Starting phenix.real_space_refine on Sat Mar 2 00:22:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k51_22670/03_2024/7k51_22670_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k51_22670/03_2024/7k51_22670.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k51_22670/03_2024/7k51_22670.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k51_22670/03_2024/7k51_22670.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k51_22670/03_2024/7k51_22670_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k51_22670/03_2024/7k51_22670_updated.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.019 sd= 1.404 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 4731 5.49 5 Mg 1 5.21 5 S 180 5.16 5 C 77766 2.51 5 N 28487 2.21 5 O 42205 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 ARG 33": "NH1" <-> "NH2" Residue "c ARG 59": "NH1" <-> "NH2" Residue "c ARG 77": "NH1" <-> "NH2" Residue "c ARG 83": "NH1" <-> "NH2" Residue "c ASP 103": "OD1" <-> "OD2" Residue "c ASP 108": "OD1" <-> "OD2" Residue "c ARG 169": "NH1" <-> "NH2" Residue "c ARG 184": "NH1" <-> "NH2" Residue "d ARG 21": "NH1" <-> "NH2" Residue "d ASP 22": "OD1" <-> "OD2" Residue "d ARG 44": "NH1" <-> "NH2" Residue "d ARG 49": "NH1" <-> "NH2" Residue "d ARG 61": "NH1" <-> "NH2" Residue "d ARG 88": "NH1" <-> "NH2" Residue "d ARG 102": "NH1" <-> "NH2" Residue "d ARG 162": "NH1" <-> "NH2" Residue "d ASP 168": "OD1" <-> "OD2" Residue "d ARG 170": "NH1" <-> "NH2" Residue "e ARG 70": "NH1" <-> "NH2" Residue "e ARG 79": "NH1" <-> "NH2" Residue "e ARG 91": "NH1" <-> "NH2" Residue "e GLU 93": "OE1" <-> "OE2" Residue "e ARG 101": "NH1" <-> "NH2" Residue "e ARG 109": "NH1" <-> "NH2" Residue "e ARG 111": "NH1" <-> "NH2" Residue "e ARG 114": "NH1" <-> "NH2" Residue "e ARG 132": "NH1" <-> "NH2" Residue "f ARG 2": "NH1" <-> "NH2" Residue "f ARG 152": "NH1" <-> "NH2" Residue "f ARG 162": "NH1" <-> "NH2" Residue "f ARG 169": "NH1" <-> "NH2" Residue "g PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 48": "OE1" <-> "OE2" Residue "h GLU 47": "OE1" <-> "OE2" Residue "i PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 GLU 86": "OE1" <-> "OE2" Residue "l ARG 126": "NH1" <-> "NH2" Residue "m ARG 10": "NH1" <-> "NH2" Residue "m ARG 18": "NH1" <-> "NH2" Residue "m PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 ASP 70": "OD1" <-> "OD2" Residue "m GLU 111": "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 ARG 118": "NH1" <-> "NH2" Residue "o ARG 10": "NH1" <-> "NH2" Residue "o ARG 16": "NH1" <-> "NH2" Residue "o ARG 25": "NH1" <-> "NH2" Residue "o TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o ARG 81": "NH1" <-> "NH2" Residue "o GLU 84": "OE1" <-> "OE2" Residue "o ARG 94": "NH1" <-> "NH2" Residue "o ARG 102": "NH1" <-> "NH2" Residue "o ARG 111": "NH1" <-> "NH2" Residue "p ARG 20": "NH1" <-> "NH2" Residue "p ARG 38": "NH1" <-> "NH2" Residue "p ARG 61": "NH1" <-> "NH2" Residue "p ARG 88": "NH1" <-> "NH2" Residue "p ARG 100": "NH1" <-> "NH2" Residue "p GLU 101": "OE1" <-> "OE2" Residue "p ARG 108": "NH1" <-> "NH2" Residue "q ARG 2": "NH1" <-> "NH2" Residue "q ARG 5": "NH1" <-> "NH2" Residue "q ARG 12": "NH1" <-> "NH2" Residue "q ARG 32": "NH1" <-> "NH2" Residue "q ARG 47": "NH1" <-> "NH2" Residue "q ARG 69": "NH1" <-> "NH2" Residue "r ARG 21": "NH1" <-> "NH2" Residue "r ARG 68": "NH1" <-> "NH2" Residue "r ARG 78": "NH1" <-> "NH2" Residue "r ARG 79": "NH1" <-> "NH2" Residue "r ARG 84": "NH1" <-> "NH2" Residue "s ASP 62": "OD1" <-> "OD2" Residue "s GLU 78": "OE1" <-> "OE2" Residue "s ARG 84": "NH1" <-> "NH2" Residue "s ARG 88": "NH1" <-> "NH2" Residue "s ARG 95": "NH1" <-> "NH2" Residue "s ARG 110": "NH1" <-> "NH2" Residue "t ARG 73": "NH1" <-> "NH2" Residue "u ARG 5": "NH1" <-> "NH2" Residue "u ARG 6": "NH1" <-> "NH2" Residue "u ARG 81": "NH1" <-> "NH2" Residue "u ARG 85": "NH1" <-> "NH2" Residue "u ARG 93": "NH1" <-> "NH2" Residue "v GLU 55": "OE1" <-> "OE2" Residue "y ARG 29": "NH1" <-> "NH2" Residue "y ARG 47": "NH1" <-> "NH2" Residue "y ARG 52": "NH1" <-> "NH2" Residue "z ARG 10": "NH1" <-> "NH2" Residue "z ARG 29": "NH1" <-> "NH2" Residue "z ARG 44": "NH1" <-> "NH2" Residue "A ASP 31": "OD1" <-> "OD2" Residue "A ARG 49": "NH1" <-> "NH2" Residue "A ARG 56": "NH1" <-> "NH2" Residue "B ARG 9": "NH1" <-> "NH2" Residue "B ARG 15": "NH1" <-> "NH2" Residue "B ARG 39": "NH1" <-> "NH2" Residue "B ARG 51": "NH1" <-> "NH2" Residue "C ARG 43": "NH1" <-> "NH2" Residue "D ARG 3": "NH1" <-> "NH2" Residue "D ARG 12": "NH1" <-> "NH2" Residue "D ARG 14": "NH1" <-> "NH2" Residue "D ARG 19": "NH1" <-> "NH2" Residue "D ARG 21": "NH1" <-> "NH2" Residue "D ARG 33": "NH1" <-> "NH2" Residue "D ARG 41": "NH1" <-> "NH2" Residue "E ARG 12": "NH1" <-> "NH2" Residue "E ARG 29": "NH1" <-> "NH2" Residue "E ARG 39": "NH1" <-> "NH2" Residue "E ARG 41": "NH1" <-> "NH2" Residue "F ARG 12": "NH1" <-> "NH2" Residue "F ARG 24": "NH1" <-> "NH2" Residue "G GLU 43": "OE1" <-> "OE2" Residue "G PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 107": "NH1" <-> "NH2" Residue "G ASP 203": "OD1" <-> "OD2" Residue "G GLU 222": "OE1" <-> "OE2" Residue "G ARG 224": "NH1" <-> "NH2" Residue "H GLU 81": "OE1" <-> "OE2" Residue "H ARG 106": "NH1" <-> "NH2" Residue "H ARG 130": "NH1" <-> "NH2" Residue "J PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 156": "NH1" <-> "NH2" Residue "L GLU 20": "OE1" <-> "OE2" Residue "L ASP 139": "OD1" <-> "OD2" Residue "M GLU 123": "OE1" <-> "OE2" Residue "N ASP 55": "OD1" <-> "OD2" Residue "N GLU 111": "OE1" <-> "OE2" Residue "N ARG 123": "NH1" <-> "NH2" Residue "P PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 55": "NH1" <-> "NH2" Residue "Q GLU 69": "OE1" <-> "OE2" Residue "S TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 37": "OD1" <-> "OD2" Residue "U ARG 28": "NH1" <-> "NH2" Residue "U PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 51": "OE1" <-> "OE2" Residue "V GLU 59": "OE1" <-> "OE2" Residue "W ARG 11": "NH1" <-> "NH2" Residue "W TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 64": "OE1" <-> "OE2" Residue "X GLU 72": "OE1" <-> "OE2" Residue "Z GLU 38": "OE1" <-> "OE2" Residue "Z ARG 66": "NH1" <-> "NH2" Residue "a ARG 7": "NH1" <-> "NH2" Residue "a ARG 12": "NH1" <-> "NH2" Residue "a ASP 16": "OD1" <-> "OD2" Residue "a ARG 162": "NH1" <-> "NH2" Residue "a TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 166": "OD1" <-> "OD2" Residue "8 ASP 20": "OD1" <-> "OD2" Residue "8 TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 ASP 51": "OD1" <-> "OD2" Residue "8 GLU 58": "OE1" <-> "OE2" Residue "8 PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 GLU 80": "OE1" <-> "OE2" Residue "8 ASP 94": "OD1" <-> "OD2" Residue "8 GLU 100": "OE1" <-> "OE2" Residue "8 PHE 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 GLU 203": "OE1" <-> "OE2" Residue "8 TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 GLU 205": "OE1" <-> "OE2" Residue "8 ASP 206": "OD1" <-> "OD2" Residue "8 GLU 358": "OE1" <-> "OE2" Residue "8 ASP 395": "OD1" <-> "OD2" Residue "8 GLU 476": "OE1" <-> "OE2" Residue "8 ASP 554": "OD1" <-> "OD2" Residue "8 ASP 585": "OD1" <-> "OD2" Residue "8 TYR 687": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 GLU 700": "OE1" <-> "OE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 153370 Number of models: 1 Model: "" Number of chains: 62 Chain: "b" Number of atoms: 2083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2083 Classifications: {'peptide': 271} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 253} Chain: "c" Number of atoms: 1565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1565 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 202} Chain: "d" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1552 Classifications: {'peptide': 201} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 195} Chain: "e" Number of atoms: 1411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1411 Classifications: {'peptide': 177} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 170} Chain: "f" Number of atoms: 1323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1323 Classifications: {'peptide': 176} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "g" Number of atoms: 936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 936 Classifications: {'peptide': 125} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain breaks: 1 Chain: "h" Number of atoms: 633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 633 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 2, 'TRANS': 81} Chain: "i" Number of atoms: 551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 551 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 8, 'TRANS': 65} Chain: "j" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1129 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 135} Chain: "k" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 939 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "l" Number of atoms: 1045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1045 Classifications: {'peptide': 143} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 138} Chain: "m" Number of atoms: 1074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1074 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 128} Chain: "n" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 961 Classifications: {'peptide': 120} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "o" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 892 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "p" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 917 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "q" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 947 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'TRANS': 116} Chain: "r" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 816 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 101} Chain: "s" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 857 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 107} Chain: "t" Number of atoms: 739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 739 Classifications: {'peptide': 93} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 91} Chain: "u" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 780 Classifications: {'peptide': 102} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "v" Number of atoms: 753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 753 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "w" Number of atoms: 575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 575 Classifications: {'peptide': 75} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "x" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 625 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "y" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 509 Classifications: {'peptide': 63} Modifications used: {'COO': 1} Link IDs: {'TRANS': 62} Chain: "z" Number of atoms: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 449 Classifications: {'peptide': 58} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "A" Number of atoms: 523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 523 Classifications: {'peptide': 66} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "B" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 444 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 54} Chain: "C" Number of atoms: 410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 410 Classifications: {'peptide': 50} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "D" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 377 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "E" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 504 Classifications: {'peptide': 64} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "F" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 302 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "G" Number of atoms: 1705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1705 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 210} Chain: "H" Number of atoms: 1625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1625 Classifications: {'peptide': 206} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 198} Chain: "I" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1643 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 198} Chain: "J" Number of atoms: 1157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1157 Classifications: {'peptide': 157} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 151} Chain: "K" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 818 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "L" Number of atoms: 1182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1182 Classifications: {'peptide': 151} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain: "M" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 979 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "N" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1022 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "O" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 787 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 92} Chain: "P" Number of atoms: 870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 870 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 108} Chain: "Q" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 955 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 115} Chain: "R" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 884 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 109} Chain: "S" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 805 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "T" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 714 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'TRANS': 87} Chain: "U" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 649 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "V" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 649 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain: "W" Number of atoms: 536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 536 Classifications: {'peptide': 65} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "X" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 638 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 73} Chain: "Y" Number of atoms: 665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 665 Classifications: {'peptide': 85} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 83} Chain: "Z" Number of atoms: 545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 545 Classifications: {'peptide': 65} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "a" Number of atoms: 1027 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1027 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 131} Chain breaks: 1 Chain: "3" Number of atoms: 33012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1539, 33012 Classifications: {'RNA': 1539} Modifications used: {'5*END': 1, 'rna2p_pur': 93, 'rna2p_pyr': 60, 'rna3p_pur': 781, 'rna3p_pyr': 605} Link IDs: {'rna2p': 153, 'rna3p': 1385} 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': 217, 'rna2p_pyr': 98, 'rna3p_pur': 1457, 'rna3p_pyr': 1131} Link IDs: {'rna2p': 315, 'rna3p': 2587} Chain: "2" Number of atoms: 2568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 2568 Classifications: {'RNA': 120} Modifications used: {'5*END': 1, 'rna2p_pur': 5, 'rna2p_pyr': 2, 'rna3p_pur': 60, 'rna3p_pyr': 53} Link IDs: {'rna2p': 7, 'rna3p': 112} Chain: "5" Number of atoms: 1647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1647 Classifications: {'RNA': 77} Modifications used: {'rna2p_pur': 10, 'rna2p_pyr': 5, 'rna3p_pur': 30, 'rna3p_pyr': 32} Link IDs: {'rna2p': 14, 'rna3p': 62} Chain: "6" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1640 Classifications: {'RNA': 77} Modifications used: {'5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 5, 'rna3p_pur': 33, 'rna3p_pyr': 33} Link IDs: {'rna2p': 11, 'rna3p': 65} Chain: "4" Number of atoms: 348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 348 Classifications: {'RNA': 16} Modifications used: {'rna2p_pur': 2, 'rna3p_pur': 10, 'rna3p_pyr': 4} Link IDs: {'rna2p': 1, 'rna3p': 14} Chain: "8" Number of atoms: 5312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 685, 5312 Classifications: {'peptide': 685} Link IDs: {'PTRANS': 33, 'TRANS': 651} Chain breaks: 1 Chain: "1" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "5" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Classifications: {'peptide': 1} Chain: "8" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GCP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 55.06, per 1000 atoms: 0.36 Number of scatterers: 153370 At special positions: 0 Unit cell: (271.95, 254.1, 243.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 180 16.00 P 4731 15.00 Mg 1 11.99 O 42205 8.00 N 28487 7.00 C 77766 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 60.52 Conformation dependent library (CDL) restraints added in 7.2 seconds 13034 Ramachandran restraints generated. 6517 Oldfield, 0 Emsley, 6517 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 12184 Finding SS restraints... Warning!!! ksdssp method is not applicable for structures that cannot fit in PDB format. Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 194 helices and 72 sheets defined 37.4% alpha, 17.7% beta 1397 base pairs and 2283 stacking pairs defined. Time for finding SS restraints: 72.32 Creating SS restraints... Processing helix chain 'b' and resid 10 through 15 removed outlier: 7.403A pdb=" N HIS b 14 " --> pdb=" O PRO b 10 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N VAL b 15 " --> pdb=" O GLY b 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 10 through 15' Processing helix chain 'b' and resid 29 through 34 removed outlier: 4.231A pdb=" N LEU b 33 " --> pdb=" O PHE b 29 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N GLU b 34 " --> pdb=" O ALA b 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 29 through 34' Processing helix chain 'b' and resid 130 through 135 removed outlier: 3.610A pdb=" N ILE b 134 " --> pdb=" O PRO b 130 " (cutoff:3.500A) Proline residue: b 135 - end of helix No H-bonds generated for 'chain 'b' and resid 130 through 135' Processing helix chain 'b' and resid 206 through 214 removed outlier: 3.721A pdb=" N ALA b 210 " --> pdb=" O LYS b 206 " (cutoff:3.500A) Processing helix chain 'b' and resid 220 through 225 removed outlier: 3.929A pdb=" N MET b 224 " --> pdb=" O ARG b 220 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N ASN b 225 " --> pdb=" O GLY b 221 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 220 through 225' Processing helix chain 'b' and resid 259 through 267 removed outlier: 5.645A pdb=" N ASP b 263 " --> pdb=" O ASN b 259 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N LYS b 264 " --> pdb=" O LYS b 260 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N PHE b 265 " --> pdb=" O ARG b 261 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE b 266 " --> pdb=" O THR b 262 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N VAL b 267 " --> pdb=" O ASP b 263 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 259 through 267' Processing helix chain 'b' and resid 196 through 201 removed outlier: 4.110A pdb=" N MET b 200 " --> pdb=" O ALA b 197 " (cutoff:3.500A) Processing helix chain 'c' and resid 62 through 72 Processing helix chain 'c' and resid 120 through 125 Processing helix chain 'c' and resid 39 through 44 Processing helix chain 'd' and resid 15 through 20 Processing helix chain 'd' and resid 24 through 40 removed outlier: 3.652A pdb=" N ALA d 39 " --> pdb=" O TYR d 35 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG d 40 " --> pdb=" O ALA d 36 " (cutoff:3.500A) Processing helix chain 'd' and resid 97 through 116 Processing helix chain 'd' and resid 130 through 142 removed outlier: 3.505A pdb=" N LEU d 134 " --> pdb=" O LYS d 130 " (cutoff:3.500A) Processing helix chain 'd' and resid 154 through 162 removed outlier: 4.438A pdb=" N ALA d 160 " --> pdb=" O ASN d 156 " (cutoff:3.500A) Processing helix chain 'd' and resid 176 through 183 Processing helix chain 'd' and resid 189 through 201 removed outlier: 3.792A pdb=" N ALA d 201 " --> pdb=" O GLU d 197 " (cutoff:3.500A) Processing helix chain 'e' and resid 1 through 20 removed outlier: 5.552A pdb=" N VAL e 12 " --> pdb=" O LYS e 8 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LYS e 13 " --> pdb=" O ASP e 9 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N GLU e 18 " --> pdb=" O LYS e 14 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N PHE e 19 " --> pdb=" O LEU e 15 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N ASN e 20 " --> pdb=" O MET e 16 " (cutoff:3.500A) Processing helix chain 'e' and resid 45 through 60 removed outlier: 3.659A pdb=" N LEU e 49 " --> pdb=" O ASP e 45 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ASP e 50 " --> pdb=" O LYS e 46 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASP e 55 " --> pdb=" O ASN e 51 " (cutoff:3.500A) Processing helix chain 'e' and resid 92 through 110 removed outlier: 4.200A pdb=" N ILE e 105 " --> pdb=" O ARG e 101 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N VAL e 107 " --> pdb=" O ILE e 103 " (cutoff:3.500A) Proline residue: e 108 - end of helix Processing helix chain 'e' and resid 141 through 146 removed outlier: 6.951A pdb=" N VAL e 145 " --> pdb=" O ASP e 141 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N ASP e 146 " --> pdb=" O TYR e 142 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 141 through 146' Processing helix chain 'e' and resid 161 through 173 removed outlier: 3.619A pdb=" N PHE e 172 " --> pdb=" O LEU e 168 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ASP e 173 " --> pdb=" O LEU e 169 " (cutoff:3.500A) Processing helix chain 'f' and resid 1 through 7 removed outlier: 3.506A pdb=" N ALA f 6 " --> pdb=" O ARG f 2 " (cutoff:3.500A) Proline residue: f 7 - end of helix Processing helix chain 'f' and resid 59 through 80 Processing helix chain 'f' and resid 136 through 152 removed outlier: 4.520A pdb=" N ARG f 151 " --> pdb=" O LEU f 147 " (cutoff:3.500A) Processing helix chain 'g' and resid 22 through 28 Processing helix chain 'g' and resid 29 through 34 Processing helix chain 'g' and resid 40 through 49 Processing helix chain 'g' and resid 95 through 107 removed outlier: 3.634A pdb=" N ALA g 102 " --> pdb=" O ASP g 98 " (cutoff:3.500A) Processing helix chain 'h' and resid 3 through 21 removed outlier: 3.640A pdb=" N ALA h 19 " --> pdb=" O VAL h 15 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N LYS h 20 " --> pdb=" O SER h 16 " (cutoff:3.500A) Processing helix chain 'h' and resid 33 through 48 removed outlier: 4.765A pdb=" N THR h 39 " --> pdb=" O VAL h 35 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLU h 40 " --> pdb=" O ASP h 36 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N ARG h 42 " --> pdb=" O MET h 38 " (cutoff:3.500A) Processing helix chain 'h' and resid 62 through 68 removed outlier: 3.733A pdb=" N THR h 67 " --> pdb=" O ALA h 63 " (cutoff:3.500A) Proline residue: h 68 - end of helix Processing helix chain 'h' and resid 74 through 79 removed outlier: 3.547A pdb=" N GLY h 78 " --> pdb=" O ALA h 75 " (cutoff:3.500A) Proline residue: h 79 - end of helix Processing helix chain 'i' and resid 23 through 29 removed outlier: 3.555A pdb=" N LEU i 27 " --> pdb=" O VAL i 23 " (cutoff:3.500A) Processing helix chain 'i' and resid 33 through 46 removed outlier: 3.562A pdb=" N PHE i 37 " --> pdb=" O ASN i 33 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N CYS i 38 " --> pdb=" O ILE i 34 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LYS i 39 " --> pdb=" O MET i 35 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ALA i 40 " --> pdb=" O GLU i 36 " (cutoff:3.500A) Processing helix chain 'j' and resid 24 through 38 removed outlier: 3.681A pdb=" N GLU j 31 " --> pdb=" O ARG j 27 " (cutoff:3.500A) Processing helix chain 'j' and resid 67 through 72 Processing helix chain 'j' and resid 88 through 96 Processing helix chain 'j' and resid 97 through 110 removed outlier: 4.071A pdb=" N ILE j 101 " --> pdb=" O PRO j 97 " (cutoff:3.500A) Proline residue: j 110 - end of helix Processing helix chain 'j' and resid 112 through 122 removed outlier: 4.591A pdb=" N LEU j 122 " --> pdb=" O MET j 118 " (cutoff:3.500A) Processing helix chain 'k' and resid 104 through 109 removed outlier: 4.717A pdb=" N ARG k 108 " --> pdb=" O THR k 104 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N SER k 109 " --> pdb=" O ARG k 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 104 through 109' Processing helix chain 'k' and resid 110 through 120 removed outlier: 5.153A pdb=" N LYS k 114 " --> pdb=" O GLU k 110 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N ILE k 115 " --> pdb=" O LYS k 111 " (cutoff:3.500A) Proline residue: k 120 - end of helix Processing helix chain 'l' and resid 37 through 42 removed outlier: 3.966A pdb=" N ARG l 41 " --> pdb=" O GLY l 37 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N SER l 42 " --> pdb=" O GLN l 38 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 37 through 42' Processing helix chain 'l' and resid 56 through 62 removed outlier: 3.637A pdb=" N LEU l 61 " --> pdb=" O LEU l 57 " (cutoff:3.500A) Proline residue: l 62 - end of helix Processing helix chain 'l' and resid 68 through 75 removed outlier: 3.710A pdb=" N ALA l 72 " --> pdb=" O SER l 68 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ILE l 73 " --> pdb=" O ARG l 69 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N THR l 74 " --> pdb=" O LYS l 70 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ALA l 75 " --> pdb=" O ALA l 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 68 through 75' Processing helix chain 'l' and resid 78 through 83 removed outlier: 3.839A pdb=" N LEU l 82 " --> pdb=" O ARG l 78 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ALA l 83 " --> pdb=" O LEU l 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 78 through 83' Processing helix chain 'l' and resid 91 through 99 removed outlier: 4.246A pdb=" N LEU l 95 " --> pdb=" O ASP l 91 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N LYS l 96 " --> pdb=" O LEU l 92 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N ALA l 97 " --> pdb=" O ASN l 93 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA l 98 " --> pdb=" O THR l 94 " (cutoff:3.500A) Processing helix chain 'l' and resid 128 through 139 removed outlier: 3.817A pdb=" N ARG l 132 " --> pdb=" O THR l 128 " (cutoff:3.500A) Processing helix chain 'm' and resid 42 through 58 removed outlier: 4.025A pdb=" N MET m 53 " --> pdb=" O ALA m 49 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N ALA m 56 " --> pdb=" O ALA m 52 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS m 58 " --> pdb=" O THR m 54 " (cutoff:3.500A) Processing helix chain 'm' and resid 109 through 125 removed outlier: 3.569A pdb=" N LYS m 123 " --> pdb=" O LEU m 119 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU m 124 " --> pdb=" O ALA m 120 " (cutoff:3.500A) Proline residue: m 125 - end of helix Processing helix chain 'n' and resid 13 through 32 Processing helix chain 'n' and resid 38 through 57 removed outlier: 4.098A pdb=" N ARG n 46 " --> pdb=" O LYS n 42 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N VAL n 47 " --> pdb=" O GLU n 43 " (cutoff:3.500A) Proline residue: n 50 - end of helix removed outlier: 4.114A pdb=" N THR n 57 " --> pdb=" O THR n 53 " (cutoff:3.500A) Processing helix chain 'n' and resid 59 through 71 removed outlier: 4.373A pdb=" N THR n 70 " --> pdb=" O ALA n 66 " (cutoff:3.500A) Processing helix chain 'n' and resid 72 through 88 removed outlier: 4.086A pdb=" N PHE n 80 " --> pdb=" O VAL n 76 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ASN n 81 " --> pdb=" O ALA n 77 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N LEU n 83 " --> pdb=" O LEU n 79 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N GLY n 84 " --> pdb=" O PHE n 80 " (cutoff:3.500A) Proline residue: n 85 - end of helix Processing helix chain 'o' and resid 2 through 22 removed outlier: 4.866A pdb=" N ARG o 13 " --> pdb=" O ARG o 9 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N ALA o 14 " --> pdb=" O ARG o 10 " (cutoff:3.500A) Processing helix chain 'o' and resid 55 through 63 removed outlier: 5.377A pdb=" N GLN o 61 " --> pdb=" O ALA o 57 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N LYS o 63 " --> pdb=" O ALA o 59 " (cutoff:3.500A) Processing helix chain 'o' and resid 67 through 86 Processing helix chain 'o' and resid 101 through 114 Processing helix chain 'p' and resid 1 through 12 removed outlier: 4.089A pdb=" N GLN p 11 " --> pdb=" O LEU p 7 " (cutoff:3.500A) Processing helix chain 'p' and resid 96 through 102 removed outlier: 3.838A pdb=" N ARG p 100 " --> pdb=" O LEU p 96 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N GLU p 101 " --> pdb=" O TYR p 97 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ARG p 102 " --> pdb=" O TYR p 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'p' and resid 96 through 102' Processing helix chain 'p' and resid 103 through 108 removed outlier: 4.512A pdb=" N ARG p 108 " --> pdb=" O THR p 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'p' and resid 103 through 108' Processing helix chain 'q' and resid 5 through 21 removed outlier: 4.413A pdb=" N GLN q 19 " --> pdb=" O LYS q 15 " (cutoff:3.500A) Processing helix chain 'q' and resid 31 through 56 removed outlier: 4.718A pdb=" N GLN q 36 " --> pdb=" O ARG q 32 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ARG q 50 " --> pdb=" O TYR q 46 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N LYS q 53 " --> pdb=" O ARG q 49 " (cutoff:3.500A) Processing helix chain 'q' and resid 58 through 71 Processing helix chain 'q' and resid 74 through 86 Processing helix chain 'q' and resid 90 through 100 removed outlier: 3.839A pdb=" N ASP q 96 " --> pdb=" O LYS q 92 " (cutoff:3.500A) Processing helix chain 'q' and resid 101 through 117 Processing helix chain 's' and resid 13 through 25 removed outlier: 3.619A pdb=" N LEU s 19 " --> pdb=" O GLN s 15 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL s 20 " --> pdb=" O LYS s 16 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU s 23 " --> pdb=" O LEU s 19 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ILE s 24 " --> pdb=" O VAL s 20 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N ARG s 25 " --> pdb=" O ALA s 21 " (cutoff:3.500A) Processing helix chain 's' and resid 28 through 39 Processing helix chain 's' and resid 41 through 62 removed outlier: 3.657A pdb=" N VAL s 45 " --> pdb=" O LYS s 41 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL s 50 " --> pdb=" O LEU s 46 " (cutoff:3.500A) Processing helix chain 't' and resid 1 through 11 removed outlier: 4.257A pdb=" N LYS t 9 " --> pdb=" O GLU t 5 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N LEU t 11 " --> pdb=" O LEU t 7 " (cutoff:3.500A) Processing helix chain 't' and resid 17 through 26 Processing helix chain 't' and resid 39 through 51 Processing helix chain 'u' and resid 65 through 70 removed outlier: 4.289A pdb=" N VAL u 69 " --> pdb=" O GLN u 65 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N ALA u 70 " --> pdb=" O VAL u 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'u' and resid 65 through 70' Processing helix chain 'v' and resid 13 through 24 removed outlier: 4.427A pdb=" N ALA v 23 " --> pdb=" O ARG v 19 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ASN v 24 " --> pdb=" O LEU v 20 " (cutoff:3.500A) Processing helix chain 'v' and resid 43 through 52 removed outlier: 4.315A pdb=" N VAL v 47 " --> pdb=" O ASP v 43 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA v 52 " --> pdb=" O MET v 48 " (cutoff:3.500A) Processing helix chain 'v' and resid 53 through 59 removed outlier: 4.479A pdb=" N TYR v 57 " --> pdb=" O LYS v 53 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N SER v 58 " --> pdb=" O ALA v 54 " (cutoff:3.500A) Processing helix chain 'x' and resid 51 through 62 removed outlier: 4.344A pdb=" N GLY x 62 " --> pdb=" O ILE x 58 " (cutoff:3.500A) Processing helix chain 'x' and resid 63 through 74 Processing helix chain 'y' and resid 1 through 7 removed outlier: 3.510A pdb=" N LEU y 6 " --> pdb=" O LYS y 2 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N ARG y 7 " --> pdb=" O ALA y 3 " (cutoff:3.500A) Processing helix chain 'y' and resid 9 through 35 removed outlier: 3.948A pdb=" N GLU y 24 " --> pdb=" O ASN y 20 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLN y 25 " --> pdb=" O LEU y 21 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N PHE y 26 " --> pdb=" O LEU y 22 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N SER y 34 " --> pdb=" O MET y 30 " (cutoff:3.500A) Processing helix chain 'y' and resid 39 through 62 removed outlier: 4.384A pdb=" N LEU y 43 " --> pdb=" O GLN y 39 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N GLY y 62 " --> pdb=" O ASN y 58 " (cutoff:3.500A) Processing helix chain 'z' and resid 16 through 27 Processing helix chain 'z' and resid 40 through 51 Processing helix chain 'A' and resid 43 through 51 removed outlier: 3.872A pdb=" N GLN A 48 " --> pdb=" O PHE A 44 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASP A 50 " --> pdb=" O GLY A 46 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL A 51 " --> pdb=" O