Starting phenix.real_space_refine on Fri Mar 1 23:11:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k54_22673/03_2024/7k54_22673_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k54_22673/03_2024/7k54_22673.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k54_22673/03_2024/7k54_22673.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k54_22673/03_2024/7k54_22673.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k54_22673/03_2024/7k54_22673_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k54_22673/03_2024/7k54_22673_updated.pdb" } resolution = 3.2 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= 0.019 sd= 1.364 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 GLU 81": "OE1" <-> "OE2" Residue "b ASP 263": "OD1" <-> "OD2" Residue "c ARG 13": "NH1" <-> "NH2" Residue "c ARG 33": "NH1" <-> "NH2" Residue "c ARG 59": "NH1" <-> "NH2" Residue "c ARG 77": "NH1" <-> "NH2" Residue "c ARG 83": "NH1" <-> "NH2" Residue "c GLU 168": "OE1" <-> "OE2" Residue "c ARG 169": "NH1" <-> "NH2" Residue "c ARG 184": "NH1" <-> "NH2" 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 ASP 91": "OD1" <-> "OD2" Residue "d ARG 102": "NH1" <-> "NH2" Residue "d GLU 122": "OE1" <-> "OE2" Residue "d ARG 162": "NH1" <-> "NH2" Residue "d ASP 168": "OD1" <-> "OD2" Residue "d ARG 170": "NH1" <-> "NH2" Residue "e GLU 18": "OE1" <-> "OE2" Residue "e GLU 31": "OE1" <-> "OE2" Residue "e ARG 70": "NH1" <-> "NH2" Residue "e ARG 79": "NH1" <-> "NH2" Residue "e ARG 91": "NH1" <-> "NH2" Residue "e ARG 101": "NH1" <-> "NH2" Residue "e ARG 109": "NH1" <-> "NH2" Residue "e ARG 111": "NH1" <-> "NH2" Residue "e ARG 114": "NH1" <-> "NH2" Residue "e ARG 132": "NH1" <-> "NH2" Residue "e GLU 133": "OE1" <-> "OE2" Residue "e PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ARG 2": "NH1" <-> "NH2" Residue "f GLU 41": "OE1" <-> "OE2" Residue "f ASP 55": "OD1" <-> "OD2" Residue "f ARG 152": "NH1" <-> "NH2" Residue "f ARG 162": "NH1" <-> "NH2" Residue "f ARG 169": "NH1" <-> "NH2" Residue "h ASP 36": "OD1" <-> "OD2" Residue "h PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i GLU 49": "OE1" <-> "OE2" 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 "k PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k GLU 92": "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 ARG 78": "NH1" <-> "NH2" Residue "l ARG 126": "NH1" <-> "NH2" Residue "m ARG 10": "NH1" <-> "NH2" Residue "m ARG 18": "NH1" <-> "NH2" Residue "m ARG 40": "NH1" <-> "NH2" Residue "m ARG 44": "NH1" <-> "NH2" Residue "m ARG 50": "NH1" <-> "NH2" Residue "m ARG 55": "NH1" <-> "NH2" Residue "m ARG 59": "NH1" <-> "NH2" Residue "m GLU 110": "OE1" <-> "OE2" Residue "m GLU 111": "OE1" <-> "OE2" Residue "m ARG 114": "NH1" <-> "NH2" Residue "m PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n ARG 8": "NH1" <-> "NH2" Residue "n ARG 12": "NH1" <-> "NH2" Residue "n ARG 17": "NH1" <-> "NH2" Residue "n ARG 22": "NH1" <-> "NH2" Residue "n ARG 46": "NH1" <-> "NH2" Residue "n ARG 63": "NH1" <-> "NH2" Residue "n ARG 64": "NH1" <-> "NH2" Residue "n ARG 69": "NH1" <-> "NH2" Residue "n ARG 71": "NH1" <-> "NH2" Residue "n GLU 82": "OE1" <-> "OE2" Residue "n ARG 96": "NH1" <-> "NH2" Residue "n ARG 118": "NH1" <-> "NH2" Residue "o ARG 10": "NH1" <-> "NH2" Residue "o ARG 16": "NH1" <-> "NH2" Residue "o ARG 25": "NH1" <-> "NH2" Residue "o 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 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 90": "OD1" <-> "OD2" Residue "q ASP 96": "OD1" <-> "OD2" Residue "r ARG 21": "NH1" <-> "NH2" Residue "r GLU 23": "OE1" <-> "OE2" 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 "s GLU 52": "OE1" <-> "OE2" 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 "x PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y ARG 29": "NH1" <-> "NH2" Residue "y ARG 47": "NH1" <-> "NH2" Residue "y ARG 52": "NH1" <-> "NH2" Residue "z ARG 10": "NH1" <-> "NH2" Residue "z ARG 29": "NH1" <-> "NH2" Residue "z ARG 44": "NH1" <-> "NH2" Residue "A ARG 49": "NH1" <-> "NH2" Residue "A ARG 56": "NH1" <-> "NH2" Residue "B ARG 9": "NH1" <-> "NH2" Residue "B ARG 15": "NH1" <-> "NH2" Residue "B 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 ARG 107": "NH1" <-> "NH2" Residue "G GLU 132": "OE1" <-> "OE2" Residue "G GLU 144": "OE1" <-> "OE2" Residue "G PHE 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 224": "NH1" <-> "NH2" Residue "H ARG 106": "NH1" <-> "NH2" Residue "H GLU 124": "OE1" <-> "OE2" Residue "H ARG 130": "NH1" <-> "NH2" Residue "H GLU 151": "OE1" <-> "OE2" Residue "H GLU 205": "OE1" <-> "OE2" Residue "I GLU 56": "OE1" <-> "OE2" Residue "I GLU 68": "OE1" <-> "OE2" Residue "I GLU 87": "OE1" <-> "OE2" Residue "J ASP 40": "OD1" <-> "OD2" Residue "J ARG 156": "NH1" <-> "NH2" Residue "L GLU 62": "OE1" <-> "OE2" Residue "M GLU 46": "OE1" <-> "OE2" Residue "M GLU 59": "OE1" <-> "OE2" Residue "N TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 96": "OE1" <-> "OE2" Residue "N ARG 123": "NH1" <-> "NH2" Residue "O GLU 27": "OE1" <-> "OE2" Residue "O ASP 97": "OD1" <-> "OD2" Residue "Q ARG 55": "NH1" <-> "NH2" Residue "R ASP 57": "OD1" <-> "OD2" Residue "R GLU 71": "OE1" <-> "OE2" Residue "R ASP 81": "OD1" <-> "OD2" Residue "S ASP 39": "OD1" <-> "OD2" Residue "U ARG 28": "NH1" <-> "NH2" Residue "W ARG 11": "NH1" <-> "NH2" Residue "W ASP 21": "OD1" <-> "OD2" Residue "Z GLU 43": "OE1" <-> "OE2" Residue "Z ARG 66": "NH1" <-> "NH2" Residue "a ARG 7": "NH1" <-> "NH2" Residue "a ARG 12": "NH1" <-> "NH2" Residue "a ARG 162": "NH1" <-> "NH2" Residue "8 GLU 100": "OE1" <-> "OE2" Residue "8 PHE 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 ASP 471": "OD1" <-> "OD2" Residue "8 ASP 500": "OD1" <-> "OD2" Residue "8 TYR 523": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 TYR 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 PHE 605": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 ASP 630": "OD1" <-> "OD2" Residue "8 GLU 648": "OE1" <-> "OE2" Residue "8 PHE 664": "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': 92, 'rna2p_pyr': 56, 'rna3p_pur': 782, 'rna3p_pyr': 609} Link IDs: {'rna2p': 148, 'rna3p': 1390} 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': 211, 'rna2p_pyr': 97, 'rna3p_pur': 1463, 'rna3p_pyr': 1132} Link IDs: {'rna2p': 308, 'rna3p': 2594} 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_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 10, '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: 56.09, per 1000 atoms: 0.37 Number of scatterers: 153368 At special positions: 0 Unit cell: (273, 256.2, 244.65, 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: 61.47 Conformation dependent library (CDL) restraints added in 7.1 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: 202 helices and 75 sheets defined 38.1% alpha, 18.3% beta 1457 base pairs and 2353 stacking pairs defined. Time for finding SS restraints: 74.05 Creating SS restraints... Processing helix chain 'b' and resid 10 through 16 removed outlier: 7.935A pdb=" N HIS b 14 " --> pdb=" O PRO b 10 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N VAL b 15 " --> pdb=" O GLY b 11 " (cutoff:3.500A) removed outlier: 6.558A 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: 3.822A pdb=" N LEU b 33 " --> pdb=" O PHE b 29 " (cutoff:3.500A) removed outlier: 5.691A 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: 4.140A 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: 3.973A pdb=" N ALA b 210 " --> pdb=" O LYS b 206 " (cutoff:3.500A) Processing helix chain 'b' and resid 220 through 225 removed outlier: 3.785A pdb=" N MET b 224 " --> pdb=" O ARG b 220 " (cutoff:3.500A) removed outlier: 5.276A 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: 5.972A pdb=" N ASP b 263 " --> pdb=" O ASN b 259 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N LYS b 264 " --> pdb=" O LYS b 260 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N PHE b 265 " --> pdb=" O ARG b 261 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ILE b 266 " --> pdb=" O THR b 262 " (cutoff:3.500A) removed outlier: 5.435A 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: 6.649A pdb=" N THR c 61 " --> pdb=" O ALA c 57 " (cutoff:3.500A) Processing helix chain 'c' and resid 62 through 72 removed outlier: 3.720A pdb=" N ALA c 71 " --> pdb=" O HIS c 67 " (cutoff:3.500A) Processing helix chain 'c' and resid 98 through 105 removed outlier: 4.172A pdb=" N ALA c 102 " --> pdb=" O VAL c 98 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N ASP c 103 " --> pdb=" O GLU c 99 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N VAL c 104 " --> pdb=" O LEU c 100 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N LYS c 105 " --> pdb=" O PHE c 101 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 98 through 105' Processing helix chain 'c' and resid 120 through 125 Processing helix chain 'c' and resid 39 through 44 Processing helix chain 'd' and resid 15 through 20 Processing helix chain 'd' and resid 24 through 41 removed outlier: 5.661A 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 removed outlier: 4.328A pdb=" N LEU d 134 " --> pdb=" O LYS d 130 " (cutoff:3.500A) Processing helix chain 'd' and resid 154 through 163 removed outlier: 4.768A pdb=" N ASN d 163 " --> pdb=" O LEU d 159 " (cutoff:3.500A) Processing helix chain 'd' and resid 176 through 184 removed outlier: 6.442A pdb=" N ASP d 184 " --> pdb=" O LEU d 180 " (cutoff:3.500A) Processing helix chain 'd' and resid 189 through 200 removed outlier: 3.535A pdb=" N GLN d 195 " --> pdb=" O ASP d 191 " (cutoff:3.500A) Processing helix chain 'e' and resid 1 through 19 removed outlier: 4.509A pdb=" N ASP e 5 " --> pdb=" O ALA e 1 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N VAL e 12 " --> pdb=" O LYS e 8 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N THR e 17 " --> pdb=" O LYS e 13 " (cutoff:3.500A) Processing helix chain 'e' and resid 41 through 46 removed outlier: 4.398A pdb=" N ASP e 45 " --> pdb=" O GLU e 41 " (cutoff:3.500A) Processing helix chain 'e' and resid 47 through 61 Processing helix chain 'e' and resid 92 through 110 removed outlier: 4.139A pdb=" N ILE e 105 " --> pdb=" O ARG e 101 " (cutoff:3.500A) removed outlier: 4.408A 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: 6.168A pdb=" N VAL e 145 " --> pdb=" O ASP e 141 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N ASP e 146 " --> pdb=" O TYR e 142 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 141 through 146' Processing helix chain 'e' and resid 161 through 173 removed outlier: 3.892A pdb=" N LEU e 168 " --> pdb=" O GLU e 164 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N PHE e 172 " --> pdb=" O LEU e 168 " (cutoff:3.500A) Processing helix chain 'e' and resid 133 through 138 removed outlier: 4.925A pdb=" N ILE e 136 " --> pdb=" O GLU e 133 " (cutoff:3.500A) Proline residue: e 138 - end of helix Processing helix chain 'f' and resid 1 through 6 removed outlier: 3.841A pdb=" N ALA f 6 " --> pdb=" O ARG f 2 " (cutoff:3.500A) Processing helix chain 'f' and resid 59 through 80 Processing helix chain 'f' and resid 136 through 152 removed outlier: 3.965A pdb=" N ARG f 151 " --> pdb=" O LEU f 147 " (cutoff:3.500A) Processing helix chain 'g' and resid 22 through 28 Processing helix chain 'g' and resid 29 through 34 Processing helix chain 'g' and resid 40 through 48 removed outlier: 5.141A pdb=" N ILE g 44 " --> pdb=" O THR g 40 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLU g 45 " --> pdb=" O LYS g 41 " (cutoff:3.500A) Processing helix chain 'g' and resid 95 through 107 removed outlier: 3.999A pdb=" N ILE g 99 " --> pdb=" O GLY g 95 " (cutoff:3.500A) Processing helix chain 'h' and resid 3 through 19 removed outlier: 3.506A pdb=" N ILE h 11 " --> pdb=" O ASP h 7 " (cutoff:3.500A) Processing helix chain 'h' and resid 33 through 48 removed outlier: 4.006A pdb=" N ARG h 42 " --> pdb=" O MET h 38 " (cutoff:3.500A) Processing helix chain 'h' and resid 59 through 68 removed outlier: 4.160A pdb=" N VAL h 64 " --> pdb=" O LEU h 60 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLU h 65 " --> pdb=" O ARG h 61 " (cutoff:3.500A) Proline residue: h 68 - end of helix Processing helix chain 'h' and resid 71 through 78 removed outlier: 4.464A pdb=" N ALA h 75 " --> pdb=" O CYS h 71 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N PHE h 76 " --> pdb=" O LEU h 72 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N VAL h 77 " --> pdb=" O LYS h 73 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N GLY h 78 " --> pdb=" O ASP h 74 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 71 through 78' Processing helix chain 'i' and resid 23 through 28 removed outlier: 4.875A pdb=" N LEU i 27 " --> pdb=" O VAL i 23 " (cutoff:3.500A) Processing helix chain 'i' and resid 33 through 49 removed outlier: 3.548A pdb=" N LYS i 44 " --> pdb=" O ALA i 40 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N SER i 47 " --> pdb=" O ALA i 43 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ILE i 48 " --> pdb=" O LYS i 44 " (cutoff:3.500A) removed outlier: 3.562A 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 Processing helix chain 'j' and resid 97 through 110 removed outlier: 3.908A pdb=" N ILE j 101 " --> pdb=" O PRO j 97 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N MET j 108 " --> pdb=" O ALA j 104 " (cutoff:3.500A) Proline residue: j 110 - end of helix Processing helix chain 'j' and resid 112 through 123 removed outlier: 3.759A pdb=" N LYS j 121 " --> pdb=" O ALA j 117 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N LEU j 122 " --> pdb=" O MET j 118 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N LYS j 123 " --> pdb=" O PHE j 119 " (cutoff:3.500A) Processing helix chain 'k' and resid 109 through 120 removed outlier: 6.435A pdb=" N MET k 113 " --> pdb=" O SER k 109 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N LYS k 114 " --> pdb=" O GLU k 110 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N ILE k 115 " --> pdb=" O LYS k 111 " (cutoff:3.500A) Proline residue: k 120 - end of helix Processing helix chain 'l' and resid 56 through 62 Proline residue: l 62 - end of helix Processing helix chain 'l' and resid 68 through 75 removed outlier: 4.096A pdb=" N ALA l 72 " --> pdb=" O SER l 68 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N ILE l 73 " --> pdb=" O ARG l 69 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N THR l 74 " --> pdb=" O LYS l 70 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N ALA l 75 " --> pdb=" O ALA l 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 68 through 75' Processing helix chain 'l' and resid 78 through 83 removed outlier: 3.801A pdb=" N LEU l 82 " --> pdb=" O ARG l 78 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ALA l 83 " --> pdb=" O LEU l 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 78 through 83' Processing helix chain 'l' and resid 91 through 99 removed outlier: 4.634A pdb=" N LEU l 95 " --> pdb=" O ASP l 91 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LYS l 96 " --> pdb=" O LEU l 92 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N ALA l 97 " --> pdb=" O ASN l 93 " (cutoff:3.500A) Processing helix chain 'l' and resid 128 through 139 Processing helix chain 'm' and resid 42 through 58 removed outlier: 3.822A pdb=" N ALA m 56 " --> pdb=" O ALA m 52 " (cutoff:3.500A) Processing helix chain 'm' and resid 109 through 125 removed outlier: 3.503A pdb=" N LEU m 119 " --> pdb=" O GLU m 115 " (cutoff:3.500A) Proline residue: m 125 - end of helix Processing helix chain 'n' and resid 13 through 32 Processing helix chain 'n' and resid 38 through 57 removed outlier: 4.666A pdb=" N ARG n 46 " --> pdb=" O LYS n 42 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N VAL n 47 " --> pdb=" O GLU n 43 " (cutoff:3.500A) Proline residue: n 50 - end of helix removed outlier: 4.374A pdb=" N THR n 57 " --> pdb=" O THR n 53 " (cutoff:3.500A) Processing helix chain 'n' and resid 59 through 71 removed outlier: 4.738A pdb=" N THR n 70 " --> pdb=" O ALA n 66 " (cutoff:3.500A) Processing helix chain 'n' and resid 72 through 82 removed outlier: 4.288A pdb=" N PHE n 80 " --> pdb=" O VAL n 76 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ASN n 81 " --> pdb=" O ALA n 77 " (cutoff:3.500A) Processing helix chain 'n' and resid 83 through 88 Processing helix chain 'o' and resid 2 through 22 removed outlier: 4.794A pdb=" N ARG o 13 " --> pdb=" O ARG o 9 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N ALA o 14 " --> pdb=" O ARG o 10 " (cutoff:3.500A) Processing helix chain 'o' and resid 55 through 63 removed outlier: 4.699A pdb=" N GLN o 61 " --> pdb=" O ALA o 57 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N LYS o 63 " --> pdb=" O ALA o 59 " (cutoff:3.500A) Processing helix chain 'o' and resid 67 through 86 removed outlier: 3.579A pdb=" N GLU o 80 " --> pdb=" O LYS o 76 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ARG o 81 " --> pdb=" O ALA o 77 " (cutoff:3.500A) Processing helix chain 'o' and resid 101 through 114 Processing helix chain 'p' and resid 1 through 13 removed outlier: 4.704A pdb=" N GLN p 11 " --> pdb=" O LEU p 7 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N LYS p 13 " --> pdb=" O GLN p 9 " (cutoff:3.500A) Processing helix chain 'p' and resid 98 through 103 removed outlier: 4.341A pdb=" N ARG p 102 " --> pdb=" O TYR p 98 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N THR p 103 " --> pdb=" O LEU p 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'p' and resid 98 through 103' Processing helix chain 'p' and resid 104 through 109 removed outlier: 6.177A pdb=" N ILE p 109 " --> pdb=" O LYS p 105 " (cutoff:3.500A) Processing helix chain 'q' and resid 5 through 21 removed outlier: 4.883A pdb=" N LYS q 21 " --> pdb=" O LEU q 17 " (cutoff:3.500A) Processing helix chain 'q' and resid 25 through 30 removed outlier: 3.949A pdb=" N ARG q 29 " --> pdb=" O GLY q 25 " (cutoff:3.500A) Processing helix chain 'q' and resid 31 through 36 removed outlier: 3.659A pdb=" N GLN q 36 " --> pdb=" O ARG q 32 " (cutoff:3.500A) Processing helix chain 'q' and resid 38 through 72 removed outlier: 4.173A pdb=" N ARG q 50 " --> pdb=" O TYR q 46 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N LYS q 53 " --> pdb=" O ARG q 49 " (cutoff:3.500A) Processing helix chain 'q' and resid 74 through 86 Processing helix chain 'q' and resid 90 through 101 removed outlier: 3.933A pdb=" N ASP q 96 " --> pdb=" O LYS q 92 " (cutoff:3.500A) Processing helix chain 'q' and resid 102 through 117 Processing helix chain 's' and resid 13 through 25 removed outlier: 4.828A pdb=" N LEU s 23 " --> pdb=" O LEU s 19 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ILE s 24 " --> pdb=" O VAL s 20 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ARG s 25 " --> pdb=" O ALA s 21 " (cutoff:3.500A) Processing helix chain 's' and resid 28 through 39 removed outlier: 4.968A pdb=" N TYR s 38 " --> pdb=" O ASP s 34 " (cutoff:3.500A) Processing helix chain 's' and resid 41 through 61 removed outlier: 3.514A pdb=" N VAL s 45 " --> pdb=" O LYS s 41 " (cutoff:3.500A) Processing helix chain 's' and resid 65 through 70 removed outlier: 3.979A pdb=" N LEU s 69 " --> pdb=" O ASP s 65 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N LYS s 70 " --> pdb=" O ILE s 66 " (cutoff:3.500A) No H-bonds generated for 'chain 's' and resid 65 through 70' Processing helix chain 't' and resid 1 through 11 removed outlier: 4.430A pdb=" N GLU t 5 " --> pdb=" O MET t 1 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU t 8 " --> pdb=" O GLU t 4 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N LYS t 9 " --> pdb=" O GLU t 5 " (cutoff:3.500A) removed outlier: 4.141A 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: 4.022A pdb=" N VAL u 69 " --> pdb=" O GLN u 65 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N ALA u 70 " --> pdb=" O VAL u 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'u' and resid 65 through 70' Processing helix chain 'v' and resid 13 through 24 removed outlier: 3.505A pdb=" N ASN v 24 " --> pdb=" O LEU v 20 " (cutoff:3.500A) Processing helix chain 'v' and resid 43 through 52 removed outlier: 3.568A pdb=" N VAL v 47 " --> pdb=" O ASP v 43 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ALA v 52 " --> pdb=" O MET v 48 " (cutoff:3.500A) Processing helix chain 'v' and resid 53 through 59 removed outlier: 4.472A pdb=" N TYR v 57 " --> pdb=" O LYS v 53 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N SER v 58 " --> pdb=" O ALA v 54 " (cutoff:3.500A) Processing helix chain 'x' and resid 51 through 61 Processing helix chain 'x' and resid 62 through 74 Processing helix chain 'y' and resid 1 through 7 removed outlier: 4.731A pdb=" N LEU y 6 " --> pdb=" O LYS y 2 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N ARG y 7 " --> pdb=" O ALA y 3 " (cutoff:3.500A) Processing helix chain 'y' and resid 9 through 35 removed outlier: 3.606A pdb=" N ARG y 23 " --> pdb=" O LEU y 19 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLN y 25 " --> pdb=" O LEU y 21 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N PHE y 26 " --> pdb=" O LEU y 22 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLY y 35 " --> pdb=" O GLN y 31 " (cutoff:3.500A) Processing helix chain 'y' and resid 40 through 62 removed outlier: 3.603A 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 Processing helix chain 'A' and resid 45 through 52 removed outlier: 3.611A pdb=" N ARG A 49 " --> pdb=" O THR A 45 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N ALA A 52 " --> pdb=" O GLN A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 65 removed outlier: 4.334A pdb=" N ARG A 59 " --> pdb=" O GLY A 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 18 removed outlier: 4.450A pdb=" N HIS B 18 " --> pdb=" O MET B 14 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 16 Processing helix chain 'D' and resid 17 through 24 removed outlier: 4.190A 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 Processing helix chain 'E' and resid 36 through 45 removed outlier: 4.388A 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: 4.575A pdb=" N GLY E 55 " --> pdb=" O LYS E 51 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N LEU E 56 " --> pdb=" O GLY E 52 " (cutoff:3.500A) Proline residue: E 62 - end of helix Processing helix chain 'F' and resid 30 through 35 removed outlier: 4.058A pdb=" N LYS F 34 " --> pdb=" O GLU F 30 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N GLN F 35 " --> pdb=" O PRO F 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 30 through 35' Processing helix chain 'G' and resid 43 through 62 Proline residue: G 47 - end of helix Processing helix chain 'G' and resid 75 through 87 removed outlier: 4.113A pdb=" N CYS G 86 " --> pdb=" O ALA G 82 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASP G 87 " --> pdb=" O ALA G 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 98 through 103 Processing helix chain 'G' and resid 104 through 122 removed outlier: 3.977A pdb=" N GLN G 108 " --> pdb=" O LYS G 104 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N GLN G 121 " --> pdb=" O GLU G 117 " (cutoff:3.500A) Processing helix chain 'G' and resid 129 through 147 Processing helix chain 'G' and resid 148 through 154 removed outlier: 3.798A pdb=" N ASP G 152 " --> pdb=" O GLY G 148 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N GLY G 154 " --> pdb=" O ILE G 150 " (cutoff:3.500A) Processing helix chain 'G' and resid 164 through 169 Processing helix chain 'G' and resid 170 through 179 removed outlier: 3.579A pdb=" N ASN G 177 " --> pdb=" O LYS G 173 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LEU G 178 " --> pdb=" O GLU G 174 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N GLY G 179 " --> pdb=" O ALA G 175 " (cutoff:3.500A) Processing helix chain 'G' and resid 205 through 225 removed outlier: 3.658A pdb=" N VAL G 209 " --> pdb=" O ALA G 205 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR G 210 " --> pdb=" O ILE G 206 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N SER G 225 " --> pdb=" O ARG G 221 " (cutoff:3.500A) Processing helix chain 'H' and resid 5 through 11 removed outlier: 3.950A pdb=" N ARG H 10 " --> pdb=" O PRO H 6 " (cutoff:3.500A) Processing helix chain 'H' and resid 27 through 47 Processing helix chain 'H' and resid 71 through 77 Processing helix chain 'H' and resid 80 through 95 Processing helix chain 'H' and resid 111 through 126 removed outlier: 3.699A pdb=" N ARG H 126 " --> pdb=" O GLN H 122 " (cutoff:3.500A) Processing helix chain 'H' and resid 128 through 144 Processing helix chain 'I' and resid 6 through 15 removed outlier: 3.952A pdb=" N LEU I 10 " --> pdb=" O PRO I 6 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N SER I 11 " --> pdb=" O LYS I 7 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 65 Processing helix chain 'I' and resid 67 through 82 removed outlier: 4.603A pdb=" N LYS I 82 " --> pdb=" O ALA I 78 " (cutoff:3.500A) Processing helix chain 'I' and resid 84 through 96 removed outlier: 3.582A 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: 3.700A pdb=" N LYS I 120 " --> pdb=" O LEU I 116 " (cutoff:3.500A) Processing helix chain 'I' and resid 151 through 165 removed outlier: 6.089A pdb=" N LYS I 155 " --> pdb=" O GLN I 151 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N ALA I 156 " --> pdb=" O SER I 152 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA I 161 " --> pdb=" O ALA I 157 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N GLU I 162 " --> pdb=" O LEU I 158 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N GLN I 163 " --> pdb=" O GLU I 159 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ARG I 164 " --> pdb=" O LEU I 160 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N GLU I 165 " --> pdb=" O ALA I 161 " (cutoff:3.500A) Processing helix chain 'I' and resid 186 through 191 removed outlier: 3.577A pdb=" N LEU I 190 " --> pdb=" O GLU I 186 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N SER I 191 " --> pdb=" O ARG I 187 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 186 through 191' Processing helix chain 'I' and resid 195 through 205 removed outlier: 4.284A pdb=" N ILE I 199 " --> pdb=" O ASN I 195 " (cutoff:3.500A) Processing helix chain 'J' and resid 54 through 70 removed outlier: 3.950A pdb=" N GLU J 64 " --> pdb=" O GLN J 60 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N LYS J 65 " --> pdb=" O LYS J 61 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N MET J 70 " --> pdb=" O ALA J 66 " (cutoff:3.500A) Processing helix chain 'J' and resid 108 through 118 removed outlier: 6.102A pdb=" N ALA J 112 " --> pdb=" O GLY J 108 " (cutoff:3.500A) removed outlier: 3.510A 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 removed outlier: 3.934A pdb=" N ALA J 154 " --> pdb=" O GLU J 150 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS J 155 " --> pdb=" O MET J 151 " (cutoff:3.500A) Processing helix chain 'J' and resid 159 through 165 Processing helix chain 'K' and resid 12 through 33 removed outlier: 3.768A pdb=" N GLN K 17 " --> pdb=" O ASP K 13 " (cutoff:3.500A) Proline residue: K 19 - end of helix Processing helix chain 'K' and resid 67 through 82 removed outlier: 5.118A pdb=" N ASP K 82 " --> pdb=" O PHE K 78 " (cutoff:3.500A) Processing helix chain 'L' and resid 20 through 30 Processing helix chain 'L' and resid 34 through 54 removed outlier: 4.083A pdb=" N ARG L 52 " --> pdb=" O THR L 48 " (cutoff:3.500A) Processing helix chain 'L' and resid 57 through 69 removed outlier: 4.936A pdb=" N GLU L 62 " --> pdb=" O LEU L 58 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA L 64 " --> pdb=" O ALA L 60 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N ASN L 67 " --> pdb=" O VAL L 63 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N VAL L 68 " --> pdb=" O ALA L 64 " (cutoff:3.500A) Processing helix chain 'L' and resid 91 through 109 removed outlier: 4.146A pdb=" N ALA L 97 " --> pdb=" O VAL L 93 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ARG L 108 " --> pdb=" O VAL L 104 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N LYS L 109 " --> pdb=" O GLU L 105 " (cutoff:3.500A) Processing helix chain 'L' and resid 114 through 129 Processing helix chain 'L' and resid 131 through 148 removed outlier: 3.535A pdb=" N GLU L 145 " --> pdb=" O HIS L 141 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ALA L 146 " --> pdb=" O ARG L 142 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N ASN L 147 " --> pdb=" O MET L 143 " (cutoff:3.500A) Processing helix chain 'M' and resid 4 through 20 Processing helix chain 'M' and resid 29 through 43 removed outlier: 3.507A pdb=" N LEU M 39 " --> pdb=" O ILE M 35 " (cutoff:3.500A) Processing helix chain 'M' and resid 111 through 119 Processing helix chain 'N' and resid 33 through 38 Processing helix chain 'N' and resid 43 through 53 removed outlier: 4.922A pdb=" N VAL N 47 " --> pdb=" O ALA N 43 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N ARG N 48 " --> pdb=" O ARG N 44 " (cutoff:3.500A) Proline residue: N 50 - end of helix Processing helix chain 'N' and resid 70 through 87 removed outlier: 4.781A pdb=" N MET N 87 " --> pdb=" O THR N 83 " (cutoff:3.500A) Processing helix chain 'N' and resid 92 through 101 removed outlier: 4.928A pdb=" N GLU N 96 " --> pdb=" O SER N 92 " (cutoff:3.500A) Processing helix chain 'O' and resid 14 through 33 removed outlier: 3.727A pdb=" N GLN O 20 " --> pdb=" O ARG O 16 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA O 29 " --> pdb=" O ILE O 25 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N THR O 32 " --> pdb=" O THR O 28 " (cutoff:3.500A) Processing helix chain 'O' and resid 80 through 90 removed outlier: 3.569A pdb=" N VAL O 84 " --> pdb=" O THR O 80 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N