb=" O ASP E 256 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL E 307 " --> pdb=" O LEU E 253 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA E 309 " --> pdb=" O ILE E 255 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ASN E 257 " --> pdb=" O ALA E 309 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLN E 308 " --> pdb=" O ILE E 153 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 133 through 134 removed outlier: 3.842A pdb=" N TYR E 147 " --> pdb=" O LEU E 134 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 84 through 87 removed outlier: 4.154A pdb=" N LEU F 113 " --> pdb=" O VAL F 87 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 95 through 96 removed outlier: 4.271A pdb=" N PHE F 219 " --> pdb=" O ILE F 96 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ALA F 216 " --> pdb=" O VAL F 183 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N THR F 185 " --> pdb=" O ALA F 216 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N VAL F 218 " --> pdb=" O THR F 185 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N VAL F 187 " --> pdb=" O VAL F 218 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N GLY F 220 " --> pdb=" O VAL F 187 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N THR F 305 " --> pdb=" O VAL F 251 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N LYS F 152 " --> pdb=" O ALA F 331 " (cutoff:3.500A) removed outlier: 8.152A pdb=" N THR F 333 " --> pdb=" O LYS F 152 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N GLY F 154 " --> pdb=" O THR F 333 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N LEU F 335 " --> pdb=" O GLY F 154 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N PHE F 156 " --> pdb=" O LEU F 335 " (cutoff:3.500A) removed outlier: 10.793A pdb=" N THR F 332 " --> pdb=" O LEU F 351 " (cutoff:3.500A) removed outlier: 9.307A pdb=" N LEU F 351 " --> pdb=" O THR F 332 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N VAL F 334 " --> pdb=" O ASP F 349 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 132 through 134 removed outlier: 4.813A pdb=" N GLU F 132 " --> pdb=" O ARG F 149 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TYR F 147 " --> pdb=" O LEU F 134 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 174 through 181 removed outlier: 6.355A pdb=" N SER G 174 " --> pdb=" O VAL G 170 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL G 170 " --> pdb=" O SER G 174 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N LEU G 73 " --> pdb=" O SER G 163 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N PHE G 165 " --> pdb=" O LEU G 73 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N VAL G 75 " --> pdb=" O PHE G 165 " (cutoff:3.500A) removed outlier: 8.866A pdb=" N ASN G 167 " --> pdb=" O VAL G 75 " (cutoff:3.500A) removed outlier: 9.094A pdb=" N ILE G 77 " --> pdb=" O ASN G 167 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N GLU G 72 " --> pdb=" O ASP G 106 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N VAL G 108 " --> pdb=" O GLU G 72 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N ILE G 74 " --> pdb=" O VAL G 108 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N ILE G 110 " --> pdb=" O ILE G 74 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N ALA G 76 " --> pdb=" O ILE G 110 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ILE G 126 " --> pdb=" O ALA G 105 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ILE G 107 " --> pdb=" O ILE G 126 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N LEU G 128 " --> pdb=" O ILE G 107 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 12 through 15 Processing sheet with id=AC8, first strand: chain 'H' and resid 37 through 42 removed outlier: 6.565A pdb=" N VAL H 56 " --> pdb=" O PRO H 33 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'O' and resid 119 through 120 removed outlier: 6.785A pdb=" N LEU O 119 " --> pdb=" O LYS O 154 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'O' and resid 157 through 159 removed outlier: 3.533A pdb=" N THR O 124 " --> pdb=" O ILE O 168 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE O 168 " --> pdb=" O THR O 124 " (cutoff:3.500A) 2327 hydrogen bonds defined for protein. 