Starting phenix.real_space_refine on Tue Feb 20 21:36:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ys3_10891/02_2024/6ys3_10891.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ys3_10891/02_2024/6ys3_10891.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ys3_10891/02_2024/6ys3_10891.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ys3_10891/02_2024/6ys3_10891.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ys3_10891/02_2024/6ys3_10891.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ys3_10891/02_2024/6ys3_10891.pdb" } resolution = 2.58 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= -0.000 sd= 0.003 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 3080 5.49 5 S 78 5.16 5 C 44817 2.51 5 N 16862 2.21 5 O 25716 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "0 ARG 3": "NH1" <-> "NH2" Residue "0 ARG 11": "NH1" <-> "NH2" Residue "0 ARG 18": "NH1" <-> "NH2" Residue "0 ARG 37": "NH1" <-> "NH2" Residue "0 PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 ARG 50": "NH1" <-> "NH2" Residue "0 ARG 57": "NH1" <-> "NH2" Residue "0 ASP 65": "OD1" <-> "OD2" Residue "0 ARG 74": "NH1" <-> "NH2" Residue "0 GLU 76": "OE1" <-> "OE2" Residue "1 ARG 29": "NH1" <-> "NH2" Residue "1 ARG 47": "NH1" <-> "NH2" Residue "1 ARG 52": "NH1" <-> "NH2" Residue "2 ARG 11": "NH1" <-> "NH2" Residue "2 ARG 30": "NH1" <-> "NH2" Residue "2 ASP 40": "OD1" <-> "OD2" Residue "2 ARG 45": "NH1" <-> "NH2" Residue "3 ARG 10": "NH1" <-> "NH2" Residue "3 ARG 16": "NH1" <-> "NH2" Residue "3 ARG 52": "NH1" <-> "NH2" Residue "4 ARG 44": "NH1" <-> "NH2" Residue "6 ARG 3": "NH1" <-> "NH2" Residue "6 ARG 12": "NH1" <-> "NH2" Residue "6 ARG 14": "NH1" <-> "NH2" Residue "6 ARG 19": "NH1" <-> "NH2" Residue "6 ARG 21": "NH1" <-> "NH2" Residue "6 ARG 33": "NH1" <-> "NH2" Residue "6 ARG 41": "NH1" <-> "NH2" Residue "7 ARG 13": "NH1" <-> "NH2" Residue "7 ARG 30": "NH1" <-> "NH2" Residue "7 ARG 40": "NH1" <-> "NH2" Residue "7 ARG 42": "NH1" <-> "NH2" Residue "8 ARG 24": "NH1" <-> "NH2" Residue "c ARG 52": "NH1" <-> "NH2" Residue "c ARG 63": "NH1" <-> "NH2" Residue "c ASP 66": "OD1" <-> "OD2" Residue "c ASP 72": "OD1" <-> "OD2" Residue "c ARG 80": "NH1" <-> "NH2" Residue "c TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ASP 114": "OD1" <-> "OD2" Residue "c ARG 133": "NH1" <-> "NH2" Residue "c GLU 145": "OE1" <-> "OE2" Residue "c ARG 167": "NH1" <-> "NH2" Residue "c ARG 177": "NH1" <-> "NH2" Residue "c GLU 180": "OE1" <-> "OE2" Residue "c ARG 182": "NH1" <-> "NH2" Residue "c ARG 189": "NH1" <-> "NH2" Residue "c ARG 203": "NH1" <-> "NH2" Residue "c ARG 212": "NH1" <-> "NH2" Residue "c ASP 264": "OD1" <-> "OD2" Residue "d ARG 13": "NH1" <-> "NH2" Residue "d GLU 30": "OE1" <-> "OE2" Residue "d ARG 33": "NH1" <-> "NH2" Residue "d ASP 39": "OD1" <-> "OD2" Residue "d ARG 59": "NH1" <-> "NH2" Residue "d ARG 77": "NH1" <-> "NH2" Residue "d ARG 83": "NH1" <-> "NH2" Residue "d ASP 131": "OD1" <-> "OD2" Residue "d GLU 168": "OE1" <-> "OE2" Residue "d ARG 169": "NH1" <-> "NH2" Residue "d ARG 184": "NH1" <-> "NH2" Residue "e PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ARG 21": "NH1" <-> "NH2" Residue "e ASP 22": "OD1" <-> "OD2" Residue "e ARG 44": "NH1" <-> "NH2" Residue "e ARG 49": "NH1" <-> "NH2" Residue "e ARG 61": "NH1" <-> "NH2" Residue "e ARG 67": "NH1" <-> "NH2" Residue "e ARG 88": "NH1" <-> "NH2" Residue "e ARG 102": "NH1" <-> "NH2" Residue "e GLU 127": "OE1" <-> "OE2" Residue "e ARG 162": "NH1" <-> "NH2" Residue "e ASP 168": "OD1" <-> "OD2" Residue "e ARG 170": "NH1" <-> "NH2" Residue "f ASP 51": "OD1" <-> "OD2" Residue "f ARG 71": "NH1" <-> "NH2" Residue "f ARG 80": "NH1" <-> "NH2" Residue "f ARG 92": "NH1" <-> "NH2" Residue "f GLU 101": "OE1" <-> "OE2" Residue "f ARG 102": "NH1" <-> "NH2" Residue "f ARG 110": "NH1" <-> "NH2" Residue "f ARG 112": "NH1" <-> "NH2" Residue "f ARG 115": "NH1" <-> "NH2" Residue "f PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ARG 133": "NH1" <-> "NH2" Residue "f GLU 165": "OE1" <-> "OE2" Residue "f ASP 174": "OD1" <-> "OD2" Residue "f PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ARG 3": "NH1" <-> "NH2" Residue "g ASP 16": "OD1" <-> "OD2" Residue "g GLU 32": "OE1" <-> "OE2" Residue "g ASP 60": "OD1" <-> "OD2" Residue "g GLU 124": "OE1" <-> "OE2" Residue "g ARG 153": "NH1" <-> "NH2" Residue "g GLU 155": "OE1" <-> "OE2" Residue "g ARG 163": "NH1" <-> "NH2" Residue "g ARG 170": "NH1" <-> "NH2" Residue "g GLU 173": "OE1" <-> "OE2" Residue "h ARG 27": "NH1" <-> "NH2" Residue "j GLU 9": "OE1" <-> "OE2" Residue "j ARG 13": "NH1" <-> "NH2" Residue "j ASP 19": "OD1" <-> "OD2" Residue "j ARG 37": "NH1" <-> "NH2" Residue "j GLU 91": "OE1" <-> "OE2" Residue "j ARG 96": "NH1" <-> "NH2" Residue "j ARG 120": "NH1" <-> "NH2" Residue "j ASP 141": "OD1" <-> "OD2" Residue "k ASP 37": "OD1" <-> "OD2" Residue "k GLU 45": "OE1" <-> "OE2" Residue "k GLU 92": "OE1" <-> "OE2" Residue "k GLU 110": "OE1" <-> "OE2" Residue "l ARG 21": "NH1" <-> "NH2" Residue "l ARG 33": "NH1" <-> "NH2" Residue "l ARG 41": "NH1" <-> "NH2" Residue "l ARG 47": "NH1" <-> "NH2" Residue "l ARG 60": "NH1" <-> "NH2" Residue "l ARG 78": "NH1" <-> "NH2" Residue "l GLU 106": "OE1" <-> "OE2" Residue "l ARG 126": "NH1" <-> "NH2" Residue "m ARG 10": "NH1" <-> "NH2" Residue "m ARG 18": "NH1" <-> "NH2" Residue "m ASP 25": "OD1" <-> "OD2" Residue "m PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m ARG 40": "NH1" <-> "NH2" Residue "m ARG 44": "NH1" <-> "NH2" Residue "m ARG 50": "NH1" <-> "NH2" Residue "m ARG 55": "NH1" <-> "NH2" Residue "m ARG 59": "NH1" <-> "NH2" Residue "m ASP 70": "OD1" <-> "OD2" Residue "m TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m GLU 104": "OE1" <-> "OE2" Residue "m ARG 114": "NH1" <-> "NH2" Residue "n ARG 8": "NH1" <-> "NH2" Residue "n ARG 12": "NH1" <-> "NH2" Residue "n ARG 17": "NH1" <-> "NH2" Residue "n ARG 22": "NH1" <-> "NH2" Residue "n GLU 43": "OE1" <-> "OE2" Residue "n ARG 46": "NH1" <-> "NH2" Residue "n ARG 63": "NH1" <-> "NH2" Residue "n ARG 64": "NH1" <-> "NH2" Residue "n ARG 69": "NH1" <-> "NH2" Residue "n ARG 71": "NH1" <-> "NH2" Residue "n 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 ASP 108": "OD1" <-> "OD2" Residue "o ARG 111": "NH1" <-> "NH2" Residue "o GLU 112": "OE1" <-> "OE2" Residue "o PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p ARG 21": "NH1" <-> "NH2" Residue "p ARG 39": "NH1" <-> "NH2" Residue "p GLU 44": "OE1" <-> "OE2" Residue "p ARG 51": "NH1" <-> "NH2" Residue "p ARG 62": "NH1" <-> "NH2" Residue "p ARG 89": "NH1" <-> "NH2" Residue "p ARG 101": "NH1" <-> "NH2" Residue "p ARG 109": "NH1" <-> "NH2" Residue "q ARG 3": "NH1" <-> "NH2" Residue "q ARG 6": "NH1" <-> "NH2" Residue "q ARG 13": "NH1" <-> "NH2" Residue "q ARG 33": "NH1" <-> "NH2" Residue "q ARG 48": "NH1" <-> "NH2" Residue "q ARG 70": "NH1" <-> "NH2" Residue "q ASP 97": "OD1" <-> "OD2" Residue "r ARG 21": "NH1" <-> "NH2" Residue "r GLU 23": "OE1" <-> "OE2" Residue "r ARG 68": "NH1" <-> "NH2" Residue "r GLU 70": "OE1" <-> "OE2" 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 ASP 65": "OD1" <-> "OD2" Residue "s ASP 77": "OD1" <-> "OD2" Residue "s ARG 84": "NH1" <-> "NH2" Residue "s ARG 88": "NH1" <-> "NH2" Residue "s ARG 95": "NH1" <-> "NH2" Residue "t ARG 12": "NH1" <-> "NH2" Residue "t ARG 73": "NH1" <-> "NH2" Residue "t TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u ARG 6": "NH1" <-> "NH2" Residue "u ARG 7": "NH1" <-> "NH2" Residue "u ASP 8": "OD1" <-> "OD2" Residue "u ASP 9": "OD1" <-> "OD2" Residue "u ASP 18": "OD1" <-> "OD2" Residue "u ARG 82": "NH1" <-> "NH2" Residue "u ARG 86": "NH1" <-> "NH2" Residue "u ASP 89": "OD1" <-> "OD2" Residue "u ARG 94": "NH1" <-> "NH2" Residue "u GLU 101": "OE1" <-> "OE2" Residue "w ASP 43": "OD1" <-> "OD2" Residue "w ASP 45": "OD1" <-> "OD2" Residue "w GLU 55": "OE1" <-> "OE2" Residue "w GLU 69": "OE1" <-> "OE2" Residue "w ASP 76": "OD1" <-> "OD2" Residue "z ARG 31": "NH1" <-> "NH2" Residue "z PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 90553 Number of models: 1 Model: "" Number of chains: 32 Chain: "0" 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: "1" Number of atoms: 495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 495 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Chain: "2" Number of atoms: 439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 439 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 2, 'TRANS': 54} Chain: "3" Number of atoms: 434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 434 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 1, 'TRANS': 53} Chain: "4" Number of atoms: 409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 409 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "6" 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: "7" 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: "8" 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: "a" Number of atoms: 2528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 2528 Classifications: {'RNA': 118} Modifications used: {'rna2p_pur': 9, 'rna2p_pyr': 6, 'rna3p_pur': 55, 'rna3p_pyr': 48} Link IDs: {'rna2p': 15, 'rna3p': 102} Unresolved chain links: 1 Unresolved chain link angles: 4 Unresolved chain link dihedrals: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "b" Number of atoms: 62008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2888, 62008 Classifications: {'RNA': 2888} Modifications used: {'p5*END': 1, 'rna2p_pur': 272, 'rna2p_pyr': 147, 'rna3p_pur': 1396, 'rna3p_pyr': 1073} Link IDs: {'rna2p': 419, 'rna3p': 2468} Chain breaks: 5 Chain: "c" Number of atoms: 2082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2082 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 17, 'TRANS': 253} Chain: "d" 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: "e" 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: "f" Number of atoms: 1410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1410 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 6, 'TRANS': 170} Chain: "g" 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: "h" Number of atoms: 287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 287 Classifications: {'peptide': 39} Link IDs: {'PTRANS': 2, 'TRANS': 36} Chain: "j" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1129 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 135} Chain: "k" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 938 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "l" Number of atoms: 1042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1042 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 4, 'TRANS': 138} Chain: "m" Number of atoms: 1074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1074 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 128} Chain: "n" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 960 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "o" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 892 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "p" Number of atoms: 908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 908 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 3, 'TRANS': 109} 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: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 791 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 1, 'TRANS': 97} Chain breaks: 1 Chain: "s" Number of atoms: 845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 845 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 2, 'TRANS': 106} Chain: "t" Number of atoms: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 738 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 1, 'TRANS': 91} Chain: "u" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 779 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "v" Number of atoms: 1583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1583 Classifications: {'RNA': 75} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 5, 'rna3p_pur': 25, 'rna3p_pyr': 38} Link IDs: {'rna2p': 11, 'rna3p': 63} Chain: "w" 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: "y" Number of atoms: 559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 559 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 72} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "z" Number of atoms: 275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 275 Classifications: {'peptide': 35} Link IDs: {'PTRANS': 3, 'TRANS': 31} Time building chain proxies: 35.40, per 1000 atoms: 0.39 Number of scatterers: 90553 At special positions: 0 Unit cell: (207.9, 203.7, 223.65, 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 78 16.00 P 3080 15.00 O 25716 8.00 N 16862 7.00 C 44817 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS 8 14 " - pdb=" SG CYS 8 27 " distance=2.05 Simple disulfide: pdb=" SG CYS z 22 " - pdb=" SG CYS z 32 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 44.19 Conformation dependent library (CDL) restraints added in 3.7 seconds 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5716 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 48 sheets defined 25.4% alpha, 21.0% beta 925 base pairs and 1637 stacking pairs defined. Time for finding SS restraints: 35.80 Creating SS restraints... Processing helix chain '0' and resid 53 through 63 removed outlier: 3.636A pdb=" N ARG 0 57 " --> pdb=" O ALA 0 53 " (cutoff:3.500A) Processing helix chain '0' and resid 63 through 73 Processing helix chain '1' and resid 5 through 9 removed outlier: 3.676A pdb=" N GLU 1 8 " --> pdb=" O GLU 1 5 " (cutoff:3.500A) Processing helix chain '1' and resid 10 through 34 removed outlier: 3.565A pdb=" N GLU 1 17 " --> pdb=" O GLU 1 13 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA 1 33 " --> pdb=" O ARG 1 29 " (cutoff:3.500A) Processing helix chain '1' and resid 41 through 61 removed outlier: 3.924A pdb=" N LYS 1 60 " --> pdb=" O LEU 1 56 " (cutoff:3.500A) Processing helix chain '2' and resid 17 through 28 Processing helix chain '2' and resid 41 through 51 removed outlier: 3.766A pdb=" N MET 2 47 " --> pdb=" O ALA 2 43 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL 2 51 " --> pdb=" O MET 2 47 " (cutoff:3.500A) Processing helix chain '3' and resid 9 through 17 removed outlier: 3.539A pdb=" N ARG 3 17 " --> pdb=" O ARG 3 13 " (cutoff:3.500A) Processing helix chain '6' and resid 8 through 16 Processing helix chain '6' and resid 17 through 22 Processing helix chain '6' and resid 24 through 38 removed outlier: 3.669A pdb=" N VAL 6 30 " --> pdb=" O ASN 6 26 " (cutoff:3.500A) Processing helix chain '7' and resid 37 through 44 removed outlier: 3.536A pdb=" N LEU 7 44 " --> pdb=" O ARG 7 40 " (cutoff:3.500A) Processing helix chain '7' and resid 54 through 62 removed outlier: 3.515A pdb=" N ALA 7 60 " --> pdb=" O GLY 7 56 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N CYS 7 61 " --> pdb=" O LEU 7 57 " (cutoff:3.500A) Processing helix chain '8' and resid 30 through 33 Processing helix chain 'c' and resid 30 through 32 No H-bonds generated for 'chain 'c' and resid 30 through 32' Processing helix chain 'c' and resid 199 through 203 Processing helix chain 'c' and resid 207 through 213 removed outlier: 3.826A pdb=" N ALA c 211 " --> pdb=" O LYS c 207 " (cutoff:3.500A) Processing helix chain 'c' and resid 221 through 225 Processing helix chain 'd' and resid 61 through 72 removed outlier: 3.729A pdb=" N HIS d 67 " --> pdb=" O PRO d 63 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA d 71 " --> pdb=" O HIS d 67 " (cutoff:3.500A) Processing helix chain 'd' and resid 97 through 104 removed outlier: 3.687A pdb=" N ALA d 102 " --> pdb=" O GLU d 99 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ASP d 103 " --> pdb=" O LEU d 100 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N VAL d 104 " --> pdb=" O PHE d 101 " (cutoff:3.500A) Processing helix chain 'd' and resid 120 through 126 Processing helix chain 'e' and resid 15 through 20 Processing helix chain 'e' and resid 24 through 38 Processing helix chain 'e' and resid 97 through 113 removed outlier: 3.515A pdb=" N GLU e 111 " --> pdb=" O SER e 107 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL e 113 " --> pdb=" O LEU e 109 " (cutoff:3.500A) Processing helix chain 'e' and resid 130 through 138 removed outlier: 3.578A pdb=" N LEU e 134 " --> pdb=" O LYS e 130 " (cutoff:3.500A) Processing helix chain 'e' and resid 154 through 161 removed outlier: 3.536A pdb=" N ALA e 161 " --> pdb=" O LEU e 157 " (cutoff:3.500A) Processing helix chain 'e' and resid 176 through 182 removed outlier: 3.616A pdb=" N LEU e 180 " --> pdb=" O ASP e 176 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE e 181 " --> pdb=" O PRO e 177 " (cutoff:3.500A) Processing helix chain 'e' and resid 189 through 200 removed outlier: 3.575A pdb=" N GLN e 195 " --> pdb=" O ASP e 191 " (cutoff:3.500A) Processing helix chain 'f' and resid 3 through 11 removed outlier: 3.842A pdb=" N TYR f 8 " --> pdb=" O LEU f 4 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N LYS f 9 " --> pdb=" O HIS f 5 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASP f 10 " --> pdb=" O ASP f 6 " (cutoff:3.500A) Processing helix chain 'f' and resid 49 through 61 removed outlier: 3.585A pdb=" N ASP f 56 " --> pdb=" O ASN f 52 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU f 57 " --> pdb=" O ALA f 53 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ALA f 59 " --> pdb=" O ALA f 55 " (cutoff:3.500A) Processing helix chain 'f' and resid 93 through 102 removed outlier: 3.978A pdb=" N TRP f 97 " --> pdb=" O GLY f 93 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N PHE f 99 " --> pdb=" O ARG f 95 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG f 102 " --> pdb=" O GLU f 98 " (cutoff:3.500A) Processing helix chain 'f' and resid 162 through 171 removed outlier: 3.635A pdb=" N LEU f 170 " --> pdb=" O GLY f 166 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ALA f 171 " --> pdb=" O ARG f 167 " (cutoff:3.500A) Processing helix chain 'f' and resid 172 through 174 No H-bonds generated for 'chain 'f' and resid 172 through 174' Processing helix chain 'g' and resid 61 through 77 Processing helix chain 'g' and resid 137 through 150 Processing helix chain 'j' and resid 24 through 38 removed outlier: 3.559A pdb=" N THR j 30 " --> pdb=" O GLY j 26 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLU j 31 " --> pdb=" O ARG j 27 " (cutoff:3.500A) Processing helix chain 'j' and resid 58 through 62 Processing helix chain 'j' and resid 67 through 72 Processing helix chain 'j' and resid 89 through 96 Processing helix chain 'j' and resid 97 through 109 removed outlier: 4.384A pdb=" N ILE j 101 " --> pdb=" O PRO j 97 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N MET j 108 " --> pdb=" O ALA j 104 " (cutoff:3.500A) Processing helix chain 'j' and resid 112 through 119 Processing helix chain 'k' and resid 104 through 108 removed outlier: 3.684A pdb=" N LEU k 107 " --> pdb=" O THR k 104 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ARG k 108 " --> pdb=" O ARG k 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 104 through 108' Processing helix chain 'k' and resid 112 through 117 Processing helix chain 'l' and resid 56 through 61 Processing helix chain 'l' and resid 78 through 83 removed outlier: 4.111A pdb=" N ALA l 83 " --> pdb=" O SER l 80 " (cutoff:3.500A) Processing helix chain 'l' and resid 92 through 98 removed outlier: 3.613A pdb=" N LYS l 96 " --> pdb=" O LEU l 92 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA l 98 " --> pdb=" O THR l 94 " (cutoff:3.500A) Processing helix chain 'l' and resid 128 through 136 Processing helix chain 'm' and resid 43 through 57 removed outlier: 3.551A pdb=" N ALA m 56 " --> pdb=" O ALA m 52 " (cutoff:3.500A) Processing helix chain 'm' and resid 109 through 122 removed outlier: 3.714A pdb=" N ALA m 122 " --> pdb=" O LYS m 118 " (cutoff:3.500A) Processing helix chain 'n' and resid 13 through 31 Processing helix chain 'n' and resid 44 through 55 Proline residue: n 50 - end of helix Processing helix chain 'n' and resid 59 through 70 removed outlier: 3.888A pdb=" N LEU n 65 " --> pdb=" O ALA n 61 " (cutoff:3.500A) Processing helix chain 'n' and resid 72 through 82 Processing helix chain 'n' and resid 82 through 87 Processing helix chain 'o' and resid 3 through 15 removed outlier: 3.756A pdb=" N ARG o 9 " --> pdb=" O SER o 5 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ARG o 13 " --> pdb=" O ARG o 9 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ALA o 14 " --> pdb=" O ARG o 10 " (cutoff:3.500A) Processing helix chain 'o' and resid 55 through 59 removed outlier: 3.702A pdb=" N ALA o 59 " --> pdb=" O LYS o 56 " (cutoff:3.500A) Processing helix chain 'o' and resid 67 through 84 removed outlier: 3.680A pdb=" N ALA o 79 " --> pdb=" O GLY o 75 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLU o 84 " --> pdb=" O GLU o 80 " (cutoff:3.500A) Processing helix chain 'o' and resid 101 through 114 removed outlier: 3.738A pdb=" N ALA o 113 " --> pdb=" O ALA o 109 " (cutoff:3.500A) Processing helix chain 'p' and resid 3 through 10 Processing helix chain 'p' and resid 97 through 102 Processing helix chain 'q' and resid 6 through 20 removed outlier: 3.586A pdb=" N ILE q 17 " --> pdb=" O ARG q 13 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLN q 20 " --> pdb=" O LYS q 16 " (cutoff:3.500A) Processing helix chain 'q' and resid 25 through 29 Processing helix chain 'q' and resid 31 through 72 removed outlier: 3.868A pdb=" N GLN q 37 " --> pdb=" O ARG q 33 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ARG q 51 " --> pdb=" O TYR q 47 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N LYS q 54 " --> pdb=" O ARG q 50 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ARG q 55 " --> pdb=" O ARG q 51 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ARG q 58 " --> pdb=" O LYS q 54 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASN q 72 " --> pdb=" O ALA q 68 " (cutoff:3.500A) Processing helix chain 'q' and resid 75 through 86 Processing helix chain 'q' and resid 91 through 102 removed outlier: 3.618A pdb=" N VAL q 100 " --> pdb=" O ALA q 96 " (cutoff:3.500A) Processing helix chain 'q' and resid 103 through 118 removed outlier: 3.597A pdb=" N ALA q 108 " --> pdb=" O VAL q 104 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU q 109 " --> pdb=" O ALA q 105 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA q 116 " --> pdb=" O LYS q 112 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA q 118 " --> pdb=" O LYS q 114 " (cutoff:3.500A) Processing helix chain 's' and resid 13 through 22 removed outlier: 3.530A pdb=" N LEU s 19 " --> pdb=" O GLN s 15 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N VAL s 20 " --> pdb=" O LYS s 16 " (cutoff:3.500A) Processing helix chain 's' and resid 28 through 34 removed outlier: 3.736A pdb=" N ASP s 34 " --> pdb=" O SER s 30 " (cutoff:3.500A) Processing helix chain 's' and resid 41 through 61 removed outlier: 3.755A pdb=" N VAL s 45 " --> pdb=" O LYS s 41 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS s 49 " --> pdb=" O VAL s 45 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL s 50 " --> pdb=" O LEU s 46 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASN s 61 " --> pdb=" O ASN s 57 " (cutoff:3.500A) Processing helix chain 's' and resid 65 through 69 removed outlier: 3.744A pdb=" N ASP s 68 " --> pdb=" O ASP s 65 " (cutoff:3.500A) Processing helix chain 's' and resid 89 through 91 No H-bonds generated for 'chain 's' and resid 89 through 91' Processing helix chain 't' and resid 3 through 8 Processing helix chain 't' and resid 19 through 27 Processing helix chain 't' and resid 39 through 51 Processing helix chain 'w' and resid 13 through 23 Processing helix chain 'w' and resid 44 through 48 Processing helix chain 'z' and resid 28 through 150 removed outlier: 4.422A pdb=" N PHE z 150 " --> pdb=" O PHE z 29 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain '0' and resid 13 through 18 Processing sheet with id=AA2, first strand: chain '0' and resid 33 through 40 Processing sheet with id=AA3, first strand: chain '2' and resid 35 through 38 removed outlier: 3.997A pdb=" N LYS 2 6 " --> pdb=" O GLU 2 58 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain '3' and resid 29 through 30 Processing sheet with id=AA5, first strand: chain '3' and resid 48 through 49 Processing sheet with id=AA6, first strand: chain '4' and resid 7 through 12 Processing sheet with id=AA7, first strand: chain '4' and resid 36 through 40 removed outlier: 3.664A pdb=" N GLN 4 45 " --> pdb=" O ASP 4 40 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain '7' and resid 14 through 16 Processing sheet with id=AA9, first strand: chain '8' and resid 2 through 4 removed outlier: 6.250A pdb=" N LYS 8 2 " --> pdb=" O ARG 8 36 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain '8' and resid 14 through 19 Processing sheet with id=AB2, first strand: chain 'c' and resid 3 through 5 Processing sheet with id=AB3, first strand: chain 'c' and resid 34 through 37 removed outlier: 3.993A pdb=" N ASN c 37 " --> pdb=" O GLN c 60 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N GLN c 60 " --> pdb=" O ASN c 37 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'c' and resid 101 through 105 removed outlier: 6.546A pdb=" N LEU c 95 " --> pdb=" O VAL c 78 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N VAL c 78 " --> pdb=" O LEU c 95 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'c' and resid 129 through 131 removed outlier: 6.105A pdb=" N ILE c 164 " --> pdb=" O ARG c 175 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ARG c 175 " --> pdb=" O ILE c 164 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA c 166 " --> pdb=" O THR c 173 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N LYS c 183 " --> pdb=" O ILE c 267 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N ILE c 267 " --> pdb=" O LYS c 183 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'c' and resid 144 through 145 Processing sheet with id=AB7, first strand: chain 'd' and resid 4 through 15 removed outlier: 6.617A pdb=" N VAL d 26 " --> pdb=" O VAL d 9 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N MET d 11 " --> pdb=" O VAL d 24 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N VAL d 24 " --> pdb=" O MET d 11 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N ARG d 13 " --> pdb=" O ILE d 22 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ILE d 22 " --> pdb=" O ARG d 13 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N LEU d 186 " --> pdb=" O VAL d 180 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N VAL d 180 " --> pdb=" O LEU d 186 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N LEU d 188 " --> pdb=" O VAL d 178 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ASP d 176 " --> pdb=" O LYS d 190 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N THR d 171 " --> pdb=" O GLY d 111 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N GLY d 111 " --> pdb=" O THR d 171 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N GLN d 173 " --> pdb=" O VAL d 109 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N VAL d 109 " --> pdb=" O GLN d 173 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N THR d 112 " --> pdb=" O ASP d 200 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N ASP d 200 " --> pdb=" O THR d 112 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'd' and resid 80 through 83 removed outlier: 6.283A pdb=" N ALA d 47 " --> pdb=" O VAL d 37 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N VAL d 37 " --> pdb=" O ALA d 47 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N GLN d 49 " --> pdb=" O THR d 35 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'd' and resid 117 through 119 removed outlier: 3.562A pdb=" N GLY d 117 " --> pdb=" O MET d 165 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'e' and resid 2 through 3 removed outlier: 3.560A pdb=" N LEU e 3 " --> pdb=" O LEU e 12 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'e' and resid 118 through 120 removed outlier: 6.151A pdb=" N LEU e 147 " --> pdb=" O VAL e 187 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'f' and resid 66 through 68 removed outlier: 4.031A pdb=" N GLY f 86 " --> pdb=" O THR f 68 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'g' and resid 9 through 10 Processing sheet with id=AC5, first strand: chain 'g' and resid 19 through 20 removed outlier: 3.519A pdb=" N ASN g 20 " --> pdb=" O VAL g 23 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N VAL g 23 " --> pdb=" O ASN g 20 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'g' and resid 122 through 124 removed outlier: 3.650A pdb=" N GLY g 135 " --> pdb=" O PHE g 83 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE g 83 " --> pdb=" O GLY g 135 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'g' and resid 95 through 98 Processing sheet with id=AC8, first strand: chain 'h' and resid 18 through 20 Processing sheet with id=AC9, first strand: chain 'j' and resid 122 through 124 removed outlier: 6.731A pdb=" N TYR j 16 " --> pdb=" O ILE j 55 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N LEU j 57 " --> pdb=" O TYR j 16 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N VAL j 18 " --> pdb=" O LEU j 57 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'j' and resid 73 through 77 Processing sheet with id=AD2, first strand: chain 'k' and resid 7 through 10 removed outlier: 3.579A pdb=" N VAL k 10 " --> pdb=" O ARG k 17 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ARG k 17 " --> pdb=" O VAL k 10 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N GLU k 45 " --> pdb=" O ARG k 17 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N VAL k 19 " --> pdb=" O ILE k 43 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ILE k 43 " --> pdb=" O VAL k 19 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N CYS k 21 " --> pdb=" O ILE k 41 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ILE k 41 " --> pdb=" O CYS k 21 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N LYS k 23 " --> pdb=" O ILE k 39 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N ILE k 39 " --> pdb=" O LYS k 23 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ALA k 83 " --> pdb=" O VAL k 63 " (cutoff:3.500A) removed outlier: 8.229A pdb=" N CYS k 84 " --> pdb=" O MET k 7 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ASN k 9 " --> pdb=" O CYS k 84 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N LEU k 86 " --> pdb=" O ASN k 9 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'k' and resid 69 through 70 removed outlier: 3.594A pdb=" N ILE k 77 " --> pdb=" O VAL k 69 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ALA p 49 " --> pdb=" O THR p 60 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ARG p 62 " --> pdb=" O VAL p 47 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N VAL p 47 " --> pdb=" O ARG p 62 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N ILE p 64 " --> pdb=" O GLY p 45 " (cutoff:3.500A) removed outlier: 8.242A pdb=" N GLY p 45 " --> pdb=" O ILE p 64 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N THR p 25 " --> pdb=" O LYS p 87 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER p 83 " --> pdb=" O LYS p 29 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N TRP p 31 " --> pdb=" O VAL p 81 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N VAL p 81 " --> pdb=" O TRP p 31 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'l' and resid 74 through 77 Processing sheet with id=AD5, first strand: chain 'l' and resid 89 through 90 removed outlier: 6.690A pdb=" N VAL l 122 " --> pdb=" O GLU l 143 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'm' and resid 62 through 65 removed outlier: 5.859A pdb=" N VAL m 101 " --> pdb=" O ALA m 35 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N ALA m 35 " --> pdb=" O VAL m 101 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TYR m 103 " --> pdb=" O LEU m 33 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'm' and resid 39 through 42 removed outlier: 3.957A pdb=" N ASN m 88 " --> pdb=" O GLU m 75 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N ILE m 73 " --> pdb=" O GLU m 90 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N TRP m 92 " --> pdb=" O LYS m 71 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N LYS m 71 " --> pdb=" O TRP m 92 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'n' and resid 33 through 37 removed outlier: 6.382A pdb=" N MET n 110 " --> pdb=" O CYS n 100 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'o' and resid 47 through 52 removed outlier: 6.725A pdb=" N VAL o 39 " --> pdb=" O LEU o 48 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N ALA o 50 " --> pdb=" O ALA o 37 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N ALA o 37 " --> pdb=" O ALA o 50 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N SER o 52 " --> pdb=" O ILE o 35 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N ILE o 35 " --> pdb=" O SER o 52 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N HIS o 34 " --> pdb=" O THR o 31 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N THR o 31 " --> pdb=" O HIS o 34 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N LEU o 26 " --> pdb=" O ASP o 93 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'r' and resid 11 through 15 removed outlier: 7.584A pdb=" N GLN r 6 " --> pdb=" O VAL r 38 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N VAL r 38 " --> pdb=" O GLN r 6 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'r' and resid 19 through 23 removed outlier: 6.525A pdb=" N ASP r 95 " --> pdb=" O VAL r 64 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N LYS r 60 " --> pdb=" O THR r 99 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'r' and resid 72 through 78 removed outlier: 4.030A pdb=" N TYR r 83 " --> pdb=" O ARG r 78 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 's' and resid 3 through 10 removed outlier: 5.287A pdb=" N SER s 101 " --> pdb=" O HIS s 9 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N THR s 100 " --> pdb=" O PRO s 80 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N HIS s 102 " --> pdb=" O GLU s 78 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N GLU s 78 " --> pdb=" O HIS s 102 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N THR s 104 " --> pdb=" O VAL s 76 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N VAL s 76 " --> pdb=" O THR s 104 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N VAL s 106 " --> pdb=" O ILE s 74 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N ILE s 74 " --> pdb=" O VAL s 106 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N SER s 108 " --> pdb=" O THR s 72 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N THR s 72 " --> pdb=" O SER s 108 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 't' and resid 11 through 14 removed outlier: 4.013A pdb=" N LYS t 81 " --> pdb=" O VAL t 34 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL t 57 " --> pdb=" O THR t 86 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 't' and resid 67 through 68 Processing sheet with id=AE7, first strand: chain 'u' and resid 65 through 66 removed outlier: 7.241A pdb=" N LYS u 33 " --> pdb=" O VAL u 28 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N VAL u 28 " --> pdb=" O LYS u 33 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ILE u 35 " --> pdb=" O LYS u 26 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N GLU u 10 " --> pdb=" O PHE u 73 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ILE u 72 " --> pdb=" O ASP u 81 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'u' and resid 41 through 45 Processing sheet with id=AE9, first strand: chain 'u' and resid 83 through 88 Processing sheet with id=AF1, first strand: chain 'w' and resid 3 through 8 removed outlier: 7.757A pdb=" N ASN w 5 " --> pdb=" O ASP w 43 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N ASP w 43 " --> pdb=" O ASN w 5 " (cutoff:3.500A) removed outlier: 9.489A pdb=" N LYS w 25 " --> pdb=" O GLN w 87 " (cutoff:3.500A) removed outlier: 9.908A pdb=" N ILE w 89 " --> pdb=" O LYS w 25 " (cutoff:3.500A) removed outlier: 8.645A pdb=" N PHE w 91 " --> pdb=" O PRO w 27 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N ILE w 29 " --> pdb=" O PHE w 91 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N ARG w 93 " --> pdb=" O ILE w 29 " (cutoff:3.500A) removed outlier: 8.268A pdb=" N TYR w 31 " --> pdb=" O ARG w 93 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N LEU w 86 " --> pdb=" O ARG w 79 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N ARG w 79 " --> pdb=" O LEU w 86 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N HIS w 88 " --> pdb=" O VAL w 77 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N VAL w 77 " --> pdb=" O HIS w 88 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ASP w 90 " --> pdb=" O GLN w 75 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'y' and resid 22 through 23 removed outlier: 6.985A pdb=" N LEU y 59 " --> pdb=" O ILE y 37 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'y' and resid 30 through 31 780 hydrogen bonds defined for protein. 2133 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2303 hydrogen bonds 3574 hydrogen bond angles 0 basepair planarities 925 basepair parallelities 1637 stacking parallelities Total time for adding SS restraints: 164.43 Time building geometry restraints manager: 47.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 11992 1.32 - 1.45: 44823 1.45 - 1.58: 36677 1.58 - 1.71: 5174 1.71 - 1.84: 139 Bond restraints: 98805 Sorted by residual: bond pdb=" C1' U a 89 " pdb=" N1 U a 89 " ideal model delta sigma weight residual 1.480 1.532 -0.052 1.50e-02 4.44e+03 1.18e+01 bond pdb=" CA GLN z 160 " pdb=" C GLN z 160 " ideal model delta sigma weight residual 1.521 1.565 -0.044 1.29e-02 6.01e+03 1.15e+01 bond pdb=" N PRO z 153 " pdb=" CD PRO z 153 " ideal model delta sigma weight residual 1.473 1.516 -0.043 1.40e-02 5.10e+03 9.55e+00 bond pdb=" CB ARG c 221 " pdb=" CG ARG c 221 " ideal model delta sigma weight residual 1.520 1.433 0.087 3.00e-02 1.11e+03 8.45e+00 bond pdb=" N ARG f 30 " pdb=" CA ARG f 30 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.21e-02 6.83e+03 7.88e+00 ... (remaining 98800 not shown) Histogram of bond angle deviations from ideal: 77.55 - 89.43: 4 89.43 - 101.30: 1684 101.30 - 113.18: 73328 113.18 - 125.06: 61731 125.06 - 136.93: 11919 Bond angle restraints: 148666 Sorted by residual: angle pdb=" N HIS g 45 " pdb=" CA HIS g 45 " pdb=" C HIS g 45 " ideal model delta sigma weight residual 110.35 77.55 32.80 1.38e+00 5.25e-01 5.65e+02 angle pdb=" N ALA z 159 " pdb=" CA ALA z 159 " pdb=" C ALA z 159 " ideal model delta sigma weight residual 108.26 79.94 28.32 1.66e+00 3.63e-01 2.91e+02 angle pdb=" N ILE z 156 " pdb=" CA ILE z 156 " pdb=" C ILE z 156 " ideal model delta sigma weight residual 109.34 136.93 -27.59 2.08e+00 2.31e-01 1.76e+02 angle pdb=" N TYR z 28 " pdb=" CA TYR z 28 " pdb=" C TYR z 28 " ideal model delta sigma weight residual 107.44 86.76 20.68 1.93e+00 2.68e-01 1.15e+02 angle pdb=" N ALA g 46 " pdb=" CA ALA g 46 " pdb=" C ALA g 46 " ideal model delta sigma weight residual 110.80 88.78 22.02 2.13e+00 2.20e-01 1.07e+02 ... (remaining 148661 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.88: 54734 35.88 - 71.75: 7743 71.75 - 107.63: 839 107.63 - 143.50: 23 143.50 - 179.38: 29 Dihedral angle restraints: 63368 sinusoidal: 54487 harmonic: 8881 Sorted by residual: dihedral pdb=" O4' U b2888 " pdb=" C1' U b2888 " pdb=" N1 U b2888 " pdb=" C2 U b2888 " ideal model delta sinusoidal sigma weight residual 200.00 25.29 174.71 1 1.50e+01 4.44e-03 8.52e+01 dihedral pdb=" O4' U b 99 " pdb=" C1' U b 99 " pdb=" N1 U b 99 " pdb=" C2 U b 99 " ideal model delta sinusoidal sigma weight residual 200.00 28.11 171.89 1 1.50e+01 4.44e-03 8.49e+01 dihedral pdb=" O4' C b1732 " pdb=" C1' C b1732 " pdb=" N1 C b1732 " pdb=" C2 C b1732 " ideal model delta sinusoidal sigma weight residual 200.00 39.93 160.07 1 1.50e+01 4.44e-03 8.28e+01 ... (remaining 63365 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.155: 18627 0.155 - 0.309: 463 0.309 - 0.464: 27 0.464 - 0.618: 1 0.618 - 0.773: 1 Chirality restraints: 19119 Sorted by residual: chirality pdb=" CA ILE z 156 " pdb=" N ILE z 156 " pdb=" C ILE z 156 " pdb=" CB ILE z 156 " both_signs ideal model delta sigma weight residual False 2.43 1.66 0.77 2.00e-01 2.50e+01 1.49e+01 chirality pdb=" CB ILE j 84 " pdb=" CA ILE j 84 " pdb=" CG1 ILE j 84 " pdb=" CG2 ILE j 84 " both_signs ideal model delta sigma weight residual False 2.64 2.18 0.47 2.00e-01 2.50e+01 5.46e+00 chirality pdb=" C1' G b2736 " pdb=" O4' G b2736 " pdb=" C2' G b2736 " pdb=" N9 G b2736 " both_signs ideal model delta sigma weight residual False 2.46 2.01 0.45 2.00e-01 2.50e+01 5.01e+00 ... (remaining 19116 not shown) Planarity restraints: 7352 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA z 159 " -0.025 2.00e-02 2.50e+03 5.13e-02 2.63e+01 pdb=" C ALA z 159 " 0.089 2.00e-02 2.50e+03 pdb=" O ALA z 159 " -0.034 2.00e-02 2.50e+03 pdb=" N GLN z 160 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G b2462 " 0.061 2.00e-02 2.50e+03 2.55e-02 1.95e+01 pdb=" N9 G b2462 " -0.056 2.00e-02 2.50e+03 pdb=" C8 G b2462 " -0.011 2.00e-02 2.50e+03 pdb=" N7 G b2462 " -0.001 2.00e-02 2.50e+03 pdb=" C5 G b2462 " -0.001 2.00e-02 2.50e+03 pdb=" C6 G b2462 " 0.018 2.00e-02 2.50e+03 pdb=" O6 G b2462 " 0.012 2.00e-02 2.50e+03 pdb=" N1 G b2462 " 0.005 2.00e-02 2.50e+03 pdb=" C2 G b2462 " -0.009 2.00e-02 2.50e+03 pdb=" N2 G b2462 " 0.002 2.00e-02 2.50e+03 pdb=" N3 G b2462 " -0.011 2.00e-02 2.50e+03 pdb=" C4 G b2462 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A b 912 " 0.057 2.00e-02 2.50e+03 2.62e-02 1.89e+01 pdb=" N9 A b 912 " -0.059 2.00e-02 2.50e+03 pdb=" C8 A b 912 " -0.004 2.00e-02 2.50e+03 pdb=" N7 A b 912 " -0.001 2.00e-02 2.50e+03 pdb=" C5 A b 912 " 0.008 2.00e-02 2.50e+03 pdb=" C6 A b 912 " 0.015 2.00e-02 2.50e+03 pdb=" N6 A b 912 " 0.009 2.00e-02 2.50e+03 pdb=" N1 A b 912 " 0.000 2.00e-02 2.50e+03 pdb=" C2 A b 912 " 0.004 2.00e-02 2.50e+03 pdb=" N3 A b 912 " -0.015 2.00e-02 2.50e+03 pdb=" C4 A b 912 " -0.013 2.00e-02 2.50e+03 ... (remaining 7349 not shown) Histogram of nonbonded interaction distances: 1.21 - 1.94: 8 1.94 - 2.68: 7474 2.68 - 3.42: 109401 3.42 - 4.16: 319407 4.16 - 4.90: 426153 Nonbonded interactions: 862443 Sorted by model distance: nonbonded pdb=" C2 A b2455 " pdb=" O ALA z 164 " model vdw 1.205 3.340 nonbonded pdb=" N2 G b2065 " pdb=" CB ALA z 164 " model vdw 1.310 3.540 nonbonded pdb=" NH2 ARG s 95 " pdb=" CE2 PHE z 150 " model vdw 1.557 3.420 nonbonded pdb=" N1 G b2065 " pdb=" CB ALA z 164 " model vdw 1.687 3.540 nonbonded pdb=" C2 G b2065 " pdb=" CB ALA z 164 " model vdw 1.701 3.680 ... (remaining 862438 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.080 Extract box with map and model: 24.720 Check model and map are aligned: 0.990 Set scattering table: 0.640 Process input model: 346.560 Find NCS groups from input model: 1.530 Set up NCS constraints: 0.250 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:11.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 391.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8723 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.116 98805 Z= 0.736 Angle : 1.101 32.798 148666 Z= 0.564 Chirality : 0.065 0.773 19119 Planarity : 0.007 0.090 7352 Dihedral : 24.574 179.375 57646 Min Nonbonded Distance : 1.205 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.15 % Favored : 92.82 % Rotamer: Outliers : 0.90 % Allowed : 8.76 % Favored : 90.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.18 (0.12), residues: 3076 helix: -4.24 (0.09), residues: 764 sheet: -2.05 (0.18), residues: 632 loop : -2.32 (0.12), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.003 TRP c 213 HIS 0.025 0.003 HIS s 7 PHE 0.023 0.003 PHE q 57 TYR 0.021 0.003 TYR 0 78 ARG 0.017 0.001 ARG q 6 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 937 residues out of total 2547 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 914 time to evaluate : 3.707 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: 4 27 LYS cc_start: 0.8406 (tppp) cc_final: 0.8008 (tppp) REVERT: e 141 MET cc_start: 0.8014 (mmm) cc_final: 0.7676 (mmt) REVERT: f 159 THR cc_start: 0.9048 (p) cc_final: 0.8218 (m) REVERT: f 165 GLU cc_start: 0.8633 (mp0) cc_final: 0.8267 (mp0) REVERT: g 62 TRP cc_start: 0.8027 (m100) cc_final: 0.7668 (m100) REVERT: g 64 GLN cc_start: 0.8880 (mm-40) cc_final: 0.8547 (mm-40) REVERT: g 88 GLN cc_start: 0.8031 (tm-30) cc_final: 0.7768 (tp40) REVERT: g 139 GLN cc_start: 0.8928 (tm-30) cc_final: 0.8703 (tm130) REVERT: m 6 ARG cc_start: 0.7117 (ptm-80) cc_final: 0.6738 (ptm-80) REVERT: p 82 ASP cc_start: 0.8594 (t70) cc_final: 0.8298 (t0) REVERT: p 109 ARG cc_start: 0.8237 (mtm180) cc_final: 0.7787 (ttt180) REVERT: r 6 GLN cc_start: 0.8185 (tt0) cc_final: 0.7845 (tt0) REVERT: s 65 ASP cc_start: 0.7452 (t70) cc_final: 0.7176 (p0) REVERT: u 100 SER cc_start: 0.8388 (p) cc_final: 0.8186 (t) REVERT: w 2 PHE cc_start: 0.8969 (m-80) cc_final: 0.8647 (m-80) REVERT: w 59 GLU cc_start: 0.7901 (pt0) cc_final: 0.6572 (pt0) outliers start: 23 outliers final: 11 residues processed: 931 average time/residue: 1.8292 time to fit residues: 2272.2215 Evaluate side-chains 707 residues out of total 2547 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 696 time to evaluate : 3.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 33 LEU Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 151 THR Chi-restraints excluded: chain e residue 116 ASP Chi-restraints excluded: chain e residue 138 LEU Chi-restraints excluded: chain f residue 36 LEU Chi-restraints excluded: chain f residue 94 GLU Chi-restraints excluded: chain m residue 25 ASP Chi-restraints excluded: chain n residue 114 GLU Chi-restraints excluded: chain r residue 72 VAL Chi-restraints excluded: chain s residue 29 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 606 random chunks: chunk 511 optimal weight: 3.9990 chunk 459 optimal weight: 0.0980 chunk 254 optimal weight: 0.7980 chunk 156 optimal weight: 20.0000 chunk 309 optimal weight: 0.6980 chunk 245 optimal weight: 1.9990 chunk 474 optimal weight: 0.7980 chunk 183 optimal weight: 0.6980 chunk 288 optimal weight: 5.9990 chunk 353 optimal weight: 4.9990 chunk 550 optimal weight: 4.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 20 ASN 1 27 ASN 1 39 GLN 1 58 ASN 4 26 ASN 7 28 ASN 8 13 ASN d 32 ASN d 94 GLN e 165 HIS f 27 GLN f 81 GLN f 127 ASN ** f 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 73 ASN ** g 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 143 GLN h 2 GLN n 23 ASN o 104 GLN p 10 GLN p 15 GLN q 20 GLN q 44 GLN q 56 GLN q 71 GLN q 72 ASN r 87 GLN s 7 HIS u 66 GLN w 12 GLN y 76 ASN z 160 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.2112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.072 98805 Z= 0.150 Angle : 0.599 7.902 148666 Z= 0.314 Chirality : 0.035 0.306 19119 Planarity : 0.005 0.065 7352 Dihedral : 24.761 179.054 51527 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 2.71 % Allowed : 20.54 % Favored : 76.75 % 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: -2.87 (0.13), residues: 3076 helix: -2.36 (0.15), residues: 795 sheet: -1.59 (0.18), residues: 664 loop : -1.74 (0.14), residues: 1617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP c 213 HIS 0.006 0.001 HIS o 34 PHE 0.011 0.001 PHE m 68 TYR 0.013 0.001 TYR f 7 ARG 0.008 0.001 ARG z 163 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 892 residues out of total 2547 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 823 time to evaluate : 3.698 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: f 23 ASN cc_start: 0.7119 (p0) cc_final: 0.6435 (p0) REVERT: g 62 TRP cc_start: 0.7941 (m100) cc_final: 0.7607 (m100) REVERT: g 115 HIS cc_start: 0.8731 (t70) cc_final: 0.8352 (t-90) REVERT: g 130 GLU cc_start: 0.7233 (tp30) cc_final: 0.6996 (tp30) REVERT: l 106 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.7354 (mt-10) REVERT: m 6 ARG cc_start: 0.7149 (ptm-80) cc_final: 0.6740 (ptm-80) REVERT: p 82 ASP cc_start: 0.8478 (t70) cc_final: 0.8210 (t0) REVERT: p 85 SER cc_start: 0.8723 (OUTLIER) cc_final: 0.8422 (p) REVERT: q 97 ASP cc_start: 0.7855 (t70) cc_final: 0.7651 (t70) REVERT: q 101 PHE cc_start: 0.7766 (m-80) cc_final: 0.7407 (m-10) REVERT: s 59 GLU cc_start: 0.7530 (pp20) cc_final: 0.7309 (tm-30) REVERT: t 1 MET cc_start: 0.5174 (pmm) cc_final: 0.4932 (pmm) REVERT: u 6 ARG cc_start: 0.8738 (OUTLIER) cc_final: 0.8497 (mtt-85) REVERT: u 9 ASP cc_start: 0.7865 (m-30) cc_final: 0.7510 (m-30) REVERT: w 53 LYS cc_start: 0.8051 (mppt) cc_final: 0.7513 (mtmm) outliers start: 69 outliers final: 31 residues processed: 845 average time/residue: 1.7217 time to fit residues: 1991.6791 Evaluate side-chains 769 residues out of total 2547 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 735 time to evaluate : 3.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 15 ASN Chi-restraints excluded: chain 1 residue 49 ASP Chi-restraints excluded: chain 4 residue 25 LYS Chi-restraints excluded: chain c residue 173 THR Chi-restraints excluded: chain d residue 17 GLU Chi-restraints excluded: chain d residue 21 SER Chi-restraints excluded: chain d residue 60 VAL Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain e residue 136 GLN Chi-restraints excluded: chain f residue 12 VAL Chi-restraints excluded: chain f residue 94 GLU Chi-restraints excluded: chain f residue 158 THR Chi-restraints excluded: chain g residue 2 SER Chi-restraints excluded: chain h residue 12 LEU Chi-restraints excluded: chain l residue 81 ASP Chi-restraints excluded: chain l residue 91 ASP Chi-restraints excluded: chain l residue 106 GLU Chi-restraints excluded: chain m residue 54 THR Chi-restraints excluded: chain m residue 63 ILE Chi-restraints excluded: chain n residue 57 THR Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain o residue 40 ILE Chi-restraints excluded: chain o residue 55 GLU Chi-restraints excluded: chain o residue 69 ASP Chi-restraints excluded: chain o residue 100 HIS Chi-restraints excluded: chain p residue 41 GLN Chi-restraints excluded: chain p residue 76 THR Chi-restraints excluded: chain p residue 85 SER Chi-restraints excluded: chain q residue 104 VAL Chi-restraints excluded: chain t residue 18 GLU Chi-restraints excluded: chain u residue 6 ARG Chi-restraints excluded: chain u residue 102 THR Chi-restraints excluded: chain w residue 42 LEU Chi-restraints excluded: chain z residue 22 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 606 random chunks: chunk 305 optimal weight: 6.9990 chunk 170 optimal weight: 6.9990 chunk 458 optimal weight: 6.9990 chunk 374 optimal weight: 9.9990 chunk 151 optimal weight: 6.9990 chunk 551 optimal weight: 0.8980 chunk 595 optimal weight: 5.9990 chunk 490 optimal weight: 7.9990 chunk 546 optimal weight: 6.9990 chunk 187 optimal weight: 6.9990 chunk 442 optimal weight: 0.0670 overall best weight: 4.1924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 58 ASN 2 9 GLN 4 26 ASN 7 28 ASN c 142 HIS d 58 ASN d 94 GLN e 165 HIS ** f 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 73 ASN g 128 GLN ** g 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 20 ASN j 86 GLN k 93 GLN n 107 ASN o 38 GLN p 75 GLN q 20 GLN q 44 GLN q 56 GLN r 87 GLN t 59 ASN w 12 GLN z 158 GLN z 160 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8743 moved from start: 0.2441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.077 98805 Z= 0.418 Angle : 0.664 8.348 148666 Z= 0.347 Chirality : 0.041 0.338 19119 Planarity : 0.005 0.058 7352 Dihedral : 24.601 179.035 51511 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 4.75 % Allowed : 21.92 % Favored : 73.33 % 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: -1.97 (0.14), residues: 3076 helix: -1.14 (0.17), residues: 812 sheet: -1.22 (0.18), residues: 684 loop : -1.35 (0.15), residues: 1580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP c 213 HIS 0.007 0.002 HIS s 7 PHE 0.018 0.002 PHE q 36 TYR 0.017 0.002 TYR s 38 ARG 0.007 0.001 ARG 6 41 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 887 residues out of total 2547 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 766 time to evaluate : 3.713 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: 3 31 ASP cc_start: 0.8384 (t70) cc_final: 0.8156 (t70) REVERT: 4 7 GLU cc_start: 0.6712 (tm-30) cc_final: 0.6308 (tm-30) REVERT: 4 27 LYS cc_start: 0.8444 (mmmm) cc_final: 0.8200 (mmtm) REVERT: c 133 ARG cc_start: 0.8027 (mtt-85) cc_final: 0.7772 (mtt-85) REVERT: c 201 MET cc_start: 0.8051 (ptp) cc_final: 0.7836 (ptm) REVERT: d 1 MET cc_start: 0.7865 (OUTLIER) cc_final: 0.7015 (tmt) REVERT: d 2 ILE cc_start: 0.8702 (pt) cc_final: 0.7535 (pt) REVERT: e 136 GLN cc_start: 0.8437 (OUTLIER) cc_final: 0.7651 (tm-30) REVERT: e 156 ASN cc_start: 0.8926 (t0) cc_final: 0.8623 (t0) REVERT: f 23 ASN cc_start: 0.7716 (p0) cc_final: 0.7484 (p0) REVERT: g 62 TRP cc_start: 0.8094 (m100) cc_final: 0.7647 (m100) REVERT: g 115 HIS cc_start: 0.8751 (t70) cc_final: 0.8521 (t-90) REVERT: g 139 GLN cc_start: 0.9036 (tm-30) cc_final: 0.8722 (tm130) REVERT: h 12 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.8373 (pp) REVERT: h 20 ASN cc_start: 0.7932 (t0) cc_final: 0.7669 (t0) REVERT: k 106 GLU cc_start: 0.7538 (mp0) cc_final: 0.7337 (mp0) REVERT: k 114 LYS cc_start: 0.8216 (OUTLIER) cc_final: 0.7871 (ttmm) REVERT: l 106 GLU cc_start: 0.7692 (OUTLIER) cc_final: 0.7301 (mt-10) REVERT: m 6 ARG cc_start: 0.7396 (ptm-80) cc_final: 0.6887 (ptm-80) REVERT: m 112 LEU cc_start: 0.9405 (tp) cc_final: 0.9140 (tp) REVERT: p 85 SER cc_start: 0.8677 (OUTLIER) cc_final: 0.8460 (p) REVERT: p 106 LYS cc_start: 0.6751 (OUTLIER) cc_final: 0.4120 (mptt) REVERT: r 13 ARG cc_start: 0.8791 (ttt-90) cc_final: 0.8549 (ttt-90) REVERT: r 60 LYS cc_start: 0.8865 (ptpp) cc_final: 0.8660 (mtmm) REVERT: u 6 ARG cc_start: 0.8820 (OUTLIER) cc_final: 0.7896 (mtm-85) REVERT: u 7 ARG cc_start: 0.7720 (tpp-160) cc_final: 0.7416 (tpt170) REVERT: u 9 ASP cc_start: 0.7932 (m-30) cc_final: 0.7730 (m-30) REVERT: w 24 ASN cc_start: 0.7762 (t0) cc_final: 0.7442 (t0) REVERT: w 53 LYS cc_start: 0.8184 (mppt) cc_final: 0.7601 (mtmm) REVERT: z 158 GLN cc_start: 0.6464 (OUTLIER) cc_final: 0.5036 (mm-40) outliers start: 121 outliers final: 48 residues processed: 820 average time/residue: 1.7075 time to fit residues: 1908.3352 Evaluate side-chains 767 residues out of total 2547 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 710 time to evaluate : 3.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 35 SER Chi-restraints excluded: chain 0 residue 66 THR Chi-restraints excluded: chain 2 residue 36 VAL Chi-restraints excluded: chain 4 residue 9 ILE Chi-restraints excluded: chain 4 residue 24 THR Chi-restraints excluded: chain 6 residue 8 SER Chi-restraints excluded: chain c residue 173 THR Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 60 VAL Chi-restraints excluded: chain d residue 97 SER Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain e residue 3 LEU Chi-restraints excluded: chain e residue 136 GLN Chi-restraints excluded: chain e residue 141 MET Chi-restraints excluded: chain e residue 178 VAL Chi-restraints excluded: chain f residue 12 VAL Chi-restraints excluded: chain f residue 68 THR Chi-restraints excluded: chain f residue 158 THR Chi-restraints excluded: chain g residue 36 THR Chi-restraints excluded: chain h residue 12 LEU Chi-restraints excluded: chain k residue 20 MET Chi-restraints excluded: chain k residue 69 VAL Chi-restraints excluded: chain k residue 104 THR Chi-restraints excluded: chain k residue 114 LYS Chi-restraints excluded: chain l residue 42 SER Chi-restraints excluded: chain l residue 91 ASP Chi-restraints excluded: chain l residue 93 ASN Chi-restraints excluded: chain l residue 106 GLU Chi-restraints excluded: chain l residue 120 VAL Chi-restraints excluded: chain m residue 54 THR Chi-restraints excluded: chain m residue 78 LEU Chi-restraints excluded: chain m residue 132 THR Chi-restraints excluded: chain n residue 57 THR Chi-restraints excluded: chain n residue 89 SER Chi-restraints excluded: chain n residue 113 ILE Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain o residue 47 VAL Chi-restraints excluded: chain o residue 69 ASP Chi-restraints excluded: chain o residue 74 VAL Chi-restraints excluded: chain o residue 100 HIS Chi-restraints excluded: chain p residue 33 VAL Chi-restraints excluded: chain p residue 41 GLN Chi-restraints excluded: chain p residue 76 THR Chi-restraints excluded: chain p residue 85 SER Chi-restraints excluded: chain p residue 106 LYS Chi-restraints excluded: chain q residue 18 LEU Chi-restraints excluded: chain q residue 104 VAL Chi-restraints excluded: chain s residue 53 SER Chi-restraints excluded: chain s residue 68 ASP Chi-restraints excluded: chain t residue 18 GLU Chi-restraints excluded: chain u residue 6 ARG Chi-restraints excluded: chain u residue 12 ILE Chi-restraints excluded: chain u residue 41 LEU Chi-restraints excluded: chain u residue 102 THR Chi-restraints excluded: chain y residue 81 SER Chi-restraints excluded: chain z residue 22 CYS Chi-restraints excluded: chain z residue 158 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 606 random chunks: chunk 544 optimal weight: 5.9990 chunk 414 optimal weight: 10.0000 chunk 286 optimal weight: 5.9990 chunk 61 optimal weight: 10.0000 chunk 263 optimal weight: 50.0000 chunk 370 optimal weight: 7.9990 chunk 553 optimal weight: 2.9990 chunk 585 optimal weight: 30.0000 chunk 289 optimal weight: 5.9990 chunk 524 optimal weight: 0.9990 chunk 157 optimal weight: 50.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 26 ASN 7 28 ASN d 58 ASN d 94 GLN d 130 GLN e 136 GLN e 165 HIS ** f 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 22 GLN ** g 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 73 ASN ** g 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 67 ASN j 86 GLN q 20 GLN q 44 GLN u 66 GLN w 12 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8750 moved from start: 0.2764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.077 98805 Z= 0.429 Angle : 0.657 11.108 148666 Z= 0.344 Chirality : 0.042 0.337 19119 Planarity : 0.005 0.088 7352 Dihedral : 24.514 178.664 51508 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 4.75 % Allowed : 23.29 % Favored : 71.96 % 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: -1.52 (0.14), residues: 3076 helix: -0.59 (0.18), residues: 818 sheet: -0.95 (0.19), residues: 684 loop : -1.18 (0.15), residues: 1574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP c 213 HIS 0.007 0.001 HIS s 7 PHE 0.015 0.002 PHE q 36 TYR 0.015 0.002 TYR s 38 ARG 0.010 0.001 ARG e 67 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 868 residues out of total 2547 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 747 time to evaluate : 3.843 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: d 1 MET cc_start: 0.7961 (OUTLIER) cc_final: 0.7149 (tmt) REVERT: e 156 ASN cc_start: 0.8915 (m-40) cc_final: 0.8445 (t0) REVERT: e 178 VAL cc_start: 0.9288 (OUTLIER) cc_final: 0.9080 (t) REVERT: f 100 PHE cc_start: 0.8258 (t80) cc_final: 0.8011 (t80) REVERT: g 62 TRP cc_start: 0.8153 (m100) cc_final: 0.7710 (m100) REVERT: g 88 GLN cc_start: 0.8147 (OUTLIER) cc_final: 0.7853 (tp-100) REVERT: g 101 ASN cc_start: 0.8661 (p0) cc_final: 0.8401 (p0) REVERT: g 115 HIS cc_start: 0.8632 (t70) cc_final: 0.8428 (t-90) REVERT: g 139 GLN cc_start: 0.9060 (tm-30) cc_final: 0.8777 (tm130) REVERT: h 12 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8287 (pp) REVERT: h 20 ASN cc_start: 0.8118 (t0) cc_final: 0.7812 (t0) REVERT: k 13 ASN cc_start: 0.9203 (p0) cc_final: 0.8984 (p0) REVERT: k 93 GLN cc_start: 0.8242 (mm-40) cc_final: 0.7982 (mm-40) REVERT: l 106 GLU cc_start: 0.7731 (OUTLIER) cc_final: 0.7347 (mt-10) REVERT: m 112 LEU cc_start: 0.9427 (tp) cc_final: 0.9180 (tp) REVERT: p 106 LYS cc_start: 0.6799 (OUTLIER) cc_final: 0.4434 (mptt) REVERT: u 6 ARG cc_start: 0.8776 (OUTLIER) cc_final: 0.7910 (mtt-85) REVERT: u 10 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.6985 (tt0) REVERT: u 22 ARG cc_start: 0.8829 (mtp180) cc_final: 0.8524 (mtp180) REVERT: w 24 ASN cc_start: 0.7916 (t0) cc_final: 0.7513 (t0) REVERT: w 53 LYS cc_start: 0.8240 (OUTLIER) cc_final: 0.7836 (mtmm) outliers start: 121 outliers final: 61 residues processed: 799 average time/residue: 1.7349 time to fit residues: 1908.2191 Evaluate side-chains 779 residues out of total 2547 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 709 time to evaluate : 3.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 2 SER Chi-restraints excluded: chain 0 residue 33 LEU Chi-restraints excluded: chain 0 residue 35 SER Chi-restraints excluded: chain 0 residue 66 THR Chi-restraints excluded: chain 2 residue 7 ILE Chi-restraints excluded: chain 2 residue 36 VAL Chi-restraints excluded: chain 3 residue 28 LEU Chi-restraints excluded: chain 4 residue 9 ILE Chi-restraints excluded: chain 4 residue 24 THR Chi-restraints excluded: chain 6 residue 8 SER Chi-restraints excluded: chain c residue 94 VAL Chi-restraints excluded: chain c residue 173 THR Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 16 THR Chi-restraints excluded: chain d residue 21 SER Chi-restraints excluded: chain d residue 60 VAL Chi-restraints excluded: chain d residue 97 SER Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain e residue 3 LEU Chi-restraints excluded: chain e residue 178 VAL Chi-restraints excluded: chain e residue 199 MET Chi-restraints excluded: chain f residue 12 VAL Chi-restraints excluded: chain f residue 13 VAL Chi-restraints excluded: chain f residue 40 VAL Chi-restraints excluded: chain f residue 44 ILE Chi-restraints excluded: chain f residue 68 THR Chi-restraints excluded: chain g residue 36 THR Chi-restraints excluded: chain g residue 88 GLN Chi-restraints excluded: chain h residue 12 LEU Chi-restraints excluded: chain h residue 37 VAL Chi-restraints excluded: chain k residue 20 MET Chi-restraints excluded: chain k residue 69 VAL Chi-restraints excluded: chain k residue 97 THR Chi-restraints excluded: chain k residue 104 THR Chi-restraints excluded: chain l residue 42 SER Chi-restraints excluded: chain l residue 73 ILE Chi-restraints excluded: chain l residue 91 ASP Chi-restraints excluded: chain l residue 93 ASN Chi-restraints excluded: chain l residue 106 GLU Chi-restraints excluded: chain l residue 116 VAL Chi-restraints excluded: chain l residue 118 THR Chi-restraints excluded: chain l residue 135 ILE Chi-restraints excluded: chain m residue 132 THR Chi-restraints excluded: chain n residue 57 THR Chi-restraints excluded: chain n residue 75 ILE Chi-restraints excluded: chain n residue 89 SER Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain o residue 47 VAL Chi-restraints excluded: chain o residue 69 ASP Chi-restraints excluded: chain o residue 74 VAL Chi-restraints excluded: chain o residue 100 HIS Chi-restraints excluded: chain p residue 5 ILE Chi-restraints excluded: chain p residue 33 VAL Chi-restraints excluded: chain p residue 41 GLN Chi-restraints excluded: chain p residue 76 THR Chi-restraints excluded: chain p residue 106 LYS Chi-restraints excluded: chain q residue 18 LEU Chi-restraints excluded: chain s residue 53 SER Chi-restraints excluded: chain s residue 107 VAL Chi-restraints excluded: chain t residue 18 GLU Chi-restraints excluded: chain t residue 33 LYS Chi-restraints excluded: chain u residue 6 ARG Chi-restraints excluded: chain u residue 10 GLU Chi-restraints excluded: chain u residue 41 LEU Chi-restraints excluded: chain u residue 102 THR Chi-restraints excluded: chain w residue 53 LYS Chi-restraints excluded: chain w residue 65 VAL Chi-restraints excluded: chain y residue 35 SER Chi-restraints excluded: chain z residue 22 CYS Chi-restraints excluded: chain z residue 157 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 606 random chunks: chunk 487 optimal weight: 6.9990 chunk 332 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 436 optimal weight: 6.9990 chunk 241 optimal weight: 8.9990 chunk 499 optimal weight: 3.9990 chunk 404 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 299 optimal weight: 5.9990 chunk 525 optimal weight: 3.9990 chunk 147 optimal weight: 4.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 26 ASN 7 28 ASN c 243 HIS d 94 GLN d 130 GLN e 136 GLN e 165 HIS ** f 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 135 GLN ** g 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 73 ASN g 143 GLN ** h 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 67 ASN p 75 GLN q 20 GLN q 44 GLN t 59 ASN w 12 GLN w 87 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8751 moved from start: 0.2975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.074 98805 Z= 0.413 Angle : 0.647 9.839 148666 Z= 0.338 Chirality : 0.041 0.341 19119 Planarity : 0.005 0.053 7352 Dihedral : 24.457 178.645 51508 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 4.95 % Allowed : 23.80 % Favored : 71.25 % 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: -1.20 (0.14), residues: 3076 helix: -0.21 (0.18), residues: 812 sheet: -0.74 (0.19), residues: 664 loop : -1.07 (0.15), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP g 62 HIS 0.006 0.001 HIS s 7 PHE 0.014 0.002 PHE f 99 TYR 0.016 0.002 TYR f 8 ARG 0.011 0.001 ARG 6 41 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 858 residues out of total 2547 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 732 time to evaluate : 3.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 10 ARG cc_start: 0.8920 (OUTLIER) cc_final: 0.8439 (mtt90) REVERT: c 132 MET cc_start: 0.8727 (OUTLIER) cc_final: 0.7997 (mmm) REVERT: c 269 ARG cc_start: 0.8183 (OUTLIER) cc_final: 0.7693 (ttm-80) REVERT: d 1 MET cc_start: 0.7883 (OUTLIER) cc_final: 0.7127 (tmt) REVERT: d 2 ILE cc_start: 0.8696 (pt) cc_final: 0.7288 (pp) REVERT: e 156 ASN cc_start: 0.8774 (m-40) cc_final: 0.8199 (t0) REVERT: e 178 VAL cc_start: 0.9295 (OUTLIER) cc_final: 0.9056 (t) REVERT: f 26 MET cc_start: 0.8826 (mmm) cc_final: 0.8603 (mmm) REVERT: g 62 TRP cc_start: 0.8181 (m100) cc_final: 0.7607 (m100) REVERT: g 88 GLN cc_start: 0.8088 (tt0) cc_final: 0.7865 (tp40) REVERT: g 101 ASN cc_start: 0.8666 (p0) cc_final: 0.8414 (p0) REVERT: g 130 GLU cc_start: 0.7237 (tp30) cc_final: 0.6848 (tp30) REVERT: g 139 GLN cc_start: 0.9065 (tm-30) cc_final: 0.8802 (tm130) REVERT: h 12 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.8181 (pp) REVERT: l 106 GLU cc_start: 0.7779 (OUTLIER) cc_final: 0.7392 (mt-10) REVERT: m 112 LEU cc_start: 0.9440 (tp) cc_final: 0.9205 (tp) REVERT: o 4 LYS cc_start: 0.8515 (OUTLIER) cc_final: 0.8308 (ttpp) REVERT: o 31 THR cc_start: 0.8923 (t) cc_final: 0.8645 (t) REVERT: p 106 LYS cc_start: 0.6910 (OUTLIER) cc_final: 0.4563 (mptt) REVERT: u 6 ARG cc_start: 0.8795 (OUTLIER) cc_final: 0.7860 (mtt-85) REVERT: u 10 GLU cc_start: 0.7879 (OUTLIER) cc_final: 0.7116 (tt0) REVERT: w 24 ASN cc_start: 0.7916 (t0) cc_final: 0.7492 (t0) REVERT: w 53 LYS cc_start: 0.8259 (OUTLIER) cc_final: 0.7888 (mtmm) outliers start: 126 outliers final: 60 residues processed: 793 average time/residue: 1.6831 time to fit residues: 1828.3375 Evaluate side-chains 780 residues out of total 2547 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 708 time to evaluate : 3.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 2 SER Chi-restraints excluded: chain 0 residue 33 LEU Chi-restraints excluded: chain 0 residue 35 SER Chi-restraints excluded: chain 0 residue 66 THR Chi-restraints excluded: chain 2 residue 7 ILE Chi-restraints excluded: chain 2 residue 36 VAL Chi-restraints excluded: chain 3 residue 10 ARG Chi-restraints excluded: chain 4 residue 9 ILE Chi-restraints excluded: chain 4 residue 24 THR Chi-restraints excluded: chain 6 residue 8 SER Chi-restraints excluded: chain c residue 94 VAL Chi-restraints excluded: chain c residue 132 MET Chi-restraints excluded: chain c residue 173 THR Chi-restraints excluded: chain c residue 268 VAL Chi-restraints excluded: chain c residue 269 ARG Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 16 THR Chi-restraints excluded: chain d residue 21 SER Chi-restraints excluded: chain d residue 60 VAL Chi-restraints excluded: chain d residue 97 SER Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain e residue 3 LEU Chi-restraints excluded: chain e residue 153 LEU Chi-restraints excluded: chain e residue 178 VAL Chi-restraints excluded: chain f residue 12 VAL Chi-restraints excluded: chain f residue 40 VAL Chi-restraints excluded: chain f residue 68 THR Chi-restraints excluded: chain g residue 36 THR Chi-restraints excluded: chain h residue 12 LEU Chi-restraints excluded: chain h residue 15 LEU Chi-restraints excluded: chain h residue 37 VAL Chi-restraints excluded: chain k residue 20 MET Chi-restraints excluded: chain k residue 69 VAL Chi-restraints excluded: chain k residue 97 THR Chi-restraints excluded: chain k residue 104 THR Chi-restraints excluded: chain k residue 113 MET Chi-restraints excluded: chain l residue 42 SER Chi-restraints excluded: chain l residue 73 ILE Chi-restraints excluded: chain l residue 106 GLU Chi-restraints excluded: chain l residue 116 VAL Chi-restraints excluded: chain m residue 54 THR Chi-restraints excluded: chain m residue 132 THR Chi-restraints excluded: chain n residue 57 THR Chi-restraints excluded: chain n residue 75 ILE Chi-restraints excluded: chain n residue 89 SER Chi-restraints excluded: chain o residue 4 LYS Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain o residue 47 VAL Chi-restraints excluded: chain o residue 69 ASP Chi-restraints excluded: chain o residue 74 VAL Chi-restraints excluded: chain o residue 100 HIS Chi-restraints excluded: chain p residue 5 ILE Chi-restraints excluded: chain p residue 33 VAL Chi-restraints excluded: chain p residue 41 GLN Chi-restraints excluded: chain p residue 76 THR Chi-restraints excluded: chain p residue 106 LYS Chi-restraints excluded: chain q residue 18 LEU Chi-restraints excluded: chain s residue 53 SER Chi-restraints excluded: chain s residue 101 SER Chi-restraints excluded: chain s residue 107 VAL Chi-restraints excluded: chain t residue 18 GLU Chi-restraints excluded: chain t residue 33 LYS Chi-restraints excluded: chain u residue 6 ARG Chi-restraints excluded: chain u residue 10 GLU Chi-restraints excluded: chain u residue 40 ASN Chi-restraints excluded: chain u residue 41 LEU Chi-restraints excluded: chain u residue 102 THR Chi-restraints excluded: chain w residue 53 LYS Chi-restraints excluded: chain w residue 55 GLU Chi-restraints excluded: chain w residue 65 VAL Chi-restraints excluded: chain y residue 35 SER Chi-restraints excluded: chain z residue 157 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 606 random chunks: chunk 197 optimal weight: 7.9990 chunk 527 optimal weight: 2.9990 chunk 115 optimal weight: 6.9990 chunk 343 optimal weight: 0.9990 chunk 144 optimal weight: 7.9990 chunk 586 optimal weight: 30.0000 chunk 486 optimal weight: 9.9990 chunk 271 optimal weight: 8.9990 chunk 48 optimal weight: 5.9990 chunk 193 optimal weight: 6.9990 chunk 307 optimal weight: 5.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 6 GLN 4 26 ASN 7 28 ASN d 94 GLN d 130 GLN e 165 HIS ** f 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 20 ASN j 67 ASN k 9 ASN o 98 GLN q 20 GLN q 44 GLN q 81 ASN t 59 ASN w 12 GLN z 158 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8760 moved from start: 0.3086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.083 98805 Z= 0.449 Angle : 0.665 8.747 148666 Z= 0.347 Chirality : 0.042 0.345 19119 Planarity : 0.005 0.052 7352 Dihedral : 24.447 178.241 51508 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 4.75 % Allowed : 24.86 % Favored : 70.38 % 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: -1.07 (0.15), residues: 3076 helix: -0.08 (0.18), residues: 818 sheet: -0.65 (0.20), residues: 653 loop : -1.01 (0.15), residues: 1605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP g 62 HIS 0.005 0.001 HIS s 7 PHE 0.018 0.002 PHE z 150 TYR 0.017 0.002 TYR f 8 ARG 0.010 0.001 ARG 6 41 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 838 residues out of total 2547 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 717 time to evaluate : 3.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 10 ARG cc_start: 0.8938 (OUTLIER) cc_final: 0.8482 (mtt90) REVERT: 8 36 ARG cc_start: 0.8712 (OUTLIER) cc_final: 0.8126 (ttt-90) REVERT: c 132 MET cc_start: 0.8695 (OUTLIER) cc_final: 0.7970 (mmm) REVERT: c 269 ARG cc_start: 0.8217 (OUTLIER) cc_final: 0.7719 (ttm-80) REVERT: d 1 MET cc_start: 0.7871 (OUTLIER) cc_final: 0.7055 (tmt) REVERT: d 2 ILE cc_start: 0.8682 (pt) cc_final: 0.7210 (pp) REVERT: e 88 ARG cc_start: 0.7856 (OUTLIER) cc_final: 0.7585 (mmm160) REVERT: e 156 ASN cc_start: 0.8816 (m-40) cc_final: 0.8228 (t0) REVERT: e 178 VAL cc_start: 0.9295 (OUTLIER) cc_final: 0.9071 (t) REVERT: f 26 MET cc_start: 0.8867 (mmm) cc_final: 0.8639 (mmm) REVERT: f 141 ILE cc_start: 0.5965 (OUTLIER) cc_final: 0.5559 (tt) REVERT: g 62 TRP cc_start: 0.8270 (m100) cc_final: 0.7816 (m100) REVERT: g 88 GLN cc_start: 0.8105 (OUTLIER) cc_final: 0.7799 (tp-100) REVERT: g 139 GLN cc_start: 0.9097 (tm-30) cc_final: 0.8853 (tm130) REVERT: h 12 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8199 (pp) REVERT: l 106 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.7417 (mt-10) REVERT: m 10 ARG cc_start: 0.8151 (OUTLIER) cc_final: 0.7381 (mtp85) REVERT: m 40 ARG cc_start: 0.9026 (OUTLIER) cc_final: 0.8637 (mtm180) REVERT: m 112 LEU cc_start: 0.9451 (tp) cc_final: 0.9218 (tp) REVERT: o 4 LYS cc_start: 0.8520 (OUTLIER) cc_final: 0.8305 (ttpp) REVERT: o 31 THR cc_start: 0.8985 (t) cc_final: 0.8755 (t) REVERT: t 93 LEU cc_start: 0.5628 (OUTLIER) cc_final: 0.5097 (tm) REVERT: u 6 ARG cc_start: 0.8800 (OUTLIER) cc_final: 0.7822 (mtm-85) REVERT: u 10 GLU cc_start: 0.7839 (OUTLIER) cc_final: 0.7168 (tt0) REVERT: w 24 ASN cc_start: 0.7861 (t0) cc_final: 0.7394 (t0) REVERT: w 53 LYS cc_start: 0.8243 (OUTLIER) cc_final: 0.7872 (mtmm) outliers start: 121 outliers final: 70 residues processed: 776 average time/residue: 1.7158 time to fit residues: 1823.0365 Evaluate side-chains 791 residues out of total 2547 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 703 time to evaluate : 3.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 2 SER Chi-restraints excluded: chain 0 residue 33 LEU Chi-restraints excluded: chain 0 residue 35 SER Chi-restraints excluded: chain 0 residue 66 THR Chi-restraints excluded: chain 1 residue 60 LYS Chi-restraints excluded: chain 2 residue 7 ILE Chi-restraints excluded: chain 2 residue 36 VAL Chi-restraints excluded: chain 3 residue 10 ARG Chi-restraints excluded: chain 4 residue 9 ILE Chi-restraints excluded: chain 6 residue 8 SER Chi-restraints excluded: chain 8 residue 36 ARG Chi-restraints excluded: chain c residue 94 VAL Chi-restraints excluded: chain c residue 132 MET Chi-restraints excluded: chain c residue 165 VAL Chi-restraints excluded: chain c residue 173 THR Chi-restraints excluded: chain c residue 269 ARG Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 16 THR Chi-restraints excluded: chain d residue 21 SER Chi-restraints excluded: chain d residue 60 VAL Chi-restraints excluded: chain d residue 97 SER Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain e residue 3 LEU Chi-restraints excluded: chain e residue 88 ARG Chi-restraints excluded: chain e residue 153 LEU Chi-restraints excluded: chain e residue 178 VAL Chi-restraints excluded: chain f residue 40 VAL Chi-restraints excluded: chain f residue 68 THR Chi-restraints excluded: chain f residue 81 GLN Chi-restraints excluded: chain f residue 103 LEU Chi-restraints excluded: chain f residue 141 ILE Chi-restraints excluded: chain g residue 36 THR Chi-restraints excluded: chain g residue 39 ASP Chi-restraints excluded: chain g residue 88 GLN Chi-restraints excluded: chain h residue 12 LEU Chi-restraints excluded: chain h residue 37 VAL Chi-restraints excluded: chain j residue 45 THR Chi-restraints excluded: chain k residue 20 MET Chi-restraints excluded: chain k residue 69 VAL Chi-restraints excluded: chain k residue 97 THR Chi-restraints excluded: chain k residue 104 THR Chi-restraints excluded: chain k residue 113 MET Chi-restraints excluded: chain l residue 42 SER Chi-restraints excluded: chain l residue 73 ILE Chi-restraints excluded: chain l residue 91 ASP Chi-restraints excluded: chain l residue 106 GLU Chi-restraints excluded: chain l residue 116 VAL Chi-restraints excluded: chain m residue 10 ARG Chi-restraints excluded: chain m residue 40 ARG Chi-restraints excluded: chain m residue 54 THR Chi-restraints excluded: chain m residue 63 ILE Chi-restraints excluded: chain m residue 132 THR Chi-restraints excluded: chain n residue 1 MET Chi-restraints excluded: chain n residue 57 THR Chi-restraints excluded: chain n residue 75 ILE Chi-restraints excluded: chain n residue 89 SER Chi-restraints excluded: chain o residue 4 LYS Chi-restraints excluded: chain o residue 5 SER Chi-restraints excluded: chain o residue 12 THR Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain o residue 47 VAL Chi-restraints excluded: chain o residue 69 ASP Chi-restraints excluded: chain o residue 74 VAL Chi-restraints excluded: chain o residue 98 GLN Chi-restraints excluded: chain o residue 100 HIS Chi-restraints excluded: chain p residue 5 ILE Chi-restraints excluded: chain p residue 33 VAL Chi-restraints excluded: chain p residue 36 SER Chi-restraints excluded: chain p residue 41 GLN Chi-restraints excluded: chain p residue 76 THR Chi-restraints excluded: chain q residue 18 LEU Chi-restraints excluded: chain s residue 53 SER Chi-restraints excluded: chain s residue 101 SER Chi-restraints excluded: chain s residue 107 VAL Chi-restraints excluded: chain t residue 18 GLU Chi-restraints excluded: chain t residue 26 LYS Chi-restraints excluded: chain t residue 30 ILE Chi-restraints excluded: chain t residue 33 LYS Chi-restraints excluded: chain t residue 93 LEU Chi-restraints excluded: chain u residue 6 ARG Chi-restraints excluded: chain u residue 10 GLU Chi-restraints excluded: chain u residue 34 VAL Chi-restraints excluded: chain u residue 41 LEU Chi-restraints excluded: chain u residue 102 THR Chi-restraints excluded: chain w residue 53 LYS Chi-restraints excluded: chain w residue 55 GLU Chi-restraints excluded: chain w residue 65 VAL Chi-restraints excluded: chain y residue 35 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 606 random chunks: chunk 565 optimal weight: 2.9990 chunk 66 optimal weight: 10.0000 chunk 334 optimal weight: 5.9990 chunk 428 optimal weight: 20.0000 chunk 331 optimal weight: 10.0000 chunk 493 optimal weight: 0.8980 chunk 327 optimal weight: 5.9990 chunk 584 optimal weight: 30.0000 chunk 365 optimal weight: 3.9990 chunk 356 optimal weight: 3.9990 chunk 269 optimal weight: 40.0000 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 26 ASN 7 28 ASN d 94 GLN d 130 GLN e 165 HIS g 30 ASN ** g 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 20 ASN j 67 ASN k 9 ASN o 98 GLN p 75 GLN q 20 GLN q 44 GLN t 59 ASN u 40 ASN w 12 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8741 moved from start: 0.3170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 98805 Z= 0.359 Angle : 0.626 8.715 148666 Z= 0.329 Chirality : 0.039 0.330 19119 Planarity : 0.005 0.052 7352 Dihedral : 24.435 178.583 51508 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 4.44 % Allowed : 26.28 % Favored : 69.29 % 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: -0.91 (0.15), residues: 3076 helix: 0.06 (0.18), residues: 820 sheet: -0.52 (0.20), residues: 648 loop : -0.93 (0.15), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP c 248 HIS 0.004 0.001 HIS r 89 PHE 0.012 0.002 PHE m 68 TYR 0.018 0.002 TYR h 25 ARG 0.012 0.001 ARG 6 41 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 830 residues out of total 2547 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 717 time to evaluate : 3.801 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: 3 10 ARG cc_start: 0.8887 (OUTLIER) cc_final: 0.8404 (mtt90) REVERT: 4 27 LYS cc_start: 0.8349 (mmmm) cc_final: 0.8029 (mmmm) REVERT: 8 36 ARG cc_start: 0.8687 (OUTLIER) cc_final: 0.8146 (ttt-90) REVERT: c 132 MET cc_start: 0.8700 (OUTLIER) cc_final: 0.7984 (mmm) REVERT: c 269 ARG cc_start: 0.8185 (OUTLIER) cc_final: 0.7694 (ttm-80) REVERT: d 1 MET cc_start: 0.7866 (OUTLIER) cc_final: 0.7056 (tmt) REVERT: d 2 ILE cc_start: 0.8675 (OUTLIER) cc_final: 0.7209 (pp) REVERT: e 88 ARG cc_start: 0.7850 (OUTLIER) cc_final: 0.7648 (mmm160) REVERT: e 156 ASN cc_start: 0.8842 (m-40) cc_final: 0.8234 (t0) REVERT: e 178 VAL cc_start: 0.9283 (OUTLIER) cc_final: 0.9066 (t) REVERT: f 141 ILE cc_start: 0.5884 (OUTLIER) cc_final: 0.5497 (tt) REVERT: g 62 TRP cc_start: 0.8243 (m100) cc_final: 0.7694 (m100) REVERT: g 139 GLN cc_start: 0.9082 (tm-30) cc_final: 0.8858 (tm130) REVERT: k 106 GLU cc_start: 0.7643 (mp0) cc_final: 0.7432 (mp0) REVERT: l 106 GLU cc_start: 0.7786 (OUTLIER) cc_final: 0.7408 (mt-10) REVERT: m 10 ARG cc_start: 0.8140 (OUTLIER) cc_final: 0.7557 (mtp85) REVERT: m 40 ARG cc_start: 0.8993 (OUTLIER) cc_final: 0.8603 (mtm180) REVERT: m 112 LEU cc_start: 0.9463 (tp) cc_final: 0.9238 (tp) REVERT: o 4 LYS cc_start: 0.8498 (OUTLIER) cc_final: 0.8285 (ttpp) REVERT: o 31 THR cc_start: 0.8939 (t) cc_final: 0.8680 (t) REVERT: u 6 ARG cc_start: 0.8779 (OUTLIER) cc_final: 0.7805 (mtm-85) REVERT: u 10 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.7159 (tt0) REVERT: w 24 ASN cc_start: 0.7827 (t0) cc_final: 0.7370 (t0) REVERT: w 53 LYS cc_start: 0.8185 (OUTLIER) cc_final: 0.7857 (mtmm) outliers start: 113 outliers final: 70 residues processed: 766 average time/residue: 1.6975 time to fit residues: 1779.8911 Evaluate side-chains 796 residues out of total 2547 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 710 time to evaluate : 3.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 2 SER Chi-restraints excluded: chain 0 residue 33 LEU Chi-restraints excluded: chain 0 residue 35 SER Chi-restraints excluded: chain 2 residue 36 VAL Chi-restraints excluded: chain 3 residue 10 ARG Chi-restraints excluded: chain 4 residue 9 ILE Chi-restraints excluded: chain 6 residue 8 SER Chi-restraints excluded: chain 8 residue 36 ARG Chi-restraints excluded: chain c residue 94 VAL Chi-restraints excluded: chain c residue 132 MET Chi-restraints excluded: chain c residue 165 VAL Chi-restraints excluded: chain c residue 173 THR Chi-restraints excluded: chain c residue 268 VAL Chi-restraints excluded: chain c residue 269 ARG Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 2 ILE Chi-restraints excluded: chain d residue 16 THR Chi-restraints excluded: chain d residue 21 SER Chi-restraints excluded: chain d residue 60 VAL Chi-restraints excluded: chain d residue 97 SER Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 151 THR Chi-restraints excluded: chain e residue 3 LEU Chi-restraints excluded: chain e residue 88 ARG Chi-restraints excluded: chain e residue 153 LEU Chi-restraints excluded: chain e residue 178 VAL Chi-restraints excluded: chain f residue 40 VAL Chi-restraints excluded: chain f residue 81 GLN Chi-restraints excluded: chain f residue 103 LEU Chi-restraints excluded: chain f residue 141 ILE Chi-restraints excluded: chain g residue 36 THR Chi-restraints excluded: chain g residue 39 ASP Chi-restraints excluded: chain g residue 47 ASP Chi-restraints excluded: chain h residue 37 VAL Chi-restraints excluded: chain j residue 45 THR Chi-restraints excluded: chain k residue 20 MET Chi-restraints excluded: chain k residue 69 VAL Chi-restraints excluded: chain k residue 97 THR Chi-restraints excluded: chain k residue 104 THR Chi-restraints excluded: chain k residue 113 MET Chi-restraints excluded: chain l residue 42 SER Chi-restraints excluded: chain l residue 73 ILE Chi-restraints excluded: chain l residue 91 ASP Chi-restraints excluded: chain l residue 106 GLU Chi-restraints excluded: chain l residue 116 VAL Chi-restraints excluded: chain l residue 117 THR Chi-restraints excluded: chain m residue 10 ARG Chi-restraints excluded: chain m residue 40 ARG Chi-restraints excluded: chain m residue 54 THR Chi-restraints excluded: chain m residue 119 LEU Chi-restraints excluded: chain m residue 132 THR Chi-restraints excluded: chain n residue 1 MET Chi-restraints excluded: chain n residue 57 THR Chi-restraints excluded: chain n residue 89 SER Chi-restraints excluded: chain o residue 4 LYS Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain o residue 47 VAL Chi-restraints excluded: chain o residue 69 ASP Chi-restraints excluded: chain o residue 74 VAL Chi-restraints excluded: chain o residue 95 SER Chi-restraints excluded: chain o residue 100 HIS Chi-restraints excluded: chain p residue 33 VAL Chi-restraints excluded: chain p residue 36 SER Chi-restraints excluded: chain p residue 41 GLN Chi-restraints excluded: chain p residue 76 THR Chi-restraints excluded: chain p residue 85 SER Chi-restraints excluded: chain q residue 18 LEU Chi-restraints excluded: chain r residue 32 THR Chi-restraints excluded: chain s residue 53 SER Chi-restraints excluded: chain s residue 101 SER Chi-restraints excluded: chain s residue 107 VAL Chi-restraints excluded: chain s residue 109 ASP Chi-restraints excluded: chain t residue 18 GLU Chi-restraints excluded: chain t residue 26 LYS Chi-restraints excluded: chain t residue 30 ILE Chi-restraints excluded: chain u residue 6 ARG Chi-restraints excluded: chain u residue 10 GLU Chi-restraints excluded: chain u residue 12 ILE Chi-restraints excluded: chain u residue 34 VAL Chi-restraints excluded: chain u residue 40 ASN Chi-restraints excluded: chain u residue 41 LEU Chi-restraints excluded: chain u residue 102 THR Chi-restraints excluded: chain w residue 53 LYS Chi-restraints excluded: chain w residue 55 GLU Chi-restraints excluded: chain y residue 35 SER Chi-restraints excluded: chain y residue 81 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 606 random chunks: chunk 361 optimal weight: 1.9990 chunk 233 optimal weight: 5.9990 chunk 348 optimal weight: 3.9990 chunk 175 optimal weight: 5.9990 chunk 114 optimal weight: 5.9990 chunk 113 optimal weight: 6.9990 chunk 371 optimal weight: 3.9990 chunk 397 optimal weight: 4.9990 chunk 288 optimal weight: 6.9990 chunk 54 optimal weight: 5.9990 chunk 459 optimal weight: 0.7980 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 26 ASN 7 28 ASN c 117 GLN d 94 GLN d 130 GLN e 165 HIS ** g 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 88 GLN g 143 GLN h 20 ASN j 67 ASN k 9 ASN q 20 GLN q 44 GLN t 48 GLN t 59 ASN w 12 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.3201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 98805 Z= 0.325 Angle : 0.615 9.702 148666 Z= 0.323 Chirality : 0.038 0.323 19119 Planarity : 0.005 0.051 7352 Dihedral : 24.428 178.791 51508 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 4.36 % Allowed : 26.32 % Favored : 69.32 % 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: -0.86 (0.15), residues: 3076 helix: 0.14 (0.19), residues: 820 sheet: -0.54 (0.20), residues: 665 loop : -0.90 (0.15), residues: 1591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP c 248 HIS 0.004 0.001 HIS s 60 PHE 0.012 0.001 PHE m 68 TYR 0.023 0.002 TYR h 25 ARG 0.012 0.001 ARG 6 41 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 834 residues out of total 2547 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 723 time to evaluate : 3.773 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: 3 10 ARG cc_start: 0.8873 (OUTLIER) cc_final: 0.8395 (mtt90) REVERT: 3 31 ASP cc_start: 0.8292 (t70) cc_final: 0.8090 (t70) REVERT: 4 27 LYS cc_start: 0.8372 (mmmm) cc_final: 0.8040 (mmmm) REVERT: 6 1 MET cc_start: 0.7382 (mpp) cc_final: 0.7042 (mpp) REVERT: 8 36 ARG cc_start: 0.8683 (OUTLIER) cc_final: 0.8137 (ttt-90) REVERT: c 72 ASP cc_start: 0.7772 (m-30) cc_final: 0.7556 (m-30) REVERT: c 269 ARG cc_start: 0.8190 (OUTLIER) cc_final: 0.7699 (ttm-80) REVERT: d 1 MET cc_start: 0.7862 (OUTLIER) cc_final: 0.7039 (tmt) REVERT: d 2 ILE cc_start: 0.8672 (OUTLIER) cc_final: 0.7197 (pp) REVERT: e 156 ASN cc_start: 0.8843 (m-40) cc_final: 0.8218 (t0) REVERT: e 178 VAL cc_start: 0.9281 (OUTLIER) cc_final: 0.9069 (t) REVERT: f 141 ILE cc_start: 0.5878 (OUTLIER) cc_final: 0.5493 (tt) REVERT: g 62 TRP cc_start: 0.8107 (m100) cc_final: 0.7687 (m100) REVERT: g 139 GLN cc_start: 0.9078 (tm-30) cc_final: 0.8863 (tm130) REVERT: l 106 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.7382 (mt-10) REVERT: m 10 ARG cc_start: 0.8144 (OUTLIER) cc_final: 0.7386 (mtp85) REVERT: m 40 ARG cc_start: 0.8991 (OUTLIER) cc_final: 0.8598 (mtm180) REVERT: m 112 LEU cc_start: 0.9447 (tp) cc_final: 0.9221 (tp) REVERT: o 4 LYS cc_start: 0.8494 (OUTLIER) cc_final: 0.8280 (ttpp) REVERT: o 31 THR cc_start: 0.8907 (t) cc_final: 0.8642 (t) REVERT: t 18 GLU cc_start: 0.7311 (OUTLIER) cc_final: 0.7101 (tm-30) REVERT: t 93 LEU cc_start: 0.5466 (OUTLIER) cc_final: 0.4998 (tm) REVERT: u 6 ARG cc_start: 0.8780 (OUTLIER) cc_final: 0.7799 (mtm-85) REVERT: u 10 GLU cc_start: 0.7811 (OUTLIER) cc_final: 0.7150 (tt0) REVERT: w 24 ASN cc_start: 0.7909 (t0) cc_final: 0.7443 (t0) outliers start: 111 outliers final: 69 residues processed: 768 average time/residue: 1.6893 time to fit residues: 1783.5703 Evaluate side-chains 793 residues out of total 2547 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 709 time to evaluate : 3.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 2 SER Chi-restraints excluded: chain 0 residue 33 LEU Chi-restraints excluded: chain 0 residue 35 SER Chi-restraints excluded: chain 2 residue 36 VAL Chi-restraints excluded: chain 3 residue 10 ARG Chi-restraints excluded: chain 4 residue 9 ILE Chi-restraints excluded: chain 6 residue 8 SER Chi-restraints excluded: chain 8 residue 36 ARG Chi-restraints excluded: chain c residue 94 VAL Chi-restraints excluded: chain c residue 165 VAL Chi-restraints excluded: chain c residue 173 THR Chi-restraints excluded: chain c residue 268 VAL Chi-restraints excluded: chain c residue 269 ARG Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 2 ILE Chi-restraints excluded: chain d residue 16 THR Chi-restraints excluded: chain d residue 21 SER Chi-restraints excluded: chain d residue 60 VAL Chi-restraints excluded: chain d residue 97 SER Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 151 THR Chi-restraints excluded: chain e residue 3 LEU Chi-restraints excluded: chain e residue 153 LEU Chi-restraints excluded: chain e residue 178 VAL Chi-restraints excluded: chain f residue 13 VAL Chi-restraints excluded: chain f residue 40 VAL Chi-restraints excluded: chain f residue 68 THR Chi-restraints excluded: chain f residue 81 GLN Chi-restraints excluded: chain f residue 103 LEU Chi-restraints excluded: chain f residue 141 ILE Chi-restraints excluded: chain f residue 144 ASP Chi-restraints excluded: chain g residue 36 THR Chi-restraints excluded: chain g residue 39 ASP Chi-restraints excluded: chain g residue 47 ASP Chi-restraints excluded: chain h residue 37 VAL Chi-restraints excluded: chain j residue 45 THR Chi-restraints excluded: chain k residue 20 MET Chi-restraints excluded: chain k residue 69 VAL Chi-restraints excluded: chain k residue 104 THR Chi-restraints excluded: chain k residue 113 MET Chi-restraints excluded: chain l residue 42 SER Chi-restraints excluded: chain l residue 73 ILE Chi-restraints excluded: chain l residue 91 ASP Chi-restraints excluded: chain l residue 106 GLU Chi-restraints excluded: chain l residue 116 VAL Chi-restraints excluded: chain l residue 117 THR Chi-restraints excluded: chain m residue 10 ARG Chi-restraints excluded: chain m residue 40 ARG Chi-restraints excluded: chain m residue 54 THR Chi-restraints excluded: chain m residue 132 THR Chi-restraints excluded: chain n residue 1 MET Chi-restraints excluded: chain n residue 57 THR Chi-restraints excluded: chain n residue 89 SER Chi-restraints excluded: chain o residue 4 LYS Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain o residue 47 VAL Chi-restraints excluded: chain o residue 69 ASP Chi-restraints excluded: chain o residue 74 VAL Chi-restraints excluded: chain o residue 100 HIS Chi-restraints excluded: chain p residue 5 ILE Chi-restraints excluded: chain p residue 33 VAL Chi-restraints excluded: chain p residue 36 SER Chi-restraints excluded: chain p residue 41 GLN Chi-restraints excluded: chain p residue 76 THR Chi-restraints excluded: chain q residue 18 LEU Chi-restraints excluded: chain r residue 32 THR Chi-restraints excluded: chain r residue 48 LYS Chi-restraints excluded: chain r residue 102 SER Chi-restraints excluded: chain s residue 53 SER Chi-restraints excluded: chain s residue 101 SER Chi-restraints excluded: chain s residue 107 VAL Chi-restraints excluded: chain s residue 109 ASP Chi-restraints excluded: chain t residue 18 GLU Chi-restraints excluded: chain t residue 26 LYS Chi-restraints excluded: chain t residue 93 LEU Chi-restraints excluded: chain u residue 6 ARG Chi-restraints excluded: chain u residue 10 GLU Chi-restraints excluded: chain u residue 12 ILE Chi-restraints excluded: chain u residue 34 VAL Chi-restraints excluded: chain u residue 102 THR Chi-restraints excluded: chain w residue 55 GLU Chi-restraints excluded: chain w residue 65 VAL Chi-restraints excluded: chain y residue 35 SER Chi-restraints excluded: chain y residue 81 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 606 random chunks: chunk 531 optimal weight: 6.9990 chunk 559 optimal weight: 5.9990 chunk 510 optimal weight: 3.9990 chunk 544 optimal weight: 0.9990 chunk 327 optimal weight: 6.9990 chunk 237 optimal weight: 10.0000 chunk 427 optimal weight: 4.9990 chunk 167 optimal weight: 6.9990 chunk 491 optimal weight: 3.9990 chunk 514 optimal weight: 7.9990 chunk 542 optimal weight: 0.7980 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 26 ASN 7 28 ASN c 117 GLN d 94 GLN d 130 GLN e 165 HIS g 22 GLN ** g 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 20 ASN j 67 ASN k 9 ASN o 98 GLN q 20 GLN q 44 GLN t 59 ASN u 40 ASN w 12 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.3250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 98805 Z= 0.307 Angle : 0.608 9.063 148666 Z= 0.319 Chirality : 0.038 0.320 19119 Planarity : 0.005 0.051 7352 Dihedral : 24.409 179.054 51508 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 3.97 % Allowed : 27.02 % Favored : 69.01 % 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: -0.78 (0.15), residues: 3076 helix: 0.21 (0.19), residues: 816 sheet: -0.51 (0.20), residues: 660 loop : -0.84 (0.15), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP c 248 HIS 0.005 0.001 HIS w 44 PHE 0.012 0.001 PHE m 68 TYR 0.031 0.002 TYR g 58 ARG 0.013 0.001 ARG 6 41 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 820 residues out of total 2547 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 719 time to evaluate : 3.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 10 ARG cc_start: 0.8840 (OUTLIER) cc_final: 0.8355 (mtt90) REVERT: 3 31 ASP cc_start: 0.8289 (t70) cc_final: 0.8084 (t70) REVERT: 4 27 LYS cc_start: 0.8371 (mmmm) cc_final: 0.8137 (mmmm) REVERT: 6 1 MET cc_start: 0.7422 (mpp) cc_final: 0.7074 (mpp) REVERT: 8 36 ARG cc_start: 0.8675 (OUTLIER) cc_final: 0.8128 (ttt-90) REVERT: c 269 ARG cc_start: 0.8188 (OUTLIER) cc_final: 0.7697 (ttm-80) REVERT: d 1 MET cc_start: 0.7857 (OUTLIER) cc_final: 0.7037 (tmt) REVERT: d 2 ILE cc_start: 0.8681 (OUTLIER) cc_final: 0.7226 (pp) REVERT: e 156 ASN cc_start: 0.8844 (m-40) cc_final: 0.8210 (t0) REVERT: e 178 VAL cc_start: 0.9273 (OUTLIER) cc_final: 0.9067 (t) REVERT: f 103 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8573 (tt) REVERT: f 141 ILE cc_start: 0.5958 (OUTLIER) cc_final: 0.5565 (tt) REVERT: g 62 TRP cc_start: 0.8126 (m100) cc_final: 0.7698 (m100) REVERT: g 139 GLN cc_start: 0.9071 (tm-30) cc_final: 0.8861 (tm130) REVERT: l 106 GLU cc_start: 0.7712 (OUTLIER) cc_final: 0.7354 (mt-10) REVERT: m 10 ARG cc_start: 0.8150 (OUTLIER) cc_final: 0.7381 (mtp85) REVERT: m 40 ARG cc_start: 0.8991 (OUTLIER) cc_final: 0.8591 (mtm180) REVERT: m 112 LEU cc_start: 0.9445 (tp) cc_final: 0.9221 (tp) REVERT: o 4 LYS cc_start: 0.8493 (OUTLIER) cc_final: 0.8279 (ttpp) REVERT: o 31 THR cc_start: 0.8880 (t) cc_final: 0.8615 (t) REVERT: s 59 GLU cc_start: 0.7568 (tp30) cc_final: 0.7153 (tp30) REVERT: t 18 GLU cc_start: 0.7294 (OUTLIER) cc_final: 0.7084 (tm-30) REVERT: t 93 LEU cc_start: 0.5409 (OUTLIER) cc_final: 0.4962 (tm) REVERT: u 6 ARG cc_start: 0.8772 (OUTLIER) cc_final: 0.7800 (mtm-85) REVERT: u 10 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.7140 (tt0) REVERT: w 24 ASN cc_start: 0.7903 (t0) cc_final: 0.7435 (t0) outliers start: 101 outliers final: 68 residues processed: 762 average time/residue: 1.6665 time to fit residues: 1740.7785 Evaluate side-chains 795 residues out of total 2547 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 711 time to evaluate : 3.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 2 SER Chi-restraints excluded: chain 0 residue 33 LEU Chi-restraints excluded: chain 0 residue 35 SER Chi-restraints excluded: chain 2 residue 36 VAL Chi-restraints excluded: chain 3 residue 10 ARG Chi-restraints excluded: chain 4 residue 9 ILE Chi-restraints excluded: chain 6 residue 8 SER Chi-restraints excluded: chain 8 residue 36 ARG Chi-restraints excluded: chain c residue 94 VAL Chi-restraints excluded: chain c residue 165 VAL Chi-restraints excluded: chain c residue 173 THR Chi-restraints excluded: chain c residue 268 VAL Chi-restraints excluded: chain c residue 269 ARG Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 2 ILE Chi-restraints excluded: chain d residue 16 THR Chi-restraints excluded: chain d residue 21 SER Chi-restraints excluded: chain d residue 97 SER Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 151 THR Chi-restraints excluded: chain e residue 3 LEU Chi-restraints excluded: chain e residue 153 LEU Chi-restraints excluded: chain e residue 178 VAL Chi-restraints excluded: chain f residue 13 VAL Chi-restraints excluded: chain f residue 40 VAL Chi-restraints excluded: chain f residue 68 THR Chi-restraints excluded: chain f residue 90 THR Chi-restraints excluded: chain f residue 103 LEU Chi-restraints excluded: chain f residue 141 ILE Chi-restraints excluded: chain g residue 36 THR Chi-restraints excluded: chain g residue 47 ASP Chi-restraints excluded: chain h residue 37 VAL Chi-restraints excluded: chain j residue 45 THR Chi-restraints excluded: chain k residue 20 MET Chi-restraints excluded: chain k residue 69 VAL Chi-restraints excluded: chain k residue 97 THR Chi-restraints excluded: chain k residue 104 THR Chi-restraints excluded: chain k residue 113 MET Chi-restraints excluded: chain l residue 42 SER Chi-restraints excluded: chain l residue 73 ILE Chi-restraints excluded: chain l residue 106 GLU Chi-restraints excluded: chain l residue 116 VAL Chi-restraints excluded: chain l residue 117 THR Chi-restraints excluded: chain m residue 10 ARG Chi-restraints excluded: chain m residue 40 ARG Chi-restraints excluded: chain m residue 132 THR Chi-restraints excluded: chain n residue 1 MET Chi-restraints excluded: chain n residue 57 THR Chi-restraints excluded: chain n residue 89 SER Chi-restraints excluded: chain o residue 4 LYS Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain o residue 47 VAL Chi-restraints excluded: chain o residue 69 ASP Chi-restraints excluded: chain o residue 74 VAL Chi-restraints excluded: chain o residue 98 GLN Chi-restraints excluded: chain o residue 100 HIS Chi-restraints excluded: chain p residue 5 ILE Chi-restraints excluded: chain p residue 33 VAL Chi-restraints excluded: chain p residue 36 SER Chi-restraints excluded: chain p residue 41 GLN Chi-restraints excluded: chain p residue 76 THR Chi-restraints excluded: chain q residue 18 LEU Chi-restraints excluded: chain r residue 32 THR Chi-restraints excluded: chain r residue 48 LYS Chi-restraints excluded: chain r residue 102 SER Chi-restraints excluded: chain s residue 53 SER Chi-restraints excluded: chain s residue 66 ILE Chi-restraints excluded: chain s residue 101 SER Chi-restraints excluded: chain s residue 107 VAL Chi-restraints excluded: chain s residue 109 ASP Chi-restraints excluded: chain t residue 18 GLU Chi-restraints excluded: chain t residue 26 LYS Chi-restraints excluded: chain t residue 93 LEU Chi-restraints excluded: chain u residue 6 ARG Chi-restraints excluded: chain u residue 10 GLU Chi-restraints excluded: chain u residue 12 ILE Chi-restraints excluded: chain u residue 34 VAL Chi-restraints excluded: chain u residue 40 ASN Chi-restraints excluded: chain u residue 102 THR Chi-restraints excluded: chain w residue 55 GLU Chi-restraints excluded: chain w residue 65 VAL Chi-restraints excluded: chain y residue 35 SER Chi-restraints excluded: chain y residue 66 LYS Chi-restraints excluded: chain y residue 81 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 606 random chunks: chunk 357 optimal weight: 6.9990 chunk 575 optimal weight: 20.0000 chunk 351 optimal weight: 3.9990 chunk 273 optimal weight: 6.9990 chunk 400 optimal weight: 3.9990 chunk 603 optimal weight: 30.0000 chunk 555 optimal weight: 0.8980 chunk 480 optimal weight: 6.9990 chunk 49 optimal weight: 6.9990 chunk 371 optimal weight: 0.8980 chunk 294 optimal weight: 6.9990 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 26 ASN 7 28 ASN d 94 GLN d 130 GLN e 165 HIS g 22 GLN h 20 ASN j 67 ASN k 9 ASN o 98 GLN q 20 GLN u 40 ASN w 12 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 moved from start: 0.3292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 98805 Z= 0.342 Angle : 0.619 9.226 148666 Z= 0.325 Chirality : 0.038 0.322 19119 Planarity : 0.005 0.050 7352 Dihedral : 24.377 179.042 51508 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 3.73 % Allowed : 27.34 % Favored : 68.93 % 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: -0.74 (0.15), residues: 3076 helix: 0.25 (0.19), residues: 816 sheet: -0.46 (0.20), residues: 644 loop : -0.83 (0.15), residues: 1616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP c 248 HIS 0.004 0.001 HIS c 200 PHE 0.020 0.002 PHE o 97 TYR 0.027 0.002 TYR h 25 ARG 0.010 0.001 ARG 2 11 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 806 residues out of total 2547 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 711 time to evaluate : 3.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 10 ARG cc_start: 0.8890 (OUTLIER) cc_final: 0.8417 (mtt90) REVERT: 3 31 ASP cc_start: 0.8292 (t70) cc_final: 0.8086 (t70) REVERT: 4 7 GLU cc_start: 0.6719 (tm-30) cc_final: 0.6417 (pp20) REVERT: 8 36 ARG cc_start: 0.8671 (OUTLIER) cc_final: 0.8109 (ttt-90) REVERT: d 1 MET cc_start: 0.7855 (OUTLIER) cc_final: 0.7053 (tmt) REVERT: d 2 ILE cc_start: 0.8683 (OUTLIER) cc_final: 0.7233 (pp) REVERT: e 88 ARG cc_start: 0.7835 (OUTLIER) cc_final: 0.7607 (mmm160) REVERT: e 156 ASN cc_start: 0.8852 (m-40) cc_final: 0.8232 (t0) REVERT: e 178 VAL cc_start: 0.9268 (OUTLIER) cc_final: 0.9062 (t) REVERT: f 141 ILE cc_start: 0.5808 (OUTLIER) cc_final: 0.5429 (tt) REVERT: g 62 TRP cc_start: 0.8137 (m100) cc_final: 0.7701 (m100) REVERT: g 139 GLN cc_start: 0.9081 (tm-30) cc_final: 0.8873 (tm130) REVERT: k 106 GLU cc_start: 0.7444 (mp0) cc_final: 0.7057 (mp0) REVERT: m 10 ARG cc_start: 0.8151 (OUTLIER) cc_final: 0.7381 (mtp85) REVERT: m 40 ARG cc_start: 0.8999 (OUTLIER) cc_final: 0.8607 (mtm180) REVERT: m 112 LEU cc_start: 0.9462 (tp) cc_final: 0.9250 (tp) REVERT: o 4 LYS cc_start: 0.8504 (OUTLIER) cc_final: 0.8282 (ttpp) REVERT: o 31 THR cc_start: 0.8886 (t) cc_final: 0.8622 (t) REVERT: t 18 GLU cc_start: 0.7300 (OUTLIER) cc_final: 0.7096 (tm-30) REVERT: t 93 LEU cc_start: 0.5192 (OUTLIER) cc_final: 0.4763 (tm) REVERT: u 6 ARG cc_start: 0.8807 (OUTLIER) cc_final: 0.7815 (mtm-85) REVERT: u 10 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.7140 (tt0) REVERT: w 24 ASN cc_start: 0.7914 (t0) cc_final: 0.7439 (t0) outliers start: 95 outliers final: 72 residues processed: 755 average time/residue: 1.7186 time to fit residues: 1786.5488 Evaluate side-chains 791 residues out of total 2547 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 705 time to evaluate : 3.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 2 SER Chi-restraints excluded: chain 0 residue 33 LEU Chi-restraints excluded: chain 0 residue 35 SER Chi-restraints excluded: chain 2 residue 36 VAL Chi-restraints excluded: chain 3 residue 10 ARG Chi-restraints excluded: chain 4 residue 9 ILE Chi-restraints excluded: chain 6 residue 8 SER Chi-restraints excluded: chain 8 residue 36 ARG Chi-restraints excluded: chain c residue 94 VAL Chi-restraints excluded: chain c residue 165 VAL Chi-restraints excluded: chain c residue 173 THR Chi-restraints excluded: chain c residue 268 VAL Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 2 ILE Chi-restraints excluded: chain d residue 16 THR Chi-restraints excluded: chain d residue 21 SER Chi-restraints excluded: chain d residue 60 VAL Chi-restraints excluded: chain d residue 97 SER Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 151 THR Chi-restraints excluded: chain e residue 3 LEU Chi-restraints excluded: chain e residue 88 ARG Chi-restraints excluded: chain e residue 153 LEU Chi-restraints excluded: chain e residue 178 VAL Chi-restraints excluded: chain f residue 13 VAL Chi-restraints excluded: chain f residue 40 VAL Chi-restraints excluded: chain f residue 68 THR Chi-restraints excluded: chain f residue 81 GLN Chi-restraints excluded: chain f residue 90 THR Chi-restraints excluded: chain f residue 141 ILE Chi-restraints excluded: chain g residue 36 THR Chi-restraints excluded: chain g residue 39 ASP Chi-restraints excluded: chain g residue 47 ASP Chi-restraints excluded: chain h residue 37 VAL Chi-restraints excluded: chain j residue 45 THR Chi-restraints excluded: chain k residue 20 MET Chi-restraints excluded: chain k residue 69 VAL Chi-restraints excluded: chain k residue 97 THR Chi-restraints excluded: chain k residue 104 THR Chi-restraints excluded: chain k residue 113 MET Chi-restraints excluded: chain l residue 42 SER Chi-restraints excluded: chain l residue 73 ILE Chi-restraints excluded: chain l residue 116 VAL Chi-restraints excluded: chain l residue 117 THR Chi-restraints excluded: chain l residue 135 ILE Chi-restraints excluded: chain m residue 10 ARG Chi-restraints excluded: chain m residue 40 ARG Chi-restraints excluded: chain m residue 132 THR Chi-restraints excluded: chain n residue 1 MET Chi-restraints excluded: chain n residue 57 THR Chi-restraints excluded: chain n residue 89 SER Chi-restraints excluded: chain n residue 113 ILE Chi-restraints excluded: chain o residue 4 LYS Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain o residue 47 VAL Chi-restraints excluded: chain o residue 69 ASP Chi-restraints excluded: chain o residue 74 VAL Chi-restraints excluded: chain o residue 100 HIS Chi-restraints excluded: chain p residue 5 ILE Chi-restraints excluded: chain p residue 33 VAL Chi-restraints excluded: chain p residue 36 SER Chi-restraints excluded: chain p residue 41 GLN Chi-restraints excluded: chain p residue 76 THR Chi-restraints excluded: chain q residue 18 LEU Chi-restraints excluded: chain r residue 32 THR Chi-restraints excluded: chain r residue 41 ILE Chi-restraints excluded: chain r residue 102 SER Chi-restraints excluded: chain s residue 53 SER Chi-restraints excluded: chain s residue 66 ILE Chi-restraints excluded: chain s residue 101 SER Chi-restraints excluded: chain s residue 107 VAL Chi-restraints excluded: chain s residue 109 ASP Chi-restraints excluded: chain t residue 18 GLU Chi-restraints excluded: chain t residue 26 LYS Chi-restraints excluded: chain t residue 93 LEU Chi-restraints excluded: chain u residue 6 ARG Chi-restraints excluded: chain u residue 10 GLU Chi-restraints excluded: chain u residue 12 ILE Chi-restraints excluded: chain u residue 34 VAL Chi-restraints excluded: chain u residue 39 ILE Chi-restraints excluded: chain u residue 40 ASN Chi-restraints excluded: chain u residue 102 THR Chi-restraints excluded: chain w residue 55 GLU Chi-restraints excluded: chain w residue 65 VAL Chi-restraints excluded: chain y residue 35 SER Chi-restraints excluded: chain y residue 81 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 606 random chunks: chunk 381 optimal weight: 3.9990 chunk 512 optimal weight: 2.9990 chunk 147 optimal weight: 5.9990 chunk 443 optimal weight: 7.9990 chunk 70 optimal weight: 6.9990 chunk 133 optimal weight: 4.9990 chunk 481 optimal weight: 1.9990 chunk 201 optimal weight: 10.0000 chunk 494 optimal weight: 1.9990 chunk 60 optimal weight: 8.9990 chunk 88 optimal weight: 20.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 26 ASN 7 28 ASN c 117 GLN d 94 GLN d 130 GLN e 165 HIS g 22 GLN h 20 ASN j 67 ASN k 9 ASN o 98 GLN q 20 GLN u 40 ASN w 12 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.089539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.061319 restraints weight = 191244.969| |-----------------------------------------------------------------------------| r_work (start): 0.2869 rms_B_bonded: 0.89 r_work: 0.2743 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2641 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.2641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8981 moved from start: 0.3321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 98805 Z= 0.328 Angle : 0.614 10.029 148666 Z= 0.323 Chirality : 0.038 0.320 19119 Planarity : 0.005 0.067 7352 Dihedral : 24.375 179.085 51508 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 3.61 % Allowed : 27.49 % Favored : 68.89 % 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: -0.71 (0.15), residues: 3076 helix: 0.25 (0.19), residues: 819 sheet: -0.45 (0.20), residues: 650 loop : -0.80 (0.15), residues: 1607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP c 248 HIS 0.004 0.001 HIS w 44 PHE 0.013 0.001 PHE m 68 TYR 0.027 0.002 TYR h 25 ARG 0.013 0.001 ARG 6 41 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 28066.67 seconds wall clock time: 492 minutes 56.97 seconds (29576.97 seconds total)