ASP O 85 " --> pdb=" O GLU O 81 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N ALA O 86 " --> pdb=" O LYS O 82 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ARG O 89 " --> pdb=" O ASP O 85 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N LEU O 90 " --> pdb=" O ALA O 86 " (cutoff:3.500A) Processing helix chain 'P' and resid 45 through 50 removed outlier: 3.952A pdb=" N GLY P 50 " --> pdb=" O ALA P 46 " (cutoff:3.500A) Processing helix chain 'P' and resid 52 through 57 removed outlier: 4.987A pdb=" N LYS P 56 " --> pdb=" O ARG P 52 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N SER P 57 " --> pdb=" O GLY P 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 52 through 57' Processing helix chain 'P' and resid 58 through 73 removed outlier: 5.517A pdb=" N ALA P 72 " --> pdb=" O ARG P 68 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N VAL P 73 " --> pdb=" O CYS P 69 " (cutoff:3.500A) Processing helix chain 'P' and resid 91 through 103 removed outlier: 4.753A pdb=" N ILE P 96 " --> pdb=" O ARG P 92 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ARG P 97 " --> pdb=" O GLU P 93 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLY P 103 " --> pdb=" O LEU P 99 " (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: 5.170A pdb=" N TYR Q 116 " --> pdb=" O ALA Q 112 " (cutoff:3.500A) removed outlier: 4.118A 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 21 removed outlier: 3.598A pdb=" N SER R 20 " --> pdb=" O ILE R 16 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N ILE R 21 " --> pdb=" O ALA R 17 " (cutoff:3.500A) Processing helix chain 'R' and resid 25 through 37 Processing helix chain 'R' and resid 43 through 48 removed outlier: 5.274A pdb=" N SER R 48 " --> pdb=" O ILE R 44 " (cutoff:3.500A) Processing helix chain 'R' and resid 49 through 63 removed outlier: 4.531A pdb=" N THR R 54 " --> pdb=" O GLY R 50 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N LYS R 61 " --> pdb=" O ASP R 57 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N PHE R 62 " --> pdb=" O GLU R 58 " (cutoff:3.500A) removed outlier: 4.997A 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 92 Processing helix chain 'R' and resid 105 through 110 Processing helix chain 'S' and resid 2 through 24 removed outlier: 5.246A pdb=" N PHE S 20 " --> pdb=" O ALA S 16 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N ALA S 21 " --> pdb=" O ASP S 17 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N LYS S 22 " --> pdb=" O LYS S 18 " (cutoff:3.500A) Processing helix chain 'S' and resid 37 through 50 removed outlier: 3.965A pdb=" N TRP S 41 " --> pdb=" O ASP S 37 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N GLN S 48 " --> pdb=" O VAL S 44 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N THR S 49 " --> pdb=" O LEU S 45 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LEU S 50 " --> pdb=" O LYS S 46 " (cutoff:3.500A) Processing helix chain 'S' and resid 55 through 60 removed outlier: 3.907A pdb=" N GLN S 59 " --> pdb=" O SER S 55 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N ARG S 60 " --> pdb=" O PRO S 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 55 through 60' Processing helix chain 'S' and resid 79 through 90 removed outlier: 4.290A pdb=" N ARG S 89 " --> pdb=" O GLU S 85 " (cutoff:3.500A) Processing helix chain 'S' and resid 25 through 31 removed outlier: 4.570A pdb=" N SER S 31 " --> pdb=" O LEU S 26 " (cutoff:3.500A) Processing helix chain 'T' and resid 3 through 15 Processing helix chain 'T' and resid 23 through 43 removed outlier: 3.527A pdb=" N GLY T 40 " --> pdb=" O ASN T 36 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N HIS T 41 " --> pdb=" O HIS T 37 " (cutoff:3.500A) Processing helix chain 'T' and resid 48 through 73 Processing helix chain 'T' and resid 74 through 85 Processing helix chain 'U' and resid 53 through 64 Processing helix chain 'U' and resid 68 through 79 Processing helix chain 'W' and resid 12 through 17 removed outlier: 3.923A pdb=" N GLY W 16 " --> pdb=" O PHE W 12 " (cutoff:3.500A) Processing helix chain 'W' and resid 24 through 33 removed outlier: 3.841A pdb=" N LEU W 28 " --> pdb=" O ASP W 24 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASN W 30 " --> pdb=" O ALA W 26 " (cutoff:3.500A) removed outlier: 5.348A 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 Processing helix chain 'X' and resid 40 through 45 removed outlier: 5.828A pdb=" N GLY X 45 " --> pdb=" O PRO X 41 " (cutoff:3.500A) Processing helix chain 'X' and resid 70 through 75 removed outlier: 3.826A 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 70 through 75' Processing helix chain 'Y' and resid 7 through 41 removed outlier: 4.091A pdb=" N ILE Y 11 " --> pdb=" O LYS Y 7 " (cutoff:3.500A) Processing helix chain 'Y' and resid 42 through 64 Proline residue: Y 55 - end of helix Processing helix chain 'Y' and resid 67 through 86 removed outlier: 6.936A pdb=" N ALA Y 71 " --> pdb=" O HIS Y 67 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ALA Y 72 " --> pdb=" O LYS Y 68 " (cutoff:3.500A) Processing helix chain 'Z' and resid 16 through 23 removed outlier: 4.001A pdb=" N ARG Z 20 " --> pdb=" O ARG Z 16 " (cutoff:3.500A) Processing helix chain 'Z' and resid 24 through 32 removed outlier: 5.834A pdb=" N LEU Z 28 " --> pdb=" O LYS Z 24 " (cutoff:3.500A) Processing helix chain 'Z' and resid 36 through 61 Proline residue: Z 40 - end of helix Processing helix chain 'a' and resid 6 through 16 removed outlier: 3.896A pdb=" N VAL a 15 " --> pdb=" O ILE a 11 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N ASP a 16 " --> pdb=" O ARG a 12 " (cutoff:3.500A) Processing helix chain 'a' and resid 23 through 35 removed outlier: 3.802A pdb=" N ALA a 28 " --> pdb=" O ASN a 24 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N GLU a 32 " --> pdb=" O ALA a 28 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU a 33 " --> pdb=" O LEU a 29 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N THR a 35 " --> pdb=" O LYS a 31 " (cutoff:3.500A) Processing helix chain 'a' and resid 181 through 200 removed outlier: 3.705A pdb=" N LEU a 185 " --> pdb=" O ASP a 181 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA a 199 " --> pdb=" O ALA a 195 " (cutoff:3.500A) Processing helix chain '8' and resid 22 through 35 Processing helix chain '8' and resid 53 through 60 removed outlier: 4.491A pdb=" N GLN 8 57 " --> pdb=" O MET 8 53 " (cutoff:3.500A) Processing helix chain '8' and resid 95 through 107 removed outlier: 3.509A pdb=" N VAL 8 99 " --> pdb=" O PHE 8 95 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG 8 104 " --> pdb=" O GLU 8 100 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N ASP 8 107 " --> pdb=" O MET 8 103 " (cutoff:3.500A) Processing helix chain '8' and resid 121 through 134 removed outlier: 4.535A pdb=" N THR 8 125 " --> pdb=" O PRO 8 121 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL 8 126 " --> pdb=" O GLN 8 122 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N TRP 8 127 " --> pdb=" O SER 8 123 " (cutoff:3.500A) Processing helix chain '8' and resid 150 through 161 removed outlier: 4.344A pdb=" N LYS 8 159 " --> pdb=" O VAL 8 155 " (cutoff:3.500A) Processing helix chain '8' and resid 211 through 228 removed outlier: 3.951A pdb=" N ALA 8 227 " --> pdb=" O ILE 8 223 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N GLU 8 228 " --> pdb=" O GLU 8 224 " (cutoff:3.500A) Processing helix chain '8' and resid 230 through 240 Processing helix chain '8' and resid 244 through 259 Processing helix chain '8' and resid 274 through 285 Processing helix chain '8' and resid 288 through 293 Proline residue: 8 293 - end of helix Processing helix chain '8' and resid 424 through 443 removed outlier: 3.625A pdb=" N LYS 8 430 " --> pdb=" O ALA 8 426 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU 8 441 " --> pdb=" O ARG 8 437 " (cutoff:3.500A) Proline residue: 8 443 - end of helix Processing helix chain '8' and resid 462 through 476 Processing helix chain '8' and resid 546 through 564 removed outlier: 4.280A pdb=" N ILE 8 550 " --> pdb=" O PRO 8 546 " (cutoff:3.500A) Proline residue: 8 551 - end of helix removed outlier: 3.753A pdb=" N LYS 8 562 " --> pdb=" O GLN 8 558 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ALA 8 563 " --> pdb=" O GLU 8 559 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLY 8 564 " --> pdb=" O GLN 8 560 " (cutoff:3.500A) Processing helix chain '8' and resid 589 through 609 removed outlier: 3.501A pdb=" N PHE 8 593 " --> pdb=" O SER 8 589 " (cutoff:3.500A) Processing helix chain '8' and resid 627 through 639 removed outlier: 3.959A pdb=" N ARG 8 639 " --> pdb=" O LEU 8 635 " (cutoff:3.500A) Processing helix chain '8' and resid 659 through 664 removed outlier: 4.125A pdb=" N PHE 8 664 " --> pdb=" O LEU 8 660 " (cutoff:3.500A) Processing helix chain '8' and resid 665 through 675 removed outlier: 3.605A pdb=" N GLN 8 669 " --> pdb=" O GLY 8 665 " (cutoff:3.500A) Processing helix chain '8' and resid 691 through 699 removed outlier: 3.792A 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: 6.694A pdb=" N LEU b 92 " --> pdb=" O GLU b 78 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N ILE b 73 " --> pdb=" O SER b 117 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N SER b 117 " --> pdb=" O ILE b 73 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ASP b 113 " --> pdb=" O VAL b 77 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N GLY b 126 " --> pdb=" O GLN b 114 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N GLN b 116 " --> pdb=" O GLY b 126 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'b' and resid 136 through 141 removed outlier: 7.929A pdb=" N VAL b 136 " --> pdb=" O ALA b 165 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N ALA b 165 " --> pdb=" O VAL b 136 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N SER b 138 " --> pdb=" O ILE b 163 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N ILE b 163 " --> pdb=" O ARG b 174 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ARG b 174 " --> pdb=" O ILE b 163 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU b 179 " --> pdb=" O LEU b 175 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'b' and resid 89 through 95 removed outlier: 5.827A pdb=" N ASN b 89 " --> pdb=" O ALA b 105 " (cutoff:3.500A) removed outlier: 3.588A 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 8 removed outlier: 4.439A pdb=" N SER c 199 " --> pdb=" O LYS c 8 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N ASP c 200 " --> pdb=" O THR c 112 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N THR c 112 " --> pdb=" O ASP c 200 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'c' and resid 11 through 16 removed outlier: 4.603A pdb=" N VAL c 20 " --> pdb=" O THR c 16 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'c' and resid 79 through 84 removed outlier: 6.328A pdb=" N ARG c 46 " --> pdb=" O LEU c 84 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N GLN c 49 " --> pdb=" O THR c 35 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N GLN c 94 " --> pdb=" O VAL c 34 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'd' and resid 117 through 120 removed outlier: 3.822A pdb=" N VAL d 187 " --> pdb=" O LEU d 147 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'e' and resid 64 through 68 removed outlier: 5.716A pdb=" N GLY e 38 " --> pdb=" O GLY e 150 " (cutoff:3.500A) removed outlier: 8.329A pdb=" N GLY e 150 " --> pdb=" O GLY e 38 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'f' and resid 15 through 18 Processing sheet with id= 10, first strand: chain 'f' and resid 40 through 44 Processing sheet with id= 11, first strand: chain 'f' and resid 93 through 98 removed outlier: 5.900A pdb=" N ASN f 100 " --> pdb=" O LEU f 116 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL f 112 " --> pdb=" O LEU f 104 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'f' and resid 120 through 124 removed outlier: 5.499A pdb=" N THR f 128 " --> pdb=" O LEU f 88 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'g' and resid 3 through 6 removed outlier: 5.507A pdb=" N LYS g 35 " --> pdb=" O LEU g 6 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'g' and resid 78 through 82 removed outlier: 4.774A pdb=" N SER g 82 " --> pdb=" O VAL g 147 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'i' and resid 54 through 61 removed outlier: 3.668A pdb=" N SER i 65 " --> pdb=" O TYR i 61 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'j' and resid 50 through 56 Processing sheet with id= 17, first strand: chain 'k' and resid 6 through 9 removed outlier: 3.745A pdb=" N THR k 6 " --> pdb=" O CYS k 21 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'm' and resid 62 through 66 removed outlier: 7.946A pdb=" N LEU m 102 " --> pdb=" O ARG m 66 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N TYR m 103 " --> pdb=" O LEU m 33 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N SER m 30 " --> pdb=" O LYS m 133 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N LYS m 127 " --> pdb=" O VAL m 36 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'n' and resid 33 through 37 removed outlier: 7.106A pdb=" N MET n 110 " --> pdb=" O CYS n 100 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N CYS n 100 " --> pdb=" O MET n 110 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'o' and resid 24 through 30 removed outlier: 3.820A pdb=" N ARG o 25 " --> pdb=" O ILE o 40 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ILE o 35 " --> pdb=" O THR o 53 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'p' and resid 37 through 44 removed outlier: 4.452A pdb=" N THR p 24 " --> pdb=" O LYS p 86 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'p' and resid 48 through 52 removed outlier: 4.078A pdb=" N ALA p 48 " --> pdb=" O THR p 59 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N ARG p 52 " --> pdb=" O HIS p 55 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N SER p 56 " --> pdb=" O THR p 75 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'r' and resid 11 through 14 removed outlier: 3.645A pdb=" N PHE r 5 " --> pdb=" O HIS r 12 " (cutoff:3.500A) removed outlier: 8.740A pdb=" N LEU r 39 " --> pdb=" O ILE r 49 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'r' and resid 18 through 21 removed outlier: 4.146A pdb=" N GLN r 18 " --> pdb=" O ILE r 98 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ASP r 95 " --> pdb=" O VAL r 64 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N LYS r 60 " --> pdb=" O THR r 99 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N GLU r 31 " --> pdb=" O VAL r 63 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'r' and resid 57 through 60 removed outlier: 5.452A pdb=" N VAL r 58 " --> pdb=" O SER r 102 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'r' and resid 65 through 72 removed outlier: 5.472A pdb=" N GLN r 91 " --> pdb=" O GLY r 69 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N LYS r 71 " --> pdb=" O HIS r 89 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N HIS r 89 " --> pdb=" O LYS r 71 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 's' and resid 2 through 8 removed outlier: 4.463A pdb=" N THR s 3 " --> pdb=" O VAL s 107 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL s 107 " --> pdb=" O THR s 3 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N THR s 100 " --> pdb=" O GLY s 79 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY s 79 " --> pdb=" O THR s 100 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 's' and resid 81 through 88 removed outlier: 3.692A pdb=" N ARG s 92 " --> pdb=" O ARG s 88 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 't' and resid 12 through 15 removed outlier: 3.835A pdb=" N ALA t 13 " --> pdb=" O LYS t 33 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N VAL t 31 " --> pdb=" O HIS t 15 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N LYS t 81 " --> pdb=" O VAL t 34 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N SER t 78 " --> pdb=" O GLY t 65 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N GLY t 65 " --> pdb=" O SER t 78 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N LYS t 66 " --> pdb=" O ARG t 77 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'u' and resid 39 through 44 removed outlier: 5.233A pdb=" N ASN u 39 " --> pdb=" O ALA u 62 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'u' and resid 81 through 86 removed outlier: 4.775A pdb=" N ARG u 81 " --> pdb=" O LYS u 96 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'v' and resid 68 through 72 removed outlier: 3.769A pdb=" N ILE v 4 " --> pdb=" O THR v 62 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ILE v 89 " --> pdb=" O PRO v 27 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'w' and resid 30 through 33 removed outlier: 4.109A pdb=" N SER w 31 " --> pdb=" O ALA w 57 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N LEU w 55 " --> pdb=" O ILE w 33 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N THR w 54 " --> pdb=" O GLY w 50 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N ASN w 46 " --> pdb=" O LYS w 58 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'w' and resid 41 through 44 removed outlier: 6.674A pdb=" N ILE w 78 " --> pdb=" O GLY w 44 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'x' and resid 11 through 18 removed outlier: 5.093A pdb=" N THR x 24 " --> pdb=" O ASN x 16 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N SER x 18 " --> pdb=" O ASN x 22 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N ASN x 22 " --> pdb=" O SER x 18 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'x' and resid 34 through 40 Processing sheet with id= 37, first strand: chain 'z' and resid 33 through 38 removed outlier: 4.846A pdb=" N HIS z 33 " --> pdb=" O GLN z 8 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LYS z 5 " --> pdb=" O GLU z 57 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N MET z 53 " --> pdb=" O THR z 9 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'A' and resid 13 through 17 Processing sheet with id= 39, first strand: chain 'C' and resid 5 through 11 Processing sheet with id= 40, first strand: chain 'C' and resid 33 through 38 removed outlier: 7.002A pdb=" N LEU C 33 " --> pdb=" O GLU C 50 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'E' and resid 21 through 24 removed outlier: 5.703A pdb=" N PHE E 21 " --> pdb=" O VAL E 49 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'F' and resid 13 through 18 removed outlier: 7.820A pdb=" N ASN F 13 " --> pdb=" O SER F 28 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'G' and resid 29 through 33 removed outlier: 7.427A pdb=" N PHE G 29 " --> pdb=" O ASN G 41 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N VAL G 37 " --> pdb=" O ALA G 33 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'G' and resid 88 through 91 Processing sheet with id= 45, first strand: chain 'H' and resid 52 through 58 Processing sheet with id= 46, first strand: chain 'H' and resid 147 through 154 removed outlier: 3.698A pdb=" N SER H 186 " --> pdb=" O VAL H 197 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASN H 184 " --> pdb=" O VAL H 199 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'I' and resid 139 through 143 removed outlier: 6.185A pdb=" N GLU I 178 " --> pdb=" O ASP I 173 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N TRP I 169 " --> pdb=" O LYS I 182 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'J' and resid 11 through 15 removed outlier: 4.047A pdb=" N GLN J 11 " --> pdb=" O GLY J 39 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N LEU J 35 " --> pdb=" O ILE J 15 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N ILE J 29 " --> pdb=" O LYS J 22 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA J 16 " --> pdb=" O LEU J 35 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'J' and resid 83 through 87 removed outlier: 4.361A pdb=" N VAL J 93 " --> pdb=" O GLY J 86 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N TYR J 127 " --> pdb=" O ARG J 92 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'J' and resid 32 through 39 removed outlier: 4.571A pdb=" N GLY J 50 " --> pdb=" O ALA J 34 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'K' and resid 34 through 37 removed outlier: 7.093A pdb=" N ASN K 63 " --> pdb=" O HIS K 37 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ILE K 6 " --> pdb=" O MET K 62 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLU K 5 " --> pdb=" O MET K 90 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N MET K 90 " --> pdb=" O GLU K 5 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N ARG K 86 " --> pdb=" O MET K 9 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'K' and resid 39 through 43 removed outlier: 6.394A pdb=" N TYR K 59 " --> pdb=" O TRP K 42 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'K' and resid 44 through 47 removed outlier: 4.024A pdb=" N LEU K 47 " --> pdb=" O HIS K 55 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N HIS K 55 " --> pdb=" O LEU K 47 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'M' and resid 23 through 27 removed outlier: 3.787A pdb=" N GLU M 51 " --> pdb=" O GLU M 57 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'M' and resid 73 through 76 removed outlier: 6.555A pdb=" N VAL M 102 " --> pdb=" O ILE M 125 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'N' and resid 4 through 10 removed outlier: 4.412A pdb=" N GLY N 9 " --> pdb=" O ALA N 16 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA N 15 " --> pdb=" O LYS N 67 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'O' and resid 42 through 46 removed outlier: 5.782A pdb=" N LEU O 71 " --> pdb=" O PRO O 43 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'P' and resid 28 through 35 removed outlier: 3.967A pdb=" N ASN P 28 " --> pdb=" O SER P 25 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ASN P 108 " --> pdb=" O LEU P 81 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N GLY P 87 " --> pdb=" O VAL P 112 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'Q' and resid 28 through 31 removed outlier: 5.356A pdb=" N LEU Q 80 " --> pdb=" O VAL Q 97 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'Q' and resid 35 through 40 removed outlier: 4.797A pdb=" N ARG Q 35 " --> pdb=" O ARG Q 53 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'U' and resid 4 through 10 removed outlier: 3.705A pdb=" N ALA U 7 " --> pdb=" O GLN U 18 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'U' and resid 37 through 40 removed outlier: 5.550A pdb=" N GLY U 49 " --> pdb=" O ASN U 40 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'V' and resid 6 through 10 removed outlier: 6.978A pdb=" N GLU V 59 " --> pdb=" O VAL V 75 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'V' and resid 18 through 29 No H-bonds generated for sheet with id= 64 Processing sheet with id= 65, first strand: chain 'X' and resid 46 through 51 removed outlier: 4.413A pdb=" N LEU X 46 " --> pdb=" O VAL X 61 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ILE X 48 " --> pdb=" O VAL X 59 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'a' and resid 43 through 48 removed outlier: 6.606A pdb=" N GLY a 169 " --> pdb=" O LEU a 48 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain '8' and resid 65 through 72 removed outlier: 4.306A pdb=" N THR 8 89 " --> pdb=" O ILE 8 15 " (cutoff:3.500A) removed outlier: 8.387A pdb=" N ALA 8 17 " --> pdb=" O THR 8 89 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N GLY 8 14 " --> pdb=" O GLY 8 108 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL 8 110 " --> pdb=" O GLY 8 14 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain '8' and resid 169 through 173 removed outlier: 6.114A pdb=" N LEU 8 169 " --> pdb=" O LEU 8 185 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU 8 171 " --> pdb=" O VAL 8 183 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLY 8 181 " --> pdb=" O ILE 8 173 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain '8' and resid 318 through 322 Processing sheet with id= 70, first strand: chain '8' and resid 323 through 327 removed outlier: 3.620A pdb=" N LYS 8 323 " --> pdb=" O PHE 8 335 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain '8' and resid 346 through 350 removed outlier: 4.159A pdb=" N ASP 8 347 " --> pdb=" O PHE 8 360 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain '8' and resid 363 through 366 removed outlier: 4.228A pdb=" N ILE 8 363 " --> pdb=" O ILE 8 374 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain '8' and resid 445 through 450 removed outlier: 6.808A pdb=" N ARG 8 446 " --> pdb=" O ILE 8 458 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N ILE 8 458 " --> pdb=" O ARG 8 446 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N TRP 8 448 " --> pdb=" O THR 8 456 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N THR 8 456 " --> pdb=" O TRP 8 448 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N ASP 8 450 " --> pdb=" O ASN 8 454 " (cutoff:3.500A) removed outlier: 14.376A pdb=" N ASN 8 454 " --> pdb=" O PRO 8 422 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N THR 8 456 " --> pdb=" O VAL 8 420 " (cutoff:3.500A) removed outlier: 18.979A pdb=" N VAL 8 415 " --> pdb=" O VAL 8 488 " (cutoff:3.500A) removed outlier: 15.230A pdb=" N VAL 8 488 " --> pdb=" O VAL 8 415 " (cutoff:3.500A) removed outlier: 10.737A pdb=" N SER 8 417 " --> pdb=" O PRO 8 486 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA 8 419 " --> pdb=" O GLY 8 484 " (cutoff:3.500A) removed outlier: 38.214A pdb=" N ALA 8 481 " --> pdb=" O THR 8 623 " (cutoff:3.500A) removed outlier: 33.581A pdb=" N THR 8 623 " --> pdb=" O ALA 8 481 " (cutoff:3.500A) removed outlier: 30.819A pdb=" N VAL 8 483 " --> pdb=" O VAL 8 621 " (cutoff:3.500A) removed outlier: 27.444A pdb=" N VAL 8 621 " --> pdb=" O VAL 8 483 " (cutoff:3.500A) removed outlier: 23.837A pdb=" N LYS 8 485 " --> pdb=" O VAL 8 619 " (cutoff:3.500A) removed outlier: 20.530A pdb=" N VAL 8 619 " --> pdb=" O LYS 8 485 " (cutoff:3.500A) removed outlier: 15.594A pdb=" N GLN 8 487 " --> pdb=" O MET 8 617 " (cutoff:3.500A) removed outlier: 11.765A pdb=" N MET 8 617 " --> pdb=" O GLN 8 487 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N ALA 8 489 " --> pdb=" O PRO 8 615 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE 8 654 " --> pdb=" O VAL 8 621 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain '8' and resid 502 through 508 removed outlier: 7.093A pdb=" N VAL 8 519 " --> pdb=" O HIS 8 579 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain '8' and resid 613 through 618 No H-bonds generated for sheet with id= 75 2077 hydrogen bonds defined for protein. 6126 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3676 hydrogen bonds 5946 hydrogen bond angles 0 basepair planarities 1457 basepair parallelities 2353 stacking parallelities Total time for adding SS restraints: 220.44 Time building geometry restraints manager: 66.