Starting phenix.real_space_refine on Thu Mar 21 21:29:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ogi_20058/03_2024/6ogi_20058.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ogi_20058/03_2024/6ogi_20058.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ogi_20058/03_2024/6ogi_20058.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ogi_20058/03_2024/6ogi_20058.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ogi_20058/03_2024/6ogi_20058.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ogi_20058/03_2024/6ogi_20058.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.400 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 4651 5.49 5 S 142 5.16 5 C 72739 2.51 5 N 27022 2.21 5 O 40341 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "c ARG 13": "NH1" <-> "NH2" Residue "c GLU 28": "OE1" <-> "OE2" Residue "c ARG 33": "NH1" <-> "NH2" Residue "c ARG 59": "NH1" <-> "NH2" Residue "c ARG 77": "NH1" <-> "NH2" Residue "c ARG 83": "NH1" <-> "NH2" Residue "c GLU 88": "OE1" <-> "OE2" Residue "c ASP 131": "OD1" <-> "OD2" Residue "c ARG 169": "NH1" <-> "NH2" Residue "c GLU 183": "OE1" <-> "OE2" Residue "c ARG 184": "NH1" <-> "NH2" Residue "d ARG 21": "NH1" <-> "NH2" Residue "d GLU 25": "OE1" <-> "OE2" Residue "d ARG 44": "NH1" <-> "NH2" Residue "d ARG 49": "NH1" <-> "NH2" Residue "d GLU 51": "OE1" <-> "OE2" Residue "d ARG 61": "NH1" <-> "NH2" Residue "d ARG 88": "NH1" <-> "NH2" Residue "d ASP 91": "OD1" <-> "OD2" Residue "d ARG 102": "NH1" <-> "NH2" Residue "d GLU 144": "OE1" <-> "OE2" Residue "d ARG 162": "NH1" <-> "NH2" Residue "d ARG 170": "NH1" <-> "NH2" Residue "e ASP 9": "OD1" <-> "OD2" 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 ASP 112": "OD1" <-> "OD2" Residue "e PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ARG 114": "NH1" <-> "NH2" Residue "e ARG 132": "NH1" <-> "NH2" Residue "e ASP 146": "OD1" <-> "OD2" Residue "e PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ARG 2": "NH1" <-> "NH2" Residue "f ASP 46": "OD1" <-> "OD2" Residue "f ASP 55": "OD1" <-> "OD2" Residue "f ASP 59": "OD1" <-> "OD2" Residue "f GLU 80": "OE1" <-> "OE2" Residue "f TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ARG 152": "NH1" <-> "NH2" Residue "f ARG 162": "NH1" <-> "NH2" Residue "f ARG 169": "NH1" <-> "NH2" Residue "g GLU 48": "OE1" <-> "OE2" Residue "g GLU 70": "OE1" <-> "OE2" Residue "g GLU 76": "OE1" <-> "OE2" Residue "g PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 127": "OE1" <-> "OE2" Residue "j GLU 9": "OE1" <-> "OE2" Residue "j ARG 13": "NH1" <-> "NH2" Residue "j ARG 37": "NH1" <-> "NH2" Residue "j GLU 43": "OE1" <-> "OE2" Residue "j ARG 96": "NH1" <-> "NH2" Residue "j ARG 120": "NH1" <-> "NH2" Residue "k GLU 45": "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 "l GLU 144": "OE1" <-> "OE2" Residue "m ARG 10": "NH1" <-> "NH2" Residue "m ARG 18": "NH1" <-> "NH2" Residue "m ARG 40": "NH1" <-> "NH2" Residue "m ARG 44": "NH1" <-> "NH2" Residue "m ARG 50": "NH1" <-> "NH2" Residue "m ARG 55": "NH1" <-> "NH2" Residue "m ARG 59": "NH1" <-> "NH2" Residue "m GLU 104": "OE1" <-> "OE2" Residue "m ARG 114": "NH1" <-> "NH2" Residue "n ARG 8": "NH1" <-> "NH2" Residue "n ARG 12": "NH1" <-> "NH2" Residue "n ARG 17": "NH1" <-> "NH2" Residue "n ARG 22": "NH1" <-> "NH2" Residue "n ARG 46": "NH1" <-> "NH2" Residue "n ARG 63": "NH1" <-> "NH2" Residue "n ARG 64": "NH1" <-> "NH2" Residue "n ARG 69": "NH1" <-> "NH2" Residue "n ARG 71": "NH1" <-> "NH2" Residue "n GLU 82": "OE1" <-> "OE2" Residue "n ARG 96": "NH1" <-> "NH2" Residue "n GLU 114": "OE1" <-> "OE2" 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 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 ARG 69": "NH1" <-> "NH2" Residue "r PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r ARG 21": "NH1" <-> "NH2" Residue "r GLU 34": "OE1" <-> "OE2" Residue "r ARG 68": "NH1" <-> "NH2" Residue "r ARG 78": "NH1" <-> "NH2" Residue "r ARG 79": "NH1" <-> "NH2" Residue "r ARG 84": "NH1" <-> "NH2" Residue "r ASP 95": "OD1" <-> "OD2" Residue "s ARG 84": "NH1" <-> "NH2" Residue "s ARG 88": "NH1" <-> "NH2" Residue "s ARG 95": "NH1" <-> "NH2" Residue "s ARG 110": "NH1" <-> "NH2" Residue "t ARG 73": "NH1" <-> "NH2" Residue "u ARG 5": "NH1" <-> "NH2" Residue "u ARG 6": "NH1" <-> "NH2" Residue "u GLU 61": "OE1" <-> "OE2" Residue "u ARG 81": "NH1" <-> "NH2" Residue "u ARG 85": "NH1" <-> "NH2" Residue "u ARG 93": "NH1" <-> "NH2" Residue "v GLU 59": "OE1" <-> "OE2" Residue "w GLU 25": "OE1" <-> "OE2" Residue "w ASP 60": "OD1" <-> "OD2" 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 GLU 38": "OE1" <-> "OE2" Residue "z ARG 44": "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 "C TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 ASP 81": "OD1" <-> "OD2" Residue "G GLU 117": "OE1" <-> "OE2" Residue "G ASP 126": "OD1" <-> "OD2" Residue "G GLU 141": "OE1" <-> "OE2" Residue "G GLU 222": "OE1" <-> "OE2" Residue "G ARG 224": "NH1" <-> "NH2" Residue "H ASP 33": "OD1" <-> "OD2" Residue "H GLU 57": "OE1" <-> "OE2" Residue "H GLU 81": "OE1" <-> "OE2" Residue "H GLU 84": "OE1" <-> "OE2" Residue "H ARG 106": "NH1" <-> "NH2" Residue "H ARG 130": "NH1" <-> "NH2" Residue "I GLU 34": "OE1" <-> "OE2" Residue "J ARG 156": "NH1" <-> "NH2" Residue "J GLU 161": "OE1" <-> "OE2" Residue "K ASP 13": "OD1" <-> "OD2" Residue "K GLU 65": "OE1" <-> "OE2" Residue "K GLU 69": "OE1" <-> "OE2" Residue "K ASP 72": "OD1" <-> "OD2" Residue "L ASP 32": "OD1" <-> "OD2" Residue "L GLU 62": "OE1" <-> "OE2" Residue "L GLU 122": "OE1" <-> "OE2" Residue "L ASP 125": "OD1" <-> "OD2" Residue "L GLU 145": "OE1" <-> "OE2" Residue "M ASP 8": "OD1" <-> "OD2" Residue "M GLU 46": "OE1" <-> "OE2" Residue "N GLU 52": "OE1" <-> "OE2" Residue "N ASP 55": "OD1" <-> "OD2" Residue "N ARG 123": "NH1" <-> "NH2" Residue "O ASP 14": "OD1" <-> "OD2" Residue "O ASP 97": "OD1" <-> "OD2" Residue "P GLU 82": "OE1" <-> "OE2" Residue "Q TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 55": "NH1" <-> "NH2" Residue "Q ASP 108": "OD1" <-> "OD2" Residue "R GLU 46": "OE1" <-> "OE2" Residue "R ASP 57": "OD1" <-> "OD2" Residue "S ASP 32": "OD1" <-> "OD2" Residue "T GLU 82": "OE1" <-> "OE2" Residue "U ARG 28": "NH1" <-> "NH2" Residue "W ARG 11": "NH1" <-> "NH2" Residue "Y ASP 42": "OD1" <-> "OD2" Residue "Z PHE 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 66": "NH1" <-> "NH2" Residue "a ARG 7": "NH1" <-> "NH2" Residue "a ARG 12": "NH1" <-> "NH2" Residue "a PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ARG 162": "NH1" <-> "NH2" Residue "a ASP 181": "OD1" <-> "OD2" Residue "a ASP 183": "OD1" <-> "OD2" Residue "a GLU 187": "OE1" <-> "OE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 144895 Number of models: 1 Model: "" Number of chains: 54 Chain: "b" Number of atoms: 2082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2082 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 17, 'TRANS': 253} Chain: "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: 1410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1410 Classifications: {'peptide': 177} 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: 1111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1111 Classifications: {'peptide': 149} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 145} Chain: "j" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1129 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 135} Chain: "k" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 938 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "l" Number of atoms: 1045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1045 Classifications: {'peptide': 143} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 138} Chain: "m" Number of atoms: 1074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1074 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 128} Chain: "n" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 960 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "o" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 892 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "p" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 917 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "q" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 947 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'TRANS': 116} Chain: "r" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 816 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 101} Chain: "s" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 857 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 107} Chain: "t" Number of atoms: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 738 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 1, 'TRANS': 91} Chain: "u" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 779 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "v" Number of atoms: 753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 753 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "w" Number of atoms: 575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 575 Classifications: {'peptide': 75} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "x" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 625 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "y" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 509 Classifications: {'peptide': 63} Modifications used: {'COO': 1} Link IDs: {'TRANS': 62} Chain: "z" Number of atoms: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 449 Classifications: {'peptide': 58} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "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: 409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 409 Classifications: {'peptide': 50} 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: 1756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1756 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 7, 'TRANS': 217} Chain: "H" Number of atoms: 1624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1624 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 7, 'TRANS': 198} Chain: "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: 1156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1156 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 5, 'TRANS': 151} Chain: "K" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 824 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 5, 'TRANS': 95} Chain: "L" Number of atoms: 1181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1181 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain: "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: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 786 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 5, 'TRANS': 92} Chain: "P" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 869 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 7, 'TRANS': 108} Chain: "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: 883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 883 Classifications: {'peptide': 114} 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: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 648 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain: "W" Number of atoms: 535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 535 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "X" Number of atoms: 637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 637 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 5, 'TRANS': 73} Chain: "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: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 544 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "a" Number of atoms: 1026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1026 Classifications: {'peptide': 134} 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': 89, 'rna2p_pyr': 50, 'rna3p_pur': 785, 'rna3p_pyr': 615} Link IDs: {'rna2p': 139, 'rna3p': 1399} 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': 216, 'rna2p_pyr': 97, 'rna3p_pur': 1458, 'rna3p_pyr': 1132} Link IDs: {'rna2p': 313, 'rna3p': 2589} 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': 3, 'rna3p_pur': 61, 'rna3p_pyr': 52} Link IDs: {'rna2p': 7, 'rna3p': 112} Chain: "5" Number of atoms: 1578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1578 Classifications: {'RNA': 74} Modifications used: {'5*END': 1, 'rna2p_pur': 7, 'rna2p_pyr': 5, 'rna3p_pur': 31, 'rna3p_pyr': 31} Link IDs: {'rna2p': 12, 'rna3p': 61} Chain: "4" Number of atoms: 437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 437 Classifications: {'RNA': 20} Modifications used: {'5*END': 1, 'rna2p_pur': 3, 'rna3p_pur': 14, 'rna3p_pyr': 3} Link IDs: {'rna2p': 3, 'rna3p': 16} Time building chain proxies: 55.43, per 1000 atoms: 0.38 Number of scatterers: 144895 At special positions: 0 Unit cell: (237.452, 260.13, 269.468, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 142 16.00 P 4651 15.00 O 40341 8.00 N 27022 7.00 C 72739 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=0, symmetry=0 Time building additional restraints: 59.78 Conformation dependent library (CDL) restraints added in 8.0 seconds 11304 Ramachandran restraints generated. 5652 Oldfield, 0 Emsley, 5652 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10570 Finding SS restraints... Secondary structure from input PDB file: 175 helices and 75 sheets defined 33.8% alpha, 17.3% beta 881 base pairs and 2363 stacking pairs defined. Time for finding SS restraints: 44.85 Creating SS restraints... Processing helix chain 'b' and resid 29 through 31 No H-bonds generated for 'chain 'b' and resid 29 through 31' Processing helix chain 'b' and resid 132 through 134 No H-bonds generated for 'chain 'b' and resid 132 through 134' Processing helix chain 'b' and resid 196 through 202 removed outlier: 4.157A pdb=" N MET b 200 " --> pdb=" O ALA b 197 " (cutoff:3.500A) Processing helix chain 'b' and resid 206 through 212 removed outlier: 4.188A pdb=" N ALA b 210 " --> pdb=" O LYS b 206 " (cutoff:3.500A) Processing helix chain 'c' and resid 61 through 72 removed outlier: 3.530A pdb=" N ALA c 71 " --> pdb=" O HIS c 67 " (cutoff:3.500A) Processing helix chain 'c' and resid 97 through 102 removed outlier: 3.543A pdb=" N LEU c 100 " --> pdb=" O SER c 97 " (cutoff:3.500A) Processing helix chain 'c' and resid 120 through 125 Processing helix chain 'd' and resid 15 through 20 Processing helix chain 'd' and resid 24 through 40 Processing helix chain 'd' and resid 97 through 115 removed outlier: 3.701A pdb=" N ARG d 114 " --> pdb=" O SER d 110 " (cutoff:3.500A) Processing helix chain 'd' and resid 130 through 141 Processing helix chain 'd' and resid 154 through 159 Processing helix chain 'd' and resid 160 through 162 No H-bonds generated for 'chain 'd' and resid 160 through 162' Processing helix chain 'd' and resid 176 through 183 Processing helix chain 'd' and resid 190 through 200 Processing helix chain 'e' and resid 2 through 8 Processing helix chain 'e' and resid 9 through 17 removed outlier: 3.725A pdb=" N LYS e 13 " --> pdb=" O ASP e 9 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR e 17 " --> pdb=" O LYS e 13 " (cutoff:3.500A) Processing helix chain 'e' and resid 23 through 27 removed outlier: 3.812A pdb=" N VAL e 27 " --> pdb=" O VAL e 24 " (cutoff:3.500A) Processing helix chain 'e' and resid 45 through 59 removed outlier: 3.820A pdb=" N LEU e 49 " --> pdb=" O ASP e 45 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE e 59 " --> pdb=" O ASP e 55 " (cutoff:3.500A) Processing helix chain 'e' and resid 73 through 77 removed outlier: 3.581A pdb=" N PHE e 76 " --> pdb=" O VAL e 73 " (cutoff:3.500A) Processing helix chain 'e' and resid 92 through 106 removed outlier: 3.583A pdb=" N ILE e 103 " --> pdb=" O PHE e 99 " (cutoff:3.500A) Processing helix chain 'e' and resid 161 through 171 removed outlier: 3.706A pdb=" N LEU e 168 " --> pdb=" O GLU e 164 " (cutoff:3.500A) Processing helix chain 'f' and resid 57 through 80 removed outlier: 3.956A pdb=" N TRP f 61 " --> pdb=" O TYR f 57 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ALA f 62 " --> pdb=" O ALA f 58 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLY f 65 " --> pdb=" O TRP f 61 " (cutoff:3.500A) Processing helix chain 'f' and resid 136 through 151 removed outlier: 3.788A pdb=" N ARG f 151 " --> pdb=" O LEU f 147 " (cutoff:3.500A) Processing helix chain 'g' and resid 22 through 30 Processing helix chain 'g' and resid 40 through 49 removed outlier: 3.506A pdb=" N ALA g 49 " --> pdb=" O GLU g 45 " (cutoff:3.500A) Processing helix chain 'g' and resid 54 through 70 Processing helix chain 'g' and resid 71 through 73 No H-bonds generated for 'chain 'g' and resid 71 through 73' Processing helix chain 'g' and resid 95 through 105 Processing helix chain 'g' and resid 111 through 113 No H-bonds generated for 'chain 'g' and resid 111 through 113' Processing helix chain 'j' and resid 24 through 38 Processing helix chain 'j' and resid 67 through 72 Processing helix chain 'j' and resid 89 through 96 Processing helix chain 'j' and resid 98 through 107 Processing helix chain 'j' and resid 112 through 120 removed outlier: 3.752A pdb=" N ARG j 120 " --> pdb=" O ARG j 116 " (cutoff:3.500A) Processing helix chain 'k' and resid 104 through 108 removed outlier: 3.563A pdb=" N LEU k 107 " --> pdb=" O THR k 104 " (cutoff:3.500A) Processing helix chain 'k' and resid 109 through 111 No H-bonds generated for 'chain 'k' and resid 109 through 111' Processing helix chain 'k' and resid 112 through 119 Processing helix chain 'l' and resid 2 through 6 removed outlier: 3.912A pdb=" N LEU l 6 " --> pdb=" O LEU l 3 " (cutoff:3.500A) Processing helix chain 'l' and resid 37 through 41 Processing helix chain 'l' and resid 56 through 61 Processing helix chain 'l' and resid 68 through 73 removed outlier: 3.839A pdb=" N ALA l 72 " --> pdb=" O SER l 68 " (cutoff:3.500A) Processing helix chain 'l' and resid 78 through 82 Processing helix chain 'l' and resid 128 through 138 Processing helix chain 'm' and resid 43 through 57 removed outlier: 3.726A pdb=" N ALA m 56 " --> pdb=" O ALA m 52 " (cutoff:3.500A) Processing helix chain 'm' and resid 109 through 123 removed outlier: 3.647A pdb=" N ALA m 121 " --> pdb=" O PHE m 117 " (cutoff:3.500A) Processing helix chain 'n' and resid 13 through 32 Processing helix chain 'n' and resid 38 through 56 removed outlier: 4.219A pdb=" N ARG n 46 " --> pdb=" O LYS n 42 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N VAL n 47 " --> pdb=" O GLU n 43 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLU n 49 " --> pdb=" O ARG n 45 " (cutoff:3.500A) Proline residue: n 50 - end of helix Processing helix chain 'n' and resid 60 through 69 Processing helix chain 'n' and resid 72 through 79 Processing helix chain 'n' and resid 82 through 87 Processing helix chain 'o' and resid 3 through 22 removed outlier: 3.521A pdb=" N ALA o 11 " --> pdb=" O ARG o 7 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N ARG o 13 " --> pdb=" O ARG o 9 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N ALA o 14 " --> pdb=" O ARG o 10 " (cutoff:3.500A) Processing helix chain 'o' and resid 55 through 60 Processing helix chain 'o' and resid 67 through 86 Processing helix chain 'o' and resid 101 through 112 Processing helix chain 'p' and resid 2 through 10 Processing helix chain 'p' and resid 52 through 55 Processing helix chain 'p' and resid 96 through 101 Processing helix chain 'q' and resid 6 through 20 removed outlier: 3.779A pdb=" N GLN q 19 " --> pdb=" O LYS q 15 " (cutoff:3.500A) Processing helix chain 'q' and resid 24 through 29 Processing helix chain 'q' and resid 30 through 71 removed outlier: 4.133A pdb=" N GLN q 36 " --> pdb=" O ARG q 32 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ARG q 50 " --> pdb=" O TYR q 46 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LYS q 53 " --> pdb=" O ARG q 49 " (cutoff:3.500A) Processing helix chain 'q' and resid 74 through 84 Processing helix chain 'q' and resid 90 through 100 Processing helix chain 'q' and resid 101 through 117 Processing helix chain 's' and resid 13 through 22 removed outlier: 3.568A pdb=" N VAL s 17 " --> pdb=" O SER s 13 " (cutoff:3.500A) Processing helix chain 's' and resid 28 through 37 Processing helix chain 's' and resid 41 through 62 Processing helix chain 's' and resid 89 through 91 No H-bonds generated for 'chain 's' and resid 89 through 91' Processing helix chain 't' and resid 2 through 8 Processing helix chain 't' and resid 17 through 28 Processing helix chain 't' and resid 39 through 51 Processing helix chain 'v' and resid 13 through 22 Processing helix chain 'v' and resid 44 through 53 removed outlier: 3.737A pdb=" N ALA v 52 " --> pdb=" O MET v 48 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LYS v 53 " --> pdb=" O ASN v 49 " (cutoff:3.500A) Processing helix chain 'v' and resid 54 through 58 Processing helix chain 