Starting phenix.real_space_refine on Tue Mar 26 03:37:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k50_22669/03_2024/7k50_22669_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k50_22669/03_2024/7k50_22669.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k50_22669/03_2024/7k50_22669.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k50_22669/03_2024/7k50_22669.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k50_22669/03_2024/7k50_22669_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k50_22669/03_2024/7k50_22669_updated.pdb" } resolution = 3.4 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= 0.018 sd= 1.404 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 4805 5.49 5 S 155 5.16 5 C 75151 2.51 5 N 27877 2.21 5 O 41712 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "b TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 184": "OE1" <-> "OE2" Residue "c ARG 13": "NH1" <-> "NH2" Residue "c ARG 33": "NH1" <-> "NH2" Residue "c ARG 59": "NH1" <-> "NH2" Residue "c ARG 77": "NH1" <-> "NH2" Residue "c ARG 83": "NH1" <-> "NH2" Residue "c ARG 169": "NH1" <-> "NH2" Residue "c ASP 176": "OD1" <-> "OD2" Residue "c ARG 184": "NH1" <-> "NH2" Residue "d ARG 21": "NH1" <-> "NH2" Residue "d GLU 25": "OE1" <-> "OE2" Residue "d ARG 44": "NH1" <-> "NH2" Residue "d ARG 49": "NH1" <-> "NH2" Residue "d GLU 51": "OE1" <-> "OE2" Residue "d ARG 61": "NH1" <-> "NH2" Residue "d ARG 88": "NH1" <-> "NH2" Residue "d ARG 102": "NH1" <-> "NH2" Residue "d ARG 162": "NH1" <-> "NH2" Residue "d ARG 170": "NH1" <-> "NH2" Residue "d GLU 197": "OE1" <-> "OE2" Residue "e ARG 70": "NH1" <-> "NH2" Residue "e ARG 79": "NH1" <-> "NH2" Residue "e ARG 91": "NH1" <-> "NH2" Residue "e ARG 101": "NH1" <-> "NH2" Residue "e ARG 109": "NH1" <-> "NH2" Residue "e ARG 111": "NH1" <-> "NH2" Residue "e ARG 114": "NH1" <-> "NH2" Residue "e ARG 132": "NH1" <-> "NH2" Residue "e ASP 141": "OD1" <-> "OD2" Residue "f ARG 2": "NH1" <-> "NH2" Residue "f GLU 41": "OE1" <-> "OE2" Residue "f ASP 136": "OD1" <-> "OD2" Residue "f ARG 152": "NH1" <-> "NH2" Residue "f ARG 162": "NH1" <-> "NH2" Residue "f ARG 169": "NH1" <-> "NH2" Residue "j ARG 13": "NH1" <-> "NH2" Residue "j ARG 37": "NH1" <-> "NH2" Residue "j ARG 96": "NH1" <-> "NH2" Residue "j ARG 120": "NH1" <-> "NH2" Residue "j TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ARG 21": "NH1" <-> "NH2" Residue "l ARG 33": "NH1" <-> "NH2" Residue "l ARG 41": "NH1" <-> "NH2" Residue "l ARG 47": "NH1" <-> "NH2" Residue "l ARG 60": "NH1" <-> "NH2" Residue "l ARG 78": "NH1" <-> "NH2" Residue "l GLU 106": "OE1" <-> "OE2" Residue "l ARG 126": "NH1" <-> "NH2" Residue "m ARG 10": "NH1" <-> "NH2" Residue "m ARG 18": "NH1" <-> "NH2" Residue "m ARG 40": "NH1" <-> "NH2" Residue "m ARG 44": "NH1" <-> "NH2" Residue "m GLU 47": "OE1" <-> "OE2" Residue "m ARG 50": "NH1" <-> "NH2" Residue "m ARG 55": "NH1" <-> "NH2" Residue "m ARG 59": "NH1" <-> "NH2" 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 GLU 49": "OE1" <-> "OE2" 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 ARG 96": "NH1" <-> "NH2" Residue "n PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n ARG 118": "NH1" <-> "NH2" Residue "o ARG 10": "NH1" <-> "NH2" Residue "o ARG 16": "NH1" <-> "NH2" Residue "o ARG 25": "NH1" <-> "NH2" Residue "o TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o ARG 81": "NH1" <-> "NH2" Residue "o ARG 94": "NH1" <-> "NH2" Residue "o ARG 102": "NH1" <-> "NH2" Residue "o ARG 111": "NH1" <-> "NH2" Residue "p GLU 10": "OE1" <-> "OE2" Residue "p ARG 20": "NH1" <-> "NH2" Residue "p ARG 38": "NH1" <-> "NH2" Residue "p ARG 61": "NH1" <-> "NH2" Residue "p ARG 88": "NH1" <-> "NH2" Residue "p ARG 100": "NH1" <-> "NH2" Residue "p ARG 108": "NH1" <-> "NH2" Residue "q ARG 2": "NH1" <-> "NH2" Residue "q ARG 5": "NH1" <-> "NH2" Residue "q ARG 12": "NH1" <-> "NH2" Residue "q ARG 32": "NH1" <-> "NH2" Residue "q ARG 47": "NH1" <-> "NH2" Residue "q ARG 69": "NH1" <-> "NH2" Residue "r ARG 21": "NH1" <-> "NH2" Residue "r GLU 34": "OE1" <-> "OE2" 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 "r PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s ARG 84": "NH1" <-> "NH2" Residue "s ARG 88": "NH1" <-> "NH2" Residue "s ARG 95": "NH1" <-> "NH2" Residue "s ARG 110": "NH1" <-> "NH2" Residue "t GLU 52": "OE1" <-> "OE2" Residue "t ARG 73": "NH1" <-> "NH2" Residue "u ARG 5": "NH1" <-> "NH2" Residue "u ARG 6": "NH1" <-> "NH2" Residue "u ASP 7": "OD1" <-> "OD2" Residue "u ARG 81": "NH1" <-> "NH2" Residue "u ARG 85": "NH1" <-> "NH2" Residue "u ARG 93": "NH1" <-> "NH2" Residue "u PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w ASP 60": "OD1" <-> "OD2" Residue "w GLU 66": "OE1" <-> "OE2" Residue "w PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y ARG 29": "NH1" <-> "NH2" Residue "y ARG 47": "NH1" <-> "NH2" Residue "y ARG 52": "NH1" <-> "NH2" Residue "z ARG 10": "NH1" <-> "NH2" Residue "z ARG 29": "NH1" <-> "NH2" Residue "z ARG 44": "NH1" <-> "NH2" Residue "A ARG 49": "NH1" <-> "NH2" Residue "A ARG 56": "NH1" <-> "NH2" Residue "B ARG 9": "NH1" <-> "NH2" Residue "B ARG 15": "NH1" <-> "NH2" Residue "B ASP 19": "OD1" <-> "OD2" Residue "B ARG 39": "NH1" <-> "NH2" Residue "B ARG 51": "NH1" <-> "NH2" Residue "C ARG 43": "NH1" <-> "NH2" Residue "D ARG 3": "NH1" <-> "NH2" Residue "D ARG 12": "NH1" <-> "NH2" Residue "D ARG 14": "NH1" <-> "NH2" Residue "D ARG 19": "NH1" <-> "NH2" Residue "D ARG 21": "NH1" <-> "NH2" Residue "D ARG 33": "NH1" <-> "NH2" Residue "D ARG 41": "NH1" <-> "NH2" Residue "E ARG 12": "NH1" <-> "NH2" Residue "E ARG 29": "NH1" <-> "NH2" Residue "E ARG 39": "NH1" <-> "NH2" Residue "E ARG 41": "NH1" <-> "NH2" Residue "F ARG 12": "NH1" <-> "NH2" Residue "F ARG 24": "NH1" <-> "NH2" Residue "G GLU 77": "OE1" <-> "OE2" Residue "G ARG 107": "NH1" <-> "NH2" Residue "G ASP 164": "OD1" <-> "OD2" Residue "G ASP 196": "OD1" <-> "OD2" Residue "G ARG 224": "NH1" <-> "NH2" Residue "H ARG 106": "NH1" <-> "NH2" Residue "H ARG 130": "NH1" <-> "NH2" Residue "H GLU 165": "OE1" <-> "OE2" Residue "I GLU 14": "OE1" <-> "OE2" Residue "I TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 87": "OE1" <-> "OE2" Residue "I GLU 112": "OE1" <-> "OE2" Residue "I TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 156": "NH1" <-> "NH2" Residue "K ASP 41": "OD1" <-> "OD2" Residue "L PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 105": "OE1" <-> "OE2" Residue "L ASP 139": "OD1" <-> "OD2" Residue "M GLU 41": "OE1" <-> "OE2" Residue "M GLU 51": "OE1" <-> "OE2" Residue "M ASP 53": "OD1" <-> "OD2" Residue "M GLU 57": "OE1" <-> "OE2" Residue "N GLU 91": "OE1" <-> "OE2" Residue "N ARG 123": "NH1" <-> "NH2" Residue "O ASP 75": "OD1" <-> "OD2" Residue "O GLU 81": "OE1" <-> "OE2" Residue "O ASP 85": "OD1" <-> "OD2" Residue "Q ARG 55": "NH1" <-> "NH2" Residue "R GLU 58": "OE1" <-> "OE2" Residue "S ASP 39": "OD1" <-> "OD2" Residue "T GLU 5": "OE1" <-> "OE2" Residue "U ARG 28": "NH1" <-> "NH2" Residue "V GLU 17": "OE1" <-> "OE2" Residue "W ARG 11": "NH1" <-> "NH2" Residue "X PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 66": "NH1" <-> "NH2" Residue "a ARG 7": "NH1" <-> "NH2" Residue "a ARG 12": "NH1" <-> "NH2" Residue "a ARG 162": "NH1" <-> "NH2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 149700 Number of models: 1 Model: "" Number of chains: 60 Chain: "b" Number of atoms: 2083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2083 Classifications: {'peptide': 271} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 253} Chain: "c" Number of atoms: 1565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1565 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 202} Chain: "d" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1552 Classifications: {'peptide': 201} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 195} Chain: "e" Number of atoms: 1411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1411 Classifications: {'peptide': 177} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 170} Chain: "f" Number of atoms: 1323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1323 Classifications: {'peptide': 176} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "g" Number of atoms: 936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 936 Classifications: {'peptide': 125} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain breaks: 1 Chain: "h" Number of atoms: 633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 633 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 2, 'TRANS': 81} Chain: "i" Number of atoms: 551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 551 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 8, 'TRANS': 65} Chain: "j" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1129 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 135} Chain: "k" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 939 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "l" Number of atoms: 1045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1045 Classifications: {'peptide': 143} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 138} Chain: "m" Number of atoms: 1074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1074 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 128} Chain: "n" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 961 Classifications: {'peptide': 120} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "o" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 892 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "p" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 917 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "q" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 947 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'TRANS': 116} Chain: "r" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 816 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 101} Chain: "s" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 857 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 107} Chain: "t" Number of atoms: 739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 739 Classifications: {'peptide': 93} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 91} Chain: "u" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 780 Classifications: {'peptide': 102} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "v" Number of atoms: 753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 753 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "w" Number of atoms: 575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 575 Classifications: {'peptide': 75} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "x" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 625 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "y" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 509 Classifications: {'peptide': 63} Modifications used: {'COO': 1} Link IDs: {'TRANS': 62} Chain: "z" Number of atoms: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 449 Classifications: {'peptide': 58} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "A" Number of atoms: 523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 523 Classifications: {'peptide': 66} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "B" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 444 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 54} Chain: "C" Number of atoms: 410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 410 Classifications: {'peptide': 50} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "D" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 377 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "E" 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: "F" 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: "G" Number of atoms: 1705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1705 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 210} Chain: "H" Number of atoms: 1625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1625 Classifications: {'peptide': 206} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 198} Chain: "I" 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: "J" Number of atoms: 1157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1157 Classifications: {'peptide': 157} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 151} Chain: "K" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 818 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "L" Number of atoms: 1182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1182 Classifications: {'peptide': 151} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain: "M" 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: "N" 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: "O" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 787 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 92} Chain: "P" Number of atoms: 870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 870 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 108} Chain: "Q" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 955 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 115} Chain: "R" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 884 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 109} Chain: "S" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 805 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "T" 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: "U" 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: "V" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 649 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain: "W" Number of atoms: 536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 536 Classifications: {'peptide': 65} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "X" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 638 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 73} Chain: "Y" 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: "Z" Number of atoms: 545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 545 Classifications: {'peptide': 65} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "a" Number of atoms: 1027 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1027 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 131} Chain breaks: 1 Chain: "3" Number of atoms: 33012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1539, 33012 Classifications: {'RNA': 1539} Modifications used: {'5*END': 1, 'rna2p_pur': 97, 'rna2p_pyr': 54, 'rna3p_pur': 777, 'rna3p_pyr': 611} Link IDs: {'rna2p': 151, 'rna3p': 1387} Chain: "1" Number of atoms: 62317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2903, 62317 Classifications: {'RNA': 2903} Modifications used: {'5*END': 1, 'rna2p_pur': 227, 'rna2p_pyr': 99, 'rna3p_pur': 1447, 'rna3p_pyr': 1130} Link IDs: {'rna2p': 326, 'rna3p': 2576} Chain: "2" Number of atoms: 2568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 2568 Classifications: {'RNA': 120} Modifications used: {'5*END': 1, 'rna2p_pur': 5, 'rna2p_pyr': 2, 'rna3p_pur': 60, 'rna3p_pyr': 53} Link IDs: {'rna2p': 7, 'rna3p': 112} Chain: "5" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1640 Classifications: {'RNA': 77} Modifications used: {'5*END': 1, 'rna2p_pur': 5, 'rna2p_pyr': 4, 'rna3p_pur': 34, 'rna3p_pyr': 34} Link IDs: {'rna2p': 9, 'rna3p': 67} Chain: "6" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1640 Classifications: {'RNA': 77} Modifications used: {'5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 5, 'rna3p_pur': 33, 'rna3p_pyr': 33} Link IDs: {'rna2p': 10, 'rna3p': 66} Chain: "4" Number of atoms: 390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 390 Classifications: {'RNA': 18} Modifications used: {'5*END': 1, 'rna3p_pur': 14, 'rna3p_pyr': 4} Link IDs: {'rna3p': 17} Chain: "7" Number of atoms: 1647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1647 Classifications: {'RNA': 77} Modifications used: {'rna2p_pur': 10, 'rna2p_pyr': 5, 'rna3p_pur': 30, 'rna3p_pyr': 32} Link IDs: {'rna2p': 14, 'rna3p': 62} Chain: "5" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} 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 Time building chain proxies: 55.40, per 1000 atoms: 0.37 Number of scatterers: 149700 At special positions: 0 Unit cell: (271.95, 255.15, 244.65, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 155 16.00 P 4805 15.00 O 41712 8.00 N 27877 7.00 C 75151 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: 67.00 Conformation dependent library (CDL) restraints added in 6.9 seconds 11672 Ramachandran restraints generated. 5836 Oldfield, 0 Emsley, 5836 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10924 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: 179 helices and 75 sheets defined 38.0% alpha, 18.6% beta 1485 base pairs and 2355 stacking pairs defined. Time for finding SS restraints: 76.40 Creating SS restraints... Processing helix chain 'b' and resid 9 through 15 removed outlier: 7.499A pdb=" N HIS b 14 " --> pdb=" O PRO b 10 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N VAL b 15 " --> pdb=" O GLY b 11 " (cutoff:3.500A) Processing helix chain 'b' and resid 130 through 135 removed outlier: 3.736A pdb=" N ILE b 134 " --> pdb=" O PRO b 130 " (cutoff:3.500A) Proline residue: b 135 - end of helix No H-bonds generated for 'chain 'b' and resid 130 through 135' Processing helix chain 'b' and resid 206 through 214 removed outlier: 4.336A pdb=" N ALA b 210 " --> pdb=" O LYS b 206 " (cutoff:3.500A) Processing helix chain 'b' and resid 220 through 225 removed outlier: 3.812A pdb=" N MET b 224 " --> pdb=" O ARG b 220 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N ASN b 225 " --> pdb=" O GLY b 221 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 220 through 225' Processing helix chain 'b' and resid 259 through 267 removed outlier: 6.270A pdb=" N ASP b 263 " --> pdb=" O ASN b 259 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N LYS b 264 " --> pdb=" O LYS b 260 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N PHE b 265 " --> pdb=" O ARG b 261 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE b 266 " --> pdb=" O THR b 262 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N VAL b 267 " --> pdb=" O ASP b 263 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 259 through 267' Processing helix chain 'b' and resid 196 through 201 Processing helix chain 'c' and resid 56 through 61 removed outlier: 3.751A pdb=" N VAL c 60 " --> pdb=" O LYS c 56 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N THR c 61 " --> pdb=" O ALA c 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 56 through 61' Processing helix chain 'c' and resid 62 through 72 Processing helix chain 'c' and resid 98 through 105 removed outlier: 4.101A pdb=" N ALA c 102 " --> pdb=" O VAL c 98 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N ASP c 103 " --> pdb=" O GLU c 99 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N VAL c 104 " --> pdb=" O LEU c 100 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N LYS c 105 " --> pdb=" O PHE c 101 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 98 through 105' Processing helix chain 'c' and resid 120 through 125 Processing helix chain 'c' and resid 39 through 44 Processing helix chain 'd' and resid 15 through 20 Processing helix chain 'd' and resid 24 through 40 Processing helix chain 'd' and resid 97 through 116 removed outlier: 3.980A pdb=" N ARG d 114 " --> pdb=" O SER d 110 " (cutoff:3.500A) Processing helix chain 'd' and resid 130 through 142 removed outlier: 4.198A pdb=" N LEU d 134 " --> pdb=" O LYS d 130 " (cutoff:3.500A) Processing helix chain 'd' and resid 154 through 163 removed outlier: 4.365A pdb=" N ASN d 163 " --> pdb=" O LEU d 159 " (cutoff:3.500A) Processing helix chain 'd' and resid 176 through 183 Processing helix chain 'd' and resid 189 through 200 Processing helix chain 'e' and resid 2 through 20 removed outlier: 5.525A pdb=" N VAL e 12 " --> pdb=" O LYS e 8 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LYS e 13 " --> pdb=" O ASP e 9 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N THR e 17 " --> pdb=" O LYS e 13 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLU e 18 " --> pdb=" O LYS e 14 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ASN e 20 " --> pdb=" O MET e 16 " (cutoff:3.500A) Processing helix chain 'e' and resid 41 through 46 removed outlier: 4.092A pdb=" N ASP e 45 " --> pdb=" O GLU e 41 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LYS e 46 " --> pdb=" O ALA e 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 41 through 46' Processing helix chain 'e' and resid 47 through 60 Processing helix chain 'e' and resid 92 through 111 removed outlier: 3.538A pdb=" N TRP e 96 " --> pdb=" O GLY e 92 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ILE e 105 " --> pdb=" O ARG e 101 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N VAL e 107 " --> pdb=" O ILE e 103 " (cutoff:3.500A) Proline residue: e 108 - end of helix removed outlier: 5.551A pdb=" N ARG e 111 " --> pdb=" O VAL e 107 " (cutoff:3.500A) Processing helix chain 'e' and resid 141 through 146 removed outlier: 6.844A pdb=" N VAL e 145 " --> pdb=" O ASP e 141 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N ASP e 146 " --> pdb=" O TYR e 142 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 141 through 146' Processing helix chain 'e' and resid 161 through 173 removed outlier: 4.585A pdb=" N ALA e 167 " --> pdb=" O GLU e 163 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N LEU e 168 " --> pdb=" O GLU e 164 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N PHE e 172 " --> pdb=" O LEU e 168 " (cutoff:3.500A) Processing helix chain 'e' and resid 133 through 138 removed outlier: 3.944A pdb=" N ILE e 136 " --> pdb=" O GLU e 133 " (cutoff:3.500A) Proline residue: e 138 - end of helix Processing helix chain 'f' and resid 1 through 6 removed outlier: 3.600A pdb=" N ALA f 6 " --> pdb=" O ARG f 2 " (cutoff:3.500A) Processing helix chain 'f' and resid 59 through 80 Processing helix chain 'f' and resid 136 through 152 removed outlier: 4.014A pdb=" N ARG f 151 " --> pdb=" O LEU f 147 " (cutoff:3.500A) Processing helix chain 'g' and resid 22 through 28 Processing helix chain 'g' and resid 29 through 34 Processing helix chain 'g' and resid 40 through 50 removed outlier: 4.822A pdb=" N ILE g 44 " --> pdb=" O THR g 40 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU g 45 " --> pdb=" O LYS g 41 " (cutoff:3.500A) Processing helix chain 'g' and resid 95 through 107 removed outlier: 3.746A pdb=" N ILE g 99 " --> pdb=" O GLY g 95 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ASP g 101 " --> pdb=" O ARG g 97 " (cutoff:3.500A) Processing helix chain 'g' and resid 111 through 116 removed outlier: 3.571A pdb=" N VAL g 115 " --> pdb=" O ALA g 111 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N ARG g 116 " --> pdb=" O LYS g 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 111 through 116' Processing helix chain 'h' and resid 3 through 21 Processing helix chain 'h' and resid 33 through 48 removed outlier: 3.898A pdb=" N THR h 39 " --> pdb=" O VAL h 35 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ARG h 42 " --> pdb=" O MET h 38 " (cutoff:3.500A) Processing helix chain 'h' and resid 62 through 71 removed outlier: 3.684A pdb=" N GLY h 66 " --> pdb=" O ARG h 62 " (cutoff:3.500A) Proline residue: h 68 - end of helix removed outlier: 4.737A pdb=" N CYS h 71 " --> pdb=" O THR h 67 " (cutoff:3.500A) Processing helix chain 'h' and resid 72 through 78 removed outlier: 3.635A pdb=" N VAL h 77 " --> pdb=" O ASP h 74 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLY h 78 " --> pdb=" O ALA h 75 " (cutoff:3.500A) Processing helix chain 'i' and resid 23 through 31 removed outlier: 4.293A pdb=" N LEU i 27 " --> pdb=" O VAL i 23 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLN i 30 " --> pdb=" O ALA i 26 " (cutoff:3.500A) Processing helix chain 'i' and resid 33 through 43 removed outlier: 3.641A pdb=" N PHE i 37 " --> pdb=" O ASN i 33 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA i 40 " --> pdb=" O GLU i 36 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ALA i 43 " --> pdb=" O LYS i 39 " (cutoff:3.500A) Processing helix chain 'j' and resid 7 through 12 removed outlier: 5.104A pdb=" N LYS j 12 " --> pdb=" O PRO j 8 " (cutoff:3.500A) Processing helix chain 'j' and resid 25 through 38 removed outlier: 3.773A 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: 4.738A pdb=" N ILE j 101 " --> pdb=" O PRO j 97 " (cutoff:3.500A) removed outlier: 4.737A 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: 3.502A pdb=" N ARG j 120 " --> pdb=" O ARG j 116 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LYS j 121 " --> pdb=" O ALA j 117 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N LEU j 122 " --> pdb=" O MET j 118 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N LYS j 123 " --> pdb=" O PHE j 119 " (cutoff:3.500A) Processing helix chain 'k' and resid 112 through 120 Proline residue: k 120 - end of helix Processing helix chain 'l' and resid 37 through 42 removed outlier: 3.703A pdb=" N ARG l 41 " --> pdb=" O GLY l 37 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N SER l 42 " --> pdb=" O GLN l 38 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 37 through 42' Processing helix chain 'l' and resid 56 through 62 removed outlier: 3.504A pdb=" N LEU l 61 " --> pdb=" O LEU l 57 " (cutoff:3.500A) Proline residue: l 62 - end of helix Processing helix chain 'l' and resid 68 through 75 removed outlier: 4.665A pdb=" N ALA l 72 " --> pdb=" O SER l 68 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ILE l 73 " --> pdb=" O ARG l 69 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N THR l 74 " --> pdb=" O LYS l 70 " (cutoff:3.500A) removed outlier: 5.595A 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 85 removed outlier: 3.572A pdb=" N ALA l 83 " --> pdb=" O LEU l 79 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N LYS l 84 " --> pdb=" O SER l 80 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N VAL l 85 " --> pdb=" O ASP l 81 " (cutoff:3.500A) Processing helix chain 'l' and resid 91 through 99 removed outlier: 4.468A pdb=" N LEU l 95 " --> pdb=" O ASP l 91 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LYS l 96 " --> pdb=" O LEU l 92 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N ALA l 97 " --> pdb=" O ASN l 93 " (cutoff:3.500A) Processing helix chain 'l' and resid 128 through 139 Processing helix chain 'm' and resid 42 through 58 removed outlier: 4.333A pdb=" N ALA m 56 " --> pdb=" O ALA m 52 " (cutoff:3.500A) Processing helix chain 'm' and resid 109 through 125 removed outlier: 3.856A pdb=" N LYS m 123 " --> pdb=" O LEU m 119 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU m 124 " --> pdb=" O ALA m 120 " (cutoff:3.500A) Proline residue: m 125 - end of helix Processing helix chain 'n' and resid 13 through 32 Processing helix chain 'n' and resid 37 through 58 removed outlier: 5.136A pdb=" N ARG n 46 " --> pdb=" O LYS n 42 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N VAL n 47 " --> pdb=" O GLU n 43 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLU n 49 " --> pdb=" O ARG n 45 " (cutoff:3.500A) Proline residue: n 50 - end of helix removed outlier: 4.324A pdb=" N THR n 57 " --> pdb=" O THR n 53 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N ASP n 58 " --> pdb=" O LEU n 54 " (cutoff:3.500A) Processing helix chain 'n' and resid 59 through 71 removed outlier: 4.748A pdb=" N THR n 70 " --> pdb=" O ALA n 66 " (cutoff:3.500A) Processing helix chain 'n' and resid 72 through 82 removed outlier: 4.362A pdb=" N PHE n 80 " --> pdb=" O VAL n 76 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ASN n 81 " --> pdb=" O ALA n 77 " (cutoff:3.500A) Processing helix chain 'n' and resid 83 through 88 Processing helix chain 'o' and resid 2 through 22 removed outlier: 4.248A pdb=" N ARG o 13 " --> pdb=" O ARG o 9 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N ALA o 14 " --> pdb=" O ARG o 10 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N LEU o 21 " --> pdb=" O LYS o 17 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY o 22 " --> pdb=" O LEU o 18 " (cutoff:3.500A) Processing helix chain 'o' and resid 55 through 62 removed outlier: 4.956A pdb=" N GLN o 61 " --> pdb=" O ALA o 57 " (cutoff:3.500A) Processing helix chain 'o' and resid 67 through 86 removed outlier: 4.370A pdb=" N LEU o 83 " --> pdb=" O ALA o 79 " (cutoff:3.500A) Processing helix chain 'o' and resid 101 through 114 removed outlier: 3.756A pdb=" N GLY o 114 " --> pdb=" O ALA o 110 " (cutoff:3.500A) Processing helix chain 'p' and resid 1 through 12 removed outlier: 3.895A pdb=" N GLN p 11 " --> pdb=" O LEU p 7 " (cutoff:3.500A) Processing helix chain 'p' and resid 98 through 103 removed outlier: 4.343A pdb=" N ARG p 102 " --> pdb=" O TYR p 98 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N THR p 103 " --> pdb=" O LEU p 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'p' and resid 98 through 103' Processing helix chain 'q' and resid 5 through 21 removed outlier: 4.034A pdb=" N ALA q 9 " --> pdb=" O ARG q 5 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLN q 19 " --> pdb=" O LYS q 15 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LYS q 21 " --> pdb=" O LEU q 17 " (cutoff:3.500A) Processing helix chain 'q' and resid 24 through 30 removed outlier: 4.640A pdb=" N SER q 28 " --> pdb=" O TYR q 24 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N ARG q 29 " --> pdb=" O GLY q 25 " (cutoff:3.500A) Processing helix chain 'q' and resid 39 through 72 removed outlier: 4.156A pdb=" N ARG q 50 " --> pdb=" O TYR q 46 " (cutoff:3.500A) Processing helix chain 'q' and resid 74 through 86 Processing helix chain 'q' and resid 90 through 101 removed outlier: 3.736A pdb=" N ASP q 96 " --> pdb=" O LYS q 92 " (cutoff:3.500A) Processing helix chain 'q' and resid 102 through 117 Processing helix chain 's' and resid 13 through 25 removed outlier: 4.215A pdb=" N LEU s 23 " --> pdb=" O LEU s 19 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N ILE s 24 " --> pdb=" O VAL s 20 " (cutoff:3.500A) removed outlier: 5.418A 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 Processing helix chain 't' and resid 2 through 11 removed outlier: 4.161A pdb=" N LYS t 9 " --> pdb=" O GLU t 5 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N LEU t 11 " --> pdb=" O LEU t 7 " (cutoff:3.500A) Processing helix chain 't' and resid 17 through 27 Processing helix chain 't' and resid 39 through 50 Processing helix chain 'u' and resid 65 through 70 removed outlier: 3.934A pdb=" N VAL u 69 " --> pdb=" O GLN u 65 " (cutoff:3.500A) removed outlier: 4.820A 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: 4.093A pdb=" N ALA v 23 " --> pdb=" O ARG v 19 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ASN v 24 " --> pdb=" O LEU v 20 " (cutoff:3.500A) Processing helix chain 'v' and resid 43 through 52 removed outlier: 4.062A pdb=" N VAL v 47 " --> pdb=" O ASP v 43 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ALA v 52 " --> pdb=" O MET v 48 " (cutoff:3.500A) Processing helix chain 'v' and resid 53 through 59 removed outlier: 4.060A pdb=" N TYR v 57 " --> pdb=" O LYS v 53 " (cutoff:3.500A) Processing helix chain 'x' and resid 51 through 61 Processing helix chain 'x' and resid 62 through 74 Processing helix chain 'y' and resid 1 through 6 Processing helix chain 'y' and resid 9 through 35 removed outlier: 3.716A pdb=" N GLU y 24 " --> pdb=" O ASN y 20 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N GLN y 25 " --> pdb=" O LEU y 21 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N PHE y 26 " --> pdb=" O LEU y 22 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ASN y 27 " --> pdb=" O ARG y 23 " (cutoff:3.500A) Processing helix chain 'y' and resid 39 through 63 removed outlier: 4.366A pdb=" N LEU y 43 " --> pdb=" O GLN y 39 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU y 59 " --> pdb=" O THR y 55 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N GLY y 62 " --> pdb=" O ASN y 58 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ALA y 63 " --> pdb=" O GLU y 59 " (cutoff:3.500A) Processing helix chain 'z' and resid 16 through 27 Processing helix chain 'z' and resid 40 through 51 removed outlier: 3.587A pdb=" N GLY z 45 " --> pdb=" O PRO z 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 52 removed outlier: 4.480A pdb=" N GLN A 48 " --> pdb=" O PHE A 44 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ALA A 52 " --> pdb=" O GLN A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 65 removed outlier: 5.470A pdb=" N ARG A 59 " --> pdb=" O GLY A 55 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG A 63 " --> pdb=" O ARG A 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 18 removed outlier: 4.797A pdb=" N HIS B 18 " --> pdb=" O MET B 14 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 16 Processing helix chain 'D' and resid 17 through 24 removed outlier: 4.416A pdb=" N THR D 24 " --> pdb=" O ALA D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 25 through 38 Processing helix chain 'E' and resid 6 through 14 removed outlier: 3.762A pdb=" N LYS E 11 " --> pdb=" O ARG E 7 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ARG E 12 " --> pdb=" O GLY E 8 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N LYS E 14 " --> pdb=" O ALA E 10 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 45 removed outlier: 3.712A pdb=" N ARG E 44 " --> pdb=" O LYS E 40 " (cutoff:3.500A) Proline residue: E 45 - end of helix Processing helix chain 'E' and resid 50 through 62 removed outlier: 5.071A pdb=" N GLY E 55 " --> pdb=" O LYS E 51 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LEU E 56 " --> pdb=" O GLY E 52 " (cutoff:3.500A) Proline residue: E 62 - end of helix Processing helix chain 'G' and resid 41 through 