Starting phenix.real_space_refine on Sun Mar 24 19:51:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wd0_21619/03_2024/6wd0_21619_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wd0_21619/03_2024/6wd0_21619.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wd0_21619/03_2024/6wd0_21619.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wd0_21619/03_2024/6wd0_21619.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wd0_21619/03_2024/6wd0_21619_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wd0_21619/03_2024/6wd0_21619_updated.pdb" } resolution = 3.0 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= 0.110 sd= 1.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 4728 5.49 5 S 154 5.16 5 C 74754 2.51 5 N 27669 2.21 5 O 41287 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "b GLU 235": "OE1" <-> "OE2" Residue "c ARG 13": "NH1" <-> "NH2" Residue "c ARG 33": "NH1" <-> "NH2" Residue "c ARG 59": "NH1" <-> "NH2" Residue "c ARG 77": "NH1" <-> "NH2" Residue "c ARG 83": "NH1" <-> "NH2" Residue "c GLU 86": "OE1" <-> "OE2" Residue "c ARG 169": "NH1" <-> "NH2" Residue "c ARG 184": "NH1" <-> "NH2" Residue "d ARG 21": "NH1" <-> "NH2" Residue "d ARG 44": "NH1" <-> "NH2" Residue "d ARG 49": "NH1" <-> "NH2" Residue "d ARG 61": "NH1" <-> "NH2" Residue "d ARG 88": "NH1" <-> "NH2" Residue "d ARG 102": "NH1" <-> "NH2" Residue "d ASP 116": "OD1" <-> "OD2" Residue "d ARG 162": "NH1" <-> "NH2" Residue "d ASP 168": "OD1" <-> "OD2" Residue "d ARG 170": "NH1" <-> "NH2" Residue "d ASP 191": "OD1" <-> "OD2" Residue "e ASP 50": "OD1" <-> "OD2" Residue "e ASP 55": "OD1" <-> "OD2" Residue "e ARG 70": "NH1" <-> "NH2" Residue "e ARG 79": "NH1" <-> "NH2" Residue "e ARG 91": "NH1" <-> "NH2" Residue "e GLU 97": "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 "e ASP 141": "OD1" <-> "OD2" Residue "f ARG 2": "NH1" <-> "NH2" Residue "f ASP 55": "OD1" <-> "OD2" Residue "f GLU 123": "OE1" <-> "OE2" Residue "f ARG 152": "NH1" <-> "NH2" Residue "f ARG 162": "NH1" <-> "NH2" Residue "f ARG 169": "NH1" <-> "NH2" Residue "g GLU 137": "OE1" <-> "OE2" Residue "h GLU 17": "OE1" <-> "OE2" Residue "h PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h GLU 116": "OE1" <-> "OE2" Residue "i ASP 46": "OD1" <-> "OD2" Residue "i ASP 115": "OD1" <-> "OD2" Residue "i ASP 120": "OD1" <-> "OD2" Residue "j ARG 13": "NH1" <-> "NH2" Residue "j ARG 37": "NH1" <-> "NH2" Residue "j TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j ARG 96": "NH1" <-> "NH2" Residue "j ARG 120": "NH1" <-> "NH2" 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 ASP 91": "OD1" <-> "OD2" Residue "l ARG 126": "NH1" <-> "NH2" Residue "m ARG 10": "NH1" <-> "NH2" Residue "m ARG 18": "NH1" <-> "NH2" Residue "m ASP 25": "OD1" <-> "OD2" Residue "m ARG 40": "NH1" <-> "NH2" Residue "m ARG 44": "NH1" <-> "NH2" Residue "m ARG 50": "NH1" <-> "NH2" Residue "m ARG 55": "NH1" <-> "NH2" Residue "m ARG 59": "NH1" <-> "NH2" Residue "m ARG 114": "NH1" <-> "NH2" Residue "n ARG 8": "NH1" <-> "NH2" Residue "n ARG 12": "NH1" <-> "NH2" Residue "n ARG 17": "NH1" <-> "NH2" Residue "n ARG 22": "NH1" <-> "NH2" Residue "n GLU 43": "OE1" <-> "OE2" 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 GLU 20": "OE1" <-> "OE2" Residue "o ARG 25": "NH1" <-> "NH2" Residue "o ARG 81": "NH1" <-> "NH2" Residue "o ARG 94": "NH1" <-> "NH2" Residue "o ARG 102": "NH1" <-> "NH2" Residue "o ARG 111": "NH1" <-> "NH2" Residue "p ARG 20": "NH1" <-> "NH2" Residue "p ARG 38": "NH1" <-> "NH2" Residue "p ARG 61": "NH1" <-> "NH2" Residue "p ARG 88": "NH1" <-> "NH2" Residue "p TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p ARG 100": "NH1" <-> "NH2" Residue "p ARG 108": "NH1" <-> "NH2" Residue "q ARG 2": "NH1" <-> "NH2" Residue "q ARG 5": "NH1" <-> "NH2" Residue "q ARG 12": "NH1" <-> "NH2" Residue "q ARG 32": "NH1" <-> "NH2" Residue "q ARG 47": "NH1" <-> "NH2" Residue "q ARG 69": "NH1" <-> "NH2" Residue "q ASP 96": "OD1" <-> "OD2" Residue "q ASP 101": "OD1" <-> "OD2" Residue "r ARG 21": "NH1" <-> "NH2" Residue "r GLU 31": "OE1" <-> "OE2" Residue "r ARG 68": "NH1" <-> "NH2" Residue "r ARG 78": "NH1" <-> "NH2" Residue "r ARG 79": "NH1" <-> "NH2" Residue "r ARG 84": "NH1" <-> "NH2" Residue "s ASP 22": "OD1" <-> "OD2" Residue "s ASP 65": "OD1" <-> "OD2" Residue "s ASP 68": "OD1" <-> "OD2" Residue "s ARG 84": "NH1" <-> "NH2" Residue "s ARG 88": "NH1" <-> "NH2" Residue "s ARG 95": "NH1" <-> "NH2" Residue "s ARG 110": "NH1" <-> "NH2" Residue "t ASP 37": "OD1" <-> "OD2" Residue "t GLU 54": "OE1" <-> "OE2" Residue "t ARG 73": "NH1" <-> "NH2" Residue "u ARG 5": "NH1" <-> "NH2" Residue "u ARG 6": "NH1" <-> "NH2" Residue "u ASP 80": "OD1" <-> "OD2" Residue "u ARG 81": "NH1" <-> "NH2" Residue "u ARG 85": "NH1" <-> "NH2" Residue "u GLU 87": "OE1" <-> "OE2" Residue "u ARG 93": "NH1" <-> "NH2" Residue "v GLU 7": "OE1" <-> "OE2" Residue "v TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v ASP 76": "OD1" <-> "OD2" Residue "w GLU 25": "OE1" <-> "OE2" Residue "x ASP 59": "OD1" <-> "OD2" Residue "y GLU 17": "OE1" <-> "OE2" Residue "y ARG 29": "NH1" <-> "NH2" Residue "y ARG 47": "NH1" <-> "NH2" Residue "y ASP 49": "OD1" <-> "OD2" 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 "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 TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 31": "OE1" <-> "OE2" Residue "C ASP 39": "OD1" <-> "OD2" Residue "C ARG 43": "NH1" <-> "NH2" Residue "C TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 50": "OE1" <-> "OE2" 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 PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 115": "OD1" <-> "OD2" Residue "G ASP 152": "OD1" <-> "OD2" Residue "G ASP 158": "OD1" <-> "OD2" Residue "G ASP 166": "OD1" <-> "OD2" Residue "G ASP 193": "OD1" <-> "OD2" Residue "G ARG 224": "NH1" <-> "NH2" Residue "H ASP 33": "OD1" <-> "OD2" Residue "H ARG 106": "NH1" <-> "NH2" Residue "H ARG 130": "NH1" <-> "NH2" Residue "H GLU 165": "OE1" <-> "OE2" Residue "H GLU 169": "OE1" <-> "OE2" Residue "H ASP 182": "OD1" <-> "OD2" Residue "I GLU 14": "OE1" <-> "OE2" Residue "I ASP 193": "OD1" <-> "OD2" Residue "J GLU 54": "OE1" <-> "OE2" Residue "J ASP 141": "OD1" <-> "OD2" Residue "J ARG 156": "NH1" <-> "NH2" Residue "J GLU 162": "OE1" <-> "OE2" Residue "K GLU 33": "OE1" <-> "OE2" Residue "K TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 69": "OE1" <-> "OE2" Residue "L PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 20": "OE1" <-> "OE2" Residue "L GLU 57": "OE1" <-> "OE2" Residue "L TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 8": "OD1" <-> "OD2" Residue "N ARG 123": "NH1" <-> "NH2" Residue "O GLU 27": "OE1" <-> "OE2" Residue "O GLU 78": "OE1" <-> "OE2" Residue "Q ARG 55": "NH1" <-> "NH2" Residue "R GLU 40": "OE1" <-> "OE2" Residue "S ASP 39": "OD1" <-> "OD2" Residue "S ASP 53": "OD1" <-> "OD2" Residue "T GLU 13": "OE1" <-> "OE2" Residue "T GLU 25": "OE1" <-> "OE2" Residue "T ASP 67": "OD1" <-> "OD2" Residue "U ARG 28": "NH1" <-> "NH2" Residue "U GLU 34": "OE1" <-> "OE2" Residue "U GLU 47": "OE1" <-> "OE2" Residue "U ASP 55": "OD1" <-> "OD2" Residue "U GLU 77": "OE1" <-> "OE2" Residue "W PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 11": "NH1" <-> "NH2" Residue "W ASP 21": "OD1" <-> "OD2" Residue "X ASP 63": "OD1" <-> "OD2" Residue "Y ASP 42": "OD1" <-> "OD2" Residue "Z ARG 66": "NH1" <-> "NH2" Residue "a ARG 7": "NH1" <-> "NH2" Residue "a ARG 12": "NH1" <-> "NH2" Residue "a ASP 51": "OD1" <-> "OD2" Residue "a ASP 56": "OD1" <-> "OD2" Residue "a ARG 162": "NH1" <-> "NH2" Residue "a TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 183": "OD1" <-> "OD2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 148592 Number of models: 1 Model: "" Number of chains: 58 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: 1111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1111 Classifications: {'peptide': 149} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 145} Chain: "h" Number of atoms: 989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 989 Classifications: {'peptide': 131} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 125} Chain: "i" Number of atoms: 1032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1032 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 131} 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: "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: 1757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1757 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 217} 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': 89, 'rna2p_pyr': 48, 'rna3p_pur': 785, 'rna3p_pyr': 617} Link IDs: {'rna2p': 137, 'rna3p': 1401} 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': 210, 'rna2p_pyr': 94, 'rna3p_pur': 1464, 'rna3p_pyr': 1135} Link IDs: {'rna2p': 304, 'rna3p': 2598} Chain: "2" Number of atoms: 2568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 2568 Classifications: {'RNA': 120} Modifications used: {'5*END': 1, 'rna2p_pur': 4, 'rna2p_pyr': 2, 'rna3p_pur': 61, 'rna3p_pyr': 53} Link IDs: {'rna2p': 6, 'rna3p': 113} Chain: "5" Number of atoms: 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': 4, 'rna3p_pur': 33, 'rna3p_pyr': 34} Link IDs: {'rna2p': 9, 'rna3p': 67} Chain: "6" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1640 Classifications: {'RNA': 77} Modifications used: {'5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 5, 'rna3p_pur': 33, 'rna3p_pyr': 33} Link IDs: {'rna2p': 11, 'rna3p': 65} Chain: "4" Number of atoms: 388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 388 Classifications: {'RNA': 18} Modifications used: {'5*END': 1, 'rna2p_pur': 1, 'rna3p_pur': 12, 'rna3p_pyr': 5} Link IDs: {'rna2p': 1, 'rna3p': 16} Chain: "5" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 58.50, per 1000 atoms: 0.39 Number of scatterers: 148592 At special positions: 0 Unit cell: (281.263, 269.266, 241.273, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 154 16.00 P 4728 15.00 O 41287 8.00 N 27669 7.00 C 74754 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 61.20 Conformation dependent library (CDL) restraints added in 7.1 seconds 11838 Ramachandran restraints generated. 5919 Oldfield, 0 Emsley, 5919 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11074 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: 184 helices and 70 sheets defined 38.9% alpha, 18.5% beta 1491 base pairs and 2885 stacking pairs defined. Time for finding SS restraints: 76.10 Creating SS restraints... Processing helix chain 'b' and resid 9 through 16 removed outlier: 7.406A pdb=" N HIS b 14 " --> pdb=" O PRO b 10 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N VAL b 15 " --> pdb=" O GLY b 11 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N VAL b 16 " --> pdb=" O ARG b 12 " (cutoff:3.500A) Processing helix chain 'b' and resid 29 through 34 removed outlier: 3.938A pdb=" N LEU b 33 " --> pdb=" O PHE b 29 " (cutoff:3.500A) removed outlier: 5.571A 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: 3.979A 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: 3.817A pdb=" N ALA b 210 " --> pdb=" O LYS b 206 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ARG b 213 " --> pdb=" O ALA b 209 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY b 214 " --> pdb=" O ALA b 210 " (cutoff:3.500A) Processing helix chain 'b' and resid 220 through 225 removed outlier: 3.846A pdb=" N MET b 224 " --> pdb=" O ARG b 220 " (cutoff:3.500A) removed outlier: 5.203A 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: 5.845A pdb=" N ASP b 263 " --> pdb=" O ASN b 259 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N LYS b 264 " --> pdb=" O LYS b 260 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N PHE b 265 " --> pdb=" O ARG b 261 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ILE b 266 " --> pdb=" O THR b 262 " (cutoff:3.500A) removed outlier: 5.598A 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: 4.219A pdb=" N MET b 200 " --> pdb=" O ALA b 197 " (cutoff:3.500A) Processing helix chain 'c' and resid 56 through 61 removed outlier: 5.859A pdb=" N THR c 61 " --> pdb=" O ALA c 57 " (cutoff:3.500A) Processing helix chain 'c' and resid 62 through 72 removed outlier: 3.688A pdb=" N ALA c 71 " --> pdb=" O HIS c 67 " (cutoff:3.500A) Processing helix chain 'c' and resid 98 through 105 removed outlier: 4.219A pdb=" N ALA c 102 " --> pdb=" O VAL c 98 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N ASP c 103 " --> pdb=" O GLU c 99 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N VAL c 104 " --> pdb=" O LEU c 100 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N LYS c 105 " --> pdb=" O PHE c 101 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 98 through 105' Processing helix chain 'c' and resid 120 through 125 Processing helix chain 'c' and resid 39 through 44 Processing helix chain 'd' and resid 15 through 20 Processing helix chain 'd' and resid 24 through 40 removed outlier: 3.507A pdb=" N ALA d 34 " --> pdb=" O GLN d 30 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG d 40 " --> pdb=" O ALA d 36 " (cutoff:3.500A) Processing helix chain 'd' and resid 48 through 53 removed outlier: 7.251A pdb=" N THR d 53 " --> pdb=" O ARG d 49 " (cutoff:3.500A) Processing helix chain 'd' and resid 97 through 116 removed outlier: 3.708A pdb=" N ARG d 114 " --> pdb=" O SER d 110 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASP d 116 " --> pdb=" O LEU d 112 " (cutoff:3.500A) Processing helix chain 'd' and resid 130 through 142 removed outlier: 3.527A pdb=" N ASP d 140 " --> pdb=" O GLN d 136 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N MET d 141 " --> pdb=" O LYS d 137 " (cutoff:3.500A) Processing helix chain 'd' and resid 154 through 163 removed outlier: 3.767A pdb=" N ALA d 160 " --> pdb=" O ASN d 156 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N ASN d 163 " --> pdb=" O LEU d 159 " (cutoff:3.500A) Processing helix chain 'd' and resid 176 through 184 removed outlier: 3.531A pdb=" N LEU d 180 " --> pdb=" O ASP d 176 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N ASP d 184 " --> pdb=" O LEU d 180 " (cutoff:3.500A) Processing helix chain 'd' and resid 189 through 201 Processing helix chain 'e' and resid 1 through 20 removed outlier: 3.538A pdb=" N ASP e 5 " --> pdb=" O ALA e 1 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N VAL e 12 " --> pdb=" O LYS e 8 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LYS e 13 " --> pdb=" O ASP e 9 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N THR e 17 " --> pdb=" O LYS e 13 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N GLU e 18 " --> pdb=" O LYS e 14 " (cutoff:3.500A) Processing helix chain 'e' and resid 41 through 46 removed outlier: 4.468A pdb=" N LYS e 46 " --> pdb=" O ALA e 42 " (cutoff:3.500A) Processing helix chain 'e' and resid 47 through 61 removed outlier: 3.535A pdb=" N ASN e 51 " --> pdb=" O LYS e 47 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N GLY e 61 " --> pdb=" O ALA e 57 " (cutoff:3.500A) Processing helix chain 'e' and resid 92 through 110 removed outlier: 4.138A pdb=" N TRP e 96 " --> pdb=" O GLY e 92 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU e 97 " --> pdb=" O GLU e 93 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N PHE e 98 " --> pdb=" O ARG e 94 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ILE e 105 " --> pdb=" O ARG e 101 " (cutoff:3.500A) removed outlier: 5.409A 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 161 through 173 removed outlier: 3.839A pdb=" N ALA e 167 " --> pdb=" O GLU e 163 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU e 168 " --> pdb=" O GLU e 164 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU e 169 " --> pdb=" O GLY e 165 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA e 171 " --> pdb=" O ALA e 167 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N PHE e 172 " --> pdb=" O LEU e 168 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ASP e 173 " --> pdb=" O LEU e 169 " (cutoff:3.500A) Processing helix chain 'e' and resid 133 through 138 removed outlier: 3.783A pdb=" N ILE e 136 " --> pdb=" O GLU e 133 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N PHE e 137 " --> pdb=" O GLN e 134 " (cutoff:3.500A) Proline residue: e 138 - end of helix No H-bonds generated for 'chain 'e' and resid 133 through 138' Processing helix chain 'f' and resid 1 through 7 removed outlier: 4.267A 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: 4.005A 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 50 through 73 removed outlier: 4.830A pdb=" N ALA g 56 " --> pdb=" O ALA g 52 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N LYS g 57 " --> pdb=" O GLU g 53 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLU g 60 " --> pdb=" O ALA g 56 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU g 62 " --> pdb=" O LEU g 58 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA g 63 " --> pdb=" O ALA g 59 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA g 69 " --> pdb=" O ALA g 65 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N LYS g 71 " --> pdb=" O ALA g 67 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE g 72 " --> pdb=" O ARG g 68 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N ASN g 73 " --> pdb=" O ALA g 69 " (cutoff:3.500A) Processing helix chain 'g' and resid 95 through 107 removed outlier: 3.502A pdb=" N ILE g 99 " --> pdb=" O GLY g 95 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL g 103 " --> pdb=" O ILE g 99 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ALA g 105 " --> pdb=" O ASP g 101 " (cutoff:3.500A) Processing helix chain 'h' and resid 3 through 21 removed outlier: 3.842A pdb=" N ALA h 10 " --> pdb=" O GLN h 6 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU h 17 " --> pdb=" O ALA h 13 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LYS h 20 " --> pdb=" O SER h 16 " (cutoff:3.500A) Processing helix chain 'h' and resid 33 through 48 removed outlier: 3.638A pdb=" N MET h 38 " --> pdb=" O THR h 34 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N THR h 39 " --> pdb=" O VAL h 35 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLU h 40 " --> pdb=" O ASP h 36 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ARG h 42 " --> pdb=" O MET h 38 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS h 43 " --> pdb=" O THR h 39 " (cutoff:3.500A) Processing helix chain 'h' and resid 62 through 71 Proline residue: h 68 - end of helix removed outlier: 4.460A pdb=" N CYS h 71 " --> pdb=" O THR h 67 " (cutoff:3.500A) Processing helix chain 'h' and resid 95 through 106 removed outlier: 4.591A pdb=" N PHE h 99 " --> pdb=" O LEU h 95 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N ALA h 100 " --> pdb=" O PHE h 96 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ALA h 104 " --> pdb=" O ALA h 100 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N PHE h 106 " --> pdb=" O ALA h 102 " (cutoff:3.500A) Processing helix chain 'h' and resid 109 through 114 removed outlier: 6.376A pdb=" N ALA h 112 " --> pdb=" O LYS h 109 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLU h 114 " --> pdb=" O ALA h 111 " (cutoff:3.500A) Processing helix chain 'i' and resid 23 through 31 removed outlier: 5.138A pdb=" N LEU i 27 " --> pdb=" O VAL i 23 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY i 28 " --> pdb=" O GLY i 24 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N GLN i 30 " --> pdb=" O ALA i 26 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N GLY i 31 " --> pdb=" O LEU i 27 " (cutoff:3.500A) Processing helix chain 'i' and resid 33 through 46 removed outlier: 3.707A pdb=" N ALA i 43 " --> pdb=" O LYS i 39 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASP i 46 " --> pdb=" O ASN i 42 " (cutoff:3.500A) Processing helix chain 'i' and resid 74 through 84 removed outlier: 3.664A pdb=" N ALA i 83 " --> pdb=" O LEU i 79 " (cutoff:3.500A) Processing helix chain 'i' and resid 101 through 114 removed outlier: 3.991A pdb=" N ALA i 114 " --> pdb=" O GLN i 110 " (cutoff:3.500A) Processing helix chain 'i' and resid 120 through 136 removed outlier: 3.602A pdb=" N ILE i 128 " --> pdb=" O MET i 124 " (cutoff:3.500A) Processing helix chain 'j' and resid 24 through 38 Processing helix chain 'j' and resid 88 through 96 Processing helix chain 'j' and resid 97 through 110 removed outlier: 4.485A pdb=" N ILE j 101 " --> pdb=" O PRO j 97 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS j 106 " --> pdb=" O GLU j 102 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N MET j 108 " --> pdb=" O ALA j 104 " (cutoff:3.500A) Proline residue: j 110 - end of helix Processing helix chain 'j' and resid 112 through 122 removed outlier: 4.485A pdb=" N LYS j 121 " --> pdb=" O ALA j 117 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N LEU j 122 " --> pdb=" O MET j 118 " (cutoff:3.500A) Processing helix chain 'k' and resid 109 through 119 removed outlier: 5.912A pdb=" N MET k 113 " --> pdb=" O SER k 109 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N LYS k 114 " --> pdb=" O GLU k 110 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N ILE k 115 " --> pdb=" O LYS k 111 " (cutoff:3.500A) Processing helix chain 'l' and resid 56 through 62 Proline residue: l 62 - end of helix Processing helix chain 'l' and resid 68 through 75 removed outlier: 4.043A pdb=" N ALA l 72 " --> pdb=" O SER l 68 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ILE l 73 " --> pdb=" O ARG l 69 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N THR l 74 " --> pdb=" O LYS l 70 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N ALA l 75 " --> pdb=" O ALA l 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 68 through 75' Processing helix chain 'l' and resid 78 through 85 removed outlier: 3.744A pdb=" N LEU l 82 " --> pdb=" O ARG l 78 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ALA l 83 " --> pdb=" O LEU l 79 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N LYS l 84 " --> pdb=" O SER l 80 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VAL l 85 " --> pdb=" O ASP l 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 78 through 85' Processing helix chain 'l' and resid 93 through 99 removed outlier: 5.803A pdb=" N ALA l 97 " --> pdb=" O ASN l 93 " (cutoff:3.500A) Processing helix chain 'l' and resid 128 through 139 Processing helix chain 'm' and resid 42 through 58 removed outlier: 4.317A pdb=" N ALA m 56 " --> pdb=" O ALA m 52 " (cutoff:3.500A) Processing helix chain 'm' and resid 109 through 125 removed outlier: 3.921A pdb=" N LYS m 118 " --> pdb=" O ARG m 114 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LYS m 123 " --> pdb=" O LEU m 119 " (cutoff:3.500A) Proline residue: m 125 - end of helix Processing helix chain 'n' and resid 13 through 32 Processing helix chain 'n' and resid 37 through 58 removed outlier: 3.617A pdb=" N ARG n 45 " --> pdb=" O ALA n 41 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ARG n 46 " --> pdb=" O LYS n 42 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N VAL n 47 " --> pdb=" O GLU n 43 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU n 49 " --> pdb=" O ARG n 45 " (cutoff:3.500A) Proline residue: n 50 - end of helix removed outlier: 4.294A pdb=" N THR n 57 " --> pdb=" O THR n 53 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N ASP n 58 " --> pdb=" O LEU n 54 " (cutoff:3.500A) Processing helix chain 'n' and resid 59 through 71 removed outlier: 3.533A pdb=" N ARG n 63 " --> pdb=" O SER n 59 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ARG n 69 " --> pdb=" O LEU n 65 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N THR n 70 " --> pdb=" O ALA n 66 " (cutoff:3.500A) Processing helix chain 'n' and resid 72 through 82 removed outlier: 4.503A pdb=" N PHE n 80 " --> pdb=" O VAL n 76 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ASN n 81 " --> pdb=" O ALA n 77 " (cutoff:3.500A) Processing helix chain 'n' and resid 83 through 89 removed outlier: 3.577A pdb=" N PHE n 87 " --> pdb=" O LEU n 83 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA n 88 " --> pdb=" O GLY n 84 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N SER n 89 " --> pdb=" O PRO n 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'n' and resid 83 through 89' Processing helix chain 'o' and resid 2 through 22 removed outlier: 3.673A pdb=" N ALA o 6 " --> pdb=" O ASP o 2 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N ARG o 13 " --> pdb=" O ARG o 9 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N ALA o 14 " --> pdb=" O ARG o 10 " (cutoff:3.500A) Processing helix chain 'o' and resid 55 through 63 removed outlier: 5.506A pdb=" N GLN o 61 " --> pdb=" O ALA o 57 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LEU o 62 " --> pdb=" O ILE o 58 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N LYS o 63 " --> pdb=" O ALA o 59 " (cutoff:3.500A) Processing helix chain 'o' and resid 67 through 86 removed outlier: 3.551A pdb=" N LEU o 83 " --> pdb=" O ALA o 79 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU o 84 " --> pdb=" O GLU o 80 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LYS o 85 " --> pdb=" O ARG o 81 " (cutoff:3.500A) Processing helix chain 'o' and resid 101 through 114 Processing helix chain 'p' and resid 1 through 13 removed outlier: 4.541A pdb=" N GLN p 11 " --> pdb=" O LEU p 7 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N LYS p 13 " --> pdb=" O GLN p 9 " (cutoff:3.500A) Processing helix chain 'p' and resid 97 through 103 removed outlier: 4.625A pdb=" N GLU p 101 " --> pdb=" O TYR p 97 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N THR p 103 " --> pdb=" O LEU p 99 " (cutoff:3.500A) Processing helix chain 'q' and resid 5 through 21 removed outlier: 4.397A pdb=" N ALA q 9 " --> pdb=" O ARG q 5 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLN q 19 " --> pdb=" O LYS q 15 " (cutoff:3.500A) Processing helix chain 'q' and resid 25 through 30 removed outlier: 3.917A pdb=" N ARG q 29 " --> pdb=" O GLY q 25 " (cutoff:3.500A) Processing helix chain 'q' and resid 38 through 60 removed outlier: 4.126A pdb=" N ARG q 50 " --> pdb=" O TYR q 46 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLN q 51 " --> pdb=" O ARG q 47 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N LYS q 53 " --> pdb=" O ARG q 49 " (cutoff:3.500A) Processing helix chain 'q' and resid 62 through 72 Processing helix chain 'q' and resid 74 through 86 Processing helix chain 'q' and resid 90 through 101 Processing helix chain 'q' and resid 102 through 117 removed outlier: 3.546A pdb=" N GLU q 110 " --> pdb=" O THR q 106 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LYS q 111 " --> pdb=" O ALA q 107 " (cutoff:3.500A) Processing helix chain 's' and resid 13 through 25 removed outlier: 3.527A pdb=" N LEU s 19 " --> pdb=" O GLN s 15 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL s 20 " --> pdb=" O LYS s 16 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N LEU s 23 " --> pdb=" O LEU s 19 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ILE s 24 " --> pdb=" O VAL s 20 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG s 25 " --> pdb=" O ALA s 21 " (cutoff:3.500A) Processing helix chain 's' and resid 28 through 40 removed outlier: 3.791A pdb=" N ASP s 34 " --> pdb=" O SER s 30 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N TYR s 38 " --> pdb=" O ASP s 34 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N ASN s 40 " --> pdb=" O LEU s 36 " (cutoff:3.500A) Processing helix chain 's' and resid 41 through 61 removed outlier: 3.565A pdb=" N VAL s 45 " --> pdb=" O LYS s 41 " (cutoff:3.500A) Processing helix chain 's' and resid 65 through 70 removed outlier: 4.360A pdb=" N LEU s 69 " --> pdb=" O ASP s 65 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N LYS s 70 " --> pdb=" O ILE s 66 " (cutoff:3.500A) No H-bonds generated for 'chain 's' and resid 65 through 70' Processing helix chain 't' and resid 1 through 11 removed outlier: 4.151A pdb=" N LYS t 9 " --> pdb=" O GLU t 5 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N LEU t 11 " --> pdb=" O LEU t 7 " (cutoff:3.500A) Processing helix chain 't' and resid 17 through 27 Processing helix chain 't' and resid 39 through 51 Processing helix chain 'u' and resid 65 through 70 removed outlier: 3.838A pdb=" N VAL u 69 " --> pdb=" O GLN u 65 " (cutoff:3.500A) removed outlier: 5.207A 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: 4.185A pdb=" N ALA v 23 " --> pdb=" O ARG v 19 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ASN v 24 " --> pdb=" O LEU v 20 " (cutoff:3.500A) Processing helix chain 'v' and resid 43 through 53 removed outlier: 3.924A pdb=" N VAL v 47 " --> pdb=" O ASP v 43 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ALA v 52 " --> pdb=" O MET v 48 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N LYS v 53 " --> pdb=" O ASN v 49 " (cutoff:3.500A) Processing helix chain 'v' and resid 54 through 59 removed outlier: 4.081A pdb=" N SER v 58 " --> pdb=" O ALA v 54 " (cutoff:3.500A) Processing helix chain 'x' and resid 51 through 61 removed outlier: 3.613A pdb=" N ARG x 56 " --> pdb=" O ALA x 52 " (cutoff:3.500A) Processing helix chain 'x' and resid 62 through 74 Processing helix chain 'y' and resid 1 through 7 removed outlier: 5.479A pdb=" N ARG y 7 " --> pdb=" O ALA y 3 " (cutoff:3.500A) Processing helix chain 'y' and resid 9 through 35 removed outlier: 3.804A pdb=" N ASN y 15 " --> pdb=" O VAL y 11 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N THR y 16 " --> pdb=" O GLU y 12 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG y 23 " --> pdb=" O LEU y 19 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU y 24 " --> pdb=" O ASN y 20 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLN y 25 " --> pdb=" O LEU y 21 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N PHE y 26 " --> pdb=" O LEU y 22 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU y 28 " --> pdb=" O GLU y 24 " (cutoff:3.500A) Processing helix chain 'y' and resid 39 through 62 removed outlier: 4.645A pdb=" N LEU y 43 " --> pdb=" O GLN y 39 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LYS y 44 " --> pdb=" O SER y 40 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALA y 51 " --> pdb=" O ARG y 47 " (cutoff:3.500A) removed outlier: 5.259A 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 'B' and resid 8 through 20 removed outlier: 4.459A pdb=" N HIS B 18 " --> pdb=" O MET B 14 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N ASP B 19 " --> pdb=" O ARG B 15 " (cutoff:3.500A) removed outlier: 4.249A 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: 4.772A 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: 3.531A pdb=" N LYS E 11 " --> pdb=" O ARG E 7 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ARG E 12 " --> pdb=" O GLY E 8 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 36 removed outlier: 4.911A pdb=" N LYS E 35 " --> pdb=" O ILE E 31 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N ALA E 36 " --> pdb=" O LEU E 32 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 31 through 36' Processing helix chain 'E' and resid 37 through 45 removed outlier: 3.569A 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: 4.588A pdb=" N GLY E 55 " --> pdb=" O LYS E 51 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N LEU E 56 " --> pdb=" O GLY E 52 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL E 57 " --> pdb=" O ASP E 53 " (cutoff:3.500A) Proline residue: E 62 - end of helix Processing helix chain 'G' and resid 4 through 12 removed outlier: 4.101A pdb=" N MET G 8 " --> pdb=" O SER G 4 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 31 removed outlier: 3.527A pdb=" N ILE G 30 " --> pdb=" O MET G 26 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N PHE G 31 " --> pdb=" O LYS G 27 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 26 through 31' Processing helix chain 'G' and resid 41 through 63 removed outlier: 3.641A pdb=" N THR G 45 " --> pdb=" O ASN G 41 " (cutoff:3.500A) Proline residue: G 47 - end of helix removed outlier: 3.516A pdb=" N LYS G 58 " --> pdb=" O ALA G 54 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE G 59 " --> pdb=" O GLU G 55 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N LYS G 63 " --> pdb=" O ILE G 59 " (cutoff:3.500A) Processing helix chain 'G' and resid 73 through 87 removed outlier: 5.446A pdb=" N GLU G 77 " --> pdb=" O ARG G 73 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ALA G 78 " --> pdb=" O ALA G 74 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N LYS G 80 " --> pdb=" O SER G 76 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU G 84 " --> pdb=" O LYS G 80 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N SER G 85 " --> pdb=" O ASP G 81 " (cutoff:3.500A) Processing helix chain 'G' and resid 102 through 123 removed outlier: 4.375A pdb=" N GLN G 108 " --> pdb=" O LYS G 104 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N SER G 109 " --> pdb=" O THR G 105 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LYS G 111 " --> pdb=" O ARG G 107 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU G 116 " --> pdb=" O ARG G 112 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLY G 123 " --> pdb=" O GLN G 119 " (cutoff:3.500A) Processing helix chain 'G' and resid 124 through 129 removed outlier: 4.116A pdb=" N LEU G 128 " --> pdb=" O THR G 124 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N THR G 129 " --> pdb=" O PHE G 125 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 124 through 129' Processing helix chain 'G' and resid 130 through 147 removed outlier: 3.945A pdb=" N MET G 135 " --> pdb=" O LYS G 131 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ARG G 136 " --> pdb=" O GLU G 132 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N SER G 146 " --> pdb=" O LYS G 142 " (cutoff:3.500A) Processing helix chain 'G' and resid 164 through 169 Processing helix chain 'G' and resid 170 through 179 removed outlier: 3.663A pdb=" N GLU G 174 " --> pdb=" O ILE G 170 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA G 175 " --> pdb=" O ALA G 171 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU G 178 " --> pdb=" O GLU G 174 " (cutoff:3.500A) Processing helix chain 'G' and resid 205 through 225 removed outlier: 3.646A pdb=" N ALA G 215 " --> pdb=" O LEU G 211 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA G 218 " --> pdb=" O GLY G 214 " (cutoff:3.500A) Processing helix chain 'H' and resid 5 through 11 removed outlier: 3.981A pdb=" N ARG H 10 " --> pdb=" O PRO H 6 " (cutoff:3.500A) Processing helix chain 'H' and resid 27 through 47 removed outlier: 3.635A pdb=" N ASP H 33 " --> pdb=" O ALA H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 71 through 77 removed outlier: 3.624A pdb=" N VAL H 75 " --> pdb=" O ARG H 71 " (cutoff:3.500A) Processing helix chain 'H' and resid 80 through 95 removed outlier: 3.525A pdb=" N LYS H 88 " --> pdb=" O GLU H 84 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL H 90 " --> pdb=" O LEU H 86 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ILE H 93 " --> pdb=" O VAL H 89 " (cutoff:3.500A) Processing helix chain 'H' and resid 107 through 112 removed outlier: 4.308A pdb=" N ASP H 111 " --> pdb=" O LYS H 107 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N ALA H 112 " --> pdb=" O PRO H 108 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 107 through 112' Processing helix chain 'H' and resid 113 through 126 removed outlier: 4.242A pdb=" N ARG H 125 " --> pdb=" O SER H 121 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ARG H 126 " --> pdb=" O GLN H 122 " (cutoff:3.500A) Processing helix chain 'H' and resid 128 through 144 removed outlier: 3.526A pdb=" N GLN H 138 " --> pdb=" O LYS H 134 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA H 140 " --> pdb=" O ALA H 136 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N MET H 141 " --> pdb=" O VAL H 137 " (cutoff:3.500A) Processing helix chain 'I' and resid 6 through 15 removed outlier: 3.896A pdb=" N SER I 11 " --> pdb=" O LYS I 7 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLU I 14 " --> pdb=" O LEU I 10 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 65 removed outlier: 3.528A pdb=" N VAL I 60 " --> pdb=" O GLU I 56 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG I 61 " --> pdb=" O LYS I 57 " (cutoff:3.500A) Processing helix chain 'I' and resid 67 through 82 removed outlier: 5.571A pdb=" N LYS I 82 " --> pdb=" O ALA I 78 " (cutoff:3.500A) Processing helix chain 'I' and resid 84 through 96 removed outlier: 3.504A pdb=" N LEU I 90 " --> pdb=" O GLY I 86 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU I 93 " --> pdb=" O LEU I 89 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU I 94 " --> pdb=" O LEU I 90 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLY I 95 " --> pdb=" O ALA I 91 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ARG I 96 " --> pdb=" O LEU I 92 " (cutoff:3.500A) Processing helix chain 'I' and resid 97 through 105 removed outlier: 4.019A pdb=" N TYR I 102 " --> pdb=" O ASP I 98 " (cutoff:3.500A) Processing helix chain 'I' and resid 109 through 120 removed outlier: 3.622A pdb=" N LYS I 120 " --> pdb=" O LEU I 116 " (cutoff:3.500A) Processing helix chain 'I' and resid 151 through 165 removed outlier: 6.363A pdb=" N LYS I 155 " --> pdb=" O GLN I 151 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA I 156 " --> pdb=" O SER I 152 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA I 157 " --> pdb=" O ARG I 153 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N GLU I 162 " --> pdb=" O LEU I 158 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N GLN I 163 " --> pdb=" O GLU I 159 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ARG I 164 " --> pdb=" O LEU I 160 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N GLU I 165 " --> pdb=" O ALA I 161 " (cutoff:3.500A) Processing helix chain 'I' and resid 195 through 205 removed outlier: 4.416A pdb=" N ILE I 199 " --> pdb=" O ASN I 195 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLU I 201 " --> pdb=" O HIS I 197 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N TYR I 203 " --> pdb=" O ILE I 199 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N SER I 204 " --> pdb=" O VAL I 200 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LYS I 205 " --> pdb=" O GLU I 201 " (cutoff:3.500A) Processing helix chain 'J' and resid 54 through 70 removed outlier: 3.610A pdb=" N GLU J 64 " --> pdb=" O GLN J 60 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYS J 65 " --> pdb=" O LYS J 61 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ARG J 68 " --> pdb=" O GLU J 64 " (cutoff:3.500A) Processing helix chain 'J' and resid 108 through 118 removed outlier: 6.378A pdb=" N ALA J 112 " --> pdb=" O GLY J 108 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL J 116 " --> pdb=" O ALA J 112 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA J 117 " --> pdb=" O VAL J 113 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLY J 118 " --> pdb=" O LEU J 114 " (cutoff:3.500A) Processing helix chain 'J' and resid 131 through 147 removed outlier: 3.597A pdb=" N ILE J 140 " --> pdb=" O VAL J 136 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASN J 145 " --> pdb=" O ASP J 141 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N ASN J 147 " --> pdb=" O LEU J 143 " (cutoff:3.500A) Processing helix chain 'J' and resid 148 through 156 removed outlier: 3.620A pdb=" N ALA J 154 " --> pdb=" O GLU J 150 " (cutoff:3.500A) Processing helix chain 'J' and resid 159 through 165 removed outlier: 4.102A pdb=" N ILE J 163 " --> pdb=" O SER J 159 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LEU J 164 " --> pdb=" O VAL J 160 " (cutoff:3.500A) Processing helix chain 'K' and resid 12 through 33 removed outlier: 4.278A pdb=" N GLU K 16 " --> pdb=" O PRO K 12 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N GLN K 17 " --> pdb=" O ASP K 13 " (cutoff:3.500A) Proline residue: K 19 - end of helix removed outlier: 3.622A pdb=" N THR K 26 " --> pdb=" O ILE K 22 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA K 28 " --> pdb=" O ARG K 24 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU K 33 " --> pdb=" O ILE K 29 " (cutoff:3.500A) Processing helix chain 'K' and resid 67 through 82 removed outlier: 3.626A pdb=" N ILE K 71 " --> pdb=" O PRO K 67 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N GLU K 73 " --> pdb=" O GLU K 69 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU K 74 " --> pdb=" O VAL K 70 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N ASP K 82 " --> pdb=" O PHE K 78 " (cutoff:3.500A) Processing helix chain 'L' and resid 19 through 30 Processing helix chain 'L' and resid 34 through 54 Processing helix chain 'L' and resid 56 through 69 removed outlier: 3.756A pdb=" N PHE L 61 " --> pdb=" O GLU L 57 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU L 62 " --> pdb=" O LEU L 58 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL L 63 " --> pdb=" O GLU L 59 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ALA L 64 " --> pdb=" O ALA L 60 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N ASN L 67 " --> pdb=" O VAL L 63 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N VAL L 68 " --> pdb=" O ALA L 64 " (cutoff:3.500A) Processing helix chain 'L' and resid 91 through 111 removed outlier: 3.667A pdb=" N ASN L 96 " --> pdb=" O PRO L 92 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ALA L 97 " --> pdb=" O VAL L 93 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LYS L 109 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N ARG L 110 " --> pdb=" O ALA L 106 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N GLY L 111 " --> pdb=" O ALA L 107 " (cutoff:3.500A) Processing helix chain 'L' and resid 114 through 129 removed outlier: 3.799A pdb=" N GLU L 128 " --> pdb=" O SER L 124 " (cutoff:3.500A) Processing helix chain 'L' and resid 131 through 148 removed outlier: 3.784A pdb=" N ARG L 137 " --> pdb=" O ALA L 133 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ALA L 146 " --> pdb=" O ARG L 142 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ASN L 147 " --> pdb=" O MET L 143 " (cutoff:3.500A) Processing helix chain 'M' and resid 4 through 20 Processing helix chain 'M' and resid 29 through 43 Processing helix chain 'M' and resid 111 through 119 removed outlier: 3.763A pdb=" N GLN M 117 " --> pdb=" O ARG M 113 " (cutoff:3.500A) Processing helix chain 'N' and resid 33 through 38 removed outlier: 3.801A pdb=" N PHE N 38 " --> pdb=" O LEU N 34 " (cutoff:3.500A) Processing helix chain 'N' and resid 43 through 55 removed outlier: 5.247A pdb=" N VAL N 47 " --> pdb=" O ALA N 43 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N ARG N 48 " --> pdb=" O ARG N 44 " (cutoff:3.500A) Proline residue: N 50 - end of helix removed outlier: 4.004A pdb=" N LEU N 53 " --> pdb=" O GLN N 49 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N VAL N 54 " --> pdb=" O PRO N 50 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ASP N 55 " --> pdb=" O LEU N 51 " (cutoff:3.500A) Processing helix chain 'N' and resid 70 through 86 removed outlier: 3.562A pdb=" N ARG N 79 " --> pdb=" O ALA N 75 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N THR N 83 " --> pdb=" O ARG N 79 " (cutoff:3.500A) Processing helix chain 'N' and resid 90 through 99 removed outlier: 4.659A pdb=" N GLU N 96 " --> pdb=" O SER N 92 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LYS N 99 " --> pdb=" O SER N 95 " (cutoff:3.500A) Processing helix chain 'O' and resid 14 through 33 removed outlier: 3.800A pdb=" N GLN O 20 " --> pdb=" O ARG O 16 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU O 24 " --> pdb=" O GLN O 20 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLU O 27 " --> pdb=" O ALA O 23 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ALA O 29 " --> pdb=" O ILE O 25 