Starting phenix.real_space_refine on Sun Feb 25 08:52:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6osq_20187/02_2024/6osq_20187_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6osq_20187/02_2024/6osq_20187.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6osq_20187/02_2024/6osq_20187_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6osq_20187/02_2024/6osq_20187_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6osq_20187/02_2024/6osq_20187_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6osq_20187/02_2024/6osq_20187.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6osq_20187/02_2024/6osq_20187.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6osq_20187/02_2024/6osq_20187_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6osq_20187/02_2024/6osq_20187_updated.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.016 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 436 5.21 5 S 157 5.16 5 C 73663 2.51 5 N 27283 2.21 5 O 40573 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 "O PHE 117": "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 "S ARG 84": "NH1" <-> "NH2" Residue "S ARG 88": "NH1" <-> "NH2" Residue "S ARG 92": "NH1" <-> "NH2" Residue "S ARG 110": "NH1" <-> "NH2" Residue "T ARG 3": "NH1" <-> "NH2" Residue "T ARG 6": "NH1" <-> "NH2" Residue "U ARG 6": "NH1" <-> "NH2" Residue "U ARG 82": "NH1" <-> "NH2" Residue "U ARG 86": "NH1" <-> "NH2" Residue "U ARG 94": "NH1" <-> "NH2" Residue "V ARG 19": "NH1" <-> "NH2" Residue "X ARG 3": "NH1" <-> "NH2" Residue "X ARG 18": "NH1" <-> "NH2" Residue "X ARG 37": "NH1" <-> "NH2" Residue "X ARG 45": "NH1" <-> "NH2" Residue "X ARG 50": "NH1" <-> "NH2" Residue "X ARG 57": "NH1" <-> "NH2" Residue "X ARG 74": "NH1" <-> "NH2" Residue "Y ARG 29": "NH1" <-> "NH2" Residue "Y ARG 47": "NH1" <-> "NH2" Residue "Y ARG 52": "NH1" <-> "NH2" Residue "Z ARG 11": "NH1" <-> "NH2" Residue "Z ARG 30": "NH1" <-> "NH2" Residue "Z ARG 45": "NH1" <-> "NH2" Residue "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 PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u ARG 51": "NH1" <-> "NH2" Residue "v ARG 11": "NH1" <-> "NH2" Residue "v ARG 27": "NH1" <-> "NH2" Residue "v ARG 65": "NH1" <-> "NH2" Residue "v ARG 77": "NH1" <-> "NH2" Residue "w ARG 61": "NH1" <-> "NH2" Residue "x ARG 32": "NH1" <-> "NH2" Residue "y ARG 60": "NH1" <-> "NH2" Residue "y ARG 74": "NH1" <-> "NH2" Residue "z ARG 33": "NH1" <-> "NH2" Residue "z ARG 45": "NH1" <-> "NH2" Residue "z ARG 55": "NH1" <-> "NH2" Residue "z ARG 62": "NH1" <-> "NH2" Residue "z ARG 67": "NH1" <-> "NH2" Residue "z ARG 69": "NH1" <-> "NH2" Residue "A ARG 137": "NH1" <-> "NH2" Residue "A ARG 142": "NH1" <-> "NH2" Residue "A ARG 195": "NH1" <-> "NH2" Residue "A GLU 213": "OE1" <-> "OE2" Residue "A ARG 294": "NH1" <-> "NH2" Residue "A ARG 316": "NH1" <-> "NH2" Time to flip residues: 0.25s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 146756 Number of models: 1 Model: "" Number of chains: 68 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: "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': 5, 'rna2p_pyr': 6, 'rna3p': 3, 'rna3p_pur': 35, '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: "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: "1" Number of atoms: 289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 289 Unusual residues: {' MG': 289} Classifications: {'undetermined': 289} Link IDs: {None: 288} Chain: "2" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 126 Unusual residues: {' MG': 126} Classifications: {'undetermined': 126} Link IDs: {None: 125} 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: "5" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" 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} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "Q" 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: "h" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "i" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM A0HM9 SG CYS a 16 71.871 78.232 68.907 1.00 63.05 S ATOM A0HML SG CYS a 18 69.537 78.203 65.265 1.00 61.89 S ATOM A0HQJ SG CYS a 37 73.193 79.787 65.875 1.00 54.45 S ATOM A0HR4 SG CYS a 40 70.875 81.604 68.168 1.00 63.34 S ATOM A0JC5 SG CYS f 11 137.315 167.171 59.772 1.00 33.05 S ATOM A0JCU SG CYS f 14 140.711 166.012 60.006 1.00 33.66 S ATOM A0JFP SG CYS f 27 140.734 169.468 61.082 1.00 34.64 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb="MG MG 13145 " occ=0.50 Time building chain proxies: 57.98, per 1000 atoms: 0.40 Number of scatterers: 146756 At special positions: 0 Unit cell: (285.52, 273.9, 227.42, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 157 16.00 P 4642 15.00 Mg 436 11.99 O 40573 8.00 N 27283 7.00 C 73663 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: 63.50 Conformation dependent library (CDL) restraints added in 7.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN a 101 " pdb="ZN ZN a 101 " - pdb=" SG CYS a 40 " pdb="ZN ZN a 101 " - pdb=" SG CYS a 18 " pdb="ZN ZN a 101 " - pdb=" SG CYS a 37 " 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 14 " pdb="ZN ZN f 102 " - pdb=" SG CYS f 27 " pdb="ZN ZN f 102 " - pdb=" SG CYS f 11 " Number of angles added : 9 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: 10958 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: 178 helices and 67 sheets defined 38.7% alpha, 19.3% beta 1271 base pairs and 2575 stacking pairs defined. Time for finding SS restraints: 78.46 Creating SS restraints... Processing helix chain 'B' and resid 10 through 17 removed outlier: 7.569A pdb=" N HIS B 15 " --> pdb=" O PRO B 11 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N VAL B 16 " --> pdb=" O GLY B 12 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N VAL B 17 " --> pdb=" O ARG B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 35 removed outlier: 3.835A pdb=" N LEU B 34 " --> pdb=" O PHE B 30 " (cutoff:3.500A) removed outlier: 5.943A 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 Proline residue: B 136 - end of helix Processing helix chain 'B' and resid 207 through 215 removed outlier: 4.164A pdb=" N ALA B 211 " --> pdb=" O LYS B 207 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ARG B 212 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TRP B 213 " --> pdb=" O GLY B 209 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ARG B 214 " --> pdb=" O ALA B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 226 removed outlier: 4.411A pdb=" N MET B 225 " --> pdb=" O ARG B 221 " (cutoff:3.500A) removed outlier: 5.651A 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: 4.244A pdb=" N ASP B 264 " --> pdb=" O ASN B 260 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N LYS B 265 " --> pdb=" O LYS B 261 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N PHE B 266 " --> pdb=" O ARG B 262 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N ILE B 267 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 5.645A 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: 4.597A pdb=" N MET B 201 " --> pdb=" O ALA B 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 61 removed outlier: 6.327A pdb=" N THR C 61 " --> pdb=" O ALA C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 72 removed outlier: 3.657A pdb=" N HIS C 67 " --> pdb=" O PRO C 63 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N PHE C 68 " --> pdb=" O GLU C 64 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS C 70 " --> pdb=" O GLY C 66 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ALA C 71 " --> pdb=" O HIS C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 103 removed outlier: 3.966A pdb=" N ALA C 102 " --> pdb=" O VAL C 98 " (cutoff:3.500A) removed outlier: 5.140A 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 39 through 44 Processing helix chain 'C' and resid 120 through 126 removed outlier: 4.578A 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: 3.938A pdb=" N GLY D 38 " --> pdb=" O ALA D 34 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA D 39 " --> pdb=" O TYR D 35 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ARG D 40 " --> pdb=" O ALA D 36 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N GLN D 41 " --> pdb=" O ALA D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 116 removed outlier: 3.641A pdb=" N GLY D 103 " --> pdb=" O LYS D 99 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER D 107 " --> pdb=" O GLY D 103 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N SER D 110 " --> pdb=" O LYS D 106 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL D 113 " --> pdb=" O LEU D 109 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ARG D 114 " --> pdb=" O SER D 110 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASP D 116 " --> pdb=" O LEU D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 142 removed outlier: 3.734A pdb=" N LEU D 134 " --> pdb=" O LYS D 130 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLN D 136 " --> pdb=" O LYS D 132 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LYS D 139 " --> pdb=" O ALA D 135 " (cutoff:3.500A) Processing helix chain 'D' and resid 154 through 163 removed outlier: 3.512A pdb=" N ALA D 161 " --> pdb=" O LEU D 157 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ARG D 162 " --> pdb=" O PHE D 158 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N ASN D 163 " --> pdb=" O LEU D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 184 removed outlier: 4.192A pdb=" N ILE D 181 " --> pdb=" O PRO D 177 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N PHE D 183 " --> pdb=" O SER D 179 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ASP D 184 " --> pdb=" O LEU D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 201 removed outlier: 4.110A pdb=" N LYS D 194 " --> pdb=" O ALA D 190 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 21 removed outlier: 3.670A pdb=" N ASP E 10 " --> pdb=" O ASP E 6 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU E 11 " --> pdb=" O TYR E 7 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N VAL E 13 " --> pdb=" O LYS E 9 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N LYS E 14 " --> pdb=" O ASP E 10 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 62 removed outlier: 4.575A pdb=" N LEU E 50 " --> pdb=" O ASP E 46 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASN E 52 " --> pdb=" O LYS E 48 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ALA E 53 " --> pdb=" O LEU E 49 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ILE E 60 " --> pdb=" O ASP E 56 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLY E 62 " --> pdb=" O ALA E 58 " (cutoff:3.500A) Processing helix chain 'E' and resid 93 through 111 removed outlier: 3.548A pdb=" N GLU E 98 " --> pdb=" O GLU E 94 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N PHE E 99 " --> pdb=" O ARG E 95 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE E 104 " --> pdb=" O PHE E 100 " (cutoff:3.500A) removed outlier: 5.431A 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 162 through 174 removed outlier: 4.799A pdb=" N GLY E 166 " --> pdb=" O SER E 162 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA E 171 " --> pdb=" O ARG E 167 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N PHE E 173 " --> pdb=" O LEU E 169 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASP E 174 " --> pdb=" O LEU E 170 " (cutoff:3.500A) Processing helix chain 'E' and resid 134 through 139 removed outlier: 3.689A pdb=" N ILE E 137 " --> pdb=" O GLU E 134 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N PHE E 138 " --> pdb=" O GLN E 135 " (cutoff:3.500A) Proline residue: E 139 - end of helix No H-bonds generated for 'chain 'E' and resid 134 through 139' Processing helix chain 'F' and resid 2 through 8 removed outlier: 4.267A pdb=" N ALA F 7 " --> pdb=" O ARG F 3 " (cutoff:3.500A) Proline residue: F 8 - end of helix Processing helix chain 'F' and resid 60 through 81 removed outlier: 3.559A pdb=" N SER F 74 " --> pdb=" O ALA F 70 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ILE F 77 " --> pdb=" O ASN F 73 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 153 removed outlier: 3.696A pdb=" N TYR F 151 " --> pdb=" O ASP F 147 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N ARG F 152 " --> pdb=" O LEU F 148 " (cutoff:3.500A) Processing helix chain 'G' and resid 22 through 29 removed outlier: 3.576A pdb=" N ARG G 27 " --> pdb=" O ALA G 23 " (cutoff:3.500A) Processing helix chain 'G' and resid 40 through 48 removed outlier: 4.035A pdb=" N GLU G 45 " --> pdb=" O LYS G 41 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N PHE G 46 " --> pdb=" O LYS G 42 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N PHE G 47 " --> pdb=" O ASN G 43 " (cutoff:3.500A) Processing helix chain 'G' and resid 51 through 74 removed outlier: 3.681A pdb=" N GLU G 55 " --> pdb=" O ARG G 51 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N ALA G 56 " --> pdb=" O ALA G 52 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LYS G 57 " --> pdb=" O GLU G 53 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU G 58 " --> pdb=" O LEU G 54 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLU G 60 " --> pdb=" O ALA G 56 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL G 61 " --> pdb=" O LYS G 57 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ALA G 63 " --> pdb=" O ALA G 59 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ALA G 65 " --> pdb=" O VAL G 61 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ASN G 66 " --> pdb=" O LEU G 62 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ALA G 67 " --> pdb=" O ALA G 63 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ARG G 68 " --> pdb=" O ALA G 64 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N ILE G 72 " --> pdb=" O ARG G 68 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N ASN G 73 " --> pdb=" O ALA G 69 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N ALA G 74 " --> pdb=" O GLU G 70 " (cutoff:3.500A) Processing helix chain 'G' and resid 95 through 107 removed outlier: 3.884A pdb=" N ILE G 99 " --> pdb=" O GLY G 95 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA G 102 " --> pdb=" O ASP G 98 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N THR G 104 " --> pdb=" O ALA G 100 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLY G 107 " --> pdb=" O VAL G 103 " (cutoff:3.500A) Processing helix chain 'J' and resid 24 through 38 removed outlier: 4.690A pdb=" N GLU J 31 " --> pdb=" O ARG J 27 " (cutoff:3.500A) Processing helix chain 'J' and resid 88 through 96 removed outlier: 3.547A pdb=" N ALA J 94 " --> pdb=" O GLU J 90 " (cutoff:3.500A) Processing helix chain 'J' and resid 97 through 110 removed outlier: 4.876A pdb=" N ILE J 101 " --> pdb=" O PRO J 97 " (cutoff:3.500A) Proline residue: J 110 - end of helix Processing helix chain 'J' and resid 112 through 123 removed outlier: 3.664A pdb=" N ALA J 117 " --> pdb=" O PRO J 113 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N PHE J 119 " --> pdb=" O GLY J 115 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG J 120 " --> pdb=" O ARG J 116 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N LYS J 121 " --> pdb=" O ALA J 117 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N LEU J 122 " --> pdb=" O MET J 118 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N LYS J 123 " --> pdb=" O PHE J 119 " (cutoff:3.500A) Processing helix chain 'K' and resid 112 through 119 removed outlier: 3.568A pdb=" N ILE K 116 " --> pdb=" O PHE K 112 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N LEU K 118 " --> pdb=" O LYS K 114 " (cutoff:3.500A) Processing helix chain 'L' and resid 56 through 62 Proline residue: L 62 - end of helix Processing helix chain 'L' and resid 68 through 75 removed outlier: 4.313A pdb=" N ALA L 72 " --> pdb=" O SER L 68 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N ILE L 73 " --> pdb=" O ARG L 69 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N THR L 74 " --> pdb=" O LYS L 70 " (cutoff:3.500A) removed outlier: 5.668A 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: 3.837A pdb=" N LEU L 82 " --> pdb=" O ARG L 78 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ALA L 83 " --> pdb=" O LEU L 79 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N LYS L 84 " --> pdb=" O SER L 80 " (cutoff:3.500A) removed outlier: 4.519A 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: 4.157A pdb=" N LEU L 95 " --> pdb=" O ASP L 91 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ALA L 97 " --> pdb=" O ASN L 93 " (cutoff:3.500A) Processing helix chain 'L' and resid 128 through 139 removed outlier: 3.724A pdb=" N ALA L 133 " --> pdb=" O LYS L 129 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ALA L 134 " --> pdb=" O GLY L 130 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE L 135 " --> pdb=" O ALA L 131 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ALA L 138 " --> pdb=" O ALA L 134 " (cutoff:3.500A) Processing helix chain 'M' and resid 42 through 58 removed outlier: 3.617A pdb=" N ILE M 46 " --> pdb=" O THR M 42 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLU M 47 " --> pdb=" O ALA M 43 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA M 52 " --> pdb=" O ALA M 48 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N MET M 53 " --> pdb=" O ALA M 49 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA M 56 " --> pdb=" O ALA M 52 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL M 57 " --> pdb=" O MET M 53 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LYS M 58 " --> pdb=" O THR M 54 " (cutoff:3.500A) Processing helix chain 'M' and resid 109 through 125 removed outlier: 4.350A pdb=" N GLU M 115 " --> pdb=" O GLU M 111 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N PHE M 117 " --> pdb=" O ALA M 113 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYS M 118 " --> pdb=" O ARG M 114 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALA M 120 " --> pdb=" O ALA M 116 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ALA M 122 " --> pdb=" O LYS M 118 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N LYS M 123 " --> pdb=" O LEU M 119 " (cutoff:3.500A) removed outlier: 4.343A 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: 3.741A pdb=" N GLN N 18 " --> pdb=" O SER N 14 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ALA N 19 " --> pdb=" O SER N 15 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ASN N 23 " --> pdb=" O ALA N 19 " (cutoff:3.500A) Processing helix chain 'N' and resid 37 through 57 removed outlier: 4.504A pdb=" N ARG N 46 " --> pdb=" O LYS N 42 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N VAL N 47 " --> pdb=" O GLU N 43 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU N 49 " --> pdb=" O ARG N 45 " (cutoff:3.500A) Proline residue: N 50 - end of helix removed outlier: 4.097A pdb=" N ALA N 55 " --> pdb=" O LEU N 51 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYS N 56 " --> pdb=" O ILE N 52 " (cutoff:3.500A) removed outlier: 5.037A 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: 3.917A pdb=" N ASN N 81 " --> pdb=" O ALA N 77 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU N 83 " --> pdb=" O LEU N 79 " (cutoff:3.500A) removed outlier: 4.160A 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: 4.098A pdb=" N ALA O 6 " --> pdb=" O ASP O 2 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARG O 10 " --> pdb=" O ALA O 6 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N ARG O 13 " --> pdb=" O ARG O 9 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N ALA O 14 " --> pdb=" O ARG O 10 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ARG O 16 " --> pdb=" O THR O 12 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU O 18 " --> pdb=" O ALA O 14 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N GLU O 20 " --> pdb=" O ARG O 16 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLY O 22 " --> pdb=" O LEU O 18 " (cutoff:3.500A) Processing helix chain 'O' and resid 55 through 63 removed outlier: 3.704A pdb=" N GLU O 60 " --> pdb=" O LYS O 56 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N GLN O 61 " --> pdb=" O ALA O 57 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N LEU O 62 " --> pdb=" O ILE O 58 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N LYS O 63 " --> pdb=" O ALA O 59 " (cutoff:3.500A) Processing helix chain 'O' and resid 67 through 86 removed outlier: 3.646A pdb=" N LYS O 76 " --> pdb=" O ALA O 72 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA O 77 " --> pdb=" O ALA O 73 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ALA O 79 " --> pdb=" O GLY O 75 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA O 82 " --> pdb=" O VAL O 78 " (cutoff:3.500A) Processing helix chain 'O' and resid 101 through 114 removed outlier: 3.797A pdb=" N ALA O 109 " --> pdb=" O ALA O 105 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA O 110 " --> pdb=" O LEU O 106 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY O 114 " --> pdb=" O ALA O 110 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 13 removed outlier: 4.399A pdb=" N GLN P 10 " --> pdb=" O LYS P 6 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLU P 11 " --> pdb=" O GLN P 7 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N GLN P 12 " --> pdb=" O LEU P 8 " (cutoff:3.500A) Processing helix chain 'P' and resid 97 through 104 removed outlier: 4.905A pdb=" N ARG P 101 " --> pdb=" O LEU P 97 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N GLU P 102 " --> pdb=" O TYR P 98 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ARG P 103 " --> pdb=" O TYR P 99 " (cutoff:3.500A) removed outlier: 5.328A 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: 3.530A pdb=" N ALA Q 10 " --> pdb=" O ARG Q 6 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LYS Q 16 " --> pdb=" O ALA Q 12 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE Q 17 " --> pdb=" O ARG Q 13 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N LYS Q 22 " --> pdb=" O LEU Q 18 " (cutoff:3.500A) Processing helix chain 'Q' and resid 26 through 31 removed outlier: 4.353A pdb=" N ARG Q 30 " --> pdb=" O GLY Q 26 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL Q 31 " --> pdb=" O ALA Q 27 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 26 through 31' Processing helix chain 'Q' and resid 39 through 73 removed outlier: 3.609A pdb=" N ALA Q 46 " --> pdb=" O ALA Q 42 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N ARG Q 51 " --> pdb=" O TYR Q 47 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N LYS Q 54 " --> pdb=" O ARG Q 50 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ARG Q 55 " --> pdb=" O ARG Q 51 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ARG Q 58 " --> pdb=" O LYS Q 54 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ALA Q 67 " --> pdb=" O ALA Q 63 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ARG Q 70 " --> pdb=" O ASN Q 66 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLN Q 71 " --> pdb=" O ALA Q 67 " (cutoff:3.500A) Processing helix chain 'Q' and resid 75 through 87 removed outlier: 3.863A pdb=" N ASN Q 81 " --> pdb=" O SER Q 77 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLY Q 82 " --> pdb=" O LYS Q 78 " (cutoff:3.500A) Processing helix chain 'Q' and resid 91 through 102 removed outlier: 3.840A pdb=" N ALA Q 96 " --> pdb=" O ARG Q 92 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N VAL Q 100 " --> pdb=" O ALA Q 96 " (cutoff:3.500A) Processing helix chain 'Q' and resid 103 through 118 removed outlier: 3.820A pdb=" N THR Q 107 " --> pdb=" O LYS Q 103 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ALA Q 116 " --> pdb=" O LYS Q 112 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU Q 117 " --> pdb=" O ALA Q 113 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ALA Q 118 " --> pdb=" O LYS Q 114 " (cutoff:3.500A) Processing helix chain 'S' and resid 13 through 25 removed outlier: 4.273A pdb=" N VAL S 17 " --> pdb=" O SER S 13 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ARG S 18 " --> pdb=" O ALA S 14 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU S 19 " --> pdb=" O GLN S 15 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N VAL S 20 " --> pdb=" O LYS S 16 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASP S 22 " --> pdb=" O ARG S 18 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N LEU S 23 " --> pdb=" O LEU S 19 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ILE S 24 " --> pdb=" O VAL S 20 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ARG S 25 " --> pdb=" O ALA S 21 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 39 removed outlier: 3.929A pdb=" N ASP S 34 " --> pdb=" O SER S 30 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N TYR S 38 " --> pdb=" O ASP S 34 " (cutoff:3.500A) Processing helix chain 'S' and resid 41 through 61 removed outlier: 3.952A pdb=" N VAL S 45 " --> pdb=" O LYS S 41 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER S 53 " --> pdb=" O LYS S 49 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA S 58 " --> pdb=" O ALA S 54 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N HIS S 60 " --> pdb=" O ALA S 56 " (cutoff:3.500A) Processing helix chain 'S' and resid 65 through 70 removed outlier: 3.524A pdb=" N LEU S 69 " --> pdb=" O ASP S 65 " (cutoff:3.500A) removed outlier: 6.256A 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: 3.533A pdb=" N LEU T 7 " --> pdb=" O ARG T 3 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LEU T 8 " --> pdb=" O GLU T 4 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LYS T 9 " --> pdb=" O GLU T 5 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N LEU T 11 " --> pdb=" O LEU T 7 " (cutoff:3.500A) Processing helix chain 'T' and resid 17 through 27 removed outlier: 3.515A pdb=" N SER T 21 " --> pdb=" O SER T 17 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N MET T 24 " --> pdb=" O ALA T 20 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLU T 25 " --> pdb=" O SER T 21 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N SER T 27 " --> pdb=" O ALA T 23 " (cutoff:3.500A) Processing helix chain 'T' and resid 39 through 50 