Starting phenix.real_space_refine on Fri Dec 15 06:56:36 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eti_24395/12_2023/8eti_24395.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eti_24395/12_2023/8eti_24395.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eti_24395/12_2023/8eti_24395.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eti_24395/12_2023/8eti_24395.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eti_24395/12_2023/8eti_24395.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eti_24395/12_2023/8eti_24395.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 1812 5.49 5 S 97 5.16 5 C 49511 2.51 5 N 16965 2.21 5 O 22070 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "4 GLU 37": "OE1" <-> "OE2" Residue "4 GLU 89": "OE1" <-> "OE2" Residue "4 GLU 149": "OE1" <-> "OE2" Residue "A GLU 275": "OE1" <-> "OE2" Residue "A GLU 287": "OE1" <-> "OE2" Residue "E TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 176": "OE1" <-> "OE2" Residue "L GLU 106": "OE1" <-> "OE2" Residue "L GLU 114": "OE1" <-> "OE2" Residue "M GLU 9": "OE1" <-> "OE2" Residue "M GLU 20": "OE1" <-> "OE2" Residue "M GLU 97": "OE1" <-> "OE2" Residue "O GLU 184": "OE1" <-> "OE2" Residue "P GLU 75": "OE1" <-> "OE2" Residue "P GLU 99": "OE1" <-> "OE2" Residue "P GLU 103": "OE1" <-> "OE2" Residue "P GLU 152": "OE1" <-> "OE2" Residue "P GLU 154": "OE1" <-> "OE2" Residue "Y GLU 37": "OE1" <-> "OE2" Residue "e GLU 80": "OE1" <-> "OE2" Residue "e GLU 92": "OE1" <-> "OE2" Residue "h GLU 22": "OE1" <-> "OE2" Residue "h GLU 62": "OE1" <-> "OE2" Residue "m GLU 251": "OE1" <-> "OE2" Residue "m GLU 255": "OE1" <-> "OE2" Residue "m GLU 257": "OE1" <-> "OE2" Residue "n GLU 75": "OE1" <-> "OE2" Residue "n GLU 83": "OE1" <-> "OE2" Residue "n PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n GLU 101": "OE1" <-> "OE2" Residue "n GLU 107": "OE1" <-> "OE2" Residue "v GLU 143": "OE1" <-> "OE2" Residue "v GLU 144": "OE1" <-> "OE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 90456 Number of models: 1 Model: "" Number of chains: 46 Chain: "1" Number of atoms: 33816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1579, 33816 Classifications: {'RNA': 1579} Modifications used: {'rna2p_pur': 171, 'rna2p_pyr': 102, 'rna3p_pur': 722, 'rna3p_pyr': 584} Link IDs: {'rna2p': 272, 'rna3p': 1306} Chain breaks: 28 Chain: "2" Number of atoms: 3229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 3229 Classifications: {'RNA': 152} Modifications used: {'rna2p_pur': 15, 'rna2p_pyr': 11, 'rna3p_pur': 62, 'rna3p_pyr': 64} Link IDs: {'rna2p': 25, 'rna3p': 126} Chain breaks: 1 Chain: "3" Number of atoms: 1576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1576 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 7, 'TRANS': 182} Chain: "4" Number of atoms: 1762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1762 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 8, 'TRANS': 200} Chain: "5" Number of atoms: 2686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2686 Classifications: {'peptide': 340} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 325} Chain breaks: 1 Chain: "6" Number of atoms: 1717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 1717 Classifications: {'RNA': 81} Modifications used: {'rna2p_pur': 13, 'rna2p_pyr': 15, 'rna3p_pur': 28, 'rna3p_pyr': 25} Link IDs: {'rna2p': 28, 'rna3p': 52} Chain breaks: 3 Chain: "A" Number of atoms: 1427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 1427 Classifications: {'peptide': 254} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 181} Link IDs: {'PTRANS': 12, 'TRANS': 241} Chain breaks: 1 Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 665 Unresolved non-hydrogen angles: 845 Unresolved non-hydrogen dihedrals: 553 Unresolved non-hydrogen chiralities: 61 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 10, 'TYR:plan': 5, 'ASN:plan1': 12, 'TRP:plan': 1, 'HIS:plan': 6, 'PHE:plan': 12, 'GLU:plan': 11, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 351 Chain: "B" Number of atoms: 2641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2641 Classifications: {'peptide': 332} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 318} Chain breaks: 1 Chain: "C" Number of atoms: 2571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2571 Classifications: {'peptide': 328} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 310} Chain breaks: 1 Chain: "D" Number of atoms: 1931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 391, 1931 Classifications: {'peptide': 391} Incomplete info: {'truncation_to_alanine': 338} Link IDs: {'PTRANS': 16, 'TRANS': 374} Chain breaks: 2 Unresolved chain link angles: 16 Unresolved non-hydrogen bonds: 1241 Unresolved non-hydrogen angles: 1573 Unresolved non-hydrogen dihedrals: 1030 Unresolved non-hydrogen chiralities: 116 Planarities with less than four sites: {'GLN:plan1': 17, 'HIS:plan': 6, 'TYR:plan': 14, 'ASN:plan1': 19, 'TRP:plan': 1, 'ASP:plan': 19, 'PHE:plan': 22, 'GLU:plan': 21, 'ARG:plan': 21} Unresolved non-hydrogen planarities: 640 Chain: "E" Number of atoms: 1328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1328 Classifications: {'peptide': 170} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 156} Chain: "F" Number of atoms: 1939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1939 Classifications: {'peptide': 239} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 227} Chain: "G" Number of atoms: 1464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1464 Classifications: {'peptide': 186} Link IDs: {'PTRANS': 8, 'TRANS': 177} Chain: "H" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 902 Classifications: {'peptide': 183} Incomplete info: {'truncation_to_alanine': 164} Link IDs: {'PTRANS': 4, 'TRANS': 178} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 569 Unresolved non-hydrogen angles: 726 Unresolved non-hydrogen dihedrals: 456 Unresolved non-hydrogen chiralities: 64 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 4, 'TYR:plan': 5, 'ASN:plan1': 16, 'TRP:plan': 1, 'ASP:plan': 7, 'PHE:plan': 5, 'GLU:plan': 10, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 288 Chain: "J" Number of atoms: 564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 564 Classifications: {'peptide': 113} Incomplete info: {'truncation_to_alanine': 100} Link IDs: {'PTRANS': 3, 'TRANS': 109} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 367 Unresolved non-hydrogen angles: 461 Unresolved non-hydrogen dihedrals: 300 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 2, 'TYR:plan': 4, 'ASN:plan1': 6, 'ASP:plan': 7, 'PHE:plan': 4, 'GLU:plan': 13, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 207 Chain: "K" Number of atoms: 1190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1190 Classifications: {'peptide': 240} Incomplete info: {'truncation_to_alanine': 213} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 225} Chain breaks: 1 Unresolved chain link angles: 14 Unresolved non-hydrogen bonds: 728 Unresolved non-hydrogen angles: 920 Unresolved non-hydrogen dihedrals: 612 Unresolved non-hydrogen chiralities: 71 Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 3, 'TYR:plan': 7, 'ASN:plan1': 11, 'TRP:plan': 3, 'ASP:plan': 8, 'PHE:plan': 7, 'GLU:plan': 13, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 328 Chain: "L" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 938 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 9, 'TRANS': 105} Chain: "M" Number of atoms: 1007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1007 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain: "N" Number of atoms: 1401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1401 Classifications: {'peptide': 166} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 160} Chain breaks: 2 Chain: "O" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1557 Classifications: {'peptide': 196} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 186} Chain: "P" Number of atoms: 1154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1154 Classifications: {'peptide': 147} Link IDs: {'PTRANS': 6, 'TRANS': 140} Chain breaks: 1 Chain: "Q" Number of atoms: 1057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1057 Classifications: {'peptide': 136} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 5, 'TRANS': 130} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "S" Number of atoms: 1395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1395 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 11, 'TRANS': 155} Chain breaks: 1 Chain: "V" Number of atoms: 624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 624 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 99} Link IDs: {'PTRANS': 7, 'TRANS': 119} Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 353 Unresolved non-hydrogen angles: 447 Unresolved non-hydrogen dihedrals: 296 Unresolved non-hydrogen chiralities: 34 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 4, 'ASN:plan1': 7, 'TRP:plan': 2, 'ASP:plan': 6, 'PHE:plan': 2, 'GLU:plan': 3, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 162 Chain: "W" Number of atoms: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 850 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 146} Link IDs: {'PTRANS': 6, 'TRANS': 166} Chain breaks: 8 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 552 Unresolved non-hydrogen angles: 707 Unresolved non-hydrogen dihedrals: 467 Unresolved non-hydrogen chiralities: 54 Planarities with less than four sites: {'GLN:plan1': 9, 'ARG:plan': 9, 'TYR:plan': 6, 'ASN:plan1': 5, 'TRP:plan': 2, 'ASP:plan': 6, 'PHE:plan': 12, 'GLU:plan': 6, 'HIS:plan': 4} Unresolved non-hydrogen planarities: 290 Chain: "X" Number of atoms: 750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 750 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 64} Link IDs: {'PTRANS': 6, 'TRANS': 115} Chain breaks: 3 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 233 Unresolved non-hydrogen angles: 294 Unresolved non-hydrogen dihedrals: 193 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'ARG:plan': 3, 'TYR:plan': 2, 'ASN:plan1': 6, 'HIS:plan': 2, 'PHE:plan': 4, 'GLU:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 103 Chain: "Y" Number of atoms: 998 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 998 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 4, 'TRANS': 120} Chain: "b" Number of atoms: 1939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 391, 1939 Classifications: {'peptide': 391} Incomplete info: {'truncation_to_alanine': 346} Link IDs: {'PTRANS': 14, 'TRANS': 376} Chain breaks: 3 Unresolved chain link angles: 14 Unresolved non-hydrogen bonds: 1250 Unresolved non-hydrogen angles: 1597 Unresolved non-hydrogen dihedrals: 1022 Unresolved non-hydrogen chiralities: 127 Planarities with less than four sites: {'GLN:plan1': 17, 'HIS:plan': 8, 'TYR:plan': 15, 'ASN:plan1': 15, 'TRP:plan': 2, 'ASP:plan': 28, 'PHE:plan': 15, 'GLU:plan': 19, 'ARG:plan': 26} Unresolved non-hydrogen planarities: 656 Chain: "d" Number of atoms: 483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 483 Classifications: {'peptide': 97} Incomplete info: {'truncation_to_alanine': 89} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain breaks: 1 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 343 Unresolved non-hydrogen angles: 433 Unresolved non-hydrogen dihedrals: 288 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 4, 'TYR:plan': 4, 'ASN:plan1': 3, 'TRP:plan': 1, 'HIS:plan': 4, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 186 Chain: "e" Number of atoms: 986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 986 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 4, 'TRANS': 118} Chain: "f" Number of atoms: 839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 839 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 101} Chain: "h" Number of atoms: 994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 994 Classifications: {'peptide': 120} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "i" Number of atoms: 696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 696 Classifications: {'peptide': 85} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 