'x' and resid 52 through 61 Processing helix chain 'x' and resid 62 through 74 Processing helix chain 'y' and resid 9 through 23 Processing helix chain 'y' and resid 23 through 34 removed outlier: 3.698A pdb=" N LEU y 28 " --> pdb=" O GLU y 24 " (cutoff:3.500A) Processing helix chain 'y' and resid 40 through 61 Processing helix chain 'z' and resid 16 through 27 Processing helix chain 'z' and resid 40 through 50 Processing helix chain 'B' and resid 8 through 16 Processing helix chain 'B' and resid 17 through 20 removed outlier: 4.027A pdb=" N ALA B 20 " --> pdb=" O SER B 17 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 17 through 20' Processing helix chain 'D' and resid 8 through 17 Processing helix chain 'D' and resid 17 through 23 Processing helix chain 'D' and resid 24 through 38 Processing helix chain 'E' and resid 6 through 11 Processing helix chain 'E' and resid 36 through 43 Processing helix chain 'E' and resid 50 through 61 removed outlier: 4.425A pdb=" N GLY E 55 " --> pdb=" O LYS E 51 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N LEU E 56 " --> pdb=" O GLY E 52 " (cutoff:3.500A) Processing helix chain 'F' and resid 18 through 22 Processing helix chain 'G' and resid 33 through 37 Processing helix chain 'G' and resid 41 through 43 No H-bonds generated for 'chain 'G' and resid 41 through 43' Processing helix chain 'G' and resid 44 through 62 removed outlier: 4.813A pdb=" N MET G 48 " --> pdb=" O LYS G 44 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA G 60 " --> pdb=" O LEU G 56 " (cutoff:3.500A) Processing helix chain 'G' and resid 75 through 84 removed outlier: 3.513A pdb=" N LEU G 84 " --> pdb=" O LYS G 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 102 through 120 removed outlier: 4.194A pdb=" N GLN G 108 " --> pdb=" O LYS G 104 " (cutoff:3.500A) Processing helix chain 'G' and resid 129 through 148 Processing helix chain 'G' and resid 164 through 177 removed outlier: 3.758A pdb=" N GLU G 168 " --> pdb=" O ASP G 164 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ILE G 170 " --> pdb=" O ASP G 166 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N ALA G 171 " --> pdb=" O HIS G 167 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ILE G 172 " --> pdb=" O GLU G 168 " (cutoff:3.500A) Processing helix chain 'G' and resid 206 through 222 Processing helix chain 'G' and resid 223 through 225 No H-bonds generated for 'chain 'G' and resid 223 through 225' Processing helix chain 'H' and resid 5 through 10 removed outlier: 3.538A pdb=" N ARG H 10 " --> pdb=" O PRO H 6 " (cutoff:3.500A) Processing helix chain 'H' and resid 27 through 45 Processing helix chain 'H' and resid 46 through 49 Processing helix chain 'H' and resid 80 through 95 removed outlier: 4.151A pdb=" N ILE H 93 " --> pdb=" O VAL H 89 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 124 Processing helix chain 'H' and resid 128 through 144 Processing helix chain 'I' and resid 8 through 14 removed outlier: 3.564A pdb=" N ARG I 12 " --> pdb=" O LEU I 8 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 65 removed outlier: 3.551A pdb=" N VAL I 60 " --> pdb=" O GLU I 56 " (cutoff:3.500A) Processing helix chain 'I' and resid 67 through 81 Processing helix chain 'I' and resid 84 through 95 Processing helix chain 'I' and resid 96 through 104 Processing helix chain 'I' and resid 109 through 119 Processing helix chain 'I' and resid 153 through 162 Processing helix chain 'I' and resid 186 through 190 removed outlier: 3.601A pdb=" N LEU I 190 " --> pdb=" O ARG I 187 " (cutoff:3.500A) Processing helix chain 'I' and resid 195 through 203 removed outlier: 4.014A pdb=" N ILE I 199 " --> pdb=" O ASN I 195 " (cutoff:3.500A) Processing helix chain 'J' and resid 54 through 69 removed outlier: 3.521A pdb=" N GLU J 64 " --> pdb=" O GLN J 60 " (cutoff:3.500A) Processing helix chain 'J' and resid 109 through 118 removed outlier: 3.565A pdb=" N VAL J 116 " --> pdb=" O ALA J 112 " (cutoff:3.500A) Processing helix chain 'J' and resid 131 through 145 Processing helix chain 'J' and resid 148 through 156 removed outlier: 3.570A pdb=" N LYS J 155 " --> pdb=" O MET J 151 " (cutoff:3.500A) Processing helix chain 'K' and resid 11 through 16 Processing helix chain 'K' and resid 17 through 31 removed outlier: 3.666A pdb=" N MET K 21 " --> pdb=" O GLN K 17 " (cutoff:3.500A) Processing helix chain 'K' and resid 67 through 80 removed outlier: 3.606A pdb=" N PHE K 80 " --> pdb=" O THR K 76 " (cutoff:3.500A) Processing helix chain 'L' and resid 19 through 30 removed outlier: 3.545A pdb=" N LEU L 29 " --> pdb=" O PHE L 25 " (cutoff:3.500A) Processing helix chain 'L' and resid 34 through 48 removed outlier: 3.625A pdb=" N ALA L 38 " --> pdb=" O LYS L 34 " (cutoff:3.500A) Processing helix chain 'L' and resid 48 through 53 removed outlier: 4.092A pdb=" N ARG L 52 " --> pdb=" O THR L 48 " (cutoff:3.500A) Processing helix chain 'L' and resid 59 through 67 removed outlier: 3.810A pdb=" N ASN L 67 " --> pdb=" O VAL L 63 " (cutoff:3.500A) Processing helix chain 'L' and resid 91 through 109 removed outlier: 4.195A pdb=" N ALA L 97 " --> pdb=" O VAL L 93 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N MET L 100 " --> pdb=" O ASN L 96 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LYS L 109 " --> pdb=" O GLU L 105 " (cutoff:3.500A) Processing helix chain 'L' and resid 114 through 128 removed outlier: 3.521A pdb=" N ASN L 121 " --> pdb=" O LEU L 117 " (cutoff:3.500A) Processing helix chain 'L' and resid 131 through 146 removed outlier: 3.567A pdb=" N GLU L 145 " --> pdb=" O HIS L 141 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA L 146 " --> pdb=" O ARG L 142 " (cutoff:3.500A) Processing helix chain 'M' and resid 4 through 19 Processing helix chain 'M' and resid 29 through 41 Processing helix chain 'M' and resid 87 through 91 Processing helix chain 'M' and resid 112 through 119 removed outlier: 3.941A pdb=" N GLN M 117 " --> pdb=" O ARG M 113 " (cutoff:3.500A) Processing helix chain 'N' and resid 48 through 52 Processing helix chain 'N' and resid 70 through 86 removed outlier: 3.559A pdb=" N THR N 83 " --> pdb=" O ARG N 79 " (cutoff:3.500A) Processing helix chain 'N' and resid 90 through 95 Processing helix chain 'N' and resid 96 through 99 Processing helix chain 'O' and resid 15 through 31 removed outlier: 3.603A pdb=" N ALA O 21 " --> pdb=" O LEU O 17 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLU O 24 " --> pdb=" O GLN O 20 " (cutoff:3.500A) Processing helix chain 'O' and resid 80 through 85 removed outlier: 3.928A pdb=" N ASP O 85 " --> pdb=" O GLU O 81 " (cutoff:3.500A) Processing helix chain 'P' and resid 52 through 57 removed outlier: 3.547A pdb=" N LYS P 56 " --> pdb=" O GLY P 53 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER P 57 " --> pdb=" O SER P 54 " (cutoff:3.500A) Processing helix chain 'P' and resid 58 through 68 removed outlier: 3.541A pdb=" N ALA P 62 " --> pdb=" O THR P 58 " (cutoff:3.500A) Processing helix chain 'P' and resid 94 through 102 removed outlier: 4.047A pdb=" N LEU P 99 " --> pdb=" O THR P 95 " (cutoff:3.500A) Processing helix chain 'Q' and resid 2 through 9 removed outlier: 3.544A pdb=" N LEU Q 6 " --> pdb=" O THR Q 2 " (cutoff:3.500A) Processing helix chain 'Q' and resid 114 through 118 removed outlier: 4.173A pdb=" N GLY Q 117 " --> pdb=" O SER Q 114 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N VAL Q 118 " --> pdb=" O LYS Q 115 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 114 through 118' Processing helix chain 'R' and resid 15 through 20 Processing helix chain 'R' and resid 25 through 37 Processing helix chain 'R' and resid 48 through 60 removed outlier: 3.897A pdb=" N ASP R 53 " --> pdb=" O GLU R 49 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N THR R 54 " --> pdb=" O GLY R 50 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU R 58 " --> pdb=" O THR R 54 " (cutoff:3.500A) Processing helix chain 'R' and resid 64 through 83 Processing helix chain 'R' and resid 84 through 92 removed outlier: 3.596A pdb=" N ARG R 89 " --> pdb=" O TYR R 85 " (cutoff:3.500A) Processing helix chain 'S' and resid 2 through 19 removed outlier: 3.540A pdb=" N ALA S 16 " --> pdb=" O ARG S 12 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N TYR S 19 " --> pdb=" O LEU S 15 " (cutoff:3.500A) Processing helix chain 'S' and resid 24 through 29 Processing helix chain 'S' and resid 37 through 47 Processing helix chain 'S' and resid 55 through 59 Processing helix chain 'S' and resid 79 through 86 Processing helix chain 'T' and resid 3 through 15 removed outlier: 3.859A pdb=" N SER T 12 " --> pdb=" O ALA T 8 " (cutoff:3.500A) Processing helix chain 'T' and resid 17 through 22 removed outlier: 3.909A pdb=" N THR T 21 " --> pdb=" O ALA T 18 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N GLY T 22 " --> pdb=" O ASN T 19 " (cutoff:3.500A) Processing helix chain 'T' and resid 23 through 44 removed outlier: 4.373A pdb=" N GLY T 40 " --> pdb=" O ASN T 36 " (cutoff:3.500A) removed outlier: 5.262A 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 73 through 85 Processing helix chain 'U' and resid 53 through 62 Processing helix chain 'U' and resid 68 through 78 Processing helix chain 'W' and resid 24 through 31 removed outlier: 4.005A pdb=" N TYR W 31 " --> pdb=" O THR W 27 " (cutoff:3.500A) Processing helix chain 'W' and resid 40 through 45 Processing helix chain 'W' and resid 47 through 64 Processing helix chain 'X' and resid 11 through 25 removed outlier: 3.506A pdb=" N ALA X 21 " --> pdb=" O LYS X 17 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N VAL X 22 " --> pdb=" O VAL X 18 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLU X 23 " --> pdb=" O GLU X 19 " (cutoff:3.500A) Processing helix chain 'X' and resid 40 through 44 removed outlier: 3.633A pdb=" N ILE X 44 " --> pdb=" O PRO X 41 " (cutoff:3.500A) Processing helix chain 'Y' and resid 4 through 6 No H-bonds generated for 'chain 'Y' and resid 4 through 6' Processing helix chain 'Y' and resid 7 through 39 removed outlier: 3.823A pdb=" N ILE Y 11 " --> pdb=" O LYS Y 7 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA Y 16 " --> pdb=" O GLN Y 12 " (cutoff:3.500A) Processing helix chain 'Y' and resid 42 through 63 Proline residue: Y 55 - end of helix Processing helix chain 'Y' and resid 68 through 86 Processing helix chain 'Z' and resid 17 through 23 Processing helix chain 'Z' and resid 39 through 60 removed outlier: 3.583A pdb=" N GLU Z 43 " --> pdb=" O LYS Z 39 " (cutoff:3.500A) Processing helix chain 'a' and resid 5 through 14 removed outlier: 3.783A pdb=" N LYS a 14 " --> pdb=" O VAL a 10 " (cutoff:3.500A) Processing helix chain 'a' and resid 22 through 32 removed outlier: 3.610A pdb=" N ALA a 26 " --> pdb=" O ASP a 22 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE a 27 " --> pdb=" O ILE a 23 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N ALA a 28 " --> pdb=" O ASN a 24 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS a 31 " --> pdb=" O ILE a 27 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N GLU a 32 " --> pdb=" O ALA a 28 " (cutoff:3.500A) Processing helix chain 'a' and resid 54 through 58 removed outlier: 3.500A pdb=" N GLN a 57 " --> pdb=" O LYS a 54 " (cutoff:3.500A) Processing helix chain 'a' and resid 181 through 200 removed outlier: 3.535A pdb=" N VAL a 194 " --> pdb=" O GLU a 190 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA a 195 " --> pdb=" O ALA a 191 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'b' and resid 2 through 4 Processing sheet with id=AA2, first strand: chain 'b' and resid 33 through 34 Processing sheet with id=AA3, first strand: chain 'b' and resid 99 through 104 removed outlier: 6.615A pdb=" N ILE b 90 " --> pdb=" O LEU b 80 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N LEU b 80 " --> pdb=" O ILE b 90 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N LEU b 92 " --> pdb=" O GLU b 78 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'b' and resid 128 through 130 removed outlier: 6.785A pdb=" N THR b 172 " --> pdb=" O VAL b 164 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N ARG b 166 " --> pdb=" O TYR b 170 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N TYR b 170 " --> pdb=" O ARG b 166 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N MET b 180 " --> pdb=" O VAL b 267 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'c' and resid 4 through 15 removed outlier: 5.799A pdb=" N LYS c 8 " --> pdb=" O GLU c 28 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N GLU c 28 " --> pdb=" O LYS c 8 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N GLY c 10 " --> pdb=" O VAL c 26 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N LEU c 186 " --> pdb=" O VAL c 180 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N VAL c 180 " --> pdb=" O LEU c 186 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N LEU c 188 " --> pdb=" O VAL c 178 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ASP c 176 " --> pdb=" O LYS c 190 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N VAL c 107 " --> pdb=" O SER c 174 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N THR c 112 " --> pdb=" O ASP c 200 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ASP c 200 " --> pdb=" O THR c 112 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'c' and resid 80 through 83 removed outlier: 6.694A pdb=" N ALA c 47 " --> pdb=" O VAL c 37 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N VAL c 37 " --> pdb=" O ALA c 47 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N GLN c 49 " --> pdb=" O THR c 35 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'c' and resid 115 through 119 Processing sheet with id=AA8, first strand: chain 'd' and resid 2 through 4 Processing sheet with id=AA9, first strand: chain 'd' and resid 118 through 121 removed outlier: 8.196A pdb=" N ARG d 170 " --> pdb=" O VAL d 146 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N ILE d 148 " --> pdb=" O ARG d 170 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'e' and resid 89 through 90 removed outlier: 3.616A pdb=" N ILE e 33 " --> pdb=" O LEU e 90 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LYS e 32 " --> pdb=" O THR e 156 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'f' and resid 15 through 19 removed outlier: 3.554A pdb=" N LYS f 17 " --> pdb=" O THR f 24 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR f 24 " --> pdb=" O LYS f 17 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'f' and resid 40 through 43 Processing sheet with id=AB4, first strand: chain 'f' and resid 121 through 126 removed outlier: 7.237A pdb=" N GLU f 129 " --> pdb=" O PRO f 125 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'f' and resid 94 through 98 Processing sheet with id=AB6, first strand: chain 'g' and resid 18 through 20 Processing sheet with id=AB7, first strand: chain 'g' and resid 77 through 81 removed outlier: 6.975A pdb=" N VAL g 78 " --> pdb=" O ASN g 145 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N VAL g 147 " --> pdb=" O VAL g 78 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N ILE g 80 " --> pdb=" O VAL g 147 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N SER g 131 " --> pdb=" O ARG g 116 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'j' and resid 122 through 125 removed outlier: 6.383A pdb=" N TYR j 16 " --> pdb=" O ILE j 55 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N LEU j 57 " --> pdb=" O TYR j 16 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N VAL j 18 " --> pdb=" O LEU j 57 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'j' and resid 73 through 77 Processing sheet with id=AC1, first strand: chain 'k' and resid 7 through 10 removed outlier: 6.585A pdb=" N ARG k 17 " --> pdb=" O VAL k 10 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N GLU k 45 " --> pdb=" O ARG k 17 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N VAL k 19 " --> pdb=" O ILE k 43 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N ILE k 43 " --> pdb=" O VAL k 19 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N CYS k 21 " --> pdb=" O ILE k 41 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ILE k 41 " --> pdb=" O CYS k 21 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N LYS k 23 " --> pdb=" O ILE k 39 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N ILE k 39 " --> pdb=" O LYS k 23 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N VAL k 62 " --> pdb=" O VAL k 85 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N VAL k 85 " --> pdb=" O VAL k 62 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N CYS k 84 " --> pdb=" O MET k 7 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ASN k 9 " --> pdb=" O CYS k 84 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N LEU k 86 " --> pdb=" O ASN k 9 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'k' and resid 69 through 70 removed outlier: 3.663A pdb=" N VAL k 69 " --> pdb=" O ILE k 77 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N VAL k 76 " --> pdb=" O VAL p 72 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA p 48 " --> pdb=" O THR p 59 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ARG p 61 " --> pdb=" O VAL p 46 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N VAL p 46 " --> pdb=" O ARG p 61 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N ILE p 63 " --> pdb=" O GLY p 44 " (cutoff:3.500A) removed outlier: 8.253A pdb=" N GLY p 44 " --> pdb=" O ILE p 63 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LYS p 36 " --> pdb=" O GLU p 33 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N LYS p 28 " --> pdb=" O ASP p 81 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'k' and resid 69 through 70 removed outlier: 3.663A pdb=" N VAL k 69 " --> pdb=" O ILE k 77 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N VAL k 76 " --> pdb=" O VAL p 72 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA p 48 " --> pdb=" O THR p 59 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ARG p 61 " --> pdb=" O VAL p 46 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N VAL p 46 " --> pdb=" O ARG p 61 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N ILE p 63 " --> pdb=" O GLY p 44 " (cutoff:3.500A) removed outlier: 8.253A pdb=" N GLY p 44 " --> pdb=" O ILE p 63 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LYS p 36 " --> pdb=" O GLU p 33 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N THR p 24 " --> pdb=" O LYS p 86 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'l' and resid 74 through 77 Processing sheet with id=AC5, first strand: chain 'l' and resid 89 through 90 removed outlier: 5.490A pdb=" N VAL l 122 " --> pdb=" O GLU l 143 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'm' and resid 62 through 65 removed outlier: 5.734A pdb=" N VAL m 101 " --> pdb=" O ALA m 35 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ALA m 35 " --> pdb=" O VAL m 101 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N TYR m 103 " --> pdb=" O LEU m 33 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'm' and resid 39 through 42 removed outlier: 6.800A pdb=" N ILE m 73 " --> pdb=" O GLU m 90 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N TRP m 92 " --> pdb=" O LYS m 71 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N LYS m 71 " --> pdb=" O TRP m 92 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'n' and resid 33 through 37 Processing sheet with id=AC9, first strand: chain 'o' and resid 47 through 50 Processing sheet with id=AD1, first strand: chain 'r' and resid 11 through 14 removed outlier: 7.119A pdb=" N GLN r 6 " --> pdb=" O VAL r 38 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N VAL r 38 " --> pdb=" O GLN r 6 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'r' and resid 19 through 22 removed outlier: 6.852A pdb=" N PHE r 93 " --> pdb=" O HIS r 66 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N HIS r 66 " --> pdb=" O PHE r 93 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ASP r 95 " --> pdb=" O VAL r 64 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'r' and resid 72 through 78 removed outlier: 4.390A pdb=" N TYR r 83 " --> pdb=" O ARG r 78 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 's' and resid 4 through 10 removed outlier: 5.440A pdb=" N ILE s 4 " --> pdb=" O VAL s 107 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N VAL s 107 " --> pdb=" O ILE s 4 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N LYS s 6 " --> pdb=" O VAL s 105 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N VAL s 105 " --> pdb=" O LYS s 6 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N ARG s 8 " --> pdb=" O ILE s 103 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N ILE s 103 " --> pdb=" O ARG s 8 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N ARG s 92 " --> pdb=" O PRO s 87 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ASP