Starting phenix.real_space_refine on Sun Sep 29 17:33:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qtt_14146/09_2024/7qtt_14146.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qtt_14146/09_2024/7qtt_14146.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qtt_14146/09_2024/7qtt_14146.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qtt_14146/09_2024/7qtt_14146.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qtt_14146/09_2024/7qtt_14146.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qtt_14146/09_2024/7qtt_14146.cif" } resolution = 3.1 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= 0.001 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 898 atoms to isotropic. 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: 7 Type Number sf(0) Gaussians Zn 12 6.06 5 P 352 5.49 5 Mg 7 5.21 5 S 251 5.16 5 C 44800 2.51 5 N 13330 2.21 5 O 14785 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 73537 Number of models: 1 Model: "" Number of chains: 46 Chain: "A" Number of atoms: 5744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1164, 5744 Classifications: {'peptide': 1164} Incomplete info: {'truncation_to_alanine': 1014} Link IDs: {'PCIS': 2, 'PTRANS': 58, 'TRANS': 1103} Chain breaks: 6 Unresolved chain link angles: 60 Unresolved non-hydrogen bonds: 3591 Unresolved non-hydrogen angles: 4622 Unresolved non-hydrogen dihedrals: 2944 Unresolved non-hydrogen chiralities: 352 Planarities with less than four sites: {'GLN:plan1': 47, 'ASP:plan': 63, 'TYR:plan': 37, 'ASN:plan1': 54, 'TRP:plan': 7, 'HIS:plan': 26, 'PHE:plan': 56, 'GLU:plan': 85, 'ARG:plan': 60} Unresolved non-hydrogen planarities: 1967 Chain: "B" Number of atoms: 350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 350 Classifications: {'peptide': 70} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 3, 'TRANS': 66} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 241 Unresolved non-hydrogen angles: 310 Unresolved non-hydrogen dihedrals: 213 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 3, 'TYR:plan': 4, 'ASN:plan1': 4, 'TRP:plan': 2, 'ASP:plan': 3, 'PHE:plan': 3, 'GLU:plan': 5, 'HIS:plan': 4} Unresolved non-hydrogen planarities: 152 Chain: "C" Number of atoms: 5115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 815, 5115 Classifications: {'peptide': 815} Incomplete info: {'truncation_to_alanine': 359} Link IDs: {'PCIS': 2, 'PTRANS': 32, 'TRANS': 780} Unresolved non-hydrogen bonds: 1400 Unresolved non-hydrogen angles: 1735 Unresolved non-hydrogen dihedrals: 1141 Unresolved non-hydrogen chiralities: 103 Planarities with less than four sites: {'GLN:plan1': 21, 'HIS:plan': 3, 'TYR:plan': 14, 'ASN:plan1': 14, 'TRP:plan': 2, 'ASP:plan': 36, 'PHE:plan': 7, 'GLU:plan': 54, 'ARG:plan': 35} Unresolved non-hydrogen planarities: 798 Chain: "D" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 649 Classifications: {'peptide': 89} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 4, 'TRANS': 84} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "E" Number of atoms: 1350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1350 Classifications: {'peptide': 198} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 76} Link IDs: {'PTRANS': 20, 'TRANS': 177} Chain breaks: 3 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 285 Unresolved non-hydrogen angles: 355 Unresolved non-hydrogen dihedrals: 233 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 8, 'TYR:plan': 3, 'ASN:plan1': 2, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 7, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 138 Chain: "F" Number of atoms: 383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 383 Classifications: {'peptide': 78} Incomplete info: {'truncation_to_alanine': 66} Link IDs: {'PTRANS': 4, 'TRANS': 73} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 250 Unresolved non-hydrogen angles: 322 Unresolved non-hydrogen dihedrals: 211 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 2, 'TYR:plan': 4, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 5, 'PHE:plan': 3, 'GLU:plan': 6, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 135 Chain: "G" Number of atoms: 364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 364 Classifications: {'peptide': 67} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 4, 'TRANS': 62} Chain breaks: 1 Unresolved non-hydrogen bonds: 139 Unresolved non-hydrogen angles: 170 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 8, 'ARG:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 68 Chain: "I" Number of atoms: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 533 Classifications: {'peptide': 84} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 2, 'TRANS': 81} Chain breaks: 1 Unresolved non-hydrogen bonds: 135 Unresolved non-hydrogen angles: 169 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 5, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 5, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 79 Chain: "J" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 510 Classifications: {'peptide': 72} Incomplete info: {'backbone_only': 2, 'truncation_to_alanine': 17} Link IDs: {'PTRANS': 3, 'TRANS': 68} Unresolved non-hydrogen bonds: 93 Unresolved non-hydrogen angles: 122 Unresolved non-hydrogen dihedrals: 83 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 2, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 64 Chain: "L" Number of atoms: 177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 177 Classifications: {'peptide': 28} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 1, 'TRANS': 26} Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 43 Chain: "N" Number of atoms: 6157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 792, 6157 Classifications: {'peptide': 792} Incomplete info: {'truncation_to_alanine': 57} Link IDs: {'PTRANS': 36, 'TRANS': 755} Chain breaks: 4 Unresolved non-hydrogen bonds: 233 Unresolved non-hydrogen angles: 286 Unresolved non-hydrogen dihedrals: 185 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 12, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 15, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 184 Chain: "O" Number of atoms: 2517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2517 Classifications: {'peptide': 320} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 306} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Chain: "P" Number of atoms: 1151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1151 Classifications: {'peptide': 148} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 18} Link IDs: {'PTRANS': 5, 'TRANS': 142} Chain breaks: 2 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 101 Unresolved non-hydrogen dihedrals: 71 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 4, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 59 Chain: "Q" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 823 Classifications: {'peptide': 100} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 2, 'TRANS': 97} Chain breaks: 1 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 16 Chain: "T" Number of atoms: 1176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1176 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 6, 'TRANS': 135} Chain: "U" Number of atoms: 2080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2080 Classifications: {'peptide': 295} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 82} Link IDs: {'PTRANS': 17, 'TRANS': 277} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 320 Unresolved non-hydrogen angles: 409 Unresolved non-hydrogen dihedrals: 260 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 8, 'PHE:plan': 6, 'GLU:plan': 7, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 195 Chain: "V" Number of atoms: 1996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 1996 Classifications: {'peptide': 285} Incomplete info: {'truncation_to_alanine': 75} Link IDs: {'PTRANS': 10, 'TRANS': 274} Chain breaks: 2 Unresolved non-hydrogen bonds: 298 Unresolved non-hydrogen angles: 374 Unresolved non-hydrogen dihedrals: 246 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 12, 'PHE:plan': 6, 'GLU:plan': 11, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 183 Chain: "W" Number of atoms: 2921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 2921 Classifications: {'peptide': 459} Incomplete info: {'truncation_to_alanine': 237} Link IDs: {'PTRANS': 14, 'TRANS': 444} Chain breaks: 1 Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 854 Unresolved non-hydrogen angles: 1084 Unresolved non-hydrogen dihedrals: 691 Unresolved non-hydrogen chiralities: 88 Planarities with less than four sites: {'GLN:plan1': 11, 'ASP:plan': 13, 'TYR:plan': 6, 'ASN:plan1': 17, 'TRP:plan': 1, 'HIS:plan': 6, 'PHE:plan': 11, 'GLU:plan': 22, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 439 Chain: "X" Number of atoms: 1587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1587 Classifications: {'peptide': 241} Incomplete info: {'truncation_to_alanine': 134} Link IDs: {'PTRANS': 3, 'TRANS': 237} Chain breaks: 1 Unresolved non-hydrogen bonds: 574 Unresolved non-hydrogen angles: 717 Unresolved non-hydrogen dihedrals: 483 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 5, 'TYR:plan': 8, 'ASN:plan1': 10, 'ASP:plan': 11, 'PHE:plan': 9, 'GLU:plan': 31, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 407 Chain: "Y" Number of atoms: 2250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2250 Classifications: {'peptide': 306} Incomplete info: {'truncation_to_alanine': 61} Link IDs: {'PTRANS': 21, 'TRANS': 284} Chain breaks: 5 Unresolved non-hydrogen bonds: 251 Unresolved non-hydrogen angles: 301 Unresolved non-hydrogen dihedrals: 203 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 7, 'ASN:plan1': 5, 'HIS:plan': 1, 'GLU:plan': 13, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 184 Chain: "Z" Number of atoms: 607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 607 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 53} Link IDs: {'PTRANS': 4, 'TRANS': 90} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 200 Unresolved non-hydrogen angles: 254 Unresolved non-hydrogen dihedrals: 169 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 3, 'HIS:plan': 2, 'PHE:plan': 5, 'GLU:plan': 3, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 137 Chain: "a" Number of atoms: 15194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1936, 15194 Classifications: {'peptide': 1936} Incomplete info: {'truncation_to_alanine': 257} Link IDs: {'PCIS': 2, 'PTRANS': 103, 'TRANS': 1830} Chain breaks: 4 Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 947 Unresolved non-hydrogen angles: 1218 Unresolved non-hydrogen dihedrals: 778 Unresolved non-hydrogen chiralities: 93 Planarities with less than four sites: {'GLN:plan1': 14, 'HIS:plan': 6, 'TYR:plan': 5, 'ASN:plan1': 14, 'TRP:plan': 6, 'ASP:plan': 20, 'PHE:plan': 11, 'GLU:plan': 28, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 515 Chain: "b" Number of atoms: 7046 Number of conformers: 1 Conformer: "" Number of residues, atoms: 898, 7046 Classifications: {'peptide': 898} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 54, 'TRANS': 843} Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 47 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 40 Chain: "d" Number of atoms: 1989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 1989 Classifications: {'RNA': 93} Modifications used: {'rna2p_pur': 10, 'rna2p_pyr': 7, 'rna3p_pur': 42, 'rna3p_pyr': 34} Link IDs: {'rna2p': 17, 'rna3p': 75} Chain breaks: 1 Chain: "e" Number of atoms: 2070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 2070 Classifications: {'RNA': 98} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 11, 'rna3p_pur': 38, 'rna3p_pyr': 43} Link IDs: {'rna2p': 16, 'rna3p': 81} Chain breaks: 2 Chain: "f" Number of atoms: 1600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1600 Classifications: {'RNA': 76} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 3, 'rna3p_pur': 29, 'rna3p_pyr': 41} Link IDs: {'rna2p': 6, 'rna3p': 69} Chain breaks: 3 Chain: "g" Number of atoms: 1559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1559 Classifications: {'RNA': 76} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 15, 'rna3p_pur': 24, 'rna3p_pyr': 30} Link IDs: {'rna2p': 22, 'rna3p': 53} Chain breaks: 1 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {' G%rna3p_pur:plan2': 2, ' G%rna3p_pur:plan': 2, ' U%rna3p_pyr:plan': 2} Unresolved non-hydrogen planarities: 42 Chain: "h" Number of atoms: 322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 322 Classifications: {'peptide': 66} Incomplete info: {'truncation_to_alanine': 57} Link IDs: {'PTRANS': 3, 'TRANS': 62} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 212 Unresolved non-hydrogen angles: 273 Unresolved non-hydrogen dihedrals: 180 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'TYR:plan': 5, 'ASN:plan1': 6, 'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 4, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 106 Chain: "i" Number of atoms: 346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 346 Classifications: {'peptide': 70} Incomplete info: {'truncation_to_alanine': 65} Link IDs: {'PTRANS': 1, 'TRANS': 68} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 249 Unresolved non-hydrogen angles: 319 Unresolved non-hydrogen dihedrals: 202 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 148 Chain: "j" Number of atoms: 335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 335 Classifications: {'peptide': 68} Incomplete info: {'truncation_to_alanine': 60} Link IDs: {'PTRANS': 1, 'TRANS': 66} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 213 Unresolved non-hydrogen angles: 273 Unresolved non-hydrogen dihedrals: 169 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'TYR:plan': 3, 'ASN:plan1': 4, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 120 Chain: "k" Number of atoms: 388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 388 Classifications: {'peptide': 78} Incomplete info: {'truncation_to_alanine': 72} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 235 Unresolved non-hydrogen angles: 301 Unresolved non-hydrogen dihedrals: 184 Unresolved non-hydrogen chiralities: 34 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 3, 'TYR:plan': 1, 'ASN:plan1': 5, 'HIS:plan': 3, 'PHE:plan': 2, 'GLU:plan': 4, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 97 Chain: "l" Number of atoms: 337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 337 Classifications: {'peptide': 68} Incomplete info: {'truncation_to_alanine': 64} Link IDs: {'PTRANS': 1, 'TRANS': 66} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 222 Unresolved non-hydrogen angles: 279 Unresolved non-hydrogen dihedrals: 182 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 6, 'TYR:plan': 1, 'ASN:plan1': 7, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 109 Chain: "m" Number of atoms: 309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 309 Classifications: {'peptide': 63} Incomplete info: {'truncation_to_alanine': 54} Link IDs: {'PTRANS': 3, 'TRANS': 59} Chain breaks: 2 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 184 Unresolved non-hydrogen angles: 230 Unresolved non-hydrogen dihedrals: 149 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 4, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 85 Chain: "n" Number of atoms: 315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 315 Classifications: {'peptide': 64} Incomplete info: {'truncation_to_alanine': 58} Link IDs: {'TRANS': 63} Chain breaks: 1 Unresolved non-hydrogen bonds: 207 Unresolved