LYS A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 64 removed outlier: 3.507A pdb=" N ARG A 59 " --> pdb=" O GLY A 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 20 removed outlier: 3.986A pdb=" N HIS B 18 " --> pdb=" O MET B 14 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ASP B 19 " --> pdb=" O ARG B 15 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ALA B 20 " --> pdb=" O ARG B 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 16 Processing helix chain 'D' and resid 17 through 24 removed outlier: 4.135A pdb=" N THR D 24 " --> pdb=" O ALA D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 25 through 38 Processing helix chain 'E' and resid 6 through 13 removed outlier: 3.636A pdb=" N ARG E 12 " --> pdb=" O GLY E 8 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 45 removed outlier: 3.608A pdb=" N ARG E 44 " --> pdb=" O LYS E 40 " (cutoff:3.500A) Proline residue: E 45 - end of helix Processing helix chain 'E' and resid 50 through 62 removed outlier: 4.727A pdb=" N GLY E 55 " --> pdb=" O LYS E 51 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N LEU E 56 " --> pdb=" O GLY E 52 " (cutoff:3.500A) Proline residue: E 62 - end of helix Processing helix chain 'G' and resid 23 through 28 removed outlier: 3.910A pdb=" N LYS G 27 " --> pdb=" O ASN G 23 " (cutoff:3.500A) Proline residue: G 28 - end of helix No H-bonds generated for 'chain 'G' and resid 23 through 28' Processing helix chain 'G' and resid 41 through 60 removed outlier: 3.894A pdb=" N THR G 45 " --> pdb=" O ASN G 41 " (cutoff:3.500A) Proline residue: G 47 - end of helix Processing helix chain 'G' and resid 73 through 87 removed outlier: 4.519A pdb=" N GLU G 77 " --> pdb=" O ARG G 73 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N ALA G 78 " --> pdb=" O ALA G 74 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N CYS G 86 " --> pdb=" O ALA G 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 104 through 122 removed outlier: 4.097A pdb=" N GLN G 108 " --> pdb=" O LYS G 104 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER G 109 " --> pdb=" O THR G 105 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLN G 121 " --> pdb=" O GLU G 117 " (cutoff:3.500A) Processing helix chain 'G' and resid 129 through 151 removed outlier: 4.906A pdb=" N GLY G 149 " --> pdb=" O ASN G 145 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N ILE G 150 " --> pdb=" O SER G 146 " (cutoff:3.500A) Processing helix chain 'G' and resid 168 through 179 removed outlier: 3.643A pdb=" N LEU G 178 " --> pdb=" O GLU G 174 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N GLY G 179 " --> pdb=" O ALA G 175 " (cutoff:3.500A) Processing helix chain 'G' and resid 206 through 225 removed outlier: 3.714A pdb=" N THR G 210 " --> pdb=" O ILE G 206 " (cutoff:3.500A) Processing helix chain 'G' and resid 98 through 103 removed outlier: 4.304A pdb=" N TRP G 103 " --> pdb=" O GLY G 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 98 through 103' Processing helix chain 'H' and resid 5 through 14 removed outlier: 4.149A pdb=" N GLY H 12 " --> pdb=" O GLY H 8 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N ILE H 13 " --> pdb=" O ILE H 9 " (cutoff:3.500A) Processing helix chain 'H' and resid 27 through 50 removed outlier: 3.523A pdb=" N SER H 34 " --> pdb=" O ASP H 30 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N LYS H 48 " --> pdb=" O LYS H 44 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ALA H 49 " --> pdb=" O GLU H 45 " (cutoff:3.500A) Processing helix chain 'H' and resid 71 through 77 Processing helix chain 'H' and resid 80 through 95 Processing helix chain 'H' and resid 111 through 126 removed outlier: 4.555A pdb=" N ARG H 126 " --> pdb=" O GLN H 122 " (cutoff:3.500A) Processing helix chain 'H' and resid 128 through 144 removed outlier: 3.551A pdb=" N ALA H 132 " --> pdb=" O MET H 128 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N MET H 133 " --> pdb=" O PHE H 129 " (cutoff:3.500A) Processing helix chain 'I' and resid 6 through 15 removed outlier: 3.699A pdb=" N LEU I 10 " --> pdb=" O PRO I 6 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N SER I 11 " --> pdb=" O LYS I 7 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 65 Processing helix chain 'I' and resid 67 through 82 removed outlier: 3.566A pdb=" N ASN I 73 " --> pdb=" O ARG I 69 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N LYS I 82 " --> pdb=" O ALA I 78 " (cutoff:3.500A) Processing helix chain 'I' and resid 84 through 96 Processing helix chain 'I' and resid 97 through 105 Processing helix chain 'I' and resid 109 through 120 removed outlier: 3.866A pdb=" N HIS I 119 " --> pdb=" O GLN I 115 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N LYS I 120 " --> pdb=" O LEU I 116 " (cutoff:3.500A) Processing helix chain 'I' and resid 151 through 164 removed outlier: 5.310A pdb=" N LYS I 155 " --> pdb=" O GLN I 151 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N ALA I 156 " --> pdb=" O SER I 152 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLU I 162 " --> pdb=" O LEU I 158 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N GLN I 163 " --> pdb=" O GLU I 159 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ARG I 164 " --> pdb=" O LEU I 160 " (cutoff:3.500A) Processing helix chain 'I' and resid 186 through 191 removed outlier: 5.038A pdb=" N SER I 191 " --> pdb=" O ARG I 187 " (cutoff:3.500A) Processing helix chain 'I' and resid 195 through 205 removed outlier: 3.816A pdb=" N ILE I 199 " --> pdb=" O ASN I 195 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU I 202 " --> pdb=" O LEU I 198 " (cutoff:3.500A) Processing helix chain 'J' and resid 54 through 70 removed outlier: 3.528A pdb=" N ASN J 69 " --> pdb=" O LYS J 65 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N MET J 70 " --> pdb=" O ALA J 66 " (cutoff:3.500A) Processing helix chain 'J' and resid 107 through 118 removed outlier: 6.191A pdb=" N ALA J 112 " --> pdb=" O GLY J 108 " (cutoff:3.500A) Processing helix chain 'J' and resid 131 through 146 Processing helix chain 'J' and resid 148 through 156 Processing helix chain 'J' and resid 159 through 164 Processing helix chain 'K' and resid 11 through 19 removed outlier: 3.983A pdb=" N GLU K 16 " --> pdb=" O PRO K 12 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N GLN K 17 " --> pdb=" O ASP K 13 " (cutoff:3.500A) Proline residue: K 19 - end of helix Processing helix chain 'K' and resid 20 through 33 removed outlier: 3.542A pdb=" N ARG K 24 " --> pdb=" O GLY K 20 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TYR K 25 " --> pdb=" O MET K 21 " (cutoff:3.500A) Processing helix chain 'K' and resid 67 through 81 removed outlier: 3.539A pdb=" N THR K 76 " --> pdb=" O ASP K 72 " (cutoff:3.500A) Processing helix chain 'L' and resid 19 through 30 removed outlier: 3.561A pdb=" N PHE L 25 " --> pdb=" O LEU L 21 " (cutoff:3.500A) Processing helix chain 'L' and resid 34 through 54 Processing helix chain 'L' and resid 57 through 69 removed outlier: 3.643A pdb=" N PHE L 61 " --> pdb=" O GLU L 57 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N GLU L 62 " --> pdb=" O LEU L 58 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA L 64 " --> pdb=" O ALA L 60 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N ASN L 67 " --> pdb=" O VAL L 63 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N VAL L 68 " --> pdb=" O ALA L 64 " (cutoff:3.500A) Processing helix chain 'L' and resid 91 through 111 removed outlier: 3.772A pdb=" N LYS L 109 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N ARG L 110 " --> pdb=" O ALA L 106 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N GLY L 111 " --> pdb=" O ALA L 107 " (cutoff:3.500A) Processing helix chain 'L' and resid 114 through 129 removed outlier: 3.661A pdb=" N GLU L 128 " --> pdb=" O SER L 124 " (cutoff:3.500A) Processing helix chain 'L' and resid 132 through 146 removed outlier: 3.858A pdb=" N ALA L 144 " --> pdb=" O VAL L 140 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N ALA L 146 " --> pdb=" O ARG L 142 " (cutoff:3.500A) Processing helix chain 'M' and resid 4 through 20 Processing helix chain 'M' and resid 29 through 43 Processing helix chain 'M' and resid 111 through 119 removed outlier: 4.117A pdb=" N GLN M 117 " --> pdb=" O ARG M 113 " (cutoff:3.500A) Processing helix chain 'N' and resid 33 through 38 Processing helix chain 'N' and resid 46 through 53 Proline residue: N 50 - end of helix Processing helix chain 'N' and resid 70 through 87 removed outlier: 3.665A pdb=" N ARG N 79 " --> pdb=" O ALA N 75 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N MET N 87 " --> pdb=" O THR N 83 " (cutoff:3.500A) Processing helix chain 'N' and resid 93 through 101 removed outlier: 3.871A pdb=" N ALA N 100 " --> pdb=" O GLU N 96 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLY N 101 " --> pdb=" O LEU N 97 " (cutoff:3.500A) Processing helix chain 'O' and resid 14 through 33 removed outlier: 4.051A pdb=" N GLN O 20 " --> pdb=" O ARG O 16 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ALA O 29 " --> pdb=" O ILE O 25 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N THR O 32 " --> pdb=" O THR O 28 " (cutoff:3.500A) Processing helix chain 'O' and resid 80 through 90 removed outlier: 4.823A pdb=" N ASP O 85 " --> pdb=" O GLU O 81 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA O 86 " --> pdb=" O LYS O 82 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N MET O 88 " --> pdb=" O VAL O 84 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N ARG O 89 " --> pdb=" O ASP O 85 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N LEU O 90 " --> pdb=" O ALA O 86 " (cutoff:3.500A) Processing helix chain 'P' and resid 45 through 50 removed outlier: 4.011A pdb=" N GLY P 50 " --> pdb=" O ALA P 46 " (cutoff:3.500A) Processing helix chain 'P' and resid 52 through 58 removed outlier: 4.520A pdb=" N LYS P 56 " --> pdb=" O ARG P 52 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N SER P 57 " --> pdb=" O GLY P 53 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N THR P 58 " --> pdb=" O SER P 54 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 52 through 58' Processing helix chain 'P' and resid 59 through 77 removed outlier: 3.835A pdb=" N ASP P 71 " --> pdb=" O GLU P 67 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ALA P 72 " --> pdb=" O ARG P 68 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N VAL P 73 " --> pdb=" O CYS P 69 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N LYS P 74 " --> pdb=" O ALA P 70 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N GLU P 75 " --> pdb=" O ASP P 71 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N TYR P 76 " --> pdb=" O ALA P 72 " (cutoff:3.500A) Processing helix chain 'P' and resid 93 through 102 Processing helix chain 'Q' and resid 2 through 10 Proline residue: Q 10 - end of helix Processing helix chain 'Q' and resid 112 through 117 removed outlier: 5.067A pdb=" N TYR Q 116 " --> pdb=" O ALA Q 112 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLY Q 117 " --> pdb=" O ARG Q 113 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 112 through 117' Processing helix chain 'R' and resid 13 through 23 removed outlier: 4.219A pdb=" N ILE R 21 " --> pdb=" O ALA R 17 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N TYR R 22 " --> pdb=" O LEU R 18 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N GLY R 23 " --> pdb=" O THR R 19 " (cutoff:3.500A) Processing helix chain 'R' and resid 25 through 37 Processing helix chain 'R' and resid 43 through 48 removed outlier: 5.581A pdb=" N SER R 48 " --> pdb=" O ILE R 44 " (cutoff:3.500A) Processing helix chain 'R' and resid 49 through 62 removed outlier: 3.709A pdb=" N ASP R 53 " --> pdb=" O GLU R 49 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N THR R 54 " --> pdb=" O GLY R 50 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA R 60 " --> pdb=" O ARG R 56 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N LYS R 61 " --> pdb=" O ASP R 57 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N PHE R 62 " --> pdb=" O GLU R 58 " (cutoff:3.500A) Processing helix chain 'R' and resid 65 through 83 removed outlier: 3.511A pdb=" N LEU R 79 " --> pdb=" O SER R 75 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N MET R 80 " --> pdb=" O ILE R 76 " (cutoff:3.500A) Processing helix chain 'R' and resid 84 through 93 Processing helix chain 'R' and resid 105 through 110 Processing helix chain 'S' and resid 2 through 23 removed outlier: 3.684A pdb=" N VAL S 10 " --> pdb=" O LYS S 6 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS S 11 " --> pdb=" O ALA S 7 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N PHE S 20 " --> pdb=" O ALA S 16 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ALA S 21 " --> pdb=" O ASP S 17 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N LYS S 22 " --> pdb=" O LYS S 18 " (cutoff:3.500A) Processing helix chain 'S' and resid 37 through 50 removed outlier: 3.567A pdb=" N ALA S 43 " --> pdb=" O ASP S 39 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N GLN S 48 " --> pdb=" O VAL S 44 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N THR S 49 " --> pdb=" O LEU S 45 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N LEU S 50 " --> pdb=" O LYS S 46 " (cutoff:3.500A) Processing helix chain 'S' and resid 79 through 90 removed outlier: 3.723A pdb=" N ALA S 86 " --> pdb=" O LYS S 82 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N ARG S 89 " --> pdb=" O GLU S 85 " (cutoff:3.500A) Processing helix chain 'S' and resid 24 through 29 removed outlier: 4.473A pdb=" N ILE S 29 " --> pdb=" O ALA S 24 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 24 through 29' Processing helix chain 'T' and resid 3 through 15 removed outlier: 3.602A pdb=" N VAL T 11 " --> pdb=" O THR T 7 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N SER T 12 " --> pdb=" O ALA T 8 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLU T 13 " --> pdb=" O LYS T 9 " (cutoff:3.500A) Processing helix chain 'T' and resid 24 through 46 removed outlier: 3.900A pdb=" N GLY T 40 " --> pdb=" O ASN T 36 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N HIS T 41 " --> pdb=" O HIS T 37 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N LYS T 46 " --> pdb=" O PHE T 42 " (cutoff:3.500A) Processing helix chain 'T' and resid 49 through 74 removed outlier: 3.712A pdb=" N VAL T 74 " --> pdb=" O LYS T 70 " (cutoff:3.500A) Processing helix chain 'T' and resid 75 through 85 Processing helix chain 'U' and resid 53 through 64 removed outlier: 3.835A pdb=" N GLN U 63 " --> pdb=" O HIS U 59 " (cutoff:3.500A) Processing helix chain 'U' and resid 68 through 79 removed outlier: 3.533A pdb=" N ASN U 79 " --> pdb=" O ILE U 75 " (cutoff:3.500A) Processing helix chain 'W' and resid 24 through 33 removed outlier: 3.927A pdb=" N ASN W 30 " --> pdb=" O ALA W 26 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N TYR W 31 " --> pdb=" O THR W 27 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ILE W 32 " --> pdb=" O LEU W 28 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N THR W 33 " --> pdb=" O LYS W 29 " (cutoff:3.500A) Processing helix chain 'W' and resid 40 through 45 Processing helix chain 'W' and resid 47 through 65 Processing helix chain 'W' and resid 12 through 17 removed outlier: 5.204A pdb=" N VAL W 17 " --> pdb=" O PHE W 12 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 12 through 17' Processing helix chain 'X' and resid 11 through 25 removed outlier: 3.611A pdb=" N GLU X 23 " --> pdb=" O GLU X 19 " (cutoff:3.500A) Processing helix chain 'X' and resid 70 through 75 removed outlier: 4.295A pdb=" N ALA X 74 " --> pdb=" O LEU X 70 " (cutoff:3.500A) Proline residue: X 75 - end of helix No H-bonds generated for 'chain 'X' and resid 70 through 75' Processing helix chain 'Y' and resid 7 through 41 removed outlier: 4.006A pdb=" N ILE Y 11 " --> pdb=" O LYS Y 7 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N TYR Y 35 " --> pdb=" O ILE Y 31 " (cutoff:3.500A) Processing helix chain 'Y' and resid 42 through 64 Proline residue: Y 55 - end of helix removed outlier: 4.128A pdb=" N LYS Y 63 " --> pdb=" O ARG Y 59 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N GLY Y 64 " --> pdb=" O GLN Y 60 " (cutoff:3.500A) Processing helix chain 'Y' and resid 67 through 86 removed outlier: 6.048A pdb=" N ALA Y 71 " --> pdb=" O HIS Y 67 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ALA Y 72 " --> pdb=" O LYS Y 68 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASN Y 77 " --> pdb=" O ARG Y 73 " (cutoff:3.500A) Processing helix chain 'Z' and resid 16 through 23 removed outlier: 3.521A pdb=" N CYS Z 22 " --> pdb=" O PHE Z 18 " (cutoff:3.500A) Processing helix chain 'Z' and resid 24 through 32 removed outlier: 4.601A pdb=" N LEU Z 28 " --> pdb=" O LYS Z 24 " (cutoff:3.500A) Processing helix chain 'Z' and resid 36 through 62 Proline residue: Z 40 - end of helix removed outlier: 4.937A pdb=" N GLU Z 62 " --> pdb=" O LYS Z 58 " (cutoff:3.500A) Processing helix chain 'a' and resid 6 through 16 removed outlier: 3.894A pdb=" N VAL a 15 " --> pdb=" O ILE a 11 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N ASP a 16 " --> pdb=" O ARG a 12 " (cutoff:3.500A) Processing helix chain 'a' and resid 23 through 34 removed outlier: 4.640A pdb=" N ALA a 28 " --> pdb=" O ASN a 24 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LYS a 31 " --> pdb=" O ILE a 27 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLU a 32 " --> pdb=" O ALA a 28 " (cutoff:3.500A) Processing helix chain 'a' and resid 181 through 200 removed outlier: 4.004A pdb=" N LEU a 185 " --> pdb=" O ASP a 181 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU a 187 " --> pdb=" O ASP a 183 " (cutoff:3.500A) Processing helix chain '8' and resid 22 through 36 Processing helix chain '8' and resid 53 through 60 removed outlier: 3.505A pdb=" N ARG 8 59 " --> pdb=" O GLN 8 55 " (cutoff:3.500A) Processing helix chain '8' and resid 95 through 107 removed outlier: 4.051A pdb=" N ARG 8 101 " --> pdb=" O ILE 8 97 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ASP 8 107 " --> pdb=" O MET 8 103 " (cutoff:3.500A) Processing helix chain '8' and resid 122 through 134 Processing helix chain '8' and resid 150 through 161 removed outlier: 3.788A pdb=" N LYS 8 159 " --> pdb=" O VAL 8 155 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR 8 160 " --> pdb=" O ASN 8 156 " (cutoff:3.500A) Processing helix chain '8' and resid 211 through 228 removed outlier: 4.192A pdb=" N TRP 8 218 " --> pdb=" O LEU 8 214 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ALA 8 227 " --> pdb=" O ILE 8 223 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N GLU 8 228 " --> pdb=" O GLU 8 224 " (cutoff:3.500A) Processing helix chain '8' and resid 230 through 240 Processing helix chain '8' and resid 244 through 259 Processing helix chain '8' and resid 272 through 286 removed outlier: 6.458A pdb=" N GLN 8 276 " --> pdb=" O ASN 8 272 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ALA 8 277 " --> pdb=" O LYS 8 273 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASP 8 280 " --> pdb=" O GLN 8 276 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TYR 8 285 " --> pdb=" O ALA 8 281 " (cutoff:3.500A) Processing helix chain '8' and resid 426 through 443 removed outlier: 5.175A pdb=" N LYS 8 430 " --> pdb=" O ALA 8 426 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU 8 433 " --> pdb=" O GLU 8 429 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LEU 8 438 " --> pdb=" O ALA 8 434 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU 8 441 " --> pdb=" O ARG 8 437 " (cutoff:3.500A) Proline residue: 8 443 - end of helix Processing helix chain '8' and resid 462 through 476 Processing helix chain '8' and resid 546 through 562 removed outlier: 5.231A pdb=" N ILE 8 550 " --> pdb=" O PRO 8 546 " (cutoff:3.500A) Proline residue: 8 551 - end of helix removed outlier: 3.558A pdb=" N GLY 8 556 " --> pdb=" O ALA 8 552 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE 8 557 " --> pdb=" O VAL 8 553 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N LYS 8 562 " --> pdb=" O GLN 8 558 " (cutoff:3.500A) Processing helix chain '8' and resid 589 through 609 removed outlier: 3.549A pdb=" N ILE 8 599 " --> pdb=" O LEU 8 595 " (cutoff:3.500A) Processing helix chain '8' and resid 627 through 639 Processing helix chain '8' and resid 659 through 664 removed outlier: 3.529A pdb=" N MET 8 663 " --> pdb=" O PRO 8 659 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N PHE 8 664 " --> pdb=" O LEU 8 660 " (cutoff:3.500A) No H-bonds generated for 'chain '8' and resid 659 through 664' Processing helix chain '8' and resid 665 through 675 removed outlier: 3.557A pdb=" N GLN 8 669 " --> pdb=" O GLY 8 665 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N LEU 8 673 " --> pdb=" O GLN 8 669 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N THR 8 674 " --> pdb=" O LEU 8 670 " (cutoff:3.500A) Processing helix chain '8' and resid 691 through 698 removed outlier: 3.797A pdb=" N ALA 8 697 " --> pdb=" O ASN 8 693 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N VAL 8 698 " --> pdb=" O VAL 8 694 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'b' and resid 100 through 104 removed outlier: 6.929A pdb=" N LEU b 92 " --> pdb=" O GLU b 78 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N ASP b 113 " --> pdb=" O VAL b 77 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'b' and resid 161 through 164 removed outlier: 3.581A pdb=" N GLN b 162 " --> pdb=" O ARG b 174 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N THR b 172 " --> pdb=" O VAL b 164 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'c' and resid 49 through 52 removed outlier: 6.821A pdb=" N GLN c 49 " --> pdb=" O THR c 35 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N GLN c 94 " --> pdb=" O VAL c 34 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'c' and resid 169 through 173 removed outlier: 4.561A pdb=" N THR c 112 " --> pdb=" O ASP c 200 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ASP c 200 " --> pdb=" O THR c 112 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N SER c 199 " --> pdb=" O LYS c 8 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N VAL c 26 " --> pdb=" O VAL c 9 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'd' and resid 117 through 120 removed outlier: 5.311A pdb=" N ARG d 117 " --> pdb=" O ASP d 184 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'e' and resid 64 through 68 removed outlier: 8.583A pdb=" N ILE e 84 " --> pdb=" O VAL e 39 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N GLY e 38 " --> pdb=" O GLY e 150 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N GLY e 150 " --> pdb=" O GLY e 38 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'f' and resid 15 through 18 Processing sheet with id= 8, first strand: chain 'f' and resid 81 through 88 removed outlier: 6.538A pdb=" N THR f 128 " --> pdb=" O LEU f 88 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'f' and resid 93 through 97 Processing sheet with id= 10, first strand: chain 'g' and resid 2 through 6 removed outlier: 6.667A pdb=" N GLN g 2 " --> pdb=" O ALA g 39 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ALA g 39 " --> pdb=" O GLN g 2 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N LYS g 35 " --> pdb=" O LEU g 6 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'g' and resid 78 through 81 Processing sheet with id= 12, first strand: chain 'i' and resid 6 through 10 removed outlier: 3.925A pdb=" N ALA i 6 " --> pdb=" O VAL i 60 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N VAL i 60 " --> pdb=" O ALA i 6 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL i 57 " --> pdb=" O VAL i 69 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'j' and resid 52 through 57 removed outlier: 3.692A pdb=" N GLN j 138 " --> pdb=" O TRP j 15 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N ASP j 19 " --> pdb=" O LEU j 140 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'k' and resid 17 through 21 removed outlier: 7.232A pdb=" N ARG k 17 " --> pdb=" O VAL k 10 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N THR k 6 " --> pdb=" O CYS k 21 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N ASN k 82 " --> pdb=" O MET k 7 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'm' and resid 61 through 65 removed outlier: 3.864A pdb=" N TYR m 103 " --> pdb=" O LEU m 33 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N LEU m 33 " --> pdb=" O LEU m 102 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LYS m 100 " --> pdb=" O ALA m 35 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'm' and resid 30 through 36 removed outlier: 7.310A pdb=" N SER m 30 " --> pdb=" O LYS m 133 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N LYS m 127 " --> pdb=" O VAL m 36 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'n' and resid 33 through 37 removed outlier: 4.976A pdb=" N MET n 110 " --> pdb=" O CYS n 100 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N CYS n 100 " --> pdb=" O MET n 110 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'o' and resid 49 through 52 removed outlier: 3.685A pdb=" N VAL o 49 " --> pdb=" O VAL o 39 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N HIS o 34 " --> pdb=" O THR o 31 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ARG o 25 " --> pdb=" O ILE o 40 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N VAL o 28 " --> pdb=" O ASP o 93 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'p' and resid 37 through 44 Processing sheet with id= 20, first strand: chain 'p' and resid 48 through 51 removed outlier: 3.877A pdb=" N ALA p 48 " --> pdb=" O THR p 59 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N SER p 56 " --> pdb=" O THR p 75 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'r' and resid 11 through 15 removed outlier: 3.940A pdb=" N PHE r 5 " --> pdb=" O HIS r 12 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'r' and resid 29 through 36 removed outlier: 6.929A pdb=" N THR r 29 " --> pdb=" O ALA r 65 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N ALA r 65 " --> pdb=" O THR r 29 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N GLU r 31 " --> pdb=" O VAL r 63 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ASP r 95 " --> pdb=" O VAL r 64 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N HIS r 66 " --> pdb=" O PHE r 93 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N PHE r 93 " --> pdb=" O HIS r 66 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N TYR r 83 " --> pdb=" O ARG r 78 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'r' and resid 58 through 61 removed outlier: 6.387A pdb=" N VAL r 58 " --> pdb=" O SER r 102 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N SER r 102 " --> pdb=" O VAL r 58 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY r 100 " --> pdb=" O LYS r 60 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 's' and resid 2 through 8 removed outlier: 4.516A pdb=" N THR s 3 " --> pdb=" O VAL s 107 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N THR s 100 " --> pdb=" O GLY s 79 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLY s 79 " --> pdb=" O THR s 100 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 's' and resid 81 through 88 removed outlier: 3.864A pdb=" N ARG s 92 " --> pdb=" O ARG s 88 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 't' and resid 12 through 15 removed outlier: 5.479A pdb=" N VAL t 31 " --> pdb=" O HIS t 15 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ASN t 28 " --> pdb=" O LEU t 87 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N LYS t 81 " --> pdb=" O VAL t 34 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N LYS t 66 " --> pdb=" O ARG t 77 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N ASP t 79 " --> pdb=" O LYS t 64 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N LYS t 64 " --> pdb=" O ASP t 79 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N LYS t 81 " --> pdb=" O VAL t 62 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N VAL t 62 " --> pdb=" O LYS t 81 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ALA t 83 " --> pdb=" O THR t 60 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N THR t 60 " --> pdb=" O ALA t 83 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N VAL t 85 " --> pdb=" O VAL t 58 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N VAL t 58 " --> pdb=" O VAL t 85 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'u' and resid 39 through 42 removed outlier: 4.563A pdb=" N ASN u 39 " --> pdb=" O ALA u 62 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'u' and resid 82 through 86 Processing sheet with id= 29, first strand: chain 'v' and resid 68 through 73 removed outlier: 4.224A pdb=" N ILE v 89 " --> pdb=" O PRO v 27 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N HIS v 88 " --> pdb=" O GLN v 78 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'w' and resid 47 through 50 removed outlier: 3.756A pdb=" N THR w 54 " --> pdb=" O GLY w 50 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'w' and resid 61 through 67 Processing sheet with id= 32, first strand: chain 'x' and resid 11 through 18 removed outlier: 3.545A pdb=" N THR x 24 " --> pdb=" O ASN x 16 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N SER x 18 " --> pdb=" O ASN x 22 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N ASN x 22 " --> pdb=" O SER x 18 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'x' and resid 34 through 40 Processing sheet with id= 34, first strand: chain 'z' and resid 34 through 38 removed outlier: 5.822A pdb=" N LYS z 5 " --> pdb=" O GLU z 57 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N MET z 53 " --> pdb=" O THR z 9 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'A' and resid 21 through 25 Processing sheet with id= 36, first strand: chain 'C' and resid 18 through 25 removed outlier: 5.390A pdb=" N HIS C 18 " --> pdb=" O SER C 12 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU C 35 " --> pdb=" O TYR C 48 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'E' and resid 21 through 24 removed outlier: 5.880A pdb=" N PHE E 21 " --> pdb=" O VAL E 49 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'F' and resid 14 through 18 removed outlier: 5.647A pdb=" N CYS F 27 " --> pdb=" O HIS F 33 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N HIS F 33 " --> pdb=" O CYS F 27 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'G' and resid 30 through 33 removed outlier: 3.582A pdb=" N VAL G 37 " --> pdb=" O ALA G 33 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'G' and resid 65 through 70 removed outlier: 3.824A pdb=" N VAL G 162 " --> pdb=" O PHE G 183 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'H' and resid 52 through 58 removed outlier: 3.517A pdb=" N THR H 69 " --> pdb=" O ALA H 103 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'H' and resid 163 through 168 Processing sheet with id= 43, first strand: chain 'I' and resid 141 through 144 removed outlier: 7.345A pdb=" N MET I 177 " --> pdb=" O ILE I 144 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N GLU I 178 " --> pdb=" O ASP I 173 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'J' and resid 10 through 15 removed outlier: 3.643A pdb=" N GLN J 11 " --> pdb=" O GLY J 39 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N LYS J 13 " --> pdb=" O VAL J 37 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL J 37 " --> pdb=" O LYS J 13 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N LEU J 35 " --> pdb=" O ILE J 15 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'J' and resid 82 through 87 removed outlier: 7.917A pdb=" N HIS J 82 " --> pdb=" O PRO J 97 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N VAL J 93 " --> pdb=" O GLY J 86 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N TYR J 127 " --> pdb=" O ARG J 92 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'J' and resid 31 through 40 removed outlier: 4.625A pdb=" N GLY J 50 " --> pdb=" O ALA J 34 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N ARG J 44 " --> pdb=" O ASP J 40 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'K' and resid 35 through 39 removed outlier: 6.640A pdb=" N ILE K 36 " --> pdb=" O VAL K 64 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N VAL K 64 " --> pdb=" O ILE K 36 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N MET K 62 " --> pdb=" O ARG K 38 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ILE K 6 " --> pdb=" O MET K 62 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N GLU K 5 " --> pdb=" O MET K 90 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N MET K 90 " --> pdb=" O GLU K 5 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'L' and resid 71 through 76 No H-bonds generated for sheet with id= 48 Processing sheet with id= 49, first strand: chain 'M' and resid 46 through 52 removed outlier: 4.594A pdb=" N ASP M 47 " --> pdb=" O THR M 61 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N THR M 61 " --> pdb=" O ASP M 47 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N GLU M 51 " --> pdb=" O GLU M 57 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'M' and resid 102 through 105 removed outlier: 6.961A pdb=" N VAL M 102 " --> pdb=" O ILE M 125 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'N' and resid 4 through 10 removed outlier: 4.308A pdb=" N GLY N 9 " --> pdb=" O ALA N 16 