Starting phenix.real_space_refine on Sat Sep 28 12:24:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cb1_7445/09_2024/6cb1_7445_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cb1_7445/09_2024/6cb1_7445.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/6cb1_7445/09_2024/6cb1_7445.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cb1_7445/09_2024/6cb1_7445.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cb1_7445/09_2024/6cb1_7445_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cb1_7445/09_2024/6cb1_7445_neut.cif" } 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= 0.000 sd= 0.003 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: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 1615 5.49 5 S 8 5.16 5 C 36518 2.51 5 N 13352 2.21 5 O 18450 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 69945 Number of models: 1 Model: "" Number of chains: 45 Chain: "1" Number of atoms: 29343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1370, 29343 Classifications: {'RNA': 1370} Modifications used: {'rna2p_pur': 140, 'rna2p_pyr': 99, 'rna3p_pur': 626, 'rna3p_pyr': 505} Link IDs: {'rna2p': 238, 'rna3p': 1131} Chain breaks: 12 Chain: "2" Number of atoms: 3353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 3353 Classifications: {'RNA': 158} Modifications used: {'rna2p_pur': 17, 'rna2p_pyr': 17, 'rna3p_pur': 61, 'rna3p_pyr': 63} Link IDs: {'rna2p': 33, 'rna3p': 124} Chain: "6" Number of atoms: 1838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 1838 Classifications: {'RNA': 87} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 19, 'rna3p_pur': 32, 'rna3p_pyr': 28} Link IDs: {'rna2p': 26, 'rna3p': 60} Chain breaks: 1 Chain: "A" Number of atoms: 1946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 1946 Classifications: {'peptide': 394} Incomplete info: {'truncation_to_alanine': 352} Link IDs: {'PTRANS': 12, 'TRANS': 381} Chain breaks: 1 Unresolved chain link angles: 12 Unresolved non-hydrogen bonds: 1238 Unresolved non-hydrogen angles: 1573 Unresolved non-hydrogen dihedrals: 1030 Unresolved non-hydrogen chiralities: 119 Planarities with less than four sites: {'GLN:plan1': 11, 'HIS:plan': 8, 'TYR:plan': 11, 'ASN:plan1': 17, 'TRP:plan': 4, 'ASP:plan': 29, 'PHE:plan': 19, 'GLU:plan': 25, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 624 Chain: "C" Number of atoms: 1553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 1553 Classifications: {'peptide': 314} Incomplete info: {'truncation_to_alanine': 257} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 298} Chain breaks: 1 Unresolved chain link angles: 15 Unresolved non-hydrogen bonds: 911 Unresolved non-hydrogen angles: 1160 Unresolved non-hydrogen dihedrals: 760 Unresolved non-hydrogen chiralities: 94 Planarities with less than four sites: {'GLN:plan1': 10, 'ASP:plan': 6, 'TYR:plan': 6, 'ASN:plan1': 16, 'TRP:plan': 5, 'HIS:plan': 8, 'PHE:plan': 7, 'GLU:plan': 14, 'ARG:plan': 21} Unresolved non-hydrogen planarities: 436 Chain: "D" Number of atoms: 948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 948 Classifications: {'peptide': 190} Incomplete info: {'truncation_to_alanine': 167} Link IDs: {'PTRANS': 6, 'TRANS': 183} Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 662 Unresolved non-hydrogen angles: 832 Unresolved non-hydrogen dihedrals: 569 Unresolved non-hydrogen chiralities: 45 Planarities with less than four sites: {'GLN:plan1': 9, 'ARG:plan': 16, 'TYR:plan': 7, 'ASN:plan1': 10, 'TRP:plan': 4, 'ASP:plan': 6, 'PHE:plan': 5, 'GLU:plan': 15, 'HIS:plan': 6} Unresolved non-hydrogen planarities: 369 Chain: "E" Number of atoms: 843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 843 Classifications: {'peptide': 170} Incomplete info: {'truncation_to_alanine': 149} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 161} Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 548 Unresolved non-hydrogen angles: 685 Unresolved non-hydrogen dihedrals: 460 Unresolved non-hydrogen chiralities: 49 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 2, 'TYR:plan': 5, 'ASN:plan1': 8, 'TRP:plan': 1, 'ASP:plan': 5, 'PHE:plan': 7, 'GLU:plan': 13, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 257 Chain: "F" Number of atoms: 1195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1195 Classifications: {'peptide': 242} Incomplete info: {'truncation_to_alanine': 204} Link IDs: {'PTRANS': 11, 'TRANS': 230} Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 785 Unresolved non-hydrogen angles: 989 Unresolved non-hydrogen dihedrals: 664 Unresolved non-hydrogen chiralities: 64 Planarities with less than four sites: {'GLN:plan1': 12, 'HIS:plan': 4, 'TYR:plan': 10, 'ASN:plan1': 14, 'TRP:plan': 2, 'ASP:plan': 4, 'PHE:plan': 10, 'GLU:plan': 16, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 409 Chain: "G" Number of atoms: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 926 Classifications: {'peptide': 187} Incomplete info: {'truncation_to_alanine': 152} Link IDs: {'CIS': 2, 'PTRANS': 8, 'TRANS': 176} Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 552 Unresolved non-hydrogen angles: 698 Unresolved non-hydrogen dihedrals: 457 Unresolved non-hydrogen chiralities: 55 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 2, 'TYR:plan': 7, 'ASN:plan1': 7, 'TRP:plan': 1, 'ASP:plan': 8, 'PHE:plan': 5, 'GLU:plan': 13, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 259 Chain: "I" Number of atoms: 1428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 1428 Classifications: {'peptide': 288} Incomplete info: {'truncation_to_alanine': 271} Link IDs: {'PTRANS': 12, 'TRANS': 275} Unresolved chain link angles: 12 Unresolved non-hydrogen bonds: 1049 Unresolved non-hydrogen angles: 1322 Unresolved non-hydrogen dihedrals: 871 Unresolved non-hydrogen chiralities: 81 Planarities with less than four sites: {'GLN:plan1': 12, 'HIS:plan': 8, 'TYR:plan': 8, 'ASN:plan1': 21, 'TRP:plan': 1, 'ASP:plan': 12, 'PHE:plan': 18, 'GLU:plan': 31, 'ARG:plan': 23} Unresolved non-hydrogen planarities: 599 Chain: "K" Number of atoms: 1293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 1293 Classifications: {'peptide': 260} Incomplete info: {'truncation_to_alanine': 241} Link IDs: {'PTRANS': 10, 'TRANS': 249} Chain breaks: 1 Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 842 Unresolved non-hydrogen angles: 1069 Unresolved non-hydrogen dihedrals: 691 Unresolved non-hydrogen chiralities: 87 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 3, 'TYR:plan': 8, 'ASN:plan1': 16, 'TRP:plan': 2, 'ASP:plan': 17, 'PHE:plan': 11, 'GLU:plan': 20, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 402 Chain: "L" Number of atoms: 525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 525 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 85} Link IDs: {'PTRANS': 5, 'TRANS': 100} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 334 Unresolved non-hydrogen angles: 420 Unresolved non-hydrogen dihedrals: 274 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 2, 'TYR:plan': 3, 'ASN:plan1': 5, 'ASP:plan': 4, 'PHE:plan': 4, 'GLU:plan': 3, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 189 Chain: "M" Number of atoms: 633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 633 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 100} Link IDs: {'PTRANS': 4, 'TRANS': 123} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 380 Unresolved non-hydrogen angles: 479 Unresolved non-hydrogen dihedrals: 322 Unresolved non-hydrogen chiralities: 38 Planarities with less than four sites: {'GLN:plan1': 7, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 4, 'ASP:plan': 3, 'PHE:plan': 3, 'GLU:plan': 5, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 179 Chain: "N" Number of atoms: 871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 871 Classifications: {'peptide': 176} Incomplete info: {'truncation_to_alanine': 153} Link IDs: {'PTRANS': 4, 'TRANS': 171} Chain breaks: 1 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 671 Unresolved non-hydrogen angles: 848 Unresolved non-hydrogen dihedrals: 581 Unresolved non-hydrogen chiralities: 39 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 5, 'TYR:plan': 10, 'ASN:plan1': 9, 'TRP:plan': 5, 'ASP:plan': 6, 'PHE:plan': 4, 'GLU:plan': 7, 'ARG:plan': 31} Unresolved non-hydrogen planarities: 424 Chain: "O" Number of atoms: 908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 908 Classifications: {'peptide': 184} Incomplete info: {'truncation_to_alanine': 150} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 176} Chain breaks: 1 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 570 Unresolved non-hydrogen angles: 715 Unresolved non-hydrogen dihedrals: 483 Unresolved non-hydrogen chiralities: 51 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 5, 'TYR:plan': 8, 'ASN:plan1': 4, 'TRP:plan': 1, 'HIS:plan': 3, 'PHE:plan': 7, 'GLU:plan': 10, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 280 Chain: "P" Number of atoms: 616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 616 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 100} Link IDs: {'PTRANS': 5, 'TRANS': 118} Chain breaks: 2 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 378 Unresolved non-hydrogen angles: 478 Unresolved non-hydrogen dihedrals: 320 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 3, 'TYR:plan': 3, 'ASN:plan1': 7, 'TRP:plan': 2, 'ASP:plan': 2, 'PHE:plan': 4, 'GLU:plan': 9, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 217 Chain: "Q" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 653 Classifications: {'peptide': 132} Incomplete info: {'truncation_to_alanine': 108} Link IDs: {'PTRANS': 7, 'TRANS': 124} Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 378 Unresolved non-hydrogen angles: 479 Unresolved non-hydrogen dihedrals: 304 Unresolved non-hydrogen chiralities: 45 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 6, 'ASP:plan': 5, 'PHE:plan': 6, 'GLU:plan': 3, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 172 Chain: "S" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 851 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 155} Link IDs: {'PTRANS': 7, 'TRANS': 163} Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 623 Unresolved non-hydrogen angles: 787 Unresolved non-hydrogen dihedrals: 541 Unresolved non-hydrogen chiralities: 43 Planarities with less than four sites: {'GLN:plan1': 7, 'ASP:plan': 5, 'TYR:plan': 9, 'ASN:plan1': 5, 'TRP:plan': 2, 'HIS:plan': 7, 'PHE:plan': 10, 'GLU:plan': 10, 'ARG:plan': 16} Unresolved non-hydrogen planarities: 354 Chain: "X" Number of atoms: 700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 700 Classifications: {'peptide': 141} Incomplete info: {'truncation_to_alanine': 117} Link IDs: {'PTRANS': 6, 'TRANS': 134} Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 417 Unresolved non-hydrogen angles: 523 Unresolved non-hydrogen dihedrals: 347 Unresolved non-hydrogen chiralities: 42 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 7, 'TYR:plan': 8, 'ASN:plan1': 7, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 5, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 179 Chain: "Y" Number of atoms: 623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 623 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 109} Link IDs: {'PTRANS': 5, 'TRANS': 120} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 382 Unresolved non-hydrogen angles: 471 Unresolved non-hydrogen dihedrals: 315 Unresolved non-hydrogen chiralities: 35 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 2, 'TYR:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 7, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 174 Chain: "Z" Number of atoms: 667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 667 Classifications: {'peptide': 135} Incomplete info: {'truncation_to_alanine': 115} Link IDs: {'CIS': 1, 'PTRANS': 6, 'TRANS': 127} Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 452 Unresolved non-hydrogen angles: 565 Unresolved non-hydrogen dihedrals: 394 Unresolved non-hydrogen chiralities: 34 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 6, 'TYR:plan': 4, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 9, 'GLU:plan': 9, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 228 Chain: "7" Number of atoms: 773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 773 Classifications: {'peptide': 156} Incomplete info: {'truncation_to_alanine': 141} Link IDs: {'PTRANS': 5, 'TRANS': 150} Chain breaks: 1 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 541 Unresolved non-hydrogen angles: 667 Unresolved non-hydrogen dihedrals: 462 Unresolved non-hydrogen chiralities: 36 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 1, 'TYR:plan': 5, 'ASN:plan1': 8, 'TRP:plan': 3, 'ASP:plan': 7, 'PHE:plan': 2, 'GLU:plan': 11, 'ARG:plan': 16} Unresolved non-hydrogen planarities: 276 Chain: "b" Number of atoms: 457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 457 Classifications: {'peptide': 92} Incomplete info: {'truncation_to_alanine': 87} Link IDs: {'PTRANS': 5, 'TRANS': 86} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 334 Unresolved non-hydrogen angles: 427 Unresolved non-hydrogen dihedrals: 281 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 5, 'TYR:plan': 4, 'ASN:plan1': 7, 'TRP:plan': 1, 'ASP:plan': 5, 'PHE:plan': 3, 'GLU:plan': 5, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 190 Chain: "b" Number of atoms: 208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 208 Classifications: {'peptide': 42} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 4, 'TRANS': 37} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 134 Unresolved non-hydrogen angles: 176 Unresolved