non-hydrogen angles: 259 Unresolved non-hydrogen dihedrals: 170 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 5, 'PHE:plan': 4, 'GLU:plan': 3, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 107 Chain: "p" Number of atoms: 776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 776 Classifications: {'peptide': 159} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 129} Link IDs: {'PTRANS': 9, 'TRANS': 149} Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 493 Unresolved non-hydrogen angles: 635 Unresolved non-hydrogen dihedrals: 423 Unresolved non-hydrogen chiralities: 40 Planarities with less than four sites: {'GLN:plan1': 7, 'ASP:plan': 9, 'TYR:plan': 6, 'ASN:plan1': 7, 'TRP:plan': 3, 'HIS:plan': 4, 'PHE:plan': 8, 'GLU:plan': 6, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 272 Chain: "q" Number of atoms: 461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 461 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 3, 'TRANS': 70} Chain breaks: 1 Unresolved non-hydrogen bonds: 148 Unresolved non-hydrogen angles: 182 Unresolved non-hydrogen dihedrals: 117 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'GLU:plan': 11, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 101 Chain: "u" Number of atoms: 1963 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 1963 Classifications: {'peptide': 367} Incomplete info: {'truncation_to_alanine': 279} Link IDs: {'PTRANS': 19, 'TRANS': 347} Chain breaks: 3 Unresolved chain link angles: 17 Unresolved non-hydrogen bonds: 1033 Unresolved non-hydrogen angles: 1324 Unresolved non-hydrogen dihedrals: 867 Unresolved non-hydrogen chiralities: 86 Planarities with less than four sites: {'GLN:plan1': 10, 'ARG:plan': 17, 'TYR:plan': 12, 'ASN:plan1': 19, 'TRP:plan': 2, 'HIS:plan': 9, 'PHE:plan': 20, 'GLU:plan': 18, 'ASP:plan': 20} Unresolved non-hydrogen planarities: 581 Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" 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} Chain: "T" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "U" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "Z" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "a" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'IHP': 1} Classifications: {'undetermined': 1} Chain: "b" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "d" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Unusual residues: {' MG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 11279 SG CYS D 11 101.760 84.326 215.246 1.00231.57 S ATOM 11536 SG CYS D 46 98.680 85.210 217.853 1.00230.57 S ATOM 11559 SG CYS D 49 100.582 87.671 215.395 1.00228.78 S ATOM 11811 SG CYS D 85 98.302 84.609 214.349 1.00231.87 S ATOM 11417 SG CYS D 30 92.309 77.591 204.043 1.00196.48 S ATOM 11438 SG CYS D 33 92.992 74.491 201.835 1.00201.37 S ATOM 11727 SG CYS D 72 89.666 74.799 203.506 1.00191.16 S ATOM 11743 SG CYS D 75 92.628 74.048 205.505 1.00189.41 S ATOM 11366 SG CYS D 23 97.069 91.364 200.257 1.00220.37 S ATOM 11390 SG CYS D 26 96.978 87.711 200.449 1.00214.05 S ATOM 11631 SG CYS D 58 97.582 89.680 203.505 1.00232.39 S ATOM 11652 SG CYS D 61 100.416 89.483 200.681 1.00236.60 S ATOM 14326 SG CYS I 56 119.575 52.353 174.150 1.00176.05 S ATOM 14342 SG CYS I 59 122.920 52.425 175.983 1.00176.49 S ATOM 14635 SG CYS J 408 119.922 26.550 206.315 1.00260.71 S ATOM 14658 SG CYS J 411 121.109 24.497 203.561 1.00262.22 S ATOM 26712 SG CYS T 105 43.895 91.908 103.379 1.00124.41 S ATOM 26806 SG CYS T 117 43.909 87.990 103.513 1.00125.44 S ATOM 26820 SG CYS T 119 40.933 90.374 103.026 1.00123.86 S ATOM 26939 SG CYS T 134 43.212 89.745 106.437 1.00121.17 S ATOM 26681 SG CYS T 101 41.105 94.159 103.628 1.00122.75 S ATOM 26820 SG CYS T 119 40.933 90.374 103.026 1.00123.86 S ATOM 26972 SG CYS T 139 37.866 92.327 104.283 1.00122.74 S ATOM 26993 SG CYS T 142 39.173 93.011 100.789 1.00125.29 S ATOM 26681 SG CYS T 101 41.105 94.159 103.628 1.00122.75 S ATOM 26687 SG CYS T 102 44.178 95.450 105.509 1.00121.64 S ATOM 26712 SG CYS T 105 43.895 91.908 103.379 1.00124.41 S ATOM 26962 SG CYS T 137 41.951 93.113 106.816 1.00120.58 S ATOM 27125 SG CYS U 24 56.790 59.439 105.186 1.00153.49 S ATOM 27147 SG CYS U 27 55.512 63.179 104.600 1.00149.94 S ATOM 27590 SG CYS U 81 58.378 62.228 106.730 1.00163.48 S ATOM 27612 SG CYS U 84 54.683 61.423 107.745 1.00159.67 S ATOM 27296 SG CYS U 45 67.759 65.883 114.311 1.00147.76 S ATOM 27319 SG CYS U 48 71.447 65.743 114.674 1.00152.43 S ATOM 27515 SG CYS U 71 70.039 65.528 111.197 1.00155.85 S ATOM 27537 SG CYS U 74 69.660 62.590 113.369 1.00172.53 S ATOM 28221 SG CYS U 165 39.456 74.997 120.201 1.00122.20 S ATOM 28287 SG CYS U 173 36.704 77.323 118.905 1.00121.71 S ATOM 28335 SG CYS U 179 39.438 76.194 116.462 1.00121.79 S ATOM 37935 SG CYS Z 202 87.324 92.838 157.254 1.00118.86 S ATOM 38010 SG CYS Z 211 90.988 92.448 157.973 1.00113.72 S ATOM 38049 SG CYS Z 217 89.749 95.560 156.160 1.00107.64 S Time building chain proxies: 30.17, per 1000 atoms: 0.41 Number of scatterers: 73537 At special positions: 0 Unit cell: (211.05, 227.85, 286.65, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 12 29.99 S 251 16.00 P 352 15.00 Mg 7 11.99 O 14785 8.00 N 13330 7.00 C 44800 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 12.80 Conformation dependent library (CDL) restraints added in 7.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D 201 " pdb="ZN ZN D 201 " - pdb=" SG CYS D 85 " pdb="ZN ZN D 201 " - pdb=" SG CYS D 11 " pdb="ZN ZN D 201 " - pdb=" SG CYS D 49 " pdb="ZN ZN D 201 " - pdb=" SG CYS D 46 " pdb=" ZN D 202 " pdb="ZN ZN D 202 " - pdb=" SG CYS D 75 " pdb="ZN ZN D 202 " - pdb=" SG CYS D 72 " pdb="ZN ZN D 202 " - pdb=" SG CYS D 33 " pdb="ZN ZN D 202 " - pdb=" SG CYS D 30 " pdb=" ZN D 203 " pdb="ZN ZN D 203 " - pdb=" SG CYS D 23 " pdb="ZN ZN D 203 " - pdb=" SG CYS D 26 " pdb="ZN ZN D 203 " - pdb=" SG CYS D 58 " pdb="ZN ZN D 203 " - pdb=" SG CYS D 61 " pdb=" ZN I 600 " pdb="ZN ZN I 600 " - pdb=" NE2 HIS I 72 " pdb="ZN ZN I 600 " - pdb=" ND1 HIS I 78 " pdb="ZN ZN I 600 " - pdb=" SG CYS I 56 " pdb="ZN ZN I 600 " - pdb=" SG CYS I 59 " pdb=" ZN J1401 " pdb="ZN ZN J1401 " - pdb=" ND1 HIS J 425 " pdb="ZN ZN J1401 " - pdb=" ND1 HIS J 431 " pdb="ZN ZN J1401 " - pdb=" SG CYS J 408 " pdb="ZN ZN J1401 " - pdb=" SG CYS J 411 " pdb=" ZN T1000 " pdb="ZN ZN T1000 " - pdb=" SG CYS T 105 " pdb="ZN ZN T1000 " - pdb=" SG CYS T 117 " pdb="ZN ZN T1000 " - pdb=" SG CYS T 134 " pdb="ZN ZN T1000 " - pdb=" SG CYS T 119 " pdb=" ZN T1001 " pdb="ZN ZN T1001 " - pdb=" SG CYS T 101 " pdb="ZN ZN T1001 " - pdb=" SG CYS T 142 " pdb="ZN ZN T1001 " - pdb=" SG CYS T 139 " pdb="ZN ZN T1001 " - pdb=" SG CYS T 119 " pdb=" ZN T1002 " pdb="ZN ZN T1002 " - pdb=" SG CYS T 101 " pdb="ZN ZN T1002 " - pdb=" SG CYS T 137 " pdb="ZN ZN T1002 " - pdb=" SG CYS T 102 " pdb="ZN ZN T1002 " - pdb=" SG CYS T 105 " pdb=" ZN U 501 " pdb="ZN ZN U 501 " - pdb=" SG CYS U 81 " pdb="ZN ZN U 501 " - pdb=" SG CYS U 84 " pdb="ZN ZN U 501 " - pdb=" SG CYS U 27 " pdb="ZN ZN U 501 " - pdb=" SG CYS U 24 " pdb=" ZN U 502 " pdb="ZN ZN U 502 " - pdb=" SG CYS U 48 " pdb="ZN ZN U 502 " - pdb=" SG CYS U 71 " pdb="ZN ZN U 502 " - pdb=" SG CYS U 45 " pdb="ZN ZN U 502 " - pdb=" SG CYS U 74 " pdb=" ZN U 503 " pdb="ZN ZN U 503 " - pdb=" NE2 HIS U 183 " pdb="ZN ZN U 503 " - pdb=" SG CYS U 173 " pdb="ZN ZN U 503 " - pdb=" SG CYS U 165 " pdb="ZN ZN U 503 " - pdb=" SG CYS U 179 " pdb=" ZN Z 701 " pdb="ZN ZN Z 701 " - pdb=" NE2 HIS Z 221 " pdb="ZN ZN Z 701 " - pdb=" SG CYS Z 202 " pdb="ZN ZN Z 701 " - pdb=" SG CYS Z 211 " pdb="ZN ZN Z 701 " - pdb=" SG CYS Z 217 " Number of angles added : 57 19214 Ramachandran restraints generated. 9607 Oldfield, 0 Emsley, 9607 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 18428 Finding SS restraints... Secondary structure from input PDB file: 338 helices and 76 sheets defined 43.0% alpha, 15.4% beta 85 base pairs and 183 stacking pairs defined. Time for finding SS restraints: 19.62 Creating SS restraints... Processing helix chain 'A' and resid 189 through 195 Processing helix chain 'A' and resid 198 through 204 removed outlier: 3.542A pdb=" N ALA A 202 " --> pdb=" O GLY A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 244 removed outlier: 4.041A pdb=" N ASP A 243 " --> pdb=" O GLY A 240 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLY A 244 " --> pdb=" O GLY A 241 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 240 through 244' Processing helix chain 'A' and resid 808 through 823 Processing helix chain 'A' and resid 834 through 845 Processing helix chain 'A' and resid 1116 through 1134 removed outlier: 3.860A pdb=" N SER A1132 " --> pdb=" O MET A1128 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1146 Processing helix chain 'A' and resid 1158 through 1166 removed outlier: 3.866A pdb=" N ASN A1165 " --> pdb=" O CYS A1161 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER A1166 " --> pdb=" O GLU A1162 " (cutoff:3.500A) Processing helix chain 'A' and resid 1168 through 1179 Processing helix chain 'A' and resid 1182 through 1197 removed outlier: 3.893A pdb=" N TYR A1197 " --> pdb=" O ILE A1193 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 16 Processing helix chain 'B' and resid 27 through 46 Processing helix chain 'B' and resid 46 through 55 Processing helix chain 'B' and resid 60 through 74 removed outlier: 3.607A pdb=" N LEU B 73 " --> pdb=" O MET B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 77 No H-bonds generated for 'chain 'B' and resid 75 through 77' Processing helix chain 'C' and resid 491 through 507 Processing helix chain 'C' and resid 508 through 522 Processing helix chain 'C' and resid 522 through 527 Processing helix chain 'C' and resid 527 through 540 removed outlier: 3.722A pdb=" N LEU C 531 " --> pdb=" O GLY C 527 " (cutoff:3.500A) Proline residue: C 537 - end of helix Processing helix chain 'C' and resid 545 through 564 Processing helix chain 'C' and resid 565 through 568 Processing helix chain 'C' and resid 570 through 582 Proline residue: C 580 - end of helix Processing helix chain 'C' and resid 586 through 604 Processing helix chain 'C' and resid 605 through 618 removed outlier: 3.733A pdb=" N MET C 609 " --> pdb=" O GLY C 605 " (cutoff:3.500A) Proline residue: C 615 - end of helix removed outlier: 4.219A pdb=" N ASP C 618 " --> pdb=" O ARG C 614 " (cutoff:3.500A) Processing helix chain 'C' and resid 621 through 640 Processing helix chain 'C' and resid 640 through 653 removed outlier: 4.151A pdb=" N LEU C 644 " --> pdb=" O GLY C 640 " (cutoff:3.500A) Proline residue: C 646 - end of helix Processing helix chain 'C' and resid 657 through 676 Processing helix chain 'C' and resid 677 through 680 removed outlier: 3.577A pdb=" N LEU C 680 " --> pdb=" O CYS C 677 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 677 through 680' Processing helix chain 'C' and resid 682 through 695 removed outlier: 4.464A pdb=" N HIS C 692 " --> pdb=" O GLU C 688 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N GLY C 693 " --> pdb=" O ILE C 689 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N VAL C 695 " --> pdb=" O GLU C 691 " (cutoff:3.500A) Processing helix chain 'C' and resid 698 through 716 Processing helix chain 'C' and resid 724 through 726 No H-bonds generated for 'chain 'C' and resid 724 through 726' Processing helix chain 'C' and resid 727 through 735 removed outlier: 3.639A pdb=" N LEU C 731 " --> pdb=" O VAL C 727 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N TRP C 732 " --> pdb=" O LEU C 728 " (cutoff:3.500A) Processing helix chain 'C' and resid 740 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 777 removed outlier: 4.403A pdb=" N LEU C 771 " --> pdb=" O ARG C 767 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ILE C 772 " --> pdb=" O GLU C 768 " (cutoff:3.500A) Processing helix chain 'C' and resid 781 through 798 Processing helix chain 'C' and resid 803 through 810 Processing helix chain 'C' and resid 810 through 818 Processing helix chain 'C' and resid 820 through 826 removed outlier: 3.890A pdb=" N ASP C 826 " --> pdb=" O ARG C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 827 through 845 Processing helix chain 'C' and resid 845 through 853 removed outlier: 4.419A pdb=" N ILE C 849 " --> pdb=" O GLY C 845 " (cutoff:3.500A) Processing helix chain 'C' and resid 854 through 859 removed outlier: 3.509A pdb=" N LEU C 857 " --> pdb=" O VAL C 854 " (cutoff:3.500A) Processing helix chain 'C' and resid 861 through 879 Processing helix chain 'C' and resid 885 through 902 Processing helix chain 'C' and resid 907 through 922 Processing helix chain 'C' and resid 923 through 926 removed outlier: 3.839A pdb=" N LYS C 926 " --> pdb=" O LYS C 923 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 923 through 926' Processing helix chain 'C' and resid 928 through 940 Processing helix chain 'C' and resid 944 through 965 removed outlier: 3.692A pdb=" N ARG C 948 " --> pdb=" O SER C 944 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N VAL C 960 " --> pdb=" O SER C 956 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N VAL C 961 " --> pdb=" O ARG C 957 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N CYS C 965 " --> pdb=" O VAL C 961 " (cutoff:3.500A) Processing helix chain 'C' and resid 967 through 981 removed outlier: 3.513A pdb=" N MET C 971 " --> pdb=" O GLU C 967 " (cutoff:3.500A) Processing helix chain 'C' and resid 982 through 984 No H-bonds generated for 'chain 'C' and resid 982 through 984' Processing helix chain 'C' and resid 986 through 1005 Processing helix chain 'C' and resid 1012 through 1021 Proline residue: C1018 - end of helix Processing helix chain 'C' and resid 1022 through 1026 Processing helix chain 'C' and resid 1028 through 1046 Processing helix chain 'C' and resid 1047 through 1050 removed outlier: 3.586A pdb=" N VAL C1050 " --> pdb=" O ALA C1047 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1047 through 1050' Processing helix chain 'C' and resid 1051 through 1066 removed outlier: 3.877A pdb=" N GLU C1064 " --> pdb=" O PHE C1060 " (cutoff:3.500A) Processing helix chain 'C' and resid 1070 through 1089 removed outlier: 3.504A pdb=" N ARG C1074 " --> pdb=" O LYS C1070 " (cutoff:3.500A) Processing helix chain 'C' and resid 1091 through 1104 Processing helix chain 'C' and resid 1109 through 1123 Processing helix chain 'C' and resid 1128 through 1135 Processing helix chain 'C' and resid 1136 through 1138 No H-bonds generated for 'chain 'C' and resid 1136 through 1138' Processing helix chain 'C' and resid 1142 through 1159 Processing helix chain 'C' and resid 1160 through 1164 removed outlier: 4.257A pdb=" N LYS C1163 " --> pdb=" O GLU C1160 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ASP C1164 " --> pdb=" O MET C1161 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1160 through 1164' Processing helix chain 'C' and resid 1165 through 1178 Proline residue: C1171 - end of helix removed outlier: 3.595A pdb=" N MET C1178 " --> pdb=" O GLU C1174 " (cutoff:3.500A) Processing helix chain 'C' and resid 1181 through 1199 removed outlier: 3.682A pdb=" N ARG C1185 " --> pdb=" O ASP C1181 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL C1199 " --> pdb=" O MET C1195 " (cutoff:3.500A) Processing helix chain 'C' and resid 1204 through 1216 removed outlier: 3.731A pdb=" N TYR C1214 " --> pdb=" O HIS C1210 " (cutoff:3.500A) Processing helix chain 'C' and resid 1217 through 1221 removed outlier: 4.236A pdb=" N PHE C1220 " --> pdb=" O PRO C1217 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLU C1221 " --> pdb=" O ASN C1218 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1217 through 1221' Processing helix chain 'C' and resid 1223 through 1241 Processing helix chain 'C' and