Starting phenix.real_space_refine on Sat Feb 24 19:02:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6orl_20174/02_2024/6orl_20174_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6orl_20174/02_2024/6orl_20174.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6orl_20174/02_2024/6orl_20174_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6orl_20174/02_2024/6orl_20174_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6orl_20174/02_2024/6orl_20174_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6orl_20174/02_2024/6orl_20174.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6orl_20174/02_2024/6orl_20174.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6orl_20174/02_2024/6orl_20174_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6orl_20174/02_2024/6orl_20174_updated.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.138 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: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 4642 5.49 5 Mg 295 5.21 5 S 152 5.16 5 C 73315 2.51 5 N 27169 2.21 5 O 40465 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ARG 52": "NH1" <-> "NH2" Residue "B ARG 63": "NH1" <-> "NH2" Residue "B ARG 80": "NH1" <-> "NH2" Residue "B ARG 167": "NH1" <-> "NH2" Residue "B ARG 177": "NH1" <-> "NH2" Residue "B ARG 182": "NH1" <-> "NH2" Residue "B ARG 212": "NH1" <-> "NH2" Residue "B ARG 269": "NH1" <-> "NH2" Residue "C ARG 13": "NH1" <-> "NH2" Residue "C ARG 33": "NH1" <-> "NH2" Residue "C ARG 59": "NH1" <-> "NH2" Residue "C ARG 77": "NH1" <-> "NH2" Residue "C ARG 83": "NH1" <-> "NH2" Residue "C ARG 169": "NH1" <-> "NH2" Residue "C ARG 184": "NH1" <-> "NH2" Residue "D ARG 21": "NH1" <-> "NH2" Residue "D ARG 44": "NH1" <-> "NH2" Residue "D ARG 49": "NH1" <-> "NH2" Residue "D ARG 102": "NH1" <-> "NH2" Residue "D ARG 162": "NH1" <-> "NH2" Residue "E ARG 30": "NH1" <-> "NH2" Residue "E ARG 71": "NH1" <-> "NH2" Residue "E ARG 92": "NH1" <-> "NH2" Residue "E ARG 102": "NH1" <-> "NH2" Residue "E ARG 110": "NH1" <-> "NH2" Residue "E ARG 112": "NH1" <-> "NH2" Residue "E ARG 115": "NH1" <-> "NH2" Residue "E ARG 148": "NH1" <-> "NH2" Residue "F ARG 3": "NH1" <-> "NH2" Residue "F ARG 152": "NH1" <-> "NH2" Residue "F ARG 153": "NH1" <-> "NH2" Residue "F ARG 163": "NH1" <-> "NH2" Residue "F ARG 170": "NH1" <-> "NH2" Residue "G ARG 50": "NH1" <-> "NH2" Residue "G ARG 51": "NH1" <-> "NH2" Residue "G ARG 68": "NH1" <-> "NH2" Residue "J ARG 13": "NH1" <-> "NH2" Residue "J ARG 34": "NH1" <-> "NH2" Residue "J ARG 37": "NH1" <-> "NH2" Residue "J ARG 95": "NH1" <-> "NH2" Residue "J ARG 96": "NH1" <-> "NH2" Residue "J ARG 120": "NH1" <-> "NH2" Residue "K ARG 17": "NH1" <-> "NH2" Residue "K ARG 18": "NH1" <-> "NH2" Residue "L ARG 21": "NH1" <-> "NH2" Residue "L ARG 33": "NH1" <-> "NH2" Residue "L ARG 41": "NH1" <-> "NH2" Residue "L ARG 47": "NH1" <-> "NH2" Residue "L ARG 60": "NH1" <-> "NH2" Residue "L ARG 78": "NH1" <-> "NH2" Residue "L ARG 123": "NH1" <-> "NH2" Residue "L ARG 126": "NH1" <-> "NH2" Residue "M ARG 10": "NH1" <-> "NH2" Residue "M ARG 18": "NH1" <-> "NH2" Residue "M ARG 40": "NH1" <-> "NH2" Residue "M ARG 50": "NH1" <-> "NH2" Residue "M ARG 55": "NH1" <-> "NH2" Residue "M ARG 114": "NH1" <-> "NH2" Residue "N ARG 8": "NH1" <-> "NH2" Residue "N ARG 12": "NH1" <-> "NH2" Residue "N ARG 17": "NH1" <-> "NH2" Residue "N ARG 22": "NH1" <-> "NH2" Residue "N ARG 46": "NH1" <-> "NH2" Residue "N ARG 63": "NH1" <-> "NH2" Residue "N ARG 64": "NH1" <-> "NH2" Residue "N ARG 69": "NH1" <-> "NH2" Residue "N ARG 96": "NH1" <-> "NH2" Residue "N ARG 118": "NH1" <-> "NH2" 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 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 ARG 62": "NH1" <-> "NH2" Residue "P ARG 89": "NH1" <-> "NH2" Residue "P ARG 101": "NH1" <-> "NH2" Residue "P ARG 109": "NH1" <-> "NH2" Residue "Q ARG 3": "NH1" <-> "NH2" Residue "Q ARG 6": "NH1" <-> "NH2" Residue "Q ARG 13": "NH1" <-> "NH2" Residue "Q ARG 33": "NH1" <-> "NH2" Residue "Q ARG 48": "NH1" <-> "NH2" Residue "Q ARG 70": "NH1" <-> "NH2" Residue "R ARG 21": "NH1" <-> "NH2" Residue "R ARG 68": "NH1" <-> "NH2" Residue "R ARG 78": "NH1" <-> "NH2" Residue "R ARG 79": "NH1" <-> "NH2" Residue "R ARG 84": "NH1" <-> "NH2" Residue "S PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 84": "NH1" <-> "NH2" Residue "S ARG 88": "NH1" <-> "NH2" Residue "S ARG 92": "NH1" <-> "NH2" Residue "S ARG 110": "NH1" <-> "NH2" Residue "T ARG 3": "NH1" <-> "NH2" Residue "T ARG 6": "NH1" <-> "NH2" Residue "U ARG 6": "NH1" <-> "NH2" Residue "U ARG 82": "NH1" <-> "NH2" Residue "U ARG 86": "NH1" <-> "NH2" Residue "U ARG 94": "NH1" <-> "NH2" Residue "V ARG 19": "NH1" <-> "NH2" Residue "X ARG 3": "NH1" <-> "NH2" Residue "X ARG 18": "NH1" <-> "NH2" Residue "X ARG 37": "NH1" <-> "NH2" Residue "X ARG 45": "NH1" <-> "NH2" Residue "X ARG 50": "NH1" <-> "NH2" Residue "X ARG 57": "NH1" <-> "NH2" Residue "X ARG 74": "NH1" <-> "NH2" Residue "Y ARG 29": "NH1" <-> "NH2" Residue "Y ARG 47": "NH1" <-> "NH2" Residue "Y ARG 52": "NH1" <-> "NH2" Residue "Z ARG 11": "NH1" <-> "NH2" Residue "Z ARG 30": "NH1" <-> "NH2" Residue "Z ARG 45": "NH1" <-> "NH2" Residue "b ARG 10": "NH1" <-> "NH2" Residue "b ARG 16": "NH1" <-> "NH2" Residue "b ARG 52": "NH1" <-> "NH2" Residue "c ARG 28": "NH1" <-> "NH2" Residue "c ARG 44": "NH1" <-> "NH2" Residue "d ARG 3": "NH1" <-> "NH2" Residue "d ARG 14": "NH1" <-> "NH2" Residue "d ARG 19": "NH1" <-> "NH2" Residue "d ARG 21": "NH1" <-> "NH2" Residue "d ARG 33": "NH1" <-> "NH2" Residue "d ARG 41": "NH1" <-> "NH2" Residue "e ARG 13": "NH1" <-> "NH2" Residue "e ARG 30": "NH1" <-> "NH2" Residue "e ARG 40": "NH1" <-> "NH2" Residue "e ARG 42": "NH1" <-> "NH2" Residue "f ARG 24": "NH1" <-> "NH2" Residue "g ARG 63": "NH1" <-> "NH2" Residue "g ARG 74": "NH1" <-> "NH2" Residue "g ARG 208": "NH1" <-> "NH2" Residue "g ARG 225": "NH1" <-> "NH2" Residue "h ARG 54": "NH1" <-> "NH2" Residue "h ARG 72": "NH1" <-> "NH2" Residue "h ARG 88": "NH1" <-> "NH2" Residue "h ARG 127": "NH1" <-> "NH2" Residue "h ARG 131": "NH1" <-> "NH2" Residue "h ARG 132": "NH1" <-> "NH2" Residue "h ARG 164": "NH1" <-> "NH2" Residue "i ARG 73": "NH1" <-> "NH2" Residue "i ARG 81": "NH1" <-> "NH2" Residue "i GLU 147": "OE1" <-> "OE2" Residue "j ARG 45": "NH1" <-> "NH2" Residue "j ARG 68": "NH1" <-> "NH2" Residue "j ARG 69": "NH1" <-> "NH2" Residue "j ARG 93": "NH1" <-> "NH2" Residue "j ARG 157": "NH1" <-> "NH2" Residue "k PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k ARG 45": "NH1" <-> "NH2" Residue "k ARG 79": "NH1" <-> "NH2" Residue "l ARG 4": "NH1" <-> "NH2" Residue "l ARG 53": "NH1" <-> "NH2" Residue "l ARG 78": "NH1" <-> "NH2" Residue "l ARG 79": "NH1" <-> "NH2" Residue "l ARG 92": "NH1" <-> "NH2" Residue "n ARG 11": "NH1" <-> "NH2" Residue "n ARG 41": "NH1" <-> "NH2" Residue "n ARG 130": "NH1" <-> "NH2" Residue "o ARG 5": "NH1" <-> "NH2" Residue "o ARG 45": "NH1" <-> "NH2" Residue "o ARG 89": "NH1" <-> "NH2" Residue "p ARG 37": "NH1" <-> "NH2" Residue "p ARG 69": "NH1" <-> "NH2" Residue "p ARG 93": "NH1" <-> "NH2" Residue "p ARG 106": "NH1" <-> "NH2" Residue "q ARG 9": "NH1" <-> "NH2" Residue "q ARG 14": "NH1" <-> "NH2" Residue "q ARG 50": "NH1" <-> "NH2" Residue "q ARG 83": "NH1" <-> "NH2" Residue "r ARG 29": "NH1" <-> "NH2" Residue "r ARG 70": "NH1" <-> "NH2" Residue "r ARG 87": "NH1" <-> "NH2" Residue "r ARG 109": "NH1" <-> "NH2" Residue "s ARG 59": "NH1" <-> "NH2" Residue "s ARG 63": "NH1" <-> "NH2" Residue "s ARG 65": "NH1" <-> "NH2" Residue "s ARG 69": "NH1" <-> "NH2" Residue "s ARG 85": "NH1" <-> "NH2" Residue "t ARG 72": "NH1" <-> "NH2" Residue "t ARG 89": "NH1" <-> "NH2" Residue "u ARG 28": "NH1" <-> "NH2" Residue "u PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u ARG 51": "NH1" <-> "NH2" Residue "v ARG 11": "NH1" <-> "NH2" Residue "v ARG 27": "NH1" <-> "NH2" Residue "v ARG 65": "NH1" <-> "NH2" Residue "v ARG 77": "NH1" <-> "NH2" Residue "w ARG 61": "NH1" <-> "NH2" Residue "x ARG 32": "NH1" <-> "NH2" Residue "y ARG 60": "NH1" <-> "NH2" Residue "y ARG 74": "NH1" <-> "NH2" Residue "z ARG 33": "NH1" <-> "NH2" Residue "z ARG 45": "NH1" <-> "NH2" Residue "z ARG 55": "NH1" <-> "NH2" Residue "z ARG 62": "NH1" <-> "NH2" Residue "z ARG 67": "NH1" <-> "NH2" Residue "z ARG 69": "NH1" <-> "NH2" Residue "A ARG 109": "NH1" <-> "NH2" Residue "A ARG 133": "NH1" <-> "NH2" Residue "A ARG 137": "NH1" <-> "NH2" Residue "A ARG 142": "NH1" <-> "NH2" Residue "A ARG 143": "NH1" <-> "NH2" Residue "A ARG 145": "NH1" <-> "NH2" Residue "A ARG 174": "NH1" <-> "NH2" Residue "A ARG 228": "NH1" <-> "NH2" Residue "A ARG 286": "NH1" <-> "NH2" Residue "A ARG 294": "NH1" <-> "NH2" Residue "A ARG 295": "NH1" <-> "NH2" Residue "A ARG 328": "NH1" <-> "NH2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 146039 Number of models: 1 Model: "" Number of chains: 62 Chain: "1" Number of atoms: 62336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2903, 62336 Classifications: {'RNA': 2903} Modifications used: {'rna2p': 6, 'rna2p_pur': 288, 'rna2p_pyr': 165, 'rna3p': 16, 'rna3p_pur': 1379, 'rna3p_pyr': 1049} Link IDs: {'rna2p': 458, 'rna3p': 2444} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 9 Chain: "2" Number of atoms: 32929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1534, 32929 Classifications: {'RNA': 1534} Modifications used: {'rna2p': 1, 'rna2p_pur': 119, 'rna2p_pyr': 89, 'rna3p': 10, 'rna3p_pur': 750, 'rna3p_pyr': 564} Link IDs: {'rna2p': 208, 'rna3p': 1325} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 2 Chain: "3" Number of atoms: 2569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 2569 Classifications: {'RNA': 120} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 8, 'rna3p_pur': 57, 'rna3p_pyr': 48} Link IDs: {'rna2p': 14, 'rna3p': 105} Chain: "B" 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: "C" Number of atoms: 1565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1565 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 202} Chain: "D" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1552 Classifications: {'peptide': 201} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 195} Chain: "E" Number of atoms: 1410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1410 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 6, 'TRANS': 170} Chain: "F" Number of atoms: 1313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1313 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 8, 'TRANS': 166} Chain: "G" Number of atoms: 1111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1111 Classifications: {'peptide': 149} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 145} Chain: "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: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 946 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 5, 'TRANS': 117} Chain: "L" Number of atoms: 1053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1053 Classifications: {'peptide': 144} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 139} 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: 951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 951 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain: "O" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 892 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "P" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 917 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "Q" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 947 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'TRANS': 116} Chain: "R" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 816 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 101} Chain: "S" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 857 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 107} Chain: "T" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 746 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 1, 'TRANS': 92} Chain: "U" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 788 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 3, 'TRANS': 99} Chain: "V" Number of atoms: 753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 753 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "W" Number of atoms: 582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 582 Classifications: {'peptide': 76} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 74} Chain: "X" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 625 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "Y" Number of atoms: 501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 501 Classifications: {'peptide': 62} Modifications used: {'COO': 1} Link IDs: {'TRANS': 61} Chain: "Z" Number of atoms: 448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 448 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "b" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 444 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 54} Chain: "c" Number of atoms: 426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 426 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 2, 'TRANS': 49} Chain: "d" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 377 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "e" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 504 Classifications: {'peptide': 64} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "f" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 302 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "g" Number of atoms: 1760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1760 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 7, 'TRANS': 217} Chain: "h" Number of atoms: 1636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1636 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 7, 'TRANS': 200} Chain: "i" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1643 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 198} Chain: "j" Number of atoms: 1152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1152 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 5, 'TRANS': 150} Chain: "k" Number of atoms: 848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 848 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "l" Number of atoms: 1181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1181 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain: "m" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 979 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "n" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1022 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "o" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 790 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 5, 'TRANS': 93} Chain: "p" Number of atoms: 877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 877 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 109} Chain: "q" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 957 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 115} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'0TD:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "r" Number of atoms: 900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 900 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain: "s" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 805 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "t" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 714 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'TRANS': 87} Chain: "u" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 649 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "v" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 648 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain: "w" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 544 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "x" Number of atoms: 663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 663 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 5, 'TRANS': 77} Chain: "y" Number of atoms: 669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 669 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "z" Number of atoms: 589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 589 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "5" Number of atoms: 1627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1627 Classifications: {'RNA': 76} Modifications used: {'rna2p': 2, 'rna2p_pur': 6, 'rna2p_pyr': 6, 'rna3p': 3, 'rna3p_pur': 34, 'rna3p_pyr': 25} Link IDs: {'rna2p': 13, 'rna3p': 62} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 3 Chain: "H" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 1929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1929 Classifications: {'peptide': 246} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 235} Chain breaks: 1 Chain: "4" Number of atoms: 184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 184 Classifications: {'RNA': 9} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 1, 'rna3p_pyr': 6} Link IDs: {'rna2p': 1, 'rna3p': 7} Chain: "1" Number of atoms: 283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 283 Unusual residues: {' MG': 283} Classifications: {'undetermined': 283} Link IDs: {None: 282} Chain: "2" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "3" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Unusual residues: {' MG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "b" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "f" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "i" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM A0HJC SG CYS f 11 139.184 163.217 58.688 1.00148.92 S ATOM A0HK1 SG CYS f 14 141.948 160.955 58.631 1.00145.48 S ATOM A0HMW SG CYS f 27 141.904 165.427 59.440 1.00137.58 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb="MG MG 13142 " occ=0.50 Time building chain proxies: 55.35, per 1000 atoms: 0.38 Number of scatterers: 146039 At special positions: 0 Unit cell: (285.52, 268.92, 227.42, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 152 16.00 P 4642 15.00 Mg 295 11.99 O 40465 8.00 N 27169 7.00 C 73315 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 73.10 Conformation dependent library (CDL) restraints added in 7.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN f 101 " pdb="ZN ZN f 101 " - pdb=" ND1 HIS f 33 " pdb="ZN ZN f 101 " - pdb=" SG CYS f 27 " pdb="ZN ZN f 101 " - pdb=" SG CYS f 14 " pdb="ZN ZN f 101 " - pdb=" SG CYS f 11 " Number of angles added : 3 11568 Ramachandran restraints generated. 5784 Oldfield, 0 Emsley, 5784 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10822 Finding SS restraints... Warning!!! ksdssp method is not applicable for structures that cannot fit in PDB format. Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 180 helices and 69 sheets defined 39.4% alpha, 19.0% beta 1321 base pairs and 2510 stacking pairs defined. Time for finding SS restraints: 78.99 Creating SS restraints... Processing helix chain 'B' and resid 10 through 17 removed outlier: 3.728A pdb=" N ARG B 14 " --> pdb=" O SER B 10 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N HIS B 15 " --> pdb=" O PRO B 11 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N VAL B 16 " --> pdb=" O GLY B 12 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N VAL B 17 " --> pdb=" O ARG B 13 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 10 through 17' Processing helix chain 'B' and resid 30 through 35 removed outlier: 3.885A pdb=" N LEU B 34 " --> pdb=" O PHE B 30 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N GLU B 35 " --> pdb=" O ALA B 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 30 through 35' Processing helix chain 'B' and resid 131 through 136 removed outlier: 3.938A pdb=" N ILE B 135 " --> pdb=" O PRO B 131 " (cutoff:3.500A) Proline residue: B 136 - end of helix No H-bonds generated for 'chain 'B' and resid 131 through 136' Processing helix chain 'B' and resid 207 through 215 removed outlier: 3.870A pdb=" N ALA B 211 " --> pdb=" O LYS B 207 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG B 214 " --> pdb=" O ALA B 210 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLY B 215 " --> pdb=" O ALA B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 268 removed outlier: 4.719A pdb=" N ASP B 264 " --> pdb=" O ASN B 260 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N LYS B 265 " --> pdb=" O LYS B 261 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N PHE B 266 " --> pdb=" O ARG B 262 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ILE B 267 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N VAL B 268 " --> pdb=" O ASP B 264 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 260 through 268' Processing helix chain 'C' and resid 61 through 72 Processing helix chain 'C' and resid 98 through 103 removed outlier: 4.233A pdb=" N ALA C 102 " --> pdb=" O VAL C 98 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N ASP C 103 " --> pdb=" O GLU C 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 98 through 103' Processing helix chain 'C' and resid 120 through 125 Processing helix chain 'D' and resid 15 through 20 Processing helix chain 'D' and resid 24 through 41 removed outlier: 3.569A pdb=" N VAL D 33 " --> pdb=" O HIS D 29 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N GLN D 41 " --> pdb=" O ALA D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 116 removed outlier: 4.186A pdb=" N SER D 110 " --> pdb=" O LYS D 106 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLU D 111 " --> pdb=" O SER D 107 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL D 113 " --> pdb=" O LEU D 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 142 Processing helix chain 'D' and resid 154 through 163 removed outlier: 3.682A pdb=" N ARG D 162 " --> pdb=" O PHE D 158 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ASN D 163 " --> pdb=" O LEU D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 183 removed outlier: 3.630A pdb=" N LEU D 180 " --> pdb=" O ASP D 176 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE D 181 " --> pdb=" O PRO D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 201 Processing helix chain 'E' and resid 2 through 21 removed outlier: 3.729A pdb=" N GLU E 11 " --> pdb=" O TYR E 7 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N VAL E 13 " --> pdb=" O LYS E 9 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LYS E 14 " --> pdb=" O ASP E 10 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 62 removed outlier: 4.369A pdb=" N LEU E 50 " --> pdb=" O ASP E 46 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA E 53 " --> pdb=" O LEU E 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 93 through 111 removed outlier: 3.586A pdb=" N THR E 105 " --> pdb=" O GLU E 101 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ILE E 106 " --> pdb=" O ARG E 102 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N VAL E 108 " --> pdb=" O ILE E 104 " (cutoff:3.500A) Proline residue: E 109 - end of helix Processing helix chain 'E' and resid 142 through 147 removed outlier: 4.013A pdb=" N VAL E 146 " --> pdb=" O ASP E 142 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N ASP E 147 " --> pdb=" O TYR E 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 142 through 147' Processing helix chain 'E' and resid 162 through 174 removed outlier: 4.675A pdb=" N GLY E 166 " --> pdb=" O SER E 162 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ARG E 167 " --> pdb=" O ASP E 163 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA E 172 " --> pdb=" O ALA E 168 " (cutoff:3.500A) Processing helix chain 'E' and resid 40 through 45 removed outlier: 3.835A pdb=" N ILE E 44 " --> pdb=" O GLY E 41 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ALA E 45 " --> pdb=" O GLU E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 123 removed outlier: 5.664A pdb=" N SER E 121 " --> pdb=" O SER E 118 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N PHE E 122 " --> pdb=" O ALA E 119 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ASP E 123 " --> pdb=" O LYS E 120 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 118 through 123' Processing helix chain 'E' and resid 134 through 139 removed outlier: 3.890A pdb=" N ILE E 137 " --> pdb=" O GLU E 134 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N PHE E 138 " --> pdb=" O GLN E 135 " (cutoff:3.500A) Proline residue: E 139 - end of helix No H-bonds generated for 'chain 'E' and resid 134 through 139' Processing helix chain 'F' and resid 2 through 8 Proline residue: F 8 - end of helix Processing helix chain 'F' and resid 60 through 81 removed outlier: 3.654A pdb=" N GLN F 64 " --> pdb=" O ASP F 60 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE F 77 " --> pdb=" O ASN F 73 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 153 removed outlier: 3.760A pdb=" N TYR F 151 " --> pdb=" O ASP F 147 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N ARG F 152 " --> pdb=" O LEU F 148 " (cutoff:3.500A) Processing helix chain 'G' and resid 22 through 28 Processing helix chain 'G' and resid 29 through 34 Processing helix chain 'G' and resid 40 through 50 removed outlier: 3.980A pdb=" N GLU G 45 " --> pdb=" O LYS G 41 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N PHE G 46 " --> pdb=" O LYS G 42 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ARG G 50 " --> pdb=" O PHE G 46 " (cutoff:3.500A) Processing helix chain 'G' and resid 51 through 74 removed outlier: 4.582A pdb=" N ALA G 56 " --> pdb=" O ALA G 52 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS G 57 " --> pdb=" O GLU G 53 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLU G 60 " --> pdb=" O ALA G 56 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N LEU G 62 " --> pdb=" O LEU G 58 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ALA G 65 " --> pdb=" O VAL G 61 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ALA G 67 " --> pdb=" O ALA G 63 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ARG G 68 " --> pdb=" O ALA G 64 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA G 69 " --> pdb=" O ALA G 65 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N GLU G 70 " --> pdb=" O ASN G 66 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ASN G 73 " --> pdb=" O ALA G 69 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA G 74 " --> pdb=" O GLU G 70 " (cutoff:3.500A) Processing helix chain 'G' and resid 95 through 107 removed outlier: 3.642A pdb=" N VAL G 103 " --> pdb=" O ILE G 99 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N THR G 104 " --> pdb=" O ALA G 100 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLY G 107 " --> pdb=" O VAL G 103 " (cutoff:3.500A) Processing helix chain 'J' and resid 24 through 38 removed outlier: 4.960A pdb=" N GLU J 31 " --> pdb=" O ARG J 27 " (cutoff:3.500A) Processing helix chain 'J' and resid 88 through 96 removed outlier: 4.078A pdb=" N MET J 92 " --> pdb=" O THR J 88 " (cutoff:3.500A) Processing helix chain 'J' and resid 97 through 110 removed outlier: 4.469A pdb=" N ILE J 101 " --> pdb=" O PRO J 97 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N MET J 108 " --> pdb=" O ALA J 104 " (cutoff:3.500A) Proline residue: J 110 - end of helix Processing helix chain 'J' and resid 112 through 122 removed outlier: 3.526A pdb=" N ARG J 120 " --> pdb=" O ARG J 116 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N LYS J 121 " --> pdb=" O ALA J 117 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N LEU J 122 " --> pdb=" O MET J 118 " (cutoff:3.500A) Processing helix chain 'K' and resid 112 through 120 Proline residue: K 120 - end of helix Processing helix chain 'L' and resid 37 through 42 removed outlier: 3.836A pdb=" N ARG L 41 " --> pdb=" O GLY L 37 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N SER L 42 " --> pdb=" O GLN L 38 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 37 through 42' Processing helix chain 'L' and resid 56 through 62 Proline residue: L 62 - end of helix Processing helix chain 'L' and resid 68 through 75 removed outlier: 3.908A pdb=" N ALA L 72 " --> pdb=" O SER L 68 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ILE L 73 " --> pdb=" O ARG L 69 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N THR L 74 " --> pdb=" O LYS L 70 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N ALA L 75 " --> pdb=" O ALA L 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 68 through 75' Processing helix chain 'L' and resid 78 through 86 removed outlier: 3.573A pdb=" N LEU L 82 " --> pdb=" O ARG L 78 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ALA L 83 " --> pdb=" O LEU L 79 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N LYS L 84 " --> pdb=" O SER L 80 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N VAL L 85 " --> pdb=" O ASP L 81 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N GLU L 86 " --> pdb=" O LEU L 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 78 through 86' Processing helix chain 'L' and resid 91 through 99 Processing helix chain 'L' and resid 128 through 139 Processing helix chain 'M' and resid 42 through 58 removed outlier: 3.501A pdb=" N LYS M 58 " --> pdb=" O THR M 54 " (cutoff:3.500A) Processing helix chain 'M' and resid 109 through 125 removed outlier: 4.181A pdb=" N LYS M 123 " --> pdb=" O LEU M 119 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU M 124 " --> pdb=" O ALA M 120 " (cutoff:3.500A) Proline residue: M 125 - end of helix Processing helix chain 'N' and resid 13 through 32 removed outlier: 3.609A pdb=" N HIS N 31 " --> pdb=" O SER N 27 " (cutoff:3.500A) Processing helix chain 'N' and resid 38 through 58 removed outlier: 3.727A pdb=" N ARG N 45 " --> pdb=" O ALA N 41 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N ARG N 46 " --> pdb=" O LYS N 42 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N VAL N 47 " --> pdb=" O GLU N 43 " (cutoff:3.500A) Proline residue: N 50 - end of helix removed outlier: 3.571A pdb=" N LYS N 56 " --> pdb=" O ILE N 52 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N THR N 57 " --> pdb=" O THR N 53 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N ASP N 58 " --> pdb=" O LEU N 54 " (cutoff:3.500A) Processing helix chain 'N' and resid 59 through 71 Processing helix chain 'N' and resid 72 through 88 removed outlier: 3.853A pdb=" N GLY N 84 " --> pdb=" O PHE N 80 " (cutoff:3.500A) Proline residue: N 85 - end of helix Processing helix chain 'O' and resid 2 through 22 removed outlier: 4.592A pdb=" N ARG O 13 " --> pdb=" O ARG O 9 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N ALA O 14 " --> pdb=" O ARG O 10 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLY O 22 " --> pdb=" O LEU O 18 " (cutoff:3.500A) Processing helix chain 'O' and resid 55 through 63 removed outlier: 4.942A pdb=" N GLN O 61 " --> pdb=" O ALA O 57 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N LEU O 62 " --> pdb=" O ILE O 58 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N LYS O 63 " --> pdb=" O ALA O 59 " (cutoff:3.500A) Processing helix chain 'O' and resid 67 through 86 removed outlier: 3.595A pdb=" N LYS O 76 " --> pdb=" O ALA O 72 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ALA O 79 " --> pdb=" O GLY O 75 " (cutoff:3.500A) Processing helix chain 'O' and resid 101 through 114 removed outlier: 3.785A pdb=" N ALA O 113 " --> pdb=" O ALA O 109 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLY O 114 " --> pdb=" O ALA O 110 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 13 removed outlier: 3.545A pdb=" N GLN P 7 " --> pdb=" O ASN P 3 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N GLU P 11 " --> pdb=" O GLN P 7 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLN P 12 " --> pdb=" O LEU P 8 " (cutoff:3.500A) Processing helix chain 'P' and resid 97 through 104 removed outlier: 4.856A pdb=" N ARG P 101 " --> pdb=" O LEU P 97 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N GLU P 102 " --> pdb=" O TYR P 98 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ARG P 103 " --> pdb=" O TYR P 99 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N THR P 104 " --> pdb=" O LEU P 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 97 through 104' Processing helix chain 'Q' and resid 6 through 22 removed outlier: 3.814A pdb=" N ALA Q 10 " --> pdb=" O ARG Q 6 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLN Q 20 " --> pdb=" O LYS Q 16 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LYS Q 22 " --> pdb=" O LEU Q 18 " (cutoff:3.500A) Processing helix chain 'Q' and resid 26 through 31 removed outlier: 4.327A pdb=" N ARG Q 30 " --> pdb=" O GLY Q 26 " (cutoff:3.500A) Processing helix chain 'Q' and resid 36 through 73 removed outlier: 4.006A pdb=" N ARG Q 51 " --> pdb=" O TYR Q 47 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LYS Q 54 " --> pdb=" O ARG Q 50 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG Q 58 " --> pdb=" O LYS Q 54 " (cutoff:3.500A) Processing helix chain 'Q' and resid 75 through 87 removed outlier: 3.556A pdb=" N GLY Q 82 " --> pdb=" O LYS Q 78 " (cutoff:3.500A) Processing helix chain 'Q' and resid 91 through 102 Processing helix chain 'Q' and resid 103 through 118 Processing helix chain 'S' and resid 13 through 25 removed outlier: 3.858A pdb=" N ARG S 18 " --> pdb=" O ALA S 14 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU S 19 " --> pdb=" O GLN S 15 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL S 20 " --> pdb=" O LYS S 16 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N LEU S 23 " --> pdb=" O LEU S 19 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ILE S 24 " --> pdb=" O VAL S 20 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ARG S 25 " --> pdb=" O ALA S 21 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 39 removed outlier: 3.745A pdb=" N ASP S 34 " --> pdb=" O SER S 30 " (cutoff:3.500A) Processing helix chain 'S' and resid 41 through 61 removed outlier: 3.851A pdb=" N VAL S 45 " --> pdb=" O LYS S 41 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU S 46 " --> pdb=" O LYS S 42 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N SER S 53 " --> pdb=" O LYS S 49 " (cutoff:3.500A) Processing helix chain 'S' and resid 65 through 70 removed outlier: 3.506A pdb=" N LEU S 69 " --> pdb=" O ASP S 65 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N LYS S 70 " --> pdb=" O ILE S 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 65 through 70' Processing helix chain 'T' and resid 3 through 11 removed outlier: 3.817A pdb=" N LYS T 9 " --> pdb=" O GLU T 5 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL T 10 " --> pdb=" O ARG T 6 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N LEU T 11 " --> pdb=" O LEU T 7 " (cutoff:3.500A) Processing helix chain 'T' and resid 17 through 26 removed outlier: 3.675A pdb=" N MET T 24 " --> pdb=" O ALA T 20 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU T 25 " --> pdb=" O SER T 21 " (cutoff:3.500A) Processing helix chain 'T' and resid 39 through 51 removed outlier: 3.519A pdb=" N GLN T 48 " --> pdb=" O LYS T 44 " (cutoff:3.500A) Processing helix chain 'U' and resid 66 through 71 removed outlier: 4.043A pdb=" N VAL U 70 " --> pdb=" O GLN U 66 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N ALA U 71 " --> pdb=" O VAL U 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 66 through 71' Processing helix chain 'V' and resid 13 through 24 Processing helix chain 'V' and resid 43 through 52 removed outlier: 3.629A pdb=" N VAL V 47 " --> pdb=" O ASP V 43 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASN V 49 " --> pdb=" O ASP V 45 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ALA V 52 " --> pdb=" O MET V 48 " (cutoff:3.500A) Processing helix chain 'V' and resid 53 through 59 removed outlier: 3.803A pdb=" N TYR V 57 " --> pdb=" O LYS V 53 " (cutoff:3.500A) Processing helix chain 'X' and resid 52 through 63 Processing helix chain 'X' and resid 64 through 75 removed outlier: 3.566A pdb=" N GLU X 70 " --> pdb=" O THR X 66 " (cutoff:3.500A) Processing helix chain 'Y' and resid 2 through 9 removed outlier: 3.923A pdb=" N GLU Y 8 " --> pdb=" O LYS Y 4 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N LYS Y 9 " --> pdb=" O GLU Y 5 " (cutoff:3.500A) Processing helix chain 'Y' and resid 10 through 35 removed outlier: 4.584A pdb=" N GLY Y 35 " --> pdb=" O GLN Y 31 " (cutoff:3.500A) Processing helix chain 'Y' and resid 39 through 61 removed outlier: 4.654A pdb=" N LEU Y 43 " --> pdb=" O GLN Y 39 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N LYS Y 44 " --> pdb=" O SER Y 40 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL Y 53 " --> pdb=" O ASP Y 49 " (cutoff:3.500A) Processing helix chain 'Z' and resid 17 through 28 Processing helix chain 'Z' and resid 41 through 52 removed outlier: 3.552A pdb=" N VAL Z 51 " --> pdb=" O MET Z 47 " (cutoff:3.500A) Processing helix chain 'b' and resid 9 through 19 removed outlier: 5.029A pdb=" N HIS b 19 " --> pdb=" O MET b 15 " (cutoff:3.500A) Processing helix chain 'c' and resid 26 through 31 Proline residue: c 31 - end of helix No H-bonds generated for 'chain 'c' and resid 26 through 31' Processing helix chain 'd' and resid 8 through 16 Processing helix chain 'd' and resid 17 through 25 removed outlier: 3.640A pdb=" N ALA d 23 " --> pdb=" O ARG d 19 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N THR d 24 " --> pdb=" O ALA d 20 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N LYS d 25 " --> pdb=" O ARG d 21 " (cutoff:3.500A) Processing helix chain 'd' and resid 26 through 38 Processing helix chain 'e' and resid 7 through 14 removed outlier: 3.782A pdb=" N LYS e 12 " --> pdb=" O ARG e 8 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ARG e 13 " --> pdb=" O GLY e 9 " (cutoff:3.500A) Processing helix chain 'e' and resid 37 through 46 removed outlier: 3.535A pdb=" N LEU e 44 " --> pdb=" O ARG e 40 " (cutoff:3.500A) Proline residue: e 46 - end of helix Processing helix chain 'e' and resid 54 through 63 removed outlier: 3.698A pdb=" N VAL e 58 " --> pdb=" O ASP e 54 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE e 59 " --> pdb=" O LEU e 55 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N CYS e 61 " --> pdb=" O LEU e 57 " (cutoff:3.500A) Proline residue: e 63 - end of helix Processing helix chain 'g' and resid 5 through 13 removed outlier: 3.508A pdb=" N MET g 9 " --> pdb=" O SER g 5 " (cutoff:3.500A) Processing helix chain 'g' and