81} Chain: "j" Number of atoms: 563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 563 Classifications: {'peptide': 71} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 68} Chain: "m" Number of atoms: 859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 859 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PTRANS': 13, 'TRANS': 107} Chain breaks: 2 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 172 Unresolved non-hydrogen angles: 218 Unresolved non-hydrogen dihedrals: 152 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ASP:plan': 1, 'TYR:plan': 5, 'ASN:plan1': 2, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 94 Chain: "n" Number of atoms: 2215 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 2215 Classifications: {'peptide': 369} Incomplete info: {'truncation_to_alanine': 218} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 348} Chain breaks: 1 Unresolved chain link angles: 14 Unresolved non-hydrogen bonds: 835 Unresolved non-hydrogen angles: 1077 Unresolved non-hydrogen dihedrals: 720 Unresolved non-hydrogen chiralities: 68 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 7, 'TYR:plan': 12, 'ASN:plan1': 7, 'TRP:plan': 3, 'ASP:plan': 13, 'PHE:plan': 21, 'GLU:plan': 14, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 475 Chain: "o" Number of atoms: 666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 666 Classifications: {'peptide': 134} Incomplete info: {'truncation_to_alanine': 119} Link IDs: {'PTRANS': 6, 'TRANS': 127} Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 471 Unresolved non-hydrogen angles: 588 Unresolved non-hydrogen dihedrals: 406 Unresolved non-hydrogen chiralities: 32 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 4, 'TYR:plan': 6, 'ASN:plan1': 5, 'HIS:plan': 7, 'PHE:plan': 7, 'GLU:plan': 8, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 253 Chain: "r" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 823 Classifications: {'peptide': 166} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 145} Link IDs: {'PTRANS': 5, 'TRANS': 160} Chain breaks: 3 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 554 Unresolved non-hydrogen angles: 688 Unresolved non-hydrogen dihedrals: 460 Unresolved non-hydrogen chiralities: 44 Planarities with less than four sites: {'GLN:plan1': 10, 'ASP:plan': 3, 'TYR:plan': 6, 'ASN:plan1': 8, 'HIS:plan': 5, 'PHE:plan': 3, 'GLU:plan': 15, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 288 Chain: "t" Number of atoms: 1115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1115 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 200} Link IDs: {'PTRANS': 7, 'TRANS': 217} Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 780 Unresolved non-hydrogen angles: 976 Unresolved non-hydrogen dihedrals: 649 Unresolved non-hydrogen chiralities: 62 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 5, 'TYR:plan': 7, 'ASN:plan1': 17, 'TRP:plan': 1, 'ASP:plan': 5, 'PHE:plan': 10, 'GLU:plan': 21, 'ARG:plan': 22} Unresolved non-hydrogen planarities: 427 Chain: "u" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 546 Classifications: {'peptide': 110} Incomplete info: {'truncation_to_alanine': 97} Link IDs: {'PTRANS': 4, 'TRANS': 105} Chain breaks: 1 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 393 Unresolved non-hydrogen angles: 491 Unresolved non-hydrogen dihedrals: 346 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 5, 'TYR:plan': 6, 'ASN:plan1': 6, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 6, 'GLU:plan': 2, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 221 Chain: "v" Number of atoms: 1299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1299 Classifications: {'peptide': 161} Link IDs: {'PTRANS': 7, 'TRANS': 153} Chain breaks: 1 Chain: "x" Number of atoms: 2503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2503 Classifications: {'peptide': 303} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 291} Chain: "y" Number of atoms: 1107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1107 Classifications: {'peptide': 225} Incomplete info: {'truncation_to_alanine': 189} Link IDs: {'PTRANS': 7, 'TRANS': 217} Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 614 Unresolved non-hydrogen angles: 802 Unresolved non-hydrogen dihedrals: 474 Unresolved non-hydrogen chiralities: 79 Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 4, 'TYR:plan': 4, 'ASN:plan1': 14, 'TRP:plan': 1, 'ASP:plan': 13, 'PHE:plan': 7, 'GLU:plan': 16, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 335 Chain: "z" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 173 Classifications: {'peptide': 35} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 1, 'TRANS': 33} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 125 Unresolved non-hydrogen angles: 149 Unresolved non-hydrogen dihedrals: 115 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 1, 'ASN:plan1': 5, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 59 Chain: "T" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 175 Classifications: {'peptide': 23} Link IDs: {'PTRANS': 5, 'TRANS': 17} Chain: "j" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 78457 SG CYS j 19 97.717 109.878 172.551 1.00 25.11 S ATOM 78485 SG CYS j 22 100.284 110.485 169.750 1.00 22.23 S ATOM 78581 SG CYS j 34 99.284 106.940 170.462 1.00 23.35 S ATOM 78598 SG CYS j 37 101.179 108.716 173.068 1.00 19.70 S Time building chain proxies: 36.40, per 1000 atoms: 0.40 Number of scatterers: 90456 At special positions: 0 Unit cell: (236.38, 213.06, 320.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 97 16.00 P 1812 15.00 O 22070 8.00 N 16965 7.00 C 49511 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 38.10 Conformation dependent library (CDL) restraints added in 10.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN j 101 " pdb="ZN ZN j 101 " - pdb=" SG CYS j 37 " pdb="ZN ZN j 101 " - pdb=" SG CYS j 19 " pdb="ZN ZN j 101 " - pdb=" SG CYS j 22 " pdb="ZN ZN j 101 " - pdb=" SG CYS j 34 " Number of angles added : 6 14974 Ramachandran restraints generated. 7487 Oldfield, 0 Emsley, 7487 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14478 Finding SS restraints... Secondary structure from input PDB file: 294 helices and 83 sheets defined 40.7% alpha, 12.7% beta 508 base pairs and 929 stacking pairs defined. Time for finding SS restraints: 27.76 Creating SS restraints... Processing helix chain '3' and resid 66 through 70 removed outlier: 3.615A pdb=" N ARG 3 69 " --> pdb=" O THR 3 66 " (cutoff:3.500A) Processing helix chain '3' and resid 85 through 97 removed outlier: 3.744A pdb=" N GLN 3 95 " --> pdb=" O GLU 3 91 " (cutoff:3.500A) Processing helix chain '3' and resid 101 through 128 removed outlier: 3.501A pdb=" N LEU 3 115 " --> pdb=" O ARG 3 111 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N TYR 3 118 " --> pdb=" O ARG 3 114 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ARG 3 124 " --> pdb=" O LEU 3 120 " (cutoff:3.500A) Processing helix chain '3' and resid 137 through 153 removed outlier: 3.522A pdb=" N ARG 3 143 " --> pdb=" O LYS 3 139 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N GLU 3 144 " --> pdb=" O GLN 3 140 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ARG 3 149 " --> pdb=" O ALA 3 145 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS 3 150 " --> pdb=" O SER 3 146 " (cutoff:3.500A) Processing helix chain '3' and resid 156 through 171 removed outlier: 3.586A pdb=" N ILE 3 161 " --> pdb=" O LEU 3 157 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLU 3 164 " --> pdb=" O ASN 3 160 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS 3 167 " --> pdb=" O LYS 3 163 " (cutoff:3.500A) Processing helix chain '3' and resid 185 through 192 Processing helix chain '4' and resid 7 through 12 removed outlier: 3.825A pdb=" N LEU 4 11 " --> pdb=" O PHE 4 7 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA 4 12 " --> pdb=" O ILE 4 8 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 7 through 12' Processing helix chain '4' and resid 15 through 31 removed outlier: 4.116A pdb=" N LYS 4 21 " --> pdb=" O LYS 4 17 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N SER 4 25 " --> pdb=" O LYS 4 21 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLN 4 27 " --> pdb=" O LEU 4 23 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ARG 4 28 " --> pdb=" O GLU 4 24 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER 4 31 " --> pdb=" O GLN 4 27 " (cutoff:3.500A) Processing helix chain '4' and resid 37 through 45 Processing helix chain '4' and resid 46 through 54 removed outlier: 3.925A pdb=" N TYR 4 50 " --> pdb=" O LYS 4 46 " (cutoff:3.500A) Processing helix chain '4' and resid 60 through 70 removed outlier: 4.322A pdb=" N ASP 4 66 " --> pdb=" O GLN 4 62 " (cutoff:3.500A) Processing helix chain '4' and resid 71 through 75 Processing helix chain '4' and resid 79 through 91 removed outlier: 3.600A pdb=" N GLN 4 84 " --> pdb=" O ARG 4 80 " (cutoff:3.500A) Processing helix chain '4' and resid 99 through 125 removed outlier: 3.948A pdb=" N ASP 4 104 " --> pdb=" O ILE 4 100 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N LYS 4 105 " --> pdb=" O LEU 4 101 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N LEU 4 108 " --> pdb=" O ASP 4 104 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU 4 109 " --> pdb=" O LYS 4 105 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N MET 4 110 " --> pdb=" O PHE 4 106 " (cutoff:3.500A) Processing helix chain '4' and resid 129 through 144 removed outlier: 3.913A pdb=" N VAL 4 133 " --> pdb=" O LEU 4 129 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ALA 4 135 " --> pdb=" O ASP 4 131 " (cutoff:3.500A) Processing helix chain '4' and resid 154 through 164 removed outlier: 4.167A pdb=" N LEU 4 158 " --> pdb=" O PRO 4 154 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N HIS 4 160 " --> pdb=" O GLY 4 156 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASP 4 163 " --> pdb=" O PHE 4 159 " (cutoff:3.500A) Processing helix chain '4' and resid 166 through 173 removed outlier: 3.779A pdb=" N VAL 4 172 " --> pdb=" O GLU 4 168 " (cutoff:3.500A) Processing helix chain '4' and resid 183 through 193 removed outlier: 3.563A pdb=" N ILE 4 190 " --> pdb=" O PHE 4 186 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N SER 4 192 " --> pdb=" O SER 4 188 " (cutoff:3.500A) Processing helix chain '4' and resid 195 through 201 Processing helix chain '4' and resid 201 through 206 Processing helix chain '5' and resid 84 through 89 removed outlier: 4.072A pdb=" N THR 5 89 " --> pdb=" O SER 5 85 " (cutoff:3.500A) Processing helix chain '5' and resid 166 through 170 Processing helix chain 'A' and resid 54 through 68 removed outlier: 3.690A pdb=" N LEU A 60 " --> pdb=" O ARG A 56 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LEU A 61 " --> pdb=" O GLN A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 94 removed outlier: 4.185A pdb=" N LEU A 89 " --> pdb=" O GLN A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 107 removed outlier: 3.693A pdb=" N ARG A 106 " --> pdb=" O SER A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 158 removed outlier: 3.680A pdb=" N ALA A 158 " --> pdb=" O THR A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 172 Processing helix chain 'A' and resid 251 through 253 No H-bonds generated for 'chain 'A' and resid 251 through 253' Processing helix chain 'A' and resid 254 through 273 removed outlier: 3.806A pdb=" N ILE A 258 " --> pdb=" O VAL A 254 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N GLN A 261 " --> pdb=" O ALA A 257 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N ALA A 262 " --> pdb=" O ILE A 258 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TYR A 266 " --> pdb=" O ALA A 262 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL A 267 " --> pdb=" O ALA A 263 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ARG A 269 " --> pdb=" O ARG A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 283 Processing helix chain 'B' and resid 111 through 116 Processing helix chain 'B' and resid 130 through 140 Processing helix chain 'B' and resid 140 through 155 removed outlier: 3.961A