removed outlier: 3.591A pdb=" N ILE T 43 " --> pdb=" O THR T 39 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LYS T 44 " --> pdb=" O LYS T 40 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ALA T 46 " --> pdb=" O GLU T 42 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LYS T 49 " --> pdb=" O ALA T 45 " (cutoff:3.500A) Processing helix chain 'U' and resid 66 through 71 removed outlier: 3.715A pdb=" N VAL U 70 " --> pdb=" O GLN U 66 " (cutoff:3.500A) removed outlier: 5.183A 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 removed outlier: 3.611A pdb=" N ARG V 18 " --> pdb=" O LYS V 14 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG V 19 " --> pdb=" O GLY V 15 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ALA V 22 " --> pdb=" O ARG V 18 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA V 23 " --> pdb=" O ARG V 19 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ASN V 24 " --> pdb=" O LEU V 20 " (cutoff:3.500A) Processing helix chain 'V' and resid 43 through 52 removed outlier: 3.889A pdb=" N ASN V 49 " --> pdb=" O ASP V 45 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ALA V 52 " --> pdb=" O MET V 48 " (cutoff:3.500A) Processing helix chain 'V' and resid 53 through 59 removed outlier: 4.434A pdb=" N TYR V 57 " --> pdb=" O LYS V 53 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N SER V 58 " --> pdb=" O ALA V 54 " (cutoff:3.500A) Processing helix chain 'X' and resid 52 through 63 removed outlier: 3.562A pdb=" N MET X 56 " --> pdb=" O SER X 52 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ARG X 57 " --> pdb=" O ALA X 53 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE X 59 " --> pdb=" O GLY X 55 " (cutoff:3.500A) Processing helix chain 'X' and resid 64 through 75 removed outlier: 3.582A pdb=" N ARG X 72 " --> pdb=" O LEU X 68 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ALA X 73 " --> pdb=" O ALA X 69 " (cutoff:3.500A) Processing helix chain 'Y' and resid 2 through 9 removed outlier: 3.532A pdb=" N ARG Y 7 " --> pdb=" O ALA Y 3 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU Y 8 " --> pdb=" O LYS Y 4 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N LYS Y 9 " --> pdb=" O GLU Y 5 " (cutoff:3.500A) Processing helix chain 'Y' and resid 10 through 35 removed outlier: 3.768A pdb=" N ASN Y 15 " --> pdb=" O VAL Y 11 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU Y 19 " --> pdb=" O ASN Y 15 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASN Y 20 " --> pdb=" O THR Y 16 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLN Y 31 " --> pdb=" O ASN Y 27 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA Y 33 " --> pdb=" O ARG Y 29 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N SER Y 34 " --> pdb=" O MET Y 30 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N GLY Y 35 " --> pdb=" O GLN Y 31 " (cutoff:3.500A) Processing helix chain 'Y' and resid 39 through 61 removed outlier: 4.683A pdb=" N LEU Y 43 " --> pdb=" O GLN Y 39 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N LYS Y 44 " --> pdb=" O SER Y 40 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA Y 51 " --> pdb=" O ARG Y 47 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU Y 56 " --> pdb=" O ARG Y 52 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA Y 61 " --> pdb=" O LEU Y 57 " (cutoff:3.500A) Processing helix chain 'Z' and resid 17 through 28 removed outlier: 4.024A pdb=" N LEU Z 24 " --> pdb=" O HIS Z 20 " (cutoff:3.500A) Processing helix chain 'Z' and resid 41 through 52 removed outlier: 3.595A pdb=" N GLY Z 46 " --> pdb=" O PRO Z 42 " (cutoff:3.500A) Processing helix chain 'a' and resid 46 through 51 removed outlier: 4.703A pdb=" N VAL a 51 " --> pdb=" O LYS a 47 " (cutoff:3.500A) Processing helix chain 'a' and resid 55 through 65 removed outlier: 4.106A pdb=" N ARG a 59 " --> pdb=" O GLY a 55 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LYS a 62 " --> pdb=" O ASP a 58 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ARG a 63 " --> pdb=" O ARG a 59 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N PHE a 64 " --> pdb=" O PHE a 60 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N ASN a 65 " --> pdb=" O ASN a 61 " (cutoff:3.500A) Processing helix chain 'b' and resid 9 through 19 removed outlier: 5.088A pdb=" N HIS b 19 " --> pdb=" O MET b 15 " (cutoff:3.500A) Processing helix chain 'c' and resid 26 through 31 Proline residue: c 31 - end of helix No H-bonds generated for 'chain 'c' and resid 26 through 31' Processing helix chain 'd' and resid 8 through 16 Processing helix chain 'd' and resid 17 through 24 removed outlier: 3.699A pdb=" N ALA d 23 " --> pdb=" O ARG d 19 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N THR d 24 " --> pdb=" O ALA d 20 " (cutoff:3.500A) Processing helix chain 'd' and resid 25 through 38 removed outlier: 3.670A pdb=" N ALA d 36 " --> pdb=" O ALA d 32 " (cutoff:3.500A) Processing helix chain 'e' and resid 7 through 14 removed outlier: 3.885A pdb=" N LYS e 12 " --> pdb=" O ARG e 8 " (cutoff:3.500A) Processing helix chain 'e' and resid 32 through 37 removed outlier: 4.757A pdb=" N LYS e 36 " --> pdb=" O ILE e 32 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N ALA e 37 " --> pdb=" O LEU e 33 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 32 through 37' Processing helix chain 'e' and resid 38 through 46 removed outlier: 3.501A pdb=" N HIS e 43 " --> pdb=" O LYS e 39 " (cutoff:3.500A) Proline residue: e 46 - end of helix Processing helix chain 'e' and resid 51 through 63 removed outlier: 4.562A pdb=" N GLY e 56 " --> pdb=" O LYS e 52 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N LEU e 57 " --> pdb=" O GLY e 53 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N VAL e 58 " --> pdb=" O ASP e 54 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE e 59 " --> pdb=" O LEU e 55 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA e 60 " --> pdb=" O GLY e 56 " (cutoff:3.500A) Proline residue: e 63 - end of helix Processing helix chain 'g' and resid 5 through 13 removed outlier: 3.645A pdb=" N ALA g 12 " --> pdb=" O ASP g 8 " (cutoff:3.500A) Processing helix chain 'g' and resid 24 through 29 removed outlier: 4.188A 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 Proline residue: g 48 - end of helix removed outlier: 4.191A pdb=" N GLU g 52 " --> pdb=" O PRO g 48 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLU g 56 " --> pdb=" O GLU g 52 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG g 63 " --> pdb=" O LYS g 59 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LYS g 64 " --> pdb=" O ILE g 60 " (cutoff:3.500A) Processing helix chain 'g' and resid 76 through 88 removed outlier: 3.786A pdb=" N VAL g 80 " --> pdb=" O ALA g 76 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS g 81 " --> pdb=" O SER g 77 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA g 84 " --> pdb=" O VAL g 80 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N CYS g 87 " --> pdb=" O ALA g 83 " (cutoff:3.500A) Processing helix chain 'g' and resid 103 through 123 removed outlier: 5.288A pdb=" N GLN g 109 " --> pdb=" O LYS g 105 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N SER g 110 " --> pdb=" O THR g 106 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER g 121 " --> pdb=" O LEU g 117 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLN g 122 " --> pdb=" O GLU g 118 " (cutoff:3.500A) Processing helix chain 'g' and resid 130 through 148 removed outlier: 3.846A pdb=" N ALA g 134 " --> pdb=" O THR g 130 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU g 135 " --> pdb=" O LYS g 131 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N MET g 136 " --> pdb=" O LYS g 132 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG g 139 " --> pdb=" O LEU g 135 " (cutoff:3.500A) Processing helix chain 'g' and resid 165 through 170 removed outlier: 3.841A pdb=" N GLU g 169 " --> pdb=" O ASP g 165 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N HIS g 170 " --> pdb=" O ALA g 166 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 165 through 170' Processing helix chain 'g' and resid 171 through 180 removed outlier: 3.856A pdb=" N ALA g 176 " --> pdb=" O ALA g 172 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU g 179 " --> pdb=" O GLU g 175 " (cutoff:3.500A) Processing helix chain 'g' and resid 206 through 227 removed outlier: 3.577A pdb=" N LEU g 212 " --> pdb=" O ARG g 208 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA g 216 " --> pdb=" O LEU g 212 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ALA g 219 " --> pdb=" O GLY g 215 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLU g 223 " --> pdb=" O ALA g 219 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLN g 227 " --> pdb=" O GLU g 223 " (cutoff:3.500A) Processing helix chain 'h' and resid 6 through 12 removed outlier: 4.558A pdb=" N ARG h 11 " --> pdb=" O PRO h 7 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU h 12 " --> pdb=" O ASN h 8 " (cutoff:3.500A) Processing helix chain 'h' and resid 28 through 48 removed outlier: 3.709A pdb=" N ASN h 32 " --> pdb=" O GLU h 28 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N SER h 35 " --> pdb=" O ASP h 31 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL h 39 " --> pdb=" O SER h 35 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR h 44 " --> pdb=" O ARG h 40 " (cutoff:3.500A) Processing helix chain 'h' and resid 72 through 78 removed outlier: 4.357A pdb=" N VAL h 76 " --> pdb=" O ARG h 72 " (cutoff:3.500A) Processing helix chain 'h' and resid 81 through 96 removed outlier: 4.115A pdb=" N LYS h 86 " --> pdb=" O GLU h 82 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N VAL h 90 " --> pdb=" O LYS h 86 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL h 91 " --> pdb=" O LEU h 87 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ASP h 93 " --> pdb=" O LYS h 89 " (cutoff:3.500A) Processing helix chain 'h' and resid 108 through 113 removed outlier: 4.030A pdb=" N ASP h 112 " --> pdb=" O LYS h 108 " (cutoff:3.500A) removed outlier: 5.743A 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 removed outlier: 3.519A pdb=" N THR h 121 " --> pdb=" O ALA h 117 " (cutoff:3.500A) Processing helix chain 'h' and resid 129 through 145 removed outlier: 3.817A pdb=" N ARG h 136 " --> pdb=" O ARG h 132 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ALA h 137 " --> pdb=" O ALA h 133 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA h 141 " --> pdb=" O ALA h 137 " (cutoff:3.500A) Processing helix chain 'i' and resid 7 through 16 removed outlier: 4.252A pdb=" N LEU i 11 " --> pdb=" O PRO i 7 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N SER i 12 " --> pdb=" O LYS i 8 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG i 14 " --> pdb=" O LYS i 10 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU i 15 " --> pdb=" O LEU i 11 " (cutoff:3.500A) Processing helix chain 'i' and resid 27 through 32 removed outlier: 3.573A pdb=" N LYS i 31 " --> pdb=" O ALA i 27 " (cutoff:3.500A) Processing helix chain 'i' and resid 49 through 66 removed outlier: 4.806A pdb=" N GLN i 54 " --> pdb=" O ASP i 50 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLU i 57 " --> pdb=" O VAL i 53 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS i 58 " --> pdb=" O GLN i 54 " (cutoff:3.500A) Processing helix chain 'i' and resid 68 through 83 removed outlier: 5.514A pdb=" N LYS i 83 " --> pdb=" O ALA i 79 " (cutoff:3.500A) Processing helix chain 'i' and resid 85 through 97 removed outlier: 3.536A pdb=" N LEU i 91 " --> pdb=" O GLY i 87 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ARG i 97 " --> pdb=" O LEU i 93 " (cutoff:3.500A) Processing helix chain 'i' and resid 98 through 106 removed outlier: 3.657A pdb=" N TYR i 103 " --> pdb=" O ASP i 99 " (cutoff:3.500A) Processing helix chain 'i' and resid 110 through 121 removed outlier: 4.012A pdb=" N VAL i 118 " --> pdb=" O ALA i 114 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LYS i 121 " --> pdb=" O LEU i 117 " (cutoff:3.500A) Processing helix chain 'i' and resid 152 through 166 removed outlier: 4.789A pdb=" N LYS i 156 " --> pdb=" O GLN i 152 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ALA i 157 " --> pdb=" O SER i 153 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ALA i 158 " --> pdb=" O ARG i 154 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLN i 164 " --> pdb=" O GLU i 160 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N GLU i 166 " --> pdb=" O ALA i 162 " (cutoff:3.500A) Processing helix chain 'i' and resid 187 through 192 removed outlier: 3.630A pdb=" N LEU i 191 " --> pdb=" O GLU i 187 " (cutoff:3.500A) removed outlier: 5.022A 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: 4.202A pdb=" N ILE i 200 " --> pdb=" O ASN i 196 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL i 201 " --> pdb=" O GLU i 197 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU i 202 " --> pdb=" O HIS i 198 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N LEU i 203 " --> pdb=" O LEU i 199 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER i 205 " --> pdb=" O VAL i 201 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N LYS i 206 " --> pdb=" O GLU i 202 " (cutoff:3.500A) Processing helix chain 'j' and resid 55 through 71 removed outlier: 3.817A pdb=" N LYS j 62 " --> pdb=" O ALA j 58 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ARG j 69 " --> pdb=" O GLU j 65 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N ASN j 70 " --> pdb=" O LYS j 66 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N MET j 71 " --> pdb=" O ALA j 67 " (cutoff:3.500A) Processing helix chain 'j' and resid 109 through 119 removed outlier: 4.073A pdb=" N ALA j 113 " --> pdb=" O GLY j 109 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N VAL j 117 " --> pdb=" O ALA j 113 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLY j 119 " --> pdb=" O LEU j 115 " (cutoff:3.500A) Processing helix chain 'j' and resid 132 through 148 removed outlier: 3.573A pdb=" N VAL j 137 " --> pdb=" O PRO j 133 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N THR j 140 " --> pdb=" O VAL j 136 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ILE j 141 " --> pdb=" O VAL j 137 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ASN j 146 " --> pdb=" O ASP j 142 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N MET j 147 " --> pdb=" O GLY j 143 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N ASN j 148 " --> pdb=" O LEU j 144 " (cutoff:3.500A) Processing helix chain 'j' and resid 149 through 158 removed outlier: 3.942A pdb=" N ALA j 154 " --> pdb=" O PRO j 150 " (cutoff:3.500A) Processing helix chain 'j' and resid 160 through 165 removed outlier: 3.830A pdb=" N ILE j 164 " --> pdb=" O SER j 160 " (cutoff:3.500A) Processing helix chain 'k' and resid 11 through 19 removed outlier: 3.703A pdb=" N SER k 15 " --> pdb=" O HIS k 11 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N GLU k 16 " --> pdb=" O PRO k 12 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N GLN k 17 " --> pdb=" O ASP k 13 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL k 18 " --> pdb=" O GLN k 14 " (cutoff:3.500A) Proline residue: k 19 - end of helix No H-bonds generated for 'chain 'k' and resid 11 through 19' Processing helix chain 'k' and resid 20 through 33 removed outlier: 4.753A pdb=" N ARG k 24 " --> pdb=" O GLY k 20 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ALA k 27 " --> pdb=" O GLU k 23 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU k 33 " --> pdb=" O ILE k 29 " (cutoff:3.500A) Processing helix chain 'k' and resid 67 through 82 removed outlier: 4.045A pdb=" N ILE k 71 " --> pdb=" O PRO k 67 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASP k 72 " --> pdb=" O GLN k 68 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLU k 73 " --> pdb=" O GLU k 69 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU k 74 " --> pdb=" O VAL k 70 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N PHE k 80 " --> pdb=" O THR k 76 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N ASP k 82 " --> pdb=" O PHE k 78 " (cutoff:3.500A) Processing helix chain 'l' and resid 20 through 31 removed outlier: 3.545A pdb=" N ASN l 28 " --> pdb=" O ALA l 24 " (cutoff:3.500A) Processing helix chain 'l' and resid 35 through 55 removed outlier: 3.702A pdb=" N SER l 45 " --> pdb=" O SER l 41 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N THR l 49 " --> pdb=" O SER l 45 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLN l 52 " --> pdb=" O GLU l 48 " (cutoff:3.500A) Processing helix chain 'l' and resid 57 through 70 removed outlier: 3.575A pdb=" N GLU l 63 " --> pdb=" O LEU l 59 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA l 65 " --> pdb=" O ALA l 61 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ASN l 68 " --> pdb=" O VAL l 64 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N VAL l 69 " --> pdb=" O ALA l 65 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG l 70 " --> pdb=" O LEU l 66 " (cutoff:3.500A) Processing helix chain 'l' and resid 92 through 111 removed outlier: 3.898A pdb=" N ASN l 97 " --> pdb=" O PRO l 93 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL l 105 " --> pdb=" O MET l 101 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS l 110 " --> pdb=" O GLU l 106 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N ARG l 111 " --> pdb=" O ALA l 107 " (cutoff:3.500A) Processing helix chain 'l' and resid 115 through 130 removed outlier: 3.680A pdb=" N ALA l 121 " --> pdb=" O ALA l 117 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASP l 126 " --> pdb=" O ASN l 122 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ALA l 128 " --> pdb=" O LEU l 124 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N GLU l 129 " --> pdb=" O SER l 125 " (cutoff:3.500A) Processing helix chain 'l' and resid 132 through 149 removed outlier: 3.715A pdb=" N MET l 144 " --> pdb=" O ASP l 140 " (cutoff:3.500A) Processing helix chain 'm' and resid 5 through 21 removed outlier: 3.500A pdb=" N MET m 10 " --> pdb=" O PRO m 6 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ARG m 15 " --> pdb=" O LEU m 11 " (cutoff:3.500A) Processing helix chain 'm' and resid 30 through 44 removed outlier: 3.690A pdb=" N VAL m 34 " --> pdb=" O SER m 30 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL m 39 " --> pdb=" O ALA m 35 " (cutoff:3.500A) Processing helix chain 'm' and resid 112 through 120 removed outlier: 3.582A pdb=" N ARG m 117 " --> pdb=" O ASP m 113 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N GLN m 118 " --> pdb=" O ARG m 114 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N ALA m 119 " --> pdb=" O ALA m 115 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLY m 120 " --> pdb=" O ALA m 116 " (cutoff:3.500A) Processing helix chain 'n' and resid 34 through 39 removed outlier: 3.635A pdb=" N PHE n 39 " --> pdb=" O LEU n 35 " (cutoff:3.500A) Processing helix chain 'n' and resid 41 through 56 removed outlier: 3.539A pdb=" N MET n 46 " --> pdb=" O GLU n 42 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL n 48 " --> pdb=" O ALA n 44 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG n 49 " --> pdb=" O ARG n 45 " (cutoff:3.500A) Proline residue: n 51 - end of helix removed outlier: 3.763A pdb=" N VAL n 55 " --> pdb=" O PRO n 51 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N ASP n 56 " --> pdb=" O LEU n 52 " (cutoff:3.500A) Processing helix chain 'n' and resid 71 through 92 removed outlier: 3.557A pdb=" N GLN n 75 " --> pdb=" O GLY n 71 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLY n 77 " --> pdb=" O SER n 73 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLU n 89 " --> pdb=" O ARG n 85 " (cutoff:3.500A) Processing helix chain 'n' and resid 94 through 102 removed outlier: 3.584A pdb=" N LYS n 100 " --> pdb=" O SER n 96 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ALA n 101 " --> pdb=" O GLU n 97 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLY n 102 " --> pdb=" O LEU n 98 " (cutoff:3.500A) Processing helix chain 'o' and resid 14 through 33 removed outlier: 3.667A pdb=" N ASP o 19 " --> pdb=" O HIS o 15 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLN o 20 " --> pdb=" O ARG o 16 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ALA o 21 " --> pdb=" O LEU o 17 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA o 23 " --> pdb=" O ASP o 19 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N GLU o 24 " --> pdb=" O GLN o 20 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ARG o 31 " --> pdb=" O GLU o 27 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR o 32 " --> pdb=" O THR o 28 " (cutoff:3.500A) Processing helix chain 'o' and resid 80 through 91 removed outlier: 3.620A pdb=" N VAL o 84 " --> pdb=" O THR o 80 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ASP o 85 " --> pdb=" O GLU o 81 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA o 86 " --> pdb=" O LYS o 82 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N LEU o 87 " --> pdb=" O THR o 83 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N MET o 88 " --> pdb=" O VAL o 84 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N ASP o 91 " --> pdb=" O LEU o 87 " (cutoff:3.500A) Processing helix chain 'p' and resid 46 through 51 removed outlier: 3.621A pdb=" N SER p 50 " --> pdb=" O THR p 46 " (cutoff:3.500A) removed outlier: 5.415A 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: 4.214A pdb=" N SER p 58 " --> pdb=" O GLY p 54 " (cutoff:3.500A) removed outlier: 4.395A 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: 3.588A pdb=" N GLN p 64 " --> pdb=" O PRO p 60 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N GLU p 68 " --> pdb=" O GLN p 64 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N CYS p 70 " --> pdb=" O ALA p 66 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASP p 72 " --> pdb=" O GLU p 68 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA p 73 " --> pdb=" O ARG p 69 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LYS p 75 " --> pdb=" O ALA p 71 " (cutoff:3.500A) Processing helix chain 'p' and resid 94 through 104 removed outlier: 3.828A pdb=" N ALA p 99 " --> pdb=" O SER p 95 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASN p 101 " --> pdb=" O ILE p 97 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ALA p 102 " --> pdb=" O ARG p 98 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ALA p 103 " --> pdb=" O ALA p 99 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N GLY p 104 " --> pdb=" O LEU p 100 " (cutoff:3.500A) Processing helix chain 'q' and resid 3 through 10 removed outlier: 3.781A pdb=" N LYS q 10 " --> pdb=" O GLN q 6 " (cutoff:3.500A) Processing helix chain 'q' and resid 113 through 118 removed outlier: 3.835A pdb=" N TYR q 117 " --> pdb=" O ALA q 113 " (cutoff:3.500A) Processing helix chain 'r' and resid 14 through 22 removed outlier: 4.559A pdb=" N THR r 20 " --> pdb=" O VAL r 16 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N SER r 21 " --> pdb=" O ILE r 17 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N ILE r 22 " --> pdb=" O ALA r 18 " (cutoff:3.500A) Processing helix chain 'r' and resid 26 through 38 removed outlier: 4.069A pdb=" N SER r 30 " --> pdb=" O GLY r 26 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ALA r 36 " --> pdb=" O ALA r 32 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA r 37 " --> pdb=" O ILE r 33 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLY r 38 " --> pdb=" O LEU r 34 " (cutoff:3.500A) Processing helix chain 'r' and resid 49 through 64 removed outlier: 3.592A pdb=" N THR r 55 " --> pdb=" O GLY r 51 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ASP r 58 " --> pdb=" O ASP r 54 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLU r 59 " --> pdb=" O THR r 55 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N PHE r 63 " --> pdb=" O GLU r 59 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N VAL r 64 " --> pdb=" O VAL r 60 " (cutoff:3.500A) Processing helix chain 'r' and resid 66 through 84 removed outlier: 3.915A pdb=" N ARG r 70 " --> pdb=" O GLU r 66 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ARG r 71 " --> pdb=" O GLY r 67 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU r 72 " --> pdb=" O ASP r 68 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU r 80 " --> pdb=" O SER r 76 " (cutoff:3.500A) Processing helix chain 'r' and resid 85 through 94 removed outlier: 3.585A pdb=" N GLY r 94 " --> pdb=" O ARG r 90 " (cutoff:3.500A) Processing helix chain 'r' and resid 106 through 111 Processing helix chain 's' and resid 3 through 21 removed outlier: 3.511A pdb=" N LYS s 7 " --> pdb=" O LYS s 3 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU s 10 " --> pdb=" O MET s 6 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ARG s 13 " --> pdb=" O ARG s 9 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA s 15 " --> pdb=" O VAL s 11 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA s 17 " --> pdb=" O ARG s 13 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N PHE s 21 " --> pdb=" O ALA s 17 " (cutoff:3.500A) Processing helix chain 's' and resid 22 through 33 removed outlier: 3.953A pdb=" N GLU s 26 " --> pdb=" O ALA s 22 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LYS s 28 " --> pdb=" O ARG s 24 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ALA s 29 " --> pdb=" O ALA s 25 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASP s 33 " --> pdb=" O ALA s 29 " (cutoff:3.500A) Processing helix chain 's' and resid 37 through 51 removed outlier: 3.801A pdb=" N TRP s 42 " --> pdb=" O ASP s 38 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N VAL s 45 " --> pdb=" O ARG s 41 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU s 48 " --> pdb=" O ALA s 44 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N GLN s 49 " --> pdb=" O VAL s 45 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR s 50 " --> pdb=" O LEU s 46 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LEU s 51 " --> pdb=" O LYS s 47 " (cutoff:3.500A) Processing helix chain 's' and resid 80 through 91 removed outlier: 