Starting phenix.real_space_refine on Sat Mar 2 00:10:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k52_22671/03_2024/7k52_22671_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k52_22671/03_2024/7k52_22671.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k52_22671/03_2024/7k52_22671.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k52_22671/03_2024/7k52_22671.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k52_22671/03_2024/7k52_22671_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k52_22671/03_2024/7k52_22671_updated.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.018 sd= 1.385 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 4731 5.49 5 Mg 1 5.21 5 S 180 5.16 5 C 77766 2.51 5 N 28487 2.21 5 O 42205 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "b GLU 22": "OE1" <-> "OE2" Residue "c ARG 13": "NH1" <-> "NH2" Residue "c ARG 33": "NH1" <-> "NH2" Residue "c ARG 59": "NH1" <-> "NH2" Residue "c GLU 64": "OE1" <-> "OE2" Residue "c ARG 77": "NH1" <-> "NH2" Residue "c ARG 83": "NH1" <-> "NH2" Residue "c ARG 169": "NH1" <-> "NH2" Residue "c ASP 176": "OD1" <-> "OD2" Residue "c GLU 183": "OE1" <-> "OE2" 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 ARG 162": "NH1" <-> "NH2" Residue "d ARG 170": "NH1" <-> "NH2" Residue "e ARG 70": "NH1" <-> "NH2" Residue "e ARG 79": "NH1" <-> "NH2" Residue "e ARG 91": "NH1" <-> "NH2" Residue "e ARG 101": "NH1" <-> "NH2" Residue "e ARG 109": "NH1" <-> "NH2" Residue "e ARG 111": "NH1" <-> "NH2" Residue "e ARG 114": "NH1" <-> "NH2" Residue "e ARG 132": "NH1" <-> "NH2" Residue "f ARG 2": "NH1" <-> "NH2" 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 149": "OE1" <-> "OE2" Residue "j GLU 9": "OE1" <-> "OE2" Residue "j ARG 13": "NH1" <-> "NH2" Residue "j ARG 37": "NH1" <-> "NH2" Residue "j ARG 96": "NH1" <-> "NH2" Residue "j ARG 120": "NH1" <-> "NH2" Residue "l ARG 21": "NH1" <-> "NH2" Residue "l ARG 33": "NH1" <-> "NH2" Residue "l ARG 41": "NH1" <-> "NH2" Residue "l ARG 47": "NH1" <-> "NH2" Residue "l ARG 60": "NH1" <-> "NH2" Residue "l ARG 78": "NH1" <-> "NH2" Residue "l ARG 126": "NH1" <-> "NH2" Residue "m ARG 10": "NH1" <-> "NH2" Residue "m ARG 18": "NH1" <-> "NH2" Residue "m ARG 40": "NH1" <-> "NH2" Residue "m ARG 44": "NH1" <-> "NH2" Residue "m ARG 50": "NH1" <-> "NH2" Residue "m ARG 55": "NH1" <-> "NH2" Residue "m ARG 59": "NH1" <-> "NH2" Residue "m ASP 70": "OD1" <-> "OD2" Residue "m GLU 75": "OE1" <-> "OE2" Residue "m ARG 114": "NH1" <-> "NH2" Residue "n ARG 8": "NH1" <-> "NH2" Residue "n ARG 12": "NH1" <-> "NH2" Residue "n ARG 17": "NH1" <-> "NH2" Residue "n ARG 22": "NH1" <-> "NH2" Residue "n ARG 46": "NH1" <-> "NH2" Residue "n ARG 63": "NH1" <-> "NH2" Residue "n ARG 64": "NH1" <-> "NH2" Residue "n ARG 69": "NH1" <-> "NH2" Residue "n ARG 71": "NH1" <-> "NH2" Residue "n ARG 96": "NH1" <-> "NH2" Residue "n ARG 118": "NH1" <-> "NH2" Residue "o ARG 10": "NH1" <-> "NH2" Residue "o ARG 16": "NH1" <-> "NH2" Residue "o ARG 25": "NH1" <-> "NH2" Residue "o GLU 80": "OE1" <-> "OE2" 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 GLU 67": "OE1" <-> "OE2" Residue "p ARG 88": "NH1" <-> "NH2" Residue "p ARG 100": "NH1" <-> "NH2" Residue "p ARG 108": "NH1" <-> "NH2" Residue "q ARG 2": "NH1" <-> "NH2" Residue "q ARG 5": "NH1" <-> "NH2" Residue "q ARG 12": "NH1" <-> "NH2" Residue "q ARG 32": "NH1" <-> "NH2" Residue "q ARG 47": "NH1" <-> "NH2" Residue "q ARG 69": "NH1" <-> "NH2" Residue "q GLU 110": "OE1" <-> "OE2" Residue "r ARG 21": "NH1" <-> "NH2" Residue "r GLU 46": "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 ARG 84": "NH1" <-> "NH2" Residue "s ARG 88": "NH1" <-> "NH2" Residue "s ARG 95": "NH1" <-> "NH2" Residue "s ARG 110": "NH1" <-> "NH2" Residue "t ARG 73": "NH1" <-> "NH2" Residue "u ARG 5": "NH1" <-> "NH2" Residue "u ARG 6": "NH1" <-> "NH2" Residue "u ARG 81": "NH1" <-> "NH2" Residue "u ARG 85": "NH1" <-> "NH2" Residue "u ARG 93": "NH1" <-> "NH2" Residue "w ASP 52": "OD1" <-> "OD2" Residue "x PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x GLU 69": "OE1" <-> "OE2" Residue "y ARG 29": "NH1" <-> "NH2" Residue "y ARG 47": "NH1" <-> "NH2" Residue "y ARG 52": "NH1" <-> "NH2" Residue "z ARG 10": "NH1" <-> "NH2" Residue "z ARG 29": "NH1" <-> "NH2" Residue "z ARG 44": "NH1" <-> "NH2" Residue "A ARG 49": "NH1" <-> "NH2" Residue "A ARG 56": "NH1" <-> "NH2" Residue "B ARG 9": "NH1" <-> "NH2" Residue "B ARG 15": "NH1" <-> "NH2" Residue "B GLU 35": "OE1" <-> "OE2" Residue "B ARG 39": "NH1" <-> "NH2" Residue "B ARG 51": "NH1" <-> "NH2" Residue "C TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 43": "NH1" <-> "NH2" Residue "C TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 3": "NH1" <-> "NH2" Residue "D ARG 12": "NH1" <-> "NH2" Residue "D ARG 14": "NH1" <-> "NH2" Residue "D ARG 19": "NH1" <-> "NH2" Residue "D ARG 21": "NH1" <-> "NH2" Residue "D ARG 33": "NH1" <-> "NH2" Residue "D ARG 41": "NH1" <-> "NH2" Residue "E ARG 12": "NH1" <-> "NH2" Residue "E ARG 29": "NH1" <-> "NH2" Residue "E ARG 39": "NH1" <-> "NH2" Residue "E ARG 41": "NH1" <-> "NH2" Residue "F ARG 12": "NH1" <-> "NH2" Residue "F ARG 24": "NH1" <-> "NH2" Residue "G GLU 43": "OE1" <-> "OE2" Residue "G ARG 107": "NH1" <-> "NH2" Residue "G GLU 139": "OE1" <-> "OE2" Residue "G ASP 187": "OD1" <-> "OD2" Residue "G ASP 193": "OD1" <-> "OD2" Residue "G TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 224": "NH1" <-> "NH2" Residue "H ARG 106": "NH1" <-> "NH2" Residue "H ARG 130": "NH1" <-> "NH2" Residue "H GLU 151": "OE1" <-> "OE2" Residue "H GLU 187": "OE1" <-> "OE2" Residue "I TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 146": "OE1" <-> "OE2" Residue "J ARG 156": "NH1" <-> "NH2" Residue "K TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 138": "OE1" <-> "OE2" Residue "M ASP 4": "OD1" <-> "OD2" Residue "M GLU 42": "OE1" <-> "OE2" Residue "N PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 123": "NH1" <-> "NH2" Residue "O GLU 47": "OE1" <-> "OE2" Residue "O PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 55": "NH1" <-> "NH2" Residue "Q GLU 75": "OE1" <-> "OE2" Residue "Q TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 28": "NH1" <-> "NH2" Residue "U PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 17": "OE1" <-> "OE2" Residue "V GLU 25": "OE1" <-> "OE2" Residue "V PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 11": "NH1" <-> "NH2" Residue "Z ARG 66": "NH1" <-> "NH2" Residue "a ARG 7": "NH1" <-> "NH2" Residue "a ARG 12": "NH1" <-> "NH2" Residue "a ARG 162": "NH1" <-> "NH2" Residue "8 TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 ASP 88": "OD1" <-> "OD2" Residue "8 ASP 107": "OD1" <-> "OD2" Residue "8 ASP 197": "OD1" <-> "OD2" Residue "8 PHE 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 ASP 347": "OD1" <-> "OD2" Residue "8 GLU 502": "OE1" <-> "OE2" Residue "8 GLU 559": "OE1" <-> "OE2" Residue "8 ASP 573": "OD1" <-> "OD2" Residue "8 PHE 605": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 GLU 625": "OE1" <-> "OE2" Residue "8 TYR 680": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 153370 Number of models: 1 Model: "" Number of chains: 62 Chain: "b" Number of atoms: 2083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2083 Classifications: {'peptide': 271} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 253} Chain: "c" Number of atoms: 1565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1565 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 202} Chain: "d" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1552 Classifications: {'peptide': 201} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 195} Chain: "e" Number of atoms: 1411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1411 Classifications: {'peptide': 177} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 170} Chain: "f" Number of atoms: 1323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1323 Classifications: {'peptide': 176} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "g" Number of atoms: 936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 936 Classifications: {'peptide': 125} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain breaks: 1 Chain: "h" Number of atoms: 633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 633 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 2, 'TRANS': 81} Chain: "i" Number of atoms: 551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 551 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 8, 'TRANS': 65} Chain: "j" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1129 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 135} Chain: "k" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 939 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "l" Number of atoms: 1045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1045 Classifications: {'peptide': 143} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 138} Chain: "m" Number of atoms: 1074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1074 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 128} Chain: "n" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 961 Classifications: {'peptide': 120} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "o" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 892 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "p" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 917 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "q" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 947 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'TRANS': 116} Chain: "r" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 816 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 101} Chain: "s" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 857 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 107} Chain: "t" Number of atoms: 739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 739 Classifications: {'peptide': 93} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 91} Chain: "u" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 780 Classifications: {'peptide': 102} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "v" Number of atoms: 753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 753 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "w" Number of atoms: 575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 575 Classifications: {'peptide': 75} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "x" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 625 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "y" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 509 Classifications: {'peptide': 63} Modifications used: {'COO': 1} Link IDs: {'TRANS': 62} Chain: "z" Number of atoms: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 449 Classifications: {'peptide': 58} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "A" Number of atoms: 523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 523 Classifications: {'peptide': 66} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "B" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 444 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 54} Chain: "C" Number of atoms: 410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 410 Classifications: {'peptide': 50} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "D" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 377 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "E" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 504 Classifications: {'peptide': 64} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "F" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 302 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "G" Number of atoms: 1705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1705 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 210} Chain: "H" Number of atoms: 1625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1625 Classifications: {'peptide': 206} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 198} Chain: "I" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1643 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 198} Chain: "J" Number of atoms: 1157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1157 Classifications: {'peptide': 157} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 151} Chain: "K" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 818 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "L" Number of atoms: 1182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1182 Classifications: {'peptide': 151} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain: "M" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 979 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "N" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1022 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "O" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 787 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 92} Chain: "P" Number of atoms: 870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 870 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 108} Chain: "Q" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 955 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 115} Chain: "R" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 884 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 109} Chain: "S" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 805 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "T" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 714 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'TRANS': 87} Chain: "U" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 649 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "V" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 649 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain: "W" Number of atoms: 536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 536 Classifications: {'peptide': 65} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "X" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 638 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 73} Chain: "Y" Number of atoms: 665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 665 Classifications: {'peptide': 85} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 83} Chain: "Z" Number of atoms: 545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 545 Classifications: {'peptide': 65} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "a" Number of atoms: 1027 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1027 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 131} Chain breaks: 1 Chain: "3" Number of atoms: 33012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1539, 33012 Classifications: {'RNA': 1539} Modifications used: {'5*END': 1, 'rna2p_pur': 91, 'rna2p_pyr': 49, 'rna3p_pur': 783, 'rna3p_pyr': 616} Link IDs: {'rna2p': 140, 'rna3p': 1398} 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': 212, 'rna2p_pyr': 96, 'rna3p_pur': 1462, 'rna3p_pyr': 1133} Link IDs: {'rna2p': 308, 'rna3p': 2594} Chain: "2" Number of atoms: 2568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 2568 Classifications: {'RNA': 120} Modifications used: {'5*END': 1, 'rna2p_pur': 4, 'rna2p_pyr': 2, 'rna3p_pur': 61, 'rna3p_pyr': 53} Link IDs: {'rna2p': 6, 'rna3p': 113} Chain: "5" Number of atoms: 1647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1647 Classifications: {'RNA': 77} Modifications used: {'rna2p_pur': 10, 'rna2p_pyr': 5, 'rna3p_pur': 30, 'rna3p_pyr': 32} Link IDs: {'rna2p': 14, 'rna3p': 62} Chain: "6" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1640 Classifications: {'RNA': 77} Modifications used: {'5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 5, 'rna3p_pur': 33, 'rna3p_pyr': 33} Link IDs: {'rna2p': 11, 'rna3p': 65} Chain: "4" Number of atoms: 348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 348 Classifications: {'RNA': 16} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 11, 'rna3p_pyr': 4} Link IDs: {'rna3p': 15} Chain: "8" Number of atoms: 5312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 685, 5312 Classifications: {'peptide': 685} Link IDs: {'PTRANS': 33, 'TRANS': 651} Chain breaks: 1 Chain: "1" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "5" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Classifications: {'peptide': 1} Chain: "8" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GCP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 59.58, per 1000 atoms: 0.39 Number of scatterers: 153370 At special positions: 0 Unit cell: (271.95, 255.15, 246.75, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 180 16.00 P 4731 15.00 Mg 1 11.99 O 42205 8.00 N 28487 7.00 C 77766 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 65.65 Conformation dependent library (CDL) restraints added in 7.8 seconds 13034 Ramachandran restraints generated. 6517 Oldfield, 0 Emsley, 6517 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 12184 Finding SS restraints... Warning!!! ksdssp method is not applicable for structures that cannot fit in PDB format. Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 196 helices and 80 sheets defined 37.4% alpha, 17.6% beta 1450 base pairs and 2323 stacking pairs defined. Time for finding SS restraints: 78.10 Creating SS restraints... Processing helix chain 'b' and resid 9 through 16 removed outlier: 7.461A pdb=" N HIS b 14 " --> pdb=" O PRO b 10 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N VAL b 15 " --> pdb=" O GLY b 11 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N VAL b 16 " --> pdb=" O ARG b 12 " (cutoff:3.500A) Processing helix chain 'b' and resid 29 through 34 removed outlier: 4.634A pdb=" N LEU b 33 " --> pdb=" O PHE b 29 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N GLU b 34 " --> pdb=" O ALA b 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 29 through 34' Processing helix chain 'b' and resid 130 through 135 removed outlier: 4.063A 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: 3.904A pdb=" N ALA b 210 " --> pdb=" O LYS b 206 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG b 213 " --> pdb=" O ALA b 209 " (cutoff:3.500A) Processing helix chain 'b' and resid 220 through 225 removed outlier: 3.884A pdb=" N MET b 224 " --> pdb=" O ARG b 220 " (cutoff:3.500A) removed outlier: 5.285A 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: 5.751A pdb=" N ASP b 263 " --> pdb=" O ASN b 259 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N LYS b 264 " --> pdb=" O LYS b 260 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N PHE b 265 " --> pdb=" O ARG b 261 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE b 266 " --> pdb=" O THR b 262 " (cutoff:3.500A) removed outlier: 5.586A 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: 4.179A pdb=" N MET b 200 " --> pdb=" O ALA b 197 " (cutoff:3.500A) Processing helix chain 'c' and resid 56 through 61 removed outlier: 5.376A pdb=" N THR c 61 " --> pdb=" O ALA c 57 " (cutoff:3.500A) Processing helix chain 'c' and resid 62 through 72 Processing helix chain 'c' and resid 120 through 125 Processing helix chain 'c' and resid 97 through 103 removed outlier: 3.937A pdb=" N ASP c 103 " --> pdb=" O LEU c 100 " (cutoff:3.500A) Processing helix chain 'd' and resid 15 through 20 Processing helix chain 'd' and resid 24 through 41 removed outlier: 3.582A pdb=" N ALA d 39 " --> pdb=" O TYR d 35 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG d 40 " --> pdb=" O ALA d 36 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N GLN d 41 " --> pdb=" O ALA d 37 " (cutoff:3.500A) Processing helix chain 'd' and resid 97 through 116 removed outlier: 3.581A pdb=" N ARG d 114 " --> pdb=" O SER d 110 " (cutoff:3.500A) Processing helix chain 'd' and resid 130 through 142 Processing helix chain 'd' and resid 154 through 162 Processing helix chain 'd' and resid 176 through 183 Processing helix chain 'd' and resid 189 through 201 removed outlier: 3.536A pdb=" N GLU d 198 " --> pdb=" O LYS d 194 " (cutoff:3.500A) Processing helix chain 'e' and resid 1 through 20 removed outlier: 3.906A pdb=" N ASP e 5 " --> pdb=" O ALA e 1 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N VAL e 12 " --> pdb=" O LYS e 8 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LYS e 13 " --> pdb=" O ASP e 9 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ASN e 20 " --> pdb=" O MET e 16 " (cutoff:3.500A) Processing helix chain 'e' and resid 41 through 46 Processing helix chain 'e' and resid 47 through 61 removed outlier: 3.522A pdb=" N ALA e 54 " --> pdb=" O ASP e 50 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASP e 55 " --> pdb=" O ASN e 51 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU e 56 " --> pdb=" O ALA e 52 " (cutoff:3.500A) Processing helix chain 'e' and resid 92 through 110 removed outlier: 3.514A pdb=" N TRP e 96 " --> pdb=" O GLY e 92 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N ILE e 105 " --> pdb=" O ARG e 101 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N VAL e 107 " --> pdb=" O ILE e 103 " (cutoff:3.500A) Proline residue: e 108 - end of helix Processing helix chain 'e' and resid 141 through 146 removed outlier: 6.709A pdb=" N VAL e 145 " --> pdb=" O ASP e 141 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N ASP e 146 " --> pdb=" O TYR e 142 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 141 through 146' Processing helix chain 'e' and resid 161 through 173 removed outlier: 3.813A pdb=" N LEU e 168 " --> pdb=" O GLU e 164 " (cutoff:3.500A) Processing helix chain 'e' and resid 133 through 138 removed outlier: 5.198A pdb=" N ILE e 136 " --> pdb=" O GLU e 133 " (cutoff:3.500A) removed outlier: 3.609A 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 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: 4.348A 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 40 through 50 removed outlier: 5.174A pdb=" N ILE g 44 " --> pdb=" O THR g 40 " (cutoff:3.500A) Processing helix chain 'g' and resid 95 through 107 Processing helix chain 'h' and resid 3 through 22 removed outlier: 3.604A pdb=" N GLU h 14 " --> pdb=" O ALA h 10 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N LYS h 20 " --> pdb=" O SER h 16 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N ALA h 22 " --> pdb=" O VAL h 18 " (cutoff:3.500A) Processing helix chain 'h' and resid 33 through 48 removed outlier: 3.942A pdb=" N THR h 39 " --> pdb=" O VAL h 35 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N ARG h 42 " --> pdb=" O MET h 38 " (cutoff:3.500A) Processing helix chain 'h' and resid 60 through 68 removed outlier: 4.123A pdb=" N VAL h 64 " --> pdb=" O LEU h 60 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLU h 65 " --> pdb=" O ARG h 61 " (cutoff:3.500A) Proline residue: h 68 - end of helix Processing helix chain 'h' and resid 71 through 76 removed outlier: 4.375A pdb=" N ALA h 75 " --> pdb=" O CYS h 71 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N PHE h 76 " --> pdb=" O LEU h 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 71 through 76' Processing helix chain 'i' and resid 23 through 29 removed outlier: 5.118A pdb=" N LEU i 27 " --> pdb=" O VAL i 23 " (cutoff:3.500A) Processing helix chain 'i' and resid 33 through 49 removed outlier: 3.533A pdb=" N ALA i 40 " --> pdb=" O GLU i 36 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N SER i 47 " --> pdb=" O ALA i 43 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N GLU i 49 " --> pdb=" O THR i 45 " (cutoff:3.500A) Processing helix chain 'j' and resid 24 through 38 Processing helix chain 'j' and resid 88 through 96 Processing helix chain 'j' and resid 97 through 110 removed outlier: 4.685A pdb=" N ILE j 101 " --> pdb=" O PRO j 97 " (cutoff:3.500A) removed outlier: 3.590A 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: 5.351A pdb=" N LEU j 122 " --> pdb=" O MET j 118 " (cutoff:3.500A) Processing helix chain 'j' and resid 67 through 72 removed outlier: 4.564A pdb=" N LYS j 72 " --> pdb=" O ASN j 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'j' and resid 67 through 72' Processing helix chain 'k' and resid 112 through 120 Proline residue: k 120 - end of helix Processing helix chain 'l' and resid 56 through 62 removed outlier: 3.647A pdb=" N LEU l 61 " --> pdb=" O LEU l 57 " (cutoff:3.500A) Proline residue: l 62 - end of helix Processing helix chain 'l' and resid 68 through 75 removed outlier: 3.814A pdb=" N ILE l 73 " --> pdb=" O ARG l 69 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ALA l 75 " --> pdb=" O ALA l 71 " (cutoff:3.500A) Processing helix chain 'l' and resid 78 through 83 removed outlier: 3.656A pdb=" N LEU l 82 " --> pdb=" O ARG l 78 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ALA l 83 " --> pdb=" O LEU l 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 78 through 83' Processing helix chain 'l' and resid 91 through 99 removed outlier: 3.908A pdb=" N LEU l 95 " --> pdb=" O ASP l 91 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LYS l 96 " --> pdb=" O LEU l 92 " (cutoff:3.500A) removed outlier: 6.071A 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 Processing helix chain 'm' and resid 109 through 125 removed outlier: 3.587A pdb=" N LEU m 119 " --> pdb=" O GLU m 115 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA m 122 " --> pdb=" O LYS m 118 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS m 123 " --> pdb=" O LEU m 119 " (cutoff:3.500A) Proline residue: m 125 - end of helix Processing helix chain 'n' and resid 13 through 32 Processing helix chain 'n' and resid 38 through 58 removed outlier: 4.538A pdb=" N ARG n 46 " --> pdb=" O LYS n 42 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL n 47 " --> pdb=" O GLU n 43 " (cutoff:3.500A) Proline residue: n 50 - end of helix removed outlier: 4.352A pdb=" N THR n 57 " --> pdb=" O THR n 53 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N ASP n 58 " --> pdb=" O LEU n 54 " (cutoff:3.500A) Processing helix chain 'n' and resid 59 through 71 removed outlier: 4.579A pdb=" N ARG n 63 " --> pdb=" O SER n 59 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N THR n 70 " --> pdb=" O ALA n 66 " (cutoff:3.500A) Processing helix chain 'n' and resid 72 through 82 removed outlier: 4.467A pdb=" N PHE n 80 " --> pdb=" O VAL n 76 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ASN n 81 " --> pdb=" O ALA n 77 " (cutoff:3.500A) Processing helix chain 'n' and resid 83 through 88 Processing helix chain 'o' and resid 3 through 22 removed outlier: 4.516A pdb=" N ARG o 13 " --> pdb=" O ARG o 9 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N ALA o 14 " --> pdb=" O ARG o 10 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY o 22 " --> pdb=" O LEU o 18 " (cutoff:3.500A) Processing helix chain 'o' and resid 55 through 63 removed outlier: 6.001A pdb=" N GLN o 61 " --> pdb=" O ALA o 57 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N LYS o 63 " --> pdb=" O ALA o 59 " (cutoff:3.500A) Processing helix chain 'o' and resid 67 through 86 Processing helix chain 'o' and resid 101 through 114 Processing helix chain 'p' and resid 1 through 12 removed outlier: 3.709A pdb=" N GLN p 11 " --> pdb=" O LEU p 7 " (cutoff:3.500A) Processing helix chain 'p' and resid 96 through 103 removed outlier: 4.533A pdb=" N ARG p 100 " --> pdb=" O LEU p 96 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N GLU p 101 " --> pdb=" O TYR p 97 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ARG p 102 " --> pdb=" O TYR p 98 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N THR p 103 " --> pdb=" O LEU p 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'p' and resid 96 through 103' Processing helix chain 'q' and resid 6 through 21 removed outlier: 3.880A pdb=" N GLN q 19 " --> pdb=" O LYS q 15 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS q 21 " --> pdb=" O LEU q 17 " (cutoff:3.500A) Processing helix chain 'q' and resid 25 through 30 removed outlier: 4.232A pdb=" N ARG q 29 " --> pdb=" O GLY q 25 " (cutoff:3.500A) Processing helix chain 'q' and resid 35 through 40 Processing helix chain 'q' and resid 42 through 60 removed outlier: 3.769A pdb=" N ARG q 50 " --> pdb=" O TYR q 46 " (cutoff:3.500A) removed outlier: 4.739A 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 Processing helix chain 's' and resid 13 through 25 removed outlier: 4.468A pdb=" N LEU s 23 " --> pdb=" O LEU s 19 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ILE s 24 " --> pdb=" O VAL s 20 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG s 25 " --> pdb=" O ALA s 21 " (cutoff:3.500A) Processing helix chain 's' and resid 28 through 39 removed outlier: 4.879A pdb=" N TYR s 38 " --> pdb=" O ASP s 34 " (cutoff:3.500A) Processing helix chain 's' and resid 41 through 61 removed outlier: 3.513A pdb=" N VAL s 45 " --> pdb=" O LYS s 41 " (cutoff:3.500A) Processing helix chain 't' and resid 2 through 11 removed outlier: 3.921A 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: 4.097A pdb=" N VAL u 69 " --> pdb=" O GLN u 65 " (cutoff:3.500A) removed outlier: 5.096A 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: 4.361A pdb=" N ALA v 23 " --> pdb=" O ARG v 19 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ASN v 24 " --> pdb=" O LEU v 20 " (cutoff:3.500A) Processing helix chain 'v' and resid 43 through 54 removed outlier: 4.556A pdb=" N VAL v 47 " --> pdb=" O ASP v 43 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA v 52 " --> pdb=" O MET v 48 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N LYS v 53 " --> pdb=" O ASN v 49 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N ALA v 54 " --> pdb=" O MET v 50 " (cutoff:3.500A) Processing helix chain 'v' and resid 55 through 60 removed outlier: 5.998A pdb=" N VAL v 60 " --> pdb=" O PHE v 56 " (cutoff:3.500A) Processing helix chain 'x' and resid 51 through 62 removed outlier: 4.706A pdb=" N GLY x 62 " --> pdb=" O ILE x 58 " (cutoff:3.500A) Processing helix chain 'x' and resid 63 through 74 removed outlier: 3.604A pdb=" N GLU x 69 " --> pdb=" O THR x 65 " (cutoff:3.500A) Processing helix chain 'y' and resid 2 through 7 removed outlier: 3.973A pdb=" N LEU y 6 " --> pdb=" O LYS y 2 