63 Proline residue: G 47 - end of helix removed outlier: 3.571A pdb=" N ARG G 62 " --> pdb=" O LYS G 58 " (cutoff:3.500A) Processing helix chain 'G' and resid 72 through 87 removed outlier: 4.094A pdb=" N SER G 76 " --> pdb=" O LYS G 72 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N GLU G 77 " --> pdb=" O ARG G 73 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N ALA G 78 " --> pdb=" O ALA G 74 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N CYS G 86 " --> pdb=" O ALA G 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 102 through 122 removed outlier: 3.790A pdb=" N VAL G 106 " --> pdb=" O ASN G 102 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N GLN G 108 " --> pdb=" O LYS G 104 " (cutoff:3.500A) Processing helix chain 'G' and resid 129 through 148 Processing helix chain 'G' and resid 164 through 169 Processing helix chain 'G' and resid 170 through 179 removed outlier: 4.777A pdb=" N GLY G 179 " --> pdb=" O ALA G 175 " (cutoff:3.500A) Processing helix chain 'G' and resid 191 through 196 removed outlier: 4.565A pdb=" N VAL G 195 " --> pdb=" O ASP G 191 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N ASP G 196 " --> pdb=" O PRO G 192 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 191 through 196' Processing helix chain 'G' and resid 205 through 225 removed outlier: 3.550A pdb=" N VAL G 220 " --> pdb=" O VAL G 216 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG G 221 " --> pdb=" O ALA G 217 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N SER G 225 " --> pdb=" O ARG G 221 " (cutoff:3.500A) Processing helix chain 'H' and resid 5 through 12 removed outlier: 3.971A pdb=" N ARG H 10 " --> pdb=" O PRO H 6 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N GLY H 12 " --> pdb=" O GLY H 8 " (cutoff:3.500A) Processing helix chain 'H' and resid 27 through 46 Processing helix chain 'H' and resid 71 through 77 Processing helix chain 'H' and resid 80 through 95 removed outlier: 3.503A pdb=" N ASP H 92 " --> pdb=" O LYS H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 126 removed outlier: 3.917A pdb=" N ARG H 125 " --> pdb=" O SER H 121 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ARG H 126 " --> pdb=" O GLN H 122 " (cutoff:3.500A) Processing helix chain 'H' and resid 128 through 144 Processing helix chain 'I' and resid 6 through 15 removed outlier: 4.239A pdb=" N LEU I 10 " --> pdb=" O PRO I 6 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N SER I 11 " --> pdb=" O LYS I 7 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 63 Processing helix chain 'I' and resid 67 through 82 removed outlier: 3.507A pdb=" N ASN I 73 " --> pdb=" O ARG I 69 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N LYS I 82 " --> pdb=" O ALA I 78 " (cutoff:3.500A) Processing helix chain 'I' and resid 84 through 96 removed outlier: 3.747A pdb=" N LEU I 90 " --> pdb=" O GLY I 86 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ARG I 96 " --> pdb=" O LEU I 92 " (cutoff:3.500A) Processing helix chain 'I' and resid 97 through 105 Processing helix chain 'I' and resid 109 through 120 removed outlier: 3.832A pdb=" N HIS I 119 " --> pdb=" O GLN I 115 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N LYS I 120 " --> pdb=" O LEU I 116 " (cutoff:3.500A) Processing helix chain 'I' and resid 152 through 165 removed outlier: 5.323A pdb=" N ALA I 156 " --> pdb=" O SER I 152 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA I 161 " --> pdb=" O ALA I 157 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N GLU I 165 " --> pdb=" O ALA I 161 " (cutoff:3.500A) Processing helix chain 'I' and resid 186 through 191 removed outlier: 5.325A pdb=" N SER I 191 " --> pdb=" O ARG I 187 " (cutoff:3.500A) Processing helix chain 'I' and resid 195 through 205 removed outlier: 4.405A pdb=" N ILE I 199 " --> pdb=" O ASN I 195 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS I 205 " --> pdb=" O GLU I 201 " (cutoff:3.500A) Processing helix chain 'J' and resid 54 through 70 removed outlier: 3.510A pdb=" N ILE J 59 " --> pdb=" O VAL J 55 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLU J 64 " --> pdb=" O GLN J 60 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N LYS J 65 " --> pdb=" O LYS J 61 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N MET J 70 " --> pdb=" O ALA J 66 " (cutoff:3.500A) Processing helix chain 'J' and resid 108 through 118 removed outlier: 5.541A pdb=" N ALA J 112 " --> pdb=" O GLY J 108 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N VAL J 116 " --> pdb=" O ALA J 112 " (cutoff:3.500A) Processing helix chain 'J' and resid 131 through 147 removed outlier: 5.724A pdb=" N ASN J 147 " --> pdb=" O LEU J 143 " (cutoff:3.500A) Processing helix chain 'J' and resid 148 through 156 removed outlier: 3.815A pdb=" N ALA J 154 " --> pdb=" O GLU J 150 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N LYS J 155 " --> pdb=" O MET J 151 " (cutoff:3.500A) Processing helix chain 'J' and resid 159 through 165 Processing helix chain 'K' and resid 12 through 18 removed outlier: 3.697A pdb=" N GLU K 16 " --> pdb=" O PRO K 12 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLN K 17 " --> pdb=" O ASP K 13 " (cutoff:3.500A) Processing helix chain 'K' and resid 19 through 30 Processing helix chain 'K' and resid 67 through 81 removed outlier: 3.566A pdb=" N PHE K 78 " --> pdb=" O LEU K 74 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASN K 81 " --> pdb=" O THR K 77 " (cutoff:3.500A) Processing helix chain 'L' and resid 19 through 30 removed outlier: 3.629A pdb=" N LEU L 29 " --> pdb=" O PHE L 25 " (cutoff:3.500A) Processing helix chain 'L' and resid 34 through 54 Processing helix chain 'L' and resid 56 through 69 removed outlier: 4.628A pdb=" N ALA L 64 " --> pdb=" O ALA L 60 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ASN L 67 " --> pdb=" O VAL L 63 " (cutoff:3.500A) Processing helix chain 'L' and resid 91 through 110 removed outlier: 4.767A pdb=" N ALA L 97 " --> pdb=" O VAL L 93 " (cutoff:3.500A) Processing helix chain 'L' and resid 114 through 129 Processing helix chain 'L' and resid 131 through 149 removed outlier: 4.004A pdb=" N GLU L 145 " --> pdb=" O HIS L 141 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASN L 147 " --> pdb=" O MET L 143 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LYS L 148 " --> pdb=" O ALA L 144 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N ALA L 149 " --> pdb=" O GLU L 145 " (cutoff:3.500A) Processing helix chain 'M' and resid 4 through 20 removed outlier: 3.526A pdb=" N ASP M 8 " --> pdb=" O ASP M 4 " (cutoff:3.500A) Processing helix chain 'M' and resid 29 through 43 Processing helix chain 'M' and resid 111 through 119 Processing helix chain 'N' and resid 33 through 38 Processing helix chain 'N' and resid 48 through 55 removed outlier: 4.064A pdb=" N LEU N 53 " --> pdb=" O GLN N 49 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL N 54 " --> pdb=" O PRO N 50 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N ASP N 55 " --> pdb=" O LEU N 51 " (cutoff:3.500A) Processing helix chain 'N' and resid 70 through 87 removed outlier: 4.843A pdb=" N MET N 87 " --> pdb=" O THR N 83 " (cutoff:3.500A) Processing helix chain 'N' and resid 90 through 101 removed outlier: 5.610A pdb=" N GLU N 96 " --> pdb=" O SER N 92 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA N 100 " --> pdb=" O GLU N 96 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLY N 101 " --> pdb=" O LEU N 97 " (cutoff:3.500A) Processing helix chain 'O' and resid 14 through 32 removed outlier: 3.641A pdb=" N THR O 32 " --> pdb=" O THR O 28 " (cutoff:3.500A) Processing helix chain 'O' and resid 81 through 90 removed outlier: 6.793A pdb=" N ASP O 85 " --> pdb=" O GLU O 81 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N ALA O 86 " --> pdb=" O LYS O 82 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N MET O 88 " --> pdb=" O VAL O 84 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N ARG O 89 " --> pdb=" O ASP O 85 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N LEU O 90 " --> pdb=" O ALA O 86 " (cutoff:3.500A) Processing helix chain 'P' and resid 45 through 50 removed outlier: 4.459A pdb=" N GLY P 50 " --> pdb=" O ALA P 46 " (cutoff:3.500A) Processing helix chain 'P' and resid 58 through 77 removed outlier: 4.237A pdb=" N ALA P 72 " --> pdb=" O ARG P 68 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N VAL P 73 " --> pdb=" O CYS P 69 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N LYS P 74 " --> pdb=" O ALA P 70 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N GLU P 75 " --> pdb=" O ASP P 71 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N TYR P 76 " --> pdb=" O ALA P 72 " (cutoff:3.500A) Processing helix chain 'P' and resid 91 through 103 removed outlier: 4.412A pdb=" N ILE P 96 " --> pdb=" O ARG P 92 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ARG P 97 " --> pdb=" O GLU P 93 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA P 98 " --> pdb=" O SER P 94 " (cutoff:3.500A) Processing helix chain 'Q' and resid 2 through 9 Processing helix chain 'Q' and resid 21 through 26 removed outlier: 6.992A pdb=" N ALA Q 25 " --> pdb=" O PRO Q 21 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N CYS Q 26 " --> pdb=" O ALA Q 22 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 21 through 26' Processing helix chain 'R' and resid 13 through 21 removed outlier: 3.524A pdb=" N SER R 20 " --> pdb=" O ILE R 16 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N ILE R 21 " --> pdb=" O ALA R 17 " (cutoff:3.500A) Processing helix chain 'R' and resid 25 through 37 Processing helix chain 'R' and resid 43 through 48 removed outlier: 5.880A pdb=" N SER R 48 " --> pdb=" O ILE R 44 " (cutoff:3.500A) Processing helix chain 'R' and resid 49 through 63 removed outlier: 3.702A pdb=" N LYS R 61 " --> pdb=" O ASP R 57 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N PHE R 62 " --> pdb=" O GLU R 58 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N VAL R 63 " --> pdb=" O VAL R 59 " (cutoff:3.500A) Processing helix chain 'R' and resid 65 through 83 Processing helix chain 'R' and resid 84 through 93 Processing helix chain 'R' and resid 105 through 110 Processing helix chain 'S' and resid 2 through 22 removed outlier: 3.558A pdb=" N ALA S 16 " --> pdb=" O ARG S 12 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS S 18 " --> pdb=" O ALA S 14 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N PHE S 20 " --> pdb=" O ALA S 16 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N ALA S 21 " --> pdb=" O ASP S 17 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LYS S 22 " --> pdb=" O LYS S 18 " (cutoff:3.500A) Processing helix chain 'S' and resid 24 through 29 Processing helix chain 'S' and resid 37 through 51 removed outlier: 3.889A pdb=" N TRP S 41 " --> pdb=" O ASP S 37 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N GLN S 48 " --> pdb=" O VAL S 44 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N THR S 49 " --> pdb=" O LEU S 45 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LEU S 50 " --> pdb=" O LYS S 46 " (cutoff:3.500A) Proline residue: S 51 - end of helix Processing helix chain 'S' and resid 79 through 90 Processing helix chain 'T' and resid 3 through 15 removed outlier: 3.772A pdb=" N SER T 12 " --> pdb=" O ALA T 8 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLU T 13 " --> pdb=" O LYS T 9 " (cutoff:3.500A) Processing helix chain 'T' and resid 23 through 46 removed outlier: 4.431A pdb=" N GLY T 40 " --> pdb=" O ASN T 36 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N HIS T 41 " --> pdb=" O HIS T 37 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N HIS T 45 " --> pdb=" O HIS T 41 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS T 46 " --> pdb=" O PHE T 42 " (cutoff:3.500A) Processing helix chain 'T' and resid 48 through 73 Processing helix chain 'T' and resid 74 through 85 Processing helix chain 'U' and resid 53 through 64 removed outlier: 3.836A pdb=" N GLN U 63 " --> pdb=" O HIS U 59 " (cutoff:3.500A) Processing helix chain 'U' and resid 68 through 79 Processing helix chain 'W' and resid 12 through 17 Processing helix chain 'W' and resid 24 through 32 removed outlier: 3.794A pdb=" N ASN W 30 " --> pdb=" O ALA W 26 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N TYR W 31 " --> pdb=" O THR W 27 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ILE W 32 " --> pdb=" O LEU W 28 " (cutoff:3.500A) Processing helix chain 'W' and resid 40 through 45 Processing helix chain 'W' and resid 47 through 65 Processing helix chain 'X' and resid 11 through 25 Processing helix chain 'X' and resid 69 through 75 removed outlier: 4.805A pdb=" N PHE X 73 " --> pdb=" O LYS X 69 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ALA X 74 " --> pdb=" O LEU X 70 " (cutoff:3.500A) Proline residue: X 75 - end of helix No H-bonds generated for 'chain 'X' and resid 69 through 75' Processing helix chain 'Y' and resid 5 through 41 removed outlier: 5.098A pdb=" N ARG Y 9 " --> pdb=" O SER Y 5 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N ALA Y 10 " --> pdb=" O ALA Y 6 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ILE Y 11 " --> pdb=" O LYS Y 7 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA Y 40 " --> pdb=" O ALA Y 36 " (cutoff:3.500A) Processing helix chain 'Y' and resid 43 through 64 Proline residue: Y 55 - end of helix Processing helix chain 'Y' and resid 67 through 86 removed outlier: 6.147A pdb=" N ALA Y 71 " --> pdb=" O HIS Y 67 " (cutoff:3.500A) Processing helix chain 'Z' and resid 17 through 23 removed outlier: 3.573A pdb=" N CYS Z 22 " --> pdb=" O PHE Z 18 " (cutoff:3.500A) Processing helix chain 'Z' and resid 24 through 33 removed outlier: 5.619A pdb=" N ARG Z 33 " --> pdb=" O ALA Z 29 " (cutoff:3.500A) Processing helix chain 'Z' and resid 38 through 61 removed outlier: 3.501A pdb=" N LYS Z 53 " --> pdb=" O ALA Z 49 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS Z 58 " --> pdb=" O ARG Z 54 " (cutoff:3.500A) Processing helix chain 'a' and resid 6 through 16 removed outlier: 3.633A pdb=" N ARG a 12 " --> pdb=" O MET a 8 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N LYS a 14 " --> pdb=" O VAL a 10 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ASP a 16 " --> pdb=" O ARG a 12 " (cutoff:3.500A) Processing helix chain 'a' and resid 23 through 34 removed outlier: 3.613A pdb=" N ALA a 28 " --> pdb=" O ASN a 24 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLU a 32 " --> pdb=" O ALA a 28 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N LEU a 33 " --> pdb=" O LEU a 29 " (cutoff:3.500A) Processing helix chain 'a' and resid 181 through 200 removed outlier: 3.698A pdb=" N LEU a 196 " --> pdb=" O LEU a 192 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'b' and resid 1 through 4 Processing sheet with id= 2, first strand: chain 'b' and resid 32 through 35 No H-bonds generated for sheet with id= 2 Processing sheet with id= 3, first strand: chain 'b' and resid 79 through 82 removed outlier: 6.853A pdb=" N LEU b 92 " --> pdb=" O GLU b 78 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N ILE b 73 " --> pdb=" O SER b 117 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N SER b 117 " --> pdb=" O ILE b 73 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ASP b 113 " --> pdb=" O VAL b 77 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'b' and resid 137 through 141 removed outlier: 4.503A pdb=" N SER b 138 " --> pdb=" O ILE b 163 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N GLU b 179 " --> pdb=" O LEU b 175 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'b' and resid 90 through 95 removed outlier: 4.360A pdb=" N GLU b 99 " --> pdb=" O TYR b 95 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'c' and resid 11 through 16 removed outlier: 4.252A pdb=" N VAL c 20 " --> pdb=" O THR c 16 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N VAL c 26 " --> pdb=" O VAL c 9 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER c 199 " --> pdb=" O LYS c 8 " (cutoff:3.500A) removed outlier: 13.573A pdb=" N GLY c 198 " --> pdb=" O LYS c 114 " (cutoff:3.500A) removed outlier: 10.787A pdb=" N LYS c 114 " --> pdb=" O GLY c 198 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N ASP c 200 " --> pdb=" O THR c 112 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N THR c 112 " --> pdb=" O ASP c 200 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N GLU c 168 " --> pdb=" O SER c 113 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'c' and resid 79 through 83 removed outlier: 6.446A pdb=" N GLN c 49 " --> pdb=" O THR c 35 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N GLN c 94 " --> pdb=" O VAL c 34 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'c' and resid 179 through 182 removed outlier: 3.569A pdb=" N ARG c 179 " --> pdb=" O LEU c 188 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'c' and resid 24 through 28 No H-bonds generated for sheet with id= 9 Processing sheet with id= 10, first strand: chain 'd' and resid 2 through 5 removed outlier: 4.925A pdb=" N LEU d 5 " --> pdb=" O SER d 10 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N SER d 10 " --> pdb=" O LEU d 5 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'd' and resid 117 through 120 removed outlier: 5.842A pdb=" N ARG d 117 " --> pdb=" O ASP d 184 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASP d 168 " --> pdb=" O VAL d 146 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'e' and resid 32 through 38 removed outlier: 3.535A pdb=" N GLY e 85 " --> pdb=" O THR e 67 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'e' and resid 126 through 132 Processing sheet with id= 14, first strand: chain 'f' and resid 15 through 18 removed outlier: 3.511A pdb=" N THR f 24 " --> pdb=" O LYS f 17 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'f' and resid 40 through 44 Processing sheet with id= 16, first strand: chain 'f' and resid 94 through 97 removed outlier: 6.770A pdb=" N ASN f 100 " --> pdb=" O LEU f 116 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'f' and resid 120 through 124 removed outlier: 5.546A pdb=" N THR f 128 " --> pdb=" O LEU f 88 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'g' and resid 15 through 20 No H-bonds generated for sheet with id= 18 Processing sheet with id= 19, first strand: chain 'g' and resid 78 through 83 removed outlier: 3.776A pdb=" N GLU g 149 " --> pdb=" O SER g 82 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'i' and resid 6 through 12 removed outlier: 3.759A pdb=" N VAL i 57 " --> pdb=" O VAL i 69 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL i 69 " --> pdb=" O VAL i 57 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N SER i 65 " --> pdb=" O TYR i 61 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'j' and resid 52 through 57 removed outlier: 5.717A pdb=" N ASP j 19 " --> pdb=" O LEU j 140 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'j' and resid 74 through 77 Processing sheet with id= 23, first strand: chain 'k' and resid 18 through 21 removed outlier: 3.895A pdb=" N THR k 6 " --> pdb=" O CYS k 21 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ASN k 82 " --> pdb=" O MET k 7 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'k' and resid 38 through 42 Processing sheet with id= 25, first strand: chain 'k' and resid 68 through 71 removed outlier: 3.863A pdb=" N SER k 75 " --> pdb=" O ARG k 71 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'm' and resid 62 through 66 removed outlier: 6.499A pdb=" N LEU m 102 " --> pdb=" O ARG m 66 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N TYR m 103 " --> pdb=" O LEU m 33 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N SER m 30 " --> pdb=" O LYS m 133 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N LYS m 127 " --> pdb=" O VAL m 36 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'm' and resid 71 through 74 Processing sheet with id= 28, first strand: chain 'n' and resid 33 through 36 removed outlier: 4.879A pdb=" N MET n 110 " --> pdb=" O CYS n 100 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'o' and resid 49 through 53 removed outlier: 6.842A pdb=" N ILE o 35 " --> pdb=" O THR o 53 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N HIS o 34 " --> pdb=" O THR o 31 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N VAL o 28 " --> pdb=" O ASP o 93 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'p' and resid 37 through 44 removed outlier: 6.401A pdb=" N THR p 24 " --> pdb=" O LYS p 86 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'p' and resid 48 through 52 removed outlier: 3.986A pdb=" N ALA p 48 " --> pdb=" O THR p 59 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N ARG p 52 " --> pdb=" O HIS p 55 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'r' and resid 2 through 6 removed outlier: 3.617A pdb=" N PHE r 5 " --> pdb=" O HIS r 12 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'r' and resid 18 through 23 removed outlier: 4.901A pdb=" N GLN r 18 " --> pdb=" O ILE r 98 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N GLN r 91 " --> pdb=" O ARG r 68 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N ARG r 68 " --> pdb=" O GLN r 91 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N PHE r 93 " --> pdb=" O HIS r 66 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N HIS r 66 " --> pdb=" O PHE r 93 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ASP r 95 " --> pdb=" O VAL r 64 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N LYS r 60 " --> pdb=" O THR r 99 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N GLU r 31 " --> pdb=" O VAL r 63 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'r' and resid 71 through 77 Processing sheet with id= 35, first strand: chain 's' and resid 3 through 8 removed outlier: 4.789A pdb=" N THR s 3 " --> pdb=" O VAL s 107 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N ARG s 99 " --> pdb=" O SER s 12 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER s 12 " --> pdb=" O ARG s 99 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 's' and resid 73 through 79 removed outlier: 5.419A pdb=" N THR s 100 " --> pdb=" O GLY s 79 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 's' and resid 80 through 88 Processing sheet with id= 38, first strand: chain 't' and resid 12 through 15 removed outlier: 5.046A pdb=" N ALA t 13 " --> pdb=" O LYS t 33 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N VAL t 31 " --> pdb=" O HIS t 15 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LYS t 81 " --> pdb=" O VAL t 34 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N LYS t 66 " --> pdb=" O ARG t 77 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ASP t 79 " --> pdb=" O LYS t 64 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N LYS t 64 " --> pdb=" O ASP t 79 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N LYS t 81 " --> pdb=" O VAL t 62 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VAL t 62 " --> pdb=" O LYS t 81 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ALA t 83 " --> pdb=" O THR t 60 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N THR t 60 " --> pdb=" O ALA t 83 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N VAL t 85 " --> pdb=" O VAL t 58 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N VAL t 58 " --> pdb=" O VAL t 85 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'u' and resid 39 through 44 removed outlier: 4.587A pdb=" N ASN u 39 " --> pdb=" O ALA u 62 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'u' and resid 82 through 86 Processing sheet with id= 41, first strand: chain 'v' and resid 2 through 5 Processing sheet with id= 42, first strand: chain 'v' and resid 37 through 41 removed outlier: 3.794A pdb=" N ILE v 89 " --> pdb=" O PRO v 27 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'w' and resid 47 through 50 removed outlier: 4.010A pdb=" N THR w 54 " --> pdb=" O GLY w 50 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'w' and resid 62 through 67 removed outlier: 3.528A pdb=" N GLU w 79 " --> pdb=" O LYS w 62 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'x' and resid 11 through 18 removed outlier: 4.356A pdb=" N SER x 18 " --> pdb=" O ASN x 22 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N ASN x 22 " --> pdb=" O SER x 18 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'x' and resid 34 through 40 Processing sheet with id= 47, first strand: chain 'z' and resid 32 through 38 removed outlier: 4.017A pdb=" N HIS z 33 " --> pdb=" O GLN z 8 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N LYS z 5 " --> pdb=" O GLU z 57 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N MET z 53 " --> pdb=" O THR z 9 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'A' and resid 11 through 15 Processing sheet with id= 49, first strand: chain 'B' and resid 28 through 31 removed outlier: 4.018A pdb=" N GLU B 35 " --> pdb=" O ASP B 30 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'C' and resid 19 through 23 removed outlier: 7.001A pdb=" N ILE C 47 " --> pdb=" O SER C 13 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N LEU C 35 " --> pdb=" O TYR C 48 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU C 50 " --> pdb=" O LEU C 33 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N LEU C 33 " --> pdb=" O GLU C 50 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'E' and resid 21 through 24 removed outlier: 6.175A pdb=" N PHE E 21 " --> pdb=" O VAL E 49 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'F' and resid 13 through 18 removed outlier: 8.338A pdb=" N ASN F 13 " --> pdb=" O SER F 28 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'G' and resid 30 through 33 removed outlier: 3.856A pdb=" N VAL G 37 " --> pdb=" O ALA G 33 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'G' and resid 88 through 91 Processing sheet with id= 55, first strand: chain 'H' and resid 52 through 58 Processing sheet with id= 56, first strand: chain 'H' and resid 162 through 169 removed outlier: 4.045A pdb=" N ILE H 206 " --> pdb=" O ARG H 178 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N ARG H 178 " --> pdb=" O ILE H 206 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'I' and resid 139 through 144 removed outlier: 4.004A pdb=" N VAL I 142 " --> pdb=" O GLY I 179 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N MET I 177 " --> pdb=" O ILE I 144 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N GLU I 178 " --> pdb=" O ASP I 173 " (cutoff:3.500A) removed outlier: 8.978A pdb=" N TRP I 169 " --> pdb=" O LYS I 182 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'J' and resid 10 through 15 removed outlier: 3.805A pdb=" N GLN J 11 " --> pdb=" O GLY J 39 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N LEU J 35 " --> pdb=" O ILE J 15 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'J' and resid 82 through 87 removed outlier: 6.699A pdb=" N HIS J 82 " --> pdb=" O PRO J 97 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N VAL J 93 " --> pdb=" O GLY J 86 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N TYR J 127 " --> pdb=" O ARG J 92 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'J' and resid 31 through 40 removed outlier: 4.522A pdb=" N GLY J 50 " --> pdb=" O ALA J 34 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ARG J 44 " --> pdb=" O ASP J 40 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'K' and resid 38 through 42 removed outlier: 3.738A pdb=" N ARG K 38 " --> pdb=" O ASN K 63 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ASN K 63 " --> pdb=" O ARG K 38 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLU K 40 " --> pdb=" O LEU K 61 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LEU K 61 " --> pdb=" O GLU K 40 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N TYR K 59 " --> pdb=" O TRP K 42 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ILE K 6 " --> pdb=" O MET K 62 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N HIS K 3 " --> pdb=" O THR K 92 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N GLU K 5 " --> pdb=" O MET K 90 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N MET K 90 " --> pdb=" O GLU K 5 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N MET K 9 " --> pdb=" O ARG K 86 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N ARG K 86 " --> pdb=" O MET K 9 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'L' and resid 71 through 76 removed outlier: 6.170A pdb=" N THR L 71 " --> pdb=" O VAL L 90 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'M' and resid 22 through 28 removed outlier: 7.114A pdb=" N ALA M 22 " --> pdb=" O LEU M 62 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N THR M 61 " --> pdb=" O ASP M 47 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N ASP M 47 " --> pdb=" O THR M 61 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'M' and resid 102 through 105 removed outlier: 6.578A pdb=" N VAL M 102 " --> pdb=" O ILE M 125 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'N' and resid 4 through 10 removed outlier: 3.962A pdb=" N GLY N 9 " --> pdb=" O ALA N 16 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'O' and resid 44 through 52 removed outlier: 3.861A pdb=" N GLU O 47 " --> pdb=" O ILE O 67 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N ILE O 8 " --> pdb=" O VAL O 74 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'P' and resid 41 through 44 removed outlier: 7.335A pdb=" N VAL P 83 " --> pdb=" O THR P 107 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'Q' and resid 28 through 33 removed outlier: 4.430A pdb=" N CYS Q 33 " --> pdb=" O SER Q 77 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N SER Q 77 " --> pdb=" O CYS Q 33 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N LEU Q 80 " --> pdb=" O VAL Q 97 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'Q' and resid 36 through 40 removed outlier: 3.504A pdb=" N TYR Q 37 " --> pdb=" O VAL Q 51 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N LYS Q 50 " --> pdb=" O ILE Q 66 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N PHE Q 60 " --> pdb=" O LEU Q 56 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'U' and resid 3 through 10 removed outlier: 3.986A pdb=" N VAL U 19 " --> pdb=" O GLY U 37 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N GLY U 37 " --> pdb=" O VAL U 19 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N GLY U 49 " --> pdb=" O ASN U 40 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'V' and resid 6 through 9 removed outlier: 3.601A pdb=" N GLY V 9 " --> pdb=" O VAL V 58 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N GLU V 59 " --> pdb=" O VAL V 75 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'V' and resid 19 through 27 No H-bonds generated for sheet with id= 72 Processing sheet with id= 73, first strand: chain 'X' and resid 29 through 33 removed outlier: 4.857A pdb=" N LEU X 30 " --> pdb=" O THR X 47 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ILE X 48 " --> pdb=" O VAL X 59 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain 'a' and resid 59 through 64 removed outlier: 7.680A pdb=" N VAL a 59 " --> pdb=" O ASN a 165 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ASN a 165 " --> pdb=" O VAL a 59 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TYR a 163 " --> pdb=" O GLY a 61 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain 'a' and resid 170 through 174 removed outlier: 3.623A pdb=" N THR a 173 " --> pdb=" O VAL a 44 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N LYS a 211 " --> pdb=" O ASN a 47 " (cutoff:3.500A) 1822 hydrogen bonds defined for protein. 5367 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3729 hydrogen bonds 6022 hydrogen bond angles 0 basepair planarities 1485 basepair parallelities 2355 stacking parallelities Total time for adding SS restraints: 238.42 Time building geometry restraints manager: 72.