Starting phenix.real_space_refine on Sun Mar 3 00:19:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wfs_8829/03_2024/5wfs_8829_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wfs_8829/03_2024/5wfs_8829.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wfs_8829/03_2024/5wfs_8829_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wfs_8829/03_2024/5wfs_8829_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wfs_8829/03_2024/5wfs_8829_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wfs_8829/03_2024/5wfs_8829.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wfs_8829/03_2024/5wfs_8829.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wfs_8829/03_2024/5wfs_8829_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wfs_8829/03_2024/5wfs_8829_updated.pdb" } resolution = 3.0 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= 0.001 sd= 0.010 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: 7 Type Number sf(0) Gaussians K 7 8.98 5 P 4805 5.49 5 Mg 1471 5.21 5 S 171 5.16 5 C 76935 2.51 5 N 28329 2.21 5 O 43382 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C GLU 78": "OE1" <-> "OE2" Residue "C GLU 99": "OE1" <-> "OE2" Residue "C ARG 211": "NH1" <-> "NH2" Residue "C GLU 235": "OE1" <-> "OE2" Residue "C ARG 261": "NH1" <-> "NH2" Residue "C ARG 270": "NH1" <-> "NH2" Residue "D ARG 13": "NH1" <-> "NH2" Residue "D GLU 17": "OE1" <-> "OE2" Residue "D ARG 59": "NH1" <-> "NH2" Residue "D ARG 77": "NH1" <-> "NH2" Residue "D ARG 83": "NH1" <-> "NH2" Residue "D GLU 88": "OE1" <-> "OE2" Residue "D GLU 99": "OE1" <-> "OE2" Residue "D GLU 183": "OE1" <-> "OE2" Residue "D ARG 184": "NH1" <-> "NH2" Residue "E GLU 2": "OE1" <-> "OE2" Residue "E ARG 21": "NH1" <-> "NH2" Residue "E ARG 40": "NH1" <-> "NH2" Residue "E ARG 44": "NH1" <-> "NH2" Residue "E ARG 49": "NH1" <-> "NH2" Residue "E GLU 51": "OE1" <-> "OE2" Residue "E ARG 61": "NH1" <-> "NH2" Residue "E ARG 67": "NH1" <-> "NH2" Residue "E ARG 88": "NH1" <-> "NH2" Residue "E ARG 102": "NH1" <-> "NH2" Residue "E GLU 127": "OE1" <-> "OE2" Residue "E GLU 152": "OE1" <-> "OE2" Residue "E GLU 155": "OE1" <-> "OE2" Residue "E ARG 162": "NH1" <-> "NH2" Residue "E ARG 170": "NH1" <-> "NH2" Residue "F ARG 70": "NH1" <-> "NH2" Residue "F ARG 91": "NH1" <-> "NH2" Residue "F ARG 109": "NH1" <-> "NH2" Residue "F ARG 111": "NH1" <-> "NH2" Residue "F ARG 114": "NH1" <-> "NH2" Residue "F ARG 132": "NH1" <-> "NH2" Residue "F GLU 163": "OE1" <-> "OE2" Residue "F GLU 164": "OE1" <-> "OE2" Residue "G ARG 2": "NH1" <-> "NH2" Residue "G GLU 31": "OE1" <-> "OE2" Residue "G ARG 54": "NH1" <-> "NH2" Residue "G ARG 152": "NH1" <-> "NH2" Residue "G ARG 169": "NH1" <-> "NH2" Residue "H GLU 60": "OE1" <-> "OE2" Residue "H GLU 87": "OE1" <-> "OE2" Residue "H GLU 137": "OE1" <-> "OE2" Residue "H GLU 149": "OE1" <-> "OE2" Residue "J ARG 13": "NH1" <-> "NH2" Residue "J ARG 34": "NH1" <-> "NH2" Residue "J ARG 37": "NH1" <-> "NH2" Residue "J ARG 96": "NH1" <-> "NH2" Residue "J ARG 120": "NH1" <-> "NH2" Residue "J GLU 129": "OE1" <-> "OE2" Residue "K GLU 121": "OE1" <-> "OE2" Residue "L ARG 2": "NH1" <-> "NH2" Residue "L GLU 10": "OE1" <-> "OE2" 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 GLU 51": "OE1" <-> "OE2" Residue "L ARG 60": "NH1" <-> "NH2" Residue "L PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 76": "OE1" <-> "OE2" Residue "L ARG 78": "NH1" <-> "NH2" Residue "L ARG 126": "NH1" <-> "NH2" Residue "M ARG 10": "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 GLU 110": "OE1" <-> "OE2" Residue "M ARG 114": "NH1" <-> "NH2" Residue "N ARG 8": "NH1" <-> "NH2" Residue "N ARG 12": "NH1" <-> "NH2" Residue "N ARG 17": "NH1" <-> "NH2" Residue "N ARG 22": "NH1" <-> "NH2" Residue "N ARG 46": "NH1" <-> "NH2" Residue "N ARG 63": "NH1" <-> "NH2" Residue "N ARG 64": "NH1" <-> "NH2" Residue "N ARG 69": "NH1" <-> "NH2" Residue "N ARG 71": "NH1" <-> "NH2" Residue "N PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 82": "OE1" <-> "OE2" Residue "N ARG 96": "NH1" <-> "NH2" 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 GLU 46": "OE1" <-> "OE2" 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 "P GLU 8": "OE1" <-> "OE2" Residue "P GLU 10": "OE1" <-> "OE2" Residue "P ARG 20": "NH1" <-> "NH2" Residue "P GLU 33": "OE1" <-> "OE2" Residue "P ARG 38": "NH1" <-> "NH2" Residue "P GLU 43": "OE1" <-> "OE2" Residue "P ARG 61": "NH1" <-> "NH2" Residue "P GLU 67": "OE1" <-> "OE2" Residue "P GLU 70": "OE1" <-> "OE2" Residue "P ARG 88": "NH1" <-> "NH2" Residue "P TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 32": "NH1" <-> "NH2" Residue "Q TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 47": "NH1" <-> "NH2" Residue "Q GLU 88": "OE1" <-> "OE2" Residue "R TYR 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 16": "OE1" <-> "OE2" 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 ARG 84": "NH1" <-> "NH2" Residue "S ARG 88": "NH1" <-> "NH2" Residue "S ARG 95": "NH1" <-> "NH2" Residue "T GLU 5": "OE1" <-> "OE2" Residue "T ARG 6": "NH1" <-> "NH2" Residue "T GLU 52": "OE1" <-> "OE2" Residue "T ARG 73": "NH1" <-> "NH2" Residue "U ARG 5": "NH1" <-> "NH2" Residue "U ARG 6": "NH1" <-> "NH2" Residue "U ARG 21": "NH1" <-> "NH2" Residue "U ARG 85": "NH1" <-> "NH2" Residue "U ARG 93": "NH1" <-> "NH2" Residue "W ARG 16": "NH1" <-> "NH2" Residue "W ARG 37": "NH1" <-> "NH2" Residue "W ARG 73": "NH1" <-> "NH2" Residue "X ARG 36": "NH1" <-> "NH2" Residue "X ARG 44": "NH1" <-> "NH2" 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 15": "NH1" <-> "NH2" Residue "Z ARG 29": "NH1" <-> "NH2" Residue "Z ARG 30": "NH1" <-> "NH2" Residue "Z ARG 44": "NH1" <-> "NH2" Residue "0 ARG 9": "NH1" <-> "NH2" Residue "0 ARG 15": "NH1" <-> "NH2" Residue "0 ARG 39": "NH1" <-> "NH2" Residue "0 ARG 51": "NH1" <-> "NH2" Residue "1 ARG 43": "NH1" <-> "NH2" Residue "2 ARG 3": "NH1" <-> "NH2" Residue "2 ARG 12": "NH1" <-> "NH2" Residue "2 ARG 14": "NH1" <-> "NH2" Residue "2 ARG 19": "NH1" <-> "NH2" Residue "2 ARG 21": "NH1" <-> "NH2" Residue "2 ARG 33": "NH1" <-> "NH2" Residue "2 ARG 41": "NH1" <-> "NH2" Residue "3 ARG 12": "NH1" <-> "NH2" Residue "3 ARG 29": "NH1" <-> "NH2" Residue "3 ARG 39": "NH1" <-> "NH2" Residue "3 ARG 41": "NH1" <-> "NH2" Residue "4 ARG 12": "NH1" <-> "NH2" Residue "4 ARG 24": "NH1" <-> "NH2" Residue "6 ARG 49": "NH1" <-> "NH2" Residue "6 ARG 56": "NH1" <-> "NH2" Residue "b GLU 51": "OE1" <-> "OE2" Residue "b ARG 94": "NH1" <-> "NH2" Residue "b ARG 107": "NH1" <-> "NH2" Residue "b GLU 139": "OE1" <-> "OE2" Residue "b ARG 224": "NH1" <-> "NH2" Residue "c GLU 57": "OE1" <-> "OE2" Residue "c ARG 64": "NH1" <-> "NH2" Residue "c ARG 106": "NH1" <-> "NH2" Residue "c ARG 130": "NH1" <-> "NH2" Residue "c GLU 151": "OE1" <-> "OE2" Residue "e ARG 44": "NH1" <-> "NH2" Residue "e GLU 115": "OE1" <-> "OE2" Residue "e GLU 150": "OE1" <-> "OE2" Residue "f GLU 16": "OE1" <-> "OE2" Residue "f GLU 23": "OE1" <-> "OE2" Residue "f ARG 38": "NH1" <-> "NH2" Residue "f GLU 65": "OE1" <-> "OE2" Residue "g ARG 2": "NH1" <-> "NH2" Residue "g GLU 62": "OE1" <-> "OE2" Residue "g GLU 66": "OE1" <-> "OE2" Residue "g GLU 73": "OE1" <-> "OE2" Residue "g GLU 89": "OE1" <-> "OE2" Residue "g ARG 95": "NH1" <-> "NH2" Residue "h GLU 90": "OE1" <-> "OE2" Residue "h ARG 113": "NH1" <-> "NH2" Residue "h GLU 123": "OE1" <-> "OE2" Residue "i GLU 88": "OE1" <-> "OE2" Residue "i ARG 123": "NH1" <-> "NH2" Residue "j ARG 7": "NH1" <-> "NH2" Residue "k ARG 12": "NH1" <-> "NH2" Residue "k ARG 55": "NH1" <-> "NH2" Residue "k GLU 67": "OE1" <-> "OE2" Residue "k GLU 82": "OE1" <-> "OE2" Residue "k GLU 93": "OE1" <-> "OE2" Residue "k ARG 97": "NH1" <-> "NH2" Residue "k ARG 126": "NH1" <-> "NH2" Residue "k ARG 127": "NH1" <-> "NH2" Residue "l ARG 35": "NH1" <-> "NH2" Residue "l ARG 53": "NH1" <-> "NH2" Residue "l ARG 55": "NH1" <-> "NH2" Residue "l GLU 61": "OE1" <-> "OE2" Residue "l GLU 75": "OE1" <-> "OE2" Residue "m ARG 70": "NH1" <-> "NH2" Residue "m ARG 89": "NH1" <-> "NH2" Residue "m ARG 108": "NH1" <-> "NH2" Residue "n GLU 9": "OE1" <-> "OE2" Residue "n ARG 12": "NH1" <-> "NH2" Residue "n ARG 90": "NH1" <-> "NH2" Residue "o ARG 83": "NH1" <-> "NH2" Residue "o ARG 88": "NH1" <-> "NH2" Residue "p ARG 8": "NH1" <-> "NH2" Residue "p ARG 14": "NH1" <-> "NH2" Residue "p ARG 25": "NH1" <-> "NH2" Residue "p ARG 28": "NH1" <-> "NH2" Residue "q ARG 5": "NH1" <-> "NH2" Residue "q GLU 25": "OE1" <-> "OE2" Residue "q GLU 48": "OE1" <-> "OE2" Residue "q GLU 51": "OE1" <-> "OE2" Residue "q GLU 79": "OE1" <-> "OE2" Residue "r ARG 11": "NH1" <-> "NH2" Residue "r GLU 19": "OE1" <-> "OE2" Residue "s PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s GLU 72": "OE1" <-> "OE2" Residue "t GLU 14": "OE1" <-> "OE2" Residue "u GLU 7": "OE1" <-> "OE2" Residue "u ARG 34": "NH1" <-> "NH2" Residue "u GLU 35": "OE1" <-> "OE2" Residue "u GLU 38": "OE1" <-> "OE2" Residue "u GLU 62": "OE1" <-> "OE2" Residue "z ARG 44": "NH1" <-> "NH2" Residue "z GLU 117": "OE1" <-> "OE2" Residue "z ARG 123": "NH1" <-> "NH2" Residue "z ARG 154": "NH1" <-> "NH2" Residue "z ARG 171": "NH1" <-> "NH2" Residue "z GLU 183": "OE1" <-> "OE2" Residue "z ARG 223": "NH1" <-> "NH2" Residue "z ARG 233": "NH1" <-> "NH2" Residue "z GLU 240": "OE1" <-> "OE2" Residue "z GLU 249": "OE1" <-> "OE2" Residue "z ARG 269": "NH1" <-> "NH2" Residue "z ARG 279": "NH1" <-> "NH2" Residue "z GLU 285": "OE1" <-> "OE2" Residue "z ARG 288": "NH1" <-> "NH2" Residue "z ARG 318": "NH1" <-> "NH2" Residue "z GLU 342": "OE1" <-> "OE2" Residue "z GLU 345": "OE1" <-> "OE2" Residue "z ARG 373": "NH1" <-> "NH2" Residue "z ARG 377": "NH1" <-> "NH2" Residue "z ARG 381": "NH1" <-> "NH2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 155100 Number of models: 1 Model: "" Number of chains: 114 Chain: "A" Number of atoms: 62277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2900, 62277 Classifications: {'RNA': 2900} Modifications used: {'p5*END': 1, 'rna2p': 7, 'rna2p_pur': 262, 'rna2p_pyr': 130, 'rna3p': 17, 'rna3p_pur': 1405, 'rna3p_pyr': 1078} Link IDs: {'rna2p': 399, 'rna3p': 2500} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 3 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': 8, 'rna2p_pyr': 5, 'rna3p_pur': 57, 'rna3p_pyr': 50} Link IDs: {'rna2p': 13, 'rna3p': 106} 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: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1557 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 201} Chain: "E" Number of atoms: 1544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1544 Classifications: {'peptide': 200} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 194} 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: 1304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1304 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 8, 'TRANS': 165} 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: 1120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1120 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 6, 'TRANS': 134} 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: 1043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1043 Classifications: {'peptide': 143} 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: 951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 951 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 4, 'TRANS': 114} 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: 933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 933 Classifications: {'peptide': 115} Link IDs: {'TRANS': 114} Chain: "R" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 810 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 1, 'TRANS': 100} Chain: "S" Number of atoms: 845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 845 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 2, 'TRANS': 106} Chain: "T" Number of atoms: 730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 730 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 1, 'TRANS': 90} 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: 739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 739 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "W" Number of atoms: 572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 572 Classifications: {'peptide': 75} 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: 494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 494 Classifications: {'peptide': 60} Link IDs: {'TRANS': 59} Chain: "Z" Number of atoms: 434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 434 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 2, 'TRANS': 53} Chain: "0" Number of atoms: 434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 434 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 1, 'TRANS': 53} Chain: "1" Number of atoms: 417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 417 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 2, 'TRANS': 48} Chain: "2" Number of atoms: 367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 367 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 1, 'TRANS': 43} 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: "a" Number of atoms: 33050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1540, 33050 Classifications: {'RNA': 1540} Modifications used: {'rna2p': 1, 'rna2p_pur': 117, 'rna2p_pyr': 74, 'rna3p': 10, 'rna3p_pur': 752, 'rna3p_pyr': 586} Link IDs: {'rna2p': 192, 'rna3p': 1347} 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: "c" Number of atoms: 1624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1624 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 7, 'TRANS': 198} Chain: "d" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1643 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 198} Chain: "e" Number of atoms: 1164 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 157, 1156 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 5, 'TRANS': 151} Conformer: "B" Number of residues, atoms: 157, 1156 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 5, 'TRANS': 151} bond proxies already assigned to first conformer: 1160 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: "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: "h" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 979 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "i" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1022 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "j" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 786 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 5, 'TRANS': 92} 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: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 940 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 7, 'TRANS': 113} Chain: "m" Number of atoms: 891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 891 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 4, 'TRANS': 110} Chain: "n" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 810 Classifications: {'peptide': 101} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 96} 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: 535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 535 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 2, 'TRANS': 62} 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: "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: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 544 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 2, 'TRANS': 62} 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': 1, 'rna3p': 3, 'rna3p_pur': 34, 'rna3p_pyr': 33} Link IDs: {'rna2p': 6, 'rna3p': 70} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 2 Chain: "w" 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': 6, 'rna2p_pyr': 4, 'rna3p': 3, 'rna3p_pur': 33, 'rna3p_pyr': 30} Link IDs: {'rna2p': 10, 'rna3p': 66} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 2 Chain: "x" Number of atoms: 252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 252 Classifications: {'RNA': 12} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 1, 'rna3p_pur': 3, 'rna3p_pyr': 6} Link IDs: {'rna2p': 2, 'rna3p': 9} Chain: "y" Number of atoms: 1632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1632 Classifications: {'RNA': 76} Modifications used: {'p5*END': 1, 'rna2p': 2, 'rna2p_pur': 6, 'rna2p_pyr': 2, 'rna3p': 7, 'rna3p_pur': 31, 'rna3p_pyr': 28} Link IDs: {'rna2p': 9, 'rna3p': 66} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 4 Chain: "z" Number of atoms: 3031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 3031 Classifications: {'peptide': 393} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 372} Chain: "A" Number of atoms: 1027 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1018, 1027 Unusual residues: {' K': 6, ' MG': 1011} Classifications: {'peptide': 1, 'undetermined': 1017} Link IDs: {None: 1017} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 37 Unusual residues: {' MG': 37} Classifications: {'undetermined': 37} Link IDs: {None: 36} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "0" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "2" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "a" Number of atoms: 393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 393 Unusual residues: {' K': 1, ' MG': 392} Classifications: {'undetermined': 393} Link IDs: {None: 392} Chain: "d" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "e" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "i" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "u" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "v" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Unusual residues: {' MG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "w" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "x" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "y" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "z" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 45 Unusual residues: {' MG': 2, 'GTP': 1} Classifications: {'peptide': 1, 'undetermined': 3} Link IDs: {None: 3} Chain: "A" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 828, 828 Classifications: {'water': 828} Link IDs: {None: 827} Chain: "B" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 29 Classifications: {'water': 29} Link IDs: {None: 28} Chain: "C" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "D" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "E" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "J" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "L" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "O" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "Q" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "S" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "W" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "X" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "Y" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "0" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "1" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "2" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "3" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "a" Number of atoms: 253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 253 Classifications: {'water': 253} Link IDs: {None: 252} Chain: "c" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "i" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "j" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "l" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "m" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "o" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "s" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "u" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "v" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "w" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "x" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "y" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 62.35, per 1000 atoms: 0.40 Number of scatterers: 155100 At special positions: 0 Unit cell: (277.34, 268.52, 241.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) K 7 19.00 S 171 16.00 P 4805 15.00 Mg 1471 11.99 O 43382 8.00 N 28329 7.00 C 76935 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 65.58 Conformation dependent library (CDL) restraints added in 9.0 seconds 12438 Ramachandran restraints generated. 6219 Oldfield, 0 Emsley, 6219 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11606 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: 193 helices and 78 sheets defined 38.3% alpha, 19.3% beta 1405 base pairs and 2390 stacking pairs defined. Time for finding SS restraints: 85.42 Creating SS restraints... Processing helix chain 'C' and resid 9 through 15 removed outlier: 7.546A pdb=" N HIS C 14 " --> pdb=" O PRO C 10 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N VAL C 15 " --> pdb=" O GLY C 11 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 34 removed outlier: 4.111A pdb=" N LEU C 33 " --> pdb=" O PHE C 29 " (cutoff:3.500A) removed outlier: 5.344A 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 Proline residue: C 135 - end of helix Processing helix chain 'C' and resid 206 through 214 removed outlier: 3.985A pdb=" N ALA C 210 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG C 213 " --> pdb=" O ALA C 209 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLY C 214 " --> pdb=" O ALA C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 225 removed outlier: 3.595A pdb=" N MET C 224 " --> pdb=" O ARG C 220 " (cutoff:3.500A) removed outlier: 5.022A 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: 6.377A pdb=" N ASP C 263 " --> pdb=" O ASN C 259 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N LYS C 264 " --> pdb=" O LYS C 260 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N PHE C 265 " --> pdb=" O ARG C 261 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ILE C 266 " --> pdb=" O THR C 262 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N VAL C 267 " --> pdb=" O ASP C 263 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 259 through 267' Processing helix chain 'D' and resid 56 through 61 removed outlier: 5.941A pdb=" N THR D 61 " --> pdb=" O ALA D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 72 removed outlier: 4.004A pdb=" N ALA D 71 " --> pdb=" O HIS D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 103 removed outlier: 4.203A pdb=" N ALA D 102 " --> pdb=" O VAL D 98 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N ASP D 103 " --> pdb=" O GLU D 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 98 through 103' Processing helix chain 'D' and resid 120 through 125 Processing helix chain 'E' and resid 15 through 20 Processing helix chain 'E' and resid 24 through 40 removed outlier: 3.849A pdb=" N ARG E 40 " --> pdb=" O ALA E 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 53 removed outlier: 6.337A pdb=" N THR E 53 " --> pdb=" O ARG E 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 116 removed outlier: 4.165A pdb=" N VAL E 113 " --> pdb=" O LEU E 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 130 through 142 removed outlier: 3.614A pdb=" N LEU E 134 " --> pdb=" O LYS E 130 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ASP E 140 " --> pdb=" O GLN E 136 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N MET E 141 " --> pdb=" O LYS E 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 154 through 163 removed outlier: 3.619A pdb=" N ALA E 160 " --> pdb=" O ASN E 156 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ARG E 162 " --> pdb=" O PHE E 158 " (cutoff:3.500A) removed outlier: 5.839A 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 Processing helix chain 'F' and resid 1 through 10 Processing helix chain 'F' and resid 11 through 20 removed outlier: 3.965A pdb=" N MET F 16 " --> pdb=" O VAL F 12 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N THR F 17 " --> pdb=" O LYS F 13 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLU F 18 " --> pdb=" O LYS F 14 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N PHE F 19 " --> pdb=" O LEU F 15 " (cutoff:3.500A) Processing helix chain 'F' and resid 41 through 46 removed outlier: 3.657A pdb=" N ASP F 45 " --> pdb=" O GLU F 41 " (cutoff:3.500A) removed outlier: 4.011A 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 61 removed outlier: 4.514A pdb=" N GLY F 61 " --> pdb=" O ALA F 57 " (cutoff:3.500A) Processing helix chain 'F' and resid 92 through 110 removed outlier: 3.753A pdb=" N TRP F 96 " --> pdb=" O GLY F 92 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE F 105 " --> pdb=" O ARG F 101 " (cutoff:3.500A) removed outlier: 4.578A 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 161 through 173 removed outlier: 3.810A pdb=" N ALA F 167 " --> pdb=" O GLU F 163 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LEU F 168 " --> pdb=" O GLU F 164 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU F 169 " --> pdb=" O GLY F 165 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N PHE F 172 " --> pdb=" O LEU F 168 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ASP F 173 " --> pdb=" O LEU F 169 " (cutoff:3.500A) Processing helix chain 'F' and resid 133 through 138 removed outlier: 4.423A pdb=" N ILE F 136 " --> pdb=" O GLU F 133 " (cutoff:3.500A) Proline residue: F 138 - end of helix Processing helix chain 'G' and resid 1 through 7 removed outlier: 3.565A pdb=" N LYS G 5 " --> pdb=" O SER G 1 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ALA G 6 " --> pdb=" O ARG G 2 " (cutoff:3.500A) Proline residue: G 7 - end of helix No H-bonds generated for 'chain 'G' and resid 1 through 7' Processing helix chain 'G' and resid 59 through 80 removed outlier: 4.060A pdb=" N GLN G 63 " --> pdb=" O ASP G 59 " (cutoff:3.500A) Processing helix chain 'G' and resid 136 through 152 removed outlier: 3.657A pdb=" N ILE G 140 " --> pdb=" O ASP G 136 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N TYR G 150 " --> pdb=" O ASP G 146 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ARG G 151 " --> pdb=" O LEU G 147 " (cutoff:3.500A) Processing helix chain 'H' and resid 22 through 28 Processing helix chain 'H' and resid 29 through 34 Processing helix chain 'H' and resid 40 through 50 removed outlier: 4.944A pdb=" N ILE H 44 " --> pdb=" O THR H 40 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N GLU H 45 " --> pdb=" O LYS H 41 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA H 49 " --> pdb=" O GLU H 45 " (cutoff:3.500A) Processing helix chain 'H' and resid 53 through 73 removed outlier: 5.120A pdb=" N LYS H 57 " --> pdb=" O GLU H 53 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU H 70 " --> pdb=" O ASN H 66 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LYS H 71 " --> pdb=" O ALA H 67 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N ASN H 73 " --> pdb=" O ALA H 69 " (cutoff:3.500A) Processing helix chain 'H' and resid 95 through 107 removed outlier: 3.837A pdb=" N ILE H 99 " --> pdb=" O GLY H 95 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA H 106 " --> pdb=" O ALA H 102 " (cutoff:3.500A) Processing helix chain 'I' and resid 23 through 29 removed outlier: 4.692A pdb=" N LEU I 27 " --> pdb=" O VAL I 23 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY I 28 " --> pdb=" O GLY I 24 " (cutoff:3.500A) Processing helix chain 'I' and resid 33 through 49 removed outlier: 4.961A pdb=" N PHE I 37 " --> pdb=" O ASN I 33 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N CYS I 38 " --> pdb=" O ILE I 34 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LYS I 39 " --> pdb=" O MET I 35 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N PHE I 41 " --> pdb=" O PHE I 37 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ASN I 42 " --> pdb=" O CYS I 38 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA I 43 " --> pdb=" O LYS I 39 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N LYS I 44 " --> pdb=" O ALA I 40 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N THR I 45 " --> pdb=" O PHE I 41 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASP I 46 " --> pdb=" O ASN I 42 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N SER I 47 " --> pdb=" O ALA I 43 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ILE I 48 " --> pdb=" O LYS I 44 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU I 49 " --> pdb=" O THR I 45 " (cutoff:3.500A) Processing helix chain 'I' and resid 74 through 83 removed outlier: 3.513A pdb=" N LYS I 80 " --> pdb=" O ALA I 76 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N LYS I 81 " --> pdb=" O VAL I 77 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ALA I 83 " --> pdb=" O LEU I 79 " (cutoff:3.500A) Processing helix chain 'I' and resid 101 through 114 removed outlier: 3.754A pdb=" N LEU I 105 " --> pdb=" O SER I 101 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU I 107 " --> pdb=" O ALA I 103 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLN I 110 " --> pdb=" O GLN I 106 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N THR I 111 " --> pdb=" O GLU I 107 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N LYS I 112 " --> pdb=" O ILE I 108 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ALA I 113 " --> pdb=" O ALA I 109 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N ALA I 114 " --> pdb=" O GLN I 110 " (cutoff:3.500A) Processing helix chain 'I' and resid 120 through 136 removed outlier: 3.677A pdb=" N MET I 124 " --> pdb=" O ASP I 120 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG I 126 " --> pdb=" O GLU I 122 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N SER I 127 " --> pdb=" O ALA I 123 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ALA I 132 " --> pdb=" O ILE I 128 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ARG I 133 " --> pdb=" O GLU I 129 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N SER I 134 " --> pdb=" O GLY I 130 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N MET I 135 " --> pdb=" O THR I 131 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N GLY I 136 " --> pdb=" O ALA I 132 " (cutoff:3.500A) Processing helix chain 'I' and resid 91 through 96 removed outlier: 4.138A pdb=" N LYS I 96 " --> pdb=" O LYS I 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 91 through 96' Processing helix chain 'J' and resid 24 through 38 removed outlier: 3.578A pdb=" N GLU J 31 " --> pdb=" O ARG J 27 " (cutoff:3.500A) Processing helix chain 'J' and resid 88 through 96 Processing helix chain 'J' and resid 97 through 110 removed outlier: 4.413A pdb=" N ILE J 101 " --> pdb=" O PRO J 97 " (cutoff:3.500A) removed outlier: 3.908A 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: 3.944A pdb=" N LYS J 121 " --> pdb=" O ALA J 117 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N LEU J 122 " --> pdb=" O MET J 118 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N LYS J 123 " --> pdb=" O PHE J 119 " (cutoff:3.500A) Processing helix chain 'J' and resid 67 through 72 removed outlier: 4.482A 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 109 through 119 removed outlier: 5.574A pdb=" N MET K 113 " --> pdb=" O SER K 109 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N LYS K 114 " --> pdb=" O GLU K 110 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N ILE K 115 " --> pdb=" O LYS K 111 " (cutoff:3.500A) Processing helix chain 'L' and resid 37 through 42 removed outlier: 5.582A pdb=" N SER L 42 " --> pdb=" O GLN L 38 " (cutoff:3.500A) Processing helix chain 'L' and resid 56 through 62 Proline residue: L 62 - end of helix Processing helix chain 'L' and resid 68 through 75 removed outlier: 4.032A pdb=" N ALA L 72 " --> pdb=" O SER L 68 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ILE L 73 " --> pdb=" O ARG L 69 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR L 74 " --> pdb=" O LYS L 70 " (cutoff:3.500A) removed outlier: 5.745A 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: 4.011A pdb=" N LEU L 82 " --> pdb=" O ARG L 78 " (cutoff:3.500A) removed outlier: 4.866A 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: 6.089A pdb=" N LEU L 95 " --> pdb=" O ASP L 91 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ASN L 99 " --> pdb=" O LEU L 95 " (cutoff:3.500A) Processing helix chain 'L' and resid 128 through 139 Processing helix chain 'M' and resid 42 through 58 Processing helix chain 'M' and resid 109 through 125 removed outlier: 3.678A pdb=" N GLU M 115 " --> pdb=" O GLU M 111 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA M 116 " --> pdb=" O LEU M 112 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU M 119 " --> pdb=" O GLU M 115 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LYS M 123 " --> pdb=" O LEU M 119 " (cutoff:3.500A) Proline residue: M 125 - end of helix Processing helix chain 'N' and resid 13 through 32 removed outlier: 3.513A pdb=" N GLY N 26 " --> pdb=" O ARG N 22 " (cutoff:3.500A) Processing helix chain 'N' and resid 37 through 57 removed outlier: 4.420A pdb=" N ARG N 46 " --> pdb=" O LYS N 42 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N VAL N 47 " --> pdb=" O GLU N 43 " (cutoff:3.500A) Proline residue: N 50 - end of helix removed outlier: 3.505A pdb=" N LYS N 56 " --> pdb=" O ILE N 52 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N THR N 57 " --> pdb=" O THR N 53 " (cutoff:3.500A) Processing helix chain 'N' and resid 59 through 71 removed outlier: 5.246A pdb=" N ARG N 63 " --> pdb=" O SER N 59 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N THR N 70 " --> pdb=" O ALA N 66 " (cutoff:3.500A) Processing helix chain 'N' and resid 72 through 88 removed outlier: 4.391A pdb=" N PHE N 80 " --> pdb=" O VAL N 76 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ASN N 81 " --> pdb=" O ALA N 77 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N LEU N 83 " --> pdb=" O LEU N 79 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N GLY N 84 " --> pdb=" O PHE N 80 " (cutoff:3.500A) Proline residue: N 85 - end of helix removed outlier: 3.604A pdb=" N ALA N 88 " --> pdb=" O GLY N 84 " (cutoff:3.500A) Processing helix chain 'O' and resid 2 through 22 removed outlier: 4.277A pdb=" N ALA O 6 " --> pdb=" O ASP O 2 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N ARG O 13 " --> pdb=" O ARG O 9 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N ALA O 14 " --> pdb=" O ARG O 10 " (cutoff:3.500A) Processing helix chain 'O' and resid 55 through 63 removed outlier: 4.688A pdb=" N GLN O 61 " --> pdb=" O ALA O 57 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU O 62 " --> pdb=" O ILE O 58 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N LYS O 63 " --> pdb=" O ALA O 59 " (cutoff:3.500A) Processing helix chain 'O' and resid 67 through 86 removed outlier: 3.725A pdb=" N ALA O 79 " --> pdb=" O GLY O 75 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLU O 84 " --> pdb=" O GLU O 80 " (cutoff:3.500A) Processing helix chain 'O' and resid 101 through 114 removed outlier: 3.605A pdb=" N GLY O 114 " --> pdb=" O ALA O 110 " (cutoff:3.500A) Processing helix chain 'P' and resid 1 through 13 removed outlier: 3.913A pdb=" N GLN P 11 " --> pdb=" O LEU P 7 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N LYS P 13 " --> pdb=" O GLN P 9 " (cutoff:3.500A) Processing helix chain 'P' and resid 96 through 103 removed outlier: 4.604A pdb=" N ARG P 100 " --> pdb=" O LEU P 96 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N GLU P 101 " --> pdb=" O TYR P 97 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG P 102 " --> pdb=" O TYR P 98 " (cutoff:3.500A) removed outlier: 4.852A 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: 3.554A pdb=" N ILE Q 16 " --> pdb=" O ARG Q 12 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS Q 21 " --> pdb=" O LEU Q 17 " (cutoff:3.500A) Processing helix chain 'Q' and resid 25 through 30 removed outlier: 3.502A pdb=" N ARG Q 29 " --> pdb=" O GLY Q 25 " (cutoff:3.500A) Processing helix chain 'Q' and resid 31 through 36 removed outlier: 4.439A pdb=" N GLN Q 36 " --> pdb=" O ARG Q 32 " (cutoff:3.500A) Processing helix chain 'Q' and resid 38 through 72 removed outlier: 3.944A pdb=" N ARG Q 50 " --> pdb=" O TYR Q 46 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N LYS Q 53 " --> pdb=" O ARG Q 49 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ARG Q 54 " --> pdb=" O ARG Q 50 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ARG Q 57 " --> pdb=" O LYS Q 53 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ASN Q 71 " --> pdb=" O ALA Q 67 " (cutoff:3.500A) Processing helix chain 'Q' and resid 74 through 86 removed outlier: 3.513A pdb=" N ASN Q 80 " --> pdb=" O SER Q 76 " (cutoff:3.500A) Processing helix chain 'Q' and resid 90 through 101 Processing helix chain 'Q' and resid 102 through 115 removed outlier: 4.001A pdb=" N ALA Q 107 " --> pdb=" O VAL Q 103 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU Q 108 " --> pdb=" O ALA Q 104 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ALA Q 115 " --> pdb=" O LYS Q 111 " (cutoff:3.500A) Processing helix chain 'S' and resid 13 through 25 removed outlier: 3.859A pdb=" N VAL S 20 " --> pdb=" O LYS S 16 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N LEU S 23 " --> pdb=" O LEU S 19 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ILE S 24 " --> pdb=" O VAL S 20 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ARG S 25 " --> pdb=" O ALA S 21 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 39 Processing helix chain 'S' and resid 41 through 61 removed outlier: 3.811A pdb=" N VAL S 45 " --> pdb=" O LYS S 41 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL S 50 " --> pdb=" O LEU S 46 " (cutoff:3.500A) Processing helix chain 'T' and resid 4 through 11 removed outlier: 6.802A pdb=" N LEU T 8 " --> pdb=" O GLU T 4 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N LYS T 9 " --> pdb=" O GLU T 5 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL T 10 " --> pdb=" O ARG T 6 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N LEU T 11 " --> pdb=" O LEU T 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 4 through 11' Processing helix chain 'T' and resid 17 through 26 removed outlier: 3.552A pdb=" N MET T 24 " --> pdb=" O ALA T 20 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLU T 25 " --> pdb=" O SER T 21 " (cutoff:3.500A) Processing helix chain 'T' and resid 39 through 50 Processing helix chain 'U' and resid 65 through 70 removed outlier: 3.921A pdb=" N VAL U 69 " --> pdb=" O GLN U 65 " (cutoff:3.500A) removed outlier: 5.067A 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: 3.607A pdb=" N ALA V 23 " --> pdb=" O ARG V 19 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ASN V 24 " --> pdb=" O LEU V 20 " (cutoff:3.500A) Processing helix chain 'V' and resid 43 through 53 removed outlier: 3.880A pdb=" N VAL V 47 " --> pdb=" O ASP V 43 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASN V 49 " --> pdb=" O ASP V 45 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ALA V 52 " --> pdb=" O MET V 48 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N LYS V 53 " --> pdb=" O ASN V 49 " (cutoff:3.500A) Processing helix chain 'V' and resid 54 through 59 removed outlier: 4.492A pdb=" N SER V 58 " --> pdb=" O ALA V 54 " (cutoff:3.500A) Processing helix chain 'X' and resid 51 through 62 removed outlier: 4.242A pdb=" N GLY X 62 " --> pdb=" O ILE X 58 " (cutoff:3.500A) Processing helix chain 'X' and resid 63 through 74 removed outlier: 3.520A pdb=" N ARG X 73 " --> pdb=" O GLU X 69 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLY X 74 " --> pdb=" O LEU X 70 " (cutoff:3.500A) Processing helix chain 'Y' and resid 1 through 8 removed outlier: 4.101A pdb=" N ARG Y 7 " --> pdb=" O ALA Y 3 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N GLU Y 8 " --> pdb=" O LYS Y 4 " (cutoff:3.500A) Processing helix chain 'Y' and resid 9 through 35 removed outlier: 3.817A pdb=" N LEU Y 14 " --> pdb=" O SER Y 10 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ASN Y 15 " --> pdb=" O VAL Y 11 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N THR Y 16 " --> pdb=" O GLU Y 12 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ARG Y 23 " --> pdb=" O LEU Y 19 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N GLU Y 24 " --> pdb=" O ASN Y 20 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N GLN Y 25 " --> pdb=" O LEU Y 21 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N PHE Y 26 " --> pdb=" O LEU Y 22 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ASN Y 27 " --> pdb=" O ARG Y 23 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA Y 33 " --> pdb=" O ARG Y 29 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY Y 35 " --> pdb=" O GLN Y 31 " (cutoff:3.500A) Processing helix chain 'Y' and resid 40 through 59 removed outlier: 4.352A pdb=" N LYS Y 44 " --> pdb=" O SER Y 40 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ASN Y 58 " --> pdb=" O LYS Y 54 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N GLU Y 59 " --> pdb=" O THR Y 55 " (cutoff:3.500A) Processing helix chain 'Z' and resid 16 through 27 removed outlier: 3.521A pdb=" N LEU Z 24 " --> pdb=" O LYS Z 20 " (cutoff:3.500A) Processing helix chain 'Z' and resid 40 through 51 removed outlier: 3.500A pdb=" N ARG Z 44 " --> pdb=" O THR Z 40 " (cutoff:3.500A) Processing helix chain '0' and resid 8 through 18 removed outlier: 4.829A pdb=" N HIS 0 18 " --> pdb=" O MET 0 14 " (cutoff:3.500A) Processing helix chain '2' and resid 8 through 16 Processing helix chain '2' and resid 17 through 25 removed outlier: 4.253A pdb=" N THR 2 24 " --> pdb=" O ALA 2 20 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N LYS 2 25 " --> pdb=" O ARG 2 21 " (cutoff:3.500A) Processing helix chain '2' and resid 26 through 38 removed outlier: 3.516A pdb=" N LEU 2 31 " --> pdb=" O GLY 2 27 " (cutoff:3.500A) Processing helix chain '3' and resid 6 through 13 removed outlier: 3.526A pdb=" N ARG 3 12 " --> pdb=" O GLY 3 8 " (cutoff:3.500A) Processing helix chain '3' and resid 31 through 36 removed outlier: 4.651A pdb=" N LYS 3 35 " --> pdb=" O ILE 3 31 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N ALA 3 36 " --> pdb=" O LEU 3 32 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 31 through 36' Processing helix chain '3' and resid 37 through 45 Proline residue: 3 45 - end of helix Processing helix chain '3' and resid 50 through 62 removed outlier: 4.794A pdb=" N GLY 3 55 " --> pdb=" O LYS 3 51 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N LEU 3 56 " --> pdb=" O GLY 3 52 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N VAL 3 57 " --> pdb=" O ASP 3 53 " (cutoff:3.500A) Proline residue: 3 62 - end of helix Processing helix chain '5' and resid 3 through 21 Processing helix chain '5' and resid 33 through 48 removed outlier: 3.794A pdb=" N MET 5 38 " --> pdb=" O THR 5 34 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N THR 5 39 " --> pdb=" O VAL 5 35 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU 5 40 " --> pdb=" O ASP 5 36 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU 5 41 " --> pdb=" O LYS 5 37 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N ARG 5 42 " --> pdb=" O MET 5 38 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ALA 5 44 " --> pdb=" O GLU 5 40 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLY 5 45 " --> pdb=" O LEU 5 41 " (cutoff:3.500A) Processing helix chain '5' and resid 62 through 70 removed outlier: 4.310A pdb=" N GLY 5 66 " --> pdb=" O ARG 5 62 " (cutoff:3.500A) Proline residue: 5 68 - end of helix Processing helix chain '5' and resid 73 through 79 removed outlier: 4.433A pdb=" N VAL 5 77 " --> pdb=" O LYS 5 73 " (cutoff:3.500A) removed outlier: 3.676A 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 73 through 79' Processing helix chain '5' and resid 94 through 106 removed outlier: 3.756A pdb=" N GLU 5 98 " --> pdb=" O ARG 5 94 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N PHE 5 99 " --> pdb=" O LEU 5 95 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ALA 5 100 " --> pdb=" O PHE 5 96 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ALA 5 104 " --> pdb=" O ALA 5 100 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N PHE 5 106 " --> pdb=" O ALA 5 102 " (cutoff:3.500A) Processing helix chain '5' and resid 109 through 114 removed outlier: 6.584A pdb=" N ALA 5 112 " --> pdb=" O LYS 5 109 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLU 5 114 " --> pdb=" O ALA 5 111 " (cutoff:3.500A) Processing helix chain '6' and resid 43 through 53 removed outlier: 4.429A pdb=" N GLN 6 48 " --> pdb=" O PHE 6 44 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ALA 6 52 " --> pdb=" O GLN 6 48 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N THR 6 53 " --> pdb=" O ARG 6 49 " (cutoff:3.500A) Processing helix chain '6' and resid 55 through 65 removed outlier: 4.140A pdb=" N ARG 6 59 " --> pdb=" O GLY 6 55 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG 6 63 " --> pdb=" O ARG 6 59 " (cutoff:3.500A) Processing helix chain 'b' and resid 42 through 63 Proline residue: b 47 - end of helix Processing helix chain 'b' and resid 73 through 87 removed outlier: 4.239A pdb=" N GLU b 77 " --> pdb=" O ARG b 73 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ALA b 78 " --> pdb=" O ALA b 74 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N CYS b 86 " --> pdb=" O ALA b 82 " (cutoff:3.500A) Processing helix chain 'b' and resid 102 through 122 removed outlier: 3.554A pdb=" N VAL b 106 " --> pdb=" O ASN b 102 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N GLN b 108 " --> pdb=" O LYS b 104 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER b 109 " --> pdb=" O THR b 105 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N THR b 118 " --> pdb=" O LYS b 114 " (cutoff:3.500A) Processing helix chain 'b' and resid 129 through 147 removed outlier: 3.801A pdb=" N SER b 146 " --> pdb=" O LYS b 142 " (cutoff:3.500A) Processing helix chain 'b' and resid 164 through 169 Processing helix chain 'b' and resid 170 through 179 removed outlier: 3.940A pdb=" N LEU b 178 " --> pdb=" O GLU b 174 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N GLY b 179 " --> pdb=" O ALA b 175 " (cutoff:3.500A) Processing helix chain 'b' and resid 205 through 225 removed outlier: 3.595A pdb=" N THR b 210 " --> pdb=" O ILE b 206 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG b 221 " --> pdb=" O ALA b 217 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ARG b 224 " --> pdb=" O VAL b 220 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N SER b 225 " --> pdb=" O ARG b 221 " (cutoff:3.500A) Processing helix chain 'b' and resid 148 through 153 removed outlier: 3.726A pdb=" N LYS b 151 " --> pdb=" O GLY b 148 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ASP b 152 " --> pdb=" O GLY b 149 " (cutoff:3.500A) Processing helix chain 'c' and resid 5 through 11 removed outlier: 3.873A pdb=" N ARG c 10 " --> pdb=" O PRO c 6 " (cutoff:3.500A) Processing helix chain 'c' and resid 27 through 47 removed outlier: 3.949A pdb=" N ALA c 47 " --> pdb=" O THR c 43 " (cutoff:3.500A) Processing helix chain 'c' and resid 71 through 77 removed outlier: 3.769A pdb=" N VAL c 75 " --> pdb=" O ARG c 71 " (cutoff:3.500A) Processing helix chain 'c' and resid 80 through 95 removed outlier: 3.689A pdb=" N GLU c 84 " --> pdb=" O GLY c 80 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL c 89 " --> pdb=" O LYS c 85 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ILE c 93 " --> pdb=" O VAL c 89 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLY c 95 " --> pdb=" O ALA c 91 " (cutoff:3.500A) Processing helix chain 'c' and resid 111 through 126 removed outlier: 3.524A pdb=" N ARG c 125 " --> pdb=" O SER c 121 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ARG c 126 " --> pdb=" O GLN c 122 " (cutoff:3.500A) Processing helix chain 'c' and resid 128 through 144 removed outlier: 4.016A pdb=" N ARG c 135 " --> pdb=" O ARG c 131 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N MET c 141 " --> pdb=" O VAL c 137 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ARG c 142 " --> pdb=" O GLN c 138 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEU c 143 " --> pdb=" O ASN c 139 " (cutoff:3.500A) Processing helix chain 'd' and resid 6 through 15 removed outlier: 3.936A pdb=" N LEU d 10 " --> pdb=" O PRO d 6 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N SER d 11 " --> pdb=" O LYS d 7 " (cutoff:3.500A) Processing helix chain 'd' and resid 48 through 65 removed outlier: 3.508A pdb=" N TYR d 64 " --> pdb=" O VAL d 60 " (cutoff:3.500A) Processing helix chain 'd' and resid 67 through 82 removed outlier: 5.295A pdb=" N LYS d 82 " --> pdb=" O ALA d 78 " (cutoff:3.500A) Processing helix chain 'd' and resid 84 through 96 removed outlier: 3.665A pdb=" N LEU d 90 " --> pdb=" O GLY d 86 " (cutoff:3.500A) removed outlier: 3.813A 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: 4.456A pdb=" N LYS d 120 " --> pdb=" O LEU d 116 " (cutoff:3.500A) Processing helix chain 'd' and resid 151 through 165 removed outlier: 4.019A pdb=" N ALA d 156 " --> pdb=" O SER d 152 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA d 157 " --> pdb=" O ARG d 153 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU d 159 " --> pdb=" O LYS d 155 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU d 160 " --> pdb=" O ALA d 156 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA d 161 " --> pdb=" O ALA d 157 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLU d 162 " --> pdb=" O LEU d 158 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N GLN d 163 " --> pdb=" O GLU d 159 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARG d 164 " --> pdb=" O LEU d 160 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N GLU d 165 " --> pdb=" O ALA d 161 " (cutoff:3.500A) Processing helix chain 'd' and resid 186 through 191 removed outlier: 3.811A pdb=" N LEU d 190 " --> pdb=" O GLU d 186 " (cutoff:3.500A) removed outlier: 5.180A 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: 4.547A pdb=" N ILE d 199 " --> pdb=" O ASN d 195 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N TYR d 203 " --> pdb=" O ILE d 199 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYS d 205 " --> pdb=" O GLU d 201 " (cutoff:3.500A) Processing helix chain 'e' and resid 54 through 70 removed outlier: 3.556A pdb=" N GLN e 60 " --> pdb=" O PRO e 56 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS e 65 " --> pdb=" O LYS e 61 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ARG e 68 " --> pdb=" O GLU e 64 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N MET e 70 " --> pdb=" O ALA e 66 " (cutoff:3.500A) Processing helix chain 'e' and resid 108 through 118 removed outlier: 6.240A pdb=" N ALA e 112 " --> pdb=" O GLY e 108 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL e 113 " --> pdb=" O ALA e 109 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU e 114 " --> pdb=" O MET e 110 " (cutoff:3.500A) Processing helix chain 'e' and resid 131 through 146 Processing helix chain 'e' and resid 148 through 157 Processing helix chain 'e' and resid 159 through 165 removed outlier: 3.540A pdb=" N LEU e 164 " --> pdb=" O VAL e 160 " (cutoff:3.500A) Processing helix chain 'f' and resid 14 through 33 removed outlier: 3.731A pdb=" N VAL f 18 " --> pdb=" O GLN f 14 " (cutoff:3.500A) Proline residue: f 19 - end of helix removed outlier: 3.563A pdb=" N GLU f 23 " --> pdb=" O PRO f 19 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLY f 31 " --> pdb=" O ALA f 27 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ALA f 32 " --> pdb=" O ALA f 28 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N GLU f 33 " --> pdb=" O ILE f 29 " (cutoff:3.500A) Processing helix chain 'f' and resid 67 through 82 removed outlier: 3.525A pdb=" N PHE f 78 " --> pdb=" O LEU f 74 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ARG f 79 " --> pdb=" O GLU f 75 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ASN f 81 " --> pdb=" O THR f 77 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N ASP f 82 " --> pdb=" O PHE f 78 " (cutoff:3.500A) Processing helix chain 'g' and resid 19 through 30 removed outlier: 5.985A pdb=" N ALA g 23 " --> pdb=" O SER g 19 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASN g 27 " --> pdb=" O ALA g 23 " (cutoff:3.500A) Processing helix chain 'g' and resid 34 through 54 removed outlier: 3.501A pdb=" N ARG g 52 " --> pdb=" O THR g 48 " (cutoff:3.500A) Processing helix chain 'g' and resid 56 through 69 removed outlier: 4.079A pdb=" N ALA g 60 " --> pdb=" O SER g 56 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ALA g 64 " --> pdb=" O ALA g 60 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ASN g 67 " --> pdb=" O VAL g 63 " (cutoff:3.500A) Processing helix chain 'g' and resid 91 through 111 removed outlier: 4.005A pdb=" N ASN g 96 " --> pdb=" O PRO g 92 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ALA g 97 " --> pdb=" O VAL g 93 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LYS g 109 " --> pdb=" O GLU g 105 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ARG g 110 " --> pdb=" O ALA g 106 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N GLY g 111 " --> pdb=" O ALA g 107 " (cutoff:3.500A) Processing helix chain 'g' and resid 114 through 129 Processing helix chain 'g' and resid 131 through 148 removed outlier: 3.904A pdb=" N LYS g 135 " --> pdb=" O GLY g 131 " (cutoff:3.500A) Processing helix chain 'h' and resid 4 through 20 removed outlier: 3.761A pdb=" N ASP h 8 " --> pdb=" O ASP h 4 " (cutoff:3.500A) Processing helix chain 'h' and resid 29 through 43 Processing helix chain 'h' and resid 111 through 119 removed outlier: 3.609A pdb=" N GLN h 117 " --> pdb=" O ARG h 113 " (cutoff:3.500A) Processing helix chain 'i' and resid 33 through 39 removed outlier: 4.242A pdb=" N GLY i 39 " --> pdb=" O GLU i 35 " (cutoff:3.500A) Processing helix chain 'i' and resid 44 through 53 removed outlier: 4.628A pdb=" N ARG i 48 " --> pdb=" O ARG i 44 " (cutoff:3.500A) Proline residue: i 50 - end of helix removed outlier: 4.587A pdb=" N LEU i 53 " --> pdb=" O GLN i 49 " (cutoff:3.500A) Processing helix chain 'i' and resid 70 through 87 removed outlier: 3.914A pdb=" N GLN i 74 " --> pdb=" O GLY i 70 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N MET i 87 " --> pdb=" O THR i 83 " (cutoff:3.500A) Processing helix chain 'i' and resid 90 through 101 removed outlier: 4.019A pdb=" N ARG i 94 " --> pdb=" O ASP i 90 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER i 95 " --> pdb=" O GLU i 91 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N GLU i 96 " --> pdb=" O SER i 92 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LYS i 99 " --> pdb=" O SER i 95 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ALA i 100 " --> pdb=" O GLU i 96 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLY i 101 " --> pdb=" O LEU i 97 " (cutoff:3.500A) Processing helix chain 'j' and resid 14 through 31 removed outlier: 3.677A pdb=" N ILE j 18 " --> pdb=" O ASP j 14 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ASP j 19 " --> pdb=" O HIS j 15 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N GLN j 20 " --> pdb=" O ARG j 16 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ALA j 29 " --> pdb=" O ILE j 25 " (cutoff:3.500A) Processing helix chain 'j' and resid 80 through 90 removed outlier: 3.752A pdb=" N ASP j 85 " --> pdb=" O GLU j 81 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N MET j 88 " --> pdb=" O VAL j 84 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N ARG j 89 " --> pdb=" O ASP j 85 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N LEU j 90 " --> pdb=" O ALA j 86 " (cutoff:3.500A) Processing helix chain 'k' and resid 45 through 50 removed outlier: 3.820A pdb=" N GLY k 50 " --> pdb=" O ALA k 46 " (cutoff:3.500A) Processing helix chain 'k' and resid 53 through 58 removed outlier: 4.064A pdb=" N SER k 57 " --> pdb=" O GLY k 53 " (cutoff:3.500A) removed outlier: 4.865A 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 74 removed outlier: 3.510A pdb=" N ASP k 71 " --> pdb=" O GLU k 67 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N ALA k 72 " --> pdb=" O ARG k 68 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N VAL k 73 " --> pdb=" O CYS k 69 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N LYS k 74 " --> pdb=" O ALA k 70 " (cutoff:3.500A) Processing helix chain 'k' and resid 91 through 103 removed outlier: 5.733A pdb=" N THR k 95 " --> pdb=" O GLY k 91 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE k 96 " --> pdb=" O ARG k 92 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ARG k 97 " --> pdb=" O GLU k 93 " (cutoff:3.500A) removed outlier: 3.501A 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: 5.087A pdb=" N TYR l 116 " --> pdb=" O ALA l 112 " (cutoff:3.500A) Processing helix chain 'm' and resid 13 through 22 removed outlier: 3.754A pdb=" N THR m 19 " --> pdb=" O VAL m 15 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N SER m 20 " --> pdb=" O ILE m 16 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N ILE m 21 " --> pdb=" O ALA m 17 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N TYR m 22 " --> pdb=" O LEU m 18 " (cutoff:3.500A) Processing helix chain 'm' and resid 25 through 37 removed outlier: 3.529A pdb=" N SER m 29 " --> pdb=" O GLY m 25 " (cutoff:3.500A) Processing helix chain 'm' and resid 43 through 48 removed outlier: 5.206A pdb=" N SER m 48 " --> pdb=" O ILE m 44 " (cutoff:3.500A) Processing helix chain 'm' and resid 49 through 63 removed outlier: 4.321A pdb=" N THR m 54 " --> pdb=" O GLY m 50 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU m 55 " --> pdb=" O GLN m 51 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASP m 57 " --> pdb=" O ASP m 53 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LYS m 61 " --> pdb=" O ASP m 57 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N PHE m 62 " --> pdb=" O GLU m 58 " (cutoff:3.500A) removed outlier: 5.105A 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 23 removed outlier: 3.546A pdb=" N VAL n 10 " --> pdb=" O LYS n 6 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LYS n 11 " --> pdb=" O ALA n 7 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ALA n 21 " --> pdb=" O ASP n 17 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N LYS n 22 " --> pdb=" O LYS n 18 " (cutoff:3.500A) Processing helix chain 'n' and resid 38 through 51 removed outlier: 3.748A pdb=" N TRP n 42 " --> pdb=" O ASP n 38 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL n 45 " --> pdb=" O ARG n 41 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N GLN n 49 " --> pdb=" O VAL n 45 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N THR n 50 " --> pdb=" O LEU n 46 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU n 51 " --> pdb=" O LYS n 47 " (cutoff:3.500A) Processing helix chain 'n' and resid 56 through 61 removed outlier: 4.101A pdb=" N GLN n 60 " --> pdb=" O SER n 56 " (cutoff:3.500A) removed outlier: 5.927A 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: 3.869A pdb=" N ARG n 85 " --> pdb=" O ARG n 81 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N ARG n 90 " --> pdb=" O GLU n 86 " (cutoff:3.500A) Processing helix chain 'n' and resid 24 through 31 removed outlier: 4.180A pdb=" N ILE n 29 " --> pdb=" O ALA n 24 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N SER n 31 " --> pdb=" O LEU n 26 " (cutoff:3.500A) Processing helix chain 'o' and resid 3 through 15 removed outlier: 3.985A pdb=" N GLU o 13 " --> pdb=" O LYS o 9 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLY o 15 " --> pdb=" O VAL o 11 " (cutoff:3.500A) Processing helix chain 'o' and resid 23 through 43 removed outlier: 4.291A pdb=" N GLY o 40 " --> pdb=" O ASN o 36 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N HIS o 41 " --> pdb=" O HIS o 37 " (cutoff:3.500A) Processing helix chain 'o' and resid 48 through 73 removed outlier: 3.643A pdb=" N GLY o 54 " --> pdb=" O HIS o 50 " (cutoff:3.500A) Processing helix chain 'o' and resid 74 through 85 removed outlier: 3.591A pdb=" N ARG o 83 " --> pdb=" O GLN o 79 " (cutoff:3.500A) Processing helix chain 'p' and resid 53 through 64 removed outlier: 3.732A pdb=" N ILE p 57 " --> pdb=" O ASP p 53 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N HIS p 59 " --> pdb=" O ASP p 55 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLN p 63 " --> pdb=" O HIS p 59 " (cutoff:3.500A) Processing helix chain 'p' and resid 68 through 79 removed outlier: 3.760A pdb=" N ALA p 73 " --> pdb=" O ASP p 69 " (cutoff:3.500A) Processing helix chain 'r' and resid 24 through 33 removed outlier: 4.422A pdb=" N LEU r 28 " --> pdb=" O ASP r 24 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ASN r 30 " --> pdb=" O ALA r 26 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N TYR r 31 " --> pdb=" O THR r 27 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ILE r 32 " --> pdb=" O LEU r 28 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N THR r 33 " --> pdb=" O LYS r 29 " (cutoff:3.500A) Processing helix chain 'r' and resid 40 through 45 removed outlier: 3.544A pdb=" N THR r 44 " --> pdb=" O PRO r 40 " (cutoff:3.500A) Processing helix chain 'r' and resid 47 through 65 Processing helix chain 's' and resid 11 through 25 removed outlier: 3.523A pdb=" N SER s 24 " --> pdb=" O LYS s 20 " (cutoff:3.500A) Processing helix chain 's' and resid 69 through 75 removed outlier: 4.468A pdb=" N PHE s 73 " --> pdb=" O LYS s 69 " (cutoff:3.500A) removed outlier: 4.451A 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 't' and resid 7 through 39 removed outlier: 3.525A pdb=" N ILE t 11 " --> pdb=" O LYS t 7 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N HIS t 19 " --> pdb=" O LYS t 15 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER t 22 " --> pdb=" O LYS t 18 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N GLU t 39 " --> pdb=" O TYR t 35 " (cutoff:3.500A) Processing helix chain 't' and resid 44 through 64 Proline residue: t 55 - end of helix removed outlier: 3.881A pdb=" N GLY t 64 " --> pdb=" O GLN t 60 " (cutoff:3.500A) Processing helix chain 't' and resid 67 through 85 removed outlier: 4.103A pdb=" N LEU t 78 " --> pdb=" O HIS t 74 " (cutoff:3.500A) Processing helix chain 'u' and resid 16 through 23 removed outlier: 3.761A pdb=" N ARG u 20 " --> pdb=" O ARG u 16 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N CYS u 22 " --> pdb=" O PHE u 18 " (cutoff:3.500A) Processing helix chain 'u' and resid 24 through 34 removed outlier: 4.762A pdb=" N GLU u 30 " --> pdb=" O GLY u 26 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL u 31 " --> pdb=" O VAL u 27 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N ARG u 33 " --> pdb=" O ALA u 29 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N ARG u 34 " --> pdb=" O GLU u 30 " (cutoff:3.500A) Processing helix chain 'u' and resid 36 through 61 Proline residue: u 40 - end of helix removed outlier: 3.577A pdb=" N LEU u 59 " --> pdb=" O HIS u 55 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA u 60 " --> pdb=" O ALA u 56 " (cutoff:3.500A) Processing helix chain 'z' and resid 24 through 39 removed outlier: 3.819A pdb=" N THR z 28 " --> pdb=" O LYS z 24 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR z 33 " --> pdb=" O ALA z 29 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR z 38 " --> pdb=" O VAL z 34 " (cutoff:3.500A) Processing helix chain 'z' and resid 45 through 51 removed outlier: 4.005A pdb=" N ILE z 49 " --> pdb=" O ALA z 45 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ASP z 50 " --> pdb=" O PHE z 46 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASN z 51 " --> pdb=" O ASN z 47 " (cutoff:3.500A) No H-bonds generated for 'chain 'z' and resid 45 through 51' Processing helix chain 'z' and resid 52 through 57 removed outlier: 4.134A pdb=" N LYS z 56 " --> pdb=" O ALA z 52 " (cutoff:3.500A) Processing helix chain 'z' and resid 87 through 99 removed outlier: 3.837A pdb=" N THR z 93 " --> pdb=" O LYS z 89 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLY z 94 " --> pdb=" O ASN z 90 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLN z 97 " --> pdb=" O THR z 93 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N MET z 98 " --> pdb=" O GLY z 94 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N ASP z 99 " --> pdb=" O ALA z 95 " (cutoff:3.500A) Processing helix chain 'z' and resid 112 through 126 removed outlier: 3.977A pdb=" N ARG z 116 " --> pdb=" O MET z 112 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLN z 124 " --> pdb=" O LEU z 120 " (cutoff:3.500A) Processing helix chain 'z' and resid 136 through 141 removed outlier: 6.244A pdb=" N VAL z 140 " --> pdb=" O LYS z 136 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N ASP z 141 " --> pdb=" O CYS z 137 " (cutoff:3.500A) No H-bonds generated for 'chain 'z' and resid 136 through 141' Processing helix chain 'z' and resid 142 through 161 removed outlier: 4.038A pdb=" N LEU z 146 " --> pdb=" O ASP z 142 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLU z 147 " --> pdb=" O GLU z 143 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N VAL z 149 " --> pdb=" O LEU z 145 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLU z 150 " --> pdb=" O LEU z 146 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N MET z 151 " --> pdb=" O GLU z 147 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLU z 152 " --> pdb=" O LEU z 148 " (cutoff:3.500A) Processing helix chain 'z' and resid 173 through 180 removed outlier: 3.590A pdb=" N ALA z 177 " --> pdb=" O SER z 173 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLU z 179 " --> pdb=" O LEU z 175 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLY z 180 " --> pdb=" O LYS z 176 " (cutoff:3.500A) Processing helix chain 'z' and resid 181 through 198 removed outlier: 3.674A pdb=" N LEU z 191 " --> pdb=" O LYS z 187 " (cutoff:3.500A) Processing helix chain 'z' and resid 282 through 287 removed outlier: 3.717A pdb=" N ILE z 286 " --> pdb=" O LYS z 282 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N GLU z 287 " --> pdb=" O ARG z 283 " (cutoff:3.500A) No H-bonds generated for 'chain 'z' and resid 282 through 287' Processing sheet with id= 1, first strand: chain 'C' and resid 1 through 4 Processing sheet with id= 2, first strand: chain 'C' and resid 74 through 77 removed outlier: 4.394A pdb=" N ASP C 113 " --> pdb=" O VAL C 77 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'C' and resid 79 through 82 removed outlier: 3.672A pdb=" N ARG C 79 " --> pdb=" O LEU C 92 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N ASN C 89 " --> pdb=" O ALA C 105 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'C' and resid 161 through 164 removed outlier: 6.742A pdb=" N THR C 172 " --> pdb=" O VAL C 164 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLU C 179 " --> pdb=" O LEU C 175 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'D' and resid 3 through 9 removed outlier: 4.243A pdb=" N SER D 199 " --> pdb=" O LYS D 8 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LYS D 204 " --> pdb=" O ASP D 108 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N LYS D 105 " --> pdb=" O VAL D 177 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'D' and resid 11 through 16 removed outlier: 3.587A pdb=" N VAL D 20 " --> pdb=" O THR D 16 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ARG D 179 " --> pdb=" O LEU D 188 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'D' and resid 36 through 40 removed outlier: 4.079A pdb=" N LEU D 40 " --> pdb=" O TYR D 45 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N TYR D 45 " --> pdb=" O LEU D 40 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N GLN D 49 " --> pdb=" O THR D 35 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N GLN D 94 " --> pdb=" O VAL D 34 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'D' and resid 46 through 51 removed outlier: 6.206A pdb=" N ARG D 46 " --> pdb=" O LEU D 84 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'E' and resid 42 through 46 removed outlier: 4.791A pdb=" N GLY E 42 " --> pdb=" O GLN E 90 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N ARG E 44 " --> pdb=" O ARG E 88 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ARG E 88 " --> pdb=" O ARG E 44 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N GLN E 46 " --> pdb=" O ALA E 86 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N ALA E 86 " --> pdb=" O GLN E 46 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'E' and resid 117 through 120 removed outlier: 5.474A pdb=" N ARG E 117 " --> pdb=" O ASP E 184 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG E 170 " --> pdb=" O ILE E 148 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'F' and resid 28 through 31 removed outlier: 5.972A pdb=" N ARG F 29 " --> pdb=" O THR F 158 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N THR F 156 " --> pdb=" O GLU F 31 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY F 85 " --> pdb=" O THR F 67 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'F' and resid 126 through 132 removed outlier: 3.523A pdb=" N LEU F 151 " --> pdb=" O VAL F 131 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'G' and resid 15 through 18 Processing sheet with id= 14, first strand: chain 'G' and resid 40 through 44 Processing sheet with id= 15, first strand: chain 'G' and resid 93 through 97 removed outlier: 3.862A pdb=" N ARG G 94 " --> pdb=" O SER G 105 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL G 112 " --> pdb=" O LEU G 104 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'G' and resid 120 through 124 removed outlier: 5.902A pdb=" N THR G 128 " --> pdb=" O LEU G 88 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU G 88 " --> pdb=" O THR G 128 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'H' and resid 3 through 6 removed outlier: 7.534A pdb=" N LYS H 35 " --> pdb=" O LEU H 6 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'H' and resid 76 through 81 removed outlier: 6.659A pdb=" N GLU H 76 " --> pdb=" O LYS H 141 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ALA H 140 " --> pdb=" O PHE H 132 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N PHE H 132 " --> pdb=" O ALA H 140 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N SER H 131 " --> pdb=" O ARG H 116 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N GLU H 114 " --> pdb=" O GLN H 133 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'I' and resid 54 through 60 No H-bonds generated for sheet with id= 19 Processing sheet with id= 20, first strand: chain 'J' and resid 52 through 57 removed outlier: 4.901A pdb=" N ASP J 19 " --> pdb=" O LEU J 140 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'J' and resid 74 through 78 removed outlier: 7.200A pdb=" N GLY J 83 " --> pdb=" O THR J 78 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'K' and resid 18 through 21 removed outlier: 4.189A pdb=" N THR K 6 " --> pdb=" O CYS K 21 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N ASN K 82 " --> pdb=" O MET K 7 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N GLY K 81 " --> pdb=" O LYS K 66 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N LYS K 66 " --> pdb=" O GLY K 81 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'K' and resid 68 through 71 removed outlier: 4.056A pdb=" N SER K 75 " --> pdb=" O ARG K 71 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'M' and resid 62 through 65 removed outlier: 3.669A pdb=" N TYR M 103 " --> pdb=" O LEU M 33 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N LEU M 33 " --> pdb=" O LEU M 102 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LYS M 100 " --> pdb=" O ALA M 35 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'M' and resid 30 through 36 removed outlier: 7.361A pdb=" N SER M 30 " --> pdb=" O LYS M 133 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N LYS M 127 " --> pdb=" O VAL M 36 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'N' and resid 33 through 36 removed outlier: 5.865A pdb=" N ALA N 108 " --> pdb=" O PHE N 102 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N PHE N 102 " --> pdb=" O ALA N 108 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N MET N 110 " --> pdb=" O CYS N 100 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'O' and resid 49 through 52 Processing sheet with id= 28, first strand: chain 'P' and resid 37 through 44 removed outlier: 6.475A pdb=" N THR P 24 " --> pdb=" O LYS P 86 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER P 82 " --> pdb=" O LYS P 28 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'P' and resid 48 through 52 removed outlier: 3.725A pdb=" N ALA P 48 " --> pdb=" O THR P 59 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N ARG P 52 " --> pdb=" O HIS P 55 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N SER P 56 " --> pdb=" O THR P 75 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'R' and resid 11 through 15 removed outlier: 3.678A pdb=" N TYR R 2 " --> pdb=" O ALA R 42 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'R' and resid 30 through 36 removed outlier: 4.678A pdb=" N GLU R 31 " --> pdb=" O VAL R 63 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N VAL R 63 " --> pdb=" O GLU R 31 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N LYS R 60 " --> pdb=" O THR R 99 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ASP R 95 " --> pdb=" O VAL R 64 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'R' and resid 71 through 78 removed outlier: 4.163A pdb=" N TYR R 83 " --> pdb=" O ARG R 78 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'S' and resid 2 through 8 removed outlier: 4.797A pdb=" N THR S 3 " --> pdb=" O VAL S 107 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL S 107 " --> pdb=" O THR S 3 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N VAL S 106 " --> pdb=" O THR S 72 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'S' and resid 73 through 79 removed outlier: 4.801A pdb=" N THR S 100 " --> pdb=" O GLY S 79 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'S' and resid 80 through 88 removed outlier: 3.614A pdb=" N THR S 100 " --> pdb=" O PRO S 80 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ARG S 92 " --> pdb=" O ARG S 88 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'T' and resid 28 through 33 removed outlier: 6.289A pdb=" N ASN T 28 " --> pdb=" O LEU T 87 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N LYS T 66 " --> pdb=" O ARG T 77 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ASP T 79 " --> pdb=" O LYS T 64 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N LYS T 64 " --> pdb=" O ASP T 79 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N LYS T 81 " --> pdb=" O VAL T 62 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N VAL T 62 " --> pdb=" O LYS T 81 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ALA T 83 " --> pdb=" O THR T 60 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N THR T 60 " --> pdb=" O ALA T 83 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N VAL T 85 " --> pdb=" O VAL T 58 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N VAL T 58 " --> pdb=" O VAL T 85 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'U' and resid 41 through 44 Processing sheet with id= 38, first strand: chain 'U' and resid 82 through 86 Processing sheet with id= 39, first strand: chain 'V' and resid 69 through 72 removed outlier: 3.649A pdb=" N ILE V 4 " --> pdb=" O THR V 62 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N ALA V 39 " --> pdb=" O ARG V 9 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE V 89 " --> pdb=" O PRO V 27 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'W' and resid 47 through 50 removed outlier: 3.631A pdb=" N PHE W 56 " --> pdb=" O GLY W 48 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N THR W 54 " --> pdb=" O GLY W 50 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'W' and resid 61 through 67 Processing sheet with id= 42, first strand: chain 'X' and resid 11 through 18 removed outlier: 3.607A pdb=" N GLY X 14 " --> pdb=" O ARG X 26 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N THR X 24 " --> pdb=" O ASN X 16 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N SER X 18 " --> pdb=" O ASN X 22 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ASN X 22 " --> pdb=" O SER X 18 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'X' and resid 34 through 40 Processing sheet with id= 44, first strand: chain 'Z' and resid 32 through 38 removed outlier: 4.234A pdb=" N HIS Z 33 " --> pdb=" O GLN Z 8 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLN Z 8 " --> pdb=" O HIS Z 33 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N LYS Z 5 " --> pdb=" O GLU Z 57 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N MET Z 53 " --> pdb=" O THR Z 9 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain '0' and resid 27 through 30 removed outlier: 6.397A pdb=" N SER 0 28 " --> pdb=" O LYS 0 36 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N LYS 0 36 " --> pdb=" O SER 0 28 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N ASP 0 30 " --> pdb=" O GLY 0 34 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain '1' and resid 19 through 24 Processing sheet with id= 47, first strand: chain '3' and resid 21 through 24 removed outlier: 5.698A pdb=" N PHE 3 21 " --> pdb=" O VAL 3 49 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain '4' and resid 13 through 19 removed outlier: 8.562A pdb=" N ASN 4 13 " --> pdb=" O SER 4 28 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N SER 4 28 " --> pdb=" O ASN 4 13 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N ILE 4 23 " --> pdb=" O GLN 4 37 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N CYS 4 27 " --> pdb=" O HIS 4 33 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N HIS 4 33 " --> pdb=" O CYS 4 27 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain '5' and resid 24 through 28 No H-bonds generated for sheet with id= 49 Processing sheet with id= 50, first strand: chain '6' and resid 21 through 25 Processing sheet with id= 51, first strand: chain 'b' and resid 29 through 33 removed outlier: 6.658A pdb=" N PHE b 29 " --> pdb=" O ASN b 41 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N VAL b 37 " --> pdb=" O ALA b 33 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'b' and resid 66 through 70 removed outlier: 3.871A pdb=" N PHE b 183 " --> pdb=" O LEU b 160 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N VAL b 162 " --> pdb=" O PHE b 183 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N PHE b 197 " --> pdb=" O VAL b 182 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA b 184 " --> pdb=" O PHE b 197 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'c' and resid 53 through 58 removed outlier: 3.665A pdb=" N ARG c 53 " --> pdb=" O HIS c 68 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ILE c 63 " --> pdb=" O PRO c 97 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'c' and resid 163 through 170 removed outlier: 3.679A pdb=" N GLU c 169 " --> pdb=" O ILE c 148 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N ILE c 148 " --> pdb=" O GLU c 169 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY c 147 " --> pdb=" O PHE c 202 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N PHE c 202 " --> pdb=" O GLY c 147 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLY c 193 " --> pdb=" O THR c 190 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'd' and resid 139 through 143 removed outlier: 3.594A pdb=" N VAL d 142 " --> pdb=" O GLY d 179 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N GLU d 178 " --> pdb=" O ASP d 173 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'e' and resid 11 through 15 removed outlier: 4.020A pdb=" N GLN e 11 " --> pdb=" O GLY e 39 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLY e 39 " --> pdb=" O GLN e 11 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N LEU e 35 " --> pdb=" O ILE e 15 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'e' and resid 82 through 87 removed outlier: 7.579A pdb=" N HIS e 82 " --> pdb=" O PRO e 97 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N VAL e 93 " --> pdb=" O GLY e 86 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N TYR e 127 " --> pdb=" O ARG e 92 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'e' and resid 31 through 39 removed outlier: 4.578A pdb=" N GLY e 50 " --> pdb=" O ALA e 34 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'f' and resid 38 through 42 removed outlier: 3.614A pdb=" N ARG f 38 " --> pdb=" O ASN f 63 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N ASN f 63 " --> pdb=" O ARG f 38 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLU f 40 " --> pdb=" O LEU f 61 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N TYR f 59 " --> pdb=" O TRP f 42 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N ILE f 6 " --> pdb=" O MET f 62 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N HIS f 3 " --> pdb=" O THR f 92 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N THR f 92 " --> pdb=" O HIS f 3 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLU f 5 " --> pdb=" O MET f 90 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N MET f 90 " --> pdb=" O GLU f 5 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N ARG f 86 " --> pdb=" O MET f 9 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'f' and resid 43 through 47 removed outlier: 3.539A pdb=" N GLY f 43 " --> pdb=" O TYR f 59 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N LEU f 47 " --> pdb=" O HIS f 55 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N HIS f 55 " --> pdb=" O LEU f 47 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'g' and resid 72 through 76 Processing sheet with id= 62, first strand: chain 'h' and resid 22 through 28 removed outlier: 6.086A pdb=" N ALA h 22 " --> pdb=" O LEU h 62 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLU h 51 " --> pdb=" O GLU h 57 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N ASP h 47 " --> pdb=" O THR h 61 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'h' and resid 73 through 76 removed outlier: 3.930A pdb=" N SER h 73 " --> pdb=" O ALA h 129 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N CYS h 126 " --> pdb=" O VAL h 102 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N VAL h 102 " --> pdb=" O ILE h 125 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'i' and resid 4 through 10 removed outlier: 4.543A pdb=" N GLY i 9 " --> pdb=" O ALA i 16 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LYS i 67 " --> pdb=" O ALA i 15 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N LYS i 26 " --> pdb=" O LEU i 60 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'j' and resid 39 through 42 removed outlier: 4.944A pdb=" N LEU j 42 " --> pdb=" O LEU j 71 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N LEU j 71 " --> pdb=" O LEU j 42 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ILE j 8 " --> pdb=" O VAL j 74 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE j 76 " --> pdb=" O ILE j 6 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ILE j 6 " --> pdb=" O ILE j 76 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'j' and resid 44 through 52 removed outlier: 3.800A pdb=" N GLU j 47 " --> pdb=" O ILE j 67 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'k' and resid 29 through 34 Processing sheet with id= 68, first strand: chain 'l' and resid 28 through 31 removed outlier: 5.006A pdb=" N LEU l 80 " --> pdb=" O VAL l 97 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'l' and resid 35 through 40 removed outlier: 5.053A pdb=" N ARG l 35 " --> pdb=" O ARG l 53 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N LYS l 50 " --> pdb=" O ILE l 66 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N PHE l 60 " --> pdb=" O LEU l 56 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'p' and resid 4 through 10 removed outlier: 6.000A pdb=" N GLN p 18 " --> pdb=" O ALA p 7 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N VAL p 19 " --> pdb=" O GLY p 37 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLY p 37 " --> pdb=" O VAL p 19 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ARG p 51 " --> pdb=" O PHE p 38 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N GLY p 49 " --> pdb=" O ASN p 40 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'q' and resid 6 through 10 removed outlier: 7.257A pdb=" N GLU q 59 " --> pdb=" O VAL q 75 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'q' and resid 18 through 29 No H-bonds generated for sheet with id= 72 Processing sheet with id= 73, first strand: chain 's' and resid 29 through 33 removed outlier: 4.195A pdb=" N LEU s 30 " --> pdb=" O THR s 47 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N LEU s 46 " --> pdb=" O VAL s 61 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N GLN s 55 " --> pdb=" O ASN s 52 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain 'z' and resid 64 through 71 removed outlier: 3.603A pdb=" N SER z 65 " --> pdb=" O ASP z 80 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N TYR z 69 " --> pdb=" O TYR z 76 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG z 74 " --> pdb=" O THR z 71 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLY z 15 " --> pdb=" O GLY z 100 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL z 105 " --> pdb=" O PHE z 133 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ASN z 135 " --> pdb=" O VAL z 105 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain 'z' and resid 210 through 214 removed outlier: 6.681A pdb=" N PHE z 210 " --> pdb=" O LYS z 294 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N GLN z 290 " --> pdb=" O ILE z 214 " (cutoff:3.500A) Processing sheet with id= 76, first strand: chain 'z' and resid 216 through 220 removed outlier: 4.064A pdb=" N ASP z 216 " --> pdb=" O THR z 228 " (cutoff:3.500A) Processing sheet with id= 77, first strand: chain 'z' and resid 234 through 237 removed outlier: 7.316A pdb=" N GLY z 234 " --> pdb=" O ALA z 270 " (cutoff:3.500A) Processing sheet with id= 78, first strand: chain 'z' and resid 336 through 340 removed outlier: 3.664A pdb=" N GLY z 339 " --> pdb=" O PRO z 328 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N LEU z 372 " --> pdb=" O VAL z 387 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N VAL z 387 " --> pdb=" O LEU z 372 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N PHE z 374 " --> pdb=" O ALA z 385 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N ALA z 385 " --> pdb=" O PHE z 374 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ILE z 376 " --> pdb=" O VAL z 383 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ARG z 381 " --> pdb=" O GLU z 378 " (cutoff:3.500A) 1807 hydrogen bonds defined for protein. 