Starting phenix.real_space_refine on Fri Dec 8 03:30:40 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b9v_12106/12_2023/7b9v_12106_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b9v_12106/12_2023/7b9v_12106.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b9v_12106/12_2023/7b9v_12106.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b9v_12106/12_2023/7b9v_12106.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b9v_12106/12_2023/7b9v_12106_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b9v_12106/12_2023/7b9v_12106_updated.pdb" } resolution = 2.8 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= 0.011 sd= 1.810 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: 8 Type Number sf(0) Gaussians K 1 8.98 5 Zn 8 6.06 5 P 552 5.49 5 Mg 6 5.21 5 S 388 5.16 5 C 67397 2.51 5 N 18746 2.21 5 O 22007 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 619": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 883": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 982": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1880": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1989": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 677": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 698": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1779": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 254": "OD1" <-> "OD2" Residue "o TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o TYR 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o ASP 277": "OD1" <-> "OD2" Residue "o PHE 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.20s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 109105 Number of models: 1 Model: "" Number of chains: 58 Chain: "2" Number of atoms: 4120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 4120 Inner-chain residues flagged as termini: ['pdbres=" U 2 54 "', 'pdbres=" U 2 138 "'] Classifications: {'RNA': 196} Modifications used: {'5*END': 2, 'rna2p_pur': 9, 'rna2p_pyr': 22, 'rna3p_pur': 73, 'rna3p_pyr': 92} Link IDs: {'rna2p': 31, 'rna3p': 164} Chain breaks: 6 Chain: "5" Number of atoms: 3777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 3777 Classifications: {'RNA': 178} Modifications used: {'5*END': 1, 'rna2p_pur': 15, 'rna2p_pyr': 10, 'rna3p_pur': 74, 'rna3p_pyr': 79} Link IDs: {'rna2p': 25, 'rna3p': 152} Chain: "6" Number of atoms: 2170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 2170 Classifications: {'RNA': 102} Modifications used: {'rna2p_pur': 10, 'rna2p_pyr': 15, 'rna3p_pur': 44, 'rna3p_pyr': 33} Link IDs: {'rna2p': 25, 'rna3p': 76} Chain: "A" Number of atoms: 18036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2191, 18036 Classifications: {'peptide': 2191} Link IDs: {'PCIS': 4, 'PTRANS': 108, 'TRANS': 2078} Chain breaks: 2 Chain: "B" Number of atoms: 13675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1707, 13675 Classifications: {'peptide': 1707} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 71, 'TRANS': 1635} Chain breaks: 1 Chain: "C" Number of atoms: 7139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 898, 7139 Classifications: {'peptide': 898} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 50, 'TRANS': 847} Chain breaks: 4 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "D" Number of atoms: 1547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1547 Classifications: {'peptide': 194} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 7, 'TRANS': 186} Chain breaks: 3 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'UNK:plan-1': 17} Unresolved non-hydrogen planarities: 17 Chain: "E" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 304 Classifications: {'RNA': 14} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 2, 'rna3p_pur': 6, 'rna3p_pyr': 2} Link IDs: {'rna2p': 6, 'rna3p': 7} Chain: "F" Number of atoms: 505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 505 Classifications: {'peptide': 64} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 1, 'TRANS': 62} Chain breaks: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'UNK:plan-1': 10} Unresolved non-hydrogen planarities: 10 Chain: "G" Number of atoms: 1090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1090 Classifications: {'peptide': 138} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 1, 'TRANS': 136} Chain breaks: 4 Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 114 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASN:plan1': 1, 'TYR:plan': 1, 'UNK:plan-1': 11, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 49 Chain: "H" Number of atoms: 3705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3705 Classifications: {'peptide': 453} Link IDs: {'PTRANS': 7, 'TRANS': 445} Chain breaks: 1 Chain: "I" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 1068 Classifications: {'RNA': 55} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 10, 'rna3p_pur': 20, 'rna3p_pyr': 19} Link IDs: {'rna2p': 16, 'rna3p': 38} Chain breaks: 1 Unresolved non-hydrogen bonds: 106 Unresolved non-hydrogen angles: 167 Unresolved non-hydrogen dihedrals: 98 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {' G%rna3p_pur:plan2': 1, ' C%rna3p_pyr:plan': 3, ' A%rna3p_pur:plan2': 4, ' U%rna3p_pyr:plan': 2, ' C%rna3p_pyr:plan2': 3, ' G%rna3p_pur:plan': 1, ' A%rna3p_pur:plan': 4} Unresolved non-hydrogen planarities: 107 Chain: "J" Number of atoms: 2926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2926 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 356} Chain breaks: 1 Chain: "K" Number of atoms: 1455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1455 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 13, 'TRANS': 168} Chain breaks: 4 Chain: "L" Number of atoms: 1283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1283 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 151} Chain: "M" Number of atoms: 2048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 2048 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 10, 'TRANS': 244} Chain: "N" Number of atoms: 2092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2092 Classifications: {'peptide': 264} Link IDs: {'PTRANS': 11, 'TRANS': 252} Chain breaks: 3 Chain: "O" Number of atoms: 2143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2143 Classifications: {'peptide': 280} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 9, 'TRANS': 270} Chain breaks: 3 Unresolved non-hydrogen bonds: 149 Unresolved non-hydrogen angles: 202 Unresolved non-hydrogen dihedrals: 102 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 9, 'UNK:plan-1': 24, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 91 Chain: "P" Number of atoms: 607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 607 Classifications: {'peptide': 74} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 70} Chain breaks: 2 Chain: "Q" Number of atoms: 4959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 624, 4959 Classifications: {'peptide': 624} Link IDs: {'PTRANS': 26, 'TRANS': 597} Chain breaks: 2 Chain: "R" Number of atoms: 555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 555 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain breaks: 1 Unresolved non-hydrogen bonds: 93 Unresolved non-hydrogen angles: 117 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 1, 'GLU:plan': 8, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 60 Chain: "S" Number of atoms: 4170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 549, 4170 Classifications: {'peptide': 549} Incomplete info: {'truncation_to_alanine': 137} Link IDs: {'PTRANS': 9, 'TRANS': 539} Chain breaks: 11 Unresolved non-hydrogen bonds: 569 Unresolved non-hydrogen angles: 724 Unresolved non-hydrogen dihedrals: 480 Unresolved non-hydrogen chiralities: 43 Planarities with less than four sites: {'GLN:plan1': 9, 'TYR:plan': 9, 'ASN:plan1': 4, 'TRP:plan': 3, 'ASP:plan': 7, 'PHE:plan': 9, 'GLU:plan': 22, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 351 Chain: "T" Number of atoms: 5387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 720, 5387 Classifications: {'peptide': 720} Incomplete info: {'truncation_to_alanine': 158} Link IDs: {'PTRANS': 22, 'TRANS': 697} Chain breaks: 13 Unresolved non-hydrogen bonds: 639 Unresolved non-hydrogen angles: 819 Unresolved non-hydrogen dihedrals: 558 Unresolved non-hydrogen chiralities: 49 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 2, 'TYR:plan': 7, 'ASN:plan1': 3, 'TRP:plan': 8, 'ASP:plan': 9, 'PHE:plan': 9, 'GLU:plan': 20, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 375 Chain: "W" Number of atoms: 1734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1734 Classifications: {'peptide': 214} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 204} Chain breaks: 1 Chain: "X" Number of atoms: 355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 355 Classifications: {'peptide': 71} Incomplete info: {'truncation_to_alanine': 71} Link IDs: {'TRANS': 70} Chain breaks: 2 Unresolved non-hydrogen bonds: 142 Unresolved non-hydrogen angles: 213 Unresolved non-hydrogen dihedrals: 71 Planarities with less than four sites: {'UNK:plan-1': 71} Unresolved non-hydrogen planarities: 71 Chain: "Y" Number of atoms: 713 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 713 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 86} Chain: "Z" Number of atoms: 446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 446 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 1, 'TRANS': 53} Chain breaks: 1 Chain: "a" Number of atoms: 1132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1132 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 7, 'TRANS': 130} Chain breaks: 2 Chain: "b" Number of atoms: 752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 752 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 3, 'TRANS': 89} Chain breaks: 1 Chain: "c" Number of atoms: 293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 293 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 1, 'TRANS': 35} Chain breaks: 1 Chain: "d" Number of atoms: 633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 633 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 4, 'TRANS': 77} Chain: "e" Number of atoms: 606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 606 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 5, 'TRANS': 71} Chain breaks: 1 Chain: "f" Number of atoms: 601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 601 Classifications: {'peptide': 75} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "g" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 557 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 1, 'TRANS': 70} Chain: "h" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 819 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "j" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 795 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "k" Number of atoms: 830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 830 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain breaks: 1 Chain: "l" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 819 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "m" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 795 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "n" Number of atoms: 633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 633 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 4, 'TRANS': 77} Chain: "o" Number of atoms: 2673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2673 Classifications: {'peptide': 330} Link IDs: {'PTRANS': 18, 'TRANS': 311} Chain breaks: 2 Chain: "p" Number of atoms: 606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 606 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 5, 'TRANS': 71} Chain breaks: 1 Chain: "q" Number of atoms: 601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 601 Classifications: {'peptide': 75} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "r" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 557 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 1, 'TRANS': 70} Chain: "s" Number of atoms: 426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 426 Classifications: {'peptide': 61} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 1, 'TRANS': 59} Chain breaks: 1 Unresolved non-hydrogen bonds: 95 Unresolved non-hydrogen angles: 128 Unresolved non-hydrogen dihedrals: 71 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 5, 'TYR:plan': 3, 'ASN:plan1': 3, 'ASP:plan': 3, 'GLU:plan': 4, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 74 Chain: "t" Number of atoms: 794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 794 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain breaks: 1 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 3, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "u" Number of atoms: 856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 856 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 7, 'TRANS': 109} Chain breaks: 1 Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ASN:plan1': 4, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 35 Chain: "v" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 827 Classifications: {'peptide': 113} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 106} Chain breaks: 1 Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 4, 'ASP:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "w" Number of atoms: 3405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3405 Classifications: {'peptide': 438} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 20, 'TRANS': 417} Chain breaks: 5 Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ASN:plan1': 4, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 35 Chain: "y" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1003 Classifications: {'peptide': 134} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'TRANS': 133} Chain breaks: 4 Unresolved non-hydrogen bonds: 126 Unresolved non-hydrogen angles: 153 Unresolved non-hydrogen dihedrals: 104 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 65 Chain: "6" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Unusual residues: {' K': 1, ' MG': 5} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'KGN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "c" 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 49327 SG CYS D 51 149.809 133.147 131.169 1.00104.52 S ATOM 49350 SG CYS D 54 152.601 131.590 133.184 1.00108.73 S ATOM 49639 SG CYS D 88 152.667 135.265 132.680 1.00103.55 S ATOM 49663 SG CYS D 91 153.562 133.065 129.946 1.00106.56 S ATOM 62397 SG CYS L 104 208.439 196.897 113.315 1.00 77.20 S ATOM 62403 SG CYS L 105 205.291 196.645 115.611 1.00 76.82 S ATOM 62428 SG CYS L 108 207.983 194.084 115.667 1.00 77.85 S ATOM 62742 SG CYS L 148 205.592 194.629 112.532 1.00 75.93 S ATOM 62397 SG CYS L 104 208.439 196.897 113.315 1.00 77.20 S ATOM 62531 SG CYS L 122 211.030 193.854 113.419 1.00 80.12 S ATOM 62752 SG CYS L 150 210.063 195.185 110.111 1.00 77.88 S ATOM 62773 SG CYS L 153 211.956 197.332 112.505 1.00 80.52 S ATOM 62428 SG CYS L 108 207.983 194.084 115.667 1.00 77.85 S ATOM 62517 SG CYS L 120 210.202 190.974 115.657 1.00 79.67 S ATOM 62531 SG CYS L 122 211.030 193.854 113.419 1.00 80.12 S ATOM 62719 SG CYS L 145 207.966 191.396 112.831 1.00 77.78 S ATOM 63367 SG CYS M 73 201.575 171.454 102.518 1.00 76.72 S ATOM 63429 SG CYS M 81 200.187 174.241 100.405 1.00 79.13 S ATOM 63469 SG CYS M 87 203.302 174.792 102.604 1.00 82.35 S ATOM 65058 SG CYS N 34 203.857 158.207 129.034 1.00 81.95 S ATOM 65081 SG CYS N 37 202.146 157.332 132.023 1.00 83.84 S ATOM 65280 SG CYS N 61 205.890 158.712 132.475 1.00 84.49 S ATOM 65304 SG CYS N 64 205.442 155.532 131.197 1.00 86.59 S ATOM 64900 SG CYS N 13 219.100 160.932 122.122 1.00 99.21 S ATOM 64924 SG CYS N 16 216.430 163.104 120.825 1.00 97.28 S ATOM 65358 SG CYS N 71 215.881 160.929 123.812 1.00 92.05 S ATOM 65379 SG CYS N 74 215.794 159.222 120.463 1.00 91.85 S ATOM 89916 SG CYS c 122 163.061 230.525 143.303 1.00146.14 S ATOM 89941 SG CYS c 125 161.642 231.764 139.971 1.00137.42 S ATOM 90014 SG CYS c 135 164.032 228.831 139.986 1.00110.13 S Time building chain proxies: 39.69, per 1000 atoms: 0.36 Number of scatterers: 109105 At special positions: 0 Unit cell: (309.15, 308.005, 280.525, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 8 29.99 K 1 19.00 S 388 16.00 P 552 15.00 Mg 6 11.99 O 22007 8.00 N 18746 7.00 C 67397 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: 29.96 Conformation dependent library (CDL) restraints added in 12.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1001 " pdb="ZN ZN D1001 " - pdb=" SG CYS D 54 " pdb="ZN ZN D1001 " - pdb=" SG CYS D 91 " pdb="ZN ZN D1001 " - pdb=" SG CYS D 88 " pdb="ZN ZN D1001 " - pdb=" SG CYS D 51 " pdb=" ZN L1000 " pdb="ZN ZN L1000 " - pdb=" SG CYS L 148 " pdb="ZN ZN L1000 " - pdb=" SG CYS L 104 " pdb="ZN ZN L1000 " - pdb=" SG CYS L 105 " pdb="ZN ZN L1000 " - pdb=" SG CYS L 108 " pdb=" ZN L1001 " pdb="ZN ZN L1001 " - pdb=" SG CYS L 153 " pdb="ZN ZN L1001 " - pdb=" SG CYS L 122 " pdb="ZN ZN L1001 " - pdb=" SG CYS L 150 " pdb="ZN ZN L1001 " - pdb=" SG CYS L 104 " pdb=" ZN L1002 " pdb="ZN ZN L1002 " - pdb=" SG CYS L 120 " pdb="ZN ZN L1002 " - pdb=" SG CYS L 108 " pdb="ZN ZN L1002 " - pdb=" SG CYS L 122 " pdb="ZN ZN L1002 " - pdb=" SG CYS L 145 " pdb=" ZN M1000 " pdb="ZN ZN M1000 " - pdb=" NE2 HIS M 91 " pdb="ZN ZN M1000 " - pdb=" SG CYS M 81 " pdb="ZN ZN M1000 " - pdb=" SG CYS M 73 " pdb="ZN ZN M1000 " - pdb=" SG CYS M 87 " pdb=" ZN N 401 " pdb="ZN ZN N 401 " - pdb=" SG CYS N 64 " pdb="ZN ZN N 401 " - pdb=" SG CYS N 37 " pdb="ZN ZN N 401 " - pdb=" SG CYS N 34 " pdb="ZN ZN N 401 " - pdb=" SG CYS N 61 " pdb=" ZN N 402 " pdb="ZN ZN N 402 " - pdb=" SG CYS N 16 " pdb="ZN ZN N 402 " - pdb=" SG CYS N 74 " pdb="ZN ZN N 402 " - pdb=" SG CYS N 13 " pdb="ZN ZN N 402 " - pdb=" SG CYS N 71 " pdb=" ZN c 400 " pdb="ZN ZN c 400 " - pdb=" NE2 HIS c 130 " pdb="ZN ZN c 400 " - pdb=" SG CYS c 125 " pdb="ZN ZN c 400 " - pdb=" SG CYS c 135 " pdb="ZN ZN c 400 " - pdb=" SG CYS c 122 " Number of angles added : 42 23880 Ramachandran restraints generated. 11940 Oldfield, 0 Emsley, 11940 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 23592 Finding SS restraints... Warning!!! ksdssp method is not applicable for structures that cannot fit in PDB format. Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 463 helices and 101 sheets defined 52.8% alpha, 14.8% beta 149 base pairs and 253 stacking pairs defined. Time for finding SS restraints: 74.49 Creating SS restraints... Processing helix chain 'A' and resid 135 through 147 removed outlier: 4.004A pdb=" N LEU A 139 " --> pdb=" O PRO A 135 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N SER A 147 " --> pdb=" O ILE A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 169 removed outlier: 3.564A pdb=" N LEU A 165 " --> pdb=" O PHE A 161 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N LYS A 166 " --> pdb=" O LEU A 162 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N TYR A 167 " --> pdb=" O GLY A 163 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU A 168 " --> pdb=" O ALA A 164 " (cutoff:3.500A) Proline residue: A 169 - end of helix Processing helix chain 'A' and resid 170 through 179 removed outlier: 3.533A pdb=" N MET A 179 " --> pdb=" O LEU A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 231 Processing helix chain 'A' and resid 253 through 259 removed outlier: 5.516A pdb=" N ASN A 257 " --> pdb=" O GLN A 253 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N ILE A 258 " --> pdb=" O HIS A 254 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N GLU A 259 " --> pdb=" O ILE A 255 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 253 through 259' Processing helix chain 'A' and resid 304 through 316 removed outlier: 3.747A pdb=" N THR A 316 " --> pdb=" O TYR A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 329 removed outlier: 4.902A pdb=" N TYR A 328 " --> pdb=" O ASP A 324 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N TYR A 329 " --> pdb=" O LYS A 325 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 324 through 329' Processing helix chain 'A' and resid 332 through 343 Processing helix chain 'A' and resid 369 through 374 removed outlier: 5.805A pdb=" N ILE A 374 " --> pdb=" O ILE A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 388 Proline residue: A 388 - end of helix Processing helix chain 'A' and resid 472 through 483 removed outlier: 3.701A pdb=" N HIS A 481 " --> pdb=" O MET A 477 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER A 482 " --> pdb=" O SER A 478 " (cutoff:3.500A) Proline residue: A 483 - end of helix Processing helix chain 'A' and resid 484 through 489 removed outlier: 7.806A pdb=" N ARG A 488 " --> pdb=" O PHE A 484 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N THR A 489 " --> pdb=" O PRO A 485 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 484 through 489' Processing helix chain 'A' and resid 495 through 500 removed outlier: 3.608A pdb=" N VAL A 499 " --> pdb=" O ARG A 495 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N ALA A 500 " --> pdb=" O ALA A 496 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 495 through 500' Processing helix chain 'A' and resid 502 through 509 removed outlier: 3.898A pdb=" N PHE A 506 " --> pdb=" O ALA A 502 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLN A 508 " --> pdb=" O LYS A 504 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N HIS A 509 " --> pdb=" O TRP A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 536 removed outlier: 3.663A pdb=" N HIS A 535 " --> pdb=" O LEU A 531 " (cutoff:3.500A) Proline residue: A 536 - end of helix Processing helix chain 'A' and resid 546 through 555 removed outlier: 4.204A pdb=" N THR A 554 " --> pdb=" O SER A 550 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N LYS A 555 " --> pdb=" O LEU A 551 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 587 Processing helix chain 'A' and resid 606 through 614 