3.735A pdb=" N VAL s 84 " --> pdb=" O SER s 80 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ARG s 85 " --> pdb=" O ARG s 81 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N ARG s 90 " --> pdb=" O GLU s 86 " (cutoff:3.500A) Processing helix chain 't' and resid 4 through 16 removed outlier: 3.647A pdb=" N LYS t 10 " --> pdb=" O GLU t 6 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N SER t 13 " --> pdb=" O ALA t 9 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N GLU t 14 " --> pdb=" O LYS t 10 " (cutoff:3.500A) Processing helix chain 't' and resid 24 through 43 removed outlier: 3.921A pdb=" N GLN t 35 " --> pdb=" O LEU t 31 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N HIS t 38 " --> pdb=" O ALA t 34 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLY t 41 " --> pdb=" O ASN t 37 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N HIS t 42 " --> pdb=" O HIS t 38 " (cutoff:3.500A) Processing helix chain 't' and resid 49 through 74 removed outlier: 3.658A pdb=" N ARG t 54 " --> pdb=" O HIS t 50 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLY t 55 " --> pdb=" O HIS t 51 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER t 61 " --> pdb=" O LEU t 57 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU t 70 " --> pdb=" O LEU t 66 " (cutoff:3.500A) Processing helix chain 't' and resid 75 through 86 removed outlier: 3.654A pdb=" N GLN t 80 " --> pdb=" O ALA t 76 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU t 83 " --> pdb=" O THR t 79 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG t 84 " --> pdb=" O GLN t 80 " (cutoff:3.500A) Processing helix chain 'u' and resid 53 through 64 removed outlier: 3.705A pdb=" N GLY u 62 " --> pdb=" O ALA u 58 " (cutoff:3.500A) Processing helix chain 'u' and resid 68 through 82 removed outlier: 4.288A pdb=" N ALA u 73 " --> pdb=" O ASP u 69 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU u 77 " --> pdb=" O ALA u 73 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N LYS u 80 " --> pdb=" O LYS u 76 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ALA u 82 " --> pdb=" O VAL u 78 " (cutoff:3.500A) Processing helix chain 'w' and resid 11 through 17 removed outlier: 4.209A pdb=" N ALA w 15 " --> pdb=" O CYS w 11 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLY w 17 " --> pdb=" O PHE w 13 " (cutoff:3.500A) Processing helix chain 'w' and resid 25 through 34 removed outlier: 4.288A pdb=" N ASN w 31 " --> pdb=" O ALA w 27 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N TYR w 32 " --> pdb=" O THR w 28 " (cutoff:3.500A) removed outlier: 6.339A 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: 3.971A pdb=" N ARG w 53 " --> pdb=" O ALA w 49 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU w 55 " --> pdb=" O TYR w 51 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA w 58 " --> pdb=" O GLN w 54 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TYR w 64 " --> pdb=" O LYS w 60 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LEU w 65 " --> pdb=" O ARG w 61 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER w 66 " --> pdb=" O ALA w 62 " (cutoff:3.500A) Processing helix chain 'x' and resid 12 through 26 removed outlier: 3.909A pdb=" N LYS x 18 " --> pdb=" O HIS x 14 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N LYS x 21 " --> pdb=" O LYS x 17 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLY x 26 " --> pdb=" O ALA x 22 " (cutoff:3.500A) Processing helix chain 'x' and resid 70 through 76 removed outlier: 4.446A pdb=" N PHE x 74 " --> pdb=" O LYS x 70 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ALA x 75 " --> pdb=" O LEU x 71 " (cutoff:3.500A) Proline residue: x 76 - end of helix No H-bonds generated for 'chain 'x' and resid 70 through 76' Processing helix chain 'y' and resid 7 through 41 removed outlier: 4.030A pdb=" N ILE y 12 " --> pdb=" O LYS y 8 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLU y 15 " --> pdb=" O ALA y 11 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LYS y 16 " --> pdb=" O ILE y 12 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASN y 21 " --> pdb=" O ALA y 17 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N SER y 23 " --> pdb=" O LYS y 19 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE y 32 " --> pdb=" O MET y 28 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL y 35 " --> pdb=" O PHE y 31 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALA y 41 " --> pdb=" O ALA y 37 " (cutoff:3.500A) Processing helix chain 'y' and resid 44 through 65 removed outlier: 3.876A pdb=" N GLU y 53 " --> pdb=" O LYS y 49 " (cutoff:3.500A) Proline residue: y 56 - end of helix removed outlier: 3.609A pdb=" N ARG y 60 " --> pdb=" O PRO y 56 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLY y 65 " --> pdb=" O GLN y 61 " (cutoff:3.500A) Processing helix chain 'y' and resid 68 through 87 removed outlier: 3.808A pdb=" N ALA y 81 " --> pdb=" O ALA y 77 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLN y 82 " --> pdb=" O ASN y 78 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LYS y 85 " --> pdb=" O ALA y 81 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N ALA y 87 " --> pdb=" O ILE y 83 " (cutoff:3.500A) Processing helix chain 'z' and resid 11 through 27 removed outlier: 3.559A pdb=" N ALA z 15 " --> pdb=" O PRO z 11 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LYS z 25 " --> pdb=" O ARG z 21 " (cutoff:3.500A) Processing helix chain 'z' and resid 28 through 37 removed outlier: 3.816A pdb=" N ARG z 33 " --> pdb=" O LEU z 29 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N PHE z 37 " --> pdb=" O ARG z 33 " (cutoff:3.500A) Processing helix chain 'z' and resid 40 through 65 removed outlier: 3.718A pdb=" N ARG z 45 " --> pdb=" O PRO z 41 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ALA z 48 " --> pdb=" O GLU z 44 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA z 50 " --> pdb=" O LYS z 46 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA z 52 " --> pdb=" O ALA z 48 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LYS z 54 " --> pdb=" O ALA z 50 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N LYS z 59 " --> pdb=" O ARG z 55 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ALA z 61 " --> pdb=" O ALA z 57 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLU z 63 " --> pdb=" O LYS z 59 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ASN z 64 " --> pdb=" O LEU z 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 143 removed outlier: 3.615A pdb=" N LEU A 126 " --> pdb=" O ASP A 122 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N GLY A 129 " --> pdb=" O ALA A 125 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ASP A 130 " --> pdb=" O LEU A 126 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ARG A 133 " --> pdb=" O GLY A 129 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG A 137 " --> pdb=" O ARG A 133 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLU A 140 " --> pdb=" O SER A 136 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ARG A 142 " --> pdb=" O TYR A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 176 Processing helix chain 'A' and resid 218 through 223 removed outlier: 3.907A pdb=" N LEU A 222 " --> pdb=" O ASN A 218 " (cutoff:3.500A) removed outlier: 7.324A 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: 3.886A pdb=" N ASN A 238 " --> pdb=" O GLY A 234 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR A 240 " --> pdb=" O HIS A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 299 removed outlier: 3.547A pdb=" N ASN A 266 " --> pdb=" O SER A 262 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA A 268 " --> pdb=" O HIS A 264 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N LYS A 269 " --> pdb=" O LYS A 265 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ALA A 270 " --> pdb=" O ASN A 266 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N VAL A 273 " --> pdb=" O LYS A 269 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU A 274 " --> pdb=" O ALA A 270 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLY A 275 " --> pdb=" O LEU A 271 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ALA A 276 " --> pdb=" O SER A 272 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE A 278 " --> pdb=" O LEU A 274 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ALA A 280 " --> pdb=" O ALA A 276 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ALA A 281 " --> pdb=" O ARG A 277 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ALA A 284 " --> pdb=" O ALA A 280 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LYS A 285 " --> pdb=" O ALA A 281 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLN A 287 " --> pdb=" O MET A 283 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N GLN A 288 " --> pdb=" O ALA A 284 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLU A 290 " --> pdb=" O ARG A 286 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N THR A 293 " --> pdb=" O ALA A 289 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N ASN A 296 " --> pdb=" O SER A 292 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU A 297 " --> pdb=" O THR A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 335 removed outlier: 4.459A pdb=" N VAL A 332 " --> pdb=" O ARG A 328 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLU A 334 " --> pdb=" O ASP A 330 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLY A 335 " --> pdb=" O GLU A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 353 removed outlier: 4.255A pdb=" N GLU A 342 " --> pdb=" O ASP A 338 " (cutoff:3.500A) Proline residue: A 343 - end of helix removed outlier: 3.651A pdb=" N GLU A 347 " --> pdb=" O PRO A 343 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLN A 352 " --> pdb=" O HIS A 348 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'B' and resid 80 through 83 removed outlier: 3.681A pdb=" N ARG B 80 " --> pdb=" O LEU B 93 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N LEU B 93 " --> pdb=" O GLU B 79 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N ILE B 74 " --> pdb=" O SER B 118 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N SER B 118 " --> pdb=" O ILE B 74 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'B' and resid 138 through 142 removed outlier: 4.597A pdb=" N SER B 139 " --> pdb=" O ILE B 164 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'B' and resid 171 through 175 Processing sheet with id= 4, first strand: chain 'B' and resid 90 through 96 removed outlier: 5.754A pdb=" N ASN B 90 " --> pdb=" O ALA B 106 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N GLU B 100 " --> pdb=" O TYR B 96 " (cutoff:3.500A) Processing sheet with id= 5, 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: 4.339A pdb=" N SER C 199 " --> pdb=" O LYS C 8 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N LYS C 105 " --> pdb=" O VAL C 177 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'C' and resid 10 through 16 removed outlier: 3.576A pdb=" N GLY C 10 " --> pdb=" O VAL C 26 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N VAL C 20 " --> pdb=" O THR C 16 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL C 189 " --> pdb=" O THR C 25 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASP C 181 " --> pdb=" O LEU C 186 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'C' and resid 79 through 84 removed outlier: 5.801A pdb=" N ARG C 46 " --> pdb=" O LEU C 84 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N GLN C 49 " --> pdb=" O THR C 35 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N GLN C 94 " --> pdb=" O VAL C 34 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'D' and resid 1 through 5 removed outlier: 4.709A pdb=" N MET D 1 " --> pdb=" O VAL D 14 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL D 14 " --> pdb=" O MET D 1 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N SER D 10 " --> pdb=" O LEU D 5 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'D' and resid 117 through 120 removed outlier: 4.145A pdb=" N VAL D 146 " --> pdb=" O LYS D 166 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'E' and resid 65 through 69 removed outlier: 3.592A pdb=" N GLY E 86 " --> pdb=" O THR E 68 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N ILE E 85 " --> pdb=" O VAL E 40 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASN E 37 " --> pdb=" O ASP E 153 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'F' and resid 16 through 19 removed outlier: 3.791A pdb=" N LYS F 18 " --> pdb=" O THR F 25 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'F' and resid 82 through 89 removed outlier: 6.045A pdb=" N THR F 129 " --> pdb=" O LEU F 89 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'F' and resid 95 through 98 removed outlier: 3.643A pdb=" N ARG F 95 " --> pdb=" O SER F 106 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA F 97 " --> pdb=" O ASN F 104 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N VAL F 113 " --> pdb=" O LEU F 105 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'G' and resid 1 through 5 removed outlier: 3.563A pdb=" N MET G 1 " --> pdb=" O VAL G 21 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N ASP G 17 " --> pdb=" O LEU G 5 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'G' and resid 76 through 83 removed outlier: 7.480A pdb=" N GLU G 76 " --> pdb=" O LYS G 141 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N ILE G 143 " --> pdb=" O GLU G 76 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N VAL G 78 " --> pdb=" O ILE G 143 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER G 82 " --> pdb=" O VAL G 147 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL G 142 " --> pdb=" O VAL G 130 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N HIS G 128 " --> pdb=" O VAL G 144 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER G 131 " --> pdb=" O ARG G 116 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N GLU G 114 " --> pdb=" O GLN G 133 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'J' and resid 52 through 57 removed outlier: 4.794A pdb=" N ASP J 19 " --> pdb=" O LEU J 140 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'J' and resid 74 through 78 removed outlier: 7.634A pdb=" N GLY J 83 " --> pdb=" O THR J 78 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'K' and resid 56 through 61 removed outlier: 4.761A pdb=" N ASP K 56 " --> pdb=" O ILE K 43 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N LYS K 40 " --> pdb=" O ILE K 22 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N THR K 6 " --> pdb=" O CYS K 21 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N ASN K 82 " --> pdb=" O MET K 7 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'L' and resid 120 through 123 removed outlier: 3.654A pdb=" N VAL L 122 " --> pdb=" O LYS L 141 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'M' and resid 62 through 65 removed outlier: 3.623A pdb=" N TYR M 103 " --> pdb=" O LEU M 33 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N LEU M 33 " --> pdb=" O LEU M 102 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LYS M 100 " --> pdb=" O ALA M 35 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'M' and resid 30 through 36 removed outlier: 8.316A pdb=" N SER M 30 " --> pdb=" O LYS M 133 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N LYS M 127 " --> pdb=" O VAL M 36 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'N' and resid 33 through 36 removed outlier: 5.270A pdb=" N ARG N 103 " --> pdb=" O ASN N 107 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N GLY N 101 " --> pdb=" O PRO N 109 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ALA N 111 " --> pdb=" O LYS N 99 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N LYS N 99 " --> pdb=" O ALA N 111 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ILE N 113 " --> pdb=" O ILE N 97 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ILE N 97 " --> pdb=" O ILE N 113 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N LEU N 115 " --> pdb=" O THR N 95 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N THR N 95 " --> pdb=" O LEU N 115 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'O' and resid 49 through 53 removed outlier: 3.653A pdb=" N VAL O 49 " --> pdb=" O VAL O 39 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N ILE O 35 " --> pdb=" O THR O 53 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'P' and resid 49 through 53 removed outlier: 3.585A pdb=" N ALA P 49 " --> pdb=" O THR P 60 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N ARG P 53 " --> pdb=" O HIS P 56 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N HIS P 56 " --> pdb=" O ARG P 53 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N THR P 60 " --> pdb=" O ILE P 48 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ASP P 24 " --> pdb=" O VAL P 47 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N THR P 25 " --> pdb=" O LYS P 87 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER P 85 " --> pdb=" O GLU P 27 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER P 83 " --> pdb=" O LYS P 29 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'P' and resid 57 through 64 removed outlier: 7.245A pdb=" N SER P 57 " --> pdb=" O THR P 76 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'R' and resid 11 through 15 removed outlier: 3.634A pdb=" N MET R 40 " --> pdb=" O VAL R 4 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N LEU R 39 " --> pdb=" O GLY R 50 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE R 41 " --> pdb=" O LYS R 48 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'R' and resid 31 through 36 removed outlier: 4.574A pdb=" N GLU R 31 " --> pdb=" O VAL R 63 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N LYS R 60 " --> pdb=" O THR R 99 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ASP R 95 " --> pdb=" O VAL R 64 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N TYR R 83 " --> pdb=" O ARG R 78 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS R 76 " --> pdb=" O LYS R 85 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'R' and resid 57 through 60 removed outlier: 3.694A pdb=" N GLY R 100 " --> pdb=" O LYS R 60 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'S' and resid 2 through 8 Processing sheet with id= 30, first strand: chain 'T' and resid 12 through 15 removed outlier: 5.390A pdb=" N VAL T 31 " --> pdb=" O HIS T 15 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N ASN T 28 " --> pdb=" O LEU T 87 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS T 81 " --> pdb=" O VAL T 34 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG T 73 " --> pdb=" O HIS T 70 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N LYS T 66 " --> pdb=" O ARG T 77 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ASP T 79 " --> pdb=" O LYS T 64 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N LYS T 64 " --> pdb=" O ASP T 79 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N LYS T 81 " --> pdb=" O VAL T 62 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N VAL T 62 " --> pdb=" O LYS T 81 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ALA T 83 " --> pdb=" O THR T 60 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N THR T 60 " --> pdb=" O ALA T 83 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N VAL T 85 " --> pdb=" O VAL T 58 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N VAL T 58 " --> pdb=" O VAL T 85 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'U' and resid 40 through 44 removed outlier: 4.881A pdb=" N ASN U 40 " --> pdb=" O ALA U 63 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'U' and resid 83 through 87 Processing sheet with id= 33, first strand: chain 'V' and resid 69 through 72 removed outlier: 3.523A pdb=" N VAL V 72 " --> pdb=" O LEU V 61 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA V 6 " --> pdb=" O VAL V 64 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ALA V 39 " --> pdb=" O ARG V 9 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N PHE V 26 " --> pdb=" O LEU V 42 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ILE V 89 " --> pdb=" O PRO V 27 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'W' and resid 51 through 54 removed outlier: 4.420A pdb=" N THR W 58 " --> pdb=" O GLY W 54 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'W' and resid 65 through 71 Processing sheet with id= 36, first strand: chain 'X' and resid 12 through 16 removed outlier: 3.522A pdb=" N VAL X 13 " --> pdb=" O PHE X 29 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'X' and resid 35 through 39 Processing sheet with id= 38, first strand: chain 'Z' and resid 33 through 39 removed outlier: 4.016A pdb=" N HIS Z 34 " --> pdb=" O GLN Z 9 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLN Z 9 " --> pdb=" O HIS Z 34 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N MET Z 54 " --> pdb=" O THR Z 10 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'a' and resid 20 through 25 removed outlier: 4.065A pdb=" N ASN a 20 " --> pdb=" O CYS a 16 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N CYS a 16 " --> pdb=" O ASN a 20 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'c' and resid 19 through 25 removed outlier: 6.362A pdb=" N HIS c 19 " --> pdb=" O SER c 13 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ILE c 48 " --> pdb=" O SER c 14 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N LEU c 34 " --> pdb=" O GLU c 51 " (cutoff:3.500A) Processing sheet with id= 41, 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= 42, first strand: chain 'f' and resid 14 through 19 Processing sheet with id= 43, first strand: chain 'g' and resid 15 through 18 removed outlier: 5.166A pdb=" N HIS g 15 " --> pdb=" O ILE g 41 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N HIS g 39 " --> pdb=" O GLY g 17 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'g' and resid 67 through 71 removed outlier: 3.842A pdb=" N ALA g 185 " --> pdb=" O PHE g 198 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'h' and resid 54 through 59 removed outlier: 3.685A pdb=" N ILE h 64 " --> pdb=" O PRO h 98 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'h' and resid 164 through 170 removed outlier: 5.842A pdb=" N ARG h 164 " --> pdb=" O GLY h 155 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N GLY h 194 " --> pdb=" O THR h 191 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VAL h 200 " --> pdb=" O ASN h 185 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASN h 185 " --> pdb=" O VAL h 200 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LYS h 204 " --> pdb=" O ASP h 181 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N ASP h 181 " --> pdb=" O LYS h 204 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'i' and resid 141 through 145 removed outlier: 3.789A pdb=" N ASP i 141 " --> pdb=" O PHE i 182 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL i 143 " --> pdb=" O GLY i 180 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N MET i 178 " --> pdb=" O ILE i 145 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N GLU i 179 " --> pdb=" O ASP i 174 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'j' and resid 12 through 16 removed outlier: 6.768A pdb=" N LEU j 36 " --> pdb=" O ILE j 16 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'j' and resid 84 through 88 removed outlier: 3.524A pdb=" N VAL j 94 " --> pdb=" O GLY j 87 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ARG j 93 " --> pdb=" O TYR j 128 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLN j 97 " --> pdb=" O LEU j 124 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ASN j 122 " --> pdb=" O ALA j 99 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'j' and resid 33 through 40 removed outlier: 3.747A pdb=" N GLY j 47 " --> pdb=" O VAL j 39 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'k' and resid 38 through 42 removed outlier: 4.230A pdb=" N ARG k 38 " --> pdb=" O ASN k 63 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N TYR k 59 " --> pdb=" O TRP k 42 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N HIS k 3 " --> pdb=" O THR k 92 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG k 86 " --> pdb=" O MET k 9 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'k' and resid 43 through 47 removed outlier: 3.578A pdb=" N GLY k 43 " --> pdb=" O TYR k 59 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N HIS k 55 " --> pdb=" O LEU k 47 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'l' and resid 73 through 79 removed outlier: 5.912A pdb=" N TYR l 85 " --> pdb=" O ARG l 78 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'm' and resid 23 through 29 removed outlier: 6.396A pdb=" N ALA m 23 " --> pdb=" O LEU m 63 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLU m 60 " --> pdb=" O LYS m 50 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASP m 48 " --> pdb=" O THR m 62 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'm' and resid 74 through 77 removed outlier: 3.755A pdb=" N TYR m 128 " --> pdb=" O GLN m 76 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N CYS m 127 " --> pdb=" O VAL m 103 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N VAL m 103 " --> pdb=" O ILE m 126 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'n' and resid 5 through 11 removed outlier: 3.848A pdb=" N VAL n 19 " --> pdb=" O GLY n 8 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ARG n 18 " --> pdb=" O THR n 66 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'o' and resid 42 through 52 removed outlier: 4.637A pdb=" N LEU o 71 " --> pdb=" O PRO o 43 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N ARG o 5 " --> pdb=" O GLY o 103 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLN o 99 " --> pdb=" O ARG o 9 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'p' and resid 42 through 45 removed outlier: 4.269A pdb=" N ASN p 29 " --> pdb=" O SER p 26 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ASN p 109 " --> pdb=" O LEU p 82 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N GLY p 88 " --> pdb=" O VAL p 113 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'q' and resid 29 through 33 removed outlier: 5.159A pdb=" N LEU q 81 " --> pdb=" O VAL q 98 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N HIS q 96 " --> pdb=" O ARG q 83 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'q' and resid 36 through 41 removed outlier: 5.062A pdb=" N LYS q 51 " --> pdb=" O ILE q 67 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N PHE q 61 " --> pdb=" O LEU q 57 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'u' and resid 4 through 10 removed outlier: 4.092A pdb=" N PHE u 16 " --> pdb=" O HIS u 9 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY u 37 " --> pdb=" O VAL u 19 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARG u 51 " --> pdb=" O PHE u 38 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N GLY u 49 " --> pdb=" O ASN u 40 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'v' and resid 7 through 11 removed outlier: 3.501A pdb=" N GLY v 10 " --> pdb=" O VAL v 59 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N GLU v 60 " --> pdb=" O VAL v 76 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'v' and resid 19 through 30 No H-bonds generated for sheet with id= 63 Processing sheet with id= 64, first strand: chain 'x' and resid 30 through 33 removed outlier: 4.546A pdb=" N LEU x 47 " --> pdb=" O VAL x 62 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL x 62 " --> pdb=" O LEU x 47 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'A' and resid 144 through 149 removed outlier: 6.883A pdb=" N ILE A 163 " --> pdb=" O MET A 149 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N LYS A 160 " --> pdb=" O ALA A 117 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N ASN A 110 " --> pdb=" O GLU A 208 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ARG A 308 " --> pdb=" O GLY A 181 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N THR A 309 " --> pdb=" O THR A 318 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'A' and resid 224 through 227 removed outlier: 3.848A pdb=" N ILE A 253 " --> pdb=" O HIS A 248 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'A' and resid 150 through 153 removed outlier: 3.556A pdb=" N SER A 150 " --> pdb=" O ILE A 163 " (cutoff:3.500A) 1593 hydrogen bonds defined for protein. 