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'O' and resid 44 through 52 removed outlier: 4.775A pdb=" N GLU O 47 " --> pdb=" O ILE O 67 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU O 10 " --> pdb=" O ARG O 72 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'P' and resid 41 through 44 removed outlier: 4.394A pdb=" N ASN P 108 " --> pdb=" O LEU P 81 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'Q' and resid 28 through 31 removed outlier: 5.270A pdb=" N LEU Q 80 " --> pdb=" O VAL Q 97 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N ARG Q 93 " --> pdb=" O GLY Q 84 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'Q' and resid 35 through 40 removed outlier: 4.799A pdb=" N ARG Q 35 " --> pdb=" O ARG Q 53 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N LYS Q 50 " --> pdb=" O ILE Q 66 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'U' and resid 4 through 10 Processing sheet with id= 57, first strand: chain 'U' and resid 37 through 40 No H-bonds generated for sheet with id= 57 Processing sheet with id= 58, first strand: chain 'V' and resid 6 through 10 removed outlier: 6.551A pdb=" N GLU V 59 " --> pdb=" O VAL V 75 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'V' and resid 19 through 29 No H-bonds generated for sheet with id= 59 Processing sheet with id= 60, first strand: chain 'X' and resid 47 through 52 removed outlier: 5.391A pdb=" N GLN X 55 " --> pdb=" O ASN X 52 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'a' and resid 43 through 47 removed outlier: 3.569A pdb=" N SER a 215 " --> pdb=" O ASP a 43 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N LYS a 211 " --> pdb=" O ASN a 47 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain '8' and resid 67 through 73 removed outlier: 5.808A pdb=" N ARG 8 9 " --> pdb=" O PRO 8 81 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE 8 15 " --> pdb=" O ILE 8 87 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL 8 112 " --> pdb=" O SER 8 16 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N LEU 8 263 " --> pdb=" O ARG 8 137 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain '8' and resid 169 through 172 removed outlier: 3.607A pdb=" N VAL 8 182 " --> pdb=" O ILE 8 191 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU 8 205 " --> pdb=" O ALA 8 190 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N THR 8 201 " --> pdb=" O ASN 8 194 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain '8' and resid 296 through 299 removed outlier: 5.076A pdb=" N GLY 8 297 " --> pdb=" O PRO 8 306 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N ASP 8 304 " --> pdb=" O LEU 8 299 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain '8' and resid 341 through 344 No H-bonds generated for sheet with id= 65 Processing sheet with id= 66, first strand: chain '8' and resid 346 through 352 removed outlier: 4.348A pdb=" N ASP 8 347 " --> pdb=" O PHE 8 360 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA 8 356 " --> pdb=" O ASN 8 351 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain '8' and resid 363 through 367 removed outlier: 3.770A pdb=" N ILE 8 363 " --> pdb=" O ILE 8 374 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU 8 372 " --> pdb=" O GLN 8 365 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N LYS 8 370 " --> pdb=" O HIS 8 367 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain '8' and resid 381 through 386 removed outlier: 4.509A pdb=" N ASP 8 381 " --> pdb=" O VAL 8 338 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA 8 385 " --> pdb=" O THR 8 334 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR 8 334 " --> pdb=" O ALA 8 385 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LYS 8 323 " --> pdb=" O PHE 8 335 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ARG 8 337 " --> pdb=" O ALA 8 321 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N ALA 8 321 " --> pdb=" O ARG 8 337 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N TYR 8 339 " --> pdb=" O ALA 8 319 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N ALA 8 319 " --> pdb=" O TYR 8 339 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain '8' and resid 445 through 450 removed outlier: 4.165A pdb=" N THR 8 456 " --> pdb=" O VAL 8 420 " (cutoff:3.500A) removed outlier: 20.252A pdb=" N VAL 8 415 " --> pdb=" O VAL 8 488 " (cutoff:3.500A) removed outlier: 15.464A pdb=" N VAL 8 488 " --> pdb=" O VAL 8 415 " (cutoff:3.500A) removed outlier: 10.907A pdb=" N SER 8 417 " --> pdb=" O PRO 8 486 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N ALA 8 419 " --> pdb=" O GLY 8 484 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N GLU 8 421 " --> pdb=" O ASN 8 482 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ASN 8 482 " --> pdb=" O GLU 8 421 " (cutoff:3.500A) removed outlier: 38.144A pdb=" N ALA 8 481 " --> pdb=" O THR 8 623 " (cutoff:3.500A) removed outlier: 33.864A pdb=" N THR 8 623 " --> pdb=" O ALA 8 481 " (cutoff:3.500A) removed outlier: 30.640A pdb=" N VAL 8 483 " --> pdb=" O VAL 8 621 " (cutoff:3.500A) removed outlier: 27.825A pdb=" N VAL 8 621 " --> pdb=" O VAL 8 483 " (cutoff:3.500A) removed outlier: 22.961A pdb=" N LYS 8 485 " --> pdb=" O VAL 8 619 " (cutoff:3.500A) removed outlier: 20.352A pdb=" N VAL 8 619 " --> pdb=" O LYS 8 485 " (cutoff:3.500A) removed outlier: 15.780A pdb=" N GLN 8 487 " --> pdb=" O MET 8 617 " (cutoff:3.500A) removed outlier: 11.416A pdb=" N MET 8 617 " --> pdb=" O GLN 8 487 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N ALA 8 489 " --> pdb=" O PRO 8 615 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL 8 652 " --> pdb=" O THR 8 623 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLY 8 644 " --> pdb=" O HIS 8 655 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain '8' and resid 500 through 508 removed outlier: 3.864A pdb=" N VAL 8 501 " --> pdb=" O ILE 8 520 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ILE 8 520 " --> pdb=" O VAL 8 501 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL 8 518 " --> pdb=" O GLY 8 503 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N VAL 8 519 " --> pdb=" O HIS 8 579 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain '8' and resid 516 through 519 removed outlier: 3.627A pdb=" N SER 8 582 " --> pdb=" O HIS 8 517 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain '8' and resid 613 through 623 removed outlier: 6.202A pdb=" N GLU 8 614 " --> pdb=" O TYR 8 687 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N TYR 8 687 " --> pdb=" O GLU 8 614 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N ILE 8 616 " --> pdb=" O LEU 8 685 " (cutoff:3.500A) 1955 hydrogen bonds defined for protein. 5799 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3508 hydrogen bonds 5740 hydrogen bond angles 0 basepair planarities 1397 basepair parallelities 2283 stacking parallelities Total time for adding SS restraints: 202.04 Time building geometry restraints manager: 65.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.09 - 1.24: 8940 1.24 - 1.40: 51429 1.40 - 1.55: 94546 1.55 - 1.70: 11033 1.70 - 1.85: 324 Bond restraints: 166272 Sorted by residual: bond pdb=" C ASP K 13 " pdb=" O ASP K 13 " ideal model delta sigma weight residual 1.236 1.511 -0.274 1.15e-02 7.56e+03 5.69e+02 bond pdb=" C VAL g 142 " pdb=" O VAL g 142 " ideal model delta sigma weight residual 1.236 1.473 -0.237 1.04e-02 9.25e+03 5.18e+02 bond pdb=" N ILE O 40 " pdb=" CA ILE O 40 " ideal model delta sigma weight residual 1.461 1.737 -0.276 1.23e-02 6.61e+03 5.03e+02 bond pdb=" C LEU O 73 " pdb=" O LEU O 73 " ideal model delta sigma weight residual 1.234 1.499 -0.265 1.22e-02 6.72e+03 4.72e+02 bond pdb=" C PRO O 39 " pdb=" N ILE O 40 " ideal model delta sigma weight residual 1.329 1.574 -0.245 1.13e-02 7.83e+03 4.70e+02 ... (remaining 166267 not shown) Histogram of bond angle deviations from ideal: 94.39 - 105.15: 22239 105.15 - 115.90: 120895 115.90 - 126.66: 91162 126.66 - 137.42: 13664 137.42 - 148.18: 2 Bond angle restraints: 247962 Sorted by residual: angle pdb=" CA ASP K 13 " pdb=" C ASP K 13 " pdb=" O ASP K 13 " ideal model delta sigma weight residual 120.82 137.20 -16.38 1.05e+00 9.07e-01 2.43e+02 angle pdb=" CA PRO O 39 " pdb=" C PRO O 39 " pdb=" O PRO O 39 " ideal model delta sigma weight residual 121.32 105.07 16.25 1.09e+00 8.42e-01 2.22e+02 angle pdb=" C HIS 8 178 " pdb=" N PHE 8 179 " pdb=" CA PHE 8 179 " ideal model delta sigma weight residual 121.50 102.15 19.35 1.43e+00 4.89e-01 1.83e+02 angle pdb=" C PHE i 37 " pdb=" N CYS i 38 " pdb=" CA CYS i 38 " ideal model delta sigma weight residual 122.26 99.60 22.66 1.73e+00 3.34e-01 1.72e+02 angle pdb=" C VAL h 18 " pdb=" N ALA h 19 " pdb=" CA ALA h 19 " ideal model delta sigma weight residual 120.31 100.43 19.88 1.52e+00 4.33e-01 1.71e+02 ... (remaining 247957 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.55: 94508 35.55 - 71.10: 10647 71.10 - 106.65: 1207 106.65 - 142.20: 10 142.20 - 177.76: 21 Dihedral angle restraints: 106393 sinusoidal: 87501 harmonic: 18892 Sorted by residual: dihedral pdb=" C4' G 12391 " pdb=" C3' G 12391 " pdb=" C2' G 12391 " pdb=" C1' G 12391 " ideal model delta sinusoidal sigma weight residual -35.00 33.34 -68.34 1 8.00e+00 1.56e-02 9.46e+01 dihedral pdb=" C4' U 11130 " pdb=" C3' U 11130 " pdb=" C2' U 11130 " pdb=" C1' U 11130 " ideal model delta sinusoidal sigma weight residual -35.00 33.03 -68.03 1 8.00e+00 1.56e-02 9.39e+01 dihedral pdb=" O4' U 31165 " pdb=" C4' U 31165 " pdb=" C3' U 31165 " pdb=" C2' U 31165 " ideal model delta sinusoidal sigma weight residual -35.00 32.89 -67.89 1 8.00e+00 1.56e-02 9.36e+01 ... (remaining 106390 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.183: 29905 0.183 - 0.366: 1596 0.366 - 0.549: 62 0.549 - 0.732: 9 0.732 - 0.915: 4 Chirality restraints: 31576 Sorted by residual: chirality pdb=" C1' U 2 1 " pdb=" O4' U 2 1 " pdb=" C2' U 2 1 " pdb=" N1 U 2 1 " both_signs ideal model delta sigma weight residual False 2.47 1.55 0.92 2.00e-01 2.50e+01 2.09e+01 chirality pdb=" CA ILE O 40 " pdb=" N ILE O 40 " pdb=" C ILE O 40 " pdb=" CB ILE O 40 " both_signs ideal model delta sigma weight residual False 2.43 3.32 -0.89 2.00e-01 2.50e+01 1.98e+01 chirality pdb=" C3' A 31396 " pdb=" C4' A 31396 " pdb=" O3' A 31396 " pdb=" C2' A 31396 " both_signs ideal model delta sigma weight residual False -2.74 -1.91 -0.84 2.00e-01 2.50e+01 1.76e+01 ... (remaining 31573 not shown) Planarity restraints: 13872 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' U 2 1 " 0.529 2.00e-02 2.50e+03 2.89e-01 1.88e+03 pdb=" N1 U 2 1 " -0.019 2.00e-02 2.50e+03 pdb=" C2 U 2 1 " -0.089 2.00e-02 2.50e+03 pdb=" O2 U 2 1 " -0.208 2.00e-02 2.50e+03 pdb=" N3 U 2 1 " -0.058 2.00e-02 2.50e+03 pdb=" C4 U 2 1 " -0.068 2.00e-02 2.50e+03 pdb=" O4 U 2 1 " 0.494 2.00e-02 2.50e+03 pdb=" C5 U 2 1 " -0.303 2.00e-02 2.50e+03 pdb=" C6 U 2 1 " -0.279 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A 31150 " 0.395 2.00e-02 2.50e+03 1.70e-01 7.99e+02 pdb=" N9 A 31150 " -0.015 2.00e-02 2.50e+03 pdb=" C8 A 31150 " -0.145 2.00e-02 2.50e+03 pdb=" N7 A 31150 " -0.132 2.00e-02 2.50e+03 pdb=" C5 A 31150 " -0.071 2.00e-02 2.50e+03 pdb=" C6 A 31150 " 0.063 2.00e-02 2.50e+03 pdb=" N6 A 31150 " 0.255 2.00e-02 2.50e+03 pdb=" N1 A 31150 " 0.028 2.00e-02 2.50e+03 pdb=" C2 A 31150 " -0.090 2.00e-02 2.50e+03 pdb=" N3 A 31150 " -0.157 2.00e-02 2.50e+03 pdb=" C4 A 31150 " -0.129 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A 2 119 " 0.297 2.00e-02 2.50e+03 1.27e-01 4.46e+02 pdb=" N9 A 2 119 " -0.022 2.00e-02 2.50e+03 pdb=" C8 A 2 119 " -0.119 2.00e-02 2.50e+03 pdb=" N7 A 2 119 " -0.096 2.00e-02 2.50e+03 pdb=" C5 A 2 119 " -0.052 2.00e-02 2.50e+03 pdb=" C6 A 2 119 " 0.048 2.00e-02 2.50e+03 pdb=" N6 A 2 119 " 0.186 2.00e-02 2.50e+03 pdb=" N1 A 2 119 " 0.028 2.00e-02 2.50e+03 pdb=" C2 A 2 119 " -0.056 2.00e-02 2.50e+03 pdb=" N3 A 2 119 " -0.114 2.00e-02 2.50e+03 pdb=" C4 A 2 119 " -0.099 2.00e-02 2.50e+03 ... (remaining 13869 not shown) Histogram of nonbonded interaction distances: 1.35 - 2.06: 14 2.06 - 2.77: 24815 2.77 - 3.48: 213174 3.48 - 4.19: 484491 4.19 - 4.90: 643570 Nonbonded interactions: 1366064 Sorted by model distance: nonbonded pdb=" N ILE O 40 " pdb=" N1 U 31123 " model vdw 1.352 3.200 nonbonded pdb=" N ILE O 40 " pdb=" C2 U 31123 " model vdw 1.384 3.340 nonbonded pdb=" O3' A 5 76 " pdb=" C PRO 5 101 " model vdw 1.417 3.270 nonbonded pdb=" N ILE O 40 " pdb=" N3 U 31123 " model vdw 1.516 3.200 nonbonded pdb=" N ILE O 40 " pdb=" C6 U 31123 " model vdw 1.647 3.420 ... (remaining 1366059 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.69 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.170 Extract box with map and model: 18.990 Check model and map are aligned: 1.630 Set scattering table: 1.020 Process input model: 491.540 Find NCS groups from input model: 3.020 Set up NCS constraints: 0.350 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 522.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.287 166272 Z= 0.731 Angle : 1.252 23.714 247962 Z= 0.837 Chirality : 0.097 0.915 31576 Planarity : 0.014 0.289 13872 Dihedral : 22.761 177.756 94209 Min Nonbonded Distance : 1.352 Molprobity Statistics. All-atom Clashscore : 25.15 Ramachandran Plot: Outliers : 1.81 % Allowed : 16.57 % Favored : 81.62 % Rotamer: Outliers : 2.06 % Allowed : 8.18 % Favored : 89.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.44 % 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: -4.69 (0.08), residues: 6517 helix: -2.62 (0.10), residues: 1717 sheet: -3.02 (0.14), residues: 1093 loop : -3.52 (0.08), residues: 3707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.075 0.008 TRP b 212 HIS 0.004 0.000 HIS E 30 PHE 0.060 0.005 PHE Z 36 TYR 0.097 0.009 TYR Z 37 ARG 0.009 0.001 ARG p 52 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13034 Ramachandran restraints generated. 6517 Oldfield, 0 Emsley, 6517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13034 Ramachandran restraints generated. 6517 Oldfield, 0 Emsley, 6517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1440 residues out of total 5429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 1328 time to evaluate : 6.007 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: b 186 ASP cc_start: 0.8347 (m-30) cc_final: 0.8002 (m-30) REVERT: d 195 GLN cc_start: 0.8289 (mt0) cc_final: 0.7692 (mm-40) REVERT: e 37 MET cc_start: 0.7063 (ttm) cc_final: 0.6791 (ttp) REVERT: e 139 GLU cc_start: 0.4964 (pm20) cc_final: 0.3843 (tp30) REVERT: e 174 PHE cc_start: 0.6989 (m-80) cc_final: 0.6712 (m-10) REVERT: f 25 ILE cc_start: 0.8640 (mt) cc_final: 0.8232 (pt) REVERT: f 71 LEU cc_start: 0.9238 (tt) cc_final: 0.9021 (tt) REVERT: g 2 GLN cc_start: 0.6972 (mm110) cc_final: 0.6710 (mm110) REVERT: g 17 ASP cc_start: 0.7551 (m-30) cc_final: 0.7160 (m-30) REVERT: g 41 LYS cc_start: 0.8013 (mmmm) cc_final: 0.7678 (pttt) REVERT: g 42 LYS cc_start: 0.7521 (tttp) cc_final: 0.7147 (tppt) REVERT: i 35 MET cc_start: 0.3588 (ppp) cc_final: 0.3307 (ppp) REVERT: i 59 THR cc_start: 0.6156 (OUTLIER) cc_final: 0.5932 (p) REVERT: j 14 ASP cc_start: 0.7667 (t70) cc_final: 0.7281 (t70) REVERT: k 73 ASP cc_start: 0.8255 (p0) cc_final: 0.7826 (p0) REVERT: k 113 MET cc_start: 0.7319 (mmm) cc_final: 0.6836 (mmm) REVERT: k 121 GLU cc_start: 0.7819 (tm-30) cc_final: 0.7079 (mp0) REVERT: l 23 ILE cc_start: 0.9208 (OUTLIER) cc_final: 0.8989 (mp) REVERT: l 91 ASP cc_start: 0.6520 (m-30) cc_final: 0.6054 (m-30) REVERT: m 17 ASN cc_start: 0.8370 (t0) cc_final: 0.7903 (t0) REVERT: n 42 LYS cc_start: 0.8766 (mttm) cc_final: 0.8470 (mmtt) REVERT: o 95 SER cc_start: 0.9035 (m) cc_final: 0.8742 (p) REVERT: p 40 GLN cc_start: 0.8173 (OUTLIER) cc_final: 0.7869 (pp30) REVERT: p 92 ARG cc_start: 0.8046 (OUTLIER) cc_final: 0.7781 (ptt180) REVERT: r 95 ASP cc_start: 0.8313 (m-30) cc_final: 0.8113 (m-30) REVERT: s 86 MET cc_start: 0.7921 (tpt) cc_final: 0.7463 (tpt) REVERT: t 21 SER cc_start: 0.9010 (m) cc_final: 0.8476 (p) REVERT: u 40 LEU cc_start: 0.8808 (pt) cc_final: 0.8474 (pp) REVERT: v 55 GLU cc_start: 0.8438 (mm-30) cc_final: 0.7961 (mm-30) REVERT: v 72 VAL cc_start: 0.8122 (m) cc_final: 0.7696 (m) REVERT: x 70 LEU cc_start: 0.9142 (mt) cc_final: 0.8780 (mt) REVERT: C 10 LEU cc_start: 0.8895 (mm) cc_final: 0.8680 (mm) REVERT: C 38 PHE cc_start: 0.8131 (t80) cc_final: 0.7841 (t80) REVERT: C 48 TYR cc_start: 0.6456 (m-80) cc_final: 0.5315 (m-80) REVERT: D 1 MET cc_start: 0.5836 (ptp) cc_final: 0.5599 (ptm) REVERT: E 21 PHE cc_start: 0.8067 (m-80) cc_final: 0.7456 (m-80) REVERT: F 37 GLN cc_start: 0.8967 (mm-40) cc_final: 0.8695 (tp-100) REVERT: G 8 MET cc_start: 0.7896 (tpt) cc_final: 0.7613 (tpt) REVERT: G 68 PHE cc_start: 0.7082 (m-80) cc_final: 0.6604 (m-80) REVERT: G 87 ASP cc_start: 0.7098 (t70) cc_final: 0.6845 (t0) REVERT: H 71 ARG cc_start: 0.4990 (mtt180) cc_final: 0.4748 (mtm180) REVERT: H 128 MET cc_start: 0.6866 (ptm) cc_final: 0.5573 (mmt) REVERT: H 139 ASN cc_start: 0.6696 (m-40) cc_final: 0.6358 (m110) REVERT: H 155 ARG cc_start: 0.0378 (OUTLIER) cc_final: -0.1052 (mtm110) REVERT: I 89 LEU cc_start: 0.6794 (tp) cc_final: 0.6287 (tt) REVERT: J 12 GLU cc_start: 0.7092 (pt0) cc_final: 0.6799 (pm20) REVERT: J 44 ARG cc_start: 0.8438 (mmm160) cc_final: 0.8183 (tpp80) REVERT: J 63 MET cc_start: 0.7707 (mmm) cc_final: 0.7424 (mmm) REVERT: J 70 MET cc_start: 0.7921 (mmm) cc_final: 0.7644 (mmm) REVERT: L 4 ARG cc_start: 0.3578 (mtt180) cc_final: 0.0639 (tpt170) REVERT: M 84 ILE cc_start: 0.8944 (mt) cc_final: 0.8644 (mp) REVERT: M 110 MET cc_start: 0.8041 (tmm) cc_final: 0.7618 (tmm) REVERT: M 125 ILE cc_start: 0.8639 (mp) cc_final: 0.8409 (tt) REVERT: N 24 ASN cc_start: 0.7643 (m110) cc_final: 0.7192 (t0) REVERT: N 30 ASN cc_start: 0.6998 (t0) cc_final: 0.6756 (m-40) REVERT: N 60 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8490 (tp) REVERT: O 24 GLU cc_start: 0.8094 (mt-10) cc_final: 0.7829 (pt0) REVERT: O 31 ARG cc_start: 0.7416 (ttt180) cc_final: 0.6705 (mmp-170) REVERT: O 59 LYS cc_start: 0.6728 (tppt) cc_final: 0.5576 (tmtt) REVERT: O 96 VAL cc_start: 0.7089 (t) cc_final: 0.6832 (t) REVERT: P 107 THR cc_start: 0.6967 (m) cc_final: 0.6726 (m) REVERT: Q 2 THR cc_start: 0.7580 (OUTLIER) cc_final: 0.7212 (p) REVERT: Q 24 GLU cc_start: 0.7720 (pm20) cc_final: 0.7367 (mm-30) REVERT: Q 73 LEU cc_start: 0.7670 (OUTLIER) cc_final: 0.7449 (mt) REVERT: Q 75 GLU cc_start: 0.8911 (mp0) cc_final: 0.8642 (mp0) REVERT: T 5 GLU cc_start: 0.7990 (tp30) cc_final: 0.7655 (pm20) REVERT: T 86 LEU cc_start: 0.8189 (OUTLIER) cc_final: 0.7942 (pp) REVERT: U 5 ARG cc_start: 0.7899 (ptt180) cc_final: 0.7598 (ptt180) REVERT: U 21 VAL cc_start: 0.8372 (t) cc_final: 0.8024 (m) REVERT: U 36 VAL cc_start: 0.9368 (p) cc_final: 0.9110 (m) REVERT: U 48 GLU cc_start: 0.6110 (tt0) cc_final: 0.5868 (tt0) REVERT: V 15 LYS cc_start: 0.7137 (tptt) cc_final: 0.6821 (mmtt) REVERT: W 18 GLN cc_start: 0.4900 (OUTLIER) cc_final: 0.4191 (pt0) REVERT: W 34 GLU cc_start: 0.7167 (tp30) cc_final: 0.6695 (pm20) REVERT: W 67 LEU cc_start: 0.8733 (mt) cc_final: 0.8394 (mp) REVERT: X 17 LYS cc_start: 0.7442 (ttmt) cc_final: 0.7088 (tttt) REVERT: X 36 ARG cc_start: 0.6963 (ptt-90) cc_final: 0.6530 (ptt90) REVERT: X 38 THR cc_start: 0.4028 (p) cc_final: 0.3712 (t) REVERT: X 39 ILE cc_start: 0.6744 (mt) cc_final: 0.6360 (mm) REVERT: X 40 PHE cc_start: 0.5926 (m-80) cc_final: 0.5670 (m-80) REVERT: X 79 TYR cc_start: 0.7712 (t80) cc_final: 0.7098 (t80) REVERT: Y 28 ARG cc_start: 0.8765 (ttm170) cc_final: 0.8539 (mtm180) REVERT: Y 67 HIS cc_start: 0.5630 (t-90) cc_final: 0.5051 (t-170) REVERT: Z 32 ARG cc_start: 0.7500 (OUTLIER) cc_final: 0.7171 (mpp80) REVERT: 8 75 MET cc_start: 0.7692 (tmm) cc_final: 0.7182 (tmm) REVERT: 8 103 MET cc_start: 0.8599 (mpp) cc_final: 0.8117 (mpp) REVERT: 8 144 MET cc_start: 0.8058 (mmm) cc_final: 0.7711 (mmm) REVERT: 8 336 PHE cc_start: 0.8944 (p90) cc_final: 0.8448 (p90) REVERT: 8 641 MET cc_start: 0.8156 (pmm) cc_final: 0.7919 (pmm) REVERT: 8 646 GLU cc_start: 0.8243 (mp0) cc_final: 0.7946 (tp30) outliers start: 112 outliers final: 36 residues processed: 1413 average time/residue: 1.3158 time to fit residues: 3229.9597 Evaluate side-chains 893 residues out of total 5429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 846 time to evaluate : 6.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 129 LEU Chi-restraints excluded: chain b residue 180 MET Chi-restraints excluded: chain b residue 228 ASP Chi-restraints excluded: chain e residue 10 GLU Chi-restraints excluded: chain e residue 18 GLU Chi-restraints excluded: chain i residue 8 VAL Chi-restraints excluded: chain i residue 59 THR Chi-restraints excluded: chain i residue 67 THR Chi-restraints excluded: chain l residue 23 ILE Chi-restraints excluded: chain l residue 57 LEU Chi-restraints excluded: chain p residue 40 GLN Chi-restraints excluded: chain p residue 92 ARG Chi-restraints excluded: chain u residue 34 ILE Chi-restraints excluded: chain v residue 26 PHE Chi-restraints excluded: chain x residue 32 LEU Chi-restraints excluded: chain x residue 47 THR Chi-restraints excluded: chain H residue 155 ARG Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain J residue 22 LYS Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 97 PRO Chi-restraints excluded: chain M residue 6 ILE Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain N residue 60 LEU Chi-restraints excluded: chain N residue 119 LYS Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain Q residue 2 THR Chi-restraints excluded: chain Q residue 40 THR Chi-restraints excluded: chain Q residue 73 LEU Chi-restraints excluded: chain R residue 97 ARG Chi-restraints excluded: chain R residue 99 GLN Chi-restraints excluded: chain T residue 86 LEU Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain U residue 79 ASN Chi-restraints excluded: chain W residue 13 THR Chi-restraints excluded: chain W residue 18 GLN Chi-restraints excluded: chain Z residue 8 ASN Chi-restraints excluded: chain Z residue 32 ARG Chi-restraints excluded: chain 8 residue 141 VAL Chi-restraints excluded: chain 8 residue 167 VAL Chi-restraints excluded: chain 8 residue 179 PHE Chi-restraints excluded: chain 8 residue 265 THR Chi-restraints excluded: chain 8 residue 348 THR Chi-restraints excluded: chain 8 residue 499 THR Chi-restraints excluded: chain 8 residue 518 VAL Chi-restraints excluded: chain 5 residue 101 PRO Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1109 random chunks: chunk 936 optimal weight: 30.0000 chunk 840 optimal weight: 20.0000 chunk 466 optimal weight: 9.9990 chunk 287 optimal weight: 7.9990 chunk 567 optimal weight: 8.9990 chunk 449 optimal weight: 9.9990 chunk 869 optimal weight: 20.0000 chunk 336 optimal weight: 9.9990 chunk 528 optimal weight: 10.0000 chunk 646 optimal weight: 20.0000 chunk 1007 optimal weight: 20.0000 overall best weight: 9.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 44 ASN ** b 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 162 GLN b 196 ASN d 9 GLN ** d 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 4 HIS ** f 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 127 GLN i 11 GLN j 128 ASN ** k 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 38 GLN l 104 GLN n 23 ASN n 62 ASN o 19 GLN ** o 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 72 GLN ** u 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 46 ASN ** x 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** y 41 HIS ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 41 ASN ** G 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 31 ASN ** H 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 35 GLN I 58 GLN ** I 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 81 ASN K 94 HIS ** L 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 75 GLN N 4 GLN P 118 ASN ** S 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 61 ASN ** T 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 34 GLN ** X 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 19 HIS Y 74 HIS a 67 HIS a 168 ASN ** 8 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 178 HIS 8 194 ASN 8 465 HIS ** 8 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.515 166272 Z= 0.376 Angle : 0.819 37.435 247962 Z= 0.419 Chirality : 0.045 0.338 31576 Planarity : 0.006 0.070 13872 Dihedral : 23.421 176.844 81326 Min Nonbonded Distance : 1.666 Molprobity Statistics. All-atom Clashscore : 20.01 Ramachandran Plot: Outliers : 0.34 % Allowed : 13.30 % Favored : 86.36 % Rotamer: Outliers : 4.57 % Allowed : 14.81 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.44 % Cis-general : 0.00 % Twisted Proline : 0.44 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.95 (0.09), residues: 6517 helix: -1.72 (0.10), residues: 2015 sheet: -2.59 (0.15), residues: 1009 loop : -3.28 (0.09), residues: 3493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP U 60 HIS 0.013 0.002 HIS O 15 PHE 0.040 0.003 PHE f 108 TYR 0.033 0.003 TYR I 74 ARG 0.010 0.001 ARG K 24 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13034 Ramachandran restraints generated. 6517 Oldfield, 0 Emsley, 6517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13034 Ramachandran restraints generated. 6517 Oldfield, 0 Emsley, 6517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1226 residues out of total 5429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 248 poor density : 978 time to evaluate : 6.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 33 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8548 (mm) REVERT: b 170 TYR cc_start: 0.6170 (m-80) cc_final: 0.5677 (m-80) REVERT: d 195 GLN cc_start: 0.8028 (mt0) cc_final: 0.7650 (mm110) REVERT: e 21 TYR cc_start: 0.5794 (t80) cc_final: 0.5023 (t80) REVERT: e 37 MET cc_start: 0.6700 (ttm) cc_final: 0.6447 (ttm) REVERT: e 127 TYR cc_start: 0.7797 (OUTLIER) cc_final: 0.6876 (t80) REVERT: e 129 MET cc_start: 0.5027 (mmm) cc_final: 0.4156 (mmm) REVERT: e 174 PHE cc_start: 0.7193 (m-80) cc_final: 0.6502 (m-80) REVERT: f 34 ARG cc_start: 0.7007 (tpm170) cc_final: 0.6580 (tpp-160) REVERT: f 36 LEU cc_start: 0.7239 (mt) cc_final: 0.7034 (mt) REVERT: f 74 MET cc_start: 0.7922 (mtp) cc_final: 0.7668 (ptp) REVERT: g 17 ASP cc_start: 0.6856 (m-30) cc_final: 0.6433 (m-30) REVERT: g 25 TYR cc_start: 0.6937 (t80) cc_final: 0.6195 (t80) REVERT: g 41 LYS cc_start: 0.7933 (mmmm) cc_final: 0.7614 (pttt) REVERT: i 16 MET cc_start: 0.1999 (tpt) cc_final: 0.1610 (tpt) REVERT: i 35 MET cc_start: 0.3681 (ppp) cc_final: 0.3476 (ppp) REVERT: j 14 ASP cc_start: 0.7506 (t70) cc_final: 0.7278 (t70) REVERT: j 136 GLN cc_start: 0.8117 (mp10) cc_final: 0.7868 (mp10) REVERT: k 73 ASP cc_start: 0.8151 (p0) cc_final: 0.7844 (p0) REVERT: k 121 GLU cc_start: 0.7744 (tm-30) cc_final: 0.7063 (mp0) REVERT: l 142 ILE cc_start: 0.9056 (mm) cc_final: 0.8838 (mm) REVERT: m 17 ASN cc_start: 0.8274 (t0) cc_final: 0.7738 (t0) REVERT: o 80 GLU cc_start: 0.8677 (mt-10) cc_final: 0.8182 (mp0) REVERT: o 89 ASP cc_start: 0.7453 (OUTLIER) cc_final: 0.7238 (t0) REVERT: r 27 ILE cc_start: 0.8349 (OUTLIER) cc_final: 0.8093 (pt) REVERT: r 40 MET cc_start: 0.8003 (tmm) cc_final: 0.7749 (tmm) REVERT: s 78 GLU cc_start: 0.7502 (mm-30) cc_final: 0.7270 (mm-30) REVERT: u 9 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.7517 (tp30) REVERT: y 13 GLU cc_start: 0.8432 (pt0) cc_final: 0.8213 (pp20) REVERT: C 10 LEU cc_start: 0.8802 (mm) cc_final: 0.8531 (mm) REVERT: C 20 TYR cc_start: 0.6648 (m-10) cc_final: 0.6270 (m-10) REVERT: C 38 PHE cc_start: 0.7967 (t80) cc_final: 0.6677 (t80) REVERT: C 40 PRO cc_start: 0.5187 (Cg_endo) cc_final: 0.4728 (Cg_exo) REVERT: E 58 ILE cc_start: 0.9308 (mt) cc_final: 0.9035 (tp) REVERT: F 37 GLN cc_start: 0.8945 (mm-40) cc_final: 0.8708 (tp-100) REVERT: G 68 PHE cc_start: 0.7534 (m-80) cc_final: 0.7230 (m-80) REVERT: G 87 ASP cc_start: 0.7170 (t70) cc_final: 0.6812 (t0) REVERT: G 192 PRO cc_start: 0.7728 (Cg_endo) cc_final: 0.7280 (Cg_exo) REVERT: H 71 ARG cc_start: 0.4259 (mtt180) cc_final: 0.4043 (mtm180) REVERT: H 200 TRP cc_start: 0.6694 (m-10) cc_final: 0.5580 (m-90) REVERT: J 70 MET cc_start: 0.7783 (mmm) cc_final: 0.7348 (mmm) REVERT: K 49 TYR cc_start: 0.6478 (p90) cc_final: 0.6254 (p90) REVERT: L 4 ARG cc_start: 0.3707 (mtt180) cc_final: 0.0695 (tpt170) REVERT: M 47 ASP cc_start: 0.8131 (t0) cc_final: 0.7922 (t0) REVERT: M 75 GLN cc_start: 0.8234 (mp-120) cc_final: 0.8021 (mp10) REVERT: N 24 ASN cc_start: 0.7568 (m110) cc_final: 0.7152 (t0) REVERT: N 65 THR cc_start: 0.1716 (p) cc_final: 0.1446 (p) REVERT: O 31 ARG cc_start: 0.7699 (ttt180) cc_final: 0.6917 (mmp-170) REVERT: O 59 LYS cc_start: 0.6199 (tppt) cc_final: 0.5428 (tttm) REVERT: P 13 LYS cc_start: 0.7523 (mmmm) cc_final: 0.7243 (mttt) REVERT: P 84 MET cc_start: 0.7468 (mtm) cc_final: 0.6676 (mtp) REVERT: Q 24 GLU cc_start: 0.7818 (pm20) cc_final: 0.7531 (mm-30) REVERT: Q 75 GLU cc_start: 0.9070 (mp0) cc_final: 0.8538 (mp0) REVERT: S 88 MET cc_start: 0.2049 (mtt) cc_final: 0.1805 (mtt) REVERT: U 5 ARG cc_start: 0.7664 (ptt180) cc_final: 0.6604 (ptt180) REVERT: U 21 VAL cc_start: 0.7659 (t) cc_final: 0.7424 (m) REVERT: U 32 PHE cc_start: 0.8394 (p90) cc_final: 0.7735 (m-80) REVERT: U 36 VAL cc_start: 0.9375 (p) cc_final: 0.9043 (m) REVERT: V 54 ILE cc_start: 0.8161 (OUTLIER) cc_final: 0.7844 (mm) REVERT: W 69 TYR cc_start: 0.5155 (m-80) cc_final: 0.4448 (m-10) REVERT: X 13 HIS cc_start: 0.3378 (OUTLIER) cc_final: 0.3019 (m90) REVERT: X 17 LYS cc_start: 0.7235 (ttmt) cc_final: 0.6778 (tttt) REVERT: X 55 GLN cc_start: 0.8183 (mm110) cc_final: 0.7981 (mm110) REVERT: Y 23 ARG cc_start: 0.9019 (mmm160) cc_final: 0.8780 (mmm160) REVERT: Y 47 GLN cc_start: 0.8605 (tp-100) cc_final: 0.8405 (mt0) REVERT: Z 8 ASN cc_start: 0.5726 (OUTLIER) cc_final: 0.5305 (p0) REVERT: Z 9 GLU cc_start: 0.4816 (OUTLIER) cc_final: 0.4321 (pt0) REVERT: 8 103 MET cc_start: 0.8792 (mpp) cc_final: 0.8414 (mpp) REVERT: 8 144 MET cc_start: 0.8006 (mmm) cc_final: 0.7388 (mmm) REVERT: 8 179 PHE cc_start: 0.7883 (OUTLIER) cc_final: 0.7507 (t80) REVERT: 8 211 MET cc_start: 0.7711 (ppp) cc_final: 0.6481 (ppp) REVERT: 8 336 PHE cc_start: 0.8960 (p90) cc_final: 0.8510 (p90) REVERT: 8 464 LEU cc_start: 0.8929 (mt) cc_final: 0.8534 (tp) outliers start: 248 outliers final: 136 residues processed: 1130 average time/residue: 1.2929 time to fit residues: 2576.2472 Evaluate side-chains 940 residues out of total 5429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 794 time to evaluate : 6.