non-hydrogen dihedrals: 109 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 2, 'ASN:plan1': 1, 'TYR:plan': 1, 'UNK:plan-1': 9, 'ASP:plan': 1, 'PHE:plan': 3, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 76 Chain: "b" Number of atoms: 536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 536 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 94} Link IDs: {'PTRANS': 4, 'TRANS': 103} Chain breaks: 1 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 329 Unresolved non-hydrogen angles: 422 Unresolved non-hydrogen dihedrals: 266 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 4, 'ASN:plan1': 4, 'ASP:plan': 5, 'TYR:plan': 3, 'UNK:plan-1': 9, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 4, 'GLU:plan': 9, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 182 Chain: "c" Number of atoms: 476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 476 Classifications: {'peptide': 97} Incomplete info: {'truncation_to_alanine': 81} Link IDs: {'PTRANS': 1, 'TRANS': 95} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 275 Unresolved non-hydrogen angles: 349 Unresolved non-hydrogen dihedrals: 224 Unresolved non-hydrogen chiralities: 35 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 6, 'ASN:plan1': 4, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 4, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 115 Chain: "d" Number of atoms: 2288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 465, 2288 Classifications: {'peptide': 465} Incomplete info: {'backbone_only': 37, 'truncation_to_alanine': 428} Link IDs: {'TRANS': 464} Chain breaks: 2 Unresolved non-hydrogen bonds: 967 Unresolved non-hydrogen angles: 1469 Unresolved non-hydrogen dihedrals: 465 Unresolved non-hydrogen chiralities: 37 Planarities with less than four sites: {'UNK:plan-1': 465} Unresolved non-hydrogen planarities: 465 Chain: "e" Number of atoms: 564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 564 Classifications: {'peptide': 114} Incomplete info: {'truncation_to_alanine': 97} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 369 Unresolved non-hydrogen angles: 460 Unresolved non-hydrogen dihedrals: 318 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 7, 'TYR:plan': 3, 'ASN:plan1': 7, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 3, 'GLU:plan': 4, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 174 Chain: "f" Number of atoms: 522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 522 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 90} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 101} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 347 Unresolved non-hydrogen angles: 441 Unresolved non-hydrogen dihedrals: 296 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 1, 'TYR:plan': 6, 'ASN:plan1': 7, 'TRP:plan': 1, 'HIS:plan': 3, 'PHE:plan': 4, 'GLU:plan': 3, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 193 Chain: "g" Number of atoms: 498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 498 Classifications: {'peptide': 101} Incomplete info: {'truncation_to_alanine': 86} Link IDs: {'PTRANS': 4, 'TRANS': 96} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 309 Unresolved non-hydrogen angles: 384 Unresolved non-hydrogen dihedrals: 255 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 4, 'HIS:plan': 2, 'PHE:plan': 2, 'GLU:plan': 3, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 155 Chain: "h" Number of atoms: 593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 593 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 104} Link IDs: {'PTRANS': 4, 'TRANS': 114} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 386 Unresolved non-hydrogen angles: 471 Unresolved non-hydrogen dihedrals: 321 Unresolved non-hydrogen chiralities: 32 Planarities with less than four sites: {'GLN:plan1': 11, 'TYR:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 8, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 180 Chain: "i" Number of atoms: 416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 416 Classifications: {'peptide': 84} Incomplete info: {'truncation_to_alanine': 70} Link IDs: {'PTRANS': 3, 'TRANS': 80} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 257 Unresolved non-hydrogen angles: 314 Unresolved non-hydrogen dihedrals: 215 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 4, 'ASP:plan': 1, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 126 Chain: "j" Number of atoms: 357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 357 Classifications: {'peptide': 72} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PCIS': 1, 'TRANS': 70} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 231 Unresolved non-hydrogen angles: 286 Unresolved non-hydrogen dihedrals: 207 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 3, 'ASN:plan1': 3, 'TRP:plan': 1, 'HIS:plan': 4, 'PHE:plan': 3, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 135 Chain: "k" Number of atoms: 382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 382 Classifications: {'peptide': 77} Incomplete info: {'truncation_to_alanine': 68} Link IDs: {'PTRANS': 3, 'TRANS': 73} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 237 Unresolved non-hydrogen angles: 293 Unresolved non-hydrogen dihedrals: 193 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASN:plan1': 4, 'ASP:plan': 3, 'PHE:plan': 3, 'GLU:plan': 2, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 96 Chain: "m" Number of atoms: 370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 370 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 74} Link IDs: {'TRANS': 73} Unresolved non-hydrogen bonds: 148 Unresolved non-hydrogen angles: 222 Unresolved non-hydrogen dihedrals: 74 Planarities with less than four sites: {'UNK:plan-1': 74} Unresolved non-hydrogen planarities: 74 Chain: "n" Number of atoms: 1693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 1693 Classifications: {'peptide': 341} Incomplete info: {'truncation_to_alanine': 309} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 18, 'TRANS': 320} Chain breaks: 3 Unresolved chain link angles: 19 Unresolved non-hydrogen bonds: 1173 Unresolved non-hydrogen angles: 1500 Unresolved non-hydrogen dihedrals: 1001 Unresolved non-hydrogen chiralities: 99 Planarities with less than four sites: {'GLN:plan1': 11, 'HIS:plan': 6, 'TYR:plan': 18, 'ASN:plan1': 13, 'TRP:plan': 4, 'ASP:plan': 19, 'PHE:plan': 21, 'GLU:plan': 17, 'ARG:plan': 21} Unresolved non-hydrogen planarities: 631 Chain: "o" Number of atoms: 656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 656 Classifications: {'peptide': 133} Incomplete info: {'truncation_to_alanine': 118} Link IDs: {'CIS': 1, 'PTRANS': 3, 'TRANS': 128} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 474 Unresolved non-hydrogen angles: 589 Unresolved non-hydrogen dihedrals: 412 Unresolved non-hydrogen chiralities: 31 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 3, 'TYR:plan': 7, 'ASN:plan1': 6, 'TRP:plan': 1, 'HIS:plan': 5, 'PHE:plan': 6, 'GLU:plan': 12, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 249 Chain: "p" Number of atoms: 2158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 2158 Classifications: {'peptide': 437} Incomplete info: {'truncation_to_alanine': 381} Link IDs: {'PTRANS': 21, 'TRANS': 415} Chain breaks: 1 Unresolved chain link angles: 21 Unresolved non-hydrogen bonds: 1396 Unresolved non-hydrogen angles: 1769 Unresolved non-hydrogen dihedrals: 1155 Unresolved non-hydrogen chiralities: 135 Planarities with less than four sites: {'GLN:plan1': 20, 'ASP:plan': 20, 'TYR:plan': 14, 'ASN:plan1': 18, 'TRP:plan': 1, 'HIS:plan': 7, 'PHE:plan': 24, 'GLU:plan': 26, 'ARG:plan': 24} Unresolved non-hydrogen planarities: 704 Chain: "s" Number of atoms: 299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 299 Classifications: {'peptide': 60} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PTRANS': 7, 'TRANS': 52} Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 219 Unresolved non-hydrogen angles: 272 Unresolved non-hydrogen dihedrals: 190 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 2, 'GLU:plan': 7, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 102 Chain: "s" Number of atoms: 2238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 2238 Classifications: {'peptide': 452} Incomplete info: {'truncation_to_alanine': 410} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 429} Chain breaks: 3 Unresolved chain link angles: 22 Unresolved non-hydrogen bonds: 1406 Unresolved non-hydrogen angles: 1841 Unresolved non-hydrogen dihedrals: 1157 Unresolved non-hydrogen chiralities: 109 Planarities with less than four sites: {'GLN:plan1': 11, 'HIS:plan': 15, 'ASN:plan1': 14, 'TYR:plan': 12, 'UNK:plan-1': 73, 'TRP:plan': 10, 'ASP:plan': 27, 'PHE:plan': 14, 'GLU:plan': 15, 'ARG:plan': 20} Unresolved non-hydrogen planarities: 733 Chain: "t" Number of atoms: 1397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 1397 Classifications: {'peptide': 282} Incomplete info: {'truncation_to_alanine': 253} Link IDs: {'PTRANS': 9, 'TRANS': 272} Chain breaks: 1 Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 834 Unresolved non-hydrogen angles: 1068 Unresolved non-hydrogen dihedrals: 651 Unresolved non-hydrogen chiralities: 83 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 4, 'ASN:plan1': 14, 'TYR:plan': 4, 'UNK:plan-1': 34, 'ASP:plan': 8, 'PHE:plan': 11, 'GLU:plan': 21, 'ARG:plan': 17} Unresolved non-hydrogen planarities: 407 Chain: "x" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 140 Classifications: {'peptide': 28} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'TRANS': 27} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'UNK:plan-1': 28} Unresolved non-hydrogen planarities: 28 Chain: "z" Number of atoms: 1209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1209 Classifications: {'peptide': 243} Incomplete info: {'truncation_to_alanine': 225} Link IDs: {'PTRANS': 7, 'TRANS': 235} Chain breaks: 1 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 897 Unresolved non-hydrogen angles: 1142 Unresolved non-hydrogen dihedrals: 775 Unresolved non-hydrogen chiralities: 66 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 2, 'TYR:plan': 10, 'ASN:plan1': 14, 'TRP:plan': 8, 'ASP:plan': 17, 'PHE:plan': 13, 'GLU:plan': 17, 'ARG:plan': 16} Unresolved non-hydrogen planarities: 503 Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "j" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 38104 SG CYS D 15 198.208 105.767 129.296 1.00 29.65 S ATOM 38169 SG CYS D 28 198.769 107.522 126.205 1.00 34.38 S ATOM 38219 SG CYS D 38 198.610 104.491 125.925 1.00 28.02 S ATOM 38245 SG CYS D 43 201.235 105.729 127.106 1.00 24.55 S ATOM 59075 SG CYS j 19 133.908 90.733 174.532 1.00 59.22 S ATOM 59091 SG CYS j 22 136.352 91.431 171.902 1.00 84.99 S ATOM 59151 SG CYS j 34 135.011 88.055 172.312 1.00 86.47 S ATOM 59167 SG CYS j 37 137.233 89.394 174.735 1.00 68.53 S Time building chain proxies: 31.51, per 1000 atoms: 0.45 Number of scatterers: 69945 At special positions: 0 Unit cell: (273, 200.2, 321.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 8 16.00 P 1615 15.00 O 18450 8.00 N 13352 7.00 C 36518 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "ATOM 21319 O5' A 11559 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied TRANS " UNK b 123 " - " GLU b 122 " " UNK b 165 " - " PRO b 164 " " UNK s 299 " - " LYS s 298 " Time building additional restraints: 13.49 Conformation dependent library (CDL) restraints added in 5.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D 401 " pdb="ZN ZN D 401 " - pdb=" SG CYS D 38 " pdb="ZN ZN D 401 " - pdb=" SG CYS D 28 " pdb="ZN ZN D 401 " - pdb=" SG CYS D 43 " pdb="ZN ZN D 401 " - pdb=" SG CYS D 15 " pdb=" ZN j 101 " pdb="ZN ZN j 101 " - pdb=" SG CYS j 37 " pdb="ZN ZN j 101 " - pdb=" SG CYS j 34 " pdb="ZN ZN j 101 " - pdb=" SG CYS j 22 " pdb="ZN ZN j 101 " - pdb=" SG CYS j 19 " Number of angles added : 12 12694 Ramachandran restraints generated. 