4698 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3061 hydrogen bonds 4882 hydrogen bond angles 0 basepair planarities 1271 basepair parallelities 2575 stacking parallelities Total time for adding SS restraints: 295.98 Time building geometry restraints manager: 68.66 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: 12085 1.29 - 1.42: 70791 1.42 - 1.55: 66462 1.55 - 1.69: 9289 1.69 - 1.82: 278 Bond restraints: 158905 Sorted by residual: bond pdb=" C5 5MU 11939 " pdb=" C6 5MU 11939 " ideal model delta sigma weight residual 1.155 1.434 -0.279 2.00e-02 2.50e+03 1.94e+02 bond pdb=" C5 5MU 5 54 " pdb=" C6 5MU 5 54 " ideal model delta sigma weight residual 1.155 1.430 -0.275 2.00e-02 2.50e+03 1.89e+02 bond pdb=" C5 5MU 1 747 " pdb=" C6 5MU 1 747 " ideal model delta sigma weight residual 1.155 1.423 -0.268 2.00e-02 2.50e+03 1.80e+02 bond pdb=" C4 5MU 1 747 " pdb=" C5 5MU 1 747 " ideal model delta sigma weight residual 1.802 1.601 0.201 2.00e-02 2.50e+03 1.01e+02 bond pdb=" C4 5MU 11939 " pdb=" C5 5MU 11939 " ideal model delta sigma weight residual 1.802 1.603 0.199 2.00e-02 2.50e+03 9.94e+01 ... (remaining 158900 not shown) Histogram of bond angle deviations from ideal: 93.78 - 102.95: 9546 102.95 - 112.13: 99603 112.13 - 121.31: 87204 121.31 - 130.49: 39297 130.49 - 139.66: 1871 Bond angle restraints: 237521 Sorted by residual: angle pdb=" C1' G7M 12069 " pdb=" N9 G7M 12069 " pdb=" C8 G7M 12069 " ideal model delta sigma weight residual 94.96 137.47 -42.51 3.00e+00 1.11e-01 2.01e+02 angle pdb=" C1' G7M 2 527 " pdb=" N9 G7M 2 527 " pdb=" C8 G7M 2 527 " ideal model delta sigma weight residual 94.96 125.60 -30.64 3.00e+00 1.11e-01 1.04e+02 angle pdb=" C1' G7M 12069 " pdb=" N9 G7M 12069 " pdb=" C4 G7M 12069 " ideal model delta sigma weight residual 142.80 114.98 27.82 3.00e+00 1.11e-01 8.60e+01 angle pdb=" C1' 2MG 21516 " pdb=" N9 2MG 21516 " pdb=" C8 2MG 21516 " ideal model delta sigma weight residual 110.07 135.19 -25.12 3.00e+00 1.11e-01 7.01e+01 angle pdb=" C1' 2MG 12445 " pdb=" N9 2MG 12445 " pdb=" C8 2MG 12445 " ideal model delta sigma weight residual 110.07 133.11 -23.04 3.00e+00 1.11e-01 5.90e+01 ... (remaining 237516 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.94: 90049 35.94 - 71.87: 10280 71.87 - 107.81: 1253 107.81 - 143.74: 12 143.74 - 179.68: 33 Dihedral angle restraints: 101627 sinusoidal: 84637 harmonic: 16990 Sorted by residual: dihedral pdb=" O4' U 2 439 " pdb=" C1' U 2 439 " pdb=" N1 U 2 439 " pdb=" C2 U 2 439 " ideal model delta sinusoidal sigma weight residual 200.00 35.40 164.60 1 1.50e+01 4.44e-03 8.38e+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 40.18 159.82 1 1.50e+01 4.44e-03 8.27e+01 dihedral pdb=" O4' U 1 138 " pdb=" C1' U 1 138 " pdb=" N1 U 1 138 " pdb=" C2 U 1 138 " ideal model delta sinusoidal sigma weight residual 200.00 43.27 156.73 1 1.50e+01 4.44e-03 8.19e+01 ... (remaining 101624 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.123: 29442 0.123 - 0.245: 740 0.245 - 0.368: 31 0.368 - 0.490: 1 0.490 - 0.613: 3 Chirality restraints: 30217 Sorted by residual: chirality pdb=" C3' A 1 404 " pdb=" C4' A 1 404 " pdb=" O3' A 1 404 " pdb=" C2' A 1 404 " both_signs ideal model delta sigma weight residual False -2.74 -2.13 -0.61 2.00e-01 2.50e+01 9.39e+00 chirality pdb=" C3' U 1 894 " pdb=" C4' U 1 894 " pdb=" O3' U 1 894 " pdb=" C2' U 1 894 " both_signs ideal model delta sigma weight residual False -2.74 -2.20 -0.55 2.00e-01 2.50e+01 7.44e+00 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 -1.96 -0.52 2.00e-01 2.50e+01 6.76e+00 ... (remaining 30214 not shown) Planarity restraints: 12870 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 5MC 21407 " -0.086 2.00e-02 2.50e+03 6.21e-01 8.66e+03 pdb=" C4' 5MC 21407 " -0.452 2.00e-02 2.50e+03 pdb=" O4' 5MC 21407 " -0.590 2.00e-02 2.50e+03 pdb=" C3' 5MC 21407 " 0.586 2.00e-02 2.50e+03 pdb=" O3' 5MC 21407 " 0.717 2.00e-02 2.50e+03 pdb=" C2' 5MC 21407 " 0.144 2.00e-02 2.50e+03 pdb=" O2' 5MC 21407 " -1.046 2.00e-02 2.50e+03 pdb=" C1' 5MC 21407 " -0.213 2.00e-02 2.50e+03 pdb=" N1 5MC 21407 " 0.942 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG 12445 " -0.037 2.00e-02 2.50e+03 6.12e-01 8.42e+03 pdb=" C4' 2MG 12445 " -0.469 2.00e-02 2.50e+03 pdb=" O4' 2MG 12445 " -0.839 2.00e-02 2.50e+03 pdb=" C3' 2MG 12445 " 0.586 2.00e-02 2.50e+03 pdb=" O3' 2MG 12445 " 0.565 2.00e-02 2.50e+03 pdb=" C2' 2MG 12445 " 0.260 2.00e-02 2.50e+03 pdb=" O2' 2MG 12445 " -0.866 2.00e-02 2.50e+03 pdb=" C1' 2MG 12445 " -0.166 2.00e-02 2.50e+03 pdb=" N9 2MG 12445 " 0.966 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' H2U 5 20 " -0.887 2.00e-02 2.50e+03 6.09e-01 8.34e+03 pdb=" C4' H2U 5 20 " 0.213 2.00e-02 2.50e+03 pdb=" O4' H2U 5 20 " 0.615 2.00e-02 2.50e+03 pdb=" C3' H2U 5 20 " -0.163 2.00e-02 2.50e+03 pdb=" O3' H2U 5 20 " 1.032 2.00e-02 2.50e+03 pdb=" C2' H2U 5 20 " -0.626 2.00e-02 2.50e+03 pdb=" O2' H2U 5 20 " -0.679 2.00e-02 2.50e+03 pdb=" C1' H2U 5 20 " 0.420 2.00e-02 2.50e+03 pdb=" N1 H2U 5 20 " 0.075 2.00e-02 2.50e+03 ... (remaining 12867 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 2522 2.59 - 3.16: 107161 3.16 - 3.74: 278244 3.74 - 4.32: 403425 4.32 - 4.90: 556149 Nonbonded interactions: 1347501 Sorted by model distance: nonbonded pdb=" OP1 C 1 510 " pdb="MG MG 13097 " model vdw 2.007 2.170 nonbonded pdb=" O6 G 1 776 " pdb="MG MG 13119 " model vdw 2.009 2.170 nonbonded pdb=" O4 U 11671 " pdb="MG MG 13142 " model vdw 2.020 2.170 nonbonded pdb=" OP2 G 11186 " pdb="MG MG 13069 " model vdw 2.024 2.170 nonbonded pdb=" O CYS g 87 " pdb=" OD1 ASP g 88 " model vdw 2.029 3.040 ... (remaining 1347496 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: 1.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.090 Extract box with map and model: 10.150 Check model and map are aligned: 1.640 Set scattering table: 1.000 Process input model: 624.140 Find NCS groups from input model: 3.030 Set up NCS constraints: 0.390 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:2.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 644.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 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 0.279 158905 Z= 0.497 Angle : 0.890 42.510 237521 Z= 0.457 Chirality : 0.049 0.613 30217 Planarity : 0.020 0.621 12870 Dihedral : 22.616 179.678 90669 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.97 % Favored : 93.98 % Rotamer: Outliers : 0.37 % Allowed : 3.32 % Favored : 96.31 % 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: -4.90 (0.08), residues: 5863 helix: -4.51 (0.05), residues: 1855 sheet: -2.86 (0.13), residues: 1125 loop : -2.40 (0.10), residues: 2883 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.004 TRP D 78 HIS 0.030 0.003 HIS M 13 PHE 0.047 0.004 PHE N 80 TYR 0.034 0.003 TYR B 103 ARG 0.015 0.002 ARG e 13 *********************** 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 2011 residues out of total 4878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 1993 time to evaluate : 6.472 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 23 GLU cc_start: 0.8000 (mm-30) cc_final: 0.7443 (mt-10) REVERT: B 49 ILE cc_start: 0.9405 (mt) cc_final: 0.8673 (tt) REVERT: B 64 ILE cc_start: 0.9465 (mt) cc_final: 0.9242 (mt) REVERT: B 74 ILE cc_start: 0.8425 (mt) cc_final: 0.8167 (mt) REVERT: B 96 TYR cc_start: 0.8795 (m-80) cc_final: 0.8386 (m-80) REVERT: B 178 SER cc_start: 0.8873 (p) cc_final: 0.8610 (t) REVERT: C 142 VAL cc_start: 0.9520 (m) cc_final: 0.9223 (m) REVERT: D 27 LEU cc_start: 0.9252 (tp) cc_final: 0.8930 (tt) REVERT: D 100 MET cc_start: 0.8344 (mtp) cc_final: 0.8090 (mtp) REVERT: E 123 ASP cc_start: 0.8491 (p0) cc_final: 0.8068 (p0) REVERT: E 128 TYR cc_start: 0.8825 (t80) cc_final: 0.8445 (t80) REVERT: E 129 SER cc_start: 0.9184 (t) cc_final: 0.8952 (p) REVERT: E 145 LYS cc_start: 0.7595 (mmtt) cc_final: 0.7053 (mtpt) REVERT: F 20 ASN cc_start: 0.7984 (t0) cc_final: 0.7444 (t0) REVERT: F 99 LYS cc_start: 0.8154 (mmmt) cc_final: 0.7767 (mptt) REVERT: F 157 TYR cc_start: 0.8532 (m-80) cc_final: 0.8090 (m-80) REVERT: F 163 ARG cc_start: 0.9137 (ptp-170) cc_final: 0.8695 (ptp-110) REVERT: G 1 MET cc_start: 0.7781 (tpt) cc_final: 0.7377 (tpp) REVERT: G 5 LEU cc_start: 0.8252 (mp) cc_final: 0.8046 (mm) REVERT: G 22 LYS cc_start: 0.8830 (mttm) cc_final: 0.8487 (mmtp) REVERT: G 28 ASN cc_start: 0.9148 (m-40) cc_final: 0.8455 (m-40) REVERT: G 70 GLU cc_start: 0.6383 (tt0) cc_final: 0.5193 (tp30) REVERT: J 81 ILE cc_start: 0.9437 (tp) cc_final: 0.9228 (tp) REVERT: J 139 VAL cc_start: 0.8418 (t) cc_final: 0.8174 (p) REVERT: K 12 ASP cc_start: 0.8571 (p0) cc_final: 0.8281 (p0) REVERT: K 57 VAL cc_start: 0.9054 (t) cc_final: 0.8792 (p) REVERT: K 89 ASN cc_start: 0.9022 (m-40) cc_final: 0.8723 (m-40) REVERT: K 108 ARG cc_start: 0.7969 (ptm160) cc_final: 0.7688 (ptm-80) REVERT: L 40 SER cc_start: 0.8993 (p) cc_final: 0.8769 (p) REVERT: M 27 SER cc_start: 0.8869 (m) cc_final: 0.8583 (t) REVERT: N 51 LEU cc_start: 0.9213 (mm) cc_final: 0.8840 (mt) REVERT: P 8 LEU cc_start: 0.8926 (mp) cc_final: 0.8630 (mt) REVERT: P 97 LEU cc_start: 0.9240 (mt) cc_final: 0.8886 (mp) REVERT: Q 25 TYR cc_start: 0.9338 (t80) cc_final: 0.9131 (t80) REVERT: Q 76 TYR cc_start: 0.9093 (t80) cc_final: 0.8813 (t80) REVERT: R 73 LYS cc_start: 0.8561 (mmtp) cc_final: 0.8206 (mmtt) REVERT: R 79 ARG cc_start: 0.8776 (ptt180) cc_final: 0.8545 (ptp90) REVERT: R 87 GLN cc_start: 0.7901 (tt0) cc_final: 0.7502 (tt0) REVERT: R 99 THR cc_start: 0.7533 (p) cc_final: 0.7205 (p) REVERT: S 97 LEU cc_start: 0.9170 (mm) cc_final: 0.8902 (mm) REVERT: S 99 ARG cc_start: 0.8863 (mmt90) cc_final: 0.8621 (mmt90) REVERT: S 100 THR cc_start: 0.8786 (p) cc_final: 0.8575 (p) REVERT: T 2 ILE cc_start: 0.8955 (mp) cc_final: 0.8669 (tp) REVERT: T 24 MET cc_start: 0.7850 (ttm) cc_final: 0.7612 (ttp) REVERT: U 58 ILE cc_start: 0.9280 (mt) cc_final: 0.8929 (mt) REVERT: U 73 PHE cc_start: 0.8966 (t80) cc_final: 0.8732 (t80) REVERT: V 29 ILE cc_start: 0.9180 (tt) cc_final: 0.8946 (tt) REVERT: W 14 ARG cc_start: 0.8476 (mpp-170) cc_final: 0.8116 (mtm-85) REVERT: W 29 GLU cc_start: 0.8574 (tt0) cc_final: 0.8331 (tt0) REVERT: W 55 ARG cc_start: 0.8733 (ttp80) cc_final: 0.8336 (ttp80) REVERT: W 71 VAL cc_start: 0.9359 (t) cc_final: 0.9007 (p) REVERT: X 8 THR cc_start: 0.9594 (p) cc_final: 0.9351 (m) REVERT: X 68 LEU cc_start: 0.9102 (mt) cc_final: 0.8873 (mt) REVERT: X 77 LYS cc_start: 0.8584 (mttt) cc_final: 0.8278 (mmmt) REVERT: Y 40 SER cc_start: 0.8894 (m) cc_final: 0.8273 (t) REVERT: Z 25 LEU cc_start: 0.8386 (tm) cc_final: 0.7932 (tp) REVERT: Z 38 ARG cc_start: 0.8063 (mmt-90) cc_final: 0.7741 (mpt180) REVERT: b 10 ARG cc_start: 0.9254 (pmm-80) cc_final: 0.8892 (ptp-170) REVERT: b 11 SER cc_start: 0.9097 (t) cc_final: 0.8300 (p) REVERT: b 49 TYR cc_start: 0.8343 (t80) cc_final: 0.8129 (t80) REVERT: b 50 ARG cc_start: 0.9017 (mtp180) cc_final: 0.8751 (mtm110) REVERT: d 2 LYS cc_start: 0.8928 (tttt) cc_final: 0.8576 (tttt) REVERT: d 10 LEU cc_start: 0.9123 (tp) cc_final: 0.8780 (tp) REVERT: d 11 LYS cc_start: 0.9156 (ttmt) cc_final: 0.8478 (ttpt) REVERT: d 12 ARG cc_start: 0.8808 (tpt-90) cc_final: 0.8508 (ttt90) REVERT: d 14 ARG cc_start: 0.8282 (mtt180) cc_final: 0.7868 (mtt180) REVERT: e 49 MET cc_start: 0.8842 (mmm) cc_final: 0.8641 (mmm) REVERT: e 64 TYR cc_start: 0.8845 (m-80) cc_final: 0.8281 (m-80) REVERT: f 24 ARG cc_start: 0.8344 (mtt-85) cc_final: 0.7948 (mmt90) REVERT: g 6 MET cc_start: 0.7298 (ttp) cc_final: 0.7074 (tmm) REVERT: g 27 MET cc_start: 0.8374 (mmm) cc_final: 0.7291 (mmm) REVERT: g 58 ASN cc_start: 0.7443 (t0) cc_final: 0.6768 (m-40) REVERT: g 141 LEU cc_start: 0.8508 (tp) cc_final: 0.8290 (tt) REVERT: g 223 GLU cc_start: 0.6480 (tm-30) cc_final: 0.6188 (tm-30) REVERT: h 142 MET cc_start: 0.8387 (mmm) cc_final: 0.7839 (mmm) REVERT: h 169 ARG cc_start: 0.7403 (ttm170) cc_final: 0.7077 (ttp80) REVERT: h 199 LYS cc_start: 0.8749 (mttt) cc_final: 0.8412 (mtmt) REVERT: i 5 LEU cc_start: 0.9039 (mp) cc_final: 0.8756 (mt) REVERT: i 49 SER cc_start: 0.8987 (p) cc_final: 0.8732 (p) REVERT: i 51 TYR cc_start: 0.9110 (t80) cc_final: 0.8775 (t80) REVERT: i 57 GLU cc_start: 0.8061 (tp30) cc_final: 0.7795 (tp30) REVERT: i 145 ILE cc_start: 0.9332 (mm) cc_final: 0.9080 (mm) REVERT: i 198 HIS cc_start: 0.7741 (p90) cc_final: 0.7314 (p-80) REVERT: j 71 MET cc_start: 0.6759 (mmm) cc_final: 0.6520 (tpp) REVERT: j 105 ILE cc_start: 0.9340 (mt) cc_final: 0.9042 (mt) REVERT: j 130 SER cc_start: 0.9093 (t) cc_final: 0.8773 (p) REVERT: j 156 LYS cc_start: 0.8691 (ttpt) cc_final: 0.8463 (ttpp) REVERT: k 25 TYR cc_start: 0.8790 (m-10) cc_final: 0.8522 (m-10) REVERT: k 35 LYS cc_start: 0.8364 (mmtm) cc_final: 0.8139 (mtpp) REVERT: k 102 MET cc_start: 0.7339 (ptm) cc_final: 0.6950 (ptp) REVERT: l 22 LEU cc_start: 0.7728 (tp) cc_final: 0.7339 (mm) REVERT: l 120 LEU cc_start: 0.9264 (tt) cc_final: 0.9023 (tt) REVERT: m 79 SER cc_start: 0.8855 (t) cc_final: 0.8262 (p) REVERT: m 111 MET cc_start: 0.7659 (ptp) cc_final: 0.7220 (ptp) REVERT: n 38 TYR cc_start: 0.8238 (t80) cc_final: 0.7985 (t80) REVERT: n 61 LEU cc_start: 0.8190 (pp) cc_final: 0.7860 (pp) REVERT: n 73 SER cc_start: 0.8810 (p) cc_final: 0.8537 (t) REVERT: n 124 ARG cc_start: 0.8712 (ttm-80) cc_final: 0.8505 (mtt-85) REVERT: o 40 ILE cc_start: 0.9338 (mt) cc_final: 0.9104 (mm) REVERT: o 44 THR cc_start: 0.9369 (m) cc_final: 0.9011 (p) REVERT: o 69 THR cc_start: 0.9075 (m) cc_final: 0.8575 (p) REVERT: o 80 THR cc_start: 0.7503 (p) cc_final: 0.7166 (p) REVERT: p 15 GLN cc_start: 0.8613 (tm-30) cc_final: 0.8361 (tm-30) REVERT: p 50 SER cc_start: 0.8794 (m) cc_final: 0.8412 (t) REVERT: p 87 LYS cc_start: 0.8719 (ttmt) cc_final: 0.7974 (mtpp) REVERT: q 70 GLU cc_start: 0.8670 (mt-10) cc_final: 0.8408 (mt-10) REVERT: r 13 LYS cc_start: 0.8708 (mttt) cc_final: 0.8499 (mttt) REVERT: r 16 VAL cc_start: 0.8948 (m) cc_final: 0.8566 (p) REVERT: r 31 LYS cc_start: 0.8827 (mttt) cc_final: 0.8535 (mtpp) REVERT: r 56 LEU cc_start: 0.9012 (tp) cc_final: 0.8763 (tp) REVERT: s 20 TYR cc_start: 0.8049 (m-80) cc_final: 0.7711 (m-80) REVERT: t 38 HIS cc_start: 0.8145 (t70) cc_final: 0.7931 (t-170) REVERT: v 19 LYS cc_start: 0.8249 (mttt) cc_final: 0.8039 (mmmt) REVERT: v 39 LYS cc_start: 0.8123 (mttt) cc_final: 0.7899 (mtmt) REVERT: v 80 GLU cc_start: 0.7952 (tm-30) cc_final: 0.7433 (tm-30) REVERT: x 27 ASP cc_start: 0.6347 (p0) cc_final: 0.5383 (t0) REVERT: x 37 ARG cc_start: 0.8240 (ptt180) cc_final: 0.8015 (ptt-90) REVERT: x 41 PHE cc_start: 0.8421 (m-10) cc_final: 0.8205 (m-80) REVERT: x 60 VAL cc_start: 0.8966 (t) cc_final: 0.8708 (p) REVERT: y 57 ILE cc_start: 0.8949 (tt) cc_final: 0.8695 (tt) REVERT: z 12 PHE cc_start: 0.7605 (t80) cc_final: 0.7327 (t80) REVERT: A 165 LYS cc_start: 0.8634 (tttt) cc_final: 0.8396 (ttmm) REVERT: A 202 THR cc_start: 0.9647 (t) cc_final: 0.9378 (p) REVERT: A 208 GLU cc_start: 0.8165 (tt0) cc_final: 0.7922 (tt0) REVERT: A 317 VAL cc_start: 0.8801 (t) cc_final: 0.8467 (p) REVERT: A 345 ILE cc_start: 0.8003 (mt) cc_final: 0.7757 (mt) outliers start: 18 outliers final: 5 residues processed: 2004 average time/residue: 1.5287 time to fit residues: 5180.1346 Evaluate side-chains 1389 residues out of total 4878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 1384 time to evaluate : 6.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 168 VAL Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain h residue 200 VAL Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 217 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1034 random chunks: chunk 873 optimal weight: 9.9990 chunk 783 optimal weight: 9.9990 chunk 434 optimal weight: 10.0000 chunk 267 optimal weight: 7.9990 chunk 528 optimal weight: 9.9990 chunk 418 optimal weight: 10.0000 chunk 810 optimal weight: 0.9980 chunk 313 optimal weight: 8.9990 chunk 492 optimal weight: 3.9990 chunk 603 optimal weight: 8.9990 chunk 938 optimal weight: 2.9990 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 86 ASN ** C 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 136 ASN D 24 ASN D 115 GLN ** D 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 163 ASN F 45 HIS F 73 ASN F 128 GLN G 11 ASN G 33 GLN K 3 GLN L 35 HIS L 54 GLN ** M 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 62 ASN O 29 HIS O 38 GLN O 61 GLN ** Q 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 60 HIS T 70 HIS U 46 GLN V 49 ASN V 78 GLN Y 45 GLN ** Z 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 34 HIS a 20 ASN ** a 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 19 HIS c 26 ASN d 6 GLN ** f 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 51 ASN g 94 HIS g 109 GLN g 120 GLN g 177 ASN h 102 ASN i 59 GLN i 74 ASN ** i 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 126 ASN i 131 ASN i 152 GLN j 12 GLN j 132 ASN k 55 HIS ** k 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 15 HIS ** o 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 64 GLN p 22 HIS p 40 ASN q 59 ASN r 8 ASN s 62 ASN t 20 ASN t 40 GLN u 9 HIS u 29 ASN x 14 HIS x 52 HIS x 69 HIS ** y 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 78 ASN z 56 HIS A 218 ASN ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 349 GLN Total number of N/Q/H flips: 60 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 158905 Z= 0.392 Angle : 0.756 16.646 237521 Z= 0.395 Chirality : 0.041 0.305 30217 Planarity : 0.007 0.132 12870 Dihedral : 23.521 179.370 78939 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.36 % Favored : 94.63 % Rotamer: Outliers : 4.41 % Allowed : 11.93 % Favored : 83.66 % 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: -3.64 (0.09), residues: 5863 helix: -2.89 (0.09), residues: 1914 sheet: -2.41 (0.14), residues: 1122 loop : -1.92 (0.11), residues: 2827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 78 HIS 0.015 0.002 HIS M 13 PHE 0.024 0.002 PHE O 117 TYR 0.031 0.002 TYR B 103 ARG 0.009 0.001 ARG O 102 *********************** 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 1691 residues out of total 4878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 215 poor density : 1476 time to evaluate : 6.457 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: B 18 LYS cc_start: 0.9207 (mttt) cc_final: 0.8919 (mtpt) REVERT: B 23 GLU cc_start: 0.7955 (mm-30) cc_final: 0.7647 (mt-10) REVERT: B 30 PHE cc_start: 0.8587 (t80) cc_final: 0.8092 (t80) REVERT: B 74 ILE cc_start: 0.8337 (mt) cc_final: 0.8112 (mt) REVERT: B 96 TYR cc_start: 0.8915 (m-80) cc_final: 0.8589 (m-80) REVERT: B 255 LYS cc_start: 0.8919 (tttm) cc_final: 0.8716 (tttp) REVERT: B 269 ARG cc_start: 0.7522 (mtp-110) cc_final: 0.7317 (mtm110) REVERT: C 45 TYR cc_start: 0.8353 (p90) cc_final: 0.7795 (p90) REVERT: C 176 ASP cc_start: 0.7837 (t0) cc_final: 0.7495 (t0) REVERT: D 19 PHE cc_start: 0.9090 (m-80) cc_final: 0.8834 (m-10) REVERT: D 139 LYS cc_start: 0.8323 (ttpt) cc_final: 0.8105 (ttmm) REVERT: E 57 LEU cc_start: 0.9331 (OUTLIER) cc_final: 0.9118 (tt) REVERT: E 129 SER cc_start: 0.9463 (t) cc_final: 0.9057 (p) REVERT: E 145 LYS cc_start: 0.7804 (mmtt) cc_final: 0.7180 (mtpt) REVERT: F 20 ASN cc_start: 0.7965 (t0) cc_final: 0.7579 (t0) REVERT: F 117 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8347 (mm) REVERT: F 130 GLU cc_start: 0.7834 (mm-30) cc_final: 0.7044 (mm-30) REVERT: F 157 TYR cc_start: 0.8586 (m-80) cc_final: 0.8101 (m-80) REVERT: F 163 ARG cc_start: 0.9258 (ptp-170) cc_final: 0.9023 (ptp-170) REVERT: G 22 LYS cc_start: 0.8787 (mttm) cc_final: 0.8542 (mmtp) REVERT: J 17 VAL cc_start: 0.9195 (t) cc_final: 0.8836 (p) REVERT: J 81 ILE cc_start: 0.9409 (tp) cc_final: 0.9169 (tp) REVERT: J 98 GLU cc_start: 0.8319 (mp0) cc_final: 0.8021 (mp0) REVERT: J 101 ILE cc_start: 0.9572 (mm) cc_final: 0.9252 (mm) REVERT: J 139 VAL cc_start: 0.8473 (t) cc_final: 0.8109 (p) REVERT: K 12 ASP cc_start: 0.8809 (p0) cc_final: 0.8435 (p0) REVERT: K 89 ASN cc_start: 0.8906 (m-40) cc_final: 0.8690 (m-40) REVERT: K 108 ARG cc_start: 0.7956 (ptm160) cc_final: 0.7713 (ptm-80) REVERT: M 17 ASN cc_start: 0.8996 (t0) cc_final: 0.7795 (t0) REVERT: M 27 SER cc_start: 0.8762 (m) cc_final: 0.8432 (t) REVERT: M 53 MET cc_start: 0.7691 (ptp) cc_final: 0.7315 (ptp) REVERT: M 76 LYS cc_start: 0.8797 (mtpp) cc_final: 0.8439 (mmmm) REVERT: N 51 LEU cc_start: 0.9018 (mm) cc_final: 0.8776 (mt) REVERT: N 78 LYS cc_start: 0.8955 (tttt) cc_final: 0.8748 (tttt) REVERT: O 17 LYS cc_start: 0.8815 (tppt) cc_final: 0.8491 (tppt) REVERT: O 48 LEU cc_start: 0.8870 (mm) cc_final: 0.8668 (mt) REVERT: P 87 LYS cc_start: 0.8108 (mmtm) cc_final: 0.7705 (mptt) REVERT: Q 66 ASN cc_start: 0.9001 (t0) cc_final: 0.8679 (t0) REVERT: Q 87 SER cc_start: 0.8812 (t) cc_final: 0.8569 (p) REVERT: R 79 ARG cc_start: 0.8817 (ptt180) cc_final: 0.8518 (ptp90) REVERT: R 80 ARG cc_start: 0.8848 (ptp90) cc_final: 0.8353 (ptp90) REVERT: S 49 LYS cc_start: 0.9055 (ttmt) cc_final: 0.8817 (mtpp) REVERT: S 84 ARG cc_start: 0.9144 (mmt-90) cc_final: 0.8884 (mmt-90) REVERT: S 99 ARG cc_start: 0.9002 (mmt90) cc_final: 0.8703 (mtt-85) REVERT: T 1 MET cc_start: 0.6881 (tpt) cc_final: 0.5540 (ppp) REVERT: T 3 ARG cc_start: 0.7906 (ttp80) cc_final: 0.7700 (ttp-110) REVERT: T 24 MET cc_start: 0.7864 (ttm) cc_final: 0.7646 (ttp) REVERT: T 28 ASN cc_start: 0.8939 (t0) cc_final: 0.8710 (m-40) REVERT: U 58 ILE cc_start: 0.9232 (mt) cc_final: 0.8975 (mt) REVERT: V 11 GLU cc_start: 0.6639 (pm20) cc_final: 0.6282 (pt0) REVERT: V 29 ILE cc_start: 0.9284 (tt) cc_final: 0.8952 (tt) REVERT: V 71 LYS cc_start: 0.8996 (mtpp) cc_final: 0.8766 (mmmt) REVERT: W 55 ARG cc_start: 0.8697 (ttp80) cc_final: 0.8446 (ttp80) REVERT: W 75 LYS cc_start: 0.9103 (mtpp) cc_final: 0.8882 (mtpp) REVERT: X 8 THR cc_start: 0.9555 (p) cc_final: 0.9328 (m) REVERT: X 68 LEU cc_start: 0.9164 (mt) cc_final: 0.8919 (mt) REVERT: X 77 LYS cc_start: 0.8503 (mttt) cc_final: 0.8070 (mmmt) REVERT: Y 49 ASP cc_start: 0.7396 (m-30) cc_final: 0.7104 (m-30) REVERT: Z 25 LEU cc_start: 0.8559 (tm) cc_final: 0.8101 (tp) REVERT: Z 47 MET cc_start: 0.7526 (mtm) cc_final: 0.7180 (mtp) REVERT: a 13 THR cc_start: 0.8045 (OUTLIER) cc_final: 0.7668 (m) REVERT: b 11 SER cc_start: 0.8996 (t) cc_final: 0.8747 (p) REVERT: b 40 ARG cc_start: 0.9153 (OUTLIER) cc_final: 0.8641 (tpt90) REVERT: b 49 TYR cc_start: 0.8371 (t80) cc_final: 0.7994 (t80) REVERT: d 14 ARG cc_start: 0.8226 (mtt180) cc_final: 0.7870 (mtt180) REVERT: d 33 ARG cc_start: 0.8987 (mtm-85) cc_final: 0.8764 (mtm180) REVERT: f 1 MET cc_start: 0.8181 (tpp) cc_final: 0.7941 (tpp) REVERT: f 9 LYS cc_start: 0.8276 (mtpt) cc_final: 0.7998 (mttt) REVERT: g 6 MET cc_start: 0.7228 (ttp) cc_final: 0.7005 (tmm) REVERT: g 27 MET cc_start: 0.8488 (mmm) cc_final: 0.7649 (mmm) REVERT: g 120 GLN cc_start: 0.7385 (OUTLIER) cc_final: 0.7058 (tt0) REVERT: g 136 MET cc_start: 0.7613 (mmt) cc_final: 0.7200 (mmm) REVERT: g 223 GLU cc_start: 0.6507 (tm-30) cc_final: 0.6033 (tp30) REVERT: h 142 MET cc_start: 0.8683 (mmm) cc_final: 0.7696 (mmm) REVERT: h 169 ARG cc_start: 0.7507 (ttm170) cc_final: 0.7164 (ttp80) REVERT: h 188 GLU cc_start: 0.7852 (mt-10) cc_final: 0.7636 (mt-10) REVERT: i 5 LEU cc_start: 0.9035 (mp) cc_final: 0.8767 (mt) REVERT: i 51 TYR cc_start: 0.8935 (t80) cc_final: 0.8542 (t80) REVERT: i 57 GLU cc_start: 0.7964 (tp30) cc_final: 0.7561 (tp30) REVERT: i 145 ILE cc_start: 0.9370 (mm) cc_final: 0.9131 (mt) REVERT: j 45 ARG cc_start: 0.7627 (mtp-110) cc_final: 0.7426 (mtp-110) REVERT: j 130 SER cc_start: 0.9267 (t) cc_final: 0.8866 (p) REVERT: j 156 LYS cc_start: 0.8920 (ttpt) cc_final: 0.8578 (ttmm) REVERT: k 2 ARG cc_start: 0.8043 (mtp85) cc_final: 0.7495 (mtp85) REVERT: k 14 GLN cc_start: 0.7552 (mm-40) cc_final: 0.7059 (tm-30) REVERT: k 38 ARG cc_start: 0.8228 (ptt-90) cc_final: 0.7957 (ptt-90) REVERT: k 65 GLU cc_start: 0.7226 (tt0) cc_final: 0.6769 (tt0) REVERT: k 91 ARG cc_start: 0.8001 (ttt180) cc_final: 0.7722 (ttt180) REVERT: l 22 LEU cc_start: 0.7725 (tp) cc_final: 0.7011 (mm) REVERT: l 50 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8373 (tm) REVERT: l 118 LEU cc_start: 0.7747 (tt) cc_final: 0.7286 (mp) REVERT: m 9 ASP cc_start: 0.7943 (t0) cc_final: 0.7540 (t0) REVERT: m 79 SER cc_start: 0.8733 (t) cc_final: 0.8311 (p) REVERT: m 83 LEU cc_start: 0.9465 (OUTLIER) cc_final: 0.9226 (tp) REVERT: m 111 MET cc_start: 0.7588 (ptp) cc_final: 0.7225 (ptp) REVERT: n 35 LEU cc_start: 0.9331 (tp) cc_final: 0.9018 (tp) REVERT: n 38 TYR cc_start: 0.8324 (t80) cc_final: 0.8062 (t80) REVERT: n 57 MET cc_start: 0.7633 (mtt) cc_final: 0.7428 (mtp) REVERT: n 61 LEU cc_start: 0.8360 (pp) cc_final: 0.7928 (pp) REVERT: n 124 ARG cc_start: 0.8891 (ttm-80) cc_final: 0.8550 (mtt-85) REVERT: o 69 THR cc_start: 0.9017 (m) cc_final: 0.8434 (p) REVERT: o 100 ILE cc_start: 0.8843 (mp) cc_final: 0.8449 (mt) REVERT: p 85 MET cc_start: 0.7877 (mtp) cc_final: 0.7592 (mmt) REVERT: p 119 ASN cc_start: 0.8173 (OUTLIER) cc_final: 0.7957 (m-40) REVERT: q 35 THR cc_start: 0.8958 (m) cc_final: 0.8690 (m) REVERT: q 51 LYS cc_start: 0.8344 (mptt) cc_final: 0.7928 (mmtm) REVERT: q 53 CYS cc_start: 0.8790 (p) cc_final: 0.8338 (p) REVERT: q 55 VAL cc_start: 0.9179 (OUTLIER) cc_final: 0.8835 (p) REVERT: q 70 GLU cc_start: 0.8646 (mt-10) cc_final: 0.8433 (mt-10) REVERT: r 13 LYS cc_start: 0.8735 (mttt) cc_final: 0.8530 (mttt) REVERT: r 17 ILE cc_start: 0.8740 (OUTLIER) cc_final: 0.8322 (mp) REVERT: r 31 LYS cc_start: 0.8811 (mttt) cc_final: 0.8553 (mtpp) REVERT: r 55 THR cc_start: 0.7151 (m) cc_final: 0.6906 (m) REVERT: s 69 ARG cc_start: 0.9085 (ttt90) cc_final: 0.8700 (ttt90) REVERT: s 92 GLU cc_start: 0.7319 (mp0) cc_final: 0.6871 (mm-30) REVERT: t 10 LYS cc_start: 0.7807 (mmmm) cc_final: 0.7491 (mtpt) REVERT: t 38 HIS cc_start: 0.8310 (t70) cc_final: 0.8039 (t-170) REVERT: t 67 LEU cc_start: 0.9210 (OUTLIER) cc_final: 0.8402 (mm) REVERT: v 19 LYS cc_start: 0.7821 (mttt) cc_final: 0.7222 (mmmt) REVERT: v 80 GLU cc_start: 0.8319 (tm-30) cc_final: 0.7468 (tm-30) REVERT: x 16 LEU cc_start: 0.7940 (OUTLIER) cc_final: 0.7717 (tp) REVERT: x 27 ASP cc_start: 0.6229 (p0) cc_final: 0.5027 (t0) REVERT: x 35 SER cc_start: 0.8552 (m) cc_final: 0.8203 (p) REVERT: y 39 ILE cc_start: 0.8939 (mt) cc_final: 0.8586 (mt) REVERT: y 61 GLN cc_start: 0.8569 (mm-40) cc_final: 0.8103 (mm-40) REVERT: z 12 PHE cc_start: 0.7462 (t80) cc_final: 0.7143 (t80) REVERT: z 36 GLU cc_start: 0.7180 (tt0) cc_final: 0.6964 (tt0) REVERT: A 165 LYS cc_start: 0.8485 (tttt) cc_final: 0.8232 (ttmm) REVERT: A 196 ILE cc_start: 0.8955 (OUTLIER) cc_final: 0.8701 (pt) REVERT: A 305 ASP cc_start: 0.8258 (p0) cc_final: 0.7923 (p0) REVERT: A 317 VAL cc_start: 0.8947 (t) cc_final: 0.8630 (p) outliers start: 215 outliers final: 153 residues processed: 1578 average time/residue: 1.4449 time to fit residues: 3945.1451 Evaluate side-chains 1493 residues out of total 4878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 1327 time to evaluate : 6.