Starting phenix.real_space_refine on Tue Mar 26 02:59:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k53_22672/03_2024/7k53_22672_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k53_22672/03_2024/7k53_22672.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k53_22672/03_2024/7k53_22672.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k53_22672/03_2024/7k53_22672.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k53_22672/03_2024/7k53_22672_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k53_22672/03_2024/7k53_22672_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.018 sd= 1.346 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 4805 5.49 5 S 155 5.16 5 C 75150 2.51 5 N 27875 2.21 5 O 41713 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "b TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 235": "OE1" <-> "OE2" Residue "c ARG 13": "NH1" <-> "NH2" Residue "c ARG 33": "NH1" <-> "NH2" Residue "c ARG 59": "NH1" <-> "NH2" Residue "c ARG 77": "NH1" <-> "NH2" Residue "c ARG 83": "NH1" <-> "NH2" Residue "c PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 169": "NH1" <-> "NH2" Residue "c ARG 184": "NH1" <-> "NH2" Residue "d GLU 2": "OE1" <-> "OE2" 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 GLU 152": "OE1" <-> "OE2" Residue "d ARG 162": "NH1" <-> "NH2" Residue "d ARG 170": "NH1" <-> "NH2" Residue "e GLU 31": "OE1" <-> "OE2" Residue "e ARG 70": "NH1" <-> "NH2" Residue "e ARG 79": "NH1" <-> "NH2" Residue "e ARG 91": "NH1" <-> "NH2" Residue "e GLU 93": "OE1" <-> "OE2" Residue "e PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ARG 101": "NH1" <-> "NH2" Residue "e ARG 109": "NH1" <-> "NH2" Residue "e ARG 111": "NH1" <-> "NH2" Residue "e ARG 114": "NH1" <-> "NH2" Residue "e ARG 132": "NH1" <-> "NH2" Residue "f ARG 2": "NH1" <-> "NH2" Residue "f ARG 152": "NH1" <-> "NH2" Residue "f ARG 162": "NH1" <-> "NH2" Residue "f ARG 169": "NH1" <-> "NH2" Residue "h PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i GLU 49": "OE1" <-> "OE2" Residue "i PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j ARG 13": "NH1" <-> "NH2" Residue "j ARG 37": "NH1" <-> "NH2" Residue "j ARG 96": "NH1" <-> "NH2" Residue "j ARG 120": "NH1" <-> "NH2" Residue "k GLU 4": "OE1" <-> "OE2" Residue "l ARG 21": "NH1" <-> "NH2" Residue "l ARG 33": "NH1" <-> "NH2" Residue "l ARG 41": "NH1" <-> "NH2" Residue "l ARG 47": "NH1" <-> "NH2" Residue "l ARG 60": "NH1" <-> "NH2" Residue "l ARG 78": "NH1" <-> "NH2" Residue "l ARG 126": "NH1" <-> "NH2" Residue "m ARG 10": "NH1" <-> "NH2" Residue "m ARG 18": "NH1" <-> "NH2" Residue "m ARG 40": "NH1" <-> "NH2" Residue "m ARG 44": "NH1" <-> "NH2" Residue "m ARG 50": "NH1" <-> "NH2" Residue "m ARG 55": "NH1" <-> "NH2" Residue "m ARG 59": "NH1" <-> "NH2" Residue "m GLU 111": "OE1" <-> "OE2" Residue "m ARG 114": "NH1" <-> "NH2" Residue "n ARG 8": "NH1" <-> "NH2" Residue "n ARG 12": "NH1" <-> "NH2" Residue "n ARG 17": "NH1" <-> "NH2" Residue "n ARG 22": "NH1" <-> "NH2" Residue "n ARG 46": "NH1" <-> "NH2" Residue "n ARG 63": "NH1" <-> "NH2" Residue "n ARG 64": "NH1" <-> "NH2" Residue "n ARG 69": "NH1" <-> "NH2" Residue "n ARG 71": "NH1" <-> "NH2" Residue "n ARG 96": "NH1" <-> "NH2" Residue "n ARG 118": "NH1" <-> "NH2" Residue "o ARG 10": "NH1" <-> "NH2" Residue "o ARG 16": "NH1" <-> "NH2" Residue "o ARG 25": "NH1" <-> "NH2" Residue "o ARG 81": "NH1" <-> "NH2" Residue "o ARG 94": "NH1" <-> "NH2" Residue "o ARG 102": "NH1" <-> "NH2" Residue "o ARG 111": "NH1" <-> "NH2" Residue "o PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p ARG 20": "NH1" <-> "NH2" Residue "p ARG 38": "NH1" <-> "NH2" Residue "p PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p ARG 61": "NH1" <-> "NH2" Residue "p ARG 88": "NH1" <-> "NH2" Residue "p ARG 100": "NH1" <-> "NH2" Residue "p ARG 108": "NH1" <-> "NH2" Residue "q ARG 2": "NH1" <-> "NH2" Residue "q ARG 5": "NH1" <-> "NH2" Residue "q ARG 12": "NH1" <-> "NH2" Residue "q ARG 32": "NH1" <-> "NH2" Residue "q ARG 47": "NH1" <-> "NH2" Residue "q ARG 69": "NH1" <-> "NH2" Residue "q PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r TYR 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r ARG 21": "NH1" <-> "NH2" Residue "r ASP 26": "OD1" <-> "OD2" 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 "r PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s GLU 2": "OE1" <-> "OE2" Residue "s PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 GLU 18": "OE1" <-> "OE2" Residue "t GLU 56": "OE1" <-> "OE2" 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 "y ARG 29": "NH1" <-> "NH2" Residue "y ARG 47": "NH1" <-> "NH2" Residue "y ARG 52": "NH1" <-> "NH2" Residue "z ARG 10": "NH1" <-> "NH2" Residue "z ARG 29": "NH1" <-> "NH2" Residue "z ARG 44": "NH1" <-> "NH2" Residue "A ASP 31": "OD1" <-> "OD2" Residue "A ARG 49": "NH1" <-> "NH2" Residue "A ARG 56": "NH1" <-> "NH2" Residue "A ASP 58": "OD1" <-> "OD2" Residue "B ARG 9": "NH1" <-> "NH2" Residue "B ARG 15": "NH1" <-> "NH2" Residue "B ARG 39": "NH1" <-> "NH2" Residue "B ARG 51": "NH1" <-> "NH2" Residue "C TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 43": "NH1" <-> "NH2" Residue "C GLU 50": "OE1" <-> "OE2" Residue "D ARG 3": "NH1" <-> "NH2" Residue "D ARG 12": "NH1" <-> "NH2" Residue "D ARG 14": "NH1" <-> "NH2" Residue "D ARG 19": "NH1" <-> "NH2" Residue "D ARG 21": "NH1" <-> "NH2" Residue "D ARG 33": "NH1" <-> "NH2" Residue "D ARG 41": "NH1" <-> "NH2" Residue "E ARG 12": "NH1" <-> "NH2" Residue "E ARG 29": "NH1" <-> "NH2" Residue "E ARG 39": "NH1" <-> "NH2" Residue "E ARG 41": "NH1" <-> "NH2" Residue "F ARG 12": "NH1" <-> "NH2" Residue "F ARG 24": "NH1" <-> "NH2" Residue "G ARG 107": "NH1" <-> "NH2" Residue "G ASP 187": "OD1" <-> "OD2" Residue "G ARG 224": "NH1" <-> "NH2" Residue "H ARG 106": "NH1" <-> "NH2" Residue "H ARG 130": "NH1" <-> "NH2" Residue "I PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 146": "OE1" <-> "OE2" Residue "J GLU 54": "OE1" <-> "OE2" Residue "J ARG 156": "NH1" <-> "NH2" Residue "K GLU 98": "OE1" <-> "OE2" Residue "M TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 52": "OE1" <-> "OE2" Residue "N ARG 123": "NH1" <-> "NH2" Residue "O ASP 97": "OD1" <-> "OD2" Residue "Q ARG 55": "NH1" <-> "NH2" Residue "Q PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 10": "OD1" <-> "OD2" Residue "S GLU 38": "OE1" <-> "OE2" Residue "U ARG 28": "NH1" <-> "NH2" Residue "U PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 47": "OE1" <-> "OE2" Residue "U ASP 55": "OD1" <-> "OD2" Residue "V GLU 25": "OE1" <-> "OE2" Residue "V GLU 48": "OE1" <-> "OE2" Residue "W ARG 11": "NH1" <-> "NH2" Residue "X ASP 11": "OD1" <-> "OD2" Residue "X GLU 72": "OE1" <-> "OE2" Residue "Z ASP 12": "OD1" <-> "OD2" Residue "Z GLU 23": "OE1" <-> "OE2" Residue "Z ARG 66": "NH1" <-> "NH2" Residue "a ARG 7": "NH1" <-> "NH2" Residue "a ARG 12": "NH1" <-> "NH2" Residue "a GLU 32": "OE1" <-> "OE2" Residue "a ARG 162": "NH1" <-> "NH2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 149698 Number of models: 1 Model: "" Number of chains: 60 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': 94, 'rna2p_pyr': 57, 'rna3p_pur': 780, 'rna3p_pyr': 608} Link IDs: {'rna2p': 151, 'rna3p': 1387} 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': 221, 'rna2p_pyr': 100, 'rna3p_pur': 1453, 'rna3p_pyr': 1129} Link IDs: {'rna2p': 321, 'rna3p': 2581} 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': 6, 'rna2p_pyr': 2, 'rna3p_pur': 59, 'rna3p_pyr': 53} Link IDs: {'rna2p': 8, 'rna3p': 111} Chain: "5" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1640 Classifications: {'RNA': 77} Modifications used: {'5*END': 1, 'rna2p_pur': 5, 'rna2p_pyr': 4, 'rna3p_pur': 34, 'rna3p_pyr': 34} Link IDs: {'rna2p': 9, 'rna3p': 67} Chain: "6" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1640 Classifications: {'RNA': 77} Modifications used: {'5*END': 1, 'rna2p_pur': 7, 'rna2p_pyr': 6, 'rna3p_pur': 32, 'rna3p_pyr': 32} Link IDs: {'rna2p': 12, 'rna3p': 64} Chain: "4" Number of atoms: 388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 388 Classifications: {'RNA': 18} Modifications used: {'5*END': 1, 'rna2p_pur': 1, 'rna3p_pur': 12, 'rna3p_pyr': 5} Link IDs: {'rna2p': 1, 'rna3p': 16} Chain: "7" Number of atoms: 1647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1647 Classifications: {'RNA': 77} Modifications used: {'rna2p_pur': 9, 'rna2p_pyr': 5, 'rna3p_pur': 31, 'rna3p_pyr': 32} Link IDs: {'rna2p': 14, 'rna3p': 62} Chain: "5" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 59.15, per 1000 atoms: 0.40 Number of scatterers: 149698 At special positions: 0 Unit cell: (273, 253.05, 245.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 155 16.00 P 4805 15.00 O 41713 8.00 N 27875 7.00 C 75150 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: 64.92 Conformation dependent library (CDL) restraints added in 6.4 seconds 11672 Ramachandran restraints generated. 5836 Oldfield, 0 Emsley, 5836 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10924 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: 181 helices and 67 sheets defined 38.2% alpha, 17.8% beta 1517 base pairs and 2421 stacking pairs defined. Time for finding SS restraints: 79.04 Creating SS restraints... Processing helix chain 'b' and resid 9 through 15 removed outlier: 7.647A pdb=" N HIS b 14 " --> pdb=" O PRO b 10 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N VAL b 15 " --> pdb=" O GLY b 11 " (cutoff:3.500A) Processing helix chain 'b' and resid 29 through 34 removed outlier: 4.555A pdb=" N LEU b 33 " --> pdb=" O PHE b 29 " (cutoff:3.500A) removed outlier: 5.490A 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: 4.221A 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: 3.565A pdb=" N ALA b 210 " --> pdb=" O LYS b 206 " (cutoff:3.500A) Processing helix chain 'b' and resid 220 through 225 removed outlier: 3.801A pdb=" N MET b 224 " --> pdb=" O ARG b 220 " (cutoff:3.500A) removed outlier: 5.471A 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: 6.717A pdb=" N ASP b 263 " --> pdb=" O ASN b 259 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N LYS b 264 " --> pdb=" O LYS b 260 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N PHE b 265 " --> pdb=" O ARG b 261 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ILE b 266 " --> pdb=" O THR b 262 " (cutoff:3.500A) removed outlier: 4.969A 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: 4.305A pdb=" N MET b 200 " --> pdb=" O ALA b 197 " (cutoff:3.500A) Processing helix chain 'c' and resid 61 through 72 Processing helix chain 'c' and resid 98 through 105 removed outlier: 3.820A pdb=" N ALA c 102 " --> pdb=" O VAL c 98 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N ASP c 103 " --> pdb=" O GLU c 99 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N VAL c 104 " --> pdb=" O LEU c 100 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N LYS c 105 " --> pdb=" O PHE c 101 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 98 through 105' Processing helix chain 'c' and resid 120 through 125 Processing helix chain 'c' and resid 39 through 44 Processing helix chain 'd' and resid 15 through 20 Processing helix chain 'd' and resid 24 through 40 Processing helix chain 'd' and resid 97 through 116 Processing helix chain 'd' and resid 130 through 142 removed outlier: 3.702A pdb=" N LEU d 134 " --> pdb=" O LYS d 130 " (cutoff:3.500A) 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 Processing helix chain 'e' and resid 1 through 20 removed outlier: 3.960A pdb=" N ASP e 5 " --> pdb=" O ALA e 1 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N VAL e 12 " --> pdb=" O LYS e 8 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LYS e 13 " --> pdb=" O ASP e 9 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLU e 18 " --> pdb=" O LYS e 14 " (cutoff:3.500A) Processing helix chain 'e' and resid 41 through 46 removed outlier: 3.799A pdb=" N LYS e 46 " --> pdb=" O ALA e 42 " (cutoff:3.500A) Processing helix chain 'e' and resid 47 through 61 removed outlier: 4.591A pdb=" N GLY e 61 " --> pdb=" O ALA e 57 " (cutoff:3.500A) Processing helix chain 'e' and resid 92 through 110 removed outlier: 3.637A pdb=" N ILE e 105 " --> pdb=" O ARG e 101 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N VAL e 107 " --> pdb=" O ILE e 103 " (cutoff:3.500A) Proline residue: e 108 - end of helix Processing helix chain 'e' and resid 161 through 173 Processing helix chain 'e' and resid 133 through 138 removed outlier: 3.857A pdb=" N ILE e 136 " --> pdb=" O GLU e 133 " (cutoff:3.500A) Proline residue: e 138 - end of helix Processing helix chain 'f' and resid 1 through 6 removed outlier: 5.483A pdb=" N ALA f 6 " --> pdb=" O ARG f 2 " (cutoff:3.500A) Processing helix chain 'f' and resid 58 through 80 removed outlier: 4.529A pdb=" N ALA f 62 " --> pdb=" O ALA f 58 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL f 78 " --> pdb=" O MET f 74 " (cutoff:3.500A) Processing helix chain 'f' and resid 136 through 152 removed outlier: 4.071A pdb=" N ARG f 151 " --> pdb=" O LEU f 147 " (cutoff:3.500A) Processing helix chain 'g' and resid 22 through 29 Processing helix chain 'g' and resid 40 through 50 removed outlier: 4.051A pdb=" N ALA g 49 " --> pdb=" O GLU g 45 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ARG g 50 " --> pdb=" O PHE g 46 " (cutoff:3.500A) Processing helix chain 'g' and resid 95 through 107 removed outlier: 3.767A pdb=" N ALA g 106 " --> pdb=" O ALA g 102 " (cutoff:3.500A) Processing helix chain 'g' and resid 111 through 116 removed outlier: 5.052A pdb=" N ARG g 116 " --> pdb=" O LYS g 112 " (cutoff:3.500A) Processing helix chain 'h' and resid 3 through 19 removed outlier: 3.610A pdb=" N GLN h 9 " --> pdb=" O LEU h 5 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N SER h 16 " --> pdb=" O VAL h 12 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLU h 17 " --> pdb=" O ALA h 13 " (cutoff:3.500A) Processing helix chain 'h' and resid 33 through 48 removed outlier: 4.273A pdb=" N ARG h 42 " --> pdb=" O MET h 38 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA h 48 " --> pdb=" O ALA h 44 " (cutoff:3.500A) Processing helix chain 'h' and resid 62 through 68 Proline residue: h 68 - end of helix Processing helix chain 'i' and resid 23 through 31 removed outlier: 5.148A pdb=" N LEU i 27 " --> pdb=" O VAL i 23 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N GLN i 30 " --> pdb=" O ALA i 26 " (cutoff:3.500A) Processing helix chain 'i' and resid 35 through 49 removed outlier: 3.506A pdb=" N LYS i 44 " --> pdb=" O ALA i 40 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N SER i 47 " --> pdb=" O ALA i 43 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ILE i 48 " --> pdb=" O LYS i 44 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N GLU i 49 " --> pdb=" O THR i 45 " (cutoff:3.500A) Processing helix chain 'j' and resid 24 through 38 Processing helix chain 'j' and resid 67 through 72 Processing helix chain 'j' and resid 88 through 96 Processing helix chain 'j' and resid 97 through 110 removed outlier: 3.993A pdb=" N ILE j 101 " --> pdb=" O PRO j 97 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N MET j 108 " --> pdb=" O ALA j 104 " (cutoff:3.500A) Proline residue: j 110 - end of helix Processing helix chain 'j' and resid 112 through 123 removed outlier: 3.915A pdb=" N LYS j 121 " --> pdb=" O ALA j 117 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N LEU j 122 " --> pdb=" O MET j 118 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N LYS j 123 " --> pdb=" O PHE j 119 " (cutoff:3.500A) Processing helix chain 'j' and resid 130 through 135 removed outlier: 4.087A pdb=" N ALA j 133 " --> pdb=" O HIS j 130 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N ALA j 134 " --> pdb=" O ASN j 131 " (cutoff:3.500A) Processing helix chain 'k' and resid 109 through 120 removed outlier: 6.618A pdb=" N MET k 113 " --> pdb=" O SER k 109 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N LYS k 114 " --> pdb=" O GLU k 110 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ILE k 115 " --> pdb=" O LYS k 111 " (cutoff:3.500A) Proline residue: k 120 - end of helix Processing helix chain 'l' and resid 56 through 62 removed outlier: 3.513A 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: 4.157A pdb=" N ALA l 72 " --> pdb=" O SER l 68 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N ALA l 75 " --> pdb=" O ALA l 71 " (cutoff:3.500A) Processing helix chain 'l' and resid 78 through 83 removed outlier: 3.992A pdb=" N LEU l 82 " --> pdb=" O ARG l 78 " (cutoff:3.500A) removed outlier: 4.755A 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: 3.610A pdb=" N LEU l 95 " --> pdb=" O ASP l 91 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS l 96 " --> pdb=" O LEU l 92 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N ALA l 97 " --> pdb=" O ASN l 93 " (cutoff:3.500A) Processing helix chain 'l' and resid 128 through 139 Processing helix chain 'm' and resid 42 through 58 removed outlier: 5.664A pdb=" N ALA m 56 " --> pdb=" O ALA m 52 " (cutoff:3.500A) Processing helix chain 'm' and resid 109 through 125 removed outlier: 3.605A pdb=" N LEU m 119 " --> pdb=" O GLU m 115 " (cutoff:3.500A) Proline residue: m 125 - end of helix Processing helix chain 'n' and resid 13 through 32 Processing helix chain 'n' and resid 37 through 58 removed outlier: 4.200A pdb=" N ARG n 46 " --> pdb=" O LYS n 42 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N VAL n 47 " --> pdb=" O GLU n 43 " (cutoff:3.500A) Proline residue: n 50 - end of helix removed outlier: 4.402A pdb=" N THR n 57 " --> pdb=" O THR n 53 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N ASP n 58 " --> pdb=" O LEU n 54 " (cutoff:3.500A) Processing helix chain 'n' and resid 59 through 71 removed outlier: 4.516A pdb=" N THR n 70 " --> pdb=" O ALA n 66 " (cutoff:3.500A) Processing helix chain 'n' and resid 72 through 82 removed outlier: 4.073A pdb=" N PHE n 80 " --> pdb=" O VAL n 76 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ASN n 81 " --> pdb=" O ALA n 77 " (cutoff:3.500A) Processing helix chain 'n' and resid 83 through 88 Processing helix chain 'o' and resid 2 through 22 removed outlier: 5.583A pdb=" N ARG o 13 " --> pdb=" O ARG o 9 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N ALA o 14 " --> pdb=" O ARG o 10 " (cutoff:3.500A) Processing helix chain 'o' and resid 55 through 63 removed outlier: 5.030A pdb=" N GLN o 61 " --> pdb=" O ALA o 57 " (cutoff:3.500A) removed outlier: 5.088A 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 13 removed outlier: 4.429A pdb=" N GLN p 11 " --> pdb=" O LEU p 7 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N LYS p 13 " --> pdb=" O GLN p 9 " (cutoff:3.500A) Processing helix chain 'p' and resid 96 through 103 removed outlier: 4.823A pdb=" N ARG p 100 " --> pdb=" O LEU p 96 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N GLU p 101 " --> pdb=" O TYR p 97 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ARG p 102 " --> pdb=" O TYR p 98 " (cutoff:3.500A) removed outlier: 4.936A 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 5 through 21 removed outlier: 4.515A pdb=" N GLN q 19 " --> pdb=" O LYS q 15 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS q 21 " --> pdb=" O LEU q 17 " (cutoff:3.500A) Processing helix chain 'q' and resid 25 through 30 removed outlier: 4.320A pdb=" N ARG q 29 " --> pdb=" O GLY q 25 " (cutoff:3.500A) Processing helix chain 'q' and resid 38 through 60 removed outlier: 4.049A pdb=" N ARG q 50 " --> pdb=" O TYR q 46 " (cutoff:3.500A) removed outlier: 3.691A 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 removed outlier: 3.763A pdb=" N ASP q 96 " --> pdb=" O LYS q 92 " (cutoff:3.500A) Processing helix chain 'q' and resid 102 through 117 Processing helix chain 's' and resid 13 through 25 removed outlier: 4.663A pdb=" N LEU s 23 " --> pdb=" O LEU s 19 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ILE s 24 " --> pdb=" O VAL s 20 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ARG s 25 " --> pdb=" O ALA s 21 " (cutoff:3.500A) Processing helix chain 's' and resid 28 through 40 removed outlier: 3.535A pdb=" N ASP s 34 " --> pdb=" O SER s 30 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N ASN s 40 " --> pdb=" O LEU s 36 " (cutoff:3.500A) Processing helix chain 's' and resid 41 through 61 Processing helix chain 't' and resid 1 through 11 removed outlier: 4.145A pdb=" N GLU t 5 " --> pdb=" O MET t 1 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LYS t 9 " --> pdb=" O GLU t 5 " (cutoff:3.500A) removed outlier: 4.197A 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: 4.120A pdb=" N VAL u 69 " --> pdb=" O GLN u 65 " (cutoff:3.500A) removed outlier: 5.271A 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: 4.032A pdb=" N ALA v 23 " --> pdb=" O ARG v 19 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ASN v 24 " --> pdb=" O LEU v 20 " (cutoff:3.500A) Processing helix chain 'v' and resid 43 through 53 removed outlier: 3.501A pdb=" N VAL v 47 " --> pdb=" O ASP v 43 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ALA v 52 " --> pdb=" O MET v 48 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N LYS v 53 " --> pdb=" O ASN v 49 " (cutoff:3.500A) Processing helix chain 'v' and resid 54 through 59 removed outlier: 4.101A pdb=" N SER v 58 " --> pdb=" O ALA v 54 " (cutoff:3.500A) Processing helix chain 'x' and resid 51 through 62 removed outlier: 4.229A pdb=" N GLY x 62 " --> pdb=" O ILE x 58 " (cutoff:3.500A) Processing helix chain 'x' and resid 63 through 74 Processing helix chain 'y' and resid 1 through 6 Processing helix chain 'y' and resid 9 through 23 Processing helix chain 'y' and resid 25 through 35 removed outlier: 3.859A pdb=" N GLY y 35 " --> pdb=" O GLN y 31 " (cutoff:3.500A) Processing helix chain 'y' and resid 40 through 61 removed outlier: 3.540A pdb=" N LYS y 44 " --> pdb=" O SER y 40 " (cutoff:3.500A) Processing helix chain 'z' and resid 16 through 27 Processing helix chain 'z' and resid 40 through 51 Processing helix chain 'A' and resid 45 through 52 removed outlier: 3.522A pdb=" N ASP A 50 " --> pdb=" O GLY A 46 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N ALA A 52 " --> pdb=" O GLN A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 65 removed outlier: 4.923A pdb=" N ARG A 59 " --> pdb=" O GLY A 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 18 removed outlier: 4.727A pdb=" N HIS B 18 " --> pdb=" O MET B 14 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 16 Processing helix chain 'D' and resid 17 through 24 removed outlier: 4.184A 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: 3.667A pdb=" N ARG E 12 " --> pdb=" O GLY E 8 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 45 removed outlier: 3.980A pdb=" N ARG E 44 " --> pdb=" O LYS E 40 " (cutoff:3.500A) Proline residue: E 45 - end of helix Processing helix chain 'E' and resid 50 through 62 removed outlier: 4.063A pdb=" N GLY E 55 " --> pdb=" O LYS E 51 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N LEU E 56 " --> pdb=" O GLY E 52 " (cutoff:3.500A) Proline residue: E 62 - end of helix Processing helix chain 'G' and resid 23 through 28 removed outlier: 4.409A pdb=" N LYS G 27 " --> pdb=" O ASN G 23 " (cutoff:3.500A) Proline residue: G 28 - end of helix No H-bonds generated for 'chain 'G' and resid 23 through 28' Processing helix chain 'G' and resid 43 through 63 Proline residue: G 47 - end of helix Processing helix chain 'G' and resid 72 through 87 removed outlier: 6.126A pdb=" N SER G 76 " --> pdb=" O LYS G 72 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N GLU G 77 " --> pdb=" O ARG G 73 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N ALA G 78 " --> pdb=" O ALA G 74 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N CYS G 86 " --> pdb=" O ALA G 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 98 through 103 Processing helix chain 'G' and resid 104 through 122 removed outlier: 4.763A pdb=" N GLN G 108 " --> pdb=" O LYS G 104 " (cutoff:3.500A) Processing helix chain 'G' and resid 129 through 147 Processing helix chain 'G' and resid 164 through 169 removed outlier: 3.709A pdb=" N GLU G 168 " --> pdb=" O ASP G 164 " (cutoff:3.500A) Processing helix chain 'G' and resid 170 through 179 removed outlier: 4.527A pdb=" N GLY G 179 " --> pdb=" O ALA G 175 " (cutoff:3.500A) Processing helix chain 'G' and resid 191 through 196 removed outlier: 4.572A pdb=" N VAL G 195 " --> pdb=" O ASP G 191 " (cutoff:3.500A) removed outlier: 5.015A 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 224 removed outlier: 3.560A pdb=" N VAL G 209 " --> pdb=" O ALA G 205 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ARG G 224 " --> pdb=" O VAL G 220 " (cutoff:3.500A) Processing helix chain 'H' and resid 5 through 12 removed outlier: 3.571A pdb=" N ARG H 10 " --> pdb=" O PRO H 6 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N GLY H 12 " --> pdb=" O GLY H 8 " (cutoff:3.500A) Processing helix chain 'H' and resid 24 through 46 removed outlier: 4.920A pdb=" N ALA H 29 " --> pdb=" O THR H 25 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N ASP H 30 " --> pdb=" O LYS H 26 " (cutoff:3.500A) Processing helix chain 'H' and resid 71 through 77 Processing helix chain 'H' and resid 80 through 95 removed outlier: 3.654A pdb=" N VAL H 89 " --> pdb=" O LYS H 85 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 126 Processing helix chain 'H' and resid 128 through 144 Processing helix chain 'I' and resid 6 through 15 removed outlier: 4.008A pdb=" N LEU I 10 " --> pdb=" O PRO I 6 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 65 Processing helix chain 'I' and resid 67 through 81 removed outlier: 3.821A pdb=" N LEU I 81 " --> pdb=" O GLU I 77 " (cutoff:3.500A) Processing helix chain 'I' and resid 84 through 96 Processing helix chain 'I' and resid 97 through 105 Processing helix chain 'I' and resid 109 through 120 removed outlier: 3.540A pdb=" N HIS I 119 " --> pdb=" O GLN I 115 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LYS I 120 " --> pdb=" O LEU I 116 " (cutoff:3.500A) Processing helix chain 'I' and resid 151 through 165 removed outlier: 6.390A pdb=" N LYS I 155 " --> pdb=" O GLN I 151 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ALA I 156 " --> pdb=" O SER I 152 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N GLN I 163 " --> pdb=" O GLU I 159 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARG I 164 " --> pdb=" O LEU I 160 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N GLU I 165 " --> pdb=" O ALA I 161 " (cutoff:3.500A) Processing helix chain 'I' and resid 195 through 205 removed outlier: 4.923A pdb=" N ILE I 199 " --> pdb=" O ASN I 195 " (cutoff:3.500A) Processing helix chain 'I' and resid 38 through 43 removed outlier: 4.491A pdb=" N ALA I 42 " --> pdb=" O GLN I 39 " (cutoff:3.500A) Processing helix chain 'J' and resid 54 through 70 removed outlier: 3.646A pdb=" N GLU J 64 " --> pdb=" O GLN J 60 " (cutoff:3.500A) Processing helix chain 'J' and resid 108 through 118 removed outlier: 6.745A pdb=" N ALA J 112 " --> pdb=" O GLY J 108 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL J 113 " --> pdb=" O ALA J 109 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA J 117 " --> pdb=" O VAL J 113 " (cutoff:3.500A) Processing helix chain 'J' and resid 131 through 147 removed outlier: 5.112A pdb=" N ASN J 147 " --> pdb=" O LEU J 143 " (cutoff:3.500A) Processing helix chain 'J' and resid 148 through 156 Processing helix chain 'J' and resid 159 through 165 Processing helix chain 'K' and resid 11 through 18 removed outlier: 3.782A pdb=" N GLU K 16 " --> pdb=" O PRO K 12 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLN K 17 " --> pdb=" O ASP K 13 " (cutoff:3.500A) Processing helix chain 'K' and resid 19 through 33 Processing helix chain 'K' and resid 67 through 82 removed outlier: 5.530A 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: 4.627A pdb=" N ARG L 52 " --> pdb=" O THR L 48 " (cutoff:3.500A) Processing helix chain 'L' and resid 57 through 69 removed outlier: 4.074A pdb=" N ALA L 64 " --> pdb=" O ALA L 60 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ASN L 67 " --> pdb=" O VAL L 63 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N VAL L 68 " --> pdb=" O ALA L 64 " (cutoff:3.500A) Processing helix chain 'L' and resid 91 through 110 removed outlier: 3.822A pdb=" N ALA L 97 " --> pdb=" O VAL L 93 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LYS L 109 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ARG L 110 " --> pdb=" O ALA L 106 " (cutoff:3.500A) Processing helix chain 'L' and resid 114 through 129 Processing helix chain 'L' and resid 131 through 148 removed outlier: 3.806A pdb=" N ALA L 146 " --> pdb=" O ARG L 142 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ASN L 147 " --> pdb=" O MET L 143 " (cutoff:3.500A) Processing helix chain 'M' and resid 4 through 20 Processing helix chain 'M' and resid 29 through 43 Processing helix chain 'M' and resid 111 through 119 Processing helix chain 'N' and resid 33 