pdb=" N ILE B 144 " --> pdb=" O SER B 140 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N TYR B 154 " --> pdb=" O ARG B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 197 Processing helix chain 'B' and resid 204 through 208 removed outlier: 3.578A pdb=" N SER B 207 " --> pdb=" O ASP B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 300 removed outlier: 4.052A pdb=" N ALA B 300 " --> pdb=" O ASP B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 352 Processing helix chain 'B' and resid 372 through 380 removed outlier: 3.705A pdb=" N LYS B 377 " --> pdb=" O PRO B 373 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLN B 378 " --> pdb=" O ALA B 374 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 30 removed outlier: 3.606A pdb=" N LYS C 29 " --> pdb=" O PHE C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 45 removed outlier: 3.592A pdb=" N ALA C 43 " --> pdb=" O SER C 39 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 130 removed outlier: 3.522A pdb=" N ALA C 125 " --> pdb=" O ARG C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 139 removed outlier: 3.683A pdb=" N LEU C 137 " --> pdb=" O VAL C 133 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LEU C 138 " --> pdb=" O PRO C 134 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA C 139 " --> pdb=" O SER C 135 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 133 through 139' Processing helix chain 'C' and resid 155 through 161 removed outlier: 3.661A pdb=" N PHE C 161 " --> pdb=" O VAL C 158 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 166 Processing helix chain 'C' and resid 167 through 174 Processing helix chain 'C' and resid 176 through 185 removed outlier: 3.838A pdb=" N VAL C 180 " --> pdb=" O ALA C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 198 removed outlier: 4.092A pdb=" N ASN C 198 " --> pdb=" O LYS C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 222 Processing helix chain 'C' and resid 236 through 241 Processing helix chain 'C' and resid 242 through 245 Processing helix chain 'C' and resid 254 through 258 Processing helix chain 'C' and resid 259 through 264 removed outlier: 3.791A pdb=" N PHE C 264 " --> pdb=" O LEU C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 331 Processing helix chain 'C' and resid 353 through 361 Processing helix chain 'D' and resid 97 through 108 Processing helix chain 'D' and resid 113 through 118 Processing helix chain 'D' and resid 119 through 125 removed outlier: 3.503A pdb=" N ALA D 125 " --> pdb=" O PRO D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 155 removed outlier: 3.887A pdb=" N PHE D 143 " --> pdb=" O LYS D 139 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU D 144 " --> pdb=" O THR D 140 " (cutoff:3.500A) Proline residue: D 146 - end of helix removed outlier: 3.508A pdb=" N GLU D 149 " --> pdb=" O ILE D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 185 removed outlier: 3.837A pdb=" N VAL D 180 " --> pdb=" O GLN D 176 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU D 185 " --> pdb=" O ALA D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 186 through 188 No H-bonds generated for 'chain 'D' and resid 186 through 188' Processing helix chain 'D' and resid 204 through 209 removed outlier: 3.577A pdb=" N LEU D 208 " --> pdb=" O GLU D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 227 removed outlier: 3.878A pdb=" N GLN D 227 " --> pdb=" O LEU D 223 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 249 Processing helix chain 'D' and resid 250 through 252 No H-bonds generated for 'chain 'D' and resid 250 through 252' Processing helix chain 'D' and resid 255 through 261 removed outlier: 3.636A pdb=" N MET D 261 " --> pdb=" O MET D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 322 through 334 removed outlier: 3.938A pdb=" N LEU D 326 " --> pdb=" O LYS D 322 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LEU D 327 " --> pdb=" O ARG D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 359 removed outlier: 3.542A pdb=" N MET D 352 " --> pdb=" O SER D 348 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N GLU D 354 " --> pdb=" O LYS D 350 " (cutoff:3.500A) Processing helix chain 'D' and resid 371 through 385 Processing helix chain 'D' and resid 394 through 398 Processing helix chain 'D' and resid 416 through 425 removed outlier: 3.554A pdb=" N TYR D 420 " --> pdb=" O ASP D 416 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ILE D 421 " --> pdb=" O PRO D 417 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N VAL D 424 " --> pdb=" O TYR D 420 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N GLY D 425 " --> pdb=" O ILE D 421 " (cutoff:3.500A) Processing helix chain 'D' and resid 446 through 455 Processing helix chain 'D' and resid 465 through 469 Processing helix chain 'D' and resid 474 through 483 removed outlier: 3.673A pdb=" N VAL D 480 " --> pdb=" O LEU D 476 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N SER D 481 " --> pdb=" O GLU D 477 " (cutoff:3.500A) Processing helix chain 'D' and resid 483 through 503 removed outlier: 3.534A pdb=" N TYR D 494 " --> pdb=" O ALA D 490 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N SER D 496 " --> pdb=" O ASP D 492 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLN D 499 " --> pdb=" O ARG D 495 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N TYR D 501 " --> pdb=" O TYR D 497 " (cutoff:3.500A) Processing helix chain 'D' and resid 511 through 515 removed outlier: 3.741A pdb=" N LEU D 515 " --> pdb=" O ILE D 512 " (cutoff:3.500A) Processing helix chain 'D' and resid 518 through 523 removed outlier: 3.859A pdb=" N LYS D 522 " --> pdb=" O ALA D 518 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N SER D 523 " --> pdb=" O LYS D 519 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 518 through 523' Processing helix chain 'E' and resid 85 through 90 Processing helix chain 'E' and resid 115 through 119 removed outlier: 3.687A pdb=" N LYS E 118 " --> pdb=" O SER E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 135 through 140 Processing helix chain 'E' and resid 150 through 163 Processing helix chain 'E' and resid 164 through 171 removed outlier: 3.777A pdb=" N ILE E 171 " --> pdb=" O ALA E 167 " (cutoff:3.500A) Processing helix chain 'E' and resid 174 through 180 removed outlier: 3.766A pdb=" N ALA E 179 " --> pdb=" O LYS E 175 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ALA E 180 " --> pdb=" O GLU E 176 " (cutoff:3.500A) Processing helix chain 'F' and resid 16 through 42 removed outlier: 3.771A pdb=" N ALA F 25 " --> pdb=" O LYS F 21 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LYS F 27 " --> pdb=" O THR F 23 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG F 30 " --> pdb=" O GLN F 26 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE F 33 " --> pdb=" O SER F 29 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ALA F 36 " --> pdb=" O GLN F 32 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ALA F 38 " --> pdb=" O VAL F 34 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N LYS F 40 " --> pdb=" O ALA F 36 " (cutoff:3.500A) Processing helix chain 'F' and resid 45 through 80 removed outlier: 3.807A pdb=" N GLU F 49 " --> pdb=" O GLN F 45 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ALA F 52 " --> pdb=" O ARG F 48 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA F 57 " --> pdb=" O LYS F 53 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG F 63 " --> pdb=" O GLU F 59 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLU F 68 " --> pdb=" O ALA F 64 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLN F 69 " --> pdb=" O ALA F 65 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALA F 73 " --> pdb=" O GLN F 69 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ALA F 76 " --> pdb=" O LEU F 72 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA F 78 " --> pdb=" O ARG F 74 " (cutoff:3.500A) Processing helix chain 'F' and resid 103 through 112 removed outlier: 3.800A pdb=" N ILE F 109 " --> pdb=" O LYS F 105 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N MET F 110 " --> pdb=" O ALA F 106 " (cutoff:3.500A) Processing helix chain 'F' and resid 127 through 135 removed outlier: 3.840A pdb=" N MET F 133 " --> pdb=" O ALA F 129 " (cutoff:3.500A) Processing helix chain 'F' and resid 136 through 140 Proline residue: F 139 - end of helix No H-bonds generated for 'chain 'F' and resid 136 through 140' Processing helix chain 'F' and resid 149 through 157 removed outlier: 4.252A pdb=" N ILE F 155 " --> pdb=" O VAL F 151 " (cutoff:3.500A) Processing helix chain 'F' and resid 172 through 181 removed outlier: 3.659A pdb=" N ILE F 176 " --> pdb=" O ASP F 172 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ALA F 179 " --> pdb=" O ILE F 175 " (cutoff:3.500A) Processing helix chain 'F' and resid 182 through 184 No H-bonds generated for 'chain 'F' and resid 182 through 184' Processing helix chain 'F' and resid 187 through 197 Processing helix chain 'F' and resid 201 through 207 Processing helix chain 'F' and resid 228 through 232 Processing helix chain 'F' and resid 242 through 250 removed outlier: 4.476A pdb=" N LYS F 248 " --> pdb=" O GLY F 244 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 60 Processing helix chain 'G' and resid 60 through 69 removed outlier: 3.883A pdb=" N ASN G 66 " --> pdb=" O ARG G 62 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LEU G 67 " --> pdb=" O LYS G 63 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU G 69 " --> pdb=" O LEU G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 72 through 77 removed outlier: 3.999A pdb=" N GLN G 77 " --> pdb=" O PRO G 73 " (cutoff:3.500A) Processing helix chain 'G' and resid 89 through 95 Processing helix chain 'G' and resid 101 through 117 removed outlier: 3.664A pdb=" N LYS G 106 " --> pdb=" O ALA G 102 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N ALA G 115 " --> pdb=" O ALA G 111 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL G 116 " --> pdb=" O GLU G 112 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA G 117 " --> pdb=" O ALA G 113 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 126 removed outlier: 3.524A pdb=" N SER G 126 " --> pdb=" O GLN G 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 135 through 145 removed outlier: 3.851A pdb=" N ALA G 141 " --> pdb=" O ASN G 137 " (cutoff:3.500A) Processing helix chain 'G' and resid 159 through 163 removed outlier: 3.528A pdb=" N VAL G 163 " --> pdb=" O ILE G 160 " (cutoff:3.500A) Processing helix chain 'G' and resid 165 through 174 Processing helix chain 'G' and resid 182 through 190 removed outlier: 3.607A pdb=" N VAL G 189 " --> pdb=" O ARG G 185 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE G 190 " --> pdb=" O LEU G 186 " (cutoff:3.500A) Processing helix chain 'G' and resid 207 through 222 removed outlier: 3.689A pdb=" N SER G 213 " --> pdb=" O ASN G 209 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N SER G 216 " --> pdb=" O ALA G 212 " (cutoff:3.500A) Processing helix chain 'H' and resid 21 through 23 No H-bonds generated for 'chain 'H' and resid 21 through 23' Processing helix chain 'H' and resid 61 through 66 Processing helix chain 'H' and resid 67 through 84 removed outlier: 3.520A pdb=" N VAL H 71 " --> pdb=" O CYS H 67 " (cutoff:3.500A) Processing helix chain 'H' and resid 114 through 118 Processing helix chain 'H' and resid 148 through 163 removed outlier: 3.634A pdb=" N CYS H 163 " --> pdb=" O ILE H 159 " (cutoff:3.500A) Processing helix chain 'J' and resid 96 through 107 Processing helix chain 'J' and resid 114 through 119 Processing helix chain 'J' and resid 134 through 161 removed outlier: 3.639A pdb=" N ARG J 138 " --> pdb=" O ASP J 134 " (cutoff:3.500A) Processing helix chain 'J' and resid 177 through 205 removed outlier: 3.923A pdb=" N LYS J 190 " --> pdb=" O GLN J 186 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLU J 191 " --> pdb=" O GLU J 187 " (cutoff:3.500A) Processing helix chain 'K' and resid 15 through 27 Processing helix chain 'K' and resid 94 through 105 removed outlier: 4.382A pdb=" N TYR K 98 " --> pdb=" O PRO K 94 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ASP