resid 24 through 29 removed outlier: 3.883A pdb=" N LYS g 28 " --> pdb=" O ASN g 24 " (cutoff:3.500A) Proline residue: g 29 - end of helix No H-bonds generated for 'chain 'g' and resid 24 through 29' Processing helix chain 'g' and resid 43 through 64 Proline residue: g 48 - end of helix removed outlier: 3.560A pdb=" N ALA g 55 " --> pdb=" O ASN g 51 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLU g 56 " --> pdb=" O GLU g 52 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ARG g 63 " --> pdb=" O LYS g 59 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LYS g 64 " --> pdb=" O ILE g 60 " (cutoff:3.500A) Processing helix chain 'g' and resid 74 through 88 removed outlier: 6.337A pdb=" N GLU g 78 " --> pdb=" O ARG g 74 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N ALA g 79 " --> pdb=" O ALA g 75 " (cutoff:3.500A) Processing helix chain 'g' and resid 103 through 121 removed outlier: 3.674A pdb=" N GLN g 109 " --> pdb=" O LYS g 105 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER g 121 " --> pdb=" O LEU g 117 " (cutoff:3.500A) Processing helix chain 'g' and resid 130 through 148 removed outlier: 3.862A pdb=" N ALA g 134 " --> pdb=" O THR g 130 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLU g 140 " --> pdb=" O MET g 136 " (cutoff:3.500A) Processing helix chain 'g' and resid 165 through 170 Processing helix chain 'g' and resid 171 through 180 Processing helix chain 'g' and resid 206 through 227 removed outlier: 3.735A pdb=" N GLY g 215 " --> pdb=" O THR g 211 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA g 216 " --> pdb=" O LEU g 212 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR g 220 " --> pdb=" O ALA g 216 " (cutoff:3.500A) Processing helix chain 'h' and resid 6 through 13 removed outlier: 3.604A pdb=" N ILE h 10 " --> pdb=" O HIS h 6 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG h 11 " --> pdb=" O PRO h 7 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N GLY h 13 " --> pdb=" O GLY h 9 " (cutoff:3.500A) Processing helix chain 'h' and resid 26 through 48 removed outlier: 3.771A pdb=" N ALA h 30 " --> pdb=" O THR h 26 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N ASP h 31 " --> pdb=" O LYS h 27 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASN h 32 " --> pdb=" O GLU h 28 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LEU h 43 " --> pdb=" O VAL h 39 " (cutoff:3.500A) Processing helix chain 'h' and resid 72 through 78 removed outlier: 4.303A pdb=" N VAL h 76 " --> pdb=" O ARG h 72 " (cutoff:3.500A) Processing helix chain 'h' and resid 81 through 96 removed outlier: 3.775A pdb=" N LEU h 87 " --> pdb=" O ASP h 83 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N VAL h 90 " --> pdb=" O LYS h 86 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA h 92 " --> pdb=" O ARG h 88 " (cutoff:3.500A) Processing helix chain 'h' and resid 108 through 113 removed outlier: 4.165A pdb=" N ASP h 112 " --> pdb=" O LYS h 108 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N ALA h 113 " --> pdb=" O PRO h 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 108 through 113' Processing helix chain 'h' and resid 114 through 127 Processing helix chain 'h' and resid 129 through 145 removed outlier: 3.777A pdb=" N ARG h 136 " --> pdb=" O ARG h 132 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA h 137 " --> pdb=" O ALA h 133 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA h 141 " --> pdb=" O ALA h 137 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N MET h 142 " --> pdb=" O VAL h 138 " (cutoff:3.500A) Processing helix chain 'i' and resid 7 through 16 removed outlier: 3.769A pdb=" N LEU i 11 " --> pdb=" O PRO i 7 " (cutoff:3.500A) Processing helix chain 'i' and resid 27 through 32 Processing helix chain 'i' and resid 49 through 66 removed outlier: 4.059A pdb=" N VAL i 61 " --> pdb=" O GLU i 57 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG i 63 " --> pdb=" O GLN i 59 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE i 64 " --> pdb=" O LYS i 60 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N TYR i 65 " --> pdb=" O VAL i 61 " (cutoff:3.500A) Processing helix chain 'i' and resid 68 through 83 removed outlier: 3.586A pdb=" N ARG i 81 " --> pdb=" O LYS i 77 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N LYS i 83 " --> pdb=" O ALA i 79 " (cutoff:3.500A) Processing helix chain 'i' and resid 85 through 97 removed outlier: 3.652A pdb=" N LEU i 93 " --> pdb=" O ASN i 89 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ARG i 97 " --> pdb=" O LEU i 93 " (cutoff:3.500A) Processing helix chain 'i' and resid 98 through 106 removed outlier: 3.627A pdb=" N GLY i 106 " --> pdb=" O VAL i 102 " (cutoff:3.500A) Processing helix chain 'i' and resid 110 through 121 removed outlier: 3.528A pdb=" N GLN i 116 " --> pdb=" O ALA i 112 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU i 117 " --> pdb=" O GLU i 113 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N VAL i 118 " --> pdb=" O ALA i 114 " (cutoff:3.500A) Processing helix chain 'i' and resid 147 through 152 removed outlier: 4.152A pdb=" N LYS i 151 " --> pdb=" O GLU i 147 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N GLN i 152 " --> pdb=" O LYS i 148 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 147 through 152' Processing helix chain 'i' and resid 154 through 166 removed outlier: 4.987A pdb=" N ALA i 158 " --> pdb=" O ARG i 154 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N LEU i 159 " --> pdb=" O VAL i 155 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N GLU i 160 " --> pdb=" O LYS i 156 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LEU i 161 " --> pdb=" O ALA i 157 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLN i 164 " --> pdb=" O GLU i 160 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N GLU i 166 " --> pdb=" O ALA i 162 " (cutoff:3.500A) Processing helix chain 'i' and resid 187 through 192 removed outlier: 4.569A pdb=" N SER i 192 " --> pdb=" O ARG i 188 " (cutoff:3.500A) Processing helix chain 'i' and resid 196 through 206 removed outlier: 3.855A pdb=" N ILE i 200 " --> pdb=" O ASN i 196 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N LYS i 206 " --> pdb=" O GLU i 202 " (cutoff:3.500A) Processing helix chain 'j' and resid 55 through 71 removed outlier: 3.619A pdb=" N GLN j 61 " --> pdb=" O PRO j 57 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ASN j 70 " --> pdb=" O LYS j 66 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N MET j 71 " --> pdb=" O ALA j 67 " (cutoff:3.500A) Processing helix chain 'j' and resid 109 through 119 Processing helix chain 'j' and resid 132 through 148 removed outlier: 3.512A pdb=" N VAL j 137 " --> pdb=" O PRO j 133 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ASP j 142 " --> pdb=" O ARG j 138 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASN j 146 " --> pdb=" O ASP j 142 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N MET j 147 " --> pdb=" O GLY j 143 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N ASN j 148 " --> pdb=" O LEU j 144 " (cutoff:3.500A) Processing helix chain 'j' and resid 149 through 158 removed outlier: 3.517A pdb=" N VAL j 153 " --> pdb=" O SER j 149 " (cutoff:3.500A) Processing helix chain 'j' and resid 160 through 165 removed outlier: 4.062A pdb=" N ILE j 164 " --> pdb=" O SER j 160 " (cutoff:3.500A) Processing helix chain 'k' and resid 11 through 19 removed outlier: 3.652A pdb=" N SER k 15 " --> pdb=" O HIS k 11 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N GLU k 16 " --> pdb=" O PRO k 12 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N GLN k 17 " --> pdb=" O ASP k 13 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N VAL k 18 " --> pdb=" O GLN k 14 " (cutoff:3.500A) Proline residue: k 19 - end of helix No H-bonds generated for 'chain 'k' and resid 11 through 19' Processing helix chain 'k' and resid 20 through 33 removed outlier: 3.527A pdb=" N ARG k 24 " --> pdb=" O GLY k 20 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ALA k 32 " --> pdb=" O ALA k 28 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N GLU k 33 " --> pdb=" O ILE k 29 " (cutoff:3.500A) Processing helix chain 'k' and resid 67 through 81 removed outlier: 3.942A pdb=" N ILE k 71 " --> pdb=" O PRO k 67 " (cutoff:3.500A) Processing helix chain 'l' and resid 20 through 31 removed outlier: 3.542A pdb=" N ASN l 28 " --> pdb=" O ALA l 24 " (cutoff:3.500A) Processing helix chain 'l' and resid 35 through 55 removed outlier: 3.964A pdb=" N SER l 41 " --> pdb=" O SER l 37 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N THR l 49 " --> pdb=" O SER l 45 " (cutoff:3.500A) Processing helix chain 'l' and resid 57 through 70 removed outlier: 3.545A pdb=" N GLU l 63 " --> pdb=" O LEU l 59 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL l 64 " --> pdb=" O GLU l 60 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA l 65 " --> pdb=" O ALA l 61 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASN l 68 " --> pdb=" O VAL l 64 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL l 69 " --> pdb=" O ALA l 65 " (cutoff:3.500A) Processing helix chain 'l' and resid 92 through 111 removed outlier: 4.016A pdb=" N LYS l 110 " --> pdb=" O GLU l 106 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ARG l 111 " --> pdb=" O ALA l 107 " (cutoff:3.500A) Processing helix chain 'l' and resid 115 through 130 removed outlier: 3.621A pdb=" N GLU l 123 " --> pdb=" O ARG l 119 " (cutoff:3.500A) Processing helix chain 'l' and resid 132 through 149 removed outlier: 3.707A pdb=" N VAL l 141 " --> pdb=" O LYS l 137 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N HIS l 142 " --> pdb=" O ARG l 138 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLU l 146 " --> pdb=" O HIS l 142 " (cutoff:3.500A) Processing helix chain 'm' and resid 5 through 21 removed outlier: 3.822A pdb=" N ASP m 9 " --> pdb=" O ASP m 5 " (cutoff:3.500A) Processing helix chain 'm' and resid 30 through 44 removed outlier: 3.549A pdb=" N GLU m 42 " --> pdb=" O ASN m 38 " (cutoff:3.500A) Processing helix chain 'm' and resid 112 through 120 Processing helix chain 'n' and resid 34 through 39 removed outlier: 3.694A pdb=" N TYR n 38 " --> pdb=" O SER n 34 " (cutoff:3.500A) Processing helix chain 'n' and resid 41 through 52 removed outlier: 3.860A pdb=" N VAL n 48 " --> pdb=" O ALA n 44 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N ARG n 49 " --> pdb=" O ARG n 45 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLN n 50 " --> pdb=" O MET n 46 " (cutoff:3.500A) Proline residue: n 51 - end of helix Processing helix chain 'n' and resid 71 through 91 removed outlier: 3.630A pdb=" N ILE n 79 " --> pdb=" O GLN n 75 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ARG n 80 " --> pdb=" O ALA n 76 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLY n 82 " --> pdb=" O ALA n 78 " (cutoff:3.500A) Processing helix chain 'n' and resid 93 through 102 removed outlier: 4.694A pdb=" N GLU n 97 " --> pdb=" O SER n 93 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LYS n 100 " --> pdb=" O SER n 96 " (cutoff:3.500A) Processing helix chain 'o' and resid 14 through 31 removed outlier: 3.660A pdb=" N ALA o 29 " --> pdb=" O ILE o 25 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N ARG o 31 " --> pdb=" O GLU o 27 " (cutoff:3.500A) Processing helix chain 'o' and resid 80 through 91 removed outlier: 3.724A pdb=" N ASP o 85 " --> pdb=" O GLU o 81 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU o 87 " --> pdb=" O THR o 83 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N MET o 88 " --> pdb=" O VAL o 84 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N ASP o 91 " --> pdb=" O LEU o 87 " (cutoff:3.500A) Processing helix chain 'p' and resid 46 through 51 removed outlier: 4.111A pdb=" N GLY p 51 " --> pdb=" O ALA p 47 " (cutoff:3.500A) Processing helix chain 'p' and resid 54 through 59 removed outlier: 4.228A pdb=" N THR p 59 " --> pdb=" O SER p 55 " (cutoff:3.500A) Processing helix chain 'p' and resid 60 through 76 removed outlier: 3.670A pdb=" N GLU p 68 " --> pdb=" O GLN p 64 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASP p 72 " --> pdb=" O GLU p 68 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N GLU p 76 " --> pdb=" O ASP p 72 " (cutoff:3.500A) Processing helix chain 'p' and resid 92 through 104 removed outlier: 3.965A pdb=" N THR p 96 " --> pdb=" O GLY p 92 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N ILE p 97 " --> pdb=" O ARG p 93 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASN p 101 " --> pdb=" O ILE p 97 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLY p 104 " --> pdb=" O LEU p 100 " (cutoff:3.500A) Processing helix chain 'q' and resid 3 through 10 Processing helix chain 'q' and resid 113 through 118 removed outlier: 4.782A pdb=" N TYR q 117 " --> pdb=" O ALA q 113 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLY q 118 " --> pdb=" O ARG q 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'q' and resid 113 through 118' Processing helix chain 'r' and resid 14 through 22 removed outlier: 4.353A pdb=" N SER r 21 " --> pdb=" O ILE r 17 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N ILE r 22 " --> pdb=" O ALA r 18 " (cutoff:3.500A) Processing helix chain 'r' and resid 26 through 38 removed outlier: 3.601A pdb=" N LEU r 34 " --> pdb=" O SER r 30 " (cutoff:3.500A) Processing helix chain 'r' and resid 49 through 64 removed outlier: 3.769A pdb=" N LYS r 62 " --> pdb=" O ASP r 58 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N PHE r 63 " --> pdb=" O GLU r 59 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N VAL r 64 " --> pdb=" O VAL r 60 " (cutoff:3.500A) Processing helix chain 'r' and resid 66 through 84 removed outlier: 5.966A pdb=" N ARG r 70 " --> pdb=" O GLU r 66 " (cutoff:3.500A) Processing helix chain 'r' and resid 85 through 94 Processing helix chain 'r' and resid 106 through 111 Processing helix chain 's' and resid 3 through 21 removed outlier: 3.550A pdb=" N TYR s 20 " --> pdb=" O LEU s 16 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N PHE s 21 " --> pdb=" O ALA s 17 " (cutoff:3.500A) Processing helix chain 's' and resid 22 through 32 removed outlier: 3.808A pdb=" N ILE s 30 " --> pdb=" O GLU s 26 " (cutoff:3.500A) Processing helix chain 's' and resid 37 through 52 Proline residue: s 52 - end of helix Processing helix chain 's' and resid 80 through 91 Processing helix chain 't' and resid 4 through 16 removed outlier: 3.742A pdb=" N ILE t 11 " --> pdb=" O ALA t 7 " (cutoff:3.500A) Processing helix chain 't' and resid 24 through 47 removed outlier: 4.877A pdb=" N GLY t 41 " --> pdb=" O ASN t 37 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N HIS t 42 " --> pdb=" O HIS t 38 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N PHE t 43 " --> pdb=" O LEU t 39 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N LYS t 47 " --> pdb=" O PHE t 43 " (cutoff:3.500A) Processing helix chain 't' and resid 49 through 74 removed outlier: 4.203A pdb=" N GLY t 55 " --> pdb=" O HIS t 51 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU t 70 " --> pdb=" O LEU t 66 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ARG t 72 " --> pdb=" O ASP t 68 " (cutoff:3.500A) Processing helix chain 't' and resid 75 through 86 Processing helix chain 'u' and resid 53 through 64 Processing helix chain 'u' and resid 68 through 82 removed outlier: 3.512A pdb=" N LYS u 76 " --> pdb=" O ALA u 72 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ALA u 81 " --> pdb=" O GLU u 77 " (cutoff:3.500A) Processing helix chain 'w' and resid 11 through 17 removed outlier: 4.915A pdb=" N ALA w 15 " --> pdb=" O CYS w 11 " (cutoff:3.500A) Processing helix chain 'w' and resid 25 through 34 removed outlier: 4.243A pdb=" N ASN w 31 " --> pdb=" O ALA w 27 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N TYR w 32 " --> pdb=" O THR w 28 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE w 33 " --> pdb=" O LEU w 29 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N THR w 34 " --> pdb=" O LYS w 30 " (cutoff:3.500A) Processing helix chain 'w' and resid 41 through 46 removed outlier: 3.526A pdb=" N THR w 45 " --> pdb=" O PRO w 41 " (cutoff:3.500A) Processing helix chain 'w' and resid 48 through 66 removed outlier: 3.580A pdb=" N SER w 66 " --> pdb=" O ALA w 62 " (cutoff:3.500A) Processing helix chain 'x' and resid 12 through 25 removed outlier: 4.452A pdb=" N GLU x 24 " --> pdb=" O GLU x 20 " (cutoff:3.500A) Processing helix chain 'x' and resid 63 through 68 removed outlier: 3.614A pdb=" N VAL x 67 " --> pdb=" O THR x 63 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N GLY x 68 " --> pdb=" O ASP x 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'x' and resid 63 through 68' Processing helix chain 'x' and resid 70 through 76 removed outlier: 4.688A pdb=" N PHE x 74 " --> pdb=" O LYS x 70 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ALA x 75 " --> pdb=" O LEU x 71 " (cutoff:3.500A) Proline residue: x 76 - end of helix No H-bonds generated for 'chain 'x' and resid 70 through 76' Processing helix chain 'y' and resid 4 through 42 removed outlier: 3.520A pdb=" N LYS y 8 " --> pdb=" O ILE y 4 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LYS y 9 " --> pdb=" O LYS y 5 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N ARG y 10 " --> pdb=" O SER y 6 " (cutoff:3.500A) Processing helix chain 'y' and resid 43 through 65 Proline residue: y 56 - end of helix removed outlier: 3.528A pdb=" N GLN y 61 " --> pdb=" O ILE y 57 " (cutoff:3.500A) Processing helix chain 'y' and resid 68 through 87 removed outlier: 3.644A pdb=" N LEU y 79 " --> pdb=" O HIS y 75 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N LYS y 85 " --> pdb=" O ALA y 81 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ALA y 87 " --> pdb=" O ILE y 83 " (cutoff:3.500A) Processing helix chain 'z' and resid 11 through 27 Processing helix chain 'z' and resid 28 through 37 removed outlier: 3.879A pdb=" N ARG z 33 " --> pdb=" O LEU z 29 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N PHE z 37 " --> pdb=" O ARG z 33 " (cutoff:3.500A) Processing helix chain 'z' and resid 40 through 67 removed outlier: 3.772A pdb=" N ALA z 48 " --> pdb=" O GLU z 44 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ARG z 66 " --> pdb=" O ARG z 62 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N ARG z 67 " --> pdb=" O GLU z 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 110 removed outlier: 4.808A pdb=" N GLU A 108 " --> pdb=" O ASP A 104 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N ARG A 109 " --> pdb=" O PRO A 105 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N ASN A 110 " --> pdb=" O ASP A 106 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 104 through 110' Processing helix chain 'A' and resid 121 through 143 removed outlier: 3.611A pdb=" N PHE A 132 " --> pdb=" O ALA A 128 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARG A 133 " --> pdb=" O GLY A 129 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N MET A 134 " --> pdb=" O ASP A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 176 Processing helix chain 'A' and resid 210 through 215 Proline residue: A 215 - end of helix Processing helix chain 'A' and resid 218 through 223 removed outlier: 4.832A pdb=" N ARG A 223 " --> pdb=" O PRO A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 291 removed outlier: 3.749A pdb=" N ASN A 266 " --> pdb=" O SER A 262 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA A 268 " --> pdb=" O HIS A 264 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL A 273 " --> pdb=" O LYS A 269 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU A 274 " --> pdb=" O ALA A 270 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA A 284 " --> pdb=" O ALA A 280 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA A 289 " --> pdb=" O LYS A 285 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N ALA A 291 " --> pdb=" O GLN A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 298 removed outlier: 4.754A pdb=" N ASN A 296 " --> pdb=" O SER A 292 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N LEU A 297 " --> pdb=" O THR A 293 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N LEU A 298 " --> pdb=" O ARG A 294 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 292 through 298' Processing helix chain 'A' and resid 328 through 335 removed outlier: 3.528A pdb=" N GLU A 334 " --> pdb=" O ASP A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 356 removed outlier: 4.981A pdb=" N LEU A 340 " --> pdb=" O LYS A 336 " (cutoff:3.500A) Proline residue: A 343 - end of helix removed outlier: 3.781A pdb=" N ALA A 355 " --> pdb=" O ASP A 351 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU A 356 " --> pdb=" O GLN A 352 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'B' and resid 80 through 83 removed outlier: 6.837A pdb=" N LEU B 93 " --> pdb=" O GLU B 79 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N ILE B 74 " --> pdb=" O SER B 118 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N SER B 118 " --> pdb=" O ILE B 74 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ASP B 114 " --> pdb=" O VAL B 78 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'B' and resid 138 through 142 removed outlier: 4.628A pdb=" N SER B 139 " --> pdb=" O ILE B 164 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ILE B 164 " --> pdb=" O SER B 139 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN B 163 " --> pdb=" O ARG B 175 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N THR B 173 " --> pdb=" O VAL B 165 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLU B 180 " --> pdb=" O LEU B 176 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'B' and resid 91 through 96 removed outlier: 4.994A pdb=" N GLU B 100 " --> pdb=" O TYR B 96 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'C' and resid 11 through 16 removed outlier: 4.865A pdb=" N VAL C 20 " --> pdb=" O THR C 16 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N VAL C 26 " --> pdb=" O VAL C 9 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N SER C 199 " --> pdb=" O LYS C 8 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N LYS C 105 " --> pdb=" O VAL C 177 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'C' and resid 36 through 40 removed outlier: 4.361A pdb=" N LEU C 40 " --> pdb=" O TYR C 45 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N TYR C 45 " --> pdb=" O LEU C 40 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N GLN C 94 " --> pdb=" O VAL C 34 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'C' and resid 24 through 29 No H-bonds generated for sheet with id= 6 Processing sheet with id= 7, first strand: chain 'C' and resid 46 through 51 removed outlier: 5.703A pdb=" N ARG C 46 " --> pdb=" O LEU C 84 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'D' and resid 1 through 6 removed outlier: 4.294A pdb=" N SER D 10 " --> pdb=" O LEU D 5 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'D' and resid 117 through 120 removed outlier: 5.528A pdb=" N ARG D 117 " --> pdb=" O ASP D 184 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASP D 168 " --> pdb=" O VAL D 146 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'E' and resid 33 through 39 removed outlier: 3.769A pdb=" N VAL E 89 " --> pdb=" O LEU E 36 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N CYS E 87 " --> pdb=" O MET E 38 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLY E 86 " --> pdb=" O THR E 68 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'F' and resid 16 through 19 removed outlier: 3.597A pdb=" N ASP F 16 " --> pdb=" O LYS F 27 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'F' and resid 95 through 98 removed outlier: 3.730A pdb=" N ALA F 97 " --> pdb=" O ASN F 104 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'F' and resid 121 through 125 removed outlier: 6.178A pdb=" N THR F 129 " --> pdb=" O LEU F 89 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL F 90 " --> pdb=" O GLY F 161 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'G' and resid 1 through 5 removed outlier: 3.908A pdb=" N MET G 1 " --> pdb=" O VAL G 21 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU G 5 " --> pdb=" O ASP G 17 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N ASP G 17 " --> pdb=" O LEU G 5 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'G' and resid 76 through 83 removed outlier: 6.495A pdb=" N GLU G 76 " --> pdb=" O LYS G 141 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ILE G 143 " --> pdb=" O GLU G 76 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N VAL G 78 " --> pdb=" O ILE G 143 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA G 140 " --> pdb=" O PHE G 132 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N GLU G 114 " --> pdb=" O GLN G 133 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'J' and resid 52 through 57 removed outlier: 5.189A pdb=" N ASP J 19 " --> pdb=" O LEU J 140 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'J' and resid 74 through 78 removed outlier: 3.912A pdb=" N HIS J 76 " --> pdb=" O LYS J 85 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N GLY J 83 " --> pdb=" O THR J 78 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'K' and resid 18 through 21 removed outlier: 4.021A pdb=" N VAL K 19 " --> pdb=" O LEU K 8 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N THR K 6 " --> pdb=" O CYS K 21 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N ASN K 82 " --> pdb=" O MET K 7 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'K' and resid 68 through 71 removed outlier: 4.028A pdb=" N SER K 75 " --> pdb=" O ARG K 71 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'M' and resid 62 through 66 removed outlier: 6.895A pdb=" N LEU M 102 " --> pdb=" O ARG M 66 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N LYS M 127 " --> pdb=" O VAL M 36 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'N' and resid 33 through 37 removed outlier: 5.178A pdb=" N ARG N 103 " --> pdb=" O ASN N 107 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N GLY N 101 " --> pdb=" O PRO N 109 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ALA N 111 " --> pdb=" O LYS N 99 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N LYS N 99 " --> pdb=" O ALA N 111 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ILE N 113 " --> pdb=" O ILE N 97 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N ILE N 97 " --> pdb=" O ILE N 113 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N LEU N 115 " --> pdb=" O THR N 95 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N THR N 95 " --> pdb=" O LEU N 115 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'O' and resid 49 through 52 removed outlier: 3.742A pdb=" N VAL O 49 " --> pdb=" O VAL O 39 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ARG O 25 " --> pdb=" O ILE O 40 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL O 28 " --> pdb=" O ASP O 93 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'P' and resid 38 through 45 removed outlier: 6.606A pdb=" N THR P 25 " --> pdb=" O LYS P 87 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'P' and resid 49 through 53 removed outlier: 3.803A pdb=" N ALA P 49 " --> pdb=" O THR P 60 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N ARG P 53 " --> pdb=" O HIS P 56 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N HIS P 56 " --> pdb=" O ARG P 53 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N SER P 57 " --> pdb=" O THR P 76 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'R' and resid 11 through 15 removed outlier: 3.736A pdb=" N ASN R 43 " --> pdb=" O GLU R 46 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLU R 46 " --> pdb=" O ASN R 43 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'R' and resid 18 through 23 removed outlier: 4.450A pdb=" N GLN R 18 " --> pdb=" O ILE R 98 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ASP R 95 " --> pdb=" O VAL R 64 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N LYS R 60 " --> pdb=" O THR R 99 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N GLU R 31 " --> pdb=" O VAL R 63 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'R' and resid 57 through 60 removed outlier: 3.535A pdb=" N VAL R 58 " --> pdb=" O SER R 102 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'R' and resid 65 through 68 Processing sheet with id= 29, first strand: chain 'R' and resid 69 through 78 removed outlier: 5.371A pdb=" N GLU R 70 " --> pdb=" O GLN R 91 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N GLN R 91 " --> pdb=" O GLU R 70 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N TYR R 83 " --> pdb=" O ARG R 78 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'S' and resid 2 through 8 Processing sheet with id= 31, first strand: chain 'T' and resid 12 through 15 removed outlier: 5.178A pdb=" N VAL T 31 " --> pdb=" O HIS T 15 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ASN T 28 " --> pdb=" O LEU T 87 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LYS T 81 " --> pdb=" O VAL T 34 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N LYS T 66 " --> pdb=" O ARG T 77 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ASP T 79 " --> pdb=" O LYS T 64 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N LYS T 64 " --> pdb=" O ASP T 79 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N LYS T 81 " --> pdb=" O VAL T 62 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N VAL T 62 " --> pdb=" O LYS T 81 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ALA T 83 " --> pdb=" O THR T 60 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N THR T 60 " --> pdb=" O ALA T 83 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N VAL T 85 " --> pdb=" O VAL T 58 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N VAL T 58 " --> pdb=" O VAL T 85 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'U' and resid 40 through 45 No H-bonds generated for sheet with id= 32 Processing sheet with id= 33, first strand: chain 'U' and resid 83 through 87 Processing sheet with id= 34, first strand: chain 'V' and resid 6 through 9 removed outlier: 6.491A pdb=" N ALA V 39 " --> pdb=" O ARG V 9 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE V 89 " --> pdb=" O PRO V 27 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'V' and resid 61 through 64 Processing sheet with id= 36, first strand: chain 'W' and resid 51 through 54 removed outlier: 4.939A pdb=" N THR W 58 " --> pdb=" O GLY W 54 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'W' and resid 67 through 71 Processing sheet with id= 38, first strand: chain 'X' and resid 12 through 19 removed outlier: 4.447A pdb=" N ASN X 23 " --> pdb=" O SER X 19 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'Z' and resid 34 through 39 removed outlier: 4.681A pdb=" N HIS Z 34 " --> pdb=" O GLN Z 9 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N MET Z 54 " --> pdb=" O THR Z 10 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'b' and resid 29 through 32 removed outlier: 4.422A pdb=" N GLU b 36 " --> pdb=" O ASP b 31 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'c' and resid 7 through 13 No H-bonds generated for sheet with id= 41 Processing sheet with id= 42, first strand: chain 'c' and resid 34 through 39 removed outlier: 6.214A pdb=" N LEU c 34 " --> pdb=" O GLU c 51 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU c 36 " --> pdb=" O TYR c 49 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'e' and resid 22 through 25 removed outlier: 6.135A pdb=" N PHE e 22 " --> pdb=" O VAL e 50 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'f' and resid 1 through 5 removed outlier: 5.310A pdb=" N HIS f 33 " --> pdb=" O CYS f 27 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N CYS f 27 " --> pdb=" O HIS f 33 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N ILE f 23 " --> pdb=" O GLN f 37 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'g' and resid 15 through 18 removed outlier: 4.938A pdb=" N HIS g 15 " --> pdb=" O ILE g 41 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N HIS g 39 " --> pdb=" O GLY g 17 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'g' and resid 90 through 93 removed outlier: 3.699A pdb=" N ALA g 185 " --> pdb=" O PHE g 198 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'h' and resid 53 through 59 Processing sheet with id= 48, first strand: chain 'h' and resid 164 through 170 removed outlier: 5.476A pdb=" N ARG h 164 " --> pdb=" O GLY h 155 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ASP h 181 " --> pdb=" O LYS h 204 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'i' and resid 140 through 143 removed outlier: 3.943A pdb=" N ASP i 141 " --> pdb=" O PHE i 182 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLU i 179 " --> pdb=" O ASP i 174 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N TRP i 170 " --> pdb=" O LYS i 183 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'j' and resid 11 through 16 removed outlier: 6.755A pdb=" N LEU j 36 " --> pdb=" O ILE j 16 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'j' and resid 84 through 88 removed outlier: 5.891A pdb=" N ASN j 122 " --> pdb=" O ALA j 99 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'j' and resid 33 through 41 removed outlier: 7.252A pdb=" N ARG j 45 " --> pdb=" O ASP j 41 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'k' and resid 38 through 43 removed outlier: 3.897A pdb=" N ARG k 38 " --> pdb=" O ASN k 63 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N TYR k 59 " --> pdb=" O TRP k 42 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N HIS k 3 " --> pdb=" O THR k 92 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL k 7 " --> pdb=" O MET k 88 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'k' and resid 44 through 47 removed outlier: 7.137A pdb=" N HIS k 55 " --> pdb=" O LEU k 47 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'l' and resid 73 through 79 removed outlier: 5.778A pdb=" N TYR l 85 " --> pdb=" O ARG l 78 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'm' and resid 23 through 27 removed outlier: 7.523A pdb=" N ALA m 23 " --> pdb=" O LEU m 63 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASP m 48 " --> pdb=" O THR m 62 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'm' and resid 74 through 77 removed outlier: 4.213A pdb=" N TYR m 128 " --> pdb=" O GLN m 76 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N CYS m 127 " --> pdb=" O VAL m 103 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N VAL m 103 " --> pdb=" O ILE m 126 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'n' and resid 5 through 11 removed outlier: 3.568A pdb=" N GLY n 10 " --> pdb=" O ALA n 17 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LYS n 22 " --> pdb=" O ASP n 62 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'o' and resid 39 through 42 removed outlier: 5.227A pdb=" N LEU o 71 " --> pdb=" O LEU o 42 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N ARG o 5 " --> pdb=" O GLY o 103 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'o' and resid 44 through 50 Processing sheet with id= 61, first strand: chain 'p' and resid 42 through 45 removed outlier: 4.145A pdb=" N ASN p 29 " --> pdb=" O SER p 26 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N PHE p 27 " --> pdb=" O PRO p 89 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ASN p 109 " --> pdb=" O LEU p 82 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N GLY p 88 " --> pdb=" O VAL p 113 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'q' and resid 29 through 33 removed outlier: 3.593A pdb=" N LYS q 30 " --> pdb=" O ILE q 82 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N LEU q 81 " --> pdb=" O VAL q 98 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N HIS q 96 " --> pdb=" O ARG q 83 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N ARG q 94 " --> pdb=" O GLY q 85 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'q' and resid 36 through 41 removed outlier: 4.984A pdb=" N LYS q 51 " --> pdb=" O ILE q 67 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'u' and resid 4 through 10 removed outlier: 3.875A pdb=" N PHE u 16 " --> pdb=" O HIS u 9 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'v' and resid 7 through 11 removed outlier: 7.085A pdb=" N GLU v 60 " --> pdb=" O VAL v 76 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'v' and resid 20 through 30 Processing sheet with id= 67, first strand: chain 'x' and resid 30 through 34 removed outlier: 3.513A pdb=" N LEU x 31 " --> pdb=" O THR x 48 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU x 47 " --> pdb=" O VAL x 62 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'A' and resid 144 through 149 removed outlier: 6.515A pdb=" N ILE A 163 " --> pdb=" O MET A 149 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ARG A 116 " --> pdb=" O THR A 202 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N THR A 202 " --> pdb=" O ARG A 116 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG A 308 " --> pdb=" O GLY A 181 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N ASN A 307 " --> pdb=" O HIS A 320 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU A 324 " --> pdb=" O ASP A 319 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'A' and resid 224 through 227 1823 hydrogen bonds defined for protein. 5388 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3158 hydrogen bonds 4510 hydrogen bond angles 0 basepair planarities 1321 basepair parallelities 2510 stacking parallelities Total time for adding SS restraints: 254.11 Time building geometry restraints manager: 78.