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.85 - 1.06: 1 1.06 - 1.26: 12091 1.26 - 1.47: 87772 1.47 - 1.67: 66082 1.67 - 1.88: 323 Bond restraints: 166269 Sorted by residual: bond pdb=" C VAL a 59 " pdb=" O VAL a 59 " ideal model delta sigma weight residual 1.236 1.590 -0.354 1.07e-02 8.73e+03 1.09e+03 bond pdb=" C LYS g 8 " pdb=" O LYS g 8 " ideal model delta sigma weight residual 1.235 0.852 0.383 1.26e-02 6.30e+03 9.26e+02 bond pdb=" C VAL i 56 " pdb=" O VAL i 56 " ideal model delta sigma weight residual 1.233 1.523 -0.290 1.08e-02 8.57e+03 7.23e+02 bond pdb=" C LEU O 73 " pdb=" O LEU O 73 " ideal model delta sigma weight residual 1.235 1.509 -0.274 1.14e-02 7.69e+03 5.79e+02 bond pdb=" C TYR a 163 " pdb=" O TYR a 163 " ideal model delta sigma weight residual 1.234 1.506 -0.273 1.25e-02 6.40e+03 4.77e+02 ... (remaining 166264 not shown) Histogram of bond angle deviations from ideal: 95.19 - 106.31: 29279 106.31 - 117.44: 123814 117.44 - 128.56: 88602 128.56 - 139.69: 6260 139.69 - 150.81: 2 Bond angle restraints: 247957 Sorted by residual: angle pdb=" CA PHE W 12 " pdb=" C PHE W 12 " pdb=" O PHE W 12 " ideal model delta sigma weight residual 120.19 130.50 -10.31 7.20e-01 1.93e+00 2.05e+02 angle pdb=" C VAL I 154 " pdb=" N LYS I 155 " pdb=" CA LYS I 155 " ideal model delta sigma weight residual 120.29 100.68 19.61 1.42e+00 4.96e-01 1.91e+02 angle pdb=" N ILE 8 86 " pdb=" CA ILE 8 86 " pdb=" C ILE 8 86 " ideal model delta sigma weight residual 106.88 124.69 -17.81 1.52e+00 4.33e-01 1.37e+02 angle pdb=" N VAL R 96 " pdb=" CA VAL R 96 " pdb=" C VAL R 96 " ideal model delta sigma weight residual 113.10 124.14 -11.04 9.70e-01 1.06e+00 1.30e+02 angle pdb=" N ILE s 35 " pdb=" CA ILE s 35 " pdb=" C ILE s 35 " ideal model delta sigma weight residual 112.96 101.81 11.15 1.00e+00 1.00e+00 1.24e+02 ... (remaining 247952 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.85: 94836 35.85 - 71.70: 10449 71.70 - 107.55: 1078 107.55 - 143.40: 15 143.40 - 179.25: 19 Dihedral angle restraints: 106397 sinusoidal: 87505 harmonic: 18892 Sorted by residual: dihedral pdb=" C5' C 3 280 " pdb=" C4' C 3 280 " pdb=" C3' C 3 280 " pdb=" O3' C 3 280 " ideal model delta sinusoidal sigma weight residual 147.00 77.20 69.80 1 8.00e+00 1.56e-02 9.82e+01 dihedral pdb=" C4' C 3 280 " pdb=" C3' C 3 280 " pdb=" C2' C 3 280 " pdb=" C1' C 3 280 " ideal model delta sinusoidal sigma weight residual -35.00 34.79 -69.79 1 8.00e+00 1.56e-02 9.82e+01 dihedral pdb=" C4' U 12296 " pdb=" C3' U 12296 " pdb=" C2' U 12296 " pdb=" C1' U 12296 " ideal model delta sinusoidal sigma weight residual -35.00 34.62 -69.62 1 8.00e+00 1.56e-02 9.78e+01 ... (remaining 106394 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.230: 30936 0.230 - 0.460: 622 0.460 - 0.689: 16 0.689 - 0.919: 1 0.919 - 1.149: 1 Chirality restraints: 31576 Sorted by residual: chirality pdb=" C3' G 31061 " pdb=" C4' G 31061 " pdb=" O3' G 31061 " pdb=" C2' G 31061 " both_signs ideal model delta sigma weight residual False -2.48 -1.33 -1.15 2.00e-01 2.50e+01 3.30e+01 chirality pdb=" CA PRO O 39 " pdb=" N PRO O 39 " pdb=" C PRO O 39 " pdb=" CB PRO O 39 " both_signs ideal model delta sigma weight residual False 2.72 2.02 0.70 2.00e-01 2.50e+01 1.22e+01 chirality pdb=" CA VAL i 8 " pdb=" N VAL i 8 " pdb=" C VAL i 8 " pdb=" CB VAL i 8 " both_signs ideal model delta sigma weight residual False 2.44 3.06 -0.62 2.00e-01 2.50e+01 9.49e+00 ... (remaining 31573 not shown) Planarity restraints: 13872 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A 2 119 " 0.329 2.00e-02 2.50e+03 1.40e-01 5.40e+02 pdb=" N9 A 2 119 " -0.029 2.00e-02 2.50e+03 pdb=" C8 A 2 119 " -0.123 2.00e-02 2.50e+03 pdb=" N7 A 2 119 " -0.094 2.00e-02 2.50e+03 pdb=" C5 A 2 119 " -0.061 2.00e-02 2.50e+03 pdb=" C6 A 2 119 " 0.054 2.00e-02 2.50e+03 pdb=" N6 A 2 119 " 0.185 2.00e-02 2.50e+03 pdb=" N1 A 2 119 " 0.055 2.00e-02 2.50e+03 pdb=" C2 A 2 119 " -0.043 2.00e-02 2.50e+03 pdb=" N3 A 2 119 " -0.146 2.00e-02 2.50e+03 pdb=" C4 A 2 119 " -0.127 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U 2 1 " 0.239 2.00e-02 2.50e+03 1.31e-01 3.85e+02 pdb=" N1 U 2 1 " -0.008 2.00e-02 2.50e+03 pdb=" C2 U 2 1 " -0.041 2.00e-02 2.50e+03 pdb=" O2 U 2 1 " -0.102 2.00e-02 2.50e+03 pdb=" N3 U 2 1 " -0.024 2.00e-02 2.50e+03 pdb=" C4 U 2 1 " -0.034 2.00e-02 2.50e+03 pdb=" O4 U 2 1 " 0.224 2.00e-02 2.50e+03 pdb=" C5 U 2 1 " -0.134 2.00e-02 2.50e+03 pdb=" C6 U 2 1 " -0.121 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G 12061 " -0.271 2.00e-02 2.50e+03 1.11e-01 3.70e+02 pdb=" N9 G 12061 " 0.019 2.00e-02 2.50e+03 pdb=" C8 G 12061 " 0.117 2.00e-02 2.50e+03 pdb=" N7 G 12061 " 0.098 2.00e-02 2.50e+03 pdb=" C5 G 12061 " 0.049 2.00e-02 2.50e+03 pdb=" C6 G 12061 " -0.051 2.00e-02 2.50e+03 pdb=" O6 G 12061 " -0.164 2.00e-02 2.50e+03 pdb=" N1 G 12061 " -0.040 2.00e-02 2.50e+03 pdb=" C2 G 12061 " 0.031 2.00e-02 2.50e+03 pdb=" N2 G 12061 " 0.036 2.00e-02 2.50e+03 pdb=" N3 G 12061 " 0.089 2.00e-02 2.50e+03 pdb=" C4 G 12061 " 0.086 2.00e-02 2.50e+03 ... (remaining 13869 not shown) Histogram of nonbonded interaction distances: 1.40 - 2.10: 5 2.10 - 2.80: 32507 2.80 - 3.50: 214382 3.50 - 4.20: 486612 4.20 - 4.90: 644919 Nonbonded interactions: 1378425 Sorted by model distance: nonbonded pdb=" O3' A 5 76 " pdb=" C PRO 5 101 " model vdw 1.400 3.270 nonbonded pdb=" O ASP 8 585 " pdb=" N ASP 8 587 " model vdw 1.978 2.520 nonbonded pdb=" O GLN 8 120 " pdb=" O PRO 8 121 " model vdw 1.995 3.040 nonbonded pdb=" O3' A 5 76 " pdb=" CA PRO 5 101 " model vdw 2.005 3.470 nonbonded pdb=" O PRO 8 121 " pdb=" N SER 8 123 " model vdw 2.006 2.520 ... (remaining 1378420 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: 4.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.120 Extract box with map and model: 19.090 Check model and map are aligned: 1.660 Set scattering table: 1.040 Process input model: 513.610 Find NCS groups from input model: 3.030 Set up NCS constraints: 0.360 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 545.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 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 : 0.011 0.383 166269 Z= 0.655 Angle : 1.169 26.045 247957 Z= 0.777 Chirality : 0.093 1.149 31576 Planarity : 0.014 0.140 13872 Dihedral : 22.565 179.253 94213 Min Nonbonded Distance : 1.400 Molprobity Statistics. All-atom Clashscore : 21.96 Ramachandran Plot: Outliers : 1.61 % Allowed : 14.10 % Favored : 84.29 % Rotamer: Outliers : 1.81 % Allowed : 6.96 % Favored : 91.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.93 (0.09), residues: 6517 helix: -2.10 (0.10), residues: 1860 sheet: -2.54 (0.14), residues: 1139 loop : -2.97 (0.09), residues: 3518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.007 TRP c 80 HIS 0.003 0.000 HIS 8 18 PHE 0.038 0.004 PHE Z 11 TYR 0.069 0.008 TYR q 31 ARG 0.016 0.001 ARG R 97 *********************** 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 1509 residues out of total 5429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 1411 time to evaluate : 8.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 250 GLN cc_start: 0.7580 (tm-30) cc_final: 0.7375 (tm-30) REVERT: c 38 LYS cc_start: 0.8391 (mttt) cc_final: 0.8088 (mtmm) REVERT: d 1 MET cc_start: 0.7428 (OUTLIER) cc_final: 0.6842 (tpt) REVERT: e 82 TYR cc_start: 0.7785 (m-10) cc_final: 0.7555 (m-80) REVERT: e 134 GLN cc_start: 0.3867 (OUTLIER) cc_final: 0.3487 (pm20) REVERT: f 1 SER cc_start: 0.6102 (t) cc_final: 0.5679 (m) REVERT: f 23 ILE cc_start: 0.7720 (mt) cc_final: 0.7508 (tp) REVERT: n 72 ASP cc_start: 0.8009 (t70) cc_final: 0.7468 (t0) REVERT: n 75 ILE cc_start: 0.8880 (mm) cc_final: 0.8564 (mm) REVERT: o 108 ASP cc_start: 0.8712 (m-30) cc_final: 0.8187 (m-30) REVERT: p 30 TRP cc_start: 0.8799 (OUTLIER) cc_final: 0.8192 (m100) REVERT: p 54 LEU cc_start: 0.8799 (tp) cc_final: 0.8441 (tp) REVERT: s 66 ILE cc_start: 0.9064 (mm) cc_final: 0.8737 (mm) REVERT: t 1 MET cc_start: 0.5521 (ptm) cc_final: 0.5261 (ptm) REVERT: t 24 MET cc_start: 0.8726 (tmm) cc_final: 0.8511 (tmm) REVERT: u 9 GLU cc_start: 0.7556 (tp30) cc_final: 0.7309 (tp30) REVERT: u 67 SER cc_start: 0.8867 (m) cc_final: 0.8498 (t) REVERT: u 81 ARG cc_start: 0.7687 (mpt-90) cc_final: 0.7402 (mmt90) REVERT: u 98 ASN cc_start: 0.8013 (t0) cc_final: 0.7624 (t0) REVERT: v 56 PHE cc_start: 0.8633 (t80) cc_final: 0.8393 (t80) REVERT: v 93 ARG cc_start: 0.7944 (ttm110) cc_final: 0.7630 (ttp-110) REVERT: y 45 GLN cc_start: 0.8946 (pt0) cc_final: 0.8663 (pm20) REVERT: y 49 ASP cc_start: 0.8262 (m-30) cc_final: 0.7706 (m-30) REVERT: A 5 ILE cc_start: 0.7484 (pt) cc_final: 0.7096 (mm) REVERT: A 24 ILE cc_start: 0.7942 (pt) cc_final: 0.7607 (pt) REVERT: B 47 TYR cc_start: 0.7789 (m-80) cc_final: 0.7585 (m-80) REVERT: C 19 PHE cc_start: 0.7865 (p90) cc_final: 0.7565 (p90) REVERT: G 26 MET cc_start: 0.7961 (mtm) cc_final: 0.7553 (ppp) REVERT: G 30 ILE cc_start: 0.8631 (pt) cc_final: 0.8074 (pt) REVERT: G 48 MET cc_start: 0.8535 (mmp) cc_final: 0.8295 (mmp) REVERT: G 49 PHE cc_start: 0.7543 (p90) cc_final: 0.6930 (p90) REVERT: G 167 HIS cc_start: 0.8354 (t-90) cc_final: 0.8083 (t-90) REVERT: H 17 TRP cc_start: 0.8287 (m-10) cc_final: 0.7930 (m-10) REVERT: H 41 TYR cc_start: 0.8655 (t80) cc_final: 0.8423 (t80) REVERT: I 50 TYR cc_start: 0.8443 (t80) cc_final: 0.8071 (t80) REVERT: I 74 TYR cc_start: 0.8612 (m-80) cc_final: 0.8386 (m-80) REVERT: I 104 MET cc_start: 0.8560 (mmm) cc_final: 0.8028 (tpt) REVERT: I 106 PHE cc_start: 0.7903 (m-80) cc_final: 0.7511 (m-80) REVERT: I 140 ASP cc_start: 0.7444 (m-30) cc_final: 0.6877 (m-30) REVERT: J 59 ILE cc_start: 0.9477 (pt) cc_final: 0.8915 (mt) REVERT: J 155 LYS cc_start: 0.9201 (ptpp) cc_final: 0.8567 (ptpp) REVERT: K 24 ARG cc_start: 0.8323 (mtp-110) cc_final: 0.8110 (mtp-110) REVERT: K 35 LYS cc_start: 0.8413 (mttm) cc_final: 0.8201 (mttp) REVERT: K 58 HIS cc_start: 0.8142 (OUTLIER) cc_final: 0.7665 (m90) REVERT: K 65 GLU cc_start: 0.6895 (tt0) cc_final: 0.6596 (tt0) REVERT: K 90 MET cc_start: 0.7196 (mmp) cc_final: 0.6981 (mtp) REVERT: K 93 LYS cc_start: 0.7800 (mttt) cc_final: 0.7385 (mmtm) REVERT: M 104 SER cc_start: 0.9149 (t) cc_final: 0.8912 (t) REVERT: N 35 GLU cc_start: 0.7920 (mm-30) cc_final: 0.7242 (mm-30) REVERT: N 62 LEU cc_start: 0.8926 (mp) cc_final: 0.8689 (mp) REVERT: N 106 ASP cc_start: 0.7177 (t0) cc_final: 0.6892 (t0) REVERT: O 49 PHE cc_start: 0.7515 (m-80) cc_final: 0.7031 (m-80) REVERT: O 78 GLU cc_start: 0.5887 (tt0) cc_final: 0.5661 (pt0) REVERT: P 82 GLU cc_start: 0.8511 (OUTLIER) cc_final: 0.8055 (pp20) REVERT: P 111 ASP cc_start: 0.5644 (t70) cc_final: 0.5150 (t70) REVERT: S 49 THR cc_start: 0.8530 (m) cc_final: 0.8306 (p) REVERT: S 53 ASP cc_start: 0.7251 (m-30) cc_final: 0.6636 (m-30) REVERT: S 72 PHE cc_start: 0.6138 (t80) cc_final: 0.5787 (t80) REVERT: S 88 MET cc_start: 0.8881 (mpp) cc_final: 0.8574 (mpp) REVERT: T 27 GLN cc_start: 0.8781 (OUTLIER) cc_final: 0.8511 (mm-40) REVERT: T 36 ASN cc_start: 0.8933 (m-40) cc_final: 0.8551 (p0) REVERT: W 52 ARG cc_start: 0.7587 (mtm-85) cc_final: 0.7070 (mtt-85) REVERT: X 42 ASN cc_start: 0.7595 (p0) cc_final: 0.7370 (p0) REVERT: X 43 MET cc_start: 0.7859 (mpp) cc_final: 0.7585 (mpp) REVERT: Y 24 ARG cc_start: 0.9333 (ttm-80) cc_final: 0.9127 (ttm110) REVERT: Z 39 LYS cc_start: 0.6536 (mmmt) cc_final: 0.6320 (mmmt) REVERT: Z 42 THR cc_start: 0.8922 (m) cc_final: 0.8701 (p) REVERT: 8 53 MET cc_start: 0.8374 (tmm) cc_final: 0.8016 (tmm) REVERT: 8 111 MET cc_start: 0.7803 (mpp) cc_final: 0.7026 (mpp) REVERT: 8 322 PHE cc_start: 0.9263 (OUTLIER) cc_final: 0.8705 (p90) REVERT: 8 409 MET cc_start: 0.5837 (pmm) cc_final: 0.5412 (pmm) REVERT: 8 626 GLU cc_start: 0.7152 (OUTLIER) cc_final: 0.6911 (pm20) REVERT: 8 663 MET cc_start: 0.9085 (mmm) cc_final: 0.8882 (mmm) outliers start: 98 outliers final: 34 residues processed: 1477 average time/residue: 1.3994 time to fit residues: 3628.6110 Evaluate side-chains 1008 residues out of total 5429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 966 time to evaluate : 5.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 52 HIS Chi-restraints excluded: chain b residue 129 LEU Chi-restraints excluded: chain c residue 146 ILE Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain e residue 71 LYS Chi-restraints excluded: chain e residue 84 ILE Chi-restraints excluded: chain e residue 134 GLN Chi-restraints excluded: chain k residue 58 LEU Chi-restraints excluded: chain k residue 65 THR Chi-restraints excluded: chain k residue 104 THR Chi-restraints excluded: chain n residue 37 THR Chi-restraints excluded: chain p residue 30 TRP Chi-restraints excluded: chain z residue 16 LEU Chi-restraints excluded: chain A residue 58 ASP Chi-restraints excluded: chain E residue 30 HIS Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain H residue 156 LEU Chi-restraints excluded: chain J residue 28 ARG Chi-restraints excluded: chain J residue 123 LEU Chi-restraints excluded: chain J residue 133 ILE Chi-restraints excluded: chain K residue 58 HIS Chi-restraints excluded: chain K residue 86 ARG Chi-restraints excluded: chain M residue 60 LEU Chi-restraints excluded: chain O residue 20 GLN Chi-restraints excluded: chain O residue 36 VAL Chi-restraints excluded: chain O residue 43 PRO Chi-restraints excluded: chain O residue 75 ASP Chi-restraints excluded: chain P residue 30 ILE Chi-restraints excluded: chain P residue 82 GLU Chi-restraints excluded: chain R residue 95 PRO Chi-restraints excluded: chain R residue 97 ARG Chi-restraints excluded: chain R residue 104 ASN Chi-restraints excluded: chain T residue 27 GLN Chi-restraints excluded: chain T residue 86 LEU Chi-restraints excluded: chain W residue 51 GLN Chi-restraints excluded: chain Y residue 29 THR Chi-restraints excluded: chain 8 residue 19 ILE Chi-restraints excluded: chain 8 residue 322 PHE Chi-restraints excluded: chain 8 residue 334 THR Chi-restraints excluded: chain 8 residue 587 ASP Chi-restraints excluded: chain 8 residue 626 GLU 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: 30.0000 chunk 287 optimal weight: 5.9990 chunk 567 optimal weight: 8.9990 chunk 449 optimal weight: 7.9990 chunk 869 optimal weight: 20.0000 chunk 336 optimal weight: 7.9990 chunk 528 optimal weight: 4.9990 chunk 646 optimal weight: 20.0000 chunk 1007 optimal weight: 10.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 134 HIS c 173 GLN d 30 GLN d 195 GLN f 19 ASN g 28 ASN ** j 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 3 GLN k 5 GLN ** k 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 31 HIS ** n 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 14 GLN q 36 GLN r 87 GLN ** s 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 15 GLN u 53 GLN u 73 ASN ** w 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** x 35 HIS ** y 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 45 HIS ** H 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 70 GLN I 130 ASN J 96 GLN J 145 ASN ** K 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 20 ASN N 36 GLN N 49 GLN ** R 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 3 GLN U 9 HIS U 18 GLN U 26 ASN U 63 GLN ** X 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 20 ASN Y 47 GLN Y 51 ASN Z 63 ASN 8 55 GLN 8 216 ASN 8 332 ASN ** 8 530 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 627 ASN ** 8 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 166269 Z= 0.302 Angle : 0.741 13.217 247957 Z= 0.384 Chirality : 0.042 0.399 31576 Planarity : 0.006 0.074 13872 Dihedral : 23.146 179.966 81331 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 15.63 Ramachandran Plot: Outliers : 0.23 % Allowed : 10.79 % Favored : 88.98 % Rotamer: Outliers : 3.72 % Allowed : 13.69 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.98 (0.10), residues: 6517 helix: -0.91 (0.11), residues: 2065 sheet: -2.24 (0.14), residues: 1122 loop : -2.61 (0.10), residues: 3330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP b 212 HIS 0.009 0.002 HIS H 189 PHE 0.040 0.002 PHE Z 36 TYR 0.026 0.002 TYR S 19 ARG 0.034 0.001 ARG B 12 *********************** 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 1303 residues out of total 5429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 202 poor density : 1101 time to evaluate : 6.767 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 131 MET cc_start: 0.8222 (mpp) cc_final: 0.7800 (mtm) REVERT: c 38 LYS cc_start: 0.8354 (mttt) cc_final: 0.8099 (mtmm) REVERT: e 82 TYR cc_start: 0.8072 (m-10) cc_final: 0.7791 (m-80) REVERT: e 95 MET cc_start: 0.7613 (OUTLIER) cc_final: 0.6326 (tmm) REVERT: e 134 GLN cc_start: 0.3606 (OUTLIER) cc_final: 0.2460 (pm20) REVERT: f 74 MET cc_start: 0.8339 (mtp) cc_final: 0.8110 (mtp) REVERT: g 45 GLU cc_start: 0.8285 (mt-10) cc_final: 0.7987 (mm-30) REVERT: n 72 ASP cc_start: 0.7973 (t70) cc_final: 0.7625 (t0) REVERT: n 75 ILE cc_start: 0.8969 (mm) cc_final: 0.8294 (mm) REVERT: o 108 ASP cc_start: 0.8288 (m-30) cc_final: 0.8012 (m-30) REVERT: p 54 LEU cc_start: 0.8790 (tp) cc_final: 0.8469 (tp) REVERT: r 34 GLU cc_start: 0.8302 (mm-30) cc_final: 0.7751 (mm-30) REVERT: r 60 LYS cc_start: 0.8861 (ttpt) cc_final: 0.8619 (ttpp) REVERT: t 4 GLU cc_start: 0.7952 (mp0) cc_final: 0.7446 (mp0) REVERT: u 6 ARG cc_start: 0.8460 (tpt90) cc_final: 0.8162 (tpt90) REVERT: u 9 GLU cc_start: 0.7436 (tp30) cc_final: 0.6946 (tp30) REVERT: u 67 SER cc_start: 0.8958 (m) cc_final: 0.8537 (t) REVERT: u 100 GLU cc_start: 0.7869 (mt-10) cc_final: 0.7581 (mt-10) REVERT: v 56 PHE cc_start: 0.8700 (t80) cc_final: 0.8470 (t80) REVERT: v 93 ARG cc_start: 0.8015 (ttm110) cc_final: 0.7716 (ttm-80) REVERT: y 26 PHE cc_start: 0.8312 (t80) cc_final: 0.7781 (t80) REVERT: y 45 GLN cc_start: 0.8913 (pt0) cc_final: 0.8547 (pp30) REVERT: y 58 ASN cc_start: 0.8058 (t0) cc_final: 0.7657 (t0) REVERT: A 1 MET cc_start: 0.8223 (tpp) cc_final: 0.7700 (tpp) REVERT: A 5 ILE cc_start: 0.7554 (pt) cc_final: 0.7296 (mm) REVERT: C 9 LYS cc_start: 0.7450 (mtpt) cc_final: 0.7016 (mtpt) REVERT: C 19 PHE cc_start: 0.7912 (p90) cc_final: 0.7629 (p90) REVERT: C 27 ARG cc_start: 0.8224 (mtp-110) cc_final: 0.7774 (ptp-170) REVERT: G 8 MET cc_start: 0.7770 (ttm) cc_final: 0.7438 (tmm) REVERT: H 17 TRP cc_start: 0.8138 (m-10) cc_final: 0.7748 (m-10) REVERT: H 122 GLN cc_start: 0.8808 (mm-40) cc_final: 0.8377 (mm-40) REVERT: H 128 MET cc_start: 0.7374 (mpp) cc_final: 0.7076 (mpp) REVERT: I 50 TYR cc_start: 0.8357 (t80) cc_final: 0.8106 (t80) REVERT: I 73 ASN cc_start: 0.8544 (m110) cc_final: 0.8278 (m-40) REVERT: I 104 MET cc_start: 0.8880 (mmm) cc_final: 0.8461 (mmm) REVERT: I 177 MET cc_start: 0.8329 (mpp) cc_final: 0.7845 (mpp) REVERT: I 203 TYR cc_start: 0.7121 (m-10) cc_final: 0.6855 (m-10) REVERT: J 22 LYS cc_start: 0.8101 (ttmt) cc_final: 0.7662 (tptp) REVERT: J 59 ILE cc_start: 0.9509 (pt) cc_final: 0.9172 (pt) REVERT: J 61 LYS cc_start: 0.9426 (mptt) cc_final: 0.9165 (mmtm) REVERT: K 5 GLU cc_start: 0.7606 (mp0) cc_final: 0.7021 (mp0) REVERT: K 58 HIS cc_start: 0.7548 (OUTLIER) cc_final: 0.6272 (m90) REVERT: K 60 VAL cc_start: 0.7911 (t) cc_final: 0.7683 (t) REVERT: K 62 MET cc_start: 0.7830 (mpp) cc_final: 0.7514 (mpp) REVERT: K 65 GLU cc_start: 0.6266 (tt0) cc_final: 0.5942 (tt0) REVERT: K 72 ASP cc_start: 0.9231 (t0) cc_final: 0.9020 (t0) REVERT: K 93 LYS cc_start: 0.7872 (mttt) cc_final: 0.7440 (mmtt) REVERT: N 5 TYR cc_start: 0.7243 (m-80) cc_final: 0.6844 (m-80) REVERT: N 55 ASP cc_start: 0.7230 (m-30) cc_final: 0.6907 (m-30) REVERT: N 62 LEU cc_start: 0.8919 (mp) cc_final: 0.8576 (mp) REVERT: N 90 ASP cc_start: 0.8285 (p0) cc_final: 0.8014 (p0) REVERT: N 96 GLU cc_start: 0.8413 (pp20) cc_final: 0.7769 (pp20) REVERT: N 106 ASP cc_start: 0.7311 (t0) cc_final: 0.7069 (t0) REVERT: N 112 ARG cc_start: 0.7188 (OUTLIER) cc_final: 0.6899 (mtm180) REVERT: O 49 PHE cc_start: 0.7577 (m-80) cc_final: 0.7083 (m-80) REVERT: O 59 LYS cc_start: 0.7213 (OUTLIER) cc_final: 0.6637 (tppt) REVERT: O 63 ASP cc_start: 0.7627 (t0) cc_final: 0.7397 (t0) REVERT: Q 36 VAL cc_start: 0.9169 (t) cc_final: 0.8862 (m) REVERT: Q 101 LEU cc_start: 0.6986 (tp) cc_final: 0.6694 (tt) REVERT: Q 102 ASP cc_start: 0.6293 (t0) cc_final: 0.5917 (m-30) REVERT: R 33 LEU cc_start: 0.7164 (mp) cc_final: 0.6869 (tp) REVERT: S 49 THR cc_start: 0.8628 (m) cc_final: 0.8378 (p) REVERT: S 53 ASP cc_start: 0.6939 (m-30) cc_final: 0.6267 (m-30) REVERT: S 72 PHE cc_start: 0.6265 (t80) cc_final: 0.6017 (t80) REVERT: S 85 GLU cc_start: 0.7195 (OUTLIER) cc_final: 0.6888 (pp20) REVERT: T 27 GLN cc_start: 0.8676 (OUTLIER) cc_final: 0.8073 (mm-40) REVERT: T 36 ASN cc_start: 0.8675 (m-40) cc_final: 0.8439 (p0) REVERT: U 1 MET cc_start: 0.7518 (tpp) cc_final: 0.7301 (tpt) REVERT: X 42 ASN cc_start: 0.7937 (p0) cc_final: 0.7609 (p0) REVERT: X 43 MET cc_start: 0.8046 (mpp) cc_final: 0.7776 (mpp) REVERT: Y 14 GLU cc_start: 0.8627 (tm-30) cc_final: 0.8418 (tm-30) REVERT: Y 17 ARG cc_start: 0.8726 (ttp80) cc_final: 0.8298 (ttp80) REVERT: Y 24 ARG cc_start: 0.9263 (ttm-80) cc_final: 0.8765 (ttm110) REVERT: 8 53 MET cc_start: 0.8119 (tmm) cc_final: 0.7652 (tmm) REVERT: 8 106 LEU cc_start: 0.8123 (pp) cc_final: 0.7916 (pp) REVERT: 8 111 MET cc_start: 0.8123 (mpp) cc_final: 0.7489 (mpp) REVERT: 8 322 PHE cc_start: 0.9154 (OUTLIER) cc_final: 0.8925 (p90) REVERT: 8 409 MET cc_start: 0.5497 (pmm) cc_final: 0.5028 (pmm) REVERT: 8 431 MET cc_start: 0.8451 (ttt) cc_final: 0.8090 (ttt) REVERT: 8 441 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7820 (pp20) outliers start: 202 outliers final: 121 residues processed: 1215 average time/residue: 1.3747 time to fit residues: 2968.2992 Evaluate side-chains 1066 residues out of total 5429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 936 time to evaluate : 6.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 37 SER Chi-restraints excluded: chain b residue 71 ASP Chi-restraints excluded: chain b residue 129 LEU Chi-restraints excluded: chain c residue 146 ILE Chi-restraints excluded: chain c residue 176 ASP Chi-restraints excluded: chain c residue 185 ASN Chi-restraints excluded: chain e residue 39 VAL Chi-restraints excluded: chain e residue 71 LYS Chi-restraints excluded: chain e residue 84 ILE Chi-restraints excluded: chain e residue 89 THR Chi-restraints excluded: chain e residue 95 MET Chi-restraints excluded: chain e residue 134 GLN Chi-restraints excluded: chain e residue 154 THR Chi-restraints excluded: chain e residue 157 THR Chi-restraints excluded: chain e residue 158 THR Chi-restraints excluded: chain e residue 173 ASP Chi-restraints excluded: chain f residue 113 ASP Chi-restraints excluded: chain f residue 130 ILE Chi-restraints excluded: chain f residue 147 LEU Chi-restraints excluded: chain g residue 6 LEU Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain h residue 15 VAL Chi-restraints excluded: chain j residue 54 ILE Chi-restraints excluded: chain j residue 86 GLN Chi-restraints excluded: chain k residue 37 ASP Chi-restraints excluded: chain k residue 42 THR Chi-restraints excluded: chain k residue 65 THR Chi-restraints excluded: chain k residue 77 ILE Chi-restraints excluded: chain k residue 90 ASN Chi-restraints excluded: chain l residue 118 THR Chi-restraints excluded: chain m residue 134 THR Chi-restraints excluded: chain n residue 27 SER Chi-restraints excluded: chain n residue 37 THR Chi-restraints excluded: chain n residue 47 VAL Chi-restraints excluded: chain n residue 57 THR Chi-restraints excluded: chain o residue 49 VAL Chi-restraints excluded: chain o residue 69 ASP Chi-restraints excluded: chain o residue 87 ILE Chi-restraints excluded: chain p residue 18 SER Chi-restraints excluded: chain p residue 35 SER Chi-restraints excluded: chain p residue 96 LEU Chi-restraints excluded: chain q residue 86 SER Chi-restraints excluded: chain q residue 101 ASP Chi-restraints excluded: chain s residue 4 ILE Chi-restraints excluded: chain t residue 32 LEU Chi-restraints excluded: chain t residue 78 SER Chi-restraints excluded: chain u residue 27 VAL Chi-restraints excluded: chain v residue 40 ILE Chi-restraints excluded: chain w residue 77 SER Chi-restraints excluded: chain z residue 16 LEU Chi-restraints excluded: chain z residue 47 ILE Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain E residue 30 HIS Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain F residue 20 ASP Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 191 ASP Chi-restraints excluded: chain H residue 206 ILE Chi-restraints excluded: chain I residue 68 GLU Chi-restraints excluded: chain I residue 109 THR Chi-restraints excluded: chain I residue 130 ASN Chi-restraints excluded: chain I residue 168 THR Chi-restraints excluded: chain J residue 10 LEU Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 71 ILE Chi-restraints excluded: chain J residue 79 THR Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain J residue 144 GLU Chi-restraints excluded: chain K residue 9 MET Chi-restraints excluded: chain K residue 56 LYS Chi-restraints excluded: chain K residue 58 HIS Chi-restraints excluded: chain K residue 61 LEU Chi-restraints excluded: chain L residue 72 VAL Chi-restraints excluded: chain M residue 111 THR Chi-restraints excluded: chain M residue 125 ILE Chi-restraints excluded: chain N residue 112 ARG Chi-restraints excluded: chain O residue 15 HIS Chi-restraints excluded: chain O residue 20 GLN Chi-restraints excluded: chain O residue 40 ILE Chi-restraints excluded: chain O residue 56 HIS Chi-restraints excluded: chain O residue 59 LYS Chi-restraints excluded: chain P residue 30 ILE Chi-restraints excluded: chain P residue 56 LYS Chi-restraints excluded: chain P residue 71 ASP Chi-restraints excluded: chain P residue 85 VAL Chi-restraints excluded: chain P residue 104 PHE Chi-restraints excluded: chain P residue 109 ILE Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain Q residue 38 THR Chi-restraints excluded: chain Q residue 106 VAL Chi-restraints excluded: chain R residue 97 ARG Chi-restraints excluded: chain R residue 104 ASN Chi-restraints excluded: chain S residue 33 VAL Chi-restraints excluded: chain S residue 58 ARG Chi-restraints excluded: chain S residue 85 GLU Chi-restraints excluded: chain T residue 4 THR Chi-restraints excluded: chain T residue 24 THR Chi-restraints excluded: chain T residue 27 GLN Chi-restraints excluded: chain T residue 74 VAL Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain U residue 23 ASP Chi-restraints excluded: chain U residue 29 ASN Chi-restraints excluded: chain U residue 45 GLU Chi-restraints excluded: chain U residue 66 THR Chi-restraints excluded: chain V residue 54 ILE Chi-restraints excluded: chain V residue 71 SER Chi-restraints excluded: chain W residue 27 THR Chi-restraints excluded: chain X residue 12 LEU Chi-restraints excluded: chain X residue 47 THR Chi-restraints excluded: chain Y residue 29 THR Chi-restraints excluded: chain Y residue 52 GLU Chi-restraints excluded: chain a residue 64 VAL Chi-restraints excluded: chain 8 residue 4 THR Chi-restraints excluded: chain 8 residue 19 ILE Chi-restraints excluded: chain 8 residue 105 VAL Chi-restraints excluded: chain 8 residue 154 VAL Chi-restraints excluded: chain 8 residue 322 PHE Chi-restraints excluded: chain 8 residue 334 THR Chi-restraints excluded: chain 8 residue 401 ASP Chi-restraints excluded: chain 8 residue 441 GLU Chi-restraints excluded: chain 8 residue 466 LEU Chi-restraints excluded: chain 8 residue 544 VAL Chi-restraints excluded: chain 8 residue 626 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1109 random chunks: chunk 559 optimal weight: 9.9990 chunk 312 optimal weight: 20.0000 chunk 838 optimal weight: 10.0000 chunk 685 optimal weight: 50.0000 chunk 277 optimal weight: 4.9990 chunk 1008 optimal weight: 20.0000 chunk 1089 optimal weight: 20.0000 chunk 898 optimal weight: 20.0000 chunk 1000 optimal weight: 20.0000 chunk 343 optimal weight: 30.0000 chunk 809 optimal weight: 10.0000 overall best weight: 10.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 20 ASN ** b 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 49 GLN c 173 GLN f 72 ASN ** j 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 3 GLN k 5 GLN ** k 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 14 GLN ** s 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 35 GLN ** H 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 88 HIS ** J 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 37 HIS ** K 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 67 ASN M 117 GLN N 36 GLN N 49 GLN N 80 HIS O 70 HIS P 118 ASN ** Q 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 61 GLN ** U 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 194 ASN 8 332 ASN 8 365 GLN 8 369 ASN 8 478 ASN ** 8 530 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 627 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.3044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.112 166269 Z= 0.412 Angle : 0.793 13.205 247957 Z= 0.408 Chirality : 0.044 0.389 31576 Planarity : 0.006 0.088 13872 Dihedral : 23.483 179.742 81279 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 19.78 Ramachandran Plot: Outliers : 0.20 % Allowed : 13.43 % Favored : 86.37 % Rotamer: Outliers : 5.71 % Allowed : 15.84 % Favored : 78.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.81 (0.10), residues: 6517 helix: -0.72 (0.11), residues: 2056 sheet: -2.05 (0.15), residues: 1104 loop : -2.58 (0.10), residues: 3357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP H 200 HIS 0.015 0.002 HIS a 67 PHE 0.043 0.003 PHE Z 36 TYR 0.028 0.003 TYR 8 113 ARG 0.012 0.001 ARG R 89 *********************** 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 1312 residues out of total 5429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 310 poor density : 1002 time to evaluate : 6.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 38 LYS cc_start: 0.8452 (mttt) cc_final: 0.8221 (mtmm) REVERT: e 82 TYR cc_start: 0.8200 (OUTLIER) cc_final: 0.7925 (m-10) REVERT: e 95 MET cc_start: 0.7688 (OUTLIER) cc_final: 0.6379 (tmm) REVERT: e 134 GLN cc_start: 0.3355 (OUTLIER) cc_final: 0.1944 (pm20) REVERT: f 59 ASP cc_start: 0.8249 (p0) cc_final: 0.8025 (p0) REVERT: f 169 ARG cc_start: 0.7788 (mmp80) cc_final: 0.7462 (mmp80) REVERT: g 14 SER cc_start: 0.7864 (t) cc_final: 0.7625 (p) REVERT: m 105 MET cc_start: 0.7290 (OUTLIER) cc_final: 0.6708 (mtm) REVERT: m 124 LEU cc_start: 0.9057 (OUTLIER) cc_final: 0.8842 (mp) REVERT: n 72 ASP cc_start: 0.8085 (t70) cc_final: 0.7689 (t0) REVERT: n 75 ILE cc_start: 0.9009 (mm) cc_final: 0.8400 (mm) REVERT: o 108 ASP cc_start: 0.8427 (m-30) cc_final: 0.7860 (m-30) REVERT: r 34 GLU cc_start: 0.8299 (mm-30) cc_final: 0.7719 (mm-30) REVERT: r 60 LYS cc_start: 0.8823 (ttpt) cc_final: 0.8461 (ttpp) REVERT: t 4 GLU cc_start: 0.8276 (mp0) cc_final: 0.7648 (mp0) REVERT: u 6 ARG cc_start: 0.8590 (tpt90) cc_final: 0.8333 (mmm-85) REVERT: u 67 SER cc_start: 0.8960 (m) cc_final: 0.8465 (t) REVERT: v 56 PHE cc_start: 0.8736 (t80) cc_final: 0.8419 (t80) REVERT: y 49 ASP cc_start: 0.8413 (m-30) cc_final: 0.8140 (m-30) REVERT: y 58 ASN cc_start: 0.7868 (t0) cc_final: 0.7444 (t0) REVERT: A 1 MET cc_start: 0.8149 (tpp) cc_final: 0.7542 (tpp) REVERT: A 5 ILE cc_start: 0.7746 (pt) cc_final: 0.7536 (mm) REVERT: C 9 LYS cc_start: 0.7470 (mtpt) cc_final: 0.6988 (mtpt) REVERT: C 48 TYR cc_start: 0.7848 (m-80) cc_final: 0.7282 (m-80) REVERT: G 8 MET cc_start: 0.8178 (ttm) cc_final: 0.7853 (tmm) REVERT: G 135 MET cc_start: 0.7629 (ptp) cc_final: 0.7318 (ptp) REVERT: G 207 ARG cc_start: 0.7865 (OUTLIER) cc_final: 0.6996 (tmm160) REVERT: H 17 TRP cc_start: 0.8089 (m-10) cc_final: 0.7716 (m-10) REVERT: H 122 GLN cc_start: 0.8787 (mm-40) cc_final: 0.8280 (mm-40) REVERT: H 166 TRP cc_start: 0.8460 (p-90) cc_final: 0.8118 (p-90) REVERT: H 183 TYR cc_start: 0.7745 (t80) cc_final: 0.7190 (t80) REVERT: I 177 MET cc_start: 0.8316 (mpp) cc_final: 0.7868 (mpp) REVERT: I 195 ASN cc_start: 0.8082 (t0) cc_final: 0.7723 (p0) REVERT: J 60 GLN cc_start: 0.8632 (tp40) cc_final: 0.8323 (tp-100) REVERT: J 155 LYS cc_start: 0.9055 (OUTLIER) cc_final: 0.8688 (pttm) REVERT: K 58 HIS cc_start: 0.7658 (OUTLIER) cc_final: 0.6542 (m90) REVERT: K 62 MET cc_start: 0.7820 (mpp) cc_final: 0.7466 (mpp) REVERT: K 93 LYS cc_start: 0.8001 (mttt) cc_final: 0.7405 (mmtt) REVERT: L 100 MET cc_start: 0.7493 (mtm) cc_final: 0.6833 (mtm) REVERT: N 5 TYR cc_start: 0.7273 (m-80) cc_final: 0.6909 (m-80) REVERT: N 49 GLN cc_start: 0.7718 (tt0) cc_final: 0.7517 (tt0) REVERT: N 62 LEU cc_start: 0.8822 (mp) cc_final: 0.8547 (mp) REVERT: N 90 ASP cc_start: 0.8264 (p0) cc_final: 0.7974 (p0) REVERT: N 102 PHE cc_start: 0.7687 (m-10) cc_final: 0.7259 (m-80) REVERT: N 106 ASP cc_start: 0.7424 (t0) cc_final: 0.7146 (t0) REVERT: N 112 ARG cc_start: 0.7302 (OUTLIER) cc_final: 0.7022 (mtm180) REVERT: N 127 SER cc_start: 0.7692 (t) cc_final: 0.7410 (p) REVERT: O 49 PHE cc_start: 0.7788 (m-80) cc_final: 0.7357 (m-80) REVERT: O 63 ASP cc_start: 0.7749 (t0) cc_final: 0.7537 (t0) REVERT: P 80 ASN cc_start: 0.3329 (OUTLIER) cc_final: 0.2753 (p0) REVERT: P 112 VAL cc_start: 0.5545 (OUTLIER) cc_final: 0.5318 (m) REVERT: Q 36 VAL cc_start: 0.9253 (t) cc_final: 0.9042 (m) REVERT: Q 75 GLU cc_start: 0.7647 (mp0) cc_final: 0.7298 (mp0) REVERT: R 33 LEU cc_start: 0.7023 (OUTLIER) cc_final: 0.6700 (tt) REVERT: S 53 ASP cc_start: 0.7234 (m-30) cc_final: 0.6470 (m-30) REVERT: S 72 PHE cc_start: 0.6496 (t80) cc_final: 0.6158 (t80) REVERT: S 73 LEU cc_start: 0.7511 (OUTLIER) cc_final: 0.7238 (tt) REVERT: S 85 GLU cc_start: 0.7211 (OUTLIER) cc_final: 0.6941 (pp20) REVERT: U 1 MET cc_start: 0.7676 (tpp) cc_final: 0.7421 (tpt) REVERT: U 31 ARG cc_start: 0.8037 (ttt180) cc_final: 0.7672 (ttm170) REVERT: U 53 ASP cc_start: 0.6977 (OUTLIER) cc_final: 0.6770 (p0) REVERT: V 80 LYS cc_start: 0.8030 (OUTLIER) cc_final: 0.7726 (tttp) REVERT: X 2 ARG cc_start: 0.6481 (tpm170) cc_final: 0.6116 (tpm170) REVERT: X 15 LEU cc_start: 0.8208 (tp) cc_final: 0.7615 (tt) REVERT: X 19 GLU cc_start: 0.8761 (OUTLIER) cc_final: 0.7920 (pt0) REVERT: Y 24 ARG cc_start: 0.9304 (ttm-80) cc_final: 0.8825 (ttm110) REVERT: Z 30 GLU cc_start: 0.7812 (tm-30) cc_final: 0.7521 (tm-30) REVERT: Z 48 LYS cc_start: 0.7046 (tttp) cc_final: 0.6586 (ttmm) REVERT: 8 53 MET cc_start: 0.8564 (tmm) cc_final: 0.8103 (tmm) REVERT: 8 75 MET cc_start: 0.6285 (ppp) cc_final: 0.4886 (tpp) REVERT: 8 106 LEU cc_start: 0.8291 (pp) cc_final: 0.8082 (pp) REVERT: 8 111 MET cc_start: 0.8329 (mpp) cc_final: 0.7449 (mpp) REVERT: 8 431 MET cc_start: 0.8429 (ttt) cc_final: 0.8174 (ttt) REVERT: 8 441 GLU cc_start: 0.8257 (OUTLIER) cc_final: 0.7886 (pp20) outliers start: 310 outliers final: 208 residues processed: 1187 average time/residue: 1.2450 time to fit residues: 2619.9845 Evaluate side-chains 1143 residues out of total 5429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 226 poor density : 917 time to evaluate : 6.