5330 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3482 hydrogen bonds 5592 hydrogen bond angles 0 basepair planarities 1405 basepair parallelities 2390 stacking parallelities Total time for adding SS restraints: 411.81 Time building geometry restraints manager: 71.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 12630 1.30 - 1.43: 68968 1.43 - 1.56: 73901 1.56 - 1.69: 9679 1.69 - 1.81: 301 Bond restraints: 165479 Sorted by residual: bond pdb=" O4' 3TD A1915 " pdb=" C1' 3TD A1915 " ideal model delta sigma weight residual 1.412 1.657 -0.245 1.50e-02 4.44e+03 2.68e+02 bond pdb=" C4 5MU A1939 " pdb=" C5 5MU A1939 " ideal model delta sigma weight residual 1.802 1.480 0.322 2.00e-02 2.50e+03 2.59e+02 bond pdb=" C4 5MU y 54 " pdb=" C5 5MU y 54 " ideal model delta sigma weight residual 1.802 1.483 0.319 2.00e-02 2.50e+03 2.54e+02 bond pdb=" C4 5MU v 54 " pdb=" C5 5MU v 54 " ideal model delta sigma weight residual 1.802 1.484 0.318 2.00e-02 2.50e+03 2.52e+02 bond pdb=" C4 5MU w 54 " pdb=" C5 5MU w 54 " ideal model delta sigma weight residual 1.802 1.488 0.314 2.00e-02 2.50e+03 2.46e+02 ... (remaining 165474 not shown) Histogram of bond angle deviations from ideal: 74.78 - 90.49: 3 90.49 - 106.20: 27750 106.20 - 121.91: 178163 121.91 - 137.63: 41289 137.63 - 153.34: 4 Bond angle restraints: 247209 Sorted by residual: angle pdb=" O3' U w 117 " pdb=" P G w 18 " pdb=" O5' G w 18 " ideal model delta sigma weight residual 104.00 139.25 -35.25 1.50e+00 4.44e-01 5.52e+02 angle pdb=" C3' U w 117 " pdb=" O3' U w 117 " pdb=" P G w 18 " ideal model delta sigma weight residual 120.20 153.34 -33.14 1.50e+00 4.44e-01 4.88e+02 angle pdb=" O3' 6MZ A1618 " pdb=" P G A1619 " pdb=" O5' G A1619 " ideal model delta sigma weight residual 104.00 83.82 20.18 1.50e+00 4.44e-01 1.81e+02 angle pdb=" O3' 6MZ A2030 " pdb=" P A A2031 " pdb=" OP2 A A2031 " ideal model delta sigma weight residual 108.00 141.88 -33.88 3.00e+00 1.11e-01 1.28e+02 angle pdb=" O3' 6MZ A2030 " pdb=" P A A2031 " pdb=" OP1 A A2031 " ideal model delta sigma weight residual 108.00 74.78 33.22 3.00e+00 1.11e-01 1.23e+02 ... (remaining 247204 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.95: 92035 35.95 - 71.90: 12225 71.90 - 107.85: 1431 107.85 - 143.80: 54 143.80 - 179.75: 49 Dihedral angle restraints: 105794 sinusoidal: 87793 harmonic: 18001 Sorted by residual: dihedral pdb=" C5' G a1305 " pdb=" C4' G a1305 " pdb=" C3' G a1305 " pdb=" O3' G a1305 " ideal model delta sinusoidal sigma weight residual 147.00 67.91 79.09 1 8.00e+00 1.56e-02 1.22e+02 dihedral pdb=" C5' U w 27 " pdb=" C4' U w 27 " pdb=" C3' U w 27 " pdb=" O3' U w 27 " ideal model delta sinusoidal sigma weight residual 147.00 73.54 73.46 1 8.00e+00 1.56e-02 1.07e+02 dihedral pdb=" C4' G w 18 " pdb=" C3' G w 18 " pdb=" C2' G w 18 " pdb=" C1' G w 18 " ideal model delta sinusoidal sigma weight residual -35.00 35.99 -70.99 1 8.00e+00 1.56e-02 1.01e+02 ... (remaining 105791 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.165: 27259 0.165 - 0.330: 4111 0.330 - 0.494: 27 0.494 - 0.659: 11 0.659 - 0.824: 10 Chirality restraints: 31418 Sorted by residual: chirality pdb=" C3' C a1399 " pdb=" C4' C a1399 " pdb=" O3' C a1399 " pdb=" C2' C a1399 " both_signs ideal model delta sigma weight residual False -2.74 -1.92 -0.82 2.00e-01 2.50e+01 1.70e+01 chirality pdb=" C3' G A 242 " pdb=" C4' G A 242 " pdb=" O3' G A 242 " pdb=" C2' G A 242 " both_signs ideal model delta sigma weight residual False -2.74 -1.95 -0.79 2.00e-01 2.50e+01 1.58e+01 chirality pdb=" C3' A a1201 " pdb=" C4' A a1201 " pdb=" O3' A a1201 " pdb=" C2' A a1201 " both_signs ideal model delta sigma weight residual False -2.74 -2.01 -0.74 2.00e-01 2.50e+01 1.35e+01 ... (remaining 31415 not shown) Planarity restraints: 13503 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 7MG A2069 " 0.062 2.00e-02 2.50e+03 6.34e-01 9.04e+03 pdb=" C4' 7MG A2069 " 0.450 2.00e-02 2.50e+03 pdb=" O4' 7MG A2069 " 0.654 2.00e-02 2.50e+03 pdb=" C3' 7MG A2069 " -0.615 2.00e-02 2.50e+03 pdb=" O3' 7MG A2069 " -0.714 2.00e-02 2.50e+03 pdb=" C2' 7MG A2069 " -0.121 2.00e-02 2.50e+03 pdb=" O2' 7MG A2069 " 1.032 2.00e-02 2.50e+03 pdb=" C1' 7MG A2069 " 0.231 2.00e-02 2.50e+03 pdb=" N9 7MG A2069 " -0.980 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG A2445 " -0.042 2.00e-02 2.50e+03 6.17e-01 8.57e+03 pdb=" C4' 2MG A2445 " -0.467 2.00e-02 2.50e+03 pdb=" O4' 2MG A2445 " -0.747 2.00e-02 2.50e+03 pdb=" C3' 2MG A2445 " 0.613 2.00e-02 2.50e+03 pdb=" O3' 2MG A2445 " 0.648 2.00e-02 2.50e+03 pdb=" C2' 2MG A2445 " 0.189 2.00e-02 2.50e+03 pdb=" O2' 2MG A2445 " -0.926 2.00e-02 2.50e+03 pdb=" C1' 2MG A2445 " -0.224 2.00e-02 2.50e+03 pdb=" N9 2MG A2445 " 0.955 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 7MG a 527 " -0.017 2.00e-02 2.50e+03 5.99e-01 8.08e+03 pdb=" C4' 7MG a 527 " 0.456 2.00e-02 2.50e+03 pdb=" O4' 7MG a 527 " 0.751 2.00e-02 2.50e+03 pdb=" C3' 7MG a 527 " -0.583 2.00e-02 2.50e+03 pdb=" O3' 7MG a 527 " -0.570 2.00e-02 2.50e+03 pdb=" C2' 7MG a 527 " -0.198 2.00e-02 2.50e+03 pdb=" O2' 7MG a 527 " 0.879 2.00e-02 2.50e+03 pdb=" C1' 7MG a 527 " 0.242 2.00e-02 2.50e+03 pdb=" N9 7MG a 527 " -0.961 2.00e-02 2.50e+03 ... (remaining 13500 not shown) Histogram of nonbonded interaction distances: 1.32 - 2.09: 114 2.09 - 2.85: 44438 2.85 - 3.61: 277161 3.61 - 4.38: 575383 4.38 - 5.14: 787538 Nonbonded interactions: 1684634 Sorted by model distance: nonbonded pdb=" O4 U A1105 " pdb=" C5 G A1106 " model vdw 1.324 3.260 nonbonded pdb=" O4 U a 437 " pdb=" N1 A a 495 " model vdw 1.365 2.496 nonbonded pdb=" O4 U A1105 " pdb=" N7 G A1106 " model vdw 1.433 3.120 nonbonded pdb=" N1 A a 182 " pdb=" O4 U a 185 " model vdw 1.633 3.120 nonbonded pdb=" N1 A A1054 " pdb=" C4 G A1106 " model vdw 1.668 3.340 ... (remaining 1684629 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'v' and (resid 0 through 76 or resid 101 through 102)) selection = chain 'w' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.100 Extract box with map and model: 18.230 Check model and map are aligned: 1.760 Set scattering table: 1.070 Process input model: 740.340 Find NCS groups from input model: 3.530 Set up NCS constraints: 0.450 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:8.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 778.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.322 165479 Z= 0.493 Angle : 1.160 35.252 247209 Z= 0.764 Chirality : 0.098 0.824 31418 Planarity : 0.023 0.634 13503 Dihedral : 24.588 179.755 94188 Min Nonbonded Distance : 1.324 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 2.44 % Allowed : 9.34 % Favored : 88.21 % Rotamer: Outliers : 3.10 % Allowed : 7.70 % Favored : 89.20 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.11 (0.08), residues: 6219 helix: -2.67 (0.09), residues: 1849 sheet: -2.82 (0.13), residues: 1056 loop : -2.74 (0.09), residues: 3314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 212 HIS 0.009 0.002 HIS C 229 PHE 0.021 0.002 PHE M 31 TYR 0.026 0.002 TYR l 116 ARG 0.021 0.001 ARG l 120 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12438 Ramachandran restraints generated. 6219 Oldfield, 0 Emsley, 6219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12438 Ramachandran restraints generated. 6219 Oldfield, 0 Emsley, 6219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1878 residues out of total 5164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 1718 time to evaluate : 6.555 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: C 4 LYS cc_start: 0.8033 (tttt) cc_final: 0.7562 (ttmm) REVERT: C 22 GLU cc_start: 0.7446 (mm-30) cc_final: 0.6613 (mm-30) REVERT: C 27 LYS cc_start: 0.7266 (mttt) cc_final: 0.6906 (mppt) REVERT: C 110 LYS cc_start: 0.7866 (OUTLIER) cc_final: 0.7581 (mtpt) REVERT: C 113 ASP cc_start: 0.6673 (m-30) cc_final: 0.6238 (t0) REVERT: C 114 GLN cc_start: 0.7461 (tt0) cc_final: 0.6818 (mm-40) REVERT: C 184 GLU cc_start: 0.7092 (tt0) cc_final: 0.6453 (mt-10) REVERT: C 187 CYS cc_start: 0.8107 (m) cc_final: 0.7904 (m) REVERT: C 202 ARG cc_start: 0.8122 (ttm110) cc_final: 0.7855 (ptp-110) REVERT: C 203 VAL cc_start: 0.7350 (OUTLIER) cc_final: 0.7076 (p) REVERT: C 224 MET cc_start: 0.9002 (mtt) cc_final: 0.8692 (mtt) REVERT: C 235 GLU cc_start: 0.8251 (mm-30) cc_final: 0.8029 (mm-30) REVERT: C 254 LYS cc_start: 0.7686 (tptt) cc_final: 0.7223 (tppt) REVERT: C 269 ARG cc_start: 0.7680 (mtp180) cc_final: 0.7475 (mmt90) REVERT: D 7 LYS cc_start: 0.7226 (ttmt) cc_final: 0.6833 (ttpm) REVERT: D 30 GLU cc_start: 0.7202 (OUTLIER) cc_final: 0.6867 (tt0) REVERT: D 56 LYS cc_start: 0.6968 (OUTLIER) cc_final: 0.6750 (mtmm) REVERT: D 61 THR cc_start: 0.7918 (p) cc_final: 0.7692 (t) REVERT: D 108 ASP cc_start: 0.7865 (m-30) cc_final: 0.6882 (p0) REVERT: D 197 THR cc_start: 0.8342 (m) cc_final: 0.7569 (p) REVERT: D 204 LYS cc_start: 0.7721 (OUTLIER) cc_final: 0.7468 (ptmt) REVERT: E 21 ARG cc_start: 0.7069 (mtp-110) cc_final: 0.6786 (mtp-110) REVERT: E 22 ASP cc_start: 0.7689 (t0) cc_final: 0.7003 (p0) REVERT: E 88 ARG cc_start: 0.7794 (ttm-80) cc_final: 0.7239 (mmp80) REVERT: E 106 LYS cc_start: 0.7999 (mtpt) cc_final: 0.7558 (mttm) REVERT: E 139 LYS cc_start: 0.7707 (OUTLIER) cc_final: 0.7321 (mtmt) REVERT: E 159 LEU cc_start: 0.8490 (tp) cc_final: 0.8221 (mm) REVERT: E 170 ARG cc_start: 0.7998 (mmt90) cc_final: 0.7797 (mpt-90) REVERT: E 194 LYS cc_start: 0.8197 (tptt) cc_final: 0.7950 (mmtp) REVERT: F 14 LYS cc_start: 0.7644 (tptp) cc_final: 0.7430 (mptt) REVERT: F 25 MET cc_start: 0.7663 (mmp) cc_final: 0.7430 (tpp) REVERT: F 31 GLU cc_start: 0.8460 (tt0) cc_final: 0.8165 (tt0) REVERT: F 37 MET cc_start: 0.7216 (ttt) cc_final: 0.6972 (tpp) REVERT: F 41 GLU cc_start: 0.6771 (mm-30) cc_final: 0.6248 (mp0) REVERT: F 46 LYS cc_start: 0.7849 (mttt) cc_final: 0.7447 (tptp) REVERT: F 47 LYS cc_start: 0.7397 (ptmt) cc_final: 0.7087 (pmtt) REVERT: F 59 ILE cc_start: 0.7942 (mt) cc_final: 0.7653 (mp) REVERT: F 63 LYS cc_start: 0.6926 (ttpt) cc_final: 0.6713 (ttmt) REVERT: F 67 THR cc_start: 0.7699 (OUTLIER) cc_final: 0.7352 (p) REVERT: F 68 LYS cc_start: 0.7583 (mptt) cc_final: 0.7212 (mppt) REVERT: F 71 LYS cc_start: 0.7345 (mmmt) cc_final: 0.6980 (ttpt) REVERT: F 100 GLU cc_start: 0.7911 (tt0) cc_final: 0.7569 (pp20) REVERT: F 111 ARG cc_start: 0.6607 (ttp80) cc_final: 0.6369 (ptm160) REVERT: F 133 GLU cc_start: 0.7671 (mt-10) cc_final: 0.7237 (mt-10) REVERT: F 137 PHE cc_start: 0.7411 (m-80) cc_final: 0.7143 (m-80) REVERT: F 147 ARG cc_start: 0.6944 (tpp80) cc_final: 0.6252 (ttt180) REVERT: F 149 ARG cc_start: 0.6965 (ptt180) cc_final: 0.6749 (ptp90) REVERT: F 151 LEU cc_start: 0.7727 (pp) cc_final: 0.7310 (pt) REVERT: F 160 LYS cc_start: 0.7680 (mtmm) cc_final: 0.7118 (ptpp) REVERT: G 35 THR cc_start: 0.8122 (m) cc_final: 0.7764 (p) REVERT: G 37 ASN cc_start: 0.7138 (t0) cc_final: 0.6921 (t0) REVERT: G 98 LYS cc_start: 0.7031 (ttpt) cc_final: 0.6694 (mtpm) REVERT: G 101 VAL cc_start: 0.7590 (t) cc_final: 0.7386 (m) REVERT: G 105 SER cc_start: 0.7986 (t) cc_final: 0.7764 (m) REVERT: G 146 ASP cc_start: 0.7137 (m-30) cc_final: 0.6765 (m-30) REVERT: G 154 GLU cc_start: 0.7064 (tt0) cc_final: 0.6530 (pt0) REVERT: G 169 ARG cc_start: 0.6467 (OUTLIER) cc_final: 0.6252 (mmt90) REVERT: I 135 MET cc_start: 0.1978 (mtp) cc_final: 0.1428 (tmt) REVERT: J 12 LYS cc_start: 0.7432 (OUTLIER) cc_final: 0.7116 (tptp) REVERT: J 31 GLU cc_start: 0.7744 (tp30) cc_final: 0.7352 (mp0) REVERT: J 43 GLU cc_start: 0.7987 (mt-10) cc_final: 0.7545 (mp0) REVERT: J 61 LYS cc_start: 0.8400 (mmtp) cc_final: 0.8044 (mtpt) REVERT: J 125 TYR cc_start: 0.7565 (m-80) cc_final: 0.7313 (m-80) REVERT: K 18 ARG cc_start: 0.8096 (mmt180) cc_final: 0.7735 (tpp-160) REVERT: K 20 MET cc_start: 0.8549 (ttt) cc_final: 0.8047 (ttp) REVERT: K 75 SER cc_start: 0.8023 (p) cc_final: 0.6769 (m) REVERT: L 12 SER cc_start: 0.8643 (t) cc_final: 0.8349 (m) REVERT: L 14 LYS cc_start: 0.7861 (OUTLIER) cc_final: 0.7653 (ttpt) REVERT: L 27 LEU cc_start: 0.8577 (pp) cc_final: 0.8291 (pp) REVERT: L 39 LYS cc_start: 0.8532 (mtpt) cc_final: 0.8210 (mtmp) REVERT: L 70 LYS cc_start: 0.7764 (tttp) cc_final: 0.7558 (ttmt) REVERT: L 94 THR cc_start: 0.8387 (p) cc_final: 0.7853 (p) REVERT: L 123 ARG cc_start: 0.6813 (mtm180) cc_final: 0.6589 (ptp-170) REVERT: L 141 LYS cc_start: 0.7148 (mmmt) cc_final: 0.6653 (ptpp) REVERT: M 2 LEU cc_start: 0.8723 (mt) cc_final: 0.8413 (mt) REVERT: M 3 GLN cc_start: 0.7585 (tt0) cc_final: 0.7102 (mt0) REVERT: M 10 ARG cc_start: 0.7951 (mtp180) cc_final: 0.7743 (mtm-85) REVERT: M 12 MET cc_start: 0.8522 (ttm) cc_final: 0.8159 (ttm) REVERT: M 41 LEU cc_start: 0.8609 (mt) cc_final: 0.8267 (mm) REVERT: M 51 ARG cc_start: 0.7853 (mtt90) cc_final: 0.7286 (mpt-90) REVERT: M 75 GLU cc_start: 0.8369 (tt0) cc_final: 0.7806 (tt0) REVERT: M 104 GLU cc_start: 0.7901 (mt-10) cc_final: 0.7622 (mt-10) REVERT: M 115 GLU cc_start: 0.7577 (mm-30) cc_final: 0.6788 (pp20) REVERT: M 133 LYS cc_start: 0.7467 (ttpp) cc_final: 0.7253 (ttpt) REVERT: N 30 ARG cc_start: 0.8249 (ttp-110) cc_final: 0.7573 (ttm-80) REVERT: N 35 LYS cc_start: 0.8048 (tttt) cc_final: 0.7644 (tttp) REVERT: N 65 LEU cc_start: 0.7699 (OUTLIER) cc_final: 0.7481 (mt) REVERT: N 118 ARG cc_start: 0.6582 (OUTLIER) cc_final: 0.5579 (mmm-85) REVERT: O 13 ARG cc_start: 0.6667 (ttt90) cc_final: 0.6138 (tpp-160) REVERT: O 28 VAL cc_start: 0.8538 (OUTLIER) cc_final: 0.8244 (m) REVERT: O 98 GLN cc_start: 0.8059 (tt0) cc_final: 0.7834 (tm-30) REVERT: P 6 GLN cc_start: 0.7820 (tt0) cc_final: 0.7574 (tm-30) REVERT: P 26 GLU cc_start: 0.7510 (OUTLIER) cc_final: 0.7143 (tp30) REVERT: P 37 LYS cc_start: 0.7123 (tttp) cc_final: 0.6386 (ttpp) REVERT: P 62 LYS cc_start: 0.7630 (tttt) cc_final: 0.7294 (ttpt) REVERT: P 92 ARG cc_start: 0.8321 (ptm160) cc_final: 0.7631 (ptm160) REVERT: Q 12 ARG cc_start: 0.7602 (ttm-80) cc_final: 0.7210 (ttt180) REVERT: Q 14 LYS cc_start: 0.7947 (tttt) cc_final: 0.7647 (mtpp) REVERT: Q 77 LYS cc_start: 0.8057 (mttt) cc_final: 0.7610 (mtpt) REVERT: R 1 MET cc_start: 0.6634 (tpp) cc_final: 0.5537 (ptm) REVERT: R 16 GLU cc_start: 0.7524 (tt0) cc_final: 0.7261 (tm-30) REVERT: R 18 GLN cc_start: 0.7698 (pt0) cc_final: 0.7262 (pt0) REVERT: R 59 ILE cc_start: 0.7779 (mt) cc_final: 0.7349 (mp) REVERT: R 79 ARG cc_start: 0.8348 (ttp-170) cc_final: 0.8056 (ttp-170) REVERT: R 85 LYS cc_start: 0.8341 (tttt) cc_final: 0.8077 (mttt) REVERT: R 91 GLN cc_start: 0.8903 (tp40) cc_final: 0.8599 (tp40) REVERT: S 6 LYS cc_start: 0.7703 (ptpt) cc_final: 0.7132 (pttp) REVERT: S 52 GLU cc_start: 0.8192 (tt0) cc_final: 0.7579 (tp30) REVERT: S 86 MET cc_start: 0.8462 (tmm) cc_final: 0.7859 (tpt) REVERT: S 92 ARG cc_start: 0.7371 (ptp90) cc_final: 0.6727 (tmt90) REVERT: S 98 LYS cc_start: 0.7646 (mmtp) cc_final: 0.7234 (mmmt) REVERT: T 24 MET cc_start: 0.6899 (mmm) cc_final: 0.6455 (mtm) REVERT: T 28 ASN cc_start: 0.7769 (t0) cc_final: 0.6958 (t0) REVERT: T 33 LYS cc_start: 0.6773 (mtpp) cc_final: 0.6557 (tttp) REVERT: T 51 PHE cc_start: 0.7398 (m-80) cc_final: 0.7093 (m-10) REVERT: T 54 GLU cc_start: 0.7171 (mt-10) cc_final: 0.6243 (mm-30) REVERT: T 69 ARG cc_start: 0.7458 (OUTLIER) cc_final: 0.6813 (tmt-80) REVERT: T 76 ARG cc_start: 0.7429 (OUTLIER) cc_final: 0.6699 (ptm-80) REVERT: U 5 ARG cc_start: 0.6358 (ptp-170) cc_final: 0.5868 (mtt180) REVERT: U 9 GLU cc_start: 0.7450 (tp30) cc_final: 0.7163 (mm-30) REVERT: U 25 LYS cc_start: 0.7499 (mmmt) cc_final: 0.6831 (mtpm) REVERT: U 36 GLU cc_start: 0.7561 (pt0) cc_final: 0.7306 (pp20) REVERT: U 71 ILE cc_start: 0.8239 (pt) cc_final: 0.7820 (mt) REVERT: V 8 VAL cc_start: 0.7988 (t) cc_final: 0.7174 (m) REVERT: V 11 GLU cc_start: 0.7019 (mt-10) cc_final: 0.6698 (pt0) REVERT: V 30 ILE cc_start: 0.7653 (mt) cc_final: 0.7303 (tt) REVERT: V 41 GLU cc_start: 0.7138 (tt0) cc_final: 0.6509 (pt0) REVERT: V 43 ASP cc_start: 0.7613 (t70) cc_final: 0.7152 (t70) REVERT: V 45 ASP cc_start: 0.7667 (m-30) cc_final: 0.7373 (m-30) REVERT: V 49 ASN cc_start: 0.6848 (m-40) cc_final: 0.6531 (p0) REVERT: V 50 MET cc_start: 0.7454 (mmm) cc_final: 0.7078 (mtt) REVERT: V 71 LYS cc_start: 0.7260 (mtpp) cc_final: 0.7002 (mppt) REVERT: V 73 LYS cc_start: 0.7282 (mttt) cc_final: 0.6833 (mmmt) REVERT: V 82 TYR cc_start: 0.7147 (p90) cc_final: 0.6713 (p90) REVERT: V 83 LYS cc_start: 0.6603 (mttt) cc_final: 0.6336 (mttp) REVERT: V 87 GLN cc_start: 0.8428 (mt0) cc_final: 0.8152 (mt0) REVERT: W 8 ASN cc_start: 0.8130 (OUTLIER) cc_final: 0.7865 (p0) REVERT: W 21 ARG cc_start: 0.7679 (mmt-90) cc_final: 0.6836 (mmp80) REVERT: W 25 GLU cc_start: 0.7941 (tt0) cc_final: 0.7711 (mt-10) REVERT: W 35 ARG cc_start: 0.7949 (mtt-85) cc_final: 0.7687 (mmt-90) REVERT: W 51 ARG cc_start: 0.8290 (ptm-80) cc_final: 0.8084 (ptm-80) REVERT: W 62 LYS cc_start: 0.8127 (mttt) cc_final: 0.7707 (mtpt) REVERT: W 66 GLU cc_start: 0.7622 (mm-30) cc_final: 0.6974 (mt-10) REVERT: X 19 HIS cc_start: 0.7832 (t70) cc_final: 0.6822 (m170) REVERT: X 69 GLU cc_start: 0.7612 (mt-10) cc_final: 0.7307 (mm-30) REVERT: Y 58 ASN cc_start: 0.7775 (t0) cc_final: 0.7499 (t0) REVERT: 0 35 GLU cc_start: 0.7028 (mt-10) cc_final: 0.6823 (mt-10) REVERT: 1 27 ARG cc_start: 0.7517 (mtm180) cc_final: 0.6879 (mmp80) REVERT: 1 29 LYS cc_start: 0.7236 (mmmt) cc_final: 0.6973 (mmmm) REVERT: 1 53 ILE cc_start: 0.5433 (mt) cc_final: 0.5193 (mt) REVERT: 2 8 SER cc_start: 0.8544 (t) cc_final: 0.8257 (t) REVERT: 2 41 ARG cc_start: 0.7787 (mmt180) cc_final: 0.7353 (mtm-85) REVERT: 2 44 VAL cc_start: 0.7734 (p) cc_final: 0.7521 (m) REVERT: 3 14 LYS cc_start: 0.8290 (tttt) cc_final: 0.7855 (mmtm) REVERT: 3 15 LYS cc_start: 0.8528 (tptm) cc_final: 0.8257 (tptm) REVERT: 4 18 LYS cc_start: 0.8046 (tttt) cc_final: 0.7799 (mtpp) REVERT: 4 22 VAL cc_start: 0.7341 (t) cc_final: 0.7053 (p) REVERT: 4 36 ARG cc_start: 0.7758 (ttp80) cc_final: 0.7529 (ptm-80) REVERT: 5 1 MET cc_start: 0.3191 (tpt) cc_final: 0.2736 (tmm) REVERT: 6 10 GLU cc_start: 0.7710 (tp30) cc_final: 0.7199 (tt0) REVERT: 6 22 MET cc_start: 0.6060 (ttp) cc_final: 0.5401 (tpt) REVERT: 6 24 ILE cc_start: 0.7317 (pt) cc_final: 0.6527 (mt) REVERT: 6 61 ASN cc_start: 0.6435 (m110) cc_final: 0.5499 (p0) REVERT: 6 62 LYS cc_start: 0.7195 (mtpt) cc_final: 0.6626 (mmmt) REVERT: b 36 LYS cc_start: 0.5761 (mtpp) cc_final: 0.4975 (pptt) REVERT: b 41 ASN cc_start: 0.7229 (t0) cc_final: 0.6838 (t0) REVERT: b 63 LYS cc_start: 0.6920 (tptt) cc_final: 0.6417 (mtmt) REVERT: b 73 ARG cc_start: 0.5921 (mmt-90) cc_final: 0.5442 (mmm-85) REVERT: b 107 ARG cc_start: 0.7032 (ttp-110) cc_final: 0.6555 (ttm-80) REVERT: b 141 GLU cc_start: 0.7283 (mt-10) cc_final: 0.7058 (pp20) REVERT: b 142 LYS cc_start: 0.8193 (tttm) cc_final: 0.7655 (ttpt) REVERT: b 143 LEU cc_start: 0.7313 (mt) cc_final: 0.7080 (mm) REVERT: b 145 ASN cc_start: 0.7675 (p0) cc_final: 0.6162 (m-40) REVERT: b 146 SER cc_start: 0.8525 (t) cc_final: 0.8206 (p) REVERT: b 152 ASP cc_start: 0.6961 (m-30) cc_final: 0.6708 (t0) REVERT: b 158 ASP cc_start: 0.7759 (t70) cc_final: 0.7433 (t0) REVERT: c 24 ASN cc_start: 0.6068 (t0) cc_final: 0.5674 (p0) REVERT: c 31 ASN cc_start: 0.6742 (t0) cc_final: 0.6336 (t0) REVERT: c 33 ASP cc_start: 0.7596 (t70) cc_final: 0.7202 (t0) REVERT: c 45 GLU cc_start: 0.7772 (tt0) cc_final: 0.7286 (mm-30) REVERT: c 71 ARG cc_start: 0.6816 (mtt90) cc_final: 0.6579 (mtp85) REVERT: c 131 ARG cc_start: 0.7711 (mmm160) cc_final: 0.6017 (tpt90) REVERT: c 134 LYS cc_start: 0.7377 (mttt) cc_final: 0.7172 (tmmt) REVERT: c 135 ARG cc_start: 0.5605 (ttt-90) cc_final: 0.5113 (tpp80) REVERT: c 138 GLN cc_start: 0.6328 (OUTLIER) cc_final: 0.6095 (pp30) REVERT: c 141 MET cc_start: 0.7884 (mmm) cc_final: 0.7506 (mmm) REVERT: c 149 LYS cc_start: 0.7875 (tttt) cc_final: 0.7594 (tttm) REVERT: c 151 GLU cc_start: 0.8074 (tt0) cc_final: 0.7492 (tm-30) REVERT: c 156 LEU cc_start: 0.7835 (OUTLIER) cc_final: 0.7530 (pt) REVERT: c 163 ARG cc_start: 0.5484 (mtt180) cc_final: 0.4730 (mtp180) REVERT: c 167 TYR cc_start: 0.7545 (m-80) cc_final: 0.7318 (m-80) REVERT: c 169 GLU cc_start: 0.7895 (mt-10) cc_final: 0.6784 (tp30) REVERT: d 47 LEU cc_start: 0.7629 (tp) cc_final: 0.6682 (pp) REVERT: d 55 ARG cc_start: 0.5922 (mmm160) cc_final: 0.5281 (mmt-90) REVERT: d 73 ASN cc_start: 0.6912 (m-40) cc_final: 0.6609 (m-40) REVERT: d 76 LYS cc_start: 0.7426 (mtpt) cc_final: 0.7081 (mtpm) REVERT: d 77 GLU cc_start: 0.7633 (mt-10) cc_final: 0.7101 (tp30) REVERT: d 81 LEU cc_start: 0.5270 (mt) cc_final: 0.4689 (mt) REVERT: d 123 MET cc_start: 0.5919 (ttt) cc_final: 0.5481 (pp-130) REVERT: d 198 LEU cc_start: 0.5372 (mt) cc_final: 0.4748 (mt) REVERT: d 204 SER cc_start: 0.7672 (t) cc_final: 0.7279 (p) REVERT: e 11 GLN cc_start: 0.7985 (OUTLIER) cc_final: 0.7450 (tp-100) REVERT: e 12 GLU cc_start: 0.7956 (pt0) cc_final: 0.7236 (mt-10) REVERT: e 60 GLN cc_start: 0.7152 (mm-40) cc_final: 0.6311 (mt0) REVERT: e 63 MET cc_start: 0.8150 (tpp) cc_final: 0.7734 (mmt) REVERT: e 65 LYS cc_start: 0.7552 (mttm) cc_final: 0.7326 (mttp) REVERT: e 71 ILE cc_start: 0.7465 (mm) cc_final: 0.7123 (tt) REVERT: e 73 VAL cc_start: 0.8092 (t) cc_final: 0.7777 (p) REVERT: e 76 ASN cc_start: 0.7265 (t0) cc_final: 0.7037 (t0) REVERT: e 81 GLN cc_start: 0.8256 (mm-40) cc_final: 0.7448 (mp10) REVERT: e 96 GLN cc_start: 0.8588 (tt0) cc_final: 0.8371 (mt0) REVERT: e 116 VAL cc_start: 0.8030 (m) cc_final: 0.7781 (p) REVERT: e 144 GLU cc_start: 0.7949 (tt0) cc_final: 0.7411 (tp30) REVERT: f 5 GLU cc_start: 0.7142 (tt0) cc_final: 0.6725 (mt-10) REVERT: f 58 HIS cc_start: 0.7458 (t70) cc_final: 0.6927 (t70) REVERT: f 62 MET cc_start: 0.6415 (mtp) cc_final: 0.5942 (mpt) REVERT: g 34 LYS cc_start: 0.7703 (mttt) cc_final: 0.7450 (mtpm) REVERT: g 69 ARG cc_start: 0.6440 (ttm170) cc_final: 0.6149 (ttt-90) REVERT: g 71 THR cc_start: 0.8495 (m) cc_final: 0.8131 (p) REVERT: g 73 GLU cc_start: 0.7363 (pt0) cc_final: 0.7063 (pp20) REVERT: g 89 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7876 (mm-30) REVERT: g 95 ARG cc_start: 0.6929 (ttt180) cc_final: 0.6527 (ttm-80) REVERT: g 105 GLU cc_start: 0.7777 (tp30) cc_final: 0.7431 (tt0) REVERT: g 122 GLU cc_start: 0.7136 (mm-30) cc_final: 0.6689 (tt0) REVERT: g 135 LYS cc_start: 0.7183 (tptm) cc_final: 0.6972 (tmmt) REVERT: g 148 LYS cc_start: 0.8058 (tttt) cc_final: 0.7767 (tttp) REVERT: h 37 ASN cc_start: 0.7163 (t0) cc_final: 0.6879 (t0) REVERT: h 40 LYS cc_start: 0.7566 (tttp) cc_final: 0.7158 (ttpt) REVERT: h 41 GLU cc_start: 0.7653 (OUTLIER) cc_final: 0.7336 (mm-30) REVERT: h 49 LYS cc_start: 0.7399 (mttp) cc_final: 0.6966 (ptpp) REVERT: h 51 GLU cc_start: 0.6976 (mt-10) cc_final: 0.6622 (pp20) REVERT: h 60 LEU cc_start: 0.6971 (mt) cc_final: 0.6487 (mt) REVERT: h 61 THR cc_start: 0.7929 (m) cc_final: 0.7723 (m) REVERT: h 86 LYS cc_start: 0.8576 (mmtp) cc_final: 0.7868 (mtpt) REVERT: i 32 ARG cc_start: 0.7307 (mmt-90) cc_final: 0.7048 (mpt-90) REVERT: i 44 ARG cc_start: 0.5451 (mtt180) cc_final: 0.4738 (mpp-170) REVERT: i 56 MET cc_start: 0.4487 (ttp) cc_final: 0.4218 (ttp) REVERT: i 63 TYR cc_start: 0.7107 (t80) cc_final: 0.6507 (t80) REVERT: i 67 LYS cc_start: 0.7396 (pttm) cc_final: 0.6694 (mtmt) REVERT: i 123 ARG cc_start: 0.7686 (mtp-110) cc_final: 0.7010 (mtt90) REVERT: j 53 ILE cc_start: 0.7518 (tt) cc_final: 0.7202 (OUTLIER) REVERT: j 63 ASP cc_start: 0.7443 (m-30) cc_final: 0.6993 (m-30) REVERT: k 74 LYS cc_start: 0.8028 (mttt) cc_final: 0.7491 (mptt) REVERT: k 76 TYR cc_start: 0.7422 (m-80) cc_final: 0.7058 (m-80) REVERT: k 125 LYS cc_start: 0.7678 (OUTLIER) cc_final: 0.7461 (tttp) REVERT: l 30 ARG cc_start: 0.5872 (mtt180) cc_final: 0.5658 (mtm110) REVERT: l 60 PHE cc_start: 0.6984 (m-80) cc_final: 0.6702 (m-80) REVERT: l 106 VAL cc_start: 0.3879 (t) cc_final: 0.3617 (p) REVERT: l 110 LYS cc_start: 0.6382 (mmtt) cc_final: 0.5885 (mmmm) REVERT: l 111 GLN cc_start: 0.6912 (mt0) cc_final: 0.6335 (mt0) REVERT: m 56 ARG cc_start: 0.4553 (mtt90) cc_final: 0.4184 (mpt-90) REVERT: m 70 ARG cc_start: 0.7441 (ttm-80) cc_final: 0.6523 (mtt90) REVERT: m 73 SER cc_start: 0.7847 (m) cc_final: 0.7595 (p) REVERT: m 89 ARG cc_start: 0.7429 (OUTLIER) cc_final: 0.7149 (tpt170) REVERT: n 6 LYS cc_start: 0.7261 (mtpt) cc_final: 0.6871 (mtmm) REVERT: n 8 ARG cc_start: 0.7152 (ptp-170) cc_final: 0.6699 (ptp-170) REVERT: n 39 GLU cc_start: 0.7690 (mt-10) cc_final: 0.7336 (mm-30) REVERT: n 48 LEU cc_start: 0.7554 (tp) cc_final: 0.7051 (tp) REVERT: n 83 LYS cc_start: 0.7751 (mmmt) cc_final: 0.7495 (mmtt) REVERT: n 89 MET cc_start: 0.7461 (ptp) cc_final: 0.6740 (mmp) REVERT: n 90 ARG cc_start: 0.7336 (ttt90) cc_final: 0.7013 (ttp80) REVERT: n 98 LYS cc_start: 0.8132 (mtpp) cc_final: 0.7599 (tttt) REVERT: o 36 ASN cc_start: 0.8369 (m-40) cc_final: 0.8082 (m110) REVERT: o 61 GLN cc_start: 0.7943 (tp40) cc_final: 0.7647 (tt0) REVERT: p 39 PHE cc_start: 0.6898 (t80) cc_final: 0.6593 (t80) REVERT: p 40 ASN cc_start: 0.5933 (t0) cc_final: 0.5404 (p0) REVERT: q 15 LYS cc_start: 0.7306 (mttt) cc_final: 0.7054 (ptmt) REVERT: q 20 ILE cc_start: 0.6098 (tt) cc_final: 0.5858 (tp) REVERT: q 25 GLU cc_start: 0.6747 (mm-30) cc_final: 0.6260 (tm-30) REVERT: q 39 ARG cc_start: 0.6489 (mmt90) cc_final: 0.6216 (tpp-160) REVERT: r 13 THR cc_start: 0.2955 (OUTLIER) cc_final: 0.2604 (m) REVERT: r 30 ASN cc_start: 0.7454 (m-40) cc_final: 0.7228 (t0) REVERT: r 47 ARG cc_start: 0.5767 (mmt-90) cc_final: 0.5420 (mmt-90) REVERT: s 6 LYS cc_start: 0.6014 (OUTLIER) cc_final: 0.4374 (pmtt) REVERT: s 43 MET cc_start: 0.8507 (mtp) cc_final: 0.8280 (mtp) REVERT: s 62 THR cc_start: 0.7663 (p) cc_final: 0.7078 (t) REVERT: s 72 GLU cc_start: 0.8279 (mt-10) cc_final: 0.7779 (tt0) REVERT: t 20 ASN cc_start: 0.8251 (t0) cc_final: 0.7837 (m-40) REVERT: t 27 MET cc_start: 0.7885 (ttp) cc_final: 0.7362 (ttm) REVERT: t 54 GLN cc_start: 0.7165 (tt0) cc_final: 0.6964 (tm-30) REVERT: t 59 ARG cc_start: 0.5332 (ttm110) cc_final: 0.4953 (ttp-110) REVERT: t 68 LYS cc_start: 0.6483 (OUTLIER) cc_final: 0.6126 (tptp) REVERT: u 36 PHE cc_start: 0.7160 (t80) cc_final: 0.6864 (t80) REVERT: z 55 GLU cc_start: 0.3790 (mt-10) cc_final: 0.2917 (mp0) REVERT: z 171 ARG cc_start: 0.3948 (ptp-110) cc_final: 0.3668 (mpt90) REVERT: z 181 ASP cc_start: 0.5723 (m-30) cc_final: 0.4932 (t0) REVERT: z 207 ASP cc_start: 0.5715 (t0) cc_final: 0.5175 (p0) REVERT: z 237 LYS cc_start: 0.4471 (mtmt) cc_final: 0.3360 (tptt) REVERT: z 238 VAL cc_start: 0.3839 (t) cc_final: 0.3508 (m) REVERT: z 240 GLU cc_start: 0.4576 (tt0) cc_final: 0.4304 (tt0) REVERT: z 241 GLU cc_start: 0.4980 (tp30) cc_final: 0.4490 (tm-30) REVERT: z 243 GLU cc_start: 0.6250 (tt0) cc_final: 0.5585 (tp30) REVERT: z 245 VAL cc_start: 0.6034 (t) cc_final: 0.5639 (m) REVERT: z 258 VAL cc_start: 0.7400 (t) cc_final: 0.6664 (m) REVERT: z 259 GLU cc_start: 0.6116 (mt-10) cc_final: 0.2042 (mm-30) REVERT: z 260 MET cc_start: 0.6532 (tpp) cc_final: 0.5586 (mmt) REVERT: z 267 GLU cc_start: 0.2453 (mt-10) cc_final: 0.2143 (mt-10) REVERT: z 282 LYS cc_start: 0.7249 (mttt) cc_final: 0.6770 (mmmt) REVERT: z 283 ARG cc_start: 0.4875 (tpt90) cc_final: 0.4553 (tpt90) REVERT: z 310 ILE cc_start: 0.4188 (mm) cc_final: 0.3548 (mm) REVERT: z 333 ARG cc_start: 0.5205 (mtt90) cc_final: 0.4059 (tpp-160) REVERT: z 354 ASP cc_start: 0.5977 (t70) cc_final: 0.5609 (p0) REVERT: z 369 ASP cc_start: 0.4195 (m-30) cc_final: 0.2778 (p0) outliers start: 160 outliers final: 21 residues processed: 1831 average time/residue: 2.3784 time to fit residues: 6164.0574 Evaluate side-chains 1255 residues out of total 5164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 1208 time to evaluate : 6.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 35 LYS Chi-restraints excluded: chain C residue 69 ASN Chi-restraints excluded: chain C residue 110 LYS Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 56 LYS Chi-restraints excluded: chain D residue 204 LYS Chi-restraints excluded: chain E residue 139 LYS Chi-restraints excluded: chain F residue 67 THR Chi-restraints excluded: chain G residue 169 ARG Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain H residue 145 ASN Chi-restraints excluded: chain I residue 30 GLN Chi-restraints excluded: chain J residue 12 LYS Chi-restraints excluded: chain K residue 2 ILE Chi-restraints excluded: chain L residue 14 LYS Chi-restraints excluded: chain N residue 65 LEU Chi-restraints excluded: chain N residue 118 ARG Chi-restraints excluded: chain O residue 28 VAL Chi-restraints excluded: chain P residue 26 GLU Chi-restraints excluded: chain S residue 29 VAL Chi-restraints excluded: chain T residue 69 ARG Chi-restraints excluded: chain T residue 76 ARG Chi-restraints excluded: chain T residue 91 GLN Chi-restraints excluded: chain W residue 8 ASN Chi-restraints excluded: chain 6 residue 37 CYS Chi-restraints excluded: chain c residue 138 GLN Chi-restraints excluded: chain c residue 156 LEU Chi-restraints excluded: chain c residue 181 ILE Chi-restraints excluded: chain e residue 11 GLN Chi-restraints excluded: chain e residue 38 VAL Chi-restraints excluded: chain e residue 45 VAL Chi-restraints excluded: chain e residue 136 VAL Chi-restraints excluded: chain g residue 89 GLU Chi-restraints excluded: chain h residue 41 GLU Chi-restraints excluded: chain h residue 111 THR Chi-restraints excluded: chain i residue 42 THR Chi-restraints excluded: chain j residue 67 ILE Chi-restraints excluded: chain k residue 125 LYS Chi-restraints excluded: chain m residue 89 ARG Chi-restraints excluded: chain q residue 47 ASP Chi-restraints excluded: chain r residue 13 THR Chi-restraints excluded: chain s residue 6 LYS Chi-restraints excluded: chain t residue 68 LYS Chi-restraints excluded: chain u residue 62 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1087 random chunks: chunk 917 optimal weight: 0.9980 chunk 823 optimal weight: 3.9990 chunk 457 optimal weight: 0.8980 chunk 281 optimal weight: 8.9990 chunk 555 optimal weight: 20.0000 chunk 440 optimal weight: 0.9980 chunk 851 optimal weight: 4.9990 chunk 329 optimal weight: 9.9990 chunk 518 optimal weight: 3.9990 chunk 634 optimal weight: 50.0000 chunk 987 optimal weight: 0.0070 overall best weight: 1.3800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 59 GLN C 199 HIS D 32 ASN D 150 GLN E 156 ASN E 165 HIS G 37 ASN G 87 GLN G 103 ASN H 135 HIS I 42 ASN J 128 ASN K 29 HIS K 88 ASN L 104 GLN N 18 GLN P 76 HIS P 114 ASN R 6 GLN R 82 HIS R 89 HIS T 91 GLN U 65 GLN U 73 ASN V 80 HIS ** Y 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 27 ASN 4 35 GLN 6 41 HIS b 176 ASN c 7 ASN c 138 GLN d 35 GLN d 58 GLN ** d 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 18 ASN f 17 GLN f 52 ASN ** g 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 58 ASN k 39 ASN l 4 ASN o 27 GLN p 79 ASN q 30 HIS q 46 HIS ** s 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 51 HIS s 55 GLN s 68 HIS t 19 HIS t 54 GLN ** z 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 135 ASN Total number of N/Q/H flips: 49 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 165479 Z= 0.185 Angle : 0.776 17.133 247209 Z= 0.416 Chirality : 0.041 0.479 31418 Planarity : 0.007 0.132 13503 Dihedral : 24.664 179.152 81939 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.79 % Allowed : 7.30 % Favored : 91.91 % Rotamer: Outliers : 5.01 % Allowed : 18.43 % Favored : 76.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.54 (0.09), residues: 6219 helix: -0.42 (0.11), residues: 1927 sheet: -2.21 (0.14), residues: 1132 loop : -2.31 (0.10), residues: 3160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP c 200 HIS 0.018 0.001 HIS b 14 PHE 0.019 0.002 PHE r 12 TYR 0.030 0.002 TYR I 7 ARG 0.009 0.001 ARG m 92 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12438 Ramachandran restraints generated. 6219 Oldfield, 0 Emsley, 6219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12438 Ramachandran restraints generated. 6219 Oldfield, 0 Emsley, 6219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1555 residues out of total 5164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 259 poor density : 1296 time to evaluate : 6.725 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: C 3 VAL cc_start: 0.8255 (p) cc_final: 0.8053 (m) REVERT: C 4 LYS cc_start: 0.8018 (tttt) cc_final: 0.7620 (ttmm) REVERT: C 27 LYS cc_start: 0.7384 (mttt) cc_final: 0.7005 (mppt) REVERT: C 65 ASP cc_start: 0.7680 (t70) cc_final: 0.6769 (m-30) REVERT: C 113 ASP cc_start: 0.6786 (m-30) cc_final: 0.6259 (t0) REVERT: C 114 GLN cc_start: 0.7436 (tt0) cc_final: 0.6824 (mm-40) REVERT: C 116 GLN cc_start: 0.7576 (OUTLIER) cc_final: 0.6762 (tt0) REVERT: C 132 ARG cc_start: 0.6497 (ttp-110) cc_final: 0.6147 (ttp-170) REVERT: C 159 THR cc_start: 0.9229 (m) cc_final: 0.8719 (p) REVERT: C 184 GLU cc_start: 0.7124 (tt0) cc_final: 0.6425 (mt-10) REVERT: C 187 CYS cc_start: 0.8257 (m) cc_final: 0.7999 (m) REVERT: C 263 ASP cc_start: 0.7775 (OUTLIER) cc_final: 0.7440 (m-30) REVERT: D 17 GLU cc_start: 0.7499 (mm-30) cc_final: 0.7090 (mm-30) REVERT: D 30 GLU cc_start: 0.7407 (OUTLIER) cc_final: 0.7041 (tt0) REVERT: D 99 GLU cc_start: 0.8181 (mt-10) cc_final: 0.7649 (mm-30) REVERT: D 108 ASP cc_start: 0.7496 (m-30) cc_final: 0.7016 (p0) REVERT: D 197 THR cc_start: 0.8283 (m) cc_final: 0.7525 (p) REVERT: E 51 GLU cc_start: 0.7933 (mt-10) cc_final: 0.7427 (mt-10) REVERT: E 88 ARG cc_start: 0.7666 (ttm-80) cc_final: 0.7191 (mmp80) REVERT: E 106 LYS cc_start: 0.7888 (mtpt) cc_final: 0.7352 (mttt) REVERT: E 140 ASP cc_start: 0.6765 (OUTLIER) cc_final: 0.6560 (m-30) REVERT: E 143 LEU cc_start: 0.7566 (mt) cc_final: 0.7319 (mp) REVERT: E 145 ASP cc_start: 0.6903 (t0) cc_final: 0.6655 (t0) REVERT: E 158 PHE cc_start: 0.7431 (t80) cc_final: 0.7161 (t80) REVERT: E 159 LEU cc_start: 0.8529 (tp) cc_final: 0.8250 (mm) REVERT: E 175 ILE cc_start: 0.7541 (pt) cc_final: 0.7123 (mm) REVERT: E 194 LYS cc_start: 0.7777 (tptt) cc_final: 0.7559 (mmtt) REVERT: F 16 MET cc_start: 0.6564 (OUTLIER) cc_final: 0.5648 (mpp) REVERT: F 31 GLU cc_start: 0.8269 (tt0) cc_final: 0.7922 (tt0) REVERT: F 37 MET cc_start: 0.7303 (ttt) cc_final: 0.6816 (tpp) REVERT: F 41 GLU cc_start: 0.6760 (mm-30) cc_final: 0.6125 (mp0) REVERT: F 46 LYS cc_start: 0.7906 (mttt) cc_final: 0.7610 (tptm) REVERT: F 47 LYS cc_start: 0.7483 (ptmt) cc_final: 0.7081 (pmtt) REVERT: F 68 LYS cc_start: 0.7546 (mptt) cc_final: 0.7230 (mppt) REVERT: F 71 LYS cc_start: 0.7297 (mmmt) cc_final: 0.6964 (ttpt) REVERT: F 96 TRP cc_start: 0.8107 (m100) cc_final: 0.7905 (m100) REVERT: F 100 GLU cc_start: 0.8217 (tt0) cc_final: 0.7635 (tm-30) REVERT: F 104 THR cc_start: 0.7715 (t) cc_final: 0.7432 (p) REVERT: F 111 ARG cc_start: 0.6580 (ttp80) cc_final: 0.6322 (ptm160) REVERT: F 119 LYS cc_start: 0.7519 (ttpp) cc_final: 0.7197 (ttpp) REVERT: F 133 GLU cc_start: 0.7775 (mt-10) cc_final: 0.6956 (pt0) REVERT: F 137 PHE cc_start: 0.7286 (m-80) cc_final: 0.7083 (m-80) REVERT: F 147 ARG cc_start: 0.6805 (tpp80) cc_final: 0.6218 (ttt180) REVERT: F 151 LEU cc_start: 0.7436 (pp) cc_final: 0.7233 (pt) REVERT: F 160 LYS cc_start: 0.7465 (mtmm) cc_final: 0.7141 (mmtm) REVERT: F 164 GLU cc_start: 0.7149 (tt0) cc_final: 0.6946 (tt0) REVERT: G 35 THR cc_start: 0.8164 (m) cc_final: 0.7797 (p) REVERT: G 37 ASN cc_start: 0.6964 (t0) cc_final: 0.6452 (t0) REVERT: G 98 LYS cc_start: 0.7039 (ttpt) cc_final: 0.6704 (mtpm) REVERT: G 105 SER cc_start: 0.7965 (t) cc_final: 0.7655 (m) REVERT: I 135 MET cc_start: 0.2098 (mtp) cc_final: 0.1322 (tmt) REVERT: J 7 LYS cc_start: 0.6921 (OUTLIER) cc_final: 0.6719 (mmtt) REVERT: J 12 LYS cc_start: 0.7513 (OUTLIER) cc_final: 0.7090 (tptp) REVERT: J 43 GLU cc_start: 0.7945 (mt-10) cc_final: 0.7276 (pm20) REVERT: J 61 LYS cc_start: 0.8358 (mmtp) cc_final: 0.8042 (mtpt) REVERT: J 95 ARG cc_start: 0.6247 (mtp-110) cc_final: 0.5818 (ttp-110) REVERT: J 131 ASN cc_start: 0.7113 (p0) cc_final: 0.6902 (p0) REVERT: K 7 MET cc_start: 0.8341 (tpp) cc_final: 0.8004 (tpp) REVERT: K 18 ARG cc_start: 0.7871 (mmt180) cc_final: 0.7468 (tpp-160) REVERT: K 20 MET cc_start: 0.8503 (ttt) cc_final: 0.7990 (ttp) REVERT: K 51 LYS cc_start: 0.6670 (mttp) cc_final: 0.6202 (mtpp) REVERT: K 61 VAL cc_start: 0.8316 (OUTLIER) cc_final: 0.8061 (p) REVERT: K 93 GLN cc_start: 0.7943 (mm-40) cc_final: 0.7703 (mp10) REVERT: L 10 GLU cc_start: 0.7206 (mm-30) cc_final: 0.6991 (tp30) REVERT: L 12 SER cc_start: 0.8524 (t) cc_final: 0.8308 (m) REVERT: L 14 LYS cc_start: 0.7802 (OUTLIER) cc_final: 0.7575 (ttpt) REVERT: L 105 ILE cc_start: 0.8413 (mt) cc_final: 0.8191 (mm) REVERT: L 126 ARG cc_start: 0.6905 (ttp-170) cc_final: 0.6499 (mtp180) REVERT: L 141 LYS cc_start: 0.6954 (mmmt) cc_final: 0.6545 (ptpp) REVERT: M 2 LEU cc_start: 0.8684 (mt) cc_final: 0.8296 (mt) REVERT: M 3 GLN cc_start: 0.7513 (tt0) cc_final: 0.6995 (mt0) REVERT: M 6 ARG cc_start: 0.7124 (OUTLIER) cc_final: 0.6620 (ptp-110) REVERT: M 12 MET cc_start: 0.8392 (ttm) cc_final: 0.8032 (ttm) REVERT: M 30 SER cc_start: 0.8383 (OUTLIER) cc_final: 0.8170 (p) REVERT: M 41 LEU cc_start: 0.8601 (mt) cc_final: 0.8278 (mm) REVERT: M 51 ARG cc_start: 0.7648 (mtt90) cc_final: 0.7144 (mpt-90) REVERT: M 75 GLU cc_start: 0.8324 (tt0) cc_final: 0.7753 (tt0) REVERT: M 103 TYR cc_start: 0.7789 (m-80) cc_final: 0.7511 (m-80) REVERT: N 13 ASN cc_start: 0.8351 (p0) cc_final: 0.8117 (p0) REVERT: N 30 ARG cc_start: 0.8134 (ttp-110) cc_final: 0.7470 (ttm-80) REVERT: N 35 LYS cc_start: 0.7887 (tttt) cc_final: 0.7447 (tttp) REVERT: O 13 ARG cc_start: 0.6888 (ttt90) cc_final: 0.6683 (tpp-160) REVERT: O 48 LEU cc_start: 0.8286 (mm) cc_final: 0.8016 (mt) REVERT: O 76 LYS cc_start: 0.5622 (ttmp) cc_final: 0.5419 (ttmt) REVERT: O 98 GLN cc_start: 0.8124 (tt0) cc_final: 0.7893 (tt0) REVERT: P 5 LYS cc_start: 0.7386 (mttt) cc_final: 0.7184 (mttt) REVERT: P 6 GLN cc_start: 0.7703 (tt0) cc_final: 0.7449 (tm-30) REVERT: P 10 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.7501 (pt0) REVERT: P 26 GLU cc_start: 0.7312 (tt0) cc_final: 0.6886 (tm-30) REVERT: P 37 LYS cc_start: 0.7235 (tttp) cc_final: 0.6643 (ttpp) REVERT: P 47 ILE cc_start: 0.8028 (OUTLIER) cc_final: 0.7679 (mp) REVERT: P 62 LYS cc_start: 0.7617 (tttt) cc_final: 0.7363 (ttpt) REVERT: P 77 SER cc_start: 0.8417 (t) cc_final: 0.8096 (p) REVERT: P 92 ARG cc_start: 0.7970 (ptm160) cc_final: 0.7593 (ptm160) REVERT: Q 12 ARG cc_start: 0.7865 (ttm-80) cc_final: 0.7433 (ttt180) REVERT: Q 14 LYS cc_start: 0.7492 (tttt) cc_final: 0.7222 (mtpp) REVERT: Q 48 ASP cc_start: 0.8144 (m-30) cc_final: 0.7553 (m-30) REVERT: Q 77 LYS cc_start: 0.8099 (mttt) cc_final: 0.7753 (mtmt) REVERT: R 1 MET cc_start: 0.6788 (tpp) cc_final: 0.5588 (ptm) REVERT: R 18 GLN cc_start: 0.7574 (pt0) cc_final: 0.7352 (pt0) REVERT: R 66 HIS cc_start: 0.8245 (OUTLIER) cc_final: 0.6948 (m-70) REVERT: R 85 LYS cc_start: 0.8223 (tttt) cc_final: 0.7954 (mttt) REVERT: R 91 GLN cc_start: 0.8908 (tp40) cc_final: 0.8614 (tp40) REVERT: S 52 GLU cc_start: 0.7880 (tt0) cc_final: 0.7414 (mm-30) REVERT: S 62 ASP cc_start: 0.7749 (OUTLIER) cc_final: 0.7526 (p0) REVERT: S 86 MET cc_start: 0.8401 (tmm) cc_final: 0.7873 (tpt) REVERT: S 92 ARG cc_start: 0.7153 (ptp90) cc_final: 0.6566 (ptm160) REVERT: S 98 LYS cc_start: 0.7711 (mmtp) cc_final: 0.7490 (mmmt) REVERT: T 28 ASN cc_start: 0.7630 (t0) cc_final: 0.7054 (t0) REVERT: T 51 PHE cc_start: 0.7077 (m-80) cc_final: 0.6839 (m-10) REVERT: T 54 GLU cc_start: 0.7189 (mt-10) cc_final: 0.5869 (tm-30) REVERT: T 76 ARG cc_start: 0.7263 (ptt90) cc_final: 0.6697 (ptm-80) REVERT: U 25 LYS cc_start: 0.7271 (mmmt) cc_final: 0.6671 (mtpt) REVERT: U 36 GLU cc_start: 0.7311 (pt0) cc_final: 0.7102 (pp20) REVERT: U 61 GLU cc_start: 0.7611 (mt-10) cc_final: 0.7235 (mt-10) REVERT: U 71 ILE cc_start: 0.7990 (pt) cc_final: 0.7412 (mt) REVERT: U 96 LYS cc_start: 0.7047 (OUTLIER) cc_final: 0.6724 (mttp) REVERT: V 7 GLU cc_start: 0.6350 (mp0) cc_final: 0.6086 (pm20) REVERT: V 8 VAL cc_start: 0.8031 (t) cc_final: 0.7466 (m) REVERT: V 11 GLU cc_start: 0.6987 (mt-10) cc_final: 0.6709 (pt0) REVERT: V 12 GLN cc_start: 0.7939 (OUTLIER) cc_final: 0.7345 (mt0) REVERT: V 30 ILE cc_start: 0.7455 (mt) cc_final: 0.7019 (tt) REVERT: V 43 ASP cc_start: 0.7597 (t70) cc_final: 0.7227 (t70) REVERT: V 48 MET cc_start: 0.7359 (mmm) cc_final: 0.7143 (mmm) REVERT: V 49 ASN cc_start: 0.7018 (m-40) cc_final: 0.6576 (p0) REVERT: V 71 LYS cc_start: 0.7303 (mtpp) cc_final: 0.7029 (mppt) REVERT: V 73 LYS cc_start: 0.7373 (mttt) cc_final: 0.6933 (mmmt) REVERT: V 82 TYR cc_start: 0.7013 (p90) cc_final: 0.6603 (p90) REVERT: V 83 LYS cc_start: 0.6304 (mttt) cc_final: 0.6054 (mttp) REVERT: W 7 ARG cc_start: 0.7744 (tpp80) cc_final: 0.7273 (ttt90) REVERT: W 25 GLU cc_start: 0.8005 (tt0) cc_final: 0.7726 (mt-10) REVERT: W 64 LYS cc_start: 0.7910 (tptm) cc_final: 0.7466 (ttmm) REVERT: W 66 GLU cc_start: 0.7839 (mm-30) cc_final: 0.7107 (mt-10) REVERT: W 71 LYS cc_start: 0.8482 (mttt) cc_final: 0.8165 (mttp) REVERT: W 79 GLU cc_start: 0.6771 (tt0) cc_final: 0.6566 (tp30) REVERT: X 19 HIS cc_start: 0.7689 (t70) cc_final: 0.6803 (m-70) REVERT: X 67 LEU cc_start: 0.7181 (mm) cc_final: 0.6870 (mm) REVERT: X 69 GLU cc_start: 0.7695 (mt-10) cc_final: 0.7467 (mm-30) REVERT: Y 58 ASN cc_start: 0.7640 (t0) cc_final: 0.7348 (t0) REVERT: 0 11 LYS cc_start: 0.8302 (mmmt) cc_final: 0.7982 (tppp) REVERT: 1 22 THR cc_start: 0.8408 (p) cc_final: 0.7831 (t) REVERT: 1 27 ARG cc_start: 0.7576 (mtm180) cc_final: 0.7270 (mpt90) REVERT: 1 36 LYS cc_start: 0.7196 (tttt) cc_final: 0.6785 (tttt) REVERT: 2 8 SER cc_start: 0.8637 (t) cc_final: 0.8371 (t) REVERT: 2 41 ARG cc_start: 0.7790 (mmt180) cc_final: 0.7235 (mtm-85) REVERT: 2 44 VAL cc_start: 0.7723 (p) cc_final: 0.7473 (m) REVERT: 3 14 LYS cc_start: 0.8233 (tttt) cc_final: 0.7946 (mmtm) REVERT: 4 18 LYS cc_start: 0.7993 (tttt) cc_final: 0.7762 (mtpp) REVERT: 4 35 GLN cc_start: 0.7526 (pt0) cc_final: 0.7182 (pm20) REVERT: 4 36 ARG cc_start: 0.7549 (ttp80) cc_final: 0.7280 (ptm-80) REVERT: 6 10 GLU cc_start: 0.7665 (tp30) cc_final: 0.7212 (tt0) REVERT: 6 61 ASN cc_start: 0.6186 (m110) cc_final: 0.5262 (p0) REVERT: 6 62 LYS cc_start: 0.7199 (mtpt) cc_final: 0.6678 (mmmt) REVERT: b 41 ASN cc_start: 0.6214 (t0) cc_final: 0.5578 (t0) REVERT: b 65 LYS cc_start: 0.6740 (OUTLIER) cc_final: 0.6238 (mmmm) REVERT: b 87 ASP cc_start: 0.7080 (m-30) cc_final: 0.6497 (p0) REVERT: b 107 ARG cc_start: 0.7025 (ttp-170) cc_final: 0.6701 (ttm-80) REVERT: b 134 LEU cc_start: 0.6278 (OUTLIER) cc_final: 0.6036 (mm) REVERT: b 136 ARG cc_start: 0.5362 (mmm-85) cc_final: 0.4537 (ttp80) REVERT: b 141 GLU cc_start: 0.7287 (mt-10) cc_final: 0.6958 (tp30) REVERT: b 146 SER cc_start: 0.8469 (t) cc_final: 0.8208 (p) REVERT: b 158 ASP cc_start: 0.7827 (t70) cc_final: 0.7582 (t0) REVERT: b 187 ASP cc_start: 0.7355 (t0) cc_final: 0.7128 (t70) REVERT: c 33 ASP cc_start: 0.7164 (t70) cc_final: 0.6882 (t0) REVERT: c 71 ARG cc_start: 0.6842 (mtt90) cc_final: 0.6612 (mtp85) REVERT: c 128 MET cc_start: 0.7534 (mmp) cc_final: 0.6741 (mtt) REVERT: c 130 ARG cc_start: 0.7627 (OUTLIER) cc_final: 0.6943 (mtt-85) REVERT: c 141 MET cc_start: 0.7709 (mmm) cc_final: 0.7388 (mmm) REVERT: c 151 GLU cc_start: 0.8059 (tt0) cc_final: 0.7496 (tm-30) REVERT: c 156 LEU cc_start: 0.7423 (OUTLIER) cc_final: 0.7089 (mt) REVERT: c 163 ARG cc_start: 0.5155 (mtt180) cc_final: 0.4477 (mtp180) REVERT: c 169 GLU cc_start: 0.8025 (mt-10) cc_final: 0.6897 (tp30) REVERT: d 47 LEU cc_start: 0.7928 (tp) cc_final: 0.7702 (tm) REVERT: d 55 ARG cc_start: 0.5984 (mmm160) cc_final: 0.5072 (mmt-90) REVERT: d 69 ARG cc_start: 0.6956 (ttm170) cc_final: 0.6536 (ttm-80) REVERT: d 72 ARG cc_start: 0.6867 (tmm-80) cc_final: 0.6618 (tmm-80) REVERT: d 123 MET cc_start: 0.5495 (ttt) cc_final: 0.5293 (pp-130) REVERT: d 135 GLN cc_start: 0.4903 (tm-30) cc_final: 0.3565 (mm110) REVERT: e 11 GLN cc_start: 0.7996 (OUTLIER) cc_final: 0.7640 (tp-100) REVERT: e 71 ILE cc_start: 0.7317 (mm) cc_final: 0.6879 (tt) REVERT: e 81 GLN cc_start: 0.8190 (mm-40) cc_final: 0.7725 (mm-40) REVERT: e 144 GLU cc_start: 0.7850 (tt0) cc_final: 0.7522 (tt0) REVERT: f 14 GLN cc_start: 0.7616 (mt0) cc_final: 0.7397 (mm-40) REVERT: f 58 HIS cc_start: 0.7624 (t70) cc_final: 0.7131 (t-170) REVERT: f 62 MET cc_start: 0.6963 (mtp) cc_final: 0.6436 (mpt) REVERT: f 69 GLU cc_start: 0.7858 (mp0) cc_final: 0.7630 (mp0) REVERT: f 73 GLU cc_start: 0.7168 (mt-10) cc_final: 0.6914 (mt-10) REVERT: f 88 MET cc_start: 0.7438 (ptm) cc_final: 0.7233 (ptm) REVERT: g 3 ARG cc_start: 0.6554 (ttt180) cc_final: 0.5863 (mmt180) REVERT: g 20 GLU cc_start: 0.5440 (mm-30) cc_final: 0.5152 (mp0) REVERT: g 59 GLU cc_start: 0.6724 (tt0) cc_final: 0.6294 (tt0) REVERT: g 62 GLU cc_start: 0.6391 (OUTLIER) cc_final: 0.5411 (mt-10) REVERT: g 69 ARG cc_start: 0.6755 (ttm170) cc_final: 0.6322 (mtp180) REVERT: g 71 THR cc_start: 0.8325 (m) cc_final: 0.8003 (p) REVERT: g 73 GLU cc_start: 0.7106 (pt0) cc_final: 0.6636 (pp20) REVERT: g 105 GLU cc_start: 0.7728 (tp30) cc_final: 0.7281 (tp30) REVERT: g 117 LEU cc_start: 0.6344 (OUTLIER) cc_final: 0.6142 (tt) REVERT: g 122 GLU cc_start: 0.7446 (mm-30) cc_final: 0.6982 (tt0) REVERT: g 134 VAL cc_start: 0.7164 (m) cc_final: 0.6885 (t) REVERT: g 135 LYS cc_start: 0.7085 (tptm) cc_final: 0.6869 (tmmt) REVERT: g 137 ARG cc_start: 0.6484 (OUTLIER) cc_final: 0.6236 (ttp80) REVERT: g 148 LYS cc_start: 0.8086 (tttt) cc_final: 0.7800 (tttp) REVERT: h 2 MET cc_start: 0.8071 (tpp) cc_final: 0.7833 (tpp) REVERT: h 28 SER cc_start: 0.8256 (t) cc_final: 0.7540 (p) REVERT: h 37 ASN cc_start: 0.7536 (t0) cc_final: 0.7320 (t0) REVERT: h 40 LYS cc_start: 0.7546 (tttp) cc_final: 0.7104 (ttpt) REVERT: h 41 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.7479 (mm-30) REVERT: h 86 LYS cc_start: 0.8536 (mmtp) cc_final: 0.8272 (tppp) REVERT: h 90 GLU cc_start: 0.8053 (tt0) cc_final: 0.7301 (mp0) REVERT: h 93 LYS cc_start: 0.7359 (ptpt) cc_final: 0.6987 (ptpp) REVERT: i 32 ARG cc_start: 0.7206 (mmt-90) cc_final: 0.6977 (mpt-90) REVERT: i 63 TYR cc_start: 0.7018 (t80) cc_final: 0.6433 (t80) REVERT: i 123 ARG cc_start: 0.7709 (mtp-110) cc_final: 0.6883 (mtt90) REVERT: k 74 LYS cc_start: 0.7765 (mttt) cc_final: 0.7329 (mptt) REVERT: k 76 TYR cc_start: 0.7377 (m-80) cc_final: 0.7026 (m-80) REVERT: k 125 LYS cc_start: 0.7768 (ttmt) cc_final: 0.7547 (ttmp) REVERT: k 126 ARG cc_start: 0.8320 (OUTLIER) cc_final: 0.8067 (ptm-80) REVERT: l 35 ARG cc_start: 0.6098 (ttt90) cc_final: 0.5780 (ttt90) REVERT: l 111 GLN cc_start: 0.6845 (mt0) cc_final: 0.6586 (mp10) REVERT: m 26 LYS cc_start: 0.7208 (tttp) cc_final: 0.6956 (ttmm) REVERT: m 38 ILE cc_start: 0.7294 (mm) cc_final: 0.7045 (tp) REVERT: m 56 ARG cc_start: 0.3811 (mtt90) cc_final: 0.3521 (mpt-90) REVERT: m 70 ARG cc_start: 0.7205 (ttm-80) cc_final: 0.6543 (mtt180) REVERT: m 73 SER cc_start: 0.7767 (m) cc_final: 0.7529 (p) REVERT: n 39 GLU cc_start: 0.7764 (mt-10) cc_final: 0.7304 (mm-30) REVERT: n 89 MET cc_start: 0.7280 (ptp) cc_final: 0.6855 (mmp) REVERT: n 90 ARG cc_start: 0.7364 (ttt90) cc_final: 0.6877 (ttp-170) REVERT: o 25 GLU cc_start: 0.7813 (mp0) cc_final: 0.7523 (mp0) REVERT: o 39 GLN cc_start: 0.7939 (mm-40) cc_final: 0.7544 (mm-40) REVERT: o 52 ARG cc_start: 0.7357 (ttt-90) cc_final: 0.7031 (tpp80) REVERT: o 61 GLN cc_start: 0.7902 (tp40) cc_final: 0.7427 (tt0) REVERT: o 82 GLU cc_start: 0.7926 (mt-10) cc_final: 0.7618 (tm-30) REVERT: p 40 ASN cc_start: 0.5622 (t0) cc_final: 0.5152 (p0) REVERT: q 18 LYS cc_start: 0.5237 (ttpt) cc_final: 0.4708 (ttmt) REVERT: q 25 GLU cc_start: 0.6685 (mm-30) cc_final: 0.6467 (tm-30) REVERT: r 21 ASP cc_start: 0.8486 (t0) cc_final: 0.8108 (t70) REVERT: r 30 ASN cc_start: 0.7574 (m-40) cc_final: 0.7313 (t0) REVERT: s 17 LYS cc_start: 0.7971 (ttmm) cc_final: 0.7729 (ttmm) REVERT: s 43 MET cc_start: 0.8223 (mtp) cc_final: 0.8022 (mtp) REVERT: s 62 THR cc_start: 0.7700 (p) cc_final: 0.7392 (t) REVERT: s 72 GLU cc_start: 0.8230 (mt-10) cc_final: 0.7750 (mt-10) REVERT: t 14 GLU cc_start: 0.7428 (tm-30) cc_final: 0.7091 (tp30) REVERT: t 20 ASN cc_start: 0.8107 (t0) cc_final: 0.7729 (m110) REVERT: t 59 ARG cc_start: 0.5384 (ttm110) cc_final: 0.4949 (ttp-110) REVERT: u 33 ARG cc_start: 0.8004 (mtt180) cc_final: 0.7764 (mtm-85) REVERT: u 35 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.7974 (tt0) REVERT: u 36 PHE cc_start: 0.6790 (t80) cc_final: 0.6500 (t80) REVERT: u 44 ARG cc_start: 0.7103 (mtt180) cc_final: 0.6833 (mtt180) REVERT: z 54 GLU cc_start: 0.5562 (OUTLIER) cc_final: 0.4379 (pm20) REVERT: z 55 GLU cc_start: 0.3865 (mt-10) cc_final: 0.3307 (mp0) REVERT: z 117 GLU cc_start: 0.4774 (tm-30) cc_final: 0.4394 (mp0) REVERT: z 171 ARG cc_start: 0.3664 (ptp-110) cc_final: 0.3184 (mpp-170) REVERT: z 201 GLU cc_start: 0.2581 (mt-10) cc_final: 0.2072 (tp30) REVERT: z 211 LEU cc_start: 0.4534 (tp) cc_final: 0.4159 (mp) REVERT: z 218 PHE cc_start: 0.5045 (m-80) cc_final: 0.4834 (m-80) REVERT: z 237 LYS cc_start: 0.4501 (mtmt) cc_final: 0.3393 (tptt) REVERT: z 238 VAL cc_start: 0.3694 (t) cc_final: 0.3354 (m) REVERT: z 240 GLU cc_start: 0.4425 (tt0) cc_final: 0.4132 (tt0) REVERT: z 262 ARG cc_start: 0.4846 (OUTLIER) cc_final: 0.4630 (mpt-90) REVERT: z 282 LYS cc_start: 0.7273 (mttt) cc_final: 0.6726 (mmmm) REVERT: z 283 ARG cc_start: 0.4769 (tpt90) cc_final: 0.4555 (tpt90) REVERT: z 310 ILE cc_start: 0.4023 (mm) cc_final: 0.3384 (mm) REVERT: z 354 ASP cc_start: 0.6225 (t70) cc_final: 0.5682 (p0) REVERT: z 369 ASP cc_start: 0.4039 (m-30) cc_final: 0.2900 (p0) outliers start: 259 outliers final: 78 residues processed: 1442 average time/residue: 2.2564 time to fit residues: 4705.5974 Evaluate side-chains 1258 residues out of total 5164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 1150 time to evaluate : 6.