Processing helix chain 'A' and resid 616 through 642 Processing helix chain 'A' and resid 645 through 660 Processing helix chain 'A' and resid 665 through 671 removed outlier: 4.766A pdb=" N TYR A 669 " --> pdb=" O GLY A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 692 removed outlier: 4.413A pdb=" N GLN A 676 " --> pdb=" O LYS A 672 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 710 Processing helix chain 'A' and resid 713 through 734 removed outlier: 3.794A pdb=" N GLY A 717 " --> pdb=" O ASN A 713 " (cutoff:3.500A) Proline residue: A 720 - end of helix Processing helix chain 'A' and resid 746 through 770 removed outlier: 5.183A pdb=" N ASP A 751 " --> pdb=" O LYS A 747 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N ALA A 752 " --> pdb=" O GLN A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 776 through 796 removed outlier: 4.616A pdb=" N ARG A 780 " --> pdb=" O GLN A 776 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLN A 784 " --> pdb=" O ARG A 780 " (cutoff:3.500A) Processing helix chain 'A' and resid 805 through 837 Processing helix chain 'A' and resid 841 through 871 removed outlier: 3.856A pdb=" N LYS A 846 " --> pdb=" O LYS A 842 " (cutoff:3.500A) Processing helix chain 'A' and resid 875 through 894 Processing helix chain 'A' and resid 907 through 924 removed outlier: 4.217A pdb=" N VAL A 922 " --> pdb=" O ASP A 918 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N TYR A 923 " --> pdb=" O LEU A 919 " (cutoff:3.500A) Processing helix chain 'A' and resid 930 through 947 removed outlier: 3.583A pdb=" N LEU A 937 " --> pdb=" O GLU A 933 " (cutoff:3.500A) Proline residue: A 947 - end of helix Processing helix chain 'A' and resid 948 through 960 Processing helix chain 'A' and resid 986 through 1007 removed outlier: 3.752A pdb=" N THR A 991 " --> pdb=" O LEU A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1020 through 1035 Processing helix chain 'A' and resid 1056 through 1061 removed outlier: 3.831A pdb=" N ILE A1061 " --> pdb=" O MET A1057 " (cutoff:3.500A) Processing helix chain 'A' and resid 1062 through 1074 removed outlier: 3.935A pdb=" N LEU A1072 " --> pdb=" O ARG A1068 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ILE A1073 " --> pdb=" O LEU A1069 " (cutoff:3.500A) Processing helix chain 'A' and resid 1075 through 1088 removed outlier: 3.559A pdb=" N ASN A1087 " --> pdb=" O THR A1083 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N VAL A1088 " --> pdb=" O ALA A1084 " (cutoff:3.500A) Processing helix chain 'A' and resid 1109 through 1127 Processing helix chain 'A' and resid 1128 through 1136 Processing helix chain 'A' and resid 1149 through 1156 removed outlier: 3.543A pdb=" N ALA A1155 " --> pdb=" O GLU A1151 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N HIS A1156 " --> pdb=" O VAL A1152 " (cutoff:3.500A) Processing helix chain 'A' and resid 1175 through 1190 Processing helix chain 'A' and resid 1216 through 1235 removed outlier: 3.805A pdb=" N SER A1232 " --> pdb=" O TRP A1228 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ARG A1233 " --> pdb=" O GLU A1229 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N VAL A1234 " --> pdb=" O ILE A1230 " (cutoff:3.500A) Proline residue: A1235 - end of helix Processing helix chain 'A' and resid 1242 through 1247 removed outlier: 3.606A pdb=" N ALA A1246 " --> pdb=" O LYS A1242 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N PHE A1247 " --> pdb=" O TRP A1243 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1242 through 1247' Processing helix chain 'A' and resid 1271 through 1276 removed outlier: 5.704A pdb=" N GLU A1276 " --> pdb=" O ARG A1272 " (cutoff:3.500A) Processing helix chain 'A' and resid 1305 through 1324 removed outlier: 4.641A pdb=" N GLY A1324 " --> pdb=" O LEU A1320 " (cutoff:3.500A) Processing helix chain 'A' and resid 1327 through 1347 Processing helix chain 'A' and resid 1348 through 1354 removed outlier: 4.459A pdb=" N ALA A1352 " --> pdb=" O GLU A1348 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N THR A1353 " --> pdb=" O ALA A1349 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N GLU A1354 " --> pdb=" O ILE A1350 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1348 through 1354' Processing helix chain 'A' and resid 1355 through 1376 removed outlier: 3.561A pdb=" N VAL A1371 " --> pdb=" O ILE A1367 " (cutoff:3.500A) Processing helix chain 'A' and resid 1379 through 1384 removed outlier: 4.053A pdb=" N PHE A1383 " --> pdb=" O MET A1379 " (cutoff:3.500A) Proline residue: A1384 - end of helix No H-bonds generated for 'chain 'A' and resid 1379 through 1384' Processing helix chain 'A' and resid 1411 through 1418 Processing helix chain 'A' and resid 1439 through 1445 removed outlier: 4.526A pdb=" N TYR A1443 " --> pdb=" O THR A1439 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ILE A1444 " --> pdb=" O ILE A1440 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N THR A1445 " --> pdb=" O PHE A1441 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1439 through 1445' Processing helix chain 'A' and resid 1446 through 1472 Processing helix chain 'A' and resid 1476 through 1481 Processing helix chain 'A' and resid 1490 through 1496 removed outlier: 4.489A pdb=" N LEU A1494 " --> pdb=" O ARG A1490 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N PHE A1495 " --> pdb=" O ILE A1491 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN A1496 " --> pdb=" O SER A1492 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1490 through 1496' Processing helix chain 'A' and resid 1498 through 1506 removed outlier: 5.075A pdb=" N TYR A1504 " --> pdb=" O HIS A1500 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ASP A1505 " --> pdb=" O THR A1501 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N ARG A1506 " --> pdb=" O LEU A1502 " (cutoff:3.500A) Processing helix chain 'A' and resid 1507 through 1519 removed outlier: 4.799A pdb=" N GLN A1516 " --> pdb=" O ARG A1512 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N TYR A1517 " --> pdb=" O GLU A1513 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N SER A1518 " --> pdb=" O PHE A1514 " (cutoff:3.500A) Processing helix chain 'A' and resid 1539 through 1551 removed outlier: 4.283A pdb=" N ARG A1543 " --> pdb=" O LEU A1539 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N THR A1544 " --> pdb=" O ASN A1540 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLY A1551 " --> pdb=" O ILE A1547 " (cutoff:3.500A) Processing helix chain 'A' and resid 1552 through 1561 removed outlier: 3.918A pdb=" N HIS A1559 " --> pdb=" O THR A1555 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N THR A1560 " --> pdb=" O ILE A1556 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N LEU A1561 " --> pdb=" O LEU A1557 " (cutoff:3.500A) Processing helix chain 'A' and resid 1580 through 1585 removed outlier: 3.642A pdb=" N SER A1584 " --> pdb=" O GLY A1580 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N MET A1585 " --> pdb=" O PHE A1581 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1580 through 1585' Processing helix chain 'A' and resid 1586 through 1592 Processing helix chain 'A' and resid 1602 through 1611 Processing helix chain 'A' and resid 1640 through 1650 Processing helix chain 'A' and resid 1652 through 1677 removed outlier: 3.717A pdb=" N GLY A1671 " --> pdb=" O GLN A1667 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU A1672 " --> pdb=" O ILE A1668 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N ASP A1674 " --> pdb=" O ASP A1670 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N VAL A1675 " --> pdb=" O GLY A1671 " (cutoff:3.500A) Processing helix chain 'A' and resid 1747 through 1762 removed outlier: 3.878A pdb=" N THR A1761 " --> pdb=" O LEU A1757 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ASP A1762 " --> pdb=" O ASP A1758 " (cutoff:3.500A) Processing helix chain 'A' and resid 1793 through 1808 removed outlier: 3.622A pdb=" N LEU A1797 " --> pdb=" O GLY A1793 " (cutoff:3.500A) Processing helix chain 'A' and resid 1809 through 1824 Processing helix chain 'A' and resid 1839 through 1845 removed outlier: 4.729A pdb=" N LEU A1843 " --> pdb=" O ASN A1839 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N PHE A1844 " --> pdb=" O TYR A1840 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N ASN A1845 " --> pdb=" O ALA A1841 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1839 through 1845' Processing helix chain 'A' and resid 1895 through 1900 removed outlier: 4.615A pdb=" N TRP A1899 " --> pdb=" O HIS A1895 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ALA A1900 " --> pdb=" O THR A1896 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1895 through 1900' Processing helix chain 'A' and resid 1904 through 1925 removed outlier: 3.559A pdb=" N LEU A1908 " --> pdb=" O ARG A1904 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LYS A1910 " --> pdb=" O SER A1906 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU A1924 " --> pdb=" O LEU A1920 " (cutoff:3.500A) Proline residue: A1925 - end of helix Processing helix chain 'A' and resid 1937 through 1949 removed outlier: 4.543A pdb=" N LEU A1941 " --> pdb=" O ARG A1937 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N ASP A1942 " --> pdb=" O LYS A1938 " (cutoff:3.500A) Proline residue: A1943 - end of helix Processing helix chain 'A' and resid 1964 through 1972 removed outlier: 4.616A pdb=" N ALA A1968 " --> pdb=" O PRO A1964 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N MET A1969 " --> pdb=" O PHE A1965 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N SER A1970 " --> pdb=" O SER A1966 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ILE A1971 " --> pdb=" O ALA A1967 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N ASP A1972 " --> pdb=" O ALA A1968 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1964 through 1972' Processing helix chain 'A' and resid 1973 through 1981 removed outlier: 3.829A pdb=" N ALA A1981 " --> pdb=" O VAL A1977 " (cutoff:3.500A) Processing helix chain 'A' and resid 1994 through 1999 removed outlier: 4.698A pdb=" N ARG A1998 " --> pdb=" O ASP A1994 " (cutoff:3.500A) Processing helix chain 'A' and resid 2000 through 2018 Processing helix chain 'A' and resid 2019 through 2028 removed outlier: 4.201A pdb=" N SER A2028 " --> pdb=" O MET A2024 " (cutoff:3.500A) Processing helix chain 'A' and resid 2044 through 2068 Processing helix chain 'A' and resid 2075 through 2085 Processing helix chain 'A' and resid 2151 through 2169 removed outlier: 3.538A pdb=" N SER A2155 " --> pdb=" O GLU A2151 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR A2160 " --> pdb=" O ALA A2156 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N LEU A2161 " --> pdb=" O ILE A2157 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N LEU A2162 " --> pdb=" O ALA A2158 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N TYR A2163 " --> pdb=" O ASN A2159 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N LEU A2164 " --> pdb=" O THR A2160 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ARG A2165 " --> pdb=" O LEU A2161 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU A2166 " --> pdb=" O LEU A2162 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N LYS A2167 " --> pdb=" O TYR A2163 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N ASN A2168 " --> pdb=" O LEU A2164 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N ILE A2169 " --> pdb=" O ARG A2165 " (cutoff:3.500A) Processing helix chain 'A' and resid 2186 through 2197 Processing helix chain 'A' and resid 2270 through 2281 Processing helix chain 'A' and resid 2308 through 2319 removed outlier: 3.974A pdb=" N LYS A2319 " --> pdb=" O GLY A2315 " (cutoff:3.500A) Processing helix chain 'A' and resid 2362 through 2367 removed outlier: 5.299A pdb=" N ASN A2367 " --> pdb=" O GLY A2363 " (cutoff:3.500A) Processing helix chain 'A' and resid 2384 through 2389 Proline residue: A2389 - end of helix Processing helix chain 'A' and resid 2390 through 2395 Processing helix chain 'A' and resid 1195 through 1200 removed outlier: 4.095A pdb=" N SER A1198 " --> pdb=" O PHE A1195 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N GLY A1200 " --> pdb=" O ASN A1197 " (cutoff:3.500A) Processing helix chain 'A' and resid 1687 through 1692 removed outlier: 4.083A pdb=" N SER A1691 " --> pdb=" O PRO A1688 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 274 removed outlier: 3.912A pdb=" N GLU A 274 " --> pdb=" O ASP A 269 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 269 through 274' Processing helix chain 'A' and resid 1529 through 1534 removed outlier: 3.951A pdb=" N GLY A1534 " --> pdb=" O ASN A1529 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1529 through 1534' Processing helix chain 'B' and resid 479 through 484 removed outlier: 4.220A pdb=" N LEU B 483 " --> pdb=" O GLU B 479 " (cutoff:3.500A) Proline residue: B 484 - end of helix No H-bonds generated for 'chain 'B' and resid 479 through 484' Processing helix chain 'B' and resid 485 through 492 removed outlier: 4.952A pdb=" N GLU B 489 " --> pdb=" O ASP B 485 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N ALA B 490 " --> pdb=" O TRP B 486 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N PHE B 491 " --> pdb=" O CYS B 487 " (cutoff:3.500A) Proline residue: B 492 - end of helix No H-bonds generated for 'chain 'B' and resid 485 through 492' Processing helix chain 'B' and resid 500 through 511 removed outlier: 4.770A pdb=" N HIS B 508 " --> pdb=" O SER B 504 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N ALA B 509 " --> pdb=" O LYS B 505 " (cutoff:3.500A) Processing helix chain 'B' and resid 526 through 542 removed outlier: 4.078A pdb=" N ILE B 530 " --> pdb=" O GLY B 526 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N HIS B 541 " --> pdb=" O LYS B 537 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N HIS B 542 " --> pdb=" O ALA B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 563 through 579 Processing helix chain 'B' and resid 594 through 602 removed outlier: 3.623A pdb=" N GLN B 598 " --> pdb=" O LEU B 594 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ASP B 600 " --> pdb=" O ARG B 596 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 619 removed outlier: 5.812A pdb=" N SER B 619 " --> pdb=" O THR B 615 " (cutoff:3.500A) Processing helix chain 'B' and resid 620 through 629 removed outlier: 5.835A pdb=" N ILE B 624 " --> pdb=" O ASN B 620 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLU B 626 " --> pdb=" O LEU B 622 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N LEU B 627 " --> pdb=" O ALA B 623 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N VAL B 628 " --> pdb=" O ILE B 624 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N ARG B 629 " --> pdb=" O VAL B 625 " (cutoff:3.500A) Processing helix chain 'B' and resid 637 through 642 removed outlier: 4.628A pdb=" N ASP B 641 " --> pdb=" O HIS B 637 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N ASP B 642 " --> pdb=" O LEU B 638 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 637 through 642' Processing helix chain 'B' and resid 643 through 656 removed outlier: 4.244A pdb=" N LEU B 647 " --> pdb=" O ARG B 643 " (cutoff:3.500A) Processing helix chain 'B' and resid 676 through 685 Processing helix chain 'B' and resid 687 through 692 removed outlier: 5.630A pdb=" N PHE B 692 " --> pdb=" O LYS B 688 " (cutoff:3.500A) Processing helix chain 'B' and resid 714 through 737 Processing helix chain 'B' and resid 746 through 765 removed outlier: 3.584A pdb=" N THR B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N SER B 751 " --> pdb=" O ARG B 747 " (cutoff:3.500A) Processing helix chain 'B' and resid 774 through 789 removed outlier: 4.024A pdb=" N ILE B 780 " --> pdb=" O GLY B 776 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ASN B 787 " --> pdb=" O THR B 783 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL B 788 " --> pdb=" O GLU B 784 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N LEU B 789 " --> pdb=" O ALA B 785 " (cutoff:3.500A) Processing helix chain 'B' and resid 790 through 800 removed outlier: 3.681A pdb=" N LEU B 796 " --> pdb=" O SER B 792 " (cutoff:3.500A) Processing helix chain 'B' and resid 809 through 823 Processing helix chain 'B' and resid 832 through 837 removed outlier: 3.851A pdb=" N TRP B 836 " --> pdb=" O ALA B 832 " (cutoff:3.500A) Processing helix chain 'B' and resid 864 through 876 removed outlier: 3.837A pdb=" N ARG B 874 " --> pdb=" O GLN B 870 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ALA B 875 " --> pdb=" O MET B 871 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N GLY B 876 " --> pdb=" O LEU B 872 " (cutoff:3.500A) Processing helix chain 'B' and resid 891 through 904 removed outlier: 3.731A pdb=" N VAL B 895 " --> pdb=" O ASP B 891 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N GLN B 896 " --> pdb=" O GLN B 892 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N TYR B 897 " --> pdb=" O SER B 893 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLN B 904 " --> pdb=" O SER B 900 " (cutoff:3.500A) Processing helix chain 'B' and resid 911 through 927 removed outlier: 4.381A pdb=" N LYS B 915 " --> pdb=" O GLN B 911 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N VAL B 917 " --> pdb=" O VAL B 913 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N ASP B 918 " --> pdb=" O SER B 914 " (cutoff:3.500A) Processing helix chain 'B' and resid 931 through 943 removed outlier: 3.738A pdb=" N ALA B 935 " --> pdb=" O CYS B 931 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N TYR B 941 " --> pdb=" O ASN B 937 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N THR B 942 " --> pdb=" O TRP B 938 " (cutoff:3.500A) removed outlier: 5.728A pdb=" N TYR B 943 " --> pdb=" O LEU B 939 " (cutoff:3.500A) Processing helix chain 'B' and resid 944 through 951 Processing helix chain 'B' and resid 959 through 964 Processing helix chain 'B' and resid 966 through 985 Processing helix chain 'B' and resid 999 through 1009 Processing helix chain 'B' and resid 1011 through 1022 Processing helix chain 'B' and resid 1027 through 1038 removed outlier: 3.566A pdb=" N PHE B1032 " --> pdb=" O GLN B1028 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG B1033 " --> pdb=" O ILE B1029 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER B1038 " --> pdb=" O ILE B1034 " (cutoff:3.500A) Processing helix chain 'B' and resid 1047 through 1061 removed outlier: 4.449A pdb=" N ARG B1052 " --> pdb=" O TYR B1048 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N GLU B1053 " --> pdb=" O GLU B1049 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N LYS B1060 " --> pdb=" O GLN B1056 " (cutoff:3.500A) Processing helix chain 'B' and resid 1071 through 1086 removed outlier: 3.594A pdb=" N LYS B1075 " --> pdb=" O ASP B1071 " (cutoff:3.500A) Processing helix chain 'B' and resid 1091 through 1120 removed outlier: 4.764A pdb=" N VAL B1099 " --> pdb=" O ASN B1095 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N GLY B1106 " --> pdb=" O HIS B1102 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N ARG B1107 " --> pdb=" O GLN B1103 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU B1108 " --> pdb=" O ASN B1104 " (cutoff:3.500A) Processing helix chain 'B' and resid 1121 through 1138 Processing helix chain 'B' and resid 1144 through 1150 removed outlier: 4.073A pdb=" N GLN B1148 " --> pdb=" O CYS B1144 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N LYS B1150 " --> pdb=" O LEU B1146 " (cutoff:3.500A) Processing helix chain 'B' and resid 1153 through 1164 removed outlier: 3.679A pdb=" N ILE B1157 " --> pdb=" O PRO B1153 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N THR B1164 " --> pdb=" O LEU B1160 " (cutoff:3.500A) Processing helix chain 'B' and resid 1166 through 1173 removed outlier: 4.347A pdb=" N GLN B1172 " --> pdb=" O GLY B1168 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N LEU B1173 " --> pdb=" O ASP B1169 " (cutoff:3.500A) Processing helix chain 'B' and resid 1175 through 1184 Processing helix chain 'B' and resid 1186 through 1197 removed outlier: 3.748A pdb=" N LYS B1190 " --> pdb=" O GLU B1186 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N GLN B1191 " --> pdb=" O LYS B1187 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASP B1194 " --> pdb=" O LYS B1190 " (cutoff:3.500A) Processing helix chain 'B' and resid 1260 through 1265 removed outlier: 6.310A pdb=" N GLY B1265 " --> pdb=" O PRO B1261 " (cutoff:3.500A) Processing helix chain 'B' and resid 1277 through 1284 Processing helix chain 'B' and resid 1336 through 1343 removed outlier: 3.772A pdb=" N GLU B1341 " --> pdb=" O ASP B1337 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N VAL B1342 " --> pdb=" O ASP B1338 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N PHE B1343 " --> pdb=" O PHE B1339 " (cutoff:3.500A) Processing helix chain 'B' and resid 1349 through 1360 removed outlier: 3.701A pdb=" N GLN B1354 " --> pdb=" O LYS B1350 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL B1355 " --> pdb=" O ILE B1351 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N GLU B1357 " --> pdb=" O SER B1353 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N SER B1358 " --> pdb=" O GLN B1354 " (cutoff:3.500A) Processing helix chain 'B' and resid 1375 through 1391 removed outlier: 3.562A pdb=" N MET B1379 " --> pdb=" O GLY B1375 " (cutoff:3.500A) Processing helix chain 'B' and resid 1401 through 1421 removed outlier: 4.129A pdb=" N SER B1410 " --> pdb=" O ASP B1406 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N SER B1417 " --> pdb=" O ASN B1413 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N HIS B1418 " --> pdb=" O LYS B1414 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N LEU B1419 " --> pdb=" O ARG B1415 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N ALA B1420 " --> pdb=" O PHE B1416 " (cutoff:3.500A) Processing helix chain 'B' and resid 1431 through 1442 Processing helix chain 'B' and resid 1448 through 1460 removed outlier: 5.279A