Starting phenix.real_space_refine on Wed Apr 17 12:54:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lza_4121/04_2024/5lza_4121_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lza_4121/04_2024/5lza_4121.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lza_4121/04_2024/5lza_4121_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lza_4121/04_2024/5lza_4121_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lza_4121/04_2024/5lza_4121_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lza_4121/04_2024/5lza_4121.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lza_4121/04_2024/5lza_4121.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lza_4121/04_2024/5lza_4121_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lza_4121/04_2024/5lza_4121_updated.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.015 sd= 0.265 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 4689 5.49 5 S 151 5.16 5 C 73316 2.51 5 N 27198 2.21 5 O 40681 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "b PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 107": "NH1" <-> "NH2" Residue "b PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 224": "NH1" <-> "NH2" Residue "c PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 125": "NH1" <-> "NH2" Residue "c PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 135": "NH1" <-> "NH2" Residue "d ASP 173": "OD1" <-> "OD2" Residue "f PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ARG 123": "NH1" <-> "NH2" Residue "l TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ARG 55": "NH1" <-> "NH2" Residue "l PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o ASP 20": "OD1" <-> "OD2" Residue "p PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p ARG 28": "NH1" <-> "NH2" Residue "p PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u PHE 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 13": "NH1" <-> "NH2" Residue "D ARG 33": "NH1" <-> "NH2" Residue "D TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 59": "NH1" <-> "NH2" Residue "D ARG 77": "NH1" <-> "NH2" Residue "D ARG 83": "NH1" <-> "NH2" Residue "D PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 169": "NH1" <-> "NH2" Residue "D ARG 184": "NH1" <-> "NH2" Residue "E PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 21": "NH1" <-> "NH2" Residue "E ARG 44": "NH1" <-> "NH2" Residue "E ARG 49": "NH1" <-> "NH2" Residue "E ARG 61": "NH1" <-> "NH2" Residue "E ARG 88": "NH1" <-> "NH2" Residue "E ARG 102": "NH1" <-> "NH2" Residue "E ARG 162": "NH1" <-> "NH2" Residue "E ARG 170": "NH1" <-> "NH2" Residue "F PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 70": "NH1" <-> "NH2" Residue "F ARG 79": "NH1" <-> "NH2" Residue "F TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 91": "NH1" <-> "NH2" Residue "F ARG 101": "NH1" <-> "NH2" Residue "F ARG 109": "NH1" <-> "NH2" Residue "F ARG 111": "NH1" <-> "NH2" Residue "F ARG 114": "NH1" <-> "NH2" Residue "F ARG 132": "NH1" <-> "NH2" Residue "F PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 13": "NH1" <-> "NH2" Residue "J ARG 37": "NH1" <-> "NH2" Residue "J ARG 96": "NH1" <-> "NH2" Residue "J ARG 120": "NH1" <-> "NH2" Residue "L ARG 21": "NH1" <-> "NH2" Residue "L ARG 33": "NH1" <-> "NH2" Residue "L ARG 41": "NH1" <-> "NH2" Residue "L ARG 47": "NH1" <-> "NH2" Residue "L ARG 60": "NH1" <-> "NH2" Residue "L PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 78": "NH1" <-> "NH2" Residue "L PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 126": "NH1" <-> "NH2" Residue "M ARG 10": "NH1" <-> "NH2" Residue "M ARG 18": "NH1" <-> "NH2" Residue "M ARG 40": "NH1" <-> "NH2" Residue "M ARG 44": "NH1" <-> "NH2" Residue "M ARG 50": "NH1" <-> "NH2" Residue "M ARG 55": "NH1" <-> "NH2" Residue "M ARG 59": "NH1" <-> "NH2" Residue "M TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 114": "NH1" <-> "NH2" Residue "N ARG 8": "NH1" <-> "NH2" Residue "N ARG 12": "NH1" <-> "NH2" Residue "N ARG 17": "NH1" <-> "NH2" Residue "N ARG 22": "NH1" <-> "NH2" Residue "N ARG 46": "NH1" <-> "NH2" Residue "N ARG 63": "NH1" <-> "NH2" Residue "N ARG 64": "NH1" <-> "NH2" Residue "N ARG 69": "NH1" <-> "NH2" Residue "N ARG 71": "NH1" <-> "NH2" Residue "N PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 96": "NH1" <-> "NH2" Residue "N PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 118": "NH1" <-> "NH2" Residue "O ARG 10": "NH1" <-> "NH2" Residue "O ARG 16": "NH1" <-> "NH2" Residue "O ARG 25": "NH1" <-> "NH2" Residue "O TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 81": "NH1" <-> "NH2" Residue "O PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 94": "NH1" <-> "NH2" Residue "O TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 102": "NH1" <-> "NH2" Residue "O ARG 111": "NH1" <-> "NH2" Residue "O PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 20": "NH1" <-> "NH2" Residue "P ARG 38": "NH1" <-> "NH2" Residue "P PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 61": "NH1" <-> "NH2" Residue "P ARG 88": "NH1" <-> "NH2" Residue "P ARG 100": "NH1" <-> "NH2" Residue "P ARG 108": "NH1" <-> "NH2" Residue "Q ARG 2": "NH1" <-> "NH2" Residue "Q ARG 5": "NH1" <-> "NH2" Residue "Q ARG 12": "NH1" <-> "NH2" Residue "Q ARG 32": "NH1" <-> "NH2" Residue "Q ARG 47": "NH1" <-> "NH2" Residue "Q ARG 69": "NH1" <-> "NH2" Residue "Q TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 21": "NH1" <-> "NH2" Residue "R ARG 68": "NH1" <-> "NH2" Residue "R ARG 78": "NH1" <-> "NH2" Residue "R ARG 79": "NH1" <-> "NH2" Residue "R ARG 84": "NH1" <-> "NH2" Residue "S PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 84": "NH1" <-> "NH2" Residue "S ARG 88": "NH1" <-> "NH2" Residue "S ARG 95": "NH1" <-> "NH2" Residue "S ARG 110": "NH1" <-> "NH2" Residue "T ARG 73": "NH1" <-> "NH2" Residue "U ARG 5": "NH1" <-> "NH2" Residue "U ARG 6": "NH1" <-> "NH2" Residue "U ARG 81": "NH1" <-> "NH2" Residue "U ARG 85": "NH1" <-> "NH2" Residue "U ARG 93": "NH1" <-> "NH2" Residue "U PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 29": "NH1" <-> "NH2" Residue "Y ARG 47": "NH1" <-> "NH2" Residue "Y ARG 52": "NH1" <-> "NH2" Residue "Z ARG 10": "NH1" <-> "NH2" Residue "Z ARG 29": "NH1" <-> "NH2" Residue "Z ARG 44": "NH1" <-> "NH2" Residue "0 ARG 9": "NH1" <-> "NH2" Residue "0 ARG 15": "NH1" <-> "NH2" Residue "0 ARG 39": "NH1" <-> "NH2" Residue "0 ARG 51": "NH1" <-> "NH2" Residue "1 ARG 43": "NH1" <-> "NH2" Residue "2 ARG 3": "NH1" <-> "NH2" Residue "2 ARG 12": "NH1" <-> "NH2" Residue "2 ARG 14": "NH1" <-> "NH2" Residue "2 ARG 19": "NH1" <-> "NH2" Residue "2 ARG 21": "NH1" <-> "NH2" Residue "2 ARG 33": "NH1" <-> "NH2" Residue "2 ARG 41": "NH1" <-> "NH2" Residue "3 ARG 12": "NH1" <-> "NH2" Residue "3 PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 29": "NH1" <-> "NH2" Residue "3 ARG 39": "NH1" <-> "NH2" Residue "3 ARG 41": "NH1" <-> "NH2" Residue "4 ARG 12": "NH1" <-> "NH2" Residue "4 ARG 24": "NH1" <-> "NH2" Residue "6 ARG 49": "NH1" <-> "NH2" Residue "6 ARG 56": "NH1" <-> "NH2" Time to flip residues: 0.22s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 146037 Number of models: 1 Model: "" Number of chains: 57 Chain: "a" Number of atoms: 33119 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1539, 33029 Classifications: {'RNA': 1539} Modifications used: {'p5*END': 1, 'rna2p': 1, 'rna2p_pur': 106, 'rna2p_pyr': 67, 'rna3p': 10, 'rna3p_pur': 762, 'rna3p_pyr': 593} Link IDs: {'rna2p': 174, 'rna3p': 1364} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 7 Conformer: "C" Number of residues, atoms: 1539, 33029 Classifications: {'RNA': 1539} Modifications used: {'p5*END': 1, 'rna2p': 1, 'rna2p_pur': 106, 'rna2p_pyr': 67, 'rna3p': 10, 'rna3p_pur': 762, 'rna3p_pyr': 593} Link IDs: {'rna2p': 174, 'rna3p': 1364} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 7 bond proxies already assigned to first conformer: 36877 Chain: "b" Number of atoms: 1705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1705 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 210} Chain: "c" Number of atoms: 1625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1625 Classifications: {'peptide': 206} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 198} Chain: "d" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1643 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 198} Chain: "e" Number of atoms: 1157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1157 Classifications: {'peptide': 157} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 151} Chain: "f" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 818 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "g" Number of atoms: 1182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1182 Classifications: {'peptide': 151} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain: "h" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 979 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "i" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1022 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "j" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 787 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 92} Chain: "k" Number of atoms: 870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 870 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 108} Chain: "l" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 955 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 115} Chain: "m" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 884 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 109} Chain: "n" Number of atoms: 794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 794 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 95} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "o" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 714 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'TRANS': 87} Chain: "p" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 649 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "q" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 649 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain: "r" Number of atoms: 505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 505 Classifications: {'peptide': 65} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 2, 'TRANS': 62} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 1, 'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 25 Chain: "s" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 638 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 73} Chain: "t" Number of atoms: 665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 665 Classifications: {'peptide': 85} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 83} Chain: "u" Number of atoms: 496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 496 Classifications: {'peptide': 65} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 2, 'TRANS': 62} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 4, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "v" Number of atoms: 1644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1644 Classifications: {'RNA': 77} Modifications used: {'p5*END': 1, 'rna2p': 1, 'rna2p_pur': 5, 'rna2p_pyr': 2, 'rna3p': 3, 'rna3p_pur': 34, 'rna3p_pyr': 32} Link IDs: {'rna2p': 7, 'rna3p': 69} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 2 Chain: "x" Number of atoms: 1025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 1025 Classifications: {'RNA': 48} Modifications used: {'p5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 4, 'rna3p_pur': 19, 'rna3p_pyr': 19} Link IDs: {'rna2p': 10, 'rna3p': 37} Chain: "A" Number of atoms: 62296 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 2900, 62274 Classifications: {'RNA': 2900} Modifications used: {'p5*END': 1, 'rna2p': 7, 'rna2p_pur': 221, 'rna2p_pyr': 106, 'rna3p': 17, 'rna3p_pur': 1445, 'rna3p_pyr': 1104} Link IDs: {'rna2p': 334, 'rna3p': 2565} Chain breaks: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen planarities: 1 Conformer: "C" Number of residues, atoms: 2900, 62274 Classifications: {'RNA': 2900} Modifications used: {'p5*END': 1, 'rna2p': 7, 'rna2p_pur': 221, 'rna2p_pyr': 106, 'rna3p': 17, 'rna3p_pur': 1445, 'rna3p_pyr': 1104} Link IDs: {'rna2p': 334, 'rna3p': 2565} Chain breaks: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 69719 Chain: "B" Number of atoms: 2570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 2570 Classifications: {'RNA': 120} Modifications used: {'p5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 3, 'rna3p_pur': 58, 'rna3p_pyr': 53} Link IDs: {'rna2p': 9, 'rna3p': 110} Chain: "C" Number of atoms: 2083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2083 Classifications: {'peptide': 271} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 253} Chain: "D" Number of atoms: 1565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1565 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 202} Chain: "E" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1552 Classifications: {'peptide': 201} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 195} Chain: "F" Number of atoms: 1411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1411 Classifications: {'peptide': 177} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 170} Chain: "G" Number of atoms: 1323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1323 Classifications: {'peptide': 176} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "I" Number of atoms: 1032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1032 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 131} Chain: "H" Number of atoms: 1111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1111 Classifications: {'peptide': 149} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 145} Chain: "J" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1129 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 135} Chain: "K" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 939 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "L" Number of atoms: 1045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1045 Classifications: {'peptide': 143} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 