Starting phenix.real_space_refine on Mon Mar 25 10:20:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9y_6311/03_2024/3j9y_6311_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9y_6311/03_2024/3j9y_6311.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9y_6311/03_2024/3j9y_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_6311/03_2024/3j9y_6311_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9y_6311/03_2024/3j9y_6311_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9y_6311/03_2024/3j9y_6311.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9y_6311/03_2024/3j9y_6311.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9y_6311/03_2024/3j9y_6311_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9y_6311/03_2024/3j9y_6311_updated.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 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. 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: 0.25s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: {'p5*END': 1, 'rna2p': 1, 'rna2p_pur': 87, 'rna2p_pyr': 42, 'rna3p': 10, 'rna3p_pur': 781, 'rna3p_pyr': 618} Link IDs: {'rna2p': 130, 'rna3p': 1408} 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: {'p5*END': 1, 'rna2p': 1, 'rna2p_pur': 5, 'rna2p_pyr': 2, 'rna3p': 3, 'rna3p_pur': 34, 'rna3p_pyr': 32} Link IDs: {'rna2p': 7, 'rna3p': 69} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 2 Chain: "x" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 189 Classifications: {'RNA': 9} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 3, 'rna3p_pyr': 5} Link IDs: {'rna2p': 1, 'rna3p': 7} 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, 'PCIS': 1, 'PTRANS': 27, 'TRANS': 594} 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: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 198} 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: {'p5*END': 1, 'rna2p': 7, 'rna2p_pur': 203, 'rna2p_pyr': 87, 'rna3p': 17, 'rna3p_pur': 1463, 'rna3p_pyr': 1123} Link IDs: {'rna2p': 297, 'rna3p': 2602} 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: {'p5*END': 1, 'rna2p_pur': 3, 'rna2p_pyr': 2, 'rna3p_pur': 62, 'rna3p_pyr': 53} Link IDs: {'rna2p': 5, 'rna3p': 114} 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: {'PCIS': 1, 'TRANS': 67} 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: 57.70, per 1000 atoms: 0.39 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: 65.97 Conformation dependent library (CDL) restraints added in 7.1 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 for structures that cannot fit in PDB format. 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: 78.00 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: 258.47 Time building geometry restraints manager: 71.20 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 1.802 1.470 0.332 2.00e-02 2.50e+03 2.76e+02 bond pdb=" C4 5MU v 54 " pdb=" C5 5MU v 54 " ideal model delta sigma weight residual 1.802 1.476 0.326 2.00e-02 2.50e+03 2.66e+02 bond pdb=" N1 5MU A1939 " pdb=" C6 5MU A1939 " ideal model delta sigma weight residual 1.635 1.327 0.308 2.00e-02 2.50e+03 2.37e+02 bond pdb=" N1 5MU v 54 " pdb=" C6 5MU v 54 " ideal model delta sigma weight residual 1.635 1.337 0.298 2.00e-02 2.50e+03 2.22e+02 bond pdb=" C5 5MU v 54 " pdb=" C6 5MU v 54 " ideal model delta sigma weight residual 1.155 1.387 -0.232 2.00e-02 2.50e+03 1.34e+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=" P G a 530 " pdb=" O5' G a 530 " pdb=" C5' G a 530 " ideal model delta sigma weight residual 120.90 109.85 11.05 1.50e+00 4.44e-01 5.43e+01 ... (remaining 240774 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.13: 89227 35.13 - 70.25: 11563 70.25 - 105.38: 1367 105.38 - 140.51: 46 140.51 - 175.64: 30 Dihedral angle restraints: 102233 sinusoidal: 84570 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 102230 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 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: 2.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.140 Extract box with map and model: 16.590 Check model and map are aligned: 1.600 Set scattering table: 1.030 Process input model: 564.580 Find NCS groups from input model: 3.190 Set up NCS constraints: 0.430 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.030 Load rotamer database and sin/cos tables:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 592.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 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 0.332 161499 Z= 0.391 Angle : 0.837 19.077 240779 Z= 0.512 Chirality : 0.037 0.557 30208 Planarity : 0.021 0.608 13518 Dihedral : 23.315 175.635 91286 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 % Allowed : 6.30 % Favored : 90.49 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 78 HIS 0.033 0.002 HIS d 119 PHE 0.020 0.002 PHE g 25 TYR 0.021 0.002 TYR M 91 ARG 0.017 0.001 ARG g 137 *********************** 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 : 6.441 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 REVERT: b 80 LYS cc_start: 0.8991 (tttt) cc_final: 0.8532 (ptpt) REVERT: b 107 ARG cc_start: 0.6935 (ttp-170) cc_final: 0.6727 (mtm110) REVERT: b 114 LYS cc_start: 0.8286 (ttmt) cc_final: 0.7934 (ttpt) REVERT: b 152 ASP cc_start: 0.6675 (m-30) cc_final: 0.6258 (t0) REVERT: b 185 ILE cc_start: 0.8817 (OUTLIER) cc_final: 0.8162 (mm) REVERT: d 46 ARG cc_start: 0.4799 (tpp-160) cc_final: 0.4547 (tpt170) REVERT: d 115 GLN cc_start: -0.0967 (OUTLIER) cc_final: -0.1642 (mm-40) REVERT: e 71 ILE cc_start: 0.8074 (mm) cc_final: 0.7770 (pt) REVERT: e 81 GLN cc_start: 0.6785 (mm110) cc_final: 0.6357 (mm-40) REVERT: e 102 THR cc_start: 0.8869 (m) cc_final: 0.8521 (p) REVERT: e 121 ASN cc_start: 0.5702 (p0) cc_final: 0.5190 (p0) REVERT: e 145 ASN cc_start: 0.7264 (t0) cc_final: 0.6913 (t0) REVERT: f 54 LEU cc_start: 0.7778 (OUTLIER) cc_final: 0.7365 (tp) REVERT: h 8 ASP cc_start: 0.8226 (t70) cc_final: 0.7760 (t0) REVERT: h 17 GLN cc_start: 0.7129 (mm110) cc_final: 0.6389 (mp10) REVERT: h 63 LYS cc_start: 0.7665 (mtpm) cc_final: 0.7037 (mtpp) REVERT: h 88 LYS cc_start: 0.7612 (tttm) cc_final: 0.7384 (tptm) REVERT: h 93 LYS cc_start: 0.7420 (ptpt) cc_final: 0.7214 (mmtt) REVERT: h 128 VAL cc_start: 0.8884 (t) cc_final: 0.8437 (t) REVERT: o 14 PHE cc_start: 0.7993 (m-80) cc_final: 0.7743 (m-80) REVERT: p 23 ASP cc_start: 0.5370 (t70) cc_final: 0.4762 (t70) REVERT: q 49 ASN cc_start: 0.6437 (p0) cc_final: 0.5227 (p0) REVERT: q 51 GLU cc_start: 0.5420 (OUTLIER) cc_final: 0.5096 (pm20) REVERT: r 20 ILE cc_start: 0.8793 (mm) cc_final: 0.8572 (mm) REVERT: r 24 ASP cc_start: 0.7137 (OUTLIER) cc_final: 0.6886 (p0) REVERT: t 28 ARG cc_start: 0.7965 (ptp-170) cc_final: 0.7689 (ptp-170) REVERT: t 58 ASP cc_start: 0.7855 (m-30) cc_final: 0.7625 (t0) REVERT: u 30 GLU cc_start: 0.7239 (tm-30) cc_final: 0.6270 (tt0) REVERT: w 508 SER cc_start: 0.9263 (m) cc_final: 0.8985 (p) REVERT: c 36 PHE cc_start: 0.8923 (t80) cc_final: 0.8669 (t80) REVERT: c 161 ILE cc_start: 0.8678 (OUTLIER) cc_final: 0.8351 (mm) REVERT: c 164 THR cc_start: 0.8446 (p) cc_final: 0.7974 (p) REVERT: g 6 ILE cc_start: 0.4451 (OUTLIER) cc_final: 0.4181 (tt) REVERT: g 46 LEU cc_start: 0.8927 (mp) cc_final: 0.8694 (pp) REVERT: g 88 VAL cc_start: 0.8227 (p) cc_final: 0.7904 (m) REVERT: g 96 ASN cc_start: 0.8366 (p0) cc_final: 0.8032 (p0) REVERT: g 104 VAL cc_start: 0.8901 (t) cc_final: 0.8471 (m) REVERT: i 61 ASP cc_start: 0.7537 (p0) cc_final: 0.6783 (t70) REVERT: j 17 LEU cc_start: 0.8569 (tt) cc_final: 0.8195 (tp) REVERT: n 54 ASP cc_start: 0.8633 (m-30) cc_final: 0.8314 (p0) REVERT: s 68 HIS cc_start: 0.8097 (m90) cc_final: 0.7662 (m-70) REVERT: C 146 LYS cc_start: 0.8513 (mttt) cc_final: 0.8300 (mtpp) REVERT: C 170 TYR cc_start: 0.7804 (m-80) cc_final: 0.6050 (m-80) REVERT: C 212 TRP cc_start: 0.9048 (p90) cc_final: 0.8371 (p90) REVERT: C 224 MET cc_start: 0.8807 (mtt) cc_final: 0.8421 (mtt) REVERT: D 8 LYS cc_start: 0.6999 (tttt) cc_final: 0.6629 (ttpp) REVERT: D 21 SER cc_start: 0.8842 (t) cc_final: 0.8608 (p) REVERT: D 110 THR cc_start: 0.8589 (m) cc_final: 0.8353 (p) REVERT: D 128 ARG cc_start: 0.8006 (mtm-85) cc_final: 0.7515 (ttm110) REVERT: D 149 ASN cc_start: 0.7993 (t0) cc_final: 0.7601 (t0) REVERT: E 1 MET cc_start: 0.4994 (tpp) cc_final: 0.4023 (ttp) REVERT: E 23 PHE cc_start: 0.7745 (t80) cc_final: 0.7309 (t80) REVERT: E 24 ASN cc_start: 0.7594 (t0) cc_final: 0.7384 (t0) REVERT: E 25 GLU cc_start: 0.7616 (tt0) cc_final: 0.7290 (tp30) REVERT: E 116 ASP cc_start: 0.8689 (m-30) cc_final: 0.8213 (t0) REVERT: E 125 SER cc_start: 0.6771 (p) cc_final: 0.6566 (m) REVERT: E 131 THR cc_start: 0.8344 (p) cc_final: 0.8045 (t) REVERT: E 189 THR cc_start: 0.7955 (m) cc_final: 0.6617 (m) REVERT: F 4 HIS cc_start: 0.7438 (t-170) cc_final: 0.7233 (t-170) REVERT: F 9 ASP cc_start: 0.6951 (OUTLIER) cc_final: 0.6496 (p0) REVERT: F 34 THR cc_start: 0.7400 (m) cc_final: 0.7148 (p) REVERT: F 72 SER cc_start: 0.4504 (t) cc_final: 0.4231 (p) REVERT: F 77 LYS cc_start: 0.8462 (mtmt) cc_final: 0.8033 (tttt) REVERT: F 109 ARG cc_start: 0.7492 (mtp85) cc_final: 0.7252 (mtp85) REVERT: F 119 LYS cc_start: 0.8361 (mttp) cc_final: 0.8161 (tmtt) REVERT: F 151 LEU cc_start: 0.6221 (pp) cc_final: 0.5965 (pp) REVERT: F 154 THR cc_start: 0.7417 (m) cc_final: 0.6788 (p) REVERT: F 169 LEU cc_start: 0.7975 (mt) cc_final: 0.7737 (mt) REVERT: F 172 PHE cc_start: 0.7684 (m-80) cc_final: 0.7404 (m-80) REVERT: F 173 ASP cc_start: 0.8605 (m-30) cc_final: 0.8341 (t70) REVERT: F 174 PHE cc_start: 0.7544 (t80) cc_final: 0.7318 (t80) REVERT: G 61 TRP cc_start: 0.6369 (m100) cc_final: 0.5727 (m100) REVERT: G 76 ILE cc_start: 0.7671 (mm) cc_final: 0.7164 (mm) REVERT: G 108 PHE cc_start: 0.6326 (m-10) cc_final: 0.6071 (m-10) REVERT: G 114 HIS cc_start: 0.6436 (t70) cc_final: 0.6150 (t70) REVERT: H 27 ARG cc_start: 0.7014 (ttp-110) cc_final: 0.6766 (ttp-110) REVERT: H 43 ASN cc_start: 0.8284 (m-40) cc_final: 0.7986 (t0) REVERT: I 85 ILE cc_start: 0.5815 (OUTLIER) cc_final: 0.5332 (tp) REVERT: I 121 ILE cc_start: 0.7950 (mt) cc_final: 0.7612 (tp) REVERT: I 124 MET cc_start: 0.4427 (mtm) cc_final: 0.3961 (ptm) REVERT: I 134 SER cc_start: 0.7441 (OUTLIER) cc_final: 0.7100 (t) REVERT: J 14 ASP cc_start: 0.7571 (t0) cc_final: 0.7075 (t0) REVERT: J 36 LEU cc_start: 0.9067 (mt) cc_final: 0.8664 (mt) REVERT: J 48 VAL cc_start: 0.8752 (t) cc_final: 0.8508 (t) REVERT: J 64 VAL cc_start: 0.7176 (OUTLIER) cc_final: 0.6792 (m) REVERT: J 89 PHE cc_start: 0.8366 (t80) cc_final: 0.8092 (t80) REVERT: K 29 HIS cc_start: 0.8233 (t-90) cc_final: 0.7780 (t-90) REVERT: K 32 TYR cc_start: 0.8382 (OUTLIER) cc_final: 0.8097 (p90) REVERT: K 58 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8670 (pp) REVERT: L 121 THR cc_start: 0.6569 (m) cc_final: 0.6208 (t) REVERT: M 38 ARG cc_start: 0.8468 (ttm-80) cc_final: 0.8246 (ttm-80) REVERT: M 54 THR cc_start: 0.9121 (m) cc_final: 0.8894 (t) REVERT: M 60 GLN cc_start: 0.8209 (pt0) cc_final: 0.7994 (pm20) REVERT: M 65 ILE cc_start: 0.9181 (mt) cc_final: 0.8927 (mt) REVERT: M 75 GLU cc_start: 0.7863 (tp30) cc_final: 0.7401 (tt0) REVERT: M 97 GLN cc_start: 0.8568 (mp10) cc_final: 0.8321 (mp10) REVERT: N 94 TYR cc_start: 0.7772 (m-80) cc_final: 0.7181 (m-80) REVERT: N 100 CYS cc_start: 0.8193 (p) cc_final: 0.7961 (t) REVERT: N 107 ASN cc_start: 0.8014 (t0) cc_final: 0.7666 (t0) REVERT: N 110 MET cc_start: 0.8337 (mmp) cc_final: 0.7990 (mmm) REVERT: O 47 VAL cc_start: 0.6334 (m) cc_final: 0.5398 (m) REVERT: O 95 SER cc_start: 0.8271 (m) cc_final: 0.7966 (t) REVERT: Q 27 ARG cc_start: 0.8643 (mtp-110) cc_final: 0.8347 (ttm110) REVERT: Q 60 TRP cc_start: 0.9242 (m-10) cc_final: 0.8533 (m-10) REVERT: Q 89 ILE cc_start: 0.7906 (mt) cc_final: 0.7570 (mt) REVERT: Q 100 PHE cc_start: 0.6980 (m-80) cc_final: 0.6763 (m-80) REVERT: R 2 TYR cc_start: 0.7035 (p90) cc_final: 0.6325 (p90) REVERT: S 23 LEU cc_start: 0.8369 (mt) cc_final: 0.8158 (mt) REVERT: S 78 GLU cc_start: 0.8744 (pt0) cc_final: 0.8289 (pt0) REVERT: S 86 MET cc_start: 0.8836 (tpt) cc_final: 0.8511 (ttp) REVERT: S 102 HIS cc_start: 0.8453 (m-70) cc_final: 0.8098 (m-70) REVERT: S 107 VAL cc_start: 0.8602 (OUTLIER) cc_final: 0.8249 (t) REVERT: S 108 SER cc_start: 0.8032 (t) cc_final: 0.7776 (t) REVERT: T 1 MET cc_start: 0.2689 (ptm) cc_final: 0.1979 (mmm) REVERT: T 37 ASP cc_start: 0.8190 (p0) cc_final: 0.7891 (p0) REVERT: U 4 ILE cc_start: 0.9230 (mp) cc_final: 0.8973 (tp) REVERT: U 6 ARG cc_start: 0.8187 (tpt90) cc_final: 0.7953 (tmm-80) REVERT: U 36 GLU cc_start: 0.7958 (pm20) cc_final: 0.7534 (pm20) REVERT: V 24 ASN cc_start: 0.8368 (m-40) cc_final: 0.7907 (t0) REVERT: V 31 TYR cc_start: 0.7186 (p90) cc_final: 0.6922 (p90) REVERT: V 48 MET cc_start: 0.8873 (tpt) cc_final: 0.8658 (tpt) REVERT: W 19 VAL cc_start: 0.8619 (t) cc_final: 0.8231 (m) REVERT: W 78 ILE cc_start: 0.8818 (mt) cc_final: 0.8615 (mt) REVERT: X 37 PHE cc_start: 0.7783 (m-80) cc_final: 0.7555 (m-80) REVERT: Y 6 LEU cc_start: 0.6657 (tp) cc_final: 0.6411 (tp) REVERT: Y 21 LEU cc_start: 0.9057 (mt) cc_final: 0.8736 (mt) REVERT: Y 39 GLN cc_start: 0.6830 (pt0) cc_final: 0.6431 (pt0) REVERT: Y 40 SER cc_start: 0.7609 (OUTLIER) cc_final: 0.7216 (p) REVERT: Y 42 LEU cc_start: 0.8468 (mt) cc_final: 0.7916 (mt) REVERT: 2 19 ARG cc_start: 0.8966 (mtp85) cc_final: 0.8613 (mmm160) REVERT: 3 6 VAL cc_start: 0.9425 (t) cc_final: 0.9188 (m) REVERT: 3 63 TYR cc_start: 0.7237 (m-80) cc_final: 0.6828 (m-80) REVERT: 4 35 GLN cc_start: 0.8234 (pt0) cc_final: 0.7896 (pt0) REVERT: 5 1 MET cc_start: 0.0957 (tpt) cc_final: -0.0078 (mmt) REVERT: 5 3 LEU cc_start: 0.4533 (OUTLIER) cc_final: 0.4168 (mp) REVERT: 5 38 MET cc_start: 0.4685 (mtm) cc_final: 0.4437 (ptm) REVERT: 5 59 LEU cc_start: 0.6338 (tp) cc_final: 0.5987 (mt) REVERT: 5 122 GLN cc_start: 0.5973 (OUTLIER) cc_final: 0.5631 (pp30) REVERT: 6 16 CYS cc_start: 0.3350 (OUTLIER) cc_final: 0.3093 (t) outliers start: 155 outliers final: 35 residues processed: 2807 average time/residue: 1.5029 time to fit residues: 7080.1971 Evaluate side-chains 1840 residues out of total 5475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 1787 time to evaluate : 6.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 71 THR Chi-restraints excluded: chain b residue 185 ILE Chi-restraints excluded: chain b residue 198 VAL Chi-restraints excluded: chain d residue 16 THR Chi-restraints excluded: chain d residue 115 GLN Chi-restraints excluded: chain e residue 45 VAL Chi-restraints excluded: chain e residue 122 VAL Chi-restraints excluded: chain e residue 158 LYS Chi-restraints excluded: chain f residue 54 LEU Chi-restraints excluded: chain h residue 58 LEU Chi-restraints excluded: chain k residue 30 ILE Chi-restraints excluded: chain k residue 39 ASN Chi-restraints excluded: chain k residue 109 ILE Chi-restraints excluded: chain l residue 54 VAL Chi-restraints excluded: chain p residue 19 VAL Chi-restraints excluded: chain q residue 51 GLU Chi-restraints excluded: chain r residue 24 ASP Chi-restraints excluded: chain c residue 105 VAL Chi-restraints excluded: chain c residue 161 ILE Chi-restraints excluded: chain g residue 6 ILE Chi-restraints excluded: chain i residue 54 VAL Chi-restraints excluded: chain i residue 60 LEU Chi-restraints excluded: chain m residue 24 VAL Chi-restraints excluded: chain n residue 60 GLN Chi-restraints excluded: chain C residue 45 ASN Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain F residue 3 LEU Chi-restraints excluded: chain F residue 9 ASP Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 134 GLN Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain I residue 85 ILE Chi-restraints excluded: chain I residue 95 ASP Chi-restraints excluded: chain I residue 100 ILE Chi-restraints excluded: chain I residue 134 SER Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain J residue 64 VAL Chi-restraints excluded: chain K residue 32 TYR Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 110 VAL Chi-restraints excluded: chain P residue 7 LEU Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain Q residue 48 ASP Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 107 VAL Chi-restraints excluded: chain U residue 48 VAL Chi-restraints excluded: chain Y residue 40 SER Chi-restraints excluded: chain 0 residue 24 VAL Chi-restraints excluded: chain 5 residue 3 LEU Chi-restraints excluded: chain 5 residue 122 GLN Chi-restraints excluded: chain 6 residue 16 CYS 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: 2.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 14 HIS d 73 ASN d 115 GLN e 72 ASN e 88 HIS e 96 GLN ** e 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ** s 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 41 GLN E 156 ASN ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 134 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 29 HIS ** 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** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Y 58 ASN Z 8 GLN 0 5 ASN 5 88 HIS 5 122 GLN 6 6 HIS 6 65 ASN Total number of N/Q/H flips: 47 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.3513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.122 161499 Z= 0.323 Angle : 0.871 15.866 240779 Z= 0.455 Chirality : 0.044 0.365 30208 Planarity : 0.008 0.126 13518 Dihedral : 23.730 179.330 79766 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 20.93 Ramachandran Plot: Outliers : 1.02 % Allowed : 8.38 % Favored : 90.60 % Rotamer: Outliers : 7.27 % Allowed : 20.15 % Favored : 72.58 % 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: -2.58 (0.10), residues: 6551 helix: -1.09 (0.10), residues: 2091 sheet: -2.76 (0.14), residues: 1080 loop : -1.69 (0.10), residues: 3380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP d 169 HIS 0.018 0.002 HIS E 165 PHE 0.036 0.003 PHE b 15 TYR 0.033 0.003 TYR s 79 ARG 0.020 0.001 ARG t 59 *********************** 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 2375 residues out of total 5475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 351 poor density : 2024 time to evaluate : 6.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 18 GLN cc_start: 0.7530 (mm110) cc_final: 0.6786 (mp10) REVERT: b 22 TRP cc_start: 0.8430 (p-90) cc_final: 0.8228 (p-90) REVERT: b 114 LYS cc_start: 0.8244 (ttmt) cc_final: 0.7537 (pptt) REVERT: b 185 ILE cc_start: 0.8747 (OUTLIER) cc_final: 0.8542 (tp) REVERT: b 191 ASP cc_start: 0.7929 (p0) cc_final: 0.7452 (t0) REVERT: d 8 LEU cc_start: 0.2548 (tp) cc_final: 0.2094 (mp) REVERT: d 46 ARG cc_start: 0.5041 (tpp-160) cc_final: 0.4741 (tpt170) REVERT: d 115 GLN cc_start: 0.0750 (OUTLIER) cc_final: -0.1798 (mm-40) REVERT: d 177 MET cc_start: -0.0210 (mmt) cc_final: -0.0923 (mmt) REVERT: e 18 ASN cc_start: 0.8029 (t0) cc_final: 0.7781 (t0) REVERT: e 155 LYS cc_start: 0.8005 (mtpt) cc_final: 0.7739 (mtpt) REVERT: f 25 TYR cc_start: 0.7645 (m-10) cc_final: 0.7339 (m-10) REVERT: f 36 ILE cc_start: 0.8400 (tp) cc_final: 0.8192 (tp) REVERT: f 90 MET cc_start: 0.7931 (OUTLIER) cc_final: 0.7697 (tpt) REVERT: h 63 LYS cc_start: 0.8359 (mtpm) cc_final: 0.7882 (mtpp) REVERT: h 93 LYS cc_start: 0.7609 (ptpt) cc_final: 0.7363 (mmtt) REVERT: h 117 GLN cc_start: 0.8684 (mm-40) cc_final: 0.8363 (mm-40) REVERT: h 128 VAL cc_start: 0.8817 (t) cc_final: 0.8586 (t) REVERT: o 13 GLU cc_start: 0.8066 (tp30) cc_final: 0.7817 (tm-30) REVERT: o 14 PHE cc_start: 0.7687 (m-80) cc_final: 0.7177 (m-80) REVERT: p 15 PRO cc_start: 0.6154 (Cg_endo) cc_final: 0.5812 (Cg_exo) REVERT: p 18 GLN cc_start: 0.7777 (pt0) cc_final: 0.7573 (pt0) REVERT: p 34 GLU cc_start: 0.7594 (pp20) cc_final: 0.7036 (pp20) REVERT: p 54 LEU cc_start: 0.8270 (tt) cc_final: 0.8002 (tt) REVERT: r 20 ILE cc_start: 0.8817 (mm) cc_final: 0.8585 (tp) REVERT: r 29 LYS cc_start: 0.7970 (ptpp) cc_final: 0.7594 (mttp) REVERT: r 31 TYR cc_start: 0.8029 (m-80) cc_final: 0.7715 (m-10) REVERT: r 63 TYR cc_start: 0.8831 (t80) cc_final: 0.8568 (t80) REVERT: t 23 ARG cc_start: 0.8551 (mmp80) cc_final: 0.8232 (tpp80) REVERT: t 26 MET cc_start: 0.8923 (tmm) cc_final: 0.8664 (tmm) REVERT: t 28 ARG cc_start: 0.8320 (ptp-170) cc_final: 0.7550 (ptp-170) REVERT: t 59 ARG cc_start: 0.8643 (OUTLIER) cc_final: 0.7834 (mtm180) REVERT: w 508 SER cc_start: 0.9185 (m) cc_final: 0.8964 (p) REVERT: c 21 TRP cc_start: 0.8376 (p-90) cc_final: 0.7941 (p-90) REVERT: c 36 PHE cc_start: 0.8928 (t80) cc_final: 0.8568 (t80) REVERT: c 120 THR cc_start: 0.9021 (OUTLIER) cc_final: 0.8766 (m) REVERT: c 151 GLU cc_start: 0.8539 (tp30) cc_final: 0.8232 (tp30) REVERT: c 156 LEU cc_start: 0.8048 (pp) cc_final: 0.7746 (pp) REVERT: c 200 TRP cc_start: 0.8387 (m-90) cc_final: 0.8168 (m-90) REVERT: g 6 ILE cc_start: 0.4980 (OUTLIER) cc_final: 0.4441 (pp) REVERT: g 46 LEU cc_start: 0.9202 (mp) cc_final: 0.8970 (pp) REVERT: g 90 VAL cc_start: 0.8518 (OUTLIER) cc_final: 0.8224 (p) REVERT: g 96 ASN cc_start: 0.7828 (p0) cc_final: 0.7430 (p0) REVERT: i 35 GLU cc_start: 0.8071 (pp20) cc_final: 0.7455 (pp20) REVERT: i 78 ILE cc_start: 0.8977 (mt) cc_final: 0.8705 (tt) REVERT: j 62 ARG cc_start: 0.8519 (mtm-85) cc_final: 0.8215 (mtm-85) REVERT: j 81 GLU cc_start: 0.8186 (mp0) cc_final: 0.7901 (pp20) REVERT: m 22 TYR cc_start: 0.8088 (t80) cc_final: 0.7177 (t80) REVERT: m 30 LYS cc_start: 0.8871 (ttmm) cc_final: 0.8609 (ttmm) REVERT: m 54 THR cc_start: 0.8213 (p) cc_final: 0.7870 (p) REVERT: m 58 GLU cc_start: 0.8281 (mt-10) cc_final: 0.7938 (mt-10) REVERT: m 69 ARG cc_start: 0.8652 (mtt-85) cc_final: 0.8352 (mmt90) REVERT: m 91 ARG cc_start: 0.7739 (mtm180) cc_final: 0.7510 (ttm170) REVERT: s 55 GLN cc_start: 0.8105 (pt0) cc_final: 0.7849 (pm20) REVERT: C 186 ASP cc_start: 0.8301 (m-30) cc_final: 0.7699 (m-30) REVERT: C 212 TRP cc_start: 0.9276 (p90) cc_final: 0.8309 (p90) REVERT: C 224 MET cc_start: 0.8678 (mtt) cc_final: 0.8340 (mtt) REVERT: D 74 GLU cc_start: 0.7149 (pm20) cc_final: 0.6888 (pm20) REVERT: D 77 ARG cc_start: 0.8120 (OUTLIER) cc_final: 0.7514 (ptt-90) REVERT: D 128 ARG cc_start: 0.8510 (mtm-85) cc_final: 0.7980 (ttm110) REVERT: D 149 ASN cc_start: 0.7934 (t0) cc_final: 0.7630 (t0) REVERT: E 24 ASN cc_start: 0.7655 (t0) cc_final: 0.7050 (t0) REVERT: E 25 GLU cc_start: 0.7849 (tt0) cc_final: 0.7565 (tp30) REVERT: E 131 THR cc_start: 0.8348 (p) cc_final: 0.8030 (t) REVERT: F 9 ASP cc_start: 0.6922 (OUTLIER) cc_final: 0.5712 (p0) REVERT: F 18 GLU cc_start: 0.8912 (mm-30) cc_final: 0.8635 (mp0) REVERT: F 77 LYS cc_start: 0.8431 (mtmt) cc_final: 0.8040 (tttt) REVERT: F 97 GLU cc_start: 0.8936 (mm-30) cc_final: 0.8710 (mm-30) REVERT: F 99 PHE cc_start: 0.8353 (t80) cc_final: 0.7835 (t80) REVERT: F 119 LYS cc_start: 0.8551 (mttp) cc_final: 0.8295 (tmtt) REVERT: F 147 ARG cc_start: 0.7433 (tpp-160) cc_final: 0.7232 (tpp80) REVERT: F 151 LEU cc_start: 0.7409 (pp) cc_final: 0.7084 (pp) REVERT: F 173 ASP cc_start: 0.8738 (m-30) cc_final: 0.8309 (t70) REVERT: F 176 PHE cc_start: 0.6755 (m-80) cc_final: 0.6553 (m-80) REVERT: G 61 TRP cc_start: 0.7030 (m100) cc_final: 0.6560 (m100) REVERT: G 103 ASN cc_start: 0.8322 (t0) cc_final: 0.7994 (m110) REVERT: G 114 HIS cc_start: 0.6811 (t70) cc_final: 0.6419 (t70) REVERT: G 146 ASP cc_start: 0.7774 (t0) cc_final: 0.7309 (t0) REVERT: G 150 TYR cc_start: 0.6704 (m-80) cc_final: 0.6001 (m-80) REVERT: G 152 ARG cc_start: 0.8399 (ttp80) cc_final: 0.8195 (ttt90) REVERT: H 27 ARG cc_start: 0.7217 (ttp-110) cc_final: 0.6924 (ttp80) REVERT: H 43 ASN cc_start: 0.8423 (m-40) cc_final: 0.8055 (t0) REVERT: I 54 ILE cc_start: 0.6542 (mt) cc_final: 0.6286 (pt) REVERT: J 15 TRP cc_start: 0.8684 (m100) cc_final: 0.8170 (m100) REVERT: J 98 GLU cc_start: 0.8670 (mp0) cc_final: 0.7913 (tm-30) REVERT: K 1 MET cc_start: 0.8081 (mtt) cc_final: 0.7811 (mtp) REVERT: K 32 TYR cc_start: 0.8418 (OUTLIER) cc_final: 0.8120 (p90) REVERT: K 40 LYS cc_start: 0.8251 (tptm) cc_final: 0.8038 (tptm) REVERT: K 45 GLU cc_start: 0.8914 (tm-30) cc_final: 0.8681 (tm-30) REVERT: K 112 PHE cc_start: 0.8541 (m-80) cc_final: 0.8287 (m-10) REVERT: K 114 LYS cc_start: 0.8839 (tptp) cc_final: 0.8494 (ptpt) REVERT: L 121 THR cc_start: 0.7170 (m) cc_final: 0.6515 (p) REVERT: L 123 ARG cc_start: 0.6974 (ttm110) cc_final: 0.6382 (mtt90) REVERT: L 141 LYS cc_start: 0.7663 (tptt) cc_final: 0.7333 (mtmt) REVERT: L 142 ILE cc_start: 0.7923 (mt) cc_final: 0.7116 (mt) REVERT: M 53 MET cc_start: 0.9333 (tmm) cc_final: 0.8923 (tmm) REVERT: N 74 GLU cc_start: 0.9007 (tp30) cc_final: 0.8782 (tp30) REVERT: N 94 TYR cc_start: 0.8473 (m-80) cc_final: 0.7565 (m-10) REVERT: N 107 ASN cc_start: 0.8187 (t0) cc_final: 0.7799 (t0) REVERT: N 110 MET cc_start: 0.8730 (mmp) cc_final: 0.8312 (mmt) REVERT: O 95 SER cc_start: 0.8511 (m) cc_final: 0.7904 (t) REVERT: O 115 LEU cc_start: 0.7195 (OUTLIER) cc_final: 0.6794 (mt) REVERT: P 86 LYS cc_start: 0.7993 (tppt) cc_final: 0.7624 (tppt) REVERT: P 97 TYR cc_start: 0.8162 (m-10) cc_final: 0.7710 (m-80) REVERT: Q 27 ARG cc_start: 0.8712 (mtp-110) cc_final: 0.8471 (ttm110) REVERT: Q 60 TRP cc_start: 0.9170 (m-10) cc_final: 0.8967 (m-10) REVERT: Q 75 TYR cc_start: 0.8820 (t80) cc_final: 0.8380 (t80) REVERT: R 1 MET cc_start: 0.7660 (ttp) cc_final: 0.7458 (mmm) REVERT: R 18 GLN cc_start: 0.7581 (pt0) cc_final: 0.7258 (pt0) REVERT: R 24 LYS cc_start: 0.8043 (ttpt) cc_final: 0.7778 (ttmt) REVERT: S 78 GLU cc_start: 0.8656 (pt0) cc_final: 0.8229 (pt0) REVERT: S 86 MET cc_start: 0.8868 (tpt) cc_final: 0.8618 (ttp) REVERT: T 1 MET cc_start: 0.2653 (ptm) cc_final: 0.2152 (mmt) REVERT: T 6 ARG cc_start: 0.7678 (ttp80) cc_final: 0.7222 (ttp80) REVERT: T 37 ASP cc_start: 0.8461 (OUTLIER) cc_final: 0.8212 (p0) REVERT: U 4 ILE cc_start: 0.9250 (mp) cc_final: 0.8991 (tp) REVERT: U 38 ILE cc_start: 0.7868 (mm) cc_final: 0.7652 (mm) REVERT: U 72 PHE cc_start: 0.7518 (t80) cc_final: 0.7163 (t80) REVERT: V 17 SER cc_start: 0.8197 (t) cc_final: 0.7977 (t) REVERT: V 55 GLU cc_start: 0.8901 (mp0) cc_final: 0.8411 (mp0) REVERT: V 85 LYS cc_start: 0.8694 (ttpt) cc_final: 0.8466 (ttpt) REVERT: W 12 SER cc_start: 0.8642 (m) cc_final: 0.8381 (p) REVERT: W 73 ARG cc_start: 0.8618 (mtm110) cc_final: 0.8316 (mtm110) REVERT: X 37 PHE cc_start: 0.7785 (m-80) cc_final: 0.7485 (m-80) REVERT: Y 17 GLU cc_start: 0.8521 (tp30) cc_final: 0.8101 (tm-30) REVERT: Y 21 LEU cc_start: 0.9000 (mt) cc_final: 0.8775 (mm) REVERT: Y 25 GLN cc_start: 0.8501 (tp40) cc_final: 0.8047 (mm-40) REVERT: Y 29 ARG cc_start: 0.8385 (ptp-110) cc_final: 0.8091 (ptp-110) REVERT: Y 30 MET cc_start: 0.8583 (ptm) cc_final: 0.8335 (ptm) REVERT: Y 42 LEU cc_start: 0.8584 (mt) cc_final: 0.8319 (mt) REVERT: Y 44 LYS cc_start: 0.8257 (tttm) cc_final: 0.7902 (tttm) REVERT: Y 50 VAL cc_start: 0.9195 (t) cc_final: 0.8929 (p) REVERT: Z 20 LYS cc_start: 0.9244 (mtmm) cc_final: 0.9015 (mtmm) REVERT: 0 47 TYR cc_start: 0.8358 (m-10) cc_final: 0.8146 (m-10) REVERT: 2 19 ARG cc_start: 0.9119 (mtp85) cc_final: 0.8680 (mmm-85) REVERT: 3 5 THR cc_start: 0.9231 (m) cc_final: 0.8959 (p) REVERT: 3 63 TYR cc_start: 0.7288 (m-80) cc_final: 0.6878 (m-80) REVERT: 5 1 MET cc_start: 0.1108 (tpt) cc_final: -0.0576 (mmt) REVERT: 5 38 MET cc_start: 0.6083 (mtm) cc_final: 0.5853 (ptm) REVERT: 5 99 PHE cc_start: 0.3852 (m-80) cc_final: 0.3594 (m-80) REVERT: 6 2 LYS cc_start: 0.7477 (mtmt) cc_final: 0.7199 (mtmt) outliers start: 351 outliers final: 201 residues processed: 2181 average time/residue: 1.3706 time to fit residues: 5181.0146 Evaluate side-chains 1993 residues out of total 5475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 213 poor density : 1780 time to evaluate : 6.