6753 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.51 Time building geometry restraints manager: 2.13 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 - 1.34: 1063 1.34 - 1.41: 3957 1.41 - 1.48: 5100 1.48 - 1.54: 5012 Bond restraints: 20192 Sorted by residual: bond pdb=" CA GLY D 11 " pdb=" C GLY D 11 " ideal model delta sigma weight residual 1.516 1.475 0.041 8.20e-03 1.49e+04 2.49e+01 bond pdb=" N LYS O 160 " pdb=" CA LYS O 160 " ideal model delta sigma weight residual 1.462 1.416 0.046 9.30e-03 1.16e+04 2.47e+01 bond pdb=" CA HIS E 178 " pdb=" C HIS E 178 " ideal model delta sigma weight residual 1.519 1.470 0.049 1.01e-02 9.80e+03 2.36e+01 bond pdb=" CA SER E 306 " pdb=" C SER E 306 " ideal model delta sigma weight residual 1.520 1.462 0.058 1.20e-02 6.94e+03 2.35e+01 bond pdb=" CA ALA C 236 " pdb=" C ALA C 236 " ideal model delta sigma weight residual 1.530 1.478 0.052 1.08e-02 8.57e+03 2.31e+01 ... (remaining 20187 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.02: 21443 3.02 - 6.04: 3119 6.04 - 9.05: 543 9.05 - 12.07: 72 12.07 - 15.09: 3 Bond angle restraints: 25180 Sorted by residual: angle pdb=" N VAL A 376 " pdb=" CA VAL A 376 " pdb=" C VAL A 376 " ideal model delta sigma weight residual 111.56 102.68 8.88 8.60e-01 1.35e+00 1.07e+02 angle pdb=" N VAL X 58 " pdb=" CA VAL X 58 " pdb=" C VAL X 58 " ideal model delta sigma weight residual 112.17 102.40 9.77 9.50e-01 1.11e+00 1.06e+02 angle pdb=" N VAL B 159 " pdb=" CA VAL B 159 " pdb=" C VAL B 159 " ideal model delta sigma weight residual 108.15 98.29 9.86 9.90e-01 1.02e+00 9.92e+01 angle pdb=" N PRO W 6 " pdb=" CA PRO W 6 " pdb=" C PRO W 6 " ideal model delta sigma weight residual 110.70 122.54 -11.84 1.22e+00 6.72e-01 9.42e+01 angle pdb=" N ILE E 258 " pdb=" CA ILE E 258 " pdb=" C ILE E 258 " ideal model delta sigma weight residual 113.22 102.19 11.03 1.23e+00 6.61e-01 8.05e+01 ... (remaining 25175 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.22: 5001 24.22 - 48.44: 21 48.44 - 72.66: 0 72.66 - 96.88: 1 96.88 - 121.10: 1 Dihedral angle restraints: 5024 sinusoidal: 4 harmonic: 5020 Sorted by residual: dihedral pdb=" CA ASP D 256 " pdb=" C ASP D 256 " pdb=" N ASN D 257 " pdb=" CA ASN D 257 " ideal model delta harmonic sigma weight residual -180.00 -58.90 -121.10 0 5.00e+00 4.00e-02 5.87e+02 dihedral pdb=" CA ASN 7 40 " pdb=" C ASN 7 40 " pdb=" N PRO 7 41 " pdb=" CA PRO 7 41 " ideal model delta harmonic sigma weight residual -180.00 -137.31 -42.69 0 5.00e+00 4.00e-02 7.29e+01 dihedral pdb=" CA ASN 6 40 " pdb=" C ASN 6 40 " pdb=" N PRO 6 41 " pdb=" CA PRO 6 41 " ideal model delta harmonic sigma weight residual 180.00 -139.63 -40.37 0 5.00e+00 4.00e-02 6.52e+01 ... (remaining 5021 not shown) Chirality restraints: 0 Planarity restraints: 5024 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL E 206 " 0.021 2.00e-02 2.50e+03 4.23e-02 1.79e+01 pdb=" C VAL E 206 " -0.073 2.00e-02 2.50e+03 pdb=" O VAL E 206 " 0.028 2.00e-02 2.50e+03 pdb=" N ILE E 207 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY E 154 " -0.019 2.00e-02 2.50e+03 3.86e-02 1.49e+01 pdb=" C GLY E 154 " 0.067 2.00e-02 2.50e+03 pdb=" O GLY E 154 " -0.025 2.00e-02 2.50e+03 pdb=" N LEU E 155 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR X 7 " -0.019 2.00e-02 2.50e+03 3.81e-02 1.46e+01 pdb=" C TYR X 7 " 0.066 2.00e-02 2.50e+03 pdb=" O TYR X 7 " -0.025 2.00e-02 2.50e+03 pdb=" N LEU X 8 " -0.022 2.00e-02 2.50e+03 ... (remaining 5021 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.89: 9870 2.89 - 3.39: 17547 3.39 - 3.89: 26480 3.89 - 4.40: 27496 4.40 - 4.90: 39992 Nonbonded interactions: 121385 Sorted by model distance: nonbonded pdb=" N SER C 129 " pdb=" O SER C 129 " model vdw 2.384 2.496 nonbonded pdb=" N TYR A 296 " pdb=" O TYR A 296 " model vdw 2.386 2.496 nonbonded pdb=" N TYR G 166 " pdb=" O TYR G 166 " model vdw 2.396 2.496 nonbonded pdb=" N GLY A 321 " pdb=" O GLY A 321 " model vdw 2.397 2.496 nonbonded pdb=" N LEU H 16 " pdb=" O LEU H 16 " model vdw 2.398 2.496 ... (remaining 121380 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain '0' and resid 2 through 73) selection = (chain '1' and resid 2 through 73) selection = (chain '2' and resid 2 through 73) selection = (chain '3' and resid 2 through 73) selection = (chain '4' and resid 2 through 73) selection = (chain '5' and resid 2 through 73) selection = (chain '6' and resid 2 through 73) selection = (chain '7' and resid 2 through 73) selection = (chain '8' and resid 2 through 73) selection = (chain '9' and resid 2 through 73) } ncs_group { reference = (chain 'A' and resid 12 through 509) selection = (chain 'B' and resid 12 through 509) selection = (chain 'C' and (resid 12 through 407 or resid 410 