6347 Oldfield, 0 Emsley, 6347 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13594 Finding SS restraints... Secondary structure from input PDB file: 252 helices and 71 sheets defined 45.9% alpha, 19.0% beta 506 base pairs and 847 stacking pairs defined. Time for finding SS restraints: 25.03 Creating SS restraints... Processing helix chain 'A' and resid 42 through 46 removed outlier: 4.006A pdb=" N TYR A 46 " --> pdb=" O LEU A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 126 Processing helix chain 'A' and resid 327 through 331 Processing helix chain 'C' and resid 31 through 44 removed outlier: 3.682A pdb=" N SER C 41 " --> pdb=" O THR C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 132 removed outlier: 3.925A pdb=" N ALA C 130 " --> pdb=" O ILE C 126 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N VAL C 131 " --> pdb=" O ALA C 127 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ALA C 132 " --> pdb=" O ALA C 128 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 139 Processing helix chain 'C' and resid 153 through 159 Processing helix chain 'C' and resid 161 through 173 Processing helix chain 'C' and resid 174 through 184 Processing helix chain 'C' and resid 190 through 195 removed outlier: 3.776A pdb=" N LYS C 193 " --> pdb=" O GLY C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 219 Processing helix chain 'C' and resid 234 through 239 Processing helix chain 'C' and resid 240 through 243 Processing helix chain 'C' and resid 252 through 263 removed outlier: 4.259A pdb=" N ASP C 259 " --> pdb=" O PHE C 255 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLN C 260 " --> pdb=" O THR C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 285 through 291 removed outlier: 3.670A pdb=" N ILE C 289 " --> pdb=" O ASP C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 299 Processing helix chain 'C' and resid 320 through 327 removed outlier: 3.524A pdb=" N LEU C 327 " --> pdb=" O VAL C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 338 removed outlier: 4.378A pdb=" N VAL C 333 " --> pdb=" O PRO C 329 " (cutoff:3.500A) Processing helix chain 'C' and resid 339 through 342 Processing helix chain 'D' and resid 3 through 13 Processing helix chain 'D' and resid 66 through 70 Processing helix chain 'D' and resid 85 through 97 Processing helix chain 'D' and resid 101 through 128 removed outlier: 3.614A pdb=" N ARG D 105 " --> pdb=" O SER D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 156 Processing helix chain 'D' and resid 157 through 173 removed outlier: 3.528A pdb=" N ALA D 161 " --> pdb=" O LYS D 157 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY D 173 " --> pdb=" O ARG D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 191 Processing helix chain 'E' and resid 68 through 73 Processing helix chain 'E' and resid 97 through 101 removed outlier: 3.669A pdb=" N LYS E 100 " --> pdb=" O ASN E 97 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N PHE E 101 " --> pdb=" O VAL E 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 97 through 101' Processing helix chain 'E' and resid 103 through 107 Processing helix chain 'E' and resid 112 through 122 removed outlier: 3.861A pdb=" N GLU E 118 " --> pdb=" O LYS E 114 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA E 119 " --> pdb=" O GLU E 115 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ASN E 120 " --> pdb=" O LYS E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 131 through 150 removed outlier: 3.743A pdb=" N VAL E 135 " --> pdb=" O LYS E 131 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA E 144 " --> pdb=" O VAL E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 154 through 161 Processing helix chain 'F' and resid 9 through 73 removed outlier: 3.652A pdb=" N ALA F 35 " --> pdb=" O ALA F 31 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 106 Processing helix chain 'F' and resid 120 through 131 Processing helix chain 'F' and resid 140 through 151 Processing helix chain 'F' and resid 165 through 174 removed outlier: 3.640A pdb=" N ILE F 169 " --> pdb=" O ASP F 165 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASN F 172 " --> pdb=" O ILE F 168 " (cutoff:3.500A) Processing helix chain 'F' and resid 180 through 190 removed outlier: 3.508A pdb=" N LEU F 184 " --> pdb=" O SER F 180 " (cutoff:3.500A) Processing helix chain 'F' and resid 194 through 202 Processing helix chain 'F' and resid 234 through 244 removed outlier: 3.866A pdb=" N LYS F 238 " --> pdb=" O GLU F 234 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LYS F 241 " --> pdb=" O ASN F 237 " (cutoff:3.500A) Processing helix chain 'G' and resid 54 through 62 Processing helix chain 'G' and resid 63 through 69 removed outlier: 3.727A pdb=" N ILE G 67 " --> pdb=" O LYS G 63 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU G 69 " --> pdb=" O LEU G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 95 Processing helix chain 'G' and resid 101 through 119 Processing helix chain 'G' and resid 135 through 143 Processing helix chain 'G' and resid 159 through 163 Processing helix chain 'G' and resid 164 through 173 removed outlier: 4.659A pdb=" N ALA G 168 " --> pdb=" O VAL G 164 " (cutoff:3.500A) Processing helix chain 'G' and resid 182 through 189 removed outlier: 3.518A pdb=" N LEU G 189 " --> pdb=" O ARG G 185 " (cutoff:3.500A) Processing helix chain 'G' and resid 207 through 222 Processing helix chain 'G' and resid 226 through 231 removed outlier: 3.839A pdb=" N LYS G 231 " --> pdb=" O ASP G 227 " (cutoff:3.500A) Processing helix chain 'I' and resid 11 through 44 Processing helix chain 'I' and resid 44 through 55 removed outlier: 4.317A pdb=" N ARG I 48 " --> pdb=" O ASN I 44 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLU I 49 " --> pdb=" O PRO I 45 " (cutoff:3.500A) Processing helix chain 'I' and resid 76 through 84 Processing helix chain 'I' and resid 104 through 118 removed outlier: 3.862A pdb=" N TYR I 108 " --> pdb=" O LYS I 104 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLU I 116 " --> pdb=" O ASN I 112 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ILE I 117 " --> pdb=" O ILE I 113 " (cutoff:3.500A) Processing helix chain 'I' and resid 131 through 142 Processing helix chain 'I' and resid 204 through 218 Processing helix chain 'I' and resid 283 through 288 Processing helix chain 'K' and resid 33 through 49 Processing helix chain 'K' and resid 70 through 76 Processing helix chain 'K' and resid 106 through 117 removed outlier: 4.026A pdb=" N THR K 116 " --> pdb=" O GLU K 112 " (cutoff:3.500A) Processing helix chain 'K' and resid 128 through 135 Processing helix chain 'K' and resid 136 through 148 removed outlier: 3.517A pdb=" N LEU K 140 " --> pdb=" O SER K 136 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLN K 143 " --> pdb=" O ASP K 139 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER K 146 " --> pdb=" O ASP K 142 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N GLU K 147 " --> pdb=" O GLN K 143 " (cutoff:3.500A) Processing helix chain 'K' and resid 157 through 163 Processing helix chain 'K' and resid 166 through 176 removed outlier: 3.548A pdb=" N GLN K 176 " --> pdb=" O ALA K 172 " (cutoff:3.500A) Processing helix chain 'K' and resid 184 through 188 removed outlier: 3.928A pdb=" N THR K 188 " --> pdb=" O ASP K 184 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 184 through 188' Processing helix chain 'K' and resid 190 through 195 removed outlier: 3.984A pdb=" N GLY K 195 " --> pdb=" O PRO K 191 " (cutoff:3.500A) Processing helix chain 'K' and resid 195 through 201 removed outlier: 3.506A pdb=" N TYR K 199 " --> pdb=" O GLY K 195 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N LYS K 201 " --> pdb=" O LYS K 197 " (cutoff:3.500A) Processing helix chain 'K' and resid 218 through 232 removed outlier: 3.627A pdb=" N LYS K 227 " --> pdb=" O THR K 223 " (cutoff:3.500A) Processing helix chain 'K' and resid 255 through 274 Processing helix chain 'K' and resid 296 through 302 removed outlier: 4.162A pdb=" N GLU K 302 " --> pdb=" O LEU K 298 " (cutoff:3.500A) Processing helix chain 'L' and resid 27 through 46 removed outlier: 3.755A pdb=" N LYS L 32 " --> pdb=" O GLN L 28 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL L 33 " --> pdb=" O ALA L 29 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ALA L 43 " --> pdb=" O ARG L 39 " (cutoff:3.500A) Processing helix chain 'L' and resid 76 through 84 removed outlier: 3.520A pdb=" N VAL L 80 " --> pdb=" O THR L 76 " (cutoff:3.500A) Processing helix chain 'L' and resid 86 through 91 Processing helix chain 'L' and resid 105 through 123 removed outlier: 3.520A pdb=" N ILE L 123 " --> pdb=" O TYR L 119 " (cutoff:3.500A) Processing helix chain 'M' and resid 61 through 63 No H-bonds generated for 'chain 'M' and resid 61 through 63' Processing helix chain 'M' and resid 77 through 89 Processing helix chain 'M' and resid 89 through 96 Processing helix chain 'M' and resid 97 through 111 Processing helix chain 'M' and resid 113 through 135 Processing helix chain 'N' and resid 3 through 12 Processing helix chain 'N' and resid 16 through 33 removed outlier: 3.816A pdb=" N TRP N 28 " --> pdb=" O ARG N 24 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LYS N 33 " --> pdb=" O GLU N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 44 through 52 Processing helix chain 'N' and resid 97 through 110 removed outlier: 3.615A pdb=" N VAL N 106 " --> pdb=" O ALA N 102 " (cutoff:3.500A) Processing helix chain 'N' and resid 139 through 144 Processing helix chain 'N' and resid 148 through 157 Proline residue: N 154 - end of helix removed outlier: 3.591A pdb=" N LYS N 157 " --> pdb=" O PRO N 154 " (cutoff:3.500A) Processing helix chain 'N' and resid 165 through 173 Processing helix chain 'N' and resid 183 through 196 Processing helix chain 'O' and resid 16 through 29 removed outlier: 3.503A pdb=" N LEU O 28 " --> pdb=" O ALA O 24 " (cutoff:3.500A) Processing helix chain 'O' and resid 37 through 39 No H-bonds generated for 'chain 'O' and resid 37 through 39' Processing helix chain 'O' and resid 46 through 59 removed outlier: 3.665A pdb=" N ASN O 50 " --> pdb=" O GLU O 46 " (cutoff:3.500A) Processing helix chain 'O' and resid 75 through 88 removed outlier: 3.623A pdb=" N MET O 87 " --> pdb=" O ALA O 83 " (cutoff:3.500A) Processing helix chain 'O' and resid 92 through 101 Processing helix chain 'O' and resid 111 through 115 Processing helix chain 'O' and resid 120 through 123 Processing helix chain 'O' and resid 124 through 129 Processing helix chain 'O' and resid 138 through 146 Processing helix chain 'O' and resid 149 through 186 Processing helix chain 'O' and resid 188 through 198 Processing helix chain 'P' and resid 25 through 37 removed outlier: 3.580A pdb=" N ILE P 36 " --> pdb=" O THR P 32 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASN P 37 " --> pdb=" O ALA P 33 " (cutoff:3.500A) Processing helix chain 'P' and resid 40 through 53 Processing helix chain 'P' and resid 84 through 106 removed outlier: 3.534A pdb=" N VAL P 88 " --> pdb=" O PRO P 84 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE P 90 " --> pdb=" O LYS P 86 " (cutoff:3.500A) Processing helix chain 'Q' and resid 23 through 40 Processing helix chain 'Q' and resid 42 through 53 removed outlier: 4.445A pdb=" N LYS Q 46 " --> pdb=" O ALA Q 42 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N PHE Q 53 " --> pdb=" O LEU Q 49 " (cutoff:3.500A) Processing helix chain 'Q' and resid 64 through 72 Processing helix chain 'Q' and resid 107 through 117 Processing helix chain 'Q' and resid 124 through 131 Processing helix chain 'S' and resid 33 through 49 removed outlier: 3.895A pdb=" N LYS S 47 " --> pdb=" O TYR S 43 " (cutoff:3.500A) Processing helix chain 'S' and resid 98 through 115 removed outlier: 3.523A pdb=" N ALA S 102 " --> pdb=" O SER S 98 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ARG S 115 " --> pdb=" O ALA S 111 " (cutoff:3.500A) Processing helix chain 'S' and resid 137 through 142 Processing helix chain 'S' and resid 143 through 145 No H-bonds generated for 'chain 'S' and resid 143 through 145' Processing helix chain 'X' and resid 4 through 16 removed outlier: 3.871A pdb=" N THR X 8 " --> pdb=" O SER X 4 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA X 10 " --> pdb=" O LYS X 6 " (cutoff:3.500A) Processing helix chain 'X' and resid 58 through 62 Processing helix chain 'X' and resid 69 through 78 removed outlier: 3.595A pdb=" N VAL X 76 " --> pdb=" O ALA X 72 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLU X 77 " --> pdb=" O MET X 73 " (cutoff:3.500A) Processing helix chain 'X' and resid 91 through 104 Processing helix chain 'X' and resid 131 through 140 removed outlier: 3.791A pdb=" N ILE X 135 " --> pdb=" O ASP X 131 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLY X 140 " --> pdb=" O ALA X 136 " (cutoff:3.500A) Processing helix chain 'Y' and resid 11 through 21 removed outlier: 3.521A pdb=" N THR Y 21 " --> pdb=" O LYS Y 17 " (cutoff:3.500A) Processing helix chain 'Y' and resid 23 through 31 removed outlier: 3.916A pdb=" N VAL Y 29 " --> pdb=" O SER Y 25 " (cutoff:3.500A) Processing helix chain 'Y' and resid 36 through 44 Processing helix chain 'Y' and resid 75 through 78 Processing helix chain 'Y' and resid 100 through 102 No H-bonds generated for 'chain 'Y' and resid 100 through 102' Processing helix chain 'Y' and resid 112 through 122 Processing helix chain 'Z' and resid 59 through 66 Processing helix chain 'Z' and resid 89 through 93 removed outlier: 3.872A pdb=" N LYS Z 93 " --> pdb=" O GLU Z 90 " (cutoff:3.500A) Processing helix chain 'Z' and resid 105 through 123 removed outlier: 3.805A pdb=" N GLU Z 109 " --> pdb=" O SER Z 105 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N VAL Z 113 " --> pdb=" O GLU Z 109 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLU Z 120 " --> pdb=" O LYS Z 116 " (cutoff:3.500A) Processing helix chain 'Z' and resid 127 through 132 removed outlier: 3.894A pdb=" N PHE Z 131 " --> pdb=" O ASN Z 127 " (cutoff:3.500A) Processing helix chain '7' and resid 3 through 12 Processing helix chain '7' and resid 33 through 40 Processing helix chain '7' and resid 45 through 54 Processing helix chain '7' and resid 157 through 168 Processing helix chain '7' and resid 178 through 192 Processing helix chain '7' and resid 196 through 201 removed outlier: 3.512A pdb=" N PHE 7 201 " --> pdb=" O LYS 7 197 " (cutoff:3.500A) Processing helix chain '7' and resid 213 through 226 Processing helix chain 'b' and resid 42 through 56 removed outlier: 4.141A pdb=" N LEU b 48 " --> pdb=" O ARG b 44 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N ILE b 49 " --> pdb=" O HIS b 45 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLN b 50 " --> pdb=" O ARG b 46 " (cutoff:3.500A) Processing helix chain 'b' and resid 71 through 82 removed outlier: 4.201A pdb=" N ASN b 75 " --> pdb=" O LEU b 71 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLU b 76 " --> pdb=" O GLN b 72 " (cutoff:3.500A) Processing helix chain 'b' and resid 146 through 161 Processing helix chain 'b' and resid 244 through 276 removed outlier: 3.512A pdb=" N VAL b 248 " --> pdb=" O SER b 244 " (cutoff:3.500A) Processing helix chain 'b' and resid 285 through 290 Processing helix chain 'c' and resid 10 through 20 removed outlier: 3.614A pdb=" N LEU c 16 " --> pdb=" O GLN c 12 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL c 17 " --> pdb=" O LYS c 13 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LYS c 19 " --> pdb=" O ALA c 15 " (cutoff:3.500A) Processing helix chain 'c' and resid 26 through 36 Processing helix chain 'c' and resid 49 through 64 removed outlier: 3.522A pdb=" N TYR c 58 " --> pdb=" O SER c 54 " (cutoff:3.500A) Processing helix chain 'c' and resid 73 through 82 Processing helix chain 'c' and resid 99 through 103 removed outlier: 3.719A pdb=" N THR c 102 " --> pdb=" O ASP c 99 " (cutoff:3.500A) Processing helix chain 'd' and resid 23 through 27 removed outlier: 4.252A pdb=" N UNK d 27 " --> pdb=" O UNK d 24 " (cutoff:3.500A) Processing helix chain 'd' and resid 29 through 32 Processing helix chain 'd' and resid 42 through 52 Processing helix chain 'd' and resid 75 through 83 Processing helix chain 'd' and resid 124 through 132 removed outlier: 3.709A pdb=" N UNK d 132 " --> pdb=" O UNK d 128 " (cutoff:3.500A) Processing helix chain 'd' and resid 170 through 174 removed outlier: 3.818A pdb=" N UNK d 174 " --> pdb=" O UNK d 171 " (cutoff:3.500A) Processing helix chain 'd' and resid 263 through 267 Processing helix chain 'd' and resid 425 through 429 Processing helix chain 'd' and resid 443 through 448 Processing helix chain 'd' and resid 455 through 459 removed outlier: 4.082A pdb=" N UNK d 458 " --> pdb=" O UNK d 455 " (cutoff:3.500A) Processing helix chain 'e' and resid 54 through 58 Processing helix chain 'e' and resid 78 through 83 Processing helix chain 'e' and resid 84 through 86 No H-bonds generated for 'chain 'e' and resid 84 through 86' Processing helix chain 'e' and resid 101 through 116 removed outlier: 3.727A pdb=" N VAL e 106 " --> pdb=" O ALA e 102 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL e 107 " --> pdb=" O LYS e 103 " (cutoff:3.500A) Processing helix chain 'f' and resid 37 through 44 removed outlier: 3.970A pdb=" N PHE f 43 " --> pdb=" O GLN f 39 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N TYR f 44 " --> pdb=" O ASP f 40 " (cutoff:3.500A) Processing helix chain 'g' and resid 59 through 63 removed outlier: 3.634A pdb=" N TYR g 62 " --> pdb=" O PRO g 59 " (cutoff:3.500A) Processing helix chain 'g' and resid 66 through 71 removed outlier: 3.816A pdb=" N LYS g 70 " --> pdb=" O SER g 66 " (cutoff:3.500A) Processing helix chain 'g' and resid 82 through 102 removed outlier: 3.656A pdb=" N ARG g 88 " --> pdb=" O CYS g 84 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ILE g 100 " --> pdb=" O GLU g 96 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL g 101 " --> pdb=" O GLU g 97 " (cutoff:3.500A) Processing helix chain 'h' and resid 5 through 11 removed outlier: 3.880A pdb=" N LEU h 9 " --> pdb=" O LYS h 5 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N THR h 11 " --> pdb=" O TYR h 7 " (cutoff:3.500A) Processing helix chain 'h' and resid 13 through 36 removed outlier: 3.556A pdb=" N VAL h 33 " --> pdb=" O ALA h 29 " (cutoff:3.500A) Processing helix chain 'h' and resid 41 through 70 removed outlier: 4.494A pdb=" N LYS h 45 " --> pdb=" O LEU h 41 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR h 46 " --> pdb=" O PRO h 42 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LYS h 49 " --> pdb=" O LYS h 45 " (cutoff:3.500A) Processing helix chain 'h' and resid 77 through 81 Processing helix chain 'h' and resid 94 through 99 Processing helix chain 'h' and resid 101 through 111 Processing helix chain 'i' and resid 27 through 31 Processing helix chain 'i' and resid 34 through 49 removed outlier: 3.582A pdb=" N GLU i 46 " --> pdb=" O SER i 42 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE i 47 " --> pdb=" O LEU i 43 " (cutoff:3.500A) Processing helix chain 'i' and resid 51 through 77 removed outlier: 3.647A pdb=" N ASP i 59 " --> pdb=" O ARG i 55 " (cutoff:3.500A) removed outlier: 8.198A pdb=" N GLU i 66 " --> pdb=" O ARG i 62 " (cutoff:3.500A) removed outlier: 9.352A pdb=" N LYS i 67 " --> pdb=" O ASN i 63 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ARG i 68 " --> pdb=" O SER i 64 " (cutoff:3.500A) Processing helix chain 'i' and resid 80 through 98 Processing helix chain 'j' and resid 50 through 56 Processing helix chain 'j' and resid 66 through 68 No H-bonds generated for 'chain 'j' and resid 66 through 68' Processing helix chain 'j' and resid 69 through 77 removed outlier: 3.665A pdb=" N ARG j 73 " --> pdb=" O HIS j 69 " (cutoff:3.500A) Processing helix chain 'k' and resid 7 through 16 removed outlier: 3.823A pdb=" N PHE k 11 " --> pdb=" O ASP k 7 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU k 12 " --> pdb=" O ILE k 8 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLU k 13 " --> pdb=" O LYS k 9 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU k 14 " --> pdb=" O GLN k 10 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ARG k 16 " --> pdb=" O LEU k 12 " (cutoff:3.500A) Processing helix chain 'k' and resid 58 through 69 removed outlier: 3.663A pdb=" N LYS k 64 " --> pdb=" O GLY k 60 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLN k 67 " --> pdb=" O LYS k 63 " (cutoff:3.500A) Processing helix chain 'm' and resid 197 through 208 Processing helix chain 'm' and resid 234 through 258 Processing helix chain 'm' and resid 261 through 269 Processing helix chain 'n' and resid 17 through 25 Processing helix chain 'n' and resid 28 through 40 Processing helix chain 'n' and resid 64 through 72 Processing helix chain 'n' and resid 74 through 96 Processing helix chain 'n' and resid 98 through 108 removed outlier: 3.591A pdb=" N ALA n 102 " --> pdb=" O GLU n 98 " (cutoff:3.500A) Processing helix chain 'n' and resid 114 through 120 Processing helix chain 'n' and resid 124 through 145 removed outlier: 4.769A pdb=" N ASP n 133 " --> pdb=" O ILE n 129 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N ASP n 134 " --> pdb=" O ARG n 130 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ALA n 135 " --> pdb=" O ASP n 131 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ASN n 137 " --> pdb=" O ASP n 133 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N MET n 138 " --> pdb=" O ASP n 134 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LEU n 139 " --> pdb=" O ALA n 135 " (cutoff:3.500A) Processing helix chain 'n' and resid 152 through 174 removed outlier: 3.506A pdb=" N LYS n 172 " --> pdb=" O ALA n 168 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLU n 173 " --> pdb=" O TYR n 169 " (cutoff:3.500A) Processing helix chain 'n' and resid 214 through 240 removed outlier: 4.378A pdb=" N MET n 218 " --> pdb=" O ASP n 214 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N THR n 220 " --> pdb=" O ARG n 216 " (cutoff:3.500A) Processing helix chain 'n' and resid 249 through 256 Processing helix chain 'n' and resid 258 through 262 Processing helix chain 'n' and resid 372 through 384 removed outlier: 4.029A pdb=" N LEU n 376 " --> pdb=" O PRO n 372 " (cutoff:3.500A) Processing helix chain 'n' and resid 389 through 394 Processing helix chain 'n' and resid 429 through 439 removed outlier: 3.650A pdb=" N ASN n 437 " --> pdb=" O PHE n 433 " (cutoff:3.500A) Processing helix chain 'o' and resid 103 through 112 Processing helix chain 'o' and resid 141 through 151 Processing helix chain 'o' and resid 192 through 215 removed outlier: 4.581A pdb=" N GLY o 215 " --> pdb=" O LEU o 211 " (cutoff:3.500A) Processing helix chain 'p' and resid 50 through 60 Processing helix chain 'p' and resid 66 through 79 Proline residue: p 74 - end of helix Processing helix chain 'p' and resid 91 through 108 removed outlier: 3.583A pdb=" N PHE p 96 " --> pdb=" O LYS p 92 " (cutoff:3.500A) Proline residue: p 99 - end of helix Processing helix chain 'p' and resid 123 through 141 removed outlier: 4.597A pdb=" N GLU p 136 " --> pdb=" O GLY p 132 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N LEU p 137 " --> pdb=" O VAL p 133 " (cutoff:3.500A) Processing helix chain 'p' and resid 153 through 164 Processing helix chain 'p' and resid 171 through 182 removed outlier: 3.664A pdb=" N LEU p 175 " --> pdb=" O THR p 171 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LEU p 176 " --> pdb=" O PRO p 172 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ASP p 177 " --> pdb=" O GLY p 173 " (cutoff:3.500A) Processing helix chain 'p' and resid 197 through 205 Processing helix chain 'p' and resid 206 through 217 Processing helix chain 'p' and resid 232 through 243 Processing helix chain 'p' and resid 275 through 287 Processing helix chain 'p' and resid 298 through 312 Processing helix chain 'p' and resid 324 through 339 Processing helix chain 'p' and resid 347 through 352 Processing helix chain 'p' and resid 369 through 384 Processing helix chain 'p' and resid 398 through 409 removed outlier: 4.057A pdb=" N LEU p 402 " --> pdb=" O GLU p 398 " (cutoff:3.500A) Processing helix chain 'p' and resid 425 through 436 Processing helix chain 'p' and resid 436 through 456 Processing helix chain 'p' and resid 464 through 468 Processing helix chain 'p' and resid 469 through 478 Processing helix chain 's' and resid 269 through 285 Processing helix chain 's' and resid 290 through 308 Processing helix chain 's' and resid 344 through 350 Processing helix chain 's' and resid 350 through 357 Processing helix chain 's' and resid 358 through 366 removed outlier: 4.403A pdb=" N UNK s 364 " --> pdb=" O UNK s 360 " (cutoff:3.500A) Processing helix chain 's' and resid 380 through 395 removed outlier: 4.653A pdb=" N ILE s 384 " --> pdb=" O TYR s 380 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ARG s 385 " --> pdb=" O GLY s 381 " (cutoff:3.500A) Processing helix chain 's' and resid 418 through 423 removed outlier: 4.169A pdb=" N ARG s 423 " --> pdb=" O LYS s 420 " (cutoff:3.500A) Processing helix chain 's' and resid 519 through 533 removed outlier: 4.610A pdb=" N GLY s 533 " --> pdb=" O LYS s 529 " (cutoff:3.500A) Processing helix chain 's' and resid 579 through 584 Processing helix chain 's' and resid 616 through 619 Processing helix chain 's' and resid 627 through 629 No H-bonds generated for 'chain 's' and resid 627 through 629' Processing helix chain 't' and resid 21 through 52 removed outlier: 3.515A pdb=" N UNK t 31 " --> pdb=" O UNK t 27 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N UNK t 45 " --> pdb=" O UNK t 41 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N UNK t 46 " --> pdb=" O UNK t 42 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N UNK t 47 " --> pdb=" O UNK t 43 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N UNK t 49 " --> pdb=" O UNK t 45 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N UNK t 50 " --> pdb=" O UNK t 46 " (cutoff:3.500A) Processing helix chain 't' and resid 59 through 88 removed outlier: 3.704A pdb=" N THR t 65 " --> pdb=" O ILE t 61 " (cutoff:3.500A) Processing helix chain 't' and resid 156 through 166 Processing helix chain 't' and resid 183 through 191 removed outlier: 3.876A pdb=" N LEU t 187 " --> pdb=" O VAL t 183 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LYS t 188 " --> pdb=" O TYR t 184 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N VAL t 189 " --> pdb=" O PRO t 185 " (cutoff:3.500A) Processing helix chain 't' and resid 200 through 211 Processing helix chain 't' and resid 231 through 239 Processing helix chain 't' and resid 247 through 257 Processing helix chain 't' and resid 261 through 268 Processing helix chain 't' and resid 281 through 299 removed outlier: 3.562A pdb=" N LEU t 286 " --> pdb=" O SER t 282 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ARG t 287 " --> pdb=" O LEU t 283 " (cutoff:3.500A) Processing helix chain 't' and resid 313 through 322 removed outlier: 3.582A pdb=" N LEU t 317 " --> pdb=" O ASP t 313 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA t 319 " --> pdb=" O ASP t 315 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LYS t 320 " --> pdb=" O SER t 316 " (cutoff:3.500A) Processing helix chain 'x' and resid 175 through 189 Processing helix chain 'z' and resid 2 through 11 Processing helix chain 'z' and resid 14 through 29 removed outlier: 3.570A pdb=" N ARG z 18 " --> pdb=" O ASN z 14 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS z 27 " --> pdb=" O GLU z 23 " (cutoff:3.500A) Processing helix chain 'z' and resid 31 through 37 removed outlier: 3.698A pdb=" N LYS z 35 " --> pdb=" O ALA z 31 " (cutoff:3.500A) Processing helix chain 'z' and resid 38 through 55 removed outlier: 3.725A pdb=" N PHE z 42 " --> pdb=" O LYS z 38 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE z 55 " --> pdb=" O TYR z 51 " (cutoff:3.500A) Processing helix chain 'z' and resid 58 through 76 removed outlier: 3.607A pdb=" N HIS z 73 " --> pdb=" O LEU z 69 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N TYR z 76 " --> pdb=" O LEU z 72 " (cutoff:3.500A) Processing helix chain 'z' and resid 78 through 85 removed outlier: 3.846A pdb=" N ASN z 82 " --> pdb=" O ASP z 78 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER z 83 " --> pdb=" O PRO z 79 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ALA z 85 " --> pdb=" O ASP z 81 " (cutoff:3.500A) Processing helix chain 'z' and resid 89 through 110 Processing helix chain 'z' and resid 111 through 113 No H-bonds generated for 'chain 'z' and resid 111 through 113' Processing helix chain 'z' and resid 117 through 139 removed outlier: 4.072A pdb=" N TYR z 121 " --> pdb=" O ARG z 117 " (cutoff:3.500A) Processing helix chain 'z' and resid 142 through 152 Processing helix chain 'z' and resid 157 through 161 removed outlier: 4.113A pdb=" N GLY z 161 " --> pdb=" O PRO z 158 " (cutoff:3.500A) Processing helix chain 'z' and resid 167 through 186 removed outlier: 5.045A pdb=" N LEU z 178 " --> pdb=" O VAL z 174 