Starting phenix.real_space_refine on Sun Feb 25 06:43:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6osk_20184/02_2024/6osk_20184_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6osk_20184/02_2024/6osk_20184.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6osk_20184/02_2024/6osk_20184_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6osk_20184/02_2024/6osk_20184_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6osk_20184/02_2024/6osk_20184_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6osk_20184/02_2024/6osk_20184.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6osk_20184/02_2024/6osk_20184.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6osk_20184/02_2024/6osk_20184_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6osk_20184/02_2024/6osk_20184_updated.pdb" } resolution = 3.6 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= 0.019 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 2 6.06 5 P 4642 5.49 5 Mg 307 5.21 5 S 158 5.16 5 C 73687 2.51 5 N 27286 2.21 5 O 40577 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 "D ARG 170": "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 PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 "R PHE 93": "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 "V PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 "Z PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ARG 56": "NH1" <-> "NH2" Residue "a ARG 63": "NH1" <-> "NH2" Residue "b ARG 10": "NH1" <-> "NH2" Residue "b ARG 16": "NH1" <-> "NH2" Residue "b ARG 52": "NH1" <-> "NH2" Residue "c PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 "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 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 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 137": "NH1" <-> "NH2" Residue "A ARG 142": "NH1" <-> "NH2" Residue "A ARG 195": "NH1" <-> "NH2" Residue "A ARG 294": "NH1" <-> "NH2" Residue "A ARG 316": "NH1" <-> "NH2" Time to flip residues: 0.22s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 146659 Number of models: 1 Model: "" Number of chains: 65 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': 289, 'rna2p_pyr': 165, 'rna3p': 16, 'rna3p_pur': 1378, 'rna3p_pyr': 1049} Link IDs: {'rna2p': 459, 'rna3p': 2443} 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: 14 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: "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: "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: "a" Number of atoms: 522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 522 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "b" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 444 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 54} Chain: "c" Number of atoms: 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: "A" Number of atoms: 2014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 2014 Classifications: {'peptide': 259} Link IDs: {'PTRANS': 10, 'TRANS': 248} 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: "6" 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: "1" Number of atoms: 292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 292 Unusual residues: {' MG': 292} Classifications: {'undetermined': 292} Link IDs: {None: 291} 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: "a" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 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: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 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} Chain: "5" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM A0GD2 SG CYS a 16 71.960 76.370 68.344 1.00156.09 S ATOM A0GDE SG CYS a 18 69.350 77.533 65.748 1.00159.75 S ATOM A0GHX SG CYS a 40 70.067 80.739 67.307 1.00164.00 S ATOM A0I2Y SG CYS f 11 139.476 164.748 59.220 1.00 75.32 S ATOM A0I3N SG CYS f 14 142.689 163.131 59.449 1.00 69.59 S ATOM A0I6I SG CYS f 27 142.195 167.196 60.345 1.00 65.12 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb="MG MG 13144 " occ=0.50 Time building chain proxies: 57.51, per 1000 atoms: 0.39 Number of scatterers: 146659 At special positions: 0 Unit cell: (284.585, 273.07, 227.01, 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 2 29.99 S 158 16.00 P 4642 15.00 Mg 307 11.99 O 40577 8.00 N 27286 7.00 C 73687 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: 63.52 Conformation dependent library (CDL) restraints added in 6.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN a 101 " pdb="ZN ZN a 101 " - pdb=" SG CYS a 18 " pdb="ZN ZN a 101 " - pdb=" SG CYS a 40 " pdb="ZN ZN a 101 " - pdb=" SG CYS a 16 " pdb=" ZN f 102 " pdb="ZN ZN f 102 " - pdb=" ND1 HIS f 33 " pdb="ZN ZN f 102 " - pdb=" SG CYS f 27 " pdb="ZN ZN f 102 " - pdb=" SG CYS f 14 " pdb="ZN ZN f 102 " - pdb=" SG CYS f 11 " Number of angles added : 3 11726 Ramachandran restraints generated. 5863 Oldfield, 0 Emsley, 5863 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10964 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: 177 helices and 75 sheets defined 38.7% alpha, 19.5% beta 1342 base pairs and 2537 stacking pairs defined. Time for finding SS restraints: 79.20 Creating SS restraints... Processing helix chain 'B' and resid 10 through 17 removed outlier: 3.591A pdb=" N ARG B 14 " --> pdb=" O SER B 10 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N HIS B 15 " --> pdb=" O PRO B 11 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N VAL B 16 " --> pdb=" O GLY B 12 " (cutoff:3.500A) removed outlier: 6.196A 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: 4.047A pdb=" N LEU B 34 " --> pdb=" O PHE B 30 " (cutoff:3.500A) removed outlier: 5.842A 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: 3.562A 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: 4.213A pdb=" N ALA B 211 " --> pdb=" O LYS B 207 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ARG B 212 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ARG B 214 " --> pdb=" O ALA B 210 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLY B 215 " --> pdb=" O ALA B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 226 removed outlier: 4.303A pdb=" N MET B 225 " --> pdb=" O ARG B 221 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N ASN B 226 " --> pdb=" O GLY B 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 221 through 226' Processing helix chain 'B' and resid 260 through 268 removed outlier: 4.715A pdb=" N ASP B 264 " --> pdb=" O ASN B 260 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N LYS B 265 " --> pdb=" O LYS B 261 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N PHE B 266 " --> pdb=" O ARG B 262 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ILE B 267 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 5.553A 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 'B' and resid 197 through 202 removed outlier: 4.241A pdb=" N MET B 201 " --> pdb=" O ALA B 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 72 removed outlier: 3.562A pdb=" N GLY C 66 " --> pdb=" O LYS C 62 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N HIS C 67 " --> pdb=" O PRO C 63 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA C 71 " --> pdb=" O HIS C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 103 removed outlier: 4.060A pdb=" N ALA C 102 " --> pdb=" O VAL C 98 " (cutoff:3.500A) removed outlier: 5.222A 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 126 removed outlier: 4.495A pdb=" N TRP C 125 " --> pdb=" O GLY C 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 15 through 20 Processing helix chain 'D' and resid 24 through 41 removed outlier: 3.546A pdb=" N GLN D 30 " --> pdb=" O ALA D 26 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG D 40 " --> pdb=" O ALA D 36 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N GLN D 41 " --> pdb=" O ALA D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 116 removed outlier: 3.692A pdb=" N SER D 110 " --> pdb=" O LYS D 106 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N VAL D 113 " --> pdb=" O LEU D 109 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ARG D 114 " --> pdb=" O SER D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 142 removed outlier: 3.549A pdb=" N LEU D 134 " --> pdb=" O LYS D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 154 through 163 removed outlier: 3.652A pdb=" N ALA D 161 " --> pdb=" O LEU D 157 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ASN D 163 " --> pdb=" O LEU D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 184 removed outlier: 3.695A pdb=" N ILE D 181 " --> pdb=" O PRO D 177 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N PHE D 183 " --> pdb=" O SER D 179 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ASP D 184 " --> pdb=" O LEU D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 201 removed outlier: 3.761A pdb=" N LYS D 194 " --> pdb=" O ALA D 190 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLN D 195 " --> pdb=" O ASP D 191 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 21 removed outlier: 3.700A pdb=" N ASP E 10 " --> pdb=" O ASP E 6 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLU E 11 " --> pdb=" O TYR E 7 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N VAL E 13 " --> pdb=" O LYS E 9 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N LYS E 14 " --> pdb=" O ASP E 10 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N PHE E 20 " --> pdb=" O LEU E 16 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 62 removed outlier: 4.585A pdb=" N LEU E 50 " --> pdb=" O ASP E 46 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA E 55 " --> pdb=" O ASP E 51 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLY E 62 " --> pdb=" O ALA E 58 " (cutoff:3.500A) Processing helix chain 'E' and resid 93 through 111 removed outlier: 4.224A pdb=" N TRP E 97 " --> pdb=" O GLY E 93 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE E 104 " --> pdb=" O PHE E 100 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA E 107 " --> pdb=" O LEU E 103 " (cutoff:3.500A) removed outlier: 5.789A 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: 5.345A pdb=" N ASP E 147 " --> pdb=" O TYR E 143 " (cutoff:3.500A) Processing helix chain 'E' and resid 162 through 174 removed outlier: 4.571A pdb=" N GLY E 166 " --> pdb=" O SER E 162 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N PHE E 173 " --> pdb=" O LEU E 169 " (cutoff:3.500A) Processing helix chain 'E' and resid 134 through 139 Proline residue: E 139 - end of helix Processing helix chain 'F' and resid 2 through 7 removed outlier: 4.311A pdb=" N ALA F 7 " --> pdb=" O ARG F 3 " (cutoff:3.500A) Processing helix chain 'F' and resid 60 through 81 removed outlier: 3.725A pdb=" N ALA F 70 " --> pdb=" O GLY F 66 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU F 72 " --> pdb=" O ALA F 68 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N ILE F 77 " --> pdb=" O ASN F 73 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N VAL F 79 " --> pdb=" O MET F 75 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 153 removed outlier: 3.637A pdb=" N GLN F 143 " --> pdb=" O GLN F 139 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N TYR F 151 " --> pdb=" O ASP F 147 " (cutoff:3.500A) removed outlier: 4.390A 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 removed outlier: 3.638A pdb=" N GLN G 33 " --> pdb=" O PHE G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 40 through 48 Processing helix chain 'G' and resid 51 through 74 removed outlier: 3.713A pdb=" N ALA G 56 " --> pdb=" O ALA G 52 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLU G 60 " --> pdb=" O ALA G 56 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU G 62 " --> pdb=" O LEU G 58 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA G 63 " --> pdb=" O ALA G 59 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ALA G 64 " --> pdb=" O GLU G 60 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ALA G 65 " --> pdb=" O VAL G 61 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ALA G 69 " --> pdb=" O ALA G 65 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N GLU G 70 " --> pdb=" O ASN G 66 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS G 71 " --> pdb=" O ALA G 67 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ILE G 72 " --> pdb=" O ARG G 68 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N ASN G 73 " --> pdb=" O ALA G 69 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ALA G 74 " --> pdb=" O GLU G 70 " (cutoff:3.500A) Processing helix chain 'G' and resid 95 through 107 removed outlier: 4.206A pdb=" N ILE G 99 " --> pdb=" O GLY G 95 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ALA G 102 " --> pdb=" O ASP G 98 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL G 103 " --> pdb=" O ILE G 99 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N THR G 104 " --> pdb=" O ALA G 100 " (cutoff:3.500A) Processing helix chain 'J' and resid 24 through 38 removed outlier: 4.754A pdb=" N GLU J 31 " --> pdb=" O ARG J 27 " (cutoff:3.500A) Processing helix chain 'J' and resid 88 through 96 Processing helix chain 'J' and resid 97 through 110 removed outlier: 4.503A pdb=" N ILE J 101 " --> pdb=" O PRO J 97 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N MET J 108 " --> pdb=" O ALA J 104 " (cutoff:3.500A) Proline residue: J 110 - end of helix Processing helix chain 'J' and resid 112 through 123 removed outlier: 3.517A pdb=" N ALA J 117 " --> pdb=" O PRO J 113 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ARG J 120 " --> pdb=" O ARG J 116 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N LYS J 121 " --> pdb=" O ALA J 117 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N LEU J 122 " --> pdb=" O MET J 118 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N LYS J 123 " --> pdb=" O PHE J 119 " (cutoff:3.500A) Processing helix chain 'K' and resid 112 through 120 removed outlier: 3.636A pdb=" N ILE K 116 " --> pdb=" O PHE K 112 " (cutoff:3.500A) Proline residue: K 120 - end of helix Processing helix chain 'L' and resid 37 through 42 removed outlier: 4.319A pdb=" N ARG L 41 " --> pdb=" O GLY L 37 " (cutoff:3.500A) removed outlier: 5.609A 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 removed outlier: 3.657A pdb=" N LEU L 61 " --> pdb=" O LEU L 57 " (cutoff:3.500A) Proline residue: L 62 - end of helix Processing helix chain 'L' and resid 68 through 75 removed outlier: 4.206A pdb=" N ALA L 72 " --> pdb=" O SER L 68 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ILE L 73 " --> pdb=" O ARG L 69 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N THR L 74 " --> pdb=" O LYS L 70 " (cutoff:3.500A) removed outlier: 5.804A 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 85 removed outlier: 3.578A pdb=" N LEU L 82 " --> pdb=" O ARG L 78 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ALA L 83 " --> pdb=" O LEU L 79 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N LYS L 84 " --> pdb=" O SER L 80 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N VAL L 85 " --> pdb=" O ASP L 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 78 through 85' Processing helix chain 'L' and resid 91 through 99 removed outlier: 3.671A pdb=" N LEU L 95 " --> pdb=" O ASP L 91 " (cutoff:3.500A) Processing helix chain 'L' and resid 128 through 139 removed outlier: 4.122A pdb=" N ALA L 134 " --> pdb=" O GLY L 130 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ALA L 138 " --> pdb=" O ALA L 134 " (cutoff:3.500A) Processing helix chain 'M' and resid 42 through 58 removed outlier: 3.771A pdb=" N GLU M 47 " --> pdb=" O ALA M 43 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N MET M 53 " --> pdb=" O ALA M 49 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL M 57 " --> pdb=" O MET M 53 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LYS M 58 " --> pdb=" O THR M 54 " (cutoff:3.500A) Processing helix chain 'M' and resid 109 through 125 removed outlier: 3.502A pdb=" N PHE M 117 " --> pdb=" O ALA M 113 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ALA M 122 " --> pdb=" O LYS M 118 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N LYS M 123 " --> pdb=" O LEU M 119 " (cutoff:3.500A) removed outlier: 3.806A 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: 3.825A pdb=" N ALA N 19 " --> pdb=" O SER N 15 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER N 27 " --> pdb=" O ASN N 23 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ARG N 30 " --> pdb=" O GLY N 26 " (cutoff:3.500A) Processing helix chain 'N' and resid 38 through 57 removed outlier: 3.790A pdb=" N GLU N 43 " --> pdb=" O PRO N 39 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG N 45 " --> pdb=" O ALA N 41 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N ARG N 46 " --> pdb=" O LYS N 42 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N VAL N 47 " --> pdb=" O GLU N 43 " (cutoff:3.500A) Proline residue: N 50 - end of helix removed outlier: 4.837A pdb=" N THR N 57 " --> pdb=" O THR N 53 " (cutoff:3.500A) Processing helix chain 'N' and resid 59 through 71 Processing helix chain 'N' and resid 72 through 88 removed outlier: 3.984A pdb=" N ASN N 81 " --> pdb=" O ALA N 77 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU N 83 " --> pdb=" O LEU N 79 " (cutoff:3.500A) removed outlier: 4.412A 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: 4.354A pdb=" N ALA O 6 " --> pdb=" O ASP O 2 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ARG O 10 " --> pdb=" O ALA O 6 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ARG O 13 " --> pdb=" O ARG O 9 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N ALA O 14 " --> pdb=" O ARG O 10 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ARG O 15 " --> pdb=" O ALA O 11 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ARG O 16 " --> pdb=" O THR O 12 " (cutoff:3.500A) Processing helix chain 'O' and resid 55 through 62 removed outlier: 3.744A pdb=" N GLU O 60 " --> pdb=" O LYS O 56 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N GLN O 61 " --> pdb=" O ALA O 57 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N LEU O 62 " --> pdb=" O ILE O 58 " (cutoff:3.500A) Processing helix chain 'O' and resid 67 through 86 removed outlier: 3.518A pdb=" N ALA O 73 " --> pdb=" O ASP O 69 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL O 74 " --> pdb=" O ALA O 70 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA O 77 " --> pdb=" O ALA O 73 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA O 79 " --> pdb=" O GLY O 75 " (cutoff:3.500A) Processing helix chain 'O' and resid 101 through 114 removed outlier: 3.506A pdb=" N GLU O 112 " --> pdb=" O ASP O 108 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA O 113 " --> pdb=" O ALA O 109 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 13 removed outlier: 3.795A pdb=" N GLU P 11 " --> pdb=" O GLN P 7 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLN P 12 " --> pdb=" O LEU P 8 " (cutoff:3.500A) Processing helix chain 'P' and resid 97 through 104 removed outlier: 4.823A pdb=" N ARG P 101 " --> pdb=" O LEU P 97 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N GLU P 102 " --> pdb=" O TYR P 98 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ARG P 103 " --> pdb=" O TYR P 99 " (cutoff:3.500A) removed outlier: 5.643A 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: 3.728A pdb=" N ILE Q 17 " --> pdb=" O ARG Q 13 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLN Q 20 " --> pdb=" O LYS Q 16 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LYS Q 22 " --> pdb=" O LEU Q 18 " (cutoff:3.500A) Processing helix chain 'Q' and resid 26 through 31 removed outlier: 4.137A pdb=" N ARG Q 30 " --> pdb=" O GLY Q 26 " (cutoff:3.500A) Processing helix chain 'Q' and resid 39 through 73 removed outlier: 4.089A pdb=" N ARG Q 51 " --> pdb=" O TYR Q 47 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N LYS Q 54 " --> pdb=" O ARG Q 50 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG Q 55 " --> pdb=" O ARG Q 51 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA Q 67 " --> pdb=" O ALA Q 63 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ARG Q 70 " --> pdb=" O ASN Q 66 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASN Q 72 " --> pdb=" O ALA Q 68 " (cutoff:3.500A) Processing helix chain 'Q' and resid 75 through 87 removed outlier: 3.602A pdb=" N ASN Q 81 " --> pdb=" O SER Q 77 " (cutoff:3.500A) Processing helix chain 'Q' and resid 91 through 102 removed outlier: 3.657A pdb=" N VAL Q 100 " --> pdb=" O ALA Q 96 " (cutoff:3.500A) Processing helix chain 'Q' and resid 103 through 118 removed outlier: 3.794A pdb=" N ALA Q 116 " --> pdb=" O LYS Q 112 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N LEU Q 117 " --> pdb=" O ALA Q 113 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA Q 118 " --> pdb=" O LYS Q 114 " (cutoff:3.500A) Processing helix chain 'S' and resid 13 through 25 removed outlier: 3.527A pdb=" N VAL S 17 " --> pdb=" O SER S 13 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ARG S 18 " --> pdb=" O ALA S 14 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU S 19 " --> pdb=" O GLN S 15 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N VAL S 20 " --> pdb=" O LYS S 16 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N LEU S 23 " --> pdb=" O LEU S 19 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ILE S 24 " --> pdb=" O VAL S 20 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ARG S 25 " --> pdb=" O ALA S 21 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 39 removed outlier: 4.069A pdb=" N ASP S 34 " --> pdb=" O SER S 30 " (cutoff:3.500A) Processing helix chain 'S' and resid 41 through 61 removed outlier: 4.057A pdb=" N VAL S 45 " --> pdb=" O LYS S 41 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU S 46 " --> pdb=" O LYS S 42 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASN S 57 " --> pdb=" O SER S 53 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N HIS S 60 " --> pdb=" O ALA S 56 " (cutoff:3.500A) Processing helix chain 'S' and resid 65 through 70 removed outlier: 3.893A pdb=" N LEU S 69 " --> pdb=" O ASP S 65 " (cutoff:3.500A) removed outlier: 6.096A 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: 3.578A pdb=" N LEU T 7 " --> pdb=" O ARG T 3 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU T 8 " --> pdb=" O GLU T 4 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LYS T 9 " --> pdb=" O GLU T 5 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N LEU T 11 " --> pdb=" O LEU T 7 " (cutoff:3.500A) Processing helix chain 'T' and resid 17 through 27 removed outlier: 3.540A pdb=" N MET T 24 " --> pdb=" O ALA T 20 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU T 25 " --> pdb=" O SER T 21 " (cutoff:3.500A) Processing helix chain 'T' and resid 39 through 50 removed outlier: 3.982A pdb=" N ALA T 45 " --> pdb=" O ALA T 41 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU T 50 " --> pdb=" O ALA T 46 " (cutoff:3.500A) Processing helix chain 'U' and resid 66 through 71 removed outlier: 3.719A pdb=" N VAL U 70 " --> pdb=" O GLN U 66 " (cutoff:3.500A) removed outlier: 5.135A 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: 3.534A pdb=" N VAL V 47 " --> pdb=" O ASP V 43 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ASN V 49 " --> pdb=" O ASP V 45 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N MET V 50 " --> pdb=" O LYS V 46 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA V 52 " --> pdb=" O MET V 48 " (cutoff:3.500A) Processing helix chain 'V' and resid 53 through 59 removed outlier: 4.608A pdb=" N TYR V 57 " --> pdb=" O LYS V 53 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N SER V 58 " --> pdb=" O ALA V 54 " (cutoff:3.500A) Processing helix chain 'X' and resid 52 through 63 removed outlier: 3.736A pdb=" N ARG X 57 " --> pdb=" O ALA X 53 " (cutoff:3.500A) Processing helix chain 'X' and resid 64 through 75 removed outlier: 4.085A pdb=" N ALA X 69 " --> pdb=" O ASP X 65 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARG X 72 " --> pdb=" O LEU X 68 " (cutoff:3.500A) Processing helix chain 'Y' and resid 2 through 9 removed outlier: 3.753A pdb=" N ARG Y 7 " --> pdb=" O ALA Y 3 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLU Y 8 " --> pdb=" O LYS Y 4 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N LYS Y 9 " --> pdb=" O GLU Y 5 " (cutoff:3.500A) Processing helix chain 'Y' and resid 10 through 35 removed outlier: 3.517A pdb=" N LEU Y 14 " --> pdb=" O SER Y 10 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG Y 23 " --> pdb=" O LEU Y 19 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N SER Y 34 " --> pdb=" O MET Y 30 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N GLY Y 35 " --> pdb=" O GLN Y 31 " (cutoff:3.500A) Processing helix chain 'Y' and resid 40 through 62 removed outlier: 4.395A pdb=" N LYS Y 44 " --> pdb=" O SER Y 40 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA Y 51 " --> pdb=" O ARG Y 47 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA Y 61 " --> pdb=" O LEU Y 57 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N GLY Y 62 " --> pdb=" O ASN Y 58 " (cutoff:3.500A) Processing helix chain 'Z' and resid 17 through 28 Processing helix chain 'Z' and resid 41 through 52 removed outlier: 3.604A pdb=" N VAL Z 51 " --> pdb=" O MET Z 47 " (cutoff:3.500A) Processing helix chain 'a' and resid 46 through 52 removed outlier: 3.725A pdb=" N VAL a 51 " --> pdb=" O LYS a 47 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N ALA a 52 " --> pdb=" O GLN a 48 " (cutoff:3.500A) Processing helix chain 'a' and resid 55 through 65 removed outlier: 3.568A pdb=" N ARG a 59 " --> pdb=" O GLY a 55 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N LYS a 62 " --> pdb=" O ASP a 58 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ARG a 63 " --> pdb=" O ARG a 59 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N PHE a 64 " --> pdb=" O PHE a 60 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N ASN a 65 " --> pdb=" O ASN a 61 " (cutoff:3.500A) Processing helix chain 'b' and resid 9 through 19 removed outlier: 5.115A pdb=" N HIS b 19 " --> pdb=" O MET b 15 " (cutoff:3.500A) Processing helix chain 'd' and resid 8 through 16 Processing helix chain 'd' and resid 17 through 24 removed outlier: 3.666A pdb=" N ALA d 23 " --> pdb=" O ARG d 19 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N THR d 24 " --> pdb=" O ALA d 20 " (cutoff:3.500A) Processing helix chain 'd' and resid 25 through 38 removed outlier: 3.587A pdb=" N GLN d 29 " --> pdb=" O LYS d 25 " (cutoff:3.500A) Processing helix chain 'e' and resid 7 through 14 removed outlier: 4.217A pdb=" N LYS e 12 " --> pdb=" O ARG e 8 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ARG e 13 " --> pdb=" O GLY e 9 " (cutoff:3.500A) Processing helix chain 'e' and resid 37 through 46 Proline residue: e 46 - end of helix Processing helix chain 'e' and resid 52 through 63 removed outlier: 4.541A pdb=" N GLY e 56 " --> pdb=" O LYS e 52 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N LEU e 57 " --> pdb=" O GLY e 53 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N VAL e 58 " --> pdb=" O ASP e 54 " (cutoff:3.500A) removed outlier: 4.123A 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: 3.589A pdb=" N MET g 9 " --> pdb=" O SER g 5 " (cutoff:3.500A) Processing helix chain 'g' and resid 24 through 29 removed outlier: 4.193A 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 42 through 64 removed outlier: 3.661A pdb=" N VAL g 47 " --> pdb=" O LEU g 43 " (cutoff:3.500A) Proline residue: g 48 - end of helix removed outlier: 3.548A pdb=" N GLU g 56 " --> pdb=" O GLU g 52 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LYS g 59 " --> pdb=" O ALA g 55 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N ARG g 63 " --> pdb=" O LYS g 59 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N LYS g 64 " --> pdb=" O ILE g 60 " (cutoff:3.500A) Processing helix chain 'g' and resid 73 through 88 removed outlier: 6.127A pdb=" N SER g 77 " --> pdb=" O LYS g 73 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N GLU g 78 " --> pdb=" O ARG g 74 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N ALA g 79 " --> pdb=" O ALA g 75 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LYS g 81 " --> pdb=" O SER g 77 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA g 84 " --> pdb=" O VAL g 80 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU g 85 " --> pdb=" O LYS g 81 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N SER g 86 " --> pdb=" O ASP g 82 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N CYS g 87 " --> pdb=" O ALA g 83 " (cutoff:3.500A) Processing helix chain 'g' and resid 103 through 123 removed outlier: 3.753A pdb=" N VAL g 107 " --> pdb=" O ASN g 103 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N GLN g 109 " --> pdb=" O LYS g 105 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N THR g 119 " --> pdb=" O LYS g 115 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLN g 122 " --> pdb=" O GLU g 118 " (cutoff:3.500A) Processing helix chain 'g' and resid 130 through 148 Processing helix chain 'g' and resid 165 through 170 removed outlier: 3.784A pdb=" N HIS g 170 " --> pdb=" O ALA g 166 " (cutoff:3.500A) Processing helix chain 'g' and resid 171 through 180 Processing helix chain 'g' and resid 206 through 227 removed outlier: 3.614A pdb=" N VAL g 210 " --> pdb=" O ALA g 206 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU g 212 " --> pdb=" O ARG g 208 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ALA g 219 " --> pdb=" O GLY g 215 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N THR g 220 " --> pdb=" O ALA g 216 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLU g 223 " --> pdb=" O ALA g 219 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N SER g 226 " --> pdb=" O ARG g 222 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLN g 227 " --> pdb=" O GLU g 223 " (cutoff:3.500A) Processing helix chain 'h' and resid 6 through 13 removed outlier: 3.934A pdb=" N ARG h 11 " --> pdb=" O PRO h 7 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N GLY h 13 " --> pdb=" O GLY h 9 " (cutoff:3.500A) Processing helix chain 'h' and resid 28 through 48 removed outlier: 3.658A pdb=" N ASN h 32 " --> pdb=" O GLU h 28 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TYR h 42 " --> pdb=" O LYS h 38 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA h 48 " --> pdb=" O THR h 44 " (cutoff:3.500A) Processing helix chain 'h' and resid 72 through 78 removed outlier: 3.905A pdb=" N VAL h 76 " --> pdb=" O ARG h 72 " (cutoff:3.500A) Processing helix chain 'h' and resid 81 through 96 removed outlier: 4.035A pdb=" N LYS h 86 " --> pdb=" O GLU h 82 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N VAL h 90 " --> pdb=" O LYS h 86 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ASP h 93 " --> pdb=" O LYS h 89 " (cutoff:3.500A) Processing helix chain 'h' and resid 108 through 113 removed outlier: 4.635A pdb=" N ASP h 112 " --> pdb=" O LYS h 108 " (cutoff:3.500A) removed outlier: 6.103A 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: 3.568A pdb=" N ARG h 143 " --> pdb=" O GLN h 139 " (cutoff:3.500A) Processing helix chain 'i' and resid 7 through 16 removed outlier: 4.017A 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: 3.809A pdb=" N LYS i 58 " --> pdb=" O GLN i 54 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL i 61 " --> pdb=" O GLU i 57 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE i 64 " --> pdb=" O LYS i 60 " (cutoff:3.500A) Processing helix chain 'i' and resid 68 through 83 removed outlier: 3.683A pdb=" N GLU i 78 " --> pdb=" O ASN i 74 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N LYS i 83 " --> pdb=" O ALA i 79 " (cutoff:3.500A) Processing helix chain 'i' and resid 85 through 97 removed outlier: 3.969A pdb=" N ARG i 97 " --> pdb=" O LEU i 93 " (cutoff:3.500A) Processing helix chain 'i' and resid 98 through 106 removed outlier: 3.937A pdb=" N TYR i 103 " --> pdb=" O ASP i 99 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLY i 106 " --> pdb=" O VAL i 102 " (cutoff:3.500A) Processing helix chain 'i' and resid 110 through 121 removed outlier: 4.431A pdb=" N VAL i 118 " --> pdb=" O ALA i 114 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS i 121 " --> pdb=" O LEU i 117 " (cutoff:3.500A) Processing helix chain 'i' and resid 152 through 166 removed outlier: 4.588A pdb=" N LYS i 156 " --> pdb=" O GLN i 152 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ALA i 157 " --> pdb=" O SER i 153 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA i 158 " --> pdb=" O ARG i 154 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLU i 160 " --> pdb=" O LYS i 156 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU i 161 " --> pdb=" O ALA i 157 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLU i 163 " --> pdb=" O LEU i 159 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLN i 164 " --> pdb=" O GLU i 160 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLU i 166 " --> pdb=" O ALA i 162 " (cutoff:3.500A) Processing helix chain 'i' and resid 187 through 192 removed outlier: 4.011A pdb=" N LEU i 191 " --> pdb=" O GLU i 187 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N SER i 192 " --> pdb=" O ARG i 188 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 187 through 192' Processing helix chain 'i' and resid 196 through 206 removed outlier: 4.302A pdb=" N ILE i 200 " --> pdb=" O ASN i 196 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL i 201 " --> pdb=" O GLU i 197 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLU i 202 " --> pdb=" O HIS i 198 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N LYS i 206 " --> pdb=" O GLU i 202 " (cutoff:3.500A) Processing helix chain 'j' and resid 55 through 71 removed outlier: 3.744A pdb=" N LYS j 62 " --> pdb=" O ALA j 58 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ASN j 70 " --> pdb=" O LYS j 66 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N MET j 71 " --> pdb=" O ALA j 67 " (cutoff:3.500A) Processing helix chain 'j' and resid 109 through 119 removed outlier: 3.598A pdb=" N ALA j 113 " --> pdb=" O GLY j 109 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL j 117 " --> pdb=" O ALA j 113 " (cutoff:3.500A) Processing helix chain 'j' and resid 132 through 148 removed outlier: 3.777A pdb=" N THR j 140 " --> pdb=" O VAL j 136 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASN j 146 " --> pdb=" O ASP j 142 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N MET j 147 " --> pdb=" O GLY j 143 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N ASN j 148 " --> pdb=" O LEU j 144 " (cutoff:3.500A) Processing helix chain 'j' and resid 149 through 158 removed outlier: 3.593A pdb=" N ALA j 155 " --> pdb=" O GLU j 151 " (cutoff:3.500A) Processing helix chain 'j' and resid 160 through 165 removed outlier: 4.021A pdb=" N ILE j 164 " --> pdb=" O SER j 160 " (cutoff:3.500A) Processing helix chain 'k' and resid 11 through 19 removed outlier: 3.630A pdb=" N SER k 15 " --> pdb=" O HIS k 11 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N GLU k 16 " --> pdb=" O PRO k 12 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N GLN k 17 " --> pdb=" O ASP k 13 " (cutoff:3.500A) Proline residue: k 19 - end of helix Processing helix chain 'k' and resid 20 through 33 removed outlier: 4.151A pdb=" N ARG k 24 " --> pdb=" O GLY k 20 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ALA k 27 " --> pdb=" O GLU k 23 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA k 32 " --> pdb=" O ALA k 28 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLU k 33 " --> pdb=" O ILE k 29 " (cutoff:3.500A) Processing helix chain 'k' and resid 67 through 81 removed outlier: 3.557A pdb=" N ILE k 71 " --> pdb=" O PRO k 67 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU k 74 " --> pdb=" O VAL k 70 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N THR k 77 " --> pdb=" O GLU k 73 " (cutoff:3.500A) Processing helix chain 'l' and resid 20 through 31 removed outlier: 3.727A pdb=" N ASN l 28 " --> pdb=" O ALA l 24 " (cutoff:3.500A) Processing helix chain 'l' and resid 35 through 55 removed outlier: 3.981A pdb=" N ILE l 42 " --> pdb=" O THR l 38 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL l 43 " --> pdb=" O ALA l 39 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N SER l 45 " --> pdb=" O SER l 41 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU l 48 " --> pdb=" O TYR l 44 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N THR l 49 " --> pdb=" O SER l 45 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA l 51 " --> pdb=" O LEU l 47 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N GLN l 52 " --> pdb=" O GLU l 48 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ARG l 53 " --> pdb=" O THR l 49 " (cutoff:3.500A) Processing helix chain 'l' and resid 57 through 70 removed outlier: 3.677A pdb=" N GLU l 63 " --> pdb=" O LEU l 59 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASN l 68 " --> pdb=" O VAL l 64 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N VAL l 69 " --> pdb=" O ALA l 65 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ARG l 70 " --> pdb=" O LEU l 66 " (cutoff:3.500A) Processing helix chain 'l' and resid 92 through 111 removed outlier: 3.995A pdb=" N ASN l 97 " --> pdb=" O PRO l 93 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA l 98 " --> pdb=" O VAL l 94 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL l 105 " --> pdb=" O MET l 101 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N LYS l 110 " --> pdb=" O GLU l 106 