pdb=" N ARG B1458 " --> pdb=" O LEU B1454 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N TRP B1459 " --> pdb=" O LEU B1455 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N ARG B1460 " --> pdb=" O SER B1456 " (cutoff:3.500A) Processing helix chain 'B' and resid 1462 through 1468 removed outlier: 3.911A pdb=" N LEU B1468 " --> pdb=" O ASN B1464 " (cutoff:3.500A) Processing helix chain 'B' and resid 1477 through 1482 removed outlier: 4.949A pdb=" N GLN B1481 " --> pdb=" O HIS B1477 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N GLY B1482 " --> pdb=" O GLU B1478 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1477 through 1482' Processing helix chain 'B' and resid 1483 through 1503 Processing helix chain 'B' and resid 1518 through 1526 Processing helix chain 'B' and resid 1528 through 1533 removed outlier: 5.539A pdb=" N TYR B1533 " --> pdb=" O LYS B1529 " (cutoff:3.500A) Processing helix chain 'B' and resid 1560 through 1578 Processing helix chain 'B' and resid 1587 through 1606 removed outlier: 4.544A pdb=" N GLU B1606 " --> pdb=" O SER B1602 " (cutoff:3.500A) Processing helix chain 'B' and resid 1613 through 1625 removed outlier: 4.119A pdb=" N ILE B1617 " --> pdb=" O GLU B1613 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N VAL B1618 " --> pdb=" O GLU B1614 " (cutoff:3.500A) Proline residue: B1619 - end of helix removed outlier: 5.625A pdb=" N THR B1625 " --> pdb=" O ILE B1621 " (cutoff:3.500A) Processing helix chain 'B' and resid 1626 through 1636 removed outlier: 4.201A pdb=" N ARG B1630 " --> pdb=" O ASP B1626 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ALA B1631 " --> pdb=" O GLY B1627 " (cutoff:3.500A) Proline residue: B1632 - end of helix Processing helix chain 'B' and resid 1645 through 1659 Processing helix chain 'B' and resid 1699 through 1710 removed outlier: 4.802A pdb=" N LEU B1709 " --> pdb=" O GLU B1705 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ALA B1710 " --> pdb=" O MET B1706 " (cutoff:3.500A) Processing helix chain 'B' and resid 1726 through 1738 removed outlier: 4.227A pdb=" N ALA B1730 " --> pdb=" O HIS B1726 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N TYR B1731 " --> pdb=" O ASN B1727 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ILE B1737 " --> pdb=" O LYS B1733 " (cutoff:3.500A) Processing helix chain 'B' and resid 1745 through 1750 removed outlier: 4.403A pdb=" N ILE B1749 " --> pdb=" O TYR B1745 " (cutoff:3.500A) Processing helix chain 'B' and resid 1751 through 1761 Processing helix chain 'B' and resid 1765 through 1777 removed outlier: 4.086A pdb=" N TYR B1775 " --> pdb=" O ASP B1771 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N SER B1776 " --> pdb=" O TRP B1772 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N TYR B1777 " --> pdb=" O PHE B1773 " (cutoff:3.500A) Processing helix chain 'B' and resid 1778 through 1785 removed outlier: 3.724A pdb=" N HIS B1783 " --> pdb=" O TYR B1779 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL B1784 " --> pdb=" O ARG B1780 " (cutoff:3.500A) Processing helix chain 'B' and resid 1795 through 1818 Processing helix chain 'B' and resid 1847 through 1857 Processing helix chain 'B' and resid 1859 through 1870 Processing helix chain 'B' and resid 1875 through 1891 removed outlier: 3.975A pdb=" N ALA B1886 " --> pdb=" O VAL B1882 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N VAL B1887 " --> pdb=" O LEU B1883 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N GLU B1888 " --> pdb=" O SER B1884 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N PHE B1889 " --> pdb=" O THR B1885 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N GLU B1890 " --> pdb=" O ALA B1886 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N SER B1891 " --> pdb=" O VAL B1887 " (cutoff:3.500A) Processing helix chain 'B' and resid 1897 through 1910 removed outlier: 3.902A pdb=" N LYS B1907 " --> pdb=" O VAL B1903 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ARG B1908 " --> pdb=" O LYS B1904 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU B1909 " --> pdb=" O LEU B1905 " (cutoff:3.500A) Proline residue: B1910 - end of helix Processing helix chain 'B' and resid 1921 through 1936 removed outlier: 3.907A pdb=" N LYS B1925 " --> pdb=" O SER B1921 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLN B1931 " --> pdb=" O PHE B1927 " (cutoff:3.500A) Processing helix chain 'B' and resid 1940 through 1969 removed outlier: 4.227A pdb=" N LYS B1953 " --> pdb=" O ASP B1949 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N VAL B1955 " --> pdb=" O LEU B1951 " (cutoff:3.500A) Proline residue: B1956 - end of helix Processing helix chain 'B' and resid 1971 through 1986 removed outlier: 4.598A pdb=" N THR B1975 " --> pdb=" O LEU B1971 " (cutoff:3.500A) Processing helix chain 'B' and resid 1992 through 1998 removed outlier: 4.260A pdb=" N GLN B1996 " --> pdb=" O ASN B1992 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N ILE B1997 " --> pdb=" O PRO B1993 " (cutoff:3.500A) Proline residue: B1998 - end of helix No H-bonds generated for 'chain 'B' and resid 1992 through 1998' Processing helix chain 'B' and resid 2001 through 2012 Processing helix chain 'B' and resid 2015 through 2022 Processing helix chain 'B' and resid 2023 through 2032 removed outlier: 4.060A pdb=" N GLU B2029 " --> pdb=" O GLU B2025 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N THR B2032 " --> pdb=" O ASP B2028 " (cutoff:3.500A) Processing helix chain 'B' and resid 2034 through 2048 Processing helix chain 'B' and resid 1330 through 1335 removed outlier: 3.873A pdb=" N LEU B1334 " --> pdb=" O THR B1331 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N GLY B1335 " --> pdb=" O SER B1332 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 114 removed outlier: 3.563A pdb=" N ILE C 113 " --> pdb=" O LEU C 109 " (cutoff:3.500A) Proline residue: C 114 - end of helix No H-bonds generated for 'chain 'C' and resid 109 through 114' Processing helix chain 'C' and resid 119 through 128 removed outlier: 3.611A pdb=" N MET C 123 " --> pdb=" O ASN C 119 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ASN C 128 " --> pdb=" O LEU C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 134 removed outlier: 3.971A pdb=" N ILE C 133 " --> pdb=" O ILE C 129 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N ILE C 134 " --> pdb=" O PRO C 130 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 129 through 134' Processing helix chain 'C' and resid 145 through 159 removed outlier: 5.314A pdb=" N LYS C 159 " --> pdb=" O ILE C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 171 Processing helix chain 'C' and resid 181 through 188 Processing helix chain 'C' and resid 221 through 232 removed outlier: 3.583A pdb=" N THR C 225 " --> pdb=" O PHE C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 260 Processing helix chain 'C' and resid 269 through 275 removed outlier: 4.211A pdb=" N LEU C 273 " --> pdb=" O LYS C 269 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE C 274 " --> pdb=" O LEU C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 300 removed outlier: 3.882A pdb=" N PHE C 298 " --> pdb=" O ASN C 294 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N LYS C 300 " --> pdb=" O ASN C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 323 through 331 Processing helix chain 'C' and resid 332 through 337 removed outlier: 3.675A pdb=" N ILE C 336 " --> pdb=" O TYR C 332 " (cutoff:3.500A) Proline residue: C 337 - end of helix No H-bonds generated for 'chain 'C' and resid 332 through 337' Processing helix chain 'C' and resid 338 through 349 removed outlier: 5.193A pdb=" N ASP C 342 " --> pdb=" O SER C 338 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N ASP C 343 " --> pdb=" O SER C 339 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ARG C 347 " --> pdb=" O ASP C 343 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU C 348 " --> pdb=" O PHE C 344 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N TRP C 349 " --> pdb=" O THR C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 371 through 390 removed outlier: 3.501A pdb=" N LEU C 378 " --> pdb=" O VAL C 374 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N ILE C 379 " --> pdb=" O GLU C 375 " (cutoff:3.500A) Proline residue: C 380 - end of helix Processing helix chain 'C' and resid 392 through 404 Processing helix chain 'C' and resid 409 through 415 removed outlier: 3.551A pdb=" N GLN C 414 " --> pdb=" O GLN C 410 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N TYR C 415 " --> pdb=" O GLU C 411 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 430 Processing helix chain 'C' and resid 432 through 449 removed outlier: 3.558A pdb=" N TYR C 443 " --> pdb=" O ILE C 439 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N GLN C 444 " --> pdb=" O THR C 440 " (cutoff:3.500A) Proline residue: C 445 - end of helix removed outlier: 3.831A pdb=" N LEU C 448 " --> pdb=" O GLN C 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 457 Processing helix chain 'C' and resid 503 through 516 removed outlier: 3.800A pdb=" N SER C 507 " --> pdb=" O ASP C 503 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N GLU C 508 " --> pdb=" O THR C 504 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N SER C 509 " --> pdb=" O SER C 505 " (cutoff:3.500A) Processing helix chain 'C' and resid 567 through 572 removed outlier: 4.674A pdb=" N TYR C 571 " --> pdb=" O ILE C 567 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N ILE C 572 " --> pdb=" O SER C 568 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 567 through 572' Processing helix chain 'C' and resid 582 through 589 Processing helix chain 'C' and resid 614 through 629 Processing helix chain 'C' and resid 648 through 662 Processing helix chain 'C' and resid 716 through 726 removed outlier: 3.901A pdb=" N ARG C 725 " --> pdb=" O GLN C 721 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASN C 726 " --> pdb=" O ASP C 722 " (cutoff:3.500A) Processing helix chain 'C' and resid 743 through 754 Processing helix chain 'C' and resid 758 through 765 Processing helix chain 'C' and resid 784 through 793 removed outlier: 4.155A pdb=" N TYR C 791 " --> pdb=" O LEU C 787 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N GLU C 793 " --> pdb=" O SER C 789 " (cutoff:3.500A) Processing helix chain 'C' and resid 794 through 806 removed outlier: 4.002A pdb=" N GLY C 806 " --> pdb=" O ALA C 802 " (cutoff:3.500A) Processing helix chain 'C' and resid 833 through 854 removed outlier: 3.673A pdb=" N GLN C 837 " --> pdb=" O VAL C 833 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ILE C 839 " --> pdb=" O LYS C 835 " (cutoff:3.500A) Proline residue: C 840 - end of helix removed outlier: 4.136A pdb=" N ILE C 854 " --> pdb=" O LEU C 850 " (cutoff:3.500A) Processing helix chain 'C' and resid 872 through 884 removed outlier: 3.515A pdb=" N VAL C 876 " --> pdb=" O LEU C 872 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N ARG C 884 " --> pdb=" O MET C 880 " (cutoff:3.500A) Processing helix chain 'C' and resid 907 through 912 removed outlier: 4.351A pdb=" N ALA C 912 " --> pdb=" O VAL C 908 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 923 Processing helix chain 'C' and resid 958 through 975 removed outlier: 3.595A pdb=" N LEU C 962 " --> pdb=" O PRO C 958 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N SER C 963 " --> pdb=" O ILE C 959 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N ARG C 964 " --> pdb=" O ASN C 960 " (cutoff:3.500A) Processing helix chain 'C' and resid 988 through 993 removed outlier: 4.725A pdb=" N TYR C 992 " --> pdb=" O THR C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 994 through 1005 Processing helix chain 'D' and resid 16 through 31 removed outlier: 3.759A pdb=" N LYS D 29 " --> pdb=" O ARG D 25 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N LYS D 30 " --> pdb=" O LYS D 26 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU D 31 " --> pdb=" O MET D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 133 through 151 Processing helix chain 'D' and resid 161 through 201 removed outlier: 4.200A pdb=" N ASP D 180 " --> pdb=" O GLU D 176 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N GLU D 181 " --> pdb=" O GLN D 177 " (cutoff:3.500A) Processing helix chain 'F' and resid 5 through 11 removed outlier: 4.735A pdb=" N LEU F 9 " --> pdb=" O ASP F 5 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N LYS F 10 " --> pdb=" O LEU F 6 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N SER F 11 " --> pdb=" O ASN F 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 5 through 11' Processing helix chain 'F' and resid 16 through 55 Processing helix chain 'G' and resid 3 through 10 removed outlier: 3.529A pdb=" N SER G 10 " --> pdb=" O ASP G 6 " (cutoff:3.500A) Processing helix chain 'G' and resid 11 through 24 Processing helix chain 'G' and resid 28 through 33 removed outlier: 4.416A pdb=" N TYR G 32 " --> pdb=" O ASP G 28 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N GLN G 33 " --> pdb=" O TYR G 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 28 through 33' Processing helix chain 'G' and resid 43 through 66 removed outlier: 3.567A pdb=" N ARG G 64 " --> pdb=" O GLN G 60 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N TYR G 66 " --> pdb=" O SER G 62 " (cutoff:3.500A) Processing helix chain 'G' and resid 73 through 98 Processing helix chain 'G' and resid 175 through 191 removed outlier: 3.572A pdb=" N PHE G 179 " --> pdb=" O ALA G 175 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER G 185 " --> pdb=" O ALA G 181 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N ILE G 186 " --> pdb=" O ASN G 182 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N LEU G 187 " --> pdb=" O TRP G 183 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA G 189 " --> pdb=" O SER G 185 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N TYR G 191 " --> pdb=" O LEU G 187 " (cutoff:3.500A) Processing helix chain 'G' and resid 214 through 231 removed outlier: 3.799A pdb=" N HIS G 219 " --> pdb=" O ALA G 215 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N TRP G 220 " --> pdb=" O ASP G 216 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ASP G 231 " --> pdb=" O LYS G 227 " (cutoff:3.500A) Processing helix chain 'H' and resid 10 through 29 removed outlier: 3.684A pdb=" N GLN H 14 " --> pdb=" O ASP H 10 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE H 21 " --> pdb=" O ASN H 17 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N SER H 26 " --> pdb=" O ARG H 22 " (cutoff:3.500A) Proline residue: H 27 - end of helix Processing helix chain 'H' and resid 36 through 47 removed outlier: 3.908A pdb=" N PHE H 45 " --> pdb=" O HIS H 41 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLN H 46 " --> pdb=" O ARG H 42 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N VAL H 47 " --> pdb=" O ASP H 43 " (cutoff:3.500A) Processing helix chain 'H' and resid 48 through 53 Processing helix chain 'H' and resid 54 through 66 Processing helix chain 'H' and resid 72 through 87 removed outlier: 3.733A pdb=" N LEU H 76 " --> pdb=" O LEU H 72 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ASP H 86 " --> pdb=" O LEU H 82 " (cutoff:3.500A) Processing helix chain 'H' and resid 88 through 109 removed outlier: 4.246A pdb=" N LYS H 96 " --> pdb=" O GLU H 92 " (cutoff:3.500A) Processing helix chain 'H' and resid 110 through 128 removed outlier: 4.620A pdb=" N ASP H 128 " --> pdb=" O LEU H 124 " (cutoff:3.500A) Processing helix chain 'H' and resid 131 through 146 removed outlier: 4.031A pdb=" N ILE H 135 " --> pdb=" O HIS H 131 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS H 145 " --> pdb=" O LEU H 141 " (cutoff:3.500A) Processing helix chain 'H' and resid 147 through 158 removed outlier: 3.537A pdb=" N VAL H 151 " --> pdb=" O SER H 147 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA H 153 " --> pdb=" O ARG H 149 " (cutoff:3.500A) Processing helix chain 'H' and resid 159 through 166 Processing helix chain 'H' and resid 167 through 183 removed outlier: 4.136A pdb=" N MET H 172 " --> pdb=" O LYS H 168 " (cutoff:3.500A) Processing helix chain 'H' and resid 187 through 204 Processing helix chain 'H' and resid 212 through 220 removed outlier: 4.799A pdb=" N ASP H 216 " --> pdb=" O LEU H 212 " (cutoff:3.500A) Proline residue: H 217 - end of helix Processing helix chain 'H' and resid 247 through 263 Processing helix chain 'H' and resid 288 through 303 removed outlier: 3.566A pdb=" N SER H 302 " --> pdb=" O VAL H 298 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N LEU H 303 " --> pdb=" O LEU H 299 " (cutoff:3.500A) Processing helix chain 'H' and resid 304 through 316 removed outlier: 3.775A pdb=" N LEU H 315 " --> pdb=" O LYS H 311 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N LYS H 316 " --> pdb=" O LEU H 312 " (cutoff:3.500A) Processing helix chain 'H' and resid 319 through 336 removed outlier: 4.645A pdb=" N LYS H 323 " --> pdb=" O ASN H 319 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N SER H 324 " --> pdb=" O ASN H 320 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLU H 336 " --> pdb=" O SER H 332 " (cutoff:3.500A) Processing helix chain 'H' and resid 340 through 355 removed outlier: 3.720A pdb=" N SER H 344 " --> pdb=" O SER H 340 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N HIS H 354 " --> pdb=" O MET H 350 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N ARG H 355 " --> pdb=" O ILE H 351 " (cutoff:3.500A) Processing helix chain 'H' and resid 356 through 371 Processing helix chain 'H' and resid 372 through 377 removed outlier: 4.095A pdb=" N TYR H 376 " --> pdb=" O ASP H 372 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N GLU H 377 " --> pdb=" O ILE H 373 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 372 through 377' Processing helix chain 'H' and resid 378 through 395 Processing helix chain 'H' and resid 398 through 404 removed outlier: 4.643A pdb=" N LEU H 402 " --> pdb=" O PRO H 398 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N LYS H 403 " --> pdb=" O MET H 399 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N ILE H 404 " --> pdb=" O ASP H 400 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 398 through 404' Processing helix chain 'H' and resid 413 through 431 Processing helix chain 'H' and resid 432 through 444 removed outlier: 3.835A pdb=" N LYS H 444 " --> pdb=" O LEU H 440 " (cutoff:3.500A) Processing helix chain 'H' and resid 454 through 469 removed outlier: 3.514A pdb=" N GLY H 469 " --> pdb=" O PHE H 465 " (cutoff:3.500A) Processing helix chain 'H' and resid 470 through 486 removed outlier: 4.182A pdb=" N THR H 474 " --> pdb=" O LEU H 470 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLU H 475 " --> pdb=" O GLY H 471 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N ASP H 476 " --> pdb=" O LEU H 472 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N MET H 477 " --> pdb=" O LEU H 473 " (cutoff:3.500A) Processing helix chain 'H' and resid 236 through 241 removed outlier: 4.400A pdb=" N GLY H 240 " --> pdb=" O LYS H 237 " (cutoff:3.500A) Processing helix chain 'J' and resid 46 through 59 removed outlier: 3.933A pdb=" N SER J 59 " --> pdb=" O ARG J 55 " (cutoff:3.500A) Processing helix chain 'J' and resid 96 through 102 removed outlier: 3.918A pdb=" N LYS J 100 " --> pdb=" O ALA J 96 " (cutoff:3.500A) Processing helix chain 'J' and resid 110 through 122 removed outlier: 3.668A pdb=" N ARG J 114 " --> pdb=" O LEU J 110 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLN J 121 " --> pdb=" O LYS J 117 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N ARG J 122 " --> pdb=" O LEU J 118 " (cutoff:3.500A) Processing helix chain 'J' and resid 396 through 401 removed outlier: 3.588A pdb=" N SER J 401 " --> pdb=" O GLY J 398 " (cutoff:3.500A) Processing helix chain 'K' and resid 1 through 6 removed outlier: 3.587A pdb=" N ARG K 5 " --> pdb=" O MET K 1 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N LEU K 6 " --> pdb=" O PHE K 2 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 1 through 6' Processing helix chain 'K' and resid 39 through 45 removed outlier: 3.993A pdb=" N PHE K 43 " --> pdb=" O LYS K 39 " (cutoff:3.500A) Proline residue: K 45 - end of helix Processing helix chain 'K' and resid 59 through 85 removed outlier: 3.727A pdb=" N GLU K 65 " --> pdb=" O ALA K 61 " (cutoff:3.500A) Processing helix chain 'K' and resid 89 through 95 removed outlier: 4.309A pdb=" N TYR K 93 " --> pdb=" O ALA K 89 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N THR K 95 " --> pdb=" O SER K 91 " (cutoff:3.500A) Processing helix chain 'K' and resid 159 through 164 removed outlier: 4.659A pdb=" N TRP K 163 " --> pdb=" O ASP K 159 " (cutoff:3.500A) Processing helix chain 'K' and resid 181 through 186 removed outlier: 3.637A pdb=" N ARG K 185 " --> pdb=" O ALA K 181 " (cutoff:3.500A) Processing helix chain 'K' and resid 198 through 224 removed outlier: 4.182A pdb=" N MET K 202 " --> pdb=" O ASN K 198 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N GLU K 224 " --> pdb=" O ARG K 220 " (cutoff:3.500A) Processing helix chain 'L' and resid 15 through 35 Proline residue: L 21 - end of helix removed outlier: 4.405A pdb=" N LYS L 35 " --> pdb=" O ARG L 31 " (cutoff:3.500A) Processing helix chain 'L' and resid 41 through 68 removed outlier: 3.665A pdb=" N LEU L 49 " --> pdb=" O SER L 45 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE L 52 " --> pdb=" O GLN L 48 " (cutoff:3.500A) Processing helix chain 'L' and resid 74 through 85 Processing helix chain 'L' and resid 88 through 98 removed outlier: 3.944A pdb=" N LYS L 97 " --> pdb=" O ALA L 93 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N THR L 98 " --> pdb=" O LYS L 94 " (cutoff:3.500A) Processing helix chain 'L' and resid 105 through 111 removed outlier: 4.439A pdb=" N ILE L 109 " --> pdb=" O CYS L 105 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLN L 110 " --> pdb=" O LEU L 106 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N