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 6 CYS Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 201 MET Chi-restraints excluded: chain C residue 18 ASP Chi-restraints excluded: chain C residue 28 GLU Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 7 ASP Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain D residue 80 SER Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 87 CYS Chi-restraints excluded: chain E residue 141 ILE Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 39 ASP Chi-restraints excluded: chain F residue 49 THR Chi-restraints excluded: chain F residue 77 ILE Chi-restraints excluded: chain F residue 84 THR Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 127 THR Chi-restraints excluded: chain F residue 168 VAL Chi-restraints excluded: chain F residue 171 THR Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 61 VAL Chi-restraints excluded: chain K residue 110 GLU Chi-restraints excluded: chain K residue 117 SER Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 23 ILE Chi-restraints excluded: chain L residue 80 SER Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 30 SER Chi-restraints excluded: chain M residue 36 VAL Chi-restraints excluded: chain M residue 42 THR Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 78 LEU Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain N residue 33 ILE Chi-restraints excluded: chain O residue 19 GLN Chi-restraints excluded: chain O residue 63 LYS Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain P residue 32 VAL Chi-restraints excluded: chain P residue 76 THR Chi-restraints excluded: chain P residue 80 VAL Chi-restraints excluded: chain P residue 83 SER Chi-restraints excluded: chain P residue 114 LEU Chi-restraints excluded: chain S residue 3 THR Chi-restraints excluded: chain S residue 37 THR Chi-restraints excluded: chain S residue 53 SER Chi-restraints excluded: chain S residue 85 ILE Chi-restraints excluded: chain T residue 21 SER Chi-restraints excluded: chain T residue 27 SER Chi-restraints excluded: chain T residue 57 VAL Chi-restraints excluded: chain T residue 63 VAL Chi-restraints excluded: chain T residue 74 ILE Chi-restraints excluded: chain U residue 15 THR Chi-restraints excluded: chain U residue 18 ASP Chi-restraints excluded: chain U residue 22 ARG Chi-restraints excluded: chain U residue 28 VAL Chi-restraints excluded: chain U residue 31 SER Chi-restraints excluded: chain W residue 12 ASN Chi-restraints excluded: chain W residue 21 LEU Chi-restraints excluded: chain W residue 30 SER Chi-restraints excluded: chain W residue 43 THR Chi-restraints excluded: chain W residue 67 VAL Chi-restraints excluded: chain X residue 19 SER Chi-restraints excluded: chain X residue 48 THR Chi-restraints excluded: chain X residue 66 THR Chi-restraints excluded: chain Y residue 22 LEU Chi-restraints excluded: chain a residue 13 THR Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain b residue 40 ARG Chi-restraints excluded: chain b residue 54 VAL Chi-restraints excluded: chain c residue 13 SER Chi-restraints excluded: chain c residue 29 THR Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 42 LEU Chi-restraints excluded: chain e residue 32 ILE Chi-restraints excluded: chain e residue 51 SER Chi-restraints excluded: chain g residue 109 GLN Chi-restraints excluded: chain g residue 120 GLN Chi-restraints excluded: chain g residue 137 ARG Chi-restraints excluded: chain g residue 138 THR Chi-restraints excluded: chain g residue 199 VAL Chi-restraints excluded: chain h residue 35 SER Chi-restraints excluded: chain h residue 105 GLU Chi-restraints excluded: chain h residue 165 THR Chi-restraints excluded: chain h residue 177 THR Chi-restraints excluded: chain h residue 200 VAL Chi-restraints excluded: chain i residue 144 SER Chi-restraints excluded: chain i residue 152 GLN Chi-restraints excluded: chain i residue 153 SER Chi-restraints excluded: chain j residue 78 ASN Chi-restraints excluded: chain j residue 103 THR Chi-restraints excluded: chain j residue 120 VAL Chi-restraints excluded: chain k residue 7 VAL Chi-restraints excluded: chain k residue 55 HIS Chi-restraints excluded: chain k residue 70 VAL Chi-restraints excluded: chain k residue 73 GLU Chi-restraints excluded: chain k residue 84 VAL Chi-restraints excluded: chain l residue 20 SER Chi-restraints excluded: chain l residue 50 LEU Chi-restraints excluded: chain l residue 77 SER Chi-restraints excluded: chain m residue 51 VAL Chi-restraints excluded: chain m residue 55 THR Chi-restraints excluded: chain m residue 83 LEU Chi-restraints excluded: chain m residue 104 VAL Chi-restraints excluded: chain m residue 105 SER Chi-restraints excluded: chain n residue 22 LYS Chi-restraints excluded: chain n residue 29 VAL Chi-restraints excluded: chain n residue 116 VAL Chi-restraints excluded: chain o residue 77 VAL Chi-restraints excluded: chain p residue 16 VAL Chi-restraints excluded: chain p residue 35 THR Chi-restraints excluded: chain p residue 40 ASN Chi-restraints excluded: chain p residue 55 SER Chi-restraints excluded: chain p residue 83 GLU Chi-restraints excluded: chain p residue 110 ILE Chi-restraints excluded: chain p residue 119 ASN Chi-restraints excluded: chain p residue 125 LYS Chi-restraints excluded: chain q residue 33 VAL Chi-restraints excluded: chain q residue 55 VAL Chi-restraints excluded: chain q residue 59 ASN Chi-restraints excluded: chain r residue 7 ILE Chi-restraints excluded: chain r residue 17 ILE Chi-restraints excluded: chain r residue 19 LEU Chi-restraints excluded: chain r residue 30 SER Chi-restraints excluded: chain r residue 65 VAL Chi-restraints excluded: chain t residue 67 LEU Chi-restraints excluded: chain t residue 75 VAL Chi-restraints excluded: chain t residue 87 LEU Chi-restraints excluded: chain u residue 24 SER Chi-restraints excluded: chain v residue 14 SER Chi-restraints excluded: chain v residue 38 ILE Chi-restraints excluded: chain v residue 55 ILE Chi-restraints excluded: chain v residue 58 VAL Chi-restraints excluded: chain v residue 67 LEU Chi-restraints excluded: chain v residue 70 THR Chi-restraints excluded: chain x residue 13 LEU Chi-restraints excluded: chain x residue 16 LEU Chi-restraints excluded: chain x residue 79 THR Chi-restraints excluded: chain y residue 23 SER Chi-restraints excluded: chain y residue 26 SER Chi-restraints excluded: chain z residue 22 SER Chi-restraints excluded: chain A residue 110 ASN Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 221 ASP Chi-restraints excluded: chain A residue 282 GLU Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 323 ASN Chi-restraints excluded: chain A residue 341 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1034 random chunks: chunk 521 optimal weight: 0.9980 chunk 291 optimal weight: 7.9990 chunk 781 optimal weight: 9.9990 chunk 639 optimal weight: 7.9990 chunk 259 optimal weight: 6.9990 chunk 940 optimal weight: 0.9990 chunk 1016 optimal weight: 0.9990 chunk 837 optimal weight: 3.9990 chunk 932 optimal weight: 2.9990 chunk 320 optimal weight: 10.0000 chunk 754 optimal weight: 0.0970 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 9 GLN D 24 ASN F 45 HIS G 28 ASN G 33 GLN K 3 GLN L 54 GLN N 18 GLN N 62 ASN O 67 ASN Q 37 GLN R 87 GLN T 70 HIS U 46 GLN V 24 ASN Y 41 HIS Y 45 GLN ** a 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 102 ASN h 190 HIS i 71 GLN i 74 ASN i 131 ASN ** i 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 198 HIS j 12 GLN k 63 ASN ** l 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 16 ASN p 40 ASN q 20 ASN q 75 GLN u 9 HIS x 43 ASN y 21 ASN y 78 ASN A 197 HIS A 348 HIS Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.3012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 158905 Z= 0.144 Angle : 0.576 14.289 237521 Z= 0.314 Chirality : 0.032 0.237 30217 Planarity : 0.006 0.124 12870 Dihedral : 23.378 178.742 78938 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 3.38 % Allowed : 15.89 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.72 (0.10), residues: 5863 helix: -1.76 (0.11), residues: 1924 sheet: -1.92 (0.14), residues: 1135 loop : -1.65 (0.11), residues: 2804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP s 42 HIS 0.032 0.001 HIS k 55 PHE 0.021 0.002 PHE y 51 TYR 0.016 0.001 TYR B 103 ARG 0.008 0.001 ARG M 59 *********************** 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 1672 residues out of total 4878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 1507 time to evaluate : 6.442 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: B 96 TYR cc_start: 0.8792 (m-80) cc_final: 0.7621 (m-80) REVERT: B 177 ARG cc_start: 0.8445 (tpt170) cc_final: 0.8195 (tpt90) REVERT: D 22 ASP cc_start: 0.7767 (m-30) cc_final: 0.7463 (m-30) REVERT: D 116 ASP cc_start: 0.7994 (t0) cc_final: 0.7600 (t0) REVERT: D 158 PHE cc_start: 0.8103 (t80) cc_final: 0.7864 (t80) REVERT: E 128 TYR cc_start: 0.8899 (t80) cc_final: 0.8629 (t80) REVERT: E 129 SER cc_start: 0.9194 (t) cc_final: 0.8941 (p) REVERT: E 145 LYS cc_start: 0.7563 (mmtt) cc_final: 0.7060 (mtpt) REVERT: F 20 ASN cc_start: 0.7944 (t0) cc_final: 0.7546 (t0) REVERT: F 117 LEU cc_start: 0.8505 (mm) cc_final: 0.8150 (mm) REVERT: F 130 GLU cc_start: 0.8021 (mm-30) cc_final: 0.7557 (mp0) REVERT: F 153 ARG cc_start: 0.7450 (mtp180) cc_final: 0.7240 (mtp-110) REVERT: F 157 TYR cc_start: 0.8584 (m-80) cc_final: 0.8062 (m-80) REVERT: G 1 MET cc_start: 0.7652 (tpp) cc_final: 0.7007 (ttt) REVERT: G 28 ASN cc_start: 0.9370 (m-40) cc_final: 0.8738 (m-40) REVERT: G 55 GLU cc_start: 0.7518 (mm-30) cc_final: 0.7131 (mm-30) REVERT: J 17 VAL cc_start: 0.9032 (OUTLIER) cc_final: 0.8702 (p) REVERT: J 81 ILE cc_start: 0.9237 (tp) cc_final: 0.8973 (tp) REVERT: J 98 GLU cc_start: 0.8191 (mp0) cc_final: 0.7946 (mp0) REVERT: J 101 ILE cc_start: 0.9403 (mm) cc_final: 0.9117 (mm) REVERT: J 139 VAL cc_start: 0.8301 (t) cc_final: 0.7909 (p) REVERT: K 12 ASP cc_start: 0.8708 (p0) cc_final: 0.8373 (p0) REVERT: K 108 ARG cc_start: 0.7858 (ptm160) cc_final: 0.7613 (ptm-80) REVERT: L 105 ILE cc_start: 0.9045 (mm) cc_final: 0.8816 (mt) REVERT: M 27 SER cc_start: 0.8565 (m) cc_final: 0.8309 (t) REVERT: M 76 LYS cc_start: 0.8743 (mtpp) cc_final: 0.8363 (mmmm) REVERT: M 124 LEU cc_start: 0.8970 (mp) cc_final: 0.8707 (mt) REVERT: P 11 GLU cc_start: 0.7950 (pt0) cc_final: 0.7688 (pt0) REVERT: P 53 ARG cc_start: 0.8297 (mmt-90) cc_final: 0.7944 (mmt-90) REVERT: P 106 LYS cc_start: 0.8835 (mmtt) cc_final: 0.8080 (mmtp) REVERT: Q 66 ASN cc_start: 0.8887 (t0) cc_final: 0.8471 (t0) REVERT: Q 71 GLN cc_start: 0.8513 (tp-100) cc_final: 0.8211 (tp40) REVERT: S 99 ARG cc_start: 0.8956 (mmt90) cc_final: 0.8441 (mtt-85) REVERT: T 1 MET cc_start: 0.6640 (tpt) cc_final: 0.5302 (ppp) REVERT: T 3 ARG cc_start: 0.7734 (ttp80) cc_final: 0.7522 (ttp-110) REVERT: T 28 ASN cc_start: 0.8916 (t0) cc_final: 0.8577 (m-40) REVERT: T 86 THR cc_start: 0.8653 (m) cc_final: 0.8379 (t) REVERT: U 73 PHE cc_start: 0.8868 (t80) cc_final: 0.8607 (t80) REVERT: V 29 ILE cc_start: 0.9277 (tt) cc_final: 0.8901 (tt) REVERT: W 55 ARG cc_start: 0.8552 (ttp80) cc_final: 0.8349 (ttp80) REVERT: W 75 LYS cc_start: 0.9049 (mtpp) cc_final: 0.8654 (mttp) REVERT: W 82 ILE cc_start: 0.8767 (mm) cc_final: 0.8552 (mm) REVERT: X 68 LEU cc_start: 0.9288 (mt) cc_final: 0.9079 (mt) REVERT: X 77 LYS cc_start: 0.8423 (mttt) cc_final: 0.7993 (mmmt) REVERT: Y 4 LYS cc_start: 0.8363 (mptt) cc_final: 0.7627 (mptt) REVERT: Y 49 ASP cc_start: 0.7334 (m-30) cc_final: 0.7105 (m-30) REVERT: Z 25 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.8051 (tp) REVERT: b 11 SER cc_start: 0.9152 (t) cc_final: 0.8714 (p) REVERT: b 49 TYR cc_start: 0.8146 (t80) cc_final: 0.7632 (t80) REVERT: d 14 ARG cc_start: 0.8333 (mtt180) cc_final: 0.7901 (mtt180) REVERT: d 25 LYS cc_start: 0.9268 (tmmt) cc_final: 0.8846 (ttpp) REVERT: f 1 MET cc_start: 0.8166 (tpp) cc_final: 0.7965 (tpt) REVERT: f 9 LYS cc_start: 0.8225 (mtpt) cc_final: 0.7965 (mttt) REVERT: f 19 ARG cc_start: 0.9013 (mtm-85) cc_final: 0.8804 (mtm-85) REVERT: g 15 HIS cc_start: 0.8769 (p-80) cc_final: 0.8526 (p-80) REVERT: g 27 MET cc_start: 0.8356 (mmm) cc_final: 0.7064 (mmm) REVERT: g 50 PHE cc_start: 0.8193 (t80) cc_final: 0.7940 (t80) REVERT: g 138 THR cc_start: 0.8528 (OUTLIER) cc_final: 0.8075 (m) REVERT: h 100 GLN cc_start: 0.8408 (tt0) cc_final: 0.7831 (tt0) REVERT: h 110 GLU cc_start: 0.8359 (mp0) cc_final: 0.8111 (mp0) REVERT: h 142 MET cc_start: 0.8606 (mmm) cc_final: 0.8226 (mmm) REVERT: h 169 ARG cc_start: 0.7421 (ttm170) cc_final: 0.7188 (ttp80) REVERT: h 188 GLU cc_start: 0.7732 (mt-10) cc_final: 0.7445 (mt-10) REVERT: i 19 LEU cc_start: 0.8782 (mt) cc_final: 0.8578 (mp) REVERT: i 51 TYR cc_start: 0.8694 (t80) cc_final: 0.8329 (t80) REVERT: i 57 GLU cc_start: 0.7902 (tp30) cc_final: 0.7452 (tp30) REVERT: i 118 VAL cc_start: 0.9124 (t) cc_final: 0.8893 (m) REVERT: i 145 ILE cc_start: 0.9071 (mm) cc_final: 0.8655 (mt) REVERT: i 187 GLU cc_start: 0.7012 (mm-30) cc_final: 0.6660 (mp0) REVERT: i 195 ILE cc_start: 0.8322 (mm) cc_final: 0.8115 (mm) REVERT: j 86 LYS cc_start: 0.7718 (mtmt) cc_final: 0.7491 (mttt) REVERT: j 152 MET cc_start: 0.7403 (ttm) cc_final: 0.7200 (ttm) REVERT: j 156 LYS cc_start: 0.8881 (ttpt) cc_final: 0.8641 (ttmm) REVERT: k 24 ARG cc_start: 0.8109 (mtm-85) cc_final: 0.7868 (mtm180) REVERT: k 49 TYR cc_start: 0.8490 (p90) cc_final: 0.8234 (p90) REVERT: k 65 GLU cc_start: 0.6774 (tt0) cc_final: 0.6567 (tt0) REVERT: l 22 LEU cc_start: 0.7007 (tp) cc_final: 0.6346 (mm) REVERT: l 50 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8380 (tm) REVERT: l 118 LEU cc_start: 0.7675 (tt) cc_final: 0.7116 (mp) REVERT: m 9 ASP cc_start: 0.7934 (t0) cc_final: 0.7433 (t0) REVERT: m 79 SER cc_start: 0.8507 (t) cc_final: 0.8131 (p) REVERT: m 83 LEU cc_start: 0.9293 (OUTLIER) cc_final: 0.9040 (tp) REVERT: n 27 LYS cc_start: 0.8202 (mtmm) cc_final: 0.7094 (tptt) REVERT: n 38 TYR cc_start: 0.8296 (t80) cc_final: 0.7947 (t80) REVERT: n 61 LEU cc_start: 0.8322 (OUTLIER) cc_final: 0.7857 (mt) REVERT: n 83 ILE cc_start: 0.8730 (mm) cc_final: 0.8429 (mt) REVERT: o 31 ARG cc_start: 0.7124 (mtp-110) cc_final: 0.6915 (mtm-85) REVERT: o 69 THR cc_start: 0.9025 (m) cc_final: 0.8463 (p) REVERT: o 100 ILE cc_start: 0.8967 (mp) cc_final: 0.8271 (mm) REVERT: p 40 ASN cc_start: 0.8041 (m110) cc_final: 0.7439 (m110) REVERT: p 85 MET cc_start: 0.7608 (mtp) cc_final: 0.7406 (mmm) REVERT: p 87 LYS cc_start: 0.8173 (ttmm) cc_final: 0.7727 (ttpp) REVERT: q 56 ARG cc_start: 0.8078 (tpp-160) cc_final: 0.7592 (tpp-160) REVERT: q 61 PHE cc_start: 0.8641 (m-10) cc_final: 0.8425 (m-10) REVERT: q 62 GLU cc_start: 0.7439 (tp30) cc_final: 0.6417 (tp30) REVERT: q 67 ILE cc_start: 0.9324 (mp) cc_final: 0.9073 (mp) REVERT: r 16 VAL cc_start: 0.8957 (m) cc_final: 0.8554 (p) REVERT: r 31 LYS cc_start: 0.8736 (mttt) cc_final: 0.8420 (mtpp) REVERT: r 71 ARG cc_start: 0.8000 (mtm110) cc_final: 0.7625 (mtm110) REVERT: r 81 MET cc_start: 0.7263 (mmm) cc_final: 0.6650 (mtt) REVERT: s 6 MET cc_start: 0.8536 (mmt) cc_final: 0.8269 (mmt) REVERT: t 10 LYS cc_start: 0.8270 (mmmm) cc_final: 0.7645 (ttpt) REVERT: t 38 HIS cc_start: 0.8279 (t70) cc_final: 0.8037 (t-170) REVERT: t 74 ASP cc_start: 0.7020 (t70) cc_final: 0.6728 (t0) REVERT: t 77 ARG cc_start: 0.7995 (mtp180) cc_final: 0.7745 (mtm180) REVERT: v 17 MET cc_start: 0.9104 (ptt) cc_final: 0.8825 (ptt) REVERT: v 19 LYS cc_start: 0.7564 (mttt) cc_final: 0.7175 (mmmt) REVERT: v 39 LYS cc_start: 0.8628 (mtmt) cc_final: 0.8338 (mtmt) REVERT: v 80 GLU cc_start: 0.8141 (tm-30) cc_final: 0.7483 (tm-30) REVERT: x 16 LEU cc_start: 0.8080 (OUTLIER) cc_final: 0.7810 (tp) REVERT: x 18 LYS cc_start: 0.8145 (mttm) cc_final: 0.7829 (mtpp) REVERT: x 32 ARG cc_start: 0.6943 (OUTLIER) cc_final: 0.6050 (ptt-90) REVERT: x 38 SER cc_start: 0.7956 (m) cc_final: 0.7624 (p) REVERT: x 55 ARG cc_start: 0.7909 (ttp-170) cc_final: 0.7502 (ttp-170) REVERT: y 12 ILE cc_start: 0.9346 (pt) cc_final: 0.9127 (pt) REVERT: y 61 GLN cc_start: 0.8595 (mm-40) cc_final: 0.8211 (mm-40) REVERT: z 12 PHE cc_start: 0.7372 (t80) cc_final: 0.7035 (t80) REVERT: A 167 SER cc_start: 0.7914 (m) cc_final: 0.7555 (m) REVERT: A 179 SER cc_start: 0.8347 (m) cc_final: 0.7985 (p) REVERT: A 196 ILE cc_start: 0.8775 (OUTLIER) cc_final: 0.8516 (pt) REVERT: A 199 SER cc_start: 0.9036 (m) cc_final: 0.8755 (p) REVERT: A 317 VAL cc_start: 0.8814 (t) cc_final: 0.8530 (p) REVERT: A 327 TYR cc_start: 0.8615 (m-80) cc_final: 0.8238 (m-80) outliers start: 165 outliers final: 87 residues processed: 1587 average time/residue: 1.3092 time to fit residues: 3549.4683 Evaluate side-chains 1421 residues out of total 4878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 1325 time to evaluate : 6.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain C residue 18 ASP Chi-restraints excluded: chain C residue 28 GLU Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 87 CYS Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 39 ASP Chi-restraints excluded: chain F residue 84 THR Chi-restraints excluded: chain F residue 127 THR Chi-restraints excluded: chain F residue 168 VAL Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain K residue 28 SER Chi-restraints excluded: chain K residue 117 SER Chi-restraints excluded: chain K residue 123 LEU Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 80 SER Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 36 VAL Chi-restraints excluded: chain M residue 132 THR Chi-restraints excluded: chain O residue 19 GLN Chi-restraints excluded: chain O residue 28 VAL Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain P residue 114 LEU Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain S residue 85 ILE Chi-restraints excluded: chain T residue 21 SER Chi-restraints excluded: chain U residue 15 THR Chi-restraints excluded: chain U residue 18 ASP Chi-restraints excluded: chain U residue 22 ARG Chi-restraints excluded: chain U residue 77 THR Chi-restraints excluded: chain V residue 41 GLU Chi-restraints excluded: chain W residue 12 ASN Chi-restraints excluded: chain W residue 21 LEU Chi-restraints excluded: chain W residue 30 SER Chi-restraints excluded: chain W residue 43 THR Chi-restraints excluded: chain X residue 40 VAL Chi-restraints excluded: chain Y residue 19 LEU Chi-restraints excluded: chain Z residue 25 LEU Chi-restraints excluded: chain Z residue 36 VAL Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain b residue 40 ARG Chi-restraints excluded: chain b residue 54 VAL Chi-restraints excluded: chain c residue 13 SER Chi-restraints excluded: chain c residue 22 THR Chi-restraints excluded: chain c residue 47 VAL Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain g residue 137 ARG Chi-restraints excluded: chain g residue 138 THR Chi-restraints excluded: chain g residue 199 VAL Chi-restraints excluded: chain g residue 205 ASP Chi-restraints excluded: chain h residue 35 SER Chi-restraints excluded: chain h residue 122 SER Chi-restraints excluded: chain h residue 186 THR Chi-restraints excluded: chain h residue 200 VAL Chi-restraints excluded: chain i residue 12 SER Chi-restraints excluded: chain j residue 76 LEU Chi-restraints excluded: chain j residue 78 ASN Chi-restraints excluded: chain k residue 7 VAL Chi-restraints excluded: chain k residue 51 ILE Chi-restraints excluded: chain k residue 55 HIS Chi-restraints excluded: chain k residue 84 VAL Chi-restraints excluded: chain k residue 96 VAL Chi-restraints excluded: chain l residue 50 LEU Chi-restraints excluded: chain m residue 83 LEU Chi-restraints excluded: chain m residue 104 VAL Chi-restraints excluded: chain n residue 61 LEU Chi-restraints excluded: chain o residue 77 VAL Chi-restraints excluded: chain p residue 35 THR Chi-restraints excluded: chain p residue 55 SER Chi-restraints excluded: chain p residue 83 GLU Chi-restraints excluded: chain p residue 110 ILE Chi-restraints excluded: chain r residue 7 ILE Chi-restraints excluded: chain r residue 64 VAL Chi-restraints excluded: chain r residue 65 VAL Chi-restraints excluded: chain s residue 45 VAL Chi-restraints excluded: chain t residue 87 LEU Chi-restraints excluded: chain u residue 24 SER Chi-restraints excluded: chain v residue 38 ILE Chi-restraints excluded: chain v residue 55 ILE Chi-restraints excluded: chain v residue 67 LEU Chi-restraints excluded: chain x residue 16 LEU Chi-restraints excluded: chain x residue 32 ARG Chi-restraints excluded: chain x residue 79 THR Chi-restraints excluded: chain y residue 26 SER Chi-restraints excluded: chain y residue 57 ILE Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 341 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1034 random chunks: chunk 929 optimal weight: 7.9990 chunk 707 optimal weight: 0.8980 chunk 488 optimal weight: 0.0070 chunk 104 optimal weight: 20.0000 chunk 448 optimal weight: 10.0000 chunk 631 optimal weight: 0.7980 chunk 944 optimal weight: 10.0000 chunk 999 optimal weight: 0.9980 chunk 493 optimal weight: 5.9990 chunk 894 optimal weight: 6.9990 chunk 269 optimal weight: 10.0000 overall best weight: 1.7400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 45 HIS F 73 ASN G 33 GLN J 86 GLN N 18 GLN O 61 GLN O 67 ASN P 12 GLN Q 37 GLN ** R 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 70 HIS U 46 GLN V 24 ASN ** a 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 16 HIS ** f 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 109 GLN g 120 GLN ** h 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 131 ASN i 198 HIS j 12 GLN k 55 HIS q 20 ASN r 12 HIS u 9 HIS x 14 HIS ** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 349 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.3240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 158905 Z= 0.169 Angle : 0.566 13.874 237521 Z= 0.307 Chirality : 0.031 0.229 30217 Planarity : 0.006 0.125 12870 Dihedral : 23.277 179.190 78933 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 4.06 % Allowed : 17.71 % Favored : 78.