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ARG l 111 " --> pdb=" O ALA l 107 " (cutoff:3.500A) Processing helix chain 'l' and resid 115 through 130 removed outlier: 3.768A pdb=" N GLU l 123 " --> pdb=" O ARG l 119 " (cutoff:3.500A) Processing helix chain 'l' and resid 132 through 149 removed outlier: 3.526A pdb=" N LYS l 137 " --> pdb=" O THR l 133 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLU l 146 " --> pdb=" O HIS l 142 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASN l 148 " --> pdb=" O MET l 144 " (cutoff:3.500A) Processing helix chain 'm' and resid 5 through 21 removed outlier: 3.832A pdb=" N ASP m 9 " --> pdb=" O ASP m 5 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASN m 21 " --> pdb=" O GLY m 17 " (cutoff:3.500A) Processing helix chain 'm' and resid 30 through 44 removed outlier: 3.620A pdb=" N ALA m 35 " --> pdb=" O LYS m 31 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL m 39 " --> pdb=" O ALA m 35 " (cutoff:3.500A) Processing helix chain 'm' and resid 112 through 120 removed outlier: 3.832A pdb=" N GLN m 118 " --> pdb=" O ARG m 114 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ALA m 119 " --> pdb=" O ALA m 115 " (cutoff:3.500A) Processing helix chain 'n' and resid 34 through 39 Processing helix chain 'n' and resid 41 through 56 removed outlier: 3.685A pdb=" N VAL n 48 " --> pdb=" O ALA n 44 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ARG n 49 " --> pdb=" O ARG n 45 " (cutoff:3.500A) Proline residue: n 51 - end of helix removed outlier: 3.525A pdb=" N VAL n 55 " --> pdb=" O PRO n 51 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N ASP n 56 " --> pdb=" O LEU n 52 " (cutoff:3.500A) Processing helix chain 'n' and resid 71 through 91 removed outlier: 3.647A pdb=" N ARG n 80 " --> pdb=" O ALA n 76 " (cutoff:3.500A) Processing helix chain 'n' and resid 92 through 102 removed outlier: 5.247A pdb=" N SER n 96 " --> pdb=" O GLU n 92 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N GLU n 97 " --> pdb=" O SER n 93 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS n 100 " --> pdb=" O SER n 96 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ALA n 101 " --> pdb=" O GLU n 97 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLY n 102 " --> pdb=" O LEU n 98 " (cutoff:3.500A) Processing helix chain 'o' and resid 14 through 32 removed outlier: 4.136A pdb=" N GLN o 20 " --> pdb=" O ARG o 16 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ALA o 21 " --> pdb=" O LEU o 17 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA o 23 " --> pdb=" O ASP o 19 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLU o 24 " --> pdb=" O GLN o 20 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ARG o 31 " --> pdb=" O GLU o 27 " (cutoff:3.500A) Processing helix chain 'o' and resid 80 through 90 removed outlier: 3.925A pdb=" N VAL o 84 " --> pdb=" O THR o 80 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ASP o 85 " --> pdb=" O GLU o 81 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LEU o 87 " --> pdb=" O THR o 83 " (cutoff:3.500A) Processing helix chain 'p' and resid 46 through 51 removed outlier: 3.889A pdb=" N SER p 50 " --> pdb=" O THR p 46 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N GLY p 51 " --> pdb=" O ALA p 47 " (cutoff:3.500A) No H-bonds generated for 'chain 'p' and resid 46 through 51' Processing helix chain 'p' and resid 54 through 59 removed outlier: 4.160A pdb=" N SER p 58 " --> pdb=" O GLY p 54 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N THR p 59 " --> pdb=" O SER p 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'p' and resid 54 through 59' Processing helix chain 'p' and resid 60 through 75 removed outlier: 3.677A pdb=" N GLN p 64 " --> pdb=" O PRO p 60 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA p 66 " --> pdb=" O ALA p 62 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ARG p 69 " --> pdb=" O VAL p 65 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA p 73 " --> pdb=" O ARG p 69 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL p 74 " --> pdb=" O CYS p 70 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LYS p 75 " --> pdb=" O ALA p 71 " (cutoff:3.500A) Processing helix chain 'p' and resid 90 through 104 removed outlier: 5.303A pdb=" N GLU p 94 " --> pdb=" O GLY p 90 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N SER p 95 " --> pdb=" O PRO p 91 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N THR p 96 " --> pdb=" O GLY p 92 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N ILE p 97 " --> pdb=" O ARG p 93 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ARG p 98 " --> pdb=" O GLU p 94 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ALA p 99 " --> pdb=" O SER p 95 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA p 103 " --> pdb=" O ALA p 99 " (cutoff:3.500A) removed outlier: 4.135A 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: 4.131A pdb=" N TYR q 117 " --> pdb=" O ALA q 113 " (cutoff:3.500A) Processing helix chain 'r' and resid 14 through 21 removed outlier: 4.474A pdb=" N SER r 21 " --> pdb=" O ILE r 17 " (cutoff:3.500A) Processing helix chain 'r' and resid 26 through 38 removed outlier: 3.641A pdb=" N ALA r 36 " --> pdb=" O ALA r 32 " (cutoff:3.500A) Processing helix chain 'r' and resid 49 through 64 removed outlier: 4.130A pdb=" N ASP r 58 " --> pdb=" O ASP r 54 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N PHE r 63 " --> pdb=" O GLU r 59 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N VAL r 64 " --> pdb=" O VAL r 60 " (cutoff:3.500A) Processing helix chain 'r' and resid 66 through 84 removed outlier: 3.836A pdb=" N ARG r 70 " --> pdb=" O GLU r 66 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLY r 84 " --> pdb=" O LEU r 80 " (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: 3.545A pdb=" N LYS s 7 " --> pdb=" O LYS s 3 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS s 12 " --> pdb=" O ALA s 8 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ARG s 13 " --> pdb=" O ARG s 9 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N PHE s 21 " --> pdb=" O ALA s 17 " (cutoff:3.500A) Processing helix chain 's' and resid 22 through 33 removed outlier: 3.892A pdb=" N ALA s 29 " --> pdb=" O ALA s 25 " (cutoff:3.500A) Processing helix chain 's' and resid 37 through 52 removed outlier: 3.756A pdb=" N LYS s 47 " --> pdb=" O ASN s 43 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLN s 49 " --> pdb=" O VAL s 45 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N THR s 50 " --> pdb=" O LEU s 46 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU s 51 " --> pdb=" O LYS s 47 " (cutoff:3.500A) Proline residue: s 52 - end of helix Processing helix chain 's' and resid 80 through 91 removed outlier: 3.913A pdb=" N ARG s 85 " --> pdb=" O ARG s 81 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ARG s 90 " --> pdb=" O GLU s 86 " (cutoff:3.500A) Processing helix chain 't' and resid 4 through 16 Processing helix chain 't' and resid 24 through 43 removed outlier: 3.663A pdb=" N HIS t 38 " --> pdb=" O ALA t 34 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLY t 41 " --> pdb=" O ASN t 37 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N HIS t 42 " --> pdb=" O HIS t 38 " (cutoff:3.500A) Processing helix chain 't' and resid 49 through 74 removed outlier: 4.113A pdb=" N ARG t 54 " --> pdb=" O HIS t 50 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLY t 55 " --> pdb=" O HIS t 51 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N MET t 59 " --> pdb=" O GLY t 55 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU t 66 " --> pdb=" O GLN t 62 " (cutoff:3.500A) Processing helix chain 't' and resid 75 through 86 removed outlier: 3.648A pdb=" N GLN t 80 " --> pdb=" O ALA t 76 " (cutoff:3.500A) Processing helix chain 'u' and resid 53 through 64 removed outlier: 3.586A pdb=" N ALA u 58 " --> pdb=" O LEU u 54 " (cutoff:3.500A) Processing helix chain 'u' and resid 68 through 82 removed outlier: 3.743A pdb=" N ALA u 72 " --> pdb=" O SER u 68 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA u 73 " --> pdb=" O ASP u 69 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ALA u 81 " --> pdb=" O GLU u 77 " (cutoff:3.500A) Processing helix chain 'w' and resid 11 through 17 removed outlier: 4.640A pdb=" N ALA w 15 " --> pdb=" O CYS w 11 " (cutoff:3.500A) Processing helix chain 'w' and resid 25 through 34 removed outlier: 4.166A pdb=" N ASN w 31 " --> pdb=" O ALA w 27 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N TYR w 32 " --> pdb=" O THR w 28 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N THR w 34 " --> pdb=" O LYS w 30 " (cutoff:3.500A) Processing helix chain 'w' and resid 41 through 46 Processing helix chain 'w' and resid 48 through 66 removed outlier: 3.765A pdb=" N ARG w 53 " --> pdb=" O ALA w 49 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLN w 54 " --> pdb=" O LYS w 50 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU w 55 " --> pdb=" O TYR w 51 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N TYR w 64 " --> pdb=" O LYS w 60 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU w 65 " --> pdb=" O ARG w 61 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N SER w 66 " --> pdb=" O ALA w 62 " (cutoff:3.500A) Processing helix chain 'x' and resid 12 through 26 removed outlier: 3.708A pdb=" N LYS x 18 " --> pdb=" O HIS x 14 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYS x 21 " --> pdb=" O LYS x 17 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLY x 26 " --> pdb=" O ALA x 22 " (cutoff:3.500A) Processing helix chain 'x' and resid 71 through 76 removed outlier: 4.392A 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 71 through 76' Processing helix chain 'y' and resid 5 through 41 removed outlier: 3.647A pdb=" N ILE y 12 " --> pdb=" O LYS y 8 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N GLU y 15 " --> pdb=" O ALA y 11 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER y 23 " --> pdb=" O LYS y 19 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N PHE y 31 " --> pdb=" O MET y 27 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL y 35 " --> pdb=" O PHE y 31 " (cutoff:3.500A) Processing helix chain 'y' and resid 45 through 65 removed outlier: 3.751A pdb=" N LYS y 49 " --> pdb=" O ALA y 45 " (cutoff:3.500A) Proline residue: y 56 - end of helix removed outlier: 3.635A pdb=" N ASP y 59 " --> pdb=" O GLN y 55 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ARG y 60 " --> pdb=" O PRO y 56 " (cutoff:3.500A) Processing helix chain 'y' and resid 68 through 87 removed outlier: 3.563A pdb=" N LEU y 79 " --> pdb=" O HIS y 75 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N GLN y 82 " --> pdb=" O ASN y 78 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LYS y 85 " --> pdb=" O ALA y 81 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU y 86 " --> pdb=" O GLN y 82 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N ALA y 87 " --> pdb=" O ILE y 83 " (cutoff:3.500A) Processing helix chain 'z' and resid 11 through 27 removed outlier: 4.218A pdb=" N PHE z 19 " --> pdb=" O ALA z 15 " (cutoff:3.500A) Processing helix chain 'z' and resid 28 through 37 removed outlier: 3.897A pdb=" N ARG z 35 " --> pdb=" O GLU z 31 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N PHE z 37 " --> pdb=" O ARG z 33 " (cutoff:3.500A) Processing helix chain 'z' and resid 40 through 69 removed outlier: 3.611A pdb=" N ALA z 48 " --> pdb=" O GLU z 44 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N HIS z 56 " --> pdb=" O ALA z 52 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N LYS z 59 " --> pdb=" O ARG z 55 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLU z 63 " --> pdb=" O LYS z 59 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ASN z 64 " --> pdb=" O LEU z 60 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ARG z 66 " --> pdb=" O ARG z 62 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ARG z 67 " --> pdb=" O GLU z 63 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N THR z 68 " --> pdb=" O ASN z 64 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N ARG z 69 " --> pdb=" O ALA z 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 143 removed outlier: 4.204A pdb=" N LEU A 126 " --> pdb=" O ASP A 122 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N GLY A 129 " --> pdb=" O ALA A 125 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ASP A 130 " --> pdb=" O LEU A 126 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ARG A 142 " --> pdb=" O TYR A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 176 removed outlier: 3.674A pdb=" N ARG A 174 " --> pdb=" O GLY A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 223 removed outlier: 4.072A pdb=" N LEU A 222 " --> pdb=" O ASN A 218 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N ARG A 223 " --> pdb=" O PRO A 219 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 218 through 223' Processing helix chain 'A' and resid 234 through 240 removed outlier: 3.911A pdb=" N THR A 240 " --> pdb=" O HIS A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 299 removed outlier: 3.579A pdb=" N ALA A 268 " --> pdb=" O HIS A 264 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LYS A 269 " --> pdb=" O LYS A 265 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA A 270 " --> pdb=" O ASN A 266 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N VAL A 273 " --> pdb=" O LYS A 269 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ALA A 280 " --> pdb=" O ALA A 276 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N ALA A 281 " --> pdb=" O ARG A 277 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ALA A 284 " --> pdb=" O ALA A 280 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA A 289 " --> pdb=" O LYS A 285 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N GLU A 290 " --> pdb=" O ARG A 286 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N ALA A 291 " --> pdb=" O GLN A 287 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N THR A 293 " --> pdb=" O ALA A 289 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ASN A 296 " --> pdb=" O SER A 292 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU A 297 " --> pdb=" O THR A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 335 removed outlier: 3.815A pdb=" N VAL A 332 " --> pdb=" O ARG A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 355 removed outlier: 3.851A pdb=" N GLU A 342 " --> pdb=" O ASP A 338 " (cutoff:3.500A) Proline residue: A 343 - end of helix removed outlier: 5.046A pdb=" N ALA A 355 " --> pdb=" O ASP A 351 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'B' and resid 80 through 83 removed outlier: 6.881A pdb=" N LEU B 93 " --> pdb=" O GLU B 79 " (cutoff:3.500A) removed outlier: 4.694A 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: 4.486A pdb=" N SER B 139 " --> pdb=" O ILE B 164 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N THR B 173 " --> pdb=" O VAL B 165 " (cutoff:3.500A) removed outlier: 4.026A 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: 4.624A pdb=" N GLU B 100 " --> pdb=" O TYR B 96 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'C' and resid 3 through 9 removed outlier: 3.670A pdb=" N LEU C 201 " --> pdb=" O GLY C 6 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N SER C 199 " --> pdb=" O LYS C 8 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N LYS C 105 " --> pdb=" O VAL C 177 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'C' and resid 10 through 16 removed outlier: 4.920A pdb=" N VAL C 20 " --> pdb=" O THR C 16 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASP C 181 " --> pdb=" O LEU C 186 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'C' and resid 36 through 40 removed outlier: 3.533A pdb=" N GLN C 36 " --> pdb=" O GLN C 49 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LEU C 40 " --> pdb=" O TYR C 45 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N TYR C 45 " --> pdb=" O LEU C 40 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N GLN C 49 " --> pdb=" O THR C 35 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N GLN C 94 " --> pdb=" O VAL C 34 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'C' and resid 46 through 51 removed outlier: 5.746A pdb=" N ARG C 46 " --> pdb=" O LEU C 84 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'D' and resid 2 through 6 removed outlier: 4.216A 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 Processing sheet with id= 10, first strand: chain 'E' and resid 29 through 32 removed outlier: 4.974A pdb=" N ARG E 30 " --> pdb=" O THR E 159 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N THR E 157 " --> pdb=" O GLU E 32 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ASN E 37 " --> pdb=" O ASP E 153 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N ILE E 85 " --> pdb=" O VAL E 40 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'E' and resid 127 through 133 removed outlier: 3.632A pdb=" N LEU E 152 " --> pdb=" O VAL E 132 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'F' and resid 16 through 19 removed outlier: 3.547A pdb=" N LYS F 18 " --> pdb=" O THR F 25 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'F' and resid 41 through 45 removed outlier: 3.521A pdb=" N THR F 51 " --> pdb=" O LYS F 44 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'F' and resid 82 through 89 removed outlier: 5.704A pdb=" N THR F 129 " --> pdb=" O LEU F 89 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'F' and resid 94 through 98 removed outlier: 3.501A pdb=" N HIS F 115 " --> pdb=" O ILE F 103 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'G' and resid 1 through 5 removed outlier: 3.544A pdb=" N MET G 1 " --> pdb=" O VAL G 21 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N ASP G 17 " --> pdb=" O LEU G 5 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'G' and resid 76 through 83 removed outlier: 7.255A pdb=" N GLU G 76 " --> pdb=" O LYS G 141 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N ILE G 143 " --> pdb=" O GLU G 76 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N VAL G 78 " --> pdb=" O ILE G 143 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE G 80 " --> pdb=" O ASN G 145 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ALA G 140 " --> pdb=" O PHE G 132 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N PHE G 132 " --> pdb=" O ALA G 140 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL G 142 " --> pdb=" O VAL G 130 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N GLU G 114 " --> pdb=" O GLN G 133 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'J' and resid 52 through 57 removed outlier: 4.993A pdb=" N ASP J 19 " --> pdb=" O LEU J 140 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'J' and resid 74 through 78 removed outlier: 3.520A pdb=" N HIS J 76 " --> pdb=" O LYS J 85 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N GLY J 83 " --> pdb=" O THR J 78 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'K' and resid 56 through 60 removed outlier: 4.992A pdb=" N ASP K 56 " --> pdb=" O ILE K 43 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LYS K 40 " --> pdb=" O ILE K 22 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N THR K 6 " --> pdb=" O CYS K 21 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N ASN K 82 " --> pdb=" O MET K 7 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'K' and resid 68 through 71 removed outlier: 3.583A pdb=" N VAL K 69 " --> pdb=" O ILE K 77 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N SER K 75 " --> pdb=" O ARG K 71 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'L' and resid 120 through 123 Processing sheet with id= 23, first strand: chain 'M' and resid 37 through 40 No H-bonds generated for sheet with id= 23 Processing sheet with id= 24, first strand: chain 'M' and resid 99 through 102 removed outlier: 4.057A pdb=" N LYS M 100 " --> pdb=" O ALA M 35 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N LEU M 33 " --> pdb=" O LEU M 102 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N TYR M 103 " --> pdb=" O LEU M 33 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'M' and resid 31 through 36 removed outlier: 6.492A pdb=" N LYS M 127 " --> pdb=" O VAL M 36 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'N' and resid 33 through 37 removed outlier: 6.158A pdb=" N MET N 110 " --> pdb=" O CYS N 100 " (cutoff:3.500A) removed outlier: 8.997A pdb=" N TYR N 94 " --> pdb=" O VAL N 116 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'O' and resid 49 through 52 removed outlier: 3.849A pdb=" N VAL O 49 " --> pdb=" O VAL O 39 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'P' and resid 49 through 53 removed outlier: 3.706A pdb=" N ALA P 49 " --> pdb=" O THR P 60 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N ARG P 53 " --> pdb=" O HIS P 56 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N HIS P 56 " --> pdb=" O ARG P 53 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N THR P 60 " --> pdb=" O ILE P 48 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N THR P 25 " --> pdb=" O LYS P 87 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N SER P 83 " --> pdb=" O LYS P 29 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'P' and resid 57 through 64 removed outlier: 7.451A pdb=" N SER P 57 " --> pdb=" O THR P 76 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'R' and resid 11 through 15 removed outlier: 3.535A pdb=" N MET R 40 " --> pdb=" O VAL R 4 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N LEU R 39 " --> pdb=" O GLY R 50 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'R' and resid 18 through 21 removed outlier: 4.518A pdb=" N GLN R 18 " --> pdb=" O ILE R 98 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ASP R 95 " --> pdb=" O VAL R 64 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N LYS R 60 " --> pdb=" O THR R 99 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE R 59 " --> pdb=" O PHE R 35 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N GLU R 31 " --> pdb=" O VAL R 63 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'R' and resid 57 through 60 Processing sheet with id= 33, first strand: chain 'R' and resid 65 through 77 removed outlier: 3.546A pdb=" N ALA R 65 " --> pdb=" O ASP R 95 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLY R 67 " --> pdb=" O PHE R 93 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N GLN R 91 " --> pdb=" O GLY R 69 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N LYS R 71 " --> pdb=" O HIS R 89 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N HIS R 89 " --> pdb=" O LYS R 71 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N LYS R 73 " --> pdb=" O GLN R 87 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N GLN R 87 " --> pdb=" O LYS R 73 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N VAL R 75 " --> pdb=" O LYS R 85 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N LYS R 85 " --> pdb=" O VAL R 75 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N PHE R 77 " --> pdb=" O TYR R 83 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N TYR R 83 " --> pdb=" O PHE R 77 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'S' and resid 2 through 8 Processing sheet with id= 35, first strand: chain 'T' and resid 12 through 15 removed outlier: 5.293A pdb=" N VAL T 31 " --> pdb=" O HIS T 15 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N ASN T 28 " --> pdb=" O LEU T 87 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LYS T 81 " --> pdb=" O VAL T 34 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N LYS T 66 " --> pdb=" O ARG T 77 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N ASP T 79 " --> pdb=" O LYS T 64 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N LYS T 64 " --> pdb=" O ASP T 79 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N LYS T 81 " --> pdb=" O VAL T 62 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N VAL T 62 " --> pdb=" O LYS T 81 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ALA T 83 " --> pdb=" O THR T 60 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N THR T 60 " --> pdb=" O ALA T 83 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N VAL T 85 " --> pdb=" O VAL T 58 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N VAL T 58 " --> pdb=" O VAL T 85 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'U' and resid 40 through 44 removed outlier: 5.114A pdb=" N ASN U 40 " --> pdb=" O ALA U 63 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'V' and resid 2 through 5 Processing sheet with id= 38, first strand: chain 'V' and resid 37 through 42 removed outlier: 4.065A pdb=" N PHE V 26 " --> pdb=" O LEU V 42 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ILE V 89 " --> pdb=" O PRO V 27 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE V 29 " --> pdb=" O ILE V 89 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'W' and resid 51 through 54 No H-bonds generated for sheet with id= 39 Processing sheet with id= 40, first strand: chain 'W' and resid 67 through 71 Processing sheet with id= 41, first strand: chain 'X' and resid 12 through 16 removed outlier: 3.612A pdb=" N VAL X 13 " --> pdb=" O PHE X 29 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'X' and resid 35 through 41 Processing sheet with id= 43, first strand: chain 'Z' and resid 33 through 39 removed outlier: 4.045A pdb=" N HIS Z 34 " --> pdb=" O GLN Z 9 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N THR Z 8 " --> pdb=" O LYS Z 56 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N MET Z 54 " --> pdb=" O THR Z 10 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'a' and resid 11 through 16 removed outlier: 5.036A pdb=" N ASN a 20 " --> pdb=" O CYS a 16 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'b' and resid 29 through 32 removed outlier: 4.379A pdb=" N GLU b 36 " --> pdb=" O ASP b 31 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'c' and resid 7 through 13 No H-bonds generated for sheet with id= 46 Processing sheet with id= 47, first strand: chain 'c' and resid 34 through 39 removed outlier: 6.111A pdb=" N LEU c 34 " --> pdb=" O GLU c 51 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'e' and resid 22 through 25 removed outlier: 5.462A pdb=" N PHE e 22 " --> pdb=" O VAL e 50 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'f' and resid 14 through 19 Processing sheet with id= 50, first strand: chain 'g' and resid 15 through 18 removed outlier: 5.301A pdb=" N HIS g 15 " --> pdb=" O ILE g 41 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N HIS g 39 " --> pdb=" O GLY g 17 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'g' and resid 89 through 93 Processing sheet with id= 52, first strand: chain 'h' and resid 54 through 59 removed outlier: 3.517A pdb=" N ILE h 64 " --> pdb=" O PRO h 98 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'h' and resid 164 through 169 removed outlier: 5.944A pdb=" N ARG h 164 " --> pdb=" O GLY h 155 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLY h 194 " --> pdb=" O THR h 191 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ASP h 181 " --> pdb=" O LYS h 204 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'i' and resid 141 through 145 removed outlier: 6.779A pdb=" N MET i 178 " --> pdb=" O ILE i 145 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLU i 179 " --> pdb=" O ASP i 174 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'j' and resid 11 through 16 removed outlier: 6.718A pdb=" N LEU j 36 " --> pdb=" O ILE j 16 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'j' and resid 84 through 88 removed outlier: 3.801A pdb=" N ARG j 93 " --> pdb=" O TYR j 128 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ASN j 122 " --> pdb=" O ALA j 99 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'j' and resid 33 through 40 Processing sheet with id= 58, first strand: chain 'k' and resid 38 through 42 removed outlier: 4.095A pdb=" N ARG k 38 " --> pdb=" O ASN k 63 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N TYR k 59 " --> pdb=" O TRP k 42 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL k 64 " --> pdb=" O TYR k 4 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N HIS k 3 " --> pdb=" O THR k 92 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG k 86 " --> pdb=" O MET k 9 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'k' and resid 43 through 47 removed outlier: 3.891A pdb=" N GLY k 43 " --> pdb=" O TYR k 59 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N HIS k 55 " --> pdb=" O LEU k 47 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'l' and resid 73 through 79 removed outlier: 6.197A pdb=" N TYR l 85 " --> pdb=" O ARG l 78 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'm' and resid 23 through 29 removed outlier: 6.714A pdb=" N ALA m 23 " --> pdb=" O LEU m 63 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASP m 48 " --> pdb=" O THR m 62 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'm' and resid 74 through 77 removed outlier: 6.597A pdb=" N VAL m 103 " --> pdb=" O ILE m 126 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'n' and resid 5 through 11 Processing sheet with id= 64, first strand: chain 'o' and resid 39 through 42 removed outlier: 4.247A pdb=" N LEU o 71 " --> pdb=" O LEU o 42 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N ARG o 5 " --> pdb=" O GLY o 103 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG o 7 " --> pdb=" O SER o 101 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'o' and resid 44 through 50 Processing sheet with id= 66, first strand: chain 'p' and resid 42 through 45 removed outlier: 4.361A pdb=" N ASN p 109 " --> pdb=" O LEU p 82 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N GLY p 88 " --> pdb=" O VAL p 113 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'q' and resid 29 through 33 removed outlier: 5.331A pdb=" N LEU q 81 " --> pdb=" O VAL q 98 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N HIS q 96 " --> pdb=" O ARG q 83 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'q' and resid 36 through 41 removed outlier: 5.094A pdb=" N LYS q 51 " --> pdb=" O ILE q 67 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N PHE q 61 " --> pdb=" O LEU q 57 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'u' and resid 4 through 10 removed outlier: 4.178A pdb=" N PHE u 16 " --> pdb=" O HIS u 9 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL u 19 " --> pdb=" O GLY u 37 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLY u 37 " --> pdb=" O VAL u 19 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG u 51 " --> pdb=" O PHE u 38 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N GLY u 49 " --> pdb=" O ASN u 40 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'v' and resid 7 through 11 Processing sheet with id= 71, first strand: chain 'v' and resid 19 through 30 No H-bonds generated for sheet with id= 71 Processing sheet with id= 72, first strand: chain 'x' and resid 30 through 33 removed outlier: 3.645A pdb=" N LEU x 31 " --> pdb=" O THR x 48 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N LEU x 47 " --> pdb=" O VAL x 62 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'A' and resid 144 through 149 removed outlier: 6.880A pdb=" N ILE A 163 " --> pdb=" O MET A 149 " (cutoff:3.500A) removed outlier: 8.432A pdb=" N LYS A 160 " --> pdb=" O ALA A 117 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ALA A 111 " --> pdb=" O ILE A 166 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N ASN A 110 " --> pdb=" O GLU A 208 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ARG A 308 " --> pdb=" O GLY A 181 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N ASN A 307 " --> pdb=" O HIS A 320 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR A 318 " --> pdb=" O THR A 309 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain 'A' and resid 224 through 227 removed outlier: 3.501A pdb=" N ALA A 243 " --> pdb=" O PHE A 227 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ILE A 253 " --> pdb=" O HIS A 248 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain 'A' and resid 150 through 153 removed outlier: 3.560A pdb=" N SER A 150 " --> pdb=" O ILE A 163 " (cutoff:3.500A) 1718 hydrogen bonds defined for protein. 5061 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3284 hydrogen bonds 5196 hydrogen bond angles 0 basepair planarities 1342 basepair parallelities 2537 stacking parallelities Total time for adding SS restraints: 291.80 Time building geometry restraints manager: 68.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 12113 1.29 - 1.42: 70661 1.42 - 1.55: 66592 1.55 - 1.68: 9292 1.68 - 1.81: 280 Bond restraints: 158938 Sorted by residual: bond pdb=" C5 5MU 5 54 " pdb=" C6 5MU 5 54 " ideal model delta sigma weight residual 1.155 1.435 -0.280 2.00e-02 2.50e+03 1.96e+02 bond pdb=" C5 5MU 11939 " pdb=" C6 5MU 11939 " ideal model delta sigma weight residual 1.155 1.433 -0.278 2.00e-02 2.50e+03 1.94e+02 bond pdb=" C5 5MU 1 747 " pdb=" C6 5MU 1 747 " ideal model delta sigma weight residual 1.155 1.417 -0.262 2.00e-02 2.50e+03 1.72e+02 bond pdb=" C4 5MU 1 747 " pdb=" C5 5MU 1 747 " ideal model delta sigma weight residual 1.802 1.597 0.205 2.00e-02 2.50e+03 1.05e+02 bond pdb=" C4 5MU 11939 " pdb=" C5 5MU 11939 " ideal model delta sigma weight residual 1.802 1.598 0.204 2.00e-02 2.50e+03 1.04e+02 ... (remaining 158933 not shown) Histogram of bond angle deviations from ideal: 96.08 - 105.07: 21799 105.07 - 114.05: 105007 114.05 - 123.03: 84332 123.03 - 132.02: 25390 132.02 - 141.00: 1034 Bond angle restraints: 237562 Sorted by residual: angle pdb=" C1' G7M 12069 " pdb=" N9 G7M 12069 " pdb=" C8 G7M 12069 " ideal model delta sigma weight residual 94.96 136.28 -41.32 3.00e+00 1.11e-01 1.90e+02 angle pdb=" C1' G7M 2 527 " pdb=" N9 G7M 2 527 " pdb=" C8 G7M 2 527 " ideal model delta sigma weight residual 94.96 125.32 -30.36 3.00e+00 1.11e-01 1.02e+02 angle pdb=" C1' G7M 12069 " pdb=" N9 G7M 12069 " pdb=" C4 G7M 12069 " ideal model delta sigma weight residual 142.80 115.88 26.92 3.00e+00 1.11e-01 8.05e+01 angle pdb=" C4' A 1 404 " pdb=" C3' A 1 404 " pdb=" O3' A 1 404 " ideal model delta sigma weight residual 109.40 122.58 -13.18 1.50e+00 4.44e-01 7.72e+01 angle pdb=" C1' 2MG 21516 " pdb=" N9 2MG 21516 " pdb=" C8 2MG 21516 " ideal model delta sigma weight residual 110.07 136.03 -25.96 3.00e+00 1.11e-01 7.49e+01 ... (remaining 237557 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.93: 89745 35.93 - 71.86: 10583 71.86 - 107.78: 1265 107.78 - 143.71: 15 143.71 - 179.64: 32 Dihedral angle restraints: 101640 sinusoidal: 84642 harmonic: 16998 Sorted by residual: dihedral pdb=" O4' C 21109 " pdb=" C2' C 21109 " pdb=" C1' C 21109 " pdb=" C3' C 21109 " ideal model delta sinusoidal sigma weight residual 25.59 61.59 -35.99 3 3.80e+00 6.93e-02 9.67e+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 36.99 163.01 1 1.50e+01 4.44e-03 8.35e+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 36.99 163.01 1 1.50e+01 4.44e-03 8.35e+01 ... (remaining 101637 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.117: 29451 0.117 - 0.235: 739 0.235 - 0.352: 25 0.352 - 0.470: 4 0.470 - 0.587: 1 Chirality restraints: 30220 Sorted by residual: chirality pdb=" C3* PSU 2 516 " pdb=" C4* PSU 2 516 " pdb=" O3* PSU 2 516 " pdb=" C2* PSU 2 516 " both_signs ideal model delta sigma weight residual False -2.48 -1.89 -0.59 2.00e-01 2.50e+01 8.63e+00 chirality pdb=" C3' A 12820 " pdb=" C4' A 12820 " pdb=" O3' A 12820 " pdb=" C2' A 12820 " both_signs ideal model delta sigma weight residual False -2.48 -2.90 0.42 2.00e-01 2.50e+01 4.44e+00 chirality pdb=" CB ILE J 84 " pdb=" CA ILE J 84 " pdb=" CG1 ILE J 84 " pdb=" CG2 ILE J 84 " both_signs ideal model delta sigma weight residual False 2.64 2.25 0.39 2.00e-01 2.50e+01 3.82e+00 ... (remaining 30217 not shown) Planarity restraints: 12875 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 2MG 21516 " -0.075 2.00e-02 2.50e+03 6.28e-01 8.86e+03 pdb=" C4' 2MG 21516 " -0.453 2.00e-02 2.50e+03 pdb=" O4' 2MG 21516 " -0.670 2.00e-02 2.50e+03 pdb=" C3' 2MG 21516 " 0.599 2.00e-02 2.50e+03 pdb=" O3' 2MG 21516 " 0.691 2.00e-02 2.50e+03 pdb=" C2' 2MG 21516 " 0.160 2.00e-02 2.50e+03 pdb=" O2' 2MG 21516 " -1.017 2.00e-02 2.50e+03 pdb=" C1' 2MG 21516 " -0.209 2.00e-02 2.50e+03 pdb=" N9 2MG 21516 " 0.973 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG 12445 " -0.052 2.00e-02 2.50e+03 6.24e-01 8.75e+03 pdb=" C4' 2MG 12445 " -0.465 2.00e-02 2.50e+03 pdb=" O4' 2MG 12445 " -0.813 2.00e-02 2.50e+03 pdb=" C3' 2MG 12445 " 0.594 2.00e-02 2.50e+03 pdb=" O3' 2MG 12445 " 0.601 2.00e-02 2.50e+03 pdb=" C2' 2MG 12445 " 0.230 2.00e-02 2.50e+03 pdb=" O2' 2MG 12445 " -0.914 2.00e-02 2.50e+03 pdb=" C1' 2MG 12445 " -0.173 2.00e-02 2.50e+03 pdb=" N9 2MG 12445 " 0.992 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG 11835 " 0.054 2.00e-02 2.50e+03 6.15e-01 8.52e+03 pdb=" C4' 2MG 11835 " 0.462 2.00e-02 2.50e+03 pdb=" O4' 2MG 11835 " 0.783 2.00e-02 2.50e+03 pdb=" C3' 2MG 11835 " -0.594 2.00e-02 2.50e+03 pdb=" O3' 2MG 11835 " -0.602 2.00e-02 2.50e+03 pdb=" C2' 2MG 11835 " -0.225 2.00e-02 2.50e+03 pdb=" O2' 2MG 11835 " 0.910 2.00e-02 2.50e+03 pdb=" C1' 2MG 11835 " 0.186 2.00e-02 2.50e+03 pdb=" N9 2MG 11835 " -0.974 2.00e-02 2.50e+03 ... (remaining 12872 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.45: 880 2.45 - 3.06: 84233 3.06 - 3.67: 272495 3.67 - 4.29: 422369 4.29 - 4.90: 576945 Nonbonded interactions: 1356922 Sorted by model distance: nonbonded pdb=" OP1 A 12448 " pdb="MG MG 13083 " model vdw 1.837 2.170 nonbonded pdb=" O PRO R 52 " pdb=" CD2 PHE R 53 " model vdw 1.839 3.340 nonbonded pdb=" OP2 A 11784 " pdb="MG MG 13086 " model vdw 1.888 2.170 nonbonded pdb=" O PRO R 52 " pdb=" CG PHE R 53 " model vdw 2.000 3.260 nonbonded pdb=" OP1 C 1 948 " pdb="MG MG 13023 " model vdw 2.010 2.170 ... (remaining 1356917 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: 1.