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 11641 1.28 - 1.42: 57812 1.42 - 1.56: 83191 1.56 - 1.70: 9780 1.70 - 1.84: 276 Bond restraints: 162700 Sorted by residual: bond pdb=" C ASP K 13 " pdb=" O ASP K 13 " ideal model delta sigma weight residual 1.236 1.469 -0.232 1.25e-02 6.40e+03 3.46e+02 bond pdb=" N GLN K 17 " pdb=" CA GLN K 17 " ideal model delta sigma weight residual 1.457 1.647 -0.190 1.16e-02 7.43e+03 2.68e+02 bond pdb=" C LEU m 119 " pdb=" O LEU m 119 " ideal model delta sigma weight residual 1.237 1.428 -0.191 1.17e-02 7.31e+03 2.66e+02 bond pdb=" C ARG j 27 " pdb=" O ARG j 27 " ideal model delta sigma weight residual 1.236 1.427 -0.191 1.18e-02 7.18e+03 2.63e+02 bond pdb=" C ILE G 59 " pdb=" O ILE G 59 " ideal model delta sigma weight residual 1.237 1.430 -0.193 1.19e-02 7.06e+03 2.63e+02 ... (remaining 162695 not shown) Histogram of bond angle deviations from ideal: 98.92 - 106.23: 28682 106.23 - 113.54: 96303 113.54 - 120.85: 69658 120.85 - 128.16: 40641 128.16 - 135.48: 8224 Bond angle restraints: 243508 Sorted by residual: angle pdb=" C PRO K 50 " pdb=" N ILE K 51 " pdb=" CA ILE K 51 " ideal model delta sigma weight residual 122.96 110.89 12.07 9.50e-01 1.11e+00 1.61e+02 angle pdb=" O GLY c 144 " pdb=" C GLY c 144 " pdb=" N SER c 145 " ideal model delta sigma weight residual 123.52 114.47 9.05 7.40e-01 1.83e+00 1.50e+02 angle pdb=" C VAL I 154 " pdb=" N LYS I 155 " pdb=" CA LYS I 155 " ideal model delta sigma weight residual 120.65 104.65 16.00 1.32e+00 5.74e-01 1.47e+02 angle pdb=" C PHE k 112 " pdb=" N MET k 113 " pdb=" CA MET k 113 " ideal model delta sigma weight residual 120.28 104.35 15.93 1.34e+00 5.57e-01 1.41e+02 angle pdb=" C ALA g 52 " pdb=" N GLU g 53 " pdb=" CA GLU g 53 " ideal model delta sigma weight residual 121.70 100.87 20.83 1.80e+00 3.09e-01 1.34e+02 ... (remaining 243503 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.67: 92744 35.67 - 71.34: 10303 71.34 - 107.02: 1232 107.02 - 142.69: 17 142.69 - 178.36: 20 Dihedral angle restraints: 104316 sinusoidal: 87386 harmonic: 16930 Sorted by residual: dihedral pdb=" C4' U 11130 " pdb=" C3' U 11130 " pdb=" C2' U 11130 " pdb=" C1' U 11130 " ideal model delta sinusoidal sigma weight residual -35.00 34.25 -69.25 1 8.00e+00 1.56e-02 9.68e+01 dihedral pdb=" C5' U 11130 " pdb=" C4' U 11130 " pdb=" C3' U 11130 " pdb=" O3' U 11130 " ideal model delta sinusoidal sigma weight residual 147.00 78.60 68.40 1 8.00e+00 1.56e-02 9.48e+01 dihedral pdb=" O4' C 11730 " pdb=" C1' C 11730 " pdb=" N1 C 11730 " pdb=" C2 C 11730 " ideal model delta sinusoidal sigma weight residual 200.00 34.66 165.34 1 1.50e+01 4.44e-03 8.39e+01 ... (remaining 104313 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.147: 28524 0.147 - 0.293: 2470 0.293 - 0.440: 137 0.440 - 0.587: 13 0.587 - 0.733: 2 Chirality restraints: 31146 Sorted by residual: chirality pdb=" C1' U 2 1 " pdb=" O4' U 2 1 " pdb=" C2' U 2 1 " pdb=" N1 U 2 1 " both_signs ideal model delta sigma weight residual False 2.47 1.73 0.73 2.00e-01 2.50e+01 1.34e+01 chirality pdb=" CA ILE K 51 " pdb=" N ILE K 51 " pdb=" C ILE K 51 " pdb=" CB ILE K 51 " both_signs ideal model delta sigma weight residual False 2.43 3.07 -0.64 2.00e-01 2.50e+01 1.03e+01 chirality pdb=" P C 7 1 " pdb=" OP1 C 7 1 " pdb=" OP2 C 7 1 " pdb=" O5' C 7 1 " both_signs ideal model delta sigma weight residual True 2.41 -2.99 -0.58 2.00e-01 2.50e+01 8.54e+00 ... (remaining 31143 not shown) Planarity restraints: 12986 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' U 2 1 " 0.489 2.00e-02 2.50e+03 2.86e-01 1.84e+03 pdb=" N1 U 2 1 " -0.011 2.00e-02 2.50e+03 pdb=" C2 U 2 1 " -0.088 2.00e-02 2.50e+03 pdb=" O2 U 2 1 " -0.159 2.00e-02 2.50e+03 pdb=" N3 U 2 1 " -0.103 2.00e-02 2.50e+03 pdb=" C4 U 2 1 " -0.103 2.00e-02 2.50e+03 pdb=" O4 U 2 1 " 0.534 2.00e-02 2.50e+03 pdb=" C5 U 2 1 " -0.304 2.00e-02 2.50e+03 pdb=" C6 U 2 1 " -0.255 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A 2 119 " 0.447 2.00e-02 2.50e+03 1.95e-01 1.05e+03 pdb=" N9 A 2 119 " -0.024 2.00e-02 2.50e+03 pdb=" C8 A 2 119 " -0.182 2.00e-02 2.50e+03 pdb=" N7 A 2 119 " -0.164 2.00e-02 2.50e+03 pdb=" C5 A 2 119 " -0.089 2.00e-02 2.50e+03 pdb=" C6 A 2 119 " 0.065 2.00e-02 2.50e+03 pdb=" N6 A 2 119 " 0.306 2.00e-02 2.50e+03 pdb=" N1 A 2 119 " 0.025 2.00e-02 2.50e+03 pdb=" C2 A 2 119 " -0.087 2.00e-02 2.50e+03 pdb=" N3 A 2 119 " -0.154 2.00e-02 2.50e+03 pdb=" C4 A 2 119 " -0.142 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U 11647 " 0.195 2.00e-02 2.50e+03 1.07e-01 2.57e+02 pdb=" N1 U 11647 " -0.006 2.00e-02 2.50e+03 pdb=" C2 U 11647 " -0.037 2.00e-02 2.50e+03 pdb=" O2 U 11647 " -0.078 2.00e-02 2.50e+03 pdb=" N3 U 11647 " -0.030 2.00e-02 2.50e+03 pdb=" C4 U 11647 " -0.033 2.00e-02 2.50e+03 pdb=" O4 U 11647 " 0.188 2.00e-02 2.50e+03 pdb=" C5 U 11647 " -0.107 2.00e-02 2.50e+03 pdb=" C6 U 11647 " -0.092 2.00e-02 2.50e+03 ... (remaining 12983 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 14606 2.73 - 3.28: 142945 3.28 - 3.82: 301602 3.82 - 4.36: 376873 4.36 - 4.90: 503091 Nonbonded interactions: 1339117 Sorted by model distance: nonbonded pdb=" N1 G 11063 " pdb=" N4 C 11075 " model vdw 2.194 3.200 nonbonded pdb=" O ALA e 1 " pdb=" N ASP e 5 " model vdw 2.218 2.520 nonbonded pdb=" OG1 THR s 3 " pdb=" O VAL s 107 " model vdw 2.261 2.440 nonbonded pdb=" NE2 HIS I 40 " pdb=" O2' C 3 511 " model vdw 2.262 2.520 nonbonded pdb=" O2' U 12506 " pdb=" O3' A 7 76 " model vdw 2.264 2.440 ... (remaining 1339112 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 '5' and resid 1 through 76) selection = chain '6' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.160 Extract box with map and model: 19.350 Check model and map are aligned: 1.540 Set scattering table: 0.970 Process input model: 546.390 Find NCS groups from input model: 3.100 Set up NCS constraints: 0.460 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.030 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 580.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.232 162700 Z= 0.613 Angle : 1.127 20.826 243508 Z= 0.747 Chirality : 0.090 0.733 31146 Planarity : 0.013 0.286 12986 Dihedral : 22.612 178.358 93392 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 19.55 Ramachandran Plot: Outliers : 1.68 % Allowed : 13.33 % Favored : 84.99 % Rotamer: Outliers : 1.75 % Allowed : 8.00 % Favored : 90.25 % Cbeta Deviations : 0.00 % 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: -4.02 (0.09), residues: 5836 helix: -2.05 (0.11), residues: 1615 sheet: -2.58 (0.15), residues: 983 loop : -3.12 (0.10), residues: 3238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.006 TRP b 212 HIS 0.003 0.000 HIS E 30 PHE 0.039 0.005 PHE l 50 TYR 0.065 0.008 TYR W 69 ARG 0.009 0.001 ARG T 88 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11672 Ramachandran restraints generated. 5836 Oldfield, 0 Emsley, 5836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11672 Ramachandran restraints generated. 5836 Oldfield, 0 Emsley, 5836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1575 residues out of total 4862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 1490 time to evaluate : 6.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 96 ILE cc_start: 0.9085 (mt) cc_final: 0.8802 (pt) REVERT: c 190 LYS cc_start: 0.8920 (tttt) cc_final: 0.8665 (ttpt) REVERT: d 1 MET cc_start: 0.5325 (mmm) cc_final: 0.4775 (mmm) REVERT: d 22 ASP cc_start: 0.8625 (m-30) cc_final: 0.8198 (p0) REVERT: d 30 GLN cc_start: 0.8952 (tm-30) cc_final: 0.8312 (tm-30) REVERT: d 119 ILE cc_start: 0.8613 (mm) cc_final: 0.8362 (mt) REVERT: e 7 TYR cc_start: 0.8565 (t80) cc_final: 0.8307 (t80) REVERT: e 37 MET cc_start: 0.7638 (tmm) cc_final: 0.6908 (tmm) REVERT: e 86 CYS cc_start: 0.7509 (p) cc_final: 0.6497 (p) REVERT: e 98 PHE cc_start: 0.8264 (t80) cc_final: 0.8000 (t80) REVERT: e 164 GLU cc_start: 0.8456 (mt-10) cc_final: 0.8147 (mt-10) REVERT: f 87 GLN cc_start: 0.8347 (tp-100) cc_final: 0.7909 (tp-100) REVERT: f 146 ASP cc_start: 0.8685 (m-30) cc_final: 0.8244 (m-30) REVERT: f 169 ARG cc_start: 0.7977 (mmm160) cc_final: 0.7039 (ttt90) REVERT: g 2 GLN cc_start: 0.6132 (mp10) cc_final: 0.5796 (pp30) REVERT: g 43 ASN cc_start: 0.7680 (m110) cc_final: 0.7399 (m110) REVERT: g 45 GLU cc_start: 0.8337 (tp30) cc_final: 0.8056 (tm-30) REVERT: j 16 TYR cc_start: 0.8888 (m-80) cc_final: 0.8487 (m-10) REVERT: j 27 ARG cc_start: 0.8355 (OUTLIER) cc_final: 0.7249 (mmt180) REVERT: j 28 LEU cc_start: 0.9210 (tp) cc_final: 0.8963 (tp) REVERT: j 136 GLN cc_start: 0.8865 (pt0) cc_final: 0.8638 (pp30) REVERT: k 3 GLN cc_start: 0.7961 (pt0) cc_final: 0.7742 (pt0) REVERT: l 90 VAL cc_start: 0.9012 (t) cc_final: 0.8806 (m) REVERT: l 94 THR cc_start: 0.8295 (m) cc_final: 0.7998 (m) REVERT: l 120 VAL cc_start: 0.9095 (m) cc_final: 0.8852 (t) REVERT: n 72 ASP cc_start: 0.8933 (t70) cc_final: 0.8505 (t0) REVERT: n 106 ASP cc_start: 0.7963 (p0) cc_final: 0.7576 (p0) REVERT: o 12 THR cc_start: 0.9273 (m) cc_final: 0.9016 (p) REVERT: o 17 LYS cc_start: 0.8647 (mmmt) cc_final: 0.8330 (mmmt) REVERT: o 19 GLN cc_start: 0.8818 (tt0) cc_final: 0.8422 (tp40) REVERT: o 34 HIS cc_start: 0.8369 (OUTLIER) cc_final: 0.7562 (m-70) REVERT: o 43 ASN cc_start: 0.9038 (p0) cc_final: 0.8555 (p0) REVERT: o 56 LYS cc_start: 0.8773 (pptt) cc_final: 0.8175 (pptt) REVERT: o 85 LYS cc_start: 0.9036 (mmtt) cc_final: 0.8694 (mmtm) REVERT: o 88 LYS cc_start: 0.8605 (tttt) cc_final: 0.8387 (tmmt) REVERT: p 8 GLU cc_start: 0.8852 (mt-10) cc_final: 0.8628 (mt-10) REVERT: p 40 GLN cc_start: 0.7717 (OUTLIER) cc_final: 0.7356 (pp30) REVERT: p 70 GLU cc_start: 0.8175 (mp0) cc_final: 0.7847 (mp0) REVERT: p 86 LYS cc_start: 0.8524 (mmtm) cc_final: 0.8233 (mmmt) REVERT: q 30 VAL cc_start: 0.8066 (t) cc_final: 0.7788 (m) REVERT: q 58 GLN cc_start: 0.9078 (tt0) cc_final: 0.8877 (tt0) REVERT: q 96 ASP cc_start: 0.8455 (m-30) cc_final: 0.7988 (m-30) REVERT: r 15 SER cc_start: 0.8758 (t) cc_final: 0.8415 (p) REVERT: r 16 GLU cc_start: 0.8412 (tt0) cc_final: 0.7735 (tt0) REVERT: r 83 TYR cc_start: 0.8656 (t80) cc_final: 0.8416 (t80) REVERT: s 68 ASP cc_start: 0.7788 (m-30) cc_final: 0.7358 (m-30) REVERT: t 15 HIS cc_start: 0.7554 (t-90) cc_final: 0.7349 (t-90) REVERT: t 78 SER cc_start: 0.8835 (m) cc_final: 0.8468 (t) REVERT: u 53 GLN cc_start: 0.8292 (mt0) cc_final: 0.8077 (mp10) REVERT: v 7 GLU cc_start: 0.8152 (pt0) cc_final: 0.7934 (pt0) REVERT: v 55 GLU cc_start: 0.9114 (mp0) cc_final: 0.8864 (mp0) REVERT: v 82 TYR cc_start: 0.7350 (p90) cc_final: 0.7111 (p90) REVERT: w 21 ARG cc_start: 0.7202 (mmp-170) cc_final: 0.6884 (mmp-170) REVERT: w 79 GLU cc_start: 0.7747 (OUTLIER) cc_final: 0.7372 (mp0) REVERT: x 22 ASN cc_start: 0.9413 (m110) cc_final: 0.9034 (m-40) REVERT: y 13 GLU cc_start: 0.8269 (pt0) cc_final: 0.7976 (mt-10) REVERT: y 40 SER cc_start: 0.9438 (p) cc_final: 0.9029 (t) REVERT: z 37 ARG cc_start: 0.8533 (mmt-90) cc_final: 0.8172 (mmt90) REVERT: A 34 LEU cc_start: 0.8207 (mt) cc_final: 0.7887 (mt) REVERT: B 16 ARG cc_start: 0.8176 (mtt180) cc_final: 0.7974 (mtt180) REVERT: B 35 GLU cc_start: 0.8078 (mt-10) cc_final: 0.7770 (mt-10) REVERT: C 23 THR cc_start: 0.8145 (p) cc_final: 0.7894 (p) REVERT: D 10 LEU cc_start: 0.9103 (tp) cc_final: 0.8815 (tt) REVERT: E 53 ASP cc_start: 0.8027 (m-30) cc_final: 0.7644 (m-30) REVERT: G 15 PHE cc_start: 0.7454 (OUTLIER) cc_final: 0.6917 (p90) REVERT: G 34 ARG cc_start: 0.7145 (mmp80) cc_final: 0.6525 (tpm170) REVERT: G 93 HIS cc_start: 0.8386 (m90) cc_final: 0.7878 (m-70) REVERT: G 99 MET cc_start: 0.8238 (ptp) cc_final: 0.8015 (ptp) REVERT: G 119 GLN cc_start: 0.8245 (mt0) cc_final: 0.7375 (pp30) REVERT: G 135 MET cc_start: 0.8393 (tpt) cc_final: 0.8189 (tpp) REVERT: H 55 VAL cc_start: 0.8689 (t) cc_final: 0.8409 (t) REVERT: H 92 ASP cc_start: 0.8943 (t70) cc_final: 0.8589 (p0) REVERT: H 111 ASP cc_start: 0.8153 (t70) cc_final: 0.7875 (t0) REVERT: I 3 TYR cc_start: 0.7446 (t80) cc_final: 0.6941 (t80) REVERT: I 168 THR cc_start: 0.7521 (p) cc_final: 0.7292 (p) REVERT: I 189 ASP cc_start: 0.6320 (m-30) cc_final: 0.5896 (m-30) REVERT: J 71 ILE cc_start: 0.8720 (mm) cc_final: 0.8266 (mp) REVERT: J 89 THR cc_start: 0.8868 (m) cc_final: 0.8532 (p) REVERT: J 127 TYR cc_start: 0.8623 (m-80) cc_final: 0.8398 (m-10) REVERT: J 151 MET cc_start: 0.8740 (mtp) cc_final: 0.8465 (mtp) REVERT: K 40 GLU cc_start: 0.6240 (tm-30) cc_final: 0.5972 (tm-30) REVERT: K 62 MET cc_start: 0.8001 (mmm) cc_final: 0.7738 (mmm) REVERT: L 10 LYS cc_start: 0.8638 (mmtp) cc_final: 0.8133 (ttpt) REVERT: L 12 LEU cc_start: 0.8557 (pt) cc_final: 0.8300 (pt) REVERT: L 51 GLN cc_start: 0.8865 (tt0) cc_final: 0.8507 (mm110) REVERT: M 4 ASP cc_start: 0.8213 (t70) cc_final: 0.7962 (t0) REVERT: M 41 GLU cc_start: 0.8806 (mm-30) cc_final: 0.8594 (mm-30) REVERT: M 59 GLU cc_start: 0.7950 (pt0) cc_final: 0.7452 (pt0) REVERT: M 79 ARG cc_start: 0.8760 (ptt-90) cc_final: 0.8409 (ptm-80) REVERT: M 95 MET cc_start: 0.8943 (mpp) cc_final: 0.8578 (mpp) REVERT: M 125 ILE cc_start: 0.8614 (mm) cc_final: 0.8370 (mm) REVERT: N 12 LYS cc_start: 0.8760 (ttmt) cc_final: 0.8205 (ttmt) REVERT: N 19 PHE cc_start: 0.8150 (m-80) cc_final: 0.7874 (m-10) REVERT: N 35 GLU cc_start: 0.8988 (mp0) cc_final: 0.8714 (mm-30) REVERT: N 53 LEU cc_start: 0.8223 (tp) cc_final: 0.7579 (tt) REVERT: O 20 GLN cc_start: 0.9123 (tp40) cc_final: 0.8907 (tm-30) REVERT: O 49 PHE cc_start: 0.8377 (m-80) cc_final: 0.8167 (m-10) REVERT: O 65 TYR cc_start: 0.8360 (m-80) cc_final: 0.7851 (m-80) REVERT: P 19 VAL cc_start: 0.7482 (t) cc_final: 0.7126 (t) REVERT: P 63 GLN cc_start: 0.8827 (tt0) cc_final: 0.8190 (tt0) REVERT: P 118 ASN cc_start: 0.8317 (m-40) cc_final: 0.8107 (m-40) REVERT: P 124 LYS cc_start: 0.7578 (pptt) cc_final: 0.7319 (ptmt) REVERT: Q 28 GLN cc_start: 0.8437 (mp10) cc_final: 0.8175 (mt0) REVERT: Q 111 GLN cc_start: 0.8223 (mt0) cc_final: 0.7858 (mt0) REVERT: R 92 ARG cc_start: 0.7665 (mmt180) cc_final: 0.7419 (mmt180) REVERT: R 96 VAL cc_start: 0.9061 (t) cc_final: 0.8816 (m) REVERT: R 99 GLN cc_start: 0.8942 (OUTLIER) cc_final: 0.7841 (mp10) REVERT: S 13 VAL cc_start: 0.8935 (t) cc_final: 0.7995 (t) REVERT: S 47 LEU cc_start: 0.8849 (tp) cc_final: 0.8632 (tp) REVERT: U 63 GLN cc_start: 0.8809 (mm110) cc_final: 0.8423 (mm-40) REVERT: V 10 ARG cc_start: 0.8831 (ptm-80) cc_final: 0.8579 (ptm-80) REVERT: V 38 LYS cc_start: 0.8901 (mtpp) cc_final: 0.8683 (pttt) REVERT: V 68 LYS cc_start: 0.8939 (tttt) cc_final: 0.8568 (mtpt) REVERT: W 37 LYS cc_start: 0.9051 (mtpt) cc_final: 0.8796 (mtpp) REVERT: W 56 ARG cc_start: 0.9169 (ttm-80) cc_final: 0.8697 (ttm110) REVERT: X 9 PHE cc_start: 0.8815 (t80) cc_final: 0.8615 (t80) REVERT: X 12 LEU cc_start: 0.8550 (tp) cc_final: 0.8286 (tt) REVERT: X 16 LYS cc_start: 0.8964 (mmmt) cc_final: 0.8246 (mtmt) REVERT: X 47 THR cc_start: 0.8021 (p) cc_final: 0.7757 (m) REVERT: X 55 GLN cc_start: 0.8693 (mm-40) cc_final: 0.8424 (mm110) REVERT: Y 24 ARG cc_start: 0.8915 (mtt-85) cc_final: 0.8655 (mtt-85) REVERT: Y 58 ASP cc_start: 0.9024 (t70) cc_final: 0.8609 (t70) REVERT: Z 33 ARG cc_start: 0.7024 (mpt180) cc_final: 0.6712 (mmt180) REVERT: Z 46 ARG cc_start: 0.7936 (mpt180) cc_final: 0.7158 (tpt-90) outliers start: 85 outliers final: 32 residues processed: 1548 average time/residue: 1.3190 time to fit residues: 3525.6524 Evaluate side-chains 1067 residues out of total 4862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 1029 time to evaluate : 6.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 125 PRO Chi-restraints excluded: chain b residue 129 LEU Chi-restraints excluded: chain c residue 138 LEU Chi-restraints excluded: chain e residue 175 PRO Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain j residue 27 ARG Chi-restraints excluded: chain l residue 111 ILE Chi-restraints excluded: chain m residue 91 TYR Chi-restraints excluded: chain o residue 34 HIS Chi-restraints excluded: chain p residue 40 GLN Chi-restraints excluded: chain r residue 45 GLU Chi-restraints excluded: chain w residue 79 GLU Chi-restraints excluded: chain y residue 12 GLU Chi-restraints excluded: chain z residue 56 VAL Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain G residue 15 PHE Chi-restraints excluded: chain G residue 21 TYR Chi-restraints excluded: chain H residue 169 GLU Chi-restraints excluded: chain I residue 30 LYS Chi-restraints excluded: chain J residue 15 ILE Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 123 LEU Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain M residue 74 ILE Chi-restraints excluded: chain M residue 77 VAL Chi-restraints excluded: chain N residue 42 THR Chi-restraints excluded: chain N residue 60 LEU Chi-restraints excluded: chain P residue 126 ARG Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain Q residue 33 CYS Chi-restraints excluded: chain Q residue 39 THR Chi-restraints excluded: chain R residue 99 GLN Chi-restraints excluded: chain U residue 2 VAL Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain U residue 66 THR Chi-restraints excluded: chain W residue 17 VAL Chi-restraints excluded: chain W residue 70 THR Chi-restraints excluded: chain a residue 178 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1048 random chunks: chunk 884 optimal weight: 20.0000 chunk 794 optimal weight: 10.0000 chunk 440 optimal weight: 7.9990 chunk 271 optimal weight: 5.9990 chunk 535 optimal weight: 7.9990 chunk 424 optimal weight: 5.9990 chunk 821 optimal weight: 10.0000 chunk 317 optimal weight: 4.9990 chunk 499 optimal weight: 8.9990 chunk 611 optimal weight: 20.0000 chunk 951 optimal weight: 10.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 45 ASN ** b 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 136 GLN ** d 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 51 ASN f 63 GLN f 87 GLN g 11 ASN g 18 GLN ** j 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 62 ASN o 38 GLN o 100 HIS p 9 GLN r 18 GLN r 86 GLN r 87 GLN y 25 GLN ** y 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 25 ASN G 18 GLN G 176 ASN ** G 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 68 HIS H 99 GLN ** I 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 53 GLN I 139 ASN I 195 ASN ** J 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 94 HIS ** L 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 109 GLN ** O 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 27 GLN ** U 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 68 HIS Y 2 ASN ** Y 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 60 GLN Z 55 HIS a 47 ASN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.2089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 162700 Z= 0.265 Angle : 0.706 12.152 243508 Z= 0.368 Chirality : 0.040 0.342 31146 Planarity : 0.006 0.094 12986 Dihedral : 23.231 177.616 81786 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 14.74 Ramachandran Plot: Outliers : 0.38 % Allowed : 12.11 % Favored : 87.51 % Rotamer: Outliers : 4.15 % Allowed : 15.01 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.51 % Twisted General : 0.30 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.07 (0.10), residues: 5836 helix: -0.89 (0.11), residues: 1833 sheet: -2.05 (0.16), residues: 984 loop : -2.83 (0.10), residues: 3019 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP b 212 HIS 0.020 0.002 HIS X 56 PHE 0.031 0.002 PHE W 12 TYR 0.034 0.002 TYR K 25 ARG 0.012 0.001 ARG X 31 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11672 Ramachandran restraints generated. 5836 Oldfield, 0 Emsley, 5836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11672 Ramachandran restraints generated. 5836 Oldfield, 0 Emsley, 5836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1383 residues out of total 4862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 202 poor density : 1181 time to evaluate : 6.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 64 GLU cc_start: 0.8623 (tp30) cc_final: 0.8376 (tp30) REVERT: c 190 LYS cc_start: 0.9020 (tttt) cc_final: 0.8765 (ttpt) REVERT: d 1 MET cc_start: 0.4487 (mmm) cc_final: 0.4228 (mmm) REVERT: d 30 GLN cc_start: 0.8737 (tm-30) cc_final: 0.8174 (tm-30) REVERT: d 115 GLN cc_start: 0.8868 (tp-100) cc_final: 0.8402 (tp-100) REVERT: d 183 PHE cc_start: 0.8596 (m-80) cc_final: 0.8261 (m-80) REVERT: d 195 GLN cc_start: 0.8637 (OUTLIER) cc_final: 0.7972 (mp10) REVERT: e 4 HIS cc_start: 0.8529 (t-170) cc_final: 0.7939 (t70) REVERT: e 31 GLU cc_start: 0.8814 (mt-10) cc_final: 0.8211 (mp0) REVERT: f 150 TYR cc_start: 0.8470 (m-10) cc_final: 0.8264 (m-10) REVERT: f 169 ARG cc_start: 0.8029 (mmm160) cc_final: 0.7103 (ttt90) REVERT: g 43 ASN cc_start: 0.7608 (m110) cc_final: 0.7229 (m110) REVERT: j 28 LEU cc_start: 0.8995 (tp) cc_final: 0.8769 (tp) REVERT: j 49 ASP cc_start: 0.8567 (t0) cc_final: 0.8242 (t0) REVERT: n 72 ASP cc_start: 0.8612 (t70) cc_final: 0.8032 (t0) REVERT: o 34 HIS cc_start: 0.8225 (m-70) cc_final: 0.7642 (m-70) REVERT: o 55 GLU cc_start: 0.8492 (OUTLIER) cc_final: 0.8233 (mm-30) REVERT: o 58 ILE cc_start: 0.8574 (mt) cc_final: 0.8208 (tp) REVERT: o 88 LYS cc_start: 0.8650 (tttt) cc_final: 0.7689 (ttmm) REVERT: p 8 GLU cc_start: 0.8808 (mt-10) cc_final: 0.8543 (mt-10) REVERT: p 40 GLN cc_start: 0.7681 (OUTLIER) cc_final: 0.7258 (pp30) REVERT: p 70 GLU cc_start: 0.8178 (mp0) cc_final: 0.7858 (mp0) REVERT: q 30 VAL cc_start: 0.7984 (t) cc_final: 0.7644 (m) REVERT: r 16 GLU cc_start: 0.8436 (tt0) cc_final: 0.8155 (tt0) REVERT: s 52 GLU cc_start: 0.8688 (mt-10) cc_final: 0.8314 (tt0) REVERT: v 12 GLN cc_start: 0.8027 (pm20) cc_final: 0.7629 (pp30) REVERT: v 41 GLU cc_start: 0.6388 (tm-30) cc_final: 0.6164 (tm-30) REVERT: v 55 GLU cc_start: 0.9083 (mp0) cc_final: 0.8663 (mp0) REVERT: v 64 VAL cc_start: 0.8338 (t) cc_final: 0.8126 (p) REVERT: y 25 GLN cc_start: 0.8793 (OUTLIER) cc_final: 0.8149 (tp-100) REVERT: y 40 SER cc_start: 0.9312 (p) cc_final: 0.8764 (t) REVERT: z 22 THR cc_start: 0.9544 (m) cc_final: 0.9280 (p) REVERT: B 16 ARG cc_start: 0.8059 (mtt180) cc_final: 0.7843 (mtt-85) REVERT: B 35 GLU cc_start: 0.7827 (mt-10) cc_final: 0.7420 (mt-10) REVERT: C 47 ILE cc_start: 0.8220 (mt) cc_final: 0.7829 (pt) REVERT: D 10 LEU cc_start: 0.9039 (tp) cc_final: 0.8753 (tt) REVERT: E 53 ASP cc_start: 0.8326 (m-30) cc_final: 0.7988 (m-30) REVERT: E 54 LEU cc_start: 0.9187 (mt) cc_final: 0.8858 (mp) REVERT: G 15 PHE cc_start: 0.7693 (OUTLIER) cc_final: 0.7406 (p90) REVERT: G 34 ARG cc_start: 0.7444 (mmp80) cc_final: 0.6749 (tpm170) REVERT: G 88 GLN cc_start: 0.8067 (mm-40) cc_final: 0.7773 (mp10) REVERT: G 93 HIS cc_start: 0.8344 (m90) cc_final: 0.7972 (m-70) REVERT: G 95 TRP cc_start: 0.8221 (t60) cc_final: 0.7852 (t60) REVERT: G 99 MET cc_start: 0.8580 (ptp) cc_final: 0.8304 (ptp) REVERT: G 135 MET cc_start: 0.8163 (tpt) cc_final: 0.7681 (tpp) REVERT: G 139 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.7221 (mp0) REVERT: H 34 SER cc_start: 0.9107 (t) cc_final: 0.8780 (p) REVERT: H 55 VAL cc_start: 0.8798 (t) cc_final: 0.8595 (t) REVERT: H 61 LYS cc_start: 0.8009 (mptt) cc_final: 0.7573 (pttm) REVERT: H 92 ASP cc_start: 0.9002 (t70) cc_final: 0.8624 (p0) REVERT: H 111 ASP cc_start: 0.7505 (t70) cc_final: 0.7237 (t0) REVERT: H 122 GLN cc_start: 0.8347 (mp-120) cc_final: 0.7891 (mp10) REVERT: I 3 TYR cc_start: 0.7781 (t80) cc_final: 0.7089 (t80) REVERT: I 50 TYR cc_start: 0.8233 (t80) cc_final: 0.7873 (t80) REVERT: I 189 ASP cc_start: 0.6365 (m-30) cc_final: 0.5905 (m-30) REVERT: J 21 SER cc_start: 0.9017 (OUTLIER) cc_final: 0.8645 (t) REVERT: J 60 GLN cc_start: 0.8900 (tt0) cc_final: 0.8483 (pp30) REVERT: J 89 THR cc_start: 0.8757 (m) cc_final: 0.8440 (p) REVERT: J 127 TYR cc_start: 0.8517 (m-80) cc_final: 0.8257 (m-10) REVERT: J 151 MET cc_start: 0.8715 (mtp) cc_final: 0.8412 (mtp) REVERT: K 5 GLU cc_start: 0.7459 (mp0) cc_final: 0.7216 (mp0) REVERT: K 13 ASP cc_start: 0.8592 (m-30) cc_final: 0.7962 (p0) REVERT: K 62 MET cc_start: 0.7979 (mmm) cc_final: 0.7730 (mmm) REVERT: L 10 LYS cc_start: 0.8560 (mmtp) cc_final: 0.8155 (ttpt) REVERT: L 12 LEU cc_start: 0.8580 (pt) cc_final: 0.8338 (pt) REVERT: L 27 ASN cc_start: 0.8809 (m110) cc_final: 0.8558 (m-40) REVERT: L 51 GLN cc_start: 0.8683 (tt0) cc_final: 0.8332 (mm110) REVERT: L 100 MET cc_start: 0.8998 (mtt) cc_final: 0.8748 (mtt) REVERT: M 4 ASP cc_start: 0.8216 (t70) cc_final: 0.7951 (t0) REVERT: M 11 THR cc_start: 0.9145 (m) cc_final: 0.8912 (p) REVERT: M 41 GLU cc_start: 0.8850 (mm-30) cc_final: 0.8648 (mm-30) REVERT: M 42 GLU cc_start: 0.8034 (tp30) cc_final: 0.7739 (tp30) REVERT: M 95 MET cc_start: 0.9051 (mpp) cc_final: 0.8587 (mpp) REVERT: N 19 PHE cc_start: 0.8295 (m-80) cc_final: 0.8023 (m-10) REVERT: N 45 MET cc_start: 0.8548 (mpp) cc_final: 0.8290 (mpp) REVERT: O 11 LYS cc_start: 0.8446 (ptpt) cc_final: 0.7854 (mtmm) REVERT: O 19 ASP cc_start: 0.8772 (m-30) cc_final: 0.7961 (p0) REVERT: O 20 GLN cc_start: 0.9057 (tp40) cc_final: 0.8643 (tm-30) REVERT: O 46 LYS cc_start: 0.8506 (mttp) cc_final: 0.8288 (mmtp) REVERT: O 63 ASP cc_start: 0.6702 (t0) cc_final: 0.6044 (t0) REVERT: O 65 TYR cc_start: 0.8306 (m-80) cc_final: 0.7940 (m-80) REVERT: P 19 VAL cc_start: 0.7807 (t) cc_final: 0.7395 (t) REVERT: P 51 PHE cc_start: 0.8636 (m-80) cc_final: 0.8379 (m-80) REVERT: P 74 LYS cc_start: 0.8627 (ptpt) cc_final: 0.8370 (mmmt) REVERT: P 86 LYS cc_start: 0.8381 (ptpp) cc_final: 0.8047 (pttm) REVERT: P 124 LYS cc_start: 0.7582 (pptt) cc_final: 0.7141 (ptmt) REVERT: Q 28 GLN cc_start: 0.8553 (mp10) cc_final: 0.7902 (mt0) REVERT: Q 111 GLN cc_start: 0.8188 (mt0) cc_final: 0.7676 (mt0) REVERT: R 10 ASP cc_start: 0.8763 (m-30) cc_final: 0.8117 (m-30) REVERT: R 79 LEU cc_start: 0.8928 (mt) cc_final: 0.8678 (tp) REVERT: S 13 VAL cc_start: 0.8832 (t) cc_final: 0.8549 (t) REVERT: T 5 GLU cc_start: 0.8567 (tp30) cc_final: 0.8333 (tp30) REVERT: T 9 LYS cc_start: 0.9505 (mttt) cc_final: 0.9101 (mttm) REVERT: U 1 MET cc_start: 0.6954 (tmm) cc_final: 0.6091 (ttt) REVERT: V 10 ARG cc_start: 0.8865 (ptm-80) cc_final: 0.8619 (ptm-80) REVERT: V 68 LYS cc_start: 0.8911 (tttt) cc_final: 0.8633 (mtpt) REVERT: W 22 TYR cc_start: 0.7707 (p90) cc_final: 0.7208 (p90) REVERT: X 9 PHE cc_start: 0.8815 (t80) cc_final: 0.8574 (t80) REVERT: X 16 LYS cc_start: 0.8974 (mmmt) cc_final: 0.8697 (mmmm) REVERT: X 17 LYS cc_start: 0.8695 (ttmm) cc_final: 0.8418 (mttp) REVERT: X 47 THR cc_start: 0.7695 (p) cc_final: 0.7406 (m) REVERT: Y 54 GLN cc_start: 0.8584 (tm-30) cc_final: 0.8147 (tm-30) REVERT: Y 58 ASP cc_start: 0.8854 (t70) cc_final: 0.8238 (t70) REVERT: Z 39 LYS cc_start: 0.7877 (tttt) cc_final: 0.7525 (tptp) REVERT: Z 46 ARG cc_start: 0.7810 (mpt180) cc_final: 0.7079 (tpt-90) REVERT: a 58 ASN cc_start: 0.5997 (p0) cc_final: 0.5734 (t0) outliers start: 202 outliers final: 125 residues processed: 1285 average time/residue: 1.2905 time to fit residues: 2925.8651 Evaluate side-chains 1134 residues out of total 4862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 1002 time to evaluate : 6.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 159 THR Chi-restraints excluded: chain b residue 228 ASP Chi-restraints excluded: chain b residue 256 THR Chi-restraints excluded: chain c residue 108 ASP Chi-restraints excluded: chain c residue 139 SER Chi-restraints excluded: chain c residue 175 LEU Chi-restraints excluded: chain d residue 140 ASP Chi-restraints excluded: chain d residue 195 GLN Chi-restraints excluded: chain e residue 16 MET Chi-restraints excluded: chain e residue 67 THR Chi-restraints excluded: chain e residue 117 SER Chi-restraints excluded: chain j residue 36 LEU Chi-restraints excluded: chain j residue 55 ILE Chi-restraints excluded: chain k residue 24 VAL Chi-restraints excluded: chain k residue 62 VAL Chi-restraints excluded: chain k residue 97 THR Chi-restraints excluded: chain k residue 104 THR Chi-restraints excluded: chain l residue 42 SER Chi-restraints excluded: chain l residue 111 ILE Chi-restraints excluded: chain l residue 116 VAL Chi-restraints excluded: chain l residue 122 VAL Chi-restraints excluded: chain m residue 7 THR Chi-restraints excluded: chain m residue 41 LEU Chi-restraints excluded: chain n residue 37 THR Chi-restraints excluded: chain o residue 2 ASP Chi-restraints excluded: chain o residue 36 TYR Chi-restraints excluded: chain o residue 39 VAL Chi-restraints excluded: chain o residue 55 GLU Chi-restraints excluded: chain o residue 69 ASP Chi-restraints excluded: chain p residue 35 SER Chi-restraints excluded: chain p residue 40 GLN Chi-restraints excluded: chain p residue 64 SER Chi-restraints excluded: chain p residue 103 THR Chi-restraints excluded: chain p residue 109 ILE Chi-restraints excluded: chain q residue 19 GLN Chi-restraints excluded: chain q residue 73 ILE Chi-restraints excluded: chain r residue 19 THR Chi-restraints excluded: chain r residue 41 ILE Chi-restraints excluded: chain r residue 101 ILE Chi-restraints excluded: chain s residue 33 LEU Chi-restraints excluded: chain s residue 69 LEU Chi-restraints excluded: chain s residue 74 ILE Chi-restraints excluded: chain s residue 81 SER Chi-restraints excluded: chain t residue 32 LEU Chi-restraints excluded: chain t residue 87 LEU Chi-restraints excluded: chain u residue 17 ASP Chi-restraints excluded: chain u residue 29 SER Chi-restraints excluded: chain v residue 8 VAL Chi-restraints excluded: chain v residue 45 ASP Chi-restraints excluded: chain w residue 8 ASN Chi-restraints excluded: chain w residue 17 LEU Chi-restraints excluded: chain w residue 72 ASN Chi-restraints excluded: chain w residue 79 GLU Chi-restraints excluded: chain x residue 7 THR Chi-restraints excluded: chain x residue 58 ILE Chi-restraints excluded: chain x residue 67 LEU Chi-restraints excluded: chain y residue 25 GLN Chi-restraints excluded: chain z residue 48 ASN Chi-restraints excluded: chain z residue 56 VAL Chi-restraints excluded: chain A residue 33 ASN Chi-restraints excluded: chain A residue 58 ASP Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 17 VAL Chi-restraints excluded: chain G residue 15 PHE Chi-restraints excluded: chain G residue 30 ILE Chi-restraints excluded: chain G residue 139 GLU Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 50 SER Chi-restraints excluded: chain H residue 68 HIS Chi-restraints excluded: chain H residue 138 GLN Chi-restraints excluded: chain H residue 153 SER Chi-restraints excluded: chain H residue 186 SER Chi-restraints excluded: chain I residue 30 LYS Chi-restraints excluded: chain I residue 140 ASP Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 29 ILE Chi-restraints excluded: chain J residue 95 MET Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 141 ASP Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain L residue 66 GLU Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain M residue 74 ILE Chi-restraints excluded: chain M residue 77 VAL Chi-restraints excluded: chain M residue 84 ILE Chi-restraints excluded: chain M residue 111 THR Chi-restraints excluded: chain M residue 124 ILE Chi-restraints excluded: chain N residue 42 THR Chi-restraints excluded: chain N residue 61 ASP Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain O residue 22 THR Chi-restraints excluded: chain O residue 36 VAL Chi-restraints excluded: chain O residue 57 VAL Chi-restraints excluded: chain O residue 92 LEU Chi-restraints excluded: chain P residue 29 THR Chi-restraints excluded: chain P residue 39 ASN Chi-restraints excluded: chain P residue 57 SER Chi-restraints excluded: chain P residue 95 THR Chi-restraints excluded: chain P residue 126 ARG Chi-restraints excluded: chain Q residue 2 THR Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain Q residue 33 CYS Chi-restraints excluded: chain Q residue 54 VAL Chi-restraints excluded: chain Q residue 101 LEU Chi-restraints excluded: chain R residue 3 ILE Chi-restraints excluded: chain R residue 15 VAL Chi-restraints excluded: chain R residue 19 THR Chi-restraints excluded: chain R residue 24 VAL Chi-restraints excluded: chain R residue 101 THR Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain T residue 56 LEU Chi-restraints excluded: chain T residue 59 VAL Chi-restraints excluded: chain T residue 69 LEU Chi-restraints excluded: chain T residue 88 ARG Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain U residue 66 THR Chi-restraints excluded: chain V residue 52 CYS Chi-restraints excluded: chain V residue 54 ILE Chi-restraints excluded: chain V residue 82 VAL Chi-restraints excluded: chain W residue 17 VAL Chi-restraints excluded: chain W residue 70 THR Chi-restraints excluded: chain X residue 57 VAL Chi-restraints excluded: chain Y residue 82 ILE Chi-restraints excluded: chain Z residue 18 PHE Chi-restraints excluded: chain a residue 8 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1048 random chunks: chunk 528 optimal weight: 20.0000 chunk 295 optimal weight: 4.9990 chunk 792 optimal weight: 10.0000 chunk 648 optimal weight: 10.0000 chunk 262 optimal weight: 0.0060 chunk 953 optimal weight: 20.0000 chunk 1029 optimal weight: 20.0000 chunk 849 optimal weight: 10.0000 chunk 945 optimal weight: 20.0000 chunk 325 optimal weight: 9.9990 chunk 764 optimal weight: 20.0000 overall best weight: 7.0008 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 44 ASN b 45 ASN ** b 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 44 HIS j 40 HIS ** l 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 38 GLN ** p 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 51 GLN q 58 GLN r 43 ASN u 73 ASN ** y 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 8 GLN G 50 ASN G 119 GLN ** G 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 53 GLN I 70 GLN ** J 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 48 GLN S 65 GLN ** X 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 20 ASN ** Y 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 55 HIS ** a 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.2680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 162700 Z= 0.267 Angle : 0.663 11.975 243508 Z= 0.345 Chirality : 0.038 0.287 31146 Planarity : 0.005 0.066 12986 Dihedral : 23.358 178.960 81744 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 15.26 Ramachandran Plot: Outliers : 0.29 % Allowed : 12.41 % Favored : 87.30 % Rotamer: Outliers : 5.59 % Allowed : 17.71 % Favored : 76.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.51 % Twisted General : 0.28 % 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: -2.67 (0.10), residues: 5836 helix: -0.49 (0.12), residues: 1846 sheet: -1.74 (0.16), residues: 966 loop : -2.68 (0.11), residues: 3024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP b 212 HIS 0.040 0.002 HIS H 68 PHE 0.027 0.002 PHE Z 36 TYR 0.026 0.002 TYR I 75 ARG 0.011 0.001 ARG Y 17 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11672 Ramachandran restraints generated. 5836 Oldfield, 0 Emsley, 5836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11672 Ramachandran restraints generated. 