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 37 SER Chi-restraints excluded: chain b residue 50 THR Chi-restraints excluded: chain b residue 52 HIS Chi-restraints excluded: chain b residue 71 ASP Chi-restraints excluded: chain b residue 113 ASP Chi-restraints excluded: chain b residue 120 ASP Chi-restraints excluded: chain b residue 129 LEU Chi-restraints excluded: chain b residue 191 LEU Chi-restraints excluded: chain b residue 215 VAL Chi-restraints excluded: chain c residue 22 ILE Chi-restraints excluded: chain c residue 146 ILE Chi-restraints excluded: chain c residue 176 ASP Chi-restraints excluded: chain c residue 185 ASN Chi-restraints excluded: chain d residue 4 VAL Chi-restraints excluded: chain d residue 84 THR Chi-restraints excluded: chain d residue 176 ASP Chi-restraints excluded: chain d residue 181 ILE Chi-restraints excluded: chain e residue 13 LYS Chi-restraints excluded: chain e residue 17 THR Chi-restraints excluded: chain e residue 39 VAL Chi-restraints excluded: chain e residue 82 TYR Chi-restraints excluded: chain e residue 84 ILE Chi-restraints excluded: chain e residue 89 THR Chi-restraints excluded: chain e residue 95 MET Chi-restraints excluded: chain e residue 134 GLN Chi-restraints excluded: chain e residue 148 VAL Chi-restraints excluded: chain e residue 153 ILE Chi-restraints excluded: chain e residue 154 THR Chi-restraints excluded: chain e residue 157 THR Chi-restraints excluded: chain e residue 158 THR Chi-restraints excluded: chain e residue 173 ASP Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 18 ILE Chi-restraints excluded: chain f residue 35 THR Chi-restraints excluded: chain f residue 42 VAL Chi-restraints excluded: chain f residue 113 ASP Chi-restraints excluded: chain f residue 130 ILE Chi-restraints excluded: chain f residue 147 LEU Chi-restraints excluded: chain f residue 167 VAL Chi-restraints excluded: chain g residue 134 VAL Chi-restraints excluded: chain i residue 8 VAL Chi-restraints excluded: chain i residue 46 ASP Chi-restraints excluded: chain j residue 5 THR Chi-restraints excluded: chain j residue 54 ILE Chi-restraints excluded: chain j residue 71 ASP Chi-restraints excluded: chain j residue 84 ILE Chi-restraints excluded: chain j residue 86 GLN Chi-restraints excluded: chain k residue 37 ASP Chi-restraints excluded: chain k residue 42 THR Chi-restraints excluded: chain k residue 45 GLU Chi-restraints excluded: chain k residue 65 THR Chi-restraints excluded: chain k residue 69 VAL Chi-restraints excluded: chain k residue 77 ILE Chi-restraints excluded: chain k residue 90 ASN Chi-restraints excluded: chain l residue 89 VAL Chi-restraints excluded: chain l residue 110 VAL Chi-restraints excluded: chain l residue 118 THR Chi-restraints excluded: chain m residue 67 VAL Chi-restraints excluded: chain m residue 105 MET Chi-restraints excluded: chain m residue 124 LEU Chi-restraints excluded: chain m residue 134 THR Chi-restraints excluded: chain n residue 15 SER Chi-restraints excluded: chain n residue 27 SER Chi-restraints excluded: chain n residue 37 THR Chi-restraints excluded: chain n residue 47 VAL Chi-restraints excluded: chain n residue 57 THR Chi-restraints excluded: chain o residue 39 VAL Chi-restraints excluded: chain o residue 40 ILE Chi-restraints excluded: chain o residue 60 GLU Chi-restraints excluded: chain o residue 69 ASP Chi-restraints excluded: chain o residue 74 VAL Chi-restraints excluded: chain o residue 87 ILE Chi-restraints excluded: chain p residue 7 LEU Chi-restraints excluded: chain p residue 18 SER Chi-restraints excluded: chain p residue 35 SER Chi-restraints excluded: chain p residue 85 VAL Chi-restraints excluded: chain p residue 109 ILE Chi-restraints excluded: chain q residue 86 SER Chi-restraints excluded: chain q residue 94 LEU Chi-restraints excluded: chain r residue 22 LEU Chi-restraints excluded: chain s residue 4 ILE Chi-restraints excluded: chain s residue 109 ASP Chi-restraints excluded: chain t residue 63 VAL Chi-restraints excluded: chain u residue 27 VAL Chi-restraints excluded: chain v residue 92 VAL Chi-restraints excluded: chain x residue 65 THR Chi-restraints excluded: chain y residue 11 VAL Chi-restraints excluded: chain z residue 13 ILE Chi-restraints excluded: chain z residue 16 LEU Chi-restraints excluded: chain z residue 24 LEU Chi-restraints excluded: chain z residue 47 ILE Chi-restraints excluded: chain z residue 54 VAL Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain E residue 3 ILE Chi-restraints excluded: chain E residue 30 HIS Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain F residue 20 ASP Chi-restraints excluded: chain F residue 35 GLN Chi-restraints excluded: chain G residue 59 ILE Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 191 ASP Chi-restraints excluded: chain G residue 207 ARG Chi-restraints excluded: chain H residue 180 ASP Chi-restraints excluded: chain H residue 199 VAL Chi-restraints excluded: chain H residue 206 ILE Chi-restraints excluded: chain I residue 109 THR Chi-restraints excluded: chain I residue 124 VAL Chi-restraints excluded: chain I residue 154 VAL Chi-restraints excluded: chain I residue 168 THR Chi-restraints excluded: chain J residue 10 LEU Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 71 ILE Chi-restraints excluded: chain J residue 79 THR Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 144 GLU Chi-restraints excluded: chain J residue 155 LYS Chi-restraints excluded: chain J residue 160 VAL Chi-restraints excluded: chain K residue 56 LYS Chi-restraints excluded: chain K residue 58 HIS Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain L residue 44 SER Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 72 VAL Chi-restraints excluded: chain L residue 93 VAL Chi-restraints excluded: chain M residue 73 SER Chi-restraints excluded: chain M residue 74 ILE Chi-restraints excluded: chain M residue 75 GLN Chi-restraints excluded: chain M residue 98 LEU Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain M residue 111 THR Chi-restraints excluded: chain M residue 125 ILE Chi-restraints excluded: chain N residue 60 LEU Chi-restraints excluded: chain N residue 74 GLN Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 112 ARG Chi-restraints excluded: chain N residue 126 PHE Chi-restraints excluded: chain O residue 15 HIS Chi-restraints excluded: chain O residue 20 GLN Chi-restraints excluded: chain O residue 42 LEU Chi-restraints excluded: chain O residue 56 HIS Chi-restraints excluded: chain O residue 59 LYS Chi-restraints excluded: chain O residue 69 THR Chi-restraints excluded: chain O residue 100 ILE Chi-restraints excluded: chain P residue 30 ILE Chi-restraints excluded: chain P residue 57 SER Chi-restraints excluded: chain P residue 80 ASN Chi-restraints excluded: chain P residue 104 PHE Chi-restraints excluded: chain P residue 109 ILE Chi-restraints excluded: chain P residue 112 VAL Chi-restraints excluded: chain P residue 126 ARG Chi-restraints excluded: chain Q residue 2 THR Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain Q residue 38 THR Chi-restraints excluded: chain Q residue 56 LEU Chi-restraints excluded: chain Q residue 76 HIS Chi-restraints excluded: chain Q residue 106 VAL Chi-restraints excluded: chain R residue 33 LEU Chi-restraints excluded: chain R residue 72 ILE Chi-restraints excluded: chain R residue 97 ARG Chi-restraints excluded: chain R residue 104 ASN Chi-restraints excluded: chain S residue 5 MET Chi-restraints excluded: chain S residue 33 VAL Chi-restraints excluded: chain S residue 58 ARG Chi-restraints excluded: chain S residue 73 LEU Chi-restraints excluded: chain S residue 85 GLU Chi-restraints excluded: chain T residue 24 THR Chi-restraints excluded: chain T residue 58 MET Chi-restraints excluded: chain T residue 74 VAL Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain U residue 23 ASP Chi-restraints excluded: chain U residue 29 ASN Chi-restraints excluded: chain U residue 42 ILE Chi-restraints excluded: chain U residue 45 GLU Chi-restraints excluded: chain U residue 53 ASP Chi-restraints excluded: chain U residue 54 LEU Chi-restraints excluded: chain U residue 66 THR Chi-restraints excluded: chain V residue 47 ASP Chi-restraints excluded: chain V residue 54 ILE Chi-restraints excluded: chain V residue 58 VAL Chi-restraints excluded: chain V residue 71 SER Chi-restraints excluded: chain V residue 80 LYS Chi-restraints excluded: chain W residue 27 THR Chi-restraints excluded: chain W residue 54 LEU Chi-restraints excluded: chain X residue 12 LEU Chi-restraints excluded: chain X residue 19 GLU Chi-restraints excluded: chain X residue 47 THR Chi-restraints excluded: chain Y residue 31 ILE Chi-restraints excluded: chain Y residue 52 GLU Chi-restraints excluded: chain Y residue 57 VAL Chi-restraints excluded: chain Z residue 3 ILE Chi-restraints excluded: chain Z residue 11 PHE Chi-restraints excluded: chain Z residue 63 ASN Chi-restraints excluded: chain Z residue 67 THR Chi-restraints excluded: chain a residue 163 TYR Chi-restraints excluded: chain a residue 212 VAL Chi-restraints excluded: chain a residue 216 THR Chi-restraints excluded: chain 8 residue 4 THR Chi-restraints excluded: chain 8 residue 19 ILE Chi-restraints excluded: chain 8 residue 80 GLU Chi-restraints excluded: chain 8 residue 105 VAL Chi-restraints excluded: chain 8 residue 141 VAL Chi-restraints excluded: chain 8 residue 154 VAL Chi-restraints excluded: chain 8 residue 158 ILE Chi-restraints excluded: chain 8 residue 334 THR Chi-restraints excluded: chain 8 residue 338 VAL Chi-restraints excluded: chain 8 residue 401 ASP Chi-restraints excluded: chain 8 residue 441 GLU Chi-restraints excluded: chain 8 residue 466 LEU Chi-restraints excluded: chain 8 residue 519 VAL Chi-restraints excluded: chain 8 residue 544 VAL Chi-restraints excluded: chain 8 residue 681 THR 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: 40.0000 chunk 481 optimal weight: 4.9990 chunk 677 optimal weight: 20.0000 chunk 1012 optimal weight: 20.0000 chunk 1071 optimal weight: 9.9990 chunk 529 optimal weight: 9.9990 chunk 959 optimal weight: 10.0000 chunk 288 optimal weight: 7.9990 overall best weight: 8.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 94 GLN c 173 GLN f 19 ASN f 72 ASN g 18 GLN ** j 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 62 ASN ** s 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 39 ASN ** w 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 18 HIS ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 17 HIS ** H 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 70 GLN ** I 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 130 ASN ** J 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 20 ASN ** N 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 80 HIS P 118 ASN Q 76 HIS ** U 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 530 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 627 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.3311 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= 0.318 Angle : 0.694 13.692 247957 Z= 0.360 Chirality : 0.040 0.399 31576 Planarity : 0.005 0.074 13872 Dihedral : 23.493 179.560 81266 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 17.70 Ramachandran Plot: Outliers : 0.11 % Allowed : 11.69 % Favored : 88.20 % Rotamer: Outliers : 5.62 % Allowed : 17.79 % Favored : 76.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.55 (0.10), residues: 6517 helix: -0.47 (0.11), residues: 2058 sheet: -1.92 (0.15), residues: 1107 loop : -2.45 (0.10), residues: 3352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP b 212 HIS 0.016 0.001 HIS L 141 PHE 0.034 0.002 PHE Z 36 TYR 0.028 0.002 TYR q 31 ARG 0.008 0.001 ARG G 94 *********************** 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 1285 residues out of total 5429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 305 poor density : 980 time to evaluate : 6.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 212 TRP cc_start: 0.8626 (OUTLIER) cc_final: 0.7892 (p90) REVERT: c 29 VAL cc_start: 0.9100 (OUTLIER) cc_final: 0.8882 (p) REVERT: c 168 GLU cc_start: 0.7116 (tp30) cc_final: 0.6873 (tp30) REVERT: e 82 TYR cc_start: 0.8222 (OUTLIER) cc_final: 0.7938 (m-10) REVERT: e 95 MET cc_start: 0.7647 (OUTLIER) cc_final: 0.6307 (tmm) REVERT: e 134 GLN cc_start: 0.3835 (OUTLIER) cc_final: 0.2529 (pm20) REVERT: f 59 ASP cc_start: 0.8234 (p0) cc_final: 0.7979 (p0) REVERT: g 14 SER cc_start: 0.7938 (t) cc_final: 0.7737 (p) REVERT: h 38 MET cc_start: -0.5380 (mmt) cc_final: -0.5644 (mmt) REVERT: m 105 MET cc_start: 0.6722 (OUTLIER) cc_final: 0.6482 (mtm) REVERT: n 72 ASP cc_start: 0.8059 (t70) cc_final: 0.7581 (t0) REVERT: n 75 ILE cc_start: 0.8960 (mm) cc_final: 0.8496 (mm) REVERT: n 94 TYR cc_start: 0.8616 (m-10) cc_final: 0.8393 (m-10) REVERT: o 36 TYR cc_start: 0.8456 (OUTLIER) cc_final: 0.8246 (m-80) REVERT: o 108 ASP cc_start: 0.8320 (m-30) cc_final: 0.7801 (m-30) REVERT: r 34 GLU cc_start: 0.8345 (mm-30) cc_final: 0.7769 (mm-30) REVERT: r 60 LYS cc_start: 0.8937 (ttpt) cc_final: 0.8592 (ttpp) REVERT: t 4 GLU cc_start: 0.8399 (mp0) cc_final: 0.7938 (mp0) REVERT: u 6 ARG cc_start: 0.8510 (tpt90) cc_final: 0.8289 (mmm-85) REVERT: u 67 SER cc_start: 0.8899 (m) cc_final: 0.8377 (t) REVERT: v 7 GLU cc_start: 0.7270 (tp30) cc_final: 0.7044 (tp30) REVERT: v 56 PHE cc_start: 0.8676 (t80) cc_final: 0.8386 (t80) REVERT: x 55 MET cc_start: 0.8539 (mmt) cc_final: 0.8125 (mmm) REVERT: y 36 GLN cc_start: 0.8094 (OUTLIER) cc_final: 0.7762 (mm-40) REVERT: y 45 GLN cc_start: 0.8884 (pt0) cc_final: 0.8670 (pp30) REVERT: A 5 ILE cc_start: 0.7548 (pt) cc_final: 0.7283 (mm) REVERT: A 22 MET cc_start: 0.7210 (ppp) cc_final: 0.6984 (ppp) REVERT: A 64 PHE cc_start: 0.6686 (OUTLIER) cc_final: 0.6395 (m-80) REVERT: C 9 LYS cc_start: 0.7480 (mtpt) cc_final: 0.7025 (mtpt) REVERT: C 27 ARG cc_start: 0.8316 (mtp-110) cc_final: 0.7841 (ptp-170) REVERT: G 8 MET cc_start: 0.8131 (ttm) cc_final: 0.7741 (tmm) REVERT: G 26 MET cc_start: 0.8087 (ppp) cc_final: 0.7822 (ppp) REVERT: G 207 ARG cc_start: 0.7828 (OUTLIER) cc_final: 0.7186 (tmm160) REVERT: H 17 TRP cc_start: 0.8041 (m-10) cc_final: 0.7673 (m-10) REVERT: H 122 GLN cc_start: 0.8863 (mm-40) cc_final: 0.8530 (mm-40) REVERT: H 166 TRP cc_start: 0.8462 (p-90) cc_final: 0.8147 (p-90) REVERT: H 183 TYR cc_start: 0.7442 (t80) cc_final: 0.7026 (t80) REVERT: I 35 GLN cc_start: 0.7902 (mm110) cc_final: 0.7324 (tm-30) REVERT: I 73 ASN cc_start: 0.8643 (m110) cc_final: 0.8384 (m-40) REVERT: I 177 MET cc_start: 0.8278 (mpp) cc_final: 0.7646 (mpp) REVERT: I 195 ASN cc_start: 0.8272 (t0) cc_final: 0.7570 (p0) REVERT: K 13 ASP cc_start: 0.7907 (p0) cc_final: 0.7690 (p0) REVERT: K 58 HIS cc_start: 0.7754 (OUTLIER) cc_final: 0.7007 (m90) REVERT: K 93 LYS cc_start: 0.7934 (mttt) cc_final: 0.7390 (mmtt) REVERT: N 49 GLN cc_start: 0.7707 (tt0) cc_final: 0.7433 (tt0) REVERT: N 62 LEU cc_start: 0.8793 (mp) cc_final: 0.8433 (mp) REVERT: N 90 ASP cc_start: 0.8344 (p0) cc_final: 0.8060 (p0) REVERT: N 102 PHE cc_start: 0.7673 (m-10) cc_final: 0.7281 (m-80) REVERT: N 106 ASP cc_start: 0.7415 (t0) cc_final: 0.7127 (t0) REVERT: N 127 SER cc_start: 0.7507 (t) cc_final: 0.7255 (p) REVERT: O 49 PHE cc_start: 0.7776 (m-80) cc_final: 0.7442 (m-80) REVERT: O 59 LYS cc_start: 0.7198 (OUTLIER) cc_final: 0.6635 (tppt) REVERT: O 63 ASP cc_start: 0.7916 (t0) cc_final: 0.7624 (t0) REVERT: O 70 HIS cc_start: 0.8950 (m-70) cc_final: 0.8634 (m90) REVERT: Q 75 GLU cc_start: 0.7359 (mp0) cc_final: 0.7067 (mp0) REVERT: Q 102 ASP cc_start: 0.6367 (m-30) cc_final: 0.6080 (m-30) REVERT: R 16 ILE cc_start: 0.7051 (OUTLIER) cc_final: 0.6829 (mt) REVERT: R 70 ARG cc_start: 0.8444 (ttp80) cc_final: 0.8123 (ttp80) REVERT: R 74 MET cc_start: 0.8395 (mmt) cc_final: 0.8166 (mmt) REVERT: S 53 ASP cc_start: 0.7284 (m-30) cc_final: 0.6506 (m-30) REVERT: S 72 PHE cc_start: 0.6667 (t80) cc_final: 0.6341 (t80) REVERT: S 85 GLU cc_start: 0.7160 (OUTLIER) cc_final: 0.6863 (pp20) REVERT: U 1 MET cc_start: 0.7721 (OUTLIER) cc_final: 0.7510 (tpt) REVERT: V 27 PHE cc_start: 0.7740 (OUTLIER) cc_final: 0.7444 (t80) REVERT: X 2 ARG cc_start: 0.6752 (tpm170) cc_final: 0.6301 (tpm170) REVERT: X 15 LEU cc_start: 0.8183 (tp) cc_final: 0.7775 (tp) REVERT: X 19 GLU cc_start: 0.8800 (OUTLIER) cc_final: 0.7985 (pt0) REVERT: Y 17 ARG cc_start: 0.8775 (ttp80) cc_final: 0.8393 (ttp80) REVERT: Y 24 ARG cc_start: 0.9179 (ttm-80) cc_final: 0.8718 (ttm110) REVERT: Z 19 LYS cc_start: 0.7816 (ttmt) cc_final: 0.7500 (ttpt) REVERT: Z 30 GLU cc_start: 0.7925 (tm-30) cc_final: 0.7714 (tm-30) REVERT: Z 48 LYS cc_start: 0.7177 (tttp) cc_final: 0.6855 (ttmm) REVERT: 8 53 MET cc_start: 0.8525 (tmm) cc_final: 0.8104 (tmm) REVERT: 8 106 LEU cc_start: 0.8281 (pp) cc_final: 0.8067 (pp) REVERT: 8 111 MET cc_start: 0.8263 (mpp) cc_final: 0.7355 (mpp) REVERT: 8 184 ASP cc_start: 0.7631 (OUTLIER) cc_final: 0.7372 (t0) REVERT: 8 204 TYR cc_start: 0.7228 (OUTLIER) cc_final: 0.6295 (t80) REVERT: 8 409 MET cc_start: 0.5660 (pmm) cc_final: 0.5297 (pmm) REVERT: 8 431 MET cc_start: 0.8319 (ttt) cc_final: 0.8084 (ttt) REVERT: 8 441 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7890 (pp20) outliers start: 305 outliers final: 212 residues processed: 1161 average time/residue: 1.2663 time to fit residues: 2608.3485 Evaluate side-chains 1149 residues out of total 5429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 232 poor density : 917 time to evaluate : 6.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 37 SER Chi-restraints excluded: chain b residue 52 HIS Chi-restraints excluded: chain b residue 71 ASP Chi-restraints excluded: chain b residue 113 ASP Chi-restraints excluded: chain b residue 120 ASP Chi-restraints excluded: chain b residue 129 LEU Chi-restraints excluded: chain b residue 191 LEU Chi-restraints excluded: chain b residue 204 LEU Chi-restraints excluded: chain b residue 212 TRP Chi-restraints excluded: chain c residue 29 VAL Chi-restraints excluded: chain c residue 146 ILE Chi-restraints excluded: chain c residue 185 ASN Chi-restraints excluded: chain d residue 4 VAL Chi-restraints excluded: chain d residue 53 THR Chi-restraints excluded: chain d residue 79 ARG Chi-restraints excluded: chain d residue 84 THR Chi-restraints excluded: chain d residue 176 ASP Chi-restraints excluded: chain e residue 39 VAL Chi-restraints excluded: chain e residue 82 TYR Chi-restraints excluded: chain e residue 84 ILE Chi-restraints excluded: chain e residue 89 THR Chi-restraints excluded: chain e residue 95 MET Chi-restraints excluded: chain e residue 134 GLN Chi-restraints excluded: chain e residue 148 VAL Chi-restraints excluded: chain e residue 154 THR Chi-restraints excluded: chain e residue 157 THR Chi-restraints excluded: chain e residue 158 THR Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 19 ASN Chi-restraints excluded: chain f residue 91 VAL Chi-restraints excluded: chain f residue 113 ASP Chi-restraints excluded: chain f residue 130 ILE Chi-restraints excluded: chain f residue 147 LEU Chi-restraints excluded: chain g residue 134 VAL Chi-restraints excluded: chain i residue 46 ASP Chi-restraints excluded: chain j residue 54 ILE Chi-restraints excluded: chain j residue 57 LEU Chi-restraints excluded: chain j residue 71 ASP Chi-restraints excluded: chain j residue 86 GLN Chi-restraints excluded: chain j residue 109 LEU Chi-restraints excluded: chain k residue 42 THR Chi-restraints excluded: chain k residue 45 GLU Chi-restraints excluded: chain k residue 65 THR Chi-restraints excluded: chain k residue 77 ILE Chi-restraints excluded: chain k residue 86 LEU Chi-restraints excluded: chain k residue 90 ASN Chi-restraints excluded: chain l residue 89 VAL Chi-restraints excluded: chain l residue 90 VAL Chi-restraints excluded: chain l residue 118 THR Chi-restraints excluded: chain m residue 12 MET Chi-restraints excluded: chain m residue 67 VAL Chi-restraints excluded: chain m residue 75 GLU Chi-restraints excluded: chain m residue 105 MET Chi-restraints excluded: chain m residue 134 THR Chi-restraints excluded: chain m residue 136 MET Chi-restraints excluded: chain n residue 15 SER Chi-restraints excluded: chain n residue 33 ILE Chi-restraints excluded: chain n residue 37 THR Chi-restraints excluded: chain n residue 57 THR Chi-restraints excluded: chain o residue 18 LEU Chi-restraints excluded: chain o residue 36 TYR Chi-restraints excluded: chain o residue 39 VAL Chi-restraints excluded: chain o residue 60 GLU Chi-restraints excluded: chain o residue 69 ASP Chi-restraints excluded: chain o residue 74 VAL Chi-restraints excluded: chain o residue 87 ILE Chi-restraints excluded: chain p residue 18 SER Chi-restraints excluded: chain p residue 35 SER Chi-restraints excluded: chain p residue 85 VAL Chi-restraints excluded: chain p residue 99 LEU Chi-restraints excluded: chain p residue 109 ILE Chi-restraints excluded: chain q residue 86 SER Chi-restraints excluded: chain q residue 94 LEU Chi-restraints excluded: chain q residue 101 ASP Chi-restraints excluded: chain r residue 6 GLN Chi-restraints excluded: chain r residue 22 LEU Chi-restraints excluded: chain r residue 54 VAL Chi-restraints excluded: chain s residue 4 ILE Chi-restraints excluded: chain s residue 109 ASP Chi-restraints excluded: chain t residue 2 ILE Chi-restraints excluded: chain t residue 15 HIS Chi-restraints excluded: chain t residue 32 LEU Chi-restraints excluded: chain t residue 63 VAL Chi-restraints excluded: chain t residue 78 SER Chi-restraints excluded: chain u residue 11 ILE Chi-restraints excluded: chain u residue 27 VAL Chi-restraints excluded: chain v residue 40 ILE Chi-restraints excluded: chain x residue 39 VAL Chi-restraints excluded: chain x residue 65 THR Chi-restraints excluded: chain y residue 11 VAL Chi-restraints excluded: chain y residue 36 GLN Chi-restraints excluded: chain z residue 13 ILE Chi-restraints excluded: chain z residue 16 LEU Chi-restraints excluded: chain z residue 47 ILE Chi-restraints excluded: chain z residue 50 VAL Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 24 ILE Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 64 PHE Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain C residue 4 ILE Chi-restraints excluded: chain C residue 8 ILE Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain E residue 3 ILE Chi-restraints excluded: chain E residue 30 HIS Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain F residue 13 ASN Chi-restraints excluded: chain F residue 20 ASP Chi-restraints excluded: chain G residue 59 ILE Chi-restraints excluded: chain G residue 191 ASP Chi-restraints excluded: chain G residue 207 ARG Chi-restraints excluded: chain H residue 180 ASP Chi-restraints excluded: chain H residue 199 VAL Chi-restraints excluded: chain H residue 206 ILE Chi-restraints excluded: chain I residue 124 VAL Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 168 THR Chi-restraints excluded: chain I residue 205 LYS Chi-restraints excluded: chain J residue 10 LEU Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 71 ILE Chi-restraints excluded: chain J residue 79 THR Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain J residue 123 LEU Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 144 GLU Chi-restraints excluded: chain K residue 15 SER Chi-restraints excluded: chain K residue 56 LYS Chi-restraints excluded: chain K residue 58 HIS Chi-restraints excluded: chain K residue 61 LEU Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain L residue 44 SER Chi-restraints excluded: chain L residue 72 VAL Chi-restraints excluded: chain L residue 93 VAL Chi-restraints excluded: chain M residue 73 SER Chi-restraints excluded: chain M residue 74 ILE Chi-restraints excluded: chain M residue 75 GLN Chi-restraints excluded: chain M residue 98 LEU Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain M residue 111 THR Chi-restraints excluded: chain M residue 124 ILE Chi-restraints excluded: chain M residue 125 ILE Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain N residue 74 GLN Chi-restraints excluded: chain N residue 83 THR Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 119 LYS Chi-restraints excluded: chain N residue 126 PHE Chi-restraints excluded: chain O residue 15 HIS Chi-restraints excluded: chain O residue 20 GLN Chi-restraints excluded: chain O residue 56 HIS Chi-restraints excluded: chain O residue 59 LYS Chi-restraints excluded: chain O residue 69 THR Chi-restraints excluded: chain P residue 30 ILE Chi-restraints excluded: chain P residue 51 PHE Chi-restraints excluded: chain P residue 57 SER Chi-restraints excluded: chain P residue 71 ASP Chi-restraints excluded: chain P residue 104 PHE Chi-restraints excluded: chain P residue 109 ILE Chi-restraints excluded: chain Q residue 2 THR Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain Q residue 38 THR Chi-restraints excluded: chain Q residue 96 THR Chi-restraints excluded: chain Q residue 106 VAL Chi-restraints excluded: chain R residue 16 ILE Chi-restraints excluded: chain R residue 42 VAL Chi-restraints excluded: chain R residue 63 VAL Chi-restraints excluded: chain R residue 72 ILE Chi-restraints excluded: chain R residue 97 ARG Chi-restraints excluded: chain R residue 104 ASN Chi-restraints excluded: chain S residue 17 ASP Chi-restraints excluded: chain S residue 58 ARG Chi-restraints excluded: chain S residue 85 GLU Chi-restraints excluded: chain T residue 24 THR Chi-restraints excluded: chain T residue 44 GLU Chi-restraints excluded: chain U residue 1 MET Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain U residue 23 ASP Chi-restraints excluded: chain U residue 29 ASN Chi-restraints excluded: chain U residue 42 ILE Chi-restraints excluded: chain U residue 45 GLU Chi-restraints excluded: chain U residue 46 LYS Chi-restraints excluded: chain U residue 54 LEU Chi-restraints excluded: chain U residue 66 THR Chi-restraints excluded: chain V residue 27 PHE Chi-restraints excluded: chain V residue 54 ILE Chi-restraints excluded: chain V residue 58 VAL Chi-restraints excluded: chain V residue 71 SER Chi-restraints excluded: chain W residue 27 THR Chi-restraints excluded: chain W residue 54 LEU Chi-restraints excluded: chain X residue 19 GLU Chi-restraints excluded: chain X residue 47 THR Chi-restraints excluded: chain Y residue 31 ILE Chi-restraints excluded: chain Z residue 3 ILE Chi-restraints excluded: chain Z residue 11 PHE Chi-restraints excluded: chain Z residue 63 ASN Chi-restraints excluded: chain Z residue 67 THR Chi-restraints excluded: chain a residue 8 MET Chi-restraints excluded: chain a residue 44 VAL Chi-restraints excluded: chain a residue 64 VAL Chi-restraints excluded: chain a residue 175 ILE Chi-restraints excluded: chain 8 residue 4 THR Chi-restraints excluded: chain 8 residue 19 ILE Chi-restraints excluded: chain 8 residue 36 VAL Chi-restraints excluded: chain 8 residue 105 VAL Chi-restraints excluded: chain 8 residue 141 VAL Chi-restraints excluded: chain 8 residue 154 VAL Chi-restraints excluded: chain 8 residue 176 GLU Chi-restraints excluded: chain 8 residue 182 VAL Chi-restraints excluded: chain 8 residue 183 VAL Chi-restraints excluded: chain 8 residue 184 ASP Chi-restraints excluded: chain 8 residue 204 TYR Chi-restraints excluded: chain 8 residue 234 MET Chi-restraints excluded: chain 8 residue 334 THR Chi-restraints excluded: chain 8 residue 338 VAL Chi-restraints excluded: chain 8 residue 401 ASP Chi-restraints excluded: chain 8 residue 441 GLU Chi-restraints excluded: chain 8 residue 466 LEU Chi-restraints excluded: chain 8 residue 498 VAL Chi-restraints excluded: chain 8 residue 519 VAL Chi-restraints excluded: chain 8 residue 544 VAL Chi-restraints excluded: chain 8 residue 681 THR 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: 20.0000 chunk 15 optimal weight: 7.9990 chunk 798 optimal weight: 10.0000 chunk 442 optimal weight: 30.0000 chunk 914 optimal weight: 10.0000 chunk 740 optimal weight: 20.0000 chunk 1 optimal weight: 2.9990 chunk 547 optimal weight: 20.0000 chunk 962 optimal weight: 10.0000 chunk 270 optimal weight: 8.9990 overall best weight: 7.