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.120 Extract box with map and model: 9.690 Check model and map are aligned: 1.600 Set scattering table: 0.970 Process input model: 621.300 Find NCS groups from input model: 2.960 Set up NCS constraints: 0.380 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: 0.030 Load rotamer database and sin/cos tables:2.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 640.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 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 : 0.008 0.280 158938 Z= 0.479 Angle : 0.869 41.324 237562 Z= 0.454 Chirality : 0.047 0.587 30220 Planarity : 0.020 0.628 12875 Dihedral : 22.811 179.639 90676 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.22 % Favored : 94.64 % Rotamer: Outliers : 0.51 % Allowed : 3.32 % Favored : 96.17 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.40 (0.09), residues: 5863 helix: -4.04 (0.06), residues: 1826 sheet: -2.38 (0.14), residues: 1100 loop : -2.27 (0.10), residues: 2937 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.003 TRP D 78 HIS 0.030 0.003 HIS M 13 PHE 0.047 0.003 PHE N 80 TYR 0.029 0.003 TYR J 74 ARG 0.017 0.002 ARG q 50 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11726 Ramachandran restraints generated. 5863 Oldfield, 0 Emsley, 5863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11726 Ramachandran restraints generated. 5863 Oldfield, 0 Emsley, 5863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2417 residues out of total 4880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 2392 time to evaluate : 6.357 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: B 97 LYS cc_start: 0.8328 (mmmt) cc_final: 0.7970 (mtpp) REVERT: B 111 LYS cc_start: 0.9209 (pttt) cc_final: 0.8773 (pttt) REVERT: B 114 ASP cc_start: 0.8365 (m-30) cc_final: 0.8003 (m-30) REVERT: B 132 MET cc_start: 0.8929 (mtm) cc_final: 0.8665 (mtp) REVERT: B 161 TYR cc_start: 0.8613 (p90) cc_final: 0.8323 (p90) REVERT: B 191 THR cc_start: 0.8746 (m) cc_final: 0.8316 (p) REVERT: B 201 MET cc_start: 0.9082 (ptt) cc_final: 0.8653 (ptt) REVERT: B 266 PHE cc_start: 0.7936 (m-10) cc_final: 0.7564 (m-10) REVERT: C 88 GLU cc_start: 0.7919 (tt0) cc_final: 0.7432 (tt0) REVERT: C 100 LEU cc_start: 0.8670 (tt) cc_final: 0.8371 (tt) REVERT: C 208 LYS cc_start: 0.8604 (mttt) cc_final: 0.8387 (mttm) REVERT: D 3 LEU cc_start: 0.8549 (mt) cc_final: 0.8186 (mp) REVERT: D 41 GLN cc_start: 0.8721 (tt0) cc_final: 0.8401 (tt0) REVERT: D 111 GLU cc_start: 0.8563 (tp30) cc_final: 0.7453 (tp30) REVERT: D 136 GLN cc_start: 0.8514 (tp-100) cc_final: 0.8075 (tp40) REVERT: D 139 LYS cc_start: 0.8722 (ttpt) cc_final: 0.8427 (ttmm) REVERT: E 26 MET cc_start: 0.6933 (mmm) cc_final: 0.6581 (mmt) REVERT: E 27 GLN cc_start: 0.7999 (tt0) cc_final: 0.7470 (tt0) REVERT: E 33 LYS cc_start: 0.9054 (pttt) cc_final: 0.8716 (pttm) REVERT: E 38 MET cc_start: 0.8575 (mtt) cc_final: 0.8060 (ptp) REVERT: E 48 LYS cc_start: 0.8092 (mttt) cc_final: 0.7600 (mmmt) REVERT: E 85 ILE cc_start: 0.8832 (tp) cc_final: 0.8574 (tt) REVERT: E 112 ARG cc_start: 0.8061 (ttp-110) cc_final: 0.7653 (ptp90) REVERT: E 155 THR cc_start: 0.9275 (m) cc_final: 0.8767 (p) REVERT: E 159 THR cc_start: 0.8670 (p) cc_final: 0.8296 (t) REVERT: E 177 PHE cc_start: 0.6824 (m-10) cc_final: 0.6619 (m-80) REVERT: F 22 GLN cc_start: 0.7902 (mm-40) cc_final: 0.6996 (mm-40) REVERT: F 39 ASP cc_start: 0.8735 (m-30) cc_final: 0.8297 (t0) REVERT: F 58 TYR cc_start: 0.7834 (m-80) cc_final: 0.6522 (m-80) REVERT: F 73 ASN cc_start: 0.8794 (t160) cc_final: 0.8070 (t0) REVERT: F 139 GLN cc_start: 0.8472 (tm-30) cc_final: 0.8035 (tm-30) REVERT: F 149 ARG cc_start: 0.8769 (ttt-90) cc_final: 0.8377 (ttt90) REVERT: F 153 ARG cc_start: 0.8409 (ttm110) cc_final: 0.7795 (mtt90) REVERT: F 163 ARG cc_start: 0.8490 (ptp-170) cc_final: 0.8276 (ptp-170) REVERT: G 4 ILE cc_start: 0.8906 (tp) cc_final: 0.8594 (mm) REVERT: G 11 ASN cc_start: 0.8127 (t160) cc_final: 0.7720 (t0) REVERT: G 29 PHE cc_start: 0.8548 (t80) cc_final: 0.8172 (t80) REVERT: G 42 LYS cc_start: 0.8018 (mmmt) cc_final: 0.7431 (ptmm) REVERT: G 44 ILE cc_start: 0.7304 (mm) cc_final: 0.6977 (mt) REVERT: G 115 VAL cc_start: 0.7446 (t) cc_final: 0.7234 (m) REVERT: J 31 GLU cc_start: 0.7708 (tp30) cc_final: 0.7101 (tp30) REVERT: J 35 ARG cc_start: 0.8723 (mtt-85) cc_final: 0.8456 (mtt-85) REVERT: J 55 ILE cc_start: 0.9390 (mt) cc_final: 0.9173 (mt) REVERT: J 57 LEU cc_start: 0.9431 (OUTLIER) cc_final: 0.9229 (pp) REVERT: J 60 ASP cc_start: 0.8285 (p0) cc_final: 0.8041 (p0) REVERT: J 67 ASN cc_start: 0.8385 (m-40) cc_final: 0.7971 (m-40) REVERT: J 109 LEU cc_start: 0.9367 (mt) cc_final: 0.9041 (mt) REVERT: J 128 ASN cc_start: 0.8537 (t0) cc_final: 0.8267 (t0) REVERT: K 3 GLN cc_start: 0.8338 (pt0) cc_final: 0.7998 (pt0) REVERT: K 53 LYS cc_start: 0.8347 (tmmm) cc_final: 0.7378 (ttpt) REVERT: K 77 ILE cc_start: 0.9445 (mt) cc_final: 0.9208 (mt) REVERT: L 39 LYS cc_start: 0.8318 (mttt) cc_final: 0.8116 (mttt) REVERT: L 55 MET cc_start: 0.8578 (tpp) cc_final: 0.8252 (tpp) REVERT: L 70 LYS cc_start: 0.9053 (tttp) cc_final: 0.8599 (tttt) REVERT: L 105 ILE cc_start: 0.9336 (mm) cc_final: 0.9015 (mp) REVERT: L 127 VAL cc_start: 0.9282 (t) cc_final: 0.8995 (m) REVERT: L 128 THR cc_start: 0.8729 (p) cc_final: 0.8401 (p) REVERT: L 132 ARG cc_start: 0.7489 (ttm-80) cc_final: 0.7128 (ttm-80) REVERT: M 28 PHE cc_start: 0.8939 (m-10) cc_final: 0.8729 (m-80) REVERT: M 34 LYS cc_start: 0.8814 (ttmt) cc_final: 0.8614 (ttmm) REVERT: M 47 GLU cc_start: 0.8115 (tm-30) cc_final: 0.7831 (tp30) REVERT: M 55 ARG cc_start: 0.7639 (ttm110) cc_final: 0.7435 (ttp-110) REVERT: M 78 LEU cc_start: 0.9186 (tp) cc_final: 0.8980 (mt) REVERT: M 82 MET cc_start: 0.8421 (mmp) cc_final: 0.7802 (mmm) REVERT: N 2 ARG cc_start: 0.8158 (OUTLIER) cc_final: 0.7638 (ptm160) REVERT: N 35 LYS cc_start: 0.8700 (tttt) cc_final: 0.8403 (tttt) REVERT: N 75 ILE cc_start: 0.8927 (mm) cc_final: 0.8631 (mm) REVERT: O 10 ARG cc_start: 0.8765 (ttm110) cc_final: 0.7781 (ttp80) REVERT: O 12 THR cc_start: 0.9223 (t) cc_final: 0.8828 (m) REVERT: O 95 SER cc_start: 0.9346 (m) cc_final: 0.9051 (p) REVERT: P 12 GLN cc_start: 0.8628 (mt0) cc_final: 0.8306 (mt0) REVERT: P 27 GLU cc_start: 0.8384 (tm-30) cc_final: 0.7262 (tm-30) REVERT: P 36 SER cc_start: 0.7328 (t) cc_final: 0.7008 (p) REVERT: P 63 LYS cc_start: 0.8912 (ptmt) cc_final: 0.8619 (ptmt) REVERT: Q 18 LEU cc_start: 0.9178 (mm) cc_final: 0.8904 (mt) REVERT: Q 25 TYR cc_start: 0.9213 (t80) cc_final: 0.8920 (t80) REVERT: Q 52 GLN cc_start: 0.8740 (mt0) cc_final: 0.8504 (mt0) REVERT: Q 59 GLN cc_start: 0.8627 (tt0) cc_final: 0.8393 (tt0) REVERT: Q 87 SER cc_start: 0.8680 (t) cc_final: 0.8424 (p) REVERT: Q 107 THR cc_start: 0.9292 (m) cc_final: 0.8796 (p) REVERT: Q 111 GLU cc_start: 0.7072 (tp30) cc_final: 0.6763 (tp30) REVERT: R 6 GLN cc_start: 0.8646 (mt0) cc_final: 0.8266 (mt0) REVERT: R 7 SER cc_start: 0.8282 (t) cc_final: 0.7622 (p) REVERT: R 21 ARG cc_start: 0.9158 (ttm170) cc_final: 0.8594 (ttm170) REVERT: R 43 ASN cc_start: 0.8159 (t0) cc_final: 0.7916 (t0) REVERT: R 48 LYS cc_start: 0.8707 (mttp) cc_final: 0.8435 (mtpp) REVERT: R 51 VAL cc_start: 0.8010 (OUTLIER) cc_final: 0.7765 (p) REVERT: R 81 LYS cc_start: 0.9291 (mmtm) cc_final: 0.9081 (mmtt) REVERT: R 97 LYS cc_start: 0.9202 (tttt) cc_final: 0.8867 (ttpt) REVERT: R 99 THR cc_start: 0.8495 (p) cc_final: 0.7790 (p) REVERT: R 101 ILE cc_start: 0.8987 (mt) cc_final: 0.8780 (mt) REVERT: S 3 THR cc_start: 0.9151 (m) cc_final: 0.8666 (p) REVERT: S 66 ILE cc_start: 0.8996 (mm) cc_final: 0.8722 (mm) REVERT: T 21 SER cc_start: 0.9114 (m) cc_final: 0.8688 (p) REVERT: T 29 THR cc_start: 0.9055 (m) cc_final: 0.8820 (p) REVERT: T 49 LYS cc_start: 0.8113 (tttt) cc_final: 0.7803 (tttm) REVERT: T 73 ARG cc_start: 0.8155 (ttm110) cc_final: 0.7617 (ptp-110) REVERT: T 77 ARG cc_start: 0.8405 (mtt180) cc_final: 0.8021 (mtt180) REVERT: U 18 ASP cc_start: 0.8303 (m-30) cc_final: 0.7823 (m-30) REVERT: U 62 GLU cc_start: 0.7799 (mt-10) cc_final: 0.7590 (mt-10) REVERT: V 24 ASN cc_start: 0.8556 (t160) cc_final: 0.8164 (t0) REVERT: V 41 GLU cc_start: 0.7566 (pp20) cc_final: 0.7336 (pm20) REVERT: V 86 LEU cc_start: 0.8893 (mt) cc_final: 0.8620 (mp) REVERT: V 90 ASP cc_start: 0.8911 (m-30) cc_final: 0.8119 (m-30) REVERT: W 19 LYS cc_start: 0.9298 (mmtt) cc_final: 0.8827 (mmtm) REVERT: W 76 ASN cc_start: 0.8475 (m-40) cc_final: 0.8099 (m110) REVERT: X 20 HIS cc_start: 0.7536 (t70) cc_final: 0.7071 (t70) REVERT: X 23 ASN cc_start: 0.8915 (m110) cc_final: 0.8604 (m-40) REVERT: X 62 LYS cc_start: 0.9188 (mttt) cc_final: 0.8722 (mttt) REVERT: X 74 ARG cc_start: 0.8965 (ttm170) cc_final: 0.8756 (ttm170) REVERT: Y 2 LYS cc_start: 0.8105 (mtpm) cc_final: 0.7610 (mtpp) REVERT: Y 25 GLN cc_start: 0.9189 (tt0) cc_final: 0.8973 (tt0) REVERT: Y 44 LYS cc_start: 0.8971 (tttt) cc_final: 0.8639 (ttmm) REVERT: Y 52 ARG cc_start: 0.8751 (mtt90) cc_final: 0.8337 (mtm180) REVERT: Y 58 ASN cc_start: 0.8452 (m-40) cc_final: 0.7615 (m110) REVERT: Z 19 LYS cc_start: 0.8575 (ttmm) cc_final: 0.8322 (mttp) REVERT: Z 21 LYS cc_start: 0.9057 (mttt) cc_final: 0.8618 (mtmm) REVERT: Z 40 ASP cc_start: 0.7671 (t0) cc_final: 0.7149 (t0) REVERT: b 31 ASP cc_start: 0.8273 (t70) cc_final: 0.7692 (t0) REVERT: b 36 GLU cc_start: 0.8424 (pt0) cc_final: 0.7592 (pt0) REVERT: c 7 GLU cc_start: 0.8153 (mt-10) cc_final: 0.7832 (mm-30) REVERT: c 27 LYS cc_start: 0.8660 (mttt) cc_final: 0.8347 (mmtt) REVERT: c 34 LEU cc_start: 0.8705 (tp) cc_final: 0.8360 (tp) REVERT: c 53 LYS cc_start: 0.8011 (ttmm) cc_final: 0.7670 (pttm) REVERT: d 6 GLN cc_start: 0.9110 (mm-40) cc_final: 0.8805 (mm110) REVERT: d 25 LYS cc_start: 0.8490 (tmmt) cc_final: 0.8230 (tppt) REVERT: e 29 LEU cc_start: 0.9033 (tp) cc_final: 0.8739 (tp) REVERT: e 49 MET cc_start: 0.8841 (mmm) cc_final: 0.8613 (mmm) REVERT: f 6 SER cc_start: 0.9229 (t) cc_final: 0.9009 (p) REVERT: f 18 LYS cc_start: 0.9097 (tttt) cc_final: 0.8887 (ttmt) REVERT: f 30 GLU cc_start: 0.8723 (tp30) cc_final: 0.7895 (mp0) REVERT: g 56 GLU cc_start: 0.8036 (tp30) cc_final: 0.7508 (tp30) REVERT: g 62 SER cc_start: 0.7998 (p) cc_final: 0.7768 (m) REVERT: g 70 VAL cc_start: 0.8216 (t) cc_final: 0.7723 (m) REVERT: g 131 LYS cc_start: 0.7403 (pttm) cc_final: 0.6264 (mmtt) REVERT: g 152 LYS cc_start: 0.8564 (pttt) cc_final: 0.8074 (tmtt) REVERT: g 178 ASN cc_start: 0.7891 (m-40) cc_final: 0.7538 (m110) REVERT: h 32 ASN cc_start: 0.8883 (m-40) cc_final: 0.8293 (m-40) REVERT: h 34 ASP cc_start: 0.8311 (t0) cc_final: 0.8041 (t0) REVERT: h 35 SER cc_start: 0.9000 (t) cc_final: 0.8649 (p) REVERT: h 41 GLN cc_start: 0.8563 (tt0) cc_final: 0.8233 (tt0) REVERT: h 121 THR cc_start: 0.9064 (m) cc_final: 0.8156 (m) REVERT: h 122 SER cc_start: 0.9077 (m) cc_final: 0.8513 (p) REVERT: h 123 GLN cc_start: 0.9075 (mt0) cc_final: 0.8808 (mt0) REVERT: h 142 MET cc_start: 0.8201 (mmm) cc_final: 0.7984 (mmm) REVERT: h 144 LEU cc_start: 0.8893 (mm) cc_final: 0.8685 (mp) REVERT: h 164 ARG cc_start: 0.8496 (pmt170) cc_final: 0.8168 (ptt90) REVERT: h 207 ILE cc_start: 0.8766 (mm) cc_final: 0.8547 (mt) REVERT: i 8 LYS cc_start: 0.8297 (mttm) cc_final: 0.8079 (mtmm) REVERT: i 59 GLN cc_start: 0.7341 (mm-40) cc_final: 0.6905 (mm110) REVERT: i 95 GLU cc_start: 0.8345 (mm-30) cc_final: 0.7301 (mm-30) REVERT: i 103 TYR cc_start: 0.7639 (t80) cc_final: 0.7202 (t80) REVERT: i 107 PHE cc_start: 0.7989 (m-10) cc_final: 0.7720 (m-10) REVERT: i 134 SER cc_start: 0.7485 (p) cc_final: 0.7235 (m) REVERT: j 19 ASN cc_start: 0.8902 (t0) cc_final: 0.8559 (t0) REVERT: j 60 ILE cc_start: 0.9085 (pp) cc_final: 0.8828 (pt) REVERT: j 62 LYS cc_start: 0.8655 (mttt) cc_final: 0.8300 (ttmm) REVERT: j 72 ILE cc_start: 0.9334 (tp) cc_final: 0.9021 (tt) REVERT: j 77 ASN cc_start: 0.8024 (t0) cc_final: 0.7820 (t0) REVERT: k 5 GLU cc_start: 0.8502 (tt0) cc_final: 0.7949 (tt0) REVERT: k 7 VAL cc_start: 0.8949 (p) cc_final: 0.8679 (m) REVERT: k 26 THR cc_start: 0.8780 (m) cc_final: 0.8396 (p) REVERT: k 38 ARG cc_start: 0.7643 (ptt180) cc_final: 0.7317 (ptp90) REVERT: k 55 HIS cc_start: 0.7226 (m90) cc_final: 0.6476 (m-70) REVERT: k 91 ARG cc_start: 0.7684 (ttt90) cc_final: 0.6502 (ttt90) REVERT: l 27 VAL cc_start: 0.9196 (m) cc_final: 0.8895 (p) REVERT: l 37 SER cc_start: 0.8472 (t) cc_final: 0.7939 (p) REVERT: l 42 ILE cc_start: 0.9006 (mt) cc_final: 0.8682 (mm) REVERT: l 48 GLU cc_start: 0.8298 (tm-30) cc_final: 0.7620 (tm-30) REVERT: l 49 THR cc_start: 0.8192 (p) cc_final: 0.7864 (p) REVERT: l 86 GLN cc_start: 0.6949 (mm110) cc_final: 0.6217 (mm-40) REVERT: l 114 LYS cc_start: 0.8092 (mttt) cc_final: 0.7552 (mmtt) REVERT: l 122 ASN cc_start: 0.7818 (m-40) cc_final: 0.7366 (m110) REVERT: l 126 ASP cc_start: 0.8307 (m-30) cc_final: 0.7973 (m-30) REVERT: l 130 ASN cc_start: 0.8448 (OUTLIER) cc_final: 0.7750 (t0) REVERT: l 131 LYS cc_start: 0.7349 (OUTLIER) cc_final: 0.7108 (ttpt) REVERT: l 144 MET cc_start: 0.8070 (ttm) cc_final: 0.7597 (tpt) REVERT: m 22 LYS cc_start: 0.8889 (mmmt) cc_final: 0.8483 (mmmm) REVERT: m 43 GLU cc_start: 0.8418 (tp30) cc_final: 0.8152 (tp30) REVERT: m 56 LYS cc_start: 0.7870 (pttt) cc_final: 0.7532 (pttp) REVERT: m 60 GLU cc_start: 0.7869 (tt0) cc_final: 0.7581 (tm-30) REVERT: m 62 THR cc_start: 0.9213 (m) cc_final: 0.8225 (p) REVERT: m 87 LYS cc_start: 0.9010 (mmtt) cc_final: 0.8583 (mmtp) REVERT: m 88 ARG cc_start: 0.6904 (mtp180) cc_final: 0.6601 (mtp180) REVERT: m 94 LYS cc_start: 0.8002 (mttm) cc_final: 0.7492 (mtmt) REVERT: m 106 THR cc_start: 0.8314 (p) cc_final: 0.7906 (p) REVERT: m 107 SER cc_start: 0.8316 (m) cc_final: 0.8084 (m) REVERT: n 6 TYR cc_start: 0.6973 (m-10) cc_final: 0.6595 (m-10) REVERT: n 35 LEU cc_start: 0.9044 (tp) cc_final: 0.8744 (pp) REVERT: n 62 ASP cc_start: 0.7080 (m-30) cc_final: 0.6735 (p0) REVERT: n 64 TYR cc_start: 0.7092 (t80) cc_final: 0.6739 (t80) REVERT: n 65 ILE cc_start: 0.8826 (mt) cc_final: 0.8623 (mm) REVERT: n 80 ARG cc_start: 0.9035 (ttp-170) cc_final: 0.8685 (ttp-170) REVERT: n 87 LEU cc_start: 0.9365 (mp) cc_final: 0.9135 (mp) REVERT: n 90 TYR cc_start: 0.7931 (t80) cc_final: 0.7598 (t80) REVERT: n 107 ASP cc_start: 0.7998 (t70) cc_final: 0.7674 (t0) REVERT: o 6 ILE cc_start: 0.7913 (mt) cc_final: 0.7706 (mm) REVERT: o 64 GLN cc_start: 0.8353 (mt0) cc_final: 0.8083 (mt0) REVERT: o 69 THR cc_start: 0.9484 (m) cc_final: 0.9200 (p) REVERT: o 73 LEU cc_start: 0.6317 (tm) cc_final: 0.5710 (tp) REVERT: o 96 VAL cc_start: 0.8038 (t) cc_final: 0.7477 (m) REVERT: o 100 ILE cc_start: 0.6715 (OUTLIER) cc_final: 0.6503 (pp) REVERT: p 24 HIS cc_start: 0.8509 (t70) cc_final: 0.8299 (t-90) REVERT: p 31 ILE cc_start: 0.9541 (mt) cc_final: 0.9333 (mm) REVERT: p 64 GLN cc_start: 0.8787 (pt0) cc_final: 0.8568 (pt0) REVERT: p 84 VAL cc_start: 0.8780 (t) cc_final: 0.8505 (p) REVERT: q 25 GLU cc_start: 0.8296 (mt-10) cc_final: 0.8025 (mt-10) REVERT: q 58 THR cc_start: 0.8583 (m) cc_final: 0.8331 (m) REVERT: q 59 ASN cc_start: 0.8690 (p0) cc_final: 0.8341 (p0) REVERT: r 23 TYR cc_start: 0.8379 (t80) cc_final: 0.8025 (t80) REVERT: r 28 THR cc_start: 0.7634 (m) cc_final: 0.7427 (p) REVERT: r 46 SER cc_start: 0.8989 (m) cc_final: 0.8739 (p) REVERT: r 56 LEU cc_start: 0.9295 (tp) cc_final: 0.8987 (tp) REVERT: r 59 GLU cc_start: 0.7763 (mm-30) cc_final: 0.7548 (mp0) REVERT: r 68 ASP cc_start: 0.7649 (m-30) cc_final: 0.7424 (m-30) REVERT: r 75 MET cc_start: 0.8585 (tpt) cc_final: 0.8186 (tpt) REVERT: r 76 SER cc_start: 0.8942 (m) cc_final: 0.8561 (p) REVERT: r 78 LYS cc_start: 0.8923 (mtpt) cc_final: 0.8442 (tptp) REVERT: r 100 GLN cc_start: 0.8625 (mp10) cc_final: 0.7994 (mp10) REVERT: s 5 SER cc_start: 0.8633 (p) cc_final: 0.8410 (t) REVERT: s 100 SER cc_start: 0.8174 (p) cc_final: 0.7856 (p) REVERT: t 48 LYS cc_start: 0.8532 (mmtm) cc_final: 0.8201 (mtpt) REVERT: t 57 LEU cc_start: 0.9320 (mt) cc_final: 0.9118 (mt) REVERT: t 58 ARG cc_start: 0.7843 (ttt180) cc_final: 0.7416 (ttp80) REVERT: t 64 ARG cc_start: 0.8068 (tpm-80) cc_final: 0.7528 (tpp-160) REVERT: u 56 ARG cc_start: 0.8312 (mmm160) cc_final: 0.7918 (mmm-85) REVERT: u 59 HIS cc_start: 0.8280 (t-90) cc_final: 0.8076 (t-90) REVERT: u 76 LYS cc_start: 0.8786 (ttmt) cc_final: 0.8514 (ttmt) REVERT: w 23 TYR cc_start: 0.8755 (p90) cc_final: 0.8113 (p90) REVERT: w 24 LYS cc_start: 0.8078 (mtmm) cc_final: 0.7491 (mttt) REVERT: w 45 THR cc_start: 0.8942 (p) cc_final: 0.8679 (p) REVERT: w 47 THR cc_start: 0.8647 (m) cc_final: 0.8347 (m) REVERT: w 50 LYS cc_start: 0.9274 (tttt) cc_final: 0.8458 (ttmt) REVERT: w 52 GLN cc_start: 0.9061 (tp40) cc_final: 0.8807 (tp-100) REVERT: w 61 ARG cc_start: 0.9244 (mtm-85) cc_final: 0.8802 (mtm180) REVERT: x 11 ILE cc_start: 0.9056 (tt) cc_final: 0.8710 (tt) REVERT: x 17 LYS cc_start: 0.8064 (mmmt) cc_final: 0.7768 (mtmt) REVERT: x 35 SER cc_start: 0.9390 (m) cc_final: 0.8942 (t) REVERT: x 66 MET cc_start: 0.7730 (mtt) cc_final: 0.7414 (mtp) REVERT: x 71 LEU cc_start: 0.9265 (mt) cc_final: 0.8831 (mt) REVERT: y 51 PHE cc_start: 0.8636 (t80) cc_final: 0.8020 (t80) REVERT: y 55 GLN cc_start: 0.8633 (tt0) cc_final: 0.8359 (tm-30) REVERT: y 60 ARG cc_start: 0.8088 (ttm110) cc_final: 0.7826 (ttp-170) REVERT: z 16 LEU cc_start: 0.7928 (tt) cc_final: 0.7288 (tt) REVERT: z 17 ARG cc_start: 0.8166 (ttm110) cc_final: 0.7634 (tpt170) REVERT: z 19 PHE cc_start: 0.8317 (t80) cc_final: 0.7887 (t80) REVERT: z 28 VAL cc_start: 0.8916 (t) cc_final: 0.8520 (p) REVERT: z 62 ARG cc_start: 0.6644 (tmm160) cc_final: 0.5671 (ttt180) REVERT: z 71 TYR cc_start: 0.7781 (p90) cc_final: 0.7452 (p90) REVERT: A 114 GLU cc_start: 0.8294 (mt-10) cc_final: 0.7962 (mt-10) REVERT: A 123 GLU cc_start: 0.8413 (tm-30) cc_final: 0.8184 (tm-30) REVERT: A 133 ARG cc_start: 0.8384 (ttt-90) cc_final: 0.8159 (ttt90) REVERT: A 137 ARG cc_start: 0.8425 (mmm-85) cc_final: 0.7752 (mmt-90) REVERT: A 162 ILE cc_start: 0.9362 (tt) cc_final: 0.9046 (tt) REVERT: A 165 LYS cc_start: 0.9265 (tttt) cc_final: 0.9046 (ttmt) REVERT: A 177 PHE cc_start: 0.7824 (m-80) cc_final: 0.7452 (m-80) REVERT: A 193 GLN cc_start: 0.7994 (mt0) cc_final: 0.7205 (tm-30) REVERT: A 206 MET cc_start: 0.8444 (mtp) cc_final: 0.7478 (mtm) REVERT: A 213 GLU cc_start: 0.2950 (mm-30) cc_final: 0.2641 (tm-30) REVERT: A 248 HIS cc_start: 0.8432 (t-90) cc_final: 0.7702 (t-90) REVERT: A 263 GLN cc_start: 0.8844 (pt0) cc_final: 0.8541 (pt0) REVERT: A 277 ARG cc_start: 0.7938 (mtt180) cc_final: 0.7252 (mtp-110) REVERT: A 283 MET cc_start: 0.8512 (mmm) cc_final: 0.8015 (mtt) REVERT: A 293 THR cc_start: 0.8469 (t) cc_final: 0.8268 (m) REVERT: A 307 ASN cc_start: 0.8241 (m110) cc_final: 0.7961 (m110) REVERT: A 352 GLN cc_start: 0.6895 (mt0) cc_final: 0.6380 (tm-30) outliers start: 25 outliers final: 8 residues processed: 2403 average time/residue: 1.3618 time to fit residues: 5498.7232 Evaluate side-chains 1749 residues out of total 4880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 1735 time to evaluate : 7.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain N residue 2 ARG Chi-restraints excluded: chain P residue 114 LEU Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain e residue 32 ILE Chi-restraints excluded: chain l residue 130 ASN Chi-restraints excluded: chain l residue 131 LYS Chi-restraints excluded: chain o residue 100 ILE Chi-restraints excluded: chain u residue 2 VAL Chi-restraints excluded: chain A residue 184 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1034 random chunks: chunk 873 optimal weight: 4.9990 chunk 783 optimal weight: 10.0000 chunk 434 optimal weight: 20.0000 chunk 267 optimal weight: 8.9990 chunk 528 optimal weight: 7.9990 chunk 418 optimal weight: 20.0000 chunk 810 optimal weight: 20.0000 chunk 313 optimal weight: 10.0000 chunk 492 optimal weight: 1.9990 chunk 603 optimal weight: 6.9990 chunk 938 optimal weight: 6.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 58 HIS B 60 GLN B 86 ASN B 153 GLN B 239 ASN B 260 ASN C 49 GLN C 94 GLN C 136 ASN D 90 GLN ** F 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 45 HIS F 88 GLN ** F 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 11 ASN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 3 GLN K 9 ASN M 3 GLN M 17 ASN N 31 HIS O 38 GLN O 98 GLN O 100 HIS ** P 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 52 ASN ** Q 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 6 GLN R 86 GLN S 61 ASN T 48 GLN U 40 ASN V 24 ASN X 6 GLN X 17 ASN Z 20 HIS a 20 ASN b 42 HIS c 19 HIS ** d 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 31 HIS f 35 GLN g 39 HIS g 177 ASN h 8 ASN h 19 ASN h 140 ASN i 41 HIS i 59 GLN i 71 GLN i 140 ASN ** i 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 97 GLN k 63 ASN l 28 ASN l 68 ASN l 130 ASN m 38 ASN n 50 GLN q 77 HIS r 8 ASN r 14 HIS w 74 HIS x 14 HIS ** x 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** y 13 GLN y 21 ASN y 78 ASN A 197 HIS A 218 ASN ** A 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 62 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 158938 Z= 0.317 Angle : 0.719 14.453 237562 Z= 0.377 Chirality : 0.039 0.288 30220 Planarity : 0.007 0.133 12875 Dihedral : 23.814 179.665 78959 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.83 % Favored : 95.14 % Rotamer: Outliers : 4.24 % Allowed : 13.89 % Favored : 81.86 % 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: -3.02 (0.10), residues: 5863 helix: -2.07 (0.10), residues: 1886 sheet: -1.89 (0.15), residues: 1085 loop : -1.90 (0.10), residues: 2892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 78 HIS 0.016 0.002 HIS M 13 PHE 0.024 0.002 PHE x 74 TYR 0.025 0.002 TYR V 57 ARG 0.008 0.001 ARG z 62 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11726 Ramachandran restraints generated. 5863 Oldfield, 0 Emsley, 5863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11726 Ramachandran restraints generated. 5863 Oldfield, 0 Emsley, 5863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2048 residues out of total 4880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 207 poor density : 1841 time to evaluate : 6.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 98 ASP cc_start: 0.8047 (p0) cc_final: 0.7839 (p0) REVERT: B 110 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8418 (mp) REVERT: B 111 LYS cc_start: 0.9038 (pttt) cc_final: 0.8710 (pttt) REVERT: B 114 ASP cc_start: 0.8272 (m-30) cc_final: 0.7854 (m-30) REVERT: B 132 MET cc_start: 0.8918 (mtm) cc_final: 0.8551 (mtp) REVERT: B 201 MET cc_start: 0.9010 (ptt) cc_final: 0.8683 (ptt) REVERT: C 204 LYS cc_start: 0.8799 (mtpp) cc_final: 0.8505 (mttm) REVERT: D 41 GLN cc_start: 0.8747 (tt0) cc_final: 0.8486 (tt0) REVERT: D 139 LYS cc_start: 0.8852 (ttpt) cc_final: 0.8569 (ttmm) REVERT: D 188 MET cc_start: 0.8175 (mtp) cc_final: 0.7961 (mtp) REVERT: E 27 GLN cc_start: 0.8000 (tt0) cc_final: 0.7730 (tt0) REVERT: E 38 MET cc_start: 0.8263 (mtt) cc_final: 0.7522 (ptm) REVERT: E 48 LYS cc_start: 0.7591 (mttt) cc_final: 0.7374 (mtpp) REVERT: E 85 ILE cc_start: 0.8901 (tp) cc_final: 0.8560 (tp) REVERT: E 112 ARG cc_start: 0.8044 (ttp-110) cc_final: 0.7715 (mtm110) REVERT: E 155 THR cc_start: 0.9290 (m) cc_final: 0.8831 (p) REVERT: E 175 PHE cc_start: 0.8078 (OUTLIER) cc_final: 0.7504 (m-80) REVERT: F 22 GLN cc_start: 0.7827 (mm-40) cc_final: 0.6663 (mm-40) REVERT: F 25 THR cc_start: 0.8488 (OUTLIER) cc_final: 0.7808 (t) REVERT: F 39 ASP cc_start: 0.8784 (m-30) cc_final: 0.8282 (t0) REVERT: F 58 TYR cc_start: 0.7899 (m-80) cc_final: 0.6406 (m-80) REVERT: F 64 GLN cc_start: 0.8565 (mm-40) cc_final: 0.8343 (mm110) REVERT: F 73 ASN cc_start: 0.8651 (t160) cc_final: 0.8398 (t0) REVERT: F 130 GLU cc_start: 0.7421 (tm-30) cc_final: 0.7006 (tm-30) REVERT: F 139 GLN cc_start: 0.8425 (tm-30) cc_final: 0.7841 (tm-30) REVERT: F 149 ARG cc_start: 0.8526 (ttt-90) cc_final: 0.8301 (ttt90) REVERT: G 4 ILE cc_start: 0.8827 (tp) cc_final: 0.8551 (mm) REVERT: G 11 ASN cc_start: 0.8212 (t0) cc_final: 0.7857 (t0) REVERT: G 29 PHE cc_start: 0.8506 (t80) cc_final: 0.8070 (t80) REVERT: G 44 ILE cc_start: 0.7249 (mm) cc_final: 0.6996 (mt) REVERT: G 46 PHE cc_start: 0.6729 (m-10) cc_final: 0.6520 (m-80) REVERT: J 57 LEU cc_start: 0.9549 (OUTLIER) cc_final: 0.9188 (pp) REVERT: J 60 ASP cc_start: 0.8304 (p0) cc_final: 0.8084 (p0) REVERT: J 75 TYR cc_start: 0.8755 (m-80) cc_final: 0.8488 (m-80) REVERT: J 111 LYS cc_start: 0.8576 (mptt) cc_final: 0.8018 (mmmt) REVERT: J 128 ASN cc_start: 0.8558 (t0) cc_final: 0.8256 (t0) REVERT: K 3 GLN cc_start: 0.8276 (pt0) cc_final: 0.8049 (pt0) REVERT: K 77 ILE cc_start: 0.9416 (mt) cc_final: 0.9164 (mt) REVERT: L 69 ARG cc_start: 0.8025 (mtp-110) cc_final: 0.7580 (mmm-85) REVERT: L 70 LYS cc_start: 0.8987 (tttp) cc_final: 0.8524 (tttt) REVERT: L 105 ILE cc_start: 0.9098 (mm) cc_final: 0.8709 (mp) REVERT: L 127 VAL cc_start: 0.9173 (t) cc_final: 0.8956 (m) REVERT: M 2 LEU cc_start: 0.8858 (mt) cc_final: 0.8567 (mt) REVERT: M 33 LEU cc_start: 0.8867 (tp) cc_final: 0.8587 (tp) REVERT: M 78 LEU cc_start: 0.9291 (tp) cc_final: 0.8968 (mt) REVERT: N 2 ARG cc_start: 0.8038 (OUTLIER) cc_final: 0.6346 (ppp-140) REVERT: N 35 LYS cc_start: 0.8862 (tttt) cc_final: 0.8582 (tttt) REVERT: N 72 ASP cc_start: 0.8998 (t0) cc_final: 0.8682 (t0) REVERT: O 12 THR cc_start: 0.9210 (t) cc_final: 0.8958 (m) REVERT: O 98 GLN cc_start: 0.8699 (tp-100) cc_final: 0.8437 (mm-40) REVERT: O 99 TYR cc_start: 0.7922 (t80) cc_final: 0.7528 (t80) REVERT: O 104 GLN cc_start: 0.6902 (tt0) cc_final: 0.6676 (tp40) REVERT: P 11 GLU cc_start: 0.7942 (pt0) cc_final: 0.7603 (pt0) REVERT: P 27 GLU cc_start: 0.8208 (tm-30) cc_final: 0.7802 (tm-30) REVERT: P 100 LEU cc_start: 0.9413 (mt) cc_final: 0.9194 (mp) REVERT: Q 25 TYR cc_start: 0.9238 (t80) cc_final: 0.8844 (t80) REVERT: Q 29 SER cc_start: 0.9110 (p) cc_final: 0.8799 (m) REVERT: Q 47 TYR cc_start: 0.9297 (t80) cc_final: 0.9081 (t80) REVERT: Q 52 GLN cc_start: 0.8735 (mt0) cc_final: 0.8383 (mt0) REVERT: Q 59 GLN cc_start: 0.8699 (tt0) cc_final: 0.8223 (mt0) REVERT: Q 71 GLN cc_start: 0.8204 (tp40) cc_final: 0.7513 (tm-30) REVERT: Q 87 SER cc_start: 0.8810 (t) cc_final: 0.8434 (p) REVERT: Q 101 PHE cc_start: 0.7763 (m-80) cc_final: 0.7398 (m-80) REVERT: R 7 SER cc_start: 0.8181 (t) cc_final: 0.7633 (p) REVERT: R 21 ARG cc_start: 0.9141 (ttm170) cc_final: 0.8591 (ttm170) REVERT: R 48 LYS cc_start: 0.8465 (mttp) cc_final: 0.8125 (mtpp) REVERT: R 51 VAL cc_start: 0.8246 (OUTLIER) cc_final: 0.7888 (p) REVERT: R 97 LYS cc_start: 0.9167 (tttt) cc_final: 0.8771 (ttpt) REVERT: R 99 THR cc_start: 0.8510 (p) cc_final: 0.7637 (p) REVERT: R 101 ILE cc_start: 0.9131 (mt) cc_final: 0.8914 (mt) REVERT: S 109 ASP cc_start: 0.8873 (OUTLIER) cc_final: 0.8630 (m-30) REVERT: T 21 SER cc_start: 0.9013 (m) cc_final: 0.8621 (p) REVERT: T 73 ARG cc_start: 0.8199 (ttm110) cc_final: 0.7793 (ptp-110) REVERT: T 77 ARG cc_start: 0.8396 (mtt180) cc_final: 0.7961 (mmm-85) REVERT: V 11 GLU cc_start: 0.7055 (pt0) cc_final: 0.6690 (pt0) REVERT: W 29 GLU cc_start: 0.8041 (tt0) cc_final: 0.7747 (tt0) REVERT: W 39 ARG cc_start: 0.8510 (mtp85) cc_final: 0.8074 (mtt180) REVERT: W 76 ASN cc_start: 0.8537 (m-40) cc_final: 0.8141 (m110) REVERT: X 20 HIS cc_start: 0.7468 (t70) cc_final: 0.7075 (t70) REVERT: X 23 ASN cc_start: 0.8879 (m110) cc_final: 0.8556 (m-40) REVERT: X 62 LYS cc_start: 0.9157 (mttt) cc_final: 0.8746 (mttt) REVERT: Y 13 GLU cc_start: 0.7849 (mt-10) cc_final: 0.7629 (mt-10) REVERT: Y 17 GLU cc_start: 0.8085 (tp30) cc_final: 0.7844 (tp30) REVERT: Y 21 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8553 (mm) REVERT: Y 38 GLN cc_start: 0.7704 (mm110) cc_final: 0.7198 (mm-40) REVERT: Y 44 LYS cc_start: 0.8917 (tttt) cc_final: 0.8692 (ttmm) REVERT: Y 49 ASP cc_start: 0.8638 (m-30) cc_final: 0.7997 (m-30) REVERT: Y 52 ARG cc_start: 0.8927 (mtt90) cc_final: 0.8695 (mtm180) REVERT: Y 58 ASN cc_start: 0.8093 (m-40) cc_final: 0.7738 (m110) REVERT: Y 59 GLU cc_start: 0.8699 (tt0) cc_final: 0.8393 (tt0) REVERT: Z 19 LYS cc_start: 0.8519 (ttmm) cc_final: 0.8316 (mttp) REVERT: Z 21 LYS cc_start: 0.9134 (mttt) cc_final: 0.8515 (mtmm) REVERT: Z 40 ASP cc_start: 0.7780 (t0) cc_final: 0.7166 (t0) REVERT: b 36 GLU cc_start: 0.8245 (pt0) cc_final: 0.6950 (pt0) REVERT: c 27 LYS cc_start: 0.8736 (mttt) cc_final: 0.8458 (tppt) REVERT: c 34 LEU cc_start: 0.8649 (tp) cc_final: 0.8396 (tp) REVERT: c 53 LYS cc_start: 0.7851 (ttmm) cc_final: 0.7576 (pttm) REVERT: d 6 GLN cc_start: 0.9195 (mm-40) cc_final: 0.8730 (mm110) REVERT: e 31 HIS cc_start: 0.8061 (OUTLIER) cc_final: 0.7715 (p90) REVERT: e 49 MET cc_start: 0.8787 (mmm) cc_final: 0.8072 (mmm) REVERT: e 55 LEU cc_start: 0.9307 (tp) cc_final: 0.9022 (tp) REVERT: f 6 SER cc_start: 0.9243 (t) cc_final: 0.9008 (p) REVERT: f 30 GLU cc_start: 0.8671 (tp30) cc_final: 0.7738 (mp0) REVERT: g 70 VAL cc_start: 0.8317 (t) cc_final: 0.7479 (p) REVERT: g 74 ARG cc_start: 0.7005 (mmp80) cc_final: 0.5886 (ttp80) REVERT: g 120 GLN cc_start: 0.8249 (mt0) cc_final: 0.7838 (mt0) REVERT: g 131 LYS cc_start: 0.7831 (pttm) cc_final: 0.6593 (mmtt) REVERT: g 143 LYS cc_start: 0.7840 (tptt) cc_final: 0.7523 (mmtm) REVERT: g 152 LYS cc_start: 0.8285 (pttt) cc_final: 0.7782 (tmtt) REVERT: g 154 MET cc_start: 0.7822 (ttp) cc_final: 0.7536 (ttm) REVERT: g 184 PHE cc_start: 0.8286 (m-80) cc_final: 0.8080 (m-80) REVERT: h 32 ASN cc_start: 0.8666 (m-40) cc_final: 0.8421 (m-40) REVERT: h 35 SER cc_start: 0.8711 (t) cc_final: 0.8409 (p) REVERT: h 79 LYS cc_start: 0.6840 (mmtm) cc_final: 0.6595 (tmtt) REVERT: h 86 LYS cc_start: 0.8692 (ttmt) cc_final: 0.8416 (mtpp) REVERT: h 122 SER cc_start: 0.9406 (m) cc_final: 0.8890 (p) REVERT: h 123 GLN cc_start: 0.9103 (mt0) cc_final: 0.8861 (mt0) REVERT: h 135 LYS cc_start: 0.8908 (mmtp) cc_final: 0.8636 (mmtm) REVERT: h 164 ARG cc_start: 0.8418 (pmt170) cc_final: 0.8212 (ptt90) REVERT: h 172 ARG cc_start: 0.8602 (OUTLIER) cc_final: 0.8287 (ptm-80) REVERT: h 207 ILE cc_start: 0.8763 (mm) cc_final: 0.8541 (mt) REVERT: i 88 GLU cc_start: 0.8436 (mt-10) cc_final: 0.8222 (mm-30) REVERT: i 103 TYR cc_start: 0.7883 (t80) cc_final: 0.7132 (t80) REVERT: i 107 PHE cc_start: 0.8064 (m-10) cc_final: 0.7702 (m-10) REVERT: i 134 SER cc_start: 0.7695 (p) cc_final: 0.7321 (m) REVERT: j 19 ASN cc_start: 0.8778 (t0) cc_final: 0.8559 (t0) REVERT: j 62 LYS cc_start: 0.8703 (mttt) cc_final: 0.8285 (ttmm) REVERT: j 69 ARG cc_start: 0.8268 (mtm180) cc_final: 0.7866 (mtm180) REVERT: j 72 ILE cc_start: 0.9265 (tp) cc_final: 0.8932 (tt) REVERT: j 128 TYR cc_start: 0.8078 (m-80) cc_final: 0.7814 (m-80) REVERT: k 5 GLU cc_start: 0.8781 (tt0) cc_final: 0.8224 (tt0) REVERT: k 30 THR cc_start: 0.8178 (m) cc_final: 0.7634 (t) REVERT: k 38 ARG cc_start: 0.7789 (ptt180) cc_final: 0.7464 (ptt180) REVERT: k 52 ASN cc_start: 0.9014 (m-40) cc_final: 0.8504 (m110) REVERT: k 55 HIS cc_start: 0.7237 (m90) cc_final: 0.6560 (m-70) REVERT: k 79 ARG cc_start: 0.7697 (mtp85) cc_final: 0.6851 (ttm110) REVERT: l 23 LEU cc_start: 0.8939 (mm) cc_final: 0.8652 (mm) REVERT: l 37 SER cc_start: 0.8292 (t) cc_final: 0.7770 (p) REVERT: l 42 ILE cc_start: 0.9210 (mt) cc_final: 0.8929 (mm) REVERT: l 48 GLU cc_start: 0.8278 (tm-30) cc_final: 0.7513 (tm-30) REVERT: l 86 GLN cc_start: 0.6923 (mm110) cc_final: 0.6279 (mm-40) REVERT: l 90 GLU cc_start: 0.7449 (tp30) cc_final: 0.7102 (tp30) REVERT: l 122 ASN cc_start: 0.7848 (m-40) cc_final: 0.7362 (m110) REVERT: l 126 ASP cc_start: 0.7850 (m-30) cc_final: 0.7648 (m-30) REVERT: l 130 ASN cc_start: 0.8318 (t0) cc_final: 0.7982 (t0) REVERT: l 144 MET cc_start: 0.7792 (ttm) cc_final: 0.7399 (tpt) REVERT: m 18 GLN cc_start: 0.8775 (mm-40) cc_final: 0.8336 (mm-40) REVERT: m 60 GLU cc_start: 0.7851 (tt0) cc_final: 0.7606 (tm-30) REVERT: m 62 THR cc_start: 0.9052 (m) cc_final: 0.8305 (p) REVERT: m 88 ARG cc_start: 0.7008 (mtp180) cc_final: 0.6247 (mtm180) REVERT: m 106 THR cc_start: 0.8679 (p) cc_final: 0.8472 (p) REVERT: m 111 MET cc_start: 0.7427 (ptt) cc_final: 0.7218 (ptt) REVERT: n 6 TYR cc_start: 0.6926 (m-10) cc_final: 0.6513 (m-10) REVERT: n 32 GLN cc_start: 0.7906 (mp10) cc_final: 0.7458 (mp10) REVERT: n 35 LEU cc_start: 0.9009 (tp) cc_final: 0.8749 (pp) REVERT: n 62 ASP cc_start: 0.6658 (m-30) cc_final: 0.6023 (p0) REVERT: n 80 ARG cc_start: 0.9072 (ttp-170) cc_final: 0.8719 (ttp80) REVERT: n 107 ASP cc_start: 0.8024 (t70) cc_final: 0.7613 (t0) REVERT: o 6 ILE cc_start: 0.7720 (mt) cc_final: 0.7513 (mm) REVERT: o 31 ARG cc_start: 0.7484 (mtm180) cc_final: 0.7218 (mtm180) REVERT: o 58 ASN cc_start: 0.8631 (m110) cc_final: 0.8299 (m110) REVERT: o 69 THR cc_start: 0.9251 (m) cc_final: 0.8832 (p) REVERT: o 100 ILE cc_start: 0.6554 (OUTLIER) cc_final: 0.6334 (pt) REVERT: p 24 HIS cc_start: 0.8389 (t70) cc_final: 0.8139 (t-90) REVERT: p 50 SER cc_start: 0.8250 (m) cc_final: 0.7422 (p) REVERT: p 61 PHE cc_start: 0.9111 (t80) cc_final: 0.8619 (t80) REVERT: q 58 THR cc_start: 0.8629 (m) cc_final: 0.8310 (m) REVERT: q 59 ASN cc_start: 0.8804 (p0) cc_final: 0.8419 (p0) REVERT: r 19 LEU cc_start: 0.8627 (mt) cc_final: 0.8237 (tp) REVERT: r 46 SER cc_start: 0.9050 (m) cc_final: 0.8755 (p) REVERT: r 68 ASP cc_start: 0.7781 (m-30) cc_final: 0.7487 (m-30) REVERT: r 75 MET cc_start: 0.8533 (tpt) cc_final: 0.8317 (tpt) REVERT: r 76 SER cc_start: 0.8856 (m) cc_final: 0.8568 (p) REVERT: s 10 GLU cc_start: 0.8009 (tp30) cc_final: 0.7767 (tp30) REVERT: s 33 ASP cc_start: 0.7942 (t0) cc_final: 0.7483 (t0) REVERT: t 17 ARG cc_start: 0.7589 (mmt180) cc_final: 0.7362 (mmt180) REVERT: t 48 LYS cc_start: 0.8566 (mmtm) cc_final: 0.8204 (mtpt) REVERT: t 64 ARG cc_start: 0.7976 (tpm-80) cc_final: 0.7677 (tpt170) REVERT: t 68 ASP cc_start: 0.7963 (m-30) cc_final: 0.7484 (m-30) REVERT: u 56 ARG cc_start: 0.8679 (mmm160) cc_final: 0.8258 (mmm-85) REVERT: u 59 HIS cc_start: 0.8444 (t-90) cc_final: 0.8157 (t-90) REVERT: u 61 VAL cc_start: 0.8669 (t) cc_final: 0.8455 (m) REVERT: u 63 GLN cc_start: 0.8783 (mm110) cc_final: 0.8437 (mt0) REVERT: v 15 ASP cc_start: 0.6081 (p0) cc_final: 0.4628 (t70) REVERT: w 47 THR cc_start: 0.8508 (m) cc_final: 0.8204 (m) REVERT: w 52 GLN cc_start: 0.9074 (tp40) cc_final: 0.8696 (tp-100) REVERT: x 71 LEU cc_start: 0.9191 (mt) cc_final: 0.8723 (mt) REVERT: y 28 MET cc_start: 0.8635 (tmm) cc_final: 0.8383 (ttm) REVERT: y 51 PHE cc_start: 0.8440 (t80) cc_final: 0.8134 (t80) REVERT: z 17 ARG cc_start: 0.8410 (ttm110) cc_final: 0.8040 (tpt170) REVERT: z 19 PHE cc_start: 0.8152 (t80) cc_final: 0.7807 (t80) REVERT: z 28 VAL cc_start: 0.9073 (t) cc_final: 0.8858 (p) REVERT: z 35 ARG cc_start: 0.8679 (mtt-85) cc_final: 0.8408 (ttm-80) REVERT: z 66 ARG cc_start: 0.4560 (OUTLIER) cc_final: 0.4076 (mtt180) REVERT: A 114 GLU cc_start: 0.8338 (mt-10) cc_final: 0.8092 (mt-10) REVERT: A 137 ARG cc_start: 0.8606 (mmm-85) cc_final: 0.7890 (mmt-90) REVERT: A 162 ILE cc_start: 0.9324 (tt) cc_final: 0.8991 (tt) REVERT: A 193 GLN cc_start: 0.8268 (mt0) cc_final: 0.7291 (tm-30) REVERT: A 206 MET cc_start: 0.8729 (mtp) cc_final: 0.7604 (mtm) REVERT: A 248 HIS cc_start: 0.8420 (t-90) cc_final: 0.7026 (t-90) REVERT: A 256 GLU cc_start: 0.8459 (mt-10) cc_final: 0.8253 (tt0) REVERT: A 274 LEU cc_start: 0.8234 (mt) cc_final: 0.7961 (tt) REVERT: A 277 ARG cc_start: 0.7819 (mtt180) cc_final: 0.7154 (mtp-110) REVERT: A 290 GLU cc_start: 0.8074 (tp30) cc_final: 0.7670 (tp30) REVERT: A 311 ASN cc_start: 0.8705 (OUTLIER) cc_final: 0.7833 (t0) REVERT: A 325 THR cc_start: 0.7247 (m) cc_final: 0.6997 (m) outliers start: 207 outliers final: 138 residues processed: 1929 average time/residue: 1.3253 time to fit residues: 4366.6287 Evaluate side-chains 1808 residues out of total 4880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 1657 time to evaluate : 6.