resid 1242 through 1252 removed outlier: 3.849A pdb=" N MET C1246 " --> pdb=" O GLY C1242 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N GLN C1252 " --> pdb=" O GLN C1248 " (cutoff:3.500A) Processing helix chain 'C' and resid 1258 through 1276 Processing helix chain 'D' and resid 23 through 27 removed outlier: 3.606A pdb=" N CYS D 26 " --> pdb=" O CYS D 23 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASP D 27 " --> pdb=" O GLU D 24 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 23 through 27' Processing helix chain 'D' and resid 79 through 84 removed outlier: 3.783A pdb=" N ARG D 82 " --> pdb=" O GLU D 79 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N GLY D 84 " --> pdb=" O ASP D 81 " (cutoff:3.500A) Processing helix chain 'E' and resid 461 through 469 Processing helix chain 'E' and resid 471 through 475 Processing helix chain 'E' and resid 478 through 482 removed outlier: 3.582A pdb=" N THR E 481 " --> pdb=" O HIS E 478 " (cutoff:3.500A) Processing helix chain 'E' and resid 484 through 493 Processing helix chain 'E' and resid 501 through 505 removed outlier: 3.588A pdb=" N TRP E 504 " --> pdb=" O PRO E 501 " (cutoff:3.500A) Processing helix chain 'E' and resid 525 through 532 Processing helix chain 'E' and resid 532 through 546 removed outlier: 4.441A pdb=" N MET E 536 " --> pdb=" O GLY E 532 " (cutoff:3.500A) Processing helix chain 'E' and resid 548 through 558 Processing helix chain 'E' and resid 568 through 576 Processing helix chain 'E' and resid 610 through 617 Processing helix chain 'E' and resid 632 through 639 Processing helix chain 'F' and resid 25 through 36 Processing helix chain 'F' and resid 63 through 73 Processing helix chain 'G' and resid 102 through 136 removed outlier: 3.914A pdb=" N LYS G 106 " --> pdb=" O SER G 102 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ASP G 125 " --> pdb=" O ASN G 121 " (cutoff:3.500A) Proline residue: G 126 - end of helix Proline residue: G 131 - end of helix removed outlier: 4.049A pdb=" N GLY G 136 " --> pdb=" O MET G 132 " (cutoff:3.500A) Processing helix chain 'G' and resid 166 through 176 Processing helix chain 'I' and resid 18 through 42 Processing helix chain 'I' and resid 65 through 71 removed outlier: 3.695A pdb=" N TYR I 69 " --> pdb=" O ASN I 65 " (cutoff:3.500A) Processing helix chain 'I' and resid 78 through 87 removed outlier: 4.167A pdb=" N ALA I 87 " --> pdb=" O ALA I 83 " (cutoff:3.500A) Processing helix chain 'J' and resid 394 through 399 Processing helix chain 'J' and resid 418 through 424 removed outlier: 3.636A pdb=" N PHE J 422 " --> pdb=" O GLY J 418 " (cutoff:3.500A) Processing helix chain 'J' and resid 429 through 439 removed outlier: 3.529A pdb=" N GLY J 439 " --> pdb=" O MET J 435 " (cutoff:3.500A) Processing helix chain 'J' and resid 444 through 448 removed outlier: 3.804A pdb=" N ASN J 448 " --> pdb=" O HIS J 445 " (cutoff:3.500A) Processing helix chain 'J' and resid 452 through 458 removed outlier: 3.667A pdb=" N ALA J 455 " --> pdb=" O ILE J 452 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU J 458 " --> pdb=" O ALA J 455 " (cutoff:3.500A) Processing helix chain 'L' and resid 531 through 540 Processing helix chain 'L' and resid 543 through 557 Processing helix chain 'N' and resid 162 through 193 Processing helix chain 'N' and resid 224 through 257 removed outlier: 4.452A pdb=" N GLU N 248 " --> pdb=" O LEU N 244 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ALA N 249 " --> pdb=" O GLU N 245 " (cutoff:3.500A) Processing helix chain 'N' and resid 265 through 296 Processing helix chain 'N' and resid 324 through 338 Processing helix chain 'N' and resid 385 through 398 Processing helix chain 'N' and resid 404 through 415 Processing helix chain 'N' and resid 427 through 438 Proline residue: N 433 - end of helix Processing helix chain 'N' and resid 454 through 470 Processing helix chain 'N' and resid 498 through 508 Processing helix chain 'N' and resid 526 through 543 Processing helix chain 'N' and resid 557 through 564 Processing helix chain 'N' and resid 592 through 605 removed outlier: 3.811A pdb=" N VAL N 596 " --> pdb=" O LEU N 592 " (cutoff:3.500A) Processing helix chain 'N' and resid 617 through 634 removed outlier: 3.705A pdb=" N ALA N 623 " --> pdb=" O GLU N 619 " (cutoff:3.500A) Processing helix chain 'N' and resid 652 through 658 Processing helix chain 'N' and resid 675 through 680 Processing helix chain 'N' and resid 715 through 727 Processing helix chain 'N' and resid 739 through 745 Processing helix chain 'N' and resid 753 through 758 removed outlier: 3.700A pdb=" N ARG N 757 " --> pdb=" O PRO N 753 " (cutoff:3.500A) Processing helix chain 'N' and resid 763 through 770 Processing helix chain 'N' and resid 785 through 799 Processing helix chain 'N' and resid 809 through 818 removed outlier: 4.452A pdb=" N LEU N 818 " --> pdb=" O LYS N 814 " (cutoff:3.500A) Processing helix chain 'N' and resid 821 through 831 removed outlier: 5.058A pdb=" N MET N 827 " --> pdb=" O MET N 823 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N ILE N 828 " --> pdb=" O LEU N 824 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU N 829 " --> pdb=" O SER N 825 " (cutoff:3.500A) Processing helix chain 'N' and resid 836 through 848 removed outlier: 3.504A pdb=" N ILE N 840 " --> pdb=" O CYS N 836 " (cutoff:3.500A) Processing helix chain 'N' and resid 861 through 870 Processing helix chain 'N' and resid 877 through 889 Processing helix chain 'N' and resid 894 through 901 removed outlier: 3.731A pdb=" N CYS N 898 " --> pdb=" O SER N 894 " (cutoff:3.500A) Processing helix chain 'N' and resid 907 through 921 Processing helix chain 'N' and resid 935 through 947 Processing helix chain 'P' and resid 12 through 27 Processing helix chain 'P' and resid 31 through 36 Processing helix chain 'P' and resid 42 through 53 Processing helix chain 'P' and resid 64 through 78 Processing helix chain 'P' and resid 81 through 90 Proline residue: P 87 - end of helix Processing helix chain 'P' and resid 92 through 108 Processing helix chain 'P' and resid 171 through 190 Processing helix chain 'Q' and resid 31 through 35 removed outlier: 3.925A pdb=" N LEU Q 35 " --> pdb=" O SER Q 32 " (cutoff:3.500A) Processing helix chain 'Q' and resid 50 through 55 Processing helix chain 'Q' and resid 58 through 75 removed outlier: 4.154A pdb=" N GLU Q 62 " --> pdb=" O ASP Q 58 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ASN Q 75 " --> pdb=" O ALA Q 71 " (cutoff:3.500A) Processing helix chain 'Q' and resid 203 through 209 removed outlier: 3.967A pdb=" N ASP Q 207 " --> pdb=" O GLN Q 204 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARG Q 209 " --> pdb=" O LYS Q 206 " (cutoff:3.500A) Processing helix chain 'Q' and resid 217 through 228 Processing helix chain 'T' and resid 12 through 16 removed outlier: 3.506A pdb=" N TRP T 15 " --> pdb=" O PRO T 12 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N GLU T 16 " --> pdb=" O ASP T 13 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 12 through 16' Processing helix chain 'T' and resid 18 through 35 removed outlier: 3.856A pdb=" N LEU T 22 " --> pdb=" O ILE T 18 " (cutoff:3.500A) Processing helix chain 'T' and resid 46 through 65 removed outlier: 4.036A pdb=" N PHE T 50 " --> pdb=" O LEU T 46 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ARG T 51 " --> pdb=" O TRP T 47 " (cutoff:3.500A) Processing helix chain 'T' and resid 71 through 81 Processing helix chain 'T' and resid 85 through 93 Processing helix chain 'T' and resid 103 through 107 removed outlier: 3.755A pdb=" N ILE T 106 " --> pdb=" O LEU T 103 " (cutoff:3.500A) Processing helix chain 'T' and resid 117 through 121 Processing helix chain 'T' and resid 122 through 126 removed outlier: 3.639A pdb=" N LEU T 126 " --> pdb=" O LYS T 123 " (cutoff:3.500A) Processing helix chain 'U' and resid 24 through 29 Processing helix chain 'U' and resid 71 through 79 Processing helix chain 'U' and resid 93 through 101 Processing helix chain 'U' and resid 110 through 127 Processing helix chain 'U' and resid 156 through 160 removed outlier: 3.830A pdb=" N ARG U 159 " --> pdb=" O TYR U 156 " (cutoff:3.500A) Processing helix chain 'U' and resid 165 through 170 Processing helix chain 'U' and resid 175 through 179 Processing helix chain 'U' and resid 191 through 195 removed outlier: 3.906A pdb=" N ASP U 195 " --> pdb=" O PRO U 192 " (cutoff:3.500A) Processing helix chain 'U' and resid 197 through 204 Processing helix chain 'U' and resid 207 through 219 Processing helix chain 'U' and resid 244 through 253 removed outlier: 3.612A pdb=" N LEU U 248 " --> pdb=" O THR U 244 " (cutoff:3.500A) Processing helix chain 'U' and resid 276 through 287 Processing helix chain 'V' and resid 21 through 34 Processing helix chain 'V' and resid 132 through 141 Processing helix chain 'V' and resid 204 through 228 Processing helix chain 'V' and resid 252 through 261 Processing helix chain 'V' and resid 290 through 299 Processing helix chain 'W' and resid 150 through 172 Processing helix chain 'W' and resid 177 through 188 removed outlier: 3.930A pdb=" N ILE W 181 " --> pdb=" O ASN W 177 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLU W 188 " --> pdb=" O GLU W 184 " (cutoff:3.500A) Processing helix chain 'W' and resid 193 through 208 Processing helix chain 'W' and resid 211 through 226 Processing helix chain 'W' and resid 226 through 247 removed outlier: 3.552A pdb=" N GLY W 230 " --> pdb=" O PHE W 226 " (cutoff:3.500A) Processing helix chain 'W' and resid 249 through 266 Processing helix chain 'W' and resid 270 through 284 removed outlier: 4.116A pdb=" N CYS W 274 " --> pdb=" O HIS W 270 " (cutoff:3.500A) Processing helix chain 'W' and resid 286 through 300 Processing helix chain 'W' and resid 300 through 308 Processing helix chain 'W' and resid 309 through 324 Processing helix chain 'W' and resid 329 through 346 Processing helix chain 'W' and resid 390 through 406 Processing helix chain 'W' and resid 451 through 466 removed outlier: 3.587A pdb=" N SER W 466 " --> pdb=" O ALA W 462 " (cutoff:3.500A) Processing helix chain 'W' and resid 468 through 479 removed outlier: 3.640A pdb=" N MET W 479 " --> pdb=" O LYS W 475 " (cutoff:3.500A) Processing helix chain 'W' and resid 482 through 484 No H-bonds generated for 'chain 'W' and resid 482 through 484' Processing helix chain 'W' and resid 485 through 499 Processing helix chain 'W' and resid 504 through 518 removed outlier: 4.162A pdb=" N GLY W 508 " --> pdb=" O GLU W 504 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LYS W 518 " --> pdb=" O PHE W 514 " (cutoff:3.500A) Processing helix chain 'W' and resid 518 through 535 removed outlier: 3.708A pdb=" N MET W 522 " --> pdb=" O LYS W 518 " (cutoff:3.500A) Processing helix chain 'W' and resid 540 through 557 Processing helix chain 'W' and resid 561 through 568 removed outlier: 3.935A pdb=" N VAL W 564 " --> pdb=" O PRO W 561 " (cutoff:3.500A) Processing helix chain 'W' and resid 576 through 594 Processing helix chain 'W' and resid 595 through 604 Processing helix chain 'W' and resid 620 through 634 Processing helix chain 'W' and resid 640 through 649 Processing helix chain 'X' and resid 217 through 238 Processing helix chain 'X' and resid 241 through 255 removed outlier: 4.133A pdb=" N TRP X 245 " --> pdb=" O VAL X 241 " (cutoff:3.500A) Processing helix chain 'X' and resid 257 through 272 Processing helix chain 'X' and resid 275 through 289 removed outlier: 3.952A pdb=" N TRP X 279 " --> pdb=" O ASN X 275 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASN X 289 " --> pdb=" O MET X 285 " (cutoff:3.500A) Processing helix chain 'X' and resid 291 through 306 Processing helix chain 'X' and resid 309 through 322 removed outlier: 3.938A pdb=" N TRP X 313 " --> pdb=" O VAL X 309 " (cutoff:3.500A) Processing helix chain 'X' and resid 328 through 338 removed outlier: 3.567A pdb=" N ARG X 335 " --> pdb=" O GLN X 331 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N TRP X 336 " --> pdb=" O VAL X 332 " (cutoff:3.500A) Processing helix chain 'X' and resid 342 through 356 removed outlier: 3.820A pdb=" N TRP X 346 " --> pdb=" O GLU X 342 " (cutoff:3.500A) Processing helix chain 'X' and resid 359 through 373 Processing helix chain 'X' and resid 375 through 389 Processing helix chain 'X' and resid 391 through 406 Processing helix chain 'X' and resid 414 through 427 Processing helix chain 'X' and resid 427 through 442 Processing helix chain 'X' and resid 449 through 461 Processing helix chain 'Y' and resid 98 through 103 Processing helix chain 'Y' and resid 115 through 119 Processing helix chain 'Y' and resid 136 through 163 Processing helix chain 'Y' and resid 238 through 245 Processing helix chain 'Y' and resid 286 through 337 Processing helix chain 'Y' and resid 353 through 373 Processing helix chain 'Y' and resid 377 through 382 Processing helix chain 'Y' and resid 388 through 394 Processing helix chain 'Z' and resid 202 through 207 Processing helix chain 'Z' and resid 213 through 217 removed outlier: 3.526A pdb=" N CYS Z 217 " --> pdb=" O GLY Z 214 " (cutoff:3.500A) Processing helix chain 'Z' and resid 228 through 235 Processing helix chain 'Z' and resid 283 through 293 Processing helix chain 'a' and resid 62 through 72 removed outlier: 4.334A pdb=" N VAL a 66 " --> pdb=" O PRO a 62 " (cutoff:3.500A) Processing helix chain 'a' and resid 73 through 77 removed outlier: 3.545A pdb=" N THR a 77 " --> pdb=" O GLY a 74 " (cutoff:3.500A) Processing helix chain 'a' and resid 84 through 91 removed outlier: 3.966A pdb=" N ALA a 91 " --> pdb=" O VAL a 87 " (cutoff:3.500A) Processing helix chain 'a' and resid 94 through 104 Processing helix chain 'a' and resid 136 through 158 Processing helix chain 'a' and resid 177 through 182 Processing helix chain 'a' and resid 200 through 204 removed outlier: 3.829A pdb=" N VAL a 203 " --> pdb=" O ASP a 200 " (cutoff:3.500A) Processing helix chain 'a' and resid 231 through 242 Processing helix chain 'a' and resid 251 through 255 removed outlier: 4.145A pdb=" N TYR a 254 " --> pdb=" O ASP a 251 " (cutoff:3.500A) Processing helix chain 'a' and resid 259 through 270 Processing helix chain 'a' and resid 294 through 298 Processing helix chain 'a' and resid 309 through 316 removed outlier: 3.604A pdb=" N LYS a 313 " --> pdb=" O ARG a 309 " (cutoff:3.500A) Processing helix chain 'a' and resid 397 through 406 removed outlier: 3.776A pdb=" N TRP a 406 " --> pdb=" O ILE a 402 " (cutoff:3.500A) Processing helix chain 'a' and resid 408 through 412 removed outlier: 3.871A pdb=" N ASN a 412 " --> pdb=" O ARG a 409 " (cutoff:3.500A) Processing helix chain 'a' and resid 427 through 433 removed outlier: 3.740A pdb=" N TYR a 431 " --> pdb=" O VAL a 427 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU a 433 " --> pdb=" O ASN a 429 " (cutoff:3.500A) Processing helix chain 'a' and resid 440 through 460 removed outlier: 3.561A pdb=" N ARG a 444 " --> pdb=" O PRO a 440 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS a 460 " --> pdb=" O LEU a 456 " (cutoff:3.500A) Processing helix chain 'a' and resid 471 through 478 Processing helix chain 'a' and resid 489 through 511 Processing helix chain 'a' and resid 531 through 538 Processing helix chain 'a' and resid 541 through 566 Processing helix chain 'a' and resid 570 through 584 Processing helix chain 'a' and resid 584 through 589 Processing helix chain 'a' and resid 590 through 594 removed outlier: 3.787A pdb=" N ARG a 593 " --> pdb=" O GLY a 590 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N TYR a 594 " --> pdb=" O MET a 591 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 590 through 594' Processing helix chain 'a' and resid 595 through 596 