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N ASP z 179 " --> pdb=" O ASP z 175 " (cutoff:3.500A) Processing helix chain 'z' and resid 198 through 211 Processing helix chain 'z' and resid 213 through 227 removed outlier: 3.794A pdb=" N VAL z 217 " --> pdb=" O PRO z 213 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ALA z 219 " --> pdb=" O ALA z 215 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ILE z 220 " --> pdb=" O ASP z 216 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N PHE z 221 " --> pdb=" O VAL z 217 " (cutoff:3.500A) Processing helix chain 'z' and resid 231 through 242 Processing helix chain 'z' and resid 245 through 251 removed outlier: 4.198A pdb=" N VAL z 249 " --> pdb=" O ASP z 245 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 34 through 38 removed outlier: 4.299A pdb=" N PHE A 406 " --> pdb=" O SER A 6 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 50 through 53 removed outlier: 3.593A pdb=" N GLU A 57 " --> pdb=" O ILE A 53 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N VAL A 67 " --> pdb=" O SER A 113 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N SER A 113 " --> pdb=" O VAL A 67 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LEU A 69 " --> pdb=" O THR A 111 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 142 through 145 removed outlier: 3.714A pdb=" N THR A 142 " --> pdb=" O ALA A 158 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N CYS A 144 " --> pdb=" O VAL A 156 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N LEU A 164 " --> pdb=" O SER A 180 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N SER A 180 " --> pdb=" O LEU A 164 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N ILE A 166 " --> pdb=" O LEU A 178 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 189 through 192 removed outlier: 3.865A pdb=" N PHE A 189 " --> pdb=" O GLY A 208 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLY A 208 " --> pdb=" O PHE A 189 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N TYR A 203 " --> pdb=" O GLU A 218 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N GLU A 218 " --> pdb=" O TYR A 203 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N PHE A 205 " --> pdb=" O LEU A 216 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N LEU A 216 " --> pdb=" O PHE A 205 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N TYR A 207 " --> pdb=" O ILE A 214 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ILE A 214 " --> pdb=" O TYR A 207 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N ILE A 214 " --> pdb=" O GLU A 231 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N GLU A 231 " --> pdb=" O ILE A 214 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N LEU A 216 " --> pdb=" O ILE A 229 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 248 through 253 removed outlier: 6.569A pdb=" N ILE A 273 " --> pdb=" O MET A 249 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N LEU A 251 " --> pdb=" O ALA A 271 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ALA A 271 " --> pdb=" O LEU A 251 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N PHE A 253 " --> pdb=" O GLN A 269 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N GLN A 269 " --> pdb=" O PHE A 253 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N HIS A 278 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ALA A 292 " --> pdb=" O LYS A 281 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 303 through 308 removed outlier: 6.367A pdb=" N THR A 336 " --> pdb=" O SER A 304 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N MET A 306 " --> pdb=" O ILE A 334 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ILE A 334 " --> pdb=" O MET A 306 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLY A 353 " --> pdb=" O LYS A 344 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 366 through 370 removed outlier: 6.459A pdb=" N VAL A 384 " --> pdb=" O LYS A 397 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LYS A 397 " --> pdb=" O VAL A 384 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N ILE A 386 " --> pdb=" O LEU A 395 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 5 through 9 removed outlier: 5.939A pdb=" N ASN C 18 " --> pdb=" O VAL C 8 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 150 through 152 removed outlier: 4.266A pdb=" N LEU C 150 " --> pdb=" O VAL C 248 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N LEU C 206 " --> pdb=" O ILE C 249 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N THR C 251 " --> pdb=" O LEU C 206 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N VAL C 208 " --> pdb=" O THR C 251 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N VAL C 207 " --> pdb=" O ALA C 228 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 186 through 187 Processing sheet with id=AB2, first strand: chain 'D' and resid 18 through 20 Processing sheet with id=AB3, first strand: chain 'D' and resid 50 through 55 Processing sheet with id=AB4, first strand: chain 'D' and resid 133 through 135 removed outlier: 3.667A pdb=" N HIS D 133 " --> pdb=" O GLU e 129 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 77 through 80 removed outlier: 3.592A pdb=" N LYS E 56 " --> pdb=" O LEU E 64 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N SER E 66 " --> pdb=" O TYR E 54 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N TYR E 54 " --> pdb=" O SER E 66 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N THR E 38 " --> pdb=" O TYR E 54 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N VAL E 39 " --> pdb=" O THR E 87 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 205 through 206 removed outlier: 4.570A pdb=" N SER F 113 " --> pdb=" O ARG F 88 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 153 through 154 Processing sheet with id=AB8, first strand: chain 'G' and resid 177 through 180 removed outlier: 6.060A pdb=" N VAL G 151 " --> pdb=" O ALA G 178 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N VAL G 180 " --> pdb=" O VAL G 151 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N ILE G 153 " --> pdb=" O VAL G 180 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 121 through 125 removed outlier: 4.162A pdb=" N THR I 99 " --> pdb=" O VAL I 124 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ILE I 147 " --> pdb=" O PHE I 162 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N PHE I 162 " --> pdb=" O ILE I 147 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ILE I 149 " --> pdb=" O LEU I 160 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N LEU I 160 " --> pdb=" O ILE I 149 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ASN I 151 " --> pdb=" O THR I 158 " (cutoff:3.500A) removed outlier: 12.272A pdb=" N LYS I 156 " --> pdb=" O SER I 177 " (cutoff:3.500A) removed outlier: 10.222A pdb=" N SER I 177 " --> pdb=" O LYS I 156 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N THR I 158 " --> pdb=" O LEU I 175 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N THR I 170 " --> pdb=" O LEU I 270 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N LEU I 270 " --> pdb=" O THR I 170 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N TYR I 172 " --> pdb=" O LYS I 268 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N THR I 264 " --> pdb=" O SER I 176 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N PHE I 178 " --> pdb=" O GLN I 262 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N GLN I 262 " --> pdb=" O PHE I 178 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 121 through 125 removed outlier: 4.162A pdb=" N THR I 99 " --> pdb=" O VAL I 124 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ILE I 147 " --> pdb=" O PHE I 162 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N PHE I 162 " --> pdb=" O ILE I 147 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ILE I 149 " --> pdb=" O LEU I 160 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N LEU I 160 " --> pdb=" O ILE I 149 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ASN I 151 " --> pdb=" O THR I 158 " (cutoff:3.500A) removed outlier: 12.272A pdb=" N LYS I 156 " --> pdb=" O SER I 177 " (cutoff:3.500A) removed outlier: 10.222A pdb=" N SER I 177 " --> pdb=" O LYS I 156 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N THR I 158 " --> pdb=" O LEU I 175 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N THR I 170 " --> pdb=" O LEU I 270 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N LEU I 270 " --> pdb=" O THR I 170 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N TYR I 172 " --> pdb=" O LYS I 268 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N THR I 264 " --> pdb=" O SER I 176 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N PHE I 178 " --> pdb=" O GLN I 262 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N GLN I 262 " --> pdb=" O PHE I 178 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N LYS I 268 " --> pdb=" O GLU I 281 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N GLU I 281 " --> pdb=" O LYS I 268 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N LEU I 270 " --> pdb=" O GLU I 279 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 247 through 248 Processing sheet with id=AC3, first strand: chain 'K' and resid 243 through 250 removed outlier: 6.222A pdb=" N GLN K 79 " --> pdb=" O LEU K 248 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N ARG K 277 " --> pdb=" O TYR K 293 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N TYR K 293 " --> pdb=" O ARG K 277 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N ILE K 279 " --> pdb=" O LEU K 291 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'K' and resid 100 through 101 Processing sheet with id=AC5, first strand: chain 'K' and resid 153 through 156 removed outlier: 6.297A pdb=" N VAL K 123 " --> pdb=" O GLU K 153 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N ILE K 155 " --> pdb=" O VAL K 123 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N LEU K 125 " --> pdb=" O ILE K 155 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 23 through 24 removed outlier: 6.620A pdb=" N LYS L 23 " --> pdb=" O LEU N 199 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'L' and resid 57 through 59 Processing sheet with id=AC8, first strand: chain 'L' and resid 124 through 126 removed outlier: 4.438A pdb=" N LYS h 115 " --> pdb=" O PHE L 126 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'M' and resid 53 through 59 removed outlier: 4.207A pdb=" N GLY M 48 " --> pdb=" O PRO M 54 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ASP M 47 " --> pdb=" O ILE M 35 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N ILE M 35 " --> pdb=" O ASP M 47 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N ARG M 19 " --> pdb=" O ILE M 35 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N VAL M 20 " --> pdb=" O THR M 66 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'N' and resid 36 through 39 removed outlier: 4.566A pdb=" N ILE N 61 " --> pdb=" O ALA N 39 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N TYR N 127 " --> pdb=" O ASN N 122 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N ASN N 122 " --> pdb=" O TYR N 127 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N TYR N 129 " --> pdb=" O TRP N 120 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N TRP N 120 " --> pdb=" O TYR N 129 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N GLU N 131 " --> pdb=" O SER N 118 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N SER N 118 " --> pdb=" O GLU N 131 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ILE N 133 " --> pdb=" O LEU N 116 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'O' and resid 6 through 10 Processing sheet with id=AD3, first strand: chain 'O' and resid 14 through 15 removed outlier: 5.716A pdb=" N HIS O 14 " --> pdb=" O ASN O 42 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N SER O 44 " --> pdb=" O HIS O 14 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'P' and resid 14 through 22 removed outlier: 5.041A pdb=" N SER P 144 " --> pdb=" O TYR P 21 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N HIS P 145 " --> pdb=" O VAL P 119 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N VAL P 119 " --> pdb=" O HIS P 145 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLU P 147 " --> pdb=" O ILE P 117 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N ILE P 117 " --> pdb=" O GLU P 147 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N VAL P 149 " --> pdb=" O SER P 115 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'P' and resid 58 through 59 Processing sheet with id=AD6, first strand: chain 'Q' and resid 62 through 63 removed outlier: 6.294A pdb=" N VAL Q 81 " --> pdb=" O ALA Q 102 " (cutoff:3.500A) removed outlier: 8.624A pdb=" N LEU Q 104 " --> pdb=" O VAL Q 81 " (cutoff:3.500A) removed outlier: 9.186A pdb=" N VAL Q 83 " --> pdb=" O LEU Q 104 " (cutoff:3.500A) removed outlier: 8.427A pdb=" N PHE Q 106 " --> pdb=" O VAL Q 83 " (cutoff:3.500A) removed outlier: 11.232A pdb=" N GLY Q 85 " --> pdb=" O PHE Q 106 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N VAL Q 101 " --> pdb=" O ILE Q 122 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'Q' and resid 62 through 63 Processing sheet with id=AD8, first strand: chain 'S' and resid 25 through 31 removed outlier: 7.324A pdb=" N GLU S 6 " --> pdb=" O GLN S 63 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N GLN S 63 " --> pdb=" O GLU S 6 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N GLN S 8 " --> pdb=" O ILE S 61 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ILE S 61 " --> pdb=" O GLN S 8 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ILE