LYS L 111 " --> pdb=" O ARG L 107 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 105 through 111' Processing helix chain 'L' and resid 125 through 137 Processing helix chain 'M' and resid 3 through 8 removed outlier: 4.530A pdb=" N LYS M 7 " --> pdb=" O SER M 3 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N SER M 8 " --> pdb=" O TRP M 4 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 3 through 8' Processing helix chain 'M' and resid 62 through 68 removed outlier: 3.750A pdb=" N ASN M 66 " --> pdb=" O THR M 62 " (cutoff:3.500A) Processing helix chain 'M' and resid 73 through 79 Processing helix chain 'M' and resid 95 through 103 Processing helix chain 'M' and resid 141 through 147 Processing helix chain 'M' and resid 152 through 168 removed outlier: 3.632A pdb=" N ARG M 166 " --> pdb=" O PHE M 162 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N LEU M 167 " --> pdb=" O VAL M 163 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLY M 168 " --> pdb=" O PHE M 164 " (cutoff:3.500A) Processing helix chain 'M' and resid 188 through 200 removed outlier: 3.603A pdb=" N GLU M 197 " --> pdb=" O GLU M 193 " (cutoff:3.500A) Processing helix chain 'M' and resid 231 through 257 removed outlier: 3.689A pdb=" N VAL M 251 " --> pdb=" O LEU M 247 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N HIS M 252 " --> pdb=" O ASN M 248 " (cutoff:3.500A) Processing helix chain 'M' and resid 54 through 59 removed outlier: 4.543A pdb=" N SER M 59 " --> pdb=" O GLN M 54 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 54 through 59' Processing helix chain 'N' and resid 13 through 18 Processing helix chain 'N' and resid 61 through 69 Processing helix chain 'N' and resid 83 through 96 removed outlier: 3.636A pdb=" N VAL N 94 " --> pdb=" O LEU N 90 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N GLU N 96 " --> pdb=" O SER N 92 " (cutoff:3.500A) Processing helix chain 'N' and resid 106 through 116 removed outlier: 3.837A pdb=" N LEU N 115 " --> pdb=" O ARG N 111 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LYS N 116 " --> pdb=" O PHE N 112 " (cutoff:3.500A) Processing helix chain 'N' and resid 122 through 127 Processing helix chain 'N' and resid 128 through 145 removed outlier: 3.835A pdb=" N ASN N 141 " --> pdb=" O ASP N 137 " (cutoff:3.500A) Processing helix chain 'N' and resid 182 through 191 removed outlier: 4.891A pdb=" N LYS N 188 " --> pdb=" O SER N 184 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LYS N 189 " --> pdb=" O HIS N 185 " (cutoff:3.500A) Proline residue: N 191 - end of helix Processing helix chain 'N' and resid 215 through 228 removed outlier: 3.851A pdb=" N ILE N 219 " --> pdb=" O PRO N 215 " (cutoff:3.500A) Processing helix chain 'N' and resid 255 through 266 removed outlier: 3.778A pdb=" N LYS N 265 " --> pdb=" O ARG N 261 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N ILE N 266 " --> pdb=" O PHE N 262 " (cutoff:3.500A) Processing helix chain 'N' and resid 298 through 303 removed outlier: 4.912A pdb=" N PHE N 302 " --> pdb=" O SER N 298 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N GLY N 303 " --> pdb=" O ALA N 299 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 298 through 303' Processing helix chain 'N' and resid 305 through 324 Processing helix chain 'O' and resid 14 through 28 removed outlier: 3.642A pdb=" N LYS O 27 " --> pdb=" O ALA O 23 " (cutoff:3.500A) Processing helix chain 'O' and resid 32 through 41 removed outlier: 3.914A pdb=" N LEU O 39 " --> pdb=" O LYS O 35 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N GLN O 41 " --> pdb=" O ALA O 37 " (cutoff:3.500A) Processing helix chain 'O' and resid 44 through 55 Processing helix chain 'O' and resid 66 through 81 Proline residue: O 81 - end of helix Processing helix chain 'O' and resid 83 through 92 Processing helix chain 'O' and resid 94 through 107 Processing helix chain 'O' and resid 147 through 161 removed outlier: 4.620A pdb=" N MET O 151 " --> pdb=" O GLU O 147 " (cutoff:3.500A) Processing helix chain 'O' and resid 164 through 195 Processing helix chain 'O' and resid 212 through 217 removed outlier: 4.318A pdb=" N ASP O 216 " --> pdb=" O ASP O 212 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N ILE O 217 " --> pdb=" O TYR O 213 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 212 through 217' Processing helix chain 'O' and resid 230 through 251 Processing helix chain 'O' and resid 497 through 536 removed outlier: 4.218A pdb=" N THR O 501 " --> pdb=" O ILE O 497 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ALA O 502 " --> pdb=" O GLN O 498 " (cutoff:3.500A) Proline residue: O 504 - end of helix removed outlier: 3.771A pdb=" N GLU O 518 " --> pdb=" O GLN O 514 " (cutoff:3.500A) Proline residue: O 532 - end of helix Processing helix chain 'P' and resid 13 through 20 removed outlier: 4.399A pdb=" N ALA P 17 " --> pdb=" O SER P 13 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA P 19 " --> pdb=" O ALA P 15 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N TYR P 20 " --> pdb=" O LYS P 16 " (cutoff:3.500A) Processing helix chain 'P' and resid 163 through 174 Processing helix chain 'P' and resid 126 through 131 removed outlier: 3.748A pdb=" N LYS P 129 " --> pdb=" O SER P 126 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N GLY P 130 " --> pdb=" O TRP P 127 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N THR P 131 " --> pdb=" O ARG P 128 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 126 through 131' Processing helix chain 'Q' and resid 339 through 350 removed outlier: 3.735A pdb=" N ILE Q 343 " --> pdb=" O SER Q 339 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N LYS Q 344 " --> pdb=" O LYS Q 340 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N HIS Q 345 " --> pdb=" O ASP Q 341 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU Q 350 " --> pdb=" O THR Q 346 " (cutoff:3.500A) Processing helix chain 'Q' and resid 351 through 356 removed outlier: 3.960A pdb=" N CYS Q 355 " --> pdb=" O PRO Q 351 " (cutoff:3.500A) Processing helix chain 'Q' and resid 357 through 366 removed outlier: 3.658A pdb=" N ARG Q 364 " --> pdb=" O LEU Q 360 " (cutoff:3.500A) Processing helix chain 'Q' and resid 378 through 391 removed outlier: 4.521A pdb=" N ALA Q 384 " --> pdb=" O THR Q 380 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLN Q 385 " --> pdb=" O THR Q 381 " (cutoff:3.500A) Processing helix chain 'Q' and resid 406 through 422 Processing helix chain 'Q' and resid 450 through 461 removed outlier: 3.797A pdb=" N LEU Q 459 " --> pdb=" O LEU Q 455 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LEU Q 460 " --> pdb=" O ARG Q 456 " (cutoff:3.500A) Processing helix chain 'Q' and resid 479 through 493 removed outlier: 3.597A pdb=" N GLY Q 487 " --> pdb=" O ASP Q 483 " (cutoff:3.500A) Processing helix chain 'Q' and resid 509 through 518 Processing helix chain 'Q' and resid 543 through 560 removed outlier: 3.793A pdb=" N ASN Q 559 " --> pdb=" O ILE Q 555 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N ASP Q 560 " --> pdb=" O HIS Q 556 " (cutoff:3.500A) Processing helix chain 'Q' and resid 572 through 590 removed outlier: 3.813A pdb=" N ASP Q 581 " --> pdb=" O GLU Q 577 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLU Q 585 " --> pdb=" O ASP Q 581 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LYS Q 586 " --> pdb=" O THR Q 582 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N PHE Q 587 " --> pdb=" O LEU Q 583 " (cutoff:3.500A) Processing helix chain 'Q' and resid 616 through 626 removed outlier: 3.518A pdb=" N LYS Q 622 " --> pdb=" O ASP Q 618 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N ILE Q 623 " --> pdb=" O LEU Q 619 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N PHE Q 624 " --> pdb=" O GLN Q 620 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLN Q 625 " --> pdb=" O PHE Q 621 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N ASP Q 626 " --> pdb=" O LYS Q 622 " (cutoff:3.500A) Processing helix chain 'Q' and resid 638 through 644 removed outlier: 4.573A pdb=" N GLU Q 642 " --> pdb=" O THR Q 638 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N THR Q 643 " --> pdb=" O ASN Q 639 " (cutoff:3.500A) Processing helix chain 'Q' and resid 679 through 692 removed outlier: 3.635A pdb=" N ARG Q 689 " --> pdb=" O GLN Q 685 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ALA Q 690 " --> pdb=" O ARG Q 686 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N GLY Q 691 " --> pdb=" O SER Q 687 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N ARG Q 692 " --> pdb=" O GLY Q 688 " (cutoff:3.500A) Processing helix chain 'Q' and resid 703 through 710 Processing helix chain 'Q' and resid 717 through 722 removed outlier: 3.803A pdb=" N ARG Q 721 " --> pdb=" O PRO Q 717 " (cutoff:3.500A) Processing helix chain 'Q' and resid 724 through 735 removed outlier: 5.047A pdb=" N ASP Q 735 " --> pdb=" O LEU Q 731 " (cutoff:3.500A) Processing helix chain 'Q' and resid 737 through 743 removed outlier: 3.726A pdb=" N SER Q 741 " --> pdb=" O THR Q 737 " (cutoff:3.500A) Processing helix chain 'Q' and resid 750 through 765 Processing helix chain 'Q' and resid 774 through 784 removed outlier: 3.628A pdb=" N LYS Q 782 " --> pdb=" O LEU Q 778 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N PHE Q 783 " --> pdb=" O GLN Q 779 " (cutoff:3.500A) Proline residue: Q 784 - end of helix Processing helix chain 'Q' and resid 786 through 800 removed outlier: 3.752A pdb=" N ARG Q 798 " --> pdb=" O LEU Q 794 " (cutoff:3.500A) Processing helix chain 'Q' and resid 801 through 815 removed outlier: 3.839A pdb=" N THR Q 807 " --> pdb=" O ASP Q 803 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N VAL Q 814 " --> pdb=" O SER Q 810 " (cutoff:3.500A) Proline residue: Q 815 - end of helix Processing helix chain 'Q' and resid 824 through 836 removed outlier: 4.489A pdb=" N PHE Q 835 " --> pdb=" O ALA Q 831 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N PHE Q 836 " --> pdb=" O ARG Q 832 " (cutoff:3.500A) Processing helix chain 'Q' and resid 840 through 856 removed outlier: 3.539A pdb=" N THR Q 844 " --> pdb=" O SER Q 840 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU Q 846 " --> pdb=" O HIS Q 842 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ASN Q 856 " --> pdb=" O TRP Q 852 " (cutoff:3.500A) Processing helix chain 'Q' and resid 858 through 866 Processing helix chain 'Q' and resid 868 through 890 Processing helix chain 'Q' and resid 899 through 911 removed outlier: 4.414A pdb=" N ILE Q 903 " --> pdb=" O ASP Q 899 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER Q 909 " --> pdb=" O LYS Q 905 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLY Q 910 " --> pdb=" O CYS Q 906 " (cutoff:3.500A) Processing helix chain 'Q' and resid 971 through 979 removed outlier: 3.891A pdb=" N LEU Q 975 " --> pdb=" O ASP Q 971 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N MET Q 976 " --> pdb=" O PRO Q 972 " (cutoff:3.500A) Processing helix chain 'R' and resid 58 through 86 removed outlier: 3.581A pdb=" N LYS R 62 " --> pdb=" O LEU R 58 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLN R 63 " --> pdb=" O ALA R 59 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ILE R 64 " --> pdb=" O VAL R 60 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLU R 65 " --> pdb=" O GLN R 61 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLU R 69 " --> pdb=" O GLU R 65 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LYS R 70 " --> pdb=" O THR R 66 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ILE R 73 " --> pdb=" O GLU R 69 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLU R 74 " --> pdb=" O LYS R 70 " (cutoff:3.500A) Processing helix chain 'R' and resid 91 through 111 removed outlier: 3.663A pdb=" N LYS R 98 " --> pdb=" O GLN R 94 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LEU R 102 " --> pdb=" O LYS R 98 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ARG R 103 " --> pdb=" O CYS R 99 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS R 105 " --> pdb=" O ALA R 101 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N ASN R 108 " --> pdb=" O ALA R 104 " (cutoff:3.500A) Processing helix chain 'S' and resid 39 through 62 Processing helix chain 'S' and resid 64 through 79 Processing helix chain 'S' and resid 80 through 96 Processing helix chain 'S' and resid 98 through 113 removed outlier: 3.576A pdb=" N TRP S 102 " --> pdb=" O PHE S 98 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL S 112 " --> pdb=" O ALA S 108 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS S 113 " --> pdb=" O GLU S 109 " (cutoff:3.500A) Processing helix chain 'S' and resid 114 through 130 Proline residue: S 130 - end of helix Processing helix chain 'S' and resid 132 through 147 removed outlier: 3.826A pdb=" N TRP S 136 " --> pdb=" O VAL S 132 " (cutoff:3.500A) Processing helix chain 'S' and resid 148 through 163 removed outlier: 3.757A pdb=" N LEU S 162 " --> pdb=" O LYS S 158 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N GLU S 163 " --> pdb=" O TRP S 159 " (cutoff:3.500A) Processing helix chain 'S' and resid 165 through 180 removed outlier: 3.968A pdb=" N TRP S 169 " --> pdb=" O GLY S 165 " (cutoff:3.500A) Processing helix chain 'S' and resid 181 through 196 removed outlier: 4.181A pdb=" N MET S 194 " --> pdb=" O SER S 190 " (cutoff:3.500A) Processing helix chain 'S' and resid 198 through 213 removed outlier: 3.931A pdb=" N TRP S 202 " --> pdb=" O GLN S 198 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N HIS S 212 " --> pdb=" O PHE S 208 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLY S 213 " --> pdb=" O GLU S 209 " (cutoff:3.500A) Processing helix chain 'S' and resid 214 through 233 Processing helix chain 'S' and resid 239 through 258 Processing helix chain 'S' and resid 259 through 275 removed outlier: 3.549A pdb=" N TYR S 267 " --> pdb=" O SER S 263 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN S 268 " --> pdb=" O SER S 264 " (cutoff:3.500A) Proline residue: S 275 - end of helix Processing helix chain 'S' and resid 277 through 291 Processing helix chain 'S' and resid 293 through 317 removed outlier: 3.941A pdb=" N ILE S 297 " --> pdb=" O ASP S 293 " (cutoff:3.500A) Processing helix chain 'S' and resid 319 through 333 removed outlier: 3.807A pdb=" N GLU S 332 " --> pdb=" O ASP S 328 " (cutoff:3.500A) Processing helix chain 'S' and resid 334 through 348 removed outlier: 3.768A pdb=" N ILE S 338 " --> pdb=" O PHE S 334 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N MET S 339 " --> pdb=" O PRO S 335 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N GLN S 340 " --> pdb=" O LYS S 336 " (cutoff:3.500A) Processing helix chain 'S' and resid 357 through 377 removed outlier: 4.574A pdb=" N TYR S 365 " --> pdb=" O LYS S 361 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N LEU S 366 " --> pdb=" O ARG S 362 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N TRP S 367 " --> pdb=" O TYR S 363 " (cutoff:3.500A) Processing helix chain 'S' and resid 380 through 395 removed outlier: 3.938A pdb=" N GLU S 384 " --> pdb=" O ASN S 380 " (cutoff:3.500A) Processing helix chain 'S' and resid 403 through 417 removed outlier: 3.660A pdb=" N TRP S 407 " --> pdb=" O PHE S 403 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ILE S 415 " --> pdb=" O ALA S 411 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ARG S 416 " --> pdb=" O LYS S 412 " (cutoff:3.500A) Processing helix chain 'S' and resid 422 through 431 removed outlier: 3.694A pdb=" N ILE S 426 " --> pdb=" O LYS S 422 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA S 430 " --> pdb=" O ILE S 426 " (cutoff:3.500A) Processing helix chain 'S' and resid 436 through 450 removed outlier: 3.902A pdb=" N PHE S 440 " --> pdb=" O LYS S 436 " (cutoff:3.500A) Processing helix chain 'S' and resid 455 through 466 removed outlier: 4.183A pdb=" N GLU S 465 " --> pdb=" O GLU S 461 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N PHE S 466 " --> pdb=" O LYS S 462 " (cutoff:3.500A) Processing helix chain 'S' and resid 472 through 484 removed outlier: 4.173A pdb=" N GLN S 476 " --> pdb=" O GLN S 472 " (cutoff:3.500A) Processing helix chain 'S' and resid 487 through 501 removed outlier: 4.571A pdb=" N ASN S 501 " --> pdb=" O ALA S 497 " (cutoff:3.500A) Processing helix chain 'S' and resid 507 through 523 removed outlier: 4.305A pdb=" N ILE S 511 " --> pdb=" O LYS S 507 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N LEU S 514 " --> pdb=" O LYS S 510 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N GLN S 515 " --> pdb=" O ILE S 511 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N LYS S 516 " --> pdb=" O VAL S 512 " (cutoff:3.500A) Processing helix chain 'S' and resid 528 through 539 removed outlier: 4.295A pdb=" N LYS S 532 " --> pdb=" O GLU S 528 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU S 538 " --> pdb=" O TYR S 534 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N GLU S 539 " --> pdb=" O ARG S 535 " (cutoff:3.500A) Processing helix chain 'S' and resid 548 through 558 removed outlier: 4.514A pdb=" N ALA S 552 " --> pdb=" O TRP S 548 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N MET S 553 " --> pdb=" O ILE S 549 " (cutoff:3.500A) Processing helix chain 'S' and resid 561 through 579 Processing helix chain 'S' and resid 586 through 602 Processing helix chain 'S' and resid 608 through 625 Processing helix chain 'T' and resid 22 through 33 removed outlier: 3.681A pdb=" N LYS T 32 " --> pdb=" O TYR T 28 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N THR T 33 " --> pdb=" O GLU T 29 " (cutoff:3.500A) Processing helix chain 'T' and resid 35 through 49 removed outlier: 3.613A pdb=" N GLU T 49 " --> pdb=" O GLU T 45 " (cutoff:3.500A) Processing helix chain 'T' and resid 54 through 68 Processing helix chain 'T' and resid 72 through 84 Processing helix chain 'T' and resid 90 through 104 removed outlier: 3.964A pdb=" N SER T 103 " --> pdb=" O ARG T 99 " (cutoff:3.500A) Processing helix chain 'T' and resid 107 through 121 removed outlier: 3.983A pdb=" N GLU T 121 " --> pdb=" O GLU T 117 " (cutoff:3.500A) Processing helix chain 'T' and resid 125 through 136 removed outlier: 4.666A pdb=" N ARG T 129 " --> pdb=" O LEU T 125 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N LEU T 136 " --> pdb=" O LEU T 132 " (cutoff:3.500A) Processing helix chain 'T' and resid 144 through 164 removed outlier: 4.003A pdb=" N TRP T 148 " --> pdb=" O HIS T 144 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N ASP T 149 " --> pdb=" O ARG T 145 " (cutoff:3.500A) Proline residue: T 150 - end of helix Proline residue: T 161 - end of helix Processing helix chain 'T' and resid 176 through 190 removed outlier: 3.758A pdb=" N LEU T 181 " --> pdb=" O ASP T 177 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS T 188 " --> pdb=" O VAL T 184 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLY T 189 " --> pdb=" O LEU T 185 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N PHE T 190 " --> pdb=" O LEU T 186 " (cutoff:3.500A) Processing helix chain 'T' and resid 209 through 222 removed outlier: 3.564A pdb=" N LYS T 220 " --> pdb=" O GLU T 216 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N VAL T 221 " --> pdb=" O ARG T 217 " (cutoff:3.500A) Processing helix chain 'T' and resid 224 through 234 removed outlier: 3.845A pdb=" N ASN T 228 " --> pdb=" O GLN T 224 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N SER T 230 " --> pdb=" O LYS T 226 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N THR T 233 " --> pdb=" O GLU T 229 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N LEU T 234 " --> pdb=" O SER T 230 " (cutoff:3.500A) Processing helix chain 'T' and resid 239 through 251 removed outlier: 4.483A pdb=" N LYS T 249 " --> pdb=" O SER T 245 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N TYR T 250 " --> pdb=" O VAL T 246 " (cutoff:3.500A) Processing helix chain 'T' and resid 267 through 282 Processing helix chain 'T' and resid 283 through 299 removed outlier: 3.609A pdb=" N GLN T 293 " --> pdb=" O GLU T 289 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N TYR T 298 " --> pdb=" O MET T 294 " (cutoff:3.500A) Proline residue: T 299 - end of helix Processing helix chain 'T' and resid 301 through 317 removed outlier: 3.606A pdb=" N ILE T 306 " --> pdb=" O TRP T 302 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N GLY T 317 " --> pdb=" O TYR T 313 " (cutoff:3.500A) Processing helix chain 'T' and resid 318 through 333 removed outlier: 3.524A pdb=" N CYS T 322 " --> pdb=" O ARG T 318 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLY T 323 " --> pdb=" O LEU T 319 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N GLN T 332 " --> pdb=" O LYS T 328 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N THR T 333 " --> pdb=" O SER T 329 " (cutoff:3.500A) Processing helix chain 'T' and resid 335 through 362 removed outlier: 3.950A pdb=" N LEU T 361 " --> pdb=" O ILE T 357 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N LYS T 362 " --> pdb=" O LEU T 358 " (cutoff:3.500A) Processing helix chain 'T' and resid 369 through 392 removed outlier: 5.059A pdb=" N SER T 387 " --> pdb=" O ALA T 383 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N LEU T 388 " --> pdb=" O THR T 384 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N ILE T 389 " --> pdb=" O PHE T 385 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ASN T 390 " --> pdb=" O GLU T 386 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N TYR T 392 " --> pdb=" O LEU T 388 " (cutoff:3.500A) Processing helix chain 'T' and resid 393 through 405 removed outlier: 3.946A pdb=" N ALA T 400 " --> pdb=" O LEU T 396 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER T 405 " --> pdb=" O LEU T 401 " (cutoff:3.500A) Processing helix chain 'T' and resid 407 through 418 removed outlier: 3.823A pdb=" N TRP T 411 " --> pdb=" O LEU T 407 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N GLN T 418 " --> pdb=" O ARG T 414 " (cutoff:3.500A) Processing helix chain 'T' and resid 