K 100 " --> pdb=" O ARG K 96 " (cutoff:3.500A) Processing helix chain 'K' and resid 117 through 123 Processing helix chain 'K' and resid 126 through 137 removed outlier: 4.035A pdb=" N PHE K 137 " --> pdb=" O LEU K 133 " (cutoff:3.500A) Processing helix chain 'K' and resid 145 through 148 Proline residue: K 148 - end of helix No H-bonds generated for 'chain 'K' and resid 145 through 148' Processing helix chain 'K' and resid 149 through 154 removed outlier: 3.727A pdb=" N ILE K 153 " --> pdb=" O MET K 149 " (cutoff:3.500A) Processing helix chain 'K' and resid 155 through 160 Processing helix chain 'K' and resid 174 through 187 removed outlier: 3.605A pdb=" N GLU K 181 " --> pdb=" O GLN K 177 " (cutoff:3.500A) Processing helix chain 'K' and resid 209 through 228 Processing helix chain 'K' and resid 231 through 234 removed outlier: 3.562A pdb=" N LYS K 234 " --> pdb=" O ASP K 231 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 231 through 234' Processing helix chain 'K' and resid 256 through 265 Processing helix chain 'L' and resid 27 through 46 removed outlier: 3.667A pdb=" N ALA L 43 " --> pdb=" O ARG L 39 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N LYS L 45 " --> pdb=" O THR L 41 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE L 46 " --> pdb=" O LYS L 42 " (cutoff:3.500A) Processing helix chain 'L' and resid 76 through 82 Processing helix chain 'L' and resid 86 through 91 removed outlier: 4.563A pdb=" N SER L 91 " --> pdb=" O ARG L 87 " (cutoff:3.500A) Processing helix chain 'L' and resid 105 through 123 removed outlier: 4.246A pdb=" N ASN L 112 " --> pdb=" O SER L 108 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLU L 114 " --> pdb=" O GLN L 110 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG L 115 " --> pdb=" O ARG L 111 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N VAL L 118 " --> pdb=" O GLU L 114 " (cutoff:3.500A) Processing helix chain 'M' and resid 52 through 54 No H-bonds generated for 'chain 'M' and resid 52 through 54' Processing helix chain 'M' and resid 70 through 81 Processing helix chain 'M' and resid 90 through 102 removed outlier: 3.527A pdb=" N LYS M 94 " --> pdb=" O SER M 90 " (cutoff:3.500A) Processing helix chain 'M' and resid 106 through 122 removed outlier: 4.067A pdb=" N MET M 114 " --> pdb=" O ARG M 110 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N GLU M 122 " --> pdb=" O LYS M 118 " (cutoff:3.500A) Processing helix chain 'M' and resid 123 through 125 No H-bonds generated for 'chain 'M' and resid 123 through 125' Processing helix chain 'N' and resid 3 through 11 removed outlier: 3.559A pdb=" N ALA N 11 " --> pdb=" O LEU N 7 " (cutoff:3.500A) Processing helix chain 'N' and resid 16 through 33 Processing helix chain 'N' and resid 46 through 52 Processing helix chain 'N' and resid 97 through 110 removed outlier: 3.623A pdb=" N VAL N 106 " --> pdb=" O ALA N 102 " (cutoff:3.500A) Processing helix chain 'N' and resid 148 through 152 removed outlier: 3.612A pdb=" N VAL N 152 " --> pdb=" O ASN N 149 " (cutoff:3.500A) Processing helix chain 'N' and resid 153 through 157 removed outlier: 3.508A pdb=" N LYS N 157 " --> pdb=" O PRO N 154 " (cutoff:3.500A) Processing helix chain 'N' and resid 158 through 163 removed outlier: 3.646A pdb=" N ARG N 162 " --> pdb=" O HIS N 158 " (cutoff:3.500A) Processing helix chain 'N' and resid 165 through 172 removed outlier: 3.824A pdb=" N LYS N 170 " --> pdb=" O SER N 166 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ARG N 172 " --> pdb=" O GLY N 168 " (cutoff:3.500A) Processing helix chain 'O' and resid 16 through 30 removed outlier: 3.867A pdb=" N SER O 22 " --> pdb=" O GLY O 18 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS O 26 " --> pdb=" O SER O 22 " (cutoff:3.500A) Processing helix chain 'O' and resid 38 through 41 Processing helix chain 'O' and resid 47 through 60 removed outlier: 4.258A pdb=" N ASN O 51 " --> pdb=" O HIS O 47 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LYS O 52 " --> pdb=" O PHE O 48 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LYS O 54 " --> pdb=" O ARG O 50 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N TYR O 58 " --> pdb=" O LYS O 54 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ARG O 60 " --> pdb=" O LEU O 56 " (cutoff:3.500A) Processing helix chain 'O' and resid 66 through 70 removed outlier: 3.719A pdb=" N GLY O 70 " --> pdb=" O PRO O 67 " (cutoff:3.500A) Processing helix chain 'O' and resid 76 through 85 removed outlier: 3.602A pdb=" N PHE O 81 " --> pdb=" O PRO O 77 " (cutoff:3.500A) Processing helix chain 'O' and resid 95 through 100 Processing helix chain 'O' and resid 101 through 103 No H-bonds generated for 'chain 'O' and resid 101 through 103' Processing helix chain 'O' and resid 110 through 115 removed outlier: 4.017A pdb=" N LYS O 115 " --> pdb=" O PRO O 111 " (cutoff:3.500A) Processing helix chain 'O' and resid 125 through 130 Processing helix chain 'O' and resid 139 through 143 Processing helix chain 'O' and resid 144 through 147 Processing helix chain 'O' and resid 150 through 186 removed outlier: 3.793A pdb=" N VAL O 154 " --> pdb=" O TYR O 150 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU O 159 " --> pdb=" O ALA O 155 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL O 163 " --> pdb=" O GLU O 159 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA O 171 " --> pdb=" O ALA O 167 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LYS O 178 " --> pdb=" O ALA O 174 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE O 179 " --> pdb=" O LYS O 175 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLU O 184 " --> pdb=" O ALA O 180 " (cutoff:3.500A) Processing helix chain 'O' and resid 187 through 192 removed outlier: 3.668A pdb=" N LYS O 191 " --> pdb=" O PRO O 187 " (cutoff:3.500A) Processing helix chain 'P' and resid 25 through 37 removed outlier: 3.846A pdb=" N SER P 29 " --> pdb=" O HIS P 25 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG P 30 " --> pdb=" O PHE P 26 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N GLU P 31 " --> pdb=" O LYS P 27 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL P 32 " --> pdb=" O ASN P 28 " (cutoff:3.500A) Processing helix chain 'P' and resid 40 through 53 removed outlier: 3.730A pdb=" N ASN P 50 " --> pdb=" O ILE P 46 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL P 51 " --> pdb=" O PHE P 47 " (cutoff:3.500A) Processing helix chain 'P' and resid 71 through 76 removed outlier: 4.181A pdb=" N LYS P 74 " --> pdb=" O ALA P 71 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N PHE P 76 " --> pdb=" O GLY P 73 " (cutoff:3.500A) Processing helix chain 'P' and resid 85 through 106 removed outlier: 3.544A pdb=" N ASN P 97 " --> pdb=" O ASP P 93 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ALA P 102 " --> pdb=" O ALA P 98 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ALA P 104 " --> pdb=" O ALA P 100 " (cutoff:3.500A) Processing helix chain 'P' and resid 108 through 110 No H-bonds generated for 'chain 'P' and resid 108 through 110' Processing helix chain 'Q' and resid 25 through 36 removed outlier: 3.537A pdb=" N VAL Q 29 " --> pdb=" O LEU Q 25 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N PHE Q 34 " --> pdb=" O LYS Q 30 " (cutoff:3.500A) Processing helix chain 'Q' and resid 43 through 52 removed outlier: 4.565A pdb=" N LYS Q 49 " --> pdb=" O LYS Q 45 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ARG Q 50 " --> pdb=" O ALA Q 46 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N PHE Q 52 " --> pdb=" O LEU Q 48 " (cutoff:3.500A) Processing helix chain 'Q' and resid 62 through 71 removed outlier: 3.592A pdb=" N SER Q 71 " --> pdb=" O ALA Q 67 " (cutoff:3.500A) Processing helix chain 'Q' and resid 111 through 116 removed outlier: 3.608A pdb=" N LEU Q 116 " --> pdb=" O ARG Q 112 " (cutoff:3.500A) Processing helix chain 'Q' and resid 117 through 119 No H-bonds generated for 'chain 'Q' and resid 117 through 119' Processing helix chain 'Q' and resid 124 through 130 Processing helix chain 'S' and resid 32 through 48 removed outlier: 3.701A pdb=" N ALA S 36 " --> pdb=" O ASN S 32 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER S 38 " --> pdb=" O SER S 34 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N TRP S 41 " --> pdb=" O LYS S 37 " (cutoff:3.500A) Processing helix chain 'S' and resid 97 through 113 removed outlier: 3.559A pdb=" N VAL S 102 " --> pdb=" O ARG S 98 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU S 103 " --> pdb=" O VAL S 99 " (cutoff:3.500A) Processing helix chain 'S' and resid 136 through 142 removed outlier: 3.543A pdb=" N LEU S 142 " --> pdb=" O TYR S 138 " (cutoff:3.500A) Processing helix chain 'V' and resid 121 through 128 removed outlier: 3.675A pdb=" N ASP V 126 " --> pdb=" O LYS V 122 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N LEU V 127 " --> pdb=" O GLU V 123 " (cutoff:3.500A) Processing helix chain 'V' and resid 128 through 134 removed outlier: 3.939A pdb=" N ASN V 134 " --> pdb=" O ARG V 130 " (cutoff:3.500A) Processing helix chain 'W' and resid 21 through 35 Processing helix chain 'W' and resid 49 through 59 removed outlier: 3.807A pdb=" N LEU W 53 " --> pdb=" O ARG W 49 " (cutoff:3.500A) Processing helix chain 'W' and resid 71 through 78 Processing helix chain 'W' and resid 89 through 95 Processing helix chain 'W' and resid 113 through 119 Processing helix chain 'W' and resid 161 through 169 removed outlier: 3.816A pdb=" N ARG W 166 " --> pdb=" O GLU W 162 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLY W 169 " --> pdb=" O VAL W 165 " (cutoff:3.500A) Processing helix chain 'W' and resid 195 through 205 removed outlier: 3.533A pdb=" N LEU W 204 " --> pdb=" O ARG W 200 " (cutoff:3.500A) Processing helix chain 'X' and resid 3 through 8 Processing helix chain 'X' and resid 12 through 16 Processing helix chain 'X' and resid 57 through 62 removed outlier: 4.820A pdb=" N ILE X 62 " --> pdb=" O GLU X 58 " (cutoff:3.500A) Processing helix chain 'X' and resid 68 through 77 removed outlier: 3.651A pdb=" N LYS X 73 " --> pdb=" O GLU X 69 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLU X 76 " --> pdb=" O MET X 72 " (cutoff:3.500A) Processing helix chain 'X' and resid 90 through 101 removed outlier: 3.828A pdb=" N GLU X 96 " --> pdb=" O PHE X 92 " (cutoff:3.500A) Processing helix chain 'X' and resid 132 through 138 Processing helix chain 'Y' and resid 10 through 20 removed outlier: 3.750A pdb=" N PHE Y 19 " --> pdb=" O ARG Y 15 " (cutoff:3.500A) Processing helix chain 'Y' and resid 24 through 29 removed outlier: 4.160A pdb=" N VAL Y 28 " --> pdb=" O SER Y 24 " (cutoff:3.500A) Processing helix chain 'Y' and resid 111 through 119 Processing helix chain 'b' and resid 14 through 29 Processing helix chain 'b' and resid 39 through 69 removed outlier: 3.721A pdb=" N LYS b 50 " --> pdb=" O PHE b 46 " (cutoff:3.500A) Processing helix chain 'b' and resid 76 through 88 removed outlier: 3.544A pdb=" N TYR b 87 " --> pdb=" O LEU b 83 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ASP b 88 " --> pdb=" O ASN b 84 " (cutoff:3.500A) Processing helix chain 'b' and resid 88 through 118 removed outlier: 3.609A pdb=" N THR b 101 " --> pdb=" O SER b 97 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALA b 102 " --> pdb=" O GLN b 98 " (cutoff:3.500A) Processing helix chain 'b' and resid 122 through 144 removed outlier: 3.690A pdb=" N LEU b 134 " --> pdb=" O LYS b 130 " (cutoff:3.500A) Processing helix chain 'b' and resid 146 through 161 removed outlier: 3.639A pdb=" N PHE b 150 " --> pdb=" O SER b 146 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU b 151 " --> pdb=" O SER b 147 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLN b 153 " --> pdb=" O GLU b 149 " (cutoff:3.500A) Processing helix chain 'b' and resid 180 through 187 Processing helix chain 'b' and resid 235 through 246 removed outlier: 3.925A pdb=" N HIS b 246 " --> pdb=" O THR b 242 " (cutoff:3.500A) Processing helix chain 'b' and resid 264 through 275 Processing helix chain 'b' and resid 306 through 311 Processing helix chain 'b' and resid 328 through 344 Processing helix chain 'b' and resid 398 through 407 