through 38 Processing helix chain 'N' and resid 44 through 55 removed outlier: 4.470A pdb=" N ARG N 48 " --> pdb=" O ARG N 44 " (cutoff:3.500A) Proline residue: N 50 - end of helix removed outlier: 4.353A pdb=" N LEU N 53 " --> pdb=" O GLN N 49 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N VAL N 54 " --> pdb=" O PRO N 50 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ASP N 55 " --> pdb=" O LEU N 51 " (cutoff:3.500A) Processing helix chain 'N' and resid 70 through 88 removed outlier: 4.052A pdb=" N MET N 87 " --> pdb=" O THR N 83 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N GLU N 88 " --> pdb=" O ARG N 84 " (cutoff:3.500A) Processing helix chain 'N' and resid 90 through 101 removed outlier: 4.721A pdb=" N GLU N 96 " --> pdb=" O SER N 92 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N ALA N 100 " --> pdb=" O GLU N 96 " (cutoff:3.500A) Processing helix chain 'O' and resid 14 through 33 removed outlier: 3.543A pdb=" N ALA O 29 " --> pdb=" O ILE O 25 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N THR O 32 " --> pdb=" O THR O 28 " (cutoff:3.500A) Processing helix chain 'O' and resid 80 through 90 removed outlier: 4.592A pdb=" N ASP O 85 " --> pdb=" O GLU O 81 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N ALA O 86 " --> pdb=" O LYS O 82 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N MET O 88 " --> pdb=" O VAL O 84 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N ARG O 89 " --> pdb=" O ASP O 85 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N LEU O 90 " --> pdb=" O ALA O 86 " (cutoff:3.500A) Processing helix chain 'P' and resid 45 through 50 removed outlier: 3.830A pdb=" N GLY P 50 " --> pdb=" O ALA P 46 " (cutoff:3.500A) Processing helix chain 'P' and resid 53 through 59 removed outlier: 4.013A pdb=" N SER P 57 " --> pdb=" O GLY P 53 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N THR P 58 " --> pdb=" O SER P 54 " (cutoff:3.500A) Proline residue: P 59 - end of helix No H-bonds generated for 'chain 'P' and resid 53 through 59' Processing helix chain 'P' and resid 60 through 74 removed outlier: 5.568A pdb=" N ALA P 72 " --> pdb=" O ARG P 68 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N VAL P 73 " --> pdb=" O CYS P 69 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N LYS P 74 " --> pdb=" O ALA P 70 " (cutoff:3.500A) Processing helix chain 'P' and resid 91 through 103 removed outlier: 5.597A pdb=" N THR P 95 " --> pdb=" O GLY P 91 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N ILE P 96 " --> pdb=" O ARG P 92 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLY P 103 " --> pdb=" O LEU P 99 " (cutoff:3.500A) Processing helix chain 'Q' and resid 2 through 10 Proline residue: Q 10 - end of helix Processing helix chain 'Q' and resid 112 through 117 removed outlier: 4.963A pdb=" N TYR Q 116 " --> pdb=" O ALA Q 112 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLY Q 117 " --> pdb=" O ARG Q 113 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 112 through 117' Processing helix chain 'R' and resid 13 through 21 removed outlier: 4.531A 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: 5.178A pdb=" N SER R 48 " --> pdb=" O ILE R 44 " (cutoff:3.500A) Processing helix chain 'R' and resid 49 through 63 removed outlier: 4.252A pdb=" N THR R 54 " --> pdb=" O GLY R 50 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LYS R 61 " --> pdb=" O ASP R 57 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N PHE R 62 " --> pdb=" O GLU R 58 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N VAL R 63 " --> pdb=" O VAL R 59 " (cutoff:3.500A) Processing helix chain 'R' and resid 65 through 83 Processing helix chain 'R' and resid 84 through 93 Processing helix chain 'R' and resid 105 through 110 Processing helix chain 'S' and resid 2 through 25 removed outlier: 4.118A pdb=" N PHE S 20 " --> pdb=" O ALA S 16 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N ALA S 21 " --> pdb=" O ASP S 17 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N LYS S 22 " --> pdb=" O LYS S 18 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N ALA S 24 " --> pdb=" O PHE S 20 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N GLU S 25 " --> pdb=" O ALA S 21 " (cutoff:3.500A) Processing helix chain 'S' and resid 37 through 52 removed outlier: 4.170A pdb=" N TRP S 41 " --> pdb=" O ASP S 37 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N GLN S 48 " --> pdb=" O VAL S 44 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR S 49 " --> pdb=" O LEU S 45 " (cutoff:3.500A) Proline residue: S 51 - end of helix Processing helix chain 'S' and resid 79 through 90 Processing helix chain 'S' and resid 26 through 31 Processing helix chain 'T' and resid 3 through 15 removed outlier: 4.196A pdb=" N SER T 12 " --> pdb=" O ALA T 8 " (cutoff:3.500A) Processing helix chain 'T' and resid 23 through 46 removed outlier: 4.291A pdb=" N GLY T 40 " --> pdb=" O ASN T 36 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N HIS T 41 " --> pdb=" O HIS T 37 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N HIS T 45 " --> pdb=" O HIS T 41 " (cutoff:3.500A) removed outlier: 3.642A 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 Processing helix chain 'U' and resid 68 through 79 Processing helix chain 'W' and resid 12 through 17 removed outlier: 3.675A pdb=" N GLY W 16 " --> pdb=" O PHE W 12 " (cutoff:3.500A) Processing helix chain 'W' and resid 24 through 33 removed outlier: 3.931A pdb=" N LEU W 28 " --> pdb=" O ASP W 24 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ASN W 30 " --> pdb=" O ALA W 26 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N TYR W 31 " --> pdb=" O THR W 27 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE W 32 " --> pdb=" O LEU W 28 " (cutoff:3.500A) removed outlier: 5.228A 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: 3.520A pdb=" N GLU X 23 " --> pdb=" O GLU X 19 " (cutoff:3.500A) Processing helix chain 'X' and resid 69 through 75 removed outlier: 4.845A pdb=" N PHE X 73 " --> pdb=" O LYS X 69 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ALA X 74 " --> pdb=" O LEU X 70 " (cutoff:3.500A) Proline residue: X 75 - end of helix No H-bonds generated for 'chain 'X' and resid 69 through 75' Processing helix chain 'Y' and resid 6 through 41 removed outlier: 4.888A pdb=" N ALA Y 10 " --> pdb=" O ALA Y 6 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ILE Y 11 " --> pdb=" O LYS Y 7 " (cutoff:3.500A) Processing helix chain 'Y' and resid 42 through 62 Proline residue: Y 55 - end of helix Processing helix chain 'Y' and resid 67 through 86 removed outlier: 5.802A pdb=" N ALA Y 71 " --> pdb=" O HIS Y 67 " (cutoff:3.500A) Processing helix chain 'Z' and resid 16 through 23 removed outlier: 4.428A pdb=" N ARG Z 20 " --> pdb=" O ARG Z 16 " (cutoff:3.500A) Processing helix chain 'Z' and resid 24 through 31 removed outlier: 5.766A pdb=" N LEU Z 28 " --> pdb=" O LYS Z 24 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N GLU Z 30 " --> pdb=" O GLY Z 26 " (cutoff:3.500A) Processing helix chain 'Z' and resid 36 through 61 Proline residue: Z 40 - end of helix Processing helix chain 'a' and resid 6 through 16 removed outlier: 3.711A pdb=" N VAL a 10 " --> pdb=" O LYS a 6 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL a 15 " --> pdb=" O ILE a 11 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N ASP a 16 " --> pdb=" O ARG a 12 " (cutoff:3.500A) Processing helix chain 'a' and resid 23 through 34 removed outlier: 4.272A pdb=" N ALA a 28 " --> pdb=" O ASN a 24 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU a 30 " --> pdb=" O ALA a 26 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N LYS a 31 " --> pdb=" O ILE a 27 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N GLU a 32 " --> pdb=" O ALA a 28 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N LEU a 33 " --> pdb=" O LEU a 29 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ALA a 34 " --> pdb=" O LEU a 30 " (cutoff:3.500A) Processing helix chain 'a' and resid 181 through 200 removed outlier: 3.567A pdb=" N ASN a 188 " --> pdb=" O LYS a 184 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'b' and resid 1 through 4 Processing sheet with id= 2, first strand: chain 'b' and resid 79 through 82 removed outlier: 6.688A pdb=" N LEU b 92 " --> pdb=" O GLU b 78 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N ASP b 113 " --> pdb=" O VAL b 77 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'b' and resid 137 through 141 removed outlier: 4.164A pdb=" N SER b 138 " --> pdb=" O ILE b 163 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N THR b 172 " --> pdb=" O VAL b 164 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N GLU b 179 " --> pdb=" O LEU b 175 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'b' and resid 90 through 95 removed outlier: 4.545A pdb=" N GLU b 99 " --> pdb=" O TYR b 95 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'c' and resid 3 through 9 removed outlier: 4.233A pdb=" N SER c 199 " --> pdb=" O LYS c 8 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N ASP c 200 " --> pdb=" O THR c 112 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N THR c 112 " --> pdb=" O ASP c 200 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'c' and resid 10 through 16 removed outlier: 3.784A pdb=" N GLY c 10 " --> pdb=" O VAL c 26 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N VAL c 20 " --> pdb=" O THR c 16 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'c' and resid 79 through 84 removed outlier: 6.351A pdb=" N ARG c 46 " --> pdb=" O LEU c 84 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N GLN c 94 " --> pdb=" O VAL c 34 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'd' and resid 1 through 5 removed outlier: 6.009A pdb=" N MET d 1 " --> pdb=" O THR d 13 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N THR d 13 " --> pdb=" O MET d 1 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N LEU d 3 " --> pdb=" O ALA d 11 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ALA d 11 " --> pdb=" O LEU d 3 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N LEU d 5 " --> pdb=" O GLN d 9 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'd' and resid 117 through 120 removed outlier: 5.280A pdb=" N ARG d 117 " --> pdb=" O ASP d 184 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL d 187 " --> pdb=" O LEU d 147 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASP d 168 " --> pdb=" O VAL d 146 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'e' and resid 64 through 68 removed outlier: 3.941A pdb=" N GLY e 85 " --> pdb=" O THR e 67 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LYS e 32 " --> pdb=" O THR e 156 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N GLY e 38 " --> pdb=" O GLY e 150 " (cutoff:3.500A) removed outlier: 8.576A pdb=" N GLY e 150 " --> pdb=" O GLY e 38 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LEU e 151 " --> pdb=" O VAL e 131 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'f' and resid 15 through 18 Processing sheet with id= 12, first strand: chain 'f' and resid 40 through 44 Processing sheet with id= 13, first strand: chain 'f' and resid 81 through 88 Processing sheet with id= 14, first strand: chain 'f' and resid 93 through 97 Processing sheet with id= 15, first strand: chain 'g' and resid 16 through 20 removed outlier: 4.052A pdb=" N ASP g 17 " --> pdb=" O LEU g 5 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N LYS g 35 " --> pdb=" O LEU g 6 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'g' and resid 78 through 83 removed outlier: 4.362A pdb=" N SER g 82 " --> pdb=" O VAL g 147 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'i' and resid 8 through 11 removed outlier: 3.687A pdb=" N VAL i 8 " --> pdb=" O ILE i 58 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N VAL i 56 " --> pdb=" O LEU i 10 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N SER i 65 " --> pdb=" O TYR i 61 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'j' and resid 14 through 19 Processing sheet with id= 19, first strand: chain 'j' and resid 74 through 78 removed outlier: 5.734A pdb=" N GLY j 83 " --> pdb=" O THR j 78 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'k' and resid 17 through 21 removed outlier: 6.794A pdb=" N ARG k 17 " --> pdb=" O VAL k 10 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N THR k 6 " --> pdb=" O CYS k 21 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N ASN k 82 " --> pdb=" O MET k 7 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'k' and resid 39 through 42 Processing sheet with id= 22, first strand: chain 'm' and resid 62 through 65 removed outlier: 4.270A pdb=" N TYR m 103 " --> pdb=" O LEU m 33 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N LEU m 33 " --> pdb=" O LEU m 102 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'm' and resid 73 through 76 removed outlier: 6.866A pdb=" N ILE m 73 " --> pdb=" O GLU m 90 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'm' and resid 31 through 36 removed outlier: 6.966A pdb=" N LYS m 127 " --> pdb=" O VAL m 36 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'o' and resid 49 through 53 removed outlier: 3.590A pdb=" N VAL o 49 " --> pdb=" O VAL o 39 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N ILE o 35 " --> pdb=" O THR o 53 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N VAL o 28 " --> pdb=" O ASP o 93 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'p' and resid 37 through 44 removed outlier: 6.455A pdb=" N THR p 24 " --> pdb=" O LYS p 86 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER p 82 " --> pdb=" O LYS p 28 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'p' and resid 48 through 52 removed outlier: 3.804A pdb=" N ALA p 48 " --> pdb=" O THR p 59 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N ARG p 52 " --> pdb=" O HIS p 55 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N SER p 56 " --> pdb=" O THR p 75 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'r' and resid 2 through 6 Processing sheet with id= 29, first strand: chain 'r' and resid 18 through 23 removed outlier: 3.576A pdb=" N GLN r 18 " --> pdb=" O ILE r 98 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ASP r 95 " --> pdb=" O VAL r 64 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N LYS r 60 " --> pdb=" O THR r 99 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL r 33 " --> pdb=" O ALA r 61 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLU r 31 " --> pdb=" O VAL r 63 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'r' and resid 57 through 60 removed outlier: 4.415A pdb=" N VAL r 58 " --> pdb=" O SER r 102 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N SER r 102 " --> pdb=" O VAL r 58 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY r 100 " --> pdb=" O LYS r 60 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'r' and resid 65 through 73 removed outlier: 5.226A pdb=" N GLN r 91 " --> pdb=" O GLY r 69 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N LYS r 71 " --> pdb=" O HIS r 89 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N HIS r 89 " --> pdb=" O LYS r 71 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N LYS r 73 " --> pdb=" O GLN r 87 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N GLN r 87 " --> pdb=" O LYS r 73 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 's' and resid 2 through 8 removed outlier: 3.930A pdb=" N THR s 3 " --> pdb=" O VAL s 107 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N THR s 100 " --> pdb=" O GLY s 79 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLY s 79 " --> pdb=" O THR s 100 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 't' and resid 12 through 15 removed outlier: 6.086A pdb=" N VAL t 31 " --> pdb=" O HIS t 15 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N LYS t 81 " --> pdb=" O VAL t 34 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N LYS t 66 " --> pdb=" O ARG t 77 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N ASP t 79 " --> pdb=" O LYS t 64 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N LYS t 64 " --> pdb=" O ASP t 79 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N LYS t 81 " --> pdb=" O VAL t 62 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N VAL t 62 " --> pdb=" O LYS t 81 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ALA t 83 " --> pdb=" O THR t 60 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N THR t 60 " --> pdb=" O ALA t 83 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N VAL t 85 " --> pdb=" O VAL t 58 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N VAL t 58 " --> pdb=" O VAL t 85 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'u' and resid 39 through 43 removed outlier: 4.882A pdb=" N ASN u 39 " --> pdb=" O ALA u 62 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'u' and resid 81 through 84 removed outlier: 4.763A pdb=" N ARG u 81 " --> pdb=" O LYS u 96 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N ARG u 93 " --> pdb=" O ILE u 102 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'v' and resid 69 through 72 removed outlier: 3.913A pdb=" N ARG v 9 " --> pdb=" O ALA v 39 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ALA v 39 " --> pdb=" O ARG v 9 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE v 89 " --> pdb=" O PRO v 27 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'w' and resid 47 through 50 removed outlier: 4.179A pdb=" N THR w 54 " --> pdb=" O GLY w 50 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'w' and resid 62 through 67 Processing sheet with id= 39, first strand: chain 'x' and resid 11 through 18 removed outlier: 3.883A pdb=" N THR x 24 " --> pdb=" O ASN x 16 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ASN x 22 " --> pdb=" O SER x 18 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'x' and resid 34 through 40 Processing sheet with id= 41, first strand: chain 'z' and resid 33 through 38 removed outlier: 4.266A pdb=" N HIS z 33 " --> pdb=" O GLN z 8 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N LYS z 5 " --> pdb=" O GLU z 57 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N MET z 53 " --> pdb=" O THR z 9 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'A' and resid 21 through 25 removed outlier: 3.864A pdb=" N LEU A 32 " --> pdb=" O THR A 13 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'C' and resid 18 through 23 removed outlier: 5.890A pdb=" N HIS C 18 " --> pdb=" O SER C 12 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N ILE C 47 " --> pdb=" O SER C 13 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU C 35 " --> pdb=" O TYR C 48 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'G' and resid 29 through 33 No H-bonds generated for sheet with id= 44 Processing sheet with id= 45, first strand: chain 'G' and resid 88 through 92 Processing sheet with id= 46, first strand: chain 'H' and resid 52 through 58 Processing sheet with id= 47, first strand: chain 'H' and resid 163 through 170 removed outlier: 3.537A pdb=" N GLY H 147 " --> pdb=" O PHE H 202 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N ARG H 178 " --> pdb=" O ILE H 206 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ILE H 206 " --> pdb=" O ARG H 178 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'I' and resid 139 through 143 removed outlier: 6.307A pdb=" N GLU I 178 " --> pdb=" O ASP I 173 " (cutoff:3.500A) removed outlier: 9.114A pdb=" N TRP I 169 " --> pdb=" O LYS I 182 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'J' and resid 10 through 15 removed outlier: 3.939A pdb=" N GLN J 11 " --> pdb=" O GLY J 39 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N LEU J 35 " --> pdb=" O ILE J 15 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'J' and resid 82 through 87 removed outlier: 7.326A pdb=" N HIS J 82 " --> pdb=" O PRO J 97 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N VAL J 93 " --> pdb=" O GLY J 86 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ARG J 92 " --> pdb=" O TYR J 127 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N TYR J 127 " --> pdb=" O ARG J 92 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'J' and resid 32 through 40 removed outlier: 4.438A pdb=" N GLY J 50 " --> pdb=" O ALA J 34 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ARG J 44 " --> pdb=" O ASP J 40 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'K' and resid 38 through 42 removed outlier: 4.427A pdb=" N ASN K 63 " --> pdb=" O ARG K 38 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLU K 40 " --> pdb=" O LEU K 61 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU K 61 " --> pdb=" O GLU K 40 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N TYR K 59 " --> pdb=" O TRP K 42 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL K 10 " --> pdb=" O HIS K 58 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N ILE K 6 " --> pdb=" O MET K 62 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N HIS K 3 " --> pdb=" O THR K 92 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N GLU K 5 " --> pdb=" O MET K 90 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N MET K 90 " --> pdb=" O GLU K 5 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'K' and resid 43 through 47 removed outlier: 5.984A pdb=" N LEU K 47 " --> pdb=" O HIS K 55 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N HIS K 55 " --> pdb=" O LEU K 47 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'L' and resid 72 through 76 Processing sheet with id= 55, first strand: chain 'M' and resid 22 through 28 removed outlier: 6.634A pdb=" N ALA M 22 " --> pdb=" O LEU M 62 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLU M 51 " --> pdb=" O GLU M 57 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N THR M 61 " --> pdb=" O ASP M 47 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N ASP M 47 " --> pdb=" O THR M 61 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'M' and resid 73 through 76 removed outlier: 3.944A pdb=" N SER M 73 " --> pdb=" O ALA M 129 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N VAL M 102 " --> pdb=" O ILE M 125 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'N' and resid 4 through 10 removed outlier: 4.427A pdb=" N GLY N 9 " --> pdb=" O ALA N 16 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N LYS N 26 " --> pdb=" O LEU N 60 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'O' and resid 42 through 52 removed outlier: 5.259A pdb=" N LEU O 71 " --> pdb=" O PRO O 43 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N ILE O 8 " --> pdb=" O VAL O 74 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'P' and resid 41 through 44 removed outlier: 4.714A pdb=" N ASN P 108 " --> pdb=" O LEU P 81 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N GLY P 87 " --> pdb=" O VAL P 112 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'Q' and resid 28 through 31 removed outlier: 5.456A pdb=" N LEU Q 80 " --> pdb=" O VAL Q 97 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N ARG Q 93 " --> pdb=" O GLY Q 84 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'Q' and resid 35 through 41 removed outlier: 4.781A pdb=" N ARG Q 35 " --> pdb=" O ARG Q 53 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N ALA Q 47 " --> pdb=" O PRO Q 41 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N LYS Q 50 " --> pdb=" O ILE Q 66 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N PHE Q 60 " --> pdb=" O LEU Q 56 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'U' and resid 4 through 11 removed outlier: 4.205A pdb=" N ALA U 7 " --> pdb=" O GLN U 18 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'U' and resid 37 through 40 No H-bonds generated for sheet with id= 63 Processing sheet with id= 64, first strand: chain 'V' and resid 6 through 11 removed outlier: 3.797A pdb=" N ASP V 56 " --> pdb=" O VAL V 11 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N GLU V 59 " --> pdb=" O VAL V 75 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'V' and resid 18 through 29 No H-bonds generated for sheet with id= 65 Processing sheet with id= 66, first strand: chain 'X' and resid 29 through 33 removed outlier: 3.603A pdb=" N ILE X 48 " --> pdb=" O VAL X 59 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'a' and resid 169 through 175 removed outlier: 5.761A pdb=" N GLY a 169 " --> pdb=" O LEU a 48 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N VAL a 42 " --> pdb=" O ILE a 175 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA a 45 " --> pdb=" O SER a 213 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N LYS a 211 " --> pdb=" O ASN a 47 " (cutoff:3.500A) 1845 hydrogen bonds defined for protein. 5430 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3817 hydrogen bonds 6134 hydrogen bond angles 0 basepair planarities 1517 basepair parallelities 2421 stacking parallelities Total time for adding SS restraints: 223.16 Time building geometry restraints manager: 69.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.28: 11787 1.28 - 1.42: 60903 1.42 - 1.57: 80079 1.57 - 1.71: 9652 1.71 - 1.86: 276 Bond restraints: 162697 Sorted by residual: bond pdb=" C ASP K 13 " pdb=" O ASP K 13 " ideal model delta sigma weight residual 1.236 1.448 -0.211 1.25e-02 6.40e+03 2.85e+02 bond pdb=" C ALA h 44 " pdb=" O ALA h 44 " ideal model delta sigma weight residual 1.236 1.443 -0.207 1.29e-02 6.01e+03 2.58e+02 bond pdb=" C VAL h 12 " pdb=" O VAL h 12 " ideal model delta sigma weight residual 1.237 1.424 -0.186 1.17e-02 7.31e+03 2.54e+02 bond pdb=" C ALA a 26 " pdb=" O ALA a 26 " ideal model delta sigma weight residual 1.236 1.410 -0.174 1.15e-02 7.56e+03 2.29e+02 bond pdb=" C GLU g 114 " pdb=" O GLU g 114 " ideal model delta sigma weight residual 1.236 1.422 -0.186 1.32e-02 5.74e+03 1.99e+02 ... (remaining 162692 not shown) Histogram of bond angle deviations from ideal: 98.90 - 106.24: 28799 106.24 - 113.58: 96703 113.58 - 120.93: 70396 120.93 - 128.27: 39504 128.27 - 135.61: 8101 Bond angle restraints: 243503 Sorted by residual: angle pdb=" N LEU L 29 " pdb=" CA LEU L 29 " pdb=" C LEU L 29 " ideal model delta sigma weight residual 114.62 98.90 15.72 1.14e+00 7.69e-01 1.90e+02 angle pdb=" N ILE j 81 " pdb=" CA ILE j 81 " pdb=" C ILE j 81 " ideal model delta sigma weight residual 110.62 125.43 -14.81 1.14e+00 7.69e-01 1.69e+02 angle pdb=" CA ASP K 13 " pdb=" C ASP K 13 " pdb=" O ASP K 13 " ideal model delta sigma weight residual 120.10 131.78 -11.68 1.13e+00 7.83e-01 1.07e+02 angle pdb=" C TYR f 163 " pdb=" N ALA f 164 " pdb=" CA ALA f 164 " ideal model delta sigma weight residual 120.44 107.44 13.00 1.30e+00 5.92e-01 1.00e+02 angle pdb=" O GLN N 31 " pdb=" C GLN N 31 " pdb=" N ARG N 32 " ideal model delta sigma weight residual 121.87 111.53 10.34 1.05e+00 9.07e-01 9.71e+01 ... (remaining 243498 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.51: 92787 35.51 - 71.02: 10274 71.02 - 106.54: 1219 106.54 - 142.05: 18 142.05 - 177.56: 22 Dihedral angle restraints: 104320 sinusoidal: 87390 harmonic: 16930 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 32.85 -67.85 1 8.00e+00 1.56e-02 9.34e+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 80.75 66.25 1 8.00e+00 1.56e-02 8.96e+01 dihedral pdb=" O4' C 6 34 " pdb=" C1' C 6 34 " pdb=" N1 C 6 34 " pdb=" C2 C 6 34 " ideal model delta sinusoidal sigma weight residual -160.00 8.94 -168.94 1 1.50e+01 4.44e-03 8.45e+01 ... (remaining 104317 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.119: 26507 0.119 - 0.238: 4207 0.238 - 0.357: 394 0.357 - 0.476: 33 0.476 - 0.595: 5 Chirality restraints: 31146 Sorted by residual: chirality pdb=" P C 7 1 " pdb=" OP1 C 7 1 " pdb=" OP2 C 7 1 " pdb=" O5' C 7 1 " both_signs ideal model delta sigma weight residual True 2.41 -3.01 -0.59 2.00e-01 2.50e+01 8.85e+00 chirality pdb=" C3' G 31190 " pdb=" C4' G 31190 " pdb=" O3' G 31190 " pdb=" C2' G 31190 " both_signs ideal model delta sigma weight residual False -2.74 -2.22 -0.52 2.00e-01 2.50e+01 6.86e+00 chirality pdb=" C3' A 31201 " pdb=" C4' A 31201 " pdb=" O3' A 31201 " pdb=" C2' A 31201 " both_signs ideal model delta sigma weight residual False -2.74 -2.23 -0.51 2.00e-01 2.50e+01 6.63e+00 ... (remaining 31143 not shown) Planarity restraints: 12986 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A 2 119 " 0.319 2.00e-02 2.50e+03 1.40e-01 5.42e+02 pdb=" N9 A 2 119 " -0.017 2.00e-02 2.50e+03 pdb=" C8 A 2 119 " -0.128 2.00e-02 2.50e+03 pdb=" N7 A 2 119 " -0.114 2.00e-02 2.50e+03 pdb=" C5 A 2 119 " -0.062 2.00e-02 2.50e+03 pdb=" C6 A 2 119 " 0.049 2.00e-02 2.50e+03 pdb=" N6 A 2 119 " 0.222 2.00e-02 2.50e+03 pdb=" N1 A 2 119 " 0.019 2.00e-02 2.50e+03 pdb=" C2 A 2 119 " -0.064 2.00e-02 2.50e+03 pdb=" N3 A 2 119 " -0.117 2.00e-02 2.50e+03 pdb=" C4 A 2 119 " -0.105 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U 2 1 " -0.229 2.00e-02 2.50e+03 1.30e-01 3.79e+02 pdb=" N1 U 2 1 " 0.004 2.00e-02 2.50e+03 pdb=" C2 U 2 1 " 0.044 2.00e-02 2.50e+03 pdb=" O2 U 2 1 " 0.087 2.00e-02 2.50e+03 pdb=" N3 U 2 1 " 0.047 2.00e-02 2.50e+03 pdb=" C4 U 2 1 " 0.052 2.00e-02 2.50e+03 pdb=" O4 U 2 1 " -0.239 2.00e-02 2.50e+03 pdb=" C5 U 2 1 " 0.128 2.00e-02 2.50e+03 pdb=" C6 U 2 1 " 0.105 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U 11647 " 0.220 2.00e-02 2.50e+03 1.17e-01 3.09e+02 pdb=" N1 U 11647 " -0.012 2.00e-02 2.50e+03 pdb=" C2 U 11647 " -0.043 2.00e-02 2.50e+03 pdb=" O2 U 11647 " -0.086 2.00e-02 2.50e+03 pdb=" N3 U 11647 " -0.030 2.00e-02 2.50e+03 pdb=" C4 U 11647 " -0.028 2.00e-02 2.50e+03 pdb=" O4 U 11647 " 0.199 2.00e-02 2.50e+03 pdb=" C5 U 11647 " -0.111 2.00e-02 2.50e+03 pdb=" C6 U 11647 " -0.109 2.00e-02 2.50e+03 ... (remaining 12983 not shown) Histogram of nonbonded interaction distances: 1.86 - 2.47: 134 2.47 - 3.08: 95797 3.08 - 3.69: 278099 3.69 - 4.29: 408938 4.29 - 4.90: 561950 Nonbonded interactions: 1344918 Sorted by model distance: nonbonded pdb=" O LYS a 6 " pdb=" N MET a 8 " model vdw 1.865 2.520 nonbonded pdb=" O THR a 5 " pdb=" O LYS a 6 " model vdw 2.036 3.040 nonbonded pdb=" O ARG J 92 " pdb=" O VAL J 93 " model vdw 2.157 3.040 nonbonded pdb=" O LYS g 8 " pdb=" O GLY g 13 " model vdw 2.221 3.040 nonbonded pdb=" O ASN U 79 " pdb=" N ALA U 82 " model vdw 2.253 2.520 ... (remaining 1344913 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain '5' and resid 1 through 76) selection = chain '6' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.530 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: 0.110 Extract box with map and model: 19.670 Check model and map are aligned: 1.690 Set scattering table: 1.050 Process input model: 534.600 Find NCS groups from input model: 3.070 Set up NCS constraints: 0.430 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:2.