S 10 " --> pdb=" O VAL S 59 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'S' and resid 86 through 96 removed outlier: 3.641A pdb=" N TYR S 81 " --> pdb=" O HIS S 88 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ASN S 74 " --> pdb=" O ILE S 129 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N ARG S 80 " --> pdb=" O ILE S 123 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N ILE S 123 " --> pdb=" O ARG S 80 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'X' and resid 63 through 66 removed outlier: 6.809A pdb=" N GLN X 85 " --> pdb=" O GLU X 64 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N VAL X 83 " --> pdb=" O PRO X 66 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LYS X 120 " --> pdb=" O VAL X 86 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'Y' and resid 32 through 34 Processing sheet with id=AE3, first strand: chain 'Y' and resid 94 through 99 removed outlier: 6.839A pdb=" N VAL Y 85 " --> pdb=" O ILE Y 97 " (cutoff:3.500A) removed outlier: 9.932A pdb=" N LEU Y 99 " --> pdb=" O ASP Y 83 " (cutoff:3.500A) removed outlier: 10.558A pdb=" N ASP Y 83 " --> pdb=" O LEU Y 99 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ALA Y 79 " --> pdb=" O VAL Y 73 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N VAL Y 73 " --> pdb=" O ALA Y 79 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N GLN Y 81 " --> pdb=" O SER Y 71 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N LYS Y 69 " --> pdb=" O ASP Y 83 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N VAL Y 85 " --> pdb=" O GLU Y 67 " (cutoff:3.500A) removed outlier: 9.217A pdb=" N GLU Y 67 " --> pdb=" O VAL Y 85 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N LEU Y 57 " --> pdb=" O ILE Y 106 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N ILE Y 106 " --> pdb=" O LEU Y 57 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'Z' and resid 69 through 76 removed outlier: 6.938A pdb=" N LYS Z 69 " --> pdb=" O GLU Z 47 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS Z 27 " --> pdb=" O LEU Z 42 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ALA Z 44 " --> pdb=" O ILE Z 25 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N ILE Z 25 " --> pdb=" O ALA Z 44 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N ILE Z 46 " --> pdb=" O VAL Z 23 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N VAL Z 23 " --> pdb=" O ILE Z 46 " (cutoff:3.500A) removed outlier: 9.614A pdb=" N ARG Z 48 " --> pdb=" O LYS Z 21 " (cutoff:3.500A) removed outlier: 10.709A pdb=" N LYS Z 21 " --> pdb=" O ARG Z 48 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LYS Z 21 " --> pdb=" O VAL Z 13 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N LYS Z 9 " --> pdb=" O ILE Z 25 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N VAL Z 10 " --> pdb=" O THR Z 83 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'b' and resid 33 through 37 removed outlier: 6.036A pdb=" N LEU b 34 " --> pdb=" O LEU b 87 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N PHE b 89 " --> pdb=" O LEU b 34 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ILE b 36 " --> pdb=" O PHE b 89 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N ALA b 91 " --> pdb=" O ILE b 36 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N LEU b 97 " --> pdb=" O ILE b 114 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU b 101 " --> pdb=" O ILE b 110 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE b 110 " --> pdb=" O LEU b 101 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N THR b 109 " --> pdb=" O ILE b 226 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ILE b 226 " --> pdb=" O THR b 109 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N LYS b 111 " --> pdb=" O ILE b 224 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N LEU b 117 " --> pdb=" O ARG b 218 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ARG b 218 " --> pdb=" O LEU b 117 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'b' and resid 213 through 214 removed outlier: 3.838A pdb=" N VAL b 213 " --> pdb=" O GLU b 192 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'b' and resid 218 through 227 current: chain 'b' and resid 136 through 139 Processing sheet with id=AE7, first strand: chain 'c' and resid 23 through 25 removed outlier: 3.689A pdb=" N LEU c 41 " --> pdb=" O ILE c 92 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ILE c 42 " --> pdb=" O TYR c 68 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'd' and resid 34 through 38 Processing sheet with id=AE9, first strand: chain 'd' and resid 103 through 109 removed outlier: 6.638A pdb=" N UNK d 484 " --> pdb=" O UNK d 105 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N UNK d 107 " --> pdb=" O UNK d 482 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N UNK d 482 " --> pdb=" O UNK d 107 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N UNK d 481 " --> pdb=" O UNK d 477 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N UNK d 477 " --> pdb=" O UNK d 481 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'd' and resid 114 through 120 removed outlier: 3.570A pdb=" N UNK d 116 " --> pdb=" O UNK d 149 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N UNK d 155 " --> pdb=" O UNK d 167 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N UNK d 167 " --> pdb=" O UNK d 155 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N UNK d 157 " --> pdb=" O UNK d 165 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'd' and resid 180 through 187 removed outlier: 6.517A pdb=" N UNK d 190 " --> pdb=" O UNK d 186 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N UNK d 195 " --> pdb=" O UNK d 199 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N UNK d 199 " --> pdb=" O UNK d 195 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N UNK d 200 " --> pdb=" O UNK d 220 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N UNK d 220 " --> pdb=" O UNK d 200 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N UNK d 202 " --> pdb=" O UNK d 218 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N UNK d 285 " --> pdb=" O UNK d 218 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'd' and resid 228 through 234 Processing sheet with id=AF4, first strand: chain 'd' and resid 300 through 305 removed outlier: 3.930A pdb=" N UNK d 321 " --> pdb=" O UNK d 317 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N UNK d 334 " --> pdb=" O UNK d 324 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N UNK d 326 " --> pdb=" O UNK d 332 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N UNK d 332 " --> pdb=" O UNK d 326 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'd' and resid 342 through 348 removed outlier: 3.501A pdb=" N UNK d 357 " --> pdb=" O UNK d 348 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N UNK d 382 " --> pdb=" O UNK d 369 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'd' and resid 391 through 396 removed outlier: 3.531A pdb=" N UNK d 439 " --> pdb=" O UNK d 415 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N UNK d 417 " --> pdb=" O UNK d 437 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N UNK d 437 " --> pdb=" O UNK d 417 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'e' and resid 72 through 76 removed outlier: 6.143A pdb=" N LYS e 72 " --> pdb=" O ALA e 93 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N GLU e 95 " --> pdb=" O LYS e 72 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N PHE e 74 " --> pdb=" O GLU e 95 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF7 Processing sheet with id=AF8, first strand: chain 'f' and resid 8 through 18 removed outlier: 9.821A pdb=" N VAL f 9 " --> pdb=" O ILE f 32 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N ILE f 32 " --> pdb=" O VAL f 9 " (cutoff:3.500A) removed outlier: 8.483A pdb=" N GLY f 11 " --> pdb=" O ILE f 30 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N ILE f 30 " --> pdb=" O GLY f 11 " (cutoff:3.500A) removed outlier: 8.748A pdb=" N HIS f 13 " --> pdb=" O SER f 28 " (cutoff:3.500A) removed outlier: 9.772A pdb=" N SER f 28 " --> pdb=" O HIS f 13 " (cutoff:3.500A) removed outlier: 10.538A pdb=" N SER f 15 " --> pdb=" O ASN f 26 " (cutoff:3.500A) removed outlier: 8.226A pdb=" N ASN f 26 " --> pdb=" O SER f 15 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N ASN f 26 " --> pdb=" O PHE f 85 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N PHE f 85 " --> pdb=" O ASN f 26 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL f 80 " --> pdb=" O HIS f 75 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ARG f 73 " --> pdb=" O ARG f 82 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N THR f 84 " --> pdb=" O VAL f 71 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N VAL f 71 " --> pdb=" O THR f 84 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ARG f 48 " --> pdb=" O PHE f 101 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N VAL f 52 " --> pdb=" O SER f 97 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N SER f 97 " --> pdb=" O VAL f 52 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ALA f 96 " --> pdb=" O HIS f 13 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'g' and resid 21 through 24 Processing sheet with id=AG1, first strand: chain 'j' and resid 16 through 17 Processing sheet with id=AG2, first strand: chain 'k' and resid 3 through 5 removed outlier: 4.544A pdb=" N VAL k 55 " --> pdb=" O ILE k 5 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LYS k 36 " --> pdb=" O ASN k 32 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'n' and resid 187 through 191 Processing sheet with id=AG4, first strand: chain 'n' and resid 365 through 367 Processing sheet with id=AG5, first strand: chain 'o' and resid 117 through 124 removed outlier: 4.758A pdb=" N LEU o 117 " --> pdb=" O GLU o 138 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N GLU o 138 " --> pdb=" O LEU o 117 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N GLU o 119 " --> pdb=" O PHE o 136 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N PHE o 136 " --> pdb=" O GLU o 119 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N ARG o 121 " --> pdb=" O TYR o 134 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N TYR o 134 " --> pdb=" O ARG o 121 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ALA o 123 " --> pdb=" O ARG o 132 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE o 139 " --> pdb=" O GLY o 91 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N GLY o 91 " --> pdb=" O PHE o 139 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N ILE o 92 " --> pdb=" O LEU o 167 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLN o 163 " --> pdb=" O SER o 96 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'p' and resid 146 through 148 removed outlier: 3.602A pdb=" N ILE p 169 " --> pdb=" O GLY p 146 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ILE p 117 " --> pdb=" O LEU p 168 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N ALA p 170 " --> pdb=" O ILE p 117 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N VAL p 119 " --> pdb=" O ALA p 170 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N LEU p 193 " --> pdb=" O MET p 225 " (cutoff:3.500A) removed outlier: 8.325A pdb=" N PHE p 227 " --> pdb=" O LEU p 193 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ILE p 195 " --> pdb=" O PHE p 227 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ILE p 250 " --> pdb=" O LEU p 83 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'p' and resid 316 through 319 removed outlier: 3.662A pdb=" N THR p 346 " --> pdb=" O LEU p 319 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N GLN p 266 " --> pdb=" O ASN p 413 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 's' and resid 429 through 433 removed outlier: 3.714A pdb=" N THR s 431 " --> pdb=" O LEU s 804 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASP s 783 " --> pdb=" O ALA s 796 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 's' and resid 440 through 445 removed outlier: 3.536A pdb=" N THR s 442 " --> pdb=" O GLY s 455 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N THR s 460 " --> pdb=" O SER s 456 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N VAL s 461 " --> pdb=" O ARG s 474 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ARG s 474 " --> pdb=" O VAL s 461 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N VAL s 463 " --> pdb=" O VAL s 472 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 's' and resid 488 through 493 removed outlier: 6.355A pdb=" N ILE s 510 " --> pdb=" O THR s 590 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N THR s 590 " --> pdb=" O ILE s 510 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N LEU s 512 " --> pdb=" O CYS s 588 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 's' and resid 599 through 602 removed outlier: 3.614A pdb=" N LYS s 599 " --> pdb=" O VAL s 612 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 's' and resid 642 through 647 removed outlier: 6.672A pdb=" N CYS s 657 " --> pdb=" O MET s 643 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ALA s 645 " --> pdb=" O PHE s 655 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N PHE s 655 " --> pdb=" O ALA s 645 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N PHE s 647 " --> pdb=" O GLN s 653 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N GLN s 653 " --> pdb=" O PHE s 647 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N ASP s 666 " --> pdb=" O LEU s 672 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N LEU s 672 " --> pdb=" O ASP s 666 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 's' and resid 683 through 688 removed outlier: 6.575A pdb=" N SER s 698 " --> pdb=" O SER s 684 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ILE s 686 " --> pdb=" O ILE s 696 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ILE s 696 " --> pdb=" O ILE s 686 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N ILE s 688 " --> pdb=" O ASN s 694 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N ASN s 694 " --> pdb=" O ILE s 688 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 's' and resid 726 through 731 removed outlier: 5.776A pdb=" N HIS s 751 " --> pdb=" O PRO s 766 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N THR s 753 " --> pdb=" O ILE s 764 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N ILE s 764 " --> pdb=" O THR s 753 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 't' and resid 129 through 134 Processing sheet with id=AH7, first strand: chain 't' and resid 174 through 179 Processing sheet with id=AH8, first strand: chain 't' and resid 214 through 216 removed outlier: 4.548A pdb=" N HIS t 225 " --> pdb=" O TYR t 216 " (cutoff:3.500A) 2443 hydrogen bonds defined for protein. 