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 11930 1.28 - 1.42: 64021 1.42 - 1.55: 72764 1.55 - 1.68: 9333 1.68 - 1.81: 272 Bond restraints: 158320 Sorted by residual: bond pdb=" C5 5MU 5 54 " pdb=" C6 5MU 5 54 " ideal model delta sigma weight residual 1.155 1.431 -0.276 2.00e-02 2.50e+03 1.90e+02 bond pdb=" C5 5MU 11939 " pdb=" C6 5MU 11939 " ideal model delta sigma weight residual 1.155 1.430 -0.275 2.00e-02 2.50e+03 1.89e+02 bond pdb=" C5 5MU 1 747 " pdb=" C6 5MU 1 747 " ideal model delta sigma weight residual 1.155 1.421 -0.266 2.00e-02 2.50e+03 1.77e+02 bond pdb=" C4 5MU 1 747 " pdb=" C5 5MU 1 747 " ideal model delta sigma weight residual 1.802 1.586 0.216 2.00e-02 2.50e+03 1.17e+02 bond pdb=" C4 5MU 11939 " pdb=" C5 5MU 11939 " ideal model delta sigma weight residual 1.802 1.597 0.205 2.00e-02 2.50e+03 1.05e+02 ... (remaining 158315 not shown) Histogram of bond angle deviations from ideal: 96.64 - 105.53: 23771 105.53 - 114.43: 105843 114.43 - 123.32: 83055 123.32 - 132.21: 23301 132.21 - 141.11: 764 Bond angle restraints: 236734 Sorted by residual: angle pdb=" C1' G7M 12069 " pdb=" N9 G7M 12069 " pdb=" C8 G7M 12069 " ideal model delta sigma weight residual 94.96 135.87 -40.91 3.00e+00 1.11e-01 1.86e+02 angle pdb=" C1' G7M 12069 " pdb=" N9 G7M 12069 " pdb=" C4 G7M 12069 " ideal model delta sigma weight residual 142.80 116.28 26.52 3.00e+00 1.11e-01 7.81e+01 angle pdb=" C1' 2MG 21207 " pdb=" N9 2MG 21207 " pdb=" C8 2MG 21207 " ideal model delta sigma weight residual 110.07 135.74 -25.67 3.00e+00 1.11e-01 7.32e+01 angle pdb=" C1' 2MG 21516 " pdb=" N9 2MG 21516 " pdb=" C8 2MG 21516 " ideal model delta sigma weight residual 110.07 134.10 -24.03 3.00e+00 1.11e-01 6.42e+01 angle pdb=" C4' A 12425 " pdb=" C3' A 12425 " pdb=" O3' A 12425 " ideal model delta sigma weight residual 109.40 120.97 -11.57 1.50e+00 4.44e-01 5.95e+01 ... (remaining 236729 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.92: 88360 35.92 - 71.85: 11494 71.85 - 107.77: 1363 107.77 - 143.70: 16 143.70 - 179.62: 36 Dihedral angle restraints: 101269 sinusoidal: 84493 harmonic: 16776 Sorted by residual: dihedral pdb=" O4' U 4 19 " pdb=" C1' U 4 19 " pdb=" N1 U 4 19 " pdb=" C2 U 4 19 " ideal model delta sinusoidal sigma weight residual -160.00 10.60 -170.60 1 1.50e+01 4.44e-03 8.48e+01 dihedral pdb=" O4' U 1 102 " pdb=" C1' U 1 102 " pdb=" N1 U 1 102 " pdb=" C2 U 1 102 " ideal model delta sinusoidal sigma weight residual 200.00 33.97 166.03 1 1.50e+01 4.44e-03 8.41e+01 dihedral pdb=" O4' U 1 139 " pdb=" C1' U 1 139 " pdb=" N1 U 1 139 " pdb=" C2 U 1 139 " ideal model delta sinusoidal sigma weight residual 200.00 36.19 163.81 1 1.50e+01 4.44e-03 8.36e+01 ... (remaining 101266 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.118: 29375 0.118 - 0.235: 727 0.235 - 0.353: 22 0.353 - 0.470: 2 0.470 - 0.588: 1 Chirality restraints: 30127 Sorted by residual: chirality pdb=" C3' U 1 894 " pdb=" C4' U 1 894 " pdb=" O3' U 1 894 " pdb=" C2' U 1 894 " both_signs ideal model delta sigma weight residual False -2.74 -2.16 -0.59 2.00e-01 2.50e+01 8.63e+00 chirality pdb=" C3' A 12425 " pdb=" C4' A 12425 " pdb=" O3' A 12425 " pdb=" C2' A 12425 " both_signs ideal model delta sigma weight residual False -2.74 -2.32 -0.43 2.00e-01 2.50e+01 4.52e+00 chirality pdb=" C3' G 12193 " pdb=" C4' G 12193 " pdb=" O3' G 12193 " pdb=" C2' G 12193 " both_signs ideal model delta sigma weight residual False -2.48 -2.11 -0.37 2.00e-01 2.50e+01 3.42e+00 ... (remaining 30124 not shown) Planarity restraints: 12767 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 7MG 2 527 " 0.032 2.00e-02 2.50e+03 6.07e-01 8.29e+03 pdb=" C4' 7MG 2 527 " 0.465 2.00e-02 2.50e+03 pdb=" O4' 7MG 2 527 " 0.789 2.00e-02 2.50e+03 pdb=" C3' 7MG 2 527 " -0.586 2.00e-02 2.50e+03 pdb=" O3' 7MG 2 527 " -0.576 2.00e-02 2.50e+03 pdb=" C2' 7MG 2 527 " -0.237 2.00e-02 2.50e+03 pdb=" O2' 7MG 2 527 " 0.884 2.00e-02 2.50e+03 pdb=" C1' 7MG 2 527 " 0.191 2.00e-02 2.50e+03 pdb=" N9 7MG 2 527 " -0.962 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG 21516 " -0.048 2.00e-02 2.50e+03 6.05e-01 8.24e+03 pdb=" C4' 2MG 21516 " -0.451 2.00e-02 2.50e+03 pdb=" O4' 2MG 21516 " -0.684 2.00e-02 2.50e+03 pdb=" C3' 2MG 21516 " 0.598 2.00e-02 2.50e+03 pdb=" O3' 2MG 21516 " 0.629 2.00e-02 2.50e+03 pdb=" C2' 2MG 21516 " 0.192 2.00e-02 2.50e+03 pdb=" O2' 2MG 21516 " -0.955 2.00e-02 2.50e+03 pdb=" C1' 2MG 21516 " -0.216 2.00e-02 2.50e+03 pdb=" N9 2MG 21516 " 0.935 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 5MC 21407 " -0.071 2.00e-02 2.50e+03 6.01e-01 8.14e+03 pdb=" C4' 5MC 21407 " -0.441 2.00e-02 2.50e+03 pdb=" O4' 5MC 21407 " -0.589 2.00e-02 2.50e+03 pdb=" C3' 5MC 21407 " 0.595 2.00e-02 2.50e+03 pdb=" O3' 5MC 21407 " 0.670 2.00e-02 2.50e+03 pdb=" C2' 5MC 21407 " 0.159 2.00e-02 2.50e+03 pdb=" O2' 5MC 21407 " -1.001 2.00e-02 2.50e+03 pdb=" C1' 5MC 21407 " -0.230 2.00e-02 2.50e+03 pdb=" N1 5MC 21407 " 0.908 2.00e-02 2.50e+03 ... (remaining 12764 not shown) Histogram of nonbonded interaction distances: 1.47 - 2.16: 366 2.16 - 2.84: 47881 2.84 - 3.53: 240308 3.53 - 4.21: 487713 4.21 - 4.90: 637838 Nonbonded interactions: 1414106 Sorted by model distance: nonbonded pdb=" O3' A 5 76 " pdb=" C PHE H 79 " model vdw 1.473 3.270 nonbonded pdb=" OP2 G 11776 " pdb="MG MG 13041 " model vdw 1.850 2.170 nonbonded pdb=" O2' C 1 893 " pdb=" O4' U 1 894 " model vdw 1.894 2.440 nonbonded pdb=" O2' A 1 404 " pdb=" OP1 U 1 405 " model vdw 1.941 2.440 nonbonded pdb=" OP2 A 1 783 " pdb="MG MG 13017 " model vdw 1.977 2.170 ... (remaining 1414101 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.100 Extract box with map and model: 9.590 Check model and map are aligned: 1.550 Set scattering table: 0.980 Process input model: 589.530 Find NCS groups from input model: 2.820 Set up NCS constraints: 0.360 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 608.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 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 0.276 158320 Z= 0.528 Angle : 0.882 40.906 236734 Z= 0.450 Chirality : 0.048 0.588 30127 Planarity : 0.020 0.607 12767 Dihedral : 23.652 179.619 90447 Min Nonbonded Distance : 1.473 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.00 % Favored : 93.88 % Rotamer: Outliers : 0.33 % Allowed : 3.03 % Favored : 96.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.76 (0.09), residues: 5784 helix: -3.08 (0.08), residues: 1854 sheet: -2.16 (0.14), residues: 1098 loop : -2.11 (0.10), residues: 2832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.004 TRP D 78 HIS 0.029 0.003 HIS M 13 PHE 0.028 0.003 PHE E 77 TYR 0.022 0.003 TYR m 65 ARG 0.016 0.001 ARG x 36 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11568 Ramachandran restraints generated. 5784 Oldfield, 0 Emsley, 5784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11568 Ramachandran restraints generated. 5784 Oldfield, 0 Emsley, 5784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1868 residues out of total 4812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 1852 time to evaluate : 6.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 114 ASP cc_start: 0.8408 (m-30) cc_final: 0.8119 (m-30) REVERT: B 161 TYR cc_start: 0.9205 (p90) cc_final: 0.8950 (p90) REVERT: B 187 ASP cc_start: 0.9139 (m-30) cc_final: 0.8594 (m-30) REVERT: B 216 VAL cc_start: 0.9631 (t) cc_final: 0.9431 (p) REVERT: B 229 ASP cc_start: 0.8727 (m-30) cc_final: 0.8524 (m-30) REVERT: B 251 GLN cc_start: 0.8833 (tp40) cc_final: 0.8509 (tm-30) REVERT: B 255 LYS cc_start: 0.9375 (tttm) cc_final: 0.8964 (tptm) REVERT: B 267 ILE cc_start: 0.9577 (mm) cc_final: 0.9372 (mm) REVERT: C 4 LEU cc_start: 0.9270 (mp) cc_final: 0.9011 (mt) REVERT: C 88 GLU cc_start: 0.7643 (tt0) cc_final: 0.5943 (tt0) REVERT: C 136 ASN cc_start: 0.8781 (t160) cc_final: 0.8417 (t0) REVERT: C 137 SER cc_start: 0.9522 (m) cc_final: 0.8966 (p) REVERT: C 149 ASN cc_start: 0.8797 (t0) cc_final: 0.8374 (t0) REVERT: C 164 GLN cc_start: 0.8802 (tp40) cc_final: 0.8520 (tp40) REVERT: C 186 LEU cc_start: 0.9562 (mt) cc_final: 0.9166 (mp) REVERT: D 51 GLU cc_start: 0.8118 (mt-10) cc_final: 0.7737 (mt-10) REVERT: D 62 GLN cc_start: 0.9168 (tp40) cc_final: 0.8560 (tp40) REVERT: D 111 GLU cc_start: 0.9225 (tp30) cc_final: 0.8872 (tp30) REVERT: D 191 ASP cc_start: 0.9052 (t70) cc_final: 0.8675 (t0) REVERT: D 194 LYS cc_start: 0.9532 (tppt) cc_final: 0.9275 (mmmt) REVERT: D 195 GLN cc_start: 0.9278 (mt0) cc_final: 0.8530 (mp10) REVERT: E 90 THR cc_start: 0.9615 (m) cc_final: 0.9381 (p) REVERT: E 96 MET cc_start: 0.9549 (ttp) cc_final: 0.9114 (ttp) REVERT: E 100 PHE cc_start: 0.9311 (t80) cc_final: 0.9096 (t80) REVERT: E 101 GLU cc_start: 0.9363 (tt0) cc_final: 0.9076 (tm-30) REVERT: E 105 THR cc_start: 0.9768 (m) cc_final: 0.9564 (p) REVERT: E 127 ASN cc_start: 0.8521 (m-40) cc_final: 0.8177 (m-40) REVERT: E 143 TYR cc_start: 0.8902 (t80) cc_final: 0.8667 (t80) REVERT: E 157 THR cc_start: 0.8646 (m) cc_final: 0.8001 (m) REVERT: F 26 ILE cc_start: 0.9346 (mt) cc_final: 0.8840 (mm) REVERT: F 60 ASP cc_start: 0.8989 (p0) cc_final: 0.8704 (p0) REVERT: F 88 GLN cc_start: 0.9159 (pt0) cc_final: 0.8924 (pm20) REVERT: F 101 ASN cc_start: 0.9292 (p0) cc_final: 0.8500 (p0) REVERT: F 116 GLN cc_start: 0.8744 (tp40) cc_final: 0.8278 (tp-100) REVERT: F 147 ASP cc_start: 0.9295 (m-30) cc_final: 0.9021 (m-30) REVERT: J 14 ASP cc_start: 0.8544 (m-30) cc_final: 0.8004 (m-30) REVERT: J 31 GLU cc_start: 0.8929 (tp30) cc_final: 0.8364 (tp30) REVERT: J 36 LEU cc_start: 0.9753 (mt) cc_final: 0.9510 (mm) REVERT: J 49 ASP cc_start: 0.8414 (t70) cc_final: 0.8027 (t70) REVERT: J 75 TYR cc_start: 0.9290 (m-80) cc_final: 0.8714 (m-10) REVERT: J 81 ILE cc_start: 0.9436 (tp) cc_final: 0.9214 (tp) REVERT: J 103 ILE cc_start: 0.9541 (mt) cc_final: 0.9340 (tp) REVERT: J 114 LEU cc_start: 0.9454 (tp) cc_final: 0.9008 (tt) REVERT: J 118 MET cc_start: 0.8949 (mtt) cc_final: 0.8470 (mtt) REVERT: J 136 GLN cc_start: 0.9313 (mt0) cc_final: 0.8928 (mp10) REVERT: J 141 ASP cc_start: 0.8750 (t0) cc_final: 0.8498 (t0) REVERT: K 3 GLN cc_start: 0.8771 (pt0) cc_final: 0.8455 (pt0) REVERT: K 7 MET cc_start: 0.8941 (mmt) cc_final: 0.8543 (mmt) REVERT: K 21 CYS cc_start: 0.9288 (t) cc_final: 0.8793 (t) REVERT: K 23 LYS cc_start: 0.9318 (tppt) cc_final: 0.8600 (tptp) REVERT: K 25 LEU cc_start: 0.9595 (mt) cc_final: 0.9371 (mp) REVERT: K 37 ASP cc_start: 0.8404 (m-30) cc_final: 0.8138 (m-30) REVERT: K 44 LYS cc_start: 0.9480 (mmtt) cc_final: 0.9122 (mmtp) REVERT: K 70 ARG cc_start: 0.9272 (mtp85) cc_final: 0.9046 (mtp180) REVERT: K 87 LEU cc_start: 0.9542 (mt) cc_final: 0.9036 (mp) REVERT: K 89 ASN cc_start: 0.9189 (m-40) cc_final: 0.8775 (m-40) REVERT: L 1 MET cc_start: 0.8298 (ttp) cc_final: 0.8039 (ttp) REVERT: L 58 TYR cc_start: 0.8387 (p90) cc_final: 0.8069 (p90) REVERT: L 105 ILE cc_start: 0.9574 (mm) cc_final: 0.9243 (mm) REVERT: L 122 VAL cc_start: 0.9575 (t) cc_final: 0.9103 (p) REVERT: M 3 GLN cc_start: 0.9179 (tt0) cc_final: 0.8758 (tt0) REVERT: M 17 ASN cc_start: 0.8813 (t0) cc_final: 0.8528 (t0) REVERT: M 88 ASN cc_start: 0.9170 (m-40) cc_final: 0.8277 (m-40) REVERT: N 6 SER cc_start: 0.9320 (t) cc_final: 0.9118 (p) REVERT: N 9 GLN cc_start: 0.8692 (tt0) cc_final: 0.8228 (tt0) REVERT: N 40 LYS cc_start: 0.9487 (mttt) cc_final: 0.9220 (mttp) REVERT: N 49 GLU cc_start: 0.8022 (mt-10) cc_final: 0.7707 (mt-10) REVERT: N 54 LEU cc_start: 0.9727 (tp) cc_final: 0.9478 (tp) REVERT: N 57 THR cc_start: 0.9166 (m) cc_final: 0.8917 (p) REVERT: N 72 ASP cc_start: 0.8693 (t0) cc_final: 0.8288 (t0) REVERT: N 78 LYS cc_start: 0.9515 (tttt) cc_final: 0.8709 (tttt) REVERT: O 17 LYS cc_start: 0.9612 (tptp) cc_final: 0.9211 (tptt) REVERT: O 19 GLN cc_start: 0.9458 (tm130) cc_final: 0.9073 (tm-30) REVERT: O 69 ASP cc_start: 0.9523 (m-30) cc_final: 0.9213 (p0) REVERT: P 9 GLU cc_start: 0.8857 (mt-10) cc_final: 0.8623 (mt-10) REVERT: P 25 THR cc_start: 0.9223 (m) cc_final: 0.8858 (p) REVERT: P 27 GLU cc_start: 0.9086 (tm-30) cc_final: 0.8729 (tm-30) REVERT: P 29 LYS cc_start: 0.9711 (mttm) cc_final: 0.9385 (mmmm) REVERT: P 40 LEU cc_start: 0.9520 (tp) cc_final: 0.9004 (tp) REVERT: P 41 GLN cc_start: 0.9281 (tt0) cc_final: 0.9070 (tt0) REVERT: P 63 LYS cc_start: 0.8833 (ptmt) cc_final: 0.8239 (ptpp) REVERT: P 87 LYS cc_start: 0.9497 (mmtm) cc_final: 0.8987 (mmmm) REVERT: Q 31 VAL cc_start: 0.9426 (t) cc_final: 0.9171 (p) REVERT: Q 32 TYR cc_start: 0.8801 (t80) cc_final: 0.8303 (t80) REVERT: Q 45 TYR cc_start: 0.8580 (m-10) cc_final: 0.8079 (m-10) REVERT: Q 49 ASP cc_start: 0.7076 (m-30) cc_final: 0.5589 (m-30) REVERT: Q 59 GLN cc_start: 0.9056 (tt0) cc_final: 0.8840 (tt0) REVERT: Q 97 ASP cc_start: 0.8948 (t70) cc_final: 0.8383 (t0) REVERT: Q 101 PHE cc_start: 0.8281 (m-80) cc_final: 0.8021 (m-10) REVERT: R 2 TYR cc_start: 0.9021 (p90) cc_final: 0.8511 (p90) REVERT: R 13 ARG cc_start: 0.9007 (tmm-80) cc_final: 0.8348 (ttt-90) REVERT: R 41 ILE cc_start: 0.9284 (mt) cc_final: 0.8925 (mm) REVERT: R 48 LYS cc_start: 0.9113 (mttp) cc_final: 0.8816 (mmtp) REVERT: R 85 LYS cc_start: 0.9130 (mttt) cc_final: 0.8483 (mtpm) REVERT: R 86 GLN cc_start: 0.8831 (mm110) cc_final: 0.8207 (mm-40) REVERT: R 87 GLN cc_start: 0.8155 (tt0) cc_final: 0.7798 (tt0) REVERT: R 95 ASP cc_start: 0.8731 (m-30) cc_final: 0.8393 (m-30) REVERT: R 98 ILE cc_start: 0.9672 (mm) cc_final: 0.9020 (mm) REVERT: R 101 ILE cc_start: 0.9204 (mt) cc_final: 0.7848 (mt) REVERT: S 65 ASP cc_start: 0.8342 (t0) cc_final: 0.7858 (t70) REVERT: S 68 ASP cc_start: 0.9121 (m-30) cc_final: 0.8578 (m-30) REVERT: S 85 ILE cc_start: 0.9481 (mt) cc_final: 0.9246 (mm) REVERT: S 99 ARG cc_start: 0.9372 (mmt90) cc_final: 0.9137 (mpt180) REVERT: T 1 MET cc_start: 0.8350 (tpt) cc_final: 0.6922 (tpp) REVERT: T 7 LEU cc_start: 0.9687 (mt) cc_final: 0.9429 (mt) REVERT: T 11 LEU cc_start: 0.9449 (mt) cc_final: 0.9054 (mt) REVERT: T 12 ARG cc_start: 0.8851 (mmp-170) cc_final: 0.7730 (mmp80) REVERT: T 42 GLU cc_start: 0.8483 (mt-10) cc_final: 0.8209 (mm-30) REVERT: U 4 LYS cc_start: 0.8633 (mttt) cc_final: 0.8144 (mttt) REVERT: V 4 ILE cc_start: 0.9413 (mt) cc_final: 0.9123 (mp) REVERT: V 40 ILE cc_start: 0.9650 (pt) cc_final: 0.8889 (mm) REVERT: V 41 GLU cc_start: 0.8799 (pp20) cc_final: 0.8511 (pm20) REVERT: V 42 LEU cc_start: 0.9515 (mt) cc_final: 0.9148 (mt) REVERT: V 65 VAL cc_start: 0.9256 (p) cc_final: 0.9043 (p) REVERT: W 36 ILE cc_start: 0.9386 (mt) cc_final: 0.8957 (mp) REVERT: W 38 VAL cc_start: 0.9679 (t) cc_final: 0.9289 (p) REVERT: W 44 LYS cc_start: 0.9604 (ttmt) cc_final: 0.9248 (ttmm) REVERT: W 68 LYS cc_start: 0.9159 (tptp) cc_final: 0.8760 (tptp) REVERT: W 78 LYS cc_start: 0.9120 (mttp) cc_final: 0.8915 (mttt) REVERT: X 6 GLN cc_start: 0.9090 (mt0) cc_final: 0.8833 (mt0) REVERT: X 16 ASN cc_start: 0.9331 (m-40) cc_final: 0.9026 (t0) REVERT: X 17 ASN cc_start: 0.9009 (m-40) cc_final: 0.8534 (m-40) REVERT: X 54 LYS cc_start: 0.9537 (tppp) cc_final: 0.9277 (tptt) REVERT: X 56 MET cc_start: 0.9099 (mtp) cc_final: 0.8372 (mtp) REVERT: X 59 ILE cc_start: 0.9639 (mt) cc_final: 0.9390 (tt) REVERT: X 64 ILE cc_start: 0.9547 (tp) cc_final: 0.9250 (tp) REVERT: Y 25 GLN cc_start: 0.9521 (tt0) cc_final: 0.9279 (tm-30) REVERT: Y 27 ASN cc_start: 0.8973 (m-40) cc_final: 0.8617 (m110) REVERT: Y 44 LYS cc_start: 0.9549 (tttt) cc_final: 0.9285 (ttmm) REVERT: Z 21 LYS cc_start: 0.9431 (mttt) cc_final: 0.9145 (mttp) REVERT: Z 49 ASN cc_start: 0.9506 (t0) cc_final: 0.9213 (t0) REVERT: b 46 ASP cc_start: 0.8547 (m-30) cc_final: 0.8277 (m-30) REVERT: d 2 LYS cc_start: 0.9101 (tttt) cc_final: 0.8683 (tttm) REVERT: d 8 SER cc_start: 0.9149 (t) cc_final: 0.8867 (p) REVERT: d 12 ARG cc_start: 0.8836 (tpt-90) cc_final: 0.8622 (tpt-90) REVERT: d 45 SER cc_start: 0.8225 (m) cc_final: 0.7910 (p) REVERT: e 32 ILE cc_start: 0.8780 (mm) cc_final: 0.8377 (mm) REVERT: f 8 LYS cc_start: 0.8987 (mttt) cc_final: 0.8774 (mmmt) REVERT: f 9 LYS cc_start: 0.9231 (mttt) cc_final: 0.8906 (mttm) REVERT: f 18 LYS cc_start: 0.9425 (tttt) cc_final: 0.9093 (mtmm) REVERT: f 36 ARG cc_start: 0.9121 (ttt-90) cc_final: 0.8753 (tmm-80) REVERT: g 27 MET cc_start: 0.9041 (mmm) cc_final: 0.8209 (mmm) REVERT: g 49 MET cc_start: 0.9622 (mtp) cc_final: 0.9411 (mtp) REVERT: g 100 MET cc_start: 0.8828 (ttm) cc_final: 0.8283 (ttm) REVERT: g 213 TYR cc_start: 0.9451 (m-10) cc_final: 0.9192 (m-10) REVERT: h 8 ASN cc_start: 0.9443 (t0) cc_final: 0.9215 (t0) REVERT: h 25 ASN cc_start: 0.9154 (m-40) cc_final: 0.8868 (p0) REVERT: h 29 PHE cc_start: 0.9186 (t80) cc_final: 0.8592 (t80) REVERT: h 102 ASN cc_start: 0.9050 (m-40) cc_final: 0.8681 (m-40) REVERT: h 123 GLN cc_start: 0.9674 (mt0) cc_final: 0.9302 (mt0) REVERT: h 129 MET cc_start: 0.7138 (mtt) cc_final: 0.6686 (ttt) REVERT: h 130 PHE cc_start: 0.9206 (p90) cc_final: 0.8823 (p90) REVERT: h 134 MET cc_start: 0.8728 (mtp) cc_final: 0.7398 (mtp) REVERT: h 152 GLU cc_start: 0.8946 (tt0) cc_final: 0.8738 (tm-30) REVERT: h 162 ILE cc_start: 0.9034 (mm) cc_final: 0.8815 (tt) REVERT: h 181 ASP cc_start: 0.9477 (t0) cc_final: 0.9148 (t0) REVERT: i 40 GLN cc_start: 0.8574 (tt0) cc_final: 0.8358 (tt0) REVERT: i 51 TYR cc_start: 0.9361 (t80) cc_final: 0.9037 (t80) REVERT: i 54 GLN cc_start: 0.9637 (mt0) cc_final: 0.9003 (mt0) REVERT: i 59 GLN cc_start: 0.9137 (mm-40) cc_final: 0.8927 (mm110) REVERT: i 73 ARG cc_start: 0.9584 (tpt-90) cc_final: 0.9109 (mmm160) REVERT: i 75 TYR cc_start: 0.9345 (m-80) cc_final: 0.8728 (m-80) REVERT: i 123 ILE cc_start: 0.9441 (mm) cc_final: 0.8838 (tp) REVERT: i 135 TYR cc_start: 0.9311 (t80) cc_final: 0.8928 (t80) REVERT: i 136 GLN cc_start: 0.9359 (mm-40) cc_final: 0.8991 (pm20) REVERT: i 146 ARG cc_start: 0.9032 (OUTLIER) cc_final: 0.8589 (ttp-110) REVERT: i 182 PHE cc_start: 0.9508 (t80) cc_final: 0.8530 (t80) REVERT: j 11 LEU cc_start: 0.9352 (mp) cc_final: 0.9119 (mt) REVERT: j 14 LYS cc_start: 0.9581 (mtpp) cc_final: 0.9097 (mmtm) REVERT: j 23 LYS cc_start: 0.8742 (tttm) cc_final: 0.8535 (tttp) REVERT: j 24 THR cc_start: 0.9132 (m) cc_final: 0.8761 (p) REVERT: j 31 PHE cc_start: 0.8973 (m-80) cc_final: 0.7946 (m-80) REVERT: j 54 ARG cc_start: 0.8614 (mmt90) cc_final: 0.8139 (mmt-90) REVERT: j 131 THR cc_start: 0.9308 (p) cc_final: 0.8893 (t) REVERT: j 138 ARG cc_start: 0.9222 (mtt-85) cc_final: 0.8832 (mtt90) REVERT: j 142 ASP cc_start: 0.9481 (t70) cc_final: 0.9173 (t0) REVERT: j 156 LYS cc_start: 0.9555 (ttpt) cc_final: 0.8774 (tppt) REVERT: k 21 MET cc_start: 0.9004 (mtm) cc_final: 0.8357 (mtp) REVERT: k 24 ARG cc_start: 0.8968 (mtm180) cc_final: 0.8766 (ptt-90) REVERT: k 25 TYR cc_start: 0.9662 (m-10) cc_final: 0.9416 (m-10) REVERT: k 61 LEU cc_start: 0.9411 (tp) cc_final: 0.9168 (tt) REVERT: k 74 LEU cc_start: 0.9447 (tp) cc_final: 0.9166 (tp) REVERT: l 26 PHE cc_start: 0.9721 (t80) cc_final: 0.9416 (t80) REVERT: l 31 MET cc_start: 0.8969 (ttp) cc_final: 0.8466 (ttp) REVERT: l 62 PHE cc_start: 0.9634 (t80) cc_final: 0.9359 (t80) REVERT: l 106 GLU cc_start: 0.9348 (tt0) cc_final: 0.9117 (tm-30) REVERT: l 137 LYS cc_start: 0.9692 (tppt) cc_final: 0.8887 (tppt) REVERT: l 140 ASP cc_start: 0.9416 (m-30) cc_final: 0.9160 (p0) REVERT: m 14 ILE cc_start: 0.9799 (mt) cc_final: 0.9472 (mm) REVERT: m 27 MET cc_start: 0.8853 (ptp) cc_final: 0.8613 (ptm) REVERT: m 38 ASN cc_start: 0.9396 (t0) cc_final: 0.9156 (m-40) REVERT: m 74 SER cc_start: 0.8947 (t) cc_final: 0.8012 (t) REVERT: m 76 GLN cc_start: 0.9168 (mt0) cc_final: 0.8925 (mp10) REVERT: m 111 MET cc_start: 0.8799 (ptp) cc_final: 0.8506 (ptp) REVERT: m 124 GLU cc_start: 0.9028 (tt0) cc_final: 0.8444 (tm-30) REVERT: m 125 ILE cc_start: 0.9265 (mt) cc_final: 0.8903 (mp) REVERT: m 126 ILE cc_start: 0.9645 (mt) cc_final: 0.8715 (mp) REVERT: m 128 TYR cc_start: 0.8905 (m-10) cc_final: 0.8215 (m-10) REVERT: n 46 MET cc_start: 0.9502 (ttp) cc_final: 0.9230 (tmm) REVERT: n 47 VAL cc_start: 0.9453 (m) cc_final: 0.9106 (p) REVERT: n 53 GLU cc_start: 0.9632 (mt-10) cc_final: 0.9425 (mt-10) REVERT: n 59 GLU cc_start: 0.9129 (mm-30) cc_final: 0.8664 (mm-30) REVERT: n 89 GLU cc_start: 0.9696 (tp30) cc_final: 0.9223 (tp30) REVERT: n 110 GLN cc_start: 0.8799 (mm110) cc_final: 0.8403 (mm-40) REVERT: n 112 GLU cc_start: 0.8417 (tt0) cc_final: 0.8187 (tp30) REVERT: n 127 PHE cc_start: 0.9351 (t80) cc_final: 0.8739 (t80) REVERT: o 10 LEU cc_start: 0.9367 (mp) cc_final: 0.9134 (mp) REVERT: o 27 GLU cc_start: 0.9612 (mm-30) cc_final: 0.9405 (mm-30) REVERT: o 53 ILE cc_start: 0.9335 (pt) cc_final: 0.9014 (pt) REVERT: o 63 ASP cc_start: 0.7968 (m-30) cc_final: 0.7504 (m-30) REVERT: o 65 TYR cc_start: 0.9108 (m-80) cc_final: 0.8691 (m-80) REVERT: o 66 GLU cc_start: 0.9210 (pt0) cc_final: 0.8619 (pt0) REVERT: o 67 ILE cc_start: 0.9212 (mt) cc_final: 0.8671 (mm) REVERT: o 71 LEU cc_start: 0.9594 (mm) cc_final: 0.9385 (mm) REVERT: o 97 ASP cc_start: 0.8398 (t70) cc_final: 0.7747 (t0) REVERT: o 99 GLN cc_start: 0.9260 (tt0) cc_final: 0.9023 (tm-30) REVERT: p 34 ILE cc_start: 0.9621 (mm) cc_final: 0.9420 (mm) REVERT: p 64 GLN cc_start: 0.9189 (pt0) cc_final: 0.8946 (pp30) REVERT: p 76 GLU cc_start: 0.9257 (pm20) cc_final: 0.8996 (pm20) REVERT: p 79 ILE cc_start: 0.9563 (mt) cc_final: 0.9148 (tp) REVERT: p 83 GLU cc_start: 0.9100 (pt0) cc_final: 0.8709 (pm20) REVERT: q 29 GLN cc_start: 0.9034 (mp10) cc_final: 0.8559 (mp10) REVERT: q 38 TYR cc_start: 0.8485 (p90) cc_final: 0.8050 (p90) REVERT: q 40 THR cc_start: 0.9589 (m) cc_final: 0.9373 (p) REVERT: q 59 ASN cc_start: 0.9129 (p0) cc_final: 0.8367 (p0) REVERT: q 61 PHE cc_start: 0.9400 (m-10) cc_final: 0.9098 (m-80) REVERT: q 66 TYR cc_start: 0.9444 (t80) cc_final: 0.8780 (t80) REVERT: q 67 ILE cc_start: 0.8349 (mt) cc_final: 0.7934 (mt) REVERT: q 70 GLU cc_start: 0.8947 (mt-10) cc_final: 0.8715 (mp0) REVERT: q 78 SER cc_start: 0.8926 (t) cc_final: 0.8341 (m) REVERT: q 79 VAL cc_start: 0.9724 (t) cc_final: 0.9467 (p) REVERT: q 82 ILE cc_start: 0.9436 (pt) cc_final: 0.9139 (mm) REVERT: q 88 LYS cc_start: 0.9451 (tttm) cc_final: 0.9101 (ttmt) REVERT: q 96 HIS cc_start: 0.9136 (m90) cc_final: 0.8878 (m90) REVERT: q 105 SER cc_start: 0.8431 (p) cc_final: 0.7678 (p) REVERT: q 116 LYS cc_start: 0.9527 (mttt) cc_final: 0.8962 (mtmp) REVERT: q 117 TYR cc_start: 0.9246 (m-80) cc_final: 0.8664 (m-80) REVERT: r 13 LYS cc_start: 0.9554 (mttt) cc_final: 0.9152 (tptt) REVERT: r 23 TYR cc_start: 0.8984 (t80) cc_final: 0.8471 (t80) REVERT: r 27 LYS cc_start: 0.9509 (tttt) cc_final: 0.9305 (tppt) REVERT: r 31 LYS cc_start: 0.9829 (mttt) cc_final: 0.9619 (mtmm) REVERT: r 42 ASP cc_start: 0.9307 (p0) cc_final: 0.8888 (t0) REVERT: r 50 GLU cc_start: 0.9366 (mm-30) cc_final: 0.8709 (tp30) REVERT: r 65 VAL cc_start: 0.8752 (m) cc_final: 0.8238 (m) REVERT: r 69 LEU cc_start: 0.9352 (tp) cc_final: 0.9024 (tp) REVERT: r 82 ASP cc_start: 0.9475 (m-30) cc_final: 0.9135 (p0) REVERT: r 100 GLN cc_start: 0.8517 (mp10) cc_final: 0.8088 (mp10) REVERT: s 6 MET cc_start: 0.9211 (mmm) cc_final: 0.8896 (tpp) REVERT: s 16 LEU cc_start: 0.9626 (mt) cc_final: 0.9143 (mm) REVERT: s 33 ASP cc_start: 0.9411 (t0) cc_final: 0.9026 (t70) REVERT: s 54 ASP cc_start: 0.8460 (m-30) cc_final: 0.7827 (p0) REVERT: s 62 ASN cc_start: 0.9493 (m-40) cc_final: 0.9185 (m-40) REVERT: s 67 THR cc_start: 0.9271 (p) cc_final: 0.8681 (t) REVERT: s 82 ILE cc_start: 0.9184 (mt) cc_final: 0.8530 (mt) REVERT: s 86 GLU cc_start: 0.9021 (mt-10) cc_final: 0.8708 (mt-10) REVERT: s 89 MET cc_start: 0.9110 (mmp) cc_final: 0.8819 (mmp) REVERT: s 96 LEU cc_start: 0.9299 (tp) cc_final: 0.9016 (tp) REVERT: t 2 SER cc_start: 0.6919 (m) cc_final: 0.6717 (m) REVERT: t 4 SER cc_start: 0.9449 (p) cc_final: 0.9081 (p) REVERT: t 28 GLN cc_start: 0.9444 (mt0) cc_final: 0.8594 (mp10) REVERT: t 37 ASN cc_start: 0.9315 (m-40) cc_final: 0.9097 (m-40) REVERT: t 43 PHE cc_start: 0.9386 (m-80) cc_final: 0.8397 (m-80) REVERT: t 48 LYS cc_start: 0.8969 (mmtm) cc_final: 0.8542 (mmtt) REVERT: t 59 MET cc_start: 0.9286 (mtt) cc_final: 0.9047 (mmp) REVERT: t 64 ARG cc_start: 0.8512 (tpm-80) cc_final: 0.8225 (tpp-160) REVERT: t 65 LYS cc_start: 0.9502 (mttt) cc_final: 0.9235 (tptp) REVERT: t 72 ARG cc_start: 0.9107 (ttp-110) cc_final: 0.8579 (ptt90) REVERT: u 12 LYS cc_start: 0.9262 (ttpt) cc_final: 0.8800 (ptmm) REVERT: u 18 GLN cc_start: 0.7187 (mm-40) cc_final: 0.6877 (mp10) REVERT: u 44 SER cc_start: 0.9122 (t) cc_final: 0.8734 (p) REVERT: u 53 ASP cc_start: 0.9329 (t0) cc_final: 0.8579 (t70) REVERT: u 55 ASP cc_start: 0.9574 (m-30) cc_final: 0.9305 (m-30) REVERT: u 60 TRP cc_start: 0.9342 (m100) cc_final: 0.8935 (m100) REVERT: u 76 LYS cc_start: 0.9610 (ttmt) cc_final: 0.9050 (pttm) REVERT: v 9 GLN cc_start: 0.7248 (mt0) cc_final: 0.6830 (tp-100) REVERT: v 31 HIS cc_start: 0.9140 (t-90) cc_final: 0.8475 (t-90) REVERT: v 69 LYS cc_start: 0.8766 (tttt) cc_final: 0.8447 (mtpt) REVERT: v 77 ARG cc_start: 0.8779 (ptm-80) cc_final: 0.8542 (ttp80) REVERT: w 29 LEU cc_start: 0.9742 (mp) cc_final: 0.9528 (mp) REVERT: w 54 GLN cc_start: 0.9477 (mt0) cc_final: 0.9241 (pt0) REVERT: w 57 ARG cc_start: 0.9329 (ttm110) cc_final: 0.9048 (ttp-110) REVERT: w 68 LEU cc_start: 0.9558 (mt) cc_final: 0.9336 (mt) REVERT: x 60 VAL cc_start: 0.8250 (t) cc_final: 0.7874 (p) REVERT: y 4 ILE cc_start: 0.8317 (mt) cc_final: 0.8024 (mp) REVERT: y 12 ILE cc_start: 0.9721 (pt) cc_final: 0.9231 (pt) REVERT: y 18 ARG cc_start: 0.9676 (ttp80) cc_final: 0.9386 (ttp80) REVERT: y 32 ILE cc_start: 0.9696 (mt) cc_final: 0.9303 (mm) REVERT: y 36 TYR cc_start: 0.9546 (m-80) cc_final: 0.8895 (m-80) REVERT: y 39 ILE cc_start: 0.8979 (mt) cc_final: 0.8587 (pt) REVERT: y 48 GLN cc_start: 0.9364 (tp40) cc_final: 0.9134 (tp-100) REVERT: y 49 LYS cc_start: 0.9706 (tppt) cc_final: 0.9496 (ttpp) REVERT: y 59 ASP cc_start: 0.9277 (m-30) cc_final: 0.8935 (m-30) REVERT: y 79 LEU cc_start: 0.9737 (mt) cc_final: 0.9319 (mp) REVERT: y 83 ILE cc_start: 0.9554 (mt) cc_final: 0.9297 (tt) REVERT: z 8 GLU cc_start: 0.9041 (tt0) cc_final: 0.8729 (pm20) REVERT: z 29 LEU cc_start: 0.9166 (mm) cc_final: 0.8779 (pp) REVERT: z 31 GLU cc_start: 0.8419 (tp30) cc_final: 0.7692 (tp30) REVERT: z 39 GLU cc_start: 0.7243 (tt0) cc_final: 0.6090 (tt0) REVERT: z 44 GLU cc_start: 0.8968 (tt0) cc_final: 0.8496 (tp30) REVERT: z 49 LYS cc_start: 0.9644 (tttm) cc_final: 0.9419 (ttpp) REVERT: z 58 LYS cc_start: 0.9537 (ttpt) cc_final: 0.8903 (tmtt) REVERT: z 59 LYS cc_start: 0.9081 (ttmm) cc_final: 0.8599 (tttt) REVERT: z 60 LEU cc_start: 0.9338 (mm) cc_final: 0.9117 (pp) REVERT: H 79 PHE cc_start: 0.8252 (OUTLIER) cc_final: 0.8012 (p90) REVERT: A 104 ASP cc_start: 0.7464 (t0) cc_final: 0.7151 (t70) REVERT: A 130 ASP cc_start: 0.9492 (m-30) cc_final: 0.9238 (m-30) REVERT: A 184 VAL cc_start: 0.7172 (p) cc_final: -0.0287 (p) REVERT: A 186 ARG cc_start: 0.8312 (ptt180) cc_final: 0.7754 (ptt90) REVERT: A 195 ARG cc_start: 0.2790 (mtt-85) cc_final: 0.2448 (mtt-85) REVERT: A 206 MET cc_start: 0.7685 (mtm) cc_final: 0.7435 (ptp) REVERT: A 320 HIS cc_start: 0.7707 (m-70) cc_final: 0.7475 (m90) REVERT: A 337 LEU cc_start: 0.9581 (tp) cc_final: 0.9343 (mt) REVERT: A 338 ASP cc_start: 0.9350 (m-30) cc_final: 0.8767 (m-30) outliers start: 16 outliers final: 3 residues processed: 1864 average time/residue: 1.3412 time to fit residues: 4243.4555 Evaluate side-chains 1294 residues out of total 4812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 1289 time to evaluate : 6.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain R residue 54 VAL Chi-restraints excluded: chain h residue 200 VAL Chi-restraints excluded: chain i residue 146 ARG Chi-restraints excluded: chain H residue 79 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1027 random chunks: chunk 867 optimal weight: 5.9990 chunk 778 optimal weight: 30.0000 chunk 431 optimal weight: 10.0000 chunk 265 optimal weight: 20.0000 chunk 525 optimal weight: 10.0000 chunk 415 optimal weight: 30.0000 chunk 804 optimal weight: 20.0000 chunk 311 optimal weight: 40.0000 chunk 489 optimal weight: 10.0000 chunk 599 optimal weight: 5.9990 chunk 932 optimal weight: 30.0000 overall best weight: 8.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 60 GLN B 86 ASN ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 260 ASN ** C 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 36 GLN C 136 ASN D 115 GLN ** E 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 30 ASN F 45 HIS F 104 ASN F 116 GLN G 2 GLN ** J 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 128 ASN K 3 GLN K 9 ASN ** K 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 35 HIS O 29 HIS O 38 GLN O 100 HIS ** P 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 71 GLN S 7 HIS ** S 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 61 ASN ** T 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 46 HIS Y 15 ASN Y 20 ASN Y 39 GLN b 4 GLN c 26 ASN c 45 GLN e 26 HIS e 43 HIS ** g 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 109 GLN g 177 ASN h 190 HIS i 36 GLN i 89 ASN ** j 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 46 GLN l 28 ASN ** l 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 5 ASN q 6 GLN t 37 ASN t 40 GLN ** w 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 14 HIS ** x 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** x 83 HIS y 3 ASN y 48 GLN y 52 ASN ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 287 GLN Total number of N/Q/H flips: 47 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.103 158320 Z= 0.326 Angle : 0.732 15.237 236734 Z= 0.385 Chirality : 0.038 0.258 30127 Planarity : 0.007 0.150 12767 Dihedral : 24.763 179.803 78861 Min Nonbonded Distance : 1.774 Molprobity Statistics. All-atom Clashscore : 25.82 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.89 % Favored : 95.07 % Rotamer: Outliers : 3.53 % Allowed : 14.40 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.30 (0.10), residues: 5784 helix: -0.95 (0.11), residues: 1957 sheet: -1.87 (0.15), residues: 1066 loop : -1.72 (0.11), residues: 2761 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP P 31 HIS 0.019 0.002 HIS t 46 PHE 0.036 0.002 PHE i 107 TYR 0.024 0.002 TYR B 83 ARG 0.013 0.001 ARG T 69 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11568 Ramachandran restraints generated. 5784 Oldfield, 0 Emsley, 5784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11568 Ramachandran restraints generated. 5784 Oldfield, 0 Emsley, 5784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1573 residues out of total 4812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 1403 time to evaluate : 6.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 16 VAL cc_start: 0.9081 (t) cc_final: 0.8868 (p) REVERT: B 23 GLU cc_start: 0.8930 (mm-30) cc_final: 0.8556 (mm-30) REVERT: B 79 GLU cc_start: 0.7687 (mt-10) cc_final: 0.6726 (mp0) REVERT: B 96 TYR cc_start: 0.9239 (m-80) cc_final: 0.8477 (m-80) REVERT: B 100 GLU cc_start: 0.7531 (tm-30) cc_final: 0.6922 (tm-30) REVERT: B 185 GLU cc_start: 0.7850 (tm-30) cc_final: 0.7598 (tm-30) REVERT: B 229 ASP cc_start: 0.8708 (m-30) cc_final: 0.8471 (m-30) REVERT: B 251 GLN cc_start: 0.8850 (tp40) cc_final: 0.8558 (tm-30) REVERT: B 255 LYS cc_start: 0.9351 (tttm) cc_final: 0.8947 (tptm) REVERT: C 1 MET cc_start: 0.7934 (tpp) cc_final: 0.7727 (tpp) REVERT: C 30 GLU cc_start: 0.8489 (mt-10) cc_final: 0.8276 (mm-30) REVERT: C 149 ASN cc_start: 0.8576 (t0) cc_final: 0.7900 (t0) REVERT: C 164 GLN cc_start: 0.8798 (tp40) cc_final: 0.8525 (tp40) REVERT: C 187 LEU cc_start: 0.9705 (tp) cc_final: 0.9501 (tp) REVERT: D 1 MET cc_start: 0.8539 (tpt) cc_final: 0.8281 (tpt) REVERT: D 46 GLN cc_start: 0.9525 (mp10) cc_final: 0.8459 (mp10) REVERT: D 61 ARG cc_start: 0.9110 (ptt-90) cc_final: 0.8821 (ptt-90) REVERT: D 62 GLN cc_start: 0.9025 (tp40) cc_final: 0.8459 (tp40) REVERT: D 100 MET cc_start: 0.8712 (mtp) cc_final: 0.8415 (mtp) REVERT: D 115 GLN cc_start: 0.8182 (mm110) cc_final: 0.7884 (mm110) REVERT: E 7 TYR cc_start: 0.9509 (t80) cc_final: 0.9307 (t80) REVERT: E 26 MET cc_start: 0.9052 (mtp) cc_final: 0.8410 (mtt) REVERT: E 83 TYR cc_start: 0.9053 (m-10) cc_final: 0.8628 (m-80) REVERT: E 90 THR cc_start: 0.9593 (m) cc_final: 0.9231 (p) REVERT: E 96 MET cc_start: 0.9551 (ttp) cc_final: 0.9141 (ttp) REVERT: E 100 PHE cc_start: 0.9114 (t80) cc_final: 0.8201 (t80) REVERT: E 127 ASN cc_start: 0.8563 (m-40) cc_final: 0.8045 (m-40) REVERT: E 143 TYR cc_start: 0.9056 (t80) cc_final: 0.8752 (t80) REVERT: E 157 THR cc_start: 0.8691 (m) cc_final: 0.6913 (m) REVERT: F 60 ASP cc_start: 0.9083 (p0) cc_final: 0.8745 (p0) REVERT: F 75 MET cc_start: 0.9026 (ttt) cc_final: 0.8660 (ttt) REVERT: F 101 ASN cc_start: 0.9284 (p0) cc_final: 0.8917 (p0) REVERT: F 147 ASP cc_start: 0.9234 (m-30) cc_final: 0.8982 (m-30) REVERT: J 75 TYR cc_start: 0.9142 (m-80) cc_final: 0.8626 (m-10) REVERT: J 102 GLU cc_start: 0.8455 (mt-10) cc_final: 0.7974 (pt0) REVERT: J 141 ASP cc_start: 0.8730 (t0) cc_final: 0.8473 (t0) REVERT: K 1 MET cc_start: 0.8714 (ttm) cc_final: 0.8204 (ttm) REVERT: K 3 GLN cc_start: 0.8750 (pt0) cc_final: 0.8272 (pt0) REVERT: K 4 GLU cc_start: 0.7839 (mm-30) cc_final: 0.7520 (mm-30) REVERT: K 23 LYS cc_start: 0.9364 (tppt) cc_final: 0.8594 (tptp) REVERT: K 25 LEU cc_start: 0.9555 (mt) cc_final: 0.9344 (mp) REVERT: K 29 HIS cc_start: 0.7666 (m90) cc_final: 0.7051 (m90) REVERT: K 37 ASP cc_start: 0.8348 (m-30) cc_final: 0.8133 (m-30) REVERT: K 44 LYS cc_start: 0.9420 (mmtt) cc_final: 0.9197 (mmmm) REVERT: K 87 LEU cc_start: 0.9510 (mt) cc_final: 0.9241 (mt) REVERT: K 88 ASN cc_start: 0.8688 (t0) cc_final: 0.8388 (t0) REVERT: L 1 MET cc_start: 0.8261 (ttp) cc_final: 0.8048 (ttp) REVERT: L 136 GLU cc_start: 0.8677 (OUTLIER) cc_final: 0.8284 (mm-30) REVERT: L 142 ILE cc_start: 0.9474 (mt) cc_final: 0.8948 (mt) REVERT: M 1 MET cc_start: 0.8799 (mmp) cc_final: 0.8492 (mmp) REVERT: M 17 ASN cc_start: 0.8585 (t0) cc_final: 0.8294 (t0) REVERT: M 45 GLN cc_start: 0.9515 (mt0) cc_final: 0.9299 (mt0) REVERT: M 53 MET cc_start: 0.8761 (ptp) cc_final: 0.8456 (ptt) REVERT: M 96 ILE cc_start: 0.9830 (mm) cc_final: 0.9572 (mp) REVERT: M 119 LEU cc_start: 0.9750 (mm) cc_final: 0.9494 (mm) REVERT: N 9 GLN cc_start: 0.8531 (tt0) cc_final: 0.8058 (tt0) REVERT: N 40 LYS cc_start: 0.9496 (mttt) cc_final: 0.8982 (mttp) REVERT: N 48 VAL cc_start: 0.9747 (t) cc_final: 0.9513 (p) REVERT: N 57 THR cc_start: 0.9115 (m) cc_final: 0.8842 (p) REVERT: N 72 ASP cc_start: 0.8731 (t0) cc_final: 0.8443 (t70) REVERT: N 75 ILE cc_start: 0.9602 (mm) cc_final: 0.9398 (mm) REVERT: O 19 GLN cc_start: 0.9561 (tm130) cc_final: 0.9152 (tm-30) REVERT: O 88 LYS cc_start: 0.9395 (tptt) cc_final: 0.8008 (tptp) REVERT: O 108 ASP cc_start: 0.9243 (m-30) cc_final: 0.8893 (p0) REVERT: O 115 LEU cc_start: 0.7945 (mm) cc_final: 0.7547 (tp) REVERT: P 25 THR cc_start: 0.9050 (m) cc_final: 0.8643 (p) REVERT: P 29 LYS cc_start: 0.9698 (mttm) cc_final: 0.9357 (mmmm) REVERT: P 40 LEU cc_start: 0.9627 (tp) cc_final: 0.8900 (tp) REVERT: P 41 GLN cc_start: 0.9213 (tt0) cc_final: 0.8913 (tt0) REVERT: Q 32 TYR cc_start: 0.8881 (t80) cc_final: 0.8444 (t80) REVERT: Q 34 VAL cc_start: 0.9810 (t) cc_final: 0.9587 (p) REVERT: Q 45 TYR cc_start: 0.8514 (m-10) cc_final: 0.8297 (m-80) REVERT: Q 52 GLN cc_start: 0.8201 (mt0) cc_final: 0.7874 (mp10) REVERT: Q 97 ASP cc_start: 0.8768 (t70) cc_final: 0.8380 (t70) REVERT: Q 101 PHE cc_start: 0.8263 (m-80) cc_final: 0.7863 (m-10) REVERT: R 13 ARG cc_start: 0.8902 (tmm-80) cc_final: 0.8354 (ttt-90) REVERT: R 46 GLU cc_start: 0.8125 (mp0) cc_final: 0.7643 (mp0) REVERT: R 85 LYS cc_start: 0.9013 (mttt) cc_final: 0.8701 (mtpp) REVERT: R 86 GLN cc_start: 0.8681 (mm110) cc_final: 0.7958 (mm-40) REVERT: R 95 ASP cc_start: 0.8642 (m-30) cc_final: 0.8338 (m-30) REVERT: S 2 GLU cc_start: 0.8173 (mp0) cc_final: 0.7878 (mp0) REVERT: S 46 LEU cc_start: 0.9624 (mt) cc_final: 0.9263 (mp) REVERT: S 65 ASP cc_start: 0.8160 (t0) cc_final: 0.7670 (t70) REVERT: S 68 ASP cc_start: 0.9109 (m-30) cc_final: 0.8579 (m-30) REVERT: S 92 ARG cc_start: 0.8957 (tmm-80) cc_final: 0.8689 (tmm-80) REVERT: T 50 LEU cc_start: 0.9462 (mt) cc_final: 0.9244 (mt) REVERT: T 92 ASN cc_start: 0.8677 (OUTLIER) cc_final: 0.8353 (t0) REVERT: U 4 LYS cc_start: 0.8926 (mttt) cc_final: 0.8440 (mttt) REVERT: V 40 ILE cc_start: 0.9621 (pt) cc_final: 0.9000 (mm) REVERT: V 48 MET cc_start: 0.9106 (tpt) cc_final: 0.8867 (tpt) REVERT: W 36 ILE cc_start: 0.9411 (mt) cc_final: 0.8943 (mt) REVERT: W 38 VAL cc_start: 0.9673 (t) cc_final: 0.9316 (p) REVERT: W 44 LYS cc_start: 0.9600 (ttmt) cc_final: 0.9229 (ttmm) REVERT: W 68 LYS cc_start: 0.8992 (tptp) cc_final: 0.8778 (tptp) REVERT: X 16 ASN cc_start: 0.9385 (m-40) cc_final: 0.9016 (t0) REVERT: X 17 ASN cc_start: 0.8719 (m-40) cc_final: 0.8131 (m-40) REVERT: X 23 ASN cc_start: 0.9002 (m110) cc_final: 0.8546 (m-40) REVERT: X 41 GLU cc_start: 0.8052 (tp30) cc_final: 0.7429 (tp30) REVERT: X 76 GLU cc_start: 0.7394 (tm-30) cc_final: 0.7132 (tm-30) REVERT: Y 25 GLN cc_start: 0.9527 (tt0) cc_final: 0.9277 (tm-30) REVERT: Y 30 MET cc_start: 0.9215 (mmp) cc_final: 0.8801 (mmm) REVERT: Y 44 LYS cc_start: 0.9584 (tttt) cc_final: 0.9296 (ttmm) REVERT: Z 3 LYS cc_start: 0.8349 (tppt) cc_final: 0.8097 (tppt) REVERT: Z 19 LYS cc_start: 0.8974 (mmtt) cc_final: 0.8608 (mmtt) REVERT: Z 21 LYS cc_start: 0.9488 (mttt) cc_final: 0.9167 (mttp) REVERT: Z 49 ASN cc_start: 0.9541 (t0) cc_final: 0.9325 (t0) REVERT: Z 56 LYS cc_start: 0.8599 (tmtt) cc_final: 0.8239 (tptp) REVERT: b 46 ASP cc_start: 0.8528 (m-30) cc_final: 0.8289 (m-30) REVERT: d 2 LYS cc_start: 0.9024 (tttt) cc_final: 0.8505 (tttp) REVERT: d 11 LYS cc_start: 0.9347 (ttmt) cc_final: 0.9023 (mtpt) REVERT: d 22 MET cc_start: 0.9029 (mmm) cc_final: 0.8802 (tpp) REVERT: e 14 PHE cc_start: 0.9772 (m-80) cc_final: 0.9547 (m-10) REVERT: e 32 ILE cc_start: 0.8818 (mm) cc_final: 0.8554 (mm) REVERT: f 9 LYS cc_start: 0.9330 (mttt) cc_final: 0.8965 (mttm) REVERT: f 18 LYS cc_start: 0.9356 (tttt) cc_final: 0.8920 (mtmm) REVERT: g 27 MET cc_start: 0.9095 (mmm) cc_final: 0.8411 (mmm) REVERT: g 49 MET cc_start: 0.9600 (mtp) cc_final: 0.9242 (mtp) REVERT: g 96 TRP cc_start: 0.9060 (t-100) cc_final: 0.8815 (t-100) REVERT: g 100 MET cc_start: 0.8986 (ttm) cc_final: 0.8780 (ttm) REVERT: g 120 GLN cc_start: 0.9526 (tt0) cc_final: 0.9296 (pp30) REVERT: g 213 TYR cc_start: 0.9426 (m-10) cc_final: 0.8855 (m-10) REVERT: h 29 PHE cc_start: 0.9325 (t80) cc_final: 0.8556 (t80) REVERT: h 129 MET cc_start: 0.7353 (mtt) cc_final: 0.6995 (ttt) REVERT: h 130 PHE cc_start: 0.9239 (p90) cc_final: 0.8748 (p90) REVERT: h 168 TYR cc_start: 0.7902 (m-80) cc_final: 0.6955 (m-80) REVERT: h 181 ASP cc_start: 0.9430 (t0) cc_final: 0.9061 (t0) REVERT: h 185 ASN cc_start: 0.9126 (t0) cc_final: 0.8810 (t0) REVERT: i 40 GLN cc_start: 0.8590 (tt0) cc_final: 0.7313 (mt0) REVERT: i 51 TYR cc_start: 0.9497 (t80) cc_final: 0.9203 (t80) REVERT: i 54 GLN cc_start: 0.9515 (mt0) cc_final: 0.9084 (mt0) REVERT: i 75 TYR cc_start: 0.9491 (m-80) cc_final: 0.8841 (m-80) REVERT: i 135 TYR cc_start: 0.9283 (t80) cc_final: 0.8926 (t80) REVERT: i 136 GLN cc_start: 0.9368 (mm-40) cc_final: 0.9004 (pm20) REVERT: i 141 ASP cc_start: 0.8316 (p0) cc_final: 0.8006 (p0) REVERT: i 182 PHE cc_start: 