through 509)) } ncs_group { reference = (chain 'D' and resid 8 through 475) selection = chain 'E' selection = (chain 'F' and resid 8 through 475) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 20.910 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6399 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 0.064 20192 Z= 1.519 Angle : 2.212 15.089 25180 Z= 1.594 Chirality : 0.000 0.000 0 Planarity : 0.010 0.042 5024 Dihedral : 6.670 121.103 5024 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 0.19 Ramachandran Plot: Outliers : 1.61 % Allowed : 4.15 % Favored : 94.24 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.96 % Cis-general : 0.08 % Twisted Proline : 3.45 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.41 (0.11), residues: 4984 helix: 0.98 (0.09), residues: 2757 sheet: -1.52 (0.21), residues: 569 loop : -1.91 (0.13), residues: 1658 Details of bonding type rmsd covalent geometry : bond 0.01934 (20192) covalent geometry : angle 2.21195 (25180) hydrogen bonds : bond 0.21177 ( 2301) hydrogen bonds : angle 8.04025 ( 6753) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9968 Ramachandran restraints generated. 4984 Oldfield, 0 Emsley, 4984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9968 Ramachandran restraints generated. 4984 Oldfield, 0 Emsley, 4984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 4114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.501 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.0839 time to fit residues: 14.0926 Evaluate side-chains 82 residues out of total 4114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 432 optimal weight: 8.9990 chunk 197 optimal weight: 5.9990 chunk 388 optimal weight: 30.0000 chunk 455 optimal weight: 9.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 5.9990 chunk 470 optimal weight: 7.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- 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 = 0.2442 r_free = 0.2442 target = 0.027986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2341 r_free = 0.2341 target = 0.023386 restraints weight = 326055.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2325 r_free = 0.2325 target = 0.023069 restraints weight = 410620.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2321 r_free = 0.2321 target = 0.022945 restraints weight = 519255.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2321 r_free = 0.2321 target = 0.022943 restraints weight = 555050.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2321 r_free = 0.2321 target = 0.022943 restraints weight = 555404.081| |-----------------------------------------------------------------------------| r_work (final): 0.2258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20192 Z= 0.197 Angle : 0.535 9.098 25180 Z= 0.338 Chirality : 0.000 0.000 0 Planarity : 0.003 0.030 5024 Dihedral : 4.897 72.702 5024 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 0.15 Ramachandran Plot: Outliers : 0.38 % Allowed : 2.65 % Favored : 96.97 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.96 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.37 (0.12), residues: 4984 helix: 2.48 (0.10), residues: 2782 sheet: -1.24 (0.21), residues: 565 loop : -1.09 (0.15), residues: 1637 Details of bonding type rmsd covalent geometry : bond 0.00257 (20192) covalent geometry : angle 0.53536 (25180) hydrogen bonds : bond 0.04435 ( 2301) hydrogen bonds : angle 4.59253 ( 6753) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9968 Ramachandran restraints generated. 4984 Oldfield, 0 Emsley, 4984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9968 Ramachandran restraints generated. 4984 Oldfield, 0 Emsley, 4984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 4114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.689 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.0826 time to fit residues: 13.9642 Evaluate side-chains 82 residues out of total 4114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 217 optimal weight: 50.0000 chunk 149 optimal weight: 30.0000 chunk 38 optimal weight: 50.0000 chunk 234 optimal weight: 30.0000 chunk 169 optimal weight: 60.0000 chunk 77 optimal weight: 20.0000 chunk 454 optimal weight: 50.0000 chunk 352 optimal weight: 30.0000 chunk 275 optimal weight: 40.0000 chunk 389 optimal weight: 6.9990 chunk 56 optimal weight: 50.0000 overall best weight: 23.3998 ------------------------------------------------------------------------------- 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 = 0.2360 r_free = 0.2360 target = 0.026058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2264 r_free = 0.2264 target = 0.021763 restraints weight = 336195.