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.17 (0.10), residues: 5863 helix: -1.17 (0.11), residues: 1921 sheet: -1.59 (0.15), residues: 1064 loop : -1.47 (0.11), residues: 2878 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP s 42 HIS 0.007 0.001 HIS i 198 PHE 0.024 0.001 PHE V 26 TYR 0.014 0.001 TYR B 103 ARG 0.008 0.000 ARG v 27 *********************** 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 1583 residues out of total 4878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 198 poor density : 1385 time to evaluate : 6.699 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: B 177 ARG cc_start: 0.8458 (tpt170) cc_final: 0.8252 (tpt90) REVERT: B 221 ARG cc_start: 0.8657 (ptt-90) cc_final: 0.8240 (ptt90) REVERT: C 91 THR cc_start: 0.7673 (p) cc_final: 0.7472 (t) REVERT: D 116 ASP cc_start: 0.8039 (t0) cc_final: 0.7669 (t0) REVERT: D 158 PHE cc_start: 0.8335 (t80) cc_final: 0.8131 (t80) REVERT: E 48 LYS cc_start: 0.7729 (mmmm) cc_final: 0.7244 (mptt) REVERT: E 97 TRP cc_start: 0.9015 (m100) cc_final: 0.8757 (m100) REVERT: E 128 TYR cc_start: 0.8929 (t80) cc_final: 0.8584 (t80) REVERT: E 145 LYS cc_start: 0.7576 (mmtt) cc_final: 0.7036 (mtpt) REVERT: F 20 ASN cc_start: 0.7898 (t0) cc_final: 0.7576 (t0) REVERT: F 117 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.8147 (mm) REVERT: F 130 GLU cc_start: 0.8123 (mm-30) cc_final: 0.7751 (mp0) REVERT: F 157 TYR cc_start: 0.8580 (m-80) cc_final: 0.8102 (m-80) REVERT: G 1 MET cc_start: 0.7599 (tpp) cc_final: 0.7263 (ttt) REVERT: G 2 GLN cc_start: 0.7726 (mm-40) cc_final: 0.7366 (mm110) REVERT: G 5 LEU cc_start: 0.8246 (mm) cc_final: 0.7986 (mt) REVERT: G 28 ASN cc_start: 0.9332 (m-40) cc_final: 0.8743 (m-40) REVERT: J 58 ASN cc_start: 0.8563 (m-40) cc_final: 0.8201 (m110) REVERT: J 81 ILE cc_start: 0.9261 (tp) cc_final: 0.9050 (tp) REVERT: J 98 GLU cc_start: 0.8189 (mp0) cc_final: 0.7971 (mp0) REVERT: J 101 ILE cc_start: 0.9393 (mm) cc_final: 0.9137 (mm) REVERT: K 12 ASP cc_start: 0.8684 (p0) cc_final: 0.8381 (p0) REVERT: K 80 ASP cc_start: 0.8235 (OUTLIER) cc_final: 0.7962 (t0) REVERT: K 108 ARG cc_start: 0.7757 (ptm160) cc_final: 0.7439 (ptp-170) REVERT: M 17 ASN cc_start: 0.8947 (t0) cc_final: 0.8166 (t0) REVERT: M 27 SER cc_start: 0.8006 (m) cc_final: 0.7697 (t) REVERT: M 76 LYS cc_start: 0.8662 (mtpp) cc_final: 0.8411 (mmmm) REVERT: P 106 LYS cc_start: 0.8873 (mmtt) cc_final: 0.8234 (mmtp) REVERT: Q 15 LYS cc_start: 0.8301 (ttpt) cc_final: 0.7771 (tttm) REVERT: Q 66 ASN cc_start: 0.8903 (t0) cc_final: 0.8467 (t0) REVERT: Q 71 GLN cc_start: 0.8420 (tp-100) cc_final: 0.8076 (tp40) REVERT: S 99 ARG cc_start: 0.8924 (mmt90) cc_final: 0.8502 (mtt-85) REVERT: T 28 ASN cc_start: 0.8856 (t0) cc_final: 0.8518 (m-40) REVERT: T 86 THR cc_start: 0.8905 (m) cc_final: 0.8628 (t) REVERT: U 73 PHE cc_start: 0.8919 (t80) cc_final: 0.8660 (t80) REVERT: V 29 ILE cc_start: 0.9304 (tt) cc_final: 0.8891 (tt) REVERT: V 55 GLU cc_start: 0.7223 (mp0) cc_final: 0.7016 (mp0) REVERT: W 75 LYS cc_start: 0.9101 (mtpp) cc_final: 0.8865 (mtpp) REVERT: W 82 ILE cc_start: 0.9190 (mm) cc_final: 0.8849 (mm) REVERT: X 77 LYS cc_start: 0.8381 (mttt) cc_final: 0.7958 (mmmt) REVERT: Y 49 ASP cc_start: 0.7374 (m-30) cc_final: 0.7125 (m-30) REVERT: b 11 SER cc_start: 0.9136 (t) cc_final: 0.8709 (p) REVERT: b 40 ARG cc_start: 0.9014 (OUTLIER) cc_final: 0.8734 (ttt90) REVERT: b 49 TYR cc_start: 0.8215 (t80) cc_final: 0.7658 (t80) REVERT: d 14 ARG cc_start: 0.8367 (mtt180) cc_final: 0.7878 (mtt180) REVERT: d 15 SER cc_start: 0.8252 (m) cc_final: 0.7886 (p) REVERT: f 1 MET cc_start: 0.8037 (tpp) cc_final: 0.7731 (tpp) REVERT: g 11 LYS cc_start: 0.7684 (pttp) cc_final: 0.6957 (ttpt) REVERT: g 15 HIS cc_start: 0.8863 (p-80) cc_final: 0.8595 (p90) REVERT: g 27 MET cc_start: 0.8469 (mmm) cc_final: 0.7228 (mmm) REVERT: g 213 TYR cc_start: 0.8369 (m-80) cc_final: 0.8130 (m-80) REVERT: h 107 ARG cc_start: 0.7966 (mtp85) cc_final: 0.7667 (ttp-170) REVERT: h 142 MET cc_start: 0.8638 (mmm) cc_final: 0.8246 (mmm) REVERT: h 169 ARG cc_start: 0.7417 (ttm170) cc_final: 0.7103 (ttp80) REVERT: h 177 THR cc_start: 0.8827 (m) cc_final: 0.8522 (p) REVERT: h 185 ASN cc_start: 0.8090 (t0) cc_final: 0.7851 (t0) REVERT: h 188 GLU cc_start: 0.7802 (mt-10) cc_final: 0.7466 (mt-10) REVERT: i 19 LEU cc_start: 0.8926 (mt) cc_final: 0.8722 (mp) REVERT: i 51 TYR cc_start: 0.8606 (t80) cc_final: 0.8249 (t80) REVERT: i 57 GLU cc_start: 0.7937 (tp30) cc_final: 0.7520 (tp30) REVERT: i 145 ILE cc_start: 0.9029 (mm) cc_final: 0.8799 (mm) REVERT: i 187 GLU cc_start: 0.7003 (mm-30) cc_final: 0.6690 (mp0) REVERT: i 195 ILE cc_start: 0.8439 (mm) cc_final: 0.8184 (mm) REVERT: j 156 LYS cc_start: 0.8915 (ttpt) cc_final: 0.8632 (ttmm) REVERT: k 7 VAL cc_start: 0.8563 (OUTLIER) cc_final: 0.8200 (t) REVERT: l 2 PRO cc_start: 0.9105 (Cg_endo) cc_final: 0.8624 (Cg_exo) REVERT: l 20 SER cc_start: 0.8176 (t) cc_final: 0.7691 (t) REVERT: l 22 LEU cc_start: 0.6978 (tp) cc_final: 0.6364 (mm) REVERT: l 50 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8334 (tm) REVERT: l 118 LEU cc_start: 0.7770 (tt) cc_final: 0.6987 (mp) REVERT: m 79 SER cc_start: 0.8374 (t) cc_final: 0.8015 (p) REVERT: m 83 LEU cc_start: 0.9353 (OUTLIER) cc_final: 0.9125 (tp) REVERT: n 38 TYR cc_start: 0.8316 (t80) cc_final: 0.7959 (t80) REVERT: n 54 LEU cc_start: 0.8706 (tp) cc_final: 0.8416 (tp) REVERT: n 61 LEU cc_start: 0.8314 (OUTLIER) cc_final: 0.7780 (mt) REVERT: n 63 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.7669 (pp) REVERT: n 83 ILE cc_start: 0.8819 (mm) cc_final: 0.8585 (mt) REVERT: n 124 ARG cc_start: 0.8644 (mtt-85) cc_final: 0.8359 (mmt180) REVERT: o 69 THR cc_start: 0.9033 (m) cc_final: 0.8500 (p) REVERT: o 100 ILE cc_start: 0.8790 (mp) cc_final: 0.8454 (mt) REVERT: p 40 ASN cc_start: 0.8259 (m110) cc_final: 0.7357 (m-40) REVERT: p 85 MET cc_start: 0.7545 (mtp) cc_final: 0.7320 (mmm) REVERT: p 87 LYS cc_start: 0.8472 (ttmm) cc_final: 0.7964 (ttpp) REVERT: q 61 PHE cc_start: 0.8567 (m-10) cc_final: 0.8280 (m-10) REVERT: q 67 ILE cc_start: 0.9319 (mp) cc_final: 0.9060 (mp) REVERT: r 16 VAL cc_start: 0.8956 (m) cc_final: 0.8629 (p) REVERT: r 31 LYS cc_start: 0.8684 (mttt) cc_final: 0.8418 (mtpp) REVERT: r 52 GLN cc_start: 0.7240 (mt0) cc_final: 0.7018 (mt0) REVERT: r 81 MET cc_start: 0.7232 (mmm) cc_final: 0.6828 (mtt) REVERT: s 6 MET cc_start: 0.8449 (mmt) cc_final: 0.8129 (mmt) REVERT: s 20 TYR cc_start: 0.8002 (m-80) cc_final: 0.7664 (m-80) REVERT: t 10 LYS cc_start: 0.8331 (mmmm) cc_final: 0.7828 (ttpt) REVERT: t 14 GLU cc_start: 0.7435 (tm-30) cc_final: 0.6972 (tm-30) REVERT: v 17 MET cc_start: 0.8927 (ptt) cc_final: 0.8318 (ptt) REVERT: v 19 LYS cc_start: 0.7492 (mttt) cc_final: 0.7031 (mmmt) REVERT: v 28 PHE cc_start: 0.8813 (OUTLIER) cc_final: 0.8271 (t80) REVERT: v 80 GLU cc_start: 0.7808 (tm-30) cc_final: 0.7186 (tm-30) REVERT: w 65 LEU cc_start: 0.9061 (mt) cc_final: 0.8617 (mt) REVERT: x 32 ARG cc_start: 0.6943 (OUTLIER) cc_final: 0.6117 (ptt-90) REVERT: x 38 SER cc_start: 0.7593 (m) cc_final: 0.7256 (p) REVERT: y 12 ILE cc_start: 0.9327 (pt) cc_final: 0.9125 (pt) REVERT: y 61 GLN cc_start: 0.8363 (mm-40) cc_final: 0.8119 (mm-40) REVERT: y 78 ASN cc_start: 0.7813 (t0) cc_final: 0.7302 (t0) REVERT: z 12 PHE cc_start: 0.7516 (t80) cc_final: 0.7218 (t80) REVERT: z 19 PHE cc_start: 0.7698 (t80) cc_final: 0.7314 (t80) REVERT: A 199 SER cc_start: 0.9095 (m) cc_final: 0.8820 (p) REVERT: A 305 ASP cc_start: 0.7929 (p0) cc_final: 0.7534 (p0) REVERT: A 327 TYR cc_start: 0.8691 (m-80) cc_final: 0.8227 (m-80) outliers start: 198 outliers final: 134 residues processed: 1463 average time/residue: 1.3227 time to fit residues: 3315.7845 Evaluate side-chains 1452 residues out of total 4878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 1308 time to evaluate : 6.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain C residue 18 ASP Chi-restraints excluded: chain C residue 28 GLU Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain D residue 80 SER Chi-restraints excluded: chain D residue 181 ILE Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 87 CYS Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 39 ASP Chi-restraints excluded: chain F residue 71 LEU Chi-restraints excluded: chain F residue 84 THR Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 127 THR Chi-restraints excluded: chain F residue 168 VAL Chi-restraints excluded: chain G residue 6 LEU Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 61 VAL Chi-restraints excluded: chain K residue 80 ASP Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 110 GLU Chi-restraints excluded: chain K residue 123 LEU Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 23 ILE Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 40 SER Chi-restraints excluded: chain L residue 80 SER Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 36 VAL Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 78 LEU Chi-restraints excluded: chain M residue 132 THR Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 33 ILE Chi-restraints excluded: chain O residue 19 GLN Chi-restraints excluded: chain O residue 28 VAL Chi-restraints excluded: chain O residue 52 SER Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain P residue 40 LEU Chi-restraints excluded: chain P residue 76 THR Chi-restraints excluded: chain P residue 80 VAL Chi-restraints excluded: chain P residue 114 LEU Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain S residue 3 THR Chi-restraints excluded: chain S residue 53 SER Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain S residue 82 MET Chi-restraints excluded: chain S residue 85 ILE Chi-restraints excluded: chain T residue 74 ILE Chi-restraints excluded: chain U residue 15 THR Chi-restraints excluded: chain U residue 18 ASP Chi-restraints excluded: chain U residue 28 VAL Chi-restraints excluded: chain U residue 77 THR Chi-restraints excluded: chain W residue 12 ASN Chi-restraints excluded: chain W residue 21 LEU Chi-restraints excluded: chain W residue 30 SER Chi-restraints excluded: chain W residue 43 THR Chi-restraints excluded: chain X residue 19 SER Chi-restraints excluded: chain X residue 40 VAL Chi-restraints excluded: chain X residue 66 THR Chi-restraints excluded: chain Z residue 10 THR Chi-restraints excluded: chain Z residue 36 VAL Chi-restraints excluded: chain a residue 17 SER Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain b residue 40 ARG Chi-restraints excluded: chain b residue 54 VAL Chi-restraints excluded: chain c residue 13 SER Chi-restraints excluded: chain c residue 29 THR Chi-restraints excluded: chain c residue 47 VAL Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 42 LEU Chi-restraints excluded: chain e residue 58 VAL Chi-restraints excluded: chain g residue 137 ARG Chi-restraints excluded: chain g residue 138 THR Chi-restraints excluded: chain g residue 199 VAL Chi-restraints excluded: chain g residue 205 ASP Chi-restraints excluded: chain h residue 35 SER Chi-restraints excluded: chain h residue 53 SER Chi-restraints excluded: chain h residue 128 VAL Chi-restraints excluded: chain h residue 156 ARG Chi-restraints excluded: chain h residue 186 THR Chi-restraints excluded: chain h residue 200 VAL Chi-restraints excluded: chain i residue 12 SER Chi-restraints excluded: chain i residue 131 ASN Chi-restraints excluded: chain j residue 76 LEU Chi-restraints excluded: chain j residue 78 ASN Chi-restraints excluded: chain j residue 100 SER Chi-restraints excluded: chain j residue 103 THR Chi-restraints excluded: chain j residue 120 VAL Chi-restraints excluded: chain k residue 7 VAL Chi-restraints excluded: chain k residue 51 ILE Chi-restraints excluded: chain k residue 84 VAL Chi-restraints excluded: chain k residue 96 VAL Chi-restraints excluded: chain k residue 100 SER Chi-restraints excluded: chain l residue 38 THR Chi-restraints excluded: chain l residue 50 LEU Chi-restraints excluded: chain l residue 120 LEU Chi-restraints excluded: chain m residue 55 THR Chi-restraints excluded: chain m residue 83 LEU Chi-restraints excluded: chain m residue 104 VAL Chi-restraints excluded: chain n residue 61 LEU Chi-restraints excluded: chain n residue 63 LEU Chi-restraints excluded: chain o residue 73 LEU Chi-restraints excluded: chain o residue 77 VAL Chi-restraints excluded: chain o residue 90 LEU Chi-restraints excluded: chain p residue 35 THR Chi-restraints excluded: chain p residue 110 ILE Chi-restraints excluded: chain r residue 19 LEU Chi-restraints excluded: chain r residue 30 SER Chi-restraints excluded: chain r residue 56 LEU Chi-restraints excluded: chain r residue 64 VAL Chi-restraints excluded: chain r residue 65 VAL Chi-restraints excluded: chain s residue 80 SER Chi-restraints excluded: chain t residue 75 VAL Chi-restraints excluded: chain t residue 87 LEU Chi-restraints excluded: chain u residue 24 SER Chi-restraints excluded: chain v residue 14 SER Chi-restraints excluded: chain v residue 28 PHE Chi-restraints excluded: chain v residue 38 ILE Chi-restraints excluded: chain v residue 55 ILE Chi-restraints excluded: chain v residue 67 LEU Chi-restraints excluded: chain x residue 32 ARG Chi-restraints excluded: chain y residue 23 SER Chi-restraints excluded: chain y residue 26 SER Chi-restraints excluded: chain z residue 22 SER Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 134 MET Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 341 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1034 random chunks: chunk 832 optimal weight: 9.9990 chunk 567 optimal weight: 7.9990 chunk 14 optimal weight: 10.0000 chunk 744 optimal weight: 5.9990 chunk 412 optimal weight: 10.0000 chunk 852 optimal weight: 0.7980 chunk 690 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 510 optimal weight: 9.9990 chunk 897 optimal weight: 5.9990 chunk 252 optimal weight: 10.0000 overall best weight: 6.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 134 ASN ** B 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 73 ASN G 18 GLN G 33 GLN ** G 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 54 GLN M 13 HIS N 18 GLN N 62 ASN R 43 ASN U 46 GLN V 24 ASN ** V 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 120 GLN h 100 GLN h 102 ASN ** h 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 71 GLN i 131 ASN i 198 HIS ** j 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 55 HIS ** l 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 59 ASN t 38 HIS ** t 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 9 HIS x 69 HIS A 110 ASN ** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 349 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.3273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.093 158905 Z= 0.466 Angle : 0.771 14.755 237521 Z= 0.397 Chirality : 0.041 0.307 30217 Planarity : 0.007 0.136 12870 Dihedral : 23.439 179.854 78933 Min Nonbonded Distance : 1.769 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 5.82 % Allowed : 17.88 % Favored : 76.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.24 (0.10), residues: 5863 helix: -1.17 (0.11), residues: 1918 sheet: -1.67 (0.15), residues: 1104 loop : -1.53 (0.11), residues: 2841 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP s 42 HIS 0.014 0.002 HIS S 7 PHE 0.031 0.003 PHE N 80 TYR 0.024 0.003 TYR G 25 ARG 0.010 0.001 ARG e 13 *********************** 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 1624 residues out of total 4878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 284 poor density : 1340 time to evaluate : 6.656 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: B 23 GLU cc_start: 0.7959 (mm-30) cc_final: 0.7645 (mt-10) REVERT: B 30 PHE cc_start: 0.8518 (t80) cc_final: 0.8252 (t80) REVERT: B 88 SER cc_start: 0.9341 (OUTLIER) cc_final: 0.9141 (p) REVERT: B 177 ARG cc_start: 0.8611 (tpt170) cc_final: 0.8393 (tpt90) REVERT: C 45 TYR cc_start: 0.8326 (p90) cc_final: 0.7868 (p90) REVERT: C 91 THR cc_start: 0.7790 (p) cc_final: 0.7523 (t) REVERT: D 116 ASP cc_start: 0.8117 (t0) cc_final: 0.7691 (t0) REVERT: D 158 PHE cc_start: 0.8558 (t80) cc_final: 0.8351 (t80) REVERT: E 128 TYR cc_start: 0.8758 (t80) cc_final: 0.8369 (t80) REVERT: E 145 LYS cc_start: 0.7732 (mmtt) cc_final: 0.7191 (mtpt) REVERT: F 20 ASN cc_start: 0.7940 (t0) cc_final: 0.7616 (t0) REVERT: F 117 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8408 (mm) REVERT: F 157 TYR cc_start: 0.8590 (m-80) cc_final: 0.8247 (m-80) REVERT: G 53 GLU cc_start: 0.6630 (mp0) cc_final: 0.5342 (mm-30) REVERT: J 17 VAL cc_start: 0.9337 (t) cc_final: 0.9030 (p) REVERT: J 52 ASP cc_start: 0.8378 (m-30) cc_final: 0.8136 (m-30) REVERT: J 98 GLU cc_start: 0.8427 (mp0) cc_final: 0.8032 (mp0) REVERT: J 101 ILE cc_start: 0.9424 (mm) cc_final: 0.9168 (mm) REVERT: K 12 ASP cc_start: 0.8688 (p0) cc_final: 0.8434 (p0) REVERT: K 80 ASP cc_start: 0.8401 (OUTLIER) cc_final: 0.8074 (t0) REVERT: K 114 LYS cc_start: 0.9037 (tttt) cc_final: 0.8740 (ttmt) REVERT: K 123 LEU cc_start: 0.8197 (OUTLIER) cc_final: 0.7859 (mt) REVERT: M 17 ASN cc_start: 0.9203 (t0) cc_final: 0.8475 (t0) REVERT: M 27 SER cc_start: 0.8626 (m) cc_final: 0.8335 (t) REVERT: M 76 LYS cc_start: 0.8804 (mtpp) cc_final: 0.8481 (mmmm) REVERT: M 106 ASP cc_start: 0.8376 (t0) cc_final: 0.8016 (t0) REVERT: N 51 LEU cc_start: 0.9115 (OUTLIER) cc_final: 0.8899 (mt) REVERT: P 11 GLU cc_start: 0.7945 (pt0) cc_final: 0.6873 (mt-10) REVERT: Q 66 ASN cc_start: 0.8980 (t0) cc_final: 0.8693 (t0) REVERT: Q 71 GLN cc_start: 0.8428 (tp-100) cc_final: 0.8032 (tp40) REVERT: R 71 LYS cc_start: 0.8998 (tppp) cc_final: 0.8777 (tppt) REVERT: S 99 ARG cc_start: 0.9028 (mmt90) cc_final: 0.8578 (mtt-85) REVERT: T 28 ASN cc_start: 0.8920 (m-40) cc_final: 0.8672 (m-40) REVERT: T 86 THR cc_start: 0.8831 (m) cc_final: 0.8560 (t) REVERT: V 29 ILE cc_start: 0.9326 (tt) cc_final: 0.9102 (tt) REVERT: W 32 LEU cc_start: 0.8837 (mt) cc_final: 0.8622 (mt) REVERT: X 74 ARG cc_start: 0.8825 (ttm170) cc_final: 0.8347 (mtp180) REVERT: X 77 LYS cc_start: 0.8427 (mttt) cc_final: 0.7978 (mmmt) REVERT: Y 15 ASN cc_start: 0.8558 (OUTLIER) cc_final: 0.8056 (m-40) REVERT: Y 21 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8268 (mm) REVERT: Y 24 GLU cc_start: 0.7678 (tp30) cc_final: 0.7288 (tp30) REVERT: Y 49 ASP cc_start: 0.7455 (m-30) cc_final: 0.7244 (m-30) REVERT: Z 27 LEU cc_start: 0.9075 (mt) cc_final: 0.8557 (tp) REVERT: Z 56 LYS cc_start: 0.8468 (tptt) cc_final: 0.8241 (tttm) REVERT: a 10 GLU cc_start: 0.6252 (tt0) cc_final: 0.6004 (mt-10) REVERT: b 11 SER cc_start: 0.9096 (t) cc_final: 0.8700 (p) REVERT: b 40 ARG cc_start: 0.9146 (OUTLIER) cc_final: 0.8677 (tpp80) REVERT: d 3 ARG cc_start: 0.8916 (mmt180) cc_final: 0.8054 (tpp-160) REVERT: d 14 ARG cc_start: 0.8278 (mtt180) cc_final: 0.7856 (mtt180) REVERT: g 15 HIS cc_start: 0.8856 (p-80) cc_final: 0.8540 (p90) REVERT: g 27 MET cc_start: 0.8606 (mmm) cc_final: 0.6908 (mmm) REVERT: g 120 GLN cc_start: 0.7743 (OUTLIER) cc_final: 0.7145 (tt0) REVERT: h 142 MET cc_start: 0.8633 (mmm) cc_final: 0.7838 (mmm) REVERT: h 169 ARG cc_start: 0.7477 (ttm170) cc_final: 0.7242 (ttp80) REVERT: h 185 ASN cc_start: 0.8476 (t0) cc_final: 0.8256 (t0) REVERT: h 188 GLU cc_start: 0.7741 (mt-10) cc_final: 0.7521 (mt-10) REVERT: i 51 TYR cc_start: 0.8725 (t80) cc_final: 0.8367 (t80) REVERT: i 57 GLU cc_start: 0.7866 (tp30) cc_final: 0.7627 (tp30) REVERT: i 145 ILE cc_start: 0.9188 (mm) cc_final: 0.8869 (mt) REVERT: i 187 GLU cc_start: 0.7086 (mm-30) cc_final: 0.6792 (mp0) REVERT: j 156 LYS cc_start: 0.8988 (ttpt) cc_final: 0.8713 (ttmm) REVERT: l 12 ILE cc_start: 0.8027 (OUTLIER) cc_final: 0.7678 (tt) REVERT: l 20 SER cc_start: 0.8302 (OUTLIER) cc_final: 0.8017 (t) REVERT: l 22 LEU cc_start: 0.7215 (tp) cc_final: 0.6606 (mm) REVERT: l 50 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8369 (tm) REVERT: m 79 SER cc_start: 0.8630 (t) cc_final: 0.8150 (p) REVERT: n 27 LYS cc_start: 0.8352 (mtmm) cc_final: 0.7183 (tptt) REVERT: n 35 LEU cc_start: 0.9197 (tp) cc_final: 0.8983 (tp) REVERT: n 38 TYR cc_start: 0.8547 (t80) cc_final: 0.8274 (t80) REVERT: n 63 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.7985 (pp) REVERT: o 69 THR cc_start: 0.9028 (m) cc_final: 0.8535 (p) REVERT: o 100 ILE cc_start: 0.8917 (mp) cc_final: 0.8328 (mm) REVERT: p 87 LYS cc_start: 0.8626 (ttmm) cc_final: 0.8101 (ttpp) REVERT: p 125 LYS cc_start: 0.9041 (OUTLIER) cc_final: 0.8778 (pttp) REVERT: q 56 ARG cc_start: 0.8079 (ttm-80) cc_final: 0.7614 (tpp-160) REVERT: q 58 THR cc_start: 0.8547 (OUTLIER) cc_final: 0.8260 (p) REVERT: q 67 ILE cc_start: 0.9325 (mp) cc_final: 0.9026 (mp) REVERT: r 16 VAL cc_start: 0.9136 (m) cc_final: 0.8794 (p) REVERT: r 31 LYS cc_start: 0.8756 (mttt) cc_final: 0.8498 (mtpp) REVERT: r 52 GLN cc_start: 0.7268 (mt0) cc_final: 0.7050 (mt0) REVERT: s 20 TYR cc_start: 0.8148 (m-80) cc_final: 0.7852 (m-80) REVERT: s 60 GLN cc_start: 0.8873 (OUTLIER) cc_final: 0.8431 (pt0) REVERT: t 10 LYS cc_start: 0.8400 (mmmm) cc_final: 0.8055 (mtpt) REVERT: t 14 GLU cc_start: 0.7578 (tm-30) cc_final: 0.6995 (tm-30) REVERT: t 74 ASP cc_start: 0.7590 (t70) cc_final: 0.6844 (p0) REVERT: v 19 LYS cc_start: 0.7869 (mttt) cc_final: 0.7192 (mmmt) REVERT: v 80 GLU cc_start: 0.7902 (tm-30) cc_final: 0.7327 (tm-30) REVERT: x 32 ARG cc_start: 0.7177 (OUTLIER) cc_final: 0.6699 (ptt-90) REVERT: y 12 ILE cc_start: 0.9422 (pt) cc_final: 0.9157 (pt) REVERT: y 24 ARG cc_start: 0.7634 (mmp80) cc_final: 0.7413 (mmm160) REVERT: y 78 ASN cc_start: 0.8066 (t0) cc_final: 0.7855 (t0) REVERT: z 12 PHE cc_start: 0.8099 (t80) cc_final: 0.7610 (t80) REVERT: z 19 PHE cc_start: 0.8019 (t80) cc_final: 0.7664 (t80) REVERT: A 126 LEU cc_start: 0.9075 (tt) cc_final: 0.8739 (tt) REVERT: A 347 GLU cc_start: 0.7378 (OUTLIER) cc_final: 0.6753 (mp0) outliers start: 284 outliers final: 212 residues processed: 1480 average time/residue: 1.3101 time to fit residues: 3329.5936 Evaluate side-chains 1526 residues out of total 4878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 230 poor density : 1296 time to evaluate : 6.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 6 CYS Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 201 MET Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain C residue 18 ASP Chi-restraints excluded: chain C residue 28 GLU Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 150 GLN Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 7 ASP Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain D residue 80 SER Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain D residue 181 ILE Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 87 CYS Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain F residue 9 VAL Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 39 ASP Chi-restraints excluded: chain F residue 49 THR Chi-restraints excluded: chain F residue 71 LEU Chi-restraints excluded: chain F residue 84 THR Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 122 THR Chi-restraints excluded: chain F residue 127 THR Chi-restraints excluded: chain F residue 168 VAL Chi-restraints excluded: chain F residue 171 THR Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 28 SER Chi-restraints excluded: chain K residue 35 VAL Chi-restraints excluded: chain K residue 61 VAL Chi-restraints excluded: chain K residue 73 ASP Chi-restraints excluded: chain K residue 80 ASP Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 110 GLU Chi-restraints excluded: chain K residue 123 LEU Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 23 ILE Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 40 SER Chi-restraints excluded: chain L residue 67 THR Chi-restraints excluded: chain L residue 80 SER Chi-restraints excluded: chain L residue 93 ASN Chi-restraints excluded: chain L residue 106 GLU Chi-restraints excluded: chain L residue 123 ARG Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 36 VAL Chi-restraints excluded: chain M residue 42 THR Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 78 LEU Chi-restraints excluded: chain M residue 82 MET Chi-restraints excluded: chain M residue 102 LEU Chi-restraints excluded: chain M residue 132 THR Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 33 ILE Chi-restraints excluded: chain N residue 45 ARG Chi-restraints excluded: chain N residue 51 LEU Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 89 SER Chi-restraints excluded: chain O residue 19 GLN Chi-restraints excluded: chain O residue 28 VAL Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 52 SER Chi-restraints excluded: chain P residue 32 VAL Chi-restraints excluded: chain P residue 80 VAL Chi-restraints excluded: chain P residue 83 SER Chi-restraints excluded: chain P residue 110 ILE Chi-restraints excluded: chain P residue 114 LEU Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain R residue 54 VAL Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain S residue 3 THR Chi-restraints excluded: chain S residue 29 VAL Chi-restraints excluded: chain S residue 47 VAL Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain S residue 82 MET Chi-restraints excluded: chain T residue 21 SER Chi-restraints excluded: chain T residue 27 SER Chi-restraints excluded: chain T residue 34 VAL Chi-restraints excluded: chain T residue 60 THR Chi-restraints excluded: chain T residue 63 VAL Chi-restraints excluded: chain T residue 74 ILE Chi-restraints excluded: chain U residue 15 THR Chi-restraints excluded: chain U residue 28 VAL Chi-restraints excluded: chain U residue 31 SER Chi-restraints excluded: chain U residue 77 THR Chi-restraints excluded: chain V residue 30 ILE Chi-restraints excluded: chain V residue 50 MET Chi-restraints excluded: chain W residue 12 ASN Chi-restraints excluded: chain W residue 21 LEU Chi-restraints excluded: chain W residue 30 SER Chi-restraints excluded: chain W residue 41 ARG Chi-restraints excluded: chain W residue 43 THR Chi-restraints excluded: chain X residue 19 SER Chi-restraints excluded: chain X residue 40 VAL Chi-restraints excluded: chain X residue 62 LYS Chi-restraints excluded: chain X residue 66 THR Chi-restraints excluded: chain Y residue 15 ASN Chi-restraints excluded: chain Y residue 21 LEU Chi-restraints excluded: chain Z residue 10 THR Chi-restraints excluded: chain Z residue 25 LEU Chi-restraints excluded: chain Z residue 36 VAL Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain b residue 40 ARG Chi-restraints excluded: chain b residue 44 THR Chi-restraints excluded: chain b residue 54 VAL Chi-restraints excluded: chain c residue 13 SER Chi-restraints excluded: chain c residue 29 THR Chi-restraints excluded: chain c residue 47 VAL Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 42 LEU Chi-restraints excluded: chain e residue 32 ILE Chi-restraints excluded: chain e residue 51 SER Chi-restraints excluded: chain e residue 58 VAL Chi-restraints excluded: chain g residue 120 GLN Chi-restraints excluded: chain g residue 137 ARG Chi-restraints excluded: chain g residue 138 THR Chi-restraints excluded: chain g residue 199 VAL Chi-restraints excluded: chain h residue 35 SER Chi-restraints excluded: chain h residue 51 SER Chi-restraints excluded: chain h residue 52 VAL Chi-restraints excluded: chain h residue 53 SER Chi-restraints excluded: chain h residue 100 GLN Chi-restraints excluded: chain h residue 105 GLU Chi-restraints excluded: chain h residue 128 VAL Chi-restraints excluded: chain h residue 152 GLU Chi-restraints