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 566.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.211 162697 Z= 0.590 Angle : 1.103 19.301 243503 Z= 0.732 Chirality : 0.089 0.595 31146 Planarity : 0.013 0.140 12986 Dihedral : 22.552 177.559 93396 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 18.16 Ramachandran Plot: Outliers : 1.15 % Allowed : 14.08 % Favored : 84.77 % Rotamer: Outliers : 1.50 % Allowed : 6.81 % Favored : 91.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.74 (0.10), residues: 5836 helix: -1.71 (0.11), residues: 1723 sheet: -2.64 (0.15), residues: 972 loop : -2.94 (0.10), residues: 3141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.083 0.007 TRP b 212 HIS 0.002 0.000 HIS Y 67 PHE 0.030 0.004 PHE k 79 TYR 0.064 0.008 TYR E 63 ARG 0.008 0.001 ARG k 30 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11672 Ramachandran restraints generated. 5836 Oldfield, 0 Emsley, 5836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11672 Ramachandran restraints generated. 5836 Oldfield, 0 Emsley, 5836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1579 residues out of total 4862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 1506 time to evaluate : 6.751 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: c 1 MET cc_start: 0.7797 (ppp) cc_final: 0.7573 (ppp) REVERT: c 2 ILE cc_start: 0.8408 (pt) cc_final: 0.8051 (pt) REVERT: d 1 MET cc_start: 0.6565 (mmm) cc_final: 0.6334 (mmm) REVERT: e 82 TYR cc_start: 0.8152 (t80) cc_final: 0.7919 (t80) REVERT: e 89 THR cc_start: 0.8904 (m) cc_final: 0.8381 (p) REVERT: e 143 ASP cc_start: 0.7009 (m-30) cc_final: 0.6540 (m-30) REVERT: f 115 GLN cc_start: 0.8361 (OUTLIER) cc_final: 0.8107 (pp30) REVERT: g 18 GLN cc_start: 0.7639 (tt0) cc_final: 0.7389 (tp-100) REVERT: j 67 ASN cc_start: 0.8164 (m-40) cc_final: 0.7890 (m-40) REVERT: m 17 ASN cc_start: 0.8859 (OUTLIER) cc_final: 0.8361 (t0) REVERT: m 103 TYR cc_start: 0.7995 (m-80) cc_final: 0.7788 (m-80) REVERT: n 75 ILE cc_start: 0.9497 (mm) cc_final: 0.9271 (mm) REVERT: n 82 GLU cc_start: 0.7746 (mp0) cc_final: 0.7522 (mp0) REVERT: o 55 GLU cc_start: 0.7952 (mt-10) cc_final: 0.7583 (mp0) REVERT: o 56 LYS cc_start: 0.7646 (mppt) cc_final: 0.7180 (mppt) REVERT: o 61 GLN cc_start: 0.8747 (mp10) cc_final: 0.8393 (pp30) REVERT: o 87 ILE cc_start: 0.8795 (mm) cc_final: 0.8438 (mp) REVERT: r 2 TYR cc_start: 0.7870 (p90) cc_final: 0.7564 (p90) REVERT: r 24 LYS cc_start: 0.9052 (ttmt) cc_final: 0.8453 (ttmt) REVERT: r 37 GLU cc_start: 0.8240 (mm-30) cc_final: 0.7330 (tm-30) REVERT: r 97 LYS cc_start: 0.9188 (tttt) cc_final: 0.8913 (ttmm) REVERT: t 42 GLU cc_start: 0.8798 (mt-10) cc_final: 0.8598 (mt-10) REVERT: t 87 LEU cc_start: 0.8760 (mp) cc_final: 0.8487 (mp) REVERT: u 39 ASN cc_start: 0.8198 (m-40) cc_final: 0.7744 (t0) REVERT: u 48 VAL cc_start: 0.8700 (OUTLIER) cc_final: 0.8200 (p) REVERT: u 80 ASP cc_start: 0.6854 (m-30) cc_final: 0.6384 (m-30) REVERT: v 8 VAL cc_start: 0.9013 (t) cc_final: 0.8753 (p) REVERT: v 60 VAL cc_start: 0.8952 (t) cc_final: 0.8331 (t) REVERT: w 53 HIS cc_start: 0.8384 (m170) cc_final: 0.8182 (m170) REVERT: w 54 THR cc_start: 0.8961 (m) cc_final: 0.8687 (t) REVERT: y 1 MET cc_start: 0.5129 (ttm) cc_final: 0.4527 (ttt) REVERT: y 8 GLU cc_start: 0.8236 (mp0) cc_final: 0.7389 (mp0) REVERT: y 15 ASN cc_start: 0.9034 (t0) cc_final: 0.8815 (m110) REVERT: y 24 GLU cc_start: 0.8502 (mp0) cc_final: 0.7952 (mp0) REVERT: y 59 GLU cc_start: 0.8675 (mt-10) cc_final: 0.8430 (mt-10) REVERT: B 31 LYS cc_start: 0.8770 (pttt) cc_final: 0.8547 (pttm) REVERT: C 16 THR cc_start: 0.8087 (t) cc_final: 0.7846 (p) REVERT: C 24 LYS cc_start: 0.8396 (ttpt) cc_final: 0.8149 (ptmt) REVERT: C 35 LEU cc_start: 0.7922 (mt) cc_final: 0.7594 (mp) REVERT: C 38 PHE cc_start: 0.7836 (t80) cc_final: 0.7242 (t80) REVERT: D 8 SER cc_start: 0.8782 (t) cc_final: 0.8543 (p) REVERT: G 15 PHE cc_start: 0.7176 (p90) cc_final: 0.6950 (p90) REVERT: G 22 TRP cc_start: 0.8959 (p-90) cc_final: 0.8344 (p-90) REVERT: G 49 PHE cc_start: 0.7533 (p90) cc_final: 0.7314 (t80) REVERT: G 135 MET cc_start: 0.9367 (ttp) cc_final: 0.8850 (tmm) REVERT: G 183 PHE cc_start: 0.7913 (m-80) cc_final: 0.7425 (m-80) REVERT: H 111 ASP cc_start: 0.8697 (t70) cc_final: 0.8496 (t0) REVERT: H 153 SER cc_start: 0.9023 (p) cc_final: 0.8765 (p) REVERT: H 182 ASP cc_start: 0.8669 (t0) cc_final: 0.8393 (t0) REVERT: I 3 TYR cc_start: 0.6944 (t80) cc_final: 0.6596 (t80) REVERT: I 85 THR cc_start: 0.9371 (m) cc_final: 0.9139 (t) REVERT: I 140 ASP cc_start: 0.7991 (m-30) cc_final: 0.7504 (m-30) REVERT: J 28 ARG cc_start: 0.7923 (ptp-170) cc_final: 0.7243 (ptt-90) REVERT: K 1 MET cc_start: 0.8293 (tmm) cc_final: 0.7964 (tmm) REVERT: K 26 THR cc_start: 0.8917 (p) cc_final: 0.8695 (p) REVERT: K 62 MET cc_start: 0.8654 (tpt) cc_final: 0.8308 (tmm) REVERT: L 100 MET cc_start: 0.8848 (mpp) cc_final: 0.8246 (mpp) REVERT: M 57 GLU cc_start: 0.8630 (mm-30) cc_final: 0.7602 (mm-30) REVERT: M 113 ARG cc_start: 0.8860 (ttp80) cc_final: 0.8430 (ttm-80) REVERT: N 18 VAL cc_start: 0.8735 (t) cc_final: 0.8438 (m) REVERT: N 29 ILE cc_start: 0.8735 (tt) cc_final: 0.8340 (tp) REVERT: N 52 GLU cc_start: 0.9070 (tp30) cc_final: 0.8672 (tp30) REVERT: N 53 LEU cc_start: 0.8813 (mp) cc_final: 0.8358 (tt) REVERT: N 63 TYR cc_start: 0.7728 (t80) cc_final: 0.6826 (t80) REVERT: N 106 ASP cc_start: 0.8184 (t70) cc_final: 0.7926 (t0) REVERT: N 109 GLN cc_start: 0.8038 (OUTLIER) cc_final: 0.7506 (tm-30) REVERT: O 11 LYS cc_start: 0.9079 (ptpt) cc_final: 0.8787 (ptpp) REVERT: Q 39 THR cc_start: 0.8369 (p) cc_final: 0.8141 (p) REVERT: R 74 MET cc_start: 0.7910 (ppp) cc_final: 0.7664 (ppp) REVERT: S 85 GLU cc_start: 0.8354 (tp30) cc_final: 0.8033 (tp30) REVERT: T 37 HIS cc_start: 0.8469 (t-90) cc_final: 0.8259 (t-170) REVERT: T 47 LYS cc_start: 0.9077 (mmtm) cc_final: 0.8829 (mmtp) REVERT: V 56 ASP cc_start: 0.7342 (p0) cc_final: 0.7099 (p0) REVERT: W 31 TYR cc_start: 0.9105 (m-80) cc_final: 0.8870 (m-10) REVERT: W 49 LYS cc_start: 0.9596 (ttpt) cc_final: 0.9301 (ttmt) REVERT: W 53 GLN cc_start: 0.8917 (mt0) cc_final: 0.8525 (mt0) REVERT: X 19 GLU cc_start: 0.8597 (mm-30) cc_final: 0.8252 (mm-30) REVERT: X 54 ARG cc_start: 0.8035 (ptt-90) cc_final: 0.7799 (ptt90) REVERT: Y 20 ASN cc_start: 0.9040 (m-40) cc_final: 0.8707 (t0) REVERT: Y 24 ARG cc_start: 0.9220 (ttm170) cc_final: 0.8897 (mtm-85) REVERT: Y 26 MET cc_start: 0.8979 (ptp) cc_final: 0.8734 (ptp) REVERT: Y 65 LEU cc_start: 0.8626 (tt) cc_final: 0.8349 (tt) REVERT: Y 69 ASN cc_start: 0.8287 (m-40) cc_final: 0.7893 (m110) outliers start: 73 outliers final: 24 residues processed: 1558 average time/residue: 1.3931 time to fit residues: 3869.8791 Evaluate side-chains 1130 residues out of total 4862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 1102 time to evaluate : 6.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 48 ILE Chi-restraints excluded: chain b residue 104 LEU Chi-restraints excluded: chain b residue 129 LEU Chi-restraints excluded: chain b residue 267 VAL Chi-restraints excluded: chain c residue 51 THR Chi-restraints excluded: chain f residue 115 GLN Chi-restraints excluded: chain k residue 10 VAL Chi-restraints excluded: chain l residue 23 ILE Chi-restraints excluded: chain l residue 76 GLU Chi-restraints excluded: chain m residue 2 LEU Chi-restraints excluded: chain m residue 17 ASN Chi-restraints excluded: chain m residue 89 VAL Chi-restraints excluded: chain u residue 27 VAL Chi-restraints excluded: chain u residue 48 VAL Chi-restraints excluded: chain x residue 12 VAL Chi-restraints excluded: chain z residue 56 VAL Chi-restraints excluded: chain D residue 16 HIS Chi-restraints excluded: chain K residue 75 GLU Chi-restraints excluded: chain L residue 96 ASN Chi-restraints excluded: chain N residue 109 GLN Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain P residue 64 VAL Chi-restraints excluded: chain R residue 15 VAL Chi-restraints excluded: chain T residue 44 GLU Chi-restraints excluded: chain T residue 88 ARG Chi-restraints excluded: chain U residue 36 VAL Chi-restraints excluded: chain W residue 13 THR Chi-restraints excluded: chain a residue 174 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1048 random chunks: chunk 884 optimal weight: 10.0000 chunk 794 optimal weight: 10.0000 chunk 440 optimal weight: 6.9990 chunk 271 optimal weight: 9.9990 chunk 535 optimal weight: 5.9990 chunk 424 optimal weight: 6.9990 chunk 821 optimal weight: 10.0000 chunk 317 optimal weight: 10.0000 chunk 499 optimal weight: 30.0000 chunk 611 optimal weight: 20.0000 chunk 951 optimal weight: 10.0000 overall best weight: 7.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 238 ASN c 49 GLN c 94 GLN c 167 ASN c 173 GLN ** e 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 37 ASN f 72 ASN i 11 GLN ** j 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 19 GLN o 38 GLN ** q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 9 HIS ** s 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 59 ASN ** u 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 49 ASN ** C 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 122 GLN ** I 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 3 HIS K 68 GLN ** L 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 121 ASN L 147 ASN N 3 ASN O 58 ASN Q 111 GLN U 26 ASN U 29 ASN ** V 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 54 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.1940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 162697 Z= 0.330 Angle : 0.716 10.133 243503 Z= 0.372 Chirality : 0.042 0.338 31146 Planarity : 0.006 0.064 12986 Dihedral : 23.165 177.995 81765 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.17 % Allowed : 11.41 % Favored : 88.42 % Rotamer: Outliers : 4.36 % Allowed : 14.27 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -2.88 (0.10), residues: 5836 helix: -0.63 (0.11), residues: 1900 sheet: -2.30 (0.15), residues: 973 loop : -2.68 (0.10), residues: 2963 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP b 212 HIS 0.010 0.002 HIS I 197 PHE 0.037 0.002 PHE K 78 TYR 0.028 0.002 TYR Q 65 ARG 0.011 0.001 ARG f 169 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11672 Ramachandran restraints generated. 5836 Oldfield, 0 Emsley, 5836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11672 Ramachandran restraints generated. 5836 Oldfield, 0 Emsley, 5836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1425 residues out of total 4862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 212 poor density : 1213 time to evaluate : 6.800 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: c 2 ILE cc_start: 0.8455 (pt) cc_final: 0.8013 (pt) REVERT: c 27 ILE cc_start: 0.9279 (mm) cc_final: 0.8834 (tp) REVERT: d 195 GLN cc_start: 0.7983 (tp40) cc_final: 0.7757 (tp40) REVERT: e 82 TYR cc_start: 0.8063 (t80) cc_final: 0.7641 (t80) REVERT: e 89 THR cc_start: 0.8877 (m) cc_final: 0.8471 (p) REVERT: e 127 TYR cc_start: 0.8841 (t80) cc_final: 0.8598 (t80) REVERT: e 143 ASP cc_start: 0.6997 (m-30) cc_final: 0.6503 (m-30) REVERT: f 43 LYS cc_start: 0.8487 (mmmt) cc_final: 0.8269 (mmmm) REVERT: f 115 GLN cc_start: 0.8448 (OUTLIER) cc_final: 0.8120 (pp30) REVERT: f 142 GLN cc_start: 0.8309 (tp40) cc_final: 0.8089 (tp40) REVERT: g 18 GLN cc_start: 0.7776 (tt0) cc_final: 0.7313 (tp-100) REVERT: h 9 GLN cc_start: 0.5457 (OUTLIER) cc_final: 0.4904 (mm-40) REVERT: k 113 MET cc_start: 0.7557 (mmp) cc_final: 0.7311 (mmp) REVERT: l 29 LYS cc_start: 0.8948 (OUTLIER) cc_final: 0.8544 (tmtt) REVERT: m 6 ARG cc_start: 0.7225 (tpt90) cc_final: 0.6659 (tpt90) REVERT: n 29 VAL cc_start: 0.9545 (t) cc_final: 0.9339 (m) REVERT: n 75 ILE cc_start: 0.9257 (mm) cc_final: 0.8869 (mm) REVERT: n 78 LYS cc_start: 0.8445 (tttt) cc_final: 0.7893 (tttt) REVERT: n 82 GLU cc_start: 0.7482 (mp0) cc_final: 0.7199 (mp0) REVERT: o 56 LYS cc_start: 0.7629 (mppt) cc_final: 0.7118 (mppt) REVERT: o 83 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8421 (mm) REVERT: o 87 ILE cc_start: 0.8593 (mm) cc_final: 0.8274 (mp) REVERT: r 6 GLN cc_start: 0.8239 (pp30) cc_final: 0.7899 (pp30) REVERT: r 11 GLN cc_start: 0.8591 (mm-40) cc_final: 0.8182 (mt0) REVERT: r 60 LYS cc_start: 0.8952 (mmmm) cc_final: 0.8742 (mmmm) REVERT: t 6 ARG cc_start: 0.8569 (tpt170) cc_final: 0.8358 (ptp-110) REVERT: t 42 GLU cc_start: 0.8756 (mt-10) cc_final: 0.8455 (mt-10) REVERT: t 69 ARG cc_start: 0.7180 (ttp80) cc_final: 0.6517 (ttp80) REVERT: v 8 VAL cc_start: 0.9070 (t) cc_final: 0.8830 (p) REVERT: v 63 ILE cc_start: 0.9144 (mt) cc_final: 0.8872 (tp) REVERT: w 54 THR cc_start: 0.8910 (m) cc_final: 0.8523 (t) REVERT: w 62 LYS cc_start: 0.8620 (mmmt) cc_final: 0.7990 (mmmt) REVERT: y 5 GLU cc_start: 0.8403 (pt0) cc_final: 0.7963 (pt0) REVERT: y 24 GLU cc_start: 0.8093 (mp0) cc_final: 0.7519 (mp0) REVERT: C 24 LYS cc_start: 0.8367 (ttpt) cc_final: 0.7943 (tttm) REVERT: C 38 PHE cc_start: 0.7958 (t80) cc_final: 0.7737 (t80) REVERT: G 22 TRP cc_start: 0.8902 (p-90) cc_final: 0.8337 (p-90) REVERT: G 135 MET cc_start: 0.9264 (ttp) cc_final: 0.8986 (tmm) REVERT: G 161 PHE cc_start: 0.7588 (t80) cc_final: 0.7351 (t80) REVERT: H 24 ASN cc_start: 0.8009 (OUTLIER) cc_final: 0.7749 (m-40) REVERT: H 106 ARG cc_start: 0.7992 (mmp80) cc_final: 0.7781 (mmp80) REVERT: I 85 THR cc_start: 0.9266 (m) cc_final: 0.9036 (t) REVERT: I 140 ASP cc_start: 0.8062 (m-30) cc_final: 0.7422 (m-30) REVERT: J 11 GLN cc_start: 0.8222 (tt0) cc_final: 0.7933 (tt0) REVERT: J 160 VAL cc_start: 0.8238 (OUTLIER) cc_final: 0.8023 (t) REVERT: K 70 VAL cc_start: 0.9249 (t) cc_final: 0.9041 (t) REVERT: L 30 MET cc_start: 0.8336 (ttp) cc_final: 0.7836 (ttp) REVERT: L 67 ASN cc_start: 0.7284 (m-40) cc_final: 0.6891 (m110) REVERT: L 119 LEU cc_start: 0.9181 (tp) cc_final: 0.8966 (tt) REVERT: L 124 SER cc_start: 0.8591 (m) cc_final: 0.8316 (p) REVERT: M 57 GLU cc_start: 0.8257 (mm-30) cc_final: 0.8017 (mm-30) REVERT: M 113 ARG cc_start: 0.8852 (ttp80) cc_final: 0.8270 (ttm-80) REVERT: N 18 VAL cc_start: 0.8721 (t) cc_final: 0.8254 (p) REVERT: N 52 GLU cc_start: 0.9041 (tp30) cc_final: 0.8619 (tp30) REVERT: N 53 LEU cc_start: 0.8986 (mp) cc_final: 0.8390 (tt) REVERT: N 54 VAL cc_start: 0.8714 (m) cc_final: 0.8505 (m) REVERT: N 106 ASP cc_start: 0.8139 (t70) cc_final: 0.7801 (t0) REVERT: N 109 GLN cc_start: 0.8004 (OUTLIER) cc_final: 0.7523 (tm-30) REVERT: Q 2 THR cc_start: 0.8458 (m) cc_final: 0.7854 (p) REVERT: Q 69 GLU cc_start: 0.6875 (mp0) cc_final: 0.6604 (mp0) REVERT: R 68 LEU cc_start: 0.9439 (tp) cc_final: 0.9211 (tp) REVERT: T 5 GLU cc_start: 0.8197 (mm-30) cc_final: 0.7973 (mm-30) REVERT: T 70 LYS cc_start: 0.9284 (OUTLIER) cc_final: 0.8561 (ttpp) REVERT: T 88 ARG cc_start: 0.5569 (OUTLIER) cc_final: 0.1977 (mpp80) REVERT: U 35 ARG cc_start: 0.8278 (ppt170) cc_final: 0.7883 (ptt90) REVERT: V 56 ASP cc_start: 0.7249 (p0) cc_final: 0.6837 (p0) REVERT: X 14 LEU cc_start: 0.8787 (tp) cc_final: 0.8527 (tt) REVERT: X 18 VAL cc_start: 0.9011 (t) cc_final: 0.8785 (p) REVERT: X 35 ARG cc_start: 0.8729 (mtp-110) cc_final: 0.7982 (mtp-110) REVERT: X 36 ARG cc_start: 0.8494 (OUTLIER) cc_final: 0.8163 (ptm160) REVERT: X 42 ASN cc_start: 0.8239 (p0) cc_final: 0.7844 (p0) REVERT: X 54 ARG cc_start: 0.8325 (ptt-90) cc_final: 0.7359 (ptt90) REVERT: Y 20 ASN cc_start: 0.9075 (m-40) cc_final: 0.8702 (t0) REVERT: Y 65 LEU cc_start: 0.8848 (tt) cc_final: 0.8636 (tt) REVERT: Z 4 LYS cc_start: 0.8216 (tttp) cc_final: 0.7880 (tptm) REVERT: Z 19 LYS cc_start: 0.6006 (mptt) cc_final: 0.5476 (mptt) outliers start: 212 outliers final: 131 residues processed: 1314 average time/residue: 1.3039 time to fit residues: 3058.8575 Evaluate side-chains 1228 residues out of total 4862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 1087 time to evaluate : 6.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 267 VAL Chi-restraints excluded: chain c residue 60 VAL Chi-restraints excluded: chain c residue 95 SER Chi-restraints excluded: chain c residue 131 ASP Chi-restraints excluded: chain c residue 176 ASP Chi-restraints excluded: chain c residue 199 SER Chi-restraints excluded: chain c residue 200 ASP Chi-restraints excluded: chain d residue 120 VAL Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 66 ILE Chi-restraints excluded: chain e residue 86 CYS Chi-restraints excluded: chain f residue 38 ASP Chi-restraints excluded: chain f residue 115 GLN Chi-restraints excluded: chain g residue 17 ASP Chi-restraints excluded: chain g residue 20 ASN Chi-restraints excluded: chain g residue 130 VAL Chi-restraints excluded: chain h residue 9 GLN Chi-restraints excluded: chain h residue 77 VAL Chi-restraints excluded: chain j residue 60 ASP Chi-restraints excluded: chain j residue 62 VAL Chi-restraints excluded: chain k residue 10 VAL Chi-restraints excluded: chain l residue 29 LYS Chi-restraints excluded: chain l residue 76 GLU Chi-restraints excluded: chain l residue 80 SER Chi-restraints excluded: chain l residue 118 THR Chi-restraints excluded: chain l residue 142 ILE Chi-restraints excluded: chain l residue 143 GLU Chi-restraints excluded: chain m residue 2 LEU Chi-restraints excluded: chain m residue 42 THR Chi-restraints excluded: chain m residue 70 ASP Chi-restraints excluded: chain m residue 89 VAL Chi-restraints excluded: chain m residue 106 ASP Chi-restraints excluded: chain m residue 127 LYS Chi-restraints excluded: chain n residue 6 SER Chi-restraints excluded: chain n residue 53 THR Chi-restraints excluded: chain n residue 76 VAL Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain o residue 31 THR Chi-restraints excluded: chain o residue 38 GLN Chi-restraints excluded: chain o residue 58 ILE Chi-restraints excluded: chain o residue 83 LEU Chi-restraints excluded: chain o residue 91 SER Chi-restraints excluded: chain o residue 93 ASP Chi-restraints excluded: chain o residue 95 SER Chi-restraints excluded: chain p residue 8 GLU Chi-restraints excluded: chain p residue 18 SER Chi-restraints excluded: chain q residue 16 ILE Chi-restraints excluded: chain r residue 51 VAL Chi-restraints excluded: chain s residue 67 ASP Chi-restraints excluded: chain s residue 74 ILE Chi-restraints excluded: chain t residue 27 SER Chi-restraints excluded: chain t residue 79 ASP Chi-restraints excluded: chain u residue 9 GLU Chi-restraints excluded: chain u residue 11 ILE Chi-restraints excluded: chain u residue 14 THR Chi-restraints excluded: chain u residue 27 VAL Chi-restraints excluded: chain u residue 67 SER Chi-restraints excluded: chain v residue 43 ASP Chi-restraints excluded: chain v residue 62 THR Chi-restraints excluded: chain v residue 64 VAL Chi-restraints excluded: chain v residue 65 VAL Chi-restraints excluded: chain v residue 76 ASP Chi-restraints excluded: chain v residue 90 ASP Chi-restraints excluded: chain w residue 72 ASN Chi-restraints excluded: chain w residue 77 SER Chi-restraints excluded: chain x residue 12 VAL Chi-restraints excluded: chain x residue 24 THR Chi-restraints excluded: chain x residue 39 VAL Chi-restraints excluded: chain x residue 47 THR Chi-restraints excluded: chain y residue 10 SER Chi-restraints excluded: chain z residue 24 LEU Chi-restraints excluded: chain z residue 56 VAL Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 44 PHE Chi-restraints excluded: chain B residue 19 ASP Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 162 VAL Chi-restraints excluded: chain G residue 196 ASP Chi-restraints excluded: chain G residue 209 VAL Chi-restraints excluded: chain H residue 24 ASN Chi-restraints excluded: chain H residue 133 MET Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 159 GLU Chi-restraints excluded: chain I residue 168 THR Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 72 ASN Chi-restraints excluded: chain J residue 79 THR Chi-restraints excluded: chain J residue 89 THR Chi-restraints excluded: chain J residue 160 VAL Chi-restraints excluded: chain J residue 162 GLU Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain K residue 93 LYS Chi-restraints excluded: chain L residue 96 ASN Chi-restraints excluded: chain L residue 132 THR Chi-restraints excluded: chain M residue 1 SER Chi-restraints excluded: chain M residue 35 ILE Chi-restraints excluded: chain M residue 61 THR Chi-restraints excluded: chain M residue 73 SER Chi-restraints excluded: chain N residue 20 ILE Chi-restraints excluded: chain N residue 109 GLN Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain O residue 51 VAL Chi-restraints excluded: chain P residue 29 THR Chi-restraints excluded: chain P residue 34 THR Chi-restraints excluded: chain P residue 45 THR Chi-restraints excluded: chain P residue 64 VAL Chi-restraints excluded: chain P residue 94 SER Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain P residue 110 THR Chi-restraints excluded: chain P residue 112 VAL Chi-restraints excluded: chain Q residue 89 LEU Chi-restraints excluded: chain R residue 41 ASP Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 64 VAL Chi-restraints excluded: chain R residue 67 ASP Chi-restraints excluded: chain R residue 71 GLU Chi-restraints excluded: chain S residue 13 VAL Chi-restraints excluded: chain S residue 44 VAL Chi-restraints excluded: chain S residue 49 THR Chi-restraints excluded: chain S residue 55 SER Chi-restraints excluded: chain S residue 99 SER Chi-restraints excluded: chain T residue 44 GLU Chi-restraints excluded: chain T residue 70 LYS Chi-restraints excluded: chain T residue 88 ARG Chi-restraints excluded: chain U residue 36 VAL Chi-restraints excluded: chain U residue 78 VAL Chi-restraints excluded: chain V residue 49 ASN Chi-restraints excluded: chain V residue 52 CYS Chi-restraints excluded: chain W residue 13 THR Chi-restraints excluded: chain X residue 30 LEU Chi-restraints excluded: chain X residue 36 ARG Chi-restraints excluded: chain X residue 70 LEU Chi-restraints excluded: chain X residue 78 THR Chi-restraints excluded: chain Y residue 11 ILE Chi-restraints excluded: chain Z residue 12 ASP Chi-restraints excluded: chain Z residue 18 PHE Chi-restraints excluded: chain a residue 174 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1048 random chunks: chunk 528 optimal weight: 7.9990 chunk 295 optimal weight: 20.0000 chunk 792 optimal weight: 10.0000 chunk 648 optimal weight: 10.0000 chunk 262 optimal weight: 7.9990 chunk 953 optimal weight: 20.0000 chunk 1029 optimal weight: 10.0000 chunk 849 optimal weight: 10.0000 chunk 945 optimal weight: 10.0000 chunk 325 optimal weight: 7.9990 chunk 764 optimal weight: 10.0000 overall best weight: 8.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 94 GLN d 46 GLN ** e 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 72 ASN ** m 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 17 ASN ** m 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 19 GLN o 38 GLN ** q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 73 ASN y 15 ASN A 61 ASN ** C 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 53 GLN ** J 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 36 GLN N 49 GLN ** P 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 46 HIS Y 19 HIS Y 54 GLN Y 81 GLN a 160 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.106 162697 Z= 0.350 Angle : 0.686 10.576 243503 Z= 0.357 Chirality : 0.040 0.339 31146 Planarity : 0.006 0.063 12986 Dihedral : 23.358 179.439 81747 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 14.36 Ramachandran Plot: Outliers : 0.17 % Allowed : 11.98 % Favored : 87.85 % Rotamer: Outliers : 5.47 % Allowed : 16.78 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -2.59 (0.10), residues: 5836 helix: -0.31 (0.12), residues: 1900 sheet: -2.19 (0.15), residues: 995 loop : -2.55 (0.11), residues: 2941 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP G 103 HIS 0.010 0.002 HIS T 37 PHE 0.048 0.002 PHE Z 36 TYR 0.028 0.002 TYR Q 65 ARG 0.008 0.001 ARG S 62 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11672 Ramachandran restraints generated. 5836 Oldfield, 0 Emsley, 5836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11672 Ramachandran restraints generated. 5836 Oldfield, 0 Emsley, 5836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1421 residues out of total 4862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 266 poor density : 1155 time to evaluate : 6.753 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: d 46 GLN cc_start: 0.8633 (OUTLIER) cc_final: 0.8037 (mt0) REVERT: d 195 GLN cc_start: 0.8009 (tp40) cc_final: 0.7789 (tp40) REVERT: e 82 TYR cc_start: 0.8008 (t80) cc_final: 0.7513 (t80) REVERT: e 89 THR cc_start: 0.8784 (m) cc_final: 0.8470 (p) REVERT: e 134 GLN cc_start: 0.7783 (OUTLIER) cc_final: 0.7509 (pm20) REVERT: e 143 ASP cc_start: 0.6915 (m-30) cc_final: 0.6456 (m-30) REVERT: f 41 GLU cc_start: 0.8806 (mt-10) cc_final: 0.8148 (pp20) REVERT: f 43 LYS cc_start: 0.8256 (mmmt) cc_final: 0.7924 (mmmm) REVERT: f 68 ARG cc_start: 0.8890 (tmt170) cc_final: 0.8623 (ttp80) REVERT: f 115 GLN cc_start: 0.8393 (OUTLIER) cc_final: 0.7933 (pp30) REVERT: f 142 GLN cc_start: 0.8471 (tp40) cc_final: 0.8201 (tp40) REVERT: f 169 ARG cc_start: 0.7927 (mmm-85) cc_final: 0.7588 (mmm160) REVERT: h 9 GLN cc_start: 0.5398 (OUTLIER) cc_final: 0.4889 (mm-40) REVERT: j 30 THR cc_start: 0.9322 (OUTLIER) cc_final: 0.9032 (p) REVERT: l 29 LYS cc_start: 0.8969 (OUTLIER) cc_final: 0.8368 (tmtt) REVERT: m 6 ARG cc_start: 0.7065 (tpt90) cc_final: 0.6540 (tpt90) REVERT: n 75 ILE cc_start: 0.9283 (mm) cc_final: 0.8803 (mm) REVERT: n 112 TYR cc_start: 0.8274 (m-80) cc_final: 0.8039 (m-80) REVERT: o 49 VAL cc_start: 0.8946 (t) cc_final: 0.8701 (m) REVERT: o 56 LYS cc_start: 0.7539 (mppt) cc_final: 0.7083 (mppt) REVERT: o 61 GLN cc_start: 0.8661 (mp10) cc_final: 0.8334 (pp30) REVERT: o 80 GLU cc_start: 0.9315 (mm-30) cc_final: 0.9109 (mm-30) REVERT: o 83 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.8409 (mm) REVERT: r 6 GLN cc_start: 0.8366 (pp30) cc_final: 0.8105 (tm-30) REVERT: r 11 GLN cc_start: 0.8559 (mm-40) cc_final: 0.8153 (mt0) REVERT: r 18 GLN cc_start: 0.8438 (tm-30) cc_final: 0.8065 (tm-30) REVERT: r 60 LYS cc_start: 0.8880 (mmmm) cc_final: 0.8410 (mmmm) REVERT: s 52 GLU cc_start: 0.7854 (tp30) cc_final: 0.7643 (tm-30) REVERT: t 69 ARG cc_start: 0.7263 (ttp80) cc_final: 0.6744 (ttp80) REVERT: v 8 VAL cc_start: 0.9102 (t) cc_final: 0.8846 (p) REVERT: v 50 MET cc_start: 0.8539 (mtt) cc_final: 0.8253 (mtt) REVERT: v 63 ILE cc_start: 0.9143 (mt) cc_final: 0.8919 (tp) REVERT: v 70 ILE cc_start: 0.9100 (mm) cc_final: 0.8820 (mm) REVERT: w 54 THR cc_start: 0.8901 (m) cc_final: 0.8532 (t) REVERT: w 64 LYS cc_start: 0.8884 (ttmm) cc_final: 0.8680 (ttmm) REVERT: w 66 GLU cc_start: 0.7226 (tm-30) cc_final: 0.6938 (tm-30) REVERT: w 79 GLU cc_start: 0.7039 (mp0) cc_final: 0.6602 (mp0) REVERT: y 24 GLU cc_start: 0.7942 (mp0) cc_final: 0.7279 (mp0) REVERT: y 30 MET cc_start: 0.8651 (mmm) cc_final: 0.8419 (mmp) REVERT: z 5 LYS cc_start: 0.8795 (mmmt) cc_final: 0.8477 (mtpp) REVERT: C 24 LYS cc_start: 0.8385 (ttpt) cc_final: 0.7947 (tttm) REVERT: G 22 TRP cc_start: 0.8883 (p-90) cc_final: 0.8278 (p-90) REVERT: G 135 MET cc_start: 0.9187 (ttp) cc_final: 0.8962 (tmm) REVERT: G 161 PHE cc_start: 0.7640 (t80) cc_final: 0.7293 (t80) REVERT: H 106 ARG cc_start: 0.8023 (mmp80) cc_final: 0.7774 (mmp80) REVERT: H 167 TYR cc_start: 0.7034 (OUTLIER) cc_final: 0.6120 (t80) REVERT: I 85 THR cc_start: 0.9252 (m) cc_final: 0.9034 (t) REVERT: I 140 ASP cc_start: 0.8010 (m-30) cc_final: 0.7399 (m-30) REVERT: J 11 GLN cc_start: 0.8164 (tt0) cc_final: 0.7768 (tt0) REVERT: J 161 GLU cc_start: 0.8600 (tp30) cc_final: 0.8347 (pm20) REVERT: K 1 MET cc_start: 0.7780 (tmm) cc_final: 0.7482 (tmm) REVERT: K 11 HIS cc_start: 0.7861 (OUTLIER) cc_final: 0.7251 (m-70) REVERT: M 113 ARG cc_start: 0.8892 (ttp80) cc_final: 0.8284 (ttm-80) REVERT: N 28 VAL cc_start: 0.7423 (t) cc_final: 0.7182 (p) REVERT: N 52 GLU cc_start: 0.9064 (tp30) cc_final: 0.8628 (tp30) REVERT: N 53 LEU cc_start: 0.8918 (mp) cc_final: 0.8460 (tt) REVERT: N 106 ASP cc_start: 0.8084 (t70) cc_final: 0.7712 (t0) REVERT: N 109 GLN cc_start: 0.7941 (tm130) cc_final: 0.7590 (tm-30) REVERT: R 68 LEU cc_start: 0.9443 (tp) cc_final: 0.9215 (tp) REVERT: R 102 LYS cc_start: 0.8507 (mttt) cc_final: 0.8250 (mttt) REVERT: S 88 MET cc_start: 0.8815 (mmt) cc_final: 0.8360 (mmt) REVERT: T 5 GLU cc_start: 0.8219 (mm-30) cc_final: 0.7985 (mm-30) REVERT: T 70 LYS cc_start: 0.9317 (OUTLIER) cc_final: 0.8540 (ttpp) REVERT: U 35 ARG cc_start: 0.8276 (ppt170) cc_final: 0.7922 (ptt90) REVERT: V 56 ASP cc_start: 0.7143 (p0) cc_final: 0.6641 (p0) REVERT: X 16 LYS cc_start: 0.8543 (mtpt) cc_final: 0.7888 (mmtt) REVERT: X 19 GLU cc_start: 0.8626 (mm-30) cc_final: 0.8408 (mm-30) REVERT: X 36 ARG cc_start: 0.8460 (OUTLIER) cc_final: 0.7951 (ptm160) REVERT: X 42 ASN cc_start: 0.8369 (p0) cc_final: 0.7988 (p0) REVERT: X 72 GLU cc_start: 0.8156 (mp0) cc_final: 0.7329 (mp0) REVERT: Y 20 ASN cc_start: 0.9107 (m-40) cc_final: 0.8524 (t0) REVERT: Y 24 ARG cc_start: 0.8934 (ttm170) cc_final: 0.8395 (mtm-85) REVERT: Y 26 MET cc_start: 0.8934 (OUTLIER) cc_final: 0.8403 (ttp) REVERT: Y 65 LEU cc_start: 0.8806 (tt) cc_final: 0.8418 (tt) outliers start: 266 outliers final: 189 residues processed: 1296 average time/residue: 1.2993 time to fit residues: 3043.3088 Evaluate side-chains 1256 residues out of total 4862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 201 poor density : 1055 time to evaluate : 6.