Starting phenix.real_space_refine (version: dev) on Tue Apr 12 19:50:54 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9y_6311/04_2022/3j9y_6311_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9y_6311/04_2022/3j9y_6311.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9y_6311/04_2022/3j9y_6311_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9y_6311/04_2022/3j9y_6311_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9y_6311/04_2022/3j9y_6311_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9y_6311/04_2022/3j9y_6311.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9y_6311/04_2022/3j9y_6311.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9y_6311/04_2022/3j9y_6311_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9y_6311/04_2022/3j9y_6311_updated.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "b PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 107": "NH1" <-> "NH2" Residue "b PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 224": "NH1" <-> "NH2" Residue "e PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ARG 156": "NH1" <-> "NH2" Residue "f TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k ASP 111": "OD1" <-> "OD2" Residue "l TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ARG 55": "NH1" <-> "NH2" Residue "l PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p ARG 28": "NH1" <-> "NH2" Residue "p PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r TYR 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u PHE 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w TYR 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 106": "NH1" <-> "NH2" Residue "c PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 130": "NH1" <-> "NH2" Residue "g PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ARG 123": "NH1" <-> "NH2" Residue "C PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 265": "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 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 TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 102": "NH1" <-> "NH2" Residue "E ARG 162": "NH1" <-> "NH2" Residue "E ARG 170": "NH1" <-> "NH2" Residue "E PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 70": "NH1" <-> "NH2" Residue "F ARG 79": "NH1" <-> "NH2" 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 PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 132": "NH1" <-> "NH2" Residue "G ARG 2": "NH1" <-> "NH2" Residue "G PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 152": "NH1" <-> "NH2" Residue "G ARG 162": "NH1" <-> "NH2" Residue "G ARG 169": "NH1" <-> "NH2" Residue "I TYR 7": "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 TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 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 "M PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 ARG 94": "NH1" <-> "NH2" 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 "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 ASP 77": "OD1" <-> "OD2" 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 PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 85": "NH1" <-> "NH2" Residue "U ARG 93": "NH1" <-> "NH2" Residue "U PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 45": "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 "Z PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 "1 TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 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 "5 TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ASP 124": "OD1" <-> "OD2" Residue "6 PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ARG 49": "NH1" <-> "NH2" Residue "6 ARG 56": "NH1" <-> "NH2" Residue "6 PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 148915 Number of models: 1 Model: "" Number of chains: 58 Chain: "a" Number of atoms: 33029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1539, 33029 Classifications: {'RNA': 1539} Modifications used: {'rna3p': 10, 'rna2p_pyr': 42, 'p5*END': 1, 'rna3p_pur': 781, 'rna2p': 1, 'rna3p_pyr': 618, 'rna2p_pur': 87} Link IDs: {'rna3p': 1408, 'rna2p': 130} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 8 Chain: "b" Number of atoms: 1704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1704 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 7, 'TRANS': 210} 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: 1141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1141 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 151} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "f" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 817 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 4, 'TRANS': 95} 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: "k" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 869 Classifications: {'peptide': 116} 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: "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: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 648 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain: "r" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 504 Classifications: {'peptide': 65} 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: "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: 495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 495 Classifications: {'peptide': 65} Incomplete info: {'truncation_to_alanine': 11} 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: {'rna3p': 3, 'rna2p': 1, 'p5*END': 1, 'rna3p_pur': 34, 'rna3p_pyr': 32, 'rna2p_pur': 5, 'rna2p_pyr': 2} Link IDs: {'rna3p': 69, 'rna2p': 7} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 2 Chain: "x" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 189 Classifications: {'RNA': 9} Modifications used: {'rna3p_pyr': 5, 'rna2p_pur': 1, 'rna3p_pur': 3} Link IDs: {'rna3p': 7, 'rna2p': 1} Chain: "w" Number of atoms: 2590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 639, 2590 Classifications: {'peptide': 639} Incomplete info: {'backbone_only': 596} Link IDs: {'CIS': 16, 'PTRANS': 27, 'TRANS': 594, 'PCIS': 1} Unresolved chain link angles: 27 Unresolved non-hydrogen bonds: 2600 Unresolved non-hydrogen angles: 3760 Unresolved non-hydrogen dihedrals: 1640 Unresolved non-hydrogen chiralities: 801 Planarities with less than four sites: {'GLN:plan1': 27, 'HIS:plan': 11, 'TYR:plan': 30, 'ASN:plan1': 31, 'TRP:plan': 3, 'ASP:plan': 27, 'PHE:plan': 20, 'GLU:plan': 52, 'ARG:plan': 28} Unresolved non-hydrogen planarities: 1164 Chain: "c" Number of atoms: 1624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1624 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 6, 'TRANS': 198, 'PCIS': 1} Chain: "g" Number of atoms: 1181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1181 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} 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: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 786 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 5, 'TRANS': 92} Chain: "m" Number of atoms: 883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 883 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 4, 'TRANS': 109} Chain: "n" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 799 Classifications: {'peptide': 101} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 96} 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: "s" Number of atoms: 637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 637 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 5, 'TRANS': 73} Chain: "A" Number of atoms: 62276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2900, 62276 Classifications: {'RNA': 2900} Modifications used: {'rna3p': 17, 'rna2p_pyr': 87, 'p5*END': 1, 'rna3p_pur': 1463, 'rna2p': 7, 'rna3p_pyr': 1123, 'rna2p_pur': 203} Link IDs: {'rna3p': 2602, 'rna2p': 297} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 11 Chain: "B" Number of atoms: 2572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 2572 Classifications: {'RNA': 120} Modifications used: {'rna3p_pyr': 53, 'p5*END': 1, 'rna2p_pur': 3, 'rna3p_pur': 62, 'rna2p_pyr': 2} Link IDs: {'rna3p': 114, 'rna2p': 5} Chain: "C" Number of atoms: 2082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2082 Classifications: {'peptide': 271} 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: 1410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1410 Classifications: {'peptide': 177} 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: "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: "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: "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: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 938 Classifications: {'peptide': 122} 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: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 960 Classifications: {'peptide': 120} 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: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 738 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 1, 'TRANS': 91} Chain: "U" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 779 Classifications: {'peptide': 102} 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: 409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 409 Classifications: {'peptide': 50} 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: "5" Number of atoms: 988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 988 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 5, 'TRANS': 125} Chain: "6" Number of atoms: 522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 522 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "7" Number of atoms: 276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 276 Classifications: {'peptide': 69} Incomplete info: {'backbone_only': 63} Link IDs: {'TRANS': 67, 'PCIS': 1} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 219 Unresolved non-hydrogen angles: 319 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 82 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 9, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 68 Time building chain proxies: 60.31, per 1000 atoms: 0.40 Number of scatterers: 148915 At special positions: 0 Unit cell: (267.028, 278.108, 241.544, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 156 16.00 P 4645 15.00 O 41244 8.00 N 27910 7.00 C 74960 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS 6 18 " - pdb=" SG CYS 6 40 " distance=2.95 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: 55.82 Conformation dependent library (CDL) restraints added in 8.0 seconds 13102 Ramachandran restraints generated. 6551 Oldfield, 0 Emsley, 6551 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10944 Finding SS restraints... Warning!!! ksdssp method is not applicable forstructures with more than 99999 atoms! Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 202 helices and 81 sheets defined 38.6% alpha, 18.2% beta 1390 base pairs and 2553 stacking pairs defined. Time for finding SS restraints: 63.04 Creating SS restraints... Processing helix chain 'b' and resid 42 through 63 Proline residue: b 47 - end of helix Processing helix chain 'b' and resid 72 through 87 removed outlier: 5.073A pdb=" N SER b 76 " --> pdb=" O LYS b 72 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLU b 77 " --> pdb=" O ARG b 73 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ALA b 78 " --> pdb=" O ALA b 74 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N CYS b 86 " --> pdb=" O ALA b 82 " (cutoff:3.500A) Processing helix chain 'b' and resid 102 through 122 removed outlier: 3.903A pdb=" N VAL b 106 " --> pdb=" O ASN b 102 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLN b 108 " --> pdb=" O LYS b 104 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLN b 121 " --> pdb=" O GLU b 117 " (cutoff:3.500A) removed outlier: 3.623A 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: 3.625A pdb=" N ILE b 172 " --> pdb=" O GLU b 168 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASN b 177 " --> pdb=" O LYS b 173 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N LEU b 178 " --> pdb=" O GLU b 174 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N GLY b 179 " --> pdb=" O ALA b 175 " (cutoff:3.500A) Processing helix chain 'b' and resid 205 through 225 removed outlier: 3.609A pdb=" N VAL b 209 " --> pdb=" O ALA b 205 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLY b 223 " --> pdb=" O THR b 219 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ARG b 224 " --> pdb=" O VAL b 220 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N SER b 225 " --> pdb=" O ARG b 221 " (cutoff:3.500A) Processing helix chain 'd' and resid 6 through 15 removed outlier: 4.003A pdb=" N LEU d 10 " --> pdb=" O PRO d 6 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N SER d 11 " --> pdb=" O LYS d 7 " (cutoff:3.500A) Processing helix chain 'd' and resid 48 through 65 Processing helix chain 'd' and resid 67 through 82 removed outlier: 3.626A pdb=" N LEU d 81 " --> pdb=" O GLU d 77 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N LYS d 82 " --> pdb=" O ALA d 78 " (cutoff:3.500A) Processing helix chain 'd' and resid 84 through 96 removed outlier: 3.797A pdb=" N LEU d 90 " --> pdb=" O GLY d 86 " (cutoff:3.500A) removed outlier: 3.547A 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: 3.614A pdb=" N HIS d 119 " --> pdb=" O GLN d 115 