Starting phenix.real_space_refine on Fri Mar 1 22:46:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k55_22674/03_2024/7k55_22674_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k55_22674/03_2024/7k55_22674.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k55_22674/03_2024/7k55_22674.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k55_22674/03_2024/7k55_22674.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k55_22674/03_2024/7k55_22674_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k55_22674/03_2024/7k55_22674_updated.pdb" } resolution = 3.3 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= 1.395 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 4731 5.49 5 Mg 1 5.21 5 S 180 5.16 5 C 77765 2.51 5 N 28485 2.21 5 O 42206 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "b TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 263": "OD1" <-> "OD2" Residue "c ARG 13": "NH1" <-> "NH2" Residue "c GLU 30": "OE1" <-> "OE2" 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 ASP 108": "OD1" <-> "OD2" Residue "c PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 169": "NH1" <-> "NH2" Residue "c ARG 184": "NH1" <-> "NH2" Residue "d GLU 16": "OE1" <-> "OE2" Residue "d ARG 21": "NH1" <-> "NH2" Residue "d ARG 44": "NH1" <-> "NH2" Residue "d ARG 49": "NH1" <-> "NH2" Residue "d ARG 61": "NH1" <-> "NH2" Residue "d ARG 88": "NH1" <-> "NH2" Residue "d ARG 102": "NH1" <-> "NH2" Residue "d ASP 140": "OD1" <-> "OD2" Residue "d GLU 152": "OE1" <-> "OE2" Residue "d ARG 162": "NH1" <-> "NH2" Residue "d ARG 170": "NH1" <-> "NH2" 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 TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ASP 173": "OD1" <-> "OD2" Residue "f ARG 2": "NH1" <-> "NH2" Residue "f GLU 80": "OE1" <-> "OE2" Residue "f ARG 152": "NH1" <-> "NH2" Residue "f ARG 162": "NH1" <-> "NH2" Residue "f ARG 169": "NH1" <-> "NH2" Residue "g PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h GLU 65": "OE1" <-> "OE2" Residue "h GLU 70": "OE1" <-> "OE2" Residue "i ASP 46": "OD1" <-> "OD2" 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 GLU 129": "OE1" <-> "OE2" Residue "l ARG 21": "NH1" <-> "NH2" Residue "l ARG 33": "NH1" <-> "NH2" Residue "l ARG 41": "NH1" <-> "NH2" Residue "l ARG 47": "NH1" <-> "NH2" Residue "l ARG 60": "NH1" <-> "NH2" Residue "l GLU 76": "OE1" <-> "OE2" Residue "l ARG 78": "NH1" <-> "NH2" Residue "l ARG 126": "NH1" <-> "NH2" Residue "l GLU 136": "OE1" <-> "OE2" Residue "m ARG 10": "NH1" <-> "NH2" Residue "m ARG 18": "NH1" <-> "NH2" Residue "m ARG 40": "NH1" <-> "NH2" Residue "m ARG 44": "NH1" <-> "NH2" Residue "m ARG 50": "NH1" <-> "NH2" Residue "m ARG 55": "NH1" <-> "NH2" Residue "m ARG 59": "NH1" <-> "NH2" Residue "m ARG 114": "NH1" <-> "NH2" Residue "n ARG 8": "NH1" <-> "NH2" Residue "n ARG 12": "NH1" <-> "NH2" Residue "n ARG 17": "NH1" <-> "NH2" Residue "n ARG 22": "NH1" <-> "NH2" Residue "n ARG 46": "NH1" <-> "NH2" Residue "n ARG 63": "NH1" <-> "NH2" Residue "n ARG 64": "NH1" <-> "NH2" Residue "n ARG 69": "NH1" <-> "NH2" Residue "n ARG 71": "NH1" <-> "NH2" Residue "n ARG 96": "NH1" <-> "NH2" Residue "n ARG 118": "NH1" <-> "NH2" Residue "o ARG 10": "NH1" <-> "NH2" Residue "o ARG 16": "NH1" <-> "NH2" Residue "o ARG 25": "NH1" <-> "NH2" Residue "o TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o ASP 69": "OD1" <-> "OD2" Residue "o ARG 81": "NH1" <-> "NH2" Residue "o GLU 84": "OE1" <-> "OE2" Residue "o ARG 94": "NH1" <-> "NH2" Residue "o ARG 102": "NH1" <-> "NH2" Residue "o ARG 111": "NH1" <-> "NH2" Residue "p ARG 20": "NH1" <-> "NH2" Residue "p ARG 38": "NH1" <-> "NH2" Residue "p PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p ARG 61": "NH1" <-> "NH2" Residue "p ARG 88": "NH1" <-> "NH2" Residue "p ARG 100": "NH1" <-> "NH2" Residue "p ARG 108": "NH1" <-> "NH2" Residue "q ARG 2": "NH1" <-> "NH2" Residue "q ARG 5": "NH1" <-> "NH2" Residue "q ARG 12": "NH1" <-> "NH2" Residue "q ARG 32": "NH1" <-> "NH2" Residue "q ARG 47": "NH1" <-> "NH2" Residue "q ASP 48": "OD1" <-> "OD2" Residue "q ARG 69": "NH1" <-> "NH2" Residue "q ASP 101": "OD1" <-> "OD2" Residue "r ARG 21": "NH1" <-> "NH2" Residue "r GLU 31": "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 ARG 73": "NH1" <-> "NH2" Residue "u ARG 5": "NH1" <-> "NH2" Residue "u ARG 6": "NH1" <-> "NH2" Residue "u ARG 81": "NH1" <-> "NH2" Residue "u ARG 85": "NH1" <-> "NH2" Residue "u ARG 93": "NH1" <-> "NH2" Residue "w ASP 11": "OD1" <-> "OD2" Residue "y ARG 29": "NH1" <-> "NH2" Residue "y ARG 47": "NH1" <-> "NH2" Residue "y ARG 52": "NH1" <-> "NH2" Residue "z ARG 10": "NH1" <-> "NH2" Residue "z ARG 29": "NH1" <-> "NH2" Residue "z ARG 44": "NH1" <-> "NH2" Residue "z GLU 57": "OE1" <-> "OE2" 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 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 PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 193": "OD1" <-> "OD2" Residue "G ARG 224": "NH1" <-> "NH2" Residue "H ARG 106": "NH1" <-> "NH2" Residue "H ASP 111": "OD1" <-> "OD2" Residue "H GLU 124": "OE1" <-> "OE2" Residue "H ARG 130": "NH1" <-> "NH2" Residue "H GLU 165": "OE1" <-> "OE2" Residue "H GLU 169": "OE1" <-> "OE2" Residue "I GLU 56": "OE1" <-> "OE2" Residue "I GLU 112": "OE1" <-> "OE2" Residue "J PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 156": "NH1" <-> "NH2" Residue "K GLU 73": "OE1" <-> "OE2" Residue "L PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 62": "OE1" <-> "OE2" Residue "L TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 122": "OE1" <-> "OE2" Residue "M ASP 47": "OD1" <-> "OD2" Residue "N ASP 55": "OD1" <-> "OD2" Residue "N GLU 96": "OE1" <-> "OE2" Residue "N ARG 123": "NH1" <-> "NH2" Residue "O GLU 27": "OE1" <-> "OE2" Residue "O ASP 60": "OD1" <-> "OD2" Residue "O ASP 75": "OD1" <-> "OD2" Residue "O ASP 97": "OD1" <-> "OD2" Residue "P GLU 82": "OE1" <-> "OE2" Residue "Q ARG 55": "NH1" <-> "NH2" Residue "Q GLU 69": "OE1" <-> "OE2" Residue "Q TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 67": "OD1" <-> "OD2" Residue "S GLU 91": "OE1" <-> "OE2" Residue "T ASP 20": "OD1" <-> "OD2" Residue "U TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 23": "OD1" <-> "OD2" Residue "U ARG 28": "NH1" <-> "NH2" Residue "U PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 34": "OE1" <-> "OE2" Residue "V GLU 25": "OE1" <-> "OE2" Residue "V PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 79": "OE1" <-> "OE2" Residue "W ARG 11": "NH1" <-> "NH2" Residue "W TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 64": "OE1" <-> "OE2" Residue "X GLU 72": "OE1" <-> "OE2" Residue "X TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 42": "OD1" <-> "OD2" Residue "Z ARG 66": "NH1" <-> "NH2" Residue "a ARG 7": "NH1" <-> "NH2" Residue "a ARG 12": "NH1" <-> "NH2" Residue "a GLU 32": "OE1" <-> "OE2" Residue "a ARG 162": "NH1" <-> "NH2" Residue "8 ASP 94": "OD1" <-> "OD2" Residue "8 PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 GLU 100": "OE1" <-> "OE2" Residue "8 GLU 242": "OE1" <-> "OE2" Residue "8 PHE 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 GLU 376": "OE1" <-> "OE2" Residue "8 PHE 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 TYR 490": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 153368 Number of models: 1 Model: "" Number of chains: 62 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': 220, 'rna2p_pyr': 103, 'rna3p_pur': 1454, 'rna3p_pyr': 1126} Link IDs: {'rna2p': 323, 'rna3p': 2579} 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': 4, 'rna2p_pyr': 2, 'rna3p_pur': 61, 'rna3p_pyr': 53} Link IDs: {'rna2p': 6, 'rna3p': 113} Chain: "5" 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: "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': 11, 'rna3p': 65} Chain: "4" Number of atoms: 346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 346 Classifications: {'RNA': 16} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 11, 'rna3p_pyr': 4} Link IDs: {'rna2p': 1, 'rna3p': 14} Chain: "8" Number of atoms: 5312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 685, 5312 Classifications: {'peptide': 685} Link IDs: {'PTRANS': 33, 'TRANS': 651} Chain breaks: 1 Chain: "1" 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 Chain: "5" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Classifications: {'peptide': 1} Chain: "8" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GCP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 57.50, per 1000 atoms: 0.37 Number of scatterers: 153368 At special positions: 0 Unit cell: (274.05, 256.2, 246.75, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 180 16.00 P 4731 15.00 Mg 1 11.99 O 42206 8.00 N 28485 7.00 C 77765 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: 60.96 Conformation dependent library (CDL) restraints added in 7.3 seconds 13034 Ramachandran restraints generated. 6517 Oldfield, 0 Emsley, 6517 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 12184 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: 194 helices and 80 sheets defined 37.4% alpha, 17.6% beta 1436 base pairs and 2282 stacking pairs defined. Time for finding SS restraints: 75.93 Creating SS restraints... Processing helix chain 'b' and resid 10 through 16 removed outlier: 7.196A pdb=" N HIS b 14 " --> pdb=" O PRO b 10 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VAL b 15 " --> pdb=" O GLY b 11 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N VAL b 16 " --> pdb=" O ARG b 12 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 10 through 16' Processing helix chain 'b' and resid 29 through 34 removed outlier: 4.426A pdb=" N LEU b 33 " --> pdb=" O PHE b 29 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N GLU b 34 " --> pdb=" O ALA b 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 29 through 34' Processing helix chain 'b' and resid 130 through 135 removed outlier: 4.002A 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: 4.038A pdb=" N ALA b 210 " --> pdb=" O LYS b 206 " (cutoff:3.500A) Processing helix chain 'b' and resid 220 through 225 removed outlier: 3.786A pdb=" N MET b 224 " --> pdb=" O ARG b 220 " (cutoff:3.500A) removed outlier: 5.504A 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: 6.145A pdb=" N ASP b 263 " --> pdb=" O ASN b 259 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N LYS b 264 " --> pdb=" O LYS b 260 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N PHE b 265 " --> pdb=" O ARG b 261 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE b 266 " --> pdb=" O THR b 262 " (cutoff:3.500A) removed outlier: 5.474A 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 'c' and resid 56 through 61 removed outlier: 6.021A pdb=" N THR c 61 " --> pdb=" O ALA c 57 " (cutoff:3.500A) Processing helix chain 'c' and resid 62 through 72 removed outlier: 4.017A pdb=" N ALA c 71 " --> pdb=" O HIS c 67 " (cutoff:3.500A) Processing helix chain 'c' and resid 98 through 103 removed outlier: 4.351A pdb=" N ALA c 102 " --> pdb=" O VAL c 98 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N ASP c 103 " --> pdb=" O GLU c 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 98 through 103' Processing helix chain 'c' and resid 120 through 125 Processing helix chain 'd' and resid 15 through 20 Processing helix chain 'd' and resid 24 through 41 removed outlier: 5.944A pdb=" N GLN d 41 " --> pdb=" O ALA d 37 " (cutoff:3.500A) Processing helix chain 'd' and resid 97 through 116 Processing helix chain 'd' and resid 130 through 142 Processing helix chain 'd' and resid 154 through 162 removed outlier: 3.640A pdb=" N ALA d 160 " --> pdb=" O ASN d 156 " (cutoff:3.500A) Processing helix chain 'd' and resid 176 through 184 removed outlier: 3.586A pdb=" N ILE d 181 " --> pdb=" O PRO d 177 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N ASP d 184 " --> pdb=" O LEU d 180 " (cutoff:3.500A) Processing helix chain 'd' and resid 189 through 201 Processing helix chain 'e' and resid 1 through 20 removed outlier: 4.656A pdb=" N VAL e 12 " --> pdb=" O LYS e 8 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU e 18 " --> pdb=" O LYS e 14 " (cutoff:3.500A) Processing helix chain 'e' and resid 41 through 46 removed outlier: 3.652A pdb=" N ASP e 45 " --> pdb=" O GLU e 41 " (cutoff:3.500A) removed outlier: 4.351A 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 61 Processing helix chain 'e' and resid 92 through 110 removed outlier: 4.106A pdb=" N ILE e 105 " --> pdb=" O ARG e 101 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N VAL e 107 " --> pdb=" O ILE e 103 " (cutoff:3.500A) Proline residue: e 108 - end of helix Processing helix chain 'e' and resid 141 through 146 removed outlier: 6.706A pdb=" N VAL e 145 " --> pdb=" O ASP e 141 " (cutoff:3.500A) removed outlier: 4.887A 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 Processing helix chain 'f' and resid 1 through 7 Proline residue: f 7 - end of helix Processing helix chain 'f' and resid 59 through 80 Processing helix chain 'f' and resid 136 through 152 removed outlier: 3.625A pdb=" N ARG f 151 " --> pdb=" O LEU f 147 " (cutoff:3.500A) Processing helix chain 'g' and resid 22 through 29 Processing helix chain 'g' and resid 40 through 50 removed outlier: 3.650A pdb=" N GLU g 48 " --> pdb=" O ILE g 44 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ALA g 49 " --> pdb=" O GLU g 45 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ARG g 50 " --> pdb=" O PHE g 46 " (cutoff:3.500A) Processing helix chain 'g' and resid 95 through 107 removed outlier: 4.236A pdb=" N ILE g 99 " --> pdb=" O GLY g 95 " (cutoff:3.500A) Processing helix chain 'h' and resid 4 through 21 removed outlier: 3.729A pdb=" N ILE h 11 " --> pdb=" O ASP h 7 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N LYS h 20 " --> pdb=" O SER h 16 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY h 21 " --> pdb=" O GLU h 17 " (cutoff:3.500A) Processing helix chain 'h' and resid 33 through 48 removed outlier: 3.631A pdb=" N LYS h 37 " --> pdb=" O VAL h 33 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N THR h 39 " --> pdb=" O VAL h 35 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ARG h 42 " --> pdb=" O MET h 38 " (cutoff:3.500A) Processing helix chain 'h' and resid 62 through 68 removed outlier: 3.584A pdb=" N GLY h 66 " --> pdb=" O ARG h 62 " (cutoff:3.500A) Proline residue: h 68 - end of helix Processing helix chain 'h' and resid 71 through 76 removed outlier: 4.292A pdb=" N ALA h 75 " --> pdb=" O CYS h 71 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N PHE h 76 " --> pdb=" O LEU h 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 71 through 76' Processing helix chain 'i' and resid 24 through 29 removed outlier: 3.844A pdb=" N GLY i 28 " --> pdb=" O GLY i 24 " (cutoff:3.500A) Processing helix chain 'i' and resid 33 through 49 removed outlier: 3.621A pdb=" N ALA i 40 " --> pdb=" O GLU i 36 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA i 43 " --> pdb=" O LYS i 39 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LYS i 44 " --> pdb=" O ALA i 40 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N SER i 47 " --> pdb=" O ALA i 43 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N ILE i 48 " --> pdb=" O LYS i 44 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N GLU i 49 " --> pdb=" O THR i 45 " (cutoff:3.500A) Processing helix chain 'j' and resid 24 through 38 Processing helix chain 'j' and resid 67 through 72 Processing helix chain 'j' and resid 88 through 96 removed outlier: 3.528A pdb=" N ALA j 94 " --> pdb=" O GLU j 90 " (cutoff:3.500A) Processing helix chain 'j' and resid 97 through 110 removed outlier: 4.852A pdb=" N ILE j 101 " --> pdb=" O PRO j 97 " (cutoff:3.500A) Proline residue: j 110 - end of helix Processing helix chain 'j' and resid 112 through 122 removed outlier: 4.375A pdb=" N LYS j 121 " --> pdb=" O ALA j 117 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N LEU j 122 " --> pdb=" O MET j 118 " (cutoff:3.500A) Processing helix chain 'j' and resid 130 through 135 removed outlier: 4.902A pdb=" N ALA j 133 " --> pdb=" O HIS j 130 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ALA j 134 " --> pdb=" O ASN j 131 " (cutoff:3.500A) Processing helix chain 'k' and resid 112 through 119 Processing helix chain 'k' and resid 104 through 109 removed outlier: 5.420A pdb=" N SER k 109 " --> pdb=" O GLU k 106 " (cutoff:3.500A) Processing helix chain 'l' and resid 2 through 7 removed outlier: 3.730A pdb=" N LEU l 6 " --> pdb=" O ARG l 2 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N SER l 7 " --> pdb=" O LEU l 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 2 through 7' Processing helix chain 'l' and resid 56 through 61 Processing helix chain 'l' and resid 68 through 75 removed outlier: 4.658A pdb=" N ALA l 72 " --> pdb=" O SER l 68 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE l 73 " --> pdb=" O ARG l 69 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR l 74 " --> pdb=" O LYS l 70 " (cutoff:3.500A) removed outlier: 4.870A 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 86 removed outlier: 4.070A pdb=" N LEU l 82 " --> pdb=" O ARG l 78 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N ALA l 83 " --> pdb=" O LEU l 79 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N LYS l 84 " --> pdb=" O SER l 80 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL l 85 " --> pdb=" O ASP l 81 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N GLU l 86 " --> pdb=" O LEU l 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 78 through 86' Processing helix chain 'l' and resid 91 through 99 removed outlier: 4.251A pdb=" N LEU l 95 " --> pdb=" O ASP l 91 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LYS l 96 " --> pdb=" O LEU l 92 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N ALA l 97 " --> pdb=" O ASN l 93 " (cutoff:3.500A) Processing helix chain 'l' and resid 128 through 139 removed outlier: 3.534A pdb=" N ALA l 138 " --> pdb=" O ALA l 134 " (cutoff:3.500A) Processing helix chain 'm' and resid 42 through 58 removed outlier: 4.667A pdb=" N ALA m 56 " --> pdb=" O ALA m 52 " (cutoff:3.500A) Processing helix chain 'm' and resid 109 through 125 removed outlier: 3.617A pdb=" N LYS m 118 " --> pdb=" O ARG m 114 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU m 119 " --> pdb=" O GLU m 115 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS m 123 " --> pdb=" O LEU m 119 " (cutoff:3.500A) Proline residue: m 125 - end of helix Processing helix chain 'n' and resid 13 through 32 Processing helix chain 'n' and resid 38 through 56 removed outlier: 4.269A pdb=" N ARG n 46 " --> pdb=" O LYS n 42 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL n 47 " --> pdb=" O GLU n 43 " (cutoff:3.500A) Proline residue: n 50 - end of helix Processing helix chain 'n' and resid 59 through 71 removed outlier: 4.340A pdb=" N ARG n 63 " --> pdb=" O SER n 59 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N THR n 70 " --> pdb=" O ALA n 66 " (cutoff:3.500A) Processing helix chain 'n' and resid 72 through 88 removed outlier: 3.751A pdb=" N PHE n 80 " --> pdb=" O VAL n 76 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ASN n 81 " --> pdb=" O ALA n 77 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N LEU n 83 " --> pdb=" O LEU n 79 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N GLY n 84 " --> pdb=" O PHE n 80 " (cutoff:3.500A) Proline residue: n 85 - end of helix Processing helix chain 'o' and resid 2 through 22 removed outlier: 4.421A pdb=" N ARG o 13 " --> pdb=" O ARG o 9 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N ALA o 14 " --> pdb=" O ARG o 10 " (cutoff:3.500A) Processing helix chain 'o' and resid 55 through 63 removed outlier: 4.538A pdb=" N GLN o 61 " --> pdb=" O ALA o 57 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N LYS o 63 " --> pdb=" O ALA o 59 " (cutoff:3.500A) Processing helix chain 'o' and resid 67 through 86 removed outlier: 3.527A pdb=" N ALA o 79 " --> pdb=" O GLY o 75 " (cutoff:3.500A) Processing helix chain 'o' and resid 101 through 114 removed outlier: 3.841A pdb=" N GLY o 114 " --> pdb=" O ALA o 110 " (cutoff:3.500A) Processing helix chain 'p' and resid 1 through 13 removed outlier: 4.522A pdb=" N GLN p 11 " --> pdb=" O LEU p 7 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N LYS p 13 " --> pdb=" O GLN p 9 " (cutoff:3.500A) Processing helix chain 'p' and resid 96 through 103 removed outlier: 4.547A pdb=" N ARG p 100 " --> pdb=" O LEU p 96 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N GLU p 101 " --> pdb=" O TYR p 97 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N ARG p 102 " --> pdb=" O TYR p 98 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N THR p 103 " --> pdb=" O LEU p 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'p' and resid 96 through 103' Processing helix chain 'q' and resid 5 through 21 removed outlier: 3.792A pdb=" N GLN q 19 " --> pdb=" O LYS q 15 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LYS q 21 " --> pdb=" O LEU q 17 " (cutoff:3.500A) Processing helix chain 'q' and resid 25 through 30 removed outlier: 4.113A pdb=" N ARG q 29 " --> pdb=" O GLY q 25 " (cutoff:3.500A) Processing helix chain 'q' and resid 35 through 71 removed outlier: 3.838A pdb=" N ARG q 50 " --> pdb=" O TYR q 46 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N LYS q 53 " --> pdb=" O ARG q 49 " (cutoff:3.500A) Processing helix chain 'q' and resid 74 through 86 Processing helix chain 'q' and resid 90 through 101 Processing helix chain 'q' and resid 102 through 117 Processing helix chain 's' and resid 13 through 25 removed outlier: 4.855A pdb=" N LEU s 23 " --> pdb=" O LEU s 19 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ILE s 24 " --> pdb=" O VAL s 20 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ARG s 25 " --> pdb=" O ALA s 21 " (cutoff:3.500A) Processing helix chain 's' and resid 28 through 40 removed outlier: 5.664A pdb=" N ASN s 40 " --> pdb=" O LEU s 36 " (cutoff:3.500A) Processing helix chain 's' and resid 41 through 61 removed outlier: 3.739A pdb=" N VAL s 50 " --> pdb=" O LEU s 46 " (cutoff:3.500A) Processing helix chain 't' and resid 1 through 11 removed outlier: 4.021A pdb=" N LYS t 9 " --> pdb=" O GLU t 5 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N LEU t 11 " --> pdb=" O LEU t 7 " (cutoff:3.500A) Processing helix chain 't' and resid 17 through 26 Processing helix chain 't' and resid 39 through 51 Processing helix chain 'u' and resid 65 through 70 removed outlier: 3.994A pdb=" N VAL u 69 " --> pdb=" O GLN u 65 " (cutoff:3.500A) removed outlier: 4.999A 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: 4.224A pdb=" N ALA v 23 " --> pdb=" O ARG v 19 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ASN v 24 " --> pdb=" O LEU v 20 " (cutoff:3.500A) Processing helix chain 'v' and resid 43 through 54 removed outlier: 3.710A pdb=" N ALA v 52 " --> pdb=" O MET v 48 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N LYS v 53 " --> pdb=" O ASN v 49 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N ALA v 54 " --> pdb=" O MET v 50 " (cutoff:3.500A) Processing helix chain 'x' and resid 51 through 62 removed outlier: 3.978A pdb=" N GLY x 62 " --> pdb=" O ILE x 58 " (cutoff:3.500A) Processing helix chain 'x' and resid 63 through 74 Processing helix chain 'y' and resid 1 through 9 removed outlier: 3.701A pdb=" N LEU y 6 " --> pdb=" O LYS y 2 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N GLU y 8 " --> pdb=" O LYS y 4 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N LYS y 9 " --> pdb=" O GLU y 5 " (cutoff:3.500A) Processing helix chain 'y' and resid 10 through 35 removed outlier: 4.272A pdb=" N GLU y 24 " --> pdb=" O ASN y 20 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N GLN y 25 " --> pdb=" O LEU y 21 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N PHE y 26 " --> pdb=" O LEU y 22 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASN y 27 " --> pdb=" O ARG y 23 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLY y 35 " --> pdb=" O GLN y 31 " (cutoff:3.500A) Processing helix chain 'y' and resid 39 through 61 removed outlier: 4.781A pdb=" N LEU y 43 " --> pdb=" O GLN y 39 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LYS y 44 " --> pdb=" O SER y 40 " (cutoff:3.500A) Processing helix chain 'z' and resid 16 through 27 Processing helix chain 'z' and resid 40 through 51 removed outlier: 3.551A pdb=" N MET z 46 " --> pdb=" O ALA z 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 53 removed outlier: 5.128A pdb=" N GLN A 48 " --> pdb=" O PHE A 44 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ARG A 49 " --> pdb=" O THR A 45 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL A 51 " --> pdb=" O LYS A 47 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA A 52 " --> pdb=" O GLN A 48 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N THR A 53 " --> pdb=" O ARG A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 64 removed outlier: 4.282A pdb=" N ARG A 59 " --> pdb=" O GLY A 55 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ARG A 63 " --> pdb=" O ARG A 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 18 removed outlier: 5.126A pdb=" N HIS B 18 " --> pdb=" O MET B 14 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 30 Proline residue: C 30 - end of helix Processing helix chain 'D' and resid 8 through 16 Processing helix chain 'D' and resid 17 through 24 removed outlier: 3.538A pdb=" N ALA D 23 " --> pdb=" O ARG D 19 " (cutoff:3.500A) removed outlier: 5.178A 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 13 removed outlier: 3.984A pdb=" N ARG E 12 " --> pdb=" O GLY E 8 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 45 removed outlier: 3.581A 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: 4.416A pdb=" N GLY E 55 " --> pdb=" O LYS E 51 " (cutoff:3.500A) removed outlier: 5.891A 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 43 through 63 Proline residue: G 47 - end of helix removed outlier: 3.547A pdb=" N GLU G 51 " --> pdb=" O PRO G 47 " (cutoff:3.500A) Processing helix chain 'G' and resid 75 through 86 Processing helix chain 'G' and resid 103 through 122 removed outlier: 4.388A pdb=" N GLN G 108 " --> pdb=" O LYS G 104 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLN G 121 " --> pdb=" O GLU G 117 " (cutoff:3.500A) Processing helix chain 'G' and resid 129 through 148 removed outlier: 3.627A pdb=" N LEU G 134 " --> pdb=" O LYS G 130 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N MET G 135 " --> pdb=" O LYS G 131 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER G 146 " --> pdb=" O LYS G 142 " (cutoff:3.500A) Processing helix chain 'G' and resid 164 through 169 removed outlier: 3.579A pdb=" N GLU G 168 " --> pdb=" O ASP G 164 " (cutoff:3.500A) Processing helix chain 'G' and resid 170 through 179 removed outlier: 3.696A pdb=" N GLU G 174 " --> pdb=" O ILE G 170 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU G 178 " --> pdb=" O GLU G 174 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N GLY G 179 " --> pdb=" O ALA G 175 " (cutoff:3.500A) Processing helix chain 'G' and resid 205 through 225 removed outlier: 3.664A pdb=" N LEU G 213 " --> pdb=" O VAL G 209 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N SER G 225 " --> pdb=" O ARG G 221 " (cutoff:3.500A) Processing helix chain 'H' and resid 5 through 11 removed outlier: 4.188A pdb=" N ARG H 10 " --> pdb=" O PRO H 6 " (cutoff:3.500A) Processing helix chain 'H' and resid 27 through 47 removed outlier: 3.528A pdb=" N LYS H 44 " --> pdb=" O GLN H 40 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA H 47 " --> pdb=" O THR H 43 " (cutoff:3.500A) Processing helix chain 'H' and resid 71 through 77 Processing helix chain 'H' and resid 80 through 95 removed outlier: 3.563A pdb=" N VAL H 89 " --> pdb=" O LYS H 85 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ILE H 93 " --> pdb=" O VAL H 89 " (cutoff:3.500A) Processing helix chain 'H' and resid 107 through 112 removed outlier: 5.084A pdb=" N ALA H 112 " --> pdb=" O PRO H 108 " (cutoff:3.500A) Processing helix chain 'H' and resid 113 through 126 Processing helix chain 'H' and resid 128 through 144 removed outlier: 3.519A pdb=" N ARG H 142 " --> pdb=" O GLN H 138 " (cutoff:3.500A) Processing helix chain 'I' and resid 6 through 14 removed outlier: 4.635A pdb=" N LEU I 10 " --> pdb=" O PRO I 6 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N SER I 11 " --> pdb=" O LYS I 7 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 65 removed outlier: 3.693A pdb=" N GLN I 53 " --> pdb=" O ASP I 49 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TYR I 64 " --> pdb=" O VAL I 60 " (cutoff:3.500A) Processing helix chain 'I' and resid 67 through 82 removed outlier: 6.271A pdb=" N LYS I 82 " --> pdb=" O ALA I 78 " (cutoff:3.500A) Processing helix chain 'I' and resid 84 through 96 removed outlier: 4.998A pdb=" N LEU I 90 " --> pdb=" O GLY I 86 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY I 95 " --> pdb=" O ALA I 91 " (cutoff:3.500A) removed outlier: 5.177A 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: 3.583A pdb=" N VAL I 117 " --> pdb=" O ALA I 113 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS I 120 " --> pdb=" O LEU I 116 " (cutoff:3.500A) Processing helix chain 'I' and resid 151 through 165 removed outlier: 7.221A pdb=" N LYS I 155 " --> pdb=" O GLN I 151 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ALA I 156 " --> pdb=" O SER I 152 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU I 160 " --> pdb=" O ALA I 156 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N ALA I 161 " --> pdb=" O ALA I 157 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N GLU I 162 " --> pdb=" O LEU I 158 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLN I 163 " --> pdb=" O GLU I 159 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLU I 165 " --> pdb=" O ALA I 161 " (cutoff:3.500A) Processing helix chain 'I' and resid 196 through 205 Processing helix chain 'I' and resid 38 through 43 removed outlier: 4.188A pdb=" N ALA I 42 " --> pdb=" O GLN I 39 " (cutoff:3.500A) Processing helix chain 'J' and resid 54 through 70 removed outlier: 5.449A pdb=" N GLU J 64 " --> pdb=" O GLN J 60 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N LYS J 65 " --> pdb=" O LYS J 61 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N MET J 70 " --> pdb=" O ALA J 66 " (cutoff:3.500A) Processing helix chain 'J' and resid 108 through 118 removed outlier: 6.481A pdb=" N ALA J 112 " --> pdb=" O GLY J 108 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL J 113 " --> pdb=" O ALA J 109 " (cutoff:3.500A) Processing helix chain 'J' and resid 131 through 146 Processing helix chain 'J' and resid 148 through 156 Processing helix chain 'J' and resid 159 through 165 Processing helix chain 'K' and resid 17 through 32 removed outlier: 4.431A pdb=" N MET K 21 " --> pdb=" O GLN K 17 " (cutoff:3.500A) Processing helix chain 'K' and resid 67 through 81 removed outlier: 5.255A pdb=" N ASN K 81 " --> pdb=" O THR K 77 " (cutoff:3.500A) Processing helix chain 'L' and resid 19 through 30 Processing helix chain 'L' and resid 34 through 54 Processing helix chain 'L' and resid 57 through 69 removed outlier: 4.740A pdb=" N ALA L 64 " --> pdb=" O ALA L 60 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ASN L 67 " --> pdb=" O VAL L 63 " (cutoff:3.500A) Processing helix chain 'L' and resid 92 through 110 removed outlier: 4.685A pdb=" N ALA L 97 " --> pdb=" O VAL L 93 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TRP L 102 " --> pdb=" O LEU L 98 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS L 109 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ARG L 110 " --> pdb=" O ALA L 106 " (cutoff:3.500A) Processing helix chain 'L' and resid 114 through 129 removed outlier: 3.784A pdb=" N GLU L 128 " --> pdb=" O SER L 124 " (cutoff:3.500A) Processing helix chain 'L' and resid 131 through 145 removed outlier: 3.556A pdb=" N ARG L 137 " --> pdb=" O ALA L 133 " (cutoff:3.500A) Processing helix chain 'M' and resid 4 through 20 Processing helix chain 'M' and resid 29 through 43 Processing helix chain 'M' and resid 111 through 119 removed outlier: 4.192A pdb=" N GLN M 117 " --> pdb=" O ARG M 113 " (cutoff:3.500A) Processing helix chain 'N' and resid 33 through 38 removed outlier: 4.153A pdb=" N PHE N 38 " --> pdb=" O LEU N 34 " (cutoff:3.500A) Processing helix chain 'N' and resid 45 through 53 Proline residue: N 50 - end of helix removed outlier: 5.399A pdb=" N LEU N 53 " --> pdb=" O GLN N 49 " (cutoff:3.500A) Processing helix chain 'N' and resid 70 through 86 Processing helix chain 'N' and resid 89 through 101 removed outlier: 3.809A pdb=" N LEU N 93 " --> pdb=" O TYR N 89 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N GLU N 96 " --> pdb=" O SER N 92 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LYS N 99 " --> pdb=" O SER N 95 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA N 100 " --> pdb=" O GLU N 96 " (cutoff:3.500A) Processing helix chain 'O' and resid 14 through 33 removed outlier: 3.728A pdb=" N ARG O 31 " --> pdb=" O GLU O 27 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N THR O 32 " --> pdb=" O THR O 28 " (cutoff:3.500A) Processing helix chain 'O' and resid 80 through 90 removed outlier: 3.735A pdb=" N ASP O 85 " --> pdb=" O GLU O 81 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ALA O 86 " --> pdb=" O LYS O 82 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N MET O 88 " --> pdb=" O VAL O 84 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ARG O 89 " --> pdb=" O ASP O 85 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N LEU O 90 " --> pdb=" O ALA O 86 " (cutoff:3.500A) Processing helix chain 'P' and resid 45 through 50 removed outlier: 4.305A pdb=" N GLY P 50 " --> pdb=" O ALA P 46 " (cutoff:3.500A) Processing helix chain 'P' and resid 58 through 75 removed outlier: 3.691A pdb=" N ALA P 72 " --> pdb=" O ARG P 68 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL P 73 " --> pdb=" O CYS P 69 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N LYS P 74 " --> pdb=" O ALA P 70 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N GLU P 75 " --> pdb=" O ASP P 71 " (cutoff:3.500A) Processing helix chain 'P' and resid 91 through 102 removed outlier: 3.698A pdb=" N THR P 95 " --> pdb=" O GLY P 91 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ALA P 98 " --> pdb=" O SER P 94 " (cutoff:3.500A) Processing helix chain 'Q' and resid 2 through 10 Proline residue: Q 10 - end of helix Processing helix chain 'Q' and resid 112 through 117 removed outlier: 4.983A pdb=" N TYR Q 116 " --> pdb=" O ALA Q 112 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLY Q 117 " --> pdb=" O ARG Q 113 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 112 through 117' Processing helix chain 'R' and resid 13 through 20 removed outlier: 3.741A pdb=" N SER R 20 " --> pdb=" O ILE R 16 " (cutoff:3.500A) Processing helix chain 'R' and resid 26 through 37 removed outlier: 3.581A pdb=" N ALA R 35 " --> pdb=" O ALA R 31 " (cutoff:3.500A) Processing helix chain 'R' and resid 48 through 63 removed outlier: 3.611A pdb=" N ASP R 53 " --> pdb=" O GLU R 49 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N THR R 54 " --> pdb=" O GLY R 50 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU R 55 " --> pdb=" O GLN R 51 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG R 56 " --> pdb=" O ILE R 52 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N LYS R 61 " --> pdb=" O ASP R 57 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N PHE R 62 " --> pdb=" O GLU R 58 " (cutoff:3.500A) removed outlier: 4.987A 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 23 removed outlier: 3.580A pdb=" N LYS S 6 " --> pdb=" O LYS S 2 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ALA S 21 " --> pdb=" O ASP S 17 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N LYS S 22 " --> pdb=" O LYS S 18 " (cutoff:3.500A) Processing helix chain 'S' and resid 24 through 29 removed outlier: 3.527A pdb=" N ALA S 28 " --> pdb=" O ALA S 24 " (cutoff:3.500A) Processing helix chain 'S' and resid 37 through 50 removed outlier: 4.301A pdb=" N GLN S 48 " --> pdb=" O VAL S 44 " (cutoff:3.500A) Processing helix chain 'S' and resid 55 through 60 removed outlier: 5.121A pdb=" N ARG S 60 " --> pdb=" O PRO S 56 " (cutoff:3.500A) Processing helix chain 'S' and resid 79 through 90 Processing helix chain 'T' and resid 3 through 15 Processing helix chain 'T' and resid 23 through 46 removed outlier: 4.336A pdb=" N GLY T 40 " --> pdb=" O ASN T 36 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N HIS T 41 " --> pdb=" O HIS T 37 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N HIS T 45 " --> pdb=" O HIS T 41 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N LYS T 46 " --> pdb=" O PHE T 42 " (cutoff:3.500A) Processing helix chain 'T' and resid 48 through 73 removed outlier: 3.560A pdb=" N ARG T 71 " --> pdb=" O ASP T 67 " (cutoff:3.500A) Processing helix chain 'T' and resid 74 through 85 Processing helix chain 'U' and resid 53 through 64 removed outlier: 4.314A pdb=" N GLN U 63 " --> pdb=" O HIS U 59 " (cutoff:3.500A) Processing helix chain 'U' and resid 68 through 79 removed outlier: 3.993A pdb=" N GLU U 77 " --> pdb=" O ALA U 73 " (cutoff:3.500A) Processing helix chain 'W' and resid 12 through 17 Processing helix chain 'W' and resid 24 through 33 removed outlier: 3.759A pdb=" N LEU W 28 " --> pdb=" O ASP W 24 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ASN W 30 " --> pdb=" O ALA W 26 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N TYR W 31 " --> pdb=" O THR W 27 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ILE W 32 " --> pdb=" O LEU W 28 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N THR W 33 " --> pdb=" O LYS W 29 " (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 removed outlier: 3.604A pdb=" N GLU X 23 " --> pdb=" O GLU X 19 " (cutoff:3.500A) Processing helix chain 'X' and resid 69 through 75 removed outlier: 4.483A pdb=" N PHE X 73 " --> pdb=" O LYS X 69 " (cutoff:3.500A) removed outlier: 4.201A 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 6 through 41 removed outlier: 4.629A pdb=" N ALA Y 10 " --> pdb=" O ALA Y 6 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N MET Y 27 " --> pdb=" O ARG Y 23 " (cutoff:3.500A) Processing helix chain 'Y' and resid 42 through 64 removed outlier: 3.680A pdb=" N MET Y 53 " --> pdb=" O ALA Y 49 " (cutoff:3.500A) Proline residue: Y 55 - end of helix removed outlier: 3.554A pdb=" N ARG Y 59 " --> pdb=" O PRO Y 55 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LYS Y 63 " --> pdb=" O ARG Y 59 " (cutoff:3.500A) Processing helix chain 'Y' and resid 67 through 86 removed outlier: 6.100A pdb=" N ALA Y 71 " --> pdb=" O HIS Y 67 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ALA Y 86 " --> pdb=" O ILE Y 82 " (cutoff:3.500A) Processing helix chain 'Z' and resid 16 through 22 removed outlier: 4.589A pdb=" N ARG Z 20 " --> pdb=" O ARG Z 16 " (cutoff:3.500A) Processing helix chain 'Z' and resid 24 through 33 removed outlier: 4.196A pdb=" N LEU Z 28 " --> pdb=" O LYS Z 24 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N ARG Z 33 " --> pdb=" O ALA Z 29 " (cutoff:3.500A) Processing helix chain 'Z' and resid 36 through 61 Proline residue: Z 40 - end of helix removed outlier: 3.571A pdb=" N ALA Z 49 " --> pdb=" O LYS Z 45 " (cutoff:3.500A) Processing helix chain 'a' and resid 6 through 16 removed outlier: 4.703A pdb=" N ASP a 16 " --> pdb=" O ARG a 12 " (cutoff:3.500A) Processing helix chain 'a' and resid 23 through 34 removed outlier: 4.248A pdb=" N ALA a 28 " --> pdb=" O ASN a 24 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N LYS a 31 " --> pdb=" O ILE a 27 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N GLU a 32 " --> pdb=" O ALA a 28 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N LEU a 33 " --> pdb=" O LEU a 29 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ALA a 34 " --> pdb=" O LEU a 30 " (cutoff:3.500A) Processing helix chain 'a' and resid 181 through 200 Processing helix chain '8' and resid 6 through 11 removed outlier: 5.589A pdb=" N ARG 8 11 " --> pdb=" O ILE 8 7 " (cutoff:3.500A) Processing helix chain '8' and resid 22 through 36 removed outlier: 3.560A pdb=" N GLY 8 35 " --> pdb=" O LEU 8 31 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N VAL 8 36 " --> pdb=" O PHE 8 32 " (cutoff:3.500A) Processing helix chain '8' and resid 53 through 60 Processing helix chain '8' and resid 95 through 106 removed outlier: 3.664A pdb=" N VAL 8 105 " --> pdb=" O ARG 8 101 " (cutoff:3.500A) Processing helix chain '8' and resid 120 through 134 removed outlier: 4.228A pdb=" N VAL 8 126 " --> pdb=" O GLN 8 122 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TRP 8 127 " --> pdb=" O SER 8 123 " (cutoff:3.500A) Processing helix chain '8' and resid 150 through 161 removed outlier: 3.534A pdb=" N GLN 8 157 " --> pdb=" O LYS 8 153 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N LYS 8 159 " --> pdb=" O VAL 8 155 " (cutoff:3.500A) Processing helix chain '8' and resid 211 through 227 Processing helix chain '8' and resid 230 through 240 removed outlier: 3.515A pdb=" N MET 8 234 " --> pdb=" O SER 8 230 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLU 8 235 " --> pdb=" O GLU 8 231 " (cutoff:3.500A) Processing helix chain '8' and resid 244 through 259 removed outlier: 4.062A pdb=" N ASN 8 259 " --> pdb=" O ARG 8 255 " (cutoff:3.500A) Processing helix chain '8' and resid 274 through 285 Processing helix chain '8' and resid 424 through 440 removed outlier: 5.129A pdb=" N LYS 8 430 " --> pdb=" O ALA 8 426 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N MET 8 431 " --> pdb=" O ASP 8 427 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N LYS 8 440 " --> pdb=" O GLY 8 436 " (cutoff:3.500A) Processing helix chain '8' and resid 462 through 476 removed outlier: 3.618A pdb=" N ARG 8 475 " --> pdb=" O ASP 8 471 " (cutoff:3.500A) Processing helix chain '8' and resid 541 through 546 removed outlier: 6.815A pdb=" N ILE 8 545 " --> pdb=" O LYS 8 541 " (cutoff:3.500A) Proline residue: 8 546 - end of helix No H-bonds generated for 'chain '8' and resid 541 through 546' Processing helix chain '8' and resid 549 through 564 removed outlier: 3.570A pdb=" N GLN 8 560 " --> pdb=" O GLY 8 556 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N LYS 8 562 " --> pdb=" O GLN 8 558 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N ALA 8 563 " --> pdb=" O GLU 8 559 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N GLY 8 564 " --> pdb=" O GLN 8 560 " (cutoff:3.500A) Processing helix chain '8' and resid 589 through 609 removed outlier: 4.073A pdb=" N LYS 8 602 " --> pdb=" O SER 8 598 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLU 8 603 " --> pdb=" O ILE 8 599 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS 8 609 " --> pdb=" O PHE 8 605 " (cutoff:3.500A) Processing helix chain '8' and resid 626 through 639 removed outlier: 4.205A pdb=" N ASP 8 630 " --> pdb=" O GLU 8 626 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLY 8 633 " --> pdb=" O GLY 8 629 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ASP 8 634 " --> pdb=" O ASP 8 630 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ARG 8 639 " --> pdb=" O LEU 8 635 " (cutoff:3.500A) Processing helix chain '8' and resid 659 through 664 removed outlier: 4.008A pdb=" N PHE 8 664 " --> pdb=" O LEU 8 660 " (cutoff:3.500A) Processing helix chain '8' and resid 665 through 675 Processing helix chain '8' and resid 691 through 699 removed outlier: 4.831A pdb=" N ALA 8 697 " --> pdb=" O ASN 8 693 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N VAL 8 698 " --> pdb=" O VAL 8 694 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ILE 8 699 " --> pdb=" O ALA 8 695 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'b' and resid 79 through 82 removed outlier: 6.519A pdb=" N LEU b 92 " --> pdb=" O GLU b 78 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ASP b 113 " --> pdb=" O VAL b 77 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'b' and resid 137 through 141 removed outlier: 4.769A pdb=" N SER b 138 " --> pdb=" O ILE b 163 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N THR b 172 " --> pdb=" O VAL b 164 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLU b 179 " --> pdb=" O LEU b 175 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'b' and resid 90 through 95 removed outlier: 4.521A pdb=" N GLU b 99 " --> pdb=" O TYR b 95 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'c' and resid 3 through 9 removed outlier: 4.248A pdb=" N SER c 199 " --> pdb=" O LYS c 8 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'c' and resid 10 through 16 removed outlier: 3.688A pdb=" N GLY c 10 " --> pdb=" O VAL c 26 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N VAL c 20 " --> pdb=" O THR c 16 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG c 179 " --> pdb=" O LEU c 188 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'c' and resid 32 through 35 removed outlier: 6.695A pdb=" N GLN c 49 " --> pdb=" O THR c 35 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N TYR c 45 " --> pdb=" O LEU c 40 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LEU c 40 " --> pdb=" O TYR c 45 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'c' and resid 108 through 112 Processing sheet with id= 8, first strand: chain 'c' and resid 46 through 51 removed outlier: 5.817A pdb=" N ARG c 46 " --> pdb=" O LEU c 84 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'd' and resid 117 through 120 removed outlier: 3.508A pdb=" N ASP d 168 " --> pdb=" O VAL d 146 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'e' and resid 64 through 68 removed outlier: 4.144A pdb=" N THR e 157 " --> pdb=" O GLY e 125 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N GLY e 125 " --> pdb=" O THR e 157 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'f' and resid 15 through 18 removed outlier: 3.546A pdb=" N LYS f 26 " --> pdb=" O ASP f 15 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N GLN f 21 " --> pdb=" O LEU f 36 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'f' and resid 39 through 44 removed outlier: 7.241A pdb=" N ALA f 39 " --> pdb=" O ARG f 54 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY f 52 " --> pdb=" O GLU f 41 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYS f 43 " --> pdb=" O THR f 50 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'f' and resid 93 through 98 removed outlier: 6.313A pdb=" N ASN f 100 " --> pdb=" O LEU f 116 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'f' and resid 120 through 124 removed outlier: 5.127A pdb=" N THR f 128 " --> pdb=" O LEU f 88 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLY f 134 " --> pdb=" O PHE f 82 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE f 82 " --> pdb=" O GLY f 134 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'g' and resid 3 through 6 No H-bonds generated for sheet with id= 15 Processing sheet with id= 16, first strand: chain 'g' and resid 78 through 82 removed outlier: 3.775A pdb=" N SER g 82 " --> pdb=" O VAL g 147 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'h' and resid 25 through 28 No H-bonds generated for sheet with id= 17 Processing sheet with id= 18, first strand: chain 'i' and resid 55 through 60 Processing sheet with id= 19, first strand: chain 'j' and resid 52 through 57 removed outlier: 4.722A pdb=" N ASP j 19 " --> pdb=" O LEU j 140 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'k' and resid 18 through 21 removed outlier: 4.337A pdb=" N THR k 6 " --> pdb=" O CYS k 21 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N ASN k 82 " --> pdb=" O MET k 7 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'm' and resid 37 through 41 removed outlier: 7.201A pdb=" N GLY m 37 " --> pdb=" O PRO m 98 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'm' and resid 99 through 102 removed outlier: 6.420A pdb=" N LEU m 33 " --> pdb=" O LEU m 102 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N TYR m 103 " --> pdb=" O LEU m 33 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'm' and resid 30 through 36 removed outlier: 8.116A pdb=" N SER m 30 " --> pdb=" O LYS m 133 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N LYS m 127 " --> pdb=" O VAL m 36 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'n' and resid 33 through 36 removed outlier: 3.875A pdb=" N ALA n 108 " --> pdb=" O ARG n 103 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N GLY n 101 " --> pdb=" O MET n 110 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'o' and resid 49 through 52 removed outlier: 3.568A pdb=" N VAL o 49 " --> pdb=" O VAL o 39 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ARG o 25 " --> pdb=" O ILE o 40 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'p' and resid 37 through 44 removed outlier: 6.357A pdb=" N THR p 24 " --> pdb=" O LYS p 86 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'p' and resid 48 through 51 removed outlier: 4.196A pdb=" N ALA p 48 " --> pdb=" O THR p 59 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'r' and resid 11 through 14 removed outlier: 3.595A pdb=" N PHE r 5 " --> pdb=" O HIS r 12 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N TYR r 2 " --> pdb=" O ALA r 42 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N ASN r 43 " --> pdb=" O GLU r 45 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N GLU r 45 " --> pdb=" O ASN r 43 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'r' and resid 18 through 23 removed outlier: 4.334A pdb=" N GLN r 18 " --> pdb=" O ILE r 98 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N PHE r 93 " --> pdb=" O HIS r 66 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N HIS r 66 " --> pdb=" O PHE r 93 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N ASP r 95 " --> pdb=" O VAL r 64 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N LYS r 60 " --> pdb=" O THR r 99 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N ILE r 101 " --> pdb=" O VAL r 58 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N VAL r 58 " --> pdb=" O ILE r 101 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N ALA r 103 " --> pdb=" O GLY r 56 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLY r 56 " --> pdb=" O ALA r 103 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N GLU r 31 " --> pdb=" O VAL r 63 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'r' and resid 71 through 77 Processing sheet with id= 31, first strand: chain 's' and resid 2 through 8 removed outlier: 4.375A pdb=" N THR s 3 " --> pdb=" O VAL s 107 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL s 107 " --> pdb=" O THR s 3 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 't' and resid 12 through 15 removed outlier: 3.775A pdb=" N ALA t 13 " --> pdb=" O LYS t 33 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N VAL t 31 " --> pdb=" O HIS t 15 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N LYS t 81 " --> pdb=" O VAL t 34 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N LYS t 66 " --> pdb=" O ARG t 77 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ASP t 79 " --> pdb=" O LYS t 64 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N LYS t 64 " --> pdb=" O ASP t 79 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N LYS t 81 " --> pdb=" O VAL t 62 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N VAL t 62 " --> pdb=" O LYS t 81 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ALA t 83 " --> pdb=" O THR t 60 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N THR t 60 " --> pdb=" O ALA t 83 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N VAL t 85 " --> pdb=" O VAL t 58 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N VAL t 58 " --> pdb=" O VAL t 85 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'u' and resid 9 through 12 removed outlier: 3.782A pdb=" N LYS u 20 " --> pdb=" O VAL u 12 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'u' and resid 39 through 44 removed outlier: 5.037A pdb=" N ASN u 39 " --> pdb=" O ALA u 62 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'v' and resid 2 through 5 removed outlier: 3.681A pdb=" N ILE v 4 " --> pdb=" O THR v 62 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE v 63 " --> pdb=" O ILE v 70 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'v' and resid 37 through 42 removed outlier: 3.879A pdb=" N ILE v 89 " --> pdb=" O PRO v 27 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'w' and resid 62 through 67 Processing sheet with id= 38, first strand: chain 'x' and resid 11 through 18 removed outlier: 3.609A pdb=" N ARG x 26 " --> pdb=" O GLY x 14 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N ASN x 22 " --> pdb=" O SER x 18 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'x' and resid 33 through 40 Processing sheet with id= 40, first strand: chain 'z' and resid 34 through 38 removed outlier: 4.858A pdb=" N LYS z 5 " --> pdb=" O GLU z 57 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N MET z 53 " --> pdb=" O THR z 9 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'A' and resid 22 through 26 removed outlier: 3.574A pdb=" N MET A 22 " --> pdb=" O ALA A 14 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N HIS A 30 " --> pdb=" O GLU A 11 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N THR A 13 " --> pdb=" O HIS A 30 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N LEU A 32 " --> pdb=" O THR A 13 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N SER A 15 " --> pdb=" O LEU A 32 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'C' and resid 6 through 11 Processing sheet with id= 43, first strand: chain 'C' and resid 34 through 37 Processing sheet with id= 44, first strand: chain 'E' and resid 21 through 24 No H-bonds generated for sheet with id= 44 Processing sheet with id= 45, first strand: chain 'G' and resid 29 through 32 No H-bonds generated for sheet with id= 45 Processing sheet with id= 46, first strand: chain 'G' and resid 66 through 70 removed outlier: 3.697A pdb=" N ALA G 184 " --> pdb=" O PHE G 197 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'H' and resid 53 through 58 removed outlier: 3.579A pdb=" N ARG H 53 " --> pdb=" O HIS H 68 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLN H 99 " --> pdb=" O ILE H 63 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'H' and resid 163 through 170 removed outlier: 3.562A pdb=" N GLY H 147 " --> pdb=" O PHE H 202 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N SER H 186 " --> pdb=" O VAL H 197 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'I' and resid 170 through 174 removed outlier: 6.085A pdb=" N GLU I 178 " --> pdb=" O ASP I 173 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'J' and resid 15 through 23 removed outlier: 6.019A pdb=" N ILE J 29 " --> pdb=" O LYS J 22 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'J' and resid 92 through 97 removed outlier: 4.398A pdb=" N ARG J 92 " --> pdb=" O TYR J 127 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N TYR J 127 " --> pdb=" O ARG J 92 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'K' and resid 34 through 37 removed outlier: 3.797A pdb=" N LYS K 35 " --> pdb=" O GLU K 65 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N ASN K 63 " --> pdb=" O HIS K 37 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL K 60 " --> pdb=" O PHE K 8 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N PHE K 8 " --> pdb=" O VAL K 60 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ILE K 6 " --> pdb=" O MET K 62 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLU K 5 " --> pdb=" O MET K 90 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N MET K 90 " --> pdb=" O GLU K 5 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N ARG K 86 " --> pdb=" O MET K 9 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'K' and resid 38 through 42 removed outlier: 3.647A pdb=" N ARG K 38 " --> pdb=" O ASN K 63 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ASN K 63 " --> pdb=" O ARG K 38 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N GLU K 40 " --> pdb=" O LEU K 61 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N LEU K 61 " --> pdb=" O GLU K 40 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N TYR K 59 " --> pdb=" O TRP K 42 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'K' and resid 43 through 46 Processing sheet with id= 55, first strand: chain 'L' and resid 72 through 76 removed outlier: 3.822A pdb=" N LYS L 75 " --> pdb=" O VAL L 86 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N VAL L 86 " --> pdb=" O LYS L 75 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'M' and resid 22 through 27 removed outlier: 6.755A pdb=" N ALA M 22 " --> pdb=" O LEU M 62 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLU M 51 " --> pdb=" O GLU M 57 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N THR M 61 " --> pdb=" O ASP M 47 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N ASP M 47 " --> pdb=" O THR M 61 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'M' and resid 102 through 105 removed outlier: 7.026A pdb=" N VAL M 102 " --> pdb=" O ILE M 125 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'N' and resid 4 through 10 removed outlier: 3.979A pdb=" N GLY N 9 " --> pdb=" O ALA N 16 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'O' and resid 36 through 40 removed outlier: 8.502A pdb=" N VAL O 36 " --> pdb=" O VAL O 77 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N VAL O 77 " --> pdb=" O VAL O 36 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N GLY O 38 " --> pdb=" O ASP O 75 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ASP O 75 " --> pdb=" O GLY O 38 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N ILE O 8 " --> pdb=" O VAL O 74 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'P' and resid 29 through 35 Processing sheet with id= 61, first strand: chain 'Q' and resid 28 through 31 removed outlier: 5.937A pdb=" N LEU Q 80 " --> pdb=" O VAL Q 97 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'Q' and resid 35 through 40 removed outlier: 4.659A pdb=" N ARG Q 35 " --> pdb=" O ARG Q 53 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N LYS Q 50 " --> pdb=" O ILE Q 66 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'U' and resid 4 through 9 removed outlier: 4.099A pdb=" N ALA U 7 " --> pdb=" O GLN U 18 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLN U 18 " --> pdb=" O ALA U 7 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N VAL U 19 " --> pdb=" O GLY U 37 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N GLY U 37 " --> pdb=" O VAL U 19 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'V' and resid 6 through 11 removed outlier: 3.530A pdb=" N GLY V 9 " --> pdb=" O VAL V 58 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N ASP V 56 " --> pdb=" O VAL V 11 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N GLU V 59 " --> pdb=" O VAL V 75 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N SER V 71 " --> pdb=" O CYS V 63 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'V' and resid 19 through 30 No H-bonds generated for sheet with id= 65 Processing sheet with id= 66, first strand: chain 'X' and resid 46 through 51 removed outlier: 3.763A pdb=" N LEU X 46 " --> pdb=" O VAL X 61 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'a' and resid 59 through 63 removed outlier: 6.616A pdb=" N VAL a 59 " --> pdb=" O ASN a 165 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'a' and resid 169 through 175 removed outlier: 5.774A pdb=" N GLY a 169 " --> pdb=" O LEU a 48 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N VAL a 42 " --> pdb=" O ILE a 175 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N LYS a 211 " --> pdb=" O ASN a 47 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain '8' and resid 66 through 71 removed outlier: 5.941A pdb=" N ARG 8 137 " --> pdb=" O ILE 8 261 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU 8 263 " --> pdb=" O ARG 8 137 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ILE 8 262 " --> pdb=" O ASN 8 165 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N CYS 8 266 " --> pdb=" O LEU 8 169 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain '8' and resid 170 through 173 removed outlier: 4.378A pdb=" N GLY 8 181 " --> pdb=" O ILE 8 173 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL 8 182 " --> pdb=" O ILE 8 191 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N THR 8 201 " --> pdb=" O ASN 8 194 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain '8' and resid 294 through 299 No H-bonds generated for sheet with id= 71 Processing sheet with id= 72, first strand: chain '8' and resid 346 through 350 removed outlier: 4.727A pdb=" N ASP 8 347 " --> pdb=" O PHE 8 360 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE 8 360 " --> pdb=" O ASP 8 347 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain '8' and resid 362 through 365 removed outlier: 4.111A pdb=" N ARG 8 362 " --> pdb=" O ILE 8 386 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N PHE 8 335 " --> pdb=" O PHE 8 322 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N LEU 8 320 " --> pdb=" O ARG 8 337 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N PHE 8 317 " --> pdb=" O CYS 8 398 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N CYS 8 398 " --> pdb=" O PHE 8 317 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ALA 8 319 " --> pdb=" O THR 8 396 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N THR 8 396 " --> pdb=" O ALA 8 319 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N ALA 8 321 " --> pdb=" O GLY 8 394 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain '8' and resid 415 through 420 removed outlier: 4.613A pdb=" N THR 8 456 " --> pdb=" O VAL 8 420 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N GLN 8 455 " --> pdb=" O ASP 8 450 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ILE 8 457 " --> pdb=" O TRP 8 448 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain '8' and resid 490 through 494 removed outlier: 4.189A pdb=" N VAL 8 652 " --> pdb=" O THR 8 623 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N HIS 8 655 " --> pdb=" O LYS 8 643 " (cutoff:3.500A) Processing sheet with id= 76, first strand: chain '8' and resid 500 through 508 removed outlier: 3.506A pdb=" N VAL 8 501 " --> pdb=" O ILE 8 520 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N VAL 8 519 " --> pdb=" O HIS 8 579 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU 8 578 " --> pdb=" O ILE 8 537 " (cutoff:3.500A) Processing sheet with id= 77, first strand: chain '8' and resid 516 through 519 removed outlier: 3.672A pdb=" N PHE 8 580 " --> pdb=" O VAL 8 519 " (cutoff:3.500A) Processing sheet with id= 78, first strand: chain '8' and resid 616 through 623 No H-bonds generated for sheet with id= 78 Processing sheet with id= 79, first strand: chain '8' and resid 612 through 616 No H-bonds generated for sheet with id= 79 Processing sheet with id= 80, first strand: chain '8' and resid 644 through 648 1965 hydrogen bonds defined for protein. 