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 48 ILE Chi-restraints excluded: chain b residue 183 VAL Chi-restraints excluded: chain b residue 258 SER Chi-restraints excluded: chain b residue 267 VAL Chi-restraints excluded: chain c residue 29 VAL Chi-restraints excluded: chain c residue 43 ASP Chi-restraints excluded: chain c residue 95 SER Chi-restraints excluded: chain c residue 131 ASP Chi-restraints excluded: chain c residue 139 SER Chi-restraints excluded: chain c residue 161 MET Chi-restraints excluded: chain c residue 176 ASP Chi-restraints excluded: chain c residue 199 SER Chi-restraints excluded: chain c residue 200 ASP Chi-restraints excluded: chain d residue 46 GLN Chi-restraints excluded: chain d residue 65 THR Chi-restraints excluded: chain e residue 3 LEU Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 134 GLN Chi-restraints excluded: chain f residue 113 ASP Chi-restraints excluded: chain f residue 115 GLN Chi-restraints excluded: chain f residue 124 CYS Chi-restraints excluded: chain f residue 130 ILE Chi-restraints excluded: chain g residue 4 ILE Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain g residue 17 ASP Chi-restraints excluded: chain g residue 20 ASN Chi-restraints excluded: chain g residue 130 VAL Chi-restraints excluded: chain h residue 9 GLN Chi-restraints excluded: chain h residue 60 LEU Chi-restraints excluded: chain h residue 77 VAL Chi-restraints excluded: chain i residue 23 VAL Chi-restraints excluded: chain j residue 14 ASP Chi-restraints excluded: chain j residue 30 THR Chi-restraints excluded: chain j residue 60 ASP Chi-restraints excluded: chain j residue 62 VAL Chi-restraints excluded: chain j residue 131 ASN Chi-restraints excluded: chain k residue 10 VAL Chi-restraints excluded: chain k residue 24 VAL Chi-restraints excluded: chain k residue 56 ASP Chi-restraints excluded: chain k residue 97 THR Chi-restraints excluded: chain k residue 110 GLU Chi-restraints excluded: chain l residue 29 LYS Chi-restraints excluded: chain l residue 76 GLU Chi-restraints excluded: chain l residue 118 THR Chi-restraints excluded: chain l residue 142 ILE Chi-restraints excluded: chain l residue 143 GLU Chi-restraints excluded: chain m residue 2 LEU Chi-restraints excluded: chain m residue 42 THR Chi-restraints excluded: chain m residue 70 ASP Chi-restraints excluded: chain m residue 89 VAL Chi-restraints excluded: chain m residue 127 LYS Chi-restraints excluded: chain n residue 6 SER Chi-restraints excluded: chain n residue 76 VAL Chi-restraints excluded: chain n residue 106 ASP Chi-restraints excluded: chain o residue 24 THR Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain o residue 31 THR Chi-restraints excluded: chain o residue 58 ILE Chi-restraints excluded: chain o residue 65 THR Chi-restraints excluded: chain o residue 83 LEU Chi-restraints excluded: chain o residue 91 SER Chi-restraints excluded: chain o residue 93 ASP Chi-restraints excluded: chain o residue 95 SER Chi-restraints excluded: chain o residue 106 LEU Chi-restraints excluded: chain p residue 8 GLU Chi-restraints excluded: chain p residue 18 SER Chi-restraints excluded: chain p residue 59 THR Chi-restraints excluded: chain p residue 60 VAL Chi-restraints excluded: chain q residue 7 VAL Chi-restraints excluded: chain q residue 16 ILE Chi-restraints excluded: chain r residue 19 THR Chi-restraints excluded: chain r residue 46 GLU Chi-restraints excluded: chain r residue 51 VAL Chi-restraints excluded: chain r residue 95 ASP Chi-restraints excluded: chain s residue 67 ASP Chi-restraints excluded: chain s residue 74 ILE Chi-restraints excluded: chain t residue 27 SER Chi-restraints excluded: chain t residue 39 THR Chi-restraints excluded: chain t residue 79 ASP Chi-restraints excluded: chain t residue 87 LEU Chi-restraints excluded: chain u residue 11 ILE Chi-restraints excluded: chain u residue 14 THR Chi-restraints excluded: chain u residue 27 VAL Chi-restraints excluded: chain u residue 35 VAL Chi-restraints excluded: chain u residue 67 SER Chi-restraints excluded: chain v residue 62 THR Chi-restraints excluded: chain v residue 64 VAL Chi-restraints excluded: chain v residue 65 VAL Chi-restraints excluded: chain v residue 76 ASP Chi-restraints excluded: chain v residue 90 ASP Chi-restraints excluded: chain w residue 72 ASN Chi-restraints excluded: chain w residue 77 SER Chi-restraints excluded: chain x residue 12 VAL Chi-restraints excluded: chain x residue 24 THR Chi-restraints excluded: chain x residue 39 VAL Chi-restraints excluded: chain x residue 47 THR Chi-restraints excluded: chain x residue 65 THR Chi-restraints excluded: chain y residue 10 SER Chi-restraints excluded: chain z residue 4 ILE Chi-restraints excluded: chain z residue 31 ILE Chi-restraints excluded: chain z residue 56 VAL Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 44 PHE Chi-restraints excluded: chain B residue 19 ASP Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain D residue 29 GLN Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 122 ASP Chi-restraints excluded: chain G residue 162 VAL Chi-restraints excluded: chain G residue 196 ASP Chi-restraints excluded: chain G residue 209 VAL Chi-restraints excluded: chain H residue 133 MET Chi-restraints excluded: chain H residue 167 TYR Chi-restraints excluded: chain I residue 53 GLN Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 159 GLU Chi-restraints excluded: chain I residue 180 THR Chi-restraints excluded: chain J residue 72 ASN Chi-restraints excluded: chain J residue 79 THR Chi-restraints excluded: chain J residue 116 VAL Chi-restraints excluded: chain J residue 133 ILE Chi-restraints excluded: chain J residue 162 GLU Chi-restraints excluded: chain K residue 6 ILE Chi-restraints excluded: chain K residue 11 HIS Chi-restraints excluded: chain K residue 26 THR Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 55 HIS Chi-restraints excluded: chain K residue 64 VAL Chi-restraints excluded: chain K residue 85 ILE Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain K residue 93 LYS Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain L residue 5 VAL Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 84 TYR Chi-restraints excluded: chain L residue 96 ASN Chi-restraints excluded: chain L residue 132 THR Chi-restraints excluded: chain L residue 139 ASP Chi-restraints excluded: chain M residue 35 ILE Chi-restraints excluded: chain M residue 59 GLU Chi-restraints excluded: chain M residue 61 THR Chi-restraints excluded: chain M residue 73 SER Chi-restraints excluded: chain M residue 125 ILE Chi-restraints excluded: chain N residue 20 ILE Chi-restraints excluded: chain N residue 38 PHE Chi-restraints excluded: chain N residue 46 VAL Chi-restraints excluded: chain N residue 65 THR Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain O residue 19 ASP Chi-restraints excluded: chain O residue 51 VAL Chi-restraints excluded: chain P residue 34 THR Chi-restraints excluded: chain P residue 64 VAL Chi-restraints excluded: chain P residue 94 SER Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain P residue 110 THR Chi-restraints excluded: chain P residue 112 VAL Chi-restraints excluded: chain Q residue 39 THR Chi-restraints excluded: chain Q residue 86 VAL Chi-restraints excluded: chain Q residue 89 LEU Chi-restraints excluded: chain R residue 6 ILE Chi-restraints excluded: chain R residue 41 ASP Chi-restraints excluded: chain R residue 49 GLU Chi-restraints excluded: chain R residue 64 VAL Chi-restraints excluded: chain R residue 71 GLU Chi-restraints excluded: chain R residue 82 LEU Chi-restraints excluded: chain R residue 84 CYS Chi-restraints excluded: chain S residue 5 MET Chi-restraints excluded: chain S residue 15 LEU Chi-restraints excluded: chain S residue 44 VAL Chi-restraints excluded: chain S residue 55 SER Chi-restraints excluded: chain S residue 83 VAL Chi-restraints excluded: chain S residue 99 SER Chi-restraints excluded: chain T residue 44 GLU Chi-restraints excluded: chain T residue 70 LYS Chi-restraints excluded: chain T residue 88 ARG Chi-restraints excluded: chain U residue 36 VAL Chi-restraints excluded: chain U residue 78 VAL Chi-restraints excluded: chain V residue 12 VAL Chi-restraints excluded: chain V residue 28 VAL Chi-restraints excluded: chain V residue 46 HIS Chi-restraints excluded: chain V residue 52 CYS Chi-restraints excluded: chain W residue 13 THR Chi-restraints excluded: chain W residue 27 THR Chi-restraints excluded: chain X residue 30 LEU Chi-restraints excluded: chain X residue 36 ARG Chi-restraints excluded: chain X residue 43 MET Chi-restraints excluded: chain X residue 59 VAL Chi-restraints excluded: chain X residue 70 LEU Chi-restraints excluded: chain X residue 78 THR Chi-restraints excluded: chain Y residue 26 MET Chi-restraints excluded: chain Y residue 58 ASP Chi-restraints excluded: chain Y residue 85 LEU Chi-restraints excluded: chain Z residue 12 ASP Chi-restraints excluded: chain Z residue 18 PHE Chi-restraints excluded: chain Z residue 42 THR Chi-restraints excluded: chain a residue 39 VAL Chi-restraints excluded: chain a residue 59 VAL Chi-restraints excluded: chain a residue 174 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1048 random chunks: chunk 941 optimal weight: 50.0000 chunk 716 optimal weight: 20.0000 chunk 494 optimal weight: 6.9990 chunk 105 optimal weight: 9.9990 chunk 455 optimal weight: 6.9990 chunk 640 optimal weight: 10.0000 chunk 956 optimal weight: 10.0000 chunk 1013 optimal weight: 20.0000 chunk 499 optimal weight: 2.9990 chunk 906 optimal weight: 10.0000 chunk 272 optimal weight: 6.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 44 HIS ** f 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 72 ASN ** m 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 17 ASN ** m 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 19 GLN q 58 GLN ** q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 92 ASN u 45 GLN ** u 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 139 ASN ** I 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 53 GLN J 76 ASN N 36 GLN ** P 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 19 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.2801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 162697 Z= 0.280 Angle : 0.635 11.176 243503 Z= 0.332 Chirality : 0.038 0.304 31146 Planarity : 0.005 0.059 12986 Dihedral : 23.398 178.158 81744 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 14.13 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.80 % Favored : 89.08 % Rotamer: Outliers : 5.72 % Allowed : 18.76 % Favored : 75.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.35 (0.11), residues: 5836 helix: -0.09 (0.12), residues: 1892 sheet: -2.09 (0.15), residues: 1009 loop : -2.39 (0.11), residues: 2935 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP G 103 HIS 0.019 0.001 HIS V 46 PHE 0.050 0.002 PHE K 78 TYR 0.025 0.002 TYR d 35 ARG 0.008 0.001 ARG d 88 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11672 Ramachandran restraints generated. 5836 Oldfield, 0 Emsley, 5836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11672 Ramachandran restraints generated. 5836 Oldfield, 0 Emsley, 5836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1416 residues out of total 4862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 278 poor density : 1138 time to evaluate : 6.784 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: e 82 TYR cc_start: 0.7888 (t80) cc_final: 0.7374 (t80) REVERT: e 89 THR cc_start: 0.8796 (m) cc_final: 0.8480 (p) REVERT: e 134 GLN cc_start: 0.7743 (OUTLIER) cc_final: 0.7530 (pm20) REVERT: e 143 ASP cc_start: 0.6898 (m-30) cc_final: 0.6452 (m-30) REVERT: f 41 GLU cc_start: 0.8804 (mt-10) cc_final: 0.8201 (pp20) REVERT: f 43 LYS cc_start: 0.8249 (mmmt) cc_final: 0.7926 (mmmm) REVERT: f 68 ARG cc_start: 0.8867 (tmt170) cc_final: 0.8616 (ttp80) REVERT: f 115 GLN cc_start: 0.8336 (OUTLIER) cc_final: 0.7876 (pp30) REVERT: f 142 GLN cc_start: 0.8375 (tp40) cc_final: 0.8093 (tp40) REVERT: g 8 LYS cc_start: 0.8466 (tptp) cc_final: 0.8180 (ptmm) REVERT: h 9 GLN cc_start: 0.5341 (OUTLIER) cc_final: 0.4850 (mm-40) REVERT: l 29 LYS cc_start: 0.8982 (OUTLIER) cc_final: 0.8367 (tmtt) REVERT: m 6 ARG cc_start: 0.7278 (tpt90) cc_final: 0.6858 (tpt90) REVERT: o 61 GLN cc_start: 0.8674 (mp10) cc_final: 0.8353 (pp30) REVERT: o 80 GLU cc_start: 0.9227 (mm-30) cc_final: 0.8994 (mm-30) REVERT: o 83 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8333 (mm) REVERT: o 97 PHE cc_start: 0.8502 (m-80) cc_final: 0.8287 (m-80) REVERT: r 6 GLN cc_start: 0.8480 (pp30) cc_final: 0.8222 (tm-30) REVERT: r 11 GLN cc_start: 0.8591 (mm-40) cc_final: 0.8140 (mt0) REVERT: r 18 GLN cc_start: 0.8470 (tm-30) cc_final: 0.8088 (tm-30) REVERT: r 60 LYS cc_start: 0.8901 (mmmm) cc_final: 0.8159 (mmmm) REVERT: t 69 ARG cc_start: 0.7182 (ttp80) cc_final: 0.6728 (ttp80) REVERT: v 8 VAL cc_start: 0.9093 (t) cc_final: 0.8829 (p) REVERT: v 63 ILE cc_start: 0.9171 (mt) cc_final: 0.8893 (tp) REVERT: v 70 ILE cc_start: 0.9154 (mm) cc_final: 0.8830 (mm) REVERT: w 54 THR cc_start: 0.8871 (OUTLIER) cc_final: 0.8538 (t) REVERT: y 5 GLU cc_start: 0.8545 (pt0) cc_final: 0.8269 (pm20) REVERT: y 8 GLU cc_start: 0.7978 (mp0) cc_final: 0.7280 (mp0) REVERT: y 24 GLU cc_start: 0.7897 (mp0) cc_final: 0.7165 (mp0) REVERT: C 24 LYS cc_start: 0.8414 (ttpt) cc_final: 0.8179 (ptmt) REVERT: G 22 TRP cc_start: 0.8872 (p-90) cc_final: 0.8303 (p-90) REVERT: G 135 MET cc_start: 0.9159 (ttp) cc_final: 0.8939 (tmm) REVERT: G 161 PHE cc_start: 0.7590 (t80) cc_final: 0.7258 (t80) REVERT: H 106 ARG cc_start: 0.7957 (mmp80) cc_final: 0.7687 (mmp80) REVERT: H 167 TYR cc_start: 0.6983 (OUTLIER) cc_final: 0.6107 (t80) REVERT: I 54 LEU cc_start: 0.9232 (tp) cc_final: 0.8921 (tp) REVERT: I 123 MET cc_start: 0.7948 (mpp) cc_final: 0.7641 (mpp) REVERT: I 140 ASP cc_start: 0.8101 (m-30) cc_final: 0.7410 (m-30) REVERT: J 11 GLN cc_start: 0.8239 (tt0) cc_final: 0.7928 (tt0) REVERT: K 1 MET cc_start: 0.7758 (tmm) cc_final: 0.7306 (tmm) REVERT: K 11 HIS cc_start: 0.7837 (OUTLIER) cc_final: 0.7071 (m-70) REVERT: K 69 GLU cc_start: 0.8735 (pm20) cc_final: 0.8459 (pm20) REVERT: L 30 MET cc_start: 0.8420 (ttp) cc_final: 0.8073 (ptp) REVERT: L 100 MET cc_start: 0.8706 (mpp) cc_final: 0.8392 (mmm) REVERT: M 113 ARG cc_start: 0.8908 (ttp80) cc_final: 0.8280 (ttm-80) REVERT: N 52 GLU cc_start: 0.9109 (tp30) cc_final: 0.8661 (tp30) REVERT: N 53 LEU cc_start: 0.8962 (mp) cc_final: 0.8478 (tt) REVERT: N 106 ASP cc_start: 0.8052 (t70) cc_final: 0.7664 (t0) REVERT: N 109 GLN cc_start: 0.7932 (OUTLIER) cc_final: 0.7519 (tm-30) REVERT: O 73 LEU cc_start: 0.7805 (mt) cc_final: 0.7457 (tt) REVERT: Q 2 THR cc_start: 0.8505 (m) cc_final: 0.7744 (p) REVERT: R 102 LYS cc_start: 0.8455 (tttt) cc_final: 0.8205 (mttt) REVERT: S 25 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7670 (pm20) REVERT: T 5 GLU cc_start: 0.8130 (mm-30) cc_final: 0.7898 (mm-30) REVERT: T 70 LYS cc_start: 0.9295 (OUTLIER) cc_final: 0.8551 (ttpp) REVERT: U 35 ARG cc_start: 0.8279 (ppt170) cc_final: 0.7958 (ptt90) REVERT: V 56 ASP cc_start: 0.7066 (p0) cc_final: 0.6571 (p0) REVERT: X 19 GLU cc_start: 0.8700 (mm-30) cc_final: 0.8425 (mm-30) REVERT: X 36 ARG cc_start: 0.8459 (OUTLIER) cc_final: 0.8132 (ptm160) REVERT: X 42 ASN cc_start: 0.8360 (p0) cc_final: 0.8055 (p0) REVERT: X 72 GLU cc_start: 0.8150 (mp0) cc_final: 0.7316 (mp0) REVERT: Y 20 ASN cc_start: 0.9096 (m-40) cc_final: 0.8442 (t0) REVERT: Y 24 ARG cc_start: 0.8953 (ttm170) cc_final: 0.8421 (ttm170) REVERT: Y 26 MET cc_start: 0.8949 (OUTLIER) cc_final: 0.8438 (ttp) REVERT: Y 65 LEU cc_start: 0.8819 (tt) cc_final: 0.8502 (tt) outliers start: 278 outliers final: 196 residues processed: 1279 average time/residue: 1.2260 time to fit residues: 2819.8549 Evaluate side-chains 1269 residues out of total 4862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 209 poor density : 1060 time to evaluate : 6.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 76 VAL Chi-restraints excluded: chain b residue 179 GLU Chi-restraints excluded: chain b residue 228 ASP Chi-restraints excluded: chain b residue 267 VAL Chi-restraints excluded: chain c residue 9 VAL Chi-restraints excluded: chain c residue 60 VAL Chi-restraints excluded: chain c residue 95 SER Chi-restraints excluded: chain c residue 131 ASP Chi-restraints excluded: chain c residue 139 SER Chi-restraints excluded: chain c residue 145 SER Chi-restraints excluded: chain c residue 176 ASP Chi-restraints excluded: chain c residue 180 VAL Chi-restraints excluded: chain c residue 199 SER Chi-restraints excluded: chain c residue 200 ASP Chi-restraints excluded: chain d residue 65 THR Chi-restraints excluded: chain d residue 77 ILE Chi-restraints excluded: chain d residue 120 VAL Chi-restraints excluded: chain e residue 3 LEU Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 39 VAL Chi-restraints excluded: chain e residue 66 ILE Chi-restraints excluded: chain e residue 86 CYS Chi-restraints excluded: chain e residue 134 GLN Chi-restraints excluded: chain f residue 38 ASP Chi-restraints excluded: chain f residue 42 VAL Chi-restraints excluded: chain f residue 115 GLN Chi-restraints excluded: chain f residue 120 ILE Chi-restraints excluded: chain f residue 124 CYS Chi-restraints excluded: chain f residue 130 ILE Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain g residue 17 ASP Chi-restraints excluded: chain g residue 20 ASN Chi-restraints excluded: chain g residue 130 VAL Chi-restraints excluded: chain h residue 9 GLN Chi-restraints excluded: chain h residue 77 VAL Chi-restraints excluded: chain i residue 23 VAL Chi-restraints excluded: chain j residue 60 ASP Chi-restraints excluded: chain j residue 62 VAL Chi-restraints excluded: chain k residue 10 VAL Chi-restraints excluded: chain k residue 24 VAL Chi-restraints excluded: chain k residue 56 ASP Chi-restraints excluded: chain k residue 89 ASN Chi-restraints excluded: chain k residue 97 THR Chi-restraints excluded: chain l residue 29 LYS Chi-restraints excluded: chain l residue 76 GLU Chi-restraints excluded: chain l residue 118 THR Chi-restraints excluded: chain l residue 142 ILE Chi-restraints excluded: chain l residue 143 GLU Chi-restraints excluded: chain m residue 2 LEU Chi-restraints excluded: chain m residue 42 THR Chi-restraints excluded: chain m residue 70 ASP Chi-restraints excluded: chain m residue 74 THR Chi-restraints excluded: chain m residue 89 VAL Chi-restraints excluded: chain m residue 127 LYS Chi-restraints excluded: chain n residue 6 SER Chi-restraints excluded: chain n residue 76 VAL Chi-restraints excluded: chain n residue 106 ASP Chi-restraints excluded: chain o residue 31 THR Chi-restraints excluded: chain o residue 58 ILE Chi-restraints excluded: chain o residue 65 THR Chi-restraints excluded: chain o residue 83 LEU Chi-restraints excluded: chain o residue 91 SER Chi-restraints excluded: chain o residue 93 ASP Chi-restraints excluded: chain o residue 95 SER Chi-restraints excluded: chain p residue 18 SER Chi-restraints excluded: chain p residue 59 THR Chi-restraints excluded: chain q residue 7 VAL Chi-restraints excluded: chain q residue 16 ILE Chi-restraints excluded: chain q residue 17 LEU Chi-restraints excluded: chain r residue 19 THR Chi-restraints excluded: chain r residue 46 GLU Chi-restraints excluded: chain r residue 51 VAL Chi-restraints excluded: chain r residue 54 VAL Chi-restraints excluded: chain s residue 67 ASP Chi-restraints excluded: chain s residue 74 ILE Chi-restraints excluded: chain s residue 103 ILE Chi-restraints excluded: chain t residue 27 SER Chi-restraints excluded: chain t residue 52 GLU Chi-restraints excluded: chain t residue 79 ASP Chi-restraints excluded: chain t residue 87 LEU Chi-restraints excluded: chain u residue 14 THR Chi-restraints excluded: chain u residue 27 VAL Chi-restraints excluded: chain u residue 67 SER Chi-restraints excluded: chain u residue 82 VAL Chi-restraints excluded: chain v residue 62 THR Chi-restraints excluded: chain v residue 64 VAL Chi-restraints excluded: chain v residue 65 VAL Chi-restraints excluded: chain v residue 76 ASP Chi-restraints excluded: chain v residue 90 ASP Chi-restraints excluded: chain w residue 54 THR Chi-restraints excluded: chain w residue 60 ASP Chi-restraints excluded: chain w residue 72 ASN Chi-restraints excluded: chain x residue 12 VAL Chi-restraints excluded: chain x residue 24 THR Chi-restraints excluded: chain x residue 39 VAL Chi-restraints excluded: chain x residue 47 THR Chi-restraints excluded: chain x residue 67 LEU Chi-restraints excluded: chain y residue 10 SER Chi-restraints excluded: chain z residue 4 ILE Chi-restraints excluded: chain z residue 24 LEU Chi-restraints excluded: chain z residue 31 ILE Chi-restraints excluded: chain z residue 56 VAL Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 44 PHE Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 19 ASP Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain D residue 29 GLN Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain G residue 29 PHE Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 162 VAL Chi-restraints excluded: chain G residue 196 ASP Chi-restraints excluded: chain G residue 209 VAL Chi-restraints excluded: chain H residue 133 MET Chi-restraints excluded: chain H residue 156 LEU Chi-restraints excluded: chain H residue 167 TYR Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 159 GLU Chi-restraints excluded: chain I residue 168 THR Chi-restraints excluded: chain I residue 180 THR Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 72 ASN Chi-restraints excluded: chain J residue 79 THR Chi-restraints excluded: chain J residue 116 VAL Chi-restraints excluded: chain J residue 133 ILE Chi-restraints excluded: chain J residue 162 GLU Chi-restraints excluded: chain K residue 6 ILE Chi-restraints excluded: chain K residue 11 HIS Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 55 HIS Chi-restraints excluded: chain K residue 64 VAL Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain K residue 93 LYS Chi-restraints excluded: chain L residue 5 VAL Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 84 TYR Chi-restraints excluded: chain L residue 96 ASN Chi-restraints excluded: chain L residue 103 ILE Chi-restraints excluded: chain L residue 112 ASP Chi-restraints excluded: chain L residue 132 THR Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain M residue 61 THR Chi-restraints excluded: chain M residue 73 SER Chi-restraints excluded: chain N residue 20 ILE Chi-restraints excluded: chain N residue 42 THR Chi-restraints excluded: chain N residue 46 VAL Chi-restraints excluded: chain N residue 54 VAL Chi-restraints excluded: chain N residue 109 GLN Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain O residue 19 ASP Chi-restraints excluded: chain O residue 51 VAL Chi-restraints excluded: chain P residue 34 THR Chi-restraints excluded: chain P residue 64 VAL Chi-restraints excluded: chain P residue 93 GLU Chi-restraints excluded: chain P residue 94 SER Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain P residue 110 THR Chi-restraints excluded: chain P residue 112 VAL Chi-restraints excluded: chain Q residue 39 THR Chi-restraints excluded: chain Q residue 80 LEU Chi-restraints excluded: chain Q residue 89 LEU Chi-restraints excluded: chain R residue 8 ILE Chi-restraints excluded: chain R residue 41 ASP Chi-restraints excluded: chain R residue 49 GLU Chi-restraints excluded: chain R residue 64 VAL Chi-restraints excluded: chain R residue 67 ASP Chi-restraints excluded: chain R residue 71 GLU Chi-restraints excluded: chain R residue 82 LEU Chi-restraints excluded: chain S residue 13 VAL Chi-restraints excluded: chain S residue 15 LEU Chi-restraints excluded: chain S residue 25 GLU Chi-restraints excluded: chain S residue 55 SER Chi-restraints excluded: chain S residue 99 SER Chi-restraints excluded: chain T residue 26 VAL Chi-restraints excluded: chain T residue 44 GLU Chi-restraints excluded: chain T residue 70 LYS Chi-restraints excluded: chain T residue 88 ARG Chi-restraints excluded: chain U residue 36 VAL Chi-restraints excluded: chain U residue 50 THR Chi-restraints excluded: chain U residue 78 VAL Chi-restraints excluded: chain V residue 18 LYS Chi-restraints excluded: chain V residue 28 VAL Chi-restraints excluded: chain V residue 46 HIS Chi-restraints excluded: chain V residue 52 CYS Chi-restraints excluded: chain V residue 73 THR Chi-restraints excluded: chain V residue 74 LEU Chi-restraints excluded: chain W residue 13 THR Chi-restraints excluded: chain X residue 30 LEU Chi-restraints excluded: chain X residue 36 ARG Chi-restraints excluded: chain X residue 48 ILE Chi-restraints excluded: chain X residue 50 VAL Chi-restraints excluded: chain X residue 59 VAL Chi-restraints excluded: chain X residue 65 MET Chi-restraints excluded: chain X residue 70 LEU Chi-restraints excluded: chain X residue 78 THR Chi-restraints excluded: chain Y residue 11 ILE Chi-restraints excluded: chain Y residue 26 MET Chi-restraints excluded: chain Y residue 58 ASP Chi-restraints excluded: chain Y residue 85 LEU Chi-restraints excluded: chain Z residue 12 ASP Chi-restraints excluded: chain Z residue 18 PHE Chi-restraints excluded: chain a residue 39 VAL Chi-restraints excluded: chain a residue 174 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1048 random chunks: chunk 843 optimal weight: 10.0000 chunk 575 optimal weight: 20.0000 chunk 14 optimal weight: 7.9990 chunk 754 optimal weight: 20.0000 chunk 417 optimal weight: 5.9990 chunk 864 optimal weight: 20.0000 chunk 700 optimal weight: 30.0000 chunk 1 optimal weight: 1.9990 chunk 517 optimal weight: 30.0000 chunk 909 optimal weight: 10.0000 chunk 255 optimal weight: 5.9990 overall best weight: 6.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 94 GLN ** f 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 3 GLN l 99 ASN ** m 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 17 ASN ** m 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 19 GLN p 74 GLN ** q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 45 GLN u 73 ASN v 49 ASN v 51 GLN H 139 ASN ** I 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 18 GLN Y 19 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.2962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 162697 Z= 0.264 Angle : 0.623 11.760 243503 Z= 0.325 Chirality : 0.037 0.296 31146 Planarity : 0.005 0.058 12986 Dihedral : 23.404 178.177 81744 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 14.07 Ramachandran Plot: Outliers : 0.10 % Allowed : 11.09 % Favored : 88.81 % Rotamer: Outliers : 6.05 % Allowed : 19.74 % Favored : 74.