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N THR O 32 " --> pdb=" O THR O 28 " (cutoff:3.500A) Processing helix chain 'O' and resid 80 through 88 removed outlier: 3.897A pdb=" N ASP O 85 " --> pdb=" O GLU O 81 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ALA O 86 " --> pdb=" O LYS O 82 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N MET O 88 " --> pdb=" O VAL O 84 " (cutoff:3.500A) Processing helix chain 'P' and resid 45 through 50 removed outlier: 3.609A pdb=" N SER P 49 " --> pdb=" O THR P 45 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N GLY P 50 " --> pdb=" O ALA P 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 45 through 50' Processing helix chain 'P' and resid 53 through 59 removed outlier: 4.124A pdb=" N SER P 57 " --> pdb=" O GLY P 53 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N THR P 58 " --> pdb=" O SER P 54 " (cutoff:3.500A) Proline residue: P 59 - end of helix No H-bonds generated for 'chain 'P' and resid 53 through 59' Processing helix chain 'P' and resid 60 through 75 removed outlier: 4.766A pdb=" N ALA P 72 " --> pdb=" O ARG P 68 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N VAL P 73 " --> pdb=" O CYS P 69 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N LYS P 74 " --> pdb=" O ALA P 70 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N GLU P 75 " --> pdb=" O ASP P 71 " (cutoff:3.500A) Processing helix chain 'P' and resid 91 through 103 removed outlier: 5.128A pdb=" N THR P 95 " --> pdb=" O GLY P 91 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N ILE P 96 " --> pdb=" O ARG P 92 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ARG P 97 " --> pdb=" O GLU P 93 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N GLY P 103 " --> pdb=" O LEU P 99 " (cutoff:3.500A) Processing helix chain 'Q' and resid 2 through 10 removed outlier: 3.518A pdb=" N LEU Q 6 " --> pdb=" O THR Q 2 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ARG Q 8 " --> pdb=" O ASN Q 4 " (cutoff:3.500A) Proline residue: Q 10 - end of helix Processing helix chain 'Q' and resid 112 through 117 removed outlier: 4.872A pdb=" N TYR Q 116 " --> pdb=" O ALA Q 112 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLY Q 117 " --> pdb=" O ARG Q 113 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 112 through 117' Processing helix chain 'R' and resid 13 through 21 removed outlier: 4.861A pdb=" N ILE R 21 " --> pdb=" O ALA R 17 " (cutoff:3.500A) Processing helix chain 'R' and resid 25 through 37 removed outlier: 3.602A pdb=" N SER R 29 " --> pdb=" O GLY R 25 " (cutoff:3.500A) Processing helix chain 'R' and resid 48 through 63 removed outlier: 3.806A pdb=" N THR R 54 " --> pdb=" O GLY R 50 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLU R 58 " --> pdb=" O THR R 54 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA R 60 " --> pdb=" O ARG R 56 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N LYS R 61 " --> pdb=" O ASP R 57 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N PHE R 62 " --> pdb=" O GLU R 58 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N VAL R 63 " --> pdb=" O VAL R 59 " (cutoff:3.500A) Processing helix chain 'R' and resid 65 through 83 removed outlier: 3.782A pdb=" N ARG R 70 " --> pdb=" O GLY R 66 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER R 73 " --> pdb=" O ARG R 69 " (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 20 removed outlier: 3.561A pdb=" N VAL S 10 " --> pdb=" O LYS S 6 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU S 15 " --> pdb=" O LYS S 11 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS S 18 " --> pdb=" O ALA S 14 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N PHE S 20 " --> pdb=" O ALA S 16 " (cutoff:3.500A) Processing helix chain 'S' and resid 23 through 29 removed outlier: 5.025A pdb=" N LYS S 27 " --> pdb=" O ARG S 23 " (cutoff:3.500A) Processing helix chain 'S' and resid 37 through 51 removed outlier: 3.815A pdb=" N TRP S 41 " --> pdb=" O ASP S 37 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N GLN S 48 " --> pdb=" O VAL S 44 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N THR S 49 " --> pdb=" O LEU S 45 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LEU S 50 " --> pdb=" O LYS S 46 " (cutoff:3.500A) Proline residue: S 51 - end of helix Processing helix chain 'S' and resid 79 through 90 Processing helix chain 'T' and resid 3 through 15 removed outlier: 3.612A pdb=" N LYS T 9 " --> pdb=" O GLU T 5 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ILE T 10 " --> pdb=" O ALA T 6 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N SER T 12 " --> pdb=" O ALA T 8 " (cutoff:3.500A) Processing helix chain 'T' and resid 23 through 43 removed outlier: 4.432A pdb=" N GLY T 40 " --> pdb=" O ASN T 36 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N HIS T 41 " --> pdb=" O HIS T 37 " (cutoff:3.500A) Processing helix chain 'T' and resid 49 through 73 removed outlier: 3.676A pdb=" N GLY T 54 " --> pdb=" O HIS T 50 " (cutoff:3.500A) Processing helix chain 'T' and resid 74 through 85 removed outlier: 4.507A pdb=" N GLU T 82 " --> pdb=" O THR T 78 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ARG T 83 " --> pdb=" O GLN T 79 " (cutoff:3.500A) Processing helix chain 'U' and resid 53 through 64 removed outlier: 3.843A pdb=" N ILE U 57 " --> pdb=" O ASP U 53 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLN U 63 " --> pdb=" O HIS U 59 " (cutoff:3.500A) Processing helix chain 'U' and resid 68 through 79 removed outlier: 3.658A pdb=" N LYS U 76 " --> pdb=" O ALA U 72 " (cutoff:3.500A) Processing helix chain 'W' and resid 12 through 17 removed outlier: 3.936A pdb=" N GLY W 16 " --> pdb=" O PHE W 12 " (cutoff:3.500A) Processing helix chain 'W' and resid 24 through 33 removed outlier: 4.229A pdb=" N ASN W 30 " --> pdb=" O ALA W 26 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N TYR W 31 " --> pdb=" O THR W 27 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ILE W 32 " --> pdb=" O LEU W 28 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N THR W 33 " --> pdb=" O LYS W 29 " (cutoff:3.500A) Processing helix chain 'W' and resid 40 through 45 Processing helix chain 'W' and resid 47 through 65 Processing helix chain 'X' and resid 11 through 25 removed outlier: 3.635A pdb=" N LYS X 17 " --> pdb=" O HIS X 13 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA X 21 " --> pdb=" O LYS X 17 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU X 23 " --> pdb=" O GLU X 19 " (cutoff:3.500A) Processing helix chain 'X' and resid 69 through 75 removed outlier: 4.596A pdb=" N PHE X 73 " --> pdb=" O LYS X 69 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ALA X 74 " --> pdb=" O LEU X 70 " (cutoff:3.500A) Proline residue: X 75 - end of helix No H-bonds generated for 'chain 'X' and resid 69 through 75' Processing helix chain 'Y' and resid 6 through 41 removed outlier: 4.646A pdb=" N ALA Y 10 " --> pdb=" O ALA Y 6 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ILE Y 11 " --> pdb=" O LYS Y 7 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N HIS Y 19 " --> pdb=" O LYS Y 15 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER Y 22 " --> pdb=" O LYS Y 18 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU Y 39 " --> pdb=" O TYR Y 35 " (cutoff:3.500A) Processing helix chain 'Y' and resid 42 through 64 Proline residue: Y 55 - end of helix Processing helix chain 'Y' and resid 67 through 86 removed outlier: 6.157A pdb=" N ALA Y 71 " --> pdb=" O HIS Y 67 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LEU Y 85 " --> pdb=" O GLN Y 81 " (cutoff:3.500A) Processing helix chain 'Z' and resid 16 through 22 removed outlier: 4.274A pdb=" N ARG Z 20 " --> pdb=" O ARG Z 16 " (cutoff:3.500A) Processing helix chain 'Z' and resid 25 through 33 removed outlier: 6.065A pdb=" N ARG Z 33 " --> pdb=" O ALA Z 29 " (cutoff:3.500A) Processing helix chain 'Z' and resid 38 through 61 removed outlier: 3.724A pdb=" N THR Z 42 " --> pdb=" O GLU Z 38 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LYS Z 48 " --> pdb=" O ARG Z 44 " (cutoff:3.500A) Processing helix chain 'a' and resid 5 through 16 removed outlier: 3.646A pdb=" N LYS a 14 " --> pdb=" O VAL a 10 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL a 15 " --> pdb=" O ILE a 11 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ASP a 16 " --> pdb=" O ARG a 12 " (cutoff:3.500A) Processing helix chain 'a' and resid 23 through 34 removed outlier: 4.538A pdb=" N ILE a 27 " --> pdb=" O ILE a 23 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N ALA a 28 " --> pdb=" O ASN a 24 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N LYS a 31 " --> pdb=" O ILE a 27 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N GLU a 32 " --> pdb=" O ALA a 28 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ALA a 34 " --> pdb=" O LEU a 30 " (cutoff:3.500A) Processing helix chain 'a' and resid 181 through 200 removed outlier: 3.747A pdb=" N LEU a 185 " --> pdb=" O ASP a 181 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LYS a 186 " --> pdb=" O ALA a 182 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLU a 187 " --> pdb=" O ASP a 183 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU a 193 " --> pdb=" O LEU a 189 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL a 194 " --> pdb=" O GLU a 190 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA a 195 " --> pdb=" O ALA a 191 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LYS a 198 " --> pdb=" O VAL a 194 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'b' and resid 79 through 82 removed outlier: 6.867A pdb=" N LEU b 92 " --> pdb=" O GLU b 78 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N ASP b 113 " --> pdb=" O VAL b 77 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'b' and resid 137 through 141 removed outlier: 4.291A pdb=" N SER b 138 " --> pdb=" O ILE b 163 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N THR b 172 " --> pdb=" O VAL b 164 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLU b 179 " --> pdb=" O LEU b 175 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'b' and resid 89 through 95 removed outlier: 5.519A pdb=" N ASN b 89 " --> pdb=" O ALA b 105 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N GLU b 99 " --> pdb=" O TYR b 95 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'c' and resid 11 through 16 removed outlier: 4.202A pdb=" N VAL c 20 " --> pdb=" O THR c 16 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N VAL c 26 " --> pdb=" O VAL c 9 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N SER c 199 " --> pdb=" O LYS c 8 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ASP c 200 " --> pdb=" O THR c 112 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N THR c 112 " --> pdb=" O ASP c 200 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS c 204 " --> pdb=" O ASP c 108 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N GLU c 168 " --> pdb=" O SER c 113 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'c' and resid 79 through 84 removed outlier: 6.073A pdb=" N ARG c 46 " --> pdb=" O LEU c 84 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N GLN c 49 " --> pdb=" O THR c 35 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N GLN c 94 " --> pdb=" O VAL c 34 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'c' and resid 179 through 182 Processing sheet with id= 7, first strand: chain 'c' and resid 24 through 28 Processing sheet with id= 8, first strand: chain 'd' and resid 1 through 5 No H-bonds generated for sheet with id= 8 Processing sheet with id= 9, first strand: chain 'd' and resid 117 through 120 Processing sheet with id= 10, first strand: chain 'e' and resid 64 through 68 removed outlier: 3.693A pdb=" N GLY e 85 " --> pdb=" O THR e 67 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE e 33 " --> pdb=" O LEU e 90 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N GLY e 38 " --> pdb=" O GLY e 150 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N GLY e 150 " --> pdb=" O GLY e 38 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N THR e 157 " --> pdb=" O GLY e 125 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N GLY e 125 " --> pdb=" O THR e 157 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'f' and resid 15 through 18 Processing sheet with id= 12, first strand: chain 'f' and resid 93 through 97 removed outlier: 3.652A pdb=" N ARG f 94 " --> pdb=" O SER f 105 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'f' and resid 120 through 124 removed outlier: 3.671A pdb=" N LYS f 133 " --> pdb=" O THR f 121 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N THR f 128 " --> pdb=" O LEU f 88 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'g' and resid 16 through 20 removed outlier: 6.141A pdb=" N GLN g 2 " --> pdb=" O ALA g 39 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N ALA g 39 " --> pdb=" O GLN g 2 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N LYS g 35 " --> pdb=" O LEU g 6 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'g' and resid 76 through 83 removed outlier: 6.782A pdb=" N GLU g 76 " --> pdb=" O LYS g 141 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N VAL g 78 " --> pdb=" O ILE g 143 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASN g 145 " --> pdb=" O VAL g 78 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N GLU g 114 " --> pdb=" O GLN g 133 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'h' and resid 22 through 28 No H-bonds generated for sheet with id= 16 Processing sheet with id= 17, first strand: chain 'i' and resid 55 through 61 removed outlier: 3.953A pdb=" N VAL i 57 " --> pdb=" O VAL i 69 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N VAL i 69 " --> pdb=" O VAL i 57 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N SER i 65 " --> pdb=" O TYR i 61 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'j' and resid 52 through 57 removed outlier: 5.426A pdb=" N ASP j 19 " --> pdb=" O LEU j 140 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'k' and resid 18 through 21 removed outlier: 4.063A pdb=" N THR k 6 " --> pdb=" O CYS k 21 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N ASN k 82 " --> pdb=" O MET k 7 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N CYS k 84 " --> pdb=" O ASN k 9 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N LEU k 86 " --> pdb=" O ALA k 11 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LYS k 59 " --> pdb=" O LEU k 87 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N ASP k 37 " --> pdb=" O VAL k 62 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'k' and resid 68 through 71 removed outlier: 3.945A pdb=" N SER k 75 " --> pdb=" O ARG k 71 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'm' and resid 37 through 40 No H-bonds generated for sheet with id= 21 Processing sheet with id= 22, first strand: chain 'm' and resid 62 through 65 removed outlier: 4.122A pdb=" N TYR m 103 " --> pdb=" O LEU m 33 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N LEU m 33 " --> pdb=" O LEU m 102 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS m 100 " --> pdb=" O ALA m 35 " (cutoff:3.500A) Processing sheet with id= 23, 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: 6.236A pdb=" N LYS m 127 " --> pdb=" O VAL m 36 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'n' and resid 33 through 36 removed outlier: 6.389A pdb=" N MET n 110 " --> pdb=" O CYS n 100 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'o' and resid 49 through 52 removed outlier: 3.974A pdb=" N VAL o 49 " --> pdb=" O VAL o 39 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ASP o 93 " --> pdb=" O LEU o 26 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N VAL o 28 " --> pdb=" O ASP o 93 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'p' and resid 37 through 44 removed outlier: 6.368A pdb=" N THR p 24 " --> pdb=" O LYS p 86 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N SER p 82 " --> pdb=" O LYS p 28 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'p' and resid 48 through 52 removed outlier: 3.736A pdb=" N ALA p 48 " --> pdb=" O THR p 59 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N ARG p 52 " --> pdb=" O HIS p 55 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N SER p 56 " --> pdb=" O THR p 75 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'r' and resid 11 through 15 removed outlier: 3.505A pdb=" N MET r 40 " --> pdb=" O VAL r 4 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'r' and resid 18 through 23 removed outlier: 4.374A pdb=" N GLN r 18 " --> pdb=" O ILE r 98 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU r 22 " --> pdb=" O THR r 94 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N ASP r 95 " --> pdb=" O VAL r 64 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N LYS r 60 " --> pdb=" O THR r 99 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N GLU r 31 " --> pdb=" O VAL r 63 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'r' and resid 57 through 60 removed outlier: 4.212A pdb=" N VAL r 58 " --> pdb=" O SER r 102 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER r 102 " --> pdb=" O VAL r 58 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'r' and resid 71 through 78 removed outlier: 4.097A pdb=" N TYR r 83 " --> pdb=" O ARG r 78 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 's' and resid 2 through 8 removed outlier: 4.638A pdb=" N THR s 3 " --> pdb=" O VAL s 107 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL s 107 " --> pdb=" O THR s 3 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 't' and resid 29 through 33 removed outlier: 4.925A pdb=" N LYS t 66 " --> pdb=" O ARG t 77 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ASP t 79 " --> pdb=" O LYS t 64 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N LYS t 64 " --> pdb=" O ASP t 79 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N LYS t 81 " --> pdb=" O VAL t 62 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N VAL t 62 " --> pdb=" O LYS t 81 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N ALA t 83 " --> pdb=" O THR t 60 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N THR t 60 " --> pdb=" O ALA t 83 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N VAL t 85 " --> pdb=" O VAL t 58 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N VAL t 58 " --> pdb=" O VAL t 85 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'u' and resid 39 through 45 removed outlier: 4.707A pdb=" N ASN u 39 " --> pdb=" O ALA u 62 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLY u 56 " --> pdb=" O GLN u 45 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'u' and resid 82 through 85 Processing sheet with id= 36, first strand: chain 'v' and resid 69 through 72 removed outlier: 6.448A pdb=" N ALA v 39 " --> pdb=" O ARG v 9 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE v 89 " --> pdb=" O PRO v 27 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'w' and resid 47 through 50 removed outlier: 4.268A pdb=" N THR w 54 " --> pdb=" O GLY w 50 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'w' and resid 62 through 67 Processing sheet with id= 39, first strand: chain 'x' and resid 11 through 18 removed outlier: 4.456A pdb=" N THR x 24 " --> pdb=" O ASN x 16 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N SER x 18 " --> pdb=" O ASN x 22 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N ASN x 22 " --> pdb=" O SER x 18 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'x' and resid 34 through 40 Processing sheet with id= 41, first strand: chain 'z' and resid 32 through 38 removed outlier: 4.262A pdb=" N HIS z 33 " --> pdb=" O GLN z 8 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N MET z 53 " --> pdb=" O THR z 9 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'B' and resid 27 through 30 removed outlier: 6.112A pdb=" N SER B 28 " --> pdb=" O LYS B 36 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LYS B 36 " --> pdb=" O SER B 28 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N ASP B 30 " --> pdb=" O GLY B 34 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'C' and resid 5 through 11 No H-bonds generated for sheet with id= 43 Processing sheet with id= 44, first strand: chain 'C' and resid 34 through 38 removed outlier: 3.584A pdb=" N LEU C 35 " --> pdb=" O TYR C 48 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'E' and resid 21 through 24 removed outlier: 5.738A pdb=" N PHE E 21 " --> pdb=" O VAL E 49 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'F' and resid 13 through 18 removed outlier: 8.254A pdb=" N ASN F 13 " --> pdb=" O SER F 28 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N SER F 28 " --> pdb=" O ASN F 13 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N ILE F 23 " --> pdb=" O GLN F 37 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N CYS F 27 " --> pdb=" O HIS F 33 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N HIS F 33 " --> pdb=" O CYS F 27 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'G' and resid 14 through 17 removed outlier: 5.567A pdb=" N HIS G 14 " --> pdb=" O ILE G 40 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N HIS G 38 " --> pdb=" O GLY G 16 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'G' and resid 66 through 70 Processing sheet with id= 49, first strand: chain 'H' and resid 53 through 58 removed outlier: 3.585A pdb=" N VAL H 55 " --> pdb=" O THR H 66 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N THR H 69 " --> pdb=" O ALA H 103 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'H' and resid 163 through 170 removed outlier: 3.529A pdb=" N GLY H 147 " --> pdb=" O PHE H 202 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N ASP H 180 " --> pdb=" O LYS H 203 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'I' and resid 140 through 143 removed outlier: 3.511A pdb=" N ASP I 140 " --> pdb=" O PHE I 181 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N GLU I 178 " --> pdb=" O ASP I 173 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'J' and resid 11 through 15 removed outlier: 3.749A pdb=" N GLN J 11 " --> pdb=" O GLY J 39 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLY J 39 " --> pdb=" O GLN J 11 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N LEU J 35 " --> pdb=" O ILE J 15 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'J' and resid 82 through 87 removed outlier: 7.268A pdb=" N HIS J 82 " --> pdb=" O PRO J 97 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N VAL J 93 " --> pdb=" O GLY J 86 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N TYR J 127 " --> pdb=" O ARG J 92 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'J' and resid 31 through 39 removed outlier: 4.564A pdb=" N GLY J 50 " --> pdb=" O ALA J 34 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'K' and resid 34 through 37 removed outlier: 7.394A pdb=" N ASN K 63 " --> pdb=" O HIS K 37 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N ILE K 6 " --> pdb=" O MET K 62 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N HIS K 3 " --> pdb=" O THR K 92 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLU K 5 " --> pdb=" O MET K 90 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N MET K 90 " --> pdb=" O GLU K 5 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'K' and resid 38 through 42 removed outlier: 3.557A pdb=" N ARG K 38 " --> pdb=" O ASN K 63 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N ASN K 63 " --> pdb=" O ARG K 38 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N TYR K 59 " --> pdb=" O TRP K 42 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'L' and resid 71 through 76 No H-bonds generated for sheet with id= 57 Processing sheet with id= 58, first strand: chain 'M' and resid 23 through 28 removed outlier: 4.365A pdb=" N GLU M 51 " --> pdb=" O GLU M 57 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'M' and resid 73 through 76 removed outlier: 4.326A pdb=" N SER M 73 " --> pdb=" O ALA M 129 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N VAL M 102 " --> pdb=" O ILE M 125 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'N' and resid 4 through 10 removed outlier: 4.281A pdb=" N GLY N 9 " --> pdb=" O ALA N 16 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N LYS N 26 " --> pdb=" O LEU N 60 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'O' and resid 44 through 52 removed outlier: 3.738A pdb=" N ARG O 45 " --> pdb=" O THR O 69 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR O 69 " --> pdb=" O ARG O 45 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ILE O 8 " --> pdb=" O VAL O 74 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLN O 99 " --> pdb=" O ARG O 9 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'P' and resid 41 through 44 Processing sheet with id= 63, first strand: chain 'Q' and resid 28 through 32 removed outlier: 5.286A pdb=" N LEU Q 80 " --> pdb=" O VAL Q 97 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'Q' and resid 34 through 40 removed outlier: 4.856A pdb=" N ARG Q 35 " --> pdb=" O ARG Q 53 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N LYS Q 50 " --> pdb=" O ILE Q 66 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'U' and resid 4 through 10 removed outlier: 3.842A pdb=" N ALA U 7 " --> pdb=" O GLN U 18 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N GLY U 37 " --> pdb=" O VAL U 19 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N GLY U 49 " --> pdb=" O ASN U 40 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'V' and resid 6 through 10 removed outlier: 3.647A pdb=" N ILE V 60 " --> pdb=" O LEU V 7 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N GLU V 59 " --> pdb=" O VAL V 75 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'V' and resid 19 through 29 Processing sheet with id= 68, first strand: chain 'X' and resid 29 through 33 removed outlier: 4.137A pdb=" N LEU X 30 " --> pdb=" O THR X 47 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N LEU X 46 " --> pdb=" O VAL X 61 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE X 48 " --> pdb=" O VAL X 59 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'a' and resid 59 through 65 removed outlier: 7.044A pdb=" N VAL a 59 " --> pdb=" O ASN a 165 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR a 63 " --> pdb=" O VAL a 161 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL a 161 " --> pdb=" O THR a 63 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'a' and resid 169 through 174 removed outlier: 6.931A pdb=" N GLY a 169 " --> pdb=" O LEU a 48 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE a 171 " --> pdb=" O VAL a 46 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL a 46 " --> pdb=" O ILE a 171 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER a 213 " --> pdb=" O ALA a 45 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N LYS a 211 " --> pdb=" O ASN a 47 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N VAL a 212 " --> pdb=" O VAL a 224 " (cutoff:3.500A) 1747 hydrogen bonds defined for protein. 5163 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3720 hydrogen bonds 5974 hydrogen bond angles 0 basepair planarities 1491 basepair parallelities 2885 stacking parallelities Total time for adding SS restraints: 278.34 Time building geometry restraints manager: 66.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 33324 1.34 - 1.47: 65817 1.47 - 1.59: 52551 1.59 - 1.71: 9429 1.71 - 1.84: 278 Bond restraints: 161399 Sorted by residual: bond pdb=" CA THR O 32 " pdb=" CB THR O 32 " ideal model delta sigma weight residual 1.527 1.553 -0.026 7.60e-03 1.73e+04 1.13e+01 bond pdb=" CA PRO i 73 " pdb=" C PRO i 73 " ideal model delta sigma weight residual 1.514 1.532 -0.017 5.50e-03 3.31e+04 9.90e+00 bond pdb=" CA VAL J 55 " pdb=" CB VAL J 55 " ideal model delta sigma weight residual 1.534 1.554 -0.020 6.80e-03 2.16e+04 8.31e+00 bond pdb=" N GLY H 1 " pdb=" CA GLY H 1 " ideal model delta sigma weight residual 1.451 1.495 -0.044 1.60e-02 3.91e+03 7.67e+00 bond pdb=" N GLY a 159 " pdb=" CA GLY a 159 " ideal model delta sigma weight residual 1.451 1.491 -0.040 1.60e-02 3.91e+03 6.28e+00 ... (remaining 161394 not shown) Histogram of bond angle deviations from ideal: 97.78 - 105.02: 22060 105.02 - 112.25: 89147 112.25 - 119.49: 54454 119.49 - 126.72: 62258 126.72 - 133.96: 13451 Bond angle restraints: 241370 Sorted by residual: angle pdb=" N LYS I 9 " pdb=" CA LYS I 9 " pdb=" C LYS I 9 " ideal model delta sigma weight residual 112.23 97.78 14.45 1.26e+00 6.30e-01 1.31e+02 angle pdb=" N ALA g 67 " pdb=" CA ALA g 67 " pdb=" C ALA g 67 " ideal model delta sigma weight residual 112.23 98.30 13.93 1.26e+00 6.30e-01 1.22e+02 angle pdb=" N GLY M 67 " pdb=" CA GLY M 67 " pdb=" C GLY M 67 " ideal model delta sigma weight residual 114.16 101.31 12.85 1.21e+00 6.83e-01 1.13e+02 angle pdb=" N GLU J 161 " pdb=" CA GLU J 161 " pdb=" C GLU J 161 " ideal model delta sigma weight residual 111.07 120.14 -9.07 1.07e+00 8.73e-01 7.19e+01 angle pdb=" N VAL a 178 " pdb=" CA VAL a 178 " pdb=" C VAL a 178 " ideal model delta sigma weight residual 110.42 118.34 -7.92 9.60e-01 1.09e+00 6.80e+01 ... (remaining 241365 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.50: 92522 35.50 - 71.01: 9662 71.01 - 106.51: 1234 106.51 - 142.01: 9 142.01 - 177.51: 18 Dihedral angle restraints: 103445 sinusoidal: 86285 harmonic: 17160 Sorted by residual: dihedral pdb=" C4' U 11130 " pdb=" C3' U 11130 " pdb=" C2' U 11130 " pdb=" C1' U 11130 " ideal model delta sinusoidal sigma weight residual -35.00 33.60 -68.60 1 8.00e+00 1.56e-02 9.53e+01 dihedral pdb=" C5' U 11130 " pdb=" C4' U 11130 " pdb=" C3' U 11130 " pdb=" O3' U 11130 " ideal model delta sinusoidal sigma weight residual 147.00 79.70 67.30 1 8.00e+00 1.56e-02 9.21e+01 dihedral pdb=" O4' C 2 12 " pdb=" C1' C 2 12 " pdb=" N1 C 2 12 " pdb=" C2 C 2 12 " ideal model delta sinusoidal sigma weight residual 200.00 37.55 162.45 1 1.50e+01 4.44e-03 8.33e+01 ... (remaining 103442 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 21415 0.088 - 0.176: 8645 0.176 - 0.264: 705 0.264 - 0.352: 84 0.352 - 0.440: 7 Chirality restraints: 30856 Sorted by residual: chirality pdb=" C3' A 31201 " pdb=" C4' A 31201 " pdb=" O3' A 31201 " pdb=" C2' A 31201 " both_signs ideal model delta sigma weight residual False -2.74 -2.31 -0.44 2.00e-01 2.50e+01 4.83e+00 chirality pdb=" C3' U 11130 " pdb=" C4' U 11130 " pdb=" O3' U 11130 " pdb=" C2' U 11130 " both_signs ideal model delta sigma weight residual False -2.74 -2.34 -0.41 2.00e-01 2.50e+01 4.18e+00 chirality pdb=" CA ASN V 49 " pdb=" N ASN V 49 " pdb=" C ASN V 49 " pdb=" CB ASN V 49 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.41 2.00e-01 2.50e+01 4.11e+00 ... (remaining 30853 not shown) Planarity restraints: 13007 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G 1 775 " 0.110 2.00e-02 2.50e+03 4.52e-02 6.14e+01 pdb=" N9 G 1 775 " -0.007 2.00e-02 2.50e+03 pdb=" C8 G 1 775 " -0.043 2.00e-02 2.50e+03 pdb=" N7 G 1 775 " -0.039 2.00e-02 2.50e+03 pdb=" C5 G 1 775 " -0.023 2.00e-02 2.50e+03 pdb=" C6 G 1 775 " 0.019 2.00e-02 2.50e+03 pdb=" O6 G 1 775 " 0.069 2.00e-02 2.50e+03 pdb=" N1 G 1 775 " 0.015 2.00e-02 2.50e+03 pdb=" C2 G 1 775 " -0.013 2.00e-02 2.50e+03 pdb=" N2 G 1 775 " -0.011 2.00e-02 2.50e+03 pdb=" N3 G 1 775 " -0.038 2.00e-02 2.50e+03 pdb=" C4 G 1 775 " -0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U 11818 " -0.092 2.00e-02 2.50e+03 5.08e-02 5.82e+01 pdb=" N1 U 11818 " 0.005 2.00e-02 2.50e+03 pdb=" C2 U 11818 " 0.019 2.00e-02 2.50e+03 pdb=" O2 U 11818 " 0.032 2.00e-02 2.50e+03 pdb=" N3 U 11818 " 0.019 2.00e-02 2.50e+03 pdb=" C4 U 11818 " 0.019 2.00e-02 2.50e+03 pdb=" O4 U 11818 " -0.092 2.00e-02 2.50e+03 pdb=" C5 U 11818 " 0.048 2.00e-02 2.50e+03 pdb=" C6 U 11818 " 0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A 12725 " 0.101 2.00e-02 2.50e+03 4.44e-02 5.42e+01 pdb=" N9 A 12725 " -0.007 2.00e-02 2.50e+03 pdb=" C8 A 12725 " -0.041 2.00e-02 2.50e+03 pdb=" N7 A 12725 " -0.038 2.00e-02 2.50e+03 pdb=" C5 A 12725 " -0.019 2.00e-02 2.50e+03 pdb=" C6 A 12725 " 0.015 2.00e-02 2.50e+03 pdb=" N6 A 12725 " 0.072 2.00e-02 2.50e+03 pdb=" N1 A 12725 " 0.002 2.00e-02 2.50e+03 pdb=" C2 A 12725 " -0.022 2.00e-02 2.50e+03 pdb=" N3 A 12725 " -0.033 2.00e-02 2.50e+03 pdb=" C4 A 12725 " -0.030 2.00e-02 2.50e+03 ... (remaining 13004 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 13042 2.73 - 3.27: 133546 3.27 - 3.81: 294335 3.81 - 4.36: 383386 4.36 - 4.90: 514024 Nonbonded interactions: 1338333 Sorted by model distance: nonbonded pdb=" O ARG n 69 " pdb=" OG1 THR n 70 " model vdw 2.187 2.440 nonbonded pdb=" O2' U 11130 " pdb=" OP1 G 11131 " model vdw 2.272 2.440 nonbonded pdb=" O GLU K 69 " pdb=" OD1 ASP K 72 " model vdw 2.282 3.040 nonbonded pdb=" O GLU K 69 " pdb=" OE1 GLU K 73 " model vdw 2.286 3.040 nonbonded pdb=" OG SER Q 114 " pdb=" O3' C 3 501 " model vdw 2.300 2.440 ... (remaining 1338328 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain '5' and resid 1 through 76) selection = chain '6' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.120 Extract box with map and model: 11.780 Check model and map are aligned: 1.670 Set scattering table: 1.080 Process input model: 584.250 Find NCS groups from input model: 3.290 Set up NCS constraints: 0.530 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.040 Load rotamer database and sin/cos tables:11.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 616.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 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 : 0.006 0.057 161399 Z= 0.347 Angle : 0.971 14.449 241370 Z= 0.639 Chirality : 0.080 0.440 30856 Planarity : 0.008 0.089 13007 Dihedral : 21.934 177.514 92371 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 2.06 % Allowed : 10.05 % Favored : 87.89 % Rotamer: Outliers : 0.75 % Allowed : 6.44 % Favored : 92.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.83 (0.08), residues: 5919 helix: -3.70 (0.07), residues: 1796 sheet: -2.88 (0.14), residues: 1048 loop : -3.01 (0.09), residues: 3075 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.005 TRP b 212 HIS 0.002 0.000 HIS E 30 PHE 0.029 0.004 PHE G 90 TYR 0.064 0.005 TYR N 5 ARG 0.006 0.001 ARG s 88 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11838 Ramachandran restraints generated. 5919 Oldfield, 0 Emsley, 5919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11838 Ramachandran restraints generated. 5919 Oldfield, 0 Emsley, 5919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2244 residues out of total 4908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 2207 time to evaluate : 6.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 22 GLU cc_start: 0.7762 (pp20) cc_final: 0.7529 (pp20) REVERT: b 73 ILE cc_start: 0.9205 (mt) cc_final: 0.8897 (mm) REVERT: b 97 ASP cc_start: 0.8855 (p0) cc_final: 0.8568 (p0) REVERT: b 131 MET cc_start: 0.8936 (mtm) cc_final: 0.8624 (mtm) REVERT: b 228 ASP cc_start: 0.8164 (m-30) cc_final: 0.7953 (m-30) REVERT: b 256 THR cc_start: 0.9154 (p) cc_final: 0.8833 (p) REVERT: b 270 ARG cc_start: 0.8356 (ttp-110) cc_final: 0.7733 (ptt90) REVERT: c 167 ASN cc_start: 0.9393 (t0) cc_final: 0.9048 (t0) REVERT: d 2 GLU cc_start: 0.8083 (mm-30) cc_final: 0.7766 (mm-30) REVERT: d 16 GLU cc_start: 0.8643 (tt0) cc_final: 0.8243 (pp20) REVERT: d 30 GLN cc_start: 0.8874 (tp40) cc_final: 0.8515 (tp40) REVERT: d 51 GLU cc_start: 0.8039 (pm20) cc_final: 0.7768 (pm20) REVERT: d 91 ASP cc_start: 0.8277 (t70) cc_final: 0.7957 (t0) REVERT: d 111 GLU cc_start: 0.7938 (tp30) cc_final: 0.7466 (tp30) REVERT: d 181 ILE cc_start: 0.9392 (mt) cc_final: 0.9144 (mm) REVERT: e 19 PHE cc_start: 0.9016 (m-80) cc_final: 0.7464 (m-10) REVERT: e 80 GLN cc_start: 0.8879 (tp40) cc_final: 0.8641 (tp40) REVERT: e 95 MET cc_start: 0.8599 (ppp) cc_final: 0.8276 (ppp) REVERT: e 97 GLU cc_start: 0.8097 (pm20) cc_final: 0.7146 (pm20) REVERT: e 117 SER cc_start: 0.8138 (p) cc_final: 0.7582 (t) REVERT: e 133 GLU cc_start: 0.8011 (tp30) cc_final: 0.7638 (tp30) REVERT: e 164 GLU cc_start: 0.8528 (tt0) cc_final: 0.8191 (tp30) REVERT: f 21 GLN cc_start: 0.8335 (tp40) cc_final: 0.8073 (tp-100) REVERT: f 54 ARG cc_start: 0.8691 (ttm170) cc_final: 0.8409 (ttm110) REVERT: f 68 ARG cc_start: 0.8950 (tmt170) cc_final: 0.8558 (tmt-80) REVERT: f 82 PHE cc_start: 0.8180 (m-80) cc_final: 0.7849 (m-80) REVERT: f 85 LYS cc_start: 0.8850 (ttmm) cc_final: 0.8642 (tppp) REVERT: f 93 TYR cc_start: 0.8764 (m-10) cc_final: 0.8512 (m-10) REVERT: f 123 GLU cc_start: 0.7819 (tm-30) cc_final: 0.7617 (tm-30) REVERT: f 129 GLU cc_start: 0.8793 (tt0) cc_final: 0.8368 (tt0) REVERT: f 130 ILE cc_start: 0.8598 (mt) cc_final: 0.8394 (mp) REVERT: f 146 ASP cc_start: 0.8920 (m-30) cc_final: 0.8582 (m-30) REVERT: g 22 LYS cc_start: 0.7885 (mmtp) cc_final: 0.7634 (mmtp) REVERT: g 122 LEU cc_start: 0.7902 (tp) cc_final: 0.7643 (pp) REVERT: i 35 MET cc_start: 0.9015 (mmt) cc_final: 0.8775 (pmm) REVERT: i 116 MET cc_start: -0.2279 (tpt) cc_final: -0.2955 (tpp) REVERT: i 139 VAL cc_start: 0.6259 (t) cc_final: 0.6031 (p) REVERT: j 31 GLU cc_start: 0.7911 (tp30) cc_final: 0.7633 (tp30) REVERT: j 71 ASP cc_start: 0.8354 (m-30) cc_final: 0.8123 (m-30) REVERT: j 103 ILE cc_start: 0.9479 (mt) cc_final: 0.9228 (mt) REVERT: k 12 ASP cc_start: 0.8148 (p0) cc_final: 0.7891 (p0) REVERT: k 88 ASN cc_start: 0.8544 (t0) cc_final: 0.8000 (p0) REVERT: k 111 LYS cc_start: 0.9118 (ptpt) cc_final: 0.8805 (ptmt) REVERT: k 118 LEU cc_start: 0.9141 (mt) cc_final: 0.8926 (mp) REVERT: l 55 MET cc_start: 0.8252 (tpp) cc_final: 0.7868 (tpp) REVERT: l 76 GLU cc_start: 0.7730 (mt-10) cc_final: 0.7199 (mt-10) REVERT: l 77 ILE cc_start: 0.9329 (mp) cc_final: 0.9036 (tp) REVERT: l 82 LEU cc_start: 0.9391 (tp) cc_final: 0.9000 (tm) REVERT: l 105 ILE cc_start: 0.9244 (mm) cc_final: 0.8983 (mm) REVERT: m 17 ASN cc_start: 0.8609 (t0) cc_final: 0.7889 (t0) REVERT: m 36 VAL cc_start: 0.9342 (t) cc_final: 0.9111 (p) REVERT: m 45 GLN cc_start: 0.9099 (mt0) cc_final: 0.8797 (mt0) REVERT: m 91 TYR cc_start: 0.9046 (p90) cc_final: 0.8660 (p90) REVERT: m 105 MET cc_start: 0.8416 (ttm) cc_final: 0.8060 (mtp) REVERT: m 106 ASP cc_start: 0.7813 (t70) cc_final: 0.7461 (t0) REVERT: n 35 LYS cc_start: 0.8762 (tttm) cc_final: 0.8548 (tptt) REVERT: o 7 ARG cc_start: 0.9114 (ttp80) cc_final: 0.8819 (tmm-80) REVERT: o 24 THR cc_start: 0.9329 (m) cc_final: 0.9054 (t) REVERT: o 33 ARG cc_start: 0.7447 (ttm170) cc_final: 0.6960 (ttm-80) REVERT: o 34 HIS cc_start: 0.8377 (m-70) cc_final: 0.7307 (m-70) REVERT: o 43 ASN cc_start: 0.8971 (p0) cc_final: 0.8654 (p0) REVERT: o 69 ASP cc_start: 0.8734 (m-30) cc_final: 0.8405 (t0) REVERT: o 94 ARG cc_start: 0.9078 (mtm110) cc_final: 0.8843 (mtm110) REVERT: o 102 ARG cc_start: 0.8603 (mtm180) cc_final: 0.8066 (mtp180) REVERT: p 14 GLN cc_start: 0.8561 (mm-40) cc_final: 0.8215 (tp-100) REVERT: p 23 ASP cc_start: 0.8474 (m-30) cc_final: 0.7971 (m-30) REVERT: p 69 VAL cc_start: 0.8940 (t) cc_final: 0.8602 (p) REVERT: q 23 TYR cc_start: 0.9009 (m-10) cc_final: 0.8796 (m-10) REVERT: q 96 ASP cc_start: 0.8316 (t0) cc_final: 0.7992 (t0) REVERT: q 106 THR cc_start: 0.8705 (p) cc_final: 0.7663 (p) REVERT: r 13 ARG cc_start: 0.8947 (ttp80) cc_final: 0.8255 (tmm-80) REVERT: r 16 GLU cc_start: 0.8191 (tt0) cc_final: 0.7990 (tp30) REVERT: r 60 LYS cc_start: 0.8939 (mtmm) cc_final: 0.8448 (mmmm) REVERT: r 62 GLU cc_start: 0.7858 (tm-30) cc_final: 0.7209 (tm-30) REVERT: r 95 ASP cc_start: 0.8204 (p0) cc_final: 0.7981 (p0) REVERT: s 38 TYR cc_start: 0.8862 (m-80) cc_final: 0.8543 (m-80) REVERT: t 21 SER cc_start: 0.9134 (m) cc_final: 0.8855 (m) REVERT: t 28 ASN cc_start: 0.8917 (t0) cc_final: 0.8411 (t0) REVERT: t 30 ILE cc_start: 0.8928 (tt) cc_final: 0.8672 (pp) REVERT: t 36 LYS cc_start: 0.8317 (tptp) cc_final: 0.8089 (tptp) REVERT: t 42 GLU cc_start: 0.8390 (mt-10) cc_final: 0.8172 (mt-10) REVERT: t 87 LEU cc_start: 0.8823 (mt) cc_final: 0.8488 (mt) REVERT: t 91 GLN cc_start: 0.8686 (mm110) cc_final: 0.8142 (mm-40) REVERT: u 23 LYS cc_start: 0.8939 (ptmt) cc_final: 0.7989 (ptmm) REVERT: u 59 GLU cc_start: 0.7990 (tp30) cc_final: 0.7711 (tp30) REVERT: u 60 LYS cc_start: 0.8108 (mtpt) cc_final: 0.7883 (mtpt) REVERT: u 93 ARG cc_start: 0.8931 (mtm180) cc_final: 0.8288 (ptp90) REVERT: v 10 LYS cc_start: 0.8074 (ptpp) cc_final: 0.7814 (mmmt) REVERT: v 38 LEU cc_start: 0.9158 (tp) cc_final: 0.8924 (tp) REVERT: v 41 GLU cc_start: 0.7417 (tm-30) cc_final: 0.6953 (tm-30) REVERT: v 46 LYS cc_start: 0.9225 (mmtm) cc_final: 0.8810 (mmpt) REVERT: v 51 GLN cc_start: 0.8806 (pt0) cc_final: 0.7905 (tt0) REVERT: v 61 LEU cc_start: 0.9157 (mp) cc_final: 0.8707 (mt) REVERT: v 63 ILE cc_start: 0.9052 (mt) cc_final: 0.8719 (mt) REVERT: v 66 ASP cc_start: 0.7770 (m-30) cc_final: 0.7411 (m-30) REVERT: v 70 ILE cc_start: 0.9019 (mt) cc_final: 0.8606 (mm) REVERT: w 39 THR cc_start: 0.8985 (m) cc_final: 0.8363 (p) REVERT: w 58 LYS cc_start: 0.9302 (mtpt) cc_final: 0.9083 (mtpt) REVERT: w 62 LYS cc_start: 0.9078 (mttt) cc_final: 0.8745 (mtmm) REVERT: x 9 LYS cc_start: 0.9022 (mttm) cc_final: 0.8636 (mttm) REVERT: x 61 LYS cc_start: 0.8892 (mttt) cc_final: 0.8405 (mtpp) REVERT: y 8 GLU cc_start: 0.7755 (mp0) cc_final: 0.7534 (mp0) REVERT: z 36 GLU cc_start: 0.7790 (tt0) cc_final: 0.7558 (pm20) REVERT: z 40 THR cc_start: 0.8865 (p) cc_final: 0.8505 (p) REVERT: B 5 ASN cc_start: 0.8912 (m-40) cc_final: 0.8525 (m110) REVERT: B 36 LYS cc_start: 0.8993 (mmtp) cc_final: 0.8607 (mptp) REVERT: D 26 ASN cc_start: 0.8875 (m-40) cc_final: 0.8358 (m110) REVERT: E 15 LYS cc_start: 0.8795 (tppp) cc_final: 0.8591 (tptp) REVERT: E 27 ASN cc_start: 0.8915 (m-40) cc_final: 0.8713 (m110) REVERT: E 41 ARG cc_start: 0.9167 (ttm110) cc_final: 0.8844 (ttp80) REVERT: F 8 LYS cc_start: 0.8813 (ptpp) cc_final: 0.8448 (pttt) REVERT: F 17 VAL cc_start: 0.8792 (p) cc_final: 0.8474 (m) REVERT: F 24 ARG cc_start: 0.8944 (mtt-85) cc_final: 0.8550 (mtt-85) REVERT: F 31 PRO cc_start: 0.9106 (Cg_exo) cc_final: 0.8863 (Cg_endo) REVERT: G 18 GLN cc_start: 0.8679 (mt0) cc_final: 0.8312 (mp10) REVERT: G 55 GLU cc_start: 0.8808 (tp30) cc_final: 0.8596 (tt0) REVERT: G 59 ILE cc_start: 0.9404 (mm) cc_final: 0.9191 (pt) REVERT: G 104 LYS cc_start: 0.8765 (tptp) cc_final: 0.8124 (tptp) REVERT: G 108 GLN cc_start: 0.9067 (mm110) cc_final: 0.8689 (mm110) REVERT: G 125 PHE cc_start: 0.7351 (m-80) cc_final: 0.6950 (m-80) REVERT: G 151 LYS cc_start: 0.9225 (ptmm) cc_final: 0.8689 (ptmm) REVERT: G 172 ILE cc_start: 0.9363 (pt) cc_final: 0.9138 (pp) REVERT: G 183 PHE cc_start: 0.8663 (m-80) cc_final: 0.8432 (m-80) REVERT: G 197 PHE cc_start: 0.8127 (m-80) cc_final: 0.6534 (m-80) REVERT: G 199 ILE cc_start: 0.8954 (mt) cc_final: 0.8749 (mm) REVERT: G 221 ARG cc_start: 0.8443 (mtm-85) cc_final: 0.8228 (mtt-85) REVERT: G 222 GLU cc_start: 0.7590 (tm-30) cc_final: 0.7327 (tm-30) REVERT: H 5 HIS cc_start: 0.9088 (t-90) cc_final: 0.8881 (t-90) REVERT: H 39 ARG cc_start: 0.8780 (ttm-80) cc_final: 0.8237 (ttm-80) REVERT: H 68 HIS cc_start: 0.8995 (m90) cc_final: 0.8624 (m-70) REVERT: H 84 GLU cc_start: 0.8251 (mm-30) cc_final: 0.7936 (mm-30) REVERT: H 141 MET cc_start: 0.8801 (mmm) cc_final: 0.8224 (mmp) REVERT: H 151 GLU cc_start: 0.8096 (tm-30) cc_final: 0.7396 (tm-30) REVERT: H 191 THR cc_start: 0.9004 (p) cc_final: 0.8583 (t) REVERT: I 9 LYS cc_start: 0.8711 (tttt) cc_final: 0.8416 (tttt) REVERT: I 18 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.8462 (pt) REVERT: I 47 LEU cc_start: 0.8809 (mm) cc_final: 0.8497 (mm) REVERT: I 68 GLU cc_start: 0.8213 (tp30) cc_final: 0.7738 (tp30) REVERT: I 69 ARG cc_start: 0.8747 (tpp80) cc_final: 0.8407 (tpp80) REVERT: I 71 PHE cc_start: 0.9365 (t80) cc_final: 0.8859 (t80) REVERT: I 73 ASN cc_start: 0.9516 (m-40) cc_final: 0.9018 (m110) REVERT: I 87 GLU cc_start: 0.7895 (mp0) cc_final: 0.7462 (mm-30) REVERT: I 112 GLU cc_start: 0.7588 (tt0) cc_final: 0.7066 (tt0) REVERT: I 137 SER cc_start: 0.8271 (t) cc_final: 0.7896 (p) REVERT: J 32 PHE cc_start: 0.9027 (m-80) cc_final: 0.8762 (m-80) REVERT: J 40 ASP cc_start: 0.8429 (p0) cc_final: 0.7920 (p0) REVERT: J 67 ARG cc_start: 0.8714 (mpt-90) cc_final: 0.8040 (mtt-85) REVERT: J 85 LYS cc_start: 0.8674 (mptt) cc_final: 0.8446 (mptt) REVERT: J 94 PHE cc_start: 0.8170 (t80) cc_final: 0.7936 (t80) REVERT: J 104 ILE cc_start: 0.9440 (mp) cc_final: 0.8953 (pp) REVERT: J 121 ASN cc_start: 0.8803 (m-40) cc_final: 0.8370 (m-40) REVERT: J 123 LEU cc_start: 0.9246 (mt) cc_final: 0.9009 (mm) REVERT: K 5 GLU cc_start: 0.8046 (pt0) cc_final: 0.7818 (pt0) REVERT: K 9 MET cc_start: 0.7870 (mtm) cc_final: 0.7664 (mtm) REVERT: K 42 TRP cc_start: 0.8549 (m-10) cc_final: 0.8345 (m-90) REVERT: K 44 ARG cc_start: 0.8222 (ttp-170) cc_final: 0.7632 (ttm-80) REVERT: K 71 ILE cc_start: 0.9010 (pt) cc_final: 0.8594 (pp) REVERT: K 85 ILE cc_start: 0.8251 (mt) cc_final: 0.7880 (mt) REVERT: K 90 MET cc_start: 0.7819 (mtt) cc_final: 0.7254 (mpp) REVERT: L 59 GLU cc_start: 0.8629 (pt0) cc_final: 0.8278 (pt0) REVERT: L 89 GLU cc_start: 0.7853 (pp20) cc_final: 0.7568 (pp20) REVERT: L 96 ASN cc_start: 0.8573 (p0) cc_final: 0.8283 (p0) REVERT: L 105 GLU cc_start: 0.8362 (pp20) cc_final: 0.7955 (pp20) REVERT: M 21 LYS cc_start: 0.8240 (ttmm) cc_final: 0.7961 (ttmm) REVERT: M 28 SER cc_start: 0.8248 (p) cc_final: 0.7905 (p) REVERT: M 40 LYS cc_start: 0.8993 (tmmt) cc_final: 0.8753 (tptp) REVERT: M 48 PHE cc_start: 0.8896 (p90) cc_final: 0.8479 (p90) REVERT: M 55 LYS cc_start: 0.7722 (mtmt) cc_final: 0.7266 (mttt) REVERT: M 61 THR cc_start: 0.8732 (OUTLIER) cc_final: 0.8470 (p) REVERT: M 62 LEU cc_start: 0.9229 (mt) cc_final: 0.8912 (mt) REVERT: M 63 LYS cc_start: 0.8619 (mtpp) cc_final: 0.8374 (mtpp) REVERT: M 75 GLN cc_start: 0.8011 (mp-120) cc_final: 0.7809 (mp10) REVERT: M 83 ARG cc_start: 0.8787 (mmt180) cc_final: 0.8567 (mpt90) REVERT: M 94 VAL cc_start: 0.8480 (t) cc_final: 0.8193 (m) REVERT: M 102 VAL cc_start: 0.9321 (t) cc_final: 0.9043 (m) REVERT: M 107 LYS cc_start: 0.9226 (mmtm) cc_final: 0.8982 (mmmt) REVERT: M 110 MET cc_start: 0.8586 (ptp) cc_final: 0.8365 (ptp) REVERT: N 20 ILE cc_start: 0.9006 (tt) cc_final: 0.8332 (tp) REVERT: N 21 LYS cc_start: 0.9020 (mtpt) cc_final: 0.8622 (mmpt) REVERT: N 27 ILE cc_start: 0.8937 (mp) cc_final: 0.8596 (mm) REVERT: N 53 LEU cc_start: 0.9183 (mm) cc_final: 0.8787 (mm) REVERT: N 60 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8498 (pp) REVERT: N 67 LYS cc_start: 0.8933 (mttp) cc_final: 0.8711 (mttp) REVERT: N 72 SER cc_start: 0.9176 (t) cc_final: 0.8615 (p) REVERT: N 84 ARG cc_start: 0.8337 (mmm-85) cc_final: 0.7971 (ttm170) REVERT: N 112 ARG cc_start: 0.8688 (ptm-80) cc_final: 0.8479 (ptm-80) REVERT: N 123 ARG cc_start: 0.8345 (mmt90) cc_final: 0.8041 (tpp80) REVERT: O 48 ARG cc_start: 0.8372 (mtt90) cc_final: 0.8142 (mtt90) REVERT: O 68 ARG cc_start: 0.7679 (mtt180) cc_final: 0.7443 (ttm170) REVERT: P 33 ILE cc_start: 0.9080 (mt) cc_final: 0.8827 (mp) REVERT: P 60 PHE cc_start: 0.9126 (t80) cc_final: 0.8902 (t80) REVERT: P 69 CYS cc_start: 0.8083 (t) cc_final: 0.7185 (t) REVERT: P 84 MET cc_start: 0.7750 (ptm) cc_final: 0.7490 (ppp) REVERT: P 127 ARG cc_start: 0.7373 (tpp80) cc_final: 0.6718 (ttm170) REVERT: Q 110 LYS cc_start: 0.8233 (mmtt) cc_final: 0.7776 (mmmm) REVERT: R 2 ARG cc_start: 0.6791 (mmt90) cc_final: 0.6590 (tpt90) REVERT: R 51 GLN cc_start: 0.9006 (mt0) cc_final: 0.8607 (pt0) REVERT: R 54 THR cc_start: 0.8508 (m) cc_final: 0.8281 (p) REVERT: R 77 LYS cc_start: 0.8938 (tttm) cc_final: 0.8363 (tptp) REVERT: R 88 LEU cc_start: 0.9352 (mp) cc_final: 0.9110 (mm) REVERT: R 111 PRO cc_start: 0.8659 (Cg_exo) cc_final: 0.8301 (Cg_endo) REVERT: S 60 ARG cc_start: 0.8441 (tpm170) cc_final: 0.8015 (tpp-160) REVERT: S 88 MET cc_start: 0.8317 (mmm) cc_final: 0.7963 (mmm) REVERT: T 25 GLU cc_start: 0.8648 (mt-10) cc_final: 0.7939 (mp0) REVERT: T 27 GLN cc_start: 0.8015 (mt0) cc_final: 0.7580 (tt0) REVERT: T 32 THR cc_start: 0.9579 (m) cc_final: 0.9209 (m) REVERT: T 36 ASN cc_start: 0.8964 (m-40) cc_final: 0.8725 (m110) REVERT: T 48 ASP cc_start: 0.8556 (t0) cc_final: 0.8088 (t0) REVERT: T 51 SER cc_start: 0.9072 (p) cc_final: 0.8694 (p) REVERT: T 76 ARG cc_start: 0.8510 (mtm180) cc_final: 0.8117 (ttm110) REVERT: U 18 GLN cc_start: 0.7915 (mt0) cc_final: 0.7670 (mt0) REVERT: U 40 ASN cc_start: 0.9423 (t0) cc_final: 0.9097 (t0) REVERT: V 66 LEU cc_start: 0.9109 (mt) cc_final: 0.8891 (mt) REVERT: V 72 TRP cc_start: 0.8569 (m100) cc_final: 0.8123 (m100) REVERT: W 23 LYS cc_start: 0.8960 (mtmm) cc_final: 0.8730 (pptt) REVERT: W 24 ASP cc_start: 0.8434 (t70) cc_final: 0.8200 (OUTLIER) REVERT: X 10 ILE cc_start: 0.9193 (pt) cc_final: 0.8400 (mm) REVERT: X 65 MET cc_start: 0.8714 (mtt) cc_final: 0.8443 (mtp) REVERT: X 69 LYS cc_start: 0.8401 (mttm) cc_final: 0.7888 (mttt) REVERT: Y 15 LYS cc_start: 0.9008 (tttm) cc_final: 0.8488 (tptp) REVERT: Y 19 HIS cc_start: 0.8067 (t-90) cc_final: 0.7625 (t70) REVERT: Y 26 MET cc_start: 0.8727 (ppp) cc_final: 0.8141 (ppp) REVERT: Y 27 MET cc_start: 0.8401 (ppp) cc_final: 0.7876 (tmt) REVERT: Y 28 ARG cc_start: 0.8625 (mtt180) cc_final: 0.8293 (mtt-85) REVERT: Y 54 GLN cc_start: 0.8946 (tt0) cc_final: 0.8510 (tt0) REVERT: Y 69 ASN cc_start: 0.8603 (m110) cc_final: 0.8212 (m110) REVERT: Z 18 PHE cc_start: 0.7701 (t80) cc_final: 0.7230 (t80) REVERT: Z 46 ARG cc_start: 0.8157 (tmt-80) cc_final: 0.7529 (tmt-80) REVERT: Z 54 ARG cc_start: 0.7276 (mtm180) cc_final: 0.7034 (ttm170) REVERT: a 218 MET cc_start: 0.4385 (mtt) cc_final: 0.3663 (mmt) outliers start: 37 outliers final: 18 residues processed: 2222 average time/residue: 2.1809 time to fit residues: 6909.6147 Evaluate side-chains 1750 residues out of total 4908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 1730 time to evaluate : 6.