excluded: chain h residue 156 ARG Chi-restraints excluded: chain h residue 186 THR Chi-restraints excluded: chain h residue 200 VAL Chi-restraints excluded: chain i residue 12 SER Chi-restraints excluded: chain j residue 16 ILE Chi-restraints excluded: chain j residue 22 SER Chi-restraints excluded: chain j residue 76 LEU Chi-restraints excluded: chain j residue 103 THR Chi-restraints excluded: chain j residue 120 VAL Chi-restraints excluded: chain j residue 140 THR Chi-restraints excluded: chain k residue 7 VAL Chi-restraints excluded: chain k residue 51 ILE Chi-restraints excluded: chain k residue 55 HIS Chi-restraints excluded: chain k residue 84 VAL Chi-restraints excluded: chain k residue 96 VAL Chi-restraints excluded: chain k residue 100 SER Chi-restraints excluded: chain l residue 6 VAL Chi-restraints excluded: chain l residue 12 ILE Chi-restraints excluded: chain l residue 20 SER Chi-restraints excluded: chain l residue 30 LEU Chi-restraints excluded: chain l residue 38 THR Chi-restraints excluded: chain l residue 50 LEU Chi-restraints excluded: chain l residue 77 SER Chi-restraints excluded: chain l residue 120 LEU Chi-restraints excluded: chain l residue 133 THR Chi-restraints excluded: chain m residue 12 THR Chi-restraints excluded: chain m residue 104 VAL Chi-restraints excluded: chain m residue 105 SER Chi-restraints excluded: chain n residue 63 LEU Chi-restraints excluded: chain o residue 54 SER Chi-restraints excluded: chain o residue 73 LEU Chi-restraints excluded: chain o residue 77 VAL Chi-restraints excluded: chain o residue 80 THR Chi-restraints excluded: chain o residue 90 LEU Chi-restraints excluded: chain p residue 35 THR Chi-restraints excluded: chain p residue 68 GLU Chi-restraints excluded: chain p residue 125 LYS Chi-restraints excluded: chain q residue 33 VAL Chi-restraints excluded: chain q residue 58 THR Chi-restraints excluded: chain q residue 70 GLU Chi-restraints excluded: chain q residue 81 LEU Chi-restraints excluded: chain r residue 30 SER Chi-restraints excluded: chain r residue 56 LEU Chi-restraints excluded: chain r residue 65 VAL Chi-restraints excluded: chain r residue 108 THR Chi-restraints excluded: chain s residue 45 VAL Chi-restraints excluded: chain s residue 60 GLN Chi-restraints excluded: chain s residue 80 SER Chi-restraints excluded: chain s residue 84 VAL Chi-restraints excluded: chain t residue 26 GLU Chi-restraints excluded: chain t residue 75 VAL Chi-restraints excluded: chain t residue 79 THR Chi-restraints excluded: chain t residue 87 LEU Chi-restraints excluded: chain u residue 24 SER Chi-restraints excluded: chain v residue 14 SER Chi-restraints excluded: chain v residue 38 ILE Chi-restraints excluded: chain v residue 55 ILE Chi-restraints excluded: chain v residue 57 ASP Chi-restraints excluded: chain v residue 67 LEU Chi-restraints excluded: chain v residue 70 THR Chi-restraints excluded: chain w residue 40 VAL Chi-restraints excluded: chain x residue 32 ARG Chi-restraints excluded: chain x residue 79 THR Chi-restraints excluded: chain y residue 23 SER Chi-restraints excluded: chain y residue 26 SER Chi-restraints excluded: chain y residue 53 GLU Chi-restraints excluded: chain y residue 57 ILE Chi-restraints excluded: chain z residue 4 ILE Chi-restraints excluded: chain z residue 22 SER Chi-restraints excluded: chain z residue 51 SER Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 134 MET Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain A residue 341 ILE 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: 20.0000 chunk 900 optimal weight: 7.9990 chunk 197 optimal weight: 6.9990 chunk 586 optimal weight: 5.9990 chunk 246 optimal weight: 7.9990 chunk 1000 optimal weight: 0.9990 chunk 830 optimal weight: 0.9990 chunk 463 optimal weight: 0.8980 chunk 83 optimal weight: 5.9990 chunk 330 optimal weight: 10.0000 chunk 525 optimal weight: 0.9980 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 73 ASN G 28 ASN G 33 GLN L 54 GLN N 18 GLN N 62 ASN R 43 ASN U 46 GLN V 24 ASN ** a 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 16 HIS ** f 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 102 ASN ** h 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 71 GLN i 131 ASN j 12 GLN k 3 HIS k 55 HIS l 142 HIS u 9 HIS x 69 HIS ** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.3513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 158905 Z= 0.176 Angle : 0.587 13.736 237521 Z= 0.317 Chirality : 0.032 0.309 30217 Planarity : 0.006 0.125 12870 Dihedral : 23.330 179.439 78933 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 4.43 % Allowed : 20.13 % Favored : 75.44 % 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: -1.82 (0.11), residues: 5863 helix: -0.69 (0.12), residues: 1918 sheet: -1.52 (0.15), residues: 1079 loop : -1.35 (0.11), residues: 2866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP s 42 HIS 0.015 0.001 HIS k 55 PHE 0.025 0.001 PHE N 80 TYR 0.019 0.002 TYR E 143 ARG 0.007 0.000 ARG y 74 *********************** 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 1534 residues out of total 4878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 216 poor density : 1318 time to evaluate : 6.459 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: B 23 GLU cc_start: 0.7920 (mm-30) cc_final: 0.7597 (mt-10) REVERT: B 88 SER cc_start: 0.9365 (OUTLIER) cc_final: 0.9045 (p) REVERT: B 177 ARG cc_start: 0.8550 (tpt170) cc_final: 0.8321 (tpt90) REVERT: C 1 MET cc_start: 0.5153 (tpp) cc_final: 0.4001 (ppp) REVERT: C 45 TYR cc_start: 0.8394 (p90) cc_final: 0.7814 (p90) REVERT: C 91 THR cc_start: 0.7765 (p) cc_final: 0.7531 (t) REVERT: D 116 ASP cc_start: 0.8055 (t0) cc_final: 0.7757 (t0) REVERT: E 8 TYR cc_start: 0.8974 (t80) cc_final: 0.8382 (t80) REVERT: E 128 TYR cc_start: 0.8773 (t80) cc_final: 0.8445 (t80) REVERT: E 140 GLU cc_start: 0.7435 (mm-30) cc_final: 0.7205 (mm-30) REVERT: E 145 LYS cc_start: 0.7618 (mmtt) cc_final: 0.7068 (mtpt) REVERT: F 20 ASN cc_start: 0.7794 (t0) cc_final: 0.7493 (t0) REVERT: F 133 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8490 (mt) REVERT: F 157 TYR cc_start: 0.8567 (m-80) cc_final: 0.8236 (m-80) REVERT: G 15 LEU cc_start: 0.8006 (tt) cc_final: 0.7763 (tt) REVERT: G 53 GLU cc_start: 0.6567 (mp0) cc_final: 0.5266 (mm-30) REVERT: J 17 VAL cc_start: 0.9232 (t) cc_final: 0.8912 (p) REVERT: J 98 GLU cc_start: 0.8219 (mp0) cc_final: 0.7933 (mp0) REVERT: K 12 ASP cc_start: 0.8669 (p0) cc_final: 0.8379 (p0) REVERT: K 123 LEU cc_start: 0.8005 (OUTLIER) cc_final: 0.7796 (mt) REVERT: L 104 GLN cc_start: 0.8541 (mm-40) cc_final: 0.8238 (tp40) REVERT: M 17 ASN cc_start: 0.9028 (t0) cc_final: 0.8264 (t0) REVERT: M 76 LYS cc_start: 0.8695 (mtpp) cc_final: 0.8350 (mmmm) REVERT: M 106 ASP cc_start: 0.8201 (t0) cc_final: 0.7767 (t0) REVERT: P 11 GLU cc_start: 0.7915 (pt0) cc_final: 0.6827 (mt-10) REVERT: Q 66 ASN cc_start: 0.8945 (t0) cc_final: 0.8620 (t0) REVERT: Q 71 GLN cc_start: 0.8430 (tp-100) cc_final: 0.8088 (tp40) REVERT: Q 92 ARG cc_start: 0.8500 (OUTLIER) cc_final: 0.8134 (mtm-85) REVERT: R 71 LYS cc_start: 0.8959 (tppp) cc_final: 0.8713 (tppt) REVERT: S 3 THR cc_start: 0.8812 (OUTLIER) cc_final: 0.8590 (p) REVERT: S 99 ARG cc_start: 0.9043 (mmt90) cc_final: 0.8595 (mtt-85) REVERT: T 1 MET cc_start: 0.6604 (tpt) cc_final: 0.5575 (ppp) REVERT: T 28 ASN cc_start: 0.8869 (m-40) cc_final: 0.8552 (m-40) REVERT: T 86 THR cc_start: 0.8881 (m) cc_final: 0.8625 (t) REVERT: U 60 GLU cc_start: 0.7726 (tt0) cc_final: 0.7353 (tt0) REVERT: V 29 ILE cc_start: 0.9296 (tt) cc_final: 0.8943 (tt) REVERT: V 46 LYS cc_start: 0.8342 (mmmm) cc_final: 0.8000 (ttpp) REVERT: W 75 LYS cc_start: 0.9143 (mtpp) cc_final: 0.8871 (mtpp) REVERT: X 58 VAL cc_start: 0.9032 (t) cc_final: 0.8774 (t) REVERT: X 74 ARG cc_start: 0.8767 (ttm170) cc_final: 0.8299 (mtp180) REVERT: X 77 LYS cc_start: 0.8337 (mttt) cc_final: 0.7938 (mmmt) REVERT: Y 15 ASN cc_start: 0.8488 (OUTLIER) cc_final: 0.8131 (m-40) REVERT: Y 21 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8157 (mt) REVERT: Y 39 GLN cc_start: 0.8439 (mt0) cc_final: 0.8215 (mt0) REVERT: Z 32 ILE cc_start: 0.9254 (pt) cc_final: 0.9040 (mt) REVERT: b 11 SER cc_start: 0.9147 (t) cc_final: 0.8786 (p) REVERT: b 40 ARG cc_start: 0.9041 (OUTLIER) cc_final: 0.8665 (tpt90) REVERT: d 3 ARG cc_start: 0.8761 (mmt180) cc_final: 0.8423 (mmp80) REVERT: d 14 ARG cc_start: 0.8377 (mtt180) cc_final: 0.7940 (mtt180) REVERT: f 1 MET cc_start: 0.8184 (tpp) cc_final: 0.7853 (tpp) REVERT: g 11 LYS cc_start: 0.7573 (pttp) cc_final: 0.7308 (ptmt) REVERT: g 15 HIS cc_start: 0.8826 (p-80) cc_final: 0.8485 (p90) REVERT: g 27 MET cc_start: 0.8667 (mmm) cc_final: 0.7131 (mmm) REVERT: h 142 MET cc_start: 0.8637 (mmm) cc_final: 0.8220 (mmm) REVERT: h 185 ASN cc_start: 0.8218 (t0) cc_final: 0.7985 (t0) REVERT: h 188 GLU cc_start: 0.7846 (mt-10) cc_final: 0.7527 (mt-10) REVERT: i 51 TYR cc_start: 0.8553 (t80) cc_final: 0.8268 (t80) REVERT: i 57 GLU cc_start: 0.7802 (tp30) cc_final: 0.7562 (tp30) REVERT: i 195 ILE cc_start: 0.8611 (mm) cc_final: 0.8408 (mm) REVERT: j 86 LYS cc_start: 0.7899 (mtmt) cc_final: 0.7652 (mttt) REVERT: j 156 LYS cc_start: 0.8904 (ttpt) cc_final: 0.8631 (ttmm) REVERT: l 12 ILE cc_start: 0.8067 (OUTLIER) cc_final: 0.7723 (tt) REVERT: l 20 SER cc_start: 0.8116 (t) cc_final: 0.7797 (t) REVERT: l 22 LEU cc_start: 0.7060 (tp) cc_final: 0.6784 (tt) REVERT: l 50 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.8329 (tm) REVERT: l 68 ASN cc_start: 0.8015 (t0) cc_final: 0.7383 (t0) REVERT: m 79 SER cc_start: 0.8667 (t) cc_final: 0.8141 (p) REVERT: n 38 TYR cc_start: 0.8489 (t80) cc_final: 0.8160 (t80) REVERT: n 79 ILE cc_start: 0.9102 (mt) cc_final: 0.8822 (mt) REVERT: n 124 ARG cc_start: 0.8656 (mtt-85) cc_final: 0.8368 (mmt180) REVERT: o 69 THR cc_start: 0.9024 (m) cc_final: 0.8504 (p) REVERT: o 100 ILE cc_start: 0.8785 (mp) cc_final: 0.8148 (mm) REVERT: p 87 LYS cc_start: 0.8600 (ttmm) cc_final: 0.8136 (ttpp) REVERT: q 58 THR cc_start: 0.8550 (OUTLIER) cc_final: 0.8254 (p) REVERT: q 61 PHE cc_start: 0.8631 (m-10) cc_final: 0.8231 (m-10) REVERT: q 67 ILE cc_start: 0.9223 (mp) cc_final: 0.8976 (mp) REVERT: q 75 GLN cc_start: 0.8476 (OUTLIER) cc_final: 0.7974 (mm110) REVERT: r 7 ILE cc_start: 0.8510 (pt) cc_final: 0.8305 (pt) REVERT: r 31 LYS cc_start: 0.8707 (mttt) cc_final: 0.8467 (mtpp) REVERT: r 52 GLN cc_start: 0.7002 (mt0) cc_final: 0.6698 (mt0) REVERT: r 81 MET cc_start: 0.7174 (mmm) cc_final: 0.6857 (mtt) REVERT: s 60 GLN cc_start: 0.8738 (OUTLIER) cc_final: 0.8372 (pt0) REVERT: t 10 LYS cc_start: 0.8513 (mmmm) cc_final: 0.8128 (mtpt) REVERT: t 74 ASP cc_start: 0.6967 (t70) cc_final: 0.6241 (p0) REVERT: v 19 LYS cc_start: 0.7820 (mttt) cc_final: 0.7182 (mmmt) REVERT: v 28 PHE cc_start: 0.8817 (OUTLIER) cc_final: 0.8314 (t80) REVERT: v 39 LYS cc_start: 0.8625 (mtpt) cc_final: 0.8362 (mtpt) REVERT: v 80 GLU cc_start: 0.7771 (tm-30) cc_final: 0.7277 (tm-30) REVERT: y 78 ASN cc_start: 0.7979 (t0) cc_final: 0.7774 (t0) REVERT: z 12 PHE cc_start: 0.7932 (t80) cc_final: 0.7532 (t80) REVERT: A 126 LEU cc_start: 0.9026 (OUTLIER) cc_final: 0.8661 (tt) REVERT: A 199 SER cc_start: 0.9167 (m) cc_final: 0.8828 (p) REVERT: A 271 LEU cc_start: 0.9004 (mt) cc_final: 0.8791 (mt) REVERT: A 347 GLU cc_start: 0.7191 (OUTLIER) cc_final: 0.6584 (mp0) outliers start: 216 outliers final: 152 residues processed: 1435 average time/residue: 1.3216 time to fit residues: 3265.4678 Evaluate side-chains 1431 residues out of total 4878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 1263 time to evaluate : 6.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain C residue 18 ASP Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 28 GLU Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain D residue 80 SER Chi-restraints excluded: chain D residue 181 ILE Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 87 CYS Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 39 ASP Chi-restraints excluded: chain F residue 49 THR Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain F residue 71 LEU Chi-restraints excluded: chain F residue 84 THR Chi-restraints excluded: chain F residue 127 THR Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain F residue 168 VAL Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 61 VAL Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 110 GLU Chi-restraints excluded: chain K residue 123 LEU Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 23 ILE Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 40 SER Chi-restraints excluded: chain L residue 67 THR Chi-restraints excluded: chain L residue 80 SER Chi-restraints excluded: chain L residue 93 ASN Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 36 VAL Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 82 MET Chi-restraints excluded: chain M residue 111 GLU Chi-restraints excluded: chain M residue 132 THR Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 33 ILE Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain O residue 19 GLN Chi-restraints excluded: chain O residue 28 VAL Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 52 SER Chi-restraints excluded: chain P residue 40 LEU Chi-restraints excluded: chain P residue 80 VAL Chi-restraints excluded: chain P residue 110 ILE Chi-restraints excluded: chain P residue 114 LEU Chi-restraints excluded: chain Q residue 92 ARG Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain S residue 3 THR Chi-restraints excluded: chain S residue 53 SER Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain T residue 21 SER Chi-restraints excluded: chain T residue 63 VAL Chi-restraints excluded: chain T residue 74 ILE Chi-restraints excluded: chain U residue 12 ILE Chi-restraints excluded: chain U residue 15 THR Chi-restraints excluded: chain U residue 31 SER Chi-restraints excluded: chain W residue 12 ASN Chi-restraints excluded: chain W residue 21 LEU Chi-restraints excluded: chain W residue 30 SER Chi-restraints excluded: chain W residue 43 THR Chi-restraints excluded: chain X residue 19 SER Chi-restraints excluded: chain X residue 40 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 40 ARG Chi-restraints excluded: chain c residue 13 SER Chi-restraints excluded: chain c residue 29 THR Chi-restraints excluded: chain c residue 47 VAL Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 42 LEU Chi-restraints excluded: chain d residue 44 VAL Chi-restraints excluded: chain e residue 58 VAL Chi-restraints excluded: chain g residue 137 ARG Chi-restraints excluded: chain g residue 138 THR Chi-restraints excluded: chain g residue 199 VAL Chi-restraints excluded: chain h residue 35 SER Chi-restraints excluded: chain h residue 128 VAL Chi-restraints excluded: chain h residue 156 ARG Chi-restraints excluded: chain h residue 186 THR Chi-restraints excluded: chain h residue 200 VAL Chi-restraints excluded: chain j residue 76 LEU Chi-restraints excluded: chain j residue 81 LEU Chi-restraints excluded: chain j residue 103 THR Chi-restraints excluded: chain j residue 120 VAL Chi-restraints excluded: chain j residue 151 GLU Chi-restraints excluded: chain k residue 7 VAL Chi-restraints excluded: chain k residue 55 HIS Chi-restraints excluded: chain k residue 84 VAL Chi-restraints excluded: chain k residue 96 VAL Chi-restraints excluded: chain l residue 6 VAL Chi-restraints excluded: chain l residue 12 ILE Chi-restraints excluded: chain l residue 30 LEU Chi-restraints excluded: chain l residue 38 THR Chi-restraints excluded: chain l residue 50 LEU Chi-restraints excluded: chain l residue 120 LEU Chi-restraints excluded: chain l residue 133 THR Chi-restraints excluded: chain l residue 144 MET Chi-restraints excluded: chain m residue 10 MET Chi-restraints excluded: chain m residue 104 VAL Chi-restraints excluded: chain n residue 111 VAL Chi-restraints excluded: chain o residue 54 SER Chi-restraints excluded: chain o residue 73 LEU Chi-restraints excluded: chain o residue 77 VAL Chi-restraints excluded: chain p residue 35 THR Chi-restraints excluded: chain q residue 33 VAL Chi-restraints excluded: chain q residue 36 ARG Chi-restraints excluded: chain q residue 58 THR Chi-restraints excluded: chain q residue 75 GLN Chi-restraints excluded: chain q residue 111 LYS Chi-restraints excluded: chain r residue 30 SER Chi-restraints excluded: chain r residue 65 VAL Chi-restraints excluded: chain r residue 68 ASP Chi-restraints excluded: chain s residue 45 VAL Chi-restraints excluded: chain s residue 60 GLN Chi-restraints excluded: chain s residue 62 ASN Chi-restraints excluded: chain t residue 75 VAL Chi-restraints excluded: chain t residue 87 LEU Chi-restraints excluded: chain u residue 24 SER Chi-restraints excluded: chain v residue 14 SER Chi-restraints excluded: chain v residue 28 PHE Chi-restraints excluded: chain v residue 29 VAL Chi-restraints excluded: chain v residue 38 ILE Chi-restraints excluded: chain v residue 55 ILE Chi-restraints excluded: chain v residue 67 LEU Chi-restraints excluded: chain v residue 70 THR Chi-restraints excluded: chain w residue 40 VAL Chi-restraints excluded: chain x residue 5 LEU Chi-restraints excluded: chain x residue 13 LEU Chi-restraints excluded: chain x residue 79 THR Chi-restraints excluded: chain y residue 23 SER Chi-restraints excluded: chain y residue 80 THR Chi-restraints excluded: chain z residue 22 SER Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 134 MET Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 256 GLU Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 341 ILE 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: 8.9990 chunk 112 optimal weight: 10.0000 chunk 570 optimal weight: 7.9990 chunk 730 optimal weight: 1.9990 chunk 566 optimal weight: 5.9990 chunk 842 optimal weight: 10.0000 chunk 558 optimal weight: 7.9990 chunk 996 optimal weight: 1.9990 chunk 623 optimal weight: 0.9990 chunk 607 optimal weight: 6.9990 chunk 460 optimal weight: 10.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 150 GLN F 22 GLN F 73 ASN G 28 ASN G 33 GLN ** G 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 40 HIS N 18 GLN Q 37 GLN R 43 ASN U 46 GLN ** f 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 120 GLN ** h 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 131 ASN j 12 GLN k 55 HIS ** l 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** x 43 ASN x 69 HIS y 52 ASN A 110 ASN ** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.3525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 158905 Z= 0.286 Angle : 0.634 13.618 237521 Z= 0.336 Chirality : 0.035 0.266 30217 Planarity : 0.006 0.129 12870 Dihedral : 23.312 179.407 78933 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 4.90 % Allowed : 20.11 % Favored : 74.99 % 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: -1.73 (0.11), residues: 5863 helix: -0.56 (0.12), residues: 1918 sheet: -1.46 (0.15), residues: 1045 loop : -1.36 (0.11), residues: 2900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP E 97 HIS 0.028 0.002 HIS k 55 PHE 0.030 0.002 PHE N 80 TYR 0.021 0.002 TYR c 49 ARG 0.010 0.001 ARG y 74 *********************** 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 1530 residues out of total 4878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 239 poor density : 1291 time to evaluate : 6.554 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: B 23 GLU cc_start: 0.7941 (mm-30) cc_final: 0.7604 (mt-10) REVERT: B 88 SER cc_start: 0.9370 (OUTLIER) cc_final: 0.9091 (p) REVERT: B 161 TYR cc_start: 0.8435 (p90) cc_final: 0.8057 (p90) REVERT: B 177 ARG cc_start: 0.8581 (tpt170) cc_final: 0.8361 (tpt90) REVERT: C 45 TYR cc_start: 0.8302 (p90) cc_final: 0.7780 (p90) REVERT: C 91 THR cc_start: 0.7827 (p) cc_final: 0.7576 (t) REVERT: D 116 ASP cc_start: 0.8091 (t0) cc_final: 0.7774 (t0) REVERT: E 8 TYR cc_start: 0.8760 (t80) cc_final: 0.8122 (t80) REVERT: E 128 TYR cc_start: 0.8748 (t80) cc_final: 0.8428 (t80) REVERT: E 140 GLU cc_start: 0.7466 (mm-30) cc_final: 0.7252 (mm-30) REVERT: E 145 LYS cc_start: 0.7662 (mmtt) cc_final: 0.7196 (mtpt) REVERT: F 20 ASN cc_start: 0.7833 (t0) cc_final: 0.7528 (t0) REVERT: F 117 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8322 (mm) REVERT: F 133 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8113 (mt) REVERT: F 157 TYR cc_start: 0.8570 (m-80) cc_final: 0.8265 (m-80) REVERT: G 15 LEU cc_start: 0.8185 (tt) cc_final: 0.7984 (tt) REVERT: G 53 GLU cc_start: 0.6632 (mp0) cc_final: 0.5299 (mm-30) REVERT: G 72 ILE cc_start: 0.3877 (OUTLIER) cc_final: 0.3132 (tp) REVERT: J 17 VAL cc_start: 0.9293 (t) cc_final: 0.8996 (p) REVERT: J 98 GLU cc_start: 0.8246 (mp0) cc_final: 0.7953 (mp0) REVERT: K 12 ASP cc_start: 0.8692 (p0) cc_final: 0.8413 (p0) REVERT: K 80 ASP cc_start: 0.8281 (OUTLIER) cc_final: 0.7993 (t0) REVERT: K 114 LYS cc_start: 0.8956 (tttt) cc_final: 0.8739 (ttmt) REVERT: K 123 LEU cc_start: 0.8043 (OUTLIER) cc_final: 0.7807 (mt) REVERT: L 104 GLN cc_start: 0.8616 (mm-40) cc_final: 0.8314 (tp40) REVERT: M 17 ASN cc_start: 0.9127 (t0) cc_final: 0.8463 (t0) REVERT: M 76 LYS cc_start: 0.8755 (mtpp) cc_final: 0.8448 (mmmm) REVERT: M 106 ASP cc_start: 0.8104 (t0) cc_final: 0.7767 (t0) REVERT: P 11 GLU cc_start: 0.7949 (pt0) cc_final: 0.6875 (mt-10) REVERT: Q 66 ASN cc_start: 0.8951 (t0) cc_final: 0.8657 (t0) REVERT: Q 71 GLN cc_start: 0.8275 (tp-100) cc_final: 0.7887 (tp40) REVERT: Q 92 ARG cc_start: 0.8456 (OUTLIER) cc_final: 0.8203 (mtm-85) REVERT: S 99 ARG cc_start: 0.9032 (mmt90) cc_final: 0.8462 (mtt-85) REVERT: T 3 ARG cc_start: 0.8149 (ttp-170) cc_final: 0.7717 (ttp-110) REVERT: T 5 GLU cc_start: 0.7536 (mp0) cc_final: 0.6936 (mp0) REVERT: T 28 ASN cc_start: 0.8874 (m-40) cc_final: 0.8571 (m-40) REVERT: T 86 THR cc_start: 0.8882 (m) cc_final: 0.8626 (t) REVERT: V 29 ILE cc_start: 0.9314 (tt) cc_final: 0.8954 (tt) REVERT: V 46 LYS cc_start: 0.8376 (mmmm) cc_final: 0.8031 (ttpp) REVERT: W 32 LEU cc_start: 0.8853 (mt) cc_final: 0.8629 (mt) REVERT: X 58 VAL cc_start: 0.9076 (t) cc_final: 0.8819 (t) REVERT: X 74 ARG cc_start: 0.8759 (ttm170) cc_final: 0.8317 (mtp180) REVERT: X 77 LYS cc_start: 0.8341 (mttt) cc_final: 0.7929 (mmmt) REVERT: Y 15 ASN cc_start: 0.8465 (OUTLIER) cc_final: 0.8020 (m-40) REVERT: Y 21 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8175 (mt) REVERT: Z 32 ILE cc_start: 0.9289 (pt) cc_final: 0.9054 (mt) REVERT: b 11 SER cc_start: 0.9131 (t) cc_final: 0.8818 (p) REVERT: b 40 ARG cc_start: 0.9037 (OUTLIER) cc_final: 0.8693 (tpt90) REVERT: d 3 ARG cc_start: 0.8783 (mmt180) cc_final: 0.8437 (mmp80) REVERT: d 14 ARG cc_start: 0.8397 (mtt180) cc_final: 0.7930 (mtt180) REVERT: g 11 LYS cc_start: 0.7763 (pttp) cc_final: 0.7479 (ptmt) REVERT: g 15 HIS cc_start: 0.8842 (p-80) cc_final: 0.8481 (p90) REVERT: g 27 MET cc_start: 0.8641 (mmm) cc_final: 0.6935 (mmm) REVERT: g 120 GLN cc_start: 0.7642 (OUTLIER) cc_final: 0.6867 (tt0) REVERT: g 213 TYR cc_start: 0.8299 (m-80) cc_final: 0.8017 (m-80) REVERT: h 142 MET cc_start: 0.8609 (mmm) cc_final: 0.8065 (mmm) REVERT: h 169 ARG cc_start: 0.7528 (ttp80) cc_final: 0.7303 (ttp80) REVERT: h 185 ASN cc_start: 0.8328 (t0) cc_final: 0.8086 (t0) REVERT: h 188 GLU cc_start: 0.7743 (mt-10) cc_final: 0.7441 (mt-10) REVERT: i 51 TYR cc_start: 0.8615 (t80) cc_final: 0.8325 (t80) REVERT: i 57 GLU cc_start: 0.7810 (tp30) cc_final: 0.7593 (tp30) REVERT: j 86 LYS cc_start: 0.7906 (mtmt) cc_final: 0.7658 (mttt) REVERT: j 156 LYS cc_start: 0.8910 (ttpt) cc_final: 0.8644 (ttmm) REVERT: k 2 ARG cc_start: 0.8102 (mtp85) cc_final: 0.7890 (mtt180) REVERT: l 12 ILE cc_start: 0.7988 (OUTLIER) cc_final: 0.7645 (tt) REVERT: l 20 SER cc_start: 0.8153 (t) cc_final: 0.7864 (t) REVERT: l 22 LEU cc_start: 0.7134 (tp) cc_final: 0.6869 (tt) REVERT: l 50 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8343 (tm) REVERT: l 68 ASN cc_start: 0.8158 (t0) cc_final: 0.7555 (t0) REVERT: m 79 SER cc_start: 0.8654 (t) cc_final: 0.8180 (p) REVERT: n 38 TYR cc_start: 0.8520 (t80) cc_final: 0.8188 (t80) REVERT: n 79 ILE cc_start: 0.9123 (mt) cc_final: 0.8850 (mt) REVERT: n 124 ARG cc_start: 0.8681 (mtt-85) cc_final: 0.8371 (mmt180) REVERT: o 69 THR cc_start: 0.8985 (m) cc_final: 0.8502 (p) REVERT: o 100 ILE cc_start: 0.8766 (mp) cc_final: 0.8444 (mt) REVERT: p 87 LYS cc_start: 0.8604 (ttmm) cc_final: 0.8136 (ttpp) REVERT: p 125 LYS cc_start: 0.9004 (OUTLIER) cc_final: 0.8764 (pttp) REVERT: q 58 THR cc_start: 0.8502 (OUTLIER) cc_final: 0.8200 (p) REVERT: q 61 PHE cc_start: 0.8657 (m-10) cc_final: 0.8237 (m-10) REVERT: q 67 ILE cc_start: 0.9314 (mp) cc_final: 0.9047 (mp) REVERT: r 48 LEU cc_start: 0.6345 (tp) cc_final: 0.6117 (tp) REVERT: r 52 GLN cc_start: 0.7087 (mt0) cc_final: 0.6881 (mt0) REVERT: r 81 MET cc_start: 0.7279 (mmm) cc_final: 0.6997 (mtt) REVERT: s 31 ILE cc_start: 0.9197 (mm) cc_final: 0.8990 (mt) REVERT: s 60 GLN cc_start: 0.8789 (OUTLIER) cc_final: 0.8396 (pt0) REVERT: t 10 LYS cc_start: 0.8622 (mmmm) cc_final: 0.8284 (mtpt) REVERT: t 14 GLU cc_start: 0.7565 (tm-30) cc_final: 0.6460 (tm-30) REVERT: v 19 LYS cc_start: 0.8263 (mttt) cc_final: 0.7598 (mmmt) REVERT: v 28 PHE cc_start: 0.8754 (OUTLIER) cc_final: 0.8382 (t80) REVERT: v 80 GLU cc_start: 0.7797 (tm-30) cc_final: 0.7138 (tm-30) REVERT: y 74 ARG cc_start: 0.7754 (ttp-110) cc_final: 0.7553 (ttp-110) REVERT: z 12 PHE cc_start: 0.8048 (t80) cc_final: 0.7584 (t80) REVERT: A 126 LEU cc_start: 0.9063 (tt) cc_final: 0.8820 (tt) REVERT: A 199 SER cc_start: 0.9202 (m) cc_final: 0.8823 (p) REVERT: A 271 LEU cc_start: 0.9015 (mt) cc_final: 0.8812 (mt) REVERT: A 347 GLU cc_start: 0.7183 (OUTLIER) cc_final: 0.6556 (mp0) outliers start: 239 outliers final: 194 residues processed: 1410 average time/residue: 1.3188 time to fit residues: 3197.0263 Evaluate side-chains 1474 residues out of total 4878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 212 poor density : 1262 time to evaluate : 6.