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 19 THR Chi-restraints excluded: chain b residue 21 TYR Chi-restraints excluded: chain b residue 42 LEU Chi-restraints excluded: chain b residue 71 THR Chi-restraints excluded: chain b residue 91 VAL Chi-restraints excluded: chain b residue 101 THR Chi-restraints excluded: chain b residue 106 VAL Chi-restraints excluded: chain b residue 129 THR Chi-restraints excluded: chain b residue 142 LYS Chi-restraints excluded: chain b residue 182 VAL Chi-restraints excluded: chain b residue 185 ILE Chi-restraints excluded: chain b residue 198 VAL Chi-restraints excluded: chain b residue 221 ARG Chi-restraints excluded: chain d residue 11 SER Chi-restraints excluded: chain d residue 16 THR Chi-restraints excluded: chain d residue 28 ASP Chi-restraints excluded: chain d residue 115 GLN Chi-restraints excluded: chain d residue 116 LEU Chi-restraints excluded: chain e residue 15 ILE Chi-restraints excluded: chain e residue 45 VAL Chi-restraints excluded: chain e residue 47 PHE Chi-restraints excluded: chain e residue 55 VAL Chi-restraints excluded: chain e residue 122 VAL Chi-restraints excluded: chain e residue 130 THR Chi-restraints excluded: chain e residue 147 ASN Chi-restraints excluded: chain e residue 152 VAL Chi-restraints excluded: chain e residue 158 LYS Chi-restraints excluded: chain e residue 160 VAL Chi-restraints excluded: chain f residue 18 VAL Chi-restraints excluded: chain f residue 89 VAL Chi-restraints excluded: chain f residue 90 MET Chi-restraints excluded: chain h residue 11 THR Chi-restraints excluded: chain h residue 24 VAL Chi-restraints excluded: chain h residue 50 VAL Chi-restraints excluded: chain h residue 58 LEU Chi-restraints excluded: chain h residue 103 VAL Chi-restraints excluded: chain h residue 125 ILE Chi-restraints excluded: chain k residue 25 SER Chi-restraints excluded: chain k residue 30 ILE Chi-restraints excluded: chain k residue 39 ASN Chi-restraints excluded: chain k residue 45 THR Chi-restraints excluded: chain k residue 109 ILE Chi-restraints excluded: chain l residue 3 VAL Chi-restraints excluded: chain l residue 7 VAL Chi-restraints excluded: chain l residue 51 VAL Chi-restraints excluded: chain l residue 54 VAL Chi-restraints excluded: chain l residue 86 VAL Chi-restraints excluded: chain o residue 4 THR Chi-restraints excluded: chain o residue 7 THR Chi-restraints excluded: chain o residue 60 SER Chi-restraints excluded: chain o residue 66 LEU Chi-restraints excluded: chain p residue 19 VAL Chi-restraints excluded: chain q residue 19 SER Chi-restraints excluded: chain q residue 45 VAL Chi-restraints excluded: chain q residue 54 ILE Chi-restraints excluded: chain q residue 56 ASP Chi-restraints excluded: chain q residue 57 VAL Chi-restraints excluded: chain r residue 27 THR Chi-restraints excluded: chain t residue 31 ILE Chi-restraints excluded: chain t residue 56 ILE Chi-restraints excluded: chain t residue 59 ARG Chi-restraints excluded: chain t residue 65 LEU Chi-restraints excluded: chain c residue 14 VAL Chi-restraints excluded: chain c residue 51 VAL Chi-restraints excluded: chain c residue 115 VAL Chi-restraints excluded: chain c residue 120 THR Chi-restraints excluded: chain c residue 121 SER Chi-restraints excluded: chain c residue 148 ILE Chi-restraints excluded: chain c residue 161 ILE Chi-restraints excluded: chain g residue 6 ILE Chi-restraints excluded: chain g residue 49 LEU Chi-restraints excluded: chain g residue 74 VAL Chi-restraints excluded: chain g residue 75 LYS Chi-restraints excluded: chain g residue 90 VAL Chi-restraints excluded: chain g residue 103 ILE Chi-restraints excluded: chain g residue 121 ASN Chi-restraints excluded: chain i residue 46 VAL Chi-restraints excluded: chain i residue 56 MET Chi-restraints excluded: chain i residue 60 LEU Chi-restraints excluded: chain i residue 66 VAL Chi-restraints excluded: chain i residue 97 LEU Chi-restraints excluded: chain i residue 113 LYS Chi-restraints excluded: chain j residue 8 ILE Chi-restraints excluded: chain j residue 44 THR Chi-restraints excluded: chain j residue 50 THR Chi-restraints excluded: chain j residue 84 VAL Chi-restraints excluded: chain m residue 3 ILE Chi-restraints excluded: chain m residue 24 VAL Chi-restraints excluded: chain m residue 96 VAL Chi-restraints excluded: chain m residue 101 THR Chi-restraints excluded: chain n residue 33 VAL Chi-restraints excluded: chain n residue 46 LEU Chi-restraints excluded: chain n residue 56 SER Chi-restraints excluded: chain n residue 60 GLN Chi-restraints excluded: chain n residue 67 THR Chi-restraints excluded: chain s residue 42 ASN Chi-restraints excluded: chain s residue 57 VAL Chi-restraints excluded: chain s residue 59 VAL Chi-restraints excluded: chain C residue 25 LYS Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 131 MET Chi-restraints excluded: chain C residue 200 MET Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 77 ARG Chi-restraints excluded: chain D residue 106 LYS Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 139 SER Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 180 VAL Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain F residue 9 ASP Chi-restraints excluded: chain F residue 15 LEU Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain F residue 145 VAL Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 18 ILE Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain G residue 137 LYS Chi-restraints excluded: chain G residue 147 LEU Chi-restraints excluded: chain I residue 32 VAL Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 59 THR Chi-restraints excluded: chain I residue 95 ASP Chi-restraints excluded: chain I residue 100 ILE Chi-restraints excluded: chain I residue 127 SER Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain J residue 67 ASN Chi-restraints excluded: chain J residue 73 VAL Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain J residue 131 ASN Chi-restraints excluded: chain K residue 12 ASP Chi-restraints excluded: chain K residue 28 SER Chi-restraints excluded: chain K residue 32 TYR Chi-restraints excluded: chain K residue 56 ASP Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 75 SER Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 76 GLU Chi-restraints excluded: chain L residue 99 ASN Chi-restraints excluded: chain L residue 100 ILE Chi-restraints excluded: chain L residue 122 VAL Chi-restraints excluded: chain M residue 42 THR Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 93 VAL Chi-restraints excluded: chain N residue 13 ASN Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain O residue 100 HIS Chi-restraints excluded: chain O residue 115 LEU Chi-restraints excluded: chain P residue 3 ILE Chi-restraints excluded: chain P residue 16 VAL Chi-restraints excluded: chain P residue 23 ASP Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 40 GLN Chi-restraints excluded: chain P residue 69 VAL Chi-restraints excluded: chain P residue 85 VAL Chi-restraints excluded: chain P residue 91 VAL Chi-restraints excluded: chain Q residue 16 ILE Chi-restraints excluded: chain Q residue 28 SER Chi-restraints excluded: chain Q residue 30 VAL Chi-restraints excluded: chain Q residue 38 VAL Chi-restraints excluded: chain Q residue 39 ILE Chi-restraints excluded: chain Q residue 71 ASN Chi-restraints excluded: chain Q residue 111 LYS Chi-restraints excluded: chain R residue 98 ILE Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain S residue 20 VAL Chi-restraints excluded: chain T residue 37 ASP Chi-restraints excluded: chain T residue 60 THR Chi-restraints excluded: chain T residue 62 VAL Chi-restraints excluded: chain T residue 85 VAL Chi-restraints excluded: chain U residue 48 VAL Chi-restraints excluded: chain U residue 68 ASN Chi-restraints excluded: chain U residue 69 VAL Chi-restraints excluded: chain U residue 78 LYS Chi-restraints excluded: chain U residue 101 THR Chi-restraints excluded: chain V residue 49 ASN Chi-restraints excluded: chain W residue 49 CYS Chi-restraints excluded: chain W residue 76 ILE Chi-restraints excluded: chain X residue 10 ARG Chi-restraints excluded: chain X residue 12 VAL Chi-restraints excluded: chain X residue 19 HIS Chi-restraints excluded: chain X residue 24 THR Chi-restraints excluded: chain X residue 39 VAL Chi-restraints excluded: chain Y residue 14 LEU Chi-restraints excluded: chain Y residue 16 THR Chi-restraints excluded: chain Z residue 40 THR Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 24 VAL Chi-restraints excluded: chain 0 residue 43 THR Chi-restraints excluded: chain 2 residue 9 VAL Chi-restraints excluded: chain 3 residue 53 ASP Chi-restraints excluded: chain 5 residue 5 LEU Chi-restraints excluded: chain 5 residue 55 VAL Chi-restraints excluded: chain 5 residue 77 VAL Chi-restraints excluded: chain 5 residue 123 ILE Chi-restraints excluded: chain 6 residue 5 ILE Chi-restraints excluded: chain 6 residue 16 CYS 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: 40.0000 chunk 833 optimal weight: 9.9990 chunk 682 optimal weight: 20.0000 chunk 276 optimal weight: 9.9990 chunk 1003 optimal weight: 7.9990 chunk 1084 optimal weight: 30.0000 chunk 893 optimal weight: 20.0000 chunk 995 optimal weight: 6.9990 chunk 342 optimal weight: 0.0040 chunk 805 optimal weight: 3.9990 overall best weight: 5.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 70 GLN d 115 GLN ** e 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 96 GLN f 46 GLN ** h 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 14 GLN ** k 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 5 GLN ** l 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 9 HIS ** r 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 60 GLN ** 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 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 70 HIS n 60 GLN ** s 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 164 GLN F 22 ASN ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 44 HIS G 47 ASN G 142 GLN I 5 GLN I 106 GLN ** J 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 135 GLN ** K 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 54 GLN ** 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** N 62 ASN ** O 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 36 GLN ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 6 GLN T 15 HIS U 65 GLN ** U 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 12 GLN V 44 HIS ** Y 41 HIS ** 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 ** 4 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.4711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.100 161499 Z= 0.286 Angle : 0.754 14.226 240779 Z= 0.402 Chirality : 0.039 0.382 30208 Planarity : 0.007 0.131 13518 Dihedral : 23.641 179.039 79727 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 18.00 Ramachandran Plot: Outliers : 0.89 % Allowed : 9.80 % Favored : 89.31 % Rotamer: Outliers : 8.01 % Allowed : 22.97 % Favored : 69.02 % 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: -2.15 (0.10), residues: 6551 helix: -0.34 (0.11), residues: 2110 sheet: -2.47 (0.13), residues: 1124 loop : -1.72 (0.10), residues: 3317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP b 103 HIS 0.011 0.002 HIS E 165 PHE 0.025 0.003 PHE k 60 TYR 0.027 0.002 TYR Q 31 ARG 0.026 0.001 ARG d 110 *********************** 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 2351 residues out of total 5475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 387 poor density : 1964 time to evaluate : 6.401 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: b 22 TRP cc_start: 0.8560 (p-90) cc_final: 0.8284 (p-90) REVERT: b 112 ARG cc_start: 0.8172 (tpp-160) cc_final: 0.7850 (tpp-160) REVERT: b 114 LYS cc_start: 0.8463 (ttmt) cc_final: 0.7750 (pptt) REVERT: b 220 VAL cc_start: 0.8374 (t) cc_final: 0.8048 (m) REVERT: d 46 ARG cc_start: 0.5395 (tpp-160) cc_final: 0.4854 (ttt90) REVERT: d 53 GLN cc_start: 0.7693 (mm-40) cc_final: 0.7490 (mm-40) REVERT: e 94 PHE cc_start: 0.8778 (t80) cc_final: 0.8521 (t80) REVERT: f 4 TYR cc_start: 0.9088 (m-10) cc_final: 0.8172 (m-10) REVERT: f 36 ILE cc_start: 0.9196 (tp) cc_final: 0.8797 (mt) REVERT: f 40 GLU cc_start: 0.7408 (tt0) cc_final: 0.7202 (tt0) REVERT: f 59 TYR cc_start: 0.6411 (m-80) cc_final: 0.5633 (m-80) REVERT: f 86 ARG cc_start: 0.7473 (OUTLIER) cc_final: 0.6721 (ttm110) REVERT: h 8 ASP cc_start: 0.8321 (t70) cc_final: 0.7162 (t0) REVERT: h 63 LYS cc_start: 0.8220 (mtpm) cc_final: 0.8011 (ttmm) REVERT: h 88 LYS cc_start: 0.7923 (tptp) cc_final: 0.7710 (tptp) REVERT: h 93 LYS cc_start: 0.7681 (ptpt) cc_final: 0.7446 (mmtt) REVERT: h 94 VAL cc_start: 0.7858 (t) cc_final: 0.7615 (t) REVERT: h 113 ARG cc_start: 0.8517 (tmm160) cc_final: 0.8110 (tmm160) REVERT: h 117 GLN cc_start: 0.8678 (mm-40) cc_final: 0.8471 (mm-40) REVERT: k 49 SER cc_start: 0.7901 (m) cc_final: 0.7429 (m) REVERT: k 124 LYS cc_start: 0.8238 (pttp) cc_final: 0.7706 (tptm) REVERT: o 13 GLU cc_start: 0.8343 (tp30) cc_final: 0.8073 (tm-30) REVERT: p 8 ARG cc_start: 0.8292 (tpt90) cc_final: 0.7995 (tpt90) REVERT: q 16 MET cc_start: 0.7363 (ptt) cc_final: 0.7093 (mtp) REVERT: r 29 LYS cc_start: 0.8183 (ptpp) cc_final: 0.7847 (mttp) REVERT: r 50 TYR cc_start: 0.8347 (m-80) cc_final: 0.8050 (m-10) REVERT: r 63 TYR cc_start: 0.8943 (t80) cc_final: 0.8581 (t80) REVERT: r 69 TYR cc_start: 0.7422 (m-80) cc_final: 0.7145 (m-10) REVERT: t 26 MET cc_start: 0.8968 (tmm) cc_final: 0.8699 (tmm) REVERT: t 28 ARG cc_start: 0.8392 (ptp-170) cc_final: 0.7777 (mtm110) REVERT: t 50 PHE cc_start: 0.8169 (t80) cc_final: 0.7327 (t80) REVERT: u 37 TYR cc_start: 0.7441 (t80) cc_final: 0.7211 (t80) REVERT: c 36 PHE cc_start: 0.8984 (t80) cc_final: 0.8610 (t80) REVERT: c 122 GLN cc_start: 0.8705 (mm-40) cc_final: 0.8409 (mm-40) REVERT: c 133 MET cc_start: 0.8668 (ptt) cc_final: 0.8191 (ptt) REVERT: g 6 ILE cc_start: 0.6026 (OUTLIER) cc_final: 0.5651 (pp) REVERT: g 46 LEU cc_start: 0.9291 (mp) cc_final: 0.9040 (pp) REVERT: g 90 VAL cc_start: 0.8591 (OUTLIER) cc_final: 0.8362 (p) REVERT: g 96 ASN cc_start: 0.8041 (p0) cc_final: 0.7516 (p0) REVERT: i 27 ILE cc_start: 0.7379 (OUTLIER) cc_final: 0.7016 (mp) REVERT: j 42 LEU cc_start: 0.8280 (mp) cc_final: 0.7999 (mt) REVERT: j 51 VAL cc_start: 0.8122 (t) cc_final: 0.7910 (p) REVERT: j 64 GLN cc_start: 0.7733 (mt0) cc_final: 0.7451 (mt0) REVERT: j 67 ILE cc_start: 0.8871 (mm) cc_final: 0.8659 (mm) REVERT: j 84 VAL cc_start: 0.6504 (OUTLIER) cc_final: 0.6041 (m) REVERT: j 85 ASP cc_start: 0.6951 (m-30) cc_final: 0.6740 (p0) REVERT: m 22 TYR cc_start: 0.8136 (t80) cc_final: 0.7174 (t80) REVERT: m 54 THR cc_start: 0.8057 (p) cc_final: 0.7753 (p) REVERT: m 55 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8650 (tt) REVERT: m 58 GLU cc_start: 0.8343 (mt-10) cc_final: 0.8033 (mt-10) REVERT: m 69 ARG cc_start: 0.8699 (mtt-85) cc_final: 0.8455 (mmt90) REVERT: m 74 MET cc_start: 0.9117 (mtt) cc_final: 0.8907 (mtp) REVERT: n 60 GLN cc_start: 0.8491 (OUTLIER) cc_final: 0.7914 (mm-40) REVERT: n 67 THR cc_start: 0.9060 (OUTLIER) cc_final: 0.8826 (p) REVERT: s 52 ASN cc_start: 0.8433 (p0) cc_final: 0.8148 (p0) REVERT: s 55 GLN cc_start: 0.8346 (pt0) cc_final: 0.8032 (pm20) REVERT: D 28 GLU cc_start: 0.7653 (pp20) cc_final: 0.7194 (tm-30) REVERT: D 74 GLU cc_start: 0.7514 (pm20) cc_final: 0.7275 (pm20) REVERT: D 77 ARG cc_start: 0.8027 (OUTLIER) cc_final: 0.7509 (ptt-90) REVERT: D 128 ARG cc_start: 0.8565 (mtm-85) cc_final: 0.8201 (mtp180) REVERT: D 184 ARG cc_start: 0.8507 (OUTLIER) cc_final: 0.8080 (mpp80) REVERT: E 23 PHE cc_start: 0.7180 (t80) cc_final: 0.6977 (t80) REVERT: E 24 ASN cc_start: 0.7905 (t0) cc_final: 0.7458 (t0) REVERT: E 25 GLU cc_start: 0.8142 (tt0) cc_final: 0.7691 (tp30) REVERT: E 35 TYR cc_start: 0.8171 (t80) cc_final: 0.7719 (t80) REVERT: E 116 ASP cc_start: 0.9077 (m-30) cc_final: 0.8174 (t70) REVERT: E 131 THR cc_start: 0.8526 (p) cc_final: 0.8216 (t) REVERT: E 159 LEU cc_start: 0.8416 (pp) cc_final: 0.8152 (pp) REVERT: F 6 TYR cc_start: 0.7790 (t80) cc_final: 0.7042 (t80) REVERT: F 9 ASP cc_start: 0.6609 (OUTLIER) cc_final: 0.6184 (p0) REVERT: F 77 LYS cc_start: 0.8548 (mtmt) cc_final: 0.8197 (tttt) REVERT: F 119 LYS cc_start: 0.8615 (mttp) cc_final: 0.8296 (tmtt) REVERT: F 120 SER cc_start: 0.8082 (t) cc_final: 0.7724 (p) REVERT: F 132 ARG cc_start: 0.7494 (OUTLIER) cc_final: 0.6514 (ptp-110) REVERT: F 141 ASP cc_start: 0.8293 (t70) cc_final: 0.8042 (t70) REVERT: F 163 GLU cc_start: 0.7783 (pm20) cc_final: 0.7528 (pm20) REVERT: F 173 ASP cc_start: 0.8516 (m-30) cc_final: 0.8178 (t70) REVERT: G 61 TRP cc_start: 0.7289 (m100) cc_final: 0.6962 (m100) REVERT: G 137 LYS cc_start: 0.8247 (OUTLIER) cc_final: 0.7842 (mtpt) REVERT: H 43 ASN cc_start: 0.8495 (m-40) cc_final: 0.8217 (t0) REVERT: H 45 GLU cc_start: 0.8254 (tm-30) cc_final: 0.7492 (pt0) REVERT: I 16 MET cc_start: 0.4665 (mpp) cc_final: 0.4311 (tpt) REVERT: I 80 LYS cc_start: 0.6136 (mmtt) cc_final: 0.5769 (mmmt) REVERT: I 86 LYS cc_start: 0.6621 (OUTLIER) cc_final: 0.6300 (ptmt) REVERT: J 15 TRP cc_start: 0.8852 (m100) cc_final: 0.8414 (m100) REVERT: J 98 GLU cc_start: 0.8794 (mp0) cc_final: 0.7977 (tm-30) REVERT: K 22 ILE cc_start: 0.9319 (pt) cc_final: 0.9112 (mt) REVERT: K 114 LYS cc_start: 0.8932 (tptp) cc_final: 0.8666 (mttp) REVERT: L 2 ARG cc_start: 0.7678 (mmm160) cc_final: 0.7435 (tmt170) REVERT: L 23 ILE cc_start: 0.8760 (mm) cc_final: 0.8553 (mt) REVERT: L 121 THR cc_start: 0.7227 (m) cc_final: 0.6905 (t) REVERT: L 142 ILE cc_start: 0.8375 (mt) cc_final: 0.7452 (mt) REVERT: M 53 MET cc_start: 0.9398 (tmm) cc_final: 0.8928 (tmm) REVERT: N 23 ASN cc_start: 0.8626 (t0) cc_final: 0.8264 (t0) REVERT: N 72 ASP cc_start: 0.8967 (t0) cc_final: 0.8608 (t0) REVERT: N 74 GLU cc_start: 0.8942 (tp30) cc_final: 0.8721 (tm-30) REVERT: N 75 ILE cc_start: 0.8946 (mm) cc_final: 0.8449 (mm) REVERT: N 107 ASN cc_start: 0.8214 (t0) cc_final: 0.7971 (t0) REVERT: N 110 MET cc_start: 0.8735 (mmp) cc_final: 0.8342 (mmt) REVERT: P 28 LYS cc_start: 0.8916 (mtpt) cc_final: 0.8547 (mppt) REVERT: P 55 HIS cc_start: 0.8801 (m-70) cc_final: 0.8458 (m170) REVERT: P 97 TYR cc_start: 0.8544 (m-10) cc_final: 0.8000 (m-80) REVERT: P 110 LYS cc_start: 0.8514 (mmmt) cc_final: 0.7964 (mtmt) REVERT: Q 23 TYR cc_start: 0.8324 (m-80) cc_final: 0.8072 (m-80) REVERT: Q 60 TRP cc_start: 0.9313 (m-10) cc_final: 0.8668 (m-10) REVERT: S 67 ASP cc_start: 0.8212 (OUTLIER) cc_final: 0.8007 (t0) REVERT: S 78 GLU cc_start: 0.8706 (pt0) cc_final: 0.8321 (pt0) REVERT: S 86 MET cc_start: 0.8987 (tpt) cc_final: 0.8688 (ttt) REVERT: T 1 MET cc_start: 0.2734 (ptm) cc_final: 0.2055 (mmt) REVERT: T 4 GLU cc_start: 0.8064 (pm20) cc_final: 0.7671 (pm20) REVERT: T 37 ASP cc_start: 0.8516 (OUTLIER) cc_final: 0.8186 (p0) REVERT: U 4 ILE cc_start: 0.9281 (mp) cc_final: 0.9033 (tp) REVERT: U 71 ILE cc_start: 0.8126 (pt) cc_final: 0.7735 (mt) REVERT: V 55 GLU cc_start: 0.8864 (mp0) cc_final: 0.8654 (mp0) REVERT: V 69 GLU cc_start: 0.8328 (mp0) cc_final: 0.8116 (mp0) REVERT: W 54 THR cc_start: 0.9157 (OUTLIER) cc_final: 0.8939 (t) REVERT: W 62 LYS cc_start: 0.8433 (mmtt) cc_final: 0.8209 (mmtt) REVERT: W 73 ARG cc_start: 0.8684 (mtm110) cc_final: 0.8133 (mtp180) REVERT: X 37 PHE cc_start: 0.7997 (m-80) cc_final: 0.7684 (m-80) REVERT: X 44 ARG cc_start: 0.7763 (ttm110) cc_final: 0.7316 (mtp-110) REVERT: Y 17 GLU cc_start: 0.8570 (tp30) cc_final: 0.8189 (tm-30) REVERT: Y 21 LEU cc_start: 0.8992 (mt) cc_final: 0.8783 (mm) REVERT: Y 26 PHE cc_start: 0.8277 (t80) cc_final: 0.7966 (t80) REVERT: Y 30 MET cc_start: 0.8738 (ptm) cc_final: 0.8272 (ptm) REVERT: Y 39 GLN cc_start: 0.7018 (pt0) cc_final: 0.6810 (pt0) REVERT: Y 42 LEU cc_start: 0.8520 (mt) cc_final: 0.8288 (mt) REVERT: Y 44 LYS cc_start: 0.8377 (tttm) cc_final: 0.8056 (mttt) REVERT: 0 47 TYR cc_start: 0.8528 (OUTLIER) cc_final: 0.8157 (m-10) REVERT: 3 63 TYR cc_start: 0.7313 (m-80) cc_final: 0.6881 (m-80) REVERT: 5 1 MET cc_start: 0.1310 (tpt) cc_final: 0.0387 (ptm) REVERT: 5 99 PHE cc_start: 0.3598 (m-80) cc_final: 0.3147 (m-80) REVERT: 5 122 GLN cc_start: 0.5829 (pm20) cc_final: 0.5103 (mp10) outliers start: 387 outliers final: 232 residues processed: 2136 average time/residue: 1.3155 time to fit residues: 4870.4246 Evaluate side-chains 2008 residues out of total 5475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 250 poor density : 1758 time to evaluate : 6.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 19 THR Chi-restraints excluded: chain b residue 21 TYR Chi-restraints excluded: chain b residue 53 LEU Chi-restraints excluded: chain b residue 71 THR Chi-restraints excluded: chain b residue 101 THR Chi-restraints excluded: chain b residue 106 VAL Chi-restraints excluded: chain b residue 129 THR Chi-restraints excluded: chain b residue 142 LYS Chi-restraints excluded: chain b residue 152 ASP Chi-restraints excluded: chain b residue 167 HIS Chi-restraints excluded: chain b residue 185 ILE Chi-restraints excluded: chain b residue 198 VAL Chi-restraints excluded: chain d residue 11 SER Chi-restraints excluded: chain d residue 16 THR Chi-restraints excluded: chain d residue 28 ASP Chi-restraints excluded: chain d residue 54 LEU Chi-restraints excluded: chain d residue 116 LEU Chi-restraints excluded: chain d residue 204 SER Chi-restraints excluded: chain e residue 14 LEU Chi-restraints excluded: chain e residue 47 PHE Chi-restraints excluded: chain e residue 55 VAL Chi-restraints excluded: chain e residue 68 ARG Chi-restraints excluded: chain e residue 89 THR Chi-restraints excluded: chain e residue 121 ASN Chi-restraints excluded: chain e residue 122 VAL Chi-restraints excluded: chain e residue 147 ASN Chi-restraints excluded: chain e residue 160 VAL Chi-restraints excluded: chain f residue 18 VAL Chi-restraints excluded: chain f residue 52 ASN Chi-restraints excluded: chain f residue 86 ARG Chi-restraints excluded: chain h residue 10 LEU Chi-restraints excluded: chain h residue 11 THR Chi-restraints excluded: chain h residue 50 VAL Chi-restraints excluded: chain h residue 53 ASP Chi-restraints excluded: chain h residue 58 LEU Chi-restraints excluded: chain h residue 73 SER Chi-restraints excluded: chain h residue 103 VAL Chi-restraints excluded: chain h residue 109 VAL Chi-restraints excluded: chain k residue 30 ILE Chi-restraints excluded: chain k residue 39 ASN Chi-restraints excluded: chain k residue 45 THR Chi-restraints excluded: chain k residue 58 THR Chi-restraints excluded: chain k residue 109 ILE Chi-restraints excluded: chain k residue 115 ILE Chi-restraints excluded: chain l residue 7 VAL Chi-restraints excluded: chain l residue 86 VAL Chi-restraints excluded: chain l residue 97 VAL Chi-restraints excluded: chain o residue 66 LEU Chi-restraints excluded: chain o residue 74 VAL Chi-restraints excluded: chain p residue 19 VAL Chi-restraints excluded: chain p residue 23 ASP Chi-restraints excluded: chain q residue 19 SER Chi-restraints excluded: chain q residue 54 ILE Chi-restraints excluded: chain q residue 56 ASP Chi-restraints excluded: chain r residue 27 THR Chi-restraints excluded: chain r residue 71 ASP Chi-restraints excluded: chain t residue 19 HIS Chi-restraints excluded: chain t residue 29 THR Chi-restraints excluded: chain t residue 31 ILE Chi-restraints excluded: chain t residue 51 ASN Chi-restraints excluded: chain c residue 14 VAL Chi-restraints excluded: chain c residue 55 VAL Chi-restraints excluded: chain c residue 100 ILE Chi-restraints excluded: chain c residue 105 VAL Chi-restraints excluded: chain c residue 121 SER Chi-restraints excluded: chain c residue 176 THR Chi-restraints excluded: chain g residue 6 ILE Chi-restraints excluded: chain g residue 11 ILE Chi-restraints excluded: chain g residue 75 LYS Chi-restraints excluded: chain g residue 90 VAL Chi-restraints excluded: chain i residue 18 VAL Chi-restraints excluded: chain i residue 27 ILE Chi-restraints excluded: chain i residue 46 VAL Chi-restraints excluded: chain i residue 56 MET Chi-restraints excluded: chain i residue 60 LEU Chi-restraints excluded: chain i residue 62 LEU Chi-restraints excluded: chain i residue 66 VAL Chi-restraints excluded: chain i residue 71 ILE Chi-restraints excluded: chain i residue 97 LEU Chi-restraints excluded: chain i residue 113 LYS Chi-restraints excluded: chain i residue 115 VAL Chi-restraints excluded: chain j residue 44 THR Chi-restraints excluded: chain j residue 46 LYS Chi-restraints excluded: chain j residue 84 VAL Chi-restraints excluded: chain m residue 3 ILE Chi-restraints excluded: chain m residue 21 ILE Chi-restraints excluded: chain m residue 24 VAL Chi-restraints excluded: chain m residue 55 LEU Chi-restraints excluded: chain m residue 82 LEU Chi-restraints excluded: chain m residue 101 THR Chi-restraints excluded: chain m residue 103 THR Chi-restraints excluded: chain n residue 56 SER Chi-restraints excluded: chain n residue 60 GLN Chi-restraints excluded: chain n residue 67 THR Chi-restraints excluded: chain s residue 5 LYS Chi-restraints excluded: chain s residue 17 LYS Chi-restraints excluded: chain s residue 39 ILE Chi-restraints excluded: chain s residue 42 ASN Chi-restraints excluded: chain s residue 59 VAL Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 85 ASN Chi-restraints excluded: chain C residue 131 MET Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain C residue 179 GLU Chi-restraints excluded: chain C residue 200 MET Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 58 ASN Chi-restraints excluded: chain D residue 77 ARG Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 106 LYS Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 139 SER Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 173 GLN Chi-restraints excluded: chain D residue 180 VAL Chi-restraints excluded: chain D residue 184 ARG Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain F residue 9 ASP Chi-restraints excluded: chain F residue 132 ARG Chi-restraints excluded: chain F residue 143 ASP Chi-restraints excluded: chain F residue 145 VAL Chi-restraints excluded: chain F residue 152 ASP Chi-restraints excluded: chain F residue 156 THR Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 18 ILE Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 37 ASN Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain G residue 137 LYS Chi-restraints excluded: chain G residue 147 LEU Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 9 VAL Chi-restraints excluded: chain H residue 44 ILE Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 59 THR Chi-restraints excluded: chain I residue 85 ILE Chi-restraints excluded: chain I residue 86 LYS Chi-restraints excluded: chain I residue 95 ASP Chi-restraints excluded: chain I residue 127 SER Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain J residue 67 ASN Chi-restraints excluded: chain J residue 81 ILE Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 28 SER Chi-restraints excluded: chain K residue 32 TYR Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 110 VAL Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 123 ARG Chi-restraints excluded: chain M residue 42 THR Chi-restraints excluded: chain M residue 54 THR Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 93 VAL Chi-restraints excluded: chain N residue 11 ASN Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain O residue 8 ILE Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 65 THR Chi-restraints excluded: chain P residue 3 ILE Chi-restraints excluded: chain P residue 7 LEU Chi-restraints excluded: chain P residue 16 VAL Chi-restraints excluded: chain P residue 23 ASP Chi-restraints excluded: chain P residue 24 THR Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 83 ILE Chi-restraints excluded: chain Q residue 7 VAL Chi-restraints excluded: chain Q residue 16 ILE Chi-restraints excluded: chain Q residue 30 VAL Chi-restraints excluded: chain Q residue 33 VAL Chi-restraints excluded: chain Q residue 38 VAL Chi-restraints excluded: chain Q residue 111 LYS Chi-restraints excluded: chain R residue 10 LYS Chi-restraints excluded: chain R residue 14 VAL Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 41 ILE Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 98 ILE Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain S residue 20 VAL Chi-restraints excluded: chain S residue 67 ASP Chi-restraints excluded: chain S residue 106 VAL Chi-restraints excluded: chain S residue 108 SER Chi-restraints excluded: chain T residue 37 ASP Chi-restraints excluded: chain T residue 39 THR Chi-restraints excluded: chain T residue 60 THR Chi-restraints excluded: chain T residue 85 VAL Chi-restraints excluded: chain U residue 27 VAL Chi-restraints excluded: chain U residue 48 VAL Chi-restraints excluded: chain U residue 68 ASN Chi-restraints excluded: chain U residue 69 VAL Chi-restraints excluded: chain U residue 78 LYS Chi-restraints excluded: chain U residue 101 THR Chi-restraints excluded: chain V residue 77 VAL Chi-restraints excluded: chain V residue 83 LYS Chi-restraints excluded: chain V residue 89 ILE Chi-restraints excluded: chain V residue 91 PHE Chi-restraints excluded: chain W residue 8 ASN Chi-restraints excluded: chain W residue 49 CYS Chi-restraints excluded: chain W residue 54 THR Chi-restraints excluded: chain W residue 63 VAL Chi-restraints excluded: chain X residue 4 CYS Chi-restraints excluded: chain X residue 10 ARG Chi-restraints excluded: chain X residue 24 THR Chi-restraints excluded: chain X residue 39 VAL Chi-restraints excluded: chain X residue 64 ASP Chi-restraints excluded: chain Y residue 15 ASN Chi-restraints excluded: chain Y residue 16 THR Chi-restraints excluded: chain Y residue 46 VAL Chi-restraints excluded: chain Y residue 55 THR Chi-restraints excluded: chain Y residue 57 LEU Chi-restraints excluded: chain Z residue 2 LYS Chi-restraints excluded: chain Z residue 40 THR Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 24 VAL Chi-restraints excluded: chain 0 residue 43 THR Chi-restraints excluded: chain 0 residue 47 TYR Chi-restraints excluded: chain 1 residue 47 ILE Chi-restraints excluded: chain 2 residue 9 VAL Chi-restraints excluded: chain 2 residue 10 LEU Chi-restraints excluded: chain 3 residue 50 SER Chi-restraints excluded: chain 5 residue 55 VAL Chi-restraints excluded: chain 5 residue 77 VAL Chi-restraints excluded: chain 6 residue 16 CYS Chi-restraints excluded: chain 6 residue 27 THR Chi-restraints excluded: chain 6 residue 35 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1103 random chunks: chunk 991 optimal weight: 8.9990 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: 0.8980 chunk 1066 optimal weight: 9.9990 chunk 526 optimal weight: 10.0000 chunk 954 optimal weight: 10.0000 chunk 287 optimal weight: 6.9990 overall best weight: 7.3790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 197 HIS ** e 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 96 GLN ** f 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 37 HIS f 46 GLN f 52 ASN ** k 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 118 ASN l 5 GLN ** l 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 71 HIS l 72 ASN ** o 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 51 GLN ** t 60 GLN ** 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 ** i 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 36 ASN C 133 ASN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 36 GLN ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 136 GLN ** F 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 47 ASN G 142 GLN ** H 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 93 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** O 38 GLN O 67 ASN P 65 ASN P 76 HIS ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 71 ASN R 18 GLN T 48 GLN ** U 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 44 HIS V 49 ASN ** V 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 15 ASN ** Y 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.6219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.170 161499 Z= 0.336 Angle : 0.815 15.696 240779 Z= 0.431 Chirality : 0.042 0.356 30208 Planarity : 0.008 0.126 13518 Dihedral : 23.658 179.141 79713 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 21.13 Ramachandran Plot: Outliers : 0.79 % Allowed : 9.34 % Favored : 89.86 % Rotamer: Outliers : 9.15 % Allowed : 25.02 % Favored : 65.83 % 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: -2.14 (0.10), residues: 6551 helix: -0.26 (0.11), residues: 2111 sheet: -2.26 (0.14), residues: 1118 loop : -1.87 (0.10), residues: 3322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP b 103 HIS 0.027 0.002 HIS E 165 PHE 0.045 0.003 PHE b 90 TYR 0.067 0.003 TYR f 59 ARG 0.018 0.001 ARG F 111 *********************** 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 2342 residues out of total 5475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 442 poor density : 1900 time to evaluate : 6.477 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: b 17 HIS cc_start: 0.3968 (OUTLIER) cc_final: 0.3457 (m170) REVERT: b 22 TRP cc_start: 0.8709 (p-90) cc_final: 0.8393 (p-90) REVERT: b 110 ILE cc_start: 0.8350 (mm) cc_final: 0.8144 (mm) REVERT: b 136 ARG cc_start: 0.7556 (ptt90) cc_final: 0.7330 (ptt90) REVERT: b 197 PHE cc_start: 0.7813 (m-80) cc_final: 0.7421 (m-80) REVERT: d 7 LYS cc_start: 0.8798 (mmtp) cc_final: 0.8454 (ttmt) REVERT: d 8 LEU cc_start: 0.6458 (tp) cc_final: 0.5678 (mt) REVERT: d 46 ARG cc_start: 0.5720 (tpp-160) cc_final: 0.4664 (ttt90) REVERT: d 72 ARG cc_start: 0.8856 (tmm-80) cc_final: 0.8477 (ttm-80) REVERT: d 177 MET cc_start: 0.1356 (mmt) cc_final: 0.0472 (mmt) REVERT: e 18 ASN cc_start: 0.8463 (OUTLIER) cc_final: 0.7771 (p0) REVERT: e 135 VAL cc_start: 0.9262 (m) cc_final: 0.9027 (p) REVERT: f 4 TYR cc_start: 0.9275 (m-80) cc_final: 0.9018 (m-10) REVERT: f 11 HIS cc_start: 0.8124 (t70) cc_final: 0.7891 (t70) REVERT: f 12 PRO cc_start: 0.8056 (Cg_exo) cc_final: 0.7694 (Cg_endo) REVERT: f 25 TYR cc_start: 0.7286 (m-10) cc_final: 0.7031 (m-10) REVERT: f 65 GLU cc_start: 0.7698 (tt0) cc_final: 0.7268 (pp20) REVERT: h 32 LYS cc_start: 0.9084 (mmmm) cc_final: 0.8769 (tppt) REVERT: h 50 VAL cc_start: 0.8309 (OUTLIER) cc_final: 0.8066 (p) REVERT: h 63 LYS cc_start: 0.8109 (mtpm) cc_final: 0.7748 (mtpp) REVERT: h 113 ARG cc_start: 0.8626 (tmm160) cc_final: 0.8110 (tmm160) REVERT: h 117 GLN cc_start: 0.8653 (mm-40) cc_final: 0.8452 (mm-40) REVERT: k 63 GLN cc_start: 0.8734 (tt0) cc_final: 0.8368 (mm110) REVERT: k 124 LYS cc_start: 0.8453 (pttp) cc_final: 0.8117 (tptm) REVERT: l 14 LYS cc_start: 0.8107 (ttmt) cc_final: 0.7493 (tppt) REVERT: l 50 LYS cc_start: 0.7854 (OUTLIER) cc_final: 0.7424 (mttm) REVERT: l 78 VAL cc_start: 0.5498 (t) cc_final: 0.5216 (m) REVERT: p 12 LYS cc_start: 0.7882 (tmtt) cc_final: 0.7602 (tmtt) REVERT: p 13 LYS cc_start: 0.8232 (mmtp) cc_final: 0.7829 (ttpp) REVERT: q 39 ARG cc_start: 0.8217 (tpp80) cc_final: 0.7995 (tpp80) REVERT: q 42 LYS cc_start: 0.7981 (mtmt) cc_final: 0.7749 (mtmt) REVERT: q 50 ASN cc_start: 0.6925 (OUTLIER) cc_final: 0.6619 (m110) REVERT: q 62 GLU cc_start: 0.8614 (tp30) cc_final: 0.8319 (tt0) REVERT: q 70 LYS cc_start: 0.8304 (OUTLIER) cc_final: 0.7292 (ttmt) REVERT: r 29 LYS cc_start: 0.8481 (ptpp) cc_final: 0.8244 (mtmm) REVERT: r 50 TYR cc_start: 0.8368 (m-80) cc_final: 0.8070 (m-10) REVERT: r 53 GLN cc_start: 0.9036 (mt0) cc_final: 0.8727 (mp10) REVERT: t 28 ARG cc_start: 0.8605 (ptp-170) cc_final: 0.8221 (mtm110) REVERT: t 50 PHE cc_start: 0.8588 (t80) cc_final: 0.8208 (t80) REVERT: t 60 GLN cc_start: 0.9276 (mm-40) cc_final: 0.8980 (mm-40) REVERT: c 13 ILE cc_start: 0.8501 (OUTLIER) cc_final: 0.8253 (mt) REVERT: c 22 PHE cc_start: 0.8516 (t80) cc_final: 0.7975 (t80) REVERT: c 36 PHE cc_start: 0.8990 (t80) cc_final: 0.8684 (t80) REVERT: c 120 THR cc_start: 0.9063 (OUTLIER) cc_final: 0.8762 (m) REVERT: c 122 GLN cc_start: 0.8680 (mm-40) cc_final: 0.8420 (mm-40) REVERT: c 133 MET cc_start: 0.8853 (ptt) cc_final: 0.8642 (ptt) REVERT: g 6 ILE cc_start: 0.6444 (OUTLIER) cc_final: 0.6148 (pp) REVERT: g 46 LEU cc_start: 0.9277 (mp) cc_final: 0.9026 (pp) REVERT: g 96 ASN cc_start: 0.7994 (p0) cc_final: 0.7628 (p0) REVERT: i 27 ILE cc_start: 0.7301 (OUTLIER) cc_final: 0.7020 (mp) REVERT: i 28 VAL cc_start: 0.8253 (t) cc_final: 0.8030 (p) REVERT: j 84 VAL cc_start: 0.7078 (OUTLIER) cc_final: 0.6461 (m) REVERT: j 85 ASP cc_start: 0.7118 (m-30) cc_final: 0.6717 (p0) REVERT: m 22 TYR cc_start: 0.8315 (t80) cc_final: 0.7161 (t80) REVERT: m 54 THR cc_start: 0.8152 (p) cc_final: 0.7815 (p) REVERT: m 55 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8653 (tt) REVERT: m 58 GLU cc_start: 0.8491 (mt-10) cc_final: 0.8064 (mt-10) REVERT: m 69 ARG cc_start: 0.8724 (mtt-85) cc_final: 0.8338 (mmt90) REVERT: m 74 MET cc_start: 0.9113 (mtt) cc_final: 0.8905 (mtp) REVERT: n 60 GLN cc_start: 0.8601 (OUTLIER) cc_final: 0.7967 (mm-40) REVERT: s 55 GLN cc_start: 0.8408 (pt0) cc_final: 0.8124 (pm20) REVERT: C 186 ASP cc_start: 0.8052 (m-30) cc_final: 0.7834 (t0) REVERT: D 30 GLU cc_start: 0.8828 (mm-30) cc_final: 0.8326 (mm-30) REVERT: D 128 ARG cc_start: 0.8548 (mtm-85) cc_final: 0.8294 (mtp180) REVERT: D 184 ARG cc_start: 0.8580 (OUTLIER) cc_final: 0.7851 (mpp80) REVERT: E 23 PHE cc_start: 0.7049 (t80) cc_final: 0.6516 (t80) REVERT: E 24 ASN cc_start: 0.7946 (t0) cc_final: 0.7391 (t0) REVERT: E 25 GLU cc_start: 0.8199 (tt0) cc_final: 0.7866 (tp30) REVERT: E 116 ASP cc_start: 0.9210 (m-30) cc_final: 0.8381 (t70) REVERT: E 189 THR cc_start: 0.8561 (m) cc_final: 0.8144 (p) REVERT: F 11 VAL cc_start: 0.8743 (t) cc_final: 0.8472 (p) REVERT: F 51 ASN cc_start: 0.8251 (m110) cc_final: 0.7720 (t0) REVERT: F 77 LYS cc_start: 0.8550 (mtmt) cc_final: 0.8248 (tttt) REVERT: F 100 GLU cc_start: 0.8734 (tm-30) cc_final: 0.8470 (tp30) REVERT: F 104 THR cc_start: 0.8610 (m) cc_final: 0.7933 (m) REVERT: F 111 ARG cc_start: 0.7403 (mmp80) cc_final: 0.6723 (mtt180) REVERT: F 119 LYS cc_start: 0.8658 (mttp) cc_final: 0.8250 (tmtt) REVERT: F 132 ARG cc_start: 0.7566 (OUTLIER) cc_final: 0.6887 (ptp90) REVERT: F 141 ASP cc_start: 0.8274 (t70) cc_final: 0.7962 (t70) REVERT: F 151 LEU cc_start: 0.8190 (pp) cc_final: 0.7689 (pp) REVERT: F 163 GLU cc_start: 0.7745 (pm20) cc_final: 0.7458 (pm20) REVERT: F 173 ASP cc_start: 0.8784 (m-30) cc_final: 0.8370 (t70) REVERT: G 82 PHE cc_start: 0.8524 (m-80) cc_final: 0.8312 (m-80) REVERT: G 146 ASP cc_start: 0.8426 (t0) cc_final: 0.8217 (t0) REVERT: H 43 ASN cc_start: 0.8551 (m-40) cc_final: 0.8219 (t0) REVERT: H 45 GLU cc_start: 0.8482 (tm-30) cc_final: 0.7656 (pt0) REVERT: I 16 MET cc_start: 0.4501 (mpp) cc_final: 0.4259 (tpt) REVERT: I 94 LYS cc_start: 0.4587 (OUTLIER) cc_final: 0.4188 (pttm) REVERT: I 99 LYS cc_start: 0.5960 (ttpt) cc_final: 0.5599 (mmtt) REVERT: I 124 MET cc_start: 0.5499 (mmp) cc_final: 0.5239 (mmp) REVERT: J 15 TRP cc_start: 0.8966 (m100) cc_final: 0.8360 (m100) REVERT: K 112 PHE cc_start: 0.8463 (m-80) cc_final: 0.8003 (m-10) REVERT: K 114 LYS cc_start: 0.9023 (tptp) cc_final: 0.8740 (mttp) REVERT: M 53 MET cc_start: 0.9383 (tmm) cc_final: 0.8981 (tmm) REVERT: M 106 ASP cc_start: 0.7796 (p0) cc_final: 0.7567 (p0) REVERT: N 5 LYS cc_start: 0.9272 (mtmm) cc_final: 0.9064 (mtmm) REVERT: N 23 ASN cc_start: 0.8831 (t0) cc_final: 0.8599 (t0) REVERT: N 72 ASP cc_start: 0.9088 (t0) cc_final: 0.8536 (t0) REVERT: N 75 ILE cc_start: 0.9087 (mm) cc_final: 0.8402 (mm) REVERT: N 99 LYS cc_start: 0.8719 (mppt) cc_final: 0.8503 (mppt) REVERT: N 107 ASN cc_start: 0.8116 (t0) cc_final: 0.7737 (t0) REVERT: N 110 MET cc_start: 0.8812 (mmp) cc_final: 0.8578 (mmm) REVERT: N 112 TYR cc_start: 0.8812 (m-80) cc_final: 0.8506 (m-80) REVERT: O 17 LYS cc_start: 0.8219 (tptt) cc_final: 0.7739 (tptt) REVERT: O 54 VAL cc_start: 0.8863 (p) cc_final: 0.8243 (p) REVERT: O 55 GLU cc_start: 0.8169 (mt-10) cc_final: 0.7837 (mm-30) REVERT: P 27 VAL cc_start: 0.9487 (t) cc_final: 0.9261 (p) REVERT: P 70 GLU cc_start: 0.8614 (tt0) cc_final: 0.8233 (tt0) REVERT: P 97 TYR cc_start: 0.8820 (m-10) cc_final: 0.8570 (m-80) REVERT: P 99 LEU cc_start: 0.9043 (OUTLIER) cc_final: 0.8806 (tt) REVERT: P 110 LYS cc_start: 0.8536 (mmmt) cc_final: 0.8034 (mtmt) REVERT: Q 90 ASP cc_start: 0.7592 (p0) cc_final: 0.7388 (p0) REVERT: R 10 LYS cc_start: 0.6304 (OUTLIER) cc_final: 0.5854 (ptmm) REVERT: R 60 LYS cc_start: 0.8810 (OUTLIER) cc_final: 0.8253 (ptpp) REVERT: R 78 ARG cc_start: 0.9203 (tpp80) cc_final: 0.8867 (tpp80) REVERT: S 67 ASP cc_start: 0.8274 (OUTLIER) cc_final: 0.8010 (t0) REVERT: S 78 GLU cc_start: 0.8738 (pt0) cc_final: 0.8219 (pt0) REVERT: S 86 MET cc_start: 0.9075 (tpt) cc_final: 0.8721 (ttp) REVERT: T 1 MET cc_start: 0.1943 (ptm) cc_final: 0.1669 (mmt) REVERT: T 6 ARG cc_start: 0.7585 (ttp80) cc_final: 0.6953 (ttp80) REVERT: T 24 MET cc_start: 0.8951 (tpt) cc_final: 0.8564 (tmm) REVERT: T 37 ASP cc_start: 0.8808 (OUTLIER) cc_final: 0.8418 (p0) REVERT: T 69 ARG cc_start: 0.6959 (ttp80) cc_final: 0.6691 (ttp80) REVERT: T 87 LEU cc_start: 0.8951 (mt) cc_final: 0.8442 (mp) REVERT: U 4 ILE cc_start: 0.9268 (mp) cc_final: 0.9057 (tp) REVERT: U 71 ILE cc_start: 0.8313 (pt) cc_final: 0.8007 (mt) REVERT: V 5 ASN cc_start: 0.8760 (m-40) cc_final: 0.7884 (p0) REVERT: V 10 LYS cc_start: 0.7331 (pttm) cc_final: 0.6908 (tptp) REVERT: W 73 ARG cc_start: 0.8790 (mtm110) cc_final: 0.8389 (ptp90) REVERT: X 44 ARG cc_start: 0.7816 (ttm110) cc_final: 0.7506 (mtp-110) REVERT: Y 17 GLU cc_start: 0.8705 (tp30) cc_final: 0.8438 (tm-30) REVERT: Y 21 LEU cc_start: 0.9074 (mt) cc_final: 0.8828 (mm) REVERT: Y 44 LYS cc_start: 0.8406 (tttm) cc_final: 0.7988 (tttt) REVERT: Y 50 VAL cc_start: 0.9472 (t) cc_final: 0.9185 (p) REVERT: Z 20 LYS cc_start: 0.9284 (mtmm) cc_final: 0.9020 (mtmm) REVERT: Z 40 THR cc_start: 0.7890 (OUTLIER) cc_final: 0.7651 (p) REVERT: 0 47 TYR cc_start: 0.8596 (OUTLIER) cc_final: 0.8079 (m-10) REVERT: 2 6 GLN cc_start: 0.8351 (tm-30) cc_final: 0.8080 (tm-30) REVERT: 3 63 TYR cc_start: 0.7527 (m-80) cc_final: 0.6988 (m-80) REVERT: 5 38 MET cc_start: 0.6830 (mtm) cc_final: 0.5924 (mmm) REVERT: 5 99 PHE cc_start: 0.4643 (m-80) cc_final: 0.3937 (m-80) REVERT: 5 122 GLN cc_start: 0.6224 (pm20) cc_final: 0.5775 (mm-40) REVERT: 6 16 CYS cc_start: 0.5995 (OUTLIER) cc_final: 0.5308 (t) REVERT: 6 41 HIS cc_start: 0.7576 (t-90) cc_final: 0.7218 (t-90) outliers start: 442 outliers final: 277 residues processed: 2117 average time/residue: 1.3412 time to fit residues: 4952.6798 Evaluate side-chains 2025 residues out of total 5475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 301 poor density : 1724 time to evaluate : 6.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 17 HIS Chi-restraints excluded: chain b residue 19 THR Chi-restraints excluded: chain b residue 21 TYR Chi-restraints excluded: chain b residue 51 GLU Chi-restraints excluded: chain b residue 53 LEU Chi-restraints excluded: chain b residue 81 ASP Chi-restraints excluded: chain b residue 104 LYS Chi-restraints excluded: chain b residue 116 LEU Chi-restraints excluded: chain b residue 119 GLN Chi-restraints excluded: chain b residue 129 THR Chi-restraints excluded: chain b residue 152 ASP Chi-restraints excluded: chain b residue 167 HIS Chi-restraints excluded: chain b residue 185 ILE Chi-restraints excluded: chain b residue 198 VAL Chi-restraints excluded: chain d residue 28 ASP Chi-restraints excluded: chain d residue 40 HIS Chi-restraints excluded: chain d residue 48 SER Chi-restraints excluded: chain d residue 116 LEU Chi-restraints excluded: chain d residue 160 LEU Chi-restraints excluded: chain e residue 18 ASN Chi-restraints excluded: chain e residue 33 THR Chi-restraints excluded: chain e residue 47 PHE Chi-restraints excluded: chain e residue 68 ARG Chi-restraints excluded: chain e residue 84 VAL Chi-restraints excluded: chain e residue 89 THR Chi-restraints excluded: chain e residue 121 ASN Chi-restraints excluded: chain e residue 122 VAL Chi-restraints excluded: chain e residue 130 THR Chi-restraints excluded: chain e residue 147 ASN Chi-restraints excluded: chain e residue 160 VAL Chi-restraints excluded: chain f residue 18 VAL Chi-restraints excluded: chain f residue 21 MET Chi-restraints excluded: chain f residue 44 ARG Chi-restraints excluded: chain f residue 52 ASN Chi-restraints excluded: chain f residue 64 VAL Chi-restraints excluded: chain f residue 89 VAL Chi-restraints excluded: chain h residue 10 LEU Chi-restraints excluded: chain h residue 25 THR Chi-restraints excluded: chain h residue 47 ASP Chi-restraints excluded: chain h residue 50 VAL Chi-restraints excluded: chain h residue 53 ASP Chi-restraints excluded: chain h residue 62 LEU Chi-restraints excluded: chain h residue 73 SER Chi-restraints excluded: chain h residue 103 VAL Chi-restraints excluded: chain h residue 109 VAL Chi-restraints excluded: chain h residue 111 THR Chi-restraints excluded: chain k residue 45 THR Chi-restraints excluded: chain k residue 58 THR Chi-restraints excluded: chain k residue 81 LEU Chi-restraints excluded: chain k residue 108 ASN Chi-restraints excluded: chain k residue 109 ILE Chi-restraints excluded: chain k residue 115 ILE Chi-restraints excluded: chain l residue 3 VAL Chi-restraints excluded: chain l residue 7 VAL Chi-restraints excluded: chain l residue 18 SER Chi-restraints excluded: chain l residue 50 LYS Chi-restraints excluded: chain l residue 77 SER Chi-restraints excluded: chain l residue 86 VAL Chi-restraints excluded: chain l residue 97 VAL Chi-restraints excluded: chain o residue 51 SER Chi-restraints excluded: chain o residue 66 LEU Chi-restraints excluded: chain o residue 82 GLU Chi-restraints excluded: chain p residue 19 VAL Chi-restraints excluded: chain p residue 42 ILE Chi-restraints excluded: chain p residue 63 GLN Chi-restraints excluded: chain q residue 50 ASN Chi-restraints excluded: chain q residue 54 ILE Chi-restraints excluded: chain q residue 56 ASP Chi-restraints excluded: chain q residue 70 LYS Chi-restraints excluded: chain r residue 27 THR Chi-restraints excluded: chain r residue 65 SER Chi-restraints excluded: chain t residue 19 HIS Chi-restraints excluded: chain t residue 31 ILE Chi-restraints excluded: chain t residue 51 ASN Chi-restraints excluded: chain t residue 57 VAL Chi-restraints excluded: chain t residue 78 LEU Chi-restraints excluded: chain w residue 508 SER Chi-restraints excluded: chain c residue 13 ILE Chi-restraints excluded: chain c residue 14 VAL Chi-restraints excluded: chain c residue 55 VAL Chi-restraints excluded: chain c residue 78 LYS Chi-restraints excluded: chain c residue 100 ILE Chi-restraints excluded: chain c residue 120 THR Chi-restraints excluded: chain c residue 121 SER Chi-restraints excluded: chain g residue 6 ILE Chi-restraints excluded: chain g residue 11 ILE Chi-restraints excluded: chain g residue 21 LEU Chi-restraints excluded: chain g residue 75 LYS Chi-restraints excluded: chain g residue 90 VAL Chi-restraints excluded: chain i residue 27 ILE Chi-restraints excluded: chain i residue 56 MET Chi-restraints excluded: chain i residue 60 LEU Chi-restraints excluded: chain i residue 62 LEU Chi-restraints excluded: chain i residue 66 VAL Chi-restraints excluded: chain i residue 71 ILE Chi-restraints excluded: chain i residue 97 LEU Chi-restraints excluded: chain i residue 113 LYS Chi-restraints excluded: chain i residue 115 VAL Chi-restraints excluded: chain j residue 8 ILE Chi-restraints excluded: chain j residue 44 THR Chi-restraints excluded: chain j residue 46 LYS Chi-restraints excluded: chain j residue 84 VAL Chi-restraints excluded: chain m residue 3 ILE Chi-restraints excluded: chain m residue 21 ILE Chi-restraints excluded: chain m residue 24 VAL Chi-restraints excluded: chain m residue 32 ILE Chi-restraints excluded: chain m residue 55 LEU Chi-restraints excluded: chain m residue 82 LEU Chi-restraints excluded: chain m residue 101 THR Chi-restraints excluded: chain m residue 107 THR Chi-restraints excluded: chain n residue 30 ILE Chi-restraints excluded: chain n residue 33 VAL Chi-restraints excluded: chain n residue 60 GLN Chi-restraints excluded: chain s residue 5 LYS Chi-restraints excluded: chain s residue 39 ILE Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 85 ASN Chi-restraints excluded: chain C residue 107 LYS Chi-restraints excluded: chain C residue 110 LYS Chi-restraints excluded: chain C residue 131 MET Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 179 GLU Chi-restraints excluded: chain C residue 200 MET Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 58 ASN Chi-restraints excluded: chain D residue 77 ARG Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 106 LYS Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 180 VAL Chi-restraints excluded: chain D residue 184 ARG Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 73 ILE Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain F residue 15 LEU Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 127 TYR Chi-restraints excluded: chain F residue 132 ARG Chi-restraints excluded: chain F residue 134 GLN Chi-restraints excluded: chain F residue 145 VAL Chi-restraints excluded: chain F residue 155 ILE Chi-restraints excluded: chain F residue 156 THR Chi-restraints excluded: chain F residue 168 LEU Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 14 VAL Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 18 ILE Chi-restraints excluded: chain G residue 37 ASN Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 48 THR Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 44 ILE Chi-restraints excluded: chain H residue 110 VAL Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 147 VAL Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 59 THR Chi-restraints excluded: chain I residue 85 ILE Chi-restraints excluded: chain I residue 94 LYS Chi-restraints excluded: chain I residue 95 ASP Chi-restraints excluded: chain I residue 97 VAL Chi-restraints excluded: chain I residue 127 SER Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain J residue 67 ASN Chi-restraints excluded: chain J residue 73 VAL Chi-restraints excluded: chain J residue 81 ILE Chi-restraints excluded: chain J residue 139 VAL Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 12 ASP Chi-restraints excluded: chain K residue 28 SER Chi-restraints excluded: chain K residue 56 ASP Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 115 ILE Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 54 GLN Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 122 VAL Chi-restraints excluded: chain L residue 123 ARG Chi-restraints excluded: chain M residue 26 VAL Chi-restraints excluded: chain M residue 42 THR Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 93 VAL Chi-restraints excluded: chain N residue 11 ASN Chi-restraints excluded: chain N residue 13 ASN Chi-restraints excluded: chain N residue 24 MET Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 106 ASP Chi-restraints excluded: chain N residue 115 LEU Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 53 THR Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain O residue 95 SER Chi-restraints excluded: chain P residue 3 ILE Chi-restraints excluded: chain P residue 7 LEU Chi-restraints excluded: chain P residue 16 VAL Chi-restraints excluded: chain P residue 23 ASP Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 39 LEU Chi-restraints excluded: chain P residue 59 THR Chi-restraints excluded: chain P residue 65 ASN Chi-restraints excluded: chain P residue 83 ILE Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain Q residue 7 VAL Chi-restraints excluded: chain Q residue 16 ILE Chi-restraints excluded: chain Q residue 17 LEU Chi-restraints excluded: chain Q residue 38 VAL Chi-restraints excluded: chain Q residue 39 ILE Chi-restraints excluded: chain Q residue 87 VAL Chi-restraints excluded: chain Q residue 111 LYS Chi-restraints excluded: chain R residue 10 LYS Chi-restraints excluded: chain R residue 14 VAL Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 27 ILE Chi-restraints excluded: chain R residue 60 LYS Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 79 ARG Chi-restraints excluded: chain R residue 98 ILE Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain S residue 33 LEU Chi-restraints excluded: chain S residue 67 ASP Chi-restraints excluded: chain S residue 106 VAL Chi-restraints excluded: chain S residue 108 SER Chi-restraints excluded: chain T residue 37 ASP Chi-restraints excluded: chain T residue 55 VAL Chi-restraints excluded: chain T residue 60 THR Chi-restraints excluded: chain T residue 78 SER Chi-restraints excluded: chain T residue 85 VAL Chi-restraints excluded: chain U residue 27 VAL Chi-restraints excluded: chain U residue 35 VAL Chi-restraints excluded: chain U residue 48 VAL Chi-restraints excluded: chain U residue 69 VAL Chi-restraints excluded: chain U residue 78 LYS Chi-restraints excluded: chain V residue 8 VAL Chi-restraints excluded: chain V residue 77 VAL Chi-restraints excluded: chain V residue 83 LYS Chi-restraints excluded: chain V residue 89 ILE Chi-restraints excluded: chain V residue 91 PHE Chi-restraints excluded: chain W residue 12 SER Chi-restraints excluded: chain W residue 49 CYS Chi-restraints excluded: chain W residue 76 ILE Chi-restraints excluded: chain W residue 78 ILE Chi-restraints excluded: chain X residue 4 CYS Chi-restraints excluded: chain X residue 10 ARG Chi-restraints excluded: chain X residue 24 THR Chi-restraints excluded: chain X residue 55 MET Chi-restraints excluded: chain X residue 64 ASP Chi-restraints excluded: chain Y residue 15 ASN Chi-restraints excluded: chain Y residue 16 THR Chi-restraints excluded: chain Y residue 55 THR Chi-restraints excluded: chain Y residue 57 LEU Chi-restraints excluded: chain Z residue 2 LYS Chi-restraints excluded: chain Z residue 31 ILE Chi-restraints excluded: chain Z residue 34 THR Chi-restraints excluded: chain Z residue 40 THR Chi-restraints excluded: chain Z residue 47 ILE Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 24 VAL Chi-restraints excluded: chain 0 residue 43 THR Chi-restraints excluded: chain 0 residue 47 TYR Chi-restraints excluded: chain 1 residue 47 ILE Chi-restraints excluded: chain 2 residue 9 VAL Chi-restraints excluded: chain 3 residue 50 SER Chi-restraints excluded: chain 4 residue 25 VAL Chi-restraints excluded: chain 4 residue 37 GLN Chi-restraints excluded: chain 5 residue 5 LEU Chi-restraints excluded: chain 5 residue 34 THR Chi-restraints excluded: chain 5 residue 50 VAL Chi-restraints excluded: chain 5 residue 77 VAL Chi-restraints excluded: chain 6 residue 5 ILE Chi-restraints excluded: chain 6 residue 16 CYS Chi-restraints excluded: chain 6 residue 27 THR Chi-restraints excluded: chain 6 residue 28 VAL Chi-restraints excluded: chain 6 residue 35 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1103 random chunks: chunk 887 optimal weight: 7.9990 chunk 605 optimal weight: 30.0000 chunk 15 optimal weight: 20.0000 chunk 793 optimal weight: 7.9990 chunk 439 optimal weight: 4.9990 chunk 909 optimal weight: 20.0000 chunk 736 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 544 optimal weight: 20.0000 chunk 956 optimal weight: 4.9990 chunk 269 optimal weight: 3.9990 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 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 96 GLN ** f 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 27 ASN ** k 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 72 ASN p 18 GLN t 60 GLN ** g 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 51 HIS ** C 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 238 ASN ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 GLN F 26 GLN ** F 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 47 ASN H 18 GLN ** J 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 128 ASN ** M 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 38 GLN P 40 GLN 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 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 27 ASN ** Y 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 58 ASN Z 33 HIS ** 4 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.6710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.166 161499 Z= 0.264 Angle : 0.734 16.551 240779 Z= 0.392 Chirality : 0.039 0.380 30208 Planarity : 0.007 0.127 13518 Dihedral : 23.624 179.764 79701 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 17.98 Ramachandran Plot: Outliers : 0.75 % Allowed : 9.49 % Favored : 89.76 % Rotamer: Outliers : 7.93 % Allowed : 28.16 % Favored : 63.91 % 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: -1.99 (0.10), residues: 6551 helix: -0.00 (0.11), residues: 2115 sheet: -2.14 (0.13), residues: 1150 loop : -1.89 (0.10), residues: 3286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP M 64 HIS 0.013 0.002 HIS o 45 PHE 0.034 0.003 PHE L 107 TYR 0.031 0.003 TYR E 35 ARG 0.012 0.001 ARG K 108 *********************** 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 2245 residues out of total 5475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 383 poor density : 1862 time to evaluate : 5.779 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: b 22 TRP cc_start: 0.8715 (p-90) cc_final: 0.8427 (p-90) REVERT: b 106 VAL cc_start: 0.8088 (m) cc_final: 0.7858 (m) REVERT: b 110 ILE cc_start: 0.8310 (mm) cc_final: 0.7989 (mm) REVERT: b 114 LYS cc_start: 0.8895 (ttmt) cc_final: 0.7977 (pptt) REVERT: d 8 LEU cc_start: 0.6608 (tp) cc_final: 0.5233 (mt) REVERT: d 46 ARG cc_start: 0.5800 (tpp-160) cc_final: 0.4732 (ttt90) REVERT: d 58 GLN cc_start: 0.7866 (mm110) cc_final: 0.7431 (tm-30) REVERT: d 72 ARG cc_start: 0.8881 (tmm-80) cc_final: 0.8529 (ttm170) REVERT: d 116 LEU cc_start: 0.5127 (OUTLIER) cc_final: 0.4044 (tt) REVERT: d 159 GLU cc_start: 0.6913 (tp30) cc_final: 0.6649 (mm-30) REVERT: d 177 MET cc_start: 0.1743 (mmt) cc_final: 0.0845 (mmt) REVERT: d 197 HIS cc_start: 0.7247 (OUTLIER) cc_final: 0.6976 (t-90) REVERT: e 18 ASN cc_start: 0.8368 (t0) cc_final: 0.7721 (p0) REVERT: e 68 ARG cc_start: 0.8605 (OUTLIER) cc_final: 0.8211 (ptm160) REVERT: e 135 VAL cc_start: 0.9201 (m) cc_final: 0.8979 (p) REVERT: e 155 LYS cc_start: 0.8386 (OUTLIER) cc_final: 0.8078 (mtmm) REVERT: f 11 HIS cc_start: 0.8403 (t70) cc_final: 0.8025 (t-90) REVERT: f 12 PRO cc_start: 0.8114 (Cg_exo) cc_final: 0.7726 (Cg_endo) REVERT: f 21 MET cc_start: 0.8803 (ttm) cc_final: 0.8216 (ttm) REVERT: f 24 ARG cc_start: 0.6990 (mmm-85) cc_final: 0.6563 (mmm-85) REVERT: f 25 TYR cc_start: 0.7503 (m-10) cc_final: 0.6866 (m-10) REVERT: f 65 GLU cc_start: 0.7769 (tt0) cc_final: 0.7240 (pp20) REVERT: f 70 VAL cc_start: 0.8065 (m) cc_final: 0.7733 (p) REVERT: h 9 MET cc_start: 0.8988 (tpp) cc_final: 0.8726 (ttm) REVERT: h 106 SER cc_start: 0.8679 (m) cc_final: 0.8233 (p) REVERT: h 113 ARG cc_start: 0.8567 (tmm160) cc_final: 0.8205 (ttp80) REVERT: k 12 ARG cc_start: 0.5238 (ptp90) cc_final: 0.4369 (ptm160) REVERT: k 37 GLN cc_start: 0.8546 (mm110) cc_final: 0.8340 (mm-40) REVERT: k 49 SER cc_start: 0.8477 (m) cc_final: 0.7934 (t) REVERT: k 124 LYS cc_start: 0.8364 (pttp) cc_final: 0.8146 (tptm) REVERT: p 12 LYS cc_start: 0.7982 (tmtt) cc_final: 0.7205 (ttmm) REVERT: p 13 LYS cc_start: 0.8294 (mmtp) cc_final: 0.7987 (ttpp) REVERT: q 17 GLU cc_start: 0.8339 (tm-30) cc_final: 0.7923 (tm-30) REVERT: q 62 GLU cc_start: 0.8601 (tp30) cc_final: 0.8250 (tt0) REVERT: q 70 LYS cc_start: 0.8558 (OUTLIER) cc_final: 0.7838 (ttmt) REVERT: r 29 LYS cc_start: 0.8490 (ptpp) cc_final: 0.8247 (mtmm) REVERT: r 53 GLN cc_start: 0.8998 (mt0) cc_final: 0.8721 (mp10) REVERT: r 71 ASP cc_start: 0.7432 (p0) cc_final: 0.7176 (p0) REVERT: t 14 GLU cc_start: 0.8821 (pp20) cc_final: 0.8318 (tp30) REVERT: t 28 ARG cc_start: 0.8586 (ptp-170) cc_final: 0.8277 (mtm110) REVERT: t 60 GLN cc_start: 0.9326 (mm110) cc_final: 0.8945 (mm-40) REVERT: u 19 LYS cc_start: 0.6158 (mmtt) cc_final: 0.5152 (pttt) REVERT: c 22 PHE cc_start: 0.8525 (t80) cc_final: 0.8308 (t80) REVERT: c 36 PHE cc_start: 0.9043 (t80) cc_final: 0.8691 (t80) REVERT: c 120 THR cc_start: 0.8959 (OUTLIER) cc_final: 0.8713 (m) REVERT: c 166 TRP cc_start: 0.8434 (p-90) cc_final: 0.8224 (p-90) REVERT: c 185 THR cc_start: 0.8588 (m) cc_final: 0.8367 (p) REVERT: g 6 ILE cc_start: 0.6366 (OUTLIER) cc_final: 0.6063 (pp) REVERT: g 46 LEU cc_start: 0.9325 (mp) cc_final: 0.9036 (pp) REVERT: g 96 ASN cc_start: 0.8096 (p0) cc_final: 0.7759 (p0) REVERT: i 27 ILE cc_start: 0.7455 (OUTLIER) cc_final: 0.7079 (mp) REVERT: i 28 VAL cc_start: 0.8228 (t) cc_final: 0.7960 (p) REVERT: i 55 ASP cc_start: 0.7558 (p0) cc_final: 0.7326 (p0) REVERT: j 15 HIS cc_start: 0.8740 (p90) cc_final: 0.8402 (t70) REVERT: j 52 LEU cc_start: 0.8456 (tt) cc_final: 0.8198 (tt) REVERT: j 84 VAL cc_start: 0.7179 (OUTLIER) cc_final: 0.6558 (m) REVERT: j 85 ASP cc_start: 0.7089 (m-30) cc_final: 0.6871 (p0) REVERT: m 54 THR cc_start: 0.8124 (p) cc_final: 0.7853 (p) REVERT: m 55 LEU cc_start: 0.8943 (OUTLIER) cc_final: 0.8657 (tt) REVERT: m 58 GLU cc_start: 0.8486 (mt-10) cc_final: 0.8139 (mt-10) REVERT: m 74 MET cc_start: 0.9158 (mtt) cc_final: 0.8862 (mtp) REVERT: m 100 ARG cc_start: 0.7901 (OUTLIER) cc_final: 0.7502 (mtm110) REVERT: s 55 GLN cc_start: 0.8624 (pt0) cc_final: 0.8180 (pm20) REVERT: C 29 PHE cc_start: 0.7910 (t80) cc_final: 0.7691 (t80) REVERT: C 36 ASN cc_start: 0.8854 (t0) cc_final: 0.7715 (p0) REVERT: C 184 GLU cc_start: 0.8483 (tp30) cc_final: 0.7967 (tm-30) REVERT: D 184 ARG cc_start: 0.8638 (OUTLIER) cc_final: 0.7858 (mpp80) REVERT: E 23 PHE cc_start: 0.7190 (t80) cc_final: 0.6831 (t80) REVERT: E 24 ASN cc_start: 0.7900 (t0) cc_final: 0.7415 (t0) REVERT: E 25 GLU cc_start: 0.8256 (tt0) cc_final: 0.7866 (tp30) REVERT: E 35 TYR cc_start: 0.8322 (t80) cc_final: 0.8014 (t80) REVERT: E 47 LYS cc_start: 0.9108 (OUTLIER) cc_final: 0.8685 (ptpt) REVERT: E 69 ARG cc_start: 0.8712 (OUTLIER) cc_final: 0.8503 (mtt180) REVERT: E 116 ASP cc_start: 0.9229 (m-30) cc_final: 0.8422 (t70) REVERT: E 195 GLN cc_start: 0.8863 (mt0) cc_final: 0.8172 (mp10) REVERT: F 51 ASN cc_start: 0.8222 (m110) cc_final: 0.7671 (t0) REVERT: F 77 LYS cc_start: 0.8595 (mtmt) cc_final: 0.8355 (tttt) REVERT: F 132 ARG cc_start: 0.7455 (OUTLIER) cc_final: 0.7093 (mmm-85) REVERT: F 151 LEU cc_start: 0.8143 (pp) cc_final: 0.7937 (pp) REVERT: F 173 ASP cc_start: 0.8731 (m-30) cc_final: 0.8342 (t70) REVERT: G 105 SER cc_start: 0.8773 (m) cc_final: 0.8308 (p) REVERT: H 27 ARG cc_start: 0.7529 (ttp80) cc_final: 0.7267 (ttp80) REVERT: H 43 ASN cc_start: 0.8467 (m-40) cc_final: 0.8033 (t0) REVERT: H 45 GLU cc_start: 0.8597 (tm-30) cc_final: 0.7884 (pt0) REVERT: I 99 LYS cc_start: 0.5779 (ttpt) cc_final: 0.5284 (mptt) REVERT: J 73 VAL cc_start: 0.8793 (OUTLIER) cc_final: 0.8565 (p) REVERT: J 98 GLU cc_start: 0.8750 (mp0) cc_final: 0.8218 (tm-30) REVERT: K 7 MET cc_start: 0.8788 (mmt) cc_final: 0.8563 (mmt) REVERT: K 112 PHE cc_start: 0.8412 (m-80) cc_final: 0.8069 (m-10) REVERT: K 114 LYS cc_start: 0.9129 (OUTLIER) cc_final: 0.8831 (mttp) REVERT: L 2 ARG cc_start: 0.8018 (mmm160) cc_final: 0.7362 (tpt90) REVERT: L 91 ASP cc_start: 0.8381 (t0) cc_final: 0.7918 (t70) REVERT: M 53 MET cc_start: 0.9319 (tmm) cc_final: 0.8916 (tmm) REVERT: M 104 GLU cc_start: 0.8666 (mm-30) cc_final: 0.8379 (mm-30) REVERT: M 136 MET cc_start: 0.7305 (mmm) cc_final: 0.7076 (mmp) REVERT: N 5 LYS cc_start: 0.9379 (mtmm) cc_final: 0.9078 (mtmm) REVERT: N 23 ASN cc_start: 0.8802 (t0) cc_final: 0.8571 (t0) REVERT: N 72 ASP cc_start: 0.8970 (t0) cc_final: 0.8530 (t0) REVERT: N 75 ILE cc_start: 0.9282 (mm) cc_final: 0.8951 (mm) REVERT: N 107 ASN cc_start: 0.8017 (t0) cc_final: 0.7688 (t0) REVERT: N 110 MET cc_start: 0.8830 (mmp) cc_final: 0.8596 (mmm) REVERT: N 112 TYR cc_start: 0.8809 (m-80) cc_final: 0.8555 (m-80) REVERT: O 116 GLN cc_start: 0.7297 (mm-40) cc_final: 0.6983 (tp40) REVERT: P 6 GLN cc_start: 0.7933 (tm-30) cc_final: 0.7213 (tm-30) REVERT: P 97 TYR cc_start: 0.8440 (m-10) cc_final: 0.8192 (m-80) REVERT: P 99 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8461 (tt) REVERT: P 110 LYS cc_start: 0.8524 (mmmt) cc_final: 0.8024 (mtmt) REVERT: S 57 ASN cc_start: 0.9124 (t0) cc_final: 0.8698 (t0) REVERT: S 67 ASP cc_start: 0.8324 (OUTLIER) cc_final: 0.8028 (t0) REVERT: S 78 GLU cc_start: 0.8721 (pt0) cc_final: 0.8318 (pt0) REVERT: S 86 MET cc_start: 0.9063 (tpt) cc_final: 0.8750 (ttt) REVERT: T 1 MET cc_start: 0.1781 (ptm) cc_final: 0.1149 (mmt) REVERT: T 5 GLU cc_start: 0.7503 (mp0) cc_final: 0.7260 (mp0) REVERT: T 24 MET cc_start: 0.8896 (tpt) cc_final: 0.8629 (tmm) REVERT: T 37 ASP cc_start: 0.8691 (OUTLIER) cc_final: 0.7890 (t0) REVERT: T 87 LEU cc_start: 0.8943 (mt) cc_final: 0.8541 (mp) REVERT: U 4 ILE cc_start: 0.9263 (mp) cc_final: 0.9029 (tp) REVERT: U 71 ILE cc_start: 0.8299 (pt) cc_final: 0.7969 (mt) REVERT: V 5 ASN cc_start: 0.8756 (m-40) cc_final: 0.7954 (p0) REVERT: V 10 LYS cc_start: 0.7377 (pttm) cc_final: 0.7058 (tptp) REVERT: V 31 TYR cc_start: 0.7634 (p90) cc_final: 0.7338 (p90) REVERT: W 21 ARG cc_start: 0.8774 (mmm-85) cc_final: 0.8552 (mmm-85) REVERT: W 54 THR cc_start: 0.9328 (OUTLIER) cc_final: 0.9088 (t) REVERT: Y 1 MET cc_start: 0.7747 (tpp) cc_final: 0.7356 (tpp) REVERT: Y 17 GLU cc_start: 0.8724 (tp30) cc_final: 0.8384 (tm-30) REVERT: Y 25 GLN cc_start: 0.8574 (mm-40) cc_final: 0.7711 (mm-40) REVERT: Y 44 LYS cc_start: 0.8357 (tttm) cc_final: 0.7947 (tttt) REVERT: Y 46 VAL cc_start: 0.9152 (OUTLIER) cc_final: 0.8499 (p) REVERT: Y 50 VAL cc_start: 0.9355 (OUTLIER) cc_final: 0.9149 (m) REVERT: Z 20 LYS cc_start: 0.9246 (mtmm) cc_final: 0.8980 (mtmm) REVERT: Z 40 THR cc_start: 0.7910 (OUTLIER) cc_final: 0.7697 (p) REVERT: 0 47 TYR cc_start: 0.8697 (OUTLIER) cc_final: 0.8029 (m-10) REVERT: 2 6 GLN cc_start: 0.8408 (tm-30) cc_final: 0.8139 (tm-30) REVERT: 3 39 ARG cc_start: 0.8522 (mtp180) cc_final: 0.7595 (mtp85) REVERT: 3 63 TYR cc_start: 0.7455 (m-80) cc_final: 0.6999 (m-80) REVERT: 4 16 ILE cc_start: 0.9130 (OUTLIER) cc_final: 0.8865 (mt) REVERT: 4 18 LYS cc_start: 0.8679 (ptmm) cc_final: 0.8445 (ttmt) REVERT: 5 86 MET cc_start: 0.3356 (mmm) cc_final: 0.3105 (mmm) REVERT: 5 122 GLN cc_start: 0.6214 (pm20) cc_final: 0.5781 (mm-40) REVERT: 6 2 LYS cc_start: 0.7870 (mtmt) cc_final: 0.7649 (mtmt) REVERT: 6 59 ARG cc_start: 0.7909 (ttt-90) cc_final: 0.7619 (tmt170) outliers start: 383 outliers final: 255 residues processed: 2042 average time/residue: 1.2971 time to fit residues: 4604.5927 Evaluate side-chains 2019 residues out of total 5475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 281 poor density : 1738 time to evaluate : 6.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 9 LEU Chi-restraints excluded: chain b residue 19 THR Chi-restraints excluded: chain b residue 21 TYR Chi-restraints excluded: chain b residue 71 THR Chi-restraints excluded: chain b residue 104 LYS Chi-restraints excluded: chain b residue 116 LEU Chi-restraints excluded: chain b residue 129 THR Chi-restraints excluded: chain b residue 152 ASP Chi-restraints excluded: chain b residue 156 LEU Chi-restraints excluded: chain b residue 167 HIS Chi-restraints excluded: chain b residue 178 LEU Chi-restraints excluded: chain b residue 185 ILE Chi-restraints excluded: chain b residue 198 VAL Chi-restraints excluded: chain d residue 28 ASP Chi-restraints excluded: chain d residue 40 HIS Chi-restraints excluded: chain d residue 116 LEU Chi-restraints excluded: chain d residue 189 ASP Chi-restraints excluded: chain d residue 197 HIS Chi-restraints excluded: chain e residue 47 PHE Chi-restraints excluded: chain e residue 68 ARG Chi-restraints excluded: chain e residue 73 VAL Chi-restraints excluded: chain e residue 121 ASN Chi-restraints excluded: chain e residue 147 ASN Chi-restraints excluded: chain e residue 155 LYS Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 18 VAL Chi-restraints excluded: chain f residue 44 ARG Chi-restraints excluded: chain f residue 64 VAL Chi-restraints excluded: chain f residue 89 VAL Chi-restraints excluded: chain h residue 10 LEU Chi-restraints excluded: chain h residue 25 THR Chi-restraints excluded: chain h residue 47 ASP Chi-restraints excluded: chain h residue 53 ASP Chi-restraints excluded: chain h residue 73 SER Chi-restraints excluded: chain h residue 103 VAL Chi-restraints excluded: chain h residue 109 VAL Chi-restraints excluded: chain h residue 111 THR Chi-restraints excluded: chain k residue 45 THR Chi-restraints excluded: chain k residue 58 THR Chi-restraints excluded: chain k residue 81 LEU Chi-restraints excluded: chain k residue 95 THR Chi-restraints excluded: chain k residue 108 ASN Chi-restraints excluded: chain k residue 109 ILE Chi-restraints excluded: chain k residue 115 ILE Chi-restraints excluded: chain l residue 7 VAL Chi-restraints excluded: chain l residue 26 CYS Chi-restraints excluded: chain l residue 50 LYS Chi-restraints excluded: chain l residue 82 ARG Chi-restraints excluded: chain l residue 96 THR Chi-restraints excluded: chain l residue 97 VAL Chi-restraints excluded: chain o residue 4 THR Chi-restraints excluded: chain o residue 51 SER Chi-restraints excluded: chain o residue 66 LEU Chi-restraints excluded: chain p residue 3 THR Chi-restraints excluded: chain p residue 19 VAL Chi-restraints excluded: chain p residue 23 ASP Chi-restraints excluded: chain p residue 55 ASP Chi-restraints excluded: chain q residue 6 THR Chi-restraints excluded: chain q residue 40 THR Chi-restraints excluded: chain q residue 54 ILE Chi-restraints excluded: chain q residue 56 ASP Chi-restraints excluded: chain q residue 70 LYS Chi-restraints excluded: chain r residue 27 THR Chi-restraints excluded: chain t residue 12 GLN Chi-restraints excluded: chain t residue 19 HIS Chi-restraints excluded: chain t residue 29 THR Chi-restraints excluded: chain t residue 78 LEU Chi-restraints excluded: chain w residue 508 SER Chi-restraints excluded: chain c residue 14 VAL Chi-restraints excluded: chain c residue 55 VAL Chi-restraints excluded: chain c residue 100 ILE Chi-restraints excluded: chain c residue 105 VAL Chi-restraints excluded: chain c residue 120 THR Chi-restraints excluded: chain c residue 206 ILE Chi-restraints excluded: chain g residue 6 ILE Chi-restraints excluded: chain g residue 11 ILE Chi-restraints excluded: chain g residue 135 LYS Chi-restraints excluded: chain i residue 27 ILE Chi-restraints excluded: chain i residue 54 VAL Chi-restraints excluded: chain i residue 56 MET Chi-restraints excluded: chain i residue 60 LEU Chi-restraints excluded: chain i residue 62 LEU Chi-restraints excluded: chain i residue 66 VAL Chi-restraints excluded: chain i residue 97 LEU Chi-restraints excluded: chain i residue 110 VAL Chi-restraints excluded: chain j residue 44 THR Chi-restraints excluded: chain j residue 51 VAL Chi-restraints excluded: chain j residue 84 VAL Chi-restraints excluded: chain m residue 3 ILE Chi-restraints excluded: chain m residue 21 ILE Chi-restraints excluded: chain m residue 24 VAL Chi-restraints excluded: chain m residue 32 ILE Chi-restraints excluded: chain m residue 44 ILE Chi-restraints excluded: chain m residue 55 LEU Chi-restraints excluded: chain m residue 82 LEU Chi-restraints excluded: chain m residue 84 CYS Chi-restraints excluded: chain m residue 100 ARG Chi-restraints excluded: chain m residue 101 THR Chi-restraints excluded: chain n residue 30 ILE Chi-restraints excluded: chain n residue 64 CYS Chi-restraints excluded: chain s residue 5 LYS Chi-restraints excluded: chain s residue 10 ILE Chi-restraints excluded: chain s residue 39 ILE Chi-restraints excluded: chain s residue 66 VAL Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 85 ASN Chi-restraints excluded: chain C residue 110 LYS Chi-restraints excluded: chain C residue 131 MET Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain C residue 179 GLU Chi-restraints excluded: chain C residue 200 MET Chi-restraints excluded: chain C residue 238 ASN Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 49 GLN Chi-restraints excluded: chain D residue 77 ARG Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 106 LYS Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 180 VAL Chi-restraints excluded: chain D residue 184 ARG Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 47 LYS Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 69 ARG Chi-restraints excluded: chain E residue 73 ILE Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 132 ARG Chi-restraints excluded: chain F residue 136 ILE Chi-restraints excluded: chain F residue 145 VAL Chi-restraints excluded: chain F residue 155 ILE Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 14 VAL Chi-restraints excluded: chain G residue 15 ASP Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 18 ILE Chi-restraints excluded: chain G residue 37 ASN Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain G residue 161 VAL Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 44 ILE Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain I residue 34 ILE Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 85 ILE Chi-restraints excluded: chain I residue 95 ASP Chi-restraints excluded: chain I residue 134 SER Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain J residue 67 ASN Chi-restraints excluded: chain J residue 73 VAL Chi-restraints excluded: chain J residue 81 ILE Chi-restraints excluded: chain J residue 139 VAL Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 12 ASP Chi-restraints excluded: chain K residue 28 SER Chi-restraints excluded: chain K residue 32 TYR Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain K residue 47 ILE Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 114 LYS Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 100 ILE Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 122 VAL Chi-restraints excluded: chain M residue 26 VAL Chi-restraints excluded: chain M residue 42 THR Chi-restraints excluded: chain M residue 54 THR Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 91 TYR Chi-restraints excluded: chain M residue 93 VAL Chi-restraints excluded: chain M residue 108 VAL Chi-restraints excluded: chain N residue 11 ASN Chi-restraints excluded: chain N residue 13 ASN Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 89 SER Chi-restraints excluded: chain O residue 8 ILE Chi-restraints excluded: chain O residue 21 LEU Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain P residue 3 ILE Chi-restraints excluded: chain P residue 7 LEU Chi-restraints excluded: chain P residue 16 VAL Chi-restraints excluded: chain P residue 23 ASP Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 59 THR Chi-restraints excluded: chain P residue 83 ILE Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain P residue 101 GLU Chi-restraints excluded: chain Q residue 7 VAL Chi-restraints excluded: chain Q residue 16 ILE Chi-restraints excluded: chain Q residue 33 VAL Chi-restraints excluded: chain Q residue 38 VAL Chi-restraints excluded: chain Q residue 111 LYS Chi-restraints excluded: chain R residue 14 VAL Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 79 ARG Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain S residue 67 ASP Chi-restraints excluded: chain S residue 68 ASP Chi-restraints excluded: chain S residue 106 VAL Chi-restraints excluded: chain T residue 37 ASP Chi-restraints excluded: chain T residue 60 THR Chi-restraints excluded: chain T residue 85 VAL Chi-restraints excluded: chain U residue 33 VAL Chi-restraints excluded: chain U residue 35 VAL Chi-restraints excluded: chain U residue 41 VAL Chi-restraints excluded: chain U residue 48 VAL Chi-restraints excluded: chain U residue 69 VAL Chi-restraints excluded: chain V residue 1 MET Chi-restraints excluded: chain V residue 64 VAL Chi-restraints excluded: chain V residue 83 LYS Chi-restraints excluded: chain V residue 89 ILE Chi-restraints excluded: chain V residue 91 PHE Chi-restraints excluded: chain W residue 8 ASN Chi-restraints excluded: chain W residue 17 LEU Chi-restraints excluded: chain W residue 32 ILE Chi-restraints excluded: chain W residue 34 VAL Chi-restraints excluded: chain W residue 49 CYS Chi-restraints excluded: chain W residue 54 THR Chi-restraints excluded: chain W residue 77 SER Chi-restraints excluded: chain X residue 4 CYS Chi-restraints excluded: chain X residue 10 ARG Chi-restraints excluded: chain X residue 24 THR Chi-restraints excluded: chain X residue 55 MET Chi-restraints excluded: chain Y residue 15 ASN Chi-restraints excluded: chain Y residue 16 THR Chi-restraints excluded: chain Y residue 31 GLN Chi-restraints excluded: chain Y residue 43 LEU Chi-restraints excluded: chain Y residue 46 VAL Chi-restraints excluded: chain Y residue 50 VAL Chi-restraints excluded: chain Y residue 55 THR Chi-restraints excluded: chain Y residue 57 LEU Chi-restraints excluded: chain Z residue 2 LYS Chi-restraints excluded: chain Z residue 31 ILE Chi-restraints excluded: chain Z residue 34 THR Chi-restraints excluded: chain Z residue 40 THR Chi-restraints excluded: chain Z residue 47 ILE Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 24 VAL Chi-restraints excluded: chain 0 residue 47 TYR Chi-restraints excluded: chain 1 residue 47 ILE Chi-restraints excluded: chain 2 residue 9 VAL Chi-restraints excluded: chain 2 residue 10 LEU Chi-restraints excluded: chain 3 residue 50 SER Chi-restraints excluded: chain 3 residue 53 ASP Chi-restraints excluded: chain 4 residue 10 LEU Chi-restraints excluded: chain 4 residue 16 ILE Chi-restraints excluded: chain 4 residue 25 VAL Chi-restraints excluded: chain 4 residue 37 GLN Chi-restraints excluded: chain 5 residue 5 LEU Chi-restraints excluded: chain 5 residue 77 VAL Chi-restraints excluded: chain 6 residue 5 ILE Chi-restraints excluded: chain 6 residue 27 THR Chi-restraints excluded: chain 6 residue 28 VAL Chi-restraints excluded: chain 6 residue 33 ASN Chi-restraints excluded: chain 6 residue 35 ASP 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: 30.0000 chunk 210 optimal weight: 20.0000 chunk 625 optimal weight: 20.0000 chunk 263 optimal weight: 0.9990 chunk 1067 optimal weight: 0.5980 chunk 885 optimal weight: 7.9990 chunk 494 optimal weight: 20.0000 chunk 88 optimal weight: 10.0000 chunk 353 optimal weight: 40.0000 chunk 560 optimal weight: 30.0000 overall best weight: 7.9192 ------------------------------------------------------------------------------- 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** e 69 ASN ** e 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 96 GLN e 145 ASN ** f 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 117 GLN ** k 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 18 GLN ** p 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 101 ASN ** g 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 31 GLN ** C 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 134 HIS F 62 GLN ** F 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 138 GLN G 142 GLN I 93 ASN ** J 40 HIS ** 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 P 40 GLN Q 19 GLN ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 71 ASN ** R 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 39 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** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.7413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.138 161499 Z= 0.330 Angle : 0.801 15.270 240779 Z= 0.423 Chirality : 0.041 0.365 30208 Planarity : 0.007 0.128 13518 Dihedral : 23.647 179.189 79696 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 21.16 Ramachandran Plot: Outliers : 0.76 % Allowed : 10.06 % Favored : 89.18 % Rotamer: Outliers : 9.13 % Allowed : 28.14 % Favored : 62.73 % 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: -2.12 (0.10), residues: 6551 helix: -0.10 (0.11), residues: 2109 sheet: -2.12 (0.14), residues: 1090 loop : -2.03 (0.10), residues: 3352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP M 64 HIS 0.015 0.002 HIS o 45 PHE 0.053 0.003 PHE 2 18 TYR 0.031 0.003 TYR b 212 ARG 0.012 0.001 ARG C 237 *********************** 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 2277 residues out of total 5475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 441 poor density : 1836 time to evaluate : 6.469 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: b 17 HIS cc_start: 0.3952 (OUTLIER) cc_final: 0.3586 (m170) REVERT: b 22 TRP cc_start: 0.8772 (p-90) cc_final: 0.8436 (p-90) REVERT: b 114 LYS cc_start: 0.8944 (ttmt) cc_final: 0.8124 (pptt) REVERT: b 135 MET cc_start: 0.8773 (mmm) cc_final: 0.8228 (ppp) REVERT: b 183 PHE cc_start: 0.6932 (p90) cc_final: 0.6715 (p90) REVERT: d 46 ARG cc_start: 0.6656 (tpp-160) cc_final: 0.5463 (ttt180) REVERT: d 70 GLN cc_start: 0.8884 (tp40) cc_final: 0.8624 (tp-100) REVERT: d 72 ARG cc_start: 0.8909 (tmm-80) cc_final: 0.8687 (ttm-80) REVERT: d 74 TYR cc_start: 0.8310 (m-80) cc_final: 0.8029 (m-10) REVERT: d 116 LEU cc_start: 0.6183 (OUTLIER) cc_final: 0.5311 (tt) REVERT: d 177 MET cc_start: 0.2161 (mmt) cc_final: 0.1904 (mmt) REVERT: e 18 ASN cc_start: 0.8402 (t0) cc_final: 0.7956 (p0) REVERT: e 68 ARG cc_start: 0.8596 (OUTLIER) cc_final: 0.8271 (ptm160) REVERT: e 70 MET cc_start: 0.8127 (mtt) cc_final: 0.7897 (mtt) REVERT: e 155 LYS cc_start: 0.8466 (OUTLIER) cc_final: 0.8233 (mtmm) REVERT: f 11 HIS cc_start: 0.8371 (t70) cc_final: 0.8005 (t70) REVERT: f 12 PRO cc_start: 0.8004 (Cg_exo) cc_final: 0.7600 (Cg_endo) REVERT: f 17 GLN cc_start: 0.7948 (mt0) cc_final: 0.7725 (tm-30) REVERT: f 21 MET cc_start: 0.8828 (ttm) cc_final: 0.8393 (ttm) REVERT: f 25 TYR cc_start: 0.7301 (m-10) cc_final: 0.6986 (m-10) REVERT: f 40 GLU cc_start: 0.7626 (tt0) cc_final: 0.6881 (tt0) REVERT: h 9 MET cc_start: 0.9001 (tpp) cc_final: 0.8718 (ttm) REVERT: h 106 SER cc_start: 0.8689 (m) cc_final: 0.8283 (p) REVERT: h 113 ARG cc_start: 0.8562 (tmm160) cc_final: 0.8361 (tmm160) REVERT: h 116 ARG cc_start: 0.8921 (mmm-85) cc_final: 0.8632 (mmm-85) REVERT: k 12 ARG cc_start: 0.4827 (ptp90) cc_final: 0.4026 (ptm160) REVERT: k 15 VAL cc_start: 0.7223 (OUTLIER) cc_final: 0.6908 (p) REVERT: k 37 GLN cc_start: 0.8732 (mm110) cc_final: 0.8494 (mm-40) REVERT: k 92 ARG cc_start: 0.7436 (ttt90) cc_final: 0.7003 (mtp-110) REVERT: k 111 ASP cc_start: 0.7458 (p0) cc_final: 0.7241 (p0) REVERT: l 69 GLU cc_start: 0.8409 (mm-30) cc_final: 0.7879 (mp0) REVERT: o 27 GLN cc_start: 0.9122 (mm-40) cc_final: 0.8507 (mm-40) REVERT: q 20 ILE cc_start: 0.8517 (tt) cc_final: 0.8134 (pt) REVERT: q 29 LYS cc_start: 0.8254 (OUTLIER) cc_final: 0.7785 (ptmm) REVERT: q 39 ARG cc_start: 0.8103 (tpp80) cc_final: 0.7849 (tpp80) REVERT: q 62 GLU cc_start: 0.8744 (tp30) cc_final: 0.8510 (tt0) REVERT: q 70 LYS cc_start: 0.8894 (OUTLIER) cc_final: 0.8229 (ttmt) REVERT: r 23 LYS cc_start: 0.8690 (tppp) cc_final: 0.8465 (mmmt) REVERT: r 29 LYS cc_start: 0.8656 (ptpp) cc_final: 0.8335 (mtmm) REVERT: r 69 TYR cc_start: 0.8175 (m-80) cc_final: 0.7937 (m-10) REVERT: c 22 PHE cc_start: 0.8599 (t80) cc_final: 0.8127 (t80) REVERT: c 36 PHE cc_start: 0.9103 (t80) cc_final: 0.8863 (t80) REVERT: c 120 THR cc_start: 0.9103 (OUTLIER) cc_final: 0.8887 (m) REVERT: c 167 TYR cc_start: 0.7953 (m-10) cc_final: 0.7735 (m-10) REVERT: c 185 THR cc_start: 0.8738 (m) cc_final: 0.8516 (p) REVERT: g 6 ILE cc_start: 0.6471 (OUTLIER) cc_final: 0.6153 (pp) REVERT: g 46 LEU cc_start: 0.9411 (mp) cc_final: 0.9130 (pp) REVERT: i 27 ILE cc_start: 0.7453 (OUTLIER) cc_final: 0.7071 (mp) REVERT: i 28 VAL cc_start: 0.8333 (t) cc_final: 0.8040 (p) REVERT: i 55 ASP cc_start: 0.7777 (p0) cc_final: 0.7569 (p0) REVERT: j 15 HIS cc_start: 0.8747 (p90) cc_final: 0.8510 (t70) REVERT: m 54 THR cc_start: 0.8072 (p) cc_final: 0.7818 (p) REVERT: m 55 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8664 (tt) REVERT: m 58 GLU cc_start: 0.8429 (mt-10) cc_final: 0.8141 (mt-10) REVERT: m 74 MET cc_start: 0.9168 (mtt) cc_final: 0.8905 (mtp) REVERT: m 100 ARG cc_start: 0.8004 (OUTLIER) cc_final: 0.7486 (mtm110) REVERT: m 101 THR cc_start: 0.8812 (OUTLIER) cc_final: 0.8610 (t) REVERT: s 55 GLN cc_start: 0.8660 (pt0) cc_final: 0.8259 (pm20) REVERT: C 29 PHE cc_start: 0.8183 (t80) cc_final: 0.7920 (t80) REVERT: C 170 TYR cc_start: 0.8546 (m-10) cc_final: 0.8276 (m-10) REVERT: C 184 GLU cc_start: 0.8524 (tp30) cc_final: 0.8239 (tm-30) REVERT: D 81 GLU cc_start: 0.9067 (pt0) cc_final: 0.8846 (pm20) REVERT: D 184 ARG cc_start: 0.8601 (OUTLIER) cc_final: 0.7834 (mpp80) REVERT: E 24 ASN cc_start: 0.7925 (t0) cc_final: 0.7390 (t0) REVERT: E 25 GLU cc_start: 0.8378 (tt0) cc_final: 0.8045 (tp30) REVERT: E 47 LYS cc_start: 0.9049 (OUTLIER) cc_final: 0.8455 (ptpt) REVERT: E 69 ARG cc_start: 0.8728 (OUTLIER) cc_final: 0.8490 (mtt180) REVERT: E 116 ASP cc_start: 0.9149 (m-30) cc_final: 0.8424 (t70) REVERT: E 195 GLN cc_start: 0.8938 (mt0) cc_final: 0.8430 (mp10) REVERT: F 36 ASN cc_start: 0.7030 (t0) cc_final: 0.6792 (t0) REVERT: F 51 ASN cc_start: 0.8238 (m110) cc_final: 0.7611 (t0) REVERT: F 77 LYS cc_start: 0.8662 (mtmt) cc_final: 0.8432 (tttt) REVERT: F 173 ASP cc_start: 0.8753 (m-30) cc_final: 0.8357 (t70) REVERT: G 23 ILE cc_start: 0.8776 (tp) cc_final: 0.8522 (tp) REVERT: G 105 SER cc_start: 0.8916 (m) cc_final: 0.8613 (p) REVERT: G 127 GLN cc_start: 0.8488 (mm-40) cc_final: 0.8182 (mm-40) REVERT: H 1 MET cc_start: 0.8359 (mmt) cc_final: 0.7902 (ttt) REVERT: H 43 ASN cc_start: 0.8481 (m-40) cc_final: 0.7908 (t0) REVERT: H 45 GLU cc_start: 0.8566 (tm-30) cc_final: 0.7857 (pt0) REVERT: H 129 GLU cc_start: 0.6781 (tt0) cc_final: 0.6261 (tm-30) REVERT: I 85 ILE cc_start: 0.7279 (OUTLIER) cc_final: 0.6489 (mt) REVERT: I 99 LYS cc_start: 0.6032 (ttpt) cc_final: 0.5633 (mmmt) REVERT: J 58 ASN cc_start: 0.8019 (m-40) cc_final: 0.7754 (m-40) REVERT: J 73 VAL cc_start: 0.8702 (OUTLIER) cc_final: 0.8422 (p) REVERT: J 98 GLU cc_start: 0.8785 (mp0) cc_final: 0.8283 (tm-30) REVERT: J 131 ASN cc_start: 0.8604 (m-40) cc_final: 0.7876 (p0) REVERT: K 111 LYS cc_start: 0.8838 (ptmt) cc_final: 0.8099 (tptt) REVERT: K 112 PHE cc_start: 0.8497 (m-80) cc_final: 0.8125 (m-10) REVERT: K 114 LYS cc_start: 0.9151 (OUTLIER) cc_final: 0.8825 (mttm) REVERT: L 2 ARG cc_start: 0.8233 (mmm160) cc_final: 0.7381 (tpt90) REVERT: L 91 ASP cc_start: 0.8580 (t0) cc_final: 0.8024 (m-30) REVERT: L 123 ARG cc_start: 0.7519 (OUTLIER) cc_final: 0.7131 (mtt90) REVERT: M 53 MET cc_start: 0.9316 (tmm) cc_final: 0.8923 (tmm) REVERT: N 71 ARG cc_start: 0.9046 (mmm160) cc_final: 0.8214 (tpp80) REVERT: N 72 ASP cc_start: 0.9015 (t0) cc_final: 0.8388 (t0) REVERT: N 75 ILE cc_start: 0.9203 (mm) cc_final: 0.8852 (mm) REVERT: N 78 LYS cc_start: 0.9214 (tppp) cc_final: 0.8961 (tppp) REVERT: N 107 ASN cc_start: 0.7984 (t0) cc_final: 0.7728 (t0) REVERT: N 110 MET cc_start: 0.8818 (mmp) cc_final: 0.8241 (mmp) REVERT: O 9 ARG cc_start: 0.8152 (ptt90) cc_final: 0.7950 (ttp80) REVERT: O 55 GLU cc_start: 0.8212 (mt-10) cc_final: 0.7937 (mm-30) REVERT: O 116 GLN cc_start: 0.7544 (mm-40) cc_final: 0.7018 (tp40) REVERT: P 7 LEU cc_start: 0.9116 (OUTLIER) cc_final: 0.8881 (tp) REVERT: P 99 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8575 (tt) REVERT: P 110 LYS cc_start: 0.8630 (mmmt) cc_final: 0.8189 (mtmt) REVERT: R 5 PHE cc_start: 0.8761 (p90) cc_final: 0.8236 (p90) REVERT: R 60 LYS cc_start: 0.8877 (OUTLIER) cc_final: 0.8402 (ptpp) REVERT: R 78 ARG cc_start: 0.9282 (tpp80) cc_final: 0.8669 (ttp80) REVERT: S 57 ASN cc_start: 0.9076 (t0) cc_final: 0.8825 (t0) REVERT: S 67 ASP cc_start: 0.8231 (OUTLIER) cc_final: 0.8021 (t0) REVERT: S 86 MET cc_start: 0.9013 (tpt) cc_final: 0.8715 (ttt) REVERT: T 1 MET cc_start: 0.1269 (ptm) cc_final: 0.1055 (tpp) REVERT: T 24 MET cc_start: 0.8866 (tpt) cc_final: 0.8539 (tmm) REVERT: T 37 ASP cc_start: 0.8725 (OUTLIER) cc_final: 0.8042 (t0) REVERT: T 69 ARG cc_start: 0.7056 (ttp80) cc_final: 0.6770 (ttp80) REVERT: T 87 LEU cc_start: 0.9008 (mt) cc_final: 0.8659 (mp) REVERT: U 4 ILE cc_start: 0.9225 (mp) cc_final: 0.8979 (tp) REVERT: U 24 VAL cc_start: 0.7659 (t) cc_final: 0.7377 (t) REVERT: U 71 ILE cc_start: 0.8368 (pt) cc_final: 0.8123 (mt) REVERT: V 5 ASN cc_start: 0.9039 (m-40) cc_final: 0.8188 (p0) REVERT: V 10 LYS cc_start: 0.7480 (OUTLIER) cc_final: 0.7042 (tptp) REVERT: W 21 ARG cc_start: 0.8821 (mmm-85) cc_final: 0.8511 (mmm-85) REVERT: W 73 ARG cc_start: 0.8827 (mtm110) cc_final: 0.8265 (mtp-110) REVERT: X 43 LYS cc_start: 0.8330 (tppt) cc_final: 0.7898 (ptmt) REVERT: Y 1 MET cc_start: 0.7903 (tpp) cc_final: 0.7478 (tpp) REVERT: Y 17 GLU cc_start: 0.8801 (tp30) cc_final: 0.8566 (tm-30) REVERT: Y 25 GLN cc_start: 0.8849 (mm-40) cc_final: 0.8571 (mm-40) REVERT: Y 31 GLN cc_start: 0.8879 (OUTLIER) cc_final: 0.8657 (mm-40) REVERT: Y 39 GLN cc_start: 0.7095 (pt0) cc_final: 0.6855 (pt0) REVERT: Y 46 VAL cc_start: 0.9199 (OUTLIER) cc_final: 0.8965 (p) REVERT: Z 3 THR cc_start: 0.7816 (p) cc_final: 0.7502 (p) REVERT: Z 48 ASN cc_start: 0.9050 (OUTLIER) cc_final: 0.8629 (m-40) REVERT: 0 47 TYR cc_start: 0.8716 (OUTLIER) cc_final: 0.7950 (m-10) REVERT: 2 6 GLN cc_start: 0.8303 (tm-30) cc_final: 0.8019 (tm-30) REVERT: 4 16 ILE cc_start: 0.9138 (OUTLIER) cc_final: 0.8866 (mt) REVERT: 4 18 LYS cc_start: 0.8786 (ptmm) cc_final: 0.8574 (ttmt) REVERT: 5 38 MET cc_start: 0.6801 (mtm) cc_final: 0.6521 (ttt) REVERT: 5 56 ARG cc_start: 0.4762 (ttm170) cc_final: 0.4410 (ttm170) REVERT: 5 86 MET cc_start: 0.2943 (mmm) cc_final: 0.2728 (mmm) REVERT: 5 122 GLN cc_start: 0.6079 (pm20) cc_final: 0.5695 (mm-40) outliers start: 441 outliers final: 310 residues processed: 2047 average time/residue: 1.4284 time to fit residues: 5165.2532 Evaluate side-chains 2065 residues out of total 5475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 341 poor density : 1724 time to evaluate : 6.