138} Chain: "M" Number of atoms: 1074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1074 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 128} Chain: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 961 Classifications: {'peptide': 120} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "O" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 892 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "P" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 917 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "Q" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 947 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'TRANS': 116} Chain: "R" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 816 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 101} Chain: "S" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 857 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 107} Chain: "T" Number of atoms: 739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 739 Classifications: {'peptide': 93} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 91} Chain: "U" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 780 Classifications: {'peptide': 102} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "V" Number of atoms: 753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 753 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "W" Number of atoms: 575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 575 Classifications: {'peptide': 75} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "X" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 625 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "Y" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 509 Classifications: {'peptide': 63} Modifications used: {'COO': 1} Link IDs: {'TRANS': 62} Chain: "Z" Number of atoms: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 449 Classifications: {'peptide': 58} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "0" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 444 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 54} Chain: "1" Number of atoms: 410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 410 Classifications: {'peptide': 50} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "2" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 377 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "3" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 504 Classifications: {'peptide': 64} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "4" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 302 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "6" Number of atoms: 523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 523 Classifications: {'peptide': 66} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "4" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "6" 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 A0YY7 SG CYS 4 11 180.958 96.568 136.784 1.00112.24 S ATOM A0YYW SG CYS 4 14 181.816 99.860 137.030 1.00109.81 S ATOM A0Z1R SG CYS 4 27 182.493 97.071 133.811 1.00108.42 S ATOM A0Z7U SG CYS 6 16 119.909 109.865 231.251 1.00199.19 S ATOM A0Z86 SG CYS 6 18 120.277 106.114 230.341 1.00137.48 S ATOM A0ZC4 SG CYS 6 37 123.069 109.249 228.929 1.00172.23 S Residues with excluded nonbonded symmetry interactions: 7 residue: pdb=" P A G a1491 " occ=0.51 ... (44 atoms not shown) pdb=" C4 C G a1491 " occ=0.49 residue: pdb=" P A A a1492 " occ=0.51 ... (42 atoms not shown) pdb=" C4 C A a1492 " occ=0.49 residue: pdb=" P A A a1493 " occ=0.51 ... (42 atoms not shown) pdb=" C4 C A a1493 " occ=0.49 residue: pdb=" P A G a1494 " occ=0.51 ... (44 atoms not shown) pdb=" C4 C G a1494 " occ=0.49 residue: pdb=" P A A A1913 " occ=0.50 ... (42 atoms not shown) pdb=" C4 C A A1913 " occ=0.50 residue: pdb="ZN ZN 4 101 " occ=0.50 residue: pdb="ZN ZN 6 100 " occ=0.76 Time building chain proxies: 87.20, per 1000 atoms: 0.60 Number of scatterers: 146037 At special positions: 0 Unit cell: (238.96, 265.64, 248.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 151 16.00 P 4689 15.00 O 40681 8.00 N 27198 7.00 C 73316 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 61.39 Conformation dependent library (CDL) restraints added in 7.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 4 101 " pdb="ZN ZN 4 101 " - pdb=" ND1 HIS 4 33 " pdb="ZN ZN 4 101 " - pdb=" SG CYS 4 11 " pdb="ZN ZN 4 101 " - pdb=" SG CYS 4 14 " pdb="ZN ZN 4 101 " - pdb=" SG CYS 4 27 " pdb=" ZN 6 100 " pdb="ZN ZN 6 100 " - pdb=" SG CYS 6 16 " pdb="ZN ZN 6 100 " - pdb=" SG CYS 6 37 " pdb="ZN ZN 6 100 " - pdb=" SG CYS 6 18 " Number of angles added : 3 11434 Ramachandran restraints generated. 5717 Oldfield, 0 Emsley, 5717 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10684 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: 182 helices and 65 sheets defined 38.7% alpha, 17.3% beta 1524 base pairs and 2405 stacking pairs defined. Time for finding SS restraints: 78.15 Creating SS restraints... Processing helix chain 'b' and resid 23 through 28 removed outlier: 4.277A pdb=" N LYS b 27 " --> pdb=" O ASN b 23 " (cutoff:3.500A) Proline residue: b 28 - end of helix No H-bonds generated for 'chain 'b' and resid 23 through 28' Processing helix chain 'b' and resid 42 through 63 Proline residue: b 47 - end of helix Processing helix chain 'b' and resid 74 through 87 removed outlier: 4.572A pdb=" N ALA b 78 " --> pdb=" O ALA b 74 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N VAL b 79 " --> pdb=" O ALA b 75 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N CYS b 86 " --> pdb=" O ALA b 82 " (cutoff:3.500A) Processing helix chain 'b' and resid 102 through 122 removed outlier: 4.414A pdb=" N VAL b 106 " --> pdb=" O ASN b 102 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N THR b 118 " --> pdb=" O LYS b 114 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ASP b 122 " --> pdb=" O THR b 118 " (cutoff:3.500A) Processing helix chain 'b' and resid 129 through 147 Processing helix chain 'b' and resid 168 through 179 removed outlier: 4.223A pdb=" N ILE b 172 " --> pdb=" O GLU b 168 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ASN b 177 " --> pdb=" O LYS b 173 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N LEU b 178 " --> pdb=" O GLU b 174 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N GLY b 179 " --> pdb=" O ALA b 175 " (cutoff:3.500A) Processing helix chain 'b' and resid 191 through 196 removed outlier: 3.756A pdb=" N VAL b 195 " --> pdb=" O ASP b 191 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N ASP b 196 " --> pdb=" O PRO b 192 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 191 through 196' Processing helix chain 'b' and resid 205 through 225 removed outlier: 3.941A pdb=" N SER b 225 " --> pdb=" O ARG b 221 " (cutoff:3.500A) Processing helix chain 'c' and resid 5 through 11 removed outlier: 3.933A pdb=" N ILE c 9 " --> pdb=" O HIS c 5 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ARG c 10 " --> pdb=" O PRO c 6 " (cutoff:3.500A) Processing helix chain 'c' and resid 24 through 47 removed outlier: 4.289A pdb=" N ALA c 29 " --> pdb=" O THR c 25 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N ASP c 30 " --> pdb=" O LYS c 26 " (cutoff:3.500A) Processing helix chain 'c' and resid 71 through 77 removed outlier: 3.677A pdb=" N VAL c 75 " --> pdb=" O ARG c 71 " (cutoff:3.500A) Processing helix chain 'c' and resid 80 through 95 removed outlier: 3.744A pdb=" N GLU c 84 " --> pdb=" O GLY c 80 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N LYS c 85 " --> pdb=" O GLU c 81 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE c 93 " --> pdb=" O VAL c 89 " (cutoff:3.500A) Processing helix chain 'c' and resid 107 through 112 removed outlier: 3.652A pdb=" N ASP c 111 " --> pdb=" O LYS c 107 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N ALA c 112 " --> pdb=" O PRO c 108 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 107 through 112' Processing helix chain 'c' and resid 113 through 126 removed outlier: 3.562A pdb=" N ARG c 125 " --> pdb=" O SER c 121 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ARG c 126 " --> pdb=" O GLN c 122 " (cutoff:3.500A) Processing helix chain 'c' and resid 128 through 144 removed outlier: 3.775A pdb=" N LYS c 134 " --> pdb=" O ARG c 130 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLY c 144 " --> pdb=" O ALA c 140 " (cutoff:3.500A) Processing helix chain 'd' and resid 6 through 15 removed outlier: 4.001A pdb=" N LEU d 10 " --> pdb=" O PRO d 6 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLU d 14 " --> pdb=" O LEU d 10 " (cutoff:3.500A) Processing helix chain 'd' and resid 48 through 65 Processing helix chain 'd' and resid 67 through 82 removed outlier: 3.700A pdb=" N ARG d 80 " --> pdb=" O LYS d 76 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N LYS d 82 " --> pdb=" O ALA d 78 " (cutoff:3.500A) Processing helix chain 'd' and resid 84 through 96 removed outlier: 3.771A pdb=" N ARG d 96 " --> pdb=" O LEU d 92 " (cutoff:3.500A) Processing helix chain 'd' and resid 97 through 105 Processing helix chain 'd' and resid 109 through 120 removed outlier: 3.654A pdb=" N HIS d 119 " --> pdb=" O GLN d 115 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LYS d 120 " --> pdb=" O LEU d 116 " (cutoff:3.500A) Processing helix chain 'd' and resid 145 through 150 removed outlier: 4.902A pdb=" N LYS d 150 " --> pdb=" O GLU d 146 " (cutoff:3.500A) Processing helix chain 'd' and resid 151 through 165 removed outlier: 6.441A pdb=" N LYS d 155 " --> pdb=" O GLN d 151 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N GLU d 165 " --> pdb=" O ALA d 161 " (cutoff:3.500A) Processing helix chain 'd' and resid 186 through 191 removed outlier: 3.899A pdb=" N SER d 191 " --> pdb=" O ARG d 187 " (cutoff:3.500A) Processing helix chain 'd' and resid 195 through 205 removed outlier: 3.945A pdb=" N ILE d 199 " --> pdb=" O ASN d 195 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N TYR d 203 " --> pdb=" O ILE d 199 " (cutoff:3.500A) Processing helix chain 'e' and resid 54 through 70 removed outlier: 3.926A pdb=" N GLN e 60 " --> pdb=" O PRO e 56 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LYS e 65 " --> pdb=" O LYS e 61 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ARG e 68 " --> pdb=" O GLU e 64 " (cutoff:3.500A) Processing helix chain 'e' and resid 108 through 118 removed outlier: 6.056A pdb=" N ALA e 112 " --> pdb=" O GLY e 108 " (cutoff:3.500A) Processing helix chain 'e' and resid 131 through 146 removed outlier: 3.563A pdb=" N ARG e 137 " --> pdb=" O ILE e 133 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N MET e 146 " --> pdb=" O GLY e 142 " (cutoff:3.500A) Processing helix chain 'e' and resid 148 through 156 Processing helix chain 'e' and resid 159 through 165 Processing helix chain 'f' and resid 14 through 33 Proline residue: f 19 - end of helix Processing helix chain 'f' and resid 67 through 81 Processing helix chain 'g' and resid 19 through 30 removed outlier: 3.965A pdb=" N LEU g 29 " --> pdb=" O PHE g 25 " (cutoff:3.500A) Processing helix chain 'g' and resid 34 through 54 removed outlier: 3.511A pdb=" N GLN g 51 " --> pdb=" O GLU g 47 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N ARG g 52 " --> pdb=" O THR g 48 " (cutoff:3.500A) Processing helix chain 'g' and resid 56 through 69 removed outlier: 3.773A pdb=" N ALA g 64 " --> pdb=" O ALA g 60 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ASN g 67 " --> pdb=" O VAL g 63 " (cutoff:3.500A) Processing helix chain 'g' and resid 91 through 110 removed outlier: 3.919A pdb=" N ASN g 96 " --> pdb=" O PRO g 92 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA g 97 " --> pdb=" O VAL g 93 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ARG g 110 " --> pdb=" O ALA g 106 " (cutoff:3.500A) Processing helix chain 'g' and resid 114 through 129 removed outlier: 3.813A pdb=" N GLU g 128 " --> pdb=" O SER g 124 " (cutoff:3.500A) Processing helix chain 'g' and resid 131 through 148 removed outlier: 3.740A pdb=" N GLU g 145 " --> pdb=" O HIS g 141 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ALA g 146 " --> pdb=" O ARG g 142 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ASN g 147 " --> pdb=" O MET g 143 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N LYS g 148 " --> pdb=" O ALA g 144 " (cutoff:3.500A) Processing helix chain 'h' and resid 4 through 20 Processing helix chain 'h' and resid 29 through 43 Processing helix chain 'h' and resid 111 through 119 Processing helix chain 'i' and resid 33 through 38 removed outlier: 3.892A pdb=" N PHE i 38 " --> pdb=" O LEU i 34 " (cutoff:3.500A) Processing helix chain 'i' and resid 45 through 55 Proline residue: i 50 - end of helix removed outlier: 3.919A pdb=" N LEU i 53 " --> pdb=" O GLN i 49 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL i 54 " --> pdb=" O PRO i 50 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N ASP i 55 " --> pdb=" O LEU i 51 " (cutoff:3.500A) Processing helix chain 'i' and resid 70 through 87 removed outlier: 4.551A pdb=" N MET i 87 " --> pdb=" O THR i 83 " (cutoff:3.500A) Processing helix chain 'i' and resid 91 through 98 removed outlier: 5.276A pdb=" N GLU i 96 " --> pdb=" O SER i 92 " (cutoff:3.500A) Processing helix chain 'j' and resid 14 through 33 removed outlier: 4.242A pdb=" N GLN j 20 " --> pdb=" O ARG j 16 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ALA j 21 " --> pdb=" O LEU j 17 " (cutoff:3.500A) Processing helix chain 'j' and resid 80 through 90 removed outlier: 4.846A pdb=" N ARG j 89 " --> pdb=" O ASP j 85 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N LEU j 90 " --> pdb=" O ALA j 86 " (cutoff:3.500A) Processing helix chain 'k' and resid 45 through 50 removed outlier: 3.620A pdb=" N SER k 49 " --> pdb=" O THR k 45 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N GLY k 50 " --> pdb=" O ALA k 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 45 through 50' Processing helix chain 'k' and resid 58 through 73 removed outlier: 3.856A pdb=" N ASP k 71 " --> pdb=" O GLU k 67 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N ALA k 72 " --> pdb=" O ARG k 68 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N VAL k 73 " --> pdb=" O CYS k 69 " (cutoff:3.500A) Processing helix chain 'k' and resid 91 through 103 removed outlier: 4.113A pdb=" N THR k 95 " --> pdb=" O GLY k 91 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ILE k 96 " --> pdb=" O ARG k 92 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ARG k 97 " --> pdb=" O GLU k 93 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ALA k 98 " --> pdb=" O SER k 94 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU k 99 " --> pdb=" O THR k 95 " (cutoff:3.500A) Processing helix chain 'l' and resid 2 through 10 Proline residue: l 10 - end of helix Processing helix chain 'l' and resid 21 through 26 removed outlier: 6.819A pdb=" N ALA l 25 " --> pdb=" O PRO l 21 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N CYS l 26 " --> pdb=" O ALA l 22 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 21 through 26' Processing helix chain 'l' and resid 112 through 117 removed outlier: 4.782A pdb=" N TYR l 116 " --> pdb=" O ALA l 112 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLY l 117 " --> pdb=" O ARG l 113 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 112 through 117' Processing helix chain 'm' and resid 13 through 21 removed outlier: 3.538A pdb=" N SER m 20 " --> pdb=" O ILE m 16 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N ILE m 21 " --> pdb=" O ALA m 17 " (cutoff:3.500A) Processing helix chain 'm' and resid 25 through 37 Processing helix chain 'm' and resid 48 through 63 removed outlier: 3.954A pdb=" N ASP m 57 " --> pdb=" O ASP m 53 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N PHE m 62 " --> pdb=" O GLU m 58 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N VAL m 63 " --> pdb=" O VAL m 59 " (cutoff:3.500A) Processing helix chain 'm' and resid 65 through 83 removed outlier: 3.636A pdb=" N GLY m 83 " --> pdb=" O LEU m 79 " (cutoff:3.500A) Processing helix chain 'm' and resid 84 through 93 Processing helix chain 'm' and resid 105 through 110 Processing helix chain 'n' and resid 2 through 20 Processing helix chain 'n' and resid 24 through 29 Processing helix chain 'n' and resid 37 through 51 Proline residue: n 51 - end of helix Processing helix chain 'n' and resid 55 through 60 removed outlier: 4.149A pdb=" N GLN n 59 " --> pdb=" O SER n 55 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N ARG n 60 " --> pdb=" O PRO n 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'n' and resid 55 through 60' Processing helix chain 'n' and resid 79 through 90 Processing helix chain 'o' and resid 3 through 15 Processing helix chain 'o' and resid 23 through 43 removed outlier: 4.070A pdb=" N GLY o 40 " --> pdb=" O ASN o 36 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N HIS o 41 " --> pdb=" O HIS o 37 " (cutoff:3.500A) Processing helix chain 'o' and resid 48 through 73 removed outlier: 3.630A pdb=" N MET o 58 " --> pdb=" O GLY o 54 " (cutoff:3.500A) Processing helix chain 'o' and resid 74 through 85 Processing helix chain 'p' and resid 53 through 64 removed outlier: 3.702A pdb=" N ILE p 57 " --> pdb=" O ASP p 53 " (cutoff:3.500A) Processing helix chain 'p' and resid 68 through 79 Processing helix chain 'r' and resid 11 through 17 removed outlier: 5.496A pdb=" N GLU r 15 " --> pdb=" O ARG r 11 " (cutoff:3.500A) Processing helix chain 'r' and resid 24 through 33 removed outlier: 5.103A pdb=" N ASN r 30 " --> pdb=" O ALA r 26 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N TYR r 31 " --> pdb=" O THR r 27 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ILE r 32 " --> pdb=" O LEU r 28 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N THR r 33 " --> pdb=" O LYS r 29 " (cutoff:3.500A) Processing helix chain 'r' and resid 40 through 45 removed outlier: 3.604A pdb=" N THR r 44 " --> pdb=" O PRO r 40 " (cutoff:3.500A) Processing helix chain 'r' and resid 47 through 65 Processing helix chain 's' and resid 11 through 25 Processing helix chain 's' and resid 69 through 75 removed outlier: 4.294A pdb=" N PHE s 73 " --> pdb=" O LYS s 69 " (cutoff:3.500A) Proline residue: s 75 - end of helix Processing helix chain 't' and resid 7 through 41 removed outlier: 3.711A pdb=" N ILE t 11 " --> pdb=" O LYS t 7 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS t 15 " --> pdb=" O ILE t 11 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N HIS t 19 " --> pdb=" O LYS t 15 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N SER t 22 " --> pdb=" O LYS t 18 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ARG t 28 " --> pdb=" O ARG t 24 " (cutoff:3.500A) Processing helix chain 't' and resid 44 through 62 Proline residue: t 55 - end of helix Processing helix chain 't' and resid 67 through 86 Processing helix chain 'u' and resid 16 through 23 removed outlier: 4.318A pdb=" N ARG u 20 " --> pdb=" O ARG u 16 " (cutoff:3.500A) Processing helix chain 'u' and resid 24 through 33 removed outlier: 3.959A pdb=" N LEU u 28 " --> pdb=" O LYS u 24 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ARG u 33 " --> pdb=" O ALA u 29 " (cutoff:3.500A) Processing helix chain 'u' and resid 38 through 62 removed outlier: 3.988A pdb=" N THR u 42 " --> pdb=" O GLU u 38 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N GLU u 62 " --> pdb=" O LYS u 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 16 removed outlier: 3.522A pdb=" N ARG C 13 " --> pdb=" O SER C 9 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N HIS C 14 " --> pdb=" O PRO C 10 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N VAL C 15 " --> pdb=" O GLY C 11 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N VAL C 16 " --> pdb=" O ARG C 12 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 9 through 16' Processing helix chain 'C' and resid 130 through 135 removed outlier: 3.841A pdb=" N ILE C 134 " --> pdb=" O PRO C 130 " (cutoff:3.500A) Proline residue: C 135 - end of helix No H-bonds generated for 'chain 'C' and resid 130 through 135' Processing helix chain 'C' and resid 206 through 214 removed outlier: 4.329A pdb=" N ALA C 210 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG C 211 " --> pdb=" O ALA C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 225 removed outlier: 3.592A pdb=" N MET C 224 " --> pdb=" O ARG C 220 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N ASN C 225 " --> pdb=" O GLY C 221 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 220 through 225' Processing helix chain 'C' and resid 259 through 267 removed outlier: 6.441A pdb=" N ASP C 263 " --> pdb=" O ASN C 259 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N LYS C 264 " --> pdb=" O LYS C 260 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N PHE C 265 " --> pdb=" O ARG C 261 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ILE C 266 " --> pdb=" O THR C 262 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N VAL C 267 " --> pdb=" O ASP C 263 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 259 through 267' Processing helix chain 'D' and resid 56 through 61 removed outlier: 5.852A pdb=" N THR D 61 " --> pdb=" O ALA D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 72 removed outlier: 3.852A pdb=" N ALA D 71 " --> pdb=" O HIS D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 105 removed outlier: 4.502A pdb=" N ALA D 102 " --> pdb=" O VAL D 98 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N ASP D 103 " --> pdb=" O GLU D 99 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N VAL D 104 " --> pdb=" O LEU D 100 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N LYS D 105 " --> pdb=" O PHE D 101 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 98 through 105' Processing helix chain 'D' and resid 120 through 125 Processing helix chain 'D' and resid 39 through 44 Processing helix chain 'E' and resid 24 through 40 removed outlier: 3.688A pdb=" N VAL E 28 " --> pdb=" O ASN E 24 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ARG E 40 " --> pdb=" O ALA E 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 116 Processing helix chain 'E' and resid 130 through 142 removed outlier: 4.053A pdb=" N LEU E 134 " --> pdb=" O LYS E 130 " (cutoff:3.500A) Processing helix chain 'E' and resid 154 through 165 removed outlier: 3.614A pdb=" N ALA E 160 " --> pdb=" O ASN E 156 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N ASN E 163 " --> pdb=" O LEU E 159 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N LEU E 164 " --> pdb=" O ALA E 160 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N HIS E 165 " --> pdb=" O ALA E 161 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 184 removed outlier: 5.854A pdb=" N ASP E 184 " --> pdb=" O LEU E 180 " (cutoff:3.500A) Processing helix chain 'E' and resid 189 through 201 removed outlier: 3.714A pdb=" N LYS E 194 " --> pdb=" O ALA E 190 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ALA E 201 " --> pdb=" O GLU E 197 " (cutoff:3.500A) Processing helix chain 'F' and resid 1 through 19 removed outlier: 4.371A pdb=" N ASP F 5 " --> pdb=" O ALA F 1 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N TYR F 6 " --> pdb=" O LYS F 2 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLU F 10 " --> pdb=" O TYR F 6 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N VAL F 11 " --> pdb=" O TYR F 7 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N VAL F 12 " --> pdb=" O LYS F 8 " (cutoff:3.500A) Processing helix chain 'F' and resid 41 through 46 removed outlier: 3.534A pdb=" N ASP F 45 " --> pdb=" O GLU F 41 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYS F 46 " --> pdb=" O ALA F 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 41 through 46' Processing helix chain 'F' and resid 47 through 60 removed outlier: 4.526A pdb=" N ASN F 51 " --> pdb=" O LYS F 47 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA F 52 " --> pdb=" O LEU F 48 " (cutoff:3.500A) Processing helix chain 'F' and resid 92 through 110 removed outlier: 4.199A pdb=" N TRP F 96 " --> pdb=" O GLY F 92 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ILE F 105 " --> pdb=" O ARG F 101 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N VAL F 107 " --> pdb=" O ILE F 103 " (cutoff:3.500A) Proline residue: F 108 - end of helix Processing helix chain 'F' and resid 141 through 146 removed outlier: 6.244A pdb=" N VAL F 145 " --> pdb=" O ASP F 141 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N ASP F 146 " --> pdb=" O TYR F 142 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 141 through 146' Processing helix chain 'F' and resid 161 through 173 removed outlier: 3.688A pdb=" N ALA F 167 " --> pdb=" O GLU F 163 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LEU F 168 " --> pdb=" O GLU F 164 " (cutoff:3.500A) Processing helix chain 'F' and resid 133 through 138 removed outlier: 3.645A pdb=" N ILE F 136 " --> pdb=" O GLU F 133 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N PHE F 137 " --> pdb=" O GLN F 134 " (cutoff:3.500A) Proline residue: F 138 - end of helix No H-bonds generated for 'chain 'F' and resid 133 through 138' Processing helix chain 'G' and resid 1 through 6 removed outlier: 4.034A pdb=" N ALA G 6 " --> pdb=" O ARG G 2 " (cutoff:3.500A) Processing helix chain 'G' and resid 59 through 80 Processing helix chain 'G' and resid 136 through 152 removed outlier: 4.160A pdb=" N ARG G 151 " --> pdb=" O LEU G 147 " (cutoff:3.500A) Processing helix chain 'I' and resid 23 through 29 removed outlier: 4.297A pdb=" N LEU I 27 " --> pdb=" O VAL I 23 " (cutoff:3.500A) Processing helix chain 'I' and resid 33 through 39 removed outlier: 4.238A pdb=" N PHE I 37 " --> pdb=" O ASN I 33 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N CYS I 38 " --> pdb=" O ILE I 34 " (cutoff:3.500A) Processing helix chain 'I' and resid 42 through 49 removed outlier: 4.938A pdb=" N SER I 47 " --> pdb=" O ALA I 43 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ILE I 48 " --> pdb=" O LYS I 44 " (cutoff:3.500A) Processing helix chain 'I' and resid 74 through 83 removed outlier: 4.355A pdb=" N LEU I 78 " --> pdb=" O PRO I 74 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LYS I 80 " --> pdb=" O ALA I 76 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N LYS I 81 " --> pdb=" O VAL I 77 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA I 82 " --> pdb=" O LEU I 78 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ALA I 83 " --> pdb=" O LEU I 79 " (cutoff:3.500A) Processing helix chain 'I' and resid 101 through 114 removed outlier: 4.520A pdb=" N GLN I 110 " --> pdb=" O GLN I 106 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N THR I 111 " --> pdb=" O GLU I 107 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LYS I 112 " --> pdb=" O ILE I 108 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ALA I 114 " --> pdb=" O GLN I 110 " (cutoff:3.500A) Processing helix chain 'I' and resid 120 through 136 removed outlier: 3.571A pdb=" N MET I 135 " --> pdb=" O THR I 131 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLY I 136 " --> pdb=" O ALA I 132 " (cutoff:3.500A) Processing helix chain 'H' and resid 22 through 29 Processing helix chain 'H' and resid 40 through 50 removed outlier: 4.924A pdb=" N ILE H 44 " --> pdb=" O THR H 40 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N GLU H 45 " --> pdb=" O LYS H 41 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ALA H 49 " --> pdb=" O GLU H 45 " (cutoff:3.500A) Processing helix chain 'H' and resid 53 through 73 removed outlier: 5.576A pdb=" N LYS H 57 " --> pdb=" O GLU H 53 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA H 67 " --> pdb=" O ALA H 63 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N ASN H 73 " --> pdb=" O ALA H 69 " (cutoff:3.500A) Processing helix chain 'H' and resid 95 through 107 removed outlier: 3.738A pdb=" N ALA H 106 " --> pdb=" O ALA H 102 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLY H 107 " --> pdb=" O VAL H 103 " (cutoff:3.500A) Processing helix chain 'J' and resid 24 through 38 removed outlier: 3.934A pdb=" N GLY J 38 " --> pdb=" O ARG J 34 " (cutoff:3.500A) Processing helix chain 'J' and resid 67 through 72 Processing helix chain 'J' and resid 88 through 96 