0.9352 (t80) cc_final: 0.9013 (t80) REVERT: j 31 PHE cc_start: 0.8933 (m-80) cc_final: 0.7922 (m-80) REVERT: j 131 THR cc_start: 0.9248 (p) cc_final: 0.8848 (t) REVERT: j 142 ASP cc_start: 0.9476 (t70) cc_final: 0.9239 (t0) REVERT: j 152 MET cc_start: 0.8817 (mtp) cc_final: 0.8351 (mtp) REVERT: k 14 GLN cc_start: 0.9454 (mm-40) cc_final: 0.9003 (mp10) REVERT: k 25 TYR cc_start: 0.9641 (m-10) cc_final: 0.9375 (m-10) REVERT: k 62 MET cc_start: 0.9411 (ptp) cc_final: 0.8918 (ptp) REVERT: l 26 PHE cc_start: 0.9729 (t80) cc_final: 0.9351 (t80) REVERT: l 29 ILE cc_start: 0.9740 (mt) cc_final: 0.9450 (pt) REVERT: l 31 MET cc_start: 0.8879 (ttp) cc_final: 0.8290 (ttp) REVERT: l 140 ASP cc_start: 0.9549 (m-30) cc_final: 0.9243 (p0) REVERT: m 3 MET cc_start: 0.9122 (tpp) cc_final: 0.8791 (tpp) REVERT: m 10 MET cc_start: 0.9096 (tmm) cc_final: 0.8541 (tmm) REVERT: m 74 SER cc_start: 0.9044 (t) cc_final: 0.8134 (p) REVERT: m 76 GLN cc_start: 0.9252 (mt0) cc_final: 0.8937 (mp10) REVERT: m 80 ARG cc_start: 0.9519 (mtm110) cc_final: 0.9318 (mtm110) REVERT: m 124 GLU cc_start: 0.8997 (tt0) cc_final: 0.8230 (tm-30) REVERT: m 125 ILE cc_start: 0.9249 (mt) cc_final: 0.8801 (mm) REVERT: m 126 ILE cc_start: 0.9668 (mt) cc_final: 0.9013 (mp) REVERT: m 128 TYR cc_start: 0.9032 (m-10) cc_final: 0.8396 (m-10) REVERT: n 57 MET cc_start: 0.9072 (mtp) cc_final: 0.8186 (tmm) REVERT: n 89 GLU cc_start: 0.9710 (tp30) cc_final: 0.9149 (tp30) REVERT: n 110 GLN cc_start: 0.8505 (mm110) cc_final: 0.8241 (mm-40) REVERT: o 10 LEU cc_start: 0.9278 (mp) cc_final: 0.8997 (mp) REVERT: o 53 ILE cc_start: 0.9267 (pt) cc_final: 0.8971 (pt) REVERT: o 63 ASP cc_start: 0.7937 (m-30) cc_final: 0.7520 (m-30) REVERT: o 66 GLU cc_start: 0.9195 (pt0) cc_final: 0.8639 (pt0) REVERT: o 71 LEU cc_start: 0.9617 (mm) cc_final: 0.9413 (mm) REVERT: o 88 MET cc_start: 0.9295 (ptm) cc_final: 0.9000 (ptt) REVERT: p 83 GLU cc_start: 0.9043 (pt0) cc_final: 0.8628 (pm20) REVERT: p 85 MET cc_start: 0.9191 (mtp) cc_final: 0.8671 (ptp) REVERT: p 87 LYS cc_start: 0.9220 (ttmm) cc_final: 0.8843 (mtmt) REVERT: p 100 LEU cc_start: 0.9558 (mt) cc_final: 0.9210 (pp) REVERT: q 6 GLN cc_start: 0.9078 (mt0) cc_final: 0.8875 (mt0) REVERT: q 29 GLN cc_start: 0.9362 (mp10) cc_final: 0.8367 (mp10) REVERT: q 38 TYR cc_start: 0.8241 (p90) cc_final: 0.7971 (p90) REVERT: q 59 ASN cc_start: 0.9179 (p0) cc_final: 0.8531 (p0) REVERT: q 61 PHE cc_start: 0.9293 (m-10) cc_final: 0.9005 (m-80) REVERT: q 66 TYR cc_start: 0.9252 (t80) cc_final: 0.8884 (t80) REVERT: q 74 LEU cc_start: 0.9325 (OUTLIER) cc_final: 0.9003 (mt) REVERT: q 81 LEU cc_start: 0.9653 (tp) cc_final: 0.9393 (mm) REVERT: q 117 TYR cc_start: 0.9238 (m-80) cc_final: 0.8640 (m-80) REVERT: r 8 ASN cc_start: 0.8380 (t0) cc_final: 0.8149 (t0) REVERT: r 13 LYS cc_start: 0.9486 (mttt) cc_final: 0.9089 (tppt) REVERT: r 23 TYR cc_start: 0.9143 (t80) cc_final: 0.8548 (t80) REVERT: r 41 GLU cc_start: 0.8794 (mt-10) cc_final: 0.8582 (mt-10) REVERT: r 42 ASP cc_start: 0.9308 (p0) cc_final: 0.8888 (t0) REVERT: r 69 LEU cc_start: 0.9415 (tp) cc_final: 0.9071 (tp) REVERT: r 81 MET cc_start: 0.9244 (mmm) cc_final: 0.8994 (mmm) REVERT: r 86 TYR cc_start: 0.8642 (t80) cc_final: 0.8349 (t80) REVERT: r 100 GLN cc_start: 0.8533 (mp10) cc_final: 0.7965 (mp10) REVERT: r 103 LYS cc_start: 0.8165 (tttt) cc_final: 0.7001 (tptt) REVERT: s 6 MET cc_start: 0.9181 (mmm) cc_final: 0.8903 (mmt) REVERT: s 33 ASP cc_start: 0.9157 (t0) cc_final: 0.8785 (t70) REVERT: s 40 ASP cc_start: 0.9062 (m-30) cc_final: 0.8739 (m-30) REVERT: s 42 TRP cc_start: 0.8800 (OUTLIER) cc_final: 0.8133 (t60) REVERT: s 62 ASN cc_start: 0.9430 (m-40) cc_final: 0.9200 (m-40) REVERT: s 67 THR cc_start: 0.9256 (p) cc_final: 0.8679 (t) REVERT: s 86 GLU cc_start: 0.9027 (mt-10) cc_final: 0.8777 (mt-10) REVERT: t 2 SER cc_start: 0.6895 (m) cc_final: 0.6656 (m) REVERT: t 14 GLU cc_start: 0.8623 (pt0) cc_final: 0.8394 (pt0) REVERT: t 43 PHE cc_start: 0.9236 (m-80) cc_final: 0.8560 (m-80) REVERT: t 48 LYS cc_start: 0.8958 (mmtm) cc_final: 0.8564 (mmtt) REVERT: t 59 MET cc_start: 0.9238 (mtt) cc_final: 0.8704 (mmp) REVERT: t 65 LYS cc_start: 0.9567 (mttt) cc_final: 0.9356 (pttt) REVERT: u 1 MET cc_start: 0.8192 (pmt) cc_final: 0.7439 (tpt) REVERT: u 34 GLU cc_start: 0.9303 (tm-30) cc_final: 0.8627 (tm-30) REVERT: u 55 ASP cc_start: 0.9538 (m-30) cc_final: 0.9330 (t0) REVERT: u 76 LYS cc_start: 0.9457 (ttmt) cc_final: 0.9103 (pttm) REVERT: u 80 LYS cc_start: 0.9060 (pttm) cc_final: 0.8825 (pttm) REVERT: v 31 HIS cc_start: 0.9164 (t-90) cc_final: 0.8570 (t-90) REVERT: v 77 ARG cc_start: 0.8637 (ptm-80) cc_final: 0.8315 (ttp80) REVERT: w 54 GLN cc_start: 0.9381 (mt0) cc_final: 0.8988 (tm-30) REVERT: x 44 MET cc_start: 0.9250 (mtt) cc_final: 0.8606 (ptp) REVERT: x 60 VAL cc_start: 0.8660 (t) cc_final: 0.8193 (p) REVERT: x 66 MET cc_start: 0.9305 (mtp) cc_final: 0.9040 (mtp) REVERT: y 4 ILE cc_start: 0.8517 (mt) cc_final: 0.8224 (mp) REVERT: y 19 LYS cc_start: 0.9838 (mttt) cc_final: 0.9382 (mtmm) REVERT: y 28 MET cc_start: 0.9482 (tmm) cc_final: 0.9258 (tmm) REVERT: y 39 ILE cc_start: 0.8646 (mt) cc_final: 0.8303 (mt) REVERT: y 59 ASP cc_start: 0.9196 (m-30) cc_final: 0.8334 (t0) REVERT: y 79 LEU cc_start: 0.9589 (mt) cc_final: 0.9181 (mt) REVERT: y 83 ILE cc_start: 0.9502 (mt) cc_final: 0.9063 (mt) REVERT: z 9 ASN cc_start: 0.8480 (p0) cc_final: 0.8154 (p0) REVERT: z 36 GLU cc_start: 0.8049 (pt0) cc_final: 0.7583 (pt0) REVERT: z 54 LYS cc_start: 0.9123 (tttt) cc_final: 0.8857 (tttt) REVERT: z 59 LYS cc_start: 0.9137 (ttmm) cc_final: 0.8602 (ptmm) REVERT: H 79 PHE cc_start: 0.7937 (OUTLIER) cc_final: 0.7723 (p90) REVERT: A 316 ARG cc_start: 0.9353 (ttp-170) cc_final: 0.8937 (ttp80) REVERT: A 333 MET cc_start: 0.8915 (tpt) cc_final: 0.8665 (tpt) outliers start: 170 outliers final: 108 residues processed: 1470 average time/residue: 1.3220 time to fit residues: 3339.2439 Evaluate side-chains 1336 residues out of total 4812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 1223 time to evaluate : 6.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 SER Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain C residue 96 ILE Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 32 GLU Chi-restraints excluded: chain F residue 155 GLU Chi-restraints excluded: chain F residue 166 ASP Chi-restraints excluded: chain J residue 109 LEU Chi-restraints excluded: chain J residue 131 ASN Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 86 LEU Chi-restraints excluded: chain K residue 90 ASN Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain L residue 136 GLU Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 124 LEU Chi-restraints excluded: chain M residue 126 ILE Chi-restraints excluded: chain M residue 132 THR Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain O residue 80 GLU Chi-restraints excluded: chain O residue 93 ASP Chi-restraints excluded: chain O residue 103 VAL Chi-restraints excluded: chain P residue 5 ILE Chi-restraints excluded: chain P residue 13 MET Chi-restraints excluded: chain P residue 48 ILE Chi-restraints excluded: chain P residue 73 VAL Chi-restraints excluded: chain P residue 85 SER Chi-restraints excluded: chain P residue 104 THR Chi-restraints excluded: chain P residue 110 ILE Chi-restraints excluded: chain P residue 114 LEU Chi-restraints excluded: chain Q residue 95 LEU Chi-restraints excluded: chain R residue 26 ASP Chi-restraints excluded: chain R residue 38 VAL Chi-restraints excluded: chain R residue 60 LYS Chi-restraints excluded: chain S residue 34 ASP Chi-restraints excluded: chain S residue 67 ASP Chi-restraints excluded: chain S residue 81 SER Chi-restraints excluded: chain T residue 60 THR Chi-restraints excluded: chain T residue 68 LYS Chi-restraints excluded: chain T residue 69 ARG Chi-restraints excluded: chain T residue 73 ARG Chi-restraints excluded: chain T residue 92 ASN Chi-restraints excluded: chain U residue 8 ASP Chi-restraints excluded: chain U residue 15 THR Chi-restraints excluded: chain U residue 28 VAL Chi-restraints excluded: chain U residue 65 ILE Chi-restraints excluded: chain U residue 72 ILE Chi-restraints excluded: chain W residue 10 THR Chi-restraints excluded: chain W residue 76 ASN Chi-restraints excluded: chain X residue 25 THR Chi-restraints excluded: chain X residue 33 LEU Chi-restraints excluded: chain X residue 48 THR Chi-restraints excluded: chain Z residue 32 ILE Chi-restraints excluded: chain Z residue 48 ILE Chi-restraints excluded: chain Z residue 57 VAL Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain b residue 23 THR Chi-restraints excluded: chain b residue 32 LYS Chi-restraints excluded: chain c residue 29 THR Chi-restraints excluded: chain d residue 4 THR Chi-restraints excluded: chain d residue 24 THR Chi-restraints excluded: chain d residue 43 THR Chi-restraints excluded: chain e residue 38 THR Chi-restraints excluded: chain g residue 123 ASP Chi-restraints excluded: chain g residue 129 LEU Chi-restraints excluded: chain h residue 83 ASP Chi-restraints excluded: chain h residue 193 TYR Chi-restraints excluded: chain h residue 200 VAL Chi-restraints excluded: chain i residue 32 CYS Chi-restraints excluded: chain j residue 134 ILE Chi-restraints excluded: chain k residue 51 ILE Chi-restraints excluded: chain l residue 50 LEU Chi-restraints excluded: chain l residue 91 VAL Chi-restraints excluded: chain m residue 54 ASP Chi-restraints excluded: chain m residue 75 ILE Chi-restraints excluded: chain n residue 35 LEU Chi-restraints excluded: chain n residue 67 VAL Chi-restraints excluded: chain n residue 111 VAL Chi-restraints excluded: chain o residue 17 LEU Chi-restraints excluded: chain o residue 32 THR Chi-restraints excluded: chain o residue 52 LEU Chi-restraints excluded: chain o residue 57 VAL Chi-restraints excluded: chain p residue 32 VAL Chi-restraints excluded: chain p residue 86 VAL Chi-restraints excluded: chain p residue 97 ILE Chi-restraints excluded: chain q residue 16 VAL Chi-restraints excluded: chain q residue 35 THR Chi-restraints excluded: chain q residue 47 SER Chi-restraints excluded: chain q residue 74 LEU Chi-restraints excluded: chain q residue 90 LEU Chi-restraints excluded: chain r residue 49 SER Chi-restraints excluded: chain r residue 64 VAL Chi-restraints excluded: chain r residue 68 ASP Chi-restraints excluded: chain r residue 104 THR Chi-restraints excluded: chain s residue 37 SER Chi-restraints excluded: chain s residue 42 TRP Chi-restraints excluded: chain t residue 11 ILE Chi-restraints excluded: chain u residue 78 VAL Chi-restraints excluded: chain v residue 67 LEU Chi-restraints excluded: chain x residue 63 THR Chi-restraints excluded: chain H residue 79 PHE Chi-restraints excluded: chain A residue 331 GLU Chi-restraints excluded: chain A residue 342 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1027 random chunks: chunk 518 optimal weight: 0.1980 chunk 289 optimal weight: 20.0000 chunk 776 optimal weight: 0.0040 chunk 635 optimal weight: 10.0000 chunk 257 optimal weight: 10.0000 chunk 934 optimal weight: 6.9990 chunk 1009 optimal weight: 8.9990 chunk 832 optimal weight: 7.9990 chunk 926 optimal weight: 50.0000 chunk 318 optimal weight: 30.0000 chunk 749 optimal weight: 20.0000 overall best weight: 4.8398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 58 HIS B 60 GLN ** C 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 164 GLN ** E 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 2 GLN ** J 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 128 ASN K 5 GLN ** K 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 116 GLN ** P 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 18 GLN ** S 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 20 ASN e 28 ASN f 35 GLN ** g 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 122 GLN ** h 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 190 HIS i 36 GLN ** j 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 126 GLN q 6 GLN q 75 GLN r 105 ASN ** s 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 52 GLN ** x 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.2677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 158320 Z= 0.211 Angle : 0.647 13.786 236734 Z= 0.347 Chirality : 0.035 0.291 30127 Planarity : 0.006 0.130 12767 Dihedral : 24.577 179.415 78856 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 21.58 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.60 % Favored : 95.37 % Rotamer: Outliers : 4.01 % Allowed : 15.73 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.11), residues: 5784 helix: -0.19 (0.11), residues: 1969 sheet: -1.55 (0.15), residues: 1067 loop : -1.47 (0.11), residues: 2748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP P 31 HIS 0.010 0.001 HIS x 57 PHE 0.043 0.002 PHE A 127 TYR 0.025 0.002 TYR e 64 ARG 0.017 0.001 ARG w 43 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11568 Ramachandran restraints generated. 5784 Oldfield, 0 Emsley, 5784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11568 Ramachandran restraints generated. 5784 Oldfield, 0 Emsley, 5784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1546 residues out of total 4812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 193 poor density : 1353 time to evaluate : 6.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 96 TYR cc_start: 0.9214 (m-80) cc_final: 0.8481 (m-80) REVERT: B 100 GLU cc_start: 0.7680 (tm-30) cc_final: 0.7094 (tm-30) REVERT: B 161 TYR cc_start: 0.8898 (p90) cc_final: 0.8488 (p90) REVERT: B 229 ASP cc_start: 0.8797 (m-30) cc_final: 0.8566 (m-30) REVERT: B 251 GLN cc_start: 0.8766 (tp40) cc_final: 0.8515 (tm-30) REVERT: B 255 LYS cc_start: 0.9332 (tttm) cc_final: 0.8957 (tptm) REVERT: C 1 MET cc_start: 0.7867 (tpp) cc_final: 0.7617 (tpp) REVERT: C 149 ASN cc_start: 0.8444 (t0) cc_final: 0.7559 (t0) REVERT: C 186 LEU cc_start: 0.9448 (mt) cc_final: 0.8858 (mp) REVERT: D 1 MET cc_start: 0.8374 (tpt) cc_final: 0.8094 (tpt) REVERT: D 46 GLN cc_start: 0.9507 (mp10) cc_final: 0.9006 (mp10) REVERT: D 62 GLN cc_start: 0.8928 (tp40) cc_final: 0.8444 (tp40) REVERT: D 100 MET cc_start: 0.8695 (mtp) cc_final: 0.8404 (mtp) REVERT: D 115 GLN cc_start: 0.8368 (mm110) cc_final: 0.8044 (mm110) REVERT: D 136 GLN cc_start: 0.9385 (tp-100) cc_final: 0.9125 (tp-100) REVERT: E 7 TYR cc_start: 0.9373 (t80) cc_final: 0.9038 (t80) REVERT: E 26 MET cc_start: 0.8999 (mtp) cc_final: 0.8482 (mtt) REVERT: E 44 ILE cc_start: 0.9342 (OUTLIER) cc_final: 0.9123 (mt) REVERT: E 83 TYR cc_start: 0.9095 (m-10) cc_final: 0.8733 (m-80) REVERT: E 90 THR cc_start: 0.9571 (m) cc_final: 0.9126 (p) REVERT: E 96 MET cc_start: 0.9504 (ttp) cc_final: 0.9118 (ttp) REVERT: E 143 TYR cc_start: 0.9076 (t80) cc_final: 0.8764 (t80) REVERT: E 157 THR cc_start: 0.8220 (m) cc_final: 0.7711 (m) REVERT: F 60 ASP cc_start: 0.9046 (p0) cc_final: 0.8780 (p0) REVERT: F 101 ASN cc_start: 0.9292 (p0) cc_final: 0.8861 (p0) REVERT: F 147 ASP cc_start: 0.9167 (m-30) cc_final: 0.8901 (m-30) REVERT: G 1 MET cc_start: 0.9294 (tpp) cc_final: 0.8989 (tpp) REVERT: J 75 TYR cc_start: 0.9103 (m-80) cc_final: 0.8577 (m-10) REVERT: J 92 MET cc_start: 0.9286 (mmm) cc_final: 0.9069 (mtp) REVERT: J 102 GLU cc_start: 0.8439 (mt-10) cc_final: 0.8023 (mt-10) REVERT: J 131 ASN cc_start: 0.9236 (OUTLIER) cc_final: 0.8660 (p0) REVERT: J 141 ASP cc_start: 0.8682 (t0) cc_final: 0.8422 (t0) REVERT: K 1 MET cc_start: 0.8714 (ttm) cc_final: 0.7946 (ttm) REVERT: K 7 MET cc_start: 0.9129 (mmt) cc_final: 0.8675 (mmm) REVERT: K 23 LYS cc_start: 0.9308 (tppt) cc_final: 0.8720 (tptp) REVERT: K 29 HIS cc_start: 0.7645 (m90) cc_final: 0.7386 (m-70) REVERT: K 44 LYS cc_start: 0.9537 (mmtt) cc_final: 0.9309 (mmmm) REVERT: K 59 LYS cc_start: 0.9345 (mttp) cc_final: 0.8950 (mttp) REVERT: K 66 LYS cc_start: 0.9394 (ttmm) cc_final: 0.8960 (ttmm) REVERT: K 82 ASN cc_start: 0.8700 (m-40) cc_final: 0.8444 (m-40) REVERT: K 87 LEU cc_start: 0.9429 (mt) cc_final: 0.9206 (mt) REVERT: K 88 ASN cc_start: 0.8776 (t0) cc_final: 0.8518 (t0) REVERT: L 35 HIS cc_start: 0.8890 (OUTLIER) cc_final: 0.8145 (m90) REVERT: M 17 ASN cc_start: 0.8480 (t0) cc_final: 0.8259 (t0) REVERT: M 136 MET cc_start: 0.8164 (ppp) cc_final: 0.7769 (ppp) REVERT: N 9 GLN cc_start: 0.8380 (tt0) cc_final: 0.7938 (tt0) REVERT: N 40 LYS cc_start: 0.9440 (mttt) cc_final: 0.8742 (mttp) REVERT: N 48 VAL cc_start: 0.9750 (t) cc_final: 0.9375 (p) REVERT: N 57 THR cc_start: 0.9046 (m) cc_final: 0.8775 (p) REVERT: N 75 ILE cc_start: 0.9548 (mm) cc_final: 0.9228 (mm) REVERT: O 19 GLN cc_start: 0.9575 (tm130) cc_final: 0.9176 (tm-30) REVERT: O 108 ASP cc_start: 0.9270 (m-30) cc_final: 0.8974 (p0) REVERT: P 11 GLU cc_start: 0.8496 (pt0) cc_final: 0.8209 (pt0) REVERT: P 25 THR cc_start: 0.9145 (m) cc_final: 0.8778 (p) REVERT: P 29 LYS cc_start: 0.9711 (mttm) cc_final: 0.9428 (mmmm) REVERT: P 40 LEU cc_start: 0.9539 (tp) cc_final: 0.9321 (tp) REVERT: P 111 LYS cc_start: 0.9135 (ptpt) cc_final: 0.8892 (ptpp) REVERT: Q 32 TYR cc_start: 0.8885 (t80) cc_final: 0.8331 (t80) REVERT: Q 45 TYR cc_start: 0.8461 (m-10) cc_final: 0.8255 (m-80) REVERT: Q 97 ASP cc_start: 0.8811 (t70) cc_final: 0.8478 (t70) REVERT: Q 101 PHE cc_start: 0.8367 (m-80) cc_final: 0.7950 (m-10) REVERT: R 13 ARG cc_start: 0.8668 (tmm-80) cc_final: 0.8261 (ttt-90) REVERT: R 40 MET cc_start: 0.8809 (tpt) cc_final: 0.8539 (tpt) REVERT: R 86 GLN cc_start: 0.8443 (mm110) cc_final: 0.8214 (mm110) REVERT: R 95 ASP cc_start: 0.8377 (m-30) cc_final: 0.7915 (m-30) REVERT: R 97 LYS cc_start: 0.9506 (tppt) cc_final: 0.8590 (tptp) REVERT: S 40 ASN cc_start: 0.8892 (m-40) cc_final: 0.8623 (m-40) REVERT: S 46 LEU cc_start: 0.9621 (mt) cc_final: 0.9238 (mp) REVERT: S 95 ARG cc_start: 0.8777 (ttp80) cc_final: 0.8395 (ttp80) REVERT: T 92 ASN cc_start: 0.8626 (OUTLIER) cc_final: 0.8345 (t0) REVERT: U 4 LYS cc_start: 0.8892 (mttt) cc_final: 0.8391 (mttt) REVERT: V 7 GLU cc_start: 0.8722 (mp0) cc_final: 0.8465 (mp0) REVERT: V 48 MET cc_start: 0.9151 (tpt) cc_final: 0.8759 (tpt) REVERT: W 36 ILE cc_start: 0.9493 (mt) cc_final: 0.9271 (mt) REVERT: W 38 VAL cc_start: 0.9683 (t) cc_final: 0.9399 (p) REVERT: W 44 LYS cc_start: 0.9597 (ttmt) cc_final: 0.9194 (ttmm) REVERT: W 68 LYS cc_start: 0.9003 (tptp) cc_final: 0.8719 (tptp) REVERT: W 78 LYS cc_start: 0.8492 (mttt) cc_final: 0.8283 (mttt) REVERT: X 16 ASN cc_start: 0.9394 (m-40) cc_final: 0.8957 (t0) REVERT: X 23 ASN cc_start: 0.8930 (m110) cc_final: 0.8460 (m-40) REVERT: X 41 GLU cc_start: 0.8760 (tp30) cc_final: 0.8217 (tp30) REVERT: Y 11 VAL cc_start: 0.9487 (t) cc_final: 0.9158 (m) REVERT: Y 12 GLU cc_start: 0.8899 (pm20) cc_final: 0.8675 (pm20) REVERT: Y 25 GLN cc_start: 0.9573 (tt0) cc_final: 0.9267 (tm-30) REVERT: Y 30 MET cc_start: 0.9260 (mmp) cc_final: 0.8807 (mmm) REVERT: Y 44 LYS cc_start: 0.9522 (tttt) cc_final: 0.9241 (ttmm) REVERT: Z 3 LYS cc_start: 0.8486 (tppt) cc_final: 0.8274 (tppt) REVERT: Z 19 LYS cc_start: 0.8871 (mmtt) cc_final: 0.8604 (mmtt) REVERT: Z 21 LYS cc_start: 0.9521 (mttt) cc_final: 0.9183 (mttp) REVERT: b 36 GLU cc_start: 0.7440 (pt0) cc_final: 0.6997 (pt0) REVERT: b 46 ASP cc_start: 0.8478 (m-30) cc_final: 0.8273 (m-30) REVERT: d 2 LYS cc_start: 0.8879 (tttt) cc_final: 0.8397 (tttm) REVERT: d 22 MET cc_start: 0.9155 (mmm) cc_final: 0.8838 (tpp) REVERT: d 25 LYS cc_start: 0.8813 (ttmt) cc_final: 0.8600 (ttmt) REVERT: e 13 ARG cc_start: 0.9309 (mpt-90) cc_final: 0.9025 (mmt-90) REVERT: e 14 PHE cc_start: 0.9710 (m-80) cc_final: 0.9177 (m-10) REVERT: e 32 ILE cc_start: 0.8822 (mm) cc_final: 0.8594 (mm) REVERT: f 9 LYS cc_start: 0.9128 (mttt) cc_final: 0.8573 (mttm) REVERT: f 34 LYS cc_start: 0.9186 (ptmt) cc_final: 0.8586 (pttt) REVERT: f 35 GLN cc_start: 0.8915 (mt0) cc_final: 0.8647 (mt0) REVERT: g 27 MET cc_start: 0.9122 (mmm) cc_final: 0.8451 (mmm) REVERT: g 49 MET cc_start: 0.9670 (mtp) cc_final: 0.9296 (mtp) REVERT: g 96 TRP cc_start: 0.9115 (t-100) cc_final: 0.8884 (t-100) REVERT: g 120 GLN cc_start: 0.9532 (tt0) cc_final: 0.9226 (pp30) REVERT: g 213 TYR cc_start: 0.9420 (m-10) cc_final: 0.8925 (m-10) REVERT: h 29 PHE cc_start: 0.9224 (t80) cc_final: 0.8437 (t80) REVERT: h 42 TYR cc_start: 0.9294 (t80) cc_final: 0.9081 (t80) REVERT: h 129 MET cc_start: 0.7142 (mtt) cc_final: 0.6697 (ttt) REVERT: h 130 PHE cc_start: 0.9294 (p90) cc_final: 0.8740 (p90) REVERT: h 168 TYR cc_start: 0.7932 (m-80) cc_final: 0.7142 (m-80) REVERT: h 181 ASP cc_start: 0.9433 (t0) cc_final: 0.9078 (t0) REVERT: h 185 ASN cc_start: 0.9285 (t0) cc_final: 0.8917 (t0) REVERT: i 40 GLN cc_start: 0.8611 (tt0) cc_final: 0.8382 (tt0) REVERT: i 51 TYR cc_start: 0.9513 (t80) cc_final: 0.9216 (t80) REVERT: i 75 TYR cc_start: 0.9505 (m-80) cc_final: 0.8987 (m-80) REVERT: i 135 TYR cc_start: 0.9292 (t80) cc_final: 0.8874 (t80) REVERT: i 136 GLN cc_start: 0.9437 (mm-40) cc_final: 0.9089 (pm20) REVERT: i 182 PHE cc_start: 0.9339 (t80) cc_final: 0.9123 (t80) REVERT: j 14 LYS cc_start: 0.9128 (mmtm) cc_final: 0.8851 (mmtm) REVERT: j 23 LYS cc_start: 0.8637 (tttm) cc_final: 0.8308 (tttp) REVERT: j 31 PHE cc_start: 0.8863 (m-80) cc_final: 0.7847 (m-80) REVERT: j 138 ARG cc_start: 0.9559 (mtt90) cc_final: 0.9294 (ttm-80) REVERT: j 142 ASP cc_start: 0.9458 (t70) cc_final: 0.9206 (t0) REVERT: k 17 GLN cc_start: 0.8798 (tm-30) cc_final: 0.8349 (tm-30) REVERT: k 21 MET cc_start: 0.9194 (mtm) cc_final: 0.8243 (mtm) REVERT: k 24 ARG cc_start: 0.9012 (ttp-110) cc_final: 0.8435 (ptt-90) REVERT: k 25 TYR cc_start: 0.9676 (m-10) cc_final: 0.9437 (m-10) REVERT: k 80 PHE cc_start: 0.9408 (m-80) cc_final: 0.8985 (m-80) REVERT: k 87 SER cc_start: 0.8849 (p) cc_final: 0.8148 (m) REVERT: k 88 MET cc_start: 0.7740 (tmm) cc_final: 0.7496 (tmm) REVERT: l 31 MET cc_start: 0.8978 (ttp) cc_final: 0.8644 (ttp) REVERT: l 116 MET cc_start: 0.9353 (tpp) cc_final: 0.9102 (mpp) REVERT: l 140 ASP cc_start: 0.9532 (m-30) cc_final: 0.9178 (p0) REVERT: m 3 MET cc_start: 0.9116 (tpp) cc_final: 0.8796 (tpp) REVERT: m 10 MET cc_start: 0.9113 (tmm) cc_final: 0.8587 (tmm) REVERT: m 80 ARG cc_start: 0.9472 (mtm110) cc_final: 0.9227 (mtm110) REVERT: m 124 GLU cc_start: 0.8936 (tt0) cc_final: 0.8167 (tm-30) REVERT: m 126 ILE cc_start: 0.9672 (mt) cc_final: 0.8689 (mt) REVERT: n 38 TYR cc_start: 0.7683 (t80) cc_final: 0.7470 (t80) REVERT: n 39 PHE cc_start: 0.9214 (m-80) cc_final: 0.8722 (m-80) REVERT: n 48 VAL cc_start: 0.9490 (m) cc_final: 0.9218 (p) REVERT: n 57 MET cc_start: 0.9246 (mtp) cc_final: 0.8322 (tmm) REVERT: n 60 LYS cc_start: 0.9506 (tppt) cc_final: 0.9205 (mmtm) REVERT: n 88 MET cc_start: 0.9075 (mmm) cc_final: 0.8786 (mmm) REVERT: n 89 GLU cc_start: 0.9673 (tp30) cc_final: 0.8873 (tp30) REVERT: o 46 LYS cc_start: 0.9201 (mttt) cc_final: 0.8726 (mtpp) REVERT: o 53 ILE cc_start: 0.9374 (pt) cc_final: 0.9050 (pt) REVERT: o 63 ASP cc_start: 0.7954 (m-30) cc_final: 0.7584 (m-30) REVERT: o 65 TYR cc_start: 0.9105 (m-80) cc_final: 0.8897 (m-80) REVERT: o 66 GLU cc_start: 0.9115 (pt0) cc_final: 0.8018 (pm20) REVERT: o 88 MET cc_start: 0.9418 (ptm) cc_final: 0.9132 (ptt) REVERT: o 97 ASP cc_start: 0.7965 (t0) cc_final: 0.7610 (t0) REVERT: p 83 GLU cc_start: 0.9011 (pt0) cc_final: 0.8584 (pm20) REVERT: p 85 MET cc_start: 0.9137 (mtp) cc_final: 0.8762 (ptp) REVERT: p 87 LYS cc_start: 0.9247 (ttmm) cc_final: 0.8996 (mtmt) REVERT: q 25 GLU cc_start: 0.8844 (OUTLIER) cc_final: 0.8215 (mp0) REVERT: q 29 GLN cc_start: 0.9286 (mp10) cc_final: 0.8365 (mp10) REVERT: q 38 TYR cc_start: 0.8496 (p90) cc_final: 0.8256 (p90) REVERT: q 59 ASN cc_start: 0.9100 (p0) cc_final: 0.8140 (p0) REVERT: q 61 PHE cc_start: 0.9309 (m-10) cc_final: 0.8891 (m-80) REVERT: q 66 TYR cc_start: 0.9128 (t80) cc_final: 0.8919 (t80) REVERT: q 67 ILE cc_start: 0.8521 (mt) cc_final: 0.8165 (mp) REVERT: q 96 HIS cc_start: 0.9110 (m90) cc_final: 0.8892 (m-70) REVERT: q 117 TYR cc_start: 0.9212 (m-80) cc_final: 0.8571 (m-80) REVERT: r 8 ASN cc_start: 0.8646 (t0) cc_final: 0.8344 (t0) REVERT: r 13 LYS cc_start: 0.9473 (mttt) cc_final: 0.9136 (tppt) REVERT: r 23 TYR cc_start: 0.9146 (t80) cc_final: 0.8441 (t80) REVERT: r 42 ASP cc_start: 0.9354 (p0) cc_final: 0.8923 (t0) REVERT: r 69 LEU cc_start: 0.9157 (tp) cc_final: 0.8732 (tp) REVERT: r 82 ASP cc_start: 0.9356 (m-30) cc_final: 0.8789 (p0) REVERT: r 100 GLN cc_start: 0.8493 (mp10) cc_final: 0.7913 (mp10) REVERT: r 105 ASN cc_start: 0.8495 (OUTLIER) cc_final: 0.7599 (t0) REVERT: r 110 LYS cc_start: 0.8638 (mtmt) cc_final: 0.8126 (mtpt) REVERT: s 6 MET cc_start: 0.9168 (mmm) cc_final: 0.8917 (mmt) REVERT: s 33 ASP cc_start: 0.9131 (t0) cc_final: 0.8729 (t70) REVERT: s 40 ASP cc_start: 0.9075 (m-30) cc_final: 0.8753 (m-30) REVERT: s 42 TRP cc_start: 0.9266 (OUTLIER) cc_final: 0.8772 (t60) REVERT: s 62 ASN cc_start: 0.9468 (m-40) cc_final: 0.9248 (m-40) REVERT: s 79 LEU cc_start: 0.8262 (OUTLIER) cc_final: 0.7910 (mt) REVERT: s 82 ILE cc_start: 0.9363 (mt) cc_final: 0.9071 (tt) REVERT: s 86 GLU cc_start: 0.8988 (mt-10) cc_final: 0.8657 (mt-10) REVERT: t 2 SER cc_start: 0.6958 (m) cc_final: 0.6724 (m) REVERT: t 14 GLU cc_start: 0.8609 (pt0) cc_final: 0.8370 (pt0) REVERT: t 18 ASP cc_start: 0.9355 (m-30) cc_final: 0.8435 (p0) REVERT: t 37 ASN cc_start: 0.9297 (m-40) cc_final: 0.9009 (p0) REVERT: t 43 PHE cc_start: 0.9270 (m-80) cc_final: 0.8679 (m-80) REVERT: t 48 LYS cc_start: 0.8925 (mmtm) cc_final: 0.8508 (mmtt) REVERT: t 59 MET cc_start: 0.9331 (mtt) cc_final: 0.8908 (mmp) REVERT: t 62 GLN cc_start: 0.8737 (OUTLIER) cc_final: 0.7869 (mp10) REVERT: t 70 LEU cc_start: 0.9411 (OUTLIER) cc_final: 0.9203 (tt) REVERT: u 1 MET cc_start: 0.8196 (pmt) cc_final: 0.7584 (tpt) REVERT: u 34 GLU cc_start: 0.9345 (tm-30) cc_final: 0.8823 (tm-30) REVERT: u 48 GLU cc_start: 0.8814 (tt0) cc_final: 0.8596 (tt0) REVERT: u 53 ASP cc_start: 0.9297 (t0) cc_final: 0.9063 (t0) REVERT: v 31 HIS cc_start: 0.9229 (t-90) cc_final: 0.8577 (t-90) REVERT: v 39 LYS cc_start: 0.9461 (mtmm) cc_final: 0.9064 (mtmm) REVERT: x 15 LEU cc_start: 0.9495 (tt) cc_final: 0.9141 (mt) REVERT: x 44 MET cc_start: 0.9288 (mtt) cc_final: 0.8629 (ptp) REVERT: y 4 ILE cc_start: 0.8412 (mt) cc_final: 0.8154 (mp) REVERT: y 18 ARG cc_start: 0.9540 (ttp80) cc_final: 0.9184 (ttp80) REVERT: y 19 LYS cc_start: 0.9728 (mttt) cc_final: 0.9289 (ptpp) REVERT: y 25 ARG cc_start: 0.9271 (mtm-85) cc_final: 0.8837 (ptp-170) REVERT: y 28 MET cc_start: 0.9429 (tmm) cc_final: 0.8846 (ppp) REVERT: y 59 ASP cc_start: 0.9042 (m-30) cc_final: 0.8068 (t0) REVERT: z 34 ARG cc_start: 0.8789 (ttp80) cc_final: 0.8475 (ttp-110) REVERT: z 36 GLU cc_start: 0.8082 (pt0) cc_final: 0.7814 (pt0) REVERT: z 39 GLU cc_start: 0.8166 (tt0) cc_final: 0.6867 (tm-30) REVERT: z 44 GLU cc_start: 0.9080 (tt0) cc_final: 0.8775 (tp30) REVERT: z 54 LYS cc_start: 0.9205 (tttt) cc_final: 0.8729 (tttt) REVERT: z 58 LYS cc_start: 0.9022 (pttt) cc_final: 0.8460 (pttm) REVERT: H 79 PHE cc_start: 0.8139 (p90) cc_final: 0.7662 (p90) REVERT: A 178 GLU cc_start: 0.6988 (OUTLIER) cc_final: 0.6182 (pp20) REVERT: A 310 TYR cc_start: 0.9341 (m-10) cc_final: 0.8999 (m-10) REVERT: A 316 ARG cc_start: 0.9438 (ttp-170) cc_final: 0.9148 (ttp80) outliers start: 193 outliers final: 126 residues processed: 1433 average time/residue: 1.3178 time to fit residues: 3322.0763 Evaluate side-chains 1318 residues out of total 4812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 1181 time to evaluate : 5.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 SER Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 264 ASP Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 176 ASP Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 90 GLN Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain E residue 138 PHE Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 32 GLU Chi-restraints excluded: chain F residue 77 ILE Chi-restraints excluded: chain F residue 166 ASP Chi-restraints excluded: chain G residue 41 LYS Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain J residue 9 GLU Chi-restraints excluded: chain J residue 109 LEU Chi-restraints excluded: chain J residue 131 ASN Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 90 ASN Chi-restraints excluded: chain K residue 107 LEU Chi-restraints excluded: chain L residue 35 HIS Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain M residue 42 THR Chi-restraints excluded: chain M residue 124 LEU Chi-restraints excluded: chain N residue 6 SER Chi-restraints excluded: chain N residue 18 GLN Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 48 LEU Chi-restraints excluded: chain O residue 53 THR Chi-restraints excluded: chain O residue 78 VAL Chi-restraints excluded: chain O residue 89 ASP Chi-restraints excluded: chain O residue 93 ASP Chi-restraints excluded: chain P residue 5 ILE Chi-restraints excluded: chain P residue 13 MET Chi-restraints excluded: chain P residue 48 ILE Chi-restraints excluded: chain P residue 60 THR Chi-restraints excluded: chain P residue 85 SER Chi-restraints excluded: chain P residue 110 ILE Chi-restraints excluded: chain Q residue 104 VAL Chi-restraints excluded: chain R residue 38 VAL Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain R residue 53 PHE Chi-restraints excluded: chain S residue 67 ASP Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain S residue 81 SER Chi-restraints excluded: chain T residue 68 LYS Chi-restraints excluded: chain T residue 69 ARG Chi-restraints excluded: chain T residue 73 ARG Chi-restraints excluded: chain T residue 92 ASN Chi-restraints excluded: chain U residue 8 ASP Chi-restraints excluded: chain U residue 12 ILE Chi-restraints excluded: chain U residue 15 THR Chi-restraints excluded: chain U residue 28 VAL Chi-restraints excluded: chain U residue 37 GLU Chi-restraints excluded: chain U residue 65 ILE Chi-restraints excluded: chain U residue 72 ILE Chi-restraints excluded: chain W residue 10 THR Chi-restraints excluded: chain W residue 58 THR Chi-restraints excluded: chain W residue 76 ASN Chi-restraints excluded: chain X residue 33 LEU Chi-restraints excluded: chain Z residue 57 VAL Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain b residue 23 THR Chi-restraints excluded: chain b residue 32 LYS Chi-restraints excluded: chain c residue 29 THR Chi-restraints excluded: chain d residue 24 THR Chi-restraints excluded: chain d residue 42 LEU Chi-restraints excluded: chain d residue 43 THR Chi-restraints excluded: chain e residue 31 HIS Chi-restraints excluded: chain f residue 22 VAL Chi-restraints excluded: chain g residue 123 ASP Chi-restraints excluded: chain g residue 129 LEU Chi-restraints excluded: chain h residue 193 TYR Chi-restraints excluded: chain h residue 200 VAL Chi-restraints excluded: chain i residue 32 CYS Chi-restraints excluded: chain i residue 174 ASP Chi-restraints excluded: chain i residue 181 THR Chi-restraints excluded: chain j residue 30 ILE Chi-restraints excluded: chain j residue 130 SER Chi-restraints excluded: chain j residue 134 ILE Chi-restraints excluded: chain j residue 144 LEU Chi-restraints excluded: chain k residue 51 ILE Chi-restraints excluded: chain l residue 50 LEU Chi-restraints excluded: chain l residue 91 VAL Chi-restraints excluded: chain m residue 27 MET Chi-restraints excluded: chain m residue 38 ASN Chi-restraints excluded: chain m residue 54 ASP Chi-restraints excluded: chain n residue 35 LEU Chi-restraints excluded: chain n residue 79 ILE Chi-restraints excluded: chain o residue 17 LEU Chi-restraints excluded: chain o residue 32 THR Chi-restraints excluded: chain o residue 52 LEU Chi-restraints excluded: chain o residue 57 VAL Chi-restraints excluded: chain o residue 98 VAL Chi-restraints excluded: chain p residue 32 VAL Chi-restraints excluded: chain p residue 97 ILE Chi-restraints excluded: chain q residue 16 VAL Chi-restraints excluded: chain q residue 25 GLU Chi-restraints excluded: chain q residue 90 LEU Chi-restraints excluded: chain r residue 55 THR Chi-restraints excluded: chain r residue 64 VAL Chi-restraints excluded: chain r residue 68 ASP Chi-restraints excluded: chain r residue 74 SER Chi-restraints excluded: chain r residue 105 ASN Chi-restraints excluded: chain s residue 37 SER Chi-restraints excluded: chain s residue 38 ASP Chi-restraints excluded: chain s residue 42 TRP Chi-restraints excluded: chain s residue 48 LEU Chi-restraints excluded: chain s residue 79 LEU Chi-restraints excluded: chain t residue 4 SER Chi-restraints excluded: chain t residue 11 ILE Chi-restraints excluded: chain t residue 60 VAL Chi-restraints excluded: chain t residue 62 GLN Chi-restraints excluded: chain t residue 70 LEU Chi-restraints excluded: chain u residue 78 VAL Chi-restraints excluded: chain v residue 67 LEU Chi-restraints excluded: chain v residue 79 VAL Chi-restraints excluded: chain x residue 13 LEU Chi-restraints excluded: chain y residue 66 LEU Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 178 GLU Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 328 ARG Chi-restraints excluded: chain A residue 331 GLU Chi-restraints excluded: chain A residue 348 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1027 random chunks: chunk 923 optimal weight: 20.0000 chunk 702 optimal weight: 6.9990 chunk 484 optimal weight: 0.9990 chunk 103 optimal weight: 20.0000 chunk 445 optimal weight: 30.0000 chunk 627 optimal weight: 5.9990 chunk 937 optimal weight: 6.9990 chunk 992 optimal weight: 20.0000 chunk 489 optimal weight: 8.9990 chunk 888 optimal weight: 50.0000 chunk 267 optimal weight: 10.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 60 GLN ** C 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 36 GLN C 134 HIS ** E 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 43 ASN ** J 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 128 ASN K 5 GLN ** K 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 4 GLN b 6 ASN ** d 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 170 HIS h 19 ASN ** h 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 190 HIS i 36 GLN ** j 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 4 GLN ** m 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 37 GLN n 126 GLN ** p 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 75 GLN t 28 GLN ** t 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 51 ASN ** x 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.2959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 158320 Z= 0.240 Angle : 0.643 13.826 236734 Z= 0.344 Chirality : 0.035 0.270 30127 Planarity : 0.006 0.128 12767 Dihedral : 24.489 179.640 78854 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 23.84 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.79 % Favored : 95.18 % Rotamer: Outliers : 4.55 % Allowed : 17.56 % Favored : 77.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.11), residues: 5784 helix: 0.24 (0.12), residues: 1966 sheet: -1.40 (0.15), residues: 1076 loop : -1.36 (0.11), residues: 2742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP s 42 HIS 0.008 0.001 HIS t 46 PHE 0.029 0.002 PHE P 59 TYR 0.021 0.002 TYR i 76 ARG 0.010 0.001 ARG T 69 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11568 Ramachandran restraints generated. 5784 Oldfield, 0 Emsley, 5784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11568 Ramachandran restraints generated. 5784 Oldfield, 0 Emsley, 5784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1481 residues out of total 4812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 219 poor density : 1262 time to evaluate : 6.