5836 Oldfield, 0 Emsley, 5836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1352 residues out of total 4862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 272 poor density : 1080 time to evaluate : 5.955 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 190 LYS cc_start: 0.8850 (tttt) cc_final: 0.8568 (ttpt) REVERT: d 1 MET cc_start: 0.4755 (mmm) cc_final: 0.4482 (mmm) REVERT: d 29 HIS cc_start: 0.8405 (OUTLIER) cc_final: 0.7968 (t70) REVERT: d 30 GLN cc_start: 0.8756 (tm-30) cc_final: 0.8183 (tm-30) REVERT: d 195 GLN cc_start: 0.8522 (OUTLIER) cc_final: 0.7965 (mp10) REVERT: e 4 HIS cc_start: 0.8492 (t-170) cc_final: 0.8053 (t-170) REVERT: e 16 MET cc_start: 0.8317 (mmm) cc_final: 0.7965 (mmm) REVERT: e 19 PHE cc_start: 0.8560 (m-10) cc_final: 0.7948 (m-10) REVERT: e 31 GLU cc_start: 0.8800 (mt-10) cc_final: 0.8114 (mp0) REVERT: e 95 MET cc_start: 0.8246 (ttp) cc_final: 0.7921 (ttp) REVERT: e 96 TRP cc_start: 0.8813 (m100) cc_final: 0.8396 (m100) REVERT: e 100 GLU cc_start: 0.8547 (pt0) cc_final: 0.8340 (pt0) REVERT: e 164 GLU cc_start: 0.8795 (OUTLIER) cc_final: 0.8358 (mm-30) REVERT: e 176 PHE cc_start: 0.7171 (OUTLIER) cc_final: 0.6628 (m-80) REVERT: f 2 ARG cc_start: 0.7841 (OUTLIER) cc_final: 0.7582 (mmt-90) REVERT: f 169 ARG cc_start: 0.8035 (mmm160) cc_final: 0.7061 (ttt90) REVERT: l 143 GLU cc_start: 0.7267 (pt0) cc_final: 0.7019 (pt0) REVERT: m 33 LEU cc_start: 0.9007 (tp) cc_final: 0.8712 (mp) REVERT: m 75 GLU cc_start: 0.8122 (tt0) cc_final: 0.7913 (mt-10) REVERT: m 90 GLU cc_start: 0.7668 (tt0) cc_final: 0.6705 (tt0) REVERT: n 72 ASP cc_start: 0.8717 (t70) cc_final: 0.8337 (t0) REVERT: o 34 HIS cc_start: 0.8242 (m-70) cc_final: 0.8000 (m-70) REVERT: o 58 ILE cc_start: 0.8372 (mt) cc_final: 0.7764 (tp) REVERT: o 116 GLN cc_start: 0.7468 (pt0) cc_final: 0.7218 (pt0) REVERT: p 8 GLU cc_start: 0.8891 (mt-10) cc_final: 0.8502 (mt-10) REVERT: p 40 GLN cc_start: 0.7548 (OUTLIER) cc_final: 0.7211 (pp30) REVERT: p 70 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7799 (mp0) REVERT: r 16 GLU cc_start: 0.8411 (tt0) cc_final: 0.8090 (tt0) REVERT: r 31 GLU cc_start: 0.8190 (tm-30) cc_final: 0.7965 (tm-30) REVERT: r 79 ARG cc_start: 0.8798 (mtm-85) cc_final: 0.8332 (mtm110) REVERT: s 52 GLU cc_start: 0.8716 (mt-10) cc_final: 0.8354 (tt0) REVERT: t 15 HIS cc_start: 0.7517 (t70) cc_final: 0.7264 (t-90) REVERT: v 87 GLN cc_start: 0.7732 (OUTLIER) cc_final: 0.7340 (mp10) REVERT: y 5 GLU cc_start: 0.7557 (mt-10) cc_final: 0.7033 (mm-30) REVERT: y 23 ARG cc_start: 0.8822 (mpt180) cc_final: 0.8487 (mpt180) REVERT: y 40 SER cc_start: 0.9289 (p) cc_final: 0.8762 (t) REVERT: y 44 LYS cc_start: 0.8583 (tptt) cc_final: 0.8382 (tptt) REVERT: y 60 LYS cc_start: 0.8944 (mmmm) cc_final: 0.8547 (mtpp) REVERT: z 55 LYS cc_start: 0.8873 (mttp) cc_final: 0.8439 (tmtt) REVERT: A 40 CYS cc_start: 0.8268 (OUTLIER) cc_final: 0.7816 (m) REVERT: B 16 ARG cc_start: 0.8018 (mtt180) cc_final: 0.7340 (mtt180) REVERT: B 35 GLU cc_start: 0.7818 (mt-10) cc_final: 0.7428 (mt-10) REVERT: D 10 LEU cc_start: 0.9059 (tp) cc_final: 0.8787 (tt) REVERT: E 53 ASP cc_start: 0.8175 (m-30) cc_final: 0.7860 (m-30) REVERT: F 37 GLN cc_start: 0.8425 (tp-100) cc_final: 0.8152 (tp-100) REVERT: G 34 ARG cc_start: 0.7485 (mmp80) cc_final: 0.6529 (tpm170) REVERT: G 88 GLN cc_start: 0.8110 (mm-40) cc_final: 0.7594 (mp10) REVERT: G 93 HIS cc_start: 0.8351 (m90) cc_final: 0.7931 (m-70) REVERT: G 95 TRP cc_start: 0.8224 (t60) cc_final: 0.7614 (t60) REVERT: G 99 MET cc_start: 0.8536 (ptp) cc_final: 0.8013 (ptp) REVERT: H 34 SER cc_start: 0.9088 (t) cc_final: 0.8755 (p) REVERT: H 40 GLN cc_start: 0.9022 (OUTLIER) cc_final: 0.8658 (pp30) REVERT: H 55 VAL cc_start: 0.8857 (t) cc_final: 0.8644 (t) REVERT: H 61 LYS cc_start: 0.7834 (mptt) cc_final: 0.7438 (pttm) REVERT: H 92 ASP cc_start: 0.9003 (t70) cc_final: 0.8640 (p0) REVERT: H 111 ASP cc_start: 0.7613 (t70) cc_final: 0.7292 (t0) REVERT: H 122 GLN cc_start: 0.8309 (mp-120) cc_final: 0.7853 (mp10) REVERT: I 3 TYR cc_start: 0.7821 (t80) cc_final: 0.7146 (t80) REVERT: I 189 ASP cc_start: 0.6296 (m-30) cc_final: 0.5844 (m-30) REVERT: J 21 SER cc_start: 0.8986 (OUTLIER) cc_final: 0.8613 (t) REVERT: J 64 GLU cc_start: 0.8888 (mt-10) cc_final: 0.8523 (tm-30) REVERT: J 89 THR cc_start: 0.8637 (m) cc_final: 0.8275 (p) REVERT: J 125 LYS cc_start: 0.8948 (tppt) cc_final: 0.8496 (tptt) REVERT: J 127 TYR cc_start: 0.8430 (m-80) cc_final: 0.8151 (m-80) REVERT: J 151 MET cc_start: 0.8757 (mtp) cc_final: 0.8548 (mtp) REVERT: K 13 ASP cc_start: 0.8684 (m-30) cc_final: 0.7945 (p0) REVERT: K 62 MET cc_start: 0.8036 (mmm) cc_final: 0.7781 (mmm) REVERT: K 90 MET cc_start: 0.8579 (mmt) cc_final: 0.8378 (tpp) REVERT: L 10 LYS cc_start: 0.8600 (mmtp) cc_final: 0.8165 (ttpt) REVERT: L 51 GLN cc_start: 0.8774 (tt0) cc_final: 0.8354 (mm110) REVERT: L 100 MET cc_start: 0.9056 (mtt) cc_final: 0.8832 (mtt) REVERT: L 143 MET cc_start: 0.9104 (tmm) cc_final: 0.8889 (ttp) REVERT: M 4 ASP cc_start: 0.8335 (t70) cc_final: 0.8035 (t0) REVERT: M 11 THR cc_start: 0.9158 (m) cc_final: 0.8895 (p) REVERT: M 41 GLU cc_start: 0.8867 (mm-30) cc_final: 0.8653 (mm-30) REVERT: M 95 MET cc_start: 0.9123 (mpp) cc_final: 0.8689 (mpp) REVERT: N 56 MET cc_start: 0.8190 (ppp) cc_final: 0.7664 (ppp) REVERT: N 102 PHE cc_start: 0.7896 (m-80) cc_final: 0.7027 (m-80) REVERT: N 104 THR cc_start: 0.7994 (t) cc_final: 0.7748 (m) REVERT: O 10 LEU cc_start: 0.8583 (pp) cc_final: 0.8305 (pt) REVERT: O 11 LYS cc_start: 0.8550 (ptpt) cc_final: 0.8055 (mtmm) REVERT: O 19 ASP cc_start: 0.8818 (m-30) cc_final: 0.8007 (p0) REVERT: O 20 GLN cc_start: 0.9072 (tp40) cc_final: 0.8684 (tm-30) REVERT: O 46 LYS cc_start: 0.8693 (mttp) cc_final: 0.8413 (mmtp) REVERT: O 63 ASP cc_start: 0.6630 (t0) cc_final: 0.6197 (t0) REVERT: O 65 TYR cc_start: 0.8451 (m-80) cc_final: 0.8085 (m-80) REVERT: P 51 PHE cc_start: 0.8714 (m-80) cc_final: 0.8503 (m-80) REVERT: P 74 LYS cc_start: 0.8670 (ptpt) cc_final: 0.8403 (mmmt) REVERT: P 86 LYS cc_start: 0.8510 (ptpp) cc_final: 0.8087 (pttm) REVERT: P 124 LYS cc_start: 0.7576 (pptt) cc_final: 0.7084 (ptmt) REVERT: R 10 ASP cc_start: 0.8830 (m-30) cc_final: 0.8232 (m-30) REVERT: R 79 LEU cc_start: 0.8986 (mt) cc_final: 0.8718 (tp) REVERT: S 13 VAL cc_start: 0.8817 (t) cc_final: 0.8504 (t) REVERT: T 9 LYS cc_start: 0.9475 (mttt) cc_final: 0.8837 (mmmt) REVERT: V 10 ARG cc_start: 0.8873 (ptm-80) cc_final: 0.8582 (ptm-80) REVERT: V 72 TRP cc_start: 0.8504 (m100) cc_final: 0.8247 (m100) REVERT: W 22 TYR cc_start: 0.7785 (p90) cc_final: 0.7535 (p90) REVERT: X 9 PHE cc_start: 0.8750 (t80) cc_final: 0.8524 (t80) REVERT: X 47 THR cc_start: 0.7605 (p) cc_final: 0.7341 (m) REVERT: X 69 LYS cc_start: 0.8398 (OUTLIER) cc_final: 0.7946 (mtmm) REVERT: Y 54 GLN cc_start: 0.8548 (tm-30) cc_final: 0.8007 (tm-30) REVERT: Y 58 ASP cc_start: 0.8997 (t70) cc_final: 0.8315 (t0) REVERT: Y 83 ASN cc_start: 0.8281 (t0) cc_final: 0.8079 (t0) REVERT: Z 32 ARG cc_start: 0.8212 (tpp-160) cc_final: 0.7986 (mmm160) REVERT: Z 46 ARG cc_start: 0.8047 (mpt180) cc_final: 0.7203 (tpt-90) outliers start: 272 outliers final: 165 residues processed: 1228 average time/residue: 1.3554 time to fit residues: 2962.6010 Evaluate side-chains 1138 residues out of total 4862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 177 poor density : 961 time to evaluate : 6.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 159 THR Chi-restraints excluded: chain b residue 228 ASP Chi-restraints excluded: chain b residue 256 THR Chi-restraints excluded: chain c residue 1 MET Chi-restraints excluded: chain c residue 108 ASP Chi-restraints excluded: chain c residue 138 LEU Chi-restraints excluded: chain c residue 139 SER Chi-restraints excluded: chain c residue 175 LEU Chi-restraints excluded: chain c residue 180 VAL Chi-restraints excluded: chain d residue 29 HIS Chi-restraints excluded: chain d residue 140 ASP Chi-restraints excluded: chain d residue 195 GLN Chi-restraints excluded: chain e residue 145 VAL Chi-restraints excluded: chain e residue 164 GLU Chi-restraints excluded: chain e residue 176 PHE Chi-restraints excluded: chain f residue 2 ARG Chi-restraints excluded: chain f residue 9 VAL Chi-restraints excluded: chain g residue 4 ILE Chi-restraints excluded: chain g residue 48 GLU Chi-restraints excluded: chain h residue 27 VAL Chi-restraints excluded: chain h residue 55 VAL Chi-restraints excluded: chain i residue 54 ILE Chi-restraints excluded: chain j residue 36 LEU Chi-restraints excluded: chain j residue 55 ILE Chi-restraints excluded: chain j residue 64 VAL Chi-restraints excluded: chain j residue 109 LEU Chi-restraints excluded: chain k residue 62 VAL Chi-restraints excluded: chain k residue 97 THR Chi-restraints excluded: chain k residue 104 THR Chi-restraints excluded: chain l residue 42 SER Chi-restraints excluded: chain l residue 111 ILE Chi-restraints excluded: chain l residue 116 VAL Chi-restraints excluded: chain l residue 120 VAL Chi-restraints excluded: chain l residue 122 VAL Chi-restraints excluded: chain m residue 7 THR Chi-restraints excluded: chain m residue 36 VAL Chi-restraints excluded: chain m residue 41 LEU Chi-restraints excluded: chain m residue 70 ASP Chi-restraints excluded: chain n residue 37 THR Chi-restraints excluded: chain n residue 106 ASP Chi-restraints excluded: chain o residue 2 ASP Chi-restraints excluded: chain o residue 36 TYR Chi-restraints excluded: chain o residue 39 VAL Chi-restraints excluded: chain o residue 69 ASP Chi-restraints excluded: chain o residue 108 ASP Chi-restraints excluded: chain p residue 31 VAL Chi-restraints excluded: chain p residue 35 SER Chi-restraints excluded: chain p residue 40 GLN Chi-restraints excluded: chain p residue 59 THR Chi-restraints excluded: chain p residue 64 SER Chi-restraints excluded: chain p residue 70 GLU Chi-restraints excluded: chain p residue 101 GLU Chi-restraints excluded: chain p residue 103 THR Chi-restraints excluded: chain p residue 109 ILE Chi-restraints excluded: chain q residue 73 ILE Chi-restraints excluded: chain r residue 19 THR Chi-restraints excluded: chain r residue 41 ILE Chi-restraints excluded: chain r residue 49 ILE Chi-restraints excluded: chain s residue 69 LEU Chi-restraints excluded: chain s residue 74 ILE Chi-restraints excluded: chain s residue 81 SER Chi-restraints excluded: chain t residue 32 LEU Chi-restraints excluded: chain t residue 50 LEU Chi-restraints excluded: chain t residue 78 SER Chi-restraints excluded: chain t residue 87 LEU Chi-restraints excluded: chain u residue 8 ASP Chi-restraints excluded: chain u residue 17 ASP Chi-restraints excluded: chain u residue 29 SER Chi-restraints excluded: chain u residue 40 LEU Chi-restraints excluded: chain u residue 73 ASN Chi-restraints excluded: chain v residue 7 GLU Chi-restraints excluded: chain v residue 8 VAL Chi-restraints excluded: chain v residue 38 LEU Chi-restraints excluded: chain v residue 45 ASP Chi-restraints excluded: chain v residue 48 MET Chi-restraints excluded: chain v residue 87 GLN Chi-restraints excluded: chain w residue 8 ASN Chi-restraints excluded: chain w residue 27 VAL Chi-restraints excluded: chain w residue 63 VAL Chi-restraints excluded: chain x residue 41 SER Chi-restraints excluded: chain x residue 58 ILE Chi-restraints excluded: chain x residue 67 LEU Chi-restraints excluded: chain z residue 11 SER Chi-restraints excluded: chain z residue 48 ASN Chi-restraints excluded: chain z residue 56 VAL Chi-restraints excluded: chain A residue 33 ASN Chi-restraints excluded: chain A residue 40 CYS Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 58 ASP Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 17 VAL Chi-restraints excluded: chain F residue 30 GLU Chi-restraints excluded: chain G residue 15 PHE Chi-restraints excluded: chain G residue 30 ILE Chi-restraints excluded: chain G residue 59 ILE Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain G residue 122 ASP Chi-restraints excluded: chain G residue 158 ASP Chi-restraints excluded: chain G residue 163 ILE Chi-restraints excluded: chain G residue 198 VAL Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 40 GLN Chi-restraints excluded: chain H residue 138 GLN Chi-restraints excluded: chain I residue 92 LEU Chi-restraints excluded: chain I residue 170 LEU Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 29 ILE Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 141 ASP Chi-restraints excluded: chain K residue 3 HIS Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 46 GLN Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 64 VAL Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain L residue 44 SER Chi-restraints excluded: chain L residue 129 ASN Chi-restraints excluded: chain L residue 132 THR Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain M residue 38 VAL Chi-restraints excluded: chain M residue 74 ILE Chi-restraints excluded: chain M residue 77 VAL Chi-restraints excluded: chain M residue 84 ILE Chi-restraints excluded: chain M residue 124 ILE Chi-restraints excluded: chain N residue 42 THR Chi-restraints excluded: chain N residue 46 VAL Chi-restraints excluded: chain N residue 54 VAL Chi-restraints excluded: chain N residue 61 ASP Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain O residue 22 THR Chi-restraints excluded: chain O residue 36 VAL Chi-restraints excluded: chain O residue 57 VAL Chi-restraints excluded: chain O residue 92 LEU Chi-restraints excluded: chain P residue 30 ILE Chi-restraints excluded: chain P residue 39 ASN Chi-restraints excluded: chain P residue 57 SER Chi-restraints excluded: chain P residue 73 VAL Chi-restraints excluded: chain P residue 95 THR Chi-restraints excluded: chain P residue 96 ILE Chi-restraints excluded: chain Q residue 2 THR Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain Q residue 33 CYS Chi-restraints excluded: chain Q residue 54 VAL Chi-restraints excluded: chain Q residue 101 LEU Chi-restraints excluded: chain R residue 3 ILE Chi-restraints excluded: chain R residue 19 THR Chi-restraints excluded: chain R residue 24 VAL Chi-restraints excluded: chain R residue 27 THR Chi-restraints excluded: chain R residue 101 THR Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain T residue 56 LEU Chi-restraints excluded: chain T residue 59 VAL Chi-restraints excluded: chain T residue 86 LEU Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain U residue 53 ASP Chi-restraints excluded: chain U residue 66 THR Chi-restraints excluded: chain V residue 4 ILE Chi-restraints excluded: chain V residue 38 LYS Chi-restraints excluded: chain V residue 52 CYS Chi-restraints excluded: chain V residue 54 ILE Chi-restraints excluded: chain W residue 17 VAL Chi-restraints excluded: chain W residue 28 LEU Chi-restraints excluded: chain W residue 70 THR Chi-restraints excluded: chain X residue 57 VAL Chi-restraints excluded: chain X residue 69 LYS Chi-restraints excluded: chain Z residue 18 PHE Chi-restraints excluded: chain Z residue 63 ASN Chi-restraints excluded: chain a residue 8 MET Chi-restraints excluded: chain a residue 64 VAL Chi-restraints excluded: chain a residue 178 VAL Chi-restraints excluded: chain a residue 193 LEU Chi-restraints excluded: chain a residue 196 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1048 random chunks: chunk 941 optimal weight: 50.0000 chunk 716 optimal weight: 20.0000 chunk 494 optimal weight: 9.9990 chunk 105 optimal weight: 10.0000 chunk 455 optimal weight: 2.9990 chunk 640 optimal weight: 10.0000 chunk 956 optimal weight: 10.0000 chunk 1013 optimal weight: 20.0000 chunk 499 optimal weight: 20.0000 chunk 906 optimal weight: 10.0000 chunk 272 optimal weight: 20.0000 overall best weight: 8.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 51 GLN y 20 ASN ** G 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 7 ASN H 68 HIS ** I 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 53 GLN ** J 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 111 GLN V 50 ASN ** X 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 68 HIS Z 55 HIS ** a 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.3027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 162700 Z= 0.313 Angle : 0.683 11.745 243508 Z= 0.353 Chirality : 0.039 0.320 31146 Planarity : 0.005 0.072 12986 Dihedral : 23.468 179.573 81733 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 16.73 Ramachandran Plot: Outliers : 0.27 % Allowed : 13.14 % Favored : 86.58 % Rotamer: Outliers : 6.11 % Allowed : 19.40 % Favored : 74.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.30 % 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: -2.56 (0.10), residues: 5836 helix: -0.41 (0.12), residues: 1855 sheet: -1.65 (0.16), residues: 995 loop : -2.62 (0.11), residues: 2986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP b 247 HIS 0.018 0.002 HIS X 56 PHE 0.023 0.002 PHE Z 36 TYR 0.022 0.002 TYR I 75 ARG 0.009 0.001 ARG S 84 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11672 Ramachandran restraints generated. 5836 Oldfield, 0 Emsley, 5836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11672 Ramachandran restraints generated. 5836 Oldfield, 0 Emsley, 5836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1312 residues out of total 4862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 297 poor density : 1015 time to evaluate : 6.675 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 190 LYS cc_start: 0.8916 (tttt) cc_final: 0.8658 (ttpt) REVERT: d 1 MET cc_start: 0.5023 (mmm) cc_final: 0.4734 (mmm) REVERT: d 29 HIS cc_start: 0.8375 (OUTLIER) cc_final: 0.7915 (t70) REVERT: d 30 GLN cc_start: 0.8797 (tm-30) cc_final: 0.8153 (tm-30) REVERT: d 115 GLN cc_start: 0.8895 (tp-100) cc_final: 0.8649 (tp-100) REVERT: d 188 MET cc_start: 0.8120 (tpp) cc_final: 0.7909 (tpp) REVERT: d 195 GLN cc_start: 0.8554 (OUTLIER) cc_final: 0.7965 (mp10) REVERT: e 4 HIS cc_start: 0.8486 (t-170) cc_final: 0.8060 (t-170) REVERT: e 9 ASP cc_start: 0.7704 (OUTLIER) cc_final: 0.7377 (m-30) REVERT: e 16 MET cc_start: 0.8467 (mmm) cc_final: 0.8026 (mmm) REVERT: e 31 GLU cc_start: 0.8909 (mt-10) cc_final: 0.8243 (mp0) REVERT: e 95 MET cc_start: 0.8421 (ttp) cc_final: 0.7926 (ttp) REVERT: e 96 TRP cc_start: 0.8795 (m100) cc_final: 0.8344 (m100) REVERT: e 176 PHE cc_start: 0.7137 (OUTLIER) cc_final: 0.6678 (m-80) REVERT: f 2 ARG cc_start: 0.7864 (OUTLIER) cc_final: 0.7609 (mmt-90) REVERT: f 41 GLU cc_start: 0.8049 (tp30) cc_final: 0.7655 (pp20) REVERT: f 57 TYR cc_start: 0.7274 (m-80) cc_final: 0.7031 (m-80) REVERT: f 169 ARG cc_start: 0.8034 (mmm160) cc_final: 0.7096 (ttt90) REVERT: g 25 TYR cc_start: 0.7782 (t80) cc_final: 0.7356 (t80) REVERT: j 28 LEU cc_start: 0.8992 (tt) cc_final: 0.8730 (tp) REVERT: l 143 GLU cc_start: 0.7216 (pt0) cc_final: 0.6981 (pt0) REVERT: m 33 LEU cc_start: 0.9021 (tp) cc_final: 0.8664 (mp) REVERT: m 75 GLU cc_start: 0.8087 (tt0) cc_final: 0.7798 (mt-10) REVERT: m 90 GLU cc_start: 0.7534 (tt0) cc_final: 0.6566 (tt0) REVERT: n 54 LEU cc_start: 0.9159 (tp) cc_final: 0.8848 (tt) REVERT: n 72 ASP cc_start: 0.8676 (t70) cc_final: 0.8017 (t0) REVERT: n 82 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.7930 (pm20) REVERT: n 110 MET cc_start: 0.8411 (mmm) cc_final: 0.8095 (mmm) REVERT: o 34 HIS cc_start: 0.8247 (m-70) cc_final: 0.7922 (m-70) REVERT: o 58 ILE cc_start: 0.8454 (mt) cc_final: 0.7883 (tp) REVERT: o 61 GLN cc_start: 0.9147 (OUTLIER) cc_final: 0.8325 (tp40) REVERT: p 8 GLU cc_start: 0.8802 (mt-10) cc_final: 0.8376 (mt-10) REVERT: p 26 GLU cc_start: 0.8151 (tt0) cc_final: 0.7715 (tm-30) REVERT: p 70 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7711 (mp0) REVERT: r 10 LYS cc_start: 0.8500 (OUTLIER) cc_final: 0.8093 (ptpp) REVERT: r 16 GLU cc_start: 0.8324 (tt0) cc_final: 0.7849 (tt0) REVERT: s 52 GLU cc_start: 0.8722 (mt-10) cc_final: 0.8364 (tt0) REVERT: t 15 HIS cc_start: 0.7545 (t70) cc_final: 0.7298 (t-90) REVERT: v 12 GLN cc_start: 0.7919 (pm20) cc_final: 0.7477 (pp30) REVERT: v 64 VAL cc_start: 0.8366 (t) cc_final: 0.8012 (m) REVERT: v 87 GLN cc_start: 0.7785 (OUTLIER) cc_final: 0.7444 (mp10) REVERT: x 69 GLU cc_start: 0.8182 (mt-10) cc_final: 0.7781 (mt-10) REVERT: y 23 ARG cc_start: 0.8732 (mpt180) cc_final: 0.8338 (mpt180) REVERT: y 40 SER cc_start: 0.9287 (p) cc_final: 0.8744 (t) REVERT: y 54 LYS cc_start: 0.8789 (mtmt) cc_final: 0.8443 (mttt) REVERT: y 60 LYS cc_start: 0.8805 (mmmm) cc_final: 0.8579 (mmmt) REVERT: z 55 LYS cc_start: 0.8929 (mttp) cc_final: 0.8378 (tmtt) REVERT: A 23 LYS cc_start: 0.8329 (mtmm) cc_final: 0.8066 (mppt) REVERT: A 40 CYS cc_start: 0.8224 (OUTLIER) cc_final: 0.7769 (m) REVERT: B 35 GLU cc_start: 0.7845 (mt-10) cc_final: 0.7437 (mt-10) REVERT: C 47 ILE cc_start: 0.8285 (mt) cc_final: 0.7890 (pt) REVERT: D 10 LEU cc_start: 0.9092 (tp) cc_final: 0.8835 (tt) REVERT: E 53 ASP cc_start: 0.8143 (m-30) cc_final: 0.7861 (m-30) REVERT: G 34 ARG cc_start: 0.7425 (mmp80) cc_final: 0.6440 (tpm170) REVERT: G 88 GLN cc_start: 0.7815 (mm-40) cc_final: 0.7517 (mp10) REVERT: G 93 HIS cc_start: 0.8353 (m90) cc_final: 0.7834 (m-70) REVERT: G 95 TRP cc_start: 0.8270 (t60) cc_final: 0.7720 (t60) REVERT: G 99 MET cc_start: 0.8579 (ptp) cc_final: 0.8058 (ptp) REVERT: G 221 ARG cc_start: 0.7786 (OUTLIER) cc_final: 0.7439 (mtt-85) REVERT: H 34 SER cc_start: 0.9092 (t) cc_final: 0.8743 (p) REVERT: H 55 VAL cc_start: 0.8804 (t) cc_final: 0.8602 (t) REVERT: H 61 LYS cc_start: 0.7952 (mptt) cc_final: 0.7520 (pttm) REVERT: H 92 ASP cc_start: 0.8966 (t70) cc_final: 0.8646 (p0) REVERT: H 111 ASP cc_start: 0.7750 (t70) cc_final: 0.7325 (t0) REVERT: H 117 ASP cc_start: 0.8561 (m-30) cc_final: 0.8199 (p0) REVERT: I 3 TYR cc_start: 0.7888 (t80) cc_final: 0.7178 (t80) REVERT: I 189 ASP cc_start: 0.6263 (m-30) cc_final: 0.5826 (m-30) REVERT: J 64 GLU cc_start: 0.8880 (mt-10) cc_final: 0.8648 (tm-30) REVERT: J 89 THR cc_start: 0.8598 (m) cc_final: 0.8234 (p) REVERT: J 125 LYS cc_start: 0.8934 (tppt) cc_final: 0.8543 (tptp) REVERT: J 127 TYR cc_start: 0.8429 (m-80) cc_final: 0.8142 (m-80) REVERT: J 146 MET cc_start: 0.7511 (ttt) cc_final: 0.7297 (ttt) REVERT: K 13 ASP cc_start: 0.8736 (m-30) cc_final: 0.7981 (p0) REVERT: K 62 MET cc_start: 0.8092 (mmm) cc_final: 0.7831 (mmm) REVERT: L 10 LYS cc_start: 0.8596 (mmtp) cc_final: 0.8147 (ttpt) REVERT: L 17 PHE cc_start: 0.7004 (OUTLIER) cc_final: 0.6096 (p90) REVERT: L 51 GLN cc_start: 0.8730 (tt0) cc_final: 0.8273 (mm-40) REVERT: L 100 MET cc_start: 0.9066 (mtt) cc_final: 0.8756 (mtt) REVERT: M 4 ASP cc_start: 0.8255 (t70) cc_final: 0.8055 (t0) REVERT: M 11 THR cc_start: 0.9141 (m) cc_final: 0.8875 (p) REVERT: M 95 MET cc_start: 0.9125 (mpp) cc_final: 0.8687 (mpp) REVERT: N 56 MET cc_start: 0.8238 (ppp) cc_final: 0.7714 (ppp) REVERT: N 102 PHE cc_start: 0.7900 (m-80) cc_final: 0.7076 (m-80) REVERT: N 104 THR cc_start: 0.8071 (t) cc_final: 0.7828 (m) REVERT: O 10 LEU cc_start: 0.8503 (pp) cc_final: 0.8198 (pt) REVERT: O 11 LYS cc_start: 0.8573 (ptpt) cc_final: 0.8087 (mtmm) REVERT: O 19 ASP cc_start: 0.8788 (m-30) cc_final: 0.8021 (p0) REVERT: O 20 GLN cc_start: 0.9111 (tp40) cc_final: 0.8692 (tm-30) REVERT: O 46 LYS cc_start: 0.8769 (mttp) cc_final: 0.8516 (mmtp) REVERT: O 63 ASP cc_start: 0.6740 (t0) cc_final: 0.6387 (t0) REVERT: P 74 LYS cc_start: 0.8705 (ptpt) cc_final: 0.8414 (mmmt) REVERT: P 86 LYS cc_start: 0.8526 (ptpp) cc_final: 0.8091 (pttm) REVERT: P 124 LYS cc_start: 0.7539 (pptt) cc_final: 0.7056 (ptmt) REVERT: Q 28 GLN cc_start: 0.8361 (mp10) cc_final: 0.7827 (mt0) REVERT: Q 111 GLN cc_start: 0.8270 (mt0) cc_final: 0.7965 (mt0) REVERT: R 10 ASP cc_start: 0.8793 (m-30) cc_final: 0.8203 (m-30) REVERT: R 51 GLN cc_start: 0.8515 (mp10) cc_final: 0.8162 (mp10) REVERT: R 79 LEU cc_start: 0.9024 (mt) cc_final: 0.8746 (tp) REVERT: S 13 VAL cc_start: 0.8791 (t) cc_final: 0.8543 (t) REVERT: S 48 GLN cc_start: 0.7931 (mt0) cc_final: 0.7575 (mt0) REVERT: T 9 LYS cc_start: 0.9444 (mttt) cc_final: 0.8870 (mmmt) REVERT: T 39 GLN cc_start: 0.8155 (mp10) cc_final: 0.7939 (mp10) REVERT: U 1 MET cc_start: 0.6466 (OUTLIER) cc_final: 0.5745 (ttt) REVERT: V 10 ARG cc_start: 0.8905 (ptm-80) cc_final: 0.8585 (ptm-80) REVERT: W 22 TYR cc_start: 0.7811 (p90) cc_final: 0.7542 (p90) REVERT: W 37 LYS cc_start: 0.8566 (mmmm) cc_final: 0.8307 (mmmt) REVERT: X 9 PHE cc_start: 0.8713 (t80) cc_final: 0.8406 (t80) REVERT: X 11 ASP cc_start: 0.7655 (t0) cc_final: 0.7350 (t0) REVERT: X 47 THR cc_start: 0.7676 (p) cc_final: 0.7403 (m) REVERT: X 69 LYS cc_start: 0.8287 (OUTLIER) cc_final: 0.7845 (mtpt) REVERT: Y 54 GLN cc_start: 0.8551 (tm-30) cc_final: 0.8020 (tm-30) REVERT: Y 58 ASP cc_start: 0.9005 (t70) cc_final: 0.8309 (t0) REVERT: Y 83 ASN cc_start: 0.8312 (t0) cc_final: 0.8073 (t0) REVERT: Z 32 ARG cc_start: 0.8260 (tpp-160) cc_final: 0.8010 (mmm160) REVERT: Z 46 ARG cc_start: 0.8073 (mpt180) cc_final: 0.7230 (tpt-90) REVERT: Z 48 LYS cc_start: 0.8474 (mmtt) cc_final: 0.8267 (mmtt) REVERT: a 167 LYS cc_start: 0.0308 (tptt) cc_final: -0.0359 (mttp) outliers start: 297 outliers final: 211 residues processed: 1188 average time/residue: 1.2580 time to fit residues: 2640.5683 Evaluate side-chains 1165 residues out of total 4862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 226 poor density : 939 time to evaluate : 6.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 44 ASN Chi-restraints excluded: chain b residue 159 THR Chi-restraints excluded: chain b residue 183 VAL Chi-restraints excluded: chain b residue 203 VAL Chi-restraints excluded: chain b residue 228 ASP Chi-restraints excluded: chain b residue 256 THR Chi-restraints excluded: chain c residue 108 ASP Chi-restraints excluded: chain c residue 138 LEU Chi-restraints excluded: chain c residue 139 SER Chi-restraints excluded: chain c residue 175 LEU Chi-restraints excluded: chain c residue 180 VAL Chi-restraints excluded: chain d residue 29 HIS Chi-restraints excluded: chain d residue 84 THR Chi-restraints excluded: chain d residue 96 VAL Chi-restraints excluded: chain d residue 140 ASP Chi-restraints excluded: chain d residue 195 GLN Chi-restraints excluded: chain e residue 9 ASP Chi-restraints excluded: chain e residue 22 ASN Chi-restraints excluded: chain e residue 24 VAL Chi-restraints excluded: chain e residue 67 THR Chi-restraints excluded: chain e residue 117 SER Chi-restraints excluded: chain e residue 176 PHE Chi-restraints excluded: chain f residue 2 ARG Chi-restraints excluded: chain f residue 9 VAL Chi-restraints excluded: chain f residue 71 LEU Chi-restraints excluded: chain g residue 4 ILE Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain g residue 48 GLU Chi-restraints excluded: chain h residue 15 VAL Chi-restraints excluded: chain h residue 27 VAL Chi-restraints excluded: chain h residue 55 VAL Chi-restraints excluded: chain i residue 54 ILE Chi-restraints excluded: chain j residue 36 LEU Chi-restraints excluded: chain j residue 55 ILE Chi-restraints excluded: chain j residue 64 VAL Chi-restraints excluded: chain j residue 105 VAL Chi-restraints excluded: chain k residue 62 VAL Chi-restraints excluded: chain k residue 76 VAL Chi-restraints excluded: chain k residue 87 LEU Chi-restraints excluded: chain k residue 104 THR Chi-restraints excluded: chain l residue 35 HIS Chi-restraints excluded: chain l residue 42 SER Chi-restraints excluded: chain l residue 81 ASP Chi-restraints excluded: chain l residue 111 ILE Chi-restraints excluded: chain l residue 116 VAL Chi-restraints excluded: chain l residue 117 THR Chi-restraints excluded: chain l residue 120 VAL Chi-restraints excluded: chain l residue 122 VAL Chi-restraints excluded: chain m residue 7 THR Chi-restraints excluded: chain m residue 36 VAL Chi-restraints excluded: chain m residue 41 LEU Chi-restraints excluded: chain n residue 18 GLN Chi-restraints excluded: chain n residue 37 THR Chi-restraints excluded: chain n residue 82 GLU Chi-restraints excluded: chain n residue 106 ASP Chi-restraints excluded: chain o residue 2 ASP Chi-restraints excluded: chain o residue 36 TYR Chi-restraints excluded: chain o residue 61 GLN Chi-restraints excluded: chain o residue 62 LEU Chi-restraints excluded: chain o residue 69 ASP Chi-restraints excluded: chain o residue 93 ASP Chi-restraints excluded: chain o residue 106 LEU Chi-restraints excluded: chain o residue 108 ASP Chi-restraints excluded: chain p residue 31 VAL Chi-restraints excluded: chain p residue 35 SER Chi-restraints excluded: chain p residue 40 GLN Chi-restraints excluded: chain p residue 59 THR Chi-restraints excluded: chain p residue 64 SER Chi-restraints excluded: chain p residue 70 GLU Chi-restraints excluded: chain p residue 103 THR Chi-restraints excluded: chain p residue 109 ILE Chi-restraints excluded: chain q residue 19 GLN Chi-restraints excluded: chain q residue 73 ILE Chi-restraints excluded: chain r residue 10 LYS Chi-restraints excluded: chain r residue 19 THR Chi-restraints excluded: chain r residue 33 VAL Chi-restraints excluded: chain r residue 40 MET Chi-restraints excluded: chain r residue 41 ILE Chi-restraints excluded: chain r residue 49 ILE Chi-restraints excluded: chain r residue 62 GLU Chi-restraints excluded: chain r residue 101 ILE Chi-restraints excluded: chain s residue 37 THR Chi-restraints excluded: chain s residue 69 LEU Chi-restraints excluded: chain s residue 81 SER Chi-restraints excluded: chain t residue 32 LEU Chi-restraints excluded: chain t residue 78 SER Chi-restraints excluded: chain t residue 87 LEU Chi-restraints excluded: chain u residue 8 ASP Chi-restraints excluded: chain u residue 17 ASP Chi-restraints excluded: chain u residue 29 SER Chi-restraints excluded: chain u residue 35 VAL Chi-restraints excluded: chain u residue 40 LEU Chi-restraints excluded: chain u residue 71 ILE Chi-restraints excluded: chain v residue 7 GLU Chi-restraints excluded: chain v residue 8 VAL Chi-restraints excluded: chain v residue 38 LEU Chi-restraints excluded: chain v residue 45 ASP Chi-restraints excluded: chain v residue 48 MET Chi-restraints excluded: chain v residue 87 GLN Chi-restraints excluded: chain v residue 89 ILE Chi-restraints excluded: chain v residue 92 VAL Chi-restraints excluded: chain w residue 8 ASN Chi-restraints excluded: chain w residue 17 LEU Chi-restraints excluded: chain w residue 27 VAL Chi-restraints excluded: chain w residue 63 VAL Chi-restraints excluded: chain x residue 41 SER Chi-restraints excluded: chain x residue 58 ILE Chi-restraints excluded: chain x residue 67 LEU Chi-restraints excluded: chain z residue 11 SER Chi-restraints excluded: chain z residue 48 ASN Chi-restraints excluded: chain z residue 56 VAL Chi-restraints excluded: chain A residue 33 ASN Chi-restraints excluded: chain A residue 40 CYS Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 58 ASP Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain E residue 51 LYS Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 17 VAL Chi-restraints excluded: chain F residue 30 GLU Chi-restraints excluded: chain G residue 30 ILE Chi-restraints excluded: chain G residue 59 ILE Chi-restraints excluded: chain G residue 122 ASP Chi-restraints excluded: chain G residue 158 ASP Chi-restraints excluded: chain G residue 163 ILE Chi-restraints excluded: chain G residue 198 VAL Chi-restraints excluded: chain G residue 221 ARG Chi-restraints excluded: chain H residue 5 HIS Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 50 SER Chi-restraints excluded: chain H residue 68 HIS Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 138 GLN Chi-restraints excluded: chain H residue 164 THR Chi-restraints excluded: chain I residue 66 VAL Chi-restraints excluded: chain I residue 92 LEU Chi-restraints excluded: chain I residue 177 MET Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 29 ILE Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 141 ASP Chi-restraints excluded: chain K residue 3 HIS Chi-restraints excluded: chain K residue 23 GLU Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 64 VAL Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain L residue 17 PHE Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain L residue 129 ASN Chi-restraints excluded: chain L residue 132 THR Chi-restraints excluded: chain M residue 38 VAL Chi-restraints excluded: chain M residue 45 ILE Chi-restraints excluded: chain M residue 74 ILE Chi-restraints excluded: chain M residue 77 VAL Chi-restraints excluded: chain M residue 84 ILE Chi-restraints excluded: chain M residue 111 THR Chi-restraints excluded: chain M residue 124 ILE Chi-restraints excluded: chain N residue 42 THR Chi-restraints excluded: chain N residue 44 ARG Chi-restraints excluded: chain N residue 46 VAL Chi-restraints excluded: chain N residue 57 VAL Chi-restraints excluded: chain N residue 61 ASP Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain O residue 22 THR Chi-restraints excluded: chain O residue 36 VAL Chi-restraints excluded: chain O residue 57 VAL Chi-restraints excluded: chain O residue 71 LEU Chi-restraints excluded: chain O residue 92 LEU Chi-restraints excluded: chain P residue 30 ILE Chi-restraints excluded: chain P residue 39 ASN Chi-restraints excluded: chain P residue 57 SER Chi-restraints excluded: chain P residue 73 VAL Chi-restraints excluded: chain P residue 95 THR Chi-restraints excluded: chain P residue 121 ARG Chi-restraints excluded: chain P residue 126 ARG Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain Q residue 33 CYS Chi-restraints excluded: chain Q residue 54 VAL Chi-restraints excluded: chain Q residue 101 LEU Chi-restraints excluded: chain Q residue 108 ASP Chi-restraints excluded: chain R residue 3 ILE Chi-restraints excluded: chain R residue 15 VAL Chi-restraints excluded: chain R residue 19 THR Chi-restraints excluded: chain R residue 24 VAL Chi-restraints excluded: chain R residue 27 THR Chi-restraints excluded: chain R residue 67 ASP Chi-restraints excluded: chain R residue 73 SER Chi-restraints excluded: chain R residue 101 THR Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain T residue 56 LEU Chi-restraints excluded: chain T residue 69 LEU Chi-restraints excluded: chain T residue 86 LEU Chi-restraints excluded: chain U residue 1 MET Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain U residue 53 ASP Chi-restraints excluded: chain U residue 66 THR Chi-restraints excluded: chain V residue 4 ILE Chi-restraints excluded: chain V residue 28 VAL Chi-restraints excluded: chain V residue 52 CYS Chi-restraints excluded: chain V residue 54 ILE Chi-restraints excluded: chain V residue 57 VAL Chi-restraints excluded: chain V residue 69 THR Chi-restraints excluded: chain V residue 77 VAL Chi-restraints excluded: chain W residue 17 VAL Chi-restraints excluded: chain W residue 28 LEU Chi-restraints excluded: chain W residue 70 THR Chi-restraints excluded: chain X residue 57 VAL Chi-restraints excluded: chain X residue 59 VAL Chi-restraints excluded: chain X residue 69 LYS Chi-restraints excluded: chain Z residue 18 PHE Chi-restraints excluded: chain Z residue 23 GLU Chi-restraints excluded: chain Z residue 30 GLU Chi-restraints excluded: chain Z residue 55 HIS Chi-restraints excluded: chain Z residue 63 ASN Chi-restraints excluded: chain a residue 8 MET Chi-restraints excluded: chain a residue 27 ILE Chi-restraints excluded: chain a residue 64 VAL Chi-restraints excluded: chain a residue 178 VAL Chi-restraints excluded: chain a residue 193 LEU Chi-restraints excluded: chain a residue 196 LEU Chi-restraints excluded: chain a residue 222 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1048 random chunks: chunk 843 optimal weight: 10.0000 chunk 575 optimal weight: 20.0000 chunk 14 optimal weight: 7.9990 chunk 754 optimal weight: 20.0000 chunk 417 optimal weight: 9.9990 chunk 864 optimal weight: 20.0000 chunk 700 optimal weight: 20.0000 chunk 1 optimal weight: 5.9990 chunk 517 optimal weight: 8.9990 chunk 909 optimal weight: 20.0000 chunk 255 optimal weight: 9.9990 overall best weight: 8.