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 17 HIS Chi-restraints excluded: chain b residue 19 THR Chi-restraints excluded: chain b residue 21 TYR Chi-restraints excluded: chain b residue 71 THR Chi-restraints excluded: chain b residue 81 ASP Chi-restraints excluded: chain b residue 104 LYS Chi-restraints excluded: chain b residue 116 LEU Chi-restraints excluded: chain b residue 129 THR Chi-restraints excluded: chain b residue 152 ASP Chi-restraints excluded: chain b residue 156 LEU Chi-restraints excluded: chain b residue 167 HIS Chi-restraints excluded: chain b residue 178 LEU Chi-restraints excluded: chain b residue 185 ILE Chi-restraints excluded: chain b residue 198 VAL Chi-restraints excluded: chain d residue 28 ASP Chi-restraints excluded: chain d residue 40 HIS Chi-restraints excluded: chain d residue 67 LEU Chi-restraints excluded: chain d residue 110 ARG Chi-restraints excluded: chain d residue 116 LEU Chi-restraints excluded: chain d residue 189 ASP Chi-restraints excluded: chain d residue 197 HIS Chi-restraints excluded: chain e residue 45 VAL Chi-restraints excluded: chain e residue 47 PHE Chi-restraints excluded: chain e residue 68 ARG Chi-restraints excluded: chain e residue 73 VAL Chi-restraints excluded: chain e residue 89 THR Chi-restraints excluded: chain e residue 121 ASN Chi-restraints excluded: chain e residue 130 THR Chi-restraints excluded: chain e residue 131 ASN Chi-restraints excluded: chain e residue 147 ASN Chi-restraints excluded: chain e residue 155 LYS Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 18 VAL Chi-restraints excluded: chain f residue 44 ARG Chi-restraints excluded: chain f residue 89 VAL Chi-restraints excluded: chain h residue 10 LEU Chi-restraints excluded: chain h residue 11 THR Chi-restraints excluded: chain h residue 47 ASP Chi-restraints excluded: chain h residue 53 ASP Chi-restraints excluded: chain h residue 73 SER Chi-restraints excluded: chain h residue 103 VAL Chi-restraints excluded: chain h residue 109 VAL Chi-restraints excluded: chain h residue 111 THR Chi-restraints excluded: chain h residue 117 GLN Chi-restraints excluded: chain h residue 128 VAL Chi-restraints excluded: chain k residue 15 VAL Chi-restraints excluded: chain k residue 30 ILE Chi-restraints excluded: chain k residue 34 THR Chi-restraints excluded: chain k residue 45 THR Chi-restraints excluded: chain k residue 58 THR Chi-restraints excluded: chain k residue 81 LEU Chi-restraints excluded: chain k residue 95 THR Chi-restraints excluded: chain k residue 109 ILE Chi-restraints excluded: chain k residue 115 ILE Chi-restraints excluded: chain l residue 3 VAL Chi-restraints excluded: chain l residue 7 VAL Chi-restraints excluded: chain l residue 26 CYS Chi-restraints excluded: chain l residue 66 ILE Chi-restraints excluded: chain l residue 82 ARG Chi-restraints excluded: chain l residue 96 THR Chi-restraints excluded: chain l residue 97 VAL Chi-restraints excluded: chain o residue 4 THR Chi-restraints excluded: chain o residue 51 SER Chi-restraints excluded: chain o residue 55 LEU Chi-restraints excluded: chain o residue 66 LEU Chi-restraints excluded: chain o residue 73 ASP Chi-restraints excluded: chain p residue 19 VAL Chi-restraints excluded: chain p residue 23 ASP Chi-restraints excluded: chain p residue 55 ASP Chi-restraints excluded: chain q residue 29 LYS Chi-restraints excluded: chain q residue 32 ILE Chi-restraints excluded: chain q residue 45 VAL Chi-restraints excluded: chain q residue 54 ILE Chi-restraints excluded: chain q residue 56 ASP Chi-restraints excluded: chain q residue 70 LYS Chi-restraints excluded: chain r residue 27 THR Chi-restraints excluded: chain t residue 19 HIS Chi-restraints excluded: chain t residue 29 THR Chi-restraints excluded: chain t residue 65 LEU Chi-restraints excluded: chain t residue 78 LEU Chi-restraints excluded: chain w residue 508 SER Chi-restraints excluded: chain c residue 14 VAL Chi-restraints excluded: chain c residue 55 VAL Chi-restraints excluded: chain c residue 78 LYS Chi-restraints excluded: chain c residue 100 ILE Chi-restraints excluded: chain c residue 101 ASN Chi-restraints excluded: chain c residue 105 VAL Chi-restraints excluded: chain c residue 120 THR Chi-restraints excluded: chain c residue 149 LYS Chi-restraints excluded: chain c residue 206 ILE Chi-restraints excluded: chain g residue 6 ILE Chi-restraints excluded: chain g residue 11 ILE Chi-restraints excluded: chain g residue 21 LEU Chi-restraints excluded: chain g residue 84 TYR Chi-restraints excluded: chain g residue 135 LYS Chi-restraints excluded: chain i residue 4 GLN Chi-restraints excluded: chain i residue 27 ILE Chi-restraints excluded: chain i residue 56 MET Chi-restraints excluded: chain i residue 60 LEU Chi-restraints excluded: chain i residue 62 LEU Chi-restraints excluded: chain i residue 66 VAL Chi-restraints excluded: chain i residue 86 LEU Chi-restraints excluded: chain i residue 97 LEU Chi-restraints excluded: chain i residue 110 VAL Chi-restraints excluded: chain i residue 115 VAL Chi-restraints excluded: chain j residue 8 ILE Chi-restraints excluded: chain j residue 44 THR Chi-restraints excluded: chain j residue 51 VAL Chi-restraints excluded: chain j residue 88 MET Chi-restraints excluded: chain m residue 3 ILE Chi-restraints excluded: chain m residue 21 ILE Chi-restraints excluded: chain m residue 24 VAL Chi-restraints excluded: chain m residue 32 ILE Chi-restraints excluded: chain m residue 33 LEU Chi-restraints excluded: chain m residue 55 LEU Chi-restraints excluded: chain m residue 82 LEU Chi-restraints excluded: chain m residue 84 CYS Chi-restraints excluded: chain m residue 88 LEU Chi-restraints excluded: chain m residue 100 ARG Chi-restraints excluded: chain m residue 101 THR Chi-restraints excluded: chain m residue 103 THR Chi-restraints excluded: chain n residue 30 ILE Chi-restraints excluded: chain n residue 33 VAL Chi-restraints excluded: chain n residue 56 SER Chi-restraints excluded: chain n residue 64 CYS Chi-restraints excluded: chain n residue 67 THR Chi-restraints excluded: chain s residue 5 LYS Chi-restraints excluded: chain s residue 10 ILE Chi-restraints excluded: chain s residue 39 ILE Chi-restraints excluded: chain s residue 42 ASN Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 85 ASN Chi-restraints excluded: chain C residue 90 ILE Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 110 LYS Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 179 GLU Chi-restraints excluded: chain C residue 200 MET Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 58 ASN Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 106 LYS Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 180 VAL Chi-restraints excluded: chain D residue 184 ARG Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 19 PHE Chi-restraints excluded: chain E residue 47 LYS Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 69 ARG Chi-restraints excluded: chain E residue 73 ILE Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 127 TYR Chi-restraints excluded: chain F residue 145 VAL Chi-restraints excluded: chain F residue 152 ASP Chi-restraints excluded: chain F residue 155 ILE Chi-restraints excluded: chain F residue 156 THR Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 14 VAL Chi-restraints excluded: chain G residue 15 ASP Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 18 ILE Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 37 ASN Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain G residue 138 GLN Chi-restraints excluded: chain G residue 161 VAL Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 44 ILE Chi-restraints excluded: chain H residue 98 ASP Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 147 VAL Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 59 THR Chi-restraints excluded: chain I residue 77 VAL Chi-restraints excluded: chain I residue 85 ILE Chi-restraints excluded: chain I residue 95 ASP Chi-restraints excluded: chain I residue 97 VAL Chi-restraints excluded: chain I residue 134 SER Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 56 VAL Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain J residue 64 VAL Chi-restraints excluded: chain J residue 67 ASN Chi-restraints excluded: chain J residue 73 VAL Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 81 ILE Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 12 ASP Chi-restraints excluded: chain K residue 28 SER Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 114 LYS Chi-restraints excluded: chain K residue 116 ILE Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 54 GLN Chi-restraints excluded: chain L residue 93 ASN Chi-restraints excluded: chain L residue 100 ILE Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 122 VAL Chi-restraints excluded: chain L residue 123 ARG Chi-restraints excluded: chain M residue 26 VAL Chi-restraints excluded: chain M residue 42 THR Chi-restraints excluded: chain M residue 78 LEU Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 93 VAL Chi-restraints excluded: chain M residue 96 ILE Chi-restraints excluded: chain M residue 108 VAL Chi-restraints excluded: chain N residue 11 ASN Chi-restraints excluded: chain N residue 13 ASN Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 89 SER Chi-restraints excluded: chain N residue 115 LEU Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 95 SER Chi-restraints excluded: chain P residue 3 ILE Chi-restraints excluded: chain P residue 7 LEU Chi-restraints excluded: chain P residue 16 VAL Chi-restraints excluded: chain P residue 23 ASP Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 59 THR Chi-restraints excluded: chain P residue 83 ILE Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain P residue 101 GLU Chi-restraints excluded: chain Q residue 7 VAL Chi-restraints excluded: chain Q residue 16 ILE Chi-restraints excluded: chain Q residue 17 LEU Chi-restraints excluded: chain Q residue 33 VAL Chi-restraints excluded: chain Q residue 38 VAL Chi-restraints excluded: chain Q residue 99 VAL Chi-restraints excluded: chain Q residue 111 LYS Chi-restraints excluded: chain R residue 14 VAL Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 27 ILE Chi-restraints excluded: chain R residue 60 LYS Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 79 ARG Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain S residue 40 ASN Chi-restraints excluded: chain S residue 67 ASP Chi-restraints excluded: chain S residue 68 ASP Chi-restraints excluded: chain S residue 69 LEU Chi-restraints excluded: chain S residue 105 VAL Chi-restraints excluded: chain S residue 106 VAL Chi-restraints excluded: chain T residue 37 ASP Chi-restraints excluded: chain T residue 53 VAL Chi-restraints excluded: chain T residue 55 VAL Chi-restraints excluded: chain T residue 60 THR Chi-restraints excluded: chain T residue 85 VAL Chi-restraints excluded: chain U residue 33 VAL Chi-restraints excluded: chain U residue 35 VAL Chi-restraints excluded: chain U residue 48 VAL Chi-restraints excluded: chain U residue 53 GLN Chi-restraints excluded: chain U residue 69 VAL Chi-restraints excluded: chain U residue 86 PHE Chi-restraints excluded: chain U residue 98 ASN Chi-restraints excluded: chain U residue 101 THR Chi-restraints excluded: chain V residue 1 MET Chi-restraints excluded: chain V residue 8 VAL Chi-restraints excluded: chain V residue 10 LYS Chi-restraints excluded: chain V residue 45 ASP Chi-restraints excluded: chain V residue 64 VAL Chi-restraints excluded: chain V residue 77 VAL Chi-restraints excluded: chain V residue 83 LYS Chi-restraints excluded: chain V residue 89 ILE Chi-restraints excluded: chain V residue 91 PHE Chi-restraints excluded: chain W residue 8 ASN Chi-restraints excluded: chain W residue 17 LEU Chi-restraints excluded: chain W residue 32 ILE Chi-restraints excluded: chain W residue 34 VAL Chi-restraints excluded: chain W residue 46 ASN Chi-restraints excluded: chain W residue 49 CYS Chi-restraints excluded: chain W residue 77 SER Chi-restraints excluded: chain X residue 4 CYS Chi-restraints excluded: chain X residue 10 ARG Chi-restraints excluded: chain X residue 24 THR Chi-restraints excluded: chain X residue 47 THR Chi-restraints excluded: chain X residue 55 MET Chi-restraints excluded: chain X residue 64 ASP Chi-restraints excluded: chain X residue 67 LEU Chi-restraints excluded: chain Y residue 15 ASN Chi-restraints excluded: chain Y residue 16 THR Chi-restraints excluded: chain Y residue 31 GLN Chi-restraints excluded: chain Y residue 43 LEU Chi-restraints excluded: chain Y residue 46 VAL Chi-restraints excluded: chain Y residue 55 THR Chi-restraints excluded: chain Y residue 57 LEU Chi-restraints excluded: chain Z residue 2 LYS Chi-restraints excluded: chain Z residue 31 ILE Chi-restraints excluded: chain Z residue 34 THR Chi-restraints excluded: chain Z residue 37 ARG Chi-restraints excluded: chain Z residue 48 ASN Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 24 VAL Chi-restraints excluded: chain 0 residue 47 TYR Chi-restraints excluded: chain 1 residue 22 THR Chi-restraints excluded: chain 1 residue 47 ILE Chi-restraints excluded: chain 2 residue 9 VAL Chi-restraints excluded: chain 2 residue 44 VAL Chi-restraints excluded: chain 3 residue 5 THR Chi-restraints excluded: chain 3 residue 50 SER Chi-restraints excluded: chain 4 residue 10 LEU Chi-restraints excluded: chain 4 residue 16 ILE Chi-restraints excluded: chain 4 residue 25 VAL Chi-restraints excluded: chain 4 residue 37 GLN Chi-restraints excluded: chain 5 residue 34 THR Chi-restraints excluded: chain 5 residue 50 VAL Chi-restraints excluded: chain 5 residue 58 THR Chi-restraints excluded: chain 5 residue 77 VAL Chi-restraints excluded: chain 6 residue 27 THR Chi-restraints excluded: chain 6 residue 28 VAL Chi-restraints excluded: chain 6 residue 35 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1103 random chunks: chunk 1028 optimal weight: 5.9990 chunk 120 optimal weight: 10.0000 chunk 608 optimal weight: 10.0000 chunk 779 optimal weight: 10.0000 chunk 603 optimal weight: 20.0000 chunk 898 optimal weight: 10.0000 chunk 595 optimal weight: 10.0000 chunk 1063 optimal weight: 7.9990 chunk 665 optimal weight: 40.0000 chunk 648 optimal weight: 9.9990 chunk 490 optimal weight: 10.0000 overall best weight: 8.7994 ------------------------------------------------------------------------------- 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 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 60 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** e 96 GLN ** f 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 46 GLN ** k 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 18 GLN ** p 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 53 GLN ** g 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 36 GLN D 49 GLN E 156 ASN ** F 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 72 ASN ** G 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 2 GLN H 43 ASN ** J 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 104 GLN ** 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 ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 18 HIS ** 4 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.7962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.124 161499 Z= 0.351 Angle : 0.817 16.155 240779 Z= 0.430 Chirality : 0.042 0.381 30208 Planarity : 0.007 0.129 13518 Dihedral : 23.699 178.285 79696 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 21.99 Ramachandran Plot: Outliers : 0.78 % Allowed : 10.73 % Favored : 88.49 % Rotamer: Outliers : 9.57 % Allowed : 29.30 % Favored : 61.13 % Cbeta Deviations : 0.02 % 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: -0.24 (0.11), residues: 2116 sheet: -2.02 (0.14), residues: 1086 loop : -2.19 (0.10), residues: 3349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP c 21 HIS 0.017 0.002 HIS o 45 PHE 0.044 0.003 PHE 2 18 TYR 0.062 0.003 TYR b 212 ARG 0.013 0.001 ARG m 69 *********************** 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 2242 residues out of total 5475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 462 poor density : 1780 time to evaluate : 6.424 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: b 22 TRP cc_start: 0.8783 (p-90) cc_final: 0.8462 (p-90) REVERT: b 114 LYS cc_start: 0.9166 (ttmt) cc_final: 0.8352 (pptt) REVERT: b 135 MET cc_start: 0.8936 (mmm) cc_final: 0.8207 (ppp) REVERT: b 141 GLU cc_start: 0.7992 (mt-10) cc_final: 0.7553 (tp30) REVERT: d 61 ARG cc_start: 0.8303 (OUTLIER) cc_final: 0.8054 (ttp-110) REVERT: d 72 ARG cc_start: 0.8967 (tmm-80) cc_final: 0.8657 (ttm-80) REVERT: d 177 MET cc_start: 0.3365 (mmt) cc_final: 0.2436 (mmt) REVERT: e 18 ASN cc_start: 0.8393 (t0) cc_final: 0.8178 (p0) REVERT: e 68 ARG cc_start: 0.8629 (OUTLIER) cc_final: 0.8348 (ptm160) REVERT: f 11 HIS cc_start: 0.8308 (t70) cc_final: 0.7976 (t70) REVERT: f 12 PRO cc_start: 0.7921 (Cg_exo) cc_final: 0.7632 (Cg_endo) REVERT: f 21 MET cc_start: 0.8884 (ttm) cc_final: 0.8555 (ttm) REVERT: f 25 TYR cc_start: 0.7409 (m-10) cc_final: 0.7029 (m-10) REVERT: f 42 TRP cc_start: 0.6985 (m100) cc_final: 0.6149 (m100) REVERT: h 9 MET cc_start: 0.8998 (tpp) cc_final: 0.8741 (tpp) REVERT: h 106 SER cc_start: 0.8667 (m) cc_final: 0.8194 (p) REVERT: k 12 ARG cc_start: 0.4838 (ptp90) cc_final: 0.3901 (mtm110) REVERT: k 37 GLN cc_start: 0.8830 (mm110) cc_final: 0.8599 (mm-40) REVERT: k 68 ARG cc_start: 0.8185 (OUTLIER) cc_final: 0.7527 (tpt90) REVERT: l 34 THR cc_start: 0.8703 (m) cc_final: 0.8336 (p) REVERT: l 69 GLU cc_start: 0.8241 (mm-30) cc_final: 0.7640 (mp0) REVERT: p 13 LYS cc_start: 0.8662 (mttp) cc_final: 0.8277 (mtmt) REVERT: q 16 MET cc_start: 0.8304 (mmm) cc_final: 0.8038 (tpp) REVERT: q 17 GLU cc_start: 0.8455 (tm-30) cc_final: 0.8063 (tm-30) REVERT: q 29 LYS cc_start: 0.8297 (OUTLIER) cc_final: 0.7755 (ptmm) REVERT: q 62 GLU cc_start: 0.8810 (OUTLIER) cc_final: 0.8610 (tt0) REVERT: q 70 LYS cc_start: 0.9051 (OUTLIER) cc_final: 0.8647 (ttmt) REVERT: r 29 LYS cc_start: 0.8747 (ptpp) cc_final: 0.8383 (mtmm) REVERT: r 69 TYR cc_start: 0.8370 (m-80) cc_final: 0.8026 (m-10) REVERT: t 14 GLU cc_start: 0.8948 (pp20) cc_final: 0.8639 (tm-30) REVERT: u 28 LEU cc_start: 0.7471 (OUTLIER) cc_final: 0.7242 (mm) REVERT: u 35 GLU cc_start: 0.7454 (tp30) cc_final: 0.7239 (tp30) REVERT: c 22 PHE cc_start: 0.8594 (t80) cc_final: 0.8118 (t80) REVERT: c 120 THR cc_start: 0.8981 (OUTLIER) cc_final: 0.8763 (m) REVERT: c 141 MET cc_start: 0.8896 (mmm) cc_final: 0.8660 (mmm) REVERT: c 167 TYR cc_start: 0.8064 (m-10) cc_final: 0.7723 (m-10) REVERT: c 185 THR cc_start: 0.8828 (m) cc_final: 0.8604 (p) REVERT: g 6 ILE cc_start: 0.6508 (OUTLIER) cc_final: 0.6198 (pp) REVERT: g 17 PHE cc_start: 0.7461 (p90) cc_final: 0.7243 (p90) REVERT: g 46 LEU cc_start: 0.9473 (mp) cc_final: 0.9136 (pp) REVERT: i 27 ILE cc_start: 0.7657 (OUTLIER) cc_final: 0.7339 (mp) REVERT: i 36 GLN cc_start: 0.8650 (tm-30) cc_final: 0.8146 (tm-30) REVERT: j 15 HIS cc_start: 0.8759 (p90) cc_final: 0.8425 (t70) REVERT: m 54 THR cc_start: 0.8187 (p) cc_final: 0.7702 (p) REVERT: m 55 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8627 (tt) REVERT: m 58 GLU cc_start: 0.8412 (mt-10) cc_final: 0.8114 (mt-10) REVERT: m 74 MET cc_start: 0.9178 (mtt) cc_final: 0.8911 (mtp) REVERT: n 11 LYS cc_start: 0.9082 (ttpt) cc_final: 0.8788 (ttmm) REVERT: n 60 GLN cc_start: 0.8669 (mp10) cc_final: 0.8324 (mp10) REVERT: s 23 GLU cc_start: 0.7960 (mm-30) cc_final: 0.7499 (mm-30) REVERT: s 55 GLN cc_start: 0.8644 (pt0) cc_final: 0.8281 (pm20) REVERT: C 29 PHE cc_start: 0.8281 (t80) cc_final: 0.7906 (t80) REVERT: C 224 MET cc_start: 0.8570 (mtt) cc_final: 0.8361 (mtt) REVERT: D 80 TRP cc_start: 0.8588 (m-90) cc_final: 0.8291 (m-90) REVERT: E 24 ASN cc_start: 0.7883 (t0) cc_final: 0.7365 (t0) REVERT: E 25 GLU cc_start: 0.8405 (tt0) cc_final: 0.8163 (tp30) REVERT: E 47 LYS cc_start: 0.9148 (OUTLIER) cc_final: 0.8543 (ptpt) REVERT: E 69 ARG cc_start: 0.8760 (OUTLIER) cc_final: 0.8457 (mtt180) REVERT: E 116 ASP cc_start: 0.9176 (m-30) cc_final: 0.8452 (t70) REVERT: E 159 LEU cc_start: 0.8404 (pp) cc_final: 0.8203 (pp) REVERT: E 195 GLN cc_start: 0.8919 (mt0) cc_final: 0.8251 (mp10) REVERT: F 51 ASN cc_start: 0.8320 (m110) cc_final: 0.7690 (t0) REVERT: F 173 ASP cc_start: 0.8725 (m-30) cc_final: 0.8423 (t70) REVERT: G 105 SER cc_start: 0.9000 (m) cc_final: 0.8705 (p) REVERT: G 127 GLN cc_start: 0.8506 (mm-40) cc_final: 0.8230 (mm-40) REVERT: G 172 GLU cc_start: 0.8470 (tp30) cc_final: 0.8200 (tm-30) REVERT: H 1 MET cc_start: 0.8233 (mmt) cc_final: 0.7746 (ttt) REVERT: H 43 ASN cc_start: 0.8432 (m110) cc_final: 0.7964 (t0) REVERT: H 45 GLU cc_start: 0.8518 (tm-30) cc_final: 0.7827 (pt0) REVERT: H 60 GLU cc_start: 0.7747 (pt0) cc_final: 0.7218 (mm-30) REVERT: H 129 GLU cc_start: 0.6781 (tt0) cc_final: 0.6321 (tm-30) REVERT: I 99 LYS cc_start: 0.6129 (ttpt) cc_final: 0.5696 (mmtt) REVERT: J 58 ASN cc_start: 0.7992 (m-40) cc_final: 0.7751 (m-40) REVERT: J 98 GLU cc_start: 0.8779 (mp0) cc_final: 0.8360 (tm-30) REVERT: K 111 LYS cc_start: 0.8779 (ptmt) cc_final: 0.7896 (tptt) REVERT: K 114 LYS cc_start: 0.9150 (OUTLIER) cc_final: 0.8869 (mttt) REVERT: L 91 ASP cc_start: 0.8324 (t0) cc_final: 0.7986 (m-30) REVERT: M 53 MET cc_start: 0.9333 (tmm) cc_final: 0.8937 (tmm) REVERT: M 82 MET cc_start: 0.8601 (mtp) cc_final: 0.8144 (ttm) REVERT: N 5 LYS cc_start: 0.9336 (mtmm) cc_final: 0.8987 (mtmm) REVERT: N 72 ASP cc_start: 0.8926 (t0) cc_final: 0.8292 (t0) REVERT: N 75 ILE cc_start: 0.9269 (mm) cc_final: 0.8909 (mm) REVERT: N 97 ILE cc_start: 0.9274 (OUTLIER) cc_final: 0.8944 (mm) REVERT: N 107 ASN cc_start: 0.7997 (t0) cc_final: 0.7730 (t0) REVERT: N 110 MET cc_start: 0.8788 (mmp) cc_final: 0.8190 (mmp) REVERT: O 80 GLU cc_start: 0.8083 (pp20) cc_final: 0.7481 (pp20) REVERT: O 115 LEU cc_start: 0.7896 (mm) cc_final: 0.7365 (mm) REVERT: P 99 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8550 (tt) REVERT: P 110 LYS cc_start: 0.8606 (mmmt) cc_final: 0.8208 (mtmt) REVERT: Q 111 LYS cc_start: 0.9270 (OUTLIER) cc_final: 0.8872 (tppp) REVERT: R 60 LYS cc_start: 0.8929 (OUTLIER) cc_final: 0.8485 (ptpp) REVERT: R 78 ARG cc_start: 0.9277 (tpp80) cc_final: 0.8627 (tpp80) REVERT: S 57 ASN cc_start: 0.8966 (t0) cc_final: 0.8730 (t0) REVERT: S 67 ASP cc_start: 0.8347 (OUTLIER) cc_final: 0.8020 (t0) REVERT: S 86 MET cc_start: 0.9037 (tpt) cc_final: 0.8669 (ttp) REVERT: T 1 MET cc_start: 0.1048 (OUTLIER) cc_final: 0.0507 (tpp) REVERT: T 24 MET cc_start: 0.8889 (tpt) cc_final: 0.8549 (tmm) REVERT: T 37 ASP cc_start: 0.8667 (OUTLIER) cc_final: 0.8071 (t0) REVERT: T 77 ARG cc_start: 0.7895 (OUTLIER) cc_final: 0.7003 (mpp80) REVERT: U 71 ILE cc_start: 0.8370 (pt) cc_final: 0.8156 (mt) REVERT: V 5 ASN cc_start: 0.9103 (m-40) cc_final: 0.8189 (p0) REVERT: V 10 LYS cc_start: 0.7454 (OUTLIER) cc_final: 0.7153 (tptt) REVERT: V 19 ARG cc_start: 0.8322 (mtm-85) cc_final: 0.7957 (ttm110) REVERT: W 21 ARG cc_start: 0.8887 (mmm-85) cc_final: 0.8511 (mmm160) REVERT: W 73 ARG cc_start: 0.8795 (mtm110) cc_final: 0.8185 (mtp-110) REVERT: X 43 LYS cc_start: 0.8567 (tppt) cc_final: 0.8118 (ptpt) REVERT: Y 1 MET cc_start: 0.7942 (tpp) cc_final: 0.7568 (tpp) REVERT: Y 25 GLN cc_start: 0.8922 (mm-40) cc_final: 0.8513 (mm-40) REVERT: Z 4 ILE cc_start: 0.9160 (OUTLIER) cc_final: 0.8924 (tp) REVERT: Z 20 LYS cc_start: 0.9308 (OUTLIER) cc_final: 0.9072 (mtmm) REVERT: Z 48 ASN cc_start: 0.8957 (OUTLIER) cc_final: 0.8642 (m-40) REVERT: 0 47 TYR cc_start: 0.8714 (OUTLIER) cc_final: 0.7927 (m-10) REVERT: 2 6 GLN cc_start: 0.8340 (tm-30) cc_final: 0.8073 (tm-30) REVERT: 4 18 LYS cc_start: 0.8770 (ptmm) cc_final: 0.8519 (ttmm) REVERT: 5 62 ARG cc_start: 0.6744 (ttm170) cc_final: 0.6204 (mtm110) REVERT: 5 86 MET cc_start: 0.2986 (mmm) cc_final: 0.2762 (mmm) REVERT: 5 122 GLN cc_start: 0.6017 (pm20) cc_final: 0.5775 (mm-40) outliers start: 462 outliers final: 347 residues processed: 1991 average time/residue: 1.3263 time to fit residues: 4644.0955 Evaluate side-chains 2061 residues out of total 5475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 374 poor density : 1687 time to evaluate : 5.