s 94 " --> pdb=" O ILE s 85 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N ILE s 85 " --> pdb=" O ASP s 94 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ILE s 96 " --> pdb=" O LYS s 83 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N LYS s 83 " --> pdb=" O ILE s 96 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N LYS s 98 " --> pdb=" O SER s 81 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N SER s 81 " --> pdb=" O LYS s 98 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N THR s 100 " --> pdb=" O GLY s 79 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N SER s 108 " --> pdb=" O VAL s 71 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N VAL s 71 " --> pdb=" O SER s 108 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 't' and resid 11 through 14 removed outlier: 4.070A pdb=" N LYS t 81 " --> pdb=" O VAL t 34 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 't' and resid 67 through 70 Processing sheet with id=AD7, first strand: chain 'u' and resid 64 through 65 Processing sheet with id=AD8, first strand: chain 'u' and resid 40 through 44 Processing sheet with id=AD9, first strand: chain 'u' and resid 82 through 85 Processing sheet with id=AE1, first strand: chain 'v' and resid 7 through 8 Processing sheet with id=AE2, first strand: chain 'v' and resid 78 through 79 removed outlier: 3.647A pdb=" N HIS v 88 " --> pdb=" O GLN v 78 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'w' and resid 18 through 19 removed outlier: 6.857A pdb=" N LEU w 55 " --> pdb=" O ILE w 33 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'w' and resid 26 through 27 removed outlier: 6.606A pdb=" N HIS w 42 " --> pdb=" O ILE w 76 " (cutoff:3.500A) removed outlier: 8.562A pdb=" N ILE w 78 " --> pdb=" O HIS w 42 " (cutoff:3.500A) removed outlier: 8.958A pdb=" N GLY w 44 " --> pdb=" O ILE w 78 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'x' and resid 12 through 15 Processing sheet with id=AE6, first strand: chain 'x' and resid 32 through 39 Processing sheet with id=AE7, first strand: chain 'z' and resid 34 through 38 Processing sheet with id=AE8, first strand: chain 'B' and resid 27 through 29 Processing sheet with id=AE9, first strand: chain 'C' and resid 19 through 24 Processing sheet with id=AF1, first strand: chain 'C' and resid 38 through 39 Processing sheet with id=AF2, first strand: chain 'E' and resid 14 through 15 Processing sheet with id=AF3, first strand: chain 'F' and resid 14 through 17 Processing sheet with id=AF4, first strand: chain 'G' and resid 66 through 69 Processing sheet with id=AF5, first strand: chain 'H' and resid 51 through 57 Processing sheet with id=AF6, first strand: chain 'H' and resid 163 through 167 removed outlier: 3.515A pdb=" N SER H 186 " --> pdb=" O VAL H 197 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL H 199 " --> pdb=" O ASN H 184 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASN H 184 " --> pdb=" O VAL H 199 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ASP H 180 " --> pdb=" O LYS H 203 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'H' and resid 189 through 190 Processing sheet with id=AF8, first strand: chain 'I' and resid 127 through 128 Processing sheet with id=AF9, first strand: chain 'J' and resid 12 through 14 Processing sheet with id=AG1, first strand: chain 'J' and resid 18 through 21 Processing sheet with id=AG2, first strand: chain 'J' and resid 94 through 95 Processing sheet with id=AG3, first strand: chain 'K' and resid 2 through 3 Processing sheet with id=AG4, first strand: chain 'K' and resid 41 through 45 removed outlier: 6.519A pdb=" N TYR K 59 " --> pdb=" O TRP K 42 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ARG K 44 " --> pdb=" O ALA K 57 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N ALA K 57 " --> pdb=" O ARG K 44 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N MET K 9 " --> pdb=" O ARG K 86 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N ARG K 86 " --> pdb=" O MET K 9 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'L' and resid 72 through 76 removed outlier: 3.601A pdb=" N LYS L 75 " --> pdb=" O VAL L 86 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'M' and resid 26 through 27 removed outlier: 3.681A pdb=" N GLU M 51 " --> pdb=" O GLU M 57 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'M' and resid 73 through 76 removed outlier: 6.867A pdb=" N VAL M 102 " --> pdb=" O ILE M 125 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N TYR M 127 " --> pdb=" O ILE M 100 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ILE M 100 " --> pdb=" O TYR M 127 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'N' and resid 10 through 11 removed outlier: 3.799A pdb=" N ARG N 11 " --> pdb=" O SER N 14 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'N' and resid 17 through 20 removed outlier: 6.483A pdb=" N VAL N 28 " --> pdb=" O ILE N 64 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'O' and resid 45 through 52 removed outlier: 3.542A pdb=" N ARG O 45 " --> pdb=" O THR O 69 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N GLU O 47 " --> pdb=" O ILE O 67 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'O' and resid 45 through 52 removed outlier: 3.542A pdb=" N ARG O 45 " --> pdb=" O THR O 69 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N GLU O 47 " --> pdb=" O ILE O 67 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N LYS S 96 " --> pdb=" O GLU O 66 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'P' and resid 29 through 32 removed outlier: 3.956A pdb=" N THR P 32 " --> pdb=" O HIS P 21 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N HIS P 21 " --> pdb=" O THR P 32 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N GLY P 18 " --> pdb=" O GLU P 82 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N MET P 84 " --> pdb=" O GLY P 18 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N ALA P 20 " --> pdb=" O MET P 84 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N LYS P 86 " --> pdb=" O ALA P 20 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N ILE P 22 " --> pdb=" O LYS P 86 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N LEU P 81 " --> pdb=" O ILE P 106 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N ASN P 108 " --> pdb=" O LEU P 81 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'Q' and resid 29 through 31 removed outlier: 4.332A pdb=" N TYR Q 94 " --> pdb=" O THR Q 63 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ARG Q 35 " --> pdb=" O ARG Q 53 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'U' and resid 32 through 35 removed outlier: 7.303A pdb=" N VAL U 21 " --> pdb=" O ILE U 33 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'U' and resid 9 through 11 Processing sheet with id=AH7, first strand: chain 'U' and resid 37 through 39 Processing sheet with id=AH8, first strand: chain 'V' and resid 10 through 13 removed outlier: 6.959A pdb=" N VAL V 21 " --> pdb=" O VAL V 12 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'V' and resid 58 through 60 removed outlier: 3.942A pdb=" N ARG V 76 " --> pdb=" O GLU V 59 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'X' and resid 31 through 32 Processing sheet with id=AI2, first strand: chain 'a' and resid 20 through 21 removed outlier: 4.255A pdb=" N VAL a 212 " --> pdb=" O VAL a 224 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N LYS a 211 " --> pdb=" O ASN a 47 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N VAL a 42 " --> pdb=" O ILE a 175 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'a' and resid 61 through 64 1732 hydrogen bonds defined for protein. 4824 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2103 hydrogen bonds 3442 hydrogen bond angles 0 basepair planarities 881 basepair parallelities 2363 stacking parallelities Total time for adding SS restraints: 207.40 Time building geometry restraints manager: 65.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.06 - 1.25: 8883 1.25 - 1.43: 69895 1.43 - 1.62: 78446 1.62 - 1.81: 146 1.81 - 1.99: 116 Bond restraints: 157486 Sorted by residual: bond pdb=" C3' C 3 967 " pdb=" O3' C 3 967 " ideal model delta sigma weight residual 1.417 1.814 -0.397 1.50e-02 4.44e+03 6.99e+02 bond pdb=" O3' A 3 968 " pdb=" P A 3 969 " ideal model delta sigma weight residual 1.607 1.993 -0.386 1.50e-02 4.44e+03 6.63e+02 bond pdb=" C THR P 32 " pdb=" O THR P 32 " ideal model delta sigma weight residual 1.234 1.504 -0.270 1.22e-02 6.72e+03 4.88e+02 bond pdb=" C VAL Q 78 " pdb=" O VAL Q 78 " ideal model delta sigma weight residual 1.236 1.490 -0.254 1.19e-02 7.06e+03 4.55e+02 bond pdb=" C HIS P 21 " pdb=" O HIS P 21 " ideal model delta sigma weight residual 1.236 1.474 -0.238 1.21e-02 6.83e+03 3.87e+02 ... (remaining 157481 not shown) Histogram of bond angle deviations from ideal: 91.59 - 101.76: 4839 101.76 - 111.92: 100971 111.92 - 122.09: 96878 122.09 - 132.25: 32321 132.25 - 142.42: 688 Bond angle restraints: 235697 Sorted by residual: angle pdb=" C PHE X 73 " pdb=" N ALA X 74 " pdb=" CA ALA X 74 " ideal model delta sigma weight residual 122.52 102.99 19.53 1.16e+00 7.43e-01 2.84e+02 angle pdb=" C4' C 3 967 " pdb=" C3' C 3 967 " pdb=" O3' C 3 967 " ideal model delta sigma weight residual 113.00 91.59 21.41 1.50e+00 4.44e-01 2.04e+02 angle pdb=" C ALA X 21 " pdb=" N VAL X 22 " pdb=" CA VAL X 22 " ideal model delta sigma weight residual 120.42 103.19 17.23 1.42e+00 4.96e-01 1.47e+02 angle pdb=" C ALA P 20 " pdb=" N HIS P 21 " pdb=" CA HIS P 21 " ideal model delta sigma weight residual 122.72 106.06 16.66 1.38e+00 5.25e-01 1.46e+02 angle pdb=" C GLY G 201 " pdb=" N ASN G 202 " pdb=" CA ASN G 202 " ideal model delta sigma weight residual 120.97 100.62 20.35 1.82e+00 3.02e-01 1.25e+02 ... (remaining 235692 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.98: 89828 35.98 - 71.97: 9959 71.97 - 107.95: 1089 107.95 - 143.94: 14 143.94 - 179.92: 18 Dihedral angle restraints: 100908 sinusoidal: 84525 harmonic: 16383 Sorted by residual: dihedral pdb=" C5' C 12326 " pdb=" C4' C 12326 " pdb=" C3' C 12326 " pdb=" O3' C 12326 " ideal model delta sinusoidal sigma weight residual 147.00 76.11 70.89 1 8.00e+00 1.56e-02 1.01e+02 dihedral pdb=" C4' C 12326 " pdb=" C3' C 12326 " pdb=" C2' C 12326 " pdb=" C1' C 12326 " ideal model delta sinusoidal sigma weight residual -35.00 35.55 -70.55 1 8.00e+00 1.56e-02 1.00e+02 dihedral pdb=" O4' G 12286 " pdb=" C4' G 12286 " pdb=" C3' G 12286 " pdb=" C2' G 12286 " ideal model delta sinusoidal sigma weight residual -35.00 32.31 -67.31 1 8.00e+00 1.56e-02 9.21e+01 ... (remaining 100905 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.195: 29192 0.195 - 0.390: 922 0.390 - 0.586: 25 0.586 - 0.781: 1 0.781 - 0.976: 1 Chirality restraints: 30141 Sorted by residual: chirality pdb=" C3' C 3 967 " pdb=" C4' C 3 967 " pdb=" O3' C 3 967 " pdb=" C2' C 3 967 " both_signs ideal model delta sigma weight residual False -2.48 -3.45 0.98 2.00e-01 2.50e+01 2.38e+01 chirality pdb=" CA THR P 32 " pdb=" N THR P 32 " pdb=" C THR P 32 " pdb=" CB THR P 32 " both_signs ideal model delta sigma weight residual False 2.53 3.18 -0.66 2.00e-01 2.50e+01 1.08e+01 chirality pdb=" CA VAL Q 106 " pdb=" N VAL Q 106 " pdb=" C VAL Q 106 " pdb=" CB VAL Q 106 " both_signs ideal model delta sigma weight residual False 2.44 3.00 -0.56 2.00e-01 2.50e+01 7.84e+00 ... (remaining 30138 not shown) Planarity restraints: 12551 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' U 11647 " -0.174 2.00e-02 2.50e+03 9.30e-02 1.95e+02 pdb=" N1 U 11647 " 0.009 2.00e-02 2.50e+03 pdb=" C2 U 11647 " 0.033 2.00e-02 2.50e+03 pdb=" O2 U 11647 " 0.069 2.00e-02 2.50e+03 pdb=" N3 U 11647 " 0.023 2.00e-02 2.50e+03 pdb=" C4 U 11647 " 0.023 2.00e-02 2.50e+03 pdb=" O4 U 11647 " -0.159 2.00e-02 2.50e+03 pdb=" C5 U 11647 " 0.089 2.00e-02 2.50e+03 pdb=" C6 U 11647 " 0.086 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A 11328 " -0.181 2.00e-02 2.50e+03 7.74e-02 1.65e+02 pdb=" N9 A 11328 " 0.016 2.00e-02 2.50e+03 pdb=" C8 A 11328 " 0.072 2.00e-02 2.50e+03 pdb=" N7 A 11328 " 0.056 2.00e-02 2.50e+03 pdb=" C5 A 11328 " 0.033 2.00e-02 2.50e+03 pdb=" C6 A 11328 " -0.028 2.00e-02 2.50e+03 pdb=" N6 A 11328 " -0.115 2.00e-02 2.50e+03 pdb=" N1 A 11328 " -0.016 2.00e-02 2.50e+03 pdb=" C2 A 11328 " 0.033 2.00e-02 2.50e+03 pdb=" N3 A 11328 " 0.068 2.00e-02 2.50e+03 pdb=" C4 A 11328 " 0.061 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G 2 24 " 0.163 2.00e-02 2.50e+03 6.87e-02 1.41e+02 pdb=" N9 G 2 24 " -0.008 2.00e-02 2.50e+03 pdb=" C8 G 2 24 " -0.078 2.00e-02 2.50e+03 pdb=" N7 G 2 24 " -0.069 2.00e-02 2.50e+03 pdb=" C5 G 2 24 " -0.032 2.00e-02 2.50e+03 pdb=" C6 G 2 24 " 0.030 2.00e-02 2.50e+03 pdb=" O6 G 2 24 " 0.105 2.00e-02 2.50e+03 pdb=" N1 G 2 24 " 0.027 2.00e-02 2.50e+03 pdb=" C2 G 2 24 " -0.015 2.00e-02 2.50e+03 pdb=" N2 G 2 24 " -0.041 2.00e-02 2.50e+03 pdb=" N3 G 2 24 " -0.039 2.00e-02 2.50e+03 pdb=" C4 G 2 24 " -0.044 2.00e-02 2.50e+03 ... (remaining 12548 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 2324 2.61 - 3.18: 117399 3.18 - 3.76: 274663 3.76 - 4.33: 379129 4.33 - 4.90: 522925 Nonbonded interactions: 1296440 Sorted by model distance: nonbonded pdb=" O HIS G 14 " pdb=" O PHE G 15 " model vdw 2.042 3.040 nonbonded pdb=" O2 C 11043 " pdb=" N2 G 11112 " model vdw 2.225 2.520 nonbonded pdb=" O LYS g 8 " pdb=" O VAL g 9 " model vdw 2.226 3.040 nonbonded pdb=" O LYS l 29 " pdb=" OG1 THR l 30 " model vdw 2.236 2.440 nonbonded pdb=" O2' G 1 858 " pdb=" OP1 G 1 859 " model vdw 2.273 2.440 ... (remaining 1296435 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.170 Extract box with map and model: 12.620 Check model and map are aligned: 1.550 Set scattering table: 1.010 Process input model: 472.220 Find NCS groups from input model: 3.000 Set up NCS constraints: 0.400 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: 0.040 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 496.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 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 : 0.009 0.397 157486 Z= 0.592 Angle : 1.114 24.702 235697 Z= 0.754 Chirality : 0.089 0.976 30141 Planarity : 0.011 0.093 12551 Dihedral : 22.502 179.922 90338 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 15.67 Ramachandran Plot: Outliers : 0.74 % Allowed : 10.26 % Favored : 89.00 % Rotamer: Outliers : 0.49 % Allowed : 4.51 % Favored : 95.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.74 (0.09), residues: 5652 helix: -3.60 (0.08), residues: 1584 sheet: -2.79 (0.15), residues: 874 loop : -3.08 (0.09), residues: 3194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.006 TRP G 103 HIS 0.001 0.000 HIS j 47 PHE 0.032 0.004 PHE K 8 TYR 0.048 0.006 TYR N 6 ARG 0.005 0.000 ARG K 86 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11304 Ramachandran restraints generated. 5652 Oldfield, 0 Emsley, 5652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11304 Ramachandran restraints generated. 5652 Oldfield, 0 Emsley, 5652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1047 residues out of total 4700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 1024 time to evaluate : 6.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 96 LYS cc_start: 0.9436 (mtpt) cc_final: 0.9146 (mmtp) REVERT: b 110 LYS cc_start: 0.9380 (mmtt) cc_final: 0.9140 (tmmt) REVERT: b 113 ASP cc_start: 0.9175 (m-30) cc_final: 0.8546 (m-30) REVERT: b 160 TYR cc_start: 0.8364 (p90) cc_final: 0.7975 (p90) REVERT: c 83 ARG cc_start: 0.9120 (OUTLIER) cc_final: 0.8770 (mmm160) REVERT: e 37 MET cc_start: 0.9011 (ttm) cc_final: 0.8770 (ttm) REVERT: e 96 TRP cc_start: 0.8280 (m100) cc_final: 0.8011 (m100) REVERT: e 174 PHE cc_start: 0.8348 (m-80) cc_final: 0.7661 (m-10) REVERT: f 57 TYR cc_start: 0.7723 (m-80) cc_final: 0.7261 (m-80) REVERT: f 87 GLN cc_start: 0.9191 (tt0) cc_final: 0.8647 (tm-30) REVERT: f 103 ASN cc_start: 0.9057 (m110) cc_final: 0.8707 (p0) REVERT: f 113 ASP cc_start: 0.7608 (m-30) cc_final: 0.7293 (m-30) REVERT: f 115 GLN cc_start: 0.9387 (tt0) cc_final: 0.9097 (mp10) REVERT: f 162 ARG cc_start: 0.8366 (ptt180) cc_final: 0.7972 (ptt-90) REVERT: g 27 ARG cc_start: 0.9064 (ptt-90) cc_final: 0.8604 (ptt-90) REVERT: g 35 LYS cc_start: 0.9397 (mptt) cc_final: 0.9051 (mptt) REVERT: g 46 PHE cc_start: 0.9363 (m-80) cc_final: 0.8973 (m-80) REVERT: g 50 ARG cc_start: 0.9253 (mtp180) cc_final: 0.8941 (tpt90) REVERT: g 112 LYS cc_start: 0.6789 (ttpt) cc_final: 0.5894 (pttt) REVERT: k 80 ASP cc_start: 0.8183 (m-30) cc_final: 0.7951 (m-30) REVERT: k 90 ASN cc_start: 0.8956 (p0) cc_final: 0.8746 (p0) REVERT: m 119 LEU cc_start: 0.9289 (mt) cc_final: 0.8807 (mt) REVERT: m 136 MET cc_start: 0.7453 (mpp) cc_final: 0.7249 (mpp) REVERT: n 37 THR cc_start: 0.9307 (p) cc_final: 0.8914 (p) REVERT: p 54 LEU cc_start: 0.9308 (tp) cc_final: 0.9041 (tt) REVERT: q 48 ASP cc_start: 0.7928 (m-30) cc_final: 0.7411 (m-30) REVERT: r 98 ILE cc_start: 0.9117 (mm) cc_final: 0.8386 (mm) REVERT: r 101 ILE cc_start: 0.9291 (mm) cc_final: 0.9006 (mm) REVERT: s 68 ASP cc_start: 0.8636 (t70) cc_final: 0.8053 (t0) REVERT: s 109 ASP cc_start: 0.8243 (p0) cc_final: 0.7752 (p0) REVERT: t 37 ASP cc_start: 0.8052 (p0) cc_final: 0.7679 (p0) REVERT: t 43 ILE cc_start: 0.9488 (mt) cc_final: 0.9287 (mm) REVERT: t 50 LEU cc_start: 0.9486 (mt) cc_final: 0.8587 (mt) REVERT: u 61 GLU cc_start: 0.8769 (mp0) cc_final: 0.8328 (mm-30) REVERT: v 45 ASP cc_start: 0.8246 (m-30) cc_final: 0.7923 (m-30) REVERT: v 76 ASP cc_start: 0.7131 (m-30) cc_final: 0.6769 (m-30) REVERT: x 70 LEU cc_start: 0.9411 (mt) cc_final: 0.9144 (mt) REVERT: B 11 LYS cc_start: 0.9260 (tppt) cc_final: 0.8908 (tppp) REVERT: C 10 LEU cc_start: 0.9559 (mt) cc_final: 0.9283 (mp) REVERT: C 24 LYS cc_start: 0.9318 (ttpt) cc_final: 0.8867 (tttp) REVERT: F 34 LYS cc_start: 0.8994 (ttpp) cc_final: 0.8791 (ttpt) REVERT: G 109 SER cc_start: 0.6513 (m) cc_final: 0.6176 (m) REVERT: I 123 MET cc_start: 0.9443 (ttp) cc_final: 0.8994 (tmm) REVERT: I 159 GLU cc_start: 0.9534 (tt0) cc_final: 0.9322 (tm-30) REVERT: I 181 PHE cc_start: 0.8645 (t80) cc_final: 0.7546 (t80) REVERT: J 47 PHE cc_start: 0.8400 (p90) cc_final: 0.8139 (p90) REVERT: J 54 GLU cc_start: 0.9351 (pt0) cc_final: 0.9093 (pm20) REVERT: J 70 MET cc_start: 0.8318 (mmm) cc_final: 0.7696 (mmm) REVERT: J 80 LEU cc_start: 0.8953 (tp) cc_final: 0.7849 (tp) REVERT: J 137 ARG cc_start: 0.8916 (mtp85) cc_final: 0.8143 (mtt-85) REVERT: J 155 LYS cc_start: 0.9033 (ptmt) cc_final: 0.8781 (ptpp) REVERT: K 1 MET cc_start: 0.6553 (mtm) cc_final: 0.5350 (tmm) REVERT: K 51 ILE cc_start: 0.6290 (mt) cc_final: 0.6011 (mt) REVERT: K 69 GLU cc_start: 0.9075 (mt-10) cc_final: 0.8833 (pm20) REVERT: K 75 GLU cc_start: 0.7350 (tt0) cc_final: 0.7104 (mm-30) REVERT: L 30 MET cc_start: 0.0735 (ttp) cc_final: 0.0023 (tmm) REVERT: L 115 MET cc_start: 0.8477 (tpp) cc_final: 0.8270 (mpp) REVERT: M 44 PHE cc_start: 0.8253 (m-80) cc_final: 0.7962 (m-80) REVERT: M 76 ARG cc_start: 0.8950 (tpt170) cc_final: 0.8390 (tpm170) REVERT: M 110 MET cc_start: 0.8227 (ptp) cc_final: 0.8022 (ptp) REVERT: M 127 TYR cc_start: 0.8873 (m-80) cc_final: 0.8632 (m-80) REVERT: N 56 MET cc_start: 0.4201 (tpt) cc_final: 0.3405 (tmm) REVERT: O 71 LEU cc_start: 0.8104 (mt) cc_final: 0.7877 (mt) REVERT: P 63 GLN cc_start: 0.8287 (mt0) cc_final: 0.8045 (tm-30) REVERT: Q 116 TYR cc_start: 0.8326 (m-80) cc_final: 0.8031 (m-80) REVERT: R 79 LEU cc_start: 0.1339 (mt) cc_final: 0.1129 (tp) REVERT: S 100 TRP cc_start: 0.7980 (p-90) cc_final: 0.7647 (p-90) REVERT: U 6 LEU cc_start: 0.9395 (mt) cc_final: 0.9133 (mt) REVERT: U 31 ARG cc_start: 0.8904 (ttp-170) cc_final: 0.8680 (ttp80) REVERT: U 47 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7600 (pm20) REVERT: U 77 GLU cc_start: 0.8590 (tp30) cc_final: 0.8364 (mm-30) REVERT: V 25 GLU cc_start: 0.8422 (mm-30) cc_final: 0.8025 (tp30) REVERT: V 36 PHE cc_start: 0.8654 (m-80) cc_final: 0.8249 (m-80) REVERT: X 10 ILE cc_start: 0.7268 (mt) cc_final: 0.6578 (mt) REVERT: Y 26 MET cc_start: 0.9444 (ttp) cc_final: 0.8858 (mmt) REVERT: Y 27 MET cc_start: 0.9204 (tpt) cc_final: 0.8983 (tpp) REVERT: Y 31 ILE cc_start: 0.9698 (mt) cc_final: 0.9333 (mt) REVERT: Y 65 LEU cc_start: 0.9021 (tp) cc_final: 0.8762 (mp) outliers start: 23 outliers final: 4 residues processed: 1044 average time/residue: 1.3575 time to fit residues: 2374.4207 Evaluate side-chains 653 residues out of total 4700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 647 time to evaluate : 5.