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 40 LEU Chi-restraints excluded: chain e residue 105 ILE Chi-restraints excluded: chain h residue 3 LEU Chi-restraints excluded: chain r residue 22 LEU Chi-restraints excluded: chain r residue 45 GLU Chi-restraints excluded: chain s residue 77 ASP Chi-restraints excluded: chain s residue 106 VAL Chi-restraints excluded: chain t residue 85 VAL Chi-restraints excluded: chain x residue 33 HIS Chi-restraints excluded: chain G residue 163 ILE Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 93 LEU Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain M residue 61 THR Chi-restraints excluded: chain N residue 60 LEU Chi-restraints excluded: chain S residue 47 LEU Chi-restraints excluded: chain T residue 81 ILE Chi-restraints excluded: chain V residue 59 GLU Chi-restraints excluded: chain a residue 53 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1050 random chunks: chunk 886 optimal weight: 30.0000 chunk 795 optimal weight: 10.0000 chunk 441 optimal weight: 6.9990 chunk 271 optimal weight: 5.9990 chunk 536 optimal weight: 20.0000 chunk 425 optimal weight: 3.9990 chunk 822 optimal weight: 50.0000 chunk 318 optimal weight: 1.9990 chunk 500 optimal weight: 7.9990 chunk 612 optimal weight: 10.0000 chunk 953 optimal weight: 10.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 24 HIS b 36 ASN b 199 HIS b 238 ASN c 94 GLN d 94 GLN d 97 ASN ** e 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 127 GLN g 33 GLN g 43 ASN g 133 GLN ** g 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 5 GLN i 29 GLN i 104 GLN j 58 ASN j 135 GLN j 138 GLN l 4 ASN m 13 HIS p 11 GLN p 114 ASN q 19 GLN q 71 ASN ** r 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 87 GLN s 61 ASN t 59 ASN u 39 ASN u 73 ASN v 12 GLN v 78 GLN ** v 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** w 8 ASN w 46 ASN x 16 ASN y 20 ASN ** y 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 6 GLN D 29 GLN F 37 GLN G 38 HIS G 50 ASN G 57 ASN G 176 ASN H 18 ASN H 122 GLN H 139 ASN I 88 ASN I 99 ASN I 115 GLN I 119 HIS I 195 ASN J 131 ASN L 147 ASN M 66 GLN N 30 ASN O 35 GLN O 56 HIS P 14 GLN ** P 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 4 ASN S 42 ASN T 36 ASN T 61 GLN U 26 ASN V 30 HIS X 68 HIS ** Y 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 12 GLN Y 47 GLN Y 51 ASN Y 60 GLN Y 67 HIS Z 8 ASN ** a 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 69 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 161399 Z= 0.362 Angle : 0.717 11.104 241370 Z= 0.371 Chirality : 0.043 0.359 30856 Planarity : 0.006 0.095 13007 Dihedral : 22.702 179.085 80607 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.41 % Allowed : 8.09 % Favored : 91.50 % Rotamer: Outliers : 6.05 % Allowed : 23.33 % Favored : 70.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.28 (0.10), residues: 5919 helix: -1.72 (0.11), residues: 1836 sheet: -2.33 (0.14), residues: 1030 loop : -2.40 (0.10), residues: 3053 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP b 212 HIS 0.008 0.001 HIS s 7 PHE 0.037 0.002 PHE Z 36 TYR 0.025 0.002 TYR N 5 ARG 0.010 0.001 ARG o 16 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11838 Ramachandran restraints generated. 5919 Oldfield, 0 Emsley, 5919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11838 Ramachandran restraints generated. 5919 Oldfield, 0 Emsley, 5919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2089 residues out of total 4908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 297 poor density : 1792 time to evaluate : 6.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 22 GLU cc_start: 0.7942 (pp20) cc_final: 0.7726 (pp20) REVERT: b 73 ILE cc_start: 0.9156 (mt) cc_final: 0.8873 (mm) REVERT: b 97 ASP cc_start: 0.8838 (p0) cc_final: 0.8508 (p0) REVERT: b 131 MET cc_start: 0.9044 (mtm) cc_final: 0.8838 (mtm) REVERT: b 152 GLN cc_start: 0.8543 (OUTLIER) cc_final: 0.7664 (mm110) REVERT: b 228 ASP cc_start: 0.8295 (m-30) cc_final: 0.8088 (m-30) REVERT: b 256 THR cc_start: 0.9076 (p) cc_final: 0.8811 (p) REVERT: c 32 ASN cc_start: 0.8816 (m-40) cc_final: 0.8347 (m110) REVERT: c 88 GLU cc_start: 0.8195 (pt0) cc_final: 0.7928 (pm20) REVERT: c 128 ARG cc_start: 0.8222 (OUTLIER) cc_final: 0.7780 (mtp180) REVERT: c 167 ASN cc_start: 0.9427 (t0) cc_final: 0.9097 (t160) REVERT: d 30 GLN cc_start: 0.8865 (tp40) cc_final: 0.8491 (tp40) REVERT: d 51 GLU cc_start: 0.8009 (pm20) cc_final: 0.7610 (pm20) REVERT: d 91 ASP cc_start: 0.8390 (t70) cc_final: 0.8086 (t0) REVERT: d 111 GLU cc_start: 0.7985 (tp30) cc_final: 0.7335 (tp30) REVERT: d 163 ASN cc_start: 0.9087 (t0) cc_final: 0.8417 (t0) REVERT: d 194 LYS cc_start: 0.8868 (pptt) cc_final: 0.8591 (pptt) REVERT: e 10 GLU cc_start: 0.8127 (mp0) cc_final: 0.7919 (mp0) REVERT: e 19 PHE cc_start: 0.8848 (m-80) cc_final: 0.8554 (m-10) REVERT: e 33 ILE cc_start: 0.8956 (OUTLIER) cc_final: 0.8641 (pt) REVERT: e 36 ASN cc_start: 0.7740 (t0) cc_final: 0.7524 (t0) REVERT: e 37 MET cc_start: 0.7888 (ttm) cc_final: 0.7683 (mtp) REVERT: e 80 GLN cc_start: 0.8995 (tp40) cc_final: 0.8752 (tp40) REVERT: e 95 MET cc_start: 0.8521 (ppp) cc_final: 0.8251 (ppp) REVERT: e 99 PHE cc_start: 0.8961 (t80) cc_final: 0.8695 (t80) REVERT: e 133 GLU cc_start: 0.7959 (tp30) cc_final: 0.7726 (tp30) REVERT: e 152 ASP cc_start: 0.7837 (OUTLIER) cc_final: 0.7567 (p0) REVERT: e 164 GLU cc_start: 0.8317 (tt0) cc_final: 0.7928 (tt0) REVERT: f 54 ARG cc_start: 0.8623 (ttm170) cc_final: 0.8381 (ttm110) REVERT: f 57 TYR cc_start: 0.7855 (m-80) cc_final: 0.7651 (m-80) REVERT: f 68 ARG cc_start: 0.9011 (tmt170) cc_final: 0.8655 (tmt-80) REVERT: f 82 PHE cc_start: 0.8174 (m-80) cc_final: 0.7715 (m-80) REVERT: f 100 ASN cc_start: 0.8496 (p0) cc_final: 0.7990 (p0) REVERT: f 103 ASN cc_start: 0.9131 (t0) cc_final: 0.8840 (t0) REVERT: f 113 ASP cc_start: 0.8227 (m-30) cc_final: 0.7990 (m-30) REVERT: f 123 GLU cc_start: 0.7839 (tm-30) cc_final: 0.7601 (tm-30) REVERT: f 129 GLU cc_start: 0.8748 (tt0) cc_final: 0.8202 (tp30) REVERT: f 131 VAL cc_start: 0.8576 (t) cc_final: 0.8039 (p) REVERT: f 146 ASP cc_start: 0.8909 (m-30) cc_final: 0.8616 (m-30) REVERT: g 4 ILE cc_start: 0.9009 (tp) cc_final: 0.8620 (mm) REVERT: g 8 LYS cc_start: 0.8517 (mtpp) cc_final: 0.7847 (tptt) REVERT: g 25 TYR cc_start: 0.8945 (t80) cc_final: 0.8402 (t80) REVERT: g 35 LYS cc_start: 0.8597 (mptt) cc_final: 0.8360 (mptm) REVERT: g 117 LEU cc_start: 0.7098 (OUTLIER) cc_final: 0.6737 (pt) REVERT: h 5 LEU cc_start: 0.9213 (tm) cc_final: 0.8906 (pt) REVERT: i 116 MET cc_start: -0.1809 (tpt) cc_final: -0.3035 (tpp) REVERT: i 124 MET cc_start: 0.6403 (tmt) cc_final: 0.6186 (ppp) REVERT: j 13 ARG cc_start: 0.8434 (mtt90) cc_final: 0.8217 (mtt90) REVERT: j 71 ASP cc_start: 0.8403 (m-30) cc_final: 0.8172 (m-30) REVERT: j 103 ILE cc_start: 0.9398 (mt) cc_final: 0.9176 (mt) REVERT: k 12 ASP cc_start: 0.8441 (p0) cc_final: 0.8238 (p0) REVERT: l 55 MET cc_start: 0.8384 (tpp) cc_final: 0.8023 (tpp) REVERT: l 76 GLU cc_start: 0.7644 (mt-10) cc_final: 0.7242 (mt-10) REVERT: l 82 LEU cc_start: 0.9445 (tp) cc_final: 0.9128 (tm) REVERT: l 104 GLN cc_start: 0.8328 (mm-40) cc_final: 0.8120 (tp-100) REVERT: l 105 ILE cc_start: 0.9248 (mm) cc_final: 0.9033 (mm) REVERT: l 143 GLU cc_start: 0.7347 (pm20) cc_final: 0.7127 (pp20) REVERT: m 17 ASN cc_start: 0.8615 (t0) cc_final: 0.7843 (t0) REVERT: m 88 ASN cc_start: 0.8546 (m-40) cc_final: 0.8281 (m110) REVERT: m 91 TYR cc_start: 0.9065 (p90) cc_final: 0.8650 (p90) REVERT: m 106 ASP cc_start: 0.8138 (t0) cc_final: 0.7798 (t0) REVERT: m 115 GLU cc_start: 0.8592 (OUTLIER) cc_final: 0.8325 (pp20) REVERT: m 118 LYS cc_start: 0.9047 (OUTLIER) cc_final: 0.8800 (ttmt) REVERT: n 32 GLU cc_start: 0.8080 (mt-10) cc_final: 0.7871 (mt-10) REVERT: n 35 LYS cc_start: 0.8865 (tttm) cc_final: 0.8524 (tptt) REVERT: n 72 ASP cc_start: 0.8757 (t0) cc_final: 0.8534 (t0) REVERT: o 17 LYS cc_start: 0.9364 (tppt) cc_final: 0.8994 (tppt) REVERT: o 19 GLN cc_start: 0.9170 (OUTLIER) cc_final: 0.8385 (tp-100) REVERT: o 46 GLU cc_start: 0.8260 (pm20) cc_final: 0.7936 (pm20) REVERT: o 80 GLU cc_start: 0.8792 (tm-30) cc_final: 0.8521 (tm-30) REVERT: o 91 SER cc_start: 0.9307 (t) cc_final: 0.9048 (m) REVERT: o 94 ARG cc_start: 0.9192 (mtm110) cc_final: 0.8954 (mtm110) REVERT: p 23 ASP cc_start: 0.8667 (m-30) cc_final: 0.8166 (m-30) REVERT: p 26 GLU cc_start: 0.7968 (tm-30) cc_final: 0.7577 (tm-30) REVERT: p 65 ASN cc_start: 0.9065 (OUTLIER) cc_final: 0.8612 (p0) REVERT: p 69 VAL cc_start: 0.9129 (t) cc_final: 0.8872 (p) REVERT: q 80 ASN cc_start: 0.9052 (t0) cc_final: 0.8832 (t0) REVERT: q 96 ASP cc_start: 0.8327 (t0) cc_final: 0.7969 (t0) REVERT: q 101 ASP cc_start: 0.8285 (t70) cc_final: 0.7802 (t0) REVERT: r 13 ARG cc_start: 0.8848 (ttp80) cc_final: 0.8100 (ttt-90) REVERT: r 31 GLU cc_start: 0.7893 (mp0) cc_final: 0.7579 (mp0) REVERT: r 35 PHE cc_start: 0.9053 (m-80) cc_final: 0.8636 (m-80) REVERT: r 62 GLU cc_start: 0.7901 (tm-30) cc_final: 0.7128 (tm-30) REVERT: r 95 ASP cc_start: 0.8206 (p0) cc_final: 0.7955 (p0) REVERT: r 101 ILE cc_start: 0.8704 (OUTLIER) cc_final: 0.8395 (tt) REVERT: s 61 ASN cc_start: 0.8717 (m-40) cc_final: 0.8439 (m-40) REVERT: t 1 MET cc_start: 0.6807 (ptp) cc_final: 0.6446 (ptp) REVERT: t 8 LEU cc_start: 0.9429 (mm) cc_final: 0.9090 (mm) REVERT: t 28 ASN cc_start: 0.8800 (t0) cc_final: 0.8338 (t0) REVERT: t 30 ILE cc_start: 0.8677 (tt) cc_final: 0.8436 (pp) REVERT: t 36 LYS cc_start: 0.8347 (tptp) cc_final: 0.8126 (tptp) REVERT: t 39 THR cc_start: 0.8800 (t) cc_final: 0.7693 (t) REVERT: t 86 THR cc_start: 0.9031 (m) cc_final: 0.8650 (p) REVERT: u 23 LYS cc_start: 0.8895 (ptmt) cc_final: 0.8484 (ptmm) REVERT: u 60 LYS cc_start: 0.7748 (mtpt) cc_final: 0.7516 (mtpt) REVERT: u 93 ARG cc_start: 0.8903 (mtm180) cc_final: 0.8202 (ptp90) REVERT: u 100 GLU cc_start: 0.8268 (mm-30) cc_final: 0.8049 (mm-30) REVERT: v 38 LEU cc_start: 0.9023 (tp) cc_final: 0.8805 (tp) REVERT: v 41 GLU cc_start: 0.7578 (tm-30) cc_final: 0.7329 (tm-30) REVERT: v 46 LYS cc_start: 0.9188 (mmtm) cc_final: 0.8796 (mmpt) REVERT: v 50 MET cc_start: 0.8808 (mtm) cc_final: 0.8550 (mtt) REVERT: v 63 ILE cc_start: 0.8896 (mt) cc_final: 0.8360 (mt) REVERT: v 69 GLU cc_start: 0.7175 (tp30) cc_final: 0.6358 (tp30) REVERT: v 71 LYS cc_start: 0.9137 (mttm) cc_final: 0.8931 (mmpt) REVERT: w 27 VAL cc_start: 0.9079 (m) cc_final: 0.8793 (m) REVERT: w 62 LYS cc_start: 0.8776 (mttt) cc_final: 0.8213 (mtmm) REVERT: w 79 GLU cc_start: 0.8074 (mp0) cc_final: 0.7771 (mp0) REVERT: x 60 LYS cc_start: 0.8952 (ttpt) cc_final: 0.8583 (tttt) REVERT: x 61 LYS cc_start: 0.8851 (mttt) cc_final: 0.8552 (mttp) REVERT: y 8 GLU cc_start: 0.7648 (mp0) cc_final: 0.7402 (mp0) REVERT: y 39 GLN cc_start: 0.8560 (OUTLIER) cc_final: 0.8307 (mt0) REVERT: B 5 ASN cc_start: 0.8924 (m-40) cc_final: 0.8502 (m110) REVERT: B 36 LYS cc_start: 0.9066 (mmtp) cc_final: 0.8822 (mptp) REVERT: F 8 LYS cc_start: 0.8862 (ptpp) cc_final: 0.8489 (pttt) REVERT: F 17 VAL cc_start: 0.9062 (p) cc_final: 0.8811 (m) REVERT: F 24 ARG cc_start: 0.8972 (mtt-85) cc_final: 0.8547 (mtt-85) REVERT: F 31 PRO cc_start: 0.9206 (Cg_exo) cc_final: 0.9002 (Cg_endo) REVERT: G 15 PHE cc_start: 0.7988 (m-80) cc_final: 0.7774 (m-10) REVERT: G 18 GLN cc_start: 0.8726 (mt0) cc_final: 0.8280 (mp10) REVERT: G 108 GLN cc_start: 0.8945 (mm110) cc_final: 0.8621 (mm110) REVERT: G 131 LYS cc_start: 0.8204 (mmmt) cc_final: 0.7900 (mmtt) REVERT: G 172 ILE cc_start: 0.9375 (pt) cc_final: 0.9153 (pp) REVERT: G 177 ASN cc_start: 0.8463 (m110) cc_final: 0.8224 (m110) REVERT: H 5 HIS cc_start: 0.9044 (t-90) cc_final: 0.8658 (t-90) REVERT: H 39 ARG cc_start: 0.8625 (ttm-80) cc_final: 0.8209 (mtt-85) REVERT: H 57 GLU cc_start: 0.8817 (mt-10) cc_final: 0.8276 (tt0) REVERT: H 84 GLU cc_start: 0.8308 (mm-30) cc_final: 0.8039 (mm-30) REVERT: H 85 LYS cc_start: 0.8586 (ttpp) cc_final: 0.8348 (ttpp) REVERT: H 139 ASN cc_start: 0.8948 (m-40) cc_final: 0.8539 (m110) REVERT: H 151 GLU cc_start: 0.8037 (tm-30) cc_final: 0.7637 (tm-30) REVERT: H 191 THR cc_start: 0.9127 (p) cc_final: 0.8771 (t) REVERT: I 9 LYS cc_start: 0.8607 (tttt) cc_final: 0.8297 (tttt) REVERT: I 43 ARG cc_start: 0.7340 (mpp-170) cc_final: 0.6945 (mpp-170) REVERT: I 68 GLU cc_start: 0.8316 (tp30) cc_final: 0.7905 (tp30) REVERT: I 71 PHE cc_start: 0.9157 (t80) cc_final: 0.8675 (t80) REVERT: I 73 ASN cc_start: 0.9481 (m-40) cc_final: 0.8632 (m110) REVERT: I 76 LYS cc_start: 0.8890 (mtmm) cc_final: 0.8150 (mppt) REVERT: I 112 GLU cc_start: 0.7511 (tt0) cc_final: 0.7093 (tt0) REVERT: I 137 SER cc_start: 0.8370 (t) cc_final: 0.7979 (p) REVERT: I 152 SER cc_start: 0.8967 (t) cc_final: 0.8726 (p) REVERT: J 13 LYS cc_start: 0.8798 (OUTLIER) cc_final: 0.8348 (ttpp) REVERT: J 94 PHE cc_start: 0.8104 (t80) cc_final: 0.7847 (t80) REVERT: K 1 MET cc_start: 0.7077 (OUTLIER) cc_final: 0.6863 (ttm) REVERT: K 44 ARG cc_start: 0.8254 (ttp-170) cc_final: 0.7622 (ttm-80) REVERT: K 56 LYS cc_start: 0.8482 (OUTLIER) cc_final: 0.7920 (mmpt) REVERT: K 65 GLU cc_start: 0.7629 (tm-30) cc_final: 0.6576 (tm-30) REVERT: K 71 ILE cc_start: 0.8892 (pt) cc_final: 0.8524 (pp) REVERT: K 88 MET cc_start: 0.7881 (OUTLIER) cc_final: 0.7614 (ptm) REVERT: K 90 MET cc_start: 0.7744 (mtm) cc_final: 0.7500 (mpp) REVERT: L 100 MET cc_start: 0.8456 (mtp) cc_final: 0.8025 (mtm) REVERT: L 105 GLU cc_start: 0.8459 (pp20) cc_final: 0.8066 (pp20) REVERT: L 125 ASP cc_start: 0.8975 (t0) cc_final: 0.8339 (t0) REVERT: L 128 GLU cc_start: 0.7629 (OUTLIER) cc_final: 0.7193 (pm20) REVERT: L 130 LYS cc_start: 0.9415 (pttt) cc_final: 0.9025 (pptt) REVERT: M 28 SER cc_start: 0.8336 (p) cc_final: 0.7998 (p) REVERT: M 37 ASN cc_start: 0.8801 (t0) cc_final: 0.8586 (t0) REVERT: M 48 PHE cc_start: 0.9125 (p90) cc_final: 0.8646 (p90) REVERT: M 83 ARG cc_start: 0.8868 (mmt180) cc_final: 0.8538 (mpt90) REVERT: M 110 MET cc_start: 0.8619 (ptp) cc_final: 0.8387 (ptp) REVERT: N 20 ILE cc_start: 0.9208 (tt) cc_final: 0.8783 (tp) REVERT: N 21 LYS cc_start: 0.8969 (mtpt) cc_final: 0.8478 (mmpt) REVERT: N 27 ILE cc_start: 0.8976 (mp) cc_final: 0.8598 (mm) REVERT: N 57 VAL cc_start: 0.7013 (OUTLIER) cc_final: 0.6029 (m) REVERT: N 60 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8533 (pp) REVERT: N 72 SER cc_start: 0.9189 (t) cc_final: 0.8663 (p) REVERT: N 123 ARG cc_start: 0.8575 (mmt90) cc_final: 0.8198 (tpp80) REVERT: O 9 ARG cc_start: 0.8164 (ttm-80) cc_final: 0.7548 (ttt180) REVERT: O 16 ARG cc_start: 0.7703 (ptt180) cc_final: 0.7223 (ptp90) REVERT: O 48 ARG cc_start: 0.8641 (mtt90) cc_final: 0.8239 (mtt-85) REVERT: P 33 ILE cc_start: 0.8995 (mt) cc_final: 0.8784 (mp) REVERT: P 60 PHE cc_start: 0.9078 (t80) cc_final: 0.8797 (t80) REVERT: P 69 CYS cc_start: 0.8364 (t) cc_final: 0.7357 (t) REVERT: P 84 MET cc_start: 0.7300 (ptm) cc_final: 0.6946 (ppp) REVERT: Q 37 TYR cc_start: 0.8013 (p90) cc_final: 0.7809 (p90) REVERT: Q 39 THR cc_start: 0.8357 (m) cc_final: 0.8082 (p) REVERT: Q 43 LYS cc_start: 0.8776 (mmmt) cc_final: 0.8465 (mmtm) REVERT: R 2 ARG cc_start: 0.6873 (mmt90) cc_final: 0.6584 (tpt170) REVERT: R 43 LYS cc_start: 0.8313 (ptpt) cc_final: 0.8086 (ptpp) REVERT: R 52 ILE cc_start: 0.8943 (mt) cc_final: 0.8429 (mp) REVERT: R 54 THR cc_start: 0.8746 (m) cc_final: 0.8200 (m) REVERT: R 77 LYS cc_start: 0.9133 (tttm) cc_final: 0.8566 (tppt) REVERT: R 88 LEU cc_start: 0.9370 (mp) cc_final: 0.9079 (mm) REVERT: T 25 GLU cc_start: 0.8567 (mt-10) cc_final: 0.8323 (mt-10) REVERT: T 36 ASN cc_start: 0.8910 (m110) cc_final: 0.8466 (m-40) REVERT: T 48 ASP cc_start: 0.8381 (t0) cc_final: 0.7985 (t0) REVERT: T 51 SER cc_start: 0.9178 (p) cc_final: 0.8738 (p) REVERT: T 73 ASP cc_start: 0.7676 (t0) cc_final: 0.7370 (t0) REVERT: T 76 ARG cc_start: 0.8438 (mtm180) cc_final: 0.8054 (ttm110) REVERT: V 16 MET cc_start: 0.7175 (ttt) cc_final: 0.6737 (ttt) REVERT: V 44 HIS cc_start: 0.8235 (m90) cc_final: 0.8009 (m-70) REVERT: V 66 LEU cc_start: 0.9157 (mt) cc_final: 0.8937 (mt) REVERT: W 23 LYS cc_start: 0.9021 (mtmm) cc_final: 0.8678 (pptt) REVERT: W 24 ASP cc_start: 0.8504 (t70) cc_final: 0.8190 (t0) REVERT: W 51 GLN cc_start: 0.8788 (tp40) cc_final: 0.8081 (tm-30) REVERT: X 10 ILE cc_start: 0.9128 (pt) cc_final: 0.8028 (mm) REVERT: X 17 LYS cc_start: 0.8390 (tptm) cc_final: 0.8012 (tttt) REVERT: X 38 THR cc_start: 0.8156 (OUTLIER) cc_final: 0.7777 (t) REVERT: X 46 LEU cc_start: 0.7606 (tm) cc_final: 0.7251 (mp) REVERT: X 69 LYS cc_start: 0.8265 (mttm) cc_final: 0.7834 (mttt) REVERT: X 72 GLU cc_start: 0.8441 (mt-10) cc_final: 0.8173 (mt-10) REVERT: Y 15 LYS cc_start: 0.8894 (tttm) cc_final: 0.8309 (tptp) REVERT: Y 17 ARG cc_start: 0.8742 (tmm-80) cc_final: 0.8150 (ttp-110) REVERT: Y 26 MET cc_start: 0.9038 (ppp) cc_final: 0.8577 (ppp) REVERT: Y 27 MET cc_start: 0.8255 (ppp) cc_final: 0.7865 (tmt) REVERT: Y 28 ARG cc_start: 0.8592 (mtt180) cc_final: 0.8177 (mtt-85) REVERT: Y 47 GLN cc_start: 0.8778 (tp40) cc_final: 0.8304 (tp-100) REVERT: Y 54 GLN cc_start: 0.8555 (tt0) cc_final: 0.8310 (tt0) REVERT: Z 18 PHE cc_start: 0.7519 (t80) cc_final: 0.6936 (t80) REVERT: a 197 LYS cc_start: 0.4948 (tttt) cc_final: 0.4590 (mmtm) REVERT: a 218 MET cc_start: 0.4519 (mtt) cc_final: 0.3765 (mmt) outliers start: 297 outliers final: 156 residues processed: 1895 average time/residue: 2.0712 time to fit residues: 5702.7151 Evaluate side-chains 1852 residues out of total 4908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 175 poor density : 1677 time to evaluate : 6.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 37 SER Chi-restraints excluded: chain b residue 48 ILE Chi-restraints excluded: chain b residue 50 THR Chi-restraints excluded: chain b residue 120 ASP Chi-restraints excluded: chain b residue 152 GLN Chi-restraints excluded: chain b residue 163 ILE Chi-restraints excluded: chain c residue 22 ILE Chi-restraints excluded: chain c residue 39 ASP Chi-restraints excluded: chain c residue 95 SER Chi-restraints excluded: chain c residue 97 SER Chi-restraints excluded: chain c residue 110 THR Chi-restraints excluded: chain c residue 128 ARG Chi-restraints excluded: chain c residue 170 VAL Chi-restraints excluded: chain c residue 199 SER Chi-restraints excluded: chain c residue 200 ASP Chi-restraints excluded: chain d residue 72 SER Chi-restraints excluded: chain d residue 157 LEU Chi-restraints excluded: chain e residue 33 ILE Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 60 SER Chi-restraints excluded: chain e residue 67 THR Chi-restraints excluded: chain e residue 152 ASP Chi-restraints excluded: chain e residue 157 THR Chi-restraints excluded: chain e residue 173 ASP Chi-restraints excluded: chain f residue 8 VAL Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 105 SER Chi-restraints excluded: chain f residue 124 CYS Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain g residue 96 THR Chi-restraints excluded: chain g residue 115 VAL Chi-restraints excluded: chain g residue 117 LEU Chi-restraints excluded: chain h residue 3 LEU Chi-restraints excluded: chain i residue 12 VAL Chi-restraints excluded: chain j residue 32 LEU Chi-restraints excluded: chain j residue 73 VAL Chi-restraints excluded: chain j residue 131 ASN Chi-restraints excluded: chain k residue 28 SER Chi-restraints excluded: chain k residue 118 LEU Chi-restraints excluded: chain l residue 5 THR Chi-restraints excluded: chain l residue 12 SER Chi-restraints excluded: chain l residue 42 SER Chi-restraints excluded: chain l residue 110 VAL Chi-restraints excluded: chain l residue 111 ILE Chi-restraints excluded: chain l residue 118 THR Chi-restraints excluded: chain l residue 120 VAL Chi-restraints excluded: chain l residue 121 THR Chi-restraints excluded: chain l residue 122 VAL Chi-restraints excluded: chain m residue 12 MET Chi-restraints excluded: chain m residue 54 THR Chi-restraints excluded: chain m residue 57 VAL Chi-restraints excluded: chain m residue 74 THR Chi-restraints excluded: chain m residue 78 LEU Chi-restraints excluded: chain m residue 93 VAL Chi-restraints excluded: chain m residue 115 GLU Chi-restraints excluded: chain m residue 118 LYS Chi-restraints excluded: chain m residue 132 THR Chi-restraints excluded: chain n residue 15 SER Chi-restraints excluded: chain n residue 27 SER Chi-restraints excluded: chain n residue 37 THR Chi-restraints excluded: chain n residue 75 ILE Chi-restraints excluded: chain n residue 76 VAL Chi-restraints excluded: chain o residue 12 THR Chi-restraints excluded: chain o residue 19 GLN Chi-restraints excluded: chain o residue 35 ILE Chi-restraints excluded: chain o residue 65 THR Chi-restraints excluded: chain o residue 103 VAL Chi-restraints excluded: chain p residue 2 ASN Chi-restraints excluded: chain p residue 35 SER Chi-restraints excluded: chain p residue 65 ASN Chi-restraints excluded: chain p residue 93 LYS Chi-restraints excluded: chain q residue 16 ILE Chi-restraints excluded: chain q residue 73 ILE Chi-restraints excluded: chain q residue 74 SER Chi-restraints excluded: chain q residue 109 VAL Chi-restraints excluded: chain r residue 22 LEU Chi-restraints excluded: chain r residue 33 VAL Chi-restraints excluded: chain r residue 43 ASN Chi-restraints excluded: chain r residue 101 ILE Chi-restraints excluded: chain s residue 3 THR Chi-restraints excluded: chain s residue 20 VAL Chi-restraints excluded: chain s residue 77 ASP Chi-restraints excluded: chain s residue 104 THR Chi-restraints excluded: chain s residue 106 VAL Chi-restraints excluded: chain s residue 108 SER Chi-restraints excluded: chain t residue 17 SER Chi-restraints excluded: chain t residue 57 VAL Chi-restraints excluded: chain t residue 85 VAL Chi-restraints excluded: chain u residue 4 ILE Chi-restraints excluded: chain u residue 11 ILE Chi-restraints excluded: chain u residue 24 VAL Chi-restraints excluded: chain v residue 45 ASP Chi-restraints excluded: chain v residue 62 THR Chi-restraints excluded: chain v residue 64 VAL Chi-restraints excluded: chain v residue 65 VAL Chi-restraints excluded: chain v residue 92 VAL Chi-restraints excluded: chain w residue 34 VAL Chi-restraints excluded: chain w residue 39 THR Chi-restraints excluded: chain w residue 76 ILE Chi-restraints excluded: chain x residue 1 SER Chi-restraints excluded: chain x residue 7 THR Chi-restraints excluded: chain x residue 13 THR Chi-restraints excluded: chain x residue 33 HIS Chi-restraints excluded: chain x residue 39 VAL Chi-restraints excluded: chain x residue 47 THR Chi-restraints excluded: chain y residue 30 MET Chi-restraints excluded: chain y residue 39 GLN Chi-restraints excluded: chain y residue 40 SER Chi-restraints excluded: chain y residue 55 THR Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain G residue 147 LEU Chi-restraints excluded: chain G residue 198 VAL Chi-restraints excluded: chain H residue 20 THR Chi-restraints excluded: chain H residue 36 PHE Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 117 ASP Chi-restraints excluded: chain H residue 118 SER Chi-restraints excluded: chain H residue 164 THR Chi-restraints excluded: chain H residue 174 LEU Chi-restraints excluded: chain I residue 93 LEU Chi-restraints excluded: chain I residue 118 SER Chi-restraints excluded: chain I residue 133 SER Chi-restraints excluded: chain I residue 204 SER Chi-restraints excluded: chain J residue 13 LYS Chi-restraints excluded: chain J residue 105 ILE Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 26 THR Chi-restraints excluded: chain K residue 39 LEU Chi-restraints excluded: chain K residue 56 LYS Chi-restraints excluded: chain K residue 68 GLN Chi-restraints excluded: chain K residue 88 MET Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain L residue 128 GLU Chi-restraints excluded: chain M residue 57 GLU Chi-restraints excluded: chain N residue 57 VAL Chi-restraints excluded: chain N residue 60 LEU Chi-restraints excluded: chain P residue 25 SER Chi-restraints excluded: chain P residue 107 THR Chi-restraints excluded: chain Q residue 32 VAL Chi-restraints excluded: chain Q residue 40 THR Chi-restraints excluded: chain Q residue 51 VAL Chi-restraints excluded: chain Q residue 63 THR Chi-restraints excluded: chain Q residue 73 LEU Chi-restraints excluded: chain Q residue 92 VAL Chi-restraints excluded: chain Q residue 97 VAL Chi-restraints excluded: chain Q residue 102 ASP Chi-restraints excluded: chain Q residue 103 CYS Chi-restraints excluded: chain R residue 20 SER Chi-restraints excluded: chain R residue 24 VAL Chi-restraints excluded: chain R residue 65 GLU Chi-restraints excluded: chain R residue 94 LEU Chi-restraints excluded: chain S residue 54 SER Chi-restraints excluded: chain T residue 12 SER Chi-restraints excluded: chain T residue 30 LEU Chi-restraints excluded: chain T residue 69 LEU Chi-restraints excluded: chain T residue 80 LEU Chi-restraints excluded: chain U residue 68 SER Chi-restraints excluded: chain V residue 24 ILE Chi-restraints excluded: chain V residue 32 ILE Chi-restraints excluded: chain V residue 54 ILE Chi-restraints excluded: chain V residue 56 ASP Chi-restraints excluded: chain W residue 35 SER Chi-restraints excluded: chain W residue 65 SER Chi-restraints excluded: chain X residue 38 THR Chi-restraints excluded: chain X residue 78 THR Chi-restraints excluded: chain Y residue 25 SER Chi-restraints excluded: chain Y residue 78 LEU Chi-restraints excluded: chain Y residue 79 THR Chi-restraints excluded: chain Z residue 12 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1050 random chunks: chunk 529 optimal weight: 10.0000 chunk 295 optimal weight: 8.9990 chunk 793 optimal weight: 10.0000 chunk 649 optimal weight: 10.0000 chunk 263 optimal weight: 5.9990 chunk 955 optimal weight: 8.9990 chunk 1031 optimal weight: 10.0000 chunk 850 optimal weight: 30.0000 chunk 947 optimal weight: 50.0000 chunk 325 optimal weight: 4.9990 chunk 766 optimal weight: 10.0000 overall best weight: 7.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** e 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 127 GLN g 2 GLN ** g 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 135 GLN n 3 HIS n 31 HIS o 29 HIS r 87 GLN t 15 HIS u 39 ASN u 68 ASN v 12 GLN v 78 GLN y 15 ASN y 20 ASN ** y 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 8 GLN B 3 GLN E 27 ASN G 38 HIS G 93 HIS H 122 GLN ** H 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 53 GLN I 73 ASN ** I 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 119 HIS ** J 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 134 ASN ** K 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 63 ASN O 56 HIS Q 4 ASN ** S 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 40 ASN ** U 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 67 HIS ** Z 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.2943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.124 161399 Z= 0.484 Angle : 0.755 11.821 241370 Z= 0.388 Chirality : 0.044 0.378 30856 Planarity : 0.006 0.081 13007 Dihedral : 23.008 178.792 80584 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.39 % Allowed : 9.87 % Favored : 89.74 % Rotamer: Outliers : 9.25 % Allowed : 24.21 % Favored : 66.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.76 (0.10), residues: 5919 helix: -1.13 (0.11), residues: 1870 sheet: -1.93 (0.15), residues: 1069 loop : -2.24 (0.11), residues: 2980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP b 212 HIS 0.010 0.002 HIS j 132 PHE 0.042 0.002 PHE Z 36 TYR 0.030 0.002 TYR G 212 ARG 0.011 0.001 ARG o 16 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11838 Ramachandran restraints generated. 5919 Oldfield, 0 Emsley, 5919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11838 Ramachandran restraints generated. 5919 Oldfield, 0 Emsley, 5919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2168 residues out of total 4908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 454 poor density : 1714 time to evaluate : 6.548 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 22 GLU cc_start: 0.8102 (pp20) cc_final: 0.7839 (pp20) REVERT: b 86 ARG cc_start: 0.9078 (OUTLIER) cc_final: 0.8229 (mtm-85) REVERT: b 97 ASP cc_start: 0.8885 (p0) cc_final: 0.8614 (p0) REVERT: b 114 GLN cc_start: 0.8764 (OUTLIER) cc_final: 0.8341 (tt0) REVERT: b 131 MET cc_start: 0.9078 (mtm) cc_final: 0.8848 (mtm) REVERT: b 152 GLN cc_start: 0.8722 (OUTLIER) cc_final: 0.7892 (mm-40) REVERT: b 180 MET cc_start: 0.7273 (mtt) cc_final: 0.6637 (mtm) REVERT: b 228 ASP cc_start: 0.8390 (m-30) cc_final: 0.8183 (m-30) REVERT: b 250 GLN cc_start: 0.8843 (OUTLIER) cc_final: 0.8226 (tt0) REVERT: c 1 MET cc_start: 0.8514 (tmm) cc_final: 0.8090 (tmm) REVERT: c 2 ILE cc_start: 0.8694 (OUTLIER) cc_final: 0.8427 (pp) REVERT: c 88 GLU cc_start: 0.8293 (pt0) cc_final: 0.8065 (pt0) REVERT: c 128 ARG cc_start: 0.8315 (OUTLIER) cc_final: 0.7724 (mtp180) REVERT: c 167 ASN cc_start: 0.9420 (t0) cc_final: 0.9083 (t160) REVERT: d 30 GLN cc_start: 0.8981 (tp40) cc_final: 0.8111 (tt0) REVERT: d 51 GLU cc_start: 0.8131 (pm20) cc_final: 0.7881 (pm20) REVERT: d 88 ARG cc_start: 0.8540 (OUTLIER) cc_final: 0.8165 (mmp80) REVERT: d 111 GLU cc_start: 0.7992 (tp30) cc_final: 0.7389 (tp30) REVERT: d 163 ASN cc_start: 0.8978 (t0) cc_final: 0.8433 (t0) REVERT: e 16 MET cc_start: 0.7950 (OUTLIER) cc_final: 0.7734 (mmm) REVERT: e 21 TYR cc_start: 0.7312 (m-80) cc_final: 0.7098 (m-80) REVERT: e 29 ARG cc_start: 0.8677 (OUTLIER) cc_final: 0.8265 (ptp-170) REVERT: e 33 ILE cc_start: 0.8995 (OUTLIER) cc_final: 0.8786 (pt) REVERT: e 36 ASN cc_start: 0.7433 (t0) cc_final: 0.7035 (t0) REVERT: e 41 GLU cc_start: 0.7798 (tp30) cc_final: 0.7444 (tp30) REVERT: e 51 ASN cc_start: 0.8221 (m-40) cc_final: 0.7922 (p0) REVERT: e 95 MET cc_start: 0.8914 (ppp) cc_final: 0.8605 (ppp) REVERT: e 99 PHE cc_start: 0.9067 (t80) cc_final: 0.8863 (t80) REVERT: e 129 MET cc_start: 0.8067 (tmt) cc_final: 0.7812 (tmm) REVERT: e 133 GLU cc_start: 0.7810 (tp30) cc_final: 0.7553 (tp30) REVERT: e 152 ASP cc_start: 0.7794 (OUTLIER) cc_final: 0.7558 (p0) REVERT: e 153 ILE cc_start: 0.9175 (mt) cc_final: 0.8677 (pp) REVERT: f 2 ARG cc_start: 0.8245 (mtt-85) cc_final: 0.7927 (ttm170) REVERT: f 19 ASN cc_start: 0.8472 (t0) cc_final: 0.8251 (t0) REVERT: f 21 GLN cc_start: 0.8537 (tp-100) cc_final: 0.8207 (tp-100) REVERT: f 54 ARG cc_start: 0.8543 (ttm170) cc_final: 0.8306 (ttm110) REVERT: f 68 ARG cc_start: 0.9005 (tmt170) cc_final: 0.8577 (tmt-80) REVERT: f 82 PHE cc_start: 0.8277 (m-80) cc_final: 0.7779 (m-80) REVERT: f 100 ASN cc_start: 0.8532 (p0) cc_final: 0.8056 (p0) REVERT: f 103 ASN cc_start: 0.9000 (t0) cc_final: 0.8736 (t0) REVERT: f 113 ASP cc_start: 0.8177 (m-30) cc_final: 0.7910 (m-30) REVERT: f 127 GLN cc_start: 0.8091 (mm110) cc_final: 0.7870 (mm-40) REVERT: f 129 GLU cc_start: 0.8579 (tt0) cc_final: 0.8147 (tp30) REVERT: f 146 ASP cc_start: 0.8949 (m-30) cc_final: 0.8691 (m-30) REVERT: g 4 ILE cc_start: 0.8914 (tp) cc_final: 0.8614 (mm) REVERT: g 8 LYS cc_start: 0.8588 (mtpp) cc_final: 0.7932 (tptt) REVERT: g 25 TYR cc_start: 0.8985 (t80) cc_final: 0.8436 (t80) REVERT: g 35 LYS cc_start: 0.8775 (mptt) cc_final: 0.8515 (mptp) REVERT: g 117 LEU cc_start: 0.7160 (OUTLIER) cc_final: 0.6656 (pt) REVERT: h 5 LEU cc_start: 0.9158 (tm) cc_final: 0.8908 (pt) REVERT: i 107 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.8071 (tm-30) REVERT: i 116 MET cc_start: -0.2338 (tpt) cc_final: -0.2625 (tpt) REVERT: j 71 ASP cc_start: 0.8463 (m-30) cc_final: 0.8219 (m-30) REVERT: k 12 ASP cc_start: 0.8465 (p0) cc_final: 0.8093 (p0) REVERT: k 77 ILE cc_start: 0.9077 (mp) cc_final: 0.8704 (tt) REVERT: k 98 ARG cc_start: 0.7879 (mtp85) cc_final: 0.7609 (ttm110) REVERT: l 55 MET cc_start: 0.8387 (tpp) cc_final: 0.8037 (tpp) REVERT: l 76 GLU cc_start: 0.7469 (mt-10) cc_final: 0.7085 (mt-10) REVERT: l 82 LEU cc_start: 0.9457 (tp) cc_final: 0.9107 (tm) REVERT: l 105 ILE cc_start: 0.9089 (mm) cc_final: 0.8829 (mm) REVERT: l 143 GLU cc_start: 0.7439 (pm20) cc_final: 0.7159 (pp20) REVERT: m 6 ARG cc_start: 0.8318 (OUTLIER) cc_final: 0.8109 (ppp80) REVERT: m 17 ASN cc_start: 0.8683 (t0) cc_final: 0.7822 (t0) REVERT: m 88 ASN cc_start: 0.8636 (m-40) cc_final: 0.8338 (m110) REVERT: m 91 TYR cc_start: 0.9115 (p90) cc_final: 0.8601 (p90) REVERT: m 97 GLN cc_start: 0.8646 (OUTLIER) cc_final: 0.8310 (mp-120) REVERT: n 32 GLU cc_start: 0.8056 (mt-10) cc_final: 0.7828 (mt-10) REVERT: n 35 LYS cc_start: 0.8869 (tttt) cc_final: 0.8616 (tptt) REVERT: n 72 ASP cc_start: 0.8877 (t0) cc_final: 0.8577 (t0) REVERT: o 17 LYS cc_start: 0.9311 (tppt) cc_final: 0.9102 (tppt) REVERT: o 19 GLN cc_start: 0.9038 (OUTLIER) cc_final: 0.8635 (tp-100) REVERT: o 38 GLN cc_start: 0.8893 (pt0) cc_final: 0.7961 (pm20) REVERT: o 43 ASN cc_start: 0.8829 (p0) cc_final: 0.8297 (p0) REVERT: o 46 GLU cc_start: 0.8209 (pm20) cc_final: 0.7893 (pm20) REVERT: o 56 LYS cc_start: 0.9297 (ptmm) cc_final: 0.9013 (tppt) REVERT: o 80 GLU cc_start: 0.8848 (tm-30) cc_final: 0.8624 (tm-30) REVERT: o 91 SER cc_start: 0.9350 (t) cc_final: 0.9018 (m) REVERT: p 23 ASP cc_start: 0.8590 (m-30) cc_final: 0.8126 (m-30) REVERT: p 26 GLU cc_start: 0.7967 (tm-30) cc_final: 0.7684 (tm-30) REVERT: p 65 ASN cc_start: 0.8957 (OUTLIER) cc_final: 0.8593 (p0) REVERT: p 110 LYS cc_start: 0.8667 (OUTLIER) cc_final: 0.8434 (ptmm) REVERT: q 50 ARG cc_start: 0.8903 (OUTLIER) cc_final: 0.7801 (mmt90) REVERT: q 96 ASP cc_start: 0.8374 (t0) cc_final: 0.7837 (t0) REVERT: q 101 ASP cc_start: 0.8368 (t70) cc_final: 0.7912 (t0) REVERT: r 13 ARG cc_start: 0.8864 (ttp80) cc_final: 0.8271 (ttt-90) REVERT: r 31 GLU cc_start: 0.8011 (mp0) cc_final: 0.7745 (mp0) REVERT: r 37 GLU cc_start: 0.7880 (pm20) cc_final: 0.7631 (pm20) REVERT: r 60 LYS cc_start: 0.8928 (mtmm) cc_final: 0.8458 (mmmm) REVERT: r 62 GLU cc_start: 0.7948 (tm-30) cc_final: 0.7153 (tm-30) REVERT: r 101 ILE cc_start: 0.8831 (OUTLIER) cc_final: 0.8610 (tt) REVERT: t 28 ASN cc_start: 0.8803 (t0) cc_final: 0.8374 (t0) REVERT: t 36 LYS cc_start: 0.8402 (tptp) cc_final: 0.8189 (tptt) REVERT: t 39 THR cc_start: 0.8774 (OUTLIER) cc_final: 0.8502 (t) REVERT: t 86 THR cc_start: 0.9104 (m) cc_final: 0.8758 (p) REVERT: t 91 GLN cc_start: 0.8961 (mm-40) cc_final: 0.8599 (mm-40) REVERT: u 33 VAL cc_start: 0.9417 (OUTLIER) cc_final: 0.9186 (t) REVERT: u 93 ARG cc_start: 0.8917 (mtm180) cc_final: 0.8345 (ptp90) REVERT: v 38 LEU cc_start: 0.9048 (tp) cc_final: 0.8704 (tp) REVERT: v 46 LYS cc_start: 0.9182 (mmtm) cc_final: 0.8723 (mmpt) REVERT: v 50 MET cc_start: 0.8619 (mtm) cc_final: 0.8230 (mtt) REVERT: v 53 LYS cc_start: 0.9075 (OUTLIER) cc_final: 0.8862 (ptpt) REVERT: v 87 GLN cc_start: 0.8617 (mt0) cc_final: 0.8144 (mt0) REVERT: v 89 ILE cc_start: 0.8792 (mp) cc_final: 0.8576 (tp) REVERT: w 16 ARG cc_start: 0.8619 (mpt-90) cc_final: 0.7740 (mmt90) REVERT: x 60 LYS cc_start: 0.9036 (ttpt) cc_final: 0.8722 (tttt) REVERT: y 1 MET cc_start: 0.6305 (tpt) cc_final: 0.5890 (tpt) REVERT: y 8 GLU cc_start: 0.7536 (mp0) cc_final: 0.7327 (mp0) REVERT: y 39 GLN cc_start: 0.8441 (OUTLIER) cc_final: 0.8096 (mt0) REVERT: z 39 ASP cc_start: 0.8190 (t0) cc_final: 0.7635 (m-30) REVERT: B 5 ASN cc_start: 0.9038 (m-40) cc_final: 0.8640 (m110) REVERT: B 36 LYS cc_start: 0.9173 (mmtp) cc_final: 0.8862 (mmtt) REVERT: D 41 ARG cc_start: 0.7997 (OUTLIER) cc_final: 0.7604 (mtp180) REVERT: E 15 LYS cc_start: 0.8793 (tptp) cc_final: 0.8543 (tptp) REVERT: F 8 LYS cc_start: 0.8877 (ptpp) cc_final: 0.8431 (pttt) REVERT: F 17 VAL cc_start: 0.9160 (p) cc_final: 0.8894 (m) REVERT: F 24 ARG cc_start: 0.8987 (mtt-85) cc_final: 0.8472 (mtt-85) REVERT: F 35 GLN cc_start: 0.9028 (OUTLIER) cc_final: 0.8580 (pt0) REVERT: G 5 MET cc_start: 0.8240 (OUTLIER) cc_final: 0.7668 (mpp) REVERT: G 18 GLN cc_start: 0.8786 (mt0) cc_final: 0.8364 (mp10) REVERT: G 144 GLU cc_start: 0.8602 (pp20) cc_final: 0.8399 (pp20) REVERT: G 150 ILE cc_start: 0.9108 (OUTLIER) cc_final: 0.8819 (tt) REVERT: G 153 MET cc_start: 0.8426 (ttm) cc_final: 0.7985 (ttm) REVERT: G 172 ILE cc_start: 0.9410 (pt) cc_final: 0.9186 (pp) REVERT: H 5 HIS cc_start: 0.9024 (t-90) cc_final: 0.8679 (t-90) REVERT: H 39 ARG cc_start: 0.8680 (ttm-80) cc_final: 0.7588 (mtt90) REVERT: H 128 MET cc_start: 0.7367 (OUTLIER) cc_final: 0.6907 (pmt) REVERT: H 129 PHE cc_start: 0.8940 (p90) cc_final: 0.8718 (p90) REVERT: H 139 ASN cc_start: 0.8988 (m-40) cc_final: 0.8572 (m110) REVERT: H 151 GLU cc_start: 0.8254 (tm-30) cc_final: 0.7705 (tm-30) REVERT: H 184 ASN cc_start: 0.8870 (t160) cc_final: 0.8647 (t160) REVERT: H 191 THR cc_start: 0.9258 (p) cc_final: 0.8870 (t) REVERT: I 43 ARG cc_start: 0.7400 (mpp-170) cc_final: 0.7031 (mpp-170) REVERT: I 68 GLU cc_start: 0.8313 (tp30) cc_final: 0.7798 (tp30) REVERT: I 71 PHE cc_start: 0.9165 (t80) cc_final: 0.8523 (t80) REVERT: I 73 ASN cc_start: 0.9462 (m110) cc_final: 0.8686 (m110) REVERT: I 76 LYS cc_start: 0.8897 (mtmm) cc_final: 0.8015 (mppt) REVERT: I 112 GLU cc_start: 0.7373 (tt0) cc_final: 0.6979 (tt0) REVERT: I 137 SER cc_start: 0.8265 (t) cc_final: 0.7831 (p) REVERT: I 152 SER cc_start: 0.8949 (t) cc_final: 0.8692 (p) REVERT: J 13 LYS cc_start: 0.8794 (OUTLIER) cc_final: 0.8315 (ttpp) REVERT: J 32 PHE cc_start: 0.9112 (m-80) cc_final: 0.8686 (m-80) REVERT: J 65 LYS cc_start: 0.8950 (OUTLIER) cc_final: 0.8458 (mtpp) REVERT: J 70 MET cc_start: 0.7977 (tpt) cc_final: 0.7712 (mmm) REVERT: J 94 PHE cc_start: 0.8312 (t80) cc_final: 0.7858 (t80) REVERT: J 95 MET cc_start: 0.7767 (mtm) cc_final: 0.7559 (mtm) REVERT: J 131 ASN cc_start: 0.8259 (t0) cc_final: 0.7756 (t0) REVERT: K 56 LYS cc_start: 0.8669 (mmtt) cc_final: 0.8451 (mmpt) REVERT: K 71 ILE cc_start: 0.9027 (pt) cc_final: 0.8805 (pp) REVERT: K 90 MET cc_start: 0.7782 (mtm) cc_final: 0.7383 (mpp) REVERT: L 105 GLU cc_start: 0.8436 (pp20) cc_final: 0.8064 (pp20) REVERT: L 139 ASP cc_start: 0.8286 (OUTLIER) cc_final: 0.7985 (t0) REVERT: M 17 GLN cc_start: 0.9083 (mm110) cc_final: 0.8734 (mm-40) REVERT: M 28 SER cc_start: 0.8625 (p) cc_final: 0.8285 (p) REVERT: M 37 ASN cc_start: 0.8782 (t0) cc_final: 0.8566 (t0) REVERT: M 57 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7897 (pp20) REVERT: M 110 MET cc_start: 0.8576 (ptp) cc_final: 0.8371 (ptp) REVERT: N 20 ILE cc_start: 0.9204 (tt) cc_final: 0.8788 (tp) REVERT: N 21 LYS cc_start: 0.9045 (mtpt) cc_final: 0.8532 (mmpt) REVERT: N 27 ILE cc_start: 0.8924 (mp) cc_final: 0.8528 (mm) REVERT: N 49 GLN cc_start: 0.9188 (tt0) cc_final: 0.8718 (tm-30) REVERT: N 123 ARG cc_start: 0.8646 (mmt90) cc_final: 0.8275 (tpp80) REVERT: O 9 ARG cc_start: 0.8209 (ttm-80) cc_final: 0.7547 (ttp-170) REVERT: O 48 ARG cc_start: 0.8658 (mtt90) cc_final: 0.8305 (mtt-85) REVERT: P 33 ILE cc_start: 0.8940 (mt) cc_final: 0.8734 (mp) REVERT: P 60 PHE cc_start: 0.9115 (t80) cc_final: 0.8754 (t80) REVERT: P 69 CYS cc_start: 0.8349 (t) cc_final: 0.7622 (t) REVERT: P 84 MET cc_start: 0.7439 (ptm) cc_final: 0.7030 (ppp) REVERT: Q 37 TYR cc_start: 0.8286 (p90) cc_final: 0.7849 (p90) REVERT: Q 39 THR cc_start: 0.8742 (m) cc_final: 0.8466 (p) REVERT: Q 43 LYS cc_start: 0.8825 (mmmt) cc_final: 0.8598 (mppt) REVERT: Q 88 ASP cc_start: 0.8141 (m-30) cc_final: 0.7409 (m-30) REVERT: R 43 LYS cc_start: 0.8468 (ptpt) cc_final: 0.8124 (ptpp) REVERT: R 52 ILE cc_start: 0.8965 (mt) cc_final: 0.8448 (mp) REVERT: R 76 ILE cc_start: 0.9359 (pp) cc_final: 0.9007 (pp) REVERT: R 77 LYS cc_start: 0.9170 (tttm) cc_final: 0.8535 (tppt) REVERT: R 88 LEU cc_start: 0.9248 (mp) cc_final: 0.9026 (mm) REVERT: T 25 GLU cc_start: 0.8570 (mt-10) cc_final: 0.8260 (mt-10) REVERT: T 36 ASN cc_start: 0.8912 (m110) cc_final: 0.8417 (m-40) REVERT: T 48 ASP cc_start: 0.8599 (t0) cc_final: 0.8098 (t0) REVERT: T 51 SER cc_start: 0.9195 (p) cc_final: 0.8872 (p) REVERT: T 76 ARG cc_start: 0.8475 (mtm180) cc_final: 0.8188 (ttm110) REVERT: U 63 GLN cc_start: 0.8255 (mm-40) cc_final: 0.8048 (mm-40) REVERT: V 38 LYS cc_start: 0.8728 (OUTLIER) cc_final: 0.8345 (ttmm) REVERT: V 44 HIS cc_start: 0.8236 (m90) cc_final: 0.7998 (m90) REVERT: V 66 LEU cc_start: 0.9130 (mt) cc_final: 0.8834 (mt) REVERT: V 80 LYS cc_start: 0.8690 (tmtt) cc_final: 0.8264 (tptt) REVERT: W 23 LYS cc_start: 0.8937 (mtmm) cc_final: 0.8707 (pptt) REVERT: W 24 ASP cc_start: 0.8501 (t70) cc_final: 0.8238 (t0) REVERT: W 42 ARG cc_start: 0.9103 (OUTLIER) cc_final: 0.8694 (mtm110) REVERT: W 69 TYR cc_start: 0.9081 (m-80) cc_final: 0.8862 (m-10) REVERT: X 10 ILE cc_start: 0.9162 (pt) cc_final: 0.8427 (mm) REVERT: X 43 MET cc_start: 0.8125 (OUTLIER) cc_final: 0.7736 (tpp) REVERT: Y 15 LYS cc_start: 0.8895 (tttm) cc_final: 0.8307 (tptp) REVERT: Y 17 ARG cc_start: 0.8833 (tmm-80) cc_final: 0.8340 (ttp-110) REVERT: Y 23 ARG cc_start: 0.8796 (mmp80) cc_final: 0.8536 (mmp80) REVERT: Y 27 MET cc_start: 0.8178 (ppp) cc_final: 0.7810 (tmt) REVERT: Y 28 ARG cc_start: 0.8441 (mtt180) cc_final: 0.8102 (mtt-85) REVERT: Y 47 GLN cc_start: 0.8788 (tp40) cc_final: 0.8265 (tp-100) REVERT: Y 50 PHE cc_start: 0.8812 (t80) cc_final: 0.8499 (t80) REVERT: Y 53 MET cc_start: 0.8471 (ppp) cc_final: 0.8177 (tmm) REVERT: Y 54 GLN cc_start: 0.8539 (tt0) cc_final: 0.8107 (tt0) REVERT: Z 18 PHE cc_start: 0.7790 (t80) cc_final: 0.7139 (t80) REVERT: Z 46 ARG cc_start: 0.8351 (tmt-80) cc_final: 0.8148 (tpt-90) REVERT: Z 54 ARG cc_start: 0.7335 (ttm170) cc_final: 0.6578 (ttm170) REVERT: a 218 MET cc_start: 0.5449 (mtt) cc_final: 0.3995 (mmt) outliers start: 454 outliers final: 245 residues processed: 1900 average time/residue: 2.0638 time to fit residues: 5703.2577 Evaluate side-chains 1927 residues out of total 4908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 281 poor density : 1646 time to evaluate : 6.