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LYS d 120 " --> pdb=" O LEU d 116 " (cutoff:3.500A) Processing helix chain 'd' and resid 151 through 165 removed outlier: 5.466A pdb=" N LYS d 155 " --> pdb=" O GLN d 151 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALA d 156 " --> pdb=" O SER d 152 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ALA d 161 " --> pdb=" O ALA d 157 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLU d 162 " --> pdb=" O LEU d 158 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N GLN d 163 " --> pdb=" O GLU d 159 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ARG d 164 " --> pdb=" O LEU d 160 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N GLU d 165 " --> pdb=" O ALA d 161 " (cutoff:3.500A) Processing helix chain 'd' and resid 186 through 191 removed outlier: 3.892A pdb=" N LEU d 190 " --> pdb=" O GLU d 186 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N SER d 191 " --> pdb=" O ARG d 187 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 186 through 191' Processing helix chain 'd' and resid 195 through 205 removed outlier: 3.831A pdb=" N ILE d 199 " --> pdb=" O ASN d 195 " (cutoff:3.500A) Processing helix chain 'e' and resid 54 through 70 removed outlier: 3.995A pdb=" N GLU e 64 " --> pdb=" O GLN e 60 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N LYS e 65 " --> pdb=" O LYS e 61 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N MET e 70 " --> pdb=" O ALA e 66 " (cutoff:3.500A) Processing helix chain 'e' and resid 108 through 118 removed outlier: 5.307A pdb=" N ALA e 112 " --> pdb=" O GLY e 108 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL e 116 " --> pdb=" O ALA e 112 " (cutoff:3.500A) Processing helix chain 'e' and resid 131 through 147 removed outlier: 5.308A pdb=" N ASN e 147 " --> pdb=" O LEU e 143 " (cutoff:3.500A) Processing helix chain 'e' and resid 148 through 156 removed outlier: 4.069A pdb=" N ALA e 154 " --> pdb=" O GLU e 150 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N LYS e 155 " --> pdb=" O MET e 151 " (cutoff:3.500A) Processing helix chain 'e' and resid 159 through 165 Processing helix chain 'f' and resid 11 through 33 Proline residue: f 19 - end of helix Processing helix chain 'f' and resid 67 through 81 removed outlier: 3.595A pdb=" N PHE f 78 " --> pdb=" O LEU f 74 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ASN f 81 " --> pdb=" O THR f 77 " (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 removed outlier: 3.892A pdb=" N GLN h 117 " --> pdb=" O ARG h 113 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY h 119 " --> pdb=" O ALA h 115 " (cutoff:3.500A) Processing helix chain 'k' and resid 45 through 50 removed outlier: 4.400A pdb=" N GLY k 50 " --> pdb=" O ALA k 46 " (cutoff:3.500A) Processing helix chain 'k' and resid 53 through 58 removed outlier: 4.346A pdb=" N SER k 57 " --> pdb=" O GLY k 53 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N THR k 58 " --> pdb=" O SER k 54 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 53 through 58' Processing helix chain 'k' and resid 59 through 73 removed outlier: 4.594A pdb=" N ALA k 72 " --> pdb=" O ARG k 68 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N VAL k 73 " --> pdb=" O CYS k 69 " (cutoff:3.500A) Processing helix chain 'k' and resid 92 through 103 removed outlier: 3.795A pdb=" N ILE k 96 " --> pdb=" O ARG k 92 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N ARG k 97 " --> pdb=" O GLU k 93 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ALA k 98 " --> pdb=" O SER k 94 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LEU k 99 " --> pdb=" O THR k 95 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ASN k 100 " --> pdb=" O ILE k 96 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N GLY k 103 " --> pdb=" O LEU k 99 " (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 112 through 117 removed outlier: 4.788A pdb=" N TYR l 116 " --> pdb=" O ALA l 112 " (cutoff:3.500A) removed outlier: 3.577A 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 'o' and resid 3 through 15 removed outlier: 3.705A pdb=" N SER o 12 " --> pdb=" O ALA o 8 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLU o 13 " --> pdb=" O LYS o 9 " (cutoff:3.500A) Processing helix chain 'o' and resid 23 through 43 removed outlier: 4.523A pdb=" N GLY o 40 " --> pdb=" O ASN o 36 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N HIS o 41 " --> pdb=" O HIS o 37 " (cutoff:3.500A) Processing helix chain 'o' and resid 48 through 73 Processing helix chain 'o' and resid 74 through 85 Processing helix chain 'p' and resid 53 through 64 removed outlier: 3.634A pdb=" N GLN p 63 " --> pdb=" O HIS p 59 " (cutoff:3.500A) Processing helix chain 'p' and resid 68 through 79 Processing helix chain 'r' and resid 11 through 16 removed outlier: 5.705A pdb=" N GLU r 15 " --> pdb=" O ARG r 11 " (cutoff:3.500A) Processing helix chain 'r' and resid 24 through 33 removed outlier: 3.611A pdb=" N LEU r 28 " --> pdb=" O ASP r 24 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ASN r 30 " --> pdb=" O ALA r 26 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N TYR r 31 " --> pdb=" O THR r 27 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ILE r 32 " --> pdb=" O LEU r 28 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N THR r 33 " --> pdb=" O LYS r 29 " (cutoff:3.500A) Processing helix chain 'r' and resid 40 through 45 Processing helix chain 'r' and resid 47 through 65 Processing helix chain 't' and resid 6 through 41 removed outlier: 5.154A pdb=" N ALA t 10 " --> pdb=" O ALA t 6 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE t 11 " --> pdb=" O LYS t 7 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N HIS t 19 " --> pdb=" O LYS t 15 " (cutoff:3.500A) Processing helix chain 't' and resid 42 through 64 Proline residue: t 55 - end of helix removed outlier: 3.529A pdb=" N LYS t 63 " --> pdb=" O ARG t 59 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLY t 64 " --> pdb=" O GLN t 60 " (cutoff:3.500A) Processing helix chain 't' and resid 67 through 86 removed outlier: 5.933A pdb=" N ALA t 71 " --> pdb=" O HIS t 67 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ALA t 72 " --> pdb=" O LYS t 68 " (cutoff:3.500A) Processing helix chain 'u' and resid 17 through 23 Processing helix chain 'u' and resid 24 through 33 removed outlier: 3.560A pdb=" N LEU u 28 " --> pdb=" O LYS u 24 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N GLU u 30 " --> pdb=" O GLY u 26 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ARG u 33 " --> pdb=" O ALA u 29 " (cutoff:3.500A) Processing helix chain 'u' and resid 37 through 61 removed outlier: 5.428A pdb=" N THR u 41 " --> pdb=" O TYR u 37 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N THR u 42 " --> pdb=" O GLU u 38 " (cutoff:3.500A) Processing helix chain 'w' and resid 15 through 28 removed outlier: 3.580A pdb=" N LEU w 19 " --> pdb=" O GLY w 15 " (cutoff:3.500A) Processing helix chain 'w' and resid 46 through 53 removed outlier: 4.384A pdb=" N ARG w 50 " --> pdb=" O THR w 46 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N GLN w 51 " --> pdb=" O LEU w 47 " (cutoff:3.500A) Processing helix chain 'w' and resid 82 through 93 removed outlier: 4.091A pdb=" N SER w 90 " --> pdb=" O TYR w 86 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL w 91 " --> pdb=" O ARG w 87 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N ASP w 93 " --> pdb=" O LEU w 89 " (cutoff:3.500A) Processing helix chain 'w' and resid 106 through 120 removed outlier: 3.814A pdb=" N ILE w 111 " --> pdb=" O ALA w 107 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU w 112 " --> pdb=" O GLN w 108 " (cutoff:3.500A) Processing helix chain 'w' and resid 137 through 149 removed outlier: 5.948A pdb=" N TYR w 141 " --> pdb=" O LEU w 137 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N GLN w 142 " --> pdb=" O SER w 138 " (cutoff:3.500A) Processing helix chain 'w' and resid 176 through 183 removed outlier: 3.518A pdb=" N ASN w 182 " --> pdb=" O VAL w 178 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N ASP w 183 " --> pdb=" O ILE w 179 " (cutoff:3.500A) Processing helix chain 'w' and resid 184 through 192 Processing helix chain 'w' and resid 198 through 209 removed outlier: 4.227A pdb=" N GLU w 203 " --> pdb=" O GLU w 199 " (cutoff:3.500A) Processing helix chain 'w' and resid 226 through 237 removed outlier: 4.134A pdb=" N ILE w 231 " --> pdb=" O ILE w 227 " (cutoff:3.500A) Processing helix chain 'w' and resid 356 through 373 removed outlier: 3.846A pdb=" N MET w 360 " --> pdb=" O GLU w 356 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASP w 363 " --> pdb=" O GLU w 359 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ASP w 372 " --> pdb=" O ILE w 368 " (cutoff:3.500A) Proline residue: w 373 - end of helix Processing helix chain 'w' and resid 392 through 406 removed outlier: 3.752A pdb=" N MET w 396 " --> pdb=" O GLY w 392 " (cutoff:3.500A) Processing helix chain 'w' and resid 470 through 488 removed outlier: 3.568A pdb=" N GLN w 474 " --> pdb=" O ASN w 470 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N ASN w 475 " --> pdb=" O GLN w 471 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N ALA w 476 " --> pdb=" O SER w 472 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N GLN w 487 " --> pdb=" O TYR w 483 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N GLY w 488 " --> pdb=" O GLY w 484 " (cutoff:3.500A) Processing helix chain 'w' and resid 512 through 532 Proline residue: w 521 - end of helix removed outlier: 3.937A pdb=" N GLY w 532 " --> pdb=" O LEU w 528 " (cutoff:3.500A) Processing helix chain 'w' and resid 547 through 562 removed outlier: 4.111A pdb=" N SER w 552 " --> pdb=" O GLN w 548 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N ARG w 553 " --> pdb=" O GLU w 549 " (cutoff:3.500A) Proline residue: w 559 - end of helix removed outlier: 4.853A pdb=" N CYS w 562 " --> pdb=" O ALA w 558 " (cutoff:3.500A) Processing helix chain 'w' and resid 582 through 598 removed outlier: 4.000A pdb=" N GLN w 587 " --> pdb=" O ALA w 583 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N GLU w 588 " --> pdb=" O ARG w 584 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N TYR w 589 " --> pdb=" O CYS w 585 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ARG w 590 " --> pdb=" O ILE w 586 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N SER w 591 " --> pdb=" O GLN w 587 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ASN w 598 " --> pdb=" O THR w 594 " (cutoff:3.500A) Processing helix chain 'w' and resid 630 through 639 removed outlier: 4.108A pdb=" N THR w 639 " --> pdb=" O PHE w 635 " (cutoff:3.500A) Processing helix chain 'c' and resid 5 through 11 removed outlier: 3.883A pdb=" N ARG c 10 " --> pdb=" O PRO c 6 " (cutoff:3.500A) Processing helix chain 'c' and resid 27 through 47 Processing helix chain 'c' and resid 71 through 77 Processing helix chain 'c' and resid 80 through 95 removed outlier: 4.010A pdb=" N ILE c 93 " --> pdb=" O VAL c 89 " (cutoff:3.500A) Processing helix chain 'c' and resid 111 through 126 removed outlier: 3.908A pdb=" N ARG c 125 " --> pdb=" O SER c 121 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ARG c 126 " --> pdb=" O GLN c 122 " (cutoff:3.500A) Processing helix chain 'c' and resid 128 through 144 Processing helix chain 'g' and resid 19 through 30 removed outlier: 3.756A pdb=" N LEU g 29 " --> pdb=" O PHE g 25 " (cutoff:3.500A) Processing helix chain 'g' and resid 34 through 54 removed outlier: 3.800A pdb=" N ARG g 52 " --> pdb=" O THR g 48 " (cutoff:3.500A) Processing helix chain 'g' and resid 57 through 69 removed outlier: 3.877A pdb=" N GLU g 62 " --> pdb=" O LEU g 58 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ALA g 64 " --> pdb=" O ALA g 60 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ASN g 67 " --> pdb=" O VAL g 63 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL g 68 " --> pdb=" O ALA g 64 " (cutoff:3.500A) Processing helix chain 'g' and resid 91 through 111 removed outlier: 4.033A pdb=" N ALA g 97 " --> pdb=" O VAL g 93 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LYS g 109 " --> pdb=" O GLU g 105 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ARG g 110 " --> pdb=" O ALA g 106 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N GLY g 111 " --> pdb=" O ALA g 107 " (cutoff:3.500A) Processing helix chain 'g' and resid 114 through 129 removed outlier: 3.960A pdb=" N GLU g 128 " --> pdb=" O SER g 124 " (cutoff:3.500A) Processing helix chain 'g' and resid 131 through 146 removed outlier: 3.538A pdb=" N ALA g 144 " --> pdb=" O VAL g 140 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLU g 145 " --> pdb=" O HIS g 141 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ALA g 146 " --> pdb=" O ARG g 142 " (cutoff:3.500A) Processing helix chain 'i' and resid 33 through 38 removed outlier: 3.912A 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: 5.169A pdb=" N LEU i 53 " --> pdb=" O GLN i 49 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N VAL i 54 " --> pdb=" O PRO i 50 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ASP i 55 " --> pdb=" O LEU i 51 " (cutoff:3.500A) Processing helix chain 'i' and resid 70 through 87 removed outlier: 5.206A pdb=" N MET i 87 " --> pdb=" O THR i 83 " (cutoff:3.500A) Processing helix chain 'i' and resid 91 through 98 removed outlier: 4.831A pdb=" N GLU i 96 " --> pdb=" O SER i 92 " (cutoff:3.500A) Processing helix chain 'j' and resid 14 through 33 removed outlier: 3.586A pdb=" N ILE j 18 " --> pdb=" O ASP j 14 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N GLN j 20 " --> pdb=" O ARG j 16 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ALA j 29 " --> pdb=" O ILE j 25 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N THR j 32 " --> pdb=" O THR j 28 " (cutoff:3.500A) Processing helix chain 'j' and resid 80 through 90 removed outlier: 3.504A pdb=" N ASP j 85 " --> pdb=" O GLU j 81 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ALA j 86 " --> pdb=" O LYS j 82 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N MET j 88 " --> pdb=" O VAL j 84 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N ARG j 89 " --> pdb=" O ASP j 85 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N LEU j 90 " --> pdb=" O ALA j 86 " (cutoff:3.500A) Processing helix chain 'm' and resid 13 through 22 removed outlier: 4.449A pdb=" N ILE m 21 " --> pdb=" O ALA m 17 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N TYR m 22 " --> pdb=" O LEU m 18 " (cutoff:3.500A) Processing helix chain 'm' and resid 25 through 37 Processing helix chain 'm' and resid 43 through 48 removed outlier: 5.130A pdb=" N SER m 48 " --> pdb=" O ILE m 44 " (cutoff:3.500A) Processing helix chain 'm' and resid 49 through 63 removed outlier: 4.172A pdb=" N THR m 54 " --> pdb=" O GLY m 50 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LYS m 61 " --> pdb=" O ASP m 57 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N PHE m 62 " --> pdb=" O GLU m 58 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N VAL m 63 " --> pdb=" O VAL m 59 " (cutoff:3.500A) Processing helix chain 'm' and resid 65 through 83 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 removed outlier: 3.581A pdb=" N TYR n 19 " --> pdb=" O LEU n 15 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE n 20 " --> pdb=" O ALA n 16 " (cutoff:3.500A) Processing helix chain 'n' and resid 24 through 29 Processing helix chain 'n' and resid 38 through 51 removed outlier: 3.706A pdb=" N TRP n 42 " --> pdb=" O ASP n 38 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N GLN n 49 " --> pdb=" O VAL n 45 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N THR n 50 " --> pdb=" O LEU n 46 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU n 51 " --> pdb=" O LYS n 47 " (cutoff:3.500A) Processing helix chain 'n' and resid 56 through 61 removed outlier: 4.370A pdb=" N GLN n 60 " --> pdb=" O SER n 56 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N ARG n 61 " --> pdb=" O PRO n 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'n' and resid 56 through 61' Processing helix chain 'n' and resid 80 through 91 removed outlier: 4.078A pdb=" N ARG n 90 " --> pdb=" O GLU n 86 " (cutoff:3.500A) Processing helix chain 's' and resid 11 through 25 Processing helix chain 's' and resid 69 through 75 removed outlier: 4.512A pdb=" N PHE s 73 " --> pdb=" O LYS s 69 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ALA s 74 " --> pdb=" O LEU s 70 " (cutoff:3.500A) Proline residue: s 75 - end of helix No H-bonds generated for 'chain 's' and resid 69 through 75' Processing helix chain 's' and resid 63 through 68 removed outlier: 4.625A pdb=" N VAL s 66 " --> pdb=" O ASP s 63 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLY s 67 " --> pdb=" O GLU s 64 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N HIS s 68 " --> pdb=" O MET s 65 " (cutoff:3.500A) No H-bonds generated for 'chain 's' and resid 63 through 68' Processing helix chain 'C' and resid 9 through 16 removed outlier: 7.386A pdb=" N HIS C 14 " --> pdb=" O PRO C 10 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N VAL C 15 " --> pdb=" O GLY C 11 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N VAL C 16 " --> pdb=" O ARG C 12 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 34 removed outlier: 3.887A pdb=" N LEU C 33 " --> pdb=" O PHE C 29 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N GLU C 34 " --> pdb=" O ALA C 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 29 through 34' Processing helix chain 'C' and resid 130 through 135 removed outlier: 3.831A 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: 3.612A pdb=" N ALA C 210 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG C 213 " --> pdb=" O ALA C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 225 removed outlier: 3.715A pdb=" N MET C 224 " --> pdb=" O ARG C 220 " (cutoff:3.500A) removed outlier: 5.285A 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: 6.089A pdb=" N ASP C 263 " --> pdb=" O ASN C 259 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N LYS C 264 " --> pdb=" O LYS C 260 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N PHE C 265 " --> pdb=" O ARG C 261 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE C 266 " --> pdb=" O THR C 262 " (cutoff:3.500A) removed outlier: 5.318A 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 61 through 72 removed outlier: 3.756A pdb=" N ALA D 71 " --> pdb=" O HIS D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 105 removed outlier: 4.575A pdb=" N ALA D 102 " --> pdb=" O VAL D 98 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N ASP D 103 " --> pdb=" O GLU D 99 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N VAL D 104 " --> pdb=" O LEU D 100 " (cutoff:3.500A) removed outlier: 5.630A 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 'E' and resid 24 through 40 Processing helix chain 'E' and resid 48 through 53 removed outlier: 6.566A pdb=" N THR E 53 " --> pdb=" O ARG E 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 116 removed outlier: 3.555A pdb=" N ARG E 114 " --> pdb=" O SER E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 130 through 142 removed outlier: 3.769A pdb=" N LEU E 134 " --> pdb=" O LYS E 130 " (cutoff:3.500A) Processing helix chain 'E' and resid 154 through 163 removed outlier: 3.732A pdb=" N ALA E 160 " --> pdb=" O ASN E 156 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ARG E 162 " --> pdb=" O PHE E 158 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ASN E 163 " --> pdb=" O LEU E 159 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 183 Processing helix chain 'E' and resid 189 through 201 removed outlier: 3.686A pdb=" N ALA E 201 " --> pdb=" O GLU E 197 " (cutoff:3.500A) Processing helix chain 'E' and resid 15 through 21 removed outlier: 4.114A pdb=" N GLY E 20 " --> pdb=" O SER E 15 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ARG E 21 " --> pdb=" O GLU E 16 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 15 through 21' Processing helix chain 'F' and resid 1 through 20 removed outlier: 3.698A pdb=" N ASP F 5 " --> pdb=" O ALA F 1 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASP F 9 " --> pdb=" O ASP F 5 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N VAL F 12 " --> pdb=" O LYS F 8 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N THR F 17 " --> pdb=" O LYS F 13 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLU F 18 " --> pdb=" O LYS F 14 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N PHE F 19 " --> pdb=" O LEU F 15 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ASN F 20 " --> pdb=" O MET F 16 " (cutoff:3.500A) Processing helix chain 'F' and resid 41 through 46 removed outlier: 3.692A pdb=" N ASP F 45 " --> pdb=" O GLU F 41 " (cutoff:3.500A) removed outlier: 3.942A 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 Processing helix chain 'F' and resid 92 through 110 removed outlier: 3.550A pdb=" N TRP F 96 " --> pdb=" O GLY F 92 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ILE F 105 " --> pdb=" O ARG F 101 " (cutoff:3.500A) removed outlier: 5.528A 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: 5.877A pdb=" N VAL F 145 " --> pdb=" O ASP F 141 " (cutoff:3.500A) removed outlier: 5.353A 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: 4.477A pdb=" N ALA F 167 " --> pdb=" O GLU F 163 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N LEU F 168 " --> pdb=" O GLU F 164 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N PHE F 172 " --> pdb=" O LEU F 168 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ASP F 173 " --> pdb=" O LEU F 169 " (cutoff:3.500A) Processing helix chain 'F' and resid 133 through 138 removed outlier: 3.861A pdb=" N ILE F 136 " --> pdb=" O GLU F 133 " (cutoff:3.500A) removed outlier: 3.580A 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: 5.017A 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: 4.093A pdb=" N ARG G 151 " --> pdb=" O LEU G 147 " (cutoff:3.500A) Processing helix chain 'H' and resid 22 through 29 removed outlier: 3.574A pdb=" N PHE H 29 " --> pdb=" O TYR H 25 " (cutoff:3.500A) Processing helix chain 'H' and resid 40 through 50 removed outlier: 4.503A pdb=" N ILE H 44 " --> pdb=" O THR H 40 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA H 49 " --> pdb=" O GLU H 45 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ARG H 50 " --> pdb=" O PHE H 46 " (cutoff:3.500A) Processing helix chain 'H' and resid 54 through 73 removed outlier: 4.742A pdb=" N ASN H 73 " --> pdb=" O ALA H 69 " (cutoff:3.500A) Processing helix chain 'H' and resid 95 through 107 removed outlier: 3.929A pdb=" N ILE H 99 " --> pdb=" O GLY H 95 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 116 removed outlier: 3.896A pdb=" N VAL H 115 " --> pdb=" O ALA H 111 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N ARG H 116 " --> pdb=" O LYS H 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 111 through 116' Processing helix chain 'I' and resid 23 through 29 removed outlier: 4.518A pdb=" N LEU I 27 " --> pdb=" O VAL I 23 " (cutoff:3.500A) Processing helix chain 'I' and resid 33 through 46 removed outlier: 4.489A pdb=" N PHE I 37 " --> pdb=" O ASN I 33 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N CYS I 38 " --> pdb=" O ILE I 34 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS I 39 " --> pdb=" O MET I 35 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ALA I 40 " --> pdb=" O GLU I 36 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N PHE I 41 " --> pdb=" O PHE I 37 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ASN I 42 " --> pdb=" O CYS I 38 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N ALA I 43 " --> pdb=" O LYS I 39 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N LYS I 44 " --> pdb=" O ALA I 40 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N THR I 45 " --> pdb=" O PHE I 41 " (cutoff:3.500A) Processing helix chain 'I' and resid 74 through 83 removed outlier: 4.623A pdb=" N LYS I 80 " --> pdb=" O ALA I 76 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N LYS I 81 " --> pdb=" O VAL I 77 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N ALA I 83 " --> pdb=" O LEU I 79 " (cutoff:3.500A) Processing helix chain 'I' and resid 101 through 114 removed outlier: 4.003A pdb=" N GLU I 107 " --> pdb=" O ALA I 103 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLN I 110 " --> pdb=" O GLN I 106 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N THR I 111 " --> pdb=" O GLU I 107 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LYS I 112 " --> pdb=" O ILE I 108 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA I 113 " --> pdb=" O ALA I 109 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N ALA I 114 " --> pdb=" O GLN I 110 " (cutoff:3.500A) Processing helix chain 'I' and resid 120 through 136 removed outlier: 3.838A pdb=" N MET I 124 " --> pdb=" O ASP I 120 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N MET I 135 " --> pdb=" O THR I 131 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N GLY I 136 " --> pdb=" O ALA I 132 " (cutoff:3.500A) Processing helix chain 'J' and resid 24 through 38 Processing helix chain 'J' and resid 88 through 96 Processing helix chain 'J' and resid 97 through 110 removed outlier: 4.210A pdb=" N ILE J 101 " --> pdb=" O PRO J 97 " (cutoff:3.500A) removed outlier: 3.898A 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 123 removed outlier: 3.625A pdb=" N ARG J 120 " --> pdb=" O ARG J 116 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LYS J 121 " --> pdb=" O ALA J 117 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N LEU J 122 " --> pdb=" O MET J 118 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N LYS J 123 " --> pdb=" O PHE J 119 " (cutoff:3.500A) Processing helix chain 'J' and resid 67 through 72 removed outlier: 4.323A pdb=" N LYS J 72 " --> pdb=" O ASN J 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 67 through 72' Processing helix chain 'K' and resid 112 through 120 Proline residue: K 120 - end of helix Processing helix chain 'K' and resid 104 through 109 removed outlier: 5.303A pdb=" N SER K 109 " --> pdb=" O GLU K 106 " (cutoff:3.500A) Processing helix chain 'L' and resid 37 through 42 removed outlier: 3.705A pdb=" N ARG L 41 " --> pdb=" O GLY L 37 " (cutoff:3.500A) removed outlier: 5.507A 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 61 removed outlier: 3.551A pdb=" N LEU L 61 " --> pdb=" O LEU L 57 " (cutoff:3.500A) Processing helix chain 'L' and resid 68 through 75 removed outlier: 3.657A pdb=" N ALA L 72 " --> pdb=" O SER L 68 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ILE L 73 " --> pdb=" O ARG L 69 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N THR L 74 " --> pdb=" O LYS L 70 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N