No H-bonds generated for 'chain 'a' and resid 595 through 596' Processing helix chain 'a' and resid 597 through 617 removed outlier: 4.027A pdb=" N GLN a 601 " --> pdb=" O LYS a 597 " (cutoff:3.500A) Processing helix chain 'a' and resid 630 through 662 Proline residue: a 646 - end of helix Processing helix chain 'a' and resid 677 through 695 Processing helix chain 'a' and resid 705 through 722 Processing helix chain 'a' and resid 732 through 763 Processing helix chain 'a' and resid 768 through 798 Processing helix chain 'a' and resid 803 through 820 Processing helix chain 'a' and resid 834 through 848 Processing helix chain 'a' and resid 857 through 873 Processing helix chain 'a' and resid 873 through 888 Processing helix chain 'a' and resid 912 through 933 Processing helix chain 'a' and resid 947 through 961 Processing helix chain 'a' and resid 984 through 988 removed outlier: 3.518A pdb=" N LYS a 987 " --> pdb=" O MET a 984 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ILE a 988 " --> pdb=" O TYR a 985 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 984 through 988' Processing helix chain 'a' and resid 989 through 998 Processing helix chain 'a' and resid 1002 through 1014 removed outlier: 3.945A pdb=" N ASN a1013 " --> pdb=" O MET a1009 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ASN a1014 " --> pdb=" O THR a1010 " (cutoff:3.500A) Processing helix chain 'a' and resid 1036 through 1054 removed outlier: 3.659A pdb=" N ILE a1040 " --> pdb=" O PHE a1036 " (cutoff:3.500A) Processing helix chain 'a' and resid 1054 through 1063 Processing helix chain 'a' and resid 1076 through 1081 Processing helix chain 'a' and resid 1102 through 1117 Processing helix chain 'a' and resid 1143 through 1161 removed outlier: 3.687A pdb=" N ARG a1160 " --> pdb=" O ASP a1156 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LEU a1161 " --> pdb=" O ILE a1157 " (cutoff:3.500A) Processing helix chain 'a' and resid 1233 through 1251 Processing helix chain 'a' and resid 1252 through 1254 No H-bonds generated for 'chain 'a' and resid 1252 through 1254' Processing helix chain 'a' and resid 1255 through 1275 Processing helix chain 'a' and resid 1276 through 1279 removed outlier: 3.601A pdb=" N VAL a1279 " --> pdb=" O GLU a1276 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 1276 through 1279' Processing helix chain 'a' and resid 1281 through 1303 removed outlier: 3.643A pdb=" N LEU a1303 " --> pdb=" O ILE a1299 " (cutoff:3.500A) Processing helix chain 'a' and resid 1313 through 1318 removed outlier: 3.605A pdb=" N THR a1318 " --> pdb=" O VAL a1314 " (cutoff:3.500A) Processing helix chain 'a' and resid 1319 through 1323 Processing helix chain 'a' and resid 1368 through 1372 Processing helix chain 'a' and resid 1374 through 1400 Processing helix chain 'a' and resid 1404 through 1409 removed outlier: 3.922A pdb=" N LEU a1408 " --> pdb=" O THR a1404 " (cutoff:3.500A) Processing helix chain 'a' and resid 1418 through 1424 removed outlier: 3.544A pdb=" N GLN a1424 " --> pdb=" O THR a1421 " (cutoff:3.500A) Processing helix chain 'a' and resid 1426 through 1431 Processing helix chain 'a' and resid 1436 through 1444 Processing helix chain 'a' and resid 1467 through 1478 removed outlier: 4.023A pdb=" N ARG a1471 " --> pdb=" O LEU a1467 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N THR a1472 " --> pdb=" O ASN a1468 " (cutoff:3.500A) Processing helix chain 'a' and resid 1479 through 1486 removed outlier: 3.545A pdb=" N GLY a1483 " --> pdb=" O GLY a1479 " (cutoff:3.500A) Processing helix chain 'a' and resid 1490 through 1494 removed outlier: 3.508A pdb=" N TYR a1494 " --> pdb=" O LYS a1491 " (cutoff:3.500A) Processing helix chain 'a' and resid 1527 through 1538 removed outlier: 4.473A pdb=" N ASN a1531 " --> pdb=" O ASN a1527 " (cutoff:3.500A) Processing helix chain 'a' and resid 1538 through 1543 Processing helix chain 'a' and resid 1566 through 1577 Processing helix chain 'a' and resid 1580 through 1600 Processing helix chain 'a' and resid 1601 through 1604 removed outlier: 3.886A pdb=" N LEU a1604 " --> pdb=" O LEU a1601 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 1601 through 1604' Processing helix chain 'a' and resid 1615 through 1619 removed outlier: 4.140A pdb=" N SER a1619 " --> pdb=" O PRO a1616 " (cutoff:3.500A) Processing helix chain 'a' and resid 1676 through 1689 Processing helix chain 'a' and resid 1721 through 1737 removed outlier: 3.960A pdb=" N LEU a1725 " --> pdb=" O GLY a1721 " (cutoff:3.500A) Processing helix chain 'a' and resid 1737 through 1752 Processing helix chain 'a' and resid 1766 through 1771 removed outlier: 3.797A pdb=" N LEU a1771 " --> pdb=" O ASN a1767 " (cutoff:3.500A) Processing helix chain 'a' and resid 1835 through 1852 Processing helix chain 'a' and resid 1869 through 1875 Processing helix chain 'a' and resid 1892 through 1896 Processing helix chain 'a' and resid 1899 through 1908 Processing helix chain 'a' and resid 1928 through 1946 Processing helix chain 'a' and resid 1946 through 1955 Processing helix chain 'a' and resid 1957 through 1961 removed outlier: 3.917A pdb=" N THR a1960 " --> pdb=" O ASP a1957 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ILE a1961 " --> pdb=" O LYS a1958 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 1957 through 1961' Processing helix chain 'a' and resid 1972 through 1996 Processing helix chain 'a' and resid 2003 through 2013 Processing helix chain 'b' and resid 68 through 74 Processing helix chain 'b' and resid 115 through 123 Processing helix chain 'b' and resid 141 through 154 Processing helix chain 'b' and resid 171 through 178 Processing helix chain 'b' and resid 208 through 210 No H-bonds generated for 'chain 'b' and resid 208 through 210' Processing helix chain 'b' and resid 211 through 222 removed outlier: 3.709A pdb=" N VAL b 215 " --> pdb=" O PHE b 211 " (cutoff:3.500A) Processing helix chain 'b' and resid 236 through 249 Processing helix chain 'b' and resid 260 through 265 removed outlier: 3.694A pdb=" N ILE b 264 " --> pdb=" O ILE b 260 " (cutoff:3.500A) Processing helix chain 'b' and resid 270 through 293 Processing helix chain 'b' and resid 319 through 331 removed outlier: 3.529A pdb=" N PHE b 323 " --> pdb=" O THR b 319 " (cutoff:3.500A) Processing helix chain 'b' and resid 335 through 344 removed outlier: 4.681A pdb=" N TRP b 344 " --> pdb=" O ALA b 340 " (cutoff:3.500A) Processing helix chain 'b' and resid 367 through 373 Processing helix chain 'b' and resid 373 through 387 Processing helix chain 'b' and resid 391 through 399 Processing helix chain 'b' and resid 411 through 425 Processing helix chain 'b' and resid 428 through 438 Processing helix chain 'b' and resid 440 through 453 removed outlier: 5.349A pdb=" N LYS b 446 " --> pdb=" O LYS b 442 " (cutoff:3.500A) Proline residue: b 447 - end of helix Processing helix chain 'b' and resid 459 through 467 Processing helix chain 'b' and resid 596 through 598 No H-bonds generated for 'chain 'b' and resid 596 through 598' Processing helix chain 'b' and resid 599 through 614 removed outlier: 3.852A pdb=" N MET b 603 " --> pdb=" O GLU b 599 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU b 604 " --> pdb=" O LEU b 600 " (cutoff:3.500A) Processing helix chain 'b' and resid 633 through 647 Processing helix chain 'b' and resid 695 through 702 Processing helix chain 'b' and resid 710 through 723 removed outlier: 3.962A pdb=" N LYS b 721 " --> pdb=" O PHE b 717 " (cutoff:3.500A) Processing helix chain 'b' and resid 725 through 730 Processing helix chain 'b' and resid 755 through 777 removed outlier: 4.453A pdb=" N ASP b 764 " --> pdb=" O GLY b 760 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N SER b 765 " --> pdb=" O SER b 761 " (cutoff:3.500A) Processing helix chain 'b' and resid 807 through 822 removed outlier: 3.733A pdb=" N THR b 811 " --> pdb=" O GLN b 807 " (cutoff:3.500A) Processing helix chain 'b' and resid 842 through 853 Processing helix chain 'b' and resid 882 through 891 Processing helix chain 'b' and resid 925 through 927 No H-bonds generated for 'chain 'b' and resid 925 through 927' Processing helix chain 'b' and resid 928 through 941 Processing helix chain 'h' and resid 7 through 14 Processing helix chain 'i' and resid 16 through 28 Processing helix chain 'j' and resid 6 through 13 Processing helix chain 'k' and resid 3 through 10 Processing helix chain 'l' and resid 28 through 40 Processing helix chain 'p' and resid 32 through 45 Processing helix chain 'p' and resid 135 through 144 Processing helix chain 'q' and resid 55 through 72 removed outlier: 3.504A pdb=" N LYS q 63 " --> pdb=" O ASP q 59 " (cutoff:3.500A) Processing helix chain 'q' and resid 81 through 100 Processing helix chain 'u' and resid 63 through 67 Processing helix chain 'u' and resid 128 through 137 Processing helix chain 'u' and resid 201 through 215 Processing helix chain 'u' and resid 234 through 238 removed outlier: 3.697A pdb=" N ALA u 238 " --> pdb=" O LYS u 235 " (cutoff:3.500A) Processing helix chain 'u' and resid 244 through 252 Processing helix chain 'u' and resid 300 through 313 Processing helix chain 'u' and resid 403 through 412 Processing helix chain 'u' and resid 436 through 451 Processing sheet with id=AA1, first strand: chain 'A' and resid 1083 through 1087 removed outlier: 3.761A pdb=" N LEU A1099 " --> pdb=" O LEU A1111 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ILE A1108 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL A1112 " --> pdb=" O TYR A 4 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N LEU A 3 " --> pdb=" O ILE A1156 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 16 through 20 removed outlier: 3.790A pdb=" N PHE A 16 " --> pdb=" O SER A 33 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 62 through 69 removed outlier: 7.374A pdb=" N ASP A 76 " --> pdb=" O TYR A 92 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N TYR A 92 " --> pdb=" O ASP A 76 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL A 88 " --> pdb=" O VAL A 80 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N SER A 82 " --> pdb=" O ARG A 86 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ARG A 86 " --> pdb=" O SER A 82 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N ILE A 87 " --> pdb=" O GLN A 104 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N GLN A 104 " --> pdb=" O ILE A 87 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ILE A 89 " --> pdb=" O ILE A 102 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 120 through 123 removed outlier: 3.612A pdb=" N VAL A 141 " --> pdb=" O LEU A 158 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 145 through 146 Processing sheet with id=AA6, first strand: chain 'A' and resid 165 through 173 removed outlier: 5.421A pdb=" N VAL A 167 " --> pdb=" O MET A 187 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N MET A 187 " --> pdb=" O VAL A 167 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N HIS A 169 " --> pdb=" O LEU A 185 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N MET A 181 " --> pdb=" O VAL A 173 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N GLU A 212 " --> pdb=" O ARG A 222 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N ARG A 222 " --> pdb=" O GLU A 212 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ASP A 214 " --> pdb=" O VAL A 220 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N VAL A 220 " --> pdb=" O ASP A 214 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 234 through 237 removed outlier: 3.886A pdb=" N PHE A 234 " --> pdb=" O CYS A 251 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N CYS A 251 " --> pdb=" O PHE A 234 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N TYR A 255 " --> pdb=" O SER A 252 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 290 through 294 removed outlier: 5.862A pdb=" N LYS A 312 " --> pdb=" O TYR A 329 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N TYR A 329 " --> pdb=" O LYS A 312 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N THR A 314 " --> pdb=" O LEU A 327 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N LEU A 327 " --> pdb=" O THR A 314 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 336 through 342 removed outlier: 3.509A pdb=" N ALA A 338 " --> pdb=" O ALA A 350 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N PHE A 346 " --> pdb=" O LEU A 342 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N HIS A 356 " --> pdb=" O GLU A 400 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N GLU A 400 " --> pdb=" O HIS A 356 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N LEU A 358 " --> pdb=" O VAL A 398 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 407 through 413 removed outlier: 6.376A pdb=" N ILE A 407 " --> pdb=" O GLY A 428 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N GLY A 428 " --> pdb=" O ILE A 407 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 458 through 461 Processing sheet with id=AB3, first strand: chain 'A' and resid 507 through 509 Processing sheet with id=AB4, first strand: chain 'A' and resid 546 through 548 Processing sheet with id=AB5, first strand: chain 'A' and resid 587 through 592 removed outlier: 7.104A pdb=" N GLY A 608 " --> pdb=" O VAL A 588 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N MET A 590 " --> pdb=" O ALA A 606 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N ALA A 606 " --> pdb=" O MET A 590 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N THR A 613 " --> pdb=" O LEU A 609 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 637 through 643 Processing sheet with id=AB7, first strand: chain 'A' and resid 703 through 706 removed outlier: 4.315A pdb=" N GLU A 710 " --> pdb=" O SER A 724 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N TRP A 720 " --> pdb=" O ALA A 714 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LEU A 721 " --> pdb=" O THR A 732 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N THR A 732 " --> pdb=" O LEU A 721 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 741 through 745 removed outlier: 3.638A pdb=" N THR A 761 " --> pdb=" O SER A 758 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 785 through 790 removed outlier: 5.080A pdb=" N THR A 802 " --> pdb=" O PRO A 785 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LYS A 787 " --> pdb=" O ILE A 800 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL A 789 " --> pdb=" O ILE A 798 " (cutoff:3.500A) removed outlier: 8.161A pdb=" N SER A 864 " --> pdb=" O GLN A 881 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N GLN A 881 " --> pdb=" O SER A 864 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ILE A 866 " --> pdb=" O LEU A 879 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N LEU A 879 " --> pdb=" O ILE A 866 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N VAL A 868 " --> pdb=" O LEU A 877 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 886 through 890 removed outlier: 6.374A pdb=" N GLY A 908 " --> pdb=" O PHE A 889 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLY A 922 " --> pdb=" O LYS A 911 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 951 through 954 removed outlier: 3.984A pdb=" N ALA A 951 " --> pdb=" O GLY A 962 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU A 967 " --> pdb=" O ASN A 983 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASN A 983 " --> pdb=" O LEU A 967 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 992 through 995 removed outlier: 3.954A pdb=" N GLY A 992 " --> pdb=" O SER A1003 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N TRP A1011 " --> pdb=" O PHE A1024 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ILE