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 83 ARG Chi-restraints excluded: chain o residue 116 GLN Chi-restraints excluded: chain G residue 51 GLU Chi-restraints excluded: chain U residue 47 GLU Chi-restraints excluded: chain V residue 51 GLU Chi-restraints excluded: chain Z residue 63 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1017 random chunks: chunk 858 optimal weight: 50.0000 chunk 770 optimal weight: 20.0000 chunk 427 optimal weight: 0.0470 chunk 263 optimal weight: 6.9990 chunk 519 optimal weight: 5.9990 chunk 411 optimal weight: 8.9990 chunk 797 optimal weight: 10.0000 chunk 308 optimal weight: 20.0000 chunk 484 optimal weight: 10.0000 chunk 593 optimal weight: 30.0000 chunk 923 optimal weight: 50.0000 overall best weight: 6.4088 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 20 ASN b 43 ASN b 44 ASN b 45 ASN ** b 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 127 ASN b 133 ASN ** b 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 238 ASN ** b 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 32 ASN c 49 GLN c 94 GLN d 41 GLN d 97 ASN d 136 GLN d 163 ASN e 126 ASN f 37 ASN ** f 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 103 ASN f 110 HIS g 66 ASN g 128 HIS g 145 ASN j 58 ASN k 3 GLN k 88 ASN l 54 GLN l 104 GLN ** m 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 45 GLN m 60 GLN n 9 GLN n 62 ASN n 81 ASN n 107 ASN p 11 GLN q 55 GLN q 71 ASN ** r 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 7 HIS s 40 ASN ** t 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 68 ASN v 49 ASN v 78 GLN y 20 ASN y 27 ASN ** y 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 5 ASN B 18 HIS ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 37 GLN G 102 ASN G 108 GLN ** H 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 18 ASN H 138 GLN H 139 ASN H 184 ASN I 39 GLN I 53 GLN I 88 ASN I 125 ASN I 151 GLN J 60 GLN J 96 GLN ** J 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 11 HIS K 17 GLN K 52 ASN K 58 HIS K 63 ASN K 94 HIS L 8 GLN L 67 ASN L 96 ASN L 121 ASN L 129 ASN L 147 ASN M 66 GLN N 36 GLN N 80 HIS O 35 GLN O 58 ASN O 64 GLN P 14 GLN P 118 ASN Q 111 GLN R 51 GLN R 104 ASN ** S 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 59 GLN S 70 HIS ** T 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 30 HIS W 51 GLN X 55 GLN X 56 HIS Y 2 ASN Y 19 HIS Y 20 ASN Y 83 ASN ** a 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 91 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.2607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.112 157486 Z= 0.257 Angle : 0.683 12.739 235697 Z= 0.357 Chirality : 0.039 0.404 30141 Planarity : 0.006 0.074 12551 Dihedral : 23.403 178.588 79035 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 17.35 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.40 % Favored : 91.49 % Rotamer: Outliers : 2.55 % Allowed : 11.21 % Favored : 86.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -3.45 (0.10), residues: 5652 helix: -1.61 (0.11), residues: 1778 sheet: -2.41 (0.16), residues: 881 loop : -2.72 (0.10), residues: 2993 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP G 95 HIS 0.008 0.002 HIS N 80 PHE 0.050 0.002 PHE T 42 TYR 0.030 0.002 TYR Q 65 ARG 0.014 0.001 ARG Q 35 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11304 Ramachandran restraints generated. 5652 Oldfield, 0 Emsley, 5652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11304 Ramachandran restraints generated. 5652 Oldfield, 0 Emsley, 5652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 891 residues out of total 4700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 771 time to evaluate : 6.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: d 9 GLN cc_start: 0.9037 (mp10) cc_final: 0.8680 (mp10) REVERT: d 156 ASN cc_start: 0.8872 (m-40) cc_final: 0.8621 (m-40) REVERT: e 37 MET cc_start: 0.8852 (ttm) cc_final: 0.8562 (tpp) REVERT: e 70 ARG cc_start: 0.7761 (ptt-90) cc_final: 0.7551 (ptt-90) REVERT: e 99 PHE cc_start: 0.8808 (t80) cc_final: 0.8532 (t80) REVERT: e 137 PHE cc_start: 0.6848 (OUTLIER) cc_final: 0.6646 (m-80) REVERT: e 174 PHE cc_start: 0.8459 (m-80) cc_final: 0.7916 (m-10) REVERT: f 57 TYR cc_start: 0.7601 (m-80) cc_final: 0.7119 (m-80) REVERT: f 63 GLN cc_start: 0.7530 (mm-40) cc_final: 0.7310 (mm-40) REVERT: f 87 GLN cc_start: 0.9132 (tt0) cc_final: 0.8561 (tm-30) REVERT: f 103 ASN cc_start: 0.9268 (m-40) cc_final: 0.8726 (p0) REVERT: f 115 GLN cc_start: 0.9364 (tt0) cc_final: 0.9062 (mp10) REVERT: f 162 ARG cc_start: 0.8386 (ptt180) cc_final: 0.7948 (ptt-90) REVERT: g 27 ARG cc_start: 0.8931 (ptt-90) cc_final: 0.8414 (ptt-90) REVERT: g 35 LYS cc_start: 0.9502 (mptt) cc_final: 0.9176 (mptt) REVERT: g 41 LYS cc_start: 0.9264 (tppt) cc_final: 0.9019 (tppt) REVERT: k 54 LYS cc_start: 0.9283 (tttm) cc_final: 0.9038 (tmtt) REVERT: o 3 LYS cc_start: 0.8784 (tttm) cc_final: 0.8373 (ttmt) REVERT: o 19 GLN cc_start: 0.8754 (tt0) cc_final: 0.8033 (tt0) REVERT: q 17 LEU cc_start: 0.9465 (mm) cc_final: 0.9252 (mm) REVERT: q 48 ASP cc_start: 0.7859 (m-30) cc_final: 0.7366 (m-30) REVERT: s 92 ARG cc_start: 0.7843 (ttp80) cc_final: 0.7605 (ttp80) REVERT: s 94 ASP cc_start: 0.7601 (m-30) cc_final: 0.7259 (m-30) REVERT: t 1 MET cc_start: 0.5798 (ttm) cc_final: 0.4384 (tmm) REVERT: t 37 ASP cc_start: 0.8156 (p0) cc_final: 0.7710 (p0) REVERT: u 17 ASP cc_start: 0.7319 (OUTLIER) cc_final: 0.7100 (p0) REVERT: v 24 ASN cc_start: 0.7079 (t0) cc_final: 0.6207 (t0) REVERT: B 11 LYS cc_start: 0.9113 (tppt) cc_final: 0.8602 (mmtm) REVERT: C 24 LYS cc_start: 0.9214 (ttpt) cc_final: 0.8959 (tttp) REVERT: F 1 MET cc_start: 0.8212 (ttp) cc_final: 0.5761 (tpp) REVERT: G 103 TRP cc_start: 0.6979 (t-100) cc_final: 0.6755 (t-100) REVERT: G 153 MET cc_start: 0.5212 (tpt) cc_final: 0.4982 (tpt) REVERT: I 74 TYR cc_start: 0.9361 (m-80) cc_final: 0.9062 (m-80) REVERT: I 134 TYR cc_start: 0.8651 (t80) cc_final: 0.8207 (t80) REVERT: I 181 PHE cc_start: 0.8223 (t80) cc_final: 0.6988 (t80) REVERT: J 67 ARG cc_start: 0.8960 (mmm160) cc_final: 0.8652 (mmm160) REVERT: J 80 LEU cc_start: 0.9257 (OUTLIER) cc_final: 0.8845 (mm) REVERT: J 94 PHE cc_start: 0.7621 (OUTLIER) cc_final: 0.6755 (m-10) REVERT: K 17 GLN cc_start: 0.8665 (OUTLIER) cc_final: 0.8255 (pm20) REVERT: K 35 LYS cc_start: 0.8639 (mmmt) cc_final: 0.8166 (ptmt) REVERT: K 73 GLU cc_start: 0.8805 (tt0) cc_final: 0.8495 (pt0) REVERT: L 30 MET cc_start: 0.1027 (ttp) cc_final: 0.0482 (tmm) REVERT: M 44 PHE cc_start: 0.8325 (m-80) cc_final: 0.8040 (m-80) REVERT: M 51 GLU cc_start: 0.8109 (pm20) cc_final: 0.6549 (pm20) REVERT: M 75 GLN cc_start: 0.7527 (pm20) cc_final: 0.7300 (mp-120) REVERT: M 76 ARG cc_start: 0.9017 (tpt170) cc_final: 0.8751 (tpm170) REVERT: N 56 MET cc_start: 0.5645 (tpt) cc_final: 0.4850 (tmm) REVERT: O 42 LEU cc_start: 0.4316 (mt) cc_final: 0.3017 (mt) REVERT: O 45 ARG cc_start: 0.4951 (mtt180) cc_final: 0.4593 (mtt180) REVERT: O 71 LEU cc_start: 0.7832 (mt) cc_final: 0.7611 (mt) REVERT: P 41 LEU cc_start: 0.8348 (mp) cc_final: 0.7976 (pp) REVERT: T 67 ASP cc_start: 0.9075 (p0) cc_final: 0.8817 (p0) REVERT: U 6 LEU cc_start: 0.9453 (mt) cc_final: 0.9206 (mt) REVERT: U 31 ARG cc_start: 0.8665 (ttp-170) cc_final: 0.8364 (ttp80) REVERT: U 47 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7618 (pm20) REVERT: U 48 GLU cc_start: 0.7148 (tp30) cc_final: 0.6746 (tp30) REVERT: U 55 ASP cc_start: 0.8902 (t70) cc_final: 0.8644 (t70) REVERT: V 25 GLU cc_start: 0.8152 (mm-30) cc_final: 0.7808 (tp30) REVERT: X 43 MET cc_start: 0.0276 (mtp) cc_final: -0.0438 (mmm) REVERT: Y 17 ARG cc_start: 0.9205 (tmm-80) cc_final: 0.8951 (ttp80) REVERT: Y 26 MET cc_start: 0.9380 (ttp) cc_final: 0.8913 (mmt) REVERT: Y 52 GLU cc_start: 0.9047 (pt0) cc_final: 0.8775 (pt0) REVERT: Z 45 LYS cc_start: 0.8083 (tptt) cc_final: 0.7697 (mmtt) outliers start: 120 outliers final: 53 residues processed: 846 average time/residue: 1.3103 time to fit residues: 1892.9257 Evaluate side-chains 662 residues out of total 4700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 603 time to evaluate : 6.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 48 ILE Chi-restraints excluded: chain b residue 153 LEU Chi-restraints excluded: chain b residue 258 SER Chi-restraints excluded: chain b residue 263 ASP Chi-restraints excluded: chain d residue 84 THR Chi-restraints excluded: chain d residue 153 LEU Chi-restraints excluded: chain e residue 6 TYR Chi-restraints excluded: chain e residue 35 LEU Chi-restraints excluded: chain e residue 137 PHE Chi-restraints excluded: chain f residue 124 CYS Chi-restraints excluded: chain f residue 174 LYS Chi-restraints excluded: chain g residue 54 LEU Chi-restraints excluded: chain k residue 56 ASP Chi-restraints excluded: chain k residue 58 LEU Chi-restraints excluded: chain k residue 114 LYS Chi-restraints excluded: chain l residue 118 THR Chi-restraints excluded: chain l residue 120 VAL Chi-restraints excluded: chain m residue 5 LYS Chi-restraints excluded: chain m residue 59 ARG Chi-restraints excluded: chain m residue 124 LEU Chi-restraints excluded: chain n residue 9 GLN Chi-restraints excluded: chain n residue 34 ILE Chi-restraints excluded: chain p residue 39 LEU Chi-restraints excluded: chain q residue 36 GLN Chi-restraints excluded: chain r residue 38 VAL Chi-restraints excluded: chain r residue 55 ASP Chi-restraints excluded: chain r residue 95 ASP Chi-restraints excluded: chain s residue 74 ILE Chi-restraints excluded: chain u residue 7 ASP Chi-restraints excluded: chain u residue 17 ASP Chi-restraints excluded: chain v residue 30 ILE Chi-restraints excluded: chain x residue 29 LEU Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain C residue 44 GLN Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain F residue 20 ASP Chi-restraints excluded: chain G residue 51 GLU Chi-restraints excluded: chain H residue 18 ASN Chi-restraints excluded: chain H residue 36 PHE Chi-restraints excluded: chain H residue 164 THR Chi-restraints excluded: chain I residue 184 LYS Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain J residue 94 PHE Chi-restraints excluded: chain J residue 110 MET Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain K residue 17 GLN Chi-restraints excluded: chain L residue 72 VAL Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain O residue 57 VAL Chi-restraints excluded: chain P residue 110 THR Chi-restraints excluded: chain Q residue 81 ILE Chi-restraints excluded: chain R residue 42 VAL Chi-restraints excluded: chain T residue 74 VAL Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain U residue 47 GLU Chi-restraints excluded: chain X residue 62 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1017 random chunks: chunk 513 optimal weight: 50.0000 chunk 286 optimal weight: 0.1980 chunk 768 optimal weight: 20.0000 chunk 628 optimal weight: 40.0000 chunk 254 optimal weight: 10.0000 chunk 925 optimal weight: 20.0000 chunk 999 optimal weight: 30.0000 chunk 823 optimal weight: 40.0000 chunk 917 optimal weight: 50.0000 chunk 315 optimal weight: 50.0000 chunk 742 optimal weight: 40.0000 overall best weight: 16.0396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 44 ASN b 85 ASN ** b 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 152 GLN ** b 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 136 ASN c 167 ASN ** e 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 88 ASN l 104 GLN ** o 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 12 HIS s 61 ASN t 48 GLN t 59 ASN u 39 ASN ** x 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 7 ASN H 18 ASN H 24 ASN ** H 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 20 GLN ** Q 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 7 ASN R 13 HIS ** S 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 53 GLN ** X 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.4230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.137 157486 Z= 0.494 Angle : 0.823 12.823 235697 Z= 0.418 Chirality : 0.043 0.368 30141 Planarity : 0.006 0.070 12551 Dihedral : 24.037 179.011 79023 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 31.14 Ramachandran Plot: Outliers : 0.12 % Allowed : 11.32 % Favored : 88.55 % Rotamer: Outliers : 3.55 % Allowed : 13.72 % Favored : 82.72 % 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: -3.13 (0.10), residues: 5652 helix: -1.08 (0.11), residues: 1782 sheet: -2.42 (0.16), residues: 859 loop : -2.66 (0.10), residues: 3011 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP P 43 HIS 0.013 0.002 HIS j 132 PHE 0.032 0.003 PHE Y 50 TYR 0.034 0.003 TYR M 127 ARG 0.016 0.001 ARG C 5 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11304 Ramachandran restraints generated. 5652 Oldfield, 0 Emsley, 5652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11304 Ramachandran restraints generated. 5652 Oldfield, 0 Emsley, 5652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 779 residues out of total 4700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 612 time to evaluate : 6.367 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: d 136 GLN cc_start: 0.8401 (tp40) cc_final: 0.8056 (tp-100) REVERT: e 96 TRP cc_start: 0.8121 (m100) cc_final: 0.7751 (m100) REVERT: e 129 MET cc_start: 0.9043 (mpp) cc_final: 0.8699 (mpp) REVERT: e 174 PHE cc_start: 0.8700 (m-80) cc_final: 0.8114 (m-10) REVERT: f 57 TYR cc_start: 0.7636 (m-80) cc_final: 0.7064 (m-80) REVERT: f 87 GLN cc_start: 0.9122 (tt0) cc_final: 0.8507 (tm-30) REVERT: f 115 GLN cc_start: 0.9311 (tt0) cc_final: 0.9057 (mp10) REVERT: f 162 ARG cc_start: 0.8332 (ptt180) cc_final: 0.7842 (ptt-90) REVERT: g 35 LYS cc_start: 0.9519 (mptt) cc_final: 0.9199 (mptt) REVERT: g 50 ARG cc_start: 0.9243 (mtp180) cc_final: 0.8910 (mtt90) REVERT: g 112 LYS cc_start: 0.6814 (ttpt) cc_final: 0.6320 (pttt) REVERT: k 113 MET cc_start: 0.8815 (mmm) cc_final: 0.8389 (mmm) REVERT: n 20 MET cc_start: 0.8640 (tmm) cc_final: 0.8385 (tmm) REVERT: o 3 LYS cc_start: 0.8958 (tttm) cc_final: 0.8633 (tttt) REVERT: o 26 LEU cc_start: 0.9329 (tp) cc_final: 0.9051 (tt) REVERT: p 14 GLN cc_start: 0.8778 (mp10) cc_final: 0.8505 (mp10) REVERT: q 17 LEU cc_start: 0.9552 (mm) cc_final: 0.9314 (mm) REVERT: q 19 GLN cc_start: 0.9104 (OUTLIER) cc_final: 0.8898 (pm20) REVERT: q 48 ASP cc_start: 0.7880 (m-30) cc_final: 0.7477 (m-30) REVERT: s 67 ASP cc_start: 0.8823 (OUTLIER) cc_final: 0.8613 (p0) REVERT: s 94 ASP cc_start: 0.7925 (m-30) cc_final: 0.7714 (m-30) REVERT: t 37 ASP cc_start: 0.8490 (p0) cc_final: 0.7896 (p0) REVERT: u 17 ASP cc_start: 0.7763 (OUTLIER) cc_final: 0.7121 (p0) REVERT: C 24 LYS cc_start: 0.9149 (ttpt) cc_final: 0.8854 (ptmm) REVERT: D 1 MET cc_start: 0.6957 (ptt) cc_final: 0.6595 (ptm) REVERT: F 1 MET cc_start: 0.8291 (ttp) cc_final: 0.5557 (tpt) REVERT: H 17 TRP cc_start: 0.7298 (m-90) cc_final: 0.6867 (m-90) REVERT: I 74 TYR cc_start: 0.9320 (m-10) cc_final: 0.8918 (m-80) REVERT: I 134 TYR cc_start: 0.8416 (t80) cc_final: 0.8206 (t80) REVERT: I 139 ASN cc_start: 0.9447 (t0) cc_final: 0.8960 (m-40) REVERT: I 181 PHE cc_start: 0.8177 (t80) cc_final: 0.7096 (t80) REVERT: J 67 ARG cc_start: 0.9072 (mmm160) cc_final: 0.8546 (mmm160) REVERT: J 70 MET cc_start: 0.8483 (mmm) cc_final: 0.8063 (mmm) REVERT: J 80 LEU cc_start: 0.9275 (tp) cc_final: 0.8904 (mm) REVERT: J 94 PHE cc_start: 0.7780 (OUTLIER) cc_final: 0.7264 (m-10) REVERT: J 137 ARG cc_start: 0.9094 (mtp85) cc_final: 0.8639 (mtp85) REVERT: J 151 MET cc_start: 0.8878 (ppp) cc_final: 0.8660 (ppp) REVERT: K 73 GLU cc_start: 0.8836 (tt0) cc_final: 0.8570 (pt0) REVERT: K 100 SER cc_start: 0.8133 (t) cc_final: 0.7837 (p) REVERT: L 30 MET cc_start: 0.1144 (ttp) cc_final: 0.0727 (tmm) REVERT: M 59 GLU cc_start: 0.8995 (mm-30) cc_final: 0.8750 (mm-30) REVERT: M 110 MET cc_start: 0.7848 (ptp) cc_final: 0.7303 (ptp) REVERT: M 116 ARG cc_start: 0.8909 (OUTLIER) cc_final: 0.8630 (mpp80) REVERT: N 45 MET cc_start: 0.5967 (tpp) cc_final: 0.5652 (ttm) REVERT: N 56 MET cc_start: 0.5538 (tpt) cc_final: 0.4614 (tmm) REVERT: N 88 GLU cc_start: 0.7569 (OUTLIER) cc_final: 0.7238 (pm20) REVERT: R 76 ILE cc_start: 0.6510 (mm) cc_final: 0.6286 (mm) REVERT: S 76 PHE cc_start: 0.0070 (OUTLIER) cc_final: -0.0260 (t80) REVERT: S 100 TRP cc_start: 0.8078 (p-90) cc_final: 0.7655 (p-90) REVERT: T 67 ASP cc_start: 0.9084 (p0) cc_final: 0.8727 (p0) REVERT: T 79 GLN cc_start: 0.9171 (tm-30) cc_final: 0.8714 (mt0) REVERT: T 88 ARG cc_start: 0.6554 (tpp-160) cc_final: 0.5990 (mmp80) REVERT: U 77 GLU cc_start: 0.8852 (mm-30) cc_final: 0.8621 (mm-30) REVERT: V 16 MET cc_start: 0.8143 (ttm) cc_final: 0.7930 (ttm) REVERT: V 49 ASN cc_start: 0.8777 (p0) cc_final: 0.8430 (p0) REVERT: Y 26 MET cc_start: 0.9281 (ttp) cc_final: 0.8756 (mmt) outliers start: 167 outliers final: 100 residues processed: 718 average time/residue: 1.3005 time to fit residues: 1606.3020 Evaluate side-chains 630 residues out of total 4700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 523 time to evaluate : 6.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 48 ILE Chi-restraints excluded: chain b residue 52 HIS Chi-restraints excluded: chain b residue 131 MET Chi-restraints excluded: chain b residue 153 LEU Chi-restraints excluded: chain b residue 258 SER Chi-restraints excluded: chain b residue 263 ASP Chi-restraints excluded: chain c residue 187 LEU Chi-restraints excluded: chain d residue 3 LEU Chi-restraints excluded: chain d residue 30 GLN Chi-restraints excluded: chain d residue 73 ILE Chi-restraints excluded: chain d residue 83 VAL Chi-restraints excluded: chain d residue 96 VAL Chi-restraints excluded: chain d residue 149 ILE Chi-restraints excluded: chain d residue 153 LEU Chi-restraints excluded: chain e residue 6 TYR Chi-restraints excluded: chain e residue 35 LEU Chi-restraints excluded: chain e residue 51 ASN Chi-restraints excluded: chain e residue 137 PHE Chi-restraints excluded: chain f residue 124 CYS Chi-restraints excluded: chain g residue 54 LEU Chi-restraints excluded: chain j residue 14 ASP Chi-restraints excluded: chain j residue 81 ILE Chi-restraints excluded: chain k residue 20 MET Chi-restraints excluded: chain k residue 56 ASP Chi-restraints excluded: chain k residue 58 LEU Chi-restraints excluded: chain k residue 76 VAL Chi-restraints excluded: chain k residue 97 THR Chi-restraints excluded: chain k residue 114 LYS Chi-restraints excluded: chain l residue 77 ILE Chi-restraints excluded: chain l residue 118 THR Chi-restraints excluded: chain l residue 120 VAL Chi-restraints excluded: chain m residue 5 LYS Chi-restraints excluded: chain m residue 12 MET Chi-restraints excluded: chain n residue 29 VAL Chi-restraints excluded: chain n residue 34 ILE Chi-restraints excluded: chain n residue 37 THR Chi-restraints excluded: chain n residue 57 THR Chi-restraints excluded: chain n residue 106 ASP Chi-restraints excluded: chain n residue 113 ILE Chi-restraints excluded: chain o residue 18 LEU Chi-restraints excluded: chain p residue 39 LEU Chi-restraints excluded: chain p residue 63 ILE Chi-restraints excluded: chain p residue 96 LEU Chi-restraints excluded: chain q residue 19 GLN Chi-restraints excluded: chain q residue 36 GLN Chi-restraints excluded: chain q residue 82 LEU Chi-restraints excluded: chain q residue 97 ILE Chi-restraints excluded: chain r residue 49 ILE Chi-restraints excluded: chain r residue 55 ASP Chi-restraints excluded: chain r residue 95 ASP Chi-restraints excluded: chain s residue 20 VAL Chi-restraints excluded: chain s residue 67 ASP Chi-restraints excluded: chain s residue 74 ILE Chi-restraints excluded: chain s residue 109 ASP Chi-restraints excluded: chain t residue 5 GLU Chi-restraints excluded: chain u residue 7 ASP Chi-restraints excluded: chain u residue 17 ASP Chi-restraints excluded: chain v residue 77 VAL Chi-restraints excluded: chain w residue 19 VAL Chi-restraints excluded: chain x residue 15 ASN Chi-restraints excluded: chain x residue 59 ASP Chi-restraints excluded: chain z residue 56 VAL Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain F residue 20 ASP Chi-restraints excluded: chain G residue 38 HIS Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 169 HIS Chi-restraints excluded: chain G residue 203 ASP Chi-restraints excluded: chain H residue 7 ASN Chi-restraints excluded: chain H residue 18 ASN Chi-restraints excluded: chain H residue 36 PHE Chi-restraints excluded: chain H residue 164 THR Chi-restraints excluded: chain I residue 123 MET Chi-restraints excluded: chain I residue 142 VAL Chi-restraints excluded: chain J residue 94 PHE Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 162 GLU Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain L residue 72 VAL Chi-restraints excluded: chain L residue 121 ASN Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain M residue 39 LEU Chi-restraints excluded: chain M residue 116 ARG Chi-restraints excluded: chain N residue 20 ILE Chi-restraints excluded: chain N residue 54 VAL Chi-restraints excluded: chain N residue 88 GLU Chi-restraints excluded: chain P residue 16 SER Chi-restraints excluded: chain P residue 110 THR Chi-restraints excluded: chain Q residue 28 GLN Chi-restraints excluded: chain Q residue 81 ILE Chi-restraints excluded: chain R residue 42 VAL Chi-restraints excluded: chain S residue 76 PHE Chi-restraints excluded: chain T residue 36 ASN Chi-restraints excluded: chain T residue 74 VAL Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain U residue 66 THR Chi-restraints excluded: chain U residue 69 ASP Chi-restraints excluded: chain X residue 66 VAL Chi-restraints excluded: chain Z residue 41 THR Chi-restraints excluded: chain Z residue 42 THR Chi-restraints excluded: chain a residue 216 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1017 random chunks: chunk 914 optimal weight: 10.0000 chunk 695 optimal weight: 20.0000 chunk 480 optimal weight: 30.0000 chunk 102 optimal weight: 0.9980 chunk 441 optimal weight: 20.0000 chunk 621 optimal weight: 30.0000 chunk 928 optimal weight: 10.0000 chunk 983 optimal weight: 10.0000 chunk 485 optimal weight: 10.0000 chunk 880 optimal weight: 20.0000 chunk 264 optimal weight: 4.9990 overall best weight: 7.