5802 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3607 hydrogen bonds 5832 hydrogen bond angles 0 basepair planarities 1436 basepair parallelities 2282 stacking parallelities Total time for adding SS restraints: 214.05 Time building geometry restraints manager: 66.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.96 - 1.13: 3 1.13 - 1.31: 14775 1.31 - 1.49: 93516 1.49 - 1.67: 57652 1.67 - 1.85: 323 Bond restraints: 166269 Sorted by residual: bond pdb=" C ASP K 13 " pdb=" O ASP K 13 " ideal model delta sigma weight residual 1.236 1.523 -0.287 1.15e-02 7.56e+03 6.23e+02 bond pdb=" C SER 8 312 " pdb=" O SER 8 312 " ideal model delta sigma weight residual 1.234 1.548 -0.314 1.26e-02 6.30e+03 6.23e+02 bond pdb=" C PRO i 19 " pdb=" O PRO i 19 " ideal model delta sigma weight residual 1.235 1.551 -0.316 1.30e-02 5.92e+03 5.90e+02 bond pdb=" C ILE i 54 " pdb=" O ILE i 54 " ideal model delta sigma weight residual 1.243 1.498 -0.254 1.08e-02 8.57e+03 5.54e+02 bond pdb=" C LEU i 27 " pdb=" O LEU i 27 " ideal model delta sigma weight residual 1.237 1.505 -0.268 1.19e-02 7.06e+03 5.08e+02 ... (remaining 166264 not shown) Histogram of bond angle deviations from ideal: 93.21 - 104.64: 21083 104.64 - 116.08: 123568 116.08 - 127.51: 93679 127.51 - 138.94: 9624 138.94 - 150.38: 3 Bond angle restraints: 247957 Sorted by residual: angle pdb=" CA GLU Z 23 " pdb=" C GLU Z 23 " pdb=" O GLU Z 23 " ideal model delta sigma weight residual 119.40 140.75 -21.35 1.10e+00 8.26e-01 3.77e+02 angle pdb=" O GLU Z 23 " pdb=" C GLU Z 23 " pdb=" N LYS Z 24 " ideal model delta sigma weight residual 121.79 104.58 17.21 9.80e-01 1.04e+00 3.08e+02 angle pdb=" C PRO K 50 " pdb=" N ILE K 51 " pdb=" CA ILE K 51 " ideal model delta sigma weight residual 123.17 103.36 19.81 1.28e+00 6.10e-01 2.40e+02 angle pdb=" CA GLY X 45 " pdb=" C GLY X 45 " pdb=" O GLY X 45 " ideal model delta sigma weight residual 118.95 134.01 -15.06 1.00e+00 1.00e+00 2.27e+02 angle pdb=" CA ASP K 13 " pdb=" C ASP K 13 " pdb=" O ASP K 13 " ideal model delta sigma weight residual 120.90 136.34 -15.44 1.07e+00 8.73e-01 2.08e+02 ... (remaining 247952 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.98: 94815 35.98 - 71.96: 10523 71.96 - 107.94: 1027 107.94 - 143.93: 15 143.93 - 179.91: 17 Dihedral angle restraints: 106397 sinusoidal: 87505 harmonic: 18892 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 31.79 -66.79 1 8.00e+00 1.56e-02 9.09e+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 82.71 64.29 1 8.00e+00 1.56e-02 8.49e+01 dihedral pdb=" O4' U 11915 " pdb=" C1' U 11915 " pdb=" N1 U 11915 " pdb=" C2 U 11915 " ideal model delta sinusoidal sigma weight residual 200.00 31.03 168.97 1 1.50e+01 4.44e-03 8.45e+01 ... (remaining 106394 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.142: 28010 0.142 - 0.284: 3250 0.284 - 0.426: 283 0.426 - 0.567: 27 0.567 - 0.709: 6 Chirality restraints: 31576 Sorted by residual: chirality pdb=" CA ASN J 121 " pdb=" N ASN J 121 " pdb=" C ASN J 121 " pdb=" CB ASN J 121 " both_signs ideal model delta sigma weight residual False 2.51 1.80 0.71 2.00e-01 2.50e+01 1.26e+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 1.01e+01 chirality pdb=" CA VAL i 12 " pdb=" N VAL i 12 " pdb=" C VAL i 12 " pdb=" CB VAL i 12 " both_signs ideal model delta sigma weight residual False 2.44 3.06 -0.62 2.00e-01 2.50e+01 9.62e+00 ... (remaining 31573 not shown) Planarity restraints: 13872 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A 2 119 " 0.368 2.00e-02 2.50e+03 1.58e-01 6.86e+02 pdb=" N9 A 2 119 " -0.026 2.00e-02 2.50e+03 pdb=" C8 A 2 119 " -0.146 2.00e-02 2.50e+03 pdb=" N7 A 2 119 " -0.118 2.00e-02 2.50e+03 pdb=" C5 A 2 119 " -0.069 2.00e-02 2.50e+03 pdb=" C6 A 2 119 " 0.060 2.00e-02 2.50e+03 pdb=" N6 A 2 119 " 0.220 2.00e-02 2.50e+03 pdb=" N1 A 2 119 " 0.053 2.00e-02 2.50e+03 pdb=" C2 A 2 119 " -0.059 2.00e-02 2.50e+03 pdb=" N3 A 2 119 " -0.152 2.00e-02 2.50e+03 pdb=" C4 A 2 119 " -0.130 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U 11647 " 0.239 2.00e-02 2.50e+03 1.30e-01 3.81e+02 pdb=" N1 U 11647 " -0.009 2.00e-02 2.50e+03 pdb=" C2 U 11647 " -0.045 2.00e-02 2.50e+03 pdb=" O2 U 11647 " -0.094 2.00e-02 2.50e+03 pdb=" N3 U 11647 " -0.037 2.00e-02 2.50e+03 pdb=" C4 U 11647 " -0.039 2.00e-02 2.50e+03 pdb=" O4 U 11647 " 0.228 2.00e-02 2.50e+03 pdb=" C5 U 11647 " -0.127 2.00e-02 2.50e+03 pdb=" C6 U 11647 " -0.116 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G 12061 " -0.240 2.00e-02 2.50e+03 9.89e-02 2.93e+02 pdb=" N9 G 12061 " 0.017 2.00e-02 2.50e+03 pdb=" C8 G 12061 " 0.103 2.00e-02 2.50e+03 pdb=" N7 G 12061 " 0.088 2.00e-02 2.50e+03 pdb=" C5 G 12061 " 0.047 2.00e-02 2.50e+03 pdb=" C6 G 12061 " -0.043 2.00e-02 2.50e+03 pdb=" O6 G 12061 " -0.152 2.00e-02 2.50e+03 pdb=" N1 G 12061 " -0.031 2.00e-02 2.50e+03 pdb=" C2 G 12061 " 0.027 2.00e-02 2.50e+03 pdb=" N2 G 12061 " 0.035 2.00e-02 2.50e+03 pdb=" N3 G 12061 " 0.073 2.00e-02 2.50e+03 pdb=" C4 G 12061 " 0.075 2.00e-02 2.50e+03 ... (remaining 13869 not shown) Histogram of nonbonded interaction distances: 1.42 - 2.12: 5 2.12 - 2.81: 36011 2.81 - 3.51: 214717 3.51 - 4.20: 482446 4.20 - 4.90: 635740 Nonbonded interactions: 1368919 Sorted by model distance: nonbonded pdb=" O3' A 5 76 " pdb=" C PRO 5 101 " model vdw 1.421 3.270 nonbonded pdb=" O LYS a 6 " pdb=" N MET a 8 " model vdw 1.822 2.520 nonbonded pdb=" O THR a 5 " pdb=" O LYS a 6 " model vdw 1.887 3.040 nonbonded pdb=" O3' A 5 76 " pdb=" CA PRO 5 101 " model vdw 2.017 3.470 nonbonded pdb=" O GLU Z 23 " pdb=" CB LYS Z 24 " model vdw 2.025 3.440 ... (remaining 1368914 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.69 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: 2.640 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: 0.110 Extract box with map and model: 18.690 Check model and map are aligned: 1.620 Set scattering table: 1.020 Process input model: 515.030 Find NCS groups from input model: 3.090 Set up NCS constraints: 0.380 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 545.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 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 : 0.012 0.316 166269 Z= 0.748 Angle : 1.259 25.606 247957 Z= 0.842 Chirality : 0.096 0.709 31576 Planarity : 0.015 0.158 13872 Dihedral : 22.662 179.906 94213 Min Nonbonded Distance : 1.421 Molprobity Statistics. All-atom Clashscore : 24.43 Ramachandran Plot: Outliers : 1.63 % Allowed : 15.73 % Favored : 82.65 % Rotamer: Outliers : 2.17 % Allowed : 8.20 % Favored : 89.63 % 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: -4.14 (0.09), residues: 6517 helix: -2.48 (0.10), residues: 1655 sheet: -2.67 (0.14), residues: 1104 loop : -2.99 (0.09), residues: 3758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.008 TRP b 247 HIS 0.002 0.000 HIS b 229 PHE 0.044 0.005 PHE i 41 TYR 0.082 0.008 TYR I 75 ARG 0.011 0.001 ARG I 114 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13034 Ramachandran restraints generated. 6517 Oldfield, 0 Emsley, 6517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13034 Ramachandran restraints generated. 6517 Oldfield, 0 Emsley, 6517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1421 residues out of total 5429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 1303 time to evaluate : 6.579 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: b 67 LYS cc_start: 0.8301 (tptp) cc_final: 0.7979 (tptp) REVERT: b 86 ARG cc_start: 0.8237 (OUTLIER) cc_final: 0.7147 (mtm-85) REVERT: b 129 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8609 (pt) REVERT: d 94 GLN cc_start: 0.7093 (pp30) cc_final: 0.6866 (pp30) REVERT: e 172 PHE cc_start: 0.7784 (t80) cc_final: 0.7469 (t80) REVERT: e 176 PHE cc_start: 0.7728 (t80) cc_final: 0.7442 (t80) REVERT: g 11 ASN cc_start: 0.7695 (t0) cc_final: 0.7432 (p0) REVERT: j 14 ASP cc_start: 0.8546 (t70) cc_final: 0.8204 (t0) REVERT: l 121 THR cc_start: 0.7709 (m) cc_final: 0.7373 (p) REVERT: n 52 ILE cc_start: 0.8713 (mm) cc_final: 0.8506 (mm) REVERT: o 46 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7902 (pp20) REVERT: o 69 ASP cc_start: 0.8339 (t0) cc_final: 0.7915 (t0) REVERT: p 23 ASP cc_start: 0.7194 (m-30) cc_final: 0.6854 (m-30) REVERT: p 105 LYS cc_start: 0.8674 (OUTLIER) cc_final: 0.8243 (mmtm) REVERT: p 109 ILE cc_start: 0.8272 (pt) cc_final: 0.8068 (mm) REVERT: r 40 MET cc_start: 0.8014 (tmm) cc_final: 0.7677 (tmm) REVERT: s 15 GLN cc_start: 0.7999 (tt0) cc_final: 0.7652 (tt0) REVERT: t 24 MET cc_start: 0.8851 (tpt) cc_final: 0.8573 (tpt) REVERT: t 29 THR cc_start: 0.8696 (m) cc_final: 0.7966 (p) REVERT: w 66 GLU cc_start: 0.7823 (tm-30) cc_final: 0.7466 (tm-30) REVERT: y 8 GLU cc_start: 0.7513 (mt-10) cc_final: 0.7243 (mt-10) REVERT: y 20 ASN cc_start: 0.8937 (m-40) cc_final: 0.8173 (m-40) REVERT: y 23 ARG cc_start: 0.7994 (mtm180) cc_final: 0.7786 (mtm110) REVERT: z 26 LEU cc_start: 0.9183 (mt) cc_final: 0.8952 (mp) REVERT: A 3 LYS cc_start: 0.8133 (mttt) cc_final: 0.7874 (tptp) REVERT: A 8 LYS cc_start: 0.7431 (tmmt) cc_final: 0.7124 (tmtt) REVERT: A 51 VAL cc_start: -0.0841 (OUTLIER) cc_final: -0.1042 (t) REVERT: C 6 GLU cc_start: 0.7897 (pt0) cc_final: 0.6666 (pm20) REVERT: F 1 MET cc_start: 0.7372 (ptp) cc_final: 0.7138 (ptp) REVERT: F 37 GLN cc_start: 0.8262 (mm-40) cc_final: 0.7754 (mm-40) REVERT: G 22 TRP cc_start: 0.8291 (p-90) cc_final: 0.8044 (p-90) REVERT: G 48 MET cc_start: 0.8602 (tmm) cc_final: 0.8371 (tmm) REVERT: G 58 LYS cc_start: 0.9420 (mmtp) cc_final: 0.9118 (tptp) REVERT: G 173 LYS cc_start: 0.8629 (ttmt) cc_final: 0.7795 (tmtt) REVERT: H 5 HIS cc_start: 0.7594 (t-90) cc_final: 0.6943 (t-90) REVERT: H 34 SER cc_start: 0.8410 (m) cc_final: 0.8066 (p) REVERT: H 40 GLN cc_start: 0.8506 (tp-100) cc_final: 0.7842 (mt0) REVERT: H 182 ASP cc_start: 0.7465 (t70) cc_final: 0.6738 (t0) REVERT: H 184 ASN cc_start: 0.7038 (m110) cc_final: 0.6454 (m110) REVERT: I 3 TYR cc_start: 0.7614 (t80) cc_final: 0.6960 (t80) REVERT: I 139 ASN cc_start: 0.4082 (OUTLIER) cc_final: 0.3862 (t0) REVERT: I 159 GLU cc_start: 0.7159 (tm-30) cc_final: 0.6806 (tm-30) REVERT: J 110 MET cc_start: 0.7616 (ttp) cc_final: 0.7403 (ttt) REVERT: J 115 GLU cc_start: 0.8025 (pt0) cc_final: 0.7624 (pt0) REVERT: K 72 ASP cc_start: 0.8532 (t70) cc_final: 0.8301 (t0) REVERT: K 84 VAL cc_start: 0.9134 (t) cc_final: 0.8611 (p) REVERT: L 98 LEU cc_start: 0.8652 (tp) cc_final: 0.8430 (tp) REVERT: L 100 MET cc_start: 0.6973 (mtm) cc_final: 0.6590 (mtp) REVERT: L 102 TRP cc_start: 0.8076 (m-10) cc_final: 0.7538 (m-90) REVERT: M 72 GLU cc_start: 0.7598 (tp30) cc_final: 0.7342 (tt0) REVERT: N 51 LEU cc_start: 0.6743 (mt) cc_final: 0.6274 (tp) REVERT: N 106 ASP cc_start: 0.7410 (t70) cc_final: 0.7071 (t0) REVERT: N 129 ARG cc_start: 0.7604 (OUTLIER) cc_final: 0.6801 (mmt180) REVERT: O 47 GLU cc_start: 0.6514 (mt-10) cc_final: 0.5600 (tm-30) REVERT: O 67 ILE cc_start: 0.4395 (pt) cc_final: 0.3632 (pt) REVERT: P 14 GLN cc_start: 0.8159 (mm110) cc_final: 0.7768 (pp30) REVERT: P 29 THR cc_start: 0.8591 (p) cc_final: 0.8346 (p) REVERT: Q 65 TYR cc_start: 0.8423 (t80) cc_final: 0.7935 (t80) REVERT: Q 88 ASP cc_start: 0.7233 (t70) cc_final: 0.6985 (t0) REVERT: R 27 THR cc_start: 0.6378 (m) cc_final: 0.6127 (p) REVERT: S 3 GLN cc_start: 0.8625 (mm-40) cc_final: 0.8416 (mm-40) REVERT: S 5 MET cc_start: 0.7147 (mpp) cc_final: 0.6749 (mpp) REVERT: S 19 TYR cc_start: 0.8041 (m-80) cc_final: 0.7748 (m-10) REVERT: S 38 GLU cc_start: 0.8830 (mt-10) cc_final: 0.8422 (mp0) REVERT: T 86 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8587 (pp) REVERT: V 16 MET cc_start: 0.7526 (tpp) cc_final: 0.7018 (tpp) REVERT: V 72 TRP cc_start: 0.6569 (m100) cc_final: 0.6356 (m100) REVERT: V 80 LYS cc_start: 0.6533 (tttm) cc_final: 0.6120 (ttpp) REVERT: Y 27 MET cc_start: 0.8377 (mtm) cc_final: 0.8167 (mtm) REVERT: 8 10 TYR cc_start: 0.7316 (m-80) cc_final: 0.6790 (m-10) REVERT: 8 241 GLU cc_start: 0.5432 (tt0) cc_final: 0.5156 (pt0) REVERT: 8 408 ARG cc_start: 0.4691 (tpt-90) cc_final: 0.3967 (mtt90) REVERT: 8 485 LYS cc_start: 0.8466 (mttm) cc_final: 0.8218 (mmmt) outliers start: 118 outliers final: 46 residues processed: 1396 average time/residue: 1.3021 time to fit residues: 3182.0198 Evaluate side-chains 927 residues out of total 5429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 873 time to evaluate : 6.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 86 ARG Chi-restraints excluded: chain b residue 129 LEU Chi-restraints excluded: chain b residue 262 THR Chi-restraints excluded: chain d residue 77 ILE Chi-restraints excluded: chain e residue 24 VAL Chi-restraints excluded: chain f residue 9 VAL Chi-restraints excluded: chain h residue 81 LEU Chi-restraints excluded: chain i residue 12 VAL Chi-restraints excluded: chain i residue 34 ILE Chi-restraints excluded: chain j residue 62 VAL Chi-restraints excluded: chain j residue 84 ILE Chi-restraints excluded: chain l residue 23 ILE Chi-restraints excluded: chain m residue 42 THR Chi-restraints excluded: chain m residue 91 TYR Chi-restraints excluded: chain n residue 2 ARG Chi-restraints excluded: chain n residue 37 THR Chi-restraints excluded: chain o residue 46 GLU Chi-restraints excluded: chain o residue 95 SER Chi-restraints excluded: chain p residue 105 LYS Chi-restraints excluded: chain r residue 43 ASN Chi-restraints excluded: chain r residue 46 GLU Chi-restraints excluded: chain s residue 76 VAL Chi-restraints excluded: chain u residue 27 VAL Chi-restraints excluded: chain u residue 87 GLU Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain G residue 169 HIS Chi-restraints excluded: chain I residue 97 LEU Chi-restraints excluded: chain I residue 139 ASN Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 162 GLU Chi-restraints excluded: chain K residue 60 VAL Chi-restraints excluded: chain M residue 60 LEU Chi-restraints excluded: chain N residue 8 THR Chi-restraints excluded: chain N residue 38 PHE Chi-restraints excluded: chain N residue 54 VAL Chi-restraints excluded: chain N residue 93 LEU Chi-restraints excluded: chain N residue 129 ARG Chi-restraints excluded: chain Q residue 66 ILE Chi-restraints excluded: chain Q residue 78 VAL Chi-restraints excluded: chain Q residue 96 THR Chi-restraints excluded: chain T residue 86 LEU Chi-restraints excluded: chain U residue 21 VAL Chi-restraints excluded: chain U residue 67 ILE Chi-restraints excluded: chain W residue 18 GLN Chi-restraints excluded: chain X residue 47 THR Chi-restraints excluded: chain X residue 65 MET Chi-restraints excluded: chain Y residue 11 ILE Chi-restraints excluded: chain Z residue 3 ILE Chi-restraints excluded: chain 8 residue 138 ILE Chi-restraints excluded: chain 8 residue 220 GLN Chi-restraints excluded: chain 8 residue 583 TYR Chi-restraints excluded: chain 5 residue 101 PRO Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1109 random chunks: chunk 936 optimal weight: 40.0000 chunk 840 optimal weight: 20.0000 chunk 466 optimal weight: 9.9990 chunk 287 optimal weight: 9.9990 chunk 567 optimal weight: 5.9990 chunk 449 optimal weight: 6.9990 chunk 869 optimal weight: 10.0000 chunk 336 optimal weight: 8.9990 chunk 528 optimal weight: 10.0000 chunk 646 optimal weight: 10.0000 chunk 1007 optimal weight: 20.0000 overall best weight: 8.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 24 HIS b 127 ASN ** c 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 150 GLN ** d 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 51 ASN g 133 GLN i 5 GLN j 128 ASN ** k 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 104 GLN o 61 GLN p 14 GLN ** p 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 36 GLN ** r 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 68 ASN v 24 ASN v 51 GLN x 15 ASN ** x 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** y 31 GLN A 33 ASN A 61 ASN D 29 GLN G 17 HIS H 122 GLN ** I 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 11 GLN ** J 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 11 HIS K 63 ASN L 129 ASN M 37 ASN N 36 GLN ** N 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 125 GLN ** R 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 99 GLN ** S 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 39 GLN ** U 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 142 ASN ** 8 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 369 ASN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 166269 Z= 0.312 Angle : 0.782 12.453 247957 Z= 0.403 Chirality : 0.044 0.362 31576 Planarity : 0.006 0.080 13872 Dihedral : 23.182 177.865 81339 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 17.72 Ramachandran Plot: Outliers : 0.35 % Allowed : 12.60 % Favored : 87.05 % Rotamer: Outliers : 4.16 % Allowed : 13.94 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.44 (0.09), residues: 6517 helix: -1.38 (0.10), residues: 2010 sheet: -2.38 (0.14), residues: 1099 loop : -2.87 (0.10), residues: 3408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP H 200 HIS 0.010 0.002 HIS n 16 PHE 0.039 0.003 PHE m 117 TYR 0.036 0.002 TYR I 75 ARG 0.014 0.001 ARG U 35 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13034 Ramachandran restraints generated. 6517 Oldfield, 0 Emsley, 6517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13034 Ramachandran restraints generated. 6517 Oldfield, 0 Emsley, 6517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1236 residues out of total 5429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 226 poor density : 1010 time to evaluate : 6.601 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: b 235 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.7591 (tp30) REVERT: e 93 GLU cc_start: 0.8522 (OUTLIER) cc_final: 0.8130 (pp20) REVERT: g 11 ASN cc_start: 0.7533 (t0) cc_final: 0.7180 (m110) REVERT: l 121 THR cc_start: 0.7498 (m) cc_final: 0.7261 (p) REVERT: m 60 GLN cc_start: 0.7700 (OUTLIER) cc_final: 0.6302 (pp30) REVERT: n 2 ARG cc_start: 0.8308 (OUTLIER) cc_final: 0.7573 (tmt-80) REVERT: n 49 GLU cc_start: 0.7151 (mt-10) cc_final: 0.6831 (mt-10) REVERT: p 24 THR cc_start: 0.8997 (p) cc_final: 0.8722 (p) REVERT: p 26 GLU cc_start: 0.7622 (tm-30) cc_final: 0.7308 (tm-30) REVERT: p 105 LYS cc_start: 0.8445 (OUTLIER) cc_final: 0.8152 (mmtm) REVERT: q 73 ILE cc_start: 0.8858 (tp) cc_final: 0.8597 (tp) REVERT: q 94 LEU cc_start: 0.9026 (mt) cc_final: 0.8627 (mt) REVERT: r 1 MET cc_start: 0.6684 (mmp) cc_final: 0.6351 (mmp) REVERT: r 48 LYS cc_start: 0.7883 (mtpt) cc_final: 0.7414 (mtpp) REVERT: u 59 GLU cc_start: 0.6897 (OUTLIER) cc_final: 0.6658 (tp30) REVERT: y 7 ARG cc_start: 0.8570 (ptm160) cc_final: 0.8344 (ptm-80) REVERT: y 8 GLU cc_start: 0.7178 (mt-10) cc_final: 0.6850 (mt-10) REVERT: y 20 ASN cc_start: 0.8804 (m-40) cc_final: 0.8371 (m-40) REVERT: A 3 LYS cc_start: 0.8127 (mttt) cc_final: 0.7795 (tptp) REVERT: A 8 LYS cc_start: 0.7287 (tmmt) cc_final: 0.6962 (tmtt) REVERT: C 6 GLU cc_start: 0.7695 (pt0) cc_final: 0.6447 (pm20) REVERT: C 9 LYS cc_start: 0.7403 (tttp) cc_final: 0.6984 (ttmt) REVERT: F 37 GLN cc_start: 0.8399 (mm-40) cc_final: 0.8060 (tp40) REVERT: G 22 TRP cc_start: 0.8245 (p-90) cc_final: 0.7897 (p-90) REVERT: G 48 MET cc_start: 0.8212 (tmm) cc_final: 0.7827 (tmm) REVERT: G 58 LYS cc_start: 0.9274 (mmtp) cc_final: 0.8859 (tptp) REVERT: G 173 LYS cc_start: 0.8505 (ttmt) cc_final: 0.7670 (tmtt) REVERT: G 191 ASP cc_start: 0.8699 (OUTLIER) cc_final: 0.8483 (t0) REVERT: H 34 SER cc_start: 0.8228 (m) cc_final: 0.7920 (p) REVERT: H 40 GLN cc_start: 0.8323 (tp-100) cc_final: 0.7739 (pt0) REVERT: H 128 MET cc_start: 0.6498 (mtp) cc_final: 0.6175 (mtt) REVERT: H 133 MET cc_start: 0.7867 (ttt) cc_final: 0.7165 (ttt) REVERT: H 167 TYR cc_start: 0.7682 (t80) cc_final: 0.7261 (t80) REVERT: H 182 ASP cc_start: 0.7247 (t0) cc_final: 0.6630 (t0) REVERT: I 3 TYR cc_start: 0.7581 (t80) cc_final: 0.6992 (t80) REVERT: J 110 MET cc_start: 0.7033 (ttp) cc_final: 0.6817 (ttt) REVERT: J 115 GLU cc_start: 0.8194 (pt0) cc_final: 0.7816 (pt0) REVERT: K 55 HIS cc_start: 0.8216 (OUTLIER) cc_final: 0.7520 (p-80) REVERT: K 73 GLU cc_start: 0.8282 (mm-30) cc_final: 0.8060 (mm-30) REVERT: L 48 THR cc_start: 0.7099 (m) cc_final: 0.6810 (m) REVERT: L 102 TRP cc_start: 0.8022 (m-10) cc_final: 0.7599 (m-90) REVERT: L 128 GLU cc_start: 0.6839 (mt-10) cc_final: 0.6135 (pt0) REVERT: M 11 THR cc_start: 0.9224 (m) cc_final: 0.8957 (p) REVERT: M 72 GLU cc_start: 0.7661 (tp30) cc_final: 0.7358 (tt0) REVERT: M 95 MET cc_start: 0.7559 (tpp) cc_final: 0.7283 (tpp) REVERT: M 117 GLN cc_start: 0.7472 (mt0) cc_final: 0.7215 (mt0) REVERT: N 87 MET cc_start: 0.7854 (mmp) cc_final: 0.7652 (mmp) REVERT: N 106 ASP cc_start: 0.7311 (t70) cc_final: 0.6932 (t0) REVERT: O 47 GLU cc_start: 0.6165 (mt-10) cc_final: 0.5248 (tm-30) REVERT: O 67 ILE cc_start: 0.4030 (pt) cc_final: 0.3164 (pt) REVERT: P 29 THR cc_start: 0.8591 (p) cc_final: 0.8360 (p) REVERT: Q 80 LEU cc_start: 0.8002 (mp) cc_final: 0.7776 (tt) REVERT: Q 88 ASP cc_start: 0.7114 (t70) cc_final: 0.6857 (t0) REVERT: R 41 ASP cc_start: 0.7594 (t0) cc_final: 0.7382 (t0) REVERT: R 102 LYS cc_start: 0.6269 (tttt) cc_final: 0.5762 (tttt) REVERT: T 86 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8623 (pp) REVERT: U 52 LEU cc_start: 0.8046 (tt) cc_final: 0.7795 (tt) REVERT: V 60 ILE cc_start: 0.8761 (pt) cc_final: 0.8206 (pt) REVERT: V 72 TRP cc_start: 0.6177 (m100) cc_final: 0.5822 (m100) REVERT: X 40 PHE cc_start: 0.6455 (m-10) cc_final: 0.5840 (m-10) REVERT: X 43 MET cc_start: 0.7200 (mtm) cc_final: 0.6751 (mtm) REVERT: 8 10 TYR cc_start: 0.7039 (m-80) cc_final: 0.6773 (m-10) REVERT: 8 234 MET cc_start: 0.6520 (tpt) cc_final: 0.6149 (tmm) REVERT: 8 241 GLU cc_start: 0.5524 (tt0) cc_final: 0.5173 (pt0) REVERT: 8 340 SER cc_start: 0.7886 (OUTLIER) cc_final: 0.7416 (p) REVERT: 8 408 ARG cc_start: 0.4800 (tpt-90) cc_final: 0.4049 (mtt90) REVERT: 8 474 LYS cc_start: 0.7459 (tptp) cc_final: 0.7242 (tptp) REVERT: 8 485 LYS cc_start: 0.8462 (mttm) cc_final: 0.8169 (mmmt) REVERT: 8 663 MET cc_start: 0.8050 (mmm) cc_final: 0.7804 (mmm) outliers start: 226 outliers final: 137 residues processed: 1160 average time/residue: 1.2975 time to fit residues: 2669.0387 Evaluate side-chains 978 residues out of total 5429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 831 time to evaluate : 6.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 37 SER Chi-restraints excluded: chain b residue 119 VAL Chi-restraints excluded: chain b residue 224 MET Chi-restraints excluded: chain b residue 235 GLU Chi-restraints excluded: chain b residue 244 VAL Chi-restraints excluded: chain b residue 262 THR Chi-restraints excluded: chain b residue 266 ILE Chi-restraints excluded: chain c residue 95 SER Chi-restraints excluded: chain c residue 176 ASP Chi-restraints excluded: chain c residue 180 VAL Chi-restraints excluded: chain c residue 186 LEU Chi-restraints excluded: chain c residue 188 LEU Chi-restraints excluded: chain c residue 197 THR Chi-restraints excluded: chain d residue 77 ILE Chi-restraints excluded: chain d residue 120 VAL Chi-restraints excluded: chain d residue 138 LEU Chi-restraints excluded: chain d residue 149 ILE Chi-restraints excluded: chain e residue 16 MET Chi-restraints excluded: chain e residue 24 VAL Chi-restraints excluded: chain e residue 93 GLU Chi-restraints excluded: chain e residue 146 ASP Chi-restraints excluded: chain f residue 9 VAL Chi-restraints excluded: chain f residue 75 VAL Chi-restraints excluded: chain i residue 12 VAL Chi-restraints excluded: chain i residue 70 THR Chi-restraints excluded: chain j residue 31 GLU Chi-restraints excluded: chain j residue 57 LEU Chi-restraints excluded: chain j residue 62 VAL Chi-restraints excluded: chain j residue 84 ILE Chi-restraints excluded: chain j residue 128 ASN Chi-restraints excluded: chain k residue 56 ASP Chi-restraints excluded: chain k residue 73 ASP Chi-restraints excluded: chain k residue 90 ASN Chi-restraints excluded: chain k residue 107 LEU Chi-restraints excluded: chain m residue 41 LEU Chi-restraints excluded: chain m residue 42 THR Chi-restraints excluded: chain m residue 45 GLN Chi-restraints excluded: chain m residue 60 GLN Chi-restraints excluded: chain m residue 70 ASP Chi-restraints excluded: chain m residue 88 ASN Chi-restraints excluded: chain m residue 91 TYR Chi-restraints excluded: chain m residue 126 ILE Chi-restraints excluded: chain n residue 2 ARG Chi-restraints excluded: chain n residue 29 VAL Chi-restraints excluded: chain n residue 33 ILE Chi-restraints excluded: chain n residue 37 THR Chi-restraints excluded: chain n residue 51 LEU Chi-restraints excluded: chain n residue 54 LEU Chi-restraints excluded: chain n residue 113 ILE Chi-restraints excluded: chain o residue 35 ILE Chi-restraints excluded: chain o residue 47 VAL Chi-restraints excluded: chain o residue 62 LEU Chi-restraints excluded: chain p residue 40 GLN Chi-restraints excluded: chain p residue 47 ILE Chi-restraints excluded: chain p residue 84 SER Chi-restraints excluded: chain p residue 96 LEU Chi-restraints excluded: chain p residue 105 LYS Chi-restraints excluded: chain q residue 86 SER Chi-restraints excluded: chain q residue 106 THR Chi-restraints excluded: chain q residue 109 VAL Chi-restraints excluded: chain r residue 43 ASN Chi-restraints excluded: chain r residue 101 ILE Chi-restraints excluded: chain s residue 3 THR Chi-restraints excluded: chain u residue 27 VAL Chi-restraints excluded: chain u residue 59 GLU Chi-restraints excluded: chain u residue 67 SER Chi-restraints excluded: chain u residue 71 ILE Chi-restraints excluded: chain u residue 99 SER Chi-restraints excluded: chain v residue 5 ASN Chi-restraints excluded: chain v residue 24 ASN Chi-restraints excluded: chain v residue 61 LEU Chi-restraints excluded: chain v residue 65 VAL Chi-restraints excluded: chain v residue 86 LEU Chi-restraints excluded: chain w residue 34 VAL Chi-restraints excluded: chain w residue 63 VAL Chi-restraints excluded: chain x residue 76 LYS Chi-restraints excluded: chain z residue 56 VAL Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain G residue 86 CYS Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 191 ASP Chi-restraints excluded: chain H residue 30 ASP Chi-restraints excluded: chain H residue 84 GLU Chi-restraints excluded: chain H residue 164 THR Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain H residue 191 THR Chi-restraints excluded: chain I residue 19 PHE Chi-restraints excluded: chain I residue 49 ASP Chi-restraints excluded: chain I residue 98 ASP Chi-restraints excluded: chain I residue 170 LEU Chi-restraints excluded: chain I residue 194 ILE Chi-restraints excluded: chain J residue 35 LEU Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 79 THR Chi-restraints excluded: chain J residue 104 ILE Chi-restraints excluded: chain J residue 123 LEU Chi-restraints excluded: chain K residue 13 ASP Chi-restraints excluded: chain K residue 55 HIS Chi-restraints excluded: chain K residue 60 VAL Chi-restraints excluded: chain K residue 96 VAL Chi-restraints excluded: chain M residue 6 ILE Chi-restraints excluded: chain N residue 8 THR Chi-restraints excluded: chain N residue 38 PHE Chi-restraints excluded: chain N residue 54 VAL Chi-restraints excluded: chain N residue 65 THR Chi-restraints excluded: chain N residue 93 LEU Chi-restraints excluded: chain O residue 66 GLU Chi-restraints excluded: chain P residue 30 ILE Chi-restraints excluded: chain P residue 95 THR Chi-restraints excluded: chain Q residue 66 ILE Chi-restraints excluded: chain Q residue 96 THR Chi-restraints excluded: chain Q residue 118 VAL Chi-restraints excluded: chain R residue 8 ILE Chi-restraints excluded: chain R residue 64 VAL Chi-restraints excluded: chain R residue 84 CYS Chi-restraints excluded: chain S residue 37 ASP Chi-restraints excluded: chain S residue 50 LEU Chi-restraints excluded: chain T residue 86 LEU Chi-restraints excluded: chain W residue 25 ILE Chi-restraints excluded: chain W residue 33 THR Chi-restraints excluded: chain W residue 58 ILE Chi-restraints excluded: chain X residue 39 ILE Chi-restraints excluded: chain X residue 47 THR Chi-restraints excluded: chain Y residue 11 ILE Chi-restraints excluded: chain Y residue 19 HIS Chi-restraints excluded: chain Y residue 57 VAL Chi-restraints excluded: chain Z residue 12 ASP Chi-restraints excluded: chain Z residue 59 LEU Chi-restraints excluded: chain 8 residue 86 ILE Chi-restraints excluded: chain 8 residue 96 THR Chi-restraints excluded: chain 8 residue 126 VAL Chi-restraints excluded: chain 8 residue 182 VAL Chi-restraints excluded: chain 8 residue 264 VAL Chi-restraints excluded: chain 8 residue 266 CYS Chi-restraints excluded: chain 8 residue 278 MET Chi-restraints excluded: chain 8 residue 292 VAL Chi-restraints excluded: chain 8 residue 298 ILE Chi-restraints excluded: chain 8 residue 340 SER Chi-restraints excluded: chain 8 residue 494 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1109 random chunks: chunk 559 optimal weight: 30.0000 chunk 312 optimal weight: 9.9990 chunk 838 optimal weight: 20.0000 chunk 685 optimal weight: 50.0000 chunk 277 optimal weight: 5.9990 chunk 1008 optimal weight: 20.0000 chunk 1089 optimal weight: 8.9990 chunk 898 optimal weight: 20.0000 chunk 1000 optimal weight: 10.0000 chunk 343 optimal weight: 30.0000 chunk 809 optimal weight: 20.0000 overall best weight: 10.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 49 GLN ** c 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 150 GLN d 46 GLN ** d 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 163 ASN e 80 GLN g 135 HIS ** k 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 61 GLN ** o 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 55 GLN r 18 GLN ** r 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 31 GLN ** A 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 3 GLN ** B 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 37 GLN G 17 HIS ** H 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 135 GLN J 11 GLN ** J 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 88 HIS L 51 GLN L 85 GLN L 96 ASN ** M 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 36 GLN ** P 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 99 GLN ** S 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 172 HIS ** 8 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 258 ASN ** 8 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 455 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.2627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.116 166269 Z= 0.384 Angle : 0.789 13.979 247957 Z= 0.405 Chirality : 0.044 0.347 31576 Planarity : 0.006 0.088 13872 Dihedral : 23.434 179.106 81278 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 19.95 Ramachandran Plot: Outliers : 0.35 % Allowed : 14.06 % Favored : 85.59 % Rotamer: Outliers : 6.00 % Allowed : 16.89 % Favored : 77.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -3.26 (0.09), residues: 6517 helix: -1.18 (0.11), residues: 2007 sheet: -2.21 (0.14), residues: 1145 loop : -2.82 (0.10), residues: 3365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP H 200 HIS 0.012 0.002 HIS a 67 PHE 0.024 0.003 PHE R 62 TYR 0.037 0.003 TYR H 167 ARG 0.011 0.001 ARG Y 73 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13034 Ramachandran restraints generated. 6517 Oldfield, 0 Emsley, 6517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13034 Ramachandran restraints generated. 6517 Oldfield, 0 Emsley, 6517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1217 residues out of total 5429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 326 poor density : 891 time to evaluate : 6.