A1022 " --> pdb=" O ARG A1013 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LYS A1015 " --> pdb=" O GLN A1020 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 1043 through 1047 removed outlier: 6.165A pdb=" N ARG A1057 " --> pdb=" O VAL A1073 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N VAL A1073 " --> pdb=" O ARG A1057 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 39 through 42 removed outlier: 3.528A pdb=" N THR D 41 " --> pdb=" O TYR D 71 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 39 through 43 Processing sheet with id=AC7, first strand: chain 'F' and resid 78 through 79 Processing sheet with id=AC8, first strand: chain 'I' and resid 46 through 48 removed outlier: 3.819A pdb=" N TYR I 54 " --> pdb=" O HIS I 63 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'J' and resid 405 through 408 Processing sheet with id=AD1, first strand: chain 'N' and resid 419 through 422 Processing sheet with id=AD2, first strand: chain 'N' and resid 484 through 486 removed outlier: 4.085A pdb=" N THR N 497 " --> pdb=" O SER N 480 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ILE N 448 " --> pdb=" O ARG N 494 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N MET N 496 " --> pdb=" O ILE N 448 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N CYS N 450 " --> pdb=" O MET N 496 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N LYS N 447 " --> pdb=" O VAL N 516 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N MET N 518 " --> pdb=" O LYS N 447 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ALA N 449 " --> pdb=" O MET N 518 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'N' and resid 644 through 645 removed outlier: 6.487A pdb=" N ILE N 611 " --> pdb=" O VAL N 671 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N ALA N 673 " --> pdb=" O ILE N 611 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N VAL N 613 " --> pdb=" O ALA N 673 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ASP N 610 " --> pdb=" O ILE N 687 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N VAL N 689 " --> pdb=" O ASP N 610 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N LEU N 612 " --> pdb=" O VAL N 689 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N ASP N 691 " --> pdb=" O LEU N 612 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N PHE N 614 " --> pdb=" O ASP N 691 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N PHE N 735 " --> pdb=" O ILE N 687 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N VAL N 689 " --> pdb=" O PHE N 735 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'N' and resid 694 through 701 Processing sheet with id=AD5, first strand: chain 'N' and resid 983 through 985 removed outlier: 3.829A pdb=" N TRP N 983 " --> pdb=" O ILE N1003 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'O' and resid 465 through 470 removed outlier: 3.969A pdb=" N ALA O 467 " --> pdb=" O ALA O 480 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N THR O 485 " --> pdb=" O GLU O 481 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N ARG O 490 " --> pdb=" O LEU O 196 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N LEU O 196 " --> pdb=" O ARG O 490 " (cutoff:3.500A) removed outlier: 9.548A pdb=" N GLU b 78 " --> pdb=" O LYS O 195 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N TYR O 197 " --> pdb=" O GLU b 78 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N ILE b 80 " --> pdb=" O TYR O 197 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N VAL O 199 " --> pdb=" O ILE b 80 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'O' and resid 207 through 212 removed outlier: 4.615A pdb=" N THR O 227 " --> pdb=" O SER O 223 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ASP O 232 " --> pdb=" O LEU O 238 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N LEU O 238 " --> pdb=" O ASP O 232 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'O' and resid 249 through 254 removed outlier: 3.619A pdb=" N GLY O 265 " --> pdb=" O GLN O 269 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N GLN O 269 " --> pdb=" O GLY O 265 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N VAL O 270 " --> pdb=" O HIS O 283 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N HIS O 283 " --> pdb=" O VAL O 270 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N CYS O 272 " --> pdb=" O ILE O 281 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'O' and resid 291 through 296 removed outlier: 3.519A pdb=" N GLY O 293 " --> pdb=" O CYS O 306 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N THR O 311 " --> pdb=" O SER O 307 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ASP O 316 " --> pdb=" O SER O 322 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N SER O 322 " --> pdb=" O ASP O 316 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'O' and resid 333 through 338 removed outlier: 4.250A pdb=" N ILE O 345 " --> pdb=" O TRP O 357 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'O' and resid 377 through 380 removed outlier: 3.857A pdb=" N PHE O 387 " --> pdb=" O TRP O 398 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N LYS O 399 " --> pdb=" O PHE O 405 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N PHE O 405 " --> pdb=" O LYS O 399 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'O' and resid 416 through 421 removed outlier: 4.746A pdb=" N THR O 435 " --> pdb=" O ALA O 431 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLN O 448 " --> pdb=" O LEU O 438 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ASP O 440 " --> pdb=" O ASN O 446 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N ASN O 446 " --> pdb=" O ASP O 440 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'U' and resid 51 through 57 removed outlier: 5.657A pdb=" N PHE U 52 " --> pdb=" O TYR U 41 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N TYR U 41 " --> pdb=" O PHE U 52 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'U' and resid 258 through 264 removed outlier: 4.178A pdb=" N LEU U 291 " --> pdb=" O LEU U 298 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N VAL U 300 " --> pdb=" O ASN U 289 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N ASN U 289 " --> pdb=" O VAL U 300 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'V' and resid 40 through 41 removed outlier: 3.608A pdb=" N CYS V 40 " --> pdb=" O ILE V 156 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N HIS V 158 " --> pdb=" O GLU V 6 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N ASP V 15 " --> pdb=" O VAL V 129 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N VAL V 129 " --> pdb=" O ASP V 15 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL V 94 " --> pdb=" O PHE V 126 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N THR V 93 " --> pdb=" O THR V 111 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'V' and resid 266 through 273 removed outlier: 4.695A pdb=" N TYR V 283 " --> pdb=" O ILE V 272 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N VAL V 304 " --> pdb=" O ILE V 311 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'Z' and resid 272 through 274 Processing sheet with id=AE9, first strand: chain 'a' and resid 127 through 129 Processing sheet with id=AF1, first strand: chain 'a' and resid 134 through 135 Processing sheet with id=AF2, first strand: chain 'a' and resid 227 through 229 Processing sheet with id=AF3, first strand: chain 'a' and resid 516 through 517 Processing sheet with id=AF4, first strand: chain 'a' and resid 905 through 910 removed outlier: 6.316A pdb=" N VAL a 894 " --> pdb=" O ASN a1018 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'a' and resid 940 through 941 removed outlier: 5.262A pdb=" N ILE a1085 " --> pdb=" O ARG a1100 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ARG a1100 " --> pdb=" O ILE a1085 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'a' and resid 1185 through 1189 removed outlier: 3.613A pdb=" N ALA a1226 " --> pdb=" O LEU a1216 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'a' and resid 1335 through 1337 Processing sheet with id=AF8, first strand: chain 'a' and resid 1501 through 1502 Processing sheet with id=AF9, first strand: chain 'a' and resid 1552 through 1554 Processing sheet with id=AG1, first strand: chain 'a' and resid 1606 through 1611 Processing sheet with id=AG2, first strand: chain 'a' and resid 1637 through 1639 Processing sheet with id=AG3, first strand: chain 'a' and resid 1779 through 1781 Processing sheet with id=AG4, first strand: chain 'a' and resid 1789 through 1790 removed outlier: 3.703A pdb=" N LYS a1801 " --> pdb=" O THR a1789 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'a' and resid 1861 through 1863 removed outlier: 5.333A pdb=" N LYS a1885 " --> pdb=" O VAL a1863 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG5 Processing sheet with id=AG6, first strand: chain 'b' and resid 184 through 191 removed outlier: 9.582A pdb=" N CYS b 308 " --> pdb=" O VAL b 253 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N VAL b 255 " --> pdb=" O CYS b 308 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N SER b 310 " --> pdb=" O VAL b 255 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N ILE b 257 " --> pdb=" O SER b 310 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'b' and resid 348 through 350 Processing sheet with id=AG8, first strand: chain 'b' and resid 523 through 525 removed outlier: 7.140A pdb=" N CYS b 476 " --> pdb=" O LEU b 497 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N LEU b 497 " --> pdb=" O CYS b 476 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N THR b 478 " --> pdb=" O ARG b 495 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N ARG b 495 " --> pdb=" O THR b 478 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LYS b 480 " --> pdb=" O PHE b 493 " (cutoff:3.500A) removed outlier: 8.866A pdb=" N TRP b 549 " --> pdb=" O SER b 533 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N SER b 533 " --> pdb=" O TRP b 549 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LEU b 530 " --> pdb=" O VAL b 541 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'b' and resid 618 through 621 removed outlier: 3.669A pdb=" N THR b 618 " --> pdb=" O LEU b 630 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N HIS b 627 " --> pdb=" O VAL b 592 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'b' and resid 618 through 621 removed outlier: 3.669A pdb=" N THR b 618 " --> pdb=" O LEU b 630 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N HIS b 627 " --> pdb=" O VAL b 592 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'b' and resid 783 through 784 removed outlier: 6.482A pdb=" N PHE b 874 " --> pdb=" O VAL b 857 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N VAL b 857 " --> pdb=" O PHE b 874 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'b' and resid 783 through 784 removed outlier: 3.586A pdb=" N HIS b 903 " --> pdb=" O TYR b 831 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N PHE b 833 " --> pdb=" O PHE b 901 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N PHE b 901 " --> pdb=" O PHE b 833 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N GLU b 835 " --> pdb=" O SER b 899 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N SER b 899 " --> pdb=" O GLU b 835 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N GLN b 837 " --> pdb=" O SER b 897 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N SER b 897 " --> pdb=" O GLN b 837 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'b' and resid 675 through 677 removed outlier: 6.169A pdb=" N LYS b 684 " --> pdb=" O ALA b 794 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ALA b 794 " --> pdb=" O LYS b 684 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N THR b 686 " --> pdb=" O LEU b 792 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N ASN b 743 " --> pdb=" O PHE b 735 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N PHE b 735 " --> pdb=" O ASN b 743 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N LEU b 745 " --> pdb=" O TRP b 733 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'i' and resid 47 through 50 removed outlier: 5.284A pdb=" N ILE i 47 " --> pdb=" O ASP i 59 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N ASP i 59 " --> pdb=" O ILE i 47 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE i 77 " --> pdb=" O LEU i 58 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ARG i 76 " --> pdb=" O GLY h 74 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N TYR h 29 " --> pdb=" O GLU h 49 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N GLU h 49 " --> pdb=" O TYR h 29 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N GLY h 31 " --> pdb=" O THR h 47 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N THR h 47 " --> pdb=" O GLY h 31 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N LEU h 33 " --> pdb=" O ALA h 45 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N ALA h 45 " --> pdb=" O LEU h 33 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N MET h 42 " --> pdb=" O ILE h 64 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N GLY h 60 " --> pdb=" O ASN h 46 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N GLU h 48 " --> pdb=" O HIS h 58 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N HIS h 58 " --> pdb=" O GLU h 48 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N LYS l 51 " --> pdb=" O GLU l 72 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N GLU l 72 " --> pdb=" O LYS l 51 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N LEU l 53 " --> pdb=" O VAL l 70 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N VAL l 70 " --> pdb=" O LEU l 53 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N VAL l 66 " --> pdb=" O LYS l 57 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N SER l 97 " --> pdb=" O ASN l 69 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N LYS l 71 " --> pdb=" O TYR l 95 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N TYR l 95 " --> pdb=" O LYS l 71 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LYS l 98 " --> pdb=" O LEU k 70 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLN k 24 " --> pdb=" O THR k 46 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N HIS k 26 " --> pdb=" O LYS k 44 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N THR k 28 " --> pdb=" O ALA k 42 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N ALA k 42 " --> pdb=" O THR k 28 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N THR k 30 " --> pdb=" O LEU k 40 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N LEU k 40 " --> pdb=" O THR k 30 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N VAL k 32 " --> pdb=" O THR k 38 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N THR k 38 " --> pdb=" O VAL k 32 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N HIS k 39 " --> pdb=" O SER k 59 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N SER k 59 " --> pdb=" O HIS k 39 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N LYS k 41 " --> pdb=" O THR k 57 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N THR k 57 " --> pdb=" O LYS k 41 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N THR k 57 " --> pdb=" O VAL n 82 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N PHE n 27 " --> pdb=" O GLU n 47 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N GLU n 47 " --> pdb=" O PHE n 27 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N GLY n 29 " --> pdb=" O CYS n 45 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N CYS n 45 " --> pdb=" O GLY n 29 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N PHE n 31 " --> pdb=" O