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 85 ASN ** b 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 73 ASN ** w 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 13 ASN ** F 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 53 GLN ** J 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 63 ASN ** N 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 50 ASN ** X 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 68 HIS ** a 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.3230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 162700 Z= 0.310 Angle : 0.682 12.233 243508 Z= 0.352 Chirality : 0.039 0.342 31146 Planarity : 0.005 0.071 12986 Dihedral : 23.531 179.173 81731 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 17.24 Ramachandran Plot: Outliers : 0.29 % Allowed : 13.02 % Favored : 86.69 % Rotamer: Outliers : 6.29 % Allowed : 20.38 % Favored : 73.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.30 % 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: -2.47 (0.11), residues: 5836 helix: -0.32 (0.12), residues: 1852 sheet: -1.60 (0.16), residues: 1012 loop : -2.58 (0.11), residues: 2972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP b 247 HIS 0.028 0.002 HIS H 68 PHE 0.026 0.002 PHE h 76 TYR 0.036 0.002 TYR W 50 ARG 0.011 0.001 ARG Z 54 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11672 Ramachandran restraints generated. 5836 Oldfield, 0 Emsley, 5836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11672 Ramachandran restraints generated. 5836 Oldfield, 0 Emsley, 5836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1295 residues out of total 4862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 306 poor density : 989 time to evaluate : 6.675 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 190 LYS cc_start: 0.8840 (tttt) cc_final: 0.8569 (ttpt) REVERT: d 1 MET cc_start: 0.5193 (mmm) cc_final: 0.4938 (mmm) REVERT: d 29 HIS cc_start: 0.8406 (OUTLIER) cc_final: 0.7949 (t70) REVERT: d 30 GLN cc_start: 0.8814 (tm-30) cc_final: 0.8167 (tm-30) REVERT: d 195 GLN cc_start: 0.8549 (OUTLIER) cc_final: 0.7944 (mp10) REVERT: e 4 HIS cc_start: 0.8469 (t-170) cc_final: 0.8051 (t-170) REVERT: e 9 ASP cc_start: 0.7698 (OUTLIER) cc_final: 0.7398 (m-30) REVERT: e 16 MET cc_start: 0.8493 (mmm) cc_final: 0.7841 (mmm) REVERT: e 19 PHE cc_start: 0.8855 (m-80) cc_final: 0.8272 (m-10) REVERT: e 95 MET cc_start: 0.8515 (ttp) cc_final: 0.8168 (ttp) REVERT: e 96 TRP cc_start: 0.8840 (m100) cc_final: 0.8373 (m100) REVERT: e 164 GLU cc_start: 0.8719 (mm-30) cc_final: 0.8437 (mm-30) REVERT: e 176 PHE cc_start: 0.7166 (OUTLIER) cc_final: 0.6764 (m-80) REVERT: f 2 ARG cc_start: 0.7894 (OUTLIER) cc_final: 0.7643 (mmt-90) REVERT: f 41 GLU cc_start: 0.8020 (tp30) cc_final: 0.7653 (pp20) REVERT: f 169 ARG cc_start: 0.8042 (mmm160) cc_final: 0.7086 (ttt90) REVERT: j 28 LEU cc_start: 0.9018 (tt) cc_final: 0.8791 (tp) REVERT: l 143 GLU cc_start: 0.7098 (OUTLIER) cc_final: 0.6852 (pt0) REVERT: m 33 LEU cc_start: 0.9025 (tp) cc_final: 0.8671 (mp) REVERT: m 75 GLU cc_start: 0.8067 (tt0) cc_final: 0.7787 (mt-10) REVERT: m 90 GLU cc_start: 0.7477 (tt0) cc_final: 0.6548 (tt0) REVERT: n 72 ASP cc_start: 0.8695 (t70) cc_final: 0.7997 (t0) REVERT: n 110 MET cc_start: 0.8194 (mmm) cc_final: 0.7985 (mmm) REVERT: o 34 HIS cc_start: 0.8285 (m-70) cc_final: 0.7862 (m-70) REVERT: o 58 ILE cc_start: 0.8441 (mt) cc_final: 0.7842 (tp) REVERT: o 61 GLN cc_start: 0.9104 (OUTLIER) cc_final: 0.8330 (tp40) REVERT: o 88 LYS cc_start: 0.8647 (tttp) cc_final: 0.8293 (ptmm) REVERT: p 8 GLU cc_start: 0.8770 (mt-10) cc_final: 0.8346 (mt-10) REVERT: p 70 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7699 (mp0) REVERT: r 10 LYS cc_start: 0.8524 (OUTLIER) cc_final: 0.8129 (ptpp) REVERT: r 16 GLU cc_start: 0.8357 (tt0) cc_final: 0.7946 (tt0) REVERT: s 2 GLU cc_start: 0.8521 (tm-30) cc_final: 0.8097 (pt0) REVERT: s 52 GLU cc_start: 0.8743 (mt-10) cc_final: 0.8404 (tt0) REVERT: t 1 MET cc_start: 0.5628 (mpt) cc_final: 0.5051 (mpt) REVERT: t 15 HIS cc_start: 0.7591 (t70) cc_final: 0.7362 (t-90) REVERT: v 7 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7821 (pm20) REVERT: v 87 GLN cc_start: 0.7762 (OUTLIER) cc_final: 0.7393 (mp10) REVERT: w 79 GLU cc_start: 0.7554 (mp0) cc_final: 0.7325 (mp0) REVERT: x 69 GLU cc_start: 0.8114 (mt-10) cc_final: 0.7758 (mt-10) REVERT: y 13 GLU cc_start: 0.8850 (mt-10) cc_final: 0.8113 (mm-30) REVERT: y 23 ARG cc_start: 0.8755 (mpt180) cc_final: 0.8362 (mpt180) REVERT: y 40 SER cc_start: 0.9286 (p) cc_final: 0.8755 (t) REVERT: y 60 LYS cc_start: 0.8874 (mmmm) cc_final: 0.8571 (mtpp) REVERT: z 55 LYS cc_start: 0.8942 (mttp) cc_final: 0.8421 (tmtt) REVERT: A 23 LYS cc_start: 0.8410 (mtmm) cc_final: 0.8146 (mppt) REVERT: B 35 GLU cc_start: 0.7819 (mt-10) cc_final: 0.7411 (mt-10) REVERT: D 10 LEU cc_start: 0.9095 (tp) cc_final: 0.8843 (tt) REVERT: E 53 ASP cc_start: 0.8045 (m-30) cc_final: 0.7779 (m-30) REVERT: G 34 ARG cc_start: 0.7476 (mmp80) cc_final: 0.6351 (tpm170) REVERT: G 88 GLN cc_start: 0.7765 (mm-40) cc_final: 0.7471 (mp10) REVERT: G 93 HIS cc_start: 0.8352 (m90) cc_final: 0.7994 (m-70) REVERT: G 95 TRP cc_start: 0.8263 (t60) cc_final: 0.7721 (t60) REVERT: G 99 MET cc_start: 0.8611 (ptp) cc_final: 0.8015 (ptp) REVERT: G 221 ARG cc_start: 0.7844 (OUTLIER) cc_final: 0.7553 (mtt-85) REVERT: H 34 SER cc_start: 0.9088 (t) cc_final: 0.8741 (p) REVERT: H 55 VAL cc_start: 0.8834 (t) cc_final: 0.8593 (t) REVERT: H 61 LYS cc_start: 0.7956 (mptt) cc_final: 0.7548 (pttm) REVERT: H 92 ASP cc_start: 0.8979 (t70) cc_final: 0.8636 (p0) REVERT: H 111 ASP cc_start: 0.7605 (t70) cc_final: 0.7349 (t0) REVERT: H 117 ASP cc_start: 0.8558 (m-30) cc_final: 0.8183 (p0) REVERT: I 3 TYR cc_start: 0.7866 (t80) cc_final: 0.7162 (t80) REVERT: J 53 ARG cc_start: 0.8049 (ttp80) cc_final: 0.7811 (ttp80) REVERT: J 64 GLU cc_start: 0.8917 (mt-10) cc_final: 0.8515 (tm-30) REVERT: J 89 THR cc_start: 0.8549 (m) cc_final: 0.8214 (p) REVERT: J 125 LYS cc_start: 0.8977 (tppt) cc_final: 0.8551 (tptp) REVERT: J 127 TYR cc_start: 0.8405 (m-80) cc_final: 0.8108 (m-80) REVERT: J 146 MET cc_start: 0.7504 (ttt) cc_final: 0.7282 (ttt) REVERT: K 13 ASP cc_start: 0.8776 (m-30) cc_final: 0.8021 (p0) REVERT: K 62 MET cc_start: 0.8149 (mmm) cc_final: 0.7895 (mmm) REVERT: L 10 LYS cc_start: 0.8575 (mmtp) cc_final: 0.8136 (ttpt) REVERT: L 17 PHE cc_start: 0.7044 (OUTLIER) cc_final: 0.5879 (p90) REVERT: L 51 GLN cc_start: 0.8708 (tt0) cc_final: 0.8246 (mm-40) REVERT: L 100 MET cc_start: 0.9115 (mtt) cc_final: 0.8755 (mtt) REVERT: M 11 THR cc_start: 0.9147 (m) cc_final: 0.8884 (p) REVERT: M 42 GLU cc_start: 0.8215 (tp30) cc_final: 0.7804 (tm-30) REVERT: M 46 GLU cc_start: 0.8159 (tm-30) cc_final: 0.7858 (tm-30) REVERT: M 90 GLU cc_start: 0.8072 (mp0) cc_final: 0.7834 (mp0) REVERT: M 95 MET cc_start: 0.9099 (mpp) cc_final: 0.8667 (mpp) REVERT: N 56 MET cc_start: 0.8201 (ppp) cc_final: 0.7702 (ppp) REVERT: N 102 PHE cc_start: 0.7909 (m-80) cc_final: 0.7085 (m-80) REVERT: N 104 THR cc_start: 0.8026 (t) cc_final: 0.7778 (m) REVERT: O 10 LEU cc_start: 0.8441 (pp) cc_final: 0.8182 (pt) REVERT: O 11 LYS cc_start: 0.8584 (ptpt) cc_final: 0.8120 (mtmm) REVERT: O 19 ASP cc_start: 0.8667 (m-30) cc_final: 0.7953 (p0) REVERT: O 20 GLN cc_start: 0.9117 (tp40) cc_final: 0.8700 (tm-30) REVERT: O 46 LYS cc_start: 0.8772 (mttp) cc_final: 0.8503 (mttm) REVERT: O 63 ASP cc_start: 0.6770 (t0) cc_final: 0.6327 (t0) REVERT: P 41 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8527 (mp) REVERT: P 74 LYS cc_start: 0.8664 (ptpt) cc_final: 0.8373 (mmmt) REVERT: P 86 LYS cc_start: 0.8537 (ptpp) cc_final: 0.8085 (pttm) REVERT: P 124 LYS cc_start: 0.7566 (pptt) cc_final: 0.7086 (ptmt) REVERT: Q 28 GLN cc_start: 0.8595 (mp10) cc_final: 0.7833 (mt0) REVERT: Q 111 GLN cc_start: 0.8237 (mt0) cc_final: 0.7907 (mt0) REVERT: R 10 ASP cc_start: 0.8791 (m-30) cc_final: 0.8237 (m-30) REVERT: R 49 GLU cc_start: 0.9090 (pm20) cc_final: 0.8890 (pm20) REVERT: R 51 GLN cc_start: 0.8527 (mp10) cc_final: 0.8159 (mp10) REVERT: S 48 GLN cc_start: 0.7884 (mt0) cc_final: 0.7651 (mt0) REVERT: S 95 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8702 (tt) REVERT: T 5 GLU cc_start: 0.8229 (tp30) cc_final: 0.7815 (tp30) REVERT: T 9 LYS cc_start: 0.9415 (mttt) cc_final: 0.8959 (mttm) REVERT: U 1 MET cc_start: 0.6437 (OUTLIER) cc_final: 0.5677 (ttp) REVERT: V 72 TRP cc_start: 0.8327 (m100) cc_final: 0.8008 (m100) REVERT: W 22 TYR cc_start: 0.7727 (p90) cc_final: 0.7463 (p90) REVERT: X 9 PHE cc_start: 0.8687 (t80) cc_final: 0.8374 (t80) REVERT: X 11 ASP cc_start: 0.7671 (t0) cc_final: 0.7446 (t0) REVERT: X 17 LYS cc_start: 0.8766 (mttp) cc_final: 0.8373 (ttmt) REVERT: X 46 LEU cc_start: 0.8456 (mt) cc_final: 0.8221 (mm) REVERT: X 69 LYS cc_start: 0.8256 (OUTLIER) cc_final: 0.7720 (mtmm) REVERT: Y 26 MET cc_start: 0.9063 (ptp) cc_final: 0.8514 (ptp) REVERT: Y 54 GLN cc_start: 0.8583 (tm-30) cc_final: 0.8062 (tm-30) REVERT: Y 58 ASP cc_start: 0.8925 (t70) cc_final: 0.8200 (t0) REVERT: Z 32 ARG cc_start: 0.8303 (tpp-160) cc_final: 0.8037 (mmm160) REVERT: Z 46 ARG cc_start: 0.8126 (mpt180) cc_final: 0.7344 (tpt-90) REVERT: a 167 LYS cc_start: 0.0817 (tptt) cc_final: 0.0137 (mttp) outliers start: 306 outliers final: 229 residues processed: 1164 average time/residue: 1.2584 time to fit residues: 2592.7902 Evaluate side-chains 1187 residues out of total 4862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 246 poor density : 941 time to evaluate : 6.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 44 ASN Chi-restraints excluded: chain b residue 159 THR Chi-restraints excluded: chain b residue 183 VAL Chi-restraints excluded: chain b residue 203 VAL Chi-restraints excluded: chain b residue 228 ASP Chi-restraints excluded: chain b residue 238 ASN Chi-restraints excluded: chain b residue 256 THR Chi-restraints excluded: chain c residue 1 MET Chi-restraints excluded: chain c residue 108 ASP Chi-restraints excluded: chain c residue 138 LEU Chi-restraints excluded: chain c residue 139 SER Chi-restraints excluded: chain c residue 175 LEU Chi-restraints excluded: chain c residue 180 VAL Chi-restraints excluded: chain d residue 29 HIS Chi-restraints excluded: chain d residue 84 THR Chi-restraints excluded: chain d residue 96 VAL Chi-restraints excluded: chain d residue 140 ASP Chi-restraints excluded: chain d residue 148 ILE Chi-restraints excluded: chain d residue 195 GLN Chi-restraints excluded: chain e residue 9 ASP Chi-restraints excluded: chain e residue 24 VAL Chi-restraints excluded: chain e residue 67 THR Chi-restraints excluded: chain e residue 77 LYS Chi-restraints excluded: chain e residue 86 CYS Chi-restraints excluded: chain e residue 176 PHE Chi-restraints excluded: chain f residue 2 ARG Chi-restraints excluded: chain g residue 4 ILE Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain g residue 48 GLU Chi-restraints excluded: chain h residue 15 VAL Chi-restraints excluded: chain h residue 27 VAL Chi-restraints excluded: chain h residue 55 VAL Chi-restraints excluded: chain i residue 54 ILE Chi-restraints excluded: chain j residue 36 LEU Chi-restraints excluded: chain j residue 55 ILE Chi-restraints excluded: chain j residue 64 VAL Chi-restraints excluded: chain j residue 105 VAL Chi-restraints excluded: chain j residue 109 LEU Chi-restraints excluded: chain j residue 142 ILE Chi-restraints excluded: chain k residue 3 GLN Chi-restraints excluded: chain k residue 62 VAL Chi-restraints excluded: chain k residue 76 VAL Chi-restraints excluded: chain k residue 87 LEU Chi-restraints excluded: chain k residue 88 ASN Chi-restraints excluded: chain k residue 97 THR Chi-restraints excluded: chain k residue 104 THR Chi-restraints excluded: chain l residue 35 HIS Chi-restraints excluded: chain l residue 42 SER Chi-restraints excluded: chain l residue 81 ASP Chi-restraints excluded: chain l residue 110 VAL Chi-restraints excluded: chain l residue 111 ILE Chi-restraints excluded: chain l residue 116 VAL Chi-restraints excluded: chain l residue 117 THR Chi-restraints excluded: chain l residue 120 VAL Chi-restraints excluded: chain l residue 122 VAL Chi-restraints excluded: chain l residue 143 GLU Chi-restraints excluded: chain m residue 7 THR Chi-restraints excluded: chain m residue 36 VAL Chi-restraints excluded: chain m residue 41 LEU Chi-restraints excluded: chain m residue 70 ASP Chi-restraints excluded: chain m residue 104 GLU Chi-restraints excluded: chain n residue 18 GLN Chi-restraints excluded: chain n residue 37 THR Chi-restraints excluded: chain n residue 106 ASP Chi-restraints excluded: chain o residue 2 ASP Chi-restraints excluded: chain o residue 28 VAL Chi-restraints excluded: chain o residue 36 TYR Chi-restraints excluded: chain o residue 61 GLN Chi-restraints excluded: chain o residue 62 LEU Chi-restraints excluded: chain o residue 69 ASP Chi-restraints excluded: chain o residue 78 VAL Chi-restraints excluded: chain o residue 93 ASP Chi-restraints excluded: chain o residue 108 ASP Chi-restraints excluded: chain p residue 31 VAL Chi-restraints excluded: chain p residue 35 SER Chi-restraints excluded: chain p residue 40 GLN Chi-restraints excluded: chain p residue 59 THR Chi-restraints excluded: chain p residue 64 SER Chi-restraints excluded: chain p residue 70 GLU Chi-restraints excluded: chain p residue 103 THR Chi-restraints excluded: chain p residue 109 ILE Chi-restraints excluded: chain q residue 8 ILE Chi-restraints excluded: chain q residue 19 GLN Chi-restraints excluded: chain q residue 73 ILE Chi-restraints excluded: chain r residue 10 LYS Chi-restraints excluded: chain r residue 19 THR Chi-restraints excluded: chain r residue 33 VAL Chi-restraints excluded: chain r residue 40 MET Chi-restraints excluded: chain r residue 41 ILE Chi-restraints excluded: chain r residue 49 ILE Chi-restraints excluded: chain r residue 62 GLU Chi-restraints excluded: chain r residue 101 ILE Chi-restraints excluded: chain s residue 37 THR Chi-restraints excluded: chain s residue 69 LEU Chi-restraints excluded: chain s residue 74 ILE Chi-restraints excluded: chain s residue 81 SER Chi-restraints excluded: chain t residue 32 LEU Chi-restraints excluded: chain t residue 50 LEU Chi-restraints excluded: chain t residue 78 SER Chi-restraints excluded: chain t residue 87 LEU Chi-restraints excluded: chain u residue 8 ASP Chi-restraints excluded: chain u residue 17 ASP Chi-restraints excluded: chain u residue 29 SER Chi-restraints excluded: chain u residue 35 VAL Chi-restraints excluded: chain u residue 40 LEU Chi-restraints excluded: chain u residue 71 ILE Chi-restraints excluded: chain v residue 7 GLU Chi-restraints excluded: chain v residue 8 VAL Chi-restraints excluded: chain v residue 38 LEU Chi-restraints excluded: chain v residue 45 ASP Chi-restraints excluded: chain v residue 59 GLU Chi-restraints excluded: chain v residue 61 LEU Chi-restraints excluded: chain v residue 87 GLN Chi-restraints excluded: chain v residue 89 ILE Chi-restraints excluded: chain v residue 92 VAL Chi-restraints excluded: chain w residue 8 ASN Chi-restraints excluded: chain w residue 17 LEU Chi-restraints excluded: chain w residue 27 VAL Chi-restraints excluded: chain w residue 63 VAL Chi-restraints excluded: chain x residue 41 SER Chi-restraints excluded: chain x residue 58 ILE Chi-restraints excluded: chain x residue 67 LEU Chi-restraints excluded: chain z residue 11 SER Chi-restraints excluded: chain z residue 48 ASN Chi-restraints excluded: chain z residue 53 MET Chi-restraints excluded: chain z residue 56 VAL Chi-restraints excluded: chain A residue 33 ASN Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 58 ASP Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain E residue 51 LYS Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 17 VAL Chi-restraints excluded: chain F residue 30 GLU Chi-restraints excluded: chain G residue 30 ILE Chi-restraints excluded: chain G residue 59 ILE Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 122 ASP Chi-restraints excluded: chain G residue 158 ASP Chi-restraints excluded: chain G residue 163 ILE Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 198 VAL Chi-restraints excluded: chain G residue 221 ARG Chi-restraints excluded: chain H residue 5 HIS Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 50 SER Chi-restraints excluded: chain H residue 138 GLN Chi-restraints excluded: chain H residue 164 THR Chi-restraints excluded: chain I residue 66 VAL Chi-restraints excluded: chain I residue 92 LEU Chi-restraints excluded: chain I residue 170 LEU Chi-restraints excluded: chain I residue 177 MET Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 29 ILE Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain J residue 87 VAL Chi-restraints excluded: chain J residue 95 MET Chi-restraints excluded: chain J residue 123 LEU Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 141 ASP Chi-restraints excluded: chain K residue 3 HIS Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 54 LEU Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain L residue 17 PHE Chi-restraints excluded: chain L residue 129 ASN Chi-restraints excluded: chain L residue 132 THR Chi-restraints excluded: chain M residue 10 LEU Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain M residue 38 VAL Chi-restraints excluded: chain M residue 45 ILE Chi-restraints excluded: chain M residue 74 ILE Chi-restraints excluded: chain M residue 77 VAL Chi-restraints excluded: chain M residue 84 ILE Chi-restraints excluded: chain M residue 111 THR Chi-restraints excluded: chain M residue 120 LEU Chi-restraints excluded: chain M residue 124 ILE Chi-restraints excluded: chain N residue 42 THR Chi-restraints excluded: chain N residue 44 ARG Chi-restraints excluded: chain N residue 46 VAL Chi-restraints excluded: chain N residue 57 VAL Chi-restraints excluded: chain N residue 61 ASP Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain O residue 14 ASP Chi-restraints excluded: chain O residue 22 THR Chi-restraints excluded: chain O residue 36 VAL Chi-restraints excluded: chain O residue 57 VAL Chi-restraints excluded: chain O residue 71 LEU Chi-restraints excluded: chain O residue 92 LEU Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 30 ILE Chi-restraints excluded: chain P residue 39 ASN Chi-restraints excluded: chain P residue 41 LEU Chi-restraints excluded: chain P residue 57 SER Chi-restraints excluded: chain P residue 73 VAL Chi-restraints excluded: chain P residue 81 LEU Chi-restraints excluded: chain P residue 95 THR Chi-restraints excluded: chain P residue 126 ARG Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain Q residue 33 CYS Chi-restraints excluded: chain Q residue 54 VAL Chi-restraints excluded: chain Q residue 76 HIS Chi-restraints excluded: chain Q residue 101 LEU Chi-restraints excluded: chain R residue 3 ILE Chi-restraints excluded: chain R residue 19 THR Chi-restraints excluded: chain R residue 24 VAL Chi-restraints excluded: chain R residue 27 THR Chi-restraints excluded: chain R residue 73 SER Chi-restraints excluded: chain R residue 101 THR Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain S residue 95 LEU Chi-restraints excluded: chain T residue 56 LEU Chi-restraints excluded: chain T residue 59 VAL Chi-restraints excluded: chain T residue 86 LEU Chi-restraints excluded: chain U residue 1 MET Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain U residue 53 ASP Chi-restraints excluded: chain U residue 66 THR Chi-restraints excluded: chain U residue 74 LEU Chi-restraints excluded: chain V residue 28 VAL Chi-restraints excluded: chain V residue 52 CYS Chi-restraints excluded: chain V residue 56 ASP Chi-restraints excluded: chain V residue 57 VAL Chi-restraints excluded: chain V residue 69 THR Chi-restraints excluded: chain V residue 77 VAL Chi-restraints excluded: chain W residue 17 VAL Chi-restraints excluded: chain W residue 28 LEU Chi-restraints excluded: chain W residue 70 THR Chi-restraints excluded: chain X residue 39 ILE Chi-restraints excluded: chain X residue 57 VAL Chi-restraints excluded: chain X residue 59 VAL Chi-restraints excluded: chain X residue 69 LYS Chi-restraints excluded: chain Z residue 18 PHE Chi-restraints excluded: chain Z residue 30 GLU Chi-restraints excluded: chain Z residue 63 ASN Chi-restraints excluded: chain a residue 8 MET Chi-restraints excluded: chain a residue 27 ILE Chi-restraints excluded: chain a residue 56 ASP Chi-restraints excluded: chain a residue 64 VAL Chi-restraints excluded: chain a residue 178 VAL Chi-restraints excluded: chain a residue 193 LEU Chi-restraints excluded: chain a residue 196 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1048 random chunks: chunk 340 optimal weight: 10.0000 chunk 912 optimal weight: 20.0000 chunk 200 optimal weight: 8.9990 chunk 594 optimal weight: 20.0000 chunk 250 optimal weight: 20.0000 chunk 1013 optimal weight: 20.0000 chunk 841 optimal weight: 30.0000 chunk 469 optimal weight: 6.9990 chunk 84 optimal weight: 10.0000 chunk 335 optimal weight: 8.9990 chunk 532 optimal weight: 8.9990 overall best weight: 8.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 150 GLN d 97 ASN ** d 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 68 HIS I 53 GLN ** J 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 134 ASN K 58 HIS ** N 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 49 HIS V 50 ASN ** X 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 68 HIS ** a 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.3366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 162700 Z= 0.318 Angle : 0.689 12.728 243508 Z= 0.356 Chirality : 0.039 0.348 31146 Planarity : 0.005 0.072 12986 Dihedral : 23.570 179.219 81731 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 17.66 Ramachandran Plot: Outliers : 0.26 % Allowed : 13.31 % Favored : 86.43 % Rotamer: Outliers : 6.83 % Allowed : 20.67 % Favored : 72.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.30 % 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: -2.46 (0.11), residues: 5836 helix: -0.34 (0.12), residues: 1851 sheet: -1.59 (0.15), residues: 1043 loop : -2.55 (0.11), residues: 2942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP b 247 HIS 0.013 0.002 HIS X 56 PHE 0.033 0.002 PHE Z 36 TYR 0.028 0.002 TYR W 50 ARG 0.010 0.001 ARG J 68 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11672 Ramachandran restraints generated. 5836 Oldfield, 0 Emsley, 5836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11672 Ramachandran restraints generated. 5836 Oldfield, 0 Emsley, 5836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1312 residues out of total 4862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 332 poor density : 980 time to evaluate : 6.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 150 GLN cc_start: 0.8317 (OUTLIER) cc_final: 0.8109 (tm-30) REVERT: c 190 LYS cc_start: 0.8852 (tttt) cc_final: 0.8565 (ttpt) REVERT: d 1 MET cc_start: 0.5320 (mmm) cc_final: 0.5064 (mmm) REVERT: d 29 HIS cc_start: 0.8403 (OUTLIER) cc_final: 0.7951 (t70) REVERT: d 30 GLN cc_start: 0.8830 (tm-30) cc_final: 0.8182 (tm-30) REVERT: d 188 MET cc_start: 0.7946 (tpp) cc_final: 0.7735 (tpt) REVERT: d 195 GLN cc_start: 0.8586 (OUTLIER) cc_final: 0.8042 (mp10) REVERT: e 4 HIS cc_start: 0.8466 (t-170) cc_final: 0.8047 (t-170) REVERT: e 16 MET cc_start: 0.8537 (mmm) cc_final: 0.8058 (mmm) REVERT: e 95 MET cc_start: 0.8541 (ttp) cc_final: 0.8179 (ttp) REVERT: e 96 TRP cc_start: 0.8821 (m100) cc_final: 0.8380 (m100) REVERT: e 176 PHE cc_start: 0.7133 (OUTLIER) cc_final: 0.6726 (m-80) REVERT: f 2 ARG cc_start: 0.7907 (OUTLIER) cc_final: 0.7603 (mmt-90) REVERT: f 41 GLU cc_start: 0.8049 (tp30) cc_final: 0.7818 (tm-30) REVERT: f 169 ARG cc_start: 0.8055 (mmm160) cc_final: 0.7139 (ttt90) REVERT: j 28 LEU cc_start: 0.9025 (OUTLIER) cc_final: 0.8800 (tp) REVERT: l 143 GLU cc_start: 0.7116 (OUTLIER) cc_final: 0.6845 (pt0) REVERT: m 75 GLU cc_start: 0.8072 (tt0) cc_final: 0.7789 (mt-10) REVERT: m 90 GLU cc_start: 0.7461 (tt0) cc_final: 0.6498 (tt0) REVERT: n 72 ASP cc_start: 0.8643 (t70) cc_final: 0.7898 (t0) REVERT: o 58 ILE cc_start: 0.8507 (mt) cc_final: 0.7890 (tp) REVERT: o 61 GLN cc_start: 0.9110 (OUTLIER) cc_final: 0.8345 (tp40) REVERT: p 8 GLU cc_start: 0.8795 (mt-10) cc_final: 0.8368 (mt-10) REVERT: p 70 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7716 (mp0) REVERT: r 10 LYS cc_start: 0.8536 (OUTLIER) cc_final: 0.8139 (ptpp) REVERT: r 16 GLU cc_start: 0.8347 (tt0) cc_final: 0.7709 (tt0) REVERT: r 31 GLU cc_start: 0.7893 (tm-30) cc_final: 0.7635 (tm-30) REVERT: r 46 GLU cc_start: 0.8789 (tp30) cc_final: 0.8212 (tm-30) REVERT: s 52 GLU cc_start: 0.8727 (mt-10) cc_final: 0.8383 (tt0) REVERT: t 1 MET cc_start: 0.5596 (mpt) cc_final: 0.5044 (mpt) REVERT: t 15 HIS cc_start: 0.7562 (t70) cc_final: 0.7334 (t-90) REVERT: v 7 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.7840 (pm20) REVERT: v 64 VAL cc_start: 0.8349 (t) cc_final: 0.7991 (m) REVERT: v 87 GLN cc_start: 0.7723 (OUTLIER) cc_final: 0.7441 (mp10) REVERT: x 69 GLU cc_start: 0.8080 (mt-10) cc_final: 0.7732 (mt-10) REVERT: y 13 GLU cc_start: 0.8886 (mt-10) cc_final: 0.8409 (tt0) REVERT: y 23 ARG cc_start: 0.8776 (mpt180) cc_final: 0.8362 (mpt180) REVERT: y 40 SER cc_start: 0.9278 (p) cc_final: 0.8741 (t) REVERT: y 60 LYS cc_start: 0.8856 (mmmm) cc_final: 0.8525 (mtpp) REVERT: z 55 LYS cc_start: 0.8935 (mttp) cc_final: 0.8423 (tmtt) REVERT: B 35 GLU cc_start: 0.7792 (mt-10) cc_final: 0.7371 (mt-10) REVERT: D 10 LEU cc_start: 0.9101 (tp) cc_final: 0.8850 (tt) REVERT: D 31 LEU cc_start: 0.9323 (OUTLIER) cc_final: 0.9050 (mt) REVERT: E 53 ASP cc_start: 0.8073 (m-30) cc_final: 0.7813 (m-30) REVERT: G 34 ARG cc_start: 0.7491 (mmp80) cc_final: 0.6333 (tpm170) REVERT: G 88 GLN cc_start: 0.7736 (mm-40) cc_final: 0.7454 (mp10) REVERT: G 93 HIS cc_start: 0.8354 (m90) cc_final: 0.7974 (m-70) REVERT: G 95 TRP cc_start: 0.8289 (t60) cc_final: 0.7776 (t60) REVERT: G 99 MET cc_start: 0.8602 (ptp) cc_final: 0.8085 (ptp) REVERT: G 221 ARG cc_start: 0.7861 (OUTLIER) cc_final: 0.7588 (mtt-85) REVERT: H 34 SER cc_start: 0.9076 (t) cc_final: 0.8728 (p) REVERT: H 55 VAL cc_start: 0.8790 (t) cc_final: 0.8569 (t) REVERT: H 92 ASP cc_start: 0.9020 (t0) cc_final: 0.8650 (p0) REVERT: H 111 ASP cc_start: 0.7790 (t70) cc_final: 0.7475 (t0) REVERT: H 169 GLU cc_start: 0.6988 (OUTLIER) cc_final: 0.6770 (pp20) REVERT: I 3 TYR cc_start: 0.7881 (t80) cc_final: 0.7194 (t80) REVERT: J 53 ARG cc_start: 0.8087 (ttp80) cc_final: 0.7869 (ttp80) REVERT: J 64 GLU cc_start: 0.8787 (mt-10) cc_final: 0.8535 (tm-30) REVERT: J 89 THR cc_start: 0.8564 (m) cc_final: 0.8264 (p) REVERT: J 125 LYS cc_start: 0.9007 (tppt) cc_final: 0.8570 (tptp) REVERT: J 127 TYR cc_start: 0.8427 (m-80) cc_final: 0.8131 (m-80) REVERT: K 13 ASP cc_start: 0.8768 (m-30) cc_final: 0.8023 (p0) REVERT: K 62 MET cc_start: 0.8112 (mmm) cc_final: 0.7843 (mmm) REVERT: L 10 LYS cc_start: 0.8591 (mmtp) cc_final: 0.8150 (ttpt) REVERT: L 17 PHE cc_start: 0.6917 (OUTLIER) cc_final: 0.5630 (p90) REVERT: L 51 GLN cc_start: 0.8750 (tt0) cc_final: 0.8275 (mm-40) REVERT: L 122 GLU cc_start: 0.7001 (OUTLIER) cc_final: 0.6787 (mm-30) REVERT: M 11 THR cc_start: 0.9121 (m) cc_final: 0.8853 (p) REVERT: M 41 GLU cc_start: 0.8712 (mm-30) cc_final: 0.8426 (mm-30) REVERT: M 42 GLU cc_start: 0.8158 (tp30) cc_final: 0.7778 (tm-30) REVERT: M 90 GLU cc_start: 0.8067 (mp0) cc_final: 0.7837 (mp0) REVERT: M 95 MET cc_start: 0.9109 (mpp) cc_final: 0.8669 (mpp) REVERT: N 56 MET cc_start: 0.8155 (ppp) cc_final: 0.7715 (ppp) REVERT: N 102 PHE cc_start: 0.7921 (m-80) cc_final: 0.7120 (m-80) REVERT: N 104 THR cc_start: 0.8009 (t) cc_final: 0.7765 (m) REVERT: O 10 LEU cc_start: 0.8408 (pp) cc_final: 0.8168 (pt) REVERT: O 11 LYS cc_start: 0.8588 (ptpt) cc_final: 0.8143 (mtmm) REVERT: O 19 ASP cc_start: 0.8666 (m-30) cc_final: 0.7957 (p0) REVERT: O 20 GLN cc_start: 0.9121 (tp40) cc_final: 0.8833 (tm-30) REVERT: O 46 LYS cc_start: 0.8768 (mttp) cc_final: 0.8472 (mttm) REVERT: O 63 ASP cc_start: 0.6680 (t0) cc_final: 0.6273 (t0) REVERT: P 41 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8528 (mp) REVERT: P 74 LYS cc_start: 0.8656 (ptpt) cc_final: 0.8379 (mmmt) REVERT: P 86 LYS cc_start: 0.8568 (ptpp) cc_final: 0.8077 (pttm) REVERT: P 124 LYS cc_start: 0.7551 (pptt) cc_final: 0.7050 (ptmt) REVERT: Q 28 GLN cc_start: 0.8587 (mp10) cc_final: 0.7845 (mt0) REVERT: Q 111 GLN cc_start: 0.8232 (mt0) cc_final: 0.7929 (mt0) REVERT: R 10 ASP cc_start: 0.8781 (m-30) cc_final: 0.8257 (m-30) REVERT: S 19 TYR cc_start: 0.8321 (OUTLIER) cc_final: 0.7633 (m-80) REVERT: S 48 GLN cc_start: 0.7887 (mt0) cc_final: 0.7660 (mt0) REVERT: S 95 LEU cc_start: 0.9090 (OUTLIER) cc_final: 0.8669 (tt) REVERT: T 5 GLU cc_start: 0.8247 (tp30) cc_final: 0.7822 (tp30) REVERT: T 9 LYS cc_start: 0.9409 (mttt) cc_final: 0.8920 (mttm) REVERT: U 1 MET cc_start: 0.6458 (OUTLIER) cc_final: 0.5641 (ttp) REVERT: V 10 ARG cc_start: 0.8891 (ptm-80) cc_final: 0.8519 (ptm-80) REVERT: V 72 TRP cc_start: 0.8382 (m100) cc_final: 0.8047 (m100) REVERT: W 22 TYR cc_start: 0.7750 (p90) cc_final: 0.7470 (p90) REVERT: X 9 PHE cc_start: 0.8713 (t80) cc_final: 0.8390 (t80) REVERT: Y 26 MET cc_start: 0.9050 (ptp) cc_final: 0.8548 (ptp) REVERT: Y 53 MET cc_start: 0.8892 (ppp) cc_final: 0.8512 (ppp) REVERT: Y 54 GLN cc_start: 0.8569 (tm-30) cc_final: 0.7934 (tm-30) REVERT: Y 58 ASP cc_start: 0.8917 (OUTLIER) cc_final: 0.8213 (t0) REVERT: Z 46 ARG cc_start: 0.8177 (mpt180) cc_final: 0.7397 (tpt-90) REVERT: a 167 LYS cc_start: 0.0801 (tptt) cc_final: 0.0119 (mttp) outliers start: 332 outliers final: 245 residues processed: 1180 average time/residue: 1.2581 time to fit residues: 2629.4024 Evaluate side-chains 1197 residues out of total 4862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 267 poor density : 930 time to evaluate : 6.