ALA L 75 " --> pdb=" O ALA L 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 68 through 75' Processing helix chain 'L' and resid 78 through 83 removed outlier: 3.660A pdb=" N LEU L 82 " --> pdb=" O ARG L 78 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ALA L 83 " --> pdb=" O LEU L 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 78 through 83' Processing helix chain 'L' and resid 91 through 99 removed outlier: 4.342A pdb=" N LEU L 95 " --> pdb=" O ASP L 91 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N LYS L 96 " --> pdb=" O LEU L 92 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N ALA L 97 " --> pdb=" O ASN L 93 " (cutoff:3.500A) Processing helix chain 'L' and resid 128 through 139 removed outlier: 4.967A pdb=" N ARG L 132 " --> pdb=" O THR L 128 " (cutoff:3.500A) Processing helix chain 'M' and resid 42 through 58 removed outlier: 3.669A pdb=" N MET M 53 " --> pdb=" O ALA M 49 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N ALA M 56 " --> pdb=" O ALA M 52 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LYS M 58 " --> pdb=" O THR M 54 " (cutoff:3.500A) Processing helix chain 'M' and resid 109 through 125 removed outlier: 3.682A pdb=" N LYS M 118 " --> pdb=" O ARG M 114 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU M 119 " --> pdb=" O GLU M 115 " (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: 4.359A pdb=" N ARG N 46 " --> pdb=" O LYS N 42 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N VAL N 47 " --> pdb=" O GLU N 43 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLU N 49 " --> pdb=" O ARG N 45 " (cutoff:3.500A) Proline residue: N 50 - end of helix removed outlier: 4.908A pdb=" N THR N 57 " --> pdb=" O THR N 53 " (cutoff:3.500A) Processing helix chain 'N' and resid 59 through 71 removed outlier: 4.822A pdb=" N ARG N 63 " --> pdb=" O SER N 59 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N THR N 70 " --> pdb=" O ALA N 66 " (cutoff:3.500A) Processing helix chain 'N' and resid 72 through 82 removed outlier: 4.232A pdb=" N PHE N 80 " --> pdb=" O VAL N 76 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ASN N 81 " --> pdb=" O ALA N 77 " (cutoff:3.500A) Processing helix chain 'N' and resid 83 through 88 removed outlier: 3.564A pdb=" N ALA N 88 " --> pdb=" O GLY N 84 " (cutoff:3.500A) Processing helix chain 'O' and resid 2 through 22 removed outlier: 4.578A pdb=" N ARG O 13 " --> pdb=" O ARG O 9 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N ALA O 14 " --> pdb=" O ARG O 10 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU O 21 " --> pdb=" O LYS O 17 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLY O 22 " --> pdb=" O LEU O 18 " (cutoff:3.500A) Processing helix chain 'O' and resid 55 through 63 removed outlier: 5.143A pdb=" N GLN O 61 " --> pdb=" O ALA O 57 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N LYS O 63 " --> pdb=" O ALA O 59 " (cutoff:3.500A) Processing helix chain 'O' and resid 67 through 86 removed outlier: 3.697A pdb=" N LEU O 83 " --> pdb=" O ALA O 79 " (cutoff:3.500A) Processing helix chain 'O' and resid 101 through 114 removed outlier: 3.692A pdb=" N GLY O 114 " --> pdb=" O ALA O 110 " (cutoff:3.500A) Processing helix chain 'P' and resid 1 through 13 removed outlier: 4.031A pdb=" N GLN P 11 " --> pdb=" O LEU P 7 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N LYS P 13 " --> pdb=" O GLN P 9 " (cutoff:3.500A) Processing helix chain 'P' and resid 96 through 103 removed outlier: 4.484A pdb=" N ARG P 100 " --> pdb=" O LEU P 96 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N GLU P 101 " --> pdb=" O TYR P 97 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ARG P 102 " --> pdb=" O TYR P 98 " (cutoff:3.500A) removed outlier: 5.343A 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 removed outlier: 4.200A pdb=" N ALA Q 9 " --> pdb=" O ARG Q 5 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N GLN Q 19 " --> pdb=" O LYS Q 15 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYS Q 21 " --> pdb=" O LEU Q 17 " (cutoff:3.500A) Processing helix chain 'Q' and resid 25 through 30 removed outlier: 3.974A pdb=" N ARG Q 29 " --> pdb=" O GLY Q 25 " (cutoff:3.500A) Processing helix chain 'Q' and resid 38 through 72 removed outlier: 4.019A pdb=" N ARG Q 50 " --> pdb=" O TYR Q 46 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N LYS Q 53 " --> pdb=" O ARG Q 49 " (cutoff:3.500A) Processing helix chain 'Q' and resid 74 through 86 Processing helix chain 'Q' and resid 90 through 101 removed outlier: 3.831A pdb=" N ASP Q 96 " --> pdb=" O LYS Q 92 " (cutoff:3.500A) Processing helix chain 'Q' and resid 102 through 117 Processing helix chain 'S' and resid 13 through 25 removed outlier: 3.503A pdb=" N VAL S 17 " --> pdb=" O SER S 13 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N LEU S 23 " --> pdb=" O LEU S 19 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ILE S 24 " --> pdb=" O VAL S 20 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ARG S 25 " --> pdb=" O ALA S 21 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 39 removed outlier: 3.744A pdb=" N TYR S 38 " --> pdb=" O ASP S 34 " (cutoff:3.500A) Processing helix chain 'S' and resid 41 through 62 removed outlier: 3.819A pdb=" N VAL S 50 " --> pdb=" O LEU S 46 " (cutoff:3.500A) Processing helix chain 'T' and resid 2 through 11 removed outlier: 3.976A pdb=" N LYS T 9 " --> pdb=" O GLU T 5 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N LEU T 11 " --> pdb=" O LEU T 7 " (cutoff:3.500A) Processing helix chain 'T' and resid 17 through 27 Processing helix chain 'T' and resid 39 through 51 Processing helix chain 'U' and resid 65 through 70 removed outlier: 3.961A pdb=" N VAL U 69 " --> pdb=" O GLN U 65 " (cutoff:3.500A) removed outlier: 5.232A 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: 3.886A pdb=" N ALA V 23 " --> pdb=" O ARG V 19 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ASN V 24 " --> pdb=" O LEU V 20 " (cutoff:3.500A) Processing helix chain 'V' and resid 43 through 53 removed outlier: 4.140A pdb=" N VAL V 47 " --> pdb=" O ASP V 43 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N ALA V 52 " --> pdb=" O MET V 48 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N LYS V 53 " --> pdb=" O ASN V 49 " (cutoff:3.500A) Processing helix chain 'V' and resid 54 through 59 removed outlier: 3.818A pdb=" N SER V 58 " --> pdb=" O ALA V 54 " (cutoff:3.500A) Processing helix chain 'X' and resid 51 through 61 Processing helix chain 'X' and resid 62 through 74 Processing helix chain 'Y' and resid 1 through 7 removed outlier: 3.671A pdb=" N LEU Y 6 " --> pdb=" O LYS Y 2 " (cutoff:3.500A) removed outlier: 4.545A 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: 3.618A pdb=" N SER Y 34 " --> pdb=" O MET Y 30 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLY Y 35 " --> pdb=" O GLN Y 31 " (cutoff:3.500A) Processing helix chain 'Y' and resid 39 through 63 removed outlier: 4.512A pdb=" N LEU Y 43 " --> pdb=" O GLN Y 39 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N GLY Y 62 " --> pdb=" O ASN Y 58 " (cutoff:3.500A) removed outlier: 5.306A 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 20 removed outlier: 4.671A pdb=" N HIS 0 18 " --> pdb=" O MET 0 14 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N ASP 0 19 " --> pdb=" O ARG 0 15 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ALA 0 20 " --> pdb=" O ARG 0 16 " (cutoff:3.500A) Processing helix chain '2' and resid 8 through 16 Processing helix chain '2' and resid 17 through 25 removed outlier: 4.277A pdb=" N THR 2 24 " --> pdb=" O ALA 2 20 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N LYS 2 25 " --> pdb=" O ARG 2 21 " (cutoff:3.500A) Processing helix chain '2' and resid 26 through 38 Processing helix chain '3' and resid 6 through 13 removed outlier: 3.672A pdb=" N LYS 3 11 " --> pdb=" O ARG 3 7 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ARG 3 12 " --> pdb=" O GLY 3 8 " (cutoff:3.500A) Processing helix chain '3' and resid 31 through 36 removed outlier: 4.337A pdb=" N LYS 3 35 " --> pdb=" O ILE 3 31 " (cutoff:3.500A) removed outlier: 5.694A 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 removed outlier: 3.860A pdb=" N ARG 3 44 " --> pdb=" O LYS 3 40 " (cutoff:3.500A) Proline residue: 3 45 - end of helix Processing helix chain '3' and resid 50 through 62 removed outlier: 4.388A pdb=" N GLY 3 55 " --> pdb=" O LYS 3 51 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N LEU 3 56 " --> pdb=" O GLY 3 52 " (cutoff:3.500A) Proline residue: 3 62 - end of helix Processing helix chain '5' and resid 3 through 21 removed outlier: 3.719A pdb=" N LYS 5 20 " --> pdb=" O SER 5 16 " (cutoff:3.500A) Processing helix chain '5' and resid 33 through 48 removed outlier: 3.879A pdb=" N THR 5 39 " --> pdb=" O VAL 5 35 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N ARG 5 42 " --> pdb=" O MET 5 38 " (cutoff:3.500A) Processing helix chain '5' and resid 62 through 71 removed outlier: 3.589A pdb=" N THR 5 67 " --> pdb=" O ALA 5 63 " (cutoff:3.500A) Proline residue: 5 68 - end of helix removed outlier: 3.895A pdb=" N CYS 5 71 " --> pdb=" O THR 5 67 " (cutoff:3.500A) Processing helix chain '5' and resid 72 through 79 removed outlier: 4.923A pdb=" N PHE 5 76 " --> pdb=" O LEU 5 72 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N VAL 5 77 " --> pdb=" O LYS 5 73 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLY 5 78 " --> pdb=" O ASP 5 74 " (cutoff:3.500A) Proline residue: 5 79 - end of helix No H-bonds generated for 'chain '5' and resid 72 through 79' Processing helix chain '5' and resid 94 through 106 removed outlier: 3.921A pdb=" N PHE 5 99 " --> pdb=" O LEU 5 95 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ALA 5 100 " --> pdb=" O PHE 5 96 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N PHE 5 106 " --> pdb=" O ALA 5 102 " (cutoff:3.500A) Processing helix chain '5' and resid 109 through 114 removed outlier: 6.587A pdb=" N ALA 5 112 " --> pdb=" O LYS 5 109 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLU 5 114 " --> pdb=" O ALA 5 111 " (cutoff:3.500A) Processing helix chain '6' and resid 43 through 54 removed outlier: 4.683A pdb=" N GLN 6 48 " --> pdb=" O PHE 6 44 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA 6 52 " --> pdb=" O GLN 6 48 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR 6 53 " --> pdb=" O ARG 6 49 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N GLY 6 54 " --> pdb=" O ASP 6 50 " (cutoff:3.500A) Processing helix chain '6' and resid 55 through 65 removed outlier: 5.134A pdb=" N ARG 6 59 " --> pdb=" O GLY 6 55 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ARG 6 63 " --> pdb=" O ARG 6 59 " (cutoff:3.500A) Processing helix chain '7' and resid 64 through 77 Processing helix chain '7' and resid 79 through 90 Processing helix chain '7' and resid 99 through 114 Processing sheet with id= 1, first strand: chain 'b' and resid 29 through 33 removed outlier: 7.262A pdb=" N PHE b 29 " --> pdb=" O ASN b 41 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N ASN b 41 " --> pdb=" O PHE b 29 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL b 37 " --> pdb=" O ALA b 33 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'b' and resid 88 through 92 removed outlier: 4.366A pdb=" N PHE b 183 " --> pdb=" O LEU b 160 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL b 162 " --> pdb=" O PHE b 183 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'd' and resid 139 through 143 removed outlier: 3.618A pdb=" N VAL d 142 " --> pdb=" O GLY d 179 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N GLU d 178 " --> pdb=" O ASP d 173 " (cutoff:3.500A) removed outlier: 8.120A pdb=" N TRP d 169 " --> pdb=" O LYS d 182 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'e' and resid 10 through 15 removed outlier: 3.579A pdb=" N GLN e 11 " --> pdb=" O GLY e 39 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LYS e 13 " --> pdb=" O VAL e 37 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N LEU e 35 " --> pdb=" O ILE e 15 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'e' and resid 82 through 87 removed outlier: 7.550A pdb=" N HIS e 82 " --> pdb=" O PRO e 97 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N MET e 95 " --> pdb=" O VAL e 84 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N VAL e 93 " --> pdb=" O GLY e 86 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG e 92 " --> pdb=" O TYR e 127 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N TYR e 127 " --> pdb=" O ARG e 92 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'e' and resid 31 through 40 removed outlier: 4.294A pdb=" N GLY e 50 " --> pdb=" O ALA e 34 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ARG e 44 " --> pdb=" O ASP e 40 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'f' and resid 39 through 42 removed outlier: 3.884A pdb=" N GLU f 40 " --> pdb=" O LEU f 61 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU f 61 " --> pdb=" O GLU f 40 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N TYR f 59 " --> pdb=" O TRP f 42 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N ILE f 6 " --> pdb=" O MET f 62 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N HIS f 3 " --> pdb=" O THR f 92 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N GLU f 5 " --> pdb=" O MET f 90 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N MET f 90 " --> pdb=" O GLU f 5 