CYS n 43 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N CYS n 43 " --> pdb=" O PHE n 31 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA n 33 " --> pdb=" O ILE n 41 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'i' and resid 47 through 50 removed outlier: 5.284A pdb=" N ILE i 47 " --> pdb=" O ASP i 59 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N ASP i 59 " --> pdb=" O ILE i 47 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE i 77 " --> pdb=" O LEU i 58 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ARG i 76 " --> pdb=" O GLY h 74 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N TYR h 29 " --> pdb=" O GLU h 49 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N GLU h 49 " --> pdb=" O TYR h 29 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N GLY h 31 " --> pdb=" O THR h 47 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N THR h 47 " --> pdb=" O GLY h 31 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N LEU h 33 " --> pdb=" O ALA h 45 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N ALA h 45 " --> pdb=" O LEU h 33 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N MET h 42 " --> pdb=" O ILE h 64 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N GLY h 60 " --> pdb=" O ASN h 46 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N GLU h 48 " --> pdb=" O HIS h 58 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N HIS h 58 " --> pdb=" O GLU h 48 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N LYS l 51 " --> pdb=" O GLU l 72 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N GLU l 72 " --> pdb=" O LYS l 51 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N LEU l 53 " --> pdb=" O VAL l 70 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N VAL l 70 " --> pdb=" O LEU l 53 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N VAL l 66 " --> pdb=" O LYS l 57 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N SER l 97 " --> pdb=" O ASN l 69 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N LYS l 71 " --> pdb=" O TYR l 95 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N TYR l 95 " --> pdb=" O LYS l 71 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LYS l 98 " --> pdb=" O LEU k 70 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLN k 24 " --> pdb=" O THR k 46 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N HIS k 26 " --> pdb=" O LYS k 44 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N THR k 28 " --> pdb=" O ALA k 42 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N ALA k 42 " --> pdb=" O THR k 28 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N THR k 30 " --> pdb=" O LEU k 40 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N LEU k 40 " --> pdb=" O THR k 30 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N VAL k 32 " --> pdb=" O THR k 38 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N THR k 38 " --> pdb=" O VAL k 32 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N HIS k 39 " --> pdb=" O SER k 59 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N SER k 59 " --> pdb=" O HIS k 39 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N LYS k 41 " --> pdb=" O THR k 57 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N THR k 57 " --> pdb=" O LYS k 41 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N THR k 57 " --> pdb=" O VAL n 82 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N PHE n 27 " --> pdb=" O GLU n 47 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N GLU n 47 " --> pdb=" O PHE n 27 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N GLY n 29 " --> pdb=" O CYS n 45 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N CYS n 45 " --> pdb=" O GLY n 29 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N PHE n 31 " --> pdb=" O CYS n 43 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N CYS n 43 " --> pdb=" O PHE n 31 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA n 33 " --> pdb=" O ILE n 41 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'i' and resid 62 through 64 removed outlier: 6.930A pdb=" N MET i 41 " --> pdb=" O LEU i 35 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLY i 45 " --> pdb=" O ILE i 31 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ILE i 31 " --> pdb=" O GLY i 45 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N GLN i 32 " --> pdb=" O LEU i 87 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N LEU i 87 " --> pdb=" O GLN i 32 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N TRP i 34 " --> pdb=" O THR i 85 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N VAL m 41 " --> pdb=" O ARG m 32 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA m 72 " --> pdb=" O GLN j 60 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N GLN j 60 " --> pdb=" O ALA m 72 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'i' and resid 62 through 64 removed outlier: 6.930A pdb=" N MET i 41 " --> pdb=" O LEU i 35 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLY i 45 " --> pdb=" O ILE i 31 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ILE i 31 " --> pdb=" O GLY i 45 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N GLN i 32 " --> pdb=" O LEU i 87 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N LEU i 87 " --> pdb=" O GLN i 32 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N TRP i 34 " --> pdb=" O THR i 85 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N VAL m 41 " --> pdb=" O ARG m 32 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA m 72 " --> pdb=" O GLN j 60 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N GLN j 60 " --> pdb=" O ALA m 72 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N GLN j 42 " --> pdb=" O ILE j 33 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'p' and resid 55 through 56 Processing sheet with id=AI1, first strand: chain 'u' and resid 60 through 62 Processing sheet with id=AI2, first strand: chain 'u' and resid 125 through 127 Processing sheet with id=AI3, first strand: chain 'u' and resid 323 through 324 removed outlier: 6.911A pdb=" N LEU u 366 " --> pdb=" O PHE u 397 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ARG u 283 " --> pdb=" O VAL u 433 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N VAL u 433 " --> pdb=" O ARG u 283 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N HIS u 285 " --> pdb=" O THR u 431 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N THR u 431 " --> pdb=" O HIS u 285 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'u' and resid 415 through 416 3651 hydrogen bonds defined for protein. 10446 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 207 hydrogen bonds 350 hydrogen bond angles 0 basepair planarities 85 basepair parallelities 183 stacking parallelities Total time for adding SS restraints: 42.97 Time building geometry restraints manager: 15.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 23325 1.34 - 1.46: 19423 1.46 - 1.59: 31750 1.59 - 1.71: 625 1.71 - 1.84: 377 Bond restraints: 75500 Sorted by residual: bond pdb=" C THR a 645 " pdb=" N PRO a 646 " ideal model delta sigma weight residual 1.336 1.389 -0.054 1.23e-02 6.61e+03 1.91e+01 bond pdb=" C ALA N 321 " pdb=" N PRO N 322 " ideal model delta sigma weight residual 1.334 1.398 -0.064 2.34e-02 1.83e+03 7.58e+00 bond pdb=" C LYS C 729 " pdb=" N PRO C 730 " ideal model delta sigma weight residual 1.334 1.395 -0.061 2.34e-02 1.83e+03 6.71e+00 bond pdb=" CA ILE C 754 " pdb=" CB ILE C 754 " ideal model delta sigma weight residual 1.534 1.551 -0.017 6.80e-03 2.16e+04 5.96e+00 bond pdb=" CA ILE C 754 " pdb=" C ILE C 754 " ideal model delta sigma weight residual 1.520 1.541 -0.021 8.80e-03 1.29e+04 5.81e+00 ... (remaining 75495 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.58: 103653 3.58 - 7.15: 861 7.15 - 10.73: 136 10.73 - 14.30: 20 14.30 - 17.88: 4 Bond angle restraints: 104674 Sorted by residual: angle pdb=" C ASP a 519 " pdb=" N TYR a 520 " pdb=" CA TYR a 520 " ideal model delta sigma weight residual 121.54 136.90 -15.36 1.91e+00 2.74e-01 6.47e+01 angle pdb=" N GLU Q 65 " pdb=" CA GLU Q 65 " pdb=" CB GLU Q 65 " ideal model delta sigma weight residual 110.40 120.15 -9.75 1.63e+00 3.76e-01 3.58e+01 angle pdb=" CB MET Y 207 " pdb=" CG MET Y 207 " pdb=" SD MET Y 207 " ideal model delta sigma weight residual 112.70 130.58 -17.88 3.00e+00 1.11e-01 3.55e+01 angle pdb=" C GLU b 56 " pdb=" N VAL b 57 " pdb=" CA VAL b 57 " ideal model delta sigma weight residual 121.97 132.03 -10.06 1.80e+00 3.09e-01 3.13e+01 angle pdb=" CB MET N 997 " pdb=" CG MET N 997 " pdb=" SD MET N 997 " ideal model delta sigma weight residual 112.70 129.10 -16.40 3.00e+00 1.11e-01 2.99e+01 ... (remaining 104669 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.84: 44064 35.84 - 71.68: 1247 71.68 - 107.52: 129 107.52 - 143.36: 3 143.36 - 179.20: 12 Dihedral angle restraints: 45455 sinusoidal: 17097 harmonic: 28358 Sorted by residual: dihedral pdb=" O4' U g 154 " pdb=" C1' U g 154 " pdb=" N1 U g 154 " pdb=" C2 U g 154 " ideal model delta sinusoidal sigma weight residual 200.00 37.94 162.06 1 1.50e+01 4.44e-03 8.33e+01 dihedral pdb=" O4' U g -14 " pdb=" C1' U g -14 " pdb=" N1 U g -14 " pdb=" C2 U g -14 " ideal model delta sinusoidal sigma weight residual 200.00 40.67 159.33 1 1.50e+01 4.44e-03 8.26e+01 dihedral pdb=" O4' C e 23 " pdb=" C1' C e 23 " pdb=" N1 C e 23 " pdb=" C2 C e 23 " ideal model delta sinusoidal sigma weight residual 200.00 74.95 125.05 1 1.50e+01 4.44e-03 6.72e+01 ... (remaining 45452 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.997: 12555 0.997 - 1.993: 0 1.993 - 2.990: 0 2.990 - 3.987: 0 3.987 - 4.984: 4 Chirality restraints: 12559 Sorted by residual: chirality pdb=" C2 IHP a3001 " pdb=" C1 IHP a3001 " pdb=" C3 IHP a3001 " pdb=" O12 IHP a3001 " both_signs ideal model delta sigma weight residual False -2.52 2.46 -4.98 2.00e-01 2.50e+01 6.21e+02 chirality pdb=" C5 IHP a3001 " pdb=" C4 IHP a3001 " pdb=" C6 IHP a3001 " pdb=" O15 IHP a3001 " both_signs ideal model delta sigma weight residual False -2.42 2.35 -4.77 2.00e-01 2.50e+01 5.69e+02 chirality pdb=" C3 IHP a3001 " pdb=" C2 IHP a3001 " pdb=" C4 IHP a3001 " pdb=" O13 IHP a3001 " both_signs ideal model delta sigma weight residual False -2.34 2.38 -4.72 2.00e-01 2.50e+01 5.56e+02 ... (remaining 12556 not shown) Planarity restraints: 12556 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL N 579 " 0.019 2.00e-02 2.50e+03 3.90e-02 1.52e+01 pdb=" C VAL N 579 " -0.068 2.00e-02 2.50e+03 pdb=" O VAL N 579 " 0.026 2.00e-02 2.50e+03 pdb=" N ASP N 580 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL Y 306 " 0.019 2.00e-02 2.50e+03 3.90e-02 1.52e+01 pdb=" C VAL Y 306 " -0.067 2.00e-02 2.50e+03 pdb=" O VAL Y 306 " 0.026 2.00e-02 2.50e+03 pdb=" N GLU Y 307 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG Y 303 " -0.019 2.00e-02 2.50e+03 3.88e-02 1.51e+01 pdb=" C ARG Y 303 " 0.067 2.00e-02 2.50e+03 pdb=" O ARG Y 303 " -0.025 2.00e-02 2.50e+03 pdb=" N GLU Y 304 " -0.023 2.00e-02 2.50e+03 ... (remaining 12553 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 1681 2.68 - 3.23: 64549 3.23 - 3.79: 121529 3.79 - 4.34: 149801 4.34 - 4.90: 240812 Nonbonded interactions: 578372 Sorted by model distance: nonbonded pdb=" OP1 C d 55 " pdb="MG MG d 205 " model vdw 2.124 2.170 nonbonded pdb=" NE2 HIS I 78 " pdb="ZN ZN I 600 " model vdw 2.126 1.848 nonbonded pdb=" O1G GTP b1500 " pdb="MG MG b1501 " model vdw 2.127 2.170 nonbonded pdb=" OP2 G d 75 " pdb="MG MG d 204 " model vdw 2.140 2.170 nonbonded pdb=" OP2 U d 74 " pdb="MG MG d 201 " model vdw 2.141 2.170 ... (remaining 578367 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=0.47 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 5.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.340 Construct map_model_manager: 0.050 Extract box with map and model: 2.070 Check model and map are aligned: 0.410 Set scattering table: 0.500 Process input model: 160.860 Find NCS groups from input model: 1.260 Set up NCS constraints: 0.230 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 173.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 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 : 0.004 0.103 75500 Z= 0.292 Angle : 0.848 17.877 104674 Z= 0.453 Chirality : 0.099 4.984 12559 Planarity : 0.007 0.077 12556 Dihedral : 16.590 179.202 27027 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.53 % Favored : 95.23 % Rotamer: Outliers : 0.04 % Allowed : 0.36 % Favored : 99.60 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % 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: -2.31 (0.07), residues: 9607 helix: -1.77 (0.06), residues: 3853 sheet: -0.15 (0.15), residues: 1315 loop : -1.64 (0.09), residues: 4439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP a 939 HIS 0.015 0.001 HIS J 425 PHE 0.031 0.002 PHE a 387 TYR 0.060 0.002 TYR X 282 ARG 0.010 0.000 ARG N 668 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19214 Ramachandran restraints generated. 9607 Oldfield, 0 Emsley, 9607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19214 Ramachandran restraints generated. 9607 Oldfield, 0 Emsley, 9607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 8630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 252 time to evaluate : 5.890 Fit side-chains revert: symmetry clash REVERT: N 823 MET cc_start: 0.8935 (tpt) cc_final: 0.8667 (tpt) REVERT: N 827 MET cc_start: 0.9516 (mmp) cc_final: 0.9281 (mmp) REVERT: N 997 MET cc_start: 0.8272 (mmm) cc_final: 0.7339 (mmm) REVERT: O 185 MET cc_start: 0.6326 (tmm) cc_final: 0.5949 (tmm) REVERT: a 1327 MET cc_start: 0.8857 (tpp) cc_final: 0.8404 (ttt) outliers start: 2 outliers final: 2 residues processed: 254 average time/residue: 0.6197 time to fit residues: 291.5544 Evaluate side-chains 249 residues out of total 8630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 247 time to evaluate : 5.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 458 THR Chi-restraints excluded: chain W residue 575 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 991 random chunks: chunk 836 optimal weight: 2.9990 chunk 751 optimal weight: 20.0000 chunk 416 optimal weight: 5.9990 chunk 256 optimal weight: 30.0000 chunk 506 optimal weight: 8.9990 chunk 401 optimal weight: 0.9990 chunk 776 optimal weight: 7.9990 chunk 300 optimal weight: 9.9990 chunk 472 optimal weight: 30.0000 chunk 578 optimal weight: 0.6980 chunk 899 optimal weight: 50.0000 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1213 ASN ** J 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 412 HIS Q 196 ASN ** V 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 629 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a1217 GLN a1218 ASN ** b 903 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 924 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.0882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 75500 Z= 0.226 Angle : 0.549 23.801 104674 Z= 0.282 Chirality : 0.044 1.386 12559 Planarity : 0.004 0.055 12556 Dihedral : 15.415 178.577 15629 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.61 % Favored : 96.17 % Rotamer: Outliers : 0.12 % Allowed : 3.76 % Favored : 96.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % 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: -0.46 (0.08), residues: 9607 helix: 0.67 (0.08), residues: 3906 sheet: -0.07 (0.15), residues: 1325 loop : -1.27 (0.09), residues: 4376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP O 315 HIS 0.005 0.001 HIS J 431 PHE 0.019 0.001 PHE a1099 TYR 0.026 0.001 TYR W 556 ARG 0.005 0.000 ARG b 852 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19214 Ramachandran restraints generated. 