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 19 THR Chi-restraints excluded: chain b residue 21 TYR Chi-restraints excluded: chain b residue 46 VAL Chi-restraints excluded: chain b residue 71 THR Chi-restraints excluded: chain b residue 81 ASP Chi-restraints excluded: chain b residue 104 LYS Chi-restraints excluded: chain b residue 116 LEU Chi-restraints excluded: chain b residue 129 THR Chi-restraints excluded: chain b residue 152 ASP Chi-restraints excluded: chain b residue 167 HIS Chi-restraints excluded: chain b residue 178 LEU Chi-restraints excluded: chain b residue 185 ILE Chi-restraints excluded: chain b residue 211 LEU Chi-restraints excluded: chain d residue 28 ASP Chi-restraints excluded: chain d residue 40 HIS Chi-restraints excluded: chain d residue 61 ARG Chi-restraints excluded: chain d residue 101 VAL Chi-restraints excluded: chain d residue 116 LEU Chi-restraints excluded: chain d residue 136 VAL Chi-restraints excluded: chain d residue 189 ASP Chi-restraints excluded: chain d residue 197 HIS Chi-restraints excluded: chain e residue 33 THR Chi-restraints excluded: chain e residue 45 VAL Chi-restraints excluded: chain e residue 68 ARG Chi-restraints excluded: chain e residue 73 VAL Chi-restraints excluded: chain e residue 89 THR Chi-restraints excluded: chain e residue 121 ASN Chi-restraints excluded: chain e residue 130 THR Chi-restraints excluded: chain e residue 131 ASN Chi-restraints excluded: chain e residue 146 MET Chi-restraints excluded: chain e residue 147 ASN Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 18 VAL Chi-restraints excluded: chain f residue 44 ARG Chi-restraints excluded: chain f residue 61 LEU Chi-restraints excluded: chain f residue 89 VAL Chi-restraints excluded: chain h residue 10 LEU Chi-restraints excluded: chain h residue 11 THR Chi-restraints excluded: chain h residue 25 THR Chi-restraints excluded: chain h residue 47 ASP Chi-restraints excluded: chain h residue 53 ASP Chi-restraints excluded: chain h residue 73 SER Chi-restraints excluded: chain h residue 74 ILE Chi-restraints excluded: chain h residue 91 LEU Chi-restraints excluded: chain h residue 100 ILE Chi-restraints excluded: chain h residue 103 VAL Chi-restraints excluded: chain h residue 109 VAL Chi-restraints excluded: chain h residue 111 THR Chi-restraints excluded: chain h residue 128 VAL Chi-restraints excluded: chain k residue 30 ILE Chi-restraints excluded: chain k residue 34 THR Chi-restraints excluded: chain k residue 45 THR Chi-restraints excluded: chain k residue 58 THR Chi-restraints excluded: chain k residue 68 ARG Chi-restraints excluded: chain k residue 81 LEU Chi-restraints excluded: chain k residue 95 THR Chi-restraints excluded: chain k residue 109 ILE Chi-restraints excluded: chain k residue 115 ILE Chi-restraints excluded: chain l residue 3 VAL Chi-restraints excluded: chain l residue 6 LEU Chi-restraints excluded: chain l residue 7 VAL Chi-restraints excluded: chain l residue 26 CYS Chi-restraints excluded: chain l residue 82 ARG Chi-restraints excluded: chain l residue 96 THR Chi-restraints excluded: chain l residue 97 VAL Chi-restraints excluded: chain o residue 4 THR Chi-restraints excluded: chain o residue 7 THR Chi-restraints excluded: chain o residue 51 SER Chi-restraints excluded: chain o residue 66 LEU Chi-restraints excluded: chain o residue 73 ASP Chi-restraints excluded: chain p residue 3 THR Chi-restraints excluded: chain p residue 18 GLN Chi-restraints excluded: chain p residue 19 VAL Chi-restraints excluded: chain p residue 23 ASP Chi-restraints excluded: chain p residue 54 LEU Chi-restraints excluded: chain q residue 6 THR Chi-restraints excluded: chain q residue 29 LYS Chi-restraints excluded: chain q residue 32 ILE Chi-restraints excluded: chain q residue 54 ILE Chi-restraints excluded: chain q residue 56 ASP Chi-restraints excluded: chain q residue 62 GLU Chi-restraints excluded: chain q residue 70 LYS Chi-restraints excluded: chain r residue 27 THR Chi-restraints excluded: chain t residue 19 HIS Chi-restraints excluded: chain t residue 65 LEU Chi-restraints excluded: chain t residue 78 LEU Chi-restraints excluded: chain u residue 28 LEU Chi-restraints excluded: chain w residue 508 SER Chi-restraints excluded: chain c residue 14 VAL Chi-restraints excluded: chain c residue 55 VAL Chi-restraints excluded: chain c residue 78 LYS Chi-restraints excluded: chain c residue 102 ILE Chi-restraints excluded: chain c residue 105 VAL Chi-restraints excluded: chain c residue 120 THR Chi-restraints excluded: chain c residue 149 LYS Chi-restraints excluded: chain c residue 183 TYR Chi-restraints excluded: chain c residue 198 LYS Chi-restraints excluded: chain c residue 206 ILE Chi-restraints excluded: chain g residue 6 ILE Chi-restraints excluded: chain g residue 11 ILE Chi-restraints excluded: chain g residue 16 LYS Chi-restraints excluded: chain g residue 21 LEU Chi-restraints excluded: chain g residue 135 LYS Chi-restraints excluded: chain i residue 18 VAL Chi-restraints excluded: chain i residue 27 ILE Chi-restraints excluded: chain i residue 54 VAL Chi-restraints excluded: chain i residue 56 MET Chi-restraints excluded: chain i residue 60 LEU Chi-restraints excluded: chain i residue 62 LEU Chi-restraints excluded: chain i residue 66 VAL Chi-restraints excluded: chain i residue 71 ILE Chi-restraints excluded: chain i residue 86 LEU Chi-restraints excluded: chain i residue 97 LEU Chi-restraints excluded: chain i residue 110 VAL Chi-restraints excluded: chain i residue 115 VAL Chi-restraints excluded: chain j residue 8 ILE Chi-restraints excluded: chain j residue 44 THR Chi-restraints excluded: chain j residue 50 THR Chi-restraints excluded: chain j residue 51 VAL Chi-restraints excluded: chain j residue 80 THR Chi-restraints excluded: chain j residue 88 MET Chi-restraints excluded: chain m residue 3 ILE Chi-restraints excluded: chain m residue 21 ILE Chi-restraints excluded: chain m residue 24 VAL Chi-restraints excluded: chain m residue 32 ILE Chi-restraints excluded: chain m residue 33 LEU Chi-restraints excluded: chain m residue 41 ASP Chi-restraints excluded: chain m residue 44 ILE Chi-restraints excluded: chain m residue 55 LEU Chi-restraints excluded: chain m residue 82 LEU Chi-restraints excluded: chain m residue 84 CYS Chi-restraints excluded: chain m residue 103 THR Chi-restraints excluded: chain n residue 30 ILE Chi-restraints excluded: chain n residue 33 VAL Chi-restraints excluded: chain n residue 56 SER Chi-restraints excluded: chain n residue 64 CYS Chi-restraints excluded: chain n residue 67 THR Chi-restraints excluded: chain s residue 5 LYS Chi-restraints excluded: chain s residue 10 ILE Chi-restraints excluded: chain s residue 39 ILE Chi-restraints excluded: chain s residue 70 LEU Chi-restraints excluded: chain C residue 44 ASN Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 85 ASN Chi-restraints excluded: chain C residue 90 ILE Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 110 LYS Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 179 GLU Chi-restraints excluded: chain C residue 200 MET Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 106 LYS Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 171 THR Chi-restraints excluded: chain D residue 180 VAL Chi-restraints excluded: chain D residue 184 ARG Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 19 PHE Chi-restraints excluded: chain E residue 47 LYS Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 69 ARG Chi-restraints excluded: chain E residue 73 ILE Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain F residue 5 ASP Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 15 LEU Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 127 TYR Chi-restraints excluded: chain F residue 145 VAL Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain F residue 155 ILE Chi-restraints excluded: chain F residue 156 THR Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain G residue 1 SER Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 14 VAL Chi-restraints excluded: chain G residue 15 ASP Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 18 ILE Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 37 ASN Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain G residue 73 SER Chi-restraints excluded: chain G residue 88 LEU Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain G residue 161 VAL Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 44 ILE Chi-restraints excluded: chain H residue 90 LEU Chi-restraints excluded: chain H residue 98 ASP Chi-restraints excluded: chain H residue 127 GLU Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 147 VAL Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 59 THR Chi-restraints excluded: chain I residue 77 VAL Chi-restraints excluded: chain I residue 95 ASP Chi-restraints excluded: chain I residue 127 SER Chi-restraints excluded: chain I residue 134 SER Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 56 VAL Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain J residue 64 VAL Chi-restraints excluded: chain J residue 67 ASN Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 81 ILE Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain J residue 142 ILE Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 12 ASP Chi-restraints excluded: chain K residue 28 SER Chi-restraints excluded: chain K residue 37 ASP Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 82 ASN Chi-restraints excluded: chain K residue 90 ASN Chi-restraints excluded: chain K residue 114 LYS Chi-restraints excluded: chain K residue 116 ILE Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 54 GLN Chi-restraints excluded: chain L residue 93 ASN Chi-restraints excluded: chain L residue 100 ILE Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 122 VAL Chi-restraints excluded: chain L residue 123 ARG Chi-restraints excluded: chain L residue 128 THR Chi-restraints excluded: chain M residue 26 VAL Chi-restraints excluded: chain M residue 42 THR Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 93 VAL Chi-restraints excluded: chain M residue 108 VAL Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 11 ASN Chi-restraints excluded: chain N residue 13 ASN Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 89 SER Chi-restraints excluded: chain N residue 97 ILE Chi-restraints excluded: chain N residue 106 ASP Chi-restraints excluded: chain N residue 115 LEU Chi-restraints excluded: chain O residue 12 THR Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 62 LEU Chi-restraints excluded: chain O residue 95 SER Chi-restraints excluded: chain P residue 16 VAL Chi-restraints excluded: chain P residue 23 ASP Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 59 THR Chi-restraints excluded: chain P residue 63 ILE Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain P residue 101 GLU Chi-restraints excluded: chain Q residue 7 VAL Chi-restraints excluded: chain Q residue 16 ILE Chi-restraints excluded: chain Q residue 17 LEU Chi-restraints excluded: chain Q residue 28 SER Chi-restraints excluded: chain Q residue 33 VAL Chi-restraints excluded: chain Q residue 38 VAL Chi-restraints excluded: chain Q residue 39 ILE Chi-restraints excluded: chain Q residue 87 VAL Chi-restraints excluded: chain Q residue 111 LYS Chi-restraints excluded: chain R residue 14 VAL Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 27 ILE Chi-restraints excluded: chain R residue 55 ASP Chi-restraints excluded: chain R residue 60 LYS Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 79 ARG Chi-restraints excluded: chain R residue 85 LYS Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain S residue 11 ARG Chi-restraints excluded: chain S residue 19 LEU Chi-restraints excluded: chain S residue 40 ASN Chi-restraints excluded: chain S residue 67 ASP Chi-restraints excluded: chain S residue 68 ASP Chi-restraints excluded: chain S residue 69 LEU Chi-restraints excluded: chain S residue 105 VAL Chi-restraints excluded: chain S residue 106 VAL Chi-restraints excluded: chain T residue 1 MET Chi-restraints excluded: chain T residue 37 ASP Chi-restraints excluded: chain T residue 53 VAL Chi-restraints excluded: chain T residue 55 VAL Chi-restraints excluded: chain T residue 60 THR Chi-restraints excluded: chain T residue 77 ARG Chi-restraints excluded: chain T residue 85 VAL Chi-restraints excluded: chain U residue 33 VAL Chi-restraints excluded: chain U residue 35 VAL Chi-restraints excluded: chain U residue 48 VAL Chi-restraints excluded: chain U residue 53 GLN Chi-restraints excluded: chain U residue 69 VAL Chi-restraints excluded: chain U residue 86 PHE Chi-restraints excluded: chain U residue 98 ASN Chi-restraints excluded: chain V residue 1 MET Chi-restraints excluded: chain V residue 8 VAL Chi-restraints excluded: chain V residue 10 LYS Chi-restraints excluded: chain V residue 45 ASP Chi-restraints excluded: chain V residue 64 VAL Chi-restraints excluded: chain V residue 77 VAL Chi-restraints excluded: chain V residue 83 LYS Chi-restraints excluded: chain V residue 89 ILE Chi-restraints excluded: chain V residue 91 PHE Chi-restraints excluded: chain W residue 8 ASN Chi-restraints excluded: chain W residue 17 LEU Chi-restraints excluded: chain W residue 32 ILE Chi-restraints excluded: chain W residue 49 CYS Chi-restraints excluded: chain W residue 76 ILE Chi-restraints excluded: chain W residue 77 SER Chi-restraints excluded: chain X residue 4 CYS Chi-restraints excluded: chain X residue 10 ARG Chi-restraints excluded: chain X residue 24 THR Chi-restraints excluded: chain X residue 47 THR Chi-restraints excluded: chain X residue 55 MET Chi-restraints excluded: chain X residue 67 LEU Chi-restraints excluded: chain Y residue 15 ASN Chi-restraints excluded: chain Y residue 16 THR Chi-restraints excluded: chain Y residue 19 LEU Chi-restraints excluded: chain Y residue 31 GLN Chi-restraints excluded: chain Y residue 43 LEU Chi-restraints excluded: chain Y residue 46 VAL Chi-restraints excluded: chain Y residue 55 THR Chi-restraints excluded: chain Y residue 57 LEU Chi-restraints excluded: chain Z residue 2 LYS Chi-restraints excluded: chain Z residue 4 ILE Chi-restraints excluded: chain Z residue 20 LYS Chi-restraints excluded: chain Z residue 31 ILE Chi-restraints excluded: chain Z residue 34 THR Chi-restraints excluded: chain Z residue 37 ARG Chi-restraints excluded: chain Z residue 48 ASN Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 24 VAL Chi-restraints excluded: chain 0 residue 47 TYR Chi-restraints excluded: chain 1 residue 22 THR Chi-restraints excluded: chain 1 residue 44 GLN Chi-restraints excluded: chain 1 residue 47 ILE Chi-restraints excluded: chain 2 residue 9 VAL Chi-restraints excluded: chain 2 residue 10 LEU Chi-restraints excluded: chain 3 residue 50 SER Chi-restraints excluded: chain 3 residue 61 LEU Chi-restraints excluded: chain 4 residue 10 LEU Chi-restraints excluded: chain 4 residue 16 ILE Chi-restraints excluded: chain 4 residue 37 GLN Chi-restraints excluded: chain 5 residue 34 THR Chi-restraints excluded: chain 5 residue 50 VAL Chi-restraints excluded: chain 5 residue 58 THR Chi-restraints excluded: chain 5 residue 77 VAL Chi-restraints excluded: chain 6 residue 27 THR Chi-restraints excluded: chain 6 residue 28 VAL Chi-restraints excluded: chain 6 residue 35 ASP 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: 5.9990 chunk 634 optimal weight: 10.0000 chunk 320 optimal weight: 50.0000 chunk 208 optimal weight: 7.9990 chunk 205 optimal weight: 10.0000 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: 8.1994 ------------------------------------------------------------------------------- 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 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 60 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** e 134 ASN ** f 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 17 GLN f 46 GLN ** h 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 14 GLN ** k 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 63 GLN r 53 GLN ** c 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 101 ASN ** g 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 4 GLN ** i 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 125 GLN ** j 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 66 GLN ** C 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 67 HIS ** E 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 104 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 ** Q 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 18 GLN ** 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 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.8338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 161499 Z= 0.331 Angle : 0.807 16.155 240779 Z= 0.426 Chirality : 0.042 0.364 30208 Planarity : 0.007 0.128 13518 Dihedral : 23.711 178.211 79695 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 22.06 Ramachandran Plot: Outliers : 0.72 % Allowed : 10.40 % Favored : 88.89 % Rotamer: Outliers : 8.80 % Allowed : 31.27 % Favored : 59.93 % 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: -0.18 (0.11), residues: 2113 sheet: -2.03 (0.14), residues: 1110 loop : -2.23 (0.10), residues: 3328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP g 102 HIS 0.015 0.002 HIS q 46 PHE 0.052 0.003 PHE F 98 TYR 0.052 0.003 TYR b 212 ARG 0.013 0.001 ARG h 116 *********************** 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 2182 residues out of total 5475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 425 poor density : 1757 time to evaluate : 6.423 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: b 17 HIS cc_start: 0.3878 (OUTLIER) cc_final: 0.3415 (m170) REVERT: b 22 TRP cc_start: 0.8857 (p-90) cc_final: 0.8527 (p-90) REVERT: b 114 LYS cc_start: 0.9241 (ttmt) cc_final: 0.8449 (pptt) REVERT: b 141 GLU cc_start: 0.7836 (mt-10) cc_final: 0.7537 (tp30) REVERT: d 3 TYR cc_start: 0.8198 (t80) cc_final: 0.7910 (t80) REVERT: d 72 ARG cc_start: 0.8984 (tmm-80) cc_final: 0.8711 (ttm-80) REVERT: d 87 GLU cc_start: 0.7587 (pm20) cc_final: 0.7346 (pm20) REVERT: d 116 LEU cc_start: 0.7844 (OUTLIER) cc_final: 0.7566 (tt) REVERT: d 119 HIS cc_start: 0.5896 (p-80) cc_final: 0.5614 (p-80) REVERT: d 177 MET cc_start: 0.3753 (mmt) cc_final: 0.2845 (mmt) REVERT: f 4 TYR cc_start: 0.9280 (m-80) cc_final: 0.9070 (m-10) REVERT: f 11 HIS cc_start: 0.8332 (t70) cc_final: 0.7932 (t70) REVERT: f 12 PRO cc_start: 0.7859 (Cg_exo) cc_final: 0.7560 (Cg_endo) REVERT: f 21 MET cc_start: 0.8821 (ttm) cc_final: 0.8377 (ttm) REVERT: f 25 TYR cc_start: 0.7450 (m-10) cc_final: 0.7012 (m-10) REVERT: f 42 TRP cc_start: 0.7454 (m100) cc_final: 0.7222 (m100) REVERT: f 44 ARG cc_start: 0.7473 (ptp-170) cc_final: 0.7137 (mtm180) REVERT: f 70 VAL cc_start: 0.8249 (m) cc_final: 0.7922 (p) REVERT: h 32 LYS cc_start: 0.8711 (OUTLIER) cc_final: 0.8298 (mmmt) REVERT: h 106 SER cc_start: 0.8597 (m) cc_final: 0.8097 (p) REVERT: k 12 ARG cc_start: 0.5167 (OUTLIER) cc_final: 0.4050 (mtm110) REVERT: k 13 LYS cc_start: 0.7348 (tppt) cc_final: 0.6896 (mppt) REVERT: l 34 THR cc_start: 0.8842 (m) cc_final: 0.8534 (p) REVERT: l 114 SER cc_start: 0.9442 (t) cc_final: 0.9204 (p) REVERT: l 120 ARG cc_start: 0.7619 (OUTLIER) cc_final: 0.6866 (tpp80) REVERT: p 13 LYS cc_start: 0.8904 (mttp) cc_final: 0.8616 (mtmt) REVERT: q 17 GLU cc_start: 0.8474 (tm-30) cc_final: 0.8074 (tm-30) REVERT: q 29 LYS cc_start: 0.8256 (OUTLIER) cc_final: 0.7749 (ptmm) REVERT: q 70 LYS cc_start: 0.9016 (OUTLIER) cc_final: 0.8516 (ttmt) REVERT: c 22 PHE cc_start: 0.8684 (t80) cc_final: 0.8248 (t80) REVERT: c 120 THR cc_start: 0.9020 (OUTLIER) cc_final: 0.8790 (m) REVERT: c 167 TYR cc_start: 0.8023 (m-10) cc_final: 0.7823 (m-80) REVERT: c 185 THR cc_start: 0.8796 (m) cc_final: 0.8583 (p) REVERT: g 6 ILE cc_start: 0.6541 (OUTLIER) cc_final: 0.6223 (pp) REVERT: g 46 LEU cc_start: 0.9493 (mp) cc_final: 0.9115 (pp) REVERT: i 27 ILE cc_start: 0.7647 (OUTLIER) cc_final: 0.7329 (mp) REVERT: i 36 GLN cc_start: 0.8631 (tm-30) cc_final: 0.8154 (tm-30) REVERT: m 12 LYS cc_start: 0.8935 (mmtt) cc_final: 0.8550 (mmmt) REVERT: m 54 THR cc_start: 0.8104 (p) cc_final: 0.7721 (p) REVERT: m 55 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8609 (tt) REVERT: m 58 GLU cc_start: 0.8422 (mt-10) cc_final: 0.8115 (mt-10) REVERT: m 74 MET cc_start: 0.9190 (mtt) cc_final: 0.8921 (mtp) REVERT: n 11 LYS cc_start: 0.9062 (ttpt) cc_final: 0.8781 (ttmm) REVERT: n 60 GLN cc_start: 0.8650 (mp10) cc_final: 0.8337 (mp10) REVERT: s 19 GLU cc_start: 0.8441 (tp30) cc_final: 0.8016 (pt0) REVERT: s 39 ILE cc_start: 0.8640 (OUTLIER) cc_final: 0.8236 (pt) REVERT: s 55 GLN cc_start: 0.8650 (pt0) cc_final: 0.8273 (pm20) REVERT: C 29 PHE cc_start: 0.8324 (t80) cc_final: 0.7961 (t80) REVERT: C 184 GLU cc_start: 0.8584 (tm-30) cc_final: 0.8044 (tm-30) REVERT: D 28 GLU cc_start: 0.8831 (pp20) cc_final: 0.8463 (pp20) REVERT: D 30 GLU cc_start: 0.9051 (mm-30) cc_final: 0.8677 (mm-30) REVERT: E 24 ASN cc_start: 0.7878 (t0) cc_final: 0.7361 (t0) REVERT: E 25 GLU cc_start: 0.8350 (tt0) cc_final: 0.8121 (tp30) REVERT: E 69 ARG cc_start: 0.8753 (OUTLIER) cc_final: 0.8352 (mtt180) REVERT: E 116 ASP cc_start: 0.9139 (m-30) cc_final: 0.8485 (t70) REVERT: F 51 ASN cc_start: 0.8379 (m110) cc_final: 0.7660 (t0) REVERT: F 173 ASP cc_start: 0.8705 (m-30) cc_final: 0.8433 (t0) REVERT: G 23 ILE cc_start: 0.8830 (tp) cc_final: 0.8501 (tp) REVERT: G 74 MET cc_start: 0.8355 (ttt) cc_final: 0.7699 (tpp) REVERT: G 105 SER cc_start: 0.9061 (m) cc_final: 0.8855 (p) REVERT: G 127 GLN cc_start: 0.8498 (mm-40) cc_final: 0.8261 (mm-40) REVERT: G 172 GLU cc_start: 0.8512 (tp30) cc_final: 0.8115 (tm-30) REVERT: H 1 MET cc_start: 0.8197 (mmt) cc_final: 0.7753 (ttt) REVERT: H 43 ASN cc_start: 0.8481 (m110) cc_final: 0.8269 (m-40) REVERT: H 45 GLU cc_start: 0.8463 (tm-30) cc_final: 0.7773 (pt0) REVERT: H 60 GLU cc_start: 0.7679 (pt0) cc_final: 0.7251 (mm-30) REVERT: H 129 GLU cc_start: 0.6747 (tt0) cc_final: 0.6295 (tm-30) REVERT: I 134 SER cc_start: 0.7184 (OUTLIER) cc_final: 0.6705 (p) REVERT: J 98 GLU cc_start: 0.8784 (mp0) cc_final: 0.8368 (tm-30) REVERT: K 111 LYS cc_start: 0.8740 (ptmt) cc_final: 0.7835 (tptt) REVERT: K 114 LYS cc_start: 0.9093 (OUTLIER) cc_final: 0.8852 (mttt) REVERT: L 91 ASP cc_start: 0.8470 (t0) cc_final: 0.7983 (m-30) REVERT: M 53 MET cc_start: 0.9267 (tmm) cc_final: 0.8853 (tmm) REVERT: M 82 MET cc_start: 0.8400 (mtp) cc_final: 0.7936 (ttm) REVERT: N 5 LYS cc_start: 0.9380 (mtmm) cc_final: 0.9062 (mtmm) REVERT: N 72 ASP cc_start: 0.8813 (t0) cc_final: 0.8267 (t0) REVERT: N 75 ILE cc_start: 0.9257 (mm) cc_final: 0.8893 (mm) REVERT: N 78 LYS cc_start: 0.9245 (tppp) cc_final: 0.9037 (tppp) REVERT: N 107 ASN cc_start: 0.8031 (t0) cc_final: 0.7755 (t0) REVERT: N 110 MET cc_start: 0.8849 (mmp) cc_final: 0.8627 (mmm) REVERT: O 56 LYS cc_start: 0.8319 (pttp) cc_final: 0.7759 (mppt) REVERT: O 115 LEU cc_start: 0.7834 (mm) cc_final: 0.7374 (mm) REVERT: P 6 GLN cc_start: 0.7740 (tm-30) cc_final: 0.7250 (pp30) REVERT: P 99 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8505 (tt) REVERT: P 110 LYS cc_start: 0.8577 (mmmt) cc_final: 0.8222 (mtmt) REVERT: Q 75 TYR cc_start: 0.8824 (t80) cc_final: 0.8420 (t80) REVERT: R 60 LYS cc_start: 0.8878 (OUTLIER) cc_final: 0.8508 (ptpp) REVERT: R 78 ARG cc_start: 0.9251 (tpp80) cc_final: 0.8997 (tpp80) REVERT: S 57 ASN cc_start: 0.8908 (t0) cc_final: 0.8694 (t0) REVERT: S 86 MET cc_start: 0.9045 (tpt) cc_final: 0.8672 (ttp) REVERT: T 1 MET cc_start: 0.1067 (ptm) cc_final: 0.0465 (tpt) REVERT: T 24 MET cc_start: 0.8880 (tpt) cc_final: 0.8541 (tmm) REVERT: T 37 ASP cc_start: 0.8687 (OUTLIER) cc_final: 0.8088 (t0) REVERT: T 87 LEU cc_start: 0.8729 (mt) cc_final: 0.8484 (mp) REVERT: V 5 ASN cc_start: 0.9109 (m-40) cc_final: 0.8207 (p0) REVERT: V 10 LYS cc_start: 0.7413 (OUTLIER) cc_final: 0.7036 (tptt) REVERT: W 73 ARG cc_start: 0.8813 (mtm110) cc_final: 0.8254 (mtp-110) REVERT: X 43 LYS cc_start: 0.8611 (tppt) cc_final: 0.8125 (ptpt) REVERT: Y 25 GLN cc_start: 0.8925 (mm-40) cc_final: 0.8685 (mm-40) REVERT: Y 31 GLN cc_start: 0.8780 (OUTLIER) cc_final: 0.8548 (mm-40) REVERT: Y 36 GLN cc_start: 0.8120 (mm-40) cc_final: 0.7809 (mp10) REVERT: Y 44 LYS cc_start: 0.8903 (tttm) cc_final: 0.8674 (mtpt) REVERT: Z 4 ILE cc_start: 0.9126 (OUTLIER) cc_final: 0.8922 (tp) REVERT: Z 20 LYS cc_start: 0.9192 (mtmm) cc_final: 0.8823 (mtmm) REVERT: Z 48 ASN cc_start: 0.8903 (OUTLIER) cc_final: 0.8547 (m-40) REVERT: 2 6 GLN cc_start: 0.8332 (tm-30) cc_final: 0.8058 (tm-30) REVERT: 5 62 ARG cc_start: 0.6688 (ttm170) cc_final: 0.6172 (mtm110) REVERT: 5 86 MET cc_start: 0.2970 (mmm) cc_final: 0.2736 (mmm) REVERT: 5 122 GLN cc_start: 0.6030 (pm20) cc_final: 0.5726 (mm-40) outliers start: 425 outliers final: 331 residues processed: 1966 average time/residue: 1.3643 time to fit residues: 4735.3394 Evaluate side-chains 2043 residues out of total 5475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 353 poor density : 1690 time to evaluate : 6.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 9 LEU Chi-restraints excluded: chain b residue 17 HIS Chi-restraints excluded: chain b residue 19 THR Chi-restraints excluded: chain b residue 21 TYR Chi-restraints excluded: chain b residue 46 VAL Chi-restraints excluded: chain b residue 71 THR Chi-restraints excluded: chain b residue 81 ASP Chi-restraints excluded: chain b residue 116 LEU Chi-restraints excluded: chain b residue 129 THR Chi-restraints excluded: chain b residue 152 ASP Chi-restraints excluded: chain b residue 167 HIS Chi-restraints excluded: chain b residue 178 LEU Chi-restraints excluded: chain b residue 185 ILE Chi-restraints excluded: chain b residue 198 VAL Chi-restraints excluded: chain b residue 211 LEU Chi-restraints excluded: chain d residue 28 ASP Chi-restraints excluded: chain d residue 40 HIS Chi-restraints excluded: chain d residue 101 VAL Chi-restraints excluded: chain d residue 110 ARG Chi-restraints excluded: chain d residue 116 LEU Chi-restraints excluded: chain d residue 189 ASP Chi-restraints excluded: chain d residue 194 ILE Chi-restraints excluded: chain d residue 197 HIS Chi-restraints excluded: chain e residue 20 VAL Chi-restraints excluded: chain e residue 33 THR Chi-restraints excluded: chain e residue 45 VAL Chi-restraints excluded: chain e residue 65 LYS Chi-restraints excluded: chain e residue 73 VAL Chi-restraints excluded: chain e residue 84 VAL Chi-restraints excluded: chain e residue 89 THR Chi-restraints excluded: chain e residue 121 ASN Chi-restraints excluded: chain e residue 131 ASN Chi-restraints excluded: chain e residue 147 ASN Chi-restraints excluded: chain f residue 18 VAL Chi-restraints excluded: chain f residue 85 ILE Chi-restraints excluded: chain f residue 89 VAL Chi-restraints excluded: chain h residue 11 THR Chi-restraints excluded: chain h residue 32 LYS Chi-restraints excluded: chain h residue 47 ASP Chi-restraints excluded: chain h residue 53 ASP Chi-restraints excluded: chain h residue 73 SER Chi-restraints excluded: chain h residue 74 ILE Chi-restraints excluded: chain h residue 91 LEU Chi-restraints excluded: chain h residue 103 VAL Chi-restraints excluded: chain h residue 109 VAL Chi-restraints excluded: chain h residue 111 THR Chi-restraints excluded: chain h residue 125 ILE Chi-restraints excluded: chain h residue 128 VAL Chi-restraints excluded: chain k residue 12 ARG Chi-restraints excluded: chain k residue 14 GLN Chi-restraints excluded: chain k residue 30 ILE Chi-restraints excluded: chain k residue 34 THR Chi-restraints excluded: chain k residue 45 THR Chi-restraints excluded: chain k residue 58 THR Chi-restraints excluded: chain k residue 68 ARG Chi-restraints excluded: chain k residue 78 ILE Chi-restraints excluded: chain k residue 81 LEU Chi-restraints excluded: chain k residue 95 THR Chi-restraints excluded: chain k residue 109 ILE Chi-restraints excluded: chain l residue 3 VAL Chi-restraints excluded: chain l residue 6 LEU Chi-restraints excluded: chain l residue 7 VAL Chi-restraints excluded: chain l residue 82 ARG Chi-restraints excluded: chain l residue 97 VAL Chi-restraints excluded: chain l residue 108 ASP Chi-restraints excluded: chain l residue 120 ARG Chi-restraints excluded: chain o residue 4 THR Chi-restraints excluded: chain o residue 51 SER Chi-restraints excluded: chain o residue 66 LEU Chi-restraints excluded: chain o residue 73 ASP Chi-restraints excluded: chain p residue 2 VAL Chi-restraints excluded: chain p residue 3 THR Chi-restraints excluded: chain p residue 19 VAL Chi-restraints excluded: chain p residue 54 LEU Chi-restraints excluded: chain p residue 55 ASP Chi-restraints excluded: chain p residue 63 GLN Chi-restraints excluded: chain q residue 6 THR Chi-restraints excluded: chain q residue 29 LYS Chi-restraints excluded: chain q residue 32 ILE Chi-restraints excluded: chain q residue 54 ILE Chi-restraints excluded: chain q residue 56 ASP Chi-restraints excluded: chain q residue 70 LYS Chi-restraints excluded: chain q residue 73 THR Chi-restraints excluded: chain r residue 27 THR Chi-restraints excluded: chain t residue 19 HIS Chi-restraints excluded: chain t residue 29 THR Chi-restraints excluded: chain t residue 65 LEU Chi-restraints excluded: chain u residue 28 LEU Chi-restraints excluded: chain w residue 508 SER Chi-restraints excluded: chain c residue 14 VAL Chi-restraints excluded: chain c residue 67 ILE Chi-restraints excluded: chain c residue 78 LYS Chi-restraints excluded: chain c residue 101 ASN Chi-restraints excluded: chain c residue 105 VAL Chi-restraints excluded: chain c residue 120 THR Chi-restraints excluded: chain c residue 177 LEU Chi-restraints excluded: chain c residue 183 TYR Chi-restraints excluded: chain c residue 198 LYS Chi-restraints excluded: chain c residue 206 ILE Chi-restraints excluded: chain g residue 6 ILE Chi-restraints excluded: chain g residue 11 ILE Chi-restraints excluded: chain g residue 16 LYS Chi-restraints excluded: chain g residue 21 LEU Chi-restraints excluded: chain g residue 135 LYS Chi-restraints excluded: chain i residue 18 VAL Chi-restraints excluded: chain i residue 27 ILE Chi-restraints excluded: chain i residue 54 VAL Chi-restraints excluded: chain i residue 56 MET Chi-restraints excluded: chain i residue 60 LEU Chi-restraints excluded: chain i residue 62 LEU Chi-restraints excluded: chain i residue 66 VAL Chi-restraints excluded: chain i residue 71 ILE Chi-restraints excluded: chain i residue 86 LEU Chi-restraints excluded: chain i residue 97 LEU Chi-restraints excluded: chain i residue 110 VAL Chi-restraints excluded: chain i residue 115 VAL Chi-restraints excluded: chain j residue 8 ILE Chi-restraints excluded: chain j residue 44 THR Chi-restraints excluded: chain j residue 46 LYS Chi-restraints excluded: chain j residue 50 THR Chi-restraints excluded: chain j residue 51 VAL Chi-restraints excluded: chain j residue 80 THR Chi-restraints excluded: chain j residue 88 MET Chi-restraints excluded: chain m residue 3 ILE Chi-restraints excluded: chain m residue 18 LEU Chi-restraints excluded: chain m residue 20 SER Chi-restraints excluded: chain m residue 21 ILE Chi-restraints excluded: chain m residue 24 VAL Chi-restraints excluded: chain m residue 32 ILE Chi-restraints excluded: chain m residue 33 LEU Chi-restraints excluded: chain m residue 55 LEU Chi-restraints excluded: chain m residue 82 LEU Chi-restraints excluded: chain m residue 84 CYS Chi-restraints excluded: chain m residue 103 THR Chi-restraints excluded: chain n residue 30 ILE Chi-restraints excluded: chain n residue 33 VAL Chi-restraints excluded: chain n residue 56 SER Chi-restraints excluded: chain n residue 64 CYS Chi-restraints excluded: chain s residue 5 LYS Chi-restraints excluded: chain s residue 10 ILE Chi-restraints excluded: chain s residue 39 ILE Chi-restraints excluded: chain s residue 42 ASN Chi-restraints excluded: chain s residue 66 VAL Chi-restraints excluded: chain s residue 70 LEU Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 85 ASN Chi-restraints excluded: chain C residue 90 ILE Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 110 LYS Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 179 GLU Chi-restraints excluded: chain C residue 200 MET Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 49 GLN Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 