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 33 LEU Chi-restraints excluded: chain b residue 48 ILE Chi-restraints excluded: chain b residue 53 ILE Chi-restraints excluded: chain b residue 63 ILE Chi-restraints excluded: chain b residue 85 ASN Chi-restraints excluded: chain b residue 129 LEU Chi-restraints excluded: chain b residue 180 MET Chi-restraints excluded: chain b residue 227 VAL Chi-restraints excluded: chain c residue 2 ILE Chi-restraints excluded: chain c residue 113 SER Chi-restraints excluded: chain c residue 165 MET Chi-restraints excluded: chain c residue 188 LEU Chi-restraints excluded: chain c residue 200 ASP Chi-restraints excluded: chain c residue 207 VAL Chi-restraints excluded: chain d residue 97 ASN Chi-restraints excluded: chain d residue 148 ILE Chi-restraints excluded: chain e residue 4 HIS Chi-restraints excluded: chain e residue 12 VAL Chi-restraints excluded: chain e residue 104 THR Chi-restraints excluded: chain e residue 127 TYR Chi-restraints excluded: chain f residue 33 THR Chi-restraints excluded: chain f residue 73 SER Chi-restraints excluded: chain f residue 154 GLU Chi-restraints excluded: chain f residue 161 VAL Chi-restraints excluded: chain g residue 5 LEU Chi-restraints excluded: chain h residue 15 VAL Chi-restraints excluded: chain h residue 27 VAL Chi-restraints excluded: chain i residue 8 VAL Chi-restraints excluded: chain i residue 58 ILE Chi-restraints excluded: chain j residue 141 ASP Chi-restraints excluded: chain k residue 37 ASP Chi-restraints excluded: chain k residue 104 THR Chi-restraints excluded: chain l residue 46 VAL Chi-restraints excluded: chain l residue 57 LEU Chi-restraints excluded: chain n residue 51 LEU Chi-restraints excluded: chain n residue 115 LEU Chi-restraints excluded: chain o residue 19 GLN Chi-restraints excluded: chain o residue 39 VAL Chi-restraints excluded: chain o residue 65 THR Chi-restraints excluded: chain o residue 78 VAL Chi-restraints excluded: chain o residue 89 ASP Chi-restraints excluded: chain p residue 23 ASP Chi-restraints excluded: chain p residue 40 GLN Chi-restraints excluded: chain q residue 90 ASP Chi-restraints excluded: chain r residue 27 ILE Chi-restraints excluded: chain r residue 32 THR Chi-restraints excluded: chain r residue 41 ILE Chi-restraints excluded: chain r residue 101 ILE Chi-restraints excluded: chain s residue 22 ASP Chi-restraints excluded: chain s residue 36 LEU Chi-restraints excluded: chain s residue 105 VAL Chi-restraints excluded: chain u residue 9 GLU Chi-restraints excluded: chain u residue 14 THR Chi-restraints excluded: chain u residue 82 VAL Chi-restraints excluded: chain v residue 24 ASN Chi-restraints excluded: chain v residue 30 ILE Chi-restraints excluded: chain v residue 61 LEU Chi-restraints excluded: chain v residue 65 VAL Chi-restraints excluded: chain w residue 27 VAL Chi-restraints excluded: chain w residue 31 SER Chi-restraints excluded: chain w residue 46 ASN Chi-restraints excluded: chain x residue 12 VAL Chi-restraints excluded: chain x residue 21 LEU Chi-restraints excluded: chain x residue 47 THR Chi-restraints excluded: chain y residue 7 ARG Chi-restraints excluded: chain z residue 56 VAL Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain F residue 20 ASP Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 144 GLU Chi-restraints excluded: chain G residue 190 SER Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain J residue 10 LEU Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 115 GLU Chi-restraints excluded: chain K residue 11 HIS Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 100 SER Chi-restraints excluded: chain L residue 85 GLN Chi-restraints excluded: chain L residue 93 VAL Chi-restraints excluded: chain M residue 37 ASN Chi-restraints excluded: chain M residue 61 THR Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain M residue 117 GLN Chi-restraints excluded: chain N residue 29 ILE Chi-restraints excluded: chain N residue 78 ILE Chi-restraints excluded: chain O residue 70 HIS Chi-restraints excluded: chain P residue 34 THR Chi-restraints excluded: chain P residue 45 THR Chi-restraints excluded: chain P residue 96 ILE Chi-restraints excluded: chain P residue 126 ARG Chi-restraints excluded: chain Q residue 38 THR Chi-restraints excluded: chain Q residue 40 THR Chi-restraints excluded: chain Q residue 79 ILE Chi-restraints excluded: chain R residue 67 ASP Chi-restraints excluded: chain R residue 97 ARG Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain S residue 83 VAL Chi-restraints excluded: chain S residue 92 ILE Chi-restraints excluded: chain T residue 21 THR Chi-restraints excluded: chain T residue 55 LEU Chi-restraints excluded: chain T residue 61 GLN Chi-restraints excluded: chain T residue 74 VAL Chi-restraints excluded: chain T residue 88 ARG Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain U residue 79 ASN Chi-restraints excluded: chain V residue 49 ASN Chi-restraints excluded: chain V residue 54 ILE Chi-restraints excluded: chain V residue 56 ASP Chi-restraints excluded: chain W residue 13 THR Chi-restraints excluded: chain X residue 4 LEU Chi-restraints excluded: chain X residue 13 HIS Chi-restraints excluded: chain X residue 47 THR Chi-restraints excluded: chain Y residue 19 HIS Chi-restraints excluded: chain Y residue 25 SER Chi-restraints excluded: chain Y residue 31 ILE Chi-restraints excluded: chain Y residue 53 MET Chi-restraints excluded: chain Z residue 8 ASN Chi-restraints excluded: chain Z residue 9 GLU Chi-restraints excluded: chain Z residue 32 ARG Chi-restraints excluded: chain Z residue 36 PHE Chi-restraints excluded: chain 8 residue 56 GLU Chi-restraints excluded: chain 8 residue 141 VAL Chi-restraints excluded: chain 8 residue 167 VAL Chi-restraints excluded: chain 8 residue 179 PHE Chi-restraints excluded: chain 8 residue 180 THR Chi-restraints excluded: chain 8 residue 182 VAL Chi-restraints excluded: chain 8 residue 244 THR Chi-restraints excluded: chain 8 residue 256 VAL Chi-restraints excluded: chain 8 residue 265 THR Chi-restraints excluded: chain 8 residue 279 LEU Chi-restraints excluded: chain 8 residue 282 VAL Chi-restraints excluded: chain 8 residue 350 LEU Chi-restraints excluded: chain 8 residue 392 THR Chi-restraints excluded: chain 8 residue 415 VAL Chi-restraints excluded: chain 8 residue 421 GLU Chi-restraints excluded: chain 8 residue 499 THR Chi-restraints excluded: chain 8 residue 518 VAL Chi-restraints excluded: chain 8 residue 519 VAL Chi-restraints excluded: chain 8 residue 664 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1109 random chunks: chunk 559 optimal weight: 30.0000 chunk 312 optimal weight: 20.0000 chunk 838 optimal weight: 20.0000 chunk 685 optimal weight: 6.9990 chunk 277 optimal weight: 10.0000 chunk 1008 optimal weight: 20.0000 chunk 1089 optimal weight: 6.9990 chunk 898 optimal weight: 20.0000 chunk 1000 optimal weight: 20.0000 chunk 343 optimal weight: 30.0000 chunk 809 optimal weight: 10.0000 overall best weight: 10.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 152 GLN b 196 ASN c 167 ASN ** f 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 18 GLN j 128 ASN ** k 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 4 ASN n 62 ASN ** n 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 43 ASN ** t 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 3 GLN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 101 ASN ** H 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 70 GLN ** I 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 82 HIS ** L 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 7 ASN T 34 GLN ** X 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 85 ASN 8 198 GLN ** 8 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.2868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.500 166272 Z= 0.399 Angle : 0.779 36.733 247962 Z= 0.402 Chirality : 0.043 0.346 31576 Planarity : 0.006 0.072 13872 Dihedral : 23.638 179.410 81268 Min Nonbonded Distance : 1.669 Molprobity Statistics. All-atom Clashscore : 21.95 Ramachandran Plot: Outliers : 0.32 % Allowed : 14.35 % Favored : 85.33 % Rotamer: Outliers : 5.45 % Allowed : 18.05 % Favored : 76.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.44 % Cis-general : 0.00 % Twisted Proline : 0.44 % Twisted General : 0.20 % 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: -3.61 (0.09), residues: 6517 helix: -1.33 (0.10), residues: 2029 sheet: -2.41 (0.15), residues: 1070 loop : -3.16 (0.09), residues: 3418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP U 60 HIS 0.036 0.002 HIS e 4 PHE 0.036 0.003 PHE Z 36 TYR 0.031 0.003 TYR Y 35 ARG 0.009 0.001 ARG d 170 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13034 Ramachandran restraints generated. 6517 Oldfield, 0 Emsley, 6517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13034 Ramachandran restraints generated. 6517 Oldfield, 0 Emsley, 6517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1141 residues out of total 5429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 296 poor density : 845 time to evaluate : 6.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 33 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8556 (mm) REVERT: b 82 TYR cc_start: 0.8322 (t80) cc_final: 0.8121 (t80) REVERT: b 200 MET cc_start: 0.8651 (mtm) cc_final: 0.8354 (mtm) REVERT: b 228 ASP cc_start: 0.8178 (OUTLIER) cc_final: 0.7957 (t0) REVERT: d 195 GLN cc_start: 0.8115 (mt0) cc_final: 0.7780 (mm-40) REVERT: e 7 TYR cc_start: 0.8150 (t80) cc_final: 0.7833 (t80) REVERT: e 21 TYR cc_start: 0.5695 (t80) cc_final: 0.5191 (t80) REVERT: f 106 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8451 (mt) REVERT: f 116 LEU cc_start: 0.8188 (OUTLIER) cc_final: 0.7877 (tp) REVERT: g 17 ASP cc_start: 0.6143 (m-30) cc_final: 0.5739 (m-30) REVERT: g 25 TYR cc_start: 0.7379 (t80) cc_final: 0.6406 (t80) REVERT: g 33 GLN cc_start: 0.8830 (tp-100) cc_final: 0.8452 (tm-30) REVERT: g 41 LYS cc_start: 0.7927 (mmmm) cc_final: 0.7365 (pttt) REVERT: g 45 GLU cc_start: 0.8813 (mm-30) cc_final: 0.8573 (mm-30) REVERT: i 8 VAL cc_start: 0.6317 (OUTLIER) cc_final: 0.6072 (p) REVERT: i 16 MET cc_start: 0.2070 (tpt) cc_final: 0.1643 (tpt) REVERT: j 136 GLN cc_start: 0.8009 (mp10) cc_final: 0.7737 (mp10) REVERT: k 73 ASP cc_start: 0.8108 (p0) cc_final: 0.7775 (p0) REVERT: k 121 GLU cc_start: 0.7706 (tm-30) cc_final: 0.7235 (mp0) REVERT: l 144 GLU cc_start: 0.8097 (tt0) cc_final: 0.7517 (tt0) REVERT: m 17 ASN cc_start: 0.8337 (t0) cc_final: 0.7753 (t0) REVERT: m 22 GLN cc_start: 0.8139 (OUTLIER) cc_final: 0.6566 (tm-30) REVERT: m 105 MET cc_start: 0.8535 (tmm) cc_final: 0.8303 (tmm) REVERT: o 80 GLU cc_start: 0.8665 (mt-10) cc_final: 0.8197 (mp0) REVERT: r 26 ASP cc_start: 0.6619 (t70) cc_final: 0.6414 (t70) REVERT: r 27 ILE cc_start: 0.8440 (OUTLIER) cc_final: 0.8184 (pt) REVERT: r 95 ASP cc_start: 0.7888 (m-30) cc_final: 0.7666 (m-30) REVERT: s 86 MET cc_start: 0.8015 (tpp) cc_final: 0.7779 (tpp) REVERT: y 13 GLU cc_start: 0.8335 (pt0) cc_final: 0.8075 (pp20) REVERT: z 28 LEU cc_start: 0.8790 (mt) cc_final: 0.8462 (mp) REVERT: B 3 GLN cc_start: 0.8790 (OUTLIER) cc_final: 0.8498 (pm20) REVERT: C 10 LEU cc_start: 0.8805 (mm) cc_final: 0.8489 (mm) REVERT: F 12 ARG cc_start: 0.8049 (mmp80) cc_final: 0.7758 (mmp-170) REVERT: H 133 MET cc_start: 0.6555 (ptt) cc_final: 0.5521 (ppp) REVERT: H 200 TRP cc_start: 0.6796 (m-10) cc_final: 0.5617 (m-90) REVERT: I 62 ARG cc_start: 0.7400 (mmt90) cc_final: 0.6988 (mtt180) REVERT: J 44 ARG cc_start: 0.8440 (mmm160) cc_final: 0.8078 (tpp80) REVERT: J 104 ILE cc_start: 0.8746 (OUTLIER) cc_final: 0.8294 (mp) REVERT: K 36 ILE cc_start: 0.6992 (OUTLIER) cc_final: 0.6730 (mp) REVERT: K 49 TYR cc_start: 0.6467 (p90) cc_final: 0.6174 (p90) REVERT: L 4 ARG cc_start: 0.3714 (mtt180) cc_final: 0.0670 (tpt170) REVERT: L 5 VAL cc_start: -0.1693 (OUTLIER) cc_final: -0.2356 (p) REVERT: M 47 ASP cc_start: 0.8262 (t0) cc_final: 0.7982 (t0) REVERT: N 24 ASN cc_start: 0.7623 (m110) cc_final: 0.7183 (t0) REVERT: N 45 MET cc_start: 0.7365 (ptm) cc_final: 0.6875 (tmm) REVERT: O 31 ARG cc_start: 0.7809 (ttt180) cc_final: 0.7038 (mmp-170) REVERT: O 59 LYS cc_start: 0.6120 (tppt) cc_final: 0.5166 (tttm) REVERT: P 81 LEU cc_start: 0.7190 (tp) cc_final: 0.6903 (mp) REVERT: Q 24 GLU cc_start: 0.7873 (pm20) cc_final: 0.7419 (mm-30) REVERT: Q 75 GLU cc_start: 0.9167 (mp0) cc_final: 0.8647 (mp0) REVERT: R 101 THR cc_start: 0.4675 (OUTLIER) cc_final: 0.4362 (p) REVERT: S 41 TRP cc_start: 0.2302 (OUTLIER) cc_final: 0.2034 (t-100) REVERT: T 14 PHE cc_start: 0.7780 (m-80) cc_final: 0.7453 (m-80) REVERT: T 34 GLN cc_start: 0.8984 (OUTLIER) cc_final: 0.8523 (mm-40) REVERT: T 86 LEU cc_start: 0.8078 (OUTLIER) cc_final: 0.7775 (pp) REVERT: U 5 ARG cc_start: 0.7722 (ptt180) cc_final: 0.6561 (ptt180) REVERT: U 21 VAL cc_start: 0.7769 (t) cc_final: 0.7142 (m) REVERT: U 32 PHE cc_start: 0.8398 (p90) cc_final: 0.7748 (p90) REVERT: U 36 VAL cc_start: 0.9319 (OUTLIER) cc_final: 0.8992 (m) REVERT: W 69 TYR cc_start: 0.5024 (m-80) cc_final: 0.4218 (m-10) REVERT: X 17 LYS cc_start: 0.7237 (ttmt) cc_final: 0.6701 (tttt) REVERT: Y 47 GLN cc_start: 0.8651 (tp-100) cc_final: 0.8420 (mt0) REVERT: Y 56 ILE cc_start: 0.8811 (mm) cc_final: 0.8404 (tp) REVERT: 8 75 MET cc_start: 0.7395 (tmm) cc_final: 0.6380 (tmm) REVERT: 8 103 MET cc_start: 0.8874 (mpp) cc_final: 0.8275 (mtp) REVERT: 8 144 MET cc_start: 0.8067 (mmm) cc_final: 0.7492 (mmm) REVERT: 8 179 PHE cc_start: 0.8065 (OUTLIER) cc_final: 0.7743 (t80) REVERT: 8 336 PHE cc_start: 0.8827 (p90) cc_final: 0.8532 (p90) REVERT: 8 431 MET cc_start: 0.8375 (mmm) cc_final: 0.8073 (mmm) outliers start: 296 outliers final: 197 residues processed: 1048 average time/residue: 1.2324 time to fit residues: 2282.9497 Evaluate side-chains 980 residues out of total 5429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 214 poor density : 766 time to evaluate : 6.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 33 LEU Chi-restraints excluded: chain b residue 48 ILE Chi-restraints excluded: chain b residue 53 ILE Chi-restraints excluded: chain b residue 85 ASN Chi-restraints excluded: chain b residue 90 ILE Chi-restraints excluded: chain b residue 93 VAL Chi-restraints excluded: chain b residue 129 LEU Chi-restraints excluded: chain b residue 180 MET Chi-restraints excluded: chain b residue 227 VAL Chi-restraints excluded: chain b residue 228 ASP Chi-restraints excluded: chain b residue 249 VAL Chi-restraints excluded: chain c residue 2 ILE Chi-restraints excluded: chain c residue 51 THR Chi-restraints excluded: chain c residue 113 SER Chi-restraints excluded: chain c residue 165 MET Chi-restraints excluded: chain c residue 167 ASN Chi-restraints excluded: chain c residue 170 VAL Chi-restraints excluded: chain c residue 188 LEU Chi-restraints excluded: chain c residue 200 ASP Chi-restraints excluded: chain d residue 73 ILE Chi-restraints excluded: chain d residue 97 ASN Chi-restraints excluded: chain d residue 116 ASP Chi-restraints excluded: chain d residue 148 ILE Chi-restraints excluded: chain e residue 12 VAL Chi-restraints excluded: chain e residue 19 PHE Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 35 LEU Chi-restraints excluded: chain e residue 104 THR Chi-restraints excluded: chain f residue 33 THR Chi-restraints excluded: chain f residue 106 LEU Chi-restraints excluded: chain f residue 116 LEU Chi-restraints excluded: chain f residue 154 GLU Chi-restraints excluded: chain f residue 161 VAL Chi-restraints excluded: chain g residue 5 LEU Chi-restraints excluded: chain g residue 90 LEU Chi-restraints excluded: chain h residue 15 VAL Chi-restraints excluded: chain h residue 50 VAL Chi-restraints excluded: chain h residue 64 VAL Chi-restraints excluded: chain h residue 77 VAL Chi-restraints excluded: chain i residue 8 VAL Chi-restraints excluded: chain i residue 56 VAL Chi-restraints excluded: chain i residue 67 THR Chi-restraints excluded: chain j residue 32 LEU Chi-restraints excluded: chain j residue 141 ASP Chi-restraints excluded: chain k residue 37 ASP Chi-restraints excluded: chain k residue 47 ILE Chi-restraints excluded: chain k residue 58 LEU Chi-restraints excluded: chain k residue 89 ASN Chi-restraints excluded: chain k residue 104 THR Chi-restraints excluded: chain l residue 4 ASN Chi-restraints excluded: chain l residue 19 LEU Chi-restraints excluded: chain l residue 46 VAL Chi-restraints excluded: chain l residue 57 LEU Chi-restraints excluded: chain m residue 22 GLN Chi-restraints excluded: chain m residue 67 VAL Chi-restraints excluded: chain n residue 51 LEU Chi-restraints excluded: chain n residue 116 VAL Chi-restraints excluded: chain o residue 39 VAL Chi-restraints excluded: chain o residue 65 THR Chi-restraints excluded: chain o residue 78 VAL Chi-restraints excluded: chain p residue 23 ASP Chi-restraints excluded: chain p residue 40 GLN Chi-restraints excluded: chain p residue 75 THR Chi-restraints excluded: chain r residue 22 LEU Chi-restraints excluded: chain r residue 27 ILE Chi-restraints excluded: chain r residue 41 ILE Chi-restraints excluded: chain r residue 96 VAL Chi-restraints excluded: chain r residue 99 THR Chi-restraints excluded: chain s residue 22 ASP Chi-restraints excluded: chain s residue 50 VAL Chi-restraints excluded: chain s residue 51 LEU Chi-restraints excluded: chain s residue 53 SER Chi-restraints excluded: chain s residue 107 VAL Chi-restraints excluded: chain t residue 7 LEU Chi-restraints excluded: chain u residue 14 THR Chi-restraints excluded: chain u residue 27 VAL Chi-restraints excluded: chain u residue 82 VAL Chi-restraints excluded: chain v residue 5 ASN Chi-restraints excluded: chain v residue 24 ASN Chi-restraints excluded: chain v residue 30 ILE Chi-restraints excluded: chain v residue 61 LEU Chi-restraints excluded: chain v residue 65 VAL Chi-restraints excluded: chain v residue 72 VAL Chi-restraints excluded: chain w residue 27 VAL Chi-restraints excluded: chain w residue 31 SER Chi-restraints excluded: chain w residue 46 ASN Chi-restraints excluded: chain w residue 62 LYS Chi-restraints excluded: chain x residue 12 VAL Chi-restraints excluded: chain x residue 21 LEU Chi-restraints excluded: chain x residue 47 THR Chi-restraints excluded: chain y residue 7 ARG Chi-restraints excluded: chain z residue 56 VAL Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain F residue 10 LEU Chi-restraints excluded: chain F residue 20 ASP Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain G residue 49 PHE Chi-restraints excluded: chain G residue 55 GLU Chi-restraints excluded: chain G residue 86 CYS Chi-restraints excluded: chain G residue 144 GLU Chi-restraints excluded: chain G residue 190 SER Chi-restraints excluded: chain G residue 210 THR Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 17 TRP Chi-restraints excluded: chain H residue 101 ASN Chi-restraints excluded: chain H residue 183 TYR Chi-restraints excluded: chain I residue 4 LEU Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 196 GLU Chi-restraints excluded: chain J residue 10 LEU Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 82 HIS Chi-restraints excluded: chain J residue 104 ILE Chi-restraints excluded: chain J residue 115 GLU Chi-restraints excluded: chain K residue 11 HIS Chi-restraints excluded: chain K residue 36 ILE Chi-restraints excluded: chain K residue 84 VAL Chi-restraints excluded: chain K residue 100 SER Chi-restraints excluded: chain L residue 5 VAL Chi-restraints excluded: chain L residue 85 GLN Chi-restraints excluded: chain M residue 25 THR Chi-restraints excluded: chain M residue 37 ASN Chi-restraints excluded: chain M residue 61 THR Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain M residue 110 MET Chi-restraints excluded: chain M residue 117 GLN Chi-restraints excluded: chain N residue 5 TYR Chi-restraints excluded: chain N residue 20 ILE Chi-restraints excluded: chain N residue 46 VAL Chi-restraints excluded: chain N residue 64 ILE Chi-restraints excluded: chain O residue 42 LEU Chi-restraints excluded: chain O residue 70 HIS Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 34 THR Chi-restraints excluded: chain P residue 45 THR Chi-restraints excluded: chain P residue 96 ILE Chi-restraints excluded: chain P residue 115 ILE Chi-restraints excluded: chain P residue 126 ARG Chi-restraints excluded: chain Q residue 38 THR Chi-restraints excluded: chain Q residue 40 THR Chi-restraints excluded: chain Q residue 79 ILE Chi-restraints excluded: chain R residue 42 VAL Chi-restraints excluded: chain R residue 67 ASP Chi-restraints excluded: chain R residue 68 LEU Chi-restraints excluded: chain R residue 97 ARG Chi-restraints excluded: chain R residue 101 THR Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain S residue 41 TRP Chi-restraints excluded: chain S residue 83 VAL Chi-restraints excluded: chain S residue 92 ILE Chi-restraints excluded: chain T residue 10 ILE Chi-restraints excluded: chain T residue 24 THR Chi-restraints excluded: chain T residue 34 GLN Chi-restraints excluded: chain T residue 55 LEU Chi-restraints excluded: chain T residue 61 GLN Chi-restraints excluded: chain T residue 74 VAL Chi-restraints excluded: chain T residue 86 LEU Chi-restraints excluded: chain T residue 88 ARG Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain U residue 20 VAL Chi-restraints excluded: chain U residue 36 VAL Chi-restraints excluded: chain U residue 66 THR Chi-restraints excluded: chain U residue 79 ASN Chi-restraints excluded: chain V residue 6 THR Chi-restraints excluded: chain V residue 49 ASN Chi-restraints excluded: chain V residue 56 ASP Chi-restraints excluded: chain W residue 13 THR Chi-restraints excluded: chain W residue 39 VAL Chi-restraints excluded: chain X residue 4 LEU Chi-restraints excluded: chain X residue 10 ILE Chi-restraints excluded: chain X residue 32 THR Chi-restraints excluded: chain X residue 47 THR Chi-restraints excluded: chain X residue 48 ILE Chi-restraints excluded: chain Y residue 11 ILE Chi-restraints excluded: chain Y residue 25 SER Chi-restraints excluded: chain Y residue 31 ILE Chi-restraints excluded: chain Y residue 53 MET Chi-restraints excluded: chain Z residue 8 ASN Chi-restraints excluded: chain Z residue 9 GLU Chi-restraints excluded: chain Z residue 32 ARG Chi-restraints excluded: chain Z residue 36 PHE Chi-restraints excluded: chain a residue 165 ASN Chi-restraints excluded: chain a residue 209 ILE Chi-restraints excluded: chain a residue 224 VAL Chi-restraints excluded: chain 8 residue 56 GLU Chi-restraints excluded: chain 8 residue 141 VAL Chi-restraints excluded: chain 8 residue 167 VAL Chi-restraints excluded: chain 8 residue 179 PHE Chi-restraints excluded: chain 8 residue 182 VAL Chi-restraints excluded: chain 8 residue 235 GLU Chi-restraints excluded: chain 8 residue 244 THR Chi-restraints excluded: chain 8 residue 265 THR Chi-restraints excluded: chain 8 residue 279 LEU Chi-restraints excluded: chain 8 residue 350 LEU Chi-restraints excluded: chain 8 residue 366 MET Chi-restraints excluded: chain 8 residue 392 THR Chi-restraints excluded: chain 8 residue 399 ASP Chi-restraints excluded: chain 8 residue 415 VAL Chi-restraints excluded: chain 8 residue 421 GLU Chi-restraints excluded: chain 8 residue 473 MET Chi-restraints excluded: chain 8 residue 499 THR Chi-restraints excluded: chain 8 residue 518 VAL Chi-restraints excluded: chain 8 residue 519 VAL Chi-restraints excluded: chain 8 residue 658 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1109 random chunks: chunk 996 optimal weight: 10.0000 chunk 758 optimal weight: 20.0000 chunk 523 optimal weight: 20.0000 chunk 111 optimal weight: 3.9990 chunk 481 optimal weight: 30.0000 chunk 677 optimal weight: 50.0000 chunk 1012 optimal weight: 20.0000 chunk 1071 optimal weight: 20.0000 chunk 529 optimal weight: 10.0000 chunk 959 optimal weight: 10.0000 chunk 288 optimal weight: 6.9990 overall best weight: 8.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 196 ASN ** e 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 128 ASN ** k 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 43 ASN t 15 HIS ** t 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 65 GLN w 46 ASN ** x 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 139 ASN ** H 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 30 ASN ** N 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 7 ASN ** X 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 55 GLN ** Y 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 69 ASN ** a 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.3177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.496 166272 Z= 0.333 Angle : 0.709 36.831 247962 Z= 0.367 Chirality : 0.040 0.330 31576 Planarity : 0.005 0.074 13872 Dihedral : 23.679 179.701 81268 Min Nonbonded Distance : 1.676 Molprobity Statistics. All-atom Clashscore : 20.33 Ramachandran Plot: Outliers : 0.23 % Allowed : 13.37 % Favored : 86.40 % Rotamer: Outliers : 5.64 % Allowed : 19.65 % Favored : 74.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.44 % Cis-general : 0.00 % Twisted Proline : 0.44 % Twisted General : 0.22 % 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: -3.29 (0.09), residues: 6517 helix: -1.00 (0.11), residues: 2043 sheet: -2.25 (0.15), residues: 1053 loop : -2.99 (0.09), residues: 3421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP U 60 HIS 0.041 0.002 HIS J 82 PHE 0.034 0.002 PHE Z 36 TYR 0.037 0.002 TYR j 16 ARG 0.009 0.001 ARG r 78 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13034 Ramachandran restraints generated. 6517 Oldfield, 0 Emsley, 6517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13034 Ramachandran restraints generated. 6517 Oldfield, 0 Emsley, 6517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1144 residues out of total 5429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 306 poor density : 838 time to evaluate : 6.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 33 LEU cc_start: 0.8816 (OUTLIER) cc_final: 0.8573 (mm) REVERT: b 186 ASP cc_start: 0.8194 (OUTLIER) cc_final: 0.7702 (t70) REVERT: b 200 MET cc_start: 0.8577 (mtm) cc_final: 0.8330 (mtm) REVERT: d 195 GLN cc_start: 0.8080 (mt0) cc_final: 0.7741 (mm110) REVERT: e 37 MET cc_start: 0.7093 (ttm) cc_final: 0.5954 (tmm) REVERT: e 127 TYR cc_start: 0.7899 (OUTLIER) cc_final: 0.6890 (t80) REVERT: e 129 MET cc_start: 0.5202 (mmm) cc_final: 0.3998 (mmm) REVERT: e 139 GLU cc_start: 0.4744 (pm20) cc_final: 0.4437 (pm20) REVERT: g 17 ASP cc_start: 0.6313 (m-30) cc_final: 0.6020 (m-30) REVERT: g 25 TYR cc_start: 0.7257 (t80) cc_final: 0.6555 (t80) REVERT: g 33 GLN cc_start: 0.8780 (tp-100) cc_final: 0.8381 (tm-30) REVERT: g 41 LYS cc_start: 0.8002 (mmmm) cc_final: 0.7485 (pttt) REVERT: g 45 GLU cc_start: 0.8750 (mm-30) cc_final: 0.8525 (mm-30) REVERT: i 8 VAL cc_start: 0.6348 (OUTLIER) cc_final: 0.6133 (p) REVERT: i 16 MET cc_start: 0.2139 (tpt) cc_final: 0.1730 (tpt) REVERT: j 136 GLN cc_start: 0.8027 (mp10) cc_final: 0.7772 (mp10) REVERT: k 73 ASP cc_start: 0.8075 (p0) cc_final: 0.7820 (p0) REVERT: k 121 GLU cc_start: 0.7890 (tm-30) cc_final: 0.7443 (mp0) REVERT: l 144 GLU cc_start: 0.8060 (tt0) cc_final: 0.7576 (tt0) REVERT: m 17 ASN cc_start: 0.8277 (t0) cc_final: 0.7682 (t0) REVERT: n 49 GLU cc_start: 0.8301 (mt-10) cc_final: 0.8010 (mm-30) REVERT: r 26 ASP cc_start: 0.6594 (t70) cc_final: 0.6304 (t70) REVERT: r 27 ILE cc_start: 0.8447 (OUTLIER) cc_final: 0.8205 (pt) REVERT: r 95 ASP cc_start: 0.7852 (m-30) cc_final: 0.7648 (m-30) REVERT: s 11 ARG cc_start: 0.7738 (OUTLIER) cc_final: 0.7461 (mtp-110) REVERT: s 86 MET cc_start: 0.8054 (tpp) cc_final: 0.7829 (tpp) REVERT: t 79 ASP cc_start: 0.8023 (m-30) cc_final: 0.7770 (m-30) REVERT: t 87 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8374 (mm) REVERT: z 28 LEU cc_start: 0.8747 (mt) cc_final: 0.8545 (mp) REVERT: A 1 MET cc_start: 0.7740 (ppp) cc_final: 0.7532 (ppp) REVERT: C 10 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8495 (mm) REVERT: C 19 PHE cc_start: 0.8182 (p90) cc_final: 0.7676 (p90) REVERT: D 12 ARG cc_start: 0.8555 (OUTLIER) cc_final: 0.7935 (ttt90) REVERT: D 15 SER cc_start: 0.9291 (t) cc_final: 0.9048 (t) REVERT: H 133 MET cc_start: 0.6559 (ptt) cc_final: 0.5552 (ppp) REVERT: H 200 TRP cc_start: 0.6731 (m-10) cc_final: 0.5542 (m-90) REVERT: I 62 ARG cc_start: 0.7364 (mmt90) cc_final: 0.6947 (mtt180) REVERT: I 196 GLU cc_start: 0.7638 (OUTLIER) cc_final: 0.7262 (pp20) REVERT: J 44 ARG cc_start: 0.8431 (mmm160) cc_final: 0.8052 (tpp80) REVERT: J 104 ILE cc_start: 0.8672 (OUTLIER) cc_final: 0.8370 (mp) REVERT: J 123 LEU cc_start: 0.6537 (OUTLIER) cc_final: 0.6271 (pt) REVERT: K 49 TYR cc_start: 0.6430 (p90) cc_final: 0.6219 (p90) REVERT: K 90 MET cc_start: 0.7602 (mmp) cc_final: 0.7149 (mmp) REVERT: M 26 MET cc_start: 0.7443 (ptp) cc_final: 0.6458 (pmm) REVERT: M 47 ASP cc_start: 0.8157 (t0) cc_final: 0.7845 (t0) REVERT: M 58 LEU cc_start: 0.8039 (tp) cc_final: 0.7618 (mt) REVERT: M 120 LEU cc_start: 0.7892 (OUTLIER) cc_final: 0.7521 (pp) REVERT: N 45 MET cc_start: 0.7386 (ptm) cc_final: 0.6924 (tmm) REVERT: O 18 ILE cc_start: 0.5911 (pt) cc_final: 0.5707 (pt) REVERT: O 31 ARG cc_start: 0.7835 (ttt180) cc_final: 0.7000 (mmp-170) REVERT: O 59 LYS cc_start: 0.5959 (tppt) cc_final: 0.5166 (tttm) REVERT: P 81 LEU cc_start: 0.7056 (tp) cc_final: 0.6827 (mp) REVERT: Q 75 GLU cc_start: 0.9138 (mp0) cc_final: 0.8496 (mp0) REVERT: S 41 TRP cc_start: 0.2237 (OUTLIER) cc_final: 0.2015 (t-100) REVERT: T 13 GLU cc_start: 0.7623 (mm-30) cc_final: 0.7379 (mm-30) REVERT: T 58 MET cc_start: 0.8502 (mmm) cc_final: 0.8231 (mmm) REVERT: T 86 LEU cc_start: 0.7959 (OUTLIER) cc_final: 0.7701 (pp) REVERT: U 5 ARG cc_start: 0.7859 (ptt180) cc_final: 0.6799 (ptt180) REVERT: U 21 VAL cc_start: 0.7418 (t) cc_final: 0.7120 (m) REVERT: U 32 PHE cc_start: 0.8267 (p90) cc_final: 0.7621 (p90) REVERT: U 36 VAL cc_start: 0.9353 (OUTLIER) cc_final: 0.9120 (m) REVERT: W 69 TYR cc_start: 0.5041 (m-80) cc_final: 0.4192 (m-10) REVERT: X 60 PHE cc_start: 0.8486 (OUTLIER) cc_final: 0.8206 (m-10) REVERT: Y 8 LYS cc_start: 0.8620 (tttt) cc_final: 0.8369 (tttt) REVERT: Y 17 ARG cc_start: 0.8735 (tmm-80) cc_final: 0.8510 (ttp80) REVERT: Y 56 ILE cc_start: 0.8633 (mm) cc_final: 0.8336 (tp) REVERT: 8 15 ILE cc_start: 0.8374 (mp) cc_final: 0.8119 (tp) REVERT: 8 50 MET cc_start: 0.7149 (ppp) cc_final: 0.6850 (ppp) REVERT: 8 75 MET cc_start: 0.7450 (tmm) cc_final: 0.6506 (tmm) REVERT: 8 103 MET cc_start: 0.8765 (mpp) cc_final: 0.8223 (mtp) REVERT: 8 144 MET cc_start: 0.8141 (mmm) cc_final: 0.7582 (mmm) REVERT: 8 211 MET cc_start: 0.7841 (ppp) cc_final: 0.7012 (ppp) REVERT: 8 336 PHE cc_start: 0.8879 (p90) cc_final: 0.8595 (p90) REVERT: 8 339 TYR cc_start: 0.7559 (OUTLIER) cc_final: 0.6247 (m-80) REVERT: 8 431 MET cc_start: 0.8423 (mmm) cc_final: 0.8047 (mmm) REVERT: 8 670 LEU cc_start: 0.9119 (tt) cc_final: 0.8849 (tp) outliers start: 306 outliers final: 210 residues processed: 1049 average time/residue: 1.2539 time to fit residues: 2335.9800 Evaluate side-chains 997 residues out of total 5429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 228 poor density : 769 time to evaluate : 6.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 33 LEU Chi-restraints excluded: chain b residue 48 ILE Chi-restraints excluded: chain b residue 53 ILE Chi-restraints excluded: chain b residue 85 ASN Chi-restraints excluded: chain b residue 90 ILE Chi-restraints excluded: chain b residue 129 LEU Chi-restraints excluded: chain b residue 180 MET Chi-restraints excluded: chain b residue 186 ASP Chi-restraints excluded: chain b residue 227 VAL Chi-restraints excluded: chain b residue 249 VAL Chi-restraints excluded: chain c residue 2 ILE Chi-restraints excluded: chain c residue 51 THR Chi-restraints excluded: chain c residue 113 SER Chi-restraints excluded: chain c residue 165 MET Chi-restraints excluded: chain c residue 170 VAL Chi-restraints excluded: chain c residue 187 LEU Chi-restraints excluded: chain c residue 200 ASP Chi-restraints excluded: chain c residue 207 VAL Chi-restraints excluded: chain d residue 73 ILE Chi-restraints excluded: chain d residue 97 ASN Chi-restraints excluded: chain d residue 116 ASP Chi-restraints excluded: chain d residue 148 ILE Chi-restraints excluded: chain e residue 12 VAL Chi-restraints excluded: chain e residue 24 VAL Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 35 LEU Chi-restraints excluded: chain e residue 90 LEU Chi-restraints excluded: chain e residue 104 THR Chi-restraints excluded: chain e residue 127 TYR Chi-restraints excluded: chain e residue 151 LEU Chi-restraints excluded: chain e residue 156 THR Chi-restraints excluded: chain e residue 162 ASP Chi-restraints excluded: chain f residue 33 THR Chi-restraints excluded: chain f residue 130 ILE Chi-restraints excluded: chain f residue 161 VAL Chi-restraints excluded: chain g residue 5 LEU Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain h residue 15 VAL Chi-restraints excluded: chain h residue 35 VAL Chi-restraints excluded: chain h residue 50 VAL Chi-restraints excluded: chain h residue 77 VAL Chi-restraints excluded: chain i residue 8 VAL Chi-restraints excluded: chain i residue 56 VAL Chi-restraints excluded: chain j residue 14 ASP Chi-restraints excluded: chain j residue 32 LEU Chi-restraints excluded: chain j residue 128 ASN Chi-restraints excluded: chain j residue 141 ASP Chi-restraints excluded: chain k residue 37 ASP Chi-restraints excluded: chain k residue 47 ILE Chi-restraints excluded: chain k residue 58 LEU Chi-restraints excluded: chain k residue 89 ASN Chi-restraints excluded: chain k residue 104 THR Chi-restraints excluded: chain l residue 46 VAL Chi-restraints excluded: chain l residue 57 LEU Chi-restraints excluded: chain l residue 122 VAL Chi-restraints excluded: chain m residue 67 VAL Chi-restraints excluded: chain m residue 78 LEU Chi-restraints excluded: chain n residue 51 LEU Chi-restraints excluded: chain n residue 97 ILE Chi-restraints excluded: chain n residue 116 VAL Chi-restraints excluded: chain o residue 39 VAL Chi-restraints excluded: chain o residue 65 THR Chi-restraints excluded: chain o residue 78 VAL Chi-restraints excluded: chain o residue 83 LEU Chi-restraints excluded: chain o residue 91 SER Chi-restraints excluded: chain p residue 23 ASP Chi-restraints excluded: chain p residue 40 GLN Chi-restraints excluded: chain p residue 75 THR Chi-restraints excluded: chain q residue 61 ILE Chi-restraints excluded: chain q residue 73 ILE Chi-restraints excluded: chain q residue 79 ILE Chi-restraints excluded: chain r residue 22 LEU Chi-restraints excluded: chain r residue 27 ILE Chi-restraints excluded: chain r residue 32 THR Chi-restraints excluded: chain r residue 41 ILE Chi-restraints excluded: chain r residue 96 VAL Chi-restraints excluded: chain s residue 11 ARG Chi-restraints excluded: chain s residue 20 VAL Chi-restraints excluded: chain s residue 22 ASP Chi-restraints excluded: chain s residue 45 VAL Chi-restraints excluded: chain s residue 50 VAL Chi-restraints excluded: chain s residue 51 LEU Chi-restraints excluded: chain s residue 107 VAL Chi-restraints excluded: chain t residue 62 VAL Chi-restraints excluded: chain t residue 77 ARG Chi-restraints excluded: chain t residue 87 LEU Chi-restraints excluded: chain u residue 14 THR Chi-restraints excluded: chain u residue 27 VAL Chi-restraints excluded: chain u residue 82 VAL Chi-restraints excluded: chain v residue 5 ASN Chi-restraints excluded: chain v residue 24 ASN Chi-restraints excluded: chain v residue 30 ILE Chi-restraints excluded: chain v residue 61 LEU Chi-restraints excluded: chain v residue 72 VAL Chi-restraints excluded: chain w residue 27 VAL Chi-restraints excluded: chain w residue 31 SER Chi-restraints excluded: chain x residue 12 VAL Chi-restraints excluded: chain x residue 39 VAL Chi-restraints excluded: chain x residue 47 THR Chi-restraints excluded: chain x residue 58 ILE Chi-restraints excluded: chain y residue 24 GLU Chi-restraints excluded: chain z residue 56 VAL Chi-restraints excluded: chain A residue 63 ARG Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 12 ARG Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain F residue 10 LEU Chi-restraints excluded: chain F residue 20 ASP Chi-restraints excluded: chain G residue 49 PHE Chi-restraints excluded: chain G residue 55 GLU Chi-restraints excluded: chain G residue 66 ILE Chi-restraints excluded: chain G residue 86 CYS Chi-restraints excluded: chain G residue 144 GLU Chi-restraints excluded: chain G residue 190 SER Chi-restraints excluded: chain G residue 210 THR Chi-restraints excluded: chain H residue 