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2249 r_free = 0.2249 target = 0.021502 restraints weight = 444853.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2244 r_free = 0.2244 target = 0.021375 restraints weight = 555069.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2244 r_free = 0.2244 target = 0.021375 restraints weight = 624996.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2244 r_free = 0.2244 target = 0.021375 restraints weight = 624996.509| |-----------------------------------------------------------------------------| r_work (final): 0.2148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.3370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 20192 Z= 0.419 Angle : 0.811 13.055 25180 Z= 0.528 Chirality : 0.000 0.000 0 Planarity : 0.005 0.037 5024 Dihedral : 5.774 76.556 5024 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 2.00 Ramachandran Plot: Outliers : 0.40 % Allowed : 5.18 % Favored : 94.42 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.96 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.67 (0.12), residues: 4984 helix: 1.84 (0.09), residues: 2790 sheet: -1.42 (0.21), residues: 535 loop : -1.35 (0.15), residues: 1659 Details of bonding type rmsd covalent geometry : bond 0.00561 (20192) covalent geometry : angle 0.81082 (25180) hydrogen bonds : bond 0.06390 ( 2301) hydrogen bonds : angle 5.99516 ( 6753) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9968 Ramachandran restraints generated. 4984 Oldfield, 0 Emsley, 4984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9968 Ramachandran restraints generated. 4984 Oldfield, 0 Emsley, 4984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 4114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.799 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.0811 time to fit residues: 13.6917 Evaluate side-chains 82 residues out of total 4114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 353 optimal weight: 7.9990 chunk 408 optimal weight: 50.0000 chunk 299 optimal weight: 0.7980 chunk 315 optimal weight: 5.9990 chunk 476 optimal weight: 50.0000 chunk 379 optimal weight: 50.0000 chunk 281 optimal weight: 20.0000 chunk 405 optimal weight: 40.0000 chunk 1 optimal weight: 120.0000 chunk 475 optimal weight: 50.0000 chunk 453 optimal weight: 20.0000 overall best weight: 10.9592 ------------------------------------------------------------------------------- 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 = 0.2370 r_free = 0.2370 target = 0.026417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2257 r_free = 0.2257 target = 0.021772 restraints weight = 359606.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2247 r_free = 0.2247 target = 0.021569 restraints weight = 442496.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 18)----------------| | r_work = 0.2243 r_free = 0.2243 target = 0.021475 restraints weight = 517973.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2242 r_free = 0.2242 target = 0.021469 restraints weight = 556526.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2242 r_free = 0.2242 target = 0.021469 restraints weight = 558422.377| |-----------------------------------------------------------------------------| r_work (final): 0.2196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.3677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 20192 Z= 0.222 Angle : 0.509 8.570 25180 Z= 0.327 Chirality : 0.000 0.000 0 Planarity : 0.003 0.033 5024 Dihedral : 4.721 86.735 5024 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 0.81 Ramachandran Plot: Outliers : 0.40 % Allowed : 4.70 % Favored : 94.90 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.96 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.50 (0.12), residues: 4984 helix: 2.65 (0.10), residues: 2792 sheet: -1.44 (0.21), residues: 540 loop : -1.11 (0.16), residues: 1652 Details of bonding type rmsd covalent geometry : bond 0.00295 (20192) covalent geometry : angle 0.50906 (25180) hydrogen bonds : bond 0.04073 ( 2301) hydrogen bonds : angle 4.53428 ( 6753) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9968 Ramachandran restraints generated. 4984 Oldfield, 0 Emsley, 4984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9968 Ramachandran restraints generated. 