Processing helix chain 'J' and resid 97 through 110 removed outlier: 3.916A pdb=" N ILE J 101 " --> pdb=" O PRO J 97 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N MET J 108 " --> pdb=" O ALA J 104 " (cutoff:3.500A) Proline residue: J 110 - end of helix Processing helix chain 'J' and resid 112 through 122 removed outlier: 3.593A pdb=" N LYS J 121 " --> pdb=" O ALA J 117 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LEU J 122 " --> pdb=" O MET J 118 " (cutoff:3.500A) Processing helix chain 'J' and resid 130 through 135 removed outlier: 4.579A pdb=" N ALA J 133 " --> pdb=" O HIS J 130 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ALA J 134 " --> pdb=" O ASN J 131 " (cutoff:3.500A) Processing helix chain 'K' and resid 112 through 119 removed outlier: 4.124A pdb=" N LEU K 118 " --> pdb=" O LYS K 114 " (cutoff:3.500A) Processing helix chain 'K' and resid 104 through 109 removed outlier: 5.141A pdb=" N SER K 109 " --> pdb=" O GLU K 106 " (cutoff:3.500A) Processing helix chain 'L' and resid 37 through 42 removed outlier: 3.691A pdb=" N ARG L 41 " --> pdb=" O GLY L 37 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N SER L 42 " --> pdb=" O GLN L 38 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 37 through 42' Processing helix chain 'L' and resid 56 through 62 Proline residue: L 62 - end of helix Processing helix chain 'L' and resid 68 through 75 removed outlier: 4.191A pdb=" N ALA L 72 " --> pdb=" O SER L 68 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ILE L 73 " --> pdb=" O ARG L 69 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N ALA L 75 " --> pdb=" O ALA L 71 " (cutoff:3.500A) Processing helix chain 'L' and resid 78 through 85 removed outlier: 3.764A pdb=" N ALA L 83 " --> pdb=" O LEU L 79 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N LYS L 84 " --> pdb=" O SER L 80 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N VAL L 85 " --> pdb=" O ASP L 81 " (cutoff:3.500A) Processing helix chain 'L' and resid 91 through 99 removed outlier: 4.415A pdb=" N LEU L 95 " --> pdb=" O ASP L 91 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N LYS L 96 " --> pdb=" O LEU L 92 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N ALA L 97 " --> pdb=" O ASN L 93 " (cutoff:3.500A) Processing helix chain 'L' and resid 128 through 139 Processing helix chain 'M' and resid 42 through 58 removed outlier: 4.303A pdb=" N ALA M 56 " --> pdb=" O ALA M 52 " (cutoff:3.500A) Processing helix chain 'M' and resid 109 through 125 removed outlier: 3.701A pdb=" N ALA M 122 " --> pdb=" O LYS M 118 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LYS M 123 " --> pdb=" O LEU M 119 " (cutoff:3.500A) Proline residue: M 125 - end of helix Processing helix chain 'N' and resid 13 through 32 Processing helix chain 'N' and resid 38 through 57 removed outlier: 4.134A pdb=" N ARG N 46 " --> pdb=" O LYS N 42 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL N 47 " --> pdb=" O GLU N 43 " (cutoff:3.500A) Proline residue: N 50 - end of helix removed outlier: 4.431A pdb=" N THR N 57 " --> pdb=" O THR N 53 " (cutoff:3.500A) Processing helix chain 'N' and resid 59 through 71 removed outlier: 4.053A pdb=" N ARG N 63 " --> pdb=" O SER N 59 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N THR N 70 " --> pdb=" O ALA N 66 " (cutoff:3.500A) Processing helix chain 'N' and resid 72 through 82 removed outlier: 4.304A pdb=" N PHE N 80 " --> pdb=" O VAL N 76 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ASN N 81 " --> pdb=" O ALA N 77 " (cutoff:3.500A) Processing helix chain 'N' and resid 83 through 89 removed outlier: 4.327A pdb=" N SER N 89 " --> pdb=" O PRO N 85 " (cutoff:3.500A) Processing helix chain 'O' and resid 2 through 22 removed outlier: 4.284A pdb=" N ARG O 13 " --> pdb=" O ARG O 9 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N ALA O 14 " --> pdb=" O ARG O 10 " (cutoff:3.500A) Processing helix chain 'O' and resid 55 through 63 removed outlier: 5.357A pdb=" N GLN O 61 " --> pdb=" O ALA O 57 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU O 62 " --> pdb=" O ILE O 58 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N LYS O 63 " --> pdb=" O ALA O 59 " (cutoff:3.500A) Processing helix chain 'O' and resid 67 through 86 removed outlier: 3.955A pdb=" N ALA O 79 " --> pdb=" O GLY O 75 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLU O 84 " --> pdb=" O GLU O 80 " (cutoff:3.500A) Processing helix chain 'O' and resid 101 through 114 Processing helix chain 'P' and resid 1 through 12 removed outlier: 3.577A pdb=" N LYS P 5 " --> pdb=" O SER P 1 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N GLU P 10 " --> pdb=" O GLN P 6 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N GLN P 11 " --> pdb=" O LEU P 7 " (cutoff:3.500A) Processing helix chain 'P' and resid 96 through 103 removed outlier: 4.480A pdb=" N ARG P 100 " --> pdb=" O LEU P 96 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N GLU P 101 " --> pdb=" O TYR P 97 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ARG P 102 " --> pdb=" O TYR P 98 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N THR P 103 " --> pdb=" O LEU P 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 96 through 103' Processing helix chain 'Q' and resid 5 through 21 Processing helix chain 'Q' and resid 25 through 30 removed outlier: 4.136A pdb=" N ARG Q 29 " --> pdb=" O GLY Q 25 " (cutoff:3.500A) Processing helix chain 'Q' and resid 35 through 40 Processing helix chain 'Q' and resid 42 through 60 removed outlier: 3.712A pdb=" N ARG Q 49 " --> pdb=" O ALA Q 45 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N ARG Q 50 " --> pdb=" O TYR Q 46 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LYS Q 53 " --> pdb=" O ARG Q 49 " (cutoff:3.500A) Processing helix chain 'Q' and resid 62 through 72 removed outlier: 3.560A pdb=" N GLN Q 70 " --> pdb=" O ALA Q 66 " (cutoff:3.500A) Processing helix chain 'Q' and resid 74 through 86 Processing helix chain 'Q' and resid 90 through 101 Processing helix chain 'Q' and resid 102 through 117 Processing helix chain 'S' and resid 13 through 25 removed outlier: 3.747A pdb=" N VAL S 20 " --> pdb=" O LYS S 16 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N LEU S 23 " --> pdb=" O LEU S 19 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ILE S 24 " --> pdb=" O VAL S 20 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG S 25 " --> pdb=" O ALA S 21 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 39 removed outlier: 3.994A pdb=" N ASP S 34 " --> pdb=" O SER S 30 " (cutoff:3.500A) Processing helix chain 'S' and resid 41 through 62 removed outlier: 3.778A pdb=" N VAL S 45 " --> pdb=" O LYS S 41 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA S 58 " --> pdb=" O ALA S 54 " (cutoff:3.500A) Processing helix chain 'T' and resid 1 through 12 removed outlier: 4.059A pdb=" N GLU T 5 " --> pdb=" O MET T 1 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU T 11 " --> pdb=" O LEU T 7 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N ARG T 12 " --> pdb=" O LEU T 8 " (cutoff:3.500A) Processing helix chain 'T' and resid 17 through 26 removed outlier: 3.721A pdb=" N GLU T 25 " --> pdb=" O SER T 21 " (cutoff:3.500A) Processing helix chain 'T' and resid 39 through 50 removed outlier: 3.544A pdb=" N LYS T 49 " --> pdb=" O ALA T 45 " (cutoff:3.500A) Processing helix chain 'U' and resid 65 through 70 removed outlier: 3.991A pdb=" N VAL U 69 " --> pdb=" O GLN U 65 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N ALA U 70 " --> pdb=" O VAL U 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 65 through 70' Processing helix chain 'V' and resid 13 through 24 removed outlier: 3.641A pdb=" N ARG V 19 " --> pdb=" O GLY V 15 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASN V 24 " --> pdb=" O LEU V 20 " (cutoff:3.500A) Processing helix chain 'V' and resid 43 through 52 removed outlier: 4.009A pdb=" N VAL V 47 " --> pdb=" O ASP V 43 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N ALA V 52 " --> pdb=" O MET V 48 " (cutoff:3.500A) Processing helix chain 'V' and resid 53 through 59 removed outlier: 4.084A pdb=" N TYR V 57 " --> pdb=" O LYS V 53 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER V 58 " --> pdb=" O ALA V 54 " (cutoff:3.500A) Processing helix chain 'X' and resid 51 through 61 removed outlier: 3.685A pdb=" N ARG X 56 " --> pdb=" O ALA X 52 " (cutoff:3.500A) Processing helix chain 'X' and resid 62 through 74 Processing helix chain 'Y' and resid 1 through 7 removed outlier: 4.218A pdb=" N ARG Y 7 " --> pdb=" O ALA Y 3 " (cutoff:3.500A) Processing helix chain 'Y' and resid 9 through 23 Processing helix chain 'Y' and resid 25 through 35 removed outlier: 3.776A pdb=" N ARG Y 29 " --> pdb=" O GLN Y 25 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER Y 34 " --> pdb=" O MET Y 30 " (cutoff:3.500A) Processing helix chain 'Y' and resid 40 through 63 removed outlier: 4.125A pdb=" N LYS Y 44 " --> pdb=" O SER Y 40 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N GLY Y 62 " --> pdb=" O ASN Y 58 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N ALA Y 63 " --> pdb=" O GLU Y 59 " (cutoff:3.500A) Processing helix chain 'Z' and resid 16 through 27 Processing helix chain 'Z' and resid 40 through 51 Processing helix chain '0' and resid 8 through 18 removed outlier: 3.931A pdb=" N ARG 0 16 " --> pdb=" O ARG 0 12 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N HIS 0 18 " --> pdb=" O MET 0 14 " (cutoff:3.500A) Processing helix chain '2' and resid 8 through 16 Processing helix chain '2' and resid 17 through 24 removed outlier: 4.876A pdb=" N THR 2 24 " --> pdb=" O ALA 2 20 " (cutoff:3.500A) Processing helix chain '2' and resid 25 through 38 Processing helix chain '3' and resid 6 through 13 Processing helix chain '3' and resid 31 through 36 removed outlier: 5.049A pdb=" N LYS 3 35 " --> pdb=" O ILE 3 31 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N ALA 3 36 " --> pdb=" O LEU 3 32 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 31 through 36' Processing helix chain '3' and resid 37 through 45 Proline residue: 3 45 - end of helix Processing helix chain '3' and resid 50 through 62 removed outlier: 4.048A pdb=" N GLY 3 55 " --> pdb=" O LYS 3 51 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N LEU 3 56 " --> pdb=" O GLY 3 52 " (cutoff:3.500A) Proline residue: 3 62 - end of helix Processing helix chain '4' and resid 30 through 35 removed outlier: 3.971A pdb=" N LYS 4 34 " --> pdb=" O GLU 4 30 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N GLN 4 35 " --> pdb=" O PRO 4 31 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 30 through 35' Processing helix chain '6' and resid 37 through 54 removed outlier: 3.523A pdb=" N HIS 6 41 " --> pdb=" O CYS 6 37 " (cutoff:3.500A) Proline residue: 6 42 - end of helix removed outlier: 6.720A pdb=" N THR 6 45 " --> pdb=" O HIS 6 41 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N GLN 6 48 " --> pdb=" O PHE 6 44 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N ARG 6 49 " --> pdb=" O THR 6 45 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N ASP 6 50 " --> pdb=" O GLY 6 46 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N GLY 6 54 " --> pdb=" O ASP 6 50 " (cutoff:3.500A) Processing helix chain '6' and resid 55 through 65 removed outlier: 5.986A pdb=" N ARG 6 59 " --> pdb=" O GLY 6 55 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'b' and resid 66 through 70 removed outlier: 3.785A pdb=" N PHE b 183 " --> pdb=" O LEU b 160 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL b 162 " --> pdb=" O PHE b 183 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N PHE b 197 " --> pdb=" O VAL b 182 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA b 184 " --> pdb=" O PHE b 197 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'c' and resid 18 through 21 removed outlier: 6.176A pdb=" N ASN c 18 " --> pdb=" O ILE c 54 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ARG c 58 " --> pdb=" O THR c 20 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE c 63 " --> pdb=" O PRO c 97 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'c' and resid 163 through 170 removed outlier: 3.630A pdb=" N VAL c 150 " --> pdb=" O TYR c 167 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N GLY c 196 " --> pdb=" O SER c 153 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N THR c 190 " --> pdb=" O GLY c 193 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N ASP c 180 " --> pdb=" O LYS c 203 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'd' and resid 139 through 144 removed outlier: 6.797A pdb=" N MET d 177 " --> pdb=" O ILE d 144 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N TRP d 169 " --> pdb=" O LYS d 182 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'e' and resid 12 through 15 removed outlier: 6.587A pdb=" N LEU e 35 " --> pdb=" O ILE e 15 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N ILE e 29 " --> pdb=" O LYS e 22 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ALA e 16 " --> pdb=" O LEU e 35 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'e' and resid 83 through 87 removed outlier: 3.581A pdb=" N VAL e 93 " --> pdb=" O GLY e 86 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N TYR e 127 " --> pdb=" O ARG e 92 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'e' and resid 32 through 39 removed outlier: 3.928A pdb=" N ALA e 34 " --> pdb=" O GLY e 50 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N GLY e 50 " --> pdb=" O ALA e 34 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'f' and resid 39 through 42 removed outlier: 5.995A pdb=" N ILE f 6 " --> pdb=" O MET f 62 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N HIS f 3 " --> pdb=" O THR f 92 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N THR f 92 " --> pdb=" O HIS f 3 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N GLU f 5 " --> pdb=" O MET f 90 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N MET f 90 " --> pdb=" O GLU f 5 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N ARG f 86 " --> pdb=" O MET f 9 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'f' and resid 43 through 47 removed