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 2 VAL Chi-restraints excluded: chain b residue 44 ASN Chi-restraints excluded: chain b residue 85 ASN Chi-restraints excluded: chain b residue 139 THR Chi-restraints excluded: chain b residue 159 THR Chi-restraints excluded: chain b residue 183 VAL Chi-restraints excluded: chain b residue 203 VAL Chi-restraints excluded: chain b residue 215 VAL Chi-restraints excluded: chain b residue 228 ASP Chi-restraints excluded: chain b residue 238 ASN Chi-restraints excluded: chain b residue 256 THR Chi-restraints excluded: chain c residue 1 MET Chi-restraints excluded: chain c residue 108 ASP Chi-restraints excluded: chain c residue 138 LEU Chi-restraints excluded: chain c residue 139 SER Chi-restraints excluded: chain c residue 150 GLN Chi-restraints excluded: chain c residue 171 THR Chi-restraints excluded: chain c residue 175 LEU Chi-restraints excluded: chain c residue 180 VAL Chi-restraints excluded: chain d residue 29 HIS Chi-restraints excluded: chain d residue 84 THR Chi-restraints excluded: chain d residue 96 VAL Chi-restraints excluded: chain d residue 140 ASP Chi-restraints excluded: chain d residue 145 ASP Chi-restraints excluded: chain d residue 148 ILE Chi-restraints excluded: chain d residue 195 GLN Chi-restraints excluded: chain e residue 22 ASN Chi-restraints excluded: chain e residue 24 VAL Chi-restraints excluded: chain e residue 67 THR Chi-restraints excluded: chain e residue 77 LYS Chi-restraints excluded: chain e residue 86 CYS Chi-restraints excluded: chain e residue 117 SER Chi-restraints excluded: chain e residue 176 PHE Chi-restraints excluded: chain f residue 2 ARG Chi-restraints excluded: chain f residue 33 THR Chi-restraints excluded: chain g residue 4 ILE Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain g residue 48 GLU Chi-restraints excluded: chain h residue 15 VAL Chi-restraints excluded: chain h residue 27 VAL Chi-restraints excluded: chain h residue 55 VAL Chi-restraints excluded: chain j residue 28 LEU Chi-restraints excluded: chain j residue 55 ILE Chi-restraints excluded: chain j residue 64 VAL Chi-restraints excluded: chain j residue 105 VAL Chi-restraints excluded: chain j residue 109 LEU Chi-restraints excluded: chain j residue 142 ILE Chi-restraints excluded: chain k residue 3 GLN Chi-restraints excluded: chain k residue 58 LEU Chi-restraints excluded: chain k residue 62 VAL Chi-restraints excluded: chain k residue 76 VAL Chi-restraints excluded: chain k residue 87 LEU Chi-restraints excluded: chain k residue 88 ASN Chi-restraints excluded: chain k residue 104 THR Chi-restraints excluded: chain l residue 35 HIS Chi-restraints excluded: chain l residue 42 SER Chi-restraints excluded: chain l residue 81 ASP Chi-restraints excluded: chain l residue 110 VAL Chi-restraints excluded: chain l residue 111 ILE Chi-restraints excluded: chain l residue 116 VAL Chi-restraints excluded: chain l residue 117 THR Chi-restraints excluded: chain l residue 120 VAL Chi-restraints excluded: chain l residue 122 VAL Chi-restraints excluded: chain l residue 143 GLU Chi-restraints excluded: chain m residue 7 THR Chi-restraints excluded: chain m residue 36 VAL Chi-restraints excluded: chain m residue 41 LEU Chi-restraints excluded: chain m residue 70 ASP Chi-restraints excluded: chain m residue 82 MET Chi-restraints excluded: chain m residue 136 MET Chi-restraints excluded: chain n residue 18 GLN Chi-restraints excluded: chain n residue 37 THR Chi-restraints excluded: chain n residue 106 ASP Chi-restraints excluded: chain o residue 2 ASP Chi-restraints excluded: chain o residue 28 VAL Chi-restraints excluded: chain o residue 36 TYR Chi-restraints excluded: chain o residue 61 GLN Chi-restraints excluded: chain o residue 62 LEU Chi-restraints excluded: chain o residue 69 ASP Chi-restraints excluded: chain o residue 78 VAL Chi-restraints excluded: chain o residue 93 ASP Chi-restraints excluded: chain o residue 108 ASP Chi-restraints excluded: chain p residue 35 SER Chi-restraints excluded: chain p residue 40 GLN Chi-restraints excluded: chain p residue 59 THR Chi-restraints excluded: chain p residue 64 SER Chi-restraints excluded: chain p residue 70 GLU Chi-restraints excluded: chain p residue 103 THR Chi-restraints excluded: chain p residue 109 ILE Chi-restraints excluded: chain q residue 2 ARG Chi-restraints excluded: chain q residue 8 ILE Chi-restraints excluded: chain q residue 19 GLN Chi-restraints excluded: chain q residue 73 ILE Chi-restraints excluded: chain r residue 10 LYS Chi-restraints excluded: chain r residue 19 THR Chi-restraints excluded: chain r residue 33 VAL Chi-restraints excluded: chain r residue 40 MET Chi-restraints excluded: chain r residue 41 ILE Chi-restraints excluded: chain r residue 49 ILE Chi-restraints excluded: chain r residue 62 GLU Chi-restraints excluded: chain s residue 37 THR Chi-restraints excluded: chain s residue 69 LEU Chi-restraints excluded: chain s residue 74 ILE Chi-restraints excluded: chain s residue 81 SER Chi-restraints excluded: chain s residue 94 ASP Chi-restraints excluded: chain t residue 32 LEU Chi-restraints excluded: chain t residue 50 LEU Chi-restraints excluded: chain t residue 87 LEU Chi-restraints excluded: chain u residue 8 ASP Chi-restraints excluded: chain u residue 17 ASP Chi-restraints excluded: chain u residue 29 SER Chi-restraints excluded: chain u residue 35 VAL Chi-restraints excluded: chain u residue 40 LEU Chi-restraints excluded: chain u residue 71 ILE Chi-restraints excluded: chain v residue 7 GLU Chi-restraints excluded: chain v residue 8 VAL Chi-restraints excluded: chain v residue 59 GLU Chi-restraints excluded: chain v residue 61 LEU Chi-restraints excluded: chain v residue 87 GLN Chi-restraints excluded: chain v residue 89 ILE Chi-restraints excluded: chain v residue 92 VAL Chi-restraints excluded: chain w residue 8 ASN Chi-restraints excluded: chain w residue 17 LEU Chi-restraints excluded: chain w residue 27 VAL Chi-restraints excluded: chain w residue 63 VAL Chi-restraints excluded: chain x residue 41 SER Chi-restraints excluded: chain x residue 58 ILE Chi-restraints excluded: chain x residue 67 LEU Chi-restraints excluded: chain z residue 11 SER Chi-restraints excluded: chain z residue 16 LEU Chi-restraints excluded: chain z residue 48 ASN Chi-restraints excluded: chain z residue 53 MET Chi-restraints excluded: chain z residue 56 VAL Chi-restraints excluded: chain A residue 33 ASN Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 58 ASP Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain E residue 51 LYS Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 17 VAL Chi-restraints excluded: chain F residue 30 GLU Chi-restraints excluded: chain G residue 29 PHE Chi-restraints excluded: chain G residue 30 ILE Chi-restraints excluded: chain G residue 59 ILE Chi-restraints excluded: chain G residue 122 ASP Chi-restraints excluded: chain G residue 158 ASP Chi-restraints excluded: chain G residue 163 ILE Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 198 VAL Chi-restraints excluded: chain G residue 221 ARG Chi-restraints excluded: chain H residue 5 HIS Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 50 SER Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 164 THR Chi-restraints excluded: chain H residue 169 GLU Chi-restraints excluded: chain I residue 66 VAL Chi-restraints excluded: chain I residue 92 LEU Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 29 ILE Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain J residue 87 VAL Chi-restraints excluded: chain J residue 95 MET Chi-restraints excluded: chain J residue 123 LEU Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 141 ASP Chi-restraints excluded: chain K residue 3 HIS Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain L residue 17 PHE Chi-restraints excluded: chain L residue 122 GLU Chi-restraints excluded: chain L residue 129 ASN Chi-restraints excluded: chain L residue 132 THR Chi-restraints excluded: chain M residue 10 LEU Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain M residue 45 ILE Chi-restraints excluded: chain M residue 74 ILE Chi-restraints excluded: chain M residue 77 VAL Chi-restraints excluded: chain M residue 84 ILE Chi-restraints excluded: chain M residue 111 THR Chi-restraints excluded: chain M residue 120 LEU Chi-restraints excluded: chain M residue 124 ILE Chi-restraints excluded: chain N residue 21 LYS Chi-restraints excluded: chain N residue 42 THR Chi-restraints excluded: chain N residue 44 ARG Chi-restraints excluded: chain N residue 46 VAL Chi-restraints excluded: chain N residue 57 VAL Chi-restraints excluded: chain N residue 61 ASP Chi-restraints excluded: chain N residue 64 ILE Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain O residue 14 ASP Chi-restraints excluded: chain O residue 22 THR Chi-restraints excluded: chain O residue 36 VAL Chi-restraints excluded: chain O residue 57 VAL Chi-restraints excluded: chain O residue 71 LEU Chi-restraints excluded: chain O residue 92 LEU Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 30 ILE Chi-restraints excluded: chain P residue 39 ASN Chi-restraints excluded: chain P residue 41 LEU Chi-restraints excluded: chain P residue 57 SER Chi-restraints excluded: chain P residue 73 VAL Chi-restraints excluded: chain P residue 81 LEU Chi-restraints excluded: chain P residue 95 THR Chi-restraints excluded: chain P residue 96 ILE Chi-restraints excluded: chain P residue 106 ILE Chi-restraints excluded: chain P residue 121 ARG Chi-restraints excluded: chain P residue 126 ARG Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain Q residue 33 CYS Chi-restraints excluded: chain Q residue 54 VAL Chi-restraints excluded: chain Q residue 101 LEU Chi-restraints excluded: chain Q residue 108 ASP Chi-restraints excluded: chain R residue 3 ILE Chi-restraints excluded: chain R residue 19 THR Chi-restraints excluded: chain R residue 24 VAL Chi-restraints excluded: chain R residue 27 THR Chi-restraints excluded: chain R residue 67 ASP Chi-restraints excluded: chain R residue 101 THR Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain S residue 19 TYR Chi-restraints excluded: chain S residue 95 LEU Chi-restraints excluded: chain T residue 32 THR Chi-restraints excluded: chain T residue 56 LEU Chi-restraints excluded: chain T residue 59 VAL Chi-restraints excluded: chain T residue 69 LEU Chi-restraints excluded: chain T residue 86 LEU Chi-restraints excluded: chain U residue 1 MET Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain U residue 29 ASN Chi-restraints excluded: chain U residue 36 VAL Chi-restraints excluded: chain U residue 53 ASP Chi-restraints excluded: chain U residue 66 THR Chi-restraints excluded: chain U residue 74 LEU Chi-restraints excluded: chain V residue 4 ILE Chi-restraints excluded: chain V residue 28 VAL Chi-restraints excluded: chain V residue 52 CYS Chi-restraints excluded: chain V residue 54 ILE Chi-restraints excluded: chain V residue 56 ASP Chi-restraints excluded: chain V residue 57 VAL Chi-restraints excluded: chain V residue 69 THR Chi-restraints excluded: chain V residue 77 VAL Chi-restraints excluded: chain W residue 17 VAL Chi-restraints excluded: chain W residue 28 LEU Chi-restraints excluded: chain W residue 70 THR Chi-restraints excluded: chain X residue 39 ILE Chi-restraints excluded: chain X residue 57 VAL Chi-restraints excluded: chain X residue 59 VAL Chi-restraints excluded: chain X residue 70 LEU Chi-restraints excluded: chain Y residue 58 ASP Chi-restraints excluded: chain Z residue 18 PHE Chi-restraints excluded: chain Z residue 19 LYS Chi-restraints excluded: chain Z residue 30 GLU Chi-restraints excluded: chain Z residue 52 VAL Chi-restraints excluded: chain Z residue 63 ASN Chi-restraints excluded: chain a residue 8 MET Chi-restraints excluded: chain a residue 27 ILE Chi-restraints excluded: chain a residue 56 ASP Chi-restraints excluded: chain a residue 64 VAL Chi-restraints excluded: chain a residue 178 VAL Chi-restraints excluded: chain a residue 193 LEU Chi-restraints excluded: chain a residue 196 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1048 random chunks: chunk 977 optimal weight: 20.0000 chunk 114 optimal weight: 8.9990 chunk 577 optimal weight: 30.0000 chunk 740 optimal weight: 20.0000 chunk 573 optimal weight: 10.0000 chunk 853 optimal weight: 10.0000 chunk 566 optimal weight: 20.0000 chunk 1010 optimal weight: 20.0000 chunk 632 optimal weight: 30.0000 chunk 615 optimal weight: 30.0000 chunk 466 optimal weight: 10.0000 overall best weight: 11.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 225 ASN ** d 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 54 GLN ** m 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 71 ASN u 39 ASN ** w 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 50 ASN ** G 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 53 GLN J 76 ASN ** J 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 134 ASN ** K 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 50 ASN ** X 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 68 HIS ** a 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.3489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.082 162700 Z= 0.411 Angle : 0.762 12.449 243508 Z= 0.389 Chirality : 0.042 0.321 31146 Planarity : 0.006 0.074 12986 Dihedral : 23.634 179.702 81731 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 19.98 Ramachandran Plot: Outliers : 0.31 % Allowed : 14.03 % Favored : 85.66 % Rotamer: Outliers : 6.99 % Allowed : 21.49 % Favored : 71.51 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.30 % 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: -2.60 (0.11), residues: 5836 helix: -0.50 (0.12), residues: 1853 sheet: -1.71 (0.16), residues: 1021 loop : -2.59 (0.11), residues: 2962 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP H 166 HIS 0.013 0.002 HIS X 56 PHE 0.024 0.002 PHE h 76 TYR 0.047 0.003 TYR W 50 ARG 0.010 0.001 ARG Z 34 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11672 Ramachandran restraints generated. 5836 Oldfield, 0 Emsley, 5836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11672 Ramachandran restraints generated. 5836 Oldfield, 0 Emsley, 5836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1299 residues out of total 4862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 340 poor density : 959 time to evaluate : 9.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 190 LYS cc_start: 0.8857 (tttt) cc_final: 0.8605 (ttpt) REVERT: d 29 HIS cc_start: 0.8410 (OUTLIER) cc_final: 0.7989 (t70) REVERT: d 30 GLN cc_start: 0.8853 (tm-30) cc_final: 0.8182 (tm-30) REVERT: d 155 GLU cc_start: 0.7292 (OUTLIER) cc_final: 0.7009 (pt0) REVERT: d 195 GLN cc_start: 0.8571 (OUTLIER) cc_final: 0.8033 (mp10) REVERT: e 4 HIS cc_start: 0.8486 (t-170) cc_final: 0.8086 (t-170) REVERT: e 9 ASP cc_start: 0.7883 (OUTLIER) cc_final: 0.7546 (m-30) REVERT: e 16 MET cc_start: 0.8695 (mmm) cc_final: 0.8282 (mmm) REVERT: e 95 MET cc_start: 0.8594 (ttp) cc_final: 0.8188 (ttp) REVERT: e 96 TRP cc_start: 0.8867 (m100) cc_final: 0.8445 (m100) REVERT: e 176 PHE cc_start: 0.7204 (OUTLIER) cc_final: 0.6836 (m-80) REVERT: f 2 ARG cc_start: 0.7983 (OUTLIER) cc_final: 0.7676 (mmt-90) REVERT: f 150 TYR cc_start: 0.8342 (m-10) cc_final: 0.8136 (m-10) REVERT: f 169 ARG cc_start: 0.8071 (mmm160) cc_final: 0.7139 (ttt90) REVERT: g 25 TYR cc_start: 0.7822 (t80) cc_final: 0.7482 (t80) REVERT: j 28 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8828 (tp) REVERT: l 143 GLU cc_start: 0.7158 (OUTLIER) cc_final: 0.6892 (pt0) REVERT: m 33 LEU cc_start: 0.9054 (tp) cc_final: 0.8734 (mp) REVERT: n 54 LEU cc_start: 0.9131 (tp) cc_final: 0.8829 (tt) REVERT: n 72 ASP cc_start: 0.8689 (t70) cc_final: 0.7931 (t0) REVERT: o 58 ILE cc_start: 0.8526 (mt) cc_final: 0.7889 (tp) REVERT: o 61 GLN cc_start: 0.9088 (OUTLIER) cc_final: 0.8298 (tp40) REVERT: p 8 GLU cc_start: 0.8799 (mt-10) cc_final: 0.8377 (mt-10) REVERT: p 70 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7736 (mp0) REVERT: q 5 ARG cc_start: 0.8469 (OUTLIER) cc_final: 0.6974 (ttp-110) REVERT: q 30 VAL cc_start: 0.8190 (t) cc_final: 0.7842 (m) REVERT: r 10 LYS cc_start: 0.8635 (OUTLIER) cc_final: 0.8420 (ptpp) REVERT: r 16 GLU cc_start: 0.8339 (tt0) cc_final: 0.7994 (tt0) REVERT: s 52 GLU cc_start: 0.8717 (mt-10) cc_final: 0.8504 (tt0) REVERT: t 1 MET cc_start: 0.5650 (mpt) cc_final: 0.5283 (mpt) REVERT: t 15 HIS cc_start: 0.7553 (t70) cc_final: 0.7325 (t-90) REVERT: v 64 VAL cc_start: 0.8362 (t) cc_final: 0.8005 (m) REVERT: w 40 LYS cc_start: 0.9069 (mttt) cc_final: 0.8729 (mttm) REVERT: x 69 GLU cc_start: 0.8093 (mt-10) cc_final: 0.7733 (mt-10) REVERT: y 13 GLU cc_start: 0.8880 (mt-10) cc_final: 0.8262 (mm-30) REVERT: y 23 ARG cc_start: 0.8847 (mpt180) cc_final: 0.8418 (mpt180) REVERT: y 40 SER cc_start: 0.9317 (p) cc_final: 0.8765 (t) REVERT: y 60 LYS cc_start: 0.8882 (mmmm) cc_final: 0.8576 (mtpp) REVERT: z 55 LYS cc_start: 0.8935 (mttp) cc_final: 0.8402 (tmtt) REVERT: B 35 GLU cc_start: 0.7872 (mt-10) cc_final: 0.7440 (mt-10) REVERT: D 10 LEU cc_start: 0.9137 (tp) cc_final: 0.8872 (tt) REVERT: D 31 LEU cc_start: 0.9321 (OUTLIER) cc_final: 0.9067 (mt) REVERT: E 53 ASP cc_start: 0.8084 (m-30) cc_final: 0.7785 (m-30) REVERT: F 36 ARG cc_start: 0.9037 (ptt90) cc_final: 0.8790 (ptt90) REVERT: G 34 ARG cc_start: 0.7553 (mmp80) cc_final: 0.6383 (tpm170) REVERT: G 88 GLN cc_start: 0.7766 (mm-40) cc_final: 0.7489 (mp10) REVERT: G 93 HIS cc_start: 0.8323 (m90) cc_final: 0.7898 (m-70) REVERT: G 95 TRP cc_start: 0.8287 (t60) cc_final: 0.7777 (t60) REVERT: G 99 MET cc_start: 0.8655 (ptp) cc_final: 0.8038 (ptp) REVERT: G 221 ARG cc_start: 0.7906 (OUTLIER) cc_final: 0.7624 (mtt-85) REVERT: H 34 SER cc_start: 0.9095 (t) cc_final: 0.8758 (p) REVERT: H 55 VAL cc_start: 0.8780 (t) cc_final: 0.8554 (t) REVERT: H 92 ASP cc_start: 0.9021 (t0) cc_final: 0.8670 (p0) REVERT: I 3 TYR cc_start: 0.7860 (t80) cc_final: 0.7244 (t80) REVERT: J 53 ARG cc_start: 0.8060 (ttp80) cc_final: 0.7848 (ttp80) REVERT: J 64 GLU cc_start: 0.8784 (mt-10) cc_final: 0.8454 (tm-30) REVERT: J 89 THR cc_start: 0.8563 (m) cc_final: 0.8260 (p) REVERT: J 125 LYS cc_start: 0.9033 (tppt) cc_final: 0.8582 (tptp) REVERT: J 127 TYR cc_start: 0.8508 (m-80) cc_final: 0.8213 (m-80) REVERT: K 13 ASP cc_start: 0.8817 (m-30) cc_final: 0.8077 (p0) REVERT: K 23 GLU cc_start: 0.8412 (pm20) cc_final: 0.8192 (pm20) REVERT: K 62 MET cc_start: 0.8217 (mmm) cc_final: 0.7934 (mmm) REVERT: L 10 LYS cc_start: 0.8608 (mmtp) cc_final: 0.8155 (ttpt) REVERT: L 17 PHE cc_start: 0.6827 (OUTLIER) cc_final: 0.5930 (p90) REVERT: L 51 GLN cc_start: 0.8783 (tt0) cc_final: 0.8307 (mm-40) REVERT: L 100 MET cc_start: 0.9143 (mtt) cc_final: 0.8807 (mtt) REVERT: M 9 MET cc_start: 0.9352 (ppp) cc_final: 0.9085 (tmm) REVERT: M 11 THR cc_start: 0.9142 (m) cc_final: 0.8881 (p) REVERT: M 41 GLU cc_start: 0.8723 (mm-30) cc_final: 0.8421 (mm-30) REVERT: M 42 GLU cc_start: 0.8177 (tp30) cc_final: 0.7800 (tm-30) REVERT: M 95 MET cc_start: 0.9114 (mpp) cc_final: 0.8669 (mpp) REVERT: N 56 MET cc_start: 0.8103 (ppp) cc_final: 0.7647 (ppp) REVERT: N 102 PHE cc_start: 0.7951 (m-80) cc_final: 0.7146 (m-80) REVERT: N 104 THR cc_start: 0.7928 (t) cc_final: 0.7677 (m) REVERT: O 10 LEU cc_start: 0.8399 (pp) cc_final: 0.8142 (pt) REVERT: O 11 LYS cc_start: 0.8600 (ptpt) cc_final: 0.8169 (mtmm) REVERT: O 19 ASP cc_start: 0.8698 (m-30) cc_final: 0.7988 (p0) REVERT: O 20 GLN cc_start: 0.9126 (tp40) cc_final: 0.8705 (tm-30) REVERT: O 46 LYS cc_start: 0.8713 (mttp) cc_final: 0.8404 (mttm) REVERT: O 53 ILE cc_start: 0.9315 (mm) cc_final: 0.9114 (mm) REVERT: O 63 ASP cc_start: 0.6802 (t0) cc_final: 0.6269 (t0) REVERT: P 41 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8525 (mp) REVERT: P 74 LYS cc_start: 0.8700 (ptpt) cc_final: 0.8419 (mmmt) REVERT: P 86 LYS cc_start: 0.8621 (ptpp) cc_final: 0.8408 (pttm) REVERT: Q 111 GLN cc_start: 0.8294 (mt0) cc_final: 0.7924 (mt0) REVERT: R 10 ASP cc_start: 0.8800 (m-30) cc_final: 0.8293 (m-30) REVERT: R 113 LYS cc_start: 0.7931 (OUTLIER) cc_final: 0.7383 (mtmm) REVERT: S 19 TYR cc_start: 0.8360 (OUTLIER) cc_final: 0.7655 (m-80) REVERT: S 48 GLN cc_start: 0.7887 (mt0) cc_final: 0.7594 (mt0) REVERT: S 78 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8434 (mt) REVERT: S 95 LEU cc_start: 0.9084 (OUTLIER) cc_final: 0.8677 (tt) REVERT: T 5 GLU cc_start: 0.8281 (tp30) cc_final: 0.7858 (tp30) REVERT: T 9 LYS cc_start: 0.9428 (mttt) cc_final: 0.8954 (mttm) REVERT: U 1 MET cc_start: 0.6517 (OUTLIER) cc_final: 0.5809 (ttp) REVERT: V 72 TRP cc_start: 0.8408 (m100) cc_final: 0.8129 (m100) REVERT: W 22 TYR cc_start: 0.7770 (p90) cc_final: 0.7492 (p90) REVERT: X 9 PHE cc_start: 0.8771 (t80) cc_final: 0.8482 (t80) REVERT: Y 3 ILE cc_start: 0.8457 (mp) cc_final: 0.7889 (mm) REVERT: Y 17 ARG cc_start: 0.8959 (ttp80) cc_final: 0.8721 (ttp80) REVERT: Y 53 MET cc_start: 0.8908 (ppp) cc_final: 0.8587 (ppp) REVERT: Y 54 GLN cc_start: 0.8615 (tm-30) cc_final: 0.8004 (tm-30) REVERT: Y 58 ASP cc_start: 0.8925 (OUTLIER) cc_final: 0.8232 (t0) REVERT: Z 46 ARG cc_start: 0.8209 (mpt180) cc_final: 0.7451 (tpt-90) outliers start: 340 outliers final: 279 residues processed: 1170 average time/residue: 1.2778 time to fit residues: 2646.7467 Evaluate side-chains 1228 residues out of total 4862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 301 poor density : 927 time to evaluate : 6.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 2 VAL Chi-restraints excluded: chain b residue 44 ASN Chi-restraints excluded: chain b residue 85 ASN Chi-restraints excluded: chain b residue 136 VAL Chi-restraints excluded: chain b residue 139 THR Chi-restraints excluded: chain b residue 159 THR Chi-restraints excluded: chain b residue 171 VAL Chi-restraints excluded: chain b residue 181 ARG Chi-restraints excluded: chain b residue 183 VAL Chi-restraints excluded: chain b residue 203 VAL Chi-restraints excluded: chain b residue 215 VAL Chi-restraints excluded: chain b residue 228 ASP Chi-restraints excluded: chain b residue 238 ASN Chi-restraints excluded: chain b residue 256 THR Chi-restraints excluded: chain c residue 1 MET Chi-restraints excluded: chain c residue 108 ASP Chi-restraints excluded: chain c residue 138 LEU Chi-restraints excluded: chain c residue 139 SER Chi-restraints excluded: chain c residue 171 THR Chi-restraints excluded: chain c residue 175 LEU Chi-restraints excluded: chain c residue 180 VAL Chi-restraints excluded: chain d residue 29 HIS Chi-restraints excluded: chain d residue 84 THR Chi-restraints excluded: chain d residue 96 VAL Chi-restraints excluded: chain d residue 140 ASP Chi-restraints excluded: chain d residue 145 ASP Chi-restraints excluded: chain d residue 155 GLU Chi-restraints excluded: chain d residue 195 GLN Chi-restraints excluded: chain e residue 9 ASP Chi-restraints excluded: chain e residue 22 ASN Chi-restraints excluded: chain e residue 24 VAL Chi-restraints excluded: chain e residue 30 VAL Chi-restraints excluded: chain e residue 67 THR Chi-restraints excluded: chain e residue 77 LYS Chi-restraints excluded: chain e residue 86 CYS Chi-restraints excluded: chain e residue 117 SER Chi-restraints excluded: chain e residue 154 THR Chi-restraints excluded: chain e residue 176 PHE Chi-restraints excluded: chain f residue 2 ARG Chi-restraints excluded: chain f residue 33 THR Chi-restraints excluded: chain f residue 147 LEU Chi-restraints excluded: chain g residue 4 ILE Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain g residue 48 GLU Chi-restraints excluded: chain h residue 15 VAL Chi-restraints excluded: chain h residue 27 VAL Chi-restraints excluded: chain h residue 55 VAL Chi-restraints excluded: chain j residue 28 LEU Chi-restraints excluded: chain j residue 36 LEU Chi-restraints excluded: chain j residue 55 ILE Chi-restraints excluded: chain j residue 64 VAL Chi-restraints excluded: chain j residue 105 VAL Chi-restraints excluded: chain j residue 109 LEU Chi-restraints excluded: chain j residue 142 ILE Chi-restraints excluded: chain k residue 3 GLN Chi-restraints excluded: chain k residue 58 LEU Chi-restraints excluded: chain k residue 62 VAL Chi-restraints excluded: chain k residue 76 VAL Chi-restraints excluded: chain k residue 87 LEU Chi-restraints excluded: chain k residue 88 ASN Chi-restraints excluded: chain k residue 104 THR Chi-restraints excluded: chain l residue 35 HIS Chi-restraints excluded: chain l residue 42 SER Chi-restraints excluded: chain l residue 81 ASP Chi-restraints excluded: chain l residue 110 VAL Chi-restraints excluded: chain l residue 111 ILE Chi-restraints excluded: chain l residue 116 VAL Chi-restraints excluded: chain l residue 117 THR Chi-restraints excluded: chain l residue 120 VAL Chi-restraints excluded: chain l residue 122 VAL Chi-restraints excluded: chain l residue 143 GLU Chi-restraints excluded: chain m residue 7 THR Chi-restraints excluded: chain m residue 36 VAL Chi-restraints excluded: chain m residue 41 LEU Chi-restraints excluded: chain m residue 70 ASP Chi-restraints excluded: chain m residue 82 MET Chi-restraints excluded: chain m residue 128 THR Chi-restraints excluded: chain m residue 136 MET Chi-restraints excluded: chain n residue 18 GLN Chi-restraints excluded: chain n residue 37 THR Chi-restraints excluded: chain n residue 106 ASP Chi-restraints excluded: chain o residue 2 ASP Chi-restraints excluded: chain o residue 28 VAL Chi-restraints excluded: chain o residue 36 TYR Chi-restraints excluded: chain o residue 61 GLN Chi-restraints excluded: chain o residue 62 LEU Chi-restraints excluded: chain o residue 69 ASP Chi-restraints excluded: chain o residue 93 ASP Chi-restraints excluded: chain o residue 108 ASP Chi-restraints excluded: chain p residue 31 VAL Chi-restraints excluded: chain p residue 35 SER Chi-restraints excluded: chain p residue 40 GLN Chi-restraints excluded: chain p residue 59 THR Chi-restraints excluded: chain p residue 64 SER Chi-restraints excluded: chain p residue 70 GLU Chi-restraints excluded: chain p residue 103 THR Chi-restraints excluded: chain p residue 109 ILE Chi-restraints excluded: chain q residue 5 ARG Chi-restraints excluded: chain q residue 8 ILE Chi-restraints excluded: chain q residue 17 LEU Chi-restraints excluded: chain q residue 19 GLN Chi-restraints excluded: chain q residue 73 ILE Chi-restraints excluded: chain q residue 82 LEU Chi-restraints excluded: chain r residue 10 LYS Chi-restraints excluded: chain r residue 19 THR Chi-restraints excluded: chain r residue 33 VAL Chi-restraints excluded: chain r residue 41 ILE Chi-restraints excluded: chain r residue 49 ILE Chi-restraints excluded: chain r residue 62 GLU Chi-restraints excluded: chain s residue 37 THR Chi-restraints excluded: chain s residue 69 LEU Chi-restraints excluded: chain s residue 74 ILE Chi-restraints excluded: chain s residue 81 SER Chi-restraints excluded: chain t residue 2 ILE Chi-restraints excluded: chain t residue 32 LEU Chi-restraints excluded: chain t residue 50 LEU Chi-restraints excluded: chain t residue 87 LEU Chi-restraints excluded: chain u residue 8 ASP Chi-restraints excluded: chain u residue 17 ASP Chi-restraints excluded: chain u residue 35 VAL Chi-restraints excluded: chain u residue 40 LEU Chi-restraints excluded: chain u residue 71 ILE Chi-restraints excluded: chain v residue 7 GLU Chi-restraints excluded: chain v residue 8 VAL Chi-restraints excluded: chain v residue 38 LEU Chi-restraints excluded: chain v residue 45 ASP Chi-restraints excluded: chain v residue 59 GLU Chi-restraints excluded: chain v residue 61 LEU Chi-restraints excluded: chain v residue 63 ILE Chi-restraints excluded: chain v residue 89 ILE Chi-restraints excluded: chain v residue 92 VAL Chi-restraints excluded: chain w residue 8 ASN Chi-restraints excluded: chain w residue 17 LEU Chi-restraints excluded: chain w residue 27 VAL Chi-restraints excluded: chain w residue 63 VAL Chi-restraints excluded: chain w residue 72 ASN Chi-restraints excluded: chain x residue 41 SER Chi-restraints excluded: chain x residue 58 ILE Chi-restraints excluded: chain x residue 67 LEU Chi-restraints excluded: chain z residue 11 SER Chi-restraints excluded: chain z residue 13 ILE Chi-restraints excluded: chain z residue 48 ASN Chi-restraints excluded: chain z residue 53 MET Chi-restraints excluded: chain z residue 56 VAL Chi-restraints excluded: chain A residue 33 ASN Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 58 ASP Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain E residue 51 LYS Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 17 VAL Chi-restraints excluded: chain F residue 30 GLU Chi-restraints excluded: chain G residue 29 PHE Chi-restraints excluded: chain G residue 30 ILE Chi-restraints excluded: chain G residue 59 ILE Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 122 ASP Chi-restraints excluded: chain G residue 158 ASP Chi-restraints excluded: chain G residue 163 ILE Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 198 VAL Chi-restraints excluded: chain G residue 221 ARG Chi-restraints excluded: chain H residue 5 HIS Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 50 SER Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 68 HIS Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain H residue 153 SER Chi-restraints excluded: chain H residue 164 THR Chi-restraints excluded: chain H residue 169 GLU Chi-restraints excluded: chain I residue 53 GLN Chi-restraints excluded: chain I residue 66 VAL Chi-restraints excluded: chain I residue 74 TYR Chi-restraints excluded: chain I residue 92 LEU Chi-restraints excluded: chain I residue 97 LEU Chi-restraints excluded: chain I residue 170 LEU Chi-restraints excluded: chain I residue 177 MET Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 29 ILE Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain J residue 87 VAL Chi-restraints excluded: chain J residue 95 MET Chi-restraints excluded: chain J residue 123 LEU Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 141 ASP Chi-restraints excluded: chain K residue 3 HIS Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 54 LEU Chi-restraints excluded: chain K residue 64 VAL Chi-restraints excluded: chain K residue 73 GLU Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain L residue 17 PHE Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain L residue 122 GLU Chi-restraints excluded: chain L residue 129 ASN Chi-restraints excluded: chain L residue 132 THR Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain M residue 45 ILE Chi-restraints excluded: chain M residue 74 ILE Chi-restraints excluded: chain M residue 77 VAL Chi-restraints excluded: chain M residue 84 ILE Chi-restraints excluded: chain M residue 111 THR Chi-restraints excluded: chain M residue 120 LEU Chi-restraints excluded: chain M residue 124 ILE Chi-restraints excluded: chain N residue 21 LYS Chi-restraints excluded: chain N residue 30 ASN Chi-restraints excluded: chain N residue 42 THR Chi-restraints excluded: chain N residue 44 ARG Chi-restraints excluded: chain N residue 46 VAL Chi-restraints excluded: chain N residue 57 VAL Chi-restraints excluded: chain N residue 61 ASP Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain O residue 14 ASP Chi-restraints excluded: chain O residue 22 THR Chi-restraints excluded: chain O residue 25 ILE Chi-restraints excluded: chain O residue 36 VAL Chi-restraints excluded: chain O residue 57 VAL Chi-restraints excluded: chain O residue 71 LEU Chi-restraints excluded: chain O residue 92 LEU Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 30 ILE Chi-restraints excluded: chain P residue 39 ASN Chi-restraints excluded: chain P residue 41 LEU Chi-restraints excluded: chain P residue 57 SER Chi-restraints excluded: chain P residue 63 GLN Chi-restraints excluded: chain P residue 73 VAL Chi-restraints excluded: chain P residue 81 LEU Chi-restraints excluded: chain P residue 95 THR Chi-restraints excluded: chain P residue 96 ILE Chi-restraints excluded: chain P residue 106 ILE Chi-restraints excluded: chain P residue 126 ARG Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain Q residue 33 CYS Chi-restraints excluded: chain Q residue 54 VAL Chi-restraints excluded: chain Q residue 101 LEU Chi-restraints excluded: chain Q residue 108 ASP Chi-restraints excluded: chain R residue 3 ILE Chi-restraints excluded: chain R residue 19 THR Chi-restraints excluded: chain R residue 24 VAL Chi-restraints excluded: chain R residue 27 THR Chi-restraints excluded: chain R residue 67 ASP Chi-restraints excluded: chain R residue 73 SER Chi-restraints excluded: chain R residue 101 THR Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain R residue 113 LYS Chi-restraints excluded: chain S residue 19 TYR Chi-restraints excluded: chain S residue 78 LEU Chi-restraints excluded: chain S residue 95 LEU Chi-restraints excluded: chain T residue 32 THR Chi-restraints excluded: chain T residue 56 LEU Chi-restraints excluded: chain T residue 59 VAL Chi-restraints excluded: chain T residue 69 LEU Chi-restraints excluded: chain T residue 86 LEU Chi-restraints excluded: chain U residue 1 MET Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain U residue 29 ASN Chi-restraints excluded: chain U residue 53 ASP Chi-restraints excluded: chain U residue 66 THR Chi-restraints excluded: chain U residue 74 LEU Chi-restraints excluded: chain V residue 4 ILE Chi-restraints excluded: chain V residue 28 VAL Chi-restraints excluded: chain V residue 38 LYS Chi-restraints excluded: chain V residue 52 CYS Chi-restraints excluded: chain V residue 54 ILE Chi-restraints excluded: chain V residue 56 ASP Chi-restraints excluded: chain V residue 57 VAL Chi-restraints excluded: chain V residue 69 THR Chi-restraints excluded: chain V residue 77 VAL Chi-restraints excluded: chain W residue 17 VAL Chi-restraints excluded: chain W residue 28 LEU Chi-restraints excluded: chain W residue 70 THR Chi-restraints excluded: chain W residue 71 ASP Chi-restraints excluded: chain X residue 39 ILE Chi-restraints excluded: chain X residue 57 VAL Chi-restraints excluded: chain X residue 59 VAL Chi-restraints excluded: chain X residue 70 LEU Chi-restraints excluded: chain X residue 78 THR Chi-restraints excluded: chain Y residue 58 ASP Chi-restraints excluded: chain Z residue 12 ASP Chi-restraints excluded: chain Z residue 18 PHE Chi-restraints excluded: chain Z residue 19 LYS Chi-restraints excluded: chain Z residue 30 GLU Chi-restraints excluded: chain Z residue 33 ARG Chi-restraints excluded: chain Z residue 52 VAL Chi-restraints excluded: chain a residue 8 MET Chi-restraints excluded: chain a residue 27 ILE Chi-restraints excluded: chain a residue 56 ASP Chi-restraints excluded: chain a residue 64 VAL Chi-restraints excluded: chain a residue 178 VAL Chi-restraints excluded: chain a residue 193 LEU Chi-restraints excluded: chain a residue 196 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1048 random chunks: chunk 624 optimal weight: 20.0000 chunk 403 optimal weight: 6.9990 chunk 603 optimal weight: 20.0000 chunk 304 optimal weight: 7.9990 chunk 198 optimal weight: 5.9990 chunk 195 optimal weight: 10.0000 chunk 642 optimal weight: 10.0000 chunk 688 optimal weight: 20.0000 chunk 499 optimal weight: 20.0000 chunk 94 optimal weight: 6.9990 chunk 793 optimal weight: 10.0000 overall best weight: 7.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 71 ASN ** v 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 53 GLN ** J 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 134 ASN ** N 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 95 HIS V 50 ASN X 56 HIS X 68 HIS ** a 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.3606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 162700 Z= 0.280 Angle : 0.670 12.711 243508 Z= 0.346 Chirality : 0.038 0.331 31146 Planarity : 0.005 0.077 12986 Dihedral : 23.639 179.605 81731 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 17.40 Ramachandran Plot: Outliers : 0.26 % Allowed : 12.65 % Favored : 87.10 % Rotamer: Outliers : 6.23 % Allowed : 22.83 % Favored : 70.94 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.51 % Twisted General : 0.30 % 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: -2.37 (0.11), residues: 5836 helix: -0.23 (0.12), residues: 1840 sheet: -1.58 (0.16), residues: 1017 loop : -2.50 (0.11), residues: 2979 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP b 247 HIS 0.012 0.001 HIS X 56 PHE 0.028 0.002 PHE Z 36 TYR 0.025 0.002 TYR H 167 ARG 0.012 0.001 ARG J 68 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11672 Ramachandran restraints generated. 5836 Oldfield, 0 Emsley, 5836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11672 Ramachandran restraints generated. 