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 86 ARG cc_start: 0.8349 (OUTLIER) cc_final: 0.7397 (mtm-85) REVERT: e 6 TYR cc_start: 0.8779 (t80) cc_final: 0.8446 (t80) REVERT: e 93 GLU cc_start: 0.8638 (OUTLIER) cc_final: 0.8232 (pp20) REVERT: h 1 MET cc_start: 0.3500 (tpt) cc_final: 0.3245 (tpt) REVERT: j 55 ILE cc_start: 0.9103 (mt) cc_final: 0.8695 (tt) REVERT: l 38 GLN cc_start: 0.8209 (tm-30) cc_final: 0.7899 (tm-30) REVERT: l 121 THR cc_start: 0.7481 (m) cc_final: 0.7276 (p) REVERT: m 60 GLN cc_start: 0.7627 (OUTLIER) cc_final: 0.6217 (pp30) REVERT: m 102 LEU cc_start: 0.9352 (mt) cc_final: 0.9122 (mt) REVERT: o 93 ASP cc_start: 0.6877 (t0) cc_final: 0.6575 (t0) REVERT: p 26 GLU cc_start: 0.7704 (tm-30) cc_final: 0.7026 (tm-30) REVERT: p 105 LYS cc_start: 0.8491 (OUTLIER) cc_final: 0.8210 (mmtm) REVERT: q 73 ILE cc_start: 0.8850 (tp) cc_final: 0.8580 (tp) REVERT: q 94 LEU cc_start: 0.9137 (mt) cc_final: 0.8762 (mt) REVERT: u 59 GLU cc_start: 0.6987 (OUTLIER) cc_final: 0.6612 (tp30) REVERT: x 19 HIS cc_start: 0.8420 (OUTLIER) cc_final: 0.7964 (t70) REVERT: x 73 ARG cc_start: 0.8474 (ttp80) cc_final: 0.7730 (mtp180) REVERT: A 3 LYS cc_start: 0.8170 (mttt) cc_final: 0.7915 (tptp) REVERT: A 8 LYS cc_start: 0.7317 (tmmt) cc_final: 0.6963 (tmtt) REVERT: C 6 GLU cc_start: 0.7699 (pt0) cc_final: 0.6374 (pm20) REVERT: C 9 LYS cc_start: 0.7265 (tttp) cc_final: 0.6926 (ttmt) REVERT: C 48 TYR cc_start: 0.6281 (m-80) cc_final: 0.5983 (m-80) REVERT: F 37 GLN cc_start: 0.8384 (mm110) cc_final: 0.8171 (tp40) REVERT: G 22 TRP cc_start: 0.8349 (p-90) cc_final: 0.8019 (p-90) REVERT: G 58 LYS cc_start: 0.9296 (mmtp) cc_final: 0.8762 (tptp) REVERT: G 173 LYS cc_start: 0.8501 (ttmt) cc_final: 0.7554 (tmtt) REVERT: G 191 ASP cc_start: 0.8658 (OUTLIER) cc_final: 0.8314 (t0) REVERT: G 196 ASP cc_start: 0.7720 (OUTLIER) cc_final: 0.7438 (m-30) REVERT: G 224 ARG cc_start: 0.8660 (mmm160) cc_final: 0.7804 (mmm-85) REVERT: H 5 HIS cc_start: 0.7264 (t-90) cc_final: 0.6151 (t-90) REVERT: H 34 SER cc_start: 0.8208 (m) cc_final: 0.7932 (p) REVERT: H 40 GLN cc_start: 0.8234 (tp-100) cc_final: 0.7714 (pt0) REVERT: H 104 GLU cc_start: 0.6434 (OUTLIER) cc_final: 0.5897 (tm-30) REVERT: H 128 MET cc_start: 0.6125 (mtp) cc_final: 0.5859 (mtt) REVERT: H 133 MET cc_start: 0.7750 (ttt) cc_final: 0.7213 (ttt) REVERT: H 182 ASP cc_start: 0.7412 (t0) cc_final: 0.6786 (t0) REVERT: H 183 TYR cc_start: 0.6918 (t80) cc_final: 0.6697 (t80) REVERT: I 3 TYR cc_start: 0.7232 (t80) cc_final: 0.6641 (t80) REVERT: I 63 ILE cc_start: 0.8636 (mt) cc_final: 0.8349 (mt) REVERT: J 82 HIS cc_start: 0.8510 (OUTLIER) cc_final: 0.7787 (p90) REVERT: J 115 GLU cc_start: 0.8180 (pt0) cc_final: 0.7823 (pt0) REVERT: K 21 MET cc_start: 0.8367 (mpp) cc_final: 0.8073 (mpp) REVERT: K 55 HIS cc_start: 0.8184 (OUTLIER) cc_final: 0.7454 (p-80) REVERT: K 73 GLU cc_start: 0.8396 (mm-30) cc_final: 0.8174 (mm-30) REVERT: L 48 THR cc_start: 0.6837 (m) cc_final: 0.6620 (m) REVERT: M 8 ASP cc_start: 0.8237 (t70) cc_final: 0.7838 (t0) REVERT: M 11 THR cc_start: 0.9249 (m) cc_final: 0.8967 (p) REVERT: M 72 GLU cc_start: 0.7719 (tp30) cc_final: 0.7316 (tt0) REVERT: M 95 MET cc_start: 0.7614 (tpp) cc_final: 0.7363 (tpp) REVERT: N 52 GLU cc_start: 0.6982 (pm20) cc_final: 0.6335 (pp20) REVERT: N 106 ASP cc_start: 0.7532 (t70) cc_final: 0.7145 (t0) REVERT: O 47 GLU cc_start: 0.6173 (mt-10) cc_final: 0.5258 (tm-30) REVERT: O 67 ILE cc_start: 0.4250 (pt) cc_final: 0.3414 (pt) REVERT: O 71 LEU cc_start: 0.8091 (pt) cc_final: 0.7829 (pp) REVERT: P 29 THR cc_start: 0.8286 (p) cc_final: 0.8054 (p) REVERT: Q 88 ASP cc_start: 0.7221 (t70) cc_final: 0.6969 (t0) REVERT: R 41 ASP cc_start: 0.8079 (t0) cc_final: 0.7864 (t0) REVERT: R 102 LYS cc_start: 0.6314 (tttt) cc_final: 0.5832 (tttt) REVERT: U 1 MET cc_start: 0.3275 (tmm) cc_final: 0.2211 (tmm) REVERT: U 39 PHE cc_start: 0.8210 (OUTLIER) cc_final: 0.7910 (t80) REVERT: V 60 ILE cc_start: 0.8894 (pt) cc_final: 0.8228 (pt) REVERT: V 72 TRP cc_start: 0.6179 (m100) cc_final: 0.5730 (m100) REVERT: V 80 LYS cc_start: 0.6607 (tttm) cc_final: 0.6097 (ttpp) REVERT: W 42 ARG cc_start: 0.6930 (OUTLIER) cc_final: 0.6671 (ptp-170) REVERT: W 43 ILE cc_start: 0.8068 (mm) cc_final: 0.7840 (mp) REVERT: X 40 PHE cc_start: 0.6549 (m-10) cc_final: 0.5928 (m-10) REVERT: X 43 MET cc_start: 0.7429 (mtm) cc_final: 0.6806 (mtm) REVERT: 8 10 TYR cc_start: 0.6869 (m-80) cc_final: 0.6111 (m-10) REVERT: 8 234 MET cc_start: 0.6399 (tpt) cc_final: 0.6074 (tmm) REVERT: 8 241 GLU cc_start: 0.6084 (tt0) cc_final: 0.5555 (pt0) REVERT: 8 278 MET cc_start: 0.6599 (OUTLIER) cc_final: 0.6082 (ptm) REVERT: 8 474 LYS cc_start: 0.7516 (tptp) cc_final: 0.7235 (tptp) REVERT: 8 485 LYS cc_start: 0.8482 (mttm) cc_final: 0.8199 (mmmt) REVERT: 8 663 MET cc_start: 0.8099 (mmm) cc_final: 0.7337 (mmm) outliers start: 326 outliers final: 209 residues processed: 1124 average time/residue: 1.2438 time to fit residues: 2493.2664 Evaluate side-chains 1029 residues out of total 5429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 223 poor density : 806 time to evaluate : 6.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 86 ARG Chi-restraints excluded: chain b residue 114 GLN Chi-restraints excluded: chain b residue 119 VAL Chi-restraints excluded: chain b residue 224 MET Chi-restraints excluded: chain b residue 244 VAL Chi-restraints excluded: chain b residue 262 THR Chi-restraints excluded: chain b residue 266 ILE Chi-restraints excluded: chain c residue 1 MET Chi-restraints excluded: chain c residue 131 ASP Chi-restraints excluded: chain c residue 150 GLN Chi-restraints excluded: chain c residue 176 ASP Chi-restraints excluded: chain c residue 180 VAL Chi-restraints excluded: chain c residue 188 LEU Chi-restraints excluded: chain c residue 197 THR Chi-restraints excluded: chain d residue 77 ILE Chi-restraints excluded: chain d residue 120 VAL Chi-restraints excluded: chain d residue 149 ILE Chi-restraints excluded: chain d residue 150 THR Chi-restraints excluded: chain d residue 180 LEU Chi-restraints excluded: chain e residue 16 MET Chi-restraints excluded: chain e residue 24 VAL Chi-restraints excluded: chain e residue 30 VAL Chi-restraints excluded: chain e residue 93 GLU Chi-restraints excluded: chain e residue 112 ASP Chi-restraints excluded: chain e residue 126 ASN Chi-restraints excluded: chain e residue 131 VAL Chi-restraints excluded: chain e residue 134 GLN Chi-restraints excluded: chain f residue 9 VAL Chi-restraints excluded: chain f residue 78 VAL Chi-restraints excluded: chain f residue 165 ASP Chi-restraints excluded: chain i residue 48 ILE Chi-restraints excluded: chain i residue 54 ILE Chi-restraints excluded: chain i residue 70 THR Chi-restraints excluded: chain j residue 57 LEU Chi-restraints excluded: chain j residue 62 VAL Chi-restraints excluded: chain k residue 51 LYS Chi-restraints excluded: chain k residue 56 ASP Chi-restraints excluded: chain k residue 73 ASP Chi-restraints excluded: chain k residue 85 VAL Chi-restraints excluded: chain k residue 90 ASN Chi-restraints excluded: chain k residue 107 LEU Chi-restraints excluded: chain k residue 111 LYS Chi-restraints excluded: chain l residue 103 ILE Chi-restraints excluded: chain m residue 7 THR Chi-restraints excluded: chain m residue 41 LEU Chi-restraints excluded: chain m residue 42 THR Chi-restraints excluded: chain m residue 60 GLN Chi-restraints excluded: chain m residue 70 ASP Chi-restraints excluded: chain m residue 75 GLU Chi-restraints excluded: chain m residue 78 LEU Chi-restraints excluded: chain m residue 88 ASN Chi-restraints excluded: chain m residue 91 TYR Chi-restraints excluded: chain m residue 124 LEU Chi-restraints excluded: chain m residue 126 ILE Chi-restraints excluded: chain m residue 129 THR Chi-restraints excluded: chain n residue 2 ARG Chi-restraints excluded: chain n residue 33 ILE Chi-restraints excluded: chain n residue 34 ILE Chi-restraints excluded: chain n residue 37 THR Chi-restraints excluded: chain n residue 51 LEU Chi-restraints excluded: chain n residue 54 LEU Chi-restraints excluded: chain o residue 35 ILE Chi-restraints excluded: chain o residue 47 VAL Chi-restraints excluded: chain o residue 52 SER Chi-restraints excluded: chain o residue 62 LEU Chi-restraints excluded: chain o residue 108 ASP Chi-restraints excluded: chain p residue 40 GLN Chi-restraints excluded: chain p residue 47 ILE Chi-restraints excluded: chain p residue 84 SER Chi-restraints excluded: chain p residue 96 LEU Chi-restraints excluded: chain p residue 103 THR Chi-restraints excluded: chain p residue 105 LYS Chi-restraints excluded: chain q residue 7 VAL Chi-restraints excluded: chain q residue 99 VAL Chi-restraints excluded: chain q residue 106 THR Chi-restraints excluded: chain q residue 109 VAL Chi-restraints excluded: chain r residue 26 ASP Chi-restraints excluded: chain r residue 101 ILE Chi-restraints excluded: chain s residue 3 THR Chi-restraints excluded: chain s residue 76 VAL Chi-restraints excluded: chain s residue 105 VAL Chi-restraints excluded: chain t residue 32 LEU Chi-restraints excluded: chain t residue 93 LEU Chi-restraints excluded: chain u residue 27 VAL Chi-restraints excluded: chain u residue 59 GLU Chi-restraints excluded: chain u residue 67 SER Chi-restraints excluded: chain u residue 69 VAL Chi-restraints excluded: chain u residue 71 ILE Chi-restraints excluded: chain u residue 88 ASP Chi-restraints excluded: chain u residue 99 SER Chi-restraints excluded: chain v residue 5 ASN Chi-restraints excluded: chain v residue 40 ILE Chi-restraints excluded: chain v residue 61 LEU Chi-restraints excluded: chain v residue 65 VAL Chi-restraints excluded: chain v residue 76 ASP Chi-restraints excluded: chain v residue 86 LEU Chi-restraints excluded: chain w residue 34 VAL Chi-restraints excluded: chain w residue 63 VAL Chi-restraints excluded: chain x residue 12 VAL Chi-restraints excluded: chain x residue 19 HIS Chi-restraints excluded: chain x residue 47 THR Chi-restraints excluded: chain x residue 76 LYS Chi-restraints excluded: chain z residue 56 VAL Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 37 LYS Chi-restraints excluded: chain C residue 50 GLU Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 60 CYS Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 23 ILE Chi-restraints excluded: chain G residue 86 CYS Chi-restraints excluded: chain G residue 169 HIS Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 191 ASP Chi-restraints excluded: chain G residue 196 ASP Chi-restraints excluded: chain H residue 7 ASN Chi-restraints excluded: chain H residue 30 ASP Chi-restraints excluded: chain H residue 84 GLU Chi-restraints excluded: chain H residue 104 GLU Chi-restraints excluded: chain H residue 164 THR Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain H residue 194 VAL Chi-restraints excluded: chain I residue 19 PHE Chi-restraints excluded: chain I residue 72 ARG Chi-restraints excluded: chain I residue 97 LEU Chi-restraints excluded: chain I residue 98 ASP Chi-restraints excluded: chain I residue 125 ASN Chi-restraints excluded: chain I residue 170 LEU Chi-restraints excluded: chain I residue 191 SER Chi-restraints excluded: chain I residue 194 ILE Chi-restraints excluded: chain J residue 35 LEU Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 38 VAL Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 61 LYS Chi-restraints excluded: chain J residue 79 THR Chi-restraints excluded: chain J residue 82 HIS Chi-restraints excluded: chain J residue 104 ILE Chi-restraints excluded: chain J residue 120 HIS Chi-restraints excluded: chain J residue 123 LEU Chi-restraints excluded: chain J residue 141 ASP Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 55 HIS Chi-restraints excluded: chain K residue 60 VAL Chi-restraints excluded: chain K residue 85 ILE Chi-restraints excluded: chain K residue 93 LYS Chi-restraints excluded: chain K residue 96 VAL Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain L residue 84 TYR Chi-restraints excluded: chain M residue 6 ILE Chi-restraints excluded: chain M residue 62 LEU Chi-restraints excluded: chain N residue 8 THR Chi-restraints excluded: chain N residue 27 ILE Chi-restraints excluded: chain N residue 38 PHE Chi-restraints excluded: chain N residue 42 THR Chi-restraints excluded: chain N residue 54 VAL Chi-restraints excluded: chain N residue 93 LEU Chi-restraints excluded: chain O residue 19 ASP Chi-restraints excluded: chain O residue 66 GLU Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain P residue 30 ILE Chi-restraints excluded: chain P residue 78 ILE Chi-restraints excluded: chain P residue 95 THR Chi-restraints excluded: chain Q residue 20 VAL Chi-restraints excluded: chain Q residue 52 CYS Chi-restraints excluded: chain Q residue 66 ILE Chi-restraints excluded: chain Q residue 82 ARG Chi-restraints excluded: chain Q residue 96 THR Chi-restraints excluded: chain Q residue 118 VAL Chi-restraints excluded: chain R residue 15 VAL Chi-restraints excluded: chain S residue 37 ASP Chi-restraints excluded: chain S residue 44 VAL Chi-restraints excluded: chain S residue 50 LEU Chi-restraints excluded: chain S residue 78 LEU Chi-restraints excluded: chain U residue 39 PHE Chi-restraints excluded: chain V residue 57 VAL Chi-restraints excluded: chain W residue 25 ILE Chi-restraints excluded: chain W residue 33 THR Chi-restraints excluded: chain W residue 42 ARG Chi-restraints excluded: chain X residue 14 LEU Chi-restraints excluded: chain X residue 39 ILE Chi-restraints excluded: chain X residue 47 THR Chi-restraints excluded: chain Y residue 11 ILE Chi-restraints excluded: chain Y residue 19 HIS Chi-restraints excluded: chain Y residue 25 SER Chi-restraints excluded: chain Y residue 31 ILE Chi-restraints excluded: chain Y residue 39 GLU Chi-restraints excluded: chain Y residue 57 VAL Chi-restraints excluded: chain Z residue 12 ASP Chi-restraints excluded: chain Z residue 18 PHE Chi-restraints excluded: chain Z residue 59 LEU Chi-restraints excluded: chain a residue 21 TYR Chi-restraints excluded: chain a residue 174 THR Chi-restraints excluded: chain 8 residue 24 THR Chi-restraints excluded: chain 8 residue 86 ILE Chi-restraints excluded: chain 8 residue 96 THR Chi-restraints excluded: chain 8 residue 105 VAL Chi-restraints excluded: chain 8 residue 110 VAL Chi-restraints excluded: chain 8 residue 112 VAL Chi-restraints excluded: chain 8 residue 126 VAL Chi-restraints excluded: chain 8 residue 167 VAL Chi-restraints excluded: chain 8 residue 182 VAL Chi-restraints excluded: chain 8 residue 184 ASP Chi-restraints excluded: chain 8 residue 186 VAL Chi-restraints excluded: chain 8 residue 201 THR Chi-restraints excluded: chain 8 residue 264 VAL Chi-restraints excluded: chain 8 residue 266 CYS Chi-restraints excluded: chain 8 residue 278 MET Chi-restraints excluded: chain 8 residue 298 ILE Chi-restraints excluded: chain 8 residue 300 ASP Chi-restraints excluded: chain 8 residue 374 ILE Chi-restraints excluded: chain 8 residue 488 VAL Chi-restraints excluded: chain 8 residue 494 ILE Chi-restraints excluded: chain 8 residue 530 ASN Chi-restraints excluded: chain 8 residue 571 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1109 random chunks: chunk 996 optimal weight: 10.0000 chunk 758 optimal weight: 20.0000 chunk 523 optimal weight: 30.0000 chunk 111 optimal weight: 30.0000 chunk 481 optimal weight: 4.9990 chunk 677 optimal weight: 30.0000 chunk 1012 optimal weight: 20.0000 chunk 1071 optimal weight: 30.0000 chunk 529 optimal weight: 10.0000 chunk 959 optimal weight: 10.0000 chunk 288 optimal weight: 9.9990 overall best weight: 8.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 46 GLN ** d 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 43 ASN ** r 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 29 GLN G 17 HIS ** I 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 11 GLN ** J 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 37 ASN N 36 GLN ** O 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 142 ASN ** 8 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.2978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 166269 Z= 0.316 Angle : 0.718 14.767 247957 Z= 0.369 Chirality : 0.041 0.341 31576 Planarity : 0.005 0.073 13872 Dihedral : 23.486 177.974 81271 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 18.46 Ramachandran Plot: Outliers : 0.31 % Allowed : 12.55 % Favored : 87.14 % Rotamer: Outliers : 5.62 % Allowed : 19.17 % Favored : 75.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -3.03 (0.10), residues: 6517 helix: -0.94 (0.11), residues: 2016 sheet: -2.19 (0.14), residues: 1105 loop : -2.67 (0.10), residues: 3396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP L 102 HIS 0.007 0.001 HIS V 30 PHE 0.047 0.002 PHE M 48 TYR 0.024 0.002 TYR I 75 ARG 0.009 0.001 ARG d 21 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13034 Ramachandran restraints generated. 6517 Oldfield, 0 Emsley, 6517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13034 Ramachandran restraints generated. 6517 Oldfield, 0 Emsley, 6517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1183 residues out of total 5429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 305 poor density : 878 time to evaluate : 6.642 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: d 189 THR cc_start: 0.8961 (OUTLIER) cc_final: 0.8683 (p) REVERT: e 93 GLU cc_start: 0.8583 (OUTLIER) cc_final: 0.8209 (pp20) REVERT: j 31 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.7524 (mp0) REVERT: j 92 MET cc_start: 0.8273 (mtp) cc_final: 0.8008 (mtt) REVERT: k 1 MET cc_start: 0.8119 (ttm) cc_final: 0.7867 (ttp) REVERT: k 111 LYS cc_start: 0.7396 (OUTLIER) cc_final: 0.7018 (tptm) REVERT: l 111 ILE cc_start: 0.8939 (mp) cc_final: 0.8418 (tt) REVERT: l 121 THR cc_start: 0.7537 (m) cc_final: 0.7251 (p) REVERT: m 45 GLN cc_start: 0.7743 (OUTLIER) cc_final: 0.7476 (mm-40) REVERT: m 60 GLN cc_start: 0.7586 (OUTLIER) cc_final: 0.6219 (pp30) REVERT: m 102 LEU cc_start: 0.9341 (mt) cc_final: 0.9119 (mt) REVERT: n 72 ASP cc_start: 0.7348 (t0) cc_final: 0.6939 (t70) REVERT: n 73 ASN cc_start: 0.7117 (p0) cc_final: 0.6863 (p0) REVERT: o 93 ASP cc_start: 0.6863 (t0) cc_final: 0.6512 (t0) REVERT: q 73 ILE cc_start: 0.8818 (tp) cc_final: 0.8554 (tp) REVERT: q 94 LEU cc_start: 0.9063 (mt) cc_final: 0.8585 (mp) REVERT: r 48 LYS cc_start: 0.7460 (mtpt) cc_final: 0.7162 (mtpt) REVERT: t 61 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8628 (pp) REVERT: x 55 MET cc_start: 0.8291 (mpp) cc_final: 0.7921 (mtm) REVERT: x 73 ARG cc_start: 0.8398 (ttp80) cc_final: 0.7747 (mtp180) REVERT: y 7 ARG cc_start: 0.8515 (ptm160) cc_final: 0.8252 (ptm160) REVERT: A 3 LYS cc_start: 0.8045 (mttt) cc_final: 0.7826 (tptp) REVERT: A 8 LYS cc_start: 0.7292 (tmmt) cc_final: 0.7044 (tmtt) REVERT: A 9 TYR cc_start: 0.6626 (m-80) cc_final: 0.6390 (m-80) REVERT: C 6 GLU cc_start: 0.7662 (pt0) cc_final: 0.6371 (pm20) REVERT: C 9 LYS cc_start: 0.7342 (tttp) cc_final: 0.7090 (ttmt) REVERT: G 22 TRP cc_start: 0.8328 (p-90) cc_final: 0.8010 (p-90) REVERT: G 58 LYS cc_start: 0.9257 (mmtp) cc_final: 0.8770 (tptp) REVERT: G 173 LYS cc_start: 0.8535 (ttmt) cc_final: 0.7570 (tmtt) REVERT: G 191 ASP cc_start: 0.8652 (OUTLIER) cc_final: 0.8400 (t0) REVERT: G 224 ARG cc_start: 0.8582 (mmm160) cc_final: 0.8148 (mmm160) REVERT: H 5 HIS cc_start: 0.7305 (t-90) cc_final: 0.6224 (t-90) REVERT: H 34 SER cc_start: 0.8220 (m) cc_final: 0.7970 (p) REVERT: H 40 GLN cc_start: 0.8211 (tp-100) cc_final: 0.7712 (pt0) REVERT: H 128 MET cc_start: 0.6151 (mtp) cc_final: 0.5866 (mtt) REVERT: H 133 MET cc_start: 0.7864 (ttt) cc_final: 0.7403 (ttt) REVERT: H 176 THR cc_start: 0.8022 (m) cc_final: 0.7795 (p) REVERT: H 182 ASP cc_start: 0.7448 (t0) cc_final: 0.6816 (t0) REVERT: I 3 TYR cc_start: 0.7327 (t80) cc_final: 0.6794 (t80) REVERT: I 63 ILE cc_start: 0.8589 (mt) cc_final: 0.8282 (mt) REVERT: J 37 VAL cc_start: 0.8754 (OUTLIER) cc_final: 0.8537 (p) REVERT: J 115 GLU cc_start: 0.8140 (pt0) cc_final: 0.7642 (pt0) REVERT: J 141 ASP cc_start: 0.8197 (m-30) cc_final: 0.7910 (p0) REVERT: K 21 MET cc_start: 0.8352 (mpp) cc_final: 0.8110 (mpp) REVERT: K 55 HIS cc_start: 0.8179 (OUTLIER) cc_final: 0.7468 (p-80) REVERT: K 73 GLU cc_start: 0.8291 (mm-30) cc_final: 0.8088 (mm-30) REVERT: L 102 TRP cc_start: 0.7891 (m-90) cc_final: 0.7461 (m-90) REVERT: L 138 GLU cc_start: 0.8567 (mp0) cc_final: 0.8289 (mp0) REVERT: M 8 ASP cc_start: 0.8187 (t70) cc_final: 0.7831 (t0) REVERT: M 11 THR cc_start: 0.9156 (OUTLIER) cc_final: 0.8912 (p) REVERT: M 26 MET cc_start: 0.4726 (ptm) cc_final: 0.4424 (ptm) REVERT: M 72 GLU cc_start: 0.7846 (tp30) cc_final: 0.7367 (tt0) REVERT: N 106 ASP cc_start: 0.7567 (t70) cc_final: 0.7177 (t0) REVERT: P 14 GLN cc_start: 0.8104 (mm-40) cc_final: 0.7895 (pp30) REVERT: P 29 THR cc_start: 0.8270 (p) cc_final: 0.8041 (p) REVERT: Q 88 ASP cc_start: 0.7653 (t70) cc_final: 0.7296 (t0) REVERT: U 1 MET cc_start: 0.3394 (tmm) cc_final: 0.2036 (tmm) REVERT: U 39 PHE cc_start: 0.8087 (OUTLIER) cc_final: 0.7802 (t80) REVERT: V 60 ILE cc_start: 0.8868 (pt) cc_final: 0.8291 (pt) REVERT: V 64 ARG cc_start: 0.7927 (ptt-90) cc_final: 0.7667 (ttp-170) REVERT: V 72 TRP cc_start: 0.6123 (m100) cc_final: 0.5638 (m100) REVERT: X 40 PHE cc_start: 0.6484 (m-10) cc_final: 0.5860 (m-10) REVERT: X 43 MET cc_start: 0.7510 (mtm) cc_final: 0.6892 (mtm) REVERT: 8 10 TYR cc_start: 0.6756 (m-80) cc_final: 0.5944 (m-10) REVERT: 8 204 TYR cc_start: 0.6022 (OUTLIER) cc_final: 0.5390 (p90) REVERT: 8 234 MET cc_start: 0.6467 (tpt) cc_final: 0.6062 (tmm) REVERT: 8 241 GLU cc_start: 0.6348 (tt0) cc_final: 0.5633 (pt0) REVERT: 8 278 MET cc_start: 0.6752 (OUTLIER) cc_final: 0.6255 (ptm) REVERT: 8 301 ASP cc_start: 0.3200 (OUTLIER) cc_final: 0.1242 (t0) REVERT: 8 474 LYS cc_start: 0.7411 (tptp) cc_final: 0.7154 (tptp) REVERT: 8 485 LYS cc_start: 0.8475 (mttm) cc_final: 0.8195 (mmmt) REVERT: 8 663 MET cc_start: 0.8164 (mmm) cc_final: 0.7463 (mmm) outliers start: 305 outliers final: 217 residues processed: 1091 average time/residue: 1.2451 time to fit residues: 2427.7627 Evaluate side-chains 1032 residues out of total 5429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 232 poor density : 800 time to evaluate : 6.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 119 VAL Chi-restraints excluded: chain b residue 203 VAL Chi-restraints excluded: chain b residue 224 MET Chi-restraints excluded: chain b residue 262 THR Chi-restraints excluded: chain b residue 266 ILE Chi-restraints excluded: chain c residue 2 ILE Chi-restraints excluded: chain c residue 60 VAL Chi-restraints excluded: chain c residue 131 ASP Chi-restraints excluded: chain c residue 146 ILE Chi-restraints excluded: chain c residue 161 MET Chi-restraints excluded: chain c residue 176 ASP Chi-restraints excluded: chain c residue 180 VAL Chi-restraints excluded: chain c residue 188 LEU Chi-restraints excluded: chain c residue 197 THR Chi-restraints excluded: chain d residue 77 ILE Chi-restraints excluded: chain d residue 108 ILE Chi-restraints excluded: chain d residue 120 VAL Chi-restraints excluded: chain d residue 180 LEU Chi-restraints excluded: chain d residue 189 THR Chi-restraints excluded: chain e residue 16 MET Chi-restraints excluded: chain e residue 24 VAL Chi-restraints excluded: chain e residue 30 VAL Chi-restraints excluded: chain e residue 56 LEU Chi-restraints excluded: chain e residue 93 GLU Chi-restraints excluded: chain e residue 126 ASN Chi-restraints excluded: chain e residue 131 VAL Chi-restraints excluded: chain e residue 146 ASP Chi-restraints excluded: chain f residue 9 VAL Chi-restraints excluded: chain f residue 75 VAL Chi-restraints excluded: chain f residue 78 VAL Chi-restraints excluded: chain f residue 165 ASP Chi-restraints excluded: chain i residue 12 VAL Chi-restraints excluded: chain i residue 48 ILE Chi-restraints excluded: chain i residue 70 THR Chi-restraints excluded: chain j residue 3 THR Chi-restraints excluded: chain j residue 31 GLU Chi-restraints excluded: chain j residue 57 LEU Chi-restraints excluded: chain j residue 62 VAL Chi-restraints excluded: chain j residue 84 ILE Chi-restraints excluded: chain j residue 90 GLU Chi-restraints excluded: chain k residue 51 LYS Chi-restraints excluded: chain k residue 56 ASP Chi-restraints excluded: chain k residue 73 ASP Chi-restraints excluded: chain k residue 90 ASN Chi-restraints excluded: chain k residue 107 LEU Chi-restraints excluded: chain k residue 111 LYS Chi-restraints excluded: chain m residue 7 THR Chi-restraints excluded: chain m residue 42 THR Chi-restraints excluded: chain m residue 45 GLN Chi-restraints excluded: chain m residue 60 GLN Chi-restraints excluded: chain m residue 70 ASP Chi-restraints excluded: chain m residue 75 GLU Chi-restraints excluded: chain m residue 78 LEU Chi-restraints excluded: chain m residue 88 ASN Chi-restraints excluded: chain m residue 91 TYR Chi-restraints excluded: chain m residue 124 LEU Chi-restraints excluded: chain m residue 126 ILE Chi-restraints excluded: chain m residue 132 THR Chi-restraints excluded: chain n residue 2 ARG Chi-restraints excluded: chain n residue 29 VAL Chi-restraints excluded: chain n residue 33 ILE Chi-restraints excluded: chain n residue 34 ILE Chi-restraints excluded: chain n residue 37 THR Chi-restraints excluded: chain n residue 51 LEU Chi-restraints excluded: chain n residue 54 LEU Chi-restraints excluded: chain o residue 35 ILE Chi-restraints excluded: chain o residue 47 VAL Chi-restraints excluded: chain o residue 62 LEU Chi-restraints excluded: chain p residue 40 GLN Chi-restraints excluded: chain p residue 47 ILE Chi-restraints excluded: chain p residue 79 VAL Chi-restraints excluded: chain p residue 84 SER Chi-restraints excluded: chain p residue 96 LEU Chi-restraints excluded: chain p residue 103 THR Chi-restraints excluded: chain p residue 105 LYS Chi-restraints excluded: chain p residue 109 ILE Chi-restraints excluded: chain q residue 7 VAL Chi-restraints excluded: chain q residue 106 THR Chi-restraints excluded: chain q residue 109 VAL Chi-restraints excluded: chain r residue 101 ILE Chi-restraints excluded: chain s residue 3 THR Chi-restraints excluded: chain s residue 76 VAL Chi-restraints excluded: chain s residue 105 VAL Chi-restraints excluded: chain t residue 24 MET Chi-restraints excluded: chain t residue 61 LEU Chi-restraints excluded: chain t residue 93 LEU Chi-restraints excluded: chain u residue 24 VAL Chi-restraints excluded: chain u residue 27 VAL Chi-restraints excluded: chain u residue 40 LEU Chi-restraints excluded: chain u residue 48 VAL Chi-restraints excluded: chain u residue 67 SER Chi-restraints excluded: chain u residue 71 ILE Chi-restraints excluded: chain u residue 88 ASP Chi-restraints excluded: chain v residue 5 ASN Chi-restraints excluded: chain v residue 40 ILE Chi-restraints excluded: chain v residue 61 LEU Chi-restraints excluded: chain v residue 65 VAL Chi-restraints excluded: chain w residue 34 VAL Chi-restraints excluded: chain w residue 63 VAL Chi-restraints excluded: chain x residue 47 THR Chi-restraints excluded: chain x residue 76 LYS Chi-restraints excluded: chain y residue 8 GLU Chi-restraints excluded: chain z residue 40 THR Chi-restraints excluded: chain z residue 56 VAL Chi-restraints excluded: chain A residue 30 HIS Chi-restraints excluded: chain A residue 33 ASN Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 58 ASP Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 50 GLU Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 60 CYS Chi-restraints excluded: chain F residue 23 ILE Chi-restraints excluded: chain G residue 86 CYS Chi-restraints excluded: chain G residue 169 HIS Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 191 ASP Chi-restraints excluded: chain G residue 203 ASP Chi-restraints excluded: chain H residue 4 VAL Chi-restraints excluded: chain H residue 30 ASP Chi-restraints excluded: chain H residue 164 THR Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain H residue 191 THR Chi-restraints excluded: chain H residue 194 VAL Chi-restraints excluded: chain H residue 197 VAL Chi-restraints excluded: chain I residue 19 PHE Chi-restraints excluded: chain I residue 49 ASP Chi-restraints excluded: chain I residue 97 LEU Chi-restraints excluded: chain I residue 98 ASP Chi-restraints excluded: chain I residue 170 LEU Chi-restraints excluded: chain I residue 194 ILE Chi-restraints excluded: chain J residue 35 LEU Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 38 VAL Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 61 LYS Chi-restraints excluded: chain J residue 104 ILE Chi-restraints excluded: chain J residue 120 HIS Chi-restraints excluded: chain J residue 123 LEU Chi-restraints excluded: chain K residue 11 HIS Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 55 HIS Chi-restraints excluded: chain K residue 60 VAL Chi-restraints excluded: chain K residue 93 LYS Chi-restraints excluded: chain K residue 96 VAL Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain L residue 84 TYR Chi-restraints excluded: chain L residue 93 VAL Chi-restraints excluded: chain M residue 6 ILE Chi-restraints excluded: chain M residue 11 THR Chi-restraints excluded: chain M residue 110 MET Chi-restraints excluded: chain N residue 8 THR Chi-restraints excluded: chain N residue 38 PHE Chi-restraints excluded: chain N residue 54 VAL Chi-restraints excluded: chain N residue 65 THR Chi-restraints excluded: chain N residue 83 THR Chi-restraints excluded: chain N residue 93 LEU Chi-restraints excluded: chain O residue 19 ASP Chi-restraints excluded: chain O residue 50 THR Chi-restraints excluded: chain O residue 66 GLU Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain O residue 83 THR Chi-restraints excluded: chain P residue 30 ILE Chi-restraints excluded: chain P residue 78 ILE Chi-restraints excluded: chain P residue 95 THR Chi-restraints excluded: chain Q residue 20 VAL Chi-restraints excluded: chain Q residue 39 THR Chi-restraints excluded: chain Q residue 42 LYS Chi-restraints excluded: chain Q residue 52 CYS Chi-restraints excluded: chain Q residue 61 GLU Chi-restraints excluded: chain Q residue 63 THR Chi-restraints excluded: chain Q residue 66 ILE Chi-restraints excluded: chain Q residue 96 THR Chi-restraints excluded: chain Q residue 118 VAL Chi-restraints excluded: chain R residue 13 HIS Chi-restraints excluded: chain R residue 15 VAL Chi-restraints excluded: chain R residue 18 LEU Chi-restraints excluded: chain R residue 64 VAL Chi-restraints excluded: chain S residue 37 ASP Chi-restraints excluded: chain S residue 44 VAL Chi-restraints excluded: chain T residue 74 VAL Chi-restraints excluded: chain U residue 39 PHE Chi-restraints excluded: chain U residue 57 ILE Chi-restraints excluded: chain U residue 75 ILE Chi-restraints excluded: chain V residue 50 ASN Chi-restraints excluded: chain W residue 25 ILE Chi-restraints excluded: chain W residue 33 THR Chi-restraints excluded: chain W residue 73 HIS Chi-restraints excluded: chain X residue 39 ILE Chi-restraints excluded: chain X residue 47 THR Chi-restraints excluded: chain X residue 66 VAL Chi-restraints excluded: chain Y residue 11 ILE Chi-restraints excluded: chain Y residue 19 HIS Chi-restraints excluded: chain Y residue 25 SER Chi-restraints excluded: chain Y residue 57 VAL Chi-restraints excluded: chain Z residue 12 ASP Chi-restraints excluded: chain Z residue 43 GLU Chi-restraints excluded: chain Z residue 59 LEU Chi-restraints excluded: chain a residue 21 TYR Chi-restraints excluded: chain a residue 24 ASN Chi-restraints excluded: chain a residue 174 THR Chi-restraints excluded: chain 8 residue 24 THR Chi-restraints excluded: chain 8 residue 86 ILE Chi-restraints excluded: chain 8 residue 96 THR Chi-restraints excluded: chain 8 residue 105 VAL Chi-restraints excluded: chain 8 residue 110 VAL Chi-restraints excluded: chain 8 residue 126 VAL Chi-restraints excluded: chain 8 residue 167 VAL Chi-restraints excluded: chain 8 residue 182 VAL Chi-restraints excluded: chain 8 residue 184 ASP Chi-restraints excluded: chain 8 residue 186 VAL Chi-restraints excluded: chain 8 residue 201 THR Chi-restraints excluded: chain 8 residue 204 TYR Chi-restraints excluded: chain 8 residue 264 VAL Chi-restraints excluded: chain 8 residue 266 CYS Chi-restraints excluded: chain 8 residue 278 MET Chi-restraints excluded: chain 8 residue 292 VAL Chi-restraints excluded: chain 8 residue 300 ASP Chi-restraints excluded: chain 8 residue 301 ASP Chi-restraints excluded: chain 8 residue 330 VAL Chi-restraints excluded: chain 8 residue 374 ILE Chi-restraints excluded: chain 8 residue 424 THR Chi-restraints excluded: chain 8 residue 494 ILE Chi-restraints excluded: chain 8 residue 571 VAL Chi-restraints excluded: chain 8 residue 585 ASP Chi-restraints excluded: chain 8 residue 622 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1109 random chunks: chunk 892 optimal weight: 10.0000 chunk 608 optimal weight: 30.0000 chunk 15 optimal weight: 10.0000 chunk 798 optimal weight: 10.0000 chunk 442 optimal weight: 20.0000 chunk 914 optimal weight: 10.0000 chunk 740 optimal weight: 20.0000 chunk 1 optimal weight: 5.9990 chunk 547 optimal weight: 6.9990 chunk 962 optimal weight: 20.0000 chunk 270 optimal weight: 5.9990 overall best weight: 7.