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 26 LYS Chi-restraints excluded: chain B residue 38 SER Chi-restraints excluded: chain B residue 70 ASN Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain C residue 18 ASP Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 176 ASP Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain E residue 23 ASN Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 87 CYS Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain E residue 175 PHE Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 106 SER Chi-restraints excluded: chain F residue 122 THR Chi-restraints excluded: chain F residue 155 GLU Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 99 ILE Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain L residue 135 ILE Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 30 SER Chi-restraints excluded: chain M residue 41 LEU Chi-restraints excluded: chain M residue 63 ILE Chi-restraints excluded: chain M residue 126 ILE Chi-restraints excluded: chain N residue 2 ARG Chi-restraints excluded: chain N residue 33 ILE Chi-restraints excluded: chain O residue 28 VAL Chi-restraints excluded: chain O residue 36 TYR Chi-restraints excluded: chain O residue 48 LEU Chi-restraints excluded: chain O residue 52 SER Chi-restraints excluded: chain O residue 78 VAL Chi-restraints excluded: chain O residue 83 LEU Chi-restraints excluded: chain P residue 2 SER Chi-restraints excluded: chain P residue 19 SER Chi-restraints excluded: chain P residue 83 SER Chi-restraints excluded: chain P residue 114 LEU Chi-restraints excluded: chain R residue 14 VAL Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain S residue 12 SER Chi-restraints excluded: chain S residue 13 SER Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 67 ASP Chi-restraints excluded: chain S residue 100 THR Chi-restraints excluded: chain S residue 108 SER Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain T residue 22 THR Chi-restraints excluded: chain T residue 50 LEU Chi-restraints excluded: chain V residue 4 ILE Chi-restraints excluded: chain V residue 17 SER Chi-restraints excluded: chain V residue 62 THR Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain V residue 77 VAL Chi-restraints excluded: chain W residue 30 SER Chi-restraints excluded: chain X residue 8 THR Chi-restraints excluded: chain X residue 25 THR Chi-restraints excluded: chain Y residue 11 VAL Chi-restraints excluded: chain Y residue 21 LEU Chi-restraints excluded: chain Z residue 36 VAL Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain b residue 23 THR Chi-restraints excluded: chain b residue 54 VAL Chi-restraints excluded: chain c residue 42 VAL Chi-restraints excluded: chain c residue 48 ILE Chi-restraints excluded: chain d residue 9 VAL Chi-restraints excluded: chain d residue 15 SER Chi-restraints excluded: chain e residue 31 HIS Chi-restraints excluded: chain e residue 38 THR Chi-restraints excluded: chain e residue 51 SER Chi-restraints excluded: chain e residue 54 ASP Chi-restraints excluded: chain g residue 36 ASN Chi-restraints excluded: chain g residue 199 VAL Chi-restraints excluded: chain h residue 165 THR Chi-restraints excluded: chain h residue 172 ARG Chi-restraints excluded: chain h residue 177 THR Chi-restraints excluded: chain h residue 192 THR Chi-restraints excluded: chain i residue 144 SER Chi-restraints excluded: chain j residue 15 LEU Chi-restraints excluded: chain j residue 22 SER Chi-restraints excluded: chain j residue 32 SER Chi-restraints excluded: chain j residue 131 THR Chi-restraints excluded: chain k residue 7 VAL Chi-restraints excluded: chain k residue 51 ILE Chi-restraints excluded: chain k residue 97 THR Chi-restraints excluded: chain l residue 6 VAL Chi-restraints excluded: chain l residue 83 SER Chi-restraints excluded: chain l residue 133 THR Chi-restraints excluded: chain m residue 12 THR Chi-restraints excluded: chain m residue 38 ASN Chi-restraints excluded: chain m residue 51 VAL Chi-restraints excluded: chain m residue 79 SER Chi-restraints excluded: chain n residue 21 ILE Chi-restraints excluded: chain n residue 58 VAL Chi-restraints excluded: chain n residue 66 THR Chi-restraints excluded: chain n residue 93 SER Chi-restraints excluded: chain o residue 54 SER Chi-restraints excluded: chain o residue 74 VAL Chi-restraints excluded: chain o residue 100 ILE Chi-restraints excluded: chain p residue 33 THR Chi-restraints excluded: chain p residue 101 ASN Chi-restraints excluded: chain p residue 107 ILE Chi-restraints excluded: chain q residue 34 CYS Chi-restraints excluded: chain q residue 119 VAL Chi-restraints excluded: chain r residue 58 ASP Chi-restraints excluded: chain r residue 65 VAL Chi-restraints excluded: chain s residue 14 VAL Chi-restraints excluded: chain s residue 16 LEU Chi-restraints excluded: chain s residue 34 VAL Chi-restraints excluded: chain t residue 56 LEU Chi-restraints excluded: chain t residue 70 LEU Chi-restraints excluded: chain t residue 75 VAL Chi-restraints excluded: chain u residue 2 VAL Chi-restraints excluded: chain u residue 3 THR Chi-restraints excluded: chain u residue 67 ILE Chi-restraints excluded: chain v residue 38 ILE Chi-restraints excluded: chain w residue 28 THR Chi-restraints excluded: chain w residue 59 ILE Chi-restraints excluded: chain w residue 71 THR Chi-restraints excluded: chain x residue 64 ASP Chi-restraints excluded: chain x residue 79 THR Chi-restraints excluded: chain y residue 30 THR Chi-restraints excluded: chain z residue 3 VAL Chi-restraints excluded: chain z residue 43 THR Chi-restraints excluded: chain z residue 66 ARG Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 311 ASN Chi-restraints excluded: chain A residue 331 GLU Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain A residue 345 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1034 random chunks: chunk 521 optimal weight: 9.9990 chunk 291 optimal weight: 10.0000 chunk 781 optimal weight: 5.9990 chunk 639 optimal weight: 20.0000 chunk 259 optimal weight: 8.9990 chunk 940 optimal weight: 7.9990 chunk 1016 optimal weight: 30.0000 chunk 837 optimal weight: 5.9990 chunk 932 optimal weight: 1.9990 chunk 320 optimal weight: 10.0000 chunk 754 optimal weight: 1.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 53 HIS B 239 ASN C 94 GLN C 126 ASN C 173 GLN F 45 HIS F 143 GLN G 73 ASN J 67 ASN ** Q 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 72 ASN S 31 GLN T 48 GLN U 40 ASN V 12 GLN X 17 ASN e 31 HIS g 120 GLN h 8 ASN i 140 ASN j 97 GLN l 148 ASN n 37 GLN n 75 GLN ** n 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 15 GLN p 38 GLN r 100 GLN ** t 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 74 HIS ** A 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 307 ASN A 320 HIS Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.2410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 158938 Z= 0.268 Angle : 0.649 13.702 237562 Z= 0.347 Chirality : 0.037 0.282 30220 Planarity : 0.006 0.131 12875 Dihedral : 23.697 179.030 78950 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.74 % Favored : 95.24 % Rotamer: Outliers : 5.31 % Allowed : 15.92 % Favored : 78.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.51 % 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: -2.22 (0.10), residues: 5863 helix: -1.03 (0.11), residues: 1889 sheet: -1.54 (0.15), residues: 1101 loop : -1.68 (0.11), residues: 2873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 248 HIS 0.026 0.001 HIS e 31 PHE 0.028 0.002 PHE g 126 TYR 0.028 0.002 TYR A 172 ARG 0.019 0.001 ARG i 63 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11726 Ramachandran restraints generated. 5863 Oldfield, 0 Emsley, 5863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11726 Ramachandran restraints generated. 5863 Oldfield, 0 Emsley, 5863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1977 residues out of total 4880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 259 poor density : 1718 time to evaluate : 5.722 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: B 98 ASP cc_start: 0.8088 (p0) cc_final: 0.7850 (p0) REVERT: B 108 LYS cc_start: 0.8373 (tttt) cc_final: 0.8082 (ttmm) REVERT: B 110 LEU cc_start: 0.9047 (OUTLIER) cc_final: 0.8579 (mp) REVERT: B 111 LYS cc_start: 0.9057 (pttt) cc_final: 0.8731 (pmtt) REVERT: B 114 ASP cc_start: 0.8273 (m-30) cc_final: 0.7843 (m-30) REVERT: B 201 MET cc_start: 0.8922 (ptt) cc_final: 0.8543 (ptt) REVERT: C 133 THR cc_start: 0.8115 (t) cc_final: 0.7759 (t) REVERT: D 108 ILE cc_start: 0.9211 (pt) cc_final: 0.8950 (mt) REVERT: D 139 LYS cc_start: 0.8811 (ttpt) cc_final: 0.8593 (ttmm) REVERT: D 156 ASN cc_start: 0.8177 (m-40) cc_final: 0.7585 (m-40) REVERT: E 13 VAL cc_start: 0.7170 (OUTLIER) cc_final: 0.6952 (t) REVERT: E 27 GLN cc_start: 0.8172 (tt0) cc_final: 0.7913 (tt0) REVERT: E 48 LYS cc_start: 0.7941 (mttt) cc_final: 0.7721 (mtpp) REVERT: E 155 THR cc_start: 0.9579 (m) cc_final: 0.9208 (p) REVERT: E 159 THR cc_start: 0.9040 (p) cc_final: 0.8442 (t) REVERT: E 175 PHE cc_start: 0.8052 (OUTLIER) cc_final: 0.7568 (m-80) REVERT: F 22 GLN cc_start: 0.7827 (mm-40) cc_final: 0.6751 (mm-40) REVERT: F 25 THR cc_start: 0.8108 (OUTLIER) cc_final: 0.7899 (t) REVERT: F 38 ASN cc_start: 0.8403 (t0) cc_final: 0.8190 (t0) REVERT: F 74 SER cc_start: 0.9545 (t) cc_final: 0.9205 (t) REVERT: F 130 GLU cc_start: 0.7661 (tm-30) cc_final: 0.7078 (tm-30) REVERT: F 139 GLN cc_start: 0.8385 (tm-30) cc_final: 0.7909 (tt0) REVERT: F 149 ARG cc_start: 0.8480 (ttt-90) cc_final: 0.8213 (ttt90) REVERT: G 4 ILE cc_start: 0.8935 (tp) cc_final: 0.8527 (mm) REVERT: G 11 ASN cc_start: 0.8069 (t0) cc_final: 0.7662 (t0) REVERT: G 29 PHE cc_start: 0.8534 (t80) cc_final: 0.8159 (t80) REVERT: G 44 ILE cc_start: 0.7310 (mm) cc_final: 0.6908 (mt) REVERT: G 46 PHE cc_start: 0.6942 (m-10) cc_final: 0.6660 (m-80) REVERT: J 81 ILE cc_start: 0.8968 (tp) cc_final: 0.8754 (tp) REVERT: J 111 LYS cc_start: 0.8410 (mptt) cc_final: 0.8017 (mmmt) REVERT: J 128 ASN cc_start: 0.8465 (t0) cc_final: 0.7906 (t0) REVERT: K 3 GLN cc_start: 0.8183 (pt0) cc_final: 0.7965 (pt0) REVERT: K 51 LYS cc_start: 0.7818 (mtpt) cc_final: 0.7557 (mmmt) REVERT: K 77 ILE cc_start: 0.9398 (mt) cc_final: 0.9133 (mt) REVERT: L 69 ARG cc_start: 0.8065 (mtp-110) cc_final: 0.7555 (mmm-85) REVERT: L 70 LYS cc_start: 0.9017 (tttp) cc_final: 0.8487 (ttpt) REVERT: L 105 ILE cc_start: 0.9157 (mm) cc_final: 0.8819 (mp) REVERT: M 2 LEU cc_start: 0.8897 (mt) cc_final: 0.8657 (mt) REVERT: M 33 LEU cc_start: 0.8778 (tp) cc_final: 0.8537 (tp) REVERT: M 78 LEU cc_start: 0.9252 (tp) cc_final: 0.8904 (mt) REVERT: M 110 GLU cc_start: 0.8223 (tm-30) cc_final: 0.7939 (tm-30) REVERT: N 2 ARG cc_start: 0.7825 (OUTLIER) cc_final: 0.4619 (ppp-140) REVERT: N 35 LYS cc_start: 0.8858 (tttt) cc_final: 0.8549 (tttt) REVERT: N 72 ASP cc_start: 0.8999 (t0) cc_final: 0.8747 (t0) REVERT: O 12 THR cc_start: 0.9159 (t) cc_final: 0.8920 (m) REVERT: O 52 SER cc_start: 0.7921 (m) cc_final: 0.7599 (m) REVERT: O 99 TYR cc_start: 0.7893 (t80) cc_final: 0.7440 (t80) REVERT: P 11 GLU cc_start: 0.7980 (pt0) cc_final: 0.7568 (pt0) REVERT: P 27 GLU cc_start: 0.8125 (tm-30) cc_final: 0.7794 (tm-30) REVERT: P 82 ASP cc_start: 0.8364 (t0) cc_final: 0.8081 (t0) REVERT: P 100 LEU cc_start: 0.9212 (mt) cc_final: 0.8980 (mp) REVERT: Q 25 TYR cc_start: 0.9262 (t80) cc_final: 0.8867 (t80) REVERT: Q 29 SER cc_start: 0.9184 (p) cc_final: 0.8924 (p) REVERT: Q 45 TYR cc_start: 0.8867 (m-80) cc_final: 0.8358 (m-10) REVERT: Q 47 TYR cc_start: 0.9306 (t80) cc_final: 0.9103 (t80) REVERT: Q 52 GLN cc_start: 0.8815 (mt0) cc_final: 0.8483 (mt0) REVERT: Q 59 GLN cc_start: 0.8669 (tt0) cc_final: 0.8184 (mt0) REVERT: Q 62 ILE cc_start: 0.9571 (mt) cc_final: 0.9190 (mm) REVERT: Q 87 SER cc_start: 0.8605 (t) cc_final: 0.8301 (p) REVERT: Q 101 PHE cc_start: 0.7939 (m-80) cc_final: 0.7341 (m-80) REVERT: R 7 SER cc_start: 0.7989 (t) cc_final: 0.7702 (p) REVERT: R 21 ARG cc_start: 0.9146 (ttm170) cc_final: 0.8566 (ttt180) REVERT: R 48 LYS cc_start: 0.8407 (mttp) cc_final: 0.8137 (mtpp) REVERT: R 62 GLU cc_start: 0.7170 (mp0) cc_final: 0.6887 (mp0) REVERT: R 97 LYS cc_start: 0.9090 (tttt) cc_final: 0.8698 (ttpt) REVERT: R 99 THR cc_start: 0.7974 (p) cc_final: 0.7639 (p) REVERT: S 109 ASP cc_start: 0.8778 (OUTLIER) cc_final: 0.8561 (m-30) REVERT: T 3 ARG cc_start: 0.7950 (ttm-80) cc_final: 0.7750 (ttm-80) REVERT: T 5 GLU cc_start: 0.7867 (OUTLIER) cc_final: 0.7013 (pm20) REVERT: T 21 SER cc_start: 0.9053 (m) cc_final: 0.8639 (p) REVERT: T 73 ARG cc_start: 0.8095 (ttm110) cc_final: 0.7534 (ptp-110) REVERT: T 77 ARG cc_start: 0.8271 (mtt180) cc_final: 0.7798 (mtp180) REVERT: U 22 ARG cc_start: 0.8242 (OUTLIER) cc_final: 0.7924 (mtm180) REVERT: V 11 GLU cc_start: 0.7042 (pt0) cc_final: 0.6712 (pt0) REVERT: W 39 ARG cc_start: 0.8440 (mtp85) cc_final: 0.8069 (mtt-85) REVERT: W 76 ASN cc_start: 0.8505 (m-40) cc_final: 0.8069 (m110) REVERT: X 20 HIS cc_start: 0.7449 (t70) cc_final: 0.7063 (t70) REVERT: X 23 ASN cc_start: 0.8889 (m110) cc_final: 0.8526 (m-40) REVERT: X 28 ARG cc_start: 0.8684 (mtp180) cc_final: 0.8442 (mtm180) REVERT: X 62 LYS cc_start: 0.9166 (mttt) cc_final: 0.8696 (mttt) REVERT: Y 13 GLU cc_start: 0.7700 (mt-10) cc_final: 0.7488 (mt-10) REVERT: Y 38 GLN cc_start: 0.7795 (mm110) cc_final: 0.7439 (mm-40) REVERT: Y 58 ASN cc_start: 0.8067 (m-40) cc_final: 0.7452 (m110) REVERT: Z 19 LYS cc_start: 0.8571 (ttmm) cc_final: 0.8355 (mttp) REVERT: Z 21 LYS cc_start: 0.9105 (mttt) cc_final: 0.8572 (mtmm) REVERT: Z 40 ASP cc_start: 0.8083 (t0) cc_final: 0.7561 (t0) REVERT: b 32 LYS cc_start: 0.8235 (pttt) cc_final: 0.7786 (mtmt) REVERT: c 27 LYS cc_start: 0.8688 (mttt) cc_final: 0.8437 (tppt) REVERT: c 34 LEU cc_start: 0.8531 (tp) cc_final: 0.8301 (tp) REVERT: c 35 GLU cc_start: 0.7792 (mm-30) cc_final: 0.7585 (mm-30) REVERT: c 45 GLN cc_start: 0.8291 (mm-40) cc_final: 0.8065 (mm-40) REVERT: c 53 LYS cc_start: 0.7632 (ttmm) cc_final: 0.7183 (pttm) REVERT: e 49 MET cc_start: 0.8744 (mmm) cc_final: 0.7799 (mmm) REVERT: f 6 SER cc_start: 0.9284 (t) cc_final: 0.9082 (p) REVERT: f 30 GLU cc_start: 0.8647 (tp30) cc_final: 0.7708 (mp0) REVERT: g 70 VAL cc_start: 0.8289 (t) cc_final: 0.7600 (p) REVERT: g 74 ARG cc_start: 0.7329 (mmp80) cc_final: 0.5825 (ttp80) REVERT: g 120 GLN cc_start: 0.8055 (mt0) cc_final: 0.7383 (mt0) REVERT: g 131 LYS cc_start: 0.7432 (pttm) cc_final: 0.6555 (mmtt) REVERT: h 31 ASP cc_start: 0.8020 (OUTLIER) cc_final: 0.7800 (p0) REVERT: h 79 LYS cc_start: 0.6983 (mmtm) cc_final: 0.6585 (ptmm) REVERT: h 86 LYS cc_start: 0.8816 (ttmt) cc_final: 0.8546 (mtpp) REVERT: h 122 SER cc_start: 0.9337 (m) cc_final: 0.8777 (p) REVERT: h 142 MET cc_start: 0.8010 (mmm) cc_final: 0.7782 (mmm) REVERT: h 147 LYS cc_start: 0.7632 (mmtm) cc_final: 0.7410 (mtmm) REVERT: h 172 ARG cc_start: 0.8572 (OUTLIER) cc_final: 0.8349 (ptm-80) REVERT: h 184 TYR cc_start: 0.9165 (t80) cc_final: 0.8844 (t80) REVERT: h 207 ILE cc_start: 0.8748 (mm) cc_final: 0.8540 (mt) REVERT: i 48 LEU cc_start: 0.7643 (tp) cc_final: 0.7275 (mp) REVERT: i 107 PHE cc_start: 0.8149 (m-10) cc_final: 0.7714 (m-10) REVERT: i 134 SER cc_start: 0.7668 (p) cc_final: 0.7296 (m) REVERT: i 135 TYR cc_start: 0.6323 (t80) cc_final: 0.6075 (t80) REVERT: j 45 ARG cc_start: 0.6862 (mtp85) cc_final: 0.6537 (ttt90) REVERT: j 61 GLN cc_start: 0.8331 (mm110) cc_final: 0.7921 (mm110) REVERT: j 62 LYS cc_start: 0.8633 (mttt) cc_final: 0.8040 (ttmm) REVERT: j 69 ARG cc_start: 0.8160 (mtm180) cc_final: 0.7762 (mtm180) REVERT: j 72 ILE cc_start: 0.9266 (tp) cc_final: 0.8918 (tt) REVERT: j 128 TYR cc_start: 0.8106 (m-80) cc_final: 0.7889 (m-80) REVERT: k 5 GLU cc_start: 0.8708 (tt0) cc_final: 0.8366 (tt0) REVERT: k 7 VAL cc_start: 0.8891 (OUTLIER) cc_final: 0.8581 (m) REVERT: k 30 THR cc_start: 0.7668 (m) cc_final: 0.7266 (t) REVERT: k 52 ASN cc_start: 0.9027 (m-40) cc_final: 0.8508 (m110) REVERT: k 55 HIS cc_start: 0.7228 (m90) cc_final: 0.6565 (m-70) REVERT: k 79 ARG cc_start: 0.7663 (mtp85) cc_final: 0.7335 (ttm110) REVERT: l 37 SER cc_start: 0.8307 (t) cc_final: 0.7807 (p) REVERT: l 42 ILE cc_start: 0.9146 (mt) cc_final: 0.8917 (mm) REVERT: l 48 GLU cc_start: 0.8390 (tm-30) cc_final: 0.8062 (tm-30) REVERT: l 86 GLN cc_start: 0.6894 (mm110) cc_final: 0.6258 (mm-40) REVERT: l 122 ASN cc_start: 0.8085 (m-40) cc_final: 0.7571 (m110) REVERT: l 136 LYS cc_start: 0.8639 (tppt) cc_final: 0.8412 (tptp) REVERT: l 144 MET cc_start: 0.7752 (ttm) cc_final: 0.7406 (tpt) REVERT: m 18 GLN cc_start: 0.8869 (mm-40) cc_final: 0.8638 (mm110) REVERT: m 60 GLU cc_start: 0.7848 (tt0) cc_final: 0.7613 (tm-30) REVERT: m 67 GLN cc_start: 0.7776 (mt0) cc_final: 0.7452 (mt0) REVERT: m 88 ARG cc_start: 0.7054 (mtp180) cc_final: 0.6302 (mtm180) REVERT: m 111 MET cc_start: 0.7396 (ptt) cc_final: 0.7086 (ptt) REVERT: n 75 GLN cc_start: 0.7192 (mt0) cc_final: 0.6955 (mt0) REVERT: n 88 MET cc_start: 0.7357 (mmt) cc_final: 0.7148 (mmm) REVERT: n 107 ASP cc_start: 0.8225 (t70) cc_final: 0.7691 (t0) REVERT: o 31 ARG cc_start: 0.7385 (mtm180) cc_final: 0.7146 (mtm180) REVERT: o 69 THR cc_start: 0.9244 (m) cc_final: 0.8879 (p) REVERT: o 88 MET cc_start: 0.7919 (mmm) cc_final: 0.7513 (mtt) REVERT: o 96 VAL cc_start: 0.8774 (m) cc_final: 0.8300 (p) REVERT: p 61 PHE cc_start: 0.9115 (t80) cc_final: 0.8674 (t80) REVERT: p 80 LYS cc_start: 0.7962 (mptt) cc_final: 0.7614 (mptt) REVERT: p 87 LYS cc_start: 0.7716 (ttmm) cc_final: 0.7504 (ptmt) REVERT: q 10 LYS cc_start: 0.8653 (tmtt) cc_final: 0.8299 (ptmm) REVERT: q 58 THR cc_start: 0.8710 (m) cc_final: 0.8441 (m) REVERT: r 46 SER cc_start: 0.8923 (m) cc_final: 0.8584 (p) REVERT: r 75 MET cc_start: 0.8531 (tpt) cc_final: 0.8006 (tpt) REVERT: r 76 SER cc_start: 0.8772 (m) cc_final: 0.8553 (p) REVERT: r 78 LYS cc_start: 0.8962 (mtpt) cc_final: 0.8554 (mtmm) REVERT: s 10 GLU cc_start: 0.7876 (tp30) cc_final: 0.7559 (tp30) REVERT: s 33 ASP cc_start: 0.8034 (t0) cc_final: 0.7632 (t0) REVERT: s 43 ASN cc_start: 0.8074 (m-40) cc_final: 0.7713 (m110) REVERT: t 48 LYS cc_start: 0.8572 (mmtm) cc_final: 0.8166 (mtpt) REVERT: t 67 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8645 (mm) REVERT: t 68 ASP cc_start: 0.8026 (m-30) cc_final: 0.7525 (m-30) REVERT: u 5 ARG cc_start: 0.8532 (ptp-170) cc_final: 0.7957 (ptp90) REVERT: u 40 ASN cc_start: 0.8028 (t0) cc_final: 0.7827 (t0) REVERT: u 56 ARG cc_start: 0.8622 (mmm160) cc_final: 0.8096 (mmm-85) REVERT: u 63 GLN cc_start: 0.8714 (mm110) cc_final: 0.8489 (mt0) REVERT: v 6 ARG cc_start: 0.5964 (mtt90) cc_final: 0.5326 (mtt90) REVERT: v 15 ASP cc_start: 0.6029 (p0) cc_final: 0.4602 (t70) REVERT: v 51 ASN cc_start: 0.8460 (OUTLIER) cc_final: 0.8257 (m-40) REVERT: w 32 TYR cc_start: 0.8679 (m-80) cc_final: 0.8372 (m-80) REVERT: w 47 THR cc_start: 0.8577 (m) cc_final: 0.8148 (m) REVERT: w 52 GLN cc_start: 0.9092 (tp40) cc_final: 0.8734 (tp-100) REVERT: x 35 SER cc_start: 0.9438 (m) cc_final: 0.8892 (t) REVERT: x 71 LEU cc_start: 0.9234 (mt) cc_final: 0.8767 (mt) REVERT: z 17 ARG cc_start: 0.8417 (ttm110) cc_final: 0.8027 (tpt170) REVERT: z 19 PHE cc_start: 0.8185 (t80) cc_final: 0.7644 (t80) REVERT: z 28 VAL cc_start: 0.9106 (t) cc_final: 0.8874 (p) REVERT: z 35 ARG cc_start: 0.8707 (mtt-85) cc_final: 0.8372 (mtm-85) REVERT: z 64 ASN cc_start: 0.7456 (t0) cc_final: 0.7151 (t0) REVERT: z 66 ARG cc_start: 0.4738 (OUTLIER) cc_final: 0.4316 (mtt180) REVERT: A 137 ARG cc_start: 0.8617 (mmm-85) cc_final: 0.7934 (mmt-90) REVERT: A 140 GLU cc_start: 0.7170 (pp20) cc_final: 0.6960 (pp20) REVERT: A 162 ILE cc_start: 0.9300 (tt) cc_final: 0.8984 (tt) REVERT: A 193 GLN cc_start: 0.8289 (mt0) cc_final: 0.7301 (tm-30) REVERT: A 206 MET cc_start: 0.8663 (mtp) cc_final: 0.8089 (mtm) REVERT: A 256 GLU cc_start: 0.8493 (mt-10) cc_final: 0.8238 (tt0) REVERT: A 274 LEU cc_start: 0.8213 (mt) cc_final: 0.7975 (tt) REVERT: A 277 ARG cc_start: 0.7682 (mtt180) cc_final: 0.7003 (mtm110) REVERT: A 311 ASN cc_start: 0.8559 (OUTLIER) cc_final: 0.7808 (t0) REVERT: A 352 GLN cc_start: 0.6729 (pt0) cc_final: 0.4651 (tm-30) outliers start: 259 outliers final: 197 residues processed: 1815 average time/residue: 1.3673 time to fit residues: 4275.0867 Evaluate side-chains 1848 residues out of total 4880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 212 poor density : 1636 time to evaluate : 6.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 SER Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 70 ASN Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain C residue 18 ASP Chi-restraints excluded: chain C residue 43 ASP Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 176 ASP Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 23 ASN Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 87 CYS Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain E residue 175 PHE Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 122 THR Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain F residue 143 GLN Chi-restraints excluded: chain F residue 147 ASP Chi-restraints excluded: chain F residue 155 GLU Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain J residue 92 MET Chi-restraints excluded: chain J residue 93 ILE Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 92 GLU Chi-restraints excluded: chain K residue 99 ILE Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 114 LYS Chi-restraints excluded: chain L residue 23 ILE Chi-restraints excluded: chain L residue 68 SER Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain L residue 135 ILE Chi-restraints excluded: chain M residue 30 SER Chi-restraints excluded: chain M residue 41 LEU Chi-restraints excluded: chain M residue 63 ILE Chi-restraints excluded: chain M residue 119 LEU Chi-restraints excluded: chain M residue 126 ILE Chi-restraints excluded: chain M residue 129 THR Chi-restraints excluded: chain N residue 2 ARG Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain N residue 33 ILE Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain O residue 28 VAL Chi-restraints excluded: chain O residue 36 TYR Chi-restraints excluded: chain O residue 48 LEU Chi-restraints excluded: chain O residue 83 LEU Chi-restraints excluded: chain P residue 2 SER Chi-restraints excluded: chain P residue 19 SER Chi-restraints excluded: chain P residue 44 GLU Chi-restraints excluded: chain P residue 114 LEU Chi-restraints excluded: chain Q residue 31 VAL Chi-restraints excluded: chain Q residue 107 THR Chi-restraints excluded: chain Q residue 117 LEU Chi-restraints excluded: chain R residue 41 ILE Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain S residue 3 THR Chi-restraints excluded: chain S residue 12 SER Chi-restraints excluded: chain S residue 13 SER Chi-restraints excluded: chain S residue 39 THR Chi-restraints excluded: chain S residue 67 ASP Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain T residue 5 GLU Chi-restraints excluded: chain T residue 11 LEU Chi-restraints excluded: chain T residue 22 THR Chi-restraints excluded: chain T residue 50 LEU Chi-restraints excluded: chain U residue 22 ARG Chi-restraints excluded: chain U residue 28 VAL Chi-restraints excluded: chain V residue 17 SER Chi-restraints excluded: chain V residue 47 VAL Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain W residue 21 LEU Chi-restraints excluded: chain W residue 30 SER Chi-restraints excluded: chain X residue 8 THR Chi-restraints excluded: chain X residue 25 THR Chi-restraints excluded: chain X residue 59 ILE Chi-restraints excluded: chain Y residue 11 VAL Chi-restraints excluded: chain Y residue 12 GLU Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain b residue 23 THR Chi-restraints excluded: chain b residue 39 LEU Chi-restraints excluded: chain b residue 54 VAL Chi-restraints excluded: chain c residue 42 VAL Chi-restraints excluded: chain c residue 48 ILE Chi-restraints excluded: chain d residue 9 VAL Chi-restraints excluded: chain d residue 15 SER Chi-restraints excluded: chain d residue 29 GLN Chi-restraints excluded: chain e residue 38 THR Chi-restraints excluded: chain e residue 44 LEU Chi-restraints excluded: chain e residue 54 ASP Chi-restraints excluded: chain g residue 6 MET Chi-restraints excluded: chain g residue 136 MET Chi-restraints excluded: chain g residue 199 VAL Chi-restraints excluded: chain h residue 31 ASP Chi-restraints excluded: chain h residue 83 ASP Chi-restraints excluded: chain h residue 102 ASN Chi-restraints excluded: chain h residue 156 ARG Chi-restraints excluded: chain h residue 165 THR Chi-restraints excluded: chain h residue 172 ARG Chi-restraints excluded: chain h residue 177 THR Chi-restraints excluded: chain h residue 192 THR Chi-restraints excluded: chain i residue 129 VAL Chi-restraints excluded: chain i residue 144 SER Chi-restraints excluded: chain j residue 15 LEU Chi-restraints excluded: chain j residue 22 SER Chi-restraints excluded: chain j residue 32 SER Chi-restraints excluded: chain j residue 88 VAL Chi-restraints excluded: chain j residue 131 THR Chi-restraints excluded: chain j residue 136 VAL Chi-restraints excluded: chain k residue 7 VAL Chi-restraints excluded: chain k residue 51 ILE Chi-restraints excluded: chain k residue 71 ILE Chi-restraints excluded: chain k residue 77 THR Chi-restraints excluded: chain k residue 85 ILE Chi-restraints excluded: chain k residue 92 THR Chi-restraints excluded: chain k residue 96 VAL Chi-restraints excluded: chain k residue 97 THR Chi-restraints excluded: chain l residue 6 VAL Chi-restraints excluded: chain l residue 106 GLU Chi-restraints excluded: chain l residue 133 THR Chi-restraints excluded: chain m residue 12 THR Chi-restraints excluded: chain m residue 38 ASN Chi-restraints excluded: chain m residue 51 VAL Chi-restraints excluded: chain m residue 52 GLU Chi-restraints excluded: chain m residue 59 LEU Chi-restraints excluded: chain m residue 79 SER Chi-restraints excluded: chain m residue 83 LEU Chi-restraints excluded: chain m residue 105 SER Chi-restraints excluded: chain m residue 107 SER Chi-restraints excluded: chain n residue 21 ILE Chi-restraints excluded: chain n residue 43 THR Chi-restraints excluded: chain n residue 52 LEU Chi-restraints excluded: chain n residue 58 VAL Chi-restraints excluded: chain n residue 66 THR Chi-restraints excluded: chain n residue 93 SER Chi-restraints excluded: chain n residue 94 LEU Chi-restraints excluded: chain n residue 116 VAL Chi-restraints excluded: chain o residue 54 SER Chi-restraints excluded: chain o residue 67 ILE Chi-restraints excluded: chain o residue 74 VAL Chi-restraints excluded: chain o residue 100 ILE Chi-restraints excluded: chain p residue 32 VAL Chi-restraints excluded: chain p residue 33 THR Chi-restraints excluded: chain p residue 58 SER Chi-restraints excluded: chain p residue 101 ASN Chi-restraints excluded: chain p residue 107 ILE Chi-restraints excluded: chain q residue 34 CYS Chi-restraints excluded: chain q residue 41 THR Chi-restraints excluded: chain q residue 70 GLU Chi-restraints excluded: chain q residue 82 ILE Chi-restraints excluded: chain q residue 119 VAL Chi-restraints excluded: chain r residue 58 ASP Chi-restraints excluded: chain r residue 65 VAL Chi-restraints excluded: chain r residue 74 SER Chi-restraints excluded: chain s residue 14 VAL Chi-restraints excluded: chain s residue 16 LEU Chi-restraints excluded: chain s residue 34 VAL Chi-restraints excluded: chain s residue 100 SER Chi-restraints excluded: chain t residue 56 LEU Chi-restraints excluded: chain t residue 67 LEU Chi-restraints excluded: chain t residue 70 LEU Chi-restraints excluded: chain t residue 89 ARG Chi-restraints excluded: chain u residue 2 VAL Chi-restraints excluded: chain u residue 3 THR Chi-restraints excluded: chain u residue 66 THR Chi-restraints excluded: chain u residue 67 ILE Chi-restraints excluded: chain u residue 74 LEU Chi-restraints excluded: chain v residue 7 THR Chi-restraints excluded: chain v residue 38 ILE Chi-restraints excluded: chain v residue 51 ASN Chi-restraints excluded: chain w residue 28 THR Chi-restraints excluded: chain w residue 40 VAL Chi-restraints excluded: chain w residue 59 ILE Chi-restraints excluded: chain w residue 71 THR Chi-restraints excluded: chain x residue 49 ILE Chi-restraints excluded: chain x residue 63 THR Chi-restraints excluded: chain x residue 64 ASP Chi-restraints excluded: chain x residue 79 THR Chi-restraints excluded: chain y residue 30 THR Chi-restraints excluded: chain z residue 43 THR Chi-restraints excluded: chain z residue 66 ARG Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 311 ASN Chi-restraints excluded: chain A residue 331 GLU Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain A residue 347 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1034 random chunks: chunk 929 optimal weight: 8.9990 chunk 707 optimal weight: 7.9990 chunk 488 optimal weight: 8.9990 chunk 104 optimal weight: 40.0000 chunk 448 optimal weight: 30.0000 chunk 631 optimal weight: 7.9990 chunk 944 optimal weight: 7.9990 chunk 999 optimal weight: 6.9990 chunk 493 optimal weight: 9.9990 chunk 894 optimal weight: 20.0000 chunk 269 optimal weight: 10.0000 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 239 ASN D 9 GLN D 90 GLN ** D 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 52 ASN ** F 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 45 HIS ** F 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 67 ASN J 131 ASN K 3 GLN ** Q 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 60 HIS T 48 GLN ** U 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 12 GLN f 13 ASN g 51 ASN h 8 ASN ** i 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 74 ASN i 140 ASN ** i 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 68 GLN l 130 ASN l 148 ASN p 38 GLN p 81 ASN ** r 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 69 HIS ** A 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 346 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.2582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.084 158938 Z= 0.416 Angle : 0.728 13.455 237562 Z= 0.381 Chirality : 0.041 0.302 30220 Planarity : 0.007 0.136 12875 Dihedral : 23.693 178.707 78949 Min Nonbonded Distance : 1.778 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.87 % Favored : 94.10 % Rotamer: Outliers : 7.03 % Allowed : 16.72 % Favored : 76.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.51 % 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: -1.94 (0.10), residues: 5863 helix: -0.67 (0.12), residues: 1887 sheet: -1.33 (0.15), residues: 1095 loop : -1.64 (0.11), residues: 2881 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP k 42 HIS 0.015 0.002 HIS S 102 PHE 0.025 0.002 PHE 6 78 TYR 0.030 0.002 TYR J 74 ARG 0.010 0.001 ARG e 13 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11726 Ramachandran restraints generated. 5863 Oldfield, 0 Emsley, 5863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11726 Ramachandran restraints generated. 5863 Oldfield, 0 Emsley, 5863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2004 residues out of total 4880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 343 poor density : 1661 time to evaluate : 6.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 98 ASP cc_start: 0.8147 (p0) cc_final: 0.7871 (p0) REVERT: B 110 LEU cc_start: 0.9028 (OUTLIER) cc_final: 0.8589 (mp) REVERT: B 111 LYS cc_start: 0.9087 (pttt) cc_final: 0.8717 (pttt) REVERT: B 114 ASP cc_start: 0.8281 (m-30) cc_final: 0.7892 (m-30) REVERT: B 161 TYR cc_start: 0.8351 (p90) cc_final: 0.7936 (p90) REVERT: B 174 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8599 (mt) REVERT: B 201 MET cc_start: 0.8944 (ptt) cc_final: 0.8515 (ptt) REVERT: B 202 LEU cc_start: 0.9309 (OUTLIER) cc_final: 0.8912 (mm) REVERT: C 133 THR cc_start: 0.8199 (t) cc_final: 0.7931 (t) REVERT: D 108 ILE cc_start: 0.9273 (OUTLIER) cc_final: 0.9031 (mt) REVERT: D 156 ASN cc_start: 0.8058 (m-40) cc_final: 0.7830 (m-40) REVERT: E 27 GLN cc_start: 0.8078 (tt0) cc_final: 0.7800 (tt0) REVERT: E 38 MET cc_start: 0.7965 (ttm) cc_final: 0.7127 (ptm) REVERT: E 69 LYS cc_start: 0.7416 (mmtt) cc_final: 0.7166 (mmtt) REVERT: E 127 ASN cc_start: 0.7551 (m-40) cc_final: 0.7325 (m-40) REVERT: E 128 TYR cc_start: 0.7451 (t80) cc_final: 0.7120 (t80) REVERT: E 155 THR cc_start: 0.9411 (m) cc_final: 0.9068 (p) REVERT: E 175 PHE cc_start: 0.8166 (OUTLIER) cc_final: 0.7566 (m-80) REVERT: F 22 GLN cc_start: 0.7810 (mm-40) cc_final: 0.6675 (mm-40) REVERT: F 25 THR cc_start: 0.8204 (OUTLIER) cc_final: 0.7975 (t) REVERT: F 39 ASP cc_start: 0.8640 (m-30) cc_final: 0.8222 (t0) REVERT: F 73 ASN cc_start: 0.8976 (t0) cc_final: 0.8765 (t0) REVERT: F 74 SER cc_start: 0.9434 (t) cc_final: 0.9109 (t) REVERT: F 139 GLN cc_start: 0.8316 (tm-30) cc_final: 0.7891 (tt0) REVERT: F 149 ARG cc_start: 0.8459 (ttt-90) cc_final: 0.8159 (ttt90) REVERT: G 11 ASN cc_start: 0.8191 (t0) cc_final: 0.7788 (t0) REVERT: G 29 PHE cc_start: 0.8717 (t80) cc_final: 0.8352 (t80) REVERT: G 46 PHE cc_start: 0.6950 (m-10) cc_final: 0.6616 (m-80) REVERT: J 111 LYS cc_start: 0.8379 (mptt) cc_final: 0.8031 (mtpt) REVERT: J 128 ASN cc_start: 0.8313 (t0) cc_final: 0.8031 (t0) REVERT: K 3 GLN cc_start: 0.8288 (pt0) cc_final: 0.8043 (pt0) REVERT: K 77 ILE cc_start: 0.9387 (mt) cc_final: 0.9136 (mt) REVERT: L 69 ARG cc_start: 0.8070 (mtp-110) cc_final: 0.7596 (mmm-85) REVERT: L 70 LYS cc_start: 0.8954 (tttp) cc_final: 0.8543 (tttt) REVERT: L 105 ILE cc_start: 0.8921 (mm) cc_final: 0.8719 (mp) REVERT: M 2 LEU cc_start: 0.8932 (mt) cc_final: 0.8672 (mt) REVERT: M 10 ARG cc_start: 0.8371 (ttp80) cc_final: 0.8110 (ttp-110) REVERT: M 20 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.8132 (mm) REVERT: M 78 LEU cc_start: 0.9282 (tp) cc_final: 0.8810 (mt) REVERT: M 105 MET cc_start: 0.7837 (OUTLIER) cc_final: 0.7605 (mtp) REVERT: N 2 ARG cc_start: 0.7738 (OUTLIER) cc_final: 0.4518 (ppp-140) REVERT: N 35 LYS cc_start: 0.8710 (tttt) cc_final: 0.8418 (tttt) REVERT: O 12 THR cc_start: 0.9186 (t) cc_final: 0.8978 (m) REVERT: P 11 GLU cc_start: 0.8031 (pt0) cc_final: 0.7623 (pt0) REVERT: P 27 GLU cc_start: 0.8088 (tm-30) cc_final: 0.7724 (tm-30) REVERT: Q 25 TYR cc_start: 0.9303 (t80) cc_final: 0.8915 (t80) REVERT: Q 29 SER cc_start: 0.9095 (p) cc_final: 0.8837 (p) REVERT: Q 52 GLN cc_start: 0.8736 (mt0) cc_final: 0.8458 (mt0) REVERT: Q 101 PHE cc_start: 0.8056 (m-80) cc_final: 0.7390 (m-80) REVERT: R 21 ARG cc_start: 0.9134 (ttm170) cc_final: 0.8548 (ttt180) REVERT: R 48 LYS cc_start: 0.8728 (mttp) cc_final: 0.8409 (mtpp) REVERT: R 62 GLU cc_start: 0.7187 (mp0) cc_final: 0.6796 (mp0) REVERT: R 97 LYS cc_start: 0.9136 (tttt) cc_final: 0.8730 (ttpt) REVERT: S 109 ASP cc_start: 0.8787 (OUTLIER) cc_final: 0.8534 (m-30) REVERT: T 5 GLU cc_start: 0.7722 (OUTLIER) cc_final: 0.7206 (pm20) REVERT: T 21 SER cc_start: 0.9048 (m) cc_final: 0.8665 (p) REVERT: T 37 ASP cc_start: 0.7283 (p0) cc_final: 0.7033 (p0) REVERT: T 73 ARG cc_start: 0.8151 (ttm110) cc_final: 0.7669 (ptp-110) REVERT: T 77 ARG cc_start: 0.8263 (mtt180) cc_final: 0.7861 (mtp180) REVERT: U 31 SER cc_start: 0.9312 (p) cc_final: 0.9089 (p) REVERT: V 45 ASP cc_start: 0.7631 (m-30) cc_final: 0.7174 (p0) REVERT: V 79 ARG cc_start: 0.8787 (mtp85) cc_final: 0.8345 (mtt-85) REVERT: W 39 ARG cc_start: 0.8466 (mtp85) cc_final: 0.8138 (mtt-85) REVERT: W 76 ASN cc_start: 0.8461 (m-40) cc_final: 0.8065 (m110) REVERT: X 20 HIS cc_start: 0.7520 (t70) cc_final: 0.7176 (t70) REVERT: X 23 ASN cc_start: 0.8952 (m110) cc_final: 0.8628 (m-40) REVERT: X 62 LYS cc_start: 0.9146 (mttt) cc_final: 0.8697 (mttt) REVERT: X 72 ARG cc_start: 0.7115 (mtm180) cc_final: 0.6866 (mtm180) REVERT: Y 13 GLU cc_start: 0.7750 (mt-10) cc_final: 0.7497 (mt-10) REVERT: Y 17 GLU cc_start: 0.8183 (tp30) cc_final: 0.7925 (tp30) REVERT: Y 21 LEU cc_start: 0.9104 (OUTLIER) cc_final: 0.8767 (mm) REVERT: Y 38 GLN cc_start: 0.7809 (mm110) cc_final: 0.7436 (mm-40) REVERT: Y 58 ASN cc_start: 0.8101 (m-40) cc_final: 0.7773 (m110) REVERT: Z 19 LYS cc_start: 0.8629 (ttmm) cc_final: 0.8418 (mttp) REVERT: Z 21 LYS cc_start: 0.9158 (mttt) cc_final: 0.8610 (mtmm) REVERT: b 32 LYS cc_start: 0.8233 (pttt) cc_final: 0.8031 (ptpt) REVERT: b 36 GLU cc_start: 0.8421 (pt0) cc_final: 0.7888 (pt0) REVERT: b 46 ASP cc_start: 0.8517 (p0) cc_final: 0.8027 (p0) REVERT: c 27 LYS cc_start: 0.8695 (mttt) cc_final: 0.8238 (tmmt) REVERT: c 34 LEU cc_start: 0.8610 (tp) cc_final: 0.8276 (tp) REVERT: c 45 GLN cc_start: 0.8337 (mm-40) cc_final: 0.8118 (mm-40) REVERT: c 53 LYS cc_start: 0.7701 (ttmm) cc_final: 0.7132 (pttm) REVERT: f 6 SER cc_start: 0.9261 (t) cc_final: 0.9031 (p) REVERT: f 15 LYS cc_start: 0.8318 (tttm) cc_final: 0.8034 (tttt) REVERT: f 30 GLU cc_start: 0.8626 (tp30) cc_final: 0.7480 (mp0) REVERT: g 56 GLU cc_start: 0.7868 (tp30) cc_final: 0.7585 (tp30) REVERT: g 74 ARG cc_start: 0.8075 (mmp80) cc_final: 0.6351 (ttp80) REVERT: g 78 GLU cc_start: 0.7861 (pm20) cc_final: 0.7515 (pm20) REVERT: g 122 GLN cc_start: 0.8122 (pm20) cc_final: 0.7675 (pm20) REVERT: g 131 LYS cc_start: 0.7447 (pttm) cc_final: 0.6635 (mmtt) REVERT: g 135 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8367 (mm) REVERT: h 31 ASP cc_start: 0.8080 (p0) cc_final: 0.7864 (p0) REVERT: h 58 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.5901 (tt0) REVERT: h 79 LYS cc_start: 0.6806 (mmtm) cc_final: 0.6391 (ptmm) REVERT: h 122 SER cc_start: 0.9272 (m) cc_final: 0.8777 (p) REVERT: h 172 ARG cc_start: 0.8646 (OUTLIER) cc_final: 0.8388 (ptm-80) REVERT: h 184 TYR cc_start: 0.9287 (t80) cc_final: 0.9010 (t80) REVERT: h 207 ILE cc_start: 0.8800 (mm) cc_final: 0.8583 (mt) REVERT: i 69 GLU cc_start: 0.8118 (tp30) cc_final: 0.7480 (tp30) REVERT: i 107 PHE cc_start: 0.8174 (m-10) cc_final: 0.7716 (m-10) REVERT: i 134 SER cc_start: 0.7599 (p) cc_final: 0.7367 (m) REVERT: i 135 TYR cc_start: 0.6732 (t80) cc_final: 0.6481 (t80) REVERT: i 200 ILE cc_start: 0.7181 (mp) cc_final: 0.6912 (mm) REVERT: j 61 GLN cc_start: 0.8503 (mm110) cc_final: 0.7858 (mm110) REVERT: j 62 LYS cc_start: 0.8520 (mttt) cc_final: 0.8068 (ttmm) REVERT: j 72 ILE cc_start: 0.9248 (tp) cc_final: 0.8872 (tt) REVERT: j 96 MET cc_start: 0.7818 (OUTLIER) cc_final: 0.7550 (ptm) REVERT: k 5 GLU cc_start: 0.8606 (tt0) cc_final: 0.8291 (tt0) REVERT: k 7 VAL cc_start: 0.8893 (OUTLIER) cc_final: 0.8591 (m) REVERT: k 30 THR cc_start: 0.7744 (m) cc_final: 0.7336 (t) REVERT: k 55 HIS cc_start: 0.7079 (m90) cc_final: 0.6603 (m90) REVERT: k 64 VAL cc_start: 0.9217 (t) cc_final: 0.8906 (m) REVERT: k 75 GLU cc_start: 0.6818 (tm-30) cc_final: 0.6421 (tm-30) REVERT: k 79 ARG cc_start: 0.7529 (mtp85) cc_final: 0.7250 (ttm110) REVERT: k 88 MET cc_start: 0.8080 (tpp) cc_final: 0.7610 (tpp) REVERT: l 37 SER cc_start: 0.8089 (t) cc_final: 0.7648 (p) REVERT: l 48 GLU cc_start: 0.8427 (tm-30) cc_final: 0.8095 (tm-30) REVERT: l 50 LEU cc_start: 0.7466 (OUTLIER) cc_final: 0.7094 (tm) REVERT: l 86 GLN cc_start: 0.7007 (mm110) cc_final: 0.5824 (mm-40) REVERT: l 122 ASN cc_start: 0.8115 (m-40) cc_final: 0.7828 (m110) REVERT: l 144 MET cc_start: 0.7764 (ttm) cc_final: 0.7300 (tpt) REVERT: m 18 GLN cc_start: 0.8732 (mm-40) cc_final: 0.8097 (mm-40) REVERT: m 60 GLU cc_start: 0.7923 (tt0) cc_final: 0.7667 (tm-30) REVERT: m 67 GLN cc_start: 0.7799 (mt0) cc_final: 0.7447 (mt0) REVERT: m 88 ARG cc_start: 0.7346 (mtp180) cc_final: 0.6422 (mtm180) REVERT: m 89 LYS cc_start: 0.8342 (OUTLIER) cc_final: 0.8031 (tptp) REVERT: m 111 MET cc_start: 0.7558 (ptt) cc_final: 0.7207 (ptt) REVERT: n 107 ASP cc_start: 0.8226 (t70) cc_final: 0.7662 (t0) REVERT: n 113 ARG cc_start: 0.9095 (OUTLIER) cc_final: 0.8873 (ptt90) REVERT: o 31 ARG cc_start: 0.7381 (mtm180) cc_final: 0.7031 (mtm180) REVERT: o 69 THR cc_start: 0.9246 (m) cc_final: 0.8868 (p) REVERT: o 96 VAL cc_start: 0.8741 (m) cc_final: 0.8480 (p) REVERT: p 50 SER cc_start: 0.8255 (m) cc_final: 0.7815 (p) REVERT: p 61 PHE cc_start: 0.9106 (t80) cc_final: 0.8736 (t80) REVERT: p 69 ARG cc_start: 0.8188 (ttm110) cc_final: 0.7889 (ttp-110) REVERT: p 80 LYS cc_start: 0.8006 (mptt) cc_final: 0.7719 (mptt) REVERT: p 87 LYS cc_start: 0.7854 (ttmm) cc_final: 0.7525 (ptmt) REVERT: q 10 LYS cc_start: 0.8721 (tmtt) cc_final: 0.8434 (ptmm) REVERT: r 23 TYR cc_start: 0.8467 (t80) cc_final: 0.8141 (t80) REVERT: r 46 SER cc_start: 0.8636 (m) cc_final: 0.8059 (p) REVERT: r 59 GLU cc_start: 0.7937 (mt-10) cc_final: 0.7460 (mt-10) REVERT: r 75 MET cc_start: 0.8415 (tpt) cc_final: 0.7792 (tpt) REVERT: r 76 SER cc_start: 0.8767 (m) cc_final: 0.8566 (p) REVERT: r 78 LYS cc_start: 0.9024 (mtpt) cc_final: 0.8671 (mtmm) REVERT: s 10 GLU cc_start: 0.7851 (tp30) cc_final: 0.7508 (tp30) REVERT: s 43 ASN cc_start: 0.8641 (m-40) cc_final: 0.8159 (m110) REVERT: s 86 GLU cc_start: 0.7955 (tt0) cc_final: 0.7298 (tm-30) REVERT: t 48 LYS cc_start: 0.8490 (mmtm) cc_final: 0.7765 (mtpt) REVERT: t 50 HIS cc_start: 0.8296 (m-70) cc_final: 0.7946 (m170) REVERT: t 67 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8683 (mm) REVERT: u 40 ASN cc_start: 0.8018 (t0) cc_final: 0.7812 (t0) REVERT: u 56 ARG cc_start: 0.8477 (mmm160) cc_final: 0.7902 (mmm-85) REVERT: u 63 GLN cc_start: 0.8753 (mm110) cc_final: 0.8443 (mm-40) REVERT: v 6 ARG cc_start: 0.5971 (mtt90) cc_final: 0.5355 (mtt90) REVERT: v 15 ASP cc_start: 0.6134 (p0) cc_final: 0.4606 (t70) REVERT: w 32 TYR cc_start: 0.8822 (m-80) cc_final: 0.8450 (m-80) REVERT: w 47 THR cc_start: 0.8672 (m) cc_final: 0.8284 (m) REVERT: w 52 GLN cc_start: 0.9049 (tp40) cc_final: 0.8647 (tp-100) REVERT: x 35 SER cc_start: 0.9339 (m) cc_final: 0.8991 (t) REVERT: x 71 LEU cc_start: 0.9372 (mt) cc_final: 0.8947 (mt) REVERT: z 17 ARG cc_start: 0.8411 (ttm110) cc_final: 0.8028 (tpt170) REVERT: z 19 PHE cc_start: 0.8354 (t80) cc_final: 0.8035 (t80) REVERT: z 35 ARG cc_start: 0.8726 (mtt-85) cc_final: 0.8339 (mtt-85) REVERT: z 64 ASN cc_start: 0.7728 (t0) cc_final: 0.7375 (t0) REVERT: A 114 GLU cc_start: 0.8199 (mt-10) cc_final: 0.7683 (mt-10) REVERT: A 137 ARG cc_start: 0.8704 (mmm-85) cc_final: 0.7933 (mmt-90) REVERT: A 162 ILE cc_start: 0.9309 (tt) cc_final: 0.9002 (tt) REVERT: A 193 GLN cc_start: 0.8442 (mt0) cc_final: 0.7378 (tm-30) REVERT: A 206 MET cc_start: 0.8554 (mtp) cc_final: 0.8200 (mtt) REVERT: A 248 HIS cc_start: 0.8629 (t-90) cc_final: 0.6989 (t-90) REVERT: A 256 GLU cc_start: 0.8484 (mt-10) cc_final: 0.8130 (tt0) REVERT: A 269 LYS cc_start: 0.8467 (tptp) cc_final: 0.8265 (tptp) REVERT: A 274 LEU cc_start: 0.8231 (mt) cc_final: 0.8013 (tt) REVERT: A 277 ARG cc_start: 0.7693 (mtt180) cc_final: 0.7037 (mtp-110) REVERT: A 288 GLN cc_start: 0.7618 (mm-40) cc_final: 0.7247 (mm-40) REVERT: A 311 ASN cc_start: 0.8611 (OUTLIER) cc_final: 0.7854 (t0) REVERT: A 337 LEU cc_start: 0.8815 (pp) cc_final: 0.8596 (pp) REVERT: A 346 GLN cc_start: 0.8285 (mm-40) cc_final: 0.8006 (mm110) REVERT: A 352 GLN cc_start: 0.6877 (pt0) cc_final: 0.4589 (tm-30) outliers start: 343 outliers final: 262 residues processed: 1813 average time/residue: 1.2865 time to fit residues: 4002.7941 Evaluate side-chains 1890 residues out of total 4880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 284 poor density : 1606 time to evaluate : 6.