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 9 SER Chi-restraints excluded: chain C residue 35 LYS Chi-restraints excluded: chain C residue 37 SER Chi-restraints excluded: chain C residue 69 ASN Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 116 GLN Chi-restraints excluded: chain C residue 263 ASP Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 28 GLU Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 140 ASP Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain F residue 16 MET Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain F residue 148 VAL Chi-restraints excluded: chain F residue 152 ASP Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain H residue 138 VAL Chi-restraints excluded: chain H residue 145 ASN Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain J residue 7 LYS Chi-restraints excluded: chain J residue 12 LYS Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain K residue 61 VAL Chi-restraints excluded: chain K residue 106 GLU Chi-restraints excluded: chain L residue 14 LYS Chi-restraints excluded: chain L residue 91 ASP Chi-restraints excluded: chain M residue 6 ARG Chi-restraints excluded: chain M residue 30 SER Chi-restraints excluded: chain M residue 105 MET Chi-restraints excluded: chain P residue 10 GLU Chi-restraints excluded: chain P residue 32 VAL Chi-restraints excluded: chain P residue 47 ILE Chi-restraints excluded: chain Q residue 108 LEU Chi-restraints excluded: chain R residue 66 HIS Chi-restraints excluded: chain S residue 29 VAL Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 82 MET Chi-restraints excluded: chain U residue 96 LYS Chi-restraints excluded: chain V residue 12 GLN Chi-restraints excluded: chain V residue 63 ILE Chi-restraints excluded: chain W residue 39 THR Chi-restraints excluded: chain X residue 34 SER Chi-restraints excluded: chain Y residue 19 LEU Chi-restraints excluded: chain Y residue 40 SER Chi-restraints excluded: chain Z residue 3 THR Chi-restraints excluded: chain Z residue 51 SER Chi-restraints excluded: chain 1 residue 42 VAL Chi-restraints excluded: chain 6 residue 40 CYS Chi-restraints excluded: chain b residue 21 TYR Chi-restraints excluded: chain b residue 65 LYS Chi-restraints excluded: chain b residue 66 ILE Chi-restraints excluded: chain b residue 134 LEU Chi-restraints excluded: chain b residue 170 ILE Chi-restraints excluded: chain b residue 190 SER Chi-restraints excluded: chain c residue 130 ARG Chi-restraints excluded: chain c residue 156 LEU Chi-restraints excluded: chain d residue 137 SER Chi-restraints excluded: chain d residue 158 LEU Chi-restraints excluded: chain d residue 168 THR Chi-restraints excluded: chain e residue 11 GLN Chi-restraints excluded: chain e residue 17 VAL Chi-restraints excluded: chain e residue 45 VAL Chi-restraints excluded: chain e residue 91 SER Chi-restraints excluded: chain e residue 129 SER Chi-restraints excluded: chain e residue 136 VAL Chi-restraints excluded: chain e residue 160 VAL Chi-restraints excluded: chain f residue 70 VAL Chi-restraints excluded: chain g residue 11 ILE Chi-restraints excluded: chain g residue 62 GLU Chi-restraints excluded: chain g residue 76 SER Chi-restraints excluded: chain g residue 117 LEU Chi-restraints excluded: chain g residue 132 THR Chi-restraints excluded: chain g residue 137 ARG Chi-restraints excluded: chain h residue 11 THR Chi-restraints excluded: chain h residue 25 THR Chi-restraints excluded: chain h residue 41 GLU Chi-restraints excluded: chain h residue 111 THR Chi-restraints excluded: chain h residue 128 VAL Chi-restraints excluded: chain i residue 42 THR Chi-restraints excluded: chain i residue 61 ASP Chi-restraints excluded: chain i residue 97 LEU Chi-restraints excluded: chain j residue 8 ILE Chi-restraints excluded: chain j residue 96 VAL Chi-restraints excluded: chain k residue 49 SER Chi-restraints excluded: chain k residue 80 ASN Chi-restraints excluded: chain k residue 126 ARG Chi-restraints excluded: chain l residue 51 VAL Chi-restraints excluded: chain l residue 54 VAL Chi-restraints excluded: chain m residue 28 ARG Chi-restraints excluded: chain m residue 67 ASP Chi-restraints excluded: chain n residue 3 GLN Chi-restraints excluded: chain p residue 2 VAL Chi-restraints excluded: chain p residue 19 VAL Chi-restraints excluded: chain r residue 67 LEU Chi-restraints excluded: chain s residue 36 ARG Chi-restraints excluded: chain u residue 35 GLU Chi-restraints excluded: chain u residue 62 GLU Chi-restraints excluded: chain z residue 54 GLU Chi-restraints excluded: chain z residue 255 CYS Chi-restraints excluded: chain z residue 260 MET Chi-restraints excluded: chain z residue 262 ARG Chi-restraints excluded: chain z residue 274 VAL Chi-restraints excluded: chain z residue 374 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1087 random chunks: chunk 548 optimal weight: 9.9990 chunk 306 optimal weight: 5.9990 chunk 821 optimal weight: 8.9990 chunk 672 optimal weight: 10.0000 chunk 272 optimal weight: 8.9990 chunk 988 optimal weight: 3.9990 chunk 1068 optimal weight: 10.0000 chunk 880 optimal weight: 0.9990 chunk 980 optimal weight: 6.9990 chunk 337 optimal weight: 0.2980 chunk 793 optimal weight: 8.9990 overall best weight: 3.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 133 ASN E 156 ASN E 165 HIS F 134 GLN ** I 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 40 HIS P 76 HIS R 6 GLN T 70 HIS U 73 ASN ** V 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 45 GLN 2 6 GLN 6 41 HIS b 18 GLN b 176 ASN d 58 GLN d 125 ASN d 197 HIS e 76 ASN f 3 HIS f 52 ASN ** g 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 129 ASN i 4 GLN i 74 GLN ** l 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 55 GLN t 19 HIS t 81 GLN z 11 HIS ** z 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 75 HIS ** z 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.2713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 165479 Z= 0.301 Angle : 0.772 14.625 247209 Z= 0.413 Chirality : 0.041 0.424 31418 Planarity : 0.008 0.181 13503 Dihedral : 24.465 178.927 81857 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.68 % Allowed : 8.20 % Favored : 91.12 % Rotamer: Outliers : 6.74 % Allowed : 20.65 % Favored : 72.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.18 (0.10), residues: 6219 helix: -0.11 (0.11), residues: 1957 sheet: -1.81 (0.14), residues: 1158 loop : -2.20 (0.10), residues: 3104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 212 HIS 0.018 0.002 HIS b 14 PHE 0.026 0.002 PHE l 60 TYR 0.045 0.002 TYR z 160 ARG 0.032 0.001 ARG n 23 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12438 Ramachandran restraints generated. 6219 Oldfield, 0 Emsley, 6219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12438 Ramachandran restraints generated. 6219 Oldfield, 0 Emsley, 6219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1583 residues out of total 5164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 348 poor density : 1235 time to evaluate : 6.665 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: C 4 LYS cc_start: 0.8052 (tttt) cc_final: 0.7626 (ttmm) REVERT: C 22 GLU cc_start: 0.7735 (OUTLIER) cc_final: 0.7380 (mm-30) REVERT: C 27 LYS cc_start: 0.7537 (mttt) cc_final: 0.7075 (mppt) REVERT: C 70 LYS cc_start: 0.6445 (OUTLIER) cc_final: 0.6185 (tttp) REVERT: C 124 LYS cc_start: 0.6994 (OUTLIER) cc_final: 0.6793 (tmmm) REVERT: C 159 THR cc_start: 0.9215 (m) cc_final: 0.8754 (p) REVERT: C 184 GLU cc_start: 0.7149 (tt0) cc_final: 0.6433 (mt-10) REVERT: C 187 CYS cc_start: 0.8316 (m) cc_final: 0.7975 (m) REVERT: C 252 LYS cc_start: 0.8307 (OUTLIER) cc_final: 0.8018 (mmtm) REVERT: D 17 GLU cc_start: 0.7226 (mm-30) cc_final: 0.6924 (mm-30) REVERT: D 58 ASN cc_start: 0.7306 (p0) cc_final: 0.7000 (t0) REVERT: D 77 ARG cc_start: 0.7306 (OUTLIER) cc_final: 0.5149 (ppt90) REVERT: D 108 ASP cc_start: 0.7517 (m-30) cc_final: 0.6924 (p0) REVERT: D 150 GLN cc_start: 0.8264 (OUTLIER) cc_final: 0.8054 (tt0) REVERT: D 186 LEU cc_start: 0.7953 (mt) cc_final: 0.7751 (mt) REVERT: E 51 GLU cc_start: 0.7859 (mt-10) cc_final: 0.7568 (mp0) REVERT: E 88 ARG cc_start: 0.7552 (ttm-80) cc_final: 0.7033 (mmp80) REVERT: E 106 LYS cc_start: 0.7679 (mtpt) cc_final: 0.7353 (mttp) REVERT: E 194 LYS cc_start: 0.7883 (tptt) cc_final: 0.7607 (mmtp) REVERT: F 16 MET cc_start: 0.6436 (OUTLIER) cc_final: 0.5473 (mpp) REVERT: F 31 GLU cc_start: 0.8282 (tt0) cc_final: 0.7969 (tt0) REVERT: F 41 GLU cc_start: 0.6893 (mm-30) cc_final: 0.6153 (mp0) REVERT: F 46 LYS cc_start: 0.7925 (mttt) cc_final: 0.7625 (tptm) REVERT: F 47 LYS cc_start: 0.7509 (ptmt) cc_final: 0.7083 (pmtt) REVERT: F 68 LYS cc_start: 0.7593 (mptt) cc_final: 0.7344 (mppt) REVERT: F 71 LYS cc_start: 0.7335 (mmmt) cc_final: 0.6965 (ttpt) REVERT: F 100 GLU cc_start: 0.8254 (tt0) cc_final: 0.7952 (tm-30) REVERT: F 114 ARG cc_start: 0.6513 (mmm160) cc_final: 0.6306 (mmm160) REVERT: F 119 LYS cc_start: 0.7591 (ttpp) cc_final: 0.7378 (ttpp) REVERT: F 133 GLU cc_start: 0.7718 (mt-10) cc_final: 0.6936 (pt0) REVERT: F 137 PHE cc_start: 0.7329 (m-80) cc_final: 0.7109 (m-80) REVERT: F 147 ARG cc_start: 0.6729 (tpp80) cc_final: 0.6124 (ttt90) REVERT: F 160 LYS cc_start: 0.7394 (mtmm) cc_final: 0.7171 (mmtp) REVERT: G 37 ASN cc_start: 0.6684 (t0) cc_final: 0.6222 (t0) REVERT: I 135 MET cc_start: 0.1785 (mtp) cc_final: 0.1126 (tmt) REVERT: J 12 LYS cc_start: 0.7507 (OUTLIER) cc_final: 0.7072 (tptp) REVERT: J 43 GLU cc_start: 0.8072 (mt-10) cc_final: 0.7371 (pm20) REVERT: J 61 LYS cc_start: 0.8358 (mmtp) cc_final: 0.7969 (mtpt) REVERT: J 91 GLU cc_start: 0.7836 (mt-10) cc_final: 0.7408 (tp30) REVERT: J 95 ARG cc_start: 0.6448 (mtp-110) cc_final: 0.5925 (ttp-110) REVERT: K 7 MET cc_start: 0.8415 (tpp) cc_final: 0.8077 (tpp) REVERT: K 20 MET cc_start: 0.8624 (ttp) cc_final: 0.8344 (ttp) REVERT: K 66 LYS cc_start: 0.8130 (mttt) cc_final: 0.7885 (mtpt) REVERT: K 93 GLN cc_start: 0.7800 (mm-40) cc_final: 0.7544 (mp10) REVERT: K 113 MET cc_start: 0.7507 (mpt) cc_final: 0.6751 (mmm) REVERT: L 10 GLU cc_start: 0.7294 (mm-30) cc_final: 0.7059 (tp30) REVERT: L 12 SER cc_start: 0.8540 (t) cc_final: 0.8276 (m) REVERT: L 14 LYS cc_start: 0.7734 (OUTLIER) cc_final: 0.7482 (ttpt) REVERT: L 105 ILE cc_start: 0.8501 (mt) cc_final: 0.8196 (mm) REVERT: L 106 GLU cc_start: 0.8228 (mt-10) cc_final: 0.8028 (mm-30) REVERT: L 141 LYS cc_start: 0.6892 (mmmt) cc_final: 0.6470 (ptpp) REVERT: M 3 GLN cc_start: 0.7699 (tt0) cc_final: 0.7317 (tt0) REVERT: M 6 ARG cc_start: 0.7245 (ttt90) cc_final: 0.6661 (ptp90) REVERT: M 10 ARG cc_start: 0.7963 (mtm110) cc_final: 0.7740 (mtp-110) REVERT: M 12 MET cc_start: 0.8312 (ttm) cc_final: 0.8000 (ttm) REVERT: M 41 LEU cc_start: 0.8652 (mt) cc_final: 0.8327 (mm) REVERT: M 55 ARG cc_start: 0.7528 (OUTLIER) cc_final: 0.6851 (ttm170) REVERT: M 75 GLU cc_start: 0.8267 (tt0) cc_final: 0.7709 (tt0) REVERT: N 35 LYS cc_start: 0.7853 (tttt) cc_final: 0.7485 (tttp) REVERT: O 13 ARG cc_start: 0.6963 (ttt90) cc_final: 0.6749 (tpp-160) REVERT: O 20 GLU cc_start: 0.7688 (tp30) cc_final: 0.7458 (tp30) REVERT: O 98 GLN cc_start: 0.8242 (tt0) cc_final: 0.7930 (tt0) REVERT: P 6 GLN cc_start: 0.7728 (tt0) cc_final: 0.7476 (tm-30) REVERT: P 10 GLU cc_start: 0.7880 (OUTLIER) cc_final: 0.7614 (pt0) REVERT: P 26 GLU cc_start: 0.7198 (tt0) cc_final: 0.6818 (tm-30) REVERT: P 62 LYS cc_start: 0.7596 (tttt) cc_final: 0.7335 (ttpt) REVERT: P 92 ARG cc_start: 0.8308 (ptm160) cc_final: 0.7864 (ptm160) REVERT: Q 12 ARG cc_start: 0.7987 (ttm-80) cc_final: 0.7558 (ttt180) REVERT: Q 14 LYS cc_start: 0.7575 (tttt) cc_final: 0.7223 (mtpp) REVERT: Q 48 ASP cc_start: 0.8365 (m-30) cc_final: 0.7756 (m-30) REVERT: Q 77 LYS cc_start: 0.8117 (mttt) cc_final: 0.7695 (mtpt) REVERT: Q 83 LYS cc_start: 0.7867 (OUTLIER) cc_final: 0.7632 (ttmm) REVERT: R 1 MET cc_start: 0.6654 (tpp) cc_final: 0.5454 (ptp) REVERT: R 18 GLN cc_start: 0.7459 (pt0) cc_final: 0.7205 (pt0) REVERT: R 66 HIS cc_start: 0.8453 (OUTLIER) cc_final: 0.7066 (m-70) REVERT: R 84 ARG cc_start: 0.8387 (OUTLIER) cc_final: 0.7883 (ptp90) REVERT: R 91 GLN cc_start: 0.8900 (tp40) cc_final: 0.8589 (tp40) REVERT: S 1 MET cc_start: 0.6719 (mmm) cc_final: 0.6416 (mmm) REVERT: S 34 ASP cc_start: 0.7316 (m-30) cc_final: 0.7079 (m-30) REVERT: S 39 THR cc_start: 0.7806 (m) cc_final: 0.7500 (m) REVERT: S 52 GLU cc_start: 0.7953 (tt0) cc_final: 0.7444 (mm-30) REVERT: S 62 ASP cc_start: 0.7064 (OUTLIER) cc_final: 0.6714 (p0) REVERT: S 86 MET cc_start: 0.8474 (OUTLIER) cc_final: 0.7842 (tpt) REVERT: S 92 ARG cc_start: 0.7230 (ptp90) cc_final: 0.6577 (ptm160) REVERT: S 94 ASP cc_start: 0.8221 (m-30) cc_final: 0.7473 (m-30) REVERT: T 28 ASN cc_start: 0.7594 (t0) cc_final: 0.7036 (t0) REVERT: T 51 PHE cc_start: 0.7256 (m-80) cc_final: 0.7050 (m-10) REVERT: T 54 GLU cc_start: 0.7072 (mt-10) cc_final: 0.6286 (mm-30) REVERT: T 76 ARG cc_start: 0.7258 (OUTLIER) cc_final: 0.6564 (ptm-80) REVERT: U 20 LYS cc_start: 0.6882 (mtpp) cc_final: 0.6655 (mtpt) REVERT: U 25 LYS cc_start: 0.7284 (mmmt) cc_final: 0.6625 (mtpp) REVERT: U 71 ILE cc_start: 0.8098 (pt) cc_final: 0.7608 (mt) REVERT: V 8 VAL cc_start: 0.7938 (t) cc_final: 0.7673 (m) REVERT: V 11 GLU cc_start: 0.6930 (mt-10) cc_final: 0.6625 (pt0) REVERT: V 30 ILE cc_start: 0.7403 (mt) cc_final: 0.6942 (tt) REVERT: V 41 GLU cc_start: 0.7277 (pt0) cc_final: 0.7033 (pt0) REVERT: V 43 ASP cc_start: 0.7609 (t70) cc_final: 0.7218 (t70) REVERT: V 71 LYS cc_start: 0.7209 (mtpp) cc_final: 0.6834 (mppt) REVERT: V 73 LYS cc_start: 0.7316 (mttt) cc_final: 0.7016 (mmmt) REVERT: V 75 GLN cc_start: 0.7662 (tp40) cc_final: 0.7306 (tp-100) REVERT: V 82 TYR cc_start: 0.7165 (p90) cc_final: 0.6763 (p90) REVERT: W 21 ARG cc_start: 0.7703 (mmt-90) cc_final: 0.6671 (mmp-170) REVERT: W 25 GLU cc_start: 0.8130 (tt0) cc_final: 0.7863 (tt0) REVERT: W 66 GLU cc_start: 0.8160 (mm-30) cc_final: 0.7138 (mt-10) REVERT: W 71 LYS cc_start: 0.8391 (mttt) cc_final: 0.8041 (mttp) REVERT: X 19 HIS cc_start: 0.7661 (t70) cc_final: 0.6786 (m-70) REVERT: X 67 LEU cc_start: 0.7103 (mm) cc_final: 0.6786 (mm) REVERT: X 69 GLU cc_start: 0.7609 (mt-10) cc_final: 0.7404 (mm-30) REVERT: X 71 ARG cc_start: 0.6293 (mtm110) cc_final: 0.5981 (ptp-110) REVERT: Y 14 LEU cc_start: 0.6102 (mm) cc_final: 0.5811 (mt) REVERT: Y 58 ASN cc_start: 0.7698 (t0) cc_final: 0.7392 (t0) REVERT: Z 5 LYS cc_start: 0.7192 (mtmm) cc_final: 0.6974 (mtpp) REVERT: 0 11 LYS cc_start: 0.8282 (mmmt) cc_final: 0.7975 (tppp) REVERT: 1 27 ARG cc_start: 0.7601 (mtm180) cc_final: 0.7050 (mmp80) REVERT: 1 32 LYS cc_start: 0.7494 (mttt) cc_final: 0.7207 (pptt) REVERT: 2 8 SER cc_start: 0.8656 (t) cc_final: 0.8375 (t) REVERT: 2 41 ARG cc_start: 0.7764 (mmt180) cc_final: 0.7188 (mtm-85) REVERT: 2 44 VAL cc_start: 0.7944 (p) cc_final: 0.7708 (m) REVERT: 3 14 LYS cc_start: 0.8360 (tttt) cc_final: 0.8018 (mmtm) REVERT: 3 15 LYS cc_start: 0.8400 (tptm) cc_final: 0.8165 (tptm) REVERT: 4 18 LYS cc_start: 0.8003 (tttt) cc_final: 0.7762 (mtpp) REVERT: 6 10 GLU cc_start: 0.7728 (tp30) cc_final: 0.7214 (tt0) REVERT: 6 61 ASN cc_start: 0.6154 (m110) cc_final: 0.5102 (p0) REVERT: 6 62 LYS cc_start: 0.7169 (mtpt) cc_final: 0.6678 (mmmt) REVERT: 6 63 ARG cc_start: 0.4928 (OUTLIER) cc_final: 0.4432 (mtt-85) REVERT: b 41 ASN cc_start: 0.6446 (t0) cc_final: 0.5738 (t0) REVERT: b 65 LYS cc_start: 0.6602 (OUTLIER) cc_final: 0.6091 (mmmm) REVERT: b 107 ARG cc_start: 0.6869 (ttp-170) cc_final: 0.6413 (ttm-80) REVERT: b 132 GLU cc_start: 0.6675 (tp30) cc_final: 0.6294 (tt0) REVERT: b 134 LEU cc_start: 0.6141 (OUTLIER) cc_final: 0.5900 (mm) REVERT: b 136 ARG cc_start: 0.5250 (mmm-85) cc_final: 0.4459 (ttp80) REVERT: b 141 GLU cc_start: 0.7380 (mt-10) cc_final: 0.7151 (tp30) REVERT: c 33 ASP cc_start: 0.7354 (t70) cc_final: 0.7067 (t0) REVERT: c 45 GLU cc_start: 0.8127 (tm-30) cc_final: 0.7306 (mm-30) REVERT: c 71 ARG cc_start: 0.7093 (mtt90) cc_final: 0.6765 (mtp85) REVERT: c 128 MET cc_start: 0.7539 (mmp) cc_final: 0.6667 (mtt) REVERT: c 130 ARG cc_start: 0.7694 (OUTLIER) cc_final: 0.6751 (mtt-85) REVERT: c 141 MET cc_start: 0.7779 (mmm) cc_final: 0.7392 (mmm) REVERT: c 151 GLU cc_start: 0.8042 (tt0) cc_final: 0.7518 (tm-30) REVERT: c 156 LEU cc_start: 0.7595 (OUTLIER) cc_final: 0.7230 (mt) REVERT: c 163 ARG cc_start: 0.5228 (mtt180) cc_final: 0.4473 (mpp-170) REVERT: c 169 GLU cc_start: 0.7896 (mt-10) cc_final: 0.6889 (tp30) REVERT: d 47 LEU cc_start: 0.8106 (tp) cc_final: 0.7787 (tm) REVERT: d 73 ASN cc_start: 0.6996 (m-40) cc_final: 0.6511 (p0) REVERT: d 77 GLU cc_start: 0.7606 (mt-10) cc_final: 0.6820 (tp30) REVERT: d 123 MET cc_start: 0.5397 (ttt) cc_final: 0.5172 (pp-130) REVERT: d 135 GLN cc_start: 0.4765 (tm-30) cc_final: 0.3534 (mm110) REVERT: d 162 GLU cc_start: 0.3054 (mm-30) cc_final: 0.1530 (pp20) REVERT: d 177 MET cc_start: 0.0063 (mtt) cc_final: -0.0831 (tpp) REVERT: e 71 ILE cc_start: 0.7044 (mm) cc_final: 0.6676 (tt) REVERT: e 81 GLN cc_start: 0.8197 (mm-40) cc_final: 0.7774 (mm-40) REVERT: e 127 TYR cc_start: 0.8402 (m-80) cc_final: 0.8055 (m-80) REVERT: e 144 GLU cc_start: 0.7880 (tt0) cc_final: 0.7653 (tt0) REVERT: f 58 HIS cc_start: 0.7588 (t70) cc_final: 0.7144 (t-170) REVERT: f 62 MET cc_start: 0.6864 (mtp) cc_final: 0.6294 (mpt) REVERT: g 3 ARG cc_start: 0.6570 (ttt180) cc_final: 0.5930 (mpt180) REVERT: g 59 GLU cc_start: 0.6777 (tt0) cc_final: 0.6335 (tt0) REVERT: g 62 GLU cc_start: 0.6328 (OUTLIER) cc_final: 0.5339 (mt-10) REVERT: g 105 GLU cc_start: 0.7791 (tp30) cc_final: 0.7266 (tp30) REVERT: g 129 ASN cc_start: 0.6452 (OUTLIER) cc_final: 0.6017 (m-40) REVERT: g 134 VAL cc_start: 0.7319 (m) cc_final: 0.6873 (t) REVERT: g 135 LYS cc_start: 0.7271 (tptm) cc_final: 0.6961 (tmmt) REVERT: g 137 ARG cc_start: 0.6595 (OUTLIER) cc_final: 0.6355 (ttp80) REVERT: g 142 ARG cc_start: 0.7167 (ttm-80) cc_final: 0.6782 (ttm110) REVERT: g 148 LYS cc_start: 0.8035 (tttt) cc_final: 0.7744 (tttp) REVERT: h 2 MET cc_start: 0.8191 (tpp) cc_final: 0.7851 (tpp) REVERT: h 28 SER cc_start: 0.8217 (t) cc_final: 0.7527 (p) REVERT: h 37 ASN cc_start: 0.7690 (t0) cc_final: 0.7418 (t0) REVERT: h 40 LYS cc_start: 0.7556 (tttp) cc_final: 0.7088 (ttpt) REVERT: h 41 GLU cc_start: 0.7686 (OUTLIER) cc_final: 0.7410 (mm-30) REVERT: h 86 LYS cc_start: 0.8481 (mmtp) cc_final: 0.8276 (mptp) REVERT: h 93 LYS cc_start: 0.7392 (ptpt) cc_final: 0.7120 (ptpp) REVERT: h 116 ARG cc_start: 0.6442 (OUTLIER) cc_final: 0.4791 (tpp-160) REVERT: i 32 ARG cc_start: 0.7095 (mmt-90) cc_final: 0.6833 (mpt-90) REVERT: i 63 TYR cc_start: 0.6981 (t80) cc_final: 0.6397 (t80) REVERT: i 123 ARG cc_start: 0.7607 (mtp-110) cc_final: 0.6938 (mtt90) REVERT: k 33 ILE cc_start: 0.7482 (mt) cc_final: 0.7257 (mp) REVERT: k 55 ARG cc_start: 0.6772 (mtp85) cc_final: 0.6523 (mtp85) REVERT: k 74 LYS cc_start: 0.7832 (mttt) cc_final: 0.7384 (mptt) REVERT: k 81 LEU cc_start: 0.7371 (OUTLIER) cc_final: 0.6923 (pp) REVERT: k 107 THR cc_start: 0.7939 (m) cc_final: 0.7679 (p) REVERT: k 125 LYS cc_start: 0.7788 (ttmt) cc_final: 0.7484 (ttmp) REVERT: l 17 LYS cc_start: 0.7095 (pttt) cc_final: 0.6817 (ptmm) REVERT: l 35 ARG cc_start: 0.6283 (ttt90) cc_final: 0.6068 (ttt90) REVERT: l 55 ARG cc_start: 0.7254 (tmm-80) cc_final: 0.6760 (tmm-80) REVERT: m 26 LYS cc_start: 0.7182 (tttp) cc_final: 0.6900 (ttmm) REVERT: m 38 ILE cc_start: 0.7373 (mm) cc_final: 0.7026 (tp) REVERT: m 73 SER cc_start: 0.7799 (m) cc_final: 0.7504 (p) REVERT: n 89 MET cc_start: 0.7147 (ptp) cc_final: 0.6845 (mmt) REVERT: n 90 ARG cc_start: 0.7398 (ttt90) cc_final: 0.6905 (ttp-170) REVERT: o 52 ARG cc_start: 0.7276 (ttt-90) cc_final: 0.6799 (ttp-170) REVERT: o 61 GLN cc_start: 0.7868 (tp40) cc_final: 0.7304 (tt0) REVERT: p 39 PHE cc_start: 0.6953 (t80) cc_final: 0.6745 (t80) REVERT: q 15 LYS cc_start: 0.6853 (mtmm) cc_final: 0.6636 (mtmm) REVERT: q 66 LEU cc_start: 0.7553 (OUTLIER) cc_final: 0.7344 (pt) REVERT: r 51 GLN cc_start: 0.8119 (tp40) cc_final: 0.7470 (tm-30) REVERT: s 17 LYS cc_start: 0.8013 (ttmm) cc_final: 0.7788 (ttmm) REVERT: s 19 GLU cc_start: 0.6611 (pp20) cc_final: 0.6362 (pp20) REVERT: s 43 MET cc_start: 0.8172 (mtp) cc_final: 0.7942 (mtm) REVERT: s 72 GLU cc_start: 0.8223 (mt-10) cc_final: 0.7878 (mt-10) REVERT: t 14 GLU cc_start: 0.7731 (tm-30) cc_final: 0.7112 (tm-30) REVERT: t 20 ASN cc_start: 0.8082 (m-40) cc_final: 0.7811 (m110) REVERT: t 59 ARG cc_start: 0.5482 (ttm110) cc_final: 0.5070 (ttp-110) REVERT: u 32 ARG cc_start: 0.7811 (OUTLIER) cc_final: 0.6888 (ppp80) REVERT: u 33 ARG cc_start: 0.7887 (mtt180) cc_final: 0.7570 (mtp180) REVERT: u 34 ARG cc_start: 0.7700 (tpt170) cc_final: 0.7488 (tpt90) REVERT: z 54 GLU cc_start: 0.5586 (OUTLIER) cc_final: 0.4287 (pm20) REVERT: z 55 GLU cc_start: 0.3778 (mt-10) cc_final: 0.3124 (mp0) REVERT: z 185 GLU cc_start: 0.4013 (OUTLIER) cc_final: 0.3413 (tt0) REVERT: z 201 GLU cc_start: 0.2511 (mt-10) cc_final: 0.1889 (tp30) REVERT: z 207 ASP cc_start: 0.5013 (t0) cc_final: 0.4388 (p0) REVERT: z 220 ILE cc_start: 0.4408 (mp) cc_final: 0.4143 (tt) REVERT: z 240 GLU cc_start: 0.4611 (tt0) cc_final: 0.4290 (tt0) REVERT: z 249 GLU cc_start: 0.5550 (OUTLIER) cc_final: 0.5048 (tt0) REVERT: z 282 LYS cc_start: 0.7127 (mttt) cc_final: 0.6701 (mmmt) REVERT: z 283 ARG cc_start: 0.4988 (tpt90) cc_final: 0.4663 (tpt90) REVERT: z 310 ILE cc_start: 0.3768 (mm) cc_final: 0.3202 (mm) REVERT: z 354 ASP cc_start: 0.6129 (t70) cc_final: 0.5617 (p0) REVERT: z 369 ASP cc_start: 0.4030 (m-30) cc_final: 0.2958 (p0) outliers start: 348 outliers final: 146 residues processed: 1424 average time/residue: 2.1894 time to fit residues: 4498.4793 Evaluate side-chains 1286 residues out of total 5164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 179 poor density : 1107 time to evaluate : 6.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 9 SER Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain C residue 35 LYS Chi-restraints excluded: chain C residue 37 SER Chi-restraints excluded: chain C residue 69 ASN Chi-restraints excluded: chain C residue 70 LYS Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 124 LYS Chi-restraints excluded: chain C residue 252 LYS Chi-restraints excluded: chain C residue 266 ILE Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 28 GLU Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 77 ARG Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 150 GLN Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 176 ASP Chi-restraints excluded: chain F residue 16 MET Chi-restraints excluded: chain F residue 25 MET Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain F residue 84 ILE Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 148 VAL Chi-restraints excluded: chain F residue 152 ASP Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 139 VAL Chi-restraints excluded: chain G residue 171 LYS Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain H residue 145 ASN Chi-restraints excluded: chain J residue 12 LYS Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain K residue 14 SER Chi-restraints excluded: chain K residue 47 ILE Chi-restraints excluded: chain K residue 61 VAL Chi-restraints excluded: chain K residue 77 ILE Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 106 GLU Chi-restraints excluded: chain K residue 107 LEU Chi-restraints excluded: chain K residue 114 LYS Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 14 LYS Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain M residue 55 ARG Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain P residue 10 GLU Chi-restraints excluded: chain P residue 32 VAL Chi-restraints excluded: chain P residue 47 ILE Chi-restraints excluded: chain P residue 56 SER Chi-restraints excluded: chain Q residue 8 ILE Chi-restraints excluded: chain Q residue 83 LYS Chi-restraints excluded: chain Q residue 108 LEU Chi-restraints excluded: chain Q residue 110 GLU Chi-restraints excluded: chain R residue 66 HIS Chi-restraints excluded: chain R residue 84 ARG Chi-restraints excluded: chain S residue 29 VAL Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 82 MET Chi-restraints excluded: chain S residue 86 MET Chi-restraints excluded: chain T residue 16 VAL Chi-restraints excluded: chain T residue 76 ARG Chi-restraints excluded: chain U residue 61 GLU Chi-restraints excluded: chain V residue 4 ILE Chi-restraints excluded: chain V residue 12 GLN Chi-restraints excluded: chain V residue 40 ILE Chi-restraints excluded: chain V residue 63 ILE Chi-restraints excluded: chain W residue 39 THR Chi-restraints excluded: chain X residue 34 SER Chi-restraints excluded: chain X residue 65 THR Chi-restraints excluded: chain Y residue 19 LEU Chi-restraints excluded: chain Z residue 3 THR Chi-restraints excluded: chain Z residue 7 THR Chi-restraints excluded: chain Z residue 51 SER Chi-restraints excluded: chain 0 residue 5 ASN Chi-restraints excluded: chain 0 residue 9 ARG Chi-restraints excluded: chain 0 residue 22 THR Chi-restraints excluded: chain 1 residue 21 THR Chi-restraints excluded: chain 1 residue 42 VAL Chi-restraints excluded: chain 1 residue 46 VAL Chi-restraints excluded: chain 2 residue 24 THR Chi-restraints excluded: chain 3 residue 61 LEU Chi-restraints excluded: chain 4 residue 6 SER Chi-restraints excluded: chain 6 residue 3 LYS Chi-restraints excluded: chain 6 residue 63 ARG Chi-restraints excluded: chain b residue 21 TYR Chi-restraints excluded: chain b residue 56 LEU Chi-restraints excluded: chain b residue 65 LYS Chi-restraints excluded: chain b residue 66 ILE Chi-restraints excluded: chain b residue 113 LEU Chi-restraints excluded: chain b residue 134 LEU Chi-restraints excluded: chain b residue 170 ILE Chi-restraints excluded: chain b residue 173 LYS Chi-restraints excluded: chain b residue 178 LEU Chi-restraints excluded: chain b residue 190 SER Chi-restraints excluded: chain b residue 219 THR Chi-restraints excluded: chain c residue 130 ARG Chi-restraints excluded: chain c residue 156 LEU Chi-restraints excluded: chain d residue 124 VAL Chi-restraints excluded: chain d residue 137 SER Chi-restraints excluded: chain d residue 143 SER Chi-restraints excluded: chain d residue 158 LEU Chi-restraints excluded: chain d residue 168 THR Chi-restraints excluded: chain e residue 17 VAL Chi-restraints excluded: chain e residue 29 ILE Chi-restraints excluded: chain e residue 33 THR Chi-restraints excluded: chain e residue 38 VAL Chi-restraints excluded: chain e residue 45 VAL Chi-restraints excluded: chain e residue 61 LYS Chi-restraints excluded: chain e residue 91 SER Chi-restraints excluded: chain e residue 121 ASN Chi-restraints excluded: chain e residue 123 LEU Chi-restraints excluded: chain e residue 160 VAL Chi-restraints excluded: chain f residue 70 VAL Chi-restraints excluded: chain f residue 96 VAL Chi-restraints excluded: chain g residue 11 ILE Chi-restraints excluded: chain g residue 24 LYS Chi-restraints excluded: chain g residue 62 GLU Chi-restraints excluded: chain g residue 76 SER Chi-restraints excluded: chain g residue 93 VAL Chi-restraints excluded: chain g residue 129 ASN Chi-restraints excluded: chain g residue 132 THR Chi-restraints excluded: chain g residue 137 ARG Chi-restraints excluded: chain h residue 11 THR Chi-restraints excluded: chain h residue 25 THR Chi-restraints excluded: chain h residue 41 GLU Chi-restraints excluded: chain h residue 58 LEU Chi-restraints excluded: chain h residue 105 THR Chi-restraints excluded: chain h residue 111 THR Chi-restraints excluded: chain h residue 116 ARG Chi-restraints excluded: chain h residue 128 VAL Chi-restraints excluded: chain i residue 20 ILE Chi-restraints excluded: chain i residue 61 ASP Chi-restraints excluded: chain i residue 78 ILE Chi-restraints excluded: chain i residue 97 LEU Chi-restraints excluded: chain j residue 40 ILE Chi-restraints excluded: chain j residue 96 VAL Chi-restraints excluded: chain k residue 15 VAL Chi-restraints excluded: chain k residue 49 SER Chi-restraints excluded: chain k residue 80 ASN Chi-restraints excluded: chain k residue 81 LEU Chi-restraints excluded: chain k residue 85 VAL Chi-restraints excluded: chain l residue 51 VAL Chi-restraints excluded: chain l residue 96 THR Chi-restraints excluded: chain l residue 97 VAL Chi-restraints excluded: chain m residue 6 ILE Chi-restraints excluded: chain m residue 15 VAL Chi-restraints excluded: chain m residue 28 ARG Chi-restraints excluded: chain m residue 52 ILE Chi-restraints excluded: chain m residue 67 ASP Chi-restraints excluded: chain n residue 3 GLN Chi-restraints excluded: chain p residue 2 VAL Chi-restraints excluded: chain p residue 19 VAL Chi-restraints excluded: chain q residue 66 LEU Chi-restraints excluded: chain q residue 67 SER Chi-restraints excluded: chain r residue 13 THR Chi-restraints excluded: chain r residue 66 LEU Chi-restraints excluded: chain r residue 70 THR Chi-restraints excluded: chain s residue 36 ARG Chi-restraints excluded: chain t residue 22 SER Chi-restraints excluded: chain u residue 32 ARG Chi-restraints excluded: chain u residue 50 SER Chi-restraints excluded: chain z residue 50 ASP Chi-restraints excluded: chain z residue 54 GLU Chi-restraints excluded: chain z residue 91 MET Chi-restraints excluded: chain z residue 185 GLU Chi-restraints excluded: chain z residue 225 THR Chi-restraints excluded: chain z residue 245 VAL Chi-restraints excluded: chain z residue 249 GLU Chi-restraints excluded: chain z residue 255 CYS Chi-restraints excluded: chain z residue 276 VAL Chi-restraints excluded: chain z residue 388 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1087 random chunks: chunk 977 optimal weight: 9.9990 chunk 743 optimal weight: 30.0000 chunk 513 optimal weight: 10.0000 chunk 109 optimal weight: 30.0000 chunk 471 optimal weight: 5.9990 chunk 664 optimal weight: 30.0000 chunk 992 optimal weight: 0.6980 chunk 1050 optimal weight: 6.9990 chunk 518 optimal weight: 6.9990 chunk 940 optimal weight: 0.9980 chunk 283 optimal weight: 10.0000 overall best weight: 4.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 238 ASN E 156 ASN E 165 HIS F 126 ASN F 134 GLN G 29 ASN G 37 ASN G 47 ASN ** G 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 6 GLN U 73 ASN 1 25 ASN b 57 ASN b 167 HIS b 176 ASN c 24 ASN c 31 ASN ** d 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 18 ASN e 76 ASN f 17 GLN f 46 GLN f 52 ASN g 85 GLN g 129 ASN h 3 GLN i 49 GLN k 39 ASN ** l 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 60 GLN s 56 HIS ** t 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.3400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.126 165479 Z= 0.333 Angle : 0.788 15.072 247209 Z= 0.418 Chirality : 0.042 0.402 31418 Planarity : 0.008 0.136 13503 Dihedral : 24.441 179.447 81849 Min Nonbonded Distance : 1.448 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.64 % Allowed : 7.91 % Favored : 91.44 % Rotamer: Outliers : 7.80 % Allowed : 21.93 % Favored : 70.27 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.08 (0.10), residues: 6219 helix: -0.14 (0.11), residues: 1956 sheet: -1.63 (0.14), residues: 1175 loop : -2.11 (0.10), residues: 3088 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 212 HIS 0.020 0.002 HIS b 14 PHE 0.024 0.002 PHE z 5 TYR 0.049 0.002 TYR z 160 ARG 0.025 0.001 ARG n 23 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12438 Ramachandran restraints generated. 6219 Oldfield, 0 Emsley, 6219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12438 Ramachandran restraints generated. 