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 96 TYR cc_start: 0.9181 (m-80) cc_final: 0.8903 (m-80) REVERT: B 225 MET cc_start: 0.9038 (mmm) cc_final: 0.8688 (mmm) REVERT: B 229 ASP cc_start: 0.8721 (m-30) cc_final: 0.8295 (m-30) REVERT: B 251 GLN cc_start: 0.8763 (tp40) cc_final: 0.8530 (tm-30) REVERT: B 255 LYS cc_start: 0.9345 (tttm) cc_final: 0.8953 (tptm) REVERT: C 1 MET cc_start: 0.7769 (tpp) cc_final: 0.7450 (tpp) REVERT: C 149 ASN cc_start: 0.8340 (t0) cc_final: 0.7528 (t0) REVERT: C 186 LEU cc_start: 0.9419 (mt) cc_final: 0.8974 (mp) REVERT: D 1 MET cc_start: 0.8256 (tpt) cc_final: 0.8006 (tpt) REVERT: D 46 GLN cc_start: 0.9543 (mp10) cc_final: 0.9018 (mp10) REVERT: D 62 GLN cc_start: 0.8927 (tp40) cc_final: 0.8420 (tp40) REVERT: D 115 GLN cc_start: 0.8368 (mm110) cc_final: 0.8052 (mm110) REVERT: D 136 GLN cc_start: 0.9369 (OUTLIER) cc_final: 0.9104 (tp-100) REVERT: E 7 TYR cc_start: 0.9396 (t80) cc_final: 0.8949 (t80) REVERT: E 26 MET cc_start: 0.9038 (mtp) cc_final: 0.8532 (mtt) REVERT: E 44 ILE cc_start: 0.9359 (OUTLIER) cc_final: 0.9123 (mt) REVERT: E 83 TYR cc_start: 0.9114 (m-10) cc_final: 0.8720 (m-10) REVERT: E 90 THR cc_start: 0.9522 (m) cc_final: 0.9001 (p) REVERT: E 96 MET cc_start: 0.9475 (ttp) cc_final: 0.9058 (ttp) REVERT: E 128 TYR cc_start: 0.8624 (t80) cc_final: 0.8273 (t80) REVERT: E 143 TYR cc_start: 0.9093 (t80) cc_final: 0.8741 (t80) REVERT: F 60 ASP cc_start: 0.9056 (p0) cc_final: 0.8743 (p0) REVERT: F 101 ASN cc_start: 0.9290 (p0) cc_final: 0.8864 (p0) REVERT: F 116 GLN cc_start: 0.8599 (tm-30) cc_final: 0.8283 (tm-30) REVERT: F 147 ASP cc_start: 0.9223 (m-30) cc_final: 0.8980 (m-30) REVERT: F 176 LYS cc_start: 0.4437 (OUTLIER) cc_final: 0.3221 (mttt) REVERT: G 1 MET cc_start: 0.9246 (tpp) cc_final: 0.8948 (tpp) REVERT: J 75 TYR cc_start: 0.9142 (m-80) cc_final: 0.8608 (m-10) REVERT: J 92 MET cc_start: 0.9219 (mmm) cc_final: 0.8643 (mmt) REVERT: J 99 ARG cc_start: 0.9085 (mmm-85) cc_final: 0.8765 (mmm-85) REVERT: J 102 GLU cc_start: 0.8369 (mt-10) cc_final: 0.7992 (mt-10) REVERT: J 108 MET cc_start: 0.9182 (mtt) cc_final: 0.8930 (mtp) REVERT: J 131 ASN cc_start: 0.9227 (OUTLIER) cc_final: 0.9015 (p0) REVERT: J 141 ASP cc_start: 0.8711 (t0) cc_final: 0.8421 (t0) REVERT: K 1 MET cc_start: 0.8630 (ttm) cc_final: 0.7856 (ttm) REVERT: K 4 GLU cc_start: 0.8078 (mm-30) cc_final: 0.7867 (mm-30) REVERT: K 7 MET cc_start: 0.9019 (mmt) cc_final: 0.8651 (mmm) REVERT: K 23 LYS cc_start: 0.9274 (tppt) cc_final: 0.8746 (tptp) REVERT: K 29 HIS cc_start: 0.7854 (OUTLIER) cc_final: 0.7518 (m-70) REVERT: K 44 LYS cc_start: 0.9573 (mmtt) cc_final: 0.9317 (mmmm) REVERT: K 59 LYS cc_start: 0.9202 (mttp) cc_final: 0.8937 (mttp) REVERT: K 82 ASN cc_start: 0.8729 (m-40) cc_final: 0.8414 (m-40) REVERT: K 87 LEU cc_start: 0.9354 (mt) cc_final: 0.9066 (mt) REVERT: K 88 ASN cc_start: 0.8868 (t0) cc_final: 0.8362 (t0) REVERT: K 112 PHE cc_start: 0.9337 (m-80) cc_final: 0.8976 (m-80) REVERT: L 35 HIS cc_start: 0.8899 (OUTLIER) cc_final: 0.8173 (m90) REVERT: M 17 ASN cc_start: 0.8518 (t0) cc_final: 0.8305 (t0) REVERT: M 45 GLN cc_start: 0.9363 (mt0) cc_final: 0.8928 (mm110) REVERT: M 96 ILE cc_start: 0.9830 (mm) cc_final: 0.9616 (mp) REVERT: M 119 LEU cc_start: 0.9702 (OUTLIER) cc_final: 0.9363 (mp) REVERT: N 9 GLN cc_start: 0.8516 (tt0) cc_final: 0.8123 (tt0) REVERT: N 40 LYS cc_start: 0.9462 (mttt) cc_final: 0.8782 (mttp) REVERT: N 57 THR cc_start: 0.9047 (m) cc_final: 0.8763 (p) REVERT: N 72 ASP cc_start: 0.8394 (t70) cc_final: 0.7717 (t0) REVERT: N 75 ILE cc_start: 0.9700 (mm) cc_final: 0.9444 (mm) REVERT: O 19 GLN cc_start: 0.9622 (tm130) cc_final: 0.9236 (tm-30) REVERT: O 85 LYS cc_start: 0.9303 (mmtm) cc_final: 0.8838 (mmmm) REVERT: O 108 ASP cc_start: 0.9272 (m-30) cc_final: 0.8671 (p0) REVERT: P 8 LEU cc_start: 0.9556 (mm) cc_final: 0.9293 (mm) REVERT: P 25 THR cc_start: 0.9037 (m) cc_final: 0.8607 (p) REVERT: P 29 LYS cc_start: 0.9726 (mttm) cc_final: 0.9475 (mmmm) REVERT: P 44 GLU cc_start: 0.8565 (tp30) cc_final: 0.8318 (mm-30) REVERT: P 111 LYS cc_start: 0.9159 (ptpt) cc_final: 0.8909 (ptpp) REVERT: P 114 LEU cc_start: 0.8766 (mt) cc_final: 0.8314 (mt) REVERT: Q 32 TYR cc_start: 0.8932 (t80) cc_final: 0.8431 (t80) REVERT: Q 52 GLN cc_start: 0.7894 (mt0) cc_final: 0.7444 (mt0) REVERT: Q 97 ASP cc_start: 0.8767 (t70) cc_final: 0.8450 (t70) REVERT: Q 101 PHE cc_start: 0.8400 (m-80) cc_final: 0.7921 (m-10) REVERT: R 85 LYS cc_start: 0.8978 (mtpp) cc_final: 0.8664 (mtpp) REVERT: R 86 GLN cc_start: 0.8410 (mm110) cc_final: 0.8058 (mm110) REVERT: R 95 ASP cc_start: 0.8680 (m-30) cc_final: 0.8386 (m-30) REVERT: S 40 ASN cc_start: 0.8960 (m-40) cc_final: 0.8682 (m-40) REVERT: S 46 LEU cc_start: 0.9618 (mt) cc_final: 0.9227 (mp) REVERT: S 86 MET cc_start: 0.8514 (tpp) cc_final: 0.8255 (tpp) REVERT: S 92 ARG cc_start: 0.9010 (tmm-80) cc_final: 0.8810 (ttp80) REVERT: S 95 ARG cc_start: 0.8732 (ttp80) cc_final: 0.8413 (ttp80) REVERT: T 92 ASN cc_start: 0.8552 (OUTLIER) cc_final: 0.8234 (t0) REVERT: U 4 LYS cc_start: 0.8917 (mttt) cc_final: 0.8433 (mttt) REVERT: V 40 ILE cc_start: 0.9455 (OUTLIER) cc_final: 0.8488 (mm) REVERT: V 48 MET cc_start: 0.9105 (tpt) cc_final: 0.8536 (tpt) REVERT: W 36 ILE cc_start: 0.9476 (mt) cc_final: 0.9254 (mt) REVERT: W 38 VAL cc_start: 0.9691 (t) cc_final: 0.9407 (p) REVERT: W 41 ARG cc_start: 0.9431 (mmt-90) cc_final: 0.9169 (mmt-90) REVERT: W 44 LYS cc_start: 0.9571 (ttmt) cc_final: 0.9177 (ttmm) REVERT: W 56 ASP cc_start: 0.9125 (p0) cc_final: 0.8892 (p0) REVERT: W 68 LYS cc_start: 0.8923 (tptp) cc_final: 0.8521 (tptp) REVERT: X 17 ASN cc_start: 0.8850 (m-40) cc_final: 0.8492 (m-40) REVERT: X 41 GLU cc_start: 0.8743 (tp30) cc_final: 0.8469 (tp30) REVERT: X 44 LYS cc_start: 0.9281 (mmmm) cc_final: 0.8907 (mmmm) REVERT: Y 12 GLU cc_start: 0.9062 (pm20) cc_final: 0.8793 (pm20) REVERT: Y 25 GLN cc_start: 0.9564 (tt0) cc_final: 0.9219 (tm-30) REVERT: Y 30 MET cc_start: 0.9229 (mmp) cc_final: 0.8897 (mmm) REVERT: Y 44 LYS cc_start: 0.9552 (tttt) cc_final: 0.9252 (ttmm) REVERT: Z 6 LYS cc_start: 0.9476 (mmmt) cc_final: 0.9133 (mmmt) REVERT: Z 21 LYS cc_start: 0.9543 (mttt) cc_final: 0.9093 (mmtm) REVERT: Z 49 ASN cc_start: 0.9503 (t0) cc_final: 0.9283 (t0) REVERT: b 36 GLU cc_start: 0.7628 (pt0) cc_final: 0.7075 (pt0) REVERT: b 46 ASP cc_start: 0.8565 (m-30) cc_final: 0.8301 (m-30) REVERT: d 1 MET cc_start: 0.7020 (mmm) cc_final: 0.6715 (mmm) REVERT: d 2 LYS cc_start: 0.8974 (tttt) cc_final: 0.8516 (tttm) REVERT: d 22 MET cc_start: 0.9173 (mmm) cc_final: 0.8836 (tpp) REVERT: d 25 LYS cc_start: 0.8816 (ttmt) cc_final: 0.8609 (ttmt) REVERT: e 13 ARG cc_start: 0.9291 (mpt-90) cc_final: 0.9044 (mmt-90) REVERT: e 14 PHE cc_start: 0.9731 (m-80) cc_final: 0.9213 (m-10) REVERT: e 32 ILE cc_start: 0.8894 (mm) cc_final: 0.8631 (mm) REVERT: e 40 ARG cc_start: 0.8787 (OUTLIER) cc_final: 0.8302 (ttt-90) REVERT: f 8 LYS cc_start: 0.8783 (mmmt) cc_final: 0.8156 (mmmt) REVERT: f 9 LYS cc_start: 0.9203 (mttt) cc_final: 0.8866 (mttm) REVERT: f 24 ARG cc_start: 0.8914 (mtt-85) cc_final: 0.8509 (mtt-85) REVERT: f 34 LYS cc_start: 0.9176 (ptmt) cc_final: 0.8974 (ptmt) REVERT: f 35 GLN cc_start: 0.8961 (mt0) cc_final: 0.8755 (mt0) REVERT: g 27 MET cc_start: 0.9147 (mmm) cc_final: 0.8482 (mmm) REVERT: g 49 MET cc_start: 0.9672 (mtp) cc_final: 0.9325 (mtp) REVERT: g 120 GLN cc_start: 0.9512 (tt0) cc_final: 0.9095 (pp30) REVERT: g 213 TYR cc_start: 0.9439 (m-10) cc_final: 0.8958 (m-10) REVERT: h 29 PHE cc_start: 0.9230 (t80) cc_final: 0.8355 (t80) REVERT: h 129 MET cc_start: 0.6987 (mtt) cc_final: 0.6521 (ttt) REVERT: h 130 PHE cc_start: 0.9406 (p90) cc_final: 0.9029 (p90) REVERT: h 168 TYR cc_start: 0.7832 (m-80) cc_final: 0.6749 (m-80) REVERT: h 181 ASP cc_start: 0.9449 (t0) cc_final: 0.9091 (t0) REVERT: h 185 ASN cc_start: 0.9238 (t0) cc_final: 0.8792 (t0) REVERT: i 40 GLN cc_start: 0.8597 (tt0) cc_final: 0.7491 (mt0) REVERT: i 51 TYR cc_start: 0.9566 (t80) cc_final: 0.9239 (t80) REVERT: i 75 TYR cc_start: 0.9493 (m-80) cc_final: 0.8943 (m-80) REVERT: i 124 MET cc_start: 0.8326 (tpp) cc_final: 0.8084 (tpp) REVERT: i 135 TYR cc_start: 0.9298 (t80) cc_final: 0.8945 (t80) REVERT: i 136 GLN cc_start: 0.9406 (mm-40) cc_final: 0.8999 (pm20) REVERT: i 164 GLN cc_start: 0.9503 (mm-40) cc_final: 0.9293 (mm110) REVERT: i 182 PHE cc_start: 0.9314 (t80) cc_final: 0.9050 (t80) REVERT: j 23 LYS cc_start: 0.8702 (tttm) cc_final: 0.8367 (tttp) REVERT: j 31 PHE cc_start: 0.8829 (m-80) cc_final: 0.7760 (m-80) REVERT: j 138 ARG cc_start: 0.9585 (mtt90) cc_final: 0.9278 (ttm-80) REVERT: j 142 ASP cc_start: 0.9484 (t70) cc_final: 0.9280 (t0) REVERT: k 17 GLN cc_start: 0.8808 (tm-30) cc_final: 0.8517 (tm-30) REVERT: k 21 MET cc_start: 0.9087 (mtm) cc_final: 0.8304 (mtm) REVERT: k 25 TYR cc_start: 0.9679 (m-10) cc_final: 0.9436 (m-10) REVERT: k 80 PHE cc_start: 0.9422 (m-80) cc_final: 0.9090 (m-80) REVERT: k 87 SER cc_start: 0.8899 (p) cc_final: 0.8194 (m) REVERT: l 26 PHE cc_start: 0.9809 (t80) cc_final: 0.9347 (t80) REVERT: l 28 ASN cc_start: 0.9648 (m110) cc_final: 0.9411 (m110) REVERT: l 31 MET cc_start: 0.8839 (ttp) cc_final: 0.8462 (ttp) REVERT: l 101 MET cc_start: 0.9445 (ttm) cc_final: 0.8881 (ttp) REVERT: l 140 ASP cc_start: 0.9489 (m-30) cc_final: 0.9132 (p0) REVERT: m 3 MET cc_start: 0.9158 (tpp) cc_final: 0.8891 (tpp) REVERT: m 10 MET cc_start: 0.9163 (tmm) cc_final: 0.8601 (tmm) REVERT: m 80 ARG cc_start: 0.9475 (mtm110) cc_final: 0.9189 (mtm110) REVERT: m 86 TYR cc_start: 0.8992 (m-10) cc_final: 0.8745 (m-80) REVERT: m 124 GLU cc_start: 0.9052 (tt0) cc_final: 0.8133 (tm-30) REVERT: m 126 ILE cc_start: 0.9663 (mt) cc_final: 0.8695 (mt) REVERT: n 43 THR cc_start: 0.9579 (p) cc_final: 0.9295 (p) REVERT: n 46 MET cc_start: 0.9032 (ppp) cc_final: 0.8763 (ppp) REVERT: n 48 VAL cc_start: 0.9366 (m) cc_final: 0.8987 (p) REVERT: n 53 GLU cc_start: 0.9285 (mt-10) cc_final: 0.8981 (mp0) REVERT: n 57 MET cc_start: 0.9244 (mtp) cc_final: 0.8381 (tmm) REVERT: n 60 LYS cc_start: 0.9487 (tppt) cc_final: 0.9171 (mmtm) REVERT: n 89 GLU cc_start: 0.9507 (tp30) cc_final: 0.8849 (tp30) REVERT: n 127 PHE cc_start: 0.9373 (t80) cc_final: 0.8734 (t80) REVERT: o 46 LYS cc_start: 0.9218 (mttt) cc_final: 0.8802 (mtpp) REVERT: o 53 ILE cc_start: 0.9311 (pt) cc_final: 0.8897 (pt) REVERT: o 63 ASP cc_start: 0.7988 (m-30) cc_final: 0.7567 (m-30) REVERT: o 66 GLU cc_start: 0.9059 (pt0) cc_final: 0.7708 (pm20) REVERT: o 88 MET cc_start: 0.9359 (ptm) cc_final: 0.9066 (ptt) REVERT: p 83 GLU cc_start: 0.8924 (pt0) cc_final: 0.8714 (pm20) REVERT: p 87 LYS cc_start: 0.9204 (ttmm) cc_final: 0.8812 (mtmt) REVERT: p 94 GLU cc_start: 0.8738 (tp30) cc_final: 0.8502 (tp30) REVERT: p 100 LEU cc_start: 0.9640 (mt) cc_final: 0.9324 (pp) REVERT: q 25 GLU cc_start: 0.8992 (OUTLIER) cc_final: 0.8565 (mp0) REVERT: q 29 GLN cc_start: 0.8863 (mp10) cc_final: 0.8467 (mp10) REVERT: q 38 TYR cc_start: 0.8470 (p90) cc_final: 0.8239 (p90) REVERT: q 61 PHE cc_start: 0.9171 (m-10) cc_final: 0.8853 (m-80) REVERT: q 67 ILE cc_start: 0.8132 (mt) cc_final: 0.7731 (mp) REVERT: q 70 GLU cc_start: 0.8574 (mt-10) cc_final: 0.8312 (mm-30) REVERT: q 82 ILE cc_start: 0.9529 (mm) cc_final: 0.8934 (tp) REVERT: q 112 GLN cc_start: 0.6550 (mt0) cc_final: 0.6107 (mp10) REVERT: q 117 TYR cc_start: 0.9242 (m-80) cc_final: 0.8568 (m-80) REVERT: r 8 ASN cc_start: 0.8585 (t0) cc_final: 0.8165 (t0) REVERT: r 23 TYR cc_start: 0.9192 (t80) cc_final: 0.8481 (t80) REVERT: r 27 LYS cc_start: 0.9260 (tppt) cc_final: 0.9026 (tppt) REVERT: r 31 LYS cc_start: 0.9739 (mtmm) cc_final: 0.9452 (mtmm) REVERT: r 69 LEU cc_start: 0.9282 (tp) cc_final: 0.8939 (tp) REVERT: r 100 GLN cc_start: 0.8424 (mp10) cc_final: 0.7907 (mp10) REVERT: r 103 LYS cc_start: 0.8489 (tttt) cc_final: 0.7220 (tptt) REVERT: r 105 ASN cc_start: 0.8612 (t0) cc_final: 0.7841 (t0) REVERT: s 6 MET cc_start: 0.9342 (mmm) cc_final: 0.8951 (mmt) REVERT: s 33 ASP cc_start: 0.9226 (t0) cc_final: 0.8779 (t70) REVERT: s 40 ASP cc_start: 0.9206 (m-30) cc_final: 0.8949 (m-30) REVERT: s 62 ASN cc_start: 0.9438 (m-40) cc_final: 0.9201 (m-40) REVERT: s 82 ILE cc_start: 0.9384 (mt) cc_final: 0.9157 (tt) REVERT: s 86 GLU cc_start: 0.8995 (mt-10) cc_final: 0.8665 (mt-10) REVERT: t 2 SER cc_start: 0.7117 (m) cc_final: 0.6868 (m) REVERT: t 14 GLU cc_start: 0.8626 (pt0) cc_final: 0.8349 (pt0) REVERT: t 18 ASP cc_start: 0.9368 (m-30) cc_final: 0.8441 (p0) REVERT: t 43 PHE cc_start: 0.9261 (m-80) cc_final: 0.8722 (m-80) REVERT: t 48 LYS cc_start: 0.8967 (mmtm) cc_final: 0.8553 (mmtt) REVERT: t 59 MET cc_start: 0.9293 (mtt) cc_final: 0.8933 (mmp) REVERT: t 62 GLN cc_start: 0.8635 (OUTLIER) cc_final: 0.8150 (pt0) REVERT: t 71 LYS cc_start: 0.9327 (OUTLIER) cc_final: 0.9006 (ttmt) REVERT: t 78 TYR cc_start: 0.9482 (t80) cc_final: 0.9101 (t80) REVERT: u 1 MET cc_start: 0.8184 (pmt) cc_final: 0.7575 (tpt) REVERT: u 32 PHE cc_start: 0.9446 (p90) cc_final: 0.9241 (p90) REVERT: u 34 GLU cc_start: 0.9324 (tm-30) cc_final: 0.8899 (tm-30) REVERT: u 51 ARG cc_start: 0.8516 (ttp-110) cc_final: 0.8008 (ptp90) REVERT: u 53 ASP cc_start: 0.9249 (t0) cc_final: 0.9007 (t0) REVERT: v 9 GLN cc_start: 0.7712 (mt0) cc_final: 0.6837 (tp-100) REVERT: v 31 HIS cc_start: 0.9250 (t-90) cc_final: 0.8589 (t-90) REVERT: v 69 LYS cc_start: 0.9212 (ttpt) cc_final: 0.8989 (mtpt) REVERT: w 30 LYS cc_start: 0.9537 (mttp) cc_final: 0.9334 (ptpp) REVERT: x 15 LEU cc_start: 0.9476 (tt) cc_final: 0.9153 (mt) REVERT: x 44 MET cc_start: 0.9198 (mtt) cc_final: 0.8774 (ptp) REVERT: y 4 ILE cc_start: 0.8432 (mt) cc_final: 0.8174 (mp) REVERT: y 21 ASN cc_start: 0.9489 (m-40) cc_final: 0.9185 (t0) REVERT: y 31 PHE cc_start: 0.9451 (m-80) cc_final: 0.9199 (m-10) REVERT: y 48 GLN cc_start: 0.9500 (mm-40) cc_final: 0.9222 (mm-40) REVERT: y 59 ASP cc_start: 0.9011 (m-30) cc_final: 0.8057 (t0) REVERT: y 66 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.7983 (mm) REVERT: y 84 ASN cc_start: 0.9234 (m-40) cc_final: 0.8672 (p0) REVERT: z 34 ARG cc_start: 0.8818 (ttp80) cc_final: 0.8460 (ttp-110) REVERT: z 39 GLU cc_start: 0.8244 (tt0) cc_final: 0.6866 (tm-30) REVERT: z 54 LYS cc_start: 0.9292 (tttt) cc_final: 0.8900 (tttt) REVERT: z 58 LYS cc_start: 0.9049 (pttt) cc_final: 0.8644 (pttp) REVERT: H 79 PHE cc_start: 0.8205 (p90) cc_final: 0.7614 (p90) REVERT: A 316 ARG cc_start: 0.9324 (ttp-170) cc_final: 0.9055 (ttp80) outliers start: 219 outliers final: 147 residues processed: 1366 average time/residue: 1.3903 time to fit residues: 3297.6072 Evaluate side-chains 1345 residues out of total 4812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 1184 time to evaluate : 6.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 38 SER Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 264 ASP Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 176 ASP Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 90 GLN Chi-restraints excluded: chain D residue 136 GLN Chi-restraints excluded: chain E residue 17 MET Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 32 GLU Chi-restraints excluded: chain F residue 42 GLU Chi-restraints excluded: chain F residue 155 GLU Chi-restraints excluded: chain F residue 166 ASP Chi-restraints excluded: chain F residue 176 LYS Chi-restraints excluded: chain G residue 41 LYS Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain J residue 9 GLU Chi-restraints excluded: chain J residue 109 LEU Chi-restraints excluded: chain J residue 118 MET Chi-restraints excluded: chain J residue 131 ASN Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 29 HIS Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 90 ASN Chi-restraints excluded: chain K residue 107 LEU Chi-restraints excluded: chain L residue 35 HIS Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain L residue 122 VAL Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 42 THR Chi-restraints excluded: chain M residue 119 LEU Chi-restraints excluded: chain M residue 124 LEU Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain N residue 6 SER Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain O residue 53 THR Chi-restraints excluded: chain O residue 89 ASP Chi-restraints excluded: chain O residue 93 ASP Chi-restraints excluded: chain P residue 48 ILE Chi-restraints excluded: chain P residue 60 THR Chi-restraints excluded: chain P residue 85 SER Chi-restraints excluded: chain P residue 110 ILE Chi-restraints excluded: chain Q residue 20 GLN Chi-restraints excluded: chain Q residue 104 VAL Chi-restraints excluded: chain R residue 38 VAL Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 67 ASP Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain S residue 81 SER Chi-restraints excluded: chain T residue 60 THR Chi-restraints excluded: chain T residue 68 LYS Chi-restraints excluded: chain T residue 73 ARG Chi-restraints excluded: chain T residue 92 ASN Chi-restraints excluded: chain U residue 8 ASP Chi-restraints excluded: chain U residue 12 ILE Chi-restraints excluded: chain U residue 15 THR Chi-restraints excluded: chain U residue 28 VAL Chi-restraints excluded: chain U residue 37 GLU Chi-restraints excluded: chain U residue 65 ILE Chi-restraints excluded: chain U residue 72 ILE Chi-restraints excluded: chain V residue 40 ILE Chi-restraints excluded: chain W residue 10 THR Chi-restraints excluded: chain W residue 58 THR Chi-restraints excluded: chain W residue 76 ASN Chi-restraints excluded: chain X residue 33 LEU Chi-restraints excluded: chain X residue 59 ILE Chi-restraints excluded: chain Z residue 32 ILE Chi-restraints excluded: chain Z residue 37 GLU Chi-restraints excluded: chain Z residue 57 VAL Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain b residue 23 THR Chi-restraints excluded: chain b residue 32 LYS Chi-restraints excluded: chain c residue 29 THR Chi-restraints excluded: chain d residue 24 THR Chi-restraints excluded: chain d residue 42 LEU Chi-restraints excluded: chain d residue 43 THR Chi-restraints excluded: chain e residue 6 THR Chi-restraints excluded: chain e residue 38 THR Chi-restraints excluded: chain e residue 40 ARG Chi-restraints excluded: chain f residue 22 VAL Chi-restraints excluded: chain g residue 123 ASP Chi-restraints excluded: chain g residue 129 LEU Chi-restraints excluded: chain h residue 102 ASN Chi-restraints excluded: chain h residue 162 ILE Chi-restraints excluded: chain h residue 193 TYR Chi-restraints excluded: chain h residue 200 VAL Chi-restraints excluded: chain i residue 32 CYS Chi-restraints excluded: chain i residue 174 ASP Chi-restraints excluded: chain i residue 190 ASP Chi-restraints excluded: chain j residue 30 ILE Chi-restraints excluded: chain j residue 37 THR Chi-restraints excluded: chain j residue 134 ILE Chi-restraints excluded: chain j residue 144 LEU Chi-restraints excluded: chain j residue 164 ILE Chi-restraints excluded: chain k residue 51 ILE Chi-restraints excluded: chain k residue 73 GLU Chi-restraints excluded: chain l residue 50 LEU Chi-restraints excluded: chain l residue 91 VAL Chi-restraints excluded: chain l residue 106 GLU Chi-restraints excluded: chain m residue 27 MET Chi-restraints excluded: chain m residue 54 ASP Chi-restraints excluded: chain m residue 75 ILE Chi-restraints excluded: chain n residue 30 ILE Chi-restraints excluded: chain n residue 35 LEU Chi-restraints excluded: chain n residue 37 GLN Chi-restraints excluded: chain n residue 111 VAL Chi-restraints excluded: chain n residue 115 LYS Chi-restraints excluded: chain o residue 17 LEU Chi-restraints excluded: chain o residue 32 THR Chi-restraints excluded: chain o residue 52 LEU Chi-restraints excluded: chain o residue 57 VAL Chi-restraints excluded: chain o residue 71 LEU Chi-restraints excluded: chain o residue 74 VAL Chi-restraints excluded: chain p residue 30 THR Chi-restraints excluded: chain p residue 97 ILE Chi-restraints excluded: chain q residue 16 VAL Chi-restraints excluded: chain q residue 25 GLU Chi-restraints excluded: chain q residue 90 LEU Chi-restraints excluded: chain r residue 49 SER Chi-restraints excluded: chain r residue 55 THR Chi-restraints excluded: chain r residue 64 VAL Chi-restraints excluded: chain r residue 74 SER Chi-restraints excluded: chain r residue 104 THR Chi-restraints excluded: chain s residue 37 SER Chi-restraints excluded: chain s residue 38 ASP Chi-restraints excluded: chain s residue 48 LEU Chi-restraints excluded: chain s residue 54 ASP Chi-restraints excluded: chain t residue 4 SER Chi-restraints excluded: chain t residue 11 ILE Chi-restraints excluded: chain t residue 62 GLN Chi-restraints excluded: chain t residue 67 LEU Chi-restraints excluded: chain t residue 71 LYS Chi-restraints excluded: chain u residue 78 VAL Chi-restraints excluded: chain v residue 67 LEU Chi-restraints excluded: chain v residue 79 VAL Chi-restraints excluded: chain x residue 13 LEU Chi-restraints excluded: chain x residue 63 THR Chi-restraints excluded: chain y residue 66 LEU Chi-restraints excluded: chain A residue 330 ASP Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 348 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1027 random chunks: chunk 826 optimal weight: 10.0000 chunk 563 optimal weight: 8.9990 chunk 14 optimal weight: 20.0000 chunk 739 optimal weight: 0.9980 chunk 409 optimal weight: 30.0000 chunk 847 optimal weight: 40.0000 chunk 686 optimal weight: 9.9990 chunk 1 optimal weight: 10.0000 chunk 506 optimal weight: 8.9990 chunk 891 optimal weight: 20.0000 chunk 250 optimal weight: 10.0000 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 60 GLN ** C 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 22 GLN ** J 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 128 ASN ** J 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 22 GLN ** M 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 17 ASN ** Y 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 39 GLN b 42 HIS ** d 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 190 HIS i 36 GLN ** j 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 75 GLN t 28 GLN ** t 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 79 ASN ** x 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.3143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.095 158320 Z= 0.289 Angle : 0.661 13.770 236734 Z= 0.352 Chirality : 0.035 0.303 30127 Planarity : 0.006 0.129 12767 Dihedral : 24.475 179.655 78854 Min Nonbonded Distance : 1.780 Molprobity Statistics. All-atom Clashscore : 25.82 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.36 % Favored : 94.61 % Rotamer: Outliers : 5.17 % Allowed : 17.79 % Favored : 77.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.11), residues: 5784 helix: 0.36 (0.12), residues: 1966 sheet: -1.31 (0.15), residues: 1050 loop : -1.33 (0.11), residues: 2768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP s 42 HIS 0.007 0.001 HIS G 135 PHE 0.026 0.002 PHE D 23 TYR 0.026 0.002 TYR Q 25 ARG 0.012 0.001 ARG C 128 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11568 Ramachandran restraints generated. 5784 Oldfield, 0 Emsley, 5784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11568 Ramachandran restraints generated. 5784 Oldfield, 0 Emsley, 5784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1471 residues out of total 4812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 249 poor density : 1222 time to evaluate : 6.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 96 TYR cc_start: 0.9278 (m-80) cc_final: 0.8502 (m-80) REVERT: B 100 GLU cc_start: 0.7685 (tm-30) cc_final: 0.6950 (tm-30) REVERT: B 229 ASP cc_start: 0.8765 (m-30) cc_final: 0.8439 (m-30) REVERT: B 255 LYS cc_start: 0.9365 (tttm) cc_final: 0.8952 (tptm) REVERT: C 1 MET cc_start: 0.7768 (tpp) cc_final: 0.7422 (tpp) REVERT: C 149 ASN cc_start: 0.8383 (t0) cc_final: 0.7605 (t0) REVERT: D 1 MET cc_start: 0.8309 (tpt) cc_final: 0.8077 (tpt) REVERT: D 46 GLN cc_start: 0.9562 (mp10) cc_final: 0.8410 (mp10) REVERT: D 62 GLN cc_start: 0.8871 (tp40) cc_final: 0.8577 (tp40) REVERT: D 115 GLN cc_start: 0.8447 (mm110) cc_final: 0.8099 (mm110) REVERT: D 136 GLN cc_start: 0.9378 (OUTLIER) cc_final: 0.9117 (tp-100) REVERT: E 7 TYR cc_start: 0.9405 (t80) cc_final: 0.8945 (t80) REVERT: E 26 MET cc_start: 0.9124 (mtp) cc_final: 0.8575 (mtt) REVERT: E 44 ILE cc_start: 0.9381 (OUTLIER) cc_final: 0.9137 (mt) REVERT: E 83 TYR cc_start: 0.9167 (m-10) cc_final: 0.8759 (m-10) REVERT: E 90 THR cc_start: 0.9489 (m) cc_final: 0.8894 (p) REVERT: E 96 MET cc_start: 0.9450 (ttp) cc_final: 0.9179 (ttp) REVERT: E 128 TYR cc_start: 0.8607 (t80) cc_final: 0.8293 (t80) REVERT: E 130 MET cc_start: 0.8625 (ppp) cc_final: 0.8186 (ppp) REVERT: E 143 TYR cc_start: 0.9128 (t80) cc_final: 0.8878 (t80) REVERT: F 60 ASP cc_start: 0.9076 (p0) cc_final: 0.8751 (p0) REVERT: F 101 ASN cc_start: 0.9272 (p0) cc_final: 0.8950 (p0) REVERT: F 147 ASP cc_start: 0.9167 (m-30) cc_final: 0.8923 (m-30) REVERT: F 176 LYS cc_start: 0.4433 (OUTLIER) cc_final: 0.3080 (mttt) REVERT: G 1 MET cc_start: 0.9274 (tpp) cc_final: 0.9001 (tpp) REVERT: J 75 TYR cc_start: 0.9192 (m-80) cc_final: 0.8690 (m-10) REVERT: J 92 MET cc_start: 0.9250 (mmm) cc_final: 0.8662 (mmt) REVERT: J 102 GLU cc_start: 0.8409 (mt-10) cc_final: 0.7902 (mt-10) REVERT: J 108 MET cc_start: 0.9221 (mtt) cc_final: 0.8818 (mtp) REVERT: J 131 ASN cc_start: 0.9233 (OUTLIER) cc_final: 0.9003 (p0) REVERT: J 141 ASP cc_start: 0.8743 (t0) cc_final: 0.8457 (t0) REVERT: K 1 MET cc_start: 0.8654 (ttm) cc_final: 0.7898 (ttm) REVERT: K 23 LYS cc_start: 0.9298 (tppt) cc_final: 0.8731 (tptp) REVERT: K 29 HIS cc_start: 0.8029 (OUTLIER) cc_final: 0.7251 (m-70) REVERT: K 44 LYS cc_start: 0.9589 (mmtt) cc_final: 0.9317 (mmmm) REVERT: K 45 GLU cc_start: 0.8449 (tm-30) cc_final: 0.8226 (tp30) REVERT: K 59 LYS cc_start: 0.9199 (mttp) cc_final: 0.8940 (mttp) REVERT: K 87 LEU cc_start: 0.9379 (mt) cc_final: 0.9142 (mt) REVERT: K 112 PHE cc_start: 0.9379 (m-80) cc_final: 0.9000 (m-80) REVERT: L 35 HIS cc_start: 0.8874 (OUTLIER) cc_final: 0.8204 (m90) REVERT: M 17 ASN cc_start: 0.8519 (t0) cc_final: 0.8305 (t0) REVERT: M 45 GLN cc_start: 0.9448 (mt0) cc_final: 0.8904 (mm110) REVERT: M 90 GLU cc_start: 0.7517 (mp0) cc_final: 0.7229 (mp0) REVERT: M 96 ILE cc_start: 0.9835 (mm) cc_final: 0.9582 (mp) REVERT: M 119 LEU cc_start: 0.9729 (OUTLIER) cc_final: 0.9416 (mp) REVERT: M 136 MET cc_start: 0.7766 (ppp) cc_final: 0.7519 (ppp) REVERT: N 9 GLN cc_start: 0.8484 (tt0) cc_final: 0.8048 (tt0) REVERT: N 40 LYS cc_start: 0.9480 (mttt) cc_final: 0.8994 (mttp) REVERT: N 57 THR cc_start: 0.9043 (m) cc_final: 0.8764 (p) REVERT: N 75 ILE cc_start: 0.9696 (mm) cc_final: 0.9396 (mm) REVERT: O 19 GLN cc_start: 0.9637 (tm130) cc_final: 0.9263 (tm-30) REVERT: P 8 LEU cc_start: 0.9529 (mm) cc_final: 0.9310 (mm) REVERT: P 25 THR cc_start: 0.9178 (m) cc_final: 0.8806 (p) REVERT: P 29 LYS cc_start: 0.9719 (mttm) cc_final: 0.9469 (mmmm) REVERT: P 34 GLU cc_start: 0.9175 (pm20) cc_final: 0.8739 (pm20) REVERT: P 111 LYS cc_start: 0.9115 (ptpt) cc_final: 0.8858 (ptpp) REVERT: P 112 GLU cc_start: 0.7840 (tm-30) cc_final: 0.7558 (tm-30) REVERT: Q 32 TYR cc_start: 0.8922 (t80) cc_final: 0.8446 (t80) REVERT: Q 52 GLN cc_start: 0.7944 (mt0) cc_final: 0.7680 (mp10) REVERT: Q 97 ASP cc_start: 0.8739 (t70) cc_final: 0.8423 (t70) REVERT: Q 101 PHE cc_start: 0.8312 (m-80) cc_final: 0.7882 (m-10) REVERT: R 85 LYS cc_start: 0.9048 (mtpp) cc_final: 0.8605 (mtpp) REVERT: R 86 GLN cc_start: 0.8475 (mm110) cc_final: 0.7918 (mm110) REVERT: R 95 ASP cc_start: 0.8493 (m-30) cc_final: 0.8179 (m-30) REVERT: S 46 LEU cc_start: 0.9664 (mt) cc_final: 0.9278 (mp) REVERT: S 86 MET cc_start: 0.8511 (tpp) cc_final: 0.8236 (tpp) REVERT: T 77 ARG cc_start: 0.9366 (ttm110) cc_final: 0.9122 (tpp80) REVERT: T 92 ASN cc_start: 0.8577 (OUTLIER) cc_final: 0.8274 (t0) REVERT: U 4 LYS cc_start: 0.8696 (mttt) cc_final: 0.8130 (mttt) REVERT: V 48 MET cc_start: 0.9138 (tpt) cc_final: 0.8789 (tpt) REVERT: W 36 ILE cc_start: 0.9394 (mt) cc_final: 0.9075 (mt) REVERT: W 38 VAL cc_start: 0.9646 (t) cc_final: 0.9365 (p) REVERT: W 44 LYS cc_start: 0.9564 (ttmt) cc_final: 0.9208 (ttmm) REVERT: W 68 LYS cc_start: 0.8957 (tptp) cc_final: 0.8637 (tptp) REVERT: X 17 ASN cc_start: 0.8863 (m110) cc_final: 0.8504 (m-40) REVERT: X 41 GLU cc_start: 0.8783 (tp30) cc_final: 0.8508 (tp30) REVERT: X 44 LYS cc_start: 0.9394 (mmmm) cc_final: 0.9090 (mmmm) REVERT: Y 12 GLU cc_start: 0.9114 (pm20) cc_final: 0.8869 (pm20) REVERT: Y 17 GLU cc_start: 0.8577 (mm-30) cc_final: 0.8337 (mm-30) REVERT: Y 25 GLN cc_start: 0.9549 (tt0) cc_final: 0.9191 (tm-30) REVERT: Y 30 MET cc_start: 0.9209 (mmp) cc_final: 0.8970 (mmm) REVERT: Y 44 LYS cc_start: 0.9572 (tttt) cc_final: 0.9279 (ttmm) REVERT: Z 6 LYS cc_start: 0.9471 (mmmt) cc_final: 0.9181 (mmmt) REVERT: Z 19 LYS cc_start: 0.8938 (mmtt) cc_final: 0.8652 (mmtt) REVERT: Z 21 LYS cc_start: 0.9553 (mttt) cc_final: 0.9098 (mmtm) REVERT: Z 49 ASN cc_start: 0.9501 (t0) cc_final: 0.9209 (t0) REVERT: b 36 GLU cc_start: 0.7635 (pt0) cc_final: 0.7123 (pt0) REVERT: b 46 ASP cc_start: 0.8728 (m-30) cc_final: 0.8480 (m-30) REVERT: d 1 MET cc_start: 0.7343 (mmm) cc_final: 0.7065 (mmm) REVERT: d 2 LYS cc_start: 0.8983 (tttt) cc_final: 0.8508 (tttm) REVERT: d 3 ARG cc_start: 0.8094 (OUTLIER) cc_final: 0.7853 (tpt170) REVERT: d 25 LYS cc_start: 0.8848 (ttmt) cc_final: 0.8581 (ttmt) REVERT: e 14 PHE cc_start: 0.9753 (m-80) cc_final: 0.9228 (m-10) REVERT: f 8 LYS cc_start: 0.8845 (mmmt) cc_final: 0.8278 (mmmt) REVERT: f 9 LYS cc_start: 0.9244 (mttt) cc_final: 0.8920 (mttm) REVERT: f 24 ARG cc_start: 0.8914 (mtt-85) cc_final: 0.8494 (mtt-85) REVERT: f 34 LYS cc_start: 0.9189 (ptmt) cc_final: 0.8916 (ptmt) REVERT: f 35 GLN cc_start: 0.8985 (mt0) cc_final: 0.8776 (mt0) REVERT: g 27 MET cc_start: 0.9157 (mmm) cc_final: 0.8481 (mmm) REVERT: g 49 MET cc_start: 0.9642 (mtp) cc_final: 0.9325 (mtp) REVERT: g 152 LYS cc_start: 0.9589 (pttt) cc_final: 0.9249 (tptt) REVERT: g 213 TYR cc_start: 0.9441 (m-10) cc_final: 0.8984 (m-10) REVERT: h 129 MET cc_start: 0.6974 (mtt) cc_final: 0.6600 (ttt) REVERT: h 130 PHE cc_start: 0.9291 (p90) cc_final: 0.9034 (p90) REVERT: h 181 ASP cc_start: 0.9292 (t0) cc_final: 0.9052 (t70) REVERT: h 185 ASN cc_start: 0.9218 (t0) cc_final: 0.8738 (t0) REVERT: i 51 TYR cc_start: 0.9538 (t80) cc_final: 0.9229 (t80) REVERT: i 75 TYR cc_start: 0.9527 (m-80) cc_final: 0.9079 (m-80) REVERT: i 135 TYR cc_start: 0.9286 (t80) cc_final: 0.8917 (t80) REVERT: i 136 GLN cc_start: 0.9413 (mm-40) cc_final: 0.9019 (pm20) REVERT: j 23 LYS cc_start: 0.8666 (tttm) cc_final: 0.8213 (tttp) REVERT: j 31 PHE cc_start: 0.8808 (m-80) cc_final: 0.7794 (m-80) REVERT: j 64 MET cc_start: 0.8853 (mtm) cc_final: 0.8599 (ptm) REVERT: j 138 ARG cc_start: 0.9573 (mtt90) cc_final: 0.9060 (ttm170) REVERT: k 8 PHE cc_start: 0.8884 (p90) cc_final: 0.8576 (p90) REVERT: k 21 MET cc_start: 0.9359 (mtm) cc_final: 0.8548 (mtm) REVERT: k 24 ARG cc_start: 0.9142 (ttp-110) cc_final: 0.8553 (ptp90) REVERT: k 80 PHE cc_start: 0.9435 (m-80) cc_final: 0.9079 (m-80) REVERT: k 87 SER cc_start: 0.8896 (p) cc_final: 0.8208 (m) REVERT: k 88 MET cc_start: 0.7739 (tmm) cc_final: 0.7516 (tmm) REVERT: l 26 PHE cc_start: 0.9803 (t80) cc_final: 0.9358 (t80) REVERT: l 28 ASN cc_start: 0.9653 (m110) cc_final: 0.9372 (m-40) REVERT: l 31 MET cc_start: 0.8792 (ttp) cc_final: 0.8378 (ttp) REVERT: l 101 MET cc_start: 0.9443 (OUTLIER) cc_final: 0.8950 (ttp) REVERT: m 3 MET cc_start: 0.9147 (tpp) cc_final: 0.8890 (tpp) REVERT: m 10 MET cc_start: 0.9191 (tmm) cc_final: 0.8607 (tmm) REVERT: m 80 ARG cc_start: 0.9493 (mtm110) cc_final: 0.9267 (mtm110) REVERT: m 86 TYR cc_start: 0.9021 (m-10) cc_final: 0.8774 (m-80) REVERT: m 96 MET cc_start: 0.9438 (tpp) cc_final: 0.8262 (tpp) REVERT: m 124 GLU cc_start: 0.9046 (tt0) cc_final: 0.8203 (tm-30) REVERT: m 126 ILE cc_start: 0.9693 (mt) cc_final: 0.8763 (mt) REVERT: n 43 THR cc_start: 0.9619 (p) cc_final: 0.9352 (p) REVERT: n 89 GLU cc_start: 0.9476 (tp30) cc_final: 0.9000 (tp30) REVERT: n 126 GLN cc_start: 0.9398 (OUTLIER) cc_final: 0.8377 (tp-100) REVERT: n 127 PHE cc_start: 0.9318 (t80) cc_final: 0.9074 (t80) REVERT: o 46 LYS cc_start: 0.9199 (mttt) cc_final: 0.8848 (mtpp) REVERT: o 65 TYR cc_start: 0.8807 (m-80) cc_final: 0.7719 (m-80) REVERT: o 66 GLU cc_start: 0.9031 (pt0) cc_final: 0.7605 (pm20) REVERT: o 88 MET cc_start: 0.9352 (OUTLIER) cc_final: 0.9057 (ptt) REVERT: p 94 GLU cc_start: 0.8808 (tp30) cc_final: 0.8485 (tp30) REVERT: p 100 LEU cc_start: 0.9584 (mt) cc_final: 0.9266 (pp) REVERT: q 25 GLU cc_start: 0.9072 (OUTLIER) cc_final: 0.8713 (mp0) REVERT: q 29 GLN cc_start: 0.8856 (mp10) cc_final: 0.8527 (mp10) REVERT: q 44 LYS cc_start: 0.8398 (mptt) cc_final: 0.7606 (tmtt) REVERT: q 70 GLU cc_start: 0.8558 (mt-10) cc_final: 0.8028 (mm-30) REVERT: q 82 ILE cc_start: 0.9566 (mm) cc_final: 0.8701 (tp) REVERT: q 86 ARG cc_start: 0.8899 (tmm-80) cc_final: 0.8641 (tmm-80) REVERT: q 112 GLN cc_start: 0.6904 (mt0) cc_final: 0.6556 (mp10) REVERT: q 117 TYR cc_start: 0.9273 (m-80) cc_final: 0.8637 (m-80) REVERT: r 8 ASN cc_start: 0.8503 (t0) cc_final: 0.8238 (m-40) REVERT: r 23 TYR cc_start: 0.9207 (t80) cc_final: 0.8455 (t80) REVERT: r 69 LEU cc_start: 0.9340 (tp) cc_final: 0.8479 (tp) REVERT: r 100 GLN cc_start: 0.8488 (mp10) cc_final: 0.7987 (mp10) REVERT: r 103 LYS cc_start: 0.8336 (tttt) cc_final: 0.7811 (tttm) REVERT: s 6 MET cc_start: 0.9350 (mmm) cc_final: 0.8909 (tpt) REVERT: s 33 ASP cc_start: 0.8974 (t0) cc_final: 0.8466 (t70) REVERT: s 40 ASP cc_start: 0.9226 (m-30) cc_final: 0.9006 (m-30) REVERT: s 62 ASN cc_start: 0.9448 (m-40) cc_final: 0.9229 (m110) REVERT: s 79 LEU cc_start: 0.8240 (mt) cc_final: 0.7789 (tp) REVERT: s 82 ILE cc_start: 0.9382 (mt) cc_final: 0.9161 (tt) REVERT: s 86 GLU cc_start: 0.9051 (mt-10) cc_final: 0.8706 (mt-10) REVERT: t 2 SER cc_start: 0.7351 (m) cc_final: 0.7106 (m) REVERT: t 6 GLU cc_start: 0.9328 (mp0) cc_final: 0.9118 (pm20) REVERT: t 14 GLU cc_start: 0.8525 (pt0) cc_final: 0.8258 (pt0) REVERT: t 18 ASP cc_start: 0.9364 (OUTLIER) cc_final: 0.8538 (p0) REVERT: t 37 ASN cc_start: 0.9251 (m-40) cc_final: 0.8919 (p0) REVERT: t 43 PHE cc_start: 0.9226 (m-80) cc_final: 0.8831 (m-80) REVERT: t 59 MET cc_start: 0.9300 (mtt) cc_final: 0.8929 (mmp) REVERT: t 62 GLN cc_start: 0.8505 (OUTLIER) cc_final: 0.8090 (pt0) REVERT: u 1 MET cc_start: 0.8165 (pmt) cc_final: 0.7576 (tpt) REVERT: u 34 GLU cc_start: 0.9509 (tm-30) cc_final: 0.9069 (tm-30) REVERT: u 51 ARG cc_start: 0.8449 (ttp-110) cc_final: 0.8137 (ttp-110) REVERT: u 53 ASP cc_start: 0.9312 (t0) cc_final: 0.9091 (t0) REVERT: v 9 GLN cc_start: 0.7761 (mt0) cc_final: 0.6787 (tp-100) REVERT: v 49 GLU cc_start: 0.7863 (mp0) cc_final: 0.7405 (mp0) REVERT: v 75 LEU cc_start: 0.7373 (OUTLIER) cc_final: 0.7073 (pt) REVERT: w 30 LYS cc_start: 0.9623 (mttp) cc_final: 0.9403 (ptpp) REVERT: x 15 LEU cc_start: 0.9532 (tt) cc_final: 0.9204 (mt) REVERT: x 44 MET cc_start: 0.9285 (mtt) cc_final: 0.8739 (ptp) REVERT: y 4 ILE cc_start: 0.8556 (mt) cc_final: 0.8302 (mp) REVERT: y 18 ARG cc_start: 0.9444 (ttp80) cc_final: 0.9143 (ttp80) REVERT: y 19 LYS cc_start: 0.9616 (mttt) cc_final: 0.9324 (mtmm) REVERT: y 25 ARG cc_start: 0.9295 (mtm-85) cc_final: 0.8760 (mtm-85) REVERT: y 31 PHE cc_start: 0.9474 (m-80) cc_final: 0.9207 (m-10) REVERT: y 48 GLN cc_start: 0.9601 (mm-40) cc_final: 0.9302 (mm110) REVERT: y 53 GLU cc_start: 0.9294 (mm-30) cc_final: 0.8991 (mm-30) REVERT: y 59 ASP cc_start: 0.8991 (m-30) cc_final: 0.8170 (t70) REVERT: y 84 ASN cc_start: 0.9175 (m-40) cc_final: 0.8659 (p0) REVERT: z 54 LYS cc_start: 0.9268 (tttt) cc_final: 0.8842 (tttt) REVERT: z 58 LYS cc_start: 0.9088 (pttt) cc_final: 0.8661 (pttp) REVERT: H 79 PHE cc_start: 0.8339 (p90) cc_final: 0.7704 (p90) outliers start: 249 outliers final: 189 residues processed: 1344 average time/residue: 1.3034 time to fit residues: 3028.2115 Evaluate side-chains 1362 residues out of total 4812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 205 poor density : 1157 time to evaluate : 6.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 38 SER Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 264 ASP Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 176 ASP Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain D residue 90 GLN Chi-restraints excluded: chain D residue 136 GLN Chi-restraints excluded: chain E residue 17 MET Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 20 ASN Chi-restraints excluded: chain F residue 42 GLU Chi-restraints excluded: chain F residue 155 GLU Chi-restraints excluded: chain F residue 166 ASP Chi-restraints excluded: chain F residue 176 LYS Chi-restraints excluded: chain G residue 41 LYS Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 103 VAL Chi-restraints excluded: chain J residue 9 GLU Chi-restraints excluded: chain J residue 109 LEU Chi-restraints excluded: chain J residue 131 ASN Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 29 HIS Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 90 ASN Chi-restraints excluded: chain K residue 107 LEU Chi-restraints excluded: chain L residue 35 HIS Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain L residue 122 VAL Chi-restraints excluded: chain M residue 42 THR Chi-restraints excluded: chain M residue 119 LEU Chi-restraints excluded: chain M residue 124 LEU Chi-restraints excluded: chain M residue 132 THR Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain N residue 6 SER Chi-restraints excluded: chain N residue 28 LEU Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 47 VAL Chi-restraints excluded: chain O residue 48 LEU Chi-restraints excluded: chain O residue 53 THR Chi-restraints excluded: chain O residue 62 LEU Chi-restraints excluded: chain O residue 69 ASP Chi-restraints excluded: chain O residue 89 ASP Chi-restraints excluded: chain O residue 90 VAL Chi-restraints excluded: chain O residue 93 ASP Chi-restraints excluded: chain P residue 48 ILE Chi-restraints excluded: chain P residue 60 THR Chi-restraints excluded: chain P residue 85 SER Chi-restraints excluded: chain P residue 104 THR Chi-restraints excluded: chain P residue 110 ILE Chi-restraints excluded: chain Q residue 20 GLN Chi-restraints excluded: chain Q residue 104 VAL Chi-restraints excluded: chain R residue 38 VAL Chi-restraints excluded: chain R residue 39 LEU Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 67 ASP Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain S residue 81 SER Chi-restraints excluded: chain T residue 60 THR Chi-restraints excluded: chain T residue 68 LYS Chi-restraints excluded: chain T residue 73 ARG Chi-restraints excluded: chain T residue 92 ASN Chi-restraints excluded: chain U residue 8 ASP Chi-restraints excluded: chain U residue 12 ILE Chi-restraints excluded: chain U residue 15 THR Chi-restraints excluded: chain U residue 28 VAL Chi-restraints excluded: chain U residue 37 GLU Chi-restraints excluded: chain U residue 65 ILE Chi-restraints excluded: chain U residue 72 ILE Chi-restraints excluded: chain W residue 10 THR Chi-restraints excluded: chain W residue 12 ASN Chi-restraints excluded: chain W residue 58 THR Chi-restraints excluded: chain W residue 76 ASN Chi-restraints excluded: chain X residue 6 GLN Chi-restraints excluded: chain X residue 22 LEU Chi-restraints excluded: chain X residue 33 LEU Chi-restraints excluded: chain X residue 40 VAL Chi-restraints excluded: chain X residue 59 ILE Chi-restraints excluded: chain X residue 71 LEU Chi-restraints excluded: chain Z residue 32 ILE Chi-restraints excluded: chain Z residue 57 VAL Chi-restraints excluded: chain b residue 23 THR Chi-restraints excluded: chain b residue 32 LYS Chi-restraints excluded: chain c residue 29 THR Chi-restraints excluded: chain d residue 3 ARG Chi-restraints excluded: chain d residue 24 THR Chi-restraints excluded: chain d residue 43 THR Chi-restraints excluded: chain d residue 44 VAL Chi-restraints excluded: chain e residue 6 THR Chi-restraints excluded: chain e residue 31 HIS Chi-restraints excluded: chain e residue 38 THR Chi-restraints excluded: chain f residue 22 VAL Chi-restraints excluded: chain g residue 9 MET Chi-restraints excluded: chain g residue 100 MET Chi-restraints excluded: chain g residue 123 ASP Chi-restraints excluded: chain g residue 129 LEU Chi-restraints excluded: chain g residue 199 VAL Chi-restraints excluded: chain h residue 83 ASP Chi-restraints excluded: chain h residue 93 ASP Chi-restraints excluded: chain h residue 102 ASN Chi-restraints excluded: chain h residue 162 ILE Chi-restraints excluded: chain h residue 172 ARG Chi-restraints excluded: chain h residue 193 TYR Chi-restraints excluded: chain h residue 200 VAL Chi-restraints excluded: chain i residue 32 CYS Chi-restraints excluded: chain i residue 174 ASP Chi-restraints excluded: chain i residue 190 ASP Chi-restraints excluded: chain j residue 30 ILE Chi-restraints excluded: chain j residue 37 THR Chi-restraints excluded: chain j residue 134 ILE Chi-restraints excluded: chain j residue 144 LEU Chi-restraints excluded: chain j residue 164 ILE Chi-restraints excluded: chain k residue 51 ILE Chi-restraints excluded: chain k residue 73 GLU Chi-restraints excluded: chain k residue 82 ASP Chi-restraints excluded: chain l residue 50 LEU Chi-restraints excluded: chain l residue 91 VAL Chi-restraints excluded: chain l residue 101 MET Chi-restraints excluded: chain l residue 106 GLU Chi-restraints excluded: chain m residue 27 MET Chi-restraints excluded: chain m residue 54 ASP Chi-restraints excluded: chain m residue 74 SER Chi-restraints excluded: chain m residue 75 ILE Chi-restraints excluded: chain n residue 30 ILE Chi-restraints excluded: chain n residue 35 LEU Chi-restraints excluded: chain n residue 37 GLN Chi-restraints excluded: chain n residue 111 VAL Chi-restraints excluded: chain n residue 115 LYS Chi-restraints excluded: chain n residue 126 GLN Chi-restraints excluded: chain o residue 17 LEU Chi-restraints excluded: chain o residue 32 THR Chi-restraints excluded: chain o residue 52 LEU Chi-restraints excluded: chain o residue 57 VAL Chi-restraints excluded: chain o residue 71 LEU Chi-restraints excluded: chain o residue 74 VAL Chi-restraints excluded: chain o residue 88 MET Chi-restraints excluded: chain p residue 18 ASP Chi-restraints excluded: chain p residue 30 THR Chi-restraints excluded: chain p residue 32 VAL Chi-restraints excluded: chain p residue 86 VAL Chi-restraints excluded: chain p residue 97 ILE Chi-restraints excluded: chain p residue 119 ASN Chi-restraints excluded: chain q residue 16 VAL Chi-restraints excluded: chain q residue 25 GLU Chi-restraints excluded: chain q residue 35 THR Chi-restraints excluded: chain q residue 81 LEU Chi-restraints excluded: chain q residue 90 LEU Chi-restraints excluded: chain r residue 49 SER Chi-restraints excluded: chain r residue 54 ASP Chi-restraints excluded: chain r residue 55 THR Chi-restraints excluded: chain r residue 64 VAL Chi-restraints excluded: chain r residue 68 ASP Chi-restraints excluded: chain r residue 74 SER Chi-restraints excluded: chain r residue 104 THR Chi-restraints excluded: chain s residue 37 SER Chi-restraints excluded: chain s residue 38 ASP Chi-restraints excluded: chain s residue 48 LEU Chi-restraints excluded: chain s residue 54 ASP Chi-restraints excluded: chain s residue 67 THR Chi-restraints excluded: chain t residue 4 SER Chi-restraints excluded: chain t residue 11 ILE Chi-restraints excluded: chain t residue 18 ASP Chi-restraints excluded: chain t residue 62 GLN Chi-restraints excluded: chain t residue 67 LEU Chi-restraints excluded: chain t residue 71 LYS Chi-restraints excluded: chain u residue 78 VAL Chi-restraints excluded: chain v residue 67 LEU Chi-restraints excluded: chain v residue 75 LEU Chi-restraints excluded: chain v residue 79 VAL Chi-restraints excluded: chain x residue 13 LEU Chi-restraints excluded: chain x residue 58 VAL Chi-restraints excluded: chain x residue 63 THR Chi-restraints excluded: chain x residue 71 LEU Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 153 GLU Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 330 ASP Chi-restraints excluded: chain A residue 348 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1027 random chunks: chunk 333 optimal weight: 50.0000 chunk 893 optimal weight: 0.5980 chunk 196 optimal weight: 9.9990 chunk 582 optimal weight: 9.9990 chunk 245 optimal weight: 10.0000 chunk 993 optimal weight: 0.9980 chunk 824 optimal weight: 7.9990 chunk 460 optimal weight: 20.0000 chunk 82 optimal weight: 10.0000 chunk 328 optimal weight: 40.0000 chunk 521 optimal weight: 9.9990 overall best weight: 5.