Starting phenix.real_space_refine on Mon Mar 18 08:36:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tkp_25977/03_2024/7tkp_25977.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tkp_25977/03_2024/7tkp_25977.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tkp_25977/03_2024/7tkp_25977.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tkp_25977/03_2024/7tkp_25977.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tkp_25977/03_2024/7tkp_25977.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tkp_25977/03_2024/7tkp_25977.pdb" } resolution = 4.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.120 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 3 Type Number sf(0) Gaussians C 10112 2.51 5 N 5056 2.21 5 O 5060 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 20228 Number of models: 1 Model: "" Number of chains: 27 Chain: "0" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 300 Classifications: {'peptide': 75} Incomplete info: {'backbone_only': 65} Link IDs: {'PTRANS': 2, 'TRANS': 72} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 246 Unresolved non-hydrogen angles: 363 Unresolved non-hydrogen dihedrals: 146 Unresolved non-hydrogen chiralities: 94 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1, 'PHE:plan': 6, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 75 Chain: "1" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 300 Classifications: {'peptide': 75} Incomplete info: {'backbone_only': 65} Link IDs: {'PTRANS': 2, 'TRANS': 72} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 246 Unresolved non-hydrogen angles: 363 Unresolved non-hydrogen dihedrals: 146 Unresolved non-hydrogen chiralities: 94 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1, 'PHE:plan': 6, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 75 Chain: "2" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 300 Classifications: {'peptide': 75} Incomplete info: {'backbone_only': 65} Link IDs: {'PTRANS': 2, 'TRANS': 72} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 246 Unresolved non-hydrogen angles: 363 Unresolved non-hydrogen dihedrals: 146 Unresolved non-hydrogen chiralities: 94 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1, 'PHE:plan': 6, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 75 Chain: "3" Number of atoms: 296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 296 Classifications: {'peptide': 74} Incomplete info: {'backbone_only': 64} Link IDs: {'PTRANS': 2, 'TRANS': 71} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 242 Unresolved non-hydrogen angles: 358 Unresolved non-hydrogen dihedrals: 143 Unresolved non-hydrogen chiralities: 93 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1, 'PHE:plan': 6, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 75 Chain: "4" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 300 Classifications: {'peptide': 75} Incomplete info: {'backbone_only': 65} Link IDs: {'PTRANS': 2, 'TRANS': 72} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 246 Unresolved non-hydrogen angles: 363 Unresolved non-hydrogen dihedrals: 146 Unresolved non-hydrogen chiralities: 94 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1, 'PHE:plan': 6, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 75 Chain: "5" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 300 Classifications: {'peptide': 75} Incomplete info: {'backbone_only': 65} Link IDs: {'PTRANS': 2, 'TRANS': 72} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 246 Unresolved non-hydrogen angles: 363 Unresolved non-hydrogen dihedrals: 146 Unresolved non-hydrogen chiralities: 94 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1, 'PHE:plan': 6, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 75 Chain: "6" Number of atoms: 296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 296 Classifications: {'peptide': 74} Incomplete info: {'backbone_only': 64} Link IDs: {'PTRANS': 2, 'TRANS': 71} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 242 Unresolved non-hydrogen angles: 358 Unresolved non-hydrogen dihedrals: 143 Unresolved non-hydrogen chiralities: 93 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1, 'PHE:plan': 6, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 75 Chain: "7" Number of atoms: 292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 292 Classifications: {'peptide': 73} Incomplete info: {'backbone_only': 64} Link IDs: {'PTRANS': 2, 'TRANS': 70} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 238 Unresolved non-hydrogen angles: 352 Unresolved non-hydrogen dihedrals: 139 Unresolved non-hydrogen chiralities: 93 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1, 'PHE:plan': 5, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 68 Chain: "8" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 300 Classifications: {'peptide': 75} Incomplete info: {'backbone_only': 65} Link IDs: {'PTRANS': 2, 'TRANS': 72} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 246 Unresolved non-hydrogen angles: 363 Unresolved non-hydrogen dihedrals: 146 Unresolved non-hydrogen chiralities: 94 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1, 'PHE:plan': 6, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 75 Chain: "9" Number of atoms: 296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 296 Classifications: {'peptide': 74} Incomplete info: {'backbone_only': 64} Link IDs: {'PTRANS': 2, 'TRANS': 71} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 242 Unresolved non-hydrogen angles: 358 Unresolved non-hydrogen dihedrals: 143 Unresolved non-hydrogen chiralities: 93 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1, 'PHE:plan': 6, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 75 Chain: "A" Number of atoms: 1996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 499, 1996 Classifications: {'peptide': 499} Incomplete info: {'backbone_only': 453} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 18, 'TRANS': 478} Chain breaks: 1 Unresolved chain link angles: 19 Unresolved non-hydrogen bonds: 1854 Unresolved non-hydrogen angles: 2698 Unresolved non-hydrogen dihedrals: 1123 Unresolved non-hydrogen chiralities: 606 Planarities with less than four sites: {'GLN:plan1': 25, 'HIS:plan': 6, 'TYR:plan': 14, 'ASN:plan1': 17, 'TRP:plan': 2, 'ASP:plan': 21, 'PHE:plan': 13, 'GLU:plan': 37, 'ARG:plan': 29} Unresolved non-hydrogen planarities: 804 Chain: "B" Number of atoms: 2028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 2028 Classifications: {'peptide': 507} Incomplete info: {'backbone_only': 460} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 485} Unresolved chain link angles: 20 Unresolved non-hydrogen bonds: 1883 Unresolved non-hydrogen angles: 2740 Unresolved non-hydrogen dihedrals: 1142 Unresolved non-hydrogen chiralities: 615 Planarities with less than four sites: {'GLN:plan1': 26, 'HIS:plan': 6, 'TYR:plan': 14, 'ASN:plan1': 17, 'TRP:plan': 2, 'ASP:plan': 21, 'PHE:plan': 14, 'GLU:plan': 37, 'ARG:plan': 29} Unresolved non-hydrogen planarities: 815 Chain: "C" Number of atoms: 1984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 1984 Classifications: {'peptide': 496} Incomplete info: {'backbone_only': 450} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 18, 'TRANS': 474} Chain breaks: 1 Unresolved chain link angles: 19 Unresolved non-hydrogen bonds: 1844 Unresolved non-hydrogen angles: 2683 Unresolved non-hydrogen dihedrals: 1118 Unresolved non-hydrogen chiralities: 602 Planarities with less than four sites: {'GLN:plan1': 25, 'HIS:plan': 6, 'TYR:plan': 14, 'ASN:plan1': 17, 'TRP:plan': 2, 'ASP:plan': 21, 'PHE:plan': 13, 'GLU:plan': 36, 'ARG:plan': 29} Unresolved non-hydrogen planarities: 800 Chain: "D" Number of atoms: 1872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 1872 Classifications: {'peptide': 468} Incomplete info: {'backbone_only': 422} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 445} Unresolved chain link angles: 22 Unresolved non-hydrogen bonds: 1721 Unresolved non-hydrogen angles: 2511 Unresolved non-hydrogen dihedrals: 1032 Unresolved non-hydrogen chiralities: 577 Planarities with less than four sites: {'GLN:plan1': 18, 'ARG:plan': 22, 'TYR:plan': 10, 'ASN:plan1': 10, 'HIS:plan': 7, 'PHE:plan': 17, 'GLU:plan': 37, 'ASP:plan': 25} Unresolved non-hydrogen planarities: 711 Chain: "E" Number of atoms: 1876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 1876 Classifications: {'peptide': 469} Incomplete info: {'backbone_only': 423} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 444} Unresolved chain link angles: 23 Unresolved non-hydrogen bonds: 1724 Unresolved non-hydrogen angles: 2516 Unresolved non-hydrogen dihedrals: 1033 Unresolved non-hydrogen chiralities: 579 Planarities with less than four sites: {'GLN:plan1': 18, 'ARG:plan': 22, 'TYR:plan': 10, 'ASN:plan1': 10, 'HIS:plan': 7, 'PHE:plan': 17, 'GLU:plan': 37, 'ASP:plan': 25} Unresolved non-hydrogen planarities: 711 Chain: "F" Number of atoms: 1880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 1880 Classifications: {'peptide': 470} Incomplete info: {'backbone_only': 424} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 446} Unresolved chain link angles: 23 Unresolved non-hydrogen bonds: 1726 Unresolved non-hydrogen angles: 2519 Unresolved non-hydrogen dihedrals: 1034 Unresolved non-hydrogen chiralities: 580 Planarities with less than four sites: {'GLN:plan1': 18, 'ARG:plan': 22, 'TYR:plan': 10, 'ASN:plan1': 10, 'HIS:plan': 7, 'PHE:plan': 17, 'GLU:plan': 37, 'ASP:plan': 25} Unresolved