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 134 HIS c 173 GLN ** d 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 51 ASN ** j 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 39 ASN w 42 HIS ** y 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 35 GLN ** H 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 70 GLN I 130 ASN ** K 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 37 ASN ** N 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 80 HIS P 118 ASN Q 76 HIS ** U 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.3601 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= 0.306 Angle : 0.680 13.360 247957 Z= 0.352 Chirality : 0.039 0.394 31576 Planarity : 0.005 0.079 13872 Dihedral : 23.499 177.574 81266 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 17.43 Ramachandran Plot: Outliers : 0.09 % Allowed : 12.29 % Favored : 87.62 % Rotamer: Outliers : 6.37 % Allowed : 18.55 % Favored : 75.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.42 (0.10), residues: 6517 helix: -0.36 (0.11), residues: 2061 sheet: -1.81 (0.15), residues: 1121 loop : -2.38 (0.10), residues: 3335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP b 212 HIS 0.021 0.002 HIS G 17 PHE 0.035 0.002 PHE Z 36 TYR 0.023 0.002 TYR q 31 ARG 0.017 0.001 ARG l 2 *********************** 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 1336 residues out of total 5429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 346 poor density : 990 time to evaluate : 6.644 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: b 212 TRP cc_start: 0.8596 (OUTLIER) cc_final: 0.7846 (p90) REVERT: b 265 PHE cc_start: 0.8612 (m-80) cc_final: 0.8264 (m-80) REVERT: c 29 VAL cc_start: 0.9088 (OUTLIER) cc_final: 0.8840 (p) REVERT: e 82 TYR cc_start: 0.8123 (OUTLIER) cc_final: 0.7841 (m-10) REVERT: e 95 MET cc_start: 0.7634 (OUTLIER) cc_final: 0.6360 (tmm) REVERT: e 134 GLN cc_start: 0.3865 (OUTLIER) cc_final: 0.2472 (pm20) REVERT: f 59 ASP cc_start: 0.8275 (p0) cc_final: 0.8068 (p0) REVERT: f 169 ARG cc_start: 0.7778 (mmp80) cc_final: 0.7363 (mmp80) REVERT: g 14 SER cc_start: 0.7961 (t) cc_final: 0.7718 (p) REVERT: h 38 MET cc_start: -0.5570 (mmt) cc_final: -0.5786 (mmt) REVERT: n 72 ASP cc_start: 0.8099 (t70) cc_final: 0.7641 (t0) REVERT: n 75 ILE cc_start: 0.8965 (mm) cc_final: 0.8438 (mm) REVERT: o 108 ASP cc_start: 0.8385 (m-30) cc_final: 0.7713 (m-30) REVERT: r 34 GLU cc_start: 0.8258 (mm-30) cc_final: 0.7594 (mm-30) REVERT: r 60 LYS cc_start: 0.8926 (ttpt) cc_final: 0.8552 (ttpp) REVERT: t 4 GLU cc_start: 0.8468 (mp0) cc_final: 0.7973 (mp0) REVERT: t 89 GLU cc_start: 0.8185 (mm-30) cc_final: 0.7864 (mm-30) REVERT: u 67 SER cc_start: 0.8883 (m) cc_final: 0.8366 (t) REVERT: v 7 GLU cc_start: 0.7246 (tp30) cc_final: 0.6961 (tp30) REVERT: v 56 PHE cc_start: 0.8674 (t80) cc_final: 0.8382 (t80) REVERT: x 55 MET cc_start: 0.8583 (mmt) cc_final: 0.8179 (mmm) REVERT: x 69 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.8011 (mp0) REVERT: y 36 GLN cc_start: 0.8308 (OUTLIER) cc_final: 0.7951 (mm-40) REVERT: A 22 MET cc_start: 0.7442 (ppp) cc_final: 0.7230 (ppp) REVERT: A 64 PHE cc_start: 0.6859 (OUTLIER) cc_final: 0.6522 (m-80) REVERT: C 9 LYS cc_start: 0.7501 (mtpt) cc_final: 0.7056 (mtpt) REVERT: C 27 ARG cc_start: 0.8357 (mtp-110) cc_final: 0.7881 (ptp-170) REVERT: G 8 MET cc_start: 0.8138 (ttm) cc_final: 0.7824 (tmm) REVERT: H 17 TRP cc_start: 0.8027 (m-10) cc_final: 0.7686 (m-10) REVERT: H 166 TRP cc_start: 0.8440 (p-90) cc_final: 0.8065 (p-90) REVERT: H 183 TYR cc_start: 0.7426 (t80) cc_final: 0.7023 (t80) REVERT: I 35 GLN cc_start: 0.7896 (mm110) cc_final: 0.7461 (tm-30) REVERT: I 50 TYR cc_start: 0.8076 (t80) cc_final: 0.7770 (t80) REVERT: I 195 ASN cc_start: 0.8181 (t0) cc_final: 0.7599 (p0) REVERT: J 60 GLN cc_start: 0.8753 (tp-100) cc_final: 0.8419 (tp-100) REVERT: J 111 ARG cc_start: 0.7899 (ttm-80) cc_final: 0.7651 (mtp85) REVERT: J 147 ASN cc_start: 0.7722 (OUTLIER) cc_final: 0.7294 (p0) REVERT: K 45 ARG cc_start: 0.7094 (ptm160) cc_final: 0.6805 (ptp-170) REVERT: K 58 HIS cc_start: 0.7764 (OUTLIER) cc_final: 0.7223 (m90) REVERT: K 93 LYS cc_start: 0.7920 (mttt) cc_final: 0.7379 (mmtt) REVERT: N 5 TYR cc_start: 0.6931 (m-80) cc_final: 0.6521 (m-80) REVERT: N 49 GLN cc_start: 0.7674 (tt0) cc_final: 0.7387 (tt0) REVERT: N 62 LEU cc_start: 0.8821 (mp) cc_final: 0.8388 (mp) REVERT: N 90 ASP cc_start: 0.8282 (p0) cc_final: 0.7958 (p0) REVERT: N 102 PHE cc_start: 0.7648 (m-80) cc_final: 0.7226 (m-80) REVERT: N 106 ASP cc_start: 0.7474 (t0) cc_final: 0.7209 (t0) REVERT: N 127 SER cc_start: 0.7572 (t) cc_final: 0.7326 (p) REVERT: O 49 PHE cc_start: 0.7855 (m-80) cc_final: 0.7591 (m-80) REVERT: O 63 ASP cc_start: 0.7936 (t0) cc_final: 0.7625 (t0) REVERT: P 56 LYS cc_start: 0.8442 (ptmt) cc_final: 0.8189 (ptmm) REVERT: R 16 ILE cc_start: 0.7095 (OUTLIER) cc_final: 0.6858 (mt) REVERT: R 56 ARG cc_start: 0.6314 (mtt90) cc_final: 0.5995 (mmt90) REVERT: R 70 ARG cc_start: 0.8422 (ttp80) cc_final: 0.8166 (ttp80) REVERT: S 32 ASP cc_start: 0.6988 (m-30) cc_final: 0.6477 (m-30) REVERT: S 72 PHE cc_start: 0.6721 (t80) cc_final: 0.6463 (t80) REVERT: S 73 LEU cc_start: 0.7556 (OUTLIER) cc_final: 0.7315 (tt) REVERT: S 85 GLU cc_start: 0.7148 (OUTLIER) cc_final: 0.6848 (pp20) REVERT: S 91 GLU cc_start: 0.7485 (mm-30) cc_final: 0.7217 (mm-30) REVERT: U 1 MET cc_start: 0.7867 (tpp) cc_final: 0.7561 (tpt) REVERT: V 25 GLU cc_start: 0.8242 (mp0) cc_final: 0.8028 (mp0) REVERT: V 27 PHE cc_start: 0.7659 (OUTLIER) cc_final: 0.7435 (t80) REVERT: X 2 ARG cc_start: 0.6844 (tpm170) cc_final: 0.6450 (tpm170) REVERT: X 15 LEU cc_start: 0.8160 (tp) cc_final: 0.7680 (tt) REVERT: X 19 GLU cc_start: 0.8793 (OUTLIER) cc_final: 0.7846 (pt0) REVERT: Y 17 ARG cc_start: 0.8758 (ttp80) cc_final: 0.8340 (ttp80) REVERT: Y 24 ARG cc_start: 0.9149 (ttm-80) cc_final: 0.8720 (ttm110) REVERT: Z 19 LYS cc_start: 0.7725 (ttmt) cc_final: 0.7409 (ttpt) REVERT: Z 48 LYS cc_start: 0.7204 (tttp) cc_final: 0.6866 (ttmm) REVERT: 8 53 MET cc_start: 0.8558 (tmm) cc_final: 0.8111 (tmm) REVERT: 8 75 MET cc_start: 0.6240 (ppp) cc_final: 0.5505 (ppp) REVERT: 8 106 LEU cc_start: 0.8332 (pp) cc_final: 0.8131 (pp) REVERT: 8 111 MET cc_start: 0.8206 (mpp) cc_final: 0.7281 (mpp) REVERT: 8 158 ILE cc_start: 0.9127 (OUTLIER) cc_final: 0.8822 (mm) REVERT: 8 204 TYR cc_start: 0.7194 (OUTLIER) cc_final: 0.6148 (t80) REVERT: 8 427 ASP cc_start: 0.7130 (t0) cc_final: 0.6886 (t0) REVERT: 8 441 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.7947 (pp20) outliers start: 346 outliers final: 250 residues processed: 1206 average time/residue: 1.2565 time to fit residues: 2692.1087 Evaluate side-chains 1198 residues out of total 5429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 268 poor density : 930 time to evaluate : 6.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 37 SER Chi-restraints excluded: chain b residue 52 HIS Chi-restraints excluded: chain b residue 71 ASP Chi-restraints excluded: chain b residue 113 ASP Chi-restraints excluded: chain b residue 120 ASP Chi-restraints excluded: chain b residue 129 LEU Chi-restraints excluded: chain b residue 191 LEU Chi-restraints excluded: chain b residue 212 TRP Chi-restraints excluded: chain c residue 22 ILE Chi-restraints excluded: chain c residue 29 VAL Chi-restraints excluded: chain c residue 146 ILE Chi-restraints excluded: chain c residue 176 ASP Chi-restraints excluded: chain c residue 185 ASN Chi-restraints excluded: chain d residue 4 VAL Chi-restraints excluded: chain d residue 53 THR Chi-restraints excluded: chain d residue 79 ARG Chi-restraints excluded: chain d residue 84 THR Chi-restraints excluded: chain d residue 96 VAL Chi-restraints excluded: chain d residue 176 ASP Chi-restraints excluded: chain e residue 39 VAL Chi-restraints excluded: chain e residue 82 TYR Chi-restraints excluded: chain e residue 84 ILE Chi-restraints excluded: chain e residue 89 THR Chi-restraints excluded: chain e residue 95 MET Chi-restraints excluded: chain e residue 134 GLN Chi-restraints excluded: chain e residue 148 VAL Chi-restraints excluded: chain e residue 154 THR Chi-restraints excluded: chain e residue 157 THR Chi-restraints excluded: chain e residue 158 THR Chi-restraints excluded: chain e residue 173 ASP Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 19 ASN Chi-restraints excluded: chain f residue 35 THR Chi-restraints excluded: chain f residue 91 VAL Chi-restraints excluded: chain f residue 113 ASP Chi-restraints excluded: chain f residue 130 ILE Chi-restraints excluded: chain f residue 147 LEU Chi-restraints excluded: chain f residue 167 VAL Chi-restraints excluded: chain g residue 6 LEU Chi-restraints excluded: chain g residue 44 ILE Chi-restraints excluded: chain g residue 134 VAL Chi-restraints excluded: chain i residue 8 VAL Chi-restraints excluded: chain j residue 5 THR Chi-restraints excluded: chain j residue 54 ILE Chi-restraints excluded: chain j residue 57 LEU Chi-restraints excluded: chain j residue 71 ASP Chi-restraints excluded: chain j residue 86 GLN Chi-restraints excluded: chain j residue 109 LEU Chi-restraints excluded: chain k residue 37 ASP Chi-restraints excluded: chain k residue 42 THR Chi-restraints excluded: chain k residue 45 GLU Chi-restraints excluded: chain k residue 65 THR Chi-restraints excluded: chain k residue 69 VAL Chi-restraints excluded: chain k residue 77 ILE Chi-restraints excluded: chain k residue 86 LEU Chi-restraints excluded: chain k residue 90 ASN Chi-restraints excluded: chain l residue 89 VAL Chi-restraints excluded: chain l residue 118 THR Chi-restraints excluded: chain l residue 122 VAL Chi-restraints excluded: chain m residue 12 MET Chi-restraints excluded: chain m residue 67 VAL Chi-restraints excluded: chain m residue 75 GLU Chi-restraints excluded: chain m residue 134 THR Chi-restraints excluded: chain m residue 136 MET Chi-restraints excluded: chain n residue 15 SER Chi-restraints excluded: chain n residue 33 ILE Chi-restraints excluded: chain n residue 37 THR Chi-restraints excluded: chain n residue 47 VAL Chi-restraints excluded: chain n residue 57 THR Chi-restraints excluded: chain o residue 18 LEU Chi-restraints excluded: chain o residue 39 VAL Chi-restraints excluded: chain o residue 40 ILE Chi-restraints excluded: chain o residue 53 THR Chi-restraints excluded: chain o residue 56 LYS Chi-restraints excluded: chain o residue 60 GLU Chi-restraints excluded: chain o residue 69 ASP Chi-restraints excluded: chain o residue 74 VAL Chi-restraints excluded: chain o residue 87 ILE Chi-restraints excluded: chain o residue 103 VAL Chi-restraints excluded: chain p residue 7 LEU Chi-restraints excluded: chain p residue 18 SER Chi-restraints excluded: chain p residue 35 SER Chi-restraints excluded: chain p residue 85 VAL Chi-restraints excluded: chain p residue 99 LEU Chi-restraints excluded: chain p residue 109 ILE Chi-restraints excluded: chain q residue 86 SER Chi-restraints excluded: chain q residue 94 LEU Chi-restraints excluded: chain q residue 101 ASP Chi-restraints excluded: chain r residue 6 GLN Chi-restraints excluded: chain r residue 22 LEU Chi-restraints excluded: chain r residue 53 PHE Chi-restraints excluded: chain r residue 54 VAL Chi-restraints excluded: chain s residue 4 ILE Chi-restraints excluded: chain s residue 109 ASP Chi-restraints excluded: chain t residue 2 ILE Chi-restraints excluded: chain t residue 32 LEU Chi-restraints excluded: chain t residue 63 VAL Chi-restraints excluded: chain u residue 11 ILE Chi-restraints excluded: chain u residue 27 VAL Chi-restraints excluded: chain u residue 88 ASP Chi-restraints excluded: chain v residue 92 VAL Chi-restraints excluded: chain x residue 39 VAL Chi-restraints excluded: chain x residue 65 THR Chi-restraints excluded: chain x residue 69 GLU Chi-restraints excluded: chain y residue 11 VAL Chi-restraints excluded: chain y residue 36 GLN Chi-restraints excluded: chain y residue 58 ASN Chi-restraints excluded: chain z residue 13 ILE Chi-restraints excluded: chain z residue 16 LEU Chi-restraints excluded: chain z residue 24 LEU Chi-restraints excluded: chain z residue 47 ILE Chi-restraints excluded: chain z residue 50 VAL Chi-restraints excluded: chain z residue 54 VAL Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 24 ILE Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 64 PHE Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain C residue 8 ILE Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain E residue 30 HIS Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain F residue 13 ASN Chi-restraints excluded: chain F residue 20 ASP Chi-restraints excluded: chain G residue 30 ILE Chi-restraints excluded: chain G residue 59 ILE Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 191 ASP Chi-restraints excluded: chain H residue 117 ASP Chi-restraints excluded: chain H residue 180 ASP Chi-restraints excluded: chain H residue 199 VAL Chi-restraints excluded: chain H residue 206 ILE Chi-restraints excluded: chain I residue 109 THR Chi-restraints excluded: chain I residue 124 VAL Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 130 ASN Chi-restraints excluded: chain I residue 168 THR Chi-restraints excluded: chain J residue 10 LEU Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 71 ILE Chi-restraints excluded: chain J residue 79 THR Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 144 GLU Chi-restraints excluded: chain J residue 147 ASN Chi-restraints excluded: chain J residue 155 LYS Chi-restraints excluded: chain K residue 15 SER Chi-restraints excluded: chain K residue 56 LYS Chi-restraints excluded: chain K residue 58 HIS Chi-restraints excluded: chain L residue 44 SER Chi-restraints excluded: chain L residue 72 VAL Chi-restraints excluded: chain L residue 88 VAL Chi-restraints excluded: chain L residue 93 VAL Chi-restraints excluded: chain L residue 112 ASP Chi-restraints excluded: chain L residue 129 ASN Chi-restraints excluded: chain M residue 73 SER Chi-restraints excluded: chain M residue 74 ILE Chi-restraints excluded: chain M residue 75 GLN Chi-restraints excluded: chain M residue 98 LEU Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain M residue 111 THR Chi-restraints excluded: chain M residue 124 ILE Chi-restraints excluded: chain M residue 125 ILE Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain N residue 20 ILE Chi-restraints excluded: chain N residue 60 LEU Chi-restraints excluded: chain N residue 74 GLN Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 119 LYS Chi-restraints excluded: chain N residue 126 PHE Chi-restraints excluded: chain O residue 15 HIS Chi-restraints excluded: chain O residue 20 GLN Chi-restraints excluded: chain O residue 56 HIS Chi-restraints excluded: chain O residue 59 LYS Chi-restraints excluded: chain O residue 100 ILE Chi-restraints excluded: chain P residue 30 ILE Chi-restraints excluded: chain P residue 51 PHE Chi-restraints excluded: chain P residue 57 SER Chi-restraints excluded: chain P residue 71 ASP Chi-restraints excluded: chain P residue 80 ASN Chi-restraints excluded: chain P residue 104 PHE Chi-restraints excluded: chain P residue 109 ILE Chi-restraints excluded: chain Q residue 2 THR Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain Q residue 34 THR Chi-restraints excluded: chain Q residue 36 VAL Chi-restraints excluded: chain Q residue 38 THR Chi-restraints excluded: chain Q residue 96 THR Chi-restraints excluded: chain Q residue 106 VAL Chi-restraints excluded: chain R residue 16 ILE Chi-restraints excluded: chain R residue 42 VAL Chi-restraints excluded: chain R residue 63 VAL Chi-restraints excluded: chain R residue 72 ILE Chi-restraints excluded: chain R residue 85 TYR Chi-restraints excluded: chain R residue 97 ARG Chi-restraints excluded: chain R residue 104 ASN Chi-restraints excluded: chain S residue 5 MET Chi-restraints excluded: chain S residue 17 ASP Chi-restraints excluded: chain S residue 58 ARG Chi-restraints excluded: chain S residue 73 LEU Chi-restraints excluded: chain S residue 85 GLU Chi-restraints excluded: chain T residue 24 THR Chi-restraints excluded: chain T residue 44 GLU Chi-restraints excluded: chain T residue 58 MET Chi-restraints excluded: chain T residue 74 VAL Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain U residue 23 ASP Chi-restraints excluded: chain U residue 29 ASN Chi-restraints excluded: chain U residue 42 ILE Chi-restraints excluded: chain U residue 45 GLU Chi-restraints excluded: chain U residue 46 LYS Chi-restraints excluded: chain U residue 54 LEU Chi-restraints excluded: chain U residue 66 THR Chi-restraints excluded: chain V residue 19 SER Chi-restraints excluded: chain V residue 27 PHE Chi-restraints excluded: chain V residue 47 ASP Chi-restraints excluded: chain V residue 54 ILE Chi-restraints excluded: chain V residue 71 SER Chi-restraints excluded: chain W residue 27 THR Chi-restraints excluded: chain W residue 54 LEU Chi-restraints excluded: chain X residue 4 LEU Chi-restraints excluded: chain X residue 12 LEU Chi-restraints excluded: chain X residue 19 GLU Chi-restraints excluded: chain X residue 39 ILE Chi-restraints excluded: chain X residue 47 THR Chi-restraints excluded: chain Y residue 31 ILE Chi-restraints excluded: chain Z residue 3 ILE Chi-restraints excluded: chain Z residue 11 PHE Chi-restraints excluded: chain Z residue 63 ASN Chi-restraints excluded: chain Z residue 67 THR Chi-restraints excluded: chain a residue 8 MET Chi-restraints excluded: chain a residue 44 VAL Chi-restraints excluded: chain a residue 50 ILE Chi-restraints excluded: chain a residue 175 ILE Chi-restraints excluded: chain a residue 216 THR Chi-restraints excluded: chain 8 residue 4 THR Chi-restraints excluded: chain 8 residue 19 ILE Chi-restraints excluded: chain 8 residue 36 VAL Chi-restraints excluded: chain 8 residue 80 GLU Chi-restraints excluded: chain 8 residue 105 VAL Chi-restraints excluded: chain 8 residue 141 VAL Chi-restraints excluded: chain 8 residue 154 VAL Chi-restraints excluded: chain 8 residue 158 ILE Chi-restraints excluded: chain 8 residue 176 GLU Chi-restraints excluded: chain 8 residue 182 VAL Chi-restraints excluded: chain 8 residue 183 VAL Chi-restraints excluded: chain 8 residue 204 TYR Chi-restraints excluded: chain 8 residue 234 MET Chi-restraints excluded: chain 8 residue 334 THR Chi-restraints excluded: chain 8 residue 338 VAL Chi-restraints excluded: chain 8 residue 401 ASP Chi-restraints excluded: chain 8 residue 441 GLU Chi-restraints excluded: chain 8 residue 466 LEU Chi-restraints excluded: chain 8 residue 498 VAL Chi-restraints excluded: chain 8 residue 518 VAL Chi-restraints excluded: chain 8 residue 519 VAL Chi-restraints excluded: chain 8 residue 544 VAL Chi-restraints excluded: chain 8 residue 681 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1109 random chunks: chunk 360 optimal weight: 20.0000 chunk 965 optimal weight: 10.0000 chunk 211 optimal weight: 10.0000 chunk 629 optimal weight: 20.0000 chunk 264 optimal weight: 5.9990 chunk 1073 optimal weight: 30.0000 chunk 890 optimal weight: 10.0000 chunk 496 optimal weight: 20.0000 chunk 89 optimal weight: 8.9990 chunk 354 optimal weight: 40.0000 chunk 563 optimal weight: 30.0000 overall best weight: 8.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 134 HIS c 173 GLN ** j 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 39 ASN ** y 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 35 GLN ** H 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 138 GLN I 130 ASN ** K 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 80 HIS P 118 ASN Q 76 HIS U 18 GLN ** W 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 172 HIS 8 122 GLN ** 8 530 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.3868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 166269 Z= 0.338 Angle : 0.701 14.651 247957 Z= 0.362 Chirality : 0.040 0.402 31576 Planarity : 0.005 0.104 13872 Dihedral : 23.551 176.859 81266 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 18.14 Ramachandran Plot: Outliers : 0.11 % Allowed : 12.09 % Favored : 87.80 % Rotamer: Outliers : 6.65 % Allowed : 19.47 % Favored : 73.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.38 (0.10), residues: 6517 helix: -0.35 (0.11), residues: 2067 sheet: -1.72 (0.15), residues: 1090 loop : -2.37 (0.10), residues: 3360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP b 212 HIS 0.015 0.002 HIS L 141 PHE 0.035 0.002 PHE Z 36 TYR 0.038 0.002 TYR H 167 ARG 0.011 0.001 ARG J 68 *********************** 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 1319 residues out of total 5429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 361 poor density : 958 time to evaluate : 6.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 212 TRP cc_start: 0.8615 (OUTLIER) cc_final: 0.7909 (p90) REVERT: c 29 VAL cc_start: 0.9088 (OUTLIER) cc_final: 0.8856 (p) REVERT: e 31 GLU cc_start: 0.8225 (mt-10) cc_final: 0.7903 (mt-10) REVERT: e 95 MET cc_start: 0.7644 (OUTLIER) cc_final: 0.6374 (tmm) REVERT: f 59 ASP cc_start: 0.8358 (p0) cc_final: 0.8137 (p0) REVERT: g 14 SER cc_start: 0.7932 (t) cc_final: 0.7670 (p) REVERT: n 72 ASP cc_start: 0.8063 (t70) cc_final: 0.7470 (t0) REVERT: n 75 ILE cc_start: 0.8976 (mm) cc_final: 0.8472 (mm) REVERT: r 34 GLU cc_start: 0.8260 (mm-30) cc_final: 0.7577 (mm-30) REVERT: r 60 LYS cc_start: 0.8939 (ttpt) cc_final: 0.8551 (ttpp) REVERT: s 31 GLN cc_start: 0.8225 (OUTLIER) cc_final: 0.7949 (pm20) REVERT: t 4 GLU cc_start: 0.8549 (mp0) cc_final: 0.7980 (mp0) REVERT: u 6 ARG cc_start: 0.8492 (tpt-90) cc_final: 0.8237 (mmm-85) REVERT: u 67 SER cc_start: 0.8914 (m) cc_final: 0.8428 (t) REVERT: v 56 PHE cc_start: 0.8699 (t80) cc_final: 0.8399 (t80) REVERT: x 69 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.7964 (mp0) REVERT: y 36 GLN cc_start: 0.8460 (OUTLIER) cc_final: 0.8040 (mm-40) REVERT: A 64 PHE cc_start: 0.7087 (OUTLIER) cc_final: 0.6773 (m-80) REVERT: C 9 LYS cc_start: 0.7493 (mtpt) cc_final: 0.7050 (mtpt) REVERT: C 27 ARG cc_start: 0.8385 (mtp-110) cc_final: 0.7869 (ptp-170) REVERT: G 8 MET cc_start: 0.8078 (ttm) cc_final: 0.7774 (tmm) REVERT: G 135 MET cc_start: 0.7725 (ptm) cc_final: 0.7469 (ptp) REVERT: H 17 TRP cc_start: 0.8021 (m-10) cc_final: 0.7681 (m-10) REVERT: H 183 TYR cc_start: 0.7479 (t80) cc_final: 0.6996 (t80) REVERT: I 35 GLN cc_start: 0.7797 (mm110) cc_final: 0.7485 (tm-30) REVERT: I 50 TYR cc_start: 0.8142 (t80) cc_final: 0.7849 (t80) REVERT: J 54 GLU cc_start: 0.8150 (tp30) cc_final: 0.7377 (pm20) REVERT: J 60 GLN cc_start: 0.8723 (tp-100) cc_final: 0.8260 (tp-100) REVERT: J 111 ARG cc_start: 0.7954 (ttm-80) cc_final: 0.7641 (mtp85) REVERT: J 147 ASN cc_start: 0.7726 (OUTLIER) cc_final: 0.7303 (p0) REVERT: K 35 LYS cc_start: 0.8121 (ptpp) cc_final: 0.7789 (ptpp) REVERT: K 45 ARG cc_start: 0.7122 (ptm160) cc_final: 0.6833 (ptp-170) REVERT: K 58 HIS cc_start: 0.7837 (OUTLIER) cc_final: 0.7323 (m90) REVERT: K 79 ARG cc_start: 0.8468 (OUTLIER) cc_final: 0.8181 (ptp90) REVERT: K 93 LYS cc_start: 0.7902 (mttt) cc_final: 0.7382 (mmtt) REVERT: N 5 TYR cc_start: 0.7070 (m-80) cc_final: 0.6758 (m-80) REVERT: N 49 GLN cc_start: 0.7522 (tt0) cc_final: 0.7255 (tt0) REVERT: N 62 LEU cc_start: 0.8824 (mp) cc_final: 0.8385 (mp) REVERT: N 87 MET cc_start: 0.5982 (ptp) cc_final: 0.5575 (pmm) REVERT: N 90 ASP cc_start: 0.8254 (p0) cc_final: 0.7922 (p0) REVERT: N 102 PHE cc_start: 0.7604 (m-80) cc_final: 0.7253 (m-80) REVERT: N 106 ASP cc_start: 0.7462 (t0) cc_final: 0.7200 (t0) REVERT: O 20 GLN cc_start: 0.7393 (OUTLIER) cc_final: 0.7156 (pp30) REVERT: O 49 PHE cc_start: 0.7869 (m-80) cc_final: 0.7651 (m-80) REVERT: O 63 ASP cc_start: 0.7944 (t0) cc_final: 0.7629 (t0) REVERT: P 56 LYS cc_start: 0.8472 (OUTLIER) cc_final: 0.8270 (ptmm) REVERT: P 80 ASN cc_start: 0.3087 (OUTLIER) cc_final: 0.2597 (p0) REVERT: R 16 ILE cc_start: 0.7179 (OUTLIER) cc_final: 0.6941 (mt) REVERT: S 32 ASP cc_start: 0.6992 (m-30) cc_final: 0.6455 (m-30) REVERT: S 72 PHE cc_start: 0.6767 (t80) cc_final: 0.6517 (t80) REVERT: S 73 LEU cc_start: 0.7516 (OUTLIER) cc_final: 0.7258 (tt) REVERT: S 85 GLU cc_start: 0.7136 (OUTLIER) cc_final: 0.6818 (pp20) REVERT: S 91 GLU cc_start: 0.7410 (mm-30) cc_final: 0.7150 (mm-30) REVERT: T 82 GLU cc_start: 0.7890 (OUTLIER) cc_final: 0.7369 (mt-10) REVERT: V 27 PHE cc_start: 0.7677 (OUTLIER) cc_final: 0.7459 (t80) REVERT: X 15 LEU cc_start: 0.8144 (tp) cc_final: 0.7717 (tt) REVERT: X 19 GLU cc_start: 0.8808 (OUTLIER) cc_final: 0.7900 (pt0) REVERT: Y 17 ARG cc_start: 0.8730 (ttp80) cc_final: 0.8508 (ttp80) REVERT: Y 24 ARG cc_start: 0.9157 (ttm-80) cc_final: 0.8808 (ttm110) REVERT: Z 19 LYS cc_start: 0.7751 (ttmt) cc_final: 0.7471 (ttpt) REVERT: Z 48 LYS cc_start: 0.7272 (tttp) cc_final: 0.6835 (ttmm) REVERT: a 163 TYR cc_start: 0.0533 (OUTLIER) cc_final: 0.0026 (p90) REVERT: 8 53 MET cc_start: 0.8578 (tmm) cc_final: 0.8117 (tmm) REVERT: 8 106 LEU cc_start: 0.8377 (pp) cc_final: 0.8170 (pp) REVERT: 8 111 MET cc_start: 0.8215 (mpp) cc_final: 0.7259 (mpp) REVERT: 8 184 ASP cc_start: 0.7562 (OUTLIER) cc_final: 0.7348 (t0) REVERT: 8 204 TYR cc_start: 0.7243 (OUTLIER) cc_final: 0.6056 (t80) REVERT: 8 366 MET cc_start: 0.5405 (mmm) cc_final: 0.4938 (mmm) REVERT: 8 373 GLU cc_start: 0.8455 (OUTLIER) cc_final: 0.7952 (pm20) REVERT: 8 427 ASP cc_start: 0.7081 (t0) cc_final: 0.6850 (t0) REVERT: 8 441 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.7844 (pp20) outliers start: 361 outliers final: 264 residues processed: 1176 average time/residue: 1.2519 time to fit residues: 2617.9783 Evaluate side-chains 1204 residues out of total 5429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 288 poor density : 916 time to evaluate : 6.