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 4 ASN ** m 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 9 GLN ** o 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 71 ASN t 15 HIS ** t 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 33 HIS z 8 GLN ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 23 ASN G 177 ASN H 7 ASN H 18 ASN ** H 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 17 GLN K 63 ASN ** L 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 85 GLN ** M 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 68 HIS ** a 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.4234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 157486 Z= 0.241 Angle : 0.617 11.387 235697 Z= 0.320 Chirality : 0.036 0.372 30141 Planarity : 0.005 0.079 12551 Dihedral : 24.017 179.970 79017 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 21.67 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.38 % Favored : 90.53 % Rotamer: Outliers : 3.17 % Allowed : 15.64 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.69 (0.10), residues: 5652 helix: -0.53 (0.12), residues: 1783 sheet: -2.27 (0.16), residues: 874 loop : -2.47 (0.10), residues: 2995 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP L 102 HIS 0.017 0.001 HIS H 5 PHE 0.026 0.002 PHE g 46 TYR 0.026 0.002 TYR Q 65 ARG 0.012 0.001 ARG J 44 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11304 Ramachandran restraints generated. 5652 Oldfield, 0 Emsley, 5652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11304 Ramachandran restraints generated. 5652 Oldfield, 0 Emsley, 5652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 767 residues out of total 4700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 618 time to evaluate : 8.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: d 136 GLN cc_start: 0.8349 (tp40) cc_final: 0.7997 (tp-100) REVERT: d 195 GLN cc_start: 0.8729 (mt0) cc_final: 0.8376 (mt0) REVERT: e 16 MET cc_start: 0.8821 (mmt) cc_final: 0.8518 (mmt) REVERT: e 96 TRP cc_start: 0.8045 (m100) cc_final: 0.7667 (m100) REVERT: e 174 PHE cc_start: 0.8639 (m-80) cc_final: 0.8114 (m-10) REVERT: f 57 TYR cc_start: 0.7651 (m-80) cc_final: 0.7155 (m-80) REVERT: f 87 GLN cc_start: 0.9092 (tt0) cc_final: 0.8478 (tm-30) REVERT: f 115 GLN cc_start: 0.9306 (tt0) cc_final: 0.9025 (mp10) REVERT: g 8 LYS cc_start: 0.9032 (tppt) cc_final: 0.8295 (mtmm) REVERT: g 27 ARG cc_start: 0.8887 (ptt-90) cc_final: 0.8493 (ptt90) REVERT: g 35 LYS cc_start: 0.9560 (mptt) cc_final: 0.9219 (mptt) REVERT: g 41 LYS cc_start: 0.9446 (ptmm) cc_final: 0.9157 (mmmt) REVERT: g 42 LYS cc_start: 0.9182 (tppt) cc_final: 0.8910 (tppt) REVERT: g 90 LEU cc_start: 0.6292 (tp) cc_final: 0.6078 (tp) REVERT: k 113 MET cc_start: 0.8824 (mmm) cc_final: 0.8456 (mmm) REVERT: n 20 MET cc_start: 0.8821 (tmm) cc_final: 0.8544 (tmm) REVERT: o 3 LYS cc_start: 0.8948 (tttm) cc_final: 0.8406 (mttt) REVERT: o 76 LYS cc_start: 0.8898 (mmmt) cc_final: 0.8607 (mmmt) REVERT: p 105 LYS cc_start: 0.7656 (mmtt) cc_final: 0.7309 (mptt) REVERT: q 17 LEU cc_start: 0.9591 (mm) cc_final: 0.9256 (mm) REVERT: q 43 GLN cc_start: 0.8890 (OUTLIER) cc_final: 0.8688 (mp10) REVERT: q 48 ASP cc_start: 0.7730 (m-30) cc_final: 0.7464 (m-30) REVERT: r 45 GLU cc_start: 0.8354 (pp20) cc_final: 0.8140 (pp20) REVERT: s 94 ASP cc_start: 0.7770 (m-30) cc_final: 0.7505 (m-30) REVERT: t 37 ASP cc_start: 0.8525 (p0) cc_final: 0.7914 (p0) REVERT: u 17 ASP cc_start: 0.7159 (OUTLIER) cc_final: 0.6911 (p0) REVERT: C 24 LYS cc_start: 0.9165 (ttpt) cc_final: 0.8927 (tttp) REVERT: C 34 GLU cc_start: 0.7400 (mm-30) cc_final: 0.6693 (mm-30) REVERT: C 49 LYS cc_start: 0.8967 (mmmt) cc_final: 0.8507 (mmmt) REVERT: G 108 GLN cc_start: 0.6970 (OUTLIER) cc_final: 0.6636 (pp30) REVERT: G 183 PHE cc_start: 0.9066 (OUTLIER) cc_final: 0.8489 (m-80) REVERT: H 17 TRP cc_start: 0.7068 (m-90) cc_final: 0.6856 (m-90) REVERT: I 74 TYR cc_start: 0.9364 (m-10) cc_final: 0.9045 (m-80) REVERT: I 134 TYR cc_start: 0.8531 (t80) cc_final: 0.8156 (t80) REVERT: I 139 ASN cc_start: 0.9477 (t0) cc_final: 0.9004 (m-40) REVERT: J 67 ARG cc_start: 0.9137 (mmm160) cc_final: 0.8801 (mmm160) REVERT: J 80 LEU cc_start: 0.9144 (tp) cc_final: 0.8833 (mm) REVERT: J 94 PHE cc_start: 0.7712 (OUTLIER) cc_final: 0.7011 (m-10) REVERT: J 137 ARG cc_start: 0.9108 (mtp85) cc_final: 0.8361 (mtp85) REVERT: K 73 GLU cc_start: 0.8866 (tt0) cc_final: 0.8578 (pt0) REVERT: K 100 SER cc_start: 0.8252 (t) cc_final: 0.7998 (p) REVERT: L 30 MET cc_start: 0.1026 (ttp) cc_final: 0.0652 (tmm) REVERT: M 48 PHE cc_start: 0.8525 (p90) cc_final: 0.8176 (p90) REVERT: M 110 MET cc_start: 0.7655 (ptp) cc_final: 0.7453 (ptp) REVERT: N 56 MET cc_start: 0.5907 (tpt) cc_final: 0.5175 (tmm) REVERT: N 88 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.7434 (pm20) REVERT: Q 111 GLN cc_start: 0.8675 (mt0) cc_final: 0.8069 (tm-30) REVERT: Q 116 TYR cc_start: 0.7888 (m-80) cc_final: 0.7446 (m-80) REVERT: S 76 PHE cc_start: -0.0105 (OUTLIER) cc_final: -0.0483 (t80) REVERT: S 100 TRP cc_start: 0.8188 (p-90) cc_final: 0.7804 (p-90) REVERT: T 67 ASP cc_start: 0.9110 (p0) cc_final: 0.8895 (p0) REVERT: T 88 ARG cc_start: 0.6582 (tpp-160) cc_final: 0.5793 (mmp80) REVERT: U 77 GLU cc_start: 0.8651 (mm-30) cc_final: 0.8259 (mm-30) REVERT: Y 26 MET cc_start: 0.9138 (ttp) cc_final: 0.8640 (mmt) outliers start: 149 outliers final: 92 residues processed: 717 average time/residue: 1.3398 time to fit residues: 1665.6542 Evaluate side-chains 651 residues out of total 4700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 552 time to evaluate : 6.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 19 VAL Chi-restraints excluded: chain b residue 44 ASN Chi-restraints excluded: chain b residue 52 HIS Chi-restraints excluded: chain b residue 113 ASP Chi-restraints excluded: chain b residue 239 PHE Chi-restraints excluded: chain b residue 258 SER Chi-restraints excluded: chain b residue 263 ASP Chi-restraints excluded: chain d residue 3 LEU Chi-restraints excluded: chain d residue 73 ILE Chi-restraints excluded: chain d residue 83 VAL Chi-restraints excluded: chain d residue 84 THR Chi-restraints excluded: chain e residue 6 TYR Chi-restraints excluded: chain e residue 51 ASN Chi-restraints excluded: chain g residue 40 THR Chi-restraints excluded: chain g residue 54 LEU Chi-restraints excluded: chain g residue 138 VAL Chi-restraints excluded: chain j residue 84 ILE Chi-restraints excluded: chain k residue 56 ASP Chi-restraints excluded: chain k residue 58 LEU Chi-restraints excluded: chain k residue 76 VAL Chi-restraints excluded: chain k residue 114 LYS Chi-restraints excluded: chain l residue 77 ILE Chi-restraints excluded: chain l residue 118 THR Chi-restraints excluded: chain l residue 120 VAL Chi-restraints excluded: chain m residue 5 LYS Chi-restraints excluded: chain m residue 12 MET Chi-restraints excluded: chain m residue 102 LEU Chi-restraints excluded: chain m residue 124 LEU Chi-restraints excluded: chain n residue 34 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 p residue 96 LEU Chi-restraints excluded: chain q residue 43 GLN Chi-restraints excluded: chain q residue 82 LEU Chi-restraints excluded: chain q residue 97 ILE Chi-restraints excluded: chain r residue 55 ASP Chi-restraints excluded: chain r residue 95 ASP Chi-restraints excluded: chain s residue 1 MET Chi-restraints excluded: chain s residue 20 VAL Chi-restraints excluded: chain s residue 74 ILE Chi-restraints excluded: chain s residue 103 ILE Chi-restraints excluded: chain s residue 109 ASP Chi-restraints excluded: chain u residue 7 ASP Chi-restraints excluded: chain u residue 17 ASP Chi-restraints excluded: chain u residue 48 VAL Chi-restraints excluded: chain w residue 17 LEU Chi-restraints excluded: chain w residue 19 VAL Chi-restraints excluded: chain x residue 15 ASN Chi-restraints excluded: chain x residue 39 VAL Chi-restraints excluded: chain y residue 31 GLN Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain F residue 20 ASP Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 108 GLN Chi-restraints excluded: chain G residue 169 HIS Chi-restraints excluded: chain G residue 183 PHE Chi-restraints excluded: chain G residue 203 ASP Chi-restraints excluded: chain H residue 18 ASN Chi-restraints excluded: chain H residue 36 PHE Chi-restraints excluded: chain H residue 164 THR Chi-restraints excluded: chain I residue 123 MET Chi-restraints excluded: chain I residue 142 VAL Chi-restraints excluded: chain J residue 68 ARG Chi-restraints excluded: chain J residue 94 PHE Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 162 GLU Chi-restraints excluded: chain K residue 11 HIS Chi-restraints excluded: chain L residue 5 VAL Chi-restraints excluded: chain L residue 72 VAL Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain L residue 100 MET Chi-restraints excluded: chain L residue 121 ASN Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain N residue 20 ILE Chi-restraints excluded: chain N residue 54 VAL Chi-restraints excluded: chain N residue 61 ASP Chi-restraints excluded: chain N residue 88 GLU Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain P residue 16 SER Chi-restraints excluded: chain P residue 110 THR Chi-restraints excluded: chain Q residue 28 GLN Chi-restraints excluded: chain Q residue 81 ILE Chi-restraints excluded: chain R residue 42 VAL Chi-restraints excluded: chain S residue 76 PHE Chi-restraints excluded: chain T residue 74 VAL Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain V residue 28 VAL Chi-restraints excluded: chain X residue 62 THR Chi-restraints excluded: chain Y residue 56 ILE Chi-restraints excluded: chain Z residue 41 THR Chi-restraints excluded: chain Z residue 42 THR Chi-restraints excluded: chain a residue 216 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1017 random chunks: chunk 818 optimal weight: 20.0000 chunk 558 optimal weight: 30.0000 chunk 14 optimal weight: 10.0000 chunk 731 optimal weight: 10.0000 chunk 405 optimal weight: 10.0000 chunk 838 optimal weight: 10.0000 chunk 679 optimal weight: 50.0000 chunk 1 optimal weight: 9.9990 chunk 501 optimal weight: 30.0000 chunk 882 optimal weight: 10.0000 chunk 248 optimal weight: 3.9990 overall best weight: 8.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 196 ASN ** b 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 62 GLN j 40 HIS ** j 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 4 ASN ** m 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 18 ASN ** H 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 131 ASN ** L 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 99 GLN Q 76 HIS ** S 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 70 HIS ** U 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.4564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 157486 Z= 0.292 Angle : 0.632 14.167 235697 Z= 0.325 Chirality : 0.036 0.359 30141 Planarity : 0.005 0.089 12551 Dihedral : 24.054 179.183 79017 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 24.22 Ramachandran Plot: Outliers : 0.07 % Allowed : 10.67 % Favored : 89.26 % Rotamer: Outliers : 3.55 % Allowed : 16.66 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.55 (0.11), residues: 5652 helix: -0.35 (0.12), residues: 1793 sheet: -2.16 (0.16), residues: 875 loop : -2.45 (0.10), residues: 2984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP L 102 HIS 0.009 0.001 HIS V 46 PHE 0.022 0.002 PHE M 65 TYR 0.023 0.002 TYR Q 65 ARG 0.017 0.001 ARG C 27 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11304 Ramachandran restraints generated. 5652 Oldfield, 0 Emsley, 5652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11304 Ramachandran restraints generated. 5652 Oldfield, 0 Emsley, 5652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 750 residues out of total 4700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 583 time to evaluate : 6.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: d 62 GLN cc_start: 0.8962 (OUTLIER) cc_final: 0.8276 (tp40) REVERT: d 136 GLN cc_start: 0.8381 (tp40) cc_final: 0.8037 (tp-100) REVERT: d 195 GLN cc_start: 0.8779 (mt0) cc_final: 0.8402 (mt0) REVERT: e 16 MET cc_start: 0.8754 (mmt) cc_final: 0.8447 (mmt) REVERT: e 157 THR cc_start: 0.7342 (OUTLIER) cc_final: 0.7090 (t) REVERT: e 174 PHE cc_start: 0.8709 (m-80) cc_final: 0.8165 (m-10) REVERT: f 34 ARG cc_start: 0.6960 (ttp80) cc_final: 0.6718 (ttp-170) REVERT: f 57 TYR cc_start: 0.7576 (m-80) cc_final: 0.7058 (m-80) REVERT: f 87 GLN cc_start: 0.9095 (tt0) cc_final: 0.8529 (tm-30) REVERT: f 163 TYR cc_start: 0.7274 (OUTLIER) cc_final: 0.7024 (p90) REVERT: g 35 LYS cc_start: 0.9564 (mptt) cc_final: 0.9235 (mptt) REVERT: g 50 ARG cc_start: 0.8607 (tpt90) cc_final: 0.8359 (tpt90) REVERT: g 90 LEU cc_start: 0.6394 (tp) cc_final: 0.6174 (tp) REVERT: k 54 LYS cc_start: 0.9343 (tmtt) cc_final: 0.9111 (tmtt) REVERT: k 113 MET cc_start: 0.8866 (mmm) cc_final: 0.8593 (mmm) REVERT: n 20 MET cc_start: 0.8813 (tmm) cc_final: 0.8500 (tmm) REVERT: o 3 LYS cc_start: 0.8991 (tttm) cc_final: 0.8478 (mttt) REVERT: q 17 LEU cc_start: 0.9579 (mm) cc_final: 0.9276 (mm) REVERT: q 48 ASP cc_start: 0.7737 (m-30) cc_final: 0.7302 (m-30) REVERT: s 9 HIS cc_start: 0.7730 (OUTLIER) cc_final: 0.7220 (m-70) REVERT: s 94 ASP cc_start: 0.7786 (m-30) cc_final: 0.7496 (m-30) REVERT: t 1 MET cc_start: 0.6091 (tpp) cc_final: 0.5393 (tpp) REVERT: t 37 ASP cc_start: 0.8527 (p0) cc_final: 0.7924 (p0) REVERT: u 17 ASP cc_start: 0.7534 (OUTLIER) cc_final: 0.7013 (p0) REVERT: C 24 LYS cc_start: 0.9169 (ttpt) cc_final: 0.8903 (ptmm) REVERT: C 49 LYS cc_start: 0.8825 (mmmt) cc_final: 0.8509 (mmmt) REVERT: F 1 MET cc_start: 0.8300 (ttp) cc_final: 0.6021 (tpt) REVERT: G 108 GLN cc_start: 0.6949 (OUTLIER) cc_final: 0.6586 (pp30) REVERT: G 183 PHE cc_start: 0.9070 (OUTLIER) cc_final: 0.8497 (m-80) REVERT: H 17 TRP cc_start: 0.7136 (m-90) cc_final: 0.6901 (m-90) REVERT: I 74 TYR cc_start: 0.9313 (m-10) cc_final: 0.8921 (m-80) REVERT: I 134 TYR cc_start: 0.8588 (t80) cc_final: 0.8206 (t80) REVERT: I 181 PHE cc_start: 0.8208 (t80) cc_final: 0.6995 (t80) REVERT: J 80 LEU cc_start: 0.9197 (tp) cc_final: 0.8937 (mm) REVERT: J 94 PHE cc_start: 0.7852 (OUTLIER) cc_final: 0.7146 (m-10) REVERT: J 137 ARG cc_start: 0.9132 (mtp85) cc_final: 0.8399 (mtp85) REVERT: K 21 MET cc_start: 0.4185 (OUTLIER) cc_final: 0.3760 (tmm) REVERT: K 33 GLU cc_start: 0.4433 (OUTLIER) cc_final: 0.3496 (tm-30) REVERT: K 35 LYS cc_start: 0.8148 (mmmt) cc_final: 0.7598 (ptmt) REVERT: K 73 GLU cc_start: 0.8888 (tt0) cc_final: 0.8596 (pt0) REVERT: L 30 MET cc_start: 0.1003 (ttp) cc_final: 0.0655 (tmm) REVERT: N 56 MET cc_start: 0.5941 (tpt) cc_final: 0.5103 (tmm) REVERT: N 88 GLU cc_start: 0.7705 (OUTLIER) cc_final: 0.7420 (pm20) REVERT: Q 111 GLN cc_start: 0.8622 (mt0) cc_final: 0.8112 (tm-30) REVERT: Q 116 TYR cc_start: 0.7807 (m-80) cc_final: 0.7444 (m-80) REVERT: S 76 PHE cc_start: -0.0211 (OUTLIER) cc_final: -0.0539 (t80) REVERT: S 100 TRP cc_start: 0.8270 (p-90) cc_final: 0.7885 (p-90) REVERT: T 42 PHE cc_start: 0.8253 (m-80) cc_final: 0.7310 (m-80) REVERT: T 79 GLN cc_start: 0.9131 (tm-30) cc_final: 0.8698 (mt0) REVERT: T 88 ARG cc_start: 0.6521 (tpp-160) cc_final: 0.5750 (mmp80) REVERT: U 51 ARG cc_start: 0.9083 (tpt90) cc_final: 0.8876 (ttt-90) REVERT: U 77 GLU cc_start: 0.8542 (mm-30) cc_final: 0.8174 (mm-30) REVERT: X 43 MET cc_start: -0.0190 (mtt) cc_final: -0.0753 (mmt) REVERT: Y 26 MET cc_start: 0.9135 (ttp) cc_final: 0.8639 (mmt) outliers start: 167 outliers final: 110 residues processed: 696 average time/residue: 1.3056 time to fit residues: 1569.3328 Evaluate side-chains 654 residues out of total 4700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 532 time to evaluate : 6.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 19 VAL Chi-restraints excluded: chain b residue 44 ASN Chi-restraints excluded: chain b residue 52 HIS Chi-restraints excluded: chain b residue 131 MET Chi-restraints excluded: chain b residue 153 LEU Chi-restraints excluded: chain b residue 239 PHE Chi-restraints excluded: chain b residue 258 SER Chi-restraints excluded: chain b residue 263 ASP Chi-restraints excluded: chain c residue 187 LEU Chi-restraints excluded: chain d residue 3 LEU Chi-restraints excluded: chain d residue 62 GLN Chi-restraints excluded: chain d residue 73 ILE Chi-restraints excluded: chain d residue 83 VAL Chi-restraints excluded: chain d residue 84 THR Chi-restraints excluded: chain e residue 6 TYR Chi-restraints excluded: chain e residue 51 ASN Chi-restraints excluded: chain e residue 140 ILE Chi-restraints excluded: chain e residue 157 THR Chi-restraints excluded: chain f residue 146 ASP Chi-restraints excluded: chain f residue 163 TYR Chi-restraints excluded: chain g residue 138 VAL Chi-restraints excluded: chain j residue 81 ILE Chi-restraints excluded: chain k residue 56 ASP Chi-restraints excluded: chain k residue 58 LEU Chi-restraints excluded: chain k residue 76 VAL Chi-restraints excluded: chain k residue 114 LYS Chi-restraints excluded: chain l residue 4 ASN Chi-restraints excluded: chain l residue 77 ILE Chi-restraints excluded: chain l residue 118 THR Chi-restraints excluded: chain l residue 120 VAL Chi-restraints excluded: chain m residue 5 LYS Chi-restraints excluded: chain m residue 12 MET Chi-restraints excluded: chain m residue 102 LEU Chi-restraints excluded: chain m residue 124 LEU Chi-restraints excluded: chain n residue 29 VAL Chi-restraints excluded: chain n residue 34 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 108 ASP Chi-restraints excluded: chain p residue 4 ILE Chi-restraints excluded: chain p residue 39 LEU Chi-restraints excluded: chain p residue 63 ILE Chi-restraints excluded: chain p residue 96 LEU Chi-restraints excluded: chain p residue 109 ILE Chi-restraints excluded: chain q residue 79 ILE Chi-restraints excluded: chain q residue 82 LEU Chi-restraints excluded: chain q residue 97 ILE Chi-restraints excluded: chain q residue 99 VAL Chi-restraints excluded: chain r residue 41 ILE Chi-restraints excluded: chain r residue 55 ASP Chi-restraints excluded: chain r residue 95 ASP Chi-restraints excluded: chain s residue 9 HIS Chi-restraints excluded: chain s residue 20 VAL Chi-restraints excluded: chain s residue 74 ILE Chi-restraints excluded: chain s residue 103 ILE Chi-restraints excluded: chain s residue 109 ASP Chi-restraints excluded: chain u residue 7 ASP Chi-restraints excluded: chain u residue 17 ASP Chi-restraints excluded: chain w residue 17 LEU Chi-restraints excluded: chain w residue 19 VAL Chi-restraints excluded: chain x residue 15 ASN Chi-restraints excluded: chain x residue 39 VAL Chi-restraints excluded: chain y residue 31 GLN Chi-restraints excluded: chain z residue 56 VAL Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain F residue 20 ASP Chi-restraints excluded: chain G residue 26 MET Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 108 GLN Chi-restraints excluded: chain G residue 169 HIS Chi-restraints excluded: chain G residue 183 PHE Chi-restraints excluded: chain G residue 203 ASP Chi-restraints excluded: chain H residue 18 ASN Chi-restraints excluded: chain H residue 36 PHE Chi-restraints excluded: chain H residue 164 THR Chi-restraints excluded: chain I residue 123 MET Chi-restraints excluded: chain I residue 142 VAL Chi-restraints excluded: chain J residue 94 PHE Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 135 VAL Chi-restraints excluded: chain J residue 162 GLU Chi-restraints excluded: chain K residue 11 HIS Chi-restraints excluded: chain K residue 21 MET Chi-restraints excluded: chain K residue 33 GLU Chi-restraints excluded: chain K residue 64 VAL Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain L residue 72 VAL Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain L residue 121 ASN Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain N residue 20 ILE Chi-restraints excluded: chain N residue 54 VAL Chi-restraints excluded: chain N residue 61 ASP Chi-restraints excluded: chain N residue 64 ILE Chi-restraints excluded: chain N residue 65 THR Chi-restraints excluded: chain N residue 88 GLU Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 71 LEU Chi-restraints excluded: chain P residue 16 SER Chi-restraints excluded: chain P residue 110 THR Chi-restraints excluded: chain Q residue 28 GLN Chi-restraints excluded: chain Q residue 81 ILE Chi-restraints excluded: chain R residue 42 VAL Chi-restraints excluded: chain S residue 76 PHE Chi-restraints excluded: chain T residue 74 VAL Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain U residue 69 ASP Chi-restraints excluded: chain V residue 20 ILE Chi-restraints excluded: chain V residue 28 VAL Chi-restraints excluded: chain X residue 62 THR Chi-restraints excluded: chain X residue 66 VAL Chi-restraints excluded: chain Y residue 56 ILE Chi-restraints excluded: chain Y residue 60 GLN Chi-restraints excluded: chain Z residue 41 THR Chi-restraints excluded: chain Z residue 42 THR Chi-restraints excluded: chain a residue 216 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1017 random chunks: chunk 330 optimal weight: 9.9990 chunk 885 optimal weight: 10.0000 chunk 194 optimal weight: 7.9990 chunk 577 optimal weight: 30.0000 chunk 242 optimal weight: 9.9990 chunk 983 optimal weight: 10.0000 chunk 816 optimal weight: 50.0000 chunk 455 optimal weight: 0.9980 chunk 81 optimal weight: 0.7980 chunk 325 optimal weight: 10.0000 chunk 516 optimal weight: 20.0000 overall best weight: 5.