6219 Oldfield, 0 Emsley, 6219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1598 residues out of total 5164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 403 poor density : 1195 time to evaluate : 6.656 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: C 2 VAL cc_start: 0.8387 (t) cc_final: 0.8128 (m) REVERT: C 4 LYS cc_start: 0.8137 (tttt) cc_final: 0.7703 (ttmm) REVERT: C 27 LYS cc_start: 0.7558 (mttt) cc_final: 0.7095 (mppt) REVERT: C 34 GLU cc_start: 0.8405 (OUTLIER) cc_final: 0.8024 (pt0) REVERT: C 65 ASP cc_start: 0.7701 (t70) cc_final: 0.6705 (m-30) REVERT: C 113 ASP cc_start: 0.6930 (m-30) cc_final: 0.6184 (t0) REVERT: C 116 GLN cc_start: 0.7858 (tt0) cc_final: 0.7638 (tt0) REVERT: C 124 LYS cc_start: 0.6885 (OUTLIER) cc_final: 0.6652 (tmmm) REVERT: C 159 THR cc_start: 0.9163 (m) cc_final: 0.8716 (p) REVERT: C 184 GLU cc_start: 0.7213 (tt0) cc_final: 0.6497 (mt-10) REVERT: C 187 CYS cc_start: 0.8304 (m) cc_final: 0.8022 (m) REVERT: C 252 LYS cc_start: 0.8241 (OUTLIER) cc_final: 0.7916 (mttp) REVERT: D 2 ILE cc_start: 0.4622 (OUTLIER) cc_final: 0.4120 (pp) REVERT: D 77 ARG cc_start: 0.7315 (OUTLIER) cc_final: 0.5056 (ppt90) REVERT: D 108 ASP cc_start: 0.7554 (m-30) cc_final: 0.6952 (p0) REVERT: D 150 GLN cc_start: 0.8261 (OUTLIER) cc_final: 0.8014 (tt0) REVERT: D 186 LEU cc_start: 0.8040 (mt) cc_final: 0.7791 (mt) REVERT: E 51 GLU cc_start: 0.7834 (mt-10) cc_final: 0.7575 (mp0) REVERT: E 88 ARG cc_start: 0.7641 (ttm-80) cc_final: 0.7155 (mmp80) REVERT: E 106 LYS cc_start: 0.7609 (mtpt) cc_final: 0.7318 (mttt) REVERT: E 159 LEU cc_start: 0.8551 (OUTLIER) cc_final: 0.8318 (mm) REVERT: E 171 ASP cc_start: 0.6975 (t0) cc_final: 0.6772 (t0) REVERT: E 194 LYS cc_start: 0.7877 (tptt) cc_final: 0.7599 (mmtp) REVERT: F 31 GLU cc_start: 0.8242 (tt0) cc_final: 0.7968 (tt0) REVERT: F 41 GLU cc_start: 0.6963 (mm-30) cc_final: 0.6215 (mp0) REVERT: F 46 LYS cc_start: 0.7976 (mttt) cc_final: 0.7633 (tppp) REVERT: F 47 LYS cc_start: 0.7510 (ptmt) cc_final: 0.7086 (pmtt) REVERT: F 68 LYS cc_start: 0.7629 (mptt) cc_final: 0.7420 (mppt) REVERT: F 71 LYS cc_start: 0.7229 (mmmt) cc_final: 0.6840 (ttpt) REVERT: F 114 ARG cc_start: 0.6426 (mmm160) cc_final: 0.6088 (mmm160) REVERT: F 133 GLU cc_start: 0.7478 (mt-10) cc_final: 0.6847 (pt0) REVERT: F 137 PHE cc_start: 0.7421 (m-80) cc_final: 0.7176 (m-80) REVERT: F 147 ARG cc_start: 0.6691 (tpp80) cc_final: 0.5991 (ttt90) REVERT: F 160 LYS cc_start: 0.7594 (mtmm) cc_final: 0.7293 (mmtp) REVERT: G 154 GLU cc_start: 0.7170 (tt0) cc_final: 0.6759 (pt0) REVERT: G 159 LYS cc_start: 0.7917 (mtpt) cc_final: 0.7437 (tttt) REVERT: I 35 MET cc_start: 0.4321 (tpt) cc_final: 0.4083 (tpt) REVERT: I 124 MET cc_start: 0.2908 (mtm) cc_final: 0.2493 (tmt) REVERT: I 135 MET cc_start: 0.1662 (mtp) cc_final: 0.1082 (tmt) REVERT: J 12 LYS cc_start: 0.7567 (OUTLIER) cc_final: 0.7137 (tptm) REVERT: J 43 GLU cc_start: 0.8063 (mt-10) cc_final: 0.7383 (pm20) REVERT: J 61 LYS cc_start: 0.8172 (mmtp) cc_final: 0.7672 (mtpt) REVERT: J 91 GLU cc_start: 0.7798 (mt-10) cc_final: 0.7389 (tp30) REVERT: J 95 ARG cc_start: 0.6533 (mtp-110) cc_final: 0.6112 (ttp-110) REVERT: K 17 ARG cc_start: 0.8334 (tpp80) cc_final: 0.7997 (tpp-160) REVERT: K 18 ARG cc_start: 0.7970 (mmt180) cc_final: 0.7482 (mtp-110) REVERT: K 53 LYS cc_start: 0.7009 (pttp) cc_final: 0.6721 (ptpp) REVERT: K 66 LYS cc_start: 0.8101 (mttt) cc_final: 0.7822 (mtpt) REVERT: K 110 GLU cc_start: 0.8191 (tm-30) cc_final: 0.7846 (tm-30) REVERT: K 113 MET cc_start: 0.7381 (OUTLIER) cc_final: 0.6723 (mmm) REVERT: L 10 GLU cc_start: 0.7342 (mm-30) cc_final: 0.7121 (tp30) REVERT: L 12 SER cc_start: 0.8589 (t) cc_final: 0.8358 (m) REVERT: L 14 LYS cc_start: 0.7508 (OUTLIER) cc_final: 0.7121 (tmtt) REVERT: L 19 LEU cc_start: 0.9057 (mp) cc_final: 0.8819 (mt) REVERT: L 105 ILE cc_start: 0.8545 (mt) cc_final: 0.8244 (mm) REVERT: L 106 GLU cc_start: 0.8420 (mt-10) cc_final: 0.8021 (mm-30) REVERT: L 117 THR cc_start: 0.8111 (m) cc_final: 0.7882 (p) REVERT: L 141 LYS cc_start: 0.6874 (mmmt) cc_final: 0.6438 (ptpp) REVERT: M 1 MET cc_start: 0.6202 (OUTLIER) cc_final: 0.4918 (ptt) REVERT: M 6 ARG cc_start: 0.7222 (OUTLIER) cc_final: 0.6652 (ptp90) REVERT: M 12 MET cc_start: 0.8258 (ttm) cc_final: 0.7991 (ttm) REVERT: M 41 LEU cc_start: 0.8582 (mt) cc_final: 0.8314 (mm) REVERT: M 55 ARG cc_start: 0.7516 (OUTLIER) cc_final: 0.6977 (ttm170) REVERT: M 75 GLU cc_start: 0.8260 (tt0) cc_final: 0.7756 (tt0) REVERT: M 88 ASN cc_start: 0.7736 (m110) cc_final: 0.7483 (m-40) REVERT: N 30 ARG cc_start: 0.7945 (ttm-80) cc_final: 0.7439 (ttm-80) REVERT: N 35 LYS cc_start: 0.7852 (tttt) cc_final: 0.7488 (tttp) REVERT: O 13 ARG cc_start: 0.7068 (ttt90) cc_final: 0.6793 (tpp-160) REVERT: O 60 GLU cc_start: 0.7155 (mt-10) cc_final: 0.6810 (mt-10) REVERT: O 98 GLN cc_start: 0.8272 (tt0) cc_final: 0.7879 (tt0) REVERT: Q 12 ARG cc_start: 0.8057 (ttm-80) cc_final: 0.7581 (ttt180) REVERT: Q 14 LYS cc_start: 0.7473 (tttt) cc_final: 0.7085 (mtpp) REVERT: Q 48 ASP cc_start: 0.8421 (m-30) cc_final: 0.7783 (m-30) REVERT: Q 77 LYS cc_start: 0.8077 (mttt) cc_final: 0.7623 (mtpt) REVERT: Q 101 ASP cc_start: 0.6452 (m-30) cc_final: 0.5985 (t0) REVERT: Q 110 GLU cc_start: 0.7113 (OUTLIER) cc_final: 0.6671 (mp0) REVERT: R 1 MET cc_start: 0.6395 (tpp) cc_final: 0.5232 (ptp) REVERT: R 10 LYS cc_start: 0.7703 (ptpp) cc_final: 0.7501 (mtmm) REVERT: R 66 HIS cc_start: 0.8292 (OUTLIER) cc_final: 0.6961 (m-70) REVERT: S 1 MET cc_start: 0.6677 (mmm) cc_final: 0.5144 (ppp) REVERT: S 34 ASP cc_start: 0.7495 (m-30) cc_final: 0.7176 (m-30) REVERT: S 39 THR cc_start: 0.7604 (m) cc_final: 0.7297 (m) REVERT: S 52 GLU cc_start: 0.7962 (tt0) cc_final: 0.7386 (mm-30) REVERT: S 86 MET cc_start: 0.8499 (OUTLIER) cc_final: 0.7861 (tpt) REVERT: S 92 ARG cc_start: 0.7161 (ptp90) cc_final: 0.6500 (ptm160) REVERT: S 95 ARG cc_start: 0.8026 (ttm-80) cc_final: 0.7784 (ttp80) REVERT: T 28 ASN cc_start: 0.7574 (t0) cc_final: 0.6904 (t0) REVERT: T 54 GLU cc_start: 0.7226 (mt-10) cc_final: 0.6119 (tp30) REVERT: T 69 ARG cc_start: 0.7782 (ttp-110) cc_final: 0.6977 (ttm-80) REVERT: T 76 ARG cc_start: 0.7236 (OUTLIER) cc_final: 0.6555 (ptm-80) REVERT: U 17 ASP cc_start: 0.6776 (m-30) cc_final: 0.6538 (m-30) REVERT: U 20 LYS cc_start: 0.6823 (OUTLIER) cc_final: 0.6570 (mtpp) REVERT: U 25 LYS cc_start: 0.7236 (mmmt) cc_final: 0.6641 (mtpp) REVERT: U 71 ILE cc_start: 0.8113 (pt) cc_final: 0.7639 (mt) REVERT: U 78 LYS cc_start: 0.7021 (OUTLIER) cc_final: 0.6589 (pmtt) REVERT: U 96 LYS cc_start: 0.7097 (OUTLIER) cc_final: 0.6825 (mttt) REVERT: V 8 VAL cc_start: 0.7958 (t) cc_final: 0.7736 (m) REVERT: V 11 GLU cc_start: 0.6958 (mt-10) cc_final: 0.6672 (pt0) REVERT: V 30 ILE cc_start: 0.7390 (mt) cc_final: 0.7020 (tt) REVERT: V 43 ASP cc_start: 0.7608 (t70) cc_final: 0.7241 (t70) REVERT: V 71 LYS cc_start: 0.7150 (mtpp) cc_final: 0.6775 (mppt) REVERT: V 73 LYS cc_start: 0.7218 (mttt) cc_final: 0.6953 (mmmt) REVERT: V 82 TYR cc_start: 0.7243 (p90) cc_final: 0.6860 (p90) REVERT: W 21 ARG cc_start: 0.7640 (mmt-90) cc_final: 0.6578 (mmp-170) REVERT: W 40 LYS cc_start: 0.7964 (ttpt) cc_final: 0.7681 (mtpp) REVERT: W 66 GLU cc_start: 0.8099 (mm-30) cc_final: 0.7037 (mt-10) REVERT: W 71 LYS cc_start: 0.8325 (mttt) cc_final: 0.7931 (mttp) REVERT: X 19 HIS cc_start: 0.7471 (t70) cc_final: 0.6690 (m-70) REVERT: X 42 GLU cc_start: 0.7027 (mt-10) cc_final: 0.6407 (tp30) REVERT: X 67 LEU cc_start: 0.7110 (mm) cc_final: 0.6836 (mm) REVERT: Y 56 LEU cc_start: 0.8153 (OUTLIER) cc_final: 0.7870 (tm) REVERT: Z 5 LYS cc_start: 0.7107 (mtmm) cc_final: 0.6784 (mttp) REVERT: 0 11 LYS cc_start: 0.8302 (mmmt) cc_final: 0.7972 (tppp) REVERT: 1 27 ARG cc_start: 0.7482 (mtm180) cc_final: 0.7165 (mpt180) REVERT: 1 32 LYS cc_start: 0.7434 (mttt) cc_final: 0.7190 (pptt) REVERT: 1 50 GLU cc_start: 0.7465 (tm-30) cc_final: 0.7109 (tm-30) REVERT: 2 8 SER cc_start: 0.8727 (t) cc_final: 0.8449 (t) REVERT: 2 41 ARG cc_start: 0.7796 (mmt180) cc_final: 0.7324 (mtm-85) REVERT: 2 44 VAL cc_start: 0.7963 (p) cc_final: 0.7727 (m) REVERT: 3 14 LYS cc_start: 0.8380 (tttt) cc_final: 0.7966 (mmtm) REVERT: 4 18 LYS cc_start: 0.7843 (tttt) cc_final: 0.7633 (mtpp) REVERT: 4 20 ASP cc_start: 0.7605 (OUTLIER) cc_final: 0.6521 (t0) REVERT: 5 1 MET cc_start: 0.3100 (tpt) cc_final: 0.2498 (tmt) REVERT: 6 1 MET cc_start: 0.7121 (mtp) cc_final: 0.6600 (ttm) REVERT: 6 10 GLU cc_start: 0.7462 (tp30) cc_final: 0.6998 (tt0) REVERT: 6 24 ILE cc_start: 0.7415 (pt) cc_final: 0.7191 (mt) REVERT: 6 61 ASN cc_start: 0.6414 (m110) cc_final: 0.5267 (p0) REVERT: 6 62 LYS cc_start: 0.6985 (mtpt) cc_final: 0.6667 (mmmt) REVERT: b 44 LYS cc_start: 0.6376 (mtpt) cc_final: 0.6166 (mtmm) REVERT: b 107 ARG cc_start: 0.6917 (ttp-110) cc_final: 0.6435 (ttm170) REVERT: b 132 GLU cc_start: 0.6721 (tp30) cc_final: 0.6137 (tt0) REVERT: b 141 GLU cc_start: 0.7362 (mt-10) cc_final: 0.7082 (mm-30) REVERT: b 145 ASN cc_start: 0.7427 (p0) cc_final: 0.6879 (m110) REVERT: c 33 ASP cc_start: 0.7393 (t70) cc_final: 0.7132 (t0) REVERT: c 45 GLU cc_start: 0.7941 (tm-30) cc_final: 0.7122 (mm-30) REVERT: c 71 ARG cc_start: 0.7254 (mtt90) cc_final: 0.6742 (mtp85) REVERT: c 128 MET cc_start: 0.7576 (mmp) cc_final: 0.6642 (mtt) REVERT: c 130 ARG cc_start: 0.7637 (OUTLIER) cc_final: 0.6911 (mtt-85) REVERT: c 151 GLU cc_start: 0.7940 (tt0) cc_final: 0.7316 (tm-30) REVERT: c 156 LEU cc_start: 0.7570 (OUTLIER) cc_final: 0.7249 (pt) REVERT: c 163 ARG cc_start: 0.5434 (mtt180) cc_final: 0.4608 (mpp-170) REVERT: c 169 GLU cc_start: 0.7884 (mt-10) cc_final: 0.6827 (tp30) REVERT: d 77 GLU cc_start: 0.7606 (mt-10) cc_final: 0.6856 (tp30) REVERT: d 116 LEU cc_start: 0.5542 (OUTLIER) cc_final: 0.5340 (mp) REVERT: d 135 GLN cc_start: 0.4791 (tm-30) cc_final: 0.3710 (mm110) REVERT: d 177 MET cc_start: -0.0747 (mtt) cc_final: -0.1113 (mtt) REVERT: e 11 GLN cc_start: 0.7524 (OUTLIER) cc_final: 0.7238 (tp-100) REVERT: e 71 ILE cc_start: 0.6901 (mm) cc_final: 0.6605 (tt) REVERT: e 127 TYR cc_start: 0.8396 (m-80) cc_final: 0.8036 (m-80) REVERT: e 144 GLU cc_start: 0.7905 (tt0) cc_final: 0.7641 (tt0) REVERT: f 24 ARG cc_start: 0.7356 (mtm110) cc_final: 0.6769 (mtm110) REVERT: f 59 TYR cc_start: 0.8148 (m-80) cc_final: 0.7778 (m-80) REVERT: g 24 LYS cc_start: 0.7029 (OUTLIER) cc_final: 0.6739 (tptm) REVERT: g 39 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.7388 (pt0) REVERT: g 59 GLU cc_start: 0.7057 (tt0) cc_final: 0.6685 (tt0) REVERT: g 62 GLU cc_start: 0.6368 (OUTLIER) cc_final: 0.5388 (mt-10) REVERT: g 75 LYS cc_start: 0.5579 (mttm) cc_final: 0.4990 (mttt) REVERT: g 89 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.7617 (mm-30) REVERT: g 105 GLU cc_start: 0.7861 (tp30) cc_final: 0.7272 (tp30) REVERT: g 148 LYS cc_start: 0.8058 (tttt) cc_final: 0.7757 (tttp) REVERT: h 2 MET cc_start: 0.8269 (tpp) cc_final: 0.7755 (tpp) REVERT: h 42 GLU cc_start: 0.7403 (mp0) cc_final: 0.7029 (mp0) REVERT: h 90 GLU cc_start: 0.7938 (tt0) cc_final: 0.7402 (mp0) REVERT: h 93 LYS cc_start: 0.7384 (ptpt) cc_final: 0.7059 (ptpp) REVERT: h 116 ARG cc_start: 0.6497 (OUTLIER) cc_final: 0.4836 (tpp-160) REVERT: i 63 TYR cc_start: 0.7066 (t80) cc_final: 0.6325 (t80) REVERT: i 64 ILE cc_start: 0.7549 (mt) cc_final: 0.7293 (mm) REVERT: i 122 ARG cc_start: 0.7441 (OUTLIER) cc_final: 0.6684 (tmt-80) REVERT: i 123 ARG cc_start: 0.7664 (mtp-110) cc_final: 0.7205 (ttm-80) REVERT: j 16 ARG cc_start: 0.6879 (ptt180) cc_final: 0.6632 (ttp-110) REVERT: j 53 ILE cc_start: 0.6758 (tp) cc_final: 0.6447 (pt) REVERT: j 62 ARG cc_start: 0.7752 (OUTLIER) cc_final: 0.6758 (mpt-90) REVERT: k 74 LYS cc_start: 0.7833 (mttt) cc_final: 0.7507 (tppt) REVERT: k 107 THR cc_start: 0.8272 (m) cc_final: 0.7988 (p) REVERT: k 125 LYS cc_start: 0.7737 (OUTLIER) cc_final: 0.7467 (ttmp) REVERT: k 126 ARG cc_start: 0.8388 (OUTLIER) cc_final: 0.7977 (ptm-80) REVERT: l 17 LYS cc_start: 0.7057 (pttt) cc_final: 0.6631 (mmtt) REVERT: l 35 ARG cc_start: 0.6179 (ttt90) cc_final: 0.5973 (ttt90) REVERT: l 94 TYR cc_start: 0.7296 (m-80) cc_final: 0.6931 (m-80) REVERT: m 12 LYS cc_start: 0.6394 (mtmt) cc_final: 0.5831 (mmtp) REVERT: m 26 LYS cc_start: 0.7226 (ttpp) cc_final: 0.6975 (ttmm) REVERT: m 73 SER cc_start: 0.7808 (m) cc_final: 0.7481 (p) REVERT: n 11 LYS cc_start: 0.6625 (OUTLIER) cc_final: 0.6327 (ptmm) REVERT: n 25 GLU cc_start: 0.7478 (pt0) cc_final: 0.7034 (mp0) REVERT: n 90 ARG cc_start: 0.7612 (ttt90) cc_final: 0.7195 (ttp-170) REVERT: o 52 ARG cc_start: 0.7241 (ttt-90) cc_final: 0.6760 (ttp-170) REVERT: o 61 GLN cc_start: 0.7732 (tp40) cc_final: 0.7251 (tt0) REVERT: o 82 GLU cc_start: 0.7900 (mm-30) cc_final: 0.7458 (tm-30) REVERT: p 34 GLU cc_start: 0.2447 (OUTLIER) cc_final: 0.2143 (tm-30) REVERT: p 39 PHE cc_start: 0.7034 (t80) cc_final: 0.6812 (t80) REVERT: q 8 GLN cc_start: 0.7988 (tt0) cc_final: 0.7395 (mp10) REVERT: q 18 LYS cc_start: 0.5626 (ttpt) cc_final: 0.5236 (ttmt) REVERT: q 25 GLU cc_start: 0.6328 (tm-30) cc_final: 0.6123 (tp30) REVERT: q 38 LYS cc_start: 0.7412 (ttpp) cc_final: 0.7212 (ttmm) REVERT: s 6 LYS cc_start: 0.5310 (OUTLIER) cc_final: 0.3973 (pmtt) REVERT: s 34 SER cc_start: 0.8932 (t) cc_final: 0.8629 (t) REVERT: t 14 GLU cc_start: 0.7345 (tm-30) cc_final: 0.6923 (tm-30) REVERT: t 20 ASN cc_start: 0.8062 (m-40) cc_final: 0.7810 (m110) REVERT: t 59 ARG cc_start: 0.5534 (ttm110) cc_final: 0.5191 (ttp-110) REVERT: u 8 ASN cc_start: 0.3292 (OUTLIER) cc_final: 0.2800 (p0) REVERT: u 33 ARG cc_start: 0.7706 (mtt180) cc_final: 0.7468 (mtm-85) REVERT: z 54 GLU cc_start: 0.5495 (OUTLIER) cc_final: 0.4711 (pm20) REVERT: z 117 GLU cc_start: 0.4873 (tm-30) cc_final: 0.4614 (mp0) REVERT: z 185 GLU cc_start: 0.4158 (OUTLIER) cc_final: 0.3073 (tm-30) REVERT: z 201 GLU cc_start: 0.2494 (mt-10) cc_final: 0.1775 (tp30) REVERT: z 207 ASP cc_start: 0.5081 (t0) cc_final: 0.4441 (p0) REVERT: z 282 LYS cc_start: 0.7081 (mttt) cc_final: 0.6629 (mmmt) REVERT: z 310 ILE cc_start: 0.4250 (mm) cc_final: 0.3901 (mm) REVERT: z 354 ASP cc_start: 0.5724 (t70) cc_final: 0.5235 (p0) outliers start: 403 outliers final: 186 residues processed: 1417 average time/residue: 2.2949 time to fit residues: 4666.1705 Evaluate side-chains 1307 residues out of total 5164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 227 poor density : 1080 time to evaluate : 6.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 9 SER Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 34 GLU Chi-restraints excluded: chain C residue 35 LYS Chi-restraints excluded: chain C residue 37 SER Chi-restraints excluded: chain C residue 69 ASN Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 124 LYS Chi-restraints excluded: chain C residue 252 LYS Chi-restraints excluded: chain C residue 266 ILE Chi-restraints excluded: chain D residue 2 ILE Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 77 ARG Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 150 GLN Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 202 ILE Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 57 LYS Chi-restraints excluded: chain E residue 159 LEU Chi-restraints excluded: chain E residue 176 ASP Chi-restraints excluded: chain F residue 16 MET Chi-restraints excluded: chain F residue 25 MET Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain F residue 84 ILE Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 104 THR Chi-restraints excluded: chain F residue 128 SER Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 152 ASP Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 24 THR Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 139 VAL Chi-restraints excluded: chain G residue 171 LYS Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain H residue 145 ASN Chi-restraints excluded: chain J residue 7 LYS Chi-restraints excluded: chain J residue 12 LYS Chi-restraints excluded: chain J residue 27 ARG Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain J residue 128 ASN Chi-restraints excluded: chain K residue 14 SER Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain K residue 47 ILE Chi-restraints excluded: chain K residue 61 VAL Chi-restraints excluded: chain K residue 90 ASN Chi-restraints excluded: chain K residue 99 ILE Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 106 GLU Chi-restraints excluded: chain K residue 107 LEU Chi-restraints excluded: chain K residue 113 MET Chi-restraints excluded: chain K residue 114 LYS Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 14 LYS Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 91 ASP Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 6 ARG Chi-restraints excluded: chain M residue 30 SER Chi-restraints excluded: chain M residue 55 ARG Chi-restraints excluded: chain N residue 24 MET Chi-restraints excluded: chain N residue 33 ILE Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain O residue 95 SER Chi-restraints excluded: chain P residue 15 ASP Chi-restraints excluded: chain P residue 32 VAL Chi-restraints excluded: chain P residue 47 ILE Chi-restraints excluded: chain Q residue 8 ILE Chi-restraints excluded: chain Q residue 39 ILE Chi-restraints excluded: chain Q residue 110 GLU Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 66 HIS Chi-restraints excluded: chain R residue 84 ARG Chi-restraints excluded: chain S residue 29 VAL Chi-restraints excluded: chain S residue 86 MET Chi-restraints excluded: chain T residue 9 LYS Chi-restraints excluded: chain T residue 76 ARG Chi-restraints excluded: chain U residue 20 LYS Chi-restraints excluded: chain U residue 61 GLU Chi-restraints excluded: chain U residue 64 ILE Chi-restraints excluded: chain U residue 78 LYS Chi-restraints excluded: chain U residue 96 LYS Chi-restraints excluded: chain V residue 4 ILE Chi-restraints excluded: chain V residue 12 GLN Chi-restraints excluded: chain V residue 40 ILE Chi-restraints excluded: chain V residue 63 ILE Chi-restraints excluded: chain V residue 64 VAL Chi-restraints excluded: chain W residue 39 THR Chi-restraints excluded: chain W residue 60 ASP Chi-restraints excluded: chain X residue 7 THR Chi-restraints excluded: chain X residue 34 SER Chi-restraints excluded: chain X residue 47 THR Chi-restraints excluded: chain X residue 65 THR Chi-restraints excluded: chain Y residue 19 LEU Chi-restraints excluded: chain Y residue 56 LEU Chi-restraints excluded: chain Z residue 3 THR Chi-restraints excluded: chain Z residue 7 THR Chi-restraints excluded: chain 0 residue 5 ASN Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 9 ARG Chi-restraints excluded: chain 0 residue 22 THR Chi-restraints excluded: chain 1 residue 21 THR Chi-restraints excluded: chain 1 residue 22 THR Chi-restraints excluded: chain 1 residue 23 THR Chi-restraints excluded: chain 1 residue 42 VAL Chi-restraints excluded: chain 1 residue 46 VAL Chi-restraints excluded: chain 2 residue 24 THR Chi-restraints excluded: chain 3 residue 61 LEU Chi-restraints excluded: chain 4 residue 6 SER Chi-restraints excluded: chain 4 residue 20 ASP Chi-restraints excluded: chain 4 residue 28 SER Chi-restraints excluded: chain b residue 21 TYR Chi-restraints excluded: chain b residue 66 ILE Chi-restraints excluded: chain b residue 105 THR Chi-restraints excluded: chain b residue 109 SER Chi-restraints excluded: chain b residue 163 ILE Chi-restraints excluded: chain b residue 178 LEU Chi-restraints excluded: chain b residue 190 SER Chi-restraints excluded: chain b residue 203 ASP Chi-restraints excluded: chain c residue 120 THR Chi-restraints excluded: chain c residue 130 ARG Chi-restraints excluded: chain c residue 156 LEU Chi-restraints excluded: chain d residue 116 LEU Chi-restraints excluded: chain d residue 143 SER Chi-restraints excluded: chain d residue 158 LEU Chi-restraints excluded: chain d residue 168 THR Chi-restraints excluded: chain e residue 11 GLN Chi-restraints excluded: chain e residue 17 VAL Chi-restraints excluded: chain e residue 29 ILE Chi-restraints excluded: chain e residue 33 THR Chi-restraints excluded: chain e residue 38 VAL Chi-restraints excluded: chain e residue 45 VAL Chi-restraints excluded: chain e residue 61 LYS Chi-restraints excluded: chain e residue 91 SER Chi-restraints excluded: chain e residue 121 ASN Chi-restraints excluded: chain e residue 123 LEU Chi-restraints excluded: chain f residue 70 VAL Chi-restraints excluded: chain f residue 86 ARG Chi-restraints excluded: chain f residue 96 VAL Chi-restraints excluded: chain g residue 11 ILE Chi-restraints excluded: chain g residue 24 LYS Chi-restraints excluded: chain g residue 32 ASP Chi-restraints excluded: chain g residue 36 SER Chi-restraints excluded: chain g residue 39 GLU Chi-restraints excluded: chain g residue 62 GLU Chi-restraints excluded: chain g residue 76 SER Chi-restraints excluded: chain g residue 89 GLU Chi-restraints excluded: chain g residue 93 VAL Chi-restraints excluded: chain g residue 132 THR Chi-restraints excluded: chain h residue 11 THR Chi-restraints excluded: chain h residue 25 THR Chi-restraints excluded: chain h residue 82 LEU Chi-restraints excluded: chain h residue 111 THR Chi-restraints excluded: chain h residue 116 ARG Chi-restraints excluded: chain h residue 128 VAL Chi-restraints excluded: chain i residue 20 ILE Chi-restraints excluded: chain i residue 61 ASP Chi-restraints excluded: chain i residue 97 LEU Chi-restraints excluded: chain i residue 122 ARG Chi-restraints excluded: chain j residue 40 ILE Chi-restraints excluded: chain j residue 62 ARG Chi-restraints excluded: chain j residue 66 GLU Chi-restraints excluded: chain j residue 96 VAL Chi-restraints excluded: chain j residue 98 VAL Chi-restraints excluded: chain k residue 15 VAL Chi-restraints excluded: chain k residue 34 THR Chi-restraints excluded: chain k residue 49 SER Chi-restraints excluded: chain k residue 80 ASN Chi-restraints excluded: chain k residue 84 MET Chi-restraints excluded: chain k residue 85 VAL Chi-restraints excluded: chain k residue 111 ASP Chi-restraints excluded: chain k residue 113 THR Chi-restraints excluded: chain k residue 125 LYS Chi-restraints excluded: chain k residue 126 ARG Chi-restraints excluded: chain l residue 15 VAL Chi-restraints excluded: chain l residue 54 VAL Chi-restraints excluded: chain l residue 96 THR Chi-restraints excluded: chain l residue 97 VAL Chi-restraints excluded: chain l residue 115 LYS Chi-restraints excluded: chain m residue 6 ILE Chi-restraints excluded: chain m residue 15 VAL Chi-restraints excluded: chain m residue 28 ARG Chi-restraints excluded: chain m residue 52 ILE Chi-restraints excluded: chain m residue 67 ASP Chi-restraints excluded: chain n residue 3 GLN Chi-restraints excluded: chain n residue 11 LYS Chi-restraints excluded: chain o residue 10 ILE Chi-restraints excluded: chain p residue 2 VAL Chi-restraints excluded: chain p residue 34 GLU Chi-restraints excluded: chain q residue 13 SER Chi-restraints excluded: chain q residue 67 SER Chi-restraints excluded: chain r residue 13 THR Chi-restraints excluded: chain r residue 25 ILE Chi-restraints excluded: chain r residue 49 LYS Chi-restraints excluded: chain r residue 66 LEU Chi-restraints excluded: chain r residue 70 THR Chi-restraints excluded: chain s residue 6 LYS Chi-restraints excluded: chain s residue 62 THR Chi-restraints excluded: chain t residue 22 SER Chi-restraints excluded: chain u residue 8 ASN Chi-restraints excluded: chain u residue 32 ARG Chi-restraints excluded: chain u residue 50 SER Chi-restraints excluded: chain z residue 54 GLU Chi-restraints excluded: chain z residue 91 MET Chi-restraints excluded: chain z residue 102 ILE Chi-restraints excluded: chain z residue 170 VAL Chi-restraints excluded: chain z residue 185 GLU Chi-restraints excluded: chain z residue 236 ILE Chi-restraints excluded: chain z residue 245 VAL Chi-restraints excluded: chain z residue 249 GLU Chi-restraints excluded: chain z residue 276 VAL Chi-restraints excluded: chain z residue 279 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1087 random chunks: chunk 875 optimal weight: 0.6980 chunk 596 optimal weight: 0.9980 chunk 15 optimal weight: 10.0000 chunk 782 optimal weight: 10.0000 chunk 433 optimal weight: 9.9990 chunk 896 optimal weight: 5.9990 chunk 726 optimal weight: 10.0000 chunk 1 optimal weight: 8.9990 chunk 536 optimal weight: 4.9990 chunk 943 optimal weight: 4.9990 chunk 265 optimal weight: 10.0000 overall best weight: 3.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 94 GLN E 165 HIS F 26 GLN ** F 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 21 GLN ** I 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 6 GLN R 6 GLN U 73 ASN V 75 GLN X 5 GLN c 24 ASN c 31 ASN ** c 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 139 ASN d 58 GLN e 76 ASN e 77 ASN f 17 GLN f 52 ASN f 63 ASN ** g 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 3 GLN k 28 ASN ** l 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 60 GLN o 19 ASN q 44 HIS ** t 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.3626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.093 165479 Z= 0.278 Angle : 0.740 15.050 247209 Z= 0.396 Chirality : 0.039 0.488 31418 Planarity : 0.007 0.132 13503 Dihedral : 24.368 179.415 81845 Min Nonbonded Distance : 1.123 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.60 % Allowed : 7.83 % Favored : 91.57 % Rotamer: Outliers : 7.07 % Allowed : 24.78 % Favored : 68.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.90 (0.10), residues: 6219 helix: 0.00 (0.11), residues: 1960 sheet: -1.46 (0.14), residues: 1181 loop : -2.03 (0.10), residues: 3078 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 212 HIS 0.021 0.001 HIS b 14 PHE 0.020 0.002 PHE f 8 TYR 0.033 0.002 TYR z 160 ARG 0.010 0.001 ARG q 61 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12438 Ramachandran restraints generated. 6219 Oldfield, 0 Emsley, 6219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12438 Ramachandran restraints generated. 6219 Oldfield, 0 Emsley, 6219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1483 residues out of total 5164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 365 poor density : 1118 time to evaluate : 6.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 4 LYS cc_start: 0.8108 (tttt) cc_final: 0.7662 (ttmm) REVERT: C 22 GLU cc_start: 0.7965 (OUTLIER) cc_final: 0.7244 (mt-10) REVERT: C 27 LYS cc_start: 0.7556 (mttt) cc_final: 0.7103 (mppt) REVERT: C 34 GLU cc_start: 0.8386 (pt0) cc_final: 0.8027 (pt0) REVERT: C 113 ASP cc_start: 0.6886 (m-30) cc_final: 0.6166 (t0) REVERT: C 116 GLN cc_start: 0.7907 (tt0) cc_final: 0.7699 (tt0) REVERT: C 124 LYS cc_start: 0.6938 (OUTLIER) cc_final: 0.6676 (tmmm) REVERT: C 159 THR cc_start: 0.9124 (m) cc_final: 0.8687 (p) REVERT: C 184 GLU cc_start: 0.7281 (tt0) cc_final: 0.6565 (mt-10) REVERT: C 187 CYS cc_start: 0.8271 (m) cc_final: 0.7977 (m) REVERT: C 252 LYS cc_start: 0.8246 (OUTLIER) cc_final: 0.7915 (mttp) REVERT: D 2 ILE cc_start: 0.4732 (OUTLIER) cc_final: 0.4342 (pp) REVERT: D 108 ASP cc_start: 0.7587 (m-30) cc_final: 0.6958 (p0) REVERT: D 150 GLN cc_start: 0.8185 (OUTLIER) cc_final: 0.7946 (tt0) REVERT: D 186 LEU cc_start: 0.7967 (mt) cc_final: 0.7729 (mt) REVERT: E 30 GLN cc_start: 0.8348 (OUTLIER) cc_final: 0.7953 (tt0) REVERT: E 51 GLU cc_start: 0.7837 (mt-10) cc_final: 0.7395 (mp0) REVERT: E 88 ARG cc_start: 0.7709 (ttm-80) cc_final: 0.7194 (mmp80) REVERT: E 95 LYS cc_start: 0.7739 (OUTLIER) cc_final: 0.7066 (tttp) REVERT: E 106 LYS cc_start: 0.7589 (mtpt) cc_final: 0.7334 (mttt) REVERT: E 159 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.8283 (mm) REVERT: E 194 LYS cc_start: 0.7898 (tptt) cc_final: 0.7592 (mmtt) REVERT: F 18 GLU cc_start: 0.5698 (OUTLIER) cc_final: 0.5118 (mt-10) REVERT: F 31 GLU cc_start: 0.8242 (tt0) cc_final: 0.7968 (tt0) REVERT: F 41 GLU cc_start: 0.7044 (mm-30) cc_final: 0.6241 (mp0) REVERT: F 46 LYS cc_start: 0.8014 (mttt) cc_final: 0.7617 (tppp) REVERT: F 47 LYS cc_start: 0.7542 (ptmt) cc_final: 0.7108 (pmtt) REVERT: F 68 LYS cc_start: 0.7582 (mptt) cc_final: 0.7377 (mppt) REVERT: F 71 LYS cc_start: 0.7210 (mmmt) cc_final: 0.6835 (ttpt) REVERT: F 133 GLU cc_start: 0.7506 (mt-10) cc_final: 0.6916 (pt0) REVERT: F 137 PHE cc_start: 0.7427 (m-80) cc_final: 0.7194 (m-80) REVERT: F 147 ARG cc_start: 0.6719 (tpp80) cc_final: 0.5980 (ttt180) REVERT: F 160 LYS cc_start: 0.7482 (mtmm) cc_final: 0.7207 (mmtp) REVERT: G 154 GLU cc_start: 0.7173 (tt0) cc_final: 0.6760 (pt0) REVERT: I 35 MET cc_start: 0.4431 (tpt) cc_final: 0.4210 (tpt) REVERT: I 124 MET cc_start: 0.2628 (mtm) cc_final: 0.2406 (tmt) REVERT: I 135 MET cc_start: 0.1511 (mtp) cc_final: 0.0970 (tmt) REVERT: J 12 LYS cc_start: 0.7543 (OUTLIER) cc_final: 0.7134 (tptp) REVERT: J 19 ASP cc_start: 0.7678 (t0) cc_final: 0.7353 (t70) REVERT: J 43 GLU cc_start: 0.8072 (mt-10) cc_final: 0.7382 (pm20) REVERT: J 61 LYS cc_start: 0.8023 (mmtp) cc_final: 0.7469 (mtpt) REVERT: J 91 GLU cc_start: 0.7762 (mt-10) cc_final: 0.7449 (tp30) REVERT: J 95 ARG cc_start: 0.6476 (mtp-110) cc_final: 0.5985 (ttp-110) REVERT: K 7 MET cc_start: 0.8551 (tpp) cc_final: 0.8252 (tpp) REVERT: K 17 ARG cc_start: 0.8350 (tpp80) cc_final: 0.8063 (tpp-160) REVERT: K 45 GLU cc_start: 0.7331 (tt0) cc_final: 0.6889 (tp30) REVERT: K 53 LYS cc_start: 0.6923 (pttp) cc_final: 0.6706 (ptpp) REVERT: K 66 LYS cc_start: 0.8115 (mttt) cc_final: 0.7855 (mtpt) REVERT: L 10 GLU cc_start: 0.7310 (mm-30) cc_final: 0.7088 (tp30) REVERT: L 14 LYS cc_start: 0.7525 (OUTLIER) cc_final: 0.7109 (tmtt) REVERT: L 19 LEU cc_start: 0.9038 (mp) cc_final: 0.8807 (mt) REVERT: L 105 ILE cc_start: 0.8476 (mt) cc_final: 0.8175 (mm) REVERT: L 106 GLU cc_start: 0.8415 (mt-10) cc_final: 0.8025 (mm-30) REVERT: L 117 THR cc_start: 0.8161 (m) cc_final: 0.7924 (p) REVERT: L 141 LYS cc_start: 0.6801 (mmmt) cc_final: 0.6367 (ptpp) REVERT: M 6 ARG cc_start: 0.7192 (OUTLIER) cc_final: 0.6669 (ptp90) REVERT: M 12 MET cc_start: 0.8285 (ttm) cc_final: 0.8026 (ttm) REVERT: M 55 ARG cc_start: 0.7478 (OUTLIER) cc_final: 0.6976 (ttm170) REVERT: M 75 GLU cc_start: 0.8264 (tt0) cc_final: 0.7756 (tt0) REVERT: M 88 ASN cc_start: 0.7739 (m110) cc_final: 0.7513 (m-40) REVERT: N 35 LYS cc_start: 0.7851 (tttt) cc_final: 0.7502 (tttp) REVERT: O 13 ARG cc_start: 0.7074 (ttt90) cc_final: 0.6781 (tpp-160) REVERT: O 98 GLN cc_start: 0.8280 (tt0) cc_final: 0.7872 (tt0) REVERT: Q 12 ARG cc_start: 0.8053 (ttm-80) cc_final: 0.7517 (ttt180) REVERT: Q 14 LYS cc_start: 0.7477 (tttt) cc_final: 0.7091 (mtpp) REVERT: Q 48 ASP cc_start: 0.8429 (m-30) cc_final: 0.7784 (m-30) REVERT: Q 77 LYS cc_start: 0.8103 (mttt) cc_final: 0.7657 (mtpt) REVERT: Q 110 GLU cc_start: 0.7097 (OUTLIER) cc_final: 0.6593 (mp0) REVERT: R 1 MET cc_start: 0.6406 (tpp) cc_final: 0.5262 (ptp) REVERT: R 10 LYS cc_start: 0.7734 (ptpp) cc_final: 0.7507 (mtmm) REVERT: R 48 LYS cc_start: 0.7184 (OUTLIER) cc_final: 0.6982 (ttmm) REVERT: R 66 HIS cc_start: 0.8402 (OUTLIER) cc_final: 0.7019 (m-70) REVERT: R 84 ARG cc_start: 0.8491 (OUTLIER) cc_final: 0.7344 (ttp80) REVERT: S 34 ASP cc_start: 0.7485 (m-30) cc_final: 0.7188 (m-30) REVERT: S 39 THR cc_start: 0.7623 (m) cc_final: 0.7337 (m) REVERT: S 52 GLU cc_start: 0.7959 (tt0) cc_final: 0.7374 (mm-30) REVERT: S 86 MET cc_start: 0.8471 (OUTLIER) cc_final: 0.7839 (tpt) REVERT: S 92 ARG cc_start: 0.7128 (ptp90) cc_final: 0.6431 (ptm160) REVERT: S 95 ARG cc_start: 0.8001 (ttm-80) cc_final: 0.7762 (ttp80) REVERT: T 28 ASN cc_start: 0.7483 (t0) cc_final: 0.6842 (t0) REVERT: T 33 LYS cc_start: 0.7369 (OUTLIER) cc_final: 0.7167 (tttt) REVERT: T 54 GLU cc_start: 0.7368 (mt-10) cc_final: 0.6435 (tp30) REVERT: T 69 ARG cc_start: 0.7744 (ttp-110) cc_final: 0.7006 (ttm-80) REVERT: T 76 ARG cc_start: 0.7267 (OUTLIER) cc_final: 0.6537 (ptm-80) REVERT: U 25 LYS cc_start: 0.7192 (mmmt) cc_final: 0.6633 (mtpp) REVERT: U 71 ILE cc_start: 0.8083 (pt) cc_final: 0.7637 (mt) REVERT: U 78 LYS cc_start: 0.7057 (OUTLIER) cc_final: 0.6565 (pmtt) REVERT: V 8 VAL cc_start: 0.7929 (t) cc_final: 0.7645 (m) REVERT: V 11 GLU cc_start: 0.6970 (mt-10) cc_final: 0.6660 (pt0) REVERT: V 30 ILE cc_start: 0.7372 (mt) cc_final: 0.6943 (tt) REVERT: V 41 GLU cc_start: 0.7457 (pt0) cc_final: 0.7037 (pm20) REVERT: V 43 ASP cc_start: 0.7637 (t70) cc_final: 0.7251 (t70) REVERT: V 71 LYS cc_start: 0.7126 (mtpp) cc_final: 0.6741 (mppt) REVERT: V 73 LYS cc_start: 0.7243 (mttt) cc_final: 0.6977 (mmmt) REVERT: V 82 TYR cc_start: 0.7203 (p90) cc_final: 0.6825 (p90) REVERT: W 40 LYS cc_start: 0.7974 (ttpt) cc_final: 0.7690 (mtpp) REVERT: W 66 GLU cc_start: 0.8011 (mm-30) cc_final: 0.7038 (mt-10) REVERT: W 71 LYS cc_start: 0.8350 (mttt) cc_final: 0.7968 (mttp) REVERT: X 19 HIS cc_start: 0.7386 (t70) cc_final: 0.6645 (m-70) REVERT: X 67 LEU cc_start: 0.7092 (mm) cc_final: 0.6804 (mm) REVERT: Y 15 ASN cc_start: 0.7089 (m-40) cc_final: 0.6695 (m110) REVERT: Z 5 LYS cc_start: 0.7097 (mtmm) cc_final: 0.6827 (mtpp) REVERT: 0 11 LYS cc_start: 0.8295 (mmmt) cc_final: 0.7972 (tppp) REVERT: 1 23 THR cc_start: 0.7945 (p) cc_final: 0.7719 (m) REVERT: 1 25 ASN cc_start: 0.7076 (t0) cc_final: 0.6847 (t160) REVERT: 1 27 ARG cc_start: 0.7478 (mtm180) cc_final: 0.7122 (mpt180) REVERT: 1 32 LYS cc_start: 0.7437 (mttt) cc_final: 0.7167 (pptt) REVERT: 2 8 SER cc_start: 0.8756 (t) cc_final: 0.8490 (t) REVERT: 2 41 ARG cc_start: 0.7909 (mmt180) cc_final: 0.7271 (mtm-85) REVERT: 3 14 LYS cc_start: 0.8328 (tttt) cc_final: 0.7985 (mmtm) REVERT: 4 18 LYS cc_start: 0.7946 (tttt) cc_final: 0.7705 (mtpp) REVERT: 4 20 ASP cc_start: 0.7511 (OUTLIER) cc_final: 0.6524 (t0) REVERT: 5 1 MET cc_start: 0.2963 (tpt) cc_final: 0.2439 (tmt) REVERT: 6 10 GLU cc_start: 0.7383 (tp30) cc_final: 0.6983 (tt0) REVERT: 6 24 ILE cc_start: 0.7407 (pt) cc_final: 0.7012 (mt) REVERT: b 44 LYS cc_start: 0.6518 (mtpt) cc_final: 0.6262 (mtmm) REVERT: b 107 ARG cc_start: 0.6976 (ttp-110) cc_final: 0.6444 (ttm170) REVERT: b 132 GLU cc_start: 0.6868 (tp30) cc_final: 0.6290 (tt0) REVERT: b 141 GLU cc_start: 0.7394 (mt-10) cc_final: 0.7019 (mm-30) REVERT: b 144 GLU cc_start: 0.7459 (tp30) cc_final: 0.7062 (tt0) REVERT: b 145 ASN cc_start: 0.7250 (p0) cc_final: 0.6716 (m110) REVERT: c 33 ASP cc_start: 0.7422 (t70) cc_final: 0.7150 (t0) REVERT: c 45 GLU cc_start: 0.8023 (tm-30) cc_final: 0.7317 (tp30) REVERT: c 71 ARG cc_start: 0.7200 (mtt90) cc_final: 0.6709 (mtp85) REVERT: c 109 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7444 (mm-30) REVERT: c 128 MET cc_start: 0.7476 (mmt) cc_final: 0.6586 (mtt) REVERT: c 130 ARG cc_start: 0.7672 (OUTLIER) cc_final: 0.7064 (mtt-85) REVERT: c 151 GLU cc_start: 0.7961 (tt0) cc_final: 0.7349 (tm-30) REVERT: c 153 SER cc_start: 0.8244 (OUTLIER) cc_final: 0.7683 (p) REVERT: c 156 LEU cc_start: 0.7500 (OUTLIER) cc_final: 0.7166 (pt) REVERT: c 163 ARG cc_start: 0.5416 (mtt180) cc_final: 0.4595 (mpp-170) REVERT: c 169 GLU cc_start: 0.7841 (mt-10) cc_final: 0.6767 (tp30) REVERT: d 33 ILE cc_start: 0.4758 (OUTLIER) cc_final: 0.4239 (mm) REVERT: d 47 LEU cc_start: 0.8081 (tp) cc_final: 0.7347 (pp) REVERT: d 73 ASN cc_start: 0.7036 (m-40) cc_final: 0.6637 (p0) REVERT: d 77 GLU cc_start: 0.7610 (mt-10) cc_final: 0.6719 (tp30) REVERT: d 135 GLN cc_start: 0.4834 (tm-30) cc_final: 0.3732 (mm110) REVERT: e 25 LYS cc_start: 0.7872 (ttpp) cc_final: 0.7464 (tttp) REVERT: e 71 ILE cc_start: 0.6863 (mm) cc_final: 0.6522 (tt) REVERT: e 127 TYR cc_start: 0.8378 (m-80) cc_final: 0.8034 (m-80) REVERT: e 144 GLU cc_start: 0.7855 (tt0) cc_final: 0.7592 (tt0) REVERT: f 24 ARG cc_start: 0.6850 (mtm110) cc_final: 0.6500 (mtm110) REVERT: f 62 MET cc_start: 0.7143 (mmm) cc_final: 0.6861 (mmm) REVERT: f 63 ASN cc_start: 0.6758 (OUTLIER) cc_final: 0.6129 (t0) REVERT: g 24 LYS cc_start: 0.7048 (OUTLIER) cc_final: 0.6806 (tptm) REVERT: g 39 GLU cc_start: 0.7769 (pt0) cc_final: 0.7434 (pt0) REVERT: g 59 GLU cc_start: 0.7126 (tt0) cc_final: 0.6713 (tt0) REVERT: g 62 GLU cc_start: 0.6363 (OUTLIER) cc_final: 0.5394 (mt-10) REVERT: g 89 GLU cc_start: 0.7974 (OUTLIER) cc_final: 0.7660 (mm-30) REVERT: g 105 GLU cc_start: 0.7848 (tp30) cc_final: 0.7304 (tp30) REVERT: h 2 MET cc_start: 0.8234 (tpp) cc_final: 0.7696 (tpp) REVERT: h 28 SER cc_start: 0.8268 (t) cc_final: 0.7600 (p) REVERT: h 42 GLU cc_start: 0.7408 (OUTLIER) cc_final: 0.7013 (mp0) REVERT: h 49 LYS cc_start: 0.7188 (mttp) cc_final: 0.6371 (ptpt) REVERT: h 86 LYS cc_start: 0.8566 (OUTLIER) cc_final: 0.8144 (mptp) REVERT: h 90 GLU cc_start: 0.7812 (tt0) cc_final: 0.7435 (mp0) REVERT: h 112 ASP cc_start: 0.7626 (p0) cc_final: 0.7370 (p0) REVERT: h 116 ARG cc_start: 0.6474 (OUTLIER) cc_final: 0.4749 (tpp-160) REVERT: i 63 TYR cc_start: 0.7121 (t80) cc_final: 0.6528 (t80) REVERT: i 123 ARG cc_start: 0.7667 (mtp-110) cc_final: 0.7029 (mtt90) REVERT: j 53 ILE cc_start: 0.6805 (tp) cc_final: 0.6431 (pt) REVERT: j 62 ARG cc_start: 0.7634 (OUTLIER) cc_final: 0.6768 (mpt-90) REVERT: k 74 LYS cc_start: 0.7802 (mttt) cc_final: 0.7440 (mptt) REVERT: k 107 THR cc_start: 0.8108 (m) cc_final: 0.7887 (p) REVERT: k 125 LYS cc_start: 0.7713 (OUTLIER) cc_final: 0.7368 (ttmp) REVERT: l 17 LYS cc_start: 0.7075 (pttt) cc_final: 0.6595 (ptmm) REVERT: l 35 ARG cc_start: 0.6224 (ttt90) cc_final: 0.6023 (ttt90) REVERT: l 94 TYR cc_start: 0.7285 (m-80) cc_final: 0.6990 (m-80) REVERT: l 111 GLN cc_start: 0.6591 (mt0) cc_final: 0.5913 (mt0) REVERT: m 12 LYS cc_start: 0.6328 (mtmt) cc_final: 0.5684 (mmtp) REVERT: m 26 LYS cc_start: 0.7184 (ttpp) cc_final: 0.6964 (ttmm) REVERT: m 73 SER cc_start: 0.7814 (m) cc_final: 0.7491 (p) REVERT: m 99 GLN cc_start: 0.7721 (OUTLIER) cc_final: 0.7255 (mt0) REVERT: n 86 GLU cc_start: 0.6863 (tm-30) cc_final: 0.6567 (tm-30) REVERT: n 90 ARG cc_start: 0.7633 (ttt90) cc_final: 0.7147 (ttp-170) REVERT: o 52 ARG cc_start: 0.7270 (ttt-90) cc_final: 0.6791 (ttp-170) REVERT: o 61 GLN cc_start: 0.7781 (tp40) cc_final: 0.7319 (tt0) REVERT: o 82 GLU cc_start: 0.7902 (mm-30) cc_final: 0.7527 (tm-30) REVERT: p 32 PHE cc_start: 0.7301 (p90) cc_final: 0.7039 (p90) REVERT: p 39 PHE cc_start: 0.7112 (t80) cc_final: 0.6911 (t80) REVERT: q 8 GLN cc_start: 0.8002 (tt0) cc_final: 0.7390 (mp10) REVERT: q 18 LYS cc_start: 0.5704 (ttpt) cc_final: 0.5259 (ttmt) REVERT: q 66 LEU cc_start: 0.7494 (OUTLIER) cc_final: 0.7251 (pp) REVERT: r 29 LYS cc_start: 0.7490 (mttp) cc_final: 0.7242 (mttp) REVERT: s 34 SER cc_start: 0.8886 (t) cc_final: 0.8605 (t) REVERT: s 43 MET cc_start: 0.8114 (mtm) cc_final: 0.7868 (mtp) REVERT: t 8 LYS cc_start: 0.6834 (OUTLIER) cc_final: 0.6422 (mtmt) REVERT: t 14 GLU cc_start: 0.7346 (tm-30) cc_final: 0.6932 (tm-30) REVERT: t 20 ASN cc_start: 0.8011 (m-40) cc_final: 0.7744 (m110) REVERT: t 59 ARG cc_start: 0.5427 (ttm110) cc_final: 0.5057 (ttp-110) REVERT: u 32 ARG cc_start: 0.7797 (OUTLIER) cc_final: 0.6888 (ppp80) REVERT: u 33 ARG cc_start: 0.7737 (mtt180) cc_final: 0.7340 (mtp180) REVERT: z 54 GLU cc_start: 0.5485 (OUTLIER) cc_final: 0.4707 (pm20) REVERT: z 185 GLU cc_start: 0.3929 (OUTLIER) cc_final: 0.3489 (tt0) REVERT: z 201 GLU cc_start: 0.2447 (mt-10) cc_final: 0.1756 (tp30) REVERT: z 207 ASP cc_start: 0.4949 (t0) cc_final: 0.4330 (p0) REVERT: z 282 LYS cc_start: 0.7030 (mttt) cc_final: 0.6616 (mmmt) REVERT: z 310 ILE cc_start: 0.4388 (mm) cc_final: 0.4102 (mm) REVERT: z 354 ASP cc_start: 0.5690 (t70) cc_final: 0.5171 (p0) outliers start: 365 outliers final: 184 residues processed: 1324 average time/residue: 2.2303 time to fit residues: 4292.3831 Evaluate side-chains 1297 residues out of total 5164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 226 poor density : 1071 time to evaluate : 6.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 9 SER Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain C residue 35 LYS Chi-restraints excluded: chain C residue 37 SER Chi-restraints excluded: chain C residue 69 ASN Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 124 LYS Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain C residue 252 LYS Chi-restraints excluded: chain D residue 2 ILE Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 99 GLU Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 150 GLN Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 30 GLN Chi-restraints excluded: chain E residue 95 LYS Chi-restraints excluded: chain E residue 137 LYS Chi-restraints excluded: chain E residue 159 LEU Chi-restraints excluded: chain E residue 176 ASP Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain F residue 16 MET Chi-restraints excluded: chain F residue 18 GLU Chi-restraints excluded: chain F residue 25 MET Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain F residue 84 ILE Chi-restraints excluded: chain F residue 122 ASP Chi-restraints excluded: chain F residue 128 SER Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 143 ASP Chi-restraints excluded: chain F residue 148 VAL Chi-restraints excluded: chain F residue 152 ASP Chi-restraints excluded: chain G residue 24 THR Chi-restraints excluded: chain G residue 120 ILE Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 139 VAL Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain H residue 145 ASN Chi-restraints excluded: chain J residue 12 LYS Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain J residue 128 ASN Chi-restraints excluded: chain K residue 14 SER Chi-restraints excluded: chain K residue 47 ILE Chi-restraints excluded: chain K residue 61 VAL Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 106 GLU Chi-restraints excluded: chain K residue 114 LYS Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 14 LYS Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 91 ASP Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain M residue 6 ARG Chi-restraints excluded: chain M residue 30 SER Chi-restraints excluded: chain M residue 55 ARG Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain O residue 95 SER Chi-restraints excluded: chain P residue 16 VAL Chi-restraints excluded: chain P residue 32 VAL Chi-restraints excluded: chain P residue 47 ILE Chi-restraints excluded: chain Q residue 108 LEU Chi-restraints excluded: chain Q residue 110 GLU Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 48 LYS Chi-restraints excluded: chain R residue 66 HIS Chi-restraints excluded: chain R residue 84 ARG Chi-restraints excluded: chain S residue 29 VAL Chi-restraints excluded: chain S residue 66 ILE Chi-restraints excluded: chain S residue 86 MET Chi-restraints excluded: chain T residue 9 LYS Chi-restraints excluded: chain T residue 16 VAL Chi-restraints excluded: chain T residue 17 SER Chi-restraints excluded: chain T residue 33 LYS Chi-restraints excluded: chain T residue 76 ARG Chi-restraints excluded: chain U residue 61 GLU Chi-restraints excluded: chain U residue 64 ILE Chi-restraints excluded: chain U residue 78 LYS Chi-restraints excluded: chain V residue 4 ILE Chi-restraints excluded: chain V residue 12 GLN Chi-restraints excluded: chain V residue 40 ILE Chi-restraints excluded: chain V residue 63 ILE Chi-restraints excluded: chain V residue 64 VAL Chi-restraints excluded: chain W residue 39 THR Chi-restraints excluded: chain W residue 60 ASP Chi-restraints excluded: chain X residue 34 SER Chi-restraints excluded: chain X residue 65 THR Chi-restraints excluded: chain Z residue 3 THR Chi-restraints excluded: chain Z residue 7 THR Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 9 ARG Chi-restraints excluded: chain 0 residue 22 THR Chi-restraints excluded: chain 0 residue 32 THR Chi-restraints excluded: chain 1 residue 21 THR Chi-restraints excluded: chain 1 residue 22 THR Chi-restraints excluded: chain 1 residue 42 VAL Chi-restraints excluded: chain 1 residue 46 VAL Chi-restraints excluded: chain 2 residue 24 THR Chi-restraints excluded: chain 3 residue 61 LEU Chi-restraints excluded: chain 4 residue 1 MET Chi-restraints excluded: chain 4 residue 6 SER Chi-restraints excluded: chain 4 residue 20 ASP Chi-restraints excluded: chain 4 residue 28 SER Chi-restraints excluded: chain 5 residue 60 LEU Chi-restraints excluded: chain 6 residue 3 LYS Chi-restraints excluded: chain 6 residue 13 THR Chi-restraints excluded: chain b residue 21 TYR Chi-restraints excluded: chain b residue 105 THR Chi-restraints excluded: chain b residue 109 SER Chi-restraints excluded: chain b residue 152 ASP Chi-restraints excluded: chain b residue 173 LYS Chi-restraints excluded: chain b residue 178 LEU Chi-restraints excluded: chain b residue 190 SER Chi-restraints excluded: chain b residue 203 ASP Chi-restraints excluded: chain b residue 222 GLU Chi-restraints excluded: chain b residue 225 SER Chi-restraints excluded: chain c residue 90 VAL Chi-restraints excluded: chain c residue 109 GLU Chi-restraints excluded: chain c residue 120 THR Chi-restraints excluded: chain c residue 130 ARG Chi-restraints excluded: chain c residue 146 LYS Chi-restraints excluded: chain c residue 153 SER Chi-restraints excluded: chain c residue 156 LEU Chi-restraints excluded: chain d residue 33 ILE Chi-restraints excluded: chain d residue 124 VAL Chi-restraints excluded: chain d residue 143 SER Chi-restraints excluded: chain d residue 158 LEU Chi-restraints excluded: chain d residue 168 THR Chi-restraints excluded: chain e residue 17 VAL Chi-restraints excluded: chain e residue 29 ILE Chi-restraints excluded: chain e residue 36 THR Chi-restraints excluded: chain e residue 38 VAL Chi-restraints excluded: chain e residue 45 VAL Chi-restraints excluded: chain e residue 61 LYS Chi-restraints excluded: chain e residue 70 MET Chi-restraints excluded: chain e residue 79 THR Chi-restraints excluded: chain e residue 91 SER Chi-restraints excluded: chain e residue 102 THR Chi-restraints excluded: chain e residue 121 ASN Chi-restraints excluded: chain e residue 129 SER Chi-restraints excluded: chain e residue 160 VAL Chi-restraints excluded: chain f residue 63 ASN Chi-restraints excluded: chain f residue 70 VAL Chi-restraints excluded: chain f residue 76 THR Chi-restraints excluded: chain f residue 96 VAL Chi-restraints excluded: chain g residue 11 ILE Chi-restraints excluded: chain g residue 24 LYS Chi-restraints excluded: chain g residue 32 ASP Chi-restraints excluded: chain g residue 62 GLU Chi-restraints excluded: chain g residue 76 SER Chi-restraints excluded: chain g residue 89 GLU Chi-restraints excluded: chain g residue 93 VAL Chi-restraints excluded: chain g residue 96 ASN Chi-restraints excluded: chain g residue 132 THR Chi-restraints excluded: chain h residue 3 GLN Chi-restraints excluded: chain h residue 11 THR Chi-restraints excluded: chain h residue 25 THR Chi-restraints excluded: chain h residue 42 GLU Chi-restraints excluded: chain h residue 58 LEU Chi-restraints excluded: chain h residue 59 GLU Chi-restraints excluded: chain h residue 82 LEU Chi-restraints excluded: chain h residue 86 LYS Chi-restraints excluded: chain h residue 105 THR Chi-restraints excluded: chain h residue 111 THR Chi-restraints excluded: chain h residue 116 ARG Chi-restraints excluded: chain h residue 128 VAL Chi-restraints excluded: chain i residue 20 ILE Chi-restraints excluded: chain i residue 61 ASP Chi-restraints excluded: chain i residue 66 VAL Chi-restraints excluded: chain i residue 97 LEU Chi-restraints excluded: chain j residue 62 ARG Chi-restraints excluded: chain j residue 96 VAL Chi-restraints excluded: chain k residue 34 THR Chi-restraints excluded: chain k residue 49 SER Chi-restraints excluded: chain k residue 80 ASN Chi-restraints excluded: chain k residue 84 MET Chi-restraints excluded: chain k residue 113 THR Chi-restraints excluded: chain k residue 125 LYS Chi-restraints excluded: chain l residue 15 VAL Chi-restraints excluded: chain l residue 96 THR Chi-restraints excluded: chain l residue 97 VAL Chi-restraints excluded: chain l residue 115 LYS Chi-restraints excluded: chain m residue 6 ILE Chi-restraints excluded: chain m residue 15 VAL Chi-restraints excluded: chain m residue 28 ARG Chi-restraints excluded: chain m residue 45 SER Chi-restraints excluded: chain m residue 52 ILE Chi-restraints excluded: chain m residue 67 ASP Chi-restraints excluded: chain m residue 99 GLN Chi-restraints excluded: chain n residue 3 GLN Chi-restraints excluded: chain n residue 60 GLN Chi-restraints excluded: chain o residue 10 ILE Chi-restraints excluded: chain p residue 2 VAL Chi-restraints excluded: chain q residue 66 LEU Chi-restraints excluded: chain q residue 67 SER Chi-restraints excluded: chain r residue 13 THR Chi-restraints excluded: chain r residue 49 LYS Chi-restraints excluded: chain r residue 66 LEU Chi-restraints excluded: chain r residue 70 THR Chi-restraints excluded: chain s residue 32 THR Chi-restraints excluded: chain s residue 48 ILE Chi-restraints excluded: chain s residue 65 MET Chi-restraints excluded: chain t residue 8 LYS Chi-restraints excluded: chain u residue 3 ILE Chi-restraints excluded: chain u residue 27 VAL Chi-restraints excluded: chain u residue 32 ARG Chi-restraints excluded: chain u residue 41 THR Chi-restraints excluded: chain u residue 50 SER Chi-restraints excluded: chain z residue 13 ASN Chi-restraints excluded: chain z residue 54 GLU Chi-restraints excluded: chain z residue 185 GLU Chi-restraints excluded: chain z residue 225 THR Chi-restraints excluded: chain z residue 233 ARG Chi-restraints excluded: chain z residue 245 VAL Chi-restraints excluded: chain z residue 249 GLU Chi-restraints excluded: chain z residue 276 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1087 random chunks: chunk 353 optimal weight: 1.9990 chunk 946 optimal weight: 0.0370 chunk 207 optimal weight: 7.9990 chunk 616 optimal weight: 4.9990 chunk 259 optimal weight: 6.9990 chunk 1051 optimal weight: 5.9990 chunk 873 optimal weight: 5.9990 chunk 486 optimal weight: 9.9990 chunk 87 optimal weight: 10.0000 chunk 347 optimal weight: 9.9990 chunk 552 optimal weight: 0.9980 overall best weight: 2.8064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 59 GLN C 238 ASN E 165 HIS ** F 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 44 HIS G 63 GLN ** I 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 6 GLN Q 19 GLN R 6 GLN U 45 GLN U 73 ASN V 75 GLN c 24 ASN c 31 ASN c 139 ASN d 58 GLN e 76 ASN ** e 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 17 GLN f 63 ASN g 27 ASN g 147 ASN ** m 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 66 HIS ** z 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.3847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 165479 Z= 0.234 Angle : 0.708 14.950 247209 Z= 0.381 Chirality : 0.037 0.413 31418 Planarity : 0.007 0.129 13503 Dihedral : 24.282 179.139 81845 Min Nonbonded Distance : 1.101 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.56 % Allowed : 7.82 % Favored : 91.62 % Rotamer: Outliers : 6.72 % Allowed : 25.42 % Favored : 67.