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N ARG f 86 " --> pdb=" O MET f 9 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'f' and resid 43 through 46 Processing sheet with id= 9, first strand: chain 'h' and resid 22 through 27 removed outlier: 6.721A pdb=" N ALA h 22 " --> pdb=" O LEU h 62 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'h' and resid 73 through 76 removed outlier: 3.510A pdb=" N SER h 73 " --> pdb=" O ALA h 129 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE h 100 " --> pdb=" O VAL h 128 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N VAL h 102 " --> pdb=" O ILE h 125 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'k' and resid 41 through 44 removed outlier: 3.849A pdb=" N GLY k 42 " --> pdb=" O ILE k 33 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'l' and resid 28 through 32 removed outlier: 3.606A pdb=" N GLY l 31 " --> pdb=" O ILE l 79 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N LEU l 80 " --> pdb=" O VAL l 97 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'l' and resid 34 through 40 removed outlier: 4.785A pdb=" N ARG l 35 " --> pdb=" O ARG l 53 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N LYS l 50 " --> pdb=" O ILE l 66 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N PHE l 60 " --> pdb=" O LEU l 56 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'p' and resid 4 through 10 removed outlier: 3.598A pdb=" N ALA p 7 " --> pdb=" O GLN p 18 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N GLN p 18 " --> pdb=" O ALA p 7 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL p 19 " --> pdb=" O GLY p 37 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N GLY p 37 " --> pdb=" O VAL p 19 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N GLY p 49 " --> pdb=" O ASN p 40 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'q' and resid 6 through 10 removed outlier: 3.765A pdb=" N GLY q 9 " --> pdb=" O VAL q 58 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N GLU q 59 " --> pdb=" O VAL q 75 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'q' and resid 18 through 29 No H-bonds generated for sheet with id= 16 Processing sheet with id= 17, first strand: chain 'w' and resid 6 through 10 removed outlier: 3.775A pdb=" N ILE w 96 " --> pdb=" O GLY w 7 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU w 9 " --> pdb=" O ILE w 96 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE w 124 " --> pdb=" O ALA w 95 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N TYR w 217 " --> pdb=" O PHE w 125 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE w 127 " --> pdb=" O TYR w 217 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'w' and resid 58 through 64 removed outlier: 4.301A pdb=" N ASP w 74 " --> pdb=" O GLY w 59 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE w 72 " --> pdb=" O THR w 61 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N PHE w 63 " --> pdb=" O VAL w 70 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'w' and resid 251 through 254 removed outlier: 4.496A pdb=" N GLY w 251 " --> pdb=" O LEU w 327 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N SER w 325 " --> pdb=" O VAL w 253 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'w' and resid 255 through 259 removed outlier: 4.032A pdb=" N LYS w 255 " --> pdb=" O TYR w 267 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N GLN w 263 " --> pdb=" O THR w 259 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N GLU w 312 " --> pdb=" O LEU w 270 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'w' and resid 279 through 283 removed outlier: 4.270A pdb=" N ASP w 279 " --> pdb=" O VAL w 291 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N VAL w 283 " --> pdb=" O GLU w 287 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N GLU w 287 " --> pdb=" O VAL w 283 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'w' and resid 295 through 298 Processing sheet with id= 23, first strand: chain 'w' and resid 348 through 352 removed outlier: 3.607A pdb=" N THR w 349 " --> pdb=" O ILE w 413 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N GLU w 351 " --> pdb=" O ILE w 411 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N ILE w 411 " --> pdb=" O GLU w 351 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'w' and resid 420 through 424 Processing sheet with id= 25, first strand: chain 'w' and resid 457 through 461 removed outlier: 3.535A pdb=" N CYS w 497 " --> pdb=" O GLY w 457 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLU w 461 " --> pdb=" O ILE w 499 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N PHE w 501 " --> pdb=" O GLU w 461 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N GLY w 446 " --> pdb=" O LYS w 502 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU w 505 " --> pdb=" O SER w 444 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N TYR w 503 " --> pdb=" O GLY w 446 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'w' and resid 540 through 546 Processing sheet with id= 27, first strand: chain 'c' and resid 53 through 58 Processing sheet with id= 28, first strand: chain 'c' and resid 163 through 170 removed outlier: 4.321A pdb=" N GLY c 154 " --> pdb=" O ARG c 163 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N SER c 186 " --> pdb=" O VAL c 197 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ASP c 180 " --> pdb=" O LYS c 203 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'g' and resid 72 through 76 removed outlier: 3.633A pdb=" N LYS g 75 " --> pdb=" O VAL g 86 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL g 86 " --> pdb=" O LYS g 75 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'i' and resid 4 through 10 removed outlier: 4.237A pdb=" N GLY i 9 " --> pdb=" O ALA i 16 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N LYS i 67 " --> pdb=" O ALA i 15 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N LYS i 26 " --> pdb=" O LEU i 60 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU i 62 " --> pdb=" O LYS i 26 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'j' and resid 39 through 42 removed outlier: 4.661A pdb=" N LEU j 42 " --> pdb=" O LEU j 71 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N LEU j 71 " --> pdb=" O LEU j 42 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ILE j 8 " --> pdb=" O VAL j 74 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'j' and resid 44 through 52 removed outlier: 3.879A pdb=" N GLU j 47 " --> pdb=" O ILE j 67 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 's' and resid 47 through 51 removed outlier: 3.855A pdb=" N ILE s 48 " --> pdb=" O VAL s 59 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'C' and resid 79 through 82 removed outlier: 6.664A pdb=" N LEU C 92 " --> pdb=" O GLU C 78 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N ILE C 73 " --> pdb=" O SER C 117 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N SER C 117 " --> pdb=" O ILE C 73 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N ASP C 113 " --> pdb=" O VAL C 77 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'C' and resid 161 through 164 removed outlier: 6.437A pdb=" N THR C 172 " --> pdb=" O VAL C 164 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLU C 179 " --> pdb=" O LEU C 175 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'C' and resid 89 through 95 removed outlier: 5.510A pdb=" N ASN C 89 " --> pdb=" O ALA C 105 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N GLU C 99 " --> pdb=" O TYR C 95 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'D' and resid 3 through 8 removed outlier: 4.469A pdb=" N SER D 199 " --> pdb=" O LYS D 8 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N ASP D 200 " --> pdb=" O THR D 112 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N THR D 112 " --> pdb=" O ASP D 200 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'D' and resid 11 through 17 removed outlier: 4.101A pdb=" N VAL D 20 " --> pdb=" O THR D 16 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE D 27 " --> pdb=" O LEU D 187 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG D 179 " --> pdb=" O LEU D 188 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'D' and resid 36 through 39 removed outlier: 3.631A pdb=" N ASN D 32 " --> pdb=" O ILE D 96 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ILE D 96 " --> pdb=" O ASN D 32 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N GLN D 94 " --> pdb=" O VAL D 34 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'D' and resid 46 through 51 removed outlier: 6.890A pdb=" N ARG D 46 " --> pdb=" O LEU D 84 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'E' and resid 1 through 5 removed outlier: 5.486A pdb=" N MET E 1 " --> pdb=" O THR E 13 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N THR E 13 " --> pdb=" O MET E 1 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N LEU E 3 " --> pdb=" O ALA E 11 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ALA E 11 " --> pdb=" O LEU E 3 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N LEU E 5 " --> pdb=" O GLN E 9 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'E' and resid 117 through 120 removed outlier: 5.462A pdb=" N ARG E 117 " --> pdb=" O ASP E 184 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL E 187 " --> pdb=" O LEU E 147 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASP E 168 " --> pdb=" O VAL E 146 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'F' and resid 64 through 68 removed outlier: 3.690A pdb=" N GLY F 85 " --> pdb=" O THR F 67 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS F 32 " --> pdb=" O THR F 156 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N THR F 157 " --> pdb=" O GLY F 125 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N GLY F 125 " --> pdb=" O THR F 157 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'G' and resid 15 through 18 Processing sheet with id= 45, first strand: chain 'G' and resid 40 through 44 Processing sheet with id= 46, first strand: chain 'G' and resid 93 through 97 removed outlier: 3.735A pdb=" N ALA G 96 " --> pdb=" O ASN G 103 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'G' and resid 120 through 124 removed outlier: 6.086A pdb=" N THR G 128 " --> pdb=" O LEU G 88 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'H' and resid 2 through 6 removed outlier: 5.591A pdb=" N GLN H 2 " --> pdb=" O ALA H 39 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N ALA H 39 " --> pdb=" O GLN H 2 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N LYS H 35 " --> pdb=" O LEU H 6 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'H' and resid 76 through 81 removed outlier: 6.846A pdb=" N GLU H 76 " --> pdb=" O LYS H 141 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N PHE H 132 " --> pdb=" O ALA H 140 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'I' and resid 6 through 9 No H-bonds generated for sheet with id= 50 Processing sheet with id= 51, first strand: chain 'J' and resid 74 through 77 Processing sheet with id= 52, first strand: chain 'K' and resid 18 through 21 removed outlier: 4.023A pdb=" N THR K 6 " --> pdb=" O CYS K 21 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N ASN K 82 " --> pdb=" O MET K 7 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'M' and resid 37 through 40 No H-bonds generated for sheet with id= 53 Processing sheet with id= 54, first strand: chain 'M' and resid 62 through 65 removed outlier: 3.682A pdb=" N TYR M 103 " --> pdb=" O LEU M 33 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N MET M 105 " --> pdb=" O PHE M 31 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N LEU M 33 " --> pdb=" O LEU M 102 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'M' and resid 30 through 36 removed outlier: 7.180A pdb=" N SER M 30 " --> pdb=" O LYS M 133 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N LYS M 34 " --> pdb=" O THR M 129 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N LYS M 127 " --> pdb=" O VAL M 36 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'N' and resid 33 through 37 removed outlier: 4.963A pdb=" N MET N 110 " --> pdb=" O CYS N 100 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N CYS N 100 " --> pdb=" O MET N 110 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'O' and resid 49 through 52 removed outlier: 4.324A pdb=" N VAL O 49 " --> pdb=" O VAL O 39 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ARG O 25 " --> pdb=" O ILE O 40 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL O 28 " --> pdb=" O ASP O 93 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'P' and resid 36 through 45 removed outlier: 3.579A pdb=" N LYS P 36 " --> pdb=" O GLU P 33 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N THR P 24 " --> pdb=" O LYS P 86 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'P' and resid 56 through 63 removed outlier: 7.871A pdb=" N SER P 56 " --> pdb=" O THR P 75 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'R' and resid 11 through 15 removed outlier: 3.684A pdb=" N PHE R 5 " --> pdb=" O HIS R 12 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N TYR R 2 " --> pdb=" O ALA R 42 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'R' and resid 18 through 21 removed outlier: 4.433A pdb=" N GLN R 18 " --> pdb=" O ILE R 98 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ASP R 95 " --> pdb=" O VAL R 64 