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ARG y 7 " --> pdb=" O ALA y 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'y' and resid 2 through 7' Processing helix chain 'y' and resid 9 through 23 Processing helix chain 'y' and resid 25 through 35 removed outlier: 3.548A pdb=" N ARG y 29 " --> pdb=" O GLN y 25 " (cutoff:3.500A) Processing helix chain 'y' and resid 40 through 62 removed outlier: 5.226A 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 removed outlier: 3.515A pdb=" N MET z 46 " --> pdb=" O ALA z 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 53 removed outlier: 4.408A pdb=" N GLN A 48 " --> pdb=" O PHE A 44 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N THR A 53 " --> pdb=" O ARG A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 65 removed outlier: 3.664A pdb=" N LYS A 62 " --> pdb=" O ASP A 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 20 removed outlier: 4.641A pdb=" N HIS B 18 " --> pdb=" O MET B 14 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N ASP B 19 " --> pdb=" O ARG B 15 " (cutoff:3.500A) removed outlier: 3.898A 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: 4.410A 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: 3.674A pdb=" N ARG E 12 " --> pdb=" O GLY E 8 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 45 Proline residue: E 45 - end of helix Processing helix chain 'E' and resid 50 through 62 removed outlier: 4.093A pdb=" N GLY E 55 " --> pdb=" O LYS E 51 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N LEU E 56 " --> pdb=" O GLY E 52 " (cutoff:3.500A) Proline residue: E 62 - end of helix Processing helix chain 'G' and resid 43 through 63 Proline residue: G 47 - end of helix removed outlier: 3.583A pdb=" N GLU G 55 " --> pdb=" O GLU G 51 " (cutoff:3.500A) Processing helix chain 'G' and resid 72 through 87 removed outlier: 5.849A pdb=" N SER G 76 " --> pdb=" O LYS G 72 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N GLU G 77 " --> pdb=" O ARG G 73 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N ALA G 78 " --> pdb=" O ALA G 74 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N CYS G 86 " --> pdb=" O ALA G 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 102 through 123 removed outlier: 4.443A pdb=" N GLN G 108 " --> pdb=" O LYS G 104 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLN G 121 " --> pdb=" O GLU G 117 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASP G 122 " --> pdb=" O THR G 118 " (cutoff:3.500A) Processing helix chain 'G' and resid 129 through 148 removed outlier: 3.620A pdb=" N LEU G 147 " --> pdb=" O LEU G 143 " (cutoff:3.500A) Processing helix chain 'G' and resid 168 through 179 removed outlier: 3.533A pdb=" N ILE G 172 " --> pdb=" O GLU G 168 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASN G 177 " --> pdb=" O LYS G 173 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU G 178 " --> pdb=" O GLU G 174 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N GLY G 179 " --> pdb=" O ALA G 175 " (cutoff:3.500A) Processing helix chain 'G' and resid 191 through 196 removed outlier: 4.195A pdb=" N VAL G 195 " --> pdb=" O ASP G 191 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N ASP G 196 " --> pdb=" O PRO G 192 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 191 through 196' Processing helix chain 'G' and resid 205 through 225 removed outlier: 3.669A pdb=" N GLY G 223 " --> pdb=" O THR G 219 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ARG G 224 " --> pdb=" O VAL G 220 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N SER G 225 " --> pdb=" O ARG G 221 " (cutoff:3.500A) Processing helix chain 'H' and resid 5 through 11 Processing helix chain 'H' and resid 27 through 47 Processing helix chain 'H' and resid 71 through 77 Processing helix chain 'H' and resid 80 through 95 removed outlier: 3.537A pdb=" N LYS H 88 " --> pdb=" O GLU H 84 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 126 removed outlier: 3.982A pdb=" N ARG H 125 " --> pdb=" O SER H 121 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ARG H 126 " --> pdb=" O GLN H 122 " (cutoff:3.500A) Processing helix chain 'H' and resid 128 through 144 Processing helix chain 'I' and resid 7 through 15 removed outlier: 4.757A pdb=" N SER I 11 " --> pdb=" O LYS I 7 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLY I 15 " --> pdb=" O SER I 11 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 65 removed outlier: 3.660A pdb=" N ILE I 63 " --> pdb=" O LYS I 59 " (cutoff:3.500A) Processing helix chain 'I' and resid 67 through 81 removed outlier: 4.290A pdb=" N LEU I 81 " --> pdb=" O GLU I 77 " (cutoff:3.500A) Processing helix chain 'I' and resid 85 through 95 removed outlier: 4.650A pdb=" N LEU I 90 " --> pdb=" O GLY I 86 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU I 92 " --> pdb=" O ASN I 88 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU I 93 " --> pdb=" O LEU I 89 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N GLU I 94 " --> pdb=" O LEU I 90 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLY I 95 " --> pdb=" O ALA I 91 " (cutoff:3.500A) Processing helix chain 'I' and resid 96 through 105 Processing helix chain 'I' and resid 109 through 120 removed outlier: 4.509A pdb=" N HIS I 119 " --> pdb=" O GLN I 115 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N LYS I 120 " --> pdb=" O LEU I 116 " (cutoff:3.500A) Processing helix chain 'I' and resid 151 through 162 removed outlier: 6.930A pdb=" N LYS I 155 " --> pdb=" O GLN I 151 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N ALA I 156 " --> pdb=" O SER I 152 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALA I 157 " --> pdb=" O ARG I 153 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU I 159 " --> pdb=" O LYS I 155 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU I 160 " --> pdb=" O ALA I 156 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLU I 162 " --> pdb=" O LEU I 158 " (cutoff:3.500A) Processing helix chain 'I' and resid 186 through 191 removed outlier: 5.310A pdb=" N SER I 191 " --> pdb=" O ARG I 187 " (cutoff:3.500A) Processing helix chain 'I' and resid 195 through 205 removed outlier: 4.214A pdb=" N ILE I 199 " --> pdb=" O ASN I 195 " (cutoff:3.500A) Processing helix chain 'J' and resid 54 through 70 removed outlier: 4.003A pdb=" N GLU J 64 " --> pdb=" O GLN J 60 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LYS J 65 " --> pdb=" O LYS J 61 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N MET J 70 " --> pdb=" O ALA J 66 " (cutoff:3.500A) Processing helix chain 'J' and resid 108 through 118 removed outlier: 5.954A pdb=" N ALA J 112 " --> pdb=" O GLY J 108 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL J 116 " --> pdb=" O ALA J 112 " (cutoff:3.500A) Processing helix chain 'J' and resid 131 through 147 removed outlier: 4.928A pdb=" N ASN J 147 " --> pdb=" O LEU J 143 " (cutoff:3.500A) Processing helix chain 'J' and resid 148 through 156 removed outlier: 4.308A pdb=" N LYS J 155 " --> pdb=" O MET J 151 " (cutoff:3.500A) Processing helix chain 'J' and resid 159 through 165 Processing helix chain 'K' and resid 12 through 33 removed outlier: 3.651A pdb=" N GLU K 16 " --> pdb=" O PRO K 12 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLN K 17 " --> pdb=" O ASP K 13 " (cutoff:3.500A) Proline residue: K 19 - end of helix removed outlier: 3.607A pdb=" N ARG K 24 " --> pdb=" O GLY K 20 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TYR K 25 " --> pdb=" O MET K 21 " (cutoff:3.500A) Processing helix chain 'K' and resid 67 through 82 removed outlier: 3.558A pdb=" N ILE K 71 " --> pdb=" O PRO K 67 " (cutoff:3.500A) removed outlier: 5.043A 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 removed outlier: 3.520A pdb=" N ILE L 41 " --> pdb=" O THR L 37 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL L 42 " --> pdb=" O ALA L 38 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TYR L 43 " --> pdb=" O GLU L 39 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ARG L 52 " --> pdb=" O THR L 48 " (cutoff:3.500A) Processing helix chain 'L' and resid 59 through 69 removed outlier: 3.501A pdb=" N VAL L 63 " --> pdb=" O GLU L 59 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ALA L 64 " --> pdb=" O ALA L 60 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N ASN L 67 " --> pdb=" O VAL L 63 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL L 68 " --> pdb=" O ALA L 64 " (cutoff:3.500A) Processing helix chain 'L' and resid 91 through 110 removed outlier: 4.340A pdb=" N ALA L 97 " --> pdb=" O VAL L 93 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TRP L 102 " --> pdb=" O LEU L 98 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ILE L 103 " --> pdb=" O ALA L 99 " (cutoff:3.500A) Processing helix chain 'L' and resid 114 through 129 removed outlier: 3.599A pdb=" N ASN L 121 " --> pdb=" O LEU L 117 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLU L 128 " --> pdb=" O SER L 124 " (cutoff:3.500A) Processing helix chain 'L' and resid 131 through 148 Processing helix chain 'M' and resid 4 through 20 removed outlier: 3.549A pdb=" N ASP M 8 " --> pdb=" O ASP M 4 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA M 19 " --> pdb=" O ASN M 15 " (cutoff:3.500A) Processing helix chain 'M' and resid 29 through 43 Processing helix chain 'M' and resid 111 through 119 Processing helix chain 'N' and resid 33 through 38 Processing helix chain 'N' and resid 45 through 53 Proline residue: N 50 - end of helix removed outlier: 4.855A pdb=" N LEU N 53 " --> pdb=" O GLN N 49 " (cutoff:3.500A) Processing helix chain 'N' and resid 70 through 86 removed outlier: 3.553A pdb=" N ALA N 85 " --> pdb=" O GLY N 81 " (cutoff:3.500A) Processing helix chain 'N' and resid 90 through 101 removed outlier: 4.933A pdb=" N GLU N 96 " --> pdb=" O SER N 92 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG N 98 " --> pdb=" O ARG N 94 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA N 100 " --> pdb=" O GLU N 96 " (cutoff:3.500A) Processing helix chain 'O' and resid 14 through 33 removed outlier: 3.501A pdb=" N GLN O 20 " --> pdb=" O ARG O 16 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA O 29 " --> pdb=" O ILE O 25 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N THR O 32 " --> pdb=" O THR O 28 " (cutoff:3.500A) Processing helix chain 'O' and resid 80 through 90 removed outlier: 3.709A pdb=" N VAL O 84 " --> pdb=" O THR O 80 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N ASP O 85 " --> pdb=" O GLU O 81 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N ALA O 86 " --> pdb=" O LYS O 82 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N MET O 88 " --> pdb=" O VAL O 84 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N ARG O 89 " --> pdb=" O ASP O 85 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N LEU O 90 " --> pdb=" O ALA O 86 " (cutoff:3.500A) Processing helix chain 'P' and resid 45 through 50 removed outlier: 4.107A pdb=" N GLY P 50 " --> pdb=" O ALA P 46 " (cutoff:3.500A) Processing helix chain 'P' and resid 53 through 58 removed outlier: 4.541A pdb=" N SER P 57 " --> pdb=" O GLY P 53 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N THR P 58 " --> pdb=" O SER P 54 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 53 through 58' Processing helix chain 'P' and resid 59 through 74 removed outlier: 4.029A pdb=" N ALA P 72 " --> pdb=" O ARG P 68 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N VAL P 73 " --> pdb=" O CYS P 69 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N LYS P 74 " --> pdb=" O ALA P 70 " (cutoff:3.500A) Processing helix chain 'P' and resid 92 through 103 removed outlier: 5.169A pdb=" N ILE P 96 " --> pdb=" O ARG P 92 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLY P 103 " --> pdb=" O LEU P 99 " (cutoff:3.500A) Processing helix chain 'Q' and resid 2 through 10 removed outlier: 3.649A 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: 5.160A pdb=" N TYR Q 116 " --> pdb=" O ALA Q 112 " (cutoff:3.500A) Processing helix chain 'R' and resid 13 through 21 removed outlier: 3.661A pdb=" N SER R 20 " --> pdb=" O ILE R 16 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N ILE R 21 " --> pdb=" O ALA R 17 " (cutoff:3.500A) Processing helix chain 'R' and resid 25 through 37 Processing helix chain 'R' and resid 43 through 48 removed outlier: 5.477A pdb=" N SER R 48 " --> pdb=" O ILE R 44 " (cutoff:3.500A) Processing helix chain 'R' and resid 49 through 63 removed outlier: 5.406A pdb=" N THR R 54 " --> pdb=" O GLY R 50 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS R 61 " --> pdb=" O ASP R 57 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N PHE R 62 " --> pdb=" O GLU R 58 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N VAL R 63 " --> pdb=" O VAL R 59 " (cutoff:3.500A) Processing helix chain 'R' and resid 65 through 82 removed outlier: 3.669A pdb=" N ARG R 70 " --> pdb=" O GLY R 66 " (cutoff:3.500A) Processing helix chain 'R' and resid 84 through 93 Processing helix chain 'R' and resid 105 through 110 Processing helix chain 'S' and resid 2 through 23 removed outlier: 3.514A pdb=" N LYS S 18 " --> pdb=" O ALA S 14 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N TYR S 19 " --> pdb=" O LEU S 15 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE S 20 " --> pdb=" O ALA S 16 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ALA S 21 " --> pdb=" O ASP S 17 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N LYS S 22 " --> pdb=" O LYS S 18 " (cutoff:3.500A) Processing helix chain 'S' and resid 24 through 29 Processing helix chain 'S' and resid 37 through 50 removed outlier: 4.979A pdb=" N GLN S 48 " --> pdb=" O VAL S 44 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N THR S 49 " --> pdb=" O LEU S 45 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N LEU S 50 " --> pdb=" O LYS S 46 " (cutoff:3.500A) Processing helix chain 'S' and resid 55 through 60 removed outlier: 4.605A pdb=" N GLN S 59 " --> pdb=" O SER S 55 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N ARG S 60 " --> pdb=" O PRO S 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 55 through 60' Processing helix chain 'S' and resid 79 through 90 Processing helix chain 'T' and resid 3 through 15 Processing helix chain 'T' and resid 23 through 46 removed outlier: 4.414A pdb=" N GLY T 40 " --> pdb=" O ASN T 36 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N HIS T 41 " --> pdb=" O HIS T 37 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N HIS T 45 " --> pdb=" O HIS T 41 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N LYS T 46 " --> pdb=" O PHE T 42 " (cutoff:3.500A) Processing helix chain 'T' and resid 48 through 73 Processing helix chain 'T' and resid 74 through 85 Processing helix chain 'U' and resid 53 through 64 removed outlier: 4.199A pdb=" N GLN U 63 " --> pdb=" O HIS U 59 " (cutoff:3.500A) Processing helix chain 'U' and resid 68 through 79 removed outlier: 3.572A pdb=" N GLU U 77 " --> pdb=" O ALA U 73 " (cutoff:3.500A) Processing helix chain 'W' and resid 12 through 17 removed outlier: 3.536A pdb=" N GLY W 16 " --> pdb=" O PHE W 12 " (cutoff:3.500A) Processing helix chain 'W' and resid 24 through 33 removed outlier: 3.805A pdb=" N TYR W 31 " --> pdb=" O THR W 27 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ILE W 32 " --> pdb=" O LEU W 28 " (cutoff:3.500A) removed outlier: 5.839A 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: 3.687A pdb=" N ALA X 21 " --> pdb=" O LYS X 17 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER X 24 " --> pdb=" O LYS X 20 " (cutoff:3.500A) Processing helix chain 'X' and resid 69 through 74 removed outlier: 3.730A pdb=" N PHE X 73 " --> pdb=" O LYS X 69 " (cutoff:3.500A) Processing helix chain 'Y' and resid 6 through 41 removed outlier: 4.494A pdb=" N ALA Y 10 " --> pdb=" O ALA Y 6 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE Y 11 " --> pdb=" O LYS Y 7 " (cutoff:3.500A) Processing helix chain 'Y' and resid 42 through 64 Proline residue: Y 55 - end of helix removed outlier: 3.649A pdb=" N ALA Y 61 " --> pdb=" O VAL Y 57 " (cutoff:3.500A) Processing helix chain 'Y' and resid 67 through 86 removed outlier: 6.369A pdb=" N ALA Y 71 " --> pdb=" O HIS Y 67 " (cutoff:3.500A) Processing helix chain 'Z' and resid 16 through 23 removed outlier: 4.072A pdb=" N ARG Z 20 " --> pdb=" O ARG Z 16 " (cutoff:3.500A) Processing helix chain 'Z' and resid 24 through 32 removed outlier: 5.939A pdb=" N LEU Z 28 " --> pdb=" O LYS Z 24 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLU Z 30 " --> pdb=" O GLY Z 26 " (cutoff:3.500A) Processing helix chain 'Z' and resid 38 through 61 removed outlier: 3.501A pdb=" N ALA Z 60 " --> pdb=" O ALA Z 56 " (cutoff:3.500A) Processing helix chain 'a' and resid 6 through 16 removed outlier: 4.724A pdb=" N ASP a 16 " --> pdb=" O ARG a 12 " (cutoff:3.500A) Processing helix chain 'a' and resid 24 through 35 removed outlier: 4.774A pdb=" N ALA a 28 " --> pdb=" O ASN a 24 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU a 30 " --> pdb=" O ALA a 26 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N LYS a 31 " --> pdb=" O ILE a 27 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N GLU a 32 " --> pdb=" O ALA a 28 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N LEU a 33 " --> pdb=" O LEU a 29 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N THR a 35 " --> pdb=" O LYS a 31 " (cutoff:3.500A) Processing helix chain 'a' and resid 181 through 200 removed outlier: 3.738A pdb=" N GLU a 190 " --> pdb=" O LYS a 186 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA a 191 " --> pdb=" O GLU a 187 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA a 199 " --> pdb=" O ALA a 195 " (cutoff:3.500A) Processing helix chain '8' and resid 22 through 35 Processing helix chain '8' and resid 53 through 60 removed outlier: 4.069A pdb=" N GLN 8 57 " --> pdb=" O MET 8 53 " (cutoff:3.500A) Processing helix chain '8' and resid 95 through 107 removed outlier: 3.794A pdb=" N ARG 8 104 " --> pdb=" O GLU 8 100 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL 8 105 " --> pdb=" O ARG 8 101 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N ASP 8 107 " --> pdb=" O MET 8 103 " (cutoff:3.500A) Processing helix chain '8' and resid 120 through 134 removed outlier: 3.804A pdb=" N GLU 8 124 " --> pdb=" O GLN 8 120 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N THR 8 125 " --> pdb=" O PRO 8 121 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TRP 8 127 " --> pdb=" O SER 8 123 " (cutoff:3.500A) Processing helix chain '8' and resid 150 through 161 removed outlier: 3.558A pdb=" N ASN 8 156 " --> pdb=" O LEU 8 152 " (cutoff:3.500A) Processing helix chain '8' and resid 211 through 228 removed outlier: 5.161A pdb=" N GLU 8 228 " --> pdb=" O GLU 8 224 " (cutoff:3.500A) Processing helix chain '8' and resid 230 through 240 Processing helix chain '8' and resid 244 through 259 Processing helix chain '8' and resid 274 through 285 Processing helix chain '8' and resid 424 through 443 removed outlier: 5.169A pdb=" N LYS 8 430 " --> pdb=" O ALA 8 426 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N LYS 8 440 " --> pdb=" O GLY 8 436 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N GLU 8 441 " --> pdb=" O ARG 8 437 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASP 8 442 " --> pdb=" O LEU 8 438 " (cutoff:3.500A) Proline residue: 8 443 - end of helix Processing helix chain '8' and resid 462 through 476 removed outlier: 3.537A pdb=" N ILE 8 468 " --> pdb=" O LEU 8 464 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE 8 469 " --> pdb=" O HIS 8 465 " (cutoff:3.500A) Processing helix chain '8' and resid 546 through 564 removed outlier: 3.902A pdb=" N ILE 8 550 " --> pdb=" O PRO 8 546 " (cutoff:3.500A) Proline residue: 8 551 - end of helix removed outlier: 4.248A pdb=" N LYS 8 562 " --> pdb=" O GLN 8 558 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ALA 8 563 " --> pdb=" O GLU 8 559 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N GLY 8 564 " --> pdb=" O GLN 8 560 " (cutoff:3.500A) Processing helix chain '8' and resid 589 through 608 removed outlier: 3.510A pdb=" N SER 8 598 " --> pdb=" O LYS 8 594 " (cutoff:3.500A) Processing helix chain '8' and resid 627 through 639 removed outlier: 3.790A pdb=" N ARG 8 639 " --> pdb=" O LEU 8 635 " (cutoff:3.500A) Processing helix chain '8' and resid 659 through 664 removed outlier: 4.312A pdb=" N PHE 8 664 " --> pdb=" O LEU 8 660 " (cutoff:3.500A) Processing helix chain '8' and resid 665 through 675 removed outlier: 4.294A pdb=" N LEU 8 673 " --> pdb=" O GLN 8 669 " (cutoff:3.500A) Processing helix chain '8' and resid 692 through 699 removed outlier: 4.784A pdb=" N ALA 8 697 " --> pdb=" O ASN 8 693 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N VAL 8 698 " --> pdb=" O VAL 8 694 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N ILE 8 699 " --> pdb=" O ALA 8 695 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'b' and resid 79 through 82 removed outlier: 6.439A pdb=" N LEU b 92 " --> pdb=" O GLU b 78 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N ILE b 73 " --> pdb=" O SER b 117 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N SER b 117 " --> pdb=" O ILE b 73 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'b' and resid 137 through 141 removed outlier: 4.579A pdb=" N SER b 138 " --> pdb=" O ILE b 163 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N THR b 172 " --> pdb=" O VAL b 164 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'b' and resid 90 through 95 removed outlier: 4.778A pdb=" N GLU b 99 " --> pdb=" O TYR b 95 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'c' and resid 3 through 9 removed outlier: 3.637A pdb=" N SER c 199 " --> pdb=" O LYS c 8 " (cutoff:3.500A) removed outlier: 13.068A pdb=" N GLY c 198 " --> pdb=" O LYS c 114 " (cutoff:3.500A) removed outlier: 11.438A pdb=" N LYS c 114 " --> pdb=" O GLY c 198 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N ASP c 200 " --> pdb=" O THR c 112 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N THR c 112 " --> pdb=" O ASP c 200 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N GLU c 168 " --> pdb=" O SER c 113 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'c' and resid 11 through 16 removed outlier: 4.316A pdb=" N VAL c 20 " --> pdb=" O THR c 16 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ARG c 179 " --> pdb=" O LEU c 188 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'c' and resid 36 through 40 removed outlier: 4.231A pdb=" N LEU c 40 " --> pdb=" O TYR c 45 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N TYR c 45 " --> pdb=" O LEU c 40 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N GLN c 49 " --> pdb=" O THR c 35 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N GLN c 94 " --> pdb=" O VAL c 34 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'c' and resid 46 through 51 removed outlier: 7.108A pdb=" N ARG c 46 " --> pdb=" O LEU c 84 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'd' and resid 1 through 4 Processing sheet with id= 9, first strand: chain 'd' and resid 117 through 120 removed outlier: 6.165A pdb=" N ARG d 117 " --> pdb=" O ASP d 184 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL d 187 " --> pdb=" O LEU d 147 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASP d 168 " --> pdb=" O VAL d 146 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'e' and resid 32 through 38 removed outlier: 3.919A pdb=" N TYR e 82 " --> pdb=" O ALA e 69 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N THR e 67 " --> pdb=" O ILE e 84 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N CYS e 86 " --> pdb=" O LEU e 65 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LEU e 65 " --> pdb=" O CYS e 86 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'e' and resid 71 through 74 removed outlier: 4.220A pdb=" N SER e 72 " --> pdb=" O ARG e 79 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N ARG e 79 " --> pdb=" O SER e 72 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ALA e 74 " --> pdb=" O LYS e 77 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'e' and resid 125 through 130 removed outlier: 5.434A pdb=" N GLY e 125 " --> pdb=" O THR e 157 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N THR e 157 " --> pdb=" O GLY e 125 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'f' and resid 15 through 18 Processing sheet with id= 14, first strand: chain 'f' and resid 40 through 44 Processing sheet with id= 15, first strand: chain 'f' and resid 81 through 88 removed outlier: 6.258A pdb=" N THR f 128 " --> pdb=" O LEU f 88 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'f' and resid 93 through 97 Processing sheet with id= 17, first strand: chain 'g' and resid 1 through 5 removed outlier: 6.279A pdb=" N MET g 1 " --> pdb=" O ASN g 20 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ASN g 20 " --> pdb=" O MET g 1 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N VAL g 3 " --> pdb=" O GLN g 18 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N GLN g 18 " --> pdb=" O VAL g 3 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N LEU g 5 " --> pdb=" O GLY g 16 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'g' and resid 78 through 83 Processing sheet with id= 19, first strand: chain 'i' and resid 53 through 60 Processing sheet with id= 20, first strand: chain 'j' and resid 74 through 78 removed outlier: 6.654A pdb=" N GLY j 83 " --> pdb=" O THR j 78 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'k' and resid 17 through 21 removed outlier: 6.867A pdb=" N ARG k 17 " --> pdb=" O VAL k 10 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N THR k 6 " --> pdb=" O CYS k 21 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N ASN k 82 " --> pdb=" O MET k 7 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'm' and resid 62 through 66 removed outlier: 7.557A pdb=" N LEU m 102 " --> pdb=" O ARG m 66 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N TYR m 103 " --> pdb=" O LEU m 33 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N SER m 30 " --> pdb=" O LYS m 133 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N LYS m 127 " --> pdb=" O VAL m 36 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'm' and resid 73 through 76 removed outlier: 6.777A pdb=" N ILE m 73 " --> pdb=" O GLU m 90 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'n' and resid 33 through 37 removed outlier: 6.058A pdb=" N ALA n 108 " --> pdb=" O PHE n 102 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N PHE n 102 " --> pdb=" O ALA n 108 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N MET n 110 " --> pdb=" O CYS n 100 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TYR n 112 " --> pdb=" O LEU n 98 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'o' and resid 49 through 52 removed outlier: 3.786A pdb=" N VAL o 49 " --> pdb=" O VAL o 39 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ARG o 25 " --> pdb=" O ILE o 40 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL o 28 " --> pdb=" O ASP o 93 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'p' and resid 48 through 52 removed outlier: 3.603A pdb=" N ALA p 48 " --> pdb=" O THR p 59 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N ARG p 52 " --> pdb=" O HIS p 55 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N THR p 59 " --> pdb=" O ILE p 47 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'p' and resid 57 through 64 removed outlier: 3.759A pdb=" N GLU p 67 " --> pdb=" O SER p 64 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'r' and resid 2 through 5 Processing sheet with id= 29, first strand: chain 'r' and resid 17 through 21 removed outlier: 4.180A pdb=" N GLN r 18 " --> pdb=" O ILE r 98 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ASP r 95 " --> pdb=" O VAL r 64 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N LYS r 60 " --> pdb=" O THR r 99 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'r' and resid 65 through 73 removed outlier: 4.027A pdb=" N GLY r 67 " --> pdb=" O PHE r 93 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N GLN r 91 " --> pdb=" O GLY r 69 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N LYS r 71 " --> pdb=" O HIS r 89 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N HIS r 89 " --> pdb=" O LYS r 71 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N LYS r 73 " --> pdb=" O GLN r 87 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N GLN r 87 " --> pdb=" O LYS r 73 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 's' and resid 2 through 8 removed outlier: 4.931A pdb=" N THR s 3 " --> pdb=" O VAL s 107 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL s 107 " --> pdb=" O THR s 3 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ARG s 99 " --> pdb=" O SER s 12 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N SER s 12 " --> pdb=" O ARG s 99 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 's' and resid 69 through 72 removed outlier: 6.660A pdb=" N VAL s 106 " --> pdb=" O THR s 72 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 's' and resid 73 through 79 removed outlier: 4.811A pdb=" N THR s 100 " --> pdb=" O GLY s 79 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 's' and resid 80 through 88 removed outlier: 3.519A pdb=" N ARG s 92 " --> pdb=" O ARG s 88 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 't' and resid 12 through 15 removed outlier: 4.078A pdb=" N ALA t 13 " --> pdb=" O LYS t 33 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N VAL t 31 " --> pdb=" O HIS t 15 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LYS t 81 " --> pdb=" O VAL t 34 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N LYS t 66 " --> pdb=" O ARG t 77 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N ASP t 79 " --> pdb=" O LYS t 64 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N LYS t 64 " --> pdb=" O ASP t 79 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N LYS t 81 " --> pdb=" O VAL t 62 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N VAL t 62 " --> pdb=" O LYS t 81 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ALA t 83 " --> pdb=" O THR t 60 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N