2 GLN Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain H residue 161 ILE Chi-restraints excluded: chain I residue 4 LEU Chi-restraints excluded: chain I residue 98 ASP Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 196 GLU Chi-restraints excluded: chain J residue 10 LEU Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 82 HIS Chi-restraints excluded: chain J residue 104 ILE Chi-restraints excluded: chain J residue 115 GLU Chi-restraints excluded: chain J residue 123 LEU Chi-restraints excluded: chain K residue 11 HIS Chi-restraints excluded: chain K residue 25 TYR Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 87 SER Chi-restraints excluded: chain K residue 100 SER Chi-restraints excluded: chain L residue 85 GLN Chi-restraints excluded: chain M residue 9 MET Chi-restraints excluded: chain M residue 25 THR Chi-restraints excluded: chain M residue 50 VAL Chi-restraints excluded: chain M residue 61 THR Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain M residue 110 MET Chi-restraints excluded: chain M residue 117 GLN Chi-restraints excluded: chain M residue 120 LEU Chi-restraints excluded: chain N residue 5 TYR Chi-restraints excluded: chain N residue 20 ILE Chi-restraints excluded: chain N residue 31 GLN Chi-restraints excluded: chain N residue 46 VAL Chi-restraints excluded: chain N residue 119 LYS Chi-restraints excluded: chain O residue 42 LEU Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 34 THR Chi-restraints excluded: chain P residue 45 THR Chi-restraints excluded: chain P residue 83 VAL Chi-restraints excluded: chain P residue 96 ILE Chi-restraints excluded: chain P residue 115 ILE Chi-restraints excluded: chain P residue 120 CYS Chi-restraints excluded: chain P residue 126 ARG Chi-restraints excluded: chain Q residue 38 THR Chi-restraints excluded: chain Q residue 40 THR Chi-restraints excluded: chain Q residue 72 ASN Chi-restraints excluded: chain Q residue 74 GLN Chi-restraints excluded: chain Q residue 79 ILE Chi-restraints excluded: chain R residue 65 GLU Chi-restraints excluded: chain R residue 67 ASP Chi-restraints excluded: chain R residue 68 LEU Chi-restraints excluded: chain R residue 97 ARG Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain S residue 41 TRP Chi-restraints excluded: chain S residue 83 VAL Chi-restraints excluded: chain S residue 92 ILE Chi-restraints excluded: chain T residue 10 ILE Chi-restraints excluded: chain T residue 24 THR Chi-restraints excluded: chain T residue 55 LEU Chi-restraints excluded: chain T residue 61 GLN Chi-restraints excluded: chain T residue 74 VAL Chi-restraints excluded: chain T residue 86 LEU Chi-restraints excluded: chain T residue 88 ARG Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain U residue 20 VAL Chi-restraints excluded: chain U residue 36 VAL Chi-restraints excluded: chain U residue 66 THR Chi-restraints excluded: chain U residue 79 ASN Chi-restraints excluded: chain V residue 6 THR Chi-restraints excluded: chain V residue 49 ASN Chi-restraints excluded: chain V residue 56 ASP Chi-restraints excluded: chain W residue 13 THR Chi-restraints excluded: chain W residue 30 ASN Chi-restraints excluded: chain W residue 39 VAL Chi-restraints excluded: chain W residue 54 LEU Chi-restraints excluded: chain X residue 4 LEU Chi-restraints excluded: chain X residue 10 ILE Chi-restraints excluded: chain X residue 32 THR Chi-restraints excluded: chain X residue 47 THR Chi-restraints excluded: chain X residue 60 PHE Chi-restraints excluded: chain Y residue 11 ILE Chi-restraints excluded: chain Y residue 25 SER Chi-restraints excluded: chain Y residue 31 ILE Chi-restraints excluded: chain Y residue 53 MET Chi-restraints excluded: chain Z residue 8 ASN Chi-restraints excluded: chain Z residue 9 GLU Chi-restraints excluded: chain Z residue 32 ARG Chi-restraints excluded: chain Z residue 36 PHE Chi-restraints excluded: chain a residue 165 ASN Chi-restraints excluded: chain a residue 209 ILE Chi-restraints excluded: chain 8 residue 56 GLU Chi-restraints excluded: chain 8 residue 141 VAL Chi-restraints excluded: chain 8 residue 167 VAL Chi-restraints excluded: chain 8 residue 180 THR Chi-restraints excluded: chain 8 residue 182 VAL Chi-restraints excluded: chain 8 residue 235 GLU Chi-restraints excluded: chain 8 residue 265 THR Chi-restraints excluded: chain 8 residue 339 TYR Chi-restraints excluded: chain 8 residue 350 LEU Chi-restraints excluded: chain 8 residue 366 MET Chi-restraints excluded: chain 8 residue 392 THR Chi-restraints excluded: chain 8 residue 399 ASP Chi-restraints excluded: chain 8 residue 415 VAL Chi-restraints excluded: chain 8 residue 518 VAL Chi-restraints excluded: chain 8 residue 519 VAL Chi-restraints excluded: chain 8 residue 628 THR Chi-restraints excluded: chain 8 residue 658 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1109 random chunks: chunk 892 optimal weight: 20.0000 chunk 608 optimal weight: 30.0000 chunk 15 optimal weight: 20.0000 chunk 798 optimal weight: 20.0000 chunk 442 optimal weight: 10.0000 chunk 914 optimal weight: 20.0000 chunk 740 optimal weight: 20.0000 chunk 1 optimal weight: 6.9990 chunk 547 optimal weight: 7.9990 chunk 962 optimal weight: 20.0000 chunk 270 optimal weight: 5.9990 overall best weight: 10.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 196 ASN e 4 HIS ** f 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 28 ASN ** k 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 4 ASN ** n 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 75 GLN ** x 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 139 ASN ** H 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 7 ASN ** T 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 49 HIS W 51 GLN ** X 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 55 GLN ** Y 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 69 ASN ** a 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 55 GLN ** 8 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 129 GLN ** 8 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 428 GLN ** 8 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.3424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.496 166272 Z= 0.378 Angle : 0.749 36.767 247962 Z= 0.385 Chirality : 0.042 0.333 31576 Planarity : 0.006 0.071 13872 Dihedral : 23.752 179.148 81265 Min Nonbonded Distance : 1.678 Molprobity Statistics. All-atom Clashscore : 22.45 Ramachandran Plot: Outliers : 0.23 % Allowed : 14.44 % Favored : 85.33 % Rotamer: Outliers : 6.69 % Allowed : 20.32 % Favored : 73.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.44 % Cis-general : 0.00 % Twisted Proline : 0.44 % Twisted General : 0.22 % 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: -3.25 (0.09), residues: 6517 helix: -1.01 (0.11), residues: 2046 sheet: -2.22 (0.15), residues: 1034 loop : -2.94 (0.09), residues: 3437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP d 78 HIS 0.014 0.002 HIS H 5 PHE 0.033 0.002 PHE Z 36 TYR 0.041 0.003 TYR j 16 ARG 0.007 0.001 ARG 8 359 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13034 Ramachandran restraints generated. 6517 Oldfield, 0 Emsley, 6517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13034 Ramachandran restraints generated. 6517 Oldfield, 0 Emsley, 6517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1164 residues out of total 5429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 363 poor density : 801 time to evaluate : 6.673 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: b 33 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8576 (mm) REVERT: b 186 ASP cc_start: 0.8303 (OUTLIER) cc_final: 0.7898 (p0) REVERT: b 200 MET cc_start: 0.8587 (mtm) cc_final: 0.8319 (mtm) REVERT: d 195 GLN cc_start: 0.8124 (mt0) cc_final: 0.7851 (mm110) REVERT: e 37 MET cc_start: 0.7151 (ttm) cc_final: 0.6124 (tmm) REVERT: e 127 TYR cc_start: 0.7928 (OUTLIER) cc_final: 0.6632 (t80) REVERT: e 129 MET cc_start: 0.5064 (mmm) cc_final: 0.4116 (mmm) REVERT: e 139 GLU cc_start: 0.4766 (pm20) cc_final: 0.4457 (pm20) REVERT: f 106 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.8205 (mt) REVERT: f 116 LEU cc_start: 0.8198 (OUTLIER) cc_final: 0.7877 (tp) REVERT: g 17 ASP cc_start: 0.6413 (m-30) cc_final: 0.6134 (m-30) REVERT: g 25 TYR cc_start: 0.7475 (t80) cc_final: 0.6902 (t80) REVERT: g 33 GLN cc_start: 0.8634 (tp-100) cc_final: 0.8328 (tm-30) REVERT: g 41 LYS cc_start: 0.7958 (mmmm) cc_final: 0.7561 (mmtp) REVERT: g 45 GLU cc_start: 0.8790 (mm-30) cc_final: 0.8582 (mm-30) REVERT: i 8 VAL cc_start: 0.6320 (OUTLIER) cc_final: 0.6111 (p) REVERT: i 16 MET cc_start: 0.1951 (tpt) cc_final: 0.1546 (tpt) REVERT: j 128 ASN cc_start: 0.8422 (t0) cc_final: 0.8217 (t0) REVERT: k 73 ASP cc_start: 0.8059 (p0) cc_final: 0.7750 (p0) REVERT: l 144 GLU cc_start: 0.7981 (tt0) cc_final: 0.7623 (tt0) REVERT: m 17 ASN cc_start: 0.8344 (t0) cc_final: 0.7740 (t0) REVERT: m 22 GLN cc_start: 0.8206 (OUTLIER) cc_final: 0.6676 (tm-30) REVERT: n 49 GLU cc_start: 0.8351 (mt-10) cc_final: 0.8067 (mm-30) REVERT: r 16 GLU cc_start: 0.7210 (tp30) cc_final: 0.6972 (tp30) REVERT: r 27 ILE cc_start: 0.8440 (OUTLIER) cc_final: 0.8206 (pt) REVERT: s 11 ARG cc_start: 0.7794 (OUTLIER) cc_final: 0.7473 (mtp-110) REVERT: s 86 MET cc_start: 0.8142 (tpp) cc_final: 0.7918 (tpp) REVERT: t 79 ASP cc_start: 0.8076 (m-30) cc_final: 0.7797 (m-30) REVERT: t 87 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8073 (mm) REVERT: y 58 ASN cc_start: 0.9049 (OUTLIER) cc_final: 0.8819 (t0) REVERT: z 28 LEU cc_start: 0.8774 (mt) cc_final: 0.8571 (mp) REVERT: A 1 MET cc_start: 0.7852 (ppp) cc_final: 0.7627 (ppp) REVERT: C 10 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8518 (mm) REVERT: D 12 ARG cc_start: 0.8597 (OUTLIER) cc_final: 0.8149 (ttt90) REVERT: D 15 SER cc_start: 0.9301 (t) cc_final: 0.9051 (t) REVERT: H 133 MET cc_start: 0.6645 (ptt) cc_final: 0.5634 (ppp) REVERT: H 151 GLU cc_start: 0.1639 (OUTLIER) cc_final: 0.0871 (mp0) REVERT: J 44 ARG cc_start: 0.8433 (mmm160) cc_final: 0.8028 (tpp80) REVERT: J 104 ILE cc_start: 0.8698 (OUTLIER) cc_final: 0.8275 (mm) REVERT: K 49 TYR cc_start: 0.6465 (p90) cc_final: 0.6242 (p90) REVERT: K 79 ARG cc_start: 0.7814 (mtm180) cc_final: 0.7536 (mtm180) REVERT: K 88 MET cc_start: 0.4692 (ttt) cc_final: 0.3895 (ttt) REVERT: M 26 MET cc_start: 0.7345 (ptp) cc_final: 0.6352 (pmm) REVERT: M 47 ASP cc_start: 0.8340 (t0) cc_final: 0.7996 (t0) REVERT: M 58 LEU cc_start: 0.7975 (tp) cc_final: 0.7624 (mt) REVERT: O 31 ARG cc_start: 0.7852 (ttt180) cc_final: 0.7010 (mmp-170) REVERT: O 59 LYS cc_start: 0.5834 (tppt) cc_final: 0.5064 (tttm) REVERT: O 73 LEU cc_start: 0.5766 (mp) cc_final: 0.5527 (tp) REVERT: Q 75 GLU cc_start: 0.9155 (mp0) cc_final: 0.8510 (mp0) REVERT: S 41 TRP cc_start: 0.2239 (OUTLIER) cc_final: 0.2020 (t-100) REVERT: T 5 GLU cc_start: 0.8136 (pm20) cc_final: 0.7912 (pm20) REVERT: T 14 PHE cc_start: 0.7637 (m-80) cc_final: 0.7340 (m-80) REVERT: T 19 ASN cc_start: 0.8427 (m-40) cc_final: 0.8203 (t0) REVERT: T 58 MET cc_start: 0.8554 (OUTLIER) cc_final: 0.8222 (mmm) REVERT: T 86 LEU cc_start: 0.8029 (OUTLIER) cc_final: 0.7825 (pp) REVERT: U 5 ARG cc_start: 0.7737 (ptt180) cc_final: 0.6750 (ptt180) REVERT: U 21 VAL cc_start: 0.7495 (t) cc_final: 0.6958 (m) REVERT: U 32 PHE cc_start: 0.8325 (p90) cc_final: 0.7670 (p90) REVERT: U 36 VAL cc_start: 0.9374 (OUTLIER) cc_final: 0.9091 (m) REVERT: W 69 TYR cc_start: 0.5117 (m-80) cc_final: 0.4166 (m-10) REVERT: X 60 PHE cc_start: 0.8599 (OUTLIER) cc_final: 0.8270 (m-10) REVERT: Y 56 ILE cc_start: 0.8697 (mm) cc_final: 0.8362 (tp) REVERT: 8 50 MET cc_start: 0.7147 (ppp) cc_final: 0.6880 (ppp) REVERT: 8 75 MET cc_start: 0.7716 (tmm) cc_final: 0.6997 (tmm) REVERT: 8 103 MET cc_start: 0.8727 (OUTLIER) cc_final: 0.8258 (mtp) REVERT: 8 144 MET cc_start: 0.8189 (mmm) cc_final: 0.7635 (mmm) REVERT: 8 203 GLU cc_start: 0.8357 (tp30) cc_final: 0.7925 (tp30) REVERT: 8 205 GLU cc_start: 0.7328 (pt0) cc_final: 0.6900 (pt0) REVERT: 8 211 MET cc_start: 0.7782 (ppp) cc_final: 0.7071 (ppp) outliers start: 363 outliers final: 262 residues processed: 1060 average time/residue: 1.2658 time to fit residues: 2387.6786 Evaluate side-chains 1041 residues out of total 5429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 283 poor density : 758 time to evaluate : 6.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 33 LEU Chi-restraints excluded: chain b residue 48 ILE Chi-restraints excluded: chain b residue 53 ILE Chi-restraints excluded: chain b residue 85 ASN Chi-restraints excluded: chain b residue 90 ILE Chi-restraints excluded: chain b residue 93 VAL Chi-restraints excluded: chain b residue 129 LEU Chi-restraints excluded: chain b residue 180 MET Chi-restraints excluded: chain b residue 186 ASP Chi-restraints excluded: chain b residue 227 VAL Chi-restraints excluded: chain b residue 249 VAL Chi-restraints excluded: chain c residue 2 ILE Chi-restraints excluded: chain c residue 51 THR Chi-restraints excluded: chain c residue 113 SER Chi-restraints excluded: chain c residue 146 ILE Chi-restraints excluded: chain c residue 165 MET Chi-restraints excluded: chain c residue 170 VAL Chi-restraints excluded: chain c residue 187 LEU Chi-restraints excluded: chain c residue 200 ASP Chi-restraints excluded: chain c residue 207 VAL Chi-restraints excluded: chain d residue 73 ILE Chi-restraints excluded: chain d residue 77 ILE Chi-restraints excluded: chain d residue 97 ASN Chi-restraints excluded: chain d residue 148 ILE Chi-restraints excluded: chain e residue 4 HIS Chi-restraints excluded: chain e residue 12 VAL Chi-restraints excluded: chain e residue 15 LEU Chi-restraints excluded: chain e residue 24 VAL Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 35 LEU Chi-restraints excluded: chain e residue 90 LEU Chi-restraints excluded: chain e residue 104 THR Chi-restraints excluded: chain e residue 127 TYR Chi-restraints excluded: chain e residue 128 SER Chi-restraints excluded: chain e residue 151 LEU Chi-restraints excluded: chain e residue 154 THR Chi-restraints excluded: chain e residue 156 THR Chi-restraints excluded: chain e residue 158 THR Chi-restraints excluded: chain f residue 33 THR Chi-restraints excluded: chain f residue 106 LEU Chi-restraints excluded: chain f residue 116 LEU Chi-restraints excluded: chain f residue 121 THR Chi-restraints excluded: chain f residue 130 ILE Chi-restraints excluded: chain f residue 161 VAL Chi-restraints excluded: chain g residue 5 LEU Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain g residue 101 ASP Chi-restraints excluded: chain h residue 15 VAL Chi-restraints excluded: chain h residue 27 VAL Chi-restraints excluded: chain h residue 35 VAL Chi-restraints excluded: chain h residue 50 VAL Chi-restraints excluded: chain h residue 77 VAL Chi-restraints excluded: chain i residue 8 VAL Chi-restraints excluded: chain i residue 56 VAL Chi-restraints excluded: chain i residue 67 THR Chi-restraints excluded: chain j residue 14 ASP Chi-restraints excluded: chain j residue 30 THR Chi-restraints excluded: chain j residue 32 LEU Chi-restraints excluded: chain j residue 141 ASP Chi-restraints excluded: chain k residue 37 ASP Chi-restraints excluded: chain k residue 47 ILE Chi-restraints excluded: chain k residue 58 LEU Chi-restraints excluded: chain k residue 82 ASN Chi-restraints excluded: chain k residue 89 ASN Chi-restraints excluded: chain k residue 104 THR Chi-restraints excluded: chain l residue 19 LEU Chi-restraints excluded: chain l residue 46 VAL Chi-restraints excluded: chain l residue 57 LEU Chi-restraints excluded: chain l residue 116 VAL Chi-restraints excluded: chain m residue 22 GLN Chi-restraints excluded: chain m residue 67 VAL Chi-restraints excluded: chain m residue 78 LEU Chi-restraints excluded: chain m residue 90 GLU Chi-restraints excluded: chain m residue 102 LEU Chi-restraints excluded: chain n residue 51 LEU Chi-restraints excluded: chain n residue 97 ILE Chi-restraints excluded: chain n residue 116 VAL Chi-restraints excluded: chain o residue 39 VAL Chi-restraints excluded: chain o residue 65 THR Chi-restraints excluded: chain o residue 78 VAL Chi-restraints excluded: chain o residue 83 LEU Chi-restraints excluded: chain o residue 91 SER Chi-restraints excluded: chain p residue 7 LEU Chi-restraints excluded: chain p residue 23 ASP Chi-restraints excluded: chain p residue 40 GLN Chi-restraints excluded: chain p residue 47 ILE Chi-restraints excluded: chain p residue 54 LEU Chi-restraints excluded: chain p residue 75 THR Chi-restraints excluded: chain q residue 61 ILE Chi-restraints excluded: chain q residue 73 ILE Chi-restraints excluded: chain q residue 79 ILE Chi-restraints excluded: chain r residue 27 ILE Chi-restraints excluded: chain r residue 32 THR Chi-restraints excluded: chain r residue 41 ILE Chi-restraints excluded: chain r residue 53 PHE Chi-restraints excluded: chain r residue 96 VAL Chi-restraints excluded: chain s residue 11 ARG Chi-restraints excluded: chain s residue 20 VAL Chi-restraints excluded: chain s residue 22 ASP Chi-restraints excluded: chain s residue 45 VAL Chi-restraints excluded: chain s residue 50 VAL Chi-restraints excluded: chain s residue 51 LEU Chi-restraints excluded: chain s residue 53 SER Chi-restraints excluded: chain s residue 107 VAL Chi-restraints excluded: chain t residue 10 VAL Chi-restraints excluded: chain t residue 62 VAL Chi-restraints excluded: chain t residue 87 LEU Chi-restraints excluded: chain u residue 14 THR Chi-restraints excluded: chain u residue 27 VAL Chi-restraints excluded: chain u residue 82 VAL Chi-restraints excluded: chain v residue 5 ASN Chi-restraints excluded: chain v residue 24 ASN Chi-restraints excluded: chain v residue 30 ILE Chi-restraints excluded: chain v residue 61 LEU Chi-restraints excluded: chain v residue 63 ILE Chi-restraints excluded: chain v residue 72 VAL Chi-restraints excluded: chain v residue 86 LEU Chi-restraints excluded: chain w residue 27 VAL Chi-restraints excluded: chain w residue 31 SER Chi-restraints excluded: chain w residue 46 ASN Chi-restraints excluded: chain w residue 55 LEU Chi-restraints excluded: chain x residue 12 VAL Chi-restraints excluded: chain x residue 21 LEU Chi-restraints excluded: chain x residue 24 THR Chi-restraints excluded: chain x residue 39 VAL Chi-restraints excluded: chain x residue 47 THR Chi-restraints excluded: chain y residue 58 ASN Chi-restraints excluded: chain z residue 9 THR Chi-restraints excluded: chain z residue 56 VAL Chi-restraints excluded: chain A residue 63 ARG Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 12 ARG Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain F residue 10 LEU Chi-restraints excluded: chain F residue 20 ASP Chi-restraints excluded: chain G residue 49 PHE Chi-restraints excluded: chain G residue 55 GLU Chi-restraints excluded: chain G residue 66 ILE Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 86 CYS Chi-restraints excluded: chain G residue 144 GLU Chi-restraints excluded: chain G residue 190 SER Chi-restraints excluded: chain G residue 210 THR Chi-restraints excluded: chain H residue 2 GLN Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain H residue 101 ASN Chi-restraints excluded: chain H residue 151 GLU Chi-restraints excluded: chain H residue 161 ILE Chi-restraints excluded: chain H residue 182 ASP Chi-restraints excluded: chain I residue 4 LEU Chi-restraints excluded: chain I residue 98 ASP Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 196 GLU Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 104 ILE Chi-restraints excluded: chain J residue 115 GLU Chi-restraints excluded: chain K residue 11 HIS Chi-restraints excluded: chain K residue 25 TYR Chi-restraints excluded: chain K residue 36 ILE Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 87 SER Chi-restraints excluded: chain K residue 90 MET Chi-restraints excluded: chain K residue 100 SER Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain L residue 85 GLN Chi-restraints excluded: chain M residue 25 THR Chi-restraints excluded: chain M residue 50 VAL Chi-restraints excluded: chain M residue 61 THR Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain M residue 110 MET Chi-restraints excluded: chain M residue 117 GLN Chi-restraints excluded: chain N residue 20 ILE Chi-restraints excluded: chain N residue 29 ILE Chi-restraints excluded: chain N residue 31 GLN Chi-restraints excluded: chain N residue 44 ARG Chi-restraints excluded: chain N residue 64 ILE Chi-restraints excluded: chain N residue 65 THR Chi-restraints excluded: chain N residue 119 LYS Chi-restraints excluded: chain O residue 42 LEU Chi-restraints excluded: chain O residue 71 LEU Chi-restraints excluded: chain P residue 34 THR Chi-restraints excluded: chain P residue 45 THR Chi-restraints excluded: chain P residue 83 VAL Chi-restraints excluded: chain P residue 96 ILE Chi-restraints excluded: chain P residue 115 ILE Chi-restraints excluded: chain P residue 120 CYS Chi-restraints excluded: chain P residue 126 ARG Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain Q residue 24 GLU Chi-restraints excluded: chain Q residue 38 THR Chi-restraints excluded: chain Q residue 40 THR Chi-restraints excluded: chain Q residue 57 THR Chi-restraints excluded: chain Q residue 72 ASN Chi-restraints excluded: chain Q residue 74 GLN Chi-restraints excluded: chain Q residue 79 ILE Chi-restraints excluded: chain R residue 42 VAL Chi-restraints excluded: chain R residue 52 ILE Chi-restraints excluded: chain R residue 63 VAL Chi-restraints excluded: chain R residue 65 GLU Chi-restraints excluded: chain R residue 67 ASP Chi-restraints excluded: chain R residue 68 LEU Chi-restraints excluded: chain R residue 97 ARG Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain R residue 107 THR Chi-restraints excluded: chain S residue 41 TRP Chi-restraints excluded: chain S residue 63 CYS Chi-restraints excluded: chain S residue 83 VAL Chi-restraints excluded: chain S residue 92 ILE Chi-restraints excluded: chain T residue 1 SER Chi-restraints excluded: chain T residue 10 ILE Chi-restraints excluded: chain T residue 24 THR Chi-restraints excluded: chain T residue 55 LEU Chi-restraints excluded: chain T residue 58 MET Chi-restraints excluded: chain T residue 61 GLN Chi-restraints excluded: chain T residue 74 VAL Chi-restraints excluded: chain T residue 86 LEU Chi-restraints excluded: chain T residue 88 ARG Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain U residue 20 VAL Chi-restraints excluded: chain U residue 36 VAL Chi-restraints excluded: chain U residue 66 THR Chi-restraints excluded: chain U residue 79 ASN Chi-restraints excluded: chain V residue 6 THR Chi-restraints excluded: chain V residue 8 GLN Chi-restraints excluded: chain V residue 49 ASN Chi-restraints excluded: chain V residue 56 ASP Chi-restraints excluded: chain V residue 82 VAL Chi-restraints excluded: chain W residue 13 THR Chi-restraints excluded: chain W residue 17 VAL Chi-restraints excluded: chain W residue 30 ASN Chi-restraints excluded: chain W residue 39 VAL Chi-restraints excluded: chain W residue 54 LEU Chi-restraints excluded: chain X residue 4 LEU Chi-restraints excluded: chain X residue 10 ILE Chi-restraints excluded: chain X residue 47 THR Chi-restraints excluded: chain X residue 60 PHE Chi-restraints excluded: chain Y residue 11 ILE Chi-restraints excluded: chain Y residue 25 SER Chi-restraints excluded: chain Y residue 31 ILE Chi-restraints excluded: chain Y residue 35 TYR Chi-restraints excluded: chain Y residue 53 MET Chi-restraints excluded: chain Z residue 8 ASN Chi-restraints excluded: chain Z residue 9 GLU Chi-restraints excluded: chain Z residue 32 ARG Chi-restraints excluded: chain Z residue 36 PHE Chi-restraints excluded: chain a residue 165 ASN Chi-restraints excluded: chain a residue 174 THR Chi-restraints excluded: chain a residue 209 ILE Chi-restraints excluded: chain 8 residue 26 THR Chi-restraints excluded: chain 8 residue 55 GLN Chi-restraints excluded: chain 8 residue 56 GLU Chi-restraints excluded: chain 8 residue 61 ILE Chi-restraints excluded: chain 8 residue 103 MET Chi-restraints excluded: chain 8 residue 141 VAL Chi-restraints excluded: chain 8 residue 167 VAL Chi-restraints excluded: chain 8 residue 182 VAL Chi-restraints excluded: chain 8 residue 235 GLU Chi-restraints excluded: chain 8 residue 244 THR Chi-restraints excluded: chain 8 residue 256 VAL Chi-restraints excluded: chain 8 residue 262 ILE Chi-restraints excluded: chain 8 residue 265 THR Chi-restraints excluded: chain 8 residue 279 LEU Chi-restraints excluded: chain 8 residue 350 LEU Chi-restraints excluded: chain 8 residue 366 MET Chi-restraints excluded: chain 8 residue 392 THR Chi-restraints excluded: chain 8 residue 399 ASP Chi-restraints excluded: chain 8 residue 415 VAL Chi-restraints excluded: chain 8 residue 499 THR Chi-restraints excluded: chain 8 residue 518 VAL Chi-restraints excluded: chain 8 residue 519 VAL Chi-restraints excluded: chain 8 residue 628 THR Chi-restraints excluded: chain 8 residue 649 VAL Chi-restraints excluded: chain 8 residue 658 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1109 random chunks: chunk 360 optimal weight: 1.9990 chunk 965 optimal weight: 20.0000 chunk 211 optimal weight: 6.9990 chunk 629 optimal weight: 20.0000 chunk 264 optimal weight: 30.0000 chunk 1073 optimal weight: 30.0000 chunk 890 optimal weight: 10.0000 chunk 496 optimal weight: 5.9990 chunk 89 optimal weight: 10.0000 chunk 354 optimal weight: 6.9990 chunk 563 optimal weight: 40.0000 overall best weight: 6.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 133 ASN b 196 ASN ** d 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 4 HIS e 26 GLN ** f 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 128 ASN ** k 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 15 HIS ** t 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 139 ASN ** H 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 27 ASN ** L 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 75 GLN R 7 ASN ** S 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 34 GLN T 41 HIS X 55 GLN Y 19 HIS Y 69 ASN ** a 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.3587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.496 166272 Z= 0.297 Angle : 0.666 36.667 247962 Z= 0.345 Chirality : 0.038 0.663 31576 Planarity : 0.005 0.071 13872 Dihedral : 23.729 175.993 81265 Min Nonbonded Distance : 1.681 Molprobity Statistics. All-atom Clashscore : 19.32 Ramachandran Plot: Outliers : 0.18 % Allowed : 12.60 % Favored : 87.22 % Rotamer: Outliers : 6.02 % Allowed : 22.16 % Favored : 71.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.44 % Cis-general : 0.00 % Twisted Proline : 0.44 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.98 (0.10), residues: 6517 helix: -0.74 (0.11), residues: 2053 sheet: -2.15 (0.15), residues: 1058 loop : -2.78 (0.10), residues: 3406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP 8 52 HIS 0.041 0.002 HIS e 4 PHE 0.034 0.002 PHE Z 36 TYR 0.035 0.002 TYR Y 35 ARG 0.011 0.001 ARG r 78 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13034 Ramachandran restraints generated. 6517 Oldfield, 0 Emsley, 6517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13034 Ramachandran restraints generated. 6517 Oldfield, 0 Emsley, 6517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1165 residues out of total 5429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 327 poor density : 838 time to evaluate : 6.697 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: b 33 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8561 (mm) REVERT: b 186 ASP cc_start: 0.8203 (OUTLIER) cc_final: 0.7740 (t70) REVERT: b 200 MET cc_start: 0.8586 (mtm) cc_final: 0.8274 (mtm) REVERT: d 195 GLN cc_start: 0.8003 (mt0) cc_final: 0.7676 (mm-40) REVERT: e 37 MET cc_start: 0.6800 (ttm) cc_final: 0.6049 (tmm) REVERT: e 127 TYR cc_start: 0.7878 (OUTLIER) cc_final: 0.6805 (t80) REVERT: e 129 MET cc_start: 0.4943 (mmm) cc_final: 0.4211 (mmm) REVERT: f 59 ASP cc_start: 0.7122 (m-30) cc_final: 0.6384 (p0) REVERT: f 106 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8204 (mt) REVERT: f 116 LEU cc_start: 0.8179 (OUTLIER) cc_final: 0.7838 (tp) REVERT: g 25 TYR cc_start: 0.7349 (t80) cc_final: 0.6815 (t80) REVERT: g 33 GLN cc_start: 0.8609 (tp-100) cc_final: 0.8287 (tm-30) REVERT: g 41 LYS cc_start: 0.8002 (mmmm) cc_final: 0.7529 (mmtp) REVERT: j 108 MET cc_start: 0.8828 (OUTLIER) cc_final: 0.8399 (mtm) REVERT: j 128 ASN cc_start: 0.8485 (OUTLIER) cc_final: 0.8274 (t0) REVERT: j 136 GLN cc_start: 0.7969 (mp10) cc_final: 0.7682 (mp10) REVERT: k 87 LEU cc_start: 0.8771 (mt) cc_final: 0.8434 (mp) REVERT: k 121 GLU cc_start: 0.7946 (tm-30) cc_final: 0.7420 (mp0) REVERT: m 17 ASN cc_start: 0.8252 (t0) cc_final: 0.7538 (t0) REVERT: m 22 GLN cc_start: 0.8188 (OUTLIER) cc_final: 0.7814 (tm-30) REVERT: m 105 MET cc_start: 0.8773 (tpp) cc_final: 0.8272 (tpp) REVERT: m 110 GLU cc_start: 0.8494 (OUTLIER) cc_final: 0.7658 (tt0) REVERT: q 5 ARG cc_start: 0.7153 (OUTLIER) cc_final: 0.6515 (ptt90) REVERT: r 27 ILE cc_start: 0.8345 (OUTLIER) cc_final: 0.8118 (pt) REVERT: r 78 ARG cc_start: 0.8125 (mmm160) cc_final: 0.7875 (mmm160) REVERT: s 11 ARG cc_start: 0.7813 (OUTLIER) cc_final: 0.7483 (mtp-110) REVERT: s 86 MET cc_start: 0.8166 (tpp) cc_final: 0.7960 (tpp) REVERT: t 24 MET cc_start: 0.7891 (mpp) cc_final: 0.7418 (mpp) REVERT: t 87 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8313 (mm) REVERT: y 58 ASN cc_start: 0.9087 (OUTLIER) cc_final: 0.8776 (t0) REVERT: z 28 LEU cc_start: 0.8731 (mt) cc_final: 0.8480 (mp) REVERT: A 1 MET cc_start: 0.7775 (ppp) cc_final: 0.7532 (ppp) REVERT: C 10 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8536 (mm) REVERT: D 12 ARG cc_start: 0.8513 (OUTLIER) cc_final: 0.8083 (ttt90) REVERT: D 15 SER cc_start: 0.9313 (t) cc_final: 0.9085 (t) REVERT: H 133 MET cc_start: 0.6684 (ptt) cc_final: 0.5627 (ppp) REVERT: H 200 TRP cc_start: 0.6939 (m-10) cc_final: 0.5596 (m-90) REVERT: J 44 ARG cc_start: 0.8363 (mmm160) cc_final: 0.7947 (tpp80) REVERT: J 104 ILE cc_start: 0.8688 (OUTLIER) cc_final: 0.8264 (mm) REVERT: K 1 MET cc_start: 0.3292 (tmm) cc_final: 0.3018 (tmm) REVERT: K 88 MET cc_start: 0.4832 (ttt) cc_final: 0.3941 (ttt) REVERT: M 26 MET cc_start: 0.7340 (ptp) cc_final: 0.6422 (pmm) REVERT: M 47 ASP cc_start: 0.8241 (t0) cc_final: 0.7919 (t0) REVERT: M 58 LEU cc_start: 0.8027 (tp) cc_final: 0.7553 (mt) REVERT: M 120 LEU cc_start: 0.7903 (OUTLIER) cc_final: 0.7404 (pp) REVERT: N 45 MET cc_start: 0.7371 (ptm) cc_final: 0.6746 (ppp) REVERT: O 31 ARG cc_start: 0.7894 (ttt180) cc_final: 0.7079 (mmp-170) REVERT: O 59 LYS cc_start: 0.5793 (tppt) cc_final: 0.5037 (tttm) REVERT: O 73 LEU cc_start: 0.5695 (mp) cc_final: 0.5424 (tp) REVERT: Q 74 GLN cc_start: 0.8335 (OUTLIER) cc_final: 0.8058 (mp10) REVERT: Q 75 GLU cc_start: 0.9146 (mp0) cc_final: 0.8498 (mp0) REVERT: R 68 LEU cc_start: 0.7761 (OUTLIER) cc_final: 0.6792 (mt) REVERT: S 41 TRP cc_start: 0.2153 (OUTLIER) cc_final: 0.1946 (t-100) REVERT: T 5 GLU cc_start: 0.8197 (pm20) cc_final: 0.7968 (pm20) REVERT: T 13 GLU cc_start: 0.7493 (mm-30) cc_final: 0.7246 (mm-30) REVERT: T 19 ASN cc_start: 0.8350 (m-40) cc_final: 0.8125 (t0) REVERT: T 58 MET cc_start: 0.8480 (OUTLIER) cc_final: 0.8219 (mmm) REVERT: T 86 LEU cc_start: 0.7806 (OUTLIER) cc_final: 0.7533 (pp) REVERT: U 5 ARG cc_start: 0.7826 (ptt180) cc_final: 0.6851 (ptt180) REVERT: U 21 VAL cc_start: 0.7398 (t) cc_final: 0.7006 (t) REVERT: U 32 PHE cc_start: 0.8212 (p90) cc_final: 0.7854 (m-80) REVERT: U 36 VAL cc_start: 0.9386 (OUTLIER) cc_final: 0.9156 (m) REVERT: W 69 TYR cc_start: 0.5037 (m-80) cc_final: 0.4135 (m-10) REVERT: Y 8 LYS cc_start: 0.8606 (tttt) cc_final: 0.8276 (tttt) REVERT: Y 14 GLU cc_start: 0.9203 (mm-30) cc_final: 0.8786 (mm-30) REVERT: Y 28 ARG cc_start: 0.8757 (ttm170) cc_final: 0.8191 (mtm180) REVERT: Y 56 ILE cc_start: 0.8727 (mm) cc_final: 0.8348 (tp) REVERT: Z 9 GLU cc_start: 0.4296 (OUTLIER) cc_final: 0.3820 (pt0) REVERT: 8 50 MET cc_start: 0.7129 (ppp) cc_final: 0.6870 (ppp) REVERT: 8 75 MET cc_start: 0.7655 (tmm) cc_final: 0.6955 (tmm) REVERT: 8 103 MET cc_start: 0.8970 (OUTLIER) cc_final: 0.8327 (mtp) REVERT: 8 144 MET cc_start: 0.8137 (mmm) cc_final: 0.7548 (mmm) REVERT: 8 203 GLU cc_start: 0.8299 (tp30) cc_final: 0.7877 (tp30) REVERT: 8 205 GLU cc_start: 0.7223 (pt0) cc_final: 0.6702 (pt0) REVERT: 8 211 MET cc_start: 0.7584 (ppp) cc_final: 0.6945 (ppp) REVERT: 8 431 MET cc_start: 0.8411 (mmm) cc_final: 0.7875 (mmm) outliers start: 327 outliers final: 234 residues processed: 1063 average time/residue: 1.2626 time to fit residues: 2391.5638 Evaluate side-chains 1048 residues out of total 5429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 260 poor density : 788 time to evaluate : 6.