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 30 GLN ** j 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 4 ASN ** n 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 43 ASN r 89 HIS ** u 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 31 GLN ** A 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 29 GLN G 17 HIS ** I 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 11 GLN ** J 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 37 ASN N 36 GLN O 15 HIS ** P 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 58 ASN ** a 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.3220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 166269 Z= 0.282 Angle : 0.687 13.945 247957 Z= 0.354 Chirality : 0.039 0.312 31576 Planarity : 0.005 0.075 13872 Dihedral : 23.499 177.527 81271 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 17.93 Ramachandran Plot: Outliers : 0.26 % Allowed : 13.03 % Favored : 86.71 % Rotamer: Outliers : 6.26 % Allowed : 19.95 % Favored : 73.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -2.86 (0.10), residues: 6517 helix: -0.75 (0.11), residues: 2033 sheet: -2.15 (0.14), residues: 1117 loop : -2.58 (0.10), residues: 3367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP L 102 HIS 0.007 0.001 HIS V 30 PHE 0.039 0.002 PHE K 78 TYR 0.021 0.002 TYR e 6 ARG 0.011 0.001 ARG q 54 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13034 Ramachandran restraints generated. 6517 Oldfield, 0 Emsley, 6517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13034 Ramachandran restraints generated. 6517 Oldfield, 0 Emsley, 6517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1204 residues out of total 5429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 340 poor density : 864 time to evaluate : 6.678 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: b 86 ARG cc_start: 0.8163 (OUTLIER) cc_final: 0.7166 (mtm-85) REVERT: b 235 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.7530 (tp30) REVERT: e 6 TYR cc_start: 0.8672 (t80) cc_final: 0.8369 (t80) REVERT: e 93 GLU cc_start: 0.8594 (OUTLIER) cc_final: 0.8247 (pp20) REVERT: e 172 PHE cc_start: 0.7291 (t80) cc_final: 0.7054 (t80) REVERT: j 31 GLU cc_start: 0.7782 (OUTLIER) cc_final: 0.7352 (mp0) REVERT: j 92 MET cc_start: 0.8251 (mtp) cc_final: 0.7976 (mtt) REVERT: m 60 GLN cc_start: 0.7548 (OUTLIER) cc_final: 0.6223 (pp30) REVERT: m 102 LEU cc_start: 0.9328 (mt) cc_final: 0.9127 (mt) REVERT: n 27 SER cc_start: 0.8725 (m) cc_final: 0.8316 (p) REVERT: n 72 ASP cc_start: 0.7279 (t0) cc_final: 0.6894 (t70) REVERT: n 73 ASN cc_start: 0.7264 (p0) cc_final: 0.7001 (p0) REVERT: o 93 ASP cc_start: 0.6903 (t0) cc_final: 0.6524 (t0) REVERT: o 116 GLN cc_start: 0.7841 (tp40) cc_final: 0.7610 (tp40) REVERT: q 73 ILE cc_start: 0.8770 (tp) cc_final: 0.8506 (tp) REVERT: q 94 LEU cc_start: 0.9081 (mt) cc_final: 0.8612 (mp) REVERT: r 40 MET cc_start: 0.7561 (tmm) cc_final: 0.7239 (tmm) REVERT: t 61 LEU cc_start: 0.8955 (OUTLIER) cc_final: 0.8604 (pp) REVERT: u 100 GLU cc_start: 0.7966 (mm-30) cc_final: 0.7680 (mm-30) REVERT: x 55 MET cc_start: 0.8273 (mpp) cc_final: 0.7944 (mtm) REVERT: x 73 ARG cc_start: 0.8351 (ttp80) cc_final: 0.7830 (mtp180) REVERT: y 7 ARG cc_start: 0.8553 (ptm160) cc_final: 0.8268 (ptm160) REVERT: y 22 LEU cc_start: 0.6994 (OUTLIER) cc_final: 0.6716 (pp) REVERT: A 3 LYS cc_start: 0.8004 (mttt) cc_final: 0.7793 (tptp) REVERT: A 8 LYS cc_start: 0.7335 (tmmt) cc_final: 0.7061 (tmtt) REVERT: C 6 GLU cc_start: 0.7702 (pt0) cc_final: 0.6365 (pm20) REVERT: C 9 LYS cc_start: 0.7259 (tttp) cc_final: 0.7046 (ttmt) REVERT: E 63 TYR cc_start: 0.8277 (OUTLIER) cc_final: 0.7935 (m-80) REVERT: F 37 GLN cc_start: 0.8383 (tp40) cc_final: 0.8051 (tp40) REVERT: G 22 TRP cc_start: 0.8300 (p-90) cc_final: 0.8046 (p-90) REVERT: G 58 LYS cc_start: 0.9262 (mmtp) cc_final: 0.8776 (tptp) REVERT: G 173 LYS cc_start: 0.8542 (ttmt) cc_final: 0.7560 (tmtt) REVERT: G 191 ASP cc_start: 0.8629 (OUTLIER) cc_final: 0.8351 (t0) REVERT: H 5 HIS cc_start: 0.7266 (t-90) cc_final: 0.6301 (t70) REVERT: H 34 SER cc_start: 0.8201 (m) cc_final: 0.7969 (p) REVERT: H 40 GLN cc_start: 0.8232 (tp-100) cc_final: 0.7742 (pt0) REVERT: H 104 GLU cc_start: 0.6374 (OUTLIER) cc_final: 0.5822 (tm-30) REVERT: H 133 MET cc_start: 0.7743 (ttt) cc_final: 0.7467 (ttt) REVERT: H 182 ASP cc_start: 0.7350 (t0) cc_final: 0.6746 (t0) REVERT: I 63 ILE cc_start: 0.8607 (mt) cc_final: 0.8279 (mt) REVERT: J 82 HIS cc_start: 0.8493 (OUTLIER) cc_final: 0.7947 (p90) REVERT: J 115 GLU cc_start: 0.8147 (pt0) cc_final: 0.7656 (pt0) REVERT: J 141 ASP cc_start: 0.8240 (m-30) cc_final: 0.7985 (p0) REVERT: K 55 HIS cc_start: 0.8143 (OUTLIER) cc_final: 0.7447 (p-80) REVERT: L 138 GLU cc_start: 0.8638 (mp0) cc_final: 0.8378 (mp0) REVERT: M 8 ASP cc_start: 0.8240 (t70) cc_final: 0.7920 (t0) REVERT: M 11 THR cc_start: 0.9171 (OUTLIER) cc_final: 0.8906 (p) REVERT: M 26 MET cc_start: 0.4382 (ptm) cc_final: 0.4064 (ptp) REVERT: M 72 GLU cc_start: 0.7830 (tp30) cc_final: 0.7330 (tt0) REVERT: M 95 MET cc_start: 0.7352 (tpp) cc_final: 0.6969 (tpp) REVERT: N 93 LEU cc_start: 0.4076 (OUTLIER) cc_final: 0.3799 (tp) REVERT: N 106 ASP cc_start: 0.7438 (t70) cc_final: 0.7071 (t0) REVERT: P 29 THR cc_start: 0.8218 (p) cc_final: 0.7982 (p) REVERT: P 58 THR cc_start: 0.8365 (p) cc_final: 0.8131 (p) REVERT: Q 88 ASP cc_start: 0.7587 (t70) cc_final: 0.7206 (t0) REVERT: U 1 MET cc_start: 0.3303 (tmm) cc_final: 0.2522 (tmm) REVERT: U 39 PHE cc_start: 0.8079 (OUTLIER) cc_final: 0.7554 (t80) REVERT: V 60 ILE cc_start: 0.8826 (pt) cc_final: 0.8249 (pt) REVERT: V 72 TRP cc_start: 0.6113 (m100) cc_final: 0.5510 (m100) REVERT: X 40 PHE cc_start: 0.6432 (m-10) cc_final: 0.5785 (m-10) REVERT: X 43 MET cc_start: 0.7454 (mtm) cc_final: 0.6859 (mtm) REVERT: Y 23 ARG cc_start: 0.8787 (mmm160) cc_final: 0.8556 (mmm160) REVERT: 8 10 TYR cc_start: 0.6715 (m-80) cc_final: 0.6055 (m-80) REVERT: 8 204 TYR cc_start: 0.6072 (OUTLIER) cc_final: 0.5536 (p90) REVERT: 8 234 MET cc_start: 0.6498 (tpt) cc_final: 0.6100 (tmm) REVERT: 8 241 GLU cc_start: 0.6439 (tt0) cc_final: 0.5713 (pt0) REVERT: 8 278 MET cc_start: 0.6892 (OUTLIER) cc_final: 0.6232 (ptt) REVERT: 8 301 ASP cc_start: 0.3243 (OUTLIER) cc_final: 0.1248 (t70) REVERT: 8 340 SER cc_start: 0.8068 (OUTLIER) cc_final: 0.7789 (p) REVERT: 8 474 LYS cc_start: 0.7440 (tptp) cc_final: 0.7177 (tptp) REVERT: 8 485 LYS cc_start: 0.8447 (mttm) cc_final: 0.8204 (mmmt) REVERT: 8 663 MET cc_start: 0.8046 (mmm) cc_final: 0.7445 (mmm) outliers start: 340 outliers final: 242 residues processed: 1109 average time/residue: 1.2464 time to fit residues: 2468.5324 Evaluate side-chains 1061 residues out of total 5429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 261 poor density : 800 time to evaluate : 6.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 86 ARG Chi-restraints excluded: chain b residue 119 VAL Chi-restraints excluded: chain b residue 203 VAL Chi-restraints excluded: chain b residue 224 MET Chi-restraints excluded: chain b residue 235 GLU Chi-restraints excluded: chain b residue 244 VAL Chi-restraints excluded: chain b residue 262 THR Chi-restraints excluded: chain b residue 266 ILE Chi-restraints excluded: chain c residue 2 ILE Chi-restraints excluded: chain c residue 25 THR Chi-restraints excluded: chain c residue 60 VAL Chi-restraints excluded: chain c residue 131 ASP Chi-restraints excluded: chain c residue 176 ASP Chi-restraints excluded: chain c residue 180 VAL Chi-restraints excluded: chain c residue 188 LEU Chi-restraints excluded: chain c residue 197 THR Chi-restraints excluded: chain d residue 77 ILE Chi-restraints excluded: chain d residue 120 VAL Chi-restraints excluded: chain d residue 188 MET Chi-restraints excluded: chain e residue 16 MET Chi-restraints excluded: chain e residue 24 VAL Chi-restraints excluded: chain e residue 30 VAL Chi-restraints excluded: chain e residue 39 VAL Chi-restraints excluded: chain e residue 56 LEU Chi-restraints excluded: chain e residue 93 GLU Chi-restraints excluded: chain e residue 112 ASP Chi-restraints excluded: chain e residue 126 ASN Chi-restraints excluded: chain e residue 128 SER Chi-restraints excluded: chain e residue 131 VAL Chi-restraints excluded: chain e residue 146 ASP Chi-restraints excluded: chain f residue 9 VAL Chi-restraints excluded: chain f residue 75 VAL Chi-restraints excluded: chain f residue 78 VAL Chi-restraints excluded: chain f residue 165 ASP Chi-restraints excluded: chain g residue 6 LEU Chi-restraints excluded: chain g residue 122 LEU Chi-restraints excluded: chain g residue 125 THR Chi-restraints excluded: chain i residue 12 VAL Chi-restraints excluded: chain i residue 34 ILE Chi-restraints excluded: chain i residue 45 THR Chi-restraints excluded: chain i residue 48 ILE Chi-restraints excluded: chain i residue 57 VAL Chi-restraints excluded: chain i residue 70 THR Chi-restraints excluded: chain j residue 3 THR Chi-restraints excluded: chain j residue 31 GLU Chi-restraints excluded: chain j residue 57 LEU Chi-restraints excluded: chain j residue 62 VAL Chi-restraints excluded: chain j residue 84 ILE Chi-restraints excluded: chain j residue 90 GLU Chi-restraints excluded: chain k residue 14 SER Chi-restraints excluded: chain k residue 51 LYS Chi-restraints excluded: chain k residue 56 ASP Chi-restraints excluded: chain k residue 73 ASP Chi-restraints excluded: chain k residue 85 VAL Chi-restraints excluded: chain k residue 90 ASN Chi-restraints excluded: chain k residue 107 LEU Chi-restraints excluded: chain k residue 111 LYS Chi-restraints excluded: chain m residue 7 THR Chi-restraints excluded: chain m residue 42 THR Chi-restraints excluded: chain m residue 60 GLN Chi-restraints excluded: chain m residue 75 GLU Chi-restraints excluded: chain m residue 78 LEU Chi-restraints excluded: chain m residue 88 ASN Chi-restraints excluded: chain m residue 91 TYR Chi-restraints excluded: chain m residue 93 VAL Chi-restraints excluded: chain m residue 124 LEU Chi-restraints excluded: chain m residue 126 ILE Chi-restraints excluded: chain m residue 129 THR Chi-restraints excluded: chain m residue 132 THR Chi-restraints excluded: chain n residue 2 ARG Chi-restraints excluded: chain n residue 33 ILE Chi-restraints excluded: chain n residue 34 ILE Chi-restraints excluded: chain n residue 51 LEU Chi-restraints excluded: chain n residue 54 LEU Chi-restraints excluded: chain n residue 115 LEU Chi-restraints excluded: chain n residue 120 GLU Chi-restraints excluded: chain o residue 35 ILE Chi-restraints excluded: chain o residue 47 VAL Chi-restraints excluded: chain o residue 52 SER Chi-restraints excluded: chain o residue 62 LEU Chi-restraints excluded: chain o residue 69 ASP Chi-restraints excluded: chain p residue 8 GLU Chi-restraints excluded: chain p residue 18 SER Chi-restraints excluded: chain p residue 40 GLN Chi-restraints excluded: chain p residue 47 ILE Chi-restraints excluded: chain p residue 79 VAL Chi-restraints excluded: chain p residue 84 SER Chi-restraints excluded: chain p residue 96 LEU Chi-restraints excluded: chain p residue 103 THR Chi-restraints excluded: chain p residue 105 LYS Chi-restraints excluded: chain q residue 7 VAL Chi-restraints excluded: chain q residue 99 VAL Chi-restraints excluded: chain q residue 106 THR Chi-restraints excluded: chain q residue 109 VAL Chi-restraints excluded: chain r residue 101 ILE Chi-restraints excluded: chain s residue 3 THR Chi-restraints excluded: chain s residue 4 ILE Chi-restraints excluded: chain s residue 76 VAL Chi-restraints excluded: chain s residue 105 VAL Chi-restraints excluded: chain t residue 24 MET Chi-restraints excluded: chain t residue 61 LEU Chi-restraints excluded: chain t residue 63 VAL Chi-restraints excluded: chain t residue 93 LEU Chi-restraints excluded: chain u residue 24 VAL Chi-restraints excluded: chain u residue 27 VAL Chi-restraints excluded: chain u residue 48 VAL Chi-restraints excluded: chain u residue 67 SER Chi-restraints excluded: chain u residue 69 VAL Chi-restraints excluded: chain u residue 71 ILE Chi-restraints excluded: chain v residue 5 ASN Chi-restraints excluded: chain v residue 40 ILE Chi-restraints excluded: chain v residue 61 LEU Chi-restraints excluded: chain v residue 65 VAL Chi-restraints excluded: chain v residue 76 ASP Chi-restraints excluded: chain v residue 86 LEU Chi-restraints excluded: chain w residue 34 VAL Chi-restraints excluded: chain w residue 63 VAL Chi-restraints excluded: chain x residue 12 VAL Chi-restraints excluded: chain x residue 47 THR Chi-restraints excluded: chain x residue 76 LYS Chi-restraints excluded: chain y residue 8 GLU Chi-restraints excluded: chain y residue 22 LEU Chi-restraints excluded: chain y residue 30 MET Chi-restraints excluded: chain z residue 40 THR Chi-restraints excluded: chain z residue 56 VAL Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 30 HIS Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 58 ASP Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 60 CYS Chi-restraints excluded: chain E residue 63 TYR Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 23 ILE Chi-restraints excluded: chain F residue 27 CYS Chi-restraints excluded: chain G residue 86 CYS Chi-restraints excluded: chain G residue 169 HIS Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 191 ASP Chi-restraints excluded: chain G residue 203 ASP Chi-restraints excluded: chain H residue 30 ASP Chi-restraints excluded: chain H residue 104 GLU Chi-restraints excluded: chain H residue 164 THR Chi-restraints excluded: chain H residue 180 ASP Chi-restraints excluded: chain H residue 191 THR Chi-restraints excluded: chain H residue 194 VAL Chi-restraints excluded: chain I residue 19 PHE Chi-restraints excluded: chain I residue 97 LEU Chi-restraints excluded: chain I residue 98 ASP Chi-restraints excluded: chain I residue 170 LEU Chi-restraints excluded: chain I residue 191 SER Chi-restraints excluded: chain I residue 194 ILE Chi-restraints excluded: chain J residue 15 ILE Chi-restraints excluded: chain J residue 35 LEU Chi-restraints excluded: chain J residue 38 VAL Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 61 LYS Chi-restraints excluded: chain J residue 79 THR Chi-restraints excluded: chain J residue 82 HIS Chi-restraints excluded: chain J residue 104 ILE Chi-restraints excluded: chain J residue 120 HIS Chi-restraints excluded: chain J residue 123 LEU Chi-restraints excluded: chain J residue 152 VAL Chi-restraints excluded: chain K residue 11 HIS Chi-restraints excluded: chain K residue 13 ASP Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 55 HIS Chi-restraints excluded: chain K residue 60 VAL Chi-restraints excluded: chain K residue 85 ILE Chi-restraints excluded: chain K residue 93 LYS Chi-restraints excluded: chain K residue 96 VAL Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain L residue 84 TYR Chi-restraints excluded: chain M residue 6 ILE Chi-restraints excluded: chain M residue 11 THR Chi-restraints excluded: chain M residue 62 LEU Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain M residue 126 CYS Chi-restraints excluded: chain N residue 8 THR Chi-restraints excluded: chain N residue 28 VAL Chi-restraints excluded: chain N residue 38 PHE Chi-restraints excluded: chain N residue 42 THR Chi-restraints excluded: chain N residue 54 VAL Chi-restraints excluded: chain N residue 83 THR Chi-restraints excluded: chain N residue 93 LEU Chi-restraints excluded: chain N residue 125 GLN Chi-restraints excluded: chain O residue 15 HIS Chi-restraints excluded: chain O residue 66 GLU Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain P residue 30 ILE Chi-restraints excluded: chain Q residue 20 VAL Chi-restraints excluded: chain Q residue 42 LYS Chi-restraints excluded: chain Q residue 61 GLU Chi-restraints excluded: chain Q residue 66 ILE Chi-restraints excluded: chain Q residue 96 THR Chi-restraints excluded: chain Q residue 118 VAL Chi-restraints excluded: chain R residue 13 HIS Chi-restraints excluded: chain R residue 15 VAL Chi-restraints excluded: chain R residue 18 LEU Chi-restraints excluded: chain R residue 64 VAL Chi-restraints excluded: chain S residue 37 ASP Chi-restraints excluded: chain S residue 44 VAL Chi-restraints excluded: chain S residue 50 LEU Chi-restraints excluded: chain S residue 78 LEU Chi-restraints excluded: chain T residue 16 ARG Chi-restraints excluded: chain T residue 74 VAL Chi-restraints excluded: chain U residue 39 PHE Chi-restraints excluded: chain U residue 57 ILE Chi-restraints excluded: chain U residue 75 ILE Chi-restraints excluded: chain V residue 50 ASN Chi-restraints excluded: chain V residue 69 THR Chi-restraints excluded: chain W residue 25 ILE Chi-restraints excluded: chain W residue 33 THR Chi-restraints excluded: chain W residue 73 HIS Chi-restraints excluded: chain X residue 39 ILE Chi-restraints excluded: chain X residue 66 VAL Chi-restraints excluded: chain Y residue 11 ILE Chi-restraints excluded: chain Y residue 19 HIS Chi-restraints excluded: chain Y residue 25 SER Chi-restraints excluded: chain Y residue 57 VAL Chi-restraints excluded: chain Z residue 12 ASP Chi-restraints excluded: chain Z residue 18 PHE Chi-restraints excluded: chain Z residue 43 GLU Chi-restraints excluded: chain Z residue 59 LEU Chi-restraints excluded: chain a residue 21 TYR Chi-restraints excluded: chain a residue 24 ASN Chi-restraints excluded: chain a residue 174 THR Chi-restraints excluded: chain 8 residue 86 ILE Chi-restraints excluded: chain 8 residue 96 THR Chi-restraints excluded: chain 8 residue 105 VAL Chi-restraints excluded: chain 8 residue 110 VAL Chi-restraints excluded: chain 8 residue 112 VAL Chi-restraints excluded: chain 8 residue 126 VAL Chi-restraints excluded: chain 8 residue 167 VAL Chi-restraints excluded: chain 8 residue 182 VAL Chi-restraints excluded: chain 8 residue 184 ASP Chi-restraints excluded: chain 8 residue 186 VAL Chi-restraints excluded: chain 8 residue 201 THR Chi-restraints excluded: chain 8 residue 204 TYR Chi-restraints excluded: chain 8 residue 247 GLU Chi-restraints excluded: chain 8 residue 264 VAL Chi-restraints excluded: chain 8 residue 266 CYS Chi-restraints excluded: chain 8 residue 278 MET Chi-restraints excluded: chain 8 residue 292 VAL Chi-restraints excluded: chain 8 residue 300 ASP Chi-restraints excluded: chain 8 residue 301 ASP Chi-restraints excluded: chain 8 residue 330 VAL Chi-restraints excluded: chain 8 residue 340 SER Chi-restraints excluded: chain 8 residue 374 ILE Chi-restraints excluded: chain 8 residue 494 ILE Chi-restraints excluded: chain 8 residue 530 ASN Chi-restraints excluded: chain 8 residue 571 VAL Chi-restraints excluded: chain 8 residue 585 ASP Chi-restraints excluded: chain 8 residue 623 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1109 random chunks: chunk 360 optimal weight: 8.9990 chunk 965 optimal weight: 20.0000 chunk 211 optimal weight: 9.9990 chunk 629 optimal weight: 20.0000 chunk 264 optimal weight: 20.0000 chunk 1073 optimal weight: 20.0000 chunk 890 optimal weight: 10.0000 chunk 496 optimal weight: 30.0000 chunk 89 optimal weight: 4.9990 chunk 354 optimal weight: 10.0000 chunk 563 optimal weight: 0.7980 overall best weight: 6.9590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 43 ASN h 9 GLN j 128 ASN m 45 GLN ** n 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 31 GLN ** A 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 11 GLN ** J 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 37 ASN M 66 GLN N 36 GLN O 15 HIS O 99 GLN ** P 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 30 HIS Y 2 ASN ** a 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.3403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 166269 Z= 0.256 Angle : 0.663 14.381 247957 Z= 0.342 Chirality : 0.038 0.317 31576 Planarity : 0.005 0.067 13872 Dihedral : 23.492 177.595 81269 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 17.40 Ramachandran Plot: Outliers : 0.25 % Allowed : 12.23 % Favored : 87.52 % Rotamer: Outliers : 6.17 % Allowed : 21.24 % Favored : 72.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -2.69 (0.10), residues: 6517 helix: -0.57 (0.11), residues: 2029 sheet: -2.05 (0.14), residues: 1103 loop : -2.51 (0.10), residues: 3385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP L 102 HIS 0.006 0.001 HIS V 30 PHE 0.038 0.002 PHE K 78 TYR 0.019 0.002 TYR X 79 ARG 0.007 0.001 ARG Q 109 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13034 Ramachandran restraints generated. 6517 Oldfield, 0 Emsley, 6517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13034 Ramachandran restraints generated. 6517 Oldfield, 0 Emsley, 6517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1195 residues out of total 5429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 335 poor density : 860 time to evaluate : 6.735 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: b 86 ARG cc_start: 0.8165 (OUTLIER) cc_final: 0.7183 (mtm-85) REVERT: e 6 TYR cc_start: 0.8681 (t80) cc_final: 0.8350 (t80) REVERT: e 37 MET cc_start: 0.6994 (ttt) cc_final: 0.6735 (ptm) REVERT: e 172 PHE cc_start: 0.7153 (t80) cc_final: 0.6947 (t80) REVERT: j 92 MET cc_start: 0.8218 (mtp) cc_final: 0.7943 (mtt) REVERT: k 1 MET cc_start: 0.8081 (ttm) cc_final: 0.7634 (ttp) REVERT: m 60 GLN cc_start: 0.7503 (OUTLIER) cc_final: 0.6198 (pp30) REVERT: n 27 SER cc_start: 0.8687 (m) cc_final: 0.8297 (p) REVERT: n 72 ASP cc_start: 0.7245 (t0) cc_final: 0.6872 (t70) REVERT: n 73 ASN cc_start: 0.7136 (p0) cc_final: 0.6850 (p0) REVERT: o 93 ASP cc_start: 0.6972 (t0) cc_final: 0.6677 (t0) REVERT: p 26 GLU cc_start: 0.7427 (mm-30) cc_final: 0.6823 (tm-30) REVERT: p 105 LYS cc_start: 0.8283 (OUTLIER) cc_final: 0.8081 (mmtm) REVERT: q 73 ILE cc_start: 0.8762 (tp) cc_final: 0.8503 (tp) REVERT: q 94 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8601 (mp) REVERT: r 40 MET cc_start: 0.7697 (tmm) cc_final: 0.7425 (tmm) REVERT: r 86 GLN cc_start: 0.8229 (tp40) cc_final: 0.7995 (tp40) REVERT: t 61 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8580 (pp) REVERT: u 98 ASN cc_start: 0.7372 (OUTLIER) cc_final: 0.6874 (p0) REVERT: x 19 HIS cc_start: 0.8402 (OUTLIER) cc_final: 0.8023 (t70) REVERT: x 73 ARG cc_start: 0.8333 (ttp80) cc_final: 0.7903 (mtp180) REVERT: y 7 ARG cc_start: 0.8546 (ptm160) cc_final: 0.8271 (ptm160) REVERT: A 3 LYS cc_start: 0.8012 (mttt) cc_final: 0.7801 (tptp) REVERT: A 8 LYS cc_start: 0.7357 (tmmt) cc_final: 0.7093 (tmtt) REVERT: C 6 GLU cc_start: 0.7801 (pt0) cc_final: 0.6493 (pm20) REVERT: C 19 PHE cc_start: 0.8533 (p90) cc_final: 0.8075 (p90) REVERT: E 63 TYR cc_start: 0.8265 (OUTLIER) cc_final: 0.7936 (m-80) REVERT: F 37 GLN cc_start: 0.8366 (tp40) cc_final: 0.8052 (tp-100) REVERT: G 22 TRP cc_start: 0.8272 (p-90) cc_final: 0.8031 (p-90) REVERT: G 58 LYS cc_start: 0.9263 (mmtp) cc_final: 0.8778 (tptp) REVERT: G 173 LYS cc_start: 0.8541 (ttmt) cc_final: 0.7547 (tmtt) REVERT: G 191 ASP cc_start: 0.8631 (OUTLIER) cc_final: 0.8319 (t0) REVERT: H 5 HIS cc_start: 0.7273 (t-90) cc_final: 0.6307 (t70) REVERT: H 40 GLN cc_start: 0.8222 (tp-100) cc_final: 0.7737 (pt0) REVERT: H 104 GLU cc_start: 0.6346 (OUTLIER) cc_final: 0.5778 (tm-30) REVERT: H 133 MET cc_start: 0.7717 (ttt) cc_final: 0.7465 (ttt) REVERT: H 182 ASP cc_start: 0.7263 (t0) cc_final: 0.6699 (t70) REVERT: I 63 ILE cc_start: 0.8616 (mt) cc_final: 0.8282 (mt) REVERT: I 202 LEU cc_start: 0.8346 (OUTLIER) cc_final: 0.8108 (tt) REVERT: J 115 GLU cc_start: 0.8158 (pt0) cc_final: 0.7658 (pt0) REVERT: J 141 ASP cc_start: 0.8190 (m-30) cc_final: 0.7985 (p0) REVERT: K 55 HIS cc_start: 0.8095 (OUTLIER) cc_final: 0.7441 (p-80) REVERT: M 8 ASP cc_start: 0.8228 (t70) cc_final: 0.7856 (t0) REVERT: M 11 THR cc_start: 0.9089 (OUTLIER) cc_final: 0.8821 (p) REVERT: M 72 GLU cc_start: 0.7824 (tp30) cc_final: 0.7342 (tt0) REVERT: N 93 LEU cc_start: 0.4052 (OUTLIER) cc_final: 0.3789 (tp) REVERT: N 106 ASP cc_start: 0.7419 (t70) cc_final: 0.7021 (t0) REVERT: N 117 LEU cc_start: 0.9222 (mp) cc_final: 0.8957 (mm) REVERT: P 58 THR cc_start: 0.8402 (p) cc_final: 0.8141 (p) REVERT: Q 88 ASP cc_start: 0.7583 (t70) cc_final: 0.7202 (t0) REVERT: T 25 GLU cc_start: 0.8681 (mp0) cc_final: 0.8411 (mp0) REVERT: T 84 LEU cc_start: 0.7761 (OUTLIER) cc_final: 0.7486 (mm) REVERT: U 1 MET cc_start: 0.3136 (tmm) cc_final: 0.2246 (tmm) REVERT: U 39 PHE cc_start: 0.8020 (OUTLIER) cc_final: 0.7485 (t80) REVERT: V 60 ILE cc_start: 0.8799 (pt) cc_final: 0.8225 (pt) REVERT: V 61 ARG cc_start: 0.8026 (ttp-110) cc_final: 0.7621 (tmt170) REVERT: V 72 TRP cc_start: 0.6107 (m100) cc_final: 0.5497 (m100) REVERT: X 40 PHE cc_start: 0.6542 (m-10) cc_final: 0.5935 (m-10) REVERT: X 43 MET cc_start: 0.7595 (mtm) cc_final: 0.6962 (mtm) REVERT: X 72 GLU cc_start: 0.5097 (mm-30) cc_final: 0.4751 (mp0) REVERT: a 186 LYS cc_start: 0.4664 (tptp) cc_final: 0.3951 (ptmt) REVERT: 8 10 TYR cc_start: 0.6702 (m-80) cc_final: 0.5994 (m-80) REVERT: 8 204 TYR cc_start: 0.6122 (OUTLIER) cc_final: 0.5660 (p90) REVERT: 8 234 MET cc_start: 0.6563 (tpt) cc_final: 0.6135 (tmm) REVERT: 8 241 GLU cc_start: 0.6472 (tt0) cc_final: 0.5748 (pt0) REVERT: 8 278 MET cc_start: 0.6938 (OUTLIER) cc_final: 0.6294 (ptt) REVERT: 8 301 ASP cc_start: 0.3558 (OUTLIER) cc_final: 0.1404 (t70) REVERT: 8 474 LYS cc_start: 0.7448 (tptp) cc_final: 0.7186 (tptp) REVERT: 8 663 MET cc_start: 0.8128 (mmm) cc_final: 0.7505 (mmm) outliers start: 335 outliers final: 257 residues processed: 1103 average time/residue: 1.2445 time to fit residues: 2458.8702 Evaluate side-chains 1078 residues out of total 5429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 276 poor density : 802 time to evaluate : 6.