6987 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1254 hydrogen bonds 1994 hydrogen bond angles 0 basepair planarities 506 basepair parallelities 847 stacking parallelities Total time for adding SS restraints: 56.94 Time building geometry restraints manager: 16.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.33: 13648 1.33 - 1.46: 31196 1.46 - 1.60: 27791 1.60 - 1.73: 1337 1.73 - 1.87: 8 Bond restraints: 73980 Sorted by residual: bond pdb=" C LEU Y 99 " pdb=" N HIS Y 100 " ideal model delta sigma weight residual 1.332 1.290 0.043 1.40e-02 5.10e+03 9.31e+00 bond pdb=" CA PRO k 70 " pdb=" C PRO k 70 " ideal model delta sigma weight residual 1.517 1.537 -0.020 6.70e-03 2.23e+04 9.08e+00 bond pdb=" C LYS G 128 " pdb=" N PRO G 129 " ideal model delta sigma weight residual 1.334 1.301 0.033 1.11e-02 8.12e+03 8.89e+00 bond pdb=" CA GLN Z 103 " pdb=" CB GLN Z 103 " ideal model delta sigma weight residual 1.525 1.548 -0.023 8.30e-03 1.45e+04 7.95e+00 bond pdb=" N ALA g 82 " pdb=" CA ALA g 82 " ideal model delta sigma weight residual 1.457 1.492 -0.034 1.29e-02 6.01e+03 7.02e+00 ... (remaining 73975 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.27: 107829 3.27 - 6.55: 1382 6.55 - 9.82: 141 9.82 - 13.10: 19 13.10 - 16.37: 1 Bond angle restraints: 109372 Sorted by residual: angle pdb=" N SER g 79 " pdb=" CA SER g 79 " pdb=" C SER g 79 " ideal model delta sigma weight residual 112.92 121.73 -8.81 1.23e+00 6.61e-01 5.13e+01 angle pdb=" O3' U 11716 " pdb=" C3' U 11716 " pdb=" C2' U 11716 " ideal model delta sigma weight residual 109.50 119.69 -10.19 1.50e+00 4.44e-01 4.61e+01 angle pdb=" O3' U 11568 " pdb=" C3' U 11568 " pdb=" C2' U 11568 " ideal model delta sigma weight residual 109.50 119.61 -10.11 1.50e+00 4.44e-01 4.54e+01 angle pdb=" C ARG S 13 " pdb=" N LEU S 14 " pdb=" CA LEU S 14 " ideal model delta sigma weight residual 121.80 138.17 -16.37 2.44e+00 1.68e-01 4.50e+01 angle pdb=" O3' A 11816 " pdb=" C3' A 11816 " pdb=" C2' A 11816 " ideal model delta sigma weight residual 113.70 123.54 -9.84 1.50e+00 4.44e-01 4.30e+01 ... (remaining 109367 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.88: 41390 35.88 - 71.77: 3874 71.77 - 107.65: 428 107.65 - 143.53: 20 143.53 - 179.42: 41 Dihedral angle restraints: 45753 sinusoidal: 25066 harmonic: 20687 Sorted by residual: dihedral pdb=" CA ALA A 185 " pdb=" C ALA A 185 " pdb=" N PRO A 186 " pdb=" CA PRO A 186 " ideal model delta harmonic sigma weight residual -180.00 -115.13 -64.87 0 5.00e+00 4.00e-02 1.68e+02 dihedral pdb=" CA UNK t 53 " pdb=" C UNK t 53 " pdb=" N LYS t 54 " pdb=" CA LYS t 54 " ideal model delta harmonic sigma weight residual 180.00 122.97 57.03 0 5.00e+00 4.00e-02 1.30e+02 dihedral pdb=" CA SER S 83 " pdb=" C SER S 83 " pdb=" N ARG S 84 " pdb=" CA ARG S 84 " ideal model delta harmonic sigma weight residual -180.00 -128.07 -51.93 0 5.00e+00 4.00e-02 1.08e+02 ... (remaining 45750 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.118: 14025 0.118 - 0.236: 804 0.236 - 0.354: 34 0.354 - 0.472: 1 0.472 - 0.590: 8 Chirality restraints: 14872 Sorted by residual: chirality pdb=" C3' C 11574 " pdb=" C4' C 11574 " pdb=" O3' C 11574 " pdb=" C2' C 11574 " both_signs ideal model delta sigma weight residual False -2.74 -2.16 -0.59 2.00e-01 2.50e+01 8.70e+00 chirality pdb=" C3' U 11716 " pdb=" C4' U 11716 " pdb=" O3' U 11716 " pdb=" C2' U 11716 " both_signs ideal model delta sigma weight residual False -2.74 -2.18 -0.56 2.00e-01 2.50e+01 7.86e+00 chirality pdb=" C3' U 11570 " pdb=" C4' U 11570 " pdb=" O3' U 11570 " pdb=" C2' U 11570 " both_signs ideal model delta sigma weight residual False -2.74 -2.20 -0.55 2.00e-01 2.50e+01 7.45e+00 ... (remaining 14869 not shown) Planarity restraints: 8708 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G 1 406 " -0.085 2.00e-02 2.50e+03 3.80e-02 4.32e+01 pdb=" N9 G 1 406 " 0.094 2.00e-02 2.50e+03 pdb=" C8 G 1 406 " 0.006 2.00e-02 2.50e+03 pdb=" N7 G 1 406 " -0.000 2.00e-02 2.50e+03 pdb=" C5 G 1 406 " -0.001 2.00e-02 2.50e+03 pdb=" C6 G 1 406 " -0.013 2.00e-02 2.50e+03 pdb=" O6 G 1 406 " -0.018 2.00e-02 2.50e+03 pdb=" N1 G 1 406 " -0.010 2.00e-02 2.50e+03 pdb=" C2 G 1 406 " -0.006 2.00e-02 2.50e+03 pdb=" N2 G 1 406 " 0.018 2.00e-02 2.50e+03 pdb=" N3 G 1 406 " 0.009 2.00e-02 2.50e+03 pdb=" C4 G 1 406 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G 2 39 " -0.057 2.00e-02 2.50e+03 2.35e-02 1.66e+01 pdb=" N9 G 2 39 " 0.053 2.00e-02 2.50e+03 pdb=" C8 G 2 39 " 0.006 2.00e-02 2.50e+03 pdb=" N7 G 2 39 " -0.000 2.00e-02 2.50e+03 pdb=" C5 G 2 39 " 0.002 2.00e-02 2.50e+03 pdb=" C6 G 2 39 " -0.008 2.00e-02 2.50e+03 pdb=" O6 G 2 39 " -0.015 2.00e-02 2.50e+03 pdb=" N1 G 2 39 " -0.006 2.00e-02 2.50e+03 pdb=" C2 G 2 39 " 0.007 2.00e-02 2.50e+03 pdb=" N2 G 2 39 " -0.001 2.00e-02 2.50e+03 pdb=" N3 G 2 39 " 0.013 2.00e-02 2.50e+03 pdb=" C4 G 2 39 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G 1 474 " -0.006 2.00e-02 2.50e+03 2.33e-02 1.64e+01 pdb=" N9 G 1 474 " 0.012 2.00e-02 2.50e+03 pdb=" C8 G 1 474 " -0.004 2.00e-02 2.50e+03 pdb=" N7 G 1 474 " 0.009 2.00e-02 2.50e+03 pdb=" C5 G 1 474 " 0.003 2.00e-02 2.50e+03 pdb=" C6 G 1 474 " -0.006 2.00e-02 2.50e+03 pdb=" O6 G 1 474 " 0.004 2.00e-02 2.50e+03 pdb=" N1 G 1 474 " 0.002 2.00e-02 2.50e+03 pdb=" C2 G 1 474 " -0.066 2.00e-02 2.50e+03 pdb=" N2 G 1 474 " 0.043 2.00e-02 2.50e+03 pdb=" N3 G 1 474 " 0.005 2.00e-02 2.50e+03 pdb=" C4 G 1 474 " 0.003 2.00e-02 2.50e+03 ... (remaining 8705 not shown) Histogram of nonbonded interaction distances: 0.27 - 1.19: 3 1.19 - 2.12: 58 2.12 - 3.05: 39321 3.05 - 3.97: 206729 3.97 - 4.90: 313566 Warning: very small nonbonded interaction distances. Nonbonded interactions: 559677 Sorted by model distance: nonbonded pdb=" CB SER Z 105 " pdb=" O PHE s 700 " model vdw 0.266 3.440 nonbonded pdb=" O3' A 11558 " pdb=" CA LEU X 34 " model vdw 0.799 3.470 nonbonded pdb=" CB LYS k 9 " pdb=" CB ASP s 710 " model vdw 1.061 3.840 nonbonded pdb=" P A 11559 " pdb=" N LEU X 34 " model vdw 1.229 3.480 nonbonded pdb=" OP1 A 11559 " pdb=" O LEU X 34 " model vdw 1.229 3.040 ... (remaining 559672 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 10.060 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: 0.050 Extract box with map and model: 2.020 Check model and map are aligned: 0.400 Set scattering table: 0.490 Process input model: 179.970 Find NCS groups from input model: 1.210 Set up NCS constraints: 0.240 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:2.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 196.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4839 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 : 0.006 0.060 73980 Z= 0.377 Angle : 1.017 16.373 109372 Z= 0.599 Chirality : 0.059 0.590 14872 Planarity : 0.005 0.038 8705 Dihedral : 23.825 179.418 32150 Min Nonbonded Distance : 0.266 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.03 % Favored : 94.85 % Rotamer: Outliers : 0.00 % Allowed : 25.00 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.08 % Twisted Proline : 1.13 % Twisted General : 0.31 % 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: -2.67 (0.09), residues: 6347 helix: -1.94 (0.08), residues: 2408 sheet: -1.01 (0.16), residues: 977 loop : -1.79 (0.10), residues: 2962 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 51 PHE 0.000 0.000 PHE A 33 TYR 0.000 0.000 TYR A 46 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12694 Ramachandran restraints generated. 6347 Oldfield, 0 Emsley, 6347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12694 Ramachandran restraints generated. 6347 Oldfield, 0 Emsley, 6347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 5634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 3.563 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 71 average time/residue: 0.5404 time to fit residues: 77.4394 Evaluate side-chains 71 residues out of total 5634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 3.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 855 random chunks: chunk 721 optimal weight: 3.9990 chunk 648 optimal weight: 5.9990 chunk 359 optimal weight: 7.9990 chunk 221 optimal weight: 5.9990 chunk 437 optimal weight: 20.0000 chunk 346 optimal weight: 20.0000 chunk 670 optimal weight: 20.0000 chunk 259 optimal weight: 20.0000 chunk 407 optimal weight: 10.0000 chunk 498 optimal weight: 10.0000 chunk 776 optimal weight: 6.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- 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: 0.6028 moved from start: 0.5392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.181 73980 Z= 0.379 Angle : 1.131 28.445 109372 Z= 0.584 Chirality : 0.054 0.907 14872 Planarity : 0.006 0.072 8705 Dihedral : 23.839 179.758 32142 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 22.94 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.72 % Favored : 94.12 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.07 % Twisted Proline : 0.38 % Twisted General : 0.20 % 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: -2.18 (0.09), residues: 6347 helix: -1.18 (0.09), residues: 2450 sheet: -1.09 (0.15), residues: 972 loop : -1.71 (0.11), residues: 2925 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 51 PHE 0.000 0.000 PHE A 33 TYR 0.000 0.000 TYR A 46 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12694 Ramachandran restraints generated. 6347 Oldfield, 0 Emsley, 6347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12694 Ramachandran restraints generated. 6347 Oldfield, 0 Emsley, 6347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 5634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 3.630 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 71 average time/residue: 0.5578 time to fit residues: 80.2363 Evaluate side-chains 71 residues out of total 5634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 3.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 855 random chunks: chunk 431 optimal weight: 8.9990 chunk 240 optimal weight: 6.9990 chunk 646 optimal weight: 6.9990 chunk 528 optimal weight: 40.0000 chunk 214 optimal weight: 10.0000 chunk 777 optimal weight: 2.9990 chunk 840 optimal weight: 0.9980 chunk 692 optimal weight: 10.0000 chunk 771 optimal weight: 2.9990 chunk 265 optimal weight: 20.0000 chunk 624 optimal weight: 0.0370 overall best weight: 2.8064 ------------------------------------------------------------------------------- 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: 0.6121 moved from start: 0.6183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.122 73980 Z= 0.186 Angle : 0.653 9.954 109372 Z= 0.344 Chirality : 0.039 0.259 14872 Planarity : 0.003 0.039 8705 Dihedral : 23.400 179.702 32142 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.11 % Favored : 95.82 % Rotamer: Outliers : 0.00 % Allowed : 25.00 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.65 (0.10), residues: 6347 helix: 0.76 (0.10), residues: 2543 sheet: -0.72 (0.16), residues: 989 loop : -1.41 (0.11), residues: 2815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 51 PHE 0.000 0.000 PHE A 33 TYR 0.000 0.000 TYR A 46 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12694 Ramachandran restraints generated. 6347 Oldfield, 0 Emsley, 6347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12694 Ramachandran restraints generated. 6347 Oldfield, 0 Emsley, 6347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 5634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 3.665 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 71 average time/residue: 0.5469 time to fit residues: 78.3870 Evaluate side-chains 71 residues out of total 5634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 3.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 855 random chunks: chunk 768 optimal weight: 8.9990 chunk 584 optimal weight: 50.0000 chunk 403 optimal weight: 20.0000 chunk 86 optimal weight: 10.0000 chunk 371 optimal weight: 5.9990 chunk 522 optimal weight: 30.0000 chunk 780 optimal weight: 40.0000 chunk 826 optimal weight: 4.9990 chunk 407 optimal weight: 6.9990 chunk 739 optimal weight: 0.8980 chunk 222 optimal weight: 0.0040 overall best weight: 3.7798 ------------------------------------------------------------------------------- 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: 0.6590 moved from start: 0.9006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.127 73980 Z= 0.282 Angle : 0.794 12.279 109372 Z= 0.415 Chirality : 0.043 0.351 14872 Planarity : 0.004 0.035 8705 Dihedral : 23.391 179.782 32142 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 17.13 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.52 % Favored : 93.35 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.10), residues: 6347 helix: 0.92 (0.10), residues: 2536 sheet: -0.93 (0.17), residues: 915 loop : -1.42 (0.11), residues: 2896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 51 PHE 0.000 0.000 PHE A 33 TYR 0.000 0.000 TYR A 46 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12694 Ramachandran restraints generated. 