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 33 LEU Chi-restraints excluded: chain b residue 48 ILE Chi-restraints excluded: chain b residue 85 ASN Chi-restraints excluded: chain b residue 90 ILE Chi-restraints excluded: chain b residue 93 VAL Chi-restraints excluded: chain b residue 129 LEU Chi-restraints excluded: chain b residue 161 VAL Chi-restraints excluded: chain b residue 180 MET Chi-restraints excluded: chain b residue 186 ASP Chi-restraints excluded: chain b residue 227 VAL Chi-restraints excluded: chain b residue 249 VAL Chi-restraints excluded: chain b residue 266 ILE Chi-restraints excluded: chain c residue 2 ILE Chi-restraints excluded: chain c residue 51 THR Chi-restraints excluded: chain c residue 113 SER Chi-restraints excluded: chain c residue 146 ILE Chi-restraints excluded: chain c residue 165 MET Chi-restraints excluded: chain c residue 170 VAL Chi-restraints excluded: chain c residue 200 ASP Chi-restraints excluded: chain c residue 207 VAL Chi-restraints excluded: chain d residue 73 ILE Chi-restraints excluded: chain d residue 148 ILE Chi-restraints excluded: chain e residue 4 HIS Chi-restraints excluded: chain e residue 12 VAL Chi-restraints excluded: chain e residue 19 PHE Chi-restraints excluded: chain e residue 24 VAL Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 35 LEU Chi-restraints excluded: chain e residue 88 VAL Chi-restraints excluded: chain e residue 90 LEU Chi-restraints excluded: chain e residue 104 THR Chi-restraints excluded: chain e residue 127 TYR Chi-restraints excluded: chain e residue 128 SER Chi-restraints excluded: chain e residue 151 LEU Chi-restraints excluded: chain e residue 158 THR Chi-restraints excluded: chain e residue 162 ASP Chi-restraints excluded: chain f residue 33 THR Chi-restraints excluded: chain f residue 106 LEU Chi-restraints excluded: chain f residue 116 LEU Chi-restraints excluded: chain f residue 130 ILE Chi-restraints excluded: chain f residue 161 VAL Chi-restraints excluded: chain f residue 167 VAL Chi-restraints excluded: chain g residue 5 LEU Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain g residue 90 LEU Chi-restraints excluded: chain h residue 15 VAL Chi-restraints excluded: chain h residue 35 VAL Chi-restraints excluded: chain i residue 56 VAL Chi-restraints excluded: chain j residue 14 ASP Chi-restraints excluded: chain j residue 30 THR Chi-restraints excluded: chain j residue 32 LEU Chi-restraints excluded: chain j residue 108 MET Chi-restraints excluded: chain j residue 128 ASN Chi-restraints excluded: chain k residue 37 ASP Chi-restraints excluded: chain k residue 47 ILE Chi-restraints excluded: chain k residue 58 LEU Chi-restraints excluded: chain k residue 92 GLU Chi-restraints excluded: chain k residue 104 THR Chi-restraints excluded: chain l residue 19 LEU Chi-restraints excluded: chain l residue 46 VAL Chi-restraints excluded: chain l residue 57 LEU Chi-restraints excluded: chain l residue 116 VAL Chi-restraints excluded: chain m residue 22 GLN Chi-restraints excluded: chain m residue 67 VAL Chi-restraints excluded: chain m residue 78 LEU Chi-restraints excluded: chain m residue 90 GLU Chi-restraints excluded: chain m residue 110 GLU Chi-restraints excluded: chain n residue 51 LEU Chi-restraints excluded: chain n residue 97 ILE Chi-restraints excluded: chain n residue 116 VAL Chi-restraints excluded: chain o residue 38 GLN Chi-restraints excluded: chain o residue 39 VAL Chi-restraints excluded: chain o residue 65 THR Chi-restraints excluded: chain o residue 78 VAL Chi-restraints excluded: chain o residue 83 LEU Chi-restraints excluded: chain o residue 91 SER Chi-restraints excluded: chain p residue 23 ASP Chi-restraints excluded: chain p residue 40 GLN Chi-restraints excluded: chain p residue 47 ILE Chi-restraints excluded: chain p residue 54 LEU Chi-restraints excluded: chain p residue 75 THR Chi-restraints excluded: chain q residue 5 ARG Chi-restraints excluded: chain q residue 73 ILE Chi-restraints excluded: chain q residue 79 ILE Chi-restraints excluded: chain r residue 27 ILE Chi-restraints excluded: chain r residue 32 THR Chi-restraints excluded: chain r residue 53 PHE Chi-restraints excluded: chain r residue 96 VAL Chi-restraints excluded: chain r residue 99 THR Chi-restraints excluded: chain r residue 101 ILE Chi-restraints excluded: chain s residue 11 ARG Chi-restraints excluded: chain s residue 15 GLN Chi-restraints excluded: chain s residue 22 ASP Chi-restraints excluded: chain s residue 45 VAL Chi-restraints excluded: chain s residue 50 VAL Chi-restraints excluded: chain s residue 53 SER Chi-restraints excluded: chain s residue 107 VAL Chi-restraints excluded: chain t residue 10 VAL Chi-restraints excluded: chain t residue 62 VAL Chi-restraints excluded: chain t residue 77 ARG Chi-restraints excluded: chain t residue 87 LEU Chi-restraints excluded: chain u residue 14 THR Chi-restraints excluded: chain u residue 27 VAL Chi-restraints excluded: chain u residue 67 SER Chi-restraints excluded: chain u residue 82 VAL Chi-restraints excluded: chain v residue 5 ASN Chi-restraints excluded: chain v residue 24 ASN Chi-restraints excluded: chain v residue 30 ILE Chi-restraints excluded: chain v residue 61 LEU Chi-restraints excluded: chain v residue 63 ILE Chi-restraints excluded: chain v residue 72 VAL Chi-restraints excluded: chain v residue 86 LEU Chi-restraints excluded: chain w residue 31 SER Chi-restraints excluded: chain x residue 12 VAL Chi-restraints excluded: chain x residue 39 VAL Chi-restraints excluded: chain x residue 47 THR Chi-restraints excluded: chain y residue 58 ASN Chi-restraints excluded: chain z residue 56 VAL Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 63 ARG Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 12 ARG Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain F residue 10 LEU Chi-restraints excluded: chain F residue 20 ASP Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 49 PHE Chi-restraints excluded: chain G residue 55 GLU Chi-restraints excluded: chain G residue 66 ILE Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 86 CYS Chi-restraints excluded: chain G residue 144 GLU Chi-restraints excluded: chain G residue 190 SER Chi-restraints excluded: chain G residue 210 THR Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain H residue 101 ASN Chi-restraints excluded: chain H residue 161 ILE Chi-restraints excluded: chain I residue 4 LEU Chi-restraints excluded: chain I residue 74 TYR Chi-restraints excluded: chain I residue 98 ASP Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain J residue 10 LEU Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 104 ILE Chi-restraints excluded: chain J residue 115 GLU Chi-restraints excluded: chain K residue 11 HIS Chi-restraints excluded: chain K residue 25 TYR Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 87 SER Chi-restraints excluded: chain K residue 90 MET Chi-restraints excluded: chain K residue 100 SER Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain L residue 85 GLN Chi-restraints excluded: chain M residue 25 THR Chi-restraints excluded: chain M residue 50 VAL Chi-restraints excluded: chain M residue 61 THR Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain M residue 117 GLN Chi-restraints excluded: chain M residue 120 LEU Chi-restraints excluded: chain N residue 5 TYR Chi-restraints excluded: chain N residue 20 ILE Chi-restraints excluded: chain N residue 29 ILE Chi-restraints excluded: chain N residue 31 GLN Chi-restraints excluded: chain N residue 119 LYS Chi-restraints excluded: chain O residue 42 LEU Chi-restraints excluded: chain O residue 71 LEU Chi-restraints excluded: chain O residue 100 ILE Chi-restraints excluded: chain P residue 34 THR Chi-restraints excluded: chain P residue 45 THR Chi-restraints excluded: chain P residue 94 SER Chi-restraints excluded: chain P residue 96 ILE Chi-restraints excluded: chain P residue 115 ILE Chi-restraints excluded: chain P residue 120 CYS Chi-restraints excluded: chain P residue 126 ARG Chi-restraints excluded: chain Q residue 38 THR Chi-restraints excluded: chain Q residue 40 THR Chi-restraints excluded: chain Q residue 72 ASN Chi-restraints excluded: chain Q residue 74 GLN Chi-restraints excluded: chain Q residue 79 ILE Chi-restraints excluded: chain R residue 42 VAL Chi-restraints excluded: chain R residue 52 ILE Chi-restraints excluded: chain R residue 63 VAL Chi-restraints excluded: chain R residue 67 ASP Chi-restraints excluded: chain R residue 68 LEU Chi-restraints excluded: chain R residue 97 ARG Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain S residue 41 TRP Chi-restraints excluded: chain S residue 63 CYS Chi-restraints excluded: chain S residue 83 VAL Chi-restraints excluded: chain S residue 92 ILE Chi-restraints excluded: chain T residue 10 ILE Chi-restraints excluded: chain T residue 24 THR Chi-restraints excluded: chain T residue 38 LEU Chi-restraints excluded: chain T residue 41 HIS Chi-restraints excluded: chain T residue 58 MET Chi-restraints excluded: chain T residue 61 GLN Chi-restraints excluded: chain T residue 74 VAL Chi-restraints excluded: chain T residue 86 LEU Chi-restraints excluded: chain T residue 88 ARG Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain U residue 20 VAL Chi-restraints excluded: chain U residue 36 VAL Chi-restraints excluded: chain U residue 79 ASN Chi-restraints excluded: chain V residue 6 THR Chi-restraints excluded: chain V residue 8 GLN Chi-restraints excluded: chain V residue 49 ASN Chi-restraints excluded: chain V residue 56 ASP Chi-restraints excluded: chain V residue 82 VAL Chi-restraints excluded: chain W residue 13 THR Chi-restraints excluded: chain W residue 17 VAL Chi-restraints excluded: chain W residue 39 VAL Chi-restraints excluded: chain W residue 54 LEU Chi-restraints excluded: chain X residue 4 LEU Chi-restraints excluded: chain X residue 10 ILE Chi-restraints excluded: chain X residue 47 THR Chi-restraints excluded: chain X residue 78 THR Chi-restraints excluded: chain Y residue 4 LYS Chi-restraints excluded: chain Y residue 11 ILE Chi-restraints excluded: chain Y residue 31 ILE Chi-restraints excluded: chain Y residue 53 MET Chi-restraints excluded: chain Y residue 69 ASN Chi-restraints excluded: chain Z residue 8 ASN Chi-restraints excluded: chain Z residue 9 GLU Chi-restraints excluded: chain Z residue 32 ARG Chi-restraints excluded: chain Z residue 36 PHE Chi-restraints excluded: chain a residue 165 ASN Chi-restraints excluded: chain a residue 174 THR Chi-restraints excluded: chain 8 residue 56 GLU Chi-restraints excluded: chain 8 residue 103 MET Chi-restraints excluded: chain 8 residue 141 VAL Chi-restraints excluded: chain 8 residue 167 VAL Chi-restraints excluded: chain 8 residue 182 VAL Chi-restraints excluded: chain 8 residue 186 VAL Chi-restraints excluded: chain 8 residue 235 GLU Chi-restraints excluded: chain 8 residue 244 THR Chi-restraints excluded: chain 8 residue 262 ILE Chi-restraints excluded: chain 8 residue 265 THR Chi-restraints excluded: chain 8 residue 338 VAL Chi-restraints excluded: chain 8 residue 350 LEU Chi-restraints excluded: chain 8 residue 353 VAL Chi-restraints excluded: chain 8 residue 366 MET Chi-restraints excluded: chain 8 residue 392 THR Chi-restraints excluded: chain 8 residue 399 ASP Chi-restraints excluded: chain 8 residue 415 VAL Chi-restraints excluded: chain 8 residue 518 VAL Chi-restraints excluded: chain 8 residue 519 VAL Chi-restraints excluded: chain 8 residue 628 THR Chi-restraints excluded: chain 8 residue 649 VAL Chi-restraints excluded: chain 8 residue 658 VAL Chi-restraints excluded: chain 8 residue 674 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1109 random chunks: chunk 1034 optimal weight: 40.0000 chunk 120 optimal weight: 0.0970 chunk 611 optimal weight: 40.0000 chunk 783 optimal weight: 20.0000 chunk 607 optimal weight: 30.0000 chunk 903 optimal weight: 10.0000 chunk 599 optimal weight: 20.0000 chunk 1068 optimal weight: 7.9990 chunk 668 optimal weight: 50.0000 chunk 651 optimal weight: 20.0000 chunk 493 optimal weight: 8.9990 overall best weight: 9.4190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 196 ASN d 62 GLN e 4 HIS e 26 GLN ** f 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 43 ASN ** t 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 2 GLN ** H 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 3 GLN ** M 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 75 GLN ** O 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 7 ASN T 34 GLN ** X 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.3762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.497 166272 Z= 0.362 Angle : 0.721 36.645 247962 Z= 0.370 Chirality : 0.040 0.389 31576 Planarity : 0.005 0.074 13872 Dihedral : 23.789 176.937 81264 Min Nonbonded Distance : 1.682 Molprobity Statistics. All-atom Clashscore : 22.10 Ramachandran Plot: Outliers : 0.21 % Allowed : 14.21 % Favored : 85.58 % Rotamer: Outliers : 6.43 % Allowed : 22.62 % Favored : 70.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.44 % Cis-general : 0.00 % Twisted Proline : 0.44 % Twisted General : 0.22 % 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: -3.02 (0.10), residues: 6517 helix: -0.77 (0.11), residues: 2036 sheet: -2.18 (0.15), residues: 1058 loop : -2.79 (0.10), residues: 3423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP 8 52 HIS 0.020 0.002 HIS e 4 PHE 0.033 0.002 PHE Z 36 TYR 0.039 0.002 TYR Y 35 ARG 0.010 0.001 ARG B 51 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13034 Ramachandran restraints generated. 6517 Oldfield, 0 Emsley, 6517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13034 Ramachandran restraints generated. 6517 Oldfield, 0 Emsley, 6517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1138 residues out of total 5429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 349 poor density : 789 time to evaluate : 6.672 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: b 33 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8554 (mm) REVERT: b 186 ASP cc_start: 0.8246 (OUTLIER) cc_final: 0.7760 (t70) REVERT: b 200 MET cc_start: 0.8563 (mtm) cc_final: 0.8276 (mtm) REVERT: d 195 GLN cc_start: 0.8042 (mt0) cc_final: 0.7736 (mm-40) REVERT: e 37 MET cc_start: 0.6723 (ttm) cc_final: 0.6031 (tmm) REVERT: e 127 TYR cc_start: 0.7978 (OUTLIER) cc_final: 0.6771 (t80) REVERT: e 129 MET cc_start: 0.4964 (mmm) cc_final: 0.4014 (mmm) REVERT: f 59 ASP cc_start: 0.7120 (m-30) cc_final: 0.6413 (p0) REVERT: f 106 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8212 (mt) REVERT: f 116 LEU cc_start: 0.8198 (OUTLIER) cc_final: 0.7888 (tp) REVERT: g 25 TYR cc_start: 0.7442 (t80) cc_final: 0.6808 (t80) REVERT: g 33 GLN cc_start: 0.8579 (tp-100) cc_final: 0.8270 (tm-30) REVERT: j 108 MET cc_start: 0.8808 (OUTLIER) cc_final: 0.8385 (mtm) REVERT: k 87 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8451 (mp) REVERT: k 110 GLU cc_start: 0.7214 (tm-30) cc_final: 0.6957 (tp30) REVERT: l 144 GLU cc_start: 0.7874 (tt0) cc_final: 0.7385 (tt0) REVERT: m 17 ASN cc_start: 0.8300 (t0) cc_final: 0.7698 (t0) REVERT: m 22 GLN cc_start: 0.8194 (OUTLIER) cc_final: 0.7806 (tm-30) REVERT: m 105 MET cc_start: 0.8792 (tpp) cc_final: 0.8487 (tpp) REVERT: m 110 GLU cc_start: 0.8500 (OUTLIER) cc_final: 0.7664 (tt0) REVERT: n 42 LYS cc_start: 0.8692 (mtmt) cc_final: 0.8421 (ptmt) REVERT: q 5 ARG cc_start: 0.7230 (OUTLIER) cc_final: 0.6597 (ptt90) REVERT: r 27 ILE cc_start: 0.8356 (OUTLIER) cc_final: 0.8127 (pt) REVERT: s 11 ARG cc_start: 0.7853 (OUTLIER) cc_final: 0.7520 (mtp-110) REVERT: s 86 MET cc_start: 0.8244 (tpp) cc_final: 0.8024 (tpp) REVERT: t 24 MET cc_start: 0.8068 (mpp) cc_final: 0.7634 (mpp) REVERT: t 87 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8261 (mm) REVERT: v 50 MET cc_start: 0.8913 (ppp) cc_final: 0.8480 (ppp) REVERT: y 58 ASN cc_start: 0.9047 (OUTLIER) cc_final: 0.8817 (t0) REVERT: z 28 LEU cc_start: 0.8765 (mt) cc_final: 0.8512 (mp) REVERT: A 1 MET cc_start: 0.7787 (ppp) cc_final: 0.7561 (ppp) REVERT: C 10 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8569 (mm) REVERT: D 12 ARG cc_start: 0.8576 (OUTLIER) cc_final: 0.8220 (ttt90) REVERT: D 15 SER cc_start: 0.9315 (t) cc_final: 0.9076 (t) REVERT: H 133 MET cc_start: 0.6839 (ptt) cc_final: 0.5761 (ppp) REVERT: H 151 GLU cc_start: 0.1722 (OUTLIER) cc_final: 0.0942 (mp0) REVERT: H 200 TRP cc_start: 0.6961 (m-10) cc_final: 0.6732 (m-10) REVERT: I 196 GLU cc_start: 0.7704 (OUTLIER) cc_final: 0.7423 (pp20) REVERT: J 44 ARG cc_start: 0.8383 (mmm160) cc_final: 0.7954 (tpp80) REVERT: J 104 ILE cc_start: 0.8723 (OUTLIER) cc_final: 0.8276 (mm) REVERT: K 78 PHE cc_start: 0.6674 (OUTLIER) cc_final: 0.6341 (m-10) REVERT: K 88 MET cc_start: 0.4950 (ttt) cc_final: 0.4055 (ttt) REVERT: M 26 MET cc_start: 0.7466 (ptp) cc_final: 0.6418 (pmm) REVERT: M 47 ASP cc_start: 0.8268 (t0) cc_final: 0.7904 (t0) REVERT: M 57 GLU cc_start: 0.6864 (mp0) cc_final: 0.6613 (mp0) REVERT: M 58 LEU cc_start: 0.8117 (tp) cc_final: 0.7638 (mt) REVERT: M 95 MET cc_start: 0.7447 (mpp) cc_final: 0.7152 (mpp) REVERT: M 120 LEU cc_start: 0.7757 (OUTLIER) cc_final: 0.7298 (pp) REVERT: N 45 MET cc_start: 0.7363 (ptm) cc_final: 0.6779 (ppp) REVERT: O 31 ARG cc_start: 0.7898 (ttt180) cc_final: 0.7085 (mmp-170) REVERT: O 59 LYS cc_start: 0.5869 (tppt) cc_final: 0.5107 (tttm) REVERT: O 73 LEU cc_start: 0.5670 (mp) cc_final: 0.5431 (tp) REVERT: Q 75 GLU cc_start: 0.9126 (mp0) cc_final: 0.8445 (mp0) REVERT: S 41 TRP cc_start: 0.2198 (OUTLIER) cc_final: 0.1975 (t-100) REVERT: T 5 GLU cc_start: 0.8186 (pm20) cc_final: 0.7957 (pm20) REVERT: T 14 PHE cc_start: 0.7562 (m-80) cc_final: 0.7266 (m-80) REVERT: T 58 MET cc_start: 0.8520 (OUTLIER) cc_final: 0.8167 (mmm) REVERT: T 86 LEU cc_start: 0.7844 (OUTLIER) cc_final: 0.7547 (pp) REVERT: U 5 ARG cc_start: 0.7811 (ptt180) cc_final: 0.6992 (ptt180) REVERT: U 32 PHE cc_start: 0.8234 (p90) cc_final: 0.7824 (m-80) REVERT: U 36 VAL cc_start: 0.9421 (OUTLIER) cc_final: 0.9200 (m) REVERT: V 21 VAL cc_start: 0.8102 (OUTLIER) cc_final: 0.7870 (p) REVERT: W 69 TYR cc_start: 0.5039 (m-80) cc_final: 0.4410 (m-10) REVERT: X 60 PHE cc_start: 0.8583 (OUTLIER) cc_final: 0.8254 (m-10) REVERT: Y 8 LYS cc_start: 0.8613 (tttt) cc_final: 0.8300 (tttt) REVERT: Y 14 GLU cc_start: 0.9189 (mm-30) cc_final: 0.8749 (mm-30) REVERT: Y 28 ARG cc_start: 0.8808 (ttm170) cc_final: 0.8267 (mtp85) REVERT: Y 56 ILE cc_start: 0.8740 (mm) cc_final: 0.8365 (tp) REVERT: Z 9 GLU cc_start: 0.4570 (OUTLIER) cc_final: 0.4193 (pt0) REVERT: 8 75 MET cc_start: 0.7782 (tmm) cc_final: 0.7147 (tmm) REVERT: 8 103 MET cc_start: 0.8840 (mpp) cc_final: 0.8263 (mtp) REVERT: 8 144 MET cc_start: 0.8146 (mmm) cc_final: 0.7588 (mmm) REVERT: 8 203 GLU cc_start: 0.8495 (tp30) cc_final: 0.8021 (tp30) REVERT: 8 205 GLU cc_start: 0.7299 (pt0) cc_final: 0.6677 (pt0) REVERT: 8 211 MET cc_start: 0.7672 (ppp) cc_final: 0.7196 (ppp) REVERT: 8 430 LYS cc_start: 0.8539 (OUTLIER) cc_final: 0.7839 (pttm) REVERT: 8 431 MET cc_start: 0.8341 (mmm) cc_final: 0.7842 (mmm) REVERT: 8 617 MET cc_start: 0.7828 (mmm) cc_final: 0.6784 (mmp) outliers start: 349 outliers final: 275 residues processed: 1041 average time/residue: 1.2600 time to fit residues: 2336.0207 Evaluate side-chains 1069 residues out of total 5429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 304 poor density : 765 time to evaluate : 6.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 33 LEU Chi-restraints excluded: chain b residue 48 ILE Chi-restraints excluded: chain b residue 53 ILE Chi-restraints excluded: chain b residue 76 VAL Chi-restraints excluded: chain b residue 85 ASN Chi-restraints excluded: chain b residue 90 ILE Chi-restraints excluded: chain b residue 93 VAL Chi-restraints excluded: chain b residue 129 LEU Chi-restraints excluded: chain b residue 136 VAL Chi-restraints excluded: chain b residue 161 VAL Chi-restraints excluded: chain b residue 180 MET Chi-restraints excluded: chain b residue 186 ASP Chi-restraints excluded: chain b residue 222 THR Chi-restraints excluded: chain b residue 227 VAL Chi-restraints excluded: chain b residue 249 VAL Chi-restraints excluded: chain c residue 2 ILE Chi-restraints excluded: chain c residue 51 THR Chi-restraints excluded: chain c residue 100 LEU Chi-restraints excluded: chain c residue 113 SER Chi-restraints excluded: chain c residue 146 ILE Chi-restraints excluded: chain c residue 165 MET Chi-restraints excluded: chain c residue 170 VAL Chi-restraints excluded: chain c residue 200 ASP Chi-restraints excluded: chain c residue 207 VAL Chi-restraints excluded: chain d residue 18 THR Chi-restraints excluded: chain d residue 73 ILE Chi-restraints excluded: chain d residue 97 ASN Chi-restraints excluded: chain d residue 148 ILE Chi-restraints excluded: chain e residue 4 HIS Chi-restraints excluded: chain e residue 12 VAL Chi-restraints excluded: chain e residue 15 LEU Chi-restraints excluded: chain e residue 19 PHE Chi-restraints excluded: chain e residue 24 VAL Chi-restraints excluded: chain e residue 26 GLN Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 35 LEU Chi-restraints excluded: chain e residue 90 LEU Chi-restraints excluded: chain e residue 104 THR Chi-restraints excluded: chain e residue 127 TYR Chi-restraints excluded: chain e residue 128 SER Chi-restraints excluded: chain e residue 151 LEU Chi-restraints excluded: chain e residue 154 THR Chi-restraints excluded: chain e residue 156 THR Chi-restraints excluded: chain e residue 158 THR Chi-restraints excluded: chain e residue 162 ASP Chi-restraints excluded: chain f residue 33 THR Chi-restraints excluded: chain f residue 106 LEU Chi-restraints excluded: chain f residue 116 LEU Chi-restraints excluded: chain f residue 121 THR Chi-restraints excluded: chain f residue 130 ILE Chi-restraints excluded: chain f residue 161 VAL Chi-restraints excluded: chain f residue 167 VAL Chi-restraints excluded: chain g residue 5 LEU Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain g residue 90 LEU Chi-restraints excluded: chain h residue 15 VAL Chi-restraints excluded: chain h residue 27 VAL Chi-restraints excluded: chain h residue 35 VAL Chi-restraints excluded: chain h residue 36 ASP Chi-restraints excluded: chain h residue 77 VAL Chi-restraints excluded: chain j residue 14 ASP Chi-restraints excluded: chain j residue 30 THR Chi-restraints excluded: chain j residue 32 LEU Chi-restraints excluded: chain j residue 98 GLU Chi-restraints excluded: chain j residue 108 MET Chi-restraints excluded: chain j residue 141 ASP Chi-restraints excluded: chain k residue 37 ASP Chi-restraints excluded: chain k residue 47 ILE Chi-restraints excluded: chain k residue 58 LEU Chi-restraints excluded: chain k residue 82 ASN Chi-restraints excluded: chain k residue 87 LEU Chi-restraints excluded: chain k residue 95 ILE Chi-restraints excluded: chain k residue 104 THR Chi-restraints excluded: chain l residue 19 LEU Chi-restraints excluded: chain l residue 46 VAL Chi-restraints excluded: chain l residue 57 LEU Chi-restraints excluded: chain l residue 74 THR Chi-restraints excluded: chain l residue 116 VAL Chi-restraints excluded: chain m residue 22 GLN Chi-restraints excluded: chain m residue 67 VAL Chi-restraints excluded: chain m residue 78 LEU Chi-restraints excluded: chain m residue 90 GLU Chi-restraints excluded: chain m residue 110 GLU Chi-restraints excluded: chain m residue 126 ILE Chi-restraints excluded: chain n residue 14 SER Chi-restraints excluded: chain n residue 51 LEU Chi-restraints excluded: chain n residue 97 ILE Chi-restraints excluded: chain n residue 116 VAL Chi-restraints excluded: chain o residue 12 THR Chi-restraints excluded: chain o residue 38 GLN Chi-restraints excluded: chain o residue 39 VAL Chi-restraints excluded: chain o residue 65 THR Chi-restraints excluded: chain o residue 78 VAL Chi-restraints excluded: chain o residue 83 LEU Chi-restraints excluded: chain o residue 91 SER Chi-restraints excluded: chain p residue 23 ASP Chi-restraints excluded: chain p residue 40 GLN Chi-restraints excluded: chain p residue 47 ILE Chi-restraints excluded: chain p residue 54 LEU Chi-restraints excluded: chain p residue 75 THR Chi-restraints excluded: chain q residue 5 ARG Chi-restraints excluded: chain q residue 73 ILE Chi-restraints excluded: chain q residue 79 ILE Chi-restraints excluded: chain r residue 27 ILE Chi-restraints excluded: chain r residue 32 THR Chi-restraints excluded: chain r residue 46 GLU Chi-restraints excluded: chain r residue 96 VAL Chi-restraints excluded: chain r residue 99 THR Chi-restraints excluded: chain r residue 101 ILE Chi-restraints excluded: chain s residue 11 ARG Chi-restraints excluded: chain s residue 15 GLN Chi-restraints excluded: chain s residue 20 VAL Chi-restraints excluded: chain s residue 22 ASP Chi-restraints excluded: chain s residue 45 VAL Chi-restraints excluded: chain s residue 50 VAL Chi-restraints excluded: chain s residue 51 LEU Chi-restraints excluded: chain s residue 53 SER Chi-restraints excluded: chain s residue 67 ASP Chi-restraints excluded: chain s residue 107 VAL Chi-restraints excluded: chain t residue 10 VAL Chi-restraints excluded: chain t residue 62 VAL Chi-restraints excluded: chain t residue 77 ARG Chi-restraints excluded: chain t residue 87 LEU Chi-restraints excluded: chain u residue 14 THR Chi-restraints excluded: chain u residue 27 VAL Chi-restraints excluded: chain u residue 67 SER Chi-restraints excluded: chain u residue 82 VAL Chi-restraints excluded: chain v residue 5 ASN Chi-restraints excluded: chain v residue 24 ASN Chi-restraints excluded: chain v residue 30 ILE Chi-restraints excluded: chain v residue 61 LEU Chi-restraints excluded: chain v residue 63 ILE Chi-restraints excluded: chain v residue 72 VAL Chi-restraints excluded: chain v residue 86 LEU Chi-restraints excluded: chain w residue 31 SER Chi-restraints excluded: chain w residue 40 LYS Chi-restraints excluded: chain w residue 46 ASN Chi-restraints excluded: chain x residue 12 VAL Chi-restraints excluded: chain x residue 24 THR Chi-restraints excluded: chain x residue 39 VAL Chi-restraints excluded: chain x residue 47 THR Chi-restraints excluded: chain y residue 14 LEU Chi-restraints excluded: chain y residue 58 ASN Chi-restraints excluded: chain z residue 56 VAL Chi-restraints excluded: chain A residue 63 ARG Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 12 ARG Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain F residue 10 LEU Chi-restraints excluded: chain F residue 20 ASP Chi-restraints excluded: chain G residue 49 PHE Chi-restraints excluded: chain G residue 55 GLU Chi-restraints excluded: chain G residue 66 ILE Chi-restraints excluded: chain G residue 86 CYS Chi-restraints excluded: chain G residue 144 GLU Chi-restraints excluded: chain G residue 190 SER Chi-restraints excluded: chain G residue 210 THR Chi-restraints excluded: chain H residue 2 GLN Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 17 TRP Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain H residue 101 ASN Chi-restraints excluded: chain H residue 151 GLU Chi-restraints excluded: chain H residue 161 ILE Chi-restraints excluded: chain H residue 182 ASP Chi-restraints excluded: chain I residue 4 LEU Chi-restraints excluded: chain I residue 74 TYR Chi-restraints excluded: chain I residue 98 ASP Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 196 GLU Chi-restraints excluded: chain I residue 199 ILE Chi-restraints excluded: chain J residue 10 LEU Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 104 ILE Chi-restraints excluded: chain J residue 115 GLU Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain K residue 11 HIS Chi-restraints excluded: chain K residue 25 TYR Chi-restraints excluded: chain K residue 36 ILE Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 78 PHE Chi-restraints excluded: chain K residue 87 SER Chi-restraints excluded: chain K residue 90 MET Chi-restraints excluded: chain K residue 100 SER Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain L residue 85 GLN Chi-restraints excluded: chain M residue 25 THR Chi-restraints excluded: chain M residue 50 VAL Chi-restraints excluded: chain M residue 61 THR Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain M residue 117 GLN Chi-restraints excluded: chain M residue 120 LEU Chi-restraints excluded: chain N residue 20 ILE Chi-restraints excluded: chain N residue 29 ILE Chi-restraints excluded: chain N residue 31 GLN Chi-restraints excluded: chain N residue 44 ARG Chi-restraints excluded: chain N residue 119 LYS Chi-restraints excluded: chain O residue 42 LEU Chi-restraints excluded: chain O residue 71 LEU Chi-restraints excluded: chain O residue 100 ILE Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 34 THR Chi-restraints excluded: chain P residue 45 THR Chi-restraints excluded: chain P residue 94 SER Chi-restraints excluded: chain P residue 96 ILE Chi-restraints excluded: chain P residue 115 ILE Chi-restraints excluded: chain P residue 120 CYS Chi-restraints excluded: chain P residue 126 ARG Chi-restraints excluded: chain Q residue 38 THR Chi-restraints excluded: chain Q residue 40 THR Chi-restraints excluded: chain Q residue 72 ASN Chi-restraints excluded: chain Q residue 74 GLN Chi-restraints excluded: chain Q residue 79 ILE Chi-restraints excluded: chain R residue 42 VAL Chi-restraints excluded: chain R residue 52 ILE Chi-restraints excluded: chain R residue 63 VAL Chi-restraints excluded: chain R residue 67 ASP Chi-restraints excluded: chain R residue 68 LEU Chi-restraints excluded: chain R residue 97 ARG Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain R residue 107 THR Chi-restraints excluded: chain S residue 41 TRP Chi-restraints excluded: chain S residue 63 CYS Chi-restraints excluded: chain S residue 83 VAL Chi-restraints excluded: chain S residue 92 ILE Chi-restraints excluded: chain T residue 1 SER Chi-restraints excluded: chain T residue 10 ILE Chi-restraints excluded: chain T residue 21 THR Chi-restraints excluded: chain T residue 24 THR Chi-restraints excluded: chain T residue 58 MET Chi-restraints excluded: chain T residue 61 GLN Chi-restraints excluded: chain T residue 74 VAL Chi-restraints excluded: chain T residue 86 LEU Chi-restraints excluded: chain T residue 88 ARG Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain U residue 20 VAL Chi-restraints excluded: chain U residue 36 VAL Chi-restraints excluded: chain U residue 66 THR Chi-restraints excluded: chain U residue 79 ASN Chi-restraints excluded: chain V residue 6 THR Chi-restraints excluded: chain V residue 7 LEU Chi-restraints excluded: chain V residue 8 GLN Chi-restraints excluded: chain V residue 21 VAL Chi-restraints excluded: chain V residue 36 PHE Chi-restraints excluded: chain V residue 49 ASN Chi-restraints excluded: chain V residue 52 CYS Chi-restraints excluded: chain V residue 82 VAL Chi-restraints excluded: chain W residue 13 THR Chi-restraints excluded: chain W residue 17 VAL Chi-restraints excluded: chain W residue 30 ASN Chi-restraints excluded: chain W residue 39 VAL Chi-restraints excluded: chain W residue 54 LEU Chi-restraints excluded: chain X residue 4 LEU Chi-restraints excluded: chain X residue 10 ILE Chi-restraints excluded: chain X residue 47 THR Chi-restraints excluded: chain X residue 60 PHE Chi-restraints excluded: chain X residue 78 THR Chi-restraints excluded: chain Y residue 11 ILE Chi-restraints excluded: chain Y residue 25 SER Chi-restraints excluded: chain Y residue 31 ILE Chi-restraints excluded: chain Y residue 53 MET Chi-restraints excluded: chain Z residue 8 ASN Chi-restraints excluded: chain Z residue 9 GLU Chi-restraints excluded: chain Z residue 32 ARG Chi-restraints excluded: chain Z residue 36 PHE Chi-restraints excluded: chain a residue 165 ASN Chi-restraints excluded: chain a residue 174 THR Chi-restraints excluded: chain 8 residue 56 GLU Chi-restraints excluded: chain 8 residue 141 VAL Chi-restraints excluded: chain 8 residue 167 VAL Chi-restraints excluded: chain 8 residue 180 THR Chi-restraints excluded: chain 8 residue 182 VAL Chi-restraints excluded: chain 8 residue 186 VAL Chi-restraints excluded: chain 8 residue 235 GLU Chi-restraints excluded: chain 8 residue 244 THR Chi-restraints excluded: chain 8 residue 262 ILE Chi-restraints excluded: chain 8 residue 265 THR Chi-restraints excluded: chain 8 residue 279 LEU Chi-restraints excluded: chain 8 residue 338 VAL Chi-restraints excluded: chain 8 residue 350 LEU Chi-restraints excluded: chain 8 residue 353 VAL Chi-restraints excluded: chain 8 residue 366 MET Chi-restraints excluded: chain 8 residue 392 THR Chi-restraints excluded: chain 8 residue 399 ASP Chi-restraints excluded: chain 8 residue 415 VAL Chi-restraints excluded: chain 8 residue 430 LYS Chi-restraints excluded: chain 8 residue 499 THR Chi-restraints excluded: chain 8 residue 518 VAL Chi-restraints excluded: chain 8 residue 519 VAL Chi-restraints excluded: chain 8 residue 605 PHE Chi-restraints excluded: chain 8 residue 628 THR Chi-restraints excluded: chain 8 residue 649 VAL Chi-restraints excluded: chain 8 residue 658 VAL Chi-restraints excluded: chain 8 residue 674 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1109 random chunks: chunk 661 optimal weight: 20.0000 chunk 426 optimal weight: 20.0000 chunk 638 optimal weight: 30.0000 chunk 321 optimal weight: 5.9990 chunk 210 optimal weight: 3.9990 chunk 207 optimal weight: 10.0000 chunk 679 optimal weight: 30.0000 chunk 728 optimal weight: 20.0000 chunk 528 optimal weight: 30.0000 chunk 99 optimal weight: 6.9990 chunk 840 optimal weight: 20.0000 overall best weight: 9.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 4 HIS ** f 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 5 GLN j 128 ASN ** k 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 72 ASN ** x 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 39 GLN I 40 HIS ** I 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 82 HIS ** L 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 75 GLN R 7 ASN T 34 GLN T 41 HIS ** X 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 19 HIS ** a 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.3907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.500 166272 Z= 0.359 Angle : 0.719 36.526 247962 Z= 0.369 Chirality : 0.040 0.603 31576 Planarity : 0.005 0.076 13872 Dihedral : 23.840 176.907 81264 Min Nonbonded Distance : 1.685 Molprobity Statistics. All-atom Clashscore : 22.10 Ramachandran Plot: Outliers : 0.23 % Allowed : 13.55 % Favored : 86.22 % Rotamer: Outliers : 6.34 % Allowed : 23.21 % Favored : 70.