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 86 ARG Chi-restraints excluded: chain b residue 119 VAL Chi-restraints excluded: chain b residue 161 VAL Chi-restraints excluded: chain b residue 224 MET Chi-restraints excluded: chain b residue 244 VAL Chi-restraints excluded: chain b residue 262 THR Chi-restraints excluded: chain b residue 266 ILE Chi-restraints excluded: chain c residue 2 ILE Chi-restraints excluded: chain c residue 25 THR Chi-restraints excluded: chain c residue 60 VAL Chi-restraints excluded: chain c residue 131 ASP Chi-restraints excluded: chain c residue 146 ILE Chi-restraints excluded: chain c residue 176 ASP Chi-restraints excluded: chain c residue 180 VAL Chi-restraints excluded: chain c residue 188 LEU Chi-restraints excluded: chain c residue 197 THR Chi-restraints excluded: chain d residue 77 ILE Chi-restraints excluded: chain d residue 120 VAL Chi-restraints excluded: chain e residue 16 MET Chi-restraints excluded: chain e residue 24 VAL Chi-restraints excluded: chain e residue 30 VAL Chi-restraints excluded: chain e residue 39 VAL Chi-restraints excluded: chain e residue 56 LEU Chi-restraints excluded: chain e residue 112 ASP Chi-restraints excluded: chain e residue 128 SER Chi-restraints excluded: chain e residue 131 VAL Chi-restraints excluded: chain e residue 146 ASP Chi-restraints excluded: chain f residue 9 VAL Chi-restraints excluded: chain f residue 78 VAL Chi-restraints excluded: chain f residue 165 ASP Chi-restraints excluded: chain g residue 4 ILE Chi-restraints excluded: chain g residue 6 LEU Chi-restraints excluded: chain g residue 121 VAL Chi-restraints excluded: chain g residue 122 LEU Chi-restraints excluded: chain g residue 125 THR Chi-restraints excluded: chain h residue 38 MET Chi-restraints excluded: chain i residue 12 VAL Chi-restraints excluded: chain i residue 23 VAL Chi-restraints excluded: chain i residue 45 THR Chi-restraints excluded: chain i residue 48 ILE Chi-restraints excluded: chain i residue 57 VAL Chi-restraints excluded: chain i residue 70 THR Chi-restraints excluded: chain j residue 3 THR Chi-restraints excluded: chain j residue 31 GLU Chi-restraints excluded: chain j residue 57 LEU Chi-restraints excluded: chain j residue 62 VAL Chi-restraints excluded: chain j residue 84 ILE Chi-restraints excluded: chain j residue 90 GLU Chi-restraints excluded: chain j residue 128 ASN Chi-restraints excluded: chain k residue 51 LYS Chi-restraints excluded: chain k residue 56 ASP Chi-restraints excluded: chain k residue 73 ASP Chi-restraints excluded: chain k residue 85 VAL Chi-restraints excluded: chain k residue 90 ASN Chi-restraints excluded: chain k residue 107 LEU Chi-restraints excluded: chain k residue 111 LYS Chi-restraints excluded: chain l residue 103 ILE Chi-restraints excluded: chain l residue 121 THR Chi-restraints excluded: chain m residue 7 THR Chi-restraints excluded: chain m residue 42 THR Chi-restraints excluded: chain m residue 45 GLN Chi-restraints excluded: chain m residue 60 GLN Chi-restraints excluded: chain m residue 63 ILE Chi-restraints excluded: chain m residue 70 ASP Chi-restraints excluded: chain m residue 75 GLU Chi-restraints excluded: chain m residue 78 LEU Chi-restraints excluded: chain m residue 88 ASN Chi-restraints excluded: chain m residue 91 TYR Chi-restraints excluded: chain m residue 124 LEU Chi-restraints excluded: chain m residue 126 ILE Chi-restraints excluded: chain m residue 129 THR Chi-restraints excluded: chain m residue 132 THR Chi-restraints excluded: chain n residue 2 ARG Chi-restraints excluded: chain n residue 33 ILE Chi-restraints excluded: chain n residue 34 ILE Chi-restraints excluded: chain n residue 51 LEU Chi-restraints excluded: chain n residue 54 LEU Chi-restraints excluded: chain n residue 115 LEU Chi-restraints excluded: chain n residue 120 GLU Chi-restraints excluded: chain o residue 35 ILE Chi-restraints excluded: chain o residue 47 VAL Chi-restraints excluded: chain o residue 52 SER Chi-restraints excluded: chain o residue 62 LEU Chi-restraints excluded: chain o residue 69 ASP Chi-restraints excluded: chain p residue 40 GLN Chi-restraints excluded: chain p residue 47 ILE Chi-restraints excluded: chain p residue 79 VAL Chi-restraints excluded: chain p residue 84 SER Chi-restraints excluded: chain p residue 96 LEU Chi-restraints excluded: chain p residue 103 THR Chi-restraints excluded: chain p residue 105 LYS Chi-restraints excluded: chain q residue 7 VAL Chi-restraints excluded: chain q residue 94 LEU Chi-restraints excluded: chain q residue 106 THR Chi-restraints excluded: chain q residue 109 VAL Chi-restraints excluded: chain r residue 101 ILE Chi-restraints excluded: chain s residue 3 THR Chi-restraints excluded: chain s residue 4 ILE Chi-restraints excluded: chain s residue 76 VAL Chi-restraints excluded: chain s residue 105 VAL Chi-restraints excluded: chain t residue 24 MET Chi-restraints excluded: chain t residue 61 LEU Chi-restraints excluded: chain t residue 63 VAL Chi-restraints excluded: chain t residue 93 LEU Chi-restraints excluded: chain u residue 27 VAL Chi-restraints excluded: chain u residue 48 VAL Chi-restraints excluded: chain u residue 67 SER Chi-restraints excluded: chain u residue 69 VAL Chi-restraints excluded: chain u residue 71 ILE Chi-restraints excluded: chain u residue 88 ASP Chi-restraints excluded: chain u residue 98 ASN Chi-restraints excluded: chain v residue 5 ASN Chi-restraints excluded: chain v residue 40 ILE Chi-restraints excluded: chain v residue 61 LEU Chi-restraints excluded: chain v residue 65 VAL Chi-restraints excluded: chain v residue 86 LEU Chi-restraints excluded: chain w residue 34 VAL Chi-restraints excluded: chain w residue 63 VAL Chi-restraints excluded: chain x residue 12 VAL Chi-restraints excluded: chain x residue 19 HIS Chi-restraints excluded: chain x residue 47 THR Chi-restraints excluded: chain x residue 76 LYS Chi-restraints excluded: chain y residue 8 GLU Chi-restraints excluded: chain y residue 30 MET Chi-restraints excluded: chain z residue 40 THR Chi-restraints excluded: chain z residue 56 VAL Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 30 HIS Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 58 ASP Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 60 CYS Chi-restraints excluded: chain E residue 63 TYR Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 23 ILE Chi-restraints excluded: chain F residue 27 CYS Chi-restraints excluded: chain G residue 86 CYS Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 191 ASP Chi-restraints excluded: chain G residue 203 ASP Chi-restraints excluded: chain H residue 4 VAL Chi-restraints excluded: chain H residue 7 ASN Chi-restraints excluded: chain H residue 30 ASP Chi-restraints excluded: chain H residue 104 GLU Chi-restraints excluded: chain H residue 164 THR Chi-restraints excluded: chain H residue 176 THR Chi-restraints excluded: chain H residue 180 ASP Chi-restraints excluded: chain H residue 194 VAL Chi-restraints excluded: chain I residue 19 PHE Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 57 LYS Chi-restraints excluded: chain I residue 97 LEU Chi-restraints excluded: chain I residue 98 ASP Chi-restraints excluded: chain I residue 170 LEU Chi-restraints excluded: chain I residue 191 SER Chi-restraints excluded: chain I residue 194 ILE Chi-restraints excluded: chain I residue 202 LEU Chi-restraints excluded: chain J residue 15 ILE Chi-restraints excluded: chain J residue 35 LEU Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 60 GLN Chi-restraints excluded: chain J residue 61 LYS Chi-restraints excluded: chain J residue 79 THR Chi-restraints excluded: chain J residue 104 ILE Chi-restraints excluded: chain J residue 120 HIS Chi-restraints excluded: chain J residue 123 LEU Chi-restraints excluded: chain K residue 11 HIS Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 55 HIS Chi-restraints excluded: chain K residue 60 VAL Chi-restraints excluded: chain K residue 85 ILE Chi-restraints excluded: chain K residue 93 LYS Chi-restraints excluded: chain K residue 96 VAL Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 48 THR Chi-restraints excluded: chain L residue 84 TYR Chi-restraints excluded: chain L residue 93 VAL Chi-restraints excluded: chain L residue 103 ILE Chi-restraints excluded: chain M residue 6 ILE Chi-restraints excluded: chain M residue 11 THR Chi-restraints excluded: chain M residue 53 ASP Chi-restraints excluded: chain M residue 62 LEU Chi-restraints excluded: chain M residue 126 CYS Chi-restraints excluded: chain N residue 8 THR Chi-restraints excluded: chain N residue 28 VAL Chi-restraints excluded: chain N residue 38 PHE Chi-restraints excluded: chain N residue 42 THR Chi-restraints excluded: chain N residue 54 VAL Chi-restraints excluded: chain N residue 65 THR Chi-restraints excluded: chain N residue 83 THR Chi-restraints excluded: chain N residue 93 LEU Chi-restraints excluded: chain O residue 15 HIS Chi-restraints excluded: chain O residue 19 ASP Chi-restraints excluded: chain O residue 50 THR Chi-restraints excluded: chain O residue 66 GLU Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain O residue 83 THR Chi-restraints excluded: chain P residue 30 ILE Chi-restraints excluded: chain Q residue 20 VAL Chi-restraints excluded: chain Q residue 39 THR Chi-restraints excluded: chain Q residue 42 LYS Chi-restraints excluded: chain Q residue 61 GLU Chi-restraints excluded: chain Q residue 66 ILE Chi-restraints excluded: chain Q residue 96 THR Chi-restraints excluded: chain Q residue 118 VAL Chi-restraints excluded: chain R residue 13 HIS Chi-restraints excluded: chain R residue 15 VAL Chi-restraints excluded: chain R residue 18 LEU Chi-restraints excluded: chain R residue 64 VAL Chi-restraints excluded: chain S residue 37 ASP Chi-restraints excluded: chain S residue 44 VAL Chi-restraints excluded: chain S residue 50 LEU Chi-restraints excluded: chain S residue 78 LEU Chi-restraints excluded: chain T residue 12 SER Chi-restraints excluded: chain T residue 16 ARG Chi-restraints excluded: chain T residue 74 VAL Chi-restraints excluded: chain T residue 84 LEU Chi-restraints excluded: chain U residue 39 PHE Chi-restraints excluded: chain U residue 57 ILE Chi-restraints excluded: chain U residue 75 ILE Chi-restraints excluded: chain V residue 28 VAL Chi-restraints excluded: chain V residue 50 ASN Chi-restraints excluded: chain V residue 57 VAL Chi-restraints excluded: chain V residue 69 THR Chi-restraints excluded: chain W residue 25 ILE Chi-restraints excluded: chain W residue 33 THR Chi-restraints excluded: chain W residue 73 HIS Chi-restraints excluded: chain X residue 39 ILE Chi-restraints excluded: chain X residue 47 THR Chi-restraints excluded: chain X residue 66 VAL Chi-restraints excluded: chain Y residue 11 ILE Chi-restraints excluded: chain Y residue 19 HIS Chi-restraints excluded: chain Y residue 25 SER Chi-restraints excluded: chain Y residue 57 VAL Chi-restraints excluded: chain Z residue 12 ASP Chi-restraints excluded: chain Z residue 18 PHE Chi-restraints excluded: chain Z residue 43 GLU Chi-restraints excluded: chain Z residue 59 LEU Chi-restraints excluded: chain a residue 21 TYR Chi-restraints excluded: chain a residue 24 ASN Chi-restraints excluded: chain a residue 39 VAL Chi-restraints excluded: chain a residue 174 THR Chi-restraints excluded: chain 8 residue 24 THR Chi-restraints excluded: chain 8 residue 86 ILE Chi-restraints excluded: chain 8 residue 96 THR Chi-restraints excluded: chain 8 residue 105 VAL Chi-restraints excluded: chain 8 residue 110 VAL Chi-restraints excluded: chain 8 residue 126 VAL Chi-restraints excluded: chain 8 residue 167 VAL Chi-restraints excluded: chain 8 residue 182 VAL Chi-restraints excluded: chain 8 residue 186 VAL Chi-restraints excluded: chain 8 residue 201 THR Chi-restraints excluded: chain 8 residue 204 TYR Chi-restraints excluded: chain 8 residue 247 GLU Chi-restraints excluded: chain 8 residue 264 VAL Chi-restraints excluded: chain 8 residue 266 CYS Chi-restraints excluded: chain 8 residue 278 MET Chi-restraints excluded: chain 8 residue 292 VAL Chi-restraints excluded: chain 8 residue 300 ASP Chi-restraints excluded: chain 8 residue 301 ASP Chi-restraints excluded: chain 8 residue 330 VAL Chi-restraints excluded: chain 8 residue 494 ILE Chi-restraints excluded: chain 8 residue 521 ASP Chi-restraints excluded: chain 8 residue 571 VAL Chi-restraints excluded: chain 8 residue 585 ASP Chi-restraints excluded: chain 8 residue 622 GLU Chi-restraints excluded: chain 8 residue 623 THR Chi-restraints excluded: chain 8 residue 673 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1109 random chunks: chunk 1034 optimal weight: 50.0000 chunk 120 optimal weight: 6.9990 chunk 611 optimal weight: 30.0000 chunk 783 optimal weight: 10.0000 chunk 607 optimal weight: 20.0000 chunk 903 optimal weight: 10.0000 chunk 599 optimal weight: 20.0000 chunk 1068 optimal weight: 5.9990 chunk 668 optimal weight: 40.0000 chunk 651 optimal weight: 10.0000 chunk 493 optimal weight: 30.0000 overall best weight: 8.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 43 ASN j 128 ASN ** n 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 65 ASN ** u 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 29 GLN G 17 HIS ** I 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 11 GLN ** J 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 96 ASN ** M 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 37 ASN ** N 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 15 HIS ** O 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 2 ASN ** a 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.3516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 166269 Z= 0.306 Angle : 0.694 14.208 247957 Z= 0.356 Chirality : 0.039 0.369 31576 Planarity : 0.005 0.064 13872 Dihedral : 23.512 176.735 81269 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 18.65 Ramachandran Plot: Outliers : 0.23 % Allowed : 13.15 % Favored : 86.62 % Rotamer: Outliers : 6.54 % Allowed : 22.09 % Favored : 71.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: 6517 helix: -0.56 (0.11), residues: 2026 sheet: -2.01 (0.14), residues: 1126 loop : -2.50 (0.10), residues: 3365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP L 102 HIS 0.006 0.001 HIS z 33 PHE 0.058 0.002 PHE R 62 TYR 0.035 0.002 TYR X 79 ARG 0.008 0.001 ARG Q 109 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13034 Ramachandran restraints generated. 6517 Oldfield, 0 Emsley, 6517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13034 Ramachandran restraints generated. 6517 Oldfield, 0 Emsley, 6517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1172 residues out of total 5429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 355 poor density : 817 time to evaluate : 6.678 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: b 86 ARG cc_start: 0.8193 (OUTLIER) cc_final: 0.7219 (mtm-85) REVERT: b 127 ASN cc_start: 0.8033 (OUTLIER) cc_final: 0.7586 (m-40) REVERT: b 235 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.7545 (tp30) REVERT: e 6 TYR cc_start: 0.8680 (t80) cc_final: 0.8370 (t80) REVERT: e 93 GLU cc_start: 0.8509 (OUTLIER) cc_final: 0.8203 (pp20) REVERT: e 172 PHE cc_start: 0.7088 (t80) cc_final: 0.6859 (t80) REVERT: j 31 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.7344 (mp0) REVERT: j 55 ILE cc_start: 0.9083 (mt) cc_final: 0.8737 (tt) REVERT: k 1 MET cc_start: 0.8091 (ttm) cc_final: 0.7639 (ttp) REVERT: l 121 THR cc_start: 0.7558 (OUTLIER) cc_final: 0.7233 (p) REVERT: m 60 GLN cc_start: 0.7525 (OUTLIER) cc_final: 0.6220 (pp30) REVERT: n 27 SER cc_start: 0.8710 (m) cc_final: 0.8325 (p) REVERT: n 72 ASP cc_start: 0.7230 (t0) cc_final: 0.6855 (t70) REVERT: n 73 ASN cc_start: 0.7248 (p0) cc_final: 0.6940 (p0) REVERT: o 93 ASP cc_start: 0.7059 (t0) cc_final: 0.6758 (t0) REVERT: p 26 GLU cc_start: 0.7521 (mm-30) cc_final: 0.6842 (tm-30) REVERT: q 73 ILE cc_start: 0.8744 (tp) cc_final: 0.8481 (tp) REVERT: q 94 LEU cc_start: 0.9092 (OUTLIER) cc_final: 0.8612 (mp) REVERT: r 40 MET cc_start: 0.7778 (tmm) cc_final: 0.7480 (tmm) REVERT: r 48 LYS cc_start: 0.7690 (OUTLIER) cc_final: 0.7455 (mtmt) REVERT: t 61 LEU cc_start: 0.8988 (OUTLIER) cc_final: 0.8630 (pp) REVERT: u 98 ASN cc_start: 0.7247 (OUTLIER) cc_final: 0.7025 (p0) REVERT: x 19 HIS cc_start: 0.8443 (OUTLIER) cc_final: 0.8039 (t70) REVERT: x 55 MET cc_start: 0.8225 (mpp) cc_final: 0.7764 (mtm) REVERT: x 73 ARG cc_start: 0.8353 (ttp80) cc_final: 0.7939 (mtp180) REVERT: y 7 ARG cc_start: 0.8568 (ptm160) cc_final: 0.8253 (ptm160) REVERT: A 3 LYS cc_start: 0.8045 (mttt) cc_final: 0.7811 (tptp) REVERT: A 8 LYS cc_start: 0.7366 (tmmt) cc_final: 0.7100 (tmtt) REVERT: A 12 ILE cc_start: 0.7841 (tp) cc_final: 0.7600 (tt) REVERT: C 6 GLU cc_start: 0.7812 (pt0) cc_final: 0.6536 (pm20) REVERT: E 63 TYR cc_start: 0.8292 (OUTLIER) cc_final: 0.7935 (m-80) REVERT: F 37 GLN cc_start: 0.8382 (tp40) cc_final: 0.8068 (tp-100) REVERT: G 22 TRP cc_start: 0.8344 (p-90) cc_final: 0.8062 (p-90) REVERT: G 58 LYS cc_start: 0.9294 (mmtp) cc_final: 0.8814 (tptp) REVERT: G 173 LYS cc_start: 0.8552 (ttmt) cc_final: 0.7569 (tmtt) REVERT: G 191 ASP cc_start: 0.8648 (OUTLIER) cc_final: 0.8342 (t0) REVERT: H 5 HIS cc_start: 0.7268 (t-90) cc_final: 0.6313 (t70) REVERT: H 40 GLN cc_start: 0.8168 (tp-100) cc_final: 0.7563 (pp30) REVERT: H 104 GLU cc_start: 0.6357 (OUTLIER) cc_final: 0.5803 (tm-30) REVERT: H 133 MET cc_start: 0.7718 (ttt) cc_final: 0.7410 (ttt) REVERT: H 182 ASP cc_start: 0.7168 (t0) cc_final: 0.6619 (t70) REVERT: I 63 ILE cc_start: 0.8639 (mt) cc_final: 0.8291 (mt) REVERT: J 82 HIS cc_start: 0.8458 (OUTLIER) cc_final: 0.7960 (p90) REVERT: J 105 ILE cc_start: 0.7987 (pt) cc_final: 0.7760 (mt) REVERT: J 115 GLU cc_start: 0.8169 (pt0) cc_final: 0.7681 (pt0) REVERT: K 55 HIS cc_start: 0.8161 (OUTLIER) cc_final: 0.7509 (p-80) REVERT: M 8 ASP cc_start: 0.8144 (t70) cc_final: 0.7931 (t0) REVERT: M 11 THR cc_start: 0.9061 (m) cc_final: 0.8824 (p) REVERT: M 72 GLU cc_start: 0.7819 (tp30) cc_final: 0.7350 (tt0) REVERT: M 95 MET cc_start: 0.7291 (tpp) cc_final: 0.6906 (tpp) REVERT: N 87 MET cc_start: 0.7832 (mmp) cc_final: 0.7617 (mmp) REVERT: N 93 LEU cc_start: 0.3915 (OUTLIER) cc_final: 0.3696 (tp) REVERT: N 106 ASP cc_start: 0.7550 (t70) cc_final: 0.7181 (t0) REVERT: N 117 LEU cc_start: 0.9211 (mp) cc_final: 0.8961 (mm) REVERT: O 20 GLN cc_start: 0.8092 (mm-40) cc_final: 0.7675 (mt0) REVERT: P 58 THR cc_start: 0.8452 (p) cc_final: 0.8170 (p) REVERT: Q 88 ASP cc_start: 0.7577 (t70) cc_final: 0.7195 (t0) REVERT: T 25 GLU cc_start: 0.8726 (mp0) cc_final: 0.8506 (mp0) REVERT: T 84 LEU cc_start: 0.7730 (OUTLIER) cc_final: 0.7506 (mm) REVERT: U 1 MET cc_start: 0.3273 (tmm) cc_final: 0.2566 (tmm) REVERT: U 39 PHE cc_start: 0.8014 (OUTLIER) cc_final: 0.7486 (t80) REVERT: V 16 MET cc_start: 0.7259 (tpp) cc_final: 0.6471 (tpt) REVERT: V 60 ILE cc_start: 0.8826 (pt) cc_final: 0.8253 (pt) REVERT: V 72 TRP cc_start: 0.6065 (m100) cc_final: 0.5509 (m100) REVERT: X 40 PHE cc_start: 0.6451 (m-10) cc_final: 0.5819 (m-10) REVERT: X 43 MET cc_start: 0.7603 (mtm) cc_final: 0.6955 (mtm) REVERT: Z 11 PHE cc_start: 0.5584 (OUTLIER) cc_final: 0.4972 (p90) REVERT: a 186 LYS cc_start: 0.4407 (tptp) cc_final: 0.3725 (ptmt) REVERT: 8 10 TYR cc_start: 0.6808 (m-80) cc_final: 0.6103 (m-80) REVERT: 8 184 ASP cc_start: 0.6184 (OUTLIER) cc_final: 0.5877 (p0) REVERT: 8 204 TYR cc_start: 0.5978 (OUTLIER) cc_final: 0.5600 (p90) REVERT: 8 234 MET cc_start: 0.6564 (tpt) cc_final: 0.6140 (tmm) REVERT: 8 241 GLU cc_start: 0.6562 (tt0) cc_final: 0.5848 (pt0) REVERT: 8 278 MET cc_start: 0.6950 (OUTLIER) cc_final: 0.6325 (ptt) REVERT: 8 301 ASP cc_start: 0.3270 (OUTLIER) cc_final: 0.1034 (t70) REVERT: 8 474 LYS cc_start: 0.7462 (tptp) cc_final: 0.7206 (tptp) REVERT: 8 663 MET cc_start: 0.8096 (mmm) cc_final: 0.7478 (mmm) outliers start: 355 outliers final: 275 residues processed: 1077 average time/residue: 1.2648 time to fit residues: 2438.1746 Evaluate side-chains 1090 residues out of total 5429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 300 poor density : 790 time to evaluate : 6.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 86 ARG Chi-restraints excluded: chain b residue 127 ASN Chi-restraints excluded: chain b residue 161 VAL Chi-restraints excluded: chain b residue 203 VAL Chi-restraints excluded: chain b residue 215 VAL Chi-restraints excluded: chain b residue 224 MET Chi-restraints excluded: chain b residue 235 GLU Chi-restraints excluded: chain b residue 244 VAL Chi-restraints excluded: chain b residue 262 THR Chi-restraints excluded: chain b residue 266 ILE Chi-restraints excluded: chain c residue 1 MET Chi-restraints excluded: chain c residue 2 ILE Chi-restraints excluded: chain c residue 25 THR Chi-restraints excluded: chain c residue 60 VAL Chi-restraints excluded: chain c residue 131 ASP Chi-restraints excluded: chain c residue 146 ILE Chi-restraints excluded: chain c residue 176 ASP Chi-restraints excluded: chain c residue 180 VAL Chi-restraints excluded: chain c residue 188 LEU Chi-restraints excluded: chain c residue 197 THR Chi-restraints excluded: chain c residue 202 ILE Chi-restraints excluded: chain d residue 77 ILE Chi-restraints excluded: chain d residue 120 VAL Chi-restraints excluded: chain d residue 188 MET Chi-restraints excluded: chain d residue 189 THR Chi-restraints excluded: chain e residue 16 MET Chi-restraints excluded: chain e residue 24 VAL Chi-restraints excluded: chain e residue 30 VAL Chi-restraints excluded: chain e residue 39 VAL Chi-restraints excluded: chain e residue 56 LEU Chi-restraints excluded: chain e residue 93 GLU Chi-restraints excluded: chain e residue 112 ASP Chi-restraints excluded: chain e residue 126 ASN Chi-restraints excluded: chain e residue 128 SER Chi-restraints excluded: chain e residue 131 VAL Chi-restraints excluded: chain e residue 146 ASP Chi-restraints excluded: chain f residue 9 VAL Chi-restraints excluded: chain f residue 78 VAL Chi-restraints excluded: chain f residue 165 ASP Chi-restraints excluded: chain g residue 4 ILE Chi-restraints excluded: chain g residue 6 LEU Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain g residue 121 VAL Chi-restraints excluded: chain g residue 122 LEU Chi-restraints excluded: chain g residue 125 THR Chi-restraints excluded: chain i residue 12 VAL Chi-restraints excluded: chain i residue 23 VAL Chi-restraints excluded: chain i residue 34 ILE Chi-restraints excluded: chain i residue 45 THR Chi-restraints excluded: chain i residue 48 ILE Chi-restraints excluded: chain i residue 57 VAL Chi-restraints excluded: chain i residue 70 THR Chi-restraints excluded: chain j residue 3 THR Chi-restraints excluded: chain j residue 31 GLU Chi-restraints excluded: chain j residue 57 LEU Chi-restraints excluded: chain j residue 62 VAL Chi-restraints excluded: chain j residue 84 ILE Chi-restraints excluded: chain k residue 51 LYS Chi-restraints excluded: chain k residue 56 ASP Chi-restraints excluded: chain k residue 73 ASP Chi-restraints excluded: chain k residue 85 VAL Chi-restraints excluded: chain k residue 90 ASN Chi-restraints excluded: chain k residue 107 LEU Chi-restraints excluded: chain k residue 111 LYS Chi-restraints excluded: chain l residue 103 ILE Chi-restraints excluded: chain l residue 121 THR Chi-restraints excluded: chain m residue 7 THR Chi-restraints excluded: chain m residue 42 THR Chi-restraints excluded: chain m residue 60 GLN Chi-restraints excluded: chain m residue 63 ILE Chi-restraints excluded: chain m residue 70 ASP Chi-restraints excluded: chain m residue 78 LEU Chi-restraints excluded: chain m residue 88 ASN Chi-restraints excluded: chain m residue 91 TYR Chi-restraints excluded: chain m residue 124 LEU Chi-restraints excluded: chain m residue 126 ILE Chi-restraints excluded: chain m residue 129 THR Chi-restraints excluded: chain m residue 132 THR Chi-restraints excluded: chain n residue 2 ARG Chi-restraints excluded: chain n residue 33 ILE Chi-restraints excluded: chain n residue 34 ILE Chi-restraints excluded: chain n residue 37 THR Chi-restraints excluded: chain n residue 51 LEU Chi-restraints excluded: chain n residue 54 LEU Chi-restraints excluded: chain n residue 115 LEU Chi-restraints excluded: chain n residue 120 GLU Chi-restraints excluded: chain o residue 35 ILE Chi-restraints excluded: chain o residue 47 VAL Chi-restraints excluded: chain o residue 52 SER Chi-restraints excluded: chain o residue 62 LEU Chi-restraints excluded: chain o residue 69 ASP Chi-restraints excluded: chain p residue 40 GLN Chi-restraints excluded: chain p residue 47 ILE Chi-restraints excluded: chain p residue 79 VAL Chi-restraints excluded: chain p residue 84 SER Chi-restraints excluded: chain p residue 96 LEU Chi-restraints excluded: chain p residue 103 THR Chi-restraints excluded: chain p residue 113 LEU Chi-restraints excluded: chain q residue 7 VAL Chi-restraints excluded: chain q residue 94 LEU Chi-restraints excluded: chain q residue 106 THR Chi-restraints excluded: chain q residue 109 VAL Chi-restraints excluded: chain r residue 1 MET Chi-restraints excluded: chain r residue 48 LYS Chi-restraints excluded: chain r residue 101 ILE Chi-restraints excluded: chain s residue 3 THR Chi-restraints excluded: chain s residue 4 ILE Chi-restraints excluded: chain s residue 76 VAL Chi-restraints excluded: chain s residue 105 VAL Chi-restraints excluded: chain t residue 24 MET Chi-restraints excluded: chain t residue 61 LEU Chi-restraints excluded: chain t residue 63 VAL Chi-restraints excluded: chain t residue 93 LEU Chi-restraints excluded: chain u residue 27 VAL Chi-restraints excluded: chain u residue 48 VAL Chi-restraints excluded: chain u residue 67 SER Chi-restraints excluded: chain u residue 69 VAL Chi-restraints excluded: chain u residue 71 ILE Chi-restraints excluded: chain u residue 88 ASP Chi-restraints excluded: chain u residue 98 ASN Chi-restraints excluded: chain v residue 5 ASN Chi-restraints excluded: chain v residue 40 ILE Chi-restraints excluded: chain v residue 61 LEU Chi-restraints excluded: chain v residue 65 VAL Chi-restraints excluded: chain v residue 76 ASP Chi-restraints excluded: chain v residue 86 LEU Chi-restraints excluded: chain w residue 34 VAL Chi-restraints excluded: chain w residue 63 VAL Chi-restraints excluded: chain x residue 12 VAL Chi-restraints excluded: chain x residue 19 HIS Chi-restraints excluded: chain x residue 47 THR Chi-restraints excluded: chain x residue 60 LYS Chi-restraints excluded: chain x residue 76 LYS Chi-restraints excluded: chain y residue 8 GLU Chi-restraints excluded: chain y residue 30 MET Chi-restraints excluded: chain z residue 6 ILE Chi-restraints excluded: chain z residue 40 THR Chi-restraints excluded: chain z residue 56 VAL Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 30 HIS Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 58 ASP Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 37 LYS Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 60 CYS Chi-restraints excluded: chain E residue 63 TYR Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 23 ILE Chi-restraints excluded: chain F residue 27 CYS Chi-restraints excluded: chain G residue 86 CYS Chi-restraints excluded: chain G residue 169 HIS Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 191 ASP Chi-restraints excluded: chain G residue 203 ASP Chi-restraints excluded: chain H residue 4 VAL Chi-restraints excluded: chain H residue 7 ASN Chi-restraints excluded: chain H residue 30 ASP Chi-restraints excluded: chain H residue 104 GLU Chi-restraints excluded: chain H residue 156 LEU Chi-restraints excluded: chain H residue 164 THR Chi-restraints excluded: chain H residue 180 ASP Chi-restraints excluded: chain H residue 194 VAL Chi-restraints excluded: chain I residue 19 PHE Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 34 GLU Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 57 LYS Chi-restraints excluded: chain I residue 97 LEU Chi-restraints excluded: chain I residue 98 ASP Chi-restraints excluded: chain I residue 170 LEU Chi-restraints excluded: chain I residue 191 SER Chi-restraints excluded: chain I residue 194 ILE Chi-restraints excluded: chain J residue 15 ILE Chi-restraints excluded: chain J residue 35 LEU Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 60 GLN Chi-restraints excluded: chain J residue 61 LYS Chi-restraints excluded: chain J residue 79 THR Chi-restraints excluded: chain J residue 82 HIS Chi-restraints excluded: chain J residue 104 ILE Chi-restraints excluded: chain J residue 120 HIS Chi-restraints excluded: chain J residue 123 LEU Chi-restraints excluded: chain K residue 11 HIS Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 55 HIS Chi-restraints excluded: chain K residue 60 VAL Chi-restraints excluded: chain K residue 85 ILE Chi-restraints excluded: chain K residue 93 LYS Chi-restraints excluded: chain K residue 96 VAL Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 29 LEU Chi-restraints excluded: chain L residue 84 TYR Chi-restraints excluded: chain L residue 93 VAL Chi-restraints excluded: chain L residue 103 ILE Chi-restraints excluded: chain M residue 53 ASP Chi-restraints excluded: chain M residue 62 LEU Chi-restraints excluded: chain M residue 126 CYS Chi-restraints excluded: chain N residue 8 THR Chi-restraints excluded: chain N residue 28 VAL Chi-restraints excluded: chain N residue 38 PHE Chi-restraints excluded: chain N residue 42 THR Chi-restraints excluded: chain N residue 54 VAL Chi-restraints excluded: chain N residue 65 THR Chi-restraints excluded: chain N residue 83 THR Chi-restraints excluded: chain N residue 93 LEU Chi-restraints excluded: chain N residue 125 GLN Chi-restraints excluded: chain O residue 10 LEU Chi-restraints excluded: chain O residue 15 HIS Chi-restraints excluded: chain O residue 19 ASP Chi-restraints excluded: chain O residue 50 THR Chi-restraints excluded: chain O residue 66 GLU Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain O residue 83 THR Chi-restraints excluded: chain P residue 29 THR Chi-restraints excluded: chain P residue 30 ILE Chi-restraints excluded: chain P residue 84 MET Chi-restraints excluded: chain Q residue 20 VAL Chi-restraints excluded: chain Q residue 39 THR Chi-restraints excluded: chain Q residue 42 LYS Chi-restraints excluded: chain Q residue 61 GLU Chi-restraints excluded: chain Q residue 66 ILE Chi-restraints excluded: chain Q residue 96 THR Chi-restraints excluded: chain Q residue 118 VAL Chi-restraints excluded: chain R residue 13 HIS Chi-restraints excluded: chain R residue 15 VAL Chi-restraints excluded: chain R residue 18 LEU Chi-restraints excluded: chain R residue 64 VAL Chi-restraints excluded: chain S residue 37 ASP Chi-restraints excluded: chain S residue 44 VAL Chi-restraints excluded: chain S residue 50 LEU Chi-restraints excluded: chain S residue 78 LEU Chi-restraints excluded: chain T residue 16 ARG Chi-restraints excluded: chain T residue 74 VAL Chi-restraints excluded: chain T residue 84 LEU Chi-restraints excluded: chain U residue 39 PHE Chi-restraints excluded: chain U residue 57 ILE Chi-restraints excluded: chain U residue 75 ILE Chi-restraints excluded: chain V residue 28 VAL Chi-restraints excluded: chain V residue 50 ASN Chi-restraints excluded: chain V residue 57 VAL Chi-restraints excluded: chain V residue 69 THR Chi-restraints excluded: chain W residue 25 ILE Chi-restraints excluded: chain W residue 33 THR Chi-restraints excluded: chain X residue 39 ILE Chi-restraints excluded: chain X residue 47 THR Chi-restraints excluded: chain X residue 66 VAL Chi-restraints excluded: chain Y residue 11 ILE Chi-restraints excluded: chain Y residue 19 HIS Chi-restraints excluded: chain Y residue 25 SER Chi-restraints excluded: chain Z residue 11 PHE Chi-restraints excluded: chain Z residue 12 ASP Chi-restraints excluded: chain Z residue 43 GLU Chi-restraints excluded: chain Z residue 59 LEU Chi-restraints excluded: chain a residue 21 TYR Chi-restraints excluded: chain a residue 24 ASN Chi-restraints excluded: chain a residue 39 VAL Chi-restraints excluded: chain a residue 56 ASP Chi-restraints excluded: chain a residue 64 VAL Chi-restraints excluded: chain a residue 174 THR Chi-restraints excluded: chain 8 residue 24 THR Chi-restraints excluded: chain 8 residue 86 ILE Chi-restraints excluded: chain 8 residue 96 THR Chi-restraints excluded: chain 8 residue 105 VAL Chi-restraints excluded: chain 8 residue 110 VAL Chi-restraints excluded: chain 8 residue 112 VAL Chi-restraints excluded: chain 8 residue 126 VAL Chi-restraints excluded: chain 8 residue 167 VAL Chi-restraints excluded: chain 8 residue 182 VAL Chi-restraints excluded: chain 8 residue 184 ASP Chi-restraints excluded: chain 8 residue 186 VAL Chi-restraints excluded: chain 8 residue 201 THR Chi-restraints excluded: chain 8 residue 204 TYR Chi-restraints excluded: chain 8 residue 247 GLU Chi-restraints excluded: chain 8 residue 264 VAL Chi-restraints excluded: chain 8 residue 266 CYS Chi-restraints excluded: chain 8 residue 278 MET Chi-restraints excluded: chain 8 residue 292 VAL Chi-restraints excluded: chain 8 residue 298 ILE Chi-restraints excluded: chain 8 residue 300 ASP Chi-restraints excluded: chain 8 residue 301 ASP Chi-restraints excluded: chain 8 residue 330 VAL Chi-restraints excluded: chain 8 residue 374 ILE Chi-restraints excluded: chain 8 residue 494 ILE Chi-restraints excluded: chain 8 residue 521 ASP Chi-restraints excluded: chain 8 residue 530 ASN Chi-restraints excluded: chain 8 residue 571 VAL Chi-restraints excluded: chain 8 residue 585 ASP Chi-restraints excluded: chain 8 residue 621 VAL Chi-restraints excluded: chain 8 residue 622 GLU Chi-restraints excluded: chain 8 residue 623 THR Chi-restraints excluded: chain 8 residue 673 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1109 random chunks: chunk 661 optimal weight: 10.0000 chunk 426 optimal weight: 30.0000 chunk 638 optimal weight: 20.0000 chunk 321 optimal weight: 8.9990 chunk 210 optimal weight: 20.0000 chunk 207 optimal weight: 2.9990 chunk 679 optimal weight: 20.0000 chunk 728 optimal weight: 20.0000 chunk 528 optimal weight: 30.0000 chunk 99 optimal weight: 20.0000 chunk 840 optimal weight: 20.0000 overall best weight: 12.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 43 ASN ** j 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 65 ASN ** u 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 29 GLN ** E 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 37 ASN ** N 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 15 HIS ** O 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 2 ASN ** a 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 165 ASN ** 8 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.3706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.111 166269 Z= 0.429 Angle : 0.809 13.758 247957 Z= 0.410 Chirality : 0.044 0.416 31576 Planarity : 0.006 0.069 13872 Dihedral : 23.688 175.323 81265 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 22.69 Ramachandran Plot: Outliers : 0.25 % Allowed : 14.30 % Favored : 85.45 % Rotamer: Outliers : 6.61 % Allowed : 22.45 % Favored : 70.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -2.92 (0.10), residues: 6517 helix: -0.83 (0.11), residues: 2030 sheet: -2.03 (0.14), residues: 1158 loop : -2.66 (0.10), residues: 3329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.003 TRP L 102 HIS 0.019 0.002 HIS O 15 PHE 0.044 0.003 PHE R 62 TYR 0.037 0.002 TYR X 79 ARG 0.010 0.001 ARG m 44 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13034 Ramachandran restraints generated. 