outlier: 3.771A pdb=" N GLY f 43 " --> pdb=" O TYR f 59 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N LEU f 47 " --> pdb=" O HIS f 55 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N HIS f 55 " --> pdb=" O LEU f 47 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'g' and resid 72 through 76 removed outlier: 3.614A pdb=" N LYS g 75 " --> pdb=" O VAL g 86 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'h' and resid 22 through 27 removed outlier: 6.292A pdb=" N ALA h 22 " --> pdb=" O LEU h 62 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N GLU h 51 " --> pdb=" O GLU h 57 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LYS h 49 " --> pdb=" O GLU h 59 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR h 61 " --> pdb=" O ASP h 47 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N ASP h 47 " --> pdb=" O THR h 61 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'h' and resid 73 through 76 removed outlier: 3.572A pdb=" N ILE h 100 " --> pdb=" O VAL h 128 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N VAL h 102 " --> pdb=" O ILE h 125 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'i' and resid 4 through 10 removed outlier: 4.259A pdb=" N GLY i 9 " --> pdb=" O ALA i 16 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LYS i 67 " --> pdb=" O ALA i 15 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'j' and resid 36 through 40 removed outlier: 6.334A pdb=" N ILE j 8 " --> pdb=" O VAL j 74 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLN j 99 " --> pdb=" O ARG j 9 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'j' and resid 44 through 52 removed outlier: 4.191A pdb=" N GLU j 47 " --> pdb=" O ILE j 67 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ILE j 67 " --> pdb=" O GLU j 47 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'k' and resid 29 through 34 Processing sheet with id= 17, first strand: chain 'l' and resid 28 through 31 removed outlier: 5.127A pdb=" N LEU l 80 " --> pdb=" O VAL l 97 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'l' and resid 35 through 40 removed outlier: 4.790A pdb=" N ARG l 35 " --> pdb=" O ARG l 53 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N LYS l 50 " --> pdb=" O ILE l 66 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'p' and resid 4 through 10 removed outlier: 5.814A pdb=" N GLN p 18 " --> pdb=" O ALA p 7 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N VAL p 19 " --> pdb=" O GLY p 37 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N GLY p 37 " --> pdb=" O VAL p 19 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N GLY p 49 " --> pdb=" O ASN p 40 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'q' and resid 6 through 10 removed outlier: 4.832A pdb=" N GLY q 9 " --> pdb=" O VAL q 58 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N VAL q 58 " --> pdb=" O GLY q 9 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N GLU q 59 " --> pdb=" O VAL q 75 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL q 75 " --> pdb=" O GLU q 59 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'q' and resid 19 through 29 No H-bonds generated for sheet with id= 21 Processing sheet with id= 22, first strand: chain 's' and resid 46 through 51 removed outlier: 4.862A pdb=" N LEU s 46 " --> pdb=" O VAL s 61 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'C' and resid 32 through 35 No H-bonds generated for sheet with id= 23 Processing sheet with id= 24, first strand: chain 'C' and resid 79 through 82 removed outlier: 4.055A pdb=" N ARG C 79 " --> pdb=" O LEU C 92 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N LEU C 92 " --> pdb=" O GLU C 78 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N ILE C 73 " --> pdb=" O SER C 117 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N SER C 117 " --> pdb=" O ILE C 73 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ASP C 113 " --> pdb=" O VAL C 77 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'C' and resid 137 through 141 removed outlier: 4.696A pdb=" N SER C 138 " --> pdb=" O ILE C 163 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N THR C 172 " --> pdb=" O VAL C 164 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N GLU C 179 " --> pdb=" O LEU C 175 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'C' and resid 90 through 95 removed outlier: 4.457A pdb=" N GLU C 99 " --> pdb=" O TYR C 95 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'D' and resid 3 through 8 removed outlier: 4.421A pdb=" N SER D 199 " --> pdb=" O LYS D 8 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'D' and resid 11 through 16 removed outlier: 4.374A pdb=" N VAL D 20 " --> pdb=" O THR D 16 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG D 179 " --> pdb=" O LEU D 188 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'D' and resid 79 through 84 removed outlier: 6.640A pdb=" N ARG D 46 " --> pdb=" O LEU D 84 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N GLN D 49 " --> pdb=" O THR D 35 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL D 34 " --> pdb=" O GLN D 94 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N GLN D 94 " --> pdb=" O VAL D 34 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'E' and resid 1 through 5 No H-bonds generated for sheet with id= 30 Processing sheet with id= 31, first strand: chain 'E' and resid 117 through 120 removed outlier: 3.528A pdb=" N LEU E 147 " --> pdb=" O LYS E 185 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL E 187 " --> pdb=" O LEU E 147 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE E 149 " --> pdb=" O VAL E 187 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASP E 168 " --> pdb=" O VAL E 146 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'F' and resid 64 through 68 removed outlier: 3.539A pdb=" N CYS F 86 " --> pdb=" O MET F 37 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL F 88 " --> pdb=" O LEU F 35 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LYS F 32 " --> pdb=" O THR F 156 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N GLY F 38 " --> pdb=" O GLY F 150 " (cutoff:3.500A) removed outlier: 8.302A pdb=" N GLY F 150 " --> pdb=" O GLY F 38 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU F 151 " --> pdb=" O VAL F 131 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N THR F 157 " --> pdb=" O GLY F 125 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N GLY F 125 " --> pdb=" O THR F 157 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'F' and resid 71 through 74 removed outlier: 5.346A pdb=" N SER F 72 " --> pdb=" O ARG F 79 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N ARG F 79 " --> pdb=" O SER F 72 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ALA F 74 " --> pdb=" O LYS F 77 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'G' and resid 15 through 18 removed outlier: 3.960A pdb=" N ILE G 23 " --> pdb=" O ARG G 34 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'G' and resid 40 through 44 Processing sheet with id= 36, first strand: chain 'G' and resid 81 through 88 removed outlier: 6.450A pdb=" N THR G 128 " --> pdb=" O LEU G 88 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'G' and resid 93 through 97 removed outlier: 3.598A pdb=" N ALA G 96 " --> pdb=" O ASN G 103 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'H' and resid 2 through 6 removed outlier: 5.773A pdb=" N GLN H 2 " --> pdb=" O ALA H 39 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N ALA H 39 " --> pdb=" O GLN H 2 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N LYS H 35 " --> pdb=" O LEU H 6 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'H' and resid 76 through 81 removed outlier: 7.471A pdb=" N GLU H 76 " --> pdb=" O LYS H 141 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N GLU H 114 " --> pdb=" O GLN H 133 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'J' and resid 52 through 57 removed outlier: 4.877A pdb=" N ASP J 19 " --> pdb=" O LEU J 140 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'J' and resid 74 through 78 removed outlier: 7.498A pdb=" N GLY J 83 " --> pdb=" O THR J 78 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'K' and resid 18 through 21 removed outlier: 4.138A pdb=" N THR K 6 " --> pdb=" O CYS K 21 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N ASN K 82 " --> pdb=" O MET K 7 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N CYS K 84 " --> pdb=" O ASN K 9 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'M' and resid 62 through 66 removed outlier: 3.558A pdb=" N ASP M 106 " --> pdb=" O LYS M 62 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N LEU M 102 " --> pdb=" O ARG M 66 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N TYR M 103 " --> pdb=" O LEU M 33 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N SER M 30 " --> pdb=" O LYS M 133 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N LYS M 127 " --> pdb=" O VAL M 36 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'O' and resid 49 through 53 removed outlier: 4.232A pdb=" N VAL O 49 " --> pdb=" O VAL O 39 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ILE O 35 " --> pdb=" O THR O 53 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL O 28 " --> pdb=" O ASP O 93 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'P' and resid 37 through 44 removed outlier: 6.089A pdb=" N THR P 24 " --> pdb=" O LYS P 86 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N SER P 82 " --> pdb=" O LYS P 28 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'P' and resid 48 through 51 removed outlier: 4.366A pdb=" N ALA P 48 " --> pdb=" O THR P 59 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N SER P 56 " --> pdb=" O THR P 75 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'R' and resid 11 through 15 removed outlier: 4.076A pdb=" N TYR R 2 " --> pdb=" O ALA R 42 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'R' and resid 32 through 36 Processing sheet with id= 49, first strand: chain 'R' and resid 65 through 69 removed outlier: 3.830A pdb=" N ALA R 65 " --> pdb=" O ASP R 95 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N GLN R 91 " --> pdb=" O GLY R 69 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N TYR R 83 " --> pdb=" O ARG R 78 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL R 72 " --> pdb=" O HIS R 89 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'S' and resid 2 through 8 removed outlier: 4.281A pdb=" N THR S 3 " --> pdb=" O VAL S 107 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N VAL S 107 " --> pdb=" O THR S 3 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N VAL S 106 " --> pdb=" O THR S 72 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'S' and resid 80 through 88 removed outlier: 4.548A pdb=" N ARG S 92 " --> pdb=" O ARG S 88 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'T' and resid 29 through 34 removed outlier: 4.088A pdb=" N LYS T 81 " --> pdb=" O VAL T 34 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LYS T 68 " --> pdb=" O GLY T 75 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N LYS T 66 " --> pdb=" O ARG T 77 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ASP T 79 " --> pdb=" O LYS T 64 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N LYS T 64 " --> pdb=" O ASP T 79 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N LYS T 81 " --> pdb=" O VAL T 62 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N VAL T 62 " --> pdb=" O LYS T 81 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N ALA T 83 " --> pdb=" O THR T 60 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N THR T 60 " --> pdb=" O ALA T 83 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N VAL T 85 " --> pdb=" O VAL T 58 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N VAL T 58 " --> pdb=" O VAL T 85 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'U' and resid 39 through 44 removed outlier: 5.476A pdb=" N ASN U 39 " --> pdb=" O ALA U 62 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'U' and resid 81 through 86 removed outlier: 5.411A pdb=" N ARG U 81 " --> pdb=" O LYS U 96 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'V' and resid 69 through 73 removed outlier: 7.271A pdb=" N PHE V 2 " --> pdb=" O VAL V 60 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N THR V 62 " --> pdb=" O PHE V 2 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA V 6 " --> pdb=" O VAL V 64 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ARG V 9 " --> pdb=" O ALA V 39 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N ALA V 39 " --> pdb=" O ARG V 9 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ILE V 89 " --> pdb=" O PRO V 27 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N HIS V 88 " --> pdb=" O GLN V 78 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'W' and resid 24 through 27 removed outlier: 4.731A pdb=" N GLU W 25 " --> pdb=" O VAL W 63 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'W' and resid 30 through 33 removed outlier: 4.337A pdb=" N SER W 31 " --> pdb=" O ALA W 57 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N LEU W 55 " --> pdb=" O ILE W 33 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N THR W 54 " --> pdb=" O GLY W 50 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N PHE W 56 " --> pdb=" O GLY W 48 " (cutoff:3.500A) removed outlier: 8.321A pdb=" N ASN W 46 " --> pdb=" O LYS W 58 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'X' and resid 11 through 18 removed outlier: 3.792A pdb=" N VAL X 12 " --> pdb=" O PHE X 28 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLY X 14 " --> pdb=" O ARG X 26 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N THR X 24 " --> pdb=" O ASN X 16 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N SER X 18 " --> pdb=" O ASN X 22 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N ASN X 22 " --> pdb=" O SER X 18 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'X' and resid 34 through 40 Processing sheet with id= 60, first strand: chain 'Z' and resid 32 through 38 removed outlier: 4.914A pdb=" N HIS Z 33 " --> pdb=" O GLN Z 8 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N GLN Z 8 " --> pdb=" O HIS Z 33 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU Z 57 " --> pdb=" O LYS Z 5 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N MET Z 53 " --> pdb=" O THR Z 9 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain '0' and resid 27 through 30 removed outlier: 6.359A pdb=" N SER 0 28 " --> pdb=" O LYS 0 36 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N LYS 0 36 " --> pdb=" O SER 0 28 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N ASP 0 30 " --> pdb=" O GLY 0 34 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain '1' and resid 19 through 23 removed outlier: 7.435A pdb=" N ILE 1 47 " --> pdb=" O SER 1 13 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL 1 46 " --> pdb=" O LYS 1 37 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LYS 1 37 " --> pdb=" O VAL 1 46 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU 1 35 " --> pdb=" O TYR 1 48 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLU 1 50 " --> pdb=" O LEU 1 33 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N LEU 1 33 " --> pdb=" O GLU 1 50 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain '3' and resid 21 through 24 No H-bonds generated for sheet with id= 63 Processing sheet with id= 64, first strand: chain '4' and resid 14 through 18 Processing sheet with id= 65, first strand: chain '6' and resid 21 through 25 1713 hydrogen bonds defined for protein. 