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.10), residues: 6219 helix: 0.17 (0.12), residues: 1967 sheet: -1.35 (0.14), residues: 1197 loop : -1.92 (0.10), residues: 3055 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 212 HIS 0.020 0.001 HIS b 14 PHE 0.022 0.002 PHE f 78 TYR 0.028 0.002 TYR z 160 ARG 0.010 0.001 ARG f 38 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12438 Ramachandran restraints generated. 6219 Oldfield, 0 Emsley, 6219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12438 Ramachandran restraints generated. 6219 Oldfield, 0 Emsley, 6219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1464 residues out of total 5164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 347 poor density : 1117 time to evaluate : 6.794 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: C 4 LYS cc_start: 0.8098 (tttt) cc_final: 0.7664 (ttmm) REVERT: C 22 GLU cc_start: 0.7922 (OUTLIER) cc_final: 0.7192 (mt-10) REVERT: C 27 LYS cc_start: 0.7562 (mttt) cc_final: 0.7106 (mppt) REVERT: C 113 ASP cc_start: 0.6891 (m-30) cc_final: 0.6168 (t0) REVERT: C 116 GLN cc_start: 0.7938 (tt0) cc_final: 0.7718 (tt0) REVERT: C 159 THR cc_start: 0.9175 (m) cc_final: 0.8706 (p) REVERT: C 184 GLU cc_start: 0.7283 (tt0) cc_final: 0.6548 (mt-10) REVERT: C 187 CYS cc_start: 0.8309 (m) cc_final: 0.8052 (m) REVERT: C 228 ASP cc_start: 0.8637 (m-30) cc_final: 0.8435 (m-30) REVERT: C 252 LYS cc_start: 0.8223 (OUTLIER) cc_final: 0.7892 (mttp) REVERT: C 260 LYS cc_start: 0.7877 (OUTLIER) cc_final: 0.7603 (ttpt) REVERT: D 2 ILE cc_start: 0.4848 (OUTLIER) cc_final: 0.4470 (pp) REVERT: D 108 ASP cc_start: 0.7582 (m-30) cc_final: 0.6930 (p0) REVERT: D 150 GLN cc_start: 0.8120 (OUTLIER) cc_final: 0.7881 (tt0) REVERT: D 186 LEU cc_start: 0.7998 (mt) cc_final: 0.7722 (mt) REVERT: E 21 ARG cc_start: 0.7467 (mtp-110) cc_final: 0.7237 (mtp-110) REVERT: E 30 GLN cc_start: 0.8333 (OUTLIER) cc_final: 0.7931 (tt0) REVERT: E 51 GLU cc_start: 0.7827 (mt-10) cc_final: 0.7390 (mp0) REVERT: E 88 ARG cc_start: 0.7704 (ttm-80) cc_final: 0.7142 (mmp80) REVERT: E 95 LYS cc_start: 0.7749 (OUTLIER) cc_final: 0.7117 (tttp) REVERT: E 106 LYS cc_start: 0.7578 (mtpt) cc_final: 0.7299 (mttt) REVERT: E 121 VAL cc_start: 0.8471 (m) cc_final: 0.8182 (p) REVERT: E 144 GLU cc_start: 0.7220 (pm20) cc_final: 0.6519 (mt-10) REVERT: E 159 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.8279 (mm) REVERT: E 194 LYS cc_start: 0.7891 (tptt) cc_final: 0.7597 (mmtt) REVERT: F 2 LYS cc_start: 0.7945 (tttm) cc_final: 0.7538 (tptt) REVERT: F 9 ASP cc_start: 0.7387 (OUTLIER) cc_final: 0.7063 (t70) REVERT: F 16 MET cc_start: 0.6540 (OUTLIER) cc_final: 0.5643 (mpp) REVERT: F 18 GLU cc_start: 0.5763 (OUTLIER) cc_final: 0.5130 (mt-10) REVERT: F 31 GLU cc_start: 0.8215 (tt0) cc_final: 0.7963 (tt0) REVERT: F 41 GLU cc_start: 0.7128 (mm-30) cc_final: 0.6358 (mp0) REVERT: F 46 LYS cc_start: 0.8026 (mttt) cc_final: 0.7623 (tppp) REVERT: F 47 LYS cc_start: 0.7517 (ptmt) cc_final: 0.7052 (pmtt) REVERT: F 68 LYS cc_start: 0.7549 (mptt) cc_final: 0.7325 (mppt) REVERT: F 71 LYS cc_start: 0.7198 (mmmt) cc_final: 0.6827 (ttpt) REVERT: F 133 GLU cc_start: 0.7501 (mt-10) cc_final: 0.6914 (pt0) REVERT: F 137 PHE cc_start: 0.7356 (m-80) cc_final: 0.7143 (m-80) REVERT: F 147 ARG cc_start: 0.6761 (tpp80) cc_final: 0.6051 (ttt180) REVERT: F 160 LYS cc_start: 0.7504 (mtmm) cc_final: 0.7180 (mmtp) REVERT: G 154 GLU cc_start: 0.7148 (tt0) cc_final: 0.6801 (pt0) REVERT: I 16 MET cc_start: 0.1483 (mmp) cc_final: 0.1138 (mpp) REVERT: I 135 MET cc_start: 0.1537 (mtp) cc_final: 0.0987 (tmt) REVERT: J 12 LYS cc_start: 0.7611 (OUTLIER) cc_final: 0.7117 (tptp) REVERT: J 31 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7611 (mp0) REVERT: J 43 GLU cc_start: 0.8052 (mt-10) cc_final: 0.7400 (pm20) REVERT: J 61 LYS cc_start: 0.7991 (mmtp) cc_final: 0.7427 (mtpt) REVERT: J 91 GLU cc_start: 0.7815 (mt-10) cc_final: 0.7386 (tp30) REVERT: J 95 ARG cc_start: 0.6473 (mtp-110) cc_final: 0.6013 (ttp-110) REVERT: K 7 MET cc_start: 0.8546 (tpp) cc_final: 0.8246 (tpp) REVERT: K 17 ARG cc_start: 0.8339 (tpp80) cc_final: 0.8048 (tpp-160) REVERT: K 18 ARG cc_start: 0.7925 (mmt180) cc_final: 0.7617 (tpp80) REVERT: K 45 GLU cc_start: 0.7289 (tt0) cc_final: 0.6804 (tp30) REVERT: K 53 LYS cc_start: 0.6908 (pttp) cc_final: 0.6707 (ptpp) REVERT: K 66 LYS cc_start: 0.8142 (mttt) cc_final: 0.7876 (mtpt) REVERT: L 14 LYS cc_start: 0.7398 (OUTLIER) cc_final: 0.7022 (tmtt) REVERT: L 19 LEU cc_start: 0.8983 (mp) cc_final: 0.8658 (mp) REVERT: L 105 ILE cc_start: 0.8470 (mt) cc_final: 0.8137 (mm) REVERT: L 106 GLU cc_start: 0.8427 (mt-10) cc_final: 0.8033 (mm-30) REVERT: L 117 THR cc_start: 0.8168 (m) cc_final: 0.7923 (p) REVERT: L 141 LYS cc_start: 0.6781 (mmmt) cc_final: 0.6335 (ptpp) REVERT: M 6 ARG cc_start: 0.7152 (OUTLIER) cc_final: 0.6689 (ptp90) REVERT: M 12 MET cc_start: 0.8355 (ttm) cc_final: 0.8111 (ttm) REVERT: M 40 ARG cc_start: 0.8577 (OUTLIER) cc_final: 0.6783 (ptp-170) REVERT: M 75 GLU cc_start: 0.8272 (tt0) cc_final: 0.7768 (tt0) REVERT: M 88 ASN cc_start: 0.7738 (m110) cc_final: 0.7520 (m-40) REVERT: N 35 LYS cc_start: 0.7892 (tttt) cc_final: 0.7553 (tttp) REVERT: O 13 ARG cc_start: 0.7050 (ttt90) cc_final: 0.6761 (tpp-160) REVERT: O 98 GLN cc_start: 0.8237 (tt0) cc_final: 0.7821 (tt0) REVERT: P 6 GLN cc_start: 0.7385 (OUTLIER) cc_final: 0.6725 (tm-30) REVERT: P 8 GLU cc_start: 0.6362 (mm-30) cc_final: 0.6144 (mp0) REVERT: Q 12 ARG cc_start: 0.8032 (ttm-80) cc_final: 0.7512 (ttt180) REVERT: Q 14 LYS cc_start: 0.7534 (tttt) cc_final: 0.7143 (mtpp) REVERT: Q 48 ASP cc_start: 0.8432 (m-30) cc_final: 0.7767 (m-30) REVERT: Q 77 LYS cc_start: 0.8085 (mttt) cc_final: 0.7634 (mtpt) REVERT: Q 101 ASP cc_start: 0.6680 (m-30) cc_final: 0.6218 (t0) REVERT: Q 110 GLU cc_start: 0.6996 (OUTLIER) cc_final: 0.6468 (mp0) REVERT: R 1 MET cc_start: 0.6405 (tpp) cc_final: 0.5271 (ptp) REVERT: R 10 LYS cc_start: 0.7740 (ptpp) cc_final: 0.7534 (mtmm) REVERT: R 66 HIS cc_start: 0.8225 (OUTLIER) cc_final: 0.6842 (m-70) REVERT: R 84 ARG cc_start: 0.8536 (OUTLIER) cc_final: 0.8196 (ptp90) REVERT: S 1 MET cc_start: 0.6725 (mmm) cc_final: 0.6208 (mpp) REVERT: S 34 ASP cc_start: 0.7353 (m-30) cc_final: 0.7102 (m-30) REVERT: S 39 THR cc_start: 0.7647 (m) cc_final: 0.7371 (m) REVERT: S 52 GLU cc_start: 0.7928 (tt0) cc_final: 0.7348 (mm-30) REVERT: S 86 MET cc_start: 0.8462 (OUTLIER) cc_final: 0.7896 (tpt) REVERT: S 92 ARG cc_start: 0.6977 (ptp90) cc_final: 0.6331 (ptm160) REVERT: S 95 ARG cc_start: 0.7983 (ttm-80) cc_final: 0.7768 (ttp80) REVERT: T 28 ASN cc_start: 0.7493 (t0) cc_final: 0.6881 (t0) REVERT: T 33 LYS cc_start: 0.7305 (OUTLIER) cc_final: 0.7092 (tttt) REVERT: T 54 GLU cc_start: 0.7354 (mt-10) cc_final: 0.6275 (tp30) REVERT: T 69 ARG cc_start: 0.7616 (ttp-110) cc_final: 0.6927 (ttm-80) REVERT: T 76 ARG cc_start: 0.7324 (OUTLIER) cc_final: 0.6665 (ptm-80) REVERT: U 20 LYS cc_start: 0.6785 (OUTLIER) cc_final: 0.6546 (mtpt) REVERT: U 25 LYS cc_start: 0.7224 (mmmt) cc_final: 0.6615 (mtpp) REVERT: U 71 ILE cc_start: 0.8070 (pt) cc_final: 0.7604 (mt) REVERT: U 78 LYS cc_start: 0.7030 (OUTLIER) cc_final: 0.6492 (pmtt) REVERT: U 96 LYS cc_start: 0.6991 (OUTLIER) cc_final: 0.6781 (mttt) REVERT: V 8 VAL cc_start: 0.7986 (t) cc_final: 0.7654 (m) REVERT: V 11 GLU cc_start: 0.6953 (mt-10) cc_final: 0.6667 (pt0) REVERT: V 30 ILE cc_start: 0.7370 (mt) cc_final: 0.6993 (tt) REVERT: V 41 GLU cc_start: 0.7592 (pt0) cc_final: 0.6941 (pm20) REVERT: V 43 ASP cc_start: 0.7631 (t70) cc_final: 0.7291 (t70) REVERT: V 71 LYS cc_start: 0.7146 (mtpp) cc_final: 0.6755 (mppt) REVERT: V 73 LYS cc_start: 0.7217 (mttt) cc_final: 0.6999 (mmmt) REVERT: V 82 TYR cc_start: 0.7186 (p90) cc_final: 0.6842 (p90) REVERT: W 40 LYS cc_start: 0.8025 (ttpt) cc_final: 0.7737 (mtpp) REVERT: W 66 GLU cc_start: 0.8049 (mm-30) cc_final: 0.7107 (mt-10) REVERT: W 71 LYS cc_start: 0.8319 (mttt) cc_final: 0.7917 (mttp) REVERT: X 19 HIS cc_start: 0.7333 (t70) cc_final: 0.6624 (m-70) REVERT: X 67 LEU cc_start: 0.7118 (mm) cc_final: 0.6852 (mm) REVERT: X 71 ARG cc_start: 0.5894 (mtm110) cc_final: 0.5640 (ptp-110) REVERT: Y 14 LEU cc_start: 0.6169 (OUTLIER) cc_final: 0.5872 (mt) REVERT: Y 15 ASN cc_start: 0.7195 (m-40) cc_final: 0.6871 (m110) REVERT: Z 5 LYS cc_start: 0.7070 (mtmm) cc_final: 0.6780 (mttp) REVERT: 0 11 LYS cc_start: 0.8290 (mmmt) cc_final: 0.7958 (tppp) REVERT: 1 25 ASN cc_start: 0.6964 (t0) cc_final: 0.6681 (t160) REVERT: 1 27 ARG cc_start: 0.7494 (mtm180) cc_final: 0.7157 (mpt180) REVERT: 1 32 LYS cc_start: 0.7410 (mttt) cc_final: 0.7139 (pptt) REVERT: 2 8 SER cc_start: 0.8734 (t) cc_final: 0.8471 (t) REVERT: 2 14 ARG cc_start: 0.8487 (OUTLIER) cc_final: 0.7502 (mtt90) REVERT: 2 41 ARG cc_start: 0.7901 (mmt180) cc_final: 0.7273 (mtm-85) REVERT: 2 44 VAL cc_start: 0.7899 (p) cc_final: 0.7665 (m) REVERT: 3 14 LYS cc_start: 0.8343 (tttt) cc_final: 0.8010 (mmtm) REVERT: 4 18 LYS cc_start: 0.7948 (tttt) cc_final: 0.7653 (mtpp) REVERT: 4 20 ASP cc_start: 0.7500 (OUTLIER) cc_final: 0.6538 (t0) REVERT: 4 37 GLN cc_start: 0.7498 (tt0) cc_final: 0.7225 (tt0) REVERT: 5 1 MET cc_start: 0.3473 (tpt) cc_final: 0.2754 (tmt) REVERT: 6 10 GLU cc_start: 0.7374 (tp30) cc_final: 0.6977 (tt0) REVERT: b 44 LYS cc_start: 0.6566 (mtpt) cc_final: 0.6284 (mtmm) REVERT: b 107 ARG cc_start: 0.6947 (ttp-110) cc_final: 0.6402 (ttm170) REVERT: b 132 GLU cc_start: 0.6677 (tp30) cc_final: 0.6035 (tt0) REVERT: b 141 GLU cc_start: 0.7366 (mt-10) cc_final: 0.7001 (mm-30) REVERT: b 144 GLU cc_start: 0.7465 (tp30) cc_final: 0.7064 (tt0) REVERT: b 145 ASN cc_start: 0.7296 (p0) cc_final: 0.6769 (m110) REVERT: c 33 ASP cc_start: 0.7332 (t70) cc_final: 0.7071 (t0) REVERT: c 45 GLU cc_start: 0.8014 (tm-30) cc_final: 0.7209 (mm-30) REVERT: c 71 ARG cc_start: 0.7200 (mtt90) cc_final: 0.6701 (mtp85) REVERT: c 109 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7471 (mm-30) REVERT: c 128 MET cc_start: 0.7389 (mmt) cc_final: 0.6501 (mtt) REVERT: c 130 ARG cc_start: 0.7608 (OUTLIER) cc_final: 0.7040 (mtt-85) REVERT: c 151 GLU cc_start: 0.7963 (tt0) cc_final: 0.7352 (tm-30) REVERT: c 153 SER cc_start: 0.8236 (OUTLIER) cc_final: 0.7717 (p) REVERT: c 156 LEU cc_start: 0.7497 (OUTLIER) cc_final: 0.7191 (pt) REVERT: c 163 ARG cc_start: 0.5455 (mtt180) cc_final: 0.4576 (mpp-170) REVERT: c 168 ARG cc_start: 0.7996 (OUTLIER) cc_final: 0.7324 (ptp90) REVERT: c 169 GLU cc_start: 0.7800 (mt-10) cc_final: 0.6740 (tp30) REVERT: d 77 GLU cc_start: 0.7605 (mt-10) cc_final: 0.6736 (tp30) REVERT: d 135 GLN cc_start: 0.4890 (tm-30) cc_final: 0.3797 (mm110) REVERT: e 25 LYS cc_start: 0.7847 (ttpp) cc_final: 0.7457 (tttp) REVERT: e 71 ILE cc_start: 0.6871 (mm) cc_final: 0.6537 (tt) REVERT: e 81 GLN cc_start: 0.8266 (OUTLIER) cc_final: 0.7246 (mp10) REVERT: e 127 TYR cc_start: 0.8419 (m-80) cc_final: 0.8082 (m-80) REVERT: e 144 GLU cc_start: 0.7867 (tt0) cc_final: 0.7633 (tt0) REVERT: f 24 ARG cc_start: 0.7053 (mtm110) cc_final: 0.6448 (mtm110) REVERT: f 58 HIS cc_start: 0.7693 (t70) cc_final: 0.6907 (t-170) REVERT: f 62 MET cc_start: 0.7003 (mmm) cc_final: 0.6782 (mmm) REVERT: f 63 ASN cc_start: 0.6610 (OUTLIER) cc_final: 0.6347 (t0) REVERT: g 20 GLU cc_start: 0.5467 (mm-30) cc_final: 0.5082 (mp0) REVERT: g 24 LYS cc_start: 0.7069 (OUTLIER) cc_final: 0.6777 (tptm) REVERT: g 59 GLU cc_start: 0.7159 (tt0) cc_final: 0.6760 (tt0) REVERT: g 62 GLU cc_start: 0.6358 (OUTLIER) cc_final: 0.5395 (mt-10) REVERT: g 89 GLU cc_start: 0.7956 (OUTLIER) cc_final: 0.7624 (mm-30) REVERT: g 105 GLU cc_start: 0.7870 (tp30) cc_final: 0.7325 (tp30) REVERT: h 2 MET cc_start: 0.8127 (tpp) cc_final: 0.7564 (tpp) REVERT: h 17 GLN cc_start: 0.8276 (mm-40) cc_final: 0.8016 (mm-40) REVERT: h 42 GLU cc_start: 0.7534 (OUTLIER) cc_final: 0.7252 (mp0) REVERT: h 86 LYS cc_start: 0.8541 (OUTLIER) cc_final: 0.8123 (mptp) REVERT: h 90 GLU cc_start: 0.7836 (tt0) cc_final: 0.7409 (mp0) REVERT: h 112 ASP cc_start: 0.7653 (p0) cc_final: 0.7392 (p0) REVERT: h 116 ARG cc_start: 0.6357 (OUTLIER) cc_final: 0.4667 (tpp-160) REVERT: i 63 TYR cc_start: 0.7090 (t80) cc_final: 0.6328 (t80) REVERT: i 64 ILE cc_start: 0.7587 (mt) cc_final: 0.7184 (mp) REVERT: i 123 ARG cc_start: 0.7593 (mtp-110) cc_final: 0.7248 (mtt-85) REVERT: j 53 ILE cc_start: 0.6724 (tp) cc_final: 0.6343 (pt) REVERT: j 62 ARG cc_start: 0.7648 (OUTLIER) cc_final: 0.6943 (mpt-90) REVERT: k 74 LYS cc_start: 0.7762 (mttt) cc_final: 0.7381 (mptt) REVERT: k 107 THR cc_start: 0.7950 (m) cc_final: 0.7741 (p) REVERT: k 125 LYS cc_start: 0.7731 (OUTLIER) cc_final: 0.7417 (ttmp) REVERT: l 13 ARG cc_start: 0.7535 (tpt170) cc_final: 0.6469 (tpt170) REVERT: l 17 LYS cc_start: 0.7094 (pttt) cc_final: 0.6532 (ptmm) REVERT: l 111 GLN cc_start: 0.6688 (mt0) cc_final: 0.6092 (mt0) REVERT: m 26 LYS cc_start: 0.7171 (ttpp) cc_final: 0.6949 (ttmm) REVERT: m 73 SER cc_start: 0.7823 (m) cc_final: 0.7514 (p) REVERT: m 99 GLN cc_start: 0.7694 (OUTLIER) cc_final: 0.7273 (mt0) REVERT: n 25 GLU cc_start: 0.7458 (pt0) cc_final: 0.6958 (mp0) REVERT: n 86 GLU cc_start: 0.6859 (tm-30) cc_final: 0.6443 (tm-30) REVERT: n 90 ARG cc_start: 0.7560 (ttt90) cc_final: 0.7070 (ttp-170) REVERT: o 52 ARG cc_start: 0.7256 (ttt-90) cc_final: 0.6777 (ttp-170) REVERT: o 61 GLN cc_start: 0.7761 (tp40) cc_final: 0.7286 (tt0) REVERT: o 67 ASP cc_start: 0.8141 (OUTLIER) cc_final: 0.7833 (m-30) REVERT: o 79 GLN cc_start: 0.7862 (mm-40) cc_final: 0.7288 (mp10) REVERT: o 82 GLU cc_start: 0.7903 (mm-30) cc_final: 0.7554 (tm-30) REVERT: p 32 PHE cc_start: 0.7308 (p90) cc_final: 0.7027 (p90) REVERT: p 39 PHE cc_start: 0.7226 (t80) cc_final: 0.6963 (t80) REVERT: q 8 GLN cc_start: 0.8094 (tt0) cc_final: 0.7559 (mp10) REVERT: q 18 LYS cc_start: 0.5634 (ttpt) cc_final: 0.5184 (ttmt) REVERT: q 40 THR cc_start: 0.7979 (OUTLIER) cc_final: 0.7699 (t) REVERT: q 66 LEU cc_start: 0.7493 (OUTLIER) cc_final: 0.7282 (pp) REVERT: r 29 LYS cc_start: 0.7539 (mttp) cc_final: 0.7247 (mttp) REVERT: s 6 LYS cc_start: 0.5111 (OUTLIER) cc_final: 0.3840 (pmtt) REVERT: s 34 SER cc_start: 0.8819 (t) cc_final: 0.8527 (t) REVERT: t 8 LYS cc_start: 0.6804 (OUTLIER) cc_final: 0.6413 (mtmt) REVERT: t 14 GLU cc_start: 0.7311 (tm-30) cc_final: 0.6977 (tm-30) REVERT: t 20 ASN cc_start: 0.8030 (m-40) cc_final: 0.7757 (m110) REVERT: t 59 ARG cc_start: 0.5444 (ttm110) cc_final: 0.5154 (ttp-110) REVERT: u 33 ARG cc_start: 0.7748 (mtt180) cc_final: 0.7418 (mtm180) REVERT: u 35 GLU cc_start: 0.8297 (mt-10) cc_final: 0.8081 (tt0) REVERT: z 54 GLU cc_start: 0.5478 (OUTLIER) cc_final: 0.4690 (pm20) REVERT: z 185 GLU cc_start: 0.4047 (OUTLIER) cc_final: 0.3704 (tt0) REVERT: z 201 GLU cc_start: 0.2423 (mt-10) cc_final: 0.1752 (tp30) REVERT: z 207 ASP cc_start: 0.4861 (t0) cc_final: 0.4326 (p0) REVERT: z 220 ILE cc_start: 0.5484 (OUTLIER) cc_final: 0.5107 (tp) REVERT: z 233 ARG cc_start: 0.5083 (OUTLIER) cc_final: 0.3973 (ptm160) REVERT: z 282 LYS cc_start: 0.7124 (mttt) cc_final: 0.6755 (mmmt) REVERT: z 310 ILE cc_start: 0.4490 (mm) cc_final: 0.4220 (mm) REVERT: z 354 ASP cc_start: 0.5594 (t70) cc_final: 0.5112 (p0) outliers start: 347 outliers final: 187 residues processed: 1307 average time/residue: 2.2539 time to fit residues: 4272.7771 Evaluate side-chains 1320 residues out of total 5164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 241 poor density : 1079 time to evaluate : 6.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 9 SER Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain C residue 35 LYS Chi-restraints excluded: chain C residue 37 SER Chi-restraints excluded: chain C residue 67 LYS Chi-restraints excluded: chain C residue 69 ASN Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain C residue 252 LYS Chi-restraints excluded: chain C residue 260 LYS Chi-restraints excluded: chain C residue 266 ILE Chi-restraints excluded: chain D residue 2 ILE Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 150 GLN Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 202 ILE Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 30 GLN Chi-restraints excluded: chain E residue 95 LYS Chi-restraints excluded: chain E residue 137 LYS Chi-restraints excluded: chain E residue 159 LEU Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 176 ASP Chi-restraints excluded: chain F residue 9 ASP Chi-restraints excluded: chain F residue 16 MET Chi-restraints excluded: chain F residue 18 GLU Chi-restraints excluded: chain F residue 25 MET Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 122 ASP Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 143 ASP Chi-restraints excluded: chain F residue 145 VAL Chi-restraints excluded: chain F residue 148 VAL Chi-restraints excluded: chain G residue 24 THR Chi-restraints excluded: chain G residue 120 ILE Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 139 VAL Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 145 ASN Chi-restraints excluded: chain I residue 56 VAL Chi-restraints excluded: chain I residue 134 SER Chi-restraints excluded: chain J residue 12 LYS Chi-restraints excluded: chain J residue 27 ARG Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 31 GLU Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain J residue 128 ASN Chi-restraints excluded: chain K residue 14 SER Chi-restraints excluded: chain K residue 47 ILE Chi-restraints excluded: chain K residue 61 VAL Chi-restraints excluded: chain K residue 90 ASN Chi-restraints excluded: chain K residue 99 ILE Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 106 GLU Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 14 LYS Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 91 ASP Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain M residue 6 ARG Chi-restraints excluded: chain M residue 30 SER Chi-restraints excluded: chain M residue 40 ARG Chi-restraints excluded: chain M residue 67 VAL Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain O residue 56 LYS Chi-restraints excluded: chain O residue 95 SER Chi-restraints excluded: chain P residue 6 GLN Chi-restraints excluded: chain P residue 15 ASP Chi-restraints excluded: chain P residue 32 VAL Chi-restraints excluded: chain P residue 47 ILE Chi-restraints excluded: chain Q residue 108 LEU Chi-restraints excluded: chain Q residue 110 GLU Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 66 HIS Chi-restraints excluded: chain R residue 84 ARG Chi-restraints excluded: chain S residue 29 VAL Chi-restraints excluded: chain S residue 66 ILE Chi-restraints excluded: chain S residue 86 MET Chi-restraints excluded: chain T residue 9 LYS Chi-restraints excluded: chain T residue 17 SER Chi-restraints excluded: chain T residue 33 LYS Chi-restraints excluded: chain T residue 61 LEU Chi-restraints excluded: chain T residue 76 ARG Chi-restraints excluded: chain U residue 20 LYS Chi-restraints excluded: chain U residue 61 GLU Chi-restraints excluded: chain U residue 78 LYS Chi-restraints excluded: chain U residue 96 LYS Chi-restraints excluded: chain V residue 4 ILE Chi-restraints excluded: chain V residue 12 GLN Chi-restraints excluded: chain V residue 40 ILE Chi-restraints excluded: chain V residue 63 ILE Chi-restraints excluded: chain V residue 64 VAL Chi-restraints excluded: chain W residue 25 GLU Chi-restraints excluded: chain W residue 60 ASP Chi-restraints excluded: chain X residue 34 SER Chi-restraints excluded: chain X residue 47 THR Chi-restraints excluded: chain X residue 65 THR Chi-restraints excluded: chain Y residue 14 LEU Chi-restraints excluded: chain Z residue 3 THR Chi-restraints excluded: chain Z residue 7 THR Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 9 ARG Chi-restraints excluded: chain 0 residue 22 THR Chi-restraints excluded: chain 0 residue 32 THR Chi-restraints excluded: chain 1 residue 21 THR Chi-restraints excluded: chain 1 residue 22 THR Chi-restraints excluded: chain 1 residue 23 THR Chi-restraints excluded: chain 1 residue 42 VAL Chi-restraints excluded: chain 1 residue 46 VAL Chi-restraints excluded: chain 2 residue 14 ARG Chi-restraints excluded: chain 2 residue 24 THR Chi-restraints excluded: chain 3 residue 61 LEU Chi-restraints excluded: chain 4 residue 1 MET Chi-restraints excluded: chain 4 residue 6 SER Chi-restraints excluded: chain 4 residue 20 ASP Chi-restraints excluded: chain 4 residue 28 SER Chi-restraints excluded: chain b residue 21 TYR Chi-restraints excluded: chain b residue 105 THR Chi-restraints excluded: chain b residue 109 SER Chi-restraints excluded: chain b residue 170 ILE Chi-restraints excluded: chain b residue 173 LYS Chi-restraints excluded: chain b residue 178 LEU Chi-restraints excluded: chain b residue 190 SER Chi-restraints excluded: chain b residue 193 ASP Chi-restraints excluded: chain b residue 203 ASP Chi-restraints excluded: chain b residue 222 GLU Chi-restraints excluded: chain b residue 225 SER Chi-restraints excluded: chain c residue 109 GLU Chi-restraints excluded: chain c residue 120 THR Chi-restraints excluded: chain c residue 130 ARG Chi-restraints excluded: chain c residue 146 LYS Chi-restraints excluded: chain c residue 153 SER Chi-restraints excluded: chain c residue 156 LEU Chi-restraints excluded: chain c residue 168 ARG Chi-restraints excluded: chain d residue 58 GLN Chi-restraints excluded: chain d residue 124 VAL Chi-restraints excluded: chain d residue 143 SER Chi-restraints excluded: chain d residue 158 LEU Chi-restraints excluded: chain d residue 168 THR Chi-restraints excluded: chain e residue 17 VAL Chi-restraints excluded: chain e residue 29 ILE Chi-restraints excluded: chain e residue 33 THR Chi-restraints excluded: chain e residue 36 THR Chi-restraints excluded: chain e residue 38 VAL Chi-restraints excluded: chain e residue 45 VAL Chi-restraints excluded: chain e residue 61 LYS Chi-restraints excluded: chain e residue 81 GLN Chi-restraints excluded: chain e residue 91 SER Chi-restraints excluded: chain e residue 123 LEU Chi-restraints excluded: chain f residue 23 GLU Chi-restraints excluded: chain f residue 38 ARG Chi-restraints excluded: chain f residue 63 ASN Chi-restraints excluded: chain f residue 70 VAL Chi-restraints excluded: chain f residue 76 THR Chi-restraints excluded: chain f residue 88 MET Chi-restraints excluded: chain f residue 96 VAL Chi-restraints excluded: chain g residue 11 ILE Chi-restraints excluded: chain g residue 24 LYS Chi-restraints excluded: chain g residue 32 ASP Chi-restraints excluded: chain g residue 62 GLU Chi-restraints excluded: chain g residue 76 SER Chi-restraints excluded: chain g residue 89 GLU Chi-restraints excluded: chain g residue 96 ASN Chi-restraints excluded: chain g residue 132 THR Chi-restraints excluded: chain h residue 25 THR Chi-restraints excluded: chain h residue 42 GLU Chi-restraints excluded: chain h residue 59 GLU Chi-restraints excluded: chain h residue 82 LEU Chi-restraints excluded: chain h residue 86 LYS Chi-restraints excluded: chain h residue 111 THR Chi-restraints excluded: chain h residue 116 ARG Chi-restraints excluded: chain h residue 128 VAL Chi-restraints excluded: chain i residue 20 ILE Chi-restraints excluded: chain i residue 61 ASP Chi-restraints excluded: chain i residue 66 VAL Chi-restraints excluded: chain i residue 97 LEU Chi-restraints excluded: chain j residue 40 ILE Chi-restraints excluded: chain j residue 62 ARG Chi-restraints excluded: chain j residue 96 VAL Chi-restraints excluded: chain j residue 98 VAL Chi-restraints excluded: chain k residue 15 VAL Chi-restraints excluded: chain k residue 34 THR Chi-restraints excluded: chain k residue 80 ASN Chi-restraints excluded: chain k residue 84 MET Chi-restraints excluded: chain k residue 85 VAL Chi-restraints excluded: chain k residue 113 THR Chi-restraints excluded: chain k residue 125 LYS Chi-restraints excluded: chain l residue 15 VAL Chi-restraints excluded: chain l residue 19 ASN Chi-restraints excluded: chain l residue 97 VAL Chi-restraints excluded: chain l residue 115 LYS Chi-restraints excluded: chain m residue 6 ILE Chi-restraints excluded: chain m residue 15 VAL Chi-restraints excluded: chain m residue 28 ARG Chi-restraints excluded: chain m residue 52 ILE Chi-restraints excluded: chain m residue 67 ASP Chi-restraints excluded: chain m residue 99 GLN Chi-restraints excluded: chain o residue 10 ILE Chi-restraints excluded: chain o residue 67 ASP Chi-restraints excluded: chain p residue 3 THR Chi-restraints excluded: chain q residue 13 SER Chi-restraints excluded: chain q residue 40 THR Chi-restraints excluded: chain q residue 66 LEU Chi-restraints excluded: chain r residue 13 THR Chi-restraints excluded: chain r residue 15 GLU Chi-restraints excluded: chain r residue 32 ILE Chi-restraints excluded: chain r residue 66 LEU Chi-restraints excluded: chain r residue 70 THR Chi-restraints excluded: chain s residue 6 LYS Chi-restraints excluded: chain s residue 32 THR Chi-restraints excluded: chain s residue 65 MET Chi-restraints excluded: chain t residue 8 LYS Chi-restraints excluded: chain t residue 22 SER Chi-restraints excluded: chain u residue 3 ILE Chi-restraints excluded: chain u residue 27 VAL Chi-restraints excluded: chain u residue 32 ARG Chi-restraints excluded: chain u residue 50 SER Chi-restraints excluded: chain z residue 13 ASN Chi-restraints excluded: chain z residue 26 THR Chi-restraints excluded: chain z residue 54 GLU Chi-restraints excluded: chain z residue 67 VAL Chi-restraints excluded: chain z residue 185 GLU Chi-restraints excluded: chain z residue 220 ILE Chi-restraints excluded: chain z residue 225 THR Chi-restraints excluded: chain z residue 233 ARG Chi-restraints excluded: chain z residue 245 VAL Chi-restraints excluded: chain z residue 249 GLU Chi-restraints excluded: chain z residue 276 VAL Chi-restraints excluded: chain z residue 279 ARG Chi-restraints excluded: chain z residue 351 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1087 random chunks: chunk 1013 optimal weight: 9.9990 chunk 118 optimal weight: 8.9990 chunk 599 optimal weight: 10.0000 chunk 768 optimal weight: 10.0000 chunk 595 optimal weight: 6.9990 chunk 885 optimal weight: 6.9990 chunk 587 optimal weight: 0.9980 chunk 1047 optimal weight: 20.0000 chunk 655 optimal weight: 10.0000 chunk 638 optimal weight: 20.0000 chunk 483 optimal weight: 0.8980 overall best weight: 4.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 59 GLN E 94 GLN E 165 HIS ** I 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 6 GLN Q 36 GLN R 6 GLN U 73 ASN V 75 GLN Y 39 GLN 6 61 ASN c 24 ASN c 139 ASN ** d 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 76 ASN f 63 ASN g 147 ASN ** i 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 28 ASN ** l 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.3958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.107 165479 Z= 0.379 Angle : 0.805 15.060 247209 Z= 0.423 Chirality : 0.043 0.392 31418 Planarity : 0.008 0.138 13503 Dihedral : 24.344 179.170 81844 Min Nonbonded Distance : 1.071 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.58 % Allowed : 8.96 % Favored : 90.46 % Rotamer: Outliers : 7.12 % Allowed : 25.73 % Favored : 67.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.92 (0.10), residues: 6219 helix: -0.10 (0.11), residues: 1959 sheet: -1.36 (0.14), residues: 1199 loop : -2.03 (0.10), residues: 3061 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 212 HIS 0.016 0.002 HIS b 14 PHE 0.023 0.002 PHE f 78 TYR 0.038 0.002 TYR n 19 ARG 0.011 0.001 ARG q 61 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12438 Ramachandran restraints generated. 6219 Oldfield, 0 Emsley, 6219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12438 Ramachandran restraints generated. 6219 Oldfield, 0 Emsley, 6219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1479 residues out of total 5164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 368 poor density : 1111 time to evaluate : 6.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 2 VAL cc_start: 0.8404 (t) cc_final: 0.8112 (m) REVERT: C 4 LYS cc_start: 0.8130 (tttt) cc_final: 0.7676 (ttmm) REVERT: C 22 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7127 (mt-10) REVERT: C 27 LYS cc_start: 0.7566 (mttt) cc_final: 0.7050 (mppt) REVERT: C 34 GLU cc_start: 0.8460 (OUTLIER) cc_final: 0.8101 (pt0) REVERT: C 113 ASP cc_start: 0.7005 (m-30) cc_final: 0.6290 (t0) REVERT: C 159 THR cc_start: 0.9160 (m) cc_final: 0.8732 (p) REVERT: C 184 GLU cc_start: 0.7296 (tt0) cc_final: 0.6588 (mt-10) REVERT: C 187 CYS cc_start: 0.8255 (m) cc_final: 0.8018 (m) REVERT: C 213 ARG cc_start: 0.8716 (OUTLIER) cc_final: 0.8388 (ttm-80) REVERT: C 260 LYS cc_start: 0.7912 (OUTLIER) cc_final: 0.7567 (ttpt) REVERT: D 108 ASP cc_start: 0.7596 (m-30) cc_final: 0.6899 (p0) REVERT: D 150 GLN cc_start: 0.8207 (OUTLIER) cc_final: 0.7996 (tt0) REVERT: D 186 LEU cc_start: 0.7981 (mt) cc_final: 0.7756 (mt) REVERT: E 61 ARG cc_start: 0.8127 (OUTLIER) cc_final: 0.7130 (ptt180) REVERT: E 88 ARG cc_start: 0.7753 (ttm-80) cc_final: 0.7189 (mmp80) REVERT: E 95 LYS cc_start: 0.7668 (OUTLIER) cc_final: 0.7046 (tttp) REVERT: E 106 LYS cc_start: 0.7579 (mtpt) cc_final: 0.7305 (mttt) REVERT: E 194 LYS cc_start: 0.7931 (tptt) cc_final: 0.7631 (mmtt) REVERT: F 2 LYS cc_start: 0.7963 (tttm) cc_final: 0.7561 (tptt) REVERT: F 9 ASP cc_start: 0.7459 (OUTLIER) cc_final: 0.7041 (t70) REVERT: F 18 GLU cc_start: 0.5671 (OUTLIER) cc_final: 0.4983 (mt-10) REVERT: F 41 GLU cc_start: 0.7074 (mm-30) cc_final: 0.6252 (mp0) REVERT: F 46 LYS cc_start: 0.8075 (mttt) cc_final: 0.7665 (tppp) REVERT: F 47 LYS cc_start: 0.7534 (ptmt) cc_final: 0.7095 (pmtt) REVERT: F 71 LYS cc_start: 0.7245 (mmmt) cc_final: 0.6843 (ttpt) REVERT: F 119 LYS cc_start: 0.7418 (ttpp) cc_final: 0.7109 (ttpp) REVERT: F 133 GLU cc_start: 0.7503 (mt-10) cc_final: 0.6924 (pt0) REVERT: F 137 PHE cc_start: 0.7381 (m-80) cc_final: 0.7155 (m-80) REVERT: F 147 ARG cc_start: 0.6591 (tpp80) cc_final: 0.5829 (ttt180) REVERT: F 160 LYS cc_start: 0.7532 (mtmm) cc_final: 0.7212 (mmtp) REVERT: G 154 GLU cc_start: 0.7143 (tt0) cc_final: 0.6828 (pt0) REVERT: I 16 MET cc_start: 0.1367 (mmp) cc_final: 0.0882 (mpp) REVERT: I 135 MET cc_start: 0.1477 (mtp) cc_final: 0.0961 (tmt) REVERT: J 12 LYS cc_start: 0.7864 (OUTLIER) cc_final: 0.7215 (tptp) REVERT: J 43 GLU cc_start: 0.8106 (mt-10) cc_final: 0.7425 (pm20) REVERT: J 61 LYS cc_start: 0.7962 (mmtp) cc_final: 0.7467 (mtpt) REVERT: J 84 ILE cc_start: 0.8155 (OUTLIER) cc_final: 0.7734 (tp) REVERT: J 91 GLU cc_start: 0.7775 (mt-10) cc_final: 0.7362 (tp30) REVERT: J 95 ARG cc_start: 0.6434 (mtp-110) cc_final: 0.6109 (ttp-110) REVERT: K 17 ARG cc_start: 0.8393 (tpp80) cc_final: 0.8061 (tpp-160) REVERT: K 18 ARG cc_start: 0.8038 (mmt180) cc_final: 0.7584 (mtp-110) REVERT: K 53 LYS cc_start: 0.6912 (pttp) cc_final: 0.6693 (ptpp) REVERT: K 66 LYS cc_start: 0.8113 (mttt) cc_final: 0.7829 (mtpt) REVERT: K 111 LYS cc_start: 0.7407 (ptpp) cc_final: 0.7002 (ttpp) REVERT: L 14 LYS cc_start: 0.7324 (tttm) cc_final: 0.6998 (tmtt) REVERT: L 19 LEU cc_start: 0.9066 (mp) cc_final: 0.8852 (mt) REVERT: L 105 ILE cc_start: 0.8485 (mt) cc_final: 0.8140 (mm) REVERT: L 106 GLU cc_start: 0.8525 (mt-10) cc_final: 0.8049 (mm-30) REVERT: L 141 LYS cc_start: 0.6808 (mmmt) cc_final: 0.6395 (ptpp) REVERT: M 6 ARG cc_start: 0.7240 (OUTLIER) cc_final: 0.6672 (ptp90) REVERT: M 12 MET cc_start: 0.8324 (ttm) cc_final: 0.8078 (ttm) REVERT: M 60 GLN cc_start: 0.7122 (pt0) cc_final: 0.6091 (mp10) REVERT: M 75 GLU cc_start: 0.8274 (tt0) cc_final: 0.7774 (tt0) REVERT: M 88 ASN cc_start: 0.7719 (m110) cc_final: 0.7486 (m-40) REVERT: N 35 LYS cc_start: 0.7873 (tttt) cc_final: 0.7493 (tttp) REVERT: O 13 ARG cc_start: 0.7142 (ttt90) cc_final: 0.6853 (tpp-160) REVERT: O 48 LEU cc_start: 0.8143 (mm) cc_final: 0.7837 (mt) REVERT: O 98 GLN cc_start: 0.8251 (tt0) cc_final: 0.7766 (tt0) REVERT: P 6 GLN cc_start: 0.7274 (tt0) cc_final: 0.6527 (tm-30) REVERT: Q 12 ARG cc_start: 0.8063 (ttm-80) cc_final: 0.7544 (ttt180) REVERT: Q 14 LYS cc_start: 0.7499 (tttt) cc_final: 0.7103 (mtpp) REVERT: Q 48 ASP cc_start: 0.8465 (m-30) cc_final: 0.7848 (m-30) REVERT: Q 77 LYS cc_start: 0.8117 (mttt) cc_final: 0.7671 (mtpt) REVERT: Q 110 GLU cc_start: 0.7093 (OUTLIER) cc_final: 0.6561 (mp0) REVERT: R 1 MET cc_start: 0.6344 (tpp) cc_final: 0.5188 (ptp) REVERT: R 10 LYS cc_start: 0.7795 (ptpp) cc_final: 0.7520 (mtmm) REVERT: R 66 HIS cc_start: 0.8415 (OUTLIER) cc_final: 0.7016 (m-70) REVERT: R 84 ARG cc_start: 0.8568 (OUTLIER) cc_final: 0.7112 (ttp80) REVERT: S 1 MET cc_start: 0.6749 (mmm) cc_final: 0.6131 (mpp) REVERT: S 34 ASP cc_start: 0.7483 (m-30) cc_final: 0.7262 (m-30) REVERT: S 52 GLU cc_start: 0.7938 (tt0) cc_final: 0.7360 (mm-30) REVERT: S 86 MET cc_start: 0.8533 (OUTLIER) cc_final: 0.7930 (tpt) REVERT: S 92 ARG cc_start: 0.7051 (ptp90) cc_final: 0.6403 (ttt90) REVERT: T 28 ASN cc_start: 0.7527 (t0) cc_final: 0.6903 (t0) REVERT: T 33 LYS cc_start: 0.7370 (OUTLIER) cc_final: 0.7156 (tttt) REVERT: T 50 LEU cc_start: 0.7741 (mm) cc_final: 0.7531 (mp) REVERT: T 54 GLU cc_start: 0.7322 (mt-10) cc_final: 0.6378 (tp30) REVERT: T 69 ARG cc_start: 0.7680 (ttp-110) cc_final: 0.6977 (ttm-80) REVERT: T 76 ARG cc_start: 0.7237 (OUTLIER) cc_final: 0.6533 (ptm-80) REVERT: U 17 ASP cc_start: 0.7862 (p0) cc_final: 0.7534 (p0) REVERT: U 25 LYS cc_start: 0.7213 (mmmt) cc_final: 0.6677 (mtpp) REVERT: U 71 ILE cc_start: 0.8084 (pt) cc_final: 0.7714 (mt) REVERT: U 78 LYS cc_start: 0.6979 (OUTLIER) cc_final: 0.6557 (pmtt) REVERT: U 96 LYS cc_start: 0.7018 (OUTLIER) cc_final: 0.6806 (mttt) REVERT: V 3 THR cc_start: 0.7705 (p) cc_final: 0.7421 (m) REVERT: V 11 GLU cc_start: 0.7030 (mt-10) cc_final: 0.6768 (pt0) REVERT: V 24 ASN cc_start: 0.8060 (OUTLIER) cc_final: 0.7130 (t0) REVERT: V 30 ILE cc_start: 0.7387 (mt) cc_final: 0.7026 (tt) REVERT: V 43 ASP cc_start: 0.7569 (t70) cc_final: 0.7235 (t70) REVERT: V 71 LYS cc_start: 0.7141 (mtpp) cc_final: 0.6749 (mppt) REVERT: V 73 LYS cc_start: 0.7133 (mttt) cc_final: 0.6925 (mmmt) REVERT: V 82 TYR cc_start: 0.7182 (p90) cc_final: 0.6854 (p90) REVERT: W 40 LYS cc_start: 0.8088 (ttpt) cc_final: 0.7736 (mtpp) REVERT: W 62 LYS cc_start: 0.7693 (mttt) cc_final: 0.7243 (mtpt) REVERT: W 66 GLU cc_start: 0.8148 (mm-30) cc_final: 0.7036 (mt-10) REVERT: W 71 LYS cc_start: 0.8339 (mttt) cc_final: 0.7989 (mttp) REVERT: X 19 HIS cc_start: 0.7464 (t70) cc_final: 0.6617 (m-70) REVERT: X 36 ARG cc_start: 0.6897 (OUTLIER) cc_final: 0.5756 (mtp85) REVERT: X 67 LEU cc_start: 0.7042 (mm) cc_final: 0.6782 (mm) REVERT: Y 14 LEU cc_start: 0.6140 (OUTLIER) cc_final: 0.5877 (mt) REVERT: Y 15 ASN cc_start: 0.7106 (m-40) cc_final: 0.6801 (m110) REVERT: Z 5 LYS cc_start: 0.7085 (mtmm) cc_final: 0.6836 (mtpp) REVERT: 0 11 LYS cc_start: 0.8286 (mmmt) cc_final: 0.7947 (tppp) REVERT: 1 6 GLU cc_start: 0.7791 (pt0) cc_final: 0.7369 (pt0) REVERT: 1 23 THR cc_start: 0.7982 (OUTLIER) cc_final: 0.7779 (m) REVERT: 1 25 ASN cc_start: 0.7001 (t0) cc_final: 0.6582 (t160) REVERT: 1 27 ARG cc_start: 0.7503 (mtm180) cc_final: 0.7139 (mpt180) REVERT: 1 32 LYS cc_start: 0.7346 (mttt) cc_final: 0.7128 (pptt) REVERT: 2 8 SER cc_start: 0.8755 (t) cc_final: 0.8485 (t) REVERT: 2 14 ARG cc_start: 0.8514 (OUTLIER) cc_final: 0.7471 (mtt90) REVERT: 2 41 ARG cc_start: 0.7951 (mmt180) cc_final: 0.7432 (mtm-85) REVERT: 2 44 VAL cc_start: 0.7924 (p) cc_final: 0.7688 (m) REVERT: 3 14 LYS cc_start: 0.8397 (tttt) cc_final: 0.7979 (mmtm) REVERT: 4 18 LYS cc_start: 0.7967 (tttt) cc_final: 0.7666 (mtpp) REVERT: 4 20 ASP cc_start: 0.7446 (OUTLIER) cc_final: 0.6526 (t0) REVERT: 5 1 MET cc_start: 0.2995 (tpt) cc_final: 0.2499 (tmt) REVERT: 6 10 GLU cc_start: 0.7342 (tp30) cc_final: 0.6977 (tt0) REVERT: 6 62 LYS cc_start: 0.7190 (mmtm) cc_final: 0.6933 (mmmt) REVERT: b 20 ARG cc_start: 0.5953 (OUTLIER) cc_final: 0.5252 (ptt-90) REVERT: b 132 GLU cc_start: 0.6746 (tp30) cc_final: 0.6059 (tt0) REVERT: b 141 GLU cc_start: 0.7366 (mt-10) cc_final: 0.7037 (mm-30) REVERT: b 144 GLU cc_start: 0.7466 (OUTLIER) cc_final: 0.7235 (tt0) REVERT: b 145 ASN cc_start: 0.7491 (p0) cc_final: 0.6979 (m110) REVERT: c 33 ASP cc_start: 0.7403 (t70) cc_final: 0.7132 (t0) REVERT: c 45 GLU cc_start: 0.7920 (tm-30) cc_final: 0.7226 (tp30) REVERT: c 71 ARG cc_start: 0.7251 (mtt90) cc_final: 0.7013 (mtp85) REVERT: c 109 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.7493 (mm-30) REVERT: c 128 MET cc_start: 0.7530 (mmp) cc_final: 0.6639 (mtt) REVERT: c 130 ARG cc_start: 0.7712 (OUTLIER) cc_final: 0.7115 (mtt-85) REVERT: c 151 GLU cc_start: 0.7967 (tt0) cc_final: 0.7336 (tm-30) REVERT: c 156 LEU cc_start: 0.7588 (OUTLIER) cc_final: 0.7351 (pt) REVERT: c 163 ARG cc_start: 0.5356 (mtt180) cc_final: 0.4494 (mpp-170) REVERT: c 168 ARG cc_start: 0.8029 (OUTLIER) cc_final: 0.7298 (ptp90) REVERT: c 169 GLU cc_start: 0.7831 (mt-10) cc_final: 0.6856 (tp30) REVERT: d 33 ILE cc_start: 0.4924 (OUTLIER) cc_final: 0.4355 (mm) REVERT: d 47 LEU cc_start: 0.8115 (tp) cc_final: 0.7450 (pt) REVERT: d 73 ASN cc_start: 0.7050 (m-40) cc_final: 0.6500 (p0) REVERT: d 77 GLU cc_start: 0.7613 (mt-10) cc_final: 0.6850 (tp30) REVERT: d 135 GLN cc_start: 0.5054 (tm-30) cc_final: 0.4001 (mm110) REVERT: e 71 ILE cc_start: 0.6921 (mm) cc_final: 0.6605 (tt) REVERT: e 81 GLN cc_start: 0.8255 (OUTLIER) cc_final: 0.7155 (mp10) REVERT: e 127 TYR cc_start: 0.8452 (m-80) cc_final: 0.8034 (m-80) REVERT: e 144 GLU cc_start: 0.7858 (tt0) cc_final: 0.7610 (tt0) REVERT: f 24 ARG cc_start: 0.6972 (mtm110) cc_final: 0.6368 (mtm110) REVERT: f 58 HIS cc_start: 0.7775 (t70) cc_final: 0.7061 (t-170) REVERT: f 62 MET cc_start: 0.7213 (mmm) cc_final: 0.6896 (mmm) REVERT: f 63 ASN cc_start: 0.6422 (OUTLIER) cc_final: 0.5891 (t0) REVERT: g 39 GLU cc_start: 0.7689 (pt0) cc_final: 0.7347 (pt0) REVERT: g 89 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7771 (mm-30) REVERT: g 105 GLU cc_start: 0.7916 (tp30) cc_final: 0.7347 (tp30) REVERT: h 2 MET cc_start: 0.7979 (tpp) cc_final: 0.7488 (tpp) REVERT: h 28 SER cc_start: 0.8330 (t) cc_final: 0.7673 (p) REVERT: h 42 GLU cc_start: 0.7569 (OUTLIER) cc_final: 0.6982 (mp0) REVERT: h 86 LYS cc_start: 0.8518 (OUTLIER) cc_final: 0.8171 (mptp) REVERT: h 90 GLU cc_start: 0.7870 (tt0) cc_final: 0.7482 (mp0) REVERT: h 112 ASP cc_start: 0.7654 (p0) cc_final: 0.7373 (p0) REVERT: h 116 ARG cc_start: 0.6479 (OUTLIER) cc_final: 0.4791 (tpp-160) REVERT: i 63 TYR cc_start: 0.7128 (t80) cc_final: 0.6381 (t80) REVERT: i 64 ILE cc_start: 0.7523 (mt) cc_final: 0.7062 (mp) REVERT: i 122 ARG cc_start: 0.7516 (OUTLIER) cc_final: 0.6764 (tmt-80) REVERT: i 123 ARG cc_start: 0.7588 (mtp-110) cc_final: 0.6821 (mtt90) REVERT: j 53 ILE cc_start: 0.6695 (tp) cc_final: 0.6344 (pt) REVERT: j 62 ARG cc_start: 0.7648 (OUTLIER) cc_final: 0.6980 (mpt-90) REVERT: j 88 MET cc_start: 0.6666 (mtm) cc_final: 0.5925 (ptt) REVERT: k 36 ARG cc_start: 0.8220 (mmm-85) cc_final: 0.7556 (mmm-85) REVERT: k 74 LYS cc_start: 0.7751 (mttt) cc_final: 0.7397 (mptt) REVERT: k 107 THR cc_start: 0.7986 (m) cc_final: 0.7780 (p) REVERT: k 125 LYS cc_start: 0.7747 (OUTLIER) cc_final: 0.7381 (ttmp) REVERT: l 13 ARG cc_start: 0.7552 (tpt170) cc_final: 0.6479 (tpt170) REVERT: l 17 LYS cc_start: 0.7068 (pttt) cc_final: 0.6719 (mmtt) REVERT: l 35 ARG cc_start: 0.6387 (ttt90) cc_final: 0.6120 (ttt90) REVERT: l 95 HIS cc_start: 0.6385 (OUTLIER) cc_final: 0.5967 (m-70) REVERT: m 26 LYS cc_start: 0.7213 (ttpp) cc_final: 0.7000 (ttmm) REVERT: m 73 SER cc_start: 0.7818 (m) cc_final: 0.7498 (p) REVERT: m 99 GLN cc_start: 0.7682 (OUTLIER) cc_final: 0.7074 (mt0) REVERT: n 25 GLU cc_start: 0.7490 (pt0) cc_final: 0.6995 (mp0) REVERT: n 90 ARG cc_start: 0.7535 (ttt90) cc_final: 0.6940 (ttp-170) REVERT: o 61 GLN cc_start: 0.7763 (tp40) cc_final: 0.7283 (tt0) REVERT: o 82 GLU cc_start: 0.7851 (mm-30) cc_final: 0.7463 (tm-30) REVERT: p 34 GLU cc_start: 0.2761 (OUTLIER) cc_final: 0.2467 (tm-30) REVERT: q 8 GLN cc_start: 0.8106 (tt0) cc_final: 0.7580 (mp10) REVERT: q 18 LYS cc_start: 0.5494 (ttpt) cc_final: 0.5074 (ttmt) REVERT: q 40 THR cc_start: 0.7968 (OUTLIER) cc_final: 0.7713 (t) REVERT: q 41 THR cc_start: 0.5634 (m) cc_final: 0.5210 (p) REVERT: s 6 LYS cc_start: 0.4998 (OUTLIER) cc_final: 0.3783 (pmtt) REVERT: s 34 SER cc_start: 0.8824 (t) cc_final: 0.8506 (t) REVERT: t 20 ASN cc_start: 0.8093 (m-40) cc_final: 0.7867 (m110) REVERT: t 59 ARG cc_start: 0.5483 (ttm110) cc_final: 0.5230 (ttp-110) REVERT: u 22 CYS cc_start: 0.7381 (t) cc_final: 0.6956 (p) REVERT: u 33 ARG cc_start: 0.7745 (mtt180) cc_final: 0.7322 (mtp180) REVERT: z 54 GLU cc_start: 0.5529 (OUTLIER) cc_final: 0.4745 (pm20) REVERT: z 179 GLU cc_start: 0.4217 (OUTLIER) cc_final: 0.3023 (mm-30) REVERT: z 185 GLU cc_start: 0.4122 (OUTLIER) cc_final: 0.3782 (tt0) REVERT: z 201 GLU cc_start: 0.2448 (mt-10) cc_final: 0.1698 (tp30) REVERT: z 207 ASP cc_start: 0.5209 (t0) cc_final: 0.4615 (p0) REVERT: z 220 ILE cc_start: 0.5725 (OUTLIER) cc_final: 0.5334 (tp) REVERT: z 282 LYS cc_start: 0.7112 (mttt) cc_final: 0.6753 (mmmt) outliers start: 368 outliers final: 214 residues processed: 1331 average time/residue: 2.2425 time to fit residues: 4346.6424 Evaluate side-chains 1345 residues out of total 5164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 265 poor density : 1080 time to evaluate : 7.