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.20 (0.11), residues: 5836 helix: 0.01 (0.12), residues: 1897 sheet: -1.94 (0.16), residues: 988 loop : -2.31 (0.11), residues: 2951 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP K 42 HIS 0.009 0.001 HIS T 37 PHE 0.043 0.002 PHE Z 36 TYR 0.024 0.002 TYR R 22 ARG 0.007 0.001 ARG U 56 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11672 Ramachandran restraints generated. 5836 Oldfield, 0 Emsley, 5836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11672 Ramachandran restraints generated. 5836 Oldfield, 0 Emsley, 5836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1413 residues out of total 4862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 294 poor density : 1119 time to evaluate : 6.735 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 51 ARG cc_start: 0.8571 (OUTLIER) cc_final: 0.7730 (ptm-80) REVERT: e 82 TYR cc_start: 0.7870 (t80) cc_final: 0.7294 (t80) REVERT: e 89 THR cc_start: 0.8811 (OUTLIER) cc_final: 0.8494 (p) REVERT: e 134 GLN cc_start: 0.7717 (OUTLIER) cc_final: 0.7511 (pm20) REVERT: e 143 ASP cc_start: 0.6903 (m-30) cc_final: 0.6468 (m-30) REVERT: f 41 GLU cc_start: 0.8774 (mt-10) cc_final: 0.8223 (pp20) REVERT: f 43 LYS cc_start: 0.8162 (mmmt) cc_final: 0.7802 (mmmm) REVERT: f 68 ARG cc_start: 0.8871 (tmt170) cc_final: 0.8628 (ttp80) REVERT: f 115 GLN cc_start: 0.8420 (OUTLIER) cc_final: 0.8048 (pp30) REVERT: g 8 LYS cc_start: 0.8636 (tptp) cc_final: 0.7913 (ptmm) REVERT: h 9 GLN cc_start: 0.5406 (OUTLIER) cc_final: 0.4898 (mm-40) REVERT: m 6 ARG cc_start: 0.7347 (tpt90) cc_final: 0.6886 (tpt90) REVERT: o 56 LYS cc_start: 0.7589 (mppt) cc_final: 0.7007 (mppt) REVERT: o 61 GLN cc_start: 0.8686 (mp10) cc_final: 0.8361 (pp30) REVERT: r 6 GLN cc_start: 0.8467 (pp30) cc_final: 0.8208 (tm-30) REVERT: r 11 GLN cc_start: 0.8587 (mm-40) cc_final: 0.8280 (mt0) REVERT: r 18 GLN cc_start: 0.8465 (tm-30) cc_final: 0.8100 (tm-30) REVERT: r 32 THR cc_start: 0.8798 (m) cc_final: 0.8563 (p) REVERT: r 35 PHE cc_start: 0.8921 (m-80) cc_final: 0.8503 (m-80) REVERT: t 7 LEU cc_start: 0.9249 (mp) cc_final: 0.9030 (mp) REVERT: t 69 ARG cc_start: 0.7193 (ttp80) cc_final: 0.6833 (ttp80) REVERT: u 61 GLU cc_start: 0.7709 (mm-30) cc_final: 0.7272 (tp30) REVERT: v 8 VAL cc_start: 0.9060 (t) cc_final: 0.8801 (p) REVERT: v 50 MET cc_start: 0.8294 (mtm) cc_final: 0.8059 (mtt) REVERT: v 59 GLU cc_start: 0.7805 (tm-30) cc_final: 0.7571 (tm-30) REVERT: v 63 ILE cc_start: 0.9143 (mt) cc_final: 0.8897 (tp) REVERT: w 54 THR cc_start: 0.8855 (OUTLIER) cc_final: 0.8506 (t) REVERT: y 8 GLU cc_start: 0.7738 (mp0) cc_final: 0.7160 (mp0) REVERT: y 24 GLU cc_start: 0.7860 (mp0) cc_final: 0.7320 (mp0) REVERT: C 24 LYS cc_start: 0.8409 (ttpt) cc_final: 0.8186 (ptmt) REVERT: G 22 TRP cc_start: 0.8867 (p-90) cc_final: 0.8368 (p-90) REVERT: G 161 PHE cc_start: 0.7574 (t80) cc_final: 0.7253 (t80) REVERT: H 106 ARG cc_start: 0.7999 (mmp80) cc_final: 0.7735 (mmp80) REVERT: H 167 TYR cc_start: 0.6938 (OUTLIER) cc_final: 0.6068 (t80) REVERT: I 123 MET cc_start: 0.7923 (mpp) cc_final: 0.7491 (mpp) REVERT: I 140 ASP cc_start: 0.8110 (m-30) cc_final: 0.7467 (m-30) REVERT: J 11 GLN cc_start: 0.8287 (tt0) cc_final: 0.7805 (tt0) REVERT: K 1 MET cc_start: 0.7758 (tmm) cc_final: 0.7443 (tmm) REVERT: K 11 HIS cc_start: 0.7802 (OUTLIER) cc_final: 0.7040 (m-70) REVERT: K 69 GLU cc_start: 0.8720 (pm20) cc_final: 0.8488 (pm20) REVERT: M 25 THR cc_start: 0.8255 (OUTLIER) cc_final: 0.7409 (m) REVERT: M 57 GLU cc_start: 0.8533 (mm-30) cc_final: 0.7500 (mm-30) REVERT: M 113 ARG cc_start: 0.8913 (ttp80) cc_final: 0.8269 (ttm-80) REVERT: N 52 GLU cc_start: 0.9088 (tp30) cc_final: 0.8630 (tp30) REVERT: N 53 LEU cc_start: 0.8963 (mp) cc_final: 0.8437 (tt) REVERT: N 106 ASP cc_start: 0.8104 (t70) cc_final: 0.7719 (t0) REVERT: N 109 GLN cc_start: 0.7917 (OUTLIER) cc_final: 0.7510 (tm-30) REVERT: O 73 LEU cc_start: 0.7782 (mt) cc_final: 0.7438 (tt) REVERT: R 102 LYS cc_start: 0.8445 (tttt) cc_final: 0.8193 (mttt) REVERT: S 25 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7638 (pm20) REVERT: T 14 PHE cc_start: 0.8014 (m-80) cc_final: 0.7619 (m-80) REVERT: T 70 LYS cc_start: 0.9286 (OUTLIER) cc_final: 0.8524 (ttpp) REVERT: U 35 ARG cc_start: 0.8278 (ppt170) cc_final: 0.7987 (ptt90) REVERT: V 56 ASP cc_start: 0.7051 (p0) cc_final: 0.6543 (p0) REVERT: X 16 LYS cc_start: 0.8579 (mtpt) cc_final: 0.8137 (mmtt) REVERT: X 36 ARG cc_start: 0.8508 (OUTLIER) cc_final: 0.7953 (ptm160) REVERT: X 42 ASN cc_start: 0.8329 (p0) cc_final: 0.8115 (p0) REVERT: X 72 GLU cc_start: 0.8142 (mp0) cc_final: 0.7427 (mp0) REVERT: Y 17 ARG cc_start: 0.8904 (ptm-80) cc_final: 0.8704 (ptm-80) REVERT: Y 20 ASN cc_start: 0.9087 (m-40) cc_final: 0.8437 (t0) REVERT: Y 24 ARG cc_start: 0.8963 (ttm170) cc_final: 0.8685 (ttm170) REVERT: Y 26 MET cc_start: 0.8933 (OUTLIER) cc_final: 0.8443 (ttp) REVERT: Y 65 LEU cc_start: 0.8805 (tt) cc_final: 0.8507 (tt) REVERT: Y 85 LEU cc_start: 0.5797 (OUTLIER) cc_final: 0.5583 (pp) outliers start: 294 outliers final: 222 residues processed: 1267 average time/residue: 1.2536 time to fit residues: 2853.3269 Evaluate side-chains 1292 residues out of total 4862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 237 poor density : 1055 time to evaluate : 6.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 39 SER Chi-restraints excluded: chain b residue 51 ARG Chi-restraints excluded: chain b residue 76 VAL Chi-restraints excluded: chain b residue 179 GLU Chi-restraints excluded: chain b residue 228 ASP Chi-restraints excluded: chain b residue 258 SER Chi-restraints excluded: chain b residue 270 ARG Chi-restraints excluded: chain c residue 2 ILE Chi-restraints excluded: chain c residue 29 VAL Chi-restraints excluded: chain c residue 60 VAL Chi-restraints excluded: chain c residue 95 SER Chi-restraints excluded: chain c residue 131 ASP Chi-restraints excluded: chain c residue 139 SER Chi-restraints excluded: chain c residue 145 SER Chi-restraints excluded: chain c residue 176 ASP Chi-restraints excluded: chain c residue 177 VAL Chi-restraints excluded: chain c residue 180 VAL Chi-restraints excluded: chain c residue 199 SER Chi-restraints excluded: chain c residue 200 ASP Chi-restraints excluded: chain d residue 22 ASP Chi-restraints excluded: chain d residue 65 THR Chi-restraints excluded: chain d residue 77 ILE Chi-restraints excluded: chain d residue 97 ASN Chi-restraints excluded: chain d residue 120 VAL Chi-restraints excluded: chain e residue 3 LEU Chi-restraints excluded: chain e residue 30 VAL Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 43 ILE Chi-restraints excluded: chain e residue 66 ILE Chi-restraints excluded: chain e residue 86 CYS Chi-restraints excluded: chain e residue 89 THR Chi-restraints excluded: chain e residue 134 GLN Chi-restraints excluded: chain e residue 136 ILE Chi-restraints excluded: chain f residue 38 ASP Chi-restraints excluded: chain f residue 85 LYS Chi-restraints excluded: chain f residue 91 VAL Chi-restraints excluded: chain f residue 113 ASP Chi-restraints excluded: chain f residue 115 GLN Chi-restraints excluded: chain f residue 120 ILE Chi-restraints excluded: chain f residue 124 CYS Chi-restraints excluded: chain f residue 130 ILE Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain g residue 17 ASP Chi-restraints excluded: chain g residue 20 ASN Chi-restraints excluded: chain g residue 130 VAL Chi-restraints excluded: chain h residue 9 GLN Chi-restraints excluded: chain h residue 60 LEU Chi-restraints excluded: chain h residue 77 VAL Chi-restraints excluded: chain i residue 23 VAL Chi-restraints excluded: chain j residue 14 ASP Chi-restraints excluded: chain j residue 30 THR Chi-restraints excluded: chain j residue 60 ASP Chi-restraints excluded: chain j residue 62 VAL Chi-restraints excluded: chain j residue 131 ASN Chi-restraints excluded: chain k residue 1 MET Chi-restraints excluded: chain k residue 10 VAL Chi-restraints excluded: chain k residue 24 VAL Chi-restraints excluded: chain k residue 56 ASP Chi-restraints excluded: chain k residue 89 ASN Chi-restraints excluded: chain k residue 97 THR Chi-restraints excluded: chain l residue 29 LYS Chi-restraints excluded: chain l residue 76 GLU Chi-restraints excluded: chain l residue 117 THR Chi-restraints excluded: chain l residue 118 THR Chi-restraints excluded: chain l residue 142 ILE Chi-restraints excluded: chain l residue 143 GLU Chi-restraints excluded: chain m residue 2 LEU Chi-restraints excluded: chain m residue 70 ASP Chi-restraints excluded: chain m residue 74 THR Chi-restraints excluded: chain m residue 89 VAL Chi-restraints excluded: chain m residue 127 LYS Chi-restraints excluded: chain n residue 6 SER Chi-restraints excluded: chain n residue 76 VAL Chi-restraints excluded: chain n residue 106 ASP Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain o residue 31 THR Chi-restraints excluded: chain o residue 58 ILE Chi-restraints excluded: chain o residue 65 THR Chi-restraints excluded: chain o residue 85 LYS Chi-restraints excluded: chain o residue 91 SER Chi-restraints excluded: chain o residue 93 ASP Chi-restraints excluded: chain o residue 95 SER Chi-restraints excluded: chain p residue 18 SER Chi-restraints excluded: chain p residue 59 THR Chi-restraints excluded: chain q residue 7 VAL Chi-restraints excluded: chain q residue 16 ILE Chi-restraints excluded: chain q residue 17 LEU Chi-restraints excluded: chain r residue 19 THR Chi-restraints excluded: chain r residue 41 ILE Chi-restraints excluded: chain r residue 46 GLU Chi-restraints excluded: chain r residue 51 VAL Chi-restraints excluded: chain r residue 54 VAL Chi-restraints excluded: chain r residue 95 ASP Chi-restraints excluded: chain s residue 67 ASP Chi-restraints excluded: chain s residue 74 ILE Chi-restraints excluded: chain s residue 103 ILE Chi-restraints excluded: chain t residue 27 SER Chi-restraints excluded: chain t residue 52 GLU Chi-restraints excluded: chain t residue 79 ASP Chi-restraints excluded: chain t residue 87 LEU Chi-restraints excluded: chain u residue 14 THR Chi-restraints excluded: chain u residue 27 VAL Chi-restraints excluded: chain u residue 67 SER Chi-restraints excluded: chain u residue 73 ASN Chi-restraints excluded: chain v residue 55 GLU Chi-restraints excluded: chain v residue 62 THR Chi-restraints excluded: chain v residue 64 VAL Chi-restraints excluded: chain v residue 65 VAL Chi-restraints excluded: chain v residue 76 ASP Chi-restraints excluded: chain v residue 90 ASP Chi-restraints excluded: chain w residue 28 LEU Chi-restraints excluded: chain w residue 54 THR Chi-restraints excluded: chain w residue 60 ASP Chi-restraints excluded: chain w residue 72 ASN Chi-restraints excluded: chain w residue 77 SER Chi-restraints excluded: chain x residue 12 VAL Chi-restraints excluded: chain x residue 24 THR Chi-restraints excluded: chain x residue 39 VAL Chi-restraints excluded: chain x residue 47 THR Chi-restraints excluded: chain y residue 10 SER Chi-restraints excluded: chain z residue 4 ILE Chi-restraints excluded: chain z residue 24 LEU Chi-restraints excluded: chain z residue 31 ILE Chi-restraints excluded: chain z residue 56 VAL Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 44 PHE Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 19 ASP Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain D residue 29 GLN Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain G residue 15 PHE Chi-restraints excluded: chain G residue 29 PHE Chi-restraints excluded: chain G residue 162 VAL Chi-restraints excluded: chain G residue 196 ASP Chi-restraints excluded: chain G residue 209 VAL Chi-restraints excluded: chain H residue 84 GLU Chi-restraints excluded: chain H residue 133 MET Chi-restraints excluded: chain H residue 156 LEU Chi-restraints excluded: chain H residue 167 TYR Chi-restraints excluded: chain I residue 49 ASP Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 159 GLU Chi-restraints excluded: chain I residue 180 THR Chi-restraints excluded: chain J residue 72 ASN Chi-restraints excluded: chain J residue 79 THR Chi-restraints excluded: chain J residue 116 VAL Chi-restraints excluded: chain J residue 123 LEU Chi-restraints excluded: chain J residue 133 ILE Chi-restraints excluded: chain J residue 162 GLU Chi-restraints excluded: chain K residue 6 ILE Chi-restraints excluded: chain K residue 11 HIS Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 55 HIS Chi-restraints excluded: chain K residue 64 VAL Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain K residue 93 LYS Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain L residue 5 VAL Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 84 TYR Chi-restraints excluded: chain L residue 96 ASN Chi-restraints excluded: chain L residue 132 THR Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain M residue 25 THR Chi-restraints excluded: chain M residue 35 ILE Chi-restraints excluded: chain M residue 61 THR Chi-restraints excluded: chain M residue 73 SER Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain N residue 20 ILE Chi-restraints excluded: chain N residue 28 VAL Chi-restraints excluded: chain N residue 42 THR Chi-restraints excluded: chain N residue 46 VAL Chi-restraints excluded: chain N residue 109 GLN Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain O residue 19 ASP Chi-restraints excluded: chain O residue 51 VAL Chi-restraints excluded: chain P residue 34 THR Chi-restraints excluded: chain P residue 93 GLU Chi-restraints excluded: chain P residue 94 SER Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain P residue 110 THR Chi-restraints excluded: chain P residue 112 VAL Chi-restraints excluded: chain Q residue 39 THR Chi-restraints excluded: chain Q residue 80 LEU Chi-restraints excluded: chain Q residue 89 LEU Chi-restraints excluded: chain R residue 6 ILE Chi-restraints excluded: chain R residue 8 ILE Chi-restraints excluded: chain R residue 41 ASP Chi-restraints excluded: chain R residue 49 GLU Chi-restraints excluded: chain R residue 64 VAL Chi-restraints excluded: chain R residue 67 ASP Chi-restraints excluded: chain R residue 71 GLU Chi-restraints excluded: chain R residue 82 LEU Chi-restraints excluded: chain S residue 5 MET Chi-restraints excluded: chain S residue 13 VAL Chi-restraints excluded: chain S residue 25 GLU Chi-restraints excluded: chain S residue 55 SER Chi-restraints excluded: chain S residue 99 SER Chi-restraints excluded: chain T residue 26 VAL Chi-restraints excluded: chain T residue 44 GLU Chi-restraints excluded: chain T residue 70 LYS Chi-restraints excluded: chain U residue 36 VAL Chi-restraints excluded: chain U residue 50 THR Chi-restraints excluded: chain U residue 78 VAL Chi-restraints excluded: chain V residue 18 LYS Chi-restraints excluded: chain V residue 28 VAL Chi-restraints excluded: chain V residue 52 CYS Chi-restraints excluded: chain V residue 73 THR Chi-restraints excluded: chain V residue 74 LEU Chi-restraints excluded: chain W residue 13 THR Chi-restraints excluded: chain X residue 30 LEU Chi-restraints excluded: chain X residue 36 ARG Chi-restraints excluded: chain X residue 48 ILE Chi-restraints excluded: chain X residue 50 VAL Chi-restraints excluded: chain X residue 59 VAL Chi-restraints excluded: chain X residue 65 MET Chi-restraints excluded: chain X residue 70 LEU Chi-restraints excluded: chain X residue 78 THR Chi-restraints excluded: chain Y residue 11 ILE Chi-restraints excluded: chain Y residue 26 MET Chi-restraints excluded: chain Y residue 53 MET Chi-restraints excluded: chain Y residue 58 ASP Chi-restraints excluded: chain Y residue 85 LEU Chi-restraints excluded: chain Z residue 12 ASP Chi-restraints excluded: chain Z residue 18 PHE Chi-restraints excluded: chain Z residue 42 THR Chi-restraints excluded: chain a residue 39 VAL Chi-restraints excluded: chain a residue 174 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1048 random chunks: chunk 340 optimal weight: 30.0000 chunk 912 optimal weight: 20.0000 chunk 200 optimal weight: 10.0000 chunk 594 optimal weight: 20.0000 chunk 250 optimal weight: 5.9990 chunk 1013 optimal weight: 20.0000 chunk 841 optimal weight: 30.0000 chunk 469 optimal weight: 7.9990 chunk 84 optimal weight: 30.0000 chunk 335 optimal weight: 9.9990 chunk 532 optimal weight: 20.0000 overall best weight: 10.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 136 GLN k 9 ASN ** m 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 17 ASN ** m 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 18 GLN ** q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 73 ASN v 88 HIS y 25 GLN ** A 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 61 ASN ** G 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 139 ASN ** I 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 53 GLN N 36 GLN O 58 ASN O 64 GLN ** P 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 18 GLN Y 19 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.3138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.121 162697 Z= 0.420 Angle : 0.718 10.421 243503 Z= 0.370 Chirality : 0.041 0.518 31146 Planarity : 0.006 0.061 12986 Dihedral : 23.495 179.130 81738 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 16.62 Ramachandran Plot: Outliers : 0.12 % Allowed : 12.39 % Favored : 87.49 % Rotamer: Outliers : 7.12 % Allowed : 19.85 % Favored : 73.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.34 (0.11), residues: 5836 helix: -0.13 (0.12), residues: 1892 sheet: -1.98 (0.15), residues: 1030 loop : -2.39 (0.11), residues: 2914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP G 103 HIS 0.010 0.002 HIS T 37 PHE 0.045 0.002 PHE Z 36 TYR 0.025 0.002 TYR m 103 ARG 0.010 0.001 ARG B 16 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11672 Ramachandran restraints generated. 5836 Oldfield, 0 Emsley, 5836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11672 Ramachandran restraints generated. 5836 Oldfield, 0 Emsley, 5836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1417 residues out of total 4862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 346 poor density : 1071 time to evaluate : 6.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 51 ARG cc_start: 0.8601 (OUTLIER) cc_final: 0.7731 (ptm-80) REVERT: c 174 SER cc_start: 0.9218 (m) cc_final: 0.8785 (p) REVERT: e 82 TYR cc_start: 0.7922 (t80) cc_final: 0.7403 (t80) REVERT: e 89 THR cc_start: 0.8917 (OUTLIER) cc_final: 0.8586 (p) REVERT: e 134 GLN cc_start: 0.7809 (OUTLIER) cc_final: 0.7557 (pm20) REVERT: e 143 ASP cc_start: 0.7026 (m-30) cc_final: 0.6606 (m-30) REVERT: f 41 GLU cc_start: 0.8797 (mt-10) cc_final: 0.8363 (pp20) REVERT: f 43 LYS cc_start: 0.8333 (mmmt) cc_final: 0.8015 (mmmm) REVERT: f 68 ARG cc_start: 0.8919 (tmt170) cc_final: 0.8689 (ttp80) REVERT: f 115 GLN cc_start: 0.8366 (OUTLIER) cc_final: 0.8070 (pp30) REVERT: g 7 ASP cc_start: 0.8355 (t70) cc_final: 0.7962 (t0) REVERT: h 9 GLN cc_start: 0.5323 (OUTLIER) cc_final: 0.4755 (mm-40) REVERT: j 30 THR cc_start: 0.9330 (OUTLIER) cc_final: 0.9012 (p) REVERT: j 136 GLN cc_start: 0.8191 (OUTLIER) cc_final: 0.7932 (mp10) REVERT: m 6 ARG cc_start: 0.7388 (tpt90) cc_final: 0.6929 (tpt90) REVERT: o 61 GLN cc_start: 0.8653 (mp10) cc_final: 0.8319 (pp30) REVERT: r 6 GLN cc_start: 0.8601 (pp30) cc_final: 0.8257 (tm-30) REVERT: r 11 GLN cc_start: 0.8547 (mm-40) cc_final: 0.8209 (mt0) REVERT: r 18 GLN cc_start: 0.8696 (tm-30) cc_final: 0.8158 (tm-30) REVERT: r 35 PHE cc_start: 0.8953 (m-80) cc_final: 0.8414 (m-80) REVERT: t 7 LEU cc_start: 0.9241 (mp) cc_final: 0.9040 (mp) REVERT: u 86 PHE cc_start: 0.7861 (OUTLIER) cc_final: 0.7620 (m-10) REVERT: v 8 VAL cc_start: 0.9083 (t) cc_final: 0.8832 (p) REVERT: v 59 GLU cc_start: 0.7818 (tm-30) cc_final: 0.7601 (tm-30) REVERT: v 63 ILE cc_start: 0.9217 (mt) cc_final: 0.8898 (tp) REVERT: w 54 THR cc_start: 0.8908 (OUTLIER) cc_final: 0.8539 (t) REVERT: w 58 LYS cc_start: 0.8792 (mmtp) cc_final: 0.8543 (mmtm) REVERT: y 5 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.7986 (pm20) REVERT: y 8 GLU cc_start: 0.7815 (mp0) cc_final: 0.7270 (mp0) REVERT: y 24 GLU cc_start: 0.7925 (mp0) cc_final: 0.7157 (mp0) REVERT: G 161 PHE cc_start: 0.7630 (t80) cc_final: 0.7342 (t80) REVERT: H 109 GLU cc_start: 0.8945 (OUTLIER) cc_final: 0.8634 (pm20) REVERT: H 111 ASP cc_start: 0.8703 (t0) cc_final: 0.8480 (t0) REVERT: H 167 TYR cc_start: 0.7043 (OUTLIER) cc_final: 0.6123 (t80) REVERT: I 123 MET cc_start: 0.7876 (mpp) cc_final: 0.7404 (mpp) REVERT: I 140 ASP cc_start: 0.8101 (m-30) cc_final: 0.7458 (m-30) REVERT: J 11 GLN cc_start: 0.8289 (tt0) cc_final: 0.7965 (tt0) REVERT: K 1 MET cc_start: 0.7826 (tmm) cc_final: 0.7469 (tmm) REVERT: K 11 HIS cc_start: 0.7865 (OUTLIER) cc_final: 0.7093 (m-70) REVERT: K 24 ARG cc_start: 0.8422 (OUTLIER) cc_final: 0.8110 (mtm-85) REVERT: K 45 ARG cc_start: 0.8374 (OUTLIER) cc_final: 0.7609 (ttp-110) REVERT: M 25 THR cc_start: 0.8213 (OUTLIER) cc_final: 0.7924 (p) REVERT: M 113 ARG cc_start: 0.8978 (ttp80) cc_final: 0.8364 (ttm-80) REVERT: N 52 GLU cc_start: 0.9042 (tp30) cc_final: 0.8596 (tp30) REVERT: N 53 LEU cc_start: 0.8935 (mp) cc_final: 0.8518 (tt) REVERT: N 106 ASP cc_start: 0.8153 (t70) cc_final: 0.7767 (t0) REVERT: N 109 GLN cc_start: 0.7922 (tm130) cc_final: 0.7513 (tm-30) REVERT: Q 2 THR cc_start: 0.8536 (m) cc_final: 0.7800 (p) REVERT: R 102 LYS cc_start: 0.8521 (tttt) cc_final: 0.8224 (mttt) REVERT: S 88 MET cc_start: 0.8769 (mmt) cc_final: 0.8470 (mmt) REVERT: T 5 GLU cc_start: 0.8179 (mm-30) cc_final: 0.7955 (mm-30) REVERT: T 70 LYS cc_start: 0.9332 (OUTLIER) cc_final: 0.8595 (ttpp) REVERT: U 35 ARG cc_start: 0.8351 (ppt170) cc_final: 0.8034 (ptt90) REVERT: V 56 ASP cc_start: 0.7096 (p0) cc_final: 0.6850 (p0) REVERT: W 17 VAL cc_start: 0.7434 (OUTLIER) cc_final: 0.7224 (m) REVERT: X 16 LYS cc_start: 0.8586 (mtpt) cc_final: 0.8066 (mmtt) REVERT: X 36 ARG cc_start: 0.8528 (OUTLIER) cc_final: 0.7934 (ptm160) REVERT: X 42 ASN cc_start: 0.8368 (p0) cc_final: 0.7947 (p0) REVERT: X 54 ARG cc_start: 0.8391 (ptt-90) cc_final: 0.7379 (ptt90) REVERT: X 72 GLU cc_start: 0.8222 (mp0) cc_final: 0.7485 (mp0) REVERT: Y 20 ASN cc_start: 0.9139 (OUTLIER) cc_final: 0.8616 (t0) REVERT: Y 26 MET cc_start: 0.8960 (OUTLIER) cc_final: 0.8400 (ttp) REVERT: Y 85 LEU cc_start: 0.6126 (OUTLIER) cc_final: 0.5616 (pp) REVERT: Z 53 LYS cc_start: 0.9184 (mttt) cc_final: 0.8983 (mmmt) outliers start: 346 outliers final: 274 residues processed: 1254 average time/residue: 1.2305 time to fit residues: 2771.3009 Evaluate side-chains 1316 residues out of total 4862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 296 poor density : 1020 time to evaluate : 6.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 39 SER Chi-restraints excluded: chain b residue 48 ILE Chi-restraints excluded: chain b residue 51 ARG Chi-restraints excluded: chain b residue 76 VAL Chi-restraints excluded: chain b residue 179 GLU Chi-restraints excluded: chain b residue 183 VAL Chi-restraints excluded: chain b residue 228 ASP Chi-restraints excluded: chain b residue 258 SER Chi-restraints excluded: chain b residue 267 VAL Chi-restraints excluded: chain b residue 270 ARG Chi-restraints excluded: chain c residue 2 ILE Chi-restraints excluded: chain c residue 9 VAL Chi-restraints excluded: chain c residue 29 VAL Chi-restraints excluded: chain c residue 43 ASP Chi-restraints excluded: chain c residue 60 VAL Chi-restraints excluded: chain c residue 95 SER Chi-restraints excluded: chain c residue 131 ASP Chi-restraints excluded: chain c residue 139 SER Chi-restraints excluded: chain c residue 145 SER Chi-restraints excluded: chain c residue 161 MET Chi-restraints excluded: chain c residue 172 VAL Chi-restraints excluded: chain c residue 176 ASP Chi-restraints excluded: chain c residue 177 VAL Chi-restraints excluded: chain c residue 180 VAL Chi-restraints excluded: chain c residue 199 SER Chi-restraints excluded: chain c residue 200 ASP Chi-restraints excluded: chain d residue 14 VAL Chi-restraints excluded: chain d residue 22 ASP Chi-restraints excluded: chain d residue 65 THR Chi-restraints excluded: chain d residue 77 ILE Chi-restraints excluded: chain d residue 97 ASN Chi-restraints excluded: chain d residue 109 LEU Chi-restraints excluded: chain d residue 120 VAL Chi-restraints excluded: chain e residue 3 LEU Chi-restraints excluded: chain e residue 30 VAL Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 39 VAL Chi-restraints excluded: chain e residue 56 LEU Chi-restraints excluded: chain e residue 66 ILE Chi-restraints excluded: chain e residue 86 CYS Chi-restraints excluded: chain e residue 89 THR Chi-restraints excluded: chain e residue 134 GLN Chi-restraints excluded: chain e residue 136 ILE Chi-restraints excluded: chain f residue 38 ASP Chi-restraints excluded: chain f residue 85 LYS Chi-restraints excluded: chain f residue 91 VAL Chi-restraints excluded: chain f residue 112 VAL Chi-restraints excluded: chain f residue 113 ASP Chi-restraints excluded: chain f residue 115 GLN Chi-restraints excluded: chain f residue 120 ILE Chi-restraints excluded: chain f residue 124 CYS Chi-restraints excluded: chain f residue 129 GLU Chi-restraints excluded: chain f residue 130 ILE Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain g residue 17 ASP Chi-restraints excluded: chain g residue 20 ASN Chi-restraints excluded: chain g residue 130 VAL Chi-restraints excluded: chain h residue 9 GLN Chi-restraints excluded: chain h residue 77 VAL Chi-restraints excluded: chain i residue 23 VAL Chi-restraints excluded: chain j residue 14 ASP Chi-restraints excluded: chain j residue 30 THR Chi-restraints excluded: chain j residue 60 ASP Chi-restraints excluded: chain j residue 62 VAL Chi-restraints excluded: chain j residue 131 ASN Chi-restraints excluded: chain j residue 136 GLN Chi-restraints excluded: chain k residue 6 THR Chi-restraints excluded: chain k residue 10 VAL Chi-restraints excluded: chain k residue 24 VAL Chi-restraints excluded: chain k residue 56 ASP Chi-restraints excluded: chain k residue 89 ASN Chi-restraints excluded: chain k residue 97 THR Chi-restraints excluded: chain k residue 110 GLU Chi-restraints excluded: chain l residue 29 LYS Chi-restraints excluded: chain l residue 76 GLU Chi-restraints excluded: chain l residue 117 THR Chi-restraints excluded: chain l residue 118 THR Chi-restraints excluded: chain l residue 142 ILE Chi-restraints excluded: chain l residue 143 GLU Chi-restraints excluded: chain m residue 2 LEU Chi-restraints excluded: chain m residue 42 THR Chi-restraints excluded: chain m residue 53 MET Chi-restraints excluded: chain m residue 67 VAL Chi-restraints excluded: chain m residue 70 ASP Chi-restraints excluded: chain m residue 74 THR Chi-restraints excluded: chain m residue 89 VAL Chi-restraints excluded: chain m residue 127 LYS Chi-restraints excluded: chain n residue 6 SER Chi-restraints excluded: chain n residue 24 MET Chi-restraints excluded: chain n residue 29 VAL Chi-restraints excluded: chain n residue 34 ILE Chi-restraints excluded: chain n residue 76 VAL Chi-restraints excluded: chain n residue 106 ASP Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain o residue 31 THR Chi-restraints excluded: chain o residue 35 ILE Chi-restraints excluded: chain o residue 58 ILE Chi-restraints excluded: chain o residue 65 THR Chi-restraints excluded: chain o residue 85 LYS Chi-restraints excluded: chain o residue 91 SER Chi-restraints excluded: chain o residue 93 ASP Chi-restraints excluded: chain o residue 95 SER Chi-restraints excluded: chain p residue 8 GLU Chi-restraints excluded: chain p residue 18 SER Chi-restraints excluded: chain p residue 59 THR Chi-restraints excluded: chain p residue 60 VAL Chi-restraints excluded: chain q residue 7 VAL Chi-restraints excluded: chain r residue 19 THR Chi-restraints excluded: chain r residue 40 MET Chi-restraints excluded: chain r residue 41 ILE Chi-restraints excluded: chain r residue 46 GLU Chi-restraints excluded: chain r residue 54 VAL Chi-restraints excluded: chain r residue 60 LYS Chi-restraints excluded: chain s residue 67 ASP Chi-restraints excluded: chain s residue 72 THR Chi-restraints excluded: chain s residue 74 ILE Chi-restraints excluded: chain s residue 103 ILE Chi-restraints excluded: chain t residue 5 GLU Chi-restraints excluded: chain t residue 27 SER Chi-restraints excluded: chain t residue 52 GLU Chi-restraints excluded: chain t residue 79 ASP Chi-restraints excluded: chain t residue 87 LEU Chi-restraints excluded: chain u residue 11 ILE Chi-restraints excluded: chain u residue 14 THR Chi-restraints excluded: chain u residue 27 VAL Chi-restraints excluded: chain u residue 67 SER Chi-restraints excluded: chain u residue 82 VAL Chi-restraints excluded: chain u residue 86 PHE Chi-restraints excluded: chain v residue 55 GLU Chi-restraints excluded: chain v residue 62 THR Chi-restraints excluded: chain v residue 64 VAL Chi-restraints excluded: chain v residue 65 VAL Chi-restraints excluded: chain v residue 76 ASP Chi-restraints excluded: chain v residue 90 ASP Chi-restraints excluded: chain