non-hydrogen planarities: 711 Chain: "G" Number of atoms: 1060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 1060 Classifications: {'peptide': 265} Incomplete info: {'backbone_only': 255} Link IDs: {'PTRANS': 9, 'TRANS': 255} Chain breaks: 1 Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 1024 Unresolved non-hydrogen angles: 1472 Unresolved non-hydrogen dihedrals: 628 Unresolved non-hydrogen chiralities: 328 Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 3, 'TYR:plan': 7, 'ASN:plan1': 18, 'ASP:plan': 14, 'PHE:plan': 8, 'GLU:plan': 16, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 413 Chain: "H" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 480 Classifications: {'peptide': 120} Incomplete info: {'backbone_only': 114} Link IDs: {'PTRANS': 6, 'TRANS': 113} Chain breaks: 4 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 439 Unresolved non-hydrogen angles: 643 Unresolved non-hydrogen dihedrals: 258 Unresolved non-hydrogen chiralities: 151 Planarities with less than four sites: {'GLN:plan1': 7, 'ASP:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 7, 'HIS:plan': 2, 'PHE:plan': 5, 'GLU:plan': 13, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 177 Chain: "I" Number of atoms: 193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 193 Classifications: {'peptide': 48} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 47} Link IDs: {'PTRANS': 2, 'TRANS': 45} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 188 Unresolved non-hydrogen angles: 278 Unresolved non-hydrogen dihedrals: 114 Unresolved non-hydrogen chiralities: 62 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 4, 'ASN:plan1': 3, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 89 Chain: "O" Number of atoms: 748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 748 Classifications: {'peptide': 187} Incomplete info: {'backbone_only': 174} Link IDs: {'PTRANS': 7, 'TRANS': 179} Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 691 Unresolved non-hydrogen angles: 1001 Unresolved non-hydrogen dihedrals: 414 Unresolved non-hydrogen chiralities: 235 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 3, 'TYR:plan': 3, 'ASN:plan1': 12, 'ASP:plan': 10, 'PHE:plan': 5, 'GLU:plan': 11, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 249 Chain: "T" Number of atoms: 897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 897 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 207} Link IDs: {'PTRANS': 7, 'TRANS': 216} Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 925 Unresolved non-hydrogen angles: 1359 Unresolved non-hydrogen dihedrals: 607 Unresolved non-hydrogen chiralities: 306 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 3, 'TYR:plan': 10, 'ASN:plan1': 11, 'TRP:plan': 5, 'ASP:plan': 2, 'PHE:plan': 18, 'GLU:plan': 3, 'ARG:plan': 3, 'HIS%COO:plan': 1} Unresolved non-hydrogen planarities: 371 Chain: "U" Number of atoms: 620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 620 Classifications: {'peptide': 155} Incomplete info: {'backbone_only': 152} Link IDs: {'PTRANS': 2, 'TRANS': 152} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 631 Unresolved non-hydrogen angles: 908 Unresolved non-hydrogen dihedrals: 388 Unresolved non-hydrogen chiralities: 198 Planarities with less than four sites: {'GLN:plan1': 11, 'HIS:plan': 2, 'TYR:plan': 3, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 8, 'PHE:plan': 6, 'GLU:plan': 16, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 283 Chain: "V" Number of atoms: 685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 685 Classifications: {'peptide': 171} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 166} Link IDs: {'PTRANS': 5, 'TRANS': 165} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 705 Unresolved non-hydrogen angles: 1009 Unresolved non-hydrogen dihedrals: 446 Unresolved non-hydrogen chiralities: 214 Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 2, 'TYR:plan': 4, 'ASN:plan1': 7, 'TRP:plan': 2, 'ASP:plan': 13, 'PHE:plan': 5, 'GLU:plan': 13, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 302 Chain: "W" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 340 Classifications: {'peptide': 85} Incomplete info: {'backbone_only': 79} Link IDs: {'PTRANS': 7, 'TRANS': 77} Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 348 Unresolved non-hydrogen angles: 503 Unresolved non-hydrogen dihedrals: 241 Unresolved non-hydrogen chiralities: 97 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 2, 'TYR:plan': 6, 'ASN:plan1': 5, 'TRP:plan': 1, 'HIS:plan': 3, 'PHE:plan': 5, 'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 162 Chain: "X" Number of atoms: 248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 248 Classifications: {'peptide': 62} Incomplete info: {'backbone_only': 60} Link IDs: {'PTRANS': 7, 'TRANS': 54} Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 257 Unresolved non-hydrogen angles: 375 Unresolved non-hydrogen dihedrals: 161 Unresolved non-hydrogen chiralities: 77 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 3, 'GLU:plan': 7, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 117 Chain: "Y" Number of atoms: 148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 148 Classifications: {'peptide': 37} Incomplete info: {'backbone_only': 35} Link IDs: {'PTRANS': 3, 'TRANS': 33} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 155 Unresolved non-hydrogen angles: 225 Unresolved non-hydrogen dihedrals: 110 Unresolved non-hydrogen chiralities: 44 Planarities with less than four sites: {'TYR:plan': 3, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 68 Chain: "Z" Number of atoms: 193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 193 Classifications: {'peptide': 48} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 46} Link IDs: {'PTRANS': 3, 'TRANS': 44} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 231 Unresolved non-hydrogen angles: 330 Unresolved non-hydrogen dihedrals: 158 Unresolved non-hydrogen chiralities: 67 Planarities with less than four sites: {'GLN:plan1': 3, 'PHE:plan': 7, 'ASN:plan1': 1, 'ARG:plan': 2, 'TYR:plan': 3} Unresolved non-hydrogen planarities: 99 Time building chain proxies: 12.63, per 1000 atoms: 0.62 Number of scatterers: 20228 At special positions: 0 Unit cell: (122.622, 146.877, 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.89 Conformation dependent library (CDL) restraints added in 6.0 seconds 9968 Ramachandran restraints generated. 4984 Oldfield, 0 Emsley, 4984 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 0 Finding SS restraints... Secondary structure from input PDB file: 204 helices and 30 sheets defined 60.3% alpha, 11.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.88 Creating SS restraints... Processing helix chain '0' and resid 1 through 17 removed outlier: 3.512A pdb=" N GLY 0 13 " --> pdb=" O TYR 0 9 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ILE 0 17 " --> pdb=" O GLY 0 13 " (cutoff:3.500A) Processing helix chain '0' and resid 18 through 40 removed outlier: 4.197A pdb=" N ALA 0 22 " --> pdb=" O GLY 0 18 " (cutoff:3.500A) removed outlier: 3.718A 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: 3.531A pdb=" N THR 0 61 " --> pdb=" O LEU 0 57 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLY 0 62 " --> pdb=" O SER 0 58 " (cutoff:3.500A) Processing helix chain '1' and resid 2 through 17 removed outlier: 3.929A pdb=" N GLY 1 13 " --> pdb=" O TYR 1 9 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ILE 1 17 " --> pdb=" O GLY 1 13 " (cutoff:3.500A) Processing helix chain '1' and resid 18 through 40 removed outlier: 4.463A pdb=" N ALA 1 22 " --> pdb=" O GLY 1 18 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA 1 27 " --> pdb=" O GLY 1 23 " (cutoff:3.500A) Processing helix chain '1' and resid 43 through 75 Proline residue: 1 49 - end of helix removed outlier: 3.500A pdb=" N GLY 1 62 " --> pdb=" O SER 1 58 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N CYS 1 65 " --> pdb=" O THR 1 61 " (cutoff:3.500A) Processing helix chain '2' and resid 2 through 16 Processing helix chain '2' and resid 18 through 40 removed outlier: 4.318A pdb=" N ALA 2 22 " --> pdb=" O GLY 2 18 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ALA 2 27 " --> pdb=" O GLY 2 23 " (cutoff:3.500A) Processing helix chain '2' and resid 43 through 75 Proline residue: 2 49 - end of helix removed outlier: 3.978A pdb=" N THR 2 61 " --> pdb=" O LEU 2 57 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N GLY 2 62 " --> pdb=" O SER 2 58 " (cutoff:3.500A) Processing helix chain '3' and resid 3 through 17 removed outlier: 3.807A pdb=" N ILE 3 17 " --> pdb=" O GLY 3 13 " (cutoff:3.500A) Processing helix chain '3' and resid 19 through 40 removed outlier: 3.885A 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: 3.880A 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: 4.088A 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: 3.891A pdb=" N THR 4 61 " --> pdb=" O LEU 4 57 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N GLY 4 62 " --> pdb=" O SER 4 58 " (cutoff:3.500A) Processing helix chain '5' and resid 2 through 16 Processing helix chain '5' and resid 18 through 40 removed outlier: 4.189A pdb=" N ALA 5 22 " --> pdb=" O GLY 5 18 " (cutoff:3.500A) Processing helix chain '5' and resid 43 through 75 Proline residue: 5 49 - end of helix removed outlier: 3.739A pdb=" N GLY 5 62 " --> pdb=" O SER 5 58 " (cutoff:3.500A) Processing helix chain '6' and resid 3 through 40 removed outlier: 3.690A pdb=" N THR 