4984 Oldfield, 0 Emsley, 4984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 4114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.632 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.0818 time to fit residues: 13.5767 Evaluate side-chains 82 residues out of total 4114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 267 optimal weight: 30.0000 chunk 167 optimal weight: 40.0000 chunk 58 optimal weight: 120.0000 chunk 442 optimal weight: 10.0000 chunk 310 optimal weight: 50.0000 chunk 251 optimal weight: 50.0000 chunk 286 optimal weight: 50.0000 chunk 109 optimal weight: 30.0000 chunk 441 optimal weight: 50.0000 chunk 111 optimal weight: 10.0000 chunk 49 optimal weight: 50.0000 overall best weight: 24.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2328 r_free = 0.2328 target = 0.025236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2221 r_free = 0.2221 target = 0.020873 restraints weight = 346885.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2211 r_free = 0.2211 target = 0.020686 restraints weight = 443950.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2209 r_free = 0.2209 target = 0.020641 restraints weight = 539363.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2209 r_free = 0.2209 target = 0.020641 restraints weight = 554965.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2209 r_free = 0.2209 target = 0.020641 restraints weight = 554965.774| |-----------------------------------------------------------------------------| r_work (final): 0.2161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.4772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 20192 Z= 0.414 Angle : 0.804 13.324 25180 Z= 0.523 Chirality : 0.000 0.000 0 Planarity : 0.005 0.037 5024 Dihedral : 6.024 78.532 5024 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.44 % Allowed : 7.78 % Favored : 91.77 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.96 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.07 (0.12), residues: 4984 helix: 1.25 (0.09), residues: 2808 sheet: -1.92 (0.24), residues: 436 loop : -1.70 (0.15), residues: 1740 Details of bonding type rmsd covalent geometry : bond 0.00550 (20192) covalent geometry : angle 0.80363 (25180) hydrogen bonds : bond 0.06482 ( 2301) hydrogen bonds : angle 6.34515 ( 6753) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9968 Ramachandran restraints generated. 4984 Oldfield, 0 Emsley, 4984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9968 Ramachandran restraints generated. 4984 Oldfield, 0 Emsley, 4984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 4114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.731 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.0833 time to fit residues: 14.0908 Evaluate side-chains 82 residues out of total 4114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 240 optimal weight: 40.0000 chunk 446 optimal weight: 120.0000 chunk 223 optimal weight: 6.9990 chunk 338 optimal weight: 7.9990 chunk 9 optimal weight: 90.0000 chunk 444 optimal weight: 6.9990 chunk 414 optimal weight: 20.0000 chunk 357 optimal weight: 30.0000 chunk 375 optimal weight: 0.0010 chunk 62 optimal weight: 120.0000 chunk 373 optimal weight: 20.0000 overall best weight: 8.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2570 r_free = 0.2570 target = 0.040717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2532 r_free = 0.2532 target = 0.035429 restraints weight = 281042.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2521 r_free = 0.2521 target = 0.035062 restraints weight = 345878.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2521 r_free = 0.2521 target = 0.035062 restraints weight = 459893.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2521 r_free = 0.2521 target = 0.035062 restraints weight = 459893.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2521 r_free = 0.2521 target = 0.035062 restraints weight = 459893.693| |-----------------------------------------------------------------------------| r_work (final): 0.2214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.4683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 20192 Z= 0.172 Angle : 0.460 9.869 25180 Z= 0.292 Chirality : 0.000 0.000 0 Planarity : 0.002 0.031 5024 Dihedral : 4.680 63.099 5024 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 0.73 Ramachandran Plot: Outliers : 0.40 % Allowed : 5.46 % Favored : 94.14 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.96 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.15 (0.13), residues: 4984 helix: 2.37 (0.10), residues: 2837 sheet: -1.89 (0.23), residues: 476 loop : -1.31 (0.16), residues: 1671 Details of bonding type rmsd covalent geometry : bond 0.00228 (20192) covalent geometry : angle 0.46034 (25180) hydrogen bonds : bond 0.03980 ( 2301) hydrogen bonds : angle 4.63071 ( 6753) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9968 Ramachandran restraints generated. 