w residue 28 LEU Chi-restraints excluded: chain w residue 34 VAL Chi-restraints excluded: chain w residue 54 THR Chi-restraints excluded: chain w residue 60 ASP Chi-restraints excluded: chain w residue 72 ASN Chi-restraints excluded: chain w residue 77 SER Chi-restraints excluded: chain x residue 12 VAL Chi-restraints excluded: chain x residue 24 THR Chi-restraints excluded: chain x residue 39 VAL Chi-restraints excluded: chain x residue 47 THR Chi-restraints excluded: chain y residue 5 GLU Chi-restraints excluded: chain y residue 10 SER Chi-restraints excluded: chain z residue 4 ILE Chi-restraints excluded: chain z residue 31 ILE Chi-restraints excluded: chain z residue 56 VAL Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 24 ILE Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 44 PHE Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 19 ASP Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 50 GLU Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 29 GLN Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain G residue 14 HIS Chi-restraints excluded: chain G residue 29 PHE Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 162 VAL Chi-restraints excluded: chain G residue 170 ILE Chi-restraints excluded: chain G residue 196 ASP Chi-restraints excluded: chain G residue 209 VAL Chi-restraints excluded: chain H residue 82 ASP Chi-restraints excluded: chain H residue 109 GLU Chi-restraints excluded: chain H residue 133 MET Chi-restraints excluded: chain H residue 156 LEU Chi-restraints excluded: chain H residue 167 TYR Chi-restraints excluded: chain I residue 29 THR Chi-restraints excluded: chain I residue 49 ASP Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 159 GLU Chi-restraints excluded: chain I residue 168 THR Chi-restraints excluded: chain I residue 180 THR Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 72 ASN Chi-restraints excluded: chain J residue 79 THR Chi-restraints excluded: chain J residue 104 ILE Chi-restraints excluded: chain J residue 116 VAL Chi-restraints excluded: chain J residue 123 LEU Chi-restraints excluded: chain J residue 133 ILE Chi-restraints excluded: chain J residue 162 GLU Chi-restraints excluded: chain K residue 6 ILE Chi-restraints excluded: chain K residue 11 HIS Chi-restraints excluded: chain K residue 24 ARG Chi-restraints excluded: chain K residue 26 THR Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 45 ARG Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 55 HIS Chi-restraints excluded: chain K residue 70 VAL Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain K residue 93 LYS Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain L residue 5 VAL Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 84 TYR Chi-restraints excluded: chain L residue 96 ASN Chi-restraints excluded: chain L residue 121 ASN Chi-restraints excluded: chain L residue 132 THR Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 139 ASP Chi-restraints excluded: chain M residue 25 THR Chi-restraints excluded: chain M residue 35 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 103 VAL Chi-restraints excluded: chain N residue 20 ILE Chi-restraints excluded: chain N residue 28 VAL Chi-restraints excluded: chain N residue 38 PHE Chi-restraints excluded: chain N residue 42 THR Chi-restraints excluded: chain N residue 46 VAL Chi-restraints excluded: chain N residue 57 VAL Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain O residue 19 ASP Chi-restraints excluded: chain O residue 51 VAL Chi-restraints excluded: chain P residue 34 THR Chi-restraints excluded: chain P residue 45 THR Chi-restraints excluded: chain P residue 64 VAL Chi-restraints excluded: chain P residue 93 GLU Chi-restraints excluded: chain P residue 94 SER Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain P residue 110 THR Chi-restraints excluded: chain P residue 112 VAL Chi-restraints excluded: chain Q residue 39 THR Chi-restraints excluded: chain Q residue 62 VAL Chi-restraints excluded: chain Q residue 80 LEU Chi-restraints excluded: chain Q residue 89 LEU Chi-restraints excluded: chain R residue 6 ILE Chi-restraints excluded: chain R residue 8 ILE Chi-restraints excluded: chain R residue 41 ASP Chi-restraints excluded: chain R residue 49 GLU Chi-restraints excluded: chain R residue 64 VAL Chi-restraints excluded: chain R residue 67 ASP Chi-restraints excluded: chain R residue 71 GLU Chi-restraints excluded: chain R residue 82 LEU Chi-restraints excluded: chain S residue 5 MET Chi-restraints excluded: chain S residue 13 VAL Chi-restraints excluded: chain S residue 25 GLU Chi-restraints excluded: chain S residue 44 VAL Chi-restraints excluded: chain S residue 55 SER Chi-restraints excluded: chain S residue 73 LEU Chi-restraints excluded: chain S residue 99 SER Chi-restraints excluded: chain T residue 26 VAL Chi-restraints excluded: chain T residue 44 GLU Chi-restraints excluded: chain T residue 70 LYS Chi-restraints excluded: chain U residue 36 VAL Chi-restraints excluded: chain U residue 50 THR Chi-restraints excluded: chain U residue 57 ILE Chi-restraints excluded: chain U residue 66 THR Chi-restraints excluded: chain U residue 78 VAL Chi-restraints excluded: chain V residue 18 LYS Chi-restraints excluded: chain V residue 28 VAL Chi-restraints excluded: chain V residue 52 CYS Chi-restraints excluded: chain V residue 73 THR Chi-restraints excluded: chain V residue 74 LEU Chi-restraints excluded: chain W residue 13 THR Chi-restraints excluded: chain W residue 17 VAL Chi-restraints excluded: chain W residue 27 THR Chi-restraints excluded: chain W residue 39 VAL Chi-restraints excluded: chain X residue 24 SER Chi-restraints excluded: chain X residue 30 LEU Chi-restraints excluded: chain X residue 36 ARG Chi-restraints excluded: chain X residue 43 MET Chi-restraints excluded: chain X residue 48 ILE Chi-restraints excluded: chain X residue 50 VAL Chi-restraints excluded: chain X residue 59 VAL Chi-restraints excluded: chain X residue 65 MET Chi-restraints excluded: chain X residue 70 LEU Chi-restraints excluded: chain X residue 78 THR Chi-restraints excluded: chain Y residue 20 ASN Chi-restraints excluded: chain Y residue 26 MET Chi-restraints excluded: chain Y residue 58 ASP Chi-restraints excluded: chain Y residue 85 LEU Chi-restraints excluded: chain Z residue 12 ASP Chi-restraints excluded: chain Z residue 15 LEU Chi-restraints excluded: chain Z residue 18 PHE Chi-restraints excluded: chain Z residue 36 PHE Chi-restraints excluded: chain Z residue 42 THR Chi-restraints excluded: chain a residue 39 VAL Chi-restraints excluded: chain a residue 59 VAL Chi-restraints excluded: chain a residue 174 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1048 random chunks: chunk 977 optimal weight: 10.0000 chunk 114 optimal weight: 0.8980 chunk 577 optimal weight: 30.0000 chunk 740 optimal weight: 20.0000 chunk 573 optimal weight: 10.0000 chunk 853 optimal weight: 10.0000 chunk 566 optimal weight: 40.0000 chunk 1010 optimal weight: 10.0000 chunk 632 optimal weight: 20.0000 chunk 615 optimal weight: 30.0000 chunk 466 optimal weight: 6.9990 overall best weight: 7.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 136 GLN l 4 ASN ** m 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 17 ASN ** m 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 59 ASN u 73 ASN y 25 GLN ** G 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 139 ASN ** I 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 36 GLN ** P 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 19 ASN ** U 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.3253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 162697 Z= 0.303 Angle : 0.649 12.983 243503 Z= 0.336 Chirality : 0.038 0.285 31146 Planarity : 0.005 0.062 12986 Dihedral : 23.519 178.230 81738 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 15.31 Ramachandran Plot: Outliers : 0.10 % Allowed : 11.48 % Favored : 88.42 % Rotamer: Outliers : 6.56 % Allowed : 21.12 % Favored : 72.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.20 (0.11), residues: 5836 helix: -0.01 (0.12), residues: 1904 sheet: -1.91 (0.16), residues: 989 loop : -2.32 (0.11), residues: 2943 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP G 103 HIS 0.010 0.001 HIS T 37 PHE 0.044 0.002 PHE Z 36 TYR 0.021 0.002 TYR m 103 ARG 0.009 0.001 ARG W 72 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11672 Ramachandran restraints generated. 5836 Oldfield, 0 Emsley, 5836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11672 Ramachandran restraints generated. 5836 Oldfield, 0 Emsley, 5836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1401 residues out of total 4862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 319 poor density : 1082 time to evaluate : 6.206 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 51 ARG cc_start: 0.8574 (OUTLIER) cc_final: 0.7721 (ptm-80) REVERT: c 174 SER cc_start: 0.9163 (OUTLIER) cc_final: 0.8712 (p) REVERT: e 82 TYR cc_start: 0.7896 (t80) cc_final: 0.7334 (t80) REVERT: e 89 THR cc_start: 0.8821 (OUTLIER) cc_final: 0.8515 (p) REVERT: e 134 GLN cc_start: 0.7786 (OUTLIER) cc_final: 0.7563 (pm20) REVERT: e 143 ASP cc_start: 0.6957 (m-30) cc_final: 0.6546 (m-30) REVERT: f 41 GLU cc_start: 0.8791 (mt-10) cc_final: 0.8358 (pp20) REVERT: f 43 LYS cc_start: 0.8402 (mmmt) cc_final: 0.8094 (mmmm) REVERT: f 68 ARG cc_start: 0.8916 (tmt170) cc_final: 0.8678 (ttp80) REVERT: f 115 GLN cc_start: 0.8416 (OUTLIER) cc_final: 0.8192 (pp30) REVERT: g 7 ASP cc_start: 0.8377 (t70) cc_final: 0.8006 (t0) REVERT: g 18 GLN cc_start: 0.7499 (tt0) cc_final: 0.7039 (tp-100) REVERT: h 9 GLN cc_start: 0.5120 (OUTLIER) cc_final: 0.4559 (mm-40) REVERT: l 29 LYS cc_start: 0.9015 (OUTLIER) cc_final: 0.8470 (tmtt) REVERT: n 112 TYR cc_start: 0.8305 (m-80) cc_final: 0.8032 (m-80) REVERT: o 56 LYS cc_start: 0.7524 (mppt) cc_final: 0.6950 (mppt) REVERT: o 61 GLN cc_start: 0.8652 (mp10) cc_final: 0.8357 (pp30) REVERT: r 6 GLN cc_start: 0.8615 (pp30) cc_final: 0.8212 (pp30) REVERT: r 11 GLN cc_start: 0.8574 (mm-40) cc_final: 0.8224 (mt0) REVERT: r 31 GLU cc_start: 0.8550 (tp30) cc_final: 0.8347 (tp30) REVERT: r 32 THR cc_start: 0.9089 (m) cc_final: 0.8705 (p) REVERT: t 69 ARG cc_start: 0.7342 (ttp80) cc_final: 0.6574 (ttp80) REVERT: u 86 PHE cc_start: 0.7848 (OUTLIER) cc_final: 0.7575 (m-10) REVERT: v 8 VAL cc_start: 0.9021 (t) cc_final: 0.8770 (p) REVERT: v 63 ILE cc_start: 0.9197 (mt) cc_final: 0.8892 (tp) REVERT: w 54 THR cc_start: 0.8883 (OUTLIER) cc_final: 0.8521 (t) REVERT: w 66 GLU cc_start: 0.7260 (tm-30) cc_final: 0.6964 (tm-30) REVERT: y 8 GLU cc_start: 0.7780 (mp0) cc_final: 0.7398 (mp0) REVERT: y 24 GLU cc_start: 0.7814 (mp0) cc_final: 0.7167 (mp0) REVERT: C 50 GLU cc_start: 0.6974 (OUTLIER) cc_final: 0.6758 (pm20) REVERT: G 161 PHE cc_start: 0.7588 (t80) cc_final: 0.7298 (t80) REVERT: H 109 GLU cc_start: 0.8942 (OUTLIER) cc_final: 0.8650 (pm20) REVERT: H 111 ASP cc_start: 0.8668 (t0) cc_final: 0.8466 (t0) REVERT: H 167 TYR cc_start: 0.7004 (OUTLIER) cc_final: 0.6129 (t80) REVERT: I 123 MET cc_start: 0.7803 (mpp) cc_final: 0.7412 (mpp) REVERT: I 140 ASP cc_start: 0.8101 (m-30) cc_final: 0.7489 (m-30) REVERT: J 11 GLN cc_start: 0.8315 (tt0) cc_final: 0.7982 (tt0) REVERT: J 70 MET cc_start: 0.8064 (tpp) cc_final: 0.7861 (tpp) REVERT: J 123 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8326 (mt) REVERT: K 1 MET cc_start: 0.7794 (tmm) cc_final: 0.7488 (tmm) REVERT: K 11 HIS cc_start: 0.7827 (OUTLIER) cc_final: 0.7014 (m-70) REVERT: K 45 ARG cc_start: 0.8348 (OUTLIER) cc_final: 0.7545 (ttp-110) REVERT: L 30 MET cc_start: 0.9020 (ptp) cc_final: 0.8378 (ptp) REVERT: M 25 THR cc_start: 0.8210 (OUTLIER) cc_final: 0.7883 (p) REVERT: M 113 ARG cc_start: 0.8935 (ttp80) cc_final: 0.8340 (ttm-80) REVERT: N 52 GLU cc_start: 0.9036 (tp30) cc_final: 0.8599 (tp30) REVERT: N 53 LEU cc_start: 0.8948 (mp) cc_final: 0.8472 (tt) REVERT: N 106 ASP cc_start: 0.8103 (t70) cc_final: 0.7720 (t0) REVERT: N 109 GLN cc_start: 0.7907 (OUTLIER) cc_final: 0.7498 (tm-30) REVERT: O 42 LEU cc_start: 0.9097 (mm) cc_final: 0.8817 (mp) REVERT: Q 2 THR cc_start: 0.8424 (m) cc_final: 0.7671 (p) REVERT: R 102 LYS cc_start: 0.8459 (tttt) cc_final: 0.8198 (mttt) REVERT: S 25 GLU cc_start: 0.7782 (OUTLIER) cc_final: 0.7520 (pm20) REVERT: T 14 PHE cc_start: 0.7991 (m-80) cc_final: 0.7697 (m-80) REVERT: T 70 LYS cc_start: 0.9301 (OUTLIER) cc_final: 0.8548 (ttpp) REVERT: U 35 ARG cc_start: 0.8348 (ppt170) cc_final: 0.8042 (ptt90) REVERT: V 56 ASP cc_start: 0.7004 (p0) cc_final: 0.6515 (p0) REVERT: X 10 ILE cc_start: 0.7926 (OUTLIER) cc_final: 0.7696 (tp) REVERT: X 16 LYS cc_start: 0.8595 (mtpt) cc_final: 0.8213 (mmtt) REVERT: X 42 ASN cc_start: 0.8317 (p0) cc_final: 0.7989 (p0) REVERT: X 72 GLU cc_start: 0.8173 (mp0) cc_final: 0.7931 (mm-30) REVERT: Y 20 ASN cc_start: 0.9141 (OUTLIER) cc_final: 0.8547 (t0) REVERT: Y 24 ARG cc_start: 0.8964 (ttm170) cc_final: 0.8630 (ttm170) REVERT: Y 26 MET cc_start: 0.8944 (OUTLIER) cc_final: 0.8453 (ttp) REVERT: Y 85 LEU cc_start: 0.6041 (OUTLIER) cc_final: 0.5580 (pp) REVERT: Z 53 LYS cc_start: 0.9224 (mttt) cc_final: 0.8994 (mmmt) outliers start: 319 outliers final: 256 residues processed: 1252 average time/residue: 1.2618 time to fit residues: 2841.1584 Evaluate side-chains 1313 residues out of total 4862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 279 poor density : 1034 time to evaluate : 5.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 39 SER Chi-restraints excluded: chain b residue 51 ARG Chi-restraints excluded: chain b residue 76 VAL Chi-restraints excluded: chain b residue 179 GLU Chi-restraints excluded: chain b residue 183 VAL Chi-restraints excluded: chain b residue 228 ASP Chi-restraints excluded: chain b residue 258 SER Chi-restraints excluded: chain b residue 270 ARG Chi-restraints excluded: chain c residue 2 ILE Chi-restraints excluded: chain c residue 9 VAL Chi-restraints excluded: chain c residue 29 VAL Chi-restraints excluded: chain c residue 60 VAL Chi-restraints excluded: chain c residue 95 SER Chi-restraints excluded: chain c residue 131 ASP Chi-restraints excluded: chain c residue 139 SER Chi-restraints excluded: chain c residue 145 SER Chi-restraints excluded: chain c residue 161 MET Chi-restraints excluded: chain c residue 172 VAL Chi-restraints excluded: chain c residue 174 SER Chi-restraints excluded: chain c residue 176 ASP Chi-restraints excluded: chain c residue 177 VAL Chi-restraints excluded: chain c residue 180 VAL Chi-restraints excluded: chain c residue 199 SER Chi-restraints excluded: chain c residue 200 ASP Chi-restraints excluded: chain d residue 14 VAL Chi-restraints excluded: chain d residue 22 ASP Chi-restraints excluded: chain d residue 65 THR Chi-restraints excluded: chain d residue 77 ILE Chi-restraints excluded: chain d residue 97 ASN Chi-restraints excluded: chain d residue 120 VAL Chi-restraints excluded: chain e residue 3 LEU Chi-restraints excluded: chain e residue 30 VAL Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 39 VAL Chi-restraints excluded: chain e residue 43 ILE Chi-restraints excluded: chain e residue 56 LEU Chi-restraints excluded: chain e residue 66 ILE Chi-restraints excluded: chain e residue 86 CYS Chi-restraints excluded: chain e residue 89 THR Chi-restraints excluded: chain e residue 112 ASP Chi-restraints excluded: chain e residue 134 GLN Chi-restraints excluded: chain e residue 136 ILE Chi-restraints excluded: chain f residue 8 VAL Chi-restraints excluded: chain f residue 38 ASP Chi-restraints excluded: chain f residue 85 LYS Chi-restraints excluded: chain f residue 91 VAL Chi-restraints excluded: chain f residue 112 VAL Chi-restraints excluded: chain f residue 113 ASP Chi-restraints excluded: chain f residue 115 GLN Chi-restraints excluded: chain f residue 129 GLU Chi-restraints excluded: chain f residue 130 ILE Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain g residue 17 ASP Chi-restraints excluded: chain g residue 20 ASN Chi-restraints excluded: chain g residue 35 LYS Chi-restraints excluded: chain g residue 130 VAL Chi-restraints excluded: chain h residue 9 GLN Chi-restraints excluded: chain h residue 77 VAL Chi-restraints excluded: chain i residue 23 VAL Chi-restraints excluded: chain j residue 14 ASP Chi-restraints excluded: chain j residue 30 THR Chi-restraints excluded: chain j residue 60 ASP Chi-restraints excluded: chain j residue 62 VAL Chi-restraints excluded: chain j residue 131 ASN Chi-restraints excluded: chain k residue 6 THR Chi-restraints excluded: chain k residue 10 VAL Chi-restraints excluded: chain k residue 24 VAL Chi-restraints excluded: chain k residue 56 ASP Chi-restraints excluded: chain k residue 89 ASN Chi-restraints excluded: chain k residue 97 THR Chi-restraints excluded: chain l residue 29 LYS Chi-restraints excluded: chain l residue 76 GLU Chi-restraints excluded: chain l residue 117 THR Chi-restraints excluded: chain l residue 118 THR Chi-restraints excluded: chain l residue 142 ILE Chi-restraints excluded: chain l residue 143 GLU Chi-restraints excluded: chain m residue 2 LEU Chi-restraints excluded: chain m residue 42 THR Chi-restraints excluded: chain m residue 70 ASP Chi-restraints excluded: chain m residue 74 THR Chi-restraints excluded: chain m residue 89 VAL Chi-restraints excluded: chain m residue 105 MET Chi-restraints excluded: chain m residue 127 LYS Chi-restraints excluded: chain n residue 6 SER Chi-restraints excluded: chain n residue 24 MET Chi-restraints excluded: chain n residue 29 VAL Chi-restraints excluded: chain n residue 34 ILE Chi-restraints excluded: chain n residue 76 VAL Chi-restraints excluded: chain n residue 106 ASP Chi-restraints excluded: chain o residue 31 THR Chi-restraints excluded: chain o residue 58 ILE Chi-restraints excluded: chain o residue 65 THR Chi-restraints excluded: chain o residue 85 LYS Chi-restraints excluded: chain o residue 91 SER Chi-restraints excluded: chain o residue 93 ASP Chi-restraints excluded: chain o residue 95 SER Chi-restraints excluded: chain p residue 59 THR Chi-restraints excluded: chain p residue 60 VAL Chi-restraints excluded: chain q residue 7 VAL Chi-restraints excluded: chain r residue 41 ILE Chi-restraints excluded: chain r residue 46 GLU Chi-restraints excluded: chain r residue 54 VAL Chi-restraints excluded: chain r residue 60 LYS Chi-restraints excluded: chain s residue 67 ASP Chi-restraints excluded: chain s residue 74 ILE Chi-restraints excluded: chain s residue 103 ILE Chi-restraints excluded: chain t residue 27 SER Chi-restraints excluded: chain t residue 39 THR Chi-restraints excluded: chain t residue 52 GLU Chi-restraints excluded: chain t residue 79 ASP Chi-restraints excluded: chain t residue 87 LEU Chi-restraints excluded: chain u residue 14 THR Chi-restraints excluded: chain u residue 27 VAL Chi-restraints excluded: chain u residue 67 SER Chi-restraints excluded: chain u residue 73 ASN Chi-restraints excluded: chain u residue 82 VAL Chi-restraints excluded: chain u residue 86 PHE Chi-restraints excluded: chain v residue 62 THR Chi-restraints excluded: chain v residue 65 VAL Chi-restraints excluded: chain v residue 76 ASP Chi-restraints excluded: chain v residue 90 ASP Chi-restraints excluded: chain w residue 28 LEU Chi-restraints excluded: chain w residue 54 THR Chi-restraints excluded: chain w residue 60 ASP Chi-restraints excluded: chain w residue 72 ASN Chi-restraints excluded: chain w residue 77 SER Chi-restraints excluded: chain x residue 12 VAL Chi-restraints excluded: chain x residue 24 THR Chi-restraints excluded: chain x residue 39 VAL Chi-restraints excluded: chain x residue 47 THR Chi-restraints excluded: chain y residue 10 SER Chi-restraints excluded: chain z residue 3 THR Chi-restraints excluded: chain z residue 4 ILE Chi-restraints excluded: chain z residue 24 LEU Chi-restraints excluded: chain z residue 31 ILE Chi-restraints excluded: chain z residue 50 VAL Chi-restraints excluded: chain z residue 56 VAL Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 24 ILE Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 44 PHE Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 19 ASP Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 50 GLU Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 29 GLN Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain G residue 15 PHE Chi-restraints excluded: chain G residue 29 PHE Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 162 VAL Chi-restraints excluded: chain G residue 170 ILE Chi-restraints excluded: chain G residue 196 ASP Chi-restraints excluded: chain G residue 204 ASP Chi-restraints excluded: chain G residue 209 VAL Chi-restraints excluded: chain H residue 82 ASP Chi-restraints excluded: chain H residue 84 GLU Chi-restraints excluded: chain H residue 109 GLU Chi-restraints excluded: chain H residue 133 MET Chi-restraints excluded: chain H residue 156 LEU Chi-restraints excluded: chain H residue 167 TYR Chi-restraints excluded: chain H residue 206 ILE Chi-restraints excluded: chain I residue 29 THR Chi-restraints excluded: chain I residue 49 ASP Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 159 GLU Chi-restraints excluded: chain I residue 180 THR Chi-restraints excluded: chain J residue 72 ASN Chi-restraints excluded: chain J residue 79 THR Chi-restraints excluded: chain J residue 104 ILE Chi-restraints excluded: chain J residue 116 VAL Chi-restraints excluded: chain J residue 123 LEU Chi-restraints excluded: chain J residue 133 ILE Chi-restraints excluded: chain J residue 162 GLU Chi-restraints excluded: chain K residue 6 ILE Chi-restraints excluded: chain K residue 11 HIS Chi-restraints excluded: chain K residue 22 ILE Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 45 ARG Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 55 HIS Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain K residue 93 LYS Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain L residue 5 VAL Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 26 VAL Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 84 TYR Chi-restraints excluded: chain L residue 96 ASN Chi-restraints excluded: chain L residue 121 ASN Chi-restraints excluded: chain L residue 132 THR Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 140 VAL Chi-restraints excluded: chain M residue 25 THR 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 103 VAL Chi-restraints excluded: chain N residue 20 ILE Chi-restraints excluded: chain N residue 28 VAL Chi-restraints excluded: chain N residue 36 GLN Chi-restraints excluded: chain N residue 38 PHE Chi-restraints excluded: chain N residue 42 THR Chi-restraints excluded: chain N residue 46 VAL Chi-restraints excluded: chain N residue 57 VAL Chi-restraints excluded: chain N residue 109 GLN Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain O residue 19 ASP Chi-restraints excluded: chain O residue 51 VAL Chi-restraints excluded: chain P residue 34 THR Chi-restraints excluded: chain P residue 45 THR Chi-restraints excluded: chain P residue 64 VAL Chi-restraints excluded: chain P residue 94 SER Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain P residue 110 THR Chi-restraints excluded: chain P residue 112 VAL Chi-restraints excluded: chain Q residue 7 VAL Chi-restraints excluded: chain Q residue 39 THR Chi-restraints excluded: chain Q residue 62 VAL Chi-restraints excluded: chain Q residue 80 LEU Chi-restraints excluded: chain Q residue 89 LEU Chi-restraints excluded: chain R residue 6 ILE Chi-restraints excluded: chain R residue 7 ASN Chi-restraints excluded: chain R residue 8 ILE Chi-restraints excluded: chain R residue 41 ASP Chi-restraints excluded: chain R residue 49 GLU Chi-restraints excluded: chain R residue 64 VAL Chi-restraints excluded: chain R residue 67 ASP Chi-restraints excluded: chain R residue 71 GLU Chi-restraints excluded: chain R residue 82 LEU Chi-restraints excluded: chain R residue 84 CYS Chi-restraints excluded: chain S residue 5 MET Chi-restraints excluded: chain S residue 13 VAL Chi-restraints excluded: chain S residue 25 GLU Chi-restraints excluded: chain S residue 55 SER Chi-restraints excluded: chain S residue 63 CYS Chi-restraints excluded: chain S residue 73 LEU Chi-restraints excluded: chain T residue 44 GLU Chi-restraints excluded: chain T residue 70 LYS Chi-restraints excluded: chain T residue 88 ARG Chi-restraints excluded: chain U residue 36 VAL Chi-restraints excluded: chain U residue 50 THR Chi-restraints excluded: chain U residue 57 ILE Chi-restraints excluded: chain U residue 78 VAL Chi-restraints excluded: chain V residue 18 LYS Chi-restraints excluded: chain V residue 28 VAL Chi-restraints excluded: chain V residue 52 CYS Chi-restraints excluded: chain V residue 73 THR Chi-restraints excluded: chain W residue 13 THR Chi-restraints excluded: chain W residue 27 THR Chi-restraints excluded: chain W residue 43 ILE Chi-restraints excluded: chain W residue 54 LEU Chi-restraints excluded: chain X residue 10 ILE Chi-restraints excluded: chain X residue 24 SER Chi-restraints excluded: chain X residue 30 LEU Chi-restraints excluded: chain X residue 43 MET Chi-restraints excluded: chain X residue 48 ILE Chi-restraints excluded: chain X residue 50 VAL Chi-restraints excluded: chain X residue 59 VAL Chi-restraints excluded: chain X residue 70 LEU Chi-restraints excluded: chain X residue 78 THR Chi-restraints excluded: chain Y residue 20 ASN Chi-restraints excluded: chain Y residue 26 MET Chi-restraints excluded: chain Y residue 58 ASP Chi-restraints excluded: chain Y residue 85 LEU Chi-restraints excluded: chain Z residue 12 ASP Chi-restraints excluded: chain Z residue 15 LEU Chi-restraints excluded: chain Z residue 18 PHE Chi-restraints excluded: chain Z residue 36 PHE Chi-restraints excluded: chain Z residue 42 THR Chi-restraints excluded: chain a residue 39 VAL Chi-restraints excluded: chain a residue 174 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1048 random chunks: chunk 624 optimal weight: 20.0000 chunk 403 optimal weight: 10.0000 chunk 603 optimal weight: 20.0000 chunk 304 optimal weight: 4.9990 chunk 198 optimal weight: 9.9990 chunk 195 optimal weight: 10.0000 chunk 642 optimal weight: 10.0000 chunk 688 optimal weight: 30.0000 chunk 499 optimal weight: 1.9990 chunk 94 optimal weight: 20.0000 chunk 793 optimal weight: 10.0000 overall best weight: 7.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 4 ASN ** m 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 17 ASN ** m 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 73 ASN y 25 GLN ** G 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 36 GLN ** P 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.3311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 162697 Z= 0.301 Angle : 0.647 12.677 243503 Z= 0.336 Chirality : 0.038 0.381 31146 Planarity : 0.005 0.061 12986 Dihedral : 23.518 178.376 81738 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 15.43 Ramachandran Plot: Outliers : 0.10 % Allowed : 11.65 % Favored : 88.25 % Rotamer: Outliers : 6.71 % Allowed : 21.12 % Favored : 72.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.18 (0.11), residues: 5836 helix: -0.02 (0.12), residues: 1917 sheet: -1.90 (0.16), residues: 993 loop : -2.30 (0.11), residues: 2926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP G 103 HIS 0.010 0.001 HIS T 37 PHE 0.044 0.002 PHE Z 36 TYR 0.024 0.002 TYR m 103 ARG 0.007 0.001 ARG U 56 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11672 Ramachandran restraints generated. 5836 Oldfield, 0 Emsley, 5836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11672 Ramachandran restraints generated. 