removed outlier: 3.626A pdb=" N GLY b 407 " --> pdb=" O GLU b 403 " (cutoff:3.500A) Processing helix chain 'b' and resid 424 through 430 Processing helix chain 'b' and resid 448 through 465 Processing helix chain 'd' and resid 21 through 25 Processing helix chain 'd' and resid 32 through 49 Processing helix chain 'd' and resid 57 through 67 removed outlier: 4.027A pdb=" N ARG d 67 " --> pdb=" O GLU d 63 " (cutoff:3.500A) Processing helix chain 'e' and resid 51 through 55 removed outlier: 3.576A pdb=" N TYR e 54 " --> pdb=" O LYS e 51 " (cutoff:3.500A) Processing helix chain 'e' and resid 79 through 84 removed outlier: 4.217A pdb=" N MET e 84 " --> pdb=" O LEU e 81 " (cutoff:3.500A) Processing helix chain 'e' and resid 100 through 110 removed outlier: 3.557A pdb=" N GLU e 104 " --> pdb=" O ARG e 100 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE e 105 " --> pdb=" O LYS e 101 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLU e 107 " --> pdb=" O VAL e 103 " (cutoff:3.500A) Processing helix chain 'f' and resid 41 through 45 removed outlier: 3.914A pdb=" N PHE f 44 " --> pdb=" O GLU f 41 " (cutoff:3.500A) Processing helix chain 'h' and resid 12 through 31 removed outlier: 4.105A pdb=" N GLN h 21 " --> pdb=" O ALA h 17 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N GLU h 22 " --> pdb=" O GLU h 18 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU h 23 " --> pdb=" O GLN h 19 " (cutoff:3.500A) Processing helix chain 'h' and resid 31 through 37 removed outlier: 3.791A pdb=" N ILE h 35 " --> pdb=" O ARG h 31 " (cutoff:3.500A) Processing helix chain 'h' and resid 41 through 72 removed outlier: 3.545A pdb=" N ILE h 56 " --> pdb=" O ASP h 52 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N THR h 58 " --> pdb=" O ALA h 54 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU h 66 " --> pdb=" O GLU h 62 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ALA h 67 " --> pdb=" O SER h 63 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU h 70 " --> pdb=" O LEU h 66 " (cutoff:3.500A) Processing helix chain 'h' and resid 87 through 92 Processing helix chain 'h' and resid 95 through 100 Processing helix chain 'h' and resid 104 through 109 Processing helix chain 'i' and resid 32 through 46 removed outlier: 3.889A pdb=" N GLU i 44 " --> pdb=" O SER i 40 " (cutoff:3.500A) Processing helix chain 'i' and resid 51 through 61 Processing helix chain 'i' and resid 63 through 76 Processing helix chain 'i' and resid 77 through 99 removed outlier: 4.279A pdb=" N ILE i 85 " --> pdb=" O ALA i 81 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N SER i 90 " --> pdb=" O GLU i 86 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL i 91 " --> pdb=" O GLU i 87 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N LEU i 97 " --> pdb=" O GLN i 93 " (cutoff:3.500A) Processing helix chain 'j' and resid 50 through 55 removed outlier: 3.892A pdb=" N ARG j 55 " --> pdb=" O ALA j 51 " (cutoff:3.500A) Processing helix chain 'j' and resid 66 through 75 removed outlier: 3.513A pdb=" N HIS j 71 " --> pdb=" O LEU j 67 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N SER j 73 " --> pdb=" O LYS j 69 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N LYS j 75 " --> pdb=" O HIS j 71 " (cutoff:3.500A) Processing helix chain 'm' and resid 221 through 225 removed outlier: 3.744A pdb=" N ARG m 224 " --> pdb=" O PRO m 221 " (cutoff:3.500A) Processing helix chain 'm' and resid 228 through 244 removed outlier: 3.516A pdb=" N ARG m 243 " --> pdb=" O ALA m 239 " (cutoff:3.500A) Processing helix chain 'm' and resid 249 through 256 removed outlier: 3.656A pdb=" N ARG m 256 " --> pdb=" O GLN m 252 " (cutoff:3.500A) Processing helix chain 'm' and resid 328 through 342 removed outlier: 3.882A pdb=" N TYR m 341 " --> pdb=" O CYS m 337 " (cutoff:3.500A) Processing helix chain 'n' and resid 11 through 15 removed outlier: 4.006A pdb=" N ILE n 15 " --> pdb=" O GLY n 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'n' and resid 11 through 15' Processing helix chain 'n' and resid 19 through 27 Processing helix chain 'n' and resid 29 through 37 removed outlier: 3.586A pdb=" N ILE n 36 " --> pdb=" O ASP n 32 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N CYS n 37 " --> pdb=" O PHE n 33 " (cutoff:3.500A) Processing helix chain 'n' and resid 49 through 54 Processing helix chain 'n' and resid 66 through 70 Processing helix chain 'n' and resid 76 through 96 removed outlier: 3.546A pdb=" N ARG n 82 " --> pdb=" O VAL n 78 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N PHE n 87 " --> pdb=" O GLU n 83 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA n 88 " --> pdb=" O TYR n 84 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N LYS n 93 " --> pdb=" O ARG n 89 " (cutoff:3.500A) Processing helix chain 'n' and resid 99 through 109 removed outlier: 3.586A pdb=" N ALA n 103 " --> pdb=" O GLU n 99 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU n 106 " --> pdb=" O THR n 102 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLU n 107 " --> pdb=" O ALA n 103 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ALA n 108 " --> pdb=" O LYS n 104 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ARG n 109 " --> pdb=" O ARG n 105 " (cutoff:3.500A) Processing helix chain 'n' and resid 116 through 123 removed outlier: 4.101A pdb=" N GLU n 121 " --> pdb=" O HIS n 117 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ARG n 122 " --> pdb=" O ILE n 118 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N TYR n 123 " --> pdb=" O ILE n 119 " (cutoff:3.500A) Processing helix chain 'n' and resid 125 through 132 Processing helix chain 'n' and resid 133 through 143 Processing helix chain 'n' and resid 153 through 175 removed outlier: 3.577A pdb=" N ALA n 158 " --> pdb=" O ALA n 154 " (cutoff:3.500A) Processing helix chain 'n' and resid 215 through 242 removed outlier: 3.576A pdb=" N ALA n 228 " --> pdb=" O GLU n 224 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LEU n 229 " --> pdb=" O PHE n 225 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASN n 239 " --> pdb=" O PHE n 235 " (cutoff:3.500A) Processing helix chain 'n' and resid 250 through 256 Processing helix chain 'n' and resid 258 through 261 Processing helix chain 'n' and resid 365 through 376 Processing helix chain 'n' and resid 420 through 431 removed outlier: 3.832A pdb=" N VAL n 424 " --> pdb=" O GLN n 420 " (cutoff:3.500A) Processing helix chain 'o' and resid 117 through 126 Processing helix chain 'o' and resid 127 through 129 No H-bonds generated for 'chain 'o' and resid 127 through 129' Processing helix chain 'o' and resid 155 through 164 Processing helix chain 'o' and resid 187 through 192 removed outlier: 4.112A pdb=" N PHE o 191 " --> pdb=" O GLU o 188 " (cutoff:3.500A) Processing helix chain 'o' and resid 202 through 212 Processing helix chain 'o' and resid 216 through 224 removed outlier: 3.590A pdb=" N LEU o 223 " --> pdb=" O LYS o 219 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE o 224 " --> pdb=" O ALA o 220 " (cutoff:3.500A) Processing helix chain 'o' and resid 226 through 238 removed outlier: 3.673A pdb=" N LEU o 238 " --> pdb=" O LYS o 234 " (cutoff:3.500A) Processing helix chain 'r' and resid 7 through 15 Processing helix chain 'r' and resid 19 through 41 removed outlier: 3.958A pdb=" N LYS r 24 " --> pdb=" O HIS r 20 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ALA r 32 " --> pdb=" O ALA r 28 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N HIS r 33 " --> pdb=" O ALA r 29 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N SER r 36 " --> pdb=" O ALA r 32 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N LEU r 37 " --> pdb=" O HIS r 33 " (cutoff:3.500A) Processing helix chain 'r' and resid 44 through 73 Processing helix chain 'r' and resid 205 through 212 Processing helix chain 'r' and resid 247 through 252 Processing helix chain 't' and resid 26 through 47 removed outlier: 3.582A pdb=" N LYS t 39 " --> pdb=" O GLN t 35 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU t 41 " --> pdb=" O ILE t 37 " (cutoff:3.500A) Processing helix chain 't' and resid 53 through 76 removed outlier: 4.087A pdb=" N PHE t 57 " --> pdb=" O ARG t 53 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ILE t 58 " --> pdb=" O ALA t 54 " (cutoff:3.500A) Processing helix chain 't' and resid 102 through 112 Processing helix chain 't' and resid 126 through 134 Processing helix chain 't' and resid 146 through 158 removed outlier: 3.546A pdb=" N VAL t 150 " --> pdb=" O ASN t 146 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TYR t 155 " --> pdb=" O ARG t 151 " (cutoff:3.500A) Processing helix chain 't' and resid 171 through 179 removed outlier: 3.635A pdb=" N ILE t 175 " --> pdb=" O ASP t 171 " (cutoff:3.500A) Processing helix chain 't' and resid 186 through 196 Processing helix chain 't' and resid 199 through 208 removed outlier: 4.462A pdb=" N GLU t 203 " --> pdb=" O SER t 199 " (cutoff:3.500A) Processing helix chain 't' and resid 238 through 249 removed outlier: 3.578A pdb=" N ASN t 242 " --> pdb=" O GLY t 238 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL t 249 " --> pdb=" O ILE t 245 " (cutoff:3.500A) Processing helix chain 'u' and resid 33 through 43 Processing helix chain 'u' and resid 45 through 49 removed outlier: 3.680A pdb=" N VAL u 49 " --> pdb=" O PRO u 46 " (cutoff:3.500A) Processing helix chain 'u' and resid 52 through 58 removed outlier: 3.942A pdb=" N ARG u 56 " --> pdb=" O THR u 52 " (cutoff:3.500A) Processing helix chain 'u' and resid 67 through 71 removed outlier: 3.970A pdb=" N ALA u 70 " --> pdb=" O THR u 67 " (cutoff:3.500A) Processing helix chain 'u' and resid 83 through 114 removed outlier: 3.721A pdb=" N MET u 94 " --> pdb=" O THR u 90 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N LYS u 95 " --> pdb=" O LEU u 91 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ARG u 96 " --> pdb=" O ASN u 92 " (cutoff:3.500A) Processing helix chain 'v' and resid 3 through 12 removed outlier: 3.725A pdb=" N ASN v 8 " --> pdb=" O PRO v 4 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LYS v 9 " --> pdb=" O ARG v 5 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLN v 10 " --> pdb=" O GLN v 6 " (cutoff:3.500A) Processing helix chain 'v' and resid 34 through 40 Processing helix chain 'v' and resid 45 through 51 Processing helix chain 'v' and resid 136 through 152 removed outlier: 3.508A pdb=" N GLU v 142 " --> pdb=" O VAL v 138 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LYS v 148 " --> pdb=" O GLU v 144 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N ALA v 149 " --> pdb=" O ALA v 145 " (cutoff:3.500A) Processing helix chain 'v' and resid 160 through 175 removed outlier: 3.918A pdb=" N LYS v 173 " --> pdb=" O ARG v 169 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TYR v 174 " --> pdb=" O LEU v 170 " (cutoff:3.500A) Processing helix chain 'v' and resid 178 through 182 removed outlier: 3.648A pdb=" N SER v 181 " --> pdb=" O ASP v 178 " (cutoff:3.500A) Processing helix chain 'v' and resid 196 through 207 removed outlier: 3.532A pdb=" N LYS v 206 " --> pdb=" O TYR v 202 " (cutoff:3.500A) Processing helix chain 'x' and resid 12 through 37 removed outlier: 3.507A pdb=" N GLN x 20 " --> pdb=" O LYS x 16 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LYS x 23 " --> pdb=" O HIS x 19 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LYS x 25 " --> pdb=" O LYS x 21 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N LEU x 26 " --> pdb=" O ASN x 22 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLU x 31 " --> pdb=" O GLU x 27 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG x 32 " --> pdb=" O ARG x 28 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS x 34 " --> pdb=" O LYS x 30 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N GLU x 35 " --> pdb=" O GLU x 31 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLU x 36 " --> pdb=" O ARG x 32 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N GLU x 37 " --> pdb=" O ALA x 33 " (cutoff:3.500A) Processing helix chain 'x' and resid 39 through 50 removed outlier: 3.950A pdb=" N LYS x 43 " --> pdb=" O ASP x 39 " (cutoff:3.500A) Processing