6 16 " --> pdb=" O ALA 6 12 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ILE 6 17 " --> pdb=" O GLY 6 13 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N GLY 6 18 " --> pdb=" O ILE 6 14 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N LEU 6 19 " --> pdb=" O SER 6 15 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU 6 20 " --> pdb=" O THR 6 16 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N GLY 6 21 " --> pdb=" O ILE 6 17 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N ALA 6 22 " --> pdb=" O GLY 6 18 " (cutoff:3.500A) removed outlier: 3.598A 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: 3.646A pdb=" N THR 6 61 " --> pdb=" O LEU 6 57 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLY 6 62 " --> pdb=" O SER 6 58 " (cutoff:3.500A) Processing helix chain '7' and resid 2 through 40 removed outlier: 4.197A pdb=" N ILE 7 17 " --> pdb=" O GLY 7 13 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N GLY 7 18 " --> pdb=" O ILE 7 14 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N LEU 7 19 " --> pdb=" O SER 7 15 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU 7 20 " --> pdb=" O THR 7 16 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N GLY 7 21 " --> pdb=" O ILE 7 17 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ALA 7 22 " --> pdb=" O GLY 7 18 " (cutoff:3.500A) removed outlier: 3.632A 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: 3.790A pdb=" N GLY 7 62 " --> pdb=" O SER 7 58 " (cutoff:3.500A) Processing helix chain '8' and resid 2 through 17 removed outlier: 3.804A pdb=" N ILE 8 17 " --> pdb=" O GLY 8 13 " (cutoff:3.500A) Processing helix chain '8' and resid 18 through 40 removed outlier: 4.119A 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: 3.793A pdb=" N THR 8 61 " --> pdb=" O LEU 8 57 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLY 8 62 " --> pdb=" O SER 8 58 " (cutoff:3.500A) Processing helix chain '9' and resid 3 through 17 removed outlier: 3.826A pdb=" N ILE 9 17 " --> pdb=" O GLY 9 13 " (cutoff:3.500A) Processing helix chain '9' and resid 18 through 40 removed outlier: 4.289A pdb=" N ALA 9 22 " --> pdb=" O GLY 9 18 " (cutoff:3.500A) Processing helix chain '9' and resid 43 through 75 Proline residue: 9 49 - end of helix removed outlier: 3.585A pdb=" N THR 9 61 " --> pdb=" O LEU 9 57 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLY 9 62 " --> pdb=" O SER 9 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 20 Processing helix chain 'A' and resid 102 through 106 removed outlier: 4.064A pdb=" N LEU A 105 " --> pdb=" O GLY A 102 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU A 106 " --> pdb=" O PRO A 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 102 through 106' Processing helix chain 'A' and resid 153 through 157 Processing helix chain 'A' and resid 176 through 188 removed outlier: 3.704A pdb=" N VAL A 180 " --> pdb=" O GLY A 176 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ALA A 181 " --> pdb=" O LYS A 177 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR A 184 " --> pdb=" O VAL A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 193 Processing helix chain 'A' and resid 196 through 200 Processing helix chain 'A' and resid 211 through 225 Processing helix chain 'A' and resid 227 through 229 No H-bonds generated for 'chain 'A' and resid 227 through 229' Processing helix chain 'A' and resid 241 through 247 Processing helix chain 'A' and resid 247 through 261 removed outlier: 3.582A pdb=" N PHE A 259 " --> pdb=" O ILE A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 287 Processing helix chain 'A' and resid 292 through 296 Processing helix chain 'A' and resid 299 through 309 Processing helix chain 'A' and resid 338 through 348 removed outlier: 3.525A pdb=" N ILE A 347 " --> pdb=" O ASN A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 361 Processing helix chain 'A' and resid 376 through 381 removed outlier: 4.360A pdb=" N ALA A 380 " --> pdb=" O VAL A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 388 Processing helix chain 'A' and resid 391 through 407 removed outlier: 3.799A pdb=" N GLU A 401 " --> pdb=" O ALA A 397 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE A 405 " --> pdb=" O GLU A 401 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N GLN A 407 " --> pdb=" O ALA A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 431 removed outlier: 3.506A pdb=" N LYS A 431 " --> pdb=" O THR A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 452 Proline residue: A 445 - end of helix Processing helix chain 'A' and resid 459 through 461 No H-bonds generated for 'chain 'A' and resid 459 through 461' Processing helix chain 'A' and resid 462 through 479 removed outlier: 3.559A pdb=" N SER A 468 " --> pdb=" O GLY A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 489 Processing helix chain 'A' and resid 492 through 509 Processing helix chain 'B' and resid 10 through 19 Processing helix chain 'B' and resid 25 through 28 Processing helix chain 'B' and resid 152 through 159 Processing helix chain 'B' and resid 176 through 188 removed outlier: 3.830A pdb=" N VAL B 180 " --> pdb=" O GLY B 176 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ALA B 181 " --> pdb=" O LYS B 177 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N THR B 184 " --> pdb=" O VAL B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 194 removed outlier: 3.530A pdb=" N GLY B 194 " --> pdb=" O ARG B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 199 Processing helix chain 'B' and resid 211 through 225 Processing helix chain 'B' and resid 241 through 263 Proline residue: B 249 - end of helix removed outlier: 3.938A pdb=" N PHE B 259 " --> pdb=" O ILE B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 286 removed outlier: 3.615A pdb=" N GLN B 276 " --> pdb=" O ASP B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 296 Processing helix chain 'B' and resid 299 through 309 Processing helix chain 'B' and resid 332 through 335 Processing helix chain 'B' and resid 338 through 348 Processing helix chain 'B' and resid 355 through 362 removed outlier: 3.650A pdb=" N PHE B 359 " --> pdb=" O GLU B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 380 removed outlier: 3.696A pdb=" N ALA B 379 " --> pdb=" O VAL B 376 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA B 380 " --> pdb=" O GLY B 377 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 376 through 380' Processing helix chain 'B' and resid 382 through 389 Processing helix chain 'B' and resid 391 through 407 removed outlier: 3.708A pdb=" N GLN B 407 " --> pdb=" O ALA B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 431 removed outlier: 3.507A pdb=" N ARG B 425 " --> pdb=" O VAL B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 442 Processing helix chain 'B' and resid 443 through 452 Processing helix chain 'B' and resid 453 through 458 removed outlier: 4.348A pdb=" N GLY B 457 " --> pdb=" O GLY B 453 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE B 458 " --> pdb=" O HIS B 454 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 453 through 458' Processing helix chain 'B' and resid 459 through 461 No H-bonds generated for 'chain 'B' and resid 459 through 461' Processing helix chain 'B' and resid 462 through 477 Processing helix chain 'B' and resid 478 through 489 Processing helix chain 'B' and resid 492 through 508 Processing helix chain 'C' and resid 13 through 22 Processing helix chain 'C' and resid 80 through 84 Processing helix chain 'C' and resid 102 through 106 removed outlier: 3.631A 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 194 removed outlier: 4.007A pdb=" N THR C 184 " --> pdb=" O VAL C 180 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE C 185 " --> pdb=" O ALA C 181 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LYS C 189 " --> pdb=" O ILE C 185 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N ARG C 190 " --> pdb=" O LEU C 186 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N TRP C 191 " --> pdb=" O ASN C 187 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLY C 194 " --> pdb=" O ARG C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 225 Processing helix chain 'C' and resid 241 through 262 Proline residue: C 249 - end of helix removed outlier: 3.685A pdb=" N ILE C 255 " --> pdb=" O THR C 251 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N PHE C 259 " --> pdb=" O ILE C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 287 removed outlier: 3.567A pdb=" N GLN C 276 " --> pdb=" O ASP C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 296 Processing helix chain 'C' and resid 297 through 298 No H-bonds generated for 'chain 'C' and resid 297 through 298' Processing helix chain 'C' and resid 299 through 309 Processing helix chain 'C' and resid 338 through 348 Processing helix chain 'C' and resid 355 through 361 Processing helix chain 'C' and resid 368 through 372 Processing helix chain 'C' and resid 376 through 381 Processing helix chain 'C' and resid 382 through 388 Processing helix chain 'C' and resid 389 through 402 removed outlier: 3.501A pdb=" N LYS C 393 " --> pdb=" O ALA C 389 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 407 Processing helix chain 'C' and resid 413 through 430 Processing helix chain 'C' and resid 439 through 452 Proline residue: C 445 - end of helix Processing helix chain 'C' and resid 459 through 478 removed outlier: 4.293A pdb=" N GLY C 464 " --> pdb=" O LEU C 460 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N