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 26 LYS Chi-restraints excluded: chain B residue 38 SER Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 58 HIS Chi-restraints excluded: chain B residue 70 ASN Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 185 GLU Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain C residue 18 ASP Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 176 ASP Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 44 ARG Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 108 ILE Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain E residue 17 MET Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 23 ASN Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 87 CYS Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain E residue 175 PHE Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 20 ASN Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 122 THR Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain F residue 155 GLU Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain J residue 60 ASP Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 92 MET Chi-restraints excluded: chain J residue 140 LEU Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 92 GLU Chi-restraints excluded: chain K residue 99 ILE Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 114 LYS Chi-restraints excluded: chain K residue 115 ILE Chi-restraints excluded: chain L residue 23 ILE Chi-restraints excluded: chain L residue 51 GLU Chi-restraints excluded: chain L residue 68 SER Chi-restraints excluded: chain L residue 103 ILE Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain L residue 135 ILE Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 30 SER Chi-restraints excluded: chain M residue 41 LEU Chi-restraints excluded: chain M residue 105 MET Chi-restraints excluded: chain M residue 119 LEU Chi-restraints excluded: chain M residue 126 ILE Chi-restraints excluded: chain N residue 2 ARG Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain N residue 33 ILE Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain O residue 28 VAL Chi-restraints excluded: chain O residue 35 ILE Chi-restraints excluded: chain O residue 36 TYR Chi-restraints excluded: chain O residue 48 LEU Chi-restraints excluded: chain O residue 83 LEU Chi-restraints excluded: chain P residue 2 SER Chi-restraints excluded: chain P residue 19 SER Chi-restraints excluded: chain P residue 44 GLU Chi-restraints excluded: chain P residue 51 ARG Chi-restraints excluded: chain P residue 66 ASN Chi-restraints excluded: chain P residue 83 SER Chi-restraints excluded: chain P residue 114 LEU Chi-restraints excluded: chain Q residue 9 ILE Chi-restraints excluded: chain Q residue 31 VAL Chi-restraints excluded: chain Q residue 107 THR Chi-restraints excluded: chain Q residue 117 LEU Chi-restraints excluded: chain R residue 14 VAL Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain S residue 3 THR Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 12 SER Chi-restraints excluded: chain S residue 13 SER Chi-restraints excluded: chain S residue 24 ILE Chi-restraints excluded: chain S residue 39 THR Chi-restraints excluded: chain S residue 67 ASP Chi-restraints excluded: chain S residue 97 LEU Chi-restraints excluded: chain S residue 100 THR Chi-restraints excluded: chain S residue 108 SER Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain T residue 5 GLU Chi-restraints excluded: chain T residue 11 LEU Chi-restraints excluded: chain T residue 22 THR Chi-restraints excluded: chain T residue 50 LEU Chi-restraints excluded: chain T residue 78 SER Chi-restraints excluded: chain U residue 28 VAL Chi-restraints excluded: chain U residue 39 ILE Chi-restraints excluded: chain U residue 52 LEU Chi-restraints excluded: chain U residue 77 THR Chi-restraints excluded: chain U residue 83 VAL Chi-restraints excluded: chain V residue 4 ILE Chi-restraints excluded: chain V residue 17 SER Chi-restraints excluded: chain V residue 62 THR Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain W residue 21 LEU Chi-restraints excluded: chain W residue 38 VAL Chi-restraints excluded: chain X residue 8 THR Chi-restraints excluded: chain X residue 13 VAL Chi-restraints excluded: chain X residue 25 THR Chi-restraints excluded: chain X residue 59 ILE Chi-restraints excluded: chain X residue 71 LEU Chi-restraints excluded: chain Y residue 11 VAL Chi-restraints excluded: chain Y residue 15 ASN Chi-restraints excluded: chain Y residue 21 LEU Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain b residue 10 ARG Chi-restraints excluded: chain b residue 23 THR Chi-restraints excluded: chain b residue 39 LEU Chi-restraints excluded: chain b residue 54 VAL Chi-restraints excluded: chain c residue 42 VAL Chi-restraints excluded: chain c residue 48 ILE Chi-restraints excluded: chain d residue 9 VAL Chi-restraints excluded: chain d residue 15 SER Chi-restraints excluded: chain e residue 38 THR Chi-restraints excluded: chain e residue 44 LEU Chi-restraints excluded: chain e residue 51 SER Chi-restraints excluded: chain e residue 54 ASP Chi-restraints excluded: chain g residue 6 MET Chi-restraints excluded: chain g residue 58 ASN Chi-restraints excluded: chain g residue 88 ASP Chi-restraints excluded: chain g residue 135 LEU Chi-restraints excluded: chain g residue 147 SER Chi-restraints excluded: chain g residue 199 VAL Chi-restraints excluded: chain g residue 210 VAL Chi-restraints excluded: chain h residue 58 GLU Chi-restraints excluded: chain h residue 83 ASP Chi-restraints excluded: chain h residue 102 ASN Chi-restraints excluded: chain h residue 149 ILE Chi-restraints excluded: chain h residue 156 ARG Chi-restraints excluded: chain h residue 161 GLU Chi-restraints excluded: chain h residue 165 THR Chi-restraints excluded: chain h residue 172 ARG Chi-restraints excluded: chain h residue 177 THR Chi-restraints excluded: chain h residue 188 GLU Chi-restraints excluded: chain h residue 192 THR Chi-restraints excluded: chain i residue 110 THR Chi-restraints excluded: chain i residue 129 VAL Chi-restraints excluded: chain i residue 144 SER Chi-restraints excluded: chain i residue 173 VAL Chi-restraints excluded: chain j residue 15 LEU Chi-restraints excluded: chain j residue 22 SER Chi-restraints excluded: chain j residue 32 SER Chi-restraints excluded: chain j residue 88 VAL Chi-restraints excluded: chain j residue 94 VAL Chi-restraints excluded: chain j residue 96 MET Chi-restraints excluded: chain j residue 131 THR Chi-restraints excluded: chain j residue 163 GLU Chi-restraints excluded: chain k residue 7 VAL Chi-restraints excluded: chain k residue 51 ILE Chi-restraints excluded: chain k residue 71 ILE Chi-restraints excluded: chain k residue 92 THR Chi-restraints excluded: chain k residue 96 VAL Chi-restraints excluded: chain k residue 97 THR Chi-restraints excluded: chain l residue 6 VAL Chi-restraints excluded: chain l residue 47 LEU Chi-restraints excluded: chain l residue 50 LEU Chi-restraints excluded: chain l residue 83 SER Chi-restraints excluded: chain l residue 106 GLU Chi-restraints excluded: chain l residue 130 ASN Chi-restraints excluded: chain l residue 133 THR Chi-restraints excluded: chain m residue 12 THR Chi-restraints excluded: chain m residue 51 VAL Chi-restraints excluded: chain m residue 52 GLU Chi-restraints excluded: chain m residue 59 LEU Chi-restraints excluded: chain m residue 62 THR Chi-restraints excluded: chain m residue 75 ILE Chi-restraints excluded: chain m residue 79 SER Chi-restraints excluded: chain m residue 83 LEU Chi-restraints excluded: chain m residue 89 LYS Chi-restraints excluded: chain m residue 96 MET Chi-restraints excluded: chain m residue 99 LEU Chi-restraints excluded: chain m residue 101 ILE Chi-restraints excluded: chain m residue 105 SER Chi-restraints excluded: chain m residue 106 THR Chi-restraints excluded: chain m residue 107 SER Chi-restraints excluded: chain m residue 112 THR Chi-restraints excluded: chain n residue 21 ILE Chi-restraints excluded: chain n residue 22 LYS Chi-restraints excluded: chain n residue 43 THR Chi-restraints excluded: chain n residue 52 LEU Chi-restraints excluded: chain n residue 58 VAL Chi-restraints excluded: chain n residue 66 THR Chi-restraints excluded: chain n residue 93 SER Chi-restraints excluded: chain n residue 94 LEU Chi-restraints excluded: chain n residue 113 ARG Chi-restraints excluded: chain n residue 116 VAL Chi-restraints excluded: chain o residue 25 ILE Chi-restraints excluded: chain o residue 54 SER Chi-restraints excluded: chain o residue 67 ILE Chi-restraints excluded: chain o residue 74 VAL Chi-restraints excluded: chain p residue 31 ILE Chi-restraints excluded: chain p residue 32 VAL Chi-restraints excluded: chain p residue 33 THR Chi-restraints excluded: chain p residue 38 GLN Chi-restraints excluded: chain p residue 46 THR Chi-restraints excluded: chain p residue 58 SER Chi-restraints excluded: chain p residue 94 GLU Chi-restraints excluded: chain p residue 101 ASN Chi-restraints excluded: chain p residue 107 ILE Chi-restraints excluded: chain q residue 15 LYS Chi-restraints excluded: chain q residue 34 CYS Chi-restraints excluded: chain q residue 52 VAL Chi-restraints excluded: chain q residue 82 ILE Chi-restraints excluded: chain q residue 119 VAL Chi-restraints excluded: chain r residue 34 LEU Chi-restraints excluded: chain r residue 58 ASP Chi-restraints excluded: chain r residue 65 VAL Chi-restraints excluded: chain r residue 74 SER Chi-restraints excluded: chain r residue 108 THR Chi-restraints excluded: chain s residue 14 VAL Chi-restraints excluded: chain s residue 16 LEU Chi-restraints excluded: chain s residue 34 VAL Chi-restraints excluded: chain s residue 100 SER Chi-restraints excluded: chain t residue 12 VAL Chi-restraints excluded: chain t residue 56 LEU Chi-restraints excluded: chain t residue 67 LEU Chi-restraints excluded: chain t residue 70 LEU Chi-restraints excluded: chain t residue 75 VAL Chi-restraints excluded: chain t residue 89 ARG Chi-restraints excluded: chain u residue 2 VAL Chi-restraints excluded: chain u residue 3 THR Chi-restraints excluded: chain u residue 19 VAL Chi-restraints excluded: chain u residue 66 THR Chi-restraints excluded: chain u residue 67 ILE Chi-restraints excluded: chain u residue 74 LEU Chi-restraints excluded: chain v residue 7 THR Chi-restraints excluded: chain v residue 51 ASN Chi-restraints excluded: chain v residue 57 ASP Chi-restraints excluded: chain v residue 67 LEU Chi-restraints excluded: chain w residue 21 ILE Chi-restraints excluded: chain w residue 28 THR Chi-restraints excluded: chain w residue 54 GLN Chi-restraints excluded: chain w residue 59 ILE Chi-restraints excluded: chain w residue 71 THR Chi-restraints excluded: chain x residue 38 SER Chi-restraints excluded: chain x residue 49 ILE Chi-restraints excluded: chain x residue 64 ASP Chi-restraints excluded: chain x residue 79 THR Chi-restraints excluded: chain y residue 30 THR Chi-restraints excluded: chain z residue 32 VAL Chi-restraints excluded: chain z residue 43 THR Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 311 ASN Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 331 GLU Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain A residue 347 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1034 random chunks: chunk 832 optimal weight: 5.9990 chunk 567 optimal weight: 9.9990 chunk 14 optimal weight: 20.0000 chunk 744 optimal weight: 0.3980 chunk 412 optimal weight: 20.0000 chunk 852 optimal weight: 1.9990 chunk 690 optimal weight: 7.9990 chunk 1 optimal weight: 10.0000 chunk 510 optimal weight: 0.1980 chunk 897 optimal weight: 10.0000 chunk 252 optimal weight: 10.0000 overall best weight: 3.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 128 ASN B 239 ASN F 45 HIS ** F 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 143 GLN K 3 GLN ** Q 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 48 GLN U 40 ASN g 120 GLN h 8 ASN i 140 ASN i 164 GLN l 148 ASN p 38 GLN ** r 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 69 HIS ** A 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 307 ASN A 352 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.2866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 158938 Z= 0.197 Angle : 0.609 13.881 237562 Z= 0.329 Chirality : 0.034 0.278 30220 Planarity : 0.006 0.126 12875 Dihedral : 23.644 179.684 78947 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.06 % Favored : 95.92 % Rotamer: Outliers : 5.45 % Allowed : 19.57 % Favored : 74.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.51 % 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: -1.57 (0.11), residues: 5863 helix: -0.25 (0.12), residues: 1898 sheet: -1.17 (0.16), residues: 1076 loop : -1.48 (0.11), residues: 2889 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP k 42 HIS 0.008 0.001 HIS M 13 PHE 0.028 0.002 PHE x 74 TYR 0.021 0.002 TYR x 80 ARG 0.010 0.001 ARG T 76 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11726 Ramachandran restraints generated. 5863 Oldfield, 0 Emsley, 5863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11726 Ramachandran restraints generated. 5863 Oldfield, 0 Emsley, 5863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2001 residues out of total 4880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 266 poor density : 1735 time to evaluate : 6.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 98 ASP cc_start: 0.8110 (p0) cc_final: 0.7832 (p0) REVERT: B 108 LYS cc_start: 0.8304 (tttt) cc_final: 0.8079 (ttmm) REVERT: B 110 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8600 (mp) REVERT: B 111 LYS cc_start: 0.9061 (pttt) cc_final: 0.8658 (pmtt) REVERT: B 114 ASP cc_start: 0.8297 (m-30) cc_final: 0.7877 (m-30) REVERT: B 201 MET cc_start: 0.8928 (ptt) cc_final: 0.8541 (ptt) REVERT: D 115 GLN cc_start: 0.8147 (OUTLIER) cc_final: 0.7091 (mp10) REVERT: D 155 GLU cc_start: 0.7054 (pm20) cc_final: 0.6744 (pm20) REVERT: D 156 ASN cc_start: 0.8213 (m-40) cc_final: 0.7457 (t0) REVERT: E 27 GLN cc_start: 0.8224 (tt0) cc_final: 0.7944 (tt0) REVERT: E 38 MET cc_start: 0.7792 (ttm) cc_final: 0.6737 (ptm) REVERT: E 69 LYS cc_start: 0.7332 (mmtt) cc_final: 0.7115 (mmtt) REVERT: E 94 GLU cc_start: 0.6670 (OUTLIER) cc_final: 0.6362 (pp20) REVERT: E 101 GLU cc_start: 0.7871 (pt0) cc_final: 0.7289 (pp20) REVERT: E 155 THR cc_start: 0.9388 (m) cc_final: 0.9056 (p) REVERT: E 164 GLU cc_start: 0.8186 (pm20) cc_final: 0.7515 (tt0) REVERT: E 175 PHE cc_start: 0.8080 (OUTLIER) cc_final: 0.7578 (m-80) REVERT: F 22 GLN cc_start: 0.7747 (mm-40) cc_final: 0.6607 (mm-40) REVERT: F 25 THR cc_start: 0.8195 (OUTLIER) cc_final: 0.7954 (t) REVERT: F 39 ASP cc_start: 0.8635 (m-30) cc_final: 0.8168 (t0) REVERT: F 73 ASN cc_start: 0.9012 (t0) cc_final: 0.8745 (t0) REVERT: F 74 SER cc_start: 0.9390 (t) cc_final: 0.9116 (t) REVERT: F 130 GLU cc_start: 0.7305 (tm-30) cc_final: 0.6460 (tm-30) REVERT: F 139 GLN cc_start: 0.8269 (tm-30) cc_final: 0.7773 (tt0) REVERT: F 149 ARG cc_start: 0.8448 (ttt-90) cc_final: 0.8192 (ttt90) REVERT: F 167 GLU cc_start: 0.7274 (pt0) cc_final: 0.7012 (pt0) REVERT: G 11 ASN cc_start: 0.8098 (t0) cc_final: 0.7882 (t0) REVERT: G 29 PHE cc_start: 0.8696 (t80) cc_final: 0.8200 (t80) REVERT: G 46 PHE cc_start: 0.7008 (m-10) cc_final: 0.6574 (m-80) REVERT: J 84 ILE cc_start: 0.9469 (OUTLIER) cc_final: 0.9111 (tp) REVERT: J 111 LYS cc_start: 0.8344 (mptt) cc_final: 0.8025 (mmmt) REVERT: K 3 GLN cc_start: 0.8186 (pt0) cc_final: 0.7940 (pt0) REVERT: K 77 ILE cc_start: 0.9385 (mt) cc_final: 0.9155 (mt) REVERT: L 69 ARG cc_start: 0.8012 (mtp-110) cc_final: 0.7570 (mmm-85) REVERT: L 70 LYS cc_start: 0.9008 (tttp) cc_final: 0.8565 (ttpt) REVERT: M 2 LEU cc_start: 0.8950 (mt) cc_final: 0.8727 (mt) REVERT: M 10 ARG cc_start: 0.8304 (ttp80) cc_final: 0.8051 (ttp-110) REVERT: M 20 LEU cc_start: 0.8415 (OUTLIER) cc_final: 0.7986 (mm) REVERT: M 33 LEU cc_start: 0.8768 (tp) cc_final: 0.8511 (tp) REVERT: M 78 LEU cc_start: 0.9285 (tp) cc_final: 0.8884 (mt) REVERT: M 110 GLU cc_start: 0.8459 (tm-30) cc_final: 0.7996 (tm-30) REVERT: N 35 LYS cc_start: 0.8678 (tttt) cc_final: 0.8372 (tttt) REVERT: N 79 LEU cc_start: 0.9210 (mt) cc_final: 0.8811 (mt) REVERT: N 89 SER cc_start: 0.7912 (p) cc_final: 0.7430 (t) REVERT: O 104 GLN cc_start: 0.7138 (tp40) cc_final: 0.6636 (tp-100) REVERT: O 116 GLN cc_start: 0.7481 (tp-100) cc_final: 0.7250 (tp-100) REVERT: P 11 GLU cc_start: 0.7992 (pt0) cc_final: 0.7672 (pt0) REVERT: P 24 ASP cc_start: 0.9102 (m-30) cc_final: 0.8819 (m-30) REVERT: P 27 GLU cc_start: 0.8069 (tm-30) cc_final: 0.7785 (tm-30) REVERT: P 51 ARG cc_start: 0.8664 (OUTLIER) cc_final: 0.8439 (tmt90) REVERT: P 100 LEU cc_start: 0.9213 (mt) cc_final: 0.9007 (mp) REVERT: Q 25 TYR cc_start: 0.9254 (t80) cc_final: 0.8772 (t80) REVERT: Q 29 SER cc_start: 0.9118 (p) cc_final: 0.8863 (p) REVERT: Q 52 GLN cc_start: 0.8746 (mt0) cc_final: 0.8425 (mt0) REVERT: Q 71 GLN cc_start: 0.8401 (tp40) cc_final: 0.7965 (tm-30) REVERT: Q 87 SER cc_start: 0.8838 (t) cc_final: 0.8344 (p) REVERT: Q 101 PHE cc_start: 0.8072 (m-80) cc_final: 0.7463 (m-80) REVERT: R 21 ARG cc_start: 0.9121 (ttm170) cc_final: 0.8530 (ttm170) REVERT: R 48 LYS cc_start: 0.8067 (mttp) cc_final: 0.7823 (mtpp) REVERT: R 84 ARG cc_start: 0.8837 (ptp90) cc_final: 0.8477 (ttp80) REVERT: R 97 LYS cc_start: 0.9072 (tttt) cc_final: 0.8746 (ttpt) REVERT: S 109 ASP cc_start: 0.8753 (OUTLIER) cc_final: 0.8490 (m-30) REVERT: T 5 GLU cc_start: 0.7894 (OUTLIER) cc_final: 0.7459 (pm20) REVERT: T 21 SER cc_start: 0.9037 (m) cc_final: 0.8655 (p) REVERT: T 73 ARG cc_start: 0.8030 (ttm110) cc_final: 0.7534 (ptp-110) REVERT: T 77 ARG cc_start: 0.8200 (mtt180) cc_final: 0.7835 (mtp180) REVERT: U 31 SER cc_start: 0.9226 (p) cc_final: 0.8999 (p) REVERT: U 40 ASN cc_start: 0.8372 (t160) cc_final: 0.8043 (t0) REVERT: U 74 ASN cc_start: 0.9306 (t0) cc_final: 0.8973 (t0) REVERT: V 30 ILE cc_start: 0.8251 (mm) cc_final: 0.8050 (mm) REVERT: V 45 ASP cc_start: 0.7326 (m-30) cc_final: 0.7037 (m-30) REVERT: V 48 MET cc_start: 0.8286 (mmm) cc_final: 0.7912 (mmm) REVERT: V 76 ASP cc_start: 0.6147 (p0) cc_final: 0.5759 (p0) REVERT: V 79 ARG cc_start: 0.8671 (mtp85) cc_final: 0.8397 (mtt-85) REVERT: W 39 ARG cc_start: 0.8410 (mtp85) cc_final: 0.8110 (mtt-85) REVERT: W 70 GLU cc_start: 0.7796 (pm20) cc_final: 0.7535 (pm20) REVERT: W 76 ASN cc_start: 0.8430 (m-40) cc_final: 0.8038 (m110) REVERT: X 20 HIS cc_start: 0.7435 (t70) cc_final: 0.7061 (t70) REVERT: X 23 ASN cc_start: 0.8883 (m110) cc_final: 0.8494 (m-40) REVERT: X 62 LYS cc_start: 0.9152 (mttt) cc_final: 0.8690 (mttt) REVERT: X 72 ARG cc_start: 0.7132 (mtm180) cc_final: 0.6865 (mtm180) REVERT: Y 13 GLU cc_start: 0.7703 (mt-10) cc_final: 0.7462 (mt-10) REVERT: Y 17 GLU cc_start: 0.8111 (tp30) cc_final: 0.7840 (tp30) REVERT: Y 21 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8419 (mm) REVERT: Y 38 GLN cc_start: 0.7852 (mm110) cc_final: 0.7340 (mm-40) REVERT: Y 58 ASN cc_start: 0.7999 (m-40) cc_final: 0.7244 (m110) REVERT: Z 19 LYS cc_start: 0.8581 (ttmm) cc_final: 0.8376 (mttp) REVERT: Z 21 LYS cc_start: 0.9086 (mttt) cc_final: 0.8782 (mtmm) REVERT: b 36 GLU cc_start: 0.8404 (pt0) cc_final: 0.7871 (pt0) REVERT: c 27 LYS cc_start: 0.8602 (mttt) cc_final: 0.8158 (tmmt) REVERT: c 34 LEU cc_start: 0.8493 (tp) cc_final: 0.8246 (tp) REVERT: c 53 LYS cc_start: 0.7705 (ttmm) cc_final: 0.7118 (pttm) REVERT: f 30 GLU cc_start: 0.8518 (tp30) cc_final: 0.7531 (mp0) REVERT: g 70 VAL cc_start: 0.8294 (t) cc_final: 0.7619 (p) REVERT: g 74 ARG cc_start: 0.8065 (mmp80) cc_final: 0.6322 (ttp80) REVERT: g 78 GLU cc_start: 0.7802 (pm20) cc_final: 0.7484 (pm20) REVERT: g 95 ARG cc_start: 0.8335 (ttp80) cc_final: 0.8115 (ttp80) REVERT: g 131 LYS cc_start: 0.6800 (pttm) cc_final: 0.6367 (mmtt) REVERT: g 135 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.8415 (mm) REVERT: h 79 LYS cc_start: 0.7016 (mmtm) cc_final: 0.6774 (tmtt) REVERT: h 122 SER cc_start: 0.9219 (m) cc_final: 0.8754 (p) REVERT: h 172 ARG cc_start: 0.8447 (OUTLIER) cc_final: 0.8237 (ptm-80) REVERT: h 184 TYR cc_start: 0.9182 (t80) cc_final: 0.8774 (t80) REVERT: h 208 LEU cc_start: 0.7887 (OUTLIER) cc_final: 0.7539 (mm) REVERT: i 48 LEU cc_start: 0.7527 (tp) cc_final: 0.7156 (mp) REVERT: i 107 PHE cc_start: 0.8218 (m-10) cc_final: 0.7833 (m-10) REVERT: i 134 SER cc_start: 0.7607 (p) cc_final: 0.7373 (m) REVERT: i 200 ILE cc_start: 0.7059 (mp) cc_final: 0.6771 (mm) REVERT: j 45 ARG cc_start: 0.7455 (ttp80) cc_final: 0.7176 (ttt90) REVERT: j 61 GLN cc_start: 0.8446 (mm110) cc_final: 0.8115 (mm110) REVERT: j 62 LYS cc_start: 0.8361 (mttt) cc_final: 0.7900 (ttmm) REVERT: j 97 GLN cc_start: 0.7754 (tt0) cc_final: 0.7450 (pt0) REVERT: k 5 GLU cc_start: 0.8610 (tt0) cc_final: 0.8279 (tt0) REVERT: k 7 VAL cc_start: 0.8920 (OUTLIER) cc_final: 0.8639 (m) REVERT: k 30 THR cc_start: 0.7848 (m) cc_final: 0.7514 (t) REVERT: k 33 GLU cc_start: 0.8060 (mp0) cc_final: 0.7739 (mp0) REVERT: k 55 HIS cc_start: 0.7088 (m90) cc_final: 0.6572 (m90) REVERT: k 64 VAL cc_start: 0.9288 (t) cc_final: 0.9049 (m) REVERT: k 75 GLU cc_start: 0.6824 (tm-30) cc_final: 0.5972 (tm-30) REVERT: k 88 MET cc_start: 0.8024 (tpp) cc_final: 0.7529 (tpp) REVERT: l 37 SER cc_start: 0.8022 (t) cc_final: 0.7577 (p) REVERT: l 42 ILE cc_start: 0.9065 (mm) cc_final: 0.8691 (mm) REVERT: l 48 GLU cc_start: 0.8379 (tm-30) cc_final: 0.8059 (tm-30) REVERT: l 50 LEU cc_start: 0.7267 (OUTLIER) cc_final: 0.6965 (tm) REVERT: l 86 GLN cc_start: 0.7216 (mm110) cc_final: 0.5875 (mm-40) REVERT: l 122 ASN cc_start: 0.8093 (m-40) cc_final: 0.7747 (m110) REVERT: m 18 GLN cc_start: 0.8650 (mm-40) cc_final: 0.8036 (mm-40) REVERT: m 43 GLU cc_start: 0.8430 (tp30) cc_final: 0.8006 (tp30) REVERT: m 60 GLU cc_start: 0.7901 (tt0) cc_final: 0.7646 (tm-30) REVERT: m 67 GLN cc_start: 0.7771 (mt0) cc_final: 0.7443 (mt0) REVERT: m 88 ARG cc_start: 0.7399 (mtp180) cc_final: 0.6590 (mtm180) REVERT: m 111 MET cc_start: 0.7452 (ptt) cc_final: 0.6833 (ptt) REVERT: o 69 THR cc_start: 0.9219 (m) cc_final: 0.8903 (p) REVERT: o 72 ARG cc_start: 0.8022 (mmm-85) cc_final: 0.7676 (mmt-90) REVERT: p 61 PHE cc_start: 0.9056 (t80) cc_final: 0.8638 (t80) REVERT: p 80 LYS cc_start: 0.8095 (mptt) cc_final: 0.7733 (mptt) REVERT: p 112 ASP cc_start: 0.6436 (m-30) cc_final: 0.6088 (m-30) REVERT: q 10 LYS cc_start: 0.8715 (tmtt) cc_final: 0.8437 (ptmm) REVERT: q 103 ASP cc_start: 0.7653 (OUTLIER) cc_final: 0.7134 (t0) REVERT: r 23 TYR cc_start: 0.8489 (t80) cc_final: 0.8207 (t80) REVERT: r 46 SER cc_start: 0.8415 (m) cc_final: 0.8107 (p) REVERT: r 59 GLU cc_start: 0.7703 (mt-10) cc_final: 0.7467 (mt-10) REVERT: r 75 MET cc_start: 0.8499 (tpt) cc_final: 0.8005 (tpt) REVERT: r 78 LYS cc_start: 0.9001 (mtpt) cc_final: 0.8605 (mtmm) REVERT: s 10 GLU cc_start: 0.7623 (tp30) cc_final: 0.7202 (tp30) REVERT: s 33 ASP cc_start: 0.8020 (t0) cc_final: 0.7693 (t0) REVERT: s 43 ASN cc_start: 0.8676 (m-40) cc_final: 0.8151 (m110) REVERT: t 48 LYS cc_start: 0.8549 (mmtm) cc_final: 0.7715 (mtpt) REVERT: t 50 HIS cc_start: 0.8265 (m-70) cc_final: 0.7904 (m170) REVERT: t 67 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8656 (mm) REVERT: u 39 PHE cc_start: 0.8489 (t80) cc_final: 0.8270 (t80) REVERT: u 56 ARG cc_start: 0.8467 (mmm160) cc_final: 0.7866 (mmm-85) REVERT: u 63 GLN cc_start: 0.8714 (mm110) cc_final: 0.8390 (mm-40) REVERT: v 6 ARG cc_start: 0.6012 (mtt90) cc_final: 0.5409 (mtt90) REVERT: v 15 ASP cc_start: 0.5996 (p0) cc_final: 0.4569 (t70) REVERT: w 47 THR cc_start: 0.8462 (m) cc_final: 0.8139 (m) REVERT: w 52 GLN cc_start: 0.9027 (tp40) cc_final: 0.8676 (tp-100) REVERT: x 31 LEU cc_start: 0.7906 (mm) cc_final: 0.7651 (pp) REVERT: x 35 SER cc_start: 0.9442 (m) cc_final: 0.9026 (t) REVERT: x 37 ARG cc_start: 0.7797 (ptt180) cc_final: 0.7489 (ptt180) REVERT: x 71 LEU cc_start: 0.9363 (mt) cc_final: 0.8863 (mt) REVERT: x 80 TYR cc_start: 0.8054 (t80) cc_final: 0.7714 (t80) REVERT: z 17 ARG cc_start: 0.8364 (ttm110) cc_final: 0.8012 (tpt170) REVERT: z 35 ARG cc_start: 0.8596 (mtt-85) cc_final: 0.8253 (mtt-85) REVERT: z 64 ASN cc_start: 0.7725 (t0) cc_final: 0.7378 (t0) REVERT: A 114 GLU cc_start: 0.8213 (mt-10) cc_final: 0.7618 (mt-10) REVERT: A 137 ARG cc_start: 0.8666 (mmm-85) cc_final: 0.7913 (mmt-90) REVERT: A 162 ILE cc_start: 0.9283 (tt) cc_final: 0.8978 (tt) REVERT: A 176 LYS cc_start: 0.8895 (ptpt) cc_final: 0.8500 (pttt) REVERT: A 193 GLN cc_start: 0.8214 (mt0) cc_final: 0.7405 (tm-30) REVERT: A 206 MET cc_start: 0.8643 (mtp) cc_final: 0.7970 (mtt) REVERT: A 256 GLU cc_start: 0.8439 (mt-10) cc_final: 0.8122 (tt0) REVERT: A 269 LYS cc_start: 0.8405 (tptp) cc_final: 0.8148 (tptp) REVERT: A 274 LEU cc_start: 0.8295 (mt) cc_final: 0.8046 (tt) REVERT: A 277 ARG cc_start: 0.7438 (mtt180) cc_final: 0.6805 (mtp-110) REVERT: A 288 GLN cc_start: 0.7647 (mm-40) cc_final: 0.7310 (mm-40) REVERT: A 307 ASN cc_start: 0.8205 (m-40) cc_final: 0.7970 (m110) REVERT: A 311 ASN cc_start: 0.8415 (OUTLIER) cc_final: 0.7502 (t0) REVERT: A 318 THR cc_start: 0.8375 (OUTLIER) cc_final: 0.8101 (m) REVERT: A 352 GLN cc_start: 0.6814 (pt0) cc_final: 0.4500 (tm-30) outliers start: 266 outliers final: 191 residues processed: 1840 average time/residue: 1.3045 time to fit residues: 4116.8386 Evaluate side-chains 1849 residues out of total 4880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 211 poor density : 1638 time to evaluate : 6.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 26 LYS Chi-restraints excluded: chain B residue 38 SER Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 70 ASN Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 185 GLU Chi-restraints excluded: chain C residue 18 ASP Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 67 ARG Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain D residue 115 GLN Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain E residue 17 MET Chi-restraints excluded: chain E residue 23 ASN Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 87 CYS Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 175 PHE Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 122 THR Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain F residue 147 ASP Chi-restraints excluded: chain F residue 155 GLU Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain K residue 92 GLU Chi-restraints excluded: chain K residue 99 ILE Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 114 LYS Chi-restraints excluded: chain L residue 23 ILE Chi-restraints excluded: chain L residue 68 SER Chi-restraints excluded: chain L residue 103 ILE Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 30 SER Chi-restraints excluded: chain M residue 41 LEU Chi-restraints excluded: chain M residue 63 ILE Chi-restraints excluded: chain N residue 2 ARG Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain N residue 33 ILE Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain O residue 28 VAL Chi-restraints excluded: chain O residue 83 LEU Chi-restraints excluded: chain P residue 2 SER Chi-restraints excluded: chain P residue 36 SER Chi-restraints excluded: chain P residue 44 GLU Chi-restraints excluded: chain P residue 51 ARG Chi-restraints excluded: chain P residue 66 ASN Chi-restraints excluded: chain P residue 114 LEU Chi-restraints excluded: chain Q residue 31 VAL Chi-restraints excluded: chain Q residue 107 THR Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain S residue 13 SER Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 39 THR Chi-restraints excluded: chain S residue 67 ASP Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain S residue 97 LEU Chi-restraints excluded: chain S residue 108 SER Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain T residue 5 GLU Chi-restraints excluded: chain T residue 11 LEU Chi-restraints excluded: chain T residue 42 GLU Chi-restraints excluded: chain T residue 50 LEU Chi-restraints excluded: chain U residue 28 VAL Chi-restraints excluded: chain U residue 39 ILE Chi-restraints excluded: chain U residue 49 VAL Chi-restraints excluded: chain U residue 52 LEU Chi-restraints excluded: chain U residue 83 VAL Chi-restraints excluded: chain V residue 4 ILE Chi-restraints excluded: chain V residue 17 SER Chi-restraints excluded: chain V residue 38 LEU Chi-restraints excluded: chain V residue 61 LEU Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain W residue 21 LEU Chi-restraints excluded: chain W residue 31 VAL Chi-restraints excluded: chain X residue 8 THR Chi-restraints excluded: chain X residue 71 LEU Chi-restraints excluded: chain Y residue 11 VAL Chi-restraints excluded: chain Y residue 12 GLU Chi-restraints excluded: chain Y residue 15 ASN Chi-restraints excluded: chain Y residue 21 LEU Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain b residue 10 ARG Chi-restraints excluded: chain b residue 23 THR Chi-restraints excluded: chain b residue 39 LEU Chi-restraints excluded: chain b residue 54 VAL Chi-restraints excluded: chain c residue 42 VAL Chi-restraints excluded: chain c residue 48 ILE Chi-restraints excluded: chain d residue 15 SER Chi-restraints excluded: chain d residue 29 GLN Chi-restraints excluded: chain e residue 38 THR Chi-restraints excluded: chain e residue 44 LEU Chi-restraints excluded: chain e residue 51 SER Chi-restraints excluded: chain g residue 135 LEU Chi-restraints excluded: chain g residue 147 SER Chi-restraints excluded: chain g residue 199 VAL Chi-restraints excluded: chain h residue 102 ASN Chi-restraints excluded: chain h residue 149 ILE Chi-restraints excluded: chain h residue 156 ARG Chi-restraints excluded: chain h residue 161 GLU Chi-restraints excluded: chain h residue 165 THR Chi-restraints excluded: chain h residue 172 ARG Chi-restraints excluded: chain h residue 177 THR Chi-restraints excluded: chain h residue 188 GLU Chi-restraints excluded: chain h residue 192 THR Chi-restraints excluded: chain h residue 208 LEU Chi-restraints excluded: chain i residue 85 ASN Chi-restraints excluded: chain i residue 129 VAL Chi-restraints excluded: chain i residue 144 SER Chi-restraints excluded: chain i residue 173 VAL Chi-restraints excluded: chain i residue 201 VAL Chi-restraints excluded: chain j residue 22 SER Chi-restraints excluded: chain j residue 32 SER Chi-restraints excluded: chain j residue 88 VAL Chi-restraints excluded: chain j residue 94 VAL Chi-restraints excluded: chain k residue 7 VAL Chi-restraints excluded: chain k residue 71 ILE Chi-restraints excluded: chain k residue 85 ILE Chi-restraints excluded: chain k residue 92 THR Chi-restraints excluded: chain k residue 96 VAL Chi-restraints excluded: chain k residue 97 THR Chi-restraints excluded: chain l residue 50 LEU Chi-restraints excluded: chain l residue 59 LEU Chi-restraints excluded: chain l residue 75 VAL Chi-restraints excluded: chain l residue 83 SER Chi-restraints excluded: chain l residue 91 VAL Chi-restraints excluded: chain l residue 106 GLU Chi-restraints excluded: chain l residue 133 THR Chi-restraints excluded: chain m residue 12 THR Chi-restraints excluded: chain m residue 38 ASN Chi-restraints excluded: chain m residue 51 VAL Chi-restraints excluded: chain m residue 52 GLU Chi-restraints excluded: chain m residue 59 LEU Chi-restraints excluded: chain m residue 83 LEU Chi-restraints excluded: chain m residue 99 LEU Chi-restraints excluded: chain m residue 101 ILE Chi-restraints excluded: chain m residue 106 THR Chi-restraints excluded: chain m residue 107 SER Chi-restraints excluded: chain n residue 21 ILE Chi-restraints excluded: chain n residue 52 LEU Chi-restraints excluded: chain n residue 58 VAL Chi-restraints excluded: chain n residue 66 THR Chi-restraints excluded: chain n residue 93 SER Chi-restraints excluded: chain n residue 94 LEU Chi-restraints excluded: chain n residue 116 VAL Chi-restraints excluded: chain o residue 25 ILE Chi-restraints excluded: chain o residue 54 SER Chi-restraints excluded: chain o residue 74 VAL Chi-restraints excluded: chain p residue 46 THR Chi-restraints excluded: chain p residue 58 SER Chi-restraints excluded: chain p residue 101 ASN Chi-restraints excluded: chain p residue 107 ILE Chi-restraints excluded: chain q residue 15 LYS Chi-restraints excluded: chain q residue 34 CYS Chi-restraints excluded: chain q residue 70 GLU Chi-restraints excluded: chain q residue 82 ILE Chi-restraints excluded: chain q residue 103 ASP Chi-restraints excluded: chain q residue 119 VAL Chi-restraints excluded: chain r residue 58 ASP Chi-restraints excluded: chain r residue 65 VAL Chi-restraints excluded: chain s residue 16 LEU Chi-restraints excluded: chain s residue 34 VAL Chi-restraints excluded: chain s residue 100 SER Chi-restraints excluded: chain t residue 12 VAL Chi-restraints excluded: chain t residue 56 LEU Chi-restraints excluded: chain t residue 67 LEU Chi-restraints excluded: chain t residue 70 LEU Chi-restraints excluded: chain t residue 89 ARG Chi-restraints excluded: chain u residue 2 VAL Chi-restraints excluded: chain u residue 3 THR Chi-restraints excluded: chain u residue 19 VAL Chi-restraints excluded: chain u residue 67 ILE Chi-restraints excluded: chain u residue 74 LEU Chi-restraints excluded: chain v residue 38 ILE Chi-restraints excluded: chain v residue 67 LEU Chi-restraints excluded: chain w residue 28 THR Chi-restraints excluded: chain w residue 59 ILE Chi-restraints excluded: chain x residue 11 ILE Chi-restraints excluded: chain x residue 49 ILE Chi-restraints excluded: chain x residue 63 THR Chi-restraints excluded: chain x residue 79 THR Chi-restraints excluded: chain y residue 30 THR Chi-restraints excluded: chain y residue 67 ILE Chi-restraints excluded: chain z residue 3 VAL Chi-restraints excluded: chain z residue 43 THR Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 311 ASN Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain A residue 347 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1034 random chunks: chunk 336 optimal weight: 50.0000 chunk 900 optimal weight: 0.8980 chunk 197 optimal weight: 10.0000 chunk 586 optimal weight: 2.9990 chunk 246 optimal weight: 10.0000 chunk 1000 optimal weight: 0.9990 chunk 830 optimal weight: 40.0000 chunk 463 optimal weight: 0.2980 chunk 83 optimal weight: 10.0000 chunk 330 optimal weight: 20.0000 chunk 525 optimal weight: 4.