helix chain 'x' and resid 54 through 58 Processing helix chain 'x' and resid 71 through 79 removed outlier: 3.661A pdb=" N GLN x 75 " --> pdb=" O ASP x 71 " (cutoff:3.500A) Processing helix chain 'x' and resid 83 through 87 Processing helix chain 'x' and resid 105 through 110 Processing helix chain 'x' and resid 113 through 119 Processing helix chain 'x' and resid 132 through 142 removed outlier: 3.721A pdb=" N GLU x 138 " --> pdb=" O HIS x 134 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LYS x 142 " --> pdb=" O GLU x 138 " (cutoff:3.500A) Processing helix chain 'x' and resid 207 through 217 removed outlier: 4.796A pdb=" N ARG x 213 " --> pdb=" O MET x 209 " (cutoff:3.500A) Processing helix chain 'y' and resid 12 through 17 removed outlier: 4.114A pdb=" N PHE y 16 " --> pdb=" O GLU y 12 " (cutoff:3.500A) Processing helix chain 'y' and resid 31 through 43 removed outlier: 3.999A pdb=" N TYR y 35 " --> pdb=" O SER y 31 " (cutoff:3.500A) Processing helix chain 'y' and resid 58 through 63 removed outlier: 3.633A pdb=" N THR y 63 " --> pdb=" O ILE y 59 " (cutoff:3.500A) Processing helix chain 'y' and resid 77 through 88 Processing helix chain 'y' and resid 103 through 108 Processing helix chain 'y' and resid 122 through 133 Processing helix chain 'y' and resid 141 through 145 removed outlier: 3.610A pdb=" N GLY y 144 " --> pdb=" O THR y 141 " (cutoff:3.500A) Processing helix chain 'y' and resid 147 through 152 Processing helix chain 'y' and resid 166 through 178 Processing helix chain 'y' and resid 211 through 222 Processing helix chain 'z' and resid 89 through 101 removed outlier: 4.084A pdb=" N TRP z 94 " --> pdb=" O ASN z 90 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ALA z 95 " --> pdb=" O ARG z 91 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYS z 97 " --> pdb=" O LYS z 93 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LYS z 101 " --> pdb=" O LYS z 97 " (cutoff:3.500A) Processing helix chain 'z' and resid 102 through 116 removed outlier: 3.824A pdb=" N LYS z 106 " --> pdb=" O GLY z 102 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N PHE z 113 " --> pdb=" O ASN z 109 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain '3' and resid 19 through 21 Processing sheet with id=AA2, first strand: chain '3' and resid 51 through 56 removed outlier: 3.749A pdb=" N LYS 3 59 " --> pdb=" O ASP 3 56 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N MET 3 64 " --> pdb=" O GLN 3 78 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '3' and resid 132 through 133 Processing sheet with id=AA4, first strand: chain '5' and resid 12 through 16 removed outlier: 3.707A pdb=" N GLY 5 6 " --> pdb=" O SER 5 338 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N SER 5 338 " --> pdb=" O GLY 5 6 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain '5' and resid 45 through 50 removed outlier: 4.589A pdb=" N PHE 5 47 " --> pdb=" O ALA 5 58 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N LEU 5 49 " --> pdb=" O PHE 5 56 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N VAL 5 57 " --> pdb=" O GLU 5 65 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N CYS 5 66 " --> pdb=" O SER 5 77 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASN 5 68 " --> pdb=" O ILE 5 75 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE 5 75 " --> pdb=" O ASN 5 68 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain '5' and resid 101 through 103 Processing sheet with id=AA7, first strand: chain '5' and resid 134 through 135 Processing sheet with id=AA8, first strand: chain '5' and resid 153 through 156 removed outlier: 3.567A pdb=" N PHE 5 180 " --> pdb=" O LEU 5 154 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N SER 5 156 " --> pdb=" O LYS 5 178 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N LYS 5 178 " --> pdb=" O SER 5 156 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain '5' and resid 198 through 202 removed outlier: 3.936A pdb=" N GLY 5 200 " --> pdb=" O ILE 5 228 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain '5' and resid 259 through 262 removed outlier: 3.542A pdb=" N GLY 5 260 " --> pdb=" O TYR 5 269 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LEU 5 268 " --> pdb=" O PHE 5 280 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE 5 270 " --> pdb=" O SER 5 278 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain '5' and resid 298 through 304 removed outlier: 7.326A pdb=" N THR 5 311 " --> pdb=" O SER 5 299 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ILE 5 301 " --> pdb=" O ALA 5 309 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ALA 5 309 " --> pdb=" O ILE 5 301 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N CYS 5 303 " --> pdb=" O VAL 5 307 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N VAL 5 307 " --> pdb=" O CYS 5 303 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE 5 310 " --> pdb=" O ARG 5 318 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ASN 5 316 " --> pdb=" O GLY 5 312 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA 5 328 " --> pdb=" O ILE 5 319 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 48 through 49 removed outlier: 7.871A pdb=" N LEU A 48 " --> pdb=" O PHE A 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 110 through 113 removed outlier: 3.811A pdb=" N ILE A 113 " --> pdb=" O VAL A 122 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N VAL A 126 " --> pdb=" O THR A 228 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N THR A 228 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N ASN A 128 " --> pdb=" O VAL A 226 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N VAL A 226 " --> pdb=" O ASN A 128 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ARG A 224 " --> pdb=" O HIS A 130 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N PHE A 225 " --> pdb=" O PHE A 200 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 110 through 113 removed outlier: 3.811A pdb=" N ILE A 113 " --> pdb=" O VAL A 122 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N VAL A 126 " --> pdb=" O THR A 228 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N THR A 228 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N ASN A 128 " --> pdb=" O VAL A 226 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N VAL A 226 " --> pdb=" O ASN A 128 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ARG A 224 " --> pdb=" O HIS A 130 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N PHE A 225 " --> pdb=" O PHE A 200 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 231 through 233 removed outlier: 6.658A pdb=" N ILE A 232 " --> pdb=" O ILE A 242 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 214 through 215 removed outlier: 5.480A pdb=" N LYS B 281 " --> pdb=" O ASN B 325 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N MET B 323 " --> pdb=" O TYR B 283 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ILE B 285 " --> pdb=" O PHE B 321 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N PHE B 321 " --> pdb=" O ILE B 285 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG B 58 " --> pdb=" O ILE B 72 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLY B 52 " --> pdb=" O VAL B 78 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N GLU B 80 " --> pdb=" O LYS B 50 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N LYS B 50 " --> pdb=" O GLU B 80 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 214 through 215 removed outlier: 5.480A pdb=" N LYS B 281 " --> pdb=" O ASN B 325 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N MET B 323 " --> pdb=" O TYR B 283 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ILE B 285 " --> pdb=" O PHE B 321 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N PHE B 321 " --> pdb=" O ILE B 285 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG B 58 " --> pdb=" O ILE B 72 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLY B 52 " --> pdb=" O VAL B 78 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N GLU B 80 " --> pdb=" O LYS B 50 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N LYS B 50 " --> pdb=" O GLU B 80 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N HIS B 55 " --> pdb=" O ILE B 359 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N ILE B 359 " --> pdb=" O HIS B 55 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N VAL B 57 " --> pdb=" O LYS B 357 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 163 through 164 removed outlier: 3.801A pdb=" N MET B 84 " --> pdb=" O VAL B 203 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 98 through 106 removed outlier: 6.545A pdb=" N GLY B 91 " --> pdb=" O LEU B 102 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N THR B 104 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N VAL B 89 " --> pdb=" O THR B 104 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N VAL B 157 " --> pdb=" O TYR B 92 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 218 through 220 Processing sheet with id=AC3, first strand: chain 'C' and resid 7 through 11 removed outlier: 3.689A pdb=" N ILE C 10 " --> pdb=" O GLU C 20 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N GLU C 20 " --> pdb=" O ILE C 10 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 152 through 154 removed outlier: 6.213A pdb=" N LEU C 152 " --> pdb=" O TRP C 252 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N LEU C 208 " --> pdb=" O ILE C 251 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N THR C 253 " --> pdb=" O LEU C 208 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N VAL C 210 " --> pdb=" O THR C 253 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 188 through 189 Processing sheet with id=AC6, first strand: chain 'D' and resid 192 through 195 removed outlier: 6.708A pdb=" N GLY D 193 " --> pdb=" O VAL D 216 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N VAL D 164 " --> pdb=" O LEU D 215 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N ALA D 217 " --> pdb=" O VAL D 164 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N ILE D 166 " --> pdb=" O ALA D 217 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LEU D 240 " --> pdb=" O GLN D 270 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LEU D 272 " --> pdb=" O LEU D 240 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 364 through 365 removed outlier: 6.662A pdb=" N LEU D 364 " --> pdb=" O LEU D 391 " (cutoff:3.500A) removed outlier: 8.895A pdb=" N THR D 393 " --> pdb=" O LEU D 364 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N LYS D 338 " --> pdb=" O TRP D 407 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N VAL D 409 " --> pdb=" O LYS D 338 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N ILE D 340 " --> pdb=" O VAL D 409 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N ILE D 408 " --> pdb=" O LEU D 438 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N PHE D 440 " --> pdb=" O ILE D 408 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N GLN D 410 " --> pdb=" O PHE D 440 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N GLY D 314 " --> pdb=" O MET D 439 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N LEU D 441 " --> pdb=" O GLY D 314 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N VAL D 316 " --> pdb=" O LEU D 441 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 93 through 97 removed outlier: 7.396A pdb=" N THR E 79 " --> pdb=" O GLN E 75 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N GLN E 75 " --> pdb=" O THR E 79 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N VAL E 81 " --> pdb=" O LEU E 73 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 82 through 84 removed outlier: 3.515A pdb=" N TYR F 82 " --> pdb=" O VAL T 141 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N HIS T 139 " --> pdb=" O VAL F 84 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 90 through 94 Processing sheet with id=AD2, first strand: chain 'F' and resid 142 through 144 removed outlier: 7.577A pdb=" N TYR F 143 " --> pdb=" O ARG F 238 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'F' and resid 160 through 163 Processing sheet with id=AD4, first strand: chain 'G' and resid 70 through 71 