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N LYS R 60 " --> pdb=" O THR R 99 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'R' and resid 57 through 60 removed outlier: 4.128A pdb=" N VAL R 58 " --> pdb=" O SER R 102 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N SER R 102 " --> pdb=" O VAL R 58 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLY R 100 " --> pdb=" O LYS R 60 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'R' and resid 68 through 78 No H-bonds generated for sheet with id= 63 Processing sheet with id= 64, first strand: chain 'S' and resid 2 through 8 removed outlier: 4.177A pdb=" N THR S 3 " --> pdb=" O VAL S 107 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N VAL S 105 " --> pdb=" O ALA S 5 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N THR S 100 " --> pdb=" O GLY S 79 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLY S 79 " --> pdb=" O THR S 100 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'S' and resid 80 through 88 removed outlier: 4.006A pdb=" N ARG S 92 " --> pdb=" O ARG S 88 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'T' and resid 12 through 15 removed outlier: 3.516A pdb=" N ALA T 13 " --> pdb=" O LYS T 33 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N VAL T 31 " --> pdb=" O HIS T 15 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N LYS T 81 " --> pdb=" O VAL T 34 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'U' and resid 39 through 44 No H-bonds generated for sheet with id= 67 Processing sheet with id= 68, first strand: chain 'U' and resid 82 through 86 Processing sheet with id= 69, first strand: chain 'V' and resid 69 through 73 removed outlier: 6.441A pdb=" N PHE V 2 " --> pdb=" O VAL V 60 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ILE V 4 " --> pdb=" O THR V 62 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ARG V 9 " --> pdb=" O ALA V 39 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ALA V 39 " --> pdb=" O ARG V 9 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ILE V 89 " --> pdb=" O PRO V 27 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N HIS V 88 " --> pdb=" O GLN V 78 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'W' and resid 30 through 33 removed outlier: 4.476A pdb=" N SER W 31 " --> pdb=" O ALA W 57 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N LEU W 55 " --> pdb=" O ILE W 33 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N THR W 54 " --> pdb=" O GLY W 50 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N ASN W 46 " --> pdb=" O LYS W 58 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'W' and resid 62 through 67 Processing sheet with id= 72, first strand: chain 'X' and resid 10 through 15 removed outlier: 7.311A pdb=" N ARG X 10 " --> pdb=" O PRO X 30 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'X' and resid 33 through 40 Processing sheet with id= 74, first strand: chain 'Z' and resid 32 through 38 removed outlier: 4.299A pdb=" N HIS Z 33 " --> pdb=" O GLN Z 8 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LYS Z 5 " --> pdb=" O GLU Z 57 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N MET Z 53 " --> pdb=" O THR Z 9 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain '0' and resid 27 through 30 removed outlier: 6.058A pdb=" N SER 0 28 " --> pdb=" O LYS 0 36 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LYS 0 36 " --> pdb=" O SER 0 28 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ASP 0 30 " --> pdb=" O GLY 0 34 " (cutoff:3.500A) Processing sheet with id= 76, first strand: chain '1' and resid 19 through 24 removed outlier: 6.850A pdb=" N ILE 1 47 " --> pdb=" O SER 1 13 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU 1 35 " --> pdb=" O TYR 1 48 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N LEU 1 33 " --> pdb=" O GLU 1 50 " (cutoff:3.500A) Processing sheet with id= 77, first strand: chain '3' and resid 21 through 24 removed outlier: 5.678A pdb=" N PHE 3 21 " --> pdb=" O VAL 3 49 " (cutoff:3.500A) Processing sheet with id= 78, first strand: chain '4' and resid 14 through 18 removed outlier: 5.016A pdb=" N ILE 4 23 " --> pdb=" O GLN 4 37 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLN 4 35 " --> pdb=" O VAL 4 25 " (cutoff:3.500A) Processing sheet with id= 79, first strand: chain '5' and resid 24 through 28 removed outlier: 3.562A pdb=" N ALA 5 25 " --> pdb=" O SER 5 85 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL 5 27 " --> pdb=" O ALA 5 83 " (cutoff:3.500A) Processing sheet with id= 80, first strand: chain '6' and resid 20 through 25 removed outlier: 4.106A pdb=" N ASN 6 20 " --> pdb=" O CYS 6 16 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N CYS 6 16 " --> pdb=" O ASN 6 20 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU 6 32 " --> pdb=" O THR 6 13 " (cutoff:3.500A) Processing sheet with id= 81, first strand: chain '7' and resid 91 through 94 removed outlier: 6.622A pdb=" N VAL 7 56 " --> pdb=" O LEU 7 94 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N GLU 7 116 " --> pdb=" O LYS 7 59 " (cutoff:3.500A) 1958 hydrogen bonds defined for protein. 5799 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3434 hydrogen bonds 5410 hydrogen bond angles 0 basepair planarities 1390 basepair parallelities 2553 stacking parallelities Total time for adding SS restraints: 277.36 Time building geometry restraints manager: 61.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 28699 1.33 - 1.46: 67127 1.46 - 1.59: 56582 1.59 - 1.72: 8814 1.72 - 1.84: 277 Bond restraints: 161499 Sorted by residual: bond pdb=" C4 5MU A1939 " pdb=" C5 5MU A1939 " ideal model delta sigma weight residual 1.805 1.470 0.335 2.00e-02 2.50e+03 2.81e+02 bond pdb=" C4 5MU v 54 " pdb=" C5 5MU v 54 " ideal model delta sigma weight residual 1.805 1.476 0.329 2.00e-02 2.50e+03 2.71e+02 bond pdb=" N1 5MU A1939 " pdb=" C6 5MU A1939 " ideal model delta sigma weight residual 1.638 1.327 0.311 2.00e-02 2.50e+03 2.42e+02 bond pdb=" N1 5MU v 54 " pdb=" C6 5MU v 54 " ideal model delta sigma weight residual 1.638 1.337 0.301 2.00e-02 2.50e+03 2.26e+02 bond pdb=" C5 5MU v 54 " pdb=" C6 5MU v 54 " ideal model delta sigma weight residual 1.150 1.387 -0.237 2.00e-02 2.50e+03 1.40e+02 ... (remaining 161494 not shown) Histogram of bond angle deviations from ideal: 93.17 - 102.20: 4895 102.20 - 111.22: 93371 111.22 - 120.25: 80044 120.25 - 129.27: 58725 129.27 - 138.30: 3744 Bond angle restraints: 240779 Sorted by residual: angle pdb=" C4' G a1491 " pdb=" C3' G a1491 " pdb=" O3' G a1491 " ideal model delta sigma weight residual 113.00 126.26 -13.26 1.50e+00 4.44e-01 7.82e+01 angle pdb=" C ILE w 121 " pdb=" N PRO w 122 " pdb=" CA PRO w 122 " ideal model delta sigma weight residual 119.78 128.84 -9.06 1.03e+00 9.43e-01 7.73e+01 angle pdb=" C3' 4OC a1402 " pdb=" C2' 4OC a1402 " pdb=" C1' 4OC a1402 " ideal model delta sigma weight residual 101.30 109.88 -8.58 1.00e+00 1.00e+00 7.37e+01 angle pdb=" O3' 4OC a1402 " pdb=" C3' 4OC a1402 " pdb=" C2' 4OC a1402 " ideal model delta sigma weight residual 113.70 126.26 -12.56 1.50e+00 4.44e-01 7.01e+01 angle pdb=" N6 MA6 a1518 " pdb=" C6 MA6 a1518 " pdb=" N1 MA6 a1518 " ideal model delta sigma weight residual 98.71 120.85 -22.14 3.00e+00 1.11e-01 5.45e+01 ... (remaining 240774 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.13: 81811 35.13 - 70.25: 3284 70.25 - 105.38: 310 105.38 - 140.51: 44 140.51 - 175.64: 29 Dihedral angle restraints: 85478 sinusoidal: 67815 harmonic: 17663 Sorted by residual: dihedral pdb=" O4' C B 12 " pdb=" C1' C B 12 " pdb=" N1 C B 12 " pdb=" C2 C B 12 " ideal model delta sinusoidal sigma weight residual -160.00 -20.25 -139.75 1 1.50e+01 4.44e-03 7.52e+01 dihedral pdb=" O4' C A1914 " pdb=" C1' C A1914 " pdb=" N1 C A1914 " pdb=" C2 C A1914 " ideal model delta sinusoidal sigma weight residual -160.00 -21.21 -138.79 1 1.50e+01 4.44e-03 7.48e+01 dihedral pdb=" O4' U A1340 " pdb=" C1' U A1340 " pdb=" N1 U A1340 " pdb=" C2 U A1340 " ideal model delta sinusoidal sigma weight residual -128.00 43.77 -171.77 1 1.70e+01 3.46e-03 6.61e+01 ... (remaining 85475 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.111: 29695 0.111 - 0.223: 479 0.223 - 0.334: 30 0.334 - 0.446: 3 0.446 - 0.557: 1 Chirality restraints: 30208 Sorted by residual: chirality pdb=" C3' 4OC a1402 " pdb=" C4' 4OC a1402 " pdb=" O3' 4OC a1402 " pdb=" C2' 4OC a1402 " both_signs ideal model delta sigma weight residual False -2.48 -1.92 -0.56 2.00e-01 2.50e+01 7.77e+00 chirality pdb=" P G a 530 " pdb=" OP1 G a 530 " pdb=" OP2 G a 530 " pdb=" O5' G a 530 " both_signs ideal model delta sigma weight residual True 2.41 -2.02 0.39 2.00e-01 2.50e+01 3.87e+00 chirality pdb=" C3' G a1297 " pdb=" C4' G a1297 " pdb=" O3' G a1297 " pdb=" C2' G a1297 " both_signs ideal model delta sigma weight residual False -2.74 -2.37 -0.38 2.00e-01 2.50e+01 3.52e+00 ... (remaining 30205 not shown) Planarity restraints: 13518 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' OMC A2498 " 0.079 2.00e-02 2.50e+03 6.08e-01 8.33e+03 pdb=" C4' OMC A2498 " 0.424 2.00e-02 2.50e+03 pdb=" O4' OMC A2498 " 0.582 2.00e-02 2.50e+03 pdb=" C3' OMC A2498 " -0.616 2.00e-02 2.50e+03 pdb=" O3' OMC A2498 " -0.675 2.00e-02 2.50e+03 pdb=" C2' OMC A2498 " -0.156 2.00e-02 2.50e+03 pdb=" O2' OMC A2498 " 1.042 2.00e-02 2.50e+03 pdb=" C1' OMC A2498 " 0.221 2.00e-02 2.50e+03 pdb=" N1 OMC A2498 " -0.901 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMG A2251 " 0.058 2.00e-02 2.50e+03 6.01e-01 8.13e+03 pdb=" C4' OMG A2251 " 0.438 2.00e-02 2.50e+03 pdb=" O4' OMG A2251 " 0.645 2.00e-02 2.50e+03 pdb=" C3' OMG A2251 " -0.595 2.00e-02 2.50e+03 pdb=" O3' OMG A2251 " -0.624 2.00e-02 2.50e+03 pdb=" C2' OMG A2251 " -0.186 2.00e-02 2.50e+03 pdb=" O2' OMG A2251 " 0.979 2.00e-02 2.50e+03 pdb=" C1' OMG A2251 " 0.211 2.00e-02 2.50e+03 pdb=" N9 OMG A2251 " -0.927 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG a1516 " -0.047 2.00e-02 2.50e+03 5.95e-01 7.96e+03 pdb=" C4' 2MG a1516 " -0.448 2.00e-02 2.50e+03 pdb=" O4' 2MG a1516 " -0.665 2.00e-02 2.50e+03 pdb=" C3' 2MG a1516 " 0.588 2.00e-02 2.50e+03 pdb=" O3' 2MG a1516 " 0.610 2.00e-02 2.50e+03 pdb=" C2' 2MG a1516 " 0.194 2.00e-02 2.50e+03 pdb=" O2' 2MG a1516 " -0.937 2.00e-02 2.50e+03 pdb=" C1' 2MG a1516 " -0.221 2.00e-02 2.50e+03 pdb=" N9 2MG a1516 " 0.926 2.00e-02 2.50e+03 ... (remaining 13515 not shown) Histogram of nonbonded interaction distances: 0.97 - 1.76: 9 1.76 - 2.54: 671 2.54 - 3.33: 168384 3.33 - 4.11: 495331 4.11 - 4.90: 702929 Warning: very small nonbonded interaction distances. Nonbonded interactions: 1367324 Sorted by model distance: nonbonded pdb=" C2 A a1493 " pdb=" O2 U x 19 " model vdw 0.974 3.340 nonbonded pdb=" N3 A a1493 " pdb=" O2 U x 19 " model vdw 1.201 3.120 nonbonded pdb=" O ASN w 598 " pdb=" O4' A A2660 " model vdw 1.527 3.040 nonbonded pdb=" N6 A a 532 " pdb=" CE1 TYR c 192 " model vdw 1.538 3.420 nonbonded pdb=" OP1 A a1080 " pdb=" NZ LYS e 51 " model vdw 1.541 2.520 ... (remaining 1367319 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 Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 4645 5.49 5 S 156 5.16 5 C 74960 2.51 5 N 27910 2.21 5 O 41244 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.160 Extract box with map and model: 20.790 Check model and map are aligned: 1.620 Convert atoms to be neutral: 0.940 Process input model: 566.840 Find NCS groups from input model: 3.190 Set up NCS constraints: 0.430 Set refine NCS operators: 0.000 Set scattering table: 0.040 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.030 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 599.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.335 161499 Z= 0.393 Angle : 0.844 22.140 240779 Z= 0.513 Chirality : 0.037 0.557 30208 Planarity : 0.021 0.608 13518 Dihedral : 15.124 175.635 74531 Min Nonbonded Distance : 0.974 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 3.43 % Allowed : 10.93 % Favored : 85.64 % Rotamer Outliers : 3.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.83 (0.09), residues: 6551 helix: -3.19 (0.08), residues: 2036 sheet: -3.38 (0.13), residues: 1060 loop : -1.74 (0.10), residues: 3455 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13102 Ramachandran restraints generated. 6551 Oldfield, 0 Emsley, 6551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13102 Ramachandran restraints generated. 6551 Oldfield, 0 Emsley, 6551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2887 residues out of total 5475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 2732 time to evaluate : 6.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 155 outliers final: 35 residues processed: 2807 average time/residue: 1.5031 time to fit residues: 7116.1388 Evaluate side-chains 1778 residues out of total 5475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 1743 time to evaluate : 6.636 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 0 residues processed: 35 average time/residue: 1.2136 time to fit residues: 89.3795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1103 random chunks: chunk 931 optimal weight: 6.9990 chunk 836 optimal weight: 6.9990 chunk 463 optimal weight: 20.0000 chunk 285 optimal weight: 9.9990 chunk 563 optimal weight: 20.0000 chunk 446 optimal weight: 5.9990 chunk 864 optimal weight: 9.9990 chunk 334 optimal weight: 10.0000 chunk 525 optimal weight: 10.0000 chunk 643 optimal weight: 10.0000 chunk 1001 optimal weight: 5.