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 239 ASN F 45 HIS ** F 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 128 GLN J 128 ASN ** L 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 18 GLN Y 31 GLN g 120 GLN h 8 ASN i 116 GLN i 140 ASN k 52 ASN l 130 ASN l 148 ASN n 75 GLN r 100 GLN ** t 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 42 HIS t 80 GLN y 82 GLN ** A 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.3253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 158938 Z= 0.150 Angle : 0.570 14.180 237562 Z= 0.310 Chirality : 0.032 0.287 30220 Planarity : 0.006 0.125 12875 Dihedral : 23.486 179.610 78947 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.09 % Favored : 95.89 % Rotamer: Outliers : 5.27 % Allowed : 20.61 % Favored : 74.12 % 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: -1.18 (0.11), residues: 5863 helix: 0.16 (0.12), residues: 1902 sheet: -1.02 (0.16), residues: 1097 loop : -1.29 (0.11), residues: 2864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP h 201 HIS 0.009 0.001 HIS t 42 PHE 0.023 0.001 PHE x 10 TYR 0.025 0.002 TYR h 168 ARG 0.011 0.000 ARG p 69 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11726 Ramachandran restraints generated. 5863 Oldfield, 0 Emsley, 5863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11726 Ramachandran restraints generated. 5863 Oldfield, 0 Emsley, 5863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1970 residues out of total 4880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 257 poor density : 1713 time to evaluate : 6.294 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: B 98 ASP cc_start: 0.8060 (p0) cc_final: 0.7853 (p0) REVERT: B 100 GLU cc_start: 0.8151 (tt0) cc_final: 0.7917 (tt0) REVERT: B 108 LYS cc_start: 0.8215 (tttt) cc_final: 0.7973 (ttmm) REVERT: B 110 LEU cc_start: 0.8975 (OUTLIER) cc_final: 0.8595 (mp) REVERT: B 111 LYS cc_start: 0.9035 (pttt) cc_final: 0.8652 (pmtt) REVERT: B 114 ASP cc_start: 0.8287 (m-30) cc_final: 0.7930 (m-30) REVERT: B 174 LEU cc_start: 0.9025 (OUTLIER) cc_final: 0.8642 (mt) REVERT: B 201 MET cc_start: 0.8979 (ptt) cc_final: 0.8608 (ptt) REVERT: B 202 LEU cc_start: 0.9287 (OUTLIER) cc_final: 0.8905 (mm) REVERT: D 24 ASN cc_start: 0.8308 (t0) cc_final: 0.8106 (t0) REVERT: D 115 GLN cc_start: 0.8209 (OUTLIER) cc_final: 0.7453 (mt0) REVERT: D 141 MET cc_start: 0.7836 (mmm) cc_final: 0.7399 (mtt) REVERT: D 155 GLU cc_start: 0.7206 (pm20) cc_final: 0.6684 (pm20) REVERT: D 156 ASN cc_start: 0.8240 (m-40) cc_final: 0.7495 (t0) REVERT: E 27 GLN cc_start: 0.8294 (tt0) cc_final: 0.7839 (tt0) REVERT: E 38 MET cc_start: 0.7692 (ttm) cc_final: 0.6671 (ptm) REVERT: E 69 LYS cc_start: 0.7496 (mmtt) cc_final: 0.7252 (mmtt) REVERT: E 94 GLU cc_start: 0.6700 (OUTLIER) cc_final: 0.6428 (pp20) REVERT: E 101 GLU cc_start: 0.7759 (pt0) cc_final: 0.7017 (pp20) REVERT: E 155 THR cc_start: 0.9528 (m) cc_final: 0.9181 (p) REVERT: E 175 PHE cc_start: 0.7863 (OUTLIER) cc_final: 0.7472 (m-80) REVERT: F 22 GLN cc_start: 0.7784 (mm-40) cc_final: 0.6703 (mm-40) REVERT: F 25 THR cc_start: 0.8194 (OUTLIER) cc_final: 0.7956 (t) REVERT: F 39 ASP cc_start: 0.8548 (m-30) cc_final: 0.7929 (t0) REVERT: F 56 ASP cc_start: 0.6594 (m-30) cc_final: 0.6287 (t0) REVERT: F 73 ASN cc_start: 0.8988 (t0) cc_final: 0.8727 (t0) REVERT: F 74 SER cc_start: 0.9320 (t) cc_final: 0.9069 (t) REVERT: F 130 GLU cc_start: 0.7302 (tm-30) cc_final: 0.6475 (tm-30) REVERT: F 139 GLN cc_start: 0.8246 (tm-30) cc_final: 0.7864 (tt0) REVERT: G 11 ASN cc_start: 0.8049 (t0) cc_final: 0.7671 (t0) REVERT: J 84 ILE cc_start: 0.9418 (OUTLIER) cc_final: 0.9031 (tp) REVERT: J 111 LYS cc_start: 0.8310 (mptt) cc_final: 0.8052 (mtpt) REVERT: J 128 ASN cc_start: 0.8255 (OUTLIER) cc_final: 0.8037 (t0) REVERT: K 13 ASN cc_start: 0.8844 (p0) cc_final: 0.8574 (p0) REVERT: K 77 ILE cc_start: 0.9350 (mt) cc_final: 0.9123 (mt) REVERT: K 113 MET cc_start: 0.6892 (tpp) cc_final: 0.6685 (tpp) REVERT: L 69 ARG cc_start: 0.8012 (mtp-110) cc_final: 0.7459 (mmm-85) REVERT: L 70 LYS cc_start: 0.9063 (tttp) cc_final: 0.8622 (ttpt) REVERT: M 2 LEU cc_start: 0.8963 (mt) cc_final: 0.8742 (mt) REVERT: M 12 MET cc_start: 0.8389 (ttm) cc_final: 0.7958 (mtp) REVERT: M 20 LEU cc_start: 0.8226 (OUTLIER) cc_final: 0.7801 (mm) REVERT: M 78 LEU cc_start: 0.9281 (tp) cc_final: 0.8938 (mt) REVERT: M 110 GLU cc_start: 0.8023 (tm-30) cc_final: 0.7676 (tm-30) REVERT: M 136 MET cc_start: 0.6366 (ttm) cc_final: 0.5954 (tmm) REVERT: N 2 ARG cc_start: 0.7633 (OUTLIER) cc_final: 0.4319 (ppp-140) REVERT: N 9 GLN cc_start: 0.8574 (tt0) cc_final: 0.8228 (tt0) REVERT: N 35 LYS cc_start: 0.8641 (tttt) cc_final: 0.8347 (tttt) REVERT: N 42 LYS cc_start: 0.8709 (mttt) cc_final: 0.8347 (mttt) REVERT: N 89 SER cc_start: 0.7885 (p) cc_final: 0.7454 (t) REVERT: O 4 LYS cc_start: 0.6507 (tptp) cc_final: 0.5972 (tttt) REVERT: O 46 GLU cc_start: 0.7791 (pt0) cc_final: 0.7424 (tm-30) REVERT: O 93 ASP cc_start: 0.7358 (t0) cc_final: 0.7089 (t0) REVERT: O 99 TYR cc_start: 0.7911 (t80) cc_final: 0.7692 (t80) REVERT: O 104 GLN cc_start: 0.7167 (tp40) cc_final: 0.6844 (tp-100) REVERT: P 11 GLU cc_start: 0.7801 (pt0) cc_final: 0.7422 (pt0) REVERT: P 24 ASP cc_start: 0.9097 (m-30) cc_final: 0.8860 (m-30) REVERT: P 27 GLU cc_start: 0.8040 (tm-30) cc_final: 0.7487 (tm-30) REVERT: Q 25 TYR cc_start: 0.9177 (t80) cc_final: 0.8526 (t80) REVERT: Q 28 ARG cc_start: 0.8623 (mtp85) cc_final: 0.8416 (mtp85) REVERT: Q 29 SER cc_start: 0.9095 (p) cc_final: 0.8860 (p) REVERT: Q 45 TYR cc_start: 0.8667 (m-10) cc_final: 0.8349 (m-10) REVERT: Q 52 GLN cc_start: 0.8673 (mt0) cc_final: 0.8355 (mt0) REVERT: Q 59 GLN cc_start: 0.8386 (tt0) cc_final: 0.7581 (mt0) REVERT: Q 71 GLN cc_start: 0.8547 (tp40) cc_final: 0.8053 (tm-30) REVERT: Q 101 PHE cc_start: 0.8052 (m-80) cc_final: 0.7489 (m-80) REVERT: R 21 ARG cc_start: 0.9111 (ttm170) cc_final: 0.8504 (ttm170) REVERT: R 40 MET cc_start: 0.8641 (ttp) cc_final: 0.8392 (ttt) REVERT: R 84 ARG cc_start: 0.8842 (ptp90) cc_final: 0.8544 (ttp80) REVERT: R 86 GLN cc_start: 0.8163 (mm-40) cc_final: 0.7899 (mm-40) REVERT: R 97 LYS cc_start: 0.9006 (tttt) cc_final: 0.8699 (ttpt) REVERT: S 109 ASP cc_start: 0.8725 (OUTLIER) cc_final: 0.8440 (m-30) REVERT: T 5 GLU cc_start: 0.7748 (OUTLIER) cc_final: 0.7228 (pm20) REVERT: T 21 SER cc_start: 0.9157 (m) cc_final: 0.8697 (p) REVERT: T 73 ARG cc_start: 0.7827 (ttm110) cc_final: 0.7454 (ptp-110) REVERT: T 77 ARG cc_start: 0.8246 (mtt180) cc_final: 0.7856 (mtp180) REVERT: U 22 ARG cc_start: 0.7918 (OUTLIER) cc_final: 0.7687 (mtp180) REVERT: U 31 SER cc_start: 0.9141 (p) cc_final: 0.8905 (p) REVERT: U 74 ASN cc_start: 0.9292 (t0) cc_final: 0.8978 (t0) REVERT: V 30 ILE cc_start: 0.8202 (mm) cc_final: 0.7977 (mm) REVERT: V 87 GLN cc_start: 0.9183 (mm-40) cc_final: 0.8141 (mt0) REVERT: W 39 ARG cc_start: 0.8332 (mtp85) cc_final: 0.8060 (mtt-85) REVERT: W 76 ASN cc_start: 0.8243 (m-40) cc_final: 0.7832 (m110) REVERT: X 20 HIS cc_start: 0.7498 (t70) cc_final: 0.7064 (t70) REVERT: X 23 ASN cc_start: 0.8887 (m110) cc_final: 0.8566 (m-40) REVERT: X 62 LYS cc_start: 0.9132 (mttt) cc_final: 0.8677 (mttt) REVERT: X 65 ASP cc_start: 0.7388 (p0) cc_final: 0.7071 (p0) REVERT: X 72 ARG cc_start: 0.7053 (mtm180) cc_final: 0.6838 (mtm180) REVERT: Y 13 GLU cc_start: 0.7701 (mt-10) cc_final: 0.7437 (mt-10) REVERT: Y 39 GLN cc_start: 0.7593 (mp10) cc_final: 0.7331 (mp10) REVERT: Y 49 ASP cc_start: 0.8702 (m-30) cc_final: 0.8403 (m-30) REVERT: Y 58 ASN cc_start: 0.7964 (m-40) cc_final: 0.7222 (m110) REVERT: Z 4 THR cc_start: 0.8413 (m) cc_final: 0.7957 (p) REVERT: Z 21 LYS cc_start: 0.9061 (mttt) cc_final: 0.8740 (mtmm) REVERT: Z 37 GLU cc_start: 0.7465 (tp30) cc_final: 0.7203 (tp30) REVERT: Z 40 ASP cc_start: 0.7907 (t0) cc_final: 0.7124 (t0) REVERT: b 15 MET cc_start: 0.8221 (mtt) cc_final: 0.7877 (mtt) REVERT: b 36 GLU cc_start: 0.8453 (pt0) cc_final: 0.8134 (pt0) REVERT: c 27 LYS cc_start: 0.8504 (mttt) cc_final: 0.8121 (tmmt) REVERT: c 45 GLN cc_start: 0.8057 (mm-40) cc_final: 0.7836 (mm-40) REVERT: c 53 LYS cc_start: 0.7741 (ttmm) cc_final: 0.7067 (pttm) REVERT: d 26 ASN cc_start: 0.8632 (m110) cc_final: 0.8313 (m-40) REVERT: e 28 ASN cc_start: 0.9043 (m-40) cc_final: 0.8727 (m-40) REVERT: f 30 GLU cc_start: 0.8477 (tp30) cc_final: 0.7442 (mp0) REVERT: g 70 VAL cc_start: 0.8294 (t) cc_final: 0.7569 (p) REVERT: g 74 ARG cc_start: 0.8265 (mmp80) cc_final: 0.6676 (ttp80) REVERT: g 78 GLU cc_start: 0.7884 (pm20) cc_final: 0.7574 (pm20) REVERT: g 89 GLN cc_start: 0.8218 (mm-40) cc_final: 0.7427 (mm110) REVERT: g 109 GLN cc_start: 0.7865 (mm-40) cc_final: 0.7508 (mm-40) REVERT: g 125 THR cc_start: 0.8050 (m) cc_final: 0.7574 (p) REVERT: g 135 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8671 (tp) REVERT: h 31 ASP cc_start: 0.8459 (p0) cc_final: 0.8215 (p0) REVERT: h 79 LYS cc_start: 0.7263 (mmtm) cc_final: 0.6848 (tmtt) REVERT: h 122 SER cc_start: 0.9203 (m) cc_final: 0.8735 (p) REVERT: h 208 LEU cc_start: 0.7920 (OUTLIER) cc_final: 0.7594 (mm) REVERT: i 69 GLU cc_start: 0.8000 (tp30) cc_final: 0.7385 (tp30) REVERT: i 95 GLU cc_start: 0.8197 (mm-30) cc_final: 0.7600 (mm-30) REVERT: i 107 PHE cc_start: 0.8294 (m-10) cc_final: 0.8075 (m-10) REVERT: i 191 LEU cc_start: 0.7100 (mt) cc_final: 0.6408 (tp) REVERT: i 200 ILE cc_start: 0.7011 (mp) cc_final: 0.6705 (mm) REVERT: j 29 ARG cc_start: 0.8421 (mtt-85) cc_final: 0.8196 (mtm-85) REVERT: j 61 GLN cc_start: 0.8459 (mm110) cc_final: 0.8207 (mm110) REVERT: j 62 LYS cc_start: 0.8215 (mttt) cc_final: 0.7810 (ttmm) REVERT: j 159 LYS cc_start: 0.8092 (mmtp) cc_final: 0.7866 (mttt) REVERT: k 4 TYR cc_start: 0.8954 (m-80) cc_final: 0.8570 (m-80) REVERT: k 5 GLU cc_start: 0.8644 (tt0) cc_final: 0.8257 (tt0) REVERT: k 30 THR cc_start: 0.7932 (m) cc_final: 0.7614 (t) REVERT: k 33 GLU cc_start: 0.8050 (mp0) cc_final: 0.7740 (mp0) REVERT: k 55 HIS cc_start: 0.7212 (m90) cc_final: 0.6596 (m-70) REVERT: k 64 VAL cc_start: 0.9209 (t) cc_final: 0.9008 (m) REVERT: l 37 SER cc_start: 0.7722 (t) cc_final: 0.7233 (p) REVERT: l 48 GLU cc_start: 0.8413 (tm-30) cc_final: 0.7832 (tm-30) REVERT: l 50 LEU cc_start: 0.7311 (OUTLIER) cc_final: 0.7051 (tm) REVERT: l 86 GLN cc_start: 0.7171 (mm110) cc_final: 0.6887 (mm-40) REVERT: l 122 ASN cc_start: 0.8221 (m-40) cc_final: 0.7902 (m110) REVERT: l 136 LYS cc_start: 0.8662 (tppt) cc_final: 0.8110 (tptp) REVERT: m 18 GLN cc_start: 0.8649 (mm-40) cc_final: 0.8037 (mm-40) REVERT: m 52 GLU cc_start: 0.7625 (OUTLIER) cc_final: 0.7238 (tm-30) REVERT: m 67 GLN cc_start: 0.7738 (mt0) cc_final: 0.7430 (mt0) REVERT: m 88 ARG cc_start: 0.7353 (mtp180) cc_final: 0.6961 (mtt180) REVERT: n 65 ILE cc_start: 0.8921 (mt) cc_final: 0.8693 (mm) REVERT: n 83 ILE cc_start: 0.8514 (mt) cc_final: 0.8247 (mt) REVERT: n 88 MET cc_start: 0.7612 (mmt) cc_final: 0.7249 (mmm) REVERT: n 113 ARG cc_start: 0.9121 (OUTLIER) cc_final: 0.8901 (ptt90) REVERT: n 114 LYS cc_start: 0.8730 (tttm) cc_final: 0.8322 (tmtm) REVERT: o 69 THR cc_start: 0.9233 (m) cc_final: 0.8922 (p) REVERT: o 88 MET cc_start: 0.7821 (mmm) cc_final: 0.6933 (mtm) REVERT: o 99 GLN cc_start: 0.7712 (tp40) cc_final: 0.7448 (tp40) REVERT: p 61 PHE cc_start: 0.9116 (t80) cc_final: 0.8761 (t80) REVERT: p 80 LYS cc_start: 0.8099 (mptt) cc_final: 0.7814 (mptt) REVERT: p 112 ASP cc_start: 0.6289 (m-30) cc_final: 0.6020 (m-30) REVERT: q 10 LYS cc_start: 0.8655 (tmtt) cc_final: 0.8355 (ptmm) REVERT: r 13 LYS cc_start: 0.7741 (mttt) cc_final: 0.7522 (mtmt) REVERT: r 46 SER cc_start: 0.8651 (m) cc_final: 0.8331 (p) REVERT: r 59 GLU cc_start: 0.7632 (mt-10) cc_final: 0.7338 (mt-10) REVERT: r 75 MET cc_start: 0.8394 (tpt) cc_final: 0.7897 (tpt) REVERT: r 78 LYS cc_start: 0.8990 (mtpt) cc_final: 0.8591 (mtmm) REVERT: s 10 GLU cc_start: 0.7555 (tp30) cc_final: 0.7246 (tp30) REVERT: s 33 ASP cc_start: 0.7963 (t0) cc_final: 0.7669 (t0) REVERT: s 43 ASN cc_start: 0.8598 (m-40) cc_final: 0.8005 (m110) REVERT: t 48 LYS cc_start: 0.8323 (mmtm) cc_final: 0.7637 (mtpt) REVERT: t 50 HIS cc_start: 0.8228 (m-70) cc_final: 0.7878 (m170) REVERT: t 67 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8582 (mm) REVERT: t 80 GLN cc_start: 0.8424 (pt0) cc_final: 0.8166 (pt0) REVERT: u 39 PHE cc_start: 0.8493 (t80) cc_final: 0.8287 (t80) REVERT: u 56 ARG cc_start: 0.8544 (mmm160) cc_final: 0.7910 (mmm-85) REVERT: u 63 GLN cc_start: 0.8642 (mm110) cc_final: 0.8248 (mt0) REVERT: v 6 ARG cc_start: 0.6120 (mtt90) cc_final: 0.5617 (mtt90) REVERT: v 15 ASP cc_start: 0.6324 (p0) cc_final: 0.4854 (t70) REVERT: v 51 ASN cc_start: 0.8388 (OUTLIER) cc_final: 0.8175 (m-40) REVERT: w 52 GLN cc_start: 0.9034 (tp40) cc_final: 0.8765 (tp-100) REVERT: x 7 LYS cc_start: 0.8949 (mtpt) cc_final: 0.8474 (ttpt) REVERT: x 37 ARG cc_start: 0.7908 (ptt180) cc_final: 0.7473 (ptt180) REVERT: x 47 LEU cc_start: 0.6216 (mp) cc_final: 0.5635 (mt) REVERT: x 65 GLU cc_start: 0.7254 (pm20) cc_final: 0.6966 (mp0) REVERT: x 66 MET cc_start: 0.8243 (ptp) cc_final: 0.7980 (ptp) REVERT: x 71 LEU cc_start: 0.9432 (mt) cc_final: 0.8956 (mt) REVERT: x 80 TYR cc_start: 0.7989 (t80) cc_final: 0.7583 (t80) REVERT: z 17 ARG cc_start: 0.8317 (ttm110) cc_final: 0.7957 (tpt170) REVERT: z 64 ASN cc_start: 0.7286 (t0) cc_final: 0.7006 (t0) REVERT: A 112 PHE cc_start: 0.8872 (m-80) cc_final: 0.8341 (m-80) REVERT: A 137 ARG cc_start: 0.8634 (mmm-85) cc_final: 0.7903 (mmt-90) REVERT: A 176 LYS cc_start: 0.8857 (ptpt) cc_final: 0.8486 (pttt) REVERT: A 193 GLN cc_start: 0.7929 (mt0) cc_final: 0.7348 (tm-30) REVERT: A 206 MET cc_start: 0.8607 (mtp) cc_final: 0.8237 (mtt) REVERT: A 256 GLU cc_start: 0.8352 (mt-10) cc_final: 0.8096 (tt0) REVERT: A 269 LYS cc_start: 0.8617 (tptp) cc_final: 0.8273 (tptp) REVERT: A 274 LEU cc_start: 0.8510 (mt) cc_final: 0.8281 (tt) REVERT: A 277 ARG cc_start: 0.7234 (mtt180) cc_final: 0.6643 (mtm110) REVERT: A 288 GLN cc_start: 0.7825 (mm-40) cc_final: 0.7384 (mm-40) REVERT: A 311 ASN cc_start: 0.8378 (OUTLIER) cc_final: 0.7560 (t0) REVERT: A 314 GLN cc_start: 0.7548 (pt0) cc_final: 0.7074 (pt0) REVERT: A 342 GLU cc_start: 0.8454 (mm-30) cc_final: 0.8249 (tp30) REVERT: A 352 GLN cc_start: 0.6644 (pt0) cc_final: 0.4235 (tm-30) outliers start: 257 outliers final: 170 residues processed: 1822 average time/residue: 1.3032 time to fit residues: 4066.0070 Evaluate side-chains 1812 residues out of total 4880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 192 poor density : 1620 time to evaluate : 6.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 SER Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 70 ASN Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 185 GLU Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain C residue 18 ASP Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 67 ARG Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain D residue 115 GLN Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 87 CYS Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 175 PHE Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 121 ILE Chi-restraints excluded: chain F residue 122 THR Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 60 ASP Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain J residue 128 ASN Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 92 GLU Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain L residue 23 ILE Chi-restraints excluded: chain L residue 68 SER Chi-restraints excluded: chain L residue 103 ILE Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 30 SER Chi-restraints excluded: chain M residue 111 GLU Chi-restraints excluded: chain N residue 2 ARG Chi-restraints excluded: chain N residue 13 ASN Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain N residue 33 ILE 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 36 TYR Chi-restraints excluded: chain P residue 2 SER Chi-restraints excluded: chain P residue 66 ASN Chi-restraints excluded: chain P residue 114 LEU Chi-restraints excluded: chain R residue 41 ILE Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain S residue 3 THR Chi-restraints excluded: chain S residue 67 ASP Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain S residue 108 SER Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain T residue 5 GLU Chi-restraints excluded: chain T residue 22 THR Chi-restraints excluded: chain T residue 50 LEU Chi-restraints excluded: chain T residue 78 SER Chi-restraints excluded: chain U residue 22 ARG Chi-restraints excluded: chain U residue 28 VAL Chi-restraints excluded: chain U residue 49 VAL Chi-restraints excluded: chain U residue 52 LEU Chi-restraints excluded: chain V residue 4 ILE Chi-restraints excluded: chain V residue 38 LEU Chi-restraints excluded: chain V residue 61 LEU Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain W residue 21 LEU Chi-restraints excluded: chain W residue 31 VAL Chi-restraints excluded: chain W residue 38 VAL Chi-restraints excluded: chain X residue 8 THR Chi-restraints excluded: chain X residue 71 LEU Chi-restraints excluded: chain Y residue 11 VAL Chi-restraints excluded: chain Y residue 12 GLU Chi-restraints excluded: chain Z residue 57 VAL Chi-restraints excluded: chain a residue 22 MET Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain b residue 10 ARG Chi-restraints excluded: chain b residue 39 LEU Chi-restraints excluded: chain b residue 54 VAL Chi-restraints excluded: chain c residue 42 VAL Chi-restraints excluded: chain c residue 48 ILE Chi-restraints excluded: chain d residue 15 SER Chi-restraints excluded: chain d residue 29 GLN Chi-restraints excluded: chain e residue 38 THR Chi-restraints excluded: chain e residue 51 SER Chi-restraints excluded: chain g residue 88 ASP Chi-restraints excluded: chain g residue 135 LEU Chi-restraints excluded: chain g residue 147 SER Chi-restraints excluded: chain g residue 199 VAL Chi-restraints excluded: chain h residue 102 ASN Chi-restraints excluded: chain h residue 149 ILE Chi-restraints excluded: chain h residue 161 GLU Chi-restraints excluded: chain h residue 165 THR Chi-restraints excluded: chain h residue 177 THR Chi-restraints excluded: chain h residue 188 GLU Chi-restraints excluded: chain h residue 192 THR Chi-restraints excluded: chain h residue 208 LEU Chi-restraints excluded: chain i residue 85 ASN Chi-restraints excluded: chain i residue 129 VAL Chi-restraints excluded: chain i residue 144 SER Chi-restraints excluded: chain i residue 173 VAL Chi-restraints excluded: chain i residue 201 VAL Chi-restraints excluded: chain j residue 22 SER Chi-restraints excluded: chain j residue 32 SER Chi-restraints excluded: chain j residue 88 VAL Chi-restraints excluded: chain j residue 96 MET Chi-restraints excluded: chain j residue 131 THR Chi-restraints excluded: chain j residue 149 SER Chi-restraints excluded: chain k residue 7 VAL Chi-restraints excluded: chain k residue 71 ILE Chi-restraints excluded: chain k residue 85 ILE Chi-restraints excluded: chain k residue 92 THR Chi-restraints excluded: chain k residue 96 VAL Chi-restraints excluded: chain k residue 97 THR Chi-restraints excluded: chain l residue 50 LEU Chi-restraints excluded: chain l residue 59 LEU Chi-restraints excluded: chain l residue 83 SER Chi-restraints excluded: chain l residue 106 GLU Chi-restraints excluded: chain l residue 130 ASN Chi-restraints excluded: chain l residue 133 THR Chi-restraints excluded: chain m residue 12 THR Chi-restraints excluded: chain m residue 38 ASN Chi-restraints excluded: chain m residue 51 VAL Chi-restraints excluded: chain m residue 52 GLU Chi-restraints excluded: chain m residue 59 LEU Chi-restraints excluded: chain m residue 79 SER Chi-restraints excluded: chain m residue 83 LEU Chi-restraints excluded: chain m residue 99 LEU Chi-restraints excluded: chain m residue 105 SER Chi-restraints excluded: chain m residue 107 SER Chi-restraints excluded: chain n residue 21 ILE Chi-restraints excluded: chain n residue 35 LEU Chi-restraints excluded: chain n residue 43 THR Chi-restraints excluded: chain n residue 58 VAL Chi-restraints excluded: chain n residue 94 LEU Chi-restraints excluded: chain n residue 113 ARG Chi-restraints excluded: chain o residue 54 SER Chi-restraints excluded: chain o residue 74 VAL Chi-restraints excluded: chain p residue 46 THR Chi-restraints excluded: chain p residue 58 SER Chi-restraints excluded: chain q residue 34 CYS Chi-restraints excluded: chain q residue 41 THR Chi-restraints excluded: chain q residue 70 GLU Chi-restraints excluded: chain q residue 82 ILE Chi-restraints excluded: chain q residue 119 VAL Chi-restraints excluded: chain r residue 34 LEU Chi-restraints excluded: chain r residue 65 VAL Chi-restraints excluded: chain s residue 16 LEU Chi-restraints excluded: chain s residue 34 VAL Chi-restraints excluded: chain s residue 100 SER Chi-restraints excluded: chain t residue 5 THR Chi-restraints excluded: chain t residue 12 VAL Chi-restraints excluded: chain t residue 42 HIS Chi-restraints excluded: chain t residue 67 LEU Chi-restraints excluded: chain t residue 70 LEU Chi-restraints excluded: chain t residue 75 VAL Chi-restraints excluded: chain t residue 89 ARG Chi-restraints excluded: chain u residue 2 VAL Chi-restraints excluded: chain u residue 3 THR Chi-restraints excluded: chain u residue 19 VAL Chi-restraints excluded: chain u residue 67 ILE Chi-restraints excluded: chain v residue 38 ILE Chi-restraints excluded: chain v residue 51 ASN Chi-restraints excluded: chain v residue 67 LEU Chi-restraints excluded: chain w residue 28 THR Chi-restraints excluded: chain w residue 54 GLN Chi-restraints excluded: chain w residue 71 THR Chi-restraints excluded: chain x residue 49 ILE Chi-restraints excluded: chain x residue 51 VAL Chi-restraints excluded: chain x residue 64 ASP Chi-restraints excluded: chain x residue 79 THR Chi-restraints excluded: chain y residue 30 THR Chi-restraints excluded: chain y residue 57 ILE Chi-restraints excluded: chain z residue 43 THR Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 263 GLN Chi-restraints excluded: chain A residue 311 ASN Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain A residue 347 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1034 random chunks: chunk 964 optimal weight: 20.0000 chunk 112 optimal weight: 10.0000 chunk 570 optimal weight: 0.7980 chunk 730 optimal weight: 7.9990 chunk 566 optimal weight: 5.9990 chunk 842 optimal weight: 8.9990 chunk 558 optimal weight: 10.0000 chunk 996 optimal weight: 2.9990 chunk 623 optimal weight: 8.9990 chunk 607 optimal weight: 8.9990 chunk 460 optimal weight: 9.9990 overall best weight: 5.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 90 GLN ** D 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 45 HIS ** F 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 128 GLN J 128 ASN ** L 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 48 GLN h 8 ASN i 140 ASN i 198 HIS l 148 ASN n 50 GLN t 28 GLN t 42 HIS y 82 GLN ** A 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.3181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 158938 Z= 0.290 Angle : 0.635 13.991 237562 Z= 0.338 Chirality : 0.035 0.274 30220 Planarity : 0.006 0.132 12875 Dihedral : 23.475 178.964 78945 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.81 % Favored : 95.17 % Rotamer: Outliers : 5.84 % Allowed : 20.84 % Favored : 73.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.51 % 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: 5863 helix: 0.18 (0.12), residues: 1897 sheet: -1.01 (0.16), residues: 1092 loop : -1.28 (0.11), residues: 2874 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP k 42 HIS 0.035 0.001 HIS t 42 PHE 0.024 0.002 PHE t 43 TYR 0.030 0.002 TYR B 83 ARG 0.012 0.001 ARG p 69 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11726 Ramachandran restraints generated. 5863 Oldfield, 0 Emsley, 5863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11726 Ramachandran restraints generated. 5863 Oldfield, 0 Emsley, 5863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1913 residues out of total 4880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 285 poor density : 1628 time to evaluate : 6.514 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: B 98 ASP cc_start: 0.8181 (p0) cc_final: 0.7913 (p0) REVERT: B 100 GLU cc_start: 0.8173 (tt0) cc_final: 0.7932 (tt0) REVERT: B 110 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8617 (mp) REVERT: B 111 LYS cc_start: 0.9022 (pttt) cc_final: 0.8704 (pttt) REVERT: B 114 ASP cc_start: 0.8274 (m-30) cc_final: 0.7929 (m-30) REVERT: B 174 LEU cc_start: 0.9042 (OUTLIER) cc_final: 0.8645 (mt) REVERT: B 201 MET cc_start: 0.8950 (ptt) cc_final: 0.8498 (ptt) REVERT: B 202 LEU cc_start: 0.9301 (OUTLIER) cc_final: 0.8891 (mm) REVERT: D 100 MET cc_start: 0.8705 (mtm) cc_final: 0.8496 (mtm) REVERT: D 115 GLN cc_start: 0.8244 (OUTLIER) cc_final: 0.7240 (mp10) REVERT: D 156 ASN cc_start: 0.8214 (m-40) cc_final: 0.7619 (t0) REVERT: E 27 GLN cc_start: 0.8215 (tt0) cc_final: 0.7740 (tt0) REVERT: E 38 MET cc_start: 0.7784 (ttm) cc_final: 0.6768 (ptm) REVERT: E 69 LYS cc_start: 0.7181 (mmtt) cc_final: 0.6893 (mmtt) REVERT: E 155 THR cc_start: 0.9444 (m) cc_final: 0.9116 (p) REVERT: E 164 GLU cc_start: 0.8280 (pm20) cc_final: 0.7606 (tt0) REVERT: F 25 THR cc_start: 0.8296 (OUTLIER) cc_final: 0.8057 (t) REVERT: F 39 ASP cc_start: 0.8525 (m-30) cc_final: 0.8003 (t0) REVERT: F 73 ASN cc_start: 0.8984 (t0) cc_final: 0.8762 (t0) REVERT: F 74 SER cc_start: 0.9362 (t) cc_final: 0.9058 (t) REVERT: F 130 GLU cc_start: 0.7313 (tm-30) cc_final: 0.6466 (tm-30) REVERT: F 139 GLN cc_start: 0.8357 (tm-30) cc_final: 0.7745 (tt0) REVERT: G 11 ASN cc_start: 0.8114 (t0) cc_final: 0.7754 (t0) REVERT: G 46 PHE cc_start: 0.7812 (t80) cc_final: 0.7281 (m-80) REVERT: J 81 ILE cc_start: 0.8999 (tp) cc_final: 0.8674 (tp) REVERT: J 84 ILE cc_start: 0.9415 (OUTLIER) cc_final: 0.9082 (tp) REVERT: J 96 ARG cc_start: 0.7605 (OUTLIER) cc_final: 0.7296 (ptm160) REVERT: J 111 LYS cc_start: 0.8327 (mptt) cc_final: 0.8037 (mtpt) REVERT: J 128 ASN cc_start: 0.8412 (t160) cc_final: 0.8065 (t0) REVERT: K 77 ILE cc_start: 0.9354 (mt) cc_final: 0.9119 (mt) REVERT: L 69 ARG cc_start: 0.7910 (mtp-110) cc_final: 0.7302 (mmm-85) REVERT: L 70 LYS cc_start: 0.9062 (tttp) cc_final: 0.8623 (ttpt) REVERT: M 2 LEU cc_start: 0.8975 (mt) cc_final: 0.8737 (mt) REVERT: M 20 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.7926 (mm) REVERT: M 78 LEU cc_start: 0.9260 (tp) cc_final: 0.8908 (mt) REVERT: M 97 GLN cc_start: 0.9104 (mp10) cc_final: 0.8851 (mp10) REVERT: N 2 ARG cc_start: 0.7879 (OUTLIER) cc_final: 0.4484 (ppp-140) REVERT: N 35 LYS cc_start: 0.8724 (tttt) cc_final: 0.8440 (tttt) REVERT: N 72 ASP cc_start: 0.9024 (t0) cc_final: 0.8542 (t0) REVERT: N 75 ILE cc_start: 0.8931 (mm) cc_final: 0.8690 (tp) REVERT: N 89 SER cc_start: 0.7970 (p) cc_final: 0.7579 (t) REVERT: O 4 LYS cc_start: 0.6619 (tptp) cc_final: 0.5879 (ttmm) REVERT: O 99 TYR cc_start: 0.7877 (t80) cc_final: 0.7643 (t80) REVERT: O 104 GLN cc_start: 0.7188 (tp40) cc_final: 0.6914 (tp-100) REVERT: O 116 GLN cc_start: 0.7280 (tp40) cc_final: 0.7037 (tp-100) REVERT: P 11 GLU cc_start: 0.7945 (pt0) cc_final: 0.7682 (pt0) REVERT: P 24 ASP cc_start: 0.9077 (m-30) cc_final: 0.8785 (m-30) REVERT: P 27 GLU cc_start: 0.8027 (tm-30) cc_final: 0.7609 (tm-30) REVERT: P 51 ARG cc_start: 0.8685 (OUTLIER) cc_final: 0.8366 (tmt90) REVERT: P 63 LYS cc_start: 0.8879 (ptmt) cc_final: 0.8442 (ptmm) REVERT: Q 25 TYR cc_start: 0.9235 (t80) cc_final: 0.8772 (t80) REVERT: Q 29 SER cc_start: 0.9042 (p) cc_final: 0.8795 (p) REVERT: Q 45 TYR cc_start: 0.8675 (m-10) cc_final: 0.8436 (m-10) REVERT: Q 52 GLN cc_start: 0.8773 (mt0) cc_final: 0.8203 (tt0) REVERT: Q 71 GLN cc_start: 0.8449 (tp40) cc_final: 0.7982 (tm-30) REVERT: Q 101 PHE cc_start: 0.7915 (m-80) cc_final: 0.7306 (m-80) REVERT: R 21 ARG cc_start: 0.9111 (ttm170) cc_final: 0.8509 (ttm170) REVERT: R 84 ARG cc_start: 0.8828 (ptp90) cc_final: 0.8446 (ttp80) REVERT: R 97 LYS cc_start: 0.8985 (tttt) cc_final: 0.8678 (ttpt) REVERT: S 82 MET cc_start: 0.6922 (mtt) cc_final: 0.6468 (mmt) REVERT: S 109 ASP cc_start: 0.8647 (OUTLIER) cc_final: 0.8343 (m-30) REVERT: T 21 SER cc_start: 0.9192 (m) cc_final: 0.8723 (p) REVERT: T 73 ARG cc_start: 0.8019 (ttm110) cc_final: 0.7412 (ptp-110) REVERT: T 77 ARG cc_start: 0.8144 (mtt180) cc_final: 0.7782 (mtp180) REVERT: U 31 SER cc_start: 0.9214 (p) cc_final: 0.8992 (p) REVERT: U 88 GLU cc_start: 0.7834 (mt-10) cc_final: 0.7545 (mt-10) REVERT: V 48 MET cc_start: 0.7998 (mmm) cc_final: 0.7788 (mmm) REVERT: W 39 ARG cc_start: 0.8397 (mtp85) cc_final: 0.8039 (mtt180) REVERT: W 76 ASN cc_start: 0.8248 (m-40) cc_final: 0.7864 (m110) REVERT: X 20 HIS cc_start: 0.7585 (t70) cc_final: 0.7175 (t70) REVERT: X 23 ASN cc_start: 0.8912 (m110) cc_final: 0.8618 (m-40) REVERT: X 45 ARG cc_start: 0.8164 (ptt-90) cc_final: 0.7964 (ptt-90) REVERT: X 62 LYS cc_start: 0.9132 (mttt) cc_final: 0.8681 (mttt) REVERT: X 72 ARG cc_start: 0.7183 (mtm180) cc_final: 0.6953 (mtm180) REVERT: Y 13 GLU cc_start: 0.7750 (mt-10) cc_final: 0.7429 (mt-10) REVERT: Y 58 ASN cc_start: 0.8049 (m-40) cc_final: 0.7320 (m110) REVERT: Z 21 LYS cc_start: 0.9104 (mttt) cc_final: 0.8767 (mtmm) REVERT: b 32 LYS cc_start: 0.8065 (mppt) cc_final: 0.7858 (mppt) REVERT: b 36 GLU cc_start: 0.8540 (pt0) cc_final: 0.7997 (pt0) REVERT: c 27 LYS cc_start: 0.8534 (mttt) cc_final: 0.8172 (tmmt) REVERT: c 53 LYS cc_start: 0.7766 (ttmm) cc_final: 0.7090 (pttm) REVERT: e 28 ASN cc_start: 0.9049 (m-40) cc_final: 0.8765 (m-40) REVERT: e 44 LEU cc_start: 0.8906 (mp) cc_final: 0.8654 (mt) REVERT: f 4 ARG cc_start: 0.8189 (mtp85) cc_final: 0.7845 (mtm180) REVERT: f 30 GLU cc_start: 0.8456 (tp30) cc_final: 0.7378 (mp0) REVERT: g 74 ARG cc_start: 0.8327 (mmp80) cc_final: 0.6791 (ttp80) REVERT: g 78 GLU cc_start: 0.7864 (pm20) cc_final: 0.7550 (pm20) REVERT: g 109 GLN cc_start: 0.8157 (mm-40) cc_final: 0.7918 (mm-40) REVERT: g 175 GLU cc_start: 0.8665 (mt-10) cc_final: 0.8238 (mt-10) REVERT: h 79 LYS cc_start: 0.7321 (mmtm) cc_final: 0.7000 (tmtt) REVERT: h 122 SER cc_start: 0.9213 (m) cc_final: 0.8758 (p) REVERT: h 142 MET cc_start: 0.7436 (mmm) cc_final: 0.7229 (mmm) REVERT: h 172 ARG cc_start: 0.8419 (OUTLIER) cc_final: 0.8162 (ptm-80) REVERT: h 184 TYR cc_start: 0.9153 (t80) cc_final: 0.8615 (t80) REVERT: h 208 LEU cc_start: 0.7778 (OUTLIER) cc_final: 0.7483 (mm) REVERT: i 48 LEU cc_start: 0.7440 (tp) cc_final: 0.6801 (mp) REVERT: i 69 GLU cc_start: 0.8009 (tp30) cc_final: 0.7395 (tp30) REVERT: i 200 ILE cc_start: 0.7088 (mp) cc_final: 0.6796 (mm) REVERT: j 61 GLN cc_start: 0.8506 (mm110) cc_final: 0.8115 (mm110) REVERT: j 62 LYS cc_start: 0.8338 (mttt) cc_final: 0.7876 (ttmm) REVERT: k 2 ARG cc_start: 0.7651 (ttm-80) cc_final: 0.7093 (mtp-110) REVERT: k 5 GLU cc_start: 0.8603 (tt0) cc_final: 0.8310 (tt0) REVERT: k 30 THR cc_start: 0.7815 (m) cc_final: 0.7485 (t) REVERT: k 33 GLU cc_start: 0.8108 (mp0) cc_final: 0.7815 (mp0) REVERT: k 55 HIS cc_start: 0.7263 (m90) cc_final: 0.6722 (m90) REVERT: k 64 VAL cc_start: 0.9294 (t) cc_final: 0.9055 (m) REVERT: l 37 SER cc_start: 0.8011 (t) cc_final: 0.7551 (p) REVERT: l 42 ILE cc_start: 0.9015 (tp) cc_final: 0.8466 (mm) REVERT: l 48 GLU cc_start: 0.8403 (tm-30) cc_final: 0.8105 (tm-30) REVERT: l 50 LEU cc_start: 0.7412 (OUTLIER) cc_final: 0.7141 (tm) REVERT: l 86 GLN cc_start: 0.7262 (mm110) cc_final: 0.7016 (mm-40) REVERT: l 136 LYS cc_start: 0.8597 (tppt) cc_final: 0.8042 (tptp) REVERT: m 18 GLN cc_start: 0.8711 (mm-40) cc_final: 0.7947 (mm-40) REVERT: m 52 GLU cc_start: 0.7802 (OUTLIER) cc_final: 0.7053 (tm-30) REVERT: m 67 GLN cc_start: 0.7782 (mt0) cc_final: 0.7433 (mt0) REVERT: n 88 MET cc_start: 0.7587 (mmt) cc_final: 0.7307 (mmm) REVERT: n 113 ARG cc_start: 0.9115 (OUTLIER) cc_final: 0.8910 (ptt90) REVERT: o 69 THR cc_start: 0.9261 (m) cc_final: 0.8930 (p) REVERT: o 99 GLN cc_start: 0.7797 (tp40) cc_final: 0.7443 (tp40) REVERT: p 61 PHE cc_start: 0.9142 (t80) cc_final: 0.8807 (t80) REVERT: p 69 ARG cc_start: 0.8074 (ttm110) cc_final: 0.7742 (ttp-110) REVERT: p 80 LYS cc_start: 0.8375 (mptt) cc_final: 0.8017 (mptt) REVERT: p 112 ASP cc_start: 0.6307 (m-30) cc_final: 0.5995 (m-30) REVERT: q 10 LYS cc_start: 0.8557 (tmtt) cc_final: 0.8242 (ptmm) REVERT: r 46 SER cc_start: 0.8662 (m) cc_final: 0.8367 (p) REVERT: r 75 MET cc_start: 0.8266 (tpt) cc_final: 0.7673 (tpt) REVERT: r 78 LYS cc_start: 0.8970 (mtpt) cc_final: 0.8533 (mtmm) REVERT: s 10 GLU cc_start: 0.7675 (tp30) cc_final: 0.7385 (tp30) REVERT: s 43 ASN cc_start: 0.8569 (m-40) cc_final: 0.7901 (m110) REVERT: t 48 LYS cc_start: 0.8582 (mmtm) cc_final: 0.8337 (mtpt) REVERT: t 67 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8662 (mm) REVERT: u 5 ARG cc_start: 0.8236 (ptp-170) cc_final: 0.7766 (ptp90) REVERT: u 56 ARG cc_start: 0.8474 (mmm160) cc_final: 0.8249 (mmm-85) REVERT: v 6 ARG cc_start: 0.6345 (mtt90) cc_final: 0.5826 (mtt90) REVERT: v 15 ASP cc_start: 0.6497 (p0) cc_final: 0.4858 (t70) REVERT: v 51 ASN cc_start: 0.8460 (OUTLIER) cc_final: 0.8230 (m-40) REVERT: x 7 LYS cc_start: 0.8933 (mtpt) cc_final: 0.8706 (mtmt) REVERT: x 37 ARG cc_start: 0.7891 (ptt180) cc_final: 0.7522 (ptt180) REVERT: x 71 LEU cc_start: 0.9391 (mt) cc_final: 0.8927 (mt) REVERT: x 80 TYR cc_start: 0.8083 (t80) cc_final: 0.7812 (t80) REVERT: y 24 ARG cc_start: 0.7891 (mmt180) cc_final: 0.7357 (mmt180) REVERT: y 57 ILE cc_start: 0.8880 (OUTLIER) cc_final: 0.8561 (tp) REVERT: z 17 ARG cc_start: 0.8322 (ttm110) cc_final: 0.8052 (tpt170) REVERT: z 64 ASN cc_start: 0.6956 (t0) cc_final: 0.6721 (t0) REVERT: A 114 GLU cc_start: 0.8170 (mt-10) cc_final: 0.7609 (mt-10) REVERT: A 137 ARG cc_start: 0.8674 (mmm-85) cc_final: 0.8028 (mmt-90) REVERT: A 169 ASP cc_start: 0.6993 (t70) cc_final: 0.6739 (t70) REVERT: A 176 LYS cc_start: 0.8908 (ptpt) cc_final: 0.8489 (pttt) REVERT: A 193 GLN cc_start: 0.8164 (mt0) cc_final: 0.7332 (tm-30) REVERT: A 206 MET cc_start: 0.8571 (mtp) cc_final: 0.7899 (mtt) REVERT: A 256 GLU cc_start: 0.8347 (mt-10) cc_final: 0.7886 (tt0) REVERT: A 269 LYS cc_start: 0.8640 (tptp) cc_final: 0.8286 (tptp) REVERT: A 274 LEU cc_start: 0.8494 (mt) cc_final: 0.8284 (tt) REVERT: A 277 ARG cc_start: 0.7337 (mtt180) cc_final: 0.6704 (mtm110) REVERT: A 288 GLN cc_start: 0.7830 (mm-40) cc_final: 0.7465 (mm-40) REVERT: A 311 ASN cc_start: 0.8317 (OUTLIER) cc_final: 0.7631 (t0) REVERT: A 352 GLN cc_start: 0.6683 (pt0) cc_final: 0.4233 (tm-30) outliers start: 285 outliers final: 230 residues processed: 1751 average time/residue: 1.4051 time to fit residues: 4262.4453 Evaluate side-chains 1831 residues out of total 4880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 250 poor density : 1581 time to evaluate : 6.