Processing sheet with id=AD5, first strand: chain 'G' and resid 133 through 134 removed outlier: 3.504A pdb=" N LEU G 150 " --> pdb=" O VAL G 200 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 8 through 12 Processing sheet with id=AD7, first strand: chain 'H' and resid 18 through 20 removed outlier: 3.925A pdb=" N ASP H 20 " --> pdb=" O THR H 27 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'H' and resid 130 through 135 removed outlier: 4.733A pdb=" N GLU H 141 " --> pdb=" O SER H 135 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N ARG H 91 " --> pdb=" O VAL H 179 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N VAL H 179 " --> pdb=" O ARG H 91 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'H' and resid 100 through 104 Processing sheet with id=AE1, first strand: chain 'K' and resid 198 through 204 removed outlier: 6.813A pdb=" N VAL K 53 " --> pdb=" O CYS K 203 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N LEU K 241 " --> pdb=" O PRO K 250 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'K' and resid 71 through 75 Processing sheet with id=AE3, first strand: chain 'K' and resid 111 through 116 removed outlier: 7.210A pdb=" N ALA K 87 " --> pdb=" O THR K 112 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N VAL K 114 " --> pdb=" O ALA K 87 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N LEU K 89 " --> pdb=" O VAL K 114 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N GLY K 116 " --> pdb=" O LEU K 89 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N VAL K 91 " --> pdb=" O GLY K 116 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N CYS K 88 " --> pdb=" O LEU K 141 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N ASP K 143 " --> pdb=" O CYS K 88 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N ILE K 90 " --> pdb=" O ASP K 143 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N VAL K 168 " --> pdb=" O PHE K 140 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N ALA K 142 " --> pdb=" O VAL K 168 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'L' and resid 57 through 58 Processing sheet with id=AE5, first strand: chain 'M' and resid 37 through 40 removed outlier: 6.299A pdb=" N LEU M 38 " --> pdb=" O VAL M 29 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ARG M 12 " --> pdb=" O ILE M 28 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N VAL M 13 " --> pdb=" O THR M 59 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'N' and resid 36 through 38 removed outlier: 6.218A pdb=" N GLU N 131 " --> pdb=" O TRP N 120 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N TRP N 120 " --> pdb=" O GLU N 131 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N ILE N 133 " --> pdb=" O SER N 118 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N SER N 118 " --> pdb=" O ILE N 133 " (cutoff:3.500A) removed outlier: 8.764A pdb=" N VAL N 135 " --> pdb=" O LEU N 116 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N LEU N 116 " --> pdb=" O VAL N 135 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'O' and resid 8 through 11 removed outlier: 6.718A pdb=" N VAL O 34 " --> pdb=" O GLN O 104 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'O' and resid 43 through 45 Processing sheet with id=AE9, first strand: chain 'P' and resid 14 through 22 removed outlier: 5.952A pdb=" N SER P 144 " --> pdb=" O TYR P 21 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N HIS P 145 " --> pdb=" O VAL P 119 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N VAL P 119 " --> pdb=" O HIS P 145 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N GLU P 147 " --> pdb=" O VAL P 117 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N VAL P 117 " --> pdb=" O GLU P 147 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ILE P 149 " --> pdb=" O LYS P 115 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'P' and resid 58 through 59 Processing sheet with id=AF2, first strand: chain 'Q' and resid 122 through 123 removed outlier: 6.761A pdb=" N ILE Q 102 " --> pdb=" O LEU Q 123 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N THR Q 82 " --> pdb=" O ALA Q 103 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'Q' and resid 87 through 88 Processing sheet with id=AF4, first strand: chain 'S' and resid 55 through 62 removed outlier: 5.111A pdb=" N ILE S 57 " --> pdb=" O ARG S 11 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ARG S 11 " --> pdb=" O ILE S 57 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ALA S 59 " --> pdb=" O VAL S 9 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU S 28 " --> pdb=" O TYR S 6 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'S' and resid 88 through 95 removed outlier: 4.269A pdb=" N VAL S 73 " --> pdb=" O VAL S 128 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N ARG S 79 " --> pdb=" O ILE S 122 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N ILE S 122 " --> pdb=" O ARG S 79 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'V' and resid 24 through 27 removed outlier: 5.990A pdb=" N ASN V 35 " --> pdb=" O LYS V 65 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N LEU V 61 " --> pdb=" O VAL V 39 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N VAL V 41 " --> pdb=" O MET V 59 " (cutoff:3.500A) removed outlier: 8.302A pdb=" N MET V 59 " --> pdb=" O VAL V 41 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ALA V 101 " --> pdb=" O VAL V 81 " (cutoff:3.500A) removed outlier: 8.546A pdb=" N GLY V 102 " --> pdb=" O ILE V 24 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N ASN V 26 " --> pdb=" O GLY V 102 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N ILE V 104 " --> pdb=" O ASN V 26 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'V' and resid 87 through 88 removed outlier: 3.693A pdb=" N TRP V 87 " --> pdb=" O LEU V 95 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LEU V 95 " --> pdb=" O TRP V 87 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF7 Processing sheet with id=AF8, first strand: chain 'W' and resid 173 through 175 Processing sheet with id=AF9, first strand: chain 'X' and resid 82 through 83 Processing sheet with id=AG1, first strand: chain 'Y' and resid 31 through 33 removed outlier: 3.525A pdb=" N LEU Y 47 " --> pdb=" O ALA Y 32 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'Y' and resid 66 through 68 removed outlier: 6.700A pdb=" N GLN Y 54 " --> pdb=" O THR Y 106 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'Y' and resid 78 through 79 removed outlier: 3.550A pdb=" N ILE Y 98 " --> pdb=" O LEU Y 79 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'Y' and resid 85 through 87 Processing sheet with id=AG5, first strand: chain 'b' and resid 207 through 208 removed outlier: 3.927A pdb=" N GLY b 208 " --> pdb=" O VAL b 219 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA b 250 " --> pdb=" O THR b 170 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'b' and resid 254 through 256 Processing sheet with id=AG7, first strand: chain 'b' and resid 435 through 436 Processing sheet with id=AG8, first strand: chain 'd' and resid 54 through 56 removed outlier: 3.822A pdb=" N GLN d 97 " --> pdb=" O ARG d 79 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ARG d 79 " --> pdb=" O GLN d 97 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'e' and resid 69 through 73 removed outlier: 6.227A pdb=" N LYS e 69 " --> pdb=" O ALA e 90 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N GLU e 92 " --> pdb=" O LYS e 69 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N PHE e 71 " --> pdb=" O GLU e 92 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N LYS e 115 " --> pdb=" O TYR e 89 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'f' and resid 11 through 19 removed outlier: 8.834A pdb=" N ALA f 12 " --> pdb=" O VAL f 31 " (cutoff:3.500A) removed outlier: 9.185A pdb=" N VAL f 31 " --> pdb=" O ALA f 12 " (cutoff:3.500A) removed outlier: 9.469A pdb=" N HIS f 14 " --> pdb=" O SER f 29 " (cutoff:3.500A) removed outlier: 10.254A pdb=" N SER f 29 " --> pdb=" O HIS f 14 " (cutoff:3.500A) removed outlier: 11.952A pdb=" N SER f 16 " --> pdb=" O GLY f 27 " (cutoff:3.500A) removed outlier: 8.825A pdb=" N GLY f 27 " --> pdb=" O SER f 16 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLN f 18 " --> pdb=" O HIS f 25 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N GLY f 27 " --> pdb=" O PHE f 86 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N PHE f 86 " --> pdb=" O GLY f 27 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N ALA f 81 " --> pdb=" O PRO f 75 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ARG f 83 " --> pdb=" O ALA f 73 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ARG f 100 " --> pdb=" O CYS f 51 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA f 12 " --> pdb=" O LEU f 99 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'f' and resid 53 through 60 removed outlier: 3.624A pdb=" N ARG f 66 " --> pdb=" O TYR f 54 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N LYS f 64 " --> pdb=" O SER f 56 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'j' and resid 17 through 18 removed outlier: 3.548A pdb=" N HIS j 28 " --> pdb=" O THR j 33 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'n' and resid 16 through 18 Processing sheet with id=AH5, first strand: chain 'n' and resid 177 through 182 removed outlier: 5.413A pdb=" N LEU n 177 " --> pdb=" O GLU n 192 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N GLU n 192 " --> pdb=" O LEU n 177 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'n' and resid 248 through 249 Processing sheet with id=AH7, first strand: chain 'o' and resid 106 through 110 removed outlier: 4.775A pdb=" N TYR o 148 " --> pdb=" O SER o 137 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER o 137 " --> pdb=" O TYR o 148 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'o' and resid 169 through 171 Processing sheet with id=AH9, first strand: chain 'r' and resid 180 through 184 removed outlier: 4.940A pdb=" N VAL r 199 " --> pdb=" O GLU r 221 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N GLU r 221 " --> pdb=" O VAL r 199 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 't' and resid 89 through 92 removed outlier: 4.023A pdb=" N VAL t 92 " --> pdb=" O VAL t 121 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N VAL t 121 " --> pdb=" O VAL t 92 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 't' and resid 159 through 162 Processing sheet with id=AI3, first strand: chain 'u' and resid 4 through 5 removed outlier: 3.608A pdb=" N HIS u 4 " --> pdb=" O VAL u 13 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'u' and resid 19 through 22 Processing sheet with id=AI5, first strand: chain 'x' and resid 122 through 124 removed outlier: 6.591A pdb=" N LEU x 96 " --> pdb=" O GLU x 123 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU x 151 " --> pdb=" O THR x 99 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA x 160 " --> pdb=" O ASN x 152 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N ASN x 159 " --> pdb=" O LEU x 176 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N HIS x 165 " --> pdb=" O PRO x 170 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N MET x 276 " --> pdb=" O TYR x 173 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N THR x 175 " --> pdb=" O LEU x 274 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N LEU x 274 " --> pdb=" O THR x 175 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N SER x 177 " --> pdb=" O MET x 272 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N MET x 272 " --> pdb=" O SER x 177 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'x' and resid 197 through 201 removed outlier: 6.270A pdb=" N GLU x 197 " --> pdb=" O VAL x 231 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N ILE x 233 " --> pdb=" O GLU x 197 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N ILE x 199 " --> pdb=" O ILE x 233 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N CYS x 235 " --> pdb=" O ILE x 199 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ASN x 201 " --> pdb=" O CYS x 235 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'y' and resid 4 through 5 Processing sheet with id=AI8, first strand: chain 'y' and resid 18 through 19 removed outlier: 6.540A pdb=" N ALA y 24 " --> pdb=" O VAL y 49 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'y' and resid 64 through 65 removed outlier: 3.676A pdb=" N GLN y 95 " --> pdb=" O LEU y 70 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'y' and resid 109 through 110 Processing sheet with id=AJ2, first strand: chain 'y' and resid 153 through 154 2128 hydrogen bonds defined for protein. 