THR t 60 " --> pdb=" O ALA t 83 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N VAL t 85 " --> pdb=" O VAL t 58 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N VAL t 58 " --> pdb=" O VAL t 85 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'u' and resid 39 through 44 No H-bonds generated for sheet with id= 36 Processing sheet with id= 37, first strand: chain 'u' and resid 81 through 84 removed outlier: 5.541A pdb=" N ARG u 81 " --> pdb=" O LYS u 96 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N ARG u 93 " --> pdb=" O ILE u 102 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'v' and resid 69 through 72 removed outlier: 3.585A pdb=" N ILE v 89 " --> pdb=" O PRO v 27 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'w' and resid 47 through 50 removed outlier: 3.973A pdb=" N THR w 54 " --> pdb=" O GLY w 50 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'x' and resid 11 through 15 Processing sheet with id= 41, first strand: chain 'x' and resid 34 through 40 Processing sheet with id= 42, first strand: chain 'z' and resid 34 through 38 removed outlier: 4.441A pdb=" N LYS z 5 " --> pdb=" O GLU z 57 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N MET z 53 " --> pdb=" O THR z 9 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'A' and resid 20 through 25 removed outlier: 3.798A pdb=" N ASN A 20 " --> pdb=" O CYS A 16 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N HIS A 30 " --> pdb=" O GLU A 11 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N THR A 13 " --> pdb=" O HIS A 30 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'C' and resid 33 through 38 removed outlier: 6.350A pdb=" N LEU C 33 " --> pdb=" O GLU C 50 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N LEU C 35 " --> pdb=" O TYR C 48 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'G' and resid 30 through 33 removed outlier: 5.869A pdb=" N PHE G 31 " --> pdb=" O HIS G 38 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N HIS G 38 " --> pdb=" O PHE G 31 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N ALA G 33 " --> pdb=" O LYS G 36 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'G' and resid 88 through 91 removed outlier: 3.760A pdb=" N LEU G 67 " --> pdb=" O ALA G 159 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE G 163 " --> pdb=" O VAL G 69 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'H' and resid 53 through 58 Processing sheet with id= 48, first strand: chain 'H' and resid 164 through 169 removed outlier: 3.562A pdb=" N GLU H 165 " --> pdb=" O VAL H 152 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY H 147 " --> pdb=" O PHE H 202 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL H 199 " --> pdb=" O ASN H 184 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ASP H 180 " --> pdb=" O LYS H 203 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'I' and resid 140 through 143 Processing sheet with id= 50, first strand: chain 'J' and resid 11 through 15 removed outlier: 3.581A pdb=" N GLN J 11 " --> pdb=" O GLY J 39 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N LEU J 35 " --> pdb=" O ILE J 15 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'J' and resid 82 through 87 removed outlier: 7.233A pdb=" N HIS J 82 " --> pdb=" O PRO J 97 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N MET J 95 " --> pdb=" O VAL J 84 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N VAL J 93 " --> pdb=" O GLY J 86 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N TYR J 127 " --> pdb=" O ARG J 92 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'J' and resid 32 through 39 removed outlier: 3.663A pdb=" N GLY J 50 " --> pdb=" O ALA J 34 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'K' and resid 34 through 37 removed outlier: 3.549A pdb=" N LYS K 35 " --> pdb=" O GLU K 65 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLU K 65 " --> pdb=" O LYS K 35 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ASN K 63 " --> pdb=" O HIS K 37 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N ILE K 6 " --> pdb=" O MET K 62 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLU K 5 " --> pdb=" O MET K 90 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N MET K 90 " --> pdb=" O GLU K 5 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N ARG K 86 " --> pdb=" O MET K 9 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'K' and resid 39 through 42 removed outlier: 3.532A pdb=" N LEU K 61 " --> pdb=" O GLU K 40 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N TYR K 59 " --> pdb=" O TRP K 42 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'L' and resid 72 through 76 Processing sheet with id= 56, first strand: chain 'M' and resid 23 through 27 removed outlier: 4.572A pdb=" N GLU M 51 " --> pdb=" O GLU M 57 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'M' and resid 73 through 76 Processing sheet with id= 58, first strand: chain 'N' and resid 4 through 10 removed outlier: 3.623A pdb=" N GLY N 7 " --> pdb=" O VAL N 18 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL N 18 " --> pdb=" O GLY N 7 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLY N 9 " --> pdb=" O ALA N 16 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA N 15 " --> pdb=" O LYS N 67 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LYS N 67 " --> pdb=" O ALA N 15 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'O' and resid 37 through 42 removed outlier: 3.674A pdb=" N GLY O 38 " --> pdb=" O ASP O 75 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ASP O 75 " --> pdb=" O GLY O 38 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE O 40 " --> pdb=" O LEU O 73 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N LEU O 42 " --> pdb=" O LEU O 71 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N LEU O 71 " --> pdb=" O LEU O 42 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU O 10 " --> pdb=" O ARG O 72 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ILE O 8 " --> pdb=" O VAL O 74 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'O' and resid 44 through 52 Processing sheet with id= 61, first strand: chain 'P' and resid 29 through 34 Processing sheet with id= 62, first strand: chain 'Q' and resid 28 through 32 removed outlier: 3.634A pdb=" N GLY Q 31 " --> pdb=" O ILE Q 79 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'Q' and resid 50 through 53 removed outlier: 4.982A pdb=" N LYS Q 50 " --> pdb=" O ILE Q 66 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER Q 64 " --> pdb=" O CYS Q 52 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'U' and resid 4 through 10 removed outlier: 3.511A pdb=" N PHE U 16 " --> pdb=" O HIS U 9 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'U' and resid 37 through 40 No H-bonds generated for sheet with id= 65 Processing sheet with id= 66, first strand: chain 'V' and resid 6 through 10 removed outlier: 7.165A 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 No H-bonds generated for sheet with id= 67 Processing sheet with id= 68, first strand: chain 'X' and resid 46 through 51 removed outlier: 4.801A pdb=" N LEU X 46 " --> pdb=" O VAL X 61 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ILE X 48 " --> pdb=" O VAL X 59 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'a' and resid 43 through 47 removed outlier: 4.080A pdb=" N LYS a 211 " --> pdb=" O ASN a 47 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N VAL a 212 " --> pdb=" O VAL a 224 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'a' and resid 60 through 65 removed outlier: 3.688A pdb=" N GLY a 61 " --> pdb=" O TYR a 163 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N TYR a 163 " --> pdb=" O GLY a 61 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N THR a 63 " --> pdb=" O VAL a 161 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL a 161 " --> pdb=" O THR a 63 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N GLY a 159 " --> pdb=" O LEU a 65 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain '8' and resid 66 through 72 removed outlier: 3.593A pdb=" N ALA 8 66 " --> pdb=" O ASP 8 88 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE 8 86 " --> pdb=" O THR 8 68 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE 8 138 " --> pdb=" O ALA 8 109 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N ARG 8 137 " --> pdb=" O ILE 8 261 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N LEU 8 263 " --> pdb=" O ARG 8 137 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE 8 262 " --> pdb=" O ASN 8 165 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N CYS 8 266 " --> pdb=" O LEU 8 169 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain '8' and resid 180 through 183 removed outlier: 6.265A pdb=" N THR 8 180 " --> pdb=" O TRP 8 193 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL 8 182 " --> pdb=" O ILE 8 191 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N THR 8 201 " --> pdb=" O ASN 8 194 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain '8' and resid 319 through 324 removed outlier: 3.766A pdb=" N THR 8 334 " --> pdb=" O ALA 8 385 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ASP 8 381 " --> pdb=" O VAL 8 338 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain '8' and resid 348 through 352 removed outlier: 3.518A pdb=" N ALA 8 356 " --> pdb=" O ASN 8 351 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain '8' and resid 363 through 366 removed outlier: 5.066A pdb=" N ILE 8 363 " --> pdb=" O ILE 8 374 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE 8 374 " --> pdb=" O ILE 8 363 " (cutoff:3.500A) Processing sheet with id= 76, first strand: chain '8' and resid 415 through 419 removed outlier: 4.517A pdb=" N GLN 8 455 " --> pdb=" O ASP 8 450 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ILE 8 457 " --> pdb=" O TRP 8 448 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ARG 8 446 " --> pdb=" O ALA 8 459 " (cutoff:3.500A) Processing sheet with id= 77, first strand: chain '8' and resid 490 through 494 removed outlier: 3.806A pdb=" N VAL 8 652 " --> pdb=" O THR 8 623 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLY 8 651 " --> pdb=" O GLU 8 648 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU 8 648 " --> pdb=" O GLY 8 651 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLY 8 644 " --> pdb=" O HIS 8 655 " (cutoff:3.500A) Processing sheet with id= 78, first strand: chain '8' and resid 500 through 508 removed outlier: 3.515A pdb=" N LYS 8 507 " --> pdb=" O GLN 8 514 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLN 8 514 " --> pdb=" O LYS 8 507 " (cutoff:3.500A) Processing sheet with id= 79, first strand: chain '8' and resid 515 through 519 removed outlier: 6.972A pdb=" N TYR 8 515 " --> pdb=" O HIS 8 584 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N HIS 8 584 " --> pdb=" O TYR 8 515 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N HIS 8 517 " --> pdb=" O SER 8 582 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE 8 580 " --> pdb=" O VAL 8 519 " (cutoff:3.500A) Processing sheet with id= 80, first strand: chain '8' and resid 612 through 618 No H-bonds generated for sheet with id= 80 1927 hydrogen bonds defined for protein. 5676 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3635 hydrogen bonds 5898 hydrogen bond angles 0 basepair planarities 1450 basepair parallelities 2323 stacking parallelities Total time for adding SS restraints: 230.29 Time building geometry restraints manager: 71.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.03 - 1.20: 62 1.20 - 1.37: 40586 1.37 - 1.54: 113022 1.54 - 1.71: 12279 1.71 - 1.88: 323 Bond restraints: 166272 Sorted by residual: bond pdb=" C ILE a 170 " pdb=" O ILE a 170 " ideal model delta sigma weight residual 1.236 1.517 -0.281 1.04e-02 9.25e+03 7.31e+02 bond pdb=" C ALA I 132 " pdb=" O ALA I 132 " ideal model delta sigma weight residual 1.236 1.524 -0.288 1.18e-02 7.18e+03 5.97e+02 bond pdb=" C ALA I 91 " pdb=" O ALA I 91 " ideal model delta sigma weight residual 1.237 1.512 -0.275 1.17e-02 7.31e+03 5.54e+02 bond pdb=" C PRO i 19 " pdb=" O PRO i 19 " ideal model delta sigma weight residual 1.235 1.517 -0.282 1.30e-02 5.92e+03 4.71e+02 bond pdb=" C LEU h 59 " pdb=" O LEU h 59 " ideal model delta sigma weight residual 1.234 1.486 -0.253 1.17e-02 7.31e+03 4.67e+02 ... (remaining 166267 not shown) Histogram of bond angle deviations from ideal: 65.30 - 82.50: 2 82.50 - 99.71: 19 99.71 - 116.91: 150322 116.91 - 134.12: 97611 134.12 - 151.33: 8 Bond angle restraints: 247962 Sorted by residual: angle pdb=" CA ASN g 11 " pdb=" C ASN g 11 " pdb=" N LEU g 12 " ideal model delta sigma weight residual 118.59 78.43 40.16 1.28e+00 6.10e-01 9.84e+02 angle pdb=" C ASN g 11 " pdb=" N LEU g 12 " pdb=" CA LEU g 12 " ideal model delta sigma weight residual 121.54 65.30 56.24 1.91e+00 2.74e-01 8.67e+02 angle pdb=" C VAL I 154 " pdb=" N LYS I 155 " pdb=" CA LYS I 155 " ideal model delta sigma weight residual 121.66 96.33 25.33 1.76e+00 3.23e-01 2.07e+02 angle pdb=" C PHE k 112 " pdb=" N MET k 113 " pdb=" CA MET k 113 " ideal model delta sigma weight residual 120.38 99.54 20.84 1.46e+00 4.69e-01 2.04e+02 angle pdb=" C ASN 8 85 " pdb=" N ILE 8 86 " pdb=" CA ILE 8 86 " ideal model delta sigma weight residual 123.10 105.03 18.07 1.33e+00 5.65e-01 1.85e+02 ... (remaining 247957 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.79: 94905 35.79 - 71.58: 10337 71.58 - 107.36: 1118 107.36 - 143.15: 14 143.15 - 178.94: 19 Dihedral angle restraints: 106393 sinusoidal: 87501 harmonic: 18892 Sorted by residual: dihedral pdb=" C4' U 11130 " pdb=" C3' U 11130 " pdb=" C2' U 11130 " pdb=" C1' U 11130 " ideal model delta sinusoidal sigma weight residual -35.00 32.67 -67.67 1 8.00e+00 1.56e-02 9.30e+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 80.96 66.04 1 8.00e+00 1.56e-02 8.91e+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 25.60 174.40 1 1.50e+01 4.44e-03 8.51e+01 ... (remaining 106390 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.144: 28252 0.144 - 0.288: 3074 0.288 - 0.432: 216 0.432 - 0.576: 28 0.576 - 0.720: 6 Chirality restraints: 31576 Sorted by residual: chirality pdb=" CA LEU g 12 " pdb=" N LEU g 12 " pdb=" C LEU g 12 " pdb=" CB LEU g 12 " both_signs ideal model delta sigma weight residual False 2.51 1.79 0.72 2.00e-01 2.50e+01 1.30e+01 chirality pdb=" CA PRO O 39 " pdb=" N PRO O 39 " pdb=" C PRO O 39 " pdb=" CB PRO O 39 " both_signs ideal model delta sigma weight residual False 2.72 2.01 0.71 2.00e-01 2.50e+01 1.27e+01 chirality pdb=" CA LYS I 155 " pdb=" N LYS I 155 " pdb=" C LYS I 155 " pdb=" CB LYS I 155 " both_signs ideal model delta sigma weight residual False 2.51 3.15 -0.64 2.00e-01 2.50e+01 1.02e+01 ... (remaining 31573 not shown) Planarity restraints: 13872 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A 2 119 " 0.289 2.00e-02 2.50e+03 1.23e-01 4.17e+02 pdb=" N9 A 2 119 " -0.024 2.00e-02 2.50e+03 pdb=" C8 A 2 119 " -0.109 2.00e-02 2.50e+03 pdb=" N7 A 2 119 " -0.081 2.00e-02 2.50e+03 pdb=" C5 A 2 119 " -0.053 2.00e-02 2.50e+03 pdb=" C6 A 2 119 " 0.048 2.00e-02 2.50e+03 pdb=" N6 A 2 119 " 0.162 2.00e-02 2.50e+03 pdb=" N1 A 2 119 " 0.047 2.00e-02 2.50e+03 pdb=" C2 A 2 119 " -0.039 2.00e-02 2.50e+03 pdb=" N3 A 2 119 " -0.129 2.00e-02 2.50e+03 pdb=" C4 A 2 119 " -0.111 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U 2 1 " 0.230 2.00e-02 2.50e+03 1.27e-01 3.64e+02 pdb=" N1 U 2 1 " -0.006 2.00e-02 2.50e+03 pdb=" C2 U 2 1 " -0.040 2.00e-02 2.50e+03 pdb=" O2 U 2 1 " -0.094 2.00e-02 2.50e+03 pdb=" N3 U 2 1 " -0.030 2.00e-02 2.50e+03 pdb=" C4 U 2 1 " -0.037 2.00e-02 2.50e+03 pdb=" O4 U 2 1 " 0.223 2.00e-02 2.50e+03 pdb=" C5 U 2 1 " -0.131 2.00e-02 2.50e+03 pdb=" C6 U 2 1 " -0.114 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G 12061 " -0.268 2.00e-02 2.50e+03 1.10e-01 3.62e+02 pdb=" N9 G 12061 " 0.019 2.00e-02 2.50e+03 pdb=" C8 G 12061 " 0.118 2.00e-02 2.50e+03 pdb=" N7 G 12061 " 0.098 2.00e-02 2.50e+03 pdb=" C5 G 12061 " 0.048 2.00e-02 2.50e+03 pdb=" C6 G 12061 " -0.050 2.00e-02 2.50e+03 pdb=" O6 G 12061 " -0.161 2.00e-02 2.50e+03 pdb=" N1 G 12061 " -0.041 2.00e-02 2.50e+03 pdb=" C2 G 12061 " 0.029 2.00e-02 2.50e+03 pdb=" N2 G 12061 " 0.042 2.00e-02 2.50e+03 pdb=" N3 G 12061 " 0.085 2.00e-02 2.50e+03 pdb=" C4 G 12061 " 0.083 2.00e-02 2.50e+03 ... (remaining 13869 not shown) Histogram of nonbonded interaction distances: 1.33 - 2.05: 6 2.05 - 2.76: 21030 2.76 - 3.47: 209655 3.47 - 4.19: 484073 4.19 - 4.90: 649923 Nonbonded interactions: 1364687 Sorted by model distance: nonbonded pdb=" N ASN g 11 " pdb=" N LEU g 12 " model vdw 1.331 2.560 nonbonded pdb=" O3' A 5 76 " pdb=" C PRO 5 101 " model vdw 1.418 3.270 nonbonded pdb=" O GLN i 11 " pdb=" O ILE i 54 " model vdw 1.906 3.040 nonbonded pdb=" O3' A 5 76 " pdb=" CA PRO 5 101 " model vdw 1.987 3.470 nonbonded pdb=" O ASP 8 585 " pdb=" N ASP 8 587 " model vdw 2.001 2.520 ... (remaining 1364682 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.69 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.350 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: 0.130 Extract box with map and model: 19.160 Check model and map are aligned: 1.680 Set scattering table: 1.020 Process input model: 541.540 Find NCS groups from input model: 3.340 Set up NCS constraints: 0.370 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 572.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.288 166272 Z= 0.713 Angle : 1.237 56.245 247962 Z= 0.825 Chirality : 0.095 0.720 31576 Planarity : 0.013 0.127 13872 Dihedral : 22.465 178.941 94209 Min Nonbonded Distance : 1.331 Molprobity Statistics. All-atom Clashscore : 22.57 Ramachandran Plot: Outliers : 1.44 % Allowed : 15.96 % Favored : 82.60 % Rotamer: Outliers : 2.03 % Allowed : 7.94 % Favored : 90.03 % 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: -4.35 (0.09), residues: 6517 helix: -2.79 (0.10), residues: 1662 sheet: -2.66 (0.15), residues: 975 loop : -3.12 (0.09), residues: 3880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.096 0.007 TRP V 72 HIS 0.003 0.000 HIS b 52 PHE 0.042 0.005 PHE T 42 TYR 0.135 0.008 TYR U 17 ARG 0.012 0.001 ARG S 62 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13034 Ramachandran restraints generated. 6517 Oldfield, 0 Emsley, 6517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13034 Ramachandran restraints generated. 6517 Oldfield, 0 Emsley, 6517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1498 residues out of total 5429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 1388 time to evaluate : 6.820 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: b 65 ASP cc_start: 0.7883 (t70) cc_final: 0.7588 (t0) REVERT: c 2 ILE cc_start: 0.8990 (pt) cc_final: 0.8659 (pt) REVERT: e 34 THR cc_start: 0.8983 (m) cc_final: 0.8598 (p) REVERT: e 89 THR cc_start: 0.7407 (m) cc_final: 0.6913 (p) REVERT: e 126 ASN cc_start: 0.7367 (p0) cc_final: 0.6720 (p0) REVERT: e 128 SER cc_start: 0.8148 (m) cc_final: 0.7721 (t) REVERT: e 137 PHE cc_start: 0.8626 (m-80) cc_final: 0.8407 (m-80) REVERT: e 140 ILE cc_start: 0.7654 (OUTLIER) cc_final: 0.7412 (mp) REVERT: f 23 ILE cc_start: 0.9140 (mm) cc_final: 0.8812 (tp) REVERT: f 87 GLN cc_start: 0.7996 (tm-30) cc_final: 0.7749 (tm-30) REVERT: i 67 THR cc_start: 0.4626 (t) cc_final: 0.3932 (p) REVERT: i 68 PHE cc_start: 0.5002 (p90) cc_final: 0.4736 (p90) REVERT: j 67 ASN cc_start: 0.8242 (m-40) cc_final: 0.7911 (m-40) REVERT: j 102 GLU cc_start: 0.7783 (tt0) cc_final: 0.7551 (tt0) REVERT: j 109 LEU cc_start: 0.9026 (mm) cc_final: 0.8804 (mm) REVERT: k 37 ASP cc_start: 0.7904 (OUTLIER) cc_final: 0.7682 (t0) REVERT: k 93 GLN cc_start: 0.7517 (mm-40) cc_final: 0.7191 (pt0) REVERT: k 104 THR cc_start: 0.8891 (m) cc_final: 0.8554 (t) REVERT: l 104 GLN cc_start: 0.7505 (mm-40) cc_final: 0.7163 (mm-40) REVERT: m 1 MET cc_start: 0.7280 (tpp) cc_final: 0.7050 (tpp) REVERT: m 42 THR cc_start: 0.9127 (p) cc_final: 0.8871 (p) REVERT: m 63 ILE cc_start: 0.8909 (OUTLIER) cc_final: 0.8692 (mp) REVERT: n 16 HIS cc_start: 0.8426 (OUTLIER) cc_final: 0.8023 (t70) REVERT: n 107 ASN cc_start: 0.8651 (OUTLIER) cc_final: 0.7996 (t0) REVERT: o 88 LYS cc_start: 0.8295 (tttt) cc_final: 0.7950 (tptt) REVERT: p 114 ASN cc_start: 0.7789 (p0) cc_final: 0.7353 (p0) REVERT: q 31 TYR cc_start: 0.8613 (t80) cc_final: 0.8306 (t80) REVERT: r 95 ASP cc_start: 0.8030 (m-30) cc_final: 0.7696 (m-30) REVERT: s 38 TYR cc_start: 0.8548 (m-80) cc_final: 0.8213 (m-10) REVERT: s 65 ASP cc_start: 0.7919 (t70) cc_final: 0.7343 (t0) REVERT: s 68 ASP cc_start: 0.8030 (m-30) cc_final: 0.7633 (p0) REVERT: t 2 ILE cc_start: 0.8550 (pt) cc_final: 0.8261 (mt) REVERT: v 57 TYR cc_start: 0.8791 (m-80) cc_final: 0.8379 (m-10) REVERT: v 75 GLN cc_start: 0.8961 (tp40) cc_final: 0.8655 (tp-100) REVERT: v 76 ASP cc_start: 0.7906 (OUTLIER) cc_final: 0.7425 (m-30) REVERT: w 11 ASP cc_start: 0.8182 (m-30) cc_final: 0.7708 (m-30) REVERT: w 25 GLU cc_start: 0.7563 (tt0) cc_final: 0.7208 (tt0) REVERT: x 46 VAL cc_start: 0.9048 (t) cc_final: 0.8748 (p) REVERT: y 8 GLU cc_start: 0.6060 (mp0) cc_final: 0.5539 (mp0) REVERT: y 50 VAL cc_start: 0.9357 (t) cc_final: 0.9152 (p) REVERT: A 53 THR cc_start: 0.5397 (p) cc_final: 0.5049 (p) REVERT: B 9 ARG cc_start: 0.8752 (ptp90) cc_final: 0.8315 (ptp90) REVERT: B 27 LEU cc_start: 0.7731 (mp) cc_final: 0.7485 (mt) REVERT: C 25 ASN cc_start: 0.8301 (t0) cc_final: 0.7777 (t0) REVERT: F 34 LYS cc_start: 0.8933 (ttpt) cc_final: 0.8698 (tttp) REVERT: G 61 SER cc_start: 0.8114 (OUTLIER) cc_final: 0.7905 (p) REVERT: G 167 HIS cc_start: 0.8698 (t-170) cc_final: 0.8221 (m-70) REVERT: H 138 GLN cc_start: 0.8139 (tm-30) cc_final: 0.7857 (pp30) REVERT: H 180 ASP cc_start: 0.7089 (m-30) cc_final: 0.6724 (m-30) REVERT: H 184 ASN cc_start: 0.6025 (m110) cc_final: 0.5723 (m110) REVERT: I 2 ARG cc_start: 0.3983 (mtp180) cc_final: 0.2553 (tpp-160) REVERT: I 10 LEU cc_start: 0.7002 (mm) cc_final: 0.6597 (mm) REVERT: I 47 LEU cc_start: 0.8614 (tp) cc_final: 0.8412 (tp) REVERT: J 47 PHE cc_start: 0.8537 (OUTLIER) cc_final: 0.8000 (p90) REVERT: J 81 GLN cc_start: 0.8602 (mm-40) cc_final: 0.8249 (mt0) REVERT: J 123 LEU cc_start: 0.8952 (mt) cc_final: 0.8289 (mp) REVERT: J 133 ILE cc_start: 0.9114 (mp) cc_final: 0.8901 (mt) REVERT: J 162 GLU cc_start: 0.8500 (mm-30) cc_final: 0.8047 (tm-30) REVERT: K 40 GLU cc_start: 0.7181 (tt0) cc_final: 0.5960 (tt0) REVERT: K 61 LEU cc_start: 0.8848 (tp) cc_final: 0.8039 (tt) REVERT: K 75 GLU cc_start: 0.8842 (tt0) cc_final: 0.8636 (pt0) REVERT: L 138 GLU cc_start: 0.8225 (mm-30) cc_final: 0.7810 (pp20) REVERT: L 143 MET cc_start: 0.4604 (tpp) cc_final: 0.4108 (mmp) REVERT: M 51 GLU cc_start: 0.7951 (mt-10) cc_final: 0.7322 (tm-30) REVERT: M 73 SER cc_start: 0.7117 (t) cc_final: 0.6655 (p) REVERT: N 45 MET cc_start: 0.7135 (mmm) cc_final: 0.6934 (mmt) REVERT: N 60 LEU cc_start: 0.7505 (pp) cc_final: 0.7287 (mt) REVERT: O 52 LEU cc_start: 0.3822 (mt) cc_final: 0.3556 (mt) REVERT: O 68 ARG cc_start: 0.7851 (mtt180) cc_final: 0.7428 (mmt180) REVERT: O 97 ASP cc_start: 0.7853 (t70) cc_final: 0.7136 (p0) REVERT: Q 50 LYS cc_start: 0.7855 (OUTLIER) cc_final: 0.7223 (mtmt) REVERT: Q 71 HIS cc_start: 0.7311 (p-80) cc_final: 0.7027 (p-80) REVERT: Q 94 TYR cc_start: 0.6363 (m-80) cc_final: 0.5641 (m-80) REVERT: R 10 ASP cc_start: 0.6991 (t70) cc_final: 0.6585 (p0) REVERT: R 22 TYR cc_start: 0.7471 (t80) cc_final: 0.6688 (t80) REVERT: R 74 MET cc_start: 0.6504 (mpp) cc_final: 0.5711 (mpp) REVERT: S 3 GLN cc_start: 0.7394 (OUTLIER) cc_final: 0.6987 (mp10) REVERT: S 61 ASN cc_start: 0.7484 (OUTLIER) cc_final: 0.6956 (p0) REVERT: S 100 TRP cc_start: 0.7184 (p90) cc_final: 0.6787 (p90) REVERT: W 56 ARG cc_start: 0.8734 (ttp-110) cc_final: 0.8010 (mmt90) REVERT: W 72 ARG cc_start: 0.8605 (mmp-170) cc_final: 0.7441 (tmt170) REVERT: X 77 ARG cc_start: 0.4005 (OUTLIER) cc_final: 0.3801 (ptp-170) REVERT: Y 28 ARG cc_start: 0.8883 (mtt180) cc_final: 0.7764 (ttm170) REVERT: Y 30 PHE cc_start: 0.8857 (m-80) cc_final: 0.8573 (m-10) REVERT: Y 35 TYR cc_start: 0.8475 (m-80) cc_final: 0.8005 (m-80) REVERT: Y 53 MET cc_start: 0.8794 (ptp) cc_final: 0.8499 (ptm) REVERT: Z 19 LYS cc_start: 0.7926 (mptt) cc_final: 0.7663 (mmtt) REVERT: Z 53 LYS cc_start: 0.9209 (ttpp) cc_final: 0.8868 (tptp) REVERT: 8 20 ASP cc_start: 0.7151 (t70) cc_final: 0.6948 (t0) REVERT: 8 280 ASP cc_start: 0.8745 (m-30) cc_final: 0.8274 (m-30) REVERT: 8 366 MET cc_start: 0.5269 (ptm) cc_final: 0.4543 (pmm) REVERT: 8 461 MET cc_start: 0.6754 (mmp) cc_final: 0.6356 (mmm) REVERT: 8 507 LYS cc_start: 0.7264 (OUTLIER) cc_final: 0.6065 (mptt) REVERT: 8 648 GLU cc_start: 0.6060 (OUTLIER) cc_final: 0.5712 (mp0) outliers start: 110 outliers final: 33 residues processed: 1473 average time/residue: 1.3158 time to fit residues: 3347.5700 Evaluate side-chains 943 residues out of total 5429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 896 time to evaluate : 6.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 53 ILE Chi-restraints excluded: chain c residue 129 THR Chi-restraints excluded: chain d residue 83 VAL Chi-restraints excluded: chain e residue 25 MET Chi-restraints excluded: chain e residue 140 ILE Chi-restraints excluded: chain g residue 12 LEU Chi-restraints excluded: chain g residue 21 VAL Chi-restraints excluded: chain h residue 50 VAL Chi-restraints excluded: chain j residue 88 THR Chi-restraints excluded: chain k residue 37 ASP Chi-restraints excluded: chain m residue 36 VAL Chi-restraints excluded: chain m residue 63 ILE Chi-restraints excluded: chain m residue 91 TYR Chi-restraints excluded: chain n residue 16 HIS Chi-restraints excluded: chain n residue 97 ILE Chi-restraints excluded: chain n residue 107 ASN Chi-restraints excluded: chain o residue 60 GLU Chi-restraints excluded: chain v residue 42 LEU Chi-restraints excluded: chain v residue 76 ASP Chi-restraints excluded: chain x residue 35 HIS Chi-restraints excluded: chain x residue 69 GLU Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain F residue 23 ILE Chi-restraints excluded: chain G residue 61 SER Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain J residue 47 PHE Chi-restraints excluded: chain J residue 160 VAL Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain M residue 3 GLN Chi-restraints excluded: chain M residue 60 LEU Chi-restraints excluded: chain O residue 32 THR Chi-restraints excluded: chain Q residue 50 LYS Chi-restraints excluded: chain S residue 3 GLN Chi-restraints excluded: chain S residue 61 ASN Chi-restraints excluded: chain T residue 55 LEU Chi-restraints excluded: chain U residue 1 MET Chi-restraints excluded: chain V residue 49 ASN Chi-restraints excluded: chain W residue 28 LEU Chi-restraints excluded: chain X residue 77 ARG Chi-restraints excluded: chain a residue 163 TYR Chi-restraints excluded: chain 8 residue 24 THR Chi-restraints excluded: chain 8 residue 244 THR Chi-restraints excluded: chain 8 residue 442 ASP Chi-restraints excluded: chain 8 residue 507 LYS Chi-restraints excluded: chain 8 residue 648 GLU Chi-restraints excluded: chain 5 residue 101 PRO Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1109 random chunks: chunk 936 optimal weight: 50.0000 chunk 840 optimal weight: 20.0000 chunk 466 optimal weight: 5.9990 chunk 287 optimal weight: 5.9990 chunk 567 optimal weight: 5.9990 chunk 449 optimal weight: 7.9990 chunk 869 optimal weight: 10.0000 chunk 336 optimal weight: 6.9990 chunk 528 optimal weight: 10.0000 chunk 646 optimal weight: 20.0000 chunk 1007 optimal weight: 20.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 44 ASN b 85 ASN b 196 ASN ** c 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 130 GLN ** d 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 90 GLN ** f 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 29 GLN j 58 ASN j 138 GLN k 3 GLN m 17 ASN ** n 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 55 HIS ** s 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 39 ASN ** v 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** x 22 ASN A 61 ASN ** G 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 58 GLN I 84 ASN I 88 ASN ** J 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 75 GLN N 125 GLN R 104 ASN S 3 GLN ** U 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 18 GLN W 30 ASN Y 47 GLN Y 51 ASN ** Y 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 508 GLN 8 560 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 166272 Z= 0.273 Angle : 0.757 21.124 247962 Z= 0.389 Chirality : 0.043 0.429 31576 Planarity : 0.006 0.089 13872 Dihedral : 23.002 178.738 81324 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 15.98 Ramachandran Plot: Outliers : 0.18 % Allowed : 11.34 % Favored : 88.48 % Rotamer: Outliers : 3.92 % Allowed : 14.37 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.53 (0.09), residues: 6517 helix: -1.69 (0.10), residues: 2038 sheet: -2.22 (0.15), residues: 1006 loop : -2.85 (0.10), residues: 3473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP V 72 HIS 0.011 0.002 HIS r 12 PHE 0.038 0.002 PHE Z 36 TYR 0.032 0.002 TYR U 17 ARG 0.010 0.001 ARG M 79 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13034 Ramachandran restraints generated. 6517 Oldfield, 0 Emsley, 6517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13034 Ramachandran restraints generated. 