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 14 HIS d 73 ASN ** e 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 96 GLN ** e 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 23 HIS k 63 GLN ** l 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 5 GLN ** l 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 19 ASN ** o 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 30 HIS q 44 HIS r 51 GLN r 53 GLN c 18 ASN c 68 HIS c 101 ASN c 189 HIS ** g 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 11 HIS ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 156 ASN ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 63 GLN H 33 GLN I 42 ASN ** J 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 77 HIS J 138 GLN ** K 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 93 ASN L 99 ASN M 3 GLN M 45 GLN O 29 HIS ** P 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 74 GLN P 76 HIS Q 71 ASN R 18 GLN S 7 HIS ** S 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 102 HIS T 15 HIS U 73 ASN ** V 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 15 ASN X 22 ASN ** Y 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 41 HIS Y 58 ASN Z 8 GLN 0 5 ASN ** 1 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 88 HIS 6 6 HIS ** 6 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.3596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.270 161499 Z= 0.367 Angle : 0.903 16.528 240779 Z= 0.467 Chirality : 0.044 0.460 30208 Planarity : 0.008 0.131 13518 Dihedral : 14.820 179.881 62920 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 21.47 Ramachandran Plot: Outliers : 1.02 % Allowed : 8.69 % Favored : 90.29 % Rotamer Outliers : 6.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.64 (0.10), residues: 6551 helix: -1.14 (0.10), residues: 2091 sheet: -2.79 (0.14), residues: 1091 loop : -1.71 (0.10), residues: 3369 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13102 Ramachandran restraints generated. 6551 Oldfield, 0 Emsley, 6551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13102 Ramachandran restraints generated. 6551 Oldfield, 0 Emsley, 6551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2334 residues out of total 5475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 333 poor density : 2001 time to evaluate : 6.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 333 outliers final: 198 residues processed: 2151 average time/residue: 1.3978 time to fit residues: 5246.1594 Evaluate side-chains 1931 residues out of total 5475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 198 poor density : 1733 time to evaluate : 6.701 Switching outliers to nearest non-outliers outliers start: 198 outliers final: 0 residues processed: 198 average time/residue: 1.1608 time to fit residues: 442.3361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1103 random chunks: chunk 556 optimal weight: 30.0000 chunk 310 optimal weight: 50.0000 chunk 833 optimal weight: 10.0000 chunk 682 optimal weight: 20.0000 chunk 276 optimal weight: 7.9990 chunk 1003 optimal weight: 3.9990 chunk 1084 optimal weight: 9.9990 chunk 893 optimal weight: 4.9990 chunk 995 optimal weight: 6.9990 chunk 342 optimal weight: 30.0000 chunk 805 optimal weight: 8.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 70 GLN ** e 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 96 GLN f 46 GLN k 14 GLN ** k 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 79 GLN r 51 GLN ** g 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 49 GLN j 58 ASN ** s 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 52 ASN ** C 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 133 ASN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 164 GLN E 41 GLN F 22 ASN ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 44 HIS G 47 ASN G 142 GLN I 5 GLN ** J 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 135 GLN ** K 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 54 GLN ** L 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 45 GLN ** N 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 38 GLN P 65 ASN P 76 HIS ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 6 GLN ** R 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 7 HIS ** T 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 12 GLN ** V 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 58 ASN ** Z 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 18 HIS 2 6 GLN ** 4 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 65 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.5049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.246 161499 Z= 0.311 Angle : 0.787 15.974 240779 Z= 0.417 Chirality : 0.040 0.326 30208 Planarity : 0.008 0.133 13518 Dihedral : 14.810 179.824 62920 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 18.51 Ramachandran Plot: Outliers : 0.90 % Allowed : 9.78 % Favored : 89.31 % Rotamer Outliers : 5.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.27 (0.10), residues: 6551 helix: -0.46 (0.11), residues: 2121 sheet: -2.42 (0.13), residues: 1160 loop : -1.82 (0.10), residues: 3270 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13102 Ramachandran restraints generated. 6551 Oldfield, 0 Emsley, 6551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13102 Ramachandran restraints generated. 6551 Oldfield, 0 Emsley, 6551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2220 residues out of total 5475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 266 poor density : 1954 time to evaluate : 6.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 266 outliers final: 143 residues processed: 2070 average time/residue: 1.3936 time to fit residues: 5035.4015 Evaluate side-chains 1833 residues out of total 5475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 1690 time to evaluate : 6.753 Switching outliers to nearest non-outliers outliers start: 143 outliers final: 0 residues processed: 143 average time/residue: 1.1656 time to fit residues: 322.0005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1103 random chunks: chunk 991 optimal weight: 5.9990 chunk 754 optimal weight: 20.0000 chunk 520 optimal weight: 10.0000 chunk 111 optimal weight: 20.0000 chunk 478 optimal weight: 20.0000 chunk 673 optimal weight: 20.0000 chunk 1007 optimal weight: 8.9990 chunk 1066 optimal weight: 10.0000 chunk 526 optimal weight: 10.0000 chunk 954 optimal weight: 9.9990 chunk 287 optimal weight: 8.9990 overall best weight: 8.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 197 HIS e 69 ASN ** e 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 37 HIS f 46 GLN f 52 ASN ** h 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 118 ASN ** l 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 71 HIS l 72 ASN l 76 HIS ** o 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 51 GLN ** g 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 4 GLN i 74 GLN m 7 ASN ** s 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 36 ASN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 GLN ** D 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 136 GLN G 47 ASN ** G 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 142 GLN ** I 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 106 GLN ** J 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 38 GLN ** O 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 67 ASN P 65 ASN P 76 HIS Q 19 GLN ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 71 ASN ** R 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 7 HIS S 102 HIS U 65 GLN ** V 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 88 HIS W 72 ASN ** Y 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 58 ASN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.6589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.208 161499 Z= 0.388 Angle : 0.873 22.489 240779 Z= 0.458 Chirality : 0.044 0.340 30208 Planarity : 0.008 0.127 13518 Dihedral : 15.187 177.902 62920 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 23.27 Ramachandran Plot: Outliers : 0.89 % Allowed : 9.45 % Favored : 89.67 % Rotamer Outliers : 6.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.44 (0.10), residues: 6551 helix: -0.51 (0.11), residues: 2110 sheet: -2.35 (0.13), residues: 1132 loop : -2.08 (0.10), residues: 3309 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13102 Ramachandran restraints generated. 6551 Oldfield, 0 Emsley, 6551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13102 Ramachandran restraints generated. 6551 Oldfield, 0 Emsley, 6551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2214 residues out of total 5475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 337 poor density : 1877 time to evaluate : 6.692 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 outliers start: 337 outliers final: 187 residues processed: 2036 average time/residue: 1.3253 time to fit residues: 4741.3694 Evaluate side-chains 1858 residues out of total 5475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 187 poor density : 1671 time to evaluate : 6.781 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 187 outliers final: 1 residues processed: 187 average time/residue: 1.0609 time to fit residues: 389.9180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1103 random chunks: chunk 887 optimal weight: 0.0980 chunk 605 optimal weight: 30.0000 chunk 15 optimal weight: 20.0000 chunk 793 optimal weight: 0.1980 chunk 439 optimal weight: 0.9990 chunk 909 optimal weight: 40.0000 chunk 736 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 544 optimal weight: 20.0000 chunk 956 optimal weight: 6.9990 chunk 269 optimal weight: 10.0000 overall best weight: 3.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 115 GLN e 60 GLN e 145 ASN f 46 GLN ** f 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 63 ASN ** h 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 27 ASN ** k 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 18 GLN r 51 GLN c 24 ASN ** c 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 4 GLN m 7 ASN s 51 HIS s 68 HIS ** C 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 238 ASN E 30 GLN E 90 GLN F 26 GLN G 47 ASN J 128 ASN ** L 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 38 GLN ** O 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 65 ASN Q 43 GLN ** Q 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 88 HIS ** W 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 33 HIS 0 40 HIS Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.6789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.178 161499 Z= 0.207 Angle : 0.715 16.945 240779 Z= 0.385 Chirality : 0.037 0.358 30208 Planarity : 0.007 0.126 13518 Dihedral : 14.897 179.593 62920 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 17.17 Ramachandran Plot: Outliers : 0.81 % Allowed : 8.99 % Favored : 90.20 % Rotamer Outliers : 3.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.07 (0.10), residues: 6551 helix: -0.07 (0.11), residues: 2120 sheet: -2.24 (0.13), residues: 1137 loop : -1.91 (0.10), residues: 3294 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13102 Ramachandran restraints generated. 6551 Oldfield, 0 Emsley, 6551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13102 Ramachandran restraints generated. 6551 Oldfield, 0 Emsley, 6551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2015 residues out of total 5475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 1853 time to evaluate : 6.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 162 outliers final: 89 residues processed: 1917 average time/residue: 1.3119 time to fit residues: 4405.0534 Evaluate side-chains 1764 residues out of total 5475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 1675 time to evaluate : 6.812 Switching outliers to nearest non-outliers outliers start: 89 outliers final: 0 residues processed: 89 average time/residue: 1.0978 time to fit residues: 192.8568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1103 random chunks: chunk 358 optimal weight: 50.0000 chunk 960 optimal weight: 5.9990 chunk 210 optimal weight: 20.0000 chunk 625 optimal weight: 20.0000 chunk 263 optimal weight: 0.8980 chunk 1067 optimal weight: 4.9990 chunk 885 optimal weight: 6.9990 chunk 494 optimal weight: 20.0000 chunk 88 optimal weight: 10.0000 chunk 353 optimal weight: 7.9990 chunk 560 optimal weight: 30.0000 overall best weight: 5.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 40 HIS ** d 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 69 ASN e 96 GLN f 37 HIS f 46 GLN k 14 GLN ** k 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 5 GLN ** o 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 18 GLN ** t 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 54 GLN c 101 ASN ** g 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 147 ASN i 74 GLN ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 116 GLN ** C 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN D 134 HIS E 30 GLN F 62 GLN G 47 ASN G 138 GLN ** I 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 128 ASN ** L 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 38 GLN ** O 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 51 GLN ** Q 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 59 ASN ** V 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 37 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.7222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.152 161499 Z= 0.255 Angle : 0.742 15.351 240779 Z= 0.397 Chirality : 0.039 0.333 30208 Planarity : 0.007 0.127 13518 Dihedral : 14.886 179.323 62920 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 19.54 Ramachandran Plot: Outliers : 0.82 % Allowed : 9.45 % Favored : 89.73 % Rotamer Outliers : 4.