GLU C 465 " --> pdb=" O SER C 461 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N SER C 468 " --> pdb=" O GLY C 464 " (cutoff:3.500A) Processing helix chain 'C' and resid 478 through 489 Processing helix chain 'C' and resid 492 through 509 Processing helix chain 'D' and resid 138 through 145 Processing helix chain 'D' and resid 162 through 178 Processing helix chain 'D' and resid 190 through 204 Processing helix chain 'D' and resid 225 through 248 removed outlier: 4.467A pdb=" N ALA D 233 " --> pdb=" O ARG D 229 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N LEU D 234 " --> pdb=" O ALA D 230 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 273 Processing helix chain 'D' and resid 277 through 281 Processing helix chain 'D' and resid 284 through 293 Processing helix chain 'D' and resid 319 through 329 removed outlier: 3.531A pdb=" N HIS D 328 " --> pdb=" O THR D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 336 through 341 Processing helix chain 'D' and resid 359 through 364 Processing helix chain 'D' and resid 364 through 392 removed outlier: 3.861A pdb=" N ILE D 387 " --> pdb=" O SER D 383 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ILE D 390 " --> pdb=" O ASP D 386 " (cutoff:3.500A) Processing helix chain 'D' and resid 393 through 396 Processing helix chain 'D' and resid 397 through 415 removed outlier: 4.050A pdb=" N SER D 415 " --> pdb=" O GLN D 411 " (cutoff:3.500A) Processing helix chain 'D' and resid 418 through 420 No H-bonds generated for 'chain 'D' and resid 418 through 420' Processing helix chain 'D' and resid 421 through 426 Processing helix chain 'D' and resid 433 through 446 Processing helix chain 'D' and resid 453 through 457 Processing helix chain 'D' and resid 462 through 475 removed outlier: 3.698A pdb=" N ALA D 468 " --> pdb=" O GLU D 464 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 92 Processing helix chain 'E' and resid 138 through 145 Processing helix chain 'E' and resid 162 through 178 removed outlier: 3.617A pdb=" N PHE E 166 " --> pdb=" O GLY E 162 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE E 167 " --> pdb=" O LYS E 163 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N LYS E 176 " --> pdb=" O ASN E 172 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALA E 177 " --> pdb=" O ASN E 173 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 204 Processing helix chain 'E' and resid 225 through 231 removed outlier: 3.622A pdb=" N ARG E 231 " --> pdb=" O GLY E 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 231 through 245 Processing helix chain 'E' and resid 257 through 273 removed outlier: 3.557A pdb=" N PHE E 261 " --> pdb=" O ASN E 257 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ALA E 270 " --> pdb=" O SER E 266 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N LEU E 271 " --> pdb=" O GLU E 267 " (cutoff:3.500A) Processing helix chain 'E' and resid 284 through 294 Processing helix chain 'E' and resid 312 through 316 Processing helix chain 'E' and resid 319 through 327 removed outlier: 4.045A pdb=" N ALA E 327 " --> pdb=" O ALA E 323 " (cutoff:3.500A) Processing helix chain 'E' and resid 336 through 342 Processing helix chain 'E' and resid 357 through 359 No H-bonds generated for 'chain 'E' and resid 357 through 359' Processing helix chain 'E' and resid 364 through 384 Processing helix chain 'E' and resid 384 through 391 Processing helix chain 'E' and resid 392 through 396 Processing helix chain 'E' and resid 397 through 415 removed outlier: 3.514A pdb=" N LEU E 402 " --> pdb=" O GLU E 398 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N SER E 415 " --> pdb=" O GLN E 411 " (cutoff:3.500A) Processing helix chain 'E' and resid 421 through 426 Processing helix chain 'E' and resid 433 through 446 Processing helix chain 'E' and resid 453 through 458 removed outlier: 3.626A pdb=" N PHE E 457 " --> pdb=" O PRO E 453 " (cutoff:3.500A) Processing helix chain 'E' and resid 462 through 475 Processing helix chain 'F' and resid 138 through 145 Processing helix chain 'F' and resid 162 through 178 removed outlier: 4.266A pdb=" N LYS F 176 " --> pdb=" O ASN F 172 " (cutoff:3.500A) Processing helix chain 'F' and resid 190 through 204 Processing helix chain 'F' and resid 225 through 245 removed outlier: 4.361A pdb=" N ALA F 233 " --> pdb=" O ARG F 229 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N LEU F 234 " --> pdb=" O ALA F 230 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR F 235 " --> pdb=" O ARG F 231 " (cutoff:3.500A) Processing helix chain 'F' and resid 257 through 273 removed outlier: 3.701A pdb=" N PHE F 261 " --> pdb=" O ASN F 257 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ALA F 270 " --> pdb=" O SER F 266 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LEU F 271 " --> pdb=" O GLU F 267 " (cutoff:3.500A) Processing helix chain 'F' and resid 277 through 281 Processing helix chain 'F' and resid 284 through 296 Processing helix chain 'F' and resid 313 through 316 Processing helix chain 'F' and resid 319 through 329 Processing helix chain 'F' and resid 336 through 342 removed outlier: 3.566A pdb=" N SER F 340 " --> pdb=" O SER F 336 " (cutoff:3.500A) Processing helix chain 'F' and resid 363 through 391 removed outlier: 3.924A pdb=" N HIS F 367 " --> pdb=" O VAL F 363 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ASP F 386 " --> pdb=" O LYS F 382 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ILE F 387 " --> pdb=" O SER F 383 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE F 390 " --> pdb=" O ASP F 386 " (cutoff:3.500A) Processing helix chain 'F' and resid 397 through 414 Processing helix chain 'F' and resid 418 through 422 Processing helix chain 'F' and resid 433 through 447 Processing helix chain 'F' and resid 453 through 457 Processing helix chain 'F' and resid 462 through 475 Processing helix chain 'G' and resid 2 through 56 removed outlier: 4.015A pdb=" N LYS G 33 " --> pdb=" O THR G 29 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N SER G 40 " --> pdb=" O LYS G 36 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU G 48 " --> pdb=" O MET G 44 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N PHE G 51 " --> pdb=" O ALA G 47 " (cutoff:3.500A) Processing helix chain 'G' and resid 86 through 102 removed outlier: 3.779A pdb=" N ASP G 101 " --> pdb=" O ARG G 97 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLN G 102 " --> pdb=" O HIS G 98 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 122 removed outlier: 3.677A pdb=" N GLN G 117 " --> pdb=" O LYS G 113 " (cutoff:3.500A) Processing helix chain 'G' and resid 139 through 155 Processing helix chain 'G' and resid 156 through 159 Processing helix chain 'G' and resid 184 through 191 Processing helix chain 'G' and resid 192 through 197 removed outlier: 3.962A pdb=" N GLY G 195 " --> pdb=" O PRO G 192 " (cutoff:3.500A) Processing helix chain 'G' and resid 204 through 276 removed outlier: 4.111A pdb=" N GLU G 211 " --> pdb=" O ARG G 207 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER G 276 " --> pdb=" O THR G 272 " (cutoff:3.500A) Processing helix chain 'H' and resid 93 through 97 Processing helix chain 'H' and resid 100 through 115 Processing helix chain 'H' and resid 119 through 136 removed outlier: 3.826A pdb=" N VAL H 136 " --> pdb=" O ASN H 132 " (cutoff:3.500A) Processing helix chain 'I' and resid 9 through 23 Processing helix chain 'I' and resid 31 through 37 removed outlier: 3.942A pdb=" N LEU I 35 " --> pdb=" O THR I 31 " (cutoff:3.500A) Processing helix chain 'O' and resid 17 through 29 Processing helix chain 'O' and resid 33 through 49 Processing helix chain 'O' and resid 64 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 180 through 191 Processing helix chain 'T' and resid 27 through 43 removed outlier: 3.539A pdb=" N SER T 42 " --> pdb=" O LEU T 38 " (cutoff:3.500A) Processing helix chain 'T' and resid 58 through 74 removed outlier: 3.894A pdb=" N GLN T 62 " --> pdb=" O TRP T 58 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N MET T 72 " --> pdb=" O THR T 68 " (cutoff:3.500A) Processing helix chain 'T' and resid 82 through 84 No H-bonds generated for 'chain 'T' and resid 82 through 84' Processing helix chain 'T' and resid 85 through 103 removed outlier: 3.954A pdb=" N ILE T 96 " --> pdb=" O LEU T 92 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LEU T 101 " --> pdb=" O PHE T 97 " (cutoff:3.500A) Processing helix chain 'T' and resid 114 through 138 removed outlier: 3.990A pdb=" N ILE T 118 " --> pdb=" O HIS T 114 " (cutoff:3.500A) Processing helix chain 'T' and resid 140 through 146 Processing helix chain 'T' and resid 151 through 155 Processing helix chain 'T' and resid 156 through 167 removed outlier: 4.019A pdb=" N GLU T 162 " --> pdb=" O LEU T 158 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N SER T 165 " --> pdb=" O ILE T 161 " (cutoff:3.500A) Processing helix chain 'T' and resid 168 through 199 removed outlier: 4.056A pdb=" N LEU T 173 " --> pdb=" O ARG T 169 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N GLY T 174 " --> pdb=" O ALA T 170 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N LEU T 177 " --> pdb=" O LEU T 173 " (cutoff:3.500A) Processing helix chain 'T' and resid 202 through 206 Processing helix chain 'T' and resid 210 through 247 removed outlier: 3.679A pdb=" N PHE T 224 " --> pdb=" O MET T 220 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA T 225 " --> pdb=" O MET T 221 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA T 239 " --> pdb=" O ALA T 235 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LEU T 242 " --> pdb=" O THR T 238 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N TYR T 247 " --> pdb=" O LYS T 243 " (cutoff:3.500A) Processing helix chain 'U' and resid 54 through 186 removed outlier: 4.099A pdb=" N LEU U 58 " --> pdb=" O ASP U 54 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ALA U 74 " --> pdb=" O ALA U 70 " (cutoff:3.500A) Proline residue: U 75 - end of helix removed outlier: 3.681A pdb=" N GLU U 118 " --> pdb=" O GLN U 114 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N LYS U 121 " --> pdb=" O ALA U 117 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N VAL U 122 " --> pdb=" O GLU U 118 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLU U 139 " --> pdb=" O SER U 135 " (cutoff:3.500A) Processing helix chain 'U' and resid 187 through 206 removed outlier: 4.026A pdb=" N VAL U 193 " --> pdb=" O PHE U 189 " (cutoff:3.500A) Processing helix chain 'V' and resid 4 through 19 Processing helix chain 'V' and resid 26 through 48 removed outlier: 3.703A pdb=" N LEU V 43 " --> pdb=" O ALA V 39 " (cutoff:3.500A) Processing helix chain 'V' and resid 56 through 62 removed outlier: 3.808A pdb=" N SER V 60 " --> pdb=" O SER V 56 " (cutoff:3.500A) Processing helix chain 'V' and resid 67 through 78 Processing helix chain 'V' and resid 90 through 127 removed outlier: 3.566A pdb=" N SER V 94 " --> pdb=" O GLN V 90 " (cutoff:3.500A) Processing helix chain 'V' and resid 134 through 142 Processing helix chain 'V' and resid 143 through 156 Processing helix chain 'V' and resid 162 through 166 Processing helix chain 'W' and resid 17 through 30 removed outlier: 4.236A pdb=" N ALA W 21 " --> pdb=" O SER W 17 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LYS W 22 " --> pdb=" O ALA W 18 " (cutoff:3.500A) removed outlier: 4.228A 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: 3.533A pdb=" N ILE W 73 " --> pdb=" O PHE W 69 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N TYR W 78 " --> pdb=" O ILE W 74 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N SER W 79 " --> pdb=" O ALA W 75 " (cutoff:3.500A) Processing helix chain 'X' and resid 2 through 14 Processing helix chain 'X' and resid 20 through 28 removed outlier: 3.969A pdb=" N GLY X 26 " --> pdb=" O GLN X 22 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ASN X 27 " --> pdb=" O ASP X 23 " (cutoff:3.500A) Processing helix chain 'X' and resid 46 through 57 removed outlier: 4.261A pdb=" N LEU X 50 " --> pdb=" O GLY X 46 " (cutoff:3.500A) Processing helix chain 'Y' and resid 13 through 35 Processing helix chain 'Z' and resid 8 through 30 Processing helix chain 'Z' and resid 30 through 48 removed outlier: 3.632A pdb=" N MET Z 34 " --> pdb=" O PHE Z 30 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE Z 35 " --> pdb=" O PHE Z 31 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 62 through 69 removed outlier: 4.586A pdb=" N GLU A 53 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N ASN A 95 " --> pdb=" O LEU A 54 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N GLU A 56 " --> pdb=" O THR A 93 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N THR A 93 " --> pdb=" O GLU A 56 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG A 32 " --> pdb=" O PHE A 44 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N ARG A 42 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N VAL A 36 " --> pdb=" O ILE A 40 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N ILE A 40 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASN A 67 " --> pdb=" O GLY A 74 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N VAL A 76 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N ALA A 65 " --> pdb=" O VAL A 76 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N PHE A 78 " --> pdb=" O GLY A 63 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N GLY A 63 " --> pdb=" O PHE A 78 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ARG E 60 " --> pdb=" O ALA E 51 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ILE E 17 " --> pdb=" O ILE E 20 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N HIS E 24 " --> pdb=" O VAL E 13 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N VAL E 13 " --> pdb=" O HIS E 24 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 98 through 101 Processing sheet with id=AA3, first strand: chain 'A' and resid 109 through 111 removed outlier: 6.148A pdb=" N CYS A 203 " --> pdb=" O ILE A 232 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N VAL A 234 " --> pdb=" O CYS A 203 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N TYR A 205 " --> pdb=" O VAL A 234 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N ALA A 236 " --> pdb=" O TYR A 205 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ALA A 207 " --> pdb=" O ALA A 236 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ALA A 266 " --> pdb=" O THR A 324 " (cutoff:3.500A) removed outlier: 8.387A pdb=" N LEU A 326 " --> pdb=" O ALA A 266 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ILE A 268 " --> pdb=" O LEU A 326 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N VAL A 328 " --> pdb=" O ILE A 268 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N TYR A 270 " --> pdb=" O VAL A 328 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N GLU A 330 " --> pdb=" O TYR A 270 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ILE A 169 " --> pdb=" O ILE A 329 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N THR A 331 " --> pdb=" O ILE A 169 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N GLY A 171 " --> pdb=" O THR A 331 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 147 through 148 removed outlier: 4.322A pdb=" N ILE A 161 " --> pdb=" O VAL A 148 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 351 through 354 removed outlier: 3.530A pdb=" N PHE A 353 " --> pdb=" O LEU A 371 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N LEU A 371 " --> pdb=" O PHE A 353 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 30 through 37 removed outlier: 6.975A pdb=" N ARG B 42 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N VAL B 36 " --> pdb=" O ILE B 40 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ILE B 40 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N VAL B 76 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N ALA B 65 " --> pdb=" O VAL B 76 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLU B 53 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N LEU B 54 " --> pdb=" O THR B 93 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 98 through 101 Processing sheet with id=AA8, first strand: chain 'B' and resid 109 through 110 removed outlier: 6.016A pdb=" N VAL B 110 " --> pdb=" O ALA B 235 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N THR B 237 " --> pdb=" O VAL B 110 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N TYR B 202 " --> pdb=" O LEU B 267 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N VAL B 269 " --> pdb=" O TYR B 202 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N VAL B 204 " --> pdb=" O VAL B 269 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N ASP B 271 " --> pdb=" O VAL B 204 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N VAL B 206 " --> pdb=" O ASP B 271 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLY B 171 " --> pdb=" O ILE B 329 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N LEU B 168 " --> pdb=" O ILE B 352 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 147 through 148 removed outlier: 3.780A pdb=" N ILE B 161 " --> pdb=" O VAL B 148 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 31 through 37 removed outlier: 6.751A pdb=" N ARG C 42 " --> pdb=" O LEU C 34 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N VAL C 36 " --> pdb=" O ILE C 40 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ILE C 40 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N GLY C 74 " --> pdb=" O LEU C 66 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LEU C 66 " --> pdb=" O GLY C 74 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 10 through 17 current: chain 'C' and resid 90 through 96 Processing sheet with id=AB2, first strand: chain 'C' and resid 31 through 37 removed outlier: 6.751A pdb=" N ARG C 42 " --> pdb=" O LEU C 34 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N VAL C 36 " --> pdb=" O ILE C 40 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ILE C 40 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N GLY C 74 " --> pdb=" O LEU C 66 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LEU C 66 " --> pdb=" O GLY C 74 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 62 through 68 current: chain 'D' and resid 36 through 41 removed outlier: 6.114A pdb=" N ARG D 60 " --> pdb=" O ALA D 51 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N HIS D 53 " --> pdb=" O THR D 58 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N THR D 58 " --> pdb=" O HIS D 53 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N VAL D 23 " --> pdb=" O VAL D 59 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ILE D 20 " --> pdb=" O VAL D 16 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N VAL D 16 " --> pdb=" O ILE D 20 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N ASP D 22 " --> pdb=" O THR D 14 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 10 through 17 current: chain 'C' and resid 90 through 96 Processing sheet with id=AB3, first