9607 Oldfield, 0 Emsley, 9607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19214 Ramachandran restraints generated. 9607 Oldfield, 0 Emsley, 9607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 8630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 246 time to evaluate : 6.009 Fit side-chains revert: symmetry clash REVERT: J 435 MET cc_start: 0.5267 (mtt) cc_final: 0.4467 (ptp) REVERT: N 500 MET cc_start: 0.9157 (mmp) cc_final: 0.8869 (mmp) REVERT: N 823 MET cc_start: 0.8912 (tpt) cc_final: 0.8632 (tpt) REVERT: O 185 MET cc_start: 0.6537 (tmm) cc_final: 0.5955 (tmm) REVERT: Y 125 MET cc_start: 0.8436 (ppp) cc_final: 0.7714 (ppp) REVERT: a 503 MET cc_start: 0.8619 (ptp) cc_final: 0.8197 (ptp) REVERT: a 1652 MET cc_start: 0.8208 (tpp) cc_final: 0.7623 (tpp) REVERT: b 105 MET cc_start: 0.9199 (mmm) cc_final: 0.8721 (mmm) REVERT: b 123 MET cc_start: 0.9043 (tpt) cc_final: 0.8810 (mmm) outliers start: 6 outliers final: 3 residues processed: 250 average time/residue: 0.6251 time to fit residues: 291.5671 Evaluate side-chains 249 residues out of total 8630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 246 time to evaluate : 5.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 64 GLU Chi-restraints excluded: chain W residue 458 THR Chi-restraints excluded: chain a residue 61 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 991 random chunks: chunk 500 optimal weight: 9.9990 chunk 279 optimal weight: 10.0000 chunk 749 optimal weight: 3.9990 chunk 612 optimal weight: 10.0000 chunk 248 optimal weight: 20.0000 chunk 901 optimal weight: 50.0000 chunk 973 optimal weight: 50.0000 chunk 802 optimal weight: 5.9990 chunk 894 optimal weight: 50.0000 chunk 307 optimal weight: 6.9990 chunk 723 optimal weight: 8.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 431 GLN N 973 ASN O 370 ASN ** V 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 157 ASN ** W 629 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a1145 HIS a1188 ASN ** a1209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 903 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.1525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 75500 Z= 0.391 Angle : 0.596 15.071 104674 Z= 0.309 Chirality : 0.042 0.387 12559 Planarity : 0.004 0.053 12556 Dihedral : 15.422 178.585 15628 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.21 % Favored : 95.58 % Rotamer: Outliers : 0.26 % Allowed : 6.59 % Favored : 93.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % 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: 0.45 (0.09), residues: 9607 helix: 1.79 (0.08), residues: 3919 sheet: -0.12 (0.15), residues: 1285 loop : -0.95 (0.09), residues: 4403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP a 637 HIS 0.006 0.001 HIS T 53 PHE 0.018 0.001 PHE a1099 TYR 0.022 0.002 TYR u 241 ARG 0.006 0.000 ARG a1427 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19214 Ramachandran restraints generated. 9607 Oldfield, 0 Emsley, 9607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19214 Ramachandran restraints generated. 9607 Oldfield, 0 Emsley, 9607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 8630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 246 time to evaluate : 6.015 Fit side-chains REVERT: N 500 MET cc_start: 0.9268 (mmp) cc_final: 0.8791 (mmp) REVERT: N 823 MET cc_start: 0.8966 (tpt) cc_final: 0.8735 (tpt) REVERT: O 185 MET cc_start: 0.6829 (tmm) cc_final: 0.5970 (tmm) REVERT: V 96 MET cc_start: 0.9119 (mmm) cc_final: 0.8722 (mmm) REVERT: W 479 MET cc_start: 0.8775 (mpp) cc_final: 0.8538 (mpp) REVERT: Y 125 MET cc_start: 0.8579 (ppp) cc_final: 0.7993 (ppp) REVERT: Y 207 MET cc_start: 0.8941 (mmm) cc_final: 0.8463 (mmm) REVERT: Z 208 THR cc_start: 0.9530 (OUTLIER) cc_final: 0.9328 (m) REVERT: a 1652 MET cc_start: 0.8449 (tpp) cc_final: 0.7794 (tpp) REVERT: b 641 MET cc_start: 0.9030 (tpp) cc_final: 0.8760 (mmm) outliers start: 13 outliers final: 3 residues processed: 254 average time/residue: 0.6253 time to fit residues: 295.6567 Evaluate side-chains 249 residues out of total 8630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 245 time to evaluate : 5.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 208 THR Chi-restraints excluded: chain a residue 61 MET Chi-restraints excluded: chain b residue 678 THR Chi-restraints excluded: chain u residue 240 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 991 random chunks: chunk 890 optimal weight: 0.0040 chunk 677 optimal weight: 4.9990 chunk 467 optimal weight: 40.0000 chunk 99 optimal weight: 50.0000 chunk 430 optimal weight: 10.0000 chunk 605 optimal weight: 0.0070 chunk 904 optimal weight: 6.9990 chunk 957 optimal weight: 0.0870 chunk 472 optimal weight: 10.0000 chunk 857 optimal weight: 20.0000 chunk 258 optimal weight: 3.9990 overall best weight: 1.8192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 973 ASN ** U 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 629 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 231 HIS ** a1209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 903 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.1483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 75500 Z= 0.140 Angle : 0.486 12.836 104674 Z= 0.250 Chirality : 0.040 0.330 12559 Planarity : 0.003 0.049 12556 Dihedral : 15.325 179.930 15627 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.66 % Favored : 96.15 % Rotamer: Outliers : 0.28 % Allowed : 7.95 % Favored : 91.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: 0.84 (0.09), residues: 9607 helix: 2.25 (0.08), residues: 3928 sheet: -0.03 (0.15), residues: 1293 loop : -0.84 (0.10), residues: 4386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP O 315 HIS 0.004 0.001 HIS u 240 PHE 0.018 0.001 PHE a1099 TYR 0.023 0.001 TYR W 556 ARG 0.004 0.000 ARG a1427 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19214 Ramachandran restraints generated. 9607 Oldfield, 0 Emsley, 9607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19214 Ramachandran restraints generated. 9607 Oldfield, 0 Emsley, 9607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 8630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 246 time to evaluate : 5.956 Fit side-chains REVERT: N 823 MET cc_start: 0.8975 (tpt) cc_final: 0.8769 (tpt) REVERT: O 185 MET cc_start: 0.6781 (tmm) cc_final: 0.6001 (tmm) REVERT: Q 64 GLU cc_start: 0.8771 (OUTLIER) cc_final: 0.8491 (mt-10) REVERT: V 96 MET cc_start: 0.9099 (mmm) cc_final: 0.8658 (mmm) REVERT: W 479 MET cc_start: 0.8709 (mpp) cc_final: 0.8503 (mpp) REVERT: W 649 ASN cc_start: 0.8488 (m-40) cc_final: 0.8287 (m110) REVERT: Y 125 MET cc_start: 0.8442 (ppp) cc_final: 0.8088 (ppp) REVERT: Z 208 THR cc_start: 0.9350 (OUTLIER) cc_final: 0.9080 (m) REVERT: a 503 MET cc_start: 0.8308 (ptp) cc_final: 0.8084 (ptt) REVERT: a 1652 MET cc_start: 0.8358 (tpp) cc_final: 0.7672 (tpp) REVERT: b 123 MET cc_start: 0.8808 (mmm) cc_final: 0.8370 (mmm) REVERT: b 641 MET cc_start: 0.8950 (tpp) cc_final: 0.8690 (mmm) outliers start: 14 outliers final: 6 residues processed: 255 average time/residue: 0.6214 time to fit residues: 295.0598 Evaluate side-chains 254 residues out of total 8630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 246 time to evaluate : 5.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 818 LEU Chi-restraints excluded: chain Q residue 64 GLU Chi-restraints excluded: chain Z residue 208 THR Chi-restraints excluded: chain a residue 61 MET Chi-restraints excluded: chain b residue 327 TYR Chi-restraints excluded: chain b residue 481 MET Chi-restraints excluded: chain q residue 19 VAL Chi-restraints excluded: chain u residue 240 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 991 random chunks: chunk 797 optimal weight: 10.0000 chunk 543 optimal weight: 4.9990 chunk 13 optimal weight: 50.0000 chunk 713 optimal weight: 10.0000 chunk 395 optimal weight: 8.9990 chunk 817 optimal weight: 9.9990 chunk 662 optimal weight: 4.9990 chunk 1 optimal weight: 50.0000 chunk 489 optimal weight: 20.0000 chunk 859 optimal weight: 10.0000 chunk 241 optimal weight: 50.0000 overall best weight: 7.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 973 ASN ** U 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 903 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.1833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 75500 Z= 0.422 Angle : 0.592 12.455 104674 Z= 0.305 Chirality : 0.042 0.264 12559 Planarity : 0.004 0.063 12556 Dihedral : 15.392 178.771 15627 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.40 % Favored : 95.40 % Rotamer: Outliers : 0.51 % Allowed : 9.02 % Favored : 90.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % 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: 0.98 (0.09), residues: 9607 helix: 2.41 (0.08), residues: 3926 sheet: -0.16 (0.15), residues: 1309 loop : -0.75 (0.10), residues: 4372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP a 637 HIS 0.007 0.001 HIS b 902 PHE 0.018 0.001 PHE a1099 TYR 0.017 0.001 TYR V 39 ARG 0.005 0.000 ARG q 11 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19214 Ramachandran restraints generated. 9607 Oldfield, 0 Emsley, 9607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19214 Ramachandran restraints generated. 9607 Oldfield, 0 Emsley, 9607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 8630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 246 time to evaluate : 6.019 Fit side-chains revert: symmetry clash REVERT: L 534 MET cc_start: 0.8812 (tpt) cc_final: 0.8570 (tmm) REVERT: N 500 MET cc_start: 0.9052 (mmp) cc_final: 0.8798 (mmp) REVERT: N 518 MET cc_start: 0.9119 (tpp) cc_final: 0.8861 (tpp) REVERT: O 185 MET cc_start: 0.7190 (tmm) cc_final: 0.6154 (tmm) REVERT: V 96 MET cc_start: 0.9145 (mmm) cc_final: 0.8766 (mmm) REVERT: Y 125 MET cc_start: 0.8302 (ppp) cc_final: 0.7914 (ppp) REVERT: Y 207 MET cc_start: 0.9342 (mmp) cc_final: 0.8614 (mmm) REVERT: Z 208 THR cc_start: 0.9545 (OUTLIER) cc_final: 0.9330 (m) REVERT: a 1591 MET cc_start: 0.8879 (mmm) cc_final: 0.8538 (mmm) REVERT: a 1652 MET cc_start: 0.8736 (tpp) cc_final: 0.8396 (tpp) REVERT: b 641 MET cc_start: 0.9062 (tpp) cc_final: 0.8749 (mmm) outliers start: 26 outliers final: 12 residues processed: 268 average time/residue: 0.6190 time to fit residues: 308.0057 Evaluate side-chains 258 residues out of total 8630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 245 time to evaluate : 5.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 818 LEU Chi-restraints excluded: chain Q residue 64 GLU Chi-restraints excluded: chain T residue 105 CYS Chi-restraints excluded: chain Z residue 192 THR Chi-restraints excluded: chain Z residue 208 THR Chi-restraints excluded: chain a residue 61 MET Chi-restraints excluded: chain a residue 330 THR Chi-restraints excluded: chain a residue 520 TYR Chi-restraints excluded: chain b residue 255 VAL Chi-restraints excluded: chain b residue 481 MET Chi-restraints excluded: chain b residue 678 THR Chi-restraints excluded: chain q residue 19 VAL Chi-restraints excluded: chain u residue 240 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 991 random chunks: chunk 322 optimal weight: 9.9990 chunk 862 optimal weight: 7.9990 chunk 189 optimal weight: 6.9990 chunk 562 optimal weight: 0.0870 chunk 236 optimal weight: 2.9990 chunk 958 optimal weight: 50.0000 chunk 795 optimal weight: 5.9990 chunk 443 optimal weight: 7.9990 chunk 79 optimal weight: 5.9990 chunk 317 optimal weight: 0.9990 chunk 503 optimal weight: 2.9990 overall best weight: 2.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 973 ASN ** U 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 903 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 75500 Z= 0.175 Angle : 0.490 11.254 104674 Z= 0.253 Chirality : 0.040 0.236 12559 Planarity : 0.003 0.048 12556 Dihedral : 15.338 179.789 15627 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.85 % Favored : 95.97 % Rotamer: Outliers : 0.45 % Allowed : 9.73 % Favored : 89.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: 1.18 (0.09), residues: 9607 helix: 2.62 (0.08), residues: 3934 sheet: -0.05 (0.15), residues: 1286 loop : -0.69 (0.10), residues: 4387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP O 315 HIS 0.004 0.001 HIS u 240 PHE 0.017 0.001 PHE a1099 TYR 0.023 0.001 TYR W 556 ARG 0.004 0.000 ARG a1427 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19214 Ramachandran restraints generated. 9607 Oldfield, 0 Emsley, 9607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19214 Ramachandran restraints generated. 9607 Oldfield, 0 Emsley, 9607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 8630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 245 time to evaluate : 5.946 Fit side-chains REVERT: C 1056 MET cc_start: 0.9169 (mmm) cc_final: 0.8969 (mmm) REVERT: L 534 MET cc_start: 0.8720 (tpt) cc_final: 0.8469 (tmm) REVERT: N 518 MET cc_start: 0.9211 (tpp) cc_final: 0.8907 (tpp) REVERT: O 185 MET cc_start: 0.7018 (tmm) cc_final: 0.6084 (tmm) REVERT: Q 64 GLU cc_start: 0.8797 (OUTLIER) cc_final: 0.8498 (mt-10) REVERT: V 96 MET cc_start: 0.9092 (mmm) cc_final: 0.8664 (mmm) REVERT: Y 125 MET cc_start: 0.8240 (ppp) cc_final: 0.7835 (ppp) REVERT: Y 207 MET cc_start: 0.9271 (mmp) cc_final: 0.8549 (mmm) REVERT: Z 208 THR cc_start: 0.9404 (OUTLIER) cc_final: 0.9140 (m) REVERT: a 1652 MET cc_start: 0.8471 (tpp) cc_final: 0.8094 (tpp) REVERT: b 641 MET cc_start: 0.9004 (tpp) cc_final: 0.8671 (mmm) outliers start: 23 outliers final: 11 residues processed: 264 average time/residue: 0.6094 time to fit residues: 298.9323 Evaluate side-chains 258 residues out of total 8630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 245 time to evaluate : 5.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 818 LEU Chi-restraints excluded: chain O residue 323 VAL Chi-restraints excluded: chain Q residue 64 GLU Chi-restraints excluded: chain T residue 105 CYS Chi-restraints excluded: chain Z residue 192 THR Chi-restraints excluded: chain Z residue 208 THR Chi-restraints excluded: chain a residue 61 MET Chi-restraints excluded: chain a residue 99 VAL Chi-restraints excluded: chain a residue 520 TYR Chi-restraints excluded: chain b residue 255 VAL Chi-restraints excluded: chain b residue 327 TYR Chi-restraints excluded: chain b residue 481 MET Chi-restraints excluded: chain q residue 19 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 991 random chunks: chunk 924 optimal weight: 50.0000 chunk 108 optimal weight: 50.0000 chunk 546 optimal weight: 20.0000 chunk 700 optimal weight: 0.9990 chunk 542 optimal weight: 10.0000 chunk 807 optimal weight: 2.9990 chunk 535 optimal weight: 50.0000 chunk 955 optimal weight: 20.0000 chunk 597 optimal weight: 0.3980 chunk 582 optimal weight: 10.0000 chunk 440 optimal weight: 10.0000 overall best weight: 4.8792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 973 ASN ** U 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 903 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.1888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 75500 Z= 0.272 Angle : 0.523 12.824 104674 Z= 0.269 Chirality : 0.040 0.244 12559 Planarity : 0.003 0.053 12556 Dihedral : 15.331 179.752 15627 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.28 % Favored : 95.54 % Rotamer: Outliers : 0.42 % Allowed : 10.28 % Favored : 89.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % 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 (0.09), residues: 9607 helix: 2.68 (0.08), residues: 3939 sheet: -0.08 (0.15), residues: 1294 loop : -0.66 (0.10), residues: 4374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP a 637 HIS 0.006 0.001 HIS u 240 PHE 0.016 0.001 PHE a1099 TYR 0.023 0.001 TYR O 197 ARG 0.004 0.000 ARG W 580 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19214 Ramachandran restraints generated. 