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 71 ASN ** r 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 18 ASN ** H 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 125 ASN ** J 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 131 ASN ** L 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 96 ASN L 129 ASN M 3 GLN Q 76 HIS ** S 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.4656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 157486 Z= 0.214 Angle : 0.582 13.839 235697 Z= 0.300 Chirality : 0.034 0.344 30141 Planarity : 0.004 0.081 12551 Dihedral : 24.036 178.951 79017 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 21.21 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.16 % Favored : 90.76 % Rotamer: Outliers : 3.36 % Allowed : 17.47 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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 (0.11), residues: 5652 helix: -0.14 (0.12), residues: 1799 sheet: -1.95 (0.17), residues: 867 loop : -2.32 (0.11), residues: 2986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP L 102 HIS 0.008 0.001 HIS V 46 PHE 0.029 0.002 PHE M 65 TYR 0.025 0.002 TYR Q 65 ARG 0.017 0.001 ARG J 68 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11304 Ramachandran restraints generated. 5652 Oldfield, 0 Emsley, 5652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11304 Ramachandran restraints generated. 5652 Oldfield, 0 Emsley, 5652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 739 residues out of total 4700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 581 time to evaluate : 6.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: d 136 GLN cc_start: 0.8352 (tp40) cc_final: 0.7989 (tp-100) REVERT: d 195 GLN cc_start: 0.8789 (mt0) cc_final: 0.8451 (mt0) REVERT: e 37 MET cc_start: 0.8473 (ppp) cc_final: 0.8194 (ppp) REVERT: e 95 MET cc_start: 0.9091 (ttp) cc_final: 0.8805 (mtp) REVERT: e 129 MET cc_start: 0.8711 (mpp) cc_final: 0.8501 (mpp) REVERT: e 157 THR cc_start: 0.7189 (OUTLIER) cc_final: 0.6954 (t) REVERT: e 174 PHE cc_start: 0.8690 (m-80) cc_final: 0.8137 (m-10) REVERT: f 57 TYR cc_start: 0.7569 (m-80) cc_final: 0.7090 (m-80) REVERT: f 68 ARG cc_start: 0.8370 (tpt-90) cc_final: 0.7868 (ttt90) REVERT: f 87 GLN cc_start: 0.9089 (tt0) cc_final: 0.8592 (tm-30) REVERT: g 33 GLN cc_start: 0.8924 (mm-40) cc_final: 0.8510 (mp10) REVERT: g 35 LYS cc_start: 0.9527 (mptt) cc_final: 0.9185 (mptt) REVERT: g 46 PHE cc_start: 0.9135 (m-80) cc_final: 0.8870 (m-80) REVERT: j 108 MET cc_start: 0.7722 (ttp) cc_final: 0.7472 (mtm) REVERT: k 113 MET cc_start: 0.8879 (mmm) cc_final: 0.8623 (mmm) REVERT: n 20 MET cc_start: 0.8773 (tmm) cc_final: 0.8543 (tmm) REVERT: o 3 LYS cc_start: 0.8973 (tttm) cc_final: 0.8699 (tttt) REVERT: q 17 LEU cc_start: 0.9564 (mm) cc_final: 0.9271 (mm) REVERT: q 43 GLN cc_start: 0.8936 (OUTLIER) cc_final: 0.8599 (mp10) REVERT: s 94 ASP cc_start: 0.7699 (m-30) cc_final: 0.7397 (m-30) REVERT: t 1 MET cc_start: 0.5347 (tpp) cc_final: 0.4617 (tpp) REVERT: t 37 ASP cc_start: 0.8441 (p0) cc_final: 0.7859 (p0) REVERT: C 24 LYS cc_start: 0.9122 (ttpt) cc_final: 0.8860 (ptmm) REVERT: F 1 MET cc_start: 0.8213 (ttp) cc_final: 0.5842 (tpt) REVERT: G 103 TRP cc_start: 0.7390 (t-100) cc_final: 0.7032 (t-100) REVERT: G 108 GLN cc_start: 0.6948 (OUTLIER) cc_final: 0.6588 (pp30) REVERT: G 183 PHE cc_start: 0.9100 (OUTLIER) cc_final: 0.8548 (m-80) REVERT: I 74 TYR cc_start: 0.9375 (m-10) cc_final: 0.9086 (m-80) REVERT: I 134 TYR cc_start: 0.8639 (t80) cc_final: 0.8230 (t80) REVERT: I 181 PHE cc_start: 0.8203 (t80) cc_final: 0.6953 (t80) REVERT: I 195 ASN cc_start: 0.8269 (m110) cc_final: 0.8015 (m-40) REVERT: J 63 MET cc_start: 0.9105 (ppp) cc_final: 0.8145 (ppp) REVERT: J 80 LEU cc_start: 0.9196 (tp) cc_final: 0.8971 (mm) REVERT: J 94 PHE cc_start: 0.7870 (OUTLIER) cc_final: 0.7158 (m-10) REVERT: J 137 ARG cc_start: 0.9109 (mtp85) cc_final: 0.8336 (mtp85) REVERT: K 21 MET cc_start: 0.4152 (OUTLIER) cc_final: 0.3724 (tmm) REVERT: K 73 GLU cc_start: 0.8885 (tt0) cc_final: 0.8607 (pt0) REVERT: L 30 MET cc_start: 0.0938 (ttp) cc_final: 0.0569 (tmm) REVERT: N 56 MET cc_start: 0.6119 (tpt) cc_final: 0.5564 (tmm) REVERT: N 88 GLU cc_start: 0.7705 (OUTLIER) cc_final: 0.7429 (pm20) REVERT: Q 111 GLN cc_start: 0.8642 (mt0) cc_final: 0.8106 (tm-30) REVERT: Q 116 TYR cc_start: 0.7790 (m-80) cc_final: 0.7445 (m-80) REVERT: S 76 PHE cc_start: -0.0319 (OUTLIER) cc_final: -0.0593 (t80) REVERT: S 88 MET cc_start: 0.4662 (tpp) cc_final: 0.4275 (tmm) REVERT: S 100 TRP cc_start: 0.8341 (p-90) cc_final: 0.7963 (p-90) REVERT: T 42 PHE cc_start: 0.8258 (m-80) cc_final: 0.7493 (m-80) REVERT: T 79 GLN cc_start: 0.9177 (tm-30) cc_final: 0.8731 (mt0) REVERT: T 88 ARG cc_start: 0.6564 (tpp-160) cc_final: 0.5726 (mmp80) REVERT: U 77 GLU cc_start: 0.8713 (mm-30) cc_final: 0.8451 (mm-30) REVERT: V 10 ARG cc_start: 0.8326 (ttm170) cc_final: 0.8018 (tpm170) REVERT: X 12 LEU cc_start: 0.2746 (pt) cc_final: 0.2077 (tp) REVERT: X 43 MET cc_start: -0.0279 (mtt) cc_final: -0.0718 (mmt) REVERT: Y 26 MET cc_start: 0.9101 (ttp) cc_final: 0.8632 (mmt) outliers start: 158 outliers final: 110 residues processed: 682 average time/residue: 1.2830 time to fit residues: 1511.8639 Evaluate side-chains 664 residues out of total 4700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 546 time to evaluate : 6.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 19 VAL Chi-restraints excluded: chain b residue 52 HIS Chi-restraints excluded: chain b residue 131 MET Chi-restraints excluded: chain b residue 153 LEU Chi-restraints excluded: chain b residue 263 ASP Chi-restraints excluded: chain c residue 187 LEU Chi-restraints excluded: chain c residue 207 VAL Chi-restraints excluded: chain d residue 3 LEU Chi-restraints excluded: chain d residue 83 VAL Chi-restraints excluded: chain d residue 84 THR Chi-restraints excluded: chain e residue 6 TYR Chi-restraints excluded: chain e residue 35 LEU Chi-restraints excluded: chain e residue 51 ASN Chi-restraints excluded: chain e residue 113 PHE Chi-restraints excluded: chain e residue 157 THR Chi-restraints excluded: chain f residue 146 ASP Chi-restraints excluded: chain g residue 5 LEU Chi-restraints excluded: chain g residue 40 THR Chi-restraints excluded: chain g residue 54 LEU Chi-restraints excluded: chain g residue 78 VAL Chi-restraints excluded: chain g residue 138 VAL Chi-restraints excluded: chain k residue 56 ASP Chi-restraints excluded: chain k residue 58 LEU Chi-restraints excluded: chain k residue 76 VAL Chi-restraints excluded: chain k residue 114 LYS Chi-restraints excluded: chain l residue 77 ILE Chi-restraints excluded: chain l residue 118 THR Chi-restraints excluded: chain l residue 120 VAL Chi-restraints excluded: chain m residue 5 LYS Chi-restraints excluded: chain m residue 12 MET Chi-restraints excluded: chain m residue 59 ARG Chi-restraints excluded: chain m residue 124 LEU Chi-restraints excluded: chain n residue 37 THR Chi-restraints excluded: chain n residue 57 THR Chi-restraints excluded: chain n residue 74 GLU Chi-restraints excluded: chain o residue 18 LEU Chi-restraints excluded: chain p residue 63 ILE Chi-restraints excluded: chain p residue 96 LEU Chi-restraints excluded: chain q residue 43 GLN Chi-restraints excluded: chain q residue 82 LEU Chi-restraints excluded: chain q residue 94 LEU Chi-restraints excluded: chain q residue 97 ILE Chi-restraints excluded: chain r residue 41 ILE Chi-restraints excluded: chain r residue 55 ASP Chi-restraints excluded: chain r residue 95 ASP Chi-restraints excluded: chain s residue 20 VAL Chi-restraints excluded: chain s residue 74 ILE Chi-restraints excluded: chain s residue 103 ILE Chi-restraints excluded: chain u residue 7 ASP Chi-restraints excluded: chain u residue 48 VAL Chi-restraints excluded: chain u residue 99 SER Chi-restraints excluded: chain w residue 19 VAL Chi-restraints excluded: chain x residue 15 ASN Chi-restraints excluded: chain x residue 39 VAL Chi-restraints excluded: chain x residue 73 ARG Chi-restraints excluded: chain y residue 31 GLN Chi-restraints excluded: chain z residue 56 VAL Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain F residue 20 ASP Chi-restraints excluded: chain G residue 26 MET Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 108 GLN Chi-restraints excluded: chain G residue 169 HIS Chi-restraints excluded: chain G residue 183 PHE Chi-restraints excluded: chain G residue 203 ASP Chi-restraints excluded: chain H residue 18 ASN Chi-restraints excluded: chain H residue 36 PHE Chi-restraints excluded: chain H residue 164 THR Chi-restraints excluded: chain H residue 182 ASP Chi-restraints excluded: chain I residue 123 MET Chi-restraints excluded: chain I residue 139 ASN Chi-restraints excluded: chain J residue 65 LYS Chi-restraints excluded: chain J residue 94 PHE Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 162 GLU Chi-restraints excluded: chain K residue 11 HIS Chi-restraints excluded: chain K residue 21 MET Chi-restraints excluded: chain K residue 64 VAL Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain K residue 100 SER Chi-restraints excluded: chain L residue 5 VAL Chi-restraints excluded: chain L residue 72 VAL Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain L residue 100 MET Chi-restraints excluded: chain L residue 121 ASN Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain M residue 89 ASP Chi-restraints excluded: chain N residue 20 ILE Chi-restraints excluded: chain N residue 54 VAL Chi-restraints excluded: chain N residue 61 ASP Chi-restraints excluded: chain N residue 65 THR Chi-restraints excluded: chain N residue 88 GLU Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 71 LEU Chi-restraints excluded: chain P residue 110 THR Chi-restraints excluded: chain P residue 115 ILE Chi-restraints excluded: chain Q residue 81 ILE Chi-restraints excluded: chain S residue 76 PHE Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain U residue 69 ASP Chi-restraints excluded: chain V residue 19 SER Chi-restraints excluded: chain V residue 20 ILE Chi-restraints excluded: chain V residue 28 VAL Chi-restraints excluded: chain V residue 51 GLU Chi-restraints excluded: chain X residue 62 THR Chi-restraints excluded: chain X residue 66 VAL Chi-restraints excluded: chain Y residue 56 ILE Chi-restraints excluded: chain Y residue 60 GLN Chi-restraints excluded: chain Z residue 41 THR Chi-restraints excluded: chain Z residue 42 THR Chi-restraints excluded: chain a residue 18 THR Chi-restraints excluded: chain a residue 216 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1017 random chunks: chunk 948 optimal weight: 20.0000 chunk 110 optimal weight: 40.0000 chunk 560 optimal weight: 50.0000 chunk 718 optimal weight: 10.0000 chunk 556 optimal weight: 40.0000 chunk 828 optimal weight: 10.0000 chunk 549 optimal weight: 30.0000 chunk 980 optimal weight: 30.0000 chunk 613 optimal weight: 40.0000 chunk 597 optimal weight: 40.0000 chunk 452 optimal weight: 50.0000 overall best weight: 20.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 94 GLN c 140 HIS ** c 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 21 GLN ** g 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 133 GLN j 76 HIS ** j 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 53 HIS ** x 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 5 ASN ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 145 ASN ** H 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 18 ASN ** H 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 131 ASN ** K 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 81 ASN ** L 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 58 ASN ** Q 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.5603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.119 157486 Z= 0.595 Angle : 0.918 13.281 235697 Z= 0.455 Chirality : 0.047 0.388 30141 Planarity : 0.007 0.086 12551 Dihedral : 24.545 179.593 79017 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 40.48 Ramachandran Plot: Outliers : 0.11 % Allowed : 12.86 % Favored : 87.03 % Rotamer: Outliers : 4.36 % Allowed : 17.87 % Favored : 77.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -2.91 (0.10), residues: 5652 helix: -0.77 (0.12), residues: 1796 sheet: -2.28 (0.16), residues: 861 loop : -2.63 (0.10), residues: 2995 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP L 102 HIS 0.014 0.002 HIS j 132 PHE 0.030 0.003 PHE M 65 TYR 0.028 0.003 TYR I 75 ARG 0.019 0.001 ARG D 3 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11304 Ramachandran restraints generated. 5652 Oldfield, 0 Emsley, 5652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11304 Ramachandran restraints generated. 5652 Oldfield, 0 Emsley, 5652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 725 residues out of total 4700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 205 poor density : 520 time to evaluate : 6.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 172 THR cc_start: 0.9597 (OUTLIER) cc_final: 0.9159 (p) REVERT: b 224 MET cc_start: 0.8987 (mmt) cc_final: 0.8611 (mmp) REVERT: d 62 GLN cc_start: 0.9111 (OUTLIER) cc_final: 0.8342 (tp40) REVERT: d 136 GLN cc_start: 0.8599 (tp40) cc_final: 0.8323 (tp-100) REVERT: d 195 GLN cc_start: 0.8772 (mt0) cc_final: 0.8442 (mt0) REVERT: e 16 MET cc_start: 0.8904 (mmt) cc_final: 0.8684 (mmt) REVERT: e 27 VAL cc_start: 0.7693 (OUTLIER) cc_final: 0.7358 (m) REVERT: e 157 THR cc_start: 0.7304 (OUTLIER) cc_final: 0.7052 (t) REVERT: e 174 PHE cc_start: 0.8870 (m-80) cc_final: 0.8557 (m-80) REVERT: f 34 ARG cc_start: 0.6467 (ttp80) cc_final: 0.6170 (ttp-170) REVERT: f 57 TYR cc_start: 0.7704 (m-80) cc_final: 0.7239 (m-80) REVERT: f 87 GLN cc_start: 0.9105 (tt0) cc_final: 0.8570 (pp30) REVERT: g 27 ARG cc_start: 0.8939 (ptt-90) cc_final: 0.8602 (ptt90) REVERT: g 46 PHE cc_start: 0.9221 (m-80) cc_final: 0.8960 (m-80) REVERT: k 113 MET cc_start: 0.8960 (mmm) cc_final: 0.8714 (mmm) REVERT: m 124 LEU cc_start: 0.9271 (OUTLIER) cc_final: 0.9055 (mm) REVERT: n 20 MET cc_start: 0.8854 (tmm) cc_final: 0.8573 (tmm) REVERT: o 83 LEU cc_start: 0.9087 (OUTLIER) cc_final: 0.8772 (pp) REVERT: p 12 MET cc_start: 0.8247 (mmm) cc_final: 0.7844 (mmm) REVERT: q 17 LEU cc_start: 0.9569 (mm) cc_final: 0.9308 (mm) REVERT: q 43 GLN cc_start: 0.9072 (OUTLIER) cc_final: 0.8840 (mp10) REVERT: q 48 ASP cc_start: 0.7943 (m-30) cc_final: 0.7570 (m-30) REVERT: r 40 MET cc_start: 0.8551 (tmm) cc_final: 0.8197 (tmm) REVERT: s 9 HIS cc_start: 0.7884 (OUTLIER) cc_final: 0.7351 (m-70) REVERT: t 1 MET cc_start: 0.6660 (tpp) cc_final: 0.6425 (tpt) REVERT: u 17 ASP cc_start: 0.7593 (OUTLIER) cc_final: 0.6964 (p0) REVERT: x 73 ARG cc_start: 0.8920 (OUTLIER) cc_final: 0.8543 (ttp-110) REVERT: C 24 LYS cc_start: 0.9186 (ttpt) cc_final: 0.8876 (ptmm) REVERT: F 1 MET cc_start: 0.8375 (ttp) cc_final: 0.6087 (tpt) REVERT: F 36 ARG cc_start: 0.8817 (ptm160) cc_final: 0.8204 (ptm-80) REVERT: G 183 PHE cc_start: 0.8925 (OUTLIER) cc_final: 0.8387 (m-80) REVERT: H 17 TRP cc_start: 0.6816 (m-90) cc_final: 0.6506 (m-90) REVERT: I 74 TYR cc_start: 0.9209 (m-10) cc_final: 0.8662 (m-80) REVERT: I 134 TYR cc_start: 0.8671 (t80) cc_final: 0.8262 (t80) REVERT: I 138 PRO cc_start: 0.8738 (Cg_exo) cc_final: 0.8472 (Cg_endo) REVERT: I 181 PHE cc_start: 0.8323 (t80) cc_final: 0.7304 (t80) REVERT: J 80 LEU cc_start: 0.9300 (tp) cc_final: 0.9013 (mm) REVERT: J 94 PHE cc_start: 0.8604 (OUTLIER) cc_final: 0.7896 (m-10) REVERT: J 137 ARG cc_start: 0.9097 (mtp85) cc_final: 0.8303 (mtp85) REVERT: K 21 MET cc_start: 0.4199 (OUTLIER) cc_final: 0.3725 (tmm) REVERT: K 45 ARG cc_start: 0.7332 (OUTLIER) cc_final: 0.6661 (ttm110) REVERT: K 73 GLU cc_start: 0.8826 (tt0) cc_final: 0.8568 (pt0) REVERT: L 30 MET cc_start: 0.1629 (ttp) cc_final: 0.1361 (tmm) REVERT: M 110 MET cc_start: 0.7185 (ptp) cc_final: 0.6523 (ptp) REVERT: N 56 MET cc_start: 0.6465 (tpt) cc_final: 0.5760 (tmm) REVERT: N 88 GLU cc_start: 0.7653 (OUTLIER) cc_final: 0.7311 (pm20) REVERT: P 60 PHE cc_start: 0.6027 (t80) cc_final: 0.5697 (t80) REVERT: S 100 TRP cc_start: 0.8433 (p-90) cc_final: 0.8188 (p-90) REVERT: T 67 ASP cc_start: 0.9087 (p0) cc_final: 0.8841 (p0) REVERT: T 79 GLN cc_start: 0.9071 (tm-30) cc_final: 0.8767 (mt0) REVERT: U 77 GLU cc_start: 0.8498 (mm-30) cc_final: 0.8183 (mm-30) REVERT: V 10 ARG cc_start: 0.8556 (ttm170) cc_final: 0.8227 (tpm170) REVERT: V 26 ARG cc_start: 0.8372 (tmm-80) cc_final: 0.8088 (tmm-80) REVERT: Y 26 MET cc_start: 0.9302 (ttp) cc_final: 0.8772 (mmt) outliers start: 205 outliers final: 144 residues processed: 668 average time/residue: 1.2724 time to fit residues: 1466.6967 Evaluate side-chains 655 residues out of total 4700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 496 time to evaluate : 6.