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 60 GLN ** C 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 80 HIS ** J 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 128 ASN ** J 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 3 GLN ** P 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 38 GLN ** g 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 168 HIS h 19 ASN ** h 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 190 HIS i 36 GLN i 164 GLN ** j 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 14 GLN ** n 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 75 GLN t 28 GLN ** t 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.3350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 158320 Z= 0.233 Angle : 0.637 13.825 236734 Z= 0.341 Chirality : 0.034 0.289 30127 Planarity : 0.006 0.126 12767 Dihedral : 24.437 179.410 78854 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 24.35 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.96 % Favored : 95.00 % Rotamer: Outliers : 4.59 % Allowed : 18.95 % Favored : 76.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.11), residues: 5784 helix: 0.46 (0.12), residues: 1959 sheet: -1.23 (0.15), residues: 1020 loop : -1.23 (0.11), residues: 2805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP s 42 HIS 0.009 0.001 HIS e 31 PHE 0.021 0.002 PHE E 175 TYR 0.026 0.002 TYR Q 25 ARG 0.010 0.001 ARG J 96 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11568 Ramachandran restraints generated. 5784 Oldfield, 0 Emsley, 5784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11568 Ramachandran restraints generated. 5784 Oldfield, 0 Emsley, 5784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1427 residues out of total 4812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 221 poor density : 1206 time to evaluate : 6.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 60 GLN cc_start: 0.8721 (mt0) cc_final: 0.8436 (mp10) REVERT: B 225 MET cc_start: 0.8936 (mmt) cc_final: 0.8718 (mmt) REVERT: B 229 ASP cc_start: 0.8722 (m-30) cc_final: 0.8519 (m-30) REVERT: C 1 MET cc_start: 0.7873 (tpp) cc_final: 0.7456 (tpp) REVERT: C 149 ASN cc_start: 0.8315 (t0) cc_final: 0.7492 (t0) REVERT: D 1 MET cc_start: 0.8286 (tpt) cc_final: 0.8059 (tpt) REVERT: D 46 GLN cc_start: 0.9550 (mp10) cc_final: 0.8908 (mp10) REVERT: D 62 GLN cc_start: 0.8850 (tp40) cc_final: 0.8559 (tp40) REVERT: D 100 MET cc_start: 0.8697 (mtp) cc_final: 0.8411 (mtp) REVERT: D 115 GLN cc_start: 0.8473 (mm110) cc_final: 0.8155 (mm110) REVERT: D 136 GLN cc_start: 0.9392 (tp-100) cc_final: 0.9084 (tp-100) REVERT: E 7 TYR cc_start: 0.9432 (t80) cc_final: 0.9003 (t80) REVERT: E 26 MET cc_start: 0.9140 (mtp) cc_final: 0.8601 (mtt) REVERT: E 44 ILE cc_start: 0.9379 (OUTLIER) cc_final: 0.9097 (mt) REVERT: E 83 TYR cc_start: 0.9151 (m-10) cc_final: 0.8722 (m-10) REVERT: E 90 THR cc_start: 0.9465 (m) cc_final: 0.8945 (p) REVERT: E 96 MET cc_start: 0.9464 (ttp) cc_final: 0.9069 (ttp) REVERT: E 128 TYR cc_start: 0.8644 (t80) cc_final: 0.8356 (t80) REVERT: E 130 MET cc_start: 0.8608 (ppp) cc_final: 0.8147 (ppp) REVERT: F 60 ASP cc_start: 0.9061 (p0) cc_final: 0.8743 (p0) REVERT: F 101 ASN cc_start: 0.9200 (p0) cc_final: 0.8926 (p0) REVERT: F 147 ASP cc_start: 0.9148 (m-30) cc_final: 0.8919 (m-30) REVERT: F 176 LYS cc_start: 0.4437 (OUTLIER) cc_final: 0.3068 (mttt) REVERT: G 1 MET cc_start: 0.9247 (tpp) cc_final: 0.8957 (tpp) REVERT: J 75 TYR cc_start: 0.9173 (m-80) cc_final: 0.8685 (m-10) REVERT: J 92 MET cc_start: 0.9243 (mmm) cc_final: 0.8692 (mmt) REVERT: J 102 GLU cc_start: 0.8412 (mt-10) cc_final: 0.7879 (mt-10) REVERT: K 1 MET cc_start: 0.8587 (ttm) cc_final: 0.8098 (ttm) REVERT: K 17 ARG cc_start: 0.8058 (mmp80) cc_final: 0.7635 (mmp80) REVERT: K 23 LYS cc_start: 0.9306 (tppt) cc_final: 0.8549 (tppp) REVERT: K 29 HIS cc_start: 0.7950 (OUTLIER) cc_final: 0.7280 (m-70) REVERT: K 44 LYS cc_start: 0.9624 (mmtt) cc_final: 0.9290 (mmmm) REVERT: K 66 LYS cc_start: 0.9480 (ttmm) cc_final: 0.9065 (ttpp) REVERT: K 87 LEU cc_start: 0.9478 (mt) cc_final: 0.9264 (mt) REVERT: K 112 PHE cc_start: 0.9346 (m-80) cc_final: 0.8981 (m-80) REVERT: L 35 HIS cc_start: 0.8810 (OUTLIER) cc_final: 0.8100 (m90) REVERT: M 17 ASN cc_start: 0.8501 (t0) cc_final: 0.8297 (t0) REVERT: M 90 GLU cc_start: 0.7510 (mp0) cc_final: 0.7229 (mp0) REVERT: M 96 ILE cc_start: 0.9828 (mm) cc_final: 0.9588 (mp) REVERT: M 119 LEU cc_start: 0.9705 (OUTLIER) cc_final: 0.9441 (mp) REVERT: M 136 MET cc_start: 0.7686 (ppp) cc_final: 0.7408 (ppp) REVERT: N 9 GLN cc_start: 0.8432 (tt0) cc_final: 0.8019 (tt0) REVERT: N 40 LYS cc_start: 0.9470 (mttt) cc_final: 0.8847 (mttp) REVERT: N 57 THR cc_start: 0.9017 (m) cc_final: 0.8742 (p) REVERT: N 75 ILE cc_start: 0.9713 (mm) cc_final: 0.9486 (mm) REVERT: O 19 GLN cc_start: 0.9635 (tm130) cc_final: 0.9266 (tm-30) REVERT: O 115 LEU cc_start: 0.8109 (OUTLIER) cc_final: 0.7837 (tp) REVERT: P 8 LEU cc_start: 0.9548 (mm) cc_final: 0.8744 (mm) REVERT: P 25 THR cc_start: 0.9148 (m) cc_final: 0.8783 (p) REVERT: P 29 LYS cc_start: 0.9670 (mttm) cc_final: 0.9428 (ttmm) REVERT: P 106 LYS cc_start: 0.9271 (mmtt) cc_final: 0.8794 (mmtt) REVERT: P 111 LYS cc_start: 0.9104 (ptpt) cc_final: 0.8837 (ptpp) REVERT: Q 32 TYR cc_start: 0.8890 (t80) cc_final: 0.8372 (t80) REVERT: Q 52 GLN cc_start: 0.7870 (mt0) cc_final: 0.7580 (mp10) REVERT: Q 97 ASP cc_start: 0.8761 (t70) cc_final: 0.8451 (t70) REVERT: Q 101 PHE cc_start: 0.8422 (m-80) cc_final: 0.7951 (m-10) REVERT: R 85 LYS cc_start: 0.9059 (mtpp) cc_final: 0.8626 (mtpt) REVERT: R 86 GLN cc_start: 0.8431 (mm110) cc_final: 0.7908 (mm-40) REVERT: R 95 ASP cc_start: 0.8455 (m-30) cc_final: 0.8141 (m-30) REVERT: S 33 LEU cc_start: 0.9566 (OUTLIER) cc_final: 0.9338 (mm) REVERT: S 46 LEU cc_start: 0.9630 (mt) cc_final: 0.9271 (mp) REVERT: S 86 MET cc_start: 0.8541 (tpp) cc_final: 0.8338 (tpp) REVERT: S 95 ARG cc_start: 0.8668 (ttp80) cc_final: 0.8355 (ttp80) REVERT: T 77 ARG cc_start: 0.9354 (ttm110) cc_final: 0.8888 (ttm-80) REVERT: T 92 ASN cc_start: 0.8535 (OUTLIER) cc_final: 0.8251 (t0) REVERT: U 4 LYS cc_start: 0.8706 (mttt) cc_final: 0.8124 (mttt) REVERT: W 36 ILE cc_start: 0.9435 (mt) cc_final: 0.9095 (mt) REVERT: W 38 VAL cc_start: 0.9655 (t) cc_final: 0.9393 (p) REVERT: W 44 LYS cc_start: 0.9566 (ttmt) cc_final: 0.9221 (ttmm) REVERT: W 68 LYS cc_start: 0.8954 (tptp) cc_final: 0.8501 (tptp) REVERT: X 17 ASN cc_start: 0.8781 (m110) cc_final: 0.8339 (m-40) REVERT: X 41 GLU cc_start: 0.8895 (tp30) cc_final: 0.8645 (tp30) REVERT: X 44 LYS cc_start: 0.9392 (mmmm) cc_final: 0.9029 (mmmm) REVERT: Y 12 GLU cc_start: 0.9059 (pm20) cc_final: 0.8711 (pm20) REVERT: Y 17 GLU cc_start: 0.8595 (mm-30) cc_final: 0.8167 (mm-30) REVERT: Y 25 GLN cc_start: 0.9581 (tt0) cc_final: 0.9258 (tm-30) REVERT: Y 30 MET cc_start: 0.9187 (mmp) cc_final: 0.8886 (mmm) REVERT: Z 6 LYS cc_start: 0.9447 (mmmt) cc_final: 0.9174 (mmmt) REVERT: Z 19 LYS cc_start: 0.8898 (mmtt) cc_final: 0.8611 (mmtt) REVERT: Z 21 LYS cc_start: 0.9544 (mttt) cc_final: 0.9081 (mmtm) REVERT: Z 49 ASN cc_start: 0.9518 (t0) cc_final: 0.9197 (t0) REVERT: b 36 GLU cc_start: 0.7586 (pt0) cc_final: 0.7135 (pt0) REVERT: b 46 ASP cc_start: 0.8699 (m-30) cc_final: 0.8469 (m-30) REVERT: d 1 MET cc_start: 0.7290 (mmm) cc_final: 0.7016 (mmm) REVERT: d 2 LYS cc_start: 0.8953 (tttt) cc_final: 0.8480 (tttm) REVERT: d 3 ARG cc_start: 0.7994 (OUTLIER) cc_final: 0.7513 (tpt170) REVERT: d 25 LYS cc_start: 0.8852 (ttmt) cc_final: 0.8542 (ttmt) REVERT: f 8 LYS cc_start: 0.8851 (mmmt) cc_final: 0.8225 (mmmt) REVERT: f 24 ARG cc_start: 0.8911 (mtt-85) cc_final: 0.8536 (mtt-85) REVERT: f 34 LYS cc_start: 0.9162 (ptmt) cc_final: 0.8902 (ptmt) REVERT: f 35 GLN cc_start: 0.8948 (mt0) cc_final: 0.8497 (mp10) REVERT: g 27 MET cc_start: 0.9163 (mmm) cc_final: 0.8482 (mmm) REVERT: g 49 MET cc_start: 0.9641 (mtp) cc_final: 0.9331 (mtp) REVERT: g 152 LYS cc_start: 0.9587 (pttt) cc_final: 0.9244 (tptt) REVERT: g 213 TYR cc_start: 0.9422 (m-10) cc_final: 0.8984 (m-10) REVERT: h 129 MET cc_start: 0.6984 (mtt) cc_final: 0.6680 (ttt) REVERT: h 130 PHE cc_start: 0.9290 (p90) cc_final: 0.9071 (p90) REVERT: h 134 MET cc_start: 0.9311 (ptm) cc_final: 0.8820 (ppp) REVERT: h 181 ASP cc_start: 0.9287 (t0) cc_final: 0.9045 (t70) REVERT: h 185 ASN cc_start: 0.9233 (t0) cc_final: 0.8744 (t0) REVERT: i 40 GLN cc_start: 0.8957 (tt0) cc_final: 0.8724 (pt0) REVERT: i 51 TYR cc_start: 0.9540 (t80) cc_final: 0.9226 (t80) REVERT: i 54 GLN cc_start: 0.9339 (mt0) cc_final: 0.9048 (mm-40) REVERT: i 75 TYR cc_start: 0.9510 (m-80) cc_final: 0.9061 (m-80) REVERT: i 135 TYR cc_start: 0.9317 (t80) cc_final: 0.8987 (t80) REVERT: i 136 GLN cc_start: 0.9382 (mm-40) cc_final: 0.9016 (pm20) REVERT: j 23 LYS cc_start: 0.8617 (tttm) cc_final: 0.8137 (tttp) REVERT: j 31 PHE cc_start: 0.8775 (m-80) cc_final: 0.7753 (m-80) REVERT: j 138 ARG cc_start: 0.9558 (mtt90) cc_final: 0.9057 (ttm170) REVERT: k 17 GLN cc_start: 0.9150 (tm-30) cc_final: 0.8773 (tm-30) REVERT: k 21 MET cc_start: 0.9569 (mtm) cc_final: 0.9017 (mtm) REVERT: k 24 ARG cc_start: 0.9145 (ttp-110) cc_final: 0.8645 (ptp90) REVERT: k 80 PHE cc_start: 0.9421 (m-80) cc_final: 0.9046 (m-80) REVERT: k 87 SER cc_start: 0.8971 (p) cc_final: 0.8281 (m) REVERT: l 26 PHE cc_start: 0.9794 (t80) cc_final: 0.9358 (t80) REVERT: l 28 ASN cc_start: 0.9640 (m110) cc_final: 0.9376 (m110) REVERT: l 31 MET cc_start: 0.8757 (ttp) cc_final: 0.8354 (ttp) REVERT: l 101 MET cc_start: 0.9434 (OUTLIER) cc_final: 0.8971 (ttp) REVERT: m 3 MET cc_start: 0.9122 (tpp) cc_final: 0.8890 (tpp) REVERT: m 10 MET cc_start: 0.9182 (tmm) cc_final: 0.8582 (tmm) REVERT: m 80 ARG cc_start: 0.9508 (mtm110) cc_final: 0.9251 (mtm110) REVERT: m 86 TYR cc_start: 0.9029 (m-10) cc_final: 0.8783 (m-80) REVERT: m 124 GLU cc_start: 0.8997 (tt0) cc_final: 0.8205 (tm-30) REVERT: m 126 ILE cc_start: 0.9695 (mt) cc_final: 0.8767 (mt) REVERT: n 39 PHE cc_start: 0.8910 (m-80) cc_final: 0.8623 (m-80) REVERT: n 57 MET cc_start: 0.9300 (ttt) cc_final: 0.8759 (tpp) REVERT: n 89 GLU cc_start: 0.9475 (tp30) cc_final: 0.9019 (tp30) REVERT: n 126 GLN cc_start: 0.9392 (OUTLIER) cc_final: 0.8326 (tp-100) REVERT: n 127 PHE cc_start: 0.9329 (t80) cc_final: 0.9123 (t80) REVERT: o 46 LYS cc_start: 0.9247 (mttt) cc_final: 0.8916 (mtpp) REVERT: o 66 GLU cc_start: 0.9049 (pt0) cc_final: 0.7550 (pm20) REVERT: o 88 MET cc_start: 0.9252 (OUTLIER) cc_final: 0.9023 (ptt) REVERT: p 87 LYS cc_start: 0.9266 (ttmm) cc_final: 0.9044 (mttt) REVERT: p 94 GLU cc_start: 0.8744 (tp30) cc_final: 0.8364 (tp30) REVERT: q 25 GLU cc_start: 0.8970 (OUTLIER) cc_final: 0.8597 (mp0) REVERT: q 29 GLN cc_start: 0.8900 (mp10) cc_final: 0.8571 (mp10) REVERT: q 38 TYR cc_start: 0.8250 (p90) cc_final: 0.7969 (p90) REVERT: q 44 LYS cc_start: 0.8385 (mptt) cc_final: 0.8171 (mptt) REVERT: q 67 ILE cc_start: 0.8184 (mt) cc_final: 0.7955 (mp) REVERT: q 70 GLU cc_start: 0.8490 (mt-10) cc_final: 0.8183 (mp0) REVERT: q 86 ARG cc_start: 0.8784 (tmm-80) cc_final: 0.8516 (tmm-80) REVERT: q 112 GLN cc_start: 0.6707 (mt0) cc_final: 0.6351 (mp10) REVERT: q 117 TYR cc_start: 0.9250 (m-80) cc_final: 0.8604 (m-80) REVERT: r 23 TYR cc_start: 0.9234 (t80) cc_final: 0.8434 (t80) REVERT: r 42 ASP cc_start: 0.9150 (p0) cc_final: 0.8819 (t0) REVERT: r 69 LEU cc_start: 0.9122 (tp) cc_final: 0.8740 (tp) REVERT: r 75 MET cc_start: 0.8925 (mmm) cc_final: 0.8723 (mmm) REVERT: r 81 MET cc_start: 0.8938 (mmm) cc_final: 0.8703 (mmm) REVERT: r 100 GLN cc_start: 0.8474 (mp10) cc_final: 0.7963 (mp10) REVERT: r 103 LYS cc_start: 0.8323 (tttt) cc_final: 0.7806 (tttm) REVERT: s 6 MET cc_start: 0.9359 (mmm) cc_final: 0.8928 (tpt) REVERT: s 33 ASP cc_start: 0.8964 (t0) cc_final: 0.8455 (t70) REVERT: s 62 ASN cc_start: 0.9447 (m-40) cc_final: 0.9219 (m110) REVERT: s 74 LEU cc_start: 0.9528 (mm) cc_final: 0.9229 (tt) REVERT: s 77 PHE cc_start: 0.9501 (m-10) cc_final: 0.8902 (m-10) REVERT: s 79 LEU cc_start: 0.8442 (mt) cc_final: 0.7676 (tp) REVERT: s 82 ILE cc_start: 0.9370 (mt) cc_final: 0.9154 (tt) REVERT: s 86 GLU cc_start: 0.9024 (mt-10) cc_final: 0.8683 (mt-10) REVERT: s 92 GLU cc_start: 0.8872 (mp0) cc_final: 0.8538 (pm20) REVERT: t 2 SER cc_start: 0.7259 (m) cc_final: 0.7001 (m) REVERT: t 6 GLU cc_start: 0.9355 (mp0) cc_final: 0.9130 (pm20) REVERT: t 14 GLU cc_start: 0.8469 (pt0) cc_final: 0.8188 (pt0) REVERT: t 18 ASP cc_start: 0.9347 (m-30) cc_final: 0.8521 (p0) REVERT: t 37 ASN cc_start: 0.9242 (m-40) cc_final: 0.8919 (p0) REVERT: t 48 LYS cc_start: 0.9236 (mmtt) cc_final: 0.8987 (mmtt) REVERT: t 59 MET cc_start: 0.9302 (mtt) cc_final: 0.8997 (mmp) REVERT: t 71 LYS cc_start: 0.9225 (OUTLIER) cc_final: 0.8885 (ttmt) REVERT: u 1 MET cc_start: 0.8171 (pmt) cc_final: 0.7690 (tpt) REVERT: u 31 ARG cc_start: 0.7071 (ttp-110) cc_final: 0.6812 (ttp-110) REVERT: u 34 GLU cc_start: 0.9507 (tm-30) cc_final: 0.8907 (tm-30) REVERT: u 51 ARG cc_start: 0.8478 (ttp-110) cc_final: 0.8210 (ttp-110) REVERT: u 53 ASP cc_start: 0.9283 (t0) cc_final: 0.9015 (t0) REVERT: v 9 GLN cc_start: 0.7509 (mt0) cc_final: 0.6692 (tp40) REVERT: w 30 LYS cc_start: 0.9666 (mttp) cc_final: 0.9364 (ptpp) REVERT: x 15 LEU cc_start: 0.9521 (tt) cc_final: 0.9186 (mt) REVERT: x 44 MET cc_start: 0.9293 (mtt) cc_final: 0.8742 (ptp) REVERT: y 4 ILE cc_start: 0.8563 (mt) cc_final: 0.8311 (mp) REVERT: y 21 ASN cc_start: 0.9426 (m-40) cc_final: 0.9139 (t0) REVERT: y 31 PHE cc_start: 0.9435 (m-80) cc_final: 0.9139 (m-10) REVERT: y 48 GLN cc_start: 0.9631 (mm-40) cc_final: 0.9324 (mm-40) REVERT: y 51 PHE cc_start: 0.9459 (t80) cc_final: 0.8752 (t80) REVERT: y 53 GLU cc_start: 0.9377 (mm-30) cc_final: 0.9159 (mm-30) REVERT: y 66 LEU cc_start: 0.8468 (mt) cc_final: 0.8061 (mm) REVERT: y 79 LEU cc_start: 0.9506 (mm) cc_final: 0.9211 (mt) REVERT: y 83 ILE cc_start: 0.9162 (mt) cc_final: 0.8846 (mt) REVERT: y 84 ASN cc_start: 0.9242 (m-40) cc_final: 0.8666 (p0) REVERT: z 36 GLU cc_start: 0.8202 (pt0) cc_final: 0.7888 (pt0) REVERT: z 44 GLU cc_start: 0.9067 (tp30) cc_final: 0.7356 (tp30) REVERT: z 54 LYS cc_start: 0.9265 (tttt) cc_final: 0.8821 (tttt) REVERT: z 58 LYS cc_start: 0.9118 (pttt) cc_final: 0.8644 (pttp) REVERT: H 79 PHE cc_start: 0.8216 (p90) cc_final: 0.7501 (p90) REVERT: A 123 GLU cc_start: 0.9018 (OUTLIER) cc_final: 0.8561 (mp0) REVERT: A 134 MET cc_start: 0.8538 (mpp) cc_final: 0.8192 (mmm) REVERT: A 186 ARG cc_start: 0.7762 (ptt180) cc_final: 0.7510 (ptt180) REVERT: A 206 MET cc_start: 0.8497 (ptp) cc_final: 0.8272 (ptt) REVERT: A 333 MET cc_start: 0.9011 (mmt) cc_final: 0.8772 (mmt) outliers start: 221 outliers final: 174 residues processed: 1307 average time/residue: 1.3065 time to fit residues: 2951.2450 Evaluate side-chains 1338 residues out of total 4812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 189 poor density : 1149 time to evaluate : 8.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 38 SER Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 264 ASP Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 176 ASP Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 90 GLN Chi-restraints excluded: chain D residue 175 ILE Chi-restraints excluded: chain E residue 17 MET Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 20 ASN Chi-restraints excluded: chain F residue 42 GLU Chi-restraints excluded: chain F residue 155 GLU Chi-restraints excluded: chain F residue 166 ASP Chi-restraints excluded: chain F residue 176 LYS Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 103 VAL Chi-restraints excluded: chain J residue 9 GLU Chi-restraints excluded: chain J residue 109 LEU Chi-restraints excluded: chain J residue 114 LEU Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 29 HIS Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 90 ASN Chi-restraints excluded: chain K residue 107 LEU Chi-restraints excluded: chain L residue 35 HIS Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain L residue 122 VAL Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 42 THR Chi-restraints excluded: chain M residue 46 ILE Chi-restraints excluded: chain M residue 119 LEU Chi-restraints excluded: chain M residue 124 LEU Chi-restraints excluded: chain M residue 132 THR Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain N residue 28 LEU Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 47 VAL Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 28 VAL Chi-restraints excluded: chain O residue 48 LEU Chi-restraints excluded: chain O residue 62 LEU Chi-restraints excluded: chain O residue 89 ASP Chi-restraints excluded: chain O residue 90 VAL Chi-restraints excluded: chain O residue 93 ASP Chi-restraints excluded: chain O residue 115 LEU Chi-restraints excluded: chain P residue 48 ILE Chi-restraints excluded: chain P residue 60 THR Chi-restraints excluded: chain P residue 85 SER Chi-restraints excluded: chain P residue 104 THR Chi-restraints excluded: chain P residue 110 ILE Chi-restraints excluded: chain Q residue 34 VAL Chi-restraints excluded: chain Q residue 104 VAL Chi-restraints excluded: chain R residue 38 VAL Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 33 LEU Chi-restraints excluded: chain S residue 34 ASP Chi-restraints excluded: chain S residue 67 ASP Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain S residue 81 SER Chi-restraints excluded: chain T residue 60 THR Chi-restraints excluded: chain T residue 68 LYS Chi-restraints excluded: chain T residue 73 ARG Chi-restraints excluded: chain T residue 92 ASN Chi-restraints excluded: chain U residue 8 ASP Chi-restraints excluded: chain U residue 12 ILE Chi-restraints excluded: chain U residue 28 VAL Chi-restraints excluded: chain U residue 37 GLU Chi-restraints excluded: chain U residue 65 ILE Chi-restraints excluded: chain U residue 72 ILE Chi-restraints excluded: chain W residue 10 THR Chi-restraints excluded: chain W residue 12 ASN Chi-restraints excluded: chain W residue 58 THR Chi-restraints excluded: chain W residue 76 ASN Chi-restraints excluded: chain X residue 22 LEU Chi-restraints excluded: chain X residue 33 LEU Chi-restraints excluded: chain X residue 40 VAL Chi-restraints excluded: chain X residue 71 LEU Chi-restraints excluded: chain Z residue 32 ILE Chi-restraints excluded: chain Z residue 57 VAL Chi-restraints excluded: chain b residue 32 LYS Chi-restraints excluded: chain c residue 29 THR Chi-restraints excluded: chain d residue 3 ARG Chi-restraints excluded: chain d residue 4 THR Chi-restraints excluded: chain d residue 24 THR Chi-restraints excluded: chain d residue 43 THR Chi-restraints excluded: chain e residue 6 THR Chi-restraints excluded: chain f residue 22 VAL Chi-restraints excluded: chain f residue 23 ILE Chi-restraints excluded: chain g residue 9 MET Chi-restraints excluded: chain g residue 100 MET Chi-restraints excluded: chain g residue 123 ASP Chi-restraints excluded: chain g residue 129 LEU Chi-restraints excluded: chain g residue 199 VAL Chi-restraints excluded: chain h residue 93 ASP Chi-restraints excluded: chain h residue 102 ASN Chi-restraints excluded: chain h residue 172 ARG Chi-restraints excluded: chain h residue 193 TYR Chi-restraints excluded: chain h residue 200 VAL Chi-restraints excluded: chain i residue 32 CYS Chi-restraints excluded: chain i residue 174 ASP Chi-restraints excluded: chain i residue 190 ASP Chi-restraints excluded: chain j residue 15 LEU Chi-restraints excluded: chain j residue 30 ILE Chi-restraints excluded: chain j residue 37 THR Chi-restraints excluded: chain j residue 134 ILE Chi-restraints excluded: chain j residue 144 LEU Chi-restraints excluded: chain j residue 148 ASN Chi-restraints excluded: chain j residue 164 ILE Chi-restraints excluded: chain k residue 51 ILE Chi-restraints excluded: chain k residue 73 GLU Chi-restraints excluded: chain k residue 96 VAL Chi-restraints excluded: chain l residue 50 LEU Chi-restraints excluded: chain l residue 91 VAL Chi-restraints excluded: chain l residue 101 MET Chi-restraints excluded: chain l residue 106 GLU Chi-restraints excluded: chain m residue 27 MET Chi-restraints excluded: chain m residue 38 ASN Chi-restraints excluded: chain m residue 54 ASP Chi-restraints excluded: chain m residue 75 ILE Chi-restraints excluded: chain n residue 30 ILE Chi-restraints excluded: chain n residue 35 LEU Chi-restraints excluded: chain n residue 111 VAL Chi-restraints excluded: chain n residue 115 LYS Chi-restraints excluded: chain n residue 126 GLN Chi-restraints excluded: chain o residue 17 LEU Chi-restraints excluded: chain o residue 32 THR Chi-restraints excluded: chain o residue 57 VAL Chi-restraints excluded: chain o residue 71 LEU Chi-restraints excluded: chain o residue 74 VAL Chi-restraints excluded: chain o residue 88 MET Chi-restraints excluded: chain p residue 18 ASP Chi-restraints excluded: chain p residue 30 THR Chi-restraints excluded: chain p residue 32 VAL Chi-restraints excluded: chain p residue 86 VAL Chi-restraints excluded: chain p residue 97 ILE Chi-restraints excluded: chain q residue 16 VAL Chi-restraints excluded: chain q residue 25 GLU Chi-restraints excluded: chain q residue 81 LEU Chi-restraints excluded: chain q residue 90 LEU Chi-restraints excluded: chain r residue 49 SER Chi-restraints excluded: chain r residue 55 THR Chi-restraints excluded: chain r residue 64 VAL Chi-restraints excluded: chain r residue 68 ASP Chi-restraints excluded: chain r residue 74 SER Chi-restraints excluded: chain r residue 104 THR Chi-restraints excluded: chain s residue 37 SER Chi-restraints excluded: chain s residue 38 ASP Chi-restraints excluded: chain s residue 48 LEU Chi-restraints excluded: chain s residue 54 ASP Chi-restraints excluded: chain s residue 67 THR Chi-restraints excluded: chain t residue 4 SER Chi-restraints excluded: chain t residue 11 ILE Chi-restraints excluded: chain t residue 67 LEU Chi-restraints excluded: chain t residue 71 LYS Chi-restraints excluded: chain u residue 78 VAL Chi-restraints excluded: chain v residue 67 LEU Chi-restraints excluded: chain v residue 79 VAL Chi-restraints excluded: chain w residue 59 ILE Chi-restraints excluded: chain x residue 13 LEU Chi-restraints excluded: chain x residue 58 VAL Chi-restraints excluded: chain x residue 63 THR Chi-restraints excluded: chain x residue 71 LEU Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 159 TYR Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 330 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1027 random chunks: chunk 958 optimal weight: 6.9990 chunk 112 optimal weight: 20.0000 chunk 566 optimal weight: 5.9990 chunk 725 optimal weight: 9.9990 chunk 562 optimal weight: 40.0000 chunk 836 optimal weight: 4.9990 chunk 554 optimal weight: 7.9990 chunk 989 optimal weight: 7.9990 chunk 619 optimal weight: 7.9990 chunk 603 optimal weight: 10.0000 chunk 457 optimal weight: 9.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 128 ASN ** P 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 39 GLN ** g 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 190 HIS i 36 GLN ** j 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 32 GLN ** n 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 75 GLN t 28 GLN ** t 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.3474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 158320 Z= 0.261 Angle : 0.647 13.861 236734 Z= 0.346 Chirality : 0.035 0.305 30127 Planarity : 0.006 0.127 12767 Dihedral : 24.411 179.247 78854 Min Nonbonded Distance : 1.787 Molprobity Statistics. All-atom Clashscore : 25.42 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.39 % Favored : 94.57 % Rotamer: Outliers : 4.80 % Allowed : 19.78 % Favored : 75.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.11), residues: 5784 helix: 0.39 (0.12), residues: 1971 sheet: -1.15 (0.15), residues: 1024 loop : -1.21 (0.12), residues: 2789 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP s 42 HIS 0.010 0.001 HIS e 31 PHE 0.029 0.002 PHE i 182 TYR 0.028 0.002 TYR Q 25 ARG 0.009 0.001 ARG y 18 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11568 Ramachandran restraints generated. 5784 Oldfield, 0 Emsley, 5784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11568 Ramachandran restraints generated. 5784 Oldfield, 0 Emsley, 5784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1414 residues out of total 4812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 231 poor density : 1183 time to evaluate : 5.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 60 GLN cc_start: 0.8746 (mt0) cc_final: 0.8446 (mp10) REVERT: B 229 ASP cc_start: 0.8704 (m-30) cc_final: 0.8426 (m-30) REVERT: C 149 ASN cc_start: 0.8357 (t0) cc_final: 0.7559 (t0) REVERT: D 46 GLN cc_start: 0.9553 (mp10) cc_final: 0.8886 (mp10) REVERT: D 62 GLN cc_start: 0.8858 (tp40) cc_final: 0.8562 (tp40) REVERT: D 115 GLN cc_start: 0.8385 (mm110) cc_final: 0.8055 (mm110) REVERT: D 136 GLN cc_start: 0.9387 (OUTLIER) cc_final: 0.9107 (tp-100) REVERT: E 7 TYR cc_start: 0.9454 (t80) cc_final: 0.9070 (t80) REVERT: E 26 MET cc_start: 0.9121 (mtp) cc_final: 0.8527 (mtt) REVERT: E 44 ILE cc_start: 0.9471 (OUTLIER) cc_final: 0.9193 (mt) REVERT: E 83 TYR cc_start: 0.9160 (m-10) cc_final: 0.8723 (m-10) REVERT: E 90 THR cc_start: 0.9510 (m) cc_final: 0.9003 (p) REVERT: E 96 MET cc_start: 0.9466 (ttp) cc_final: 0.9204 (ttp) REVERT: E 128 TYR cc_start: 0.8631 (t80) cc_final: 0.8404 (t80) REVERT: E 130 MET cc_start: 0.8596 (ppp) cc_final: 0.8139 (ppp) REVERT: F 60 ASP cc_start: 0.9067 (p0) cc_final: 0.8807 (p0) REVERT: F 101 ASN cc_start: 0.9206 (p0) cc_final: 0.8936 (p0) REVERT: F 147 ASP cc_start: 0.9152 (m-30) cc_final: 0.8935 (m-30) REVERT: F 176 LYS cc_start: 0.4428 (OUTLIER) cc_final: 0.3032 (mttt) REVERT: G 1 MET cc_start: 0.9252 (tpp) cc_final: 0.8969 (tpp) REVERT: J 75 TYR cc_start: 0.9174 (m-80) cc_final: 0.8723 (m-10) REVERT: J 92 MET cc_start: 0.9210 (mmm) cc_final: 0.8673 (mmt) REVERT: J 102 GLU cc_start: 0.8411 (mt-10) cc_final: 0.7859 (mt-10) REVERT: K 1 MET cc_start: 0.8590 (ttm) cc_final: 0.8173 (ttm) REVERT: K 23 LYS cc_start: 0.9287 (tppt) cc_final: 0.8744 (tppp) REVERT: K 29 HIS cc_start: 0.8009 (OUTLIER) cc_final: 0.7297 (m-70) REVERT: K 44 LYS cc_start: 0.9632 (mmtt) cc_final: 0.9302 (mmmm) REVERT: K 45 GLU cc_start: 0.8420 (tm-30) cc_final: 0.8145 (tp30) REVERT: K 66 LYS cc_start: 0.9482 (ttmm) cc_final: 0.9080 (ttpp) REVERT: K 87 LEU cc_start: 0.9499 (mt) cc_final: 0.9282 (mt) REVERT: K 112 PHE cc_start: 0.9356 (m-80) cc_final: 0.8982 (m-80) REVERT: L 35 HIS cc_start: 0.8816 (OUTLIER) cc_final: 0.8521 (m90) REVERT: M 17 ASN cc_start: 0.8507 (t0) cc_final: 0.8302 (t0) REVERT: M 96 ILE cc_start: 0.9825 (mm) cc_final: 0.9575 (mp) REVERT: M 136 MET cc_start: 0.7834 (ppp) cc_final: 0.7515 (ppp) REVERT: N 9 GLN cc_start: 0.8487 (tt0) cc_final: 0.8051 (tt0) REVERT: N 40 LYS cc_start: 0.9472 (mttt) cc_final: 0.8857 (mttp) REVERT: N 57 THR cc_start: 0.9013 (m) cc_final: 0.8730 (p) REVERT: N 75 ILE cc_start: 0.9712 (mm) cc_final: 0.9442 (mm) REVERT: O 19 GLN cc_start: 0.9607 (tm130) cc_final: 0.9228 (tm-30) REVERT: O 60 GLU cc_start: 0.9016 (pt0) cc_final: 0.8792 (pt0) REVERT: O 115 LEU cc_start: 0.8092 (OUTLIER) cc_final: 0.7825 (tp) REVERT: P 25 THR cc_start: 0.9028 (m) cc_final: 0.8620 (p) REVERT: P 29 LYS cc_start: 0.9656 (mttm) cc_final: 0.9422 (ttmm) REVERT: P 111 LYS cc_start: 0.9143 (ptpt) cc_final: 0.8863 (ptpp) REVERT: Q 32 TYR cc_start: 0.8908 (t80) cc_final: 0.8508 (t80) REVERT: Q 34 VAL cc_start: 0.9797 (OUTLIER) cc_final: 0.9554 (p) REVERT: Q 52 GLN cc_start: 0.7934 (mt0) cc_final: 0.7600 (mp10) REVERT: Q 97 ASP cc_start: 0.8741 (t70) cc_final: 0.8066 (t70) REVERT: Q 101 PHE cc_start: 0.8423 (m-80) cc_final: 0.7975 (m-10) REVERT: R 2 TYR cc_start: 0.9104 (p90) cc_final: 0.8700 (p90) REVERT: R 13 ARG cc_start: 0.8617 (tmm-80) cc_final: 0.7841 (ttt-90) REVERT: R 85 LYS cc_start: 0.9059 (mtpp) cc_final: 0.8542 (mtpt) REVERT: R 86 GLN cc_start: 0.8508 (mm110) cc_final: 0.7990 (mm-40) REVERT: R 95 ASP cc_start: 0.8434 (m-30) cc_final: 0.8125 (m-30) REVERT: S 33 LEU cc_start: 0.9581 (OUTLIER) cc_final: 0.9358 (mm) REVERT: S 46 LEU cc_start: 0.9625 (mt) cc_final: 0.9274 (mp) REVERT: S 86 MET cc_start: 0.8553 (tpp) cc_final: 0.8348 (tpp) REVERT: S 95 ARG cc_start: 0.8752 (ttp80) cc_final: 0.8466 (ttp80) REVERT: T 42 GLU cc_start: 0.8850 (mm-30) cc_final: 0.8544 (mm-30) REVERT: T 68 LYS cc_start: 0.6695 (OUTLIER) cc_final: 0.5992 (pttt) REVERT: T 77 ARG cc_start: 0.9365 (ttm110) cc_final: 0.8899 (ttm-80) REVERT: T 92 ASN cc_start: 0.8534 (OUTLIER) cc_final: 0.8254 (t0) REVERT: U 4 LYS cc_start: 0.8730 (mttt) cc_final: 0.8137 (mttt) REVERT: V 48 MET cc_start: 0.8803 (tpt) cc_final: 0.8484 (tpt) REVERT: W 36 ILE cc_start: 0.9416 (mt) cc_final: 0.9084 (mt) REVERT: W 38 VAL cc_start: 0.9648 (t) cc_final: 0.9384 (p) REVERT: W 41 ARG cc_start: 0.9376 (mmt-90) cc_final: 0.8694 (mmt-90) REVERT: W 44 LYS cc_start: 0.9562 (ttmt) cc_final: 0.9236 (ttmm) REVERT: W 68 LYS cc_start: 0.8936 (tptp) cc_final: 0.8508 (tptp) REVERT: X 41 GLU cc_start: 0.8847 (tp30) cc_final: 0.8580 (tp30) REVERT: X 44 LYS cc_start: 0.9411 (mmmm) cc_final: 0.9064 (mmmm) REVERT: X 54 LYS cc_start: 0.9326 (tptp) cc_final: 0.9117 (tptp) REVERT: Y 17 GLU cc_start: 0.8782 (mm-30) cc_final: 0.8499 (mm-30) REVERT: Y 25 GLN cc_start: 0.9592 (tt0) cc_final: 0.9240 (tm-30) REVERT: Y 30 MET cc_start: 0.9176 (mmp) cc_final: 0.8874 (mmm) REVERT: Y 44 LYS cc_start: 0.9567 (tttt) cc_final: 0.9275 (ttmm) REVERT: Y 54 LYS cc_start: 0.9547 (mmmm) cc_final: 0.9251 (mtpp) REVERT: Y 59 GLU cc_start: 0.8824 (pp20) cc_final: 0.8316 (pp20) REVERT: Z 6 LYS cc_start: 0.9461 (mmmt) cc_final: 0.9241 (mmmt) REVERT: Z 19 LYS cc_start: 0.8906 (mmtt) cc_final: 0.8248 (mmtt) REVERT: Z 21 LYS cc_start: 0.9547 (mttt) cc_final: 0.9087 (mmtm) REVERT: b 36 GLU cc_start: 0.7619 (pt0) cc_final: 0.7139 (pt0) REVERT: b 46 ASP cc_start: 0.8735 (m-30) cc_final: 0.8485 (m-30) REVERT: d 1 MET cc_start: 0.7412 (mmm) cc_final: 0.7140 (mmm) REVERT: d 2 LYS cc_start: 0.8941 (tttt) cc_final: 0.8469 (tttm) REVERT: d 3 ARG cc_start: 0.8012 (OUTLIER) cc_final: 0.7540 (tpt170) REVERT: d 22 MET cc_start: 0.8761 (tpp) cc_final: 0.8517 (mmm) REVERT: d 25 LYS cc_start: 0.8876 (ttmt) cc_final: 0.8616 (ttmt) REVERT: e 40 ARG cc_start: 0.8742 (ttt180) cc_final: 0.8139 (ttt-90) REVERT: f 8 LYS cc_start: 0.8880 (mmmt) cc_final: 0.8435 (mmmt) REVERT: f 34 LYS cc_start: 0.9169 (ptmt) cc_final: 0.8870 (ptmt) REVERT: f 35 GLN cc_start: 0.8974 (mt0) cc_final: 0.8729 (pt0) REVERT: g 27 MET cc_start: 0.9186 (mmm) cc_final: 0.8455 (mmm) REVERT: g 49 MET cc_start: 0.9643 (mtp) cc_final: 0.9336 (mtp) REVERT: g 152 LYS cc_start: 0.9593 (pttt) cc_final: 0.9259 (tptt) REVERT: g 213 TYR cc_start: 0.9421 (m-10) cc_final: 0.8999 (m-10) REVERT: h 129 MET cc_start: 0.6924 (mtt) cc_final: 0.6615 (ttt) REVERT: h 130 PHE cc_start: 0.9303 (p90) cc_final: 0.8989 (p90) REVERT: h 181 ASP cc_start: 0.9361 (t0) cc_final: 0.9136 (t70) REVERT: h 185 ASN cc_start: 0.9210 (t0) cc_final: 0.8714 (t0) REVERT: i 40 GLN cc_start: 0.8842 (tt0) cc_final: 0.8525 (pt0) REVERT: i 51 TYR cc_start: 0.9586 (t80) cc_final: 0.9301 (t80) REVERT: i 54 GLN cc_start: 0.9320 (mt0) cc_final: 0.9052 (mm-40) REVERT: i 75 TYR cc_start: 0.9514 (m-80) cc_final: 0.9053 (m-80) REVERT: i 135 TYR cc_start: 0.9321 (t80) cc_final: 0.8991 (t80) REVERT: i 136 GLN cc_start: 0.9370 (mm-40) cc_final: 0.9015 (pm20) REVERT: j 23 LYS cc_start: 0.8685 (tttm) cc_final: 0.8228 (tttp) REVERT: j 31 PHE cc_start: 0.8777 (m-80) cc_final: 0.7754 (m-80) REVERT: j 138 ARG cc_start: 0.9546 (mtt90) cc_final: 0.9243 (mtt90) REVERT: j 145 GLU cc_start: 0.8862 (tp30) cc_final: 0.8621 (mm-30) REVERT: j 162 GLU cc_start: 0.9013 (mp0) cc_final: 0.8744 (mp0) REVERT: k 17 GLN cc_start: 0.9189 (tm-30) cc_final: 0.8588 (tm-30) REVERT: k 21 MET cc_start: 0.9553 (mtm) cc_final: 0.8750 (mtm) REVERT: k 24 ARG cc_start: 0.9150 (ttp-110) cc_final: 0.8618 (ptp90) REVERT: k 62 MET cc_start: 0.9249 (ptp) cc_final: 0.8283 (pmm) REVERT: k 80 PHE cc_start: 0.9399 (m-80) cc_final: 0.9029 (m-80) REVERT: k 87 SER cc_start: 0.8977 (p) cc_final: 0.8287 (m) REVERT: l 26 PHE cc_start: 0.9798 (t80) cc_final: 0.9338 (t80) REVERT: l 28 ASN cc_start: 0.9641 (m110) cc_final: 0.9365 (m110) REVERT: l 31 MET cc_start: 0.8756 (ttp) cc_final: 0.8356 (ttp) REVERT: l 101 MET cc_start: 0.9447 (OUTLIER) cc_final: 0.8888 (ttp) REVERT: l 126 ASP cc_start: 0.9661 (m-30) cc_final: 0.9220 (p0) REVERT: m 3 MET cc_start: 0.9131 (tpp) cc_final: 0.8927 (tpp) REVERT: m 10 MET cc_start: 0.9183 (tmm) cc_final: 0.8576 (tmm) REVERT: m 76 GLN cc_start: 0.9291 (mt0) cc_final: 0.9084 (mp-120) REVERT: m 80 ARG cc_start: 0.9510 (mtm110) cc_final: 0.9241 (mtm110) REVERT: m 86 TYR cc_start: 0.9057 (m-10) cc_final: 0.8847 (m-80) REVERT: m 124 GLU cc_start: 0.9021 (tt0) cc_final: 0.8471 (tm-30) REVERT: m 126 ILE cc_start: 0.9702 (mt) cc_final: 0.8807 (mt) REVERT: n 39 PHE cc_start: 0.8939 (m-80) cc_final: 0.8650 (m-80) REVERT: n 46 MET cc_start: 0.8972 (ppp) cc_final: 0.8758 (ppp) REVERT: n 57 MET cc_start: 0.9273 (ttt) cc_final: 0.9023 (tpp) REVERT: n 89 GLU cc_start: 0.9478 (tp30) cc_final: 0.8979 (tp30) REVERT: n 126 GLN cc_start: 0.9402 (OUTLIER) cc_final: 0.8348 (tp-100) REVERT: o 46 LYS cc_start: 0.9248 (mttt) cc_final: 0.8918 (mtpp) REVERT: o 65 TYR cc_start: 0.8623 (m-80) cc_final: 0.8384 (m-80) REVERT: o 66 GLU cc_start: 0.9079 (pt0) cc_final: 0.7896 (pm20) REVERT: o 88 MET cc_start: 0.9245 (OUTLIER) cc_final: 0.9021 (ptt) REVERT: p 87 LYS cc_start: 0.9204 (ttmm) cc_final: 0.8954 (mttt) REVERT: p 94 GLU cc_start: 0.8843 (tp30) cc_final: 0.8431 (tp30) REVERT: p 100 LEU cc_start: 0.9620 (mt) cc_final: 0.9287 (pp) REVERT: q 29 GLN cc_start: 0.9036 (mp10) cc_final: 0.8745 (mp10) REVERT: q 38 TYR cc_start: 0.8259 (p90) cc_final: 0.7994 (p90) REVERT: q 44 LYS cc_start: 0.8369 (mptt) cc_final: 0.7594 (tmtt) REVERT: q 67 ILE cc_start: 0.8154 (mt) cc_final: 0.7928 (mp) REVERT: q 70 GLU cc_start: 0.8455 (mt-10) cc_final: 0.8204 (mp0) REVERT: q 83 ARG cc_start: 0.9431 (ppt-90) cc_final: 0.8625 (ttp-110) REVERT: q 112 GLN cc_start: 0.6838 (mt0) cc_final: 0.6551 (mp10) REVERT: q 117 TYR cc_start: 0.9258 (m-80) cc_final: 0.8609 (m-80) REVERT: r 23 TYR cc_start: 0.9172 (t80) cc_final: 0.8399 (t80) REVERT: r 69 LEU cc_start: 0.9235 (tp) cc_final: 0.8941 (tp) REVERT: r 75 MET cc_start: 0.8951 (mmm) cc_final: 0.8704 (mmm) REVERT: r 81 MET cc_start: 0.8957 (mmm) cc_final: 0.8745 (mmm) REVERT: r 100 GLN cc_start: 0.8664 (mp10) cc_final: 0.8230 (mp10) REVERT: r 103 LYS cc_start: 0.8304 (tttt) cc_final: 0.7778 (tttm) REVERT: s 6 MET cc_start: 0.9360 (mmm) cc_final: 0.8936 (tpt) REVERT: s 33 ASP cc_start: 0.8939 (t0) cc_final: 0.8432 (t70) REVERT: s 62 ASN cc_start: 0.9440 (m-40) cc_final: 0.9210 (m110) REVERT: s 74 LEU cc_start: 0.9433 (mm) cc_final: 0.9207 (tt) REVERT: s 77 PHE cc_start: 0.9496 (m-10) cc_final: 0.8901 (m-10) REVERT: s 79 LEU cc_start: 0.8469 (mt) cc_final: 0.8174 (tp) REVERT: s 82 ILE cc_start: 0.9365 (mt) cc_final: 0.9156 (tt) REVERT: s 86 GLU cc_start: 0.9029 (mt-10) cc_final: 0.8704 (mt-10) REVERT: t 2 SER cc_start: 0.7340 (m) cc_final: 0.7074 (m) REVERT: t 6 GLU cc_start: 0.9391 (mp0) cc_final: 0.9002 (pm20) REVERT: t 14 GLU cc_start: 0.8499 (pt0) cc_final: 0.8226 (pt0) REVERT: t 18 ASP cc_start: 0.9344 (OUTLIER) cc_final: 0.8518 (p0) REVERT: t 37 ASN cc_start: 0.9272 (m-40) cc_final: 0.8948 (p0) REVERT: t 48 LYS cc_start: 0.9283 (mmtt) cc_final: 0.9057 (mmtt) REVERT: t 59 MET cc_start: 0.9329 (mtt) cc_final: 0.9013 (mmp) REVERT: t 71 LYS cc_start: 0.9222 (mtpp) cc_final: 0.8879 (ttmt) REVERT: u 1 MET cc_start: 0.8145 (pmt) cc_final: 0.7677 (tpt) REVERT: u 31 ARG cc_start: 0.7235 (ttp-110) cc_final: 0.6910 (ttp-110) REVERT: u 34 GLU cc_start: 0.9507 (tm-30) cc_final: 0.9051 (tm-30) REVERT: u 51 ARG cc_start: 0.8492 (ttp-110) cc_final: 0.8223 (ttp-110) REVERT: u 53 ASP cc_start: 0.9286 (t0) cc_final: 0.9015 (t0) REVERT: v 7 THR cc_start: 0.8346 (OUTLIER) cc_final: 0.7296 (t) REVERT: v 9 GLN cc_start: 0.7576 (mt0) cc_final: 0.6438 (tp-100) REVERT: v 60 GLU cc_start: 0.8871 (tt0) cc_final: 0.8248 (tp30) REVERT: x 15 LEU cc_start: 0.9498 (tt) cc_final: 0.9137 (mt) REVERT: x 44 MET cc_start: 0.9303 (mtt) cc_final: 0.8671 (ptp) REVERT: y 4 ILE cc_start: 0.8433 (mt) cc_final: 0.8214 (mp) REVERT: y 21 ASN cc_start: 0.9511 (m-40) cc_final: 0.9234 (t0) REVERT: y 28 MET cc_start: 0.9449 (tmm) cc_final: 0.8881 (ppp) REVERT: y 31 PHE cc_start: 0.9431 (m-80) cc_final: 0.9131 (m-10) REVERT: y 48 GLN cc_start: 0.9659 (mm-40) cc_final: 0.9303 (mm-40) REVERT: y 51 PHE cc_start: 0.9431 (t80) cc_final: 0.8910 (t80) REVERT: y 52 ASN cc_start: 0.9333 (m110) cc_final: 0.9048 (m110) REVERT: y 53 GLU cc_start: 0.9386 (mm-30) cc_final: 0.9137 (mm-30) REVERT: y 66 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.7998 (mm) REVERT: y 84 ASN cc_start: 0.9244 (m-40) cc_final: 0.8704 (p0) REVERT: z 37 PHE cc_start: 0.8726 (p90) cc_final: 0.8073 (p90) REVERT: z 54 LYS cc_start: 0.9211 (tttt) cc_final: 0.8799 (tttt) REVERT: z 58 LYS cc_start: 0.9148 (pttt) cc_final: 0.8677 (pttp) REVERT: H 79 PHE cc_start: 0.8253 (p90) cc_final: 0.7523 (p90) REVERT: A 134 MET cc_start: 0.8600 (mpp) cc_final: 0.8272 (mmm) REVERT: A 186 ARG cc_start: 0.7717 (ptt180) cc_final: 0.7493 (ptt180) outliers start: 231 outliers final: 187 residues processed: 1290 average time/residue: 1.3625 time to fit residues: 3049.7197 Evaluate side-chains 1350 residues out of total 4812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 204 poor density : 1146 time to evaluate : 6.