strand: chain 'C' and resid 98 through 101 Processing sheet with id=AB4, first strand: chain 'C' and resid 109 through 110 removed outlier: 6.204A pdb=" N VAL C 110 " --> pdb=" O ALA C 235 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N THR C 237 " --> pdb=" O VAL C 110 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N TYR C 205 " --> pdb=" O VAL C 234 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N ALA C 236 " --> pdb=" O TYR C 205 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N ALA C 207 " --> pdb=" O ALA C 236 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 147 through 148 removed outlier: 4.577A pdb=" N ILE C 161 " --> pdb=" O VAL C 148 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 328 through 331 removed outlier: 7.395A pdb=" N ILE C 170 " --> pdb=" O LEU C 354 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 84 through 87 removed outlier: 4.383A pdb=" N LEU D 113 " --> pdb=" O VAL D 87 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 95 through 96 removed outlier: 3.640A pdb=" N PHE D 219 " --> pdb=" O ILE D 96 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N VAL D 183 " --> pdb=" O PHE D 254 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N ASP D 256 " --> pdb=" O VAL D 183 " (cutoff:3.500A) removed outlier: 8.306A pdb=" N THR D 185 " --> pdb=" O ASP D 256 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N PHE D 254 " --> pdb=" O VAL D 307 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N ALA D 309 " --> pdb=" O PHE D 254 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N ASP D 256 " --> pdb=" O ALA D 309 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 84 through 87 removed outlier: 4.222A 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: 5.848A pdb=" N ILE E 96 " --> pdb=" O PHE E 219 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N GLN E 221 " --> pdb=" O ILE E 96 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ALA E 216 " --> pdb=" O VAL E 183 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N THR E 185 " --> pdb=" O ALA E 216 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N VAL E 218 " --> pdb=" O THR E 185 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N VAL E 187 " --> pdb=" O VAL E 218 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N GLY E 220 " --> pdb=" O VAL E 187 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL E 251 " --> pdb=" O THR E 305 " (cutoff:3.500A) removed outlier: 8.612A pdb=" N VAL E 307 " --> pdb=" O VAL E 251 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N LEU E 253 " --> pdb=" O VAL E 307 " (cutoff:3.500A) removed outlier: 8.467A pdb=" N ALA E 309 " --> pdb=" O LEU E 253 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N ILE E 255 " --> pdb=" O ALA E 309 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 133 through 134 Processing sheet with id=AC3, first strand: chain 'E' and resid 331 through 335 removed outlier: 5.656A pdb=" N ASP E 352 " --> pdb=" O VAL E 334 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 13 through 17 removed outlier: 3.765A pdb=" N ALA F 15 " --> pdb=" O ASP F 22 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ARG F 60 " --> pdb=" O ALA F 51 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 84 through 87 Processing sheet with id=AC6, first strand: chain 'F' and resid 216 through 221 removed outlier: 6.762A pdb=" N ILE F 153 " --> pdb=" O GLN F 308 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N VAL F 310 " --> pdb=" O ILE F 153 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N LEU F 155 " --> pdb=" O VAL F 310 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LYS F 152 " --> pdb=" O ALA F 331 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N THR F 333 " --> pdb=" O LYS F 152 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N GLY F 154 " --> pdb=" O THR F 333 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N LEU F 335 " --> pdb=" O GLY F 154 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N PHE F 156 " --> pdb=" O LEU F 335 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 126 through 130 removed outlier: 7.089A pdb=" N ILE G 107 " --> pdb=" O LYS G 127 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N SER G 129 " --> pdb=" O ILE G 107 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N THR G 109 " --> pdb=" O SER G 129 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N GLU G 72 " --> pdb=" O ASP G 106 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N VAL G 108 " --> pdb=" O GLU G 72 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N ILE G 74 " --> pdb=" O VAL G 108 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N ILE G 110 " --> pdb=" O ILE G 74 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N ALA G 76 " --> pdb=" O ILE G 110 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N LEU G 73 " --> pdb=" O SER G 163 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N PHE G 165 " --> pdb=" O LEU G 73 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N VAL G 75 " --> pdb=" O PHE G 165 " (cutoff:3.500A) removed outlier: 8.904A pdb=" N ASN G 167 " --> pdb=" O VAL G 75 " (cutoff:3.500A) removed outlier: 9.004A pdb=" N ILE G 77 " --> pdb=" O ASN G 167 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N SER G 174 " --> pdb=" O VAL G 170 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 20 through 22 removed outlier: 5.633A pdb=" N GLN H 13 " --> pdb=" O VAL H 85 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N ALA H 87 " --> pdb=" O GLN H 13 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N ALA H 15 " --> pdb=" O ALA H 87 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 37 through 42 removed outlier: 6.372A pdb=" N VAL H 56 " --> pdb=" O PRO H 33 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 43 through 45 Processing sheet with id=AD2, first strand: chain 'O' and resid 118 through 119 Processing sheet with id=AD3, first strand: chain 'O' and resid 157 through 159 removed outlier: 3.520A pdb=" N VAL O 158 " --> pdb=" O VAL O 123 " (cutoff:3.500A) 2313 hydrogen bonds defined for protein. 6681 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: 8.49 Time building geometry restraints manager: 9.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.28: 5060 1.28 - 1.35: 1503 1.35 - 1.41: 3518 1.41 - 1.48: 5111 1.48 - 1.54: 5000 Bond restraints: 20192 Sorted by residual: bond pdb=" CA ALA A 157 " pdb=" C ALA A 157 " ideal model delta sigma weight residual 1.523 1.465 0.059 8.20e-03 1.49e+04 5.11e+01 bond pdb=" CA ALA C 157 " pdb=" C ALA C 157 " ideal model delta sigma weight residual 1.523 1.473 0.050 8.40e-03 1.42e+04 3.61e+01 bond pdb=" CA GLY F 220 " pdb=" C GLY F 220 " ideal model delta sigma weight residual 1.520 1.480 0.041 7.30e-03 1.88e+04 3.09e+01 bond pdb=" CA GLY F 11 " pdb=" C GLY F 11 " ideal model delta sigma weight residual 1.514 1.472 0.042 8.60e-03 1.35e+04 2.38e+01 bond pdb=" CA ALA F 148 " pdb=" C ALA F 148 " ideal model delta sigma weight residual 1.522 1.465 0.057 1.21e-02 6.83e+03 2.20e+01 ... (remaining 20187 not shown) Histogram of bond angle deviations from ideal: 96.22 - 104.34: 526 104.34 - 112.47: 3754 112.47 - 120.59: 9205 120.59 - 128.72: 11676 128.72 - 136.84: 19 Bond angle restraints: 25180 Sorted by residual: angle pdb=" N VAL V 67 " pdb=" CA VAL V 67 " pdb=" C VAL V 67 " ideal model delta sigma weight residual 113.71 102.41 11.30 9.50e-01 1.11e+00 1.41e+02 angle pdb=" N VAL T 146 " pdb=" CA VAL T 146 " pdb=" C VAL T 146 " ideal model delta sigma weight residual 108.15 98.75 9.40 9.90e-01 1.02e+00 9.02e+01 angle pdb=" N VAL C 376 " pdb=" CA VAL C 376 " pdb=" C VAL C 376 " ideal model delta sigma weight residual 111.81 103.76 8.05 8.60e-01 1.35e+00 8.76e+01 angle pdb=" N GLN A 398 " pdb=" CA GLN A 398 " pdb=" C GLN A 398 " ideal model delta sigma weight residual 113.41 102.08 11.33 1.22e+00 6.72e-01 8.62e+01 angle pdb=" C ASN G 204 " pdb=" N VAL G 205 " pdb=" CA VAL G 205 " ideal model delta sigma weight residual 120.24 125.96 -5.72 6.30e-01 2.52e+00 8.24e+01 ... (remaining 25175 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.18: 5005 24.18 - 48.36: 17 48.36 - 72.54: 0 72.54 - 96.72: 1 96.72 - 120.90: 1 Dihedral angle restraints: 5024 sinusoidal: 4 harmonic: 5020 Sorted by residual: dihedral pdb=" CA ASP F 256 " pdb=" C ASP F 256 " pdb=" N ASN F 257 " pdb=" CA ASN F 257 " ideal model delta harmonic sigma weight residual -180.00 -59.10 -120.90 0 5.00e+00 4.00e-02 5.85e+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 -136.35 -43.65 0 5.00e+00 4.00e-02 7.62e+01 dihedral pdb=" CA ASN 9 40 " pdb=" C ASN 9 40 " pdb=" N PRO 9 41 " pdb=" CA PRO 9 41 " ideal model delta harmonic sigma weight residual -180.00 -139.25 -40.75 0 5.00e+00 4.00e-02 6.64e+01 ... (remaining 5021 not shown) Chirality restraints: 0 Planarity restraints: 5024 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR G 2 " -0.020 2.00e-02 2.50e+03 4.02e-02 1.62e+01 pdb=" C THR G 2 " 0.070 2.00e-02 2.50e+03 pdb=" O THR G 2 " -0.026 2.00e-02 2.50e+03 pdb=" N LEU G 3 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY B 321 " -0.020 2.00e-02 2.50e+03 4.01e-02 1.61e+01 pdb=" C GLY B 321 " 0.069 2.00e-02 2.50e+03 pdb=" O GLY B 321 " -0.026 2.00e-02 2.50e+03 pdb=" N SER B 322 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR C 93 " -0.019 2.00e-02 2.50e+03 3.85e-02 1.49e+01 pdb=" C THR C 93 " 0.067 2.00e-02 2.50e+03 pdb=" O THR C 93 " -0.025 2.00e-02 2.50e+03 pdb=" N GLY C 94 " -0.022 2.00e-02 2.50e+03 ... (remaining 