6347 Oldfield, 0 Emsley, 6347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12694 Ramachandran restraints generated. 6347 Oldfield, 0 Emsley, 6347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 5634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 3.833 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 71 average time/residue: 0.6103 time to fit residues: 87.4378 Evaluate side-chains 71 residues out of total 5634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 3.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 855 random chunks: chunk 688 optimal weight: 0.3980 chunk 469 optimal weight: 30.0000 chunk 12 optimal weight: 10.0000 chunk 615 optimal weight: 0.8980 chunk 340 optimal weight: 20.0000 chunk 705 optimal weight: 8.9990 chunk 571 optimal weight: 50.0000 chunk 0 optimal weight: 9.9990 chunk 422 optimal weight: 8.9990 chunk 741 optimal weight: 8.9990 chunk 208 optimal weight: 0.8980 overall best weight: 4.0384 ------------------------------------------------------------------------------- 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: 0.6743 moved from start: 1.0545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 73980 Z= 0.209 Angle : 0.677 11.267 109372 Z= 0.355 Chirality : 0.040 0.271 14872 Planarity : 0.004 0.035 8705 Dihedral : 23.420 179.929 32142 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.09 % Favored : 94.80 % Rotamer: Outliers : 0.00 % Allowed : 12.50 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.11), residues: 6347 helix: 1.30 (0.10), residues: 2551 sheet: -0.95 (0.17), residues: 891 loop : -1.47 (0.11), residues: 2905 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 51 PHE 0.000 0.000 PHE A 33 TYR 0.000 0.000 TYR A 46 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12694 Ramachandran restraints generated. 6347 Oldfield, 0 Emsley, 6347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12694 Ramachandran restraints generated. 6347 Oldfield, 0 Emsley, 6347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 5634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 3.606 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 71 average time/residue: 0.5475 time to fit residues: 78.5501 Evaluate side-chains 71 residues out of total 5634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 3.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 855 random chunks: chunk 278 optimal weight: 9.9990 chunk 744 optimal weight: 0.0270 chunk 163 optimal weight: 50.0000 chunk 485 optimal weight: 10.0000 chunk 204 optimal weight: 30.0000 chunk 827 optimal weight: 10.0000 chunk 686 optimal weight: 4.9990 chunk 383 optimal weight: 6.9990 chunk 68 optimal weight: 10.0000 chunk 273 optimal weight: 40.0000 chunk 434 optimal weight: 6.9990 overall best weight: 5.8046 ------------------------------------------------------------------------------- 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: 0.7002 moved from start: 1.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.100 73980 Z= 0.304 Angle : 0.796 9.639 109372 Z= 0.417 Chirality : 0.044 0.289 14872 Planarity : 0.004 0.027 8705 Dihedral : 23.609 179.685 32142 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 17.49 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.27 % Favored : 91.65 % Rotamer: Outliers : 0.00 % Allowed : 12.50 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.11), residues: 6347 helix: 0.97 (0.10), residues: 2526 sheet: -1.14 (0.18), residues: 837 loop : -1.67 (0.11), residues: 2984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 51 PHE 0.000 0.000 PHE A 33 TYR 0.000 0.000 TYR A 46 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12694 Ramachandran restraints generated. 6347 Oldfield, 0 Emsley, 6347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12694 Ramachandran restraints generated. 6347 Oldfield, 0 Emsley, 6347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 5634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 3.623 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 71 average time/residue: 0.5311 time to fit residues: 76.2095 Evaluate side-chains 71 residues out of total 5634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 3.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 855 random chunks: chunk 797 optimal weight: 40.0000 chunk 93 optimal weight: 20.0000 chunk 471 optimal weight: 30.0000 chunk 604 optimal weight: 3.9990 chunk 468 optimal weight: 8.9990 chunk 696 optimal weight: 9.9990 chunk 461 optimal weight: 8.9990 chunk 824 optimal weight: 0.2980 chunk 515 optimal weight: 50.0000 chunk 502 optimal weight: 9.9990 chunk 380 optimal weight: 1.9990 overall best weight: 4.8588 ------------------------------------------------------------------------------- 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: 0.7090 moved from start: 1.4193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.095 73980 Z= 0.221 Angle : 0.680 10.107 109372 Z= 0.357 Chirality : 0.040 0.310 14872 Planarity : 0.003 0.027 8705 Dihedral : 23.614 179.686 32142 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.81 % Favored : 94.12 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.11), residues: 6347 helix: 1.30 (0.10), residues: 2551 sheet: -1.05 (0.18), residues: 802 loop : -1.78 (0.11), residues: 2994 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 51 PHE 0.000 0.000 PHE A 33 TYR 0.000 0.000 TYR A 46 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12694 Ramachandran restraints generated. 6347 Oldfield, 0 Emsley, 6347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12694 Ramachandran restraints generated. 6347 Oldfield, 0 Emsley, 6347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 5634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 3.663 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 71 average time/residue: 0.5394 time to fit residues: 77.4092 Evaluate side-chains 71 residues out of total 5634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 3.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 855 random chunks: chunk 509 optimal weight: 7.9990 chunk 329 optimal weight: 30.0000 chunk 492 optimal weight: 40.0000 chunk 248 optimal weight: 10.0000 chunk 161 optimal weight: 20.0000 chunk 159 optimal weight: 20.0000 chunk 523 optimal weight: 8.9990 chunk 561 optimal weight: 40.0000 chunk 407 optimal weight: 4.9990 chunk 76 optimal weight: 10.0000 chunk 647 optimal weight: 20.0000 overall best weight: 8.3994 ------------------------------------------------------------------------------- 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: 0.7301 moved from start: 1.6170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.127 73980 Z= 0.383 Angle : 0.994 10.774 109372 Z= 0.509 Chirality : 0.051 0.344 14872 Planarity : 0.005 0.029 8705 Dihedral : 24.199 179.750 32142 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 26.73 Ramachandran Plot: Outliers : 0.44 % Allowed : 10.62 % Favored : 88.94 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.76 (0.10), residues: 6347 helix: 0.10 (0.10), residues: 2484 sheet: -1.51 (0.18), residues: 736 loop : -2.18 (0.11), residues: 3127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 51 PHE 0.000 0.000 PHE A 33 TYR 0.000 0.000 TYR A 46 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12694 Ramachandran restraints generated. 6347 Oldfield, 0 Emsley, 6347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12694 Ramachandran restraints generated. 6347 Oldfield, 0 Emsley, 6347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 5634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 3.655 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 71 average time/residue: 0.6302 time to fit residues: 91.0415 Evaluate side-chains 71 residues out of total 5634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 3.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 855 random chunks: chunk 749 optimal weight: 0.0370 chunk 789 optimal weight: 40.0000 chunk 720 optimal weight: 9.9990 chunk 767 optimal weight: 50.0000 chunk 462 optimal weight: 0.1980 chunk 334 optimal weight: 30.0000 chunk 603 optimal weight: 20.0000 chunk 235 optimal weight: 0.1980 chunk 693 optimal weight: 20.0000 chunk 726 optimal weight: 8.9990 chunk 765 optimal weight: 2.9990 overall best weight: 2.4862 ------------------------------------------------------------------------------- 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: 0.7215 moved from start: 1.6171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 73980 Z= 0.152 Angle : 0.614 9.647 109372 Z= 0.322 Chirality : 0.039 0.342 14872 Planarity : 0.003 0.022 8705 Dihedral : 23.691 179.709 32142 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.11 % Favored : 93.87 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.80 (0.11), residues: 6347 helix: 1.33 (0.10), residues: 2541 sheet: -1.45 (0.18), residues: 775 loop : -1.99 (0.11), residues: 3031 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 51 PHE 0.000 0.000 PHE A 33 TYR 0.000 0.000 TYR A 46 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12694 Ramachandran restraints generated. 6347 Oldfield, 0 Emsley, 6347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12694 Ramachandran restraints generated. 6347 Oldfield, 0 Emsley, 6347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 5634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 3.786 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 71 average time/residue: 0.6056 time to fit residues: 88.5229 Evaluate side-chains 71 residues out of total 5634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 3.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 855 random chunks: chunk 504 optimal weight: 3.9990 chunk 812 optimal weight: 8.9990 chunk 495 optimal weight: 30.0000 chunk 385 optimal weight: 10.0000 chunk 564 optimal weight: 50.0000 chunk 851 optimal weight: 0.0030 chunk 783 optimal weight: 8.9990 chunk 678 optimal weight: 10.0000 chunk 70 optimal weight: 20.0000 chunk 523 optimal weight: 50.0000 chunk 415 optimal weight: 20.0000 overall best weight: 6.4000 ------------------------------------------------------------------------------- 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: 0.7323 moved from start: 1.7056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.111 73980 Z= 0.292 Angle : 0.768 10.493 109372 Z= 0.401 Chirality : 0.043 0.357 14872 Planarity : 0.004 0.025 8705 Dihedral : 23.897 179.817 32142 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 20.08 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.89 % Favored : 89.02 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.23 (0.11), residues: 6347 helix: 0.92 (0.10), residues: 2493 sheet: -1.65 (0.18), residues: 758 loop : -2.13 (0.11), residues: 3096 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 51 PHE 0.000 0.000 PHE A 33 TYR 0.000 0.000 TYR A 46 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12694 Ramachandran restraints generated. 6347 Oldfield, 0 Emsley, 6347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12694 Ramachandran restraints generated. 6347 Oldfield, 0 Emsley, 6347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 5634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 3.695 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 71 average time/residue: 0.5459 time to fit residues: 78.1863 Evaluate side-chains 71 residues out of total 5634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 3.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 855 random chunks: chunk 538 optimal weight: 8.9990 chunk 722 optimal weight: 30.0000 chunk 207 optimal weight: 6.9990 chunk 625 optimal weight: 5.9990 chunk 100 optimal weight: 10.0000 chunk 188 optimal weight: 3.9990 chunk 679 optimal weight: 2.9990 chunk 284 optimal weight: 0.3980 chunk 697 optimal weight: 30.0000 chunk 86 optimal weight: 10.0000 chunk 125 optimal weight: 20.0000 overall best weight: 4.0788 ------------------------------------------------------------------------------- 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 = 0.3685 r_free = 0.3685 target = 0.075524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.059994 restraints weight = 714995.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.059548 restraints weight = 1028511.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.059702 restraints weight = 839119.355| |-----------------------------------------------------------------------------| r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 1.7371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 73980 Z= 0.183 Angle : 0.615 10.946 109372 Z= 0.324 Chirality : 0.039 0.344 14872 Planarity : 0.003 0.022 8705 Dihedral : 23.685 179.903 32142 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 14.12 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.75 % Favored : 92.22 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.11), residues: 6347 helix: 1.51 (0.11), residues: 2505 sheet: -1.66 (0.18), residues: 797 loop : -2.08 (0.11), residues: 3045 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 51 PHE 0.000 0.000 PHE A 33 TYR 0.000 0.000 TYR A 46 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5771.62 seconds wall clock time: 105 minutes 51.23 seconds (6351.23 seconds total)