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 37 SER Chi-restraints excluded: chain b residue 48 ILE Chi-restraints excluded: chain b residue 50 THR Chi-restraints excluded: chain b residue 52 HIS Chi-restraints excluded: chain b residue 70 LYS Chi-restraints excluded: chain b residue 86 ARG Chi-restraints excluded: chain b residue 114 GLN Chi-restraints excluded: chain b residue 152 GLN Chi-restraints excluded: chain b residue 194 VAL Chi-restraints excluded: chain b residue 250 GLN Chi-restraints excluded: chain b residue 256 THR Chi-restraints excluded: chain b residue 260 LYS Chi-restraints excluded: chain b residue 269 ARG Chi-restraints excluded: chain c residue 2 ILE Chi-restraints excluded: chain c residue 9 VAL Chi-restraints excluded: chain c residue 22 ILE Chi-restraints excluded: chain c residue 39 ASP Chi-restraints excluded: chain c residue 95 SER Chi-restraints excluded: chain c residue 97 SER Chi-restraints excluded: chain c residue 104 VAL Chi-restraints excluded: chain c residue 110 THR Chi-restraints excluded: chain c residue 128 ARG Chi-restraints excluded: chain c residue 133 THR Chi-restraints excluded: chain c residue 157 LYS Chi-restraints excluded: chain c residue 170 VAL Chi-restraints excluded: chain c residue 193 VAL Chi-restraints excluded: chain c residue 199 SER Chi-restraints excluded: chain c residue 200 ASP Chi-restraints excluded: chain d residue 65 THR Chi-restraints excluded: chain d residue 72 SER Chi-restraints excluded: chain d residue 88 ARG Chi-restraints excluded: chain d residue 108 ILE Chi-restraints excluded: chain d residue 120 VAL Chi-restraints excluded: chain d residue 131 THR Chi-restraints excluded: chain d residue 157 LEU Chi-restraints excluded: chain d residue 189 THR Chi-restraints excluded: chain e residue 16 MET Chi-restraints excluded: chain e residue 23 SER Chi-restraints excluded: chain e residue 29 ARG Chi-restraints excluded: chain e residue 30 VAL Chi-restraints excluded: chain e residue 33 ILE Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 60 SER Chi-restraints excluded: chain e residue 67 THR Chi-restraints excluded: chain e residue 89 THR Chi-restraints excluded: chain e residue 117 SER Chi-restraints excluded: chain e residue 126 ASN Chi-restraints excluded: chain e residue 152 ASP Chi-restraints excluded: chain e residue 157 THR Chi-restraints excluded: chain f residue 1 SER Chi-restraints excluded: chain f residue 8 VAL Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 17 LYS Chi-restraints excluded: chain f residue 89 VAL Chi-restraints excluded: chain f residue 105 SER Chi-restraints excluded: chain f residue 126 THR Chi-restraints excluded: chain f residue 130 ILE Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain g residue 96 THR Chi-restraints excluded: chain g residue 115 VAL Chi-restraints excluded: chain g residue 117 LEU Chi-restraints excluded: chain h residue 3 LEU Chi-restraints excluded: chain h residue 128 THR Chi-restraints excluded: chain i residue 12 VAL Chi-restraints excluded: chain i residue 107 GLU Chi-restraints excluded: chain j residue 32 LEU Chi-restraints excluded: chain j residue 54 ILE Chi-restraints excluded: chain j residue 73 VAL Chi-restraints excluded: chain j residue 131 ASN Chi-restraints excluded: chain k residue 28 SER Chi-restraints excluded: chain k residue 65 THR Chi-restraints excluded: chain k residue 86 LEU Chi-restraints excluded: chain l residue 5 THR Chi-restraints excluded: chain l residue 12 SER Chi-restraints excluded: chain l residue 42 SER Chi-restraints excluded: chain l residue 85 VAL Chi-restraints excluded: chain l residue 110 VAL Chi-restraints excluded: chain l residue 111 ILE Chi-restraints excluded: chain l residue 118 THR Chi-restraints excluded: chain l residue 120 VAL Chi-restraints excluded: chain l residue 121 THR Chi-restraints excluded: chain l residue 122 VAL Chi-restraints excluded: chain m residue 6 ARG Chi-restraints excluded: chain m residue 12 MET Chi-restraints excluded: chain m residue 24 THR Chi-restraints excluded: chain m residue 42 THR Chi-restraints excluded: chain m residue 54 THR Chi-restraints excluded: chain m residue 67 VAL Chi-restraints excluded: chain m residue 74 THR Chi-restraints excluded: chain m residue 78 LEU Chi-restraints excluded: chain m residue 93 VAL Chi-restraints excluded: chain m residue 97 GLN Chi-restraints excluded: chain m residue 112 LEU Chi-restraints excluded: chain m residue 118 LYS Chi-restraints excluded: chain m residue 126 ILE Chi-restraints excluded: chain m residue 132 THR Chi-restraints excluded: chain n residue 18 GLN Chi-restraints excluded: chain n residue 27 SER Chi-restraints excluded: chain n residue 37 THR Chi-restraints excluded: chain n residue 53 THR Chi-restraints excluded: chain n residue 73 ASN Chi-restraints excluded: chain n residue 75 ILE Chi-restraints excluded: chain o residue 12 THR Chi-restraints excluded: chain o residue 19 GLN Chi-restraints excluded: chain o residue 35 ILE Chi-restraints excluded: chain o residue 39 VAL Chi-restraints excluded: chain o residue 48 LEU Chi-restraints excluded: chain o residue 65 THR Chi-restraints excluded: chain o residue 95 SER Chi-restraints excluded: chain o residue 103 VAL Chi-restraints excluded: chain p residue 65 ASN Chi-restraints excluded: chain p residue 91 VAL Chi-restraints excluded: chain p residue 93 LYS Chi-restraints excluded: chain p residue 110 LYS Chi-restraints excluded: chain q residue 16 ILE Chi-restraints excluded: chain q residue 50 ARG Chi-restraints excluded: chain q residue 73 ILE Chi-restraints excluded: chain q residue 74 SER Chi-restraints excluded: chain q residue 82 LEU Chi-restraints excluded: chain q residue 109 VAL Chi-restraints excluded: chain r residue 22 LEU Chi-restraints excluded: chain r residue 33 VAL Chi-restraints excluded: chain r residue 47 VAL Chi-restraints excluded: chain r residue 101 ILE Chi-restraints excluded: chain s residue 3 THR Chi-restraints excluded: chain s residue 7 HIS Chi-restraints excluded: chain s residue 20 VAL Chi-restraints excluded: chain s residue 23 LEU Chi-restraints excluded: chain s residue 74 ILE Chi-restraints excluded: chain s residue 77 ASP Chi-restraints excluded: chain s residue 96 ILE Chi-restraints excluded: chain s residue 104 THR Chi-restraints excluded: chain s residue 106 VAL Chi-restraints excluded: chain s residue 108 SER Chi-restraints excluded: chain t residue 17 SER Chi-restraints excluded: chain t residue 27 SER Chi-restraints excluded: chain t residue 39 THR Chi-restraints excluded: chain t residue 57 VAL Chi-restraints excluded: chain t residue 85 VAL Chi-restraints excluded: chain t residue 87 LEU Chi-restraints excluded: chain u residue 4 ILE Chi-restraints excluded: chain u residue 11 ILE Chi-restraints excluded: chain u residue 24 VAL Chi-restraints excluded: chain u residue 33 VAL Chi-restraints excluded: chain u residue 48 VAL Chi-restraints excluded: chain u residue 82 VAL Chi-restraints excluded: chain v residue 20 LEU Chi-restraints excluded: chain v residue 24 ASN Chi-restraints excluded: chain v residue 45 ASP Chi-restraints excluded: chain v residue 47 VAL Chi-restraints excluded: chain v residue 53 LYS Chi-restraints excluded: chain v residue 62 THR Chi-restraints excluded: chain v residue 64 VAL Chi-restraints excluded: chain v residue 65 VAL Chi-restraints excluded: chain v residue 92 VAL Chi-restraints excluded: chain w residue 34 VAL Chi-restraints excluded: chain w residue 39 THR Chi-restraints excluded: chain w residue 66 GLU Chi-restraints excluded: chain w residue 68 LYS Chi-restraints excluded: chain w residue 76 ILE Chi-restraints excluded: chain x residue 1 SER Chi-restraints excluded: chain x residue 7 THR Chi-restraints excluded: chain x residue 13 THR Chi-restraints excluded: chain x residue 33 HIS Chi-restraints excluded: chain x residue 39 VAL Chi-restraints excluded: chain x residue 46 VAL Chi-restraints excluded: chain x residue 47 THR Chi-restraints excluded: chain x residue 64 ASP Chi-restraints excluded: chain y residue 27 ASN Chi-restraints excluded: chain y residue 30 MET Chi-restraints excluded: chain y residue 34 SER Chi-restraints excluded: chain y residue 39 GLN Chi-restraints excluded: chain y residue 40 SER Chi-restraints excluded: chain y residue 55 THR Chi-restraints excluded: chain z residue 40 THR Chi-restraints excluded: chain z residue 56 VAL Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 35 GLU Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 41 ARG Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain F residue 35 GLN Chi-restraints excluded: chain G residue 5 MET Chi-restraints excluded: chain G residue 35 ASN Chi-restraints excluded: chain G residue 120 SER Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 158 ASP Chi-restraints excluded: chain G residue 188 THR Chi-restraints excluded: chain G residue 198 VAL Chi-restraints excluded: chain G residue 216 VAL Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 20 THR Chi-restraints excluded: chain H residue 43 THR Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain H residue 117 ASP Chi-restraints excluded: chain H residue 118 SER Chi-restraints excluded: chain H residue 128 MET Chi-restraints excluded: chain H residue 164 THR Chi-restraints excluded: chain H residue 174 LEU Chi-restraints excluded: chain I residue 60 VAL Chi-restraints excluded: chain I residue 93 LEU Chi-restraints excluded: chain I residue 118 SER Chi-restraints excluded: chain I residue 133 SER Chi-restraints excluded: chain I residue 194 ILE Chi-restraints excluded: chain J residue 13 LYS Chi-restraints excluded: chain J residue 65 LYS Chi-restraints excluded: chain J residue 105 ILE Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 147 ASN Chi-restraints excluded: chain K residue 15 SER Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 26 THR Chi-restraints excluded: chain K residue 39 LEU Chi-restraints excluded: chain K residue 84 VAL Chi-restraints excluded: chain K residue 86 ARG Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain L residue 31 VAL Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain L residue 139 ASP Chi-restraints excluded: chain M residue 6 ILE Chi-restraints excluded: chain M residue 11 THR Chi-restraints excluded: chain M residue 57 GLU Chi-restraints excluded: chain M residue 58 LEU Chi-restraints excluded: chain M residue 61 THR Chi-restraints excluded: chain N residue 28 VAL Chi-restraints excluded: chain N residue 60 LEU Chi-restraints excluded: chain N residue 84 ARG Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain O residue 50 THR Chi-restraints excluded: chain O residue 91 ASP Chi-restraints excluded: chain P residue 25 SER Chi-restraints excluded: chain P residue 45 THR Chi-restraints excluded: chain P residue 54 SER Chi-restraints excluded: chain P residue 86 LYS Chi-restraints excluded: chain Q residue 32 VAL Chi-restraints excluded: chain Q residue 34 THR Chi-restraints excluded: chain Q residue 40 THR Chi-restraints excluded: chain Q residue 46 SER Chi-restraints excluded: chain Q residue 51 VAL Chi-restraints excluded: chain Q residue 63 THR Chi-restraints excluded: chain Q residue 73 LEU Chi-restraints excluded: chain Q residue 92 VAL Chi-restraints excluded: chain Q residue 97 VAL Chi-restraints excluded: chain Q residue 102 ASP Chi-restraints excluded: chain R residue 20 SER Chi-restraints excluded: chain R residue 24 VAL Chi-restraints excluded: chain R residue 59 VAL Chi-restraints excluded: chain R residue 65 GLU Chi-restraints excluded: chain R residue 94 LEU Chi-restraints excluded: chain T residue 30 LEU Chi-restraints excluded: chain T residue 69 LEU Chi-restraints excluded: chain T residue 80 LEU Chi-restraints excluded: chain V residue 24 ILE Chi-restraints excluded: chain V residue 32 ILE Chi-restraints excluded: chain V residue 38 LYS Chi-restraints excluded: chain V residue 41 THR Chi-restraints excluded: chain V residue 54 ILE Chi-restraints excluded: chain V residue 56 ASP Chi-restraints excluded: chain V residue 71 SER Chi-restraints excluded: chain W residue 35 SER Chi-restraints excluded: chain W residue 42 ARG Chi-restraints excluded: chain W residue 44 THR Chi-restraints excluded: chain X residue 38 THR Chi-restraints excluded: chain X residue 43 MET Chi-restraints excluded: chain X residue 48 ILE Chi-restraints excluded: chain X residue 78 THR Chi-restraints excluded: chain Y residue 22 SER Chi-restraints excluded: chain Y residue 25 SER Chi-restraints excluded: chain Y residue 78 LEU Chi-restraints excluded: chain Y residue 79 THR Chi-restraints excluded: chain Z residue 12 ASP Chi-restraints excluded: chain Z residue 52 VAL Chi-restraints excluded: chain a residue 35 THR Chi-restraints excluded: chain a residue 46 VAL Chi-restraints excluded: chain a residue 53 ARG Chi-restraints excluded: chain a residue 207 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1050 random chunks: chunk 943 optimal weight: 40.0000 chunk 718 optimal weight: 10.0000 chunk 495 optimal weight: 2.9990 chunk 105 optimal weight: 7.9990 chunk 455 optimal weight: 6.9990 chunk 641 optimal weight: 20.0000 chunk 958 optimal weight: 5.9990 chunk 1014 optimal weight: 8.9990 chunk 500 optimal weight: 6.9990 chunk 908 optimal weight: 6.9990 chunk 273 optimal weight: 5.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 94 GLN ** e 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 18 GLN ** g 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 103 ASN m 3 GLN o 29 HIS r 86 GLN r 87 GLN s 57 ASN s 61 ASN u 39 ASN u 65 GLN v 12 GLN x 16 ASN y 15 ASN y 20 ASN y 27 ASN ** y 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 3 GLN E 27 ASN G 38 HIS G 177 ASN H 122 GLN ** H 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 53 GLN ** I 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 119 HIS ** J 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 11 HIS K 52 ASN ** N 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 56 HIS Q 4 ASN ** S 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 27 GLN ** T 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 12 GLN ** Y 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 67 HIS Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.3197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.096 161399 Z= 0.366 Angle : 0.675 15.966 241370 Z= 0.347 Chirality : 0.040 0.334 30856 Planarity : 0.005 0.078 13007 Dihedral : 23.074 179.452 80584 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.34 % Allowed : 8.30 % Favored : 91.37 % Rotamer: Outliers : 8.15 % Allowed : 28.08 % Favored : 63.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.38 (0.10), residues: 5919 helix: -0.72 (0.12), residues: 1866 sheet: -1.73 (0.15), residues: 1075 loop : -2.07 (0.11), residues: 2978 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP G 103 HIS 0.008 0.001 HIS f 44 PHE 0.025 0.002 PHE Z 36 TYR 0.030 0.002 TYR G 212 ARG 0.012 0.001 ARG r 80 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11838 Ramachandran restraints generated. 5919 Oldfield, 0 Emsley, 5919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11838 Ramachandran restraints generated. 5919 Oldfield, 0 Emsley, 5919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2121 residues out of total 4908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 400 poor density : 1721 time to evaluate : 6.581 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: b 22 GLU cc_start: 0.8045 (pp20) cc_final: 0.7820 (pp20) REVERT: b 86 ARG cc_start: 0.9078 (OUTLIER) cc_final: 0.8237 (mtm-85) REVERT: b 97 ASP cc_start: 0.8870 (p0) cc_final: 0.8598 (p0) REVERT: b 114 GLN cc_start: 0.8770 (OUTLIER) cc_final: 0.8357 (tt0) REVERT: b 152 GLN cc_start: 0.8634 (OUTLIER) cc_final: 0.7823 (mm110) REVERT: b 250 GLN cc_start: 0.8797 (OUTLIER) cc_final: 0.8016 (tt0) REVERT: c 1 MET cc_start: 0.8738 (tmm) cc_final: 0.8357 (tmm) REVERT: c 128 ARG cc_start: 0.8271 (OUTLIER) cc_final: 0.7704 (mtp180) REVERT: c 167 ASN cc_start: 0.9393 (t0) cc_final: 0.9045 (t160) REVERT: d 30 GLN cc_start: 0.8980 (tp40) cc_final: 0.8120 (tt0) REVERT: d 51 GLU cc_start: 0.8071 (pm20) cc_final: 0.7838 (pm20) REVERT: d 88 ARG cc_start: 0.8484 (OUTLIER) cc_final: 0.8122 (mmp80) REVERT: d 111 GLU cc_start: 0.8006 (tp30) cc_final: 0.7398 (tp30) REVERT: d 163 ASN cc_start: 0.9007 (t0) cc_final: 0.8459 (t0) REVERT: e 16 MET cc_start: 0.8195 (OUTLIER) cc_final: 0.7879 (mmm) REVERT: e 25 MET cc_start: 0.8846 (ppp) cc_final: 0.7805 (ppp) REVERT: e 29 ARG cc_start: 0.8634 (OUTLIER) cc_final: 0.8230 (ptp-170) REVERT: e 33 ILE cc_start: 0.9023 (OUTLIER) cc_final: 0.8762 (pt) REVERT: e 36 ASN cc_start: 0.7205 (t0) cc_final: 0.6905 (t0) REVERT: e 41 GLU cc_start: 0.7814 (tp30) cc_final: 0.7533 (tp30) REVERT: e 95 MET cc_start: 0.8882 (ppp) cc_final: 0.8483 (ppp) REVERT: e 99 PHE cc_start: 0.9114 (t80) cc_final: 0.8811 (t80) REVERT: e 100 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.8073 (mp0) REVERT: e 133 GLU cc_start: 0.7748 (tp30) cc_final: 0.7514 (tp30) REVERT: e 153 ILE cc_start: 0.9198 (mt) cc_final: 0.8837 (pp) REVERT: f 2 ARG cc_start: 0.8247 (mtt-85) cc_final: 0.7823 (ttm170) REVERT: f 19 ASN cc_start: 0.8745 (t0) cc_final: 0.8516 (t0) REVERT: f 21 GLN cc_start: 0.8330 (tp-100) cc_final: 0.8111 (tp-100) REVERT: f 68 ARG cc_start: 0.8995 (tmt170) cc_final: 0.8753 (tmt-80) REVERT: f 82 PHE cc_start: 0.8290 (m-80) cc_final: 0.7751 (m-80) REVERT: f 100 ASN cc_start: 0.8474 (p0) cc_final: 0.7938 (p0) REVERT: f 113 ASP cc_start: 0.8081 (m-30) cc_final: 0.7849 (m-30) REVERT: f 129 GLU cc_start: 0.8548 (tt0) cc_final: 0.8172 (tp30) REVERT: g 4 ILE cc_start: 0.8901 (tp) cc_final: 0.8580 (mm) REVERT: g 7 ASP cc_start: 0.8660 (OUTLIER) cc_final: 0.8428 (t0) REVERT: g 8 LYS cc_start: 0.8761 (mtpp) cc_final: 0.8014 (tptt) REVERT: g 25 TYR cc_start: 0.8898 (t80) cc_final: 0.8480 (t80) REVERT: g 35 LYS cc_start: 0.8745 (mptt) cc_final: 0.8498 (mptp) REVERT: g 117 LEU cc_start: 0.7066 (OUTLIER) cc_final: 0.6759 (pt) REVERT: h 5 LEU cc_start: 0.9166 (OUTLIER) cc_final: 0.8872 (pt) REVERT: i 107 GLU cc_start: 0.8303 (OUTLIER) cc_final: 0.8086 (tm-30) REVERT: j 13 ARG cc_start: 0.8354 (mtt90) cc_final: 0.8055 (mtt90) REVERT: j 71 ASP cc_start: 0.8479 (m-30) cc_final: 0.8261 (m-30) REVERT: j 95 ARG cc_start: 0.7924 (ttp-170) cc_final: 0.7658 (ttp80) REVERT: k 12 ASP cc_start: 0.8369 (p0) cc_final: 0.8094 (p0) REVERT: k 108 ARG cc_start: 0.7927 (OUTLIER) cc_final: 0.7380 (mtm110) REVERT: k 111 LYS cc_start: 0.9251 (ptmt) cc_final: 0.8942 (ptmt) REVERT: l 76 GLU cc_start: 0.7487 (mt-10) cc_final: 0.7093 (mt-10) REVERT: l 82 LEU cc_start: 0.9384 (tp) cc_final: 0.9050 (tm) REVERT: l 99 ASN cc_start: 0.8769 (t0) cc_final: 0.8500 (t0) REVERT: l 105 ILE cc_start: 0.9048 (mm) cc_final: 0.8846 (mm) REVERT: m 17 ASN cc_start: 0.8633 (t0) cc_final: 0.7828 (t0) REVERT: m 88 ASN cc_start: 0.8602 (m-40) cc_final: 0.8296 (m110) REVERT: m 91 TYR cc_start: 0.9058 (p90) cc_final: 0.8527 (p90) REVERT: m 110 GLU cc_start: 0.8283 (tm-30) cc_final: 0.7915 (tm-30) REVERT: m 115 GLU cc_start: 0.8681 (OUTLIER) cc_final: 0.8470 (pp20) REVERT: n 35 LYS cc_start: 0.8875 (tttt) cc_final: 0.8650 (tptt) REVERT: n 72 ASP cc_start: 0.8811 (t0) cc_final: 0.8489 (t0) REVERT: o 17 LYS cc_start: 0.9285 (tppt) cc_final: 0.9066 (tppt) REVERT: o 19 GLN cc_start: 0.8952 (OUTLIER) cc_final: 0.8555 (tp-100) REVERT: o 38 GLN cc_start: 0.8881 (pt0) cc_final: 0.7900 (pm20) REVERT: o 46 GLU cc_start: 0.8276 (pm20) cc_final: 0.7969 (pm20) REVERT: o 80 GLU cc_start: 0.8877 (tm-30) cc_final: 0.8617 (tm-30) REVERT: p 23 ASP cc_start: 0.8561 (m-30) cc_final: 0.8100 (m-30) REVERT: p 26 GLU cc_start: 0.7915 (tm-30) cc_final: 0.7668 (tm-30) REVERT: p 65 ASN cc_start: 0.8909 (OUTLIER) cc_final: 0.8561 (p0) REVERT: q 50 ARG cc_start: 0.8885 (OUTLIER) cc_final: 0.8059 (mmt90) REVERT: q 96 ASP cc_start: 0.8331 (t0) cc_final: 0.7776 (t0) REVERT: q 101 ASP cc_start: 0.8264 (t70) cc_final: 0.7833 (t0) REVERT: r 1 MET cc_start: 0.7149 (tpp) cc_final: 0.6949 (tpp) REVERT: r 13 ARG cc_start: 0.8833 (ttp80) cc_final: 0.8171 (ttt-90) REVERT: r 31 GLU cc_start: 0.7967 (mp0) cc_final: 0.7705 (mp0) REVERT: r 37 GLU cc_start: 0.7898 (pm20) cc_final: 0.7651 (pm20) REVERT: r 60 LYS cc_start: 0.8923 (mtmm) cc_final: 0.8467 (mmmm) REVERT: s 61 ASN cc_start: 0.8798 (m-40) cc_final: 0.8400 (m-40) REVERT: t 1 MET cc_start: 0.7640 (OUTLIER) cc_final: 0.7184 (ptp) REVERT: t 5 GLU cc_start: 0.8426 (mt-10) cc_final: 0.8099 (pm20) REVERT: t 28 ASN cc_start: 0.8797 (t0) cc_final: 0.8401 (t0) REVERT: t 36 LYS cc_start: 0.8480 (tptp) cc_final: 0.8257 (tptt) REVERT: t 86 THR cc_start: 0.9058 (m) cc_final: 0.8728 (p) REVERT: t 91 GLN cc_start: 0.8872 (mm-40) cc_final: 0.8554 (mm-40) REVERT: u 33 VAL cc_start: 0.9456 (m) cc_final: 0.9195 (t) REVERT: u 36 GLU cc_start: 0.8680 (pp20) cc_final: 0.8441 (pp20) REVERT: u 61 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.7821 (mt-10) REVERT: u 82 VAL cc_start: 0.9385 (OUTLIER) cc_final: 0.9172 (m) REVERT: v 38 LEU cc_start: 0.9015 (tp) cc_final: 0.8766 (tp) REVERT: v 40 ILE cc_start: 0.8916 (OUTLIER) cc_final: 0.8691 (pt) REVERT: v 41 GLU cc_start: 0.8234 (tt0) cc_final: 0.7830 (tm-30) REVERT: v 46 LYS cc_start: 0.9176 (mmtm) cc_final: 0.8695 (mmpt) REVERT: v 50 MET cc_start: 0.8621 (mtm) cc_final: 0.8241 (mtt) REVERT: v 87 GLN cc_start: 0.8563 (mt0) cc_final: 0.8089 (mt0) REVERT: w 16 ARG cc_start: 0.8740 (mpt-90) cc_final: 0.7848 (mmt90) REVERT: w 51 ARG cc_start: 0.9118 (OUTLIER) cc_final: 0.8702 (ppp80) REVERT: x 61 LYS cc_start: 0.8922 (mttt) cc_final: 0.8685 (mtmt) REVERT: x 69 GLU cc_start: 0.8931 (OUTLIER) cc_final: 0.8543 (mt-10) REVERT: y 1 MET cc_start: 0.6641 (tpt) cc_final: 0.6337 (tpt) REVERT: y 27 ASN cc_start: 0.8902 (OUTLIER) cc_final: 0.8585 (m-40) REVERT: y 31 GLN cc_start: 0.8959 (mt0) cc_final: 0.8753 (mp10) REVERT: y 39 GLN cc_start: 0.8421 (OUTLIER) cc_final: 0.7855 (mt0) REVERT: z 4 ILE cc_start: 0.8697 (tt) cc_final: 0.8419 (mt) REVERT: B 3 GLN cc_start: 0.8515 (pt0) cc_final: 0.8160 (pt0) REVERT: B 5 ASN cc_start: 0.8990 (m-40) cc_final: 0.8585 (m-40) REVERT: B 36 LYS cc_start: 0.9150 (mmtp) cc_final: 0.8727 (mmtt) REVERT: C 36 LYS cc_start: 0.8713 (ttpt) cc_final: 0.8363 (mtpp) REVERT: D 28 ARG cc_start: 0.8959 (mtm-85) cc_final: 0.8706 (mtm180) REVERT: D 41 ARG cc_start: 0.8040 (OUTLIER) cc_final: 0.7590 (mtp180) REVERT: E 15 LYS cc_start: 0.8736 (tptp) cc_final: 0.8462 (tptp) REVERT: F 17 VAL cc_start: 0.9166 (p) cc_final: 0.8903 (m) REVERT: F 24 ARG cc_start: 0.8929 (mtt-85) cc_final: 0.8532 (mtt-85) REVERT: G 5 MET cc_start: 0.8144 (OUTLIER) cc_final: 0.7705 (mpp) REVERT: G 18 GLN cc_start: 0.8769 (mt0) cc_final: 0.8329 (mp10) REVERT: G 26 MET cc_start: 0.8348 (mmm) cc_final: 0.7999 (mmm) REVERT: G 150 ILE cc_start: 0.9135 (OUTLIER) cc_final: 0.8882 (tt) REVERT: G 172 ILE cc_start: 0.9379 (pt) cc_final: 0.9168 (pp) REVERT: H 5 HIS cc_start: 0.9010 (t-90) cc_final: 0.8640 (t-90) REVERT: H 39 ARG cc_start: 0.8681 (ttm-80) cc_final: 0.7880 (mtt90) REVERT: H 57 GLU cc_start: 0.8990 (OUTLIER) cc_final: 0.8403 (mt-10) REVERT: H 139 ASN cc_start: 0.8910 (m-40) cc_final: 0.8461 (m110) REVERT: H 151 GLU cc_start: 0.8229 (tm-30) cc_final: 0.7740 (tm-30) REVERT: H 184 ASN cc_start: 0.8763 (OUTLIER) cc_final: 0.8514 (t160) REVERT: H 191 THR cc_start: 0.9254 (p) cc_final: 0.8875 (t) REVERT: I 68 GLU cc_start: 0.8294 (tp30) cc_final: 0.7835 (tp30) REVERT: I 71 PHE cc_start: 0.9158 (t80) cc_final: 0.8605 (t80) REVERT: I 73 ASN cc_start: 0.9461 (m110) cc_final: 0.8970 (m110) REVERT: I 76 LYS cc_start: 0.8847 (mtmm) cc_final: 0.8358 (mppt) REVERT: I 112 GLU cc_start: 0.7332 (tt0) cc_final: 0.6929 (tt0) REVERT: I 137 SER cc_start: 0.8251 (t) cc_final: 0.7836 (p) REVERT: I 152 SER cc_start: 0.8857 (t) cc_final: 0.8613 (p) REVERT: J 30 PHE cc_start: 0.9137 (m-80) cc_final: 0.8642 (m-80) REVERT: J 32 PHE cc_start: 0.9099 (m-80) cc_final: 0.8664 (m-80) REVERT: J 60 GLN cc_start: 0.8799 (tp-100) cc_final: 0.8418 (tp40) REVERT: J 70 MET cc_start: 0.7965 (tpt) cc_final: 0.7757 (mmm) REVERT: J 85 LYS cc_start: 0.8707 (mptt) cc_final: 0.8445 (mptp) REVERT: J 94 PHE cc_start: 0.8261 (t80) cc_final: 0.7664 (t80) REVERT: J 131 ASN cc_start: 0.8117 (t0) cc_final: 0.7695 (t0) REVERT: J 146 MET cc_start: 0.8388 (OUTLIER) cc_final: 0.7751 (ttp) REVERT: K 1 MET cc_start: 0.7033 (ttm) cc_final: 0.6819 (ttm) REVERT: K 44 ARG cc_start: 0.8283 (ttp-170) cc_final: 0.7795 (ttm-80) REVERT: K 56 LYS cc_start: 0.8583 (mmtt) cc_final: 0.8013 (mmpt) REVERT: K 90 MET cc_start: 0.7834 (mtm) cc_final: 0.7500 (mpp) REVERT: L 105 GLU cc_start: 0.8416 (pp20) cc_final: 0.8034 (pp20) REVERT: M 26 MET cc_start: 0.8561 (ptp) cc_final: 0.8119 (pmm) REVERT: M 28 SER cc_start: 0.8600 (p) cc_final: 0.8283 (p) REVERT: M 37 ASN cc_start: 0.8739 (t0) cc_final: 0.8452 (t0) REVERT: M 57 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7757 (pp20) REVERT: M 110 MET cc_start: 0.8552 (ptp) cc_final: 0.8345 (ptp) REVERT: N 20 ILE cc_start: 0.9123 (tt) cc_final: 0.8672 (tp) REVERT: N 21 LYS cc_start: 0.9004 (mtpt) cc_final: 0.8590 (mmpt) REVERT: N 27 ILE cc_start: 0.8920 (mp) cc_final: 0.8485 (mm) REVERT: N 49 GLN cc_start: 0.9173 (tt0) cc_final: 0.8751 (tm-30) REVERT: N 123 ARG cc_start: 0.8640 (mmt90) cc_final: 0.8195 (tpp80) REVERT: O 9 ARG cc_start: 0.8259 (ttm-80) cc_final: 0.7871 (ttp-170) REVERT: P 60 PHE cc_start: 0.9111 (t80) cc_final: 0.8721 (t80) REVERT: P 84 MET cc_start: 0.7399 (ptm) cc_final: 0.7038 (ppp) REVERT: Q 37 TYR cc_start: 0.8217 (p90) cc_final: 0.7834 (p90) REVERT: Q 43 LYS cc_start: 0.8786 (mmmt) cc_final: 0.8476 (mmtt) REVERT: Q 72 ASN cc_start: 0.8604 (OUTLIER) cc_final: 0.8117 (p0) REVERT: Q 88 ASP cc_start: 0.8452 (m-30) cc_final: 0.7666 (m-30) REVERT: R 15 VAL cc_start: 0.8170 (m) cc_final: 0.7910 (t) REVERT: R 43 LYS cc_start: 0.8555 (ptpt) cc_final: 0.8233 (ptpp) REVERT: R 52 ILE cc_start: 0.8955 (mt) cc_final: 0.8404 (mp) REVERT: R 73 SER cc_start: 0.9217 (t) cc_final: 0.8948 (m) REVERT: R 76 ILE cc_start: 0.9452 (pp) cc_final: 0.9181 (pp) REVERT: R 77 LYS cc_start: 0.9183 (tttm) cc_final: 0.8544 (tppt) REVERT: T 23 SER cc_start: 0.9025 (t) cc_final: 0.8809 (t) REVERT: T 25 GLU cc_start: 0.8568 (mt-10) cc_final: 0.8355 (mt-10) REVERT: T 36 ASN cc_start: 0.8864 (m110) cc_final: 0.8343 (m-40) REVERT: T 48 ASP cc_start: 0.8480 (t0) cc_final: 0.8060 (t0) REVERT: T 51 SER cc_start: 0.9133 (p) cc_final: 0.8827 (p) REVERT: T 76 ARG cc_start: 0.8538 (mtm180) cc_final: 0.8166 (ttm110) REVERT: T 79 GLN cc_start: 0.8828 (tp40) cc_final: 0.8594 (tp-100) REVERT: U 18 GLN cc_start: 0.8227 (mt0) cc_final: 0.7582 (mt0) REVERT: U 39 PHE cc_start: 0.9058 (t80) cc_final: 0.8357 (t80) REVERT: V 16 MET cc_start: 0.7452 (ttt) cc_final: 0.7159 (ttt) REVERT: V 44 HIS cc_start: 0.8166 (m90) cc_final: 0.7947 (m90) REVERT: V 61 ARG cc_start: 0.8107 (ppp80) cc_final: 0.7697 (ppp80) REVERT: V 80 LYS cc_start: 0.8689 (tmtt) cc_final: 0.8201 (tptt) REVERT: W 23 LYS cc_start: 0.9140 (mtmm) cc_final: 0.8833 (pptt) REVERT: W 24 ASP cc_start: 0.8477 (t70) cc_final: 0.8175 (t0) REVERT: W 42 ARG cc_start: 0.9087 (OUTLIER) cc_final: 0.8755 (mtm110) REVERT: W 51 GLN cc_start: 0.8767 (tp40) cc_final: 0.7612 (tm-30) REVERT: X 10 ILE cc_start: 0.9114 (pt) cc_final: 0.8460 (mm) REVERT: X 36 ARG cc_start: 0.8645 (OUTLIER) cc_final: 0.7529 (ptm-80) REVERT: Y 15 LYS cc_start: 0.8903 (tttm) cc_final: 0.8294 (tptp) REVERT: Y 17 ARG cc_start: 0.8815 (tmm-80) cc_final: 0.8205 (ttp-110) REVERT: Y 26 MET cc_start: 0.9253 (OUTLIER) cc_final: 0.8918 (ppp) REVERT: Y 27 MET cc_start: 0.8015 (ppp) cc_final: 0.7796 (tmt) REVERT: Y 28 ARG cc_start: 0.8376 (mtt180) cc_final: 0.7993 (mtt-85) REVERT: Y 50 PHE cc_start: 0.8805 (t80) cc_final: 0.8501 (t80) REVERT: Y 53 MET cc_start: 0.8431 (ppp) cc_final: 0.8192 (tmm) REVERT: Y 54 GLN cc_start: 0.8482 (tt0) cc_final: 0.7987 (tt0) REVERT: Z 9 GLU cc_start: 0.7243 (OUTLIER) cc_final: 0.7015 (tm-30) REVERT: a 16 ASP cc_start: 0.2100 (OUTLIER) cc_final: 0.1728 (t70) REVERT: a 218 MET cc_start: 0.5295 (mtt) cc_final: 0.3848 (mmt) outliers start: 400 outliers final: 226 residues processed: 1873 average time/residue: 2.0418 time to fit residues: 5575.8794 Evaluate side-chains 1915 residues out of total 4908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 266 poor density : 1649 time to evaluate : 6.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 37 SER Chi-restraints excluded: chain b residue 48 ILE Chi-restraints excluded: chain b residue 50 THR Chi-restraints excluded: chain b residue 52 HIS Chi-restraints excluded: chain b residue 86 ARG Chi-restraints excluded: chain b residue 114 GLN Chi-restraints excluded: chain b residue 140 VAL Chi-restraints excluded: chain b residue 152 GLN Chi-restraints excluded: chain b residue 250 GLN Chi-restraints excluded: chain b residue 269 ARG Chi-restraints excluded: chain c residue 22 ILE Chi-restraints excluded: chain c residue 39 ASP Chi-restraints excluded: chain c residue 95 SER Chi-restraints excluded: chain c residue 110 THR Chi-restraints excluded: chain c residue 128 ARG Chi-restraints excluded: chain c residue 157 LYS Chi-restraints excluded: chain c residue 170 VAL Chi-restraints excluded: chain c residue 199 SER Chi-restraints excluded: chain c residue 200 ASP Chi-restraints excluded: chain d residue 48 THR Chi-restraints excluded: chain d residue 53 THR Chi-restraints excluded: chain d residue 72 SER Chi-restraints excluded: chain d residue 88 ARG Chi-restraints excluded: chain d residue 108 ILE Chi-restraints excluded: chain d residue 146 VAL Chi-restraints excluded: chain d residue 157 LEU Chi-restraints excluded: chain d residue 189 THR Chi-restraints excluded: chain e residue 16 MET Chi-restraints excluded: chain e residue 23 SER Chi-restraints excluded: chain e residue 24 VAL Chi-restraints excluded: chain e residue 29 ARG Chi-restraints excluded: chain e residue 30 VAL Chi-restraints excluded: chain e residue 33 ILE Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 60 SER Chi-restraints excluded: chain e residue 67 THR Chi-restraints excluded: chain e residue 89 THR Chi-restraints excluded: chain e residue 100 GLU Chi-restraints excluded: chain e residue 117 SER Chi-restraints excluded: chain e residue 126 ASN Chi-restraints excluded: chain e residue 157 THR Chi-restraints excluded: chain e residue 173 ASP Chi-restraints excluded: chain f residue 1 SER Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 17 LYS Chi-restraints excluded: chain f residue 23 ILE Chi-restraints excluded: chain f residue 105 SER Chi-restraints excluded: chain f residue 130 ILE Chi-restraints excluded: chain g residue 6 LEU Chi-restraints excluded: chain g residue 7 ASP Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain g residue 96 THR Chi-restraints excluded: chain g residue 115 VAL Chi-restraints excluded: chain g residue 117 LEU Chi-restraints excluded: chain g residue 133 GLN Chi-restraints excluded: chain h residue 3 LEU Chi-restraints excluded: chain h residue 5 LEU Chi-restraints excluded: chain i residue 12 VAL Chi-restraints excluded: chain i residue 35 MET Chi-restraints excluded: chain i residue 107 GLU Chi-restraints excluded: chain j residue 54 ILE Chi-restraints excluded: chain j residue 73 VAL Chi-restraints excluded: chain j residue 131 ASN Chi-restraints excluded: chain k residue 28 SER Chi-restraints excluded: chain k residue 65 THR Chi-restraints excluded: chain k residue 69 VAL Chi-restraints excluded: chain k residue 80 ASP Chi-restraints excluded: chain k residue 108 ARG Chi-restraints excluded: chain k residue 117 SER Chi-restraints excluded: chain k residue 118 LEU Chi-restraints excluded: chain l residue 5 THR Chi-restraints excluded: chain l residue 12 SER Chi-restraints excluded: chain l residue 85 VAL Chi-restraints excluded: chain l residue 110 VAL Chi-restraints excluded: chain l residue 118 THR Chi-restraints excluded: chain l residue 120 VAL Chi-restraints excluded: chain l residue 121 THR Chi-restraints excluded: chain l residue 122 VAL Chi-restraints excluded: chain l residue 127 VAL Chi-restraints excluded: chain m residue 12 MET Chi-restraints excluded: chain m residue 54 THR Chi-restraints excluded: chain m residue 74 THR Chi-restraints excluded: chain m residue 78 LEU Chi-restraints excluded: chain m residue 93 VAL Chi-restraints excluded: chain m residue 115 GLU Chi-restraints excluded: chain m residue 118 LYS Chi-restraints excluded: chain m residue 126 ILE Chi-restraints excluded: chain m residue 132 THR Chi-restraints excluded: chain n residue 15 SER Chi-restraints excluded: chain n residue 27 SER Chi-restraints excluded: chain n residue 73 ASN Chi-restraints excluded: chain n residue 75 ILE Chi-restraints excluded: chain o residue 12 THR Chi-restraints excluded: chain o residue 19 GLN Chi-restraints excluded: chain o residue 21 LEU Chi-restraints excluded: chain o residue 35 ILE Chi-restraints excluded: chain o residue 40 ILE Chi-restraints excluded: chain o residue 48 LEU Chi-restraints excluded: chain o residue 65 THR Chi-restraints excluded: chain o residue 95 SER Chi-restraints excluded: chain o residue 103 VAL Chi-restraints excluded: chain o residue 112 GLU Chi-restraints excluded: chain p residue 2 ASN Chi-restraints excluded: chain p residue 63 ILE Chi-restraints excluded: chain p residue 65 ASN Chi-restraints excluded: chain p residue 91 VAL Chi-restraints excluded: chain p residue 93 LYS Chi-restraints excluded: chain q residue 16 ILE Chi-restraints excluded: chain q residue 50 ARG Chi-restraints excluded: chain q residue 82 LEU Chi-restraints excluded: chain q residue 109 VAL Chi-restraints excluded: chain r residue 33 VAL Chi-restraints excluded: chain r residue 38 VAL Chi-restraints excluded: chain r residue 47 VAL Chi-restraints excluded: chain s residue 20 VAL Chi-restraints excluded: chain s residue 23 LEU Chi-restraints excluded: chain s residue 77 ASP Chi-restraints excluded: chain s residue 104 THR Chi-restraints excluded: chain s residue 106 VAL Chi-restraints excluded: chain s residue 108 SER Chi-restraints excluded: chain t residue 1 MET Chi-restraints excluded: chain t residue 17 SER Chi-restraints excluded: chain t residue 57 VAL Chi-restraints excluded: chain t residue 85 VAL Chi-restraints excluded: chain t residue 87 LEU Chi-restraints excluded: chain u residue 4 ILE Chi-restraints excluded: chain u residue 11 ILE Chi-restraints excluded: chain u residue 24 VAL Chi-restraints excluded: chain u residue 61 GLU Chi-restraints excluded: chain u residue 82 VAL Chi-restraints excluded: chain v residue 20 LEU Chi-restraints excluded: chain v residue 40 ILE Chi-restraints excluded: chain v residue 45 ASP Chi-restraints excluded: chain v residue 61 LEU Chi-restraints excluded: chain v residue 64 VAL Chi-restraints excluded: chain v residue 65 VAL Chi-restraints excluded: chain v residue 73 LYS Chi-restraints excluded: chain v residue 92 VAL Chi-restraints excluded: chain w residue 32 ILE Chi-restraints excluded: chain w residue 34 VAL Chi-restraints excluded: chain w residue 39 THR Chi-restraints excluded: chain w residue 51 ARG Chi-restraints excluded: chain w residue 66 GLU Chi-restraints excluded: chain w residue 68 LYS Chi-restraints excluded: chain w residue 76 ILE Chi-restraints excluded: chain x residue 1 SER Chi-restraints excluded: chain x residue 13 THR Chi-restraints excluded: chain x residue 33 HIS Chi-restraints excluded: chain x residue 39 VAL Chi-restraints excluded: chain x residue 46 VAL Chi-restraints excluded: chain x residue 47 THR Chi-restraints excluded: chain x residue 64 ASP Chi-restraints excluded: chain x residue 69 GLU Chi-restraints excluded: chain y residue 27 ASN Chi-restraints excluded: chain y residue 30 MET Chi-restraints excluded: chain y residue 39 GLN Chi-restraints excluded: chain y residue 40 SER Chi-restraints excluded: chain y residue 43 LEU Chi-restraints excluded: chain y residue 55 THR Chi-restraints excluded: chain z residue 56 VAL Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 41 ARG Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain G residue 5 MET Chi-restraints excluded: chain G residue 35 ASN Chi-restraints excluded: chain G residue 141 GLU Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 158 ASP Chi-restraints excluded: chain G residue 198 VAL Chi-restraints excluded: chain H residue 9 ILE Chi-restraints excluded: chain H residue 43 THR Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 123 LEU Chi-restraints excluded: chain H residue 164 THR Chi-restraints excluded: chain H residue 174 LEU Chi-restraints excluded: chain H residue 184 ASN Chi-restraints excluded: chain I residue 60 VAL Chi-restraints excluded: chain I residue 93 LEU Chi-restraints excluded: chain I residue 118 SER Chi-restraints excluded: chain I residue 133 SER Chi-restraints excluded: chain J residue 31 SER Chi-restraints excluded: chain J residue 63 MET Chi-restraints excluded: chain J residue 104 ILE Chi-restraints excluded: chain J residue 105 ILE Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 146 MET Chi-restraints excluded: chain K residue 7 VAL Chi-restraints excluded: chain K residue 15 SER Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 39 LEU Chi-restraints excluded: chain K residue 75 GLU Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain L residue 31 VAL Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain L residue 117 LEU Chi-restraints excluded: chain M residue 6 ILE Chi-restraints excluded: chain M residue 57 GLU Chi-restraints excluded: chain M residue 58 LEU Chi-restraints excluded: chain N residue 28 VAL Chi-restraints excluded: chain N residue 53 LEU Chi-restraints excluded: chain N residue 60 LEU Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain O residue 18 ILE Chi-restraints excluded: chain O residue 50 THR Chi-restraints excluded: chain O residue 91 ASP Chi-restraints excluded: chain O residue 92 LEU Chi-restraints excluded: chain P residue 15 VAL Chi-restraints excluded: chain P residue 25 SER Chi-restraints excluded: chain P residue 30 ILE Chi-restraints excluded: chain P residue 45 THR Chi-restraints excluded: chain P residue 54 SER Chi-restraints excluded: chain P residue 86 LYS Chi-restraints excluded: chain Q residue 32 VAL Chi-restraints excluded: chain Q residue 40 THR Chi-restraints excluded: chain Q residue 46 SER Chi-restraints excluded: chain Q residue 51 VAL Chi-restraints excluded: chain Q residue 57 THR Chi-restraints excluded: chain Q residue 63 THR Chi-restraints excluded: chain Q residue 72 ASN Chi-restraints excluded: chain Q residue 73 LEU Chi-restraints excluded: chain Q residue 92 VAL Chi-restraints excluded: chain Q residue 97 VAL Chi-restraints excluded: chain Q residue 102 ASP Chi-restraints excluded: chain R residue 20 SER Chi-restraints excluded: chain R residue 65 GLU Chi-restraints excluded: chain R residue 94 LEU Chi-restraints excluded: chain S residue 47 LEU Chi-restraints excluded: chain T residue 4 THR Chi-restraints excluded: chain T residue 30 LEU Chi-restraints excluded: chain T residue 69 LEU Chi-restraints excluded: chain V residue 24 ILE Chi-restraints excluded: chain V residue 32 ILE Chi-restraints excluded: chain V residue 41 THR Chi-restraints excluded: chain V residue 54 ILE Chi-restraints excluded: chain V residue 56 ASP Chi-restraints excluded: chain V residue 71 SER Chi-restraints excluded: chain V residue 82 VAL Chi-restraints excluded: chain W residue 35 SER Chi-restraints excluded: chain W residue 42 ARG Chi-restraints excluded: chain W residue 43 ILE Chi-restraints excluded: chain W residue 70 THR Chi-restraints excluded: chain X residue 36 ARG Chi-restraints excluded: chain X residue 38 THR Chi-restraints excluded: chain X residue 48 ILE Chi-restraints excluded: chain X residue 78 THR Chi-restraints excluded: chain Y residue 22 SER Chi-restraints excluded: chain Y residue 25 SER Chi-restraints excluded: chain Y residue 26 MET Chi-restraints excluded: chain Y residue 78 LEU Chi-restraints excluded: chain Y residue 79 THR Chi-restraints excluded: chain Z residue 9 GLU Chi-restraints excluded: chain Z residue 12 ASP Chi-restraints excluded: chain Z residue 59 LEU Chi-restraints excluded: chain a residue 16 ASP Chi-restraints excluded: chain a residue 46 VAL Chi-restraints excluded: chain a residue 53 ARG Chi-restraints excluded: chain a residue 207 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1050 random chunks: chunk 845 optimal weight: 8.9990 chunk 576 optimal weight: 40.0000 chunk 14 optimal weight: 2.9990 chunk 755 optimal weight: 10.0000 chunk 418 optimal weight: 7.9990 chunk 866 optimal weight: 7.9990 chunk 701 optimal weight: 20.0000 chunk 1 optimal weight: 5.9990 chunk 518 optimal weight: 7.9990 chunk 910 optimal weight: 4.9990 chunk 256 optimal weight: 10.