422 through 435 removed outlier: 4.719A pdb=" N ASN T 426 " --> pdb=" O ALA T 422 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL T 427 " --> pdb=" O GLU T 423 " (cutoff:3.500A) Processing helix chain 'T' and resid 444 through 459 removed outlier: 3.557A pdb=" N TYR T 457 " --> pdb=" O TYR T 453 " (cutoff:3.500A) Processing helix chain 'T' and resid 462 through 476 removed outlier: 4.152A pdb=" N ALA T 466 " --> pdb=" O ALA T 462 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLN T 472 " --> pdb=" O GLU T 468 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU T 474 " --> pdb=" O TRP T 470 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N LYS T 475 " --> pdb=" O THR T 471 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N VAL T 476 " --> pdb=" O GLN T 472 " (cutoff:3.500A) Processing helix chain 'T' and resid 480 through 499 removed outlier: 4.340A pdb=" N LEU T 484 " --> pdb=" O TYR T 480 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N GLU T 486 " --> pdb=" O GLU T 482 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE T 487 " --> pdb=" O ASP T 483 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ASN T 490 " --> pdb=" O GLU T 486 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N ASP T 493 " --> pdb=" O LEU T 489 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N LEU T 496 " --> pdb=" O ALA T 492 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ASP T 497 " --> pdb=" O ASP T 493 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N LYS T 498 " --> pdb=" O ARG T 494 " (cutoff:3.500A) Processing helix chain 'T' and resid 500 through 513 removed outlier: 3.560A pdb=" N ALA T 504 " --> pdb=" O GLY T 500 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N SER T 506 " --> pdb=" O GLU T 502 " (cutoff:3.500A) Processing helix chain 'T' and resid 517 through 528 removed outlier: 3.541A pdb=" N LEU T 521 " --> pdb=" O ASN T 517 " (cutoff:3.500A) Processing helix chain 'T' and resid 534 through 539 removed outlier: 3.667A pdb=" N LEU T 538 " --> pdb=" O ALA T 534 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N PHE T 539 " --> pdb=" O GLN T 535 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 534 through 539' Processing helix chain 'T' and resid 541 through 556 removed outlier: 3.691A pdb=" N TRP T 545 " --> pdb=" O SER T 541 " (cutoff:3.500A) Processing helix chain 'T' and resid 564 through 581 removed outlier: 3.627A pdb=" N ASN T 575 " --> pdb=" O LYS T 571 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU T 580 " --> pdb=" O THR T 576 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG T 581 " --> pdb=" O VAL T 577 " (cutoff:3.500A) Processing helix chain 'T' and resid 584 through 599 Processing helix chain 'T' and resid 600 through 616 removed outlier: 3.531A pdb=" N SER T 604 " --> pdb=" O GLU T 600 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N PHE T 605 " --> pdb=" O VAL T 601 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLN T 606 " --> pdb=" O MET T 602 " (cutoff:3.500A) Proline residue: T 613 - end of helix Proline residue: T 616 - end of helix Processing helix chain 'T' and resid 617 through 633 removed outlier: 5.028A pdb=" N GLU T 622 " --> pdb=" O GLU T 618 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N GLU T 626 " --> pdb=" O GLU T 622 " (cutoff:3.500A) Processing helix chain 'T' and resid 640 through 659 removed outlier: 3.628A pdb=" N GLU T 649 " --> pdb=" O ARG T 645 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ASN T 658 " --> pdb=" O ASN T 654 " (cutoff:3.500A) Processing helix chain 'T' and resid 662 through 677 removed outlier: 3.608A pdb=" N ALA T 668 " --> pdb=" O THR T 664 " (cutoff:3.500A) Processing helix chain 'T' and resid 679 through 693 removed outlier: 3.603A pdb=" N ILE T 693 " --> pdb=" O ARG T 689 " (cutoff:3.500A) Processing helix chain 'T' and resid 701 through 719 removed outlier: 4.082A pdb=" N TRP T 709 " --> pdb=" O ARG T 705 " (cutoff:3.500A) Processing helix chain 'T' and resid 722 through 736 removed outlier: 3.555A pdb=" N ARG T 726 " --> pdb=" O PRO T 722 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLU T 727 " --> pdb=" O SER T 723 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU T 731 " --> pdb=" O GLU T 727 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N GLN T 734 " --> pdb=" O GLN T 730 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE T 735 " --> pdb=" O GLU T 731 " (cutoff:3.500A) Processing helix chain 'T' and resid 737 through 756 removed outlier: 4.416A pdb=" N VAL T 742 " --> pdb=" O ASN T 738 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N GLU T 743 " --> pdb=" O SER T 739 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N PHE T 744 " --> pdb=" O LYS T 740 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE T 746 " --> pdb=" O VAL T 742 " (cutoff:3.500A) Processing helix chain 'T' and resid 757 through 769 removed outlier: 4.266A pdb=" N ALA T 761 " --> pdb=" O GLU T 757 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE T 764 " --> pdb=" O ARG T 760 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N ALA T 769 " --> pdb=" O LEU T 765 " (cutoff:3.500A) Processing helix chain 'T' and resid 779 through 788 removed outlier: 4.699A pdb=" N SER T 783 " --> pdb=" O GLU T 779 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N PHE T 784 " --> pdb=" O LEU T 780 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N GLU T 788 " --> pdb=" O PHE T 784 " (cutoff:3.500A) Processing helix chain 'T' and resid 794 through 810 removed outlier: 3.821A pdb=" N SER T 809 " --> pdb=" O LYS T 805 " (cutoff:3.500A) Processing helix chain 'W' and resid 4 through 11 removed outlier: 4.319A pdb=" N VAL W 8 " --> pdb=" O THR W 4 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ILE W 9 " --> pdb=" O PRO W 5 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASP W 10 " --> pdb=" O SER W 6 " (cutoff:3.500A) Processing helix chain 'W' and resid 40 through 51 Proline residue: W 44 - end of helix removed outlier: 4.165A pdb=" N LYS W 48 " --> pdb=" O PRO W 44 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N HIS W 49 " --> pdb=" O SER W 45 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LEU W 50 " --> pdb=" O SER W 46 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N THR W 51 " --> pdb=" O LEU W 47 " (cutoff:3.500A) Processing helix chain 'W' and resid 90 through 95 removed outlier: 4.147A pdb=" N LEU W 94 " --> pdb=" O ASP W 90 " (cutoff:3.500A) Proline residue: W 95 - end of helix No H-bonds generated for 'chain 'W' and resid 90 through 95' Processing helix chain 'W' and resid 110 through 121 removed outlier: 3.730A pdb=" N LEU W 114 " --> pdb=" O ARG W 110 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N ARG W 116 " --> pdb=" O GLU W 112 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N LEU W 117 " --> pdb=" O ASP W 113 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N ARG W 118 " --> pdb=" O LEU W 114 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N ARG W 119 " --> pdb=" O GLN W 115 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ALA W 120 " --> pdb=" O ARG W 116 " (cutoff:3.500A) Proline residue: W 121 - end of helix Processing helix chain 'W' and resid 132 through 138 removed outlier: 4.576A pdb=" N HIS W 136 " --> pdb=" O ASN W 132 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU W 137 " --> pdb=" O GLN W 133 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N ALA W 138 " --> pdb=" O VAL W 134 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 132 through 138' Processing helix chain 'W' and resid 139 through 149 removed outlier: 3.586A pdb=" N ARG W 146 " --> pdb=" O GLU W 142 " (cutoff:3.500A) Proline residue: W 149 - end of helix Processing helix chain 'W' and resid 160 through 170 removed outlier: 4.234A pdb=" N MET W 168 " --> pdb=" O ARG W 164 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N SER W 169 " --> pdb=" O LYS W 165 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N PHE W 170 " --> pdb=" O SER W 166 " (cutoff:3.500A) Processing helix chain 'W' and resid 194 through 206 removed outlier: 5.089A pdb=" N ILE W 198 " --> pdb=" O LYS W 194 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N MET W 199 " --> pdb=" O THR W 195 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS W 205 " --> pdb=" O LEU W 201 " (cutoff:3.500A) Processing helix chain 'W' and resid 207 through 221 removed outlier: 4.385A pdb=" N LYS W 216 " --> pdb=" O ASN W 212 " (cutoff:3.500A) Processing helix chain 'W' and resid 223 through 236 Processing helix chain 'Y' and resid 40 through 54 removed outlier: 4.311A pdb=" N THR Y 54 " --> pdb=" O LEU Y 50 " (cutoff:3.500A) Processing helix chain 'Y' and resid 78 through 89 removed outlier: 4.190A pdb=" N LEU Y 84 " --> pdb=" O ASP Y 80 " (cutoff:3.500A) Processing helix chain 'Y' and resid 64 through 69 removed outlier: 4.220A pdb=" N ARG Y 69 " --> pdb=" O ASN Y 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 64 through 69' Processing helix chain 'Z' and resid 2 through 23 removed outlier: 4.669A pdb=" N ASP Z 6 " --> pdb=" O PRO Z 2 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LEU Z 7 " --> pdb=" O SER Z 3 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ASN Z 16 " --> pdb=" O ASP Z 12 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N GLN Z 17 " --> pdb=" O GLN Z 13 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N LEU Z 18 " --> pdb=" O GLU Z 14 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ASN Z 23 " --> pdb=" O ARG Z 19 " (cutoff:3.500A) Processing helix chain 'Z' and resid 98 through 128 removed outlier: 3.562A pdb=" N LYS Z 104 " --> pdb=" O ASP Z 100 " (cutoff:3.500A) Proline residue: Z 107 - end of helix removed outlier: 3.604A pdb=" N VAL Z 111 " --> pdb=" O PRO Z 107 " (cutoff:3.500A) Processing helix chain 'a' and resid 76 through 90 removed outlier: 4.452A pdb=" N THR a 90 " --> pdb=" O ALA a 86 " (cutoff:3.500A) Processing helix chain 'a' and resid 96 through 103 removed outlier: 5.725A pdb=" N THR a 103 " --> pdb=" O GLN a 99 " (cutoff:3.500A) Processing helix chain 'a' and resid 105 through 132 removed outlier: 5.820A pdb=" N GLU a 129 " --> pdb=" O LYS a 125 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N ALA a 130 " --> pdb=" O ALA a 126 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N TYR a 131 " --> pdb=" O SER a 127 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N HIS a 132 " --> pdb=" O LEU a 128 " (cutoff:3.500A) Processing helix chain 'a' and resid 133 through 153 removed outlier: 4.240A pdb=" N LEU a 137 " --> pdb=" O PRO a 133 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N ASP a 138 " --> pdb=" O GLU a 134 " (cutoff:3.500A) Proline residue: a 145 - end of helix Processing helix chain 'a' and resid 156 through 173 removed outlier: 3.989A pdb=" N GLN a 172 " --> pdb=" O TYR a 168 " (cutoff:3.500A) Proline residue: a 173 - end of helix Processing helix chain 'a' and resid 175 through 188 Processing helix chain 'a' and resid 223 through 247 Processing helix chain 'b' and resid 11 through 16 removed outlier: 4.234A pdb=" N LEU b 15 " --> pdb=" O ARG b 11 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ILE b 16 " --> pdb=" O LEU b 12 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 11 through 16' Processing helix chain 'b' and resid 54 through 62 removed outlier: 4.448A pdb=" N ASP b 59 " --> pdb=" O LYS b 55 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N LYS b 60 " --> pdb=" O THR b 56 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N LEU b 61 " --> pdb=" O GLN b 57 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N ARG b 62 " --> pdb=" O LEU b 58 " (cutoff:3.500A) Processing helix chain 'b' and resid 88 through 93 removed outlier: 3.805A pdb=" N ILE b 92 " --> pdb=" O ARG b 88 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N LEU b 93 " --> pdb=" O GLY b 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 88 through 93' Processing helix chain 'c' and resid 216 through 226 removed outlier: 4.108A pdb=" N LYS c 220 " --> pdb=" O ILE c 216 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N TYR c 224 " --> pdb=" O LYS c 220 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N LYS c 225 " --> pdb=" O LEU c 221 " (cutoff:3.500A) Processing helix chain 'd' and resid 5 through 15 removed outlier: 3.750A pdb=" N GLN d 15 " --> pdb=" O LEU d 11 " (cutoff:3.500A) Processing helix chain 'd' and resid 77 through 82 removed outlier: 4.293A pdb=" N ALA d 81 " --> pdb=" O LEU d 77 " (cutoff:3.500A) Proline residue: d 82 - end of helix No H-bonds generated for 'chain 'd' and resid 77 through 82' Processing helix chain 'n' and resid 5 through 15 removed outlier: 4.596A pdb=" N LEU n 11 " --> pdb=" O PRO n 7 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N GLN n 15 " --> pdb=" O LEU n 11 " (cutoff:3.500A) Processing helix chain 'n' and resid 77 through 82 removed outlier: 4.235A pdb=" N ALA n 81 " --> pdb=" O LEU n 77 " (cutoff:3.500A) Proline residue: n 82 - end of helix No H-bonds generated for 'chain 'n' and resid 77 through 82' Processing helix chain 'e' and resid 12 through 24 removed outlier: 3.960A pdb=" N GLN e 23 " --> pdb=" O ASN e 19 " (cutoff:3.500A) Processing helix chain 'e' and resid 70 through 75 removed outlier: 3.891A pdb=" N GLY e 74 " --> pdb=" O ASP e 70 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N THR e 75 " --> pdb=" O VAL e 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 70 through 75' Processing helix chain 'e' and resid 83 through 88 removed outlier: 4.089A pdb=" N ILE e 87 " --> pdb=" O LYS e 83 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N THR e 88 " --> pdb=" O GLY e 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 83 through 88' Processing helix chain 'p' and resid 12 through 24 removed outlier: 4.246A pdb=" N GLN p 23 " --> pdb=" O ASN p 19 " (cutoff:3.500A) Processing helix chain 'p' and resid 70 through 75 removed outlier: 3.927A pdb=" N GLY p 74 " --> pdb=" O ASP p 70 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N THR p 75 " --> pdb=" O VAL p 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'p' and resid 70 through 75' Processing helix chain 'p' and resid 83 through 88 removed outlier: 4.221A pdb=" N ILE p 87 " --> pdb=" O LYS p 83 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N THR p 88 " --> pdb=" O GLY p 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'p' and resid 83 through 88' Processing helix chain 'f' and resid 14 through 23 removed outlier: 3.580A pdb=" N VAL f 23 " --> pdb=" O LEU f 19 " (cutoff:3.500A) Processing helix chain 'q' and resid 14 through 23 removed outlier: 3.564A pdb=" N VAL q 23 " --> pdb=" O LEU q 19 " (cutoff:3.500A) Processing helix chain 'h' and resid 2 through 11 removed outlier: 3.664A pdb=" N LYS h 9 " --> pdb=" O ASN h 5 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU h 10 " --> pdb=" O PHE h 6 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N ARG h 11 " --> pdb=" O LEU h 7 " (cutoff:3.500A) Processing helix chain 'h' and resid 48 through 53 removed outlier: 3.663A pdb=" N ASN h 53 " --> pdb=" O GLN h 49 " (cutoff:3.500A) Processing helix chain 'h' and resid 54 through 69 removed outlier: 6.049A pdb=" N ILE h 60 " --> pdb=" O ASN h 56 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N ALA h 61 " --> pdb=" O SER h 57 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N GLY h 69 " --> pdb=" O LEU h 65 " (cutoff:3.500A) Processing helix chain 'l' and resid 2 through 11 removed outlier: 4.194A pdb=" N LYS l 9 " --> pdb=" O ASN l 5 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LEU l 10 " --> pdb=" O PHE l 6 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ARG l 11 " --> pdb=" O LEU l 7 " (cutoff:3.500A) Processing helix chain 'l' and resid 48 through 53 Processing helix chain 'l' and resid 54 through 69 removed outlier: 5.999A pdb=" N ILE l 60 " --> pdb=" O ASN l 56 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N ALA l 61 " --> pdb=" O SER l 57 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR l 68 " --> pdb=" O SER l 64 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N GLY l 69 " --> pdb=" O LEU l 65 " (cutoff:3.500A) Processing helix chain 'j' and resid 14 through 29 Processing helix chain 'j' and resid 31 through 41 Processing helix chain 'm' and resid 14 through 29 Processing helix chain 'm' and resid 31 through 41 Processing helix chain 'k' and resid 11 through 16 removed outlier: 3.540A pdb=" N LEU k 15 " --> pdb=" O ARG k 11 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ILE k 16 " --> pdb=" O LEU k 12 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 11 through 16' Processing helix chain 'k' and resid 54 through 63 removed outlier: 4.529A pdb=" N ASP k 59 " --> pdb=" O LYS k 55 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N LYS k 60 " --> pdb=" O THR k 56 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N LEU k 61 " --> pdb=" O GLN k 57 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ARG k 62 " --> pdb=" O LEU k 58 " (cutoff:3.500A) Proline residue: k 63 - end of helix Processing helix chain 'k' and resid 88 through 93 removed outlier: 4.224A pdb=" N ILE k 92 " --> pdb=" O ARG k 88 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N LEU k 93 " --> pdb=" O GLY k 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 88 through 93' Processing helix chain 'k' and resid 104 through 109 removed outlier: 3.804A pdb=" N ARG k 108 " --> pdb=" O SER k 104 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU k 109 " --> pdb=" O LYS k 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 104 through 109' Processing helix chain 'o' and resid 52 through 63 removed outlier: 3.938A pdb=" N ARG o 63 " --> pdb=" O ARG o 59 " (cutoff:3.500A) Processing helix chain 's' and resid 114 through 130 removed outlier: 3.664A pdb=" N ASP s 129 " --> pdb=" O GLU s 125 " (cutoff:3.500A) Processing helix chain 's' and resid 133 through 175 removed outlier: 4.810A pdb=" N SER s 137 " --> pdb=" O PRO s 133 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ASN s 138 " --> pdb=" O GLN s 134 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N TRP s 140 " --> pdb=" O VAL s 136 " (cutoff:3.500A) Processing helix chain 't' and resid 24 through 35 removed outlier: 3.634A pdb=" N TYR t 31 " --> pdb=" O LEU t 27 " (cutoff:3.500A) Processing helix chain 't' and resid 46 through 51 removed outlier: 5.515A pdb=" N VAL t 51 " --> pdb=" O ILE t 47 " (cutoff:3.500A) Processing helix chain 't' and resid 76 through 121 Processing helix chain 'u' and resid 24 through 35 Processing helix chain 'u' and resid 46 through 51 removed outlier: 3.637A pdb=" N ILE u 50 " --> pdb=" O SER u 46 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N VAL u 51 " --> pdb=" O ILE u 47 " (cutoff:3.500A) No H-bonds generated for 'chain 'u' and resid 46 through 51' Processing helix chain 'u' and resid 77 through 137 removed outlier: 4.579A pdb=" N LEU u 81 " --> pdb=" O ILE u 77 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N THR u 82 " --> pdb=" O PRO u 78 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASN u 131 " --> pdb=" O LEU u 127 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N LEU u 137 " --> pdb=" O ASP u 133 " (cutoff:3.500A) Processing helix chain 'v' and resid 24 through 35 Processing helix chain 'v' and resid 46 through 51 removed outlier: 3.506A pdb=" N ILE v 50 " --> pdb=" O SER v 46 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N VAL v 51 " --> pdb=" O ILE v 47 " (cutoff:3.500A) No H-bonds generated for 'chain 'v' and resid 46 through 51' Processing helix chain 'v' and resid 76 through 127 Processing helix chain 'w' and resid 24 through 35 Processing helix chain 'w' and resid 77 through 116 Processing helix chain 'w' and resid 121 through 137 Processing helix chain 'y' and resid 3 through 36 removed outlier: 3.806A pdb=" N VAL y 35 " --> pdb=" O GLU y 31 " (cutoff:3.500A) Processing helix chain 'y' and resid 65 through 70 removed outlier: 5.502A pdb=" N HIS y 69 " --> pdb=" O GLU y 65 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N TYR y 70 " --> pdb=" O LYS y 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'y' and resid 65 through 70' Processing helix chain 'y' and resid 71 through 81 removed outlier: 3.546A pdb=" N ALA y 77 " --> pdb=" O GLN y 73 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N TRP y 78 " --> pdb=" O GLU y 74 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLU y 79 " --> pdb=" O TYR y 75 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N ARG y 80 " --> pdb=" O ASP y 76 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ARG y 81 " --> pdb=" O ALA y 77 " (cutoff:3.500A) Processing helix chain 'y' and resid 96 through 116 removed outlier: 3.821A pdb=" N GLN y 115 " --> pdb=" O ASN y 111 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N THR y 116 " --> pdb=" O LEU y 112 " (cutoff:3.500A) Processing helix chain 'y' and resid 157 through 185 Processing helix chain 'y' and resid 197 through 211 Processing sheet with id= 1, first strand: chain 'A' and resid 200 through 203 removed outlier: 5.439A pdb=" N LYS A 190 " --> pdb=" O ASN A 203 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'A' and resid 299 through 302 removed outlier: 6.743A pdb=" N LYS A 299 " --> pdb=" O MET A 493 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'A' and resid 977 through 984 removed outlier: 3.561A pdb=" N ASN A 974 " --> pdb=" O ASN A 977 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'A' and resid 1159 through 1164 removed outlier: 6.180A pdb=" N ASP A1166 " --> pdb=" O LEU A1054 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'A' and resid 1257 through 1262 removed outlier: 6.576A pdb=" N GLY A1284 " --> pdb=" O LEU A1302 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'A' and resid 1405 through 1409 removed outlier: 6.924A pdb=" N ILE A1405 " --> pdb=" O GLY A1428 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'A' and resid 1679 through 1684 removed outlier: 3.711A pdb=" N SER A1680 " --> pdb=" O GLU A1704 