4984 Oldfield, 0 Emsley, 4984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9968 Ramachandran restraints generated. 4984 Oldfield, 0 Emsley, 4984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 4114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.844 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.0842 time to fit residues: 14.1237 Evaluate side-chains 82 residues out of total 4114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 154 optimal weight: 50.0000 chunk 259 optimal weight: 50.0000 chunk 235 optimal weight: 50.0000 chunk 313 optimal weight: 50.0000 chunk 490 optimal weight: 50.0000 chunk 43 optimal weight: 50.0000 chunk 212 optimal weight: 70.0000 chunk 111 optimal weight: 40.0000 chunk 134 optimal weight: 30.0000 chunk 31 optimal weight: 70.0000 chunk 430 optimal weight: 80.0000 overall best weight: 44.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2290 r_free = 0.2290 target = 0.024504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2194 r_free = 0.2194 target = 0.020601 restraints weight = 400446.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2184 r_free = 0.2184 target = 0.020410 restraints weight = 458009.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2184 r_free = 0.2184 target = 0.020410 restraints weight = 530641.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2184 r_free = 0.2184 target = 0.020410 restraints weight = 530687.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2184 r_free = 0.2184 target = 0.020410 restraints weight = 530691.684| |-----------------------------------------------------------------------------| r_work (final): 0.2184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.6134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.134 20192 Z= 0.684 Angle : 1.186 18.641 25180 Z= 0.784 Chirality : 0.000 0.000 0 Planarity : 0.008 0.043 5024 Dihedral : 7.481 45.574 5024 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.58 % Allowed : 12.16 % Favored : 87.26 % 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 : 0.49 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.35 (0.11), residues: 4984 helix: -0.77 (0.09), residues: 2714 sheet: -1.94 (0.27), residues: 369 loop : -2.56 (0.14), residues: 1901 Details of bonding type rmsd covalent geometry : bond 0.00914 (20192) covalent geometry : angle 1.18553 (25180) hydrogen bonds : bond 0.09034 ( 2301) hydrogen bonds : angle 8.43397 ( 6753) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9968 Ramachandran restraints generated. 4984 Oldfield, 0 Emsley, 4984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9968 Ramachandran restraints generated. 4984 Oldfield, 0 Emsley, 4984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 4114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.829 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.0881 time to fit residues: 14.8494 Evaluate side-chains 82 residues out of total 4114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 63 optimal weight: 40.0000 chunk 409 optimal weight: 20.0000 chunk 355 optimal weight: 7.9990 chunk 56 optimal weight: 10.0000 chunk 171 optimal weight: 30.0000 chunk 290 optimal weight: 6.9990 chunk 97 optimal weight: 10.0000 chunk 288 optimal weight: 20.0000 chunk 319 optimal weight: 8.9990 chunk 376 optimal weight: 9.9990 chunk 420 optimal weight: 50.0000 overall best weight: 8.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2563 r_free = 0.2563 target = 0.043394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2551 r_free = 0.2551 target = 0.038248 restraints weight = 303275.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2541 r_free = 0.2541 target = 0.037892 restraints weight = 412487.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2538 r_free = 0.2538 target = 0.037777 restraints weight = 508676.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2537 r_free = 0.2537 target = 0.037747 restraints weight = 555328.