5021 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 9286 2.86 - 3.37: 17245 3.37 - 3.88: 26971 3.88 - 4.39: 27447 4.39 - 4.90: 40984 Nonbonded interactions: 121933 Sorted by model distance: nonbonded pdb=" N THR T 150 " pdb=" O THR T 150 " model vdw 2.352 2.496 nonbonded pdb=" N LEU H 16 " pdb=" O LEU H 16 " model vdw 2.365 2.496 nonbonded pdb=" N GLU A 167 " pdb=" O GLU A 167 " model vdw 2.388 2.496 nonbonded pdb=" N THR D 305 " pdb=" O THR D 305 " model vdw 2.389 2.496 nonbonded pdb=" N ASP F 256 " pdb=" O ASP F 256 " model vdw 2.400 2.496 ... (remaining 121928 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain '0' and resid 2 through 73) selection = (chain '1' and resid 2 through 73) selection = (chain '2' and resid 2 through 73) selection = (chain '3' and resid 2 through 73) selection = (chain '4' and resid 2 through 73) selection = (chain '5' and resid 2 through 73) selection = (chain '6' and resid 2 through 73) selection = (chain '7' and resid 2 through 73) selection = (chain '8' and resid 2 through 73) selection = (chain '9' and resid 2 through 73) } ncs_group { reference = (chain 'A' and resid 12 through 509) selection = (chain 'B' and (resid 12 through 407 or resid 410 through 509)) selection = chain 'C' } ncs_group { reference = chain 'D' selection = (chain 'E' and resid 8 through 475) selection = (chain 'F' and resid 8 through 475) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 4.690 Check model and map are aligned: 0.280 Set scattering table: 0.180 Process input model: 61.760 Find NCS groups from input model: 1.790 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6413 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.019 0.059 20192 Z= 1.442 Angle : 2.202 15.144 25180 Z= 1.587 Chirality : 0.000 0.000 0 Planarity : 0.010 0.040 5024 Dihedral : 6.684 120.900 5024 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 0.12 Ramachandran Plot: Outliers : 1.28 % Allowed : 4.17 % Favored : 94.54 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.46 % Cis-general : 0.08 % Twisted Proline : 4.43 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.11), residues: 4984 helix: 0.82 (0.09), residues: 2800 sheet: -1.39 (0.20), residues: 575 loop : -1.92 (0.13), residues: 1609 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9968 Ramachandran restraints generated. 4984 Oldfield, 0 Emsley, 4984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9968 Ramachandran restraints generated. 4984 Oldfield, 0 Emsley, 4984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 4114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 2.218 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.1611 time to fit residues: 28.1958 Evaluate side-chains 82 residues out of total 4114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 2.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 415 optimal weight: 6.9990 chunk 372 optimal weight: 7.9990 chunk 206 optimal weight: 6.9990 chunk 127 optimal weight: 6.9990 chunk 251 optimal weight: 7.9990 chunk 199 optimal weight: 10.0000 chunk 385 optimal weight: 8.9990 chunk 149 optimal weight: 6.9990 chunk 234 optimal weight: 20.0000 chunk 287 optimal weight: 10.0000 chunk 446 optimal weight: 10.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6457 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 20192 Z= 0.192 Angle : 0.540 8.122 25180 Z= 0.346 Chirality : 0.000 0.000 0 Planarity : 0.003 0.020 5024 Dihedral : 4.877 67.205 5024 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 1.50 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.77 % Favored : 97.01 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.96 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.12), residues: 4984 helix: 2.34 (0.10), residues: 2840 sheet: -0.87 (0.22), residues: 529 loop : -0.93 (0.15), residues: 1615 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9968 Ramachandran restraints generated. 4984 Oldfield, 0 Emsley, 4984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9968 Ramachandran restraints generated. 4984 Oldfield, 0 Emsley, 4984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 4114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 2.441 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.1537 time to fit residues: 27.2059 Evaluate side-chains 82 residues out of total 4114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 2.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 248 optimal weight: 0.2980 chunk 138 optimal weight: 40.0000 chunk 371 optimal weight: 3.9990 chunk 304 optimal weight: 50.0000 chunk 123 optimal weight: 50.0000 chunk 447 optimal weight: 9.9990 chunk 483 optimal weight: 50.0000 chunk 398 optimal weight: 50.0000 chunk 443 optimal weight: 120.0000 chunk 152 optimal weight: 20.0000 chunk 359 optimal weight: 50.0000 overall best weight: 14.8592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6770 moved from start: 0.3704 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= 0.319 Angle : 0.696 12.299 25180 Z= 0.446 Chirality : 0.000 0.000 0 Planarity : 0.004 0.018 5024 Dihedral : 5.517 59.137 5024 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.38 % Favored : 94.38 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.96 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.12), residues: 4984 helix: 2.48 (0.10), residues: 2807 sheet: -1.09 (0.21), residues: 515 loop : -0.93 (0.15), residues: 1662 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9968 Ramachandran restraints generated. 4984 Oldfield, 0 Emsley, 4984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9968 Ramachandran restraints generated. 4984 Oldfield, 0 Emsley, 4984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 4114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 2.199 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.1628 time to fit residues: 28.7002 Evaluate side-chains 82 residues out of total 4114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 2.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 442 optimal weight: 50.0000 chunk 336 optimal weight: 4.9990 chunk 232 optimal weight: 0.0570 chunk 49 optimal weight: 50.0000 chunk 213 optimal weight: 40.0000 chunk 300 optimal weight: 50.0000 chunk 449 optimal weight: 110.0000 chunk 475 optimal weight: 50.0000 chunk 234 optimal weight: 30.0000 chunk 425 optimal weight: 50.0000 chunk 128 optimal weight: 40.0000 overall best weight: 23.0112 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6948 moved from start: 0.5031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.088 20192 Z= 0.426 Angle : 0.819 16.245 25180 Z= 0.536 Chirality : 0.000 0.000 0 Planarity : 0.005 0.023 5024 Dihedral : 6.342 49.598 5024 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 15.68 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.78 % Favored : 92.96 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.96 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.12), residues: 4984 helix: 1.40 (0.09), residues: 2775 sheet: -1.46 (0.25), residues: 396 loop : -1.45 (0.15), residues: 1813 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9968 Ramachandran restraints generated. 4984 Oldfield, 0 Emsley, 4984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9968 Ramachandran restraints generated. 4984 Oldfield, 0 Emsley, 4984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 4114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 2.295 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.1613 time to fit residues: 28.5009 Evaluate side-chains 82 residues out of total 4114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 2.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 396 optimal weight: 50.0000 chunk 269 optimal weight: 20.0000 chunk 6 optimal weight: 110.0000 chunk 354 optimal weight: 0.4980 chunk 196 optimal weight: 7.9990 chunk 405 optimal weight: 8.9990 chunk 328 optimal weight: 20.0000 chunk 0 optimal weight: 60.0000 chunk 242 optimal weight: 7.9990 chunk 426 optimal weight: 50.0000 chunk 120 optimal weight: 40.0000 overall best weight: 9.0990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6800 moved from start: 0.4986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 20192 Z= 0.181 Angle : 0.464 9.482 25180 Z= 0.298 Chirality : 0.000 0.000 0 Planarity : 0.002 0.012 5024 Dihedral : 4.894 40.770 5024 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.54 % 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 : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.12), residues: 4984 helix: 2.48 (0.10), residues: 2819 sheet: -1.53 (0.23), residues: 462 loop : -1.13 (0.16), residues: 1703 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9968 Ramachandran restraints generated. 4984 Oldfield, 0 Emsley, 4984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9968 Ramachandran restraints generated. 4984 Oldfield, 0 Emsley, 4984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 4114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 2.252 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.1650 time to fit residues: 29.3174 Evaluate side-chains 82 residues out of total 4114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 2.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 160 optimal weight: 30.0000 chunk 428 optimal weight: 50.0000 chunk 94 optimal weight: 30.0000 chunk 279 optimal weight: 20.0000 chunk 117 optimal weight: 50.0000 chunk 476 optimal weight: 4.9990 chunk 395 optimal weight: 20.0000 chunk 220 optimal weight: 40.0000 chunk 39 optimal weight: 50.0000 chunk 157 optimal weight: 50.0000 chunk 249 optimal weight: 7.9990 overall best weight: 16.