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 94 GLN ** e 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 63 GLN ** f 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 40 HIS o 29 HIS q 51 GLN r 86 GLN r 87 GLN ** t 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 39 ASN u 65 GLN u 68 ASN v 12 GLN x 16 ASN ** x 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** y 15 ASN y 20 ASN ** y 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 27 ASN H 122 GLN ** H 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 53 GLN I 88 ASN I 99 ASN I 115 GLN I 119 HIS ** J 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 66 GLN O 56 HIS ** P 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 4 ASN R 99 GLN S 65 GLN T 27 GLN ** T 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 55 GLN Y 12 GLN ** Y 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.3399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.094 161399 Z= 0.382 Angle : 0.685 18.475 241370 Z= 0.351 Chirality : 0.040 0.312 30856 Planarity : 0.005 0.070 13007 Dihedral : 23.110 179.353 80582 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.32 % Allowed : 9.73 % Favored : 89.95 % Rotamer: Outliers : 8.94 % Allowed : 29.05 % Favored : 62.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.16 (0.10), residues: 5919 helix: -0.53 (0.12), residues: 1863 sheet: -1.55 (0.15), residues: 1072 loop : -1.97 (0.11), residues: 2984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP G 103 HIS 0.008 0.001 HIS f 44 PHE 0.030 0.002 PHE g 46 TYR 0.030 0.002 TYR K 25 ARG 0.014 0.001 ARG x 10 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11838 Ramachandran restraints generated. 5919 Oldfield, 0 Emsley, 5919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11838 Ramachandran restraints generated. 5919 Oldfield, 0 Emsley, 5919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2106 residues out of total 4908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 439 poor density : 1667 time to evaluate : 6.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 22 GLU cc_start: 0.8077 (pp20) cc_final: 0.7834 (pp20) REVERT: b 86 ARG cc_start: 0.9084 (OUTLIER) cc_final: 0.8247 (mtm-85) REVERT: b 97 ASP cc_start: 0.8825 (p0) cc_final: 0.8507 (p0) REVERT: b 114 GLN cc_start: 0.8773 (OUTLIER) cc_final: 0.8336 (tt0) REVERT: b 152 GLN cc_start: 0.8664 (OUTLIER) cc_final: 0.7897 (mm110) REVERT: b 250 GLN cc_start: 0.8807 (OUTLIER) cc_final: 0.8045 (tt0) REVERT: c 1 MET cc_start: 0.8709 (tmm) cc_final: 0.8433 (tmm) REVERT: c 2 ILE cc_start: 0.8753 (OUTLIER) cc_final: 0.8500 (pp) REVERT: c 128 ARG cc_start: 0.8268 (OUTLIER) cc_final: 0.7666 (mtp180) REVERT: c 167 ASN cc_start: 0.9393 (t0) cc_final: 0.9050 (t160) REVERT: d 30 GLN cc_start: 0.9019 (tp40) cc_final: 0.8160 (tt0) REVERT: d 51 GLU cc_start: 0.8051 (pm20) cc_final: 0.7760 (pm20) REVERT: e 6 TYR cc_start: 0.8504 (t80) cc_final: 0.8186 (t80) REVERT: e 16 MET cc_start: 0.8193 (OUTLIER) cc_final: 0.7970 (mmm) REVERT: e 25 MET cc_start: 0.8877 (ppp) cc_final: 0.7984 (ppp) REVERT: e 29 ARG cc_start: 0.8677 (OUTLIER) cc_final: 0.8188 (ptp-170) REVERT: e 31 GLU cc_start: 0.8327 (mt-10) cc_final: 0.8076 (mm-30) REVERT: e 36 ASN cc_start: 0.7136 (OUTLIER) cc_final: 0.6883 (t0) REVERT: e 41 GLU cc_start: 0.8162 (tp30) cc_final: 0.7921 (tp30) REVERT: e 65 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.8302 (tm) REVERT: e 95 MET cc_start: 0.8938 (ppp) cc_final: 0.8580 (ppp) REVERT: e 99 PHE cc_start: 0.9063 (t80) cc_final: 0.8811 (t80) REVERT: e 100 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.8034 (mp0) REVERT: e 129 MET cc_start: 0.7885 (tmt) cc_final: 0.7676 (tmm) REVERT: e 133 GLU cc_start: 0.7773 (tp30) cc_final: 0.7499 (tp30) REVERT: e 153 ILE cc_start: 0.9224 (mt) cc_final: 0.8925 (pp) REVERT: f 19 ASN cc_start: 0.8770 (t0) cc_final: 0.8525 (t0) REVERT: f 21 GLN cc_start: 0.8352 (tp-100) cc_final: 0.8134 (tp-100) REVERT: f 63 GLN cc_start: 0.8298 (mm-40) cc_final: 0.8032 (mt0) REVERT: f 68 ARG cc_start: 0.8974 (tmt170) cc_final: 0.8728 (tmt-80) REVERT: f 82 PHE cc_start: 0.8198 (m-80) cc_final: 0.7699 (m-80) REVERT: f 100 ASN cc_start: 0.8490 (p0) cc_final: 0.7998 (p0) REVERT: f 129 GLU cc_start: 0.8575 (tt0) cc_final: 0.7985 (tp30) REVERT: g 4 ILE cc_start: 0.8885 (tp) cc_final: 0.8562 (mm) REVERT: g 7 ASP cc_start: 0.8692 (OUTLIER) cc_final: 0.8453 (t0) REVERT: g 8 LYS cc_start: 0.8773 (mtpp) cc_final: 0.8027 (tptt) REVERT: g 25 TYR cc_start: 0.8894 (t80) cc_final: 0.8427 (t80) REVERT: g 35 LYS cc_start: 0.8726 (mptt) cc_final: 0.8473 (mptp) REVERT: g 117 LEU cc_start: 0.7207 (OUTLIER) cc_final: 0.6880 (pt) REVERT: h 5 LEU cc_start: 0.9124 (OUTLIER) cc_final: 0.8874 (pt) REVERT: j 13 ARG cc_start: 0.8348 (mtt90) cc_final: 0.8096 (mtt90) REVERT: j 71 ASP cc_start: 0.8506 (m-30) cc_final: 0.8279 (m-30) REVERT: k 12 ASP cc_start: 0.8390 (p0) cc_final: 0.8119 (p0) REVERT: k 17 ARG cc_start: 0.7904 (OUTLIER) cc_final: 0.7142 (ttm170) REVERT: k 49 ARG cc_start: 0.8165 (OUTLIER) cc_final: 0.7491 (mpp-170) REVERT: k 111 LYS cc_start: 0.9172 (ptmt) cc_final: 0.8874 (ptmt) REVERT: l 76 GLU cc_start: 0.7483 (mt-10) cc_final: 0.7097 (mt-10) REVERT: l 78 ARG cc_start: 0.8453 (OUTLIER) cc_final: 0.8198 (mtp-110) REVERT: l 82 LEU cc_start: 0.9365 (tp) cc_final: 0.9080 (tm) REVERT: l 105 ILE cc_start: 0.9059 (mm) cc_final: 0.8851 (mm) REVERT: l 106 GLU cc_start: 0.7591 (mm-30) cc_final: 0.7380 (mm-30) REVERT: l 143 GLU cc_start: 0.7096 (pp20) cc_final: 0.6781 (pp20) REVERT: m 47 GLU cc_start: 0.8333 (tm-30) cc_final: 0.7930 (tm-30) REVERT: m 88 ASN cc_start: 0.8595 (m-40) cc_final: 0.8291 (m110) REVERT: m 91 TYR cc_start: 0.9121 (p90) cc_final: 0.8611 (p90) REVERT: m 97 GLN cc_start: 0.8620 (OUTLIER) cc_final: 0.8264 (mp-120) REVERT: m 110 GLU cc_start: 0.8272 (tm-30) cc_final: 0.7897 (tm-30) REVERT: n 35 LYS cc_start: 0.8870 (tttt) cc_final: 0.8593 (tptt) REVERT: n 72 ASP cc_start: 0.8826 (t0) cc_final: 0.8505 (t0) REVERT: o 19 GLN cc_start: 0.8858 (OUTLIER) cc_final: 0.8511 (tp-100) REVERT: o 38 GLN cc_start: 0.8837 (pt0) cc_final: 0.7910 (pm20) REVERT: o 80 GLU cc_start: 0.8873 (tm-30) cc_final: 0.8591 (tm-30) REVERT: p 23 ASP cc_start: 0.8551 (m-30) cc_final: 0.8118 (m-30) REVERT: p 26 GLU cc_start: 0.7903 (tm-30) cc_final: 0.7680 (tm-30) REVERT: p 65 ASN cc_start: 0.8911 (OUTLIER) cc_final: 0.8566 (p0) REVERT: q 50 ARG cc_start: 0.8903 (OUTLIER) cc_final: 0.8079 (mmt90) REVERT: q 58 GLN cc_start: 0.8907 (OUTLIER) cc_final: 0.8651 (tm-30) REVERT: q 96 ASP cc_start: 0.8305 (t0) cc_final: 0.7760 (t0) REVERT: q 101 ASP cc_start: 0.8260 (t70) cc_final: 0.7834 (t0) REVERT: r 13 ARG cc_start: 0.8818 (ttp80) cc_final: 0.8175 (ttt-90) REVERT: r 31 GLU cc_start: 0.7895 (mp0) cc_final: 0.7513 (mp0) REVERT: r 37 GLU cc_start: 0.7932 (pm20) cc_final: 0.7670 (pm20) REVERT: r 60 LYS cc_start: 0.8920 (mtmm) cc_final: 0.8472 (mmmm) REVERT: s 52 GLU cc_start: 0.8033 (mm-30) cc_final: 0.7798 (tm-30) REVERT: t 1 MET cc_start: 0.7468 (OUTLIER) cc_final: 0.7106 (ptp) REVERT: t 28 ASN cc_start: 0.8792 (t0) cc_final: 0.8378 (t0) REVERT: t 36 LYS cc_start: 0.8385 (tptp) cc_final: 0.8173 (tptp) REVERT: t 54 GLU cc_start: 0.7602 (pm20) cc_final: 0.7392 (pm20) REVERT: t 86 THR cc_start: 0.9104 (m) cc_final: 0.8669 (p) REVERT: u 33 VAL cc_start: 0.9463 (OUTLIER) cc_final: 0.9198 (t) REVERT: u 36 GLU cc_start: 0.8780 (pp20) cc_final: 0.8528 (pp20) REVERT: u 61 GLU cc_start: 0.8275 (OUTLIER) cc_final: 0.7810 (mt-10) REVERT: u 82 VAL cc_start: 0.9422 (OUTLIER) cc_final: 0.9218 (m) REVERT: u 93 ARG cc_start: 0.8943 (mtm180) cc_final: 0.8484 (mtp180) REVERT: v 38 LEU cc_start: 0.9010 (tp) cc_final: 0.8802 (tp) REVERT: v 46 LYS cc_start: 0.9186 (mmtm) cc_final: 0.8700 (mmpt) REVERT: v 50 MET cc_start: 0.8620 (mtm) cc_final: 0.8215 (mtt) REVERT: v 79 ARG cc_start: 0.8721 (mtp85) cc_final: 0.8359 (mtt-85) REVERT: v 87 GLN cc_start: 0.8478 (mt0) cc_final: 0.7985 (mt0) REVERT: w 51 ARG cc_start: 0.9096 (OUTLIER) cc_final: 0.8720 (ppp80) REVERT: x 61 LYS cc_start: 0.8917 (mttt) cc_final: 0.8710 (mtmt) REVERT: x 69 GLU cc_start: 0.8912 (OUTLIER) cc_final: 0.8535 (mt-10) REVERT: x 75 GLU cc_start: 0.7353 (mp0) cc_final: 0.7088 (mp0) REVERT: y 1 MET cc_start: 0.7045 (tpt) cc_final: 0.6647 (tpt) REVERT: y 27 ASN cc_start: 0.9039 (OUTLIER) cc_final: 0.8748 (p0) REVERT: y 28 LEU cc_start: 0.9073 (OUTLIER) cc_final: 0.8675 (mp) REVERT: y 31 GLN cc_start: 0.8860 (mt0) cc_final: 0.8608 (mp10) REVERT: y 39 GLN cc_start: 0.8398 (OUTLIER) cc_final: 0.7910 (mt0) REVERT: z 39 ASP cc_start: 0.8330 (t0) cc_final: 0.8046 (t0) REVERT: B 5 ASN cc_start: 0.8998 (m-40) cc_final: 0.8595 (m110) REVERT: B 36 LYS cc_start: 0.9147 (mmtp) cc_final: 0.8840 (mptp) REVERT: C 36 LYS cc_start: 0.8697 (ttpt) cc_final: 0.8355 (mtpp) REVERT: D 41 ARG cc_start: 0.8021 (OUTLIER) cc_final: 0.7585 (mtp180) REVERT: F 24 ARG cc_start: 0.8898 (mtt-85) cc_final: 0.8481 (mtt-85) REVERT: F 35 GLN cc_start: 0.8939 (OUTLIER) cc_final: 0.8627 (pt0) REVERT: G 5 MET cc_start: 0.8103 (OUTLIER) cc_final: 0.7545 (mpp) REVERT: G 18 GLN cc_start: 0.8761 (mt0) cc_final: 0.8345 (mp10) REVERT: G 26 MET cc_start: 0.8529 (mmm) cc_final: 0.8178 (mmm) REVERT: G 131 LYS cc_start: 0.8397 (mmmt) cc_final: 0.8134 (mmtt) REVERT: G 150 ILE cc_start: 0.9073 (OUTLIER) cc_final: 0.8809 (tt) REVERT: G 160 LEU cc_start: 0.9085 (tt) cc_final: 0.8865 (tp) REVERT: G 172 ILE cc_start: 0.9360 (pt) cc_final: 0.9155 (pp) REVERT: H 5 HIS cc_start: 0.9193 (t-90) cc_final: 0.8849 (t-90) REVERT: H 39 ARG cc_start: 0.8686 (ttm-80) cc_final: 0.7908 (mtt90) REVERT: H 40 GLN cc_start: 0.8864 (tt0) cc_final: 0.8504 (pp30) REVERT: H 57 GLU cc_start: 0.8990 (OUTLIER) cc_final: 0.8426 (mt-10) REVERT: H 139 ASN cc_start: 0.8912 (m-40) cc_final: 0.8449 (m110) REVERT: H 151 GLU cc_start: 0.8211 (tm-30) cc_final: 0.7753 (tm-30) REVERT: H 184 ASN cc_start: 0.8785 (OUTLIER) cc_final: 0.8516 (t160) REVERT: H 191 THR cc_start: 0.9269 (p) cc_final: 0.8880 (t) REVERT: I 43 ARG cc_start: 0.7210 (mpp-170) cc_final: 0.6743 (mpp-170) REVERT: I 68 GLU cc_start: 0.8313 (tp30) cc_final: 0.7719 (tp30) REVERT: I 71 PHE cc_start: 0.9220 (t80) cc_final: 0.8617 (t80) REVERT: I 73 ASN cc_start: 0.9445 (m110) cc_final: 0.8671 (m110) REVERT: I 76 LYS cc_start: 0.8828 (mtmm) cc_final: 0.7981 (mppt) REVERT: I 112 GLU cc_start: 0.7319 (tt0) cc_final: 0.6950 (tt0) REVERT: I 116 LEU cc_start: 0.8847 (tp) cc_final: 0.8572 (tt) REVERT: I 137 SER cc_start: 0.8205 (t) cc_final: 0.7774 (p) REVERT: I 138 PRO cc_start: 0.8247 (Cg_exo) cc_final: 0.7824 (Cg_endo) REVERT: I 152 SER cc_start: 0.8884 (t) cc_final: 0.8618 (p) REVERT: J 30 PHE cc_start: 0.9131 (m-80) cc_final: 0.8645 (m-80) REVERT: J 32 PHE cc_start: 0.9107 (m-80) cc_final: 0.8367 (m-80) REVERT: J 60 GLN cc_start: 0.8841 (tp-100) cc_final: 0.8347 (tp-100) REVERT: J 94 PHE cc_start: 0.8211 (t80) cc_final: 0.7567 (t80) REVERT: J 114 LEU cc_start: 0.9504 (mt) cc_final: 0.9260 (mp) REVERT: J 131 ASN cc_start: 0.8145 (t0) cc_final: 0.7768 (t0) REVERT: J 146 MET cc_start: 0.8385 (OUTLIER) cc_final: 0.7610 (ttp) REVERT: K 86 ARG cc_start: 0.8670 (OUTLIER) cc_final: 0.8345 (ttm110) REVERT: K 88 MET cc_start: 0.8052 (ptm) cc_final: 0.7681 (ptm) REVERT: K 90 MET cc_start: 0.7762 (mtm) cc_final: 0.7434 (mpp) REVERT: L 3 ARG cc_start: 0.6663 (ttm170) cc_final: 0.6337 (ttm170) REVERT: L 105 GLU cc_start: 0.8410 (pp20) cc_final: 0.8055 (pp20) REVERT: M 17 GLN cc_start: 0.9091 (mm110) cc_final: 0.8806 (mm-40) REVERT: M 26 MET cc_start: 0.8553 (ptp) cc_final: 0.8123 (pmm) REVERT: M 28 SER cc_start: 0.8634 (p) cc_final: 0.8303 (p) REVERT: M 37 ASN cc_start: 0.8771 (t0) cc_final: 0.8454 (t0) REVERT: M 48 PHE cc_start: 0.9065 (p90) cc_final: 0.8857 (p90) REVERT: M 57 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7631 (pp20) REVERT: M 98 LEU cc_start: 0.9412 (pp) cc_final: 0.9108 (pt) REVERT: N 20 ILE cc_start: 0.9061 (tt) cc_final: 0.8582 (tp) REVERT: N 21 LYS cc_start: 0.9028 (mtpt) cc_final: 0.8616 (mmpt) REVERT: N 27 ILE cc_start: 0.8903 (mp) cc_final: 0.8434 (mm) REVERT: N 49 GLN cc_start: 0.9162 (tt0) cc_final: 0.8785 (tm-30) REVERT: N 123 ARG cc_start: 0.8611 (mmt90) cc_final: 0.8343 (tpp80) REVERT: O 9 ARG cc_start: 0.8156 (ttm-80) cc_final: 0.7418 (ttt180) REVERT: O 44 THR cc_start: 0.8370 (OUTLIER) cc_final: 0.8150 (t) REVERT: O 48 ARG cc_start: 0.8727 (mtt90) cc_final: 0.8524 (mtt90) REVERT: Q 37 TYR cc_start: 0.8289 (p90) cc_final: 0.7843 (p90) REVERT: Q 43 LYS cc_start: 0.8752 (mmmt) cc_final: 0.8446 (mmtt) REVERT: Q 72 ASN cc_start: 0.8594 (OUTLIER) cc_final: 0.8048 (p0) REVERT: Q 88 ASP cc_start: 0.8532 (m-30) cc_final: 0.7750 (m-30) REVERT: R 15 VAL cc_start: 0.8195 (m) cc_final: 0.7923 (t) REVERT: R 43 LYS cc_start: 0.8557 (ptpt) cc_final: 0.8201 (ptpp) REVERT: R 52 ILE cc_start: 0.8925 (mt) cc_final: 0.8472 (mp) REVERT: R 73 SER cc_start: 0.9196 (t) cc_final: 0.8961 (m) REVERT: R 76 ILE cc_start: 0.9386 (pp) cc_final: 0.9056 (pp) REVERT: R 77 LYS cc_start: 0.9221 (tttm) cc_final: 0.8608 (tppt) REVERT: T 25 GLU cc_start: 0.8569 (mt-10) cc_final: 0.8338 (mt-10) REVERT: T 36 ASN cc_start: 0.8789 (m110) cc_final: 0.8255 (m-40) REVERT: T 48 ASP cc_start: 0.8531 (t0) cc_final: 0.7991 (t0) REVERT: T 51 SER cc_start: 0.9090 (p) cc_final: 0.8812 (p) REVERT: T 73 ASP cc_start: 0.7906 (t0) cc_final: 0.7512 (t0) REVERT: T 76 ARG cc_start: 0.8540 (mtm180) cc_final: 0.8076 (ttm110) REVERT: U 18 GLN cc_start: 0.8245 (mt0) cc_final: 0.7565 (mt0) REVERT: U 39 PHE cc_start: 0.9046 (t80) cc_final: 0.8327 (t80) REVERT: V 27 PHE cc_start: 0.8450 (t80) cc_final: 0.8232 (t80) REVERT: V 38 LYS cc_start: 0.8722 (OUTLIER) cc_final: 0.8279 (ttmm) REVERT: V 44 HIS cc_start: 0.8131 (m90) cc_final: 0.7869 (m90) REVERT: V 61 ARG cc_start: 0.8158 (ppp80) cc_final: 0.7807 (ppp80) REVERT: W 23 LYS cc_start: 0.9137 (mtmm) cc_final: 0.8852 (pptt) REVERT: W 24 ASP cc_start: 0.8481 (t70) cc_final: 0.8192 (t0) REVERT: W 42 ARG cc_start: 0.9096 (OUTLIER) cc_final: 0.8812 (mtm110) REVERT: W 51 GLN cc_start: 0.8743 (tp40) cc_final: 0.7585 (tm-30) REVERT: X 10 ILE cc_start: 0.9119 (pt) cc_final: 0.8505 (mm) REVERT: X 36 ARG cc_start: 0.8665 (OUTLIER) cc_final: 0.7589 (ptm-80) REVERT: Y 15 LYS cc_start: 0.8921 (tttm) cc_final: 0.8315 (tptp) REVERT: Y 17 ARG cc_start: 0.8868 (tmm-80) cc_final: 0.8262 (ttp-110) REVERT: Y 27 MET cc_start: 0.8008 (ppp) cc_final: 0.7786 (tmt) REVERT: Y 28 ARG cc_start: 0.8379 (mtt180) cc_final: 0.8051 (mtt-85) REVERT: Y 50 PHE cc_start: 0.8723 (t80) cc_final: 0.8452 (t80) REVERT: Y 54 GLN cc_start: 0.8564 (tt0) cc_final: 0.8094 (tt0) REVERT: Z 9 GLU cc_start: 0.7378 (OUTLIER) cc_final: 0.7154 (tm-30) REVERT: Z 46 ARG cc_start: 0.8256 (tpt-90) cc_final: 0.7931 (tpt-90) REVERT: a 218 MET cc_start: 0.5283 (mtt) cc_final: 0.3852 (mmt) outliers start: 439 outliers final: 276 residues processed: 1843 average time/residue: 2.0415 time to fit residues: 5518.2455 Evaluate side-chains 1945 residues out of total 4908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 322 poor density : 1623 time to evaluate : 6.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 37 SER Chi-restraints excluded: chain b residue 48 ILE Chi-restraints excluded: chain b residue 50 THR Chi-restraints excluded: chain b residue 52 HIS Chi-restraints excluded: chain b residue 86 ARG Chi-restraints excluded: chain b residue 114 GLN Chi-restraints excluded: chain b residue 140 VAL Chi-restraints excluded: chain b residue 152 GLN Chi-restraints excluded: chain b residue 163 ILE Chi-restraints excluded: chain b residue 164 VAL Chi-restraints excluded: chain b residue 186 ASP Chi-restraints excluded: chain b residue 194 VAL Chi-restraints excluded: chain b residue 250 GLN Chi-restraints excluded: chain b residue 269 ARG Chi-restraints excluded: chain c residue 2 ILE Chi-restraints excluded: chain c residue 9 VAL Chi-restraints excluded: chain c residue 22 ILE Chi-restraints excluded: chain c residue 39 ASP Chi-restraints excluded: chain c residue 89 GLU Chi-restraints excluded: chain c residue 95 SER Chi-restraints excluded: chain c residue 97 SER Chi-restraints excluded: chain c residue 110 THR Chi-restraints excluded: chain c residue 128 ARG Chi-restraints excluded: chain c residue 157 LYS Chi-restraints excluded: chain c residue 170 VAL Chi-restraints excluded: chain c residue 199 SER Chi-restraints excluded: chain c residue 200 ASP Chi-restraints excluded: chain d residue 48 THR Chi-restraints excluded: chain d residue 53 THR Chi-restraints excluded: chain d residue 65 THR Chi-restraints excluded: chain d residue 72 SER Chi-restraints excluded: chain d residue 80 SER Chi-restraints excluded: chain d residue 108 ILE Chi-restraints excluded: chain d residue 120 VAL Chi-restraints excluded: chain d residue 189 THR Chi-restraints excluded: chain e residue 16 MET Chi-restraints excluded: chain e residue 23 SER Chi-restraints excluded: chain e residue 24 VAL Chi-restraints excluded: chain e residue 29 ARG Chi-restraints excluded: chain e residue 30 VAL Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 36 ASN Chi-restraints excluded: chain e residue 60 SER Chi-restraints excluded: chain e residue 65 LEU Chi-restraints excluded: chain e residue 67 THR Chi-restraints excluded: chain e residue 89 THR Chi-restraints excluded: chain e residue 90 LEU Chi-restraints excluded: chain e residue 100 GLU Chi-restraints excluded: chain e residue 117 SER Chi-restraints excluded: chain e residue 126 ASN Chi-restraints excluded: chain e residue 131 VAL Chi-restraints excluded: chain e residue 157 THR Chi-restraints excluded: chain e residue 173 ASP Chi-restraints excluded: chain f residue 1 SER Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 17 LYS Chi-restraints excluded: chain f residue 23 ILE Chi-restraints excluded: chain f residue 66 THR Chi-restraints excluded: chain f residue 105 SER Chi-restraints excluded: chain f residue 126 THR Chi-restraints excluded: chain g residue 6 LEU Chi-restraints excluded: chain g residue 7 ASP Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain g residue 61 VAL Chi-restraints excluded: chain g residue 96 THR Chi-restraints excluded: chain g residue 115 VAL Chi-restraints excluded: chain g residue 117 LEU Chi-restraints excluded: chain g residue 133 GLN Chi-restraints excluded: chain h residue 3 LEU Chi-restraints excluded: chain h residue 5 LEU Chi-restraints excluded: chain h residue 77 VAL Chi-restraints excluded: chain h residue 128 THR Chi-restraints excluded: chain i residue 12 VAL Chi-restraints excluded: chain i residue 35 MET Chi-restraints excluded: chain j residue 54 ILE Chi-restraints excluded: chain j residue 73 VAL Chi-restraints excluded: chain j residue 131 ASN Chi-restraints excluded: chain k residue 17 ARG Chi-restraints excluded: chain k residue 28 SER Chi-restraints excluded: chain k residue 45 GLU Chi-restraints excluded: chain k residue 49 ARG Chi-restraints excluded: chain k residue 65 THR Chi-restraints excluded: chain k residue 69 VAL Chi-restraints excluded: chain k residue 80 ASP Chi-restraints excluded: chain k residue 86 LEU Chi-restraints excluded: chain k residue 118 LEU Chi-restraints excluded: chain l residue 12 SER Chi-restraints excluded: chain l residue 78 ARG Chi-restraints excluded: chain l residue 85 VAL Chi-restraints excluded: chain l residue 110 VAL Chi-restraints excluded: chain l residue 116 VAL Chi-restraints excluded: chain l residue 118 THR Chi-restraints excluded: chain l residue 120 VAL Chi-restraints excluded: chain l residue 121 THR Chi-restraints excluded: chain l residue 122 VAL Chi-restraints excluded: chain l residue 127 VAL Chi-restraints excluded: chain m residue 12 MET Chi-restraints excluded: chain m residue 42 THR Chi-restraints excluded: chain m residue 54 THR Chi-restraints excluded: chain m residue 57 VAL Chi-restraints excluded: chain m residue 74 THR Chi-restraints excluded: chain m residue 78 LEU Chi-restraints excluded: chain m residue 93 VAL Chi-restraints excluded: chain m residue 97 GLN Chi-restraints excluded: chain m residue 112 LEU Chi-restraints excluded: chain m residue 118 LYS Chi-restraints excluded: chain m residue 126 ILE Chi-restraints excluded: chain m residue 132 THR Chi-restraints excluded: chain n residue 6 SER Chi-restraints excluded: chain n residue 27 SER Chi-restraints excluded: chain n residue 65 LEU Chi-restraints excluded: chain n residue 73 ASN Chi-restraints excluded: chain n residue 75 ILE Chi-restraints excluded: chain o residue 12 THR Chi-restraints excluded: chain o residue 19 GLN Chi-restraints excluded: chain o residue 21 LEU Chi-restraints excluded: chain o residue 35 ILE Chi-restraints excluded: chain o residue 39 VAL Chi-restraints excluded: chain o residue 40 ILE Chi-restraints excluded: chain o residue 48 LEU Chi-restraints excluded: chain o residue 95 SER Chi-restraints excluded: chain o residue 103 VAL Chi-restraints excluded: chain p residue 2 ASN Chi-restraints excluded: chain p residue 7 LEU Chi-restraints excluded: chain p residue 63 ILE Chi-restraints excluded: chain p residue 65 ASN Chi-restraints excluded: chain p residue 91 VAL Chi-restraints excluded: chain p residue 93 LYS Chi-restraints excluded: chain q residue 16 ILE Chi-restraints excluded: chain q residue 50 ARG Chi-restraints excluded: chain q residue 58 GLN Chi-restraints excluded: chain q residue 73 ILE Chi-restraints excluded: chain q residue 82 LEU Chi-restraints excluded: chain q residue 109 VAL Chi-restraints excluded: chain r residue 33 VAL Chi-restraints excluded: chain r residue 47 VAL Chi-restraints excluded: chain s residue 20 VAL Chi-restraints excluded: chain s residue 23 LEU Chi-restraints excluded: chain s residue 74 ILE Chi-restraints excluded: chain s residue 77 ASP Chi-restraints excluded: chain s residue 104 THR Chi-restraints excluded: chain s residue 106 VAL Chi-restraints excluded: chain s residue 107 VAL Chi-restraints excluded: chain s residue 108 SER Chi-restraints excluded: chain t residue 1 MET Chi-restraints excluded: chain t residue 16 VAL Chi-restraints excluded: chain t residue 17 SER Chi-restraints excluded: chain t residue 57 VAL Chi-restraints excluded: chain t residue 85 VAL Chi-restraints excluded: chain t residue 87 LEU Chi-restraints excluded: chain u residue 4 ILE Chi-restraints excluded: chain u residue 11 ILE Chi-restraints excluded: chain u residue 24 VAL Chi-restraints excluded: chain u residue 33 VAL Chi-restraints excluded: chain u residue 48 VAL Chi-restraints excluded: chain u residue 61 GLU Chi-restraints excluded: chain u residue 82 VAL Chi-restraints excluded: chain v residue 17 SER Chi-restraints excluded: chain v residue 20 LEU Chi-restraints excluded: chain v residue 30 ILE Chi-restraints excluded: chain v residue 45 ASP Chi-restraints excluded: chain v residue 47 VAL Chi-restraints excluded: chain v residue 61 LEU Chi-restraints excluded: chain v residue 64 VAL Chi-restraints excluded: chain v residue 65 VAL Chi-restraints excluded: chain v residue 92 VAL Chi-restraints excluded: chain w residue 32 ILE Chi-restraints excluded: chain w residue 34 VAL Chi-restraints excluded: chain w residue 39 THR Chi-restraints excluded: chain w residue 51 ARG Chi-restraints excluded: chain w residue 66 GLU Chi-restraints excluded: chain w residue 68 LYS Chi-restraints excluded: chain w residue 74 LYS Chi-restraints excluded: chain w residue 76 ILE Chi-restraints excluded: chain x residue 1 SER Chi-restraints excluded: chain x residue 7 THR Chi-restraints excluded: chain x residue 13 THR Chi-restraints excluded: chain x residue 33 HIS Chi-restraints excluded: chain x residue 39 VAL Chi-restraints excluded: chain x residue 46 VAL Chi-restraints excluded: chain x residue 47 THR Chi-restraints excluded: chain x residue 64 ASP Chi-restraints excluded: chain x residue 69 GLU Chi-restraints excluded: chain y residue 27 ASN Chi-restraints excluded: chain y residue 28 LEU Chi-restraints excluded: chain y residue 30 MET Chi-restraints excluded: chain y residue 39 GLN Chi-restraints excluded: chain y residue 40 SER Chi-restraints excluded: chain y residue 43 LEU Chi-restraints excluded: chain z residue 29 ARG Chi-restraints excluded: chain z residue 56 VAL Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 25 LYS Chi-restraints excluded: chain D residue 41 ARG Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain F residue 35 GLN Chi-restraints excluded: chain G residue 5 MET Chi-restraints excluded: chain G residue 35 ASN Chi-restraints excluded: chain G residue 141 GLU Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 158 ASP Chi-restraints excluded: chain G residue 198 VAL Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain G residue 216 VAL Chi-restraints excluded: chain H residue 20 THR Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 43 THR Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 117 ASP Chi-restraints excluded: chain H residue 118 SER Chi-restraints excluded: chain H residue 123 LEU Chi-restraints excluded: chain H residue 164 THR Chi-restraints excluded: chain H residue 174 LEU Chi-restraints excluded: chain H residue 184 ASN Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 93 LEU Chi-restraints excluded: chain I residue 115 GLN Chi-restraints excluded: chain I residue 118 SER Chi-restraints excluded: chain I residue 133 SER Chi-restraints excluded: chain I residue 143 SER Chi-restraints excluded: chain J residue 89 THR Chi-restraints excluded: chain J residue 104 ILE Chi-restraints excluded: chain J residue 105 ILE Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 146 MET Chi-restraints excluded: chain K residue 7 VAL Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 39 LEU Chi-restraints excluded: chain K residue 75 GLU Chi-restraints excluded: chain K residue 86 ARG Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain L residue 117 LEU Chi-restraints excluded: chain L residue 121 ASN Chi-restraints excluded: chain M residue 6 ILE Chi-restraints excluded: chain M residue 9 MET Chi-restraints excluded: chain M residue 11 THR Chi-restraints excluded: chain M residue 57 GLU Chi-restraints excluded: chain M residue 58 LEU Chi-restraints excluded: chain M residue 61 THR Chi-restraints excluded: chain M residue 125 ILE Chi-restraints excluded: chain N residue 28 VAL Chi-restraints excluded: chain N residue 53 LEU Chi-restraints excluded: chain N residue 60 LEU Chi-restraints excluded: chain N residue 78 ILE Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain O residue 44 THR Chi-restraints excluded: chain O residue 50 THR Chi-restraints excluded: chain O residue 91 ASP Chi-restraints excluded: chain O residue 92 LEU Chi-restraints excluded: chain P residue 25 SER Chi-restraints excluded: chain P residue 30 ILE Chi-restraints excluded: chain P residue 45 THR Chi-restraints excluded: chain P residue 54 SER Chi-restraints excluded: chain P residue 86 LYS Chi-restraints excluded: chain Q residue 32 VAL Chi-restraints excluded: chain Q residue 34 THR Chi-restraints excluded: chain Q residue 39 THR Chi-restraints excluded: chain Q residue 40 THR Chi-restraints excluded: chain Q residue 46 SER Chi-restraints excluded: chain Q residue 51 VAL Chi-restraints excluded: chain Q residue 57 THR Chi-restraints excluded: chain Q residue 63 THR Chi-restraints excluded: chain Q residue 72 ASN Chi-restraints excluded: chain Q residue 73 LEU Chi-restraints excluded: chain Q residue 97 VAL Chi-restraints excluded: chain Q residue 102 ASP Chi-restraints excluded: chain Q residue 119 LYS Chi-restraints excluded: chain R residue 20 SER Chi-restraints excluded: chain R residue 24 VAL Chi-restraints excluded: chain R residue 58 GLU Chi-restraints excluded: chain R residue 65 GLU Chi-restraints excluded: chain R residue 94 LEU Chi-restraints excluded: chain S residue 47 LEU Chi-restraints excluded: chain T residue 4 THR Chi-restraints excluded: chain T residue 27 GLN Chi-restraints excluded: chain T residue 30 LEU Chi-restraints excluded: chain T residue 69 LEU Chi-restraints excluded: chain U residue 21 VAL Chi-restraints excluded: chain U residue 68 SER Chi-restraints excluded: chain U residue 78 VAL Chi-restraints excluded: chain V residue 24 ILE Chi-restraints excluded: chain V residue 32 ILE Chi-restraints excluded: chain V residue 38 LYS Chi-restraints excluded: chain V residue 41 THR Chi-restraints excluded: chain V residue 54 ILE Chi-restraints excluded: chain V residue 56 ASP Chi-restraints excluded: chain V residue 71 SER Chi-restraints excluded: chain V residue 82 VAL Chi-restraints excluded: chain W residue 35 SER Chi-restraints excluded: chain W residue 42 ARG Chi-restraints excluded: chain W residue 70 THR Chi-restraints excluded: chain X residue 31 ARG Chi-restraints excluded: chain X residue 36 ARG Chi-restraints excluded: chain X residue 37 SER Chi-restraints excluded: chain X residue 38 THR Chi-restraints excluded: chain X residue 48 ILE Chi-restraints excluded: chain X residue 78 THR Chi-restraints excluded: chain Y residue 22 SER Chi-restraints excluded: chain Y residue 25 SER Chi-restraints excluded: chain Y residue 78 LEU Chi-restraints excluded: chain Y residue 79 THR Chi-restraints excluded: chain Z residue 9 GLU Chi-restraints excluded: chain Z residue 12 ASP Chi-restraints excluded: chain Z residue 52 VAL Chi-restraints excluded: chain Z residue 59 LEU Chi-restraints excluded: chain a residue 35 THR Chi-restraints excluded: chain a residue 46 VAL Chi-restraints excluded: chain a residue 53 ARG Chi-restraints excluded: chain a residue 64 VAL Chi-restraints excluded: chain a residue 207 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1050 random chunks: chunk 341 optimal weight: 0.5980 chunk 913 optimal weight: 6.9990 chunk 200 optimal weight: 7.9990 chunk 595 optimal weight: 20.0000 chunk 250 optimal weight: 8.9990 chunk 1015 optimal weight: 7.9990 chunk 843 optimal weight: 40.0000 chunk 470 optimal weight: 50.0000 chunk 84 optimal weight: 0.2980 chunk 336 optimal weight: 4.9990 chunk 533 optimal weight: 20.0000 overall best weight: 4.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 163 ASN ** e 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 128 ASN o 29 HIS r 86 GLN s 61 ASN t 48 GLN u 39 ASN u 65 GLN v 12 GLN x 16 ASN ** x 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** y 20 ASN y 27 ASN ** y 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 27 ASN G 50 ASN H 122 GLN ** H 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 53 GLN I 88 ASN I 119 HIS ** J 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 56 HIS P 21 HIS ** P 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 4 ASN ** T 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 12 GLN ** Y 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.3522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 161399 Z= 0.281 Angle : 0.638 17.760 241370 Z= 0.327 Chirality : 0.038 0.305 30856 Planarity : 0.005 0.073 13007 Dihedral : 23.128 179.109 80582 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.29 % Allowed : 8.67 % Favored : 91.05 % Rotamer: Outliers : 8.27 % Allowed : 31.13 % Favored : 60.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.11), residues: 5919 helix: -0.32 (0.12), residues: 1862 sheet: -1.50 (0.16), residues: 1033 loop : -1.89 (0.11), residues: 3024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP G 103 HIS 0.009 0.001 HIS J 82 PHE 0.056 0.002 PHE g 46 TYR 0.031 0.002 TYR G 212 ARG 0.015 0.001 ARG x 10 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11838 Ramachandran restraints generated. 5919 Oldfield, 0 Emsley, 5919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11838 Ramachandran restraints generated. 5919 Oldfield, 0 Emsley, 5919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2080 residues out of total 4908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 406 poor density : 1674 time to evaluate : 6.456 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: b 22 GLU cc_start: 0.7994 (pp20) cc_final: 0.7742 (pp20) REVERT: b 86 ARG cc_start: 0.9051 (OUTLIER) cc_final: 0.8203 (mtm-85) REVERT: b 97 ASP cc_start: 0.8808 (p0) cc_final: 0.8479 (p0) REVERT: b 114 GLN cc_start: 0.8723 (OUTLIER) cc_final: 0.8326 (tt0) REVERT: b 152 GLN cc_start: 0.8549 (OUTLIER) cc_final: 0.8166 (mm-40) REVERT: b 250 GLN cc_start: 0.8789 (OUTLIER) cc_final: 0.8006 (tt0) REVERT: c 1 MET cc_start: 0.8695 (tmm) cc_final: 0.8280 (tmm) REVERT: c 2 ILE cc_start: 0.8746 (OUTLIER) cc_final: 0.8475 (pp) REVERT: c 167 ASN cc_start: 0.9349 (t0) cc_final: 0.9009 (t0) REVERT: d 30 GLN cc_start: 0.8998 (tp40) cc_final: 0.8411 (tt0) REVERT: d 51 GLU cc_start: 0.8036 (pm20) cc_final: 0.7734 (pm20) REVERT: d 88 ARG cc_start: 0.8455 (OUTLIER) cc_final: 0.8094 (mmp80) REVERT: e 6 TYR cc_start: 0.8466 (t80) cc_final: 0.8165 (t80) REVERT: e 16 MET cc_start: 0.8179 (OUTLIER) cc_final: 0.7971 (mmm) REVERT: e 25 MET cc_start: 0.8955 (ppp) cc_final: 0.8006 (ppp) REVERT: e 29 ARG cc_start: 0.8636 (OUTLIER) cc_final: 0.8179 (ptp-170) REVERT: e 31 GLU cc_start: 0.8356 (mt-10) cc_final: 0.8041 (mm-30) REVERT: e 36 ASN cc_start: 0.7169 (t0) cc_final: 0.6860 (t0) REVERT: e 65 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.8257 (tm) REVERT: e 87 LYS cc_start: 0.8983 (ttpp) cc_final: 0.8312 (ttmt) REVERT: e 95 MET cc_start: 0.8863 (ppp) cc_final: 0.8543 (ppp) REVERT: e 99 PHE cc_start: 0.8974 (t80) cc_final: 0.8762 (t80) REVERT: e 100 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.8016 (mp0) REVERT: e 133 GLU cc_start: 0.7742 (tp30) cc_final: 0.7479 (tp30) REVERT: e 145 VAL cc_start: 0.7439 (t) cc_final: 0.6751 (p) REVERT: e 163 GLU cc_start: 0.8194 (pm20) cc_final: 0.7808 (pp20) REVERT: f 19 ASN cc_start: 0.8749 (t0) cc_final: 0.8535 (t0) REVERT: f 21 GLN cc_start: 0.8281 (tp-100) cc_final: 0.8046 (tp-100) REVERT: f 68 ARG cc_start: 0.8973 (tmt170) cc_final: 0.8714 (tmt-80) REVERT: f 74 MET cc_start: 0.9364 (ttm) cc_final: 0.8957 (ttm) REVERT: f 82 PHE cc_start: 0.8287 (m-80) cc_final: 0.7785 (m-80) REVERT: f 100 ASN cc_start: 0.8465 (p0) cc_final: 0.7950 (p0) REVERT: f 113 ASP cc_start: 0.8327 (OUTLIER) cc_final: 0.8096 (m-30) REVERT: f 129 GLU cc_start: 0.8554 (tt0) cc_final: 0.7966 (tp30) REVERT: g 4 ILE cc_start: 0.8833 (tp) cc_final: 0.8514 (mm) REVERT: g 7 ASP cc_start: 0.8660 (OUTLIER) cc_final: 0.8414 (t0) REVERT: g 8 LYS cc_start: 0.8788 (mtpp) cc_final: 0.8075 (tptt) REVERT: g 25 TYR cc_start: 0.8858 (t80) cc_final: 0.8416 (t80) REVERT: g 35 LYS cc_start: 0.8721 (mptt) cc_final: 0.8480 (mptp) REVERT: g 117 LEU cc_start: 0.7010 (OUTLIER) cc_final: 0.6683 (pt) REVERT: h 5 LEU cc_start: 0.9103 (OUTLIER) cc_final: 0.8882 (pt) REVERT: i 139 VAL cc_start: 0.6825 (t) cc_final: 0.6600 (m) REVERT: j 13 ARG cc_start: 0.8226 (mtt90) cc_final: 0.7996 (mtt90) REVERT: j 71 ASP cc_start: 0.8465 (m-30) cc_final: 0.8257 (m-30) REVERT: k 12 ASP cc_start: 0.8335 (p0) cc_final: 0.8060 (p0) REVERT: k 17 ARG cc_start: 0.7881 (OUTLIER) cc_final: 0.7138 (ttm170) REVERT: l 76 GLU cc_start: 0.7511 (mt-10) cc_final: 0.7135 (mt-10) REVERT: l 82 LEU cc_start: 0.9341 (tp) cc_final: 0.9038 (tm) REVERT: l 105 ILE cc_start: 0.9049 (mm) cc_final: 0.8787 (mm) REVERT: l 143 GLU cc_start: 0.7523 (pp20) cc_final: 0.7181 (pp20) REVERT: m 91 TYR cc_start: 0.9058 (p90) cc_final: 0.8522 (p90) REVERT: m 97 GLN cc_start: 0.8597 (OUTLIER) cc_final: 0.8245 (mp-120) REVERT: m 110 GLU cc_start: 0.8267 (tm-30) cc_final: 0.7842 (tm-30) REVERT: n 35 LYS cc_start: 0.8809 (tttt) cc_final: 0.8584 (tptt) REVERT: n 72 ASP cc_start: 0.8782 (t0) cc_final: 0.8451 (t0) REVERT: o 38 GLN cc_start: 0.8846 (pt0) cc_final: 0.7921 (pm20) REVERT: o 80 GLU cc_start: 0.8882 (tm-30) cc_final: 0.8613 (tm-30) REVERT: p 23 ASP cc_start: 0.8531 (m-30) cc_final: 0.8096 (m-30) REVERT: p 26 GLU cc_start: 0.7879 (tm-30) cc_final: 0.7653 (tm-30) REVERT: p 65 ASN cc_start: 0.8891 (OUTLIER) cc_final: 0.8533 (p0) REVERT: p 69 VAL cc_start: 0.9071 (t) cc_final: 0.8813 (p) REVERT: q 58 GLN cc_start: 0.8870 (OUTLIER) cc_final: 0.8647 (tt0) REVERT: q 96 ASP cc_start: 0.8296 (t0) cc_final: 0.7721 (t0) REVERT: q 101 ASP cc_start: 0.8219 (t70) cc_final: 0.7826 (t0) REVERT: r 1 MET cc_start: 0.7248 (tpp) cc_final: 0.7021 (tpp) REVERT: r 13 ARG cc_start: 0.8803 (ttp80) cc_final: 0.8124 (ttt-90) REVERT: r 16 GLU cc_start: 0.8476 (tp30) cc_final: 0.8085 (tp30) REVERT: r 31 GLU cc_start: 0.7792 (mp0) cc_final: 0.7267 (mp0) REVERT: r 37 GLU cc_start: 0.7903 (pm20) cc_final: 0.7603 (pm20) REVERT: r 60 LYS cc_start: 0.8894 (mtmm) cc_final: 0.8453 (mmmm) REVERT: r 62 GLU cc_start: 0.8570 (tt0) cc_final: 0.7826 (tm-30) REVERT: s 52 GLU cc_start: 0.7957 (mm-30) cc_final: 0.7670 (tm-30) REVERT: s 61 ASN cc_start: 0.8777 (m-40) cc_final: 0.8417 (m-40) REVERT: t 1 MET cc_start: 0.7614 (OUTLIER) cc_final: 0.7107 (ptp) REVERT: t 28 ASN cc_start: 0.8768 (t0) cc_final: 0.8354 (t0) REVERT: t 36 LYS cc_start: 0.8477 (tptp) cc_final: 0.8270 (tptp) REVERT: t 42 GLU cc_start: 0.8585 (mp0) cc_final: 0.8351 (mp0) REVERT: t 86 THR cc_start: 0.9035 (m) cc_final: 0.8785 (p) REVERT: u 36 GLU cc_start: 0.8826 (pp20) cc_final: 0.8553 (pp20) REVERT: u 61 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7715 (mt-10) REVERT: u 93 ARG cc_start: 0.8887 (mtm180) cc_final: 0.8529 (mtp180) REVERT: v 38 LEU cc_start: 0.9008 (tp) cc_final: 0.8730 (tp) REVERT: v 41 GLU cc_start: 0.8222 (tt0) cc_final: 0.7934 (tm-30) REVERT: v 46 LYS cc_start: 0.9175 (mmtm) cc_final: 0.8675 (mmpt) REVERT: v 87 GLN cc_start: 0.8344 (mt0) cc_final: 0.7811 (mt0) REVERT: w 16 ARG cc_start: 0.8642 (mpt-90) cc_final: 0.7719 (mmt90) REVERT: w 51 ARG cc_start: 0.9071 (OUTLIER) cc_final: 0.8579 (ppp80) REVERT: x 69 GLU cc_start: 0.8914 (OUTLIER) cc_final: 0.8697 (mt-10) REVERT: x 75 GLU cc_start: 0.7504 (mp0) cc_final: 0.7208 (mp0) REVERT: y 27 ASN cc_start: 0.8799 (m110) cc_final: 0.8391 (m-40) REVERT: y 39 GLN cc_start: 0.8364 (OUTLIER) cc_final: 0.7787 (mt0) REVERT: B 5 ASN cc_start: 0.8930 (m-40) cc_final: 0.8536 (m-40) REVERT: B 35 GLU cc_start: 0.7408 (mt-10) cc_final: 0.5377 (mt-10) REVERT: B 36 LYS cc_start: 0.9103 (mmtp) cc_final: 0.8759 (mptp) REVERT: C 36 LYS cc_start: 0.8682 (ttpt) cc_final: 0.8339 (mtpp) REVERT: D 28 ARG cc_start: 0.8966 (OUTLIER) cc_final: 0.8399 (mtm180) REVERT: D 41 ARG cc_start: 0.8083 (OUTLIER) cc_final: 0.7605 (mtp180) REVERT: F 17 VAL cc_start: 0.9127 (p) cc_final: 0.8897 (m) REVERT: F 24 ARG cc_start: 0.8821 (mtt-85) cc_final: 0.8452 (mtt-85) REVERT: F 35 GLN cc_start: 0.8930 (OUTLIER) cc_final: 0.8621 (pt0) REVERT: G 5 MET cc_start: 0.8042 (OUTLIER) cc_final: 0.7351 (mpp) REVERT: G 18 GLN cc_start: 0.8862 (mt0) cc_final: 0.8476 (mp10) REVERT: G 26 MET cc_start: 0.8603 (mmm) cc_final: 0.8240 (mmm) REVERT: G 150 ILE cc_start: 0.9135 (OUTLIER) cc_final: 0.8861 (tt) REVERT: H 5 HIS cc_start: 0.9146 (t-90) cc_final: 0.8825 (t-90) REVERT: H 39 ARG cc_start: 0.8695 (ttm-80) cc_final: 0.7539 (mtt180) REVERT: H 40 GLN cc_start: 0.8895 (tt0) cc_final: 0.8632 (pp30) REVERT: H 139 ASN cc_start: 0.8895 (m-40) cc_final: 0.8411 (m110) REVERT: H 151 GLU cc_start: 0.8205 (tm-30) cc_final: 0.7762 (tm-30) REVERT: H 156 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8707 (mm) REVERT: H 184 ASN cc_start: 0.8822 (OUTLIER) cc_final: 0.8573 (t160) REVERT: H 191 THR cc_start: 0.9229 (p) cc_final: 0.8844 (t) REVERT: I 68 GLU cc_start: 0.8353 (tp30) cc_final: 0.7819 (tp30) REVERT: I 71 PHE cc_start: 0.9208 (t80) cc_final: 0.8550 (t80) REVERT: I 73 ASN cc_start: 0.9405 (m110) cc_final: 0.8931 (m110) REVERT: I 112 GLU cc_start: 0.7409 (tt0) cc_final: 0.7153 (tt0) REVERT: I 116 LEU cc_start: 0.8630 (tp) cc_final: 0.8391 (tt) REVERT: I 137 SER cc_start: 0.8204 (t) cc_final: 0.7797 (p) REVERT: I 152 SER cc_start: 0.8858 (t) cc_final: 0.8615 (p) REVERT: J 32 PHE cc_start: 0.9075 (m-80) cc_final: 0.8719 (m-80) REVERT: J 60 GLN cc_start: 0.8835 (tp-100) cc_final: 0.8317 (tp-100) REVERT: J 94 PHE cc_start: 0.8200 (t80) cc_final: 0.7584 (t80) REVERT: J 104 ILE cc_start: 0.9348 (OUTLIER) cc_final: 0.8898 (pp) REVERT: J 131 ASN cc_start: 0.8077 (t0) cc_final: 0.7737 (t0) REVERT: J 146 MET cc_start: 0.8307 (OUTLIER) cc_final: 0.7239 (ttp) REVERT: K 44 ARG cc_start: 0.8291 (ttp-170) cc_final: 0.7601 (ttm-80) REVERT: K 56 LYS cc_start: 0.8469 (mmtt) cc_final: 0.7832 (mmpt) REVERT: K 59 TYR cc_start: 0.8379 (m-80) cc_final: 0.8122 (m-80) REVERT: K 88 MET cc_start: 0.8035 (ptm) cc_final: 0.7577 (ptm) REVERT: K 90 MET cc_start: 0.7712 (mtm) cc_final: 0.7254 (mpp) REVERT: L 3 ARG cc_start: 0.6603 (ttm170) cc_final: 0.6291 (ttm170) REVERT: L 100 MET cc_start: 0.8541 (mtm) cc_final: 0.8332 (mtm) REVERT: L 105 GLU cc_start: 0.8414 (pp20) cc_final: 0.8058 (pp20) REVERT: M 26 MET cc_start: 0.8520 (ptp) cc_final: 0.8148 (pmm) REVERT: M 28 SER cc_start: 0.8547 (p) cc_final: 0.8202 (p) REVERT: M 37 ASN cc_start: 0.8736 (t0) cc_final: 0.8452 (t0) REVERT: M 57 GLU cc_start: 0.7857 (OUTLIER) cc_final: 0.7452 (pp20) REVERT: M 95 MET cc_start: 0.8391 (tpt) cc_final: 0.8035 (tpp) REVERT: M 98 LEU cc_start: 0.9270 (OUTLIER) cc_final: 0.8625 (pt) REVERT: M 110 MET cc_start: 0.8376 (ptp) cc_final: 0.8134 (ptp) REVERT: N 20 ILE cc_start: 0.9047 (tt) cc_final: 0.8732 (tp) REVERT: N 21 LYS cc_start: 0.9025 (mtpt) cc_final: 0.8623 (mmtt) REVERT: N 27 ILE cc_start: 0.8969 (mp) cc_final: 0.8581 (mm) REVERT: N 123 ARG cc_start: 0.8604 (mmt90) cc_final: 0.8288 (tpp80) REVERT: O 9 ARG cc_start: 0.8303 (ttm-80) cc_final: 0.7731 (ttt180) REVERT: O 16 ARG cc_start: 0.8035 (ptt180) cc_final: 0.7643 (ptp90) REVERT: O 44 THR cc_start: 0.8288 (OUTLIER) cc_final: 0.8058 (t) REVERT: Q 37 TYR cc_start: 0.8246 (p90) cc_final: 0.7844 (p90) REVERT: Q 43 LYS cc_start: 0.8770 (mmmt) cc_final: 0.8504 (mmtt) REVERT: Q 88 ASP cc_start: 0.8491 (m-30) cc_final: 0.7744 (m-30) REVERT: R 15 VAL cc_start: 0.8205 (m) cc_final: 0.7929 (t) REVERT: R 43 LYS cc_start: 0.8564 (ptpt) cc_final: 0.8227 (ptpp) REVERT: R 52 ILE cc_start: 0.8899 (mt) cc_final: 0.8462 (mp) REVERT: R 73 SER cc_start: 0.9198 (t) cc_final: 0.8948 (m) REVERT: R 76 ILE cc_start: 0.9380 (pp) cc_final: 0.9036 (pp) REVERT: R 77 LYS cc_start: 0.9211 (tttm) cc_final: 0.8624 (tppt) REVERT: R 80 MET cc_start: 0.8543 (OUTLIER) cc_final: 0.8323 (ttm) REVERT: T 25 GLU cc_start: 0.8604 (mt-10) cc_final: 0.8369 (mt-10) REVERT: T 36 ASN cc_start: 0.8740 (m110) cc_final: 0.8230 (m-40) REVERT: T 48 ASP cc_start: 0.8466 (t0) cc_final: 0.8028 (t0) REVERT: T 51 SER cc_start: 0.8981 (p) cc_final: 0.8690 (p) REVERT: T 73 ASP cc_start: 0.7850 (t0) cc_final: 0.7529 (t0) REVERT: T 76 ARG cc_start: 0.8558 (mtm180) cc_final: 0.8146 (ttm110) REVERT: U 18 GLN cc_start: 0.8198 (mt0) cc_final: 0.7531 (mm-40) REVERT: U 39 PHE cc_start: 0.9064 (t80) cc_final: 0.8351 (t80) REVERT: V 24 ILE cc_start: 0.8551 (OUTLIER) cc_final: 0.7913 (pp) REVERT: V 44 HIS cc_start: 0.8139 (m90) cc_final: 0.7894 (m90) REVERT: V 61 ARG cc_start: 0.8112 (ppp80) cc_final: 0.7776 (ppp80) REVERT: V 80 LYS cc_start: 0.8881 (tmtt) cc_final: 0.8519 (tptt) REVERT: W 24 ASP cc_start: 0.8433 (t0) cc_final: 0.8192 (t0) REVERT: W 42 ARG cc_start: 0.9076 (OUTLIER) cc_final: 0.8780 (mtm110) REVERT: W 51 GLN cc_start: 0.8725 (tp40) cc_final: 0.7876 (tm-30) REVERT: X 10 ILE cc_start: 0.9046 (pt) cc_final: 0.8394 (mm) REVERT: Y 15 LYS cc_start: 0.8877 (tttm) cc_final: 0.8261 (tptp) REVERT: Y 17 ARG cc_start: 0.8855 (tmm-80) cc_final: 0.8255 (ttp-110) REVERT: Y 18 LYS cc_start: 0.9171 (mttp) cc_final: 0.8823 (mtpp) REVERT: Y 28 ARG cc_start: 0.8323 (mtt180) cc_final: 0.8008 (mtt-85) REVERT: Y 47 GLN cc_start: 0.8787 (OUTLIER) cc_final: 0.8558 (mp10) REVERT: Y 50 PHE cc_start: 0.8638 (t80) cc_final: 0.8423 (t80) REVERT: Y 53 MET cc_start: 0.8938 (tmm) cc_final: 0.8725 (tmm) REVERT: Y 54 GLN cc_start: 0.8638 (tt0) cc_final: 0.8334 (tt0) REVERT: Y 81 GLN cc_start: 0.9205 (mm-40) cc_final: 0.8713 (mm-40) REVERT: Z 38 GLU cc_start: 0.7974 (pp20) cc_final: 0.7714 (tm-30) REVERT: a 16 ASP cc_start: 0.2141 (OUTLIER) cc_final: 0.1769 (t70) REVERT: a 218 MET cc_start: 0.5035 (mtt) cc_final: 0.3842 (mmt) outliers start: 406 outliers final: 251 residues processed: 1838 average time/residue: 2.0541 time to fit residues: 5548.5921 Evaluate side-chains 1911 residues out of total 4908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 291 poor density : 1620 time to evaluate : 6.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 37 SER Chi-restraints excluded: chain b residue 48 ILE Chi-restraints excluded: chain b residue 50 THR Chi-restraints excluded: chain b residue 52 HIS Chi-restraints excluded: chain b residue 86 ARG Chi-restraints excluded: chain b residue 114 GLN Chi-restraints excluded: chain b residue 152 GLN Chi-restraints excluded: chain b residue 164 VAL Chi-restraints excluded: chain b residue 194 VAL Chi-restraints excluded: chain b residue 250 GLN Chi-restraints excluded: chain b residue 269 ARG Chi-restraints excluded: chain c residue 2 ILE Chi-restraints excluded: chain c residue 9 VAL Chi-restraints excluded: chain c residue 30 GLU Chi-restraints excluded: chain c residue 39 ASP Chi-restraints excluded: chain c residue 95 SER Chi-restraints excluded: chain c residue 104 VAL Chi-restraints excluded: chain c residue 110 THR Chi-restraints excluded: chain c residue 157 LYS Chi-restraints excluded: chain c residue 170 VAL Chi-restraints excluded: chain c residue 193 VAL Chi-restraints excluded: chain c residue 199 SER Chi-restraints excluded: chain c residue 200 ASP Chi-restraints excluded: chain d residue 48 THR Chi-restraints excluded: chain d residue 65 THR Chi-restraints excluded: chain d residue 72 SER Chi-restraints excluded: chain d residue 84 THR Chi-restraints excluded: chain d residue 88 ARG Chi-restraints excluded: chain d residue 96 VAL Chi-restraints excluded: chain d residue 108 ILE Chi-restraints excluded: chain d residue 120 VAL Chi-restraints excluded: chain d residue 146 VAL Chi-restraints excluded: chain d residue 189 THR Chi-restraints excluded: chain e residue 16 MET Chi-restraints excluded: chain e residue 23 SER Chi-restraints excluded: chain e residue 24 VAL Chi-restraints excluded: chain e residue 29 ARG Chi-restraints excluded: chain e residue 30 VAL Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 60 SER Chi-restraints excluded: chain e residue 65 LEU Chi-restraints excluded: chain e residue 67 THR Chi-restraints excluded: chain e residue 89 THR Chi-restraints excluded: chain e residue 90 LEU Chi-restraints excluded: chain e residue 100 GLU Chi-restraints excluded: chain e residue 117 SER Chi-restraints excluded: chain e residue 131 VAL Chi-restraints excluded: chain e residue 157 THR Chi-restraints excluded: chain e residue 173 ASP Chi-restraints excluded: chain f residue 1 SER Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 23 ILE Chi-restraints excluded: chain f residue 38 ASP Chi-restraints excluded: chain f residue 105 SER Chi-restraints excluded: chain f residue 113 ASP Chi-restraints excluded: chain g residue 6 LEU Chi-restraints excluded: chain g residue 7 ASP Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain g residue 61 VAL Chi-restraints excluded: chain g residue 96 THR Chi-restraints excluded: chain g residue 115 VAL Chi-restraints excluded: chain g residue 117 LEU Chi-restraints excluded: chain g residue 133 GLN Chi-restraints excluded: chain h residue 3 LEU Chi-restraints excluded: chain h residue 5 LEU Chi-restraints excluded: chain h residue 77 VAL Chi-restraints excluded: chain h residue 128 THR Chi-restraints excluded: chain i residue 12 VAL Chi-restraints excluded: chain i residue 35 MET Chi-restraints excluded: chain j residue 54 ILE Chi-restraints excluded: chain j residue 73 VAL Chi-restraints excluded: chain j residue 131 ASN Chi-restraints excluded: chain k residue 14 SER Chi-restraints excluded: chain k residue 17 ARG Chi-restraints excluded: chain k residue 28 SER Chi-restraints excluded: chain k residue 45 GLU Chi-restraints excluded: chain k residue 69 VAL Chi-restraints excluded: chain k residue 80 ASP Chi-restraints excluded: chain k residue 118 LEU Chi-restraints excluded: chain l residue 12 SER Chi-restraints excluded: chain l residue 85 VAL Chi-restraints excluded: chain l residue 110 VAL Chi-restraints excluded: chain l residue 116 VAL Chi-restraints excluded: chain l residue 118 THR Chi-restraints excluded: chain l residue 120 VAL Chi-restraints excluded: chain l residue 121 THR Chi-restraints excluded: chain l residue 122 VAL Chi-restraints excluded: chain l residue 127 VAL Chi-restraints excluded: chain m residue 54 THR Chi-restraints excluded: chain m residue 74 THR Chi-restraints excluded: chain m residue 93 VAL Chi-restraints excluded: chain m residue 97 GLN Chi-restraints excluded: chain m residue 118 LYS Chi-restraints excluded: chain m residue 126 ILE Chi-restraints excluded: chain m residue 132 THR Chi-restraints excluded: chain n residue 27 SER Chi-restraints excluded: chain n residue 73 ASN Chi-restraints excluded: chain n residue 75 ILE Chi-restraints excluded: chain n residue 76 VAL Chi-restraints excluded: chain o residue 12 THR Chi-restraints excluded: chain o residue 21 LEU Chi-restraints excluded: chain o residue 35 ILE Chi-restraints excluded: chain o residue 39 VAL Chi-restraints excluded: chain o residue 40 ILE Chi-restraints excluded: chain o residue 48 LEU Chi-restraints excluded: chain o residue 65 THR Chi-restraints excluded: chain o residue 95 SER Chi-restraints excluded: chain o residue 103 VAL Chi-restraints excluded: chain o residue 112 GLU Chi-restraints excluded: chain p residue 2 ASN Chi-restraints excluded: chain p residue 7 LEU Chi-restraints excluded: chain p residue 63 ILE Chi-restraints excluded: chain p residue 65 ASN Chi-restraints excluded: chain p residue 91 VAL Chi-restraints excluded: chain p residue 93 LYS Chi-restraints excluded: chain q residue 58 GLN Chi-restraints excluded: chain q residue 82 LEU Chi-restraints excluded: chain q residue 109 VAL Chi-restraints excluded: chain r residue 33 VAL Chi-restraints excluded: chain r residue 47 VAL Chi-restraints excluded: chain r residue 48 LYS Chi-restraints excluded: chain r residue 63 VAL Chi-restraints excluded: chain r residue 101 ILE Chi-restraints excluded: chain s residue 20 VAL Chi-restraints excluded: chain s residue 23 LEU Chi-restraints excluded: chain s residue 77 ASP Chi-restraints excluded: chain s residue 104 THR Chi-restraints excluded: chain s residue 106 VAL Chi-restraints excluded: chain s residue 107 VAL Chi-restraints excluded: chain s residue 108 SER Chi-restraints excluded: chain t residue 1 MET Chi-restraints excluded: chain t residue 16 VAL Chi-restraints excluded: chain t residue 17 SER Chi-restraints excluded: chain t residue 39 THR Chi-restraints excluded: chain t residue 57 VAL Chi-restraints excluded: chain t residue 85 VAL Chi-restraints excluded: chain t residue 87 LEU Chi-restraints excluded: chain u residue 4 ILE Chi-restraints excluded: chain u residue 24 VAL Chi-restraints excluded: chain u residue 48 VAL Chi-restraints excluded: chain u residue 61 GLU Chi-restraints excluded: chain v residue 30 ILE Chi-restraints excluded: chain v residue 45 ASP Chi-restraints excluded: chain v residue 47 VAL Chi-restraints excluded: chain v residue 64 VAL Chi-restraints excluded: chain v residue 65 VAL Chi-restraints excluded: chain v residue 92 VAL Chi-restraints excluded: chain w residue 32 ILE Chi-restraints excluded: chain w residue 34 VAL Chi-restraints excluded: chain w residue 39 THR Chi-restraints excluded: chain w residue 51 ARG Chi-restraints excluded: chain w residue 66 GLU Chi-restraints excluded: chain w residue 67 VAL Chi-restraints excluded: chain w residue 68 LYS Chi-restraints excluded: chain x residue 1 SER Chi-restraints excluded: chain x residue 13 THR Chi-restraints excluded: chain x residue 33 HIS Chi-restraints excluded: chain x residue 39 VAL Chi-restraints excluded: chain x residue 46 VAL Chi-restraints excluded: chain x residue 47 THR Chi-restraints excluded: chain x residue 64 ASP Chi-restraints excluded: chain x residue 67 LEU Chi-restraints excluded: chain x residue 69 GLU Chi-restraints excluded: chain y residue 11 VAL Chi-restraints excluded: chain y residue 39 GLN Chi-restraints excluded: chain y residue 40 SER Chi-restraints excluded: chain y residue 43 LEU Chi-restraints excluded: chain y residue 55 THR Chi-restraints excluded: chain z residue 29 ARG Chi-restraints excluded: chain z residue 56 VAL Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 28 ARG Chi-restraints excluded: chain D residue 41 ARG Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain F residue 35 GLN Chi-restraints excluded: chain G residue 5 MET Chi-restraints excluded: chain G residue 141 GLU Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 198 VAL Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain G residue 216 VAL Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 43 THR Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 117 ASP Chi-restraints excluded: chain H residue 123 LEU Chi-restraints excluded: chain H residue 156 LEU Chi-restraints excluded: chain H residue 164 THR Chi-restraints excluded: chain H residue 174 LEU Chi-restraints excluded: chain H residue 184 ASN Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 93 LEU Chi-restraints excluded: chain I residue 118 SER Chi-restraints excluded: chain I residue 133 SER Chi-restraints excluded: chain I residue 143 SER Chi-restraints excluded: chain J residue 89 THR Chi-restraints excluded: chain J residue 104 ILE Chi-restraints excluded: chain J residue 105 ILE Chi-restraints excluded: chain J residue 123 LEU Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 146 MET Chi-restraints excluded: chain J residue 147 ASN Chi-restraints excluded: chain K residue 7 VAL Chi-restraints excluded: chain K residue 17 GLN Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 39 LEU Chi-restraints excluded: chain K residue 75 GLU Chi-restraints excluded: chain K residue 84 VAL Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain L residue 96 ASN Chi-restraints excluded: chain L residue 117 LEU Chi-restraints excluded: chain L residue 121 ASN Chi-restraints excluded: chain M residue 2 MET Chi-restraints excluded: chain M residue 6 ILE Chi-restraints excluded: chain M residue 57 GLU Chi-restraints excluded: chain M residue 58 LEU Chi-restraints excluded: chain M residue 98 LEU Chi-restraints excluded: chain M residue 104 SER Chi-restraints excluded: chain M residue 125 ILE Chi-restraints excluded: chain N residue 28 VAL Chi-restraints excluded: chain N residue 78 ILE Chi-restraints excluded: chain O residue 18 ILE Chi-restraints excluded: chain O residue 44 THR Chi-restraints excluded: chain O residue 50 THR Chi-restraints excluded: chain O residue 91 ASP Chi-restraints excluded: chain O residue 92 LEU Chi-restraints excluded: chain P residue 25 SER Chi-restraints excluded: chain P residue 30 ILE Chi-restraints excluded: chain P residue 45 THR Chi-restraints excluded: chain P residue 54 SER Chi-restraints excluded: chain P residue 63 GLN Chi-restraints excluded: chain P residue 109 ILE Chi-restraints excluded: chain Q residue 32 VAL Chi-restraints excluded: chain Q residue 34 THR Chi-restraints excluded: chain Q residue 39 THR Chi-restraints excluded: chain Q residue 40 THR Chi-restraints excluded: chain Q residue 46 SER Chi-restraints excluded: chain Q residue 51 VAL Chi-restraints excluded: chain Q residue 57 THR Chi-restraints excluded: chain Q residue 63 THR Chi-restraints excluded: chain Q residue 73 LEU Chi-restraints excluded: chain Q residue 92 VAL Chi-restraints excluded: chain Q residue 97 VAL Chi-restraints excluded: chain Q residue 102 ASP Chi-restraints excluded: chain R residue 20 SER Chi-restraints excluded: chain R residue 24 VAL Chi-restraints excluded: chain R residue 58 GLU Chi-restraints excluded: chain R residue 59 VAL Chi-restraints excluded: chain R residue 80 MET Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain S residue 47 LEU Chi-restraints excluded: chain U residue 21 VAL Chi-restraints excluded: chain U residue 68 SER Chi-restraints excluded: chain V residue 24 ILE Chi-restraints excluded: chain V residue 32 ILE Chi-restraints excluded: chain V residue 41 THR Chi-restraints excluded: chain V residue 54 ILE Chi-restraints excluded: chain V residue 56 ASP Chi-restraints excluded: chain V residue 71 SER Chi-restraints excluded: chain V residue 82 VAL Chi-restraints excluded: chain W residue 35 SER Chi-restraints excluded: chain W residue 42 ARG Chi-restraints excluded: chain W residue 70 THR Chi-restraints excluded: chain X residue 37 SER Chi-restraints excluded: chain X residue 38 THR Chi-restraints excluded: chain X residue 48 ILE Chi-restraints excluded: chain X residue 78 THR Chi-restraints excluded: chain Y residue 22 SER Chi-restraints excluded: chain Y residue 25 SER Chi-restraints excluded: chain Y residue 47 GLN Chi-restraints excluded: chain Y residue 60 GLN Chi-restraints excluded: chain Y residue 74 HIS Chi-restraints excluded: chain Y residue 78 LEU Chi-restraints excluded: chain Y residue 79 THR Chi-restraints excluded: chain Z residue 12 ASP Chi-restraints excluded: chain Z residue 59 LEU Chi-restraints excluded: chain a residue 8 MET Chi-restraints excluded: chain a residue 16 ASP Chi-restraints excluded: chain a residue 35 THR Chi-restraints excluded: chain a residue 46 VAL Chi-restraints excluded: chain a residue 53 ARG Chi-restraints excluded: chain a residue 64 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1050 random chunks: chunk 979 optimal weight: 10.0000 chunk 114 optimal weight: 20.0000 chunk 578 optimal weight: 0.0270 chunk 741 optimal weight: 10.0000 chunk 574 optimal weight: 50.0000 chunk 855 optimal weight: 10.0000 chunk 567 optimal weight: 30.0000 chunk 1012 optimal weight: 20.0000 chunk 633 optimal weight: 20.0000 chunk 616 optimal weight: 10.0000 chunk 467 optimal weight: 7.9990 overall best weight: 7.6052 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 62 GLN ** e 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 63 GLN ** f 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 18 GLN o 19 GLN ** o 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 51 GLN r 87 GLN s 57 ASN t 48 GLN u 65 GLN v 12 GLN x 16 ASN ** x 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** y 15 ASN y 20 ASN ** y 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 3 GLN G 202 ASN ** H 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 53 GLN I 88 ASN ** I 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 49 GLN O 56 HIS ** P 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 4 ASN T 27 GLN ** T 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.3677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.108 161399 Z= 0.476 Angle : 0.737 16.245 241370 Z= 0.375 Chirality : 0.043 0.317 30856 Planarity : 0.006 0.059 13007 Dihedral : 23.157 179.870 80580 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 0.30 % Allowed : 10.04 % Favored : 89.66 % Rotamer: Outliers : 9.07 % Allowed : 31.60 % Favored : 59.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.01 (0.11), residues: 5919 helix: -0.38 (0.12), residues: 1861 sheet: -1.45 (0.15), residues: 1072 loop : -1.91 (0.11), residues: 2986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP b 212 HIS 0.008 0.001 HIS X 56 PHE 0.041 0.002 PHE g 46 TYR 0.034 0.003 TYR K 25 ARG 0.017 0.001 ARG x 10 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11838 Ramachandran restraints generated. 5919 Oldfield, 0 Emsley, 5919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11838 Ramachandran restraints generated. 5919 Oldfield, 0 Emsley, 5919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2057 residues out of total 4908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 445 poor density : 1612 time to evaluate : 5.967 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: b 22 GLU cc_start: 0.8119 (pp20) cc_final: 0.7840 (pp20) REVERT: b 86 ARG cc_start: 0.9113 (OUTLIER) cc_final: 0.8259 (mtm-85) REVERT: b 97 ASP cc_start: 0.8822 (p0) cc_final: 0.8499 (p0) REVERT: b 114 GLN cc_start: 0.8768 (OUTLIER) cc_final: 0.8350 (tt0) REVERT: b 152 GLN cc_start: 0.8696 (OUTLIER) cc_final: 0.7880 (mm110) REVERT: b 250 GLN cc_start: 0.8820 (OUTLIER) cc_final: 0.8113 (tt0) REVERT: c 1 MET cc_start: 0.8633 (tmm) cc_final: 0.8213 (tmm) REVERT: c 2 ILE cc_start: 0.8839 (OUTLIER) cc_final: 0.8502 (pp) REVERT: c 128 ARG cc_start: 0.8293 (OUTLIER) cc_final: 0.7666 (mtp180) REVERT: c 167 ASN cc_start: 0.9400 (t0) cc_final: 0.9032 (t160) REVERT: d 30 GLN cc_start: 0.9056 (tp40) cc_final: 0.8217 (tt0) REVERT: d 51 GLU cc_start: 0.8054 (pm20) cc_final: 0.7758 (pm20) REVERT: d 80 SER cc_start: 0.8984 (OUTLIER) cc_final: 0.8558 (p) REVERT: d 88 ARG cc_start: 0.8489 (OUTLIER) cc_final: 0.8125 (mmp80) REVERT: d 115 GLN cc_start: 0.8546 (mm-40) cc_final: 0.8235 (mm-40) REVERT: e 25 MET cc_start: 0.8998 (ppp) cc_final: 0.8181 (ppp) REVERT: e 29 ARG cc_start: 0.8691 (OUTLIER) cc_final: 0.8227 (ptp-170) REVERT: e 31 GLU cc_start: 0.8363 (mt-10) cc_final: 0.8117 (mm-30) REVERT: e 36 ASN cc_start: 0.6961 (OUTLIER) cc_final: 0.6675 (t0) REVERT: e 65 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8357 (tm) REVERT: e 95 MET cc_start: 0.8936 (ppp) cc_final: 0.8627 (ppp) REVERT: e 99 PHE cc_start: 0.9017 (t80) cc_final: 0.8778 (t80) REVERT: e 100 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7998 (mp0) REVERT: f 19 ASN cc_start: 0.8790 (t0) cc_final: 0.8552 (t0) REVERT: f 21 GLN cc_start: 0.8235 (tp-100) cc_final: 0.8016 (tp-100) REVERT: f 37 ASN cc_start: 0.7827 (t0) cc_final: 0.7353 (t0) REVERT: f 63 GLN cc_start: 0.8284 (mm-40) cc_final: 0.8009 (mm-40) REVERT: f 68 ARG cc_start: 0.8974 (tmt170) cc_final: 0.8710 (tmt-80) REVERT: f 82 PHE cc_start: 0.8280 (m-80) cc_final: 0.7699 (m-80) REVERT: f 100 ASN cc_start: 0.8507 (p0) cc_final: 0.8035 (p0) REVERT: f 113 ASP cc_start: 0.8319 (OUTLIER) cc_final: 0.8064 (m-30) REVERT: f 129 GLU cc_start: 0.8587 (tt0) cc_final: 0.8025 (tp30) REVERT: g 4 ILE cc_start: 0.8860 (tp) cc_final: 0.8523 (mm) REVERT: g 7 ASP cc_start: 0.8729 (OUTLIER) cc_final: 0.8504 (t0) REVERT: g 8 LYS cc_start: 0.8724 (mtpp) cc_final: 0.8032 (tptt) REVERT: g 25 TYR cc_start: 0.8906 (t80) cc_final: 0.8411 (t80) REVERT: g 35 LYS cc_start: 0.8737 (mptt) cc_final: 0.8474 (mptp) REVERT: g 117 LEU cc_start: 0.7008 (OUTLIER) cc_final: 0.6644 (pt) REVERT: h 5 LEU cc_start: 0.9086 (OUTLIER) cc_final: 0.8714 (pt) REVERT: j 13 ARG cc_start: 0.8233 (mtt90) cc_final: 0.8015 (mtt90) REVERT: j 71 ASP cc_start: 0.8523 (m-30) cc_final: 0.8311 (m-30) REVERT: k 12 ASP cc_start: 0.8420 (p0) cc_final: 0.8149 (p0) REVERT: k 49 ARG cc_start: 0.8201 (OUTLIER) cc_final: 0.7620 (mpp-170) REVERT: l 76 GLU cc_start: 0.7508 (mt-10) cc_final: 0.7173 (mt-10) REVERT: l 82 LEU cc_start: 0.9378 (tp) cc_final: 0.9116 (tm) REVERT: l 143 GLU cc_start: 0.7466 (pp20) cc_final: 0.7039 (pp20) REVERT: m 88 ASN cc_start: 0.8573 (m-40) cc_final: 0.8311 (m110) REVERT: m 91 TYR cc_start: 0.9145 (p90) cc_final: 0.8665 (p90) REVERT: m 97 GLN cc_start: 0.8636 (OUTLIER) cc_final: 0.8271 (mp-120) REVERT: n 35 LYS cc_start: 0.8869 (tttt) cc_final: 0.8547 (tptt) REVERT: n 72 ASP cc_start: 0.8847 (t0) cc_final: 0.8515 (t0) REVERT: o 80 GLU cc_start: 0.8914 (tm-30) cc_final: 0.8617 (tm-30) REVERT: p 23 ASP cc_start: 0.8617 (m-30) cc_final: 0.8190 (m-30) REVERT: p 26 GLU cc_start: 0.7922 (OUTLIER) cc_final: 0.7700 (tm-30) REVERT: p 65 ASN cc_start: 0.8907 (OUTLIER) cc_final: 0.8555 (p0) REVERT: q 58 GLN cc_start: 0.8926 (OUTLIER) cc_final: 0.8697 (tt0) REVERT: q 96 ASP cc_start: 0.8319 (t0) cc_final: 0.7759 (t0) REVERT: q 101 ASP cc_start: 0.8335 (OUTLIER) cc_final: 0.7963 (t0) REVERT: r 13 ARG cc_start: 0.8825 (ttp80) cc_final: 0.8218 (ttt-90) REVERT: r 31 GLU cc_start: 0.7723 (mp0) cc_final: 0.7438 (mp0) REVERT: r 37 GLU cc_start: 0.7979 (pm20) cc_final: 0.7609 (pm20) REVERT: r 60 LYS cc_start: 0.8934 (mtmm) cc_final: 0.8505 (mmmm) REVERT: s 52 GLU cc_start: 0.8024 (mm-30) cc_final: 0.7777 (tm-30) REVERT: t 1 MET cc_start: 0.7605 (OUTLIER) cc_final: 0.7122 (ptp) REVERT: t 28 ASN cc_start: 0.8817 (t0) cc_final: 0.8370 (t0) REVERT: t 36 LYS cc_start: 0.8423 (tptp) cc_final: 0.8117 (tptt) REVERT: t 42 GLU cc_start: 0.8493 (mp0) cc_final: 0.8257 (mp0) REVERT: t 86 THR cc_start: 0.9068 (m) cc_final: 0.8786 (p) REVERT: u 33 VAL cc_start: 0.9474 (OUTLIER) cc_final: 0.9224 (t) REVERT: u 36 GLU cc_start: 0.8857 (pp20) cc_final: 0.8568 (pp20) REVERT: u 61 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.7790 (mt-10) REVERT: v 38 LEU cc_start: 0.8939 (tp) cc_final: 0.8729 (tp) REVERT: v 46 LYS cc_start: 0.9175 (mmtm) cc_final: 0.8734 (mmpt) REVERT: v 50 MET cc_start: 0.8705 (mtm) cc_final: 0.8344 (mtt) REVERT: v 87 GLN cc_start: 0.8415 (mt0) cc_final: 0.7836 (mt0) REVERT: w 20 LYS cc_start: 0.9036 (OUTLIER) cc_final: 0.8377 (mmtm) REVERT: w 51 ARG cc_start: 0.9097 (OUTLIER) cc_final: 0.8752 (ppp80) REVERT: x 58 ILE cc_start: 0.9038 (OUTLIER) cc_final: 0.8815 (mm) REVERT: x 69 GLU cc_start: 0.8911 (OUTLIER) cc_final: 0.7937 (mp0) REVERT: y 1 MET cc_start: 0.6362 (tpt) cc_final: 0.6090 (tpt) REVERT: y 39 GLN cc_start: 0.8393 (OUTLIER) cc_final: 0.7913 (mt0) REVERT: B 5 ASN cc_start: 0.9030 (m-40) cc_final: 0.8647 (m110) REVERT: B 36 LYS cc_start: 0.9125 (mmtp) cc_final: 0.8774 (mptp) REVERT: C 36 LYS cc_start: 0.8676 (ttpt) cc_final: 0.8323 (mtpp) REVERT: D 41 ARG cc_start: 0.8048 (OUTLIER) cc_final: 0.7651 (mtp180) REVERT: E 48 MET cc_start: 0.8772 (mmt) cc_final: 0.8528 (mmt) REVERT: F 15 LYS cc_start: 0.8476 (mttt) cc_final: 0.8211 (tttp) REVERT: F 24 ARG cc_start: 0.8859 (mtt-85) cc_final: 0.8557 (mtt-85) REVERT: F 35 GLN cc_start: 0.8943 (OUTLIER) cc_final: 0.8618 (pt0) REVERT: G 8 MET cc_start: 0.8877 (mtp) cc_final: 0.8016 (mpp) REVERT: G 18 GLN cc_start: 0.8847 (mt0) cc_final: 0.8466 (mp10) REVERT: G 26 MET cc_start: 0.8686 (mmm) cc_final: 0.8393 (mmm) REVERT: G 48 MET cc_start: 0.9065 (OUTLIER) cc_final: 0.8698 (pmm) REVERT: G 131 LYS cc_start: 0.8269 (mmmt) cc_final: 0.8068 (mmtt) REVERT: H 5 HIS cc_start: 0.9158 (t-90) cc_final: 0.8874 (t-90) REVERT: H 39 ARG cc_start: 0.8669 (ttm-80) cc_final: 0.7558 (mtt180) REVERT: H 40 GLN cc_start: 0.8901 (tt0) cc_final: 0.8618 (pp30) REVERT: H 139 ASN cc_start: 0.8934 (m-40) cc_final: 0.8449 (m110) REVERT: H 151 GLU cc_start: 0.8162 (tm-30) cc_final: 0.7784 (tm-30) REVERT: H 184 ASN cc_start: 0.8824 (OUTLIER) cc_final: 0.8561 (t160) REVERT: H 191 THR cc_start: 0.9271 (p) cc_final: 0.8900 (t) REVERT: I 43 ARG cc_start: 0.7365 (mpp-170) cc_final: 0.6761 (mpp-170) REVERT: I 47 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8310 (mm) REVERT: I 68 GLU cc_start: 0.8355 (tp30) cc_final: 0.7815 (tp30) REVERT: I 71 PHE cc_start: 0.9229 (t80) cc_final: 0.8623 (t80) REVERT: I 73 ASN cc_start: 0.9401 (m110) cc_final: 0.8974 (m110) REVERT: I 112 GLU cc_start: 0.7325 (tt0) cc_final: 0.6987 (tt0) REVERT: I 116 LEU cc_start: 0.8832 (tp) cc_final: 0.8552 (tt) REVERT: I 137 SER cc_start: 0.8166 (t) cc_final: 0.7753 (p) REVERT: I 138 PRO cc_start: 0.8183 (Cg_exo) cc_final: 0.7738 (Cg_endo) REVERT: I 152 SER cc_start: 0.8894 (t) cc_final: 0.8646 (p) REVERT: J 12 GLU cc_start: 0.8205 (mt-10) cc_final: 0.7491 (mt-10) REVERT: J 32 PHE cc_start: 0.9087 (m-80) cc_final: 0.8703 (m-80) REVERT: J 60 GLN cc_start: 0.8867 (tp-100) cc_final: 0.8454 (OUTLIER) REVERT: J 67 ARG cc_start: 0.8711 (OUTLIER) cc_final: 0.8211 (mtt-85) REVERT: J 94 PHE cc_start: 0.8243 (t80) cc_final: 0.7584 (t80) REVERT: J 104 ILE cc_start: 0.9308 (OUTLIER) cc_final: 0.8744 (pp) REVERT: J 131 ASN cc_start: 0.8160 (t0) cc_final: 0.7788 (t0) REVERT: J 146 MET cc_start: 0.8356 (OUTLIER) cc_final: 0.7629 (ttp) REVERT: K 44 ARG cc_start: 0.8268 (ttp-170) cc_final: 0.7671 (ttm-80) REVERT: K 62 MET cc_start: 0.8104 (mmm) cc_final: 0.7776 (mmm) REVERT: K 65 GLU cc_start: 0.8112 (tp30) cc_final: 0.7767 (tp30) REVERT: K 86 ARG cc_start: 0.8679 (OUTLIER) cc_final: 0.8258 (ttm110) REVERT: K 88 MET cc_start: 0.8208 (ptm) cc_final: 0.7635 (ptm) REVERT: K 90 MET cc_start: 0.7508 (mtm) cc_final: 0.7097 (mpp) REVERT: L 3 ARG cc_start: 0.6599 (ttm170) cc_final: 0.6295 (ttm170) REVERT: L 100 MET cc_start: 0.8480 (mtm) cc_final: 0.8214 (mtm) REVERT: L 105 GLU cc_start: 0.8598 (pp20) cc_final: 0.8217 (pp20) REVERT: M 26 MET cc_start: 0.8491 (ptp) cc_final: 0.7966 (pmm) REVERT: M 28 SER cc_start: 0.8564 (p) cc_final: 0.8222 (p) REVERT: M 42 GLU cc_start: 0.7328 (tp30) cc_final: 0.7086 (tp30) REVERT: M 57 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7479 (pp20) REVERT: M 98 LEU cc_start: 0.9304 (OUTLIER) cc_final: 0.8821 (pt) REVERT: M 110 MET cc_start: 0.8324 (ptp) cc_final: 0.8073 (ptp) REVERT: N 20 ILE cc_start: 0.9054 (tt) cc_final: 0.8647 (tt) REVERT: N 21 LYS cc_start: 0.9058 (mtpt) cc_final: 0.8649 (mmtt) REVERT: N 27 ILE cc_start: 0.8951 (mp) cc_final: 0.8534 (mm) REVERT: N 49 GLN cc_start: 0.9359 (OUTLIER) cc_final: 0.8278 (tp-100) REVERT: N 123 ARG cc_start: 0.8638 (mmt90) cc_final: 0.8375 (tpp80) REVERT: O 9 ARG cc_start: 0.8403 (ttm-80) cc_final: 0.7810 (ttt180) REVERT: O 16 ARG cc_start: 0.8118 (ptt180) cc_final: 0.7782 (ptp90) REVERT: O 44 THR cc_start: 0.8380 (OUTLIER) cc_final: 0.8153 (t) REVERT: P 86 LYS cc_start: 0.8667 (OUTLIER) cc_final: 0.8331 (ptmm) REVERT: Q 37 TYR cc_start: 0.8293 (p90) cc_final: 0.7865 (p90) REVERT: Q 87 LYS cc_start: 0.8711 (OUTLIER) cc_final: 0.7939 (tppt) REVERT: R 15 VAL cc_start: 0.8242 (m) cc_final: 0.7996 (t) REVERT: R 52 ILE cc_start: 0.8927 (mt) cc_final: 0.8483 (mp) REVERT: R 76 ILE cc_start: 0.9375 (pp) cc_final: 0.9032 (pp) REVERT: R 77 LYS cc_start: 0.9226 (tttm) cc_final: 0.8660 (tppt) REVERT: R 80 MET cc_start: 0.8187 (OUTLIER) cc_final: 0.7987 (ttt) REVERT: S 97 LYS cc_start: 0.8552 (tttt) cc_final: 0.8144 (tttt) REVERT: T 25 GLU cc_start: 0.8631 (mt-10) cc_final: 0.8248 (mt-10) REVERT: T 36 ASN cc_start: 0.8710 (m110) cc_final: 0.8047 (m-40) REVERT: T 48 ASP cc_start: 0.8681 (t0) cc_final: 0.8177 (t0) REVERT: T 51 SER cc_start: 0.9104 (p) cc_final: 0.8806 (p) REVERT: T 73 ASP cc_start: 0.7981 (t0) cc_final: 0.7755 (t0) REVERT: T 76 ARG cc_start: 0.8540 (mtm180) cc_final: 0.8210 (ttm110) REVERT: U 18 GLN cc_start: 0.8241 (mt0) cc_final: 0.7634 (mt0) REVERT: U 39 PHE cc_start: 0.9030 (t80) cc_final: 0.8318 (t80) REVERT: U 53 ASP cc_start: 0.8386 (OUTLIER) cc_final: 0.8057 (p0) REVERT: V 44 HIS cc_start: 0.8199 (m90) cc_final: 0.7957 (m90) REVERT: V 61 ARG cc_start: 0.8275 (ppp80) cc_final: 0.7964 (ppp80) REVERT: V 80 LYS cc_start: 0.8847 (tmtt) cc_final: 0.8544 (tmtt) REVERT: W 24 ASP cc_start: 0.8640 (t0) cc_final: 0.8251 (t0) REVERT: W 42 ARG cc_start: 0.9114 (OUTLIER) cc_final: 0.8861 (mtm110) REVERT: X 5 LYS cc_start: 0.7153 (tppp) cc_final: 0.6384 (tppp) REVERT: X 36 ARG cc_start: 0.8719 (OUTLIER) cc_final: 0.7656 (ptm-80) REVERT: X 69 LYS cc_start: 0.8528 (OUTLIER) cc_final: 0.8130 (mttp) REVERT: Y 14 GLU cc_start: 0.8525 (tp30) cc_final: 0.8093 (tp30) REVERT: Y 15 LYS cc_start: 0.8949 (tttm) cc_final: 0.8355 (tptp) REVERT: Y 17 ARG cc_start: 0.8885 (tmm-80) cc_final: 0.8229 (ttp-110) REVERT: Y 28 ARG cc_start: 0.8339 (mtt180) cc_final: 0.8023 (mtt-85) REVERT: Y 50 PHE cc_start: 0.8676 (t80) cc_final: 0.8467 (t80) REVERT: Y 53 MET cc_start: 0.8809 (tmm) cc_final: 0.8580 (tmm) REVERT: Y 54 GLN cc_start: 0.8641 (tt0) cc_final: 0.8326 (tt0) REVERT: Y 81 GLN cc_start: 0.9188 (mm-40) cc_final: 0.8712 (mm-40) REVERT: Z 38 GLU cc_start: 0.8189 (pp20) cc_final: 0.7811 (tm-30) REVERT: Z 46 ARG cc_start: 0.8382 (OUTLIER) cc_final: 0.8177 (tmt-80) REVERT: a 16 ASP cc_start: 0.2104 (OUTLIER) cc_final: 0.1826 (t0) REVERT: a 218 MET cc_start: 0.5013 (mtt) cc_final: 0.3800 (mmt) outliers start: 445 outliers final: 287 residues processed: 1794 average time/residue: 2.0854 time to fit residues: 5472.3529 Evaluate side-chains 1929 residues out of total 4908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 338 poor density : 1591 time to evaluate : 6.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 37 SER Chi-restraints excluded: chain b residue 48 ILE Chi-restraints excluded: chain b residue 50 THR Chi-restraints excluded: chain b residue 52 HIS Chi-restraints excluded: chain b residue 86 ARG Chi-restraints excluded: chain b residue 114 GLN Chi-restraints excluded: chain b residue 120 ASP Chi-restraints excluded: chain b residue 140 VAL Chi-restraints excluded: chain b residue 152 GLN Chi-restraints excluded: chain b residue 163 ILE Chi-restraints excluded: chain b residue 164 VAL Chi-restraints excluded: chain b residue 194 VAL Chi-restraints excluded: chain b residue 250 GLN Chi-restraints excluded: chain b residue 256 THR Chi-restraints excluded: chain b residue 269 ARG Chi-restraints excluded: chain c residue 2 ILE Chi-restraints excluded: chain c residue 9 VAL Chi-restraints excluded: chain c residue 22 ILE Chi-restraints excluded: chain c residue 39 ASP Chi-restraints excluded: chain c residue 89 GLU Chi-restraints excluded: chain c residue 95 SER Chi-restraints excluded: chain c residue 97 SER Chi-restraints excluded: chain c residue 104 VAL Chi-restraints excluded: chain c residue 110 THR Chi-restraints excluded: chain c residue 128 ARG Chi-restraints excluded: chain c residue 130 GLN Chi-restraints excluded: chain c residue 155 VAL Chi-restraints excluded: chain c residue 157 LYS Chi-restraints excluded: chain c residue 170 VAL Chi-restraints excluded: chain c residue 193 VAL Chi-restraints excluded: chain c residue 199 SER Chi-restraints excluded: chain c residue 200 ASP Chi-restraints excluded: chain d residue 48 THR Chi-restraints excluded: chain d residue 65 THR Chi-restraints excluded: chain d residue 72 SER Chi-restraints excluded: chain d residue 80 SER Chi-restraints excluded: chain d residue 84 THR Chi-restraints excluded: chain d residue 88 ARG Chi-restraints excluded: chain d residue 96 VAL Chi-restraints excluded: chain d residue 120 VAL Chi-restraints excluded: chain d residue 146 VAL Chi-restraints excluded: chain d residue 189 THR Chi-restraints excluded: chain e residue 23 SER Chi-restraints excluded: chain e residue 24 VAL Chi-restraints excluded: chain e residue 29 ARG Chi-restraints excluded: chain e residue 30 VAL Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 36 ASN Chi-restraints excluded: chain e residue 60 SER Chi-restraints excluded: chain e residue 65 LEU Chi-restraints excluded: chain e residue 67 THR Chi-restraints excluded: chain e residue 89 THR Chi-restraints excluded: chain e residue 90 LEU Chi-restraints excluded: chain e residue 100 GLU Chi-restraints excluded: chain e residue 117 SER Chi-restraints excluded: chain e residue 131 VAL Chi-restraints excluded: chain e residue 157 THR Chi-restraints excluded: chain e residue 173 ASP Chi-restraints excluded: chain f residue 1 SER Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 23 ILE Chi-restraints excluded: chain f residue 66 THR Chi-restraints excluded: chain f residue 105 SER Chi-restraints excluded: chain f residue 112 VAL Chi-restraints excluded: chain f residue 113 ASP Chi-restraints excluded: chain f residue 126 THR Chi-restraints excluded: chain g residue 6 LEU Chi-restraints excluded: chain g residue 7 ASP Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain g residue 61 VAL Chi-restraints excluded: chain g residue 96 THR Chi-restraints excluded: chain g residue 115 VAL Chi-restraints excluded: chain g residue 117 LEU Chi-restraints excluded: chain h residue 3 LEU Chi-restraints excluded: chain h residue 5 LEU Chi-restraints excluded: chain h residue 77 VAL Chi-restraints excluded: chain h residue 128 THR Chi-restraints excluded: chain i residue 12 VAL Chi-restraints excluded: chain i residue 35 MET Chi-restraints excluded: chain j residue 12 LYS Chi-restraints excluded: chain j residue 73 VAL Chi-restraints excluded: chain j residue 131 ASN Chi-restraints excluded: chain k residue 14 SER Chi-restraints excluded: chain k residue 28 SER Chi-restraints excluded: chain k residue 45 GLU Chi-restraints excluded: chain k residue 49 ARG Chi-restraints excluded: chain k residue 69 VAL Chi-restraints excluded: chain k residue 80 ASP Chi-restraints excluded: chain k residue 118 LEU Chi-restraints excluded: chain l residue 12 SER Chi-restraints excluded: chain l residue 85 VAL Chi-restraints excluded: chain l residue 110 VAL Chi-restraints excluded: chain l residue 116 VAL Chi-restraints excluded: chain l residue 118 THR Chi-restraints excluded: chain l residue 120 VAL Chi-restraints excluded: chain l residue 121 THR Chi-restraints excluded: chain l residue 122 VAL Chi-restraints excluded: chain l residue 127 VAL Chi-restraints excluded: chain m residue 24 THR Chi-restraints excluded: chain m residue 54 THR Chi-restraints excluded: chain m residue 57 VAL Chi-restraints excluded: chain m residue 74 THR Chi-restraints excluded: chain m residue 93 VAL Chi-restraints excluded: chain m residue 97 GLN Chi-restraints excluded: chain m residue 112 LEU Chi-restraints excluded: chain m residue 118 LYS Chi-restraints excluded: chain m residue 126 ILE Chi-restraints excluded: chain m residue 132 THR Chi-restraints excluded: chain n residue 6 SER Chi-restraints excluded: chain n residue 18 GLN Chi-restraints excluded: chain n residue 27 SER Chi-restraints excluded: chain n residue 37 THR Chi-restraints excluded: chain n residue 59 SER Chi-restraints excluded: chain n residue 65 LEU Chi-restraints excluded: chain n residue 73 ASN Chi-restraints excluded: chain n residue 75 ILE Chi-restraints excluded: chain o residue 12 THR Chi-restraints excluded: chain o residue 21 LEU Chi-restraints excluded: chain o residue 35 ILE Chi-restraints excluded: chain o residue 39 VAL Chi-restraints excluded: chain o residue 48 LEU Chi-restraints excluded: chain o residue 65 THR Chi-restraints excluded: chain o residue 95 SER Chi-restraints excluded: chain o residue 103 VAL Chi-restraints excluded: chain o residue 112 GLU Chi-restraints excluded: chain p residue 7 LEU Chi-restraints excluded: chain p residue 26 GLU Chi-restraints excluded: chain p residue 63 ILE Chi-restraints excluded: chain p residue 65 ASN Chi-restraints excluded: chain p residue 91 VAL Chi-restraints excluded: chain p residue 93 LYS Chi-restraints excluded: chain q residue 14 LYS Chi-restraints excluded: chain q residue 58 GLN Chi-restraints excluded: chain q residue 82 LEU Chi-restraints excluded: chain q residue 101 ASP Chi-restraints excluded: chain q residue 109 VAL Chi-restraints excluded: chain r residue 33 VAL Chi-restraints excluded: chain r residue 47 VAL Chi-restraints excluded: chain s residue 20 VAL Chi-restraints excluded: chain s residue 23 LEU Chi-restraints excluded: chain s residue 74 ILE Chi-restraints excluded: chain s residue 96 ILE Chi-restraints excluded: chain s residue 104 THR Chi-restraints excluded: chain s residue 106 VAL Chi-restraints excluded: chain s residue 107 VAL Chi-restraints excluded: chain s residue 108 SER Chi-restraints excluded: chain t residue 1 MET Chi-restraints excluded: chain t residue 16 VAL Chi-restraints excluded: chain t residue 17 SER Chi-restraints excluded: chain t residue 27 SER Chi-restraints excluded: chain t residue 39 THR Chi-restraints excluded: chain t residue 48 GLN Chi-restraints excluded: chain t residue 57 VAL Chi-restraints excluded: chain t residue 85 VAL Chi-restraints excluded: chain t residue 87 LEU Chi-restraints excluded: chain u residue 4 ILE Chi-restraints excluded: chain u residue 11 ILE Chi-restraints excluded: chain u residue 24 VAL Chi-restraints excluded: chain u residue 33 VAL Chi-restraints excluded: chain u residue 48 VAL Chi-restraints excluded: chain u residue 61 GLU Chi-restraints excluded: chain v residue 17 SER Chi-restraints excluded: chain v residue 20 LEU Chi-restraints excluded: chain v residue 45 ASP Chi-restraints excluded: chain v residue 47 VAL Chi-restraints excluded: chain v residue 53 LYS Chi-restraints excluded: chain v residue 64 VAL Chi-restraints excluded: chain v residue 65 VAL Chi-restraints excluded: chain v residue 92 VAL Chi-restraints excluded: chain w residue 20 LYS Chi-restraints excluded: chain w residue 32 ILE Chi-restraints excluded: chain w residue 34 VAL Chi-restraints excluded: chain w residue 39 THR Chi-restraints excluded: chain w residue 51 ARG Chi-restraints excluded: chain w residue 66 GLU Chi-restraints excluded: chain w residue 74 LYS Chi-restraints excluded: chain w residue 76 ILE Chi-restraints excluded: chain x residue 1 SER Chi-restraints excluded: chain x residue 7 THR Chi-restraints excluded: chain x residue 13 THR Chi-restraints excluded: chain x residue 33 HIS Chi-restraints excluded: chain x residue 39 VAL Chi-restraints excluded: chain x residue 46 VAL Chi-restraints excluded: chain x residue 47 THR Chi-restraints excluded: chain x residue 58 ILE Chi-restraints excluded: chain x residue 64 ASP Chi-restraints excluded: chain x residue 67 LEU Chi-restraints excluded: chain x residue 69 GLU Chi-restraints excluded: chain y residue 30 MET Chi-restraints excluded: chain y residue 39 GLN Chi-restraints excluded: chain y residue 40 SER Chi-restraints excluded: chain y residue 43 LEU Chi-restraints excluded: chain y residue 55 THR Chi-restraints excluded: chain z residue 29 ARG Chi-restraints excluded: chain z residue 56 VAL Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 30 ASP Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 41 ARG Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain F residue 35 GLN Chi-restraints excluded: chain G residue 48 MET Chi-restraints excluded: chain G residue 129 THR Chi-restraints excluded: chain G residue 141 GLU Chi-restraints excluded: chain G residue 158 ASP Chi-restraints excluded: chain G residue 162 VAL Chi-restraints excluded: chain G residue 188 THR Chi-restraints excluded: chain G residue 198 VAL Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain G residue 216 VAL Chi-restraints excluded: chain H residue 20 THR Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 43 THR Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain H residue 117 ASP Chi-restraints excluded: chain H residue 118 SER Chi-restraints excluded: chain H residue 123 LEU Chi-restraints excluded: chain H residue 156 LEU Chi-restraints excluded: chain H residue 164 THR Chi-restraints excluded: chain H residue 174 LEU Chi-restraints excluded: chain H residue 184 ASN Chi-restraints excluded: chain I residue 9 LYS Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 93 LEU Chi-restraints excluded: chain I residue 118 SER Chi-restraints excluded: chain I residue 133 SER Chi-restraints excluded: chain I residue 143 SER Chi-restraints excluded: chain I residue 191 SER Chi-restraints excluded: chain J residue 67 ARG Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain J residue 89 THR Chi-restraints excluded: chain J residue 104 ILE Chi-restraints excluded: chain J residue 105 ILE Chi-restraints excluded: chain J residue 123 LEU Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 146 MET Chi-restraints excluded: chain J residue 147 ASN Chi-restraints excluded: chain K residue 7 VAL Chi-restraints excluded: chain K residue 17 GLN Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 39 LEU Chi-restraints excluded: chain K residue 68 GLN Chi-restraints excluded: chain K residue 75 GLU Chi-restraints excluded: chain K residue 84 VAL Chi-restraints excluded: chain K residue 86 ARG Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain L residue 96 ASN Chi-restraints excluded: chain L residue 117 LEU Chi-restraints excluded: chain L residue 121 ASN Chi-restraints excluded: chain M residue 6 ILE Chi-restraints excluded: chain M residue 9 MET Chi-restraints excluded: chain M residue 57 GLU Chi-restraints excluded: chain M residue 61 THR Chi-restraints excluded: chain M residue 98 LEU Chi-restraints excluded: chain M residue 104 SER Chi-restraints excluded: chain M residue 125 ILE Chi-restraints excluded: chain N residue 28 VAL Chi-restraints excluded: chain N residue 49 GLN Chi-restraints excluded: chain N residue 78 ILE Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain O residue 44 THR Chi-restraints excluded: chain O residue 50 THR Chi-restraints excluded: chain O residue 91 ASP Chi-restraints excluded: chain O residue 92 LEU Chi-restraints excluded: chain P residue 25 SER Chi-restraints excluded: chain P residue 30 ILE Chi-restraints excluded: chain P residue 45 THR Chi-restraints excluded: chain P residue 54 SER Chi-restraints excluded: chain P residue 86 LYS Chi-restraints excluded: chain Q residue 32 VAL Chi-restraints excluded: chain Q residue 34 THR Chi-restraints excluded: chain Q residue 39 THR Chi-restraints excluded: chain Q residue 40 THR Chi-restraints excluded: chain Q residue 46 SER Chi-restraints excluded: chain Q residue 51 VAL Chi-restraints excluded: chain Q residue 57 THR Chi-restraints excluded: chain Q residue 63 THR Chi-restraints excluded: chain Q residue 73 LEU Chi-restraints excluded: chain Q residue 87 LYS Chi-restraints excluded: chain Q residue 92 VAL Chi-restraints excluded: chain Q residue 97 VAL Chi-restraints excluded: chain Q residue 102 ASP Chi-restraints excluded: chain R residue 20 SER Chi-restraints excluded: chain R residue 24 VAL Chi-restraints excluded: chain R residue 58 GLU Chi-restraints excluded: chain R residue 80 MET Chi-restraints excluded: chain R residue 107 THR Chi-restraints excluded: chain S residue 47 LEU Chi-restraints excluded: chain S residue 54 SER Chi-restraints excluded: chain T residue 4 THR Chi-restraints excluded: chain T residue 27 GLN Chi-restraints excluded: chain T residue 30 LEU Chi-restraints excluded: chain T residue 80 LEU Chi-restraints excluded: chain T residue 81 ILE Chi-restraints excluded: chain U residue 21 VAL Chi-restraints excluded: chain U residue 53 ASP Chi-restraints excluded: chain U residue 68 SER Chi-restraints excluded: chain V residue 24 ILE Chi-restraints excluded: chain V residue 32 ILE Chi-restraints excluded: chain V residue 41 THR Chi-restraints excluded: chain V residue 54 ILE Chi-restraints excluded: chain V residue 56 ASP Chi-restraints excluded: chain V residue 71 SER Chi-restraints excluded: chain V residue 82 VAL Chi-restraints excluded: chain W residue 35 SER Chi-restraints excluded: chain W residue 42 ARG Chi-restraints excluded: chain W residue 70 THR Chi-restraints excluded: chain X residue 36 ARG Chi-restraints excluded: chain X residue 37 SER Chi-restraints excluded: chain X residue 38 THR Chi-restraints excluded: chain X residue 48 ILE Chi-restraints excluded: chain X residue 69 LYS Chi-restraints excluded: chain X residue 78 THR Chi-restraints excluded: chain Y residue 22 SER Chi-restraints excluded: chain Y residue 25 SER Chi-restraints excluded: chain Y residue 74 HIS Chi-restraints excluded: chain Y residue 78 LEU Chi-restraints excluded: chain Y residue 79 THR Chi-restraints excluded: chain Z residue 12 ASP Chi-restraints excluded: chain Z residue 46 ARG Chi-restraints excluded: chain Z residue 59 LEU Chi-restraints excluded: chain a residue 16 ASP Chi-restraints excluded: chain a residue 35 THR Chi-restraints excluded: chain a residue 46 VAL Chi-restraints excluded: chain a residue 53 ARG Chi-restraints excluded: chain a residue 64 VAL Chi-restraints excluded: chain a residue 207 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1050 random chunks: chunk 626 optimal weight: 50.0000 chunk 404 optimal weight: 6.9990 chunk 604 optimal weight: 10.0000 chunk 304 optimal weight: 6.9990 chunk 198 optimal weight: 0.9990 chunk 196 optimal weight: 0.9980 chunk 643 optimal weight: 20.0000 chunk 689 optimal weight: 10.0000 chunk 500 optimal weight: 7.9990 chunk 94 optimal weight: 9.9990 chunk 795 optimal weight: 8.