5836 Oldfield, 0 Emsley, 5836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1282 residues out of total 4862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 303 poor density : 979 time to evaluate : 6.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 224 MET cc_start: 0.8206 (mtt) cc_final: 0.7971 (mtt) REVERT: c 190 LYS cc_start: 0.8838 (tttt) cc_final: 0.8557 (ttpt) REVERT: d 1 MET cc_start: 0.5521 (mmm) cc_final: 0.5230 (mmm) REVERT: d 29 HIS cc_start: 0.8362 (OUTLIER) cc_final: 0.7898 (t70) REVERT: d 30 GLN cc_start: 0.8815 (tm-30) cc_final: 0.8155 (tm-30) REVERT: d 115 GLN cc_start: 0.8772 (tp40) cc_final: 0.8559 (tp-100) REVERT: d 155 GLU cc_start: 0.7246 (OUTLIER) cc_final: 0.6972 (pt0) REVERT: d 195 GLN cc_start: 0.8573 (OUTLIER) cc_final: 0.8176 (mp10) REVERT: e 4 HIS cc_start: 0.8473 (t-170) cc_final: 0.8061 (t-170) REVERT: e 9 ASP cc_start: 0.7943 (OUTLIER) cc_final: 0.7607 (m-30) REVERT: e 16 MET cc_start: 0.8638 (mmm) cc_final: 0.8244 (mmm) REVERT: e 95 MET cc_start: 0.8572 (ttp) cc_final: 0.8162 (ttp) REVERT: e 96 TRP cc_start: 0.8789 (m100) cc_final: 0.8313 (m100) REVERT: e 176 PHE cc_start: 0.7121 (OUTLIER) cc_final: 0.6771 (m-80) REVERT: f 2 ARG cc_start: 0.7963 (OUTLIER) cc_final: 0.7744 (mmt-90) REVERT: f 138 GLN cc_start: 0.8008 (OUTLIER) cc_final: 0.7660 (tp40) REVERT: f 169 ARG cc_start: 0.8053 (mmm160) cc_final: 0.7092 (ttt90) REVERT: g 25 TYR cc_start: 0.7862 (t80) cc_final: 0.7512 (t80) REVERT: j 28 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8771 (tp) REVERT: l 143 GLU cc_start: 0.7005 (OUTLIER) cc_final: 0.6736 (pt0) REVERT: m 33 LEU cc_start: 0.9002 (tp) cc_final: 0.8682 (mp) REVERT: n 28 LEU cc_start: 0.9393 (tt) cc_final: 0.9188 (tp) REVERT: n 72 ASP cc_start: 0.8645 (t70) cc_final: 0.7973 (t0) REVERT: n 82 GLU cc_start: 0.8473 (mt-10) cc_final: 0.7982 (pm20) REVERT: o 58 ILE cc_start: 0.8564 (mt) cc_final: 0.7930 (tp) REVERT: o 61 GLN cc_start: 0.9051 (OUTLIER) cc_final: 0.8301 (tp40) REVERT: p 8 GLU cc_start: 0.8737 (mt-10) cc_final: 0.8350 (mt-10) REVERT: p 70 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7575 (mp0) REVERT: r 10 LYS cc_start: 0.8520 (OUTLIER) cc_final: 0.8130 (ptpp) REVERT: r 16 GLU cc_start: 0.8371 (tt0) cc_final: 0.8040 (tt0) REVERT: r 31 GLU cc_start: 0.7923 (tm-30) cc_final: 0.7619 (tm-30) REVERT: r 46 GLU cc_start: 0.8425 (tm-30) cc_final: 0.7946 (tm-30) REVERT: r 62 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.7348 (tp30) REVERT: s 2 GLU cc_start: 0.8485 (tm-30) cc_final: 0.8004 (pt0) REVERT: s 52 GLU cc_start: 0.8670 (mt-10) cc_final: 0.8348 (tt0) REVERT: t 1 MET cc_start: 0.5775 (mpt) cc_final: 0.5446 (mpt) REVERT: t 15 HIS cc_start: 0.7595 (t70) cc_final: 0.7372 (t-90) REVERT: v 87 GLN cc_start: 0.7957 (OUTLIER) cc_final: 0.7730 (mt0) REVERT: w 40 LYS cc_start: 0.9037 (mttt) cc_final: 0.8699 (mttm) REVERT: x 69 GLU cc_start: 0.8040 (mt-10) cc_final: 0.7711 (mt-10) REVERT: y 13 GLU cc_start: 0.8946 (mt-10) cc_final: 0.8407 (tt0) REVERT: y 23 ARG cc_start: 0.8809 (mpt180) cc_final: 0.8404 (mpt180) REVERT: y 40 SER cc_start: 0.9300 (p) cc_final: 0.8633 (t) REVERT: y 44 LYS cc_start: 0.8538 (tptt) cc_final: 0.7901 (tptt) REVERT: y 60 LYS cc_start: 0.8818 (mmmm) cc_final: 0.8541 (mtpp) REVERT: z 55 LYS cc_start: 0.8930 (mttp) cc_final: 0.8435 (tmtt) REVERT: B 35 GLU cc_start: 0.7725 (mt-10) cc_final: 0.7310 (mt-10) REVERT: C 20 TYR cc_start: 0.6533 (m-80) cc_final: 0.6102 (m-80) REVERT: C 29 LYS cc_start: 0.5776 (ptpt) cc_final: 0.5281 (pttt) REVERT: D 10 LEU cc_start: 0.9089 (tp) cc_final: 0.8841 (tt) REVERT: E 53 ASP cc_start: 0.7962 (m-30) cc_final: 0.7707 (m-30) REVERT: G 34 ARG cc_start: 0.7451 (mmp80) cc_final: 0.6301 (tpm170) REVERT: G 88 GLN cc_start: 0.7698 (mm-40) cc_final: 0.7431 (mp10) REVERT: G 93 HIS cc_start: 0.8309 (m90) cc_final: 0.7930 (m-70) REVERT: G 95 TRP cc_start: 0.8245 (t60) cc_final: 0.7777 (t60) REVERT: G 99 MET cc_start: 0.8653 (ptp) cc_final: 0.8110 (ptp) REVERT: G 119 GLN cc_start: 0.8236 (mt0) cc_final: 0.7880 (pp30) REVERT: G 221 ARG cc_start: 0.7852 (OUTLIER) cc_final: 0.7583 (mtt-85) REVERT: H 34 SER cc_start: 0.9073 (t) cc_final: 0.8719 (p) REVERT: H 55 VAL cc_start: 0.8776 (t) cc_final: 0.8547 (t) REVERT: H 92 ASP cc_start: 0.9007 (t0) cc_final: 0.8653 (p0) REVERT: H 111 ASP cc_start: 0.8076 (t0) cc_final: 0.7843 (t0) REVERT: H 122 GLN cc_start: 0.8349 (mp-120) cc_final: 0.7996 (mp10) REVERT: I 3 TYR cc_start: 0.7861 (t80) cc_final: 0.7165 (t80) REVERT: I 82 LYS cc_start: 0.5832 (mttt) cc_final: 0.5407 (mtmm) REVERT: I 123 MET cc_start: 0.6082 (mmm) cc_final: 0.5644 (mmm) REVERT: J 53 ARG cc_start: 0.8053 (ttp80) cc_final: 0.7839 (ttp80) REVERT: J 64 GLU cc_start: 0.8730 (mt-10) cc_final: 0.8440 (tm-30) REVERT: J 125 LYS cc_start: 0.8958 (tppt) cc_final: 0.8543 (tptp) REVERT: J 127 TYR cc_start: 0.8420 (m-80) cc_final: 0.8160 (m-80) REVERT: K 13 ASP cc_start: 0.8785 (m-30) cc_final: 0.8064 (p0) REVERT: K 62 MET cc_start: 0.8107 (mmm) cc_final: 0.7828 (mmm) REVERT: K 91 ARG cc_start: 0.8331 (OUTLIER) cc_final: 0.7306 (mmm-85) REVERT: L 10 LYS cc_start: 0.8577 (mmtp) cc_final: 0.8147 (ttpt) REVERT: L 17 PHE cc_start: 0.6864 (OUTLIER) cc_final: 0.5272 (p90) REVERT: L 51 GLN cc_start: 0.8567 (tt0) cc_final: 0.8219 (mm-40) REVERT: L 100 MET cc_start: 0.9128 (mtt) cc_final: 0.8771 (mtt) REVERT: M 4 ASP cc_start: 0.8202 (t0) cc_final: 0.7544 (t0) REVERT: M 11 THR cc_start: 0.9109 (m) cc_final: 0.8829 (p) REVERT: M 41 GLU cc_start: 0.8791 (mm-30) cc_final: 0.8493 (mm-30) REVERT: M 42 GLU cc_start: 0.8089 (tp30) cc_final: 0.7846 (tm-30) REVERT: M 46 GLU cc_start: 0.8206 (tm-30) cc_final: 0.7973 (tm-30) REVERT: M 90 GLU cc_start: 0.8133 (mp0) cc_final: 0.7892 (mp0) REVERT: M 95 MET cc_start: 0.9108 (mpp) cc_final: 0.8667 (mpp) REVERT: N 56 MET cc_start: 0.8220 (ppp) cc_final: 0.7758 (ppp) REVERT: N 102 PHE cc_start: 0.8096 (m-80) cc_final: 0.7211 (m-80) REVERT: N 104 THR cc_start: 0.7951 (t) cc_final: 0.7727 (m) REVERT: O 11 LYS cc_start: 0.8583 (ptpt) cc_final: 0.8154 (mtmm) REVERT: O 19 ASP cc_start: 0.8716 (m-30) cc_final: 0.8000 (p0) REVERT: O 20 GLN cc_start: 0.9112 (tp40) cc_final: 0.8695 (tm-30) REVERT: O 46 LYS cc_start: 0.8745 (mttp) cc_final: 0.8476 (mttm) REVERT: O 63 ASP cc_start: 0.6809 (t0) cc_final: 0.6279 (t0) REVERT: P 41 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8551 (mp) REVERT: P 74 LYS cc_start: 0.8708 (ptpt) cc_final: 0.8393 (mmmt) REVERT: P 86 LYS cc_start: 0.8532 (ptpp) cc_final: 0.7988 (pttm) REVERT: Q 28 GLN cc_start: 0.8545 (mp10) cc_final: 0.7847 (mt0) REVERT: Q 111 GLN cc_start: 0.8174 (mt0) cc_final: 0.7835 (mt0) REVERT: R 51 GLN cc_start: 0.8469 (mp10) cc_final: 0.8193 (mp10) REVERT: R 113 LYS cc_start: 0.7889 (OUTLIER) cc_final: 0.7368 (mtmm) REVERT: S 4 SER cc_start: 0.9308 (p) cc_final: 0.8751 (t) REVERT: S 48 GLN cc_start: 0.7856 (mt0) cc_final: 0.7574 (mt0) REVERT: S 78 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8525 (mt) REVERT: S 95 LEU cc_start: 0.9055 (OUTLIER) cc_final: 0.8643 (tt) REVERT: T 5 GLU cc_start: 0.8231 (tp30) cc_final: 0.7797 (tp30) REVERT: T 9 LYS cc_start: 0.9427 (mttt) cc_final: 0.8952 (mttm) REVERT: T 39 GLN cc_start: 0.8269 (mp10) cc_final: 0.7958 (mp10) REVERT: U 1 MET cc_start: 0.6509 (OUTLIER) cc_final: 0.5664 (ttp) REVERT: V 10 ARG cc_start: 0.8890 (ptm-80) cc_final: 0.8521 (ptm-80) REVERT: V 27 PHE cc_start: 0.8785 (OUTLIER) cc_final: 0.8229 (t80) REVERT: V 72 TRP cc_start: 0.8370 (m100) cc_final: 0.8113 (m100) REVERT: W 22 TYR cc_start: 0.7725 (p90) cc_final: 0.7456 (p90) REVERT: X 9 PHE cc_start: 0.8698 (t80) cc_final: 0.8409 (t80) REVERT: X 19 GLU cc_start: 0.8355 (mm-30) cc_final: 0.7900 (pp20) REVERT: Y 17 ARG cc_start: 0.8974 (ttp80) cc_final: 0.8731 (ttp80) REVERT: Y 27 MET cc_start: 0.8987 (ppp) cc_final: 0.8752 (tmm) REVERT: Y 54 GLN cc_start: 0.8559 (tm-30) cc_final: 0.8136 (tm-30) REVERT: Y 58 ASP cc_start: 0.8913 (OUTLIER) cc_final: 0.8203 (t0) REVERT: Z 46 ARG cc_start: 0.8149 (mpt180) cc_final: 0.7414 (tpt-90) outliers start: 303 outliers final: 247 residues processed: 1165 average time/residue: 1.3298 time to fit residues: 2748.4064 Evaluate side-chains 1208 residues out of total 4862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 271 poor density : 937 time to evaluate : 6.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 2 VAL Chi-restraints excluded: chain b residue 159 THR Chi-restraints excluded: chain b residue 171 VAL Chi-restraints excluded: chain b residue 181 ARG Chi-restraints excluded: chain b residue 183 VAL Chi-restraints excluded: chain b residue 203 VAL Chi-restraints excluded: chain b residue 215 VAL Chi-restraints excluded: chain b residue 228 ASP Chi-restraints excluded: chain b residue 238 ASN Chi-restraints excluded: chain b residue 256 THR Chi-restraints excluded: chain c residue 1 MET Chi-restraints excluded: chain c residue 50 VAL Chi-restraints excluded: chain c residue 108 ASP Chi-restraints excluded: chain c residue 138 LEU Chi-restraints excluded: chain c residue 139 SER Chi-restraints excluded: chain c residue 175 LEU Chi-restraints excluded: chain c residue 180 VAL Chi-restraints excluded: chain d residue 29 HIS Chi-restraints excluded: chain d residue 84 THR Chi-restraints excluded: chain d residue 140 ASP Chi-restraints excluded: chain d residue 145 ASP Chi-restraints excluded: chain d residue 155 GLU Chi-restraints excluded: chain d residue 195 GLN Chi-restraints excluded: chain e residue 9 ASP Chi-restraints excluded: chain e residue 22 ASN Chi-restraints excluded: chain e residue 24 VAL Chi-restraints excluded: chain e residue 67 THR Chi-restraints excluded: chain e residue 77 LYS Chi-restraints excluded: chain e residue 86 CYS Chi-restraints excluded: chain e residue 117 SER Chi-restraints excluded: chain e residue 176 PHE Chi-restraints excluded: chain f residue 2 ARG Chi-restraints excluded: chain f residue 33 THR Chi-restraints excluded: chain f residue 71 LEU Chi-restraints excluded: chain f residue 138 GLN Chi-restraints excluded: chain f residue 154 GLU Chi-restraints excluded: chain g residue 4 ILE Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain g residue 48 GLU Chi-restraints excluded: chain h residue 15 VAL Chi-restraints excluded: chain h residue 27 VAL Chi-restraints excluded: chain h residue 55 VAL Chi-restraints excluded: chain j residue 28 LEU Chi-restraints excluded: chain j residue 55 ILE Chi-restraints excluded: chain j residue 64 VAL Chi-restraints excluded: chain j residue 76 HIS Chi-restraints excluded: chain j residue 92 MET Chi-restraints excluded: chain j residue 105 VAL Chi-restraints excluded: chain j residue 109 LEU Chi-restraints excluded: chain j residue 142 ILE Chi-restraints excluded: chain k residue 3 GLN Chi-restraints excluded: chain k residue 58 LEU Chi-restraints excluded: chain k residue 76 VAL Chi-restraints excluded: chain k residue 87 LEU Chi-restraints excluded: chain k residue 104 THR Chi-restraints excluded: chain l residue 35 HIS Chi-restraints excluded: chain l residue 42 SER Chi-restraints excluded: chain l residue 81 ASP Chi-restraints excluded: chain l residue 110 VAL Chi-restraints excluded: chain l residue 111 ILE Chi-restraints excluded: chain l residue 116 VAL Chi-restraints excluded: chain l residue 117 THR Chi-restraints excluded: chain l residue 122 VAL Chi-restraints excluded: chain l residue 143 GLU Chi-restraints excluded: chain m residue 7 THR Chi-restraints excluded: chain m residue 36 VAL Chi-restraints excluded: chain m residue 41 LEU Chi-restraints excluded: chain m residue 70 ASP Chi-restraints excluded: chain m residue 82 MET Chi-restraints excluded: chain m residue 95 LEU Chi-restraints excluded: chain m residue 136 MET Chi-restraints excluded: chain n residue 18 GLN Chi-restraints excluded: chain n residue 37 THR Chi-restraints excluded: chain n residue 106 ASP Chi-restraints excluded: chain o residue 2 ASP Chi-restraints excluded: chain o residue 28 VAL Chi-restraints excluded: chain o residue 36 TYR Chi-restraints excluded: chain o residue 61 GLN Chi-restraints excluded: chain o residue 62 LEU Chi-restraints excluded: chain o residue 69 ASP Chi-restraints excluded: chain o residue 93 ASP Chi-restraints excluded: chain o residue 108 ASP Chi-restraints excluded: chain p residue 31 VAL Chi-restraints excluded: chain p residue 35 SER Chi-restraints excluded: chain p residue 40 GLN Chi-restraints excluded: chain p residue 59 THR Chi-restraints excluded: chain p residue 64 SER Chi-restraints excluded: chain p residue 70 GLU Chi-restraints excluded: chain p residue 103 THR Chi-restraints excluded: chain p residue 109 ILE Chi-restraints excluded: chain q residue 2 ARG Chi-restraints excluded: chain q residue 8 ILE Chi-restraints excluded: chain q residue 17 LEU Chi-restraints excluded: chain q residue 73 ILE Chi-restraints excluded: chain r residue 10 LYS Chi-restraints excluded: chain r residue 19 THR Chi-restraints excluded: chain r residue 33 VAL Chi-restraints excluded: chain r residue 40 MET Chi-restraints excluded: chain r residue 41 ILE Chi-restraints excluded: chain r residue 49 ILE Chi-restraints excluded: chain r residue 53 PHE Chi-restraints excluded: chain r residue 62 GLU Chi-restraints excluded: chain s residue 69 LEU Chi-restraints excluded: chain s residue 74 ILE Chi-restraints excluded: chain s residue 81 SER Chi-restraints excluded: chain t residue 32 LEU Chi-restraints excluded: chain t residue 50 LEU Chi-restraints excluded: chain t residue 87 LEU Chi-restraints excluded: chain u residue 17 ASP Chi-restraints excluded: chain u residue 29 SER Chi-restraints excluded: chain u residue 35 VAL Chi-restraints excluded: chain u residue 40 LEU Chi-restraints excluded: chain u residue 71 ILE Chi-restraints excluded: chain v residue 8 VAL Chi-restraints excluded: chain v residue 38 LEU Chi-restraints excluded: chain v residue 42 LEU Chi-restraints excluded: chain v residue 45 ASP Chi-restraints excluded: chain v residue 59 GLU Chi-restraints excluded: chain v residue 61 LEU Chi-restraints excluded: chain v residue 63 ILE Chi-restraints excluded: chain v residue 87 GLN Chi-restraints excluded: chain v residue 89 ILE Chi-restraints excluded: chain w residue 8 ASN Chi-restraints excluded: chain w residue 17 LEU Chi-restraints excluded: chain w residue 27 VAL Chi-restraints excluded: chain w residue 72 ASN Chi-restraints excluded: chain x residue 41 SER Chi-restraints excluded: chain x residue 58 ILE Chi-restraints excluded: chain x residue 67 LEU Chi-restraints excluded: chain z residue 11 SER Chi-restraints excluded: chain z residue 13 ILE Chi-restraints excluded: chain z residue 48 ASN Chi-restraints excluded: chain z residue 53 MET Chi-restraints excluded: chain z residue 56 VAL Chi-restraints excluded: chain A residue 33 ASN Chi-restraints excluded: chain A residue 58 ASP Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain E residue 51 LYS Chi-restraints excluded: chain F residue 17 VAL Chi-restraints excluded: chain F residue 30 GLU Chi-restraints excluded: chain G residue 29 PHE Chi-restraints excluded: chain G residue 30 ILE Chi-restraints excluded: chain G residue 59 ILE Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain G residue 122 ASP Chi-restraints excluded: chain G residue 158 ASP Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 198 VAL Chi-restraints excluded: chain G residue 221 ARG Chi-restraints excluded: chain H residue 5 HIS Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 50 SER Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 68 HIS Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 153 SER Chi-restraints excluded: chain H residue 169 GLU Chi-restraints excluded: chain I residue 53 GLN Chi-restraints excluded: chain I residue 66 VAL Chi-restraints excluded: chain I residue 92 LEU Chi-restraints excluded: chain I residue 173 ASP Chi-restraints excluded: chain I residue 177 MET Chi-restraints excluded: chain I residue 196 GLU Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 29 ILE Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain J residue 87 VAL Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 141 ASP Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 54 LEU Chi-restraints excluded: chain K residue 73 GLU Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain K residue 91 ARG Chi-restraints excluded: chain L residue 17 PHE Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain L residue 122 GLU Chi-restraints excluded: chain L residue 129 ASN Chi-restraints excluded: chain L residue 132 THR Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain M residue 74 ILE Chi-restraints excluded: chain M residue 77 VAL Chi-restraints excluded: chain M residue 84 ILE Chi-restraints excluded: chain M residue 111 THR Chi-restraints excluded: chain M residue 120 LEU Chi-restraints excluded: chain M residue 124 ILE Chi-restraints excluded: chain N residue 42 THR Chi-restraints excluded: chain N residue 44 ARG Chi-restraints excluded: chain N residue 46 VAL Chi-restraints excluded: chain N residue 57 VAL Chi-restraints excluded: chain N residue 61 ASP Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain O residue 22 THR Chi-restraints excluded: chain O residue 36 VAL Chi-restraints excluded: chain O residue 57 VAL Chi-restraints excluded: chain O residue 71 LEU Chi-restraints excluded: chain O residue 92 LEU Chi-restraints excluded: chain P residue 30 ILE Chi-restraints excluded: chain P residue 39 ASN Chi-restraints excluded: chain P residue 41 LEU Chi-restraints excluded: chain P residue 57 SER Chi-restraints excluded: chain P residue 67 GLU Chi-restraints excluded: chain P residue 73 VAL Chi-restraints excluded: chain P residue 81 LEU Chi-restraints excluded: chain P residue 95 THR Chi-restraints excluded: chain P residue 96 ILE Chi-restraints excluded: chain P residue 106 ILE Chi-restraints excluded: chain P residue 126 ARG Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain Q residue 33 CYS Chi-restraints excluded: chain Q residue 54 VAL Chi-restraints excluded: chain Q residue 101 LEU Chi-restraints excluded: chain Q residue 108 ASP Chi-restraints excluded: chain Q residue 119 LYS Chi-restraints excluded: chain R residue 3 ILE Chi-restraints excluded: chain R residue 19 THR Chi-restraints excluded: chain R residue 24 VAL Chi-restraints excluded: chain R residue 27 THR Chi-restraints excluded: chain R residue 67 ASP Chi-restraints excluded: chain R residue 73 SER Chi-restraints excluded: chain R residue 101 THR Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain R residue 113 LYS Chi-restraints excluded: chain S residue 78 LEU Chi-restraints excluded: chain S residue 95 LEU Chi-restraints excluded: chain T residue 32 THR Chi-restraints excluded: chain T residue 56 LEU Chi-restraints excluded: chain T residue 59 VAL Chi-restraints excluded: chain T residue 69 LEU Chi-restraints excluded: chain T residue 86 LEU Chi-restraints excluded: chain U residue 1 MET Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain U residue 36 VAL Chi-restraints excluded: chain U residue 53 ASP Chi-restraints excluded: chain U residue 66 THR Chi-restraints excluded: chain U residue 74 LEU Chi-restraints excluded: chain V residue 4 ILE Chi-restraints excluded: chain V residue 27 PHE Chi-restraints excluded: chain V residue 38 LYS Chi-restraints excluded: chain V residue 52 CYS Chi-restraints excluded: chain V residue 54 ILE Chi-restraints excluded: chain V residue 56 ASP Chi-restraints excluded: chain V residue 77 VAL Chi-restraints excluded: chain W residue 17 VAL Chi-restraints excluded: chain W residue 28 LEU Chi-restraints excluded: chain W residue 70 THR Chi-restraints excluded: chain W residue 71 ASP Chi-restraints excluded: chain X residue 57 VAL Chi-restraints excluded: chain X residue 59 VAL Chi-restraints excluded: chain X residue 70 LEU Chi-restraints excluded: chain X residue 78 THR Chi-restraints excluded: chain Y residue 58 ASP Chi-restraints excluded: chain Z residue 12 ASP Chi-restraints excluded: chain Z residue 18 PHE Chi-restraints excluded: chain Z residue 30 GLU Chi-restraints excluded: chain Z residue 33 ARG Chi-restraints excluded: chain a residue 8 MET Chi-restraints excluded: chain a residue 27 ILE Chi-restraints excluded: chain a residue 42 VAL Chi-restraints excluded: chain a residue 56 ASP Chi-restraints excluded: chain a residue 64 VAL Chi-restraints excluded: chain a residue 178 VAL Chi-restraints excluded: chain a residue 193 LEU Chi-restraints excluded: chain a residue 196 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1048 random chunks: chunk 918 optimal weight: 10.0000 chunk 967 optimal weight: 10.0000 chunk 882 optimal weight: 30.0000 chunk 941 optimal weight: 50.0000 chunk 566 optimal weight: 6.9990 chunk 410 optimal weight: 30.0000 chunk 739 optimal weight: 20.0000 chunk 288 optimal weight: 9.9990 chunk 850 optimal weight: 10.0000 chunk 890 optimal weight: 10.0000 chunk 938 optimal weight: 50.0000 overall best weight: 9.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 19 GLN q 51 GLN q 71 ASN ** v 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 134 ASN ** K 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 50 ASN X 68 HIS ** a 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.3663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 162700 Z= 0.337 Angle : 0.704 12.810 243508 Z= 0.362 Chirality : 0.039 0.328 31146 Planarity : 0.005 0.072 12986 Dihedral : 23.660 179.983 81731 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 18.50 Ramachandran Plot: Outliers : 0.29 % Allowed : 13.43 % Favored : 86.27 % Rotamer: Outliers : 6.48 % Allowed : 22.97 % Favored : 70.55 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.51 % Twisted General : 0.32 % 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: -2.43 (0.11), residues: 5836 helix: -0.30 (0.12), residues: 1842 sheet: -1.61 (0.16), residues: 1034 loop : -2.53 (0.11), residues: 2960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP H 166 HIS 0.008 0.001 HIS v 80 PHE 0.030 0.002 PHE C 19 TYR 0.035 0.003 TYR W 50 ARG 0.007 0.001 ARG Z 34 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11672 Ramachandran restraints generated. 5836 Oldfield, 0 Emsley, 5836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11672 Ramachandran restraints generated. 5836 Oldfield, 0 Emsley, 5836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1255 residues out of total 4862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 315 poor density : 940 time to evaluate : 6.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 224 MET cc_start: 0.8226 (mtt) cc_final: 0.7985 (mtt) REVERT: c 190 LYS cc_start: 0.8844 (tttt) cc_final: 0.8571 (ttpt) REVERT: d 1 MET cc_start: 0.5209 (mmm) cc_final: 0.4962 (mmm) REVERT: d 29 HIS cc_start: 0.8391 (OUTLIER) cc_final: 0.7932 (t70) REVERT: d 30 GLN cc_start: 0.8827 (tm-30) cc_final: 0.8170 (tm-30) REVERT: d 115 GLN cc_start: 0.8817 (tp40) cc_final: 0.8612 (tp-100) REVERT: d 155 GLU cc_start: 0.7198 (OUTLIER) cc_final: 0.6920 (pt0) REVERT: d 195 GLN cc_start: 0.8656 (OUTLIER) cc_final: 0.8079 (mp10) REVERT: e 4 HIS cc_start: 0.8473 (t-170) cc_final: 0.8048 (t-170) REVERT: e 9 ASP cc_start: 0.7919 (OUTLIER) cc_final: 0.7596 (m-30) REVERT: e 16 MET cc_start: 0.8685 (mmm) cc_final: 0.8226 (mmm) REVERT: e 95 MET cc_start: 0.8582 (ttp) cc_final: 0.8145 (ttp) REVERT: e 96 TRP cc_start: 0.8823 (m100) cc_final: 0.8345 (m100) REVERT: e 176 PHE cc_start: 0.7126 (OUTLIER) cc_final: 0.6809 (m-80) REVERT: f 2 ARG cc_start: 0.7947 (OUTLIER) cc_final: 0.7692 (mmt-90) REVERT: f 138 GLN cc_start: 0.8055 (OUTLIER) cc_final: 0.7712 (tp40) REVERT: f 169 ARG cc_start: 0.8068 (mmm160) cc_final: 0.7124 (ttt90) REVERT: g 25 TYR cc_start: 0.7859 (t80) cc_final: 0.7540 (t80) REVERT: l 143 GLU cc_start: 0.7051 (OUTLIER) cc_final: 0.6757 (pt0) REVERT: m 33 LEU cc_start: 0.9055 (tp) cc_final: 0.8730 (mp) REVERT: m 75 GLU cc_start: 0.7590 (mt-10) cc_final: 0.7022 (mt-10) REVERT: n 72 ASP cc_start: 0.8672 (t70) cc_final: 0.7990 (t0) REVERT: o 58 ILE cc_start: 0.8602 (mt) cc_final: 0.7974 (tp) REVERT: o 61 GLN cc_start: 0.9049 (OUTLIER) cc_final: 0.8307 (tp40) REVERT: p 8 GLU cc_start: 0.8754 (mt-10) cc_final: 0.8377 (mt-10) REVERT: p 70 GLU cc_start: 0.8212 (OUTLIER) cc_final: 0.7592 (mp0) REVERT: p 97 TYR cc_start: 0.7812 (m-80) cc_final: 0.7556 (m-80) REVERT: r 10 LYS cc_start: 0.8578 (OUTLIER) cc_final: 0.8214 (ptpp) REVERT: r 16 GLU cc_start: 0.8434 (tt0) cc_final: 0.8131 (tt0) REVERT: r 62 GLU cc_start: 0.8100 (OUTLIER) cc_final: 0.7333 (tp30) REVERT: s 52 GLU cc_start: 0.8679 (mt-10) cc_final: 0.8370 (tt0) REVERT: t 1 MET cc_start: 0.5839 (mpt) cc_final: 0.5276 (mpt) REVERT: t 15 HIS cc_start: 0.7578 (t70) cc_final: 0.7352 (t-90) REVERT: v 87 GLN cc_start: 0.7961 (OUTLIER) cc_final: 0.7679 (mp10) REVERT: w 40 LYS cc_start: 0.9055 (mttt) cc_final: 0.8714 (mttm) REVERT: x 69 GLU cc_start: 0.8041 (mt-10) cc_final: 0.7711 (mt-10) REVERT: y 23 ARG cc_start: 0.8820 (mpt180) cc_final: 0.8423 (mpt180) REVERT: y 40 SER cc_start: 0.9341 (p) cc_final: 0.8814 (t) REVERT: y 60 LYS cc_start: 0.8823 (mmmm) cc_final: 0.8532 (mtpp) REVERT: z 55 LYS cc_start: 0.8935 (mttp) cc_final: 0.8438 (tmtt) REVERT: B 35 GLU cc_start: 0.7774 (mt-10) cc_final: 0.7337 (mt-10) REVERT: C 20 TYR cc_start: 0.6551 (m-80) cc_final: 0.6183 (m-80) REVERT: C 29 LYS cc_start: 0.5611 (ptpt) cc_final: 0.5060 (pttt) REVERT: D 10 LEU cc_start: 0.9105 (tp) cc_final: 0.8858 (tt) REVERT: E 53 ASP cc_start: 0.7954 (m-30) cc_final: 0.7682 (m-30) REVERT: G 34 ARG cc_start: 0.7476 (mmp80) cc_final: 0.6282 (tpm170) REVERT: G 88 GLN cc_start: 0.7713 (mm-40) cc_final: 0.7428 (mp10) REVERT: G 93 HIS cc_start: 0.8360 (m90) cc_final: 0.7944 (m-70) REVERT: G 95 TRP cc_start: 0.8235 (t60) cc_final: 0.7766 (t60) REVERT: G 99 MET cc_start: 0.8664 (ptp) cc_final: 0.8073 (ptp) REVERT: G 119 GLN cc_start: 0.8296 (mt0) cc_final: 0.7864 (pp30) REVERT: G 221 ARG cc_start: 0.7866 (OUTLIER) cc_final: 0.7596 (mtt-85) REVERT: H 34 SER cc_start: 0.9084 (t) cc_final: 0.8735 (p) REVERT: H 55 VAL cc_start: 0.8746 (t) cc_final: 0.8519 (t) REVERT: H 111 ASP cc_start: 0.8135 (t0) cc_final: 0.7894 (t0) REVERT: H 133 MET cc_start: 0.8880 (OUTLIER) cc_final: 0.8636 (tmm) REVERT: I 3 TYR cc_start: 0.7856 (t80) cc_final: 0.7190 (t80) REVERT: I 123 MET cc_start: 0.6271 (mmm) cc_final: 0.5827 (mmm) REVERT: J 53 ARG cc_start: 0.8067 (ttp80) cc_final: 0.7847 (ttp80) REVERT: J 64 GLU cc_start: 0.8730 (mt-10) cc_final: 0.8444 (tm-30) REVERT: J 89 THR cc_start: 0.8744 (m) cc_final: 0.8203 (p) REVERT: J 125 LYS cc_start: 0.8988 (tppt) cc_final: 0.8555 (tptp) REVERT: J 127 TYR cc_start: 0.8447 (m-80) cc_final: 0.8149 (m-80) REVERT: K 13 ASP cc_start: 0.8814 (m-30) cc_final: 0.8099 (p0) REVERT: K 62 MET cc_start: 0.8096 (mmm) cc_final: 0.7798 (mmm) REVERT: K 91 ARG cc_start: 0.8344 (OUTLIER) cc_final: 0.7311 (mmm-85) REVERT: L 10 LYS cc_start: 0.8563 (mmtp) cc_final: 0.8138 (ttpt) REVERT: L 17 PHE cc_start: 0.6864 (OUTLIER) cc_final: 0.5386 (p90) REVERT: L 51 GLN cc_start: 0.8572 (tt0) cc_final: 0.8223 (mm-40) REVERT: L 100 MET cc_start: 0.9100 (mtt) cc_final: 0.8700 (mtt) REVERT: M 3 GLN cc_start: 0.8560 (OUTLIER) cc_final: 0.7270 (mt0) REVERT: M 41 GLU cc_start: 0.8813 (mm-30) cc_final: 0.8487 (mm-30) REVERT: M 46 GLU cc_start: 0.8206 (tm-30) cc_final: 0.7912 (tm-30) REVERT: M 90 GLU cc_start: 0.8160 (mp0) cc_final: 0.7918 (mp0) REVERT: M 95 MET cc_start: 0.9115 (mpp) cc_final: 0.8660 (mpp) REVERT: M 98 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8654 (pp) REVERT: N 56 MET cc_start: 0.8134 (ppp) cc_final: 0.7698 (ppp) REVERT: N 102 PHE cc_start: 0.8122 (m-80) cc_final: 0.7325 (m-80) REVERT: N 104 THR cc_start: 0.7862 (t) cc_final: 0.7629 (m) REVERT: O 11 LYS cc_start: 0.8561 (ptpt) cc_final: 0.8151 (mtmm) REVERT: O 19 ASP cc_start: 0.8720 (m-30) cc_final: 0.8013 (p0) REVERT: O 20 GLN cc_start: 0.9117 (tp40) cc_final: 0.8701 (tm-30) REVERT: O 46 LYS cc_start: 0.8750 (mttp) cc_final: 0.8452 (mttm) REVERT: O 63 ASP cc_start: 0.6889 (t0) cc_final: 0.6358 (t0) REVERT: P 41 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8519 (mp) REVERT: P 74 LYS cc_start: 0.8707 (ptpt) cc_final: 0.8393 (mmmt) REVERT: P 86 LYS cc_start: 0.8581 (ptpp) cc_final: 0.8084 (pttm) REVERT: Q 28 GLN cc_start: 0.8568 (mp10) cc_final: 0.7861 (mt0) REVERT: Q 111 GLN cc_start: 0.8184 (mt0) cc_final: 0.7776 (mt0) REVERT: R 51 GLN cc_start: 0.8502 (mp10) cc_final: 0.8213 (mp10) REVERT: R 113 LYS cc_start: 0.7893 (OUTLIER) cc_final: 0.7384 (mtmm) REVERT: S 4 SER cc_start: 0.9247 (p) cc_final: 0.8648 (t) REVERT: S 19 TYR cc_start: 0.8351 (OUTLIER) cc_final: 0.7657 (m-80) REVERT: S 48 GLN cc_start: 0.7857 (mt0) cc_final: 0.7587 (mt0) REVERT: S 78 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8503 (mt) REVERT: S 95 LEU cc_start: 0.9055 (OUTLIER) cc_final: 0.8667 (tt) REVERT: T 5 GLU cc_start: 0.8249 (tp30) cc_final: 0.7805 (tp30) REVERT: T 9 LYS cc_start: 0.9431 (mttt) cc_final: 0.8956 (mttm) REVERT: U 1 MET cc_start: 0.6567 (OUTLIER) cc_final: 0.5811 (ttp) REVERT: V 10 ARG cc_start: 0.8901 (ptm-80) cc_final: 0.8402 (ptm-80) REVERT: V 27 PHE cc_start: 0.8776 (OUTLIER) cc_final: 0.8215 (t80) REVERT: V 39 ARG cc_start: 0.8033 (mmm160) cc_final: 0.7798 (mmm160) REVERT: V 72 TRP cc_start: 0.8367 (m100) cc_final: 0.8126 (m100) REVERT: W 22 TYR cc_start: 0.7787 (p90) cc_final: 0.7517 (p90) REVERT: X 9 PHE cc_start: 0.8717 (t80) cc_final: 0.8424 (t80) REVERT: X 19 GLU cc_start: 0.8351 (mm-30) cc_final: 0.7863 (pp20) REVERT: Y 3 ILE cc_start: 0.8454 (mp) cc_final: 0.7887 (mm) REVERT: Y 17 ARG cc_start: 0.8964 (ttp80) cc_final: 0.8727 (ttp80) REVERT: Y 27 MET cc_start: 0.8992 (ppp) cc_final: 0.8764 (tmm) REVERT: Y 53 MET cc_start: 0.8880 (ppp) cc_final: 0.8566 (ppp) REVERT: Y 54 GLN cc_start: 0.8614 (tm-30) cc_final: 0.8012 (tm-30) REVERT: Y 58 ASP cc_start: 0.8919 (OUTLIER) cc_final: 0.8225 (t0) REVERT: Z 46 ARG cc_start: 0.8175 (mpt180) cc_final: 0.7423 (tpt-90) REVERT: a 167 LYS cc_start: 0.0288 (tptt) cc_final: -0.0409 (mttp) outliers start: 315 outliers final: 266 residues processed: 1131 average time/residue: 1.2636 time to fit residues: 2523.2408 Evaluate side-chains 1223 residues out of total 4862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 293 poor density : 930 time to evaluate : 9.