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6928 moved from start: 0.5640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 20192 Z= 0.301 Angle : 0.632 13.951 25180 Z= 0.409 Chirality : 0.000 0.000 0 Planarity : 0.004 0.017 5024 Dihedral : 5.581 50.171 5024 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.99 % Favored : 91.73 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.96 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.12), residues: 4984 helix: 2.12 (0.10), residues: 2789 sheet: -1.67 (0.26), residues: 362 loop : -1.47 (0.15), residues: 1833 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9968 Ramachandran restraints generated. 4984 Oldfield, 0 Emsley, 4984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9968 Ramachandran restraints generated. 4984 Oldfield, 0 Emsley, 4984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 4114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 2.605 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.1674 time to fit residues: 29.4225 Evaluate side-chains 82 residues out of total 4114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 2.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 458 optimal weight: 50.0000 chunk 53 optimal weight: 20.0000 chunk 271 optimal weight: 6.9990 chunk 347 optimal weight: 5.9990 chunk 269 optimal weight: 50.0000 chunk 400 optimal weight: 20.0000 chunk 265 optimal weight: 1.9990 chunk 474 optimal weight: 0.0270 chunk 296 optimal weight: 50.0000 chunk 289 optimal weight: 40.0000 chunk 218 optimal weight: 6.9990 overall best weight: 4.4046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6739 moved from start: 0.5516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.024 20192 Z= 0.112 Angle : 0.356 6.212 25180 Z= 0.229 Chirality : 0.000 0.000 0 Planarity : 0.002 0.013 5024 Dihedral : 4.227 37.290 5024 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.11 % Favored : 95.69 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.96 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.98 (0.13), residues: 4984 helix: 3.09 (0.10), residues: 2814 sheet: -1.58 (0.23), residues: 477 loop : -0.96 (0.16), residues: 1693 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9968 Ramachandran restraints generated. 4984 Oldfield, 0 Emsley, 4984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9968 Ramachandran restraints generated. 4984 Oldfield, 0 Emsley, 4984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 4114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 2.485 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.1686 time to fit residues: 29.4801 Evaluate side-chains 82 residues out of total 4114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 2.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 293 optimal weight: 0.0370 chunk 189 optimal weight: 50.0000 chunk 283 optimal weight: 30.0000 chunk 142 optimal weight: 50.0000 chunk 93 optimal weight: 40.0000 chunk 91 optimal weight: 50.0000 chunk 301 optimal weight: 9.9990 chunk 323 optimal weight: 20.0000 chunk 234 optimal weight: 30.0000 chunk 44 optimal weight: 20.0000 chunk 372 optimal weight: 20.0000 overall best weight: 14.0072 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6879 moved from start: 0.5823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 20192 Z= 0.251 Angle : 0.527 11.243 25180 Z= 0.343 Chirality : 0.000 0.000 0 Planarity : 0.003 0.013 5024 Dihedral : 4.769 42.286 5024 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.46 % Favored : 92.32 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.96 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.13), residues: 4984 helix: 2.80 (0.10), residues: 2809 sheet: -1.72 (0.24), residues: 422 loop : -1.17 (0.15), residues: 1753 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9968 Ramachandran restraints generated. 4984 Oldfield, 0 Emsley, 4984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9968 Ramachandran restraints generated. 4984 Oldfield, 0 Emsley, 4984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 4114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 2.418 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.1670 time to fit residues: 29.1148 Evaluate side-chains 82 residues out of total 4114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 2.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 431 optimal weight: 50.0000 chunk 454 optimal weight: 50.0000 chunk 414 optimal weight: 0.0060 chunk 441 optimal weight: 50.0000 chunk 265 optimal weight: 3.9990 chunk 192 optimal weight: 9.9990 chunk 346 optimal weight: 5.9990 chunk 135 optimal weight: 50.0000 chunk 399 optimal weight: 30.0000 chunk 417 optimal weight: 60.0000 chunk 440 optimal weight: 9.9990 overall best weight: 6.0004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6775 moved from start: 0.5831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 20192 Z= 0.126 Angle : 0.360 7.674 25180 Z= 0.232 Chirality : 0.000 0.000 0 Planarity : 0.002 0.013 5024 Dihedral : 4.163 38.197 5024 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.78 % Favored : 95.02 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.96 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.13 (0.13), residues: 4984 helix: 3.25 (0.10), residues: 2823 sheet: -1.65 (0.24), residues: 453 loop : -0.99 (0.16), residues: 1708 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9968 Ramachandran restraints generated. 4984 Oldfield, 0 Emsley, 4984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9968 Ramachandran restraints generated. 4984 Oldfield, 0 Emsley, 4984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 4114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 2.354 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.1690 time to fit residues: 29.6402 Evaluate side-chains 82 residues out of total 4114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 2.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 290 optimal weight: 30.0000 chunk 467 optimal weight: 50.0000 chunk 285 optimal weight: 50.0000 chunk 221 optimal weight: 30.0000 chunk 324 optimal weight: 50.0000 chunk 490 optimal weight: 50.0000 chunk 451 optimal weight: 40.0000 chunk 390 optimal weight: 50.0000 chunk 40 optimal weight: 70.0000 chunk 301 optimal weight: 9.9990 chunk 239 optimal weight: 50.0000 overall best weight: 31.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7080 moved from start: 0.6627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.102 20192 Z= 0.533 Angle : 0.915 16.013 25180 Z= 0.621 Chirality : 0.000 0.000 0 Planarity : 0.006 0.026 5024 Dihedral : 6.363 49.865 5024 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 23.81 Ramachandran Plot: Outliers : 0.44 % Allowed : 10.19 % Favored : 89.37 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.96 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.12), residues: 4984 helix: 0.94 (0.10), residues: 2772 sheet: -2.08 (0.27), residues: 325 loop : -2.04 (0.14), residues: 1887 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9968 Ramachandran restraints generated. 4984 Oldfield, 0 Emsley, 4984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9968 Ramachandran restraints generated. 4984 Oldfield, 0 Emsley, 4984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 4114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 2.613 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.1756 time to fit residues: 30.4524 Evaluate side-chains 82 residues out of total 4114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 2.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 310 optimal weight: 50.0000 chunk 415 optimal weight: 30.0000 chunk 119 optimal weight: 50.0000 chunk 359 optimal weight: 50.0000 chunk 57 optimal weight: 40.0000 chunk 108 optimal weight: 20.0000 chunk 390 optimal weight: 9.9990 chunk 163 optimal weight: 30.0000 chunk 401 optimal weight: 20.0000 chunk 49 optimal weight: 50.0000 chunk 72 optimal weight: 6.9990 overall best weight: 17.3996 ------------------------------------------------------------------------------- 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 = 0.2286 r_free = 0.2286 target = 0.027078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2182 r_free = 0.2182 target = 0.022270 restraints weight = 326096.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2182 r_free = 0.2182 target = 0.022269 restraints weight = 428079.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2182 r_free = 0.2182 target = 0.022269 restraints weight = 428475.708| |-----------------------------------------------------------------------------| r_work (final): 0.2377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.6643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 20192 Z= 0.303 Angle : 0.617 12.858 25180 Z= 0.405 Chirality : 0.000 0.000 0 Planarity : 0.003 0.020 5024 Dihedral : 5.672 54.136 5024 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 13.64 Ramachandran Plot: Outliers : 0.22 % Allowed : 9.29 % Favored : 90.49 % 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 : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.12), residues: 4984 helix: 1.41 (0.10), residues: 2798 sheet: -2.08 (0.26), residues: 342 loop : -2.03 (0.14), residues: 1844 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2376.08 seconds wall clock time: 43 minutes 35.35 seconds (2615.35 seconds total)