6517 Oldfield, 0 Emsley, 6517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1259 residues out of total 5429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 213 poor density : 1046 time to evaluate : 6.922 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: b 65 ASP cc_start: 0.7934 (t70) cc_final: 0.7572 (t0) REVERT: b 167 ASP cc_start: 0.7599 (p0) cc_final: 0.7393 (p0) REVERT: c 11 MET cc_start: 0.8430 (tpt) cc_final: 0.7606 (tpt) REVERT: e 10 GLU cc_start: 0.8803 (OUTLIER) cc_final: 0.7711 (pp20) REVERT: e 34 THR cc_start: 0.8842 (m) cc_final: 0.8295 (p) REVERT: e 89 THR cc_start: 0.7500 (m) cc_final: 0.7006 (p) REVERT: e 126 ASN cc_start: 0.7563 (OUTLIER) cc_final: 0.6914 (p0) REVERT: e 128 SER cc_start: 0.7684 (m) cc_final: 0.7465 (t) REVERT: g 28 ASN cc_start: 0.7861 (m110) cc_final: 0.7623 (m110) REVERT: i 67 THR cc_start: 0.4192 (t) cc_final: 0.3809 (p) REVERT: k 106 GLU cc_start: 0.7774 (mp0) cc_final: 0.7551 (mp0) REVERT: m 42 THR cc_start: 0.8899 (p) cc_final: 0.8670 (p) REVERT: m 136 MET cc_start: 0.5294 (ppp) cc_final: 0.4714 (ppp) REVERT: n 18 GLN cc_start: 0.8325 (tm-30) cc_final: 0.8112 (tm-30) REVERT: n 107 ASN cc_start: 0.8487 (OUTLIER) cc_final: 0.8146 (t0) REVERT: n 112 TYR cc_start: 0.8406 (m-80) cc_final: 0.8081 (m-80) REVERT: o 3 LYS cc_start: 0.7848 (tmtt) cc_final: 0.7449 (pttt) REVERT: o 55 GLU cc_start: 0.8366 (mt-10) cc_final: 0.7733 (tp30) REVERT: o 62 LEU cc_start: 0.8238 (mt) cc_final: 0.7942 (tp) REVERT: o 88 LYS cc_start: 0.8259 (tttt) cc_final: 0.8011 (tptp) REVERT: p 114 ASN cc_start: 0.7766 (p0) cc_final: 0.7324 (p0) REVERT: q 31 TYR cc_start: 0.8579 (t80) cc_final: 0.8311 (t80) REVERT: q 48 ASP cc_start: 0.8112 (m-30) cc_final: 0.7900 (m-30) REVERT: r 46 GLU cc_start: 0.7270 (tm-30) cc_final: 0.7041 (tm-30) REVERT: r 60 LYS cc_start: 0.8746 (ttpt) cc_final: 0.8336 (pttm) REVERT: s 11 ARG cc_start: 0.7194 (mmt-90) cc_final: 0.6849 (mmt-90) REVERT: s 52 GLU cc_start: 0.8655 (mt-10) cc_final: 0.8436 (mt-10) REVERT: t 74 ILE cc_start: 0.9039 (pt) cc_final: 0.8438 (pt) REVERT: u 39 ASN cc_start: 0.8111 (t0) cc_final: 0.7739 (t0) REVERT: v 24 ASN cc_start: 0.8159 (OUTLIER) cc_final: 0.7957 (t0) REVERT: v 75 GLN cc_start: 0.8957 (tp40) cc_final: 0.8652 (tp-100) REVERT: v 76 ASP cc_start: 0.7835 (OUTLIER) cc_final: 0.7501 (m-30) REVERT: B 9 ARG cc_start: 0.8733 (ptp90) cc_final: 0.8465 (ptp90) REVERT: B 14 MET cc_start: 0.8223 (ptp) cc_final: 0.7992 (ptp) REVERT: C 24 LYS cc_start: 0.8542 (tptm) cc_final: 0.8133 (tppt) REVERT: C 36 LYS cc_start: 0.7816 (ttmt) cc_final: 0.7313 (ttpp) REVERT: F 34 LYS cc_start: 0.8998 (ttpt) cc_final: 0.8704 (mtpt) REVERT: G 135 MET cc_start: 0.7407 (ptp) cc_final: 0.7142 (ptp) REVERT: G 139 GLU cc_start: 0.9055 (mp0) cc_final: 0.8703 (mp0) REVERT: G 167 HIS cc_start: 0.8549 (t-170) cc_final: 0.8219 (m90) REVERT: H 138 GLN cc_start: 0.8412 (tm-30) cc_final: 0.8113 (pp30) REVERT: H 141 MET cc_start: 0.6421 (mmm) cc_final: 0.6039 (mmm) REVERT: H 180 ASP cc_start: 0.6600 (m-30) cc_final: 0.6201 (m-30) REVERT: I 2 ARG cc_start: 0.3743 (mtp180) cc_final: 0.2965 (tpp-160) REVERT: I 10 LEU cc_start: 0.6465 (mm) cc_final: 0.6158 (mm) REVERT: J 15 ILE cc_start: 0.8619 (OUTLIER) cc_final: 0.8357 (mp) REVERT: J 25 LYS cc_start: 0.7933 (tppt) cc_final: 0.7729 (tptt) REVERT: J 81 GLN cc_start: 0.8638 (mm-40) cc_final: 0.8178 (mt0) REVERT: J 151 MET cc_start: 0.8675 (tpp) cc_final: 0.8349 (tpt) REVERT: J 161 GLU cc_start: 0.8031 (pm20) cc_final: 0.7655 (pm20) REVERT: K 30 THR cc_start: 0.7600 (m) cc_final: 0.7388 (p) REVERT: K 40 GLU cc_start: 0.6483 (tt0) cc_final: 0.5559 (tt0) REVERT: K 61 LEU cc_start: 0.8794 (tp) cc_final: 0.8495 (tt) REVERT: K 75 GLU cc_start: 0.8785 (tt0) cc_final: 0.8496 (pt0) REVERT: L 22 LEU cc_start: 0.8299 (mm) cc_final: 0.7304 (tp) REVERT: M 51 GLU cc_start: 0.7704 (mt-10) cc_final: 0.7253 (tm-30) REVERT: M 66 GLN cc_start: 0.7400 (mp10) cc_final: 0.7149 (mp10) REVERT: N 45 MET cc_start: 0.6784 (mmm) cc_final: 0.6545 (mmt) REVERT: N 51 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.7972 (tp) REVERT: N 88 GLU cc_start: 0.3413 (tt0) cc_final: 0.3005 (tt0) REVERT: O 68 ARG cc_start: 0.7718 (mtt180) cc_final: 0.7389 (mmt180) REVERT: O 97 ASP cc_start: 0.6872 (t70) cc_final: 0.6574 (t70) REVERT: Q 85 ARG cc_start: 0.7039 (ptm160) cc_final: 0.6450 (mtp180) REVERT: Q 94 TYR cc_start: 0.6488 (m-80) cc_final: 0.5896 (m-80) REVERT: R 22 TYR cc_start: 0.7352 (t80) cc_final: 0.6303 (t80) REVERT: R 65 GLU cc_start: 0.7261 (OUTLIER) cc_final: 0.6714 (tp30) REVERT: R 68 LEU cc_start: 0.8969 (tp) cc_final: 0.8571 (tp) REVERT: S 9 GLU cc_start: 0.7191 (tp30) cc_final: 0.6845 (tp30) REVERT: S 61 ASN cc_start: 0.7514 (OUTLIER) cc_final: 0.7127 (p0) REVERT: S 100 TRP cc_start: 0.7042 (p90) cc_final: 0.6656 (p90) REVERT: T 48 ASP cc_start: 0.7943 (OUTLIER) cc_final: 0.7743 (m-30) REVERT: W 53 GLN cc_start: 0.8662 (mt0) cc_final: 0.8321 (mt0) REVERT: W 72 ARG cc_start: 0.8599 (mmp-170) cc_final: 0.7576 (tmt-80) REVERT: X 65 MET cc_start: 0.8023 (tpt) cc_final: 0.7349 (tpt) REVERT: Y 35 TYR cc_start: 0.8631 (m-80) cc_final: 0.8297 (m-80) REVERT: Y 53 MET cc_start: 0.8303 (ptp) cc_final: 0.7979 (ptp) REVERT: Y 70 LYS cc_start: 0.8668 (OUTLIER) cc_final: 0.8319 (tptt) REVERT: Z 53 LYS cc_start: 0.9226 (ttpp) cc_final: 0.8833 (tptp) REVERT: 8 15 ILE cc_start: 0.8338 (mm) cc_final: 0.8124 (tp) REVERT: 8 58 GLU cc_start: 0.8479 (OUTLIER) cc_final: 0.8124 (mp0) REVERT: 8 101 ARG cc_start: 0.8093 (ttm-80) cc_final: 0.6869 (mtp85) REVERT: 8 257 LEU cc_start: 0.8161 (tt) cc_final: 0.7745 (mp) REVERT: 8 461 MET cc_start: 0.7002 (mmp) cc_final: 0.6681 (mmm) REVERT: 8 648 GLU cc_start: 0.5862 (OUTLIER) cc_final: 0.5504 (mp0) outliers start: 213 outliers final: 114 residues processed: 1170 average time/residue: 1.2977 time to fit residues: 2669.6395 Evaluate side-chains 995 residues out of total 5429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 868 time to evaluate : 8.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 8 THR Chi-restraints excluded: chain b residue 9 SER Chi-restraints excluded: chain b residue 53 ILE Chi-restraints excluded: chain b residue 69 ASN Chi-restraints excluded: chain b residue 134 ILE Chi-restraints excluded: chain b residue 155 ARG Chi-restraints excluded: chain b residue 258 SER Chi-restraints excluded: chain d residue 83 VAL Chi-restraints excluded: chain e residue 10 GLU Chi-restraints excluded: chain e residue 126 ASN Chi-restraints excluded: chain e residue 162 ASP Chi-restraints excluded: chain g residue 21 VAL Chi-restraints excluded: chain g residue 122 LEU Chi-restraints excluded: chain h residue 33 VAL Chi-restraints excluded: chain h residue 50 VAL Chi-restraints excluded: chain h residue 54 VAL Chi-restraints excluded: chain j residue 60 ASP Chi-restraints excluded: chain j residue 138 GLN Chi-restraints excluded: chain k residue 7 MET Chi-restraints excluded: chain k residue 58 LEU Chi-restraints excluded: chain l residue 25 SER Chi-restraints excluded: chain l residue 89 VAL Chi-restraints excluded: chain m residue 25 ASP Chi-restraints excluded: chain m residue 36 VAL Chi-restraints excluded: chain m residue 65 ILE Chi-restraints excluded: chain m residue 74 THR Chi-restraints excluded: chain m residue 91 TYR Chi-restraints excluded: chain m residue 95 LEU Chi-restraints excluded: chain m residue 134 THR Chi-restraints excluded: chain n residue 23 ASN Chi-restraints excluded: chain n residue 24 MET Chi-restraints excluded: chain n residue 29 VAL Chi-restraints excluded: chain n residue 37 THR Chi-restraints excluded: chain n residue 107 ASN Chi-restraints excluded: chain o residue 2 ASP Chi-restraints excluded: chain o residue 28 VAL Chi-restraints excluded: chain o residue 60 GLU Chi-restraints excluded: chain p residue 109 ILE Chi-restraints excluded: chain q residue 17 LEU Chi-restraints excluded: chain q residue 103 VAL Chi-restraints excluded: chain r residue 41 ILE Chi-restraints excluded: chain r residue 102 SER Chi-restraints excluded: chain s residue 4 ILE Chi-restraints excluded: chain s residue 55 ILE Chi-restraints excluded: chain s residue 66 ILE Chi-restraints excluded: chain s residue 101 SER Chi-restraints excluded: chain t residue 11 LEU Chi-restraints excluded: chain t residue 39 THR Chi-restraints excluded: chain t residue 92 ASN Chi-restraints excluded: chain u residue 17 ASP Chi-restraints excluded: chain u residue 51 LEU Chi-restraints excluded: chain u residue 57 ILE Chi-restraints excluded: chain v residue 24 ASN Chi-restraints excluded: chain v residue 76 ASP Chi-restraints excluded: chain x residue 12 VAL Chi-restraints excluded: chain y residue 40 SER Chi-restraints excluded: chain z residue 3 THR Chi-restraints excluded: chain z residue 34 THR Chi-restraints excluded: chain z residue 47 ILE Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain B residue 2 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 22 THR Chi-restraints excluded: chain C residue 44 GLN Chi-restraints excluded: chain C residue 45 HIS Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain G residue 38 HIS Chi-restraints excluded: chain H residue 17 TRP Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 84 GLU Chi-restraints excluded: chain I residue 4 LEU Chi-restraints excluded: chain I residue 44 LYS Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 88 ASN Chi-restraints excluded: chain J residue 15 ILE Chi-restraints excluded: chain J residue 45 VAL Chi-restraints excluded: chain J residue 64 GLU Chi-restraints excluded: chain J residue 71 ILE Chi-restraints excluded: chain J residue 160 VAL Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain M residue 3 GLN Chi-restraints excluded: chain M residue 74 ILE Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain M residue 112 ASP Chi-restraints excluded: chain M residue 125 ILE Chi-restraints excluded: chain N residue 29 ILE Chi-restraints excluded: chain N residue 38 PHE Chi-restraints excluded: chain N residue 51 LEU Chi-restraints excluded: chain N residue 65 THR Chi-restraints excluded: chain N residue 93 LEU Chi-restraints excluded: chain O residue 10 LEU Chi-restraints excluded: chain O residue 15 HIS Chi-restraints excluded: chain O residue 98 VAL Chi-restraints excluded: chain P residue 45 THR Chi-restraints excluded: chain P residue 109 ILE Chi-restraints excluded: chain R residue 65 GLU Chi-restraints excluded: chain R residue 88 LEU Chi-restraints excluded: chain S residue 61 ASN Chi-restraints excluded: chain T residue 48 ASP Chi-restraints excluded: chain T residue 55 LEU Chi-restraints excluded: chain V residue 49 ASN Chi-restraints excluded: chain V residue 61 ARG Chi-restraints excluded: chain W residue 64 LEU Chi-restraints excluded: chain Y residue 11 ILE Chi-restraints excluded: chain Y residue 70 LYS Chi-restraints excluded: chain Y residue 79 THR Chi-restraints excluded: chain 8 residue 24 THR Chi-restraints excluded: chain 8 residue 58 GLU Chi-restraints excluded: chain 8 residue 96 THR Chi-restraints excluded: chain 8 residue 167 VAL Chi-restraints excluded: chain 8 residue 200 VAL Chi-restraints excluded: chain 8 residue 244 THR Chi-restraints excluded: chain 8 residue 409 MET Chi-restraints excluded: chain 8 residue 420 VAL Chi-restraints excluded: chain 8 residue 488 VAL Chi-restraints excluded: chain 8 residue 628 THR Chi-restraints excluded: chain 8 residue 648 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1109 random chunks: chunk 559 optimal weight: 8.9990 chunk 312 optimal weight: 30.0000 chunk 838 optimal weight: 20.0000 chunk 685 optimal weight: 50.0000 chunk 277 optimal weight: 0.5980 chunk 1008 optimal weight: 20.0000 chunk 1089 optimal weight: 7.9990 chunk 898 optimal weight: 20.0000 chunk 1000 optimal weight: 10.0000 chunk 343 optimal weight: 20.0000 chunk 809 optimal weight: 10.0000 overall best weight: 7.5192 ------------------------------------------------------------------------------- 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** ** d 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 26 GLN ** f 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 38 GLN l 104 GLN m 3 GLN ** n 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 19 GLN p 14 GLN p 55 HIS ** s 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 68 ASN x 19 HIS ** y 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 17 HIS G 57 ASN ** H 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 39 GLN J 121 ASN ** J 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 75 GLN P 21 HIS R 99 GLN U 9 HIS ** V 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 188 ASN ** 8 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 560 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.2715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 166272 Z= 0.276 Angle : 0.689 23.995 247962 Z= 0.358 Chirality : 0.040 0.390 31576 Planarity : 0.006 0.152 13872 Dihedral : 23.158 178.838 81265 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 16.70 Ramachandran Plot: Outliers : 0.18 % Allowed : 11.97 % Favored : 87.85 % Rotamer: Outliers : 5.01 % Allowed : 16.23 % Favored : 78.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.12 (0.09), residues: 6517 helix: -1.19 (0.10), residues: 2052 sheet: -1.92 (0.15), residues: 1044 loop : -2.74 (0.10), residues: 3421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP V 72 HIS 0.012 0.002 HIS v 80 PHE 0.034 0.002 PHE Z 36 TYR 0.025 0.002 TYR I 64 ARG 0.013 0.001 ARG t 73 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13034 Ramachandran restraints generated. 6517 Oldfield, 0 Emsley, 6517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13034 Ramachandran restraints generated. 6517 Oldfield, 0 Emsley, 6517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1217 residues out of total 5429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 272 poor density : 945 time to evaluate : 6.729 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: b 65 ASP cc_start: 0.7861 (t70) cc_final: 0.7497 (t0) REVERT: b 167 ASP cc_start: 0.7668 (p0) cc_final: 0.7452 (p0) REVERT: c 11 MET cc_start: 0.8531 (tpt) cc_final: 0.8011 (tpt) REVERT: d 100 MET cc_start: 0.8025 (ptt) cc_final: 0.7644 (mtm) REVERT: e 10 GLU cc_start: 0.8848 (OUTLIER) cc_final: 0.7760 (pp20) REVERT: e 34 THR cc_start: 0.8871 (m) cc_final: 0.8268 (p) REVERT: e 89 THR cc_start: 0.7694 (m) cc_final: 0.7406 (t) REVERT: e 126 ASN cc_start: 0.7573 (OUTLIER) cc_final: 0.7146 (p0) REVERT: f 15 ASP cc_start: 0.7965 (OUTLIER) cc_final: 0.7761 (m-30) REVERT: f 87 GLN cc_start: 0.7770 (tm-30) cc_final: 0.7417 (pp30) REVERT: g 28 ASN cc_start: 0.7929 (m110) cc_final: 0.7709 (m110) REVERT: i 67 THR cc_start: 0.4412 (t) cc_final: 0.4000 (p) REVERT: j 102 GLU cc_start: 0.7469 (tt0) cc_final: 0.7144 (tt0) REVERT: l 104 GLN cc_start: 0.7554 (mm110) cc_final: 0.7273 (mt0) REVERT: m 42 THR cc_start: 0.8929 (p) cc_final: 0.8720 (p) REVERT: m 111 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.7707 (tm-30) REVERT: m 136 MET cc_start: 0.5355 (ppp) cc_final: 0.4807 (ppp) REVERT: n 1 MET cc_start: 0.8111 (ptp) cc_final: 0.7904 (mtm) REVERT: n 18 GLN cc_start: 0.8326 (tm-30) cc_final: 0.8055 (tm-30) REVERT: n 107 ASN cc_start: 0.8286 (OUTLIER) cc_final: 0.7988 (t0) REVERT: o 3 LYS cc_start: 0.7587 (tmtt) cc_final: 0.7203 (tttt) REVERT: o 55 GLU cc_start: 0.8360 (mt-10) cc_final: 0.7861 (tp30) REVERT: o 62 LEU cc_start: 0.8049 (mt) cc_final: 0.7820 (tp) REVERT: o 88 LYS cc_start: 0.8253 (tttt) cc_final: 0.7941 (tptt) REVERT: p 23 ASP cc_start: 0.8185 (m-30) cc_final: 0.7966 (m-30) REVERT: p 114 ASN cc_start: 0.7608 (p0) cc_final: 0.7242 (p0) REVERT: q 31 TYR cc_start: 0.8583 (t80) cc_final: 0.8329 (t80) REVERT: q 48 ASP cc_start: 0.8189 (m-30) cc_final: 0.7922 (m-30) REVERT: r 46 GLU cc_start: 0.7349 (tm-30) cc_final: 0.7132 (tm-30) REVERT: s 11 ARG cc_start: 0.7268 (mmt-90) cc_final: 0.6922 (mmt-90) REVERT: s 52 GLU cc_start: 0.8536 (mt-10) cc_final: 0.8288 (mt-10) REVERT: t 1 MET cc_start: 0.5988 (ttt) cc_final: 0.4876 (tmm) REVERT: u 39 ASN cc_start: 0.8125 (t0) cc_final: 0.7700 (t0) REVERT: v 41 GLU cc_start: 0.7377 (OUTLIER) cc_final: 0.7155 (pp20) REVERT: v 75 GLN cc_start: 0.8964 (tp40) cc_final: 0.8661 (tp-100) REVERT: v 76 ASP cc_start: 0.7788 (OUTLIER) cc_final: 0.7466 (m-30) REVERT: y 30 MET cc_start: 0.8995 (mmp) cc_final: 0.8730 (mmm) REVERT: B 9 ARG cc_start: 0.8727 (ptp90) cc_final: 0.8214 (ptp90) REVERT: B 14 MET cc_start: 0.8174 (ptp) cc_final: 0.7679 (ptp) REVERT: C 24 LYS cc_start: 0.8620 (tptm) cc_final: 0.8214 (tppt) REVERT: C 36 LYS cc_start: 0.7814 (ttmt) cc_final: 0.7057 (ttpp) REVERT: E 28 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8460 (tt) REVERT: G 139 GLU cc_start: 0.9019 (OUTLIER) cc_final: 0.8574 (mp0) REVERT: G 167 HIS cc_start: 0.8633 (t-170) cc_final: 0.8022 (m90) REVERT: H 138 GLN cc_start: 0.8416 (tm-30) cc_final: 0.8093 (pp30) REVERT: H 141 MET cc_start: 0.6498 (mmm) cc_final: 0.6037 (mmm) REVERT: H 180 ASP cc_start: 0.6398 (m-30) cc_final: 0.5993 (m-30) REVERT: I 2 ARG cc_start: 0.3152 (mtp180) cc_final: 0.2929 (tpp-160) REVERT: I 73 ASN cc_start: 0.8473 (m-40) cc_final: 0.8222 (m-40) REVERT: I 104 MET cc_start: 0.1278 (mmt) cc_final: 0.0481 (mmt) REVERT: J 151 MET cc_start: 0.8596 (tpp) cc_final: 0.8089 (tpt) REVERT: K 40 GLU cc_start: 0.6209 (tt0) cc_final: 0.5556 (tt0) REVERT: K 61 LEU cc_start: 0.8579 (tp) cc_final: 0.8297 (tt) REVERT: K 75 GLU cc_start: 0.8807 (tt0) cc_final: 0.8586 (pt0) REVERT: K 88 MET cc_start: 0.7821 (ppp) cc_final: 0.7549 (ppp) REVERT: L 22 LEU cc_start: 0.8170 (mm) cc_final: 0.7204 (tp) REVERT: M 3 GLN cc_start: 0.7436 (OUTLIER) cc_final: 0.6057 (mp10) REVERT: M 51 GLU cc_start: 0.7693 (mt-10) cc_final: 0.7211 (tm-30) REVERT: P 73 VAL cc_start: 0.8973 (m) cc_final: 0.8566 (t) REVERT: P 84 MET cc_start: 0.6959 (ppp) cc_final: 0.6747 (ppp) REVERT: Q 85 ARG cc_start: 0.7036 (ptm160) cc_final: 0.6280 (ptp-110) REVERT: Q 94 TYR cc_start: 0.6615 (m-80) cc_final: 0.6111 (m-80) REVERT: Q 111 GLN cc_start: 0.7564 (mt0) cc_final: 0.6739 (pm20) REVERT: R 22 TYR cc_start: 0.7222 (t80) cc_final: 0.6542 (t80) REVERT: R 74 MET cc_start: 0.6426 (OUTLIER) cc_final: 0.6220 (mpp) REVERT: S 9 GLU cc_start: 0.7210 (tp30) cc_final: 0.6830 (tp30) REVERT: S 61 ASN cc_start: 0.7539 (OUTLIER) cc_final: 0.7133 (p0) REVERT: S 100 TRP cc_start: 0.6852 (p90) cc_final: 0.6547 (p90) REVERT: T 14 PHE cc_start: 0.6853 (OUTLIER) cc_final: 0.5979 (m-80) REVERT: V 61 ARG cc_start: 0.5628 (OUTLIER) cc_final: 0.4918 (mmm160) REVERT: V 73 THR cc_start: 0.5003 (OUTLIER) cc_final: 0.4769 (t) REVERT: W 53 GLN cc_start: 0.8835 (mt0) cc_final: 0.8415 (mt0) REVERT: W 72 ARG cc_start: 0.8559 (mmp-170) cc_final: 0.7491 (tmt-80) REVERT: X 77 ARG cc_start: 0.4860 (ptt-90) cc_final: 0.4564 (ptt-90) REVERT: Y 12 GLN cc_start: 0.8866 (tp40) cc_final: 0.8328 (tp40) REVERT: Y 47 GLN cc_start: 0.8549 (tp40) cc_final: 0.8174 (tp-100) REVERT: Y 53 MET cc_start: 0.8401 (ptp) cc_final: 0.7963 (ptp) REVERT: Y 73 ARG cc_start: 0.7849 (ttp-170) cc_final: 0.7636 (ttp-170) REVERT: Z 53 LYS cc_start: 0.9166 (ttpp) cc_final: 0.8745 (tptp) REVERT: 8 58 GLU cc_start: 0.8655 (OUTLIER) cc_final: 0.8247 (mp0) REVERT: 8 101 ARG cc_start: 0.7963 (ttm-80) cc_final: 0.6678 (mmt180) REVERT: 8 257 LEU cc_start: 0.7999 (tt) cc_final: 0.7741 (mm) REVERT: 8 461 MET cc_start: 0.7081 (mmp) cc_final: 0.6764 (mmm) REVERT: 8 648 GLU cc_start: 0.5344 (OUTLIER) cc_final: 0.5076 (mp0) outliers start: 272 outliers final: 152 residues processed: 1107 average time/residue: 1.2871 time to fit residues: 2518.2175 Evaluate side-chains 991 residues out of total 5429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 822 time to evaluate : 6.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 9 SER Chi-restraints excluded: chain b residue 53 ILE Chi-restraints excluded: chain b residue 69 ASN Chi-restraints excluded: chain b residue 155 ARG Chi-restraints excluded: chain b residue 258 SER Chi-restraints excluded: chain c residue 207 VAL Chi-restraints excluded: chain d residue 83 VAL Chi-restraints excluded: chain e residue 10 GLU Chi-restraints excluded: chain e residue 126 ASN Chi-restraints excluded: chain f residue 1 SER Chi-restraints excluded: chain f residue 15 ASP Chi-restraints excluded: chain f residue 70 LEU Chi-restraints excluded: chain f residue 100 ASN Chi-restraints excluded: chain f residue 126 THR Chi-restraints excluded: chain f residue 168 VAL Chi-restraints excluded: chain g residue 21 VAL Chi-restraints excluded: chain g residue 90 LEU Chi-restraints excluded: chain g residue 122 LEU Chi-restraints excluded: chain h residue 50 VAL Chi-restraints excluded: chain h residue 54 VAL Chi-restraints excluded: chain i residue 57 VAL Chi-restraints excluded: chain j residue 60 ASP Chi-restraints excluded: chain k residue 7 MET Chi-restraints excluded: chain k residue 42 THR Chi-restraints excluded: chain k residue 58 LEU Chi-restraints excluded: chain k residue 116 ILE Chi-restraints excluded: chain m residue 25 ASP Chi-restraints excluded: chain m residue 26 VAL Chi-restraints excluded: chain m residue 36 VAL Chi-restraints excluded: chain m residue 41 LEU Chi-restraints excluded: chain m residue 65 ILE Chi-restraints excluded: chain m residue 74 THR Chi-restraints excluded: chain m residue 91 TYR Chi-restraints excluded: chain m residue 111 GLU Chi-restraints excluded: chain m residue 124 LEU Chi-restraints excluded: chain m residue 134 THR Chi-restraints excluded: chain n residue 23 ASN Chi-restraints excluded: chain n residue 29 VAL Chi-restraints excluded: chain n residue 37 THR Chi-restraints excluded: chain n residue 76 VAL Chi-restraints excluded: chain n residue 107 ASN Chi-restraints excluded: chain n residue 116 VAL Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain o residue 28 VAL Chi-restraints excluded: chain o residue 54 VAL Chi-restraints excluded: chain o residue 60 GLU Chi-restraints excluded: chain o residue 106 LEU Chi-restraints excluded: chain p residue 31 VAL Chi-restraints excluded: chain p residue 79 VAL Chi-restraints excluded: chain p residue 109 ILE Chi-restraints excluded: chain q residue 17 LEU Chi-restraints excluded: chain q residue 52 ARG Chi-restraints excluded: chain r residue 19 THR Chi-restraints excluded: chain r residue 41 ILE Chi-restraints excluded: chain r residue 102 SER Chi-restraints excluded: chain s residue 4 ILE Chi-restraints excluded: chain s residue 55 ILE Chi-restraints excluded: chain s residue 66 ILE Chi-restraints excluded: chain s residue 67 ASP Chi-restraints excluded: chain t residue 11 LEU Chi-restraints excluded: chain t residue 39 THR Chi-restraints excluded: chain t residue 92 ASN Chi-restraints excluded: chain u residue 51 LEU Chi-restraints excluded: chain u residue 57 ILE Chi-restraints excluded: chain v residue 41 GLU Chi-restraints excluded: chain v residue 56 PHE Chi-restraints excluded: chain v residue 62 THR Chi-restraints excluded: chain v residue 63 ILE Chi-restraints excluded: chain v residue 64 VAL Chi-restraints excluded: chain v residue 76 ASP Chi-restraints excluded: chain w residue 17 LEU Chi-restraints excluded: chain w residue 71 LYS Chi-restraints excluded: chain x residue 57 VAL Chi-restraints excluded: chain z residue 34 THR Chi-restraints excluded: chain z residue 47 ILE Chi-restraints excluded: chain z residue 56 VAL Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 18 CYS Chi-restraints excluded: chain A residue 34 LEU 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 22 THR Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 44 GLN Chi-restraints excluded: chain C residue 45 HIS Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain G residue 21 TYR Chi-restraints excluded: chain G residue 30 ILE Chi-restraints excluded: chain G residue 139 GLU Chi-restraints excluded: chain G residue 198 VAL Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain I residue 4 LEU Chi-restraints excluded: chain I residue 29 THR Chi-restraints excluded: chain I residue 44 LYS Chi-restraints excluded: chain I residue 165 GLU Chi-restraints excluded: chain I residue 172 VAL Chi-restraints excluded: chain J residue 45 VAL Chi-restraints excluded: chain J residue 64 GLU Chi-restraints excluded: chain J residue 71 ILE Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain J residue 89 THR Chi-restraints excluded: chain J residue 160 VAL Chi-restraints excluded: chain K residue 11 HIS Chi-restraints excluded: chain K residue 70 VAL Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain L residue 100 MET Chi-restraints excluded: chain M residue 1 SER Chi-restraints excluded: chain M residue 3 GLN Chi-restraints excluded: chain M residue 73 SER Chi-restraints excluded: chain M residue 111 THR Chi-restraints excluded: chain N residue 29 ILE Chi-restraints excluded: chain N residue 38 PHE Chi-restraints excluded: chain N residue 65 THR Chi-restraints excluded: chain N residue 93 LEU Chi-restraints excluded: chain O residue 10 LEU Chi-restraints excluded: chain O residue 32 THR Chi-restraints excluded: chain O residue 67 ILE Chi-restraints excluded: chain O residue 98 VAL Chi-restraints excluded: chain P residue 15 VAL Chi-restraints excluded: chain P residue 45 THR Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain Q residue 34 THR Chi-restraints excluded: chain R residue 42 VAL Chi-restraints excluded: chain R residue 64 VAL Chi-restraints excluded: chain R residue 74 MET Chi-restraints excluded: chain R residue 88 LEU Chi-restraints excluded: chain S residue 61 ASN Chi-restraints excluded: chain T residue 10 ILE Chi-restraints excluded: chain T residue 14 PHE Chi-restraints excluded: chain T residue 48 ASP Chi-restraints excluded: chain T residue 55 LEU Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain V residue 8 GLN Chi-restraints excluded: chain V residue 24 ILE Chi-restraints excluded: chain V residue 32 ILE Chi-restraints excluded: chain V residue 49 ASN Chi-restraints excluded: chain V residue 61 ARG Chi-restraints excluded: chain V residue 73 THR Chi-restraints excluded: chain X residue 18 VAL Chi-restraints excluded: chain X residue 42 ASN Chi-restraints excluded: chain X residue 66 VAL Chi-restraints excluded: chain Y residue 11 ILE Chi-restraints excluded: chain Y residue 79 THR Chi-restraints excluded: chain a residue 217 THR Chi-restraints excluded: chain 8 residue 58 GLU Chi-restraints excluded: chain 8 residue 86 ILE Chi-restraints excluded: chain 8 residue 96 THR Chi-restraints excluded: chain 8 residue 105 VAL Chi-restraints excluded: chain 8 residue 154 VAL Chi-restraints excluded: chain 8 residue 200 VAL Chi-restraints excluded: chain 8 residue 244 THR Chi-restraints excluded: chain 8 residue 409 MET Chi-restraints excluded: chain 8 residue 420 VAL Chi-restraints excluded: chain 8 residue 488 VAL Chi-restraints excluded: chain 8 residue 499 THR Chi-restraints excluded: chain 8 residue 519 VAL Chi-restraints excluded: chain 8 residue 648 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1109 random chunks: chunk 996 optimal weight: 10.0000 chunk 758 optimal weight: 30.0000 chunk 523 optimal weight: 30.0000 chunk 111 optimal weight: 10.0000 chunk 481 optimal weight: 6.9990 chunk 677 optimal weight: 40.0000 chunk 1012 optimal weight: 20.0000 chunk 1071 optimal weight: 40.0000 chunk 529 optimal weight: 4.9990 chunk 959 optimal weight: 10.0000 chunk 288 optimal weight: 2.9990 overall best weight: 6.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 225 ASN ** c 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 43 GLN ** s 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 145 ASN ** L 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 75 GLN N 80 HIS P 100 ASN R 99 GLN ** U 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 51 GLN ** Y 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 69 ASN ** Y 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.3130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.100 166272 Z= 0.258 Angle : 0.658 26.557 247962 Z= 0.341 Chirality : 0.038 0.365 31576 Planarity : 0.005 0.074 13872 Dihedral : 23.249 179.405 81264 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 16.78 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.94 % Favored : 88.92 % Rotamer: Outliers : 5.38 % Allowed : 17.13 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.81 (0.10), residues: 6517 helix: -0.87 (0.11), residues: 2049 sheet: -1.76 (0.15), residues: 1076 loop : -2.59 (0.10), residues: 3392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP V 72 HIS 0.011 0.001 HIS r 12 PHE 0.046 0.002 PHE X 40 TYR 0.020 0.002 TYR I 64 ARG 0.006 0.001 ARG y 23 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13034 Ramachandran restraints generated. 6517 Oldfield, 0 Emsley, 6517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13034 Ramachandran restraints generated. 6517 Oldfield, 0 Emsley, 6517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1220 residues out of total 5429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 292 poor density : 928 time to evaluate : 6.