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.02 (0.10), residues: 6551 helix: 0.01 (0.11), residues: 2111 sheet: -2.12 (0.13), residues: 1141 loop : -1.95 (0.10), residues: 3299 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13102 Ramachandran restraints generated. 6551 Oldfield, 0 Emsley, 6551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13102 Ramachandran restraints generated. 6551 Oldfield, 0 Emsley, 6551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2021 residues out of total 5475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 223 poor density : 1798 time to evaluate : 6.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 223 outliers final: 131 residues processed: 1882 average time/residue: 1.3721 time to fit residues: 4545.4836 Evaluate side-chains 1799 residues out of total 5475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 1668 time to evaluate : 6.740 Switching outliers to nearest non-outliers outliers start: 131 outliers final: 0 residues processed: 131 average time/residue: 1.1710 time to fit residues: 297.3496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1103 random chunks: chunk 1028 optimal weight: 20.0000 chunk 120 optimal weight: 20.0000 chunk 608 optimal weight: 10.0000 chunk 779 optimal weight: 8.9990 chunk 603 optimal weight: 20.0000 chunk 898 optimal weight: 5.9990 chunk 595 optimal weight: 20.0000 chunk 1063 optimal weight: 10.0000 chunk 665 optimal weight: 50.0000 chunk 648 optimal weight: 10.0000 chunk 490 optimal weight: 10.0000 overall best weight: 8.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 46 GLN ** k 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 18 GLN ** t 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 147 ASN ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 72 ASN G 114 HIS ** M 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 9 GLN O 38 GLN ** O 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 19 GLN ** Q 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 48 GLN V 44 HIS W 42 HIS ** Y 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.7405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 1.065 161499 Z= 0.440 Angle : 0.851 106.096 240779 Z= 0.439 Chirality : 0.042 0.327 30208 Planarity : 0.008 0.348 13518 Dihedral : 14.967 179.998 62920 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 21.04 Ramachandran Plot: Outliers : 0.81 % Allowed : 10.01 % Favored : 89.18 % Rotamer Outliers : 3.98 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.10 (0.10), residues: 6551 helix: -0.07 (0.11), residues: 2111 sheet: -2.09 (0.14), residues: 1120 loop : -2.02 (0.10), residues: 3320 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13102 Ramachandran restraints generated. 6551 Oldfield, 0 Emsley, 6551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13102 Ramachandran restraints generated. 6551 Oldfield, 0 Emsley, 6551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1901 residues out of total 5475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 192 poor density : 1709 time to evaluate : 6.765 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 outliers start: 192 outliers final: 129 residues processed: 1786 average time/residue: 1.4055 time to fit residues: 4460.5991 Evaluate side-chains 1763 residues out of total 5475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 1634 time to evaluate : 6.712 Switching outliers to nearest non-outliers outliers start: 129 outliers final: 0 residues processed: 129 average time/residue: 1.1355 time to fit residues: 285.8147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1103 random chunks: chunk 657 optimal weight: 10.0000 chunk 424 optimal weight: 0.9990 chunk 634 optimal weight: 10.0000 chunk 320 optimal weight: 50.0000 chunk 208 optimal weight: 20.0000 chunk 205 optimal weight: 0.6980 chunk 675 optimal weight: 10.0000 chunk 724 optimal weight: 10.0000 chunk 525 optimal weight: 10.0000 chunk 99 optimal weight: 30.0000 chunk 835 optimal weight: 6.9990 overall best weight: 5.7392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 17 HIS ** d 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 96 GLN e 134 ASN f 46 GLN ** k 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 18 GLN ** t 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 24 ASN c 101 ASN ** g 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 125 GLN C 36 ASN C 52 HIS ** G 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 114 HIS ** I 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 38 GLN ** O 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 19 GLN ** Q 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 80 ASN ** R 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 48 GLN ** Y 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.7455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.897 161499 Z= 0.342 Angle : 0.813 80.645 240779 Z= 0.424 Chirality : 0.039 0.461 30208 Planarity : 0.008 0.131 13518 Dihedral : 14.960 179.883 62920 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 20.63 Ramachandran Plot: Outliers : 0.76 % Allowed : 9.94 % Favored : 89.30 % Rotamer Outliers : 2.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.10 (0.10), residues: 6551 helix: -0.08 (0.11), residues: 2114 sheet: -2.06 (0.14), residues: 1131 loop : -2.04 (0.10), residues: 3306 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13102 Ramachandran restraints generated. 6551 Oldfield, 0 Emsley, 6551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13102 Ramachandran restraints generated. 6551 Oldfield, 0 Emsley, 6551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1816 residues out of total 5475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 1699 time to evaluate : 6.666 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 outliers start: 117 outliers final: 78 residues processed: 1732 average time/residue: 1.3121 time to fit residues: 4010.5246 Evaluate side-chains 1729 residues out of total 5475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 1651 time to evaluate : 6.684 Switching outliers to nearest non-outliers outliers start: 78 outliers final: 0 residues processed: 78 average time/residue: 1.1039 time to fit residues: 171.5402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1103 random chunks: chunk 967 optimal weight: 4.9990 chunk 1018 optimal weight: 20.0000 chunk 929 optimal weight: 6.9990 chunk 990 optimal weight: 6.9990 chunk 596 optimal weight: 20.0000 chunk 431 optimal weight: 4.9990 chunk 777 optimal weight: 8.9990 chunk 304 optimal weight: 30.0000 chunk 895 optimal weight: 5.9990 chunk 936 optimal weight: 20.0000 chunk 987 optimal weight: 6.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 145 ASN ** h 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 39 ASN ** k 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 18 GLN ** t 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 19 HIS c 24 ASN ** g 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 38 GLN ** O 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 19 GLN ** Q 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 48 GLN ** Y 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 19 HIS ** 0 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.7465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.795 161499 Z= 0.406 Angle : 0.834 106.099 240779 Z= 0.434 Chirality : 0.039 0.592 30208 Planarity : 0.008 0.186 13518 Dihedral : 14.960 179.898 62920 Min Nonbonded Distance : 1.814 Molprobity Statistics. All-atom Clashscore : 22.28 Ramachandran Plot: Outliers : 0.79 % Allowed : 9.97 % Favored : 89.24 % Rotamer Outliers : 1.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.10 (0.10), residues: 6551 helix: -0.07 (0.11), residues: 2114 sheet: -2.04 (0.14), residues: 1131 loop : -2.05 (0.10), residues: 3306 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13102 Ramachandran restraints generated. 6551 Oldfield, 0 Emsley, 6551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13102 Ramachandran restraints generated. 6551 Oldfield, 0 Emsley, 6551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1745 residues out of total 5475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 1669 time to evaluate : 6.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 76 outliers final: 62 residues processed: 1687 average time/residue: 1.3057 time to fit residues: 3893.9044 Evaluate side-chains 1704 residues out of total 5475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 1642 time to evaluate : 6.650 Switching outliers to nearest non-outliers outliers start: 62 outliers final: 0 residues processed: 62 average time/residue: 1.1363 time to fit residues: 138.8748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1103 random chunks: chunk 650 optimal weight: 10.0000 chunk 1047 optimal weight: 4.9990 chunk 639 optimal weight: 20.0000 chunk 496 optimal weight: 10.0000 chunk 728 optimal weight: 20.0000 chunk 1098 optimal weight: 2.9990 chunk 1011 optimal weight: 8.9990 chunk 875 optimal weight: 5.9990 chunk 90 optimal weight: 10.0000 chunk 675 optimal weight: 10.0000 chunk 536 optimal weight: 20.0000 overall best weight: 6.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 24 ASN c 101 ASN ** g 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 38 GLN ** O 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 19 GLN ** Q 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 48 GLN ** T 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.7468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 1.722 161499 Z= 0.522 Angle : 0.868 106.100 240779 Z= 0.463 Chirality : 0.039 0.592 30208 Planarity : 0.008 0.186 13518 Dihedral : 14.960 179.898 62920 Min Nonbonded Distance : 1.532 Molprobity Statistics. All-atom Clashscore : 23.09 Ramachandran Plot: Outliers : 0.79 % Allowed : 9.97 % Favored : 89.24 % Rotamer Outliers : 0.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.10 (0.10), residues: 6551 helix: -0.07 (0.11), residues: 2114 sheet: -2.04 (0.14), residues: 1131 loop : -2.05 (0.10), residues: 3306 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13102 Ramachandran restraints generated. 6551 Oldfield, 0 Emsley, 6551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13102 Ramachandran restraints generated. 6551 Oldfield, 0 Emsley, 6551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1653 residues out of total 5475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1652 time to evaluate : 6.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 1653 average time/residue: 1.3015 time to fit residues: 3844.4143 Evaluate side-chains 1643 residues out of total 5475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1642 time to evaluate : 6.785 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 1.0939 time to fit residues: 9.4894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1103 random chunks: chunk 695 optimal weight: 10.0000 chunk 932 optimal weight: 7.9990 chunk 268 optimal weight: 9.9990 chunk 806 optimal weight: 9.9990 chunk 129 optimal weight: 20.0000 chunk 243 optimal weight: 20.0000 chunk 876 optimal weight: 0.0370 chunk 366 optimal weight: 50.0000 chunk 899 optimal weight: 8.9990 chunk 110 optimal weight: 20.0000 chunk 161 optimal weight: 10.0000 overall best weight: 7.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 145 ASN ** h 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 18 GLN ** t 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 19 HIS c 24 ASN ** g 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 38 GLN ** O 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 19 GLN ** Q 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 48 GLN ** Y 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.081179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.065747 restraints weight = 566694.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 64)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.067602 restraints weight = 188062.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 70)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.068689 restraints weight = 99393.933| |-----------------------------------------------------------------------------| r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.7470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 1.722 161499 Z= 0.522 Angle : 0.868 106.100 240779 Z= 0.463 Chirality : 0.039 0.592 30208 Planarity : 0.008 0.186 13518 Dihedral : 14.960 179.898 62920 Min Nonbonded Distance : 1.532 Molprobity Statistics. All-atom Clashscore : 23.19 Ramachandran Plot: Outliers : 0.79 % Allowed : 9.97 % Favored : 89.24 % Rotamer Outliers : 0.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.10 (0.10), residues: 6551 helix: -0.07 (0.11), residues: 2114 sheet: -2.04 (0.14), residues: 1131 loop : -2.05 (0.10), residues: 3306 =============================================================================== Job complete usr+sys time: 59061.37 seconds wall clock time: 1008 minutes 11.52 seconds (60491.52 seconds total)