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 19 VAL Chi-restraints excluded: chain b residue 44 ASN Chi-restraints excluded: chain b residue 52 HIS Chi-restraints excluded: chain b residue 131 MET Chi-restraints excluded: chain b residue 153 LEU Chi-restraints excluded: chain b residue 172 THR Chi-restraints excluded: chain b residue 237 ARG Chi-restraints excluded: chain b residue 258 SER Chi-restraints excluded: chain b residue 263 ASP Chi-restraints excluded: chain c residue 187 LEU Chi-restraints excluded: chain c residue 207 VAL Chi-restraints excluded: chain d residue 3 LEU Chi-restraints excluded: chain d residue 62 GLN Chi-restraints excluded: chain d residue 73 ILE Chi-restraints excluded: chain d residue 83 VAL Chi-restraints excluded: chain d residue 84 THR Chi-restraints excluded: chain d residue 96 VAL Chi-restraints excluded: chain d residue 149 ILE Chi-restraints excluded: chain e residue 6 TYR Chi-restraints excluded: chain e residue 27 VAL Chi-restraints excluded: chain e residue 35 LEU Chi-restraints excluded: chain e residue 51 ASN Chi-restraints excluded: chain e residue 90 LEU Chi-restraints excluded: chain e residue 136 ILE Chi-restraints excluded: chain e residue 140 ILE Chi-restraints excluded: chain e residue 157 THR Chi-restraints excluded: chain f residue 146 ASP Chi-restraints excluded: chain g residue 5 LEU Chi-restraints excluded: chain g residue 54 LEU Chi-restraints excluded: chain g residue 78 VAL Chi-restraints excluded: chain g residue 91 PHE Chi-restraints excluded: chain g residue 138 VAL Chi-restraints excluded: chain g residue 139 PHE Chi-restraints excluded: chain j residue 55 ILE Chi-restraints excluded: chain j residue 84 ILE Chi-restraints excluded: chain k residue 56 ASP Chi-restraints excluded: chain k residue 58 LEU Chi-restraints excluded: chain k residue 76 VAL Chi-restraints excluded: chain k residue 97 THR Chi-restraints excluded: chain k residue 114 LYS Chi-restraints excluded: chain l residue 77 ILE Chi-restraints excluded: chain l residue 118 THR Chi-restraints excluded: chain l residue 120 VAL Chi-restraints excluded: chain m residue 12 MET Chi-restraints excluded: chain m residue 59 ARG Chi-restraints excluded: chain m residue 102 LEU Chi-restraints excluded: chain m residue 124 LEU Chi-restraints excluded: chain n residue 24 MET Chi-restraints excluded: chain n residue 29 VAL Chi-restraints excluded: chain n residue 32 GLU Chi-restraints excluded: chain n residue 34 ILE Chi-restraints excluded: chain n residue 37 THR Chi-restraints excluded: chain n residue 57 THR Chi-restraints excluded: chain n residue 74 GLU Chi-restraints excluded: chain n residue 113 ILE Chi-restraints excluded: chain o residue 18 LEU Chi-restraints excluded: chain o residue 83 LEU Chi-restraints excluded: chain o residue 108 ASP Chi-restraints excluded: chain p residue 7 LEU Chi-restraints excluded: chain p residue 63 ILE Chi-restraints excluded: chain p residue 65 ASN Chi-restraints excluded: chain p residue 96 LEU Chi-restraints excluded: chain p residue 109 ILE Chi-restraints excluded: chain q residue 43 GLN Chi-restraints excluded: chain q residue 79 ILE Chi-restraints excluded: chain q residue 82 LEU Chi-restraints excluded: chain q residue 94 LEU Chi-restraints excluded: chain q residue 97 ILE Chi-restraints excluded: chain r residue 41 ILE Chi-restraints excluded: chain r residue 55 ASP Chi-restraints excluded: chain r residue 95 ASP Chi-restraints excluded: chain s residue 9 HIS Chi-restraints excluded: chain s residue 20 VAL Chi-restraints excluded: chain s residue 55 ILE Chi-restraints excluded: chain s residue 74 ILE 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 u residue 7 ASP Chi-restraints excluded: chain u residue 17 ASP Chi-restraints excluded: chain u residue 48 VAL Chi-restraints excluded: chain v residue 66 ASP Chi-restraints excluded: chain v residue 77 VAL Chi-restraints excluded: chain w residue 19 VAL Chi-restraints excluded: chain x residue 15 ASN Chi-restraints excluded: chain x residue 59 ASP Chi-restraints excluded: chain x residue 73 ARG Chi-restraints excluded: chain y residue 31 GLN Chi-restraints excluded: chain z residue 56 VAL Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain F residue 12 ARG Chi-restraints excluded: chain F residue 20 ASP Chi-restraints excluded: chain G residue 14 HIS Chi-restraints excluded: chain G residue 26 MET Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 109 SER Chi-restraints excluded: chain G residue 152 ASP Chi-restraints excluded: chain G residue 169 HIS Chi-restraints excluded: chain G residue 183 PHE Chi-restraints excluded: chain G residue 203 ASP Chi-restraints excluded: chain H residue 18 ASN Chi-restraints excluded: chain H residue 36 PHE Chi-restraints excluded: chain H residue 182 ASP Chi-restraints excluded: chain I residue 98 ASP Chi-restraints excluded: chain I residue 123 MET Chi-restraints excluded: chain I residue 139 ASN Chi-restraints excluded: chain I residue 154 VAL Chi-restraints excluded: chain J residue 65 LYS Chi-restraints excluded: chain J residue 94 PHE Chi-restraints excluded: chain J residue 110 MET Chi-restraints excluded: chain J residue 123 LEU Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 135 VAL Chi-restraints excluded: chain J residue 162 GLU Chi-restraints excluded: chain K residue 11 HIS Chi-restraints excluded: chain K residue 21 MET Chi-restraints excluded: chain K residue 45 ARG Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain K residue 100 SER Chi-restraints excluded: chain L residue 5 VAL Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain L residue 100 MET Chi-restraints excluded: chain L residue 121 ASN Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain M residue 89 ASP Chi-restraints excluded: chain N residue 54 VAL Chi-restraints excluded: chain N residue 61 ASP Chi-restraints excluded: chain N residue 64 ILE Chi-restraints excluded: chain N residue 65 THR Chi-restraints excluded: chain N residue 88 GLU Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 71 LEU Chi-restraints excluded: chain P residue 16 SER Chi-restraints excluded: chain P residue 81 LEU Chi-restraints excluded: chain P residue 110 THR Chi-restraints excluded: chain P residue 115 ILE Chi-restraints excluded: chain Q residue 28 GLN Chi-restraints excluded: chain Q residue 39 THR Chi-restraints excluded: chain R residue 42 VAL Chi-restraints excluded: chain S residue 76 PHE Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain U residue 69 ASP Chi-restraints excluded: chain V residue 19 SER Chi-restraints excluded: chain V residue 28 VAL Chi-restraints excluded: chain X residue 62 THR Chi-restraints excluded: chain X residue 66 VAL Chi-restraints excluded: chain Y residue 14 GLU Chi-restraints excluded: chain Y residue 56 ILE Chi-restraints excluded: chain Y residue 60 GLN Chi-restraints excluded: chain Z residue 41 THR Chi-restraints excluded: chain Z residue 42 THR Chi-restraints excluded: chain a residue 18 THR Chi-restraints excluded: chain a residue 216 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1017 random chunks: chunk 606 optimal weight: 40.0000 chunk 391 optimal weight: 50.0000 chunk 585 optimal weight: 20.0000 chunk 295 optimal weight: 9.9990 chunk 192 optimal weight: 6.9990 chunk 189 optimal weight: 5.9990 chunk 623 optimal weight: 50.0000 chunk 667 optimal weight: 50.0000 chunk 484 optimal weight: 0.0870 chunk 91 optimal weight: 9.9990 chunk 770 optimal weight: 20.0000 overall best weight: 6.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 162 GLN ** b 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 133 GLN ** j 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 65 ASN ** p 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 71 ASN ** t 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 5 ASN ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 18 ASN ** H 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 131 ASN L 129 ASN ** O 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 45 ASN ** S 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.5274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 157486 Z= 0.231 Angle : 0.629 15.455 235697 Z= 0.323 Chirality : 0.036 0.293 30141 Planarity : 0.005 0.057 12551 Dihedral : 24.357 179.508 79017 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 23.97 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.97 % Favored : 90.96 % Rotamer: Outliers : 3.32 % Allowed : 19.34 % Favored : 77.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -2.48 (0.11), residues: 5652 helix: -0.33 (0.12), residues: 1790 sheet: -2.09 (0.16), residues: 855 loop : -2.40 (0.10), residues: 3007 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP L 102 HIS 0.010 0.001 HIS Q 76 PHE 0.033 0.002 PHE M 65 TYR 0.032 0.002 TYR M 127 ARG 0.041 0.001 ARG y 23 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11304 Ramachandran restraints generated. 5652 Oldfield, 0 Emsley, 5652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11304 Ramachandran restraints generated. 5652 Oldfield, 0 Emsley, 5652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 722 residues out of total 4700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 566 time to evaluate : 5.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 224 MET cc_start: 0.9109 (mmt) cc_final: 0.8707 (mmp) REVERT: d 136 GLN cc_start: 0.8416 (tp40) cc_final: 0.8051 (tp-100) REVERT: d 195 GLN cc_start: 0.8681 (mt0) cc_final: 0.8213 (mt0) REVERT: e 95 MET cc_start: 0.8742 (ttp) cc_final: 0.8482 (mtm) REVERT: e 157 THR cc_start: 0.7299 (OUTLIER) cc_final: 0.7067 (t) REVERT: e 174 PHE cc_start: 0.8845 (m-80) cc_final: 0.8429 (m-80) REVERT: f 25 ILE cc_start: 0.7813 (tt) cc_final: 0.7502 (pt) REVERT: f 34 ARG cc_start: 0.6353 (ttp80) cc_final: 0.6063 (ttp-170) REVERT: f 57 TYR cc_start: 0.7771 (m-80) cc_final: 0.7317 (m-80) REVERT: f 87 GLN cc_start: 0.9092 (tt0) cc_final: 0.8619 (pp30) REVERT: g 27 ARG cc_start: 0.8921 (ptt-90) cc_final: 0.8666 (ptt90) REVERT: g 133 GLN cc_start: 0.6705 (OUTLIER) cc_final: 0.6086 (pm20) REVERT: k 32 TYR cc_start: 0.7626 (m-80) cc_final: 0.7343 (m-80) REVERT: k 113 MET cc_start: 0.8908 (mmm) cc_final: 0.8664 (mmm) REVERT: n 20 MET cc_start: 0.8820 (tmm) cc_final: 0.8490 (tmm) REVERT: n 43 GLU cc_start: 0.7927 (mm-30) cc_final: 0.7623 (mm-30) REVERT: o 3 LYS cc_start: 0.8970 (tttm) cc_final: 0.8710 (tttt) REVERT: o 83 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8699 (pp) REVERT: q 17 LEU cc_start: 0.9579 (mm) cc_final: 0.9304 (mm) REVERT: q 43 GLN cc_start: 0.8922 (OUTLIER) cc_final: 0.8583 (mp10) REVERT: q 48 ASP cc_start: 0.7708 (m-30) cc_final: 0.7467 (m-30) REVERT: r 12 HIS cc_start: 0.8661 (OUTLIER) cc_final: 0.8362 (m-70) REVERT: s 94 ASP cc_start: 0.7774 (m-30) cc_final: 0.7437 (m-30) REVERT: t 1 MET cc_start: 0.5824 (tpp) cc_final: 0.5134 (tpp) REVERT: t 37 ASP cc_start: 0.8511 (p0) cc_final: 0.7935 (p0) REVERT: u 87 GLU cc_start: 0.8673 (OUTLIER) cc_final: 0.8119 (pm20) REVERT: C 24 LYS cc_start: 0.9136 (ttpt) cc_final: 0.8891 (ptmm) REVERT: F 1 MET cc_start: 0.8243 (ttp) cc_final: 0.6228 (tpt) REVERT: F 36 ARG cc_start: 0.8739 (ptm160) cc_final: 0.8469 (ptm160) REVERT: G 103 TRP cc_start: 0.7504 (t-100) cc_final: 0.6898 (t-100) REVERT: G 108 GLN cc_start: 0.7273 (pt0) cc_final: 0.6945 (pp30) REVERT: G 183 PHE cc_start: 0.8953 (OUTLIER) cc_final: 0.8390 (m-80) REVERT: I 74 TYR cc_start: 0.9341 (m-10) cc_final: 0.9001 (m-80) REVERT: I 134 TYR cc_start: 0.8678 (t80) cc_final: 0.8175 (t80) REVERT: I 138 PRO cc_start: 0.8801 (Cg_exo) cc_final: 0.8520 (Cg_endo) REVERT: I 181 PHE cc_start: 0.8254 (t80) cc_final: 0.7103 (t80) REVERT: J 61 LYS cc_start: 0.9498 (mtpt) cc_final: 0.9066 (mmmm) REVERT: J 80 LEU cc_start: 0.9239 (tp) cc_final: 0.9025 (mm) REVERT: J 94 PHE cc_start: 0.8167 (OUTLIER) cc_final: 0.7514 (m-10) REVERT: J 151 MET cc_start: 0.9098 (ppp) cc_final: 0.8835 (ppp) REVERT: K 1 MET cc_start: 0.4216 (ttm) cc_final: 0.3865 (tpp) REVERT: K 9 MET cc_start: 0.6076 (mmp) cc_final: 0.4933 (ptm) REVERT: K 21 MET cc_start: 0.3553 (OUTLIER) cc_final: 0.3205 (tmm) REVERT: K 73 GLU cc_start: 0.8838 (tt0) cc_final: 0.8566 (pt0) REVERT: L 30 MET cc_start: 0.0987 (ttp) cc_final: 0.0692 (tmm) REVERT: M 26 MET cc_start: 0.8491 (mpp) cc_final: 0.8270 (mpp) REVERT: N 56 MET cc_start: 0.6439 (tpt) cc_final: 0.5873 (tmm) REVERT: N 88 GLU cc_start: 0.7683 (OUTLIER) cc_final: 0.7445 (pm20) REVERT: O 45 ARG cc_start: 0.5458 (mtt180) cc_final: 0.5151 (mtt180) REVERT: P 60 PHE cc_start: 0.6000 (t80) cc_final: 0.5685 (t80) REVERT: P 108 ASN cc_start: 0.3551 (t0) cc_final: 0.3323 (t0) REVERT: Q 111 GLN cc_start: 0.8579 (mt0) cc_final: 0.8095 (tm-30) REVERT: Q 116 TYR cc_start: 0.7802 (m-80) cc_final: 0.7462 (m-80) REVERT: S 76 PHE cc_start: -0.0395 (OUTLIER) cc_final: -0.0668 (t80) REVERT: S 100 TRP cc_start: 0.8594 (p-90) cc_final: 0.8314 (p-90) REVERT: T 79 GLN cc_start: 0.9105 (tm-30) cc_final: 0.8780 (mt0) REVERT: U 77 GLU cc_start: 0.8551 (mm-30) cc_final: 0.8236 (mm-30) REVERT: V 10 ARG cc_start: 0.8416 (ttm170) cc_final: 0.8111 (tpm170) REVERT: V 26 ARG cc_start: 0.8359 (tmm-80) cc_final: 0.8035 (tmm-80) REVERT: V 76 ARG cc_start: 0.8355 (ptt90) cc_final: 0.8018 (ptm160) REVERT: X 12 LEU cc_start: 0.2985 (pt) cc_final: 0.2493 (tp) REVERT: Y 26 MET cc_start: 0.9152 (ttp) cc_final: 0.8679 (mmt) outliers start: 156 outliers final: 117 residues processed: 670 average time/residue: 1.2937 time to fit residues: 1489.5328 Evaluate side-chains 676 residues out of total 4700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 548 time to evaluate : 6.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 19 VAL Chi-restraints excluded: chain b residue 44 ASN Chi-restraints excluded: chain b residue 52 HIS Chi-restraints excluded: chain b residue 131 MET Chi-restraints excluded: chain b residue 153 LEU Chi-restraints excluded: chain b residue 237 ARG Chi-restraints excluded: chain b residue 239 PHE Chi-restraints excluded: chain b residue 258 SER Chi-restraints excluded: chain b residue 263 ASP Chi-restraints excluded: chain c residue 187 LEU Chi-restraints excluded: chain c residue 207 VAL Chi-restraints excluded: chain d residue 3 LEU Chi-restraints excluded: chain d residue 73 ILE Chi-restraints excluded: chain d residue 84 THR Chi-restraints excluded: chain d residue 178 VAL Chi-restraints excluded: chain e residue 6 TYR Chi-restraints excluded: chain e residue 35 LEU Chi-restraints excluded: chain e residue 51 ASN Chi-restraints excluded: chain e residue 113 PHE Chi-restraints excluded: chain e residue 136 ILE Chi-restraints excluded: chain e residue 140 ILE Chi-restraints excluded: chain e residue 157 THR Chi-restraints excluded: chain f residue 146 ASP Chi-restraints excluded: chain g residue 5 LEU Chi-restraints excluded: chain g residue 40 THR Chi-restraints excluded: chain g residue 78 VAL Chi-restraints excluded: chain g residue 133 GLN Chi-restraints excluded: chain g residue 138 VAL Chi-restraints excluded: chain k residue 56 ASP Chi-restraints excluded: chain k residue 58 LEU Chi-restraints excluded: chain k residue 76 VAL Chi-restraints excluded: chain k residue 114 LYS Chi-restraints excluded: chain l residue 77 ILE Chi-restraints excluded: chain l residue 118 THR Chi-restraints excluded: chain l residue 120 VAL Chi-restraints excluded: chain m residue 12 MET Chi-restraints excluded: chain m residue 59 ARG Chi-restraints excluded: chain m residue 102 LEU Chi-restraints excluded: chain m residue 124 LEU Chi-restraints excluded: chain m residue 126 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 83 LEU Chi-restraints excluded: chain p residue 7 LEU Chi-restraints excluded: chain p residue 29 VAL Chi-restraints excluded: chain p residue 63 ILE Chi-restraints excluded: chain p residue 96 LEU Chi-restraints excluded: chain q residue 43 GLN Chi-restraints excluded: chain q residue 82 LEU Chi-restraints excluded: chain q residue 94 LEU Chi-restraints excluded: chain q residue 97 ILE Chi-restraints excluded: chain r residue 12 HIS Chi-restraints excluded: chain r residue 41 ILE Chi-restraints excluded: chain r residue 95 ASP Chi-restraints excluded: chain s residue 20 VAL Chi-restraints excluded: chain s residue 74 ILE Chi-restraints excluded: chain s residue 103 ILE Chi-restraints excluded: chain u residue 7 ASP Chi-restraints excluded: chain u residue 48 VAL Chi-restraints excluded: chain u residue 87 GLU Chi-restraints excluded: chain v residue 77 VAL Chi-restraints excluded: chain w residue 19 VAL Chi-restraints excluded: chain x residue 15 ASN Chi-restraints excluded: chain x residue 39 VAL Chi-restraints excluded: chain y residue 31 GLN Chi-restraints excluded: chain z residue 56 VAL Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain E residue 30 HIS Chi-restraints excluded: chain F residue 20 ASP Chi-restraints excluded: chain G residue 26 MET Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 152 ASP Chi-restraints excluded: chain G residue 169 HIS Chi-restraints excluded: chain G residue 183 PHE Chi-restraints excluded: chain G residue 203 ASP Chi-restraints excluded: chain H residue 18 ASN Chi-restraints excluded: chain H residue 36 PHE Chi-restraints excluded: chain H residue 182 ASP Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain I residue 123 MET Chi-restraints excluded: chain I residue 139 ASN Chi-restraints excluded: chain I residue 154 VAL Chi-restraints excluded: chain J residue 67 ARG Chi-restraints excluded: chain J residue 94 PHE Chi-restraints excluded: chain J residue 123 LEU Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 162 GLU Chi-restraints excluded: chain K residue 11 HIS Chi-restraints excluded: chain K residue 21 MET Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain K residue 100 SER Chi-restraints excluded: chain L residue 5 VAL Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain L residue 100 MET Chi-restraints excluded: chain L residue 121 ASN Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain M residue 39 LEU Chi-restraints excluded: chain M residue 89 ASP Chi-restraints excluded: chain N residue 54 VAL Chi-restraints excluded: chain N residue 61 ASP Chi-restraints excluded: chain N residue 64 ILE Chi-restraints excluded: chain N residue 88 GLU Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 71 LEU Chi-restraints excluded: chain P residue 110 THR Chi-restraints excluded: chain P residue 115 ILE Chi-restraints excluded: chain Q residue 81 ILE Chi-restraints excluded: chain S residue 76 PHE Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain U residue 69 ASP Chi-restraints excluded: chain V residue 19 SER Chi-restraints excluded: chain V residue 28 VAL Chi-restraints excluded: chain V residue 51 GLU Chi-restraints excluded: chain X residue 57 VAL Chi-restraints excluded: chain X residue 62 THR Chi-restraints excluded: chain X residue 66 VAL Chi-restraints excluded: chain Y residue 56 ILE Chi-restraints excluded: chain Y residue 60 GLN Chi-restraints excluded: chain Z residue 41 THR Chi-restraints excluded: chain a residue 175 ILE Chi-restraints excluded: chain a residue 216 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1017 random chunks: chunk 891 optimal weight: 30.0000 chunk 939 optimal weight: 20.0000 chunk 856 optimal weight: 50.0000 chunk 913 optimal weight: 10.0000 chunk 938 optimal weight: 10.0000 chunk 549 optimal weight: 6.9990 chunk 397 optimal weight: 4.9990 chunk 717 optimal weight: 20.0000 chunk 280 optimal weight: 8.9990 chunk 825 optimal weight: 10.0000 chunk 863 optimal weight: 20.0000 overall best weight: 8.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 71 ASN ** t 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 18 ASN ** H 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 131 ASN ** L 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.5376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 157486 Z= 0.277 Angle : 0.642 19.097 235697 Z= 0.328 Chirality : 0.036 0.300 30141 Planarity : 0.005 0.076 12551 Dihedral : 24.318 179.828 79017 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 25.99 Ramachandran Plot: Outliers : 0.05 % Allowed : 10.60 % Favored : 89.35 % Rotamer: Outliers : 3.40 % Allowed : 19.28 % Favored : 77.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -2.45 (0.11), residues: 5652 helix: -0.28 (0.12), residues: 1788 sheet: -2.10 (0.16), residues: 902 loop : -2.38 (0.11), residues: 2962 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP L 102 HIS 0.010 0.001 HIS V 46 PHE 0.038 0.002 PHE g 29 TYR 0.028 0.002 TYR M 127 ARG 0.009 0.001 ARG x 73 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11304 Ramachandran restraints generated. 5652 Oldfield, 0 Emsley, 5652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11304 Ramachandran restraints generated. 5652 Oldfield, 0 Emsley, 5652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 704 residues out of total 4700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 544 time to evaluate : 6.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 172 THR cc_start: 0.9558 (OUTLIER) cc_final: 0.9093 (p) REVERT: b 224 MET cc_start: 0.9102 (mmt) cc_final: 0.8733 (mmp) REVERT: d 136 GLN cc_start: 0.8497 (tp40) cc_final: 0.8202 (tp-100) REVERT: d 195 GLN cc_start: 0.8770 (mt0) cc_final: 0.8511 (mt0) REVERT: e 16 MET cc_start: 0.8902 (mmt) cc_final: 0.8527 (mmm) REVERT: e 157 THR cc_start: 0.7075 (OUTLIER) cc_final: 0.6861 (t) REVERT: e 174 PHE cc_start: 0.8852 (m-80) cc_final: 0.8443 (m-80) REVERT: f 25 ILE cc_start: 0.7557 (tt) cc_final: 0.7343 (pt) REVERT: f 34 ARG cc_start: 0.6287 (ttp80) cc_final: 0.6062 (ttp-170) REVERT: f 57 TYR cc_start: 0.7775 (m-80) cc_final: 0.7325 (m-80) REVERT: f 87 GLN cc_start: 0.9142 (tt0) cc_final: 0.8646 (pp30) REVERT: g 27 ARG cc_start: 0.8883 (ptt-90) cc_final: 0.8615 (ptt90) REVERT: g 46 PHE cc_start: 0.9173 (m-80) cc_final: 0.8950 (m-80) REVERT: k 113 MET cc_start: 0.8933 (mmm) cc_final: 0.8686 (mmm) REVERT: n 20 MET cc_start: 0.8839 (tmm) cc_final: 0.8500 (tmm) REVERT: n 43 GLU cc_start: 0.7936 (mm-30) cc_final: 0.7631 (mm-30) REVERT: o 3 LYS cc_start: 0.8986 (tttm) cc_final: 0.8704 (tttt) REVERT: p 105 LYS cc_start: 0.7784 (mmtt) cc_final: 0.7431 (mmtt) REVERT: q 17 LEU cc_start: 0.9585 (mm) cc_final: 0.9308 (mm) REVERT: q 43 GLN cc_start: 0.8975 (OUTLIER) cc_final: 0.8604 (mp10) REVERT: q 48 ASP cc_start: 0.7711 (m-30) cc_final: 0.7300 (m-30) REVERT: s 94 ASP cc_start: 0.7768 (m-30) cc_final: 0.7454 (m-30) REVERT: t 1 MET cc_start: 0.5603 (tpp) cc_final: 0.5235 (tpp) REVERT: t 37 ASP cc_start: 0.8556 (p0) cc_final: 0.7951 (p0) REVERT: C 24 LYS cc_start: 0.9155 (ttpt) cc_final: 0.8925 (ptmm) REVERT: F 1 MET cc_start: 0.8290 (ttp) cc_final: 0.6179 (tpt) REVERT: G 103 TRP cc_start: 0.7534 (t-100) cc_final: 0.6917 (t-100) REVERT: G 108 GLN cc_start: 0.7283 (pt0) cc_final: 0.6979 (pp30) REVERT: G 109 SER cc_start: 0.6629 (OUTLIER) cc_final: 0.6414 (p) REVERT: G 183 PHE cc_start: 0.8950 (OUTLIER) cc_final: 0.8401 (m-80) REVERT: H 17 TRP cc_start: 0.6316 (m-90) cc_final: 0.5969 (m-90) REVERT: I 74 TYR cc_start: 0.9329 (m-10) cc_final: 0.8978 (m-80) REVERT: I 134 TYR cc_start: 0.8690 (t80) cc_final: 0.8197 (t80) REVERT: I 138 PRO cc_start: 0.8794 (Cg_exo) cc_final: 0.8518 (Cg_endo) REVERT: I 181 PHE cc_start: 0.8262 (t80) cc_final: 0.7216 (t80) REVERT: J 94 PHE cc_start: 0.8164 (OUTLIER) cc_final: 0.7505 (m-10) REVERT: J 151 MET cc_start: 0.9084 (ppp) cc_final: 0.8819 (ppp) REVERT: K 1 MET cc_start: 0.4567 (ttm) cc_final: 0.4319 (tpp) REVERT: K 73 GLU cc_start: 0.8844 (tt0) cc_final: 0.8576 (pt0) REVERT: L 30 MET cc_start: 0.1038 (ttp) cc_final: 0.0755 (tmm) REVERT: M 26 MET cc_start: 0.8461 (mpp) cc_final: 0.8220 (mpp) REVERT: N 56 MET cc_start: 0.6468 (tpt) cc_final: 0.5907 (tmm) REVERT: N 88 GLU cc_start: 0.7658 (OUTLIER) cc_final: 0.7448 (pm20) REVERT: P 60 PHE cc_start: 0.6009 (t80) cc_final: 0.5703 (t80) REVERT: Q 111 GLN cc_start: 0.8547 (mt0) cc_final: 0.8125 (tm-30) REVERT: Q 116 TYR cc_start: 0.7797 (m-80) cc_final: 0.7459 (m-80) REVERT: S 76 PHE cc_start: -0.0396 (OUTLIER) cc_final: -0.0661 (t80) REVERT: S 88 MET cc_start: 0.5253 (tmm) cc_final: 0.5023 (tpp) REVERT: S 100 TRP cc_start: 0.8480 (p-90) cc_final: 0.8231 (p-90) REVERT: T 79 GLN cc_start: 0.9107 (tm-30) cc_final: 0.8777 (mt0) REVERT: U 77 GLU cc_start: 0.8626 (mm-30) cc_final: 0.8316 (mm-30) REVERT: V 26 ARG cc_start: 0.8353 (tmm-80) cc_final: 0.8125 (tmm-80) REVERT: X 12 LEU cc_start: 0.3005 (pt) cc_final: 0.2429 (tp) REVERT: Y 26 MET cc_start: 0.9154 (ttp) cc_final: 0.8678 (mmt) REVERT: a 218 MET cc_start: -0.1946 (mmt) cc_final: -0.3141 (mtt) outliers start: 160 outliers final: 130 residues processed: 644 average time/residue: 1.2739 time to fit residues: 1419.0941 Evaluate side-chains 668 residues out of total 4700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 530 time to evaluate : 6.