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 2 VAL Chi-restraints excluded: chain b residue 85 ASN Chi-restraints excluded: chain b residue 136 VAL Chi-restraints excluded: chain b residue 159 THR Chi-restraints excluded: chain b residue 171 VAL Chi-restraints excluded: chain b residue 181 ARG Chi-restraints excluded: chain b residue 183 VAL Chi-restraints excluded: chain b residue 203 VAL Chi-restraints excluded: chain b residue 215 VAL Chi-restraints excluded: chain b residue 228 ASP Chi-restraints excluded: chain b residue 238 ASN Chi-restraints excluded: chain b residue 256 THR Chi-restraints excluded: chain c residue 1 MET Chi-restraints excluded: chain c residue 50 VAL Chi-restraints excluded: chain c residue 138 LEU Chi-restraints excluded: chain c residue 139 SER Chi-restraints excluded: chain c residue 175 LEU Chi-restraints excluded: chain c residue 180 VAL Chi-restraints excluded: chain d residue 29 HIS Chi-restraints excluded: chain d residue 84 THR Chi-restraints excluded: chain d residue 140 ASP Chi-restraints excluded: chain d residue 145 ASP Chi-restraints excluded: chain d residue 155 GLU Chi-restraints excluded: chain d residue 195 GLN Chi-restraints excluded: chain e residue 9 ASP Chi-restraints excluded: chain e residue 22 ASN Chi-restraints excluded: chain e residue 24 VAL Chi-restraints excluded: chain e residue 67 THR Chi-restraints excluded: chain e residue 77 LYS Chi-restraints excluded: chain e residue 86 CYS Chi-restraints excluded: chain e residue 117 SER Chi-restraints excluded: chain e residue 176 PHE Chi-restraints excluded: chain f residue 2 ARG Chi-restraints excluded: chain f residue 33 THR Chi-restraints excluded: chain f residue 71 LEU Chi-restraints excluded: chain f residue 138 GLN Chi-restraints excluded: chain f residue 147 LEU Chi-restraints excluded: chain f residue 154 GLU Chi-restraints excluded: chain g residue 4 ILE Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain g residue 48 GLU Chi-restraints excluded: chain h residue 15 VAL Chi-restraints excluded: chain h residue 27 VAL Chi-restraints excluded: chain h residue 55 VAL Chi-restraints excluded: chain j residue 36 LEU Chi-restraints excluded: chain j residue 55 ILE Chi-restraints excluded: chain j residue 64 VAL Chi-restraints excluded: chain j residue 76 HIS Chi-restraints excluded: chain j residue 84 ILE Chi-restraints excluded: chain j residue 92 MET Chi-restraints excluded: chain j residue 105 VAL Chi-restraints excluded: chain j residue 109 LEU Chi-restraints excluded: chain j residue 142 ILE Chi-restraints excluded: chain k residue 3 GLN Chi-restraints excluded: chain k residue 58 LEU Chi-restraints excluded: chain k residue 62 VAL Chi-restraints excluded: chain k residue 76 VAL Chi-restraints excluded: chain k residue 87 LEU Chi-restraints excluded: chain k residue 97 THR Chi-restraints excluded: chain k residue 104 THR Chi-restraints excluded: chain l residue 35 HIS Chi-restraints excluded: chain l residue 42 SER Chi-restraints excluded: chain l residue 81 ASP Chi-restraints excluded: chain l residue 110 VAL Chi-restraints excluded: chain l residue 111 ILE Chi-restraints excluded: chain l residue 116 VAL Chi-restraints excluded: chain l residue 117 THR Chi-restraints excluded: chain l residue 122 VAL Chi-restraints excluded: chain l residue 143 GLU Chi-restraints excluded: chain m residue 7 THR Chi-restraints excluded: chain m residue 36 VAL Chi-restraints excluded: chain m residue 41 LEU Chi-restraints excluded: chain m residue 70 ASP Chi-restraints excluded: chain m residue 82 MET Chi-restraints excluded: chain m residue 95 LEU Chi-restraints excluded: chain m residue 128 THR Chi-restraints excluded: chain m residue 136 MET Chi-restraints excluded: chain n residue 18 GLN Chi-restraints excluded: chain n residue 34 ILE Chi-restraints excluded: chain n residue 37 THR Chi-restraints excluded: chain n residue 106 ASP Chi-restraints excluded: chain o residue 2 ASP Chi-restraints excluded: chain o residue 28 VAL Chi-restraints excluded: chain o residue 36 TYR Chi-restraints excluded: chain o residue 61 GLN Chi-restraints excluded: chain o residue 62 LEU Chi-restraints excluded: chain o residue 69 ASP Chi-restraints excluded: chain o residue 78 VAL Chi-restraints excluded: chain o residue 93 ASP Chi-restraints excluded: chain o residue 108 ASP Chi-restraints excluded: chain p residue 31 VAL Chi-restraints excluded: chain p residue 35 SER Chi-restraints excluded: chain p residue 40 GLN Chi-restraints excluded: chain p residue 59 THR Chi-restraints excluded: chain p residue 64 SER Chi-restraints excluded: chain p residue 70 GLU Chi-restraints excluded: chain p residue 101 GLU Chi-restraints excluded: chain p residue 103 THR Chi-restraints excluded: chain p residue 109 ILE Chi-restraints excluded: chain q residue 2 ARG Chi-restraints excluded: chain q residue 5 ARG Chi-restraints excluded: chain q residue 8 ILE Chi-restraints excluded: chain q residue 17 LEU Chi-restraints excluded: chain q residue 19 GLN Chi-restraints excluded: chain q residue 73 ILE Chi-restraints excluded: chain r residue 10 LYS Chi-restraints excluded: chain r residue 19 THR Chi-restraints excluded: chain r residue 33 VAL Chi-restraints excluded: chain r residue 40 MET Chi-restraints excluded: chain r residue 41 ILE Chi-restraints excluded: chain r residue 49 ILE Chi-restraints excluded: chain r residue 53 PHE Chi-restraints excluded: chain r residue 62 GLU Chi-restraints excluded: chain s residue 37 THR Chi-restraints excluded: chain s residue 69 LEU Chi-restraints excluded: chain s residue 74 ILE Chi-restraints excluded: chain s residue 81 SER Chi-restraints excluded: chain s residue 94 ASP Chi-restraints excluded: chain t residue 32 LEU Chi-restraints excluded: chain t residue 50 LEU Chi-restraints excluded: chain t residue 78 SER Chi-restraints excluded: chain t residue 87 LEU Chi-restraints excluded: chain u residue 17 ASP Chi-restraints excluded: chain u residue 35 VAL Chi-restraints excluded: chain u residue 40 LEU Chi-restraints excluded: chain u residue 71 ILE Chi-restraints excluded: chain v residue 7 GLU Chi-restraints excluded: chain v residue 8 VAL Chi-restraints excluded: chain v residue 38 LEU Chi-restraints excluded: chain v residue 45 ASP Chi-restraints excluded: chain v residue 59 GLU Chi-restraints excluded: chain v residue 61 LEU Chi-restraints excluded: chain v residue 63 ILE Chi-restraints excluded: chain v residue 87 GLN Chi-restraints excluded: chain v residue 89 ILE Chi-restraints excluded: chain w residue 8 ASN Chi-restraints excluded: chain w residue 17 LEU Chi-restraints excluded: chain w residue 27 VAL Chi-restraints excluded: chain w residue 63 VAL Chi-restraints excluded: chain w residue 72 ASN Chi-restraints excluded: chain x residue 41 SER Chi-restraints excluded: chain x residue 58 ILE Chi-restraints excluded: chain x residue 67 LEU Chi-restraints excluded: chain z residue 11 SER Chi-restraints excluded: chain z residue 13 ILE Chi-restraints excluded: chain z residue 48 ASN Chi-restraints excluded: chain z residue 53 MET Chi-restraints excluded: chain z residue 56 VAL Chi-restraints excluded: chain A residue 33 ASN Chi-restraints excluded: chain A residue 58 ASP Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain E residue 51 LYS Chi-restraints excluded: chain F residue 17 VAL Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain F residue 30 GLU Chi-restraints excluded: chain G residue 29 PHE Chi-restraints excluded: chain G residue 30 ILE Chi-restraints excluded: chain G residue 59 ILE Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain G residue 122 ASP Chi-restraints excluded: chain G residue 158 ASP Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 198 VAL Chi-restraints excluded: chain G residue 221 ARG Chi-restraints excluded: chain H residue 5 HIS Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 50 SER Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 68 HIS Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 133 MET Chi-restraints excluded: chain H residue 153 SER Chi-restraints excluded: chain H residue 169 GLU Chi-restraints excluded: chain I residue 66 VAL Chi-restraints excluded: chain I residue 92 LEU Chi-restraints excluded: chain I residue 97 LEU Chi-restraints excluded: chain I residue 170 LEU Chi-restraints excluded: chain I residue 177 MET Chi-restraints excluded: chain I residue 196 GLU Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 29 ILE Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain J residue 87 VAL Chi-restraints excluded: chain J residue 123 LEU Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 133 ILE Chi-restraints excluded: chain J residue 141 ASP Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 54 LEU Chi-restraints excluded: chain K residue 64 VAL Chi-restraints excluded: chain K residue 73 GLU Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain K residue 91 ARG Chi-restraints excluded: chain L residue 17 PHE Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain L residue 122 GLU Chi-restraints excluded: chain L residue 129 ASN Chi-restraints excluded: chain L residue 132 THR Chi-restraints excluded: chain M residue 3 GLN Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain M residue 74 ILE Chi-restraints excluded: chain M residue 77 VAL Chi-restraints excluded: chain M residue 84 ILE Chi-restraints excluded: chain M residue 98 LEU Chi-restraints excluded: chain M residue 111 THR Chi-restraints excluded: chain M residue 120 LEU Chi-restraints excluded: chain M residue 124 ILE Chi-restraints excluded: chain N residue 42 THR Chi-restraints excluded: chain N residue 44 ARG Chi-restraints excluded: chain N residue 46 VAL Chi-restraints excluded: chain N residue 57 VAL Chi-restraints excluded: chain N residue 61 ASP Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain O residue 22 THR Chi-restraints excluded: chain O residue 36 VAL Chi-restraints excluded: chain O residue 57 VAL Chi-restraints excluded: chain O residue 71 LEU Chi-restraints excluded: chain O residue 92 LEU Chi-restraints excluded: chain P residue 30 ILE Chi-restraints excluded: chain P residue 39 ASN Chi-restraints excluded: chain P residue 41 LEU Chi-restraints excluded: chain P residue 57 SER Chi-restraints excluded: chain P residue 63 GLN Chi-restraints excluded: chain P residue 67 GLU Chi-restraints excluded: chain P residue 73 VAL Chi-restraints excluded: chain P residue 81 LEU Chi-restraints excluded: chain P residue 95 THR Chi-restraints excluded: chain P residue 96 ILE Chi-restraints excluded: chain P residue 106 ILE Chi-restraints excluded: chain P residue 126 ARG Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain Q residue 54 VAL Chi-restraints excluded: chain Q residue 101 LEU Chi-restraints excluded: chain Q residue 108 ASP Chi-restraints excluded: chain R residue 3 ILE Chi-restraints excluded: chain R residue 19 THR Chi-restraints excluded: chain R residue 24 VAL Chi-restraints excluded: chain R residue 27 THR Chi-restraints excluded: chain R residue 67 ASP Chi-restraints excluded: chain R residue 73 SER Chi-restraints excluded: chain R residue 101 THR Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain R residue 113 LYS Chi-restraints excluded: chain S residue 19 TYR Chi-restraints excluded: chain S residue 78 LEU Chi-restraints excluded: chain S residue 95 LEU Chi-restraints excluded: chain T residue 32 THR Chi-restraints excluded: chain T residue 56 LEU Chi-restraints excluded: chain T residue 59 VAL Chi-restraints excluded: chain T residue 69 LEU Chi-restraints excluded: chain T residue 86 LEU Chi-restraints excluded: chain U residue 1 MET Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain U residue 36 VAL Chi-restraints excluded: chain U residue 53 ASP Chi-restraints excluded: chain U residue 66 THR Chi-restraints excluded: chain U residue 74 LEU Chi-restraints excluded: chain V residue 4 ILE Chi-restraints excluded: chain V residue 27 PHE Chi-restraints excluded: chain V residue 38 LYS Chi-restraints excluded: chain V residue 52 CYS Chi-restraints excluded: chain V residue 54 ILE Chi-restraints excluded: chain V residue 56 ASP Chi-restraints excluded: chain V residue 77 VAL Chi-restraints excluded: chain W residue 17 VAL Chi-restraints excluded: chain W residue 28 LEU Chi-restraints excluded: chain W residue 70 THR Chi-restraints excluded: chain W residue 71 ASP Chi-restraints excluded: chain X residue 57 VAL Chi-restraints excluded: chain X residue 59 VAL Chi-restraints excluded: chain X residue 70 LEU Chi-restraints excluded: chain X residue 78 THR Chi-restraints excluded: chain Y residue 29 THR Chi-restraints excluded: chain Y residue 58 ASP Chi-restraints excluded: chain Z residue 12 ASP Chi-restraints excluded: chain Z residue 18 PHE Chi-restraints excluded: chain Z residue 30 GLU Chi-restraints excluded: chain Z residue 33 ARG Chi-restraints excluded: chain a residue 8 MET Chi-restraints excluded: chain a residue 27 ILE Chi-restraints excluded: chain a residue 42 VAL Chi-restraints excluded: chain a residue 56 ASP Chi-restraints excluded: chain a residue 64 VAL Chi-restraints excluded: chain a residue 178 VAL Chi-restraints excluded: chain a residue 193 LEU Chi-restraints excluded: chain a residue 196 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1048 random chunks: chunk 618 optimal weight: 40.0000 chunk 995 optimal weight: 10.0000 chunk 607 optimal weight: 20.0000 chunk 472 optimal weight: 6.9990 chunk 691 optimal weight: 20.0000 chunk 1044 optimal weight: 30.0000 chunk 960 optimal weight: 10.0000 chunk 831 optimal weight: 50.0000 chunk 86 optimal weight: 20.0000 chunk 642 optimal weight: 10.0000 chunk 509 optimal weight: 20.0000 overall best weight: 11.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 51 GLN ** u 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 15 ASN ** G 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 134 ASN ** K 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 50 ASN ** W 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 68 HIS ** a 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.3738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.085 162700 Z= 0.397 Angle : 0.754 13.397 243508 Z= 0.385 Chirality : 0.041 0.326 31146 Planarity : 0.006 0.072 12986 Dihedral : 23.714 178.932 81730 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 20.06 Ramachandran Plot: Outliers : 0.27 % Allowed : 14.17 % Favored : 85.56 % Rotamer: Outliers : 6.29 % Allowed : 23.18 % Favored : 70.53 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.32 % 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: -2.55 (0.11), residues: 5836 helix: -0.44 (0.12), residues: 1841 sheet: -1.64 (0.16), residues: 1023 loop : -2.59 (0.11), residues: 2972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP H 166 HIS 0.010 0.002 HIS K 3 PHE 0.028 0.002 PHE Z 36 TYR 0.036 0.003 TYR N 5 ARG 0.008 0.001 ARG Z 34 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11672 Ramachandran restraints generated. 5836 Oldfield, 0 Emsley, 5836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11672 Ramachandran restraints generated. 5836 Oldfield, 0 Emsley, 5836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1231 residues out of total 4862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 306 poor density : 925 time to evaluate : 6.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 190 LYS cc_start: 0.8847 (tttt) cc_final: 0.8573 (ttpt) REVERT: d 29 HIS cc_start: 0.8408 (OUTLIER) cc_final: 0.7981 (t70) REVERT: d 30 GLN cc_start: 0.8872 (tm-30) cc_final: 0.8200 (tm-30) REVERT: d 155 GLU cc_start: 0.7217 (OUTLIER) cc_final: 0.6949 (pt0) REVERT: d 195 GLN cc_start: 0.8649 (OUTLIER) cc_final: 0.8110 (mp10) REVERT: e 4 HIS cc_start: 0.8493 (t-170) cc_final: 0.8087 (t-170) REVERT: e 9 ASP cc_start: 0.7931 (OUTLIER) cc_final: 0.7620 (m-30) REVERT: e 16 MET cc_start: 0.8758 (mmm) cc_final: 0.8527 (mmm) REVERT: e 95 MET cc_start: 0.8440 (ttp) cc_final: 0.8030 (ttp) REVERT: e 96 TRP cc_start: 0.8808 (m100) cc_final: 0.8357 (m100) REVERT: e 176 PHE cc_start: 0.7220 (OUTLIER) cc_final: 0.6928 (m-80) REVERT: f 2 ARG cc_start: 0.7975 (OUTLIER) cc_final: 0.7707 (mmt-90) REVERT: f 138 GLN cc_start: 0.8077 (OUTLIER) cc_final: 0.7731 (tp40) REVERT: f 169 ARG cc_start: 0.8052 (mmm160) cc_final: 0.7148 (ttt90) REVERT: g 25 TYR cc_start: 0.7902 (t80) cc_final: 0.7571 (t80) REVERT: l 143 GLU cc_start: 0.7117 (OUTLIER) cc_final: 0.6883 (pt0) REVERT: m 33 LEU cc_start: 0.9075 (tp) cc_final: 0.8752 (mp) REVERT: m 75 GLU cc_start: 0.7620 (mt-10) cc_final: 0.7395 (mt-10) REVERT: n 72 ASP cc_start: 0.8691 (t70) cc_final: 0.8016 (t0) REVERT: o 58 ILE cc_start: 0.8604 (mt) cc_final: 0.7974 (tp) REVERT: o 61 GLN cc_start: 0.9031 (OUTLIER) cc_final: 0.8309 (tp40) REVERT: p 8 GLU cc_start: 0.8777 (mt-10) cc_final: 0.8381 (mt-10) REVERT: p 70 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.7715 (mp0) REVERT: r 10 LYS cc_start: 0.8589 (OUTLIER) cc_final: 0.8251 (ptpp) REVERT: r 16 GLU cc_start: 0.8443 (tt0) cc_final: 0.8121 (tt0) REVERT: r 31 GLU cc_start: 0.7837 (tm-30) cc_final: 0.7597 (tm-30) REVERT: s 52 GLU cc_start: 0.8702 (mt-10) cc_final: 0.8349 (tt0) REVERT: t 1 MET cc_start: 0.5788 (mpt) cc_final: 0.5356 (mpt) REVERT: t 15 HIS cc_start: 0.7598 (t70) cc_final: 0.7375 (t-90) REVERT: v 87 GLN cc_start: 0.8017 (OUTLIER) cc_final: 0.7748 (mp10) REVERT: w 40 LYS cc_start: 0.9056 (mttt) cc_final: 0.8707 (mttm) REVERT: x 69 GLU cc_start: 0.8039 (mt-10) cc_final: 0.7707 (mt-10) REVERT: y 23 ARG cc_start: 0.8851 (mpt180) cc_final: 0.8450 (mpt180) REVERT: y 40 SER cc_start: 0.9364 (p) cc_final: 0.8785 (t) REVERT: y 60 LYS cc_start: 0.8854 (mmmm) cc_final: 0.8587 (mtpp) REVERT: z 55 LYS cc_start: 0.8926 (mttp) cc_final: 0.8408 (tmtt) REVERT: B 35 GLU cc_start: 0.7811 (mt-10) cc_final: 0.7360 (mt-10) REVERT: C 20 TYR cc_start: 0.6656 (m-80) cc_final: 0.6212 (m-80) REVERT: D 10 LEU cc_start: 0.9121 (tp) cc_final: 0.8872 (tt) REVERT: E 53 ASP cc_start: 0.7944 (m-30) cc_final: 0.7660 (m-30) REVERT: G 34 ARG cc_start: 0.7497 (mmp80) cc_final: 0.6308 (tpm170) REVERT: G 88 GLN cc_start: 0.7722 (mm-40) cc_final: 0.7444 (mp10) REVERT: G 93 HIS cc_start: 0.8344 (m90) cc_final: 0.7906 (m-70) REVERT: G 95 TRP cc_start: 0.8276 (t60) cc_final: 0.7765 (t60) REVERT: G 99 MET cc_start: 0.8664 (ptp) cc_final: 0.8053 (ptp) REVERT: G 119 GLN cc_start: 0.8287 (mt0) cc_final: 0.7858 (pp30) REVERT: G 221 ARG cc_start: 0.7905 (OUTLIER) cc_final: 0.7609 (mtt-85) REVERT: H 34 SER cc_start: 0.9065 (t) cc_final: 0.8730 (p) REVERT: H 55 VAL cc_start: 0.8744 (t) cc_final: 0.8516 (t) REVERT: H 111 ASP cc_start: 0.8155 (t0) cc_final: 0.7925 (t0) REVERT: I 3 TYR cc_start: 0.7904 (t80) cc_final: 0.7271 (t80) REVERT: J 53 ARG cc_start: 0.8023 (ttp80) cc_final: 0.7795 (ttp80) REVERT: J 64 GLU cc_start: 0.8706 (mt-10) cc_final: 0.8413 (tm-30) REVERT: J 89 THR cc_start: 0.8740 (m) cc_final: 0.8409 (p) REVERT: J 125 LYS cc_start: 0.9052 (tppt) cc_final: 0.8592 (tptp) REVERT: J 127 TYR cc_start: 0.8450 (m-80) cc_final: 0.8144 (m-80) REVERT: K 13 ASP cc_start: 0.8845 (m-30) cc_final: 0.8098 (p0) REVERT: K 62 MET cc_start: 0.8119 (mmm) cc_final: 0.7826 (mmm) REVERT: K 91 ARG cc_start: 0.8288 (OUTLIER) cc_final: 0.7240 (mmm-85) REVERT: L 10 LYS cc_start: 0.8578 (mmtp) cc_final: 0.8160 (ttpt) REVERT: L 17 PHE cc_start: 0.6819 (OUTLIER) cc_final: 0.5323 (p90) REVERT: L 51 GLN cc_start: 0.8591 (tt0) cc_final: 0.8282 (mm-40) REVERT: L 100 MET cc_start: 0.9100 (mtt) cc_final: 0.8688 (mtt) REVERT: M 90 GLU cc_start: 0.8141 (mp0) cc_final: 0.7887 (mp0) REVERT: M 95 MET cc_start: 0.9123 (mpp) cc_final: 0.8659 (mpp) REVERT: M 98 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8699 (pp) REVERT: N 56 MET cc_start: 0.8071 (ppp) cc_final: 0.7641 (ppp) REVERT: N 102 PHE cc_start: 0.8091 (m-80) cc_final: 0.7294 (m-80) REVERT: N 104 THR cc_start: 0.7881 (t) cc_final: 0.7642 (m) REVERT: O 11 LYS cc_start: 0.8560 (ptpt) cc_final: 0.8133 (mtmm) REVERT: O 19 ASP cc_start: 0.8749 (m-30) cc_final: 0.8037 (p0) REVERT: O 20 GLN cc_start: 0.9116 (tp40) cc_final: 0.8683 (tm-30) REVERT: O 46 LYS cc_start: 0.8753 (mttp) cc_final: 0.8457 (mttm) REVERT: O 53 ILE cc_start: 0.9280 (mm) cc_final: 0.9074 (mm) REVERT: O 63 ASP cc_start: 0.6850 (t0) cc_final: 0.6315 (t0) REVERT: P 41 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8505 (mp) REVERT: P 74 LYS cc_start: 0.8735 (ptpt) cc_final: 0.8404 (mmmt) REVERT: P 86 LYS cc_start: 0.8624 (ptpp) cc_final: 0.8401 (pttm) REVERT: Q 111 GLN cc_start: 0.8267 (mt0) cc_final: 0.7865 (mt0) REVERT: R 51 GLN cc_start: 0.8486 (mp10) cc_final: 0.8211 (mp10) REVERT: R 113 LYS cc_start: 0.7905 (OUTLIER) cc_final: 0.7533 (mtmm) REVERT: S 4 SER cc_start: 0.9250 (p) cc_final: 0.8644 (t) REVERT: S 19 TYR cc_start: 0.8393 (OUTLIER) cc_final: 0.7668 (m-80) REVERT: S 48 GLN cc_start: 0.7885 (mt0) cc_final: 0.7633 (mt0) REVERT: S 78 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8498 (mt) REVERT: S 95 LEU cc_start: 0.9062 (OUTLIER) cc_final: 0.8669 (tt) REVERT: T 5 GLU cc_start: 0.8242 (tp30) cc_final: 0.7795 (tp30) REVERT: T 9 LYS cc_start: 0.9447 (mttt) cc_final: 0.9011 (mttm) REVERT: U 1 MET cc_start: 0.6594 (OUTLIER) cc_final: 0.5880 (ttp) REVERT: V 27 PHE cc_start: 0.8773 (OUTLIER) cc_final: 0.8215 (t80) REVERT: V 72 TRP cc_start: 0.8407 (m100) cc_final: 0.8158 (m100) REVERT: W 22 TYR cc_start: 0.7807 (p90) cc_final: 0.7520 (p90) REVERT: X 9 PHE cc_start: 0.8749 (t80) cc_final: 0.8470 (t80) REVERT: X 19 GLU cc_start: 0.8351 (mm-30) cc_final: 0.7856 (pp20) REVERT: Y 3 ILE cc_start: 0.8482 (mp) cc_final: 0.7898 (mm) REVERT: Y 17 ARG cc_start: 0.8972 (ttp80) cc_final: 0.8731 (ttp80) REVERT: Y 27 MET cc_start: 0.8997 (ppp) cc_final: 0.8756 (tmm) REVERT: Y 53 MET cc_start: 0.8889 (ppp) cc_final: 0.8578 (ppp) REVERT: Y 54 GLN cc_start: 0.8625 (tm-30) cc_final: 0.8011 (tm-30) REVERT: Y 58 ASP cc_start: 0.8923 (OUTLIER) cc_final: 0.8234 (t0) REVERT: Z 46 ARG cc_start: 0.8241 (mpt180) cc_final: 0.7454 (tpt-90) outliers start: 306 outliers final: 268 residues processed: 1114 average time/residue: 1.2555 time to fit residues: 2473.2757 Evaluate side-chains 1200 residues out of total 4862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 292 poor density : 908 time to evaluate : 6.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 2 VAL Chi-restraints excluded: chain b residue 85 ASN Chi-restraints excluded: chain b residue 136 VAL Chi-restraints excluded: chain b residue 159 THR Chi-restraints excluded: chain b residue 171 VAL Chi-restraints excluded: chain b residue 181 ARG Chi-restraints excluded: chain b residue 183 VAL Chi-restraints excluded: chain b residue 203 VAL Chi-restraints excluded: chain b residue 215 VAL Chi-restraints excluded: chain b residue 228 ASP Chi-restraints excluded: chain b residue 238 ASN Chi-restraints excluded: chain b residue 256 THR Chi-restraints excluded: chain c residue 1 MET Chi-restraints excluded: chain c residue 50 VAL Chi-restraints excluded: chain c residue 108 ASP Chi-restraints excluded: chain c residue 138 LEU Chi-restraints excluded: chain c residue 139 SER Chi-restraints excluded: chain c residue 175 LEU Chi-restraints excluded: chain c residue 180 VAL Chi-restraints excluded: chain d residue 29 HIS Chi-restraints excluded: chain d residue 84 THR Chi-restraints excluded: chain d residue 140 ASP Chi-restraints excluded: chain d residue 145 ASP Chi-restraints excluded: chain d residue 155 GLU Chi-restraints excluded: chain d residue 195 GLN Chi-restraints excluded: chain e residue 9 ASP Chi-restraints excluded: chain e residue 22 ASN Chi-restraints excluded: chain e residue 24 VAL Chi-restraints excluded: chain e residue 67 THR Chi-restraints excluded: chain e residue 77 LYS Chi-restraints excluded: chain e residue 86 CYS Chi-restraints excluded: chain e residue 117 SER Chi-restraints excluded: chain e residue 176 PHE Chi-restraints excluded: chain f residue 2 ARG Chi-restraints excluded: chain f residue 33 THR Chi-restraints excluded: chain f residue 138 GLN Chi-restraints excluded: chain f residue 147 LEU Chi-restraints excluded: chain f residue 154 GLU Chi-restraints excluded: chain g residue 4 ILE Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain g residue 48 GLU Chi-restraints excluded: chain h residue 15 VAL Chi-restraints excluded: chain h residue 27 VAL Chi-restraints excluded: chain h residue 55 VAL Chi-restraints excluded: chain j residue 36 LEU Chi-restraints excluded: chain j residue 55 ILE Chi-restraints excluded: chain j residue 64 VAL Chi-restraints excluded: chain j residue 76 HIS Chi-restraints excluded: chain j residue 84 ILE Chi-restraints excluded: chain j residue 92 MET Chi-restraints excluded: chain j residue 105 VAL Chi-restraints excluded: chain j residue 109 LEU Chi-restraints excluded: chain j residue 142 ILE Chi-restraints excluded: chain k residue 3 GLN Chi-restraints excluded: chain k residue 58 LEU Chi-restraints excluded: chain k residue 62 VAL Chi-restraints excluded: chain k residue 76 VAL Chi-restraints excluded: chain k residue 87 LEU Chi-restraints excluded: chain k residue 97 THR Chi-restraints excluded: chain k residue 104 THR Chi-restraints excluded: chain l residue 35 HIS Chi-restraints excluded: chain l residue 42 SER Chi-restraints excluded: chain l residue 81 ASP Chi-restraints excluded: chain l residue 110 VAL Chi-restraints excluded: chain l residue 111 ILE Chi-restraints excluded: chain l residue 116 VAL Chi-restraints excluded: chain l residue 117 THR Chi-restraints excluded: chain l residue 122 VAL Chi-restraints excluded: chain l residue 143 GLU Chi-restraints excluded: chain m residue 7 THR Chi-restraints excluded: chain m residue 36 VAL Chi-restraints excluded: chain m residue 41 LEU Chi-restraints excluded: chain m residue 42 THR Chi-restraints excluded: chain m residue 70 ASP Chi-restraints excluded: chain m residue 82 MET Chi-restraints excluded: chain m residue 95 LEU Chi-restraints excluded: chain m residue 128 THR Chi-restraints excluded: chain m residue 136 MET Chi-restraints excluded: chain n residue 18 GLN Chi-restraints excluded: chain n residue 37 THR Chi-restraints excluded: chain n residue 106 ASP Chi-restraints excluded: chain o residue 2 ASP Chi-restraints excluded: chain o residue 28 VAL Chi-restraints excluded: chain o residue 36 TYR Chi-restraints excluded: chain o residue 61 GLN Chi-restraints excluded: chain o residue 62 LEU Chi-restraints excluded: chain o residue 69 ASP Chi-restraints excluded: chain o residue 93 ASP Chi-restraints excluded: chain o residue 108 ASP Chi-restraints excluded: chain p residue 31 VAL Chi-restraints excluded: chain p residue 35 SER Chi-restraints excluded: chain p residue 40 GLN Chi-restraints excluded: chain p residue 59 THR Chi-restraints excluded: chain p residue 64 SER Chi-restraints excluded: chain p residue 70 GLU Chi-restraints excluded: chain p residue 103 THR Chi-restraints excluded: chain p residue 109 ILE Chi-restraints excluded: chain q residue 2 ARG Chi-restraints excluded: chain q residue 5 ARG Chi-restraints excluded: chain q residue 8 ILE Chi-restraints excluded: chain q residue 17 LEU Chi-restraints excluded: chain q residue 73 ILE Chi-restraints excluded: chain r residue 10 LYS Chi-restraints excluded: chain r residue 19 THR Chi-restraints excluded: chain r residue 33 VAL Chi-restraints excluded: chain r residue 40 MET Chi-restraints excluded: chain r residue 41 ILE Chi-restraints excluded: chain r residue 62 GLU Chi-restraints excluded: chain s residue 37 THR Chi-restraints excluded: chain s residue 69 LEU Chi-restraints excluded: chain s residue 74 ILE Chi-restraints excluded: chain s residue 81 SER Chi-restraints excluded: chain s residue 94 ASP Chi-restraints excluded: chain t residue 32 LEU Chi-restraints excluded: chain t residue 50 LEU Chi-restraints excluded: chain t residue 78 SER Chi-restraints excluded: chain t residue 87 LEU Chi-restraints excluded: chain u residue 17 ASP Chi-restraints excluded: chain u residue 35 VAL Chi-restraints excluded: chain u residue 40 LEU Chi-restraints excluded: chain u residue 71 ILE Chi-restraints excluded: chain v residue 8 VAL Chi-restraints excluded: chain v residue 38 LEU Chi-restraints excluded: chain v residue 42 LEU Chi-restraints excluded: chain v residue 45 ASP Chi-restraints excluded: chain v residue 59 GLU Chi-restraints excluded: chain v residue 61 LEU Chi-restraints excluded: chain v residue 63 ILE Chi-restraints excluded: chain v residue 87 GLN Chi-restraints excluded: chain v residue 89 ILE Chi-restraints excluded: chain w residue 8 ASN Chi-restraints excluded: chain w residue 17 LEU Chi-restraints excluded: chain w residue 27 VAL Chi-restraints excluded: chain w residue 63 VAL Chi-restraints excluded: chain w residue 72 ASN Chi-restraints excluded: chain x residue 41 SER Chi-restraints excluded: chain x residue 58 ILE Chi-restraints excluded: chain x residue 59 ASP Chi-restraints excluded: chain x residue 67 LEU Chi-restraints excluded: chain z residue 11 SER Chi-restraints excluded: chain z residue 13 ILE Chi-restraints excluded: chain z residue 16 LEU Chi-restraints excluded: chain z residue 48 ASN Chi-restraints excluded: chain z residue 53 MET Chi-restraints excluded: chain z residue 56 VAL Chi-restraints excluded: chain A residue 33 ASN Chi-restraints excluded: chain A residue 58 ASP Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain E residue 51 LYS Chi-restraints excluded: chain F residue 17 VAL Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain F residue 30 GLU Chi-restraints excluded: chain G residue 29 PHE Chi-restraints excluded: chain G residue 30 ILE Chi-restraints excluded: chain G residue 59 ILE Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain G residue 122 ASP Chi-restraints excluded: chain G residue 158 ASP Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 198 VAL Chi-restraints excluded: chain G residue 221 ARG Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 50 SER Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 68 HIS Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 153 SER Chi-restraints excluded: chain H residue 169 GLU Chi-restraints excluded: chain I residue 66 VAL Chi-restraints excluded: chain I residue 74 TYR Chi-restraints excluded: chain I residue 92 LEU Chi-restraints excluded: chain I residue 97 LEU Chi-restraints excluded: chain I residue 170 LEU Chi-restraints excluded: chain I residue 177 MET Chi-restraints excluded: chain I residue 196 GLU Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 29 ILE Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain J residue 87 VAL Chi-restraints excluded: chain J residue 123 LEU Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 141 ASP Chi-restraints excluded: chain K residue 3 HIS Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 54 LEU Chi-restraints excluded: chain K residue 64 VAL Chi-restraints excluded: chain K residue 73 GLU Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain K residue 91 ARG Chi-restraints excluded: chain L residue 17 PHE Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain L residue 122 GLU Chi-restraints excluded: chain L residue 129 ASN Chi-restraints excluded: chain L residue 132 THR Chi-restraints excluded: chain M residue 8 ASP Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain M residue 74 ILE Chi-restraints excluded: chain M residue 77 VAL Chi-restraints excluded: chain M residue 84 ILE Chi-restraints excluded: chain M residue 98 LEU Chi-restraints excluded: chain M residue 111 THR Chi-restraints excluded: chain M residue 120 LEU Chi-restraints excluded: chain M residue 124 ILE Chi-restraints excluded: chain N residue 21 LYS Chi-restraints excluded: chain N residue 30 ASN Chi-restraints excluded: chain N residue 42 THR Chi-restraints excluded: chain N residue 44 ARG Chi-restraints excluded: chain N residue 46 VAL Chi-restraints excluded: chain N residue 57 VAL Chi-restraints excluded: chain N residue 61 ASP Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain O residue 22 THR Chi-restraints excluded: chain O residue 36 VAL Chi-restraints excluded: chain O residue 57 VAL Chi-restraints excluded: chain O residue 71 LEU Chi-restraints excluded: chain O residue 92 LEU Chi-restraints excluded: chain P residue 30 ILE Chi-restraints excluded: chain P residue 39 ASN Chi-restraints excluded: chain P residue 41 LEU Chi-restraints excluded: chain P residue 57 SER Chi-restraints excluded: chain P residue 63 GLN Chi-restraints excluded: chain P residue 67 GLU Chi-restraints excluded: chain P residue 73 VAL Chi-restraints excluded: chain P residue 81 LEU Chi-restraints excluded: chain P residue 95 THR Chi-restraints excluded: chain P residue 96 ILE Chi-restraints excluded: chain P residue 106 ILE Chi-restraints excluded: chain P residue 126 ARG Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain Q residue 54 VAL Chi-restraints excluded: chain Q residue 101 LEU Chi-restraints excluded: chain Q residue 108 ASP Chi-restraints excluded: chain R residue 3 ILE Chi-restraints excluded: chain R residue 19 THR Chi-restraints excluded: chain R residue 24 VAL Chi-restraints excluded: chain R residue 27 THR Chi-restraints excluded: chain R residue 67 ASP Chi-restraints excluded: chain R residue 73 SER Chi-restraints excluded: chain R residue 101 THR Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain R residue 113 LYS Chi-restraints excluded: chain S residue 19 TYR Chi-restraints excluded: chain S residue 78 LEU Chi-restraints excluded: chain S residue 95 LEU Chi-restraints excluded: chain T residue 32 THR Chi-restraints excluded: chain T residue 56 LEU Chi-restraints excluded: chain T residue 59 VAL Chi-restraints excluded: chain T residue 69 LEU Chi-restraints excluded: chain T residue 86 LEU Chi-restraints excluded: chain U residue 1 MET Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain U residue 36 VAL Chi-restraints excluded: chain U residue 53 ASP Chi-restraints excluded: chain U residue 66 THR Chi-restraints excluded: chain U residue 74 LEU Chi-restraints excluded: chain V residue 4 ILE Chi-restraints excluded: chain V residue 27 PHE Chi-restraints excluded: chain V residue 38 LYS Chi-restraints excluded: chain V residue 52 CYS Chi-restraints excluded: chain V residue 54 ILE Chi-restraints excluded: chain V residue 56 ASP Chi-restraints excluded: chain V residue 77 VAL Chi-restraints excluded: chain W residue 17 VAL Chi-restraints excluded: chain W residue 25 ILE Chi-restraints excluded: chain W residue 28 LEU Chi-restraints excluded: chain W residue 70 THR Chi-restraints excluded: chain W residue 71 ASP Chi-restraints excluded: chain X residue 57 VAL Chi-restraints excluded: chain X residue 59 VAL Chi-restraints excluded: chain X residue 70 LEU Chi-restraints excluded: chain X residue 78 THR Chi-restraints excluded: chain Y residue 29 THR Chi-restraints excluded: chain Y residue 58 ASP Chi-restraints excluded: chain Z residue 12 ASP Chi-restraints excluded: chain Z residue 18 PHE Chi-restraints excluded: chain Z residue 30 GLU Chi-restraints excluded: chain Z residue 33 ARG Chi-restraints excluded: chain a residue 8 MET Chi-restraints excluded: chain a residue 27 ILE Chi-restraints excluded: chain a residue 42 VAL Chi-restraints excluded: chain a residue 56 ASP Chi-restraints excluded: chain a residue 64 VAL Chi-restraints excluded: chain a residue 178 VAL Chi-restraints excluded: chain a residue 193 LEU Chi-restraints excluded: chain a residue 196 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1048 random chunks: chunk 660 optimal weight: 10.0000 chunk 885 optimal weight: 10.0000 chunk 254 optimal weight: 20.0000 chunk 766 optimal weight: 20.0000 chunk 122 optimal weight: 0.0170 chunk 231 optimal weight: 5.9990 chunk 832 optimal weight: 50.0000 chunk 348 optimal weight: 20.0000 chunk 855 optimal weight: 10.0000 chunk 105 optimal weight: 7.9990 chunk 153 optimal weight: 6.9990 overall best weight: 6.2028 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 19 GLN q 71 ASN r 43 ASN ** v 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 3 GLN ** G 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 134 ASN ** N 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 72 ASN R 7 ASN S 59 GLN V 50 ASN X 68 HIS ** a 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.061182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 92)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.048405 restraints weight = 868222.207| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 2.31 r_work: 0.3120 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.3799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 162700 Z= 0.241 Angle : 0.651 13.147 243508 Z= 0.338 Chirality : 0.037 0.320 31146 Planarity : 0.005 0.075 12986 Dihedral : 23.675 179.713 81730 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 16.91 Ramachandran Plot: Outliers : 0.27 % Allowed : 12.20 % Favored : 87.53 % Rotamer: Outliers : 6.01 % Allowed : 23.55 % Favored : 70.44 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.51 % Twisted General : 0.30 % 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: -2.35 (0.11), residues: 5836 helix: -0.21 (0.12), residues: 1848 sheet: -1.61 (0.16), residues: 1021 loop : -2.48 (0.11), residues: 2967 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP H 166 HIS 0.007 0.001 HIS j 80 PHE 0.023 0.002 PHE Z 36 TYR 0.033 0.002 TYR N 5 ARG 0.015 0.001 ARG W 42 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 40907.02 seconds wall clock time: 714 minutes 43.24 seconds (42883.24 seconds total)