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2537 r_free = 0.2537 target = 0.037747 restraints weight = 553644.139| |-----------------------------------------------------------------------------| r_work (final): 0.2236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.5672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.063 20192 Z= 0.178 Angle : 0.501 12.990 25180 Z= 0.313 Chirality : 0.000 0.000 0 Planarity : 0.003 0.031 5024 Dihedral : 5.195 41.895 5024 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 0.89 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.62 % Favored : 93.04 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.96 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.28 (0.12), residues: 4984 helix: 1.23 (0.10), residues: 2813 sheet: -2.13 (0.25), residues: 394 loop : -2.07 (0.14), residues: 1777 Details of bonding type rmsd covalent geometry : bond 0.00238 (20192) covalent geometry : angle 0.50104 (25180) hydrogen bonds : bond 0.04343 ( 2301) hydrogen bonds : angle 5.26433 ( 6753) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9968 Ramachandran restraints generated. 4984 Oldfield, 0 Emsley, 4984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9968 Ramachandran restraints generated. 4984 Oldfield, 0 Emsley, 4984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 4114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.764 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.0824 time to fit residues: 13.8481 Evaluate side-chains 82 residues out of total 4114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 131 optimal weight: 20.0000 chunk 489 optimal weight: 60.0000 chunk 146 optimal weight: 9.9990 chunk 84 optimal weight: 40.0000 chunk 365 optimal weight: 40.0000 chunk 316 optimal weight: 50.0000 chunk 449 optimal weight: 100.0000 chunk 42 optimal weight: 40.0000 chunk 457 optimal weight: 50.0000 chunk 144 optimal weight: 40.0000 chunk 11 optimal weight: 50.0000 overall best weight: 29.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2315 r_free = 0.2315 target = 0.024935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2212 r_free = 0.2212 target = 0.020833 restraints weight = 388950.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2201 r_free = 0.2201 target = 0.020634 restraints weight = 488259.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2201 r_free = 0.2201 target = 0.020634 restraints weight = 572757.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2201 r_free = 0.2201 target = 0.020634 restraints weight = 572813.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2201 r_free = 0.2201 target = 0.020634 restraints weight = 572813.217| |-----------------------------------------------------------------------------| r_work (final): 0.2377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.6281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.091 20192 Z= 0.478 Angle : 0.866 16.979 25180 Z= 0.569 Chirality : 0.000 0.000 0 Planarity : 0.005 0.038 5024 Dihedral : 6.327 43.276 5024 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.36 % Allowed : 12.50 % Favored : 87.14 % 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 : 0.49 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.47 (0.12), residues: 4984 helix: 0.16 (0.09), residues: 2755 sheet: -2.18 (0.26), residues: 389 loop : -2.45 (0.14), residues: 1840 Details of bonding type rmsd covalent geometry : bond 0.00637 (20192) covalent geometry : angle 0.86577 (25180) hydrogen bonds : bond 0.06883 ( 2301) hydrogen bonds : angle 7.01882 ( 6753) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9968 Ramachandran restraints generated. 4984 Oldfield, 0 Emsley, 4984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9968 Ramachandran restraints generated. 4984 Oldfield, 0 Emsley, 4984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 4114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.860 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.0844 time to fit residues: 14.2249 Evaluate side-chains 82 residues out of total 4114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 288 optimal weight: 20.0000 chunk 126 optimal weight: 6.9990 chunk 403 optimal weight: 30.0000 chunk 233 optimal weight: 40.0000 chunk 2 optimal weight: 9.9990 chunk 140 optimal weight: 30.0000 chunk 316 optimal weight: 20.0000 chunk 8 optimal weight: 50.0000 chunk 228 optimal weight: 30.0000 chunk 291 optimal weight: 20.0000 chunk 391 optimal weight: 7.9990 overall best weight: 12.9994 ------------------------------------------------------------------------------- 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 = 0.2593 r_free = 0.2593 target = 0.030989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2335 r_free = 0.2335 target = 0.022847 restraints weight = 227047.