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 94 GLN ** e 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 127 GLN j 128 ASN o 29 HIS q 51 GLN r 86 GLN r 87 GLN s 61 ASN t 48 GLN u 65 GLN v 12 GLN x 16 ASN ** x 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** y 20 ASN y 27 ASN B 3 GLN ** H 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 53 GLN ** I 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 147 ASN N 49 GLN O 56 HIS Q 4 ASN U 79 ASN V 49 ASN Y 60 GLN ** Y 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.3743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 161399 Z= 0.315 Angle : 0.665 16.166 241370 Z= 0.340 Chirality : 0.039 0.310 30856 Planarity : 0.005 0.072 13007 Dihedral : 23.190 179.237 80578 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 14.30 Ramachandran Plot: Outliers : 0.25 % Allowed : 9.12 % Favored : 90.62 % Rotamer: Outliers : 8.01 % Allowed : 33.29 % Favored : 58.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.90 (0.11), residues: 5919 helix: -0.25 (0.12), residues: 1852 sheet: -1.39 (0.15), residues: 1046 loop : -1.87 (0.11), residues: 3021 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP G 103 HIS 0.006 0.001 HIS X 56 PHE 0.034 0.002 PHE g 46 TYR 0.026 0.002 TYR G 212 ARG 0.019 0.001 ARG x 10 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11838 Ramachandran restraints generated. 5919 Oldfield, 0 Emsley, 5919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11838 Ramachandran restraints generated. 5919 Oldfield, 0 Emsley, 5919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2032 residues out of total 4908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 393 poor density : 1639 time to evaluate : 6.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 22 GLU cc_start: 0.7975 (pp20) cc_final: 0.7735 (pp20) REVERT: b 86 ARG cc_start: 0.9065 (OUTLIER) cc_final: 0.8228 (mtm-85) REVERT: b 97 ASP cc_start: 0.8844 (p0) cc_final: 0.8531 (p0) REVERT: b 114 GLN cc_start: 0.8733 (OUTLIER) cc_final: 0.8315 (tt0) REVERT: b 152 GLN cc_start: 0.8613 (OUTLIER) cc_final: 0.8220 (mm-40) REVERT: b 250 GLN cc_start: 0.8835 (OUTLIER) cc_final: 0.8075 (tt0) REVERT: c 1 MET cc_start: 0.8656 (tmm) cc_final: 0.8161 (tmm) REVERT: c 2 ILE cc_start: 0.8812 (OUTLIER) cc_final: 0.8513 (pp) REVERT: c 167 ASN cc_start: 0.9351 (t0) cc_final: 0.8980 (t160) REVERT: d 30 GLN cc_start: 0.9019 (tp40) cc_final: 0.8199 (tt0) REVERT: d 51 GLU cc_start: 0.7968 (pm20) cc_final: 0.7708 (pm20) REVERT: d 88 ARG cc_start: 0.8460 (OUTLIER) cc_final: 0.8094 (mmp80) REVERT: d 115 GLN cc_start: 0.8527 (mm-40) cc_final: 0.8294 (mt0) REVERT: e 25 MET cc_start: 0.8980 (ppp) cc_final: 0.8005 (ppp) REVERT: e 29 ARG cc_start: 0.8649 (OUTLIER) cc_final: 0.8170 (ptp-170) REVERT: e 31 GLU cc_start: 0.8363 (mt-10) cc_final: 0.8068 (mm-30) REVERT: e 36 ASN cc_start: 0.6967 (OUTLIER) cc_final: 0.6607 (t0) REVERT: e 65 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8324 (tm) REVERT: e 87 LYS cc_start: 0.9001 (ttpp) cc_final: 0.8317 (ttmt) REVERT: e 95 MET cc_start: 0.8869 (ppp) cc_final: 0.8544 (ppp) REVERT: e 99 PHE cc_start: 0.8973 (t80) cc_final: 0.8734 (t80) REVERT: e 100 GLU cc_start: 0.8245 (OUTLIER) cc_final: 0.7963 (mp0) REVERT: e 145 VAL cc_start: 0.7393 (t) cc_final: 0.6726 (p) REVERT: f 19 ASN cc_start: 0.8763 (t0) cc_final: 0.8544 (t0) REVERT: f 21 GLN cc_start: 0.8211 (tp-100) cc_final: 0.7985 (tp-100) REVERT: f 63 GLN cc_start: 0.8297 (mm-40) cc_final: 0.7888 (mm-40) REVERT: f 68 ARG cc_start: 0.8966 (tmt170) cc_final: 0.8711 (tmt-80) REVERT: f 82 PHE cc_start: 0.8161 (m-80) cc_final: 0.7699 (m-80) REVERT: f 100 ASN cc_start: 0.8484 (p0) cc_final: 0.7982 (p0) REVERT: f 113 ASP cc_start: 0.8303 (OUTLIER) cc_final: 0.8066 (m-30) REVERT: f 123 GLU cc_start: 0.8076 (tm-30) cc_final: 0.7698 (pp20) REVERT: f 129 GLU cc_start: 0.8564 (tt0) cc_final: 0.8007 (tp30) REVERT: g 4 ILE cc_start: 0.8828 (tp) cc_final: 0.8509 (mm) REVERT: g 8 LYS cc_start: 0.8765 (mtpp) cc_final: 0.8128 (tptt) REVERT: g 25 TYR cc_start: 0.8858 (t80) cc_final: 0.8345 (t80) REVERT: g 35 LYS cc_start: 0.8726 (mptt) cc_final: 0.8495 (mptp) REVERT: g 117 LEU cc_start: 0.6987 (OUTLIER) cc_final: 0.6679 (pt) REVERT: h 5 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8727 (pt) REVERT: h 81 LEU cc_start: 0.5529 (OUTLIER) cc_final: 0.5176 (mt) REVERT: i 124 MET cc_start: 0.5355 (ppp) cc_final: 0.2794 (mmt) REVERT: i 139 VAL cc_start: 0.6792 (t) cc_final: 0.6579 (m) REVERT: j 71 ASP cc_start: 0.8484 (m-30) cc_final: 0.8262 (m-30) REVERT: k 12 ASP cc_start: 0.8354 (p0) cc_final: 0.8070 (p0) REVERT: k 17 ARG cc_start: 0.7899 (OUTLIER) cc_final: 0.7151 (ttm170) REVERT: l 76 GLU cc_start: 0.7515 (mt-10) cc_final: 0.7144 (mt-10) REVERT: l 82 LEU cc_start: 0.9338 (tp) cc_final: 0.9033 (tm) REVERT: l 143 GLU cc_start: 0.7497 (pp20) cc_final: 0.7210 (pp20) REVERT: m 88 ASN cc_start: 0.8573 (m-40) cc_final: 0.8258 (m110) REVERT: m 91 TYR cc_start: 0.9071 (p90) cc_final: 0.8542 (p90) REVERT: m 97 GLN cc_start: 0.8623 (OUTLIER) cc_final: 0.8262 (mp-120) REVERT: m 104 GLU cc_start: 0.8132 (mt-10) cc_final: 0.7669 (tt0) REVERT: n 35 LYS cc_start: 0.8823 (tttt) cc_final: 0.8581 (tptt) REVERT: n 72 ASP cc_start: 0.8808 (t0) cc_final: 0.8493 (t0) REVERT: o 17 LYS cc_start: 0.9402 (tppt) cc_final: 0.9151 (tppt) REVERT: o 38 GLN cc_start: 0.8834 (pt0) cc_final: 0.7943 (pm20) REVERT: o 62 LEU cc_start: 0.8913 (pt) cc_final: 0.8702 (pt) REVERT: o 80 GLU cc_start: 0.8901 (tm-30) cc_final: 0.8629 (tm-30) REVERT: p 23 ASP cc_start: 0.8534 (m-30) cc_final: 0.8082 (m-30) REVERT: p 26 GLU cc_start: 0.7897 (tm-30) cc_final: 0.7667 (tm-30) REVERT: p 65 ASN cc_start: 0.8894 (OUTLIER) cc_final: 0.8540 (p0) REVERT: q 58 GLN cc_start: 0.8874 (OUTLIER) cc_final: 0.8643 (tt0) REVERT: q 96 ASP cc_start: 0.8224 (t0) cc_final: 0.7666 (t0) REVERT: q 101 ASP cc_start: 0.8247 (t70) cc_final: 0.7828 (t0) REVERT: r 13 ARG cc_start: 0.8811 (ttp80) cc_final: 0.8194 (ttt-90) REVERT: r 16 GLU cc_start: 0.8476 (tp30) cc_final: 0.8088 (tp30) REVERT: r 31 GLU cc_start: 0.7739 (mp0) cc_final: 0.7253 (mp0) REVERT: r 37 GLU cc_start: 0.7942 (pm20) cc_final: 0.7672 (pm20) REVERT: r 40 MET cc_start: 0.8703 (ttt) cc_final: 0.8317 (tpp) REVERT: r 46 GLU cc_start: 0.7880 (tp30) cc_final: 0.7399 (tp30) REVERT: r 60 LYS cc_start: 0.8952 (mtmm) cc_final: 0.8483 (mmmm) REVERT: r 62 GLU cc_start: 0.8576 (tt0) cc_final: 0.7837 (tm-30) REVERT: s 52 GLU cc_start: 0.8038 (mm-30) cc_final: 0.7756 (tm-30) REVERT: s 61 ASN cc_start: 0.8817 (m-40) cc_final: 0.8496 (m-40) REVERT: t 1 MET cc_start: 0.7598 (OUTLIER) cc_final: 0.7064 (ptp) REVERT: t 28 ASN cc_start: 0.8814 (t0) cc_final: 0.8318 (t0) REVERT: t 36 LYS cc_start: 0.8510 (tptp) cc_final: 0.8197 (tptt) REVERT: t 42 GLU cc_start: 0.8518 (mp0) cc_final: 0.8274 (mp0) REVERT: t 69 ARG cc_start: 0.8123 (mtp-110) cc_final: 0.7888 (ttm110) REVERT: t 86 THR cc_start: 0.9091 (m) cc_final: 0.8833 (p) REVERT: u 36 GLU cc_start: 0.8867 (pp20) cc_final: 0.8571 (pp20) REVERT: u 61 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.7687 (mt-10) REVERT: u 93 ARG cc_start: 0.8685 (mtm180) cc_final: 0.8226 (ptp-170) REVERT: v 46 LYS cc_start: 0.9165 (mmtm) cc_final: 0.8724 (mmpt) REVERT: w 16 ARG cc_start: 0.8609 (mpt-90) cc_final: 0.7730 (mmt90) REVERT: w 20 LYS cc_start: 0.9045 (OUTLIER) cc_final: 0.8397 (mmtt) REVERT: w 51 ARG cc_start: 0.9074 (OUTLIER) cc_final: 0.8626 (ppp80) REVERT: x 69 GLU cc_start: 0.8933 (OUTLIER) cc_final: 0.8717 (mt-10) REVERT: x 75 GLU cc_start: 0.7240 (mp0) cc_final: 0.6886 (mp0) REVERT: y 1 MET cc_start: 0.6001 (tpt) cc_final: 0.5333 (tpt) REVERT: y 39 GLN cc_start: 0.8360 (OUTLIER) cc_final: 0.7871 (mt0) REVERT: B 3 GLN cc_start: 0.8515 (pt0) cc_final: 0.8161 (pt0) REVERT: B 5 ASN cc_start: 0.8981 (m-40) cc_final: 0.8588 (m-40) REVERT: B 36 LYS cc_start: 0.9114 (mmtp) cc_final: 0.8853 (mptp) REVERT: C 36 LYS cc_start: 0.8666 (ttpt) cc_final: 0.8308 (mtpp) REVERT: D 41 ARG cc_start: 0.8103 (OUTLIER) cc_final: 0.7646 (mtp180) REVERT: E 48 MET cc_start: 0.8762 (mmt) cc_final: 0.8460 (mmt) REVERT: F 15 LYS cc_start: 0.8466 (mttt) cc_final: 0.8210 (tttp) REVERT: F 24 ARG cc_start: 0.8798 (mtt-85) cc_final: 0.8094 (mtt-85) REVERT: G 8 MET cc_start: 0.8873 (mtp) cc_final: 0.8042 (mpp) REVERT: G 18 GLN cc_start: 0.8843 (mt0) cc_final: 0.8464 (mp10) REVERT: G 26 MET cc_start: 0.8649 (mmm) cc_final: 0.8335 (mmm) REVERT: G 51 GLU cc_start: 0.8854 (tm-30) cc_final: 0.8518 (tm-30) REVERT: H 5 HIS cc_start: 0.9158 (t-90) cc_final: 0.8808 (t-90) REVERT: H 18 ASN cc_start: 0.9050 (m-40) cc_final: 0.8646 (m110) REVERT: H 39 ARG cc_start: 0.8637 (ttm-80) cc_final: 0.7482 (mtt180) REVERT: H 40 GLN cc_start: 0.8872 (tt0) cc_final: 0.8587 (pp30) REVERT: H 139 ASN cc_start: 0.8930 (m-40) cc_final: 0.8428 (m110) REVERT: H 151 GLU cc_start: 0.8147 (tm-30) cc_final: 0.7777 (tm-30) REVERT: H 165 GLU cc_start: 0.8374 (mp0) cc_final: 0.8089 (mm-30) REVERT: H 184 ASN cc_start: 0.8824 (OUTLIER) cc_final: 0.8560 (t160) REVERT: H 191 THR cc_start: 0.9266 (p) cc_final: 0.8883 (t) REVERT: I 43 ARG cc_start: 0.7315 (mpp-170) cc_final: 0.6810 (mpp-170) REVERT: I 47 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8308 (mm) REVERT: I 68 GLU cc_start: 0.8350 (tp30) cc_final: 0.7801 (tp30) REVERT: I 71 PHE cc_start: 0.9215 (t80) cc_final: 0.8570 (t80) REVERT: I 73 ASN cc_start: 0.9351 (m110) cc_final: 0.8953 (m110) REVERT: I 112 GLU cc_start: 0.7436 (tt0) cc_final: 0.7158 (tt0) REVERT: I 116 LEU cc_start: 0.8811 (tp) cc_final: 0.8537 (tt) REVERT: I 137 SER cc_start: 0.8152 (t) cc_final: 0.7863 (p) REVERT: I 152 SER cc_start: 0.8844 (t) cc_final: 0.8598 (p) REVERT: J 32 PHE cc_start: 0.9078 (m-80) cc_final: 0.8658 (m-80) REVERT: J 60 GLN cc_start: 0.8868 (tp-100) cc_final: 0.8441 (OUTLIER) REVERT: J 94 PHE cc_start: 0.8285 (t80) cc_final: 0.7617 (t80) REVERT: J 104 ILE cc_start: 0.9282 (OUTLIER) cc_final: 0.8742 (pp) REVERT: J 131 ASN cc_start: 0.8038 (t0) cc_final: 0.7822 (t0) REVERT: J 146 MET cc_start: 0.8340 (OUTLIER) cc_final: 0.7454 (ttp) REVERT: K 56 LYS cc_start: 0.8454 (mmtt) cc_final: 0.8125 (mmpt) REVERT: K 58 HIS cc_start: 0.7444 (t70) cc_final: 0.7169 (t70) REVERT: K 62 MET cc_start: 0.8168 (mmm) cc_final: 0.7758 (mpp) REVERT: K 65 GLU cc_start: 0.8123 (tp30) cc_final: 0.7725 (tp30) REVERT: K 88 MET cc_start: 0.8103 (ptm) cc_final: 0.7525 (ptm) REVERT: K 90 MET cc_start: 0.7481 (mtm) cc_final: 0.7074 (mpp) REVERT: L 3 ARG cc_start: 0.6609 (ttm170) cc_final: 0.6296 (ttm170) REVERT: L 78 ARG cc_start: 0.6950 (OUTLIER) cc_final: 0.6680 (ptp90) REVERT: L 100 MET cc_start: 0.8466 (mtm) cc_final: 0.8238 (mtm) REVERT: L 105 GLU cc_start: 0.8577 (pp20) cc_final: 0.8194 (pp20) REVERT: M 26 MET cc_start: 0.8542 (ptp) cc_final: 0.8088 (pmm) REVERT: M 28 SER cc_start: 0.8543 (p) cc_final: 0.8088 (p) REVERT: M 56 PRO cc_start: 0.8931 (Cg_exo) cc_final: 0.8429 (Cg_endo) REVERT: M 57 GLU cc_start: 0.7832 (OUTLIER) cc_final: 0.7411 (pp20) REVERT: M 95 MET cc_start: 0.8251 (tpp) cc_final: 0.7808 (tpt) REVERT: M 98 LEU cc_start: 0.9202 (OUTLIER) cc_final: 0.8709 (pt) REVERT: M 110 MET cc_start: 0.8336 (ptp) cc_final: 0.8061 (ptp) REVERT: N 20 ILE cc_start: 0.8974 (tt) cc_final: 0.8590 (tt) REVERT: N 21 LYS cc_start: 0.9054 (mtpt) cc_final: 0.8644 (mmtt) REVERT: N 27 ILE cc_start: 0.8906 (mp) cc_final: 0.8511 (mm) REVERT: N 123 ARG cc_start: 0.8612 (mmt90) cc_final: 0.8369 (tpp80) REVERT: O 16 ARG cc_start: 0.8113 (ptt180) cc_final: 0.7813 (ptp90) REVERT: O 44 THR cc_start: 0.8313 (OUTLIER) cc_final: 0.8087 (t) REVERT: P 86 LYS cc_start: 0.8640 (OUTLIER) cc_final: 0.8361 (ptmm) REVERT: Q 37 TYR cc_start: 0.8239 (p90) cc_final: 0.7835 (p90) REVERT: Q 72 ASN cc_start: 0.8308 (OUTLIER) cc_final: 0.7589 (p0) REVERT: Q 87 LYS cc_start: 0.8683 (OUTLIER) cc_final: 0.7927 (tppt) REVERT: R 15 VAL cc_start: 0.8193 (m) cc_final: 0.7955 (t) REVERT: R 52 ILE cc_start: 0.8883 (mt) cc_final: 0.8445 (mp) REVERT: R 76 ILE cc_start: 0.9340 (pp) cc_final: 0.9000 (pp) REVERT: R 77 LYS cc_start: 0.9218 (tttm) cc_final: 0.8653 (tppt) REVERT: S 97 LYS cc_start: 0.8539 (tttt) cc_final: 0.8270 (tttt) REVERT: T 25 GLU cc_start: 0.8583 (mt-10) cc_final: 0.8311 (mt-10) REVERT: T 36 ASN cc_start: 0.8765 (m110) cc_final: 0.8216 (m-40) REVERT: T 48 ASP cc_start: 0.8514 (t0) cc_final: 0.8024 (t0) REVERT: T 51 SER cc_start: 0.8964 (p) cc_final: 0.8651 (p) REVERT: T 73 ASP cc_start: 0.7943 (t0) cc_final: 0.7527 (t0) REVERT: T 76 ARG cc_start: 0.8536 (mtm180) cc_final: 0.8124 (ttm110) REVERT: U 18 GLN cc_start: 0.8154 (mt0) cc_final: 0.7486 (mm-40) REVERT: U 39 PHE cc_start: 0.9017 (t80) cc_final: 0.8036 (t80) REVERT: U 53 ASP cc_start: 0.8384 (OUTLIER) cc_final: 0.8027 (p0) REVERT: V 7 LEU cc_start: 0.8755 (mp) cc_final: 0.8489 (pp) REVERT: V 16 MET cc_start: 0.7049 (ttt) cc_final: 0.6758 (ttt) REVERT: V 24 ILE cc_start: 0.8589 (OUTLIER) cc_final: 0.7938 (pp) REVERT: V 44 HIS cc_start: 0.8181 (m90) cc_final: 0.7970 (m90) REVERT: V 61 ARG cc_start: 0.8233 (ppp80) cc_final: 0.7927 (ppp80) REVERT: V 80 LYS cc_start: 0.8874 (tmtt) cc_final: 0.8419 (tptt) REVERT: W 24 ASP cc_start: 0.8553 (t0) cc_final: 0.8215 (t0) REVERT: W 42 ARG cc_start: 0.9087 (OUTLIER) cc_final: 0.8867 (mtm110) REVERT: W 47 ARG cc_start: 0.7360 (mtm180) cc_final: 0.7116 (mtt180) REVERT: W 51 GLN cc_start: 0.8789 (tp40) cc_final: 0.7579 (tm-30) REVERT: X 69 LYS cc_start: 0.8516 (OUTLIER) cc_final: 0.8136 (mttp) REVERT: Y 15 LYS cc_start: 0.8874 (tttm) cc_final: 0.8260 (tptp) REVERT: Y 17 ARG cc_start: 0.8872 (tmm-80) cc_final: 0.8296 (ttp-110) REVERT: Y 18 LYS cc_start: 0.9185 (mttp) cc_final: 0.8878 (mtpp) REVERT: Y 50 PHE cc_start: 0.8666 (t80) cc_final: 0.8423 (t80) REVERT: Y 53 MET cc_start: 0.8806 (tmm) cc_final: 0.8515 (tmm) REVERT: Y 54 GLN cc_start: 0.8643 (tt0) cc_final: 0.8322 (tt0) REVERT: Y 81 GLN cc_start: 0.9171 (mm-40) cc_final: 0.8716 (mm-40) REVERT: Z 19 LYS cc_start: 0.8781 (mmmt) cc_final: 0.8176 (mmmt) REVERT: Z 38 GLU cc_start: 0.8160 (pp20) cc_final: 0.7862 (tm-30) REVERT: a 16 ASP cc_start: 0.2043 (OUTLIER) cc_final: 0.1732 (t0) REVERT: a 218 MET cc_start: 0.4898 (mtt) cc_final: 0.3852 (mmt) outliers start: 393 outliers final: 270 residues processed: 1805 average time/residue: 2.0201 time to fit residues: 5362.4750 Evaluate side-chains 1918 residues out of total 4908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 310 poor density : 1608 time to evaluate : 6.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 37 SER Chi-restraints excluded: chain b residue 48 ILE Chi-restraints excluded: chain b residue 50 THR Chi-restraints excluded: chain b residue 52 HIS Chi-restraints excluded: chain b residue 86 ARG Chi-restraints excluded: chain b residue 114 GLN Chi-restraints excluded: chain b residue 140 VAL Chi-restraints excluded: chain b residue 152 GLN Chi-restraints excluded: chain b residue 163 ILE Chi-restraints excluded: chain b residue 164 VAL Chi-restraints excluded: chain b residue 194 VAL Chi-restraints excluded: chain b residue 250 GLN Chi-restraints excluded: chain b residue 256 THR Chi-restraints excluded: chain c residue 2 ILE Chi-restraints excluded: chain c residue 9 VAL Chi-restraints excluded: chain c residue 22 ILE Chi-restraints excluded: chain c residue 39 ASP Chi-restraints excluded: chain c residue 89 GLU Chi-restraints excluded: chain c residue 95 SER Chi-restraints excluded: chain c residue 97 SER Chi-restraints excluded: chain c residue 104 VAL Chi-restraints excluded: chain c residue 110 THR Chi-restraints excluded: chain c residue 155 VAL Chi-restraints excluded: chain c residue 157 LYS Chi-restraints excluded: chain c residue 170 VAL Chi-restraints excluded: chain c residue 193 VAL Chi-restraints excluded: chain c residue 199 SER Chi-restraints excluded: chain c residue 200 ASP Chi-restraints excluded: chain d residue 48 THR Chi-restraints excluded: chain d residue 53 THR Chi-restraints excluded: chain d residue 65 THR Chi-restraints excluded: chain d residue 72 SER Chi-restraints excluded: chain d residue 80 SER Chi-restraints excluded: chain d residue 84 THR Chi-restraints excluded: chain d residue 88 ARG Chi-restraints excluded: chain d residue 96 VAL Chi-restraints excluded: chain d residue 120 VAL Chi-restraints excluded: chain d residue 146 VAL Chi-restraints excluded: chain d residue 189 THR Chi-restraints excluded: chain e residue 20 ASN Chi-restraints excluded: chain e residue 23 SER Chi-restraints excluded: chain e residue 24 VAL Chi-restraints excluded: chain e residue 29 ARG Chi-restraints excluded: chain e residue 30 VAL Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 36 ASN Chi-restraints excluded: chain e residue 60 SER Chi-restraints excluded: chain e residue 65 LEU Chi-restraints excluded: chain e residue 67 THR Chi-restraints excluded: chain e residue 89 THR Chi-restraints excluded: chain e residue 90 LEU Chi-restraints excluded: chain e residue 100 GLU Chi-restraints excluded: chain e residue 117 SER Chi-restraints excluded: chain e residue 131 VAL Chi-restraints excluded: chain e residue 157 THR Chi-restraints excluded: chain e residue 173 ASP Chi-restraints excluded: chain f residue 1 SER Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 23 ILE Chi-restraints excluded: chain f residue 66 THR Chi-restraints excluded: chain f residue 91 VAL Chi-restraints excluded: chain f residue 105 SER Chi-restraints excluded: chain f residue 112 VAL Chi-restraints excluded: chain f residue 113 ASP Chi-restraints excluded: chain f residue 126 THR Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain g residue 61 VAL Chi-restraints excluded: chain g residue 96 THR Chi-restraints excluded: chain g residue 117 LEU Chi-restraints excluded: chain h residue 3 LEU Chi-restraints excluded: chain h residue 5 LEU Chi-restraints excluded: chain h residue 77 VAL Chi-restraints excluded: chain h residue 81 LEU Chi-restraints excluded: chain h residue 128 THR Chi-restraints excluded: chain i residue 12 VAL Chi-restraints excluded: chain i residue 35 MET Chi-restraints excluded: chain j residue 54 ILE Chi-restraints excluded: chain j residue 73 VAL Chi-restraints excluded: chain j residue 131 ASN Chi-restraints excluded: chain k residue 14 SER Chi-restraints excluded: chain k residue 17 ARG Chi-restraints excluded: chain k residue 28 SER Chi-restraints excluded: chain k residue 45 GLU Chi-restraints excluded: chain k residue 69 VAL Chi-restraints excluded: chain k residue 97 THR Chi-restraints excluded: chain k residue 118 LEU Chi-restraints excluded: chain l residue 12 SER Chi-restraints excluded: chain l residue 85 VAL Chi-restraints excluded: chain l residue 110 VAL Chi-restraints excluded: chain l residue 111 ILE Chi-restraints excluded: chain l residue 116 VAL Chi-restraints excluded: chain l residue 118 THR Chi-restraints excluded: chain l residue 120 VAL Chi-restraints excluded: chain l residue 121 THR Chi-restraints excluded: chain l residue 122 VAL Chi-restraints excluded: chain l residue 127 VAL Chi-restraints excluded: chain m residue 24 THR Chi-restraints excluded: chain m residue 42 THR Chi-restraints excluded: chain m residue 54 THR Chi-restraints excluded: chain m residue 74 THR Chi-restraints excluded: chain m residue 93 VAL Chi-restraints excluded: chain m residue 97 GLN Chi-restraints excluded: chain m residue 118 LYS Chi-restraints excluded: chain m residue 126 ILE Chi-restraints excluded: chain m residue 132 THR Chi-restraints excluded: chain n residue 6 SER Chi-restraints excluded: chain n residue 27 SER Chi-restraints excluded: chain n residue 37 THR Chi-restraints excluded: chain n residue 73 ASN Chi-restraints excluded: chain n residue 75 ILE Chi-restraints excluded: chain o residue 12 THR Chi-restraints excluded: chain o residue 21 LEU Chi-restraints excluded: chain o residue 35 ILE Chi-restraints excluded: chain o residue 39 VAL Chi-restraints excluded: chain o residue 40 ILE Chi-restraints excluded: chain o residue 48 LEU Chi-restraints excluded: chain o residue 65 THR Chi-restraints excluded: chain o residue 95 SER Chi-restraints excluded: chain o residue 103 VAL Chi-restraints excluded: chain o residue 112 GLU Chi-restraints excluded: chain p residue 7 LEU Chi-restraints excluded: chain p residue 63 ILE Chi-restraints excluded: chain p residue 65 ASN Chi-restraints excluded: chain p residue 91 VAL Chi-restraints excluded: chain p residue 93 LYS Chi-restraints excluded: chain q residue 58 GLN Chi-restraints excluded: chain q residue 64 ILE Chi-restraints excluded: chain q residue 82 LEU Chi-restraints excluded: chain q residue 109 VAL Chi-restraints excluded: chain r residue 32 THR Chi-restraints excluded: chain r residue 33 VAL Chi-restraints excluded: chain r residue 43 ASN Chi-restraints excluded: chain r residue 47 VAL Chi-restraints excluded: chain r residue 63 VAL Chi-restraints excluded: chain s residue 20 VAL Chi-restraints excluded: chain s residue 23 LEU Chi-restraints excluded: chain s residue 77 ASP Chi-restraints excluded: chain s residue 104 THR Chi-restraints excluded: chain s residue 106 VAL Chi-restraints excluded: chain s residue 107 VAL Chi-restraints excluded: chain s residue 108 SER Chi-restraints excluded: chain t residue 1 MET Chi-restraints excluded: chain t residue 16 VAL Chi-restraints excluded: chain t residue 17 SER Chi-restraints excluded: chain t residue 27 SER Chi-restraints excluded: chain t residue 39 THR Chi-restraints excluded: chain t residue 57 VAL Chi-restraints excluded: chain t residue 85 VAL Chi-restraints excluded: chain t residue 87 LEU Chi-restraints excluded: chain u residue 4 ILE Chi-restraints excluded: chain u residue 24 VAL Chi-restraints excluded: chain u residue 48 VAL Chi-restraints excluded: chain u residue 61 GLU Chi-restraints excluded: chain v residue 17 SER Chi-restraints excluded: chain v residue 20 LEU Chi-restraints excluded: chain v residue 30 ILE Chi-restraints excluded: chain v residue 45 ASP Chi-restraints excluded: chain v residue 47 VAL Chi-restraints excluded: chain v residue 64 VAL Chi-restraints excluded: chain v residue 92 VAL Chi-restraints excluded: chain w residue 20 LYS Chi-restraints excluded: chain w residue 32 ILE Chi-restraints excluded: chain w residue 34 VAL Chi-restraints excluded: chain w residue 39 THR Chi-restraints excluded: chain w residue 51 ARG Chi-restraints excluded: chain w residue 66 GLU Chi-restraints excluded: chain w residue 76 ILE Chi-restraints excluded: chain x residue 1 SER Chi-restraints excluded: chain x residue 13 THR Chi-restraints excluded: chain x residue 39 VAL Chi-restraints excluded: chain x residue 46 VAL Chi-restraints excluded: chain x residue 47 THR Chi-restraints excluded: chain x residue 64 ASP Chi-restraints excluded: chain x residue 67 LEU Chi-restraints excluded: chain x residue 69 GLU Chi-restraints excluded: chain y residue 11 VAL Chi-restraints excluded: chain y residue 30 MET Chi-restraints excluded: chain y residue 39 GLN Chi-restraints excluded: chain y residue 40 SER Chi-restraints excluded: chain y residue 43 LEU Chi-restraints excluded: chain y residue 55 THR Chi-restraints excluded: chain z residue 29 ARG Chi-restraints excluded: chain z residue 56 VAL Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 45 ASP Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 41 ARG Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain G residue 129 THR Chi-restraints excluded: chain G residue 153 MET Chi-restraints excluded: chain G residue 158 ASP Chi-restraints excluded: chain G residue 198 VAL Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain G residue 216 VAL Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 43 THR Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 117 ASP Chi-restraints excluded: chain H residue 123 LEU Chi-restraints excluded: chain H residue 164 THR Chi-restraints excluded: chain H residue 174 LEU Chi-restraints excluded: chain H residue 184 ASN Chi-restraints excluded: chain I residue 9 LYS Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 60 VAL Chi-restraints excluded: chain I residue 93 LEU Chi-restraints excluded: chain I residue 118 SER Chi-restraints excluded: chain I residue 133 SER Chi-restraints excluded: chain I residue 143 SER Chi-restraints excluded: chain J residue 67 ARG Chi-restraints excluded: chain J residue 89 THR Chi-restraints excluded: chain J residue 104 ILE Chi-restraints excluded: chain J residue 105 ILE Chi-restraints excluded: chain J residue 123 LEU Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 146 MET Chi-restraints excluded: chain K residue 17 GLN Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 39 LEU Chi-restraints excluded: chain K residue 75 GLU Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain L residue 78 ARG Chi-restraints excluded: chain L residue 96 ASN Chi-restraints excluded: chain L residue 117 LEU Chi-restraints excluded: chain L residue 121 ASN Chi-restraints excluded: chain M residue 6 ILE Chi-restraints excluded: chain M residue 9 MET Chi-restraints excluded: chain M residue 57 GLU Chi-restraints excluded: chain M residue 98 LEU Chi-restraints excluded: chain M residue 104 SER Chi-restraints excluded: chain M residue 125 ILE Chi-restraints excluded: chain N residue 28 VAL Chi-restraints excluded: chain N residue 78 ILE Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain O residue 18 ILE Chi-restraints excluded: chain O residue 44 THR Chi-restraints excluded: chain O residue 50 THR Chi-restraints excluded: chain O residue 91 ASP Chi-restraints excluded: chain O residue 92 LEU Chi-restraints excluded: chain P residue 25 SER Chi-restraints excluded: chain P residue 30 ILE Chi-restraints excluded: chain P residue 45 THR Chi-restraints excluded: chain P residue 54 SER Chi-restraints excluded: chain P residue 86 LYS Chi-restraints excluded: chain Q residue 32 VAL Chi-restraints excluded: chain Q residue 34 THR Chi-restraints excluded: chain Q residue 40 THR Chi-restraints excluded: chain Q residue 46 SER Chi-restraints excluded: chain Q residue 51 VAL Chi-restraints excluded: chain Q residue 57 THR Chi-restraints excluded: chain Q residue 63 THR Chi-restraints excluded: chain Q residue 72 ASN Chi-restraints excluded: chain Q residue 73 LEU Chi-restraints excluded: chain Q residue 87 LYS Chi-restraints excluded: chain Q residue 92 VAL Chi-restraints excluded: chain Q residue 97 VAL Chi-restraints excluded: chain Q residue 102 ASP Chi-restraints excluded: chain R residue 20 SER Chi-restraints excluded: chain R residue 24 VAL Chi-restraints excluded: chain R residue 58 GLU Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain R residue 107 THR Chi-restraints excluded: chain S residue 13 VAL Chi-restraints excluded: chain S residue 47 LEU Chi-restraints excluded: chain S residue 54 SER Chi-restraints excluded: chain T residue 4 THR Chi-restraints excluded: chain T residue 26 VAL Chi-restraints excluded: chain U residue 21 VAL Chi-restraints excluded: chain U residue 53 ASP Chi-restraints excluded: chain U residue 68 SER Chi-restraints excluded: chain V residue 24 ILE Chi-restraints excluded: chain V residue 32 ILE Chi-restraints excluded: chain V residue 41 THR Chi-restraints excluded: chain V residue 54 ILE Chi-restraints excluded: chain V residue 56 ASP Chi-restraints excluded: chain V residue 71 SER Chi-restraints excluded: chain V residue 82 VAL Chi-restraints excluded: chain W residue 37 LYS Chi-restraints excluded: chain W residue 42 ARG Chi-restraints excluded: chain W residue 70 THR Chi-restraints excluded: chain X residue 37 SER Chi-restraints excluded: chain X residue 38 THR Chi-restraints excluded: chain X residue 48 ILE Chi-restraints excluded: chain X residue 69 LYS Chi-restraints excluded: chain X residue 78 THR Chi-restraints excluded: chain Y residue 22 SER Chi-restraints excluded: chain Y residue 74 HIS Chi-restraints excluded: chain Y residue 78 LEU Chi-restraints excluded: chain Y residue 79 THR Chi-restraints excluded: chain Z residue 12 ASP Chi-restraints excluded: chain Z residue 52 VAL Chi-restraints excluded: chain Z residue 59 LEU Chi-restraints excluded: chain a residue 8 MET Chi-restraints excluded: chain a residue 16 ASP Chi-restraints excluded: chain a residue 35 THR Chi-restraints excluded: chain a residue 46 VAL Chi-restraints excluded: chain a residue 53 ARG Chi-restraints excluded: chain a residue 64 VAL Chi-restraints excluded: chain a residue 207 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1050 random chunks: chunk 920 optimal weight: 20.0000 chunk 969 optimal weight: 10.0000 chunk 884 optimal weight: 10.0000 chunk 943 optimal weight: 40.0000 chunk 567 optimal weight: 20.0000 chunk 410 optimal weight: 6.9990 chunk 740 optimal weight: 10.0000 chunk 289 optimal weight: 10.0000 chunk 852 optimal weight: 7.9990 chunk 891 optimal weight: 20.0000 chunk 939 optimal weight: 6.9990 overall best weight: 8.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 122 GLN j 128 ASN k 89 ASN ** o 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 6 GLN q 51 GLN r 87 GLN t 48 GLN u 65 GLN u 68 ASN v 12 GLN ** x 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** y 20 ASN y 27 ASN ** y 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 3 GLN D 13 ASN ** H 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 53 GLN I 88 ASN ** I 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 147 ASN ** M 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 49 GLN O 56 HIS Q 4 ASN ** T 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 79 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.3880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.114 161399 Z= 0.517 Angle : 0.770 15.431 241370 Z= 0.390 Chirality : 0.045 0.323 30856 Planarity : 0.006 0.071 13007 Dihedral : 23.222 178.967 80575 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 15.66 Ramachandran Plot: Outliers : 0.29 % Allowed : 10.17 % Favored : 89.54 % Rotamer: Outliers : 7.82 % Allowed : 34.05 % Favored : 58.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.06 (0.11), residues: 5919 helix: -0.43 (0.12), residues: 1853 sheet: -1.49 (0.15), residues: 1071 loop : -1.91 (0.11), residues: 2995 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP b 212 HIS 0.008 0.002 HIS X 56 PHE 0.037 0.002 PHE G 197 TYR 0.041 0.003 TYR K 25 ARG 0.019 0.001 ARG x 10 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11838 Ramachandran restraints generated. 5919 Oldfield, 0 Emsley, 5919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11838 Ramachandran restraints generated. 5919 Oldfield, 0 Emsley, 5919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1998 residues out of total 4908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 384 poor density : 1614 time to evaluate : 6.580 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: b 22 GLU cc_start: 0.8150 (pp20) cc_final: 0.7874 (pp20) REVERT: b 86 ARG cc_start: 0.9134 (OUTLIER) cc_final: 0.8307 (mtm-85) REVERT: b 97 ASP cc_start: 0.8844 (p0) cc_final: 0.8514 (p0) REVERT: b 114 GLN cc_start: 0.8762 (OUTLIER) cc_final: 0.8347 (tt0) REVERT: b 152 GLN cc_start: 0.8711 (OUTLIER) cc_final: 0.7925 (mm110) REVERT: b 250 GLN cc_start: 0.8853 (OUTLIER) cc_final: 0.8158 (tt0) REVERT: c 30 GLU cc_start: 0.8000 (mm-30) cc_final: 0.7633 (mp0) REVERT: c 167 ASN cc_start: 0.9407 (t0) cc_final: 0.9051 (t160) REVERT: d 80 SER cc_start: 0.9034 (OUTLIER) cc_final: 0.8593 (p) REVERT: d 88 ARG cc_start: 0.8485 (OUTLIER) cc_final: 0.8114 (mmp80) REVERT: d 115 GLN cc_start: 0.8582 (mm-40) cc_final: 0.8254 (mm-40) REVERT: d 156 ASN cc_start: 0.7874 (t0) cc_final: 0.7638 (t0) REVERT: e 25 MET cc_start: 0.9003 (ppp) cc_final: 0.8276 (tmm) REVERT: e 29 ARG cc_start: 0.8669 (OUTLIER) cc_final: 0.8164 (ptp-170) REVERT: e 31 GLU cc_start: 0.8370 (mt-10) cc_final: 0.8118 (mm-30) REVERT: e 36 ASN cc_start: 0.7021 (OUTLIER) cc_final: 0.6692 (t0) REVERT: e 65 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8322 (tm) REVERT: e 87 LYS cc_start: 0.9071 (ttpp) cc_final: 0.8444 (ttmt) REVERT: e 95 MET cc_start: 0.8916 (ppp) cc_final: 0.8590 (ppp) REVERT: e 99 PHE cc_start: 0.9011 (t80) cc_final: 0.8801 (t80) REVERT: e 100 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7820 (mp0) REVERT: e 145 VAL cc_start: 0.7532 (t) cc_final: 0.6850 (p) REVERT: f 19 ASN cc_start: 0.8766 (t0) cc_final: 0.8485 (t0) REVERT: f 21 GLN cc_start: 0.8257 (tp-100) cc_final: 0.8006 (tp-100) REVERT: f 68 ARG cc_start: 0.8956 (tmt170) cc_final: 0.8664 (tmt-80) REVERT: f 82 PHE cc_start: 0.8273 (m-80) cc_final: 0.7723 (m-80) REVERT: f 100 ASN cc_start: 0.8592 (p0) cc_final: 0.8351 (p0) REVERT: f 113 ASP cc_start: 0.8317 (OUTLIER) cc_final: 0.8088 (m-30) REVERT: f 123 GLU cc_start: 0.8098 (tm-30) cc_final: 0.7717 (pp20) REVERT: f 129 GLU cc_start: 0.8590 (tt0) cc_final: 0.7998 (tp30) REVERT: g 4 ILE cc_start: 0.8874 (tp) cc_final: 0.8533 (mm) REVERT: g 8 LYS cc_start: 0.8751 (mtpp) cc_final: 0.8068 (tptt) REVERT: g 25 TYR cc_start: 0.8892 (t80) cc_final: 0.8323 (t80) REVERT: g 35 LYS cc_start: 0.8733 (mptt) cc_final: 0.8454 (mptp) REVERT: g 117 LEU cc_start: 0.7094 (OUTLIER) cc_final: 0.6777 (pt) REVERT: h 5 LEU cc_start: 0.9073 (OUTLIER) cc_final: 0.8747 (pt) REVERT: h 81 LEU cc_start: 0.5696 (OUTLIER) cc_final: 0.5419 (mt) REVERT: j 71 ASP cc_start: 0.8544 (m-30) cc_final: 0.8319 (m-30) REVERT: k 12 ASP cc_start: 0.8568 (p0) cc_final: 0.8159 (p0) REVERT: k 17 ARG cc_start: 0.7974 (OUTLIER) cc_final: 0.7259 (ttm170) REVERT: l 76 GLU cc_start: 0.7527 (mt-10) cc_final: 0.7138 (mt-10) REVERT: l 84 LYS cc_start: 0.8333 (ptpp) cc_final: 0.8106 (pmmt) REVERT: l 105 ILE cc_start: 0.9001 (mm) cc_final: 0.8752 (mp) REVERT: l 143 GLU cc_start: 0.7510 (pp20) cc_final: 0.7009 (pp20) REVERT: m 17 ASN cc_start: 0.8709 (t0) cc_final: 0.7836 (t0) REVERT: m 88 ASN cc_start: 0.8584 (m-40) cc_final: 0.8330 (m110) REVERT: m 91 TYR cc_start: 0.9140 (p90) cc_final: 0.8678 (p90) REVERT: m 97 GLN cc_start: 0.8649 (OUTLIER) cc_final: 0.8312 (mp-120) REVERT: n 35 LYS cc_start: 0.8870 (tttt) cc_final: 0.8538 (tptt) REVERT: n 72 ASP cc_start: 0.8873 (t0) cc_final: 0.8563 (t0) REVERT: o 80 GLU cc_start: 0.8935 (tm-30) cc_final: 0.8618 (tm-30) REVERT: p 23 ASP cc_start: 0.8630 (m-30) cc_final: 0.8197 (m-30) REVERT: p 26 GLU cc_start: 0.7937 (tm-30) cc_final: 0.7708 (tm-30) REVERT: p 65 ASN cc_start: 0.8910 (OUTLIER) cc_final: 0.8567 (p0) REVERT: q 58 GLN cc_start: 0.8935 (OUTLIER) cc_final: 0.8709 (tt0) REVERT: q 96 ASP cc_start: 0.8302 (t0) cc_final: 0.7723 (t0) REVERT: q 101 ASP cc_start: 0.8362 (OUTLIER) cc_final: 0.7945 (t0) REVERT: r 13 ARG cc_start: 0.8811 (ttp80) cc_final: 0.8194 (ttt-90) REVERT: r 31 GLU cc_start: 0.7767 (mp0) cc_final: 0.7473 (mp0) REVERT: r 37 GLU cc_start: 0.8005 (pm20) cc_final: 0.7751 (pm20) REVERT: r 60 LYS cc_start: 0.8967 (mtmm) cc_final: 0.8515 (mmmm) REVERT: r 62 GLU cc_start: 0.8620 (tt0) cc_final: 0.7712 (tm-30) REVERT: s 52 GLU cc_start: 0.8112 (mm-30) cc_final: 0.7887 (tm-30) REVERT: t 1 MET cc_start: 0.7686 (OUTLIER) cc_final: 0.7169 (ptp) REVERT: t 28 ASN cc_start: 0.8840 (t0) cc_final: 0.8320 (t0) REVERT: t 36 LYS cc_start: 0.8432 (tptp) cc_final: 0.8084 (tptt) REVERT: t 42 GLU cc_start: 0.8456 (mp0) cc_final: 0.8254 (mp0) REVERT: u 33 VAL cc_start: 0.9482 (OUTLIER) cc_final: 0.9225 (t) REVERT: u 36 GLU cc_start: 0.8896 (pp20) cc_final: 0.8579 (pp20) REVERT: u 93 ARG cc_start: 0.8768 (mtm180) cc_final: 0.8413 (mtp180) REVERT: v 41 GLU cc_start: 0.8157 (tt0) cc_final: 0.7374 (tm-30) REVERT: v 46 LYS cc_start: 0.9192 (mmtm) cc_final: 0.8773 (mmpt) REVERT: v 50 MET cc_start: 0.8753 (mtm) cc_final: 0.8433 (mtt) REVERT: v 87 GLN cc_start: 0.8373 (mt0) cc_final: 0.7937 (mt0) REVERT: w 16 ARG cc_start: 0.8678 (mpt-90) cc_final: 0.7769 (mmt90) REVERT: w 20 LYS cc_start: 0.8954 (OUTLIER) cc_final: 0.8318 (mmtm) REVERT: w 51 ARG cc_start: 0.9098 (OUTLIER) cc_final: 0.8748 (ppp80) REVERT: x 69 GLU cc_start: 0.8872 (OUTLIER) cc_final: 0.7940 (mp0) REVERT: x 75 GLU cc_start: 0.7300 (mp0) cc_final: 0.6996 (mp0) REVERT: y 1 MET cc_start: 0.6067 (tpt) cc_final: 0.5525 (tpt) REVERT: y 27 ASN cc_start: 0.8891 (OUTLIER) cc_final: 0.8662 (m-40) REVERT: y 31 GLN cc_start: 0.8946 (OUTLIER) cc_final: 0.8585 (mp10) REVERT: y 39 GLN cc_start: 0.8443 (OUTLIER) cc_final: 0.7972 (mt0) REVERT: B 5 ASN cc_start: 0.9060 (m-40) cc_final: 0.8666 (m110) REVERT: B 36 LYS cc_start: 0.9152 (mmtp) cc_final: 0.8886 (mptp) REVERT: C 36 LYS cc_start: 0.8686 (ttpt) cc_final: 0.8326 (mtpp) REVERT: D 41 ARG cc_start: 0.8058 (OUTLIER) cc_final: 0.7648 (mtp180) REVERT: E 48 MET cc_start: 0.8799 (mmt) cc_final: 0.8548 (mmt) REVERT: F 15 LYS cc_start: 0.8474 (mttt) cc_final: 0.8204 (tttp) REVERT: F 24 ARG cc_start: 0.8896 (mtt-85) cc_final: 0.8555 (mtt-85) REVERT: G 18 GLN cc_start: 0.8848 (mt0) cc_final: 0.8487 (mp10) REVERT: G 26 MET cc_start: 0.8583 (mmm) cc_final: 0.8186 (mmm) REVERT: G 48 MET cc_start: 0.9001 (ptp) cc_final: 0.8636 (pmm) REVERT: G 108 GLN cc_start: 0.8704 (mm110) cc_final: 0.8322 (mm110) REVERT: H 5 HIS cc_start: 0.9168 (t-90) cc_final: 0.8941 (t-90) REVERT: H 39 ARG cc_start: 0.8692 (ttm-80) cc_final: 0.8490 (ttm-80) REVERT: H 40 GLN cc_start: 0.8964 (tt0) cc_final: 0.8653 (pp30) REVERT: H 139 ASN cc_start: 0.8987 (m-40) cc_final: 0.8516 (m110) REVERT: H 151 GLU cc_start: 0.8172 (tm-30) cc_final: 0.7820 (tm-30) REVERT: H 165 GLU cc_start: 0.8392 (mp0) cc_final: 0.8110 (mm-30) REVERT: H 184 ASN cc_start: 0.8823 (OUTLIER) cc_final: 0.8551 (t160) REVERT: H 191 THR cc_start: 0.9311 (p) cc_final: 0.8936 (t) REVERT: I 47 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8322 (mm) REVERT: I 68 GLU cc_start: 0.8364 (tp30) cc_final: 0.8069 (tp30) REVERT: I 71 PHE cc_start: 0.9226 (t80) cc_final: 0.8622 (t80) REVERT: I 73 ASN cc_start: 0.9413 (m110) cc_final: 0.9044 (m110) REVERT: I 112 GLU cc_start: 0.7411 (tt0) cc_final: 0.7124 (tt0) REVERT: I 116 LEU cc_start: 0.8735 (tp) cc_final: 0.8469 (tt) REVERT: I 137 SER cc_start: 0.8119 (t) cc_final: 0.7833 (p) REVERT: I 152 SER cc_start: 0.8903 (t) cc_final: 0.8655 (p) REVERT: J 32 PHE cc_start: 0.9111 (m-80) cc_final: 0.8716 (m-80) REVERT: J 60 GLN cc_start: 0.8877 (tp-100) cc_final: 0.8421 (tp-100) REVERT: J 94 PHE cc_start: 0.8323 (t80) cc_final: 0.7711 (t80) REVERT: J 131 ASN cc_start: 0.8135 (t0) cc_final: 0.7849 (t0) REVERT: J 146 MET cc_start: 0.8523 (OUTLIER) cc_final: 0.7649 (ttp) REVERT: J 156 ARG cc_start: 0.7561 (OUTLIER) cc_final: 0.7327 (ttt-90) REVERT: K 5 GLU cc_start: 0.8222 (pt0) cc_final: 0.7613 (pt0) REVERT: K 56 LYS cc_start: 0.8384 (mmtt) cc_final: 0.7980 (mmpt) REVERT: K 62 MET cc_start: 0.8142 (mmm) cc_final: 0.7738 (mpp) REVERT: K 65 GLU cc_start: 0.8162 (tp30) cc_final: 0.7785 (tp30) REVERT: K 90 MET cc_start: 0.7605 (mtm) cc_final: 0.7331 (mtp) REVERT: L 3 ARG cc_start: 0.6603 (ttm170) cc_final: 0.6297 (ttm170) REVERT: L 100 MET cc_start: 0.8494 (mtm) cc_final: 0.8260 (mtm) REVERT: L 105 GLU cc_start: 0.8625 (pp20) cc_final: 0.8252 (pp20) REVERT: M 26 MET cc_start: 0.8509 (ptp) cc_final: 0.7973 (pmm) REVERT: M 28 SER cc_start: 0.8583 (p) cc_final: 0.8228 (p) REVERT: M 57 GLU cc_start: 0.7857 (OUTLIER) cc_final: 0.7403 (pp20) REVERT: M 98 LEU cc_start: 0.9332 (OUTLIER) cc_final: 0.9009 (pt) REVERT: M 110 MET cc_start: 0.8326 (ptp) cc_final: 0.8053 (ptp) REVERT: N 20 ILE cc_start: 0.8969 (tt) cc_final: 0.8576 (tt) REVERT: N 21 LYS cc_start: 0.9066 (mtpt) cc_final: 0.8632 (mmtt) REVERT: N 49 GLN cc_start: 0.9279 (OUTLIER) cc_final: 0.8196 (tm130) REVERT: N 123 ARG cc_start: 0.8644 (mmt90) cc_final: 0.8381 (tpp80) REVERT: O 16 ARG cc_start: 0.8220 (ptt180) cc_final: 0.7870 (ptp90) REVERT: O 44 THR cc_start: 0.8404 (OUTLIER) cc_final: 0.8172 (t) REVERT: P 13 LYS cc_start: 0.8599 (mmpt) cc_final: 0.8347 (mppt) REVERT: P 86 LYS cc_start: 0.8663 (OUTLIER) cc_final: 0.8388 (ptmm) REVERT: Q 37 TYR cc_start: 0.8270 (p90) cc_final: 0.7899 (p90) REVERT: Q 87 LYS cc_start: 0.8687 (OUTLIER) cc_final: 0.7885 (tppt) REVERT: R 15 VAL cc_start: 0.8319 (m) cc_final: 0.8095 (t) REVERT: R 76 ILE cc_start: 0.9379 (pp) cc_final: 0.9038 (pp) REVERT: R 77 LYS cc_start: 0.9228 (tttm) cc_final: 0.8646 (tppt) REVERT: R 80 MET cc_start: 0.7929 (ttm) cc_final: 0.7494 (tmm) REVERT: S 97 LYS cc_start: 0.8535 (tttt) cc_final: 0.8286 (tttt) REVERT: T 25 GLU cc_start: 0.8650 (mt-10) cc_final: 0.8340 (mt-10) REVERT: T 36 ASN cc_start: 0.8824 (m110) cc_final: 0.8184 (m-40) REVERT: T 48 ASP cc_start: 0.8623 (t0) cc_final: 0.8077 (t0) REVERT: T 51 SER cc_start: 0.9112 (p) cc_final: 0.8808 (p) REVERT: T 73 ASP cc_start: 0.7958 (t0) cc_final: 0.7560 (t0) REVERT: T 76 ARG cc_start: 0.8549 (mtm180) cc_final: 0.8149 (ttm110) REVERT: U 18 GLN cc_start: 0.8230 (mt0) cc_final: 0.7622 (mt0) REVERT: U 39 PHE cc_start: 0.9034 (t80) cc_final: 0.8283 (t80) REVERT: U 51 ARG cc_start: 0.7634 (OUTLIER) cc_final: 0.7103 (ttp-110) REVERT: U 53 ASP cc_start: 0.8391 (OUTLIER) cc_final: 0.8038 (p0) REVERT: V 7 LEU cc_start: 0.8768 (mp) cc_final: 0.8514 (pp) REVERT: V 16 MET cc_start: 0.6907 (ttt) cc_final: 0.6668 (ttt) REVERT: V 44 HIS cc_start: 0.8186 (m90) cc_final: 0.7981 (m90) REVERT: V 61 ARG cc_start: 0.8375 (ppp80) cc_final: 0.8069 (ppp80) REVERT: V 80 LYS cc_start: 0.8871 (tmtt) cc_final: 0.8566 (tmtt) REVERT: W 24 ASP cc_start: 0.8607 (t0) cc_final: 0.8251 (t0) REVERT: W 47 ARG cc_start: 0.7332 (mtm180) cc_final: 0.7093 (mtt180) REVERT: W 51 GLN cc_start: 0.8815 (tp40) cc_final: 0.7858 (tm-30) REVERT: X 5 LYS cc_start: 0.7216 (tppp) cc_final: 0.6641 (tppp) REVERT: X 69 LYS cc_start: 0.8562 (OUTLIER) cc_final: 0.8225 (mttp) REVERT: Y 15 LYS cc_start: 0.8954 (tttm) cc_final: 0.8348 (tptp) REVERT: Y 53 MET cc_start: 0.8872 (tmm) cc_final: 0.8447 (tmm) REVERT: Y 54 GLN cc_start: 0.8619 (tt0) cc_final: 0.8219 (tt0) REVERT: Y 81 GLN cc_start: 0.9181 (mm-40) cc_final: 0.8718 (mm-40) REVERT: Z 38 GLU cc_start: 0.8090 (pp20) cc_final: 0.7616 (tm-30) REVERT: a 16 ASP cc_start: 0.1970 (OUTLIER) cc_final: 0.1644 (t0) REVERT: a 218 MET cc_start: 0.4893 (mtt) cc_final: 0.3830 (mmt) outliers start: 384 outliers final: 278 residues processed: 1776 average time/residue: 2.0311 time to fit residues: 5286.0380 Evaluate side-chains 1912 residues out of total 4908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 320 poor density : 1592 time to evaluate : 6.