6517 Oldfield, 0 Emsley, 6517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13034 Ramachandran restraints generated. 6517 Oldfield, 0 Emsley, 6517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1148 residues out of total 5429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 359 poor density : 789 time to evaluate : 6.051 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: b 86 ARG cc_start: 0.8314 (OUTLIER) cc_final: 0.7350 (mtm-85) REVERT: b 127 ASN cc_start: 0.8059 (OUTLIER) cc_final: 0.7598 (m-40) REVERT: e 93 GLU cc_start: 0.8554 (OUTLIER) cc_final: 0.8239 (pp20) REVERT: e 172 PHE cc_start: 0.7280 (t80) cc_final: 0.7060 (t80) REVERT: j 98 GLU cc_start: 0.7385 (mt-10) cc_final: 0.7136 (mt-10) REVERT: k 1 MET cc_start: 0.8183 (ttm) cc_final: 0.7764 (ttp) REVERT: l 121 THR cc_start: 0.7487 (OUTLIER) cc_final: 0.7181 (p) REVERT: m 60 GLN cc_start: 0.7646 (OUTLIER) cc_final: 0.6222 (pp30) REVERT: n 27 SER cc_start: 0.8789 (m) cc_final: 0.8373 (p) REVERT: n 72 ASP cc_start: 0.7381 (t0) cc_final: 0.7155 (t70) REVERT: n 73 ASN cc_start: 0.7469 (p0) cc_final: 0.7151 (p0) REVERT: o 93 ASP cc_start: 0.7193 (t0) cc_final: 0.6829 (t0) REVERT: p 26 GLU cc_start: 0.7718 (mm-30) cc_final: 0.6816 (tm-30) REVERT: q 73 ILE cc_start: 0.8821 (tp) cc_final: 0.8553 (tp) REVERT: q 94 LEU cc_start: 0.9141 (OUTLIER) cc_final: 0.8674 (mp) REVERT: t 61 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8681 (pp) REVERT: u 98 ASN cc_start: 0.7326 (OUTLIER) cc_final: 0.6992 (p0) REVERT: x 19 HIS cc_start: 0.8488 (OUTLIER) cc_final: 0.8124 (t70) REVERT: x 55 MET cc_start: 0.8313 (mpp) cc_final: 0.7897 (mtm) REVERT: x 73 ARG cc_start: 0.8387 (ttp80) cc_final: 0.7989 (mtp180) REVERT: y 7 ARG cc_start: 0.8603 (ptm160) cc_final: 0.8275 (ptm160) REVERT: A 3 LYS cc_start: 0.7970 (mttt) cc_final: 0.7499 (tptp) REVERT: A 8 LYS cc_start: 0.7389 (tmmt) cc_final: 0.7126 (tmtt) REVERT: A 12 ILE cc_start: 0.7932 (tp) cc_final: 0.7695 (tt) REVERT: C 6 GLU cc_start: 0.7802 (pt0) cc_final: 0.6521 (pm20) REVERT: C 9 LYS cc_start: 0.7544 (ptmt) cc_final: 0.7333 (ptpt) REVERT: E 63 TYR cc_start: 0.8305 (OUTLIER) cc_final: 0.7934 (m-80) REVERT: F 37 GLN cc_start: 0.8458 (tp40) cc_final: 0.8137 (tp-100) REVERT: G 22 TRP cc_start: 0.8407 (p-90) cc_final: 0.8008 (p-90) REVERT: G 58 LYS cc_start: 0.9328 (mmtp) cc_final: 0.8826 (tptp) REVERT: G 173 LYS cc_start: 0.8568 (ttmt) cc_final: 0.7589 (tmtt) REVERT: G 191 ASP cc_start: 0.8665 (OUTLIER) cc_final: 0.8355 (t70) REVERT: H 5 HIS cc_start: 0.7405 (t-90) cc_final: 0.6475 (t70) REVERT: H 40 GLN cc_start: 0.8187 (tp-100) cc_final: 0.7705 (pt0) REVERT: H 104 GLU cc_start: 0.6490 (OUTLIER) cc_final: 0.5974 (tm-30) REVERT: H 133 MET cc_start: 0.7685 (ttt) cc_final: 0.7410 (ttt) REVERT: H 182 ASP cc_start: 0.7369 (t0) cc_final: 0.6826 (t70) REVERT: I 63 ILE cc_start: 0.8651 (mt) cc_final: 0.8303 (mt) REVERT: I 202 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.8185 (tt) REVERT: J 115 GLU cc_start: 0.8204 (pt0) cc_final: 0.7762 (pt0) REVERT: K 55 HIS cc_start: 0.8225 (OUTLIER) cc_final: 0.7508 (p-80) REVERT: M 72 GLU cc_start: 0.7768 (tp30) cc_final: 0.7326 (tt0) REVERT: N 93 LEU cc_start: 0.3897 (OUTLIER) cc_final: 0.3658 (tp) REVERT: N 106 ASP cc_start: 0.7472 (t70) cc_final: 0.7110 (t0) REVERT: N 117 LEU cc_start: 0.9161 (mp) cc_final: 0.8919 (mm) REVERT: O 20 GLN cc_start: 0.8108 (mm-40) cc_final: 0.7689 (mt0) REVERT: Q 88 ASP cc_start: 0.7597 (t70) cc_final: 0.7234 (t0) REVERT: T 63 ARG cc_start: 0.8013 (OUTLIER) cc_final: 0.7182 (ttm110) REVERT: T 84 LEU cc_start: 0.7785 (OUTLIER) cc_final: 0.7504 (mm) REVERT: U 1 MET cc_start: 0.2706 (tmm) cc_final: 0.2310 (tmm) REVERT: U 39 PHE cc_start: 0.8040 (OUTLIER) cc_final: 0.7509 (t80) REVERT: V 16 MET cc_start: 0.7293 (tpp) cc_final: 0.6936 (tpp) REVERT: V 64 ARG cc_start: 0.7941 (ptt-90) cc_final: 0.7428 (ttp-170) REVERT: V 72 TRP cc_start: 0.6037 (m100) cc_final: 0.5737 (m100) REVERT: X 40 PHE cc_start: 0.6386 (m-10) cc_final: 0.5729 (m-10) REVERT: X 43 MET cc_start: 0.7624 (mtm) cc_final: 0.6957 (mtm) REVERT: X 72 GLU cc_start: 0.5209 (mm-30) cc_final: 0.4941 (mp0) REVERT: Z 11 PHE cc_start: 0.5574 (OUTLIER) cc_final: 0.4997 (p90) REVERT: a 186 LYS cc_start: 0.4358 (tptp) cc_final: 0.3650 (ptmt) REVERT: 8 10 TYR cc_start: 0.6937 (m-80) cc_final: 0.6168 (m-80) REVERT: 8 184 ASP cc_start: 0.6311 (OUTLIER) cc_final: 0.5964 (p0) REVERT: 8 204 TYR cc_start: 0.5971 (OUTLIER) cc_final: 0.5614 (p90) REVERT: 8 234 MET cc_start: 0.6498 (tpt) cc_final: 0.6078 (tmm) REVERT: 8 241 GLU cc_start: 0.6584 (tt0) cc_final: 0.5763 (pt0) REVERT: 8 278 MET cc_start: 0.6916 (OUTLIER) cc_final: 0.6333 (ptt) REVERT: 8 301 ASP cc_start: 0.3315 (OUTLIER) cc_final: 0.1173 (t70) REVERT: 8 663 MET cc_start: 0.8183 (mmm) cc_final: 0.7601 (mmm) outliers start: 359 outliers final: 277 residues processed: 1054 average time/residue: 1.2281 time to fit residues: 2318.4290 Evaluate side-chains 1068 residues out of total 5429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 300 poor density : 768 time to evaluate : 8.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 86 ARG Chi-restraints excluded: chain b residue 127 ASN Chi-restraints excluded: chain b residue 161 VAL Chi-restraints excluded: chain b residue 215 VAL Chi-restraints excluded: chain b residue 224 MET Chi-restraints excluded: chain b residue 244 VAL Chi-restraints excluded: chain b residue 262 THR Chi-restraints excluded: chain b residue 266 ILE Chi-restraints excluded: chain c residue 2 ILE Chi-restraints excluded: chain c residue 24 VAL Chi-restraints excluded: chain c residue 25 THR Chi-restraints excluded: chain c residue 60 VAL Chi-restraints excluded: chain c residue 131 ASP Chi-restraints excluded: chain c residue 146 ILE Chi-restraints excluded: chain c residue 176 ASP Chi-restraints excluded: chain c residue 180 VAL Chi-restraints excluded: chain c residue 188 LEU Chi-restraints excluded: chain c residue 197 THR Chi-restraints excluded: chain c residue 202 ILE Chi-restraints excluded: chain d residue 77 ILE Chi-restraints excluded: chain d residue 120 VAL Chi-restraints excluded: chain d residue 188 MET Chi-restraints excluded: chain d residue 189 THR Chi-restraints excluded: chain e residue 16 MET Chi-restraints excluded: chain e residue 24 VAL Chi-restraints excluded: chain e residue 30 VAL Chi-restraints excluded: chain e residue 39 VAL Chi-restraints excluded: chain e residue 93 GLU Chi-restraints excluded: chain e residue 112 ASP Chi-restraints excluded: chain e residue 126 ASN Chi-restraints excluded: chain e residue 128 SER Chi-restraints excluded: chain e residue 131 VAL Chi-restraints excluded: chain e residue 146 ASP Chi-restraints excluded: chain f residue 9 VAL Chi-restraints excluded: chain f residue 78 VAL Chi-restraints excluded: chain f residue 165 ASP Chi-restraints excluded: chain g residue 4 ILE Chi-restraints excluded: chain g residue 6 LEU Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain g residue 121 VAL Chi-restraints excluded: chain g residue 122 LEU Chi-restraints excluded: chain g residue 125 THR Chi-restraints excluded: chain h residue 38 MET Chi-restraints excluded: chain i residue 12 VAL Chi-restraints excluded: chain i residue 23 VAL Chi-restraints excluded: chain i residue 27 LEU Chi-restraints excluded: chain i residue 34 ILE Chi-restraints excluded: chain i residue 45 THR Chi-restraints excluded: chain i residue 48 ILE Chi-restraints excluded: chain i residue 57 VAL Chi-restraints excluded: chain i residue 70 THR Chi-restraints excluded: chain j residue 3 THR Chi-restraints excluded: chain j residue 57 LEU Chi-restraints excluded: chain j residue 62 VAL Chi-restraints excluded: chain j residue 84 ILE Chi-restraints excluded: chain k residue 51 LYS Chi-restraints excluded: chain k residue 56 ASP Chi-restraints excluded: chain k residue 85 VAL Chi-restraints excluded: chain k residue 90 ASN Chi-restraints excluded: chain k residue 107 LEU Chi-restraints excluded: chain k residue 111 LYS Chi-restraints excluded: chain l residue 103 ILE Chi-restraints excluded: chain l residue 121 THR Chi-restraints excluded: chain m residue 7 THR Chi-restraints excluded: chain m residue 42 THR Chi-restraints excluded: chain m residue 60 GLN Chi-restraints excluded: chain m residue 63 ILE Chi-restraints excluded: chain m residue 70 ASP Chi-restraints excluded: chain m residue 74 THR Chi-restraints excluded: chain m residue 75 GLU Chi-restraints excluded: chain m residue 78 LEU Chi-restraints excluded: chain m residue 88 ASN Chi-restraints excluded: chain m residue 91 TYR Chi-restraints excluded: chain m residue 124 LEU Chi-restraints excluded: chain m residue 126 ILE Chi-restraints excluded: chain m residue 129 THR Chi-restraints excluded: chain m residue 132 THR Chi-restraints excluded: chain n residue 2 ARG Chi-restraints excluded: chain n residue 33 ILE Chi-restraints excluded: chain n residue 37 THR Chi-restraints excluded: chain n residue 51 LEU Chi-restraints excluded: chain n residue 54 LEU Chi-restraints excluded: chain n residue 115 LEU Chi-restraints excluded: chain n residue 120 GLU Chi-restraints excluded: chain o residue 35 ILE Chi-restraints excluded: chain o residue 47 VAL Chi-restraints excluded: chain o residue 52 SER Chi-restraints excluded: chain o residue 53 THR Chi-restraints excluded: chain o residue 62 LEU Chi-restraints excluded: chain o residue 69 ASP Chi-restraints excluded: chain o residue 108 ASP Chi-restraints excluded: chain p residue 18 SER Chi-restraints excluded: chain p residue 40 GLN Chi-restraints excluded: chain p residue 47 ILE Chi-restraints excluded: chain p residue 79 VAL Chi-restraints excluded: chain p residue 84 SER Chi-restraints excluded: chain p residue 96 LEU Chi-restraints excluded: chain p residue 103 THR Chi-restraints excluded: chain p residue 113 LEU Chi-restraints excluded: chain q residue 7 VAL Chi-restraints excluded: chain q residue 94 LEU Chi-restraints excluded: chain q residue 106 THR Chi-restraints excluded: chain q residue 109 VAL Chi-restraints excluded: chain r residue 1 MET Chi-restraints excluded: chain r residue 101 ILE Chi-restraints excluded: chain s residue 3 THR Chi-restraints excluded: chain s residue 4 ILE Chi-restraints excluded: chain s residue 76 VAL Chi-restraints excluded: chain s residue 105 VAL Chi-restraints excluded: chain t residue 24 MET Chi-restraints excluded: chain t residue 61 LEU Chi-restraints excluded: chain t residue 93 LEU Chi-restraints excluded: chain u residue 27 VAL Chi-restraints excluded: chain u residue 48 VAL Chi-restraints excluded: chain u residue 67 SER Chi-restraints excluded: chain u residue 69 VAL Chi-restraints excluded: chain u residue 71 ILE Chi-restraints excluded: chain u residue 88 ASP Chi-restraints excluded: chain u residue 98 ASN Chi-restraints excluded: chain v residue 5 ASN Chi-restraints excluded: chain v residue 40 ILE Chi-restraints excluded: chain v residue 61 LEU Chi-restraints excluded: chain v residue 65 VAL Chi-restraints excluded: chain v residue 86 LEU Chi-restraints excluded: chain w residue 34 VAL Chi-restraints excluded: chain w residue 63 VAL Chi-restraints excluded: chain x residue 12 VAL Chi-restraints excluded: chain x residue 19 HIS Chi-restraints excluded: chain x residue 47 THR Chi-restraints excluded: chain x residue 76 LYS Chi-restraints excluded: chain y residue 8 GLU Chi-restraints excluded: chain y residue 30 MET Chi-restraints excluded: chain z residue 6 ILE Chi-restraints excluded: chain z residue 40 THR Chi-restraints excluded: chain z residue 56 VAL Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 30 HIS Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 58 ASP Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 30 ASP Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 60 CYS Chi-restraints excluded: chain E residue 63 TYR Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 23 ILE Chi-restraints excluded: chain F residue 27 CYS Chi-restraints excluded: chain G residue 40 ILE Chi-restraints excluded: chain G residue 86 CYS Chi-restraints excluded: chain G residue 169 HIS Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 191 ASP Chi-restraints excluded: chain G residue 203 ASP Chi-restraints excluded: chain H residue 4 VAL Chi-restraints excluded: chain H residue 7 ASN Chi-restraints excluded: chain H residue 30 ASP Chi-restraints excluded: chain H residue 104 GLU Chi-restraints excluded: chain H residue 117 ASP Chi-restraints excluded: chain H residue 156 LEU Chi-restraints excluded: chain H residue 164 THR Chi-restraints excluded: chain H residue 180 ASP Chi-restraints excluded: chain H residue 194 VAL Chi-restraints excluded: chain I residue 19 PHE Chi-restraints excluded: chain I residue 34 GLU Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 57 LYS Chi-restraints excluded: chain I residue 97 LEU Chi-restraints excluded: chain I residue 98 ASP Chi-restraints excluded: chain I residue 170 LEU Chi-restraints excluded: chain I residue 191 SER Chi-restraints excluded: chain I residue 194 ILE Chi-restraints excluded: chain I residue 202 LEU Chi-restraints excluded: chain J residue 15 ILE Chi-restraints excluded: chain J residue 35 LEU Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 60 GLN Chi-restraints excluded: chain J residue 61 LYS Chi-restraints excluded: chain J residue 79 THR Chi-restraints excluded: chain J residue 104 ILE Chi-restraints excluded: chain J residue 120 HIS Chi-restraints excluded: chain J residue 123 LEU Chi-restraints excluded: chain K residue 11 HIS Chi-restraints excluded: chain K residue 13 ASP Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 55 HIS Chi-restraints excluded: chain K residue 60 VAL Chi-restraints excluded: chain K residue 85 ILE Chi-restraints excluded: chain K residue 93 LYS Chi-restraints excluded: chain K residue 96 VAL Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 29 LEU Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain L residue 84 TYR Chi-restraints excluded: chain L residue 103 ILE Chi-restraints excluded: chain M residue 2 MET Chi-restraints excluded: chain M residue 39 LEU Chi-restraints excluded: chain M residue 53 ASP Chi-restraints excluded: chain M residue 62 LEU Chi-restraints excluded: chain M residue 126 CYS Chi-restraints excluded: chain N residue 8 THR Chi-restraints excluded: chain N residue 28 VAL Chi-restraints excluded: chain N residue 38 PHE Chi-restraints excluded: chain N residue 42 THR Chi-restraints excluded: chain N residue 54 VAL Chi-restraints excluded: chain N residue 65 THR Chi-restraints excluded: chain N residue 83 THR Chi-restraints excluded: chain N residue 93 LEU Chi-restraints excluded: chain N residue 125 GLN Chi-restraints excluded: chain O residue 10 LEU Chi-restraints excluded: chain O residue 19 ASP Chi-restraints excluded: chain O residue 50 THR Chi-restraints excluded: chain O residue 66 GLU Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain O residue 83 THR Chi-restraints excluded: chain P residue 30 ILE Chi-restraints excluded: chain Q residue 20 VAL Chi-restraints excluded: chain Q residue 39 THR Chi-restraints excluded: chain Q residue 42 LYS Chi-restraints excluded: chain Q residue 61 GLU Chi-restraints excluded: chain Q residue 66 ILE Chi-restraints excluded: chain Q residue 96 THR Chi-restraints excluded: chain Q residue 118 VAL Chi-restraints excluded: chain R residue 15 VAL Chi-restraints excluded: chain R residue 18 LEU Chi-restraints excluded: chain R residue 42 VAL Chi-restraints excluded: chain R residue 64 VAL Chi-restraints excluded: chain S residue 37 ASP Chi-restraints excluded: chain S residue 44 VAL Chi-restraints excluded: chain S residue 50 LEU Chi-restraints excluded: chain S residue 78 LEU Chi-restraints excluded: chain T residue 16 ARG Chi-restraints excluded: chain T residue 23 SER Chi-restraints excluded: chain T residue 63 ARG Chi-restraints excluded: chain T residue 74 VAL Chi-restraints excluded: chain T residue 84 LEU Chi-restraints excluded: chain U residue 39 PHE Chi-restraints excluded: chain U residue 52 LEU Chi-restraints excluded: chain U residue 57 ILE Chi-restraints excluded: chain U residue 75 ILE Chi-restraints excluded: chain V residue 28 VAL Chi-restraints excluded: chain V residue 50 ASN Chi-restraints excluded: chain V residue 57 VAL Chi-restraints excluded: chain V residue 69 THR Chi-restraints excluded: chain W residue 25 ILE Chi-restraints excluded: chain W residue 33 THR Chi-restraints excluded: chain W residue 73 HIS Chi-restraints excluded: chain X residue 39 ILE Chi-restraints excluded: chain X residue 47 THR Chi-restraints excluded: chain X residue 66 VAL Chi-restraints excluded: chain Y residue 11 ILE Chi-restraints excluded: chain Y residue 19 HIS Chi-restraints excluded: chain Y residue 25 SER Chi-restraints excluded: chain Z residue 11 PHE Chi-restraints excluded: chain Z residue 12 ASP Chi-restraints excluded: chain Z residue 18 PHE Chi-restraints excluded: chain Z residue 43 GLU Chi-restraints excluded: chain Z residue 59 LEU Chi-restraints excluded: chain a residue 5 THR Chi-restraints excluded: chain a residue 24 ASN Chi-restraints excluded: chain a residue 39 VAL Chi-restraints excluded: chain a residue 64 VAL Chi-restraints excluded: chain a residue 174 THR Chi-restraints excluded: chain 8 residue 24 THR Chi-restraints excluded: chain 8 residue 86 ILE Chi-restraints excluded: chain 8 residue 96 THR Chi-restraints excluded: chain 8 residue 105 VAL Chi-restraints excluded: chain 8 residue 110 VAL Chi-restraints excluded: chain 8 residue 112 VAL Chi-restraints excluded: chain 8 residue 126 VAL Chi-restraints excluded: chain 8 residue 167 VAL Chi-restraints excluded: chain 8 residue 182 VAL Chi-restraints excluded: chain 8 residue 184 ASP Chi-restraints excluded: chain 8 residue 186 VAL Chi-restraints excluded: chain 8 residue 201 THR Chi-restraints excluded: chain 8 residue 204 TYR Chi-restraints excluded: chain 8 residue 247 GLU Chi-restraints excluded: chain 8 residue 264 VAL Chi-restraints excluded: chain 8 residue 266 CYS Chi-restraints excluded: chain 8 residue 278 MET Chi-restraints excluded: chain 8 residue 292 VAL Chi-restraints excluded: chain 8 residue 300 ASP Chi-restraints excluded: chain 8 residue 301 ASP Chi-restraints excluded: chain 8 residue 330 VAL Chi-restraints excluded: chain 8 residue 374 ILE Chi-restraints excluded: chain 8 residue 494 ILE Chi-restraints excluded: chain 8 residue 521 ASP Chi-restraints excluded: chain 8 residue 530 ASN Chi-restraints excluded: chain 8 residue 571 VAL Chi-restraints excluded: chain 8 residue 585 ASP Chi-restraints excluded: chain 8 residue 621 VAL Chi-restraints excluded: chain 8 residue 622 GLU Chi-restraints excluded: chain 8 residue 623 THR Chi-restraints excluded: chain 8 residue 673 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1109 random chunks: chunk 972 optimal weight: 10.0000 chunk 1024 optimal weight: 20.0000 chunk 934 optimal weight: 50.0000 chunk 996 optimal weight: 10.0000 chunk 1023 optimal weight: 10.0000 chunk 599 optimal weight: 20.0000 chunk 433 optimal weight: 7.9990 chunk 782 optimal weight: 10.0000 chunk 305 optimal weight: 50.0000 chunk 900 optimal weight: 10.0000 chunk 942 optimal weight: 30.0000 overall best weight: 9.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 43 ASN j 128 ASN ** n 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 31 GLN ** A 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 29 GLN ** E 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 2 ASN ** a 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.3805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 166269 Z= 0.330 Angle : 0.726 13.628 247957 Z= 0.371 Chirality : 0.041 0.378 31576 Planarity : 0.005 0.083 13872 Dihedral : 23.681 175.913 81265 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 20.07 Ramachandran Plot: Outliers : 0.23 % Allowed : 13.44 % Favored : 86.33 % Rotamer: Outliers : 6.10 % Allowed : 23.39 % Favored : 70.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -2.78 (0.10), residues: 6517 helix: -0.70 (0.11), residues: 2030 sheet: -1.89 (0.14), residues: 1120 loop : -2.60 (0.10), residues: 3367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP L 102 HIS 0.007 0.001 HIS 8 219 PHE 0.055 0.002 PHE R 62 TYR 0.030 0.002 TYR X 79 ARG 0.008 0.001 ARG Q 109 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13034 Ramachandran restraints generated. 6517 Oldfield, 0 Emsley, 6517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13034 Ramachandran restraints generated. 6517 Oldfield, 0 Emsley, 6517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1126 residues out of total 5429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 331 poor density : 795 time to evaluate : 6.684 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: b 86 ARG cc_start: 0.8217 (OUTLIER) cc_final: 0.7246 (mtm-85) REVERT: b 127 ASN cc_start: 0.8059 (OUTLIER) cc_final: 0.7611 (m-40) REVERT: g 91 PHE cc_start: 0.4182 (OUTLIER) cc_final: 0.3829 (t80) REVERT: k 1 MET cc_start: 0.8078 (ttm) cc_final: 0.7626 (ttp) REVERT: l 121 THR cc_start: 0.7462 (OUTLIER) cc_final: 0.7162 (p) REVERT: m 60 GLN cc_start: 0.7574 (OUTLIER) cc_final: 0.6214 (pp30) REVERT: n 27 SER cc_start: 0.8718 (m) cc_final: 0.8336 (p) REVERT: n 72 ASP cc_start: 0.7326 (t0) cc_final: 0.7092 (t70) REVERT: n 73 ASN cc_start: 0.7385 (p0) cc_final: 0.7085 (p0) REVERT: o 93 ASP cc_start: 0.7008 (t0) cc_final: 0.6719 (t0) REVERT: p 26 GLU cc_start: 0.7760 (mm-30) cc_final: 0.6956 (tm-30) REVERT: q 73 ILE cc_start: 0.8787 (tp) cc_final: 0.8528 (tp) REVERT: q 94 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8626 (mp) REVERT: t 61 LEU cc_start: 0.9006 (OUTLIER) cc_final: 0.8633 (pp) REVERT: u 98 ASN cc_start: 0.7287 (OUTLIER) cc_final: 0.7005 (p0) REVERT: x 19 HIS cc_start: 0.8507 (OUTLIER) cc_final: 0.8041 (t70) REVERT: x 55 MET cc_start: 0.8249 (mpp) cc_final: 0.7871 (mtm) REVERT: x 73 ARG cc_start: 0.8378 (ttp80) cc_final: 0.8002 (mtp180) REVERT: y 7 ARG cc_start: 0.8625 (ptm160) cc_final: 0.8296 (ptm160) REVERT: A 8 LYS cc_start: 0.7354 (tmmt) cc_final: 0.7107 (tmtt) REVERT: A 12 ILE cc_start: 0.7905 (tp) cc_final: 0.7666 (tt) REVERT: C 6 GLU cc_start: 0.7776 (pt0) cc_final: 0.6472 (pm20) REVERT: C 9 LYS cc_start: 0.7644 (ptmt) cc_final: 0.7410 (ptpt) REVERT: C 48 TYR cc_start: 0.6053 (m-80) cc_final: 0.5777 (m-80) REVERT: E 63 TYR cc_start: 0.8301 (OUTLIER) cc_final: 0.7926 (m-80) REVERT: F 37 GLN cc_start: 0.8383 (tp40) cc_final: 0.8081 (tp-100) REVERT: G 22 TRP cc_start: 0.8347 (p-90) cc_final: 0.7997 (p-90) REVERT: G 58 LYS cc_start: 0.9324 (mmtp) cc_final: 0.8829 (tptp) REVERT: G 173 LYS cc_start: 0.8567 (ttmt) cc_final: 0.7590 (tmtt) REVERT: G 191 ASP cc_start: 0.8602 (OUTLIER) cc_final: 0.8275 (t70) REVERT: H 40 GLN cc_start: 0.8190 (tp-100) cc_final: 0.7701 (pt0) REVERT: H 104 GLU cc_start: 0.6457 (OUTLIER) cc_final: 0.5958 (tm-30) REVERT: H 133 MET cc_start: 0.7668 (ttt) cc_final: 0.7433 (ttt) REVERT: H 182 ASP cc_start: 0.7191 (t0) cc_final: 0.6654 (t70) REVERT: I 63 ILE cc_start: 0.8724 (mt) cc_final: 0.8466 (mt) REVERT: I 123 MET cc_start: 0.6361 (ttm) cc_final: 0.6129 (tpp) REVERT: I 202 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.8272 (tt) REVERT: J 115 GLU cc_start: 0.8163 (pt0) cc_final: 0.7714 (pt0) REVERT: J 146 MET cc_start: 0.6843 (tmm) cc_final: 0.6422 (tmm) REVERT: J 156 ARG cc_start: 0.7457 (tmm-80) cc_final: 0.7191 (tmm-80) REVERT: K 55 HIS cc_start: 0.8232 (OUTLIER) cc_final: 0.7571 (p-80) REVERT: M 72 GLU cc_start: 0.7767 (tp30) cc_final: 0.7311 (tt0) REVERT: M 95 MET cc_start: 0.7311 (tpp) cc_final: 0.6997 (tpp) REVERT: N 93 LEU cc_start: 0.3825 (OUTLIER) cc_final: 0.3587 (tp) REVERT: N 106 ASP cc_start: 0.7548 (t70) cc_final: 0.7211 (t0) REVERT: N 117 LEU cc_start: 0.9156 (mp) cc_final: 0.8901 (mm) REVERT: O 20 GLN cc_start: 0.8118 (mm-40) cc_final: 0.7775 (mt0) REVERT: Q 88 ASP cc_start: 0.7590 (t70) cc_final: 0.7222 (t0) REVERT: T 63 ARG cc_start: 0.7987 (OUTLIER) cc_final: 0.7182 (ttm110) REVERT: T 84 LEU cc_start: 0.7741 (OUTLIER) cc_final: 0.7487 (mm) REVERT: U 1 MET cc_start: 0.2508 (tmm) cc_final: 0.2021 (tmm) REVERT: U 39 PHE cc_start: 0.8032 (OUTLIER) cc_final: 0.7510 (t80) REVERT: V 16 MET cc_start: 0.7198 (tpp) cc_final: 0.6925 (tpp) REVERT: V 60 ILE cc_start: 0.8871 (pt) cc_final: 0.8281 (pt) REVERT: V 72 TRP cc_start: 0.6016 (m100) cc_final: 0.5485 (m100) REVERT: X 40 PHE cc_start: 0.6337 (m-10) cc_final: 0.5690 (m-10) REVERT: X 43 MET cc_start: 0.7599 (mtm) cc_final: 0.6939 (mtm) REVERT: X 54 ARG cc_start: 0.7995 (ptt-90) cc_final: 0.7709 (ptp90) REVERT: Y 81 GLN cc_start: 0.7839 (mm-40) cc_final: 0.7304 (mm-40) REVERT: Z 11 PHE cc_start: 0.5508 (OUTLIER) cc_final: 0.4900 (p90) REVERT: Z 44 ARG cc_start: 0.8007 (mmm-85) cc_final: 0.7491 (tpp80) REVERT: a 186 LYS cc_start: 0.4393 (tptp) cc_final: 0.3667 (ptmt) REVERT: 8 10 TYR cc_start: 0.6971 (m-80) cc_final: 0.6216 (m-80) REVERT: 8 184 ASP cc_start: 0.6327 (OUTLIER) cc_final: 0.5978 (p0) REVERT: 8 204 TYR cc_start: 0.5943 (OUTLIER) cc_final: 0.5595 (p90) REVERT: 8 234 MET cc_start: 0.6557 (tpt) cc_final: 0.6131 (tmm) REVERT: 8 241 GLU cc_start: 0.6750 (tt0) cc_final: 0.5964 (pt0) REVERT: 8 278 MET cc_start: 0.6874 (OUTLIER) cc_final: 0.6352 (ptt) REVERT: 8 301 ASP cc_start: 0.3400 (OUTLIER) cc_final: 0.1196 (t70) REVERT: 8 474 LYS cc_start: 0.7607 (tptm) cc_final: 0.7289 (tptp) outliers start: 331 outliers final: 284 residues processed: 1034 average time/residue: 1.2370 time to fit residues: 2288.2663 Evaluate side-chains 1078 residues out of total 5429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 307 poor density : 771 time to evaluate : 6.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 86 ARG Chi-restraints excluded: chain b residue 127 ASN Chi-restraints excluded: chain b residue 161 VAL Chi-restraints excluded: chain b residue 215 VAL Chi-restraints excluded: chain b residue 224 MET Chi-restraints excluded: chain b residue 244 VAL Chi-restraints excluded: chain b residue 262 THR Chi-restraints excluded: chain b residue 266 ILE Chi-restraints excluded: chain c residue 1 MET Chi-restraints excluded: chain c residue 2 ILE Chi-restraints excluded: chain c residue 24 VAL Chi-restraints excluded: chain c residue 25 THR Chi-restraints excluded: chain c residue 60 VAL Chi-restraints excluded: chain c residue 126 ASN Chi-restraints excluded: chain c residue 131 ASP Chi-restraints excluded: chain c residue 146 ILE Chi-restraints excluded: chain c residue 176 ASP Chi-restraints excluded: chain c residue 188 LEU Chi-restraints excluded: chain c residue 197 THR Chi-restraints excluded: chain c residue 202 ILE Chi-restraints excluded: chain d residue 77 ILE Chi-restraints excluded: chain d residue 120 VAL Chi-restraints excluded: chain d residue 188 MET Chi-restraints excluded: chain d residue 189 THR Chi-restraints excluded: chain e residue 16 MET Chi-restraints excluded: chain e residue 24 VAL Chi-restraints excluded: chain e residue 30 VAL Chi-restraints excluded: chain e residue 39 VAL Chi-restraints excluded: chain e residue 56 LEU Chi-restraints excluded: chain e residue 112 ASP Chi-restraints excluded: chain e residue 126 ASN Chi-restraints excluded: chain e residue 128 SER Chi-restraints excluded: chain e residue 131 VAL Chi-restraints excluded: chain e residue 146 ASP Chi-restraints excluded: chain e residue 157 THR Chi-restraints excluded: chain f residue 9 VAL Chi-restraints excluded: chain f residue 42 VAL Chi-restraints excluded: chain f residue 78 VAL Chi-restraints excluded: chain f residue 165 ASP Chi-restraints excluded: chain g residue 6 LEU Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain g residue 43 ASN Chi-restraints excluded: chain g residue 91 PHE Chi-restraints excluded: chain g residue 121 VAL Chi-restraints excluded: chain g residue 122 LEU Chi-restraints excluded: chain g residue 125 THR Chi-restraints excluded: chain h residue 38 MET Chi-restraints excluded: chain i residue 12 VAL Chi-restraints excluded: chain i residue 27 LEU Chi-restraints excluded: chain i residue 45 THR Chi-restraints excluded: chain i residue 48 ILE Chi-restraints excluded: chain i residue 57 VAL Chi-restraints excluded: chain i residue 70 THR Chi-restraints excluded: chain j residue 3 THR Chi-restraints excluded: chain j residue 57 LEU Chi-restraints excluded: chain j residue 62 VAL Chi-restraints excluded: chain j residue 84 ILE Chi-restraints excluded: chain j residue 128 ASN Chi-restraints excluded: chain k residue 35 VAL Chi-restraints excluded: chain k residue 56 ASP Chi-restraints excluded: chain k residue 73 ASP Chi-restraints excluded: chain k residue 85 VAL Chi-restraints excluded: chain k residue 90 ASN Chi-restraints excluded: chain k residue 107 LEU Chi-restraints excluded: chain k residue 111 LYS Chi-restraints excluded: chain l residue 103 ILE Chi-restraints excluded: chain l residue 121 THR Chi-restraints excluded: chain m residue 2 LEU Chi-restraints excluded: chain m residue 7 THR Chi-restraints excluded: chain m residue 42 THR Chi-restraints excluded: chain m residue 60 GLN Chi-restraints excluded: chain m residue 70 ASP Chi-restraints excluded: chain m residue 74 THR Chi-restraints excluded: chain m residue 75 GLU Chi-restraints excluded: chain m residue 78 LEU Chi-restraints excluded: chain m residue 88 ASN Chi-restraints excluded: chain m residue 91 TYR Chi-restraints excluded: chain m residue 124 LEU Chi-restraints excluded: chain m residue 126 ILE Chi-restraints excluded: chain m residue 129 THR Chi-restraints excluded: chain m residue 132 THR Chi-restraints excluded: chain n residue 2 ARG Chi-restraints excluded: chain n residue 33 ILE Chi-restraints excluded: chain n residue 37 THR Chi-restraints excluded: chain n residue 51 LEU Chi-restraints excluded: chain n residue 54 LEU Chi-restraints excluded: chain n residue 115 LEU Chi-restraints excluded: chain n residue 120 GLU Chi-restraints excluded: chain o residue 35 ILE Chi-restraints excluded: chain o residue 47 VAL Chi-restraints excluded: chain o residue 52 SER Chi-restraints excluded: chain o residue 53 THR Chi-restraints excluded: chain o residue 62 LEU Chi-restraints excluded: chain o residue 69 ASP Chi-restraints excluded: chain o residue 108 ASP Chi-restraints excluded: chain p residue 18 SER Chi-restraints excluded: chain p residue 40 GLN Chi-restraints excluded: chain p residue 47 ILE Chi-restraints excluded: chain p residue 79 VAL Chi-restraints excluded: chain p residue 84 SER Chi-restraints excluded: chain p residue 96 LEU Chi-restraints excluded: chain p residue 103 THR Chi-restraints excluded: chain p residue 113 LEU Chi-restraints excluded: chain q residue 7 VAL Chi-restraints excluded: chain q residue 94 LEU Chi-restraints excluded: chain q residue 106 THR Chi-restraints excluded: chain q residue 109 VAL Chi-restraints excluded: chain r residue 1 MET Chi-restraints excluded: chain r residue 101 ILE Chi-restraints excluded: chain s residue 3 THR Chi-restraints excluded: chain s residue 4 ILE Chi-restraints excluded: chain s residue 76 VAL Chi-restraints excluded: chain s residue 105 VAL Chi-restraints excluded: chain t residue 24 MET Chi-restraints excluded: chain t residue 61 LEU Chi-restraints excluded: chain t residue 93 LEU Chi-restraints excluded: chain u residue 27 VAL Chi-restraints excluded: chain u residue 40 LEU Chi-restraints excluded: chain u residue 48 VAL Chi-restraints excluded: chain u residue 67 SER Chi-restraints excluded: chain u residue 69 VAL Chi-restraints excluded: chain u residue 71 ILE