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 38 SER Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 125 LYS Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 264 ASP Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 176 ASP Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain D residue 90 GLN Chi-restraints excluded: chain D residue 136 GLN Chi-restraints excluded: chain D residue 175 ILE Chi-restraints excluded: chain E residue 17 MET Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain E residue 52 ASN Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 20 ASN Chi-restraints excluded: chain F residue 42 GLU Chi-restraints excluded: chain F residue 155 GLU Chi-restraints excluded: chain F residue 166 ASP Chi-restraints excluded: chain F residue 176 LYS Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain J residue 9 GLU Chi-restraints excluded: chain J residue 49 ASP Chi-restraints excluded: chain J residue 109 LEU Chi-restraints excluded: chain J residue 114 LEU Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 29 HIS Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 90 ASN Chi-restraints excluded: chain K residue 107 LEU Chi-restraints excluded: chain L residue 35 HIS Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain L residue 122 VAL Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 42 THR Chi-restraints excluded: chain M residue 124 LEU Chi-restraints excluded: chain M residue 132 THR Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain N residue 28 LEU Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain O residue 28 VAL Chi-restraints excluded: chain O residue 48 LEU Chi-restraints excluded: chain O residue 53 THR Chi-restraints excluded: chain O residue 62 LEU Chi-restraints excluded: chain O residue 69 ASP Chi-restraints excluded: chain O residue 89 ASP Chi-restraints excluded: chain O residue 93 ASP Chi-restraints excluded: chain O residue 115 LEU Chi-restraints excluded: chain P residue 13 MET Chi-restraints excluded: chain P residue 48 ILE Chi-restraints excluded: chain P residue 60 THR Chi-restraints excluded: chain P residue 85 SER Chi-restraints excluded: chain P residue 104 THR Chi-restraints excluded: chain P residue 110 ILE Chi-restraints excluded: chain Q residue 34 VAL Chi-restraints excluded: chain R residue 38 VAL Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 33 LEU Chi-restraints excluded: chain S residue 67 ASP Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain S residue 81 SER Chi-restraints excluded: chain T residue 60 THR Chi-restraints excluded: chain T residue 68 LYS Chi-restraints excluded: chain T residue 73 ARG Chi-restraints excluded: chain T residue 92 ASN Chi-restraints excluded: chain U residue 8 ASP Chi-restraints excluded: chain U residue 12 ILE Chi-restraints excluded: chain U residue 28 VAL Chi-restraints excluded: chain U residue 37 GLU Chi-restraints excluded: chain U residue 65 ILE Chi-restraints excluded: chain U residue 72 ILE Chi-restraints excluded: chain W residue 10 THR Chi-restraints excluded: chain W residue 12 ASN Chi-restraints excluded: chain W residue 58 THR Chi-restraints excluded: chain W residue 76 ASN Chi-restraints excluded: chain X residue 22 LEU Chi-restraints excluded: chain X residue 33 LEU Chi-restraints excluded: chain X residue 71 LEU Chi-restraints excluded: chain Z residue 32 ILE Chi-restraints excluded: chain Z residue 57 VAL Chi-restraints excluded: chain b residue 23 THR Chi-restraints excluded: chain b residue 32 LYS Chi-restraints excluded: chain c residue 29 THR Chi-restraints excluded: chain d residue 3 ARG Chi-restraints excluded: chain d residue 24 THR Chi-restraints excluded: chain d residue 29 GLN Chi-restraints excluded: chain d residue 43 THR Chi-restraints excluded: chain e residue 6 THR Chi-restraints excluded: chain e residue 31 HIS Chi-restraints excluded: chain e residue 38 THR Chi-restraints excluded: chain f residue 22 VAL Chi-restraints excluded: chain f residue 23 ILE Chi-restraints excluded: chain f residue 28 SER Chi-restraints excluded: chain g residue 9 MET Chi-restraints excluded: chain g residue 100 MET Chi-restraints excluded: chain g residue 123 ASP Chi-restraints excluded: chain g residue 129 LEU Chi-restraints excluded: chain g residue 199 VAL Chi-restraints excluded: chain h residue 102 ASN Chi-restraints excluded: chain h residue 162 ILE Chi-restraints excluded: chain h residue 172 ARG Chi-restraints excluded: chain h residue 193 TYR Chi-restraints excluded: chain h residue 200 VAL Chi-restraints excluded: chain i residue 32 CYS Chi-restraints excluded: chain i residue 174 ASP Chi-restraints excluded: chain i residue 190 ASP Chi-restraints excluded: chain j residue 15 LEU Chi-restraints excluded: chain j residue 30 ILE Chi-restraints excluded: chain j residue 37 THR Chi-restraints excluded: chain j residue 134 ILE Chi-restraints excluded: chain j residue 144 LEU Chi-restraints excluded: chain j residue 148 ASN Chi-restraints excluded: chain j residue 164 ILE Chi-restraints excluded: chain k residue 9 MET Chi-restraints excluded: chain k residue 51 ILE Chi-restraints excluded: chain k residue 73 GLU Chi-restraints excluded: chain k residue 82 ASP Chi-restraints excluded: chain k residue 96 VAL Chi-restraints excluded: chain l residue 50 LEU Chi-restraints excluded: chain l residue 89 VAL Chi-restraints excluded: chain l residue 91 VAL Chi-restraints excluded: chain l residue 101 MET Chi-restraints excluded: chain l residue 106 GLU Chi-restraints excluded: chain m residue 27 MET Chi-restraints excluded: chain m residue 38 ASN Chi-restraints excluded: chain m residue 54 ASP Chi-restraints excluded: chain m residue 75 ILE Chi-restraints excluded: chain n residue 30 ILE Chi-restraints excluded: chain n residue 35 LEU Chi-restraints excluded: chain n residue 53 GLU Chi-restraints excluded: chain n residue 111 VAL Chi-restraints excluded: chain n residue 115 LYS Chi-restraints excluded: chain n residue 126 GLN Chi-restraints excluded: chain o residue 17 LEU Chi-restraints excluded: chain o residue 32 THR Chi-restraints excluded: chain o residue 57 VAL Chi-restraints excluded: chain o residue 71 LEU Chi-restraints excluded: chain o residue 74 VAL Chi-restraints excluded: chain o residue 88 MET Chi-restraints excluded: chain p residue 18 ASP Chi-restraints excluded: chain p residue 23 ILE Chi-restraints excluded: chain p residue 30 THR Chi-restraints excluded: chain p residue 32 VAL Chi-restraints excluded: chain p residue 86 VAL Chi-restraints excluded: chain p residue 97 ILE Chi-restraints excluded: chain q residue 16 VAL Chi-restraints excluded: chain q residue 81 LEU Chi-restraints excluded: chain q residue 90 LEU Chi-restraints excluded: chain r residue 49 SER Chi-restraints excluded: chain r residue 55 THR Chi-restraints excluded: chain r residue 64 VAL Chi-restraints excluded: chain r residue 68 ASP Chi-restraints excluded: chain r residue 104 THR Chi-restraints excluded: chain s residue 37 SER Chi-restraints excluded: chain s residue 38 ASP Chi-restraints excluded: chain s residue 48 LEU Chi-restraints excluded: chain s residue 54 ASP Chi-restraints excluded: chain s residue 67 THR Chi-restraints excluded: chain t residue 4 SER Chi-restraints excluded: chain t residue 11 ILE Chi-restraints excluded: chain t residue 18 ASP Chi-restraints excluded: chain t residue 67 LEU Chi-restraints excluded: chain u residue 78 VAL Chi-restraints excluded: chain v residue 7 THR Chi-restraints excluded: chain v residue 67 LEU Chi-restraints excluded: chain v residue 79 VAL Chi-restraints excluded: chain w residue 59 ILE Chi-restraints excluded: chain x residue 13 LEU Chi-restraints excluded: chain x residue 58 VAL Chi-restraints excluded: chain x residue 63 THR Chi-restraints excluded: chain x residue 71 LEU Chi-restraints excluded: chain x residue 79 THR Chi-restraints excluded: chain y residue 27 MET Chi-restraints excluded: chain y residue 66 LEU Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 159 TYR Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 330 ASP Chi-restraints excluded: chain A residue 348 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1027 random chunks: chunk 612 optimal weight: 7.9990 chunk 395 optimal weight: 30.0000 chunk 591 optimal weight: 2.9990 chunk 298 optimal weight: 50.0000 chunk 194 optimal weight: 20.0000 chunk 191 optimal weight: 20.0000 chunk 629 optimal weight: 0.8980 chunk 674 optimal weight: 6.9990 chunk 489 optimal weight: 6.9990 chunk 92 optimal weight: 10.0000 chunk 778 optimal weight: 20.0000 overall best weight: 5.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 128 ASN K 9 ASN ** P 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 19 ASN h 190 HIS i 36 GLN ** j 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.3639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 158320 Z= 0.212 Angle : 0.630 13.899 236734 Z= 0.338 Chirality : 0.034 0.320 30127 Planarity : 0.006 0.125 12767 Dihedral : 24.365 179.094 78854 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 23.87 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.03 % Favored : 94.93 % Rotamer: Outliers : 4.28 % Allowed : 20.24 % Favored : 75.48 % 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: -0.92 (0.11), residues: 5784 helix: 0.45 (0.12), residues: 1972 sheet: -1.04 (0.15), residues: 1062 loop : -1.16 (0.12), residues: 2750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP s 42 HIS 0.010 0.001 HIS e 31 PHE 0.029 0.002 PHE i 182 TYR 0.032 0.002 TYR Q 25 ARG 0.011 0.000 ARG y 18 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11568 Ramachandran restraints generated. 5784 Oldfield, 0 Emsley, 5784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11568 Ramachandran restraints generated. 5784 Oldfield, 0 Emsley, 5784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1403 residues out of total 4812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 206 poor density : 1197 time to evaluate : 6.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 60 GLN cc_start: 0.8746 (mt0) cc_final: 0.8444 (mp10) REVERT: B 229 ASP cc_start: 0.8728 (m-30) cc_final: 0.8441 (m-30) REVERT: B 236 GLU cc_start: 0.7675 (mm-30) cc_final: 0.7345 (mm-30) REVERT: C 1 MET cc_start: 0.7428 (mmm) cc_final: 0.7116 (tpp) REVERT: C 149 ASN cc_start: 0.8295 (t0) cc_final: 0.7473 (t0) REVERT: D 46 GLN cc_start: 0.9502 (mp10) cc_final: 0.8396 (mp10) REVERT: D 62 GLN cc_start: 0.8835 (tp40) cc_final: 0.8554 (tp40) REVERT: D 100 MET cc_start: 0.8695 (mtp) cc_final: 0.8410 (mtp) REVERT: D 115 GLN cc_start: 0.8537 (mm110) cc_final: 0.8230 (mm110) REVERT: D 136 GLN cc_start: 0.9399 (tp-100) cc_final: 0.9073 (tp-100) REVERT: E 7 TYR cc_start: 0.9461 (t80) cc_final: 0.9080 (t80) REVERT: E 26 MET cc_start: 0.9194 (mtp) cc_final: 0.8733 (mtt) REVERT: E 44 ILE cc_start: 0.9403 (OUTLIER) cc_final: 0.9107 (mt) REVERT: E 83 TYR cc_start: 0.9167 (m-10) cc_final: 0.8717 (m-10) REVERT: E 90 THR cc_start: 0.9523 (m) cc_final: 0.9017 (p) REVERT: E 96 MET cc_start: 0.9464 (ttp) cc_final: 0.9071 (ttp) REVERT: E 99 PHE cc_start: 0.9307 (t80) cc_final: 0.9080 (t80) REVERT: E 128 TYR cc_start: 0.8703 (t80) cc_final: 0.8396 (t80) REVERT: E 130 MET cc_start: 0.8601 (ppp) cc_final: 0.8138 (ppp) REVERT: E 143 TYR cc_start: 0.9058 (t80) cc_final: 0.8834 (t80) REVERT: F 60 ASP cc_start: 0.9100 (p0) cc_final: 0.8808 (p0) REVERT: F 147 ASP cc_start: 0.9003 (m-30) cc_final: 0.8791 (m-30) REVERT: F 176 LYS cc_start: 0.4425 (OUTLIER) cc_final: 0.3039 (mttt) REVERT: G 1 MET cc_start: 0.9248 (tpp) cc_final: 0.8967 (tpp) REVERT: J 75 TYR cc_start: 0.9229 (m-80) cc_final: 0.8777 (m-10) REVERT: J 92 MET cc_start: 0.9235 (mmm) cc_final: 0.8644 (mmt) REVERT: J 102 GLU cc_start: 0.8406 (mt-10) cc_final: 0.7836 (mt-10) REVERT: K 1 MET cc_start: 0.8550 (ttm) cc_final: 0.8139 (ttm) REVERT: K 17 ARG cc_start: 0.8280 (mmp80) cc_final: 0.7867 (mmp80) REVERT: K 23 LYS cc_start: 0.9283 (tppt) cc_final: 0.8570 (tppp) REVERT: K 29 HIS cc_start: 0.8051 (OUTLIER) cc_final: 0.7237 (m-70) REVERT: K 44 LYS cc_start: 0.9625 (mmtt) cc_final: 0.9288 (mmmm) REVERT: K 45 GLU cc_start: 0.8422 (tm-30) cc_final: 0.8174 (tp30) REVERT: K 66 LYS cc_start: 0.9486 (ttmm) cc_final: 0.9095 (ttpp) REVERT: K 87 LEU cc_start: 0.9452 (mt) cc_final: 0.9213 (mt) REVERT: K 112 PHE cc_start: 0.9335 (m-80) cc_final: 0.8985 (m-80) REVERT: L 35 HIS cc_start: 0.8778 (OUTLIER) cc_final: 0.8468 (m90) REVERT: M 96 ILE cc_start: 0.9820 (mm) cc_final: 0.9575 (mp) REVERT: M 136 MET cc_start: 0.7882 (ppp) cc_final: 0.7584 (ppp) REVERT: N 40 LYS cc_start: 0.9410 (mttt) cc_final: 0.8787 (mttp) REVERT: N 57 THR cc_start: 0.8983 (m) cc_final: 0.8709 (p) REVERT: N 75 ILE cc_start: 0.9715 (mm) cc_final: 0.9438 (mm) REVERT: O 19 GLN cc_start: 0.9598 (tm130) cc_final: 0.9218 (tm-30) REVERT: O 35 ILE cc_start: 0.8720 (OUTLIER) cc_final: 0.8517 (mm) REVERT: O 60 GLU cc_start: 0.9110 (pt0) cc_final: 0.8863 (pt0) REVERT: O 115 LEU cc_start: 0.8054 (OUTLIER) cc_final: 0.7837 (tp) REVERT: P 6 LYS cc_start: 0.9018 (mmtm) cc_final: 0.8775 (mmtm) REVERT: P 25 THR cc_start: 0.8992 (m) cc_final: 0.8603 (p) REVERT: Q 32 TYR cc_start: 0.8872 (t80) cc_final: 0.8370 (t80) REVERT: Q 52 GLN cc_start: 0.7848 (mt0) cc_final: 0.7524 (mp10) REVERT: Q 97 ASP cc_start: 0.8765 (t70) cc_final: 0.8387 (t70) REVERT: Q 101 PHE cc_start: 0.8348 (m-80) cc_final: 0.7861 (m-10) REVERT: R 2 TYR cc_start: 0.9043 (p90) cc_final: 0.8774 (p90) REVERT: R 73 LYS cc_start: 0.9174 (tppp) cc_final: 0.8860 (tptp) REVERT: R 85 LYS cc_start: 0.9038 (mtpp) cc_final: 0.8642 (mtpp) REVERT: R 95 ASP cc_start: 0.8518 (m-30) cc_final: 0.8226 (m-30) REVERT: S 33 LEU cc_start: 0.9570 (OUTLIER) cc_final: 0.9348 (mm) REVERT: S 46 LEU cc_start: 0.9628 (mt) cc_final: 0.9257 (mp) REVERT: S 86 MET cc_start: 0.8562 (tpp) cc_final: 0.8307 (tpp) REVERT: S 95 ARG cc_start: 0.8727 (ttp80) cc_final: 0.8438 (ttp80) REVERT: T 42 GLU cc_start: 0.8859 (mm-30) cc_final: 0.8558 (mm-30) REVERT: T 68 LYS cc_start: 0.6530 (OUTLIER) cc_final: 0.5914 (pttt) REVERT: T 77 ARG cc_start: 0.9393 (ttm110) cc_final: 0.8904 (ttm-80) REVERT: T 92 ASN cc_start: 0.8500 (OUTLIER) cc_final: 0.8227 (t0) REVERT: U 4 LYS cc_start: 0.8727 (mttt) cc_final: 0.8124 (mttt) REVERT: V 48 MET cc_start: 0.8805 (tpt) cc_final: 0.8501 (tpt) REVERT: W 36 ILE cc_start: 0.9450 (mt) cc_final: 0.9114 (mt) REVERT: W 38 VAL cc_start: 0.9651 (t) cc_final: 0.9401 (p) REVERT: W 41 ARG cc_start: 0.9369 (mmt-90) cc_final: 0.8746 (mmt-90) REVERT: W 44 LYS cc_start: 0.9569 (ttmt) cc_final: 0.9240 (ttmm) REVERT: W 68 LYS cc_start: 0.8937 (tptp) cc_final: 0.8509 (tptp) REVERT: X 41 GLU cc_start: 0.8845 (tp30) cc_final: 0.8595 (tp30) REVERT: X 44 LYS cc_start: 0.9403 (mmmm) cc_final: 0.9104 (mmmm) REVERT: X 54 LYS cc_start: 0.9318 (tptp) cc_final: 0.9111 (tptp) REVERT: Y 12 GLU cc_start: 0.9085 (pm20) cc_final: 0.8838 (pm20) REVERT: Y 17 GLU cc_start: 0.8805 (mm-30) cc_final: 0.8483 (mm-30) REVERT: Y 25 GLN cc_start: 0.9576 (tt0) cc_final: 0.9223 (tm-30) REVERT: Y 30 MET cc_start: 0.9150 (mmp) cc_final: 0.8865 (mmm) REVERT: Z 19 LYS cc_start: 0.8884 (mmtt) cc_final: 0.8564 (mmtt) REVERT: Z 21 LYS cc_start: 0.9536 (mttt) cc_final: 0.9066 (mmtm) REVERT: b 36 GLU cc_start: 0.7570 (pt0) cc_final: 0.7154 (pt0) REVERT: b 46 ASP cc_start: 0.8695 (m-30) cc_final: 0.8461 (m-30) REVERT: d 2 LYS cc_start: 0.8911 (tttt) cc_final: 0.8422 (tttm) REVERT: d 3 ARG cc_start: 0.7970 (OUTLIER) cc_final: 0.7492 (tpt170) REVERT: e 40 ARG cc_start: 0.8769 (ttt180) cc_final: 0.8362 (ttt-90) REVERT: f 8 LYS cc_start: 0.8840 (mmmt) cc_final: 0.8337 (mmmt) REVERT: f 34 LYS cc_start: 0.9145 (ptmt) cc_final: 0.8843 (ptmt) REVERT: f 35 GLN cc_start: 0.8962 (mt0) cc_final: 0.8722 (pt0) REVERT: g 27 MET cc_start: 0.9163 (mmm) cc_final: 0.8481 (mmm) REVERT: g 49 MET cc_start: 0.9646 (mtp) cc_final: 0.9344 (mtp) REVERT: g 213 TYR cc_start: 0.9414 (m-10) cc_final: 0.8999 (m-10) REVERT: h 129 MET cc_start: 0.6669 (mtt) cc_final: 0.6283 (ttt) REVERT: h 130 PHE cc_start: 0.9223 (p90) cc_final: 0.8897 (p90) REVERT: h 181 ASP cc_start: 0.9359 (t0) cc_final: 0.9136 (t70) REVERT: h 185 ASN cc_start: 0.9209 (t0) cc_final: 0.8680 (t0) REVERT: i 40 GLN cc_start: 0.8860 (tt0) cc_final: 0.8562 (pt0) REVERT: i 51 TYR cc_start: 0.9558 (t80) cc_final: 0.9299 (t80) REVERT: i 54 GLN cc_start: 0.9309 (mt0) cc_final: 0.9047 (mm-40) REVERT: i 75 TYR cc_start: 0.9496 (m-80) cc_final: 0.9044 (m-80) REVERT: i 135 TYR cc_start: 0.9309 (t80) cc_final: 0.9091 (t80) REVERT: i 136 GLN cc_start: 0.9331 (mm-40) cc_final: 0.9075 (pm20) REVERT: j 23 LYS cc_start: 0.8719 (tttm) cc_final: 0.8351 (tttp) REVERT: j 31 PHE cc_start: 0.8747 (m-80) cc_final: 0.7767 (m-80) REVERT: j 138 ARG cc_start: 0.9522 (mtt90) cc_final: 0.9132 (mtt90) REVERT: k 17 GLN cc_start: 0.9124 (tm-30) cc_final: 0.8622 (tm-30) REVERT: k 21 MET cc_start: 0.9527 (mtm) cc_final: 0.8726 (mtm) REVERT: k 24 ARG cc_start: 0.9146 (ttp-110) cc_final: 0.8618 (ptp90) REVERT: k 80 PHE cc_start: 0.9370 (m-80) cc_final: 0.9079 (m-80) REVERT: k 87 SER cc_start: 0.8943 (p) cc_final: 0.8269 (m) REVERT: l 26 PHE cc_start: 0.9796 (t80) cc_final: 0.9339 (t80) REVERT: l 28 ASN cc_start: 0.9391 (m110) cc_final: 0.9144 (m-40) REVERT: l 31 MET cc_start: 0.8739 (ttp) cc_final: 0.8349 (ttp) REVERT: l 101 MET cc_start: 0.9438 (OUTLIER) cc_final: 0.8890 (ttp) REVERT: l 116 MET cc_start: 0.9525 (mmm) cc_final: 0.9242 (mpp) REVERT: l 126 ASP cc_start: 0.9650 (m-30) cc_final: 0.9221 (p0) REVERT: m 10 MET cc_start: 0.9163 (tmm) cc_final: 0.8552 (tmm) REVERT: m 76 GLN cc_start: 0.9280 (mt0) cc_final: 0.9076 (mp-120) REVERT: m 80 ARG cc_start: 0.9527 (mtm110) cc_final: 0.9294 (mtm110) REVERT: m 96 MET cc_start: 0.9506 (tpp) cc_final: 0.8495 (tpp) REVERT: m 124 GLU cc_start: 0.8989 (tt0) cc_final: 0.8465 (tm-30) REVERT: m 126 ILE cc_start: 0.9706 (mt) cc_final: 0.8790 (mt) REVERT: n 39 PHE cc_start: 0.8912 (m-80) cc_final: 0.8573 (m-80) REVERT: n 60 LYS cc_start: 0.9542 (tppt) cc_final: 0.9300 (mmtm) REVERT: n 89 GLU cc_start: 0.9456 (tp30) cc_final: 0.9089 (tp30) REVERT: n 126 GLN cc_start: 0.9416 (OUTLIER) cc_final: 0.8377 (tp-100) REVERT: o 46 LYS cc_start: 0.9121 (mttt) cc_final: 0.8688 (mtpp) REVERT: o 66 GLU cc_start: 0.9050 (pt0) cc_final: 0.8111 (pm20) REVERT: o 88 MET cc_start: 0.9238 (OUTLIER) cc_final: 0.8999 (ptt) REVERT: p 15 GLN cc_start: 0.8758 (tp40) cc_final: 0.8473 (tp-100) REVERT: p 94 GLU cc_start: 0.8869 (tp30) cc_final: 0.8549 (tp30) REVERT: p 100 LEU cc_start: 0.9636 (mt) cc_final: 0.9325 (pp) REVERT: q 29 GLN cc_start: 0.9016 (mp10) cc_final: 0.8739 (mp10) REVERT: q 38 TYR cc_start: 0.8552 (p90) cc_final: 0.8349 (p90) REVERT: q 44 LYS cc_start: 0.8359 (mptt) cc_final: 0.7589 (tmtt) REVERT: q 67 ILE cc_start: 0.8174 (mt) cc_final: 0.7947 (mp) REVERT: q 70 GLU cc_start: 0.8395 (mt-10) cc_final: 0.8185 (mp0) REVERT: q 83 ARG cc_start: 0.9425 (ppt-90) cc_final: 0.8610 (ttp-110) REVERT: q 117 TYR cc_start: 0.9228 (m-80) cc_final: 0.8565 (m-80) REVERT: r 23 TYR cc_start: 0.9205 (t80) cc_final: 0.8482 (t80) REVERT: r 69 LEU cc_start: 0.9200 (tp) cc_final: 0.8916 (tp) REVERT: r 75 MET cc_start: 0.8965 (mmm) cc_final: 0.8685 (mmm) REVERT: r 100 GLN cc_start: 0.8657 (mp10) cc_final: 0.8230 (mp10) REVERT: r 103 LYS cc_start: 0.8357 (tttt) cc_final: 0.7899 (tttm) REVERT: s 33 ASP cc_start: 0.8954 (t0) cc_final: 0.8457 (t70) REVERT: s 74 LEU cc_start: 0.9438 (mm) cc_final: 0.9212 (tt) REVERT: s 77 PHE cc_start: 0.9535 (m-10) cc_final: 0.9012 (m-10) REVERT: s 79 LEU cc_start: 0.8530 (mt) cc_final: 0.8076 (tp) REVERT: s 86 GLU cc_start: 0.8994 (mt-10) cc_final: 0.8670 (mt-10) REVERT: t 2 SER cc_start: 0.7217 (m) cc_final: 0.6933 (m) REVERT: t 6 GLU cc_start: 0.9400 (mp0) cc_final: 0.9005 (pm20) REVERT: t 14 GLU cc_start: 0.8457 (pt0) cc_final: 0.8181 (pt0) REVERT: t 18 ASP cc_start: 0.9325 (OUTLIER) cc_final: 0.8496 (p0) REVERT: t 37 ASN cc_start: 0.9275 (m-40) cc_final: 0.8936 (p0) REVERT: t 48 LYS cc_start: 0.9286 (mmtt) cc_final: 0.9046 (mmtt) REVERT: t 59 MET cc_start: 0.9333 (mtt) cc_final: 0.8989 (mmp) REVERT: u 1 MET cc_start: 0.8086 (pmt) cc_final: 0.7639 (tpt) REVERT: u 31 ARG cc_start: 0.7526 (ttp-110) cc_final: 0.7244 (ttp-110) REVERT: u 34 GLU cc_start: 0.9485 (tm-30) cc_final: 0.9161 (tm-30) REVERT: u 51 ARG cc_start: 0.8478 (ttp-110) cc_final: 0.8169 (ttp-110) REVERT: u 53 ASP cc_start: 0.9276 (t0) cc_final: 0.9012 (t0) REVERT: v 7 THR cc_start: 0.8397 (OUTLIER) cc_final: 0.7331 (t) REVERT: v 9 GLN cc_start: 0.7254 (mt0) cc_final: 0.6180 (tp40) REVERT: v 11 ARG cc_start: 0.9411 (mmp80) cc_final: 0.9208 (mmp80) REVERT: v 30 LYS cc_start: 0.9154 (ttmm) cc_final: 0.8716 (tppp) REVERT: v 36 LYS cc_start: 0.8839 (tptm) cc_final: 0.8445 (tptt) REVERT: v 60 GLU cc_start: 0.8901 (tt0) cc_final: 0.8321 (tp30) REVERT: x 15 LEU cc_start: 0.9492 (tt) cc_final: 0.9138 (mt) REVERT: x 44 MET cc_start: 0.9307 (mtt) cc_final: 0.8752 (ptp) REVERT: y 4 ILE cc_start: 0.8383 (mt) cc_final: 0.8160 (mp) REVERT: y 25 ARG cc_start: 0.9312 (mtm-85) cc_final: 0.8815 (mtt-85) REVERT: y 28 MET cc_start: 0.9495 (tmm) cc_final: 0.8927 (ppp) REVERT: y 31 PHE cc_start: 0.9418 (m-80) cc_final: 0.9113 (m-10) REVERT: y 48 GLN cc_start: 0.9678 (mm-40) cc_final: 0.9384 (mm-40) REVERT: y 51 PHE cc_start: 0.9412 (t80) cc_final: 0.8894 (t80) REVERT: y 52 ASN cc_start: 0.9328 (m110) cc_final: 0.9033 (m110) REVERT: y 53 GLU cc_start: 0.9389 (mm-30) cc_final: 0.9136 (mm-30) REVERT: y 84 ASN cc_start: 0.9204 (m-40) cc_final: 0.8637 (p0) REVERT: z 44 GLU cc_start: 0.8527 (mm-30) cc_final: 0.8286 (mp0) REVERT: z 54 LYS cc_start: 0.9214 (tttt) cc_final: 0.8810 (tttt) REVERT: z 58 LYS cc_start: 0.9150 (pttt) cc_final: 0.8667 (pttp) REVERT: H 79 PHE cc_start: 0.8315 (p90) cc_final: 0.7614 (p90) REVERT: A 149 MET cc_start: 0.7077 (ppp) cc_final: 0.6752 (ppp) REVERT: A 186 ARG cc_start: 0.7631 (ptt180) cc_final: 0.7413 (ptt180) REVERT: A 206 MET cc_start: 0.8272 (ptp) cc_final: 0.8054 (ptt) outliers start: 206 outliers final: 172 residues processed: 1290 average time/residue: 1.2867 time to fit residues: 2869.6917 Evaluate side-chains 1329 residues out of total 4812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 187 poor density : 1142 time to evaluate : 6.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 SER Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 125 LYS Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 264 ASP Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 176 ASP Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain D residue 90 GLN Chi-restraints excluded: chain D residue 175 ILE Chi-restraints excluded: chain E residue 17 MET Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 166 ASP Chi-restraints excluded: chain F residue 176 LYS Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain J residue 9 GLU Chi-restraints excluded: chain J residue 109 LEU Chi-restraints excluded: chain J residue 114 LEU Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 29 HIS Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain K residue 52 VAL Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 107 LEU Chi-restraints excluded: chain L residue 35 HIS Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain L residue 122 VAL Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 42 THR Chi-restraints excluded: chain M residue 124 LEU Chi-restraints excluded: chain M residue 132 THR Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain N residue 28 LEU Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain O residue 28 VAL Chi-restraints excluded: chain O residue 35 ILE Chi-restraints excluded: chain O residue 48 LEU Chi-restraints excluded: chain O residue 62 LEU Chi-restraints excluded: chain O residue 69 ASP Chi-restraints excluded: chain O residue 89 ASP Chi-restraints excluded: chain O residue 93 ASP Chi-restraints excluded: chain O residue 115 LEU Chi-restraints excluded: chain P residue 13 MET Chi-restraints excluded: chain P residue 48 ILE Chi-restraints excluded: chain P residue 60 THR Chi-restraints excluded: chain P residue 85 SER Chi-restraints excluded: chain P residue 104 THR Chi-restraints excluded: chain P residue 110 ILE Chi-restraints excluded: chain Q residue 34 VAL Chi-restraints excluded: chain Q residue 104 VAL Chi-restraints excluded: chain R residue 38 VAL Chi-restraints excluded: chain R residue 41 ILE Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 33 LEU Chi-restraints excluded: chain S residue 67 ASP Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain S residue 81 SER Chi-restraints excluded: chain T residue 60 THR Chi-restraints excluded: chain T residue 68 LYS Chi-restraints excluded: chain T residue 92 ASN Chi-restraints excluded: chain U residue 8 ASP Chi-restraints excluded: chain U residue 12 ILE Chi-restraints excluded: chain U residue 15 THR Chi-restraints excluded: chain U residue 28 VAL Chi-restraints excluded: chain U residue 65 ILE Chi-restraints excluded: chain U residue 72 ILE Chi-restraints excluded: chain V residue 42 LEU Chi-restraints excluded: chain W residue 10 THR Chi-restraints excluded: chain W residue 12 ASN Chi-restraints excluded: chain W residue 58 THR Chi-restraints excluded: chain X residue 33 LEU Chi-restraints excluded: chain X residue 71 LEU Chi-restraints excluded: chain Z residue 32 ILE Chi-restraints excluded: chain Z residue 57 VAL Chi-restraints excluded: chain b residue 23 THR Chi-restraints excluded: chain b residue 32 LYS Chi-restraints excluded: chain c residue 29 THR Chi-restraints excluded: chain c residue 48 ILE Chi-restraints excluded: chain d residue 3 ARG Chi-restraints excluded: chain d residue 4 THR Chi-restraints excluded: chain d residue 24 THR Chi-restraints excluded: chain d residue 42 LEU Chi-restraints excluded: chain e residue 6 THR Chi-restraints excluded: chain e residue 31 HIS Chi-restraints excluded: chain f residue 22 VAL Chi-restraints excluded: chain f residue 23 ILE Chi-restraints excluded: chain f residue 28 SER Chi-restraints excluded: chain g residue 9 MET Chi-restraints excluded: chain g residue 100 MET Chi-restraints excluded: chain g residue 123 ASP Chi-restraints excluded: chain g residue 129 LEU Chi-restraints excluded: chain g residue 199 VAL Chi-restraints excluded: chain h residue 102 ASN Chi-restraints excluded: chain h residue 162 ILE Chi-restraints excluded: chain h residue 172 ARG Chi-restraints excluded: chain h residue 193 TYR Chi-restraints excluded: chain h residue 200 VAL Chi-restraints excluded: chain i residue 32 CYS Chi-restraints excluded: chain i residue 174 ASP Chi-restraints excluded: chain i residue 190 ASP Chi-restraints excluded: chain j residue 15 LEU Chi-restraints excluded: chain j residue 30 ILE Chi-restraints excluded: chain j residue 37 THR Chi-restraints excluded: chain j residue 92 SER Chi-restraints excluded: chain j residue 144 LEU Chi-restraints excluded: chain j residue 148 ASN Chi-restraints excluded: chain j residue 164 ILE Chi-restraints excluded: chain k residue 9 MET Chi-restraints excluded: chain k residue 51 ILE Chi-restraints excluded: chain k residue 73 GLU Chi-restraints excluded: chain k residue 90 MET Chi-restraints excluded: chain k residue 96 VAL Chi-restraints excluded: chain l residue 89 VAL Chi-restraints excluded: chain l residue 91 VAL Chi-restraints excluded: chain l residue 101 MET Chi-restraints excluded: chain l residue 106 GLU Chi-restraints excluded: chain m residue 27 MET Chi-restraints excluded: chain m residue 38 ASN Chi-restraints excluded: chain m residue 75 ILE Chi-restraints excluded: chain n residue 30 ILE Chi-restraints excluded: chain n residue 35 LEU Chi-restraints excluded: chain n residue 53 GLU Chi-restraints excluded: chain n residue 111 VAL Chi-restraints excluded: chain n residue 115 LYS Chi-restraints excluded: chain n residue 126 GLN Chi-restraints excluded: chain o residue 10 LEU Chi-restraints excluded: chain o residue 17 LEU Chi-restraints excluded: chain o residue 32 THR Chi-restraints excluded: chain o residue 57 VAL Chi-restraints excluded: chain o residue 74 VAL Chi-restraints excluded: chain o residue 88 MET Chi-restraints excluded: chain p residue 18 ASP Chi-restraints excluded: chain p residue 23 ILE Chi-restraints excluded: chain p residue 30 THR Chi-restraints excluded: chain p residue 32 VAL Chi-restraints excluded: chain p residue 86 VAL Chi-restraints excluded: chain p residue 97 ILE Chi-restraints excluded: chain q residue 16 VAL Chi-restraints excluded: chain q residue 90 LEU Chi-restraints excluded: chain r residue 64 VAL Chi-restraints excluded: chain r residue 68 ASP Chi-restraints excluded: chain r residue 74 SER Chi-restraints excluded: chain r residue 104 THR Chi-restraints excluded: chain s residue 37 SER Chi-restraints excluded: chain s residue 38 ASP Chi-restraints excluded: chain s residue 48 LEU Chi-restraints excluded: chain s residue 54 ASP Chi-restraints excluded: chain s residue 67 THR Chi-restraints excluded: chain t residue 4 SER Chi-restraints excluded: chain t residue 11 ILE Chi-restraints excluded: chain t residue 18 ASP Chi-restraints excluded: chain t residue 67 LEU Chi-restraints excluded: chain v residue 7 THR Chi-restraints excluded: chain v residue 67 LEU Chi-restraints excluded: chain v residue 79 VAL Chi-restraints excluded: chain w residue 59 ILE Chi-restraints excluded: chain x residue 13 LEU Chi-restraints excluded: chain x residue 58 VAL Chi-restraints excluded: chain x residue 63 THR Chi-restraints excluded: chain x residue 71 LEU Chi-restraints excluded: chain y residue 27 MET Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 159 TYR Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 330 ASP Chi-restraints excluded: chain A residue 348 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1027 random chunks: chunk 900 optimal weight: 9.9990 chunk 948 optimal weight: 7.9990 chunk 865 optimal weight: 0.0060 chunk 922 optimal weight: 20.0000 chunk 555 optimal weight: 1.9990 chunk 401 optimal weight: 40.0000 chunk 724 optimal weight: 20.0000 chunk 283 optimal weight: 10.0000 chunk 833 optimal weight: 8.9990 chunk 872 optimal weight: 8.9990 chunk 919 optimal weight: 6.9990 overall best weight: 5.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 128 ASN N 9 GLN ** P 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 39 GLN ** g 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 122 GLN h 190 HIS i 36 GLN ** j 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 75 GLN ** r 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.3760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 158320 Z= 0.216 Angle : 0.642 17.974 236734 Z= 0.342 Chirality : 0.034 0.292 30127 Planarity : 0.006 0.125 12767 Dihedral : 24.328 178.950 78854 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 23.95 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.22 % Favored : 94.74 % Rotamer: Outliers : 4.34 % Allowed : 20.72 % Favored : 74.94 % 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: -0.89 (0.11), residues: 5784 helix: 0.42 (0.12), residues: 1973 sheet: -0.95 (0.16), residues: 1041 loop : -1.13 (0.12), residues: 2770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP A 144 HIS 0.011 0.001 HIS e 31 PHE 0.028 0.002 PHE i 182 TYR 0.034 0.002 TYR Q 25 ARG 0.015 0.001 ARG c 28 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11568 Ramachandran restraints generated. 5784 Oldfield, 0 Emsley, 5784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11568 Ramachandran restraints generated. 5784 Oldfield, 0 Emsley, 5784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1401 residues out of total 4812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 209 poor density : 1192 time to evaluate : 6.