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 37 SER Chi-restraints excluded: chain b residue 48 ILE Chi-restraints excluded: chain b residue 50 THR Chi-restraints excluded: chain b residue 52 HIS Chi-restraints excluded: chain b residue 86 ARG Chi-restraints excluded: chain b residue 114 GLN Chi-restraints excluded: chain b residue 140 VAL Chi-restraints excluded: chain b residue 152 GLN Chi-restraints excluded: chain b residue 163 ILE Chi-restraints excluded: chain b residue 164 VAL Chi-restraints excluded: chain b residue 194 VAL Chi-restraints excluded: chain b residue 250 GLN Chi-restraints excluded: chain b residue 256 THR Chi-restraints excluded: chain c residue 9 VAL Chi-restraints excluded: chain c residue 22 ILE Chi-restraints excluded: chain c residue 39 ASP Chi-restraints excluded: chain c residue 89 GLU Chi-restraints excluded: chain c residue 95 SER Chi-restraints excluded: chain c residue 97 SER Chi-restraints excluded: chain c residue 104 VAL Chi-restraints excluded: chain c residue 110 THR Chi-restraints excluded: chain c residue 130 GLN Chi-restraints excluded: chain c residue 155 VAL Chi-restraints excluded: chain c residue 157 LYS Chi-restraints excluded: chain c residue 170 VAL Chi-restraints excluded: chain c residue 193 VAL Chi-restraints excluded: chain c residue 200 ASP Chi-restraints excluded: chain d residue 48 THR Chi-restraints excluded: chain d residue 53 THR Chi-restraints excluded: chain d residue 65 THR Chi-restraints excluded: chain d residue 72 SER Chi-restraints excluded: chain d residue 80 SER Chi-restraints excluded: chain d residue 84 THR Chi-restraints excluded: chain d residue 88 ARG Chi-restraints excluded: chain d residue 96 VAL Chi-restraints excluded: chain d residue 120 VAL Chi-restraints excluded: chain d residue 146 VAL Chi-restraints excluded: chain d residue 189 THR Chi-restraints excluded: chain e residue 23 SER Chi-restraints excluded: chain e residue 24 VAL Chi-restraints excluded: chain e residue 29 ARG Chi-restraints excluded: chain e residue 30 VAL Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 36 ASN Chi-restraints excluded: chain e residue 60 SER Chi-restraints excluded: chain e residue 65 LEU Chi-restraints excluded: chain e residue 67 THR Chi-restraints excluded: chain e residue 89 THR Chi-restraints excluded: chain e residue 90 LEU Chi-restraints excluded: chain e residue 100 GLU Chi-restraints excluded: chain e residue 117 SER Chi-restraints excluded: chain e residue 126 ASN Chi-restraints excluded: chain e residue 131 VAL Chi-restraints excluded: chain e residue 157 THR Chi-restraints excluded: chain e residue 173 ASP Chi-restraints excluded: chain f residue 1 SER Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 17 LYS Chi-restraints excluded: chain f residue 23 ILE Chi-restraints excluded: chain f residue 66 THR Chi-restraints excluded: chain f residue 91 VAL Chi-restraints excluded: chain f residue 105 SER Chi-restraints excluded: chain f residue 112 VAL Chi-restraints excluded: chain f residue 113 ASP Chi-restraints excluded: chain f residue 126 THR Chi-restraints excluded: chain f residue 130 ILE Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain g residue 61 VAL Chi-restraints excluded: chain g residue 96 THR Chi-restraints excluded: chain g residue 117 LEU Chi-restraints excluded: chain h residue 3 LEU Chi-restraints excluded: chain h residue 5 LEU Chi-restraints excluded: chain h residue 77 VAL Chi-restraints excluded: chain h residue 81 LEU Chi-restraints excluded: chain h residue 122 GLN Chi-restraints excluded: chain i residue 12 VAL Chi-restraints excluded: chain i residue 35 MET Chi-restraints excluded: chain j residue 12 LYS Chi-restraints excluded: chain j residue 73 VAL Chi-restraints excluded: chain j residue 131 ASN Chi-restraints excluded: chain k residue 14 SER Chi-restraints excluded: chain k residue 17 ARG Chi-restraints excluded: chain k residue 28 SER Chi-restraints excluded: chain k residue 45 GLU Chi-restraints excluded: chain k residue 69 VAL Chi-restraints excluded: chain k residue 118 LEU Chi-restraints excluded: chain l residue 12 SER Chi-restraints excluded: chain l residue 85 VAL Chi-restraints excluded: chain l residue 110 VAL Chi-restraints excluded: chain l residue 116 VAL Chi-restraints excluded: chain l residue 118 THR Chi-restraints excluded: chain l residue 120 VAL Chi-restraints excluded: chain l residue 121 THR Chi-restraints excluded: chain l residue 122 VAL Chi-restraints excluded: chain l residue 127 VAL Chi-restraints excluded: chain m residue 24 THR Chi-restraints excluded: chain m residue 42 THR Chi-restraints excluded: chain m residue 54 THR Chi-restraints excluded: chain m residue 57 VAL Chi-restraints excluded: chain m residue 67 VAL Chi-restraints excluded: chain m residue 74 THR Chi-restraints excluded: chain m residue 78 LEU Chi-restraints excluded: chain m residue 93 VAL Chi-restraints excluded: chain m residue 97 GLN Chi-restraints excluded: chain m residue 118 LYS Chi-restraints excluded: chain m residue 126 ILE Chi-restraints excluded: chain m residue 132 THR Chi-restraints excluded: chain n residue 6 SER Chi-restraints excluded: chain n residue 27 SER Chi-restraints excluded: chain n residue 37 THR Chi-restraints excluded: chain n residue 59 SER Chi-restraints excluded: chain n residue 73 ASN Chi-restraints excluded: chain n residue 75 ILE Chi-restraints excluded: chain o residue 12 THR Chi-restraints excluded: chain o residue 21 LEU Chi-restraints excluded: chain o residue 35 ILE Chi-restraints excluded: chain o residue 39 VAL Chi-restraints excluded: chain o residue 48 LEU Chi-restraints excluded: chain o residue 65 THR Chi-restraints excluded: chain o residue 95 SER Chi-restraints excluded: chain o residue 103 VAL Chi-restraints excluded: chain p residue 7 LEU Chi-restraints excluded: chain p residue 63 ILE Chi-restraints excluded: chain p residue 65 ASN Chi-restraints excluded: chain p residue 91 VAL Chi-restraints excluded: chain p residue 93 LYS Chi-restraints excluded: chain q residue 14 LYS Chi-restraints excluded: chain q residue 16 ILE Chi-restraints excluded: chain q residue 58 GLN Chi-restraints excluded: chain q residue 82 LEU Chi-restraints excluded: chain q residue 101 ASP Chi-restraints excluded: chain q residue 109 VAL Chi-restraints excluded: chain r residue 33 VAL Chi-restraints excluded: chain r residue 38 VAL Chi-restraints excluded: chain r residue 43 ASN Chi-restraints excluded: chain r residue 47 VAL Chi-restraints excluded: chain r residue 63 VAL Chi-restraints excluded: chain s residue 20 VAL Chi-restraints excluded: chain s residue 23 LEU Chi-restraints excluded: chain s residue 77 ASP Chi-restraints excluded: chain s residue 96 ILE Chi-restraints excluded: chain s residue 104 THR Chi-restraints excluded: chain s residue 106 VAL Chi-restraints excluded: chain s residue 107 VAL Chi-restraints excluded: chain s residue 108 SER Chi-restraints excluded: chain t residue 1 MET Chi-restraints excluded: chain t residue 16 VAL Chi-restraints excluded: chain t residue 17 SER Chi-restraints excluded: chain t residue 39 THR Chi-restraints excluded: chain t residue 57 VAL Chi-restraints excluded: chain t residue 85 VAL Chi-restraints excluded: chain t residue 87 LEU Chi-restraints excluded: chain u residue 4 ILE Chi-restraints excluded: chain u residue 24 VAL Chi-restraints excluded: chain u residue 33 VAL Chi-restraints excluded: chain u residue 48 VAL Chi-restraints excluded: chain v residue 17 SER Chi-restraints excluded: chain v residue 30 ILE Chi-restraints excluded: chain v residue 45 ASP Chi-restraints excluded: chain v residue 47 VAL Chi-restraints excluded: chain v residue 53 LYS Chi-restraints excluded: chain v residue 64 VAL Chi-restraints excluded: chain v residue 65 VAL Chi-restraints excluded: chain v residue 92 VAL Chi-restraints excluded: chain w residue 20 LYS Chi-restraints excluded: chain w residue 32 ILE Chi-restraints excluded: chain w residue 34 VAL Chi-restraints excluded: chain w residue 39 THR Chi-restraints excluded: chain w residue 51 ARG Chi-restraints excluded: chain w residue 66 GLU Chi-restraints excluded: chain w residue 74 LYS Chi-restraints excluded: chain w residue 76 ILE Chi-restraints excluded: chain x residue 1 SER Chi-restraints excluded: chain x residue 7 THR Chi-restraints excluded: chain x residue 13 THR Chi-restraints excluded: chain x residue 39 VAL Chi-restraints excluded: chain x residue 46 VAL Chi-restraints excluded: chain x residue 47 THR Chi-restraints excluded: chain x residue 64 ASP Chi-restraints excluded: chain x residue 67 LEU Chi-restraints excluded: chain x residue 69 GLU Chi-restraints excluded: chain y residue 11 VAL Chi-restraints excluded: chain y residue 27 ASN Chi-restraints excluded: chain y residue 30 MET Chi-restraints excluded: chain y residue 31 GLN Chi-restraints excluded: chain y residue 39 GLN Chi-restraints excluded: chain y residue 40 SER Chi-restraints excluded: chain y residue 43 LEU Chi-restraints excluded: chain y residue 55 THR Chi-restraints excluded: chain z residue 29 ARG Chi-restraints excluded: chain z residue 56 VAL Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 41 ARG Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain G residue 35 ASN Chi-restraints excluded: chain G residue 129 THR Chi-restraints excluded: chain G residue 153 MET Chi-restraints excluded: chain G residue 158 ASP Chi-restraints excluded: chain G residue 188 THR Chi-restraints excluded: chain G residue 198 VAL Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain G residue 216 VAL Chi-restraints excluded: chain H residue 20 THR Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 43 THR Chi-restraints excluded: chain H residue 48 LYS Chi-restraints excluded: chain H residue 117 ASP Chi-restraints excluded: chain H residue 123 LEU Chi-restraints excluded: chain H residue 164 THR Chi-restraints excluded: chain H residue 174 LEU Chi-restraints excluded: chain H residue 184 ASN Chi-restraints excluded: chain I residue 9 LYS Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 60 VAL Chi-restraints excluded: chain I residue 93 LEU Chi-restraints excluded: chain I residue 118 SER Chi-restraints excluded: chain I residue 133 SER Chi-restraints excluded: chain J residue 67 ARG Chi-restraints excluded: chain J residue 89 THR Chi-restraints excluded: chain J residue 104 ILE Chi-restraints excluded: chain J residue 105 ILE Chi-restraints excluded: chain J residue 123 LEU Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 146 MET Chi-restraints excluded: chain J residue 156 ARG Chi-restraints excluded: chain K residue 2 ARG Chi-restraints excluded: chain K residue 15 SER Chi-restraints excluded: chain K residue 17 GLN Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 39 LEU Chi-restraints excluded: chain K residue 68 GLN Chi-restraints excluded: chain K residue 75 GLU Chi-restraints excluded: chain K residue 84 VAL Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain L residue 96 ASN Chi-restraints excluded: chain L residue 117 LEU Chi-restraints excluded: chain L residue 121 ASN Chi-restraints excluded: chain M residue 6 ILE Chi-restraints excluded: chain M residue 9 MET Chi-restraints excluded: chain M residue 11 THR Chi-restraints excluded: chain M residue 57 GLU Chi-restraints excluded: chain M residue 98 LEU Chi-restraints excluded: chain M residue 104 SER Chi-restraints excluded: chain M residue 125 ILE Chi-restraints excluded: chain N residue 28 VAL Chi-restraints excluded: chain N residue 49 GLN Chi-restraints excluded: chain N residue 78 ILE Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain O residue 44 THR Chi-restraints excluded: chain O residue 50 THR Chi-restraints excluded: chain O residue 91 ASP Chi-restraints excluded: chain O residue 92 LEU Chi-restraints excluded: chain P residue 25 SER Chi-restraints excluded: chain P residue 45 THR Chi-restraints excluded: chain P residue 54 SER Chi-restraints excluded: chain P residue 86 LYS Chi-restraints excluded: chain Q residue 32 VAL Chi-restraints excluded: chain Q residue 34 THR Chi-restraints excluded: chain Q residue 40 THR Chi-restraints excluded: chain Q residue 46 SER Chi-restraints excluded: chain Q residue 51 VAL Chi-restraints excluded: chain Q residue 57 THR Chi-restraints excluded: chain Q residue 63 THR Chi-restraints excluded: chain Q residue 73 LEU Chi-restraints excluded: chain Q residue 87 LYS Chi-restraints excluded: chain Q residue 92 VAL Chi-restraints excluded: chain Q residue 97 VAL Chi-restraints excluded: chain Q residue 102 ASP Chi-restraints excluded: chain R residue 20 SER Chi-restraints excluded: chain R residue 24 VAL Chi-restraints excluded: chain R residue 58 GLU Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain R residue 107 THR Chi-restraints excluded: chain S residue 13 VAL Chi-restraints excluded: chain S residue 47 LEU Chi-restraints excluded: chain S residue 54 SER Chi-restraints excluded: chain T residue 4 THR Chi-restraints excluded: chain U residue 21 VAL Chi-restraints excluded: chain U residue 51 ARG Chi-restraints excluded: chain U residue 53 ASP Chi-restraints excluded: chain U residue 68 SER Chi-restraints excluded: chain V residue 24 ILE Chi-restraints excluded: chain V residue 32 ILE Chi-restraints excluded: chain V residue 41 THR Chi-restraints excluded: chain V residue 54 ILE Chi-restraints excluded: chain V residue 56 ASP Chi-restraints excluded: chain V residue 71 SER Chi-restraints excluded: chain V residue 82 VAL Chi-restraints excluded: chain W residue 37 LYS Chi-restraints excluded: chain W residue 70 THR Chi-restraints excluded: chain X residue 37 SER Chi-restraints excluded: chain X residue 38 THR Chi-restraints excluded: chain X residue 48 ILE Chi-restraints excluded: chain X residue 69 LYS Chi-restraints excluded: chain X residue 78 THR Chi-restraints excluded: chain Y residue 22 SER Chi-restraints excluded: chain Y residue 60 GLN Chi-restraints excluded: chain Y residue 74 HIS Chi-restraints excluded: chain Y residue 78 LEU Chi-restraints excluded: chain Y residue 79 THR Chi-restraints excluded: chain Z residue 12 ASP Chi-restraints excluded: chain Z residue 52 VAL Chi-restraints excluded: chain Z residue 59 LEU Chi-restraints excluded: chain a residue 8 MET Chi-restraints excluded: chain a residue 16 ASP Chi-restraints excluded: chain a residue 35 THR Chi-restraints excluded: chain a residue 46 VAL Chi-restraints excluded: chain a residue 53 ARG Chi-restraints excluded: chain a residue 64 VAL Chi-restraints excluded: chain a residue 207 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1050 random chunks: chunk 619 optimal weight: 10.0000 chunk 997 optimal weight: 5.9990 chunk 608 optimal weight: 10.0000 chunk 473 optimal weight: 4.9990 chunk 693 optimal weight: 40.0000 chunk 1046 optimal weight: 50.0000 chunk 962 optimal weight: 10.0000 chunk 832 optimal weight: 3.9990 chunk 86 optimal weight: 10.0000 chunk 643 optimal weight: 10.0000 chunk 510 optimal weight: 0.8980 overall best weight: 5.1790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 94 GLN ** e 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 63 GLN ** f 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 51 GLN r 86 GLN r 87 GLN s 61 ASN ** t 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 65 GLN v 12 GLN ** x 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** y 20 ASN y 27 ASN B 3 GLN D 13 ASN H 99 GLN ** H 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 53 GLN ** I 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 147 ASN N 49 GLN O 56 HIS Q 4 ASN T 27 GLN U 79 ASN V 49 ASN Y 54 GLN ** Y 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.3922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 161399 Z= 0.336 Angle : 0.690 15.753 241370 Z= 0.352 Chirality : 0.040 0.317 30856 Planarity : 0.005 0.079 13007 Dihedral : 23.249 179.234 80575 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 14.88 Ramachandran Plot: Outliers : 0.25 % Allowed : 9.07 % Favored : 90.67 % Rotamer: Outliers : 6.83 % Allowed : 35.66 % Favored : 57.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.96 (0.11), residues: 5919 helix: -0.36 (0.12), residues: 1857 sheet: -1.41 (0.16), residues: 1043 loop : -1.86 (0.11), residues: 3019 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP G 103 HIS 0.006 0.001 HIS f 44 PHE 0.043 0.002 PHE g 46 TYR 0.031 0.002 TYR e 21 ARG 0.020 0.001 ARG x 10 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11838 Ramachandran restraints generated. 5919 Oldfield, 0 Emsley, 5919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11838 Ramachandran restraints generated. 5919 Oldfield, 0 Emsley, 5919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1964 residues out of total 4908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 335 poor density : 1629 time to evaluate : 6.609 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: b 22 GLU cc_start: 0.7957 (pp20) cc_final: 0.7745 (pp20) REVERT: b 86 ARG cc_start: 0.9069 (OUTLIER) cc_final: 0.8227 (mtm-85) REVERT: b 97 ASP cc_start: 0.8833 (p0) cc_final: 0.8505 (p0) REVERT: b 114 GLN cc_start: 0.8730 (OUTLIER) cc_final: 0.8318 (tt0) REVERT: b 152 GLN cc_start: 0.8615 (OUTLIER) cc_final: 0.8209 (mm-40) REVERT: b 250 GLN cc_start: 0.8840 (OUTLIER) cc_final: 0.8105 (tt0) REVERT: c 30 GLU cc_start: 0.7948 (mm-30) cc_final: 0.7472 (mp0) REVERT: c 88 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7717 (pt0) REVERT: c 167 ASN cc_start: 0.9356 (t0) cc_final: 0.8986 (t160) REVERT: d 65 THR cc_start: 0.8803 (OUTLIER) cc_final: 0.8497 (t) REVERT: d 88 ARG cc_start: 0.8521 (OUTLIER) cc_final: 0.8123 (mmp80) REVERT: d 100 MET cc_start: 0.8209 (mtm) cc_final: 0.7931 (mtm) REVERT: d 115 GLN cc_start: 0.8536 (mm-40) cc_final: 0.8239 (mm-40) REVERT: d 156 ASN cc_start: 0.7857 (t0) cc_final: 0.7627 (t0) REVERT: e 25 MET cc_start: 0.8963 (ppp) cc_final: 0.8137 (tmm) REVERT: e 29 ARG cc_start: 0.8633 (OUTLIER) cc_final: 0.8141 (ptp-170) REVERT: e 31 GLU cc_start: 0.8355 (mt-10) cc_final: 0.8060 (mm-30) REVERT: e 36 ASN cc_start: 0.6846 (OUTLIER) cc_final: 0.6639 (t0) REVERT: e 65 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8388 (tm) REVERT: e 87 LYS cc_start: 0.9030 (ttpp) cc_final: 0.8338 (ttmt) REVERT: e 95 MET cc_start: 0.8860 (ppp) cc_final: 0.8527 (ppp) REVERT: e 145 VAL cc_start: 0.7498 (t) cc_final: 0.6818 (p) REVERT: f 19 ASN cc_start: 0.8814 (t0) cc_final: 0.8597 (t0) REVERT: f 21 GLN cc_start: 0.8197 (tp-100) cc_final: 0.7913 (tp-100) REVERT: f 37 ASN cc_start: 0.7694 (t0) cc_final: 0.7283 (t0) REVERT: f 63 GLN cc_start: 0.8282 (mm-40) cc_final: 0.8068 (mt0) REVERT: f 68 ARG cc_start: 0.8960 (tmt170) cc_final: 0.8748 (tmt-80) REVERT: f 82 PHE cc_start: 0.8229 (m-80) cc_final: 0.7704 (m-80) REVERT: f 100 ASN cc_start: 0.8497 (p0) cc_final: 0.8217 (p0) REVERT: f 129 GLU cc_start: 0.8566 (tt0) cc_final: 0.8007 (tp30) REVERT: g 4 ILE cc_start: 0.8747 (tp) cc_final: 0.8422 (mm) REVERT: g 8 LYS cc_start: 0.8754 (mtpp) cc_final: 0.8114 (tptt) REVERT: g 25 TYR cc_start: 0.8841 (t80) cc_final: 0.8319 (t80) REVERT: g 35 LYS cc_start: 0.8772 (mptt) cc_final: 0.8538 (mptp) REVERT: g 117 LEU cc_start: 0.7039 (OUTLIER) cc_final: 0.6730 (pt) REVERT: h 5 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8767 (pt) REVERT: h 81 LEU cc_start: 0.5608 (OUTLIER) cc_final: 0.5272 (mt) REVERT: i 116 MET cc_start: -0.2591 (OUTLIER) cc_final: -0.3076 (tpt) REVERT: i 124 MET cc_start: 0.4992 (ppp) cc_final: 0.2667 (mmt) REVERT: j 31 GLU cc_start: 0.7708 (tp30) cc_final: 0.7320 (tp30) REVERT: j 35 ARG cc_start: 0.8794 (mtt90) cc_final: 0.8281 (mtm-85) REVERT: j 71 ASP cc_start: 0.8499 (m-30) cc_final: 0.8272 (m-30) REVERT: k 12 ASP cc_start: 0.8413 (p0) cc_final: 0.8124 (p0) REVERT: k 17 ARG cc_start: 0.7911 (OUTLIER) cc_final: 0.7195 (ttm170) REVERT: l 14 LYS cc_start: 0.8158 (tppp) cc_final: 0.7930 (tppp) REVERT: l 76 GLU cc_start: 0.7533 (mt-10) cc_final: 0.7133 (mt-10) REVERT: l 84 LYS cc_start: 0.8219 (ptpp) cc_final: 0.7983 (pmmt) REVERT: l 105 ILE cc_start: 0.8971 (mm) cc_final: 0.8764 (mp) REVERT: l 143 GLU cc_start: 0.7513 (pp20) cc_final: 0.7186 (pp20) REVERT: m 17 ASN cc_start: 0.8651 (t0) cc_final: 0.7844 (t0) REVERT: m 88 ASN cc_start: 0.8591 (m-40) cc_final: 0.8284 (m110) REVERT: m 91 TYR cc_start: 0.9065 (p90) cc_final: 0.8542 (p90) REVERT: m 97 GLN cc_start: 0.8628 (OUTLIER) cc_final: 0.8299 (mp-120) REVERT: m 105 MET cc_start: 0.8436 (OUTLIER) cc_final: 0.8186 (mtp) REVERT: n 35 LYS cc_start: 0.8826 (tttt) cc_final: 0.8573 (tptt) REVERT: n 72 ASP cc_start: 0.8831 (t0) cc_final: 0.8531 (t0) REVERT: o 38 GLN cc_start: 0.8851 (pt0) cc_final: 0.7955 (pm20) REVERT: o 80 GLU cc_start: 0.8913 (tm-30) cc_final: 0.8596 (tm-30) REVERT: p 23 ASP cc_start: 0.8592 (m-30) cc_final: 0.8164 (m-30) REVERT: p 26 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.7677 (tm-30) REVERT: p 65 ASN cc_start: 0.8878 (OUTLIER) cc_final: 0.8539 (p0) REVERT: q 58 GLN cc_start: 0.8880 (OUTLIER) cc_final: 0.8649 (tt0) REVERT: q 96 ASP cc_start: 0.8185 (t0) cc_final: 0.7607 (t0) REVERT: q 101 ASP cc_start: 0.8336 (OUTLIER) cc_final: 0.7911 (t0) REVERT: r 13 ARG cc_start: 0.8783 (ttp80) cc_final: 0.8147 (ttt-90) REVERT: r 16 GLU cc_start: 0.8491 (tp30) cc_final: 0.8061 (tp30) REVERT: r 18 GLN cc_start: 0.8222 (pt0) cc_final: 0.7828 (pm20) REVERT: r 31 GLU cc_start: 0.7704 (mp0) cc_final: 0.7310 (mp0) REVERT: r 37 GLU cc_start: 0.7960 (pm20) cc_final: 0.7659 (pm20) REVERT: r 40 MET cc_start: 0.8638 (ttt) cc_final: 0.8274 (tpp) REVERT: r 46 GLU cc_start: 0.8021 (tp30) cc_final: 0.7715 (tp30) REVERT: r 60 LYS cc_start: 0.8929 (mtmm) cc_final: 0.8511 (mmmm) REVERT: r 62 GLU cc_start: 0.8524 (tt0) cc_final: 0.7762 (tm-30) REVERT: s 52 GLU cc_start: 0.8054 (mm-30) cc_final: 0.7771 (tm-30) REVERT: s 61 ASN cc_start: 0.8849 (m-40) cc_final: 0.8542 (m-40) REVERT: t 1 MET cc_start: 0.7562 (OUTLIER) cc_final: 0.7037 (ptp) REVERT: t 25 GLU cc_start: 0.8221 (mm-30) cc_final: 0.7855 (mm-30) REVERT: t 28 ASN cc_start: 0.8802 (t0) cc_final: 0.8319 (t0) REVERT: t 36 LYS cc_start: 0.8373 (tptp) cc_final: 0.8047 (tptt) REVERT: t 86 THR cc_start: 0.9078 (m) cc_final: 0.8726 (p) REVERT: u 33 VAL cc_start: 0.9486 (m) cc_final: 0.9196 (t) REVERT: u 36 GLU cc_start: 0.8858 (pp20) cc_final: 0.8597 (pp20) REVERT: u 93 ARG cc_start: 0.8743 (mtm180) cc_final: 0.8407 (mtp180) REVERT: v 41 GLU cc_start: 0.8114 (tt0) cc_final: 0.7236 (tm-30) REVERT: v 46 LYS cc_start: 0.9160 (mmtm) cc_final: 0.8798 (mmpt) REVERT: v 50 MET cc_start: 0.8698 (mtm) cc_final: 0.8344 (mtt) REVERT: w 16 ARG cc_start: 0.8643 (mpt-90) cc_final: 0.7781 (mmt90) REVERT: w 20 LYS cc_start: 0.9033 (OUTLIER) cc_final: 0.8348 (mmtm) REVERT: w 51 ARG cc_start: 0.9056 (OUTLIER) cc_final: 0.8559 (ppp80) REVERT: x 10 ARG cc_start: 0.8459 (ttm110) cc_final: 0.8113 (mtp-110) REVERT: x 69 GLU cc_start: 0.8855 (OUTLIER) cc_final: 0.7956 (mp0) REVERT: x 75 GLU cc_start: 0.7338 (mp0) cc_final: 0.7018 (mp0) REVERT: y 1 MET cc_start: 0.6229 (tpt) cc_final: 0.5769 (tpt) REVERT: y 39 GLN cc_start: 0.8373 (OUTLIER) cc_final: 0.7903 (mt0) REVERT: z 4 ILE cc_start: 0.8730 (mt) cc_final: 0.8353 (mp) REVERT: B 3 GLN cc_start: 0.8524 (pt0) cc_final: 0.8166 (pt0) REVERT: B 5 ASN cc_start: 0.8973 (m-40) cc_final: 0.8571 (m110) REVERT: B 36 LYS cc_start: 0.9121 (mmtp) cc_final: 0.8860 (mptp) REVERT: C 36 LYS cc_start: 0.8667 (ttpt) cc_final: 0.8305 (mtpp) REVERT: D 41 ARG cc_start: 0.8120 (OUTLIER) cc_final: 0.7690 (mtp180) REVERT: E 48 MET cc_start: 0.8751 (mmt) cc_final: 0.8475 (mmt) REVERT: F 15 LYS cc_start: 0.8451 (mttt) cc_final: 0.8197 (tttp) REVERT: F 24 ARG cc_start: 0.8831 (mtt-85) cc_final: 0.8624 (mtt-85) REVERT: G 18 GLN cc_start: 0.8853 (mt0) cc_final: 0.8561 (mp10) REVERT: G 26 MET cc_start: 0.8673 (mmm) cc_final: 0.8313 (mmm) REVERT: G 48 MET cc_start: 0.9043 (ptp) cc_final: 0.8758 (pmm) REVERT: H 5 HIS cc_start: 0.9152 (t-90) cc_final: 0.8876 (t-90) REVERT: H 39 ARG cc_start: 0.8654 (ttm-80) cc_final: 0.8237 (ttm-80) REVERT: H 40 GLN cc_start: 0.8878 (tt0) cc_final: 0.8593 (pp30) REVERT: H 139 ASN cc_start: 0.8968 (m-40) cc_final: 0.8499 (m110) REVERT: H 151 GLU cc_start: 0.8162 (tm-30) cc_final: 0.7801 (tm-30) REVERT: H 165 GLU cc_start: 0.8370 (mp0) cc_final: 0.8059 (mm-30) REVERT: H 184 ASN cc_start: 0.8786 (OUTLIER) cc_final: 0.8528 (t160) REVERT: H 191 THR cc_start: 0.9285 (p) cc_final: 0.8913 (t) REVERT: I 18 LEU cc_start: 0.8588 (pt) cc_final: 0.8373 (pt) REVERT: I 47 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8305 (mm) REVERT: I 68 GLU cc_start: 0.8352 (tp30) cc_final: 0.7791 (tp30) REVERT: I 71 PHE cc_start: 0.9213 (t80) cc_final: 0.8568 (t80) REVERT: I 73 ASN cc_start: 0.9362 (m110) cc_final: 0.8964 (m110) REVERT: I 112 GLU cc_start: 0.7425 (tt0) cc_final: 0.7161 (tt0) REVERT: I 116 LEU cc_start: 0.8727 (tp) cc_final: 0.8463 (tt) REVERT: I 137 SER cc_start: 0.8085 (t) cc_final: 0.7788 (p) REVERT: I 152 SER cc_start: 0.8880 (t) cc_final: 0.8561 (p) REVERT: J 32 PHE cc_start: 0.9074 (m-80) cc_final: 0.8712 (m-80) REVERT: J 60 GLN cc_start: 0.8861 (tp-100) cc_final: 0.8421 (OUTLIER) REVERT: J 94 PHE cc_start: 0.8338 (t80) cc_final: 0.7750 (t80) REVERT: J 104 ILE cc_start: 0.9215 (OUTLIER) cc_final: 0.8698 (pp) REVERT: J 146 MET cc_start: 0.8543 (OUTLIER) cc_final: 0.7672 (ttp) REVERT: K 56 LYS cc_start: 0.8117 (mmtt) cc_final: 0.7733 (mmpt) REVERT: K 58 HIS cc_start: 0.7664 (t70) cc_final: 0.7372 (t70) REVERT: K 62 MET cc_start: 0.8165 (mmm) cc_final: 0.7744 (mpp) REVERT: K 65 GLU cc_start: 0.7942 (tp30) cc_final: 0.7522 (tp30) REVERT: K 90 MET cc_start: 0.7688 (mtm) cc_final: 0.7469 (mtp) REVERT: L 3 ARG cc_start: 0.6686 (ttm170) cc_final: 0.6347 (ttm170) REVERT: L 100 MET cc_start: 0.8490 (mtm) cc_final: 0.8239 (mtm) REVERT: L 105 GLU cc_start: 0.8616 (pp20) cc_final: 0.8254 (pp20) REVERT: M 17 GLN cc_start: 0.9057 (mm110) cc_final: 0.8322 (mm110) REVERT: M 26 MET cc_start: 0.8535 (ptp) cc_final: 0.8061 (pmm) REVERT: M 28 SER cc_start: 0.8543 (p) cc_final: 0.8071 (p) REVERT: M 56 PRO cc_start: 0.8943 (Cg_exo) cc_final: 0.8421 (Cg_endo) REVERT: M 57 GLU cc_start: 0.7786 (OUTLIER) cc_final: 0.7355 (pp20) REVERT: M 98 LEU cc_start: 0.9284 (OUTLIER) cc_final: 0.8939 (pt) REVERT: M 110 MET cc_start: 0.8328 (ptp) cc_final: 0.8057 (ptp) REVERT: N 20 ILE cc_start: 0.8953 (tt) cc_final: 0.8552 (tt) REVERT: N 21 LYS cc_start: 0.9060 (mtpt) cc_final: 0.8619 (mmtt) REVERT: N 27 ILE cc_start: 0.8988 (mp) cc_final: 0.8631 (mm) REVERT: N 123 ARG cc_start: 0.8617 (mmt90) cc_final: 0.8370 (tpp80) REVERT: O 16 ARG cc_start: 0.8183 (ptt180) cc_final: 0.7915 (ptp90) REVERT: O 44 THR cc_start: 0.8340 (OUTLIER) cc_final: 0.8112 (t) REVERT: O 62 ARG cc_start: 0.7937 (mtt90) cc_final: 0.7717 (mmt-90) REVERT: P 86 LYS cc_start: 0.8632 (OUTLIER) cc_final: 0.8422 (ptmm) REVERT: Q 33 CYS cc_start: 0.8529 (t) cc_final: 0.8270 (t) REVERT: Q 37 TYR cc_start: 0.8212 (p90) cc_final: 0.7893 (p90) REVERT: Q 87 LYS cc_start: 0.8649 (OUTLIER) cc_final: 0.7870 (tppt) REVERT: R 15 VAL cc_start: 0.8329 (m) cc_final: 0.8078 (t) REVERT: R 43 LYS cc_start: 0.8856 (ptpt) cc_final: 0.8409 (ptpp) REVERT: R 76 ILE cc_start: 0.9343 (pp) cc_final: 0.8987 (pp) REVERT: R 77 LYS cc_start: 0.9223 (tttm) cc_final: 0.8632 (tppt) REVERT: R 80 MET cc_start: 0.7873 (ttm) cc_final: 0.7451 (tmm) REVERT: S 97 LYS cc_start: 0.8593 (tttt) cc_final: 0.8352 (tttt) REVERT: T 25 GLU cc_start: 0.8590 (mt-10) cc_final: 0.8314 (mt-10) REVERT: T 36 ASN cc_start: 0.8806 (m110) cc_final: 0.8279 (m-40) REVERT: T 48 ASP cc_start: 0.8496 (t0) cc_final: 0.8016 (t0) REVERT: T 51 SER cc_start: 0.8975 (p) cc_final: 0.8678 (p) REVERT: T 73 ASP cc_start: 0.7876 (t0) cc_final: 0.7451 (t0) REVERT: T 76 ARG cc_start: 0.8549 (mtm180) cc_final: 0.8099 (ttm110) REVERT: U 18 GLN cc_start: 0.8163 (mt0) cc_final: 0.7510 (mm-40) REVERT: U 39 PHE cc_start: 0.9002 (t80) cc_final: 0.8014 (t80) REVERT: U 53 ASP cc_start: 0.8395 (OUTLIER) cc_final: 0.8039 (p0) REVERT: V 7 LEU cc_start: 0.8777 (mp) cc_final: 0.8539 (pp) REVERT: V 16 MET cc_start: 0.7086 (ttt) cc_final: 0.6678 (ttt) REVERT: V 24 ILE cc_start: 0.8608 (OUTLIER) cc_final: 0.7960 (pp) REVERT: V 61 ARG cc_start: 0.8241 (ppp80) cc_final: 0.7942 (ppp80) REVERT: V 80 LYS cc_start: 0.8858 (tmtt) cc_final: 0.8403 (tptt) REVERT: W 24 ASP cc_start: 0.8565 (t0) cc_final: 0.8275 (t0) REVERT: W 51 GLN cc_start: 0.8789 (tp40) cc_final: 0.7548 (tm-30) REVERT: X 5 LYS cc_start: 0.7170 (tppp) cc_final: 0.6583 (tppp) REVERT: X 32 THR cc_start: 0.8398 (t) cc_final: 0.8159 (p) REVERT: X 69 LYS cc_start: 0.8532 (OUTLIER) cc_final: 0.8185 (mttp) REVERT: X 79 TYR cc_start: 0.7953 (t80) cc_final: 0.7711 (t80) REVERT: Y 15 LYS cc_start: 0.8880 (tttm) cc_final: 0.8265 (tptp) REVERT: Y 17 ARG cc_start: 0.8862 (tmm-80) cc_final: 0.8038 (ttp-110) REVERT: Y 18 LYS cc_start: 0.9168 (mttp) cc_final: 0.8734 (mttp) REVERT: Y 53 MET cc_start: 0.8851 (tmm) cc_final: 0.8393 (ppp) REVERT: Y 81 GLN cc_start: 0.9156 (mm-40) cc_final: 0.8728 (mm-40) REVERT: Z 38 GLU cc_start: 0.8095 (pp20) cc_final: 0.7708 (tm-30) REVERT: a 16 ASP cc_start: 0.2077 (OUTLIER) cc_final: 0.1705 (t0) outliers start: 335 outliers final: 264 residues processed: 1773 average time/residue: 2.0177 time to fit residues: 5252.8557 Evaluate side-chains 1911 residues out of total 4908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 303 poor density : 1608 time to evaluate : 6.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 37 SER Chi-restraints excluded: chain b residue 48 ILE Chi-restraints excluded: chain b residue 50 THR Chi-restraints excluded: chain b residue 52 HIS Chi-restraints excluded: chain b residue 86 ARG Chi-restraints excluded: chain b residue 114 GLN Chi-restraints excluded: chain b residue 140 VAL Chi-restraints excluded: chain b residue 152 GLN Chi-restraints excluded: chain b residue 163 ILE Chi-restraints excluded: chain b residue 164 VAL Chi-restraints excluded: chain b residue 194 VAL Chi-restraints excluded: chain b residue 250 GLN Chi-restraints excluded: chain b residue 256 THR Chi-restraints excluded: chain c residue 9 VAL Chi-restraints excluded: chain c residue 22 ILE Chi-restraints excluded: chain c residue 39 ASP Chi-restraints excluded: chain c residue 88 GLU Chi-restraints excluded: chain c residue 89 GLU Chi-restraints excluded: chain c residue 95 SER Chi-restraints excluded: chain c residue 97 SER Chi-restraints excluded: chain c residue 104 VAL Chi-restraints excluded: chain c residue 110 THR Chi-restraints excluded: chain c residue 155 VAL Chi-restraints excluded: chain c residue 157 LYS Chi-restraints excluded: chain c residue 170 VAL Chi-restraints excluded: chain c residue 193 VAL Chi-restraints excluded: chain c residue 200 ASP Chi-restraints excluded: chain d residue 53 THR Chi-restraints excluded: chain d residue 65 THR Chi-restraints excluded: chain d residue 72 SER Chi-restraints excluded: chain d residue 80 SER Chi-restraints excluded: chain d residue 84 THR Chi-restraints excluded: chain d residue 88 ARG Chi-restraints excluded: chain d residue 96 VAL Chi-restraints excluded: chain d residue 120 VAL Chi-restraints excluded: chain d residue 146 VAL Chi-restraints excluded: chain d residue 189 THR Chi-restraints excluded: chain e residue 23 SER Chi-restraints excluded: chain e residue 24 VAL Chi-restraints excluded: chain e residue 29 ARG Chi-restraints excluded: chain e residue 30 VAL Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 36 ASN Chi-restraints excluded: chain e residue 60 SER Chi-restraints excluded: chain e residue 65 LEU Chi-restraints excluded: chain e residue 67 THR Chi-restraints excluded: chain e residue 89 THR Chi-restraints excluded: chain e residue 90 LEU Chi-restraints excluded: chain e residue 117 SER Chi-restraints excluded: chain e residue 131 VAL Chi-restraints excluded: chain e residue 157 THR Chi-restraints excluded: chain e residue 173 ASP Chi-restraints excluded: chain f residue 1 SER Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 17 LYS Chi-restraints excluded: chain f residue 23 ILE Chi-restraints excluded: chain f residue 66 THR Chi-restraints excluded: chain f residue 91 VAL Chi-restraints excluded: chain f residue 105 SER Chi-restraints excluded: chain f residue 112 VAL Chi-restraints excluded: chain f residue 126 THR Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain g residue 61 VAL Chi-restraints excluded: chain g residue 96 THR Chi-restraints excluded: chain g residue 117 LEU Chi-restraints excluded: chain h residue 3 LEU Chi-restraints excluded: chain h residue 5 LEU Chi-restraints excluded: chain h residue 77 VAL Chi-restraints excluded: chain h residue 81 LEU Chi-restraints excluded: chain i residue 12 VAL Chi-restraints excluded: chain i residue 35 MET Chi-restraints excluded: chain i residue 116 MET Chi-restraints excluded: chain j residue 12 LYS Chi-restraints excluded: chain j residue 54 ILE Chi-restraints excluded: chain j residue 73 VAL Chi-restraints excluded: chain k residue 14 SER Chi-restraints excluded: chain k residue 17 ARG Chi-restraints excluded: chain k residue 28 SER Chi-restraints excluded: chain k residue 45 GLU Chi-restraints excluded: chain k residue 69 VAL Chi-restraints excluded: chain k residue 80 ASP Chi-restraints excluded: chain k residue 108 ARG Chi-restraints excluded: chain k residue 118 LEU Chi-restraints excluded: chain l residue 12 SER Chi-restraints excluded: chain l residue 85 VAL Chi-restraints excluded: chain l residue 110 VAL Chi-restraints excluded: chain l residue 116 VAL Chi-restraints excluded: chain l residue 118 THR Chi-restraints excluded: chain l residue 121 THR Chi-restraints excluded: chain l residue 122 VAL Chi-restraints excluded: chain l residue 127 VAL Chi-restraints excluded: chain m residue 24 THR Chi-restraints excluded: chain m residue 42 THR Chi-restraints excluded: chain m residue 54 THR Chi-restraints excluded: chain m residue 57 VAL Chi-restraints excluded: chain m residue 74 THR Chi-restraints excluded: chain m residue 93 VAL Chi-restraints excluded: chain m residue 97 GLN Chi-restraints excluded: chain m residue 105 MET Chi-restraints excluded: chain m residue 118 LYS Chi-restraints excluded: chain m residue 126 ILE Chi-restraints excluded: chain m residue 132 THR Chi-restraints excluded: chain n residue 6 SER Chi-restraints excluded: chain n residue 27 SER Chi-restraints excluded: chain n residue 73 ASN Chi-restraints excluded: chain n residue 75 ILE Chi-restraints excluded: chain o residue 12 THR Chi-restraints excluded: chain o residue 21 LEU Chi-restraints excluded: chain o residue 35 ILE Chi-restraints excluded: chain o residue 39 VAL Chi-restraints excluded: chain o residue 40 ILE Chi-restraints excluded: chain o residue 48 LEU Chi-restraints excluded: chain o residue 65 THR Chi-restraints excluded: chain o residue 95 SER Chi-restraints excluded: chain o residue 103 VAL Chi-restraints excluded: chain p residue 7 LEU Chi-restraints excluded: chain p residue 26 GLU Chi-restraints excluded: chain p residue 63 ILE Chi-restraints excluded: chain p residue 65 ASN Chi-restraints excluded: chain p residue 91 VAL Chi-restraints excluded: chain p residue 93 LYS Chi-restraints excluded: chain q residue 16 ILE Chi-restraints excluded: chain q residue 58 GLN Chi-restraints excluded: chain q residue 64 ILE Chi-restraints excluded: chain q residue 82 LEU Chi-restraints excluded: chain q residue 101 ASP Chi-restraints excluded: chain q residue 109 VAL Chi-restraints excluded: chain r residue 38 VAL Chi-restraints excluded: chain r residue 43 ASN Chi-restraints excluded: chain r residue 63 VAL Chi-restraints excluded: chain s residue 20 VAL Chi-restraints excluded: chain s residue 23 LEU Chi-restraints excluded: chain s residue 74 ILE Chi-restraints excluded: chain s residue 77 ASP Chi-restraints excluded: chain s residue 104 THR Chi-restraints excluded: chain s residue 106 VAL Chi-restraints excluded: chain s residue 107 VAL Chi-restraints excluded: chain s residue 108 SER Chi-restraints excluded: chain t residue 1 MET Chi-restraints excluded: chain t residue 16 VAL Chi-restraints excluded: chain t residue 17 SER Chi-restraints excluded: chain t residue 39 THR Chi-restraints excluded: chain t residue 57 VAL Chi-restraints excluded: chain t residue 85 VAL Chi-restraints excluded: chain t residue 87 LEU Chi-restraints excluded: chain u residue 4 ILE Chi-restraints excluded: chain u residue 24 VAL Chi-restraints excluded: chain u residue 48 VAL Chi-restraints excluded: chain v residue 17 SER Chi-restraints excluded: chain v residue 45 ASP Chi-restraints excluded: chain v residue 47 VAL Chi-restraints excluded: chain v residue 53 LYS Chi-restraints excluded: chain v residue 64 VAL Chi-restraints excluded: chain v residue 65 VAL Chi-restraints excluded: chain v residue 92 VAL Chi-restraints excluded: chain w residue 20 LYS Chi-restraints excluded: chain w residue 32 ILE Chi-restraints excluded: chain w residue 34 VAL Chi-restraints excluded: chain w residue 39 THR Chi-restraints excluded: chain w residue 51 ARG Chi-restraints excluded: chain w residue 66 GLU Chi-restraints excluded: chain w residue 74 LYS Chi-restraints excluded: chain w residue 76 ILE Chi-restraints excluded: chain x residue 1 SER Chi-restraints excluded: chain x residue 7 THR Chi-restraints excluded: chain x residue 13 THR Chi-restraints excluded: chain x residue 39 VAL Chi-restraints excluded: chain x residue 46 VAL Chi-restraints excluded: chain x residue 47 THR Chi-restraints excluded: chain x residue 64 ASP Chi-restraints excluded: chain x residue 67 LEU Chi-restraints excluded: chain x residue 69 GLU Chi-restraints excluded: chain y residue 11 VAL Chi-restraints excluded: chain y residue 30 MET Chi-restraints excluded: chain y residue 31 GLN Chi-restraints excluded: chain y residue 39 GLN Chi-restraints excluded: chain y residue 40 SER Chi-restraints excluded: chain y residue 43 LEU Chi-restraints excluded: chain z residue 29 ARG Chi-restraints excluded: chain z residue 56 VAL Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 41 ARG Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain G residue 120 SER Chi-restraints excluded: chain G residue 153 MET Chi-restraints excluded: chain G residue 158 ASP Chi-restraints excluded: chain G residue 188 THR Chi-restraints excluded: chain G residue 198 VAL Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 43 THR Chi-restraints excluded: chain H residue 117 ASP Chi-restraints excluded: chain H residue 123 LEU Chi-restraints excluded: chain H residue 164 THR Chi-restraints excluded: chain H residue 174 LEU Chi-restraints excluded: chain H residue 184 ASN Chi-restraints excluded: chain I residue 9 LYS Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 60 VAL Chi-restraints excluded: chain I residue 93 LEU Chi-restraints excluded: chain I residue 118 SER Chi-restraints excluded: chain I residue 133 SER Chi-restraints excluded: chain J residue 67 ARG Chi-restraints excluded: chain J residue 89 THR Chi-restraints excluded: chain J residue 104 ILE Chi-restraints excluded: chain J residue 105 ILE Chi-restraints excluded: chain J residue 123 LEU Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 146 MET Chi-restraints excluded: chain K residue 15 SER Chi-restraints excluded: chain K residue 17 GLN Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 39 LEU Chi-restraints excluded: chain K residue 68 GLN Chi-restraints excluded: chain K residue 75 GLU Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain L residue 96 ASN Chi-restraints excluded: chain L residue 117 LEU Chi-restraints excluded: chain L residue 121 ASN Chi-restraints excluded: chain M residue 6 ILE Chi-restraints excluded: chain M residue 9 MET Chi-restraints excluded: chain M residue 11 THR Chi-restraints excluded: chain M residue 57 GLU Chi-restraints excluded: chain M residue 98 LEU Chi-restraints excluded: chain M residue 104 SER Chi-restraints excluded: chain M residue 125 ILE Chi-restraints excluded: chain N residue 28 VAL Chi-restraints excluded: chain N residue 78 ILE Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain O residue 44 THR Chi-restraints excluded: chain O residue 50 THR Chi-restraints excluded: chain O residue 91 ASP Chi-restraints excluded: chain O residue 92 LEU Chi-restraints excluded: chain P residue 15 VAL Chi-restraints excluded: chain P residue 25 SER Chi-restraints excluded: chain P residue 30 ILE Chi-restraints excluded: chain P residue 45 THR Chi-restraints excluded: chain P residue 54 SER Chi-restraints excluded: chain P residue 86 LYS Chi-restraints excluded: chain P residue 107 THR Chi-restraints excluded: chain Q residue 32 VAL Chi-restraints excluded: chain Q residue 34 THR Chi-restraints excluded: chain Q residue 39 THR Chi-restraints excluded: chain Q residue 40 THR Chi-restraints excluded: chain Q residue 46 SER Chi-restraints excluded: chain Q residue 51 VAL Chi-restraints excluded: chain Q residue 57 THR Chi-restraints excluded: chain Q residue 63 THR Chi-restraints excluded: chain Q residue 73 LEU Chi-restraints excluded: chain Q residue 87 LYS Chi-restraints excluded: chain Q residue 92 VAL Chi-restraints excluded: chain Q residue 97 VAL Chi-restraints excluded: chain Q residue 102 ASP Chi-restraints excluded: chain R residue 24 VAL Chi-restraints excluded: chain R residue 58 GLU Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain R residue 107 THR Chi-restraints excluded: chain S residue 13 VAL Chi-restraints excluded: chain S residue 47 LEU Chi-restraints excluded: chain S residue 54 SER Chi-restraints excluded: chain T residue 4 THR Chi-restraints excluded: chain T residue 27 GLN Chi-restraints excluded: chain U residue 21 VAL Chi-restraints excluded: chain U residue 53 ASP Chi-restraints excluded: chain U residue 68 SER Chi-restraints excluded: chain U residue 79 ASN Chi-restraints excluded: chain V residue 24 ILE Chi-restraints excluded: chain V residue 32 ILE Chi-restraints excluded: chain V residue 41 THR Chi-restraints excluded: chain V residue 54 ILE Chi-restraints excluded: chain V residue 56 ASP Chi-restraints excluded: chain V residue 71 SER Chi-restraints excluded: chain V residue 82 VAL Chi-restraints excluded: chain W residue 70 THR Chi-restraints excluded: chain X residue 37 SER Chi-restraints excluded: chain X residue 38 THR Chi-restraints excluded: chain X residue 48 ILE Chi-restraints excluded: chain X residue 69 LYS Chi-restraints excluded: chain X residue 78 THR Chi-restraints excluded: chain Y residue 22 SER Chi-restraints excluded: chain Y residue 74 HIS Chi-restraints excluded: chain Y residue 78 LEU Chi-restraints excluded: chain Y residue 79 THR Chi-restraints excluded: chain Z residue 12 ASP Chi-restraints excluded: chain Z residue 52 VAL Chi-restraints excluded: chain Z residue 59 LEU Chi-restraints excluded: chain a residue 8 MET Chi-restraints excluded: chain a residue 16 ASP Chi-restraints excluded: chain a residue 35 THR Chi-restraints excluded: chain a residue 46 VAL Chi-restraints excluded: chain a residue 53 ARG Chi-restraints excluded: chain a residue 64 VAL Chi-restraints excluded: chain a residue 207 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1050 random chunks: chunk 661 optimal weight: 10.0000 chunk 887 optimal weight: 10.0000 chunk 255 optimal weight: 1.9990 chunk 768 optimal weight: 30.0000 chunk 122 optimal weight: 40.0000 chunk 231 optimal weight: 0.7980 chunk 834 optimal weight: 10.0000 chunk 349 optimal weight: 20.0000 chunk 856 optimal weight: 10.0000 chunk 105 optimal weight: 7.9990 chunk 153 optimal weight: 5.9990 overall best weight: 5.3590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** e 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 89 ASN n 18 GLN ** o 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 51 GLN r 87 GLN ** t 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 65 GLN u 68 ASN v 12 GLN y 20 ASN y 27 ASN D 13 ASN ** H 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 147 ASN O 56 HIS Q 4 ASN T 27 GLN U 79 ASN ** V 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 60 GLN ** Y 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.128369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.086796 restraints weight = 286587.710| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 1.33 r_work: 0.3002 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8723 moved from start: 0.3924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.294 161399 Z= 0.383 Angle : 0.730 59.062 241370 Z= 0.380 Chirality : 0.041 1.006 30856 Planarity : 0.005 0.075 13007 Dihedral : 23.249 179.253 80575 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 16.32 Ramachandran Plot: Outliers : 0.29 % Allowed : 9.22 % Favored : 90.49 % Rotamer: Outliers : 6.85 % Allowed : 35.98 % Favored : 57.17 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.96 (0.11), residues: 5919 helix: -0.37 (0.12), residues: 1857 sheet: -1.40 (0.16), residues: 1043 loop : -1.86 (0.11), residues: 3019 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.160 0.003 TRP S 41 HIS 0.009 0.001 HIS V 44 PHE 0.059 0.002 PHE b 265 TYR 0.030 0.002 TYR G 212 ARG 0.018 0.001 ARG x 10 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 70200.77 seconds wall clock time: 1208 minutes 25.94 seconds (72505.94 seconds total)