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 9 SER Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain C residue 34 GLU Chi-restraints excluded: chain C residue 35 LYS Chi-restraints excluded: chain C residue 37 SER Chi-restraints excluded: chain C residue 67 LYS Chi-restraints excluded: chain C residue 69 ASN Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain C residue 213 ARG Chi-restraints excluded: chain C residue 260 LYS Chi-restraints excluded: chain C residue 266 ILE Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 150 GLN Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 61 ARG Chi-restraints excluded: chain E residue 95 LYS Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 137 LYS Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 176 ASP Chi-restraints excluded: chain F residue 9 ASP Chi-restraints excluded: chain F residue 16 MET Chi-restraints excluded: chain F residue 18 GLU Chi-restraints excluded: chain F residue 25 MET Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain F residue 84 ILE Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 122 ASP Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 143 ASP Chi-restraints excluded: chain F residue 145 VAL Chi-restraints excluded: chain F residue 148 VAL Chi-restraints excluded: chain G residue 24 THR Chi-restraints excluded: chain G residue 84 LYS Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 139 VAL Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain I residue 56 VAL Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 12 LYS Chi-restraints excluded: chain J residue 27 ARG Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain J residue 128 ASN Chi-restraints excluded: chain K residue 14 SER Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain K residue 47 ILE Chi-restraints excluded: chain K residue 61 VAL Chi-restraints excluded: chain K residue 99 ILE Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 106 GLU Chi-restraints excluded: chain K residue 107 LEU Chi-restraints excluded: chain K residue 114 LYS Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 91 ASP Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain M residue 6 ARG Chi-restraints excluded: chain M residue 30 SER Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain O residue 56 LYS Chi-restraints excluded: chain O residue 95 SER Chi-restraints excluded: chain P residue 15 ASP Chi-restraints excluded: chain P residue 16 VAL Chi-restraints excluded: chain P residue 32 VAL Chi-restraints excluded: chain P residue 47 ILE Chi-restraints excluded: chain Q residue 110 GLU Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 66 HIS Chi-restraints excluded: chain R residue 84 ARG Chi-restraints excluded: chain S residue 29 VAL Chi-restraints excluded: chain S residue 86 MET Chi-restraints excluded: chain T residue 9 LYS Chi-restraints excluded: chain T residue 17 SER Chi-restraints excluded: chain T residue 33 LYS Chi-restraints excluded: chain T residue 61 LEU Chi-restraints excluded: chain T residue 76 ARG Chi-restraints excluded: chain U residue 61 GLU Chi-restraints excluded: chain U residue 78 LYS Chi-restraints excluded: chain U residue 96 LYS Chi-restraints excluded: chain V residue 4 ILE Chi-restraints excluded: chain V residue 12 GLN Chi-restraints excluded: chain V residue 24 ASN Chi-restraints excluded: chain V residue 40 ILE Chi-restraints excluded: chain V residue 63 ILE Chi-restraints excluded: chain V residue 64 VAL Chi-restraints excluded: chain W residue 39 THR Chi-restraints excluded: chain W residue 60 ASP Chi-restraints excluded: chain X residue 34 SER Chi-restraints excluded: chain X residue 36 ARG Chi-restraints excluded: chain X residue 47 THR Chi-restraints excluded: chain X residue 65 THR Chi-restraints excluded: chain Y residue 14 LEU Chi-restraints excluded: chain Y residue 17 GLU Chi-restraints excluded: chain Y residue 57 LEU Chi-restraints excluded: chain Z residue 3 THR Chi-restraints excluded: chain Z residue 7 THR Chi-restraints excluded: chain Z residue 48 ASN Chi-restraints excluded: chain Z residue 51 SER Chi-restraints excluded: chain 0 residue 5 ASN Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 9 ARG Chi-restraints excluded: chain 0 residue 22 THR Chi-restraints excluded: chain 0 residue 32 THR Chi-restraints excluded: chain 1 residue 21 THR Chi-restraints excluded: chain 1 residue 22 THR Chi-restraints excluded: chain 1 residue 23 THR Chi-restraints excluded: chain 1 residue 42 VAL Chi-restraints excluded: chain 1 residue 46 VAL Chi-restraints excluded: chain 2 residue 14 ARG Chi-restraints excluded: chain 2 residue 24 THR Chi-restraints excluded: chain 3 residue 61 LEU Chi-restraints excluded: chain 4 residue 1 MET Chi-restraints excluded: chain 4 residue 6 SER Chi-restraints excluded: chain 4 residue 20 ASP Chi-restraints excluded: chain 4 residue 28 SER Chi-restraints excluded: chain 6 residue 3 LYS Chi-restraints excluded: chain 6 residue 13 THR Chi-restraints excluded: chain b residue 20 ARG Chi-restraints excluded: chain b residue 21 TYR Chi-restraints excluded: chain b residue 105 THR Chi-restraints excluded: chain b residue 109 SER Chi-restraints excluded: chain b residue 113 LEU Chi-restraints excluded: chain b residue 144 GLU Chi-restraints excluded: chain b residue 163 ILE Chi-restraints excluded: chain b residue 173 LYS Chi-restraints excluded: chain b residue 178 LEU Chi-restraints excluded: chain b residue 190 SER Chi-restraints excluded: chain b residue 193 ASP Chi-restraints excluded: chain b residue 203 ASP Chi-restraints excluded: chain b residue 225 SER Chi-restraints excluded: chain c residue 90 VAL Chi-restraints excluded: chain c residue 109 GLU Chi-restraints excluded: chain c residue 120 THR Chi-restraints excluded: chain c residue 130 ARG Chi-restraints excluded: chain c residue 146 LYS Chi-restraints excluded: chain c residue 153 SER Chi-restraints excluded: chain c residue 156 LEU Chi-restraints excluded: chain c residue 168 ARG Chi-restraints excluded: chain c residue 181 ILE Chi-restraints excluded: chain d residue 33 ILE Chi-restraints excluded: chain d residue 90 LEU Chi-restraints excluded: chain d residue 124 VAL Chi-restraints excluded: chain d residue 143 SER Chi-restraints excluded: chain d residue 158 LEU Chi-restraints excluded: chain d residue 168 THR Chi-restraints excluded: chain e residue 17 VAL Chi-restraints excluded: chain e residue 29 ILE Chi-restraints excluded: chain e residue 36 THR Chi-restraints excluded: chain e residue 38 VAL Chi-restraints excluded: chain e residue 45 VAL Chi-restraints excluded: chain e residue 61 LYS Chi-restraints excluded: chain e residue 81 GLN Chi-restraints excluded: chain e residue 91 SER Chi-restraints excluded: chain e residue 121 ASN Chi-restraints excluded: chain e residue 123 LEU Chi-restraints excluded: chain e residue 129 SER Chi-restraints excluded: chain e residue 160 VAL Chi-restraints excluded: chain f residue 63 ASN Chi-restraints excluded: chain f residue 70 VAL Chi-restraints excluded: chain f residue 76 THR Chi-restraints excluded: chain f residue 86 ARG Chi-restraints excluded: chain f residue 96 VAL Chi-restraints excluded: chain g residue 11 ILE Chi-restraints excluded: chain g residue 32 ASP Chi-restraints excluded: chain g residue 76 SER Chi-restraints excluded: chain g residue 89 GLU Chi-restraints excluded: chain g residue 93 VAL Chi-restraints excluded: chain g residue 96 ASN Chi-restraints excluded: chain g residue 132 THR Chi-restraints excluded: chain h residue 11 THR Chi-restraints excluded: chain h residue 25 THR Chi-restraints excluded: chain h residue 42 GLU Chi-restraints excluded: chain h residue 58 LEU Chi-restraints excluded: chain h residue 59 GLU Chi-restraints excluded: chain h residue 79 ARG Chi-restraints excluded: chain h residue 82 LEU Chi-restraints excluded: chain h residue 86 LYS Chi-restraints excluded: chain h residue 105 THR Chi-restraints excluded: chain h residue 111 THR Chi-restraints excluded: chain h residue 116 ARG Chi-restraints excluded: chain h residue 128 VAL Chi-restraints excluded: chain i residue 20 ILE Chi-restraints excluded: chain i residue 61 ASP Chi-restraints excluded: chain i residue 66 VAL Chi-restraints excluded: chain i residue 82 ILE Chi-restraints excluded: chain i residue 122 ARG Chi-restraints excluded: chain j residue 40 ILE Chi-restraints excluded: chain j residue 62 ARG Chi-restraints excluded: chain j residue 66 GLU Chi-restraints excluded: chain j residue 96 VAL Chi-restraints excluded: chain k residue 15 VAL Chi-restraints excluded: chain k residue 34 THR Chi-restraints excluded: chain k residue 71 ASP Chi-restraints excluded: chain k residue 80 ASN Chi-restraints excluded: chain k residue 84 MET Chi-restraints excluded: chain k residue 85 VAL Chi-restraints excluded: chain k residue 113 THR Chi-restraints excluded: chain k residue 125 LYS Chi-restraints excluded: chain l residue 19 ASN Chi-restraints excluded: chain l residue 95 HIS Chi-restraints excluded: chain l residue 96 THR Chi-restraints excluded: chain l residue 97 VAL Chi-restraints excluded: chain l residue 115 LYS Chi-restraints excluded: chain m residue 6 ILE Chi-restraints excluded: chain m residue 15 VAL Chi-restraints excluded: chain m residue 28 ARG Chi-restraints excluded: chain m residue 52 ILE Chi-restraints excluded: chain m residue 67 ASP Chi-restraints excluded: chain m residue 99 GLN Chi-restraints excluded: chain n residue 27 LYS Chi-restraints excluded: chain o residue 10 ILE Chi-restraints excluded: chain p residue 3 THR Chi-restraints excluded: chain p residue 34 GLU Chi-restraints excluded: chain q residue 20 ILE Chi-restraints excluded: chain q residue 40 THR Chi-restraints excluded: chain q residue 67 SER Chi-restraints excluded: chain r residue 13 THR Chi-restraints excluded: chain r residue 15 GLU Chi-restraints excluded: chain r residue 66 LEU Chi-restraints excluded: chain r residue 70 THR Chi-restraints excluded: chain s residue 6 LYS Chi-restraints excluded: chain s residue 32 THR Chi-restraints excluded: chain s residue 48 ILE Chi-restraints excluded: chain s residue 62 THR Chi-restraints excluded: chain s residue 65 MET Chi-restraints excluded: chain t residue 22 SER Chi-restraints excluded: chain u residue 3 ILE Chi-restraints excluded: chain u residue 27 VAL Chi-restraints excluded: chain u residue 32 ARG Chi-restraints excluded: chain u residue 50 SER Chi-restraints excluded: chain z residue 13 ASN Chi-restraints excluded: chain z residue 26 THR Chi-restraints excluded: chain z residue 54 GLU Chi-restraints excluded: chain z residue 67 VAL Chi-restraints excluded: chain z residue 102 ILE Chi-restraints excluded: chain z residue 179 GLU Chi-restraints excluded: chain z residue 185 GLU Chi-restraints excluded: chain z residue 220 ILE Chi-restraints excluded: chain z residue 225 THR Chi-restraints excluded: chain z residue 233 ARG Chi-restraints excluded: chain z residue 236 ILE Chi-restraints excluded: chain z residue 245 VAL Chi-restraints excluded: chain z residue 276 VAL Chi-restraints excluded: chain z residue 351 MET Chi-restraints excluded: chain z residue 358 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1087 random chunks: chunk 648 optimal weight: 10.0000 chunk 418 optimal weight: 6.9990 chunk 625 optimal weight: 6.9990 chunk 315 optimal weight: 6.9990 chunk 205 optimal weight: 5.9990 chunk 202 optimal weight: 5.9990 chunk 666 optimal weight: 10.0000 chunk 713 optimal weight: 10.0000 chunk 517 optimal weight: 2.9990 chunk 97 optimal weight: 6.9990 chunk 823 optimal weight: 0.0980 overall best weight: 4.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 59 GLN E 165 HIS G 29 ASN G 114 HIS H 28 ASN ** I 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 36 GLN R 6 GLN R 86 GLN U 73 ASN V 75 GLN 6 61 ASN c 24 ASN c 31 ASN c 139 ASN d 125 ASN ** d 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 76 ASN ** e 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 63 ASN f 68 GLN g 147 ASN l 4 ASN ** l 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 60 GLN t 2 ASN ** t 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.4117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 165479 Z= 0.333 Angle : 0.769 15.070 247209 Z= 0.408 Chirality : 0.041 0.397 31418 Planarity : 0.007 0.134 13503 Dihedral : 24.330 179.242 81838 Min Nonbonded Distance : 0.957 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.56 % Allowed : 8.20 % Favored : 91.24 % Rotamer: Outliers : 6.74 % Allowed : 26.79 % Favored : 66.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.10), residues: 6219 helix: -0.09 (0.11), residues: 1958 sheet: -1.31 (0.14), residues: 1199 loop : -2.05 (0.10), residues: 3062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 212 HIS 0.015 0.001 HIS b 14 PHE 0.023 0.002 PHE f 78 TYR 0.036 0.002 TYR z 160 ARG 0.010 0.001 ARG q 61 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12438 Ramachandran restraints generated. 6219 Oldfield, 0 Emsley, 6219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12438 Ramachandran restraints generated. 6219 Oldfield, 0 Emsley, 6219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1461 residues out of total 5164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 348 poor density : 1113 time to evaluate : 6.802 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: C 4 LYS cc_start: 0.8166 (tttt) cc_final: 0.7707 (ttmm) REVERT: C 22 GLU cc_start: 0.7928 (OUTLIER) cc_final: 0.7128 (mt-10) REVERT: C 27 LYS cc_start: 0.7576 (mttt) cc_final: 0.7029 (mppt) REVERT: C 34 GLU cc_start: 0.8423 (OUTLIER) cc_final: 0.8067 (pt0) REVERT: C 113 ASP cc_start: 0.7038 (m-30) cc_final: 0.6334 (t0) REVERT: C 159 THR cc_start: 0.9161 (m) cc_final: 0.8719 (p) REVERT: C 184 GLU cc_start: 0.7269 (tt0) cc_final: 0.6662 (mt-10) REVERT: C 187 CYS cc_start: 0.8237 (m) cc_final: 0.8020 (m) REVERT: C 260 LYS cc_start: 0.7884 (OUTLIER) cc_final: 0.7557 (ttpt) REVERT: D 2 ILE cc_start: 0.4968 (OUTLIER) cc_final: 0.4593 (pp) REVERT: D 108 ASP cc_start: 0.7585 (m-30) cc_final: 0.6873 (p0) REVERT: D 150 GLN cc_start: 0.8200 (OUTLIER) cc_final: 0.7973 (tt0) REVERT: D 186 LEU cc_start: 0.8022 (mt) cc_final: 0.7777 (mt) REVERT: E 88 ARG cc_start: 0.7754 (ttm-80) cc_final: 0.7162 (mmp80) REVERT: E 95 LYS cc_start: 0.7710 (OUTLIER) cc_final: 0.7185 (tttp) REVERT: E 121 VAL cc_start: 0.8506 (m) cc_final: 0.8142 (p) REVERT: E 194 LYS cc_start: 0.7885 (tptt) cc_final: 0.7657 (mmtp) REVERT: F 2 LYS cc_start: 0.7979 (tttm) cc_final: 0.7573 (tptt) REVERT: F 9 ASP cc_start: 0.7447 (OUTLIER) cc_final: 0.7015 (t0) REVERT: F 18 GLU cc_start: 0.5707 (OUTLIER) cc_final: 0.4998 (mt-10) REVERT: F 41 GLU cc_start: 0.7078 (mm-30) cc_final: 0.6301 (mp0) REVERT: F 46 LYS cc_start: 0.8096 (mttt) cc_final: 0.7639 (tppp) REVERT: F 47 LYS cc_start: 0.7553 (ptmt) cc_final: 0.7080 (pmtt) REVERT: F 71 LYS cc_start: 0.7237 (mmmt) cc_final: 0.6852 (ttpt) REVERT: F 133 GLU cc_start: 0.7525 (mt-10) cc_final: 0.6921 (pt0) REVERT: F 137 PHE cc_start: 0.7322 (m-80) cc_final: 0.7100 (m-80) REVERT: F 147 ARG cc_start: 0.6607 (tpp80) cc_final: 0.5839 (ttt180) REVERT: F 160 LYS cc_start: 0.7549 (mtmm) cc_final: 0.7209 (mptp) REVERT: F 177 ARG cc_start: 0.5433 (OUTLIER) cc_final: 0.4982 (mtp180) REVERT: G 154 GLU cc_start: 0.7189 (tt0) cc_final: 0.6818 (pt0) REVERT: I 16 MET cc_start: 0.1307 (mmp) cc_final: 0.0757 (mpp) REVERT: I 135 MET cc_start: 0.1516 (mtp) cc_final: 0.1002 (tmt) REVERT: J 12 LYS cc_start: 0.7846 (OUTLIER) cc_final: 0.7213 (tptp) REVERT: J 43 GLU cc_start: 0.8080 (mt-10) cc_final: 0.7407 (pm20) REVERT: J 61 LYS cc_start: 0.7926 (mmtp) cc_final: 0.7320 (mtpt) REVERT: J 84 ILE cc_start: 0.8124 (OUTLIER) cc_final: 0.7683 (tp) REVERT: J 91 GLU cc_start: 0.7840 (mt-10) cc_final: 0.7323 (tp30) REVERT: J 95 ARG cc_start: 0.6441 (mtp-110) cc_final: 0.6124 (ttp-110) REVERT: K 7 MET cc_start: 0.8596 (tpp) cc_final: 0.8277 (tpp) REVERT: K 17 ARG cc_start: 0.8428 (tpp80) cc_final: 0.8089 (tpp-160) REVERT: K 53 LYS cc_start: 0.6891 (pttp) cc_final: 0.6677 (ptpp) REVERT: K 66 LYS cc_start: 0.8121 (mttt) cc_final: 0.7835 (mtpt) REVERT: L 14 LYS cc_start: 0.7440 (tttm) cc_final: 0.7021 (tmtt) REVERT: L 19 LEU cc_start: 0.9038 (mp) cc_final: 0.8804 (mt) REVERT: L 68 SER cc_start: 0.8413 (t) cc_final: 0.8158 (p) REVERT: L 105 ILE cc_start: 0.8490 (mt) cc_final: 0.8125 (mm) REVERT: L 106 GLU cc_start: 0.8499 (mt-10) cc_final: 0.8076 (mm-30) REVERT: L 141 LYS cc_start: 0.6799 (mmmt) cc_final: 0.6443 (ptpp) REVERT: M 6 ARG cc_start: 0.7276 (OUTLIER) cc_final: 0.6731 (ptp90) REVERT: M 12 MET cc_start: 0.8319 (ttm) cc_final: 0.8072 (ttm) REVERT: M 75 GLU cc_start: 0.8268 (tt0) cc_final: 0.7729 (tt0) REVERT: M 88 ASN cc_start: 0.7692 (m110) cc_final: 0.7472 (m-40) REVERT: N 35 LYS cc_start: 0.7922 (tttt) cc_final: 0.7567 (tttp) REVERT: O 13 ARG cc_start: 0.7139 (ttt90) cc_final: 0.6848 (tpp-160) REVERT: O 48 LEU cc_start: 0.8138 (mm) cc_final: 0.7897 (mt) REVERT: O 98 GLN cc_start: 0.8223 (tt0) cc_final: 0.7729 (tt0) REVERT: P 43 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.7813 (tt0) REVERT: P 112 ARG cc_start: 0.6465 (ttm170) cc_final: 0.6211 (ttp80) REVERT: Q 12 ARG cc_start: 0.8059 (ttm-80) cc_final: 0.7531 (ttt180) REVERT: Q 14 LYS cc_start: 0.7482 (tttt) cc_final: 0.7105 (mtpp) REVERT: Q 48 ASP cc_start: 0.8450 (m-30) cc_final: 0.7794 (m-30) REVERT: Q 77 LYS cc_start: 0.8109 (mttt) cc_final: 0.7653 (mtpt) REVERT: Q 110 GLU cc_start: 0.7123 (OUTLIER) cc_final: 0.6601 (mp0) REVERT: R 1 MET cc_start: 0.6323 (tpp) cc_final: 0.5183 (ptp) REVERT: R 10 LYS cc_start: 0.7875 (ptpp) cc_final: 0.7599 (mtmm) REVERT: R 48 LYS cc_start: 0.7734 (ttmm) cc_final: 0.6973 (ttpt) REVERT: R 66 HIS cc_start: 0.8281 (OUTLIER) cc_final: 0.6917 (m-70) REVERT: R 84 ARG cc_start: 0.8564 (OUTLIER) cc_final: 0.7274 (ttp80) REVERT: S 1 MET cc_start: 0.6669 (mmm) cc_final: 0.6252 (mpp) REVERT: S 34 ASP cc_start: 0.7466 (m-30) cc_final: 0.7265 (m-30) REVERT: S 52 GLU cc_start: 0.7933 (tt0) cc_final: 0.7355 (mm-30) REVERT: S 86 MET cc_start: 0.8478 (OUTLIER) cc_final: 0.7834 (tpt) REVERT: S 92 ARG cc_start: 0.7039 (ptp90) cc_final: 0.6324 (ptm160) REVERT: T 28 ASN cc_start: 0.7547 (t0) cc_final: 0.6963 (t0) REVERT: T 33 LYS cc_start: 0.7338 (OUTLIER) cc_final: 0.7122 (tttt) REVERT: T 54 GLU cc_start: 0.7333 (mt-10) cc_final: 0.6407 (tp30) REVERT: T 69 ARG cc_start: 0.7654 (ttp-110) cc_final: 0.6942 (ttm-80) REVERT: T 76 ARG cc_start: 0.7237 (OUTLIER) cc_final: 0.6541 (ptm-80) REVERT: U 17 ASP cc_start: 0.7817 (p0) cc_final: 0.7395 (p0) REVERT: U 25 LYS cc_start: 0.7173 (mmmt) cc_final: 0.6641 (mtpp) REVERT: U 71 ILE cc_start: 0.8122 (pt) cc_final: 0.7751 (mt) REVERT: U 78 LYS cc_start: 0.7066 (OUTLIER) cc_final: 0.6534 (pmtt) REVERT: V 3 THR cc_start: 0.7670 (p) cc_final: 0.7379 (m) REVERT: V 11 GLU cc_start: 0.7076 (mt-10) cc_final: 0.6847 (pt0) REVERT: V 30 ILE cc_start: 0.7372 (mt) cc_final: 0.6994 (tt) REVERT: V 41 GLU cc_start: 0.7622 (pt0) cc_final: 0.7007 (pm20) REVERT: V 43 ASP cc_start: 0.7664 (t70) cc_final: 0.7314 (t70) REVERT: V 71 LYS cc_start: 0.7108 (mtpp) cc_final: 0.6708 (mppt) REVERT: V 82 TYR cc_start: 0.7211 (p90) cc_final: 0.6904 (p90) REVERT: W 40 LYS cc_start: 0.8123 (ttpt) cc_final: 0.7757 (mtpp) REVERT: W 62 LYS cc_start: 0.7734 (mttt) cc_final: 0.7281 (mtpt) REVERT: W 71 LYS cc_start: 0.8319 (mttt) cc_final: 0.8020 (mttp) REVERT: X 19 HIS cc_start: 0.7420 (t70) cc_final: 0.6632 (m-70) REVERT: X 36 ARG cc_start: 0.6983 (OUTLIER) cc_final: 0.5931 (mtp85) REVERT: X 71 ARG cc_start: 0.5926 (mtm110) cc_final: 0.5610 (ptp-110) REVERT: Y 14 LEU cc_start: 0.6081 (OUTLIER) cc_final: 0.5809 (mt) REVERT: Y 15 ASN cc_start: 0.7132 (m-40) cc_final: 0.6861 (m110) REVERT: Z 5 LYS cc_start: 0.7046 (mtmm) cc_final: 0.6779 (mtpp) REVERT: 0 11 LYS cc_start: 0.8293 (mmmt) cc_final: 0.7960 (tppp) REVERT: 1 23 THR cc_start: 0.7947 (OUTLIER) cc_final: 0.7725 (m) REVERT: 1 27 ARG cc_start: 0.7501 (mtm180) cc_final: 0.7192 (mpt180) REVERT: 1 32 LYS cc_start: 0.7337 (mttt) cc_final: 0.7078 (pttt) REVERT: 2 8 SER cc_start: 0.8756 (t) cc_final: 0.8490 (t) REVERT: 2 14 ARG cc_start: 0.8543 (OUTLIER) cc_final: 0.7511 (mtt90) REVERT: 2 41 ARG cc_start: 0.7920 (mmt180) cc_final: 0.7402 (mtm-85) REVERT: 2 44 VAL cc_start: 0.7933 (p) cc_final: 0.7700 (m) REVERT: 3 14 LYS cc_start: 0.8455 (tttt) cc_final: 0.8040 (mmtm) REVERT: 4 18 LYS cc_start: 0.7810 (tttt) cc_final: 0.7518 (mtpp) REVERT: 4 20 ASP cc_start: 0.7491 (OUTLIER) cc_final: 0.6555 (t0) REVERT: 5 1 MET cc_start: 0.2980 (tpt) cc_final: 0.2467 (tmt) REVERT: 6 1 MET cc_start: 0.7040 (mtp) cc_final: 0.6671 (ttm) REVERT: 6 10 GLU cc_start: 0.7307 (tp30) cc_final: 0.6990 (tt0) REVERT: 6 62 LYS cc_start: 0.7223 (mmtm) cc_final: 0.6960 (mmmt) REVERT: 6 63 ARG cc_start: 0.4874 (OUTLIER) cc_final: 0.4454 (mtt-85) REVERT: b 20 ARG cc_start: 0.5797 (OUTLIER) cc_final: 0.5076 (ptt-90) REVERT: b 36 LYS cc_start: 0.5709 (OUTLIER) cc_final: 0.4752 (pptt) REVERT: b 65 LYS cc_start: 0.6824 (OUTLIER) cc_final: 0.6193 (mttp) REVERT: b 73 ARG cc_start: 0.6820 (OUTLIER) cc_final: 0.6000 (mmp80) REVERT: b 132 GLU cc_start: 0.6816 (tp30) cc_final: 0.6256 (tt0) REVERT: b 136 ARG cc_start: 0.5213 (mmm-85) cc_final: 0.4299 (ttp80) REVERT: b 141 GLU cc_start: 0.7351 (mt-10) cc_final: 0.7052 (mm-30) REVERT: b 144 GLU cc_start: 0.7443 (OUTLIER) cc_final: 0.7206 (tt0) REVERT: b 145 ASN cc_start: 0.7618 (p0) cc_final: 0.7039 (m110) REVERT: c 33 ASP cc_start: 0.7410 (t70) cc_final: 0.7136 (t0) REVERT: c 45 GLU cc_start: 0.7956 (tm-30) cc_final: 0.7233 (tp30) REVERT: c 71 ARG cc_start: 0.7326 (mtt90) cc_final: 0.6770 (mtp85) REVERT: c 109 GLU cc_start: 0.8253 (OUTLIER) cc_final: 0.7481 (mm-30) REVERT: c 128 MET cc_start: 0.7648 (mmt) cc_final: 0.6754 (mtt) REVERT: c 130 ARG cc_start: 0.7745 (OUTLIER) cc_final: 0.7099 (mtt-85) REVERT: c 151 GLU cc_start: 0.7972 (tt0) cc_final: 0.7339 (tm-30) REVERT: c 156 LEU cc_start: 0.7529 (OUTLIER) cc_final: 0.7237 (pt) REVERT: c 163 ARG cc_start: 0.5388 (mtt180) cc_final: 0.4475 (mpp-170) REVERT: c 169 GLU cc_start: 0.7795 (mt-10) cc_final: 0.6823 (tp30) REVERT: d 33 ILE cc_start: 0.4931 (OUTLIER) cc_final: 0.4374 (mm) REVERT: d 47 LEU cc_start: 0.8092 (tp) cc_final: 0.7403 (pp) REVERT: d 73 ASN cc_start: 0.6906 (m-40) cc_final: 0.6554 (p0) REVERT: d 77 GLU cc_start: 0.7676 (mt-10) cc_final: 0.6900 (tp30) REVERT: d 135 GLN cc_start: 0.5084 (tm-30) cc_final: 0.4013 (mm110) REVERT: e 70 MET cc_start: 0.7451 (mtm) cc_final: 0.7203 (mtm) REVERT: e 71 ILE cc_start: 0.6861 (mm) cc_final: 0.6576 (tt) REVERT: e 81 GLN cc_start: 0.8271 (OUTLIER) cc_final: 0.7207 (mp10) REVERT: e 127 TYR cc_start: 0.8420 (m-80) cc_final: 0.8005 (m-80) REVERT: e 144 GLU cc_start: 0.7874 (tt0) cc_final: 0.7624 (tt0) REVERT: f 24 ARG cc_start: 0.7039 (mtm110) cc_final: 0.6431 (mtm110) REVERT: f 58 HIS cc_start: 0.7753 (t70) cc_final: 0.7262 (t-170) REVERT: f 62 MET cc_start: 0.6994 (mmm) cc_final: 0.6658 (mmm) REVERT: g 20 GLU cc_start: 0.5331 (mm-30) cc_final: 0.4837 (mp0) REVERT: g 39 GLU cc_start: 0.7794 (pt0) cc_final: 0.7514 (pt0) REVERT: g 89 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.7754 (mm-30) REVERT: g 105 GLU cc_start: 0.7900 (tp30) cc_final: 0.7324 (tp30) REVERT: h 2 MET cc_start: 0.8134 (tpp) cc_final: 0.7595 (tpp) REVERT: h 28 SER cc_start: 0.8304 (t) cc_final: 0.7635 (p) REVERT: h 42 GLU cc_start: 0.7566 (OUTLIER) cc_final: 0.6967 (mp0) REVERT: h 86 LYS cc_start: 0.8532 (OUTLIER) cc_final: 0.8188 (mptp) REVERT: h 90 GLU cc_start: 0.7866 (tt0) cc_final: 0.7469 (mp0) REVERT: h 112 ASP cc_start: 0.7628 (p0) cc_final: 0.7334 (p0) REVERT: h 116 ARG cc_start: 0.6465 (OUTLIER) cc_final: 0.4737 (tpp-160) REVERT: i 63 TYR cc_start: 0.7125 (t80) cc_final: 0.6433 (t80) REVERT: i 122 ARG cc_start: 0.7478 (OUTLIER) cc_final: 0.6641 (tmt-80) REVERT: i 123 ARG cc_start: 0.7634 (mtp-110) cc_final: 0.6877 (mtt90) REVERT: j 53 ILE cc_start: 0.6702 (tp) cc_final: 0.6312 (pt) REVERT: j 62 ARG cc_start: 0.7618 (OUTLIER) cc_final: 0.6709 (mpt-90) REVERT: j 88 MET cc_start: 0.6669 (mtm) cc_final: 0.5921 (ptt) REVERT: k 36 ARG cc_start: 0.8225 (mmm-85) cc_final: 0.7486 (mmm-85) REVERT: k 74 LYS cc_start: 0.7769 (mttt) cc_final: 0.7425 (mptt) REVERT: k 107 THR cc_start: 0.7987 (m) cc_final: 0.7783 (p) REVERT: k 125 LYS cc_start: 0.7737 (OUTLIER) cc_final: 0.7418 (ttmp) REVERT: l 13 ARG cc_start: 0.7542 (tpt170) cc_final: 0.6486 (tpt170) REVERT: l 17 LYS cc_start: 0.7055 (pttt) cc_final: 0.6624 (mttm) REVERT: l 95 HIS cc_start: 0.6321 (OUTLIER) cc_final: 0.5889 (m-70) REVERT: m 26 LYS cc_start: 0.7218 (ttpp) cc_final: 0.7007 (ttmm) REVERT: m 73 SER cc_start: 0.7799 (m) cc_final: 0.7455 (p) REVERT: m 99 GLN cc_start: 0.7667 (OUTLIER) cc_final: 0.7089 (mt0) REVERT: n 25 GLU cc_start: 0.7532 (pt0) cc_final: 0.6976 (mp0) REVERT: n 39 GLU cc_start: 0.7977 (mt-10) cc_final: 0.7689 (mm-30) REVERT: n 60 GLN cc_start: 0.7684 (OUTLIER) cc_final: 0.7238 (mp-120) REVERT: n 90 ARG cc_start: 0.7515 (ttt90) cc_final: 0.6988 (ttp-170) REVERT: o 10 ILE cc_start: 0.7600 (OUTLIER) cc_final: 0.7399 (tp) REVERT: o 52 ARG cc_start: 0.7368 (ttt180) cc_final: 0.6748 (ttp-170) REVERT: o 61 GLN cc_start: 0.7806 (tp40) cc_final: 0.7314 (tt0) REVERT: o 82 GLU cc_start: 0.7871 (mm-30) cc_final: 0.7505 (tm-30) REVERT: q 8 GLN cc_start: 0.8130 (tt0) cc_final: 0.7539 (mp10) REVERT: q 18 LYS cc_start: 0.5438 (ttpt) cc_final: 0.5020 (ttmt) REVERT: q 40 THR cc_start: 0.7945 (OUTLIER) cc_final: 0.7698 (t) REVERT: r 29 LYS cc_start: 0.7612 (mttp) cc_final: 0.7324 (mttp) REVERT: s 6 LYS cc_start: 0.5080 (OUTLIER) cc_final: 0.3847 (pmtt) REVERT: s 34 SER cc_start: 0.8795 (t) cc_final: 0.8474 (t) REVERT: t 20 ASN cc_start: 0.8102 (m-40) cc_final: 0.7874 (m110) REVERT: t 59 ARG cc_start: 0.5555 (ttm110) cc_final: 0.5268 (ttp-170) REVERT: u 22 CYS cc_start: 0.7362 (t) cc_final: 0.6927 (p) REVERT: u 33 ARG cc_start: 0.7726 (OUTLIER) cc_final: 0.7316 (mtm180) REVERT: z 4 LYS cc_start: 0.4344 (mtmm) cc_final: 0.3909 (ttmt) REVERT: z 54 GLU cc_start: 0.5581 (OUTLIER) cc_final: 0.4772 (pm20) REVERT: z 185 GLU cc_start: 0.4097 (OUTLIER) cc_final: 0.3807 (tt0) REVERT: z 201 GLU cc_start: 0.2477 (mt-10) cc_final: 0.1695 (tp30) REVERT: z 207 ASP cc_start: 0.5380 (t0) cc_final: 0.5047 (p0) REVERT: z 220 ILE cc_start: 0.5617 (OUTLIER) cc_final: 0.5212 (tp) REVERT: z 282 LYS cc_start: 0.7111 (mttt) cc_final: 0.6746 (mmmt) outliers start: 348 outliers final: 215 residues processed: 1319 average time/residue: 2.2118 time to fit residues: 4246.3894 Evaluate side-chains 1341 residues out of total 5164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 268 poor density : 1073 time to evaluate : 6.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 9 SER Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain C residue 34 GLU Chi-restraints excluded: chain C residue 35 LYS Chi-restraints excluded: chain C residue 37 SER Chi-restraints excluded: chain C residue 67 LYS Chi-restraints excluded: chain C residue 69 ASN Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain C residue 260 LYS Chi-restraints excluded: chain D residue 2 ILE Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 150 GLN Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 73 ILE Chi-restraints excluded: chain E residue 95 LYS Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 137 LYS Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 176 ASP Chi-restraints excluded: chain F residue 9 ASP Chi-restraints excluded: chain F residue 16 MET Chi-restraints excluded: chain F residue 18 GLU Chi-restraints excluded: chain F residue 45 ASP Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 122 ASP Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 143 ASP Chi-restraints excluded: chain F residue 145 VAL Chi-restraints excluded: chain F residue 148 VAL Chi-restraints excluded: chain F residue 177 ARG Chi-restraints excluded: chain G residue 24 THR Chi-restraints excluded: chain G residue 84 LYS Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 139 VAL Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain I residue 56 VAL Chi-restraints excluded: chain I residue 134 SER Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 12 LYS Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain J residue 128 ASN Chi-restraints excluded: chain K residue 14 SER Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain K residue 47 ILE Chi-restraints excluded: chain K residue 61 VAL Chi-restraints excluded: chain K residue 90 ASN Chi-restraints excluded: chain K residue 99 ILE Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 106 GLU Chi-restraints excluded: chain K residue 107 LEU Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 91 ASP Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain M residue 6 ARG Chi-restraints excluded: chain M residue 30 SER Chi-restraints excluded: chain N residue 13 ASN Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain O residue 56 LYS Chi-restraints excluded: chain O residue 95 SER Chi-restraints excluded: chain P residue 15 ASP Chi-restraints excluded: chain P residue 16 VAL Chi-restraints excluded: chain P residue 32 VAL Chi-restraints excluded: chain P residue 43 GLU Chi-restraints excluded: chain P residue 47 ILE Chi-restraints excluded: chain Q residue 110 GLU Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 66 HIS Chi-restraints excluded: chain R residue 84 ARG Chi-restraints excluded: chain S residue 29 VAL Chi-restraints excluded: chain S residue 66 ILE Chi-restraints excluded: chain S residue 86 MET Chi-restraints excluded: chain T residue 2 ILE Chi-restraints excluded: chain T residue 9 LYS Chi-restraints excluded: chain T residue 16 VAL Chi-restraints excluded: chain T residue 17 SER Chi-restraints excluded: chain T residue 33 LYS Chi-restraints excluded: chain T residue 61 LEU Chi-restraints excluded: chain T residue 76 ARG Chi-restraints excluded: chain U residue 61 GLU Chi-restraints excluded: chain U residue 78 LYS Chi-restraints excluded: chain V residue 4 ILE Chi-restraints excluded: chain V residue 12 GLN Chi-restraints excluded: chain V residue 40 ILE Chi-restraints excluded: chain V residue 63 ILE Chi-restraints excluded: chain V residue 64 VAL Chi-restraints excluded: chain W residue 25 GLU Chi-restraints excluded: chain W residue 39 THR Chi-restraints excluded: chain W residue 60 ASP Chi-restraints excluded: chain X residue 34 SER Chi-restraints excluded: chain X residue 36 ARG Chi-restraints excluded: chain X residue 47 THR Chi-restraints excluded: chain X residue 65 THR Chi-restraints excluded: chain Y residue 14 LEU Chi-restraints excluded: chain Y residue 17 GLU Chi-restraints excluded: chain Y residue 19 LEU Chi-restraints excluded: chain Y residue 57 LEU Chi-restraints excluded: chain Z residue 3 THR Chi-restraints excluded: chain Z residue 7 THR Chi-restraints excluded: chain Z residue 51 SER Chi-restraints excluded: chain 0 residue 5 ASN Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 9 ARG Chi-restraints excluded: chain 0 residue 22 THR Chi-restraints excluded: chain 0 residue 32 THR Chi-restraints excluded: chain 1 residue 21 THR Chi-restraints excluded: chain 1 residue 22 THR Chi-restraints excluded: chain 1 residue 23 THR Chi-restraints excluded: chain 1 residue 42 VAL Chi-restraints excluded: chain 1 residue 46 VAL Chi-restraints excluded: chain 1 residue 53 ILE Chi-restraints excluded: chain 2 residue 14 ARG Chi-restraints excluded: chain 2 residue 24 THR Chi-restraints excluded: chain 3 residue 61 LEU Chi-restraints excluded: chain 4 residue 1 MET Chi-restraints excluded: chain 4 residue 6 SER Chi-restraints excluded: chain 4 residue 20 ASP Chi-restraints excluded: chain 4 residue 28 SER Chi-restraints excluded: chain 6 residue 3 LYS Chi-restraints excluded: chain 6 residue 63 ARG Chi-restraints excluded: chain b residue 20 ARG Chi-restraints excluded: chain b residue 21 TYR Chi-restraints excluded: chain b residue 36 LYS Chi-restraints excluded: chain b residue 65 LYS Chi-restraints excluded: chain b residue 73 ARG Chi-restraints excluded: chain b residue 105 THR Chi-restraints excluded: chain b residue 109 SER Chi-restraints excluded: chain b residue 113 LEU Chi-restraints excluded: chain b residue 144 GLU Chi-restraints excluded: chain b residue 170 ILE Chi-restraints excluded: chain b residue 178 LEU Chi-restraints excluded: chain b residue 190 SER Chi-restraints excluded: chain b residue 193 ASP Chi-restraints excluded: chain b residue 203 ASP Chi-restraints excluded: chain b residue 222 GLU Chi-restraints excluded: chain b residue 225 SER Chi-restraints excluded: chain c residue 50 SER Chi-restraints excluded: chain c residue 90 VAL Chi-restraints excluded: chain c residue 109 GLU Chi-restraints excluded: chain c residue 120 THR Chi-restraints excluded: chain c residue 130 ARG Chi-restraints excluded: chain c residue 146 LYS Chi-restraints excluded: chain c residue 153 SER Chi-restraints excluded: chain c residue 156 LEU Chi-restraints excluded: chain c residue 181 ILE Chi-restraints excluded: chain d residue 33 ILE Chi-restraints excluded: chain d residue 90 LEU Chi-restraints excluded: chain d residue 124 VAL Chi-restraints excluded: chain d residue 143 SER Chi-restraints excluded: chain d residue 158 LEU Chi-restraints excluded: chain d residue 168 THR Chi-restraints excluded: chain e residue 17 VAL Chi-restraints excluded: chain e residue 29 ILE Chi-restraints excluded: chain e residue 33 THR Chi-restraints excluded: chain e residue 36 THR Chi-restraints excluded: chain e residue 38 VAL Chi-restraints excluded: chain e residue 45 VAL Chi-restraints excluded: chain e residue 61 LYS Chi-restraints excluded: chain e residue 81 GLN Chi-restraints excluded: chain e residue 91 SER Chi-restraints excluded: chain e residue 121 ASN Chi-restraints excluded: chain e residue 123 LEU Chi-restraints excluded: chain e residue 129 SER Chi-restraints excluded: chain f residue 70 VAL Chi-restraints excluded: chain f residue 76 THR Chi-restraints excluded: chain f residue 96 VAL Chi-restraints excluded: chain g residue 11 ILE Chi-restraints excluded: chain g residue 32 ASP Chi-restraints excluded: chain g residue 89 GLU Chi-restraints excluded: chain g residue 93 VAL Chi-restraints excluded: chain g residue 96 ASN Chi-restraints excluded: chain g residue 132 THR Chi-restraints excluded: chain h residue 25 THR Chi-restraints excluded: chain h residue 42 GLU Chi-restraints excluded: chain h residue 45 ILE Chi-restraints excluded: chain h residue 58 LEU Chi-restraints excluded: chain h residue 59 GLU Chi-restraints excluded: chain h residue 79 ARG Chi-restraints excluded: chain h residue 82 LEU Chi-restraints excluded: chain h residue 86 LYS Chi-restraints excluded: chain h residue 105 THR Chi-restraints excluded: chain h residue 111 THR Chi-restraints excluded: chain h residue 116 ARG Chi-restraints excluded: chain h residue 128 VAL Chi-restraints excluded: chain i residue 20 ILE Chi-restraints excluded: chain i residue 51 LEU Chi-restraints excluded: chain i residue 61 ASP Chi-restraints excluded: chain i residue 66 VAL Chi-restraints excluded: chain i residue 82 ILE Chi-restraints excluded: chain i residue 122 ARG Chi-restraints excluded: chain j residue 40 ILE Chi-restraints excluded: chain j residue 62 ARG Chi-restraints excluded: chain j residue 66 GLU Chi-restraints excluded: chain j residue 96 VAL Chi-restraints excluded: chain j residue 98 VAL Chi-restraints excluded: chain k residue 15 VAL Chi-restraints excluded: chain k residue 34 THR Chi-restraints excluded: chain k residue 80 ASN Chi-restraints excluded: chain k residue 84 MET Chi-restraints excluded: chain k residue 85 VAL Chi-restraints excluded: chain k residue 113 THR Chi-restraints excluded: chain k residue 125 LYS Chi-restraints excluded: chain l residue 19 ASN Chi-restraints excluded: chain l residue 95 HIS Chi-restraints excluded: chain l residue 96 THR Chi-restraints excluded: chain l residue 97 VAL Chi-restraints excluded: chain l residue 115 LYS Chi-restraints excluded: chain m residue 6 ILE Chi-restraints excluded: chain m residue 15 VAL Chi-restraints excluded: chain m residue 28 ARG Chi-restraints excluded: chain m residue 52 ILE Chi-restraints excluded: chain m residue 67 ASP Chi-restraints excluded: chain m residue 99 GLN Chi-restraints excluded: chain n residue 60 GLN Chi-restraints excluded: chain o residue 10 ILE Chi-restraints excluded: chain p residue 3 THR Chi-restraints excluded: chain q residue 20 ILE Chi-restraints excluded: chain q residue 40 THR Chi-restraints excluded: chain q residue 67 SER Chi-restraints excluded: chain r residue 13 THR Chi-restraints excluded: chain r residue 15 GLU Chi-restraints excluded: chain r residue 66 LEU Chi-restraints excluded: chain r residue 70 THR Chi-restraints excluded: chain s residue 6 LYS Chi-restraints excluded: chain s residue 32 THR Chi-restraints excluded: chain s residue 48 ILE Chi-restraints excluded: chain s residue 62 THR Chi-restraints excluded: chain s residue 65 MET Chi-restraints excluded: chain t residue 22 SER Chi-restraints excluded: chain u residue 3 ILE Chi-restraints excluded: chain u residue 27 VAL Chi-restraints excluded: chain u residue 32 ARG Chi-restraints excluded: chain u residue 33 ARG Chi-restraints excluded: chain u residue 50 SER Chi-restraints excluded: chain z residue 13 ASN Chi-restraints excluded: chain z residue 26 THR Chi-restraints excluded: chain z residue 54 GLU Chi-restraints excluded: chain z residue 102 ILE Chi-restraints excluded: chain z residue 173 SER Chi-restraints excluded: chain z residue 185 GLU Chi-restraints excluded: chain z residue 220 ILE Chi-restraints excluded: chain z residue 225 THR Chi-restraints excluded: chain z residue 236 ILE Chi-restraints excluded: chain z residue 245 VAL Chi-restraints excluded: chain z residue 276 VAL Chi-restraints excluded: chain z residue 338 THR Chi-restraints excluded: chain z residue 351 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1087 random chunks: chunk 953 optimal weight: 5.9990 chunk 1003 optimal weight: 1.9990 chunk 915 optimal weight: 3.9990 chunk 976 optimal weight: 6.9990 chunk 587 optimal weight: 0.8980 chunk 425 optimal weight: 30.0000 chunk 766 optimal weight: 10.0000 chunk 299 optimal weight: 10.0000 chunk 882 optimal weight: 2.9990 chunk 923 optimal weight: 5.9990 chunk 972 optimal weight: 0.9980 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 165 HIS H 28 ASN ** I 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 55 HIS R 6 GLN R 86 GLN U 73 ASN V 75 GLN 6 61 ASN c 24 ASN c 31 ASN c 122 GLN c 139 ASN d 58 GLN ** d 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 76 ASN ** e 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 63 ASN g 27 ASN ** g 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 28 ASN ** l 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 2 ASN t 51 ASN ** z 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.4273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 165479 Z= 0.203 Angle : 0.698 14.869 247209 Z= 0.376 Chirality : 0.036 0.413 31418 Planarity : 0.007 0.127 13503 Dihedral : 24.246 179.717 81838 Min Nonbonded Distance : 1.065 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.56 % Allowed : 7.90 % Favored : 91.54 % Rotamer: Outliers : 5.28 % Allowed : 28.63 % Favored : 66.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.10), residues: 6219 helix: 0.11 (0.12), residues: 1966 sheet: -1.19 (0.14), residues: 1192 loop : -1.94 (0.10), residues: 3061 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP P 30 HIS 0.017 0.001 HIS b 14 PHE 0.024 0.001 PHE f 78 TYR 0.025 0.002 TYR n 19 ARG 0.013 0.001 ARG C 202 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12438 Ramachandran restraints generated. 6219 Oldfield, 0 Emsley, 6219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12438 Ramachandran restraints generated. 6219 Oldfield, 0 Emsley, 6219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1381 residues out of total 5164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 273 poor density : 1108 time to evaluate : 6.