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.44 % Cis-general : 0.00 % Twisted Proline : 0.87 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.99 (0.10), residues: 6517 helix: -0.74 (0.11), residues: 2042 sheet: -2.18 (0.15), residues: 1060 loop : -2.77 (0.10), residues: 3415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.003 TRP 8 52 HIS 0.040 0.002 HIS e 4 PHE 0.029 0.002 PHE Z 36 TYR 0.046 0.002 TYR Y 35 ARG 0.013 0.001 ARG r 78 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13034 Ramachandran restraints generated. 6517 Oldfield, 0 Emsley, 6517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13034 Ramachandran restraints generated. 6517 Oldfield, 0 Emsley, 6517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1137 residues out of total 5429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 344 poor density : 793 time to evaluate : 6.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 33 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8549 (mm) REVERT: b 186 ASP cc_start: 0.8248 (OUTLIER) cc_final: 0.7768 (t70) REVERT: b 200 MET cc_start: 0.8533 (mtm) cc_final: 0.8292 (mtm) REVERT: b 228 ASP cc_start: 0.8056 (OUTLIER) cc_final: 0.7849 (t0) REVERT: d 1 MET cc_start: 0.5730 (mmp) cc_final: 0.5530 (mmm) REVERT: d 195 GLN cc_start: 0.8012 (mt0) cc_final: 0.7702 (mm110) REVERT: e 37 MET cc_start: 0.6653 (ttm) cc_final: 0.6007 (tmm) REVERT: e 95 MET cc_start: 0.8672 (ttp) cc_final: 0.8449 (ttp) REVERT: e 127 TYR cc_start: 0.7987 (OUTLIER) cc_final: 0.6732 (t80) REVERT: e 129 MET cc_start: 0.4929 (mmm) cc_final: 0.3988 (mmm) REVERT: f 59 ASP cc_start: 0.7117 (m-30) cc_final: 0.6444 (p0) REVERT: f 106 LEU cc_start: 0.8593 (OUTLIER) cc_final: 0.8296 (mt) REVERT: f 116 LEU cc_start: 0.8241 (OUTLIER) cc_final: 0.7915 (tp) REVERT: g 33 GLN cc_start: 0.8580 (tp-100) cc_final: 0.8267 (tm-30) REVERT: j 108 MET cc_start: 0.8861 (OUTLIER) cc_final: 0.8477 (mtm) REVERT: k 87 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8301 (mp) REVERT: k 121 GLU cc_start: 0.7909 (tm-30) cc_final: 0.7326 (mp0) REVERT: l 144 GLU cc_start: 0.7891 (tt0) cc_final: 0.7464 (tt0) REVERT: m 13 HIS cc_start: 0.8683 (OUTLIER) cc_final: 0.7958 (m-70) REVERT: m 17 ASN cc_start: 0.8257 (t0) cc_final: 0.7655 (t0) REVERT: m 22 GLN cc_start: 0.8225 (OUTLIER) cc_final: 0.7827 (tm-30) REVERT: m 105 MET cc_start: 0.8724 (tpp) cc_final: 0.8509 (tpp) REVERT: m 110 GLU cc_start: 0.8490 (OUTLIER) cc_final: 0.7688 (tt0) REVERT: o 88 LYS cc_start: 0.8589 (tmtt) cc_final: 0.8373 (tmtt) REVERT: q 5 ARG cc_start: 0.7227 (OUTLIER) cc_final: 0.6561 (ptt90) REVERT: r 27 ILE cc_start: 0.8361 (OUTLIER) cc_final: 0.8131 (pt) REVERT: r 78 ARG cc_start: 0.8182 (mmm160) cc_final: 0.7828 (mmm160) REVERT: s 11 ARG cc_start: 0.7854 (OUTLIER) cc_final: 0.7475 (mtp-110) REVERT: s 86 MET cc_start: 0.8251 (tpp) cc_final: 0.8031 (tpp) REVERT: t 6 ARG cc_start: 0.9042 (mmt-90) cc_final: 0.8771 (tpt170) REVERT: t 24 MET cc_start: 0.8028 (mpp) cc_final: 0.7687 (mpp) REVERT: t 87 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8206 (mm) REVERT: v 50 MET cc_start: 0.8935 (ppp) cc_final: 0.8587 (ppp) REVERT: y 7 ARG cc_start: 0.7984 (OUTLIER) cc_final: 0.6194 (mmp-170) REVERT: y 13 GLU cc_start: 0.8375 (mm-30) cc_final: 0.8077 (mm-30) REVERT: z 28 LEU cc_start: 0.8794 (mt) cc_final: 0.8546 (mp) REVERT: A 1 MET cc_start: 0.7813 (ppp) cc_final: 0.7588 (ppp) REVERT: D 12 ARG cc_start: 0.8595 (OUTLIER) cc_final: 0.8249 (ttt90) REVERT: D 15 SER cc_start: 0.9316 (t) cc_final: 0.9080 (t) REVERT: H 133 MET cc_start: 0.6854 (ptt) cc_final: 0.5810 (ppp) REVERT: H 151 GLU cc_start: 0.1748 (OUTLIER) cc_final: 0.1006 (mp0) REVERT: I 163 GLN cc_start: 0.4385 (OUTLIER) cc_final: 0.4015 (tm130) REVERT: I 196 GLU cc_start: 0.7716 (OUTLIER) cc_final: 0.7435 (pp20) REVERT: J 44 ARG cc_start: 0.8374 (mmm160) cc_final: 0.7959 (tpp80) REVERT: J 104 ILE cc_start: 0.8742 (OUTLIER) cc_final: 0.8283 (mm) REVERT: J 146 MET cc_start: 0.6739 (OUTLIER) cc_final: 0.5958 (ptm) REVERT: K 78 PHE cc_start: 0.6659 (OUTLIER) cc_final: 0.6315 (m-10) REVERT: K 88 MET cc_start: 0.5021 (ttt) cc_final: 0.4205 (ttt) REVERT: M 47 ASP cc_start: 0.8234 (t0) cc_final: 0.7911 (t0) REVERT: M 57 GLU cc_start: 0.6897 (mp0) cc_final: 0.6587 (mp0) REVERT: M 120 LEU cc_start: 0.7687 (OUTLIER) cc_final: 0.7238 (pp) REVERT: O 31 ARG cc_start: 0.7900 (ttt180) cc_final: 0.7086 (mmp-170) REVERT: O 59 LYS cc_start: 0.5896 (tppt) cc_final: 0.5017 (tttm) REVERT: O 73 LEU cc_start: 0.5814 (mp) cc_final: 0.5539 (tp) REVERT: Q 74 GLN cc_start: 0.8373 (OUTLIER) cc_final: 0.8061 (mp10) REVERT: Q 75 GLU cc_start: 0.9088 (mp0) cc_final: 0.8401 (mp0) REVERT: S 41 TRP cc_start: 0.2300 (OUTLIER) cc_final: 0.2052 (t-100) REVERT: T 5 GLU cc_start: 0.8219 (pm20) cc_final: 0.7988 (pm20) REVERT: T 14 PHE cc_start: 0.7491 (m-80) cc_final: 0.7269 (m-80) REVERT: T 58 MET cc_start: 0.8514 (OUTLIER) cc_final: 0.8213 (mmm) REVERT: T 86 LEU cc_start: 0.7779 (OUTLIER) cc_final: 0.7502 (pp) REVERT: U 5 ARG cc_start: 0.7723 (ptt180) cc_final: 0.6941 (ptt180) REVERT: U 32 PHE cc_start: 0.8292 (p90) cc_final: 0.7892 (m-80) REVERT: U 36 VAL cc_start: 0.9174 (OUTLIER) cc_final: 0.8932 (m) REVERT: W 69 TYR cc_start: 0.4975 (m-80) cc_final: 0.4399 (m-10) REVERT: X 60 PHE cc_start: 0.8583 (OUTLIER) cc_final: 0.8251 (m-10) REVERT: Y 8 LYS cc_start: 0.8601 (tttt) cc_final: 0.8283 (tttt) REVERT: Y 14 GLU cc_start: 0.9197 (mm-30) cc_final: 0.8758 (mm-30) REVERT: Y 28 ARG cc_start: 0.8784 (ttm170) cc_final: 0.8225 (mtp85) REVERT: Y 56 ILE cc_start: 0.8737 (mm) cc_final: 0.8381 (tp) REVERT: Z 9 GLU cc_start: 0.4510 (OUTLIER) cc_final: 0.4141 (pt0) REVERT: 8 75 MET cc_start: 0.7786 (tmm) cc_final: 0.7177 (tmm) REVERT: 8 103 MET cc_start: 0.8823 (mpp) cc_final: 0.8235 (mtp) REVERT: 8 144 MET cc_start: 0.8223 (mmm) cc_final: 0.7704 (mmm) REVERT: 8 211 MET cc_start: 0.7645 (ppp) cc_final: 0.7210 (ppp) REVERT: 8 218 TRP cc_start: 0.8514 (m100) cc_final: 0.8197 (m100) REVERT: 8 430 LYS cc_start: 0.8555 (OUTLIER) cc_final: 0.7852 (pttm) REVERT: 8 431 MET cc_start: 0.8473 (mmm) cc_final: 0.7956 (mmm) outliers start: 344 outliers final: 276 residues processed: 1035 average time/residue: 1.2407 time to fit residues: 2289.2600 Evaluate side-chains 1066 residues out of total 5429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 308 poor density : 758 time to evaluate : 6.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 33 LEU Chi-restraints excluded: chain b residue 48 ILE Chi-restraints excluded: chain b residue 53 ILE Chi-restraints excluded: chain b residue 85 ASN Chi-restraints excluded: chain b residue 90 ILE Chi-restraints excluded: chain b residue 93 VAL Chi-restraints excluded: chain b residue 129 LEU Chi-restraints excluded: chain b residue 136 VAL Chi-restraints excluded: chain b residue 161 VAL Chi-restraints excluded: chain b residue 180 MET Chi-restraints excluded: chain b residue 186 ASP Chi-restraints excluded: chain b residue 222 THR Chi-restraints excluded: chain b residue 227 VAL Chi-restraints excluded: chain b residue 228 ASP Chi-restraints excluded: chain b residue 249 VAL Chi-restraints excluded: chain c residue 2 ILE Chi-restraints excluded: chain c residue 51 THR Chi-restraints excluded: chain c residue 100 LEU Chi-restraints excluded: chain c residue 113 SER Chi-restraints excluded: chain c residue 146 ILE Chi-restraints excluded: chain c residue 165 MET Chi-restraints excluded: chain c residue 170 VAL Chi-restraints excluded: chain c residue 187 LEU Chi-restraints excluded: chain c residue 188 LEU Chi-restraints excluded: chain c residue 200 ASP Chi-restraints excluded: chain c residue 207 VAL Chi-restraints excluded: chain d residue 18 THR Chi-restraints excluded: chain d residue 73 ILE Chi-restraints excluded: chain d residue 97 ASN Chi-restraints excluded: chain d residue 148 ILE Chi-restraints excluded: chain d residue 150 THR Chi-restraints excluded: chain e residue 4 HIS Chi-restraints excluded: chain e residue 12 VAL Chi-restraints excluded: chain e residue 15 LEU Chi-restraints excluded: chain e residue 19 PHE Chi-restraints excluded: chain e residue 24 VAL Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 35 LEU Chi-restraints excluded: chain e residue 88 VAL Chi-restraints excluded: chain e residue 90 LEU Chi-restraints excluded: chain e residue 104 THR Chi-restraints excluded: chain e residue 127 TYR Chi-restraints excluded: chain e residue 128 SER Chi-restraints excluded: chain e residue 151 LEU Chi-restraints excluded: chain e residue 154 THR Chi-restraints excluded: chain e residue 158 THR Chi-restraints excluded: chain e residue 162 ASP Chi-restraints excluded: chain f residue 33 THR Chi-restraints excluded: chain f residue 106 LEU Chi-restraints excluded: chain f residue 116 LEU Chi-restraints excluded: chain f residue 121 THR Chi-restraints excluded: chain f residue 130 ILE Chi-restraints excluded: chain f residue 161 VAL Chi-restraints excluded: chain f residue 167 VAL Chi-restraints excluded: chain g residue 5 LEU Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain g residue 90 LEU Chi-restraints excluded: chain h residue 15 VAL Chi-restraints excluded: chain h residue 27 VAL Chi-restraints excluded: chain h residue 35 VAL Chi-restraints excluded: chain h residue 36 ASP Chi-restraints excluded: chain h residue 77 VAL Chi-restraints excluded: chain j residue 14 ASP Chi-restraints excluded: chain j residue 30 THR Chi-restraints excluded: chain j residue 32 LEU Chi-restraints excluded: chain j residue 98 GLU Chi-restraints excluded: chain j residue 108 MET Chi-restraints excluded: chain j residue 141 ASP Chi-restraints excluded: chain k residue 37 ASP Chi-restraints excluded: chain k residue 47 ILE Chi-restraints excluded: chain k residue 58 LEU Chi-restraints excluded: chain k residue 82 ASN Chi-restraints excluded: chain k residue 87 LEU Chi-restraints excluded: chain k residue 95 ILE Chi-restraints excluded: chain k residue 104 THR Chi-restraints excluded: chain l residue 19 LEU Chi-restraints excluded: chain l residue 46 VAL Chi-restraints excluded: chain l residue 57 LEU Chi-restraints excluded: chain l residue 74 THR Chi-restraints excluded: chain l residue 116 VAL Chi-restraints excluded: chain m residue 13 HIS Chi-restraints excluded: chain m residue 22 GLN Chi-restraints excluded: chain m residue 67 VAL Chi-restraints excluded: chain m residue 78 LEU Chi-restraints excluded: chain m residue 90 GLU Chi-restraints excluded: chain m residue 102 LEU Chi-restraints excluded: chain m residue 110 GLU Chi-restraints excluded: chain m residue 126 ILE Chi-restraints excluded: chain n residue 51 LEU Chi-restraints excluded: chain n residue 97 ILE Chi-restraints excluded: chain n residue 116 VAL Chi-restraints excluded: chain o residue 12 THR Chi-restraints excluded: chain o residue 38 GLN Chi-restraints excluded: chain o residue 39 VAL Chi-restraints excluded: chain o residue 47 VAL Chi-restraints excluded: chain o residue 65 THR Chi-restraints excluded: chain o residue 78 VAL Chi-restraints excluded: chain o residue 83 LEU Chi-restraints excluded: chain o residue 91 SER Chi-restraints excluded: chain p residue 23 ASP Chi-restraints excluded: chain p residue 40 GLN Chi-restraints excluded: chain p residue 47 ILE Chi-restraints excluded: chain p residue 54 LEU Chi-restraints excluded: chain p residue 75 THR Chi-restraints excluded: chain q residue 5 ARG Chi-restraints excluded: chain q residue 73 ILE Chi-restraints excluded: chain q residue 79 ILE Chi-restraints excluded: chain r residue 27 ILE Chi-restraints excluded: chain r residue 32 THR Chi-restraints excluded: chain r residue 46 GLU Chi-restraints excluded: chain r residue 96 VAL Chi-restraints excluded: chain r residue 99 THR Chi-restraints excluded: chain r residue 101 ILE Chi-restraints excluded: chain s residue 11 ARG Chi-restraints excluded: chain s residue 15 GLN Chi-restraints excluded: chain s residue 20 VAL Chi-restraints excluded: chain s residue 22 ASP Chi-restraints excluded: chain s residue 45 VAL Chi-restraints excluded: chain s residue 50 VAL Chi-restraints excluded: chain s residue 51 LEU Chi-restraints excluded: chain s residue 53 SER Chi-restraints excluded: chain s residue 67 ASP Chi-restraints excluded: chain s residue 107 VAL Chi-restraints excluded: chain t residue 10 VAL Chi-restraints excluded: chain t residue 62 VAL Chi-restraints excluded: chain t residue 77 ARG Chi-restraints excluded: chain t residue 87 LEU Chi-restraints excluded: chain u residue 14 THR Chi-restraints excluded: chain u residue 27 VAL Chi-restraints excluded: chain u residue 67 SER Chi-restraints excluded: chain u residue 82 VAL Chi-restraints excluded: chain v residue 5 ASN Chi-restraints excluded: chain v residue 24 ASN Chi-restraints excluded: chain v residue 30 ILE Chi-restraints excluded: chain v residue 61 LEU Chi-restraints excluded: chain v residue 63 ILE Chi-restraints excluded: chain v residue 72 VAL Chi-restraints excluded: chain w residue 46 ASN Chi-restraints excluded: chain w residue 55 LEU Chi-restraints excluded: chain x residue 12 VAL Chi-restraints excluded: chain x residue 24 THR Chi-restraints excluded: chain x residue 39 VAL Chi-restraints excluded: chain x residue 47 THR Chi-restraints excluded: chain y residue 7 ARG Chi-restraints excluded: chain y residue 14 LEU Chi-restraints excluded: chain z residue 56 VAL Chi-restraints excluded: chain A residue 63 ARG Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 12 ARG Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain F residue 10 LEU Chi-restraints excluded: chain F residue 20 ASP Chi-restraints excluded: chain G residue 49 PHE Chi-restraints excluded: chain G residue 55 GLU Chi-restraints excluded: chain G residue 66 ILE Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 86 CYS Chi-restraints excluded: chain G residue 144 GLU Chi-restraints excluded: chain G residue 190 SER Chi-restraints excluded: chain G residue 210 THR Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 17 TRP Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain H residue 101 ASN Chi-restraints excluded: chain H residue 151 GLU Chi-restraints excluded: chain H residue 161 ILE Chi-restraints excluded: chain I residue 4 LEU Chi-restraints excluded: chain I residue 74 TYR Chi-restraints excluded: chain I residue 98 ASP Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 163 GLN Chi-restraints excluded: chain I residue 196 GLU Chi-restraints excluded: chain J residue 10 LEU Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 82 HIS Chi-restraints excluded: chain J residue 104 ILE Chi-restraints excluded: chain J residue 115 GLU Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 146 MET Chi-restraints excluded: chain K residue 11 HIS Chi-restraints excluded: chain K residue 25 TYR Chi-restraints excluded: chain K residue 36 ILE Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 78 PHE Chi-restraints excluded: chain K residue 87 SER Chi-restraints excluded: chain K residue 90 MET Chi-restraints excluded: chain K residue 100 SER Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain L residue 85 GLN Chi-restraints excluded: chain M residue 25 THR Chi-restraints excluded: chain M residue 50 VAL Chi-restraints excluded: chain M residue 61 THR Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain M residue 117 GLN Chi-restraints excluded: chain M residue 120 LEU Chi-restraints excluded: chain N residue 20 ILE Chi-restraints excluded: chain N residue 29 ILE Chi-restraints excluded: chain N residue 31 GLN Chi-restraints excluded: chain N residue 44 ARG Chi-restraints excluded: chain N residue 119 LYS Chi-restraints excluded: chain O residue 18 ILE Chi-restraints excluded: chain O residue 42 LEU Chi-restraints excluded: chain O residue 71 LEU Chi-restraints excluded: chain O residue 100 ILE Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 34 THR Chi-restraints excluded: chain P residue 45 THR Chi-restraints excluded: chain P residue 94 SER Chi-restraints excluded: chain P residue 96 ILE Chi-restraints excluded: chain P residue 115 ILE Chi-restraints excluded: chain P residue 120 CYS Chi-restraints excluded: chain P residue 126 ARG Chi-restraints excluded: chain Q residue 38 THR Chi-restraints excluded: chain Q residue 40 THR Chi-restraints excluded: chain Q residue 57 THR Chi-restraints excluded: chain Q residue 72 ASN Chi-restraints excluded: chain Q residue 74 GLN Chi-restraints excluded: chain Q residue 79 ILE Chi-restraints excluded: chain R residue 42 VAL Chi-restraints excluded: chain R residue 52 ILE Chi-restraints excluded: chain R residue 63 VAL Chi-restraints excluded: chain R residue 67 ASP Chi-restraints excluded: chain R residue 68 LEU Chi-restraints excluded: chain R residue 97 ARG Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain R residue 107 THR Chi-restraints excluded: chain S residue 20 PHE Chi-restraints excluded: chain S residue 41 TRP Chi-restraints excluded: chain S residue 63 CYS Chi-restraints excluded: chain S residue 83 VAL Chi-restraints excluded: chain S residue 92 ILE Chi-restraints excluded: chain T residue 1 SER Chi-restraints excluded: chain T residue 10 ILE Chi-restraints excluded: chain T residue 21 THR Chi-restraints excluded: chain T residue 24 THR Chi-restraints excluded: chain T residue 34 GLN Chi-restraints excluded: chain T residue 55 LEU Chi-restraints excluded: chain T residue 58 MET Chi-restraints excluded: chain T residue 61 GLN Chi-restraints excluded: chain T residue 74 VAL Chi-restraints excluded: chain T residue 86 LEU Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain U residue 20 VAL Chi-restraints excluded: chain U residue 36 VAL Chi-restraints excluded: chain U residue 66 THR Chi-restraints excluded: chain U residue 79 ASN Chi-restraints excluded: chain V residue 6 THR Chi-restraints excluded: chain V residue 8 GLN Chi-restraints excluded: chain V residue 36 PHE Chi-restraints excluded: chain V residue 49 ASN Chi-restraints excluded: chain V residue 52 CYS Chi-restraints excluded: chain V residue 82 VAL Chi-restraints excluded: chain W residue 13 THR Chi-restraints excluded: chain W residue 17 VAL Chi-restraints excluded: chain W residue 30 ASN Chi-restraints excluded: chain W residue 39 VAL Chi-restraints excluded: chain W residue 54 LEU Chi-restraints excluded: chain X residue 4 LEU Chi-restraints excluded: chain X residue 10 ILE Chi-restraints excluded: chain X residue 47 THR Chi-restraints excluded: chain X residue 60 PHE Chi-restraints excluded: chain X residue 78 THR Chi-restraints excluded: chain Y residue 11 ILE Chi-restraints excluded: chain Y residue 31 ILE Chi-restraints excluded: chain Z residue 8 ASN Chi-restraints excluded: chain Z residue 9 GLU Chi-restraints excluded: chain Z residue 32 ARG Chi-restraints excluded: chain Z residue 36 PHE Chi-restraints excluded: chain a residue 165 ASN Chi-restraints excluded: chain a residue 174 THR Chi-restraints excluded: chain 8 residue 56 GLU Chi-restraints excluded: chain 8 residue 141 VAL Chi-restraints excluded: chain 8 residue 167 VAL Chi-restraints excluded: chain 8 residue 171 LEU Chi-restraints excluded: chain 8 residue 182 VAL Chi-restraints excluded: chain 8 residue 186 VAL Chi-restraints excluded: chain 8 residue 235 GLU Chi-restraints excluded: chain 8 residue 244 THR Chi-restraints excluded: chain 8 residue 262 ILE Chi-restraints excluded: chain 8 residue 265 THR Chi-restraints excluded: chain 8 residue 279 LEU Chi-restraints excluded: chain 8 residue 338 VAL Chi-restraints excluded: chain 8 residue 350 LEU Chi-restraints excluded: chain 8 residue 353 VAL Chi-restraints excluded: chain 8 residue 366 MET Chi-restraints excluded: chain 8 residue 392 THR Chi-restraints excluded: chain 8 residue 399 ASP Chi-restraints excluded: chain 8 residue 415 VAL Chi-restraints excluded: chain 8 residue 416 ILE Chi-restraints excluded: chain 8 residue 430 LYS Chi-restraints excluded: chain 8 residue 435 LEU Chi-restraints excluded: chain 8 residue 457 ILE Chi-restraints excluded: chain 8 residue 499 THR Chi-restraints excluded: chain 8 residue 518 VAL Chi-restraints excluded: chain 8 residue 519 VAL Chi-restraints excluded: chain 8 residue 605 PHE Chi-restraints excluded: chain 8 residue 628 THR Chi-restraints excluded: chain 8 residue 649 VAL Chi-restraints excluded: chain 8 residue 674 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1109 random chunks: chunk 972 optimal weight: 10.0000 chunk 1024 optimal weight: 20.0000 chunk 934 optimal weight: 40.0000 chunk 996 optimal weight: 10.0000 chunk 1023 optimal weight: 10.0000 chunk 599 optimal weight: 20.0000 chunk 433 optimal weight: 0.8980 chunk 782 optimal weight: 10.0000 chunk 305 optimal weight: 8.9990 chunk 900 optimal weight: 10.0000 chunk 942 optimal weight: 30.0000 overall best weight: 7.9794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 4 HIS i 33 ASN j 128 ASN ** k 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 15 HIS ** t 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 2 GLN ** I 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 82 HIS ** L 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 75 GLN R 7 ASN ** T 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 82 HIS 8 157 GLN ** 8 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.4013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.512 166272 Z= 0.327 Angle : 0.695 35.970 247962 Z= 0.357 Chirality : 0.039 0.409 31576 Planarity : 0.005 0.077 13872 Dihedral : 23.838 177.526 81264 Min Nonbonded Distance : 1.681 Molprobity Statistics. All-atom Clashscore : 21.04 Ramachandran Plot: Outliers : 0.23 % Allowed : 13.63 % Favored : 86.14 % Rotamer: Outliers : 6.26 % Allowed : 23.67 % Favored : 70.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.44 % Cis-general : 0.00 % Twisted Proline : 0.87 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.89 (0.10), residues: 6517 helix: -0.65 (0.11), residues: 2048 sheet: -2.11 (0.15), residues: 1061 loop : -2.73 (0.10), residues: 3408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.003 TRP 8 52 HIS 0.026 0.002 HIS e 4 PHE 0.047 0.002 PHE q 35 TYR 0.046 0.002 TYR Y 35 ARG 0.012 0.001 ARG B 51 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13034 Ramachandran restraints generated. 6517 Oldfield, 0 Emsley, 6517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13034 Ramachandran restraints generated. 6517 Oldfield, 0 Emsley, 6517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1132 residues out of total 5429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 340 poor density : 792 time to evaluate : 6.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 33 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8509 (mm) REVERT: b 186 ASP cc_start: 0.8239 (OUTLIER) cc_final: 0.7813 (p0) REVERT: b 200 MET cc_start: 0.8517 (mtm) cc_final: 0.8277 (mtm) REVERT: d 1 MET cc_start: 0.5672 (mmp) cc_final: 0.5452 (mmm) REVERT: d 195 GLN cc_start: 0.8009 (mt0) cc_final: 0.7717 (mm-40) REVERT: e 37 MET cc_start: 0.6377 (ttm) cc_final: 0.6050 (tmm) REVERT: e 95 MET cc_start: 0.8687 (ttp) cc_final: 0.8305 (ttp) REVERT: e 127 TYR cc_start: 0.7923 (OUTLIER) cc_final: 0.6728 (t80) REVERT: e 129 MET cc_start: 0.4976 (mmm) cc_final: 0.3982 (mmm) REVERT: f 59 ASP cc_start: 0.7098 (m-30) cc_final: 0.6448 (p0) REVERT: f 106 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8293 (mt) REVERT: f 116 LEU cc_start: 0.8235 (OUTLIER) cc_final: 0.7885 (tp) REVERT: g 33 GLN cc_start: 0.8600 (tp-100) cc_final: 0.8257 (tm-30) REVERT: g 41 LYS cc_start: 0.7888 (mmtp) cc_final: 0.7606 (pptt) REVERT: j 108 MET cc_start: 0.8850 (OUTLIER) cc_final: 0.8460 (mtm) REVERT: k 87 LEU cc_start: 0.8701 (OUTLIER) cc_final: 0.8319 (mp) REVERT: k 121 GLU cc_start: 0.7877 (tm-30) cc_final: 0.7321 (mp0) REVERT: l 144 GLU cc_start: 0.7890 (tt0) cc_final: 0.7501 (tt0) REVERT: m 13 HIS cc_start: 0.8674 (OUTLIER) cc_final: 0.7918 (m-70) REVERT: m 17 ASN cc_start: 0.8282 (t0) cc_final: 0.7706 (t0) REVERT: m 22 GLN cc_start: 0.8218 (OUTLIER) cc_final: 0.7832 (tm-30) REVERT: m 110 GLU cc_start: 0.8482 (OUTLIER) cc_final: 0.7689 (tt0) REVERT: o 88 LYS cc_start: 0.8567 (tmtt) cc_final: 0.8338 (tmtt) REVERT: q 5 ARG cc_start: 0.7199 (OUTLIER) cc_final: 0.6554 (ptt90) REVERT: r 26 ASP cc_start: 0.6449 (t70) cc_final: 0.6163 (t70) REVERT: r 27 ILE cc_start: 0.8345 (OUTLIER) cc_final: 0.8121 (pt) REVERT: r 40 MET cc_start: 0.8058 (tmm) cc_final: 0.7808 (tmm) REVERT: s 11 ARG cc_start: 0.7849 (OUTLIER) cc_final: 0.7471 (mtp-110) REVERT: s 86 MET cc_start: 0.8246 (tpp) cc_final: 0.8038 (tpp) REVERT: t 6 ARG cc_start: 0.9049 (mmt-90) cc_final: 0.8765 (tpt170) REVERT: t 24 MET cc_start: 0.8041 (mpp) cc_final: 0.7559 (mpp) REVERT: t 87 LEU cc_start: 0.8610 (OUTLIER) cc_final: 0.8219 (mm) REVERT: v 50 MET cc_start: 0.8904 (ppp) cc_final: 0.8692 (ppp) REVERT: y 7 ARG cc_start: 0.8027 (OUTLIER) cc_final: 0.6234 (mmp-170) REVERT: y 13 GLU cc_start: 0.8443 (mm-30) cc_final: 0.8176 (mm-30) REVERT: z 28 LEU cc_start: 0.8738 (mt) cc_final: 0.8528 (mp) REVERT: A 1 MET cc_start: 0.7782 (ppp) cc_final: 0.7561 (ppp) REVERT: B 47 TYR cc_start: 0.7857 (OUTLIER) cc_final: 0.6913 (m-80) REVERT: C 10 LEU cc_start: 0.8840 (mm) cc_final: 0.8605 (mm) REVERT: D 12 ARG cc_start: 0.8554 (OUTLIER) cc_final: 0.8238 (ttt90) REVERT: D 15 SER cc_start: 0.9324 (t) cc_final: 0.9096 (t) REVERT: H 133 MET cc_start: 0.6837 (ptt) cc_final: 0.5825 (ppp) REVERT: H 151 GLU cc_start: 0.1697 (OUTLIER) cc_final: 0.0949 (mp0) REVERT: I 70 GLN cc_start: 0.8089 (tm-30) cc_final: 0.7567 (mt0) REVERT: I 163 GLN cc_start: 0.4341 (OUTLIER) cc_final: 0.4032 (tm130) REVERT: I 196 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.7440 (pp20) REVERT: J 44 ARG cc_start: 0.8343 (mmm160) cc_final: 0.7967 (tpp80) REVERT: J 104 ILE cc_start: 0.8709 (OUTLIER) cc_final: 0.8286 (mm) REVERT: J 146 MET cc_start: 0.6764 (ttp) cc_final: 0.6406 (ttp) REVERT: K 78 PHE cc_start: 0.6609 (OUTLIER) cc_final: 0.6273 (m-10) REVERT: K 88 MET cc_start: 0.4932 (ttt) cc_final: 0.4362 (ttt) REVERT: M 26 MET cc_start: 0.7498 (ptp) cc_final: 0.6467 (pmm) REVERT: M 47 ASP cc_start: 0.8163 (t0) cc_final: 0.7888 (t0) REVERT: M 57 GLU cc_start: 0.6876 (mp0) cc_final: 0.6595 (mp0) REVERT: M 58 LEU cc_start: 0.8108 (tp) cc_final: 0.7680 (mt) REVERT: M 95 MET cc_start: 0.7501 (mpp) cc_final: 0.7243 (mpp) REVERT: M 120 LEU cc_start: 0.7786 (OUTLIER) cc_final: 0.7314 (pp) REVERT: O 31 ARG cc_start: 0.7882 (ttt180) cc_final: 0.7082 (mmp-170) REVERT: O 59 LYS cc_start: 0.5904 (tppt) cc_final: 0.5023 (tttm) REVERT: O 73 LEU cc_start: 0.5891 (mp) cc_final: 0.5638 (tp) REVERT: P 14 GLN cc_start: 0.7618 (tm-30) cc_final: 0.7324 (mm-40) REVERT: Q 74 GLN cc_start: 0.8370 (OUTLIER) cc_final: 0.8090 (mp10) REVERT: Q 75 GLU cc_start: 0.9105 (mp0) cc_final: 0.8425 (mp0) REVERT: R 68 LEU cc_start: 0.7786 (OUTLIER) cc_final: 0.6836 (mt) REVERT: S 5 MET cc_start: -0.1390 (mpp) cc_final: -0.1649 (ptp) REVERT: S 41 TRP cc_start: 0.2236 (OUTLIER) cc_final: 0.1992 (t-100) REVERT: T 5 GLU cc_start: 0.8232 (pm20) cc_final: 0.7999 (pm20) REVERT: T 58 MET cc_start: 0.8504 (OUTLIER) cc_final: 0.8235 (mmm) REVERT: T 86 LEU cc_start: 0.7865 (OUTLIER) cc_final: 0.7564 (pp) REVERT: U 5 ARG cc_start: 0.7715 (ptt180) cc_final: 0.6973 (ptt180) REVERT: U 32 PHE cc_start: 0.8263 (p90) cc_final: 0.7912 (m-80) REVERT: U 36 VAL cc_start: 0.9222 (OUTLIER) cc_final: 0.8972 (m) REVERT: W 69 TYR cc_start: 0.4952 (m-80) cc_final: 0.4455 (m-10) REVERT: X 54 ARG cc_start: 0.6653 (mmm160) cc_final: 0.5784 (mmm160) REVERT: X 55 GLN cc_start: 0.7958 (mm110) cc_final: 0.7703 (mm110) REVERT: X 60 PHE cc_start: 0.8600 (OUTLIER) cc_final: 0.8267 (m-10) REVERT: Y 8 LYS cc_start: 0.8601 (tttt) cc_final: 0.8265 (tttt) REVERT: Y 14 GLU cc_start: 0.9200 (mm-30) cc_final: 0.8754 (mm-30) REVERT: Y 28 ARG cc_start: 0.8785 (ttm170) cc_final: 0.8196 (mtp85) REVERT: Y 56 ILE cc_start: 0.8778 (mm) cc_final: 0.8417 (tp) REVERT: Z 9 GLU cc_start: 0.4519 (OUTLIER) cc_final: 0.4105 (pt0) REVERT: 8 54 GLU cc_start: 0.7970 (OUTLIER) cc_final: 0.7540 (pm20) REVERT: 8 75 MET cc_start: 0.7799 (tmm) cc_final: 0.7178 (tmm) REVERT: 8 103 MET cc_start: 0.8761 (OUTLIER) cc_final: 0.8243 (mtp) REVERT: 8 144 MET cc_start: 0.8205 (mmm) cc_final: 0.7810 (mmm) REVERT: 8 203 GLU cc_start: 0.8238 (tp30) cc_final: 0.8031 (tm-30) REVERT: 8 211 MET cc_start: 0.7555 (ppp) cc_final: 0.7097 (ppp) REVERT: 8 218 TRP cc_start: 0.8489 (m100) cc_final: 0.8155 (m100) REVERT: 8 430 LYS cc_start: 0.8532 (OUTLIER) cc_final: 0.7820 (pttm) REVERT: 8 431 MET cc_start: 0.8487 (mmm) cc_final: 0.7983 (mmm) REVERT: 8 641 MET cc_start: 0.7937 (pmm) cc_final: 0.7694 (pmm) outliers start: 340 outliers final: 270 residues processed: 1034 average time/residue: 1.2685 time to fit residues: 2332.6913 Evaluate side-chains 1067 residues out of total 5429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 304 poor density : 763 time to evaluate : 6.