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 37 SER Chi-restraints excluded: chain b residue 50 THR Chi-restraints excluded: chain b residue 52 HIS Chi-restraints excluded: chain b residue 71 ASP Chi-restraints excluded: chain b residue 113 ASP Chi-restraints excluded: chain b residue 120 ASP Chi-restraints excluded: chain b residue 129 LEU Chi-restraints excluded: chain b residue 191 LEU Chi-restraints excluded: chain b residue 204 LEU Chi-restraints excluded: chain b residue 212 TRP Chi-restraints excluded: chain c residue 22 ILE Chi-restraints excluded: chain c residue 29 VAL Chi-restraints excluded: chain c residue 146 ILE Chi-restraints excluded: chain c residue 176 ASP Chi-restraints excluded: chain c residue 185 ASN Chi-restraints excluded: chain c residue 200 ASP Chi-restraints excluded: chain d residue 4 VAL Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain d residue 53 THR Chi-restraints excluded: chain d residue 79 ARG Chi-restraints excluded: chain d residue 84 THR Chi-restraints excluded: chain d residue 96 VAL Chi-restraints excluded: chain d residue 108 ILE Chi-restraints excluded: chain d residue 141 MET Chi-restraints excluded: chain d residue 176 ASP Chi-restraints excluded: chain e residue 39 VAL Chi-restraints excluded: chain e residue 84 ILE Chi-restraints excluded: chain e residue 89 THR Chi-restraints excluded: chain e residue 95 MET Chi-restraints excluded: chain e residue 134 GLN Chi-restraints excluded: chain e residue 148 VAL Chi-restraints excluded: chain e residue 153 ILE Chi-restraints excluded: chain e residue 154 THR Chi-restraints excluded: chain e residue 157 THR Chi-restraints excluded: chain e residue 158 THR Chi-restraints excluded: chain e residue 173 ASP Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 35 THR Chi-restraints excluded: chain f residue 91 VAL Chi-restraints excluded: chain f residue 113 ASP Chi-restraints excluded: chain f residue 130 ILE Chi-restraints excluded: chain f residue 140 ILE Chi-restraints excluded: chain f residue 147 LEU Chi-restraints excluded: chain f residue 167 VAL Chi-restraints excluded: chain g residue 6 LEU Chi-restraints excluded: chain g residue 44 ILE Chi-restraints excluded: chain i residue 8 VAL Chi-restraints excluded: chain j residue 5 THR Chi-restraints excluded: chain j residue 54 ILE Chi-restraints excluded: chain j residue 71 ASP Chi-restraints excluded: chain j residue 86 GLN Chi-restraints excluded: chain j residue 109 LEU Chi-restraints excluded: chain k residue 37 ASP Chi-restraints excluded: chain k residue 42 THR Chi-restraints excluded: chain k residue 45 GLU Chi-restraints excluded: chain k residue 65 THR Chi-restraints excluded: chain k residue 69 VAL Chi-restraints excluded: chain k residue 77 ILE Chi-restraints excluded: chain k residue 86 LEU Chi-restraints excluded: chain k residue 90 ASN Chi-restraints excluded: chain l residue 89 VAL Chi-restraints excluded: chain l residue 90 VAL Chi-restraints excluded: chain l residue 118 THR Chi-restraints excluded: chain l residue 122 VAL Chi-restraints excluded: chain m residue 12 MET Chi-restraints excluded: chain m residue 67 VAL Chi-restraints excluded: chain m residue 75 GLU Chi-restraints excluded: chain m residue 105 MET Chi-restraints excluded: chain m residue 134 THR Chi-restraints excluded: chain m residue 136 MET Chi-restraints excluded: chain n residue 15 SER Chi-restraints excluded: chain n residue 33 ILE Chi-restraints excluded: chain n residue 37 THR Chi-restraints excluded: chain n residue 47 VAL Chi-restraints excluded: chain n residue 57 THR Chi-restraints excluded: chain o residue 18 LEU Chi-restraints excluded: chain o residue 39 VAL Chi-restraints excluded: chain o residue 40 ILE Chi-restraints excluded: chain o residue 53 THR Chi-restraints excluded: chain o residue 56 LYS Chi-restraints excluded: chain o residue 60 GLU Chi-restraints excluded: chain o residue 69 ASP Chi-restraints excluded: chain o residue 74 VAL Chi-restraints excluded: chain o residue 87 ILE Chi-restraints excluded: chain o residue 103 VAL Chi-restraints excluded: chain p residue 18 SER Chi-restraints excluded: chain p residue 35 SER Chi-restraints excluded: chain p residue 85 VAL Chi-restraints excluded: chain p residue 99 LEU Chi-restraints excluded: chain p residue 109 ILE Chi-restraints excluded: chain q residue 86 SER Chi-restraints excluded: chain q residue 94 LEU Chi-restraints excluded: chain q residue 101 ASP Chi-restraints excluded: chain r residue 6 GLN Chi-restraints excluded: chain r residue 53 PHE Chi-restraints excluded: chain r residue 54 VAL Chi-restraints excluded: chain s residue 4 ILE Chi-restraints excluded: chain s residue 31 GLN Chi-restraints excluded: chain s residue 109 ASP Chi-restraints excluded: chain t residue 2 ILE Chi-restraints excluded: chain t residue 15 HIS Chi-restraints excluded: chain t residue 32 LEU Chi-restraints excluded: chain t residue 63 VAL Chi-restraints excluded: chain t residue 78 SER Chi-restraints excluded: chain u residue 11 ILE Chi-restraints excluded: chain u residue 27 VAL Chi-restraints excluded: chain u residue 88 ASP Chi-restraints excluded: chain v residue 40 ILE Chi-restraints excluded: chain v residue 92 VAL Chi-restraints excluded: chain w residue 77 SER Chi-restraints excluded: chain x residue 39 VAL Chi-restraints excluded: chain x residue 46 VAL Chi-restraints excluded: chain x residue 65 THR Chi-restraints excluded: chain x residue 69 GLU Chi-restraints excluded: chain y residue 11 VAL Chi-restraints excluded: chain y residue 36 GLN Chi-restraints excluded: chain y residue 58 ASN Chi-restraints excluded: chain z residue 13 ILE Chi-restraints excluded: chain z residue 16 LEU Chi-restraints excluded: chain z residue 24 LEU Chi-restraints excluded: chain z residue 47 ILE Chi-restraints excluded: chain z residue 50 VAL Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 59 ARG Chi-restraints excluded: chain A residue 64 PHE Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain C residue 8 ILE Chi-restraints excluded: chain C residue 19 PHE Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain E residue 3 ILE Chi-restraints excluded: chain E residue 30 HIS Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain F residue 13 ASN Chi-restraints excluded: chain F residue 20 ASP Chi-restraints excluded: chain G residue 30 ILE Chi-restraints excluded: chain G residue 59 ILE Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 191 ASP Chi-restraints excluded: chain H residue 117 ASP Chi-restraints excluded: chain H residue 180 ASP Chi-restraints excluded: chain H residue 199 VAL Chi-restraints excluded: chain H residue 206 ILE Chi-restraints excluded: chain I residue 109 THR Chi-restraints excluded: chain I residue 124 VAL Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 168 THR Chi-restraints excluded: chain I residue 205 LYS Chi-restraints excluded: chain J residue 10 LEU Chi-restraints excluded: chain J residue 13 LYS Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 71 ILE Chi-restraints excluded: chain J residue 79 THR Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 144 GLU Chi-restraints excluded: chain J residue 147 ASN Chi-restraints excluded: chain J residue 159 SER Chi-restraints excluded: chain J residue 160 VAL Chi-restraints excluded: chain K residue 15 SER Chi-restraints excluded: chain K residue 56 LYS Chi-restraints excluded: chain K residue 58 HIS Chi-restraints excluded: chain K residue 61 LEU Chi-restraints excluded: chain K residue 79 ARG Chi-restraints excluded: chain L residue 44 SER Chi-restraints excluded: chain L residue 72 VAL Chi-restraints excluded: chain L residue 88 VAL Chi-restraints excluded: chain L residue 93 VAL Chi-restraints excluded: chain L residue 112 ASP Chi-restraints excluded: chain L residue 129 ASN Chi-restraints excluded: chain M residue 73 SER Chi-restraints excluded: chain M residue 74 ILE Chi-restraints excluded: chain M residue 75 GLN Chi-restraints excluded: chain M residue 98 LEU Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain M residue 111 THR Chi-restraints excluded: chain M residue 124 ILE Chi-restraints excluded: chain M residue 125 ILE Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain N residue 60 LEU Chi-restraints excluded: chain N residue 74 GLN Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 119 LYS Chi-restraints excluded: chain N residue 126 PHE Chi-restraints excluded: chain O residue 15 HIS Chi-restraints excluded: chain O residue 20 GLN Chi-restraints excluded: chain O residue 56 HIS Chi-restraints excluded: chain O residue 59 LYS Chi-restraints excluded: chain O residue 98 VAL Chi-restraints excluded: chain O residue 100 ILE Chi-restraints excluded: chain P residue 30 ILE Chi-restraints excluded: chain P residue 41 LEU Chi-restraints excluded: chain P residue 51 PHE Chi-restraints excluded: chain P residue 56 LYS Chi-restraints excluded: chain P residue 57 SER Chi-restraints excluded: chain P residue 71 ASP Chi-restraints excluded: chain P residue 80 ASN Chi-restraints excluded: chain P residue 104 PHE Chi-restraints excluded: chain P residue 109 ILE Chi-restraints excluded: chain Q residue 2 THR Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain Q residue 36 VAL Chi-restraints excluded: chain Q residue 38 THR Chi-restraints excluded: chain Q residue 96 THR Chi-restraints excluded: chain Q residue 106 VAL Chi-restraints excluded: chain R residue 3 ILE Chi-restraints excluded: chain R residue 16 ILE Chi-restraints excluded: chain R residue 42 VAL Chi-restraints excluded: chain R residue 63 VAL Chi-restraints excluded: chain R residue 72 ILE Chi-restraints excluded: chain R residue 97 ARG Chi-restraints excluded: chain R residue 104 ASN Chi-restraints excluded: chain S residue 15 LEU Chi-restraints excluded: chain S residue 17 ASP Chi-restraints excluded: chain S residue 53 ASP Chi-restraints excluded: chain S residue 73 LEU Chi-restraints excluded: chain S residue 85 GLU Chi-restraints excluded: chain T residue 44 GLU Chi-restraints excluded: chain T residue 74 VAL Chi-restraints excluded: chain T residue 82 GLU Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain U residue 21 VAL Chi-restraints excluded: chain U residue 23 ASP Chi-restraints excluded: chain U residue 29 ASN Chi-restraints excluded: chain U residue 42 ILE Chi-restraints excluded: chain U residue 45 GLU Chi-restraints excluded: chain U residue 46 LYS Chi-restraints excluded: chain U residue 66 THR Chi-restraints excluded: chain V residue 27 PHE Chi-restraints excluded: chain V residue 47 ASP Chi-restraints excluded: chain V residue 52 CYS Chi-restraints excluded: chain V residue 54 ILE Chi-restraints excluded: chain V residue 58 VAL Chi-restraints excluded: chain V residue 71 SER Chi-restraints excluded: chain W residue 27 THR Chi-restraints excluded: chain W residue 38 ILE Chi-restraints excluded: chain W residue 54 LEU Chi-restraints excluded: chain X residue 4 LEU Chi-restraints excluded: chain X residue 12 LEU Chi-restraints excluded: chain X residue 19 GLU Chi-restraints excluded: chain X residue 32 THR Chi-restraints excluded: chain X residue 39 ILE Chi-restraints excluded: chain X residue 47 THR Chi-restraints excluded: chain Y residue 31 ILE Chi-restraints excluded: chain Z residue 11 PHE Chi-restraints excluded: chain Z residue 63 ASN Chi-restraints excluded: chain a residue 50 ILE Chi-restraints excluded: chain a residue 56 ASP Chi-restraints excluded: chain a residue 163 TYR Chi-restraints excluded: chain a residue 175 ILE Chi-restraints excluded: chain a residue 212 VAL Chi-restraints excluded: chain 8 residue 4 THR Chi-restraints excluded: chain 8 residue 19 ILE Chi-restraints excluded: chain 8 residue 36 VAL Chi-restraints excluded: chain 8 residue 64 THR Chi-restraints excluded: chain 8 residue 105 VAL Chi-restraints excluded: chain 8 residue 141 VAL Chi-restraints excluded: chain 8 residue 154 VAL Chi-restraints excluded: chain 8 residue 176 GLU Chi-restraints excluded: chain 8 residue 182 VAL Chi-restraints excluded: chain 8 residue 183 VAL Chi-restraints excluded: chain 8 residue 184 ASP Chi-restraints excluded: chain 8 residue 204 TYR Chi-restraints excluded: chain 8 residue 234 MET Chi-restraints excluded: chain 8 residue 300 ASP Chi-restraints excluded: chain 8 residue 334 THR Chi-restraints excluded: chain 8 residue 338 VAL Chi-restraints excluded: chain 8 residue 373 GLU Chi-restraints excluded: chain 8 residue 401 ASP Chi-restraints excluded: chain 8 residue 441 GLU Chi-restraints excluded: chain 8 residue 466 LEU Chi-restraints excluded: chain 8 residue 498 VAL Chi-restraints excluded: chain 8 residue 518 VAL Chi-restraints excluded: chain 8 residue 519 VAL Chi-restraints excluded: chain 8 residue 544 VAL Chi-restraints excluded: chain 8 residue 681 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1109 random chunks: chunk 1034 optimal weight: 30.0000 chunk 120 optimal weight: 40.0000 chunk 611 optimal weight: 20.0000 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: 20.0000 chunk 668 optimal weight: 40.0000 chunk 651 optimal weight: 10.0000 chunk 493 optimal weight: 8.9990 overall best weight: 11.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 39 ASN ** y 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 122 GLN I 130 ASN ** J 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 80 HIS O 64 GLN O 70 HIS ** R 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 530 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.4192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.096 166269 Z= 0.430 Angle : 0.787 14.811 247957 Z= 0.401 Chirality : 0.044 0.415 31576 Planarity : 0.006 0.100 13872 Dihedral : 23.712 179.745 81266 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 21.25 Ramachandran Plot: Outliers : 0.12 % Allowed : 13.29 % Favored : 86.59 % Rotamer: Outliers : 6.94 % Allowed : 20.26 % Favored : 72.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.58 (0.10), residues: 6517 helix: -0.57 (0.11), residues: 2069 sheet: -1.84 (0.15), residues: 1118 loop : -2.46 (0.10), residues: 3330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP b 212 HIS 0.015 0.002 HIS L 141 PHE 0.037 0.003 PHE Z 36 TYR 0.036 0.003 TYR q 31 ARG 0.012 0.001 ARG G 207 *********************** 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 1304 residues out of total 5429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 377 poor density : 927 time to evaluate : 6.973 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: b 212 TRP cc_start: 0.8656 (OUTLIER) cc_final: 0.7887 (p90) REVERT: c 29 VAL cc_start: 0.9120 (OUTLIER) cc_final: 0.8859 (p) REVERT: f 59 ASP cc_start: 0.8308 (p0) cc_final: 0.8081 (p0) REVERT: g 14 SER cc_start: 0.8088 (t) cc_final: 0.7804 (p) REVERT: n 72 ASP cc_start: 0.8149 (t70) cc_final: 0.7456 (t0) REVERT: n 75 ILE cc_start: 0.8993 (mm) cc_final: 0.8307 (mm) REVERT: n 110 MET cc_start: 0.7697 (tpp) cc_final: 0.7368 (mmm) REVERT: s 31 GLN cc_start: 0.8230 (OUTLIER) cc_final: 0.8016 (pm20) REVERT: t 4 GLU cc_start: 0.8369 (mp0) cc_final: 0.7785 (mp0) REVERT: u 67 SER cc_start: 0.8908 (m) cc_final: 0.8447 (t) REVERT: x 69 GLU cc_start: 0.8395 (OUTLIER) cc_final: 0.8025 (mp0) REVERT: y 36 GLN cc_start: 0.8493 (OUTLIER) cc_final: 0.8051 (mm-40) REVERT: A 22 MET cc_start: 0.7600 (ppp) cc_final: 0.7347 (ppp) REVERT: A 64 PHE cc_start: 0.7181 (OUTLIER) cc_final: 0.6881 (m-80) REVERT: C 9 LYS cc_start: 0.7505 (mtpt) cc_final: 0.7035 (mtpt) REVERT: C 13 SER cc_start: 0.8845 (p) cc_final: 0.8493 (p) REVERT: C 27 ARG cc_start: 0.8328 (mtp-110) cc_final: 0.7821 (ptp-170) REVERT: D 29 GLN cc_start: 0.8737 (OUTLIER) cc_final: 0.8138 (mp10) REVERT: G 8 MET cc_start: 0.8273 (ttm) cc_final: 0.8038 (tmm) REVERT: G 49 PHE cc_start: 0.6912 (OUTLIER) cc_final: 0.6277 (p90) REVERT: H 183 TYR cc_start: 0.7400 (t80) cc_final: 0.7000 (t80) REVERT: I 35 GLN cc_start: 0.7657 (mm110) cc_final: 0.7388 (tm-30) REVERT: I 195 ASN cc_start: 0.8140 (t0) cc_final: 0.7685 (p0) REVERT: J 60 GLN cc_start: 0.8843 (tp-100) cc_final: 0.8407 (tp-100) REVERT: J 111 ARG cc_start: 0.8069 (ttm-80) cc_final: 0.7823 (mtp85) REVERT: J 147 ASN cc_start: 0.7830 (OUTLIER) cc_final: 0.7439 (p0) REVERT: K 1 MET cc_start: 0.6342 (OUTLIER) cc_final: 0.5937 (tpt) REVERT: K 40 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7474 (mp0) REVERT: K 45 ARG cc_start: 0.7129 (ptm160) cc_final: 0.6856 (ptp-170) REVERT: K 58 HIS cc_start: 0.7768 (OUTLIER) cc_final: 0.7303 (m90) REVERT: K 93 LYS cc_start: 0.7960 (mttt) cc_final: 0.7396 (mmtt) REVERT: N 5 TYR cc_start: 0.7128 (m-80) cc_final: 0.6806 (m-80) REVERT: N 49 GLN cc_start: 0.7518 (tt0) cc_final: 0.7245 (tt0) REVERT: N 62 LEU cc_start: 0.8798 (mp) cc_final: 0.8328 (mp) REVERT: N 90 ASP cc_start: 0.8219 (p0) cc_final: 0.7875 (p0) REVERT: N 102 PHE cc_start: 0.7603 (m-10) cc_final: 0.7197 (m-80) REVERT: N 106 ASP cc_start: 0.7468 (t0) cc_final: 0.7179 (t0) REVERT: O 63 ASP cc_start: 0.7876 (t0) cc_final: 0.7569 (t0) REVERT: P 56 LYS cc_start: 0.8521 (ptmt) cc_final: 0.8261 (ptmm) REVERT: P 80 ASN cc_start: 0.3014 (OUTLIER) cc_final: 0.2634 (p0) REVERT: R 16 ILE cc_start: 0.7148 (OUTLIER) cc_final: 0.6771 (mt) REVERT: S 32 ASP cc_start: 0.6935 (m-30) cc_final: 0.6696 (m-30) REVERT: S 72 PHE cc_start: 0.6873 (t80) cc_final: 0.6597 (t80) REVERT: S 73 LEU cc_start: 0.7550 (OUTLIER) cc_final: 0.7278 (tt) REVERT: S 85 GLU cc_start: 0.7190 (OUTLIER) cc_final: 0.6844 (pp20) REVERT: S 91 GLU cc_start: 0.7441 (mm-30) cc_final: 0.7194 (mm-30) REVERT: W 24 ASP cc_start: 0.5165 (OUTLIER) cc_final: 0.4340 (p0) REVERT: X 15 LEU cc_start: 0.8145 (tp) cc_final: 0.7840 (tp) REVERT: X 19 GLU cc_start: 0.8791 (OUTLIER) cc_final: 0.8086 (pt0) REVERT: Y 17 ARG cc_start: 0.8720 (ttp80) cc_final: 0.8486 (ttp80) REVERT: Y 24 ARG cc_start: 0.9212 (ttm-80) cc_final: 0.8840 (ttm110) REVERT: Y 38 ILE cc_start: 0.8443 (tt) cc_final: 0.8239 (tp) REVERT: a 163 TYR cc_start: 0.0689 (OUTLIER) cc_final: -0.0086 (p90) REVERT: 8 53 MET cc_start: 0.8598 (tmm) cc_final: 0.8108 (tmm) REVERT: 8 106 LEU cc_start: 0.8363 (pp) cc_final: 0.8120 (pp) REVERT: 8 111 MET cc_start: 0.8254 (mpp) cc_final: 0.7413 (mpp) REVERT: 8 170 GLN cc_start: 0.7422 (OUTLIER) cc_final: 0.7021 (tp-100) REVERT: 8 204 TYR cc_start: 0.7286 (OUTLIER) cc_final: 0.5908 (t80) REVERT: 8 373 GLU cc_start: 0.8440 (OUTLIER) cc_final: 0.7949 (pm20) REVERT: 8 441 GLU cc_start: 0.8229 (OUTLIER) cc_final: 0.7842 (pp20) REVERT: 8 500 ASP cc_start: 0.7179 (p0) cc_final: 0.6943 (p0) outliers start: 377 outliers final: 293 residues processed: 1167 average time/residue: 1.2504 time to fit residues: 2595.9069 Evaluate side-chains 1206 residues out of total 5429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 316 poor density : 890 time to evaluate : 6.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 37 SER Chi-restraints excluded: chain b residue 50 THR Chi-restraints excluded: chain b residue 52 HIS Chi-restraints excluded: chain b residue 71 ASP Chi-restraints excluded: chain b residue 113 ASP Chi-restraints excluded: chain b residue 120 ASP Chi-restraints excluded: chain b residue 129 LEU Chi-restraints excluded: chain b residue 191 LEU Chi-restraints excluded: chain b residue 204 LEU Chi-restraints excluded: chain b residue 212 TRP Chi-restraints excluded: chain c residue 22 ILE Chi-restraints excluded: chain c residue 29 VAL Chi-restraints excluded: chain c residue 146 ILE Chi-restraints excluded: chain c residue 176 ASP Chi-restraints excluded: chain c residue 185 ASN Chi-restraints excluded: chain c residue 200 ASP Chi-restraints excluded: chain d residue 4 VAL Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain d residue 53 THR Chi-restraints excluded: chain d residue 79 ARG Chi-restraints excluded: chain d residue 84 THR Chi-restraints excluded: chain d residue 96 VAL Chi-restraints excluded: chain d residue 108 ILE Chi-restraints excluded: chain d residue 141 MET Chi-restraints excluded: chain d residue 146 VAL Chi-restraints excluded: chain d residue 176 ASP Chi-restraints excluded: chain e residue 3 LEU Chi-restraints excluded: chain e residue 37 MET Chi-restraints excluded: chain e residue 39 VAL Chi-restraints excluded: chain e residue 66 ILE Chi-restraints excluded: chain e residue 84 ILE Chi-restraints excluded: chain e residue 89 THR Chi-restraints excluded: chain e residue 134 GLN Chi-restraints excluded: chain e residue 148 VAL Chi-restraints excluded: chain e residue 154 THR Chi-restraints excluded: chain e residue 157 THR Chi-restraints excluded: chain e residue 158 THR Chi-restraints excluded: chain e residue 173 ASP Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 35 THR Chi-restraints excluded: chain f residue 91 VAL Chi-restraints excluded: chain f residue 113 ASP Chi-restraints excluded: chain f residue 130 ILE Chi-restraints excluded: chain f residue 140 ILE Chi-restraints excluded: chain f residue 147 LEU Chi-restraints excluded: chain f residue 167 VAL Chi-restraints excluded: chain g residue 6 LEU Chi-restraints excluded: chain g residue 44 ILE Chi-restraints excluded: chain i residue 57 VAL Chi-restraints excluded: chain j residue 5 THR Chi-restraints excluded: chain j residue 54 ILE Chi-restraints excluded: chain j residue 71 ASP Chi-restraints excluded: chain j residue 84 ILE Chi-restraints excluded: chain j residue 86 GLN Chi-restraints excluded: chain j residue 109 LEU Chi-restraints excluded: chain k residue 37 ASP Chi-restraints excluded: chain k residue 42 THR Chi-restraints excluded: chain k residue 45 GLU Chi-restraints excluded: chain k residue 65 THR Chi-restraints excluded: chain k residue 77 ILE Chi-restraints excluded: chain k residue 86 LEU Chi-restraints excluded: chain k residue 90 ASN Chi-restraints excluded: chain l residue 89 VAL Chi-restraints excluded: chain l residue 90 VAL Chi-restraints excluded: chain l residue 118 THR Chi-restraints excluded: chain l residue 122 VAL Chi-restraints excluded: chain m residue 12 MET Chi-restraints excluded: chain m residue 67 VAL Chi-restraints excluded: chain m residue 75 GLU Chi-restraints excluded: chain m residue 124 LEU Chi-restraints excluded: chain m residue 134 THR Chi-restraints excluded: chain m residue 136 MET Chi-restraints excluded: chain n residue 15 SER Chi-restraints excluded: chain n residue 33 ILE Chi-restraints excluded: chain n residue 37 THR Chi-restraints excluded: chain n residue 47 VAL Chi-restraints excluded: chain n residue 57 THR Chi-restraints excluded: chain n residue 106 ASP Chi-restraints excluded: chain o residue 39 VAL Chi-restraints excluded: chain o residue 40 ILE Chi-restraints excluded: chain o residue 49 VAL Chi-restraints excluded: chain o residue 53 THR Chi-restraints excluded: chain o residue 56 LYS Chi-restraints excluded: chain o residue 69 ASP Chi-restraints excluded: chain o residue 74 VAL Chi-restraints excluded: chain o residue 87 ILE Chi-restraints excluded: chain o residue 103 VAL Chi-restraints excluded: chain p residue 7 LEU Chi-restraints excluded: chain p residue 18 SER Chi-restraints excluded: chain p residue 35 SER Chi-restraints excluded: chain p residue 85 VAL Chi-restraints excluded: chain p residue 99 LEU Chi-restraints excluded: chain p residue 109 ILE Chi-restraints excluded: chain q residue 86 SER Chi-restraints excluded: chain q residue 94 LEU Chi-restraints excluded: chain q residue 101 ASP Chi-restraints excluded: chain q residue 116 LEU Chi-restraints excluded: chain r residue 6 GLN Chi-restraints excluded: chain r residue 26 ASP Chi-restraints excluded: chain r residue 29 THR Chi-restraints excluded: chain r residue 53 PHE Chi-restraints excluded: chain r residue 54 VAL Chi-restraints excluded: chain s residue 4 ILE Chi-restraints excluded: chain s residue 31 GLN Chi-restraints excluded: chain s residue 103 ILE Chi-restraints excluded: chain s residue 109 ASP Chi-restraints excluded: chain t residue 15 HIS Chi-restraints excluded: chain t residue 25 GLU Chi-restraints excluded: chain t residue 32 LEU Chi-restraints excluded: chain t residue 63 VAL Chi-restraints excluded: chain t residue 78 SER Chi-restraints excluded: chain u residue 11 ILE Chi-restraints excluded: chain u residue 27 VAL Chi-restraints excluded: chain u residue 88 ASP Chi-restraints excluded: chain v residue 40 ILE Chi-restraints excluded: chain v residue 89 ILE Chi-restraints excluded: chain v residue 92 VAL Chi-restraints excluded: chain x residue 39 VAL Chi-restraints excluded: chain x residue 46 VAL Chi-restraints excluded: chain x residue 65 THR Chi-restraints excluded: chain x residue 69 GLU Chi-restraints excluded: chain y residue 36 GLN Chi-restraints excluded: chain y residue 58 ASN Chi-restraints excluded: chain z residue 13 ILE Chi-restraints excluded: chain z residue 16 LEU Chi-restraints excluded: chain z residue 24 LEU Chi-restraints excluded: chain z residue 47 ILE Chi-restraints excluded: chain z residue 50 VAL Chi-restraints excluded: chain z residue 54 VAL Chi-restraints excluded: chain A residue 20 ASN Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 59 ARG Chi-restraints excluded: chain A residue 64 PHE Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain C residue 8 ILE Chi-restraints excluded: chain C residue 19 PHE Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain D residue 29 GLN Chi-restraints excluded: chain E residue 3 ILE Chi-restraints excluded: chain E residue 30 HIS Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain F residue 13 ASN Chi-restraints excluded: chain F residue 20 ASP Chi-restraints excluded: chain G residue 14 HIS Chi-restraints excluded: chain G residue 30 ILE Chi-restraints excluded: chain G residue 49 PHE Chi-restraints excluded: chain G residue 59 ILE Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 191 ASP Chi-restraints excluded: chain H residue 117 ASP Chi-restraints excluded: chain H residue 180 ASP Chi-restraints excluded: chain H residue 199 VAL Chi-restraints excluded: chain H residue 206 ILE Chi-restraints excluded: chain I residue 33 ILE Chi-restraints excluded: chain I residue 109 THR Chi-restraints excluded: chain I residue 124 VAL Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 154 VAL Chi-restraints excluded: chain I residue 168 THR Chi-restraints excluded: chain I residue 205 LYS Chi-restraints excluded: chain J residue 10 LEU Chi-restraints excluded: chain J residue 13 LYS Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 71 ILE Chi-restraints excluded: chain J residue 79 THR Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 140 ILE Chi-restraints excluded: chain J residue 144 GLU Chi-restraints excluded: chain J residue 147 ASN Chi-restraints excluded: chain J residue 155 LYS Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 15 SER Chi-restraints excluded: chain K residue 29 ILE Chi-restraints excluded: chain K residue 40 GLU Chi-restraints excluded: chain K residue 56 LYS Chi-restraints excluded: chain K residue 58 HIS Chi-restraints excluded: chain K residue 61 LEU Chi-restraints excluded: chain L residue 19 SER Chi-restraints excluded: chain L residue 44 SER Chi-restraints excluded: chain L residue 72 VAL Chi-restraints excluded: chain L residue 88 VAL Chi-restraints excluded: chain L residue 93 VAL Chi-restraints excluded: chain L residue 112 ASP Chi-restraints excluded: chain L residue 129 ASN Chi-restraints excluded: chain M residue 60 LEU Chi-restraints excluded: chain M residue 73 SER Chi-restraints excluded: chain M residue 74 ILE Chi-restraints excluded: chain M residue 75 GLN Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain M residue 111 THR Chi-restraints excluded: chain M residue 124 ILE Chi-restraints excluded: chain M residue 125 ILE Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain N residue 20 ILE Chi-restraints excluded: chain N residue 60 LEU Chi-restraints excluded: chain N residue 74 GLN Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 119 LYS Chi-restraints excluded: chain N residue 126 PHE Chi-restraints excluded: chain O residue 15 HIS Chi-restraints excluded: chain O residue 20 GLN Chi-restraints excluded: chain O residue 56 HIS Chi-restraints excluded: chain O residue 59 LYS Chi-restraints excluded: chain O residue 69 THR Chi-restraints excluded: chain O residue 77 VAL Chi-restraints excluded: chain O residue 98 VAL Chi-restraints excluded: chain O residue 100 ILE Chi-restraints excluded: chain P residue 30 ILE Chi-restraints excluded: chain P residue 41 LEU Chi-restraints excluded: chain P residue 51 PHE Chi-restraints excluded: chain P residue 57 SER Chi-restraints excluded: chain P residue 71 ASP Chi-restraints excluded: chain P residue 74 LYS Chi-restraints excluded: chain P residue 80 ASN Chi-restraints excluded: chain P residue 104 PHE Chi-restraints excluded: chain P residue 109 ILE Chi-restraints excluded: chain Q residue 2 THR Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain Q residue 20 VAL Chi-restraints excluded: chain Q residue 34 THR Chi-restraints excluded: chain Q residue 36 VAL Chi-restraints excluded: chain Q residue 38 THR Chi-restraints excluded: chain Q residue 96 THR Chi-restraints excluded: chain Q residue 106 VAL Chi-restraints excluded: chain R residue 3 ILE Chi-restraints excluded: chain R residue 16 ILE Chi-restraints excluded: chain R residue 42 VAL Chi-restraints excluded: chain R residue 63 VAL Chi-restraints excluded: chain R residue 65 GLU Chi-restraints excluded: chain R residue 72 ILE Chi-restraints excluded: chain R residue 97 ARG Chi-restraints excluded: chain R residue 104 ASN Chi-restraints excluded: chain S residue 15 LEU Chi-restraints excluded: chain S residue 17 ASP Chi-restraints excluded: chain S residue 53 ASP Chi-restraints excluded: chain S residue 73 LEU Chi-restraints excluded: chain S residue 85 GLU Chi-restraints excluded: chain T residue 24 THR Chi-restraints excluded: chain T residue 44 GLU Chi-restraints excluded: chain T residue 74 VAL Chi-restraints excluded: chain T residue 82 GLU Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain U residue 21 VAL Chi-restraints excluded: chain U residue 23 ASP Chi-restraints excluded: chain U residue 29 ASN Chi-restraints excluded: chain U residue 33 ILE Chi-restraints excluded: chain U residue 42 ILE Chi-restraints excluded: chain U residue 45 GLU Chi-restraints excluded: chain U residue 46 LYS Chi-restraints excluded: chain U residue 66 THR Chi-restraints excluded: chain V residue 47 ASP Chi-restraints excluded: chain V residue 52 CYS Chi-restraints excluded: chain V residue 54 ILE Chi-restraints excluded: chain V residue 58 VAL Chi-restraints excluded: chain V residue 71 SER Chi-restraints excluded: chain W residue 24 ASP Chi-restraints excluded: chain W residue 27 THR Chi-restraints excluded: chain W residue 38 ILE Chi-restraints excluded: chain W residue 54 LEU Chi-restraints excluded: chain X residue 4 LEU Chi-restraints excluded: chain X residue 12 LEU Chi-restraints excluded: chain X residue 19 GLU Chi-restraints excluded: chain X residue 32 THR Chi-restraints excluded: chain X residue 39 ILE Chi-restraints excluded: chain X residue 47 THR Chi-restraints excluded: chain Y residue 31 ILE Chi-restraints excluded: chain Y residue 57 VAL Chi-restraints excluded: chain Z residue 11 PHE Chi-restraints excluded: chain Z residue 63 ASN Chi-restraints excluded: chain Z residue 67 THR Chi-restraints excluded: chain a residue 41 SER Chi-restraints excluded: chain a residue 50 ILE Chi-restraints excluded: chain a residue 56 ASP Chi-restraints excluded: chain a residue 163 TYR Chi-restraints excluded: chain a residue 172 HIS Chi-restraints excluded: chain a residue 175 ILE Chi-restraints excluded: chain a residue 212 VAL Chi-restraints excluded: chain a residue 216 THR Chi-restraints excluded: chain 8 residue 4 THR Chi-restraints excluded: chain 8 residue 19 ILE Chi-restraints excluded: chain 8 residue 36 VAL Chi-restraints excluded: chain 8 residue 52 TRP Chi-restraints excluded: chain 8 residue 64 THR Chi-restraints excluded: chain 8 residue 80 GLU Chi-restraints excluded: chain 8 residue 105 VAL Chi-restraints excluded: chain 8 residue 141 VAL Chi-restraints excluded: chain 8 residue 154 VAL Chi-restraints excluded: chain 8 residue 170 GLN Chi-restraints excluded: chain 8 residue 176 GLU Chi-restraints excluded: chain 8 residue 182 VAL Chi-restraints excluded: chain 8 residue 204 TYR Chi-restraints excluded: chain 8 residue 234 MET Chi-restraints excluded: chain 8 residue 266 CYS Chi-restraints excluded: chain 8 residue 300 ASP Chi-restraints excluded: chain 8 residue 334 THR Chi-restraints excluded: chain 8 residue 338 VAL Chi-restraints excluded: chain 8 residue 373 GLU Chi-restraints excluded: chain 8 residue 401 ASP Chi-restraints excluded: chain 8 residue 441 GLU Chi-restraints excluded: chain 8 residue 466 LEU Chi-restraints excluded: chain 8 residue 518 VAL Chi-restraints excluded: chain 8 residue 519 VAL Chi-restraints excluded: chain 8 residue 681 THR 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: 20.0000 chunk 638 optimal weight: 20.0000 chunk 321 optimal weight: 3.9990 chunk 210 optimal weight: 9.9990 chunk 207 optimal weight: 5.9990 chunk 679 optimal weight: 20.0000 chunk 728 optimal weight: 10.0000 chunk 528 optimal weight: 5.9990 chunk 99 optimal weight: 8.9990 chunk 840 optimal weight: 20.