Chi-restraints excluded: chain u residue 88 ASP Chi-restraints excluded: chain u residue 98 ASN Chi-restraints excluded: chain v residue 5 ASN Chi-restraints excluded: chain v residue 40 ILE Chi-restraints excluded: chain v residue 61 LEU Chi-restraints excluded: chain v residue 65 VAL Chi-restraints excluded: chain v residue 76 ASP Chi-restraints excluded: chain v residue 86 LEU Chi-restraints excluded: chain w residue 34 VAL Chi-restraints excluded: chain w residue 54 THR Chi-restraints excluded: chain w residue 63 VAL Chi-restraints excluded: chain x residue 12 VAL Chi-restraints excluded: chain x residue 19 HIS Chi-restraints excluded: chain x residue 47 THR Chi-restraints excluded: chain x residue 60 LYS Chi-restraints excluded: chain x residue 76 LYS Chi-restraints excluded: chain y residue 8 GLU Chi-restraints excluded: chain y residue 30 MET Chi-restraints excluded: chain z residue 6 ILE Chi-restraints excluded: chain z residue 40 THR Chi-restraints excluded: chain z residue 56 VAL Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 58 ASP Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 60 CYS Chi-restraints excluded: chain E residue 63 TYR Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 23 ILE Chi-restraints excluded: chain F residue 27 CYS Chi-restraints excluded: chain G residue 40 ILE Chi-restraints excluded: chain G residue 86 CYS Chi-restraints excluded: chain G residue 169 HIS Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 191 ASP Chi-restraints excluded: chain G residue 203 ASP Chi-restraints excluded: chain H residue 4 VAL Chi-restraints excluded: chain H residue 7 ASN Chi-restraints excluded: chain H residue 30 ASP Chi-restraints excluded: chain H residue 104 GLU Chi-restraints excluded: chain H residue 117 ASP Chi-restraints excluded: chain H residue 156 LEU Chi-restraints excluded: chain H residue 164 THR Chi-restraints excluded: chain H residue 180 ASP Chi-restraints excluded: chain H residue 194 VAL Chi-restraints excluded: chain I residue 19 PHE Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 34 GLU Chi-restraints excluded: chain I residue 49 ASP Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 97 LEU Chi-restraints excluded: chain I residue 98 ASP Chi-restraints excluded: chain I residue 170 LEU Chi-restraints excluded: chain I residue 191 SER Chi-restraints excluded: chain I residue 194 ILE Chi-restraints excluded: chain I residue 202 LEU Chi-restraints excluded: chain J residue 15 ILE Chi-restraints excluded: chain J residue 35 LEU Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 60 GLN Chi-restraints excluded: chain J residue 79 THR Chi-restraints excluded: chain J residue 104 ILE Chi-restraints excluded: chain J residue 120 HIS Chi-restraints excluded: chain J residue 123 LEU Chi-restraints excluded: chain K residue 11 HIS Chi-restraints excluded: chain K residue 13 ASP Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 55 HIS Chi-restraints excluded: chain K residue 60 VAL Chi-restraints excluded: chain K residue 85 ILE Chi-restraints excluded: chain K residue 93 LYS Chi-restraints excluded: chain K residue 96 VAL Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 29 LEU Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain L residue 84 TYR Chi-restraints excluded: chain L residue 103 ILE Chi-restraints excluded: chain M residue 6 ILE Chi-restraints excluded: chain M residue 53 ASP Chi-restraints excluded: chain M residue 62 LEU Chi-restraints excluded: chain M residue 126 CYS Chi-restraints excluded: chain N residue 8 THR Chi-restraints excluded: chain N residue 28 VAL Chi-restraints excluded: chain N residue 38 PHE Chi-restraints excluded: chain N residue 42 THR Chi-restraints excluded: chain N residue 54 VAL Chi-restraints excluded: chain N residue 65 THR Chi-restraints excluded: chain N residue 83 THR Chi-restraints excluded: chain N residue 93 LEU Chi-restraints excluded: chain N residue 125 GLN Chi-restraints excluded: chain O residue 10 LEU Chi-restraints excluded: chain O residue 50 THR Chi-restraints excluded: chain O residue 66 GLU Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain O residue 83 THR Chi-restraints excluded: chain P residue 29 THR Chi-restraints excluded: chain P residue 30 ILE Chi-restraints excluded: chain Q residue 20 VAL Chi-restraints excluded: chain Q residue 36 VAL Chi-restraints excluded: chain Q residue 39 THR Chi-restraints excluded: chain Q residue 42 LYS Chi-restraints excluded: chain Q residue 61 GLU Chi-restraints excluded: chain Q residue 66 ILE Chi-restraints excluded: chain Q residue 81 ILE Chi-restraints excluded: chain Q residue 96 THR Chi-restraints excluded: chain Q residue 118 VAL Chi-restraints excluded: chain R residue 13 HIS Chi-restraints excluded: chain R residue 15 VAL Chi-restraints excluded: chain R residue 18 LEU Chi-restraints excluded: chain R residue 42 VAL Chi-restraints excluded: chain R residue 64 VAL Chi-restraints excluded: chain S residue 37 ASP Chi-restraints excluded: chain S residue 44 VAL Chi-restraints excluded: chain S residue 50 LEU Chi-restraints excluded: chain S residue 78 LEU Chi-restraints excluded: chain T residue 16 ARG Chi-restraints excluded: chain T residue 23 SER Chi-restraints excluded: chain T residue 63 ARG Chi-restraints excluded: chain T residue 74 VAL Chi-restraints excluded: chain T residue 84 LEU Chi-restraints excluded: chain U residue 39 PHE Chi-restraints excluded: chain U residue 57 ILE Chi-restraints excluded: chain U residue 75 ILE Chi-restraints excluded: chain V residue 28 VAL Chi-restraints excluded: chain V residue 50 ASN Chi-restraints excluded: chain V residue 57 VAL Chi-restraints excluded: chain V residue 69 THR Chi-restraints excluded: chain W residue 25 ILE Chi-restraints excluded: chain W residue 33 THR Chi-restraints excluded: chain W residue 73 HIS Chi-restraints excluded: chain X residue 39 ILE Chi-restraints excluded: chain X residue 47 THR Chi-restraints excluded: chain X residue 66 VAL Chi-restraints excluded: chain Y residue 11 ILE Chi-restraints excluded: chain Y residue 19 HIS Chi-restraints excluded: chain Y residue 25 SER Chi-restraints excluded: chain Y residue 78 LEU Chi-restraints excluded: chain Z residue 11 PHE Chi-restraints excluded: chain Z residue 12 ASP Chi-restraints excluded: chain Z residue 18 PHE Chi-restraints excluded: chain Z residue 43 GLU Chi-restraints excluded: chain Z residue 59 LEU Chi-restraints excluded: chain a residue 5 THR Chi-restraints excluded: chain a residue 24 ASN Chi-restraints excluded: chain a residue 39 VAL Chi-restraints excluded: chain a residue 64 VAL Chi-restraints excluded: chain a residue 174 THR Chi-restraints excluded: chain 8 residue 24 THR Chi-restraints excluded: chain 8 residue 86 ILE Chi-restraints excluded: chain 8 residue 96 THR Chi-restraints excluded: chain 8 residue 105 VAL Chi-restraints excluded: chain 8 residue 110 VAL Chi-restraints excluded: chain 8 residue 112 VAL Chi-restraints excluded: chain 8 residue 126 VAL Chi-restraints excluded: chain 8 residue 167 VAL Chi-restraints excluded: chain 8 residue 182 VAL Chi-restraints excluded: chain 8 residue 184 ASP Chi-restraints excluded: chain 8 residue 186 VAL Chi-restraints excluded: chain 8 residue 201 THR Chi-restraints excluded: chain 8 residue 204 TYR Chi-restraints excluded: chain 8 residue 247 GLU Chi-restraints excluded: chain 8 residue 264 VAL Chi-restraints excluded: chain 8 residue 266 CYS Chi-restraints excluded: chain 8 residue 278 MET Chi-restraints excluded: chain 8 residue 292 VAL Chi-restraints excluded: chain 8 residue 300 ASP Chi-restraints excluded: chain 8 residue 301 ASP Chi-restraints excluded: chain 8 residue 330 VAL Chi-restraints excluded: chain 8 residue 374 ILE Chi-restraints excluded: chain 8 residue 494 ILE Chi-restraints excluded: chain 8 residue 521 ASP Chi-restraints excluded: chain 8 residue 530 ASN Chi-restraints excluded: chain 8 residue 571 VAL Chi-restraints excluded: chain 8 residue 585 ASP Chi-restraints excluded: chain 8 residue 621 VAL Chi-restraints excluded: chain 8 residue 622 GLU Chi-restraints excluded: chain 8 residue 623 THR Chi-restraints excluded: chain 8 residue 673 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1109 random chunks: chunk 992 optimal weight: 10.0000 chunk 654 optimal weight: 20.0000 chunk 1053 optimal weight: 10.0000 chunk 642 optimal weight: 20.0000 chunk 499 optimal weight: 5.9990 chunk 732 optimal weight: 20.0000 chunk 1104 optimal weight: 9.9990 chunk 1016 optimal weight: 30.0000 chunk 879 optimal weight: 20.0000 chunk 91 optimal weight: 6.9990 chunk 679 optimal weight: 20.0000 overall best weight: 8.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 128 ASN ** n 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 55 GLN ** u 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 29 GLN ** E 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 5 HIS ** H 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 2 ASN ** a 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.3904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 166269 Z= 0.305 Angle : 0.713 14.858 247957 Z= 0.365 Chirality : 0.040 0.381 31576 Planarity : 0.005 0.073 13872 Dihedral : 23.667 175.936 81265 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 19.82 Ramachandran Plot: Outliers : 0.23 % Allowed : 13.44 % Favored : 86.33 % Rotamer: Outliers : 5.84 % Allowed : 23.95 % Favored : 70.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -2.71 (0.10), residues: 6517 helix: -0.63 (0.11), residues: 2031 sheet: -1.89 (0.14), residues: 1130 loop : -2.56 (0.10), residues: 3356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP L 102 HIS 0.019 0.001 HIS j 130 PHE 0.053 0.002 PHE R 62 TYR 0.047 0.002 TYR X 79 ARG 0.009 0.001 ARG b 268 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13034 Ramachandran restraints generated. 6517 Oldfield, 0 Emsley, 6517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13034 Ramachandran restraints generated. 6517 Oldfield, 0 Emsley, 6517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1123 residues out of total 5429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 317 poor density : 806 time to evaluate : 6.636 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: b 86 ARG cc_start: 0.8205 (OUTLIER) cc_final: 0.7227 (mtm-85) REVERT: c 15 PHE cc_start: 0.8438 (OUTLIER) cc_final: 0.7788 (m-10) REVERT: e 59 ILE cc_start: 0.9121 (mp) cc_final: 0.8882 (mp) REVERT: e 93 GLU cc_start: 0.8575 (OUTLIER) cc_final: 0.8269 (pp20) REVERT: k 1 MET cc_start: 0.8073 (ttm) cc_final: 0.7619 (ttp) REVERT: k 51 LYS cc_start: 0.7975 (mtmt) cc_final: 0.7693 (mtmt) REVERT: l 121 THR cc_start: 0.7409 (OUTLIER) cc_final: 0.7122 (p) REVERT: m 60 GLN cc_start: 0.7556 (OUTLIER) cc_final: 0.6207 (pp30) REVERT: n 27 SER cc_start: 0.8707 (m) cc_final: 0.8323 (p) REVERT: n 72 ASP cc_start: 0.7411 (t0) cc_final: 0.6992 (t70) REVERT: n 73 ASN cc_start: 0.7416 (p0) cc_final: 0.7135 (p0) REVERT: o 93 ASP cc_start: 0.7007 (t0) cc_final: 0.6731 (t0) REVERT: p 26 GLU cc_start: 0.7700 (mm-30) cc_final: 0.6856 (tm-30) REVERT: p 43 GLU cc_start: 0.7434 (tm-30) cc_final: 0.7015 (tm-30) REVERT: q 73 ILE cc_start: 0.8753 (tp) cc_final: 0.8508 (tp) REVERT: q 94 LEU cc_start: 0.9114 (OUTLIER) cc_final: 0.8633 (mp) REVERT: t 61 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8635 (pp) REVERT: u 98 ASN cc_start: 0.7351 (OUTLIER) cc_final: 0.7021 (p0) REVERT: w 78 ILE cc_start: 0.8690 (mm) cc_final: 0.8414 (tt) REVERT: x 19 HIS cc_start: 0.8522 (OUTLIER) cc_final: 0.8152 (t70) REVERT: x 55 MET cc_start: 0.8250 (mpp) cc_final: 0.7873 (mtm) REVERT: y 7 ARG cc_start: 0.8622 (ptm160) cc_final: 0.8284 (ptm160) REVERT: A 8 LYS cc_start: 0.7378 (tmmt) cc_final: 0.7126 (tmtt) REVERT: A 12 ILE cc_start: 0.7862 (tp) cc_final: 0.7645 (tt) REVERT: C 6 GLU cc_start: 0.7728 (pt0) cc_final: 0.6421 (pm20) REVERT: C 43 ARG cc_start: 0.5270 (tpt170) cc_final: 0.4258 (mmm160) REVERT: C 48 TYR cc_start: 0.6090 (m-80) cc_final: 0.5844 (m-80) REVERT: E 63 TYR cc_start: 0.8260 (OUTLIER) cc_final: 0.7910 (m-80) REVERT: F 37 GLN cc_start: 0.8312 (tp40) cc_final: 0.8015 (tp-100) REVERT: G 22 TRP cc_start: 0.8313 (p-90) cc_final: 0.7969 (p-90) REVERT: G 58 LYS cc_start: 0.9319 (mmtp) cc_final: 0.8815 (tptp) REVERT: G 173 LYS cc_start: 0.8564 (ttmt) cc_final: 0.7591 (tmtt) REVERT: G 191 ASP cc_start: 0.8612 (OUTLIER) cc_final: 0.8259 (t70) REVERT: H 40 GLN cc_start: 0.8187 (tp-100) cc_final: 0.7698 (pt0) REVERT: H 104 GLU cc_start: 0.6502 (OUTLIER) cc_final: 0.5992 (tm-30) REVERT: H 133 MET cc_start: 0.7641 (ttt) cc_final: 0.7393 (ttt) REVERT: H 182 ASP cc_start: 0.7145 (t0) cc_final: 0.6623 (t70) REVERT: I 63 ILE cc_start: 0.8734 (mt) cc_final: 0.8478 (mt) REVERT: I 202 LEU cc_start: 0.8561 (OUTLIER) cc_final: 0.8331 (tt) REVERT: K 55 HIS cc_start: 0.8243 (OUTLIER) cc_final: 0.7502 (p-80) REVERT: K 65 GLU cc_start: 0.6467 (tm-30) cc_final: 0.5937 (tm-30) REVERT: M 72 GLU cc_start: 0.7765 (tp30) cc_final: 0.7313 (tt0) REVERT: M 95 MET cc_start: 0.7317 (tpp) cc_final: 0.6978 (tpp) REVERT: N 93 LEU cc_start: 0.3829 (OUTLIER) cc_final: 0.3613 (tp) REVERT: N 106 ASP cc_start: 0.7591 (t70) cc_final: 0.7210 (t0) REVERT: N 117 LEU cc_start: 0.9143 (mp) cc_final: 0.8892 (mm) REVERT: O 20 GLN cc_start: 0.8168 (mm-40) cc_final: 0.7843 (mt0) REVERT: Q 88 ASP cc_start: 0.7599 (t70) cc_final: 0.7239 (t0) REVERT: T 63 ARG cc_start: 0.7979 (OUTLIER) cc_final: 0.7037 (ttm110) REVERT: T 84 LEU cc_start: 0.7739 (OUTLIER) cc_final: 0.7500 (mm) REVERT: U 1 MET cc_start: 0.2547 (tmm) cc_final: 0.2107 (tmm) REVERT: U 39 PHE cc_start: 0.8010 (OUTLIER) cc_final: 0.7483 (t80) REVERT: V 16 MET cc_start: 0.7272 (tpp) cc_final: 0.7043 (tpp) REVERT: V 56 ASP cc_start: 0.7132 (p0) cc_final: 0.6912 (p0) REVERT: V 60 ILE cc_start: 0.8867 (pt) cc_final: 0.8308 (pt) REVERT: V 64 ARG cc_start: 0.7940 (ptt-90) cc_final: 0.7457 (ttp-170) REVERT: V 72 TRP cc_start: 0.5996 (m100) cc_final: 0.5472 (m100) REVERT: X 40 PHE cc_start: 0.6315 (m-10) cc_final: 0.5663 (m-10) REVERT: X 43 MET cc_start: 0.7592 (mtm) cc_final: 0.6932 (mtm) REVERT: X 54 ARG cc_start: 0.8064 (ptt-90) cc_final: 0.7784 (ptp90) REVERT: X 72 GLU cc_start: 0.5044 (mm-30) cc_final: 0.4706 (mp0) REVERT: Z 11 PHE cc_start: 0.5471 (OUTLIER) cc_final: 0.4933 (p90) REVERT: Z 44 ARG cc_start: 0.7979 (mmm-85) cc_final: 0.7479 (tpp80) REVERT: a 186 LYS cc_start: 0.4277 (tptp) cc_final: 0.3534 (ptmt) REVERT: a 198 LYS cc_start: 0.3345 (OUTLIER) cc_final: 0.3027 (tptp) REVERT: 8 10 TYR cc_start: 0.6921 (m-80) cc_final: 0.6148 (m-80) REVERT: 8 184 ASP cc_start: 0.6331 (OUTLIER) cc_final: 0.5891 (p0) REVERT: 8 204 TYR cc_start: 0.5941 (OUTLIER) cc_final: 0.5639 (p90) REVERT: 8 234 MET cc_start: 0.6553 (tpt) cc_final: 0.6127 (tmm) REVERT: 8 241 GLU cc_start: 0.6721 (tt0) cc_final: 0.5933 (pt0) REVERT: 8 278 MET cc_start: 0.6783 (OUTLIER) cc_final: 0.6200 (ptt) REVERT: 8 300 ASP cc_start: 0.3067 (OUTLIER) cc_final: 0.2750 (m-30) REVERT: 8 301 ASP cc_start: 0.3458 (OUTLIER) cc_final: 0.1217 (t70) REVERT: 8 474 LYS cc_start: 0.7693 (tptm) cc_final: 0.7359 (tptp) outliers start: 317 outliers final: 281 residues processed: 1037 average time/residue: 1.2366 time to fit residues: 2300.4596 Evaluate side-chains 1087 residues out of total 5429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 306 poor density : 781 time to evaluate : 6.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 86 ARG Chi-restraints excluded: chain b residue 161 VAL Chi-restraints excluded: chain b residue 215 VAL Chi-restraints excluded: chain b residue 224 MET Chi-restraints excluded: chain b residue 244 VAL Chi-restraints excluded: chain b residue 262 THR Chi-restraints excluded: chain b residue 266 ILE Chi-restraints excluded: chain c residue 2 ILE Chi-restraints excluded: chain c residue 15 PHE Chi-restraints excluded: chain c residue 24 VAL Chi-restraints excluded: chain c residue 25 THR Chi-restraints excluded: chain c residue 60 VAL Chi-restraints excluded: chain c residue 131 ASP Chi-restraints excluded: chain c residue 146 ILE Chi-restraints excluded: chain c residue 176 ASP Chi-restraints excluded: chain c residue 180 VAL Chi-restraints excluded: chain c residue 188 LEU Chi-restraints excluded: chain c residue 197 THR Chi-restraints excluded: chain c residue 202 ILE Chi-restraints excluded: chain d residue 77 ILE Chi-restraints excluded: chain d residue 120 VAL Chi-restraints excluded: chain d residue 188 MET Chi-restraints excluded: chain d residue 189 THR Chi-restraints excluded: chain e residue 16 MET Chi-restraints excluded: chain e residue 24 VAL Chi-restraints excluded: chain e residue 30 VAL Chi-restraints excluded: chain e residue 39 VAL Chi-restraints excluded: chain e residue 93 GLU Chi-restraints excluded: chain e residue 112 ASP Chi-restraints excluded: chain e residue 126 ASN Chi-restraints excluded: chain e residue 128 SER Chi-restraints excluded: chain e residue 131 VAL Chi-restraints excluded: chain e residue 146 ASP Chi-restraints excluded: chain f residue 9 VAL Chi-restraints excluded: chain f residue 42 VAL Chi-restraints excluded: chain f residue 78 VAL Chi-restraints excluded: chain f residue 165 ASP Chi-restraints excluded: chain g residue 6 LEU Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain g residue 121 VAL Chi-restraints excluded: chain g residue 122 LEU Chi-restraints excluded: chain g residue 125 THR Chi-restraints excluded: chain h residue 38 MET Chi-restraints excluded: chain i residue 12 VAL Chi-restraints excluded: chain i residue 27 LEU Chi-restraints excluded: chain i residue 45 THR Chi-restraints excluded: chain i residue 48 ILE Chi-restraints excluded: chain i residue 57 VAL Chi-restraints excluded: chain i residue 70 THR Chi-restraints excluded: chain j residue 3 THR Chi-restraints excluded: chain j residue 31 GLU Chi-restraints excluded: chain j residue 57 LEU Chi-restraints excluded: chain j residue 62 VAL Chi-restraints excluded: chain j residue 84 ILE Chi-restraints excluded: chain k residue 35 VAL Chi-restraints excluded: chain k residue 56 ASP Chi-restraints excluded: chain k residue 73 ASP Chi-restraints excluded: chain k residue 85 VAL Chi-restraints excluded: chain k residue 90 ASN Chi-restraints excluded: chain k residue 107 LEU Chi-restraints excluded: chain k residue 111 LYS Chi-restraints excluded: chain l residue 103 ILE Chi-restraints excluded: chain l residue 121 THR Chi-restraints excluded: chain m residue 2 LEU Chi-restraints excluded: chain m residue 7 THR Chi-restraints excluded: chain m residue 42 THR Chi-restraints excluded: chain m residue 60 GLN Chi-restraints excluded: chain m residue 70 ASP Chi-restraints excluded: chain m residue 74 THR Chi-restraints excluded: chain m residue 75 GLU Chi-restraints excluded: chain m residue 78 LEU Chi-restraints excluded: chain m residue 88 ASN Chi-restraints excluded: chain m residue 91 TYR Chi-restraints excluded: chain m residue 124 LEU Chi-restraints excluded: chain m residue 126 ILE Chi-restraints excluded: chain m residue 129 THR Chi-restraints excluded: chain m residue 132 THR Chi-restraints excluded: chain n residue 2 ARG Chi-restraints excluded: chain n residue 33 ILE Chi-restraints excluded: chain n residue 37 THR Chi-restraints excluded: chain n residue 51 LEU Chi-restraints excluded: chain n residue 54 LEU Chi-restraints excluded: chain n residue 115 LEU Chi-restraints excluded: chain n residue 120 GLU Chi-restraints excluded: chain o residue 35 ILE Chi-restraints excluded: chain o residue 47 VAL Chi-restraints excluded: chain o residue 52 SER Chi-restraints excluded: chain o residue 53 THR Chi-restraints excluded: chain o residue 62 LEU Chi-restraints excluded: chain o residue 69 ASP Chi-restraints excluded: chain o residue 108 ASP Chi-restraints excluded: chain p residue 18 SER Chi-restraints excluded: chain p residue 40 GLN Chi-restraints excluded: chain p residue 47 ILE Chi-restraints excluded: chain p residue 79 VAL Chi-restraints excluded: chain p residue 84 SER Chi-restraints excluded: chain p residue 96 LEU Chi-restraints excluded: chain p residue 103 THR Chi-restraints excluded: chain p residue 113 LEU Chi-restraints excluded: chain q residue 7 VAL Chi-restraints excluded: chain q residue 94 LEU Chi-restraints excluded: chain q residue 106 THR Chi-restraints excluded: chain q residue 109 VAL Chi-restraints excluded: chain r residue 1 MET Chi-restraints excluded: chain r residue 101 ILE Chi-restraints excluded: chain s residue 3 THR Chi-restraints excluded: chain s residue 4 ILE Chi-restraints excluded: chain s residue 76 VAL Chi-restraints excluded: chain s residue 105 VAL Chi-restraints excluded: chain t residue 24 MET Chi-restraints excluded: chain t residue 61 LEU Chi-restraints excluded: chain t residue 93 LEU Chi-restraints excluded: chain u residue 27 VAL Chi-restraints excluded: chain u residue 48 VAL Chi-restraints excluded: chain u residue 67 SER Chi-restraints excluded: chain u residue 69 VAL Chi-restraints excluded: chain u residue 71 ILE Chi-restraints excluded: chain u residue 88 ASP Chi-restraints excluded: chain u residue 98 ASN Chi-restraints excluded: chain v residue 5 ASN Chi-restraints excluded: chain v residue 40 ILE Chi-restraints excluded: chain v residue 61 LEU Chi-restraints excluded: chain v residue 65 VAL Chi-restraints excluded: chain v residue 76 ASP Chi-restraints excluded: chain v residue 86 LEU Chi-restraints excluded: chain w residue 54 THR Chi-restraints excluded: chain w residue 63 VAL Chi-restraints excluded: chain x residue 12 VAL Chi-restraints excluded: chain x residue 19 HIS Chi-restraints excluded: chain x residue 47 THR Chi-restraints excluded: chain x residue 60 LYS Chi-restraints excluded: chain x residue 76 LYS Chi-restraints excluded: chain y residue 8 GLU Chi-restraints excluded: chain y residue 30 MET Chi-restraints excluded: chain z residue 6 ILE Chi-restraints excluded: chain z residue 40 THR Chi-restraints excluded: chain z residue 56 VAL Chi-restraints excluded: chain A residue 30 HIS Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 58 ASP Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 60 CYS Chi-restraints excluded: chain E residue 63 TYR Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 23 ILE Chi-restraints excluded: chain F residue 27 CYS Chi-restraints excluded: chain G residue 40 ILE Chi-restraints excluded: chain G residue 86 CYS Chi-restraints excluded: chain G residue 169 HIS Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 191 ASP Chi-restraints excluded: chain G residue 203 ASP Chi-restraints excluded: chain H residue 7 ASN Chi-restraints excluded: chain H residue 30 ASP Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 104 GLU Chi-restraints excluded: chain H residue 117 ASP Chi-restraints excluded: chain H residue 156 LEU Chi-restraints excluded: chain H residue 164 THR Chi-restraints excluded: chain H residue 180 ASP Chi-restraints excluded: chain H residue 194 VAL Chi-restraints excluded: chain I residue 19 PHE Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 34 GLU Chi-restraints excluded: chain I residue 49 ASP Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 97 LEU Chi-restraints excluded: chain I residue 98 ASP Chi-restraints excluded: chain I residue 170 LEU Chi-restraints excluded: chain I residue 191 SER Chi-restraints excluded: chain I residue 194 ILE Chi-restraints excluded: chain I residue 202 LEU Chi-restraints excluded: chain J residue 15 ILE Chi-restraints excluded: chain J residue 35 LEU Chi-restraints excluded: chain J residue 45 VAL Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 60 GLN Chi-restraints excluded: chain J residue 79 THR Chi-restraints excluded: chain J residue 104 ILE Chi-restraints excluded: chain J residue 120 HIS Chi-restraints excluded: chain J residue 123 LEU Chi-restraints excluded: chain K residue 11 HIS Chi-restraints excluded: chain K residue 13 ASP Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 55 HIS Chi-restraints excluded: chain K residue 60 VAL Chi-restraints excluded: chain K residue 85 ILE Chi-restraints excluded: chain K residue 93 LYS Chi-restraints excluded: chain K residue 96 VAL Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 29 LEU Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain L residue 84 TYR Chi-restraints excluded: chain L residue 103 ILE Chi-restraints excluded: chain M residue 6 ILE Chi-restraints excluded: chain M residue 53 ASP Chi-restraints excluded: chain M residue 62 LEU Chi-restraints excluded: chain M residue 110 MET Chi-restraints excluded: chain M residue 126 CYS Chi-restraints excluded: chain N residue 8 THR Chi-restraints excluded: chain N residue 28 VAL Chi-restraints excluded: chain N residue 38 PHE Chi-restraints excluded: chain N residue 42 THR Chi-restraints excluded: chain N residue 54 VAL Chi-restraints excluded: chain N residue 65 THR Chi-restraints excluded: chain N residue 83 THR Chi-restraints excluded: chain N residue 93 LEU Chi-restraints excluded: chain N residue 125 GLN Chi-restraints excluded: chain O residue 10 LEU Chi-restraints excluded: chain O residue 50 THR Chi-restraints excluded: chain O residue 66 GLU Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain O residue 83 THR Chi-restraints excluded: chain P residue 29 THR Chi-restraints excluded: chain P residue 30 ILE Chi-restraints excluded: chain Q residue 20 VAL Chi-restraints excluded: chain Q residue 36 VAL Chi-restraints excluded: chain Q residue 39 THR Chi-restraints excluded: chain Q residue 42 LYS Chi-restraints excluded: chain Q residue 61 GLU Chi-restraints excluded: chain Q residue 66 ILE Chi-restraints excluded: chain Q residue 81 ILE Chi-restraints excluded: chain Q residue 96 THR Chi-restraints excluded: chain Q residue 118 VAL Chi-restraints excluded: chain R residue 13 HIS Chi-restraints excluded: chain R residue 15 VAL Chi-restraints excluded: chain R residue 18 LEU Chi-restraints excluded: chain R residue 42 VAL Chi-restraints excluded: chain R residue 64 VAL Chi-restraints excluded: chain S residue 37 ASP Chi-restraints excluded: chain S residue 44 VAL Chi-restraints excluded: chain S residue 50 LEU Chi-restraints excluded: chain S residue 78 LEU Chi-restraints excluded: chain T residue 16 ARG Chi-restraints excluded: chain T residue 23 SER Chi-restraints excluded: chain T residue 63 ARG Chi-restraints excluded: chain T residue 74 VAL Chi-restraints excluded: chain T residue 84 LEU Chi-restraints excluded: chain U residue 39 PHE Chi-restraints excluded: chain U residue 57 ILE Chi-restraints excluded: chain U residue 75 ILE Chi-restraints excluded: chain V residue 28 VAL Chi-restraints excluded: chain V residue 50 ASN Chi-restraints excluded: chain V residue 57 VAL Chi-restraints excluded: chain V residue 69 THR Chi-restraints excluded: chain W residue 25 ILE Chi-restraints excluded: chain W residue 33 THR Chi-restraints excluded: chain W residue 73 HIS Chi-restraints excluded: chain X residue 39 ILE Chi-restraints excluded: chain X residue 47 THR Chi-restraints excluded: chain X residue 66 VAL Chi-restraints excluded: chain Y residue 11 ILE Chi-restraints excluded: chain Y residue 19 HIS Chi-restraints excluded: chain Y residue 25 SER Chi-restraints excluded: chain Y residue 78 LEU Chi-restraints excluded: chain Z residue 11 PHE Chi-restraints excluded: chain Z residue 12 ASP Chi-restraints excluded: chain Z residue 18 PHE Chi-restraints excluded: chain Z residue 43 GLU Chi-restraints excluded: chain Z residue 59 LEU Chi-restraints excluded: chain a residue 5 THR Chi-restraints excluded: chain a residue 24 ASN Chi-restraints excluded: chain a residue 39 VAL Chi-restraints excluded: chain a residue 64 VAL Chi-restraints excluded: chain a residue 174 THR Chi-restraints excluded: chain a residue 198 LYS Chi-restraints excluded: chain 8 residue 24 THR Chi-restraints excluded: chain 8 residue 86 ILE Chi-restraints excluded: chain 8 residue 96 THR Chi-restraints excluded: chain 8 residue 105 VAL Chi-restraints excluded: chain 8 residue 110 VAL Chi-restraints excluded: chain 8 residue 112 VAL Chi-restraints excluded: chain 8 residue 126 VAL Chi-restraints excluded: chain 8 residue 167 VAL Chi-restraints excluded: chain 8 residue 182 VAL Chi-restraints excluded: chain 8 residue 184 ASP Chi-restraints excluded: chain 8 residue 186 VAL Chi-restraints excluded: chain 8 residue 201 THR Chi-restraints excluded: chain 8 residue 204 TYR Chi-restraints excluded: chain 8 residue 247 GLU Chi-restraints excluded: chain 8 residue 264 VAL Chi-restraints excluded: chain 8 residue 266 CYS Chi-restraints excluded: chain 8 residue 278 MET Chi-restraints excluded: chain 8 residue 279 LEU Chi-restraints excluded: chain 8 residue 292 VAL Chi-restraints excluded: chain 8 residue 300 ASP Chi-restraints excluded: chain 8 residue 301 ASP Chi-restraints excluded: chain 8 residue 330 VAL Chi-restraints excluded: chain 8 residue 374 ILE Chi-restraints excluded: chain 8 residue 494 ILE Chi-restraints excluded: chain 8 residue 521 ASP Chi-restraints excluded: chain 8 residue 530 ASN Chi-restraints excluded: chain 8 residue 571 VAL Chi-restraints excluded: chain 8 residue 585 ASP Chi-restraints excluded: chain 8 residue 621 VAL Chi-restraints excluded: chain 8 residue 622 GLU Chi-restraints excluded: chain 8 residue 623 THR Chi-restraints excluded: chain 8 residue 673 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1109 random chunks: chunk 539 optimal weight: 6.9990 chunk 698 optimal weight: 40.0000 chunk 937 optimal weight: 50.0000 chunk 269 optimal weight: 8.9990 chunk 811 optimal weight: 20.0000 chunk 129 optimal weight: 10.0000 chunk 244 optimal weight: 9.9990 chunk 881 optimal weight: 20.0000 chunk 368 optimal weight: 20.0000 chunk 904 optimal weight: 10.0000 chunk 111 optimal weight: 20.0000 overall best weight: 9.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 164 GLN ** d 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 18 GLN g 43 ASN ** j 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 29 GLN ** E 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 53 GLN ** I 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 81 GLN ** a 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.069287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.054691 restraints weight = 874666.344| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 2.35 r_work: 0.3278 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3272 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3272 r_free = 0.3272 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3272 r_free = 0.3272 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3272 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.3982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 166269 Z= 0.323 Angle : 0.721 14.343 247957 Z= 0.368 Chirality : 0.040 0.369 31576 Planarity : 0.005 0.076 13872 Dihedral : 23.676 175.870 81265 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 20.41 Ramachandran Plot: Outliers : 0.23 % Allowed : 13.53 % Favored : 86.24 % Rotamer: Outliers : 5.99 % Allowed : 24.11 % Favored : 69.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -2.73 (0.10), residues: 6517 helix: -0.66 (0.11), residues: 2038 sheet: -1.88 (0.14), residues: 1122 loop : -2.58 (0.10), residues: 3357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP L 102 HIS 0.006 0.001 HIS z 33 PHE 0.049 0.002 PHE R 62 TYR 0.044 0.002 TYR X 79 ARG 0.013 0.001 ARG I 72 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 38562.17 seconds wall clock time: 675 minutes 43.46 seconds (40543.46 seconds total)