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 4 LYS cc_start: 0.8190 (tttt) cc_final: 0.7740 (ttmm) REVERT: C 12 ARG cc_start: 0.7273 (OUTLIER) cc_final: 0.6680 (tpt90) REVERT: C 22 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7143 (mt-10) REVERT: C 27 LYS cc_start: 0.7514 (mttt) cc_final: 0.7033 (mppt) REVERT: C 113 ASP cc_start: 0.7041 (m-30) cc_final: 0.6320 (t0) REVERT: C 159 THR cc_start: 0.9159 (m) cc_final: 0.8685 (p) REVERT: C 184 GLU cc_start: 0.7247 (tt0) cc_final: 0.6640 (mt-10) REVERT: C 187 CYS cc_start: 0.8258 (m) cc_final: 0.8052 (m) REVERT: C 260 LYS cc_start: 0.7866 (OUTLIER) cc_final: 0.7567 (ttpt) REVERT: D 2 ILE cc_start: 0.4876 (OUTLIER) cc_final: 0.4493 (pp) REVERT: D 108 ASP cc_start: 0.7556 (m-30) cc_final: 0.6870 (p0) REVERT: D 186 LEU cc_start: 0.7965 (mt) cc_final: 0.7700 (mt) REVERT: E 51 GLU cc_start: 0.7847 (mt-10) cc_final: 0.7441 (mp0) REVERT: E 88 ARG cc_start: 0.7743 (ttm-80) cc_final: 0.7171 (mmp80) REVERT: E 95 LYS cc_start: 0.7728 (OUTLIER) cc_final: 0.7034 (tttp) REVERT: E 121 VAL cc_start: 0.8498 (m) cc_final: 0.8103 (p) REVERT: E 155 GLU cc_start: 0.7139 (mm-30) cc_final: 0.6698 (pp20) REVERT: E 194 LYS cc_start: 0.7913 (tptt) cc_final: 0.7690 (mmtp) REVERT: F 2 LYS cc_start: 0.7995 (tttm) cc_final: 0.7575 (tptt) REVERT: F 18 GLU cc_start: 0.5770 (OUTLIER) cc_final: 0.5095 (mt-10) REVERT: F 41 GLU cc_start: 0.6877 (mm-30) cc_final: 0.6101 (mp0) REVERT: F 46 LYS cc_start: 0.8083 (mttt) cc_final: 0.7650 (tppp) REVERT: F 47 LYS cc_start: 0.7543 (ptmt) cc_final: 0.7084 (pmtt) REVERT: F 71 LYS cc_start: 0.7203 (mmmt) cc_final: 0.6828 (ttpt) REVERT: F 110 ILE cc_start: 0.7807 (tt) cc_final: 0.7387 (tp) REVERT: F 133 GLU cc_start: 0.7482 (mt-10) cc_final: 0.6801 (pt0) REVERT: F 137 PHE cc_start: 0.7345 (m-80) cc_final: 0.7143 (m-80) REVERT: F 147 ARG cc_start: 0.6698 (tpp80) cc_final: 0.6009 (ttt180) REVERT: F 160 LYS cc_start: 0.7537 (mtmm) cc_final: 0.7208 (mptp) REVERT: G 82 PHE cc_start: 0.5600 (m-80) cc_final: 0.5295 (m-80) REVERT: I 16 MET cc_start: 0.1273 (mmp) cc_final: 0.0743 (mpp) REVERT: I 135 MET cc_start: 0.1549 (mtp) cc_final: 0.0974 (tmt) REVERT: J 12 LYS cc_start: 0.7927 (OUTLIER) cc_final: 0.7268 (tptp) REVERT: J 43 GLU cc_start: 0.8056 (mt-10) cc_final: 0.7431 (pm20) REVERT: J 61 LYS cc_start: 0.7903 (mmtp) cc_final: 0.7638 (mppt) REVERT: J 84 ILE cc_start: 0.8122 (OUTLIER) cc_final: 0.7665 (tp) REVERT: J 91 GLU cc_start: 0.7720 (mt-10) cc_final: 0.7298 (tp30) REVERT: J 95 ARG cc_start: 0.6432 (mtp-110) cc_final: 0.6055 (ttp-110) REVERT: K 7 MET cc_start: 0.8550 (tpp) cc_final: 0.8249 (tpp) REVERT: K 17 ARG cc_start: 0.8384 (tpp80) cc_final: 0.8091 (tpp-160) REVERT: K 66 LYS cc_start: 0.8180 (mttt) cc_final: 0.7891 (mtpt) REVERT: L 7 SER cc_start: 0.8206 (OUTLIER) cc_final: 0.7762 (t) REVERT: L 14 LYS cc_start: 0.7371 (tttm) cc_final: 0.6949 (tmtt) REVERT: L 19 LEU cc_start: 0.8942 (mp) cc_final: 0.8661 (mp) REVERT: L 105 ILE cc_start: 0.8454 (mt) cc_final: 0.8123 (mm) REVERT: L 106 GLU cc_start: 0.8474 (mt-10) cc_final: 0.8065 (mm-30) REVERT: M 6 ARG cc_start: 0.7209 (OUTLIER) cc_final: 0.6724 (ptp90) REVERT: M 12 MET cc_start: 0.8361 (ttm) cc_final: 0.8131 (ttm) REVERT: M 75 GLU cc_start: 0.8256 (tt0) cc_final: 0.7715 (tt0) REVERT: M 88 ASN cc_start: 0.7745 (m110) cc_final: 0.7531 (m-40) REVERT: N 35 LYS cc_start: 0.7870 (tttt) cc_final: 0.7555 (tttp) REVERT: O 13 ARG cc_start: 0.7099 (ttt90) cc_final: 0.6816 (tpp-160) REVERT: O 48 LEU cc_start: 0.8210 (mm) cc_final: 0.7954 (mt) REVERT: O 98 GLN cc_start: 0.8233 (tt0) cc_final: 0.7861 (tt0) REVERT: Q 12 ARG cc_start: 0.7975 (ttm-80) cc_final: 0.7496 (ttt180) REVERT: Q 14 LYS cc_start: 0.7523 (tttt) cc_final: 0.7149 (mtpp) REVERT: Q 48 ASP cc_start: 0.8405 (m-30) cc_final: 0.7722 (m-30) REVERT: Q 77 LYS cc_start: 0.8129 (mttt) cc_final: 0.7689 (mtpt) REVERT: Q 110 GLU cc_start: 0.7017 (OUTLIER) cc_final: 0.6577 (mp0) REVERT: R 1 MET cc_start: 0.6258 (tpp) cc_final: 0.5120 (ptp) REVERT: R 10 LYS cc_start: 0.7821 (ptpp) cc_final: 0.7612 (mtmm) REVERT: R 66 HIS cc_start: 0.8176 (OUTLIER) cc_final: 0.6790 (m-70) REVERT: S 1 MET cc_start: 0.6690 (mmm) cc_final: 0.6290 (mpp) REVERT: S 34 ASP cc_start: 0.7351 (m-30) cc_final: 0.7139 (m-30) REVERT: S 52 GLU cc_start: 0.7947 (tt0) cc_final: 0.7361 (mm-30) REVERT: S 86 MET cc_start: 0.8441 (OUTLIER) cc_final: 0.7816 (tpt) REVERT: S 92 ARG cc_start: 0.6962 (ptp90) cc_final: 0.6273 (ptm160) REVERT: T 28 ASN cc_start: 0.7503 (t0) cc_final: 0.6864 (t0) REVERT: T 33 LYS cc_start: 0.7238 (OUTLIER) cc_final: 0.7035 (tttt) REVERT: T 50 LEU cc_start: 0.7685 (mm) cc_final: 0.7483 (mp) REVERT: T 54 GLU cc_start: 0.7349 (mt-10) cc_final: 0.6435 (tp30) REVERT: T 69 ARG cc_start: 0.7636 (ttp-110) cc_final: 0.6899 (ttm-80) REVERT: T 76 ARG cc_start: 0.7341 (OUTLIER) cc_final: 0.6695 (ptm-80) REVERT: U 17 ASP cc_start: 0.7786 (p0) cc_final: 0.7405 (p0) REVERT: U 25 LYS cc_start: 0.7147 (mmmt) cc_final: 0.6616 (mtpp) REVERT: U 61 GLU cc_start: 0.7502 (OUTLIER) cc_final: 0.6932 (mt-10) REVERT: U 78 LYS cc_start: 0.7092 (OUTLIER) cc_final: 0.6502 (pmtt) REVERT: V 3 THR cc_start: 0.7623 (p) cc_final: 0.7357 (m) REVERT: V 30 ILE cc_start: 0.7370 (mt) cc_final: 0.7000 (tt) REVERT: V 41 GLU cc_start: 0.7524 (pt0) cc_final: 0.6911 (pm20) REVERT: V 69 GLU cc_start: 0.7164 (mt-10) cc_final: 0.6756 (tm-30) REVERT: V 71 LYS cc_start: 0.7203 (mtpp) cc_final: 0.6729 (mppt) REVERT: V 73 LYS cc_start: 0.6502 (mmmt) cc_final: 0.5949 (tptp) REVERT: V 82 TYR cc_start: 0.7051 (p90) cc_final: 0.6801 (p90) REVERT: W 40 LYS cc_start: 0.8051 (ttpt) cc_final: 0.7733 (mtpp) REVERT: W 66 GLU cc_start: 0.8156 (mm-30) cc_final: 0.7139 (mt-10) REVERT: W 71 LYS cc_start: 0.8276 (mttt) cc_final: 0.7487 (mttp) REVERT: X 19 HIS cc_start: 0.7418 (t70) cc_final: 0.6682 (m-70) REVERT: X 71 ARG cc_start: 0.6010 (mtm110) cc_final: 0.5679 (ptp-110) REVERT: Y 14 LEU cc_start: 0.6093 (OUTLIER) cc_final: 0.5813 (mt) REVERT: Y 15 ASN cc_start: 0.7122 (m-40) cc_final: 0.6847 (m110) REVERT: Z 5 LYS cc_start: 0.7047 (mtmm) cc_final: 0.6791 (mtpp) REVERT: 0 11 LYS cc_start: 0.8234 (mmmt) cc_final: 0.7931 (tppp) REVERT: 1 25 ASN cc_start: 0.6821 (t0) cc_final: 0.6471 (t160) REVERT: 1 27 ARG cc_start: 0.7491 (mtm180) cc_final: 0.7105 (mpt90) REVERT: 1 32 LYS cc_start: 0.7374 (mttt) cc_final: 0.7067 (pttt) REVERT: 2 8 SER cc_start: 0.8723 (t) cc_final: 0.8463 (t) REVERT: 2 14 ARG cc_start: 0.8467 (OUTLIER) cc_final: 0.7486 (mtt90) REVERT: 2 41 ARG cc_start: 0.7861 (mmt180) cc_final: 0.7390 (mtm-85) REVERT: 2 44 VAL cc_start: 0.7797 (p) cc_final: 0.7554 (m) REVERT: 3 14 LYS cc_start: 0.8389 (tttt) cc_final: 0.8035 (mmtm) REVERT: 4 18 LYS cc_start: 0.7964 (tttt) cc_final: 0.7676 (mtpp) REVERT: 4 20 ASP cc_start: 0.7523 (OUTLIER) cc_final: 0.6572 (t0) REVERT: 5 1 MET cc_start: 0.3334 (tpt) cc_final: 0.2705 (tmt) REVERT: 6 1 MET cc_start: 0.6930 (mtp) cc_final: 0.6642 (ttm) REVERT: 6 10 GLU cc_start: 0.7347 (tp30) cc_final: 0.7052 (tt0) REVERT: 6 61 ASN cc_start: 0.6662 (m-40) cc_final: 0.5390 (p0) REVERT: 6 62 LYS cc_start: 0.7281 (mmtm) cc_final: 0.6684 (mmmt) REVERT: 6 63 ARG cc_start: 0.4823 (OUTLIER) cc_final: 0.4475 (mtt-85) REVERT: b 62 ARG cc_start: 0.6675 (tpm170) cc_final: 0.6386 (mtm180) REVERT: b 132 GLU cc_start: 0.6737 (tp30) cc_final: 0.6202 (tt0) REVERT: b 136 ARG cc_start: 0.5192 (mmm-85) cc_final: 0.4275 (ttp80) REVERT: b 141 GLU cc_start: 0.7447 (mt-10) cc_final: 0.7147 (mm-30) REVERT: b 145 ASN cc_start: 0.7477 (p0) cc_final: 0.7050 (m110) REVERT: c 24 ASN cc_start: 0.5678 (p0) cc_final: 0.4791 (p0) REVERT: c 33 ASP cc_start: 0.7341 (t70) cc_final: 0.7063 (t0) REVERT: c 45 GLU cc_start: 0.8073 (tm-30) cc_final: 0.7320 (tp30) REVERT: c 71 ARG cc_start: 0.7281 (mtt90) cc_final: 0.6883 (mtp85) REVERT: c 109 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.7525 (mm-30) REVERT: c 128 MET cc_start: 0.7458 (mmt) cc_final: 0.6594 (mtt) REVERT: c 130 ARG cc_start: 0.7649 (OUTLIER) cc_final: 0.7077 (mtt-85) REVERT: c 151 GLU cc_start: 0.7984 (tt0) cc_final: 0.7365 (tm-30) REVERT: c 153 SER cc_start: 0.8218 (OUTLIER) cc_final: 0.7674 (p) REVERT: c 156 LEU cc_start: 0.7533 (OUTLIER) cc_final: 0.7157 (pt) REVERT: c 163 ARG cc_start: 0.5389 (mtt180) cc_final: 0.4540 (mpp-170) REVERT: c 169 GLU cc_start: 0.7755 (mt-10) cc_final: 0.6783 (tp30) REVERT: d 47 LEU cc_start: 0.7872 (tp) cc_final: 0.7307 (pp) REVERT: d 73 ASN cc_start: 0.6926 (m-40) cc_final: 0.6582 (p0) REVERT: d 77 GLU cc_start: 0.7648 (mt-10) cc_final: 0.6810 (tp30) REVERT: d 135 GLN cc_start: 0.5086 (tm-30) cc_final: 0.3957 (mm110) REVERT: e 25 LYS cc_start: 0.7865 (ttpp) cc_final: 0.7501 (tttp) REVERT: e 70 MET cc_start: 0.7457 (mtm) cc_final: 0.7128 (mtm) REVERT: e 71 ILE cc_start: 0.6819 (mm) cc_final: 0.6537 (tt) REVERT: e 81 GLN cc_start: 0.8264 (OUTLIER) cc_final: 0.7236 (mp10) REVERT: e 91 SER cc_start: 0.8807 (OUTLIER) cc_final: 0.8312 (t) REVERT: e 127 TYR cc_start: 0.8413 (m-80) cc_final: 0.8043 (m-80) REVERT: e 144 GLU cc_start: 0.7862 (tt0) cc_final: 0.7619 (tt0) REVERT: f 24 ARG cc_start: 0.7107 (mtm110) cc_final: 0.6560 (mtm110) REVERT: f 59 TYR cc_start: 0.8248 (m-80) cc_final: 0.7822 (m-80) REVERT: f 62 MET cc_start: 0.7131 (mmm) cc_final: 0.6846 (mmm) REVERT: g 20 GLU cc_start: 0.5434 (mm-30) cc_final: 0.5131 (mp0) REVERT: g 89 GLU cc_start: 0.7938 (OUTLIER) cc_final: 0.7649 (mm-30) REVERT: g 105 GLU cc_start: 0.7873 (tp30) cc_final: 0.7350 (tp30) REVERT: h 2 MET cc_start: 0.8075 (tpp) cc_final: 0.7536 (tpp) REVERT: h 90 GLU cc_start: 0.7849 (tt0) cc_final: 0.7380 (mp0) REVERT: i 63 TYR cc_start: 0.7105 (t80) cc_final: 0.6524 (t80) REVERT: i 123 ARG cc_start: 0.7589 (mtp-110) cc_final: 0.7201 (mtt-85) REVERT: j 53 ILE cc_start: 0.6580 (tp) cc_final: 0.6165 (pt) REVERT: j 66 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7288 (pp20) REVERT: k 36 ARG cc_start: 0.8222 (mmm-85) cc_final: 0.7619 (mmm-85) REVERT: k 74 LYS cc_start: 0.7802 (mttt) cc_final: 0.7473 (mptt) REVERT: k 107 THR cc_start: 0.7978 (m) cc_final: 0.7284 (p) REVERT: k 125 LYS cc_start: 0.7712 (ttmt) cc_final: 0.7392 (ttmp) REVERT: l 13 ARG cc_start: 0.7567 (tpt170) cc_final: 0.6503 (tpt170) REVERT: l 17 LYS cc_start: 0.7059 (pttt) cc_final: 0.6680 (mmtt) REVERT: l 95 HIS cc_start: 0.6307 (OUTLIER) cc_final: 0.5820 (m-70) REVERT: l 111 GLN cc_start: 0.6776 (mt0) cc_final: 0.6070 (mt0) REVERT: m 73 SER cc_start: 0.7701 (m) cc_final: 0.7340 (p) REVERT: n 39 GLU cc_start: 0.8011 (mt-10) cc_final: 0.7682 (mm-30) REVERT: n 86 GLU cc_start: 0.6703 (tm-30) cc_final: 0.6417 (tm-30) REVERT: n 90 ARG cc_start: 0.7478 (ttt90) cc_final: 0.6994 (ttp-170) REVERT: o 52 ARG cc_start: 0.7220 (ttt180) cc_final: 0.6610 (ttp-170) REVERT: o 61 GLN cc_start: 0.7776 (tp40) cc_final: 0.7291 (tt0) REVERT: o 82 GLU cc_start: 0.7859 (mm-30) cc_final: 0.7497 (tm-30) REVERT: q 8 GLN cc_start: 0.8104 (tt0) cc_final: 0.7494 (mp10) REVERT: q 18 LYS cc_start: 0.5496 (ttpt) cc_final: 0.5079 (ttmt) REVERT: q 40 THR cc_start: 0.7994 (OUTLIER) cc_final: 0.7784 (t) REVERT: r 29 LYS cc_start: 0.7586 (mttp) cc_final: 0.7296 (mttp) REVERT: s 34 SER cc_start: 0.8791 (t) cc_final: 0.8493 (t) REVERT: t 20 ASN cc_start: 0.8126 (m-40) cc_final: 0.7886 (m110) REVERT: t 59 ARG cc_start: 0.5788 (ttm110) cc_final: 0.5480 (ttp-170) REVERT: u 22 CYS cc_start: 0.7320 (t) cc_final: 0.6900 (p) REVERT: u 32 ARG cc_start: 0.7622 (OUTLIER) cc_final: 0.6858 (ppp80) REVERT: u 33 ARG cc_start: 0.7680 (OUTLIER) cc_final: 0.7224 (mtm180) REVERT: u 38 GLU cc_start: 0.7465 (pt0) cc_final: 0.7250 (pt0) REVERT: z 4 LYS cc_start: 0.4347 (mtmm) cc_final: 0.3922 (ttmt) REVERT: z 54 GLU cc_start: 0.5558 (OUTLIER) cc_final: 0.4789 (pm20) REVERT: z 185 GLU cc_start: 0.4023 (OUTLIER) cc_final: 0.3742 (tt0) REVERT: z 201 GLU cc_start: 0.2433 (mt-10) cc_final: 0.1692 (tp30) REVERT: z 207 ASP cc_start: 0.5601 (t0) cc_final: 0.5191 (p0) REVERT: z 220 ILE cc_start: 0.5558 (OUTLIER) cc_final: 0.5167 (tp) REVERT: z 233 ARG cc_start: 0.5024 (OUTLIER) cc_final: 0.3691 (ptm160) REVERT: z 282 LYS cc_start: 0.7028 (mttt) cc_final: 0.6694 (mmmt) outliers start: 273 outliers final: 168 residues processed: 1259 average time/residue: 2.2337 time to fit residues: 4096.5319 Evaluate side-chains 1279 residues out of total 5164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 205 poor density : 1074 time to evaluate : 6.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 9 SER Chi-restraints excluded: chain C residue 12 ARG Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain C residue 35 LYS Chi-restraints excluded: chain C residue 67 LYS Chi-restraints excluded: chain C residue 69 ASN Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain C residue 260 LYS Chi-restraints excluded: chain D residue 2 ILE Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 95 LYS Chi-restraints excluded: chain E residue 137 LYS Chi-restraints excluded: chain E residue 176 ASP Chi-restraints excluded: chain F residue 16 MET Chi-restraints excluded: chain F residue 18 GLU Chi-restraints excluded: chain F residue 45 ASP Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 122 ASP Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain G residue 24 THR Chi-restraints excluded: chain G residue 120 ILE Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 139 VAL Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain I residue 56 VAL Chi-restraints excluded: chain J residue 12 LYS Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain K residue 14 SER Chi-restraints excluded: chain K residue 61 VAL Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 106 GLU Chi-restraints excluded: chain K residue 114 LYS Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain M residue 6 ARG Chi-restraints excluded: chain M residue 30 SER Chi-restraints excluded: chain M residue 105 MET Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain O residue 56 LYS Chi-restraints excluded: chain O residue 95 SER Chi-restraints excluded: chain P residue 15 ASP Chi-restraints excluded: chain P residue 16 VAL Chi-restraints excluded: chain P residue 32 VAL Chi-restraints excluded: chain P residue 47 ILE Chi-restraints excluded: chain Q residue 110 GLU Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 66 HIS Chi-restraints excluded: chain S residue 29 VAL Chi-restraints excluded: chain S residue 66 ILE Chi-restraints excluded: chain S residue 86 MET Chi-restraints excluded: chain T residue 9 LYS Chi-restraints excluded: chain T residue 16 VAL Chi-restraints excluded: chain T residue 17 SER Chi-restraints excluded: chain T residue 33 LYS Chi-restraints excluded: chain T residue 76 ARG Chi-restraints excluded: chain U residue 36 GLU Chi-restraints excluded: chain U residue 61 GLU Chi-restraints excluded: chain U residue 78 LYS Chi-restraints excluded: chain V residue 4 ILE Chi-restraints excluded: chain V residue 12 GLN Chi-restraints excluded: chain V residue 40 ILE Chi-restraints excluded: chain V residue 63 ILE Chi-restraints excluded: chain V residue 64 VAL Chi-restraints excluded: chain W residue 39 THR Chi-restraints excluded: chain X residue 34 SER Chi-restraints excluded: chain X residue 47 THR Chi-restraints excluded: chain X residue 65 THR Chi-restraints excluded: chain Y residue 14 LEU Chi-restraints excluded: chain Y residue 17 GLU Chi-restraints excluded: chain Y residue 40 SER Chi-restraints excluded: chain Z residue 3 THR Chi-restraints excluded: chain Z residue 7 THR Chi-restraints excluded: chain Z residue 51 SER Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 9 ARG Chi-restraints excluded: chain 0 residue 22 THR Chi-restraints excluded: chain 0 residue 32 THR Chi-restraints excluded: chain 1 residue 21 THR Chi-restraints excluded: chain 1 residue 22 THR Chi-restraints excluded: chain 1 residue 42 VAL Chi-restraints excluded: chain 1 residue 46 VAL Chi-restraints excluded: chain 2 residue 14 ARG Chi-restraints excluded: chain 4 residue 6 SER Chi-restraints excluded: chain 4 residue 20 ASP Chi-restraints excluded: chain 4 residue 28 SER Chi-restraints excluded: chain 6 residue 3 LYS Chi-restraints excluded: chain 6 residue 13 THR Chi-restraints excluded: chain 6 residue 22 MET Chi-restraints excluded: chain 6 residue 63 ARG Chi-restraints excluded: chain b residue 21 TYR Chi-restraints excluded: chain b residue 109 SER Chi-restraints excluded: chain b residue 170 ILE Chi-restraints excluded: chain b residue 178 LEU Chi-restraints excluded: chain b residue 190 SER Chi-restraints excluded: chain b residue 193 ASP Chi-restraints excluded: chain b residue 203 ASP Chi-restraints excluded: chain b residue 225 SER Chi-restraints excluded: chain c residue 57 GLU Chi-restraints excluded: chain c residue 90 VAL Chi-restraints excluded: chain c residue 93 ILE Chi-restraints excluded: chain c residue 109 GLU Chi-restraints excluded: chain c residue 120 THR Chi-restraints excluded: chain c residue 130 ARG Chi-restraints excluded: chain c residue 153 SER Chi-restraints excluded: chain c residue 156 LEU Chi-restraints excluded: chain d residue 124 VAL Chi-restraints excluded: chain d residue 143 SER Chi-restraints excluded: chain d residue 168 THR Chi-restraints excluded: chain e residue 17 VAL Chi-restraints excluded: chain e residue 33 THR Chi-restraints excluded: chain e residue 36 THR Chi-restraints excluded: chain e residue 38 VAL Chi-restraints excluded: chain e residue 45 VAL Chi-restraints excluded: chain e residue 61 LYS Chi-restraints excluded: chain e residue 81 GLN Chi-restraints excluded: chain e residue 91 SER Chi-restraints excluded: chain e residue 123 LEU Chi-restraints excluded: chain e residue 129 SER Chi-restraints excluded: chain f residue 23 GLU Chi-restraints excluded: chain f residue 70 VAL Chi-restraints excluded: chain f residue 76 THR Chi-restraints excluded: chain f residue 96 VAL Chi-restraints excluded: chain g residue 11 ILE Chi-restraints excluded: chain g residue 32 ASP Chi-restraints excluded: chain g residue 89 GLU Chi-restraints excluded: chain g residue 93 VAL Chi-restraints excluded: chain g residue 96 ASN Chi-restraints excluded: chain g residue 132 THR Chi-restraints excluded: chain h residue 25 THR Chi-restraints excluded: chain h residue 59 GLU Chi-restraints excluded: chain h residue 79 ARG Chi-restraints excluded: chain h residue 82 LEU Chi-restraints excluded: chain h residue 111 THR Chi-restraints excluded: chain h residue 128 VAL Chi-restraints excluded: chain i residue 20 ILE Chi-restraints excluded: chain i residue 61 ASP Chi-restraints excluded: chain i residue 82 ILE Chi-restraints excluded: chain i residue 127 SER Chi-restraints excluded: chain j residue 40 ILE Chi-restraints excluded: chain j residue 66 GLU Chi-restraints excluded: chain j residue 96 VAL Chi-restraints excluded: chain j residue 98 VAL Chi-restraints excluded: chain k residue 15 VAL Chi-restraints excluded: chain k residue 34 THR Chi-restraints excluded: chain k residue 49 SER Chi-restraints excluded: chain k residue 80 ASN Chi-restraints excluded: chain k residue 84 MET Chi-restraints excluded: chain k residue 85 VAL Chi-restraints excluded: chain k residue 113 THR Chi-restraints excluded: chain l residue 95 HIS Chi-restraints excluded: chain l residue 96 THR Chi-restraints excluded: chain l residue 115 LYS Chi-restraints excluded: chain m residue 6 ILE Chi-restraints excluded: chain m residue 15 VAL Chi-restraints excluded: chain m residue 28 ARG Chi-restraints excluded: chain m residue 52 ILE Chi-restraints excluded: chain m residue 67 ASP Chi-restraints excluded: chain p residue 3 THR Chi-restraints excluded: chain q residue 20 ILE Chi-restraints excluded: chain q residue 40 THR Chi-restraints excluded: chain q residue 67 SER Chi-restraints excluded: chain r residue 13 THR Chi-restraints excluded: chain r residue 15 GLU Chi-restraints excluded: chain r residue 66 LEU Chi-restraints excluded: chain r residue 70 THR Chi-restraints excluded: chain s residue 32 THR Chi-restraints excluded: chain s residue 48 ILE Chi-restraints excluded: chain s residue 65 MET Chi-restraints excluded: chain t residue 2 ASN Chi-restraints excluded: chain t residue 22 SER Chi-restraints excluded: chain u residue 3 ILE Chi-restraints excluded: chain u residue 27 VAL Chi-restraints excluded: chain u residue 32 ARG Chi-restraints excluded: chain u residue 33 ARG Chi-restraints excluded: chain z residue 13 ASN Chi-restraints excluded: chain z residue 26 THR Chi-restraints excluded: chain z residue 54 GLU Chi-restraints excluded: chain z residue 102 ILE Chi-restraints excluded: chain z residue 185 GLU Chi-restraints excluded: chain z residue 220 ILE Chi-restraints excluded: chain z residue 225 THR Chi-restraints excluded: chain z residue 233 ARG Chi-restraints excluded: chain z residue 245 VAL Chi-restraints excluded: chain z residue 276 VAL Chi-restraints excluded: chain z residue 279 ARG Chi-restraints excluded: chain z residue 338 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1087 random chunks: chunk 641 optimal weight: 10.0000 chunk 1032 optimal weight: 10.0000 chunk 630 optimal weight: 9.9990 chunk 489 optimal weight: 0.0050 chunk 717 optimal weight: 10.0000 chunk 1082 optimal weight: 0.4980 chunk 996 optimal weight: 7.9990 chunk 862 optimal weight: 7.9990 chunk 89 optimal weight: 20.0000 chunk 666 optimal weight: 10.0000 chunk 528 optimal weight: 10.0000 overall best weight: 5.3000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 59 GLN D 150 GLN E 165 HIS ** I 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 6 GLN R 6 GLN U 39 ASN U 73 ASN V 75 GLN b 119 GLN c 31 ASN c 122 GLN c 139 ASN ** d 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 84 ASN ** d 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 76 ASN ** e 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 28 ASN ** l 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 99 GLN n 60 GLN t 2 ASN ** t 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.4272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 165479 Z= 0.387 Angle : 0.808 15.038 247209 Z= 0.424 Chirality : 0.043 0.392 31418 Planarity : 0.008 0.138 13503 Dihedral : 24.293 179.691 81838 Min Nonbonded Distance : 1.031 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.58 % Allowed : 8.97 % Favored : 90.45 % Rotamer: Outliers : 5.07 % Allowed : 29.27 % Favored : 65.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.10), residues: 6219 helix: -0.14 (0.11), residues: 1959 sheet: -1.31 (0.14), residues: 1194 loop : -2.01 (0.10), residues: 3066 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP P 30 HIS 0.020 0.002 HIS b 14 PHE 0.024 0.002 PHE f 78 TYR 0.036 0.002 TYR n 19 ARG 0.015 0.001 ARG C 202 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12438 Ramachandran restraints generated. 6219 Oldfield, 0 Emsley, 6219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12438 Ramachandran restraints generated. 6219 Oldfield, 0 Emsley, 6219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1348 residues out of total 5164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 262 poor density : 1086 time to evaluate : 6.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 2 VAL cc_start: 0.8362 (t) cc_final: 0.8036 (m) REVERT: C 4 LYS cc_start: 0.8186 (tttt) cc_final: 0.7748 (ttmm) REVERT: C 12 ARG cc_start: 0.7385 (OUTLIER) cc_final: 0.6757 (tpt90) REVERT: C 22 GLU cc_start: 0.7942 (OUTLIER) cc_final: 0.7121 (mt-10) REVERT: C 27 LYS cc_start: 0.7552 (mttt) cc_final: 0.7009 (mppt) REVERT: C 34 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.8042 (pt0) REVERT: C 113 ASP cc_start: 0.7042 (m-30) cc_final: 0.6335 (t0) REVERT: C 159 THR cc_start: 0.9142 (m) cc_final: 0.8700 (p) REVERT: C 184 GLU cc_start: 0.7270 (tt0) cc_final: 0.6668 (mt-10) REVERT: C 187 CYS cc_start: 0.8140 (m) cc_final: 0.7927 (m) REVERT: C 250 GLN cc_start: 0.7752 (tm-30) cc_final: 0.7374 (tm130) REVERT: C 260 LYS cc_start: 0.7906 (OUTLIER) cc_final: 0.7566 (ttpt) REVERT: D 2 ILE cc_start: 0.4841 (OUTLIER) cc_final: 0.4463 (pp) REVERT: D 45 TYR cc_start: 0.7378 (p90) cc_final: 0.7021 (p90) REVERT: D 108 ASP cc_start: 0.7545 (m-30) cc_final: 0.6878 (p0) REVERT: D 186 LEU cc_start: 0.8017 (mt) cc_final: 0.7779 (mt) REVERT: E 88 ARG cc_start: 0.7801 (ttm-80) cc_final: 0.7200 (mmp80) REVERT: E 95 LYS cc_start: 0.7682 (OUTLIER) cc_final: 0.7229 (tttp) REVERT: E 155 GLU cc_start: 0.7161 (mm-30) cc_final: 0.6741 (pp20) REVERT: E 194 LYS cc_start: 0.7913 (tptt) cc_final: 0.7686 (mmtp) REVERT: F 2 LYS cc_start: 0.7956 (tttm) cc_final: 0.7585 (tptt) REVERT: F 18 GLU cc_start: 0.5654 (OUTLIER) cc_final: 0.4912 (mt-10) REVERT: F 41 GLU cc_start: 0.7065 (mm-30) cc_final: 0.6265 (mp0) REVERT: F 46 LYS cc_start: 0.8066 (mttt) cc_final: 0.7656 (tppp) REVERT: F 47 LYS cc_start: 0.7543 (ptmt) cc_final: 0.7083 (pmtt) REVERT: F 71 LYS cc_start: 0.7252 (mmmt) cc_final: 0.6857 (ttpt) REVERT: F 133 GLU cc_start: 0.7480 (mt-10) cc_final: 0.7152 (mt-10) REVERT: F 137 PHE cc_start: 0.7321 (m-80) cc_final: 0.7106 (m-80) REVERT: F 147 ARG cc_start: 0.6782 (tpp80) cc_final: 0.5967 (ttt180) REVERT: F 160 LYS cc_start: 0.7558 (mtmm) cc_final: 0.7206 (mptp) REVERT: F 177 ARG cc_start: 0.5290 (OUTLIER) cc_final: 0.4924 (mtp180) REVERT: G 154 GLU cc_start: 0.7180 (tt0) cc_final: 0.6810 (pt0) REVERT: I 16 MET cc_start: 0.1322 (mmp) cc_final: 0.0741 (mpp) REVERT: I 135 MET cc_start: 0.1548 (mtp) cc_final: 0.1010 (tmt) REVERT: J 12 LYS cc_start: 0.7967 (OUTLIER) cc_final: 0.7300 (tptp) REVERT: J 43 GLU cc_start: 0.8100 (mt-10) cc_final: 0.7415 (pm20) REVERT: J 61 LYS cc_start: 0.7930 (mmtp) cc_final: 0.7333 (mtpt) REVERT: J 84 ILE cc_start: 0.8096 (OUTLIER) cc_final: 0.7640 (tp) REVERT: J 91 GLU cc_start: 0.7847 (mt-10) cc_final: 0.7369 (tp30) REVERT: J 95 ARG cc_start: 0.6443 (mtp-110) cc_final: 0.6058 (ttp-110) REVERT: K 17 ARG cc_start: 0.8470 (tpp80) cc_final: 0.8177 (tpp-160) REVERT: K 18 ARG cc_start: 0.8021 (mmt180) cc_final: 0.7554 (mtp-110) REVERT: K 66 LYS cc_start: 0.8125 (mttt) cc_final: 0.7831 (mtpt) REVERT: K 111 LYS cc_start: 0.7378 (ptpp) cc_final: 0.6838 (ttpp) REVERT: L 14 LYS cc_start: 0.7457 (tttm) cc_final: 0.7030 (tmtt) REVERT: L 19 LEU cc_start: 0.9061 (mp) cc_final: 0.8850 (mt) REVERT: L 68 SER cc_start: 0.8394 (t) cc_final: 0.8136 (p) REVERT: L 105 ILE cc_start: 0.8487 (mt) cc_final: 0.8127 (mm) REVERT: L 106 GLU cc_start: 0.8522 (mt-10) cc_final: 0.8091 (mm-30) REVERT: M 6 ARG cc_start: 0.7258 (OUTLIER) cc_final: 0.6681 (ptp90) REVERT: M 12 MET cc_start: 0.8334 (ttm) cc_final: 0.8093 (ttm) REVERT: M 75 GLU cc_start: 0.8230 (tt0) cc_final: 0.7739 (tt0) REVERT: M 88 ASN cc_start: 0.7661 (m110) cc_final: 0.7451 (m-40) REVERT: N 35 LYS cc_start: 0.7884 (tttt) cc_final: 0.7506 (tttp) REVERT: O 13 ARG cc_start: 0.7070 (ttt90) cc_final: 0.6803 (tpp-160) REVERT: O 48 LEU cc_start: 0.8153 (mm) cc_final: 0.7906 (mt) REVERT: O 98 GLN cc_start: 0.8250 (tt0) cc_final: 0.7766 (tt0) REVERT: P 6 GLN cc_start: 0.7244 (OUTLIER) cc_final: 0.6604 (tm-30) REVERT: P 43 GLU cc_start: 0.8253 (OUTLIER) cc_final: 0.7838 (tt0) REVERT: Q 12 ARG cc_start: 0.8060 (ttm-80) cc_final: 0.7544 (ttt180) REVERT: Q 14 LYS cc_start: 0.7491 (tttt) cc_final: 0.7116 (mtpp) REVERT: Q 48 ASP cc_start: 0.8462 (m-30) cc_final: 0.7824 (m-30) REVERT: Q 77 LYS cc_start: 0.8103 (mttt) cc_final: 0.7656 (mtpt) REVERT: Q 110 GLU cc_start: 0.7128 (OUTLIER) cc_final: 0.6630 (mp0) REVERT: R 1 MET cc_start: 0.6469 (tpp) cc_final: 0.5161 (ptp) REVERT: R 10 LYS cc_start: 0.7958 (ptpp) cc_final: 0.7703 (mtmm) REVERT: R 66 HIS cc_start: 0.8286 (OUTLIER) cc_final: 0.6894 (m-70) REVERT: S 1 MET cc_start: 0.6597 (mmm) cc_final: 0.6322 (mpp) REVERT: S 34 ASP cc_start: 0.7474 (m-30) cc_final: 0.7270 (m-30) REVERT: S 52 GLU cc_start: 0.7972 (tt0) cc_final: 0.7366 (mm-30) REVERT: S 86 MET cc_start: 0.8443 (OUTLIER) cc_final: 0.7816 (tpt) REVERT: S 92 ARG cc_start: 0.7057 (ptp90) cc_final: 0.6335 (ptm160) REVERT: T 28 ASN cc_start: 0.7562 (t0) cc_final: 0.6926 (t0) REVERT: T 33 LYS cc_start: 0.7361 (OUTLIER) cc_final: 0.7147 (tttt) REVERT: T 54 GLU cc_start: 0.7395 (mt-10) cc_final: 0.6510 (tp30) REVERT: T 69 ARG cc_start: 0.7613 (ttp-110) cc_final: 0.6808 (ttm-80) REVERT: T 76 ARG cc_start: 0.7222 (OUTLIER) cc_final: 0.6510 (ptm-80) REVERT: U 17 ASP cc_start: 0.7764 (p0) cc_final: 0.7338 (p0) REVERT: U 25 LYS cc_start: 0.7131 (mmmt) cc_final: 0.6672 (mtpp) REVERT: U 78 LYS cc_start: 0.7047 (OUTLIER) cc_final: 0.6614 (pmtt) REVERT: V 2 PHE cc_start: 0.4672 (m-10) cc_final: 0.3521 (p90) REVERT: V 3 THR cc_start: 0.7736 (p) cc_final: 0.7522 (m) REVERT: V 30 ILE cc_start: 0.7452 (mt) cc_final: 0.7117 (tt) REVERT: V 41 GLU cc_start: 0.7584 (pt0) cc_final: 0.6966 (pm20) REVERT: V 71 LYS cc_start: 0.7208 (mtpp) cc_final: 0.6805 (mppt) REVERT: V 73 LYS cc_start: 0.6411 (mmmt) cc_final: 0.5865 (tptp) REVERT: V 82 TYR cc_start: 0.7147 (p90) cc_final: 0.6860 (p90) REVERT: W 40 LYS cc_start: 0.8139 (ttpt) cc_final: 0.7780 (mtpp) REVERT: W 62 LYS cc_start: 0.7714 (mttt) cc_final: 0.7278 (mtpt) REVERT: W 71 LYS cc_start: 0.8320 (mttt) cc_final: 0.8022 (mttp) REVERT: X 19 HIS cc_start: 0.7447 (t70) cc_final: 0.6673 (m-70) REVERT: X 36 ARG cc_start: 0.6935 (OUTLIER) cc_final: 0.5804 (mtp85) REVERT: X 71 ARG cc_start: 0.5710 (mtm110) cc_final: 0.5399 (ptp-110) REVERT: Y 14 LEU cc_start: 0.6048 (OUTLIER) cc_final: 0.5778 (mt) REVERT: Y 15 ASN cc_start: 0.7122 (m-40) cc_final: 0.6865 (m110) REVERT: Z 5 LYS cc_start: 0.7085 (mtmm) cc_final: 0.6879 (mtpp) REVERT: 0 11 LYS cc_start: 0.8279 (mmmt) cc_final: 0.7937 (tppp) REVERT: 1 6 GLU cc_start: 0.7748 (pt0) cc_final: 0.7491 (pt0) REVERT: 1 23 THR cc_start: 0.7880 (p) cc_final: 0.7628 (m) REVERT: 1 27 ARG cc_start: 0.7486 (mtm180) cc_final: 0.7176 (mpt180) REVERT: 1 32 LYS cc_start: 0.7325 (mttt) cc_final: 0.7118 (pptt) REVERT: 2 8 SER cc_start: 0.8758 (t) cc_final: 0.8489 (t) REVERT: 2 14 ARG cc_start: 0.8541 (OUTLIER) cc_final: 0.7548 (mtt90) REVERT: 2 41 ARG cc_start: 0.7918 (mmt180) cc_final: 0.7449 (mtm-85) REVERT: 2 44 VAL cc_start: 0.7939 (p) cc_final: 0.7706 (m) REVERT: 3 14 LYS cc_start: 0.8402 (tttt) cc_final: 0.7889 (mmtm) REVERT: 4 18 LYS cc_start: 0.7974 (tttt) cc_final: 0.7670 (mtpp) REVERT: 4 20 ASP cc_start: 0.7467 (OUTLIER) cc_final: 0.6551 (t0) REVERT: 5 1 MET cc_start: 0.3082 (tpt) cc_final: 0.2514 (tmt) REVERT: 6 1 MET cc_start: 0.7015 (mtp) cc_final: 0.6709 (ttm) REVERT: 6 10 GLU cc_start: 0.7301 (tp30) cc_final: 0.7071 (tt0) REVERT: 6 62 LYS cc_start: 0.7089 (mmtm) cc_final: 0.6867 (mmmt) REVERT: 6 63 ARG cc_start: 0.4831 (OUTLIER) cc_final: 0.4462 (mtt-85) REVERT: b 107 ARG cc_start: 0.7475 (ttp-110) cc_final: 0.6774 (ttp-170) REVERT: b 136 ARG cc_start: 0.5145 (mmm-85) cc_final: 0.4194 (ttp80) REVERT: b 141 GLU cc_start: 0.7326 (mt-10) cc_final: 0.7056 (mm-30) REVERT: b 145 ASN cc_start: 0.7552 (p0) cc_final: 0.7063 (m110) REVERT: c 33 ASP cc_start: 0.7495 (t70) cc_final: 0.7222 (t0) REVERT: c 45 GLU cc_start: 0.7949 (tm-30) cc_final: 0.7231 (tp30) REVERT: c 71 ARG cc_start: 0.7331 (mtt90) cc_final: 0.6992 (mtp85) REVERT: c 109 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.7491 (mm-30) REVERT: c 128 MET cc_start: 0.7535 (mmt) cc_final: 0.6640 (mtt) REVERT: c 130 ARG cc_start: 0.7718 (OUTLIER) cc_final: 0.7121 (mtt-85) REVERT: c 151 GLU cc_start: 0.7982 (tt0) cc_final: 0.7339 (tm-30) REVERT: c 156 LEU cc_start: 0.7533 (OUTLIER) cc_final: 0.7252 (pt) REVERT: c 163 ARG cc_start: 0.5385 (mtt180) cc_final: 0.4433 (mpp-170) REVERT: c 169 GLU cc_start: 0.7811 (mt-10) cc_final: 0.6886 (tp30) REVERT: d 33 ILE cc_start: 0.4937 (OUTLIER) cc_final: 0.4385 (mm) REVERT: d 77 GLU cc_start: 0.7679 (mt-10) cc_final: 0.6916 (tp30) REVERT: d 135 GLN cc_start: 0.5061 (tm-30) cc_final: 0.3965 (mm110) REVERT: e 70 MET cc_start: 0.7454 (mtm) cc_final: 0.7182 (mtm) REVERT: e 71 ILE cc_start: 0.6873 (mm) cc_final: 0.6599 (tt) REVERT: e 81 GLN cc_start: 0.8268 (OUTLIER) cc_final: 0.7180 (mp10) REVERT: e 127 TYR cc_start: 0.8451 (m-80) cc_final: 0.8040 (m-80) REVERT: e 144 GLU cc_start: 0.7875 (tt0) cc_final: 0.7624 (tt0) REVERT: f 24 ARG cc_start: 0.7052 (mtm110) cc_final: 0.6534 (mtm110) REVERT: f 59 TYR cc_start: 0.8260 (m-80) cc_final: 0.7800 (m-80) REVERT: f 62 MET cc_start: 0.7312 (mmm) cc_final: 0.7036 (mmm) REVERT: g 89 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7810 (mm-30) REVERT: g 105 GLU cc_start: 0.7903 (tp30) cc_final: 0.7319 (tp30) REVERT: h 2 MET cc_start: 0.8079 (tpp) cc_final: 0.7614 (tpp) REVERT: h 28 SER cc_start: 0.8321 (t) cc_final: 0.7701 (p) REVERT: h 86 LYS cc_start: 0.8516 (OUTLIER) cc_final: 0.8164 (mptp) REVERT: h 90 GLU cc_start: 0.7890 (tt0) cc_final: 0.7463 (mp0) REVERT: i 63 TYR cc_start: 0.7092 (t80) cc_final: 0.6501 (t80) REVERT: i 123 ARG cc_start: 0.7677 (mtp-110) cc_final: 0.7052 (mtt90) REVERT: j 53 ILE cc_start: 0.6639 (tp) cc_final: 0.6252 (pt) REVERT: j 66 GLU cc_start: 0.7950 (OUTLIER) cc_final: 0.7186 (pp20) REVERT: k 36 ARG cc_start: 0.8129 (mmm-85) cc_final: 0.7487 (mmm-85) REVERT: k 74 LYS cc_start: 0.7657 (mttt) cc_final: 0.7329 (mptt) REVERT: k 107 THR cc_start: 0.7953 (m) cc_final: 0.7184 (p) REVERT: k 125 LYS cc_start: 0.7729 (ttmt) cc_final: 0.7384 (ttmp) REVERT: l 13 ARG cc_start: 0.7567 (tpt170) cc_final: 0.6516 (tpt170) REVERT: l 17 LYS cc_start: 0.7070 (pttt) cc_final: 0.6633 (mttm) REVERT: l 95 HIS cc_start: 0.6306 (OUTLIER) cc_final: 0.5865 (m-70) REVERT: m 73 SER cc_start: 0.7717 (m) cc_final: 0.7358 (p) REVERT: n 25 GLU cc_start: 0.7512 (pt0) cc_final: 0.6939 (mp0) REVERT: n 39 GLU cc_start: 0.7998 (mt-10) cc_final: 0.7637 (mm-30) REVERT: n 90 ARG cc_start: 0.7644 (ttt90) cc_final: 0.7026 (ttp-170) REVERT: o 52 ARG cc_start: 0.7461 (ttt180) cc_final: 0.6804 (ttp-170) REVERT: o 61 GLN cc_start: 0.7765 (tp40) cc_final: 0.7282 (tt0) REVERT: o 82 GLU cc_start: 0.7838 (mm-30) cc_final: 0.7445 (tm-30) REVERT: p 34 GLU cc_start: 0.3644 (tm-30) cc_final: 0.3182 (tp30) REVERT: q 8 GLN cc_start: 0.8135 (tt0) cc_final: 0.7598 (mp10) REVERT: q 18 LYS cc_start: 0.5402 (ttpt) cc_final: 0.4993 (ttmt) REVERT: q 40 THR cc_start: 0.8036 (OUTLIER) cc_final: 0.7831 (t) REVERT: q 41 THR cc_start: 0.5612 (m) cc_final: 0.5156 (p) REVERT: r 29 LYS cc_start: 0.7642 (mttp) cc_final: 0.7404 (mttp) REVERT: s 6 LYS cc_start: 0.4972 (OUTLIER) cc_final: 0.3731 (pmtt) REVERT: s 34 SER cc_start: 0.8794 (t) cc_final: 0.8487 (t) REVERT: t 20 ASN cc_start: 0.8119 (m-40) cc_final: 0.7873 (m110) REVERT: t 59 ARG cc_start: 0.5692 (ttm110) cc_final: 0.5386 (ttp-170) REVERT: u 6 ARG cc_start: 0.4644 (tpm170) cc_final: 0.3612 (mtt90) REVERT: u 22 CYS cc_start: 0.7365 (t) cc_final: 0.6901 (p) REVERT: u 32 ARG cc_start: 0.7649 (OUTLIER) cc_final: 0.6842 (ppp80) REVERT: u 33 ARG cc_start: 0.7804 (OUTLIER) cc_final: 0.7232 (mtp180) REVERT: z 4 LYS cc_start: 0.4379 (mtmm) cc_final: 0.3957 (ttmt) REVERT: z 54 GLU cc_start: 0.5580 (OUTLIER) cc_final: 0.4766 (pm20) REVERT: z 91 MET cc_start: 0.5310 (tmm) cc_final: 0.5054 (pp-130) REVERT: z 185 GLU cc_start: 0.3973 (OUTLIER) cc_final: 0.3723 (tt0) REVERT: z 201 GLU cc_start: 0.2619 (mt-10) cc_final: 0.1938 (tp30) REVERT: z 207 ASP cc_start: 0.5314 (t0) cc_final: 0.5038 (p0) REVERT: z 220 ILE cc_start: 0.5702 (OUTLIER) cc_final: 0.5307 (tp) REVERT: z 233 ARG cc_start: 0.5080 (OUTLIER) cc_final: 0.3840 (ptm160) REVERT: z 282 LYS cc_start: 0.7113 (mttt) cc_final: 0.6767 (mmmt) REVERT: z 351 MET cc_start: 0.4252 (OUTLIER) cc_final: 0.4037 (mmt) outliers start: 262 outliers final: 175 residues processed: 1235 average time/residue: 2.2264 time to fit residues: 4000.9773 Evaluate side-chains 1283 residues out of total 5164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 217 poor density : 1066 time to evaluate : 6.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 9 SER Chi-restraints excluded: chain C residue 12 ARG Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain C residue 34 GLU Chi-restraints excluded: chain C residue 35 LYS Chi-restraints excluded: chain C residue 67 LYS Chi-restraints excluded: chain C residue 69 ASN Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain C residue 260 LYS Chi-restraints excluded: chain D residue 2 ILE Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 95 LYS Chi-restraints excluded: chain E residue 137 LYS Chi-restraints excluded: chain E residue 176 ASP Chi-restraints excluded: chain F residue 18 GLU Chi-restraints excluded: chain F residue 45 ASP Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 122 ASP Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 152 ASP Chi-restraints excluded: chain F residue 177 ARG Chi-restraints excluded: chain G residue 24 THR Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 139 VAL Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 12 LYS Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain K residue 14 SER Chi-restraints excluded: chain K residue 61 VAL Chi-restraints excluded: chain K residue 95 ILE Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 106 GLU Chi-restraints excluded: chain K residue 114 LYS Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain M residue 6 ARG Chi-restraints excluded: chain M residue 30 SER Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain O residue 56 LYS Chi-restraints excluded: chain O residue 95 SER Chi-restraints excluded: chain P residue 6 GLN Chi-restraints excluded: chain P residue 15 ASP Chi-restraints excluded: chain P residue 16 VAL Chi-restraints excluded: chain P residue 32 VAL Chi-restraints excluded: chain P residue 43 GLU Chi-restraints excluded: chain P residue 47 ILE Chi-restraints excluded: chain Q residue 110 GLU Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 66 HIS Chi-restraints excluded: chain S residue 29 VAL Chi-restraints excluded: chain S residue 86 MET Chi-restraints excluded: chain T residue 9 LYS Chi-restraints excluded: chain T residue 16 VAL Chi-restraints excluded: chain T residue 17 SER Chi-restraints excluded: chain T residue 33 LYS Chi-restraints excluded: chain T residue 76 ARG Chi-restraints excluded: chain U residue 36 GLU Chi-restraints excluded: chain U residue 61 GLU Chi-restraints excluded: chain U residue 78 LYS Chi-restraints excluded: chain V residue 4 ILE Chi-restraints excluded: chain V residue 12 GLN Chi-restraints excluded: chain V residue 63 ILE Chi-restraints excluded: chain V residue 64 VAL Chi-restraints excluded: chain W residue 39 THR Chi-restraints excluded: chain X residue 7 THR Chi-restraints excluded: chain X residue 34 SER Chi-restraints excluded: chain X residue 36 ARG Chi-restraints excluded: chain X residue 47 THR Chi-restraints excluded: chain X residue 65 THR Chi-restraints excluded: chain Y residue 14 LEU Chi-restraints excluded: chain Y residue 17 GLU Chi-restraints excluded: chain Z residue 3 THR Chi-restraints excluded: chain Z residue 7 THR Chi-restraints excluded: chain Z residue 51 SER Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 9 ARG Chi-restraints excluded: chain 0 residue 22 THR Chi-restraints excluded: chain 0 residue 32 THR Chi-restraints excluded: chain 1 residue 21 THR Chi-restraints excluded: chain 1 residue 22 THR Chi-restraints excluded: chain 1 residue 42 VAL Chi-restraints excluded: chain 1 residue 46 VAL Chi-restraints excluded: chain 1 residue 53 ILE Chi-restraints excluded: chain 2 residue 14 ARG Chi-restraints excluded: chain 4 residue 6 SER Chi-restraints excluded: chain 4 residue 20 ASP Chi-restraints excluded: chain 4 residue 28 SER Chi-restraints excluded: chain 5 residue 3 LEU Chi-restraints excluded: chain 6 residue 3 LYS Chi-restraints excluded: chain 6 residue 13 THR Chi-restraints excluded: chain 6 residue 22 MET Chi-restraints excluded: chain 6 residue 63 ARG Chi-restraints excluded: chain b residue 21 TYR Chi-restraints excluded: chain b residue 105 THR Chi-restraints excluded: chain b residue 109 SER Chi-restraints excluded: chain b residue 178 LEU Chi-restraints excluded: chain b residue 190 SER Chi-restraints excluded: chain b residue 193 ASP Chi-restraints excluded: chain b residue 203 ASP Chi-restraints excluded: chain b residue 225 SER Chi-restraints excluded: chain c residue 57 GLU Chi-restraints excluded: chain c residue 90 VAL Chi-restraints excluded: chain c residue 93 ILE Chi-restraints excluded: chain c residue 109 GLU Chi-restraints excluded: chain c residue 120 THR Chi-restraints excluded: chain c residue 130 ARG Chi-restraints excluded: chain c residue 153 SER Chi-restraints excluded: chain c residue 156 LEU Chi-restraints excluded: chain c residue 181 ILE Chi-restraints excluded: chain d residue 33 ILE Chi-restraints excluded: chain d residue 90 LEU Chi-restraints excluded: chain d residue 124 VAL Chi-restraints excluded: chain d residue 143 SER Chi-restraints excluded: chain d residue 168 THR Chi-restraints excluded: chain e residue 17 VAL Chi-restraints excluded: chain e residue 33 THR Chi-restraints excluded: chain e residue 36 THR Chi-restraints excluded: chain e residue 38 VAL Chi-restraints excluded: chain e residue 45 VAL Chi-restraints excluded: chain e residue 61 LYS Chi-restraints excluded: chain e residue 81 GLN Chi-restraints excluded: chain e residue 91 SER Chi-restraints excluded: chain e residue 121 ASN Chi-restraints excluded: chain e residue 123 LEU Chi-restraints excluded: chain e residue 129 SER Chi-restraints excluded: chain f residue 70 VAL Chi-restraints excluded: chain f residue 76 THR Chi-restraints excluded: chain f residue 96 VAL Chi-restraints excluded: chain g residue 11 ILE Chi-restraints excluded: chain g residue 32 ASP Chi-restraints excluded: chain g residue 89 GLU Chi-restraints excluded: chain g residue 93 VAL Chi-restraints excluded: chain g residue 96 ASN Chi-restraints excluded: chain g residue 132 THR Chi-restraints excluded: chain h residue 11 THR Chi-restraints excluded: chain h residue 25 THR Chi-restraints excluded: chain h residue 45 ILE Chi-restraints excluded: chain h residue 59 GLU Chi-restraints excluded: chain h residue 79 ARG Chi-restraints excluded: chain h residue 82 LEU Chi-restraints excluded: chain h residue 86 LYS Chi-restraints excluded: chain h residue 111 THR Chi-restraints excluded: chain h residue 128 VAL Chi-restraints excluded: chain i residue 20 ILE Chi-restraints excluded: chain i residue 61 ASP Chi-restraints excluded: chain i residue 82 ILE Chi-restraints excluded: chain i residue 127 SER Chi-restraints excluded: chain j residue 40 ILE Chi-restraints excluded: chain j residue 66 GLU Chi-restraints excluded: chain j residue 96 VAL Chi-restraints excluded: chain j residue 98 VAL Chi-restraints excluded: chain k residue 15 VAL Chi-restraints excluded: chain k residue 34 THR Chi-restraints excluded: chain k residue 80 ASN Chi-restraints excluded: chain k residue 84 MET Chi-restraints excluded: chain k residue 85 VAL Chi-restraints excluded: chain k residue 113 THR Chi-restraints excluded: chain l residue 95 HIS Chi-restraints excluded: chain l residue 96 THR Chi-restraints excluded: chain l residue 115 LYS Chi-restraints excluded: chain m residue 6 ILE Chi-restraints excluded: chain m residue 15 VAL Chi-restraints excluded: chain m residue 28 ARG Chi-restraints excluded: chain m residue 52 ILE Chi-restraints excluded: chain m residue 67 ASP Chi-restraints excluded: chain q residue 20 ILE Chi-restraints excluded: chain q residue 40 THR Chi-restraints excluded: chain q residue 67 SER Chi-restraints excluded: chain r residue 13 THR Chi-restraints excluded: chain r residue 15 GLU Chi-restraints excluded: chain r residue 66 LEU Chi-restraints excluded: chain r residue 70 THR Chi-restraints excluded: chain s residue 6 LYS Chi-restraints excluded: chain s residue 32 THR Chi-restraints excluded: chain s residue 48 ILE Chi-restraints excluded: chain s residue 62 THR Chi-restraints excluded: chain s residue 65 MET Chi-restraints excluded: chain t residue 22 SER Chi-restraints excluded: chain t residue 29 THR Chi-restraints excluded: chain t residue 51 ASN Chi-restraints excluded: chain u residue 3 ILE Chi-restraints excluded: chain u residue 27 VAL Chi-restraints excluded: chain u residue 32 ARG Chi-restraints excluded: chain u residue 33 ARG Chi-restraints excluded: chain z residue 13 ASN Chi-restraints excluded: chain z residue 26 THR Chi-restraints excluded: chain z residue 54 GLU Chi-restraints excluded: chain z residue 102 ILE Chi-restraints excluded: chain z residue 185 GLU Chi-restraints excluded: chain z residue 220 ILE Chi-restraints excluded: chain z residue 225 THR Chi-restraints excluded: chain z residue 233 ARG Chi-restraints excluded: chain z residue 245 VAL Chi-restraints excluded: chain z residue 260 MET Chi-restraints excluded: chain z residue 276 VAL Chi-restraints excluded: chain z residue 351 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1087 random chunks: chunk 684 optimal weight: 20.0000 chunk 918 optimal weight: 4.9990 chunk 264 optimal weight: 8.9990 chunk 795 optimal weight: 5.9990 chunk 127 optimal weight: 8.9990 chunk 239 optimal weight: 7.9990 chunk 863 optimal weight: 1.9990 chunk 361 optimal weight: 2.9990 chunk 886 optimal weight: 2.9990 chunk 109 optimal weight: 30.0000 chunk 159 optimal weight: 10.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 59 GLN E 165 HIS ** I 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 6 GLN U 39 ASN ** U 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 75 GLN 6 61 ASN c 31 ASN c 122 GLN c 139 ASN ** d 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 76 ASN ** e 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 28 ASN ** l 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 60 GLN t 2 ASN ** t 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.151971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.118949 restraints weight = 229605.532| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 1.04 r_work: 0.3160 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3059 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3059 r_free = 0.3059 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3059 r_free = 0.3059 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3059 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.4279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.242 165479 Z= 0.359 Angle : 0.818 59.200 247209 Z= 0.433 Chirality : 0.042 0.561 31418 Planarity : 0.008 0.138 13503 Dihedral : 24.294 179.609 81838 Min Nonbonded Distance : 1.031 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.60 % Allowed : 8.88 % Favored : 90.53 % Rotamer: Outliers : 4.94 % Allowed : 29.64 % Favored : 65.43 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.10), residues: 6219 helix: -0.16 (0.11), residues: 1959 sheet: -1.32 (0.14), residues: 1194 loop : -2.01 (0.10), residues: 3066 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP g 102 HIS 0.020 0.001 HIS b 14 PHE 0.022 0.002 PHE f 78 TYR 0.034 0.002 TYR n 19 ARG 0.016 0.001 ARG C 202 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 60301.07 seconds wall clock time: 1042 minutes 44.48 seconds (62564.48 seconds total)