5836 Oldfield, 0 Emsley, 5836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1390 residues out of total 4862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 326 poor density : 1064 time to evaluate : 6.870 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 51 ARG cc_start: 0.8579 (OUTLIER) cc_final: 0.7726 (ptm-80) REVERT: c 174 SER cc_start: 0.9185 (m) cc_final: 0.8592 (t) REVERT: e 82 TYR cc_start: 0.7887 (t80) cc_final: 0.7327 (t80) REVERT: e 89 THR cc_start: 0.8816 (OUTLIER) cc_final: 0.8513 (p) REVERT: e 134 GLN cc_start: 0.7782 (OUTLIER) cc_final: 0.7562 (pm20) REVERT: e 143 ASP cc_start: 0.6952 (m-30) cc_final: 0.6544 (m-30) REVERT: f 34 ARG cc_start: 0.8543 (tpp80) cc_final: 0.8290 (tpt-90) REVERT: f 41 GLU cc_start: 0.8812 (mt-10) cc_final: 0.8385 (pp20) REVERT: f 43 LYS cc_start: 0.8429 (mmmt) cc_final: 0.8134 (mmmm) REVERT: f 68 ARG cc_start: 0.8921 (tmt170) cc_final: 0.8705 (ttp80) REVERT: f 169 ARG cc_start: 0.7880 (mmm-85) cc_final: 0.7438 (mmm160) REVERT: g 7 ASP cc_start: 0.8451 (t70) cc_final: 0.8096 (t0) REVERT: g 18 GLN cc_start: 0.7489 (tt0) cc_final: 0.7030 (tp-100) REVERT: h 9 GLN cc_start: 0.5081 (OUTLIER) cc_final: 0.4516 (mm-40) REVERT: l 29 LYS cc_start: 0.9011 (OUTLIER) cc_final: 0.8508 (tmtt) REVERT: m 6 ARG cc_start: 0.6936 (tpt90) cc_final: 0.6662 (tpt90) REVERT: n 112 TYR cc_start: 0.8322 (m-80) cc_final: 0.8084 (m-80) REVERT: o 80 GLU cc_start: 0.9227 (mm-30) cc_final: 0.8919 (pp20) REVERT: r 6 GLN cc_start: 0.8620 (pp30) cc_final: 0.8200 (pp30) REVERT: r 11 GLN cc_start: 0.8595 (mm-40) cc_final: 0.8237 (mt0) REVERT: r 18 GLN cc_start: 0.8554 (tm-30) cc_final: 0.8240 (tm-30) REVERT: r 31 GLU cc_start: 0.8627 (tp30) cc_final: 0.8372 (tp30) REVERT: r 32 THR cc_start: 0.9040 (m) cc_final: 0.8733 (p) REVERT: t 69 ARG cc_start: 0.7386 (ttp80) cc_final: 0.6687 (ttp80) REVERT: u 86 PHE cc_start: 0.7859 (OUTLIER) cc_final: 0.7589 (m-10) REVERT: v 8 VAL cc_start: 0.9014 (t) cc_final: 0.8805 (p) REVERT: v 63 ILE cc_start: 0.9207 (mt) cc_final: 0.8908 (tp) REVERT: w 54 THR cc_start: 0.8885 (OUTLIER) cc_final: 0.8514 (t) REVERT: w 66 GLU cc_start: 0.7234 (tm-30) cc_final: 0.7010 (tm-30) REVERT: y 8 GLU cc_start: 0.8040 (mp0) cc_final: 0.7384 (mp0) REVERT: y 24 GLU cc_start: 0.7786 (mp0) cc_final: 0.7122 (mp0) REVERT: G 161 PHE cc_start: 0.7565 (t80) cc_final: 0.7283 (t80) REVERT: H 109 GLU cc_start: 0.8948 (OUTLIER) cc_final: 0.8655 (pm20) REVERT: H 111 ASP cc_start: 0.8672 (t0) cc_final: 0.8464 (t0) REVERT: H 167 TYR cc_start: 0.6993 (OUTLIER) cc_final: 0.6120 (t80) REVERT: I 140 ASP cc_start: 0.8104 (m-30) cc_final: 0.7491 (m-30) REVERT: I 189 ASP cc_start: 0.7908 (m-30) cc_final: 0.7327 (m-30) REVERT: J 11 GLN cc_start: 0.8240 (tt0) cc_final: 0.7891 (tt0) REVERT: J 123 LEU cc_start: 0.8545 (tp) cc_final: 0.8306 (mt) REVERT: K 1 MET cc_start: 0.7851 (tmm) cc_final: 0.7567 (tmm) REVERT: K 11 HIS cc_start: 0.7855 (OUTLIER) cc_final: 0.7061 (m-70) REVERT: K 45 ARG cc_start: 0.8347 (OUTLIER) cc_final: 0.7550 (ttp-110) REVERT: L 30 MET cc_start: 0.9030 (ptp) cc_final: 0.8393 (ptp) REVERT: M 4 ASP cc_start: 0.7954 (t0) cc_final: 0.7604 (t0) REVERT: M 25 THR cc_start: 0.8280 (OUTLIER) cc_final: 0.8033 (p) REVERT: M 113 ARG cc_start: 0.8933 (ttp80) cc_final: 0.8342 (ttm-80) REVERT: N 45 MET cc_start: 0.8129 (pmm) cc_final: 0.7901 (pmm) REVERT: N 52 GLU cc_start: 0.9039 (tp30) cc_final: 0.8610 (tp30) REVERT: N 53 LEU cc_start: 0.8934 (mp) cc_final: 0.8415 (tt) REVERT: N 106 ASP cc_start: 0.8105 (t70) cc_final: 0.7717 (t0) REVERT: N 109 GLN cc_start: 0.7915 (OUTLIER) cc_final: 0.7619 (tm-30) REVERT: N 111 GLU cc_start: 0.8561 (mt-10) cc_final: 0.8340 (mt-10) REVERT: O 42 LEU cc_start: 0.9100 (mm) cc_final: 0.8893 (mp) REVERT: R 102 LYS cc_start: 0.8466 (tttt) cc_final: 0.8199 (mttt) REVERT: S 4 SER cc_start: 0.8283 (OUTLIER) cc_final: 0.7950 (m) REVERT: S 25 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.7504 (pm20) REVERT: T 14 PHE cc_start: 0.7988 (m-80) cc_final: 0.7743 (m-80) REVERT: T 70 LYS cc_start: 0.9306 (OUTLIER) cc_final: 0.8560 (ttpp) REVERT: U 35 ARG cc_start: 0.8326 (ppt170) cc_final: 0.8044 (ptt90) REVERT: V 56 ASP cc_start: 0.6994 (p0) cc_final: 0.6627 (p0) REVERT: X 16 LYS cc_start: 0.8563 (mtpt) cc_final: 0.8214 (mmtt) REVERT: X 42 ASN cc_start: 0.8289 (p0) cc_final: 0.7962 (p0) REVERT: X 72 GLU cc_start: 0.8137 (mp0) cc_final: 0.7552 (mp0) REVERT: Y 20 ASN cc_start: 0.9145 (OUTLIER) cc_final: 0.8655 (t0) REVERT: Y 26 MET cc_start: 0.8923 (OUTLIER) cc_final: 0.8451 (ttp) REVERT: Y 85 LEU cc_start: 0.6095 (OUTLIER) cc_final: 0.5634 (pp) REVERT: Z 53 LYS cc_start: 0.9228 (mttt) cc_final: 0.9025 (mmmt) outliers start: 326 outliers final: 272 residues processed: 1247 average time/residue: 1.2865 time to fit residues: 2895.5371 Evaluate side-chains 1321 residues out of total 4862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 291 poor density : 1030 time to evaluate : 6.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 39 SER Chi-restraints excluded: chain b residue 51 ARG Chi-restraints excluded: chain b residue 76 VAL Chi-restraints excluded: chain b residue 179 GLU Chi-restraints excluded: chain b residue 183 VAL Chi-restraints excluded: chain b residue 228 ASP Chi-restraints excluded: chain b residue 258 SER Chi-restraints excluded: chain b residue 267 VAL Chi-restraints excluded: chain b residue 270 ARG Chi-restraints excluded: chain c residue 2 ILE Chi-restraints excluded: chain c residue 9 VAL Chi-restraints excluded: chain c residue 29 VAL Chi-restraints excluded: chain c residue 60 VAL Chi-restraints excluded: chain c residue 95 SER Chi-restraints excluded: chain c residue 131 ASP Chi-restraints excluded: chain c residue 139 SER Chi-restraints excluded: chain c residue 145 SER Chi-restraints excluded: chain c residue 161 MET Chi-restraints excluded: chain c residue 172 VAL Chi-restraints excluded: chain c residue 176 ASP Chi-restraints excluded: chain c residue 177 VAL Chi-restraints excluded: chain c residue 180 VAL Chi-restraints excluded: chain c residue 199 SER Chi-restraints excluded: chain c residue 200 ASP Chi-restraints excluded: chain d residue 14 VAL Chi-restraints excluded: chain d residue 22 ASP Chi-restraints excluded: chain d residue 65 THR Chi-restraints excluded: chain d residue 77 ILE Chi-restraints excluded: chain d residue 97 ASN Chi-restraints excluded: chain d residue 120 VAL Chi-restraints excluded: chain d residue 150 THR Chi-restraints excluded: chain e residue 3 LEU Chi-restraints excluded: chain e residue 30 VAL Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 39 VAL Chi-restraints excluded: chain e residue 43 ILE Chi-restraints excluded: chain e residue 56 LEU Chi-restraints excluded: chain e residue 66 ILE Chi-restraints excluded: chain e residue 86 CYS Chi-restraints excluded: chain e residue 89 THR Chi-restraints excluded: chain e residue 112 ASP Chi-restraints excluded: chain e residue 134 GLN Chi-restraints excluded: chain e residue 136 ILE Chi-restraints excluded: chain f residue 8 VAL Chi-restraints excluded: chain f residue 38 ASP Chi-restraints excluded: chain f residue 85 LYS Chi-restraints excluded: chain f residue 91 VAL Chi-restraints excluded: chain f residue 112 VAL Chi-restraints excluded: chain f residue 113 ASP Chi-restraints excluded: chain f residue 129 GLU Chi-restraints excluded: chain f residue 130 ILE Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain g residue 17 ASP Chi-restraints excluded: chain g residue 20 ASN Chi-restraints excluded: chain g residue 35 LYS Chi-restraints excluded: chain g residue 130 VAL Chi-restraints excluded: chain h residue 9 GLN Chi-restraints excluded: chain h residue 77 VAL Chi-restraints excluded: chain i residue 23 VAL Chi-restraints excluded: chain j residue 14 ASP Chi-restraints excluded: chain j residue 30 THR Chi-restraints excluded: chain j residue 60 ASP Chi-restraints excluded: chain j residue 62 VAL Chi-restraints excluded: chain j residue 131 ASN Chi-restraints excluded: chain k residue 6 THR Chi-restraints excluded: chain k residue 10 VAL Chi-restraints excluded: chain k residue 24 VAL Chi-restraints excluded: chain k residue 56 ASP Chi-restraints excluded: chain k residue 73 ASP Chi-restraints excluded: chain k residue 89 ASN Chi-restraints excluded: chain k residue 97 THR Chi-restraints excluded: chain l residue 29 LYS Chi-restraints excluded: chain l residue 76 GLU Chi-restraints excluded: chain l residue 117 THR Chi-restraints excluded: chain l residue 118 THR Chi-restraints excluded: chain l residue 142 ILE Chi-restraints excluded: chain l residue 143 GLU Chi-restraints excluded: chain m residue 2 LEU Chi-restraints excluded: chain m residue 67 VAL Chi-restraints excluded: chain m residue 70 ASP Chi-restraints excluded: chain m residue 74 THR Chi-restraints excluded: chain m residue 89 VAL Chi-restraints excluded: chain m residue 105 MET Chi-restraints excluded: chain m residue 127 LYS Chi-restraints excluded: chain n residue 6 SER Chi-restraints excluded: chain n residue 24 MET Chi-restraints excluded: chain n residue 29 VAL Chi-restraints excluded: chain n residue 34 ILE Chi-restraints excluded: chain n residue 76 VAL Chi-restraints excluded: chain n residue 106 ASP Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain o residue 31 THR Chi-restraints excluded: chain o residue 58 ILE Chi-restraints excluded: chain o residue 65 THR Chi-restraints excluded: chain o residue 83 LEU Chi-restraints excluded: chain o residue 85 LYS Chi-restraints excluded: chain o residue 91 SER Chi-restraints excluded: chain o residue 93 ASP Chi-restraints excluded: chain o residue 95 SER Chi-restraints excluded: chain p residue 18 SER Chi-restraints excluded: chain p residue 59 THR Chi-restraints excluded: chain p residue 60 VAL Chi-restraints excluded: chain q residue 7 VAL Chi-restraints excluded: chain q residue 16 ILE Chi-restraints excluded: chain r residue 19 THR Chi-restraints excluded: chain r residue 29 THR Chi-restraints excluded: chain r residue 41 ILE Chi-restraints excluded: chain r residue 46 GLU Chi-restraints excluded: chain r residue 54 VAL Chi-restraints excluded: chain r residue 60 LYS Chi-restraints excluded: chain s residue 67 ASP Chi-restraints excluded: chain s residue 74 ILE Chi-restraints excluded: chain s residue 103 ILE Chi-restraints excluded: chain t residue 27 SER Chi-restraints excluded: chain t residue 52 GLU Chi-restraints excluded: chain t residue 79 ASP Chi-restraints excluded: chain t residue 87 LEU Chi-restraints excluded: chain u residue 14 THR Chi-restraints excluded: chain u residue 27 VAL Chi-restraints excluded: chain u residue 67 SER Chi-restraints excluded: chain u residue 73 ASN Chi-restraints excluded: chain u residue 82 VAL Chi-restraints excluded: chain u residue 86 PHE Chi-restraints excluded: chain v residue 30 ILE Chi-restraints excluded: chain v residue 55 GLU Chi-restraints excluded: chain v residue 62 THR Chi-restraints excluded: chain v residue 64 VAL Chi-restraints excluded: chain v residue 65 VAL Chi-restraints excluded: chain v residue 76 ASP Chi-restraints excluded: chain v residue 90 ASP Chi-restraints excluded: chain w residue 28 LEU Chi-restraints excluded: chain w residue 54 THR Chi-restraints excluded: chain w residue 60 ASP Chi-restraints excluded: chain w residue 72 ASN Chi-restraints excluded: chain w residue 77 SER Chi-restraints excluded: chain x residue 12 VAL Chi-restraints excluded: chain x residue 24 THR Chi-restraints excluded: chain x residue 39 VAL Chi-restraints excluded: chain x residue 47 THR Chi-restraints excluded: chain x residue 65 THR Chi-restraints excluded: chain y residue 5 GLU Chi-restraints excluded: chain z residue 4 ILE Chi-restraints excluded: chain z residue 31 ILE Chi-restraints excluded: chain z residue 40 THR Chi-restraints excluded: chain z residue 50 VAL Chi-restraints excluded: chain z residue 56 VAL Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 24 ILE Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 44 PHE Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 19 ASP Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 29 GLN Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain G residue 15 PHE Chi-restraints excluded: chain G residue 29 PHE Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 162 VAL Chi-restraints excluded: chain G residue 170 ILE Chi-restraints excluded: chain G residue 196 ASP Chi-restraints excluded: chain G residue 204 ASP Chi-restraints excluded: chain G residue 209 VAL Chi-restraints excluded: chain H residue 82 ASP Chi-restraints excluded: chain H residue 84 GLU Chi-restraints excluded: chain H residue 109 GLU Chi-restraints excluded: chain H residue 133 MET Chi-restraints excluded: chain H residue 156 LEU Chi-restraints excluded: chain H residue 167 TYR Chi-restraints excluded: chain H residue 206 ILE Chi-restraints excluded: chain I residue 29 THR Chi-restraints excluded: chain I residue 49 ASP Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 159 GLU Chi-restraints excluded: chain I residue 180 THR Chi-restraints excluded: chain J residue 72 ASN Chi-restraints excluded: chain J residue 79 THR Chi-restraints excluded: chain J residue 104 ILE Chi-restraints excluded: chain J residue 116 VAL Chi-restraints excluded: chain J residue 133 ILE Chi-restraints excluded: chain J residue 162 GLU Chi-restraints excluded: chain K residue 6 ILE Chi-restraints excluded: chain K residue 11 HIS Chi-restraints excluded: chain K residue 26 THR Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 45 ARG Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 55 HIS Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain K residue 93 LYS Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain L residue 5 VAL Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 26 VAL Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 84 TYR Chi-restraints excluded: chain L residue 96 ASN Chi-restraints excluded: chain L residue 121 ASN Chi-restraints excluded: chain L residue 132 THR Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 140 VAL Chi-restraints excluded: chain M residue 25 THR Chi-restraints excluded: chain M residue 35 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 103 VAL Chi-restraints excluded: chain M residue 125 ILE Chi-restraints excluded: chain N residue 20 ILE Chi-restraints excluded: chain N residue 28 VAL Chi-restraints excluded: chain N residue 38 PHE Chi-restraints excluded: chain N residue 42 THR Chi-restraints excluded: chain N residue 46 VAL Chi-restraints excluded: chain N residue 57 VAL Chi-restraints excluded: chain N residue 109 GLN Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain O residue 19 ASP Chi-restraints excluded: chain O residue 51 VAL Chi-restraints excluded: chain P residue 34 THR Chi-restraints excluded: chain P residue 45 THR Chi-restraints excluded: chain P residue 64 VAL Chi-restraints excluded: chain P residue 93 GLU Chi-restraints excluded: chain P residue 94 SER Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain P residue 110 THR Chi-restraints excluded: chain P residue 112 VAL Chi-restraints excluded: chain Q residue 7 VAL Chi-restraints excluded: chain Q residue 39 THR Chi-restraints excluded: chain Q residue 62 VAL Chi-restraints excluded: chain Q residue 80 LEU Chi-restraints excluded: chain Q residue 89 LEU Chi-restraints excluded: chain R residue 6 ILE Chi-restraints excluded: chain R residue 7 ASN Chi-restraints excluded: chain R residue 8 ILE Chi-restraints excluded: chain R residue 41 ASP Chi-restraints excluded: chain R residue 49 GLU Chi-restraints excluded: chain R residue 64 VAL Chi-restraints excluded: chain R residue 67 ASP Chi-restraints excluded: chain R residue 71 GLU Chi-restraints excluded: chain R residue 82 LEU Chi-restraints excluded: chain R residue 84 CYS Chi-restraints excluded: chain S residue 4 SER Chi-restraints excluded: chain S residue 5 MET Chi-restraints excluded: chain S residue 13 VAL Chi-restraints excluded: chain S residue 25 GLU Chi-restraints excluded: chain S residue 55 SER Chi-restraints excluded: chain S residue 63 CYS Chi-restraints excluded: chain S residue 73 LEU Chi-restraints excluded: chain S residue 99 SER Chi-restraints excluded: chain T residue 26 VAL Chi-restraints excluded: chain T residue 44 GLU Chi-restraints excluded: chain T residue 70 LYS Chi-restraints excluded: chain T residue 88 ARG Chi-restraints excluded: chain U residue 36 VAL Chi-restraints excluded: chain U residue 50 THR Chi-restraints excluded: chain U residue 57 ILE Chi-restraints excluded: chain U residue 78 VAL Chi-restraints excluded: chain V residue 18 LYS Chi-restraints excluded: chain V residue 28 VAL Chi-restraints excluded: chain V residue 52 CYS Chi-restraints excluded: chain V residue 73 THR Chi-restraints excluded: chain W residue 13 THR Chi-restraints excluded: chain W residue 43 ILE Chi-restraints excluded: chain W residue 54 LEU Chi-restraints excluded: chain X residue 24 SER Chi-restraints excluded: chain X residue 30 LEU Chi-restraints excluded: chain X residue 43 MET Chi-restraints excluded: chain X residue 48 ILE Chi-restraints excluded: chain X residue 50 VAL Chi-restraints excluded: chain X residue 59 VAL Chi-restraints excluded: chain X residue 65 MET Chi-restraints excluded: chain X residue 70 LEU Chi-restraints excluded: chain X residue 78 THR Chi-restraints excluded: chain Y residue 20 ASN Chi-restraints excluded: chain Y residue 26 MET Chi-restraints excluded: chain Y residue 58 ASP Chi-restraints excluded: chain Y residue 85 LEU Chi-restraints excluded: chain Z residue 12 ASP Chi-restraints excluded: chain Z residue 15 LEU Chi-restraints excluded: chain Z residue 18 PHE Chi-restraints excluded: chain Z residue 36 PHE Chi-restraints excluded: chain Z residue 42 THR Chi-restraints excluded: chain a residue 39 VAL Chi-restraints excluded: chain a residue 171 ILE Chi-restraints excluded: chain a residue 174 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1048 random chunks: chunk 918 optimal weight: 10.0000 chunk 967 optimal weight: 10.0000 chunk 882 optimal weight: 20.0000 chunk 941 optimal weight: 50.0000 chunk 566 optimal weight: 40.0000 chunk 410 optimal weight: 20.0000 chunk 739 optimal weight: 20.0000 chunk 288 optimal weight: 5.9990 chunk 850 optimal weight: 10.0000 chunk 890 optimal weight: 10.0000 chunk 938 optimal weight: 50.0000 overall best weight: 9.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 17 ASN ** m 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 58 GLN ** q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 59 ASN ** u 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 25 GLN ** A 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 37 ASN N 36 GLN N 74 GLN ** P 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.3392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.111 162697 Z= 0.366 Angle : 0.687 12.470 243503 Z= 0.354 Chirality : 0.040 0.312 31146 Planarity : 0.005 0.062 12986 Dihedral : 23.548 178.766 81735 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 16.40 Ramachandran Plot: Outliers : 0.12 % Allowed : 12.17 % Favored : 87.71 % Rotamer: Outliers : 6.62 % Allowed : 21.43 % Favored : 71.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.24 (0.11), residues: 5836 helix: -0.07 (0.12), residues: 1905 sheet: -1.91 (0.16), residues: 1017 loop : -2.35 (0.11), residues: 2914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP G 103 HIS 0.010 0.001 HIS T 37 PHE 0.045 0.002 PHE Z 36 TYR 0.023 0.002 TYR H 41 ARG 0.009 0.001 ARG K 24 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11672 Ramachandran restraints generated. 5836 Oldfield, 0 Emsley, 5836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11672 Ramachandran restraints generated. 5836 Oldfield, 0 Emsley, 5836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1359 residues out of total 4862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 322 poor density : 1037 time to evaluate : 6.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 51 ARG cc_start: 0.8587 (OUTLIER) cc_final: 0.7727 (ptm-80) REVERT: c 174 SER cc_start: 0.9247 (m) cc_final: 0.8795 (p) REVERT: e 82 TYR cc_start: 0.7920 (t80) cc_final: 0.7366 (t80) REVERT: e 89 THR cc_start: 0.8827 (OUTLIER) cc_final: 0.8536 (p) REVERT: e 134 GLN cc_start: 0.7805 (OUTLIER) cc_final: 0.7572 (pm20) REVERT: e 143 ASP cc_start: 0.6965 (m-30) cc_final: 0.6565 (m-30) REVERT: f 41 GLU cc_start: 0.8796 (mt-10) cc_final: 0.8371 (pp20) REVERT: f 142 GLN cc_start: 0.8348 (tp40) cc_final: 0.7973 (tp40) REVERT: f 169 ARG cc_start: 0.7859 (mmm-85) cc_final: 0.7425 (mmm160) REVERT: g 7 ASP cc_start: 0.8485 (t70) cc_final: 0.8195 (t70) REVERT: h 9 GLN cc_start: 0.4990 (OUTLIER) cc_final: 0.4351 (mm-40) REVERT: k 20 MET cc_start: 0.8151 (ttt) cc_final: 0.7613 (ttt) REVERT: l 29 LYS cc_start: 0.9028 (OUTLIER) cc_final: 0.8438 (tmtt) REVERT: m 6 ARG cc_start: 0.6859 (tpt90) cc_final: 0.6533 (tpt90) REVERT: n 112 TYR cc_start: 0.8314 (m-80) cc_final: 0.8074 (m-80) REVERT: o 80 GLU cc_start: 0.9259 (mm-30) cc_final: 0.8910 (pp20) REVERT: r 6 GLN cc_start: 0.8665 (pp30) cc_final: 0.8244 (pp30) REVERT: r 11 GLN cc_start: 0.8536 (mm-40) cc_final: 0.8218 (mt0) REVERT: r 18 GLN cc_start: 0.8671 (tm-30) cc_final: 0.8278 (tm-30) REVERT: r 32 THR cc_start: 0.9031 (m) cc_final: 0.8782 (p) REVERT: s 11 ARG cc_start: 0.8388 (OUTLIER) cc_final: 0.7202 (mmm160) REVERT: s 95 ARG cc_start: 0.7977 (tmm-80) cc_final: 0.7682 (tmm-80) REVERT: t 69 ARG cc_start: 0.7389 (ttp80) cc_final: 0.6688 (ttp80) REVERT: u 86 PHE cc_start: 0.7900 (OUTLIER) cc_final: 0.7609 (m-10) REVERT: v 8 VAL cc_start: 0.8967 (t) cc_final: 0.8762 (p) REVERT: v 63 ILE cc_start: 0.9173 (mt) cc_final: 0.8899 (tp) REVERT: w 54 THR cc_start: 0.8875 (OUTLIER) cc_final: 0.8511 (t) REVERT: w 66 GLU cc_start: 0.7290 (tm-30) cc_final: 0.7049 (tm-30) REVERT: y 8 GLU cc_start: 0.8069 (mp0) cc_final: 0.7398 (mp0) REVERT: C 38 PHE cc_start: 0.7564 (t80) cc_final: 0.7209 (t80) REVERT: C 50 GLU cc_start: 0.6933 (OUTLIER) cc_final: 0.6707 (pm20) REVERT: G 161 PHE cc_start: 0.7559 (t80) cc_final: 0.7292 (t80) REVERT: H 109 GLU cc_start: 0.8968 (OUTLIER) cc_final: 0.8691 (pm20) REVERT: H 111 ASP cc_start: 0.8709 (t0) cc_final: 0.8489 (t0) REVERT: H 167 TYR cc_start: 0.7019 (OUTLIER) cc_final: 0.6128 (t80) REVERT: I 140 ASP cc_start: 0.8112 (m-30) cc_final: 0.7483 (m-30) REVERT: J 11 GLN cc_start: 0.8261 (tt0) cc_final: 0.7909 (tt0) REVERT: J 123 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.8301 (mt) REVERT: K 11 HIS cc_start: 0.7875 (OUTLIER) cc_final: 0.7055 (m-70) REVERT: K 45 ARG cc_start: 0.8352 (OUTLIER) cc_final: 0.7558 (ttp-110) REVERT: M 25 THR cc_start: 0.8168 (OUTLIER) cc_final: 0.7916 (p) REVERT: M 113 ARG cc_start: 0.8958 (ttp80) cc_final: 0.8389 (ttm-80) REVERT: N 45 MET cc_start: 0.8087 (pmm) cc_final: 0.7845 (pmm) REVERT: N 52 GLU cc_start: 0.9035 (tp30) cc_final: 0.8616 (tp30) REVERT: N 53 LEU cc_start: 0.8946 (mp) cc_final: 0.8513 (tt) REVERT: N 96 GLU cc_start: 0.8703 (pt0) cc_final: 0.7991 (mp0) REVERT: N 106 ASP cc_start: 0.8115 (t70) cc_final: 0.7739 (t0) REVERT: N 109 GLN cc_start: 0.7942 (OUTLIER) cc_final: 0.7534 (tm-30) REVERT: N 111 GLU cc_start: 0.8657 (mt-10) cc_final: 0.8451 (mt-10) REVERT: O 42 LEU cc_start: 0.9108 (mm) cc_final: 0.8897 (mp) REVERT: P 71 ASP cc_start: 0.8241 (p0) cc_final: 0.8002 (p0) REVERT: R 102 LYS cc_start: 0.8463 (tttt) cc_final: 0.8171 (mttt) REVERT: S 4 SER cc_start: 0.8272 (OUTLIER) cc_final: 0.7940 (m) REVERT: S 25 GLU cc_start: 0.7791 (OUTLIER) cc_final: 0.7385 (pm20) REVERT: S 88 MET cc_start: 0.8768 (mmt) cc_final: 0.8473 (mmt) REVERT: T 5 GLU cc_start: 0.8116 (mm-30) cc_final: 0.7843 (mm-30) REVERT: T 14 PHE cc_start: 0.8060 (m-80) cc_final: 0.7678 (m-80) REVERT: T 70 LYS cc_start: 0.9322 (OUTLIER) cc_final: 0.8573 (ttpp) REVERT: U 35 ARG cc_start: 0.8359 (ppt170) cc_final: 0.8071 (ptt90) REVERT: V 56 ASP cc_start: 0.7035 (p0) cc_final: 0.6713 (p0) REVERT: W 17 VAL cc_start: 0.7497 (OUTLIER) cc_final: 0.7253 (m) REVERT: X 10 ILE cc_start: 0.7976 (OUTLIER) cc_final: 0.7747 (tp) REVERT: X 16 LYS cc_start: 0.8549 (mtpt) cc_final: 0.8212 (mmtt) REVERT: X 42 ASN cc_start: 0.8310 (p0) cc_final: 0.8012 (p0) REVERT: X 72 GLU cc_start: 0.8200 (mp0) cc_final: 0.7616 (mp0) REVERT: Y 20 ASN cc_start: 0.9124 (OUTLIER) cc_final: 0.8708 (t0) REVERT: Y 26 MET cc_start: 0.8950 (OUTLIER) cc_final: 0.8469 (ttp) REVERT: Y 85 LEU cc_start: 0.6244 (OUTLIER) cc_final: 0.5757 (pp) outliers start: 322 outliers final: 271 residues processed: 1212 average time/residue: 1.2630 time to fit residues: 2754.2610 Evaluate side-chains 1319 residues out of total 4862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 295 poor density : 1024 time to evaluate : 6.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 39 SER Chi-restraints excluded: chain b residue 51 ARG Chi-restraints excluded: chain b residue 76 VAL Chi-restraints excluded: chain b residue 183 VAL Chi-restraints excluded: chain b residue 228 ASP Chi-restraints excluded: chain b residue 258 SER Chi-restraints excluded: chain b residue 267 VAL Chi-restraints excluded: chain b residue 270 ARG Chi-restraints excluded: chain c residue 2 ILE Chi-restraints excluded: chain c residue 9 VAL Chi-restraints excluded: chain c residue 29 VAL Chi-restraints excluded: chain c residue 60 VAL Chi-restraints excluded: chain c residue 95 SER Chi-restraints excluded: chain c residue 131 ASP Chi-restraints excluded: chain c residue 139 SER Chi-restraints excluded: chain c residue 145 SER Chi-restraints excluded: chain c residue 161 MET Chi-restraints excluded: chain c residue 172 VAL Chi-restraints excluded: chain c residue 176 ASP Chi-restraints excluded: chain c residue 177 VAL Chi-restraints excluded: chain c residue 180 VAL Chi-restraints excluded: chain c residue 199 SER Chi-restraints excluded: chain c residue 200 ASP Chi-restraints excluded: chain d residue 14 VAL Chi-restraints excluded: chain d residue 22 ASP Chi-restraints excluded: chain d residue 65 THR Chi-restraints excluded: chain d residue 77 ILE Chi-restraints excluded: chain d residue 97 ASN Chi-restraints excluded: chain d residue 120 VAL Chi-restraints excluded: chain d residue 150 THR Chi-restraints excluded: chain e residue 3 LEU Chi-restraints excluded: chain e residue 30 VAL Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 39 VAL Chi-restraints excluded: chain e residue 43 ILE Chi-restraints excluded: chain e residue 56 LEU Chi-restraints excluded: chain e residue 66 ILE Chi-restraints excluded: chain e residue 86 CYS Chi-restraints excluded: chain e residue 89 THR Chi-restraints excluded: chain e residue 112 ASP Chi-restraints excluded: chain e residue 134 GLN Chi-restraints excluded: chain e residue 136 ILE Chi-restraints excluded: chain f residue 38 ASP Chi-restraints excluded: chain f residue 85 LYS Chi-restraints excluded: chain f residue 91 VAL Chi-restraints excluded: chain f residue 112 VAL Chi-restraints excluded: chain f residue 113 ASP Chi-restraints excluded: chain f residue 129 GLU Chi-restraints excluded: chain f residue 130 ILE Chi-restraints excluded: chain g residue 17 ASP Chi-restraints excluded: chain g residue 20 ASN Chi-restraints excluded: chain g residue 35 LYS Chi-restraints excluded: chain g residue 130 VAL Chi-restraints excluded: chain h residue 9 GLN Chi-restraints excluded: chain h residue 77 VAL Chi-restraints excluded: chain i residue 23 VAL Chi-restraints excluded: chain j residue 14 ASP Chi-restraints excluded: chain j residue 30 THR Chi-restraints excluded: chain j residue 60 ASP Chi-restraints excluded: chain j residue 62 VAL Chi-restraints excluded: chain j residue 101 ILE Chi-restraints excluded: chain j residue 131 ASN Chi-restraints excluded: chain k residue 6 THR Chi-restraints excluded: chain k residue 10 VAL Chi-restraints excluded: chain k residue 24 VAL Chi-restraints excluded: chain k residue 56 ASP Chi-restraints excluded: chain k residue 73 ASP Chi-restraints excluded: chain k residue 89 ASN Chi-restraints excluded: chain k residue 97 THR Chi-restraints excluded: chain l residue 29 LYS Chi-restraints excluded: chain l residue 76 GLU Chi-restraints excluded: chain l residue 117 THR Chi-restraints excluded: chain l residue 118 THR Chi-restraints excluded: chain l residue 142 ILE Chi-restraints excluded: chain l residue 143 GLU Chi-restraints excluded: chain m residue 2 LEU Chi-restraints excluded: chain m residue 42 THR Chi-restraints excluded: chain m residue 67 VAL Chi-restraints excluded: chain m residue 70 ASP Chi-restraints excluded: chain m residue 74 THR Chi-restraints excluded: chain m residue 89 VAL Chi-restraints excluded: chain m residue 127 LYS Chi-restraints excluded: chain n residue 6 SER Chi-restraints excluded: chain n residue 24 MET Chi-restraints excluded: chain n residue 29 VAL Chi-restraints excluded: chain n residue 34 ILE Chi-restraints excluded: chain n residue 76 VAL Chi-restraints excluded: chain n residue 106 ASP Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain o residue 31 THR Chi-restraints excluded: chain o residue 58 ILE Chi-restraints excluded: chain o residue 65 THR Chi-restraints excluded: chain o residue 83 LEU Chi-restraints excluded: chain o residue 91 SER Chi-restraints excluded: chain o residue 93 ASP Chi-restraints excluded: chain o residue 95 SER Chi-restraints excluded: chain p residue 8 GLU Chi-restraints excluded: chain p residue 18 SER Chi-restraints excluded: chain p residue 59 THR Chi-restraints excluded: chain p residue 60 VAL Chi-restraints excluded: chain q residue 7 VAL Chi-restraints excluded: chain r residue 19 THR Chi-restraints excluded: chain r residue 29 THR Chi-restraints excluded: chain r residue 46 GLU Chi-restraints excluded: chain r residue 54 VAL Chi-restraints excluded: chain r residue 60 LYS Chi-restraints excluded: chain s residue 11 ARG Chi-restraints excluded: chain s residue 67 ASP Chi-restraints excluded: chain s residue 74 ILE Chi-restraints excluded: chain s residue 103 ILE Chi-restraints excluded: chain t residue 5 GLU Chi-restraints excluded: chain t residue 27 SER Chi-restraints excluded: chain t residue 52 GLU Chi-restraints excluded: chain t residue 79 ASP Chi-restraints excluded: chain t residue 87 LEU Chi-restraints excluded: chain u residue 14 THR Chi-restraints excluded: chain u residue 27 