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 116 GLN ** b 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 134 HIS ** c 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 40 GLN ** s 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 39 ASN ** y 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 130 ASN ** J 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 80 HIS O 70 HIS Q 76 HIS T 79 GLN U 18 GLN ** X 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.4313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 166269 Z= 0.271 Angle : 0.666 13.313 247957 Z= 0.344 Chirality : 0.038 0.378 31576 Planarity : 0.005 0.097 13872 Dihedral : 23.652 179.380 81266 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 17.49 Ramachandran Plot: Outliers : 0.11 % Allowed : 11.16 % Favored : 88.74 % Rotamer: Outliers : 6.10 % Allowed : 21.57 % Favored : 72.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.29 (0.10), residues: 6517 helix: -0.28 (0.11), residues: 2074 sheet: -1.67 (0.15), residues: 1101 loop : -2.31 (0.10), residues: 3342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP b 212 HIS 0.012 0.001 HIS L 141 PHE 0.033 0.002 PHE Z 36 TYR 0.030 0.002 TYR q 31 ARG 0.016 0.001 ARG G 34 *********************** 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 1291 residues out of total 5429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 331 poor density : 960 time to evaluate : 6.743 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: b 212 TRP cc_start: 0.8583 (OUTLIER) cc_final: 0.7890 (p90) REVERT: c 29 VAL cc_start: 0.9064 (OUTLIER) cc_final: 0.8781 (p) REVERT: e 31 GLU cc_start: 0.8078 (mt-10) cc_final: 0.7841 (mt-10) REVERT: e 95 MET cc_start: 0.7570 (ttp) cc_final: 0.6172 (tmm) REVERT: f 169 ARG cc_start: 0.7945 (mmp80) cc_final: 0.7496 (mmp80) REVERT: g 14 SER cc_start: 0.7924 (t) cc_final: 0.7659 (p) REVERT: n 72 ASP cc_start: 0.8089 (t70) cc_final: 0.7380 (t0) REVERT: n 75 ILE cc_start: 0.8958 (mm) cc_final: 0.8299 (mm) REVERT: r 60 LYS cc_start: 0.8950 (ttpt) cc_final: 0.8695 (ttpp) REVERT: t 4 GLU cc_start: 0.8557 (mp0) cc_final: 0.8029 (mp0) REVERT: t 56 GLU cc_start: 0.8494 (mm-30) cc_final: 0.7821 (mp0) REVERT: u 67 SER cc_start: 0.8874 (m) cc_final: 0.8406 (t) REVERT: A 64 PHE cc_start: 0.7093 (OUTLIER) cc_final: 0.6749 (m-80) REVERT: C 19 PHE cc_start: 0.7678 (OUTLIER) cc_final: 0.7365 (p90) REVERT: C 27 ARG cc_start: 0.8443 (mtp-110) cc_final: 0.7901 (ptp-170) REVERT: G 8 MET cc_start: 0.8065 (ttm) cc_final: 0.7827 (tmm) REVERT: G 34 ARG cc_start: 0.5534 (mmp80) cc_final: 0.4085 (tpt170) REVERT: G 49 PHE cc_start: 0.6877 (OUTLIER) cc_final: 0.6273 (p90) REVERT: H 17 TRP cc_start: 0.7962 (m-10) cc_final: 0.7661 (m-10) REVERT: H 183 TYR cc_start: 0.7472 (t80) cc_final: 0.7070 (t80) REVERT: I 35 GLN cc_start: 0.7692 (mm110) cc_final: 0.7467 (tm-30) REVERT: I 104 MET cc_start: 0.8720 (mmm) cc_final: 0.8462 (tpt) REVERT: I 195 ASN cc_start: 0.8141 (t0) cc_final: 0.7700 (p0) REVERT: J 60 GLN cc_start: 0.8733 (tp-100) cc_final: 0.8129 (tp-100) REVERT: K 1 MET cc_start: 0.6774 (OUTLIER) cc_final: 0.6519 (tpt) REVERT: K 45 ARG cc_start: 0.7127 (ptm160) cc_final: 0.6874 (ptp-170) REVERT: K 79 ARG cc_start: 0.8356 (OUTLIER) cc_final: 0.8073 (ptp90) REVERT: K 93 LYS cc_start: 0.7911 (mttt) cc_final: 0.7428 (mttp) REVERT: L 25 PHE cc_start: 0.7493 (t80) cc_final: 0.7281 (m-80) REVERT: N 5 TYR cc_start: 0.7376 (m-80) cc_final: 0.7133 (m-80) REVERT: N 49 GLN cc_start: 0.7544 (tt0) cc_final: 0.7260 (tt0) REVERT: N 62 LEU cc_start: 0.8892 (mp) cc_final: 0.8424 (mp) REVERT: N 90 ASP cc_start: 0.8235 (p0) cc_final: 0.7881 (p0) REVERT: N 102 PHE cc_start: 0.7574 (m-80) cc_final: 0.7191 (m-80) REVERT: N 106 ASP cc_start: 0.7321 (t0) cc_final: 0.7073 (t0) REVERT: O 63 ASP cc_start: 0.7981 (t0) cc_final: 0.7655 (t0) REVERT: R 16 ILE cc_start: 0.7063 (OUTLIER) cc_final: 0.6788 (mt) REVERT: S 32 ASP cc_start: 0.6815 (m-30) cc_final: 0.6542 (m-30) REVERT: S 72 PHE cc_start: 0.6919 (t80) cc_final: 0.6593 (t80) REVERT: S 73 LEU cc_start: 0.7614 (OUTLIER) cc_final: 0.7360 (tt) REVERT: S 85 GLU cc_start: 0.7200 (OUTLIER) cc_final: 0.6953 (pp20) REVERT: S 91 GLU cc_start: 0.7500 (mm-30) cc_final: 0.7252 (mm-30) REVERT: T 78 THR cc_start: 0.8844 (m) cc_final: 0.8248 (t) REVERT: V 25 GLU cc_start: 0.8434 (mp0) cc_final: 0.8224 (mp0) REVERT: W 24 ASP cc_start: 0.4684 (OUTLIER) cc_final: 0.3924 (p0) REVERT: X 15 LEU cc_start: 0.8098 (tp) cc_final: 0.7737 (tt) REVERT: X 19 GLU cc_start: 0.8707 (OUTLIER) cc_final: 0.7879 (pt0) REVERT: Y 17 ARG cc_start: 0.8672 (ttp80) cc_final: 0.8456 (ttp80) REVERT: Y 24 ARG cc_start: 0.9138 (ttm-80) cc_final: 0.8861 (ttm110) REVERT: Y 59 ARG cc_start: 0.7281 (OUTLIER) cc_final: 0.6833 (mtm180) REVERT: a 163 TYR cc_start: 0.0554 (OUTLIER) cc_final: -0.0016 (p90) REVERT: 8 53 MET cc_start: 0.8571 (tmm) cc_final: 0.8107 (tmm) REVERT: 8 106 LEU cc_start: 0.8317 (pp) cc_final: 0.8080 (pp) REVERT: 8 111 MET cc_start: 0.8221 (mpp) cc_final: 0.7420 (mpp) REVERT: 8 170 GLN cc_start: 0.7572 (OUTLIER) cc_final: 0.6949 (tp-100) REVERT: 8 204 TYR cc_start: 0.7267 (OUTLIER) cc_final: 0.5952 (t80) REVERT: 8 366 MET cc_start: 0.5338 (mmm) cc_final: 0.4844 (mmm) REVERT: 8 427 ASP cc_start: 0.7130 (t0) cc_final: 0.6881 (t0) REVERT: 8 441 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7823 (pp20) outliers start: 331 outliers final: 264 residues processed: 1156 average time/residue: 1.3820 time to fit residues: 2861.3136 Evaluate side-chains 1202 residues out of total 5429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 281 poor density : 921 time to evaluate : 6.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 37 SER Chi-restraints excluded: chain b residue 52 HIS Chi-restraints excluded: chain b residue 71 ASP Chi-restraints excluded: chain b residue 113 ASP Chi-restraints excluded: chain b residue 120 ASP Chi-restraints excluded: chain b residue 129 LEU Chi-restraints excluded: chain b residue 191 LEU Chi-restraints excluded: chain b residue 204 LEU Chi-restraints excluded: chain b residue 212 TRP Chi-restraints excluded: chain b residue 215 VAL Chi-restraints excluded: chain b residue 227 VAL Chi-restraints excluded: chain c residue 22 ILE Chi-restraints excluded: chain c residue 29 VAL Chi-restraints excluded: chain c residue 146 ILE Chi-restraints excluded: chain c residue 177 VAL Chi-restraints excluded: chain c residue 185 ASN Chi-restraints excluded: chain c residue 200 ASP Chi-restraints excluded: chain d residue 4 VAL Chi-restraints excluded: chain d residue 53 THR Chi-restraints excluded: chain d residue 79 ARG Chi-restraints excluded: chain d residue 108 ILE Chi-restraints excluded: chain d residue 141 MET Chi-restraints excluded: chain d residue 176 ASP Chi-restraints excluded: chain e residue 39 VAL Chi-restraints excluded: chain e residue 84 ILE Chi-restraints excluded: chain e residue 89 THR Chi-restraints excluded: chain e residue 134 GLN Chi-restraints excluded: chain e residue 148 VAL Chi-restraints excluded: chain e residue 154 THR Chi-restraints excluded: chain e residue 157 THR Chi-restraints excluded: chain e residue 158 THR Chi-restraints excluded: chain e residue 173 ASP Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 91 VAL Chi-restraints excluded: chain f residue 113 ASP Chi-restraints excluded: chain f residue 130 ILE Chi-restraints excluded: chain f residue 140 ILE Chi-restraints excluded: chain f residue 147 LEU Chi-restraints excluded: chain f residue 167 VAL Chi-restraints excluded: chain g residue 6 LEU Chi-restraints excluded: chain g residue 44 ILE Chi-restraints excluded: chain g residue 87 GLU Chi-restraints excluded: chain g residue 94 ILE Chi-restraints excluded: chain i residue 8 VAL Chi-restraints excluded: chain i residue 57 VAL Chi-restraints excluded: chain j residue 5 THR Chi-restraints excluded: chain j residue 54 ILE Chi-restraints excluded: chain j residue 57 LEU Chi-restraints excluded: chain j residue 71 ASP Chi-restraints excluded: chain j residue 86 GLN Chi-restraints excluded: chain j residue 109 LEU Chi-restraints excluded: chain k residue 37 ASP Chi-restraints excluded: chain k residue 42 THR Chi-restraints excluded: chain k residue 45 GLU Chi-restraints excluded: chain k residue 65 THR Chi-restraints excluded: chain k residue 69 VAL Chi-restraints excluded: chain k residue 77 ILE Chi-restraints excluded: chain k residue 86 LEU Chi-restraints excluded: chain k residue 90 ASN Chi-restraints excluded: chain l residue 118 THR Chi-restraints excluded: chain l residue 122 VAL Chi-restraints excluded: chain m residue 12 MET Chi-restraints excluded: chain m residue 67 VAL Chi-restraints excluded: chain m residue 75 GLU Chi-restraints excluded: chain m residue 124 LEU Chi-restraints excluded: chain m residue 134 THR Chi-restraints excluded: chain m residue 136 MET Chi-restraints excluded: chain n residue 15 SER Chi-restraints excluded: chain n residue 33 ILE Chi-restraints excluded: chain n residue 37 THR Chi-restraints excluded: chain n residue 57 THR Chi-restraints excluded: chain o residue 39 VAL Chi-restraints excluded: chain o residue 40 ILE Chi-restraints excluded: chain o residue 53 THR Chi-restraints excluded: chain o residue 56 LYS Chi-restraints excluded: chain o residue 69 ASP Chi-restraints excluded: chain o residue 74 VAL Chi-restraints excluded: chain o residue 87 ILE Chi-restraints excluded: chain o residue 103 VAL Chi-restraints excluded: chain p residue 35 SER Chi-restraints excluded: chain p residue 40 GLN Chi-restraints excluded: chain p residue 85 VAL Chi-restraints excluded: chain p residue 99 LEU Chi-restraints excluded: chain p residue 109 ILE Chi-restraints excluded: chain q residue 86 SER Chi-restraints excluded: chain q residue 94 LEU Chi-restraints excluded: chain q residue 101 ASP Chi-restraints excluded: chain r residue 6 GLN Chi-restraints excluded: chain r residue 29 THR Chi-restraints excluded: chain r residue 53 PHE Chi-restraints excluded: chain r residue 54 VAL Chi-restraints excluded: chain s residue 4 ILE Chi-restraints excluded: chain s residue 103 ILE Chi-restraints excluded: chain s residue 109 ASP Chi-restraints excluded: chain t residue 25 GLU Chi-restraints excluded: chain t residue 32 LEU Chi-restraints excluded: chain t residue 63 VAL Chi-restraints excluded: chain u residue 11 ILE Chi-restraints excluded: chain v residue 92 VAL Chi-restraints excluded: chain w residue 77 SER Chi-restraints excluded: chain x residue 39 VAL Chi-restraints excluded: chain x residue 46 VAL Chi-restraints excluded: chain x residue 65 THR Chi-restraints excluded: chain x residue 69 GLU Chi-restraints excluded: chain y residue 11 VAL Chi-restraints excluded: chain y residue 58 ASN Chi-restraints excluded: chain z residue 13 ILE Chi-restraints excluded: chain z residue 16 LEU Chi-restraints excluded: chain z residue 24 LEU Chi-restraints excluded: chain z residue 47 ILE Chi-restraints excluded: chain z residue 50 VAL Chi-restraints excluded: chain z residue 54 VAL Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 59 ARG Chi-restraints excluded: chain A residue 64 PHE Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain C residue 8 ILE Chi-restraints excluded: chain C residue 19 PHE Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain E residue 3 ILE Chi-restraints excluded: chain E residue 30 HIS Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain F residue 13 ASN Chi-restraints excluded: chain F residue 20 ASP Chi-restraints excluded: chain G residue 14 HIS Chi-restraints excluded: chain G residue 30 ILE Chi-restraints excluded: chain G residue 49 PHE Chi-restraints excluded: chain G residue 59 ILE Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 191 ASP Chi-restraints excluded: chain G residue 207 ARG Chi-restraints excluded: chain H residue 180 ASP Chi-restraints excluded: chain H residue 199 VAL Chi-restraints excluded: chain H residue 206 ILE Chi-restraints excluded: chain I residue 33 ILE Chi-restraints excluded: chain I residue 124 VAL Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 130 ASN Chi-restraints excluded: chain I residue 154 VAL Chi-restraints excluded: chain I residue 168 THR Chi-restraints excluded: chain J residue 10 LEU Chi-restraints excluded: chain J residue 13 LYS Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 47 PHE Chi-restraints excluded: chain J residue 71 ILE Chi-restraints excluded: chain J residue 79 THR Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 144 GLU Chi-restraints excluded: chain J residue 155 LYS Chi-restraints excluded: chain J residue 160 VAL Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 15 SER Chi-restraints excluded: chain K residue 29 ILE Chi-restraints excluded: chain K residue 56 LYS Chi-restraints excluded: chain K residue 58 HIS Chi-restraints excluded: chain K residue 61 LEU Chi-restraints excluded: chain K residue 79 ARG Chi-restraints excluded: chain L residue 19 SER Chi-restraints excluded: chain L residue 44 SER Chi-restraints excluded: chain L residue 72 VAL Chi-restraints excluded: chain L residue 88 VAL Chi-restraints excluded: chain L residue 93 VAL Chi-restraints excluded: chain L residue 112 ASP Chi-restraints excluded: chain L residue 129 ASN Chi-restraints excluded: chain M residue 74 ILE Chi-restraints excluded: chain M residue 111 THR Chi-restraints excluded: chain M residue 124 ILE Chi-restraints excluded: chain M residue 125 ILE Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain N residue 20 ILE Chi-restraints excluded: chain N residue 60 LEU Chi-restraints excluded: chain N residue 74 GLN Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 119 LYS Chi-restraints excluded: chain N residue 126 PHE Chi-restraints excluded: chain O residue 15 HIS Chi-restraints excluded: chain O residue 20 GLN Chi-restraints excluded: chain O residue 49 PHE Chi-restraints excluded: chain O residue 56 HIS Chi-restraints excluded: chain O residue 59 LYS Chi-restraints excluded: chain O residue 64 GLN Chi-restraints excluded: chain O residue 69 THR Chi-restraints excluded: chain O residue 77 VAL Chi-restraints excluded: chain O residue 98 VAL Chi-restraints excluded: chain O residue 100 ILE Chi-restraints excluded: chain P residue 30 ILE Chi-restraints excluded: chain P residue 41 LEU Chi-restraints excluded: chain P residue 51 PHE Chi-restraints excluded: chain P residue 57 SER Chi-restraints excluded: chain P residue 71 ASP Chi-restraints excluded: chain P residue 74 LYS Chi-restraints excluded: chain P residue 80 ASN Chi-restraints excluded: chain P residue 104 PHE Chi-restraints excluded: chain P residue 109 ILE Chi-restraints excluded: chain Q residue 2 THR Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain Q residue 34 THR Chi-restraints excluded: chain Q residue 36 VAL Chi-restraints excluded: chain Q residue 38 THR Chi-restraints excluded: chain Q residue 76 HIS Chi-restraints excluded: chain Q residue 96 THR Chi-restraints excluded: chain Q residue 101 LEU Chi-restraints excluded: chain R residue 3 ILE Chi-restraints excluded: chain R residue 16 ILE Chi-restraints excluded: chain R residue 63 VAL Chi-restraints excluded: chain R residue 65 GLU Chi-restraints excluded: chain R residue 67 ASP Chi-restraints excluded: chain R residue 104 ASN Chi-restraints excluded: chain S residue 15 LEU Chi-restraints excluded: chain S residue 53 ASP Chi-restraints excluded: chain S residue 73 LEU Chi-restraints excluded: chain S residue 85 GLU Chi-restraints excluded: chain T residue 44 GLU Chi-restraints excluded: chain T residue 74 VAL Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain U residue 21 VAL Chi-restraints excluded: chain U residue 23 ASP Chi-restraints excluded: chain U residue 29 ASN Chi-restraints excluded: chain U residue 42 ILE Chi-restraints excluded: chain U residue 45 GLU Chi-restraints excluded: chain U residue 46 LYS Chi-restraints excluded: chain U residue 66 THR Chi-restraints excluded: chain U residue 75 ILE Chi-restraints excluded: chain V residue 54 ILE Chi-restraints excluded: chain V residue 58 VAL Chi-restraints excluded: chain V residue 71 SER Chi-restraints excluded: chain W residue 24 ASP Chi-restraints excluded: chain W residue 27 THR Chi-restraints excluded: chain W residue 54 LEU Chi-restraints excluded: chain X residue 4 LEU Chi-restraints excluded: chain X residue 12 LEU Chi-restraints excluded: chain X residue 19 GLU Chi-restraints excluded: chain X residue 32 THR Chi-restraints excluded: chain X residue 39 ILE Chi-restraints excluded: chain X residue 47 THR Chi-restraints excluded: chain Y residue 35 TYR Chi-restraints excluded: chain Y residue 59 ARG Chi-restraints excluded: chain Z residue 11 PHE Chi-restraints excluded: chain Z residue 63 ASN Chi-restraints excluded: chain a residue 50 ILE Chi-restraints excluded: chain a residue 56 ASP Chi-restraints excluded: chain a residue 163 TYR Chi-restraints excluded: chain a residue 172 HIS Chi-restraints excluded: chain a residue 175 ILE Chi-restraints excluded: chain a residue 212 VAL Chi-restraints excluded: chain a residue 214 ILE Chi-restraints excluded: chain a residue 216 THR Chi-restraints excluded: chain 8 residue 4 THR Chi-restraints excluded: chain 8 residue 19 ILE Chi-restraints excluded: chain 8 residue 52 TRP Chi-restraints excluded: chain 8 residue 64 THR Chi-restraints excluded: chain 8 residue 105 VAL Chi-restraints excluded: chain 8 residue 141 VAL Chi-restraints excluded: chain 8 residue 154 VAL Chi-restraints excluded: chain 8 residue 170 GLN Chi-restraints excluded: chain 8 residue 176 GLU Chi-restraints excluded: chain 8 residue 183 VAL Chi-restraints excluded: chain 8 residue 204 TYR Chi-restraints excluded: chain 8 residue 234 MET Chi-restraints excluded: chain 8 residue 300 ASP Chi-restraints excluded: chain 8 residue 334 THR Chi-restraints excluded: chain 8 residue 338 VAL Chi-restraints excluded: chain 8 residue 401 ASP Chi-restraints excluded: chain 8 residue 441 GLU Chi-restraints excluded: chain 8 residue 466 LEU Chi-restraints excluded: chain 8 residue 518 VAL Chi-restraints excluded: chain 8 residue 519 VAL Chi-restraints excluded: chain 8 residue 544 VAL Chi-restraints excluded: chain 8 residue 681 THR 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: 40.0000 chunk 996 optimal weight: 10.0000 chunk 1023 optimal weight: 10.0000 chunk 599 optimal weight: 20.0000 chunk 433 optimal weight: 8.9990 chunk 782 optimal weight: 10.0000 chunk 305 optimal weight: 40.0000 chunk 900 optimal weight: 10.0000 chunk 942 optimal weight: 20.0000 overall best weight: 9.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 134 HIS e 134 GLN i 42 ASN ** j 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 51 GLN ** s 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 39 ASN ** y 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 130 ASN J 11 GLN ** J 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 80 HIS O 70 HIS R 90 HIS ** R 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 18 GLN ** X 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 530 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.4424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.092 166269 Z= 0.366 Angle : 0.734 13.916 247957 Z= 0.376 Chirality : 0.041 0.391 31576 Planarity : 0.006 0.095 13872 Dihedral : 23.673 179.694 81262 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 19.59 Ramachandran Plot: Outliers : 0.11 % Allowed : 12.78 % Favored : 87.11 % Rotamer: Outliers : 5.99 % Allowed : 22.14 % Favored : 71.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.35 (0.10), residues: 6517 helix: -0.38 (0.11), residues: 2093 sheet: -1.69 (0.15), residues: 1100 loop : -2.34 (0.10), residues: 3324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP b 212 HIS 0.018 0.002 HIS L 141 PHE 0.091 0.002 PHE g 29 TYR 0.038 0.002 TYR q 31 ARG 0.014 0.001 ARG G 207 *********************** 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 1249 residues out of total 5429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 325 poor density : 924 time to evaluate : 6.262 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: b 212 TRP cc_start: 0.8619 (OUTLIER) cc_final: 0.7916 (p90) REVERT: b 265 PHE cc_start: 0.8622 (m-80) cc_final: 0.8399 (m-80) REVERT: c 29 VAL cc_start: 0.9097 (OUTLIER) cc_final: 0.8801 (p) REVERT: e 95 MET cc_start: 0.7478 (ttp) cc_final: 0.6333 (tmm) REVERT: g 14 SER cc_start: 0.7992 (t) cc_final: 0.7712 (p) REVERT: n 72 ASP cc_start: 0.8126 (t70) cc_final: 0.7408 (t0) REVERT: n 75 ILE cc_start: 0.8982 (mm) cc_final: 0.8359 (mm) REVERT: r 34 GLU cc_start: 0.8395 (mm-30) cc_final: 0.8059 (mm-30) REVERT: r 60 LYS cc_start: 0.8920 (ttpt) cc_final: 0.8659 (ttpp) REVERT: t 4 GLU cc_start: 0.8641 (mp0) cc_final: 0.8033 (mp0) REVERT: t 89 GLU cc_start: 0.7770 (mm-30) cc_final: 0.7531 (mm-30) REVERT: u 67 SER cc_start: 0.8895 (m) cc_final: 0.8477 (t) REVERT: x 69 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.8024 (mp0) REVERT: A 64 PHE cc_start: 0.7268 (OUTLIER) cc_final: 0.6928 (m-80) REVERT: C 9 LYS cc_start: 0.7475 (mtpt) cc_final: 0.7060 (mtpt) REVERT: C 27 ARG cc_start: 0.8425 (mtp-110) cc_final: 0.7835 (ptp-170) REVERT: F 36 ARG cc_start: 0.8825 (OUTLIER) cc_final: 0.8336 (ttm-80) REVERT: G 8 MET cc_start: 0.8208 (ttm) cc_final: 0.8003 (tmm) REVERT: G 49 PHE cc_start: 0.6901 (OUTLIER) cc_final: 0.6290 (p90) REVERT: H 17 TRP cc_start: 0.7969 (m-10) cc_final: 0.7666 (m-10) REVERT: H 183 TYR cc_start: 0.7431 (t80) cc_final: 0.7020 (t80) REVERT: I 35 GLN cc_start: 0.7711 (mm110) cc_final: 0.7479 (tm-30) REVERT: I 195 ASN cc_start: 0.8191 (t0) cc_final: 0.7674 (p0) REVERT: J 60 GLN cc_start: 0.8783 (tp-100) cc_final: 0.8268 (tp-100) REVERT: K 1 MET cc_start: 0.6830 (OUTLIER) cc_final: 0.6595 (tpt) REVERT: K 8 PHE cc_start: 0.7549 (p90) cc_final: 0.7273 (p90) REVERT: K 40 GLU cc_start: 0.7864 (OUTLIER) cc_final: 0.7441 (mp0) REVERT: K 45 ARG cc_start: 0.7154 (ptm160) cc_final: 0.6942 (ptp-170) REVERT: K 79 ARG cc_start: 0.8458 (OUTLIER) cc_final: 0.8211 (ptp90) REVERT: K 93 LYS cc_start: 0.7967 (mttt) cc_final: 0.7449 (mttp) REVERT: L 25 PHE cc_start: 0.7560 (t80) cc_final: 0.7322 (m-80) REVERT: L 102 TRP cc_start: 0.6930 (m-10) cc_final: 0.6710 (m-10) REVERT: N 5 TYR cc_start: 0.7355 (m-80) cc_final: 0.7100 (m-80) REVERT: N 49 GLN cc_start: 0.7572 (tt0) cc_final: 0.7306 (tt0) REVERT: N 62 LEU cc_start: 0.8878 (mp) cc_final: 0.8421 (mp) REVERT: N 90 ASP cc_start: 0.8229 (p0) cc_final: 0.7881 (p0) REVERT: N 102 PHE cc_start: 0.7565 (m-80) cc_final: 0.7179 (m-80) REVERT: N 106 ASP cc_start: 0.7427 (t0) cc_final: 0.7175 (t0) REVERT: O 63 ASP cc_start: 0.7924 (t0) cc_final: 0.7620 (t0) REVERT: R 16 ILE cc_start: 0.7029 (OUTLIER) cc_final: 0.6724 (mt) REVERT: S 32 ASP cc_start: 0.6899 (m-30) cc_final: 0.6632 (m-30) REVERT: S 72 PHE cc_start: 0.6915 (t80) cc_final: 0.6623 (t80) REVERT: S 73 LEU cc_start: 0.7612 (OUTLIER) cc_final: 0.7356 (tt) REVERT: S 85 GLU cc_start: 0.7145 (OUTLIER) cc_final: 0.6801 (pp20) REVERT: S 91 GLU cc_start: 0.7332 (mm-30) cc_final: 0.7073 (mm-30) REVERT: W 24 ASP cc_start: 0.4885 (OUTLIER) cc_final: 0.3980 (p0) REVERT: X 15 LEU cc_start: 0.8123 (tp) cc_final: 0.7787 (tt) REVERT: X 19 GLU cc_start: 0.8769 (OUTLIER) cc_final: 0.7930 (pt0) REVERT: Y 17 ARG cc_start: 0.8692 (ttp80) cc_final: 0.8454 (ttp80) REVERT: Y 24 ARG cc_start: 0.9181 (ttm-80) cc_final: 0.8896 (ttm110) REVERT: Y 59 ARG cc_start: 0.7335 (OUTLIER) cc_final: 0.6794 (ttm170) REVERT: a 14 LYS cc_start: 0.5776 (mmtt) cc_final: 0.5568 (mtmt) REVERT: a 163 TYR cc_start: 0.0387 (OUTLIER) cc_final: -0.0271 (p90) REVERT: 8 53 MET cc_start: 0.8589 (tmm) cc_final: 0.8120 (tmm) REVERT: 8 75 MET cc_start: 0.6177 (ppp) cc_final: 0.4235 (tpp) REVERT: 8 106 LEU cc_start: 0.8345 (pp) cc_final: 0.8110 (pp) REVERT: 8 111 MET cc_start: 0.8181 (mpp) cc_final: 0.7316 (mpp) REVERT: 8 170 GLN cc_start: 0.7666 (OUTLIER) cc_final: 0.6969 (tp-100) REVERT: 8 204 TYR cc_start: 0.7219 (OUTLIER) cc_final: 0.5987 (t80) REVERT: 8 366 MET cc_start: 0.5210 (mmm) cc_final: 0.4733 (mmm) REVERT: 8 427 ASP cc_start: 0.7142 (t0) cc_final: 0.6908 (t0) REVERT: 8 441 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.7825 (pp20) outliers start: 325 outliers final: 281 residues processed: 1122 average time/residue: 1.2404 time to fit residues: 2476.8419 Evaluate side-chains 1204 residues out of total 5429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 300 poor density : 904 time to evaluate : 6.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 37 SER Chi-restraints excluded: chain b residue 52 HIS Chi-restraints excluded: chain b residue 71 ASP Chi-restraints excluded: chain b residue 113 ASP Chi-restraints excluded: chain b residue 120 ASP Chi-restraints excluded: chain b residue 129 LEU Chi-restraints excluded: chain b residue 191 LEU Chi-restraints excluded: chain b residue 204 LEU Chi-restraints excluded: chain b residue 212 TRP Chi-restraints excluded: chain b residue 215 VAL Chi-restraints excluded: chain b residue 227 VAL Chi-restraints excluded: chain c residue 22 ILE Chi-restraints excluded: chain c residue 29 VAL Chi-restraints excluded: chain c residue 146 ILE Chi-restraints excluded: chain c residue 176 ASP Chi-restraints excluded: chain c residue 185 ASN Chi-restraints excluded: chain c residue 200 ASP Chi-restraints excluded: chain d residue 4 VAL Chi-restraints excluded: chain d residue 53 THR Chi-restraints excluded: chain d residue 79 ARG Chi-restraints excluded: chain d residue 108 ILE Chi-restraints excluded: chain d residue 141 MET Chi-restraints excluded: chain d residue 176 ASP Chi-restraints excluded: chain e residue 37 MET Chi-restraints excluded: chain e residue 39 VAL Chi-restraints excluded: chain e residue 84 ILE Chi-restraints excluded: chain e residue 89 THR Chi-restraints excluded: chain e residue 134 GLN Chi-restraints excluded: chain e residue 148 VAL Chi-restraints excluded: chain e residue 154 THR Chi-restraints excluded: chain e residue 157 THR Chi-restraints excluded: chain e residue 158 THR Chi-restraints excluded: chain e residue 173 ASP Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 42 VAL Chi-restraints excluded: chain f residue 61 TRP Chi-restraints excluded: chain f residue 91 VAL Chi-restraints excluded: chain f residue 113 ASP Chi-restraints excluded: chain f residue 130 ILE Chi-restraints excluded: chain f residue 140 ILE Chi-restraints excluded: chain f residue 147 LEU Chi-restraints excluded: chain f residue 167 VAL Chi-restraints excluded: chain g residue 6 LEU Chi-restraints excluded: chain g residue 44 ILE Chi-restraints excluded: chain g residue 87 GLU Chi-restraints excluded: chain g residue 94 ILE Chi-restraints excluded: chain g residue 134 VAL Chi-restraints excluded: chain i residue 57 VAL Chi-restraints excluded: chain j residue 5 THR Chi-restraints excluded: chain j residue 54 ILE Chi-restraints excluded: chain j residue 57 LEU Chi-restraints excluded: chain j residue 71 ASP Chi-restraints excluded: chain j residue 86 GLN Chi-restraints excluded: chain j residue 109 LEU Chi-restraints excluded: chain k residue 37 ASP Chi-restraints excluded: chain k residue 42 THR Chi-restraints excluded: chain k residue 45 GLU Chi-restraints excluded: chain k residue 65 THR Chi-restraints excluded: chain k residue 69 VAL Chi-restraints excluded: chain k residue 77 ILE Chi-restraints excluded: chain k residue 86 LEU Chi-restraints excluded: chain k residue 90 ASN Chi-restraints excluded: chain l residue 89 VAL Chi-restraints excluded: chain l residue 118 THR Chi-restraints excluded: chain l residue 122 VAL Chi-restraints excluded: chain m residue 12 MET Chi-restraints excluded: chain m residue 67 VAL Chi-restraints excluded: chain m residue 75 GLU Chi-restraints excluded: chain m residue 124 LEU Chi-restraints excluded: chain m residue 134 THR Chi-restraints excluded: chain m residue 136 MET Chi-restraints excluded: chain n residue 15 SER Chi-restraints excluded: chain n residue 33 ILE Chi-restraints excluded: chain n residue 37 THR Chi-restraints excluded: chain n residue 57 THR Chi-restraints excluded: chain o residue 39 VAL Chi-restraints excluded: chain o residue 40 ILE Chi-restraints excluded: chain o residue 49 VAL Chi-restraints excluded: chain o residue 53 THR Chi-restraints excluded: chain o residue 56 LYS Chi-restraints excluded: chain o residue 69 ASP Chi-restraints excluded: chain o residue 74 VAL Chi-restraints excluded: chain o residue 87 ILE Chi-restraints excluded: chain o residue 103 VAL Chi-restraints excluded: chain p residue 35 SER Chi-restraints excluded: chain p residue 85 VAL Chi-restraints excluded: chain p residue 99 LEU Chi-restraints excluded: chain p residue 109 ILE Chi-restraints excluded: chain q residue 86 SER Chi-restraints excluded: chain q residue 94 LEU Chi-restraints excluded: chain q residue 101 ASP Chi-restraints excluded: chain r residue 6 GLN Chi-restraints excluded: chain r residue 29 THR Chi-restraints excluded: chain r residue 53 PHE Chi-restraints excluded: chain r residue 54 VAL Chi-restraints excluded: chain s residue 4 ILE Chi-restraints excluded: chain s residue 61 ASN Chi-restraints excluded: chain s residue 65 ASP Chi-restraints excluded: chain s residue 103 ILE Chi-restraints excluded: chain s residue 109 ASP Chi-restraints excluded: chain t residue 25 GLU Chi-restraints excluded: chain t residue 32 LEU Chi-restraints excluded: chain t residue 63 VAL Chi-restraints excluded: chain u residue 11 ILE Chi-restraints excluded: chain u residue 27 VAL Chi-restraints excluded: chain u residue 88 ASP Chi-restraints