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 65 ASP cc_start: 0.7825 (t70) cc_final: 0.7464 (t0) REVERT: b 167 ASP cc_start: 0.7745 (p0) cc_final: 0.7519 (p0) REVERT: c 11 MET cc_start: 0.8570 (tpt) cc_final: 0.8037 (tpt) REVERT: d 140 ASP cc_start: 0.8016 (m-30) cc_final: 0.7807 (m-30) REVERT: e 10 GLU cc_start: 0.8811 (OUTLIER) cc_final: 0.7740 (pp20) REVERT: e 34 THR cc_start: 0.8923 (m) cc_final: 0.8294 (p) REVERT: e 89 THR cc_start: 0.7630 (m) cc_final: 0.7426 (t) REVERT: e 126 ASN cc_start: 0.7784 (OUTLIER) cc_final: 0.7444 (p0) REVERT: f 172 GLU cc_start: 0.7710 (pm20) cc_final: 0.7460 (pm20) REVERT: i 67 THR cc_start: 0.4523 (t) cc_final: 0.4106 (p) REVERT: j 102 GLU cc_start: 0.7168 (tt0) cc_final: 0.6941 (tt0) REVERT: k 7 MET cc_start: 0.8113 (OUTLIER) cc_final: 0.7867 (mmp) REVERT: l 55 MET cc_start: 0.8579 (mmm) cc_final: 0.8318 (mmm) REVERT: m 42 THR cc_start: 0.8872 (p) cc_final: 0.8660 (p) REVERT: m 136 MET cc_start: 0.5312 (ppp) cc_final: 0.4736 (ppp) REVERT: n 18 GLN cc_start: 0.8431 (tm-30) cc_final: 0.8103 (tm-30) REVERT: n 72 ASP cc_start: 0.7804 (t0) cc_final: 0.7515 (t0) REVERT: o 3 LYS cc_start: 0.7453 (tmtt) cc_final: 0.7229 (tttt) REVERT: o 55 GLU cc_start: 0.8336 (mt-10) cc_final: 0.7781 (tp30) REVERT: o 88 LYS cc_start: 0.8234 (tttt) cc_final: 0.7929 (tptt) REVERT: p 114 ASN cc_start: 0.7645 (p0) cc_final: 0.7254 (p0) REVERT: q 48 ASP cc_start: 0.8173 (m-30) cc_final: 0.7910 (m-30) REVERT: r 34 GLU cc_start: 0.8136 (mm-30) cc_final: 0.7830 (tp30) REVERT: s 11 ARG cc_start: 0.7333 (mmt-90) cc_final: 0.6980 (mmt-90) REVERT: s 52 GLU cc_start: 0.8547 (mt-10) cc_final: 0.8306 (mt-10) REVERT: t 1 MET cc_start: 0.5387 (ttt) cc_final: 0.5074 (tmm) REVERT: t 59 ASN cc_start: 0.8677 (OUTLIER) cc_final: 0.8473 (t0) REVERT: u 39 ASN cc_start: 0.8134 (t0) cc_final: 0.7744 (t0) REVERT: v 57 TYR cc_start: 0.8739 (m-10) cc_final: 0.8415 (m-10) REVERT: v 59 GLU cc_start: 0.7375 (tm-30) cc_final: 0.7163 (tm-30) REVERT: v 75 GLN cc_start: 0.8965 (tp40) cc_final: 0.8694 (tp-100) REVERT: v 76 ASP cc_start: 0.7734 (OUTLIER) cc_final: 0.7467 (m-30) REVERT: w 40 LYS cc_start: 0.8728 (tppt) cc_final: 0.8504 (mmmm) REVERT: y 30 MET cc_start: 0.8940 (mmp) cc_final: 0.8706 (mmm) REVERT: y 39 GLN cc_start: 0.7773 (mt0) cc_final: 0.7315 (mp10) REVERT: z 7 THR cc_start: 0.8551 (OUTLIER) cc_final: 0.8333 (p) REVERT: B 9 ARG cc_start: 0.8717 (ptp90) cc_final: 0.8075 (ptp90) REVERT: C 36 LYS cc_start: 0.7753 (ttmt) cc_final: 0.7174 (ttpp) REVERT: D 3 ARG cc_start: 0.6732 (tpp-160) cc_final: 0.6179 (tpp80) REVERT: E 28 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8460 (tt) REVERT: F 16 ILE cc_start: 0.8773 (mm) cc_final: 0.8542 (mm) REVERT: G 14 HIS cc_start: 0.6062 (OUTLIER) cc_final: 0.5613 (p-80) REVERT: G 139 GLU cc_start: 0.8977 (OUTLIER) cc_final: 0.8642 (mt-10) REVERT: G 167 HIS cc_start: 0.8738 (t-170) cc_final: 0.7883 (m90) REVERT: H 111 ASP cc_start: 0.5122 (m-30) cc_final: 0.4596 (m-30) REVERT: H 138 GLN cc_start: 0.8488 (tm-30) cc_final: 0.8237 (pt0) REVERT: H 141 MET cc_start: 0.6532 (mmm) cc_final: 0.6071 (mmm) REVERT: H 180 ASP cc_start: 0.6332 (m-30) cc_final: 0.5946 (m-30) REVERT: I 2 ARG cc_start: 0.3047 (mtp180) cc_final: 0.1790 (tpp-160) REVERT: I 73 ASN cc_start: 0.8354 (m-40) cc_final: 0.8113 (m-40) REVERT: J 161 GLU cc_start: 0.8102 (pm20) cc_final: 0.7697 (pm20) REVERT: K 40 GLU cc_start: 0.6010 (tt0) cc_final: 0.5429 (tt0) REVERT: L 22 LEU cc_start: 0.8070 (mm) cc_final: 0.7082 (tp) REVERT: M 2 MET cc_start: 0.7635 (OUTLIER) cc_final: 0.7134 (tpt) REVERT: M 3 GLN cc_start: 0.7271 (OUTLIER) cc_final: 0.5976 (mp-120) REVERT: M 51 GLU cc_start: 0.7665 (mt-10) cc_final: 0.7214 (tm-30) REVERT: O 88 MET cc_start: 0.2128 (mmp) cc_final: 0.0550 (mtm) REVERT: Q 85 ARG cc_start: 0.6867 (ptm160) cc_final: 0.6391 (mtp85) REVERT: Q 94 TYR cc_start: 0.6779 (m-80) cc_final: 0.6368 (m-80) REVERT: R 22 TYR cc_start: 0.7233 (t80) cc_final: 0.6565 (t80) REVERT: R 65 GLU cc_start: 0.7220 (OUTLIER) cc_final: 0.6905 (tp30) REVERT: R 74 MET cc_start: 0.6328 (OUTLIER) cc_final: 0.6102 (mpp) REVERT: R 80 MET cc_start: 0.6951 (mmt) cc_final: 0.5938 (mmt) REVERT: S 9 GLU cc_start: 0.7233 (tp30) cc_final: 0.6878 (tp30) REVERT: S 61 ASN cc_start: 0.7429 (OUTLIER) cc_final: 0.7029 (p0) REVERT: S 100 TRP cc_start: 0.6873 (p90) cc_final: 0.6627 (p90) REVERT: T 14 PHE cc_start: 0.7082 (OUTLIER) cc_final: 0.6193 (m-80) REVERT: V 61 ARG cc_start: 0.5520 (OUTLIER) cc_final: 0.4689 (mmm160) REVERT: V 73 THR cc_start: 0.4727 (OUTLIER) cc_final: 0.4444 (t) REVERT: W 53 GLN cc_start: 0.8834 (mt0) cc_final: 0.8450 (mt0) REVERT: W 72 ARG cc_start: 0.8545 (mmp-170) cc_final: 0.7502 (tmt-80) REVERT: Y 53 MET cc_start: 0.8348 (ptp) cc_final: 0.8000 (ptp) REVERT: Y 73 ARG cc_start: 0.8040 (ttp-170) cc_final: 0.7806 (ttp-170) REVERT: Z 48 LYS cc_start: 0.6101 (mmtp) cc_final: 0.4875 (mmtm) REVERT: 8 204 TYR cc_start: 0.6851 (OUTLIER) cc_final: 0.5820 (t80) REVERT: 8 257 LEU cc_start: 0.8061 (tt) cc_final: 0.7770 (mm) REVERT: 8 422 PRO cc_start: 0.6981 (Cg_exo) cc_final: 0.6752 (Cg_endo) REVERT: 8 461 MET cc_start: 0.6925 (mmp) cc_final: 0.6704 (mmm) outliers start: 292 outliers final: 178 residues processed: 1107 average time/residue: 1.2749 time to fit residues: 2492.4322 Evaluate side-chains 1029 residues out of total 5429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 196 poor density : 833 time to evaluate : 6.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 8 THR Chi-restraints excluded: chain b residue 9 SER Chi-restraints excluded: chain b residue 53 ILE Chi-restraints excluded: chain b residue 69 ASN Chi-restraints excluded: chain b residue 76 VAL Chi-restraints excluded: chain b residue 93 VAL Chi-restraints excluded: chain b residue 133 ASN Chi-restraints excluded: chain b residue 134 ILE Chi-restraints excluded: chain b residue 155 ARG Chi-restraints excluded: chain b residue 227 VAL Chi-restraints excluded: chain b residue 258 SER Chi-restraints excluded: chain c residue 4 LEU Chi-restraints excluded: chain c residue 189 VAL Chi-restraints excluded: chain c residue 207 VAL Chi-restraints excluded: chain d residue 7 ASP Chi-restraints excluded: chain d residue 83 VAL Chi-restraints excluded: chain d residue 187 VAL Chi-restraints excluded: chain e residue 10 GLU Chi-restraints excluded: chain e residue 126 ASN Chi-restraints excluded: chain e residue 145 VAL Chi-restraints excluded: chain f residue 1 SER Chi-restraints excluded: chain f residue 70 LEU Chi-restraints excluded: chain f residue 89 VAL Chi-restraints excluded: chain f residue 100 ASN Chi-restraints excluded: chain f residue 152 ARG Chi-restraints excluded: chain g residue 21 VAL Chi-restraints excluded: chain g residue 80 ILE Chi-restraints excluded: chain g residue 90 LEU Chi-restraints excluded: chain g residue 122 LEU Chi-restraints excluded: chain h residue 50 VAL Chi-restraints excluded: chain h residue 54 VAL Chi-restraints excluded: chain j residue 60 ASP Chi-restraints excluded: chain j residue 91 GLU Chi-restraints excluded: chain k residue 7 MET Chi-restraints excluded: chain k residue 42 THR Chi-restraints excluded: chain k residue 58 LEU Chi-restraints excluded: chain k residue 121 GLU Chi-restraints excluded: chain m residue 26 VAL Chi-restraints excluded: chain m residue 36 VAL Chi-restraints excluded: chain m residue 65 ILE Chi-restraints excluded: chain m residue 74 THR Chi-restraints excluded: chain m residue 91 TYR Chi-restraints excluded: chain m residue 95 LEU Chi-restraints excluded: chain m residue 124 LEU Chi-restraints excluded: chain n residue 23 ASN Chi-restraints excluded: chain n residue 29 VAL Chi-restraints excluded: chain n residue 37 THR Chi-restraints excluded: chain n residue 76 VAL Chi-restraints excluded: chain o residue 2 ASP Chi-restraints excluded: chain o residue 28 VAL Chi-restraints excluded: chain o residue 53 THR Chi-restraints excluded: chain o residue 54 VAL Chi-restraints excluded: chain o residue 60 GLU Chi-restraints excluded: chain o residue 106 LEU Chi-restraints excluded: chain p residue 7 LEU Chi-restraints excluded: chain p residue 31 VAL Chi-restraints excluded: chain p residue 72 VAL Chi-restraints excluded: chain p residue 109 ILE Chi-restraints excluded: chain q residue 17 LEU Chi-restraints excluded: chain q residue 52 ARG Chi-restraints excluded: chain r residue 19 THR Chi-restraints excluded: chain r residue 27 ILE Chi-restraints excluded: chain r residue 41 ILE Chi-restraints excluded: chain r residue 59 ILE Chi-restraints excluded: chain r residue 102 SER Chi-restraints excluded: chain s residue 4 ILE Chi-restraints excluded: chain s residue 66 ILE Chi-restraints excluded: chain s residue 67 ASP Chi-restraints excluded: chain s residue 101 SER Chi-restraints excluded: chain t residue 11 LEU Chi-restraints excluded: chain t residue 39 THR Chi-restraints excluded: chain t residue 59 ASN Chi-restraints excluded: chain t residue 92 ASN Chi-restraints excluded: chain u residue 51 LEU Chi-restraints excluded: chain u residue 57 ILE Chi-restraints excluded: chain v residue 40 ILE Chi-restraints excluded: chain v residue 62 THR Chi-restraints excluded: chain v residue 66 ASP Chi-restraints excluded: chain v residue 76 ASP Chi-restraints excluded: chain w residue 17 LEU Chi-restraints excluded: chain w residue 71 LYS Chi-restraints excluded: chain x residue 12 VAL Chi-restraints excluded: chain x residue 46 VAL Chi-restraints excluded: chain y residue 55 THR Chi-restraints excluded: chain z residue 7 THR Chi-restraints excluded: chain z residue 34 THR Chi-restraints excluded: chain z residue 47 ILE Chi-restraints excluded: chain z residue 54 VAL Chi-restraints excluded: chain z residue 56 VAL Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 44 PHE 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 22 THR Chi-restraints excluded: chain C residue 45 HIS Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain G residue 14 HIS Chi-restraints excluded: chain G residue 21 TYR Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 139 GLU Chi-restraints excluded: chain G residue 152 ASP Chi-restraints excluded: chain G residue 198 VAL Chi-restraints excluded: chain G residue 203 ASP Chi-restraints excluded: chain H residue 17 TRP Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 84 GLU Chi-restraints excluded: chain I residue 4 LEU Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 44 LYS Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 92 LEU Chi-restraints excluded: chain I residue 158 LEU Chi-restraints excluded: chain I residue 165 GLU Chi-restraints excluded: chain J residue 15 ILE Chi-restraints excluded: chain J residue 45 VAL Chi-restraints excluded: chain J residue 64 GLU Chi-restraints excluded: chain J residue 71 ILE Chi-restraints excluded: chain J residue 89 THR Chi-restraints excluded: chain J residue 160 VAL Chi-restraints excluded: chain K residue 11 HIS Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 62 MET Chi-restraints excluded: chain K residue 64 VAL Chi-restraints excluded: chain K residue 70 VAL Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain L residue 100 MET Chi-restraints excluded: chain M residue 2 MET Chi-restraints excluded: chain M residue 3 GLN Chi-restraints excluded: chain M residue 112 ASP Chi-restraints excluded: chain M residue 125 ILE Chi-restraints excluded: chain N residue 29 ILE Chi-restraints excluded: chain N residue 38 PHE Chi-restraints excluded: chain N residue 63 TYR Chi-restraints excluded: chain N residue 65 THR Chi-restraints excluded: chain N residue 93 LEU Chi-restraints excluded: chain O residue 10 LEU Chi-restraints excluded: chain O residue 15 HIS Chi-restraints excluded: chain O residue 32 THR Chi-restraints excluded: chain O residue 44 THR Chi-restraints excluded: chain O residue 67 ILE Chi-restraints excluded: chain O residue 98 VAL Chi-restraints excluded: chain P residue 45 THR Chi-restraints excluded: chain P residue 109 ILE Chi-restraints excluded: chain Q residue 34 THR Chi-restraints excluded: chain R residue 64 VAL Chi-restraints excluded: chain R residue 65 GLU Chi-restraints excluded: chain R residue 74 MET Chi-restraints excluded: chain S residue 61 ASN Chi-restraints excluded: chain T residue 10 ILE Chi-restraints excluded: chain T residue 14 PHE Chi-restraints excluded: chain T residue 44 GLU Chi-restraints excluded: chain T residue 48 ASP Chi-restraints excluded: chain T residue 55 LEU Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain U residue 35 ARG Chi-restraints excluded: chain V residue 8 GLN Chi-restraints excluded: chain V residue 24 ILE Chi-restraints excluded: chain V residue 32 ILE Chi-restraints excluded: chain V residue 49 ASN Chi-restraints excluded: chain V residue 61 ARG Chi-restraints excluded: chain V residue 73 THR Chi-restraints excluded: chain W residue 64 LEU Chi-restraints excluded: chain X residue 66 VAL Chi-restraints excluded: chain Y residue 11 ILE Chi-restraints excluded: chain Y residue 14 GLU Chi-restraints excluded: chain Y residue 78 LEU Chi-restraints excluded: chain Y residue 79 THR Chi-restraints excluded: chain Z residue 32 ARG Chi-restraints excluded: chain 8 residue 30 ILE Chi-restraints excluded: chain 8 residue 58 GLU Chi-restraints excluded: chain 8 residue 96 THR Chi-restraints excluded: chain 8 residue 110 VAL Chi-restraints excluded: chain 8 residue 135 VAL Chi-restraints excluded: chain 8 residue 138 ILE Chi-restraints excluded: chain 8 residue 141 VAL Chi-restraints excluded: chain 8 residue 154 VAL Chi-restraints excluded: chain 8 residue 200 VAL Chi-restraints excluded: chain 8 residue 204 TYR Chi-restraints excluded: chain 8 residue 244 THR Chi-restraints excluded: chain 8 residue 409 MET Chi-restraints excluded: chain 8 residue 420 VAL Chi-restraints excluded: chain 8 residue 488 VAL Chi-restraints excluded: chain 8 residue 586 VAL Chi-restraints excluded: chain 8 residue 628 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1109 random chunks: chunk 892 optimal weight: 10.0000 chunk 608 optimal weight: 30.0000 chunk 15 optimal weight: 4.9990 chunk 798 optimal weight: 10.0000 chunk 442 optimal weight: 50.0000 chunk 914 optimal weight: 10.0000 chunk 740 optimal weight: 20.0000 chunk 1 optimal weight: 6.9990 chunk 547 optimal weight: 6.9990 chunk 962 optimal weight: 20.0000 chunk 270 optimal weight: 30.0000 overall best weight: 7.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 138 GLN m 3 GLN ** m 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 19 HIS ** y 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 58 ASN G 18 GLN G 167 HIS ** H 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 145 ASN J 147 ASN ** L 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 75 GLN ** T 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 74 HIS Y 81 GLN a 168 ASN ** 8 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.3436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 166272 Z= 0.283 Angle : 0.673 28.060 247962 Z= 0.347 Chirality : 0.039 0.288 31576 Planarity : 0.005 0.066 13872 Dihedral : 23.338 178.755 81258 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 18.06 Ramachandran Plot: Outliers : 0.15 % Allowed : 12.00 % Favored : 87.85 % Rotamer: Outliers : 5.65 % Allowed : 18.57 % Favored : 75.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.72 (0.10), residues: 6517 helix: -0.75 (0.11), residues: 2053 sheet: -1.78 (0.15), residues: 1111 loop : -2.53 (0.10), residues: 3353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP V 72 HIS 0.010 0.001 HIS r 12 PHE 0.035 0.002 PHE Z 36 TYR 0.024 0.002 TYR I 64 ARG 0.012 0.001 ARG h 56 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13034 Ramachandran restraints generated. 6517 Oldfield, 0 Emsley, 6517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13034 Ramachandran restraints generated. 6517 Oldfield, 0 Emsley, 6517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1196 residues out of total 5429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 307 poor density : 889 time to evaluate : 7.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 65 ASP cc_start: 0.7821 (t70) cc_final: 0.7458 (t0) REVERT: b 162 GLN cc_start: 0.8522 (mt0) cc_final: 0.8221 (mp10) REVERT: b 167 ASP cc_start: 0.7757 (p0) cc_final: 0.7521 (p0) REVERT: c 11 MET cc_start: 0.8574 (tpt) cc_final: 0.8178 (tpt) REVERT: d 136 GLN cc_start: 0.8583 (tp-100) cc_final: 0.7941 (tp-100) REVERT: d 140 ASP cc_start: 0.7909 (m-30) cc_final: 0.7528 (m-30) REVERT: e 10 GLU cc_start: 0.8825 (OUTLIER) cc_final: 0.7726 (pp20) REVERT: e 34 THR cc_start: 0.8932 (m) cc_final: 0.8343 (p) REVERT: e 89 THR cc_start: 0.7668 (m) cc_final: 0.7446 (t) REVERT: e 97 GLU cc_start: 0.8828 (tp30) cc_final: 0.8615 (tp30) REVERT: e 126 ASN cc_start: 0.7939 (OUTLIER) cc_final: 0.7585 (p0) REVERT: f 172 GLU cc_start: 0.7871 (pm20) cc_final: 0.7641 (pm20) REVERT: i 67 THR cc_start: 0.4507 (t) cc_final: 0.4101 (p) REVERT: k 7 MET cc_start: 0.8132 (OUTLIER) cc_final: 0.7851 (mmp) REVERT: m 42 THR cc_start: 0.8920 (p) cc_final: 0.8719 (p) REVERT: m 136 MET cc_start: 0.5556 (ppp) cc_final: 0.4931 (ppp) REVERT: n 18 GLN cc_start: 0.8446 (tm-30) cc_final: 0.8089 (tm-30) REVERT: n 72 ASP cc_start: 0.7831 (t0) cc_final: 0.7486 (t0) REVERT: o 55 GLU cc_start: 0.8248 (mt-10) cc_final: 0.7683 (tp30) REVERT: o 88 LYS cc_start: 0.8220 (tttt) cc_final: 0.7943 (tptt) REVERT: p 114 ASN cc_start: 0.7707 (p0) cc_final: 0.7336 (p0) REVERT: q 48 ASP cc_start: 0.8186 (m-30) cc_final: 0.7867 (m-30) REVERT: r 34 GLU cc_start: 0.8256 (mm-30) cc_final: 0.7858 (tp30) REVERT: r 40 MET cc_start: 0.8149 (tpp) cc_final: 0.7916 (mmp) REVERT: s 11 ARG cc_start: 0.7388 (mmt-90) cc_final: 0.7018 (mmt-90) REVERT: s 40 ASN cc_start: 0.6878 (t0) cc_final: 0.6532 (t0) REVERT: s 52 GLU cc_start: 0.8523 (mt-10) cc_final: 0.8267 (mt-10) REVERT: t 1 MET cc_start: 0.5342 (ttt) cc_final: 0.5053 (tmm) REVERT: v 57 TYR cc_start: 0.8693 (m-10) cc_final: 0.8487 (m-10) REVERT: v 75 GLN cc_start: 0.8967 (tp40) cc_final: 0.8665 (tp-100) REVERT: v 76 ASP cc_start: 0.7623 (OUTLIER) cc_final: 0.7280 (m-30) REVERT: w 62 LYS cc_start: 0.8635 (mtpp) cc_final: 0.8375 (mtmt) REVERT: y 39 GLN cc_start: 0.7831 (mt0) cc_final: 0.7336 (mp10) REVERT: z 7 THR cc_start: 0.8411 (OUTLIER) cc_final: 0.8184 (p) REVERT: z 36 GLU cc_start: 0.8015 (tt0) cc_final: 0.7651 (tm-30) REVERT: B 9 ARG cc_start: 0.8719 (ptp90) cc_final: 0.8070 (ptp90) REVERT: C 36 LYS cc_start: 0.7760 (ttmt) cc_final: 0.7256 (ttpp) REVERT: D 3 ARG cc_start: 0.6824 (tpp-160) cc_final: 0.6329 (tpp80) REVERT: E 28 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8501 (tt) REVERT: F 36 ARG cc_start: 0.8239 (OUTLIER) cc_final: 0.7748 (ptt90) REVERT: G 139 GLU cc_start: 0.8963 (OUTLIER) cc_final: 0.8610 (mt-10) REVERT: G 167 HIS cc_start: 0.8727 (t70) cc_final: 0.8193 (m-70) REVERT: G 204 ASP cc_start: 0.6473 (OUTLIER) cc_final: 0.6091 (p0) REVERT: H 111 ASP cc_start: 0.4920 (m-30) cc_final: 0.4390 (m-30) REVERT: H 138 GLN cc_start: 0.8556 (tm-30) cc_final: 0.8238 (pt0) REVERT: H 141 MET cc_start: 0.6526 (mmm) cc_final: 0.6005 (mmm) REVERT: H 180 ASP cc_start: 0.6340 (m-30) cc_final: 0.5966 (m-30) REVERT: I 59 LYS cc_start: 0.5285 (ttmt) cc_final: 0.4893 (tppt) REVERT: I 61 ARG cc_start: 0.5559 (mtp180) cc_final: 0.4838 (tmt-80) REVERT: I 73 ASN cc_start: 0.8549 (m-40) cc_final: 0.8331 (m-40) REVERT: J 13 LYS cc_start: 0.7871 (tppt) cc_final: 0.7614 (tppt) REVERT: J 115 GLU cc_start: 0.7900 (pp20) cc_final: 0.7489 (pp20) REVERT: K 40 GLU cc_start: 0.5941 (tt0) cc_final: 0.5342 (tt0) REVERT: K 77 THR cc_start: 0.8440 (p) cc_final: 0.7805 (p) REVERT: L 22 LEU cc_start: 0.7999 (mm) cc_final: 0.7043 (tp) REVERT: M 2 MET cc_start: 0.7594 (OUTLIER) cc_final: 0.7054 (tpt) REVERT: M 3 GLN cc_start: 0.7613 (OUTLIER) cc_final: 0.6163 (mp10) REVERT: M 51 GLU cc_start: 0.7608 (mt-10) cc_final: 0.7159 (tm-30) REVERT: Q 94 TYR cc_start: 0.6807 (m-80) cc_final: 0.6477 (m-80) REVERT: Q 111 GLN cc_start: 0.7566 (mt0) cc_final: 0.6756 (pm20) REVERT: S 9 GLU cc_start: 0.7260 (tp30) cc_final: 0.6913 (tp30) REVERT: S 61 ASN cc_start: 0.7389 (OUTLIER) cc_final: 0.6984 (p0) REVERT: S 100 TRP cc_start: 0.6807 (p90) cc_final: 0.6599 (p90) REVERT: T 14 PHE cc_start: 0.7056 (OUTLIER) cc_final: 0.6237 (m-80) REVERT: V 61 ARG cc_start: 0.5630 (OUTLIER) cc_final: 0.4712 (mmm160) REVERT: V 73 THR cc_start: 0.4638 (OUTLIER) cc_final: 0.4391 (t) REVERT: W 53 GLN cc_start: 0.8841 (mt0) cc_final: 0.8440 (mt0) REVERT: W 72 ARG cc_start: 0.8623 (mmp-170) cc_final: 0.7544 (tmt-80) REVERT: Y 12 GLN cc_start: 0.9021 (tp40) cc_final: 0.8675 (tp40) REVERT: Y 53 MET cc_start: 0.8344 (ptp) cc_final: 0.7979 (ptp) REVERT: 8 13 ILE cc_start: 0.8608 (pt) cc_final: 0.8379 (mp) REVERT: 8 58 GLU cc_start: 0.8683 (OUTLIER) cc_final: 0.8385 (pm20) REVERT: 8 101 ARG cc_start: 0.7995 (ttm-80) cc_final: 0.7271 (mtm-85) REVERT: 8 204 TYR cc_start: 0.6856 (OUTLIER) cc_final: 0.5770 (t80) REVERT: 8 257 LEU cc_start: 0.7956 (tt) cc_final: 0.7742 (mm) REVERT: 8 410 GLU cc_start: 0.1914 (OUTLIER) cc_final: 0.0406 (pm20) REVERT: 8 413 GLU cc_start: 0.7527 (mp0) cc_final: 0.6824 (mp0) REVERT: 8 422 PRO cc_start: 0.7017 (Cg_exo) cc_final: 0.6734 (Cg_endo) REVERT: 8 490 TYR cc_start: 0.7527 (m-80) cc_final: 0.7308 (m-10) REVERT: 8 660 LEU cc_start: 0.7284 (OUTLIER) cc_final: 0.7025 (tt) outliers start: 307 outliers final: 214 residues processed: 1090 average time/residue: 1.2654 time to fit residues: 2444.3262 Evaluate side-chains 1066 residues out of total 5429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 233 poor density : 833 time to evaluate : 6.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 8 THR Chi-restraints excluded: chain b residue 9 SER Chi-restraints excluded: chain b residue 53 ILE Chi-restraints excluded: chain b residue 69 ASN Chi-restraints excluded: chain b residue 76 VAL Chi-restraints excluded: chain b residue 134 ILE Chi-restraints excluded: chain b residue 227 VAL Chi-restraints excluded: chain b residue 258 SER Chi-restraints excluded: chain c residue 4 LEU Chi-restraints excluded: chain c residue 26 VAL Chi-restraints excluded: chain c residue 50 VAL Chi-restraints excluded: chain c residue 172 VAL Chi-restraints excluded: chain c residue 178 VAL Chi-restraints excluded: chain c residue 207 VAL Chi-restraints excluded: chain d residue 7 ASP Chi-restraints excluded: chain d residue 33 VAL Chi-restraints excluded: chain d residue 83 VAL Chi-restraints excluded: chain d residue 173 THR Chi-restraints excluded: chain e residue 10 GLU Chi-restraints excluded: chain e residue 126 ASN Chi-restraints excluded: chain e residue 145 VAL Chi-restraints excluded: chain e residue 162 ASP Chi-restraints excluded: chain f residue 1 SER Chi-restraints excluded: chain f residue 18 ILE Chi-restraints excluded: chain f residue 70 LEU Chi-restraints excluded: chain f residue 100 ASN Chi-restraints excluded: chain f residue 126 THR Chi-restraints excluded: chain g residue 2 GLN Chi-restraints excluded: chain g residue 21 VAL Chi-restraints excluded: chain g residue 80 ILE Chi-restraints excluded: chain g residue 90 LEU Chi-restraints excluded: chain g residue 122 LEU Chi-restraints excluded: chain h residue 35 VAL Chi-restraints excluded: chain h residue 50 VAL Chi-restraints excluded: chain h residue 54 VAL Chi-restraints excluded: chain h residue 65 GLU Chi-restraints excluded: chain i residue 57 VAL Chi-restraints excluded: chain j residue 60 ASP Chi-restraints excluded: chain j residue 91 GLU Chi-restraints excluded: chain j residue 138 GLN Chi-restraints excluded: chain k residue 7 MET Chi-restraints excluded: chain k residue 42 THR Chi-restraints excluded: chain k residue 58 LEU Chi-restraints excluded: chain k residue 90 ASN Chi-restraints excluded: chain m residue 26 VAL Chi-restraints excluded: chain m residue 36 VAL Chi-restraints excluded: chain m residue 65 ILE Chi-restraints excluded: chain m residue 74 THR Chi-restraints excluded: chain m residue 91 TYR Chi-restraints excluded: chain m residue 95 LEU Chi-restraints excluded: chain m residue 124 LEU Chi-restraints excluded: chain n residue 23 ASN Chi-restraints excluded: chain n residue 24 MET Chi-restraints excluded: chain n residue 29 VAL Chi-restraints excluded: chain n residue 37 THR Chi-restraints excluded: chain n residue 53 THR Chi-restraints excluded: chain n residue 76 VAL Chi-restraints excluded: chain n residue 97 ILE Chi-restraints excluded: chain n residue 116 VAL Chi-restraints excluded: chain o residue 2 ASP Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain o residue 28 VAL Chi-restraints excluded: chain o residue 53 THR Chi-restraints excluded: chain o residue 60 GLU Chi-restraints excluded: chain p residue 7 LEU Chi-restraints excluded: chain p residue 31 VAL Chi-restraints excluded: chain p residue 72 VAL Chi-restraints excluded: chain p residue 79 VAL Chi-restraints excluded: chain p residue 109 ILE Chi-restraints excluded: chain q residue 17 LEU Chi-restraints excluded: chain q residue 52 ARG Chi-restraints excluded: chain r residue 19 THR Chi-restraints excluded: chain r residue 27 ILE Chi-restraints excluded: chain r residue 41 ILE Chi-restraints excluded: chain r residue 58 VAL Chi-restraints excluded: chain r residue 59 ILE Chi-restraints excluded: chain r residue 98 ILE Chi-restraints excluded: chain r residue 102 SER Chi-restraints excluded: chain s residue 4 ILE Chi-restraints excluded: chain s residue 55 ILE Chi-restraints excluded: chain s residue 66 ILE Chi-restraints excluded: chain s residue 67 ASP Chi-restraints excluded: chain s residue 101 SER Chi-restraints excluded: chain t residue 11 LEU Chi-restraints excluded: chain t residue 32 LEU Chi-restraints excluded: chain t residue 39 THR Chi-restraints excluded: chain t residue 92 ASN Chi-restraints excluded: chain u residue 11 ILE Chi-restraints excluded: chain u residue 51 LEU Chi-restraints excluded: chain u residue 57 ILE Chi-restraints excluded: chain v residue 40 ILE Chi-restraints excluded: chain v residue 56 PHE Chi-restraints excluded: chain v residue 62 THR Chi-restraints excluded: chain v residue 66 ASP Chi-restraints excluded: chain v residue 76 ASP Chi-restraints excluded: chain w residue 17 LEU Chi-restraints excluded: chain w residue 71 LYS Chi-restraints excluded: chain w residue 76 ILE Chi-restraints excluded: chain x residue 12 VAL Chi-restraints excluded: chain y residue 16 THR Chi-restraints excluded: chain z residue 7 THR Chi-restraints excluded: chain z residue 34 THR Chi-restraints excluded: chain z residue 47 ILE Chi-restraints excluded: chain z residue 56 VAL Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 18 CYS Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 44 PHE Chi-restraints excluded: chain A residue 57 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 22 THR Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 44 GLN Chi-restraints excluded: chain C residue 45 HIS Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 25 LYS Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain F residue 36 ARG Chi-restraints excluded: chain G residue 21 TYR Chi-restraints excluded: chain G residue 29 PHE Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 139 GLU Chi-restraints excluded: chain G residue 152 ASP Chi-restraints excluded: chain G residue 198 VAL Chi-restraints excluded: chain G residue 203 ASP Chi-restraints excluded: chain G residue 204 ASP Chi-restraints excluded: chain H residue 17 TRP Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 68 HIS Chi-restraints excluded: chain H residue 84 GLU Chi-restraints excluded: chain I residue 4 LEU Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 44 LYS Chi-restraints excluded: chain I residue 92 LEU Chi-restraints excluded: chain I residue 158 LEU Chi-restraints excluded: chain I residue 165 GLU Chi-restraints excluded: chain J residue 45 VAL Chi-restraints excluded: chain J residue 64 GLU Chi-restraints excluded: chain J residue 71 ILE Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain J residue 89 THR Chi-restraints excluded: chain J residue 160 VAL Chi-restraints excluded: chain K residue 11 HIS Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 62 MET Chi-restraints excluded: chain K residue 70 VAL Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain L residue 11 ILE Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain L residue 100 MET Chi-restraints excluded: chain M residue 2 MET Chi-restraints excluded: chain M residue 3 GLN Chi-restraints excluded: chain M residue 45 ILE Chi-restraints excluded: chain M residue 73 SER Chi-restraints excluded: chain M residue 111 THR Chi-restraints excluded: chain M residue 125 ILE Chi-restraints excluded: chain N residue 29 ILE Chi-restraints excluded: chain N residue 38 PHE Chi-restraints excluded: chain N residue 63 TYR Chi-restraints excluded: chain N residue 65 THR Chi-restraints excluded: chain N residue 93 LEU Chi-restraints excluded: chain O residue 32 THR Chi-restraints excluded: chain O residue 44 THR Chi-restraints excluded: chain O residue 67 ILE Chi-restraints excluded: chain O residue 98 VAL Chi-restraints excluded: chain P residue 15 VAL Chi-restraints excluded: chain P residue 45 THR Chi-restraints excluded: chain P residue 95 THR Chi-restraints excluded: chain P residue 109 ILE Chi-restraints excluded: chain Q residue 34 THR Chi-restraints excluded: chain R residue 64 VAL Chi-restraints excluded: chain S residue 44 VAL Chi-restraints excluded: chain S residue 61 ASN Chi-restraints excluded: chain T residue 10 ILE Chi-restraints excluded: chain T residue 13 GLU Chi-restraints excluded: chain T residue 14 PHE Chi-restraints excluded: chain T residue 44 GLU Chi-restraints excluded: chain T residue 48 ASP Chi-restraints excluded: chain T residue 55 LEU Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain U residue 34 GLU Chi-restraints excluded: chain U residue 35 ARG Chi-restraints excluded: chain V residue 8 GLN Chi-restraints excluded: chain V residue 24 ILE Chi-restraints excluded: chain V residue 32 ILE Chi-restraints excluded: chain V residue 49 ASN Chi-restraints excluded: chain V residue 56 ASP Chi-restraints excluded: chain V residue 61 ARG Chi-restraints excluded: chain V residue 73 THR Chi-restraints excluded: chain W residue 64 LEU Chi-restraints excluded: chain X residue 66 VAL Chi-restraints excluded: chain Y residue 11 ILE Chi-restraints excluded: chain Y residue 78 LEU Chi-restraints excluded: chain Y residue 79 THR Chi-restraints excluded: chain Z residue 5 VAL Chi-restraints excluded: chain Z residue 12 ASP Chi-restraints excluded: chain Z residue 32 ARG Chi-restraints excluded: chain Z residue 52 VAL Chi-restraints excluded: chain 8 residue 58 GLU Chi-restraints excluded: chain 8 residue 86 ILE Chi-restraints excluded: chain 8 residue 96 THR Chi-restraints excluded: chain 8 residue 105 VAL Chi-restraints excluded: chain 8 residue 135 VAL Chi-restraints excluded: chain 8 residue 138 ILE Chi-restraints excluded: chain 8 residue 141 VAL Chi-restraints excluded: chain 8 residue 154 VAL Chi-restraints excluded: chain 8 residue 200 VAL Chi-restraints excluded: chain 8 residue 204 TYR Chi-restraints excluded: chain 8 residue 244 THR Chi-restraints excluded: chain 8 residue 366 MET Chi-restraints excluded: chain 8 residue 409 MET Chi-restraints excluded: chain 8 residue 410 GLU Chi-restraints excluded: chain 8 residue 420 VAL Chi-restraints excluded: chain 8 residue 488 VAL Chi-restraints excluded: chain 8 residue 499 THR Chi-restraints excluded: chain 8 residue 519 VAL Chi-restraints excluded: chain 8 residue 586 VAL Chi-restraints excluded: chain 8 residue 628 THR Chi-restraints excluded: chain 8 residue 660 LEU Chi-restraints excluded: chain 8 residue 698 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1109 random chunks: chunk 360 optimal weight: 8.9990 chunk 965 optimal weight: 20.0000 chunk 211 optimal weight: 0.6980 chunk 629 optimal weight: 20.0000 chunk 264 optimal weight: 6.9990 chunk 1073 optimal weight: 7.9990 chunk 890 optimal weight: 10.0000 chunk 496 optimal weight: 30.0000 chunk 89 optimal weight: 9.9990 chunk 354 optimal weight: 9.9990 chunk 563 optimal weight: 0.0370 overall best weight: 4.9464 ------------------------------------------------------------------------------- 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 26 GLN ** f 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 57 ASN n 31 HIS ** n 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 9 HIS ** s 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 39 ASN ** v 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 145 ASN ** L 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 75 GLN N 4 GLN ** U 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 30 HIS ** W 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 74 HIS a 168 ASN ** 8 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 259 ASN ** 8 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.3649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 166272 Z= 0.199 Angle : 0.615 26.300 247962 Z= 0.318 Chirality : 0.036 0.344 31576 Planarity : 0.005 0.069 13872 Dihedral : 23.337 177.868 81256 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 16.04 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.36 % Favored : 89.52 % Rotamer: Outliers : 4.95 % Allowed : 20.52 % Favored : 74.