6024 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1242 hydrogen bonds 2018 hydrogen bond angles 0 basepair planarities 508 basepair parallelities 929 stacking parallelities Total time for adding SS restraints: 66.44 Time building geometry restraints manager: 41.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 14921 1.33 - 1.45: 33655 1.45 - 1.57: 43364 1.57 - 1.70: 3591 1.70 - 1.82: 156 Bond restraints: 95687 Sorted by residual: bond pdb=" CA MET B 323 " pdb=" CB MET B 323 " ideal model delta sigma weight residual 1.525 1.569 -0.044 1.47e-02 4.63e+03 9.11e+00 bond pdb=" CA ALA P 100 " pdb=" C ALA P 100 " ideal model delta sigma weight residual 1.522 1.471 0.051 1.72e-02 3.38e+03 8.74e+00 bond pdb=" CG GLN G 59 " pdb=" CD GLN G 59 " ideal model delta sigma weight residual 1.516 1.450 0.066 2.50e-02 1.60e+03 7.00e+00 bond pdb=" CG LYS X 5 " pdb=" CD LYS X 5 " ideal model delta sigma weight residual 1.520 1.599 -0.079 3.00e-02 1.11e+03 6.97e+00 bond pdb=" CB LYS X 5 " pdb=" CG LYS X 5 " ideal model delta sigma weight residual 1.520 1.584 -0.064 3.00e-02 1.11e+03 4.58e+00 ... (remaining 95682 not shown) Histogram of bond angle deviations from ideal: 97.07 - 104.46: 8395 104.46 - 111.86: 50263 111.86 - 119.26: 31486 119.26 - 126.66: 42842 126.66 - 134.06: 5548 Bond angle restraints: 138534 Sorted by residual: angle pdb=" CA LYS B 34 " pdb=" CB LYS B 34 " pdb=" CG LYS B 34 " ideal model delta sigma weight residual 114.10 123.28 -9.18 2.00e+00 2.50e-01 2.11e+01 angle pdb=" N LEU S 142 " pdb=" CA LEU S 142 " pdb=" C LEU S 142 " ideal model delta sigma weight residual 113.02 107.52 5.50 1.20e+00 6.94e-01 2.10e+01 angle pdb=" CA ARG A 255 " pdb=" CB ARG A 255 " pdb=" CG ARG A 255 " ideal model delta sigma weight residual 114.10 123.01 -8.91 2.00e+00 2.50e-01 1.99e+01 angle pdb=" C GLN M 49 " pdb=" CA GLN M 49 " pdb=" CB GLN M 49 " ideal model delta sigma weight residual 110.56 118.86 -8.30 1.88e+00 2.83e-01 1.95e+01 angle pdb=" CA GLN S 141 " pdb=" CB GLN S 141 " pdb=" CG GLN S 141 " ideal model delta sigma weight residual 114.10 122.55 -8.45 2.00e+00 2.50e-01 1.78e+01 ... (remaining 138529 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.95: 53396 35.95 - 71.89: 3976 71.89 - 107.84: 524 107.84 - 143.79: 20 143.79 - 179.73: 39 Dihedral angle restraints: 57955 sinusoidal: 35772 harmonic: 22183 Sorted by residual: dihedral pdb=" O4' U 11330 " pdb=" C1' U 11330 " pdb=" N1 U 11330 " pdb=" C2 U 11330 " ideal model delta sinusoidal sigma weight residual 200.00 21.25 178.75 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U 1 300 " pdb=" C1' U 1 300 " pdb=" N1 U 1 300 " pdb=" C2 U 1 300 " ideal model delta sinusoidal sigma weight residual 200.00 23.24 176.76 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U 11139 " pdb=" C1' U 11139 " pdb=" N1 U 11139 " pdb=" C2 U 11139 " ideal model delta sinusoidal sigma weight residual -160.00 10.99 -170.99 1 1.50e+01 4.44e-03 8.48e+01 ... (remaining 57952 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 16152 0.070 - 0.140: 1234 0.140 - 0.210: 61 0.210 - 0.280: 5 0.280 - 0.350: 2 Chirality restraints: 17454 Sorted by residual: chirality pdb=" CB THR i 16 " pdb=" CA THR i 16 " pdb=" OG1 THR i 16 " pdb=" CG2 THR i 16 " both_signs ideal model delta sigma weight residual False 2.55 2.20 0.35 2.00e-01 2.50e+01 3.07e+00 chirality pdb=" CB THR A 247 " pdb=" CA THR A 247 " pdb=" OG1 THR A 247 " pdb=" CG2 THR A 247 " both_signs ideal model delta sigma weight residual False 2.55 2.25 0.30 2.00e-01 2.50e+01 2.26e+00 chirality pdb=" CG LEU i 58 " pdb=" CB LEU i 58 " pdb=" CD1 LEU i 58 " pdb=" CD2 LEU i 58 " both_signs ideal model delta sigma weight residual False -2.59 -2.85 0.26 2.00e-01 2.50e+01 1.70e+00 ... (remaining 17451 not shown) Planarity restraints: 11238 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR N 62 " -0.015 2.00e-02 2.50e+03 2.27e-02 1.03e+01 pdb=" CG TYR N 62 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 TYR N 62 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 TYR N 62 " -0.035 2.00e-02 2.50e+03 pdb=" CE1 TYR N 62 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR N 62 " 0.023 2.00e-02 2.50e+03 pdb=" CZ TYR N 62 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR N 62 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG G 62 " 0.286 9.50e-02 1.11e+02 1.28e-01 1.01e+01 pdb=" NE ARG G 62 " -0.016 2.00e-02 2.50e+03 pdb=" CZ ARG G 62 " -0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG G 62 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG G 62 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG m 256 " 0.270 9.50e-02 1.11e+02 1.21e-01 9.37e+00 pdb=" NE ARG m 256 " -0.020 2.00e-02 2.50e+03 pdb=" CZ ARG m 256 " 0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG m 256 " -0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG m 256 " 0.006 2.00e-02 2.50e+03 ... (remaining 11235 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 2208 2.64 - 3.20: 79626 3.20 - 3.77: 166558 3.77 - 4.33: 215864 4.33 - 4.90: 305111 Nonbonded interactions: 769367 Sorted by model distance: nonbonded pdb=" O ASN x 168 " pdb=" ND2 ASN x 168 " model vdw 2.074 2.520 nonbonded pdb=" O2' G 13085 " pdb=" O5' A 13086 " model vdw 2.125 2.440 nonbonded pdb=" O ARG O 141 " pdb=" NH1 ARG O 141 " model vdw 2.145 2.520 nonbonded pdb=" O2' C 11308 " pdb=" O5' A 11309 " model vdw 2.179 2.440 nonbonded pdb=" O2' A 1 116 " pdb=" OP1 U 1 117 " model vdw 2.180 2.440 ... (remaining 769362 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.080 Extract box with map and model: 29.010 Check model and map are aligned: 1.010 Set scattering table: 0.610 Process input model: 259.890 Find NCS groups from input model: 2.850 Set up NCS constraints: 0.280 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: 0.020 Load rotamer database and sin/cos tables:2.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 305.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4415 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 0.079 95687 Z= 0.267 Angle : 0.619 9.713 138534 Z= 0.326 Chirality : 0.038 0.350 17454 Planarity : 0.005 0.128 11238 Dihedral : 21.556 179.735 43477 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.37 % Favored : 94.58 % Rotamer: Outliers : 0.78 % Allowed : 17.96 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.75 % 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: -3.47 (0.08), residues: 7487 helix: -2.66 (0.08), residues: 2718 sheet: -2.08 (0.16), residues: 920 loop : -2.03 (0.09), residues: 3849 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP 5 197 HIS 0.009 0.001 HIS m 230 PHE 0.045 0.002 PHE A 248 TYR 0.045 0.002 TYR N 62 ARG 0.022 0.001 ARG A 255 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14974 Ramachandran restraints generated. 7487 Oldfield, 0 Emsley, 7487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14974 Ramachandran restraints generated. 7487 Oldfield, 0 Emsley, 7487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1014 residues out of total 6624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 984 time to evaluate : 5.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 10 residues processed: 1008 average time/residue: 0.9697 time to fit residues: 1592.9441 Evaluate side-chains 561 residues out of total 6624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 551 time to evaluate : 5.327 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.6532 time to fit residues: 19.0902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 927 random chunks: chunk 782 optimal weight: 40.0000 chunk 702 optimal weight: 2.9990 chunk 389 optimal weight: 1.9990 chunk 240 optimal weight: 8.9990 chunk 473 optimal weight: 10.0000 chunk 375 optimal weight: 10.0000 chunk 726 optimal weight: 0.8980 chunk 281 optimal weight: 2.9990 chunk 441 optimal weight: 30.0000 chunk 540 optimal weight: 1.9990 chunk 841 optimal weight: 9.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 33 ASN ** 4 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 261 GLN ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 55 HIS ** B 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 286 ASN F 243 ASN G 123 GLN L 28 GLN ** L 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 34 HIS M 60 HIS M 119 GLN ** M 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 193 ASN O 43 ASN O 102 HIS ** P 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 145 HIS Q 57 ASN Q 127 GLN Y 54 GLN j 48 ASN ** v 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 48 GLN x 20 GLN x 168 ASN ** x 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 236 GLN T 139 HIS Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5242 moved from start: 0.4092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.154 95687 Z= 0.356 Angle : 0.797 12.553 138534 Z= 0.413 Chirality : 0.044 0.358 17454 Planarity : 0.007 0.150 11238 Dihedral : 21.835 179.804 34173 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 15.85 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.05 % Favored : 94.90 % Rotamer: Outliers : 5.53 % Allowed : 19.23 % Favored : 75.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.75 % 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: -2.47 (0.09), residues: 7487 helix: -1.40 (0.09), residues: 2825 sheet: -1.87 (0.16), residues: 945 loop : -1.69 (0.10), residues: 3717 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.004 TRP 3 100 HIS 0.019 0.002 HIS G 138 PHE 0.059 0.003 PHE B 199 TYR 0.041 0.003 TYR B 283 ARG 0.100 0.002 ARG 3 123 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14974 Ramachandran restraints generated. 7487 Oldfield, 0 Emsley, 7487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14974 Ramachandran restraints generated. 7487 Oldfield, 0 Emsley, 7487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 894 residues out of total 6624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 212 poor density : 682 time to evaluate : 5.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 212 outliers final: 91 residues processed: 829 average time/residue: 0.8843 time to fit residues: 1240.7185 Evaluate side-chains 621 residues out of total 6624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 530 time to evaluate : 5.286 Switching outliers to nearest non-outliers outliers start: 91 outliers final: 0 residues processed: 91 average time/residue: 0.6876 time to fit residues: 123.2371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 927 random chunks: chunk 467 optimal weight: 8.9990 chunk 261 optimal weight: 3.9990 chunk 700 optimal weight: 2.9990 chunk 573 optimal weight: 3.9990 chunk 232 optimal weight: 20.0000 chunk 843 optimal weight: 9.9990 chunk 911 optimal weight: 9.9990 chunk 751 optimal weight: 9.9990 chunk 836 optimal weight: 10.0000 chunk 287 optimal weight: 0.9980 chunk 676 optimal weight: 40.0000 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 39 ASN 3 160 ASN ** 4 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 175 ASN 5 230 HIS ** A 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 282 GLN B 25 GLN B 109 HIS ** B 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 314 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 127 GLN F 69 GLN F 247 GLN ** G 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 28 GLN ** L 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 178 HIS N 192 HIS O 91 HIS O 116 GLN ** P 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 144 ASN S 153 HIS ** v 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 39 ASN x 202 ASN x 236 GLN T 131 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5789 moved from start: 0.7625 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: