Starting phenix.real_space_refine on Tue Mar 19 01:40:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z20_14454/03_2024/7z20_14454.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z20_14454/03_2024/7z20_14454.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z20_14454/03_2024/7z20_14454.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z20_14454/03_2024/7z20_14454.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z20_14454/03_2024/7z20_14454.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z20_14454/03_2024/7z20_14454.pdb" } resolution = 2.29 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= 0.001 sd= 0.015 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 3096 5.49 5 S 75 5.16 5 C 45060 2.51 5 N 16961 2.21 5 O 25832 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 GLU 43": "OE1" <-> "OE2" Residue "0 ARG 50": "NH1" <-> "NH2" Residue "0 ARG 57": "NH1" <-> "NH2" Residue "0 GLU 70": "OE1" <-> "OE2" Residue "0 ARG 74": "NH1" <-> "NH2" Residue "0 GLU 76": "OE1" <-> "OE2" Residue "1 GLU 5": "OE1" <-> "OE2" Residue "1 GLU 8": "OE1" <-> "OE2" Residue "1 GLU 12": "OE1" <-> "OE2" Residue "1 GLU 13": "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 GLU 37": "OE1" <-> "OE2" Residue "2 ARG 45": "NH1" <-> "NH2" Residue "2 GLU 58": "OE1" <-> "OE2" Residue "3 ARG 10": "NH1" <-> "NH2" Residue "3 ARG 16": "NH1" <-> "NH2" Residue "3 GLU 36": "OE1" <-> "OE2" 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 GLU 35": "OE1" <-> "OE2" Residue "c ARG 52": "NH1" <-> "NH2" Residue "c ARG 63": "NH1" <-> "NH2" Residue "c ARG 80": "NH1" <-> "NH2" 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 ARG 182": "NH1" <-> "NH2" Residue "c GLU 185": "OE1" <-> "OE2" Residue "c ARG 189": "NH1" <-> "NH2" Residue "c GLU 194": "OE1" <-> "OE2" Residue "c ARG 203": "NH1" <-> "NH2" Residue "c ARG 212": "NH1" <-> "NH2" Residue "d ARG 13": "NH1" <-> "NH2" Residue "d GLU 30": "OE1" <-> "OE2" Residue "d ARG 33": "NH1" <-> "NH2" Residue "d ARG 59": "NH1" <-> "NH2" Residue "d GLU 64": "OE1" <-> "OE2" Residue "d ARG 77": "NH1" <-> "NH2" Residue "d GLU 81": "OE1" <-> "OE2" Residue "d ARG 83": "NH1" <-> "NH2" Residue "d GLU 86": "OE1" <-> "OE2" Residue "d ARG 169": "NH1" <-> "NH2" Residue "d ARG 184": "NH1" <-> "NH2" Residue "e GLU 2": "OE1" <-> "OE2" Residue "e GLU 16": "OE1" <-> "OE2" Residue "e ARG 21": "NH1" <-> "NH2" Residue "e ARG 44": "NH1" <-> "NH2" Residue "e ARG 49": "NH1" <-> "NH2" Residue "e GLU 51": "OE1" <-> "OE2" 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 111": "OE1" <-> "OE2" Residue "e GLU 122": "OE1" <-> "OE2" Residue "e GLU 152": "OE1" <-> "OE2" Residue "e ARG 162": "NH1" <-> "NH2" Residue "e ARG 170": "NH1" <-> "NH2" Residue "e GLU 197": "OE1" <-> "OE2" Residue "e GLU 198": "OE1" <-> "OE2" Residue "f GLU 11": "OE1" <-> "OE2" Residue "f GLU 19": "OE1" <-> "OE2" Residue "f GLU 42": "OE1" <-> "OE2" Residue "f ARG 71": "NH1" <-> "NH2" Residue "f ARG 80": "NH1" <-> "NH2" Residue "f ARG 92": "NH1" <-> "NH2" Residue "f GLU 94": "OE1" <-> "OE2" 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 ARG 133": "NH1" <-> "NH2" Residue "f GLU 140": "OE1" <-> "OE2" Residue "f GLU 164": "OE1" <-> "OE2" Residue "g ARG 3": "NH1" <-> "NH2" Residue "g GLU 32": "OE1" <-> "OE2" Residue "g GLU 81": "OE1" <-> "OE2" Residue "g GLU 130": "OE1" <-> "OE2" Residue "g ARG 153": "NH1" <-> "NH2" Residue "g GLU 155": "OE1" <-> "OE2" Residue "g ARG 163": "NH1" <-> "NH2" Residue "g GLU 167": "OE1" <-> "OE2" Residue "g ARG 170": "NH1" <-> "NH2" Residue "h ARG 27": "NH1" <-> "NH2" Residue "j PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j ARG 13": "NH1" <-> "NH2" Residue "j GLU 31": "OE1" <-> "OE2" Residue "j ARG 37": "NH1" <-> "NH2" Residue "j GLU 90": "OE1" <-> "OE2" Residue "j GLU 91": "OE1" <-> "OE2" Residue "j ARG 96": "NH1" <-> "NH2" Residue "j GLU 102": "OE1" <-> "OE2" Residue "j ARG 120": "NH1" <-> "NH2" Residue "j GLU 129": "OE1" <-> "OE2" Residue "k GLU 92": "OE1" <-> "OE2" Residue "k GLU 106": "OE1" <-> "OE2" Residue "k GLU 121": "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 115": "OE1" <-> "OE2" Residue "l ARG 126": "NH1" <-> "NH2" Residue "m ARG 10": "NH1" <-> "NH2" Residue "m ARG 18": "NH1" <-> "NH2" Residue "m ARG 40": "NH1" <-> "NH2" Residue "m ARG 44": "NH1" <-> "NH2" Residue "m GLU 47": "OE1" <-> "OE2" Residue "m ARG 50": "NH1" <-> "NH2" Residue "m ARG 55": "NH1" <-> "NH2" Residue "m ARG 59": "NH1" <-> "NH2" Residue "m GLU 75": "OE1" <-> "OE2" Residue "m GLU 104": "OE1" <-> "OE2" Residue "m GLU 111": "OE1" <-> "OE2" Residue "m ARG 114": "NH1" <-> "NH2" Residue "m GLU 115": "OE1" <-> "OE2" Residue "n ARG 8": "NH1" <-> "NH2" Residue "n ARG 12": "NH1" <-> "NH2" Residue "n ARG 17": "NH1" <-> "NH2" Residue "n ARG 22": "NH1" <-> "NH2" Residue "n ARG 46": "NH1" <-> "NH2" Residue "n GLU 49": "OE1" <-> "OE2" Residue "n ARG 63": "NH1" <-> "NH2" Residue "n ARG 64": "NH1" <-> "NH2" Residue "n ARG 69": "NH1" <-> "NH2" Residue "n ARG 71": "NH1" <-> "NH2" Residue "n GLU 82": "OE1" <-> "OE2" Residue "n ARG 96": "NH1" <-> "NH2" Residue "n ARG 118": "NH1" <-> "NH2" Residue "n GLU 120": "OE1" <-> "OE2" Residue "o ARG 10": "NH1" <-> "NH2" Residue "o ARG 13": "NH1" <-> "NH2" Residue "o ARG 16": "NH1" <-> "NH2" Residue "o ARG 25": "NH1" <-> "NH2" Residue "o GLU 46": "OE1" <-> "OE2" Residue "o GLU 55": "OE1" <-> "OE2" Residue "o GLU 60": "OE1" <-> "OE2" Residue "o ARG 81": "NH1" <-> "NH2" Residue "o ARG 94": "NH1" <-> "NH2" Residue "o ARG 102": "NH1" <-> "NH2" Residue "o ARG 111": "NH1" <-> "NH2" Residue "p ARG 21": "NH1" <-> "NH2" Residue "p GLU 27": "OE1" <-> "OE2" Residue "p ARG 39": "NH1" <-> "NH2" Residue "p ARG 51": "NH1" <-> "NH2" Residue "p ARG 62": "NH1" <-> "NH2" Residue "p GLU 68": "OE1" <-> "OE2" Residue "p ARG 89": "NH1" <-> "NH2" Residue "p ARG 101": "NH1" <-> "NH2" Residue "p GLU 102": "OE1" <-> "OE2" Residue "p ARG 109": "NH1" <-> "NH2" Residue "p GLU 112": "OE1" <-> "OE2" 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 "r ARG 21": "NH1" <-> "NH2" Residue "r GLU 23": "OE1" <-> "OE2" Residue "r GLU 31": "OE1" <-> "OE2" Residue "r GLU 34": "OE1" <-> "OE2" Residue "r GLU 45": "OE1" <-> "OE2" Residue "r GLU 46": "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 "s GLU 59": "OE1" <-> "OE2" Residue "s PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s ARG 84": "NH1" <-> "NH2" Residue "s ARG 88": "NH1" <-> "NH2" Residue "s ARG 95": "NH1" <-> "NH2" Residue "t GLU 5": "OE1" <-> "OE2" Residue "t ARG 12": "NH1" <-> "NH2" Residue "t GLU 25": "OE1" <-> "OE2" Residue "t GLU 52": "OE1" <-> "OE2" Residue "t GLU 54": "OE1" <-> "OE2" Residue "t GLU 56": "OE1" <-> "OE2" Residue "u ARG 6": "NH1" <-> "NH2" Residue "u ARG 7": "NH1" <-> "NH2" Residue "u GLU 62": "OE1" <-> "OE2" Residue "u ARG 82": "NH1" <-> "NH2" Residue "u ARG 86": "NH1" <-> "NH2" Residue "u ARG 94": "NH1" <-> "NH2" Residue "u PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u GLU 101": "OE1" <-> "OE2" Residue "w GLU 35": "OE1" <-> "OE2" Residue "w GLU 41": "OE1" <-> "OE2" Residue "w GLU 55": "OE1" <-> "OE2" Residue "w GLU 59": "OE1" <-> "OE2" Residue "y ARG 11": "NH1" <-> "NH2" Residue "y GLU 17": "OE1" <-> "OE2" Residue "y GLU 29": "OE1" <-> "OE2" Residue "y GLU 83": "OE1" <-> "OE2" Residue "z GLU 137": "OE1" <-> "OE2" Residue "z GLU 149": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 91024 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: 301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 301 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "a" Number of atoms: 2529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 2529 Classifications: {'RNA': 118} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 6, 'rna3p_pur': 57, 'rna3p_pyr': 48} Link IDs: {'rna2p': 13, 'rna3p': 104} Chain: "b" Number of atoms: 62279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2901, 62279 Classifications: {'RNA': 2901} Modifications used: {'rna2p_pur': 280, 'rna2p_pyr': 154, 'rna3p_pur': 1394, 'rna3p_pyr': 1073} Link IDs: {'rna2p': 434, 'rna3p': 2466} Chain breaks: 1 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: 1043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1043 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: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 810 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 1, 'TRANS': 100} 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: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 793 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 1, 'TRANS': 99} 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: "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: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 619 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "v" Number of atoms: 1646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1646 Classifications: {'RNA': 77} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 7, 'rna3p_pur': 34, 'rna3p_pyr': 30} Link IDs: {'rna2p': 12, 'rna3p': 64} Chain: "z" Number of atoms: 277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 277 Classifications: {'peptide': 33} Link IDs: {'PTRANS': 3, 'TRANS': 29} Time building chain proxies: 37.11, per 1000 atoms: 0.41 Number of scatterers: 91024 At special positions: 0 Unit cell: (202.73, 213.4, 228.338, 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 75 16.00 P 3096 15.00 O 25832 8.00 N 16961 7.00 C 45060 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS 8 14 " - pdb=" SG CYS 8 27 " distance=2.04 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: 37.83 Conformation dependent library (CDL) restraints added in 3.9 seconds 6190 Ramachandran restraints generated. 3095 Oldfield, 0 Emsley, 3095 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5740 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 47 sheets defined 29.3% alpha, 22.2% beta 1018 base pairs and 1550 stacking pairs defined. Time for finding SS restraints: 32.57 Creating SS restraints... Processing helix chain '0' and resid 53 through 63 Processing helix chain '0' and resid 63 through 75 Processing helix chain '1' and resid 3 through 9 Processing helix chain '1' and resid 10 through 34 Processing helix chain '1' and resid 41 through 61 Processing helix chain '2' and resid 17 through 28 Processing helix chain '2' and resid 41 through 51 removed outlier: 3.626A pdb=" N VAL 2 51 " --> pdb=" O MET 2 47 " (cutoff:3.500A) Processing helix chain '3' and resid 9 through 18 Processing helix chain '6' and resid 8 through 17 Processing helix chain '6' and resid 17 through 24 removed outlier: 4.369A pdb=" N THR 6 24 " --> pdb=" O ALA 6 20 " (cutoff:3.500A) Processing helix chain '6' and resid 24 through 38 Processing helix chain '7' and resid 37 through 44 Processing helix chain '7' and resid 51 through 62 removed outlier: 4.384A pdb=" N GLY 7 56 " --> pdb=" O LYS 7 52 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N LEU 7 57 " --> pdb=" O GLY 7 53 " (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 133 through 135 No H-bonds generated for 'chain 'c' and resid 133 through 135' Processing helix chain 'c' and resid 197 through 203 removed outlier: 4.125A pdb=" N MET c 201 " --> pdb=" O ALA c 198 " (cutoff:3.500A) Processing helix chain 'c' and resid 207 through 213 removed outlier: 3.840A 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 'c' and resid 263 through 265 No H-bonds generated for 'chain 'c' and resid 263 through 265' Processing helix chain 'd' and resid 39 through 44 Processing helix chain 'd' and resid 61 through 72 removed outlier: 3.694A pdb=" N ALA d 71 " --> pdb=" O HIS d 67 " (cutoff:3.500A) Processing helix chain 'd' and resid 97 through 102 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 115 Processing helix chain 'e' and resid 130 through 141 removed outlier: 3.521A pdb=" N LEU e 134 " --> pdb=" O LYS e 130 " (cutoff:3.500A) Processing helix chain 'e' and resid 154 through 162 Processing helix chain 'e' and resid 176 through 183 removed outlier: 3.503A pdb=" N PHE e 183 " --> pdb=" O SER e 179 " (cutoff:3.500A) Processing helix chain 'e' and resid 190 through 201 Processing helix chain 'f' and resid 3 through 12 Processing helix chain 'f' and resid 12 through 21 Processing helix chain 'f' and resid 24 through 28 Processing helix chain 'f' and resid 40 through 45 removed outlier: 4.003A pdb=" N ILE f 44 " --> pdb=" O GLY f 41 " (cutoff:3.500A) Processing helix chain 'f' and resid 47 through 61 Processing helix chain 'f' and resid 93 through 106 Processing helix chain 'f' and resid 134 through 138 removed outlier: 3.950A pdb=" N ILE f 137 " --> pdb=" O GLU f 134 " (cutoff:3.500A) Processing helix chain 'f' and resid 162 through 172 Processing helix chain 'g' and resid 60 through 80 removed outlier: 3.586A pdb=" N GLN g 64 " --> pdb=" O ASP g 60 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR g 80 " --> pdb=" O VAL g 76 " (cutoff:3.500A) Processing helix chain 'g' and resid 137 through 151 removed outlier: 3.755A pdb=" N TYR g 151 " --> pdb=" O ASP g 147 " (cutoff:3.500A) Processing helix chain 'h' and resid 30 through 34 Processing helix chain 'j' and resid 24 through 38 removed outlier: 3.908A pdb=" N GLU j 31 " --> pdb=" O ARG j 27 " (cutoff:3.500A) Processing helix chain 'j' and resid 58 through 62 removed outlier: 3.666A pdb=" N VAL j 62 " --> pdb=" O ALA j 59 " (cutoff:3.500A) 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 108 removed outlier: 4.360A pdb=" N ILE j 101 " --> pdb=" O PRO j 97 " (cutoff:3.500A) Processing helix chain 'j' and resid 112 through 120 Processing helix chain 'j' and resid 132 through 136 Processing helix chain 'k' and resid 104 through 108 Processing helix chain 'k' and resid 112 through 119 Processing helix chain 'l' and resid 56 through 61 removed outlier: 3.520A pdb=" N LEU l 61 " --> pdb=" O LEU l 57 " (cutoff:3.500A) Processing helix chain 'l' and resid 70 through 72 No H-bonds generated for 'chain 'l' and resid 70 through 72' Processing helix chain 'l' and resid 80 through 86 removed outlier: 4.065A pdb=" N ALA l 83 " --> pdb=" O SER l 80 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL l 85 " --> pdb=" O LEU l 82 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N GLU l 86 " --> pdb=" O ALA l 83 " (cutoff:3.500A) Processing helix chain 'l' and resid 91 through 98 Processing helix chain 'l' and resid 128 through 138 Processing helix chain 'm' and resid 43 through 57 removed outlier: 3.563A pdb=" N VAL m 57 " --> pdb=" O MET m 53 " (cutoff:3.500A) Processing helix chain 'm' and resid 109 through 122 removed outlier: 3.576A pdb=" N ALA m 122 " --> pdb=" O LYS m 118 " (cutoff:3.500A) Processing helix chain 'n' and resid 13 through 32 Processing helix chain 'n' and resid 44 through 56 Proline residue: n 50 - end of helix Processing helix chain 'n' and resid 59 through 70 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 22 removed outlier: 4.323A pdb=" N ARG o 13 " --> pdb=" O ARG o 9 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N ALA o 14 " --> pdb=" O ARG o 10 " (cutoff:3.500A) Processing helix chain 'o' and resid 55 through 61 removed outlier: 4.268A pdb=" N GLN o 61 " --> pdb=" O ALA o 57 " (cutoff:3.500A) Processing helix chain 'o' and resid 67 through 85 removed outlier: 3.517A pdb=" N LYS o 85 " --> pdb=" O ARG o 81 " (cutoff:3.500A) Processing helix chain 'o' and resid 101 through 114 Processing helix chain 'p' and resid 3 through 11 Processing helix chain 'p' and resid 53 through 56 Processing helix chain 'p' and resid 97 through 103 Processing helix chain 'p' and resid 104 through 109 Processing helix chain 'q' and resid 6 through 20 removed outlier: 3.739A pdb=" N GLN q 20 " --> pdb=" O LYS q 16 " (cutoff:3.500A) Processing helix chain 'q' and resid 25 through 30 Processing helix chain 'q' and resid 31 through 71 removed outlier: 3.691A pdb=" N GLN q 37 " --> pdb=" O ARG q 33 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ARG q 51 " --> pdb=" O TYR q 47 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N LYS q 54 " --> pdb=" O ARG q 50 " (cutoff:3.500A) Processing helix chain 'q' and resid 75 through 86 Processing helix chain 'q' and resid 91 through 102 removed outlier: 3.562A pdb=" N VAL q 100 " --> pdb=" O ALA q 96 " (cutoff:3.500A) Processing helix chain 'q' and resid 102 through 118 Processing helix chain 's' and resid 13 through 25 removed outlier: 3.770A pdb=" N VAL s 20 " --> pdb=" O LYS s 16 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N LEU s 23 " --> pdb=" O LEU s 19 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ILE s 24 " --> pdb=" O VAL s 20 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG s 25 " --> pdb=" O ALA s 21 " (cutoff:3.500A) Processing helix chain 's' and resid 28 through 38 Processing helix chain 's' and resid 41 through 62 removed outlier: 3.994A pdb=" N VAL s 45 " --> pdb=" O LYS s 41 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU s 46 " --> pdb=" O LYS s 42 " (cutoff:3.500A) Processing helix chain 's' and resid 65 through 69 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 10 Processing helix chain 't' and resid 17 through 28 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 51 Processing helix chain 'w' and resid 52 through 58 removed outlier: 6.512A pdb=" N GLU w 55 " --> pdb=" O ALA w 52 " (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: 3.670A 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 20 through 25 Processing sheet with id=AA7, first strand: chain '7' and resid 15 through 16 Processing sheet with id=AA8, first strand: chain '8' and resid 2 through 4 removed outlier: 5.848A pdb=" N LYS 8 2 " --> pdb=" O ARG 8 36 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N ILE 8 23 " --> pdb=" O GLN 8 37 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'c' and resid 3 through 5 Processing sheet with id=AB1, first strand: chain 'c' and resid 34 through 36 Processing sheet with id=AB2, first strand: chain 'c' and resid 101 through 105 removed outlier: 6.733A pdb=" N ILE c 91 " --> pdb=" O LEU c 81 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N LEU c 81 " --> pdb=" O ILE c 91 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N LEU c 93 " --> pdb=" O GLU c 79 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'c' and resid 129 through 131 removed outlier: 5.924A pdb=" N ILE c 164 " --> pdb=" O ARG c 175 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ARG c 175 " --> pdb=" O ILE c 164 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TYR c 171 " --> pdb=" O ASP c 168 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N LYS c 183 " --> pdb=" O ILE c 267 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N ILE c 267 " --> pdb=" O LYS c 183 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'c' and resid 144 through 145 removed outlier: 5.856A pdb=" N VAL c 144 " --> pdb=" O GLN c 153 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'd' and resid 4 through 15 removed outlier: 6.015A pdb=" N LYS d 8 " --> pdb=" O GLU d 28 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N GLU d 28 " --> pdb=" O LYS d 8 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLY d 10 " --> pdb=" O VAL d 26 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N LEU d 186 " --> pdb=" O VAL d 180 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N VAL d 180 " --> pdb=" O LEU d 186 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N LEU d 188 " --> pdb=" O VAL d 178 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ASP d 176 " --> pdb=" O LYS d 190 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N VAL d 107 " --> pdb=" O SER d 174 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N THR d 112 " --> pdb=" O ASP d 200 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N ASP d 200 " --> pdb=" O THR d 112 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'd' and resid 80 through 83 removed outlier: 6.581A pdb=" N ALA d 47 " --> pdb=" O VAL d 37 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N VAL d 37 " --> pdb=" O ALA d 47 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N GLN d 49 " --> pdb=" O THR d 35 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'd' and resid 117 through 119 removed outlier: 3.614A pdb=" N GLY d 117 " --> pdb=" O MET d 165 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'e' and resid 2 through 4 Processing sheet with id=AB9, first strand: chain 'e' and resid 118 through 121 Processing sheet with id=AC1, first strand: chain 'f' and resid 66 through 69 removed outlier: 3.700A pdb=" N GLY f 86 " --> pdb=" O THR f 68 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS f 33 " --> pdb=" O THR f 157 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'g' and resid 9 through 10 Processing sheet with id=AC3, first strand: chain 'g' and resid 16 through 20 removed outlier: 4.070A pdb=" N VAL g 23 " --> pdb=" O ASN g 20 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'g' and resid 122 through 124 Processing sheet with id=AC5, first strand: chain 'g' and resid 95 through 99 Processing sheet with id=AC6, first strand: chain 'h' and resid 18 through 20 Processing sheet with id=AC7, first strand: chain 'j' and resid 122 through 124 removed outlier: 6.750A pdb=" N TRP j 15 " --> pdb=" O GLN j 138 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'j' and resid 73 through 77 Processing sheet with id=AC9, first strand: chain 'k' and resid 7 through 10 removed outlier: 3.648A pdb=" N VAL k 10 " --> pdb=" O ARG k 17 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ARG k 17 " --> pdb=" O VAL k 10 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ALA k 16 " --> pdb=" O ALA k 46 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N ALA k 46 " --> pdb=" O ALA k 16 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N ARG k 18 " --> pdb=" O LYS k 44 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N LYS k 40 " --> pdb=" O ILE k 22 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N VAL k 24 " --> pdb=" O ILE k 38 " (cutoff:3.500A) removed outlier: 8.372A pdb=" N ILE k 38 " --> pdb=" O VAL k 24 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS k 59 " --> pdb=" O LEU k 87 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ALA k 83 " --> pdb=" O VAL k 63 " (cutoff:3.500A) removed outlier: 8.207A pdb=" N CYS k 84 " --> pdb=" O MET k 7 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ASN k 9 " --> pdb=" O CYS k 84 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N LEU k 86 " --> pdb=" O ASN k 9 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'k' and resid 69 through 70 removed outlier: 3.600A pdb=" N GLU p 68 " --> pdb=" O SER p 65 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ALA p 49 " --> pdb=" O THR p 60 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ARG p 62 " --> pdb=" O VAL p 47 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N VAL p 47 " --> pdb=" O ARG p 62 " (cutoff:3.500A) removed outlier: 8.605A pdb=" N ILE p 64 " --> pdb=" O GLY p 45 " (cutoff:3.500A) removed outlier: 8.357A pdb=" N GLY p 45 " --> pdb=" O ILE p 64 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N THR p 25 " --> pdb=" O LYS p 87 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N TRP p 31 " --> pdb=" O VAL p 81 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N VAL p 81 " --> pdb=" O TRP p 31 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'l' and resid 74 through 78 Processing sheet with id=AD3, first strand: chain 'l' and resid 89 through 90 Processing sheet with id=AD4, first strand: chain 'm' and resid 62 through 65 removed outlier: 6.614A pdb=" N LEU m 33 " --> pdb=" O LEU m 102 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N GLU m 104 " --> pdb=" O PHE m 31 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N PHE m 31 " --> pdb=" O GLU m 104 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'm' and resid 39 through 42 removed outlier: 6.876A pdb=" N ILE m 73 " --> pdb=" O GLU m 90 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N TRP m 92 " --> pdb=" O LYS m 71 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N LYS m 71 " --> pdb=" O TRP m 92 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'n' and resid 33 through 37 removed outlier: 5.575A pdb=" N MET n 110 " --> pdb=" O CYS n 100 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'o' and resid 47 through 52 removed outlier: 6.769A pdb=" N VAL o 39 " --> pdb=" O LEU o 48 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N ALA o 50 " --> pdb=" O ALA o 37 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ALA o 37 " --> pdb=" O ALA o 50 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N SER o 52 " --> pdb=" O ILE o 35 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N ILE o 35 " --> pdb=" O SER o 52 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N LEU o 26 " --> pdb=" O ASP o 93 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'r' and resid 11 through 15 removed outlier: 3.829A pdb=" N MET r 40 " --> pdb=" O VAL r 4 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N GLN r 6 " --> pdb=" O VAL r 38 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N VAL r 38 " --> pdb=" O GLN r 6 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'r' and resid 19 through 23 removed outlier: 6.724A pdb=" N PHE r 93 " --> pdb=" O HIS r 66 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N HIS r 66 " --> pdb=" O PHE r 93 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ASP r 95 " --> pdb=" O VAL r 64 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N LYS r 60 " --> pdb=" O THR r 99 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'r' and resid 72 through 78 removed outlier: 4.292A pdb=" N TYR r 83 " --> pdb=" O ARG r 78 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 's' and resid 2 through 10 removed outlier: 5.582A pdb=" N SER s 101 " --> pdb=" O HIS s 9 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N HIS s 102 " --> pdb=" O VAL s 76 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N VAL s 76 " --> pdb=" O HIS s 102 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N THR s 104 " --> pdb=" O ILE s 74 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N ILE s 74 " --> pdb=" O THR s 104 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N VAL s 106 " --> pdb=" O THR s 72 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 's' and resid 82 through 87 Processing sheet with id=AE4, first strand: chain 't' and resid 11 through 14 removed outlier: 3.861A pdb=" N LYS t 89 " --> pdb=" O VAL t 34 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL t 57 " --> pdb=" O THR t 94 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 't' and resid 67 through 73 Processing sheet with id=AE6, first strand: chain 'u' and resid 65 through 66 removed outlier: 6.614A pdb=" N LYS u 33 " --> pdb=" O VAL u 28 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N VAL u 28 " --> pdb=" O LYS u 33 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ILE u 35 " --> pdb=" O LYS u 26 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N GLU u 10 " --> pdb=" O PHE u 73 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ILE u 72 " --> pdb=" O ASP u 81 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'u' and resid 41 through 46 Processing sheet with id=AE8, first strand: chain 'u' and resid 83 through 88 Processing sheet with id=AE9, first strand: chain 'w' and resid 3 through 8 removed outlier: 7.961A pdb=" N ASN w 5 " --> pdb=" O ASP w 43 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N ASP w 43 " --> pdb=" O ASN w 5 " (cutoff:3.500A) removed outlier: 9.029A pdb=" N LYS w 25 " --> pdb=" O GLN w 87 " (cutoff:3.500A) removed outlier: 9.897A pdb=" N ILE w 89 " --> pdb=" O LYS w 25 " (cutoff:3.500A) removed outlier: 8.472A pdb=" N PHE w 91 " --> pdb=" O PRO w 27 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N ILE w 29 " --> pdb=" O PHE w 91 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N ARG w 93 " --> pdb=" O ILE w 29 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N TYR w 31 " --> pdb=" O ARG w 93 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N GLN w 78 " --> pdb=" O GLN w 87 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ILE w 89 " --> pdb=" O ASP w 76 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ASP w 76 " --> pdb=" O ILE w 89 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N PHE w 91 " --> pdb=" O ALA w 74 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ALA w 74 " --> pdb=" O PHE w 91 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ARG w 93 " --> pdb=" O VAL w 72 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N VAL w 72 " --> pdb=" O ARG w 93 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ILE w 4 " --> pdb=" O VAL w 64 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'y' and resid 22 through 23 removed outlier: 6.775A pdb=" N LEU y 59 " --> pdb=" O ILE y 37 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'y' and resid 30 through 31 956 hydrogen bonds defined for protein. 2595 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2561 hydrogen bonds 3984 hydrogen bond angles 0 basepair planarities 1018 basepair parallelities 1550 stacking parallelities Total time for adding SS restraints: 155.99 Time building geometry restraints manager: 40.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 10364 1.32 - 1.44: 43451 1.44 - 1.57: 39192 1.57 - 1.69: 6189 1.69 - 1.81: 137 Bond restraints: 99333 Sorted by residual: bond pdb=" N ASN u 53 " pdb=" CA ASN u 53 " ideal model delta sigma weight residual 1.457 1.489 -0.032 6.40e-03 2.44e+04 2.53e+01 bond pdb=" O3' U b1093 " pdb=" P A b1094 " ideal model delta sigma weight residual 1.607 1.662 -0.055 1.50e-02 4.44e+03 1.33e+01 bond pdb=" N VAL r 51 " pdb=" CA VAL r 51 " ideal model delta sigma weight residual 1.461 1.505 -0.044 1.23e-02 6.61e+03 1.26e+01 bond pdb=" O3' A b2799 " pdb=" P G b2800 " ideal model delta sigma weight residual 1.607 1.659 -0.052 1.50e-02 4.44e+03 1.22e+01 bond pdb=" N ILE 7 32 " pdb=" CA ILE 7 32 " ideal model delta sigma weight residual 1.459 1.502 -0.043 1.25e-02 6.40e+03 1.20e+01 ... (remaining 99328 not shown) Histogram of bond angle deviations from ideal: 95.36 - 103.10: 6371 103.10 - 110.84: 53124 110.84 - 118.59: 38754 118.59 - 126.33: 41528 126.33 - 134.07: 9699 Bond angle restraints: 149476 Sorted by residual: angle pdb=" O3' A b1625 " pdb=" C3' A b1625 " pdb=" C2' A b1625 " ideal model delta sigma weight residual 113.70 124.89 -11.19 1.50e+00 4.44e-01 5.57e+01 angle pdb=" O3' A b 63 " pdb=" C3' A b 63 " pdb=" C2' A b 63 " ideal model delta sigma weight residual 109.50 120.51 -11.01 1.50e+00 4.44e-01 5.39e+01 angle pdb=" C4' G b2654 " pdb=" C3' G b2654 " pdb=" O3' G b2654 " ideal model delta sigma weight residual 109.40 120.01 -10.61 1.50e+00 4.44e-01 5.00e+01 angle pdb=" C4' G b1929 " pdb=" C3' G b1929 " pdb=" O3' G b1929 " ideal model delta sigma weight residual 109.40 119.45 -10.05 1.50e+00 4.44e-01 4.49e+01 angle pdb=" O3' G v 5 " pdb=" C3' G v 5 " pdb=" C2' G v 5 " ideal model delta sigma weight residual 113.70 123.08 -9.38 1.50e+00 4.44e-01 3.91e+01 ... (remaining 149471 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.99: 55032 35.99 - 71.99: 7803 71.99 - 107.98: 797 107.98 - 143.98: 19 143.98 - 179.97: 25 Dihedral angle restraints: 63676 sinusoidal: 54755 harmonic: 8921 Sorted by residual: dihedral pdb=" C5' U b 826 " pdb=" C4' U b 826 " pdb=" C3' U b 826 " pdb=" O3' U b 826 " ideal model delta sinusoidal sigma weight residual 147.00 78.09 68.91 1 8.00e+00 1.56e-02 9.60e+01 dihedral pdb=" C4' U b 826 " pdb=" C3' U b 826 " pdb=" C2' U b 826 " pdb=" C1' U b 826 " ideal model delta sinusoidal sigma weight residual -35.00 30.28 -65.28 1 8.00e+00 1.56e-02 8.73e+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 26.47 173.53 1 1.50e+01 4.44e-03 8.51e+01 ... (remaining 63673 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.147: 18672 0.147 - 0.294: 502 0.294 - 0.441: 36 0.441 - 0.588: 6 0.588 - 0.735: 1 Chirality restraints: 19217 Sorted by residual: chirality pdb=" C3' G b2654 " pdb=" C4' G b2654 " pdb=" O3' G b2654 " pdb=" C2' G b2654 " both_signs ideal model delta sigma weight residual False -2.74 -2.01 -0.73 2.00e-01 2.50e+01 1.35e+01 chirality pdb=" C3' G b1929 " pdb=" C4' G b1929 " pdb=" O3' G b1929 " pdb=" C2' G b1929 " both_signs ideal model delta sigma weight residual False -2.74 -2.16 -0.59 2.00e-01 2.50e+01 8.56e+00 chirality pdb=" P G b 1 " pdb=" OP1 G b 1 " pdb=" OP2 G b 1 " pdb=" O5' G b 1 " both_signs ideal model delta sigma weight residual True 2.41 -2.99 -0.58 2.00e-01 2.50e+01 8.42e+00 ... (remaining 19214 not shown) Planarity restraints: 7388 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A b 909 " -0.049 2.00e-02 2.50e+03 2.19e-02 1.32e+01 pdb=" N9 A b 909 " 0.048 2.00e-02 2.50e+03 pdb=" C8 A b 909 " 0.004 2.00e-02 2.50e+03 pdb=" N7 A b 909 " 0.001 2.00e-02 2.50e+03 pdb=" C5 A b 909 " -0.004 2.00e-02 2.50e+03 pdb=" C6 A b 909 " -0.015 2.00e-02 2.50e+03 pdb=" N6 A b 909 " -0.008 2.00e-02 2.50e+03 pdb=" N1 A b 909 " -0.001 2.00e-02 2.50e+03 pdb=" C2 A b 909 " 0.000 2.00e-02 2.50e+03 pdb=" N3 A b 909 " 0.011 2.00e-02 2.50e+03 pdb=" C4 A b 909 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN h 20 " 0.018 2.00e-02 2.50e+03 3.61e-02 1.30e+01 pdb=" C ASN h 20 " -0.062 2.00e-02 2.50e+03 pdb=" O ASN h 20 " 0.024 2.00e-02 2.50e+03 pdb=" N VAL h 21 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C b 417 " 0.043 2.00e-02 2.50e+03 2.30e-02 1.19e+01 pdb=" N1 C b 417 " -0.051 2.00e-02 2.50e+03 pdb=" C2 C b 417 " -0.002 2.00e-02 2.50e+03 pdb=" O2 C b 417 " -0.004 2.00e-02 2.50e+03 pdb=" N3 C b 417 " 0.005 2.00e-02 2.50e+03 pdb=" C4 C b 417 " 0.009 2.00e-02 2.50e+03 pdb=" N4 C b 417 " 0.010 2.00e-02 2.50e+03 pdb=" C5 C b 417 " -0.001 2.00e-02 2.50e+03 pdb=" C6 C b 417 " -0.008 2.00e-02 2.50e+03 ... (remaining 7385 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 7098 2.69 - 3.24: 74818 3.24 - 3.79: 192803 3.79 - 4.35: 254745 4.35 - 4.90: 326739 Nonbonded interactions: 856203 Sorted by model distance: nonbonded pdb=" N GLU e 122 " pdb=" OE1 GLU e 122 " model vdw 2.134 2.520 nonbonded pdb=" OD1 ASN d 149 " pdb=" N GLN d 150 " model vdw 2.145 2.520 nonbonded pdb=" O2' G v 19 " pdb=" N2 G v 57 " model vdw 2.198 2.520 nonbonded pdb=" NH1 ARG d 184 " pdb=" OE2 GLU p 11 " model vdw 2.203 2.520 nonbonded pdb=" OG1 THR 7 34 " pdb=" OP1 C b2419 " model vdw 2.204 2.440 ... (remaining 856198 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: 2.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.120 Extract box with map and model: 14.650 Check model and map are aligned: 1.080 Set scattering table: 0.670 Process input model: 330.400 Find NCS groups from input model: 1.500 Set up NCS constraints: 0.210 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:12.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 363.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.062 99333 Z= 0.541 Angle : 0.776 11.193 149476 Z= 0.438 Chirality : 0.056 0.735 19217 Planarity : 0.005 0.050 7388 Dihedral : 24.281 179.970 57933 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.88 % Favored : 94.96 % Rotamer: Outliers : 2.34 % Allowed : 38.37 % Favored : 59.28 % Cbeta Deviations : 0.07 % 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: -0.59 (0.14), residues: 3095 helix: 0.68 (0.19), residues: 802 sheet: -0.34 (0.19), residues: 718 loop : -0.95 (0.14), residues: 1575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP c 213 HIS 0.011 0.002 HIS c 53 PHE 0.030 0.003 PHE q 57 TYR 0.022 0.002 TYR f 83 ARG 0.022 0.002 ARG m 59 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6190 Ramachandran restraints generated. 3095 Oldfield, 0 Emsley, 3095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6190 Ramachandran restraints generated. 3095 Oldfield, 0 Emsley, 3095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 568 residues out of total 2559 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 508 time to evaluate : 3.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 19 LYS cc_start: 0.8186 (mttp) cc_final: 0.7876 (mttt) REVERT: 2 35 THR cc_start: 0.9041 (t) cc_final: 0.8821 (m) REVERT: 3 37 LYS cc_start: 0.8906 (mttm) cc_final: 0.8595 (mtmp) REVERT: 4 25 LYS cc_start: 0.8849 (tttm) cc_final: 0.8404 (tttt) REVERT: 6 1 MET cc_start: 0.7867 (mtp) cc_final: 0.7632 (mtp) REVERT: 8 30 GLU cc_start: 0.8033 (tp30) cc_final: 0.7787 (tp30) REVERT: c 163 GLN cc_start: 0.7769 (tt0) cc_final: 0.7136 (mt0) REVERT: d 176 ASP cc_start: 0.8440 (m-30) cc_final: 0.8167 (m-30) REVERT: f 83 TYR cc_start: 0.8344 (m-80) cc_final: 0.8126 (m-10) REVERT: j 92 MET cc_start: 0.8887 (mmm) cc_final: 0.8286 (mmm) REVERT: j 103 ILE cc_start: 0.8217 (pt) cc_final: 0.7935 (pp) REVERT: k 73 ASP cc_start: 0.7815 (t0) cc_final: 0.7594 (t0) REVERT: k 114 LYS cc_start: 0.8459 (mtpp) cc_final: 0.7983 (ttmt) REVERT: k 121 GLU cc_start: 0.8358 (tt0) cc_final: 0.8015 (tt0) REVERT: n 14 SER cc_start: 0.9109 (t) cc_final: 0.8772 (t) REVERT: n 72 ASP cc_start: 0.8457 (t0) cc_final: 0.8133 (t0) REVERT: p 10 GLN cc_start: 0.8172 (tp-100) cc_final: 0.7962 (tp40) REVERT: p 89 ARG cc_start: 0.8096 (mtp180) cc_final: 0.7883 (mtp180) REVERT: r 43 ASN cc_start: 0.6559 (OUTLIER) cc_final: 0.6179 (p0) REVERT: r 97 LYS cc_start: 0.9041 (tttm) cc_final: 0.8801 (tttp) REVERT: t 73 ARG cc_start: 0.7570 (ptp-110) cc_final: 0.7325 (ptm-80) REVERT: y 25 ARG cc_start: 0.8265 (mmt-90) cc_final: 0.8030 (mmm-85) REVERT: y 78 LYS cc_start: 0.8730 (mtpt) cc_final: 0.8231 (mttm) outliers start: 60 outliers final: 16 residues processed: 540 average time/residue: 1.9965 time to fit residues: 1412.5786 Evaluate side-chains 503 residues out of total 2559 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 486 time to evaluate : 3.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 56 MET Chi-restraints excluded: chain 2 residue 5 ILE Chi-restraints excluded: chain 2 residue 36 VAL Chi-restraints excluded: chain c residue 115 GLN Chi-restraints excluded: chain d residue 84 LEU Chi-restraints excluded: chain j residue 30 THR Chi-restraints excluded: chain l residue 85 VAL Chi-restraints excluded: chain l residue 121 THR Chi-restraints excluded: chain m residue 41 LEU Chi-restraints excluded: chain n residue 57 THR Chi-restraints excluded: chain n residue 65 LEU Chi-restraints excluded: chain o residue 24 THR Chi-restraints excluded: chain r residue 43 ASN Chi-restraints excluded: chain r residue 47 VAL Chi-restraints excluded: chain u residue 83 VAL Chi-restraints excluded: chain y residue 43 THR Chi-restraints excluded: chain y residue 70 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 611 random chunks: chunk 515 optimal weight: 7.9990 chunk 463 optimal weight: 0.8980 chunk 256 optimal weight: 4.9990 chunk 158 optimal weight: 60.0000 chunk 312 optimal weight: 6.9990 chunk 247 optimal weight: 5.9990 chunk 478 optimal weight: 0.5980 chunk 185 optimal weight: 6.9990 chunk 291 optimal weight: 5.9990 chunk 356 optimal weight: 0.9990 chunk 554 optimal weight: 5.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 4 GLN c 142 HIS ** c 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 42 ASN d 136 ASN ** j 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 35 HIS n 18 GLN o 43 ASN r 6 GLN r 18 GLN r 86 GLN t 48 GLN w 75 GLN y 46 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.0813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 99333 Z= 0.223 Angle : 0.591 9.738 149476 Z= 0.315 Chirality : 0.037 0.347 19217 Planarity : 0.005 0.076 7388 Dihedral : 23.949 178.375 51795 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.46 % Favored : 95.41 % Rotamer: Outliers : 5.55 % Allowed : 30.17 % Favored : 64.28 % 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: -0.15 (0.15), residues: 3095 helix: 1.07 (0.19), residues: 819 sheet: -0.04 (0.19), residues: 713 loop : -0.72 (0.15), residues: 1563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP c 213 HIS 0.006 0.001 HIS c 15 PHE 0.021 0.001 PHE q 57 TYR 0.014 0.001 TYR f 83 ARG 0.009 0.001 ARG d 184 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6190 Ramachandran restraints generated. 3095 Oldfield, 0 Emsley, 3095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6190 Ramachandran restraints generated. 3095 Oldfield, 0 Emsley, 3095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 656 residues out of total 2559 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 514 time to evaluate : 3.979 Fit side-chains revert: symmetry clash REVERT: 1 24 GLU cc_start: 0.8048 (tp30) cc_final: 0.7738 (tp30) REVERT: 1 45 GLN cc_start: 0.8346 (tt0) cc_final: 0.8128 (tt0) REVERT: 2 19 LYS cc_start: 0.8232 (mttp) cc_final: 0.7910 (mttt) REVERT: 3 27 SER cc_start: 0.5343 (OUTLIER) cc_final: 0.5043 (p) REVERT: 4 25 LYS cc_start: 0.8569 (tttm) cc_final: 0.8276 (tttt) REVERT: 4 27 LYS cc_start: 0.8740 (OUTLIER) cc_final: 0.8474 (mptm) REVERT: 6 1 MET cc_start: 0.7770 (mtp) cc_final: 0.7545 (mtp) REVERT: 7 30 ARG cc_start: 0.9363 (OUTLIER) cc_final: 0.8945 (mpt180) REVERT: 8 30 GLU cc_start: 0.8098 (tp30) cc_final: 0.7794 (tp30) REVERT: c 90 ASN cc_start: 0.8191 (OUTLIER) cc_final: 0.7880 (m-40) REVERT: c 118 SER cc_start: 0.8924 (p) cc_final: 0.8700 (p) REVERT: c 163 GLN cc_start: 0.7851 (tt0) cc_final: 0.7258 (mt0) REVERT: d 84 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8269 (mp) REVERT: d 176 ASP cc_start: 0.8443 (m-30) cc_final: 0.8149 (m-30) REVERT: e 170 ARG cc_start: 0.9008 (OUTLIER) cc_final: 0.7499 (tpp80) REVERT: j 92 MET cc_start: 0.8883 (mmm) cc_final: 0.8229 (mmm) REVERT: j 103 ILE cc_start: 0.8132 (OUTLIER) cc_final: 0.7876 (pp) REVERT: k 114 LYS cc_start: 0.8476 (mtpp) cc_final: 0.8068 (ttmt) REVERT: k 121 GLU cc_start: 0.8315 (tt0) cc_final: 0.7991 (tt0) REVERT: m 12 MET cc_start: 0.8297 (mtp) cc_final: 0.7873 (mtp) REVERT: m 115 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7665 (tp30) REVERT: n 14 SER cc_start: 0.9000 (t) cc_final: 0.8637 (t) REVERT: n 72 ASP cc_start: 0.8398 (t0) cc_final: 0.8078 (t0) REVERT: o 40 ILE cc_start: 0.8698 (OUTLIER) cc_final: 0.8362 (mm) REVERT: p 10 GLN cc_start: 0.8192 (tp-100) cc_final: 0.7870 (tp40) REVERT: p 102 GLU cc_start: 0.7582 (mp0) cc_final: 0.7314 (mp0) REVERT: r 97 LYS cc_start: 0.8975 (tttm) cc_final: 0.8698 (tttp) REVERT: s 4 ILE cc_start: 0.9162 (mt) cc_final: 0.8943 (mp) REVERT: t 64 LYS cc_start: 0.8606 (OUTLIER) cc_final: 0.8269 (mmtm) REVERT: t 73 ARG cc_start: 0.7586 (ptp-110) cc_final: 0.7310 (ptm-80) REVERT: y 25 ARG cc_start: 0.8235 (mmt-90) cc_final: 0.7962 (mmm-85) REVERT: y 62 LYS cc_start: 0.8918 (mtmt) cc_final: 0.8629 (mtpt) REVERT: y 66 LYS cc_start: 0.8891 (mttp) cc_final: 0.8690 (mmmm) REVERT: y 78 LYS cc_start: 0.8802 (mtpt) cc_final: 0.8345 (mttm) REVERT: z 148 VAL cc_start: 0.3009 (OUTLIER) cc_final: 0.2725 (t) outliers start: 142 outliers final: 64 residues processed: 611 average time/residue: 1.8480 time to fit residues: 1511.2635 Evaluate side-chains 563 residues out of total 2559 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 488 time to evaluate : 3.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 12 SER Chi-restraints excluded: chain 3 residue 25 VAL Chi-restraints excluded: chain 3 residue 27 SER Chi-restraints excluded: chain 3 residue 29 SER Chi-restraints excluded: chain 4 residue 27 LYS Chi-restraints excluded: chain 4 residue 42 VAL Chi-restraints excluded: chain 7 residue 30 ARG Chi-restraints excluded: chain 7 residue 54 ASP Chi-restraints excluded: chain c residue 90 ASN Chi-restraints excluded: chain c residue 165 VAL Chi-restraints excluded: chain c residue 191 THR Chi-restraints excluded: chain d residue 7 LYS Chi-restraints excluded: chain d residue 60 VAL Chi-restraints excluded: chain d residue 84 LEU Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 151 THR Chi-restraints excluded: chain e residue 65 THR Chi-restraints excluded: chain e residue 170 ARG Chi-restraints excluded: chain e residue 191 ASP Chi-restraints excluded: chain f residue 35 THR Chi-restraints excluded: chain f residue 42 GLU Chi-restraints excluded: chain f residue 88 LYS Chi-restraints excluded: chain f residue 103 LEU Chi-restraints excluded: chain f residue 125 ARG Chi-restraints excluded: chain f residue 137 ILE Chi-restraints excluded: chain g residue 15 VAL Chi-restraints excluded: chain g residue 23 VAL Chi-restraints excluded: chain g residue 25 THR Chi-restraints excluded: chain g residue 37 LEU Chi-restraints excluded: chain g residue 41 VAL Chi-restraints excluded: chain g residue 127 THR Chi-restraints excluded: chain g residue 168 VAL Chi-restraints excluded: chain h residue 11 ASN Chi-restraints excluded: chain h residue 15 LEU Chi-restraints excluded: chain j residue 21 THR Chi-restraints excluded: chain j residue 30 THR Chi-restraints excluded: chain j residue 48 VAL Chi-restraints excluded: chain j residue 101 ILE Chi-restraints excluded: chain j residue 103 ILE Chi-restraints excluded: chain k residue 76 VAL Chi-restraints excluded: chain l residue 85 VAL Chi-restraints excluded: chain l residue 117 THR Chi-restraints excluded: chain l residue 121 THR Chi-restraints excluded: chain m residue 1 MET Chi-restraints excluded: chain m residue 22 GLN Chi-restraints excluded: chain m residue 30 SER Chi-restraints excluded: chain m residue 41 LEU Chi-restraints excluded: chain m residue 115 GLU Chi-restraints excluded: chain m residue 127 LYS Chi-restraints excluded: chain m residue 135 VAL Chi-restraints excluded: chain n residue 36 THR Chi-restraints excluded: chain n residue 57 THR Chi-restraints excluded: chain n residue 65 LEU Chi-restraints excluded: chain n residue 70 THR Chi-restraints excluded: chain o residue 24 THR Chi-restraints excluded: chain o residue 40 ILE Chi-restraints excluded: chain o residue 54 VAL Chi-restraints excluded: chain p residue 2 SER Chi-restraints excluded: chain p residue 7 GLN Chi-restraints excluded: chain p residue 52 ASN Chi-restraints excluded: chain p residue 63 LYS Chi-restraints excluded: chain p residue 70 VAL Chi-restraints excluded: chain p residue 76 THR Chi-restraints excluded: chain s residue 108 SER Chi-restraints excluded: chain t residue 27 SER Chi-restraints excluded: chain t residue 64 LYS Chi-restraints excluded: chain u residue 39 ILE Chi-restraints excluded: chain u residue 68 SER Chi-restraints excluded: chain u residue 83 VAL Chi-restraints excluded: chain w residue 65 VAL Chi-restraints excluded: chain y residue 9 SER Chi-restraints excluded: chain y residue 43 THR Chi-restraints excluded: chain z residue 135 ASN Chi-restraints excluded: chain z residue 143 SER Chi-restraints excluded: chain z residue 148 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 611 random chunks: chunk 308 optimal weight: 8.9990 chunk 172 optimal weight: 9.9990 chunk 461 optimal weight: 7.9990 chunk 377 optimal weight: 0.7980 chunk 153 optimal weight: 10.0000 chunk 555 optimal weight: 6.9990 chunk 600 optimal weight: 10.0000 chunk 495 optimal weight: 8.9990 chunk 551 optimal weight: 8.9990 chunk 189 optimal weight: 8.9990 chunk 445 optimal weight: 9.9990 overall best weight: 6.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 26 ASN 6 6 GLN c 21 ASN c 153 GLN d 42 ASN e 41 GLN f 52 ASN g 143 GLN j 67 ASN ** j 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 18 GLN o 104 GLN o 116 GLN r 6 GLN r 86 GLN r 89 HIS t 48 GLN t 69 GLN w 75 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.0818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.086 99333 Z= 0.487 Angle : 0.736 8.420 149476 Z= 0.382 Chirality : 0.047 0.430 19217 Planarity : 0.006 0.053 7388 Dihedral : 23.940 179.543 51780 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.62 % Favored : 95.28 % Rotamer: Outliers : 6.53 % Allowed : 26.77 % Favored : 66.71 % 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: -0.25 (0.15), residues: 3095 helix: 1.03 (0.18), residues: 814 sheet: -0.20 (0.18), residues: 731 loop : -0.74 (0.15), residues: 1550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP c 248 HIS 0.008 0.002 HIS c 15 PHE 0.023 0.002 PHE q 57 TYR 0.017 0.002 TYR c 161 ARG 0.008 0.001 ARG 6 39 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6190 Ramachandran restraints generated. 3095 Oldfield, 0 Emsley, 3095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6190 Ramachandran restraints generated. 3095 Oldfield, 0 Emsley, 3095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 657 residues out of total 2559 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 490 time to evaluate : 4.282 Fit side-chains REVERT: 1 24 GLU cc_start: 0.8108 (tp30) cc_final: 0.7718 (tp30) REVERT: 3 27 SER cc_start: 0.5005 (OUTLIER) cc_final: 0.4663 (p) REVERT: 3 46 ASP cc_start: 0.8366 (OUTLIER) cc_final: 0.7827 (t70) REVERT: 4 7 GLU cc_start: 0.8045 (pm20) cc_final: 0.7633 (pm20) REVERT: 4 25 LYS cc_start: 0.8654 (tttm) cc_final: 0.8111 (tttt) REVERT: 4 27 LYS cc_start: 0.8744 (OUTLIER) cc_final: 0.8485 (mptm) REVERT: 6 1 MET cc_start: 0.7775 (mtp) cc_final: 0.7536 (mtp) REVERT: 7 40 ARG cc_start: 0.8692 (OUTLIER) cc_final: 0.6928 (ttm170) REVERT: 8 30 GLU cc_start: 0.8113 (tp30) cc_final: 0.7746 (tp30) REVERT: c 36 LYS cc_start: 0.9160 (OUTLIER) cc_final: 0.8959 (pttp) REVERT: c 90 ASN cc_start: 0.8242 (OUTLIER) cc_final: 0.7842 (m110) REVERT: c 163 GLN cc_start: 0.7841 (tt0) cc_final: 0.7183 (mt0) REVERT: d 74 GLU cc_start: 0.7541 (OUTLIER) cc_final: 0.7200 (mp0) REVERT: d 176 ASP cc_start: 0.8490 (m-30) cc_final: 0.8196 (m-30) REVERT: e 21 ARG cc_start: 0.7824 (mtm110) cc_final: 0.7581 (mtp85) REVERT: e 170 ARG cc_start: 0.9036 (OUTLIER) cc_final: 0.7623 (tpp80) REVERT: f 64 LYS cc_start: 0.8806 (OUTLIER) cc_final: 0.8458 (pttt) REVERT: f 113 ASP cc_start: 0.8396 (t70) cc_final: 0.8181 (t0) REVERT: g 155 GLU cc_start: 0.8387 (OUTLIER) cc_final: 0.7862 (pp20) REVERT: g 163 ARG cc_start: 0.8318 (OUTLIER) cc_final: 0.7151 (ptt180) REVERT: h 27 ARG cc_start: 0.7894 (OUTLIER) cc_final: 0.7633 (ptt-90) REVERT: j 92 MET cc_start: 0.8880 (mmm) cc_final: 0.8279 (mmm) REVERT: j 96 ARG cc_start: 0.8331 (OUTLIER) cc_final: 0.7945 (pmt170) REVERT: j 103 ILE cc_start: 0.8191 (OUTLIER) cc_final: 0.7909 (pp) REVERT: k 30 ARG cc_start: 0.8809 (OUTLIER) cc_final: 0.8395 (ttt-90) REVERT: k 105 ARG cc_start: 0.8303 (OUTLIER) cc_final: 0.7003 (mtm-85) REVERT: k 114 LYS cc_start: 0.8523 (mtpp) cc_final: 0.8114 (ttmt) REVERT: m 12 MET cc_start: 0.8311 (mtp) cc_final: 0.7938 (mtp) REVERT: m 115 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.7422 (tt0) REVERT: n 14 SER cc_start: 0.9060 (t) cc_final: 0.8709 (t) REVERT: n 72 ASP cc_start: 0.8458 (t0) cc_final: 0.8191 (t0) REVERT: o 40 ILE cc_start: 0.8826 (OUTLIER) cc_final: 0.8579 (mm) REVERT: p 7 GLN cc_start: 0.8035 (OUTLIER) cc_final: 0.7710 (pp30) REVERT: p 10 GLN cc_start: 0.8171 (tp-100) cc_final: 0.7865 (tp40) REVERT: r 46 GLU cc_start: 0.7762 (OUTLIER) cc_final: 0.7163 (mm-30) REVERT: r 97 LYS cc_start: 0.9037 (tttm) cc_final: 0.8774 (tttp) REVERT: s 92 ARG cc_start: 0.7452 (OUTLIER) cc_final: 0.6817 (ttp-170) REVERT: t 9 LYS cc_start: 0.8710 (OUTLIER) cc_final: 0.7582 (mppt) REVERT: t 64 LYS cc_start: 0.8597 (OUTLIER) cc_final: 0.7252 (mmtp) REVERT: t 73 ARG cc_start: 0.7634 (OUTLIER) cc_final: 0.7126 (ptm-80) REVERT: w 85 LYS cc_start: 0.8756 (OUTLIER) cc_final: 0.7946 (mptp) REVERT: y 25 ARG cc_start: 0.8263 (mmt-90) cc_final: 0.7996 (mmm-85) REVERT: y 78 LYS cc_start: 0.8776 (mtpt) cc_final: 0.8295 (mttm) outliers start: 167 outliers final: 94 residues processed: 599 average time/residue: 1.9000 time to fit residues: 1516.0923 Evaluate side-chains 604 residues out of total 2559 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 485 time to evaluate : 3.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 35 SER Chi-restraints excluded: chain 1 residue 19 LEU Chi-restraints excluded: chain 1 residue 59 GLU Chi-restraints excluded: chain 2 residue 5 ILE Chi-restraints excluded: chain 2 residue 12 SER Chi-restraints excluded: chain 3 residue 25 VAL Chi-restraints excluded: chain 3 residue 27 SER Chi-restraints excluded: chain 3 residue 29 SER Chi-restraints excluded: chain 3 residue 46 ASP Chi-restraints excluded: chain 4 residue 27 LYS Chi-restraints excluded: chain 4 residue 42 VAL Chi-restraints excluded: chain 6 residue 8 SER Chi-restraints excluded: chain 6 residue 15 SER Chi-restraints excluded: chain 7 residue 40 ARG Chi-restraints excluded: chain c residue 36 LYS Chi-restraints excluded: chain c residue 90 ASN Chi-restraints excluded: chain d residue 2 ILE Chi-restraints excluded: chain d residue 7 LYS Chi-restraints excluded: chain d residue 56 LYS Chi-restraints excluded: chain d residue 58 ASN Chi-restraints excluded: chain d residue 60 VAL Chi-restraints excluded: chain d residue 74 GLU Chi-restraints excluded: chain d residue 84 LEU Chi-restraints excluded: chain d residue 97 SER Chi-restraints excluded: chain d residue 100 LEU Chi-restraints excluded: chain d residue 151 THR Chi-restraints excluded: chain e residue 10 SER Chi-restraints excluded: chain e residue 65 THR Chi-restraints excluded: chain e residue 80 SER Chi-restraints excluded: chain e residue 126 VAL Chi-restraints excluded: chain e residue 133 LEU Chi-restraints excluded: chain e residue 166 LYS Chi-restraints excluded: chain e residue 170 ARG Chi-restraints excluded: chain e residue 191 ASP Chi-restraints excluded: chain e residue 200 LEU Chi-restraints excluded: chain f residue 35 THR Chi-restraints excluded: chain f residue 42 GLU Chi-restraints excluded: chain f residue 64 LYS Chi-restraints excluded: chain f residue 88 LYS Chi-restraints excluded: chain f residue 103 LEU Chi-restraints excluded: chain f residue 125 ARG Chi-restraints excluded: chain f residue 137 ILE Chi-restraints excluded: chain g residue 15 VAL Chi-restraints excluded: chain g residue 23 VAL Chi-restraints excluded: chain g residue 25 THR Chi-restraints excluded: chain g residue 30 ASN Chi-restraints excluded: chain g residue 37 LEU Chi-restraints excluded: chain g residue 41 VAL Chi-restraints excluded: chain g residue 106 SER Chi-restraints excluded: chain g residue 110 SER Chi-restraints excluded: chain g residue 127 THR Chi-restraints excluded: chain g residue 155 GLU Chi-restraints excluded: chain g residue 163 ARG Chi-restraints excluded: chain g residue 168 VAL Chi-restraints excluded: chain h residue 11 ASN Chi-restraints excluded: chain h residue 15 LEU Chi-restraints excluded: chain h residue 27 ARG Chi-restraints excluded: chain j residue 21 THR Chi-restraints excluded: chain j residue 30 THR Chi-restraints excluded: chain j residue 48 VAL Chi-restraints excluded: chain j residue 96 ARG Chi-restraints excluded: chain j residue 101 ILE Chi-restraints excluded: chain j residue 103 ILE Chi-restraints excluded: chain k residue 30 ARG Chi-restraints excluded: chain k residue 76 VAL Chi-restraints excluded: chain k residue 105 ARG Chi-restraints excluded: chain l residue 85 VAL Chi-restraints excluded: chain l residue 117 THR Chi-restraints excluded: chain l residue 121 THR Chi-restraints excluded: chain m residue 1 MET Chi-restraints excluded: chain m residue 22 GLN Chi-restraints excluded: chain m residue 41 LEU Chi-restraints excluded: chain m residue 115 GLU Chi-restraints excluded: chain m residue 135 VAL Chi-restraints excluded: chain n residue 36 THR Chi-restraints excluded: chain n residue 57 THR Chi-restraints excluded: chain n residue 65 LEU Chi-restraints excluded: chain n residue 70 THR Chi-restraints excluded: chain o residue 5 SER Chi-restraints excluded: chain o residue 20 GLU Chi-restraints excluded: chain o residue 24 THR Chi-restraints excluded: chain o residue 40 ILE Chi-restraints excluded: chain o residue 54 VAL Chi-restraints excluded: chain p residue 4 ILE Chi-restraints excluded: chain p residue 5 ILE Chi-restraints excluded: chain p residue 7 GLN Chi-restraints excluded: chain p residue 30 VAL Chi-restraints excluded: chain p residue 52 ASN Chi-restraints excluded: chain p residue 63 LYS Chi-restraints excluded: chain p residue 70 VAL Chi-restraints excluded: chain p residue 76 THR Chi-restraints excluded: chain p residue 102 GLU Chi-restraints excluded: chain r residue 15 SER Chi-restraints excluded: chain r residue 46 GLU Chi-restraints excluded: chain r residue 71 LYS Chi-restraints excluded: chain s residue 92 ARG Chi-restraints excluded: chain s residue 101 SER Chi-restraints excluded: chain s residue 107 VAL Chi-restraints excluded: chain s residue 108 SER Chi-restraints excluded: chain t residue 9 LYS Chi-restraints excluded: chain t residue 27 SER Chi-restraints excluded: chain t residue 64 LYS Chi-restraints excluded: chain t residue 73 ARG Chi-restraints excluded: chain u residue 59 VAL Chi-restraints excluded: chain u residue 68 SER Chi-restraints excluded: chain u residue 83 VAL Chi-restraints excluded: chain u residue 89 ASP Chi-restraints excluded: chain u residue 100 SER Chi-restraints excluded: chain w residue 12 GLN Chi-restraints excluded: chain w residue 41 GLU Chi-restraints excluded: chain w residue 65 VAL Chi-restraints excluded: chain w residue 85 LYS Chi-restraints excluded: chain y residue 9 SER Chi-restraints excluded: chain y residue 43 THR Chi-restraints excluded: chain y residue 58 THR Chi-restraints excluded: chain y residue 70 GLU Chi-restraints excluded: chain z residue 135 ASN Chi-restraints excluded: chain z residue 143 SER Chi-restraints excluded: chain z residue 147 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 611 random chunks: chunk 549 optimal weight: 0.8980 chunk 417 optimal weight: 0.9990 chunk 288 optimal weight: 5.9990 chunk 61 optimal weight: 10.0000 chunk 265 optimal weight: 70.0000 chunk 373 optimal weight: 7.9990 chunk 557 optimal weight: 1.9990 chunk 590 optimal weight: 4.9990 chunk 291 optimal weight: 6.9990 chunk 528 optimal weight: 3.9990 chunk 159 optimal weight: 80.0000 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 17 ASN 6 29 GLN d 42 ASN h 33 GLN ** j 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 18 GLN o 116 GLN ** p 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 6 GLN r 86 GLN t 48 GLN w 12 GLN w 75 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.1052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 99333 Z= 0.212 Angle : 0.573 8.790 149476 Z= 0.305 Chirality : 0.037 0.313 19217 Planarity : 0.005 0.050 7388 Dihedral : 23.859 179.309 51780 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.10 % Favored : 95.80 % Rotamer: Outliers : 5.51 % Allowed : 26.85 % Favored : 67.64 % 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: 0.02 (0.15), residues: 3095 helix: 1.25 (0.19), residues: 820 sheet: -0.03 (0.19), residues: 721 loop : -0.58 (0.15), residues: 1554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP c 213 HIS 0.004 0.001 HIS r 89 PHE 0.016 0.001 PHE q 57 TYR 0.014 0.001 TYR f 83 ARG 0.007 0.000 ARG r 78 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6190 Ramachandran restraints generated. 3095 Oldfield, 0 Emsley, 3095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6190 Ramachandran restraints generated. 3095 Oldfield, 0 Emsley, 3095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 641 residues out of total 2559 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 500 time to evaluate : 3.941 Fit side-chains revert: symmetry clash REVERT: 1 24 GLU cc_start: 0.8087 (tp30) cc_final: 0.7662 (tp30) REVERT: 3 27 SER cc_start: 0.4617 (OUTLIER) cc_final: 0.4395 (p) REVERT: 4 7 GLU cc_start: 0.8008 (pm20) cc_final: 0.7607 (pm20) REVERT: 4 25 LYS cc_start: 0.8605 (tttm) cc_final: 0.8019 (tttt) REVERT: 4 27 LYS cc_start: 0.8751 (OUTLIER) cc_final: 0.8525 (mptm) REVERT: 6 1 MET cc_start: 0.7840 (mtp) cc_final: 0.7608 (mtp) REVERT: 8 30 GLU cc_start: 0.8159 (tp30) cc_final: 0.7884 (tp30) REVERT: c 90 ASN cc_start: 0.8134 (OUTLIER) cc_final: 0.7891 (m-40) REVERT: c 118 SER cc_start: 0.8936 (p) cc_final: 0.8723 (p) REVERT: c 163 GLN cc_start: 0.7803 (tt0) cc_final: 0.7172 (mt0) REVERT: c 251 GLN cc_start: 0.8526 (OUTLIER) cc_final: 0.8276 (tp40) REVERT: d 74 GLU cc_start: 0.7529 (OUTLIER) cc_final: 0.7176 (mp0) REVERT: d 176 ASP cc_start: 0.8487 (m-30) cc_final: 0.8182 (m-30) REVERT: e 141 MET cc_start: 0.8245 (mtp) cc_final: 0.8003 (mtp) REVERT: f 113 ASP cc_start: 0.8349 (t70) cc_final: 0.8120 (t0) REVERT: g 163 ARG cc_start: 0.8251 (OUTLIER) cc_final: 0.7196 (ptt180) REVERT: j 23 LYS cc_start: 0.8744 (OUTLIER) cc_final: 0.7538 (mmtm) REVERT: j 92 MET cc_start: 0.8866 (mmm) cc_final: 0.8285 (mmm) REVERT: j 96 ARG cc_start: 0.8374 (OUTLIER) cc_final: 0.7921 (pmt170) REVERT: j 103 ILE cc_start: 0.8117 (OUTLIER) cc_final: 0.7871 (pp) REVERT: k 30 ARG cc_start: 0.8772 (OUTLIER) cc_final: 0.8338 (ttt-90) REVERT: k 105 ARG cc_start: 0.8245 (OUTLIER) cc_final: 0.6952 (mtm-85) REVERT: k 114 LYS cc_start: 0.8417 (mtpp) cc_final: 0.8008 (ttmt) REVERT: k 121 GLU cc_start: 0.8336 (tt0) cc_final: 0.8084 (tt0) REVERT: k 122 VAL cc_start: 0.7907 (t) cc_final: 0.6489 (t) REVERT: m 12 MET cc_start: 0.8240 (mtp) cc_final: 0.7811 (mtp) REVERT: m 115 GLU cc_start: 0.8018 (OUTLIER) cc_final: 0.7447 (tt0) REVERT: n 72 ASP cc_start: 0.8387 (t0) cc_final: 0.8087 (t0) REVERT: o 40 ILE cc_start: 0.8651 (OUTLIER) cc_final: 0.8324 (mm) REVERT: p 7 GLN cc_start: 0.7840 (OUTLIER) cc_final: 0.7599 (pp30) REVERT: p 10 GLN cc_start: 0.8136 (tp-100) cc_final: 0.7847 (tp40) REVERT: p 68 GLU cc_start: 0.7627 (OUTLIER) cc_final: 0.7385 (pm20) REVERT: r 46 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.7260 (mm-30) REVERT: r 97 LYS cc_start: 0.9008 (tttm) cc_final: 0.8737 (tttp) REVERT: s 4 ILE cc_start: 0.9155 (mt) cc_final: 0.8937 (mp) REVERT: s 92 ARG cc_start: 0.7341 (mtp180) cc_final: 0.6658 (ttp-170) REVERT: t 9 LYS cc_start: 0.8678 (OUTLIER) cc_final: 0.7544 (mppt) REVERT: t 24 MET cc_start: 0.7219 (tpt) cc_final: 0.7009 (tpt) REVERT: t 36 LYS cc_start: 0.9009 (OUTLIER) cc_final: 0.8772 (tttt) REVERT: t 64 LYS cc_start: 0.8605 (OUTLIER) cc_final: 0.7378 (mmtp) REVERT: w 7 GLU cc_start: 0.7406 (mt-10) cc_final: 0.7087 (mp0) REVERT: w 85 LYS cc_start: 0.8678 (OUTLIER) cc_final: 0.7840 (mptp) REVERT: y 25 ARG cc_start: 0.8221 (mmt-90) cc_final: 0.7938 (mmm-85) REVERT: y 62 LYS cc_start: 0.8938 (mtmt) cc_final: 0.8632 (mtpt) REVERT: y 78 LYS cc_start: 0.8692 (mtpt) cc_final: 0.8195 (mttm) REVERT: z 157 ILE cc_start: 0.7257 (OUTLIER) cc_final: 0.6873 (mt) outliers start: 141 outliers final: 70 residues processed: 594 average time/residue: 1.8857 time to fit residues: 1486.6578 Evaluate side-chains 581 residues out of total 2559 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 490 time to evaluate : 3.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 59 GLU Chi-restraints excluded: chain 2 residue 5 ILE Chi-restraints excluded: chain 2 residue 12 SER Chi-restraints excluded: chain 2 residue 58 GLU Chi-restraints excluded: chain 3 residue 25 VAL Chi-restraints excluded: chain 3 residue 27 SER Chi-restraints excluded: chain 3 residue 29 SER Chi-restraints excluded: chain 4 residue 27 LYS Chi-restraints excluded: chain 4 residue 42 VAL Chi-restraints excluded: chain 7 residue 54 ASP Chi-restraints excluded: chain c residue 90 ASN Chi-restraints excluded: chain c residue 165 VAL Chi-restraints excluded: chain c residue 251 GLN Chi-restraints excluded: chain d residue 2 ILE Chi-restraints excluded: chain d residue 7 LYS Chi-restraints excluded: chain d residue 60 VAL Chi-restraints excluded: chain d residue 74 GLU Chi-restraints excluded: chain d residue 84 LEU Chi-restraints excluded: chain d residue 100 LEU Chi-restraints excluded: chain d residue 151 THR Chi-restraints excluded: chain e residue 10 SER Chi-restraints excluded: chain e residue 126 VAL Chi-restraints excluded: chain e residue 191 ASP Chi-restraints excluded: chain f residue 35 THR Chi-restraints excluded: chain f residue 42 GLU Chi-restraints excluded: chain f residue 88 LYS Chi-restraints excluded: chain f residue 103 LEU Chi-restraints excluded: chain f residue 125 ARG Chi-restraints excluded: chain g residue 15 VAL Chi-restraints excluded: chain g residue 23 VAL Chi-restraints excluded: chain g residue 25 THR Chi-restraints excluded: chain g residue 41 VAL Chi-restraints excluded: chain g residue 81 GLU Chi-restraints excluded: chain g residue 106 SER Chi-restraints excluded: chain g residue 163 ARG Chi-restraints excluded: chain g residue 168 VAL Chi-restraints excluded: chain h residue 15 LEU Chi-restraints excluded: chain j residue 23 LYS Chi-restraints excluded: chain j residue 30 THR Chi-restraints excluded: chain j residue 48 VAL Chi-restraints excluded: chain j residue 96 ARG Chi-restraints excluded: chain j residue 101 ILE Chi-restraints excluded: chain j residue 103 ILE Chi-restraints excluded: chain k residue 30 ARG Chi-restraints excluded: chain k residue 76 VAL Chi-restraints excluded: chain k residue 105 ARG Chi-restraints excluded: chain l residue 85 VAL Chi-restraints excluded: chain l residue 121 THR Chi-restraints excluded: chain m residue 1 MET Chi-restraints excluded: chain m residue 22 GLN Chi-restraints excluded: chain m residue 30 SER Chi-restraints excluded: chain m residue 41 LEU Chi-restraints excluded: chain m residue 115 GLU Chi-restraints excluded: chain m residue 135 VAL Chi-restraints excluded: chain n residue 36 THR Chi-restraints excluded: chain n residue 57 THR Chi-restraints excluded: chain n residue 65 LEU Chi-restraints excluded: chain n residue 70 THR Chi-restraints excluded: chain o residue 20 GLU Chi-restraints excluded: chain o residue 24 THR Chi-restraints excluded: chain o residue 40 ILE Chi-restraints excluded: chain o residue 54 VAL Chi-restraints excluded: chain p residue 7 GLN Chi-restraints excluded: chain p residue 52 ASN Chi-restraints excluded: chain p residue 63 LYS Chi-restraints excluded: chain p residue 68 GLU Chi-restraints excluded: chain p residue 70 VAL Chi-restraints excluded: chain p residue 76 THR Chi-restraints excluded: chain r residue 16 GLU Chi-restraints excluded: chain r residue 46 GLU Chi-restraints excluded: chain r residue 71 LYS Chi-restraints excluded: chain s residue 108 SER Chi-restraints excluded: chain s residue 109 ASP Chi-restraints excluded: chain t residue 9 LYS Chi-restraints excluded: chain t residue 27 SER Chi-restraints excluded: chain t residue 36 LYS Chi-restraints excluded: chain t residue 64 LYS Chi-restraints excluded: chain u residue 15 THR Chi-restraints excluded: chain u residue 39 ILE Chi-restraints excluded: chain u residue 68 SER Chi-restraints excluded: chain u residue 83 VAL Chi-restraints excluded: chain u residue 89 ASP Chi-restraints excluded: chain w residue 12 GLN Chi-restraints excluded: chain w residue 41 GLU Chi-restraints excluded: chain w residue 65 VAL Chi-restraints excluded: chain w residue 85 LYS Chi-restraints excluded: chain y residue 9 SER Chi-restraints excluded: chain y residue 43 THR Chi-restraints excluded: chain z residue 135 ASN Chi-restraints excluded: chain z residue 147 THR Chi-restraints excluded: chain z residue 157 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 611 random chunks: chunk 491 optimal weight: 0.0870 chunk 335 optimal weight: 10.0000 chunk 8 optimal weight: 5.9990 chunk 439 optimal weight: 9.9990 chunk 243 optimal weight: 10.0000 chunk 503 optimal weight: 10.0000 chunk 408 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 301 optimal weight: 10.0000 chunk 530 optimal weight: 9.9990 chunk 149 optimal weight: 7.9990 overall best weight: 6.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 17 ASN 4 26 ASN 6 29 GLN d 42 ASN g 104 ASN ** j 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 18 GLN o 104 GLN ** p 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 6 GLN r 86 GLN s 61 ASN t 48 GLN t 99 GLN w 75 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.0960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.079 99333 Z= 0.489 Angle : 0.734 8.687 149476 Z= 0.381 Chirality : 0.047 0.431 19217 Planarity : 0.006 0.055 7388 Dihedral : 23.878 179.635 51780 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.49 % Favored : 95.41 % Rotamer: Outliers : 6.76 % Allowed : 25.32 % Favored : 67.92 % 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: -0.15 (0.15), residues: 3095 helix: 1.13 (0.18), residues: 814 sheet: -0.13 (0.19), residues: 731 loop : -0.69 (0.15), residues: 1550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP c 248 HIS 0.008 0.002 HIS r 89 PHE 0.020 0.002 PHE q 57 TYR 0.017 0.002 TYR c 161 ARG 0.007 0.001 ARG z 162 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6190 Ramachandran restraints generated. 3095 Oldfield, 0 Emsley, 3095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6190 Ramachandran restraints generated. 3095 Oldfield, 0 Emsley, 3095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 660 residues out of total 2559 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 487 time to evaluate : 4.148 Fit side-chains revert: symmetry clash REVERT: 1 24 GLU cc_start: 0.8124 (tp30) cc_final: 0.7699 (tp30) REVERT: 3 27 SER cc_start: 0.4969 (OUTLIER) cc_final: 0.4637 (p) REVERT: 6 1 MET cc_start: 0.7818 (mtp) cc_final: 0.7579 (mtp) REVERT: 7 40 ARG cc_start: 0.8676 (OUTLIER) cc_final: 0.6945 (ttm170) REVERT: 8 30 GLU cc_start: 0.8175 (tp30) cc_final: 0.7787 (tp30) REVERT: c 90 ASN cc_start: 0.8233 (OUTLIER) cc_final: 0.7858 (m110) REVERT: c 163 GLN cc_start: 0.7849 (tt0) cc_final: 0.7193 (mt0) REVERT: d 74 GLU cc_start: 0.7522 (OUTLIER) cc_final: 0.7192 (mp0) REVERT: d 176 ASP cc_start: 0.8487 (m-30) cc_final: 0.8199 (m-30) REVERT: e 69 ARG cc_start: 0.8526 (OUTLIER) cc_final: 0.7280 (ptp-170) REVERT: f 64 LYS cc_start: 0.8783 (OUTLIER) cc_final: 0.8439 (pttt) REVERT: f 113 ASP cc_start: 0.8394 (t70) cc_final: 0.8149 (t0) REVERT: g 81 GLU cc_start: 0.8588 (OUTLIER) cc_final: 0.8148 (pm20) REVERT: g 163 ARG cc_start: 0.8327 (OUTLIER) cc_final: 0.7126 (ptt180) REVERT: j 23 LYS cc_start: 0.8768 (OUTLIER) cc_final: 0.7518 (mmtm) REVERT: j 92 MET cc_start: 0.8869 (mmm) cc_final: 0.8299 (mmm) REVERT: j 96 ARG cc_start: 0.8450 (OUTLIER) cc_final: 0.7927 (pmt170) REVERT: j 103 ILE cc_start: 0.8210 (OUTLIER) cc_final: 0.7916 (pp) REVERT: k 30 ARG cc_start: 0.8813 (OUTLIER) cc_final: 0.8394 (ttt-90) REVERT: k 38 ILE cc_start: 0.9139 (OUTLIER) cc_final: 0.8927 (mm) REVERT: k 105 ARG cc_start: 0.8305 (OUTLIER) cc_final: 0.6961 (mtm-85) REVERT: k 114 LYS cc_start: 0.8502 (mtpp) cc_final: 0.8057 (ttmt) REVERT: m 12 MET cc_start: 0.8344 (mtp) cc_final: 0.7943 (mtp) REVERT: m 115 GLU cc_start: 0.8002 (OUTLIER) cc_final: 0.7425 (tt0) REVERT: n 72 ASP cc_start: 0.8428 (t0) cc_final: 0.8183 (t0) REVERT: p 10 GLN cc_start: 0.8148 (tp-100) cc_final: 0.7932 (tp40) REVERT: p 68 GLU cc_start: 0.7777 (OUTLIER) cc_final: 0.7545 (pm20) REVERT: r 46 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7447 (mm-30) REVERT: r 48 LYS cc_start: 0.8489 (OUTLIER) cc_final: 0.8259 (tppp) REVERT: r 97 LYS cc_start: 0.9040 (tttm) cc_final: 0.8785 (tttp) REVERT: s 92 ARG cc_start: 0.7370 (OUTLIER) cc_final: 0.6619 (ttp-170) REVERT: t 9 LYS cc_start: 0.8713 (OUTLIER) cc_final: 0.7673 (mppt) REVERT: t 36 LYS cc_start: 0.9031 (OUTLIER) cc_final: 0.8791 (tttt) REVERT: t 64 LYS cc_start: 0.8596 (OUTLIER) cc_final: 0.7345 (mmtp) REVERT: u 24 LYS cc_start: 0.8549 (OUTLIER) cc_final: 0.8291 (ttpp) REVERT: u 37 GLU cc_start: 0.7894 (OUTLIER) cc_final: 0.7581 (mt-10) REVERT: w 85 LYS cc_start: 0.8760 (OUTLIER) cc_final: 0.7920 (mptp) REVERT: y 25 ARG cc_start: 0.8207 (mmt-90) cc_final: 0.7935 (mmm-85) REVERT: y 78 LYS cc_start: 0.8702 (mtpt) cc_final: 0.8228 (mttm) REVERT: z 157 ILE cc_start: 0.7329 (OUTLIER) cc_final: 0.6920 (mt) outliers start: 173 outliers final: 102 residues processed: 599 average time/residue: 1.9166 time to fit residues: 1528.7030 Evaluate side-chains 609 residues out of total 2559 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 481 time to evaluate : 4.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 35 SER Chi-restraints excluded: chain 1 residue 19 LEU Chi-restraints excluded: chain 1 residue 59 GLU Chi-restraints excluded: chain 2 residue 5 ILE Chi-restraints excluded: chain 2 residue 12 SER Chi-restraints excluded: chain 2 residue 58 GLU Chi-restraints excluded: chain 3 residue 25 VAL Chi-restraints excluded: chain 3 residue 27 SER Chi-restraints excluded: chain 3 residue 29 SER Chi-restraints excluded: chain 3 residue 46 ASP Chi-restraints excluded: chain 4 residue 42 VAL Chi-restraints excluded: chain 6 residue 8 SER Chi-restraints excluded: chain 7 residue 40 ARG Chi-restraints excluded: chain 7 residue 52 LYS Chi-restraints excluded: chain 8 residue 26 ILE Chi-restraints excluded: chain c residue 90 ASN Chi-restraints excluded: chain c residue 165 VAL Chi-restraints excluded: chain d residue 2 ILE Chi-restraints excluded: chain d residue 7 LYS Chi-restraints excluded: chain d residue 58 ASN Chi-restraints excluded: chain d residue 60 VAL Chi-restraints excluded: chain d residue 74 GLU Chi-restraints excluded: chain d residue 84 LEU Chi-restraints excluded: chain d residue 97 SER Chi-restraints excluded: chain d residue 100 LEU Chi-restraints excluded: chain d residue 151 THR Chi-restraints excluded: chain e residue 10 SER Chi-restraints excluded: chain e residue 65 THR Chi-restraints excluded: chain e residue 69 ARG Chi-restraints excluded: chain e residue 126 VAL Chi-restraints excluded: chain e residue 133 LEU Chi-restraints excluded: chain e residue 166 LYS Chi-restraints excluded: chain e residue 191 ASP Chi-restraints excluded: chain f residue 35 THR Chi-restraints excluded: chain f residue 42 GLU Chi-restraints excluded: chain f residue 64 LYS Chi-restraints excluded: chain f residue 88 LYS Chi-restraints excluded: chain f residue 90 THR Chi-restraints excluded: chain f residue 103 LEU Chi-restraints excluded: chain f residue 125 ARG Chi-restraints excluded: chain f residue 136 ILE Chi-restraints excluded: chain f residue 137 ILE Chi-restraints excluded: chain f residue 170 LEU Chi-restraints excluded: chain g residue 2 SER Chi-restraints excluded: chain g residue 15 VAL Chi-restraints excluded: chain g residue 23 VAL Chi-restraints excluded: chain g residue 27 LYS Chi-restraints excluded: chain g residue 37 LEU Chi-restraints excluded: chain g residue 41 VAL Chi-restraints excluded: chain g residue 81 GLU Chi-restraints excluded: chain g residue 85 LYS Chi-restraints excluded: chain g residue 106 SER Chi-restraints excluded: chain g residue 110 SER Chi-restraints excluded: chain g residue 127 THR Chi-restraints excluded: chain g residue 163 ARG Chi-restraints excluded: chain g residue 168 VAL Chi-restraints excluded: chain h residue 11 ASN Chi-restraints excluded: chain h residue 15 LEU Chi-restraints excluded: chain h residue 27 ARG Chi-restraints excluded: chain j residue 21 THR Chi-restraints excluded: chain j residue 23 LYS Chi-restraints excluded: chain j residue 30 THR Chi-restraints excluded: chain j residue 48 VAL Chi-restraints excluded: chain j residue 96 ARG Chi-restraints excluded: chain j residue 101 ILE Chi-restraints excluded: chain j residue 103 ILE Chi-restraints excluded: chain k residue 30 ARG Chi-restraints excluded: chain k residue 38 ILE Chi-restraints excluded: chain k residue 76 VAL Chi-restraints excluded: chain k residue 105 ARG Chi-restraints excluded: chain l residue 80 SER Chi-restraints excluded: chain l residue 85 VAL Chi-restraints excluded: chain l residue 117 THR Chi-restraints excluded: chain l residue 121 THR Chi-restraints excluded: chain m residue 1 MET Chi-restraints excluded: chain m residue 22 GLN Chi-restraints excluded: chain m residue 41 LEU Chi-restraints excluded: chain m residue 115 GLU Chi-restraints excluded: chain m residue 135 VAL Chi-restraints excluded: chain n residue 14 SER Chi-restraints excluded: chain n residue 36 THR Chi-restraints excluded: chain n residue 57 THR Chi-restraints excluded: chain n residue 65 LEU Chi-restraints excluded: chain n residue 70 THR Chi-restraints excluded: chain o residue 5 SER Chi-restraints excluded: chain o residue 20 GLU Chi-restraints excluded: chain o residue 24 THR Chi-restraints excluded: chain o residue 40 ILE Chi-restraints excluded: chain o residue 54 VAL Chi-restraints excluded: chain p residue 4 ILE Chi-restraints excluded: chain p residue 5 ILE Chi-restraints excluded: chain p residue 30 VAL Chi-restraints excluded: chain p residue 52 ASN Chi-restraints excluded: chain p residue 63 LYS Chi-restraints excluded: chain p residue 68 GLU Chi-restraints excluded: chain p residue 70 VAL Chi-restraints excluded: chain p residue 76 THR Chi-restraints excluded: chain r residue 46 GLU Chi-restraints excluded: chain r residue 48 LYS Chi-restraints excluded: chain r residue 71 LYS Chi-restraints excluded: chain s residue 92 ARG Chi-restraints excluded: chain s residue 101 SER Chi-restraints excluded: chain s residue 108 SER Chi-restraints excluded: chain s residue 109 ASP Chi-restraints excluded: chain t residue 9 LYS Chi-restraints excluded: chain t residue 27 SER Chi-restraints excluded: chain t residue 36 LYS Chi-restraints excluded: chain t residue 64 LYS Chi-restraints excluded: chain u residue 15 THR Chi-restraints excluded: chain u residue 24 LYS Chi-restraints excluded: chain u residue 37 GLU Chi-restraints excluded: chain u residue 59 VAL Chi-restraints excluded: chain u residue 68 SER Chi-restraints excluded: chain u residue 83 VAL Chi-restraints excluded: chain u residue 89 ASP Chi-restraints excluded: chain u residue 100 SER Chi-restraints excluded: chain w residue 11 GLU Chi-restraints excluded: chain w residue 12 GLN Chi-restraints excluded: chain w residue 41 GLU Chi-restraints excluded: chain w residue 65 VAL Chi-restraints excluded: chain w residue 85 LYS Chi-restraints excluded: chain y residue 9 SER Chi-restraints excluded: chain y residue 43 THR Chi-restraints excluded: chain y residue 70 GLU Chi-restraints excluded: chain z residue 135 ASN Chi-restraints excluded: chain z residue 143 SER Chi-restraints excluded: chain z residue 147 THR Chi-restraints excluded: chain z residue 157 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 611 random chunks: chunk 198 optimal weight: 10.0000 chunk 531 optimal weight: 0.8980 chunk 116 optimal weight: 8.9990 chunk 346 optimal weight: 4.9990 chunk 145 optimal weight: 8.9990 chunk 591 optimal weight: 7.9990 chunk 490 optimal weight: 2.9990 chunk 273 optimal weight: 10.0000 chunk 49 optimal weight: 8.9990 chunk 195 optimal weight: 7.9990 chunk 310 optimal weight: 5.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 17 ASN 6 29 GLN d 42 ASN ** j 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 18 GLN o 104 GLN r 6 GLN r 86 GLN s 61 ASN t 48 GLN w 75 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.0976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 99333 Z= 0.344 Angle : 0.654 12.921 149476 Z= 0.346 Chirality : 0.042 0.381 19217 Planarity : 0.005 0.054 7388 Dihedral : 23.891 179.125 51780 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.33 % Favored : 95.57 % Rotamer: Outliers : 6.10 % Allowed : 25.56 % Favored : 68.35 % 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: -0.11 (0.15), residues: 3095 helix: 1.17 (0.18), residues: 814 sheet: -0.12 (0.19), residues: 732 loop : -0.68 (0.15), residues: 1549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP c 248 HIS 0.006 0.001 HIS y 3 PHE 0.017 0.002 PHE q 57 TYR 0.017 0.002 TYR f 83 ARG 0.006 0.001 ARG e 21 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6190 Ramachandran restraints generated. 3095 Oldfield, 0 Emsley, 3095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6190 Ramachandran restraints generated. 3095 Oldfield, 0 Emsley, 3095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 643 residues out of total 2559 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 487 time to evaluate : 4.009 Fit side-chains revert: symmetry clash REVERT: 1 24 GLU cc_start: 0.8114 (tp30) cc_final: 0.7682 (tp30) REVERT: 6 1 MET cc_start: 0.7797 (mtp) cc_final: 0.7564 (mtp) REVERT: 7 19 LYS cc_start: 0.8790 (OUTLIER) cc_final: 0.8254 (pttt) REVERT: 7 40 ARG cc_start: 0.8656 (OUTLIER) cc_final: 0.6899 (ttm170) REVERT: 8 30 GLU cc_start: 0.8189 (tp30) cc_final: 0.7752 (tp30) REVERT: c 90 ASN cc_start: 0.8199 (OUTLIER) cc_final: 0.7862 (m110) REVERT: c 163 GLN cc_start: 0.7818 (tt0) cc_final: 0.7174 (mt0) REVERT: c 182 ARG cc_start: 0.8903 (OUTLIER) cc_final: 0.8398 (ttt90) REVERT: d 1 MET cc_start: 0.7306 (OUTLIER) cc_final: 0.6435 (tmm) REVERT: d 74 GLU cc_start: 0.7534 (OUTLIER) cc_final: 0.7181 (mp0) REVERT: d 176 ASP cc_start: 0.8482 (m-30) cc_final: 0.8188 (m-30) REVERT: e 69 ARG cc_start: 0.8487 (OUTLIER) cc_final: 0.7133 (ptp-170) REVERT: e 95 LYS cc_start: 0.8669 (OUTLIER) cc_final: 0.8413 (tttt) REVERT: e 170 ARG cc_start: 0.8993 (OUTLIER) cc_final: 0.7518 (tpp80) REVERT: f 63 GLN cc_start: 0.9060 (pt0) cc_final: 0.8842 (pt0) REVERT: f 113 ASP cc_start: 0.8331 (t70) cc_final: 0.8069 (t0) REVERT: g 81 GLU cc_start: 0.8580 (OUTLIER) cc_final: 0.8137 (pm20) REVERT: g 163 ARG cc_start: 0.8278 (OUTLIER) cc_final: 0.7132 (ptt180) REVERT: j 23 LYS cc_start: 0.8756 (OUTLIER) cc_final: 0.7518 (mmtm) REVERT: j 92 MET cc_start: 0.8869 (mmm) cc_final: 0.8319 (mmm) REVERT: j 96 ARG cc_start: 0.8439 (OUTLIER) cc_final: 0.7954 (pmt170) REVERT: j 103 ILE cc_start: 0.8152 (OUTLIER) cc_final: 0.7889 (pp) REVERT: k 30 ARG cc_start: 0.8796 (OUTLIER) cc_final: 0.8364 (ttt-90) REVERT: k 38 ILE cc_start: 0.9131 (OUTLIER) cc_final: 0.8923 (mm) REVERT: k 105 ARG cc_start: 0.8278 (OUTLIER) cc_final: 0.6925 (mtm-85) REVERT: k 114 LYS cc_start: 0.8442 (mtpp) cc_final: 0.8012 (ttmt) REVERT: m 12 MET cc_start: 0.8346 (mtp) cc_final: 0.7965 (mtp) REVERT: m 115 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.7421 (tt0) REVERT: n 72 ASP cc_start: 0.8416 (t0) cc_final: 0.8174 (t0) REVERT: o 40 ILE cc_start: 0.8779 (OUTLIER) cc_final: 0.8508 (mm) REVERT: p 10 GLN cc_start: 0.8141 (tp-100) cc_final: 0.7927 (tp40) REVERT: p 68 GLU cc_start: 0.7726 (OUTLIER) cc_final: 0.7461 (pm20) REVERT: r 46 GLU cc_start: 0.8005 (OUTLIER) cc_final: 0.7460 (mm-30) REVERT: r 97 LYS cc_start: 0.9008 (tttm) cc_final: 0.8744 (tttp) REVERT: s 4 ILE cc_start: 0.9214 (mt) cc_final: 0.8988 (mp) REVERT: s 92 ARG cc_start: 0.7309 (OUTLIER) cc_final: 0.6567 (ttp-170) REVERT: t 9 LYS cc_start: 0.8706 (OUTLIER) cc_final: 0.7685 (mppt) REVERT: t 36 LYS cc_start: 0.9023 (OUTLIER) cc_final: 0.8778 (tttt) REVERT: t 64 LYS cc_start: 0.8589 (OUTLIER) cc_final: 0.7337 (mmtp) REVERT: t 73 ARG cc_start: 0.7624 (OUTLIER) cc_final: 0.7290 (ptm-80) REVERT: u 24 LYS cc_start: 0.8537 (OUTLIER) cc_final: 0.8282 (ttpp) REVERT: u 37 GLU cc_start: 0.7879 (OUTLIER) cc_final: 0.7576 (mt-10) REVERT: w 85 LYS cc_start: 0.8722 (OUTLIER) cc_final: 0.7837 (mptp) REVERT: y 25 ARG cc_start: 0.8199 (mmt-90) cc_final: 0.7926 (mmm-85) REVERT: y 62 LYS cc_start: 0.8961 (mtmt) cc_final: 0.8643 (mtpt) REVERT: y 78 LYS cc_start: 0.8716 (mtpt) cc_final: 0.8225 (mttm) outliers start: 156 outliers final: 94 residues processed: 591 average time/residue: 1.9357 time to fit residues: 1516.6306 Evaluate side-chains 605 residues out of total 2559 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 482 time to evaluate : 4.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 19 LEU Chi-restraints excluded: chain 1 residue 34 SER Chi-restraints excluded: chain 1 residue 59 GLU Chi-restraints excluded: chain 2 residue 5 ILE Chi-restraints excluded: chain 2 residue 12 SER Chi-restraints excluded: chain 2 residue 58 GLU Chi-restraints excluded: chain 3 residue 25 VAL Chi-restraints excluded: chain 3 residue 29 SER Chi-restraints excluded: chain 4 residue 42 VAL Chi-restraints excluded: chain 6 residue 8 SER Chi-restraints excluded: chain 7 residue 19 LYS Chi-restraints excluded: chain 7 residue 40 ARG Chi-restraints excluded: chain 7 residue 52 LYS Chi-restraints excluded: chain 7 residue 54 ASP Chi-restraints excluded: chain 8 residue 26 ILE Chi-restraints excluded: chain c residue 90 ASN Chi-restraints excluded: chain c residue 165 VAL Chi-restraints excluded: chain c residue 182 ARG Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 2 ILE Chi-restraints excluded: chain d residue 7 LYS Chi-restraints excluded: chain d residue 58 ASN Chi-restraints excluded: chain d residue 60 VAL Chi-restraints excluded: chain d residue 74 GLU Chi-restraints excluded: chain d residue 84 LEU Chi-restraints excluded: chain d residue 100 LEU Chi-restraints excluded: chain d residue 151 THR Chi-restraints excluded: chain e residue 10 SER Chi-restraints excluded: chain e residue 65 THR Chi-restraints excluded: chain e residue 69 ARG Chi-restraints excluded: chain e residue 95 LYS Chi-restraints excluded: chain e residue 126 VAL Chi-restraints excluded: chain e residue 166 LYS Chi-restraints excluded: chain e residue 170 ARG Chi-restraints excluded: chain e residue 191 ASP Chi-restraints excluded: chain f residue 35 THR Chi-restraints excluded: chain f residue 42 GLU Chi-restraints excluded: chain f residue 88 LYS Chi-restraints excluded: chain f residue 103 LEU Chi-restraints excluded: chain f residue 125 ARG Chi-restraints excluded: chain f residue 137 ILE Chi-restraints excluded: chain f residue 170 LEU Chi-restraints excluded: chain g residue 2 SER Chi-restraints excluded: chain g residue 15 VAL Chi-restraints excluded: chain g residue 23 VAL Chi-restraints excluded: chain g residue 27 LYS Chi-restraints excluded: chain g residue 41 VAL Chi-restraints excluded: chain g residue 80 THR Chi-restraints excluded: chain g residue 81 GLU Chi-restraints excluded: chain g residue 85 LYS Chi-restraints excluded: chain g residue 106 SER Chi-restraints excluded: chain g residue 127 THR Chi-restraints excluded: chain g residue 163 ARG Chi-restraints excluded: chain g residue 168 VAL Chi-restraints excluded: chain h residue 15 LEU Chi-restraints excluded: chain h residue 27 ARG Chi-restraints excluded: chain j residue 23 LYS Chi-restraints excluded: chain j residue 30 THR Chi-restraints excluded: chain j residue 48 VAL Chi-restraints excluded: chain j residue 96 ARG Chi-restraints excluded: chain j residue 100 VAL Chi-restraints excluded: chain j residue 101 ILE Chi-restraints excluded: chain j residue 103 ILE Chi-restraints excluded: chain k residue 30 ARG Chi-restraints excluded: chain k residue 38 ILE Chi-restraints excluded: chain k residue 76 VAL Chi-restraints excluded: chain k residue 105 ARG Chi-restraints excluded: chain l residue 80 SER Chi-restraints excluded: chain l residue 85 VAL Chi-restraints excluded: chain l residue 117 THR Chi-restraints excluded: chain l residue 121 THR Chi-restraints excluded: chain m residue 1 MET Chi-restraints excluded: chain m residue 22 GLN Chi-restraints excluded: chain m residue 41 LEU Chi-restraints excluded: chain m residue 115 GLU Chi-restraints excluded: chain m residue 135 VAL Chi-restraints excluded: chain n residue 14 SER Chi-restraints excluded: chain n residue 36 THR Chi-restraints excluded: chain n residue 57 THR Chi-restraints excluded: chain n residue 65 LEU Chi-restraints excluded: chain n residue 70 THR Chi-restraints excluded: chain o residue 20 GLU Chi-restraints excluded: chain o residue 24 THR Chi-restraints excluded: chain o residue 40 ILE Chi-restraints excluded: chain o residue 54 VAL Chi-restraints excluded: chain p residue 4 ILE Chi-restraints excluded: chain p residue 5 ILE Chi-restraints excluded: chain p residue 52 ASN Chi-restraints excluded: chain p residue 63 LYS Chi-restraints excluded: chain p residue 68 GLU Chi-restraints excluded: chain p residue 70 VAL Chi-restraints excluded: chain p residue 76 THR Chi-restraints excluded: chain r residue 16 GLU Chi-restraints excluded: chain r residue 46 GLU Chi-restraints excluded: chain r residue 71 LYS Chi-restraints excluded: chain s residue 92 ARG Chi-restraints excluded: chain s residue 101 SER Chi-restraints excluded: chain s residue 108 SER Chi-restraints excluded: chain s residue 109 ASP Chi-restraints excluded: chain t residue 9 LYS Chi-restraints excluded: chain t residue 27 SER Chi-restraints excluded: chain t residue 36 LYS Chi-restraints excluded: chain t residue 64 LYS Chi-restraints excluded: chain t residue 73 ARG Chi-restraints excluded: chain u residue 15 THR Chi-restraints excluded: chain u residue 24 LYS Chi-restraints excluded: chain u residue 37 GLU Chi-restraints excluded: chain u residue 59 VAL Chi-restraints excluded: chain u residue 68 SER Chi-restraints excluded: chain u residue 83 VAL Chi-restraints excluded: chain u residue 89 ASP Chi-restraints excluded: chain u residue 100 SER Chi-restraints excluded: chain w residue 11 GLU Chi-restraints excluded: chain w residue 12 GLN Chi-restraints excluded: chain w residue 41 GLU Chi-restraints excluded: chain w residue 65 VAL Chi-restraints excluded: chain w residue 85 LYS Chi-restraints excluded: chain y residue 9 SER Chi-restraints excluded: chain y residue 17 GLU Chi-restraints excluded: chain y residue 43 THR Chi-restraints excluded: chain y residue 70 GLU Chi-restraints excluded: chain z residue 135 ASN Chi-restraints excluded: chain z residue 147 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 611 random chunks: chunk 569 optimal weight: 6.9990 chunk 66 optimal weight: 10.0000 chunk 336 optimal weight: 8.9990 chunk 431 optimal weight: 10.0000 chunk 334 optimal weight: 7.9990 chunk 497 optimal weight: 0.0470 chunk 330 optimal weight: 10.0000 chunk 588 optimal weight: 9.9990 chunk 368 optimal weight: 3.9990 chunk 359 optimal weight: 2.9990 chunk 271 optimal weight: 10.0000 overall best weight: 4.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 17 ASN 4 26 ASN 6 29 GLN d 42 ASN ** j 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 18 GLN o 104 GLN r 6 GLN r 86 GLN s 61 ASN t 48 GLN w 75 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.0999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 99333 Z= 0.335 Angle : 0.650 10.059 149476 Z= 0.343 Chirality : 0.041 0.369 19217 Planarity : 0.005 0.054 7388 Dihedral : 23.863 178.965 51780 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.49 % Favored : 95.41 % Rotamer: Outliers : 6.33 % Allowed : 25.24 % Favored : 68.43 % 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: -0.08 (0.15), residues: 3095 helix: 1.21 (0.18), residues: 815 sheet: -0.09 (0.19), residues: 727 loop : -0.66 (0.15), residues: 1553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP c 248 HIS 0.006 0.001 HIS r 89 PHE 0.017 0.002 PHE q 57 TYR 0.020 0.002 TYR f 83 ARG 0.006 0.001 ARG z 162 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6190 Ramachandran restraints generated. 3095 Oldfield, 0 Emsley, 3095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6190 Ramachandran restraints generated. 3095 Oldfield, 0 Emsley, 3095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 646 residues out of total 2559 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 484 time to evaluate : 3.956 Fit side-chains REVERT: 1 24 GLU cc_start: 0.8115 (tp30) cc_final: 0.7678 (tp30) REVERT: 6 1 MET cc_start: 0.7818 (mtp) cc_final: 0.7598 (mtp) REVERT: 7 19 LYS cc_start: 0.8816 (OUTLIER) cc_final: 0.8272 (pttt) REVERT: 7 52 LYS cc_start: 0.8588 (OUTLIER) cc_final: 0.8250 (tttm) REVERT: 8 30 GLU cc_start: 0.8193 (tp30) cc_final: 0.7764 (tp30) REVERT: c 90 ASN cc_start: 0.8180 (OUTLIER) cc_final: 0.7888 (m110) REVERT: c 163 GLN cc_start: 0.7823 (tt0) cc_final: 0.7179 (mt0) REVERT: c 182 ARG cc_start: 0.8877 (OUTLIER) cc_final: 0.8390 (ttt90) REVERT: d 1 MET cc_start: 0.7328 (OUTLIER) cc_final: 0.6482 (tmm) REVERT: d 2 ILE cc_start: 0.8692 (OUTLIER) cc_final: 0.7248 (pt) REVERT: d 74 GLU cc_start: 0.7533 (OUTLIER) cc_final: 0.7181 (mp0) REVERT: d 176 ASP cc_start: 0.8481 (m-30) cc_final: 0.8190 (m-30) REVERT: e 69 ARG cc_start: 0.8488 (OUTLIER) cc_final: 0.7129 (ptp-170) REVERT: e 170 ARG cc_start: 0.8995 (OUTLIER) cc_final: 0.7525 (tpp80) REVERT: f 38 MET cc_start: 0.7862 (OUTLIER) cc_final: 0.7463 (mtm) REVERT: f 63 GLN cc_start: 0.9064 (pt0) cc_final: 0.8847 (pt0) REVERT: f 64 LYS cc_start: 0.8750 (OUTLIER) cc_final: 0.8311 (pttt) REVERT: f 113 ASP cc_start: 0.8351 (t70) cc_final: 0.8090 (t0) REVERT: g 18 LYS cc_start: 0.7534 (mppt) cc_final: 0.7221 (mmtt) REVERT: g 81 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.8135 (pm20) REVERT: g 163 ARG cc_start: 0.8263 (OUTLIER) cc_final: 0.7175 (ptt180) REVERT: j 23 LYS cc_start: 0.8741 (OUTLIER) cc_final: 0.7516 (mmtm) REVERT: j 92 MET cc_start: 0.8869 (mmm) cc_final: 0.8322 (mmm) REVERT: j 96 ARG cc_start: 0.8434 (OUTLIER) cc_final: 0.7887 (pmt170) REVERT: j 103 ILE cc_start: 0.8142 (OUTLIER) cc_final: 0.7885 (pp) REVERT: k 30 ARG cc_start: 0.8797 (OUTLIER) cc_final: 0.8367 (ttt-90) REVERT: k 38 ILE cc_start: 0.9132 (OUTLIER) cc_final: 0.8926 (mm) REVERT: k 105 ARG cc_start: 0.8278 (OUTLIER) cc_final: 0.6926 (mtm-85) REVERT: k 114 LYS cc_start: 0.8436 (mtpp) cc_final: 0.8012 (ttmt) REVERT: m 12 MET cc_start: 0.8344 (mtp) cc_final: 0.7945 (mtp) REVERT: m 115 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.7418 (tt0) REVERT: n 72 ASP cc_start: 0.8425 (t0) cc_final: 0.8178 (t0) REVERT: o 40 ILE cc_start: 0.8750 (OUTLIER) cc_final: 0.8470 (mm) REVERT: p 10 GLN cc_start: 0.8134 (tp-100) cc_final: 0.7924 (tp-100) REVERT: p 68 GLU cc_start: 0.7728 (OUTLIER) cc_final: 0.7504 (pm20) REVERT: r 46 GLU cc_start: 0.8018 (OUTLIER) cc_final: 0.7528 (mm-30) REVERT: r 97 LYS cc_start: 0.9011 (tttm) cc_final: 0.8749 (tttp) REVERT: s 4 ILE cc_start: 0.9198 (mt) cc_final: 0.8973 (mp) REVERT: s 92 ARG cc_start: 0.7330 (OUTLIER) cc_final: 0.6564 (ttp-170) REVERT: t 9 LYS cc_start: 0.8690 (OUTLIER) cc_final: 0.7660 (mppt) REVERT: t 36 LYS cc_start: 0.9020 (OUTLIER) cc_final: 0.8793 (tttt) REVERT: t 64 LYS cc_start: 0.8588 (OUTLIER) cc_final: 0.7318 (mmtp) REVERT: t 73 ARG cc_start: 0.7627 (OUTLIER) cc_final: 0.7291 (ptm-80) REVERT: u 24 LYS cc_start: 0.8527 (OUTLIER) cc_final: 0.8273 (ttpp) REVERT: u 37 GLU cc_start: 0.7879 (OUTLIER) cc_final: 0.7577 (mt-10) REVERT: w 85 LYS cc_start: 0.8716 (OUTLIER) cc_final: 0.7881 (mptp) REVERT: y 25 ARG cc_start: 0.8208 (mmt-90) cc_final: 0.7931 (mmm-85) REVERT: y 62 LYS cc_start: 0.8953 (mtmt) cc_final: 0.8630 (mtpt) REVERT: y 78 LYS cc_start: 0.8702 (mtpt) cc_final: 0.8211 (mttm) REVERT: z 157 ILE cc_start: 0.7334 (OUTLIER) cc_final: 0.6937 (mt) outliers start: 162 outliers final: 103 residues processed: 595 average time/residue: 1.9327 time to fit residues: 1529.1471 Evaluate side-chains 620 residues out of total 2559 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 485 time to evaluate : 3.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 35 SER Chi-restraints excluded: chain 1 residue 19 LEU Chi-restraints excluded: chain 1 residue 34 SER Chi-restraints excluded: chain 1 residue 59 GLU Chi-restraints excluded: chain 2 residue 5 ILE Chi-restraints excluded: chain 2 residue 12 SER Chi-restraints excluded: chain 2 residue 58 GLU Chi-restraints excluded: chain 3 residue 25 VAL Chi-restraints excluded: chain 3 residue 29 SER Chi-restraints excluded: chain 3 residue 46 ASP Chi-restraints excluded: chain 4 residue 42 VAL Chi-restraints excluded: chain 6 residue 8 SER Chi-restraints excluded: chain 6 residue 15 SER Chi-restraints excluded: chain 7 residue 19 LYS Chi-restraints excluded: chain 7 residue 52 LYS Chi-restraints excluded: chain 7 residue 54 ASP Chi-restraints excluded: chain 8 residue 26 ILE Chi-restraints excluded: chain c residue 90 ASN Chi-restraints excluded: chain c residue 165 VAL Chi-restraints excluded: chain c residue 182 ARG Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 2 ILE Chi-restraints excluded: chain d residue 7 LYS Chi-restraints excluded: chain d residue 58 ASN Chi-restraints excluded: chain d residue 60 VAL Chi-restraints excluded: chain d residue 74 GLU Chi-restraints excluded: chain d residue 84 LEU Chi-restraints excluded: chain d residue 97 SER Chi-restraints excluded: chain d residue 100 LEU Chi-restraints excluded: chain d residue 151 THR Chi-restraints excluded: chain e residue 10 SER Chi-restraints excluded: chain e residue 65 THR Chi-restraints excluded: chain e residue 69 ARG Chi-restraints excluded: chain e residue 126 VAL Chi-restraints excluded: chain e residue 133 LEU Chi-restraints excluded: chain e residue 166 LYS Chi-restraints excluded: chain e residue 170 ARG Chi-restraints excluded: chain e residue 191 ASP Chi-restraints excluded: chain f residue 35 THR Chi-restraints excluded: chain f residue 38 MET Chi-restraints excluded: chain f residue 42 GLU Chi-restraints excluded: chain f residue 64 LYS Chi-restraints excluded: chain f residue 88 LYS Chi-restraints excluded: chain f residue 103 LEU Chi-restraints excluded: chain f residue 125 ARG Chi-restraints excluded: chain f residue 137 ILE Chi-restraints excluded: chain g residue 2 SER Chi-restraints excluded: chain g residue 15 VAL Chi-restraints excluded: chain g residue 23 VAL Chi-restraints excluded: chain g residue 41 VAL Chi-restraints excluded: chain g residue 80 THR Chi-restraints excluded: chain g residue 81 GLU Chi-restraints excluded: chain g residue 85 LYS Chi-restraints excluded: chain g residue 106 SER Chi-restraints excluded: chain g residue 110 SER Chi-restraints excluded: chain g residue 127 THR Chi-restraints excluded: chain g residue 163 ARG Chi-restraints excluded: chain g residue 168 VAL Chi-restraints excluded: chain h residue 15 LEU Chi-restraints excluded: chain h residue 27 ARG Chi-restraints excluded: chain j residue 2 LYS Chi-restraints excluded: chain j residue 21 THR Chi-restraints excluded: chain j residue 23 LYS Chi-restraints excluded: chain j residue 30 THR Chi-restraints excluded: chain j residue 48 VAL Chi-restraints excluded: chain j residue 96 ARG Chi-restraints excluded: chain j residue 101 ILE Chi-restraints excluded: chain j residue 103 ILE Chi-restraints excluded: chain k residue 30 ARG Chi-restraints excluded: chain k residue 38 ILE Chi-restraints excluded: chain k residue 76 VAL Chi-restraints excluded: chain k residue 105 ARG Chi-restraints excluded: chain l residue 80 SER Chi-restraints excluded: chain l residue 85 VAL Chi-restraints excluded: chain l residue 117 THR Chi-restraints excluded: chain l residue 121 THR Chi-restraints excluded: chain m residue 1 MET Chi-restraints excluded: chain m residue 22 GLN Chi-restraints excluded: chain m residue 30 SER Chi-restraints excluded: chain m residue 41 LEU Chi-restraints excluded: chain m residue 115 GLU Chi-restraints excluded: chain m residue 127 LYS Chi-restraints excluded: chain m residue 135 VAL Chi-restraints excluded: chain n residue 14 SER Chi-restraints excluded: chain n residue 36 THR Chi-restraints excluded: chain n residue 57 THR Chi-restraints excluded: chain n residue 65 LEU Chi-restraints excluded: chain n residue 70 THR Chi-restraints excluded: chain o residue 5 SER Chi-restraints excluded: chain o residue 20 GLU Chi-restraints excluded: chain o residue 24 THR Chi-restraints excluded: chain o residue 40 ILE Chi-restraints excluded: chain o residue 54 VAL Chi-restraints excluded: chain p residue 4 ILE Chi-restraints excluded: chain p residue 5 ILE Chi-restraints excluded: chain p residue 30 VAL Chi-restraints excluded: chain p residue 52 ASN Chi-restraints excluded: chain p residue 63 LYS Chi-restraints excluded: chain p residue 68 GLU Chi-restraints excluded: chain p residue 70 VAL Chi-restraints excluded: chain p residue 76 THR Chi-restraints excluded: chain r residue 15 SER Chi-restraints excluded: chain r residue 16 GLU Chi-restraints excluded: chain r residue 46 GLU Chi-restraints excluded: chain r residue 71 LYS Chi-restraints excluded: chain s residue 92 ARG Chi-restraints excluded: chain s residue 101 SER Chi-restraints excluded: chain s residue 108 SER Chi-restraints excluded: chain s residue 109 ASP Chi-restraints excluded: chain t residue 9 LYS Chi-restraints excluded: chain t residue 27 SER Chi-restraints excluded: chain t residue 36 LYS Chi-restraints excluded: chain t residue 64 LYS Chi-restraints excluded: chain t residue 73 ARG Chi-restraints excluded: chain u residue 15 THR Chi-restraints excluded: chain u residue 24 LYS Chi-restraints excluded: chain u residue 37 GLU Chi-restraints excluded: chain u residue 59 VAL Chi-restraints excluded: chain u residue 68 SER Chi-restraints excluded: chain u residue 83 VAL Chi-restraints excluded: chain u residue 89 ASP Chi-restraints excluded: chain u residue 100 SER Chi-restraints excluded: chain w residue 12 GLN Chi-restraints excluded: chain w residue 41 GLU Chi-restraints excluded: chain w residue 65 VAL Chi-restraints excluded: chain w residue 85 LYS Chi-restraints excluded: chain y residue 9 SER Chi-restraints excluded: chain y residue 17 GLU Chi-restraints excluded: chain y residue 43 THR Chi-restraints excluded: chain y residue 58 THR Chi-restraints excluded: chain y residue 70 GLU Chi-restraints excluded: chain z residue 135 ASN Chi-restraints excluded: chain z residue 143 SER Chi-restraints excluded: chain z residue 147 THR Chi-restraints excluded: chain z residue 157 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 611 random chunks: chunk 364 optimal weight: 1.9990 chunk 235 optimal weight: 8.9990 chunk 351 optimal weight: 9.9990 chunk 177 optimal weight: 6.9990 chunk 115 optimal weight: 8.9990 chunk 114 optimal weight: 7.9990 chunk 374 optimal weight: 6.9990 chunk 401 optimal weight: 10.0000 chunk 291 optimal weight: 8.9990 chunk 54 optimal weight: 6.9990 chunk 462 optimal weight: 5.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 17 ASN 6 29 GLN d 42 ASN ** j 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 18 GLN o 104 GLN r 6 GLN r 86 GLN t 48 GLN w 75 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.1012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.072 99333 Z= 0.420 Angle : 0.691 8.244 149476 Z= 0.362 Chirality : 0.044 0.400 19217 Planarity : 0.006 0.055 7388 Dihedral : 23.853 178.963 51780 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.33 % Favored : 95.57 % Rotamer: Outliers : 6.37 % Allowed : 25.09 % Favored : 68.54 % 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: -0.11 (0.15), residues: 3095 helix: 1.17 (0.18), residues: 814 sheet: -0.11 (0.19), residues: 730 loop : -0.69 (0.15), residues: 1551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP c 248 HIS 0.007 0.001 HIS c 200 PHE 0.019 0.002 PHE q 57 TYR 0.019 0.002 TYR c 161 ARG 0.007 0.001 ARG z 162 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6190 Ramachandran restraints generated. 3095 Oldfield, 0 Emsley, 3095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6190 Ramachandran restraints generated. 3095 Oldfield, 0 Emsley, 3095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 654 residues out of total 2559 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 491 time to evaluate : 4.042 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 24 GLU cc_start: 0.8120 (tp30) cc_final: 0.7685 (tp30) REVERT: 7 19 LYS cc_start: 0.8799 (OUTLIER) cc_final: 0.8232 (pttt) REVERT: 7 52 LYS cc_start: 0.8612 (OUTLIER) cc_final: 0.8277 (tttm) REVERT: 8 30 GLU cc_start: 0.8206 (tp30) cc_final: 0.7892 (tp30) REVERT: c 90 ASN cc_start: 0.8220 (OUTLIER) cc_final: 0.7912 (m110) REVERT: c 163 GLN cc_start: 0.7839 (tt0) cc_final: 0.7186 (mt0) REVERT: c 182 ARG cc_start: 0.8909 (OUTLIER) cc_final: 0.8407 (ttt90) REVERT: d 1 MET cc_start: 0.7338 (OUTLIER) cc_final: 0.6499 (tmm) REVERT: d 2 ILE cc_start: 0.8709 (OUTLIER) cc_final: 0.7256 (pt) REVERT: d 74 GLU cc_start: 0.7536 (OUTLIER) cc_final: 0.7183 (mp0) REVERT: d 176 ASP cc_start: 0.8481 (m-30) cc_final: 0.8195 (m-30) REVERT: e 69 ARG cc_start: 0.8507 (OUTLIER) cc_final: 0.7191 (ptp-170) REVERT: e 74 LYS cc_start: 0.9072 (OUTLIER) cc_final: 0.8573 (mttt) REVERT: e 170 ARG cc_start: 0.8995 (OUTLIER) cc_final: 0.7539 (tpp80) REVERT: f 64 LYS cc_start: 0.8761 (OUTLIER) cc_final: 0.8377 (pttt) REVERT: f 113 ASP cc_start: 0.8359 (t70) cc_final: 0.8100 (t0) REVERT: g 18 LYS cc_start: 0.7601 (mppt) cc_final: 0.7326 (mmtt) REVERT: g 163 ARG cc_start: 0.8284 (OUTLIER) cc_final: 0.7112 (ptt180) REVERT: j 23 LYS cc_start: 0.8749 (OUTLIER) cc_final: 0.7521 (mmtm) REVERT: j 92 MET cc_start: 0.8861 (mmm) cc_final: 0.8316 (mmm) REVERT: j 96 ARG cc_start: 0.8446 (OUTLIER) cc_final: 0.7885 (pmt170) REVERT: j 103 ILE cc_start: 0.8180 (OUTLIER) cc_final: 0.7913 (pp) REVERT: k 30 ARG cc_start: 0.8805 (OUTLIER) cc_final: 0.8378 (ttt-90) REVERT: k 105 ARG cc_start: 0.8295 (OUTLIER) cc_final: 0.6949 (mtm-85) REVERT: k 114 LYS cc_start: 0.8485 (mtpp) cc_final: 0.8054 (ttmt) REVERT: l 126 ARG cc_start: 0.8656 (mtm-85) cc_final: 0.8400 (mtp180) REVERT: m 12 MET cc_start: 0.8350 (mtp) cc_final: 0.7969 (mtp) REVERT: m 115 GLU cc_start: 0.8010 (OUTLIER) cc_final: 0.7437 (tt0) REVERT: n 72 ASP cc_start: 0.8404 (t0) cc_final: 0.8157 (t0) REVERT: r 46 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7561 (mm-30) REVERT: r 97 LYS cc_start: 0.9008 (tttm) cc_final: 0.8751 (tttp) REVERT: s 4 ILE cc_start: 0.9230 (mt) cc_final: 0.9004 (mp) REVERT: s 92 ARG cc_start: 0.7363 (OUTLIER) cc_final: 0.6580 (ttp-170) REVERT: t 9 LYS cc_start: 0.8702 (OUTLIER) cc_final: 0.7655 (mppt) REVERT: t 36 LYS cc_start: 0.9023 (OUTLIER) cc_final: 0.8779 (tttt) REVERT: t 64 LYS cc_start: 0.8591 (OUTLIER) cc_final: 0.7338 (mmtp) REVERT: t 73 ARG cc_start: 0.7632 (OUTLIER) cc_final: 0.7286 (ptm-80) REVERT: u 24 LYS cc_start: 0.8537 (OUTLIER) cc_final: 0.8283 (ttpp) REVERT: u 37 GLU cc_start: 0.7891 (OUTLIER) cc_final: 0.7589 (mt-10) REVERT: w 85 LYS cc_start: 0.8726 (OUTLIER) cc_final: 0.7921 (mptp) REVERT: y 25 ARG cc_start: 0.8340 (mmt-90) cc_final: 0.8075 (mmm-85) REVERT: y 62 LYS cc_start: 0.8971 (mtmt) cc_final: 0.8643 (mtpt) REVERT: y 78 LYS cc_start: 0.8706 (mtpt) cc_final: 0.8157 (mtmm) REVERT: z 157 ILE cc_start: 0.7373 (OUTLIER) cc_final: 0.6985 (mt) outliers start: 163 outliers final: 110 residues processed: 601 average time/residue: 1.9281 time to fit residues: 1541.9600 Evaluate side-chains 623 residues out of total 2559 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 485 time to evaluate : 3.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 35 SER Chi-restraints excluded: chain 1 residue 19 LEU Chi-restraints excluded: chain 1 residue 34 SER Chi-restraints excluded: chain 1 residue 59 GLU Chi-restraints excluded: chain 2 residue 5 ILE Chi-restraints excluded: chain 2 residue 12 SER Chi-restraints excluded: chain 2 residue 58 GLU Chi-restraints excluded: chain 3 residue 25 VAL Chi-restraints excluded: chain 3 residue 26 THR Chi-restraints excluded: chain 3 residue 29 SER Chi-restraints excluded: chain 3 residue 46 ASP Chi-restraints excluded: chain 4 residue 42 VAL Chi-restraints excluded: chain 6 residue 8 SER Chi-restraints excluded: chain 6 residue 15 SER Chi-restraints excluded: chain 7 residue 19 LYS Chi-restraints excluded: chain 7 residue 52 LYS Chi-restraints excluded: chain 8 residue 26 ILE Chi-restraints excluded: chain c residue 90 ASN Chi-restraints excluded: chain c residue 97 LYS Chi-restraints excluded: chain c residue 165 VAL Chi-restraints excluded: chain c residue 182 ARG Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 2 ILE Chi-restraints excluded: chain d residue 7 LYS Chi-restraints excluded: chain d residue 58 ASN Chi-restraints excluded: chain d residue 60 VAL Chi-restraints excluded: chain d residue 74 GLU Chi-restraints excluded: chain d residue 84 LEU Chi-restraints excluded: chain d residue 97 SER Chi-restraints excluded: chain d residue 100 LEU Chi-restraints excluded: chain d residue 151 THR Chi-restraints excluded: chain e residue 10 SER Chi-restraints excluded: chain e residue 65 THR Chi-restraints excluded: chain e residue 69 ARG Chi-restraints excluded: chain e residue 74 LYS Chi-restraints excluded: chain e residue 80 SER Chi-restraints excluded: chain e residue 126 VAL Chi-restraints excluded: chain e residue 133 LEU Chi-restraints excluded: chain e residue 166 LYS Chi-restraints excluded: chain e residue 170 ARG Chi-restraints excluded: chain e residue 191 ASP Chi-restraints excluded: chain f residue 35 THR Chi-restraints excluded: chain f residue 38 MET Chi-restraints excluded: chain f residue 42 GLU Chi-restraints excluded: chain f residue 64 LYS Chi-restraints excluded: chain f residue 88 LYS Chi-restraints excluded: chain f residue 103 LEU Chi-restraints excluded: chain f residue 125 ARG Chi-restraints excluded: chain f residue 137 ILE Chi-restraints excluded: chain f residue 170 LEU Chi-restraints excluded: chain g residue 2 SER Chi-restraints excluded: chain g residue 15 VAL Chi-restraints excluded: chain g residue 23 VAL Chi-restraints excluded: chain g residue 41 VAL Chi-restraints excluded: chain g residue 80 THR Chi-restraints excluded: chain g residue 81 GLU Chi-restraints excluded: chain g residue 85 LYS Chi-restraints excluded: chain g residue 106 SER Chi-restraints excluded: chain g residue 110 SER Chi-restraints excluded: chain g residue 127 THR Chi-restraints excluded: chain g residue 163 ARG Chi-restraints excluded: chain g residue 168 VAL Chi-restraints excluded: chain h residue 15 LEU Chi-restraints excluded: chain h residue 27 ARG Chi-restraints excluded: chain j residue 2 LYS Chi-restraints excluded: chain j residue 21 THR Chi-restraints excluded: chain j residue 23 LYS Chi-restraints excluded: chain j residue 30 THR Chi-restraints excluded: chain j residue 48 VAL Chi-restraints excluded: chain j residue 96 ARG Chi-restraints excluded: chain j residue 100 VAL Chi-restraints excluded: chain j residue 101 ILE Chi-restraints excluded: chain j residue 103 ILE Chi-restraints excluded: chain k residue 30 ARG Chi-restraints excluded: chain k residue 76 VAL Chi-restraints excluded: chain k residue 105 ARG Chi-restraints excluded: chain l residue 80 SER Chi-restraints excluded: chain l residue 85 VAL Chi-restraints excluded: chain l residue 117 THR Chi-restraints excluded: chain l residue 121 THR Chi-restraints excluded: chain m residue 1 MET Chi-restraints excluded: chain m residue 22 GLN Chi-restraints excluded: chain m residue 41 LEU Chi-restraints excluded: chain m residue 115 GLU Chi-restraints excluded: chain m residue 127 LYS Chi-restraints excluded: chain m residue 135 VAL Chi-restraints excluded: chain n residue 14 SER Chi-restraints excluded: chain n residue 36 THR Chi-restraints excluded: chain n residue 57 THR Chi-restraints excluded: chain n residue 65 LEU Chi-restraints excluded: chain n residue 70 THR Chi-restraints excluded: chain o residue 5 SER Chi-restraints excluded: chain o residue 20 GLU Chi-restraints excluded: chain o residue 24 THR Chi-restraints excluded: chain o residue 54 VAL Chi-restraints excluded: chain p residue 4 ILE Chi-restraints excluded: chain p residue 5 ILE Chi-restraints excluded: chain p residue 6 LYS Chi-restraints excluded: chain p residue 30 VAL Chi-restraints excluded: chain p residue 52 ASN Chi-restraints excluded: chain p residue 63 LYS Chi-restraints excluded: chain p residue 70 VAL Chi-restraints excluded: chain p residue 76 THR Chi-restraints excluded: chain p residue 102 GLU Chi-restraints excluded: chain r residue 16 GLU Chi-restraints excluded: chain r residue 46 GLU Chi-restraints excluded: chain r residue 71 LYS Chi-restraints excluded: chain s residue 66 ILE Chi-restraints excluded: chain s residue 92 ARG Chi-restraints excluded: chain s residue 101 SER Chi-restraints excluded: chain s residue 108 SER Chi-restraints excluded: chain s residue 109 ASP Chi-restraints excluded: chain t residue 9 LYS Chi-restraints excluded: chain t residue 27 SER Chi-restraints excluded: chain t residue 36 LYS Chi-restraints excluded: chain t residue 64 LYS Chi-restraints excluded: chain t residue 68 ARG Chi-restraints excluded: chain t residue 73 ARG Chi-restraints excluded: chain u residue 15 THR Chi-restraints excluded: chain u residue 24 LYS Chi-restraints excluded: chain u residue 37 GLU Chi-restraints excluded: chain u residue 59 VAL Chi-restraints excluded: chain u residue 68 SER Chi-restraints excluded: chain u residue 83 VAL Chi-restraints excluded: chain u residue 89 ASP Chi-restraints excluded: chain u residue 100 SER Chi-restraints excluded: chain w residue 12 GLN Chi-restraints excluded: chain w residue 41 GLU Chi-restraints excluded: chain w residue 65 VAL Chi-restraints excluded: chain w residue 85 LYS Chi-restraints excluded: chain y residue 9 SER Chi-restraints excluded: chain y residue 43 THR Chi-restraints excluded: chain y residue 58 THR Chi-restraints excluded: chain y residue 70 GLU Chi-restraints excluded: chain z residue 135 ASN Chi-restraints excluded: chain z residue 143 SER Chi-restraints excluded: chain z residue 147 THR Chi-restraints excluded: chain z residue 157 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 611 random chunks: chunk 535 optimal weight: 0.6980 chunk 564 optimal weight: 0.8980 chunk 514 optimal weight: 9.9990 chunk 548 optimal weight: 0.3980 chunk 330 optimal weight: 10.0000 chunk 239 optimal weight: 10.0000 chunk 430 optimal weight: 9.9990 chunk 168 optimal weight: 10.0000 chunk 495 optimal weight: 3.9990 chunk 519 optimal weight: 6.9990 chunk 546 optimal weight: 5.9990 overall best weight: 2.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 17 ASN 4 26 ASN 6 29 GLN d 42 ASN ** j 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 18 GLN r 6 GLN r 86 GLN t 48 GLN w 75 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.1110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 99333 Z= 0.200 Angle : 0.584 8.217 149476 Z= 0.313 Chirality : 0.038 0.318 19217 Planarity : 0.004 0.052 7388 Dihedral : 23.871 179.190 51780 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.20 % Favored : 95.70 % Rotamer: Outliers : 4.53 % Allowed : 26.89 % Favored : 68.58 % 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: 0.07 (0.15), residues: 3095 helix: 1.38 (0.19), residues: 809 sheet: -0.02 (0.19), residues: 714 loop : -0.59 (0.15), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP c 248 HIS 0.004 0.001 HIS o 100 PHE 0.012 0.001 PHE q 57 TYR 0.021 0.001 TYR f 83 ARG 0.004 0.000 ARG m 6 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6190 Ramachandran restraints generated. 3095 Oldfield, 0 Emsley, 3095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6190 Ramachandran restraints generated. 3095 Oldfield, 0 Emsley, 3095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 611 residues out of total 2559 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 495 time to evaluate : 4.060 Fit side-chains revert: symmetry clash REVERT: 1 24 GLU cc_start: 0.8092 (tp30) cc_final: 0.7645 (tp30) REVERT: 7 19 LYS cc_start: 0.8798 (OUTLIER) cc_final: 0.8257 (pttt) REVERT: 7 52 LYS cc_start: 0.8526 (OUTLIER) cc_final: 0.8251 (tttm) REVERT: 8 30 GLU cc_start: 0.8182 (tp30) cc_final: 0.7758 (tp30) REVERT: c 90 ASN cc_start: 0.8187 (OUTLIER) cc_final: 0.7869 (m-40) REVERT: c 118 SER cc_start: 0.9007 (p) cc_final: 0.8782 (p) REVERT: c 163 GLN cc_start: 0.7770 (tt0) cc_final: 0.7145 (mt0) REVERT: c 182 ARG cc_start: 0.8825 (OUTLIER) cc_final: 0.8353 (ttt90) REVERT: d 1 MET cc_start: 0.7322 (OUTLIER) cc_final: 0.6480 (tmm) REVERT: d 74 GLU cc_start: 0.7518 (OUTLIER) cc_final: 0.7169 (mp0) REVERT: d 99 GLU cc_start: 0.7647 (pm20) cc_final: 0.7370 (pm20) REVERT: d 176 ASP cc_start: 0.8484 (m-30) cc_final: 0.8190 (m-30) REVERT: e 69 ARG cc_start: 0.8337 (OUTLIER) cc_final: 0.6979 (ptp-170) REVERT: e 74 LYS cc_start: 0.9079 (OUTLIER) cc_final: 0.8557 (mttt) REVERT: e 170 ARG cc_start: 0.8983 (OUTLIER) cc_final: 0.7460 (tpp80) REVERT: f 64 LYS cc_start: 0.8745 (OUTLIER) cc_final: 0.8486 (pttt) REVERT: f 113 ASP cc_start: 0.8366 (t70) cc_final: 0.8111 (t0) REVERT: g 18 LYS cc_start: 0.7568 (mppt) cc_final: 0.7274 (mmtt) REVERT: g 163 ARG cc_start: 0.8209 (OUTLIER) cc_final: 0.7124 (ptt180) REVERT: j 23 LYS cc_start: 0.8738 (OUTLIER) cc_final: 0.7530 (mmtm) REVERT: j 92 MET cc_start: 0.8864 (mmm) cc_final: 0.8230 (mmm) REVERT: j 96 ARG cc_start: 0.8420 (OUTLIER) cc_final: 0.7897 (pmt170) REVERT: j 103 ILE cc_start: 0.8067 (OUTLIER) cc_final: 0.7835 (pp) REVERT: k 30 ARG cc_start: 0.8787 (OUTLIER) cc_final: 0.8343 (ttt-90) REVERT: k 105 ARG cc_start: 0.8254 (OUTLIER) cc_final: 0.6957 (mtm-85) REVERT: k 114 LYS cc_start: 0.8427 (mtpp) cc_final: 0.8011 (ttmt) REVERT: k 122 VAL cc_start: 0.7844 (t) cc_final: 0.6753 (t) REVERT: l 126 ARG cc_start: 0.8645 (mtm-85) cc_final: 0.8401 (mtp180) REVERT: m 12 MET cc_start: 0.8332 (mtp) cc_final: 0.7913 (mtp) REVERT: m 115 GLU cc_start: 0.8013 (OUTLIER) cc_final: 0.7435 (tt0) REVERT: n 72 ASP cc_start: 0.8420 (t0) cc_final: 0.8140 (t0) REVERT: r 46 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7584 (mm-30) REVERT: r 97 LYS cc_start: 0.8999 (tttm) cc_final: 0.8741 (tttp) REVERT: s 4 ILE cc_start: 0.9151 (mt) cc_final: 0.8928 (mp) REVERT: s 59 GLU cc_start: 0.7374 (mm-30) cc_final: 0.7140 (mm-30) REVERT: s 92 ARG cc_start: 0.7241 (OUTLIER) cc_final: 0.6467 (ttp-170) REVERT: t 9 LYS cc_start: 0.8684 (OUTLIER) cc_final: 0.7662 (mppt) REVERT: t 36 LYS cc_start: 0.9013 (OUTLIER) cc_final: 0.8774 (tttt) REVERT: t 64 LYS cc_start: 0.8587 (OUTLIER) cc_final: 0.7286 (mmtp) REVERT: t 73 ARG cc_start: 0.7574 (OUTLIER) cc_final: 0.7268 (ptm-80) REVERT: u 24 LYS cc_start: 0.8522 (OUTLIER) cc_final: 0.8284 (ttpp) REVERT: u 37 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.7582 (mt-10) REVERT: y 25 ARG cc_start: 0.8232 (mmt-90) cc_final: 0.7957 (mmm-85) REVERT: y 62 LYS cc_start: 0.8948 (mtmt) cc_final: 0.8653 (mtpt) REVERT: y 78 LYS cc_start: 0.8695 (mtpt) cc_final: 0.8202 (mttm) outliers start: 116 outliers final: 76 residues processed: 571 average time/residue: 1.9735 time to fit residues: 1492.4296 Evaluate side-chains 587 residues out of total 2559 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 486 time to evaluate : 3.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 19 LEU Chi-restraints excluded: chain 1 residue 59 GLU Chi-restraints excluded: chain 2 residue 12 SER Chi-restraints excluded: chain 2 residue 21 LYS Chi-restraints excluded: chain 3 residue 25 VAL Chi-restraints excluded: chain 3 residue 26 THR Chi-restraints excluded: chain 3 residue 29 SER Chi-restraints excluded: chain 4 residue 42 VAL Chi-restraints excluded: chain 7 residue 19 LYS Chi-restraints excluded: chain 7 residue 52 LYS Chi-restraints excluded: chain 7 residue 54 ASP Chi-restraints excluded: chain c residue 90 ASN Chi-restraints excluded: chain c residue 165 VAL Chi-restraints excluded: chain c residue 182 ARG Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 2 ILE Chi-restraints excluded: chain d residue 7 LYS Chi-restraints excluded: chain d residue 58 ASN Chi-restraints excluded: chain d residue 60 VAL Chi-restraints excluded: chain d residue 74 GLU Chi-restraints excluded: chain d residue 84 LEU Chi-restraints excluded: chain d residue 97 SER Chi-restraints excluded: chain d residue 100 LEU Chi-restraints excluded: chain d residue 151 THR Chi-restraints excluded: chain e residue 69 ARG Chi-restraints excluded: chain e residue 74 LYS Chi-restraints excluded: chain e residue 126 VAL Chi-restraints excluded: chain e residue 166 LYS Chi-restraints excluded: chain e residue 170 ARG Chi-restraints excluded: chain e residue 191 ASP Chi-restraints excluded: chain f residue 35 THR Chi-restraints excluded: chain f residue 38 MET Chi-restraints excluded: chain f residue 42 GLU Chi-restraints excluded: chain f residue 64 LYS Chi-restraints excluded: chain f residue 88 LYS Chi-restraints excluded: chain f residue 103 LEU Chi-restraints excluded: chain f residue 125 ARG Chi-restraints excluded: chain g residue 15 VAL Chi-restraints excluded: chain g residue 23 VAL Chi-restraints excluded: chain g residue 41 VAL Chi-restraints excluded: chain g residue 81 GLU Chi-restraints excluded: chain g residue 106 SER Chi-restraints excluded: chain g residue 110 SER Chi-restraints excluded: chain g residue 127 THR Chi-restraints excluded: chain g residue 163 ARG Chi-restraints excluded: chain g residue 168 VAL Chi-restraints excluded: chain h residue 15 LEU Chi-restraints excluded: chain j residue 2 LYS Chi-restraints excluded: chain j residue 23 LYS Chi-restraints excluded: chain j residue 30 THR Chi-restraints excluded: chain j residue 48 VAL Chi-restraints excluded: chain j residue 96 ARG Chi-restraints excluded: chain j residue 101 ILE Chi-restraints excluded: chain j residue 103 ILE Chi-restraints excluded: chain k residue 30 ARG Chi-restraints excluded: chain k residue 76 VAL Chi-restraints excluded: chain k residue 105 ARG Chi-restraints excluded: chain l residue 80 SER Chi-restraints excluded: chain l residue 85 VAL Chi-restraints excluded: chain l residue 117 THR Chi-restraints excluded: chain l residue 121 THR Chi-restraints excluded: chain m residue 1 MET Chi-restraints excluded: chain m residue 22 GLN Chi-restraints excluded: chain m residue 41 LEU Chi-restraints excluded: chain m residue 115 GLU Chi-restraints excluded: chain m residue 135 VAL Chi-restraints excluded: chain n residue 36 THR Chi-restraints excluded: chain n residue 57 THR Chi-restraints excluded: chain n residue 65 LEU Chi-restraints excluded: chain n residue 70 THR Chi-restraints excluded: chain o residue 24 THR Chi-restraints excluded: chain o residue 54 VAL Chi-restraints excluded: chain p residue 30 VAL Chi-restraints excluded: chain p residue 52 ASN Chi-restraints excluded: chain p residue 63 LYS Chi-restraints excluded: chain p residue 70 VAL Chi-restraints excluded: chain p residue 76 THR Chi-restraints excluded: chain p residue 102 GLU Chi-restraints excluded: chain r residue 16 GLU Chi-restraints excluded: chain r residue 46 GLU Chi-restraints excluded: chain s residue 92 ARG Chi-restraints excluded: chain t residue 9 LYS Chi-restraints excluded: chain t residue 27 SER Chi-restraints excluded: chain t residue 36 LYS Chi-restraints excluded: chain t residue 64 LYS Chi-restraints excluded: chain t residue 68 ARG Chi-restraints excluded: chain t residue 73 ARG Chi-restraints excluded: chain u residue 15 THR Chi-restraints excluded: chain u residue 24 LYS Chi-restraints excluded: chain u residue 37 GLU Chi-restraints excluded: chain u residue 68 SER Chi-restraints excluded: chain u residue 83 VAL Chi-restraints excluded: chain u residue 89 ASP Chi-restraints excluded: chain w residue 12 GLN Chi-restraints excluded: chain w residue 41 GLU Chi-restraints excluded: chain w residue 65 VAL Chi-restraints excluded: chain y residue 9 SER Chi-restraints excluded: chain y residue 43 THR Chi-restraints excluded: chain y residue 70 GLU Chi-restraints excluded: chain z residue 135 ASN Chi-restraints excluded: chain z residue 147 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 611 random chunks: chunk 360 optimal weight: 8.9990 chunk 580 optimal weight: 9.9990 chunk 354 optimal weight: 6.9990 chunk 275 optimal weight: 10.0000 chunk 403 optimal weight: 10.0000 chunk 608 optimal weight: 0.1980 chunk 560 optimal weight: 2.9990 chunk 484 optimal weight: 5.9990 chunk 50 optimal weight: 10.0000 chunk 374 optimal weight: 9.9990 chunk 297 optimal weight: 8.9990 overall best weight: 5.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 17 ASN 6 29 GLN d 42 ASN f 63 GLN ** j 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 18 GLN o 104 GLN r 6 GLN r 86 GLN t 48 GLN w 75 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.1058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 99333 Z= 0.369 Angle : 0.655 12.658 149476 Z= 0.345 Chirality : 0.042 0.372 19217 Planarity : 0.005 0.054 7388 Dihedral : 23.820 179.050 51780 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.30 % Favored : 95.61 % Rotamer: Outliers : 4.34 % Allowed : 27.24 % Favored : 68.43 % 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: -0.01 (0.15), residues: 3095 helix: 1.28 (0.18), residues: 814 sheet: -0.05 (0.19), residues: 732 loop : -0.64 (0.15), residues: 1549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP c 248 HIS 0.006 0.001 HIS c 200 PHE 0.018 0.002 PHE q 57 TYR 0.018 0.002 TYR f 83 ARG 0.007 0.001 ARG d 184 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6190 Ramachandran restraints generated. 3095 Oldfield, 0 Emsley, 3095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6190 Ramachandran restraints generated. 3095 Oldfield, 0 Emsley, 3095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 596 residues out of total 2559 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 485 time to evaluate : 4.015 Fit side-chains REVERT: 1 24 GLU cc_start: 0.8107 (tp30) cc_final: 0.7664 (tp30) REVERT: 7 19 LYS cc_start: 0.8815 (OUTLIER) cc_final: 0.8218 (pttt) REVERT: 7 40 ARG cc_start: 0.8735 (OUTLIER) cc_final: 0.7797 (ttp-170) REVERT: 7 52 LYS cc_start: 0.8550 (OUTLIER) cc_final: 0.8278 (tttm) REVERT: 8 30 GLU cc_start: 0.8190 (tp30) cc_final: 0.7873 (tp30) REVERT: c 90 ASN cc_start: 0.8138 (OUTLIER) cc_final: 0.7919 (m110) REVERT: c 118 SER cc_start: 0.8990 (p) cc_final: 0.8767 (p) REVERT: c 163 GLN cc_start: 0.7822 (tt0) cc_final: 0.7179 (mt0) REVERT: c 182 ARG cc_start: 0.8889 (OUTLIER) cc_final: 0.8396 (ttt90) REVERT: d 1 MET cc_start: 0.7336 (OUTLIER) cc_final: 0.6509 (tmm) REVERT: d 74 GLU cc_start: 0.7528 (OUTLIER) cc_final: 0.7178 (mp0) REVERT: d 99 GLU cc_start: 0.7661 (pm20) cc_final: 0.7376 (pm20) REVERT: d 176 ASP cc_start: 0.8490 (m-30) cc_final: 0.8203 (m-30) REVERT: e 21 ARG cc_start: 0.7915 (mtp85) cc_final: 0.7480 (ptm160) REVERT: e 69 ARG cc_start: 0.8492 (OUTLIER) cc_final: 0.7126 (ptp-170) REVERT: e 74 LYS cc_start: 0.9068 (OUTLIER) cc_final: 0.8527 (mttt) REVERT: e 170 ARG cc_start: 0.8997 (OUTLIER) cc_final: 0.7523 (tpp80) REVERT: f 64 LYS cc_start: 0.8725 (OUTLIER) cc_final: 0.8336 (pttt) REVERT: f 113 ASP cc_start: 0.8380 (t70) cc_final: 0.8126 (t0) REVERT: g 18 LYS cc_start: 0.7645 (mppt) cc_final: 0.7339 (mmtt) REVERT: g 81 GLU cc_start: 0.8592 (OUTLIER) cc_final: 0.8099 (pm20) REVERT: g 163 ARG cc_start: 0.8266 (OUTLIER) cc_final: 0.7153 (ptt180) REVERT: j 23 LYS cc_start: 0.8745 (OUTLIER) cc_final: 0.7522 (mmtm) REVERT: j 92 MET cc_start: 0.8859 (mmm) cc_final: 0.8314 (mmm) REVERT: j 103 ILE cc_start: 0.8148 (OUTLIER) cc_final: 0.7883 (pp) REVERT: k 30 ARG cc_start: 0.8803 (OUTLIER) cc_final: 0.8380 (ttt-90) REVERT: k 105 ARG cc_start: 0.8278 (OUTLIER) cc_final: 0.6952 (mtm-85) REVERT: k 114 LYS cc_start: 0.8435 (mtpp) cc_final: 0.8000 (ttmt) REVERT: k 122 VAL cc_start: 0.7856 (t) cc_final: 0.6836 (t) REVERT: l 126 ARG cc_start: 0.8653 (mtm-85) cc_final: 0.8410 (mtp180) REVERT: m 12 MET cc_start: 0.8337 (mtp) cc_final: 0.7951 (mtp) REVERT: m 115 GLU cc_start: 0.8032 (OUTLIER) cc_final: 0.7444 (tt0) REVERT: n 72 ASP cc_start: 0.8405 (t0) cc_final: 0.8154 (t0) REVERT: p 10 GLN cc_start: 0.8116 (tp-100) cc_final: 0.7895 (tp40) REVERT: r 46 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7598 (mm-30) REVERT: r 97 LYS cc_start: 0.9011 (tttm) cc_final: 0.8755 (tttp) REVERT: s 4 ILE cc_start: 0.9197 (mt) cc_final: 0.8969 (mp) REVERT: s 92 ARG cc_start: 0.7340 (OUTLIER) cc_final: 0.6546 (ttp-170) REVERT: t 9 LYS cc_start: 0.8703 (OUTLIER) cc_final: 0.7664 (mppt) REVERT: t 36 LYS cc_start: 0.9020 (OUTLIER) cc_final: 0.8787 (tttt) REVERT: t 64 LYS cc_start: 0.8584 (OUTLIER) cc_final: 0.7318 (mmtp) REVERT: t 73 ARG cc_start: 0.7644 (OUTLIER) cc_final: 0.7334 (ptm-80) REVERT: u 24 LYS cc_start: 0.8532 (OUTLIER) cc_final: 0.8295 (ttpp) REVERT: u 37 GLU cc_start: 0.7890 (OUTLIER) cc_final: 0.7606 (mt-10) REVERT: y 25 ARG cc_start: 0.8336 (mmt-90) cc_final: 0.8069 (mmm-85) REVERT: y 62 LYS cc_start: 0.8960 (mtmt) cc_final: 0.8628 (mtpt) REVERT: y 78 LYS cc_start: 0.8703 (mtpt) cc_final: 0.8224 (mttm) outliers start: 111 outliers final: 79 residues processed: 562 average time/residue: 1.9844 time to fit residues: 1478.7440 Evaluate side-chains 589 residues out of total 2559 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 484 time to evaluate : 4.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 35 SER Chi-restraints excluded: chain 1 residue 19 LEU Chi-restraints excluded: chain 1 residue 59 GLU Chi-restraints excluded: chain 2 residue 12 SER Chi-restraints excluded: chain 3 residue 25 VAL Chi-restraints excluded: chain 3 residue 26 THR Chi-restraints excluded: chain 3 residue 29 SER Chi-restraints excluded: chain 3 residue 46 ASP Chi-restraints excluded: chain 4 residue 42 VAL Chi-restraints excluded: chain 7 residue 19 LYS Chi-restraints excluded: chain 7 residue 40 ARG Chi-restraints excluded: chain 7 residue 52 LYS Chi-restraints excluded: chain 7 residue 54 ASP Chi-restraints excluded: chain c residue 90 ASN Chi-restraints excluded: chain c residue 165 VAL Chi-restraints excluded: chain c residue 182 ARG Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 2 ILE Chi-restraints excluded: chain d residue 7 LYS Chi-restraints excluded: chain d residue 58 ASN Chi-restraints excluded: chain d residue 60 VAL Chi-restraints excluded: chain d residue 74 GLU Chi-restraints excluded: chain d residue 84 LEU Chi-restraints excluded: chain d residue 97 SER Chi-restraints excluded: chain d residue 100 LEU Chi-restraints excluded: chain d residue 151 THR Chi-restraints excluded: chain e residue 69 ARG Chi-restraints excluded: chain e residue 74 LYS Chi-restraints excluded: chain e residue 126 VAL Chi-restraints excluded: chain e residue 166 LYS Chi-restraints excluded: chain e residue 170 ARG Chi-restraints excluded: chain e residue 191 ASP Chi-restraints excluded: chain f residue 35 THR Chi-restraints excluded: chain f residue 38 MET Chi-restraints excluded: chain f residue 42 GLU Chi-restraints excluded: chain f residue 64 LYS Chi-restraints excluded: chain f residue 88 LYS Chi-restraints excluded: chain f residue 103 LEU Chi-restraints excluded: chain f residue 125 ARG Chi-restraints excluded: chain f residue 170 LEU Chi-restraints excluded: chain g residue 15 VAL Chi-restraints excluded: chain g residue 23 VAL Chi-restraints excluded: chain g residue 41 VAL Chi-restraints excluded: chain g residue 81 GLU Chi-restraints excluded: chain g residue 106 SER Chi-restraints excluded: chain g residue 110 SER Chi-restraints excluded: chain g residue 127 THR Chi-restraints excluded: chain g residue 163 ARG Chi-restraints excluded: chain g residue 168 VAL Chi-restraints excluded: chain h residue 15 LEU Chi-restraints excluded: chain j residue 2 LYS Chi-restraints excluded: chain j residue 23 LYS Chi-restraints excluded: chain j residue 30 THR Chi-restraints excluded: chain j residue 48 VAL Chi-restraints excluded: chain j residue 101 ILE Chi-restraints excluded: chain j residue 103 ILE Chi-restraints excluded: chain k residue 30 ARG Chi-restraints excluded: chain k residue 76 VAL Chi-restraints excluded: chain k residue 105 ARG Chi-restraints excluded: chain l residue 80 SER Chi-restraints excluded: chain l residue 85 VAL Chi-restraints excluded: chain l residue 117 THR Chi-restraints excluded: chain l residue 121 THR Chi-restraints excluded: chain m residue 1 MET Chi-restraints excluded: chain m residue 22 GLN Chi-restraints excluded: chain m residue 41 LEU Chi-restraints excluded: chain m residue 115 GLU Chi-restraints excluded: chain m residue 135 VAL Chi-restraints excluded: chain n residue 36 THR Chi-restraints excluded: chain n residue 57 THR Chi-restraints excluded: chain n residue 65 LEU Chi-restraints excluded: chain n residue 70 THR Chi-restraints excluded: chain o residue 24 THR Chi-restraints excluded: chain o residue 54 VAL Chi-restraints excluded: chain p residue 4 ILE Chi-restraints excluded: chain p residue 30 VAL Chi-restraints excluded: chain p residue 52 ASN Chi-restraints excluded: chain p residue 63 LYS Chi-restraints excluded: chain p residue 70 VAL Chi-restraints excluded: chain p residue 76 THR Chi-restraints excluded: chain p residue 102 GLU Chi-restraints excluded: chain r residue 16 GLU Chi-restraints excluded: chain r residue 46 GLU Chi-restraints excluded: chain s residue 92 ARG Chi-restraints excluded: chain t residue 9 LYS Chi-restraints excluded: chain t residue 27 SER Chi-restraints excluded: chain t residue 36 LYS Chi-restraints excluded: chain t residue 64 LYS Chi-restraints excluded: chain t residue 68 ARG Chi-restraints excluded: chain t residue 73 ARG Chi-restraints excluded: chain u residue 15 THR Chi-restraints excluded: chain u residue 24 LYS Chi-restraints excluded: chain u residue 37 GLU Chi-restraints excluded: chain u residue 68 SER Chi-restraints excluded: chain u residue 83 VAL Chi-restraints excluded: chain u residue 89 ASP Chi-restraints excluded: chain u residue 100 SER Chi-restraints excluded: chain w residue 12 GLN Chi-restraints excluded: chain w residue 41 GLU Chi-restraints excluded: chain w residue 65 VAL Chi-restraints excluded: chain y residue 9 SER Chi-restraints excluded: chain y residue 43 THR Chi-restraints excluded: chain y residue 70 GLU Chi-restraints excluded: chain z residue 135 ASN Chi-restraints excluded: chain z residue 147 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 611 random chunks: chunk 385 optimal weight: 2.9990 chunk 516 optimal weight: 0.9990 chunk 148 optimal weight: 6.9990 chunk 446 optimal weight: 0.0270 chunk 71 optimal weight: 6.9990 chunk 134 optimal weight: 6.9990 chunk 485 optimal weight: 1.9990 chunk 203 optimal weight: 10.0000 chunk 498 optimal weight: 0.0670 chunk 61 optimal weight: 10.0000 chunk 89 optimal weight: 8.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 17 ASN 4 26 ASN 6 29 GLN d 42 ASN ** j 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 18 GLN r 6 GLN r 86 GLN t 48 GLN w 75 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.105918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.069064 restraints weight = 115029.474| |-----------------------------------------------------------------------------| r_work (start): 0.2833 rms_B_bonded: 0.67 r_work: 0.2716 rms_B_bonded: 1.35 restraints_weight: 0.5000 r_work: 0.2620 rms_B_bonded: 2.14 restraints_weight: 0.2500 r_work (final): 0.2620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.1240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 99333 Z= 0.148 Angle : 0.565 12.648 149476 Z= 0.301 Chirality : 0.036 0.332 19217 Planarity : 0.004 0.065 7388 Dihedral : 23.854 179.178 51780 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.36 % Favored : 95.54 % Rotamer: Outliers : 4.03 % Allowed : 27.82 % Favored : 68.15 % 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: 0.13 (0.15), residues: 3095 helix: 1.43 (0.19), residues: 817 sheet: 0.00 (0.19), residues: 720 loop : -0.54 (0.15), residues: 1558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP c 248 HIS 0.005 0.001 HIS m 13 PHE 0.015 0.001 PHE w 2 TYR 0.023 0.001 TYR f 83 ARG 0.006 0.000 ARG d 184 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 25188.29 seconds wall clock time: 441 minutes 39.94 seconds (26499.94 seconds total)