5073 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3839 hydrogen bonds 6106 hydrogen bond angles 0 basepair planarities 1524 basepair parallelities 2407 stacking parallelities Total time for adding SS restraints: 217.53 Time building geometry restraints manager: 66.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 13979 1.31 - 1.44: 70492 1.44 - 1.57: 64613 1.57 - 1.70: 9366 1.70 - 1.83: 267 Bond restraints: 158717 Sorted by residual: bond pdb=" C4 5MU A 747 " pdb=" C5 5MU A 747 " ideal model delta sigma weight residual 1.802 1.474 0.328 2.00e-02 2.50e+03 2.69e+02 bond pdb=" C4 5MU A1939 " pdb=" C5 5MU A1939 " ideal model delta sigma weight residual 1.802 1.475 0.327 2.00e-02 2.50e+03 2.68e+02 bond pdb=" C4 5MU v 54 " pdb=" C5 5MU v 54 " ideal model delta sigma weight residual 1.802 1.479 0.323 2.00e-02 2.50e+03 2.61e+02 bond pdb=" N1 5MU A1939 " pdb=" C6 5MU A1939 " ideal model delta sigma weight residual 1.635 1.333 0.302 2.00e-02 2.50e+03 2.29e+02 bond pdb=" N1 5MU v 54 " pdb=" C6 5MU v 54 " ideal model delta sigma weight residual 1.635 1.335 0.300 2.00e-02 2.50e+03 2.24e+02 ... (remaining 158712 not shown) Histogram of bond angle deviations from ideal: 91.77 - 101.53: 2676 101.53 - 111.29: 94561 111.29 - 121.05: 93587 121.05 - 130.81: 45024 130.81 - 140.57: 1696 Bond angle restraints: 237544 Sorted by residual: angle pdb=" N ASN e 77 " pdb=" CA ASN e 77 " pdb=" CB ASN e 77 " ideal model delta sigma weight residual 110.49 91.77 18.72 1.69e+00 3.50e-01 1.23e+02 angle pdb=" N GLU m 65 " pdb=" CA GLU m 65 " pdb=" CB GLU m 65 " ideal model delta sigma weight residual 110.49 93.08 17.41 1.69e+00 3.50e-01 1.06e+02 angle pdb=" N LEU U 51 " pdb=" CA LEU U 51 " pdb=" CB LEU U 51 " ideal model delta sigma weight residual 110.49 94.11 16.38 1.69e+00 3.50e-01 9.40e+01 angle pdb=" N LEU l 101 " pdb=" CA LEU l 101 " pdb=" CB LEU l 101 " ideal model delta sigma weight residual 110.49 95.06 15.43 1.69e+00 3.50e-01 8.33e+01 angle pdb=" N ARG b 73 " pdb=" CA ARG b 73 " pdb=" CB ARG b 73 " ideal model delta sigma weight residual 110.49 95.64 14.85 1.69e+00 3.50e-01 7.72e+01 ... (remaining 237539 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.50: 89460 35.50 - 71.00: 10774 71.00 - 106.50: 1311 106.50 - 142.00: 29 142.00 - 177.51: 23 Dihedral angle restraints: 101597 sinusoidal: 85035 harmonic: 16562 Sorted by residual: dihedral pdb=" O4' G7M a 527 " pdb=" C4' G7M a 527 " pdb=" C3' G7M a 527 " pdb=" C2' G7M a 527 " ideal model delta sinusoidal sigma weight residual -35.00 40.77 -75.77 1 8.00e+00 1.56e-02 1.13e+02 dihedral pdb=" O4' G7M A2069 " pdb=" C4' G7M A2069 " pdb=" C3' G7M A2069 " pdb=" C2' G7M A2069 " ideal model delta sinusoidal sigma weight residual -35.00 38.95 -73.95 1 8.00e+00 1.56e-02 1.09e+02 dihedral pdb=" CA GLY E 82 " pdb=" C GLY E 82 " pdb=" N VAL E 83 " pdb=" CA VAL E 83 " ideal model delta harmonic sigma weight residual 180.00 -128.32 -51.68 0 5.00e+00 4.00e-02 1.07e+02 ... (remaining 101594 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.948: 30267 0.948 - 1.896: 0 1.896 - 2.844: 0 2.844 - 3.791: 0 3.791 - 4.739: 4 Chirality restraints: 30271 Sorted by residual: chirality pdb=" C4' G7M A2069 " pdb=" C5' G7M A2069 " pdb=" O4' G7M A2069 " pdb=" C3' G7M A2069 " both_signs ideal model delta sigma weight residual False -2.50 2.24 -4.74 2.00e-01 2.50e+01 5.62e+02 chirality pdb=" C4' G7M a 527 " pdb=" C5' G7M a 527 " pdb=" O4' G7M a 527 " pdb=" C3' G7M a 527 " both_signs ideal model delta sigma weight residual False -2.50 1.95 -4.45 2.00e-01 2.50e+01 4.95e+02 chirality pdb=" C3' G7M A2069 " pdb=" C4' G7M A2069 " pdb=" O3' G7M A2069 " pdb=" C2' G7M A2069 " both_signs ideal model delta sigma weight residual False -2.48 1.88 -4.36 2.00e-01 2.50e+01 4.75e+02 ... (remaining 30268 not shown) Planarity restraints: 12696 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 2MG A1835 " -0.044 2.00e-02 2.50e+03 5.81e-01 7.59e+03 pdb=" C4' 2MG A1835 " -0.427 2.00e-02 2.50e+03 pdb=" O4' 2MG A1835 " -0.645 2.00e-02 2.50e+03 pdb=" C3' 2MG A1835 " 0.599 2.00e-02 2.50e+03 pdb=" O3' 2MG A1835 " 0.585 2.00e-02 2.50e+03 pdb=" C2' 2MG A1835 " 0.198 2.00e-02 2.50e+03 pdb=" O2' 2MG A1835 " -0.923 2.00e-02 2.50e+03 pdb=" C1' 2MG A1835 " -0.232 2.00e-02 2.50e+03 pdb=" N9 2MG A1835 " 0.889 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG a1207 " -0.037 2.00e-02 2.50e+03 5.80e-01 7.58e+03 pdb=" C4' 2MG a1207 " -0.451 2.00e-02 2.50e+03 pdb=" O4' 2MG a1207 " -0.682 2.00e-02 2.50e+03 pdb=" C3' 2MG a1207 " 0.586 2.00e-02 2.50e+03 pdb=" O3' 2MG a1207 " 0.578 2.00e-02 2.50e+03 pdb=" C2' 2MG a1207 " 0.226 2.00e-02 2.50e+03 pdb=" O2' 2MG a1207 " -0.894 2.00e-02 2.50e+03 pdb=" C1' 2MG a1207 " -0.214 2.00e-02 2.50e+03 pdb=" N9 2MG a1207 " 0.889 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 5MC a1407 " 0.047 2.00e-02 2.50e+03 5.78e-01 7.53e+03 pdb=" C4' 5MC a1407 " 0.444 2.00e-02 2.50e+03 pdb=" O4' 5MC a1407 " 0.584 2.00e-02 2.50e+03 pdb=" C3' 5MC a1407 " -0.584 2.00e-02 2.50e+03 pdb=" O3' 5MC a1407 " -0.616 2.00e-02 2.50e+03 pdb=" C2' 5MC a1407 " -0.183 2.00e-02 2.50e+03 pdb=" O2' 5MC a1407 " 0.947 2.00e-02 2.50e+03 pdb=" C1' 5MC a1407 " 0.236 2.00e-02 2.50e+03 pdb=" N1 5MC a1407 " -0.874 2.00e-02 2.50e+03 ... (remaining 12693 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 6189 2.66 - 3.22: 124212 3.22 - 3.78: 300990 3.78 - 4.34: 384849 4.34 - 4.90: 506277 Nonbonded interactions: 1322517 Sorted by model distance: nonbonded pdb=" O2' C a 110 " pdb=" O ARG p 25 " model vdw 2.102 2.440 nonbonded pdb=" OG SER j 54 " pdb=" O HIS j 56 " model vdw 2.139 2.440 nonbonded pdb=" O2' U a1123 " pdb=" O PRO j 39 " model vdw 2.153 2.440 nonbonded pdb=" O2' U a 407 " pdb=" OE1 GLU d 112 " model vdw 2.155 2.440 nonbonded pdb=" O2' C A1064 " pdb=" O2 C A1075 " model vdw 2.162 2.440 ... (remaining 1322512 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.49 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.980 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: 0.100 Extract box with map and model: 10.910 Check model and map are aligned: 1.530 Set scattering table: 0.930 Process input model: 571.850 Find NCS groups from input model: 2.920 Set up NCS constraints: 0.430 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 591.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 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 : 0.008 0.328 158717 Z= 0.494 Angle : 1.154 24.275 237544 Z= 0.610 Chirality : 0.074 4.739 30271 Planarity : 0.021 0.581 12696 Dihedral : 22.914 177.505 90913 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 2.10 % Allowed : 7.82 % Favored : 90.08 % Rotamer: Outliers : 0.47 % Allowed : 2.01 % Favored : 97.53 % Cbeta Deviations : 0.32 % Peptide Plane: Cis-proline : 0.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.47 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.44 (0.10), residues: 5717 helix: -3.06 (0.08), residues: 1859 sheet: -3.43 (0.12), residues: 954 loop : -1.14 (0.11), residues: 2904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.004 TRP C 212 HIS 0.031 0.004 HIS o 45 PHE 0.039 0.004 PHE M 68 TYR 0.048 0.004 TYR 3 63 ARG 0.029 0.001 ARG 1 43 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11434 Ramachandran restraints generated. 5717 Oldfield, 0 Emsley, 5717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11434 Ramachandran restraints generated. 5717 Oldfield, 0 Emsley, 5717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2427 residues out of total 4751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 2405 time to evaluate : 6.270 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: b 26 MET cc_start: 0.7872 (mtp) cc_final: 0.7617 (mmm) REVERT: b 29 PHE cc_start: 0.7422 (m-80) cc_final: 0.6779 (m-80) REVERT: b 63 LYS cc_start: 0.8016 (mmmt) cc_final: 0.7344 (tptm) REVERT: b 91 VAL cc_start: 0.8970 (t) cc_final: 0.8766 (m) REVERT: b 94 ARG cc_start: 0.6729 (mmt-90) cc_final: 0.6335 (tmm-80) REVERT: b 114 LYS cc_start: 0.7529 (ttmt) cc_final: 0.7154 (tptt) REVERT: b 117 GLU cc_start: 0.7077 (pt0) cc_final: 0.6333 (pp20) REVERT: b 164 ASP cc_start: 0.7788 (t70) cc_final: 0.7443 (t0) REVERT: b 174 GLU cc_start: 0.8105 (tt0) cc_final: 0.6900 (tt0) REVERT: c 57 GLU cc_start: 0.8080 (mt-10) cc_final: 0.7826 (mt-10) REVERT: c 87 ARG cc_start: 0.8058 (mtt180) cc_final: 0.7702 (ttt90) REVERT: c 109 GLU cc_start: 0.8166 (mt-10) cc_final: 0.7906 (mp0) REVERT: c 146 LYS cc_start: 0.8801 (mmmt) cc_final: 0.8458 (tptp) REVERT: c 155 ARG cc_start: 0.8537 (mmm-85) cc_final: 0.8206 (mmm-85) REVERT: c 163 ARG cc_start: 0.8352 (ttp80) cc_final: 0.8096 (ptp90) REVERT: c 178 ARG cc_start: 0.8899 (ttp-170) cc_final: 0.8467 (ttp80) REVERT: d 13 ARG cc_start: 0.7445 (ttm-80) cc_final: 0.6316 (ttp-110) REVERT: d 59 LYS cc_start: 0.9110 (tttt) cc_final: 0.8833 (ttpt) REVERT: d 82 LYS cc_start: 0.7999 (pttt) cc_final: 0.7765 (mmmt) REVERT: d 116 LEU cc_start: 0.8531 (tp) cc_final: 0.8215 (tt) REVERT: d 139 ASN cc_start: 0.8299 (t0) cc_final: 0.7700 (p0) REVERT: d 144 ILE cc_start: 0.8157 (mt) cc_final: 0.7936 (tt) REVERT: d 170 LEU cc_start: 0.8576 (pp) cc_final: 0.8044 (pt) REVERT: d 183 ARG cc_start: 0.8308 (ptt90) cc_final: 0.7910 (ptm-80) REVERT: e 18 ASN cc_start: 0.7976 (t0) cc_final: 0.7661 (t0) REVERT: e 19 ARG cc_start: 0.8006 (ptt90) cc_final: 0.7680 (ptt-90) REVERT: e 69 ASN cc_start: 0.7938 (t0) cc_final: 0.7246 (t0) REVERT: e 85 LYS cc_start: 0.8742 (mttt) cc_final: 0.8472 (mttm) REVERT: e 94 PHE cc_start: 0.8893 (t80) cc_final: 0.8426 (t80) REVERT: e 116 VAL cc_start: 0.8874 (m) cc_final: 0.8625 (p) REVERT: e 121 ASN cc_start: 0.7447 (m-40) cc_final: 0.6842 (m-40) REVERT: e 135 VAL cc_start: 0.9204 (t) cc_final: 0.8980 (p) REVERT: e 144 GLU cc_start: 0.8544 (tt0) cc_final: 0.8228 (tp30) REVERT: e 151 MET cc_start: 0.8360 (mtp) cc_final: 0.7865 (tpp) REVERT: e 161 GLU cc_start: 0.7984 (mt-10) cc_final: 0.7772 (tm-30) REVERT: f 24 ARG cc_start: 0.8780 (ttm-80) cc_final: 0.8512 (mtp180) REVERT: f 42 TRP cc_start: 0.7155 (m100) cc_final: 0.6869 (m100) REVERT: f 46 GLN cc_start: 0.8275 (tt0) cc_final: 0.7888 (tp40) REVERT: f 49 TYR cc_start: 0.8317 (p90) cc_final: 0.8070 (p90) REVERT: g 105 GLU cc_start: 0.7922 (tp30) cc_final: 0.7324 (tp30) REVERT: g 109 LYS cc_start: 0.7564 (mptt) cc_final: 0.7284 (mmtt) REVERT: g 115 MET cc_start: 0.7521 (tpt) cc_final: 0.7156 (tpp) REVERT: g 122 GLU cc_start: 0.8148 (mm-30) cc_final: 0.7049 (tp30) REVERT: g 142 ARG cc_start: 0.7874 (mmt-90) cc_final: 0.6744 (tpt-90) REVERT: g 143 MET cc_start: 0.6768 (mmp) cc_final: 0.6469 (tpt) REVERT: h 29 SER cc_start: 0.9163 (t) cc_final: 0.8913 (t) REVERT: h 93 LYS cc_start: 0.8686 (mtpp) cc_final: 0.8036 (mptt) REVERT: h 113 ARG cc_start: 0.8580 (ttp80) cc_final: 0.7895 (ttm110) REVERT: i 11 ARG cc_start: 0.7542 (tpt90) cc_final: 0.7109 (tpt-90) REVERT: i 17 ARG cc_start: 0.8183 (mtp-110) cc_final: 0.7804 (mtp180) REVERT: i 60 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.8301 (pp) REVERT: i 63 TYR cc_start: 0.8760 (t80) cc_final: 0.8419 (t80) REVERT: i 65 THR cc_start: 0.8699 (p) cc_final: 0.8326 (p) REVERT: i 103 VAL cc_start: 0.8909 (m) cc_final: 0.8604 (p) REVERT: i 115 VAL cc_start: 0.8262 (p) cc_final: 0.8046 (p) REVERT: i 119 LYS cc_start: 0.8887 (ptpt) cc_final: 0.8627 (pttt) REVERT: i 127 SER cc_start: 0.8178 (t) cc_final: 0.7876 (p) REVERT: j 6 ILE cc_start: 0.8842 (mt) cc_final: 0.8526 (pt) REVERT: j 63 ASP cc_start: 0.8641 (t0) cc_final: 0.8405 (t0) REVERT: j 83 THR cc_start: 0.7800 (m) cc_final: 0.7574 (p) REVERT: k 31 VAL cc_start: 0.9174 (t) cc_final: 0.8923 (m) REVERT: k 32 THR cc_start: 0.8943 (m) cc_final: 0.8595 (p) REVERT: k 36 ARG cc_start: 0.8950 (tpp-160) cc_final: 0.8732 (tpp80) REVERT: k 81 LEU cc_start: 0.8407 (pp) cc_final: 0.8078 (pt) REVERT: k 94 SER cc_start: 0.8603 (t) cc_final: 0.8383 (p) REVERT: k 110 THR cc_start: 0.8406 (p) cc_final: 0.8006 (p) REVERT: l 50 LYS cc_start: 0.8108 (mptt) cc_final: 0.7571 (mtmm) REVERT: l 61 GLU cc_start: 0.7602 (tp30) cc_final: 0.7360 (tp30) REVERT: l 66 ILE cc_start: 0.8548 (mt) cc_final: 0.8323 (mp) REVERT: m 12 LYS cc_start: 0.7154 (mttt) cc_final: 0.6466 (mptt) REVERT: m 38 ILE cc_start: 0.6866 (mm) cc_final: 0.6342 (tp) REVERT: m 69 ARG cc_start: 0.8627 (mtt-85) cc_final: 0.8397 (mmt90) REVERT: m 88 LEU cc_start: 0.9107 (tp) cc_final: 0.8859 (mt) REVERT: n 4 SER cc_start: 0.8655 (p) cc_final: 0.8066 (t) REVERT: o 7 THR cc_start: 0.8393 (p) cc_final: 0.8175 (t) REVERT: o 9 LYS cc_start: 0.8755 (ttpt) cc_final: 0.8049 (tppt) REVERT: p 36 VAL cc_start: 0.8986 (OUTLIER) cc_final: 0.8410 (m) REVERT: p 63 GLN cc_start: 0.7904 (mm-40) cc_final: 0.7593 (mm-40) REVERT: q 4 ILE cc_start: 0.5920 (OUTLIER) cc_final: 0.5692 (tt) REVERT: q 16 MET cc_start: 0.7865 (ptm) cc_final: 0.7619 (tmm) REVERT: q 39 ARG cc_start: 0.8588 (mmt90) cc_final: 0.8237 (mtp-110) REVERT: q 64 ARG cc_start: 0.7947 (ttp-110) cc_final: 0.7334 (ttp-170) REVERT: r 22 TYR cc_start: 0.8540 (p90) cc_final: 0.7963 (p90) REVERT: r 46 THR cc_start: 0.8796 (p) cc_final: 0.8564 (p) REVERT: r 65 SER cc_start: 0.9384 (m) cc_final: 0.9127 (t) REVERT: s 4 LEU cc_start: 0.6347 (OUTLIER) cc_final: 0.6021 (pt) REVERT: s 20 LYS cc_start: 0.8268 (ttpp) cc_final: 0.7591 (mmtm) REVERT: s 55 GLN cc_start: 0.7606 (pm20) cc_final: 0.7212 (pm20) REVERT: t 66 ILE cc_start: 0.8935 (mm) cc_final: 0.8727 (mt) REVERT: t 84 LYS cc_start: 0.6607 (ttmt) cc_final: 0.6385 (tppt) REVERT: u 21 SER cc_start: 0.7284 (t) cc_final: 0.6973 (p) REVERT: u 37 TYR cc_start: 0.7685 (t80) cc_final: 0.7243 (t80) REVERT: C 4 LYS cc_start: 0.9006 (ttpt) cc_final: 0.8588 (tptt) REVERT: C 36 ASN cc_start: 0.8477 (t0) cc_final: 0.8274 (t0) REVERT: C 44 ASN cc_start: 0.9368 (m110) cc_final: 0.8996 (p0) REVERT: C 81 GLU cc_start: 0.8690 (mm-30) cc_final: 0.8454 (mm-30) REVERT: C 83 ASP cc_start: 0.8913 (t0) cc_final: 0.8539 (t0) REVERT: C 102 TYR cc_start: 0.8631 (m-80) cc_final: 0.8394 (m-80) REVERT: C 124 LYS cc_start: 0.8565 (tttt) cc_final: 0.8265 (pttt) REVERT: C 156 SER cc_start: 0.9182 (t) cc_final: 0.8680 (p) REVERT: C 160 TYR cc_start: 0.8822 (p90) cc_final: 0.8513 (p90) REVERT: C 188 ARG cc_start: 0.8221 (mtt-85) cc_final: 0.7760 (mtm-85) REVERT: C 266 ILE cc_start: 0.9076 (mt) cc_final: 0.8692 (pt) REVERT: D 16 THR cc_start: 0.8225 (p) cc_final: 0.7923 (p) REVERT: D 28 GLU cc_start: 0.8710 (pt0) cc_final: 0.8376 (pt0) REVERT: D 30 GLU cc_start: 0.8055 (mp0) cc_final: 0.7516 (mp0) REVERT: D 45 TYR cc_start: 0.8378 (p90) cc_final: 0.7988 (p90) REVERT: D 89 GLU cc_start: 0.7667 (tp30) cc_final: 0.7350 (mp0) REVERT: D 106 LYS cc_start: 0.8885 (mtmt) cc_final: 0.8661 (mtpp) REVERT: D 155 VAL cc_start: 0.9277 (t) cc_final: 0.8978 (m) REVERT: D 165 MET cc_start: 0.8945 (ttp) cc_final: 0.8656 (ttt) REVERT: E 12 LEU cc_start: 0.7622 (mt) cc_final: 0.7330 (tt) REVERT: E 15 SER cc_start: 0.7853 (m) cc_final: 0.7644 (m) REVERT: E 80 SER cc_start: 0.8777 (m) cc_final: 0.8264 (p) REVERT: E 144 GLU cc_start: 0.7565 (tt0) cc_final: 0.7050 (mm-30) REVERT: E 168 ASP cc_start: 0.8134 (t0) cc_final: 0.7500 (m-30) REVERT: E 191 ASP cc_start: 0.7939 (t70) cc_final: 0.7407 (t70) REVERT: F 46 LYS cc_start: 0.8100 (tptm) cc_final: 0.7529 (mptt) REVERT: F 82 TYR cc_start: 0.8124 (t80) cc_final: 0.7882 (m-80) REVERT: F 84 ILE cc_start: 0.8965 (tp) cc_final: 0.8618 (tp) REVERT: F 88 VAL cc_start: 0.9178 (t) cc_final: 0.8965 (p) REVERT: F 97 GLU cc_start: 0.8141 (tp30) cc_final: 0.7726 (tp30) REVERT: F 100 GLU cc_start: 0.8745 (tt0) cc_final: 0.8539 (tp30) REVERT: F 101 ARG cc_start: 0.8740 (ttp-110) cc_final: 0.8526 (mtp-110) REVERT: F 105 ILE cc_start: 0.8539 (pt) cc_final: 0.8105 (tt) REVERT: F 143 ASP cc_start: 0.7073 (m-30) cc_final: 0.6585 (t0) REVERT: F 166 ARG cc_start: 0.7844 (ttm110) cc_final: 0.7603 (ttm170) REVERT: G 43 LYS cc_start: 0.7353 (mttt) cc_final: 0.6800 (mmtt) REVERT: G 47 ASN cc_start: 0.8343 (m-40) cc_final: 0.8053 (t0) REVERT: G 93 TYR cc_start: 0.7777 (m-10) cc_final: 0.7463 (m-80) REVERT: G 131 VAL cc_start: 0.9093 (t) cc_final: 0.8885 (p) REVERT: I 116 MET cc_start: -0.0048 (mmp) cc_final: -0.0545 (mpp) REVERT: H 2 GLN cc_start: 0.8149 (mm-40) cc_final: 0.7902 (mm-40) REVERT: J 2 LYS cc_start: 0.8482 (mtpp) cc_final: 0.8278 (mtmt) REVERT: J 36 LEU cc_start: 0.8927 (mt) cc_final: 0.8525 (mp) REVERT: J 57 LEU cc_start: 0.9110 (pp) cc_final: 0.8795 (mp) REVERT: J 58 ASN cc_start: 0.8686 (t0) cc_final: 0.8147 (t0) REVERT: J 74 TYR cc_start: 0.8876 (m-80) cc_final: 0.7598 (m-80) REVERT: K 56 ASP cc_start: 0.8088 (m-30) cc_final: 0.7687 (t0) REVERT: K 71 ARG cc_start: 0.8530 (mmt90) cc_final: 0.8284 (mmm-85) REVERT: K 99 ILE cc_start: 0.8591 (mt) cc_final: 0.8369 (mm) REVERT: L 55 MET cc_start: 0.8740 (tpp) cc_final: 0.8437 (tpp) REVERT: L 60 ARG cc_start: 0.8566 (mtm110) cc_final: 0.8118 (mtm180) REVERT: L 63 LYS cc_start: 0.8683 (ptpt) cc_final: 0.8470 (mtpt) REVERT: M 22 GLN cc_start: 0.8354 (mm-40) cc_final: 0.8046 (mm-40) REVERT: M 38 ARG cc_start: 0.8366 (ttm-80) cc_final: 0.7741 (ttm-80) REVERT: M 59 ARG cc_start: 0.8515 (ptt90) cc_final: 0.7722 (mmm160) REVERT: M 110 GLU cc_start: 0.7876 (tm-30) cc_final: 0.7527 (tp30) REVERT: M 133 LYS cc_start: 0.8432 (ttpp) cc_final: 0.8225 (tttp) REVERT: N 79 LEU cc_start: 0.8710 (mt) cc_final: 0.8457 (mt) REVERT: N 116 VAL cc_start: 0.8614 (t) cc_final: 0.8294 (m) REVERT: O 12 THR cc_start: 0.8679 (m) cc_final: 0.8448 (p) REVERT: O 13 ARG cc_start: 0.8645 (tpt170) cc_final: 0.7951 (tpp80) REVERT: O 16 ARG cc_start: 0.8870 (mmt-90) cc_final: 0.8391 (mmm160) REVERT: O 35 ILE cc_start: 0.8787 (tp) cc_final: 0.8518 (tp) REVERT: O 46 GLU cc_start: 0.6867 (pm20) cc_final: 0.6571 (tt0) REVERT: O 49 VAL cc_start: 0.8086 (t) cc_final: 0.7731 (p) REVERT: O 63 LYS cc_start: 0.7480 (tttm) cc_final: 0.7246 (pttt) REVERT: O 64 TYR cc_start: 0.7246 (t80) cc_final: 0.6995 (t80) REVERT: O 76 LYS cc_start: 0.7742 (ttpt) cc_final: 0.7527 (tppt) REVERT: O 94 ARG cc_start: 0.8825 (mtm110) cc_final: 0.8576 (mtp85) REVERT: P 13 LYS cc_start: 0.7512 (ptpt) cc_final: 0.7134 (pttt) REVERT: P 38 ARG cc_start: 0.7982 (ttt90) cc_final: 0.7492 (mtm110) REVERT: P 71 ARG cc_start: 0.7738 (ttt180) cc_final: 0.7158 (ttt-90) REVERT: Q 31 TYR cc_start: 0.9169 (t80) cc_final: 0.8894 (t80) REVERT: Q 44 TYR cc_start: 0.9105 (m-10) cc_final: 0.8902 (m-80) REVERT: R 7 SER cc_start: 0.8729 (t) cc_final: 0.8423 (p) REVERT: R 12 HIS cc_start: 0.8290 (m-70) cc_final: 0.8029 (m90) REVERT: R 19 THR cc_start: 0.8502 (t) cc_final: 0.8298 (m) REVERT: R 24 LYS cc_start: 0.8649 (ttpp) cc_final: 0.8171 (ptmm) REVERT: R 45 GLU cc_start: 0.7753 (tm-30) cc_final: 0.7104 (pm20) REVERT: R 46 GLU cc_start: 0.7880 (tm-30) cc_final: 0.7517 (tm-30) REVERT: R 47 VAL cc_start: 0.9099 (t) cc_final: 0.8675 (m) REVERT: S 59 GLU cc_start: 0.8298 (pt0) cc_final: 0.7971 (tp30) REVERT: S 92 ARG cc_start: 0.8434 (ptp90) cc_final: 0.8148 (mtm180) REVERT: T 6 ARG cc_start: 0.8195 (tpt90) cc_final: 0.7765 (ttm170) REVERT: T 33 LYS cc_start: 0.8336 (ptmt) cc_final: 0.8102 (ptpp) REVERT: T 40 LYS cc_start: 0.8615 (mttt) cc_final: 0.8309 (mttt) REVERT: T 80 TRP cc_start: 0.9234 (p-90) cc_final: 0.8348 (p-90) REVERT: T 88 LYS cc_start: 0.7648 (mtmm) cc_final: 0.7147 (mttt) REVERT: U 64 ILE cc_start: 0.9232 (tt) cc_final: 0.8946 (pt) REVERT: U 90 LYS cc_start: 0.7840 (mmtp) cc_final: 0.7210 (mttp) REVERT: V 38 LEU cc_start: 0.9061 (tp) cc_final: 0.8641 (mt) REVERT: V 48 MET cc_start: 0.8874 (tpt) cc_final: 0.8667 (tpp) REVERT: V 66 ASP cc_start: 0.8201 (m-30) cc_final: 0.7958 (p0) REVERT: W 19 VAL cc_start: 0.8521 (t) cc_final: 0.8270 (t) REVERT: W 28 LEU cc_start: 0.8571 (mt) cc_final: 0.8101 (mp) REVERT: X 39 VAL cc_start: 0.8719 (t) cc_final: 0.8433 (p) REVERT: X 41 SER cc_start: 0.7875 (p) cc_final: 0.7315 (p) REVERT: X 61 LYS cc_start: 0.8692 (mtmt) cc_final: 0.8462 (mtpt) REVERT: X 65 THR cc_start: 0.8671 (m) cc_final: 0.8431 (m) REVERT: X 76 LYS cc_start: 0.7817 (tttt) cc_final: 0.7221 (mtmm) REVERT: Y 17 GLU cc_start: 0.8525 (tp30) cc_final: 0.8064 (tp30) REVERT: Y 21 LEU cc_start: 0.8450 (mt) cc_final: 0.8134 (mp) REVERT: Y 27 ASN cc_start: 0.7815 (m110) cc_final: 0.7419 (m-40) REVERT: Y 56 LEU cc_start: 0.8626 (mt) cc_final: 0.8193 (mp) REVERT: Y 59 GLU cc_start: 0.8169 (tt0) cc_final: 0.7751 (mt-10) REVERT: Z 7 THR cc_start: 0.8477 (m) cc_final: 0.7926 (p) REVERT: Z 34 THR cc_start: 0.8269 (m) cc_final: 0.7990 (t) REVERT: 0 39 ARG cc_start: 0.9057 (mmm160) cc_final: 0.8841 (mmm160) REVERT: 1 5 ARG cc_start: 0.7342 (ttt90) cc_final: 0.6646 (ttt90) REVERT: 1 7 LYS cc_start: 0.8428 (ptpt) cc_final: 0.8108 (mtmt) REVERT: 1 46 VAL cc_start: 0.8785 (t) cc_final: 0.8473 (m) REVERT: 2 14 ARG cc_start: 0.8988 (mmt90) cc_final: 0.8627 (mmm-85) REVERT: 2 22 MET cc_start: 0.8640 (mmm) cc_final: 0.8407 (mmm) REVERT: 3 2 LYS cc_start: 0.9032 (ptpt) cc_final: 0.8720 (ptmt) REVERT: 6 12 ILE cc_start: 0.7692 (pt) cc_final: 0.7108 (pt) REVERT: 6 41 HIS cc_start: 0.7691 (t-90) cc_final: 0.7348 (t70) REVERT: 6 62 LYS cc_start: 0.8436 (mtpt) cc_final: 0.8214 (tppt) outliers start: 22 outliers final: 5 residues processed: 2419 average time/residue: 1.4612 time to fit residues: 5910.7496 Evaluate side-chains 1722 residues out of total 4751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 1713 time to evaluate : 6.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain h residue 103 VAL Chi-restraints excluded: chain i residue 60 LEU Chi-restraints excluded: chain l residue 33 CYS Chi-restraints excluded: chain p residue 36 VAL Chi-restraints excluded: chain q residue 4 ILE Chi-restraints excluded: chain s residue 4 LEU Chi-restraints excluded: chain s residue 48 ILE Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain X residue 4 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1025 random chunks: chunk 865 optimal weight: 0.9980 chunk 776 optimal weight: 20.0000 chunk 431 optimal weight: 20.0000 chunk 265 optimal weight: 8.9990 chunk 524 optimal weight: 9.9990 chunk 415 optimal weight: 20.0000 chunk 803 optimal weight: 30.0000 chunk 310 optimal weight: 0.7980 chunk 488 optimal weight: 10.0000 chunk 597 optimal weight: 10.0000 chunk 930 optimal weight: 6.9990 overall best weight: 5.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 57 ASN c 40 GLN c 122 GLN ** d 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 134 ASN e 145 ASN e 147 ASN f 11 HIS f 63 ASN ** h 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 31 GLN i 36 GLN i 80 HIS j 64 GLN l 5 GLN ** m 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 73 HIS t 47 GLN t 67 HIS C 44 ASN C 225 ASN D 36 GLN D 150 GLN E 29 HIS E 41 GLN E 97 ASN F 20 ASN G 21 GLN ** H 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 43 ASN K 3 GLN ** K 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 88 ASN ** L 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 18 GLN N 62 ASN N 81 ASN O 38 GLN ** P 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 36 GLN Q 80 ASN R 6 GLN R 18 GLN R 66 HIS ** U 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 87 GLN ** V 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 8 ASN X 16 ASN Y 20 ASN 1 45 HIS 4 35 GLN Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.2001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.130 158717 Z= 0.249 Angle : 0.711 14.291 237544 Z= 0.377 Chirality : 0.037 0.338 30271 Planarity : 0.007 0.126 12696 Dihedral : 23.581 179.581 79548 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.66 % Allowed : 6.89 % Favored : 92.44 % Rotamer: Outliers : 4.70 % Allowed : 15.14 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.34 % 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: -1.96 (0.10), residues: 5717 helix: -0.71 (0.11), residues: 1869 sheet: -2.74 (0.13), residues: 1010 loop : -1.01 (0.12), residues: 2838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP b 22 HIS 0.012 0.001 HIS O 34 PHE 0.054 0.002 PHE u 36 TYR 0.021 0.002 TYR E 35 ARG 0.014 0.001 ARG g 110 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11434 Ramachandran restraints generated. 5717 Oldfield, 0 Emsley, 5717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11434 Ramachandran restraints generated. 5717 Oldfield, 0 Emsley, 5717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2050 residues out of total 4751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 222 poor density : 1828 time to evaluate : 5.818 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: b 14 HIS cc_start: 0.7181 (p-80) cc_final: 0.6974 (p-80) REVERT: b 29 PHE cc_start: 0.7105 (m-80) cc_final: 0.6684 (m-80) REVERT: b 65 LYS cc_start: 0.7021 (mttp) cc_final: 0.6751 (mttp) REVERT: b 114 LYS cc_start: 0.7587 (ttmt) cc_final: 0.7250 (tptt) REVERT: b 117 GLU cc_start: 0.7253 (pt0) cc_final: 0.6466 (pp20) REVERT: b 139 GLU cc_start: 0.7809 (mm-30) cc_final: 0.7343 (mt-10) REVERT: b 174 GLU cc_start: 0.8091 (tt0) cc_final: 0.7065 (tt0) REVERT: b 212 TYR cc_start: 0.8025 (m-80) cc_final: 0.7415 (m-80) REVERT: c 45 GLU cc_start: 0.9064 (mm-30) cc_final: 0.8534 (mm-30) REVERT: c 46 LEU cc_start: 0.8551 (mm) cc_final: 0.8342 (mp) REVERT: c 129 PHE cc_start: 0.8746 (p90) cc_final: 0.8492 (p90) REVERT: c 146 LYS cc_start: 0.8836 (mmmt) cc_final: 0.8618 (tptp) REVERT: c 189 HIS cc_start: 0.7992 (m-70) cc_final: 0.7336 (m90) REVERT: d 32 LYS cc_start: 0.7389 (mttt) cc_final: 0.7175 (mttm) REVERT: d 59 LYS cc_start: 0.9018 (tttt) cc_final: 0.8783 (ttpt) REVERT: d 69 ARG cc_start: 0.8695 (mmm160) cc_final: 0.8340 (mmm160) REVERT: d 77 GLU cc_start: 0.8443 (tp30) cc_final: 0.8124 (tp30) REVERT: d 82 LYS cc_start: 0.8109 (pttt) cc_final: 0.7801 (mmmt) REVERT: d 116 LEU cc_start: 0.8492 (tp) cc_final: 0.8154 (tt) REVERT: d 139 ASN cc_start: 0.7971 (t0) cc_final: 0.7432 (p0) REVERT: e 19 ARG cc_start: 0.8026 (ptt90) cc_final: 0.7715 (ptt-90) REVERT: e 60 GLN cc_start: 0.9039 (mm-40) cc_final: 0.8540 (mm-40) REVERT: e 69 ASN cc_start: 0.7642 (t0) cc_final: 0.6960 (t0) REVERT: e 85 LYS cc_start: 0.8802 (mttt) cc_final: 0.8448 (mttm) REVERT: e 94 PHE cc_start: 0.8928 (t80) cc_final: 0.8573 (t80) REVERT: e 115 GLU cc_start: 0.8593 (mt-10) cc_final: 0.8313 (mt-10) REVERT: e 121 ASN cc_start: 0.7454 (m-40) cc_final: 0.7228 (m-40) REVERT: f 42 TRP cc_start: 0.6921 (m100) cc_final: 0.6684 (m100) REVERT: f 46 GLN cc_start: 0.8250 (tt0) cc_final: 0.7928 (tp40) REVERT: f 49 TYR cc_start: 0.8462 (p90) cc_final: 0.8226 (p90) REVERT: g 49 LEU cc_start: 0.8327 (tp) cc_final: 0.8091 (mp) REVERT: g 85 GLN cc_start: 0.7660 (mm-40) cc_final: 0.7414 (mm-40) REVERT: g 105 GLU cc_start: 0.7691 (tp30) cc_final: 0.7101 (tp30) REVERT: g 109 LYS cc_start: 0.7883 (mptt) cc_final: 0.7112 (mmtt) REVERT: g 115 MET cc_start: 0.7426 (tpt) cc_final: 0.6917 (tpp) REVERT: g 122 GLU cc_start: 0.8206 (mm-30) cc_final: 0.7796 (tp30) REVERT: g 142 ARG cc_start: 0.7913 (mmt-90) cc_final: 0.6363 (tpt-90) REVERT: g 143 MET cc_start: 0.6700 (mmp) cc_final: 0.6454 (tpt) REVERT: h 90 GLU cc_start: 0.7891 (mp0) cc_final: 0.7681 (mp0) REVERT: i 17 