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.47 (0.10), residues: 6517 helix: -0.43 (0.11), residues: 2050 sheet: -1.70 (0.15), residues: 1067 loop : -2.45 (0.10), residues: 3400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP V 72 HIS 0.009 0.001 HIS j 80 PHE 0.031 0.002 PHE Z 36 TYR 0.020 0.002 TYR C 48 ARG 0.016 0.001 ARG Y 73 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13034 Ramachandran restraints generated. 6517 Oldfield, 0 Emsley, 6517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13034 Ramachandran restraints generated. 6517 Oldfield, 0 Emsley, 6517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1173 residues out of total 5429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 269 poor density : 904 time to evaluate : 6.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 65 ASP cc_start: 0.7801 (t70) cc_final: 0.7439 (t0) REVERT: b 167 ASP cc_start: 0.7732 (p0) cc_final: 0.7517 (p0) REVERT: c 187 LEU cc_start: 0.8287 (tp) cc_final: 0.7935 (tp) REVERT: d 136 GLN cc_start: 0.8539 (tp-100) cc_final: 0.8005 (tp40) REVERT: d 140 ASP cc_start: 0.7852 (m-30) cc_final: 0.7597 (m-30) REVERT: e 34 THR cc_start: 0.8985 (m) cc_final: 0.8331 (p) REVERT: e 89 THR cc_start: 0.7584 (m) cc_final: 0.7382 (t) REVERT: e 126 ASN cc_start: 0.8005 (OUTLIER) cc_final: 0.7601 (p0) REVERT: f 172 GLU cc_start: 0.7925 (pm20) cc_final: 0.7697 (pm20) REVERT: i 35 MET cc_start: 0.1824 (ppp) cc_final: 0.1601 (ppp) REVERT: j 102 GLU cc_start: 0.7471 (tt0) cc_final: 0.7233 (tt0) REVERT: m 42 THR cc_start: 0.8894 (p) cc_final: 0.8673 (p) REVERT: m 136 MET cc_start: 0.5588 (ppp) cc_final: 0.4992 (ppp) REVERT: n 18 GLN cc_start: 0.8465 (tm-30) cc_final: 0.8067 (tm-30) REVERT: n 54 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8726 (mp) REVERT: n 72 ASP cc_start: 0.7709 (t0) cc_final: 0.7267 (t0) REVERT: n 110 MET cc_start: 0.8161 (mmt) cc_final: 0.7857 (tpp) REVERT: o 55 GLU cc_start: 0.8166 (mt-10) cc_final: 0.7611 (tp30) REVERT: o 88 LYS cc_start: 0.8234 (tttt) cc_final: 0.8030 (tptp) REVERT: p 114 ASN cc_start: 0.7684 (p0) cc_final: 0.7307 (p0) REVERT: q 48 ASP cc_start: 0.8193 (m-30) cc_final: 0.7930 (m-30) REVERT: r 34 GLU cc_start: 0.8232 (mm-30) cc_final: 0.7850 (tp30) REVERT: s 11 ARG cc_start: 0.7380 (mmt-90) cc_final: 0.7059 (mmt-90) REVERT: s 52 GLU cc_start: 0.8603 (mt-10) cc_final: 0.8403 (mt-10) REVERT: v 75 GLN cc_start: 0.8948 (tp40) cc_final: 0.8703 (tp-100) REVERT: y 39 GLN cc_start: 0.7682 (mt0) cc_final: 0.7461 (mp10) REVERT: y 49 ASP cc_start: 0.8133 (p0) cc_final: 0.7901 (p0) REVERT: y 58 ASN cc_start: 0.8348 (t160) cc_final: 0.8128 (t0) REVERT: z 7 THR cc_start: 0.8445 (OUTLIER) cc_final: 0.8215 (p) REVERT: z 36 GLU cc_start: 0.8146 (tt0) cc_final: 0.7862 (tm-30) REVERT: A 53 THR cc_start: 0.5295 (p) cc_final: 0.4979 (p) REVERT: B 9 ARG cc_start: 0.8717 (ptp90) cc_final: 0.8117 (ptp90) REVERT: C 36 LYS cc_start: 0.7653 (ttmt) cc_final: 0.7120 (ttpp) REVERT: E 5 THR cc_start: 0.9081 (OUTLIER) cc_final: 0.8678 (p) REVERT: E 28 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8435 (tt) REVERT: F 34 LYS cc_start: 0.9138 (ttmt) cc_final: 0.8785 (ttpt) REVERT: G 14 HIS cc_start: 0.6044 (OUTLIER) cc_final: 0.5745 (p-80) REVERT: G 139 GLU cc_start: 0.8949 (OUTLIER) cc_final: 0.8608 (mt-10) REVERT: H 111 ASP cc_start: 0.4829 (m-30) cc_final: 0.4328 (m-30) REVERT: H 138 GLN cc_start: 0.8527 (tm-30) cc_final: 0.8219 (pt0) REVERT: H 141 MET cc_start: 0.6284 (mmm) cc_final: 0.5857 (mmm) REVERT: H 180 ASP cc_start: 0.6346 (m-30) cc_final: 0.5973 (m-30) REVERT: H 186 SER cc_start: 0.5485 (m) cc_final: 0.5249 (m) REVERT: I 61 ARG cc_start: 0.5460 (mtp180) cc_final: 0.4887 (tmt-80) REVERT: I 66 VAL cc_start: 0.1130 (OUTLIER) cc_final: 0.0860 (t) REVERT: I 73 ASN cc_start: 0.8480 (m-40) cc_final: 0.8191 (m-40) REVERT: I 177 MET cc_start: -0.4410 (mtt) cc_final: -0.4615 (mtt) REVERT: J 115 GLU cc_start: 0.7900 (pp20) cc_final: 0.7495 (pp20) REVERT: K 84 VAL cc_start: 0.8805 (OUTLIER) cc_final: 0.8599 (p) REVERT: L 22 LEU cc_start: 0.7995 (mm) cc_final: 0.7050 (tp) REVERT: M 2 MET cc_start: 0.7512 (OUTLIER) cc_final: 0.6895 (tpt) REVERT: M 3 GLN cc_start: 0.7513 (OUTLIER) cc_final: 0.6019 (mp10) REVERT: M 51 GLU cc_start: 0.7494 (mt-10) cc_final: 0.7172 (tm-30) REVERT: O 68 ARG cc_start: 0.7311 (mtt180) cc_final: 0.7021 (mmt180) REVERT: O 88 MET cc_start: 0.2199 (mmp) cc_final: 0.0555 (mtm) REVERT: Q 94 TYR cc_start: 0.6711 (m-80) cc_final: 0.6302 (m-80) REVERT: R 22 TYR cc_start: 0.7437 (t80) cc_final: 0.6481 (t80) REVERT: R 65 GLU cc_start: 0.7273 (OUTLIER) cc_final: 0.6147 (pt0) REVERT: R 74 MET cc_start: 0.6595 (mpp) cc_final: 0.6057 (mpp) REVERT: R 80 MET cc_start: 0.6991 (mmt) cc_final: 0.6010 (mmt) REVERT: S 9 GLU cc_start: 0.7301 (tp30) cc_final: 0.6982 (tp30) REVERT: S 61 ASN cc_start: 0.7482 (OUTLIER) cc_final: 0.7122 (p0) REVERT: S 100 TRP cc_start: 0.6776 (p90) cc_final: 0.6560 (p90) REVERT: T 14 PHE cc_start: 0.7028 (OUTLIER) cc_final: 0.6263 (m-80) REVERT: V 61 ARG cc_start: 0.5732 (OUTLIER) cc_final: 0.4708 (mmm160) REVERT: V 73 THR cc_start: 0.4464 (OUTLIER) cc_final: 0.4215 (t) REVERT: W 53 GLN cc_start: 0.8844 (mt0) cc_final: 0.8462 (mt0) REVERT: W 72 ARG cc_start: 0.8614 (mmp-170) cc_final: 0.7558 (tmt-80) REVERT: X 65 MET cc_start: 0.8045 (tpt) cc_final: 0.7532 (tpt) REVERT: Y 53 MET cc_start: 0.8253 (ptp) cc_final: 0.7996 (ptp) REVERT: 8 72 TRP cc_start: 0.6441 (t-100) cc_final: 0.6120 (t-100) REVERT: 8 111 MET cc_start: 0.6742 (mmt) cc_final: 0.6519 (mmt) REVERT: 8 204 TYR cc_start: 0.6951 (OUTLIER) cc_final: 0.5628 (t80) REVERT: 8 257 LEU cc_start: 0.8021 (tt) cc_final: 0.7783 (mm) REVERT: 8 279 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.8202 (mt) REVERT: 8 410 GLU cc_start: 0.1818 (OUTLIER) cc_final: 0.0417 (pm20) REVERT: 8 490 TYR cc_start: 0.7496 (m-10) cc_final: 0.7241 (m-10) outliers start: 269 outliers final: 183 residues processed: 1071 average time/residue: 1.2503 time to fit residues: 2379.6900 Evaluate side-chains 1033 residues out of total 5429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 202 poor density : 831 time to evaluate : 6.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 9 SER Chi-restraints excluded: chain b residue 53 ILE Chi-restraints excluded: chain b residue 69 ASN Chi-restraints excluded: chain b residue 93 VAL Chi-restraints excluded: chain b residue 134 ILE Chi-restraints excluded: chain b residue 227 VAL Chi-restraints excluded: chain c residue 189 VAL Chi-restraints excluded: chain d residue 7 ASP Chi-restraints excluded: chain d residue 83 VAL Chi-restraints excluded: chain d residue 173 THR Chi-restraints excluded: chain e residue 73 VAL Chi-restraints excluded: chain e residue 126 ASN Chi-restraints excluded: chain e residue 145 VAL Chi-restraints excluded: chain e residue 176 PHE Chi-restraints excluded: chain f residue 1 SER Chi-restraints excluded: chain f residue 18 ILE Chi-restraints excluded: chain f residue 70 LEU Chi-restraints excluded: chain f residue 91 VAL Chi-restraints excluded: chain f residue 100 ASN Chi-restraints excluded: chain f residue 126 THR Chi-restraints excluded: chain g residue 2 GLN Chi-restraints excluded: chain g residue 21 VAL Chi-restraints excluded: chain g residue 90 LEU Chi-restraints excluded: chain g residue 122 LEU Chi-restraints excluded: chain h residue 50 VAL Chi-restraints excluded: chain h residue 65 GLU Chi-restraints excluded: chain i residue 54 ILE Chi-restraints excluded: chain i residue 57 VAL Chi-restraints excluded: chain j residue 60 ASP Chi-restraints excluded: chain j residue 91 GLU Chi-restraints excluded: chain k residue 7 MET Chi-restraints excluded: chain k residue 53 LYS Chi-restraints excluded: chain k residue 58 LEU Chi-restraints excluded: chain k residue 90 ASN Chi-restraints excluded: chain k residue 121 GLU Chi-restraints excluded: chain l residue 5 THR Chi-restraints excluded: chain l residue 92 LEU Chi-restraints excluded: chain l residue 93 ASN Chi-restraints excluded: chain m residue 26 VAL Chi-restraints excluded: chain m residue 36 VAL Chi-restraints excluded: chain m residue 65 ILE Chi-restraints excluded: chain m residue 74 THR Chi-restraints excluded: chain m residue 91 TYR Chi-restraints excluded: chain m residue 95 LEU Chi-restraints excluded: chain m residue 124 LEU Chi-restraints excluded: chain n residue 23 ASN Chi-restraints excluded: chain n residue 24 MET Chi-restraints excluded: chain n residue 29 VAL Chi-restraints excluded: chain n residue 37 THR Chi-restraints excluded: chain n residue 54 LEU Chi-restraints excluded: chain o residue 2 ASP Chi-restraints excluded: chain o residue 28 VAL Chi-restraints excluded: chain o residue 53 THR Chi-restraints excluded: chain o residue 54 VAL Chi-restraints excluded: chain o residue 60 GLU Chi-restraints excluded: chain o residue 106 LEU Chi-restraints excluded: chain p residue 31 VAL Chi-restraints excluded: chain p residue 109 ILE Chi-restraints excluded: chain q residue 17 LEU Chi-restraints excluded: chain q residue 52 ARG Chi-restraints excluded: chain r residue 27 ILE Chi-restraints excluded: chain r residue 41 ILE Chi-restraints excluded: chain r residue 58 VAL Chi-restraints excluded: chain r residue 59 ILE Chi-restraints excluded: chain r residue 98 ILE Chi-restraints excluded: chain r residue 99 THR Chi-restraints excluded: chain r residue 102 SER Chi-restraints excluded: chain s residue 4 ILE Chi-restraints excluded: chain s residue 66 ILE Chi-restraints excluded: chain s residue 67 ASP Chi-restraints excluded: chain s residue 101 SER Chi-restraints excluded: chain t residue 11 LEU Chi-restraints excluded: chain t residue 32 LEU Chi-restraints excluded: chain t residue 92 ASN Chi-restraints excluded: chain v residue 40 ILE Chi-restraints excluded: chain v residue 62 THR Chi-restraints excluded: chain w residue 71 LYS Chi-restraints excluded: chain w residue 76 ILE Chi-restraints excluded: chain x residue 12 VAL Chi-restraints excluded: chain z residue 7 THR Chi-restraints excluded: chain z residue 47 ILE Chi-restraints excluded: chain z residue 54 VAL Chi-restraints excluded: chain z residue 56 VAL Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 18 CYS Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 44 PHE Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 44 GLN Chi-restraints excluded: chain C residue 45 HIS Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 25 LYS Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain G residue 14 HIS Chi-restraints excluded: chain G residue 21 TYR Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 139 GLU Chi-restraints excluded: chain G residue 152 ASP Chi-restraints excluded: chain G residue 198 VAL Chi-restraints excluded: chain G residue 203 ASP Chi-restraints excluded: chain H residue 17 TRP Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 68 HIS Chi-restraints excluded: chain H residue 84 GLU Chi-restraints excluded: chain I residue 4 LEU Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 66 VAL Chi-restraints excluded: chain I residue 92 LEU Chi-restraints excluded: chain I residue 165 GLU Chi-restraints excluded: chain J residue 45 VAL Chi-restraints excluded: chain J residue 64 GLU Chi-restraints excluded: chain J residue 71 ILE Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain J residue 89 THR Chi-restraints excluded: chain J residue 145 ASN Chi-restraints excluded: chain J residue 160 VAL Chi-restraints excluded: chain K residue 11 HIS Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 62 MET Chi-restraints excluded: chain K residue 70 VAL Chi-restraints excluded: chain K residue 84 VAL Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain M residue 2 MET Chi-restraints excluded: chain M residue 3 GLN Chi-restraints excluded: chain M residue 45 ILE Chi-restraints excluded: chain M residue 61 THR Chi-restraints excluded: chain M residue 73 SER Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain M residue 111 THR Chi-restraints excluded: chain N residue 29 ILE Chi-restraints excluded: chain N residue 38 PHE Chi-restraints excluded: chain N residue 63 TYR Chi-restraints excluded: chain N residue 65 THR Chi-restraints excluded: chain N residue 93 LEU Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain O residue 15 HIS Chi-restraints excluded: chain O residue 44 THR Chi-restraints excluded: chain O residue 98 VAL Chi-restraints excluded: chain P residue 45 THR Chi-restraints excluded: chain P residue 95 THR Chi-restraints excluded: chain P residue 109 ILE Chi-restraints excluded: chain P residue 112 VAL Chi-restraints excluded: chain Q residue 34 THR Chi-restraints excluded: chain Q residue 54 VAL Chi-restraints excluded: chain R residue 64 VAL Chi-restraints excluded: chain R residue 65 GLU Chi-restraints excluded: chain S residue 44 VAL Chi-restraints excluded: chain S residue 61 ASN Chi-restraints excluded: chain T residue 10 ILE Chi-restraints excluded: chain T residue 14 PHE Chi-restraints excluded: chain T residue 44 GLU Chi-restraints excluded: chain T residue 48 ASP Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain U residue 34 GLU Chi-restraints excluded: chain V residue 8 GLN Chi-restraints excluded: chain V residue 12 VAL Chi-restraints excluded: chain V residue 24 ILE Chi-restraints excluded: chain V residue 32 ILE Chi-restraints excluded: chain V residue 49 ASN Chi-restraints excluded: chain V residue 56 ASP Chi-restraints excluded: chain V residue 61 ARG Chi-restraints excluded: chain V residue 73 THR Chi-restraints excluded: chain W residue 64 LEU Chi-restraints excluded: chain X residue 66 VAL Chi-restraints excluded: chain Y residue 11 ILE Chi-restraints excluded: chain Y residue 78 LEU Chi-restraints excluded: chain Y residue 79 THR Chi-restraints excluded: chain Z residue 5 VAL Chi-restraints excluded: chain Z residue 12 ASP Chi-restraints excluded: chain Z residue 32 ARG Chi-restraints excluded: chain 8 residue 58 GLU Chi-restraints excluded: chain 8 residue 96 THR Chi-restraints excluded: chain 8 residue 110 VAL Chi-restraints excluded: chain 8 residue 135 VAL Chi-restraints excluded: chain 8 residue 138 ILE Chi-restraints excluded: chain 8 residue 141 VAL Chi-restraints excluded: chain 8 residue 154 VAL Chi-restraints excluded: chain 8 residue 200 VAL Chi-restraints excluded: chain 8 residue 204 TYR Chi-restraints excluded: chain 8 residue 244 THR Chi-restraints excluded: chain 8 residue 279 LEU Chi-restraints excluded: chain 8 residue 334 THR Chi-restraints excluded: chain 8 residue 366 MET Chi-restraints excluded: chain 8 residue 388 LEU Chi-restraints excluded: chain 8 residue 409 MET Chi-restraints excluded: chain 8 residue 410 GLU Chi-restraints excluded: chain 8 residue 488 VAL Chi-restraints excluded: chain 8 residue 586 VAL Chi-restraints excluded: chain 8 residue 698 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1109 random chunks: chunk 1034 optimal weight: 50.0000 chunk 120 optimal weight: 0.0060 chunk 611 optimal weight: 40.0000 chunk 783 optimal weight: 20.0000 chunk 607 optimal weight: 30.0000 chunk 903 optimal weight: 10.0000 chunk 599 optimal weight: 20.0000 chunk 1068 optimal weight: 0.8980 chunk 668 optimal weight: 50.0000 chunk 651 optimal weight: 20.0000 chunk 493 optimal weight: 20.0000 overall best weight: 10.1808 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 57 ASN k 3 GLN ** n 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 39 ASN ** v 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 102 ASN G 167 HIS ** G 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 68 HIS ** H 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 145 ASN ** M 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 75 GLN ** Q 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 12 GLN ** Y 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 74 HIS ** 8 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 259 ASN ** 8 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.3830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.098 166272 Z= 0.361 Angle : 0.732 26.936 247962 Z= 0.373 Chirality : 0.041 0.289 31576 Planarity : 0.006 0.080 13872 Dihedral : 23.439 177.883 81251 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 20.11 Ramachandran Plot: Outliers : 0.12 % Allowed : 12.67 % Favored : 87.20 % Rotamer: Outliers : 5.71 % Allowed : 20.94 % Favored : 73.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.67 (0.10), residues: 6517 helix: -0.66 (0.11), residues: 2071 sheet: -1.81 (0.15), residues: 1061 loop : -2.54 (0.10), residues: 3385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP V 72 HIS 0.011 0.002 HIS q 13 PHE 0.039 0.002 PHE Z 36 TYR 0.034 0.002 TYR q 31 ARG 0.011 0.001 ARG f 162 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13034 Ramachandran restraints generated. 6517 Oldfield, 0 Emsley, 6517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13034 Ramachandran restraints generated. 6517 Oldfield, 0 Emsley, 6517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1153 residues out of total 5429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 310 poor density : 843 time to evaluate : 9.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 65 ASP cc_start: 0.7897 (t70) cc_final: 0.7551 (t0) REVERT: b 167 ASP cc_start: 0.7744 (p0) cc_final: 0.7515 (p0) REVERT: c 11 MET cc_start: 0.8671 (tpt) cc_final: 0.8257 (tpt) REVERT: d 115 GLN cc_start: 0.9089 (tt0) cc_final: 0.8805 (tt0) REVERT: d 136 GLN cc_start: 0.8545 (tp-100) cc_final: 0.8031 (tp40) REVERT: d 140 ASP cc_start: 0.7817 (m-30) cc_final: 0.7615 (m-30) REVERT: e 10 GLU cc_start: 0.8918 (OUTLIER) cc_final: 0.7791 (pp20) REVERT: e 34 THR cc_start: 0.9024 (m) cc_final: 0.8417 (p) REVERT: e 126 ASN cc_start: 0.8206 (OUTLIER) cc_final: 0.7392 (p0) REVERT: e 176 PHE cc_start: 0.7030 (OUTLIER) cc_final: 0.6092 (t80) REVERT: f 172 GLU cc_start: 0.8016 (pm20) cc_final: 0.7776 (pm20) REVERT: i 67 THR cc_start: 0.4479 (t) cc_final: 0.4089 (p) REVERT: j 102 GLU cc_start: 0.7492 (tt0) cc_final: 0.7110 (tt0) REVERT: m 136 MET cc_start: 0.5574 (ppp) cc_final: 0.4905 (ppp) REVERT: n 18 GLN cc_start: 0.8438 (tm-30) cc_final: 0.8070 (tm-30) REVERT: n 72 ASP cc_start: 0.7832 (t0) cc_final: 0.7370 (t0) REVERT: n 110 MET cc_start: 0.8116 (mmt) cc_final: 0.7825 (tpp) REVERT: o 55 GLU cc_start: 0.8381 (mt-10) cc_final: 0.7773 (tp30) REVERT: o 88 LYS cc_start: 0.8262 (tttt) cc_final: 0.8047 (tptp) REVERT: p 114 ASN cc_start: 0.7768 (p0) cc_final: 0.7339 (p0) REVERT: q 31 TYR cc_start: 0.8351 (t80) cc_final: 0.8120 (t80) REVERT: q 48 ASP cc_start: 0.8232 (m-30) cc_final: 0.7896 (m-30) REVERT: r 34 GLU cc_start: 0.8256 (mm-30) cc_final: 0.7985 (tp30) REVERT: s 40 ASN cc_start: 0.6990 (t0) cc_final: 0.6681 (t0) REVERT: v 75 GLN cc_start: 0.9023 (tp40) cc_final: 0.8498 (tm-30) REVERT: w 62 LYS cc_start: 0.8586 (mtmt) cc_final: 0.8356 (mtmt) REVERT: y 39 GLN cc_start: 0.7908 (mt0) cc_final: 0.7417 (mp10) REVERT: z 7 THR cc_start: 0.8379 (OUTLIER) cc_final: 0.8170 (p) REVERT: z 36 GLU cc_start: 0.7964 (tt0) cc_final: 0.7626 (tm-30) REVERT: A 60 PHE cc_start: 0.0207 (t80) cc_final: -0.0326 (t80) REVERT: B 9 ARG cc_start: 0.8721 (ptp90) cc_final: 0.8081 (ptp90) REVERT: C 36 LYS cc_start: 0.7686 (ttmt) cc_final: 0.7197 (ttpp) REVERT: E 28 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8520 (tt) REVERT: F 36 ARG cc_start: 0.8383 (OUTLIER) cc_final: 0.7920 (ptt90) REVERT: G 14 HIS cc_start: 0.5985 (OUTLIER) cc_final: 0.5761 (p-80) REVERT: G 139 GLU cc_start: 0.8951 (OUTLIER) cc_final: 0.8605 (mt-10) REVERT: H 111 ASP cc_start: 0.5040 (m-30) cc_final: 0.4561 (m-30) REVERT: H 138 GLN cc_start: 0.8518 (tm-30) cc_final: 0.8207 (pt0) REVERT: H 141 MET cc_start: 0.6559 (mmm) cc_final: 0.6109 (mmm) REVERT: H 180 ASP cc_start: 0.6355 (m-30) cc_final: 0.5987 (m-30) REVERT: H 186 SER cc_start: 0.5642 (m) cc_final: 0.5403 (m) REVERT: I 59 LYS cc_start: 0.4883 (ttmt) cc_final: 0.4340 (tppt) REVERT: I 73 ASN cc_start: 0.8578 (m-40) cc_final: 0.8318 (m110) REVERT: J 115 GLU cc_start: 0.7941 (pp20) cc_final: 0.7559 (pp20) REVERT: K 9 MET cc_start: 0.8153 (mpp) cc_final: 0.7684 (mmp) REVERT: L 22 LEU cc_start: 0.7956 (mm) cc_final: 0.7024 (tp) REVERT: M 2 MET cc_start: 0.7564 (OUTLIER) cc_final: 0.6969 (tpt) REVERT: M 3 GLN cc_start: 0.7684 (OUTLIER) cc_final: 0.6120 (mp10) REVERT: M 51 GLU cc_start: 0.7566 (mt-10) cc_final: 0.7109 (tm-30) REVERT: O 75 ASP cc_start: 0.1254 (OUTLIER) cc_final: 0.0224 (t70) REVERT: O 88 MET cc_start: 0.2204 (mmp) cc_final: 0.0534 (mtm) REVERT: Q 82 ARG cc_start: 0.6797 (ttp80) cc_final: 0.6538 (ttp80) REVERT: Q 94 TYR cc_start: 0.6755 (m-80) cc_final: 0.6397 (m-80) REVERT: R 74 MET cc_start: 0.6374 (mpp) cc_final: 0.5897 (mpp) REVERT: R 80 MET cc_start: 0.6716 (mmt) cc_final: 0.5714 (mmt) REVERT: S 9 GLU cc_start: 0.7287 (tp30) cc_final: 0.6978 (tp30) REVERT: S 61 ASN cc_start: 0.7529 (OUTLIER) cc_final: 0.7119 (p0) REVERT: T 14 PHE cc_start: 0.7018 (OUTLIER) cc_final: 0.6251 (m-80) REVERT: V 61 ARG cc_start: 0.5554 (OUTLIER) cc_final: 0.4608 (mmm160) REVERT: V 73 THR cc_start: 0.4560 (t) cc_final: 0.4335 (t) REVERT: W 72 ARG cc_start: 0.8614 (mmp-170) cc_final: 0.7598 (tmt-80) REVERT: Y 53 MET cc_start: 0.8320 (ptp) cc_final: 0.8044 (ptp) REVERT: Z 48 LYS cc_start: 0.5976 (mmtp) cc_final: 0.4865 (mmtm) REVERT: 8 58 GLU cc_start: 0.8793 (OUTLIER) cc_final: 0.8494 (pm20) REVERT: 8 72 TRP cc_start: 0.6587 (t-100) cc_final: 0.6198 (t-100) REVERT: 8 204 TYR cc_start: 0.6965 (OUTLIER) cc_final: 0.5807 (t80) REVERT: 8 257 LEU cc_start: 0.8017 (tt) cc_final: 0.7785 (mm) REVERT: 8 279 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.8199 (mt) REVERT: 8 410 GLU cc_start: 0.1836 (OUTLIER) cc_final: 0.0351 (pm20) REVERT: 8 413 GLU cc_start: 0.7542 (mp0) cc_final: 0.6941 (mp0) REVERT: 8 461 MET cc_start: 0.6265 (mmm) cc_final: 0.5978 (mmm) REVERT: 8 490 TYR cc_start: 0.7566 (m-10) cc_final: 0.7306 (m-10) REVERT: 8 660 LEU cc_start: 0.7445 (OUTLIER) cc_final: 0.7116 (tt) outliers start: 310 outliers final: 229 residues processed: 1051 average time/residue: 1.2580 time to fit residues: 2340.1328 Evaluate side-chains 1056 residues out of total 5429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 248 poor density : 808 time to evaluate : 6.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 8 THR Chi-restraints excluded: chain b residue 9 SER Chi-restraints excluded: chain b residue 53 ILE Chi-restraints excluded: chain b residue 69 ASN Chi-restraints excluded: chain b residue 93 VAL Chi-restraints excluded: chain b residue 152 GLN Chi-restraints excluded: chain b residue 227 VAL Chi-restraints excluded: chain b residue 258 SER Chi-restraints excluded: chain c residue 26 VAL Chi-restraints excluded: chain c residue 50 VAL Chi-restraints excluded: chain c residue 121 THR Chi-restraints excluded: chain c residue 178 VAL Chi-restraints excluded: chain c residue 189 VAL Chi-restraints excluded: chain c residue 207 VAL Chi-restraints excluded: chain d residue 7 ASP Chi-restraints excluded: chain d residue 33 VAL Chi-restraints excluded: chain d residue 83 VAL Chi-restraints excluded: chain d residue 84 THR Chi-restraints excluded: chain d residue 150 THR Chi-restraints excluded: chain d residue 173 THR Chi-restraints excluded: chain e residue 10 GLU Chi-restraints excluded: chain e residue 73 VAL Chi-restraints excluded: chain e residue 126 ASN Chi-restraints excluded: chain e residue 145 VAL Chi-restraints excluded: chain e residue 162 ASP Chi-restraints excluded: chain e residue 176 PHE Chi-restraints excluded: chain f residue 1 SER Chi-restraints excluded: chain f residue 18 ILE Chi-restraints excluded: chain f residue 70 LEU Chi-restraints excluded: chain f residue 89 VAL Chi-restraints excluded: chain f residue 100 ASN Chi-restraints excluded: chain f residue 126 THR Chi-restraints excluded: chain f residue 161 VAL Chi-restraints excluded: chain g residue 2 GLN Chi-restraints excluded: chain g residue 21 VAL Chi-restraints excluded: chain g residue 90 LEU Chi-restraints excluded: chain g residue 122 LEU Chi-restraints excluded: chain h residue 35 VAL Chi-restraints excluded: chain h residue 50 VAL Chi-restraints excluded: chain h residue 54 VAL Chi-restraints excluded: chain i residue 54 ILE Chi-restraints excluded: chain i residue 57 VAL Chi-restraints excluded: chain i residue 72 THR Chi-restraints excluded: chain j residue 60 ASP Chi-restraints excluded: chain j residue 91 GLU Chi-restraints excluded: chain k residue 7 MET Chi-restraints excluded: chain k residue 42 THR Chi-restraints excluded: chain k residue 53 LYS Chi-restraints excluded: chain k residue 58 LEU Chi-restraints excluded: chain k residue 90 ASN Chi-restraints excluded: chain k residue 115 ILE Chi-restraints excluded: chain l residue 93 ASN Chi-restraints excluded: chain m residue 26 VAL Chi-restraints excluded: chain m residue 36 VAL Chi-restraints excluded: chain m residue 65 ILE Chi-restraints excluded: chain m residue 74 THR Chi-restraints excluded: chain m residue 91 TYR Chi-restraints excluded: chain m residue 95 LEU Chi-restraints excluded: chain m residue 124 LEU Chi-restraints excluded: chain n residue 23 ASN Chi-restraints excluded: chain n residue 24 MET Chi-restraints excluded: chain n residue 29 VAL Chi-restraints excluded: chain n residue 37 THR Chi-restraints excluded: chain n residue 53 THR Chi-restraints excluded: chain n residue 54 LEU Chi-restraints excluded: chain n residue 76 VAL Chi-restraints excluded: chain n residue 116 VAL Chi-restraints excluded: chain o residue 28 VAL Chi-restraints excluded: chain o residue 54 VAL Chi-restraints excluded: chain o residue 60 GLU Chi-restraints excluded: chain o residue 106 LEU Chi-restraints excluded: chain p residue 7 LEU Chi-restraints excluded: chain p residue 31 VAL Chi-restraints excluded: chain p residue 72 VAL Chi-restraints excluded: chain p residue 79 VAL Chi-restraints excluded: chain p residue 109 ILE Chi-restraints excluded: chain q residue 3 VAL Chi-restraints excluded: chain q residue 17 LEU Chi-restraints excluded: chain q residue 52 ARG Chi-restraints excluded: chain r residue 19 THR Chi-restraints excluded: chain r residue 27 ILE Chi-restraints excluded: chain r residue 41 ILE Chi-restraints excluded: chain r residue 58 VAL Chi-restraints excluded: chain r residue 59 ILE Chi-restraints excluded: chain r residue 98 ILE Chi-restraints excluded: chain r residue 99 THR Chi-restraints excluded: chain r residue 102 SER Chi-restraints excluded: chain s residue 4 ILE Chi-restraints excluded: chain s residue 66 ILE Chi-restraints excluded: chain s residue 67 ASP Chi-restraints excluded: chain s residue 101 SER Chi-restraints excluded: chain t residue 11 LEU Chi-restraints excluded: chain t residue 32 LEU Chi-restraints excluded: chain t residue 39 THR Chi-restraints excluded: chain t residue 63 VAL Chi-restraints excluded: chain t residue 92 ASN Chi-restraints excluded: chain u residue 11 ILE Chi-restraints excluded: chain u residue 57 ILE Chi-restraints excluded: chain v residue 8 VAL Chi-restraints excluded: chain v residue 40 ILE Chi-restraints excluded: chain v residue 62 THR Chi-restraints excluded: chain v residue 66 ASP Chi-restraints excluded: chain w residue 17 LEU Chi-restraints excluded: chain w residue 36 GLN Chi-restraints excluded: chain w residue 71 LYS Chi-restraints excluded: chain w residue 76 ILE Chi-restraints excluded: chain x residue 12 VAL Chi-restraints excluded: chain y residue 16 THR Chi-restraints excluded: chain y residue 55 THR Chi-restraints excluded: chain z residue 7 THR Chi-restraints excluded: chain z residue 47 ILE Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 18 CYS Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 44 PHE Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 34 GLU Chi-restraints excluded: chain C residue 44 GLN Chi-restraints excluded: chain C residue 45 HIS Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 25 LYS Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain F residue 36 ARG Chi-restraints excluded: chain G residue 8 MET Chi-restraints excluded: chain G residue 14 HIS Chi-restraints excluded: chain G residue 21 TYR Chi-restraints excluded: chain G residue 30 ILE Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 139 GLU Chi-restraints excluded: chain G residue 152 ASP Chi-restraints excluded: chain G residue 198 VAL Chi-restraints excluded: chain G residue 203 ASP Chi-restraints excluded: chain H residue 17 TRP Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 84 GLU Chi-restraints excluded: chain I residue 4 LEU Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 89 LEU Chi-restraints excluded: chain I residue 92 LEU Chi-restraints excluded: chain I residue 158 LEU Chi-restraints excluded: chain I residue 165 GLU Chi-restraints excluded: chain J residue 15 ILE Chi-restraints excluded: chain J residue 45 VAL Chi-restraints excluded: chain J residue 64 GLU Chi-restraints excluded: chain J residue 71 ILE Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain J residue 89 THR Chi-restraints excluded: chain J residue 141 ASP Chi-restraints excluded: chain J residue 145 ASN Chi-restraints excluded: chain J residue 160 VAL Chi-restraints excluded: chain K residue 11 HIS Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 70 VAL Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 100 MET Chi-restraints excluded: chain M residue 2 MET Chi-restraints excluded: chain M residue 3 GLN Chi-restraints excluded: chain M residue 45 ILE Chi-restraints excluded: chain M residue 61 THR Chi-restraints excluded: chain M residue 73 SER Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain M residue 111 THR Chi-restraints excluded: chain M residue 125 ILE Chi-restraints excluded: chain N residue 29 ILE Chi-restraints excluded: chain N residue 38 PHE Chi-restraints excluded: chain N residue 63 TYR Chi-restraints excluded: chain N residue 65 THR Chi-restraints excluded: chain N residue 93 LEU Chi-restraints excluded: chain O residue 10 LEU Chi-restraints excluded: chain O residue 32 THR Chi-restraints excluded: chain O residue 44 THR Chi-restraints excluded: chain O residue 75 ASP Chi-restraints excluded: chain O residue 98 VAL Chi-restraints excluded: chain P residue 15 VAL Chi-restraints excluded: chain P residue 45 THR Chi-restraints excluded: chain P residue 73 VAL Chi-restraints excluded: chain P residue 78 ILE Chi-restraints excluded: chain P residue 109 ILE Chi-restraints excluded: chain P residue 112 VAL Chi-restraints excluded: chain Q residue 34 THR Chi-restraints excluded: chain Q residue 118 VAL Chi-restraints excluded: chain R residue 64 VAL Chi-restraints excluded: chain R residue 106 ARG Chi-restraints excluded: chain S residue 44 VAL Chi-restraints excluded: chain S residue 61 ASN Chi-restraints excluded: chain S residue 85 GLU Chi-restraints excluded: chain S residue 88 MET Chi-restraints excluded: chain T residue 10 ILE Chi-restraints excluded: chain T residue 13 GLU Chi-restraints excluded: chain T residue 14 PHE Chi-restraints excluded: chain T residue 44 GLU Chi-restraints excluded: chain T residue 48 ASP Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain U residue 34 GLU Chi-restraints excluded: chain U residue 35 ARG Chi-restraints excluded: chain V residue 8 GLN Chi-restraints excluded: chain V residue 24 ILE Chi-restraints excluded: chain V residue 32 ILE Chi-restraints excluded: chain V residue 49 ASN Chi-restraints excluded: chain V residue 56 ASP Chi-restraints excluded: chain V residue 61 ARG Chi-restraints excluded: chain X residue 42 ASN Chi-restraints excluded: chain X residue 66 VAL Chi-restraints excluded: chain Y residue 11 ILE 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 32 ARG Chi-restraints excluded: chain 8 residue 58 GLU Chi-restraints excluded: chain 8 residue 86 ILE Chi-restraints excluded: chain 8 residue 105 VAL Chi-restraints excluded: chain 8 residue 110 VAL Chi-restraints excluded: chain 8 residue 135 VAL Chi-restraints excluded: chain 8 residue 138 ILE Chi-restraints excluded: chain 8 residue 141 VAL Chi-restraints excluded: chain 8 residue 154 VAL Chi-restraints excluded: chain 8 residue 200 VAL Chi-restraints excluded: chain 8 residue 204 TYR Chi-restraints excluded: chain 8 residue 244 THR Chi-restraints excluded: chain 8 residue 279 LEU Chi-restraints excluded: chain 8 residue 366 MET Chi-restraints excluded: chain 8 residue 388 LEU Chi-restraints excluded: chain 8 residue 409 MET Chi-restraints excluded: chain 8 residue 410 GLU Chi-restraints excluded: chain 8 residue 420 VAL Chi-restraints excluded: chain 8 residue 488 VAL Chi-restraints excluded: chain 8 residue 499 THR Chi-restraints excluded: chain 8 residue 586 VAL Chi-restraints excluded: chain 8 residue 628 THR Chi-restraints excluded: chain 8 residue 632 ILE Chi-restraints excluded: chain 8 residue 660 LEU Chi-restraints excluded: chain 8 residue 698 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1109 random chunks: chunk 661 optimal weight: 10.0000 chunk 426 optimal weight: 30.0000 chunk 638 optimal weight: 20.0000 chunk 321 optimal weight: 2.9990 chunk 210 optimal weight: 6.9990 chunk 207 optimal weight: 9.9990 chunk 679 optimal weight: 20.0000 chunk 728 optimal weight: 20.0000 chunk 528 optimal weight: 7.9990 chunk 99 optimal weight: 7.9990 chunk 840 optimal weight: 20.