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 19 VAL Chi-restraints excluded: chain b residue 44 ASN Chi-restraints excluded: chain b residue 52 HIS Chi-restraints excluded: chain b residue 131 MET Chi-restraints excluded: chain b residue 153 LEU Chi-restraints excluded: chain b residue 172 THR Chi-restraints excluded: chain b residue 237 ARG Chi-restraints excluded: chain b residue 239 PHE Chi-restraints excluded: chain b residue 258 SER Chi-restraints excluded: chain b residue 263 ASP Chi-restraints excluded: chain c residue 187 LEU Chi-restraints excluded: chain c residue 207 VAL Chi-restraints excluded: chain d residue 3 LEU Chi-restraints excluded: chain d residue 73 ILE Chi-restraints excluded: chain d residue 83 VAL Chi-restraints excluded: chain d residue 84 THR Chi-restraints excluded: chain d residue 178 VAL Chi-restraints excluded: chain e residue 6 TYR Chi-restraints excluded: chain e residue 35 LEU Chi-restraints excluded: chain e residue 51 ASN Chi-restraints excluded: chain e residue 113 PHE Chi-restraints excluded: chain e residue 136 ILE Chi-restraints excluded: chain e residue 140 ILE Chi-restraints excluded: chain e residue 157 THR Chi-restraints excluded: chain f residue 146 ASP Chi-restraints excluded: chain g residue 5 LEU Chi-restraints excluded: chain g residue 40 THR Chi-restraints excluded: chain g residue 78 VAL Chi-restraints excluded: chain g residue 138 VAL Chi-restraints excluded: chain k residue 56 ASP Chi-restraints excluded: chain k residue 58 LEU Chi-restraints excluded: chain k residue 76 VAL Chi-restraints excluded: chain k residue 114 LYS Chi-restraints excluded: chain l residue 77 ILE Chi-restraints excluded: chain l residue 118 THR Chi-restraints excluded: chain l residue 120 VAL Chi-restraints excluded: chain m residue 12 MET Chi-restraints excluded: chain m residue 59 ARG Chi-restraints excluded: chain m residue 102 LEU Chi-restraints excluded: chain n residue 37 THR Chi-restraints excluded: chain n residue 57 THR Chi-restraints excluded: chain n residue 74 GLU Chi-restraints excluded: chain n residue 110 MET Chi-restraints excluded: chain o residue 18 LEU Chi-restraints excluded: chain o residue 83 LEU Chi-restraints excluded: chain p residue 7 LEU Chi-restraints excluded: chain p residue 29 VAL Chi-restraints excluded: chain p residue 63 ILE Chi-restraints excluded: chain p residue 96 LEU Chi-restraints excluded: chain p residue 109 ILE Chi-restraints excluded: chain q residue 43 GLN Chi-restraints excluded: chain q residue 79 ILE Chi-restraints excluded: chain q residue 82 LEU Chi-restraints excluded: chain q residue 94 LEU Chi-restraints excluded: chain q residue 97 ILE Chi-restraints excluded: chain r residue 41 ILE Chi-restraints excluded: chain r residue 95 ASP Chi-restraints excluded: chain s residue 20 VAL Chi-restraints excluded: chain s residue 74 ILE Chi-restraints excluded: chain s residue 103 ILE Chi-restraints excluded: chain u residue 7 ASP Chi-restraints excluded: chain u residue 48 VAL Chi-restraints excluded: chain v residue 30 ILE Chi-restraints excluded: chain v residue 77 VAL Chi-restraints excluded: chain w residue 17 LEU Chi-restraints excluded: chain w residue 19 VAL Chi-restraints excluded: chain x residue 15 ASN Chi-restraints excluded: chain x residue 39 VAL Chi-restraints excluded: chain y residue 31 GLN Chi-restraints excluded: chain z residue 56 VAL Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain E residue 30 HIS Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain F residue 20 ASP Chi-restraints excluded: chain G residue 26 MET Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 109 SER Chi-restraints excluded: chain G residue 152 ASP Chi-restraints excluded: chain G residue 169 HIS Chi-restraints excluded: chain G residue 183 PHE Chi-restraints excluded: chain G residue 203 ASP Chi-restraints excluded: chain H residue 36 PHE Chi-restraints excluded: chain H residue 182 ASP Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain I residue 123 MET Chi-restraints excluded: chain I residue 139 ASN Chi-restraints excluded: chain I residue 154 VAL Chi-restraints excluded: chain J residue 67 ARG Chi-restraints excluded: chain J residue 94 PHE Chi-restraints excluded: chain J residue 123 LEU Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 131 ASN Chi-restraints excluded: chain J residue 162 GLU Chi-restraints excluded: chain K residue 11 HIS Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain K residue 100 SER Chi-restraints excluded: chain L residue 5 VAL Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain L residue 93 VAL Chi-restraints excluded: chain L residue 100 MET Chi-restraints excluded: chain L residue 121 ASN Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain M residue 39 LEU Chi-restraints excluded: chain M residue 77 VAL Chi-restraints excluded: chain M residue 89 ASP Chi-restraints excluded: chain N residue 29 ILE Chi-restraints excluded: chain N residue 54 VAL Chi-restraints excluded: chain N residue 61 ASP Chi-restraints excluded: chain N residue 64 ILE Chi-restraints excluded: chain N residue 88 GLU Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 71 LEU Chi-restraints excluded: chain P residue 81 LEU Chi-restraints excluded: chain P residue 110 THR Chi-restraints excluded: chain P residue 115 ILE Chi-restraints excluded: chain Q residue 39 THR Chi-restraints excluded: chain Q residue 81 ILE Chi-restraints excluded: chain R residue 75 SER Chi-restraints excluded: chain S residue 76 PHE Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain U residue 69 ASP Chi-restraints excluded: chain V residue 19 SER Chi-restraints excluded: chain V residue 28 VAL Chi-restraints excluded: chain V residue 51 GLU Chi-restraints excluded: chain X residue 57 VAL Chi-restraints excluded: chain X residue 62 THR Chi-restraints excluded: chain X residue 66 VAL Chi-restraints excluded: chain Y residue 56 ILE Chi-restraints excluded: chain Y residue 60 GLN Chi-restraints excluded: chain Z residue 41 THR Chi-restraints excluded: chain Z residue 42 THR Chi-restraints excluded: chain a residue 175 ILE Chi-restraints excluded: chain a residue 216 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1017 random chunks: chunk 910 optimal weight: 10.0000 chunk 599 optimal weight: 50.0000 chunk 965 optimal weight: 10.0000 chunk 589 optimal weight: 30.0000 chunk 458 optimal weight: 9.9990 chunk 671 optimal weight: 50.0000 chunk 1013 optimal weight: 50.0000 chunk 932 optimal weight: 10.0000 chunk 806 optimal weight: 10.0000 chunk 83 optimal weight: 20.0000 chunk 623 optimal weight: 50.0000 overall best weight: 9.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 131 ASN ** K 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 39 GLN ** U 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 55 HIS ** a 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.5555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 157486 Z= 0.323 Angle : 0.675 17.487 235697 Z= 0.343 Chirality : 0.037 0.299 30141 Planarity : 0.005 0.070 12551 Dihedral : 24.347 179.709 79017 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 28.20 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.88 % Favored : 89.08 % Rotamer: Outliers : 3.19 % Allowed : 19.77 % Favored : 77.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -2.50 (0.11), residues: 5652 helix: -0.38 (0.12), residues: 1804 sheet: -2.06 (0.16), residues: 879 loop : -2.40 (0.11), residues: 2969 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP L 102 HIS 0.011 0.002 HIS V 46 PHE 0.052 0.002 PHE X 40 TYR 0.029 0.002 TYR M 127 ARG 0.010 0.001 ARG T 53 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11304 Ramachandran restraints generated. 5652 Oldfield, 0 Emsley, 5652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11304 Ramachandran restraints generated. 5652 Oldfield, 0 Emsley, 5652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 685 residues out of total 4700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 535 time to evaluate : 6.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 172 THR cc_start: 0.9568 (OUTLIER) cc_final: 0.9074 (p) REVERT: b 224 MET cc_start: 0.9081 (mmt) cc_final: 0.8788 (mmp) REVERT: d 136 GLN cc_start: 0.8512 (tp40) cc_final: 0.8216 (tp-100) REVERT: d 195 GLN cc_start: 0.8841 (mt0) cc_final: 0.8528 (mt0) REVERT: e 16 MET cc_start: 0.8855 (mmt) cc_final: 0.8445 (mmm) REVERT: e 157 THR cc_start: 0.7122 (OUTLIER) cc_final: 0.6894 (t) REVERT: e 174 PHE cc_start: 0.8891 (m-80) cc_final: 0.8538 (m-80) REVERT: f 57 TYR cc_start: 0.7775 (m-80) cc_final: 0.7322 (m-80) REVERT: f 87 GLN cc_start: 0.9141 (tt0) cc_final: 0.8654 (pp30) REVERT: g 27 ARG cc_start: 0.8917 (ptt-90) cc_final: 0.8651 (ptt90) REVERT: g 46 PHE cc_start: 0.9191 (m-80) cc_final: 0.8950 (m-80) REVERT: k 113 MET cc_start: 0.8952 (mmm) cc_final: 0.8701 (mmm) REVERT: n 20 MET cc_start: 0.8851 (tmm) cc_final: 0.8504 (tmm) REVERT: p 12 MET cc_start: 0.7482 (mmm) cc_final: 0.7159 (mmm) REVERT: p 105 LYS cc_start: 0.7881 (mmtt) cc_final: 0.7496 (mmtt) REVERT: q 17 LEU cc_start: 0.9587 (mm) cc_final: 0.9319 (mm) REVERT: q 43 GLN cc_start: 0.8987 (OUTLIER) cc_final: 0.8595 (mp10) REVERT: q 48 ASP cc_start: 0.7742 (m-30) cc_final: 0.7340 (m-30) REVERT: s 9 HIS cc_start: 0.7688 (OUTLIER) cc_final: 0.7139 (m-70) REVERT: t 1 MET cc_start: 0.6317 (tpp) cc_final: 0.5653 (tpp) REVERT: t 37 ASP cc_start: 0.8551 (p0) cc_final: 0.7952 (p0) REVERT: D 1 MET cc_start: 0.7274 (tmm) cc_final: 0.6399 (ptm) REVERT: D 22 MET cc_start: 0.8658 (mmm) cc_final: 0.8269 (mmm) REVERT: F 1 MET cc_start: 0.8269 (ttp) cc_final: 0.6035 (tpt) REVERT: F 36 ARG cc_start: 0.8758 (ptm160) cc_final: 0.8465 (ptm160) REVERT: G 48 MET cc_start: 0.8961 (ppp) cc_final: 0.8658 (pmm) REVERT: G 103 TRP cc_start: 0.7569 (t-100) cc_final: 0.6955 (t-100) REVERT: G 108 GLN cc_start: 0.7097 (pt0) cc_final: 0.6837 (pp30) REVERT: G 109 SER cc_start: 0.6887 (OUTLIER) cc_final: 0.6670 (p) REVERT: G 183 PHE cc_start: 0.8938 (OUTLIER) cc_final: 0.8370 (m-80) REVERT: H 17 TRP cc_start: 0.6242 (m-90) cc_final: 0.5930 (m-90) REVERT: I 74 TYR cc_start: 0.9306 (m-10) cc_final: 0.8867 (m-80) REVERT: I 134 TYR cc_start: 0.8659 (t80) cc_final: 0.8139 (t80) REVERT: I 181 PHE cc_start: 0.8261 (t80) cc_final: 0.7140 (t80) REVERT: J 94 PHE cc_start: 0.8288 (OUTLIER) cc_final: 0.7556 (m-10) REVERT: J 151 MET cc_start: 0.9107 (ppp) cc_final: 0.8840 (ppp) REVERT: K 1 MET cc_start: 0.4541 (ttm) cc_final: 0.4293 (tpp) REVERT: K 9 MET cc_start: 0.6052 (mmp) cc_final: 0.4926 (ttp) REVERT: K 73 GLU cc_start: 0.8853 (tt0) cc_final: 0.8572 (pt0) REVERT: L 30 MET cc_start: 0.1079 (ttp) cc_final: 0.0792 (tmm) REVERT: M 26 MET cc_start: 0.8457 (mpp) cc_final: 0.8209 (mpp) REVERT: N 56 MET cc_start: 0.6561 (tpt) cc_final: 0.6034 (tmm) REVERT: N 88 GLU cc_start: 0.7675 (OUTLIER) cc_final: 0.7472 (pm20) REVERT: P 60 PHE cc_start: 0.6022 (t80) cc_final: 0.5731 (t80) REVERT: Q 111 GLN cc_start: 0.8493 (mt0) cc_final: 0.8087 (tm-30) REVERT: Q 116 TYR cc_start: 0.7810 (m-80) cc_final: 0.7475 (m-80) REVERT: S 76 PHE cc_start: -0.0437 (OUTLIER) cc_final: -0.0734 (t80) REVERT: S 88 MET cc_start: 0.5338 (tmm) cc_final: 0.5107 (tpp) REVERT: S 100 TRP cc_start: 0.8431 (p-90) cc_final: 0.8202 (p-90) REVERT: T 79 GLN cc_start: 0.9139 (tm-30) cc_final: 0.8826 (mt0) REVERT: U 77 GLU cc_start: 0.8642 (mm-30) cc_final: 0.8370 (mm-30) REVERT: V 26 ARG cc_start: 0.8415 (tmm-80) cc_final: 0.8028 (tmm-80) REVERT: Y 26 MET cc_start: 0.9166 (ttp) cc_final: 0.8697 (mmt) REVERT: a 218 MET cc_start: -0.1904 (mmt) cc_final: -0.3045 (mtt) outliers start: 150 outliers final: 128 residues processed: 636 average time/residue: 1.3030 time to fit residues: 1436.6500 Evaluate side-chains 659 residues out of total 4700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 522 time to evaluate : 6.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 19 VAL Chi-restraints excluded: chain b residue 44 ASN Chi-restraints excluded: chain b residue 52 HIS Chi-restraints excluded: chain b residue 131 MET Chi-restraints excluded: chain b residue 153 LEU Chi-restraints excluded: chain b residue 172 THR Chi-restraints excluded: chain b residue 237 ARG Chi-restraints excluded: chain b residue 239 PHE Chi-restraints excluded: chain b residue 258 SER Chi-restraints excluded: chain b residue 263 ASP Chi-restraints excluded: chain c residue 187 LEU Chi-restraints excluded: chain c residue 207 VAL Chi-restraints excluded: chain d residue 3 LEU Chi-restraints excluded: chain d residue 73 ILE Chi-restraints excluded: chain d residue 83 VAL Chi-restraints excluded: chain d residue 84 THR Chi-restraints excluded: chain d residue 178 VAL Chi-restraints excluded: chain e residue 6 TYR Chi-restraints excluded: chain e residue 35 LEU Chi-restraints excluded: chain e residue 51 ASN Chi-restraints excluded: chain e residue 113 PHE Chi-restraints excluded: chain e residue 136 ILE Chi-restraints excluded: chain e residue 140 ILE Chi-restraints excluded: chain e residue 157 THR Chi-restraints excluded: chain f residue 146 ASP Chi-restraints excluded: chain g residue 5 LEU Chi-restraints excluded: chain g residue 40 THR Chi-restraints excluded: chain g residue 78 VAL Chi-restraints excluded: chain g residue 138 VAL Chi-restraints excluded: chain k residue 56 ASP Chi-restraints excluded: chain k residue 58 LEU Chi-restraints excluded: chain k residue 76 VAL Chi-restraints excluded: chain k residue 114 LYS Chi-restraints excluded: chain l residue 77 ILE Chi-restraints excluded: chain l residue 118 THR Chi-restraints excluded: chain l residue 120 VAL Chi-restraints excluded: chain m residue 12 MET Chi-restraints excluded: chain m residue 59 ARG Chi-restraints excluded: chain m residue 102 LEU Chi-restraints excluded: chain m residue 126 ILE Chi-restraints excluded: chain n residue 37 THR Chi-restraints excluded: chain n residue 57 THR Chi-restraints excluded: chain n residue 74 GLU Chi-restraints excluded: chain n residue 110 MET Chi-restraints excluded: chain o residue 18 LEU Chi-restraints excluded: chain o residue 83 LEU Chi-restraints excluded: chain p residue 29 VAL Chi-restraints excluded: chain p residue 63 ILE Chi-restraints excluded: chain p residue 96 LEU Chi-restraints excluded: chain p residue 109 ILE Chi-restraints excluded: chain q residue 43 GLN Chi-restraints excluded: chain q residue 79 ILE Chi-restraints excluded: chain q residue 82 LEU Chi-restraints excluded: chain q residue 94 LEU Chi-restraints excluded: chain q residue 97 ILE Chi-restraints excluded: chain r residue 41 ILE Chi-restraints excluded: chain r residue 55 ASP Chi-restraints excluded: chain r residue 95 ASP Chi-restraints excluded: chain s residue 9 HIS Chi-restraints excluded: chain s residue 20 VAL Chi-restraints excluded: chain s residue 74 ILE Chi-restraints excluded: chain s residue 103 ILE Chi-restraints excluded: chain u residue 7 ASP Chi-restraints excluded: chain u residue 48 VAL Chi-restraints excluded: chain v residue 30 ILE Chi-restraints excluded: chain v residue 77 VAL Chi-restraints excluded: chain w residue 19 VAL Chi-restraints excluded: chain x residue 15 ASN Chi-restraints excluded: chain x residue 39 VAL Chi-restraints excluded: chain y residue 31 GLN Chi-restraints excluded: chain z residue 56 VAL Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain E residue 30 HIS Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain F residue 20 ASP Chi-restraints excluded: chain G residue 26 MET Chi-restraints excluded: chain G residue 41 ASN Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 109 SER Chi-restraints excluded: chain G residue 152 ASP Chi-restraints excluded: chain G residue 183 PHE Chi-restraints excluded: chain G residue 203 ASP Chi-restraints excluded: chain H residue 36 PHE Chi-restraints excluded: chain H residue 182 ASP Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain I residue 123 MET Chi-restraints excluded: chain I residue 139 ASN Chi-restraints excluded: chain I residue 154 VAL Chi-restraints excluded: chain J residue 94 PHE Chi-restraints excluded: chain J residue 123 LEU Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 162 GLU Chi-restraints excluded: chain K residue 11 HIS Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain K residue 100 SER Chi-restraints excluded: chain L residue 5 VAL Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain L residue 93 VAL Chi-restraints excluded: chain L residue 100 MET Chi-restraints excluded: chain L residue 121 ASN Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain M residue 39 LEU Chi-restraints excluded: chain M residue 77 VAL Chi-restraints excluded: chain M residue 89 ASP Chi-restraints excluded: chain N residue 29 ILE Chi-restraints excluded: chain N residue 54 VAL Chi-restraints excluded: chain N residue 61 ASP Chi-restraints excluded: chain N residue 64 ILE Chi-restraints excluded: chain N residue 88 GLU Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 71 LEU Chi-restraints excluded: chain P residue 81 LEU Chi-restraints excluded: chain P residue 110 THR Chi-restraints excluded: chain P residue 115 ILE Chi-restraints excluded: chain Q residue 39 THR Chi-restraints excluded: chain S residue 76 PHE Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain U residue 69 ASP Chi-restraints excluded: chain V residue 19 SER Chi-restraints excluded: chain V residue 28 VAL Chi-restraints excluded: chain X residue 57 VAL Chi-restraints excluded: chain X residue 62 THR Chi-restraints excluded: chain X residue 66 VAL Chi-restraints excluded: chain Y residue 56 ILE Chi-restraints excluded: chain Y residue 60 GLN Chi-restraints excluded: chain Z residue 41 THR Chi-restraints excluded: chain Z residue 42 THR Chi-restraints excluded: chain Z residue 55 HIS Chi-restraints excluded: chain a residue 175 ILE Chi-restraints excluded: chain a residue 216 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1017 random chunks: chunk 494 optimal weight: 8.9990 chunk 640 optimal weight: 40.0000 chunk 859 optimal weight: 50.0000 chunk 247 optimal weight: 7.9990 chunk 743 optimal weight: 20.0000 chunk 119 optimal weight: 9.9990 chunk 224 optimal weight: 5.9990 chunk 808 optimal weight: 10.0000 chunk 338 optimal weight: 10.0000 chunk 829 optimal weight: 10.0000 chunk 102 optimal weight: 8.9990 overall best weight: 8.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 93 HIS ** H 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 131 ASN ** O 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.066034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.042034 restraints weight = 1110205.947| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 3.25 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.5615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 157486 Z= 0.278 Angle : 0.642 17.310 235697 Z= 0.327 Chirality : 0.036 0.305 30141 Planarity : 0.005 0.063 12551 Dihedral : 24.334 179.710 79017 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 26.17 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.62 % Favored : 89.35 % Rotamer: Outliers : 3.30 % Allowed : 20.15 % Favored : 76.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.43 (0.11), residues: 5652 helix: -0.31 (0.12), residues: 1801 sheet: -2.05 (0.16), residues: 885 loop : -2.35 (0.11), residues: 2966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP L 102 HIS 0.040 0.001 HIS Z 55 PHE 0.030 0.002 PHE X 40 TYR 0.028 0.002 TYR M 127 ARG 0.015 0.001 ARG Z 54 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 28137.64 seconds wall clock time: 499 minutes 40.59 seconds (29980.59 seconds total)