106 LYS Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 171 THR Chi-restraints excluded: chain D residue 180 VAL Chi-restraints excluded: chain E residue 3 LEU Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 19 PHE Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 69 ARG Chi-restraints excluded: chain E residue 73 ILE Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain F residue 5 ASP Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 15 LEU Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 145 VAL Chi-restraints excluded: chain F residue 155 ILE Chi-restraints excluded: chain F residue 156 THR Chi-restraints excluded: chain G residue 14 VAL Chi-restraints excluded: chain G residue 15 ASP Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 18 ILE Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 37 ASN Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 55 ASP Chi-restraints excluded: chain G residue 73 SER Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 161 VAL Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain G residue 170 THR Chi-restraints excluded: chain H residue 44 ILE Chi-restraints excluded: chain H residue 90 LEU Chi-restraints excluded: chain H residue 98 ASP Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 147 VAL Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 77 VAL Chi-restraints excluded: chain I residue 95 ASP Chi-restraints excluded: chain I residue 127 SER Chi-restraints excluded: chain I residue 134 SER Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 56 VAL Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain J residue 64 VAL Chi-restraints excluded: chain J residue 67 ASN Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 81 ILE Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 12 ASP Chi-restraints excluded: chain K residue 28 SER Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 82 ASN Chi-restraints excluded: chain K residue 90 ASN Chi-restraints excluded: chain K residue 114 LYS Chi-restraints excluded: chain K residue 116 ILE Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 54 GLN Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 93 ASN Chi-restraints excluded: chain L residue 100 ILE Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 122 VAL Chi-restraints excluded: chain M residue 26 VAL Chi-restraints excluded: chain M residue 42 THR Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 93 VAL Chi-restraints excluded: chain M residue 96 ILE Chi-restraints excluded: chain M residue 108 VAL Chi-restraints excluded: chain N residue 11 ASN Chi-restraints excluded: chain N residue 13 ASN Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 89 SER Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain P residue 3 ILE Chi-restraints excluded: chain P residue 16 VAL Chi-restraints excluded: chain P residue 23 ASP Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 59 THR Chi-restraints excluded: chain P residue 63 ILE Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain P residue 101 GLU Chi-restraints excluded: chain Q residue 7 VAL Chi-restraints excluded: chain Q residue 16 ILE Chi-restraints excluded: chain Q residue 17 LEU Chi-restraints excluded: chain Q residue 28 SER Chi-restraints excluded: chain Q residue 33 VAL Chi-restraints excluded: chain Q residue 38 VAL Chi-restraints excluded: chain Q residue 39 ILE Chi-restraints excluded: chain Q residue 110 GLU Chi-restraints excluded: chain Q residue 111 LYS Chi-restraints excluded: chain R residue 10 LYS Chi-restraints excluded: chain R residue 14 VAL Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 55 ASP Chi-restraints excluded: chain R residue 60 LYS Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 79 ARG Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain S residue 11 ARG Chi-restraints excluded: chain S residue 19 LEU Chi-restraints excluded: chain S residue 40 ASN Chi-restraints excluded: chain S residue 68 ASP Chi-restraints excluded: chain S residue 69 LEU Chi-restraints excluded: chain S residue 106 VAL Chi-restraints excluded: chain T residue 37 ASP Chi-restraints excluded: chain T residue 53 VAL Chi-restraints excluded: chain T residue 60 THR Chi-restraints excluded: chain T residue 73 ARG Chi-restraints excluded: chain T residue 85 VAL Chi-restraints excluded: chain U residue 33 VAL Chi-restraints excluded: chain U residue 35 VAL Chi-restraints excluded: chain U residue 48 VAL Chi-restraints excluded: chain U residue 53 GLN Chi-restraints excluded: chain U residue 69 VAL Chi-restraints excluded: chain U residue 86 PHE Chi-restraints excluded: chain U residue 98 ASN Chi-restraints excluded: chain U residue 101 THR Chi-restraints excluded: chain V residue 1 MET Chi-restraints excluded: chain V residue 8 VAL Chi-restraints excluded: chain V residue 10 LYS Chi-restraints excluded: chain V residue 42 LEU Chi-restraints excluded: chain V residue 64 VAL Chi-restraints excluded: chain V residue 77 VAL Chi-restraints excluded: chain V residue 83 LYS Chi-restraints excluded: chain V residue 89 ILE Chi-restraints excluded: chain V residue 91 PHE Chi-restraints excluded: chain W residue 8 ASN Chi-restraints excluded: chain W residue 46 ASN Chi-restraints excluded: chain W residue 49 CYS Chi-restraints excluded: chain W residue 63 VAL Chi-restraints excluded: chain W residue 77 SER Chi-restraints excluded: chain W residue 78 ILE Chi-restraints excluded: chain X residue 4 CYS Chi-restraints excluded: chain X residue 10 ARG Chi-restraints excluded: chain X residue 24 THR Chi-restraints excluded: chain X residue 47 THR Chi-restraints excluded: chain X residue 55 MET Chi-restraints excluded: chain X residue 64 ASP Chi-restraints excluded: chain X residue 67 LEU Chi-restraints excluded: chain Y residue 15 ASN Chi-restraints excluded: chain Y residue 16 THR Chi-restraints excluded: chain Y residue 31 GLN Chi-restraints excluded: chain Y residue 43 LEU Chi-restraints excluded: chain Y residue 46 VAL Chi-restraints excluded: chain Y residue 55 THR Chi-restraints excluded: chain Y residue 57 LEU Chi-restraints excluded: chain Z residue 4 ILE Chi-restraints excluded: chain Z residue 26 LEU Chi-restraints excluded: chain Z residue 31 ILE Chi-restraints excluded: chain Z residue 34 THR Chi-restraints excluded: chain Z residue 37 ARG Chi-restraints excluded: chain Z residue 48 ASN Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 24 VAL Chi-restraints excluded: chain 0 residue 43 THR Chi-restraints excluded: chain 1 residue 22 THR Chi-restraints excluded: chain 1 residue 47 ILE Chi-restraints excluded: chain 2 residue 9 VAL Chi-restraints excluded: chain 2 residue 10 LEU Chi-restraints excluded: chain 3 residue 50 SER Chi-restraints excluded: chain 4 residue 10 LEU Chi-restraints excluded: chain 4 residue 37 GLN Chi-restraints excluded: chain 5 residue 36 ASP Chi-restraints excluded: chain 5 residue 50 VAL Chi-restraints excluded: chain 5 residue 58 THR Chi-restraints excluded: chain 5 residue 77 VAL Chi-restraints excluded: chain 6 residue 5 ILE Chi-restraints excluded: chain 6 residue 27 THR Chi-restraints excluded: chain 6 residue 33 ASN Chi-restraints excluded: chain 6 residue 35 ASP Chi-restraints excluded: chain 6 residue 56 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1103 random chunks: chunk 967 optimal weight: 10.0000 chunk 1018 optimal weight: 5.9990 chunk 929 optimal weight: 9.9990 chunk 990 optimal weight: 7.9990 chunk 596 optimal weight: 20.0000 chunk 431 optimal weight: 9.9990 chunk 777 optimal weight: 6.9990 chunk 304 optimal weight: 30.0000 chunk 895 optimal weight: 9.9990 chunk 936 optimal weight: 8.9990 chunk 987 optimal weight: 6.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- 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** ** e 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 46 GLN h 66 GLN ** h 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 63 GLN ** t 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 101 ASN ** g 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 70 HIS ** n 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 138 GLN ** J 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 97 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 ** P 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 55 HIS ** Q 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.8559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.113 161499 Z= 0.305 Angle : 0.789 15.497 240779 Z= 0.417 Chirality : 0.041 0.369 30208 Planarity : 0.007 0.127 13518 Dihedral : 23.711 179.879 79694 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 21.29 Ramachandran Plot: Outliers : 0.67 % Allowed : 10.75 % Favored : 88.58 % Rotamer: Outliers : 8.01 % Allowed : 32.45 % Favored : 59.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.22 (0.10), residues: 6551 helix: -0.10 (0.11), residues: 2104 sheet: -1.98 (0.14), residues: 1128 loop : -2.23 (0.10), residues: 3319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP f 42 HIS 0.013 0.002 HIS q 46 PHE 0.053 0.003 PHE F 98 TYR 0.054 0.003 TYR b 212 ARG 0.014 0.001 ARG T 77 *********************** 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 2129 residues out of total 5475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 387 poor density : 1742 time to evaluate : 6.628 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: b 17 HIS cc_start: 0.4232 (OUTLIER) cc_final: 0.3681 (m170) REVERT: b 22 TRP cc_start: 0.8858 (p-90) cc_final: 0.8535 (p-90) REVERT: b 114 LYS cc_start: 0.9259 (ttmt) cc_final: 0.8487 (pptt) REVERT: b 141 GLU cc_start: 0.7874 (mt-10) cc_final: 0.7586 (tp30) REVERT: d 3 TYR cc_start: 0.8329 (t80) cc_final: 0.8011 (t80) REVERT: d 72 ARG cc_start: 0.8988 (tmm-80) cc_final: 0.8692 (ttm170) REVERT: d 87 GLU cc_start: 0.7519 (pm20) cc_final: 0.7117 (pm20) REVERT: d 177 MET cc_start: 0.4041 (mmt) cc_final: 0.3103 (mmt) REVERT: f 11 HIS cc_start: 0.8222 (t70) cc_final: 0.7882 (t-90) REVERT: f 21 MET cc_start: 0.8859 (ttm) cc_final: 0.8354 (ttm) REVERT: f 25 TYR cc_start: 0.7469 (m-10) cc_final: 0.7033 (m-10) REVERT: f 44 ARG cc_start: 0.7482 (ptp-170) cc_final: 0.7163 (mtm180) REVERT: f 70 VAL cc_start: 0.8189 (m) cc_final: 0.7836 (p) REVERT: f 93 LYS cc_start: 0.8160 (mmmt) cc_final: 0.7665 (mmtt) REVERT: h 32 LYS cc_start: 0.8667 (OUTLIER) cc_final: 0.8284 (mmmt) REVERT: k 12 ARG cc_start: 0.5219 (OUTLIER) cc_final: 0.3975 (mtm180) REVERT: k 13 LYS cc_start: 0.7173 (tppt) cc_final: 0.6916 (tppt) REVERT: k 52 ARG cc_start: 0.7137 (tpp-160) cc_final: 0.6866 (mmm-85) REVERT: l 34 THR cc_start: 0.8796 (OUTLIER) cc_final: 0.8500 (p) REVERT: l 63 THR cc_start: 0.9528 (t) cc_final: 0.9264 (p) REVERT: l 69 GLU cc_start: 0.8294 (mm-30) cc_final: 0.7734 (mp0) REVERT: l 114 SER cc_start: 0.9411 (t) cc_final: 0.9185 (p) REVERT: l 120 ARG cc_start: 0.7712 (OUTLIER) cc_final: 0.7044 (tpp80) REVERT: p 13 LYS cc_start: 0.8961 (mttp) cc_final: 0.8675 (mtmt) REVERT: p 14 ARG cc_start: 0.9125 (mmm-85) cc_final: 0.8807 (mmm160) REVERT: q 15 LYS cc_start: 0.7339 (ptmm) cc_final: 0.7096 (ptmm) REVERT: q 16 MET cc_start: 0.8100 (mmm) cc_final: 0.7612 (tpp) REVERT: q 17 GLU cc_start: 0.8467 (tm-30) cc_final: 0.8179 (tm-30) REVERT: q 29 LYS cc_start: 0.8291 (OUTLIER) cc_final: 0.7765 (ptmm) REVERT: q 70 LYS cc_start: 0.8977 (tttm) cc_final: 0.8557 (ttmt) REVERT: r 72 ARG cc_start: 0.8470 (mmm-85) cc_final: 0.8253 (mmm-85) REVERT: t 54 GLN cc_start: 0.8283 (mp10) cc_final: 0.7980 (mp10) REVERT: t 84 LYS cc_start: 0.8281 (tppt) cc_final: 0.7758 (pptt) REVERT: c 22 PHE cc_start: 0.8691 (t80) cc_final: 0.8256 (t80) REVERT: c 167 TYR cc_start: 0.8033 (m-10) cc_final: 0.7808 (m-10) REVERT: g 6 ILE cc_start: 0.6536 (OUTLIER) cc_final: 0.6205 (pp) REVERT: g 46 LEU cc_start: 0.9502 (mp) cc_final: 0.9105 (pp) REVERT: i 27 ILE cc_start: 0.7692 (OUTLIER) cc_final: 0.7381 (mp) REVERT: m 54 THR cc_start: 0.8125 (p) cc_final: 0.7781 (p) REVERT: m 55 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8601 (tt) REVERT: m 58 GLU cc_start: 0.8431 (mt-10) cc_final: 0.8101 (mt-10) REVERT: m 74 MET cc_start: 0.9187 (mtt) cc_final: 0.8903 (mtp) REVERT: n 60 GLN cc_start: 0.8638 (mp10) cc_final: 0.8299 (mp10) REVERT: s 39 ILE cc_start: 0.8721 (OUTLIER) cc_final: 0.8338 (pt) REVERT: s 43 MET cc_start: 0.8166 (ptp) cc_final: 0.7857 (tmm) REVERT: s 55 GLN cc_start: 0.8630 (pt0) cc_final: 0.8282 (pm20) REVERT: C 29 PHE cc_start: 0.8355 (t80) cc_final: 0.8002 (t80) REVERT: C 170 TYR cc_start: 0.8419 (m-10) cc_final: 0.8077 (m-10) REVERT: C 184 GLU cc_start: 0.8580 (tm-30) cc_final: 0.7957 (tm-30) REVERT: C 224 MET cc_start: 0.8488 (mtt) cc_final: 0.8226 (mtt) REVERT: D 80 TRP cc_start: 0.8453 (m-90) cc_final: 0.8070 (m-90) REVERT: E 24 ASN cc_start: 0.7827 (t0) cc_final: 0.7312 (t0) REVERT: E 25 GLU cc_start: 0.8317 (tt0) cc_final: 0.8094 (tp30) REVERT: E 47 LYS cc_start: 0.9189 (OUTLIER) cc_final: 0.8525 (ptpt) REVERT: E 69 ARG cc_start: 0.8770 (OUTLIER) cc_final: 0.8321 (mtt180) REVERT: E 116 ASP cc_start: 0.9132 (m-30) cc_final: 0.8492 (t70) REVERT: F 51 ASN cc_start: 0.8299 (m110) cc_final: 0.7686 (t0) REVERT: F 173 ASP cc_start: 0.8687 (m-30) cc_final: 0.8455 (t70) REVERT: G 74 MET cc_start: 0.8379 (ttt) cc_final: 0.7722 (tpp) REVERT: G 172 GLU cc_start: 0.8567 (tp30) cc_final: 0.8162 (tm-30) REVERT: H 1 MET cc_start: 0.8187 (mmt) cc_final: 0.7724 (ttt) REVERT: H 43 ASN cc_start: 0.8518 (m110) cc_final: 0.8290 (m-40) REVERT: H 45 GLU cc_start: 0.8483 (tm-30) cc_final: 0.7878 (pt0) REVERT: H 129 GLU cc_start: 0.6786 (tt0) cc_final: 0.6265 (tm-30) REVERT: I 134 SER cc_start: 0.7395 (OUTLIER) cc_final: 0.6976 (p) REVERT: J 1 MET cc_start: 0.7655 (OUTLIER) cc_final: 0.7288 (ttt) REVERT: J 98 GLU cc_start: 0.8786 (mp0) cc_final: 0.8312 (tm-30) REVERT: K 111 LYS cc_start: 0.8692 (ptmt) cc_final: 0.7748 (tptt) REVERT: K 114 LYS cc_start: 0.9057 (OUTLIER) cc_final: 0.8856 (mttt) REVERT: L 91 ASP cc_start: 0.8483 (t0) cc_final: 0.8005 (m-30) REVERT: M 1 MET cc_start: 0.8192 (tmm) cc_final: 0.7916 (tmm) REVERT: M 53 MET cc_start: 0.9295 (tmm) cc_final: 0.8904 (tmm) REVERT: M 82 MET cc_start: 0.8436 (mtp) cc_final: 0.7999 (ttm) REVERT: N 5 LYS cc_start: 0.9359 (mtmm) cc_final: 0.9047 (mtmm) REVERT: N 72 ASP cc_start: 0.8837 (t0) cc_final: 0.8267 (t0) REVERT: N 75 ILE cc_start: 0.9265 (mm) cc_final: 0.8871 (mm) REVERT: N 97 ILE cc_start: 0.9318 (mm) cc_final: 0.9031 (mm) REVERT: N 107 ASN cc_start: 0.7988 (t0) cc_final: 0.7739 (t0) REVERT: N 110 MET cc_start: 0.8767 (mmp) cc_final: 0.8214 (mmp) REVERT: O 56 LYS cc_start: 0.8313 (pttp) cc_final: 0.7799 (mppt) REVERT: O 115 LEU cc_start: 0.7868 (mm) cc_final: 0.7364 (mm) REVERT: P 99 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8466 (tt) REVERT: P 110 LYS cc_start: 0.8610 (mmmt) cc_final: 0.8202 (mtmt) REVERT: Q 75 TYR cc_start: 0.8787 (t80) cc_final: 0.8402 (t80) REVERT: R 60 LYS cc_start: 0.8890 (OUTLIER) cc_final: 0.8467 (ptpp) REVERT: R 78 ARG cc_start: 0.9247 (tpp80) cc_final: 0.8627 (tpp80) REVERT: S 82 MET cc_start: 0.8566 (mtm) cc_final: 0.8286 (mtt) REVERT: S 86 MET cc_start: 0.9046 (tpt) cc_final: 0.8673 (ttp) REVERT: T 1 MET cc_start: 0.1663 (OUTLIER) cc_final: 0.0506 (tpt) REVERT: T 24 MET cc_start: 0.8868 (tpt) cc_final: 0.8521 (tmm) REVERT: T 37 ASP cc_start: 0.8723 (OUTLIER) cc_final: 0.8171 (t0) REVERT: T 87 LEU cc_start: 0.8804 (mt) cc_final: 0.8470 (mp) REVERT: V 5 ASN cc_start: 0.9088 (m-40) cc_final: 0.8160 (p0) REVERT: V 10 LYS cc_start: 0.7306 (OUTLIER) cc_final: 0.6946 (tptt) REVERT: W 62 LYS cc_start: 0.8106 (mmmt) cc_final: 0.6746 (mmtm) REVERT: W 73 ARG cc_start: 0.8805 (mtm110) cc_final: 0.8217 (mtp-110) REVERT: X 43 LYS cc_start: 0.8612 (tppt) cc_final: 0.8121 (ptpt) REVERT: Y 13 GLU cc_start: 0.8119 (pt0) cc_final: 0.7581 (tm-30) REVERT: Y 25 GLN cc_start: 0.8975 (mm-40) cc_final: 0.8752 (mm-40) REVERT: Y 36 GLN cc_start: 0.8062 (mm-40) cc_final: 0.7772 (mp10) REVERT: Z 4 ILE cc_start: 0.9126 (OUTLIER) cc_final: 0.8924 (tp) REVERT: Z 20 LYS cc_start: 0.9175 (mtmm) cc_final: 0.8837 (mtmm) REVERT: Z 46 MET cc_start: 0.8862 (mmt) cc_final: 0.8620 (mmm) REVERT: Z 48 ASN cc_start: 0.8895 (OUTLIER) cc_final: 0.8539 (m-40) REVERT: 2 6 GLN cc_start: 0.8347 (tm-30) cc_final: 0.8105 (tm-30) REVERT: 2 18 PHE cc_start: 0.9111 (t80) cc_final: 0.8801 (t80) REVERT: 5 62 ARG cc_start: 0.6670 (ttm170) cc_final: 0.6244 (mtm110) REVERT: 5 122 GLN cc_start: 0.6099 (pm20) cc_final: 0.5843 (mm-40) REVERT: 6 22 MET cc_start: 0.7979 (pmm) cc_final: 0.7656 (pmm) outliers start: 387 outliers final: 311 residues processed: 1932 average time/residue: 1.2671 time to fit residues: 4277.8337 Evaluate side-chains 2022 residues out of total 5475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 333 poor density : 1689 time to evaluate : 6.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 9 LEU Chi-restraints excluded: chain b residue 17 HIS Chi-restraints excluded: chain b residue 21 TYR Chi-restraints excluded: chain b residue 46 VAL Chi-restraints excluded: chain b residue 71 THR Chi-restraints excluded: chain b residue 81 ASP Chi-restraints excluded: chain b residue 116 LEU Chi-restraints excluded: chain b residue 129 THR Chi-restraints excluded: chain b residue 152 ASP Chi-restraints excluded: chain b residue 167 HIS Chi-restraints excluded: chain b residue 178 LEU Chi-restraints excluded: chain b residue 185 ILE Chi-restraints excluded: chain b residue 211 LEU Chi-restraints excluded: chain d residue 40 HIS Chi-restraints excluded: chain d residue 101 VAL Chi-restraints excluded: chain d residue 110 ARG Chi-restraints excluded: chain d residue 136 VAL Chi-restraints excluded: chain d residue 189 ASP Chi-restraints excluded: chain d residue 197 HIS Chi-restraints excluded: chain e residue 20 VAL Chi-restraints excluded: chain e residue 33 THR Chi-restraints excluded: chain e residue 45 VAL Chi-restraints excluded: chain e residue 89 THR Chi-restraints excluded: chain e residue 121 ASN Chi-restraints excluded: chain e residue 130 THR Chi-restraints excluded: chain e residue 146 MET Chi-restraints excluded: chain e residue 147 ASN Chi-restraints excluded: chain f residue 18 VAL Chi-restraints excluded: chain f residue 36 ILE Chi-restraints excluded: chain f residue 89 VAL Chi-restraints excluded: chain h residue 11 THR Chi-restraints excluded: chain h residue 32 LYS Chi-restraints excluded: chain h residue 47 ASP Chi-restraints excluded: chain h residue 53 ASP Chi-restraints excluded: chain h residue 73 SER Chi-restraints excluded: chain h residue 74 ILE Chi-restraints excluded: chain h residue 91 LEU Chi-restraints excluded: chain h residue 103 VAL Chi-restraints excluded: chain h residue 111 THR Chi-restraints excluded: chain h residue 120 LEU Chi-restraints excluded: chain h residue 128 VAL Chi-restraints excluded: chain k residue 12 ARG Chi-restraints excluded: chain k residue 30 ILE Chi-restraints excluded: chain k residue 34 THR Chi-restraints excluded: chain k residue 45 THR Chi-restraints excluded: chain k residue 58 THR Chi-restraints excluded: chain k residue 68 ARG Chi-restraints excluded: chain k residue 81 LEU Chi-restraints excluded: chain k residue 95 THR Chi-restraints excluded: chain k residue 109 ILE Chi-restraints excluded: chain l residue 6 LEU Chi-restraints excluded: chain l residue 7 VAL Chi-restraints excluded: chain l residue 34 THR Chi-restraints excluded: chain l residue 82 ARG Chi-restraints excluded: chain l residue 96 THR Chi-restraints excluded: chain l residue 97 VAL Chi-restraints excluded: chain l residue 108 ASP Chi-restraints excluded: chain l residue 120 ARG Chi-restraints excluded: chain o residue 4 THR Chi-restraints excluded: chain o residue 7 THR Chi-restraints excluded: chain o residue 51 SER Chi-restraints excluded: chain o residue 59 VAL Chi-restraints excluded: chain o residue 66 LEU Chi-restraints excluded: chain o residue 73 ASP Chi-restraints excluded: chain o residue 82 GLU Chi-restraints excluded: chain p residue 2 VAL Chi-restraints excluded: chain p residue 3 THR Chi-restraints excluded: chain p residue 19 VAL Chi-restraints excluded: chain p residue 42 ILE Chi-restraints excluded: chain p residue 54 LEU Chi-restraints excluded: chain p residue 57 ILE Chi-restraints excluded: chain q residue 6 THR Chi-restraints excluded: chain q residue 29 LYS Chi-restraints excluded: chain q residue 32 ILE Chi-restraints excluded: chain q residue 54 ILE Chi-restraints excluded: chain q residue 56 ASP Chi-restraints excluded: chain r residue 27 THR Chi-restraints excluded: chain t residue 19 HIS Chi-restraints excluded: chain t residue 31 ILE Chi-restraints excluded: chain t residue 65 LEU Chi-restraints excluded: chain t residue 78 LEU Chi-restraints excluded: chain t residue 82 ILE Chi-restraints excluded: chain u residue 28 LEU Chi-restraints excluded: chain w residue 508 SER Chi-restraints excluded: chain c residue 14 VAL Chi-restraints excluded: chain c residue 67 ILE Chi-restraints excluded: chain c residue 78 LYS Chi-restraints excluded: chain c residue 100 ILE Chi-restraints excluded: chain c residue 101 ASN Chi-restraints excluded: chain c residue 105 VAL Chi-restraints excluded: chain c residue 123 LEU Chi-restraints excluded: chain c residue 177 LEU Chi-restraints excluded: chain c residue 183 TYR Chi-restraints excluded: chain c residue 198 LYS Chi-restraints excluded: chain c residue 206 ILE Chi-restraints excluded: chain g residue 6 ILE Chi-restraints excluded: chain g residue 11 ILE Chi-restraints excluded: chain g residue 16 LYS Chi-restraints excluded: chain g residue 21 LEU Chi-restraints excluded: chain g residue 135 LYS Chi-restraints excluded: chain i residue 18 VAL Chi-restraints excluded: chain i residue 27 ILE Chi-restraints excluded: chain i residue 56 MET Chi-restraints excluded: chain i residue 60 LEU Chi-restraints excluded: chain i residue 62 LEU Chi-restraints excluded: chain i residue 66 VAL Chi-restraints excluded: chain i residue 71 ILE Chi-restraints excluded: chain i residue 97 LEU Chi-restraints excluded: chain i residue 110 VAL Chi-restraints excluded: chain i residue 115 VAL Chi-restraints excluded: chain j residue 8 ILE Chi-restraints excluded: chain j residue 44 THR Chi-restraints excluded: chain j residue 50 THR Chi-restraints excluded: chain j residue 51 VAL Chi-restraints excluded: chain j residue 80 THR Chi-restraints excluded: chain j residue 88 MET Chi-restraints excluded: chain m residue 3 ILE Chi-restraints excluded: chain m residue 18 LEU Chi-restraints excluded: chain m residue 20 SER Chi-restraints excluded: chain m residue 21 ILE Chi-restraints excluded: chain m residue 24 VAL Chi-restraints excluded: chain m residue 32 ILE Chi-restraints excluded: chain m residue 55 LEU Chi-restraints excluded: chain m residue 82 LEU Chi-restraints excluded: chain m residue 84 CYS Chi-restraints excluded: chain m residue 103 THR Chi-restraints excluded: chain n residue 30 ILE Chi-restraints excluded: chain n residue 33 VAL Chi-restraints excluded: chain n residue 56 SER Chi-restraints excluded: chain n residue 64 CYS Chi-restraints excluded: chain s residue 5 LYS Chi-restraints excluded: chain s residue 10 ILE Chi-restraints excluded: chain s residue 39 ILE Chi-restraints excluded: chain s residue 42 ASN Chi-restraints excluded: chain s residue 70 LEU Chi-restraints excluded: chain C residue 44 ASN Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 85 ASN Chi-restraints excluded: chain C residue 90 ILE Chi-restraints excluded: chain C residue 110 LYS Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 200 MET Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 106 LYS Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 171 THR Chi-restraints excluded: chain D residue 180 VAL Chi-restraints excluded: chain E residue 3 LEU Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 19 PHE Chi-restraints excluded: chain E residue 47 LYS Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 69 ARG Chi-restraints excluded: chain E residue 73 ILE Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain F residue 5 ASP Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 15 LEU Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 145 VAL Chi-restraints excluded: chain F residue 155 ILE Chi-restraints excluded: chain F residue 156 THR Chi-restraints excluded: chain G residue 1 SER Chi-restraints excluded: chain G residue 14 VAL Chi-restraints excluded: chain G residue 15 ASP Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 18 ILE Chi-restraints excluded: chain G residue 37 ASN Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 55 ASP Chi-restraints excluded: chain G residue 73 SER Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 130 ILE Chi-restraints excluded: chain G residue 136 ASP Chi-restraints excluded: chain G residue 161 VAL Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain G residue 170 THR Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 44 ILE Chi-restraints excluded: chain H residue 90 LEU Chi-restraints excluded: chain H residue 98 ASP Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 147 VAL Chi-restraints excluded: chain I residue 7 TYR Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 77 VAL Chi-restraints excluded: chain I residue 95 ASP Chi-restraints excluded: chain I residue 127 SER Chi-restraints excluded: chain I residue 134 SER Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 56 VAL Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain J residue 60 ASP Chi-restraints excluded: chain J residue 64 VAL Chi-restraints excluded: chain J residue 67 ASN Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 81 ILE Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain J residue 142 ILE Chi-restraints excluded: chain K residue 12 ASP Chi-restraints excluded: chain K residue 28 SER Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 90 ASN Chi-restraints excluded: chain K residue 114 LYS Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 54 GLN Chi-restraints excluded: chain L residue 93 ASN Chi-restraints excluded: chain L residue 100 ILE Chi-restraints excluded: chain L residue 122 VAL Chi-restraints excluded: chain M residue 26 VAL Chi-restraints excluded: chain M residue 42 THR Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 93 VAL Chi-restraints excluded: chain M residue 108 VAL Chi-restraints excluded: chain N residue 11 ASN Chi-restraints excluded: chain N residue 13 ASN Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 89 SER Chi-restraints excluded: chain N residue 115 LEU Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 62 LEU Chi-restraints excluded: chain P residue 3 ILE Chi-restraints excluded: chain P residue 16 VAL Chi-restraints excluded: chain P residue 23 ASP Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 59 THR Chi-restraints excluded: chain P residue 63 ILE Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain P residue 101 GLU Chi-restraints excluded: chain Q residue 7 VAL Chi-restraints excluded: chain Q residue 16 ILE Chi-restraints excluded: chain Q residue 17 LEU Chi-restraints excluded: chain Q residue 28 SER Chi-restraints excluded: chain Q residue 33 VAL Chi-restraints excluded: chain Q residue 38 VAL Chi-restraints excluded: chain Q residue 39 ILE Chi-restraints excluded: chain Q residue 87 VAL Chi-restraints excluded: chain Q residue 108 LEU Chi-restraints excluded: chain Q residue 111 LYS Chi-restraints excluded: chain R residue 10 LYS Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 55 ASP Chi-restraints excluded: chain R residue 60 LYS Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 79 ARG Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain S residue 19 LEU Chi-restraints excluded: chain S residue 40 ASN Chi-restraints excluded: chain S residue 53 SER Chi-restraints excluded: chain S residue 68 ASP Chi-restraints excluded: chain S residue 69 LEU Chi-restraints excluded: chain T residue 1 MET Chi-restraints excluded: chain T residue 37 ASP Chi-restraints excluded: chain T residue 60 THR Chi-restraints excluded: chain T residue 85 VAL Chi-restraints excluded: chain U residue 35 VAL Chi-restraints excluded: chain U residue 48 VAL Chi-restraints excluded: chain U residue 53 GLN Chi-restraints excluded: chain U residue 69 VAL Chi-restraints excluded: chain U residue 86 PHE Chi-restraints excluded: chain U residue 98 ASN Chi-restraints excluded: chain U residue 101 THR Chi-restraints excluded: chain V residue 8 VAL Chi-restraints excluded: chain V residue 10 LYS Chi-restraints excluded: chain V residue 45 ASP Chi-restraints excluded: chain V residue 64 VAL Chi-restraints excluded: chain V residue 77 VAL Chi-restraints excluded: chain V residue 83 LYS Chi-restraints excluded: chain V residue 89 ILE Chi-restraints excluded: chain V residue 91 PHE Chi-restraints excluded: chain W residue 8 ASN Chi-restraints excluded: chain W residue 17 LEU Chi-restraints excluded: chain W residue 32 ILE Chi-restraints excluded: chain W residue 49 CYS Chi-restraints excluded: chain W residue 77 SER Chi-restraints excluded: chain X residue 4 CYS Chi-restraints excluded: chain X residue 10 ARG Chi-restraints excluded: chain X residue 24 THR Chi-restraints excluded: chain X residue 47 THR Chi-restraints excluded: chain X residue 55 MET Chi-restraints excluded: chain X residue 64 ASP Chi-restraints excluded: chain X residue 67 LEU Chi-restraints excluded: chain Y residue 15 ASN Chi-restraints excluded: chain Y residue 16 THR Chi-restraints excluded: chain Y residue 19 LEU Chi-restraints excluded: chain Y residue 31 GLN Chi-restraints excluded: chain Y residue 43 LEU Chi-restraints excluded: chain Y residue 46 VAL Chi-restraints excluded: chain Y residue 55 THR Chi-restraints excluded: chain Y residue 57 LEU Chi-restraints excluded: chain Z residue 4 ILE Chi-restraints excluded: chain Z residue 26 LEU Chi-restraints excluded: chain Z residue 31 ILE Chi-restraints excluded: chain Z residue 34 THR Chi-restraints excluded: chain Z residue 37 ARG Chi-restraints excluded: chain Z residue 48 ASN Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 24 VAL Chi-restraints excluded: chain 1 residue 47 ILE Chi-restraints excluded: chain 2 residue 9 VAL Chi-restraints excluded: chain 2 residue 10 LEU Chi-restraints excluded: chain 3 residue 50 SER Chi-restraints excluded: chain 4 residue 10 LEU Chi-restraints excluded: chain 4 residue 37 GLN Chi-restraints excluded: chain 5 residue 50 VAL Chi-restraints excluded: chain 5 residue 58 THR Chi-restraints excluded: chain 5 residue 77 VAL Chi-restraints excluded: chain 6 residue 17 SER Chi-restraints excluded: chain 6 residue 27 THR Chi-restraints excluded: chain 6 residue 33 ASN Chi-restraints excluded: chain 6 residue 35 ASP Chi-restraints excluded: chain 6 residue 40 CYS Chi-restraints excluded: chain 6 residue 56 ARG 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: 6.9990 chunk 639 optimal weight: 20.0000 chunk 496 optimal weight: 10.0000 chunk 728 optimal weight: 20.0000 chunk 1098 optimal weight: 10.0000 chunk 1011 optimal weight: 30.0000 chunk 875 optimal weight: 2.9990 chunk 90 optimal weight: 10.0000 chunk 675 optimal weight: 10.0000 chunk 536 optimal weight: 20.0000 overall best weight: 7.9996 ------------------------------------------------------------------------------- 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** ** e 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 134 ASN ** f 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 46 GLN ** h 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 14 GLN ** k 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 18 GLN r 53 GLN ** t 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 38 GLN ** P 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 14 GLN P 76 HIS ** Q 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 18 GLN ** 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 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.8749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.102 161499 Z= 0.327 Angle : 0.810 17.396 240779 Z= 0.426 Chirality : 0.041 0.362 30208 Planarity : 0.007 0.128 13518 Dihedral : 23.713 178.082 79694 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 22.23 Ramachandran Plot: Outliers : 0.64 % Allowed : 11.08 % Favored : 88.28 % Rotamer: Outliers : 7.74 % Allowed : 33.03 % Favored : 59.23 % 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: -2.25 (0.10), residues: 6551 helix: -0.12 (0.11), residues: 2097 sheet: -1.97 (0.14), residues: 1110 loop : -2.26 (0.10), residues: 3344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP g 102 HIS 0.015 0.002 HIS q 46 PHE 0.046 0.003 PHE 2 18 TYR 0.057 0.003 TYR b 212 ARG 0.011 0.001 ARG Y 29 ********************** 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 2102 residues out of total 5475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 374 poor density : 1728 time to evaluate : 6.539 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: b 17 HIS cc_start: 0.4052 (OUTLIER) cc_final: 0.3537 (m170) REVERT: b 22 TRP cc_start: 0.8846 (p-90) cc_final: 0.8481 (p-90) REVERT: b 114 LYS cc_start: 0.9264 (ttmt) cc_final: 0.8497 (pttt) REVERT: b 135 MET cc_start: 0.8964 (mmm) cc_final: 0.8156 (ppp) REVERT: b 141 GLU cc_start: 0.7886 (mt-10) cc_final: 0.7617 (tp30) REVERT: d 3 TYR cc_start: 0.8405 (t80) cc_final: 0.8019 (t80) REVERT: d 72 ARG cc_start: 0.9008 (tmm-80) cc_final: 0.8724 (ttm170) REVERT: d 87 GLU cc_start: 0.7412 (pm20) cc_final: 0.6823 (pm20) REVERT: d 110 ARG cc_start: 0.6797 (OUTLIER) cc_final: 0.6593 (mmt180) REVERT: d 112 GLU cc_start: 0.6543 (tt0) cc_final: 0.5551 (tt0) REVERT: d 177 MET cc_start: 0.4265 (mmt) cc_final: 0.3393 (mmt) REVERT: f 21 MET cc_start: 0.8867 (ttm) cc_final: 0.8206 (ttm) REVERT: f 25 TYR cc_start: 0.7608 (m-10) cc_final: 0.7054 (m-10) REVERT: f 44 ARG cc_start: 0.7560 (ptp-170) cc_final: 0.7260 (mtm180) REVERT: f 70 VAL cc_start: 0.8197 (m) cc_final: 0.7848 (p) REVERT: h 32 LYS cc_start: 0.8662 (OUTLIER) cc_final: 0.8324 (mmmt) REVERT: h 106 SER cc_start: 0.8603 (m) cc_final: 0.8169 (p) REVERT: k 12 ARG cc_start: 0.5194 (OUTLIER) cc_final: 0.3753 (mtm-85) REVERT: k 31 VAL cc_start: 0.9449 (t) cc_final: 0.9163 (p) REVERT: k 52 ARG cc_start: 0.7133 (tpp-160) cc_final: 0.6842 (mmm-85) REVERT: l 34 THR cc_start: 0.8819 (OUTLIER) cc_final: 0.8524 (p) REVERT: l 63 THR cc_start: 0.9565 (t) cc_final: 0.9306 (p) REVERT: l 69 GLU cc_start: 0.8291 (mm-30) cc_final: 0.7747 (mp0) REVERT: l 114 SER cc_start: 0.9396 (t) cc_final: 0.9167 (p) REVERT: l 120 ARG cc_start: 0.7750 (OUTLIER) cc_final: 0.7121 (tpp80) REVERT: p 13 LYS cc_start: 0.8939 (mttp) cc_final: 0.8691 (mtmt) REVERT: q 15 LYS cc_start: 0.7328 (ptmm) cc_final: 0.6993 (ptmm) REVERT: q 16 MET cc_start: 0.8105 (mmm) cc_final: 0.7840 (tpp) REVERT: q 17 GLU cc_start: 0.8501 (tm-30) cc_final: 0.8177 (tm-30) REVERT: q 20 ILE cc_start: 0.8228 (pp) cc_final: 0.7972 (pp) REVERT: q 29 LYS cc_start: 0.8299 (OUTLIER) cc_final: 0.7793 (ptmm) REVERT: q 47 ASP cc_start: 0.7449 (p0) cc_final: 0.6914 (p0) REVERT: q 70 LYS cc_start: 0.8961 (tttm) cc_final: 0.8542 (ttmt) REVERT: r 72 ARG cc_start: 0.8492 (mmm-85) cc_final: 0.8285 (mmm-85) REVERT: t 84 LYS cc_start: 0.8362 (tppt) cc_final: 0.7872 (tttt) REVERT: c 22 PHE cc_start: 0.8621 (t80) cc_final: 0.8232 (t80) REVERT: c 36 PHE cc_start: 0.9014 (t80) cc_final: 0.8782 (t80) REVERT: c 167 TYR cc_start: 0.8039 (m-10) cc_final: 0.7830 (m-10) REVERT: c 206 ILE cc_start: 0.5600 (OUTLIER) cc_final: 0.5173 (mp) REVERT: g 6 ILE cc_start: 0.6541 (OUTLIER) cc_final: 0.6205 (pp) REVERT: g 46 LEU cc_start: 0.9510 (mp) cc_final: 0.9121 (pp) REVERT: i 27 ILE cc_start: 0.7763 (OUTLIER) cc_final: 0.7446 (mp) REVERT: i 36 GLN cc_start: 0.8632 (tm-30) cc_final: 0.8173 (tm-30) REVERT: m 54 THR cc_start: 0.8110 (p) cc_final: 0.7800 (p) REVERT: m 55 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8590 (tt) REVERT: m 58 GLU cc_start: 0.8430 (mt-10) cc_final: 0.8100 (mt-10) REVERT: m 74 MET cc_start: 0.9210 (mtt) cc_final: 0.8920 (mtp) REVERT: n 9 GLU cc_start: 0.9114 (tp30) cc_final: 0.8608 (tm-30) REVERT: n 60 GLN cc_start: 0.8631 (mp10) cc_final: 0.8273 (mp10) REVERT: s 43 MET cc_start: 0.8131 (ptp) cc_final: 0.7788 (tmm) REVERT: s 55 GLN cc_start: 0.8675 (pt0) cc_final: 0.8324 (pm20) REVERT: C 29 PHE cc_start: 0.8363 (t80) cc_final: 0.8019 (t80) REVERT: C 170 TYR cc_start: 0.8434 (m-10) cc_final: 0.8089 (m-10) REVERT: C 184 GLU cc_start: 0.8589 (tm-30) cc_final: 0.7968 (tm-30) REVERT: C 224 MET cc_start: 0.8501 (mtt) cc_final: 0.8239 (mtt) REVERT: E 24 ASN cc_start: 0.7824 (t0) cc_final: 0.7306 (t0) REVERT: E 25 GLU cc_start: 0.8343 (tt0) cc_final: 0.8094 (tp30) REVERT: E 47 LYS cc_start: 0.9167 (OUTLIER) cc_final: 0.8496 (ptpt) REVERT: E 69 ARG cc_start: 0.8742 (OUTLIER) cc_final: 0.8331 (mtt180) REVERT: E 116 ASP cc_start: 0.9155 (m-30) cc_final: 0.8472 (t70) REVERT: E 195 GLN cc_start: 0.8853 (mt0) cc_final: 0.8318 (mp10) REVERT: F 51 ASN cc_start: 0.8317 (m110) cc_final: 0.7635 (t0) REVERT: F 173 ASP cc_start: 0.8622 (m-30) cc_final: 0.8395 (t70) REVERT: G 51 PHE cc_start: 0.6829 (m-80) cc_final: 0.6498 (m-10) REVERT: G 74 MET cc_start: 0.8332 (ttt) cc_final: 0.7726 (tpp) REVERT: G 127 GLN cc_start: 0.8570 (mm-40) cc_final: 0.8312 (mm-40) REVERT: G 172 GLU cc_start: 0.8503 (tp30) cc_final: 0.8108 (tm-30) REVERT: H 1 MET cc_start: 0.8080 (mmt) cc_final: 0.7607 (ttt) REVERT: H 33 GLN cc_start: 0.8859 (pm20) cc_final: 0.8443 (pm20) REVERT: H 43 ASN cc_start: 0.8508 (m110) cc_final: 0.8259 (m-40) REVERT: H 45 GLU cc_start: 0.8539 (tm-30) cc_final: 0.8138 (tm-30) REVERT: H 112 LYS cc_start: 0.6037 (ttpp) cc_final: 0.4923 (mttt) REVERT: H 129 GLU cc_start: 0.6789 (tt0) cc_final: 0.6129 (tm-30) REVERT: I 99 LYS cc_start: 0.5230 (tppt) cc_final: 0.4343 (tmtt) REVERT: I 134 SER cc_start: 0.7392 (OUTLIER) cc_final: 0.6975 (p) REVERT: J 1 MET cc_start: 0.7656 (OUTLIER) cc_final: 0.7283 (ttt) REVERT: J 44 TYR cc_start: 0.8709 (OUTLIER) cc_final: 0.8378 (t80) REVERT: J 98 GLU cc_start: 0.8820 (mp0) cc_final: 0.8325 (tm-30) REVERT: K 111 LYS cc_start: 0.8702 (ptmt) cc_final: 0.7933 (tptt) REVERT: K 112 PHE cc_start: 0.8332 (m-10) cc_final: 0.8055 (m-10) REVERT: L 91 ASP cc_start: 0.8478 (t0) cc_final: 0.8026 (m-30) REVERT: M 1 MET cc_start: 0.8196 (tmm) cc_final: 0.7909 (tmm) REVERT: M 53 MET cc_start: 0.9287 (tmm) cc_final: 0.8884 (tmm) REVERT: M 82 MET cc_start: 0.8474 (mtp) cc_final: 0.8046 (ttm) REVERT: N 5 LYS cc_start: 0.9379 (mtmm) cc_final: 0.9049 (mtmm) REVERT: N 72 ASP cc_start: 0.8842 (t0) cc_final: 0.8267 (t0) REVERT: N 75 ILE cc_start: 0.9266 (mm) cc_final: 0.8885 (mm) REVERT: N 107 ASN cc_start: 0.7980 (t0) cc_final: 0.7728 (t0) REVERT: N 110 MET cc_start: 0.8775 (mmp) cc_final: 0.8202 (mmp) REVERT: O 56 LYS cc_start: 0.8298 (pttp) cc_final: 0.7785 (mppt) REVERT: O 115 LEU cc_start: 0.7843 (mm) cc_final: 0.7291 (mm) REVERT: P 99 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8468 (tt) REVERT: P 110 LYS cc_start: 0.8581 (mmmt) cc_final: 0.8196 (mtmt) REVERT: Q 75 TYR cc_start: 0.8789 (t80) cc_final: 0.8413 (t80) REVERT: R 60 LYS cc_start: 0.8923 (OUTLIER) cc_final: 0.8531 (ptpp) REVERT: R 78 ARG cc_start: 0.9259 (tpp80) cc_final: 0.8647 (tpp80) REVERT: S 82 MET cc_start: 0.8550 (mtm) cc_final: 0.8270 (mtt) REVERT: S 86 MET cc_start: 0.9047 (tpt) cc_final: 0.8665 (ttp) REVERT: T 1 MET cc_start: 0.1533 (OUTLIER) cc_final: -0.0137 (tpt) REVERT: T 24 MET cc_start: 0.8883 (tpt) cc_final: 0.8517 (tmm) REVERT: T 37 ASP cc_start: 0.8681 (OUTLIER) cc_final: 0.8135 (t0) REVERT: V 5 ASN cc_start: 0.9069 (m-40) cc_final: 0.8167 (p0) REVERT: V 10 LYS cc_start: 0.7306 (OUTLIER) cc_final: 0.6923 (tptt) REVERT: V 19 ARG cc_start: 0.8260 (mtm-85) cc_final: 0.7996 (ttm110) REVERT: V 53 LYS cc_start: 0.9048 (mmmt) cc_final: 0.8534 (mtmt) REVERT: W 62 LYS cc_start: 0.8155 (mmmt) cc_final: 0.6709 (mmtm) REVERT: W 73 ARG cc_start: 0.8821 (mtm110) cc_final: 0.8240 (mtp-110) REVERT: X 43 LYS cc_start: 0.8560 (tppt) cc_final: 0.8110 (ptpt) REVERT: Y 25 GLN cc_start: 0.9015 (mm-40) cc_final: 0.8732 (mm-40) REVERT: Y 36 GLN cc_start: 0.8142 (mm-40) cc_final: 0.7887 (mp10) REVERT: Z 4 ILE cc_start: 0.9160 (OUTLIER) cc_final: 0.8942 (tp) REVERT: Z 20 LYS cc_start: 0.9157 (mtmm) cc_final: 0.8547 (mtmm) REVERT: Z 48 ASN cc_start: 0.8919 (OUTLIER) cc_final: 0.8568 (m-40) REVERT: 2 6 GLN cc_start: 0.8390 (tm-30) cc_final: 0.8157 (tm-30) REVERT: 2 18 PHE cc_start: 0.9125 (t80) cc_final: 0.8829 (t80) REVERT: 5 52 MET cc_start: -0.0970 (tmm) cc_final: -0.1831 (tpp) REVERT: 5 62 ARG cc_start: 0.6739 (ttm170) cc_final: 0.6368 (mtm110) REVERT: 5 122 GLN cc_start: 0.6083 (pm20) cc_final: 0.5850 (mm-40) REVERT: 6 8 LYS cc_start: 0.8358 (mmmm) cc_final: 0.7984 (mmtm) outliers start: 374 outliers final: 318 residues processed: 1907 average time/residue: 1.2745 time to fit residues: 4245.4149 Evaluate side-chains 2028 residues out of total 5475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 341 poor density : 1687 time to evaluate : 6.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 9 LEU Chi-restraints excluded: chain b residue 17 HIS Chi-restraints excluded: chain b residue 21 TYR Chi-restraints excluded: chain b residue 46 VAL Chi-restraints excluded: chain b residue 71 THR Chi-restraints excluded: chain b residue 81 ASP Chi-restraints excluded: chain b residue 116 LEU Chi-restraints excluded: chain b residue 129 THR Chi-restraints excluded: chain b residue 152 ASP Chi-restraints excluded: chain b residue 156 LEU Chi-restraints excluded: chain b residue 167 HIS Chi-restraints excluded: chain b residue 169 HIS Chi-restraints excluded: chain b residue 178 LEU Chi-restraints excluded: chain b residue 185 ILE Chi-restraints excluded: chain b residue 211 LEU Chi-restraints excluded: chain d residue 40 HIS Chi-restraints excluded: chain d residue 77 GLU Chi-restraints excluded: chain d residue 101 VAL Chi-restraints excluded: chain d residue 110 ARG Chi-restraints excluded: chain d residue 189 ASP Chi-restraints excluded: chain d residue 197 HIS Chi-restraints excluded: chain d residue 203 TYR Chi-restraints excluded: chain e residue 20 VAL Chi-restraints excluded: chain e residue 33 THR Chi-restraints excluded: chain e residue 45 VAL Chi-restraints excluded: chain e residue 73 VAL Chi-restraints excluded: chain e residue 84 VAL Chi-restraints excluded: chain e residue 89 THR Chi-restraints excluded: chain e residue 121 ASN Chi-restraints excluded: chain e residue 130 THR Chi-restraints excluded: chain e residue 131 ASN Chi-restraints excluded: chain e residue 147 ASN Chi-restraints excluded: chain f residue 18 VAL Chi-restraints excluded: chain f residue 36 ILE Chi-restraints excluded: chain f residue 85 ILE Chi-restraints excluded: chain f residue 89 VAL Chi-restraints excluded: chain h residue 10 LEU Chi-restraints excluded: chain h residue 11 THR Chi-restraints excluded: chain h residue 32 LYS Chi-restraints excluded: chain h residue 47 ASP Chi-restraints excluded: chain h residue 53 ASP Chi-restraints excluded: chain h residue 61 THR Chi-restraints excluded: chain h residue 73 SER Chi-restraints excluded: chain h residue 74 ILE Chi-restraints excluded: chain h residue 91 LEU Chi-restraints excluded: chain h residue 103 VAL Chi-restraints excluded: chain h residue 111 THR Chi-restraints excluded: chain h residue 128 VAL Chi-restraints excluded: chain k residue 12 ARG Chi-restraints excluded: chain k residue 14 GLN Chi-restraints excluded: chain k residue 30 ILE Chi-restraints excluded: chain k residue 34 THR Chi-restraints excluded: chain k residue 45 THR Chi-restraints excluded: chain k residue 58 THR Chi-restraints excluded: chain k residue 64 VAL Chi-restraints excluded: chain k residue 81 LEU Chi-restraints excluded: chain k residue 95 THR Chi-restraints excluded: chain k residue 109 ILE Chi-restraints excluded: chain l residue 3 VAL Chi-restraints excluded: chain l residue 6 LEU Chi-restraints excluded: chain l residue 7 VAL Chi-restraints excluded: chain l residue 34 THR Chi-restraints excluded: chain l residue 82 ARG Chi-restraints excluded: chain l residue 96 THR Chi-restraints excluded: chain l residue 97 VAL Chi-restraints excluded: chain l residue 108 ASP Chi-restraints excluded: chain l residue 120 ARG Chi-restraints excluded: chain o residue 4 THR Chi-restraints excluded: chain o residue 7 THR Chi-restraints excluded: chain o residue 51 SER Chi-restraints excluded: chain o residue 59 VAL Chi-restraints excluded: chain o residue 66 LEU Chi-restraints excluded: chain o residue 73 ASP Chi-restraints excluded: chain p residue 2 VAL Chi-restraints excluded: chain p residue 3 THR Chi-restraints excluded: chain p residue 19 VAL Chi-restraints excluded: chain p residue 42 ILE Chi-restraints excluded: chain q residue 6 THR Chi-restraints excluded: chain q residue 29 LYS Chi-restraints excluded: chain q residue 32 ILE Chi-restraints excluded: chain q residue 54 ILE Chi-restraints excluded: chain q residue 56 ASP Chi-restraints excluded: chain r residue 27 THR Chi-restraints excluded: chain t residue 19 HIS Chi-restraints excluded: chain t residue 29 THR Chi-restraints excluded: chain t residue 31 ILE Chi-restraints excluded: chain t residue 65 LEU Chi-restraints excluded: chain t residue 82 ILE Chi-restraints excluded: chain u residue 28 LEU Chi-restraints excluded: chain w residue 508 SER Chi-restraints excluded: chain c residue 14 VAL Chi-restraints excluded: chain c residue 67 ILE Chi-restraints excluded: chain c residue 78 LYS Chi-restraints excluded: chain c residue 100 ILE Chi-restraints excluded: chain c residue 105 VAL Chi-restraints excluded: chain c residue 123 LEU Chi-restraints excluded: chain c residue 149 LYS Chi-restraints excluded: chain c residue 177 LEU Chi-restraints excluded: chain c residue 183 TYR Chi-restraints excluded: chain c residue 198 LYS Chi-restraints excluded: chain c residue 206 ILE Chi-restraints excluded: chain g residue 6 ILE Chi-restraints excluded: chain g residue 11 ILE Chi-restraints excluded: chain g residue 16 LYS Chi-restraints excluded: chain g residue 21 LEU Chi-restraints excluded: chain g residue 135 LYS Chi-restraints excluded: chain i residue 18 VAL Chi-restraints excluded: chain i residue 27 ILE Chi-restraints excluded: chain i residue 56 MET Chi-restraints excluded: chain i residue 60 LEU Chi-restraints excluded: chain i residue 62 LEU Chi-restraints excluded: chain i residue 66 VAL Chi-restraints excluded: chain i residue 71 ILE Chi-restraints excluded: chain i residue 97 LEU Chi-restraints excluded: chain i residue 110 VAL Chi-restraints excluded: chain i residue 115 VAL Chi-restraints excluded: chain j residue 8 ILE Chi-restraints excluded: chain j residue 44 THR Chi-restraints excluded: chain j residue 50 THR Chi-restraints excluded: chain j residue 51 VAL Chi-restraints excluded: chain j residue 88 MET Chi-restraints excluded: chain m residue 3 ILE Chi-restraints excluded: chain m residue 18 LEU Chi-restraints excluded: chain m residue 20 SER Chi-restraints excluded: chain m residue 21 ILE Chi-restraints excluded: chain m residue 24 VAL Chi-restraints excluded: chain m residue 32 ILE Chi-restraints excluded: chain m residue 55 LEU Chi-restraints excluded: chain m residue 82 LEU Chi-restraints excluded: chain m residue 84 CYS Chi-restraints excluded: chain m residue 103 THR Chi-restraints excluded: chain n residue 30 ILE Chi-restraints excluded: chain n residue 33 VAL Chi-restraints excluded: chain n residue 56 SER Chi-restraints excluded: chain n residue 64 CYS Chi-restraints excluded: chain s residue 5 LYS Chi-restraints excluded: chain s residue 10 ILE Chi-restraints excluded: chain s residue 39 ILE Chi-restraints excluded: chain s residue 42 ASN Chi-restraints excluded: chain s residue 66 VAL Chi-restraints excluded: chain s residue 70 LEU Chi-restraints excluded: chain C residue 44 ASN Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 85 ASN Chi-restraints excluded: chain C residue 90 ILE Chi-restraints excluded: chain C residue 110 LYS Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 200 MET Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 106 LYS Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 171 THR Chi-restraints excluded: chain D residue 180 VAL Chi-restraints excluded: chain E residue 3 LEU Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 47 LYS Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 69 ARG Chi-restraints excluded: chain E residue 73 ILE Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain F residue 5 ASP Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 15 LEU Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 145 VAL Chi-restraints excluded: chain F residue 155 ILE Chi-restraints excluded: chain F residue 156 THR Chi-restraints excluded: chain G residue 1 SER Chi-restraints excluded: chain G residue 14 VAL Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 18 ILE Chi-restraints excluded: chain G residue 37 ASN Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 55 ASP Chi-restraints excluded: chain G residue 73 SER Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 130 ILE Chi-restraints excluded: chain G residue 136 ASP Chi-restraints excluded: chain G residue 161 VAL Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain G residue 170 THR Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 44 ILE Chi-restraints excluded: chain H residue 90 LEU Chi-restraints excluded: chain H residue 98 ASP Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 147 VAL Chi-restraints excluded: chain I residue 7 TYR Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 59 THR Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 95 ASP Chi-restraints excluded: chain I residue 116 MET Chi-restraints excluded: chain I residue 127 SER Chi-restraints excluded: chain I residue 134 SER Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 44 TYR Chi-restraints excluded: chain J residue 56 VAL Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain J residue 60 ASP Chi-restraints excluded: chain J residue 64 VAL Chi-restraints excluded: chain J residue 67 ASN Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 81 ILE Chi-restraints excluded: chain J residue 109 LEU Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 12 ASP Chi-restraints excluded: chain K residue 28 SER Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 82 ASN Chi-restraints excluded: chain K residue 90 ASN Chi-restraints excluded: chain K residue 114 LYS Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 54 GLN Chi-restraints excluded: chain L residue 93 ASN Chi-restraints excluded: chain L residue 100 ILE Chi-restraints excluded: chain L residue 122 VAL Chi-restraints excluded: chain M residue 26 VAL Chi-restraints excluded: chain M residue 42 THR Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 93 VAL Chi-restraints excluded: chain M residue 108 VAL Chi-restraints excluded: chain N residue 11 ASN Chi-restraints excluded: chain N residue 13 ASN Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 89 SER Chi-restraints excluded: chain N residue 113 ILE Chi-restraints excluded: chain N residue 115 LEU Chi-restraints excluded: chain O residue 12 THR Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 62 LEU Chi-restraints excluded: chain O residue 93 ASP Chi-restraints excluded: chain P residue 3 ILE Chi-restraints excluded: chain P residue 16 VAL Chi-restraints excluded: chain P residue 23 ASP Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 59 THR Chi-restraints excluded: chain P residue 63 ILE Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain P residue 101 GLU Chi-restraints excluded: chain Q residue 7 VAL Chi-restraints excluded: chain Q residue 16 ILE Chi-restraints excluded: chain Q residue 17 LEU Chi-restraints excluded: chain Q residue 28 SER Chi-restraints excluded: chain Q residue 33 VAL Chi-restraints excluded: chain Q residue 38 VAL Chi-restraints excluded: chain Q residue 39 ILE Chi-restraints excluded: chain Q residue 87 VAL Chi-restraints excluded: chain Q residue 108 LEU Chi-restraints excluded: chain Q residue 110 GLU Chi-restraints excluded: chain Q residue 111 LYS Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 55 ASP Chi-restraints excluded: chain R residue 60 LYS Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 79 ARG Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain S residue 19 LEU Chi-restraints excluded: chain S residue 40 ASN Chi-restraints excluded: chain S residue 53 SER Chi-restraints excluded: chain S residue 68 ASP Chi-restraints excluded: chain S residue 69 LEU Chi-restraints excluded: chain T residue 1 MET Chi-restraints excluded: chain T residue 37 ASP Chi-restraints excluded: chain T residue 57 VAL Chi-restraints excluded: chain T residue 60 THR Chi-restraints excluded: chain T residue 85 VAL Chi-restraints excluded: chain U residue 35 VAL Chi-restraints excluded: chain U residue 48 VAL Chi-restraints excluded: chain U residue 53 GLN Chi-restraints excluded: chain U residue 69 VAL Chi-restraints excluded: chain U residue 86 PHE Chi-restraints excluded: chain U residue 98 ASN Chi-restraints excluded: chain V residue 8 VAL Chi-restraints excluded: chain V residue 10 LYS Chi-restraints excluded: chain V residue 24 ASN Chi-restraints excluded: chain V residue 64 VAL Chi-restraints excluded: chain V residue 77 VAL Chi-restraints excluded: chain V residue 83 LYS Chi-restraints excluded: chain V residue 89 ILE Chi-restraints excluded: chain V residue 91 PHE Chi-restraints excluded: chain W residue 8 ASN Chi-restraints excluded: chain W residue 17 LEU Chi-restraints excluded: chain W residue 32 ILE Chi-restraints excluded: chain W residue 46 ASN Chi-restraints excluded: chain W residue 49 CYS Chi-restraints excluded: chain W residue 77 SER Chi-restraints excluded: chain X residue 4 CYS Chi-restraints excluded: chain X residue 10 ARG Chi-restraints excluded: chain X residue 24 THR Chi-restraints excluded: chain X residue 47 THR Chi-restraints excluded: chain X residue 64 ASP Chi-restraints excluded: chain X residue 67 LEU Chi-restraints excluded: chain Y residue 15 ASN Chi-restraints excluded: chain Y residue 16 THR Chi-restraints excluded: chain Y residue 31 GLN Chi-restraints excluded: chain Y residue 43 LEU Chi-restraints excluded: chain Y residue 55 THR Chi-restraints excluded: chain Z residue 4 ILE Chi-restraints excluded: chain Z residue 26 LEU Chi-restraints excluded: chain Z residue 31 ILE Chi-restraints excluded: chain Z residue 34 THR Chi-restraints excluded: chain Z residue 37 ARG Chi-restraints excluded: chain Z residue 48 ASN Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 24 VAL Chi-restraints excluded: chain 1 residue 22 THR Chi-restraints excluded: chain 1 residue 47 ILE Chi-restraints excluded: chain 2 residue 9 VAL Chi-restraints excluded: chain 2 residue 10 LEU Chi-restraints excluded: chain 3 residue 50 SER Chi-restraints excluded: chain 3 residue 61 LEU Chi-restraints excluded: chain 4 residue 10 LEU Chi-restraints excluded: chain 4 residue 37 GLN Chi-restraints excluded: chain 5 residue 50 VAL Chi-restraints excluded: chain 5 residue 58 THR Chi-restraints excluded: chain 5 residue 77 VAL Chi-restraints excluded: chain 6 residue 17 SER Chi-restraints excluded: chain 6 residue 27 THR Chi-restraints excluded: chain 6 residue 33 ASN Chi-restraints excluded: chain 6 residue 35 ASP Chi-restraints excluded: chain 6 residue 40 CYS 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: 20.0000 chunk 268 optimal weight: 6.9990 chunk 806 optimal weight: 7.9990 chunk 129 optimal weight: 20.0000 chunk 243 optimal weight: 0.0570 chunk 876 optimal weight: 4.9990 chunk 366 optimal weight: 50.0000 chunk 899 optimal weight: 20.0000 chunk 110 optimal weight: 20.0000 chunk 161 optimal weight: 5.9990 overall best weight: 5.2106 ------------------------------------------------------------------------------- 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 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 60 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 ** h 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 18 GLN ** r 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 101 ASN ** g 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 97 GLN ** N 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 38 GLN ** P 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 76 HIS ** Q 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 18 GLN ** 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** ** Y 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.078315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.063651 restraints weight = 566783.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.065441 restraints weight = 186338.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.066483 restraints weight = 96885.977| |-----------------------------------------------------------------------------| r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.8759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.356 161499 Z= 0.323 Angle : 0.823 59.158 240779 Z= 0.436 Chirality : 0.041 0.708 30208 Planarity : 0.007 0.127 13518 Dihedral : 23.713 178.106 79694 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 23.68 Ramachandran Plot: Outliers : 0.64 % Allowed : 11.22 % Favored : 88.14 % Rotamer: Outliers : 7.87 % Allowed : 33.11 % Favored : 59.02 % Cbeta Deviations : 0.02 % 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: -2.24 (0.10), residues: 6551 helix: -0.11 (0.11), residues: 2097 sheet: -1.97 (0.14), residues: 1110 loop : -2.26 (0.10), residues: 3344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP g 102 HIS 0.014 0.002 HIS q 46 PHE 0.043 0.003 PHE 2 18 TYR 0.123 0.003 TYR o 77 ARG 0.031 0.001 ARG F 124 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 59885.98 seconds wall clock time: 1035 minutes 16.56 seconds (62116.56 seconds total)