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 57 ASN l 4 ASN ** n 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 61 GLN ** s 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 39 ASN ** v 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 29 GLN G 167 HIS ** H 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 145 ASN ** L 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 75 GLN ** Q 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 18 GLN Y 12 GLN ** Y 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 74 HIS ** 8 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 259 ASN ** 8 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.3969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 166272 Z= 0.260 Angle : 0.660 25.928 247962 Z= 0.339 Chirality : 0.038 0.341 31576 Planarity : 0.005 0.067 13872 Dihedral : 23.478 177.617 81251 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 18.22 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.89 % Favored : 88.98 % Rotamer: Outliers : 5.16 % Allowed : 21.94 % Favored : 72.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.57 (0.10), residues: 6517 helix: -0.56 (0.11), residues: 2067 sheet: -1.73 (0.15), residues: 1075 loop : -2.49 (0.10), residues: 3375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP S 100 HIS 0.014 0.001 HIS Z 55 PHE 0.037 0.002 PHE Z 36 TYR 0.045 0.002 TYR I 75 ARG 0.010 0.001 ARG y 23 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13034 Ramachandran restraints generated. 6517 Oldfield, 0 Emsley, 6517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13034 Ramachandran restraints generated. 6517 Oldfield, 0 Emsley, 6517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1145 residues out of total 5429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 280 poor density : 865 time to evaluate : 6.851 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: b 65 ASP cc_start: 0.7871 (t70) cc_final: 0.7520 (t0) REVERT: b 167 ASP cc_start: 0.7689 (p0) cc_final: 0.7477 (p0) REVERT: c 11 MET cc_start: 0.8668 (tpt) cc_final: 0.8233 (tpt) REVERT: d 136 GLN cc_start: 0.8544 (tp-100) cc_final: 0.8023 (tp40) REVERT: e 34 THR cc_start: 0.8930 (m) cc_final: 0.8277 (p) REVERT: e 126 ASN cc_start: 0.8158 (OUTLIER) cc_final: 0.7513 (p0) REVERT: e 176 PHE cc_start: 0.7142 (OUTLIER) cc_final: 0.6277 (t80) REVERT: f 172 GLU cc_start: 0.7950 (pm20) cc_final: 0.7705 (pm20) REVERT: j 102 GLU cc_start: 0.7432 (tt0) cc_final: 0.7122 (tt0) REVERT: m 136 MET cc_start: 0.5637 (ppp) cc_final: 0.5020 (ppp) REVERT: n 18 GLN cc_start: 0.8443 (tm-30) cc_final: 0.8034 (tm-30) REVERT: n 72 ASP cc_start: 0.7692 (t0) cc_final: 0.7237 (t0) REVERT: n 110 MET cc_start: 0.8150 (mmt) cc_final: 0.7868 (tpp) REVERT: o 55 GLU cc_start: 0.8201 (mt-10) cc_final: 0.7703 (tp30) REVERT: o 61 GLN cc_start: 0.8269 (mm110) cc_final: 0.8027 (mm110) REVERT: o 69 ASP cc_start: 0.7595 (p0) cc_final: 0.7316 (p0) REVERT: o 88 LYS cc_start: 0.8256 (tttt) cc_final: 0.8036 (tptp) REVERT: p 114 ASN cc_start: 0.7700 (p0) cc_final: 0.7276 (p0) REVERT: q 44 TYR cc_start: 0.8864 (m-80) cc_final: 0.8400 (m-80) REVERT: q 48 ASP cc_start: 0.8201 (m-30) cc_final: 0.7895 (m-30) REVERT: r 34 GLU cc_start: 0.8424 (mm-30) cc_final: 0.7980 (tp30) REVERT: s 11 ARG cc_start: 0.7469 (mmt90) cc_final: 0.7143 (mmt-90) REVERT: s 40 ASN cc_start: 0.6851 (t0) cc_final: 0.6539 (t0) REVERT: v 75 GLN cc_start: 0.8991 (tp40) cc_final: 0.8379 (tm-30) REVERT: y 39 GLN cc_start: 0.7821 (mt0) cc_final: 0.7567 (mt0) REVERT: y 58 ASN cc_start: 0.8510 (t160) cc_final: 0.8297 (t0) REVERT: z 36 GLU cc_start: 0.7958 (tt0) cc_final: 0.7691 (tm-30) REVERT: A 60 PHE cc_start: 0.0143 (t80) cc_final: -0.0417 (t80) REVERT: B 9 ARG cc_start: 0.8677 (ptp90) cc_final: 0.8081 (ptp90) REVERT: C 36 LYS cc_start: 0.7651 (ttmt) cc_final: 0.7427 (ttpp) REVERT: D 3 ARG cc_start: 0.6798 (tpp-160) cc_final: 0.6344 (tpp80) REVERT: E 5 THR cc_start: 0.9096 (OUTLIER) cc_final: 0.8667 (p) REVERT: E 28 LEU cc_start: 0.8871 (OUTLIER) cc_final: 0.8530 (tt) REVERT: F 36 ARG cc_start: 0.8337 (OUTLIER) cc_final: 0.7897 (ptt90) REVERT: G 29 PHE cc_start: 0.7226 (OUTLIER) cc_final: 0.6931 (p90) REVERT: G 56 LEU cc_start: 0.8819 (tp) cc_final: 0.8523 (tt) REVERT: G 139 GLU cc_start: 0.8951 (OUTLIER) cc_final: 0.8628 (mt-10) REVERT: H 111 ASP cc_start: 0.4952 (m-30) cc_final: 0.4316 (m-30) REVERT: H 138 GLN cc_start: 0.8627 (tm-30) cc_final: 0.8288 (pt0) REVERT: H 141 MET cc_start: 0.6351 (mmm) cc_final: 0.5929 (mmm) REVERT: H 180 ASP cc_start: 0.6371 (m-30) cc_final: 0.6006 (m-30) REVERT: H 186 SER cc_start: 0.5577 (m) cc_final: 0.5325 (m) REVERT: I 73 ASN cc_start: 0.8525 (m-40) cc_final: 0.8265 (m-40) REVERT: J 115 GLU cc_start: 0.7958 (pp20) cc_final: 0.7567 (pp20) REVERT: L 22 LEU cc_start: 0.7907 (mm) cc_final: 0.6957 (tp) REVERT: M 2 MET cc_start: 0.7556 (OUTLIER) cc_final: 0.7033 (tpt) REVERT: M 3 GLN cc_start: 0.7559 (OUTLIER) cc_final: 0.6060 (mp10) REVERT: M 51 GLU cc_start: 0.7618 (mt-10) cc_final: 0.7160 (tm-30) REVERT: O 75 ASP cc_start: 0.1257 (OUTLIER) cc_final: 0.0191 (t70) REVERT: O 88 MET cc_start: 0.2286 (mmp) cc_final: 0.0686 (mtm) REVERT: Q 82 ARG cc_start: 0.6799 (ttp80) cc_final: 0.6555 (ttp80) REVERT: Q 94 TYR cc_start: 0.6710 (m-80) cc_final: 0.6326 (m-80) REVERT: R 74 MET cc_start: 0.6529 (mpp) cc_final: 0.6086 (mpp) REVERT: R 80 MET cc_start: 0.6934 (mmt) cc_final: 0.5953 (mmt) REVERT: S 9 GLU cc_start: 0.7281 (tp30) cc_final: 0.6985 (tp30) REVERT: S 61 ASN cc_start: 0.7512 (OUTLIER) cc_final: 0.7121 (p0) REVERT: T 14 PHE cc_start: 0.7027 (OUTLIER) cc_final: 0.6320 (m-80) REVERT: V 16 MET cc_start: 0.6497 (mtp) cc_final: 0.5297 (ttt) REVERT: V 61 ARG cc_start: 0.5543 (OUTLIER) cc_final: 0.4668 (mmm160) REVERT: W 72 ARG cc_start: 0.8633 (mmp-170) cc_final: 0.7539 (tmt-80) REVERT: X 43 MET cc_start: 0.5307 (mmt) cc_final: 0.5106 (mmt) REVERT: Y 53 MET cc_start: 0.8224 (ptp) cc_final: 0.7983 (ptp) REVERT: Y 70 LYS cc_start: 0.8573 (OUTLIER) cc_final: 0.8185 (ttmt) REVERT: Z 48 LYS cc_start: 0.5932 (mmtp) cc_final: 0.4844 (mmtm) REVERT: 8 72 TRP cc_start: 0.6622 (t-100) cc_final: 0.6170 (t-100) REVERT: 8 204 TYR cc_start: 0.7007 (OUTLIER) cc_final: 0.5741 (t80) REVERT: 8 257 LEU cc_start: 0.8023 (tt) cc_final: 0.7786 (mm) REVERT: 8 410 GLU cc_start: 0.2064 (OUTLIER) cc_final: 0.0524 (pm20) REVERT: 8 461 MET cc_start: 0.6446 (mmm) cc_final: 0.6183 (mmm) REVERT: 8 490 TYR cc_start: 0.7549 (m-10) cc_final: 0.7338 (m-10) outliers start: 280 outliers final: 223 residues processed: 1055 average time/residue: 1.3147 time to fit residues: 2472.7456 Evaluate side-chains 1064 residues out of total 5429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 239 poor density : 825 time to evaluate : 6.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 8 THR Chi-restraints excluded: chain b residue 9 SER Chi-restraints excluded: chain b residue 53 ILE Chi-restraints excluded: chain b residue 69 ASN Chi-restraints excluded: chain b residue 93 VAL Chi-restraints excluded: chain b residue 227 VAL Chi-restraints excluded: chain b residue 258 SER Chi-restraints excluded: chain c residue 50 VAL Chi-restraints excluded: chain c residue 98 VAL Chi-restraints excluded: chain c residue 121 THR Chi-restraints excluded: chain c residue 178 VAL Chi-restraints excluded: chain c residue 189 VAL Chi-restraints excluded: chain c residue 207 VAL Chi-restraints excluded: chain d residue 7 ASP Chi-restraints excluded: chain d residue 33 VAL Chi-restraints excluded: chain d residue 83 VAL Chi-restraints excluded: chain d residue 84 THR Chi-restraints excluded: chain d residue 173 THR Chi-restraints excluded: chain e residue 27 VAL Chi-restraints excluded: chain e residue 73 VAL Chi-restraints excluded: chain e residue 126 ASN Chi-restraints excluded: chain e residue 145 VAL Chi-restraints excluded: chain e residue 176 PHE Chi-restraints excluded: chain f residue 1 SER Chi-restraints excluded: chain f residue 18 ILE Chi-restraints excluded: chain f residue 70 LEU Chi-restraints excluded: chain f residue 100 ASN Chi-restraints excluded: chain f residue 126 THR Chi-restraints excluded: chain g residue 2 GLN Chi-restraints excluded: chain g residue 21 VAL Chi-restraints excluded: chain g residue 90 LEU Chi-restraints excluded: chain g residue 122 LEU Chi-restraints excluded: chain h residue 35 VAL Chi-restraints excluded: chain h residue 50 VAL Chi-restraints excluded: chain h residue 54 VAL Chi-restraints excluded: chain i residue 27 LEU Chi-restraints excluded: chain i residue 54 ILE Chi-restraints excluded: chain i residue 57 VAL Chi-restraints excluded: chain i residue 72 THR Chi-restraints excluded: chain j residue 60 ASP Chi-restraints excluded: chain j residue 91 GLU Chi-restraints excluded: chain k residue 7 MET Chi-restraints excluded: chain k residue 53 LYS Chi-restraints excluded: chain k residue 58 LEU Chi-restraints excluded: chain k residue 90 ASN Chi-restraints excluded: chain k residue 115 ILE Chi-restraints excluded: chain k residue 121 GLU Chi-restraints excluded: chain l residue 93 ASN Chi-restraints excluded: chain m residue 26 VAL Chi-restraints excluded: chain m residue 36 VAL Chi-restraints excluded: chain m residue 74 THR Chi-restraints excluded: chain m residue 91 TYR Chi-restraints excluded: chain m residue 95 LEU Chi-restraints excluded: chain m residue 124 LEU Chi-restraints excluded: chain n residue 23 ASN Chi-restraints excluded: chain n residue 24 MET Chi-restraints excluded: chain n residue 29 VAL Chi-restraints excluded: chain n residue 37 THR Chi-restraints excluded: chain n residue 53 THR Chi-restraints excluded: chain n residue 54 LEU Chi-restraints excluded: chain n residue 76 VAL Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain o residue 28 VAL Chi-restraints excluded: chain o residue 47 VAL Chi-restraints excluded: chain o residue 53 THR Chi-restraints excluded: chain o residue 54 VAL Chi-restraints excluded: chain o residue 60 GLU Chi-restraints excluded: chain p residue 7 LEU Chi-restraints excluded: chain p residue 31 VAL Chi-restraints excluded: chain p residue 72 VAL Chi-restraints excluded: chain p residue 79 VAL Chi-restraints excluded: chain p residue 109 ILE Chi-restraints excluded: chain q residue 3 VAL Chi-restraints excluded: chain q residue 17 LEU Chi-restraints excluded: chain q residue 52 ARG Chi-restraints excluded: chain q residue 82 LEU Chi-restraints excluded: chain r residue 19 THR Chi-restraints excluded: chain r residue 27 ILE Chi-restraints excluded: chain r residue 40 MET Chi-restraints excluded: chain r residue 41 ILE Chi-restraints excluded: chain r residue 53 PHE Chi-restraints excluded: chain r residue 58 VAL Chi-restraints excluded: chain r residue 59 ILE Chi-restraints excluded: chain r residue 98 ILE Chi-restraints excluded: chain r residue 99 THR Chi-restraints excluded: chain r residue 102 SER Chi-restraints excluded: chain s residue 4 ILE Chi-restraints excluded: chain s residue 66 ILE Chi-restraints excluded: chain s residue 67 ASP Chi-restraints excluded: chain s residue 101 SER Chi-restraints excluded: chain t residue 11 LEU Chi-restraints excluded: chain t residue 32 LEU Chi-restraints excluded: chain t residue 92 ASN Chi-restraints excluded: chain u residue 11 ILE Chi-restraints excluded: chain v residue 8 VAL Chi-restraints excluded: chain v residue 40 ILE Chi-restraints excluded: chain v residue 62 THR Chi-restraints excluded: chain v residue 66 ASP Chi-restraints excluded: chain w residue 34 VAL Chi-restraints excluded: chain w residue 71 LYS Chi-restraints excluded: chain w residue 76 ILE Chi-restraints excluded: chain x residue 12 VAL Chi-restraints excluded: chain y residue 16 THR Chi-restraints excluded: chain y residue 55 THR Chi-restraints excluded: chain z residue 47 ILE Chi-restraints excluded: chain z residue 54 VAL Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 18 CYS Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 44 PHE Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 45 HIS Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 25 LYS Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain F residue 36 ARG Chi-restraints excluded: chain G residue 21 TYR Chi-restraints excluded: chain G residue 29 PHE Chi-restraints excluded: chain G residue 30 ILE Chi-restraints excluded: chain G residue 139 GLU Chi-restraints excluded: chain G residue 152 ASP Chi-restraints excluded: chain G residue 203 ASP Chi-restraints excluded: chain G residue 219 THR Chi-restraints excluded: chain H residue 17 TRP Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 84 GLU Chi-restraints excluded: chain I residue 4 LEU Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 33 ILE Chi-restraints excluded: chain I residue 67 LEU Chi-restraints excluded: chain I residue 92 LEU Chi-restraints excluded: chain I residue 158 LEU Chi-restraints excluded: chain I residue 165 GLU Chi-restraints excluded: chain I residue 189 ASP Chi-restraints excluded: chain J residue 45 VAL Chi-restraints excluded: chain J residue 64 GLU Chi-restraints excluded: chain J residue 71 ILE Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain J residue 89 THR Chi-restraints excluded: chain J residue 141 ASP Chi-restraints excluded: chain J residue 145 ASN Chi-restraints excluded: chain J residue 160 VAL Chi-restraints excluded: chain K residue 11 HIS Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 62 MET Chi-restraints excluded: chain K residue 70 VAL Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain L residue 11 ILE Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain L residue 100 MET Chi-restraints excluded: chain M residue 2 MET Chi-restraints excluded: chain M residue 3 GLN Chi-restraints excluded: chain M residue 45 ILE Chi-restraints excluded: chain M residue 61 THR Chi-restraints excluded: chain M residue 73 SER Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain M residue 111 THR Chi-restraints excluded: chain N residue 38 PHE Chi-restraints excluded: chain N residue 63 TYR Chi-restraints excluded: chain N residue 65 THR Chi-restraints excluded: chain N residue 93 LEU Chi-restraints excluded: chain O residue 10 LEU Chi-restraints excluded: chain O residue 32 THR Chi-restraints excluded: chain O residue 44 THR Chi-restraints excluded: chain O residue 75 ASP Chi-restraints excluded: chain O residue 98 VAL Chi-restraints excluded: chain P residue 15 VAL Chi-restraints excluded: chain P residue 45 THR Chi-restraints excluded: chain P residue 73 VAL Chi-restraints excluded: chain P residue 95 THR Chi-restraints excluded: chain P residue 109 ILE Chi-restraints excluded: chain Q residue 34 THR Chi-restraints excluded: chain Q residue 54 VAL Chi-restraints excluded: chain R residue 64 VAL Chi-restraints excluded: chain S residue 44 VAL Chi-restraints excluded: chain S residue 61 ASN Chi-restraints excluded: chain S residue 85 GLU Chi-restraints excluded: chain T residue 10 ILE Chi-restraints excluded: chain T residue 13 GLU Chi-restraints excluded: chain T residue 14 PHE Chi-restraints excluded: chain T residue 44 GLU Chi-restraints excluded: chain T residue 48 ASP Chi-restraints excluded: chain T residue 69 LEU Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain U residue 35 ARG Chi-restraints excluded: chain V residue 8 GLN Chi-restraints excluded: chain V residue 24 ILE Chi-restraints excluded: chain V residue 32 ILE Chi-restraints excluded: chain V residue 49 ASN Chi-restraints excluded: chain V residue 52 CYS Chi-restraints excluded: chain V residue 56 ASP Chi-restraints excluded: chain V residue 61 ARG Chi-restraints excluded: chain W residue 64 LEU Chi-restraints excluded: chain X residue 18 VAL Chi-restraints excluded: chain X residue 42 ASN Chi-restraints excluded: chain X residue 66 VAL Chi-restraints excluded: chain Y residue 11 ILE Chi-restraints excluded: chain Y residue 70 LYS Chi-restraints excluded: chain Y residue 78 LEU Chi-restraints excluded: chain Y residue 79 THR Chi-restraints excluded: chain Z residue 5 VAL Chi-restraints excluded: chain Z residue 12 ASP Chi-restraints excluded: chain Z residue 32 ARG Chi-restraints excluded: chain 8 residue 58 GLU Chi-restraints excluded: chain 8 residue 105 VAL Chi-restraints excluded: chain 8 residue 110 VAL Chi-restraints excluded: chain 8 residue 135 VAL Chi-restraints excluded: chain 8 residue 138 ILE Chi-restraints excluded: chain 8 residue 141 VAL Chi-restraints excluded: chain 8 residue 154 VAL Chi-restraints excluded: chain 8 residue 200 VAL Chi-restraints excluded: chain 8 residue 204 TYR Chi-restraints excluded: chain 8 residue 244 THR Chi-restraints excluded: chain 8 residue 295 ILE Chi-restraints excluded: chain 8 residue 366 MET Chi-restraints excluded: chain 8 residue 409 MET Chi-restraints excluded: chain 8 residue 410 GLU Chi-restraints excluded: chain 8 residue 420 VAL Chi-restraints excluded: chain 8 residue 488 VAL Chi-restraints excluded: chain 8 residue 586 VAL Chi-restraints excluded: chain 8 residue 628 THR Chi-restraints excluded: chain 8 residue 632 ILE Chi-restraints excluded: chain 8 residue 660 LEU Chi-restraints excluded: chain 8 residue 698 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1109 random chunks: chunk 972 optimal weight: 10.0000 chunk 1024 optimal weight: 20.0000 chunk 934 optimal weight: 40.0000 chunk 996 optimal weight: 10.0000 chunk 1023 optimal weight: 10.0000 chunk 599 optimal weight: 20.0000 chunk 433 optimal weight: 4.9990 chunk 782 optimal weight: 10.0000 chunk 305 optimal weight: 30.0000 chunk 900 optimal weight: 10.0000 chunk 942 optimal weight: 20.0000 overall best weight: 8.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 136 GLN ** d 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 57 ASN ** m 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 167 HIS ** G 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 75 GLN ** Q 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 18 GLN Y 12 GLN ** Y 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 54 GLN Y 74 HIS ** 8 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 170 GLN 8 259 ASN ** 8 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.4112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 166272 Z= 0.316 Angle : 0.706 26.206 247962 Z= 0.361 Chirality : 0.040 0.360 31576 Planarity : 0.005 0.072 13872 Dihedral : 23.541 177.330 81251 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 19.99 Ramachandran Plot: Outliers : 0.14 % Allowed : 12.81 % Favored : 87.05 % Rotamer: Outliers : 5.14 % Allowed : 22.23 % Favored : 72.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.44 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.63 (0.10), residues: 6517 helix: -0.65 (0.11), residues: 2066 sheet: -1.74 (0.15), residues: 1067 loop : -2.51 (0.10), residues: 3384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP V 72 HIS 0.013 0.001 HIS q 13 PHE 0.040 0.002 PHE Z 36 TYR 0.038 0.002 TYR s 38 ARG 0.012 0.001 ARG y 23 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13034 Ramachandran restraints generated. 6517 Oldfield, 0 Emsley, 6517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13034 Ramachandran restraints generated. 6517 Oldfield, 0 Emsley, 6517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1113 residues out of total 5429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 279 poor density : 834 time to evaluate : 6.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 65 ASP cc_start: 0.7894 (t70) cc_final: 0.7546 (t0) REVERT: b 167 ASP cc_start: 0.7723 (p0) cc_final: 0.7493 (p0) REVERT: c 11 MET cc_start: 0.8679 (tpt) cc_final: 0.8251 (tpt) REVERT: d 115 GLN cc_start: 0.9095 (tt0) cc_final: 0.8541 (tt0) REVERT: e 34 THR cc_start: 0.8943 (m) cc_final: 0.8326 (p) REVERT: e 126 ASN cc_start: 0.8276 (OUTLIER) cc_final: 0.7437 (p0) REVERT: e 176 PHE cc_start: 0.7136 (OUTLIER) cc_final: 0.6161 (t80) REVERT: f 136 ASP cc_start: 0.8584 (OUTLIER) cc_final: 0.8224 (p0) REVERT: f 172 GLU cc_start: 0.7988 (pm20) cc_final: 0.7742 (pm20) REVERT: j 102 GLU cc_start: 0.7401 (tt0) cc_final: 0.7061 (tt0) REVERT: j 118 MET cc_start: 0.7238 (mtm) cc_final: 0.7000 (mmm) REVERT: m 136 MET cc_start: 0.5881 (ppp) cc_final: 0.5262 (ppp) REVERT: n 18 GLN cc_start: 0.8434 (tm-30) cc_final: 0.8041 (tm-30) REVERT: n 72 ASP cc_start: 0.7744 (t0) cc_final: 0.7290 (t0) REVERT: n 110 MET cc_start: 0.8169 (mmt) cc_final: 0.7889 (tpp) REVERT: o 55 GLU cc_start: 0.8383 (mt-10) cc_final: 0.7787 (tp30) REVERT: o 69 ASP cc_start: 0.7594 (p0) cc_final: 0.7329 (p0) REVERT: o 88 LYS cc_start: 0.8271 (tttt) cc_final: 0.8028 (tptp) REVERT: p 114 ASN cc_start: 0.7711 (p0) cc_final: 0.7266 (p0) REVERT: q 44 TYR cc_start: 0.8905 (m-80) cc_final: 0.8444 (m-80) REVERT: q 48 ASP cc_start: 0.8198 (m-30) cc_final: 0.7870 (m-30) REVERT: r 34 GLU cc_start: 0.8479 (mm-30) cc_final: 0.8067 (tp30) REVERT: s 11 ARG cc_start: 0.7498 (mmt90) cc_final: 0.7125 (mmt-90) REVERT: s 40 ASN cc_start: 0.6908 (t0) cc_final: 0.6569 (t0) REVERT: v 75 GLN cc_start: 0.8998 (tp40) cc_final: 0.8413 (tm-30) REVERT: y 39 GLN cc_start: 0.7823 (mt0) cc_final: 0.7558 (mt0) REVERT: y 58 ASN cc_start: 0.8601 (t160) cc_final: 0.8398 (t0) REVERT: z 36 GLU cc_start: 0.7911 (tt0) cc_final: 0.7628 (tm-30) REVERT: A 60 PHE cc_start: -0.0134 (t80) cc_final: -0.0752 (t80) REVERT: B 9 ARG cc_start: 0.8727 (ptp90) cc_final: 0.8108 (ptp90) REVERT: C 36 LYS cc_start: 0.7672 (ttmt) cc_final: 0.7451 (ttpp) REVERT: D 3 ARG cc_start: 0.6857 (tpp-160) cc_final: 0.6411 (tpp80) REVERT: E 28 LEU cc_start: 0.8890 (OUTLIER) cc_final: 0.8519 (tt) REVERT: F 36 ARG cc_start: 0.8350 (OUTLIER) cc_final: 0.7911 (ptt90) REVERT: G 56 LEU cc_start: 0.8865 (tp) cc_final: 0.8587 (tt) REVERT: G 135 MET cc_start: 0.6608 (ptp) cc_final: 0.6405 (ptp) REVERT: G 139 GLU cc_start: 0.8944 (OUTLIER) cc_final: 0.8627 (mt-10) REVERT: H 111 ASP cc_start: 0.5218 (m-30) cc_final: 0.4515 (m-30) REVERT: H 138 GLN cc_start: 0.8626 (tm-30) cc_final: 0.8286 (pt0) REVERT: H 141 MET cc_start: 0.6408 (mmm) cc_final: 0.5980 (mmm) REVERT: H 180 ASP cc_start: 0.6348 (m-30) cc_final: 0.5988 (m-30) REVERT: H 186 SER cc_start: 0.5626 (m) cc_final: 0.5369 (m) REVERT: I 73 ASN cc_start: 0.8592 (m-40) cc_final: 0.8317 (m-40) REVERT: J 115 GLU cc_start: 0.7954 (pp20) cc_final: 0.7546 (pp20) REVERT: K 9 MET cc_start: 0.8112 (mpp) cc_final: 0.7638 (mmp) REVERT: L 22 LEU cc_start: 0.7769 (mm) cc_final: 0.6826 (tp) REVERT: L 102 TRP cc_start: 0.6587 (t-100) cc_final: 0.6337 (t-100) REVERT: M 2 MET cc_start: 0.7586 (OUTLIER) cc_final: 0.7044 (tpt) REVERT: M 3 GLN cc_start: 0.7641 (OUTLIER) cc_final: 0.6149 (mp10) REVERT: M 51 GLU cc_start: 0.7707 (mt-10) cc_final: 0.7337 (tm-30) REVERT: N 29 ILE cc_start: 0.4457 (OUTLIER) cc_final: 0.4227 (mt) REVERT: O 75 ASP cc_start: 0.1262 (OUTLIER) cc_final: 0.0182 (t70) REVERT: Q 82 ARG cc_start: 0.6780 (ttp80) cc_final: 0.6555 (ttp80) REVERT: Q 94 TYR cc_start: 0.6742 (m-80) cc_final: 0.6303 (m-80) REVERT: R 74 MET cc_start: 0.6508 (mpp) cc_final: 0.6069 (mpp) REVERT: R 80 MET cc_start: 0.6712 (mmt) cc_final: 0.5686 (mmt) REVERT: S 9 GLU cc_start: 0.7202 (tp30) cc_final: 0.6695 (tp30) REVERT: S 61 ASN cc_start: 0.7512 (OUTLIER) cc_final: 0.7094 (p0) REVERT: T 14 PHE cc_start: 0.7051 (OUTLIER) cc_final: 0.6361 (m-80) REVERT: V 61 ARG cc_start: 0.5608 (OUTLIER) cc_final: 0.4724 (mmm160) REVERT: W 72 ARG cc_start: 0.8642 (mmp-170) cc_final: 0.7539 (tmt-80) REVERT: Y 53 MET cc_start: 0.8294 (ptp) cc_final: 0.8029 (ptp) REVERT: Y 70 LYS cc_start: 0.8516 (OUTLIER) cc_final: 0.8257 (ttmt) REVERT: Z 48 LYS cc_start: 0.6050 (mmtp) cc_final: 0.4923 (mmtm) REVERT: 8 58 GLU cc_start: 0.8800 (OUTLIER) cc_final: 0.8486 (pm20) REVERT: 8 72 TRP cc_start: 0.6725 (t-100) cc_final: 0.6436 (t-100) REVERT: 8 204 TYR cc_start: 0.7062 (OUTLIER) cc_final: 0.5782 (t80) REVERT: 8 257 LEU cc_start: 0.8103 (tt) cc_final: 0.7868 (mm) REVERT: 8 410 GLU cc_start: 0.2094 (OUTLIER) cc_final: 0.0590 (pm20) REVERT: 8 461 MET cc_start: 0.6662 (mmm) cc_final: 0.6320 (mmm) REVERT: 8 490 TYR cc_start: 0.7566 (m-10) cc_final: 0.7352 (m-10) outliers start: 279 outliers final: 241 residues processed: 1020 average time/residue: 1.2489 time to fit residues: 2261.4531 Evaluate side-chains 1069 residues out of total 5429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 258 poor density : 811 time to evaluate : 6.