excluded: chain v residue 92 VAL Chi-restraints excluded: chain w residue 60 ASP Chi-restraints excluded: chain w residue 77 SER Chi-restraints excluded: chain x residue 39 VAL Chi-restraints excluded: chain x residue 46 VAL Chi-restraints excluded: chain x residue 65 THR Chi-restraints excluded: chain x residue 69 GLU Chi-restraints excluded: chain y residue 11 VAL Chi-restraints excluded: chain y residue 58 ASN Chi-restraints excluded: chain z residue 13 ILE Chi-restraints excluded: chain z residue 16 LEU Chi-restraints excluded: chain z residue 24 LEU Chi-restraints excluded: chain z residue 47 ILE Chi-restraints excluded: chain z residue 50 VAL Chi-restraints excluded: chain A residue 20 ASN Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 59 ARG Chi-restraints excluded: chain A residue 64 PHE Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain C residue 8 ILE Chi-restraints excluded: chain C residue 19 PHE Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain E residue 3 ILE Chi-restraints excluded: chain E residue 30 HIS Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain F residue 13 ASN Chi-restraints excluded: chain F residue 20 ASP Chi-restraints excluded: chain F residue 36 ARG Chi-restraints excluded: chain G residue 14 HIS Chi-restraints excluded: chain G residue 30 ILE Chi-restraints excluded: chain G residue 49 PHE Chi-restraints excluded: chain G residue 59 ILE Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 191 ASP Chi-restraints excluded: chain G residue 207 ARG Chi-restraints excluded: chain H residue 180 ASP Chi-restraints excluded: chain H residue 199 VAL Chi-restraints excluded: chain H residue 206 ILE Chi-restraints excluded: chain I residue 33 ILE Chi-restraints excluded: chain I residue 124 VAL Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 154 VAL Chi-restraints excluded: chain I residue 168 THR Chi-restraints excluded: chain I residue 205 LYS Chi-restraints excluded: chain J residue 10 LEU Chi-restraints excluded: chain J residue 13 LYS Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 47 PHE Chi-restraints excluded: chain J residue 71 ILE Chi-restraints excluded: chain J residue 79 THR Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 144 GLU Chi-restraints excluded: chain J residue 160 VAL Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 15 SER Chi-restraints excluded: chain K residue 29 ILE Chi-restraints excluded: chain K residue 40 GLU Chi-restraints excluded: chain K residue 56 LYS Chi-restraints excluded: chain K residue 58 HIS Chi-restraints excluded: chain K residue 61 LEU Chi-restraints excluded: chain K residue 79 ARG Chi-restraints excluded: chain L residue 19 SER Chi-restraints excluded: chain L residue 44 SER Chi-restraints excluded: chain L residue 72 VAL Chi-restraints excluded: chain L residue 88 VAL Chi-restraints excluded: chain L residue 93 VAL Chi-restraints excluded: chain L residue 112 ASP Chi-restraints excluded: chain L residue 129 ASN Chi-restraints excluded: chain M residue 73 SER Chi-restraints excluded: chain M residue 74 ILE Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain M residue 111 THR Chi-restraints excluded: chain M residue 124 ILE Chi-restraints excluded: chain M residue 125 ILE Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain N residue 20 ILE Chi-restraints excluded: chain N residue 60 LEU Chi-restraints excluded: chain N residue 74 GLN Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 119 LYS Chi-restraints excluded: chain N residue 126 PHE Chi-restraints excluded: chain O residue 15 HIS Chi-restraints excluded: chain O residue 20 GLN Chi-restraints excluded: chain O residue 32 THR Chi-restraints excluded: chain O residue 49 PHE Chi-restraints excluded: chain O residue 56 HIS Chi-restraints excluded: chain O residue 59 LYS Chi-restraints excluded: chain O residue 64 GLN Chi-restraints excluded: chain O residue 69 THR Chi-restraints excluded: chain O residue 77 VAL Chi-restraints excluded: chain O residue 98 VAL Chi-restraints excluded: chain O residue 100 ILE Chi-restraints excluded: chain P residue 30 ILE Chi-restraints excluded: chain P residue 41 LEU Chi-restraints excluded: chain P residue 51 PHE Chi-restraints excluded: chain P residue 57 SER Chi-restraints excluded: chain P residue 71 ASP Chi-restraints excluded: chain P residue 74 LYS Chi-restraints excluded: chain P residue 80 ASN Chi-restraints excluded: chain P residue 83 VAL Chi-restraints excluded: chain P residue 104 PHE Chi-restraints excluded: chain P residue 109 ILE Chi-restraints excluded: chain Q residue 2 THR Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain Q residue 34 THR Chi-restraints excluded: chain Q residue 36 VAL Chi-restraints excluded: chain Q residue 38 THR Chi-restraints excluded: chain Q residue 76 HIS Chi-restraints excluded: chain Q residue 96 THR Chi-restraints excluded: chain Q residue 101 LEU Chi-restraints excluded: chain R residue 3 ILE Chi-restraints excluded: chain R residue 16 ILE Chi-restraints excluded: chain R residue 42 VAL Chi-restraints excluded: chain R residue 63 VAL Chi-restraints excluded: chain R residue 65 GLU Chi-restraints excluded: chain R residue 67 ASP Chi-restraints excluded: chain R residue 85 TYR Chi-restraints excluded: chain R residue 104 ASN Chi-restraints excluded: chain S residue 5 MET Chi-restraints excluded: chain S residue 15 LEU Chi-restraints excluded: chain S residue 53 ASP Chi-restraints excluded: chain S residue 73 LEU Chi-restraints excluded: chain S residue 85 GLU Chi-restraints excluded: chain T residue 44 GLU Chi-restraints excluded: chain T residue 74 VAL Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain U residue 21 VAL Chi-restraints excluded: chain U residue 23 ASP Chi-restraints excluded: chain U residue 29 ASN Chi-restraints excluded: chain U residue 42 ILE Chi-restraints excluded: chain U residue 45 GLU Chi-restraints excluded: chain U residue 46 LYS Chi-restraints excluded: chain U residue 66 THR Chi-restraints excluded: chain V residue 52 CYS Chi-restraints excluded: chain V residue 54 ILE Chi-restraints excluded: chain V residue 58 VAL Chi-restraints excluded: chain V residue 71 SER Chi-restraints excluded: chain W residue 24 ASP Chi-restraints excluded: chain W residue 27 THR Chi-restraints excluded: chain W residue 54 LEU Chi-restraints excluded: chain X residue 4 LEU Chi-restraints excluded: chain X residue 12 LEU Chi-restraints excluded: chain X residue 19 GLU Chi-restraints excluded: chain X residue 39 ILE Chi-restraints excluded: chain X residue 47 THR Chi-restraints excluded: chain Y residue 31 ILE Chi-restraints excluded: chain Y residue 35 TYR Chi-restraints excluded: chain Y residue 59 ARG Chi-restraints excluded: chain Z residue 11 PHE Chi-restraints excluded: chain Z residue 63 ASN Chi-restraints excluded: chain Z residue 67 THR Chi-restraints excluded: chain a residue 41 SER Chi-restraints excluded: chain a residue 50 ILE Chi-restraints excluded: chain a residue 56 ASP Chi-restraints excluded: chain a residue 163 TYR Chi-restraints excluded: chain a residue 172 HIS Chi-restraints excluded: chain a residue 175 ILE Chi-restraints excluded: chain a residue 212 VAL Chi-restraints excluded: chain a residue 214 ILE Chi-restraints excluded: chain a residue 216 THR Chi-restraints excluded: chain 8 residue 4 THR Chi-restraints excluded: chain 8 residue 19 ILE Chi-restraints excluded: chain 8 residue 52 TRP Chi-restraints excluded: chain 8 residue 64 THR Chi-restraints excluded: chain 8 residue 105 VAL Chi-restraints excluded: chain 8 residue 141 VAL Chi-restraints excluded: chain 8 residue 154 VAL Chi-restraints excluded: chain 8 residue 170 GLN Chi-restraints excluded: chain 8 residue 176 GLU Chi-restraints excluded: chain 8 residue 183 VAL Chi-restraints excluded: chain 8 residue 204 TYR Chi-restraints excluded: chain 8 residue 234 MET Chi-restraints excluded: chain 8 residue 266 CYS Chi-restraints excluded: chain 8 residue 300 ASP Chi-restraints excluded: chain 8 residue 334 THR Chi-restraints excluded: chain 8 residue 338 VAL Chi-restraints excluded: chain 8 residue 401 ASP Chi-restraints excluded: chain 8 residue 441 GLU Chi-restraints excluded: chain 8 residue 466 LEU Chi-restraints excluded: chain 8 residue 518 VAL Chi-restraints excluded: chain 8 residue 519 VAL Chi-restraints excluded: chain 8 residue 544 VAL Chi-restraints excluded: chain 8 residue 681 THR 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: 30.0000 chunk 1053 optimal weight: 5.9990 chunk 642 optimal weight: 20.0000 chunk 499 optimal weight: 0.9980 chunk 732 optimal weight: 20.0000 chunk 1104 optimal weight: 7.9990 chunk 1016 optimal weight: 20.0000 chunk 879 optimal weight: 10.0000 chunk 91 optimal weight: 8.9990 chunk 679 optimal weight: 20.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 28 ASN u 39 ASN ** y 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 70 GLN I 130 ASN ** J 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 85 GLN ** N 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 80 HIS O 70 HIS U 18 GLN ** X 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.4542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 166269 Z= 0.263 Angle : 0.666 27.382 247957 Z= 0.342 Chirality : 0.038 0.371 31576 Planarity : 0.005 0.093 13872 Dihedral : 23.651 179.506 81262 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 17.49 Ramachandran Plot: Outliers : 0.11 % Allowed : 11.42 % Favored : 88.48 % Rotamer: Outliers : 5.60 % Allowed : 22.80 % Favored : 71.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.19 (0.10), residues: 6517 helix: -0.21 (0.11), residues: 2084 sheet: -1.62 (0.15), residues: 1096 loop : -2.24 (0.10), residues: 3337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP b 212 HIS 0.017 0.001 HIS L 141 PHE 0.074 0.002 PHE g 29 TYR 0.030 0.002 TYR q 31 ARG 0.013 0.001 ARG G 207 ********************** 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 1258 residues out of total 5429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 304 poor density : 954 time to evaluate : 6.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 212 TRP cc_start: 0.8555 (OUTLIER) cc_final: 0.7893 (p90) REVERT: b 265 PHE cc_start: 0.8568 (m-80) cc_final: 0.8353 (m-80) REVERT: c 29 VAL cc_start: 0.9044 (OUTLIER) cc_final: 0.8732 (p) REVERT: e 31 GLU cc_start: 0.8132 (mt-10) cc_final: 0.7901 (mt-10) REVERT: e 95 MET cc_start: 0.7440 (ttp) cc_final: 0.6313 (tmm) REVERT: e 134 GLN cc_start: 0.3674 (OUTLIER) cc_final: 0.2397 (pm20) REVERT: g 14 SER cc_start: 0.7995 (t) cc_final: 0.7737 (p) REVERT: n 72 ASP cc_start: 0.8094 (t70) cc_final: 0.7370 (t0) REVERT: n 75 ILE cc_start: 0.8925 (mm) cc_final: 0.8287 (mm) REVERT: p 83 ILE cc_start: 0.9013 (OUTLIER) cc_final: 0.8736 (mp) REVERT: r 34 GLU cc_start: 0.8397 (mm-30) cc_final: 0.8067 (mm-30) REVERT: r 60 LYS cc_start: 0.8922 (ttpt) cc_final: 0.8670 (ttpp) REVERT: s 1 MET cc_start: 0.7177 (tmm) cc_final: 0.6933 (tmm) REVERT: t 4 GLU cc_start: 0.8600 (mp0) cc_final: 0.8010 (mp0) REVERT: u 67 SER cc_start: 0.8856 (m) cc_final: 0.8389 (t) REVERT: A 64 PHE cc_start: 0.7098 (OUTLIER) cc_final: 0.6740 (m-80) REVERT: C 19 PHE cc_start: 0.7618 (OUTLIER) cc_final: 0.7324 (p90) REVERT: C 27 ARG cc_start: 0.8446 (mtp-110) cc_final: 0.7897 (ptp-170) REVERT: D 29 GLN cc_start: 0.8620 (OUTLIER) cc_final: 0.8047 (mp10) REVERT: F 36 ARG cc_start: 0.8790 (OUTLIER) cc_final: 0.8342 (ttm-80) REVERT: G 8 MET cc_start: 0.8102 (ttm) cc_final: 0.7848 (tmm) REVERT: G 49 PHE cc_start: 0.6872 (OUTLIER) cc_final: 0.6274 (p90) REVERT: H 17 TRP cc_start: 0.7927 (m-10) cc_final: 0.7617 (m-10) REVERT: H 183 TYR cc_start: 0.7526 (t80) cc_final: 0.7058 (t80) REVERT: I 123 MET cc_start: 0.7428 (tpp) cc_final: 0.6819 (tpp) REVERT: I 177 MET cc_start: 0.8435 (mmp) cc_final: 0.8134 (mmp) REVERT: I 195 ASN cc_start: 0.8081 (t0) cc_final: 0.7590 (p0) REVERT: J 10 LEU cc_start: 0.8015 (OUTLIER) cc_final: 0.7733 (pp) REVERT: J 60 GLN cc_start: 0.8713 (tp-100) cc_final: 0.8112 (tp-100) REVERT: K 29 ILE cc_start: 0.8200 (OUTLIER) cc_final: 0.7971 (tt) REVERT: K 40 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.7419 (mp0) REVERT: K 45 ARG cc_start: 0.7108 (ptm160) cc_final: 0.6881 (ptp-170) REVERT: K 79 ARG cc_start: 0.8381 (OUTLIER) cc_final: 0.8120 (ptp90) REVERT: K 93 LYS cc_start: 0.7945 (mttt) cc_final: 0.7436 (mttp) REVERT: L 25 PHE cc_start: 0.7655 (t80) cc_final: 0.7373 (m-80) REVERT: N 5 TYR cc_start: 0.7411 (m-80) cc_final: 0.7168 (m-80) REVERT: N 49 GLN cc_start: 0.7515 (tt0) cc_final: 0.7249 (tt0) REVERT: N 62 LEU cc_start: 0.8909 (mp) cc_final: 0.8499 (mp) REVERT: N 90 ASP cc_start: 0.8325 (p0) cc_final: 0.7991 (p0) REVERT: N 102 PHE cc_start: 0.7550 (m-80) cc_final: 0.7122 (m-80) REVERT: N 106 ASP cc_start: 0.7248 (t0) cc_final: 0.7006 (t0) REVERT: O 63 ASP cc_start: 0.8005 (t0) cc_final: 0.7646 (t0) REVERT: P 80 ASN cc_start: 0.3138 (OUTLIER) cc_final: 0.2747 (p0) REVERT: R 16 ILE cc_start: 0.7025 (OUTLIER) cc_final: 0.6757 (mt) REVERT: S 32 ASP cc_start: 0.6758 (m-30) cc_final: 0.6480 (m-30) REVERT: S 72 PHE cc_start: 0.6883 (t80) cc_final: 0.6593 (t80) REVERT: S 73 LEU cc_start: 0.7611 (OUTLIER) cc_final: 0.7361 (tt) REVERT: S 85 GLU cc_start: 0.7148 (OUTLIER) cc_final: 0.6861 (pp20) REVERT: S 91 GLU cc_start: 0.7469 (mm-30) cc_final: 0.7199 (mm-30) REVERT: W 24 ASP cc_start: 0.4837 (OUTLIER) cc_final: 0.3937 (p0) REVERT: X 15 LEU cc_start: 0.8103 (tp) cc_final: 0.7777 (tt) REVERT: X 19 GLU cc_start: 0.8691 (OUTLIER) cc_final: 0.7864 (pt0) REVERT: Y 17 ARG cc_start: 0.8664 (ttp80) cc_final: 0.8451 (ttp80) REVERT: Y 24 ARG cc_start: 0.9167 (ttm-80) cc_final: 0.8868 (ttm110) REVERT: Y 59 ARG cc_start: 0.7307 (OUTLIER) cc_final: 0.6869 (mtm180) REVERT: Z 19 LYS cc_start: 0.7852 (ttmt) cc_final: 0.7517 (tptt) REVERT: a 14 LYS cc_start: 0.5672 (mmtt) cc_final: 0.5467 (mtmt) REVERT: a 163 TYR cc_start: 0.0608 (OUTLIER) cc_final: 0.0041 (p90) REVERT: 8 53 MET cc_start: 0.8566 (tmm) cc_final: 0.8097 (tmm) REVERT: 8 106 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.8128 (pp) REVERT: 8 170 GLN cc_start: 0.7625 (OUTLIER) cc_final: 0.7031 (tp-100) REVERT: 8 204 TYR cc_start: 0.7267 (OUTLIER) cc_final: 0.5978 (t80) REVERT: 8 366 MET cc_start: 0.5351 (mmm) cc_final: 0.4900 (mmm) REVERT: 8 441 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7747 (pp20) outliers start: 304 outliers final: 262 residues processed: 1138 average time/residue: 1.2448 time to fit residues: 2517.0367 Evaluate side-chains 1210 residues out of total 5429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 287 poor density : 923 time to evaluate : 6.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 37 SER Chi-restraints excluded: chain b residue 71 ASP Chi-restraints excluded: chain b residue 113 ASP Chi-restraints excluded: chain b residue 120 ASP Chi-restraints excluded: chain b residue 129 LEU Chi-restraints excluded: chain b residue 191 LEU Chi-restraints excluded: chain b residue 204 LEU Chi-restraints excluded: chain b residue 212 TRP Chi-restraints excluded: chain b residue 215 VAL Chi-restraints excluded: chain b residue 227 VAL Chi-restraints excluded: chain c residue 29 VAL Chi-restraints excluded: chain c residue 146 ILE Chi-restraints excluded: chain c residue 185 ASN Chi-restraints excluded: chain c residue 200 ASP Chi-restraints excluded: chain d residue 4 VAL Chi-restraints excluded: chain d residue 53 THR Chi-restraints excluded: chain d residue 79 ARG Chi-restraints excluded: chain d residue 96 VAL Chi-restraints excluded: chain d residue 108 ILE Chi-restraints excluded: chain d residue 141 MET Chi-restraints excluded: chain d residue 176 ASP Chi-restraints excluded: chain e residue 37 MET Chi-restraints excluded: chain e residue 39 VAL Chi-restraints excluded: chain e residue 84 ILE Chi-restraints excluded: chain e residue 89 THR Chi-restraints excluded: chain e residue 134 GLN Chi-restraints excluded: chain e residue 148 VAL Chi-restraints excluded: chain e residue 154 THR Chi-restraints excluded: chain e residue 157 THR Chi-restraints excluded: chain e residue 158 THR Chi-restraints excluded: chain e residue 173 ASP Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 42 VAL Chi-restraints excluded: chain f residue 91 VAL Chi-restraints excluded: chain f residue 113 ASP Chi-restraints excluded: chain f residue 130 ILE Chi-restraints excluded: chain f residue 140 ILE Chi-restraints excluded: chain f residue 147 LEU Chi-restraints excluded: chain f residue 167 VAL Chi-restraints excluded: chain g residue 44 ILE Chi-restraints excluded: chain g residue 87 GLU Chi-restraints excluded: chain g residue 94 ILE Chi-restraints excluded: chain i residue 57 VAL Chi-restraints excluded: chain j residue 5 THR Chi-restraints excluded: chain j residue 54 ILE Chi-restraints excluded: chain j residue 57 LEU Chi-restraints excluded: chain j residue 71 ASP Chi-restraints excluded: chain j residue 86 GLN Chi-restraints excluded: chain j residue 109 LEU Chi-restraints excluded: chain k residue 37 ASP Chi-restraints excluded: chain k residue 42 THR Chi-restraints excluded: chain k residue 45 GLU Chi-restraints excluded: chain k residue 65 THR Chi-restraints excluded: chain k residue 69 VAL Chi-restraints excluded: chain k residue 77 ILE Chi-restraints excluded: chain k residue 90 ASN Chi-restraints excluded: chain l residue 89 VAL Chi-restraints excluded: chain l residue 118 THR Chi-restraints excluded: chain l residue 122 VAL Chi-restraints excluded: chain m residue 12 MET Chi-restraints excluded: chain m residue 67 VAL Chi-restraints excluded: chain m residue 75 GLU Chi-restraints excluded: chain m residue 124 LEU Chi-restraints excluded: chain m residue 134 THR Chi-restraints excluded: chain m residue 136 MET Chi-restraints excluded: chain n residue 15 SER Chi-restraints excluded: chain n residue 33 ILE Chi-restraints excluded: chain n residue 37 THR Chi-restraints excluded: chain n residue 57 THR Chi-restraints excluded: chain o residue 39 VAL Chi-restraints excluded: chain o residue 40 ILE Chi-restraints excluded: chain o residue 49 VAL Chi-restraints excluded: chain o residue 53 THR Chi-restraints excluded: chain o residue 56 LYS Chi-restraints excluded: chain o residue 69 ASP Chi-restraints excluded: chain o residue 74 VAL Chi-restraints excluded: chain o residue 87 ILE Chi-restraints excluded: chain o residue 103 VAL Chi-restraints excluded: chain o residue 112 GLU Chi-restraints excluded: chain p residue 35 SER Chi-restraints excluded: chain p residue 83 ILE Chi-restraints excluded: chain p residue 85 VAL Chi-restraints excluded: chain p residue 99 LEU Chi-restraints excluded: chain p residue 109 ILE Chi-restraints excluded: chain q residue 86 SER Chi-restraints excluded: chain q residue 94 LEU Chi-restraints excluded: chain q residue 101 ASP Chi-restraints excluded: chain r residue 6 GLN Chi-restraints excluded: chain r residue 29 THR Chi-restraints excluded: chain r residue 53 PHE Chi-restraints excluded: chain r residue 54 VAL Chi-restraints excluded: chain s residue 4 ILE Chi-restraints excluded: chain s residue 61 ASN Chi-restraints excluded: chain s residue 65 ASP Chi-restraints excluded: chain s residue 103 ILE Chi-restraints excluded: chain s residue 109 ASP Chi-restraints excluded: chain t residue 32 LEU Chi-restraints excluded: chain t residue 63 VAL Chi-restraints excluded: chain u residue 11 ILE Chi-restraints excluded: chain u residue 27 VAL Chi-restraints excluded: chain u residue 88 ASP Chi-restraints excluded: chain v residue 92 VAL Chi-restraints excluded: chain w residue 60 ASP Chi-restraints excluded: chain w residue 77 SER Chi-restraints excluded: chain x residue 39 VAL Chi-restraints excluded: chain x residue 65 THR Chi-restraints excluded: chain x residue 69 GLU Chi-restraints excluded: chain y residue 11 VAL Chi-restraints excluded: chain y residue 58 ASN Chi-restraints excluded: chain z residue 13 ILE Chi-restraints excluded: chain z residue 16 LEU Chi-restraints excluded: chain z residue 24 LEU Chi-restraints excluded: chain z residue 47 ILE Chi-restraints excluded: chain z residue 50 VAL Chi-restraints excluded: chain A residue 20 ASN Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 59 ARG Chi-restraints excluded: chain A residue 64 PHE Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain C residue 8 ILE Chi-restraints excluded: chain C residue 19 PHE Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 29 GLN Chi-restraints excluded: chain E residue 3 ILE Chi-restraints excluded: chain E residue 30 HIS Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain F residue 13 ASN Chi-restraints excluded: chain F residue 20 ASP Chi-restraints excluded: chain F residue 36 ARG Chi-restraints excluded: chain G residue 14 HIS Chi-restraints excluded: chain G residue 30 ILE Chi-restraints excluded: chain G residue 49 PHE Chi-restraints excluded: chain G residue 59 ILE Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 191 ASP Chi-restraints excluded: chain G residue 207 ARG Chi-restraints excluded: chain H residue 117 ASP Chi-restraints excluded: chain H residue 180 ASP Chi-restraints excluded: chain H residue 199 VAL Chi-restraints excluded: chain H residue 206 ILE Chi-restraints excluded: chain I residue 33 ILE Chi-restraints excluded: chain I residue 124 VAL Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 130 ASN Chi-restraints excluded: chain I residue 168 THR Chi-restraints excluded: chain J residue 10 LEU Chi-restraints excluded: chain J residue 13 LYS Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 47 PHE Chi-restraints excluded: chain J residue 79 THR Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain J residue 123 LEU Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 144 GLU Chi-restraints excluded: chain K residue 15 SER Chi-restraints excluded: chain K residue 29 ILE Chi-restraints excluded: chain K residue 40 GLU Chi-restraints excluded: chain K residue 56 LYS Chi-restraints excluded: chain K residue 58 HIS Chi-restraints excluded: chain K residue 61 LEU Chi-restraints excluded: chain K residue 79 ARG Chi-restraints excluded: chain L residue 19 SER Chi-restraints excluded: chain L residue 44 SER Chi-restraints excluded: chain L residue 72 VAL Chi-restraints excluded: chain L residue 88 VAL Chi-restraints excluded: chain L residue 93 VAL Chi-restraints excluded: chain L residue 112 ASP Chi-restraints excluded: chain L residue 129 ASN Chi-restraints excluded: chain M residue 73 SER Chi-restraints excluded: chain M residue 74 ILE Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain M residue 111 THR Chi-restraints excluded: chain M residue 124 ILE Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain N residue 20 ILE Chi-restraints excluded: chain N residue 60 LEU Chi-restraints excluded: chain N residue 74 GLN Chi-restraints excluded: chain N residue 83 THR Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 119 LYS Chi-restraints excluded: chain N residue 126 PHE Chi-restraints excluded: chain O residue 15 HIS Chi-restraints excluded: chain O residue 20 GLN Chi-restraints excluded: chain O residue 32 THR Chi-restraints excluded: chain O residue 56 HIS Chi-restraints excluded: chain O residue 59 LYS Chi-restraints excluded: chain O residue 69 THR Chi-restraints excluded: chain O residue 77 VAL Chi-restraints excluded: chain O residue 98 VAL Chi-restraints excluded: chain O residue 100 ILE Chi-restraints excluded: chain P residue 30 ILE Chi-restraints excluded: chain P residue 41 LEU Chi-restraints excluded: chain P residue 51 PHE Chi-restraints excluded: chain P residue 57 SER Chi-restraints excluded: chain P residue 71 ASP Chi-restraints excluded: chain P residue 74 LYS Chi-restraints excluded: chain P residue 80 ASN Chi-restraints excluded: chain P residue 83 VAL Chi-restraints excluded: chain P residue 104 PHE Chi-restraints excluded: chain P residue 109 ILE Chi-restraints excluded: chain Q residue 2 THR Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain Q residue 36 VAL Chi-restraints excluded: chain Q residue 38 THR Chi-restraints excluded: chain Q residue 96 THR Chi-restraints excluded: chain Q residue 101 LEU Chi-restraints excluded: chain R residue 3 ILE Chi-restraints excluded: chain R residue 16 ILE Chi-restraints excluded: chain R residue 42 VAL Chi-restraints excluded: chain R residue 65 GLU Chi-restraints excluded: chain R residue 67 ASP Chi-restraints excluded: chain R residue 104 ASN Chi-restraints excluded: chain S residue 15 LEU Chi-restraints excluded: chain S residue 53 ASP Chi-restraints excluded: chain S residue 73 LEU Chi-restraints excluded: chain S residue 85 GLU Chi-restraints excluded: chain T residue 44 GLU Chi-restraints excluded: chain T residue 74 VAL Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain U residue 21 VAL Chi-restraints excluded: chain U residue 23 ASP Chi-restraints excluded: chain U residue 29 ASN Chi-restraints excluded: chain U residue 42 ILE Chi-restraints excluded: chain U residue 45 GLU Chi-restraints excluded: chain U residue 46 LYS Chi-restraints excluded: chain U residue 66 THR Chi-restraints excluded: chain V residue 52 CYS Chi-restraints excluded: chain V residue 54 ILE Chi-restraints excluded: chain V residue 58 VAL Chi-restraints excluded: chain V residue 71 SER Chi-restraints excluded: chain W residue 24 ASP Chi-restraints excluded: chain W residue 27 THR Chi-restraints excluded: chain W residue 54 LEU Chi-restraints excluded: chain X residue 4 LEU Chi-restraints excluded: chain X residue 12 LEU Chi-restraints excluded: chain X residue 19 GLU Chi-restraints excluded: chain X residue 39 ILE Chi-restraints excluded: chain X residue 47 THR Chi-restraints excluded: chain Y residue 35 TYR Chi-restraints excluded: chain Y residue 59 ARG Chi-restraints excluded: chain Z residue 11 PHE Chi-restraints excluded: chain Z residue 63 ASN Chi-restraints excluded: chain Z residue 67 THR Chi-restraints excluded: chain a residue 8 MET Chi-restraints excluded: chain a residue 41 SER Chi-restraints excluded: chain a residue 50 ILE Chi-restraints excluded: chain a residue 56 ASP Chi-restraints excluded: chain a residue 163 TYR Chi-restraints excluded: chain a residue 172 HIS Chi-restraints excluded: chain a residue 175 ILE Chi-restraints excluded: chain a residue 212 VAL Chi-restraints excluded: chain a residue 214 ILE Chi-restraints excluded: chain a residue 216 THR Chi-restraints excluded: chain 8 residue 4 THR Chi-restraints excluded: chain 8 residue 19 ILE Chi-restraints excluded: chain 8 residue 52 TRP Chi-restraints excluded: chain 8 residue 64 THR Chi-restraints excluded: chain 8 residue 105 VAL Chi-restraints excluded: chain 8 residue 106 LEU Chi-restraints excluded: chain 8 residue 141 VAL Chi-restraints excluded: chain 8 residue 154 VAL Chi-restraints excluded: chain 8 residue 170 GLN Chi-restraints excluded: chain 8 residue 176 GLU Chi-restraints excluded: chain 8 residue 183 VAL Chi-restraints excluded: chain 8 residue 204 TYR Chi-restraints excluded: chain 8 residue 234 MET Chi-restraints excluded: chain 8 residue 266 CYS Chi-restraints excluded: chain 8 residue 300 ASP Chi-restraints excluded: chain 8 residue 334 THR Chi-restraints excluded: chain 8 residue 338 VAL Chi-restraints excluded: chain 8 residue 401 ASP Chi-restraints excluded: chain 8 residue 441 GLU Chi-restraints excluded: chain 8 residue 466 LEU Chi-restraints excluded: chain 8 residue 518 VAL Chi-restraints excluded: chain 8 residue 519 VAL Chi-restraints excluded: chain 8 residue 544 VAL Chi-restraints excluded: chain 8 residue 681 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1109 random chunks: chunk 539 optimal weight: 30.0000 chunk 698 optimal weight: 30.0000 chunk 937 optimal weight: 50.0000 chunk 269 optimal weight: 10.0000 chunk 811 optimal weight: 20.0000 chunk 129 optimal weight: 5.9990 chunk 244 optimal weight: 8.9990 chunk 881 optimal weight: 20.0000 chunk 368 optimal weight: 40.0000 chunk 904 optimal weight: 10.0000 chunk 111 optimal weight: 20.0000 overall best weight: 10.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 51 GLN ** s 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 39 ASN ** y 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 80 HIS O 64 GLN O 70 HIS ** R 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 216 ASN ** 8 530 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 = 0.3645 r_free = 0.3645 target = 0.063893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.049220 restraints weight = 840421.655| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 2.19 r_work: 0.3133 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3125 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3125 r_free = 0.3125 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3125 r_free = 0.3125 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3125 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.4640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.092 166269 Z= 0.402 Angle : 0.760 27.221 247957 Z= 0.387 Chirality : 0.042 0.399 31576 Planarity : 0.006 0.092 13872 Dihedral : 23.714 179.175 81262 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 20.48 Ramachandran Plot: Outliers : 0.11 % Allowed : 13.13 % Favored : 86.76 % Rotamer: Outliers : 5.71 % Allowed : 22.93 % Favored : 71.36 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.36 (0.10), residues: 6517 helix: -0.40 (0.11), residues: 2100 sheet: -1.68 (0.15), residues: 1111 loop : -2.34 (0.10), residues: 3306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP b 212 HIS 0.019 0.002 HIS L 141 PHE 0.084 0.003 PHE g 29 TYR 0.037 0.003 TYR q 31 ARG 0.015 0.001 ARG G 207 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 41149.13 seconds wall clock time: 719 minutes 32.26 seconds (43172.26 seconds total)