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 60 GLN cc_start: 0.8752 (mt0) cc_final: 0.8443 (mp10) REVERT: B 83 TYR cc_start: 0.8592 (t80) cc_final: 0.8367 (t80) REVERT: B 236 GLU cc_start: 0.7654 (mm-30) cc_final: 0.7320 (mm-30) REVERT: C 1 MET cc_start: 0.7422 (mmm) cc_final: 0.7182 (tpp) REVERT: C 149 ASN cc_start: 0.8394 (t0) cc_final: 0.7615 (t0) REVERT: D 46 GLN cc_start: 0.9536 (mp10) cc_final: 0.8477 (mp10) REVERT: D 62 GLN cc_start: 0.8835 (tp40) cc_final: 0.8557 (tp40) REVERT: D 78 TRP cc_start: 0.9268 (m-10) cc_final: 0.9000 (m-10) REVERT: D 100 MET cc_start: 0.8689 (mtp) cc_final: 0.8406 (mtp) REVERT: D 115 GLN cc_start: 0.8515 (mm110) cc_final: 0.8214 (mm110) REVERT: D 136 GLN cc_start: 0.9388 (tp-100) cc_final: 0.9070 (tp-100) REVERT: E 7 TYR cc_start: 0.9477 (t80) cc_final: 0.9104 (t80) REVERT: E 26 MET cc_start: 0.9188 (mtp) cc_final: 0.8739 (mtt) REVERT: E 44 ILE cc_start: 0.9410 (OUTLIER) cc_final: 0.9107 (mt) REVERT: E 83 TYR cc_start: 0.9185 (m-10) cc_final: 0.8714 (m-10) REVERT: E 90 THR cc_start: 0.9556 (m) cc_final: 0.9083 (p) REVERT: E 96 MET cc_start: 0.9440 (ttp) cc_final: 0.9055 (ttp) REVERT: E 128 TYR cc_start: 0.8693 (t80) cc_final: 0.8454 (t80) REVERT: E 130 MET cc_start: 0.8596 (ppp) cc_final: 0.8154 (ppp) REVERT: F 60 ASP cc_start: 0.9098 (p0) cc_final: 0.8808 (p0) REVERT: F 147 ASP cc_start: 0.9004 (m-30) cc_final: 0.8803 (m-30) REVERT: F 176 LYS cc_start: 0.4426 (OUTLIER) cc_final: 0.3041 (mttt) REVERT: J 75 TYR cc_start: 0.9177 (m-80) cc_final: 0.8671 (m-10) REVERT: J 92 MET cc_start: 0.9313 (mmm) cc_final: 0.8600 (mmt) REVERT: J 102 GLU cc_start: 0.8412 (mt-10) cc_final: 0.7823 (mt-10) REVERT: K 1 MET cc_start: 0.8550 (ttm) cc_final: 0.8138 (ttm) REVERT: K 17 ARG cc_start: 0.8352 (mmp80) cc_final: 0.7953 (mmp80) REVERT: K 23 LYS cc_start: 0.9287 (tppt) cc_final: 0.8527 (tppp) REVERT: K 29 HIS cc_start: 0.8052 (OUTLIER) cc_final: 0.7348 (m-70) REVERT: K 44 LYS cc_start: 0.9626 (mmtt) cc_final: 0.9273 (mmmm) REVERT: K 45 GLU cc_start: 0.8429 (tm-30) cc_final: 0.8169 (tp30) REVERT: K 66 LYS cc_start: 0.9483 (ttmm) cc_final: 0.9135 (ttpp) REVERT: K 87 LEU cc_start: 0.9363 (mt) cc_final: 0.9082 (tp) REVERT: K 88 ASN cc_start: 0.8880 (t0) cc_final: 0.8469 (t0) REVERT: K 112 PHE cc_start: 0.9336 (m-80) cc_final: 0.8985 (m-80) REVERT: L 35 HIS cc_start: 0.8776 (OUTLIER) cc_final: 0.8458 (m90) REVERT: M 91 TYR cc_start: 0.8590 (p90) cc_final: 0.8274 (p90) REVERT: M 96 ILE cc_start: 0.9812 (mm) cc_final: 0.9580 (mp) REVERT: M 136 MET cc_start: 0.7873 (ppp) cc_final: 0.7569 (ppp) REVERT: N 40 LYS cc_start: 0.9381 (mttt) cc_final: 0.8915 (mttp) REVERT: N 57 THR cc_start: 0.8991 (m) cc_final: 0.8719 (p) REVERT: N 75 ILE cc_start: 0.9723 (mm) cc_final: 0.9487 (mm) REVERT: O 19 GLN cc_start: 0.9591 (tm130) cc_final: 0.9206 (tm-30) REVERT: O 115 LEU cc_start: 0.7977 (OUTLIER) cc_final: 0.7722 (tp) REVERT: P 6 LYS cc_start: 0.9050 (mmtm) cc_final: 0.8808 (mmtm) REVERT: P 25 THR cc_start: 0.8988 (m) cc_final: 0.8590 (p) REVERT: P 63 LYS cc_start: 0.8875 (ptmm) cc_final: 0.8660 (ptmm) REVERT: Q 32 TYR cc_start: 0.8878 (t80) cc_final: 0.8378 (t80) REVERT: Q 52 GLN cc_start: 0.7852 (mt0) cc_final: 0.7504 (mp10) REVERT: Q 97 ASP cc_start: 0.8753 (t70) cc_final: 0.8376 (t70) REVERT: Q 101 PHE cc_start: 0.8351 (m-80) cc_final: 0.7860 (m-10) REVERT: R 2 TYR cc_start: 0.9032 (p90) cc_final: 0.8679 (p90) REVERT: R 73 LYS cc_start: 0.9170 (tppp) cc_final: 0.8850 (tptp) REVERT: R 85 LYS cc_start: 0.9053 (mtpp) cc_final: 0.8664 (mtpp) REVERT: R 95 ASP cc_start: 0.8444 (m-30) cc_final: 0.8170 (m-30) REVERT: S 33 LEU cc_start: 0.9584 (OUTLIER) cc_final: 0.9377 (mm) REVERT: S 46 LEU cc_start: 0.9616 (mt) cc_final: 0.9255 (mp) REVERT: S 86 MET cc_start: 0.8563 (tpp) cc_final: 0.8309 (tpp) REVERT: S 95 ARG cc_start: 0.8747 (ttp80) cc_final: 0.8461 (ttp80) REVERT: T 4 GLU cc_start: 0.8410 (pm20) cc_final: 0.7960 (pm20) REVERT: T 5 GLU cc_start: 0.8314 (pm20) cc_final: 0.7894 (pm20) REVERT: T 42 GLU cc_start: 0.8853 (mm-30) cc_final: 0.8533 (mm-30) REVERT: T 68 LYS cc_start: 0.6532 (OUTLIER) cc_final: 0.6132 (pttt) REVERT: T 77 ARG cc_start: 0.9395 (ttm110) cc_final: 0.8919 (ttm-80) REVERT: U 4 LYS cc_start: 0.8739 (mttt) cc_final: 0.8133 (mttt) REVERT: V 48 MET cc_start: 0.8786 (tpt) cc_final: 0.8427 (tpt) REVERT: V 50 MET cc_start: 0.8005 (ptm) cc_final: 0.7517 (ttp) REVERT: W 36 ILE cc_start: 0.9455 (mt) cc_final: 0.9120 (mt) REVERT: W 38 VAL cc_start: 0.9649 (t) cc_final: 0.9399 (p) REVERT: W 41 ARG cc_start: 0.9358 (mmt-90) cc_final: 0.8737 (mmt-90) REVERT: W 44 LYS cc_start: 0.9564 (ttmt) cc_final: 0.9250 (ttmm) REVERT: W 68 LYS cc_start: 0.8936 (tptp) cc_final: 0.8513 (tptp) REVERT: X 41 GLU cc_start: 0.8838 (tp30) cc_final: 0.8572 (tp30) REVERT: X 44 LYS cc_start: 0.9406 (mmmm) cc_final: 0.9112 (mmmm) REVERT: Y 17 GLU cc_start: 0.8814 (mm-30) cc_final: 0.8475 (mm-30) REVERT: Y 25 GLN cc_start: 0.9554 (tt0) cc_final: 0.9182 (tm-30) REVERT: Y 30 MET cc_start: 0.9145 (mmp) cc_final: 0.8862 (mmm) REVERT: Y 54 LYS cc_start: 0.9506 (mmmm) cc_final: 0.9217 (mtpp) REVERT: Z 19 LYS cc_start: 0.8880 (mmtt) cc_final: 0.8198 (mmtt) REVERT: Z 21 LYS cc_start: 0.9534 (mttt) cc_final: 0.9057 (mmtm) REVERT: b 36 GLU cc_start: 0.7565 (pt0) cc_final: 0.7128 (pt0) REVERT: b 46 ASP cc_start: 0.8690 (m-30) cc_final: 0.8439 (m-30) REVERT: d 2 LYS cc_start: 0.8871 (tttt) cc_final: 0.8374 (tttm) REVERT: e 40 ARG cc_start: 0.8771 (ttt180) cc_final: 0.8372 (ttt-90) REVERT: f 8 LYS cc_start: 0.8829 (mmmt) cc_final: 0.8160 (mmmt) REVERT: f 35 GLN cc_start: 0.8973 (mt0) cc_final: 0.8726 (pt0) REVERT: g 27 MET cc_start: 0.9167 (mmm) cc_final: 0.8403 (mmm) REVERT: g 49 MET cc_start: 0.9648 (mtp) cc_final: 0.9346 (mtp) REVERT: g 213 TYR cc_start: 0.9412 (m-10) cc_final: 0.9002 (m-10) REVERT: h 129 MET cc_start: 0.6599 (mtt) cc_final: 0.6229 (ttt) REVERT: h 130 PHE cc_start: 0.9228 (p90) cc_final: 0.8957 (p90) REVERT: h 181 ASP cc_start: 0.9359 (t0) cc_final: 0.9133 (t70) REVERT: h 185 ASN cc_start: 0.9200 (t0) cc_final: 0.8659 (t0) REVERT: i 40 GLN cc_start: 0.8845 (tt0) cc_final: 0.8564 (pt0) REVERT: i 51 TYR cc_start: 0.9546 (t80) cc_final: 0.9327 (t80) REVERT: i 54 GLN cc_start: 0.9291 (mt0) cc_final: 0.9046 (mm-40) REVERT: i 75 TYR cc_start: 0.9495 (m-80) cc_final: 0.9045 (m-80) REVERT: i 135 TYR cc_start: 0.9272 (t80) cc_final: 0.9058 (t80) REVERT: i 136 GLN cc_start: 0.9333 (mm-40) cc_final: 0.9051 (pm20) REVERT: j 23 LYS cc_start: 0.8726 (tttm) cc_final: 0.8224 (tttp) REVERT: j 31 PHE cc_start: 0.8754 (m-80) cc_final: 0.7748 (m-80) REVERT: j 54 ARG cc_start: 0.8377 (mtt90) cc_final: 0.7888 (mpt180) REVERT: j 138 ARG cc_start: 0.9513 (mtt90) cc_final: 0.9102 (mtt90) REVERT: k 8 PHE cc_start: 0.8635 (p90) cc_final: 0.8433 (p90) REVERT: k 17 GLN cc_start: 0.9123 (tm-30) cc_final: 0.8650 (tm-30) REVERT: k 21 MET cc_start: 0.9527 (mtm) cc_final: 0.8686 (mtm) REVERT: k 24 ARG cc_start: 0.9152 (ttp-110) cc_final: 0.8630 (ptp90) REVERT: k 62 MET cc_start: 0.9289 (ptp) cc_final: 0.8232 (pmm) REVERT: k 80 PHE cc_start: 0.9361 (m-80) cc_final: 0.9059 (m-80) REVERT: k 87 SER cc_start: 0.9013 (p) cc_final: 0.8367 (m) REVERT: l 26 PHE cc_start: 0.9799 (t80) cc_final: 0.9337 (t80) REVERT: l 28 ASN cc_start: 0.9423 (m110) cc_final: 0.9195 (m110) REVERT: l 31 MET cc_start: 0.8724 (ttp) cc_final: 0.8347 (ttp) REVERT: l 101 MET cc_start: 0.9437 (OUTLIER) cc_final: 0.8887 (ttp) REVERT: m 3 MET cc_start: 0.9234 (tpp) cc_final: 0.8975 (tpp) REVERT: m 10 MET cc_start: 0.9205 (tmm) cc_final: 0.8604 (tmm) REVERT: m 76 GLN cc_start: 0.9276 (mt0) cc_final: 0.9074 (mp-120) REVERT: m 80 ARG cc_start: 0.9520 (mtm110) cc_final: 0.9280 (mtm110) REVERT: m 96 MET cc_start: 0.9501 (tpp) cc_final: 0.8643 (tpp) REVERT: m 126 ILE cc_start: 0.9713 (mt) cc_final: 0.8846 (mt) REVERT: n 39 PHE cc_start: 0.8894 (m-80) cc_final: 0.8522 (m-80) REVERT: n 54 LEU cc_start: 0.9260 (tp) cc_final: 0.8852 (pp) REVERT: n 57 MET cc_start: 0.9002 (tpp) cc_final: 0.8236 (tpp) REVERT: n 88 MET cc_start: 0.8959 (mmm) cc_final: 0.8736 (mmp) REVERT: n 89 GLU cc_start: 0.9573 (tp30) cc_final: 0.8905 (tp30) REVERT: n 126 GLN cc_start: 0.9417 (OUTLIER) cc_final: 0.8384 (tp-100) REVERT: n 127 PHE cc_start: 0.9331 (t80) cc_final: 0.9083 (t80) REVERT: o 30 LYS cc_start: 0.9372 (tttt) cc_final: 0.9139 (ptpt) REVERT: o 46 LYS cc_start: 0.9140 (mttt) cc_final: 0.8722 (mtpp) REVERT: o 66 GLU cc_start: 0.9046 (pt0) cc_final: 0.8115 (pm20) REVERT: p 15 GLN cc_start: 0.8759 (tp40) cc_final: 0.8506 (tp-100) REVERT: p 18 ASP cc_start: 0.7901 (OUTLIER) cc_final: 0.7125 (m-30) REVERT: p 81 ASN cc_start: 0.8782 (m-40) cc_final: 0.8470 (t0) REVERT: p 94 GLU cc_start: 0.8869 (tp30) cc_final: 0.8538 (tp30) REVERT: p 100 LEU cc_start: 0.9644 (mt) cc_final: 0.9334 (pp) REVERT: q 29 GLN cc_start: 0.8995 (mp10) cc_final: 0.8636 (mp10) REVERT: q 38 TYR cc_start: 0.8641 (p90) cc_final: 0.8438 (p90) REVERT: q 43 LYS cc_start: 0.8726 (mttm) cc_final: 0.8448 (mttm) REVERT: q 44 LYS cc_start: 0.8333 (mptt) cc_final: 0.7576 (tmtt) REVERT: q 67 ILE cc_start: 0.8125 (mt) cc_final: 0.7892 (mp) REVERT: q 83 ARG cc_start: 0.9407 (ppt-90) cc_final: 0.8611 (ttp-110) REVERT: q 117 TYR cc_start: 0.9201 (m-80) cc_final: 0.8513 (m-80) REVERT: r 23 TYR cc_start: 0.9153 (t80) cc_final: 0.8482 (t80) REVERT: r 69 LEU cc_start: 0.9196 (tp) cc_final: 0.8957 (tp) REVERT: r 75 MET cc_start: 0.8988 (mmm) cc_final: 0.8697 (mmm) REVERT: r 100 GLN cc_start: 0.8651 (mp10) cc_final: 0.8225 (mp10) REVERT: r 103 LYS cc_start: 0.8517 (tttt) cc_final: 0.8105 (tttm) REVERT: s 33 ASP cc_start: 0.8929 (t0) cc_final: 0.8452 (t70) REVERT: s 62 ASN cc_start: 0.9446 (m-40) cc_final: 0.9187 (m110) REVERT: s 74 LEU cc_start: 0.9443 (mm) cc_final: 0.9221 (tt) REVERT: s 77 PHE cc_start: 0.9547 (m-10) cc_final: 0.9044 (m-10) REVERT: s 79 LEU cc_start: 0.8580 (mt) cc_final: 0.8123 (tp) REVERT: s 86 GLU cc_start: 0.8930 (mt-10) cc_final: 0.8659 (mt-10) REVERT: t 2 SER cc_start: 0.7205 (m) cc_final: 0.6915 (m) REVERT: t 6 GLU cc_start: 0.9405 (mp0) cc_final: 0.9010 (pm20) REVERT: t 14 GLU cc_start: 0.8485 (pt0) cc_final: 0.8159 (pt0) REVERT: t 18 ASP cc_start: 0.9314 (OUTLIER) cc_final: 0.8487 (p0) REVERT: t 37 ASN cc_start: 0.9279 (m-40) cc_final: 0.8939 (p0) REVERT: t 48 LYS cc_start: 0.9301 (mmtt) cc_final: 0.9061 (mmtt) REVERT: t 59 MET cc_start: 0.9307 (mtt) cc_final: 0.8898 (mmp) REVERT: t 71 LYS cc_start: 0.9149 (mtpp) cc_final: 0.8772 (ttmt) REVERT: u 1 MET cc_start: 0.8111 (pmt) cc_final: 0.7677 (tpt) REVERT: u 31 ARG cc_start: 0.7594 (ttp-110) cc_final: 0.7240 (ttp-110) REVERT: u 34 GLU cc_start: 0.9481 (tm-30) cc_final: 0.9166 (tm-30) REVERT: u 51 ARG cc_start: 0.8491 (ttp-110) cc_final: 0.8117 (ttp-110) REVERT: u 53 ASP cc_start: 0.9271 (t0) cc_final: 0.9005 (t0) REVERT: v 7 THR cc_start: 0.8407 (OUTLIER) cc_final: 0.7339 (t) REVERT: v 9 GLN cc_start: 0.7289 (mt0) cc_final: 0.6213 (tp40) REVERT: v 27 ARG cc_start: 0.8565 (ptt180) cc_final: 0.8193 (ptt-90) REVERT: v 30 LYS cc_start: 0.9170 (ttmm) cc_final: 0.8696 (tppp) REVERT: v 36 LYS cc_start: 0.8806 (tptm) cc_final: 0.8419 (tptt) REVERT: v 60 GLU cc_start: 0.8885 (tt0) cc_final: 0.8336 (tp30) REVERT: x 15 LEU cc_start: 0.9489 (tt) cc_final: 0.9132 (mt) REVERT: x 44 MET cc_start: 0.9118 (mtt) cc_final: 0.8568 (ptp) REVERT: x 73 GLU cc_start: 0.8867 (mt-10) cc_final: 0.8515 (mp0) REVERT: y 4 ILE cc_start: 0.8341 (mt) cc_final: 0.8139 (mp) REVERT: y 28 MET cc_start: 0.9481 (tmm) cc_final: 0.8873 (ppp) REVERT: y 48 GLN cc_start: 0.9715 (mm-40) cc_final: 0.9368 (mm-40) REVERT: y 51 PHE cc_start: 0.9209 (t80) cc_final: 0.8833 (t80) REVERT: y 54 MET cc_start: 0.8847 (ppp) cc_final: 0.8561 (ppp) REVERT: y 84 ASN cc_start: 0.9376 (m-40) cc_final: 0.8860 (p0) REVERT: z 37 PHE cc_start: 0.8462 (p90) cc_final: 0.8210 (p90) REVERT: z 39 GLU cc_start: 0.7882 (mp0) cc_final: 0.7548 (mp0) REVERT: z 44 GLU cc_start: 0.8480 (mm-30) cc_final: 0.8236 (mp0) REVERT: z 54 LYS cc_start: 0.9138 (tttt) cc_final: 0.8820 (ptmt) REVERT: z 58 LYS cc_start: 0.9164 (pttt) cc_final: 0.8711 (pttp) REVERT: H 79 PHE cc_start: 0.8342 (p90) cc_final: 0.7691 (p90) REVERT: A 186 ARG cc_start: 0.7634 (ptt180) cc_final: 0.7413 (ptt180) outliers start: 209 outliers final: 174 residues processed: 1287 average time/residue: 1.4217 time to fit residues: 3191.0878 Evaluate side-chains 1342 residues out of total 4812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 186 poor density : 1156 time to evaluate : 6.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 SER Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 125 LYS Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 264 ASP Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 176 ASP Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain D residue 175 ILE Chi-restraints excluded: chain D residue 188 MET Chi-restraints excluded: chain E residue 17 MET Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 166 ASP Chi-restraints excluded: chain F residue 176 LYS Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain J residue 9 GLU Chi-restraints excluded: chain J residue 14 ASP Chi-restraints excluded: chain J residue 109 LEU Chi-restraints excluded: chain J residue 114 LEU Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 29 HIS Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain K residue 52 VAL Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 107 LEU Chi-restraints excluded: chain L residue 35 HIS Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain L residue 122 VAL Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 41 LEU Chi-restraints excluded: chain M residue 42 THR Chi-restraints excluded: chain M residue 124 LEU Chi-restraints excluded: chain M residue 132 THR Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain O residue 28 VAL Chi-restraints excluded: chain O residue 48 LEU Chi-restraints excluded: chain O residue 62 LEU Chi-restraints excluded: chain O residue 69 ASP Chi-restraints excluded: chain O residue 89 ASP Chi-restraints excluded: chain O residue 93 ASP Chi-restraints excluded: chain O residue 115 LEU Chi-restraints excluded: chain P residue 8 LEU Chi-restraints excluded: chain P residue 48 ILE Chi-restraints excluded: chain P residue 60 THR Chi-restraints excluded: chain P residue 85 SER Chi-restraints excluded: chain P residue 104 THR Chi-restraints excluded: chain P residue 110 ILE Chi-restraints excluded: chain Q residue 34 VAL Chi-restraints excluded: chain R residue 38 VAL Chi-restraints excluded: chain R residue 41 ILE Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 33 LEU Chi-restraints excluded: chain S residue 67 ASP Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain S residue 81 SER Chi-restraints excluded: chain T residue 60 THR Chi-restraints excluded: chain T residue 68 LYS Chi-restraints excluded: chain U residue 8 ASP Chi-restraints excluded: chain U residue 12 ILE Chi-restraints excluded: chain U residue 15 THR Chi-restraints excluded: chain U residue 28 VAL Chi-restraints excluded: chain U residue 65 ILE Chi-restraints excluded: chain U residue 72 ILE Chi-restraints excluded: chain V residue 42 LEU Chi-restraints excluded: chain W residue 10 THR Chi-restraints excluded: chain W residue 12 ASN Chi-restraints excluded: chain W residue 58 THR Chi-restraints excluded: chain W residue 76 ASN Chi-restraints excluded: chain X residue 22 LEU Chi-restraints excluded: chain X residue 33 LEU Chi-restraints excluded: chain X residue 71 LEU Chi-restraints excluded: chain Z residue 32 ILE Chi-restraints excluded: chain Z residue 57 VAL Chi-restraints excluded: chain b residue 23 THR Chi-restraints excluded: chain c residue 29 THR Chi-restraints excluded: chain c residue 48 ILE Chi-restraints excluded: chain d residue 4 THR Chi-restraints excluded: chain d residue 24 THR Chi-restraints excluded: chain d residue 42 LEU Chi-restraints excluded: chain d residue 45 SER Chi-restraints excluded: chain e residue 6 THR Chi-restraints excluded: chain e residue 31 HIS Chi-restraints excluded: chain f residue 22 VAL Chi-restraints excluded: chain f residue 23 ILE Chi-restraints excluded: chain f residue 28 SER Chi-restraints excluded: chain g residue 9 MET Chi-restraints excluded: chain g residue 100 MET Chi-restraints excluded: chain g residue 122 GLN Chi-restraints excluded: chain g residue 129 LEU Chi-restraints excluded: chain g residue 199 VAL Chi-restraints excluded: chain h residue 102 ASN Chi-restraints excluded: chain h residue 162 ILE Chi-restraints excluded: chain h residue 172 ARG Chi-restraints excluded: chain h residue 193 TYR Chi-restraints excluded: chain h residue 200 VAL Chi-restraints excluded: chain i residue 32 CYS Chi-restraints excluded: chain i residue 190 ASP Chi-restraints excluded: chain j residue 15 LEU Chi-restraints excluded: chain j residue 30 ILE Chi-restraints excluded: chain j residue 37 THR Chi-restraints excluded: chain j residue 92 SER Chi-restraints excluded: chain j residue 134 ILE Chi-restraints excluded: chain j residue 144 LEU Chi-restraints excluded: chain j residue 148 ASN Chi-restraints excluded: chain j residue 164 ILE Chi-restraints excluded: chain k residue 51 ILE Chi-restraints excluded: chain k residue 90 MET Chi-restraints excluded: chain k residue 96 VAL Chi-restraints excluded: chain l residue 89 VAL Chi-restraints excluded: chain l residue 91 VAL Chi-restraints excluded: chain l residue 101 MET Chi-restraints excluded: chain m residue 27 MET Chi-restraints excluded: chain m residue 38 ASN Chi-restraints excluded: chain m residue 54 ASP Chi-restraints excluded: chain m residue 75 ILE Chi-restraints excluded: chain n residue 30 ILE Chi-restraints excluded: chain n residue 35 LEU Chi-restraints excluded: chain n residue 53 GLU Chi-restraints excluded: chain n residue 111 VAL Chi-restraints excluded: chain n residue 115 LYS Chi-restraints excluded: chain n residue 126 GLN Chi-restraints excluded: chain o residue 17 LEU Chi-restraints excluded: chain o residue 32 THR Chi-restraints excluded: chain o residue 57 VAL Chi-restraints excluded: chain o residue 74 VAL Chi-restraints excluded: chain p residue 18 ASP Chi-restraints excluded: chain p residue 23 ILE Chi-restraints excluded: chain p residue 30 THR Chi-restraints excluded: chain p residue 32 VAL Chi-restraints excluded: chain p residue 46 THR Chi-restraints excluded: chain p residue 86 VAL Chi-restraints excluded: chain p residue 97 ILE Chi-restraints excluded: chain q residue 16 VAL Chi-restraints excluded: chain q residue 82 ILE Chi-restraints excluded: chain q residue 90 LEU Chi-restraints excluded: chain r residue 64 VAL Chi-restraints excluded: chain r residue 68 ASP Chi-restraints excluded: chain r residue 74 SER Chi-restraints excluded: chain r residue 104 THR Chi-restraints excluded: chain s residue 48 LEU Chi-restraints excluded: chain s residue 54 ASP Chi-restraints excluded: chain s residue 67 THR Chi-restraints excluded: chain t residue 4 SER Chi-restraints excluded: chain t residue 11 ILE Chi-restraints excluded: chain t residue 18 ASP Chi-restraints excluded: chain t residue 67 LEU Chi-restraints excluded: chain v residue 7 THR Chi-restraints excluded: chain v residue 67 LEU Chi-restraints excluded: chain v residue 79 VAL Chi-restraints excluded: chain w residue 59 ILE Chi-restraints excluded: chain x residue 13 LEU Chi-restraints excluded: chain x residue 58 VAL Chi-restraints excluded: chain x residue 63 THR Chi-restraints excluded: chain x residue 71 LEU Chi-restraints excluded: chain x residue 79 THR Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 159 TYR Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 330 ASP Chi-restraints excluded: chain A residue 348 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1027 random chunks: chunk 605 optimal weight: 7.9990 chunk 975 optimal weight: 6.9990 chunk 595 optimal weight: 0.8980 chunk 462 optimal weight: 6.9990 chunk 678 optimal weight: 1.9990 chunk 1023 optimal weight: 9.9990 chunk 941 optimal weight: 7.9990 chunk 814 optimal weight: 20.0000 chunk 84 optimal weight: 20.0000 chunk 629 optimal weight: 7.9990 chunk 499 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: ** C 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 128 ASN ** P 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 48 GLN Y 38 GLN ** d 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 19 ASN h 190 HIS i 36 GLN ** j 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 50 ASN ** x 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.3909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 158320 Z= 0.200 Angle : 0.641 14.680 236734 Z= 0.341 Chirality : 0.033 0.318 30127 Planarity : 0.006 0.125 12767 Dihedral : 24.282 179.520 78854 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 23.41 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.94 % Favored : 95.02 % Rotamer: Outliers : 3.91 % Allowed : 21.45 % Favored : 74.65 % 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: -0.84 (0.11), residues: 5784 helix: 0.43 (0.12), residues: 1958 sheet: -0.90 (0.16), residues: 1042 loop : -1.07 (0.12), residues: 2784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP A 144 HIS 0.012 0.001 HIS e 31 PHE 0.024 0.002 PHE n 127 TYR 0.034 0.002 TYR Q 25 ARG 0.011 0.000 ARG y 18 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11568 Ramachandran restraints generated. 5784 Oldfield, 0 Emsley, 5784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11568 Ramachandran restraints generated. 5784 Oldfield, 0 Emsley, 5784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1378 residues out of total 4812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 188 poor density : 1190 time to evaluate : 8.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 83 TYR cc_start: 0.8522 (t80) cc_final: 0.8268 (t80) REVERT: B 229 ASP cc_start: 0.8802 (m-30) cc_final: 0.8067 (m-30) REVERT: B 236 GLU cc_start: 0.7628 (mm-30) cc_final: 0.7297 (mm-30) REVERT: C 1 MET cc_start: 0.7407 (mmm) cc_final: 0.7163 (tpp) REVERT: C 149 ASN cc_start: 0.8357 (t0) cc_final: 0.7565 (t0) REVERT: D 46 GLN cc_start: 0.9540 (mp10) cc_final: 0.8334 (mp10) REVERT: D 61 ARG cc_start: 0.9139 (ptt-90) cc_final: 0.8830 (ptt90) REVERT: D 62 GLN cc_start: 0.8887 (tp40) cc_final: 0.8584 (tp40) REVERT: D 78 TRP cc_start: 0.9246 (m-10) cc_final: 0.8937 (m-10) REVERT: D 115 GLN cc_start: 0.8550 (mm110) cc_final: 0.8241 (mm110) REVERT: D 136 GLN cc_start: 0.9393 (tp-100) cc_final: 0.9067 (tp-100) REVERT: E 7 TYR cc_start: 0.9470 (t80) cc_final: 0.9190 (t80) REVERT: E 26 MET cc_start: 0.9151 (mtp) cc_final: 0.8674 (mtt) REVERT: E 44 ILE cc_start: 0.9408 (OUTLIER) cc_final: 0.9108 (mt) REVERT: E 83 TYR cc_start: 0.9188 (m-10) cc_final: 0.8705 (m-10) REVERT: E 90 THR cc_start: 0.9573 (m) cc_final: 0.9102 (p) REVERT: E 96 MET cc_start: 0.9446 (ttp) cc_final: 0.9157 (ttp) REVERT: E 128 TYR cc_start: 0.8692 (t80) cc_final: 0.8433 (t80) REVERT: E 130 MET cc_start: 0.8593 (ppp) cc_final: 0.8157 (ppp) REVERT: F 60 ASP cc_start: 0.9084 (p0) cc_final: 0.8799 (p0) REVERT: F 176 LYS cc_start: 0.4432 (OUTLIER) cc_final: 0.3047 (mttt) REVERT: G 46 PHE cc_start: 0.9540 (t80) cc_final: 0.9037 (t80) REVERT: J 75 TYR cc_start: 0.9168 (m-80) cc_final: 0.8645 (m-10) REVERT: J 92 MET cc_start: 0.9349 (mmm) cc_final: 0.8700 (mmt) REVERT: J 102 GLU cc_start: 0.8402 (mt-10) cc_final: 0.7800 (mt-10) REVERT: K 1 MET cc_start: 0.8526 (ttm) cc_final: 0.8094 (ttm) REVERT: K 5 GLN cc_start: 0.9346 (mm110) cc_final: 0.9137 (mm-40) REVERT: K 23 LYS cc_start: 0.9146 (tppt) cc_final: 0.7841 (tppp) REVERT: K 29 HIS cc_start: 0.8007 (OUTLIER) cc_final: 0.7334 (m-70) REVERT: K 40 LYS cc_start: 0.9432 (tppt) cc_final: 0.9224 (tttt) REVERT: K 44 LYS cc_start: 0.9629 (mmtt) cc_final: 0.9277 (mmmm) REVERT: K 45 GLU cc_start: 0.8518 (tm-30) cc_final: 0.8195 (tp30) REVERT: K 66 LYS cc_start: 0.9473 (ttmm) cc_final: 0.9137 (ttpp) REVERT: K 87 LEU cc_start: 0.9462 (mt) cc_final: 0.9190 (mt) REVERT: K 88 ASN cc_start: 0.8758 (t0) cc_final: 0.8277 (t0) REVERT: K 112 PHE cc_start: 0.9339 (m-80) cc_final: 0.8959 (m-80) REVERT: L 35 HIS cc_start: 0.8764 (OUTLIER) cc_final: 0.8451 (m90) REVERT: M 91 TYR cc_start: 0.8524 (p90) cc_final: 0.8308 (p90) REVERT: M 136 MET cc_start: 0.7852 (ppp) cc_final: 0.7599 (ppp) REVERT: N 40 LYS cc_start: 0.9381 (mttt) cc_final: 0.8940 (mttp) REVERT: N 57 THR cc_start: 0.8982 (m) cc_final: 0.8711 (p) REVERT: N 75 ILE cc_start: 0.9700 (mm) cc_final: 0.9395 (mm) REVERT: O 19 GLN cc_start: 0.9590 (tm130) cc_final: 0.9198 (tm-30) REVERT: P 6 LYS cc_start: 0.9065 (mmtm) cc_final: 0.8826 (mmtm) REVERT: P 25 THR cc_start: 0.8947 (m) cc_final: 0.8551 (p) REVERT: P 63 LYS cc_start: 0.8862 (ptmm) cc_final: 0.8656 (ptmm) REVERT: Q 32 TYR cc_start: 0.8868 (t80) cc_final: 0.8367 (t80) REVERT: Q 52 GLN cc_start: 0.7856 (mt0) cc_final: 0.7479 (mp10) REVERT: Q 80 ILE cc_start: 0.9814 (mm) cc_final: 0.9564 (tt) REVERT: Q 97 ASP cc_start: 0.8696 (t70) cc_final: 0.8377 (t70) REVERT: Q 101 PHE cc_start: 0.8341 (m-80) cc_final: 0.7842 (m-10) REVERT: R 2 TYR cc_start: 0.9051 (p90) cc_final: 0.8721 (p90) REVERT: R 73 LYS cc_start: 0.9154 (tppp) cc_final: 0.8850 (tptp) REVERT: R 85 LYS cc_start: 0.9058 (mtpp) cc_final: 0.8661 (mtpp) REVERT: R 95 ASP cc_start: 0.8481 (m-30) cc_final: 0.8210 (m-30) REVERT: S 33 LEU cc_start: 0.9589 (OUTLIER) cc_final: 0.9368 (mm) REVERT: S 46 LEU cc_start: 0.9607 (mt) cc_final: 0.9266 (mp) REVERT: S 86 MET cc_start: 0.8561 (tpp) cc_final: 0.8309 (tpp) REVERT: S 95 ARG cc_start: 0.8754 (ttp80) cc_final: 0.8473 (ttp80) REVERT: T 5 GLU cc_start: 0.8519 (pm20) cc_final: 0.8274 (pm20) REVERT: T 77 ARG cc_start: 0.9387 (ttm110) cc_final: 0.8924 (ttm-80) REVERT: U 4 LYS cc_start: 0.8824 (mttt) cc_final: 0.8265 (mttt) REVERT: V 48 MET cc_start: 0.8752 (tpt) cc_final: 0.8473 (tpt) REVERT: V 50 MET cc_start: 0.8118 (ptm) cc_final: 0.7631 (ttp) REVERT: W 36 ILE cc_start: 0.9473 (mt) cc_final: 0.9141 (mt) REVERT: W 38 VAL cc_start: 0.9647 (t) cc_final: 0.9439 (p) REVERT: W 41 ARG cc_start: 0.9379 (mmt-90) cc_final: 0.8785 (mmt-90) REVERT: W 44 LYS cc_start: 0.9559 (ttmt) cc_final: 0.9256 (ttmm) REVERT: W 68 LYS cc_start: 0.8907 (tptp) cc_final: 0.8475 (tptp) REVERT: X 41 GLU cc_start: 0.8835 (tp30) cc_final: 0.8591 (tp30) REVERT: X 44 LYS cc_start: 0.9398 (mmmm) cc_final: 0.9107 (mmmm) REVERT: Y 12 GLU cc_start: 0.9143 (pm20) cc_final: 0.8714 (pm20) REVERT: Y 17 GLU cc_start: 0.8855 (mm-30) cc_final: 0.8507 (mm-30) REVERT: Y 25 GLN cc_start: 0.9548 (tt0) cc_final: 0.9173 (tm-30) REVERT: Y 30 MET cc_start: 0.9141 (mmp) cc_final: 0.8872 (mmm) REVERT: Y 44 LYS cc_start: 0.9696 (tttp) cc_final: 0.9304 (tppt) REVERT: Y 54 LYS cc_start: 0.9514 (mmmm) cc_final: 0.9249 (mmmm) REVERT: Z 19 LYS cc_start: 0.8884 (mmtt) cc_final: 0.8208 (mmtt) REVERT: Z 21 LYS cc_start: 0.9528 (mttt) cc_final: 0.9055 (mmtm) REVERT: b 36 GLU cc_start: 0.7691 (pt0) cc_final: 0.7325 (pt0) REVERT: b 46 ASP cc_start: 0.8678 (m-30) cc_final: 0.8429 (m-30) REVERT: d 1 MET cc_start: 0.7304 (mmm) cc_final: 0.6932 (mmm) REVERT: d 2 LYS cc_start: 0.8958 (tttt) cc_final: 0.8425 (tttm) REVERT: e 40 ARG cc_start: 0.8763 (ttt180) cc_final: 0.8399 (ttt-90) REVERT: f 8 LYS cc_start: 0.8792 (mmmt) cc_final: 0.8431 (mmtt) REVERT: f 34 LYS cc_start: 0.9208 (ptmt) cc_final: 0.8764 (pttt) REVERT: f 35 GLN cc_start: 0.8997 (mt0) cc_final: 0.8771 (pt0) REVERT: g 27 MET cc_start: 0.9191 (mmm) cc_final: 0.8467 (mmm) REVERT: g 49 MET cc_start: 0.9654 (mtp) cc_final: 0.9354 (mtp) REVERT: g 110 SER cc_start: 0.9472 (t) cc_final: 0.9215 (p) REVERT: g 213 TYR cc_start: 0.9409 (m-10) cc_final: 0.9000 (m-10) REVERT: h 129 MET cc_start: 0.6786 (mtt) cc_final: 0.6397 (ttt) REVERT: h 130 PHE cc_start: 0.9239 (p90) cc_final: 0.8958 (p90) REVERT: h 181 ASP cc_start: 0.9355 (t0) cc_final: 0.9134 (t70) REVERT: h 185 ASN cc_start: 0.9190 (t0) cc_final: 0.8650 (t0) REVERT: i 40 GLN cc_start: 0.8867 (tt0) cc_final: 0.8415 (pt0) REVERT: i 51 TYR cc_start: 0.9534 (t80) cc_final: 0.9293 (t80) REVERT: i 54 GLN cc_start: 0.9307 (mt0) cc_final: 0.9042 (mm-40) REVERT: i 75 TYR cc_start: 0.9490 (m-80) cc_final: 0.9052 (m-80) REVERT: j 23 LYS cc_start: 0.8754 (tttm) cc_final: 0.8262 (tttp) REVERT: j 31 PHE cc_start: 0.8737 (m-80) cc_final: 0.7733 (m-80) REVERT: j 54 ARG cc_start: 0.8224 (mtt90) cc_final: 0.7974 (mtt90) REVERT: j 71 MET cc_start: 0.8232 (tpp) cc_final: 0.7792 (tpp) REVERT: j 86 LYS cc_start: 0.8317 (mttt) cc_final: 0.6840 (tptt) REVERT: j 138 ARG cc_start: 0.9505 (mtt90) cc_final: 0.9090 (mtt90) REVERT: k 17 GLN cc_start: 0.9150 (tm-30) cc_final: 0.8716 (tm-30) REVERT: k 21 MET cc_start: 0.9477 (mtm) cc_final: 0.8659 (mtm) REVERT: k 24 ARG cc_start: 0.9174 (ttp-110) cc_final: 0.8723 (ptp90) REVERT: k 60 VAL cc_start: 0.9256 (t) cc_final: 0.8627 (t) REVERT: k 62 MET cc_start: 0.9293 (ptp) cc_final: 0.8159 (pmm) REVERT: k 80 PHE cc_start: 0.9340 (m-80) cc_final: 0.9039 (m-80) REVERT: k 87 SER cc_start: 0.8952 (p) cc_final: 0.8329 (m) REVERT: l 26 PHE cc_start: 0.9795 (t80) cc_final: 0.9340 (t80) REVERT: l 28 ASN cc_start: 0.9424 (m110) cc_final: 0.9186 (m110) REVERT: l 101 MET cc_start: 0.9430 (OUTLIER) cc_final: 0.8920 (ttp) REVERT: l 126 ASP cc_start: 0.9680 (m-30) cc_final: 0.9268 (p0) REVERT: m 76 GLN cc_start: 0.9265 (mt0) cc_final: 0.9007 (mp10) REVERT: m 79 SER cc_start: 0.9201 (t) cc_final: 0.8926 (m) REVERT: m 80 ARG cc_start: 0.9519 (mtm110) cc_final: 0.9270 (mtm110) REVERT: m 85 ILE cc_start: 0.9359 (mm) cc_final: 0.8898 (mm) REVERT: m 96 MET cc_start: 0.9501 (tpp) cc_final: 0.8635 (tpp) REVERT: m 128 TYR cc_start: 0.9017 (m-10) cc_final: 0.8000 (m-10) REVERT: n 39 PHE cc_start: 0.8872 (m-80) cc_final: 0.8518 (m-80) REVERT: n 54 LEU cc_start: 0.9466 (tp) cc_final: 0.9063 (pp) REVERT: n 57 MET cc_start: 0.9273 (tpp) cc_final: 0.8325 (tpp) REVERT: n 89 GLU cc_start: 0.9403 (tp30) cc_final: 0.8921 (tp30) REVERT: n 126 GLN cc_start: 0.9415 (OUTLIER) cc_final: 0.8377 (tp-100) REVERT: n 127 PHE cc_start: 0.9319 (t80) cc_final: 0.9089 (t80) REVERT: o 46 LYS cc_start: 0.9124 (mttt) cc_final: 0.8704 (mtpp) REVERT: o 66 GLU cc_start: 0.9035 (pt0) cc_final: 0.8123 (pm20) REVERT: p 15 GLN cc_start: 0.8784 (tp40) cc_final: 0.8552 (tp-100) REVERT: p 18 ASP cc_start: 0.7900 (OUTLIER) cc_final: 0.7153 (m-30) REVERT: p 81 ASN cc_start: 0.8761 (m-40) cc_final: 0.8456 (t0) REVERT: p 94 GLU cc_start: 0.8861 (tp30) cc_final: 0.8529 (tp30) REVERT: p 100 LEU cc_start: 0.9645 (mt) cc_final: 0.9331 (pp) REVERT: q 29 GLN cc_start: 0.9002 (mp10) cc_final: 0.8619 (mp10) REVERT: q 38 TYR cc_start: 0.8724 (p90) cc_final: 0.8503 (p90) REVERT: q 44 LYS cc_start: 0.8328 (mptt) cc_final: 0.7586 (tmtt) REVERT: q 61 PHE cc_start: 0.9476 (m-10) cc_final: 0.9103 (m-80) REVERT: q 67 ILE cc_start: 0.8114 (mt) cc_final: 0.7884 (mp) REVERT: q 83 ARG cc_start: 0.9382 (ppt-90) cc_final: 0.8517 (ttp-110) REVERT: q 112 GLN cc_start: 0.6608 (mt0) cc_final: 0.6061 (pm20) REVERT: q 117 TYR cc_start: 0.9211 (m-80) cc_final: 0.8549 (m-80) REVERT: r 23 TYR cc_start: 0.9049 (t80) cc_final: 0.8570 (t80) REVERT: r 75 MET cc_start: 0.9032 (mmm) cc_final: 0.8692 (mmm) REVERT: r 86 TYR cc_start: 0.8910 (t80) cc_final: 0.8509 (t80) REVERT: r 100 GLN cc_start: 0.8646 (mp10) cc_final: 0.8220 (mp10) REVERT: r 103 LYS cc_start: 0.8603 (tttt) cc_final: 0.8222 (tttm) REVERT: s 33 ASP cc_start: 0.9178 (t0) cc_final: 0.8738 (t70) REVERT: s 62 ASN cc_start: 0.9457 (m-40) cc_final: 0.9157 (m110) REVERT: s 79 LEU cc_start: 0.8618 (mt) cc_final: 0.7889 (tp) REVERT: s 86 GLU cc_start: 0.8925 (mt-10) cc_final: 0.8642 (mt-10) REVERT: t 2 SER cc_start: 0.7113 (m) cc_final: 0.6813 (m) REVERT: t 6 GLU cc_start: 0.9416 (mp0) cc_final: 0.8968 (pm20) REVERT: t 14 GLU cc_start: 0.8492 (pt0) cc_final: 0.8169 (pt0) REVERT: t 18 ASP cc_start: 0.9298 (m-30) cc_final: 0.8468 (p0) REVERT: t 37 ASN cc_start: 0.9278 (m-40) cc_final: 0.8934 (p0) REVERT: t 48 LYS cc_start: 0.9283 (mmtt) cc_final: 0.9040 (mmtt) REVERT: t 59 MET cc_start: 0.9298 (mtt) cc_final: 0.8684 (mmp) REVERT: u 1 MET cc_start: 0.8105 (pmt) cc_final: 0.7653 (tpt) REVERT: u 31 ARG cc_start: 0.7658 (ttp-110) cc_final: 0.7309 (ttp-110) REVERT: u 34 GLU cc_start: 0.9483 (tm-30) cc_final: 0.9148 (tm-30) REVERT: u 51 ARG cc_start: 0.8497 (ttp-110) cc_final: 0.8056 (ttp-110) REVERT: u 53 ASP cc_start: 0.9329 (t0) cc_final: 0.8586 (t0) REVERT: v 7 THR cc_start: 0.8398 (OUTLIER) cc_final: 0.7340 (t) REVERT: v 9 GLN cc_start: 0.6914 (mt0) cc_final: 0.6160 (tp40) REVERT: v 27 ARG cc_start: 0.8601 (ptt180) cc_final: 0.8246 (ptt-90) REVERT: v 33 ILE cc_start: 0.9764 (mp) cc_final: 0.9321 (tp) REVERT: v 60 GLU cc_start: 0.8860 (tt0) cc_final: 0.8320 (tp30) REVERT: x 15 LEU cc_start: 0.9485 (tt) cc_final: 0.9132 (mt) REVERT: x 44 MET cc_start: 0.9129 (mtt) cc_final: 0.8563 (ptp) REVERT: y 4 ILE cc_start: 0.8487 (mt) cc_final: 0.8248 (mp) REVERT: y 28 MET cc_start: 0.9482 (tmm) cc_final: 0.8865 (ppp) REVERT: y 51 PHE cc_start: 0.9350 (t80) cc_final: 0.8892 (t80) REVERT: y 68 HIS cc_start: 0.8278 (t-90) cc_final: 0.7572 (t-170) REVERT: y 84 ASN cc_start: 0.9321 (m-40) cc_final: 0.8854 (p0) REVERT: z 44 GLU cc_start: 0.8496 (mm-30) cc_final: 0.8212 (mp0) REVERT: z 54 LYS cc_start: 0.9136 (tttt) cc_final: 0.8902 (ptmt) REVERT: z 58 LYS cc_start: 0.9176 (pttt) cc_final: 0.8717 (pttp) REVERT: A 149 MET cc_start: 0.5483 (ppp) cc_final: 0.4933 (tpt) REVERT: A 186 ARG cc_start: 0.7709 (ptt180) cc_final: 0.7495 (ptt180) outliers start: 188 outliers final: 162 residues processed: 1275 average time/residue: 1.2836 time to fit residues: 2825.2966 Evaluate side-chains 1324 residues out of total 4812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 171 poor density : 1153 time to evaluate : 6.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 SER Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 125 LYS Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 264 ASP Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 176 ASP Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain D residue 175 ILE Chi-restraints excluded: chain D residue 188 MET Chi-restraints excluded: chain E residue 17 MET Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 166 ASP Chi-restraints excluded: chain F residue 176 LYS Chi-restraints excluded: chain J residue 9 GLU Chi-restraints excluded: chain J residue 14 ASP Chi-restraints excluded: chain J residue 109 LEU Chi-restraints excluded: chain J residue 114 LEU Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 29 HIS Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain K residue 52 VAL Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 107 LEU Chi-restraints excluded: chain L residue 35 HIS Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain L residue 122 VAL Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 41 LEU Chi-restraints excluded: chain M residue 42 THR Chi-restraints excluded: chain M residue 124 LEU Chi-restraints excluded: chain M residue 128 THR Chi-restraints excluded: chain M residue 132 THR Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain N residue 6 SER Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain O residue 28 VAL Chi-restraints excluded: chain O residue 48 LEU Chi-restraints excluded: chain O residue 62 LEU Chi-restraints excluded: chain O residue 69 ASP Chi-restraints excluded: chain O residue 89 ASP Chi-restraints excluded: chain O residue 93 ASP Chi-restraints excluded: chain P residue 48 ILE Chi-restraints excluded: chain P residue 60 THR Chi-restraints excluded: chain P residue 85 SER Chi-restraints excluded: chain P residue 104 THR Chi-restraints excluded: chain P residue 110 ILE Chi-restraints excluded: chain Q residue 34 VAL Chi-restraints excluded: chain R residue 38 VAL Chi-restraints excluded: chain R residue 41 ILE Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 33 LEU Chi-restraints excluded: chain S residue 67 ASP Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain S residue 81 SER Chi-restraints excluded: chain T residue 60 THR Chi-restraints excluded: chain T residue 68 LYS Chi-restraints excluded: chain U residue 8 ASP Chi-restraints excluded: chain U residue 12 ILE Chi-restraints excluded: chain U residue 15 THR Chi-restraints excluded: chain U residue 28 VAL Chi-restraints excluded: chain U residue 37 GLU Chi-restraints excluded: chain U residue 65 ILE Chi-restraints excluded: chain U residue 72 ILE Chi-restraints excluded: chain V residue 42 LEU Chi-restraints excluded: chain W residue 10 THR Chi-restraints excluded: chain W residue 12 ASN Chi-restraints excluded: chain W residue 58 THR Chi-restraints excluded: chain X residue 22 LEU Chi-restraints excluded: chain X residue 33 LEU Chi-restraints excluded: chain X residue 71 LEU Chi-restraints excluded: chain Y residue 38 GLN Chi-restraints excluded: chain Z residue 32 ILE Chi-restraints excluded: chain Z residue 57 VAL Chi-restraints excluded: chain b residue 23 THR Chi-restraints excluded: chain c residue 48 ILE Chi-restraints excluded: chain d residue 4 THR Chi-restraints excluded: chain d residue 24 THR Chi-restraints excluded: chain d residue 42 LEU Chi-restraints excluded: chain e residue 6 THR Chi-restraints excluded: chain e residue 31 HIS Chi-restraints excluded: chain e residue 38 THR Chi-restraints excluded: chain f residue 22 VAL Chi-restraints excluded: chain f residue 23 ILE Chi-restraints excluded: chain f residue 28 SER Chi-restraints excluded: chain g residue 9 MET Chi-restraints excluded: chain g residue 100 MET Chi-restraints excluded: chain g residue 129 LEU Chi-restraints excluded: chain g residue 199 VAL Chi-restraints excluded: chain h residue 102 ASN Chi-restraints excluded: chain h residue 172 ARG Chi-restraints excluded: chain h residue 193 TYR Chi-restraints excluded: chain h residue 200 VAL Chi-restraints excluded: chain i residue 32 CYS Chi-restraints excluded: chain i residue 174 ASP Chi-restraints excluded: chain i residue 190 ASP Chi-restraints excluded: chain j residue 15 LEU Chi-restraints excluded: chain j residue 30 ILE Chi-restraints excluded: chain j residue 37 THR Chi-restraints excluded: chain j residue 144 LEU Chi-restraints excluded: chain j residue 148 ASN Chi-restraints excluded: chain j residue 164 ILE Chi-restraints excluded: chain k residue 51 ILE Chi-restraints excluded: chain k residue 96 VAL Chi-restraints excluded: chain l residue 89 VAL Chi-restraints excluded: chain l residue 91 VAL Chi-restraints excluded: chain l residue 101 MET Chi-restraints excluded: chain m residue 27 MET Chi-restraints excluded: chain m residue 75 ILE Chi-restraints excluded: chain n residue 30 ILE Chi-restraints excluded: chain n residue 35 LEU Chi-restraints excluded: chain n residue 53 GLU Chi-restraints excluded: chain n residue 111 VAL Chi-restraints excluded: chain n residue 115 LYS Chi-restraints excluded: chain n residue 126 GLN Chi-restraints excluded: chain o residue 17 LEU Chi-restraints excluded: chain o residue 32 THR Chi-restraints excluded: chain o residue 57 VAL Chi-restraints excluded: chain o residue 74 VAL Chi-restraints excluded: chain p residue 18 ASP Chi-restraints excluded: chain p residue 23 ILE Chi-restraints excluded: chain p residue 30 THR Chi-restraints excluded: chain p residue 32 VAL Chi-restraints excluded: chain p residue 46 THR Chi-restraints excluded: chain p residue 86 VAL Chi-restraints excluded: chain p residue 97 ILE Chi-restraints excluded: chain q residue 16 VAL Chi-restraints excluded: chain q residue 82 ILE Chi-restraints excluded: chain q residue 90 LEU Chi-restraints excluded: chain r residue 64 VAL Chi-restraints excluded: chain r residue 68 ASP Chi-restraints excluded: chain r residue 74 SER Chi-restraints excluded: chain s residue 48 LEU Chi-restraints excluded: chain s residue 54 ASP Chi-restraints excluded: chain s residue 67 THR Chi-restraints excluded: chain t residue 4 SER Chi-restraints excluded: chain t residue 11 ILE Chi-restraints excluded: chain t residue 67 LEU Chi-restraints excluded: chain v residue 7 THR Chi-restraints excluded: chain v residue 67 LEU Chi-restraints excluded: chain w residue 59 ILE Chi-restraints excluded: chain x residue 13 LEU Chi-restraints excluded: chain x residue 58 VAL Chi-restraints excluded: chain x residue 63 THR Chi-restraints excluded: chain x residue 71 LEU Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 198 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1027 random chunks: chunk 647 optimal weight: 7.9990 chunk 867 optimal weight: 8.9990 chunk 249 optimal weight: 10.0000 chunk 751 optimal weight: 3.9990 chunk 120 optimal weight: 10.0000 chunk 226 optimal weight: 10.0000 chunk 816 optimal weight: 8.9990 chunk 341 optimal weight: 40.0000 chunk 837 optimal weight: 30.0000 chunk 103 optimal weight: 20.0000 chunk 150 optimal weight: 30.0000 overall best weight: 7.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 128 ASN ** Q 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 48 GLN W 46 HIS Y 38 GLN ** g 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 190 HIS i 36 GLN ** j 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 28 GLN ** t 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 263 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.050797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.036058 restraints weight = 1070414.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 72)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.037029 restraints weight = 366029.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.037544 restraints weight = 207458.860| |-----------------------------------------------------------------------------| r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2883 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2883 r_free = 0.2883 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2883 r_free = 0.2883 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2883 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.3923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.094 158320 Z= 0.298 Angle : 0.686 15.321 236734 Z= 0.362 Chirality : 0.035 0.368 30127 Planarity : 0.006 0.128 12767 Dihedral : 24.311 179.738 78854 Min Nonbonded Distance : 1.772 Molprobity Statistics. All-atom Clashscore : 27.36 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.79 % Favored : 94.17 % Rotamer: Outliers : 4.26 % Allowed : 21.65 % Favored : 74.09 % 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: -0.90 (0.11), residues: 5784 helix: 0.35 (0.12), residues: 1966 sheet: -0.91 (0.16), residues: 1037 loop : -1.10 (0.12), residues: 2781 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP A 144 HIS 0.013 0.001 HIS e 31 PHE 0.029 0.002 PHE E 99 TYR 0.034 0.002 TYR Q 25 ARG 0.013 0.001 ARG j 93 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 42955.92 seconds wall clock time: 751 minutes 57.43 seconds (45117.43 seconds total)