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 8 THR Chi-restraints excluded: chain b residue 9 SER Chi-restraints excluded: chain b residue 53 ILE Chi-restraints excluded: chain b residue 69 ASN Chi-restraints excluded: chain b residue 93 VAL Chi-restraints excluded: chain b residue 227 VAL Chi-restraints excluded: chain b residue 258 SER Chi-restraints excluded: chain c residue 26 VAL Chi-restraints excluded: chain c residue 50 VAL Chi-restraints excluded: chain c residue 98 VAL Chi-restraints excluded: chain c residue 121 THR Chi-restraints excluded: chain c residue 178 VAL Chi-restraints excluded: chain c residue 189 VAL Chi-restraints excluded: chain c residue 207 VAL Chi-restraints excluded: chain d residue 7 ASP Chi-restraints excluded: chain d residue 33 VAL Chi-restraints excluded: chain d residue 83 VAL Chi-restraints excluded: chain d residue 84 THR Chi-restraints excluded: chain d residue 109 LEU Chi-restraints excluded: chain d residue 150 THR Chi-restraints excluded: chain d residue 173 THR Chi-restraints excluded: chain e residue 27 VAL Chi-restraints excluded: chain e residue 73 VAL Chi-restraints excluded: chain e residue 126 ASN Chi-restraints excluded: chain e residue 145 VAL Chi-restraints excluded: chain e residue 176 PHE Chi-restraints excluded: chain f residue 1 SER Chi-restraints excluded: chain f residue 18 ILE Chi-restraints excluded: chain f residue 70 LEU Chi-restraints excluded: chain f residue 100 ASN Chi-restraints excluded: chain f residue 126 THR Chi-restraints excluded: chain f residue 136 ASP Chi-restraints excluded: chain f residue 161 VAL Chi-restraints excluded: chain g residue 2 GLN Chi-restraints excluded: chain g residue 21 VAL Chi-restraints excluded: chain g residue 80 ILE Chi-restraints excluded: chain g residue 90 LEU Chi-restraints excluded: chain g residue 122 LEU Chi-restraints excluded: chain h residue 50 VAL Chi-restraints excluded: chain h residue 54 VAL Chi-restraints excluded: chain i residue 27 LEU Chi-restraints excluded: chain i residue 54 ILE Chi-restraints excluded: chain i residue 57 VAL Chi-restraints excluded: chain i residue 72 THR Chi-restraints excluded: chain j residue 56 VAL Chi-restraints excluded: chain j residue 60 ASP Chi-restraints excluded: chain j residue 91 GLU Chi-restraints excluded: chain k residue 7 MET Chi-restraints excluded: chain k residue 42 THR Chi-restraints excluded: chain k residue 53 LYS Chi-restraints excluded: chain k residue 58 LEU Chi-restraints excluded: chain k residue 90 ASN Chi-restraints excluded: chain k residue 115 ILE Chi-restraints excluded: chain k residue 121 GLU Chi-restraints excluded: chain m residue 26 VAL Chi-restraints excluded: chain m residue 36 VAL Chi-restraints excluded: chain m residue 74 THR Chi-restraints excluded: chain m residue 91 TYR Chi-restraints excluded: chain m residue 95 LEU Chi-restraints excluded: chain m residue 124 LEU Chi-restraints excluded: chain n residue 23 ASN Chi-restraints excluded: chain n residue 29 VAL Chi-restraints excluded: chain n residue 37 THR Chi-restraints excluded: chain n residue 53 THR Chi-restraints excluded: chain n residue 54 LEU Chi-restraints excluded: chain n residue 76 VAL Chi-restraints excluded: chain n residue 97 ILE Chi-restraints excluded: chain n residue 116 VAL Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain o residue 28 VAL Chi-restraints excluded: chain o residue 47 VAL Chi-restraints excluded: chain o residue 53 THR Chi-restraints excluded: chain o residue 54 VAL Chi-restraints excluded: chain o residue 60 GLU Chi-restraints excluded: chain o residue 106 LEU Chi-restraints excluded: chain p residue 7 LEU Chi-restraints excluded: chain p residue 31 VAL Chi-restraints excluded: chain p residue 72 VAL Chi-restraints excluded: chain p residue 79 VAL Chi-restraints excluded: chain p residue 109 ILE Chi-restraints excluded: chain q residue 3 VAL Chi-restraints excluded: chain q residue 17 LEU Chi-restraints excluded: chain q residue 52 ARG Chi-restraints excluded: chain q residue 82 LEU Chi-restraints excluded: chain r residue 19 THR Chi-restraints excluded: chain r residue 27 ILE Chi-restraints excluded: chain r residue 41 ILE Chi-restraints excluded: chain r residue 53 PHE Chi-restraints excluded: chain r residue 58 VAL Chi-restraints excluded: chain r residue 59 ILE Chi-restraints excluded: chain r residue 98 ILE Chi-restraints excluded: chain r residue 99 THR Chi-restraints excluded: chain r residue 102 SER Chi-restraints excluded: chain s residue 4 ILE Chi-restraints excluded: chain s residue 66 ILE Chi-restraints excluded: chain s residue 101 SER Chi-restraints excluded: chain t residue 11 LEU Chi-restraints excluded: chain t residue 32 LEU Chi-restraints excluded: chain t residue 39 THR Chi-restraints excluded: chain t residue 92 ASN Chi-restraints excluded: chain u residue 11 ILE Chi-restraints excluded: chain v residue 8 VAL Chi-restraints excluded: chain v residue 40 ILE Chi-restraints excluded: chain v residue 62 THR Chi-restraints excluded: chain v residue 66 ASP Chi-restraints excluded: chain w residue 17 LEU Chi-restraints excluded: chain w residue 34 VAL Chi-restraints excluded: chain w residue 71 LYS Chi-restraints excluded: chain w residue 76 ILE Chi-restraints excluded: chain x residue 12 VAL Chi-restraints excluded: chain y residue 16 THR Chi-restraints excluded: chain y residue 55 THR Chi-restraints excluded: chain z residue 8 GLN Chi-restraints excluded: chain z residue 34 THR Chi-restraints excluded: chain z residue 47 ILE Chi-restraints excluded: chain z residue 54 VAL Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 18 CYS Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 44 PHE Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 45 HIS Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 26 ASN Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain F residue 36 ARG Chi-restraints excluded: chain G residue 21 TYR Chi-restraints excluded: chain G residue 30 ILE Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 139 GLU Chi-restraints excluded: chain G residue 152 ASP Chi-restraints excluded: chain G residue 203 ASP Chi-restraints excluded: chain G residue 219 THR Chi-restraints excluded: chain H residue 17 TRP Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 84 GLU Chi-restraints excluded: chain I residue 4 LEU Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 33 ILE Chi-restraints excluded: chain I residue 67 LEU Chi-restraints excluded: chain I residue 89 LEU Chi-restraints excluded: chain I residue 92 LEU Chi-restraints excluded: chain I residue 158 LEU Chi-restraints excluded: chain I residue 165 GLU Chi-restraints excluded: chain I residue 189 ASP Chi-restraints excluded: chain J residue 15 ILE Chi-restraints excluded: chain J residue 45 VAL Chi-restraints excluded: chain J residue 64 GLU Chi-restraints excluded: chain J residue 71 ILE Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain J residue 89 THR Chi-restraints excluded: chain J residue 141 ASP Chi-restraints excluded: chain J residue 160 VAL Chi-restraints excluded: chain K residue 11 HIS Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 70 VAL Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain L residue 11 ILE Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain L residue 100 MET Chi-restraints excluded: chain M residue 2 MET Chi-restraints excluded: chain M residue 3 GLN Chi-restraints excluded: chain M residue 45 ILE Chi-restraints excluded: chain M residue 61 THR Chi-restraints excluded: chain M residue 73 SER Chi-restraints excluded: chain M residue 89 ASP Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain M residue 111 THR Chi-restraints excluded: chain N residue 29 ILE Chi-restraints excluded: chain N residue 38 PHE Chi-restraints excluded: chain N residue 63 TYR Chi-restraints excluded: chain N residue 65 THR Chi-restraints excluded: chain N residue 93 LEU Chi-restraints excluded: chain O residue 10 LEU Chi-restraints excluded: chain O residue 32 THR Chi-restraints excluded: chain O residue 44 THR Chi-restraints excluded: chain O residue 75 ASP Chi-restraints excluded: chain O residue 98 VAL Chi-restraints excluded: chain P residue 15 VAL Chi-restraints excluded: chain P residue 45 THR Chi-restraints excluded: chain P residue 73 VAL Chi-restraints excluded: chain P residue 95 THR Chi-restraints excluded: chain P residue 109 ILE Chi-restraints excluded: chain Q residue 34 THR Chi-restraints excluded: chain Q residue 54 VAL Chi-restraints excluded: chain Q residue 77 SER Chi-restraints excluded: chain Q residue 118 VAL Chi-restraints excluded: chain R residue 64 VAL Chi-restraints excluded: chain S residue 44 VAL Chi-restraints excluded: chain S residue 61 ASN Chi-restraints excluded: chain S residue 85 GLU Chi-restraints excluded: chain T residue 10 ILE Chi-restraints excluded: chain T residue 13 GLU Chi-restraints excluded: chain T residue 14 PHE Chi-restraints excluded: chain T residue 44 GLU Chi-restraints excluded: chain T residue 48 ASP Chi-restraints excluded: chain T residue 69 LEU Chi-restraints excluded: chain U residue 6 LEU Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain U residue 35 ARG Chi-restraints excluded: chain V residue 8 GLN Chi-restraints excluded: chain V residue 24 ILE Chi-restraints excluded: chain V residue 32 ILE Chi-restraints excluded: chain V residue 49 ASN Chi-restraints excluded: chain V residue 52 CYS Chi-restraints excluded: chain V residue 56 ASP Chi-restraints excluded: chain V residue 61 ARG Chi-restraints excluded: chain W residue 18 GLN Chi-restraints excluded: chain W residue 53 GLN Chi-restraints excluded: chain W residue 64 LEU Chi-restraints excluded: chain X residue 18 VAL Chi-restraints excluded: chain X residue 42 ASN Chi-restraints excluded: chain X residue 66 VAL Chi-restraints excluded: chain Y residue 11 ILE Chi-restraints excluded: chain Y residue 70 LYS Chi-restraints excluded: chain Y residue 78 LEU Chi-restraints excluded: chain Y residue 79 THR Chi-restraints excluded: chain Z residue 5 VAL Chi-restraints excluded: chain Z residue 12 ASP Chi-restraints excluded: chain Z residue 32 ARG Chi-restraints excluded: chain 8 residue 58 GLU Chi-restraints excluded: chain 8 residue 105 VAL Chi-restraints excluded: chain 8 residue 116 VAL Chi-restraints excluded: chain 8 residue 135 VAL Chi-restraints excluded: chain 8 residue 138 ILE Chi-restraints excluded: chain 8 residue 141 VAL Chi-restraints excluded: chain 8 residue 154 VAL Chi-restraints excluded: chain 8 residue 200 VAL Chi-restraints excluded: chain 8 residue 204 TYR Chi-restraints excluded: chain 8 residue 244 THR Chi-restraints excluded: chain 8 residue 279 LEU Chi-restraints excluded: chain 8 residue 295 ILE Chi-restraints excluded: chain 8 residue 366 MET Chi-restraints excluded: chain 8 residue 409 MET Chi-restraints excluded: chain 8 residue 410 GLU Chi-restraints excluded: chain 8 residue 420 VAL Chi-restraints excluded: chain 8 residue 488 VAL Chi-restraints excluded: chain 8 residue 499 THR Chi-restraints excluded: chain 8 residue 586 VAL Chi-restraints excluded: chain 8 residue 628 THR Chi-restraints excluded: chain 8 residue 632 ILE Chi-restraints excluded: chain 8 residue 660 LEU Chi-restraints excluded: chain 8 residue 698 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1109 random chunks: chunk 992 optimal weight: 10.0000 chunk 654 optimal weight: 30.0000 chunk 1053 optimal weight: 7.9990 chunk 642 optimal weight: 20.0000 chunk 499 optimal weight: 0.9990 chunk 732 optimal weight: 20.0000 chunk 1104 optimal weight: 10.0000 chunk 1016 optimal weight: 30.0000 chunk 879 optimal weight: 20.0000 chunk 91 optimal weight: 8.9990 chunk 679 optimal weight: 20.0000 overall best weight: 7.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 136 GLN ** d 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 57 ASN n 107 ASN s 40 ASN ** t 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 61 ASN ** D 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 167 HIS H 138 GLN ** J 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 75 GLN ** T 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 12 GLN ** Y 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 74 HIS ** 8 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 259 ASN ** 8 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.4243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 166272 Z= 0.271 Angle : 0.675 25.751 247962 Z= 0.345 Chirality : 0.038 0.278 31576 Planarity : 0.005 0.065 13872 Dihedral : 23.561 177.508 81251 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 18.78 Ramachandran Plot: Outliers : 0.12 % Allowed : 11.31 % Favored : 88.57 % Rotamer: Outliers : 4.83 % Allowed : 22.64 % Favored : 72.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.44 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.57 (0.10), residues: 6517 helix: -0.60 (0.11), residues: 2067 sheet: -1.74 (0.15), residues: 1118 loop : -2.45 (0.10), residues: 3332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP S 100 HIS 0.010 0.001 HIS q 13 PHE 0.040 0.002 PHE Z 36 TYR 0.037 0.002 TYR s 38 ARG 0.012 0.001 ARG y 47 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13034 Ramachandran restraints generated. 6517 Oldfield, 0 Emsley, 6517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13034 Ramachandran restraints generated. 6517 Oldfield, 0 Emsley, 6517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1116 residues out of total 5429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 262 poor density : 854 time to evaluate : 7.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 65 ASP cc_start: 0.7890 (t70) cc_final: 0.7532 (t0) REVERT: b 167 ASP cc_start: 0.7684 (p0) cc_final: 0.7470 (p0) REVERT: c 11 MET cc_start: 0.8706 (tpt) cc_final: 0.8233 (tpt) REVERT: d 115 GLN cc_start: 0.9037 (tt0) cc_final: 0.8530 (tt0) REVERT: e 34 THR cc_start: 0.8927 (m) cc_final: 0.8294 (p) REVERT: e 126 ASN cc_start: 0.8336 (OUTLIER) cc_final: 0.7487 (p0) REVERT: e 176 PHE cc_start: 0.7205 (OUTLIER) cc_final: 0.6296 (t80) REVERT: f 136 ASP cc_start: 0.8594 (OUTLIER) cc_final: 0.8237 (p0) REVERT: f 172 GLU cc_start: 0.7957 (pm20) cc_final: 0.7712 (pm20) REVERT: j 102 GLU cc_start: 0.7427 (tt0) cc_final: 0.7100 (tt0) REVERT: j 118 MET cc_start: 0.7158 (mtm) cc_final: 0.6926 (mmm) REVERT: m 1 MET cc_start: 0.6893 (tpp) cc_final: 0.6640 (tpp) REVERT: m 82 MET cc_start: 0.8041 (mmm) cc_final: 0.7822 (mmm) REVERT: m 136 MET cc_start: 0.5857 (ppp) cc_final: 0.5275 (ppp) REVERT: n 18 GLN cc_start: 0.8430 (tm-30) cc_final: 0.8025 (tm-30) REVERT: n 72 ASP cc_start: 0.7640 (t0) cc_final: 0.7194 (t0) REVERT: n 110 MET cc_start: 0.8184 (mmt) cc_final: 0.7860 (tpp) REVERT: o 55 GLU cc_start: 0.8333 (mt-10) cc_final: 0.7690 (tp30) REVERT: o 69 ASP cc_start: 0.7597 (p0) cc_final: 0.7311 (p0) REVERT: o 88 LYS cc_start: 0.8225 (tttt) cc_final: 0.7973 (tptp) REVERT: p 114 ASN cc_start: 0.7687 (p0) cc_final: 0.7237 (p0) REVERT: q 44 TYR cc_start: 0.8857 (m-80) cc_final: 0.8395 (m-80) REVERT: q 48 ASP cc_start: 0.8176 (m-30) cc_final: 0.7858 (m-30) REVERT: r 34 GLU cc_start: 0.8474 (mm-30) cc_final: 0.8058 (tp30) REVERT: s 11 ARG cc_start: 0.7488 (mmt90) cc_final: 0.7095 (mmt-90) REVERT: v 75 GLN cc_start: 0.8987 (tp40) cc_final: 0.8774 (tp-100) REVERT: y 39 GLN cc_start: 0.7838 (mt0) cc_final: 0.7387 (mp10) REVERT: y 45 GLN cc_start: 0.8538 (pp30) cc_final: 0.8319 (pp30) REVERT: y 49 ASP cc_start: 0.8500 (t0) cc_final: 0.8067 (p0) REVERT: z 36 GLU cc_start: 0.7846 (tt0) cc_final: 0.7619 (tm-30) REVERT: A 60 PHE cc_start: -0.0109 (t80) cc_final: -0.0820 (t80) REVERT: B 9 ARG cc_start: 0.8675 (ptp90) cc_final: 0.8091 (ptp90) REVERT: C 36 LYS cc_start: 0.7652 (ttmt) cc_final: 0.6880 (ttpp) REVERT: D 3 ARG cc_start: 0.6799 (tpp-160) cc_final: 0.6336 (tpp80) REVERT: E 5 THR cc_start: 0.9093 (OUTLIER) cc_final: 0.8656 (p) REVERT: E 28 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8570 (tt) REVERT: F 36 ARG cc_start: 0.8308 (OUTLIER) cc_final: 0.7887 (ptt90) REVERT: G 56 LEU cc_start: 0.8969 (tp) cc_final: 0.8687 (tt) REVERT: G 135 MET cc_start: 0.6582 (ptp) cc_final: 0.6355 (ptp) REVERT: G 139 GLU cc_start: 0.8950 (OUTLIER) cc_final: 0.8630 (mt-10) REVERT: H 111 ASP cc_start: 0.5008 (m-30) cc_final: 0.4360 (m-30) REVERT: H 138 GLN cc_start: 0.8653 (tm130) cc_final: 0.8330 (pt0) REVERT: H 141 MET cc_start: 0.6325 (mmm) cc_final: 0.5882 (mmm) REVERT: H 180 ASP cc_start: 0.6455 (m-30) cc_final: 0.6097 (m-30) REVERT: H 186 SER cc_start: 0.5708 (m) cc_final: 0.5477 (m) REVERT: I 61 ARG cc_start: 0.5979 (mtp180) cc_final: 0.5123 (tpt90) REVERT: I 73 ASN cc_start: 0.8593 (m-40) cc_final: 0.8289 (m-40) REVERT: I 104 MET cc_start: 0.1849 (mmt) cc_final: 0.0719 (mmt) REVERT: J 115 GLU cc_start: 0.7953 (pp20) cc_final: 0.7557 (pp20) REVERT: K 9 MET cc_start: 0.8172 (mpp) cc_final: 0.7698 (mmp) REVERT: K 40 GLU cc_start: 0.5941 (tt0) cc_final: 0.5343 (tt0) REVERT: L 22 LEU cc_start: 0.7774 (mm) cc_final: 0.6803 (tp) REVERT: L 102 TRP cc_start: 0.6635 (t-100) cc_final: 0.6429 (t-100) REVERT: M 2 MET cc_start: 0.7558 (OUTLIER) cc_final: 0.7018 (tpt) REVERT: M 3 GLN cc_start: 0.7596 (OUTLIER) cc_final: 0.6078 (mp10) REVERT: M 51 GLU cc_start: 0.7578 (mt-10) cc_final: 0.7271 (tm-30) REVERT: O 68 ARG cc_start: 0.7372 (mtt180) cc_final: 0.7089 (mmt180) REVERT: O 75 ASP cc_start: 0.1292 (OUTLIER) cc_final: 0.0161 (t70) REVERT: O 97 ASP cc_start: 0.6907 (t0) cc_final: 0.6142 (p0) REVERT: Q 82 ARG cc_start: 0.6764 (ttp80) cc_final: 0.6543 (ttp80) REVERT: R 74 MET cc_start: 0.6469 (mpp) cc_final: 0.6125 (mpp) REVERT: R 80 MET cc_start: 0.6732 (mmt) cc_final: 0.5760 (mmt) REVERT: S 9 GLU cc_start: 0.7300 (tp30) cc_final: 0.7009 (tp30) REVERT: S 61 ASN cc_start: 0.7471 (OUTLIER) cc_final: 0.7042 (p0) REVERT: T 14 PHE cc_start: 0.7055 (OUTLIER) cc_final: 0.6437 (m-80) REVERT: V 61 ARG cc_start: 0.5417 (OUTLIER) cc_final: 0.4512 (mmm160) REVERT: W 60 ARG cc_start: 0.8579 (mtp85) cc_final: 0.8288 (mtt90) REVERT: W 72 ARG cc_start: 0.8623 (mmp-170) cc_final: 0.7536 (tpt170) REVERT: Y 70 LYS cc_start: 0.8534 (OUTLIER) cc_final: 0.8308 (ttmt) REVERT: Z 48 LYS cc_start: 0.5994 (mmtp) cc_final: 0.4864 (mmtm) REVERT: 8 72 TRP cc_start: 0.6763 (t-100) cc_final: 0.6466 (t-100) REVERT: 8 204 TYR cc_start: 0.6988 (OUTLIER) cc_final: 0.5632 (t80) REVERT: 8 461 MET cc_start: 0.6672 (mmm) cc_final: 0.6327 (mmm) REVERT: 8 490 TYR cc_start: 0.7534 (m-10) cc_final: 0.7320 (m-10) outliers start: 262 outliers final: 230 residues processed: 1027 average time/residue: 1.2504 time to fit residues: 2271.5852 Evaluate side-chains 1065 residues out of total 5429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 245 poor density : 820 time to evaluate : 8.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 8 THR Chi-restraints excluded: chain b residue 9 SER Chi-restraints excluded: chain b residue 53 ILE Chi-restraints excluded: chain b residue 69 ASN Chi-restraints excluded: chain b residue 93 VAL Chi-restraints excluded: chain b residue 227 VAL Chi-restraints excluded: chain b residue 258 SER Chi-restraints excluded: chain c residue 26 VAL Chi-restraints excluded: chain c residue 50 VAL Chi-restraints excluded: chain c residue 98 VAL Chi-restraints excluded: chain c residue 121 THR Chi-restraints excluded: chain c residue 170 VAL Chi-restraints excluded: chain c residue 178 VAL Chi-restraints excluded: chain c residue 189 VAL Chi-restraints excluded: chain c residue 207 VAL Chi-restraints excluded: chain d residue 7 ASP Chi-restraints excluded: chain d residue 33 VAL Chi-restraints excluded: chain d residue 83 VAL Chi-restraints excluded: chain d residue 84 THR Chi-restraints excluded: chain d residue 109 LEU Chi-restraints excluded: chain d residue 150 THR Chi-restraints excluded: chain d residue 173 THR Chi-restraints excluded: chain e residue 27 VAL Chi-restraints excluded: chain e residue 73 VAL Chi-restraints excluded: chain e residue 126 ASN Chi-restraints excluded: chain e residue 145 VAL Chi-restraints excluded: chain e residue 176 PHE Chi-restraints excluded: chain f residue 1 SER Chi-restraints excluded: chain f residue 18 ILE Chi-restraints excluded: chain f residue 70 LEU Chi-restraints excluded: chain f residue 126 THR Chi-restraints excluded: chain f residue 136 ASP Chi-restraints excluded: chain g residue 2 GLN Chi-restraints excluded: chain g residue 21 VAL Chi-restraints excluded: chain g residue 80 ILE Chi-restraints excluded: chain g residue 90 LEU Chi-restraints excluded: chain g residue 122 LEU Chi-restraints excluded: chain h residue 50 VAL Chi-restraints excluded: chain h residue 54 VAL Chi-restraints excluded: chain i residue 27 LEU Chi-restraints excluded: chain i residue 54 ILE Chi-restraints excluded: chain i residue 57 VAL Chi-restraints excluded: chain i residue 72 THR Chi-restraints excluded: chain j residue 56 VAL Chi-restraints excluded: chain j residue 60 ASP Chi-restraints excluded: chain j residue 91 GLU Chi-restraints excluded: chain k residue 7 MET Chi-restraints excluded: chain k residue 42 THR Chi-restraints excluded: chain k residue 53 LYS Chi-restraints excluded: chain k residue 58 LEU Chi-restraints excluded: chain k residue 90 ASN Chi-restraints excluded: chain k residue 115 ILE Chi-restraints excluded: chain k residue 121 GLU Chi-restraints excluded: chain m residue 26 VAL Chi-restraints excluded: chain m residue 36 VAL Chi-restraints excluded: chain m residue 74 THR Chi-restraints excluded: chain m residue 91 TYR Chi-restraints excluded: chain m residue 95 LEU Chi-restraints excluded: chain m residue 124 LEU Chi-restraints excluded: chain n residue 23 ASN Chi-restraints excluded: chain n residue 29 VAL Chi-restraints excluded: chain n residue 37 THR Chi-restraints excluded: chain n residue 53 THR Chi-restraints excluded: chain n residue 54 LEU Chi-restraints excluded: chain n residue 76 VAL Chi-restraints excluded: chain n residue 116 VAL Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain o residue 28 VAL Chi-restraints excluded: chain o residue 47 VAL Chi-restraints excluded: chain o residue 53 THR Chi-restraints excluded: chain o residue 54 VAL Chi-restraints excluded: chain o residue 60 GLU Chi-restraints excluded: chain p residue 7 LEU Chi-restraints excluded: chain p residue 31 VAL Chi-restraints excluded: chain p residue 79 VAL Chi-restraints excluded: chain p residue 109 ILE Chi-restraints excluded: chain q residue 3 VAL Chi-restraints excluded: chain q residue 17 LEU Chi-restraints excluded: chain q residue 52 ARG Chi-restraints excluded: chain r residue 19 THR Chi-restraints excluded: chain r residue 27 ILE Chi-restraints excluded: chain r residue 41 ILE Chi-restraints excluded: chain r residue 53 PHE Chi-restraints excluded: chain r residue 58 VAL Chi-restraints excluded: chain r residue 59 ILE Chi-restraints excluded: chain r residue 98 ILE Chi-restraints excluded: chain r residue 99 THR Chi-restraints excluded: chain r residue 102 SER Chi-restraints excluded: chain s residue 4 ILE Chi-restraints excluded: chain s residue 66 ILE Chi-restraints excluded: chain s residue 101 SER Chi-restraints excluded: chain t residue 11 LEU Chi-restraints excluded: chain t residue 32 LEU Chi-restraints excluded: chain t residue 39 THR Chi-restraints excluded: chain t residue 63 VAL Chi-restraints excluded: chain t residue 92 ASN Chi-restraints excluded: chain u residue 11 ILE Chi-restraints excluded: chain v residue 8 VAL Chi-restraints excluded: chain v residue 40 ILE Chi-restraints excluded: chain v residue 62 THR Chi-restraints excluded: chain v residue 66 ASP Chi-restraints excluded: chain w residue 34 VAL Chi-restraints excluded: chain w residue 71 LYS Chi-restraints excluded: chain w residue 76 ILE Chi-restraints excluded: chain x residue 12 VAL Chi-restraints excluded: chain y residue 16 THR Chi-restraints excluded: chain y residue 55 THR Chi-restraints excluded: chain z residue 47 ILE Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 18 CYS Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 44 PHE Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 45 HIS Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain F residue 36 ARG Chi-restraints excluded: chain G residue 21 TYR Chi-restraints excluded: chain G residue 30 ILE Chi-restraints excluded: chain G residue 139 GLU Chi-restraints excluded: chain G residue 152 ASP Chi-restraints excluded: chain G residue 198 VAL Chi-restraints excluded: chain G residue 203 ASP Chi-restraints excluded: chain G residue 219 THR Chi-restraints excluded: chain H residue 17 TRP Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 84 GLU Chi-restraints excluded: chain I residue 4 LEU Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 33 ILE Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 67 LEU Chi-restraints excluded: chain I residue 89 LEU Chi-restraints excluded: chain I residue 92 LEU Chi-restraints excluded: chain I residue 165 GLU Chi-restraints excluded: chain I residue 189 ASP Chi-restraints excluded: chain J residue 45 VAL Chi-restraints excluded: chain J residue 64 GLU Chi-restraints excluded: chain J residue 71 ILE Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain J residue 89 THR Chi-restraints excluded: chain J residue 160 VAL Chi-restraints excluded: chain K residue 11 HIS Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 70 VAL Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain L residue 11 ILE Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain L residue 100 MET Chi-restraints excluded: chain M residue 2 MET Chi-restraints excluded: chain M residue 3 GLN Chi-restraints excluded: chain M residue 45 ILE Chi-restraints excluded: chain M residue 61 THR Chi-restraints excluded: chain M residue 73 SER Chi-restraints excluded: chain M residue 89 ASP Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain M residue 111 THR Chi-restraints excluded: chain N residue 38 PHE Chi-restraints excluded: chain N residue 63 TYR Chi-restraints excluded: chain N residue 65 THR Chi-restraints excluded: chain N residue 93 LEU Chi-restraints excluded: chain O residue 10 LEU Chi-restraints excluded: chain O residue 32 THR Chi-restraints excluded: chain O residue 44 THR Chi-restraints excluded: chain O residue 75 ASP Chi-restraints excluded: chain O residue 98 VAL Chi-restraints excluded: chain P residue 15 VAL Chi-restraints excluded: chain P residue 45 THR Chi-restraints excluded: chain P residue 73 VAL Chi-restraints excluded: chain P residue 95 THR Chi-restraints excluded: chain P residue 109 ILE Chi-restraints excluded: chain Q residue 34 THR Chi-restraints excluded: chain Q residue 54 VAL Chi-restraints excluded: chain Q residue 77 SER Chi-restraints excluded: chain Q residue 118 VAL Chi-restraints excluded: chain R residue 64 VAL Chi-restraints excluded: chain S residue 44 VAL Chi-restraints excluded: chain S residue 61 ASN Chi-restraints excluded: chain S residue 85 GLU Chi-restraints excluded: chain T residue 10 ILE Chi-restraints excluded: chain T residue 13 GLU Chi-restraints excluded: chain T residue 14 PHE Chi-restraints excluded: chain T residue 44 GLU Chi-restraints excluded: chain T residue 48 ASP Chi-restraints excluded: chain T residue 69 LEU Chi-restraints excluded: chain U residue 6 LEU Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain U residue 35 ARG Chi-restraints excluded: chain V residue 8 GLN Chi-restraints excluded: chain V residue 24 ILE Chi-restraints excluded: chain V residue 32 ILE Chi-restraints excluded: chain V residue 49 ASN Chi-restraints excluded: chain V residue 52 CYS Chi-restraints excluded: chain V residue 56 ASP Chi-restraints excluded: chain V residue 61 ARG Chi-restraints excluded: chain W residue 27 THR Chi-restraints excluded: chain W residue 53 GLN Chi-restraints excluded: chain W residue 64 LEU Chi-restraints excluded: chain X residue 10 ILE Chi-restraints excluded: chain X residue 12 LEU Chi-restraints excluded: chain X residue 18 VAL Chi-restraints excluded: chain X residue 66 VAL Chi-restraints excluded: chain Y residue 11 ILE Chi-restraints excluded: chain Y residue 70 LYS Chi-restraints excluded: chain Y residue 78 LEU Chi-restraints excluded: chain Y residue 79 THR Chi-restraints excluded: chain Z residue 5 VAL Chi-restraints excluded: chain Z residue 12 ASP Chi-restraints excluded: chain Z residue 32 ARG Chi-restraints excluded: chain 8 residue 58 GLU Chi-restraints excluded: chain 8 residue 105 VAL Chi-restraints excluded: chain 8 residue 116 VAL Chi-restraints excluded: chain 8 residue 135 VAL Chi-restraints excluded: chain 8 residue 138 ILE Chi-restraints excluded: chain 8 residue 141 VAL Chi-restraints excluded: chain 8 residue 154 VAL Chi-restraints excluded: chain 8 residue 200 VAL Chi-restraints excluded: chain 8 residue 204 TYR Chi-restraints excluded: chain 8 residue 244 THR Chi-restraints excluded: chain 8 residue 295 ILE Chi-restraints excluded: chain 8 residue 366 MET Chi-restraints excluded: chain 8 residue 409 MET Chi-restraints excluded: chain 8 residue 420 VAL Chi-restraints excluded: chain 8 residue 488 VAL Chi-restraints excluded: chain 8 residue 586 VAL Chi-restraints excluded: chain 8 residue 587 ASP Chi-restraints excluded: chain 8 residue 628 THR Chi-restraints excluded: chain 8 residue 632 ILE Chi-restraints excluded: chain 8 residue 660 LEU Chi-restraints excluded: chain 8 residue 698 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1109 random chunks: chunk 539 optimal weight: 5.9990 chunk 698 optimal weight: 40.0000 chunk 937 optimal weight: 50.0000 chunk 269 optimal weight: 8.9990 chunk 811 optimal weight: 20.0000 chunk 129 optimal weight: 9.9990 chunk 244 optimal weight: 9.9990 chunk 881 optimal weight: 20.0000 chunk 368 optimal weight: 9.9990 chunk 904 optimal weight: 10.0000 chunk 111 optimal weight: 7.9990 overall best weight: 8.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 127 ASN ** c 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 57 ASN ** m 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 39 ASN u 98 ASN ** v 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 167 HIS ** J 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 75 GLN N 36 GLN ** T 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 18 GLN Y 12 GLN ** Y 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 74 HIS ** 8 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.071252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.055151 restraints weight = 852523.929| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 2.54 r_work: 0.3248 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3242 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3242 r_free = 0.3242 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3242 r_free = 0.3242 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3242 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.4333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 166272 Z= 0.306 Angle : 0.699 26.224 247962 Z= 0.357 Chirality : 0.039 0.268 31576 Planarity : 0.005 0.069 13872 Dihedral : 23.590 177.388 81251 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 20.11 Ramachandran Plot: Outliers : 0.12 % Allowed : 12.60 % Favored : 87.28 % Rotamer: Outliers : 5.03 % Allowed : 22.66 % Favored : 72.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.44 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.60 (0.10), residues: 6517 helix: -0.63 (0.11), residues: 2066 sheet: -1.70 (0.15), residues: 1082 loop : -2.49 (0.10), residues: 3369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP V 72 HIS 0.009 0.001 HIS q 13 PHE 0.040 0.002 PHE Z 36 TYR 0.040 0.002 TYR I 75 ARG 0.011 0.001 ARG f 94 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 38134.08 seconds wall clock time: 668 minutes 30.64 seconds (40110.64 seconds total)