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 33 LEU Chi-restraints excluded: chain b residue 48 ILE Chi-restraints excluded: chain b residue 53 ILE Chi-restraints excluded: chain b residue 76 VAL Chi-restraints excluded: chain b residue 85 ASN Chi-restraints excluded: chain b residue 90 ILE Chi-restraints excluded: chain b residue 93 VAL Chi-restraints excluded: chain b residue 129 LEU Chi-restraints excluded: chain b residue 136 VAL Chi-restraints excluded: chain b residue 161 VAL Chi-restraints excluded: chain b residue 180 MET Chi-restraints excluded: chain b residue 186 ASP Chi-restraints excluded: chain b residue 222 THR Chi-restraints excluded: chain b residue 227 VAL Chi-restraints excluded: chain b residue 249 VAL Chi-restraints excluded: chain c residue 2 ILE Chi-restraints excluded: chain c residue 51 THR Chi-restraints excluded: chain c residue 100 LEU Chi-restraints excluded: chain c residue 113 SER Chi-restraints excluded: chain c residue 146 ILE Chi-restraints excluded: chain c residue 165 MET Chi-restraints excluded: chain c residue 170 VAL Chi-restraints excluded: chain c residue 187 LEU Chi-restraints excluded: chain c residue 188 LEU Chi-restraints excluded: chain c residue 200 ASP Chi-restraints excluded: chain c residue 207 VAL Chi-restraints excluded: chain d residue 7 ASP Chi-restraints excluded: chain d residue 18 THR Chi-restraints excluded: chain d residue 73 ILE Chi-restraints excluded: chain d residue 97 ASN Chi-restraints excluded: chain d residue 148 ILE Chi-restraints excluded: chain d residue 150 THR Chi-restraints excluded: chain e residue 12 VAL Chi-restraints excluded: chain e residue 15 LEU Chi-restraints excluded: chain e residue 19 PHE Chi-restraints excluded: chain e residue 24 VAL Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 88 VAL Chi-restraints excluded: chain e residue 90 LEU Chi-restraints excluded: chain e residue 104 THR Chi-restraints excluded: chain e residue 127 TYR Chi-restraints excluded: chain e residue 128 SER Chi-restraints excluded: chain e residue 151 LEU Chi-restraints excluded: chain e residue 158 THR Chi-restraints excluded: chain e residue 162 ASP Chi-restraints excluded: chain f residue 33 THR Chi-restraints excluded: chain f residue 97 VAL Chi-restraints excluded: chain f residue 106 LEU Chi-restraints excluded: chain f residue 116 LEU Chi-restraints excluded: chain f residue 130 ILE Chi-restraints excluded: chain f residue 161 VAL Chi-restraints excluded: chain f residue 167 VAL Chi-restraints excluded: chain g residue 5 LEU Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain h residue 15 VAL Chi-restraints excluded: chain h residue 27 VAL Chi-restraints excluded: chain h residue 35 VAL Chi-restraints excluded: chain h residue 77 VAL Chi-restraints excluded: chain j residue 14 ASP Chi-restraints excluded: chain j residue 30 THR Chi-restraints excluded: chain j residue 32 LEU Chi-restraints excluded: chain j residue 98 GLU Chi-restraints excluded: chain j residue 108 MET Chi-restraints excluded: chain j residue 141 ASP Chi-restraints excluded: chain k residue 37 ASP Chi-restraints excluded: chain k residue 47 ILE Chi-restraints excluded: chain k residue 58 LEU Chi-restraints excluded: chain k residue 82 ASN Chi-restraints excluded: chain k residue 87 LEU Chi-restraints excluded: chain k residue 92 GLU Chi-restraints excluded: chain k residue 95 ILE Chi-restraints excluded: chain k residue 104 THR Chi-restraints excluded: chain l residue 19 LEU Chi-restraints excluded: chain l residue 46 VAL Chi-restraints excluded: chain l residue 57 LEU Chi-restraints excluded: chain l residue 116 VAL Chi-restraints excluded: chain m residue 13 HIS Chi-restraints excluded: chain m residue 22 GLN Chi-restraints excluded: chain m residue 67 VAL Chi-restraints excluded: chain m residue 78 LEU Chi-restraints excluded: chain m residue 90 GLU Chi-restraints excluded: chain m residue 110 GLU Chi-restraints excluded: chain m residue 126 ILE Chi-restraints excluded: chain n residue 14 SER Chi-restraints excluded: chain n residue 51 LEU Chi-restraints excluded: chain n residue 60 VAL Chi-restraints excluded: chain n residue 97 ILE Chi-restraints excluded: chain o residue 12 THR Chi-restraints excluded: chain o residue 38 GLN Chi-restraints excluded: chain o residue 39 VAL Chi-restraints excluded: chain o residue 47 VAL Chi-restraints excluded: chain o residue 65 THR Chi-restraints excluded: chain o residue 78 VAL Chi-restraints excluded: chain o residue 83 LEU Chi-restraints excluded: chain o residue 91 SER Chi-restraints excluded: chain p residue 2 ASN Chi-restraints excluded: chain p residue 7 LEU Chi-restraints excluded: chain p residue 23 ASP Chi-restraints excluded: chain p residue 40 GLN Chi-restraints excluded: chain p residue 47 ILE Chi-restraints excluded: chain p residue 54 LEU Chi-restraints excluded: chain p residue 75 THR Chi-restraints excluded: chain q residue 5 ARG Chi-restraints excluded: chain q residue 73 ILE Chi-restraints excluded: chain q residue 79 ILE Chi-restraints excluded: chain r residue 27 ILE Chi-restraints excluded: chain r residue 32 THR Chi-restraints excluded: chain r residue 46 GLU Chi-restraints excluded: chain r residue 96 VAL Chi-restraints excluded: chain r residue 99 THR Chi-restraints excluded: chain r residue 101 ILE Chi-restraints excluded: chain s residue 11 ARG Chi-restraints excluded: chain s residue 15 GLN Chi-restraints excluded: chain s residue 20 VAL Chi-restraints excluded: chain s residue 22 ASP Chi-restraints excluded: chain s residue 45 VAL Chi-restraints excluded: chain s residue 50 VAL Chi-restraints excluded: chain s residue 51 LEU Chi-restraints excluded: chain s residue 53 SER Chi-restraints excluded: chain s residue 67 ASP Chi-restraints excluded: chain s residue 107 VAL Chi-restraints excluded: chain t residue 10 VAL Chi-restraints excluded: chain t residue 62 VAL Chi-restraints excluded: chain t residue 77 ARG Chi-restraints excluded: chain t residue 87 LEU Chi-restraints excluded: chain u residue 14 THR Chi-restraints excluded: chain u residue 27 VAL Chi-restraints excluded: chain u residue 41 VAL Chi-restraints excluded: chain u residue 67 SER Chi-restraints excluded: chain u residue 69 VAL Chi-restraints excluded: chain u residue 82 VAL Chi-restraints excluded: chain v residue 5 ASN Chi-restraints excluded: chain v residue 24 ASN Chi-restraints excluded: chain v residue 30 ILE Chi-restraints excluded: chain v residue 61 LEU Chi-restraints excluded: chain v residue 63 ILE Chi-restraints excluded: chain w residue 46 ASN Chi-restraints excluded: chain w residue 55 LEU Chi-restraints excluded: chain x residue 12 VAL Chi-restraints excluded: chain x residue 39 VAL Chi-restraints excluded: chain x residue 47 THR Chi-restraints excluded: chain y residue 7 ARG Chi-restraints excluded: chain y residue 14 LEU Chi-restraints excluded: chain z residue 56 VAL Chi-restraints excluded: chain A residue 63 ARG Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 47 TYR Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 12 ARG Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain F residue 20 ASP Chi-restraints excluded: chain G residue 49 PHE Chi-restraints excluded: chain G residue 55 GLU Chi-restraints excluded: chain G residue 66 ILE Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 86 CYS Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 144 GLU Chi-restraints excluded: chain G residue 190 SER Chi-restraints excluded: chain G residue 210 THR Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain H residue 101 ASN Chi-restraints excluded: chain H residue 151 GLU Chi-restraints excluded: chain H residue 161 ILE Chi-restraints excluded: chain I residue 4 LEU Chi-restraints excluded: chain I residue 98 ASP Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 163 GLN Chi-restraints excluded: chain I residue 196 GLU Chi-restraints excluded: chain I residue 199 ILE Chi-restraints excluded: chain J residue 10 LEU Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 82 HIS Chi-restraints excluded: chain J residue 104 ILE Chi-restraints excluded: chain J residue 115 GLU Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain K residue 11 HIS Chi-restraints excluded: chain K residue 25 TYR Chi-restraints excluded: chain K residue 36 ILE Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 78 PHE Chi-restraints excluded: chain K residue 87 SER Chi-restraints excluded: chain K residue 90 MET Chi-restraints excluded: chain K residue 100 SER Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain L residue 85 GLN Chi-restraints excluded: chain M residue 25 THR Chi-restraints excluded: chain M residue 50 VAL Chi-restraints excluded: chain M residue 61 THR Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain M residue 117 GLN Chi-restraints excluded: chain M residue 120 LEU Chi-restraints excluded: chain N residue 20 ILE Chi-restraints excluded: chain N residue 29 ILE Chi-restraints excluded: chain N residue 31 GLN Chi-restraints excluded: chain N residue 44 ARG Chi-restraints excluded: chain N residue 82 ILE Chi-restraints excluded: chain N residue 119 LYS Chi-restraints excluded: chain O residue 18 ILE Chi-restraints excluded: chain O residue 42 LEU Chi-restraints excluded: chain O residue 71 LEU Chi-restraints excluded: chain O residue 100 ILE Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 34 THR Chi-restraints excluded: chain P residue 45 THR Chi-restraints excluded: chain P residue 94 SER Chi-restraints excluded: chain P residue 96 ILE Chi-restraints excluded: chain P residue 115 ILE Chi-restraints excluded: chain P residue 120 CYS Chi-restraints excluded: chain P residue 126 ARG Chi-restraints excluded: chain Q residue 38 THR Chi-restraints excluded: chain Q residue 40 THR Chi-restraints excluded: chain Q residue 72 ASN Chi-restraints excluded: chain Q residue 74 GLN Chi-restraints excluded: chain Q residue 79 ILE Chi-restraints excluded: chain R residue 42 VAL Chi-restraints excluded: chain R residue 52 ILE Chi-restraints excluded: chain R residue 63 VAL Chi-restraints excluded: chain R residue 67 ASP Chi-restraints excluded: chain R residue 68 LEU Chi-restraints excluded: chain R residue 97 ARG Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain S residue 20 PHE Chi-restraints excluded: chain S residue 41 TRP Chi-restraints excluded: chain S residue 63 CYS Chi-restraints excluded: chain S residue 83 VAL Chi-restraints excluded: chain S residue 92 ILE Chi-restraints excluded: chain T residue 10 ILE Chi-restraints excluded: chain T residue 21 THR Chi-restraints excluded: chain T residue 24 THR Chi-restraints excluded: chain T residue 55 LEU Chi-restraints excluded: chain T residue 58 MET Chi-restraints excluded: chain T residue 61 GLN Chi-restraints excluded: chain T residue 74 VAL Chi-restraints excluded: chain T residue 86 LEU Chi-restraints excluded: chain T residue 88 ARG Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain U residue 20 VAL Chi-restraints excluded: chain U residue 36 VAL Chi-restraints excluded: chain U residue 60 TRP Chi-restraints excluded: chain U residue 66 THR Chi-restraints excluded: chain U residue 79 ASN Chi-restraints excluded: chain V residue 6 THR Chi-restraints excluded: chain V residue 8 GLN Chi-restraints excluded: chain V residue 36 PHE Chi-restraints excluded: chain V residue 49 ASN Chi-restraints excluded: chain V residue 52 CYS Chi-restraints excluded: chain V residue 82 VAL Chi-restraints excluded: chain W residue 13 THR Chi-restraints excluded: chain W residue 17 VAL Chi-restraints excluded: chain W residue 30 ASN Chi-restraints excluded: chain W residue 39 VAL Chi-restraints excluded: chain W residue 54 LEU Chi-restraints excluded: chain X residue 4 LEU Chi-restraints excluded: chain X residue 10 ILE Chi-restraints excluded: chain X residue 47 THR Chi-restraints excluded: chain X residue 60 PHE Chi-restraints excluded: chain X residue 78 THR Chi-restraints excluded: chain Y residue 11 ILE Chi-restraints excluded: chain Y residue 31 ILE Chi-restraints excluded: chain Z residue 8 ASN Chi-restraints excluded: chain Z residue 9 GLU Chi-restraints excluded: chain Z residue 32 ARG Chi-restraints excluded: chain Z residue 36 PHE Chi-restraints excluded: chain a residue 165 ASN Chi-restraints excluded: chain a residue 174 THR Chi-restraints excluded: chain 8 residue 54 GLU Chi-restraints excluded: chain 8 residue 56 GLU Chi-restraints excluded: chain 8 residue 103 MET Chi-restraints excluded: chain 8 residue 141 VAL Chi-restraints excluded: chain 8 residue 167 VAL Chi-restraints excluded: chain 8 residue 182 VAL Chi-restraints excluded: chain 8 residue 186 VAL Chi-restraints excluded: chain 8 residue 235 GLU Chi-restraints excluded: chain 8 residue 244 THR Chi-restraints excluded: chain 8 residue 262 ILE Chi-restraints excluded: chain 8 residue 265 THR Chi-restraints excluded: chain 8 residue 279 LEU Chi-restraints excluded: chain 8 residue 338 VAL Chi-restraints excluded: chain 8 residue 350 LEU Chi-restraints excluded: chain 8 residue 353 VAL Chi-restraints excluded: chain 8 residue 366 MET Chi-restraints excluded: chain 8 residue 392 THR Chi-restraints excluded: chain 8 residue 399 ASP Chi-restraints excluded: chain 8 residue 415 VAL Chi-restraints excluded: chain 8 residue 416 ILE Chi-restraints excluded: chain 8 residue 430 LYS Chi-restraints excluded: chain 8 residue 457 ILE Chi-restraints excluded: chain 8 residue 499 THR Chi-restraints excluded: chain 8 residue 518 VAL Chi-restraints excluded: chain 8 residue 519 VAL Chi-restraints excluded: chain 8 residue 605 PHE Chi-restraints excluded: chain 8 residue 628 THR Chi-restraints excluded: chain 8 residue 649 VAL Chi-restraints excluded: chain 8 residue 674 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1109 random chunks: chunk 992 optimal weight: 10.0000 chunk 654 optimal weight: 30.0000 chunk 1053 optimal weight: 5.9990 chunk 642 optimal weight: 20.0000 chunk 499 optimal weight: 6.9990 chunk 732 optimal weight: 30.0000 chunk 1104 optimal weight: 6.9990 chunk 1016 optimal weight: 30.0000 chunk 879 optimal weight: 20.0000 chunk 91 optimal weight: 8.9990 chunk 679 optimal weight: 30.0000 overall best weight: 7.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 15 HIS ** t 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 2 GLN ** H 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 75 GLN R 7 ASN ** T 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 19 HIS ** Y 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.4110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.534 166272 Z= 0.325 Angle : 0.693 33.881 247962 Z= 0.356 Chirality : 0.039 0.535 31576 Planarity : 0.005 0.098 13872 Dihedral : 23.835 177.568 81264 Min Nonbonded Distance : 1.685 Molprobity Statistics. All-atom Clashscore : 21.14 Ramachandran Plot: Outliers : 0.23 % Allowed : 13.53 % Favored : 86.24 % Rotamer: Outliers : 5.78 % Allowed : 24.26 % Favored : 69.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.44 % Cis-general : 0.00 % Twisted Proline : 0.87 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.86 (0.10), residues: 6517 helix: -0.63 (0.11), residues: 2055 sheet: -2.07 (0.15), residues: 1079 loop : -2.72 (0.10), residues: 3383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.003 TRP 8 52 HIS 0.040 0.002 HIS J 82 PHE 0.044 0.002 PHE q 35 TYR 0.049 0.002 TYR Y 35 ARG 0.013 0.001 ARG r 78 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13034 Ramachandran restraints generated. 6517 Oldfield, 0 Emsley, 6517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13034 Ramachandran restraints generated. 6517 Oldfield, 0 Emsley, 6517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1095 residues out of total 5429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 314 poor density : 781 time to evaluate : 6.716 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: b 33 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8508 (mm) REVERT: b 186 ASP cc_start: 0.8244 (OUTLIER) cc_final: 0.7803 (p0) REVERT: b 200 MET cc_start: 0.8510 (mtm) cc_final: 0.8290 (mtm) REVERT: d 195 GLN cc_start: 0.8002 (mt0) cc_final: 0.7713 (mm-40) REVERT: e 37 MET cc_start: 0.6350 (ttm) cc_final: 0.6055 (tmm) REVERT: e 95 MET cc_start: 0.8721 (ttp) cc_final: 0.8375 (ttp) REVERT: e 127 TYR cc_start: 0.7871 (OUTLIER) cc_final: 0.6637 (t80) REVERT: e 129 MET cc_start: 0.4955 (mmm) cc_final: 0.3974 (mmm) REVERT: f 59 ASP cc_start: 0.7124 (m-30) cc_final: 0.6469 (p0) REVERT: f 106 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.8319 (mt) REVERT: f 116 LEU cc_start: 0.8229 (OUTLIER) cc_final: 0.7879 (tp) REVERT: f 148 ARG cc_start: 0.8969 (ttp80) cc_final: 0.8077 (ttp80) REVERT: g 33 GLN cc_start: 0.8617 (tp-100) cc_final: 0.8269 (tm-30) REVERT: g 41 LYS cc_start: 0.7911 (mmtp) cc_final: 0.7611 (pptt) REVERT: j 108 MET cc_start: 0.8870 (OUTLIER) cc_final: 0.8492 (mtm) REVERT: k 121 GLU cc_start: 0.7871 (tm-30) cc_final: 0.7321 (mp0) REVERT: l 144 GLU cc_start: 0.7907 (tt0) cc_final: 0.7539 (tt0) REVERT: m 13 HIS cc_start: 0.8647 (OUTLIER) cc_final: 0.7948 (m-70) REVERT: m 17 ASN cc_start: 0.8257 (t0) cc_final: 0.7675 (t0) REVERT: m 22 GLN cc_start: 0.8207 (OUTLIER) cc_final: 0.7830 (tm-30) REVERT: m 110 GLU cc_start: 0.8449 (OUTLIER) cc_final: 0.7662 (tt0) REVERT: q 5 ARG cc_start: 0.7187 (OUTLIER) cc_final: 0.6536 (ptt90) REVERT: r 26 ASP cc_start: 0.6440 (t70) cc_final: 0.6146 (t70) REVERT: r 27 ILE cc_start: 0.8338 (OUTLIER) cc_final: 0.8115 (pt) REVERT: r 40 MET cc_start: 0.7985 (tmm) cc_final: 0.7759 (tmm) REVERT: r 60 LYS cc_start: 0.8301 (pttm) cc_final: 0.7640 (ptmt) REVERT: r 78 ARG cc_start: 0.8228 (mmm160) cc_final: 0.7910 (mmm160) REVERT: s 11 ARG cc_start: 0.7858 (OUTLIER) cc_final: 0.7494 (mtp-110) REVERT: s 86 MET cc_start: 0.8240 (tpp) cc_final: 0.8019 (tpp) REVERT: t 6 ARG cc_start: 0.8991 (mmt-90) cc_final: 0.8733 (tpt170) REVERT: t 24 MET cc_start: 0.8036 (mpp) cc_final: 0.7683 (mpp) REVERT: t 87 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.8198 (mm) REVERT: v 50 MET cc_start: 0.8902 (ppp) cc_final: 0.8656 (ppp) REVERT: y 7 ARG cc_start: 0.8023 (OUTLIER) cc_final: 0.6265 (mmp-170) REVERT: z 28 LEU cc_start: 0.8730 (mt) cc_final: 0.8519 (mp) REVERT: A 1 MET cc_start: 0.7764 (ppp) cc_final: 0.7549 (ppp) REVERT: B 47 TYR cc_start: 0.7845 (OUTLIER) cc_final: 0.6900 (m-80) REVERT: D 12 ARG cc_start: 0.8554 (OUTLIER) cc_final: 0.8239 (ttt90) REVERT: D 15 SER cc_start: 0.9315 (t) cc_final: 0.9064 (t) REVERT: G 138 ARG cc_start: 0.6288 (mmt90) cc_final: 0.5984 (mmm-85) REVERT: H 133 MET cc_start: 0.6941 (ptt) cc_final: 0.5800 (ppp) REVERT: H 151 GLU cc_start: 0.1699 (OUTLIER) cc_final: 0.0998 (mp0) REVERT: I 70 GLN cc_start: 0.8027 (tm-30) cc_final: 0.7521 (mt0) REVERT: I 163 GLN cc_start: 0.4457 (OUTLIER) cc_final: 0.4179 (tm130) REVERT: I 196 GLU cc_start: 0.7688 (OUTLIER) cc_final: 0.7337 (pp20) REVERT: J 44 ARG cc_start: 0.8370 (mmm160) cc_final: 0.7932 (tpp80) REVERT: J 104 ILE cc_start: 0.8716 (OUTLIER) cc_final: 0.8294 (mm) REVERT: J 146 MET cc_start: 0.6859 (ttp) cc_final: 0.6079 (ptm) REVERT: K 78 PHE cc_start: 0.6590 (OUTLIER) cc_final: 0.6258 (m-10) REVERT: K 79 ARG cc_start: 0.7972 (mtm180) cc_final: 0.7725 (mtm180) REVERT: K 88 MET cc_start: 0.4941 (ttt) cc_final: 0.4388 (ttt) REVERT: M 47 ASP cc_start: 0.8162 (t0) cc_final: 0.7882 (t0) REVERT: M 58 LEU cc_start: 0.8117 (tp) cc_final: 0.7840 (mt) REVERT: M 120 LEU cc_start: 0.7700 (OUTLIER) cc_final: 0.7181 (pp) REVERT: O 31 ARG cc_start: 0.7862 (ttt180) cc_final: 0.7063 (mmp-170) REVERT: O 59 LYS cc_start: 0.5889 (tppt) cc_final: 0.5012 (tttm) REVERT: O 73 LEU cc_start: 0.5839 (mp) cc_final: 0.5595 (tp) REVERT: P 14 GLN cc_start: 0.7620 (tm-30) cc_final: 0.7316 (mm-40) REVERT: Q 74 GLN cc_start: 0.8369 (OUTLIER) cc_final: 0.8090 (mp10) REVERT: Q 75 GLU cc_start: 0.9095 (mp0) cc_final: 0.8389 (mp0) REVERT: R 68 LEU cc_start: 0.7788 (OUTLIER) cc_final: 0.6836 (mt) REVERT: S 5 MET cc_start: -0.1322 (mpp) cc_final: -0.1567 (ptp) REVERT: T 5 GLU cc_start: 0.8239 (pm20) cc_final: 0.8006 (pm20) REVERT: T 58 MET cc_start: 0.8412 (OUTLIER) cc_final: 0.8178 (mmm) REVERT: T 84 LEU cc_start: 0.7786 (mm) cc_final: 0.7480 (mm) REVERT: T 86 LEU cc_start: 0.7856 (OUTLIER) cc_final: 0.7511 (pp) REVERT: U 5 ARG cc_start: 0.7712 (ptt180) cc_final: 0.6940 (ptt180) REVERT: U 32 PHE cc_start: 0.8245 (p90) cc_final: 0.7923 (m-80) REVERT: U 36 VAL cc_start: 0.9230 (OUTLIER) cc_final: 0.8958 (m) REVERT: W 69 TYR cc_start: 0.4902 (m-80) cc_final: 0.4458 (m-10) REVERT: X 54 ARG cc_start: 0.6659 (mmm160) cc_final: 0.5848 (mmm160) REVERT: X 55 GLN cc_start: 0.7990 (mm110) cc_final: 0.7694 (mm110) REVERT: Y 8 LYS cc_start: 0.8604 (tttt) cc_final: 0.8255 (tttt) REVERT: Y 14 GLU cc_start: 0.9209 (mm-30) cc_final: 0.8770 (mm-30) REVERT: Y 28 ARG cc_start: 0.8704 (ttm170) cc_final: 0.8171 (mtp85) REVERT: Y 56 ILE cc_start: 0.8812 (mm) cc_final: 0.8430 (tp) REVERT: Z 9 GLU cc_start: 0.4607 (OUTLIER) cc_final: 0.4278 (pt0) REVERT: 8 54 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.7524 (pm20) REVERT: 8 75 MET cc_start: 0.7787 (tmm) cc_final: 0.7163 (tmm) REVERT: 8 103 MET cc_start: 0.8757 (OUTLIER) cc_final: 0.8233 (mtp) REVERT: 8 144 MET cc_start: 0.8185 (mmm) cc_final: 0.7790 (mmm) REVERT: 8 211 MET cc_start: 0.7546 (ppp) cc_final: 0.6969 (ppp) REVERT: 8 218 TRP cc_start: 0.8488 (m100) cc_final: 0.8150 (m100) REVERT: 8 430 LYS cc_start: 0.8529 (OUTLIER) cc_final: 0.7818 (pttm) REVERT: 8 431 MET cc_start: 0.8514 (mmm) cc_final: 0.8005 (mmm) REVERT: 8 641 MET cc_start: 0.8001 (pmm) cc_final: 0.7754 (pmm) outliers start: 314 outliers final: 263 residues processed: 1002 average time/residue: 1.2547 time to fit residues: 2239.6603 Evaluate side-chains 1044 residues out of total 5429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 294 poor density : 750 time to evaluate : 6.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 33 LEU Chi-restraints excluded: chain b residue 48 ILE Chi-restraints excluded: chain b residue 53 ILE Chi-restraints excluded: chain b residue 76 VAL Chi-restraints excluded: chain b residue 85 ASN Chi-restraints excluded: chain b residue 90 ILE Chi-restraints excluded: chain b residue 93 VAL Chi-restraints excluded: chain b residue 129 LEU Chi-restraints excluded: chain b residue 136 VAL Chi-restraints excluded: chain b residue 161 VAL Chi-restraints excluded: chain b residue 180 MET Chi-restraints excluded: chain b residue 186 ASP Chi-restraints excluded: chain b residue 222 THR Chi-restraints excluded: chain b residue 227 VAL Chi-restraints excluded: chain b residue 249 VAL Chi-restraints excluded: chain c residue 2 ILE Chi-restraints excluded: chain c residue 51 THR Chi-restraints excluded: chain c residue 100 LEU Chi-restraints excluded: chain c residue 113 SER Chi-restraints excluded: chain c residue 146 ILE Chi-restraints excluded: chain c residue 165 MET Chi-restraints excluded: chain c residue 170 VAL Chi-restraints excluded: chain c residue 188 LEU Chi-restraints excluded: chain c residue 200 ASP Chi-restraints excluded: chain c residue 207 VAL Chi-restraints excluded: chain d residue 7 ASP Chi-restraints excluded: chain d residue 73 ILE Chi-restraints excluded: chain d residue 97 ASN Chi-restraints excluded: chain d residue 148 ILE Chi-restraints excluded: chain d residue 150 THR Chi-restraints excluded: chain e residue 12 VAL Chi-restraints excluded: chain e residue 15 LEU Chi-restraints excluded: chain e residue 19 PHE Chi-restraints excluded: chain e residue 24 VAL Chi-restraints excluded: chain e residue 90 LEU Chi-restraints excluded: chain e residue 104 THR Chi-restraints excluded: chain e residue 127 TYR Chi-restraints excluded: chain e residue 128 SER Chi-restraints excluded: chain e residue 151 LEU Chi-restraints excluded: chain e residue 154 THR Chi-restraints excluded: chain e residue 156 THR Chi-restraints excluded: chain e residue 158 THR Chi-restraints excluded: chain e residue 162 ASP Chi-restraints excluded: chain f residue 33 THR Chi-restraints excluded: chain f residue 97 VAL Chi-restraints excluded: chain f residue 106 LEU Chi-restraints excluded: chain f residue 116 LEU Chi-restraints excluded: chain f residue 121 THR Chi-restraints excluded: chain f residue 130 ILE Chi-restraints excluded: chain f residue 161 VAL Chi-restraints excluded: chain f residue 167 VAL Chi-restraints excluded: chain g residue 5 LEU Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain h residue 15 VAL Chi-restraints excluded: chain h residue 27 VAL Chi-restraints excluded: chain h residue 35 VAL Chi-restraints excluded: chain h residue 77 VAL Chi-restraints excluded: chain j residue 14 ASP Chi-restraints excluded: chain j residue 30 THR Chi-restraints excluded: chain j residue 32 LEU Chi-restraints excluded: chain j residue 98 GLU Chi-restraints excluded: chain j residue 108 MET Chi-restraints excluded: chain j residue 141 ASP Chi-restraints excluded: chain k residue 37 ASP Chi-restraints excluded: chain k residue 47 ILE Chi-restraints excluded: chain k residue 58 LEU Chi-restraints excluded: chain k residue 82 ASN Chi-restraints excluded: chain k residue 87 LEU Chi-restraints excluded: chain k residue 92 GLU Chi-restraints excluded: chain k residue 95 ILE Chi-restraints excluded: chain k residue 104 THR Chi-restraints excluded: chain l residue 19 LEU Chi-restraints excluded: chain l residue 46 VAL Chi-restraints excluded: chain l residue 57 LEU Chi-restraints excluded: chain l residue 74 THR Chi-restraints excluded: chain l residue 116 VAL Chi-restraints excluded: chain m residue 13 HIS Chi-restraints excluded: chain m residue 22 GLN Chi-restraints excluded: chain m residue 67 VAL Chi-restraints excluded: chain m residue 78 LEU Chi-restraints excluded: chain m residue 90 GLU Chi-restraints excluded: chain m residue 110 GLU Chi-restraints excluded: chain m residue 126 ILE Chi-restraints excluded: chain m residue 134 THR Chi-restraints excluded: chain n residue 14 SER Chi-restraints excluded: chain n residue 51 LEU Chi-restraints excluded: chain n residue 60 VAL Chi-restraints excluded: chain n residue 97 ILE Chi-restraints excluded: chain o residue 12 THR Chi-restraints excluded: chain o residue 38 GLN Chi-restraints excluded: chain o residue 39 VAL Chi-restraints excluded: chain o residue 47 VAL Chi-restraints excluded: chain o residue 65 THR Chi-restraints excluded: chain o residue 78 VAL Chi-restraints excluded: chain o residue 83 LEU Chi-restraints excluded: chain o residue 91 SER Chi-restraints excluded: chain p residue 2 ASN Chi-restraints excluded: chain p residue 7 LEU Chi-restraints excluded: chain p residue 23 ASP Chi-restraints excluded: chain p residue 40 GLN Chi-restraints excluded: chain p residue 47 ILE Chi-restraints excluded: chain p residue 54 LEU Chi-restraints excluded: chain p residue 75 THR Chi-restraints excluded: chain q residue 5 ARG Chi-restraints excluded: chain q residue 73 ILE Chi-restraints excluded: chain q residue 79 ILE Chi-restraints excluded: chain r residue 27 ILE Chi-restraints excluded: chain r residue 32 THR Chi-restraints excluded: chain r residue 46 GLU Chi-restraints excluded: chain r residue 96 VAL Chi-restraints excluded: chain r residue 99 THR Chi-restraints excluded: chain r residue 101 ILE Chi-restraints excluded: chain s residue 11 ARG Chi-restraints excluded: chain s residue 15 GLN Chi-restraints excluded: chain s residue 20 VAL Chi-restraints excluded: chain s residue 22 ASP Chi-restraints excluded: chain s residue 45 VAL Chi-restraints excluded: chain s residue 50 VAL Chi-restraints excluded: chain s residue 51 LEU Chi-restraints excluded: chain s residue 53 SER Chi-restraints excluded: chain s residue 107 VAL Chi-restraints excluded: chain t residue 10 VAL Chi-restraints excluded: chain t residue 77 ARG Chi-restraints excluded: chain t residue 87 LEU Chi-restraints excluded: chain u residue 14 THR Chi-restraints excluded: chain u residue 27 VAL Chi-restraints excluded: chain u residue 41 VAL Chi-restraints excluded: chain u residue 67 SER Chi-restraints excluded: chain u residue 69 VAL Chi-restraints excluded: chain u residue 82 VAL Chi-restraints excluded: chain v residue 5 ASN Chi-restraints excluded: chain v residue 24 ASN Chi-restraints excluded: chain v residue 30 ILE Chi-restraints excluded: chain v residue 61 LEU Chi-restraints excluded: chain v residue 63 ILE Chi-restraints excluded: chain v residue 72 VAL Chi-restraints excluded: chain w residue 46 ASN Chi-restraints excluded: chain x residue 12 VAL Chi-restraints excluded: chain x residue 24 THR Chi-restraints excluded: chain x residue 39 VAL Chi-restraints excluded: chain x residue 47 THR Chi-restraints excluded: chain y residue 7 ARG Chi-restraints excluded: chain y residue 14 LEU Chi-restraints excluded: chain y residue 24 GLU Chi-restraints excluded: chain z residue 56 VAL Chi-restraints excluded: chain A residue 63 ARG Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 47 TYR Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 12 ARG Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain F residue 20 ASP Chi-restraints excluded: chain G residue 49 PHE Chi-restraints excluded: chain G residue 55 GLU Chi-restraints excluded: chain G residue 66 ILE Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 86 CYS Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 144 GLU Chi-restraints excluded: chain G residue 190 SER Chi-restraints excluded: chain G residue 210 THR Chi-restraints excluded: chain H residue 2 GLN Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain H residue 101 ASN Chi-restraints excluded: chain H residue 151 GLU Chi-restraints excluded: chain H residue 161 ILE Chi-restraints excluded: chain I residue 4 LEU Chi-restraints excluded: chain I residue 98 ASP Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 163 GLN Chi-restraints excluded: chain I residue 196 GLU Chi-restraints excluded: chain I residue 199 ILE Chi-restraints excluded: chain J residue 10 LEU Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 104 ILE Chi-restraints excluded: chain J residue 115 GLU Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain K residue 11 HIS Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 78 PHE Chi-restraints excluded: chain K residue 87 SER Chi-restraints excluded: chain K residue 90 MET Chi-restraints excluded: chain K residue 100 SER Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain M residue 25 THR Chi-restraints excluded: chain M residue 50 VAL Chi-restraints excluded: chain M residue 61 THR Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain M residue 120 LEU Chi-restraints excluded: chain N residue 20 ILE Chi-restraints excluded: chain N residue 29 ILE Chi-restraints excluded: chain N residue 44 ARG Chi-restraints excluded: chain N residue 82 ILE Chi-restraints excluded: chain O residue 18 ILE Chi-restraints excluded: chain O residue 42 LEU Chi-restraints excluded: chain O residue 71 LEU Chi-restraints excluded: chain O residue 100 ILE Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 34 THR Chi-restraints excluded: chain P residue 45 THR Chi-restraints excluded: chain P residue 94 SER Chi-restraints excluded: chain P residue 96 ILE Chi-restraints excluded: chain P residue 115 ILE Chi-restraints excluded: chain P residue 120 CYS Chi-restraints excluded: chain P residue 126 ARG Chi-restraints excluded: chain Q residue 38 THR Chi-restraints excluded: chain Q residue 40 THR Chi-restraints excluded: chain Q residue 57 THR Chi-restraints excluded: chain Q residue 72 ASN Chi-restraints excluded: chain Q residue 74 GLN Chi-restraints excluded: chain Q residue 79 ILE Chi-restraints excluded: chain R residue 42 VAL Chi-restraints excluded: chain R residue 52 ILE Chi-restraints excluded: chain R residue 63 VAL Chi-restraints excluded: chain R residue 67 ASP Chi-restraints excluded: chain R residue 68 LEU Chi-restraints excluded: chain R residue 97 ARG Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain R residue 107 THR Chi-restraints excluded: chain S residue 20 PHE Chi-restraints excluded: chain S residue 63 CYS Chi-restraints excluded: chain S residue 83 VAL Chi-restraints excluded: chain T residue 10 ILE Chi-restraints excluded: chain T residue 21 THR Chi-restraints excluded: chain T residue 24 THR Chi-restraints excluded: chain T residue 55 LEU Chi-restraints excluded: chain T residue 58 MET Chi-restraints excluded: chain T residue 61 GLN Chi-restraints excluded: chain T residue 74 VAL Chi-restraints excluded: chain T residue 86 LEU Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain U residue 20 VAL Chi-restraints excluded: chain U residue 36 VAL Chi-restraints excluded: chain U residue 66 THR Chi-restraints excluded: chain U residue 79 ASN Chi-restraints excluded: chain V residue 6 THR Chi-restraints excluded: chain V residue 8 GLN Chi-restraints excluded: chain V residue 49 ASN Chi-restraints excluded: chain V residue 52 CYS Chi-restraints excluded: chain V residue 56 ASP Chi-restraints excluded: chain V residue 82 VAL Chi-restraints excluded: chain W residue 13 THR Chi-restraints excluded: chain W residue 17 VAL Chi-restraints excluded: chain W residue 30 ASN Chi-restraints excluded: chain W residue 39 VAL Chi-restraints excluded: chain W residue 54 LEU Chi-restraints excluded: chain X residue 4 LEU Chi-restraints excluded: chain X residue 10 ILE Chi-restraints excluded: chain X residue 47 THR Chi-restraints excluded: chain X residue 78 THR Chi-restraints excluded: chain Y residue 11 ILE Chi-restraints excluded: chain Z residue 8 ASN Chi-restraints excluded: chain Z residue 9 GLU Chi-restraints excluded: chain Z residue 32 ARG Chi-restraints excluded: chain Z residue 36 PHE Chi-restraints excluded: chain a residue 165 ASN Chi-restraints excluded: chain a residue 174 THR Chi-restraints excluded: chain 8 residue 54 GLU Chi-restraints excluded: chain 8 residue 56 GLU Chi-restraints excluded: chain 8 residue 103 MET Chi-restraints excluded: chain 8 residue 141 VAL Chi-restraints excluded: chain 8 residue 167 VAL Chi-restraints excluded: chain 8 residue 182 VAL Chi-restraints excluded: chain 8 residue 186 VAL Chi-restraints excluded: chain 8 residue 235 GLU Chi-restraints excluded: chain 8 residue 244 THR Chi-restraints excluded: chain 8 residue 262 ILE Chi-restraints excluded: chain 8 residue 265 THR Chi-restraints excluded: chain 8 residue 279 LEU Chi-restraints excluded: chain 8 residue 338 VAL Chi-restraints excluded: chain 8 residue 350 LEU Chi-restraints excluded: chain 8 residue 353 VAL Chi-restraints excluded: chain 8 residue 366 MET Chi-restraints excluded: chain 8 residue 392 THR Chi-restraints excluded: chain 8 residue 399 ASP Chi-restraints excluded: chain 8 residue 415 VAL Chi-restraints excluded: chain 8 residue 430 LYS Chi-restraints excluded: chain 8 residue 457 ILE Chi-restraints excluded: chain 8 residue 499 THR Chi-restraints excluded: chain 8 residue 518 VAL Chi-restraints excluded: chain 8 residue 519 VAL Chi-restraints excluded: chain 8 residue 605 PHE Chi-restraints excluded: chain 8 residue 628 THR Chi-restraints excluded: chain 8 residue 649 VAL Chi-restraints excluded: chain 8 residue 674 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1109 random chunks: chunk 539 optimal weight: 0.6980 chunk 698 optimal weight: 50.0000 chunk 937 optimal weight: 50.0000 chunk 269 optimal weight: 0.0670 chunk 811 optimal weight: 20.0000 chunk 129 optimal weight: 6.9990 chunk 244 optimal weight: 7.9990 chunk 881 optimal weight: 20.0000 chunk 368 optimal weight: 7.9990 chunk 904 optimal weight: 10.0000 chunk 111 optimal weight: 0.0570 overall best weight: 3.1640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 196 ASN d 163 ASN g 18 GLN j 128 ASN ** k 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 3 GLN ** n 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 43 ASN t 15 HIS ** t 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 73 ASN ** x 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 6 GLN ** G 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 75 GLN R 7 ASN S 42 ASN ** S 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 165 ASN ** 8 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.068944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.055731 restraints weight = 977473.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.056862 restraints weight = 362531.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.057541 restraints weight = 198429.326| |-----------------------------------------------------------------------------| r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3505 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3505 r_free = 0.3505 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3505 r_free = 0.3505 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3505 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.4199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.528 166272 Z= 0.249 Angle : 0.629 34.352 247962 Z= 0.324 Chirality : 0.035 0.467 31576 Planarity : 0.005 0.076 13872 Dihedral : 23.750 179.015 81264 Min Nonbonded Distance : 1.684 Molprobity Statistics. All-atom Clashscore : 17.88 Ramachandran Plot: Outliers : 0.14 % Allowed : 11.45 % Favored : 88.41 % Rotamer: Outliers : 4.59 % Allowed : 25.73 % Favored : 69.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.44 % Cis-general : 0.00 % Twisted Proline : 0.44 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.58 (0.10), residues: 6517 helix: -0.35 (0.11), residues: 2048 sheet: -1.92 (0.15), residues: 1084 loop : -2.57 (0.10), residues: 3385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.003 TRP 8 52 HIS 0.009 0.001 HIS H 5 PHE 0.044 0.002 PHE q 35 TYR 0.046 0.002 TYR Y 35 ARG 0.012 0.001 ARG r 78 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 35177.53 seconds wall clock time: 618 minutes 53.24 seconds (37133.24 seconds total)