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 26 LYS Chi-restraints excluded: chain B residue 38 SER Chi-restraints excluded: chain B residue 70 ASN Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 185 GLU Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain C residue 18 ASP Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 96 ILE Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 67 ARG Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 115 GLN Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 17 MET Chi-restraints excluded: chain E residue 23 ASN Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 87 CYS Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 106 SER Chi-restraints excluded: chain F residue 121 ILE Chi-restraints excluded: chain F residue 122 THR Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain F residue 155 GLU Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 60 ASP Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain J residue 96 ARG Chi-restraints excluded: chain K residue 92 GLU Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 114 LYS Chi-restraints excluded: chain L residue 23 ILE Chi-restraints excluded: chain L residue 51 GLU Chi-restraints excluded: chain L residue 100 ILE Chi-restraints excluded: chain L residue 103 ILE Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain L residue 135 ILE Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 30 SER Chi-restraints excluded: chain M residue 111 GLU Chi-restraints excluded: chain M residue 119 LEU Chi-restraints excluded: chain N residue 2 ARG Chi-restraints excluded: chain N residue 13 ASN Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain N residue 33 ILE Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain O residue 19 GLN Chi-restraints excluded: chain O residue 28 VAL Chi-restraints excluded: chain O residue 35 ILE Chi-restraints excluded: chain P residue 2 SER Chi-restraints excluded: chain P residue 19 SER Chi-restraints excluded: chain P residue 47 VAL Chi-restraints excluded: chain P residue 51 ARG Chi-restraints excluded: chain P residue 66 ASN Chi-restraints excluded: chain P residue 114 LEU Chi-restraints excluded: chain Q residue 62 ILE Chi-restraints excluded: chain Q residue 107 THR Chi-restraints excluded: chain Q residue 117 LEU Chi-restraints excluded: chain R residue 31 GLU Chi-restraints excluded: chain R residue 38 VAL Chi-restraints excluded: chain R residue 39 LEU Chi-restraints excluded: chain R residue 41 ILE Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain S residue 3 THR Chi-restraints excluded: chain S residue 13 SER Chi-restraints excluded: chain S residue 39 THR Chi-restraints excluded: chain S residue 67 ASP Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain S residue 108 SER Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain T residue 22 THR Chi-restraints excluded: chain T residue 42 GLU Chi-restraints excluded: chain T residue 50 LEU Chi-restraints excluded: chain U residue 28 VAL Chi-restraints excluded: chain U residue 39 ILE Chi-restraints excluded: chain U residue 49 VAL Chi-restraints excluded: chain U residue 52 LEU Chi-restraints excluded: chain V residue 4 ILE Chi-restraints excluded: chain V residue 17 SER Chi-restraints excluded: chain V residue 38 LEU Chi-restraints excluded: chain V residue 40 ILE Chi-restraints excluded: chain V residue 61 LEU Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain W residue 21 LEU Chi-restraints excluded: chain W residue 31 VAL Chi-restraints excluded: chain W residue 38 VAL Chi-restraints excluded: chain X residue 8 THR Chi-restraints excluded: chain X residue 25 THR Chi-restraints excluded: chain X residue 59 ILE Chi-restraints excluded: chain X residue 71 LEU Chi-restraints excluded: chain Y residue 11 VAL Chi-restraints excluded: chain Y residue 12 GLU Chi-restraints excluded: chain a residue 22 MET Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain b residue 10 ARG Chi-restraints excluded: chain b residue 39 LEU Chi-restraints excluded: chain b residue 54 VAL Chi-restraints excluded: chain c residue 42 VAL Chi-restraints excluded: chain c residue 48 ILE Chi-restraints excluded: chain d residue 9 VAL Chi-restraints excluded: chain d residue 15 SER Chi-restraints excluded: chain d residue 22 MET Chi-restraints excluded: chain d residue 29 GLN Chi-restraints excluded: chain e residue 38 THR Chi-restraints excluded: chain e residue 51 SER Chi-restraints excluded: chain f residue 15 LYS Chi-restraints excluded: chain f residue 26 ILE Chi-restraints excluded: chain g residue 88 ASP Chi-restraints excluded: chain g residue 135 LEU Chi-restraints excluded: chain g residue 147 SER Chi-restraints excluded: chain g residue 148 LEU Chi-restraints excluded: chain g residue 199 VAL Chi-restraints excluded: chain h residue 66 VAL Chi-restraints excluded: chain h residue 102 ASN Chi-restraints excluded: chain h residue 149 ILE Chi-restraints excluded: chain h residue 161 GLU Chi-restraints excluded: chain h residue 165 THR Chi-restraints excluded: chain h residue 172 ARG Chi-restraints excluded: chain h residue 177 THR Chi-restraints excluded: chain h residue 188 GLU Chi-restraints excluded: chain h residue 192 THR Chi-restraints excluded: chain h residue 208 LEU Chi-restraints excluded: chain i residue 40 GLN Chi-restraints excluded: chain i residue 85 ASN Chi-restraints excluded: chain i residue 129 VAL Chi-restraints excluded: chain i residue 144 SER Chi-restraints excluded: chain i residue 173 VAL Chi-restraints excluded: chain i residue 201 VAL Chi-restraints excluded: chain j residue 22 SER Chi-restraints excluded: chain j residue 32 SER Chi-restraints excluded: chain j residue 88 VAL Chi-restraints excluded: chain j residue 94 VAL Chi-restraints excluded: chain j residue 96 MET Chi-restraints excluded: chain j residue 131 THR Chi-restraints excluded: chain j residue 149 SER Chi-restraints excluded: chain k residue 7 VAL Chi-restraints excluded: chain k residue 51 ILE Chi-restraints excluded: chain k residue 54 LEU Chi-restraints excluded: chain k residue 70 VAL Chi-restraints excluded: chain k residue 71 ILE Chi-restraints excluded: chain k residue 85 ILE Chi-restraints excluded: chain k residue 92 THR Chi-restraints excluded: chain k residue 96 VAL Chi-restraints excluded: chain k residue 97 THR Chi-restraints excluded: chain k residue 100 SER Chi-restraints excluded: chain l residue 50 LEU Chi-restraints excluded: chain l residue 59 LEU Chi-restraints excluded: chain l residue 69 VAL Chi-restraints excluded: chain l residue 83 SER Chi-restraints excluded: chain l residue 91 VAL Chi-restraints excluded: chain l residue 106 GLU Chi-restraints excluded: chain l residue 133 THR Chi-restraints excluded: chain m residue 12 THR Chi-restraints excluded: chain m residue 51 VAL Chi-restraints excluded: chain m residue 52 GLU Chi-restraints excluded: chain m residue 59 LEU Chi-restraints excluded: chain m residue 79 SER Chi-restraints excluded: chain m residue 83 LEU Chi-restraints excluded: chain m residue 99 LEU Chi-restraints excluded: chain m residue 101 ILE Chi-restraints excluded: chain m residue 105 SER Chi-restraints excluded: chain m residue 106 THR Chi-restraints excluded: chain m residue 107 SER Chi-restraints excluded: chain m residue 112 THR Chi-restraints excluded: chain n residue 21 ILE Chi-restraints excluded: chain n residue 35 LEU Chi-restraints excluded: chain n residue 52 LEU Chi-restraints excluded: chain n residue 58 VAL Chi-restraints excluded: chain n residue 63 LEU Chi-restraints excluded: chain n residue 94 LEU Chi-restraints excluded: chain n residue 113 ARG Chi-restraints excluded: chain n residue 116 VAL Chi-restraints excluded: chain o residue 25 ILE Chi-restraints excluded: chain o residue 54 SER Chi-restraints excluded: chain o residue 67 ILE Chi-restraints excluded: chain o residue 74 VAL Chi-restraints excluded: chain p residue 31 ILE Chi-restraints excluded: chain p residue 33 THR Chi-restraints excluded: chain p residue 46 THR Chi-restraints excluded: chain p residue 58 SER Chi-restraints excluded: chain q residue 34 CYS Chi-restraints excluded: chain q residue 41 THR Chi-restraints excluded: chain q residue 70 GLU Chi-restraints excluded: chain q residue 82 ILE Chi-restraints excluded: chain q residue 119 VAL Chi-restraints excluded: chain r residue 34 LEU Chi-restraints excluded: chain r residue 39 ILE Chi-restraints excluded: chain r residue 65 VAL Chi-restraints excluded: chain r residue 108 THR Chi-restraints excluded: chain s residue 16 LEU Chi-restraints excluded: chain s residue 34 VAL Chi-restraints excluded: chain s residue 100 SER Chi-restraints excluded: chain t residue 12 VAL Chi-restraints excluded: chain t residue 67 LEU Chi-restraints excluded: chain t residue 70 LEU Chi-restraints excluded: chain t residue 75 VAL Chi-restraints excluded: chain t residue 89 ARG Chi-restraints excluded: chain u residue 2 VAL Chi-restraints excluded: chain u residue 3 THR Chi-restraints excluded: chain u residue 19 VAL Chi-restraints excluded: chain u residue 66 THR Chi-restraints excluded: chain u residue 67 ILE Chi-restraints excluded: chain u residue 74 LEU Chi-restraints excluded: chain v residue 38 ILE Chi-restraints excluded: chain v residue 51 ASN Chi-restraints excluded: chain v residue 57 ASP Chi-restraints excluded: chain v residue 67 LEU Chi-restraints excluded: chain w residue 28 THR Chi-restraints excluded: chain w residue 54 GLN Chi-restraints excluded: chain w residue 71 THR Chi-restraints excluded: chain x residue 64 ASP Chi-restraints excluded: chain x residue 79 THR Chi-restraints excluded: chain y residue 30 THR Chi-restraints excluded: chain y residue 57 ILE Chi-restraints excluded: chain z residue 3 VAL Chi-restraints excluded: chain z residue 43 THR Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 303 ARG Chi-restraints excluded: chain A residue 311 ASN Chi-restraints excluded: chain A residue 331 GLU Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain A residue 347 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1034 random chunks: chunk 616 optimal weight: 0.7980 chunk 397 optimal weight: 10.0000 chunk 595 optimal weight: 7.9990 chunk 300 optimal weight: 20.0000 chunk 195 optimal weight: 10.0000 chunk 193 optimal weight: 10.0000 chunk 633 optimal weight: 10.0000 chunk 678 optimal weight: 4.9990 chunk 492 optimal weight: 0.9980 chunk 92 optimal weight: 10.0000 chunk 783 optimal weight: 1.9990 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 239 ASN D 90 GLN F 45 HIS ** F 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 128 GLN ** N 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 86 GLN ** S 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 120 GLN h 8 ASN i 140 ASN i 198 HIS l 130 ASN l 148 ASN ** r 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 42 HIS t 80 GLN y 82 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.3316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 158938 Z= 0.201 Angle : 0.594 14.109 237562 Z= 0.320 Chirality : 0.033 0.276 30220 Planarity : 0.006 0.127 12875 Dihedral : 23.472 179.490 78945 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.08 % Favored : 95.91 % Rotamer: Outliers : 5.31 % Allowed : 21.66 % Favored : 73.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.51 % 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: -1.03 (0.11), residues: 5863 helix: 0.32 (0.12), residues: 1892 sheet: -0.92 (0.16), residues: 1107 loop : -1.23 (0.11), residues: 2864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP k 42 HIS 0.007 0.001 HIS A 264 PHE 0.022 0.001 PHE x 10 TYR 0.027 0.002 TYR B 83 ARG 0.009 0.001 ARG p 69 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11726 Ramachandran restraints generated. 5863 Oldfield, 0 Emsley, 5863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11726 Ramachandran restraints generated. 5863 Oldfield, 0 Emsley, 5863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1884 residues out of total 4880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 259 poor density : 1625 time to evaluate : 8.300 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: B 98 ASP cc_start: 0.8130 (p0) cc_final: 0.7833 (p0) REVERT: B 100 GLU cc_start: 0.8148 (tt0) cc_final: 0.7924 (tt0) REVERT: B 108 LYS cc_start: 0.8252 (tttt) cc_final: 0.8039 (ttmm) REVERT: B 110 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8584 (mp) REVERT: B 111 LYS cc_start: 0.9004 (pttt) cc_final: 0.8695 (pttt) REVERT: B 114 ASP cc_start: 0.8274 (m-30) cc_final: 0.7937 (m-30) REVERT: B 174 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8634 (mt) REVERT: B 201 MET cc_start: 0.8944 (ptt) cc_final: 0.8485 (ptt) REVERT: B 202 LEU cc_start: 0.9221 (OUTLIER) cc_final: 0.8780 (mm) REVERT: D 115 GLN cc_start: 0.8205 (OUTLIER) cc_final: 0.7220 (mp10) REVERT: D 141 MET cc_start: 0.7901 (mmm) cc_final: 0.7444 (mtt) REVERT: D 156 ASN cc_start: 0.8146 (m-40) cc_final: 0.7594 (t0) REVERT: E 22 TYR cc_start: 0.6628 (m-10) cc_final: 0.6287 (m-10) REVERT: E 27 GLN cc_start: 0.8196 (tt0) cc_final: 0.7854 (tt0) REVERT: E 38 MET cc_start: 0.7736 (ttm) cc_final: 0.6730 (ptm) REVERT: E 69 LYS cc_start: 0.7151 (mmtt) cc_final: 0.6888 (mmtt) REVERT: E 94 GLU cc_start: 0.7325 (pp20) cc_final: 0.7031 (pp20) REVERT: E 155 THR cc_start: 0.9412 (m) cc_final: 0.9092 (p) REVERT: E 164 GLU cc_start: 0.8102 (pm20) cc_final: 0.7591 (tt0) REVERT: E 175 PHE cc_start: 0.7773 (OUTLIER) cc_final: 0.6817 (m-80) REVERT: F 25 THR cc_start: 0.8301 (OUTLIER) cc_final: 0.8085 (t) REVERT: F 39 ASP cc_start: 0.8525 (m-30) cc_final: 0.8003 (t0) REVERT: F 56 ASP cc_start: 0.6811 (m-30) cc_final: 0.6485 (t0) REVERT: F 73 ASN cc_start: 0.8982 (t0) cc_final: 0.8780 (t0) REVERT: F 74 SER cc_start: 0.9327 (t) cc_final: 0.9058 (t) REVERT: F 130 GLU cc_start: 0.7281 (tm-30) cc_final: 0.6445 (tm-30) REVERT: F 139 GLN cc_start: 0.8426 (tm-30) cc_final: 0.7868 (tt0) REVERT: G 11 ASN cc_start: 0.8049 (t0) cc_final: 0.7698 (t0) REVERT: G 46 PHE cc_start: 0.7385 (t80) cc_final: 0.7133 (m-80) REVERT: J 84 ILE cc_start: 0.9404 (OUTLIER) cc_final: 0.9058 (tp) REVERT: J 111 LYS cc_start: 0.8283 (mptt) cc_final: 0.8028 (mtpt) REVERT: J 128 ASN cc_start: 0.8426 (t160) cc_final: 0.8011 (t0) REVERT: K 77 ILE cc_start: 0.9353 (mt) cc_final: 0.9121 (mt) REVERT: L 69 ARG cc_start: 0.7897 (mtp-110) cc_final: 0.7300 (mmm-85) REVERT: L 70 LYS cc_start: 0.9077 (tttp) cc_final: 0.8628 (ttpt) REVERT: M 20 LEU cc_start: 0.8336 (OUTLIER) cc_final: 0.7902 (mm) REVERT: M 78 LEU cc_start: 0.9321 (tp) cc_final: 0.8978 (mt) REVERT: M 97 GLN cc_start: 0.9120 (mp10) cc_final: 0.8914 (mp10) REVERT: M 110 GLU cc_start: 0.8031 (tm-30) cc_final: 0.7682 (tm-30) REVERT: M 136 MET cc_start: 0.6233 (ttm) cc_final: 0.5881 (tmm) REVERT: N 35 LYS cc_start: 0.8710 (tttt) cc_final: 0.8412 (tttt) REVERT: N 89 SER cc_start: 0.7914 (p) cc_final: 0.7534 (t) REVERT: O 4 LYS cc_start: 0.6506 (tptp) cc_final: 0.5839 (ttmm) REVERT: O 99 TYR cc_start: 0.7881 (t80) cc_final: 0.7636 (t80) REVERT: O 104 GLN cc_start: 0.7123 (tp40) cc_final: 0.6813 (tp-100) REVERT: O 108 ASP cc_start: 0.8009 (p0) cc_final: 0.7741 (p0) REVERT: O 116 GLN cc_start: 0.7285 (tp40) cc_final: 0.6947 (tp-100) REVERT: P 11 GLU cc_start: 0.7899 (pt0) cc_final: 0.7573 (pt0) REVERT: P 24 ASP cc_start: 0.9189 (m-30) cc_final: 0.8966 (m-30) REVERT: P 27 GLU cc_start: 0.8083 (tm-30) cc_final: 0.7524 (tm-30) REVERT: P 63 LYS cc_start: 0.8859 (ptmt) cc_final: 0.8446 (ptmm) REVERT: Q 25 TYR cc_start: 0.9211 (t80) cc_final: 0.8714 (t80) REVERT: Q 29 SER cc_start: 0.9015 (p) cc_final: 0.8766 (p) REVERT: Q 45 TYR cc_start: 0.8648 (m-10) cc_final: 0.8435 (m-10) REVERT: Q 52 GLN cc_start: 0.8739 (mt0) cc_final: 0.8525 (mt0) REVERT: Q 71 GLN cc_start: 0.8406 (tp40) cc_final: 0.7962 (tm-30) REVERT: Q 101 PHE cc_start: 0.7681 (m-80) cc_final: 0.7299 (m-80) REVERT: R 21 ARG cc_start: 0.9122 (ttm170) cc_final: 0.8527 (ttm170) REVERT: R 84 ARG cc_start: 0.8828 (ptp90) cc_final: 0.8492 (ttp80) REVERT: R 86 GLN cc_start: 0.8157 (mm-40) cc_final: 0.7903 (mm-40) REVERT: R 97 LYS cc_start: 0.8948 (tttt) cc_final: 0.8658 (ttpt) REVERT: S 82 MET cc_start: 0.7220 (mtt) cc_final: 0.6643 (mmt) REVERT: T 21 SER cc_start: 0.9093 (m) cc_final: 0.8722 (p) REVERT: T 73 ARG cc_start: 0.7995 (ttm110) cc_final: 0.7351 (ptp-110) REVERT: T 77 ARG cc_start: 0.8203 (mtt180) cc_final: 0.7876 (mtp180) REVERT: U 22 ARG cc_start: 0.8122 (mtp180) cc_final: 0.7910 (mtm180) REVERT: U 31 SER cc_start: 0.9173 (p) cc_final: 0.8945 (p) REVERT: W 29 GLU cc_start: 0.8021 (tt0) cc_final: 0.7810 (tt0) REVERT: W 39 ARG cc_start: 0.8360 (mtp85) cc_final: 0.8012 (mtt180) REVERT: W 76 ASN cc_start: 0.8233 (m-40) cc_final: 0.7797 (m110) REVERT: X 20 HIS cc_start: 0.7544 (t70) cc_final: 0.7127 (t70) REVERT: X 23 ASN cc_start: 0.8906 (m110) cc_final: 0.8573 (m-40) REVERT: X 45 ARG cc_start: 0.8132 (ptt-90) cc_final: 0.7887 (ptt-90) REVERT: X 62 LYS cc_start: 0.9138 (mttt) cc_final: 0.8676 (mttt) REVERT: X 65 ASP cc_start: 0.7564 (p0) cc_final: 0.7270 (p0) REVERT: X 72 ARG cc_start: 0.7111 (mtm180) cc_final: 0.6877 (mtm180) REVERT: Y 13 GLU cc_start: 0.7693 (mt-10) cc_final: 0.7424 (mt-10) REVERT: Y 49 ASP cc_start: 0.8647 (m-30) cc_final: 0.8136 (m-30) REVERT: Y 58 ASN cc_start: 0.8025 (m-40) cc_final: 0.7273 (m110) REVERT: Z 4 THR cc_start: 0.8490 (m) cc_final: 0.8094 (p) REVERT: Z 21 LYS cc_start: 0.9091 (mttt) cc_final: 0.8745 (mtmm) REVERT: b 36 GLU cc_start: 0.8504 (pt0) cc_final: 0.7926 (pt0) REVERT: c 27 LYS cc_start: 0.8597 (mttt) cc_final: 0.8247 (tmmt) REVERT: c 53 LYS cc_start: 0.7775 (ttmm) cc_final: 0.7107 (pttm) REVERT: e 28 ASN cc_start: 0.9011 (m-40) cc_final: 0.8738 (m-40) REVERT: f 4 ARG cc_start: 0.8178 (mtp85) cc_final: 0.7843 (mtm180) REVERT: f 30 GLU cc_start: 0.8481 (tp30) cc_final: 0.7388 (mp0) REVERT: g 74 ARG cc_start: 0.8331 (mmp80) cc_final: 0.6806 (ttp80) REVERT: g 78 GLU cc_start: 0.7852 (pm20) cc_final: 0.7540 (pm20) REVERT: g 89 GLN cc_start: 0.8378 (mm-40) cc_final: 0.7351 (mm110) REVERT: g 109 GLN cc_start: 0.7994 (mm-40) cc_final: 0.7686 (mm-40) REVERT: g 152 LYS cc_start: 0.8392 (pttt) cc_final: 0.7987 (tmtt) REVERT: h 79 LYS cc_start: 0.7306 (mmtm) cc_final: 0.6842 (tmtt) REVERT: h 122 SER cc_start: 0.9201 (m) cc_final: 0.8729 (p) REVERT: h 142 MET cc_start: 0.7409 (mmm) cc_final: 0.7179 (mmm) REVERT: h 184 TYR cc_start: 0.9141 (t80) cc_final: 0.8589 (t80) REVERT: h 208 LEU cc_start: 0.7754 (OUTLIER) cc_final: 0.7456 (mm) REVERT: i 69 GLU cc_start: 0.7989 (tp30) cc_final: 0.7379 (tp30) REVERT: i 107 PHE cc_start: 0.8173 (m-80) cc_final: 0.7675 (m-80) REVERT: i 191 LEU cc_start: 0.7095 (mt) cc_final: 0.6800 (tp) REVERT: i 200 ILE cc_start: 0.7057 (mp) cc_final: 0.6773 (mm) REVERT: j 61 GLN cc_start: 0.8485 (mm110) cc_final: 0.8111 (mm110) REVERT: j 62 LYS cc_start: 0.8298 (mttt) cc_final: 0.7844 (ttmm) REVERT: j 69 ARG cc_start: 0.8218 (mtm180) cc_final: 0.7944 (mtm110) REVERT: k 5 GLU cc_start: 0.8567 (tt0) cc_final: 0.8225 (tt0) REVERT: k 9 MET cc_start: 0.7973 (mtp) cc_final: 0.7493 (mtt) REVERT: k 30 THR cc_start: 0.7777 (m) cc_final: 0.7437 (t) REVERT: k 33 GLU cc_start: 0.7930 (mp0) cc_final: 0.7636 (mp0) REVERT: k 55 HIS cc_start: 0.7226 (m90) cc_final: 0.6816 (m90) REVERT: k 64 VAL cc_start: 0.9269 (t) cc_final: 0.9020 (m) REVERT: k 68 GLN cc_start: 0.8123 (mt0) cc_final: 0.7601 (mp10) REVERT: l 37 SER cc_start: 0.7969 (t) cc_final: 0.7478 (p) REVERT: l 40 GLU cc_start: 0.8043 (tp30) cc_final: 0.7832 (mm-30) REVERT: l 42 ILE cc_start: 0.8845 (tp) cc_final: 0.8344 (mm) REVERT: l 48 GLU cc_start: 0.8408 (tm-30) cc_final: 0.8097 (tm-30) REVERT: l 50 LEU cc_start: 0.7291 (OUTLIER) cc_final: 0.7007 (tm) REVERT: l 86 GLN cc_start: 0.7223 (mm110) cc_final: 0.6970 (mm-40) REVERT: l 136 LYS cc_start: 0.8612 (tppt) cc_final: 0.8054 (tptp) REVERT: m 18 GLN cc_start: 0.8656 (mm-40) cc_final: 0.7927 (mm110) REVERT: m 52 GLU cc_start: 0.7602 (OUTLIER) cc_final: 0.7027 (tm-30) REVERT: m 67 GLN cc_start: 0.7767 (mt0) cc_final: 0.7411 (mt0) REVERT: n 59 GLU cc_start: 0.8233 (mt-10) cc_final: 0.7238 (pm20) REVERT: n 79 ILE cc_start: 0.8459 (mt) cc_final: 0.8202 (mp) REVERT: n 83 ILE cc_start: 0.8586 (mt) cc_final: 0.8320 (mt) REVERT: n 88 MET cc_start: 0.7544 (mmt) cc_final: 0.7278 (mmm) REVERT: n 113 ARG cc_start: 0.9143 (OUTLIER) cc_final: 0.8920 (ptt90) REVERT: o 69 THR cc_start: 0.9240 (m) cc_final: 0.8899 (p) REVERT: o 99 GLN cc_start: 0.7808 (tp40) cc_final: 0.7464 (tp40) REVERT: p 61 PHE cc_start: 0.9121 (t80) cc_final: 0.8769 (t80) REVERT: p 69 ARG cc_start: 0.7810 (ttm110) cc_final: 0.7399 (ttp-110) REVERT: p 80 LYS cc_start: 0.8123 (mptt) cc_final: 0.7812 (mptt) REVERT: q 10 LYS cc_start: 0.8528 (tmtt) cc_final: 0.8199 (ptmm) REVERT: q 61 PHE cc_start: 0.7218 (m-80) cc_final: 0.6875 (m-80) REVERT: r 23 TYR cc_start: 0.8539 (t80) cc_final: 0.8204 (t80) REVERT: r 46 SER cc_start: 0.8639 (m) cc_final: 0.8336 (p) REVERT: r 59 GLU cc_start: 0.7651 (mt-10) cc_final: 0.7107 (mt-10) REVERT: r 75 MET cc_start: 0.8382 (tpt) cc_final: 0.8113 (tpp) REVERT: s 10 GLU cc_start: 0.7684 (tp30) cc_final: 0.7374 (tp30) REVERT: s 43 ASN cc_start: 0.8559 (m-40) cc_final: 0.7900 (m110) REVERT: s 79 LEU cc_start: 0.8427 (mt) cc_final: 0.8110 (mt) REVERT: t 48 LYS cc_start: 0.8531 (mmtm) cc_final: 0.8301 (mtpt) REVERT: t 67 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8652 (mm) REVERT: t 80 GLN cc_start: 0.8412 (pt0) cc_final: 0.8047 (pt0) REVERT: u 5 ARG cc_start: 0.8131 (ptp-170) cc_final: 0.7722 (ptp90) REVERT: u 56 ARG cc_start: 0.8556 (mmm160) cc_final: 0.8332 (mmm-85) REVERT: v 6 ARG cc_start: 0.6268 (mtt90) cc_final: 0.5764 (mtt90) REVERT: v 15 ASP cc_start: 0.6420 (p0) cc_final: 0.4836 (t70) REVERT: v 51 ASN cc_start: 0.8424 (OUTLIER) cc_final: 0.8192 (m-40) REVERT: w 52 GLN cc_start: 0.9119 (tp40) cc_final: 0.8838 (tp-100) REVERT: w 65 LEU cc_start: 0.9037 (mt) cc_final: 0.8814 (mp) REVERT: x 37 ARG cc_start: 0.7889 (ptt180) cc_final: 0.7498 (ptt180) REVERT: x 71 LEU cc_start: 0.9361 (mt) cc_final: 0.8932 (mt) REVERT: x 80 TYR cc_start: 0.8061 (t80) cc_final: 0.7745 (t80) REVERT: y 24 ARG cc_start: 0.7947 (mmt180) cc_final: 0.7445 (mmt180) REVERT: y 51 PHE cc_start: 0.8202 (t80) cc_final: 0.7766 (t80) REVERT: y 57 ILE cc_start: 0.8821 (OUTLIER) cc_final: 0.8508 (tp) REVERT: z 17 ARG cc_start: 0.8217 (ttm110) cc_final: 0.7988 (tpt170) REVERT: z 64 ASN cc_start: 0.6967 (t0) cc_final: 0.6723 (t0) REVERT: A 123 GLU cc_start: 0.8195 (tm-30) cc_final: 0.7895 (tm-30) REVERT: A 137 ARG cc_start: 0.8662 (mmm-85) cc_final: 0.7937 (mmt-90) REVERT: A 140 GLU cc_start: 0.7126 (pp20) cc_final: 0.6905 (pp20) REVERT: A 162 ILE cc_start: 0.9282 (tt) cc_final: 0.8982 (tt) REVERT: A 169 ASP cc_start: 0.7107 (t70) cc_final: 0.6870 (t70) REVERT: A 176 LYS cc_start: 0.8871 (ptpt) cc_final: 0.8461 (pttt) REVERT: A 193 GLN cc_start: 0.8077 (mt0) cc_final: 0.7280 (tm-30) REVERT: A 206 MET cc_start: 0.8602 (mtp) cc_final: 0.8058 (mtt) REVERT: A 256 GLU cc_start: 0.8351 (mt-10) cc_final: 0.7849 (tt0) REVERT: A 269 LYS cc_start: 0.8622 (tptp) cc_final: 0.8272 (tptp) REVERT: A 274 LEU cc_start: 0.8501 (mt) cc_final: 0.8291 (tt) REVERT: A 277 ARG cc_start: 0.7326 (mtt180) cc_final: 0.6666 (mtm110) REVERT: A 288 GLN cc_start: 0.7822 (mm-40) cc_final: 0.7539 (mm-40) REVERT: A 311 ASN cc_start: 0.8429 (OUTLIER) cc_final: 0.7669 (t0) REVERT: A 352 GLN cc_start: 0.6672 (pt0) cc_final: 0.4230 (tm-30) outliers start: 259 outliers final: 213 residues processed: 1728 average time/residue: 1.2972 time to fit residues: 3846.2015 Evaluate side-chains 1812 residues out of total 4880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 229 poor density : 1583 time to evaluate : 6.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 26 LYS Chi-restraints excluded: chain B residue 38 SER Chi-restraints excluded: chain B residue 70 ASN Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 185 GLU Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain C residue 18 ASP Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 96 ILE Chi-restraints excluded: chain C residue 131 ASP Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 44 ARG Chi-restraints excluded: chain D residue 67 ARG Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain D residue 115 GLN Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 17 MET Chi-restraints excluded: chain E residue 23 ASN Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 87 CYS Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain E residue 175 PHE Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 121 ILE Chi-restraints excluded: chain F residue 122 THR Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain F residue 155 GLU Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 60 ASP Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain K residue 92 GLU Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 114 LYS Chi-restraints excluded: chain L residue 23 ILE Chi-restraints excluded: chain L residue 51 GLU Chi-restraints excluded: chain L residue 100 ILE Chi-restraints excluded: chain L residue 103 ILE Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 30 SER Chi-restraints excluded: chain M residue 111 GLU Chi-restraints excluded: chain M residue 119 LEU Chi-restraints excluded: chain N residue 2 ARG Chi-restraints excluded: chain N residue 13 ASN Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain N residue 33 ILE 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 36 TYR Chi-restraints excluded: chain P residue 2 SER Chi-restraints excluded: chain P residue 47 VAL Chi-restraints excluded: chain P residue 66 ASN Chi-restraints excluded: chain P residue 100 LEU Chi-restraints excluded: chain P residue 114 LEU Chi-restraints excluded: chain Q residue 107 THR Chi-restraints excluded: chain Q residue 117 LEU Chi-restraints excluded: chain R residue 39 LEU Chi-restraints excluded: chain R residue 41 ILE Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain S residue 3 THR Chi-restraints excluded: chain S residue 39 THR Chi-restraints excluded: chain S residue 67 ASP Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain S residue 97 LEU Chi-restraints excluded: chain S residue 108 SER Chi-restraints excluded: chain T residue 11 LEU Chi-restraints excluded: chain T residue 22 THR Chi-restraints excluded: chain T residue 42 GLU Chi-restraints excluded: chain T residue 50 LEU Chi-restraints excluded: chain T residue 78 SER 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 39 ILE Chi-restraints excluded: chain U residue 49 VAL Chi-restraints excluded: chain U residue 52 LEU Chi-restraints excluded: chain V residue 4 ILE Chi-restraints excluded: chain V residue 17 SER Chi-restraints excluded: chain V residue 38 LEU Chi-restraints excluded: chain V residue 40 ILE Chi-restraints excluded: chain V residue 61 LEU Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain W residue 21 LEU Chi-restraints excluded: chain W residue 30 SER Chi-restraints excluded: chain W residue 31 VAL Chi-restraints excluded: chain W residue 38 VAL Chi-restraints excluded: chain W residue 70 GLU Chi-restraints excluded: chain X residue 8 THR Chi-restraints excluded: chain X residue 25 THR Chi-restraints excluded: chain X residue 59 ILE Chi-restraints excluded: chain X residue 71 LEU Chi-restraints excluded: chain Y residue 11 VAL Chi-restraints excluded: chain Y residue 12 GLU Chi-restraints excluded: chain Z residue 27 LEU Chi-restraints excluded: chain a residue 22 MET Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain b residue 10 ARG Chi-restraints excluded: chain b residue 28 LEU Chi-restraints excluded: chain b residue 39 LEU Chi-restraints excluded: chain b residue 54 VAL Chi-restraints excluded: chain c residue 42 VAL Chi-restraints excluded: chain c residue 48 ILE Chi-restraints excluded: chain d residue 15 SER Chi-restraints excluded: chain d residue 22 MET Chi-restraints excluded: chain d residue 29 GLN Chi-restraints excluded: chain e residue 38 THR Chi-restraints excluded: chain e residue 51 SER Chi-restraints excluded: chain f residue 15 LYS Chi-restraints excluded: chain g residue 88 ASP Chi-restraints excluded: chain g residue 135 LEU Chi-restraints excluded: chain g residue 147 SER Chi-restraints excluded: chain g residue 199 VAL Chi-restraints excluded: chain h residue 102 ASN Chi-restraints excluded: chain h residue 149 ILE Chi-restraints excluded: chain h residue 161 GLU Chi-restraints excluded: chain h residue 165 THR Chi-restraints excluded: chain h residue 177 THR Chi-restraints excluded: chain h residue 188 GLU Chi-restraints excluded: chain h residue 192 THR Chi-restraints excluded: chain h residue 208 LEU Chi-restraints excluded: chain i residue 40 GLN Chi-restraints excluded: chain i residue 85 ASN Chi-restraints excluded: chain i residue 124 MET Chi-restraints excluded: chain i residue 129 VAL Chi-restraints excluded: chain i residue 144 SER Chi-restraints excluded: chain i residue 173 VAL Chi-restraints excluded: chain i residue 201 VAL Chi-restraints excluded: chain j residue 22 SER Chi-restraints excluded: chain j residue 32 SER Chi-restraints excluded: chain j residue 88 VAL Chi-restraints excluded: chain j residue 131 THR Chi-restraints excluded: chain j residue 149 SER Chi-restraints excluded: chain k residue 1 MET Chi-restraints excluded: chain k residue 7 VAL Chi-restraints excluded: chain k residue 54 LEU Chi-restraints excluded: chain k residue 71 ILE Chi-restraints excluded: chain k residue 85 ILE Chi-restraints excluded: chain k residue 92 THR Chi-restraints excluded: chain k residue 96 VAL Chi-restraints excluded: chain k residue 97 THR Chi-restraints excluded: chain k residue 100 SER Chi-restraints excluded: chain l residue 50 LEU Chi-restraints excluded: chain l residue 59 LEU Chi-restraints excluded: chain l residue 69 VAL Chi-restraints excluded: chain l residue 83 SER Chi-restraints excluded: chain l residue 91 VAL Chi-restraints excluded: chain l residue 106 GLU Chi-restraints excluded: chain l residue 130 ASN Chi-restraints excluded: chain l residue 133 THR Chi-restraints excluded: chain m residue 12 THR Chi-restraints excluded: chain m residue 38 ASN Chi-restraints excluded: chain m residue 51 VAL Chi-restraints excluded: chain m residue 52 GLU Chi-restraints excluded: chain m residue 59 LEU Chi-restraints excluded: chain m residue 79 SER Chi-restraints excluded: chain m residue 83 LEU Chi-restraints excluded: chain m residue 99 LEU Chi-restraints excluded: chain m residue 105 SER Chi-restraints excluded: chain m residue 107 SER Chi-restraints excluded: chain m residue 112 THR Chi-restraints excluded: chain n residue 21 ILE Chi-restraints excluded: chain n residue 22 LYS Chi-restraints excluded: chain n residue 35 LEU Chi-restraints excluded: chain n residue 63 LEU Chi-restraints excluded: chain n residue 94 LEU Chi-restraints excluded: chain n residue 113 ARG Chi-restraints excluded: chain n residue 116 VAL Chi-restraints excluded: chain o residue 25 ILE Chi-restraints excluded: chain o residue 54 SER Chi-restraints excluded: chain o residue 74 VAL Chi-restraints excluded: chain p residue 31 ILE Chi-restraints excluded: chain p residue 32 VAL Chi-restraints excluded: chain p residue 33 THR Chi-restraints excluded: chain p residue 46 THR Chi-restraints excluded: chain p residue 58 SER Chi-restraints excluded: chain q residue 34 CYS Chi-restraints excluded: chain q residue 41 THR Chi-restraints excluded: chain q residue 70 GLU Chi-restraints excluded: chain q residue 82 ILE Chi-restraints excluded: chain q residue 119 VAL Chi-restraints excluded: chain r residue 34 LEU Chi-restraints excluded: chain r residue 65 VAL Chi-restraints excluded: chain s residue 16 LEU Chi-restraints excluded: chain s residue 34 VAL Chi-restraints excluded: chain s residue 100 SER Chi-restraints excluded: chain t residue 42 HIS Chi-restraints excluded: chain t residue 67 LEU Chi-restraints excluded: chain t residue 70 LEU Chi-restraints excluded: chain t residue 89 ARG Chi-restraints excluded: chain u residue 2 VAL Chi-restraints excluded: chain u residue 3 THR Chi-restraints excluded: chain u residue 19 VAL Chi-restraints excluded: chain u residue 67 ILE Chi-restraints excluded: chain v residue 28 PHE Chi-restraints excluded: chain v residue 38 ILE Chi-restraints excluded: chain v residue 51 ASN Chi-restraints excluded: chain v residue 57 ASP Chi-restraints excluded: chain v residue 67 LEU Chi-restraints excluded: chain w residue 59 ILE Chi-restraints excluded: chain w residue 71 THR Chi-restraints excluded: chain x residue 64 ASP Chi-restraints excluded: chain x residue 79 THR Chi-restraints excluded: chain y residue 30 THR Chi-restraints excluded: chain y residue 57 ILE Chi-restraints excluded: chain z residue 43 THR Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 311 ASN Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain A residue 347 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1034 random chunks: chunk 906 optimal weight: 8.9990 chunk 954 optimal weight: 0.9990 chunk 871 optimal weight: 20.0000 chunk 928 optimal weight: 4.9990 chunk 558 optimal weight: 0.9990 chunk 404 optimal weight: 30.0000 chunk 729 optimal weight: 1.9990 chunk 285 optimal weight: 10.0000 chunk 839 optimal weight: 8.9990 chunk 878 optimal weight: 8.9990 chunk 925 optimal weight: 0.9980 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 239 ASN D 90 GLN F 45 HIS ** F 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 128 GLN ** N 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 8 ASN i 140 ASN i 164 GLN i 198 HIS l 130 ASN l 148 ASN ** r 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 42 HIS y 82 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.3476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 158938 Z= 0.151 Angle : 0.573 14.273 237562 Z= 0.310 Chirality : 0.031 0.279 30220 Planarity : 0.005 0.125 12875 Dihedral : 23.438 178.911 78945 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.91 % Favored : 96.08 % Rotamer: Outliers : 4.61 % Allowed : 22.30 % Favored : 73.09 % 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: -0.89 (0.11), residues: 5863 helix: 0.48 (0.12), residues: 1897 sheet: -0.85 (0.16), residues: 1103 loop : -1.18 (0.11), residues: 2863 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP k 42 HIS 0.013 0.001 HIS t 42 PHE 0.017 0.001 PHE u 39 TYR 0.025 0.002 TYR B 83 ARG 0.023 0.001 ARG o 89 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11726 Ramachandran restraints generated. 5863 Oldfield, 0 Emsley, 5863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11726 Ramachandran restraints generated. 5863 Oldfield, 0 Emsley, 5863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1845 residues out of total 4880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 225 poor density : 1620 time to evaluate : 6.414 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: B 98 ASP cc_start: 0.8099 (p0) cc_final: 0.7857 (p0) REVERT: B 100 GLU cc_start: 0.8127 (tt0) cc_final: 0.7899 (tt0) REVERT: B 108 LYS cc_start: 0.8305 (tttt) cc_final: 0.8037 (ttmm) REVERT: B 110 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8546 (mp) REVERT: B 111 LYS cc_start: 0.8993 (pttt) cc_final: 0.8785 (pttt) REVERT: B 114 ASP cc_start: 0.8289 (m-30) cc_final: 0.7951 (m-30) REVERT: B 174 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8633 (mt) REVERT: B 201 MET cc_start: 0.9000 (ptt) cc_final: 0.8576 (ptt) REVERT: B 202 LEU cc_start: 0.9262 (OUTLIER) cc_final: 0.8872 (mm) REVERT: D 24 ASN cc_start: 0.8298 (t0) cc_final: 0.8091 (t0) REVERT: D 115 GLN cc_start: 0.8170 (OUTLIER) cc_final: 0.7468 (mp10) REVERT: D 141 MET cc_start: 0.7810 (mmm) cc_final: 0.7394 (mtt) REVERT: D 156 ASN cc_start: 0.8100 (m-40) cc_final: 0.7576 (t0) REVERT: E 27 GLN cc_start: 0.8179 (tt0) cc_final: 0.7846 (tt0) REVERT: E 38 MET cc_start: 0.7692 (ttm) cc_final: 0.6705 (ptm) REVERT: E 69 LYS cc_start: 0.7159 (mmtt) cc_final: 0.6892 (mmtt) REVERT: E 155 THR cc_start: 0.9410 (m) cc_final: 0.9096 (p) REVERT: E 175 PHE cc_start: 0.7823 (OUTLIER) cc_final: 0.6788 (m-80) REVERT: F 25 THR cc_start: 0.8259 (OUTLIER) cc_final: 0.8040 (t) REVERT: F 39 ASP cc_start: 0.8530 (m-30) cc_final: 0.8031 (t0) REVERT: F 56 ASP cc_start: 0.6795 (m-30) cc_final: 0.6465 (t0) REVERT: F 73 ASN cc_start: 0.8992 (t0) cc_final: 0.8760 (t0) REVERT: F 74 SER cc_start: 0.9312 (t) cc_final: 0.9027 (t) REVERT: F 130 GLU cc_start: 0.7217 (tm-30) cc_final: 0.6355 (tm-30) REVERT: F 139 GLN cc_start: 0.8395 (tm-30) cc_final: 0.7961 (tt0) REVERT: F 147 ASP cc_start: 0.8484 (m-30) cc_final: 0.8251 (m-30) REVERT: G 11 ASN cc_start: 0.8001 (t0) cc_final: 0.7684 (t0) REVERT: G 46 PHE cc_start: 0.7342 (t80) cc_final: 0.7058 (m-80) REVERT: J 81 ILE cc_start: 0.8958 (tp) cc_final: 0.8643 (tp) REVERT: J 84 ILE cc_start: 0.9390 (OUTLIER) cc_final: 0.9039 (tp) REVERT: J 96 ARG cc_start: 0.7494 (OUTLIER) cc_final: 0.7104 (ptm160) REVERT: J 111 LYS cc_start: 0.8257 (mptt) cc_final: 0.7935 (mmmt) REVERT: J 128 ASN cc_start: 0.8385 (t160) cc_final: 0.8081 (t0) REVERT: K 13 ASN cc_start: 0.8817 (p0) cc_final: 0.8589 (p0) REVERT: K 77 ILE cc_start: 0.9342 (mt) cc_final: 0.9111 (mt) REVERT: K 113 MET cc_start: 0.7071 (mmt) cc_final: 0.6804 (mmm) REVERT: L 69 ARG cc_start: 0.7890 (mtp-110) cc_final: 0.7290 (mmm-85) REVERT: L 70 LYS cc_start: 0.9100 (tttp) cc_final: 0.8648 (ttpt) REVERT: M 2 LEU cc_start: 0.8902 (mt) cc_final: 0.8539 (mt) REVERT: M 20 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.7924 (mm) REVERT: M 78 LEU cc_start: 0.9298 (tp) cc_final: 0.8967 (mt) REVERT: M 110 GLU cc_start: 0.7983 (tm-30) cc_final: 0.7701 (tm-30) REVERT: M 136 MET cc_start: 0.6202 (ttm) cc_final: 0.5912 (tmm) REVERT: N 2 ARG cc_start: 0.7712 (OUTLIER) cc_final: 0.4286 (ppp-140) REVERT: N 35 LYS cc_start: 0.8674 (tttt) cc_final: 0.8371 (tttt) REVERT: N 89 SER cc_start: 0.7879 (p) cc_final: 0.7515 (t) REVERT: O 46 GLU cc_start: 0.7688 (pt0) cc_final: 0.7459 (tm-30) REVERT: O 99 TYR cc_start: 0.7797 (t80) cc_final: 0.7555 (t80) REVERT: O 104 GLN cc_start: 0.7090 (tp40) cc_final: 0.6773 (tp-100) REVERT: O 108 ASP cc_start: 0.8024 (p0) cc_final: 0.7764 (p0) REVERT: O 116 GLN cc_start: 0.7301 (tp40) cc_final: 0.6963 (tp-100) REVERT: P 11 GLU cc_start: 0.7761 (pt0) cc_final: 0.7448 (pt0) REVERT: P 27 GLU cc_start: 0.8073 (tm-30) cc_final: 0.7553 (tm-30) REVERT: P 51 ARG cc_start: 0.8582 (OUTLIER) cc_final: 0.8351 (tmt90) REVERT: P 63 LYS cc_start: 0.8849 (ptmt) cc_final: 0.8415 (ptmm) REVERT: P 100 LEU cc_start: 0.8906 (mp) cc_final: 0.8694 (mm) REVERT: Q 25 TYR cc_start: 0.9181 (t80) cc_final: 0.8616 (t80) REVERT: Q 29 SER cc_start: 0.8994 (p) cc_final: 0.8739 (p) REVERT: Q 45 TYR cc_start: 0.8634 (m-10) cc_final: 0.8421 (m-10) REVERT: Q 52 GLN cc_start: 0.8734 (mt0) cc_final: 0.8439 (mt0) REVERT: Q 59 GLN cc_start: 0.8453 (tt0) cc_final: 0.7510 (mt0) REVERT: Q 71 GLN cc_start: 0.8555 (tp40) cc_final: 0.8082 (tm-30) REVERT: Q 101 PHE cc_start: 0.7650 (m-80) cc_final: 0.7281 (m-80) REVERT: R 21 ARG cc_start: 0.9099 (ttm170) cc_final: 0.8494 (ttm170) REVERT: R 84 ARG cc_start: 0.8835 (ptp90) cc_final: 0.8518 (ttp80) REVERT: R 86 GLN cc_start: 0.8095 (mm-40) cc_final: 0.7831 (mm-40) REVERT: R 97 LYS cc_start: 0.8911 (tttt) cc_final: 0.8661 (ttpt) REVERT: S 68 ASP cc_start: 0.8615 (m-30) cc_final: 0.8177 (m-30) REVERT: S 82 MET cc_start: 0.7187 (mtt) cc_final: 0.6761 (mmt) REVERT: T 21 SER cc_start: 0.9051 (m) cc_final: 0.8710 (p) REVERT: T 73 ARG cc_start: 0.7962 (ttm110) cc_final: 0.7296 (ptp-110) REVERT: T 77 ARG cc_start: 0.8188 (mtt180) cc_final: 0.7854 (mtp180) REVERT: U 22 ARG cc_start: 0.8042 (mtp180) cc_final: 0.7793 (mtm180) REVERT: U 31 SER cc_start: 0.9128 (p) cc_final: 0.8897 (p) REVERT: U 74 ASN cc_start: 0.9284 (t0) cc_final: 0.8991 (t0) REVERT: V 1 MET cc_start: 0.7513 (tmm) cc_final: 0.7139 (tpt) REVERT: W 39 ARG cc_start: 0.8390 (mtp85) cc_final: 0.8071 (mtt180) REVERT: W 76 ASN cc_start: 0.8181 (m-40) cc_final: 0.7742 (m110) REVERT: X 20 HIS cc_start: 0.7497 (t70) cc_final: 0.7072 (t70) REVERT: X 23 ASN cc_start: 0.8891 (m110) cc_final: 0.8584 (m-40) REVERT: X 62 LYS cc_start: 0.9130 (mttt) cc_final: 0.8663 (mttt) REVERT: X 65 ASP cc_start: 0.7566 (p0) cc_final: 0.7289 (p0) REVERT: X 72 ARG cc_start: 0.7055 (mtm180) cc_final: 0.6840 (mtm180) REVERT: Y 13 GLU cc_start: 0.7684 (mt-10) cc_final: 0.7402 (mt-10) REVERT: Y 49 ASP cc_start: 0.8646 (m-30) cc_final: 0.8113 (m-30) REVERT: Y 58 ASN cc_start: 0.8015 (m-40) cc_final: 0.7256 (m110) REVERT: Z 4 THR cc_start: 0.8578 (m) cc_final: 0.8051 (p) REVERT: Z 21 LYS cc_start: 0.9090 (mttt) cc_final: 0.8764 (mtmm) REVERT: b 36 GLU cc_start: 0.8483 (pt0) cc_final: 0.7891 (pt0) REVERT: c 27 LYS cc_start: 0.8586 (mttt) cc_final: 0.8244 (tmmt) REVERT: c 53 LYS cc_start: 0.7758 (ttmm) cc_final: 0.7092 (pttm) REVERT: e 28 ASN cc_start: 0.9018 (m-40) cc_final: 0.8770 (m-40) REVERT: f 30 GLU cc_start: 0.8507 (tp30) cc_final: 0.7444 (mp0) REVERT: g 74 ARG cc_start: 0.8325 (mmp80) cc_final: 0.6818 (ttp80) REVERT: g 78 GLU cc_start: 0.7951 (pm20) cc_final: 0.7645 (pm20) REVERT: g 89 GLN cc_start: 0.8372 (mm-40) cc_final: 0.7373 (mm110) REVERT: g 109 GLN cc_start: 0.8132 (mm-40) cc_final: 0.7822 (mm-40) REVERT: g 152 LYS cc_start: 0.8573 (pttt) cc_final: 0.8079 (tmtt) REVERT: g 175 GLU cc_start: 0.8684 (mt-10) cc_final: 0.8249 (mt-10) REVERT: h 79 LYS cc_start: 0.7341 (mmtm) cc_final: 0.6852 (tmtt) REVERT: h 122 SER cc_start: 0.9190 (m) cc_final: 0.8717 (p) REVERT: h 142 MET cc_start: 0.7392 (mmm) cc_final: 0.7153 (mmm) REVERT: h 172 ARG cc_start: 0.8340 (OUTLIER) cc_final: 0.8074 (ptm-80) REVERT: h 184 TYR cc_start: 0.9147 (t80) cc_final: 0.8577 (t80) REVERT: h 208 LEU cc_start: 0.7852 (OUTLIER) cc_final: 0.7590 (mm) REVERT: i 48 LEU cc_start: 0.7304 (tp) cc_final: 0.6823 (mp) REVERT: i 69 GLU cc_start: 0.7976 (tp30) cc_final: 0.7366 (tp30) REVERT: i 78 GLU cc_start: 0.7434 (tp30) cc_final: 0.7214 (tp30) REVERT: i 95 GLU cc_start: 0.8174 (mm-30) cc_final: 0.7502 (mm-30) REVERT: i 107 PHE cc_start: 0.8135 (m-80) cc_final: 0.7780 (m-80) REVERT: i 191 LEU cc_start: 0.7490 (mt) cc_final: 0.6831 (tp) REVERT: i 200 ILE cc_start: 0.7006 (mp) cc_final: 0.6739 (mm) REVERT: j 61 GLN cc_start: 0.8400 (mm110) cc_final: 0.8045 (mm110) REVERT: j 62 LYS cc_start: 0.8247 (mttt) cc_final: 0.7803 (ttmm) REVERT: j 106 ILE cc_start: 0.8975 (mt) cc_final: 0.8433 (tp) REVERT: k 5 GLU cc_start: 0.8543 (tt0) cc_final: 0.8213 (tt0) REVERT: k 9 MET cc_start: 0.8004 (mtp) cc_final: 0.7535 (mtt) REVERT: k 30 THR cc_start: 0.7908 (m) cc_final: 0.7560 (t) REVERT: k 33 GLU cc_start: 0.7912 (mp0) cc_final: 0.7615 (mp0) REVERT: k 55 HIS cc_start: 0.7217 (m90) cc_final: 0.6745 (m-70) REVERT: k 64 VAL cc_start: 0.9282 (t) cc_final: 0.9062 (m) REVERT: k 68 GLN cc_start: 0.8170 (mt0) cc_final: 0.7951 (mp10) REVERT: k 75 GLU cc_start: 0.7229 (mt-10) cc_final: 0.6944 (mt-10) REVERT: l 15 ASP cc_start: 0.7252 (t0) cc_final: 0.7038 (t0) REVERT: l 37 SER cc_start: 0.7523 (t) cc_final: 0.6931 (p) REVERT: l 42 ILE cc_start: 0.8777 (tp) cc_final: 0.7986 (mm) REVERT: l 48 GLU cc_start: 0.8501 (tm-30) cc_final: 0.7900 (tm-30) REVERT: l 50 LEU cc_start: 0.7331 (OUTLIER) cc_final: 0.7074 (tm) REVERT: l 86 GLN cc_start: 0.7159 (mm110) cc_final: 0.5902 (mm-40) REVERT: l 136 LYS cc_start: 0.8621 (tppt) cc_final: 0.8056 (tptp) REVERT: m 18 GLN cc_start: 0.8650 (mm-40) cc_final: 0.7942 (mm-40) REVERT: m 52 GLU cc_start: 0.7604 (OUTLIER) cc_final: 0.6989 (tm-30) REVERT: m 67 GLN cc_start: 0.7751 (mt0) cc_final: 0.7417 (mt0) REVERT: n 57 MET cc_start: 0.7494 (mpp) cc_final: 0.7059 (mmm) REVERT: n 83 ILE cc_start: 0.8603 (mt) cc_final: 0.8333 (mt) REVERT: n 88 MET cc_start: 0.7525 (mmt) cc_final: 0.7274 (mmm) REVERT: n 113 ARG cc_start: 0.9138 (OUTLIER) cc_final: 0.8921 (ptt90) REVERT: n 114 LYS cc_start: 0.8809 (tttm) cc_final: 0.8419 (tmtm) REVERT: o 69 THR cc_start: 0.9234 (m) cc_final: 0.8912 (p) REVERT: o 82 LYS cc_start: 0.8021 (tttp) cc_final: 0.7764 (tmtt) REVERT: o 88 MET cc_start: 0.8012 (mmm) cc_final: 0.7209 (mtm) REVERT: o 99 GLN cc_start: 0.7796 (tp40) cc_final: 0.7465 (tp40) REVERT: p 15 GLN cc_start: 0.8192 (tp-100) cc_final: 0.7623 (tp40) REVERT: p 61 PHE cc_start: 0.9144 (t80) cc_final: 0.8765 (t80) REVERT: p 80 LYS cc_start: 0.8133 (mptt) cc_final: 0.7785 (mptt) REVERT: p 83 GLU cc_start: 0.7298 (pm20) cc_final: 0.7008 (pm20) REVERT: q 10 LYS cc_start: 0.8525 (tmtt) cc_final: 0.8194 (ptmm) REVERT: r 23 TYR cc_start: 0.8383 (t80) cc_final: 0.8065 (t80) REVERT: r 46 SER cc_start: 0.8610 (m) cc_final: 0.8325 (p) REVERT: r 54 ASP cc_start: 0.7570 (t70) cc_final: 0.7208 (t0) REVERT: r 59 GLU cc_start: 0.7559 (mt-10) cc_final: 0.7338 (mt-10) REVERT: r 66 GLU cc_start: 0.8880 (mm-30) cc_final: 0.8494 (mm-30) REVERT: r 75 MET cc_start: 0.8377 (tpt) cc_final: 0.8095 (tpp) REVERT: s 10 GLU cc_start: 0.7715 (tp30) cc_final: 0.7384 (tp30) REVERT: s 43 ASN cc_start: 0.8556 (m-40) cc_final: 0.7891 (m110) REVERT: s 79 LEU cc_start: 0.8412 (mt) cc_final: 0.8080 (mt) REVERT: t 48 LYS cc_start: 0.8480 (mmtm) cc_final: 0.8175 (mtpt) REVERT: t 67 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8629 (mm) REVERT: u 5 ARG cc_start: 0.8091 (ptp-170) cc_final: 0.7677 (ptp90) REVERT: u 56 ARG cc_start: 0.8593 (mmm160) cc_final: 0.8353 (mmm-85) REVERT: v 6 ARG cc_start: 0.6288 (mtt90) cc_final: 0.5797 (mtt90) REVERT: v 15 ASP cc_start: 0.6429 (p0) cc_final: 0.4839 (t70) REVERT: w 52 GLN cc_start: 0.9069 (tp40) cc_final: 0.8857 (tp-100) REVERT: x 7 LYS cc_start: 0.8830 (mtpt) cc_final: 0.8506 (ttpt) REVERT: x 37 ARG cc_start: 0.7857 (ptt180) cc_final: 0.7445 (ptt180) REVERT: x 66 MET cc_start: 0.8287 (ptp) cc_final: 0.8084 (ptp) REVERT: x 71 LEU cc_start: 0.9292 (mt) cc_final: 0.9018 (tp) REVERT: x 80 TYR cc_start: 0.8048 (t80) cc_final: 0.7738 (t80) REVERT: y 24 ARG cc_start: 0.7943 (mmt180) cc_final: 0.7456 (mmt180) REVERT: y 51 PHE cc_start: 0.8125 (t80) cc_final: 0.7702 (t80) REVERT: y 57 ILE cc_start: 0.8816 (OUTLIER) cc_final: 0.8502 (tp) REVERT: z 17 ARG cc_start: 0.8221 (ttm110) cc_final: 0.7935 (tpt170) REVERT: A 112 PHE cc_start: 0.8856 (m-80) cc_final: 0.8564 (m-80) REVERT: A 123 GLU cc_start: 0.8189 (tm-30) cc_final: 0.7897 (tm-30) REVERT: A 137 ARG cc_start: 0.8668 (mmm-85) cc_final: 0.7929 (mmt-90) REVERT: A 169 ASP cc_start: 0.7115 (t70) cc_final: 0.6850 (t70) REVERT: A 176 LYS cc_start: 0.8810 (ptpt) cc_final: 0.8454 (pttt) REVERT: A 193 GLN cc_start: 0.7717 (mt0) cc_final: 0.7169 (tm-30) REVERT: A 206 MET cc_start: 0.8651 (mtp) cc_final: 0.8315 (mtm) REVERT: A 256 GLU cc_start: 0.8406 (mt-10) cc_final: 0.7954 (tt0) REVERT: A 269 LYS cc_start: 0.8616 (tptp) cc_final: 0.8245 (tptp) REVERT: A 274 LEU cc_start: 0.8497 (mt) cc_final: 0.8285 (tt) REVERT: A 277 ARG cc_start: 0.7267 (mtt180) cc_final: 0.6637 (mtm110) REVERT: A 288 GLN cc_start: 0.7820 (mm-40) cc_final: 0.7538 (mm-40) REVERT: A 311 ASN cc_start: 0.8432 (t0) cc_final: 0.7682 (t0) REVERT: A 352 GLN cc_start: 0.6647 (pt0) cc_final: 0.4204 (tm-30) outliers start: 225 outliers final: 181 residues processed: 1721 average time/residue: 1.3075 time to fit residues: 3863.4947 Evaluate side-chains 1776 residues out of total 4880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 199 poor density : 1577 time to evaluate : 6.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 SER Chi-restraints excluded: chain B residue 70 ASN Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 185 GLU Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain C residue 18 ASP Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 67 ARG Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain D residue 115 GLN Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain E residue 17 MET Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 23 ASN Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 87 CYS Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain E residue 175 PHE Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 121 ILE Chi-restraints excluded: chain F residue 122 THR Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain F residue 155 GLU Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 60 ASP Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain J residue 96 ARG Chi-restraints excluded: chain K residue 92 GLU Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain L residue 23 ILE Chi-restraints excluded: chain L residue 51 GLU Chi-restraints excluded: chain L residue 82 LEU Chi-restraints excluded: chain L residue 100 ILE Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 30 SER Chi-restraints excluded: chain M residue 42 THR Chi-restraints excluded: chain M residue 111 GLU Chi-restraints excluded: chain M residue 132 THR Chi-restraints excluded: chain N residue 2 ARG Chi-restraints excluded: chain N residue 13 ASN Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain N residue 33 ILE Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain O residue 28 VAL Chi-restraints excluded: chain P residue 2 SER Chi-restraints excluded: chain P residue 51 ARG Chi-restraints excluded: chain P residue 110 ILE Chi-restraints excluded: chain P residue 114 LEU Chi-restraints excluded: chain Q residue 107 THR Chi-restraints excluded: chain R residue 39 LEU Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain R residue 58 VAL Chi-restraints excluded: chain S residue 3 THR Chi-restraints excluded: chain S residue 67 ASP Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain S residue 108 SER Chi-restraints excluded: chain T residue 11 LEU Chi-restraints excluded: chain T residue 22 THR Chi-restraints excluded: chain T residue 42 GLU Chi-restraints excluded: chain T residue 50 LEU Chi-restraints excluded: chain U residue 12 ILE Chi-restraints excluded: chain U residue 28 VAL Chi-restraints excluded: chain U residue 39 ILE Chi-restraints excluded: chain U residue 49 VAL Chi-restraints excluded: chain U residue 52 LEU Chi-restraints excluded: chain V residue 4 ILE Chi-restraints excluded: chain V residue 17 SER Chi-restraints excluded: chain V residue 38 LEU Chi-restraints excluded: chain V residue 40 ILE Chi-restraints excluded: chain V residue 61 LEU Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain W residue 21 LEU Chi-restraints excluded: chain W residue 31 VAL Chi-restraints excluded: chain W residue 38 VAL Chi-restraints excluded: chain W residue 70 GLU Chi-restraints excluded: chain X residue 8 THR Chi-restraints excluded: chain X residue 25 THR Chi-restraints excluded: chain Y residue 11 VAL Chi-restraints excluded: chain Y residue 12 GLU Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain b residue 10 ARG Chi-restraints excluded: chain b residue 39 LEU Chi-restraints excluded: chain b residue 54 VAL Chi-restraints excluded: chain c residue 42 VAL Chi-restraints excluded: chain c residue 48 ILE Chi-restraints excluded: chain d residue 15 SER Chi-restraints excluded: chain d residue 29 GLN Chi-restraints excluded: chain e residue 38 THR Chi-restraints excluded: chain e residue 51 SER Chi-restraints excluded: chain g residue 88 ASP Chi-restraints excluded: chain g residue 135 LEU Chi-restraints excluded: chain g residue 199 VAL Chi-restraints excluded: chain h residue 66 VAL Chi-restraints excluded: chain h residue 102 ASN Chi-restraints excluded: chain h residue 149 ILE Chi-restraints excluded: chain h residue 161 GLU Chi-restraints excluded: chain h residue 165 THR Chi-restraints excluded: chain h residue 172 ARG Chi-restraints excluded: chain h residue 177 THR Chi-restraints excluded: chain h residue 188 GLU Chi-restraints excluded: chain h residue 192 THR Chi-restraints excluded: chain h residue 208 LEU Chi-restraints excluded: chain i residue 11 LEU Chi-restraints excluded: chain i residue 124 MET Chi-restraints excluded: chain i residue 129 VAL Chi-restraints excluded: chain i residue 144 SER Chi-restraints excluded: chain i residue 173 VAL Chi-restraints excluded: chain i residue 201 VAL Chi-restraints excluded: chain j residue 22 SER Chi-restraints excluded: chain j residue 32 SER Chi-restraints excluded: chain j residue 88 VAL Chi-restraints excluded: chain j residue 94 VAL Chi-restraints excluded: chain j residue 96 MET Chi-restraints excluded: chain j residue 131 THR Chi-restraints excluded: chain j residue 149 SER Chi-restraints excluded: chain k residue 7 VAL Chi-restraints excluded: chain k residue 54 LEU Chi-restraints excluded: chain k residue 85 ILE Chi-restraints excluded: chain k residue 92 THR Chi-restraints excluded: chain k residue 96 VAL Chi-restraints excluded: chain k residue 97 THR Chi-restraints excluded: chain l residue 47 LEU Chi-restraints excluded: chain l residue 50 LEU Chi-restraints excluded: chain l residue 59 LEU Chi-restraints excluded: chain l residue 69 VAL Chi-restraints excluded: chain l residue 83 SER Chi-restraints excluded: chain l residue 91 VAL Chi-restraints excluded: chain l residue 130 ASN Chi-restraints excluded: chain m residue 12 THR Chi-restraints excluded: chain m residue 38 ASN Chi-restraints excluded: chain m residue 51 VAL Chi-restraints excluded: chain m residue 52 GLU Chi-restraints excluded: chain m residue 79 SER Chi-restraints excluded: chain m residue 83 LEU Chi-restraints excluded: chain m residue 99 LEU Chi-restraints excluded: chain m residue 107 SER Chi-restraints excluded: chain m residue 112 THR Chi-restraints excluded: chain n residue 21 ILE Chi-restraints excluded: chain n residue 22 LYS Chi-restraints excluded: chain n residue 35 LEU Chi-restraints excluded: chain n residue 63 LEU Chi-restraints excluded: chain n residue 94 LEU Chi-restraints excluded: chain n residue 113 ARG Chi-restraints excluded: chain o residue 54 SER Chi-restraints excluded: chain o residue 74 VAL Chi-restraints excluded: chain p residue 31 ILE Chi-restraints excluded: chain p residue 46 THR Chi-restraints excluded: chain p residue 58 SER Chi-restraints excluded: chain p residue 111 THR Chi-restraints excluded: chain q residue 34 CYS Chi-restraints excluded: chain q residue 41 THR Chi-restraints excluded: chain q residue 70 GLU Chi-restraints excluded: chain q residue 82 ILE Chi-restraints excluded: chain q residue 119 VAL Chi-restraints excluded: chain r residue 34 LEU Chi-restraints excluded: chain r residue 39 ILE Chi-restraints excluded: chain r residue 65 VAL Chi-restraints excluded: chain s residue 16 LEU Chi-restraints excluded: chain s residue 34 VAL Chi-restraints excluded: chain s residue 100 SER Chi-restraints excluded: chain t residue 67 LEU Chi-restraints excluded: chain t residue 70 LEU Chi-restraints excluded: chain t residue 89 ARG Chi-restraints excluded: chain u residue 2 VAL Chi-restraints excluded: chain u residue 3 THR Chi-restraints excluded: chain u residue 19 VAL Chi-restraints excluded: chain u residue 67 ILE Chi-restraints excluded: chain v residue 38 ILE Chi-restraints excluded: chain v residue 67 LEU Chi-restraints excluded: chain w residue 71 THR Chi-restraints excluded: chain x residue 64 ASP Chi-restraints excluded: chain x residue 79 THR Chi-restraints excluded: chain y residue 30 THR Chi-restraints excluded: chain y residue 57 ILE Chi-restraints excluded: chain z residue 43 THR Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain A residue 347 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1034 random chunks: chunk 609 optimal weight: 7.9990 chunk 982 optimal weight: 0.9980 chunk 599 optimal weight: 9.9990 chunk 465 optimal weight: 4.9990 chunk 682 optimal weight: 0.9980 chunk 1030 optimal weight: 10.0000 chunk 948 optimal weight: 10.0000 chunk 820 optimal weight: 0.3980 chunk 85 optimal weight: 10.0000 chunk 633 optimal weight: 0.4980 chunk 502 optimal weight: 6.9990 overall best weight: 1.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 90 GLN ** D 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 45 HIS ** F 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 128 GLN K 9 ASN ** N 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 120 GLN h 8 ASN i 140 ASN k 52 ASN l 130 ASN l 148 ASN r 100 GLN t 42 HIS t 80 GLN y 82 GLN A 263 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.3718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.075 158938 Z= 0.137 Angle : 0.561 14.405 237562 Z= 0.304 Chirality : 0.031 0.282 30220 Planarity : 0.005 0.123 12875 Dihedral : 23.370 179.836 78945 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.55 % Favored : 96.44 % Rotamer: Outliers : 3.73 % Allowed : 23.36 % Favored : 72.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.11), residues: 5863 helix: 0.63 (0.12), residues: 1915 sheet: -0.77 (0.16), residues: 1072 loop : -1.11 (0.11), residues: 2876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP k 42 HIS 0.007 0.001 HIS A 264 PHE 0.017 0.001 PHE u 39 TYR 0.031 0.002 TYR E 83 ARG 0.017 0.000 ARG n 124 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11726 Ramachandran restraints generated. 5863 Oldfield, 0 Emsley, 5863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11726 Ramachandran restraints generated. 5863 Oldfield, 0 Emsley, 5863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1827 residues out of total 4880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 182 poor density : 1645 time to evaluate : 6.420 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: B 98 ASP cc_start: 0.8178 (p0) cc_final: 0.7943 (p0) REVERT: B 108 LYS cc_start: 0.8298 (tttt) cc_final: 0.8059 (ttmm) REVERT: B 110 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8514 (mp) REVERT: B 111 LYS cc_start: 0.8984 (pttt) cc_final: 0.8782 (pttt) REVERT: B 114 ASP cc_start: 0.8294 (m-30) cc_final: 0.7978 (m-30) REVERT: B 201 MET cc_start: 0.8983 (ptt) cc_final: 0.8589 (ptt) REVERT: B 202 LEU cc_start: 0.9305 (OUTLIER) cc_final: 0.8923 (mm) REVERT: D 24 ASN cc_start: 0.8376 (t0) cc_final: 0.8170 (t0) REVERT: D 97 ASN cc_start: 0.8219 (m-40) cc_final: 0.7895 (m-40) REVERT: D 100 MET cc_start: 0.8559 (mtm) cc_final: 0.8193 (mtm) REVERT: D 115 GLN cc_start: 0.8186 (OUTLIER) cc_final: 0.7564 (mt0) REVERT: D 141 MET cc_start: 0.7836 (mmm) cc_final: 0.7567 (mtt) REVERT: D 156 ASN cc_start: 0.8101 (m-40) cc_final: 0.7562 (t0) REVERT: E 22 TYR cc_start: 0.6023 (m-10) cc_final: 0.5794 (m-10) REVERT: E 27 GLN cc_start: 0.8217 (tt0) cc_final: 0.7894 (tt0) REVERT: E 38 MET cc_start: 0.7648 (ttm) cc_final: 0.6676 (ptm) REVERT: E 101 GLU cc_start: 0.7149 (pt0) cc_final: 0.6434 (pp20) REVERT: E 128 TYR cc_start: 0.7484 (t80) cc_final: 0.7085 (t80) REVERT: E 155 THR cc_start: 0.9547 (m) cc_final: 0.9226 (p) REVERT: E 164 GLU cc_start: 0.8058 (pm20) cc_final: 0.7554 (tt0) REVERT: E 175 PHE cc_start: 0.7986 (OUTLIER) cc_final: 0.6964 (m-80) REVERT: F 25 THR cc_start: 0.8192 (OUTLIER) cc_final: 0.7639 (t) REVERT: F 39 ASP cc_start: 0.8554 (m-30) cc_final: 0.7904 (t0) REVERT: F 56 ASP cc_start: 0.6784 (m-30) cc_final: 0.6458 (t0) REVERT: F 73 ASN cc_start: 0.9016 (t0) cc_final: 0.8811 (t0) REVERT: F 74 SER cc_start: 0.9315 (t) cc_final: 0.9039 (t) REVERT: F 139 GLN cc_start: 0.8326 (tm-30) cc_final: 0.7873 (tt0) REVERT: F 147 ASP cc_start: 0.8384 (m-30) cc_final: 0.8175 (m-30) REVERT: G 11 ASN cc_start: 0.7879 (t0) cc_final: 0.7581 (t0) REVERT: J 81 ILE cc_start: 0.8844 (tp) cc_final: 0.8548 (tp) REVERT: J 84 ILE cc_start: 0.9338 (OUTLIER) cc_final: 0.8954 (tp) REVERT: J 96 ARG cc_start: 0.7492 (OUTLIER) cc_final: 0.7178 (ptm160) REVERT: J 111 LYS cc_start: 0.8299 (mptt) cc_final: 0.8058 (mtpt) REVERT: J 128 ASN cc_start: 0.8376 (t160) cc_final: 0.8125 (t0) REVERT: K 13 ASN cc_start: 0.8741 (p0) cc_final: 0.8467 (p0) REVERT: K 77 ILE cc_start: 0.9422 (mt) cc_final: 0.9169 (mt) REVERT: K 113 MET cc_start: 0.7243 (mmt) cc_final: 0.6912 (mmm) REVERT: L 54 GLN cc_start: 0.8284 (tt0) cc_final: 0.8060 (tt0) REVERT: L 69 ARG cc_start: 0.8015 (mtp-110) cc_final: 0.7366 (mmm-85) REVERT: L 70 LYS cc_start: 0.9115 (tttp) cc_final: 0.8669 (ttpt) REVERT: M 5 LYS cc_start: 0.7933 (mttp) cc_final: 0.7623 (mttm) REVERT: M 12 MET cc_start: 0.8300 (ttm) cc_final: 0.7892 (mtp) REVERT: M 20 LEU cc_start: 0.8318 (OUTLIER) cc_final: 0.7938 (mm) REVERT: M 78 LEU cc_start: 0.9127 (tp) cc_final: 0.8796 (mt) REVERT: M 110 GLU cc_start: 0.7929 (tm-30) cc_final: 0.7637 (tm-30) REVERT: M 136 MET cc_start: 0.6287 (ttm) cc_final: 0.6026 (tmm) REVERT: N 2 ARG cc_start: 0.7678 (OUTLIER) cc_final: 0.4281 (ppp-140) REVERT: N 9 GLN cc_start: 0.8526 (tt0) cc_final: 0.8196 (tt0) REVERT: N 35 LYS cc_start: 0.8803 (tttt) cc_final: 0.8516 (tttt) REVERT: N 89 SER cc_start: 0.7852 (p) cc_final: 0.7486 (t) REVERT: O 99 TYR cc_start: 0.7759 (t80) cc_final: 0.7529 (t80) REVERT: O 104 GLN cc_start: 0.7081 (tp40) cc_final: 0.6760 (tp-100) REVERT: O 108 ASP cc_start: 0.8011 (p0) cc_final: 0.7719 (p0) REVERT: O 116 GLN cc_start: 0.7134 (tp40) cc_final: 0.6915 (tp-100) REVERT: P 11 GLU cc_start: 0.7583 (pt0) cc_final: 0.7362 (pt0) REVERT: P 27 GLU cc_start: 0.8080 (tm-30) cc_final: 0.7547 (tm-30) REVERT: P 63 LYS cc_start: 0.8841 (ptmt) cc_final: 0.8431 (ptmm) REVERT: Q 25 TYR cc_start: 0.9163 (t80) cc_final: 0.8630 (t80) REVERT: Q 29 SER cc_start: 0.8989 (p) cc_final: 0.8741 (p) REVERT: Q 45 TYR cc_start: 0.8641 (m-10) cc_final: 0.8421 (m-10) REVERT: Q 52 GLN cc_start: 0.8695 (mt0) cc_final: 0.8379 (mt0) REVERT: Q 59 GLN cc_start: 0.8352 (tt0) cc_final: 0.7495 (mt0) REVERT: Q 71 GLN cc_start: 0.8527 (tp40) cc_final: 0.8064 (tm-30) REVERT: Q 101 PHE cc_start: 0.7604 (m-80) cc_final: 0.7153 (m-80) REVERT: R 21 ARG cc_start: 0.8928 (ttm170) cc_final: 0.8209 (ttm170) REVERT: R 84 ARG cc_start: 0.8858 (ptp90) cc_final: 0.8569 (ttp80) REVERT: R 86 GLN cc_start: 0.8014 (mm-40) cc_final: 0.7736 (mm-40) REVERT: R 97 LYS cc_start: 0.8945 (tttt) cc_final: 0.8724 (ttpt) REVERT: S 82 MET cc_start: 0.7124 (mtt) cc_final: 0.6742 (mmt) REVERT: T 21 SER cc_start: 0.9028 (m) cc_final: 0.8752 (p) REVERT: T 73 ARG cc_start: 0.7981 (ttm110) cc_final: 0.7310 (ptp-110) REVERT: T 76 ARG cc_start: 0.7395 (ttp80) cc_final: 0.7100 (ttp80) REVERT: T 77 ARG cc_start: 0.8167 (mtt180) cc_final: 0.7785 (mtp180) REVERT: U 22 ARG cc_start: 0.8012 (mtp180) cc_final: 0.7552 (mtm180) REVERT: U 31 SER cc_start: 0.9135 (p) cc_final: 0.8903 (p) REVERT: U 74 ASN cc_start: 0.9336 (t0) cc_final: 0.9046 (t0) REVERT: W 39 ARG cc_start: 0.8348 (mtp85) cc_final: 0.8022 (mtt180) REVERT: W 76 ASN cc_start: 0.8107 (m-40) cc_final: 0.7658 (m110) REVERT: X 20 HIS cc_start: 0.7438 (t70) cc_final: 0.7003 (t70) REVERT: X 23 ASN cc_start: 0.8847 (m110) cc_final: 0.8565 (m-40) REVERT: X 62 LYS cc_start: 0.9111 (mttt) cc_final: 0.8797 (mttm) REVERT: X 65 ASP cc_start: 0.7572 (p0) cc_final: 0.7338 (p0) REVERT: X 71 LEU cc_start: 0.8383 (mt) cc_final: 0.8171 (mm) REVERT: Y 13 GLU cc_start: 0.7626 (mt-10) cc_final: 0.7381 (mt-10) REVERT: Y 49 ASP cc_start: 0.8648 (m-30) cc_final: 0.8102 (m-30) REVERT: Y 58 ASN cc_start: 0.7989 (m-40) cc_final: 0.7225 (m110) REVERT: Z 21 LYS cc_start: 0.9061 (mttt) cc_final: 0.8521 (mtmm) REVERT: Z 37 GLU cc_start: 0.7443 (tp30) cc_final: 0.7242 (tp30) REVERT: b 36 GLU cc_start: 0.8428 (pt0) cc_final: 0.7815 (pt0) REVERT: c 27 LYS cc_start: 0.8560 (mttt) cc_final: 0.8212 (tmmt) REVERT: c 53 LYS cc_start: 0.7691 (ttmm) cc_final: 0.7072 (pttm) REVERT: e 28 ASN cc_start: 0.8987 (m-40) cc_final: 0.8719 (m-40) REVERT: f 30 GLU cc_start: 0.8524 (tp30) cc_final: 0.7476 (mp0) REVERT: g 6 MET cc_start: 0.6501 (ttm) cc_final: 0.6193 (mpp) REVERT: g 27 MET cc_start: 0.7877 (mmm) cc_final: 0.7618 (mmp) REVERT: g 74 ARG cc_start: 0.8315 (mmp80) cc_final: 0.6821 (ttp80) REVERT: g 78 GLU cc_start: 0.7944 (pm20) cc_final: 0.7640 (pm20) REVERT: g 89 GLN cc_start: 0.8311 (mm-40) cc_final: 0.7190 (mm110) REVERT: g 109 GLN cc_start: 0.8004 (mm-40) cc_final: 0.7662 (mm-40) REVERT: g 135 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8640 (tp) REVERT: g 152 LYS cc_start: 0.8498 (pttt) cc_final: 0.8076 (tmtt) REVERT: h 79 LYS cc_start: 0.7589 (mmtm) cc_final: 0.6938 (tmtt) REVERT: h 122 SER cc_start: 0.9261 (m) cc_final: 0.8744 (p) REVERT: h 142 MET cc_start: 0.7452 (mmm) cc_final: 0.7237 (mmm) REVERT: h 184 TYR cc_start: 0.9108 (t80) cc_final: 0.8439 (t80) REVERT: h 208 LEU cc_start: 0.7848 (OUTLIER) cc_final: 0.7586 (mm) REVERT: i 48 LEU cc_start: 0.7332 (tp) cc_final: 0.6874 (mp) REVERT: i 69 GLU cc_start: 0.7951 (tp30) cc_final: 0.7311 (tp30) REVERT: i 95 GLU cc_start: 0.8175 (mm-30) cc_final: 0.7546 (mm-30) REVERT: i 107 PHE cc_start: 0.8088 (m-80) cc_final: 0.7788 (m-80) REVERT: i 200 ILE cc_start: 0.6992 (mp) cc_final: 0.6713 (mm) REVERT: j 61 GLN cc_start: 0.8469 (mm110) cc_final: 0.8161 (mm110) REVERT: j 62 LYS cc_start: 0.8192 (mttt) cc_final: 0.7757 (ttmm) REVERT: j 81 LEU cc_start: 0.9232 (mt) cc_final: 0.9025 (mt) REVERT: j 106 ILE cc_start: 0.8903 (mt) cc_final: 0.8464 (tp) REVERT: k 4 TYR cc_start: 0.9019 (m-80) cc_final: 0.8569 (m-80) REVERT: k 5 GLU cc_start: 0.8557 (tt0) cc_final: 0.8237 (tt0) REVERT: k 9 MET cc_start: 0.8049 (mtp) cc_final: 0.7762 (mtt) REVERT: k 30 THR cc_start: 0.7865 (m) cc_final: 0.7527 (t) REVERT: k 33 GLU cc_start: 0.8093 (mp0) cc_final: 0.7704 (mp0) REVERT: k 35 LYS cc_start: 0.8025 (mmtt) cc_final: 0.7253 (mtpp) REVERT: k 55 HIS cc_start: 0.7188 (m90) cc_final: 0.6697 (m-70) REVERT: k 64 VAL cc_start: 0.9139 (t) cc_final: 0.8889 (m) REVERT: k 75 GLU cc_start: 0.7286 (mt-10) cc_final: 0.7013 (mt-10) REVERT: l 37 SER cc_start: 0.7396 (t) cc_final: 0.6775 (p) REVERT: l 42 ILE cc_start: 0.8575 (tp) cc_final: 0.8051 (mm) REVERT: l 48 GLU cc_start: 0.8488 (tm-30) cc_final: 0.7917 (tm-30) REVERT: l 50 LEU cc_start: 0.7208 (OUTLIER) cc_final: 0.6936 (tm) REVERT: l 86 GLN cc_start: 0.7154 (mm110) cc_final: 0.5912 (mm-40) REVERT: m 18 GLN cc_start: 0.8661 (mm-40) cc_final: 0.7975 (mm-40) REVERT: m 52 GLU cc_start: 0.7653 (OUTLIER) cc_final: 0.6966 (tm-30) REVERT: m 67 GLN cc_start: 0.7739 (mt0) cc_final: 0.7422 (mt0) REVERT: n 57 MET cc_start: 0.7490 (mpp) cc_final: 0.7037 (mmm) REVERT: n 80 ARG cc_start: 0.9005 (ttp-170) cc_final: 0.8671 (ttp80) REVERT: n 88 MET cc_start: 0.7493 (mmt) cc_final: 0.7248 (mmm) REVERT: n 114 LYS cc_start: 0.8841 (tttm) cc_final: 0.8445 (tmtm) REVERT: n 124 ARG cc_start: 0.8671 (ttm110) cc_final: 0.8399 (ttp-110) REVERT: o 31 ARG cc_start: 0.8222 (ptt-90) cc_final: 0.7836 (ptt-90) REVERT: o 69 THR cc_start: 0.9141 (m) cc_final: 0.8927 (p) REVERT: o 82 LYS cc_start: 0.8357 (tttp) cc_final: 0.8124 (tmtt) REVERT: o 99 GLN cc_start: 0.7802 (tp40) cc_final: 0.7458 (tp40) REVERT: p 15 GLN cc_start: 0.8189 (tp-100) cc_final: 0.7678 (tp40) REVERT: p 61 PHE cc_start: 0.9160 (t80) cc_final: 0.8787 (t80) REVERT: p 80 LYS cc_start: 0.8402 (mptt) cc_final: 0.8010 (mptt) REVERT: r 46 SER cc_start: 0.8467 (m) cc_final: 0.8259 (p) REVERT: r 54 ASP cc_start: 0.7515 (t70) cc_final: 0.7127 (t0) REVERT: r 75 MET cc_start: 0.8366 (tpt) cc_final: 0.8088 (tpp) REVERT: s 10 GLU cc_start: 0.7719 (tp30) cc_final: 0.7373 (tp30) REVERT: s 43 ASN cc_start: 0.8544 (m-40) cc_final: 0.7808 (m110) REVERT: s 79 LEU cc_start: 0.8387 (mt) cc_final: 0.8056 (mt) REVERT: t 40 GLN cc_start: 0.8281 (mm-40) cc_final: 0.7896 (mm-40) REVERT: t 48 LYS cc_start: 0.8426 (mmtm) cc_final: 0.8121 (mtpt) REVERT: t 67 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8647 (mm) REVERT: t 80 GLN cc_start: 0.8444 (pt0) cc_final: 0.8190 (pt0) REVERT: u 5 ARG cc_start: 0.8027 (ptp-170) cc_final: 0.7684 (ptp90) REVERT: u 56 ARG cc_start: 0.8614 (mmm160) cc_final: 0.8344 (mmm-85) REVERT: u 76 LYS cc_start: 0.8892 (ttmt) cc_final: 0.8652 (ptmt) REVERT: v 6 ARG cc_start: 0.6345 (mtt90) cc_final: 0.5883 (mtt90) REVERT: v 11 ARG cc_start: 0.7776 (ttm-80) cc_final: 0.7488 (ttm-80) REVERT: w 54 GLN cc_start: 0.8545 (pt0) cc_final: 0.8207 (pt0) REVERT: w 57 ARG cc_start: 0.8985 (ttm170) cc_final: 0.8583 (mtm180) REVERT: x 7 LYS cc_start: 0.8828 (mtpt) cc_final: 0.8515 (ttpt) REVERT: x 37 ARG cc_start: 0.7896 (ptt180) cc_final: 0.7496 (ptt180) REVERT: x 41 PHE cc_start: 0.7755 (m-10) cc_final: 0.7459 (m-10) REVERT: x 71 LEU cc_start: 0.9365 (mt) cc_final: 0.8959 (mt) REVERT: x 80 TYR cc_start: 0.7997 (t80) cc_final: 0.7653 (t80) REVERT: y 51 PHE cc_start: 0.8266 (t80) cc_final: 0.7855 (t80) REVERT: z 17 ARG cc_start: 0.8485 (ttm110) cc_final: 0.8141 (tpt170) REVERT: A 112 PHE cc_start: 0.8811 (m-80) cc_final: 0.8512 (m-80) REVERT: A 114 GLU cc_start: 0.7872 (mt-10) cc_final: 0.7372 (mt-10) REVERT: A 123 GLU cc_start: 0.8178 (tm-30) cc_final: 0.7908 (tm-30) REVERT: A 137 ARG cc_start: 0.8652 (mmm-85) cc_final: 0.7950 (mmt-90) REVERT: A 169 ASP cc_start: 0.7099 (t70) cc_final: 0.6837 (t70) REVERT: A 176 LYS cc_start: 0.8805 (ptpt) cc_final: 0.8468 (pttt) REVERT: A 193 GLN cc_start: 0.7671 (mt0) cc_final: 0.7159 (tm-30) REVERT: A 206 MET cc_start: 0.8629 (mtp) cc_final: 0.8359 (mtm) REVERT: A 256 GLU cc_start: 0.8132 (mt-10) cc_final: 0.7657 (tt0) REVERT: A 274 LEU cc_start: 0.8497 (mt) cc_final: 0.8294 (tt) REVERT: A 277 ARG cc_start: 0.7171 (mtt180) cc_final: 0.6556 (mtm110) REVERT: A 288 GLN cc_start: 0.7700 (mm-40) cc_final: 0.7407 (mm-40) REVERT: A 311 ASN cc_start: 0.8449 (t0) cc_final: 0.7651 (t0) REVERT: A 352 GLN cc_start: 0.6319 (pt0) cc_final: 0.4055 (tm-30) outliers start: 182 outliers final: 145 residues processed: 1724 average time/residue: 1.3095 time to fit residues: 3892.4281 Evaluate side-chains 1752 residues out of total 4880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 1593 time to evaluate : 6.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 26 LYS Chi-restraints excluded: chain B residue 38 SER Chi-restraints excluded: chain B residue 70 ASN Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 185 GLU Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 67 ARG Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain D residue 115 GLN Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain E residue 23 ASN Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 87 CYS Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain E residue 175 PHE Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 121 ILE Chi-restraints excluded: chain F residue 122 THR Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain F residue 155 GLU Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 60 ASP Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain J residue 96 ARG Chi-restraints excluded: chain K residue 92 GLU Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain L residue 51 GLU Chi-restraints excluded: chain L residue 100 ILE Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 30 SER Chi-restraints excluded: chain M residue 42 THR Chi-restraints excluded: chain M residue 111 GLU Chi-restraints excluded: chain M residue 132 THR Chi-restraints excluded: chain N residue 2 ARG Chi-restraints excluded: chain N residue 13 ASN Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain N residue 33 ILE Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain O residue 28 VAL Chi-restraints excluded: chain P residue 2 SER Chi-restraints excluded: chain P residue 114 LEU Chi-restraints excluded: chain R residue 38 VAL Chi-restraints excluded: chain R residue 39 LEU Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain R residue 58 VAL Chi-restraints excluded: chain S residue 3 THR Chi-restraints excluded: chain S residue 67 ASP Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain S residue 108 SER Chi-restraints excluded: chain T residue 50 LEU Chi-restraints excluded: chain U residue 12 ILE Chi-restraints excluded: chain U residue 28 VAL Chi-restraints excluded: chain U residue 49 VAL Chi-restraints excluded: chain U residue 52 LEU Chi-restraints excluded: chain V residue 4 ILE Chi-restraints excluded: chain V residue 17 SER Chi-restraints excluded: chain V residue 38 LEU Chi-restraints excluded: chain V residue 40 ILE Chi-restraints excluded: chain V residue 61 LEU Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain W residue 21 LEU Chi-restraints excluded: chain W residue 31 VAL Chi-restraints excluded: chain X residue 8 THR Chi-restraints excluded: chain Y residue 11 VAL Chi-restraints excluded: chain Z residue 57 VAL Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain b residue 10 ARG Chi-restraints excluded: chain b residue 28 LEU Chi-restraints excluded: chain b residue 39 LEU Chi-restraints excluded: chain b residue 54 VAL Chi-restraints excluded: chain c residue 42 VAL Chi-restraints excluded: chain e residue 38 THR Chi-restraints excluded: chain e residue 51 SER Chi-restraints excluded: chain g residue 88 ASP Chi-restraints excluded: chain g residue 135 LEU Chi-restraints excluded: chain g residue 199 VAL Chi-restraints excluded: chain h residue 66 VAL Chi-restraints excluded: chain h residue 102 ASN Chi-restraints excluded: chain h residue 149 ILE Chi-restraints excluded: chain h residue 161 GLU Chi-restraints excluded: chain h residue 165 THR Chi-restraints excluded: chain h residue 177 THR Chi-restraints excluded: chain h residue 188 GLU Chi-restraints excluded: chain h residue 192 THR Chi-restraints excluded: chain h residue 208 LEU Chi-restraints excluded: chain i residue 11 LEU Chi-restraints excluded: chain i residue 124 MET Chi-restraints excluded: chain i residue 173 VAL Chi-restraints excluded: chain i residue 201 VAL Chi-restraints excluded: chain j residue 22 SER Chi-restraints excluded: chain j residue 32 SER Chi-restraints excluded: chain j residue 88 VAL Chi-restraints excluded: chain j residue 94 VAL Chi-restraints excluded: chain j residue 96 MET Chi-restraints excluded: chain j residue 149 SER Chi-restraints excluded: chain k residue 7 VAL Chi-restraints excluded: chain k residue 54 LEU Chi-restraints excluded: chain k residue 85 ILE Chi-restraints excluded: chain k residue 92 THR Chi-restraints excluded: chain k residue 96 VAL Chi-restraints excluded: chain k residue 97 THR Chi-restraints excluded: chain l residue 50 LEU Chi-restraints excluded: chain l residue 59 LEU Chi-restraints excluded: chain l residue 91 VAL Chi-restraints excluded: chain m residue 12 THR Chi-restraints excluded: chain m residue 38 ASN Chi-restraints excluded: chain m residue 51 VAL Chi-restraints excluded: chain m residue 52 GLU Chi-restraints excluded: chain m residue 79 SER Chi-restraints excluded: chain m residue 83 LEU Chi-restraints excluded: chain m residue 112 THR Chi-restraints excluded: chain n residue 35 LEU Chi-restraints excluded: chain n residue 63 LEU Chi-restraints excluded: chain n residue 94 LEU Chi-restraints excluded: chain o residue 54 SER Chi-restraints excluded: chain o residue 74 VAL Chi-restraints excluded: chain p residue 31 ILE Chi-restraints excluded: chain p residue 46 THR Chi-restraints excluded: chain p residue 58 SER Chi-restraints excluded: chain p residue 111 THR Chi-restraints excluded: chain q residue 34 CYS Chi-restraints excluded: chain q residue 70 GLU Chi-restraints excluded: chain q residue 82 ILE Chi-restraints excluded: chain q residue 119 VAL Chi-restraints excluded: chain r residue 39 ILE Chi-restraints excluded: chain r residue 65 VAL Chi-restraints excluded: chain s residue 16 LEU Chi-restraints excluded: chain s residue 34 VAL Chi-restraints excluded: chain t residue 42 HIS Chi-restraints excluded: chain t residue 67 LEU Chi-restraints excluded: chain t residue 70 LEU Chi-restraints excluded: chain t residue 89 ARG Chi-restraints excluded: chain u residue 2 VAL Chi-restraints excluded: chain u residue 3 THR Chi-restraints excluded: chain v residue 38 ILE Chi-restraints excluded: chain v residue 67 LEU Chi-restraints excluded: chain w residue 71 THR Chi-restraints excluded: chain x residue 64 ASP Chi-restraints excluded: chain x residue 79 THR Chi-restraints excluded: chain y residue 30 THR Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain A residue 347 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1034 random chunks: chunk 651 optimal weight: 10.0000 chunk 873 optimal weight: 5.9990 chunk 251 optimal weight: 10.0000 chunk 756 optimal weight: 3.9990 chunk 121 optimal weight: 10.0000 chunk 227 optimal weight: 10.0000 chunk 821 optimal weight: 8.9990 chunk 343 optimal weight: 20.0000 chunk 843 optimal weight: 10.0000 chunk 104 optimal weight: 40.0000 chunk 151 optimal weight: 20.0000 overall best weight: 7.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 163 GLN B 239 ASN ** C 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 128 GLN ** N 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 6 GLN h 8 ASN i 140 ASN k 52 ASN ** k 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 130 ASN l 148 ASN s 66 GLN t 42 HIS y 13 GLN y 82 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.108905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.074565 restraints weight = 306398.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.076189 restraints weight = 137175.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.076137 restraints weight = 88690.111| |-----------------------------------------------------------------------------| r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2852 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2852 r_free = 0.2852 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2852 r_free = 0.2852 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2852 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.3424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.070 158938 Z= 0.402 Angle : 0.705 14.158 237562 Z= 0.368 Chirality : 0.039 0.280 30220 Planarity : 0.007 0.137 12875 Dihedral : 23.416 179.351 78945 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.39 % Favored : 94.59 % Rotamer: Outliers : 4.47 % Allowed : 23.42 % Favored : 72.11 % 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: 5863 helix: 0.37 (0.12), residues: 1914 sheet: -0.98 (0.16), residues: 1087 loop : -1.24 (0.11), residues: 2862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP k 42 HIS 0.012 0.002 HIS S 102 PHE 0.038 0.003 PHE l 18 TYR 0.026 0.002 TYR B 103 ARG 0.014 0.001 ARG n 124 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 51154.33 seconds wall clock time: 889 minutes 41.47 seconds (53381.47 seconds total)