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2347 r_free = 0.2347 target = 0.023107 restraints weight = 189472.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2355 r_free = 0.2355 target = 0.023264 restraints weight = 160104.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.2367 r_free = 0.2367 target = 0.023516 restraints weight = 142925.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2373 r_free = 0.2373 target = 0.023636 restraints weight = 127649.970| |-----------------------------------------------------------------------------| r_work (final): 0.2379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.6143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 20192 Z= 0.233 Angle : 0.547 15.557 25180 Z= 0.347 Chirality : 0.000 0.000 0 Planarity : 0.003 0.033 5024 Dihedral : 5.232 41.400 5024 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 1.46 Ramachandran Plot: Outliers : 0.32 % Allowed : 8.29 % Favored : 91.39 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.96 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.42 (0.12), residues: 4984 helix: 1.16 (0.10), residues: 2802 sheet: -2.25 (0.25), residues: 402 loop : -2.19 (0.15), residues: 1780 Details of bonding type rmsd covalent geometry : bond 0.00312 (20192) covalent geometry : angle 0.54724 (25180) hydrogen bonds : bond 0.04564 ( 2301) hydrogen bonds : angle 5.45064 ( 6753) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9968 Ramachandran restraints generated. 4984 Oldfield, 0 Emsley, 4984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9968 Ramachandran restraints generated. 4984 Oldfield, 0 Emsley, 4984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 4114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.754 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.0823 time to fit residues: 13.9592 Evaluate side-chains 82 residues out of total 4114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 340 optimal weight: 50.0000 chunk 107 optimal weight: 50.0000 chunk 3 optimal weight: 40.0000 chunk 91 optimal weight: 40.0000 chunk 112 optimal weight: 50.0000 chunk 369 optimal weight: 20.0000 chunk 30 optimal weight: 9.9990 chunk 356 optimal weight: 40.0000 chunk 252 optimal weight: 0.2980 chunk 460 optimal weight: 50.0000 chunk 77 optimal weight: 20.0000 overall best weight: 18.0594 ------------------------------------------------------------------------------- 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 = 0.2586 r_free = 0.2586 target = 0.030839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2334 r_free = 0.2334 target = 0.022886 restraints weight = 230223.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2348 r_free = 0.2348 target = 0.023200 restraints weight = 190593.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2356 r_free = 0.2356 target = 0.023358 restraints weight = 159450.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2365 r_free = 0.2365 target = 0.023548 restraints weight = 141374.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 17)----------------| | r_work = 0.2372 r_free = 0.2372 target = 0.023694 restraints weight = 128466.966| |-----------------------------------------------------------------------------| r_work (final): 0.2376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.6407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 20192 Z= 0.306 Angle : 0.628 16.716 25180 Z= 0.403 Chirality : 0.000 0.000 0 Planarity : 0.004 0.035 5024 Dihedral : 5.380 41.501 5024 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 2.27 Ramachandran Plot: Outliers : 0.34 % Allowed : 11.50 % Favored : 88.16 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.96 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.40 (0.12), residues: 4984 helix: 1.19 (0.10), residues: 2786 sheet: -2.06 (0.26), residues: 395 loop : -2.22 (0.15), residues: 1803 Details of bonding type rmsd covalent geometry : bond 0.00409 (20192) covalent geometry : angle 0.62774 (25180) hydrogen bonds : bond 0.05112 ( 2301) hydrogen bonds : angle 5.76051 ( 6753) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2318.48 seconds wall clock time: 40 minutes 24.98 seconds (2424.98 seconds total)