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ASP A1700 " --> pdb=" O GLU A1684 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N THR A1771 " --> pdb=" O LYS A1731 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N TRP A1733 " --> pdb=" O THR A1771 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N GLY A1772 " --> pdb=" O ASN A1789 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'A' and resid 1708 through 1711 Processing sheet with id= 9, first strand: chain 'A' and resid 1857 through 1864 removed outlier: 6.231A pdb=" N VAL A1857 " --> pdb=" O GLY A1877 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N GLY A1877 " --> pdb=" O VAL A1857 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N ARG A1859 " --> pdb=" O ILE A1875 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N ASP A1854 " --> pdb=" O THR A1936 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'A' and resid 1984 through 1990 removed outlier: 3.869A pdb=" N GLN A1985 " --> pdb=" O ILE A1893 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'A' and resid 2235 through 2239 removed outlier: 3.919A pdb=" N SER A2235 " --> pdb=" O HIS A2232 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N TYR A2208 " --> pdb=" O LYS A2222 " (cutoff:3.500A) removed outlier: 8.521A pdb=" N ASN A2181 " --> pdb=" O HIS A2336 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N GLN A2338 " --> pdb=" O ASN A2181 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'A' and resid 1877 through 1884 No H-bonds generated for sheet with id= 12 Processing sheet with id= 13, first strand: chain 'A' and resid 2202 through 2208 removed outlier: 4.576A pdb=" N VAL A2203 " --> pdb=" O THR A2261 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'A' and resid 2223 through 2226 Processing sheet with id= 15, first strand: chain 'B' and resid 452 through 457 removed outlier: 3.734A pdb=" N TYR B 460 " --> pdb=" O LYS B 457 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ALA B 467 " --> pdb=" O LEU B 703 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N LEU B 703 " --> pdb=" O ALA B 467 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'B' and resid 516 through 521 removed outlier: 3.675A pdb=" N LEU B 630 " --> pdb=" O LYS B 556 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'B' and resid 851 through 855 Processing sheet with id= 18, first strand: chain 'B' and resid 987 through 991 Processing sheet with id= 19, first strand: chain 'B' and resid 1200 through 1210 removed outlier: 4.426A pdb=" N LYS B1201 " --> pdb=" O ASP B1225 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N SER B1214 " --> pdb=" O LEU B1276 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'B' and resid 1253 through 1259 Processing sheet with id= 21, first strand: chain 'B' and resid 1365 through 1370 removed outlier: 3.810A pdb=" N LEU B1470 " --> pdb=" O ARG B1394 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'B' and resid 1543 through 1551 removed outlier: 3.522A pdb=" N SER B1581 " --> pdb=" O SER B1662 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'B' and resid 1685 through 1690 No H-bonds generated for sheet with id= 23 Processing sheet with id= 24, first strand: chain 'B' and resid 1820 through 1824 Processing sheet with id= 25, first strand: chain 'B' and resid 2051 through 2057 Processing sheet with id= 26, first strand: chain 'B' and resid 2113 through 2118 removed outlier: 6.798A pdb=" N SER B2098 " --> pdb=" O ASP B2147 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'C' and resid 193 through 199 removed outlier: 3.882A pdb=" N ASN C 194 " --> pdb=" O ASP C 214 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N GLY C 140 " --> pdb=" O ALA C 215 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N ASN C 310 " --> pdb=" O MET C 263 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'C' and resid 474 through 477 removed outlier: 3.594A pdb=" N LYS C 474 " --> pdb=" O LEU C 485 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N LEU C 485 " --> pdb=" O LEU C 473 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N TRP C 469 " --> pdb=" O TYR C 489 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N VAL C 580 " --> pdb=" O THR C 498 " (cutoff:3.500A) removed outlier: 9.924A pdb=" N THR C 498 " --> pdb=" O VAL C 580 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ASP C 497 " --> pdb=" O VAL C 539 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'C' and resid 550 through 553 removed outlier: 4.212A pdb=" N ILE C 542 " --> pdb=" O VAL C 553 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N GLU C 541 " --> pdb=" O LYS C 565 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'C' and resid 632 through 637 removed outlier: 4.466A pdb=" N GLU C 641 " --> pdb=" O GLU C 637 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N VAL C 606 " --> pdb=" O SER C 671 " (cutoff:3.500A) removed outlier: 8.173A pdb=" N GLU C 667 " --> pdb=" O LEU C 610 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'C' and resid 677 through 681 removed outlier: 4.825A pdb=" N LEU C 899 " --> pdb=" O VAL C 894 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'C' and resid 688 through 692 removed outlier: 5.144A pdb=" N ILE C 689 " --> pdb=" O VAL C 710 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N VAL C 710 " --> pdb=" O ILE C 689 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N SER C 709 " --> pdb=" O LEU C 821 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'C' and resid 483 through 489 removed outlier: 3.938A pdb=" N GLN C 560 " --> pdb=" O ILE C 488 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'C' and resid 706 through 709 removed outlier: 3.567A pdb=" N SER C 822 " --> pdb=" O SER C 709 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'C' and resid 863 through 868 Processing sheet with id= 36, first strand: chain 'C' and resid 857 through 861 No H-bonds generated for sheet with id= 36 Processing sheet with id= 37, first strand: chain 'D' and resid 38 through 42 removed outlier: 7.258A pdb=" N ASN D 65 " --> pdb=" O SER D 87 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N SER D 87 " --> pdb=" O ASN D 65 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N TYR D 82 " --> pdb=" O THR D 99 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ASN D 93 " --> pdb=" O CYS D 88 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ALA D 96 " --> pdb=" O GLU D 109 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'D' and resid 55 through 60 removed outlier: 4.054A pdb=" N GLU D 56 " --> pdb=" O CYS D 51 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LYS D 60 " --> pdb=" O PHE D 47 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N PHE D 47 " --> pdb=" O LYS D 60 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N SER D 48 " --> pdb=" O ASN D 115 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N GLY D 111 " --> pdb=" O LEU D 52 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'J' and resid 128 through 132 removed outlier: 6.732A pdb=" N ILE J 425 " --> pdb=" O SER J 132 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'J' and resid 143 through 147 removed outlier: 8.436A pdb=" N GLU J 153 " --> pdb=" O LEU J 169 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N VAL J 166 " --> pdb=" O LYS J 175 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LYS J 173 " --> pdb=" O ASP J 168 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'J' and resid 186 through 191 removed outlier: 3.672A pdb=" N ASP J 187 " --> pdb=" O VAL J 200 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N TYR J 196 " --> pdb=" O SER J 191 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N THR J 205 " --> pdb=" O SER J 201 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'J' and resid 228 through 233 removed outlier: 5.399A pdb=" N LEU J 238 " --> pdb=" O HIS J 233 " (cutoff:3.500A) removed outlier: 9.177A pdb=" N ASP J 237 " --> pdb=" O MET J 253 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLY J 243 " --> pdb=" O VAL J 247 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N VAL J 247 " --> pdb=" O GLY J 243 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE J 260 " --> pdb=" O LEU J 250 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'J' and resid 270 through 275 removed outlier: 4.599A pdb=" N GLN J 280 " --> pdb=" O THR J 275 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N VAL J 281 " --> pdb=" O TRP J 293 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N THR J 289 " --> pdb=" O SER J 285 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'J' and resid 313 through 317 removed outlier: 3.699A pdb=" N ALA J 313 " --> pdb=" O ALA J 326 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N SER J 322 " --> pdb=" O HIS J 317 " (cutoff:3.500A) removed outlier: 8.877A pdb=" N PHE J 321 " --> pdb=" O LEU J 336 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N SER J 333 " --> pdb=" O LEU J 342 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'J' and resid 355 through 359 removed outlier: 3.669A pdb=" N THR J 355 " --> pdb=" O GLY J 367 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N VAL J 363 " --> pdb=" O ASN J 359 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N GLY J 371 " --> pdb=" O THR J 389 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'J' and resid 403 through 408 removed outlier: 5.654A pdb=" N ARG J 413 " --> pdb=" O ASP J 408 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'J' and resid 163 through 166 removed outlier: 3.505A pdb=" N THR J 176 " --> pdb=" O VAL J 166 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'J' and resid 413 through 418 removed outlier: 4.071A pdb=" N SER J 422 " --> pdb=" O GLU J 418 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'K' and resid 102 through 106 removed outlier: 5.103A pdb=" N ALA K 102 " --> pdb=" O VAL K 114 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'M' and resid 29 through 32 removed outlier: 3.676A pdb=" N LYS M 36 " --> pdb=" O ASN M 31 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'M' and resid 171 through 177 removed outlier: 6.118A pdb=" N LYS M 135 " --> pdb=" O PHE M 186 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N THR M 136 " --> pdb=" O ALA M 226 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'N' and resid 25 through 29 Processing sheet with id= 53, first strand: chain 'N' and resid 204 through 208 Processing sheet with id= 54, first strand: chain 'N' and resid 278 through 282 Processing sheet with id= 55, first strand: chain 'N' and resid 44 through 47 removed outlier: 5.354A pdb=" N TYR N 44 " --> pdb=" O THR N 58 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'Q' and resid 367 through 372 removed outlier: 6.403A pdb=" N GLN Q 367 " --> pdb=" O LEU Q 499 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N CYS Q 469 " --> pdb=" O SER Q 399 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'Q' and resid 605 through 611 removed outlier: 3.953A pdb=" N CYS Q 656 " --> pdb=" O PHE Q 569 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'Q' and resid 657 through 666 removed outlier: 6.302A pdb=" N TYR Q 658 " --> pdb=" O PRO Q 677 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LYS Q 660 " --> pdb=" O ILE Q 675 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N ILE Q 675 " --> pdb=" O LYS Q 660 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N LYS Q 662 " --> pdb=" O LEU Q 673 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N LEU Q 673 " --> pdb=" O LYS Q 662 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N TYR Q 664 " --> pdb=" O ASP Q 671 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ASP Q 671 " --> pdb=" O TYR Q 664 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N LEU Q 956 " --> pdb=" O GLY Q 669 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N GLU Q 955 " --> pdb=" O CYS Q 965 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'Q' and resid 914 through 917 removed outlier: 4.624A pdb=" N TYR Q 950 " --> pdb=" O VAL Q 970 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N CYS Q 966 " --> pdb=" O HIS Q 954 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'W' and resid 12 through 16 removed outlier: 3.741A pdb=" N ASP W 26 " --> pdb=" O VAL W 16 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N GLY W 82 " --> pdb=" O LEU W 59 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N SER W 104 " --> pdb=" O LEU W 81 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N ILE W 130 " --> pdb=" O LEU W 103 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'Y' and resid 29 through 33 removed outlier: 3.608A pdb=" N LYS Y 60 " --> pdb=" O THR Y 75 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'Y' and resid 90 through 93 removed outlier: 5.256A pdb=" N ASN Y 90 " --> pdb=" O VAL Y 101 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N VAL Y 101 " --> pdb=" O ASN Y 90 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N GLU Y 92 " --> pdb=" O LEU Y 99 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'b' and resid 43 through 46 Processing sheet with id= 64, first strand: chain 'b' and resid 77 through 83 removed outlier: 5.732A pdb=" N GLU b 47 " --> pdb=" O GLN b 33 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N GLN b 33 " --> pdb=" O GLU b 47 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N TYR b 18 " --> pdb=" O LEU b 34 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N LYS b 19 " --> pdb=" O GLU b 98 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N SER b 94 " --> pdb=" O LEU b 23 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'd' and resid 55 through 60 removed outlier: 4.321A pdb=" N ALA d 55 " --> pdb=" O GLU d 51 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N ASP d 46 " --> pdb=" O LYS d 32 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N LYS d 32 " --> pdb=" O ASP d 46 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N HIS d 17 " --> pdb=" O LEU d 33 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'n' and resid 55 through 60 removed outlier: 4.277A pdb=" N ALA n 55 " --> pdb=" O GLU n 51 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N ASP n 46 " --> pdb=" O LYS n 32 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N LYS n 32 " --> pdb=" O ASP n 46 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N HIS n 17 " --> pdb=" O LEU n 33 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'e' and resid 57 through 62 removed outlier: 6.083A pdb=" N GLY e 36 " --> pdb=" O VAL e 62 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'p' and resid 57 through 62 removed outlier: 6.201A pdb=" N GLY p 36 " --> pdb=" O VAL p 62 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'f' and resid 65 through 69 removed outlier: 3.953A pdb=" N GLY f 66 " --> pdb=" O GLU f 58 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N GLU f 55 " --> pdb=" O THR f 41 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N THR f 41 " --> pdb=" O GLU f 55 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N THR f 36 " --> pdb=" O LEU f 31 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N HIS f 25 " --> pdb=" O LEU f 42 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR f 80 " --> pdb=" O LYS f 30 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'q' and resid 65 through 69 removed outlier: 3.994A pdb=" N GLY q 66 " --> pdb=" O GLU q 58 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA q 56 " --> pdb=" O LEU q 68 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N GLU q 55 " --> pdb=" O THR q 41 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N THR q 41 " --> pdb=" O GLU q 55 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N THR q 36 " --> pdb=" O LEU q 31 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N HIS q 25 " --> pdb=" O LEU q 42 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TYR q 80 " --> pdb=" O LYS q 30 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'g' and resid 54 through 57 removed outlier: 7.045A pdb=" N ALA g 43 " --> pdb=" O LEU g 57 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N LYS g 24 " --> pdb=" O ILE g 46 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ARG g 23 " --> pdb=" O ILE g 19 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ILE g 19 " --> pdb=" O ARG g 23 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N LYS g 13 " --> pdb=" O LEU g 29 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'r' and resid 54 through 57 removed outlier: 7.409A pdb=" N ALA r 43 " --> pdb=" O LEU r 57 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N LYS r 24 " --> pdb=" O ILE r 46 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ARG r 23 " --> pdb=" O ILE r 19 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N LEU r 29 " --> pdb=" O LYS r 13 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N LYS r 13 " --> pdb=" O LEU r 29 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'h' and resid 79 through 82 removed outlier: 4.146A pdb=" N THR h 23 " --> pdb=" O LEU h 19 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain 'l' and resid 79 through 82 removed outlier: 3.843A pdb=" N THR l 23 " --> pdb=" O LEU l 19 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain 'j' and resid 84 through 91 removed outlier: 4.132A pdb=" N HIS j 52 " --> pdb=" O LEU j 48 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL j 103 " --> pdb=" O SER j 47 " (cutoff:3.500A) Processing sheet with id= 76, first strand: chain 'm' and resid 84 through 91 removed outlier: 3.512A pdb=" N ARG m 89 " --> pdb=" O GLU m 74 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N HIS m 52 " --> pdb=" O LEU m 48 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL m 103 " --> pdb=" O SER m 47 " (cutoff:3.500A) Processing sheet with id= 77, first strand: chain 'k' and resid 77 through 82 removed outlier: 4.335A pdb=" N ARG k 28 " --> pdb=" O THR k 24 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N LYS k 19 " --> pdb=" O GLU k 98 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N SER k 94 " --> pdb=" O LEU k 23 " (cutoff:3.500A) Processing sheet with id= 78, first strand: chain 'o' and resid 156 through 160 removed outlier: 3.710A pdb=" N GLY o 160 " --> pdb=" O GLY o 449 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N GLY o 449 " --> pdb=" O GLY o 160 " (cutoff:3.500A) Processing sheet with id= 79, first strand: chain 'o' and resid 167 through 170 removed outlier: 7.539A pdb=" N HIS o 176 " --> pdb=" O PHE o 192 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N ILE o 189 " --> pdb=" O LEU o 199 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N GLU o 197 " --> pdb=" O ASP o 191 " (cutoff:3.500A) Processing sheet with id= 80, first strand: chain 'o' and resid 211 through 215 removed outlier: 5.529A pdb=" N SER o 220 " --> pdb=" O THR o 215 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N ARG o 228 " --> pdb=" O LEU o 246 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N THR o 242 " --> pdb=" O ILE o 232 " (cutoff:3.500A) Processing sheet with id= 81, first strand: chain 'o' and resid 252 through 256 removed outlier: 3.748A pdb=" N ASP o 252 " --> pdb=" O GLY o 266 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N GLU o 262 " --> pdb=" O ARG o 256 " (cutoff:3.500A) removed outlier: 8.683A pdb=" N HIS o 261 " --> pdb=" O ASP o 277 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N LYS o 271 " --> pdb=" O LEU o 267 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLN o 287 " --> pdb=" O HIS o 274 " (cutoff:3.500A) Processing sheet with id= 82, first strand: chain 'o' and resid 298 through 302 removed outlier: 5.853A pdb=" N LYS o 307 " --> pdb=" O PHE o 302 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYS o 329 " --> pdb=" O ILE o 319 " (cutoff:3.500A) Processing sheet with id= 83, first strand: chain 'o' and resid 341 through 345 removed outlier: 3.996A pdb=" N PHE o 341 " --> pdb=" O GLN o 354 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N TYR o 350 " --> pdb=" O HIS o 345 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ASN o 349 " --> pdb=" O LEU o 365 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ARG o 359 " --> pdb=" O SER o 355 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N SER o 362 " --> pdb=" O LYS o 375 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N LYS o 375 " --> pdb=" O SER o 362 " (cutoff:3.500A) Processing sheet with id= 84, first strand: chain 'o' and resid 389 through 392 removed outlier: 5.332A pdb=" N TYR o 397 " --> pdb=" O SER o 392 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ILE o 398 " --> pdb=" O THR o 409 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N THR o 409 " --> pdb=" O ILE o 398 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N SER o 400 " --> pdb=" O LEU o 407 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N LEU o 407 " --> pdb=" O SER o 400 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N ASP o 402 " --> pdb=" O SER o 405 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASN o 419 " --> pdb=" O THR o 409 " (cutoff:3.500A) Processing sheet with id= 85, first strand: chain 'o' and resid 186 through 189 removed outlier: 3.897A pdb=" N ARG o 200 " --> pdb=" O ILE o 189 " (cutoff:3.500A) Processing sheet with id= 86, first strand: chain 't' and resid 14 through 17 Processing sheet with id= 87, first strand: chain 'u' and resid 14 through 17 removed outlier: 3.830A pdb=" N THR u 21 " --> pdb=" O SER u 16 " (cutoff:3.500A) Processing sheet with id= 88, first strand: chain 'v' and resid 14 through 17 removed outlier: 3.578A pdb=" N THR v 21 " --> pdb=" O SER v 16 " (cutoff:3.500A) Processing sheet with id= 89, first strand: chain 'w' and resid 14 through 17 removed outlier: 3.533A pdb=" N THR w 21 " --> pdb=" O SER w 16 " (cutoff:3.500A) Processing sheet with id= 90, first strand: chain 'w' and resid 179 through 183 removed outlier: 6.589A pdb=" N ILE w 498 " --> pdb=" O LEU w 183 " (cutoff:3.500A) Processing sheet with id= 91, first strand: chain 'w' and resid 196 through 