VAL Chi-restraints excluded: chain u residue 40 LEU Chi-restraints excluded: chain u residue 67 SER Chi-restraints excluded: chain u residue 82 VAL Chi-restraints excluded: chain u residue 86 PHE Chi-restraints excluded: chain v residue 30 ILE Chi-restraints excluded: chain v residue 62 THR Chi-restraints excluded: chain v residue 64 VAL Chi-restraints excluded: chain v residue 65 VAL Chi-restraints excluded: chain v residue 76 ASP Chi-restraints excluded: chain v residue 90 ASP Chi-restraints excluded: chain w residue 28 LEU Chi-restraints excluded: chain w residue 34 VAL Chi-restraints excluded: chain w residue 54 THR Chi-restraints excluded: chain w residue 60 ASP Chi-restraints excluded: chain w residue 72 ASN Chi-restraints excluded: chain w residue 77 SER Chi-restraints excluded: chain x residue 12 VAL Chi-restraints excluded: chain x residue 24 THR Chi-restraints excluded: chain x residue 39 VAL Chi-restraints excluded: chain x residue 47 THR Chi-restraints excluded: chain x residue 65 THR Chi-restraints excluded: chain y residue 5 GLU Chi-restraints excluded: chain z residue 4 ILE Chi-restraints excluded: chain z residue 31 ILE Chi-restraints excluded: chain z residue 50 VAL Chi-restraints excluded: chain z residue 56 VAL Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 24 ILE Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 44 PHE Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 19 ASP Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 50 GLU Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 29 GLN Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain G residue 14 HIS Chi-restraints excluded: chain G residue 29 PHE Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 106 VAL Chi-restraints excluded: chain G residue 162 VAL Chi-restraints excluded: chain G residue 170 ILE Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 196 ASP Chi-restraints excluded: chain G residue 204 ASP Chi-restraints excluded: chain G residue 209 VAL Chi-restraints excluded: chain H residue 82 ASP Chi-restraints excluded: chain H residue 84 GLU Chi-restraints excluded: chain H residue 109 GLU Chi-restraints excluded: chain H residue 133 MET Chi-restraints excluded: chain H residue 156 LEU Chi-restraints excluded: chain H residue 167 TYR Chi-restraints excluded: chain I residue 29 THR Chi-restraints excluded: chain I residue 49 ASP Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 123 MET Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 159 GLU Chi-restraints excluded: chain I residue 180 THR Chi-restraints excluded: chain J residue 72 ASN Chi-restraints excluded: chain J residue 79 THR Chi-restraints excluded: chain J residue 104 ILE Chi-restraints excluded: chain J residue 116 VAL Chi-restraints excluded: chain J residue 123 LEU Chi-restraints excluded: chain J residue 133 ILE Chi-restraints excluded: chain J residue 162 GLU Chi-restraints excluded: chain K residue 6 ILE Chi-restraints excluded: chain K residue 11 HIS Chi-restraints excluded: chain K residue 22 ILE Chi-restraints excluded: chain K residue 26 THR Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 45 ARG Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 55 HIS Chi-restraints excluded: chain K residue 73 GLU Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain K residue 93 LYS Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain L residue 5 VAL Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 26 VAL Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 84 TYR Chi-restraints excluded: chain L residue 96 ASN Chi-restraints excluded: chain L residue 121 ASN Chi-restraints excluded: chain L residue 132 THR Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 140 VAL Chi-restraints excluded: chain M residue 25 THR Chi-restraints excluded: chain M residue 35 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 103 VAL Chi-restraints excluded: chain N residue 20 ILE Chi-restraints excluded: chain N residue 28 VAL Chi-restraints excluded: chain N residue 36 GLN Chi-restraints excluded: chain N residue 38 PHE Chi-restraints excluded: chain N residue 42 THR Chi-restraints excluded: chain N residue 46 VAL Chi-restraints excluded: chain N residue 57 VAL Chi-restraints excluded: chain N residue 109 GLN Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain O residue 19 ASP Chi-restraints excluded: chain O residue 51 VAL Chi-restraints excluded: chain P residue 34 THR Chi-restraints excluded: chain P residue 45 THR Chi-restraints excluded: chain P residue 64 VAL Chi-restraints excluded: chain P residue 93 GLU Chi-restraints excluded: chain P residue 94 SER Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain P residue 110 THR Chi-restraints excluded: chain P residue 112 VAL Chi-restraints excluded: chain Q residue 7 VAL Chi-restraints excluded: chain Q residue 39 THR Chi-restraints excluded: chain Q residue 62 VAL Chi-restraints excluded: chain Q residue 80 LEU Chi-restraints excluded: chain Q residue 89 LEU Chi-restraints excluded: chain R residue 6 ILE Chi-restraints excluded: chain R residue 7 ASN Chi-restraints excluded: chain R residue 8 ILE Chi-restraints excluded: chain R residue 41 ASP Chi-restraints excluded: chain R residue 49 GLU Chi-restraints excluded: chain R residue 64 VAL Chi-restraints excluded: chain R residue 67 ASP Chi-restraints excluded: chain R residue 71 GLU Chi-restraints excluded: chain R residue 82 LEU Chi-restraints excluded: chain S residue 4 SER Chi-restraints excluded: chain S residue 5 MET Chi-restraints excluded: chain S residue 13 VAL Chi-restraints excluded: chain S residue 25 GLU Chi-restraints excluded: chain S residue 55 SER Chi-restraints excluded: chain S residue 63 CYS Chi-restraints excluded: chain S residue 73 LEU Chi-restraints excluded: chain S residue 99 SER Chi-restraints excluded: chain T residue 26 VAL Chi-restraints excluded: chain T residue 44 GLU Chi-restraints excluded: chain T residue 70 LYS Chi-restraints excluded: chain T residue 88 ARG Chi-restraints excluded: chain U residue 36 VAL Chi-restraints excluded: chain U residue 50 THR Chi-restraints excluded: chain U residue 78 VAL Chi-restraints excluded: chain V residue 18 LYS Chi-restraints excluded: chain V residue 28 VAL Chi-restraints excluded: chain V residue 52 CYS Chi-restraints excluded: chain V residue 73 THR Chi-restraints excluded: chain W residue 13 THR Chi-restraints excluded: chain W residue 17 VAL Chi-restraints excluded: chain W residue 23 LYS Chi-restraints excluded: chain W residue 43 ILE Chi-restraints excluded: chain W residue 54 LEU Chi-restraints excluded: chain X residue 10 ILE Chi-restraints excluded: chain X residue 24 SER Chi-restraints excluded: chain X residue 30 LEU Chi-restraints excluded: chain X residue 43 MET Chi-restraints excluded: chain X residue 48 ILE Chi-restraints excluded: chain X residue 50 VAL Chi-restraints excluded: chain X residue 59 VAL Chi-restraints excluded: chain X residue 65 MET Chi-restraints excluded: chain X residue 70 LEU Chi-restraints excluded: chain X residue 78 THR Chi-restraints excluded: chain Y residue 20 ASN Chi-restraints excluded: chain Y residue 26 MET Chi-restraints excluded: chain Y residue 58 ASP Chi-restraints excluded: chain Y residue 85 LEU Chi-restraints excluded: chain Z residue 12 ASP Chi-restraints excluded: chain Z residue 15 LEU Chi-restraints excluded: chain Z residue 18 PHE Chi-restraints excluded: chain Z residue 36 PHE Chi-restraints excluded: chain Z residue 42 THR Chi-restraints excluded: chain a residue 39 VAL Chi-restraints excluded: chain a residue 171 ILE Chi-restraints excluded: chain a residue 174 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1048 random chunks: chunk 618 optimal weight: 40.0000 chunk 995 optimal weight: 10.0000 chunk 607 optimal weight: 20.0000 chunk 472 optimal weight: 7.9990 chunk 691 optimal weight: 20.0000 chunk 1044 optimal weight: 30.0000 chunk 960 optimal weight: 10.0000 chunk 831 optimal weight: 50.0000 chunk 86 optimal weight: 8.9990 chunk 642 optimal weight: 10.0000 chunk 509 optimal weight: 20.0000 overall best weight: 9.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 17 ASN ** m 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 59 ASN u 73 ASN v 5 ASN y 25 GLN ** G 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 36 GLN ** P 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.3483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.112 162697 Z= 0.370 Angle : 0.694 13.225 243503 Z= 0.358 Chirality : 0.040 0.362 31146 Planarity : 0.005 0.063 12986 Dihedral : 23.589 178.688 81735 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 16.69 Ramachandran Plot: Outliers : 0.12 % Allowed : 12.15 % Favored : 87.73 % Rotamer: Outliers : 6.31 % Allowed : 22.01 % Favored : 71.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.27 (0.11), residues: 5836 helix: -0.09 (0.12), residues: 1903 sheet: -1.92 (0.16), residues: 1009 loop : -2.35 (0.11), residues: 2924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP G 103 HIS 0.011 0.001 HIS T 37 PHE 0.050 0.002 PHE A 64 TYR 0.062 0.002 TYR Z 37 ARG 0.013 0.001 ARG K 24 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11672 Ramachandran restraints generated. 5836 Oldfield, 0 Emsley, 5836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11672 Ramachandran restraints generated. 5836 Oldfield, 0 Emsley, 5836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1350 residues out of total 4862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 307 poor density : 1043 time to evaluate : 6.748 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 51 ARG cc_start: 0.8584 (OUTLIER) cc_final: 0.7722 (ptm-80) REVERT: c 174 SER cc_start: 0.9181 (m) cc_final: 0.8578 (t) REVERT: d 188 MET cc_start: 0.6950 (tpt) cc_final: 0.6480 (tpt) REVERT: e 82 TYR cc_start: 0.7885 (t80) cc_final: 0.7340 (t80) REVERT: e 89 THR cc_start: 0.8847 (OUTLIER) cc_final: 0.8548 (p) REVERT: e 134 GLN cc_start: 0.7809 (OUTLIER) cc_final: 0.7581 (pm20) REVERT: e 143 ASP cc_start: 0.6977 (m-30) cc_final: 0.6581 (m-30) REVERT: f 34 ARG cc_start: 0.8506 (tpp80) cc_final: 0.8206 (tpt-90) REVERT: f 41 GLU cc_start: 0.8797 (mt-10) cc_final: 0.8455 (pp20) REVERT: f 142 GLN cc_start: 0.8349 (tp40) cc_final: 0.7975 (tp40) REVERT: f 169 ARG cc_start: 0.7845 (mmm-85) cc_final: 0.7416 (mmm160) REVERT: h 9 GLN cc_start: 0.4998 (OUTLIER) cc_final: 0.4347 (mm-40) REVERT: k 20 MET cc_start: 0.8145 (OUTLIER) cc_final: 0.7541 (ttt) REVERT: l 29 LYS cc_start: 0.9030 (OUTLIER) cc_final: 0.8477 (tmtt) REVERT: o 36 TYR cc_start: 0.7825 (OUTLIER) cc_final: 0.7595 (m-80) REVERT: o 97 PHE cc_start: 0.8570 (m-80) cc_final: 0.8319 (m-80) REVERT: r 6 GLN cc_start: 0.8642 (pp30) cc_final: 0.8200 (pp30) REVERT: r 11 GLN cc_start: 0.8585 (mm-40) cc_final: 0.8265 (mt0) REVERT: r 18 GLN cc_start: 0.8788 (tm-30) cc_final: 0.8259 (tm-30) REVERT: r 31 GLU cc_start: 0.8646 (tp30) cc_final: 0.8274 (tm-30) REVERT: s 95 ARG cc_start: 0.7981 (tmm-80) cc_final: 0.7687 (tmm-80) REVERT: t 69 ARG cc_start: 0.7359 (ttp80) cc_final: 0.6682 (ttp80) REVERT: u 86 PHE cc_start: 0.7894 (OUTLIER) cc_final: 0.7622 (m-10) REVERT: v 8 VAL cc_start: 0.8964 (t) cc_final: 0.8759 (p) REVERT: v 70 ILE cc_start: 0.9094 (mm) cc_final: 0.8892 (mm) REVERT: w 54 THR cc_start: 0.8878 (OUTLIER) cc_final: 0.8518 (t) REVERT: y 8 GLU cc_start: 0.8029 (mp0) cc_final: 0.7619 (mt-10) REVERT: z 20 LYS cc_start: 0.8615 (mtpt) cc_final: 0.8334 (mttp) REVERT: C 38 PHE cc_start: 0.7376 (t80) cc_final: 0.6689 (t80) REVERT: F 30 GLU cc_start: 0.8732 (tp30) cc_final: 0.8366 (tm-30) REVERT: G 161 PHE cc_start: 0.7561 (t80) cc_final: 0.7300 (t80) REVERT: H 109 GLU cc_start: 0.8963 (OUTLIER) cc_final: 0.8697 (pm20) REVERT: H 111 ASP cc_start: 0.8692 (t0) cc_final: 0.8475 (t0) REVERT: H 167 TYR cc_start: 0.7056 (OUTLIER) cc_final: 0.6166 (t80) REVERT: I 140 ASP cc_start: 0.8140 (m-30) cc_final: 0.7491 (m-30) REVERT: J 11 GLN cc_start: 0.8255 (tt0) cc_final: 0.7903 (tt0) REVERT: J 123 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8336 (mt) REVERT: K 11 HIS cc_start: 0.7882 (OUTLIER) cc_final: 0.7043 (m-70) REVERT: K 45 ARG cc_start: 0.8382 (OUTLIER) cc_final: 0.7595 (ttp-110) REVERT: M 4 ASP cc_start: 0.7986 (t0) cc_final: 0.7625 (t0) REVERT: M 25 THR cc_start: 0.8115 (OUTLIER) cc_final: 0.7712 (p) REVERT: M 57 GLU cc_start: 0.8798 (mm-30) cc_final: 0.8075 (tp30) REVERT: M 113 ARG cc_start: 0.8950 (ttp80) cc_final: 0.8390 (ttm-80) REVERT: N 52 GLU cc_start: 0.9084 (tp30) cc_final: 0.8847 (tp30) REVERT: N 106 ASP cc_start: 0.8116 (t70) cc_final: 0.7742 (t0) REVERT: N 109 GLN cc_start: 0.7936 (OUTLIER) cc_final: 0.7533 (tm-30) REVERT: O 51 VAL cc_start: 0.8814 (OUTLIER) cc_final: 0.8604 (p) REVERT: P 71 ASP cc_start: 0.8271 (p0) cc_final: 0.8036 (p0) REVERT: Q 2 THR cc_start: 0.8556 (m) cc_final: 0.7803 (p) REVERT: R 102 LYS cc_start: 0.8460 (tttt) cc_final: 0.8167 (mttt) REVERT: S 4 SER cc_start: 0.8260 (OUTLIER) cc_final: 0.7929 (m) REVERT: T 70 LYS cc_start: 0.9319 (OUTLIER) cc_final: 0.8570 (ttpp) REVERT: U 35 ARG cc_start: 0.8360 (ppt170) cc_final: 0.8078 (ptt90) REVERT: V 56 ASP cc_start: 0.7036 (p0) cc_final: 0.6707 (p0) REVERT: X 10 ILE cc_start: 0.8004 (OUTLIER) cc_final: 0.7794 (tp) REVERT: X 16 LYS cc_start: 0.8592 (mtpt) cc_final: 0.8256 (mmtt) REVERT: X 42 ASN cc_start: 0.8291 (p0) cc_final: 0.7988 (p0) REVERT: X 54 ARG cc_start: 0.8502 (ptt-90) cc_final: 0.7337 (ptt90) REVERT: X 72 GLU cc_start: 0.8198 (mp0) cc_final: 0.7609 (mp0) REVERT: Y 12 GLN cc_start: 0.8690 (mt0) cc_final: 0.8249 (mt0) REVERT: Y 20 ASN cc_start: 0.9127 (OUTLIER) cc_final: 0.8756 (t0) REVERT: Y 26 MET cc_start: 0.8936 (OUTLIER) cc_final: 0.8428 (ttp) REVERT: Y 85 LEU cc_start: 0.6297 (OUTLIER) cc_final: 0.5728 (pp) outliers start: 307 outliers final: 269 residues processed: 1208 average time/residue: 1.3131 time to fit residues: 2864.2011 Evaluate side-chains 1307 residues out of total 4862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 292 poor density : 1015 time to evaluate : 6.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 39 SER Chi-restraints excluded: chain b residue 51 ARG Chi-restraints excluded: chain b residue 76 VAL Chi-restraints excluded: chain b residue 183 VAL Chi-restraints excluded: chain b residue 228 ASP Chi-restraints excluded: chain b residue 258 SER Chi-restraints excluded: chain b residue 267 VAL Chi-restraints excluded: chain b residue 270 ARG Chi-restraints excluded: chain c residue 2 ILE Chi-restraints excluded: chain c residue 9 VAL Chi-restraints excluded: chain c residue 29 VAL Chi-restraints excluded: chain c residue 60 VAL Chi-restraints excluded: chain c residue 95 SER Chi-restraints excluded: chain c residue 131 ASP Chi-restraints excluded: chain c residue 139 SER Chi-restraints excluded: chain c residue 145 SER Chi-restraints excluded: chain c residue 161 MET Chi-restraints excluded: chain c residue 172 VAL Chi-restraints excluded: chain c residue 176 ASP Chi-restraints excluded: chain c residue 177 VAL Chi-restraints excluded: chain c residue 180 VAL Chi-restraints excluded: chain c residue 199 SER Chi-restraints excluded: chain c residue 200 ASP Chi-restraints excluded: chain d residue 14 VAL Chi-restraints excluded: chain d residue 22 ASP Chi-restraints excluded: chain d residue 65 THR Chi-restraints excluded: chain d residue 77 ILE Chi-restraints excluded: chain d residue 97 ASN Chi-restraints excluded: chain d residue 120 VAL Chi-restraints excluded: chain d residue 150 THR Chi-restraints excluded: chain e residue 3 LEU Chi-restraints excluded: chain e residue 30 VAL Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 39 VAL Chi-restraints excluded: chain e residue 43 ILE Chi-restraints excluded: chain e residue 56 LEU Chi-restraints excluded: chain e residue 66 ILE Chi-restraints excluded: chain e residue 86 CYS Chi-restraints excluded: chain e residue 89 THR Chi-restraints excluded: chain e residue 112 ASP Chi-restraints excluded: chain e residue 134 GLN Chi-restraints excluded: chain e residue 136 ILE Chi-restraints excluded: chain f residue 38 ASP Chi-restraints excluded: chain f residue 85 LYS Chi-restraints excluded: chain f residue 91 VAL Chi-restraints excluded: chain f residue 112 VAL Chi-restraints excluded: chain f residue 113 ASP Chi-restraints excluded: chain f residue 129 GLU Chi-restraints excluded: chain f residue 130 ILE Chi-restraints excluded: chain g residue 17 ASP Chi-restraints excluded: chain g residue 20 ASN Chi-restraints excluded: chain g residue 35 LYS Chi-restraints excluded: chain g residue 130 VAL Chi-restraints excluded: chain h residue 9 GLN Chi-restraints excluded: chain h residue 77 VAL Chi-restraints excluded: chain i residue 23 VAL Chi-restraints excluded: chain j residue 14 ASP Chi-restraints excluded: chain j residue 30 THR Chi-restraints excluded: chain j residue 60 ASP Chi-restraints excluded: chain j residue 62 VAL Chi-restraints excluded: chain j residue 131 ASN Chi-restraints excluded: chain k residue 6 THR Chi-restraints excluded: chain k residue 10 VAL Chi-restraints excluded: chain k residue 20 MET Chi-restraints excluded: chain k residue 24 VAL Chi-restraints excluded: chain k residue 42 THR Chi-restraints excluded: chain k residue 56 ASP Chi-restraints excluded: chain k residue 89 ASN Chi-restraints excluded: chain k residue 97 THR Chi-restraints excluded: chain l residue 29 LYS Chi-restraints excluded: chain l residue 76 GLU Chi-restraints excluded: chain l residue 117 THR Chi-restraints excluded: chain l residue 118 THR Chi-restraints excluded: chain l residue 142 ILE Chi-restraints excluded: chain l residue 143 GLU Chi-restraints excluded: chain m residue 2 LEU Chi-restraints excluded: chain m residue 17 ASN Chi-restraints excluded: chain m residue 67 VAL Chi-restraints excluded: chain m residue 70 ASP Chi-restraints excluded: chain m residue 74 THR Chi-restraints excluded: chain m residue 89 VAL Chi-restraints excluded: chain m residue 105 MET Chi-restraints excluded: chain m residue 127 LYS Chi-restraints excluded: chain n residue 6 SER Chi-restraints excluded: chain n residue 24 MET Chi-restraints excluded: chain n residue 29 VAL Chi-restraints excluded: chain n residue 34 ILE Chi-restraints excluded: chain n residue 76 VAL Chi-restraints excluded: chain n residue 106 ASP Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain o residue 31 THR Chi-restraints excluded: chain o residue 36 TYR Chi-restraints excluded: chain o residue 58 ILE Chi-restraints excluded: chain o residue 65 THR Chi-restraints excluded: chain o residue 83 LEU Chi-restraints excluded: chain o residue 91 SER Chi-restraints excluded: chain o residue 93 ASP Chi-restraints excluded: chain o residue 95 SER Chi-restraints excluded: chain p residue 8 GLU Chi-restraints excluded: chain p residue 18 SER Chi-restraints excluded: chain p residue 59 THR Chi-restraints excluded: chain p residue 60 VAL Chi-restraints excluded: chain q residue 7 VAL Chi-restraints excluded: chain q residue 16 ILE Chi-restraints excluded: chain r residue 19 THR Chi-restraints excluded: chain r residue 29 THR Chi-restraints excluded: chain r residue 46 GLU Chi-restraints excluded: chain r residue 54 VAL Chi-restraints excluded: chain r residue 60 LYS Chi-restraints excluded: chain s residue 67 ASP Chi-restraints excluded: chain s residue 74 ILE Chi-restraints excluded: chain s residue 103 ILE Chi-restraints excluded: chain t residue 5 GLU Chi-restraints excluded: chain t residue 27 SER Chi-restraints excluded: chain t residue 52 GLU Chi-restraints excluded: chain t residue 79 ASP Chi-restraints excluded: chain t residue 87 LEU Chi-restraints excluded: chain u residue 14 THR Chi-restraints excluded: chain u residue 27 VAL Chi-restraints excluded: chain u residue 40 LEU Chi-restraints excluded: chain u residue 67 SER Chi-restraints excluded: chain u residue 73 ASN Chi-restraints excluded: chain u residue 82 VAL Chi-restraints excluded: chain u residue 86 PHE Chi-restraints excluded: chain v residue 62 THR Chi-restraints excluded: chain v residue 64 VAL Chi-restraints excluded: chain v residue 65 VAL Chi-restraints excluded: chain v residue 76 ASP Chi-restraints excluded: chain v residue 90 ASP Chi-restraints excluded: chain w residue 28 LEU Chi-restraints excluded: chain w residue 34 VAL Chi-restraints excluded: chain w residue 54 THR Chi-restraints excluded: chain w residue 60 ASP Chi-restraints excluded: chain w residue 72 ASN Chi-restraints excluded: chain x residue 12 VAL Chi-restraints excluded: chain x residue 24 THR Chi-restraints excluded: chain x residue 39 VAL Chi-restraints excluded: chain x residue 47 THR Chi-restraints excluded: chain x residue 65 THR Chi-restraints excluded: chain y residue 5 GLU Chi-restraints excluded: chain z residue 4 ILE Chi-restraints excluded: chain z residue 31 ILE Chi-restraints excluded: chain z residue 50 VAL Chi-restraints excluded: chain z residue 56 VAL Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 24 ILE Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 44 PHE Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 19 ASP Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 29 GLN Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain G residue 14 HIS Chi-restraints excluded: chain G residue 29 PHE Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 106 VAL Chi-restraints excluded: chain G residue 162 VAL Chi-restraints excluded: chain G residue 170 ILE Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 196 ASP Chi-restraints excluded: chain G residue 204 ASP Chi-restraints excluded: chain G residue 209 VAL Chi-restraints excluded: chain H residue 82 ASP Chi-restraints excluded: chain H residue 84 GLU Chi-restraints excluded: chain H residue 109 GLU Chi-restraints excluded: chain H residue 133 MET Chi-restraints excluded: chain H residue 156 LEU Chi-restraints excluded: chain H residue 167 TYR Chi-restraints excluded: chain I residue 29 THR Chi-restraints excluded: chain I residue 49 ASP Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 123 MET Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 159 GLU Chi-restraints excluded: chain I residue 180 THR Chi-restraints excluded: chain J residue 72 ASN Chi-restraints excluded: chain J residue 79 THR Chi-restraints excluded: chain J residue 104 ILE Chi-restraints excluded: chain J residue 116 VAL Chi-restraints excluded: chain J residue 123 LEU Chi-restraints excluded: chain J residue 133 ILE Chi-restraints excluded: chain J residue 162 GLU Chi-restraints excluded: chain K residue 6 ILE Chi-restraints excluded: chain K residue 11 HIS Chi-restraints excluded: chain K residue 22 ILE Chi-restraints excluded: chain K residue 26 THR Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 45 ARG Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 55 HIS Chi-restraints excluded: chain K residue 73 GLU Chi-restraints excluded: chain K residue 74 LEU Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain K residue 93 LYS Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain L residue 5 VAL Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 26 VAL Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 84 TYR Chi-restraints excluded: chain L residue 96 ASN Chi-restraints excluded: chain L residue 121 ASN Chi-restraints excluded: chain L residue 132 THR Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 140 VAL Chi-restraints excluded: chain M residue 25 THR Chi-restraints excluded: chain M residue 35 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 103 VAL Chi-restraints excluded: chain M residue 125 ILE Chi-restraints excluded: chain N residue 20 ILE Chi-restraints excluded: chain N residue 28 VAL Chi-restraints excluded: chain N residue 38 PHE Chi-restraints excluded: chain N residue 42 THR Chi-restraints excluded: chain N residue 46 VAL Chi-restraints excluded: chain N residue 57 VAL Chi-restraints excluded: chain N residue 109 GLN Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain O residue 51 VAL Chi-restraints excluded: chain P residue 34 THR Chi-restraints excluded: chain P residue 45 THR Chi-restraints excluded: chain P residue 64 VAL Chi-restraints excluded: chain P residue 93 GLU Chi-restraints excluded: chain P residue 94 SER Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain P residue 110 THR Chi-restraints excluded: chain Q residue 7 VAL Chi-restraints excluded: chain Q residue 39 THR Chi-restraints excluded: chain Q residue 62 VAL Chi-restraints excluded: chain Q residue 80 LEU Chi-restraints excluded: chain Q residue 89 LEU Chi-restraints excluded: chain R residue 6 ILE Chi-restraints excluded: chain R residue 7 ASN Chi-restraints excluded: chain R residue 8 ILE Chi-restraints excluded: chain R residue 41 ASP Chi-restraints excluded: chain R residue 49 GLU Chi-restraints excluded: chain R residue 64 VAL Chi-restraints excluded: chain R residue 67 ASP Chi-restraints excluded: chain R residue 71 GLU Chi-restraints excluded: chain R residue 82 LEU Chi-restraints excluded: chain S residue 4 SER Chi-restraints excluded: chain S residue 5 MET Chi-restraints excluded: chain S residue 13 VAL Chi-restraints excluded: chain S residue 55 SER Chi-restraints excluded: chain S residue 63 CYS Chi-restraints excluded: chain S residue 73 LEU Chi-restraints excluded: chain S residue 99 SER Chi-restraints excluded: chain T residue 26 VAL Chi-restraints excluded: chain T residue 44 GLU Chi-restraints excluded: chain T residue 58 MET Chi-restraints excluded: chain T residue 70 LYS Chi-restraints excluded: chain T residue 88 ARG Chi-restraints excluded: chain U residue 36 VAL Chi-restraints excluded: chain U residue 50 THR Chi-restraints excluded: chain U residue 78 VAL Chi-restraints excluded: chain V residue 18 LYS Chi-restraints excluded: chain V residue 28 VAL Chi-restraints excluded: chain V residue 52 CYS Chi-restraints excluded: chain V residue 73 THR Chi-restraints excluded: chain W residue 13 THR Chi-restraints excluded: chain W residue 23 LYS Chi-restraints excluded: chain W residue 43 ILE Chi-restraints excluded: chain W residue 54 LEU Chi-restraints excluded: chain X residue 10 ILE Chi-restraints excluded: chain X residue 24 SER Chi-restraints excluded: chain X residue 30 LEU Chi-restraints excluded: chain X residue 43 MET Chi-restraints excluded: chain X residue 48 ILE Chi-restraints excluded: chain X residue 50 VAL Chi-restraints excluded: chain X residue 59 VAL Chi-restraints excluded: chain X residue 65 MET Chi-restraints excluded: chain X residue 70 LEU Chi-restraints excluded: chain X residue 78 THR Chi-restraints excluded: chain Y residue 20 ASN Chi-restraints excluded: chain Y residue 26 MET Chi-restraints excluded: chain Y residue 58 ASP Chi-restraints excluded: chain Y residue 85 LEU Chi-restraints excluded: chain Z residue 12 ASP Chi-restraints excluded: chain Z residue 15 LEU Chi-restraints excluded: chain Z residue 18 PHE Chi-restraints excluded: chain Z residue 36 PHE Chi-restraints excluded: chain Z residue 42 THR Chi-restraints excluded: chain a residue 39 VAL Chi-restraints excluded: chain a residue 171 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1048 random chunks: chunk 660 optimal weight: 10.0000 chunk 885 optimal weight: 10.0000 chunk 254 optimal weight: 20.0000 chunk 766 optimal weight: 20.0000 chunk 122 optimal weight: 40.0000 chunk 231 optimal weight: 20.0000 chunk 832 optimal weight: 50.0000 chunk 348 optimal weight: 10.0000 chunk 855 optimal weight: 10.0000 chunk 105 optimal weight: 0.8980 chunk 153 optimal weight: 10.0000 overall best weight: 8.1796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 116 GLN ** c 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 17 ASN ** m 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 5 ASN y 25 GLN ** A 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.060683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.045425 restraints weight = 772599.858| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 1.94 r_work: 0.2982 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work: 0.2898 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 moved from start: 0.3531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.099 162697 Z= 0.329 Angle : 0.674 13.480 243503 Z= 0.348 Chirality : 0.039 0.360 31146 Planarity : 0.005 0.066 12986 Dihedral : 23.593 178.372 81734 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 16.32 Ramachandran Plot: Outliers : 0.14 % Allowed : 12.05 % Favored : 87.82 % Rotamer: Outliers : 6.40 % Allowed : 22.23 % Favored : 71.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.21 (0.11), residues: 5836 helix: -0.02 (0.12), residues: 1898 sheet: -1.91 (0.16), residues: 997 loop : -2.32 (0.11), residues: 2941 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP G 103 HIS 0.011 0.001 HIS T 37 PHE 0.046 0.002 PHE Z 36 TYR 0.049 0.002 TYR Z 37 ARG 0.019 0.001 ARG W 11 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 43971.59 seconds wall clock time: 766 minutes 4.56 seconds (45964.56 seconds total)