9607 Oldfield, 0 Emsley, 9607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19214 Ramachandran restraints generated. 9607 Oldfield, 0 Emsley, 9607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 8630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 245 time to evaluate : 6.009 Fit side-chains REVERT: N 500 MET cc_start: 0.9117 (mmp) cc_final: 0.8762 (mmp) REVERT: N 518 MET cc_start: 0.9189 (tpp) cc_final: 0.8904 (tpp) REVERT: N 908 MET cc_start: 0.8497 (OUTLIER) cc_final: 0.7990 (tmm) REVERT: O 185 MET cc_start: 0.7167 (tmm) cc_final: 0.6134 (tmm) REVERT: Q 64 GLU cc_start: 0.8791 (OUTLIER) cc_final: 0.8517 (mt-10) REVERT: V 96 MET cc_start: 0.9096 (mmm) cc_final: 0.8666 (mmm) REVERT: Y 207 MET cc_start: 0.9361 (mmp) cc_final: 0.8573 (mmm) REVERT: Y 412 PHE cc_start: 0.9311 (OUTLIER) cc_final: 0.8546 (t80) REVERT: Z 208 THR cc_start: 0.9482 (OUTLIER) cc_final: 0.9265 (m) REVERT: a 1591 MET cc_start: 0.8780 (mmm) cc_final: 0.8516 (mmm) REVERT: a 1652 MET cc_start: 0.8560 (tpp) cc_final: 0.8171 (tpp) REVERT: b 641 MET cc_start: 0.9041 (tpp) cc_final: 0.8678 (mmm) REVERT: b 687 MET cc_start: 0.8138 (tmm) cc_final: 0.7919 (tmm) outliers start: 21 outliers final: 12 residues processed: 262 average time/residue: 0.6554 time to fit residues: 318.9172 Evaluate side-chains 261 residues out of total 8630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 245 time to evaluate : 6.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 818 LEU Chi-restraints excluded: chain N residue 908 MET Chi-restraints excluded: chain O residue 323 VAL Chi-restraints excluded: chain Q residue 64 GLU Chi-restraints excluded: chain T residue 105 CYS Chi-restraints excluded: chain Y residue 412 PHE Chi-restraints excluded: chain Z residue 192 THR Chi-restraints excluded: chain Z residue 208 THR Chi-restraints excluded: chain a residue 61 MET Chi-restraints excluded: chain a residue 99 VAL Chi-restraints excluded: chain a residue 520 TYR Chi-restraints excluded: chain a residue 1295 ILE Chi-restraints excluded: chain b residue 255 VAL Chi-restraints excluded: chain b residue 481 MET Chi-restraints excluded: chain b residue 678 THR Chi-restraints excluded: chain q residue 19 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 991 random chunks: chunk 590 optimal weight: 0.6980 chunk 381 optimal weight: 10.0000 chunk 570 optimal weight: 20.0000 chunk 287 optimal weight: 9.9990 chunk 187 optimal weight: 4.9990 chunk 185 optimal weight: 1.9990 chunk 607 optimal weight: 1.9990 chunk 650 optimal weight: 3.9990 chunk 472 optimal weight: 50.0000 chunk 89 optimal weight: 10.0000 chunk 750 optimal weight: 30.0000 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 973 ASN U 206 ASN ** V 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 903 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 75500 Z= 0.176 Angle : 0.491 13.515 104674 Z= 0.252 Chirality : 0.040 0.235 12559 Planarity : 0.003 0.047 12556 Dihedral : 15.278 179.672 15627 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.87 % Favored : 95.97 % Rotamer: Outliers : 0.49 % Allowed : 10.56 % Favored : 88.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % 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: 1.31 (0.09), residues: 9607 helix: 2.74 (0.08), residues: 3940 sheet: -0.05 (0.15), residues: 1300 loop : -0.62 (0.10), residues: 4367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP a 750 HIS 0.007 0.001 HIS u 240 PHE 0.016 0.001 PHE a1099 TYR 0.022 0.001 TYR O 197 ARG 0.003 0.000 ARG W 580 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19214 Ramachandran restraints generated. 9607 Oldfield, 0 Emsley, 9607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19214 Ramachandran restraints generated. 9607 Oldfield, 0 Emsley, 9607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 8630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 245 time to evaluate : 5.931 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 500 MET cc_start: 0.9117 (mmp) cc_final: 0.8795 (mmp) REVERT: N 518 MET cc_start: 0.9215 (tpp) cc_final: 0.8975 (tpp) REVERT: N 846 MET cc_start: 0.9361 (mmt) cc_final: 0.9084 (mmt) REVERT: N 908 MET cc_start: 0.8511 (OUTLIER) cc_final: 0.8022 (tmm) REVERT: O 185 MET cc_start: 0.7100 (tmm) cc_final: 0.6081 (tmm) REVERT: Q 64 GLU cc_start: 0.8807 (OUTLIER) cc_final: 0.8500 (mt-10) REVERT: V 96 MET cc_start: 0.9084 (mmm) cc_final: 0.8633 (mmm) REVERT: Y 207 MET cc_start: 0.9300 (mmp) cc_final: 0.8530 (mmm) REVERT: Y 412 PHE cc_start: 0.9239 (OUTLIER) cc_final: 0.8427 (t80) REVERT: Z 208 THR cc_start: 0.9416 (OUTLIER) cc_final: 0.9148 (m) REVERT: a 1591 MET cc_start: 0.8775 (mmm) cc_final: 0.8494 (mmm) REVERT: a 1652 MET cc_start: 0.8520 (tpp) cc_final: 0.8196 (tpp) REVERT: b 105 MET cc_start: 0.8988 (mmm) cc_final: 0.8277 (mmm) REVERT: b 123 MET cc_start: 0.8948 (mmm) cc_final: 0.8466 (mmm) REVERT: b 641 MET cc_start: 0.9003 (tpp) cc_final: 0.8654 (mmm) REVERT: b 687 MET cc_start: 0.8106 (tmm) cc_final: 0.7830 (tmm) outliers start: 25 outliers final: 15 residues processed: 266 average time/residue: 0.6163 time to fit residues: 304.2726 Evaluate side-chains 264 residues out of total 8630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 245 time to evaluate : 5.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain N residue 438 GLU Chi-restraints excluded: chain N residue 818 LEU Chi-restraints excluded: chain N residue 908 MET Chi-restraints excluded: chain O residue 302 VAL Chi-restraints excluded: chain O residue 323 VAL Chi-restraints excluded: chain Q residue 64 GLU Chi-restraints excluded: chain T residue 105 CYS Chi-restraints excluded: chain Y residue 412 PHE Chi-restraints excluded: chain Z residue 192 THR Chi-restraints excluded: chain Z residue 208 THR Chi-restraints excluded: chain a residue 61 MET Chi-restraints excluded: chain a residue 99 VAL Chi-restraints excluded: chain a residue 520 TYR Chi-restraints excluded: chain a residue 1416 ILE Chi-restraints excluded: chain b residue 255 VAL Chi-restraints excluded: chain b residue 481 MET Chi-restraints excluded: chain b residue 678 THR Chi-restraints excluded: chain q residue 19 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 991 random chunks: chunk 868 optimal weight: 10.0000 chunk 915 optimal weight: 20.0000 chunk 834 optimal weight: 7.9990 chunk 890 optimal weight: 6.9990 chunk 914 optimal weight: 4.9990 chunk 535 optimal weight: 30.0000 chunk 387 optimal weight: 8.9990 chunk 698 optimal weight: 4.9990 chunk 273 optimal weight: 0.2980 chunk 804 optimal weight: 3.9990 chunk 841 optimal weight: 9.9990 overall best weight: 4.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 973 ASN ** V 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 903 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 75500 Z= 0.244 Angle : 0.516 14.365 104674 Z= 0.264 Chirality : 0.040 0.240 12559 Planarity : 0.003 0.050 12556 Dihedral : 15.278 179.826 15627 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.18 % Favored : 95.67 % Rotamer: Outliers : 0.47 % Allowed : 10.82 % Favored : 88.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % 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: 1.33 (0.09), residues: 9607 helix: 2.77 (0.08), residues: 3939 sheet: -0.08 (0.15), residues: 1301 loop : -0.61 (0.10), residues: 4367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP a 637 HIS 0.008 0.001 HIS u 240 PHE 0.016 0.001 PHE a1099 TYR 0.022 0.001 TYR O 197 ARG 0.004 0.000 ARG b 852 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19214 Ramachandran restraints generated. 9607 Oldfield, 0 Emsley, 9607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19214 Ramachandran restraints generated. 9607 Oldfield, 0 Emsley, 9607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 8630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 245 time to evaluate : 6.052 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 500 MET cc_start: 0.9186 (mmp) cc_final: 0.8806 (mmp) REVERT: N 518 MET cc_start: 0.9210 (tpp) cc_final: 0.8950 (tpp) REVERT: N 908 MET cc_start: 0.8496 (OUTLIER) cc_final: 0.7998 (tmm) REVERT: O 185 MET cc_start: 0.7154 (tmm) cc_final: 0.6085 (tmm) REVERT: Q 64 GLU cc_start: 0.8802 (OUTLIER) cc_final: 0.8527 (mt-10) REVERT: V 96 MET cc_start: 0.9091 (mmm) cc_final: 0.8689 (mmm) REVERT: Y 207 MET cc_start: 0.9315 (mmp) cc_final: 0.8651 (mmm) REVERT: Y 412 PHE cc_start: 0.9255 (OUTLIER) cc_final: 0.8489 (t80) REVERT: Z 208 THR cc_start: 0.9460 (OUTLIER) cc_final: 0.9256 (m) REVERT: a 1327 MET cc_start: 0.9078 (ttm) cc_final: 0.8878 (ttt) REVERT: a 1652 MET cc_start: 0.8660 (tpp) cc_final: 0.8342 (tpp) REVERT: b 123 MET cc_start: 0.8978 (mmm) cc_final: 0.8492 (mmm) REVERT: b 641 MET cc_start: 0.9066 (tpp) cc_final: 0.8700 (mmm) REVERT: b 687 MET cc_start: 0.8086 (tmm) cc_final: 0.7819 (tmm) outliers start: 24 outliers final: 14 residues processed: 265 average time/residue: 0.6265 time to fit residues: 309.5405 Evaluate side-chains 263 residues out of total 8630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 245 time to evaluate : 5.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain N residue 438 GLU Chi-restraints excluded: chain N residue 818 LEU Chi-restraints excluded: chain N residue 908 MET Chi-restraints excluded: chain O residue 302 VAL Chi-restraints excluded: chain O residue 323 VAL Chi-restraints excluded: chain Q residue 64 GLU Chi-restraints excluded: chain T residue 105 CYS Chi-restraints excluded: chain Y residue 412 PHE Chi-restraints excluded: chain Z residue 192 THR Chi-restraints excluded: chain Z residue 208 THR Chi-restraints excluded: chain a residue 99 VAL Chi-restraints excluded: chain a residue 520 TYR Chi-restraints excluded: chain a residue 1416 ILE Chi-restraints excluded: chain b residue 255 VAL Chi-restraints excluded: chain b residue 481 MET Chi-restraints excluded: chain b residue 678 THR Chi-restraints excluded: chain q residue 19 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 991 random chunks: chunk 886 optimal weight: 40.0000 chunk 584 optimal weight: 0.9980 chunk 941 optimal weight: 3.9990 chunk 574 optimal weight: 0.9980 chunk 446 optimal weight: 0.9990 chunk 654 optimal weight: 9.9990 chunk 987 optimal weight: 10.0000 chunk 908 optimal weight: 30.0000 chunk 786 optimal weight: 10.0000 chunk 81 optimal weight: 50.0000 chunk 607 optimal weight: 5.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 973 ASN ** V 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 903 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 75500 Z= 0.170 Angle : 0.497 14.637 104674 Z= 0.253 Chirality : 0.040 0.244 12559 Planarity : 0.003 0.047 12556 Dihedral : 15.241 179.737 15627 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.90 % Favored : 95.95 % Rotamer: Outliers : 0.45 % Allowed : 10.74 % Favored : 88.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % 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: 1.37 (0.09), residues: 9607 helix: 2.80 (0.08), residues: 3941 sheet: -0.02 (0.15), residues: 1296 loop : -0.59 (0.10), residues: 4370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP a 750 HIS 0.008 0.001 HIS u 240 PHE 0.015 0.001 PHE a1099 TYR 0.021 0.001 TYR W 556 ARG 0.003 0.000 ARG b 852 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19214 Ramachandran restraints generated. 9607 Oldfield, 0 Emsley, 9607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19214 Ramachandran restraints generated. 9607 Oldfield, 0 Emsley, 9607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 8630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 245 time to evaluate : 6.094 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 534 MET cc_start: 0.8649 (tpt) cc_final: 0.8182 (tmm) REVERT: N 500 MET cc_start: 0.9148 (mmp) cc_final: 0.8797 (mmp) REVERT: N 908 MET cc_start: 0.8512 (OUTLIER) cc_final: 0.8037 (tmm) REVERT: O 185 MET cc_start: 0.7091 (tmm) cc_final: 0.6032 (tmm) REVERT: Q 64 GLU cc_start: 0.8810 (OUTLIER) cc_final: 0.8502 (mt-10) REVERT: U 220 MET cc_start: 0.7364 (tpt) cc_final: 0.6238 (mmt) REVERT: V 96 MET cc_start: 0.9067 (mmm) cc_final: 0.8610 (mmm) REVERT: Y 207 MET cc_start: 0.9297 (mmp) cc_final: 0.8655 (mmm) REVERT: Y 412 PHE cc_start: 0.9198 (OUTLIER) cc_final: 0.8368 (t80) REVERT: Z 208 THR cc_start: 0.9403 (OUTLIER) cc_final: 0.9096 (m) REVERT: b 105 MET cc_start: 0.8810 (mmm) cc_final: 0.8329 (mmm) REVERT: b 123 MET cc_start: 0.8943 (mmm) cc_final: 0.8506 (mmm) REVERT: b 641 MET cc_start: 0.8992 (tpp) cc_final: 0.8635 (mmm) REVERT: b 687 MET cc_start: 0.8062 (tmm) cc_final: 0.7766 (tmm) outliers start: 23 outliers final: 13 residues processed: 264 average time/residue: 0.6395 time to fit residues: 315.3267 Evaluate side-chains 262 residues out of total 8630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 245 time to evaluate : 6.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain N residue 438 GLU Chi-restraints excluded: chain N residue 908 MET Chi-restraints excluded: chain O residue 302 VAL Chi-restraints excluded: chain O residue 323 VAL Chi-restraints excluded: chain Q residue 64 GLU Chi-restraints excluded: chain T residue 105 CYS Chi-restraints excluded: chain Y residue 412 PHE Chi-restraints excluded: chain Z residue 192 THR Chi-restraints excluded: chain Z residue 208 THR Chi-restraints excluded: chain a residue 99 VAL Chi-restraints excluded: chain a residue 520 TYR Chi-restraints excluded: chain a residue 1416 ILE Chi-restraints excluded: chain b residue 255 VAL Chi-restraints excluded: chain b residue 481 MET Chi-restraints excluded: chain b residue 678 THR Chi-restraints excluded: chain q residue 19 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 991 random chunks: chunk 482 optimal weight: 50.0000 chunk 624 optimal weight: 7.9990 chunk 837 optimal weight: 0.9990 chunk 240 optimal weight: 50.0000 chunk 724 optimal weight: 0.9990 chunk 116 optimal weight: 50.0000 chunk 218 optimal weight: 2.9990 chunk 787 optimal weight: 7.9990 chunk 329 optimal weight: 9.9990 chunk 808 optimal weight: 3.9990 chunk 99 optimal weight: 50.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 478 HIS ** J 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 804 HIS ** V 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 903 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.042818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.032482 restraints weight = 870024.958| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 4.11 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3326 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3326 r_free = 0.3326 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3326 r_free = 0.3326 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3326 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 75500 Z= 0.205 Angle : 0.506 14.322 104674 Z= 0.258 Chirality : 0.040 0.246 12559 Planarity : 0.003 0.046 12556 Dihedral : 15.232 179.838 15627 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.13 % Favored : 95.72 % Rotamer: Outliers : 0.42 % Allowed : 10.92 % Favored : 88.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % 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: 1.41 (0.09), residues: 9607 helix: 2.84 (0.08), residues: 3938 sheet: -0.01 (0.15), residues: 1309 loop : -0.57 (0.10), residues: 4360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP a 637 HIS 0.008 0.001 HIS u 240 PHE 0.016 0.001 PHE a1099 TYR 0.024 0.001 TYR O 197 ARG 0.003 0.000 ARG W 580 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10678.41 seconds wall clock time: 188 minutes 17.03 seconds (11297.03 seconds total)