ARG cc_start: 0.8166 (mtp-110) cc_final: 0.7710 (mtp180) REVERT: i 44 ARG cc_start: 0.8326 (ptt-90) cc_final: 0.7710 (pmt170) REVERT: i 60 LEU cc_start: 0.8337 (OUTLIER) cc_final: 0.7966 (pp) REVERT: i 79 ARG cc_start: 0.8947 (tmm-80) cc_final: 0.8516 (ttm-80) REVERT: i 119 LYS cc_start: 0.8875 (ptpt) cc_final: 0.8570 (pttt) REVERT: i 127 SER cc_start: 0.8411 (t) cc_final: 0.7967 (p) REVERT: j 6 ILE cc_start: 0.8679 (mt) cc_final: 0.8355 (pt) REVERT: j 88 MET cc_start: 0.7598 (ttp) cc_final: 0.7020 (tpt) REVERT: k 68 ARG cc_start: 0.7917 (mtp180) cc_final: 0.7366 (tpt170) REVERT: l 66 ILE cc_start: 0.8629 (mt) cc_final: 0.8304 (mp) REVERT: l 88 ASP cc_start: 0.8306 (t0) cc_final: 0.7982 (t0) REVERT: m 12 LYS cc_start: 0.7172 (mttt) cc_final: 0.6784 (mptt) REVERT: m 58 GLU cc_start: 0.7948 (tp30) cc_final: 0.6629 (mt-10) REVERT: n 41 TRP cc_start: 0.9079 (t-100) cc_final: 0.8730 (t60) REVERT: n 42 ASN cc_start: 0.8340 (m-40) cc_final: 0.7984 (p0) REVERT: o 9 LYS cc_start: 0.8997 (ttpt) cc_final: 0.8260 (tppt) REVERT: o 57 ARG cc_start: 0.8637 (ttm170) cc_final: 0.8393 (ttm170) REVERT: o 77 TYR cc_start: 0.8465 (t80) cc_final: 0.8154 (t80) REVERT: p 23 ASP cc_start: 0.8240 (t0) cc_final: 0.7957 (t0) REVERT: p 63 GLN cc_start: 0.7506 (mm-40) cc_final: 0.7086 (mt0) REVERT: p 66 THR cc_start: 0.8950 (m) cc_final: 0.8275 (p) REVERT: q 10 ARG cc_start: 0.7830 (mtm180) cc_final: 0.7605 (mtp180) REVERT: q 16 MET cc_start: 0.7683 (ptm) cc_final: 0.7337 (tmm) REVERT: q 38 LYS cc_start: 0.8546 (mmtt) cc_final: 0.8115 (ttmt) REVERT: q 39 ARG cc_start: 0.8718 (mmt90) cc_final: 0.8485 (ttm110) REVERT: q 64 ARG cc_start: 0.7682 (ttp-110) cc_final: 0.7297 (ttp-170) REVERT: r 65 SER cc_start: 0.9397 (m) cc_final: 0.9195 (t) REVERT: s 4 LEU cc_start: 0.6333 (OUTLIER) cc_final: 0.6114 (pt) REVERT: s 20 LYS cc_start: 0.8262 (ttpp) cc_final: 0.7432 (mmtm) REVERT: s 55 GLN cc_start: 0.7543 (pm20) cc_final: 0.7115 (pm20) REVERT: t 59 ARG cc_start: 0.8768 (ttm110) cc_final: 0.8554 (ptp-110) REVERT: u 21 SER cc_start: 0.7279 (t) cc_final: 0.6882 (p) REVERT: u 32 ARG cc_start: 0.8707 (ptt180) cc_final: 0.8283 (mmm160) REVERT: u 33 ARG cc_start: 0.7943 (tmm160) cc_final: 0.7678 (tmm160) REVERT: u 37 TYR cc_start: 0.7551 (t80) cc_final: 0.7153 (t80) REVERT: C 4 LYS cc_start: 0.8970 (ttpt) cc_final: 0.8352 (mttm) REVERT: C 17 LYS cc_start: 0.8433 (mtmt) cc_final: 0.8059 (mtmm) REVERT: C 63 ILE cc_start: 0.9005 (mp) cc_final: 0.8558 (tt) REVERT: C 124 LYS cc_start: 0.8506 (tttt) cc_final: 0.8252 (mtmt) REVERT: C 166 ARG cc_start: 0.8161 (mtm180) cc_final: 0.7849 (mtt180) REVERT: C 180 MET cc_start: 0.8836 (mmm) cc_final: 0.8572 (mpp) REVERT: C 202 ARG cc_start: 0.8609 (ttm170) cc_final: 0.8402 (mtp85) REVERT: C 203 VAL cc_start: 0.8266 (m) cc_final: 0.8018 (p) REVERT: C 213 ARG cc_start: 0.8678 (tpp-160) cc_final: 0.8388 (mmt90) REVERT: C 266 ILE cc_start: 0.8968 (mt) cc_final: 0.8513 (pt) REVERT: D 59 ARG cc_start: 0.7493 (tpp-160) cc_final: 0.6695 (mmt-90) REVERT: D 89 GLU cc_start: 0.7920 (tp30) cc_final: 0.7428 (mp0) REVERT: D 90 PHE cc_start: 0.8768 (m-10) cc_final: 0.8534 (m-10) REVERT: D 99 GLU cc_start: 0.8111 (mt-10) cc_final: 0.7892 (mt-10) REVERT: D 100 LEU cc_start: 0.8099 (mp) cc_final: 0.7714 (tt) REVERT: E 2 GLU cc_start: 0.6918 (pm20) cc_final: 0.6608 (pm20) REVERT: E 4 VAL cc_start: 0.7893 (m) cc_final: 0.7670 (p) REVERT: E 80 SER cc_start: 0.8482 (m) cc_final: 0.8223 (p) REVERT: E 143 LEU cc_start: 0.8726 (mt) cc_final: 0.8417 (mt) REVERT: E 162 ARG cc_start: 0.8414 (ttp-170) cc_final: 0.8173 (ttm170) REVERT: E 168 ASP cc_start: 0.8197 (t0) cc_final: 0.7594 (m-30) REVERT: F 84 ILE cc_start: 0.8667 (tp) cc_final: 0.8322 (tp) REVERT: F 105 ILE cc_start: 0.8535 (pt) cc_final: 0.8330 (mp) REVERT: F 163 GLU cc_start: 0.8665 (tm-30) cc_final: 0.8415 (tm-30) REVERT: G 120 ILE cc_start: 0.8304 (mm) cc_final: 0.7958 (pt) REVERT: I 85 ILE cc_start: 0.1582 (OUTLIER) cc_final: 0.0978 (tp) REVERT: H 22 LYS cc_start: 0.6831 (mmtt) cc_final: 0.6509 (mttp) REVERT: J 58 ASN cc_start: 0.8591 (t0) cc_final: 0.8116 (t0) REVERT: J 74 TYR cc_start: 0.8771 (m-80) cc_final: 0.7611 (m-80) REVERT: J 81 ILE cc_start: 0.8758 (tp) cc_final: 0.8527 (tp) REVERT: J 135 GLN cc_start: 0.8531 (mp10) cc_final: 0.8226 (mp10) REVERT: J 136 GLN cc_start: 0.7858 (tm-30) cc_final: 0.7544 (tm-30) REVERT: K 56 ASP cc_start: 0.8188 (m-30) cc_final: 0.7684 (t0) REVERT: K 71 ARG cc_start: 0.8469 (mmt90) cc_final: 0.8023 (mmt180) REVERT: L 105 ILE cc_start: 0.8998 (mm) cc_final: 0.8784 (tp) REVERT: M 51 ARG cc_start: 0.8762 (mtm110) cc_final: 0.8426 (mtm180) REVERT: M 59 ARG cc_start: 0.8498 (ptt90) cc_final: 0.7756 (mmp80) REVERT: M 68 PHE cc_start: 0.8922 (t80) cc_final: 0.8674 (t80) REVERT: M 105 MET cc_start: 0.9071 (ttm) cc_final: 0.8794 (mtp) REVERT: M 106 ASP cc_start: 0.8837 (t70) cc_final: 0.8571 (t0) REVERT: N 1 MET cc_start: 0.8171 (ptp) cc_final: 0.7928 (mtm) REVERT: N 21 PHE cc_start: 0.8806 (m-10) cc_final: 0.8397 (m-10) REVERT: N 116 VAL cc_start: 0.8829 (t) cc_final: 0.8525 (m) REVERT: O 13 ARG cc_start: 0.8914 (tpt170) cc_final: 0.8177 (tpp80) REVERT: O 34 HIS cc_start: 0.8015 (m-70) cc_final: 0.7690 (m-70) REVERT: O 98 GLN cc_start: 0.8388 (tp40) cc_final: 0.7934 (tp40) REVERT: P 6 GLN cc_start: 0.7366 (tm-30) cc_final: 0.7119 (tm-30) REVERT: P 9 GLN cc_start: 0.7392 (pm20) cc_final: 0.7010 (pm20) REVERT: P 13 LYS cc_start: 0.7639 (ptpt) cc_final: 0.6911 (pttt) REVERT: P 28 LYS cc_start: 0.8770 (mtpp) cc_final: 0.8512 (mtpp) REVERT: P 38 ARG cc_start: 0.8016 (ttt90) cc_final: 0.7762 (ttp80) REVERT: P 74 GLN cc_start: 0.8657 (mm-40) cc_final: 0.8455 (mm-40) REVERT: Q 44 TYR cc_start: 0.9063 (m-10) cc_final: 0.8682 (m-80) REVERT: R 26 ASP cc_start: 0.8253 (p0) cc_final: 0.7928 (p0) REVERT: R 45 GLU cc_start: 0.7800 (tm-30) cc_final: 0.7082 (pm20) REVERT: R 47 VAL cc_start: 0.9004 (t) cc_final: 0.8788 (m) REVERT: R 84 ARG cc_start: 0.8724 (ttp80) cc_final: 0.8523 (ttp80) REVERT: T 6 ARG cc_start: 0.8221 (tpt90) cc_final: 0.7798 (ttm170) REVERT: T 9 LYS cc_start: 0.9193 (mttm) cc_final: 0.8422 (mmmt) REVERT: T 12 ARG cc_start: 0.8344 (tpp-160) cc_final: 0.7910 (mmt180) REVERT: T 33 LYS cc_start: 0.8312 (ptmt) cc_final: 0.8054 (ptpp) REVERT: T 56 GLU cc_start: 0.8481 (mm-30) cc_final: 0.8278 (tm-30) REVERT: T 80 TRP cc_start: 0.9209 (p-90) cc_final: 0.8460 (p-90) REVERT: U 16 LYS cc_start: 0.8733 (ptmt) cc_final: 0.8234 (pttt) REVERT: V 18 ARG cc_start: 0.8686 (mtt90) cc_final: 0.8480 (mtt90) REVERT: V 56 PHE cc_start: 0.8398 (t80) cc_final: 0.8114 (t80) REVERT: V 66 ASP cc_start: 0.8279 (m-30) cc_final: 0.7940 (p0) REVERT: V 85 LYS cc_start: 0.8291 (ptpt) cc_final: 0.7875 (pttp) REVERT: X 76 LYS cc_start: 0.7861 (tttt) cc_final: 0.7230 (mtmm) REVERT: Y 4 LYS cc_start: 0.8959 (mtmm) cc_final: 0.8055 (mtmm) REVERT: Y 17 GLU cc_start: 0.8548 (tp30) cc_final: 0.8178 (tp30) REVERT: Y 21 LEU cc_start: 0.8353 (mt) cc_final: 0.7981 (mt) REVERT: Y 27 ASN cc_start: 0.8061 (m110) cc_final: 0.7842 (m110) REVERT: Y 59 GLU cc_start: 0.8134 (tt0) cc_final: 0.7812 (mt-10) REVERT: Z 7 THR cc_start: 0.8620 (m) cc_final: 0.8126 (p) REVERT: 0 30 ASP cc_start: 0.7815 (t0) cc_final: 0.7542 (t0) REVERT: 1 5 ARG cc_start: 0.6713 (ttt90) cc_final: 0.6479 (ttt90) REVERT: 1 7 LYS cc_start: 0.8577 (ptpt) cc_final: 0.8204 (mtmt) REVERT: 2 14 ARG cc_start: 0.8938 (mmt90) cc_final: 0.8541 (mmm-85) REVERT: 3 14 LYS cc_start: 0.9131 (mmmt) cc_final: 0.8893 (mmmt) REVERT: 3 41 ARG cc_start: 0.8882 (mtm110) cc_final: 0.8601 (ttm-80) REVERT: 6 39 LYS cc_start: 0.7843 (mmtm) cc_final: 0.7477 (mttt) outliers start: 222 outliers final: 150 residues processed: 1920 average time/residue: 1.1613 time to fit residues: 3803.4681 Evaluate side-chains 1765 residues out of total 4751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 1612 time to evaluate : 5.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 57 ASN Chi-restraints excluded: chain b residue 69 VAL Chi-restraints excluded: chain b residue 166 ASP Chi-restraints excluded: chain b residue 170 ILE Chi-restraints excluded: chain b residue 195 VAL Chi-restraints excluded: chain b residue 220 VAL Chi-restraints excluded: chain c residue 32 LEU Chi-restraints excluded: chain c residue 34 SER Chi-restraints excluded: chain c residue 63 ILE Chi-restraints excluded: chain c residue 110 LEU Chi-restraints excluded: chain c residue 176 THR Chi-restraints excluded: chain c residue 190 THR Chi-restraints excluded: chain d residue 33 ILE Chi-restraints excluded: chain d residue 184 LYS Chi-restraints excluded: chain e residue 36 THR Chi-restraints excluded: chain e residue 47 PHE Chi-restraints excluded: chain e residue 72 ASN Chi-restraints excluded: chain e residue 147 ASN Chi-restraints excluded: chain f residue 30 THR Chi-restraints excluded: chain f residue 64 VAL Chi-restraints excluded: chain f residue 96 VAL Chi-restraints excluded: chain g residue 74 VAL Chi-restraints excluded: chain g residue 119 LEU Chi-restraints excluded: chain h residue 33 VAL Chi-restraints excluded: chain h residue 78 SER Chi-restraints excluded: chain h residue 103 VAL Chi-restraints excluded: chain i residue 60 LEU Chi-restraints excluded: chain j residue 32 THR Chi-restraints excluded: chain j residue 42 LEU Chi-restraints excluded: chain j residue 51 VAL Chi-restraints excluded: chain j residue 52 LEU Chi-restraints excluded: chain j residue 67 ILE Chi-restraints excluded: chain k residue 69 CYS Chi-restraints excluded: chain k residue 108 ASN Chi-restraints excluded: chain l residue 6 LEU Chi-restraints excluded: chain l residue 32 VAL Chi-restraints excluded: chain l residue 39 THR Chi-restraints excluded: chain l residue 40 THR Chi-restraints excluded: chain l residue 77 SER Chi-restraints excluded: chain m residue 6 ILE Chi-restraints excluded: chain m residue 82 LEU Chi-restraints excluded: chain n residue 73 LEU Chi-restraints excluded: chain o residue 26 VAL Chi-restraints excluded: chain o residue 56 LEU Chi-restraints excluded: chain p residue 19 VAL Chi-restraints excluded: chain q residue 24 ILE Chi-restraints excluded: chain q residue 56 ASP Chi-restraints excluded: chain q residue 58 VAL Chi-restraints excluded: chain q residue 63 CYS Chi-restraints excluded: chain r residue 25 ILE Chi-restraints excluded: chain r residue 41 SER Chi-restraints excluded: chain s residue 4 LEU Chi-restraints excluded: chain s residue 59 VAL Chi-restraints excluded: chain s residue 78 THR Chi-restraints excluded: chain t residue 27 MET Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 139 SER Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 154 ASP Chi-restraints excluded: chain E residue 165 HIS Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 168 LEU Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 138 GLN Chi-restraints excluded: chain I residue 85 ILE Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 14 SER Chi-restraints excluded: chain K residue 21 CYS Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 90 ASN Chi-restraints excluded: chain K residue 111 LYS Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 111 ILE Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain L residue 128 THR Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 42 THR Chi-restraints excluded: chain M residue 93 VAL Chi-restraints excluded: chain M residue 126 ILE Chi-restraints excluded: chain M residue 135 VAL Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 107 ASN Chi-restraints excluded: chain O residue 62 LEU Chi-restraints excluded: chain P residue 40 GLN Chi-restraints excluded: chain P residue 72 VAL Chi-restraints excluded: chain P residue 77 SER Chi-restraints excluded: chain P residue 92 ARG Chi-restraints excluded: chain P residue 101 GLU Chi-restraints excluded: chain Q residue 79 ILE Chi-restraints excluded: chain Q residue 99 VAL Chi-restraints excluded: chain R residue 15 SER Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 32 THR Chi-restraints excluded: chain R residue 66 HIS Chi-restraints excluded: chain S residue 3 THR Chi-restraints excluded: chain S residue 19 LEU Chi-restraints excluded: chain S residue 42 LYS Chi-restraints excluded: chain S residue 49 LYS Chi-restraints excluded: chain S residue 61 ASN Chi-restraints excluded: chain S residue 77 ASP Chi-restraints excluded: chain S residue 85 ILE Chi-restraints excluded: chain T residue 10 VAL Chi-restraints excluded: chain T residue 16 VAL Chi-restraints excluded: chain T residue 29 THR Chi-restraints excluded: chain T residue 30 ILE Chi-restraints excluded: chain T residue 39 THR Chi-restraints excluded: chain T residue 60 THR Chi-restraints excluded: chain U residue 30 SER Chi-restraints excluded: chain U residue 35 VAL Chi-restraints excluded: chain V residue 3 THR Chi-restraints excluded: chain V residue 11 GLU Chi-restraints excluded: chain V residue 17 SER Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain W residue 31 SER Chi-restraints excluded: chain Y residue 6 LEU Chi-restraints excluded: chain Z residue 40 THR Chi-restraints excluded: chain Z residue 51 SER Chi-restraints excluded: chain Z residue 57 GLU Chi-restraints excluded: chain 0 residue 2 VAL Chi-restraints excluded: chain 0 residue 29 VAL Chi-restraints excluded: chain 0 residue 38 LEU Chi-restraints excluded: chain 3 residue 5 THR Chi-restraints excluded: chain 3 residue 53 ASP Chi-restraints excluded: chain 4 residue 1 MET Chi-restraints excluded: chain 4 residue 6 SER Chi-restraints excluded: chain 4 residue 22 VAL Chi-restraints excluded: chain 4 residue 28 SER Chi-restraints excluded: chain 6 residue 27 THR Chi-restraints excluded: chain 6 residue 57 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1025 random chunks: chunk 517 optimal weight: 10.0000 chunk 288 optimal weight: 9.9990 chunk 774 optimal weight: 30.0000 chunk 633 optimal weight: 20.0000 chunk 256 optimal weight: 8.9990 chunk 932 optimal weight: 30.0000 chunk 1007 optimal weight: 10.0000 chunk 830 optimal weight: 4.9990 chunk 924 optimal weight: 9.9990 chunk 317 optimal weight: 10.0000 chunk 748 optimal weight: 10.0000 overall best weight: 8.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/mod