201 removed outlier: 4.812A pdb=" N TYR w 205 " --> pdb=" O ASN w 201 " (cutoff:3.500A) Processing sheet with id= 92, first strand: chain 'w' and resid 248 through 253 removed outlier: 3.651A pdb=" N ILE w 248 " --> pdb=" O LEU w 260 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ARG w 256 " --> pdb=" O GLY w 252 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N ASN w 255 " --> pdb=" O ASP w 270 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ASP w 270 " --> pdb=" O ASN w 255 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N LEU w 257 " --> pdb=" O ILE w 268 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ILE w 268 " --> pdb=" O LEU w 257 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N LEU w 259 " --> pdb=" O ILE w 266 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ILE w 266 " --> pdb=" O LEU w 259 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N TYR w 261 " --> pdb=" O ASN w 264 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ILE w 268 " --> pdb=" O LEU w 277 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LYS w 275 " --> pdb=" O ASP w 270 " (cutoff:3.500A) Processing sheet with id= 93, first strand: chain 'w' and resid 290 through 293 removed outlier: 6.250A pdb=" N ILE w 311 " --> pdb=" O VAL w 324 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N SER w 320 " --> pdb=" O SER w 315 " (cutoff:3.500A) Processing sheet with id= 94, first strand: chain 'w' and resid 335 through 339 removed outlier: 5.492A pdb=" N LEU w 344 " --> pdb=" O HIS w 339 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N LEU w 343 " --> pdb=" O LEU w 359 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N GLY w 352 " --> pdb=" O VAL w 371 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N VAL w 371 " --> pdb=" O GLY w 352 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N LEU w 354 " --> pdb=" O PHE w 369 " (cutoff:3.500A) Processing sheet with id= 95, first strand: chain 'w' and resid 379 through 383 removed outlier: 5.179A pdb=" N TRP w 388 " --> pdb=" O ALA w 383 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N TYR w 387 " --> pdb=" O LEU w 402 " (cutoff:3.500A) Processing sheet with id= 96, first strand: chain 'w' and resid 423 through 429 removed outlier: 8.329A pdb=" N THR w 423 " --> pdb=" O ASN w 440 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N ASN w 434 " --> pdb=" O ASP w 429 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N LYS w 433 " --> pdb=" O PHE w 450 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER w 444 " --> pdb=" O SER w 439 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ILE w 447 " --> pdb=" O ASP w 460 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ASN w 456 " --> pdb=" O ASP w 451 " (cutoff:3.500A) Processing sheet with id= 97, first strand: chain 'w' and resid 476 through 481 Processing sheet with id= 98, first strand: chain 'w' and resid 264 through 268 removed outlier: 5.994A pdb=" N ASN w 264 " --> pdb=" O VAL w 282 " (cutoff:3.500A) Processing sheet with id= 99, first strand: chain 'w' and resid 443 through 447 removed outlier: 6.427A pdb=" N ASN w 443 " --> pdb=" O LEU w 465 " (cutoff:3.500A) Processing sheet with id=100, first strand: chain 'w' and resid 486 through 491 removed outlier: 4.370A pdb=" N ILE w 486 " --> pdb=" O LEU w 501 " (cutoff:3.500A) Processing sheet with id=101, first strand: chain 'y' and resid 142 through 147 removed outlier: 5.060A pdb=" N LYS y 142 " --> pdb=" O ALA y 155 " (cutoff:3.500A) 4894 hydrogen bonds defined for protein. 14472 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 365 hydrogen bonds 652 hydrogen bond angles 0 basepair planarities 149 basepair parallelities 253 stacking parallelities Total time for adding SS restraints: 63.44 Time building geometry restraints manager: 33.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 18569 1.32 - 1.46: 34486 1.46 - 1.59: 57668 1.59 - 1.72: 927 1.72 - 1.86: 630 Bond restraints: 112280 Sorted by residual: bond pdb=" CB LYS s 122 " pdb=" CG LYS s 122 " ideal model delta sigma weight residual 1.520 1.324 0.196 3.00e-02 1.11e+03 4.29e+01 bond pdb=" C ASN B 500 " pdb=" N PRO B 501 " ideal model delta sigma weight residual 1.334 1.456 -0.122 2.34e-02 1.83e+03 2.71e+01 bond pdb=" C ASP T 149 " pdb=" N PRO T 150 " ideal model delta sigma weight residual 1.334 1.445 -0.111 2.34e-02 1.83e+03 2.23e+01 bond pdb=" CB TRP B 756 " pdb=" CG TRP B 756 " ideal model delta sigma weight residual 1.498 1.644 -0.146 3.10e-02 1.04e+03 2.21e+01 bond pdb=" CB THR B 803 " pdb=" CG2 THR B 803 " ideal model delta sigma weight residual 1.521 1.370 0.151 3.30e-02 9.18e+02 2.10e+01 ... (remaining 112275 not shown) Histogram of bond angle deviations from ideal: 92.92 - 101.83: 723 101.83 - 110.75: 37001 110.75 - 119.66: 64891 119.66 - 128.57: 50356 128.57 - 137.49: 1465 Bond angle restraints: 154436 Sorted by residual: angle pdb=" CA TYR Q 712 " pdb=" CB TYR Q 712 " pdb=" CG TYR Q 712 " ideal model delta sigma weight residual 113.90 97.68 16.22 1.80e+00 3.09e-01 8.12e+01 angle pdb=" O3' G 2 120 " pdb=" C3' G 2 120 " pdb=" C2' G 2 120 " ideal model delta sigma weight residual 109.50 121.85 -12.35 1.50e+00 4.44e-01 6.78e+01 angle pdb=" C3' A 5 128 " pdb=" O3' A 5 128 " pdb=" P G 5 129 " ideal model delta sigma weight residual 120.20 132.30 -12.10 1.50e+00 4.44e-01 6.50e+01 angle pdb=" C3' G 2 120 " pdb=" O3' G 2 120 " pdb=" P C 2 121 " ideal model delta sigma weight residual 120.20 131.84 -11.64 1.50e+00 4.44e-01 6.02e+01 angle pdb=" CA ILE B1605 " pdb=" CB ILE B1605 " pdb=" CG2 ILE B1605 " ideal model delta sigma weight residual 110.50 122.19 -11.69 1.70e+00 3.46e-01 4.73e+01 ... (remaining 154431 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.96: 66432 35.96 - 71.91: 1617 71.91 - 107.87: 264 107.87 - 143.82: 28 143.82 - 179.78: 12 Dihedral angle restraints: 68353 sinusoidal: 32159 harmonic: 36194 Sorted by residual: dihedral pdb=" C4' A I 81 " pdb=" C3' A I 81 " pdb=" C2' A I 81 " pdb=" C1' A I 81 " ideal model delta sinusoidal sigma weight residual 36.00 -39.41 75.41 1 8.00e+00 1.56e-02 1.12e+02 dihedral pdb=" C4' A I 78 " pdb=" C3' A I 78 " pdb=" C2' A I 78 " pdb=" C1' A I 78 " ideal model delta sinusoidal sigma weight residual 36.00 -36.54 72.54 1 8.00e+00 1.56e-02 1.05e+02 dihedral pdb=" C4' U I 85 " pdb=" C3' U I 85 " pdb=" C2' U I 85 " pdb=" C1' U I 85 " ideal model delta sinusoidal sigma weight residual 36.00 -35.80 71.80 1 8.00e+00 1.56e-02 1.03e+02 ... (remaining 68350 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.990: 17994 0.990 - 1.981: 0 1.981 - 2.971: 0 2.971 - 3.962: 0 3.962 - 4.952: 3 Chirality restraints: 17997 Sorted by residual: chirality pdb=" C4 KGN A2500 " pdb=" C3 KGN A2500 " pdb=" C5 KGN A2500 " pdb=" O14 KGN A2500 " both_signs ideal model delta sigma weight residual False -2.50 2.45 -4.95 2.00e-01 2.50e+01 6.13e+02 chirality pdb=" C5 KGN A2500 " pdb=" C4 KGN A2500 " pdb=" C6 KGN A2500 " pdb=" O15 KGN A2500 " both_signs ideal model delta sigma weight residual False 2.36 -2.55 4.91 2.00e-01 2.50e+01 6.03e+02 chirality pdb=" C2 KGN A2500 " pdb=" C1 KGN A2500 " pdb=" C3 KGN A2500 " pdb=" O12 KGN A2500 " both_signs ideal model delta sigma weight residual False -2.37 2.47 -4.85 2.00e-01 2.50e+01 5.87e+02 ... (remaining 17994 not shown) Planarity restraints: 17650 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG T 726 " -0.036 2.00e-02 2.50e+03 7.15e-02 5.11e+01 pdb=" C ARG T 726 " 0.124 2.00e-02 2.50e+03 pdb=" O ARG T 726 " -0.046 2.00e-02 2.50e+03 pdb=" N GLU T 727 " -0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER T 546 " 0.035 2.00e-02 2.50e+03 6.93e-02 4.81e+01 pdb=" C SER T 546 " -0.120 2.00e-02 2.50e+03 pdb=" O SER T 546 " 0.045 2.00e-02 2.50e+03 pdb=" N LYS T 547 " 0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR Q 388 " -0.041 2.00e-02 2.50e+03 4.12e-02 3.39e+01 pdb=" CG TYR Q 388 " 0.007 2.00e-02 2.50e+03 pdb=" CD1 TYR Q 388 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 TYR Q 388 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR Q 388 " 0.040 2.00e-02 2.50e+03 pdb=" CE2 TYR Q 388 " 0.046 2.00e-02 2.50e+03 pdb=" CZ TYR Q 388 " 0.036 2.00e-02 2.50e+03 pdb=" OH TYR Q 388 " -0.083 2.00e-02 2.50e+03 ... (remaining 17647 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.31: 19 2.31 - 3.02: 53560 3.02 - 3.73: 200280 3.73 - 4.43: 317676 4.43 - 5.14: 508940 Nonbonded interactions: 1080475 Sorted by model distance: nonbonded pdb=" P G I 1 " pdb=" O2' A I 70 " model vdw 1.604 3.400 nonbonded pdb=" OG SER C 190 " pdb="MG MG C1100 " model vdw 2.034 2.170 nonbonded pdb=" OP1 G I 1 " pdb="MG MG 6 201 " model vdw 2.036 2.170 nonbonded pdb=" OP1 G 6 78 " pdb="MG MG 6 201 " model vdw 2.041 2.170 nonbonded pdb="MG MG C1100 " pdb=" O2B GTP C1101 " model vdw 2.048 2.170 ... (remaining 1080470 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'b' selection = (chain 'k' and resid 3 through 102) } ncs_group { reference = chain 'd' selection = chain 'n' } ncs_group { reference = chain 'e' selection = chain 'p' } ncs_group { reference = chain 'f' selection = chain 'q' } ncs_group { reference = chain 'g' selection = chain 'r' } ncs_group { reference = chain 'h' selection = chain 'l' } ncs_group { reference = chain 'j' selection = chain 'm' } ncs_group { reference = (chain 't' and (resid 1 through 54 or resid 77 through 126)) selection = (chain 'u' and (resid 1 through 54 or resid 77 through 126)) selection = (chain 'v' and (resid 1 through 54 or resid 77 through 126)) } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.260 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: 0.060 Extract box with map and model: 16.300 Check model and map are aligned: 1.160 Set scattering table: 0.730 Process input model: 307.010 Find NCS groups from input model: 2.740 Set up NCS constraints: 0.720 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 339.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6255 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 : 0.010 0.196 112280 Z= 0.636 Angle : 1.402 17.752 154436 Z= 0.791 Chirality : 0.099 4.952 17997 Planarity : 0.011 0.188 17650 Dihedral : 16.144 179.779 44761 Min Nonbonded Distance : 1.604 Molprobity Statistics. All-atom Clashscore : 0.26 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.51 % Favored : 97.44 % Rotamer: Outliers : 0.17 % Allowed : 4.59 % Favored : 95.24 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 1.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.07), residues: 11940 helix: -0.28 (0.06), residues: 5364 sheet: -0.05 (0.13), residues: 1631 loop : -0.12 (0.09), residues: 4945 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.005 TRP A2152 HIS 0.040 0.005 HIS B1279 PHE 0.081 0.006 PHE Q 763 TYR 0.084 0.007 TYR k 30 ARG 0.036 0.003 ARG C 132 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23880 Ramachandran restraints generated. 11940 Oldfield, 0 Emsley, 11940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23880 Ramachandran restraints generated. 11940 Oldfield, 0 Emsley, 11940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2765 residues out of total 11038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 2747 time to evaluate : 8.413 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 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 8 residues processed: 2759 average time/residue: 1.6943 time to fit residues: 6567.4114 Evaluate side-chains 2084 residues out of total 11038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 2076 time to evaluate : 8.426 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 7 residues processed: 3 average time/residue: 0.8476 time to fit residues: 16.1347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1264 random chunks: chunk 1067 optimal weight: 0.4980 chunk 958 optimal weight: 0.6980 chunk 531 optimal weight: 4.9990 chunk 327 optimal weight: 30.0000 chunk 646 optimal weight: 2.9990 chunk 511 optimal weight: 0.6980 chunk 990 optimal weight: 40.0000 chunk 383 optimal weight: 10.0000 chunk 602 optimal weight: 2.9990 chunk 737 optimal weight: 3.9990 chunk 1147 optimal weight: 7.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 GLN A 343 ASN A 542 HIS A 553 ASN A 559 GLN A 760 ASN A 948 HIS A 976 GLN A1033 ASN A1034 ASN A1077 ASN ** A1140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1449 ASN A1455 GLN A1522 ASN A1548 GLN A1792 ASN A1827 GLN A1990 ASN A2168 ASN ** B 618 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 862 GLN B1028 GLN ** B1481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2012 ASN C 84 GLN C 87 GLN C 128 ASN C 158 HIS C 289 ASN C 414 GLN C 776 ASN ** C 797 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 929 GLN D 35 ASN G 33 GLN ** G 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 317 HIS J 443 ASN K 84 ASN K 210 ASN L 110 GLN M 39 GLN M 189 GLN M 191 ASN N 72 GLN N 95 ASN O 26 GLN P 158 ASN Q 366 ASN Q 682 ASN Q 865 HIS ** S 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 116 ASN S 179 GLN S 248 ASN ** S 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 527 ASN T 598 HIS W 49 HIS W 200 ASN a 118 HIS a 177 ASN e 23 GLN ** g 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 74 ASN l 35 GLN ** m 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 337 HIS p 22 GLN q 77 ASN r 18 ASN r 47 ASN r 53 ASN w 265 GLN w 295 ASN y 99 GLN Total number of N/Q/H flips: 68 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6309 moved from start: 0.2305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 112280 Z= 0.271 Angle : 0.686 16.371 154436 Z= 0.360 Chirality : 0.046 0.505 17997 Planarity : 0.005 0.065 17650 Dihedral : 15.023 177.256 20903 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 3.20 % Allowed : 14.00 % Favored : 82.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.08), residues: 11940 helix: 0.85 (0.07), residues: 5449 sheet: -0.03 (0.12), residues: 1758 loop : 0.19 (0.09), residues: 4733 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP m 76 HIS 0.010 0.001 HIS H 225 PHE 0.038 0.002 PHE j 26 TYR 0.022 0.002 TYR J 54 ARG 0.011 0.001 ARG A1071 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23880 Ramachandran restraints generated. 11940 Oldfield, 0 Emsley, 11940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23880 Ramachandran restraints generated. 11940 Oldfield, 0 Emsley, 11940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2520 residues out of total 11038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 336 poor density : 2184 time to evaluate : 8.460 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 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 revert: symmetry clash outliers start: 336 outliers final: 121 residues processed: 2325 average time/residue: 1.7533 time to fit residues: 5808.7433 Evaluate side-chains 2086 residues out of total 11038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 1965 time to evaluate : 8.340 Switching outliers to nearest non-outliers outliers start: 121 outliers final: 54 residues processed: 71 average time/residue: 1.1695 time to fit residues: 144.9324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1264 random chunks: chunk 637 optimal weight: 1.9990 chunk 356 optimal weight: 5.9990 chunk 955 optimal weight: 0.9980 chunk 781 optimal weight: 8.9990 chunk 316 optimal weight: 10.0000 chunk 1149 optimal weight: 0.0970 chunk 1242 optimal weight: 4.9990 chunk 1024 optimal weight: 6.9990 chunk 1140 optimal weight: 20.0000 chunk 392 optimal weight: 20.0000 chunk 922 optimal weight: 2.9990 overall best weight: 2.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 553 ASN A 559 GLN A 864 GLN ** A 866 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1087 ASN ** A1140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1449 ASN A1522 ASN A1548 GLN A1827 GLN A2180 GLN ** B 618 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 768 HIS B1056 GLN B1280 ASN ** B1481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 GLN C 87 GLN C 119 ASN ** C 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 290 HIS C 310 ASN G 33 GLN G 37 ASN ** G 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 107 ASN H 182 GLN H 362 ASN H 425 GLN J 443 ASN L 128 GLN M 31 ASN M 134 ASN M 202 GLN N 53 ASN ** N 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 95 ASN N 134 ASN ** N 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 509 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 19 HIS S 67 GLN S 116 ASN ** S 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 273 ASN ** T 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 527 ASN Z 13 GLN e 23 GLN ** g 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 53 ASN g 66 ASN ** h 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 74 ASN ** m 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 219 GLN o 358 ASN p 22 GLN s 134 GLN Total number of N/Q/H flips: 45 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6346 moved from start: 0.2816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 112280 Z= 0.334 Angle : 0.667 13.370 154436 Z= 0.348 Chirality : 0.046 0.603 17997 Planarity : 0.005 0.066 17650 Dihedral : 14.910 175.189 20903 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 3.96 % Allowed : 15.81 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.08), residues: 11940 helix: 0.99 (0.07), residues: 5497 sheet: -0.12 (0.12), residues: 1755 loop : 0.13 (0.09), residues: 4688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 766 HIS 0.009 0.001 HIS N 89 PHE 0.045 0.002 PHE j 26 TYR 0.025 0.002 TYR T 548 ARG 0.011 0.001 ARG h 88 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23880 Ramachandran restraints generated. 11940 Oldfield, 0 Emsley, 11940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23880 Ramachandran restraints generated. 11940 Oldfield, 0 Emsley, 11940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2441 residues out of total 11038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 416 poor density : 2025 time to evaluate : 8.750 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 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: 416 outliers final: 198 residues processed: 2221 average time/residue: 1.7516 time to fit residues: 5480.4197 Evaluate side-chains 2129 residues out of total 11038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 198 poor density : 1931 time to evaluate : 8.425 Switching outliers to nearest non-outliers outliers start: 198 outliers final: 100 residues processed: 104 average time/residue: 1.1250 time to fit residues: 202.9389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1264 random chunks: chunk 1136 optimal weight: 9.9990 chunk 864 optimal weight: 0.5980 chunk 596 optimal weight: 0.8980 chunk 127 optimal weight: 3.9990 chunk 548 optimal weight: 6.9990 chunk 772 optimal weight: 3.9990 chunk 1154 optimal weight: 3.9990 chunk 1221 optimal weight: 0.0980 chunk 602 optimal weight: 0.9990 chunk 1093 optimal weight: 0.9980 chunk 329 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 553 ASN A 559 GLN A 638 GLN A 643 ASN A1077 ASN ** A1140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1449 ASN A1548 GLN A1618 ASN ** A1687 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1827 GLN A1863 HIS ** B 618 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2002 ASN ** B2124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 GLN ** C 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 770 ASN ** D 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 175 GLN G 37 ASN ** G 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 107 ASN H 425 GLN J 443 ASN L 128 GLN L 139 GLN M 147 ASN M 189 GLN N 72 GLN S 67 GLN ** S 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 379 GLN ** T 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 527 ASN W 99 GLN ** W 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 28 ASN f 77 ASN ** g 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 64 HIS ** m 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 219 GLN o 322 ASN o 323 GLN q 86 ASN s 134 GLN ** v 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 115 GLN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6277 moved from start: 0.3121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 112280 Z= 0.170 Angle : 0.595 13.978 154436 Z= 0.307 Chirality : 0.042 0.419 17997 Planarity : 0.004 0.077 17650 Dihedral : 14.763 177.513 20903 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 3.35 % Allowed : 17.45 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.08), residues: 11940 helix: 1.30 (0.07), residues: 5508 sheet: -0.06 (0.12), residues: 1760 loop : 0.21 (0.09), residues: 4672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP w 88 HIS 0.008 0.001 HIS B1102 PHE 0.044 0.001 PHE j 26 TYR 0.025 0.001 TYR A1784 ARG 0.010 0.000 ARG h 93 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23880 Ramachandran restraints generated. 11940 Oldfield, 0 Emsley, 11940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23880 Ramachandran restraints generated. 11940 Oldfield, 0 Emsley, 11940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2425 residues out of total 11038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 352 poor density : 2073 time to evaluate : 7.490 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 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: 352 outliers final: 189 residues processed: 2251 average time/residue: 1.7239 time to fit residues: 5534.2357 Evaluate side-chains 2139 residues out of total 11038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 189 poor density : 1950 time to evaluate : 8.378 Switching outliers to nearest non-outliers outliers start: 189 outliers final: 115 residues processed: 81 average time/residue: 1.1722 time to fit residues: 165.8283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1264 random chunks: chunk 1017 optimal weight: 9.9990 chunk 693 optimal weight: 2.9990 chunk 17 optimal weight: 8.9990 chunk 909 optimal weight: 6.9990 chunk 504 optimal weight: 2.9990 chunk 1042 optimal weight: 10.0000 chunk 844 optimal weight: 0.7980 chunk 1 optimal weight: 9.9990 chunk 623 optimal weight: 7.9990 chunk 1096 optimal weight: 3.9990 chunk 308 optimal weight: 50.0000 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 254 HIS ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 553 ASN A 643 ASN A 864 GLN A1449 ASN A1548 GLN A1618 ASN A1782 ASN A1827 GLN ** B 618 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1309 ASN ** B1481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 GLN C 87 GLN C 108 GLN ** C 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 410 GLN C 721 GLN C 770 ASN ** D 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 37 ASN ** G 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 219 HIS ** H 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 107 ASN ** H 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 425 GLN ** J 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 443 ASN L 128 GLN L 139 GLN M 31 ASN M 147 ASN M 191 ASN N 53 ASN O 31 HIS O 82 ASN P 5 HIS P 158 ASN Q 476 HIS S 67 GLN ** S 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 527 ASN T 596 GLN W 115 GLN W 143 HIS ** Y 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 13 GLN f 25 HIS f 34 ASN ** g 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 52 HIS k 14 ASN ** m 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 17 HIS o 219 GLN o 322 ASN o 323 GLN r 56 GLN ** s 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 134 GLN y 99 GLN Total number of N/Q/H flips: 49 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6393 moved from start: 0.3387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.102 112280 Z= 0.501 Angle : 0.730 13.477 154436 Z= 0.375 Chirality : 0.048 0.604 17997 Planarity : 0.005 0.061 17650 Dihedral : 14.899 174.552 20903 Min Nonbonded Distance : 1.771 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 4.57 % Allowed : 17.81 % Favored : 77.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.08), residues: 11940 helix: 1.01 (0.07), residues: 5496 sheet: -0.17 (0.12), residues: 1780 loop : -0.02 (0.09), residues: 4664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP t 88 HIS 0.019 0.002 HIS s 123 PHE 0.038 0.002 PHE A 691 TYR 0.028 0.002 TYR S 326 ARG 0.012 0.001 ARG Z 11 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23880 Ramachandran restraints generated. 11940 Oldfield, 0 Emsley, 11940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23880 Ramachandran restraints generated. 11940 Oldfield, 0 Emsley, 11940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2464 residues out of total 11038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 480 poor density : 1984 time to evaluate : 8.784 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 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: 480 outliers final: 266 residues processed: 2217 average time/residue: 1.7379 time to fit residues: 5477.2932 Evaluate side-chains 2164 residues out of total 11038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 266 poor density : 1898 time to evaluate : 8.153 Switching outliers to nearest non-outliers outliers start: 266 outliers final: 136 residues processed: 134 average time/residue: 1.1434 time to fit residues: 263.3565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1264 random chunks: chunk 411 optimal weight: 4.9990 chunk 1100 optimal weight: 0.8980 chunk 241 optimal weight: 50.0000 chunk 717 optimal weight: 5.9990 chunk 301 optimal weight: 50.0000 chunk 1222 optimal weight: 50.0000 chunk 1015 optimal weight: 50.0000 chunk 566 optimal weight: 2.9990 chunk 101 optimal weight: 4.9990 chunk 404 optimal weight: 0.0970 chunk 642 optimal weight: 0.8980 overall best weight: 1.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 126 ASN ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 553 ASN ** A1257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1449 ASN A1548 GLN A1618 ASN A1827 GLN ** B 618 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1565 GLN B2002 ASN B2124 GLN C 84 GLN C 87 GLN ** C 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 514 GLN ** D 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 37 ASN ** G 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 17 ASN ** H 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 68 GLN ** H 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 170 HIS ** H 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 425 GLN ** J 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 443 ASN L 128 GLN L 139 GLN M 147 ASN N 72 GLN P 158 ASN S 67 GLN ** S 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 527 ASN ** T 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 13 GLN Z 117 ASN ** g 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 14 ASN k 74 ASN ** m 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 219 GLN ** s 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 134 GLN y 99 GLN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6345 moved from start: 0.3561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 112280 Z= 0.300 Angle : 0.648 19.215 154436 Z= 0.332 Chirality : 0.044 0.490 17997 Planarity : 0.004 0.057 17650 Dihedral : 14.831 174.560 20903 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.95 % Allowed : 19.36 % Favored : 76.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.08), residues: 11940 helix: 1.19 (0.07), residues: 5493 sheet: -0.21 (0.12), residues: 1738 loop : 0.01 (0.09), residues: 4709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP t 88 HIS 0.019 0.001 HIS s 123 PHE 0.041 0.002 PHE j 26 TYR 0.024 0.002 TYR B1009 ARG 0.014 0.001 ARG H 15 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23880 Ramachandran restraints generated. 11940 Oldfield, 0 Emsley, 11940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23880 Ramachandran restraints generated. 11940 Oldfield, 0 Emsley, 11940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2358 residues out of total 11038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 415 poor density : 1943 time to evaluate : 8.366 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 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: 415 outliers final: 239 residues processed: 2168 average time/residue: 1.7132 time to fit residues: 5299.4198 Evaluate side-chains 2138 residues out of total 11038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 239 poor density : 1899 time to evaluate : 8.252 Switching outliers to nearest non-outliers outliers start: 239 outliers final: 144 residues processed: 98 average time/residue: 1.0710 time to fit residues: 186.3557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1264 random chunks: chunk 1179 optimal weight: 3.9990 chunk 137 optimal weight: 7.9990 chunk 696 optimal weight: 2.9990 chunk 893 optimal weight: 0.9990 chunk 691 optimal weight: 0.8980 chunk 1029 optimal weight: 4.9990 chunk 682 optimal weight: 3.9990 chunk 1218 optimal weight: 9.9990 chunk 762 optimal weight: 0.0870 chunk 742 optimal weight: 0.6980 chunk 562 optimal weight: 1.9990 overall best weight: 0.9362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 553 ASN A 559 GLN A 961 GLN A1077 ASN ** A1140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1257 ASN A1449 ASN A1538 ASN ** A1548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1827 GLN A2306 ASN ** B 618 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1481 GLN ** B2124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 GLN ** C 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 410 GLN C 770 ASN D 38 HIS G 37 ASN ** G 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 425 GLN ** J 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 443 ASN L 29 GLN L 110 GLN L 128 GLN L 139 GLN M 31 ASN M 147 ASN N 72 GLN N 244 HIS P 158 ASN ** Q 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 67 GLN ** S 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 406 ASN T 527 ASN W 143 HIS Y 81 GLN Z 13 GLN Z 117 ASN ** g 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 14 ASN ** m 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 219 GLN ** o 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 134 GLN y 99 GLN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6302 moved from start: 0.3723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 112280 Z= 0.196 Angle : 0.617 16.627 154436 Z= 0.314 Chirality : 0.042 0.393 17997 Planarity : 0.004 0.055 17650 Dihedral : 14.736 176.486 20903 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.37 % Allowed : 20.19 % Favored : 76.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.08), residues: 11940 helix: 1.42 (0.07), residues: 5478 sheet: -0.16 (0.12), residues: 1735 loop : 0.09 (0.09), residues: 4727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP t 88 HIS 0.015 0.001 HIS s 123 PHE 0.038 0.001 PHE J 97 TYR 0.026 0.001 TYR A1784 ARG 0.015 0.000 ARG H 15 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23880 Ramachandran restraints generated. 11940 Oldfield, 0 Emsley, 11940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23880 Ramachandran restraints generated. 11940 Oldfield, 0 Emsley, 11940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2340 residues out of total 11038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 354 poor density : 1986 time to evaluate : 8.491 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 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: 354 outliers final: 219 residues processed: 2194 average time/residue: 1.7079 time to fit residues: 5357.7905 Evaluate side-chains 2146 residues out of total 11038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 219 poor density : 1927 time to evaluate : 8.432 Switching outliers to nearest non-outliers outliers start: 219 outliers final: 140 residues processed: 80 average time/residue: 1.1585 time to fit residues: 166.5216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1264 random chunks: chunk 753 optimal weight: 5.9990 chunk 486 optimal weight: 3.9990 chunk 727 optimal weight: 10.0000 chunk 366 optimal weight: 10.0000 chunk 239 optimal weight: 9.9990 chunk 236 optimal weight: 0.7980 chunk 774 optimal weight: 50.0000 chunk 830 optimal weight: 0.3980 chunk 602 optimal weight: 2.9990 chunk 113 optimal weight: 4.9990 chunk 957 optimal weight: 0.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 553 ASN A 638 GLN A 643 ASN A1077 ASN ** A1140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1449 ASN ** A1548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1618 ASN A1827 GLN ** B 618 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 919 ASN ** B1878 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2002 ASN ** B2124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 GLN ** C 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 444 GLN D 35 ASN G 37 ASN ** G 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 425 GLN ** J 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 443 ASN L 29 GLN L 128 GLN L 139 GLN M 134 ASN M 147 ASN M 191 ASN N 72 GLN N 244 HIS P 158 ASN S 67 GLN ** S 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 398 HIS ** T 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 527 ASN W 115 GLN W 143 HIS Z 117 ASN b 33 GLN d 61 GLN ** g 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 14 ASN k 74 ASN ** m 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 219 GLN r 53 ASN ** s 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** y 99 GLN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6337 moved from start: 0.3841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 112280 Z= 0.292 Angle : 0.661 16.160 154436 Z= 0.335 Chirality : 0.044 0.405 17997 Planarity : 0.004 0.060 17650 Dihedral : 14.742 174.760 20903 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 3.26 % Allowed : 20.93 % Favored : 75.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.08), residues: 11940 helix: 1.37 (0.07), residues: 5486 sheet: -0.20 (0.12), residues: 1744 loop : 0.07 (0.09), residues: 4710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP t 88 HIS 0.012 0.001 HIS s 123 PHE 0.051 0.002 PHE Q 489 TYR 0.026 0.002 TYR C 769 ARG 0.014 0.001 ARG O 246 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23880 Ramachandran restraints generated. 11940 Oldfield, 0 Emsley, 11940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23880 Ramachandran restraints generated. 11940 Oldfield, 0 Emsley, 11940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2272 residues out of total 11038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 342 poor density : 1930 time to evaluate : 7.664 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 342 outliers final: 240 residues processed: 2121 average time/residue: 1.7214 time to fit residues: 5206.1330 Evaluate side-chains 2133 residues out of total 11038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 240 poor density : 1893 time to evaluate : 8.369 Switching outliers to nearest non-outliers outliers start: 240 outliers final: 149 residues processed: 92 average time/residue: 1.1144 time to fit residues: 181.3854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1264 random chunks: chunk 1108 optimal weight: 0.5980 chunk 1167 optimal weight: 5.9990 chunk 1064 optimal weight: 0.6980 chunk 1135 optimal weight: 9.9990 chunk 1166 optimal weight: 0.9990 chunk 683 optimal weight: 0.9990 chunk 494 optimal weight: 3.9990 chunk 891 optimal weight: 7.9990 chunk 348 optimal weight: 10.0000 chunk 1025 optimal weight: 0.3980 chunk 1073 optimal weight: 6.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 553 ASN A 638 GLN A 864 GLN A1077 ASN ** A1140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1449 ASN ** A1548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1618 ASN A1827 GLN ** B 618 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1878 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 GLN ** C 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 410 GLN C 444 GLN C 514 GLN G 37 ASN ** G 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 443 ASN L 29 GLN L 110 GLN L 128 GLN L 139 GLN M 31 ASN N 72 GLN ** N 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 244 HIS P 158 ASN Q 519 ASN S 67 GLN ** S 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 271 ASN ** T 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 527 ASN W 143 HIS Z 13 GLN Z 117 ASN b 33 GLN d 61 GLN ** g 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 14 ASN ** m 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 219 GLN ** s 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** y 99 GLN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6289 moved from start: 0.3965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 112280 Z= 0.185 Angle : 0.635 16.387 154436 Z= 0.320 Chirality : 0.042 0.387 17997 Planarity : 0.004 0.081 17650 Dihedral : 14.678 176.740 20903 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.48 % Allowed : 22.07 % Favored : 75.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.08), residues: 11940 helix: 1.52 (0.07), residues: 5486 sheet: -0.19 (0.12), residues: 1738 loop : 0.12 (0.09), residues: 4716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP t 88 HIS 0.013 0.001 HIS s 123 PHE 0.040 0.001 PHE p 20 TYR 0.055 0.001 TYR w 438 ARG 0.038 0.000 ARG H 22 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23880 Ramachandran restraints generated. 11940 Oldfield, 0 Emsley, 11940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23880 Ramachandran restraints generated. 11940 Oldfield, 0 Emsley, 11940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2235 residues out of total 11038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 261 poor density : 1974 time to evaluate : 8.499 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 261 outliers final: 195 residues processed: 2149 average time/residue: 1.7502 time to fit residues: 5398.5862 Evaluate side-chains 2116 residues out of total 11038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 195 poor density : 1921 time to evaluate : 8.328 Switching outliers to nearest non-outliers outliers start: 195 outliers final: 149 residues processed: 48 average time/residue: 1.1897 time to fit residues: 105.1967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1264 random chunks: chunk 1131 optimal weight: 10.0000 chunk 745 optimal weight: 0.7980 chunk 1200 optimal weight: 10.0000 chunk 732 optimal weight: 4.9990 chunk 569 optimal weight: 0.0370 chunk 834 optimal weight: 7.9990 chunk 1259 optimal weight: 8.9990 chunk 1159 optimal weight: 1.9990 chunk 1002 optimal weight: 0.9990 chunk 104 optimal weight: 2.9990 chunk 774 optimal weight: 40.0000 overall best weight: 1.3664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 553 ASN A 638 GLN A1077 ASN ** A1140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1449 ASN ** A1548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1618 ASN A1792 ASN A1827 GLN ** B 618 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1481 GLN ** B1878 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2002 ASN B2085 GLN ** B2124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 GLN ** C 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 444 GLN D 35 ASN G 37 ASN ** G 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 443 ASN L 29 GLN L 110 GLN L 128 GLN L 139 GLN M 134 ASN N 72 GLN ** N 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 244 HIS P 158 ASN S 67 GLN ** S 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 293 GLN T 527 ASN Z 117 ASN b 33 GLN ** g 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 14 ASN ** m 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 53 ASN ** s 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** y 99 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6313 moved from start: 0.4049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.096 112280 Z= 0.245 Angle : 0.667 16.953 154436 Z= 0.335 Chirality : 0.043 0.346 17997 Planarity : 0.004 0.069 17650 Dihedral : 14.665 174.783 20903 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.14 % Allowed : 22.60 % Favored : 75.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.08), residues: 11940 helix: 1.50 (0.07), residues: 5479 sheet: -0.16 (0.12), residues: 1711 loop : 0.10 (0.09), residues: 4750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP t 88 HIS 0.010 0.001 HIS s 123 PHE 0.050 0.002 PHE Q 489 TYR 0.034 0.001 TYR w 438 ARG 0.025 0.001 ARG H 22 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23880 Ramachandran restraints generated. 11940 Oldfield, 0 Emsley, 11940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23880 Ramachandran restraints generated. 11940 Oldfield, 0 Emsley, 11940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2154 residues out of total 11038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 225 poor density : 1929 time to evaluate : 8.578 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 225 outliers final: 186 residues processed: 2094 average time/residue: 1.7872 time to fit residues: 5363.7960 Evaluate side-chains 2087 residues out of total 11038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 186 poor density : 1901 time to evaluate : 8.372 Switching outliers to nearest non-outliers outliers start: 186 outliers final: 154 residues processed: 39 average time/residue: 1.1031 time to fit residues: 84.2171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1264 random chunks: chunk 614 optimal weight: 2.9990 chunk 796 optimal weight: 30.0000 chunk 1068 optimal weight: 4.9990 chunk 307 optimal weight: 9.9990 chunk 924 optimal weight: 0.6980 chunk 148 optimal weight: 1.9990 chunk 278 optimal weight: 30.0000 chunk 1004 optimal weight: 0.0020 chunk 420 optimal weight: 1.9990 chunk 1031 optimal weight: 0.8980 chunk 127 optimal weight: 0.9990 overall best weight: 0.9192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 ASN A 553 ASN A 638 GLN A 930 ASN A1077 ASN ** A1140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1449 ASN ** A1548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1618 ASN A1792 ASN A1827 GLN ** B 618 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1481 GLN B1727 ASN ** B1878 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 GLN ** C 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 410 GLN C 444 GLN C 721 GLN G 37 ASN ** G 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 443 ASN L 128 GLN L 139 GLN M 31 ASN M 147 ASN M 191 ASN N 72 GLN ** N 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 244 HIS P 158 ASN S 67 GLN ** S 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 293 GLN T 527 ASN Z 13 GLN Z 117 ASN ** g 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 14 ASN k 74 ASN l 30 GLN ** m 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 354 GLN r 53 ASN ** s 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4717 r_free = 0.4717 target = 0.259664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.204711 restraints weight = 158373.603| |-----------------------------------------------------------------------------| r_work (start): 0.4139 rms_B_bonded: 3.02 r_work: 0.3759 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6877 moved from start: 0.4145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 112280 Z= 0.201 Angle : 0.649 17.066 154436 Z= 0.325 Chirality : 0.042 0.342 17997 Planarity : 0.004 0.083 17650 Dihedral : 14.635 176.418 20903 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.26 % Allowed : 22.74 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.08), residues: 11940 helix: 1.54 (0.07), residues: 5497 sheet: -0.19 (0.12), residues: 1739 loop : 0.14 (0.09), residues: 4704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP w 88 HIS 0.013 0.001 HIS s 123 PHE 0.046 0.001 PHE j 26 TYR 0.044 0.001 TYR T 274 ARG 0.018 0.000 ARG T 335 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 70392.46 seconds wall clock time: 1204 minutes 6.15 seconds (72246.15 seconds total)