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 146 MET Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 201 MET Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 28 GLU Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 7 ASP Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain D residue 80 SER Chi-restraints excluded: chain D residue 176 ASP Chi-restraints excluded: chain D residue 181 ILE Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 87 CYS Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain F residue 9 VAL Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 39 ASP Chi-restraints excluded: chain F residue 49 THR Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain F residue 71 LEU Chi-restraints excluded: chain F residue 84 THR Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 127 THR Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain F residue 168 VAL Chi-restraints excluded: chain F residue 171 THR Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 72 ILE Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 35 VAL Chi-restraints excluded: chain K residue 61 VAL Chi-restraints excluded: chain K residue 73 ASP Chi-restraints excluded: chain K residue 80 ASP Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 110 GLU Chi-restraints excluded: chain K residue 123 LEU Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 23 ILE Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 40 SER Chi-restraints excluded: chain L residue 67 THR Chi-restraints excluded: chain L residue 80 SER Chi-restraints excluded: chain L residue 93 ASN Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 36 VAL Chi-restraints excluded: chain M residue 42 THR Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 78 LEU Chi-restraints excluded: chain M residue 82 MET Chi-restraints excluded: chain M residue 111 GLU Chi-restraints excluded: chain M residue 132 THR Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 33 ILE Chi-restraints excluded: chain N residue 45 ARG Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain O residue 28 VAL Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 52 SER Chi-restraints excluded: chain O residue 63 LYS Chi-restraints excluded: chain P residue 4 ILE Chi-restraints excluded: chain P residue 32 VAL Chi-restraints excluded: chain P residue 40 LEU Chi-restraints excluded: chain P residue 80 VAL Chi-restraints excluded: chain P residue 110 ILE Chi-restraints excluded: chain P residue 114 LEU Chi-restraints excluded: chain Q residue 92 ARG Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain S residue 3 THR Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain T residue 21 SER Chi-restraints excluded: chain T residue 27 SER Chi-restraints excluded: chain T residue 34 VAL Chi-restraints excluded: chain T residue 63 VAL Chi-restraints excluded: chain T residue 74 ILE 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 31 SER Chi-restraints excluded: chain U residue 72 ILE Chi-restraints excluded: chain V residue 30 ILE Chi-restraints excluded: chain V residue 41 GLU Chi-restraints excluded: chain V residue 50 MET Chi-restraints excluded: chain W residue 12 ASN Chi-restraints excluded: chain W residue 21 LEU Chi-restraints excluded: chain W residue 30 SER Chi-restraints excluded: chain W residue 43 THR Chi-restraints excluded: chain X residue 19 SER Chi-restraints excluded: chain X residue 40 VAL Chi-restraints excluded: chain X residue 66 THR Chi-restraints excluded: chain Y residue 15 ASN Chi-restraints excluded: chain Y residue 21 LEU Chi-restraints excluded: chain Y residue 22 LEU Chi-restraints excluded: chain Z residue 10 THR Chi-restraints excluded: chain Z residue 25 LEU Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain b residue 40 ARG Chi-restraints excluded: chain b residue 44 THR Chi-restraints excluded: chain c residue 13 SER Chi-restraints excluded: chain c residue 29 THR Chi-restraints excluded: chain c residue 47 VAL Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 42 LEU Chi-restraints excluded: chain d residue 44 VAL Chi-restraints excluded: chain e residue 51 SER Chi-restraints excluded: chain e residue 58 VAL Chi-restraints excluded: chain g residue 120 GLN Chi-restraints excluded: chain g residue 137 ARG Chi-restraints excluded: chain g residue 174 LYS Chi-restraints excluded: chain g residue 199 VAL Chi-restraints excluded: chain h residue 35 SER Chi-restraints excluded: chain h residue 152 GLU Chi-restraints excluded: chain h residue 156 ARG Chi-restraints excluded: chain h residue 186 THR Chi-restraints excluded: chain h residue 200 VAL Chi-restraints excluded: chain j residue 30 ILE Chi-restraints excluded: chain j residue 76 LEU Chi-restraints excluded: chain j residue 103 THR Chi-restraints excluded: chain j residue 120 VAL Chi-restraints excluded: chain j residue 140 THR Chi-restraints excluded: chain k residue 7 VAL Chi-restraints excluded: chain k residue 73 GLU Chi-restraints excluded: chain k residue 84 VAL Chi-restraints excluded: chain k residue 96 VAL Chi-restraints excluded: chain l residue 6 VAL Chi-restraints excluded: chain l residue 12 ILE Chi-restraints excluded: chain l residue 30 LEU Chi-restraints excluded: chain l residue 38 THR Chi-restraints excluded: chain l residue 50 LEU Chi-restraints excluded: chain l residue 77 SER Chi-restraints excluded: chain l residue 120 LEU Chi-restraints excluded: chain l residue 133 THR Chi-restraints excluded: chain m residue 10 MET Chi-restraints excluded: chain m residue 55 THR Chi-restraints excluded: chain m residue 104 VAL Chi-restraints excluded: chain m residue 105 SER Chi-restraints excluded: chain n residue 62 ASP Chi-restraints excluded: chain n residue 111 VAL Chi-restraints excluded: chain o residue 54 SER Chi-restraints excluded: chain o residue 73 LEU Chi-restraints excluded: chain o residue 74 VAL Chi-restraints excluded: chain o residue 77 VAL Chi-restraints excluded: chain p residue 35 THR Chi-restraints excluded: chain p residue 125 LYS Chi-restraints excluded: chain q residue 33 VAL Chi-restraints excluded: chain q residue 36 ARG Chi-restraints excluded: chain q residue 58 THR Chi-restraints excluded: chain q residue 70 GLU Chi-restraints excluded: chain q residue 111 LYS Chi-restraints excluded: chain r residue 30 SER Chi-restraints excluded: chain r residue 56 LEU Chi-restraints excluded: chain r residue 65 VAL Chi-restraints excluded: chain r residue 68 ASP Chi-restraints excluded: chain s residue 45 VAL Chi-restraints excluded: chain s residue 60 GLN Chi-restraints excluded: chain s residue 80 SER Chi-restraints excluded: chain t residue 75 VAL Chi-restraints excluded: chain t residue 87 LEU Chi-restraints excluded: chain u residue 24 SER Chi-restraints excluded: chain v residue 14 SER Chi-restraints excluded: chain v residue 28 PHE Chi-restraints excluded: chain v residue 29 VAL Chi-restraints excluded: chain v residue 38 ILE Chi-restraints excluded: chain v residue 55 ILE Chi-restraints excluded: chain v residue 67 LEU Chi-restraints excluded: chain v residue 70 THR Chi-restraints excluded: chain x residue 5 LEU Chi-restraints excluded: chain x residue 79 THR Chi-restraints excluded: chain y residue 23 SER Chi-restraints excluded: chain y residue 26 SER Chi-restraints excluded: chain y residue 53 GLU Chi-restraints excluded: chain y residue 57 ILE Chi-restraints excluded: chain y residue 80 THR Chi-restraints excluded: chain z residue 4 ILE Chi-restraints excluded: chain z residue 22 SER Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 134 MET Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 256 GLU Chi-restraints excluded: chain A residue 341 ILE 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: 3.9990 chunk 397 optimal weight: 10.0000 chunk 595 optimal weight: 0.4980 chunk 300 optimal weight: 10.0000 chunk 195 optimal weight: 7.9990 chunk 193 optimal weight: 8.9990 chunk 633 optimal weight: 2.9990 chunk 678 optimal weight: 10.0000 chunk 492 optimal weight: 7.9990 chunk 92 optimal weight: 10.0000 chunk 783 optimal weight: 6.9990 overall best weight: 4.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 22 GLN F 73 ASN G 28 ASN G 33 GLN L 4 ASN L 54 GLN R 43 ASN U 46 GLN V 5 ASN ** f 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 100 GLN h 102 ASN ** h 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 131 ASN j 12 GLN k 55 HIS ** l 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 5 GLN ** u 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** y 52 ASN ** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.3551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 158905 Z= 0.345 Angle : 0.672 13.619 237521 Z= 0.352 Chirality : 0.037 0.278 30217 Planarity : 0.006 0.131 12870 Dihedral : 23.329 179.364 78933 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 5.49 % Allowed : 20.09 % Favored : 74.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.11), residues: 5863 helix: -0.56 (0.12), residues: 1917 sheet: -1.50 (0.15), residues: 1068 loop : -1.36 (0.11), residues: 2878 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP s 42 HIS 0.010 0.002 HIS S 7 PHE 0.032 0.002 PHE N 80 TYR 0.018 0.002 TYR c 49 ARG 0.011 0.001 ARG v 27 *********************** 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 1547 residues out of total 4878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 268 poor density : 1279 time to evaluate : 6.581 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: B 23 GLU cc_start: 0.7896 (mm-30) cc_final: 0.7596 (mt-10) REVERT: B 88 SER cc_start: 0.9372 (OUTLIER) cc_final: 0.9105 (p) REVERT: C 45 TYR cc_start: 0.8296 (p90) cc_final: 0.7823 (p90) REVERT: C 91 THR cc_start: 0.7847 (p) cc_final: 0.7545 (t) REVERT: D 116 ASP cc_start: 0.8083 (t0) cc_final: 0.7773 (t0) REVERT: E 8 TYR cc_start: 0.8768 (t80) cc_final: 0.8009 (t80) REVERT: E 117 LEU cc_start: 0.8232 (OUTLIER) cc_final: 0.7702 (mt) REVERT: E 128 TYR cc_start: 0.8765 (t80) cc_final: 0.8515 (t80) REVERT: E 145 LYS cc_start: 0.7722 (mmtt) cc_final: 0.7116 (mtpt) REVERT: F 20 ASN cc_start: 0.7825 (t0) cc_final: 0.7521 (t0) REVERT: F 117 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8362 (mm) REVERT: F 130 GLU cc_start: 0.8362 (mm-30) cc_final: 0.8034 (mm-30) REVERT: F 133 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8136 (mt) REVERT: F 157 TYR cc_start: 0.8565 (m-80) cc_final: 0.8285 (m-80) REVERT: G 53 GLU cc_start: 0.6664 (mp0) cc_final: 0.5301 (mm-30) REVERT: G 72 ILE cc_start: 0.4070 (OUTLIER) cc_final: 0.3307 (tp) REVERT: J 17 VAL cc_start: 0.9333 (t) cc_final: 0.9067 (p) REVERT: J 98 GLU cc_start: 0.8286 (mp0) cc_final: 0.7999 (mp0) REVERT: K 12 ASP cc_start: 0.8681 (p0) cc_final: 0.8403 (p0) REVERT: K 80 ASP cc_start: 0.8280 (OUTLIER) cc_final: 0.7997 (t0) REVERT: K 123 LEU cc_start: 0.8127 (OUTLIER) cc_final: 0.7915 (mt) REVERT: M 17 ASN cc_start: 0.9153 (t0) cc_final: 0.8473 (t0) REVERT: M 76 LYS cc_start: 0.8776 (mtpp) cc_final: 0.8488 (mmmm) REVERT: M 106 ASP cc_start: 0.8124 (t0) cc_final: 0.7863 (t0) REVERT: N 2 ARG cc_start: 0.8480 (OUTLIER) cc_final: 0.7851 (ttp80) REVERT: N 51 LEU cc_start: 0.9149 (OUTLIER) cc_final: 0.8872 (mt) REVERT: P 11 GLU cc_start: 0.7976 (pt0) cc_final: 0.6941 (mt-10) REVERT: Q 66 ASN cc_start: 0.8965 (t0) cc_final: 0.8679 (t0) REVERT: Q 71 GLN cc_start: 0.8291 (tp-100) cc_final: 0.7908 (tp40) REVERT: Q 92 ARG cc_start: 0.8555 (OUTLIER) cc_final: 0.8354 (mtm-85) REVERT: S 99 ARG cc_start: 0.9032 (mmt90) cc_final: 0.8492 (mtt-85) REVERT: T 28 ASN cc_start: 0.8828 (m-40) cc_final: 0.8592 (m-40) REVERT: T 86 THR cc_start: 0.8877 (m) cc_final: 0.8599 (t) REVERT: V 29 ILE cc_start: 0.9341 (tt) cc_final: 0.9127 (tt) REVERT: V 46 LYS cc_start: 0.8398 (mmmm) cc_final: 0.8049 (ttpp) REVERT: W 32 LEU cc_start: 0.8878 (mt) cc_final: 0.8649 (mt) REVERT: X 74 ARG cc_start: 0.8682 (ttm170) cc_final: 0.8227 (mtp180) REVERT: X 77 LYS cc_start: 0.8356 (mttt) cc_final: 0.7941 (mmmt) REVERT: Y 15 ASN cc_start: 0.8507 (OUTLIER) cc_final: 0.8106 (m-40) REVERT: Z 32 ILE cc_start: 0.9292 (pt) cc_final: 0.9056 (mt) REVERT: b 11 SER cc_start: 0.9137 (t) cc_final: 0.8835 (p) REVERT: b 40 ARG cc_start: 0.9092 (OUTLIER) cc_final: 0.8795 (tpt90) REVERT: d 3 ARG cc_start: 0.8783 (mmt180) cc_final: 0.8435 (mmp80) REVERT: d 14 ARG cc_start: 0.8359 (mtt180) cc_final: 0.7943 (mtt180) REVERT: g 11 LYS cc_start: 0.7779 (pttp) cc_final: 0.7532 (ptmt) REVERT: g 15 HIS cc_start: 0.8849 (p-80) cc_final: 0.8507 (p90) REVERT: g 27 MET cc_start: 0.8676 (mmm) cc_final: 0.6928 (mmm) REVERT: g 213 TYR cc_start: 0.8319 (m-80) cc_final: 0.8007 (m-80) REVERT: h 142 MET cc_start: 0.8725 (mmm) cc_final: 0.8197 (mmm) REVERT: h 185 ASN cc_start: 0.8380 (t0) cc_final: 0.8144 (t0) REVERT: h 188 GLU cc_start: 0.7745 (mt-10) cc_final: 0.7478 (mt-10) REVERT: i 51 TYR cc_start: 0.8647 (t80) cc_final: 0.8348 (t80) REVERT: i 187 GLU cc_start: 0.7281 (mp0) cc_final: 0.6786 (mp0) REVERT: i 195 ILE cc_start: 0.8851 (mm) cc_final: 0.8603 (mm) REVERT: j 86 LYS cc_start: 0.7938 (mtmt) cc_final: 0.7688 (mttt) REVERT: j 156 LYS cc_start: 0.8910 (ttpt) cc_final: 0.8666 (ttmm) REVERT: k 2 ARG cc_start: 0.8006 (mtp85) cc_final: 0.7284 (mtp85) REVERT: k 39 LEU cc_start: 0.8271 (tt) cc_final: 0.8070 (tt) REVERT: l 12 ILE cc_start: 0.8037 (OUTLIER) cc_final: 0.7689 (tt) REVERT: l 20 SER cc_start: 0.8195 (t) cc_final: 0.7912 (t) REVERT: l 50 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.8329 (tm) REVERT: l 68 ASN cc_start: 0.8086 (t0) cc_final: 0.7793 (t0) REVERT: m 79 SER cc_start: 0.8664 (t) cc_final: 0.8417 (t) REVERT: n 38 TYR cc_start: 0.8541 (t80) cc_final: 0.8219 (t80) REVERT: n 79 ILE cc_start: 0.9133 (mt) cc_final: 0.8853 (mt) REVERT: n 124 ARG cc_start: 0.8664 (mtt-85) cc_final: 0.8344 (mmt180) REVERT: o 69 THR cc_start: 0.8977 (m) cc_final: 0.8522 (p) REVERT: o 100 ILE cc_start: 0.8754 (mp) cc_final: 0.8452 (mt) REVERT: p 87 LYS cc_start: 0.8626 (ttmm) cc_final: 0.8125 (ttpp) REVERT: p 125 LYS cc_start: 0.9003 (OUTLIER) cc_final: 0.8756 (pttp) REVERT: q 58 THR cc_start: 0.8571 (OUTLIER) cc_final: 0.8257 (p) REVERT: q 61 PHE cc_start: 0.8728 (m-10) cc_final: 0.8315 (m-10) REVERT: q 67 ILE cc_start: 0.9324 (mp) cc_final: 0.9071 (mp) REVERT: q 75 GLN cc_start: 0.8561 (OUTLIER) cc_final: 0.8048 (mm110) REVERT: r 48 LEU cc_start: 0.6429 (tp) cc_final: 0.6214 (tp) REVERT: r 52 GLN cc_start: 0.7226 (mt0) cc_final: 0.6971 (mt0) REVERT: r 81 MET cc_start: 0.7321 (mmm) cc_final: 0.5986 (mmm) REVERT: s 31 ILE cc_start: 0.9214 (mm) cc_final: 0.8984 (mt) REVERT: s 60 GLN cc_start: 0.8810 (OUTLIER) cc_final: 0.8390 (pt0) REVERT: t 10 LYS cc_start: 0.8565 (mmmm) cc_final: 0.8173 (mtpt) REVERT: t 14 GLU cc_start: 0.7364 (tm-30) cc_final: 0.6268 (tm-30) REVERT: t 74 ASP cc_start: 0.7578 (t70) cc_final: 0.6853 (p0) REVERT: v 19 LYS cc_start: 0.8161 (mttt) cc_final: 0.7433 (mmmt) REVERT: v 28 PHE cc_start: 0.8746 (OUTLIER) cc_final: 0.8375 (t80) REVERT: v 80 GLU cc_start: 0.7831 (tm-30) cc_final: 0.7319 (tm-30) REVERT: z 12 PHE cc_start: 0.8075 (t80) cc_final: 0.7604 (t80) REVERT: A 126 LEU cc_start: 0.9074 (OUTLIER) cc_final: 0.8868 (tt) REVERT: A 347 GLU cc_start: 0.7141 (OUTLIER) cc_final: 0.6703 (mp0) outliers start: 268 outliers final: 225 residues processed: 1423 average time/residue: 1.3199 time to fit residues: 3233.1369 Evaluate side-chains 1507 residues out of total 4878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 246 poor density : 1261 time to evaluate : 6.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 146 MET Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 201 MET Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 28 GLU Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 7 ASP Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain D residue 80 SER Chi-restraints excluded: chain D residue 141 MET Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 176 ASP Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain D residue 181 ILE Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 87 CYS Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 165 GLU Chi-restraints excluded: chain F residue 9 VAL Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain F residue 39 ASP Chi-restraints excluded: chain F residue 49 THR Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain F residue 71 LEU Chi-restraints excluded: chain F residue 84 THR Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 127 THR Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain F residue 168 VAL Chi-restraints excluded: chain F residue 171 THR Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 72 ILE Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 28 SER Chi-restraints excluded: chain K residue 35 VAL Chi-restraints excluded: chain K residue 61 VAL Chi-restraints excluded: chain K residue 73 ASP Chi-restraints excluded: chain K residue 80 ASP Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 110 GLU Chi-restraints excluded: chain K residue 123 LEU Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 23 ILE Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 40 SER Chi-restraints excluded: chain L residue 67 THR Chi-restraints excluded: chain L residue 80 SER Chi-restraints excluded: chain L residue 93 ASN Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 27 SER Chi-restraints excluded: chain M residue 36 VAL Chi-restraints excluded: chain M residue 42 THR Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 78 LEU Chi-restraints excluded: chain M residue 82 MET Chi-restraints excluded: chain M residue 111 GLU Chi-restraints excluded: chain M residue 132 THR Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 2 ARG Chi-restraints excluded: chain N residue 33 ILE Chi-restraints excluded: chain N residue 45 ARG Chi-restraints excluded: chain N residue 51 LEU Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain O residue 28 VAL Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 52 SER Chi-restraints excluded: chain O residue 63 LYS Chi-restraints excluded: chain P residue 4 ILE Chi-restraints excluded: chain P residue 32 VAL Chi-restraints excluded: chain P residue 34 GLU Chi-restraints excluded: chain P residue 40 LEU Chi-restraints excluded: chain P residue 80 VAL Chi-restraints excluded: chain P residue 110 ILE Chi-restraints excluded: chain P residue 114 LEU Chi-restraints excluded: chain Q residue 92 ARG Chi-restraints excluded: chain R residue 1 MET Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain R residue 54 VAL Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain S residue 3 THR Chi-restraints excluded: chain S residue 53 SER Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain T residue 21 SER Chi-restraints excluded: chain T residue 27 SER Chi-restraints excluded: chain T residue 34 VAL Chi-restraints excluded: chain T residue 39 THR Chi-restraints excluded: chain T residue 63 VAL Chi-restraints excluded: chain T residue 74 ILE 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 31 SER Chi-restraints excluded: chain U residue 72 ILE Chi-restraints excluded: chain V residue 4 ILE Chi-restraints excluded: chain V residue 30 ILE Chi-restraints excluded: chain V residue 50 MET Chi-restraints excluded: chain W residue 12 ASN Chi-restraints excluded: chain W residue 21 LEU Chi-restraints excluded: chain W residue 30 SER Chi-restraints excluded: chain W residue 43 THR Chi-restraints excluded: chain X residue 19 SER Chi-restraints excluded: chain X residue 40 VAL Chi-restraints excluded: chain X residue 66 THR Chi-restraints excluded: chain Y residue 15 ASN Chi-restraints excluded: chain Y residue 22 LEU Chi-restraints excluded: chain Z residue 10 THR Chi-restraints excluded: chain Z residue 25 LEU Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain b residue 40 ARG Chi-restraints excluded: chain b residue 44 THR Chi-restraints excluded: chain c residue 13 SER Chi-restraints excluded: chain c residue 29 THR Chi-restraints excluded: chain c residue 47 VAL Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 42 LEU Chi-restraints excluded: chain d residue 44 VAL Chi-restraints excluded: chain e residue 32 ILE Chi-restraints excluded: chain e residue 51 SER Chi-restraints excluded: chain e residue 58 VAL Chi-restraints excluded: chain g residue 9 MET Chi-restraints excluded: chain g residue 137 ARG Chi-restraints excluded: chain g residue 174 LYS Chi-restraints excluded: chain g residue 199 VAL Chi-restraints excluded: chain h residue 35 SER Chi-restraints excluded: chain h residue 53 SER Chi-restraints excluded: chain h residue 58 GLU Chi-restraints excluded: chain h residue 100 GLN Chi-restraints excluded: chain h residue 108 LYS Chi-restraints excluded: chain h residue 128 VAL Chi-restraints excluded: chain h residue 152 GLU Chi-restraints excluded: chain h residue 156 ARG Chi-restraints excluded: chain h residue 186 THR Chi-restraints excluded: chain h residue 200 VAL Chi-restraints excluded: chain j residue 34 THR Chi-restraints excluded: chain j residue 72 ILE Chi-restraints excluded: chain j residue 76 LEU Chi-restraints excluded: chain j residue 103 THR Chi-restraints excluded: chain j residue 120 VAL Chi-restraints excluded: chain j residue 140 THR Chi-restraints excluded: chain k residue 7 VAL Chi-restraints excluded: chain k residue 51 ILE Chi-restraints excluded: chain k residue 55 HIS Chi-restraints excluded: chain k residue 73 GLU Chi-restraints excluded: chain k residue 84 VAL Chi-restraints excluded: chain k residue 96 VAL Chi-restraints excluded: chain l residue 6 VAL Chi-restraints excluded: chain l residue 12 ILE Chi-restraints excluded: chain l residue 30 LEU Chi-restraints excluded: chain l residue 38 THR Chi-restraints excluded: chain l residue 50 LEU Chi-restraints excluded: chain l residue 77 SER Chi-restraints excluded: chain l residue 120 LEU Chi-restraints excluded: chain l residue 133 THR Chi-restraints excluded: chain m residue 10 MET Chi-restraints excluded: chain m residue 104 VAL Chi-restraints excluded: chain m residue 105 SER Chi-restraints excluded: chain n residue 111 VAL Chi-restraints excluded: chain o residue 54 SER Chi-restraints excluded: chain o residue 73 LEU Chi-restraints excluded: chain o residue 74 VAL Chi-restraints excluded: chain o residue 77 VAL Chi-restraints excluded: chain p residue 35 THR Chi-restraints excluded: chain p residue 68 GLU Chi-restraints excluded: chain p residue 125 LYS Chi-restraints excluded: chain q residue 33 VAL Chi-restraints excluded: chain q residue 36 ARG Chi-restraints excluded: chain q residue 58 THR Chi-restraints excluded: chain q residue 70 GLU Chi-restraints excluded: chain q residue 75 GLN Chi-restraints excluded: chain q residue 82 ILE Chi-restraints excluded: chain q residue 111 LYS Chi-restraints excluded: chain r residue 20 THR Chi-restraints excluded: chain r residue 30 SER Chi-restraints excluded: chain r residue 56 LEU Chi-restraints excluded: chain r residue 65 VAL Chi-restraints excluded: chain r residue 68 ASP Chi-restraints excluded: chain s residue 45 VAL Chi-restraints excluded: chain s residue 60 GLN Chi-restraints excluded: chain s residue 80 SER Chi-restraints excluded: chain t residue 75 VAL Chi-restraints excluded: chain t residue 87 LEU Chi-restraints excluded: chain u residue 3 THR Chi-restraints excluded: chain u residue 24 SER Chi-restraints excluded: chain v residue 14 SER Chi-restraints excluded: chain v residue 28 PHE Chi-restraints excluded: chain v residue 29 VAL Chi-restraints excluded: chain v residue 38 ILE Chi-restraints excluded: chain v residue 55 ILE Chi-restraints excluded: chain v residue 67 LEU Chi-restraints excluded: chain v residue 70 THR Chi-restraints excluded: chain x residue 5 LEU Chi-restraints excluded: chain x residue 13 LEU Chi-restraints excluded: chain x residue 79 THR Chi-restraints excluded: chain y residue 12 ILE Chi-restraints excluded: chain y residue 23 SER Chi-restraints excluded: chain y residue 26 SER Chi-restraints excluded: chain y residue 53 GLU Chi-restraints excluded: chain y residue 57 ILE Chi-restraints excluded: chain y residue 80 THR Chi-restraints excluded: chain z residue 4 ILE Chi-restraints excluded: chain z residue 22 SER Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 134 MET Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 256 GLU Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain A residue 341 ILE 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: 0.5980 chunk 954 optimal weight: 3.9990 chunk 871 optimal weight: 0.6980 chunk 928 optimal weight: 0.9990 chunk 558 optimal weight: 0.9980 chunk 404 optimal weight: 10.0000 chunk 729 optimal weight: 7.9990 chunk 285 optimal weight: 10.0000 chunk 839 optimal weight: 0.0070 chunk 878 optimal weight: 2.9990 chunk 925 optimal weight: 0.9990 overall best weight: 0.6600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 52 ASN F 22 GLN F 73 ASN G 28 ASN G 33 GLN L 4 ASN L 54 GLN N 62 ASN R 43 ASN U 46 GLN ** a 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 39 HIS ** g 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 102 ASN ** h 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 131 ASN ** i 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 12 GLN k 55 HIS n 5 GLN x 43 ASN y 52 ASN A 193 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.3981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.086 158905 Z= 0.116 Angle : 0.555 13.796 237521 Z= 0.300 Chirality : 0.030 0.235 30217 Planarity : 0.005 0.123 12870 Dihedral : 23.249 179.814 78933 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.83 % Allowed : 22.67 % Favored : 74.50 % 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: -1.22 (0.11), residues: 5863 helix: 0.03 (0.12), residues: 1911 sheet: -1.23 (0.15), residues: 1068 loop : -1.14 (0.11), residues: 2884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP E 97 HIS 0.037 0.001 HIS k 55 PHE 0.026 0.001 PHE J 4 TYR 0.024 0.001 TYR K 32 ARG 0.010 0.000 ARG v 27 *********************** 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 1509 residues out of total 4878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 1371 time to evaluate : 6.407 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: B 88 SER cc_start: 0.9465 (p) cc_final: 0.9059 (p) REVERT: B 96 TYR cc_start: 0.8405 (m-80) cc_final: 0.7687 (m-80) REVERT: C 91 THR cc_start: 0.7943 (p) cc_final: 0.7617 (t) REVERT: D 116 ASP cc_start: 0.7975 (t0) cc_final: 0.7722 (t0) REVERT: E 48 LYS cc_start: 0.7812 (mmmm) cc_final: 0.7550 (mptt) REVERT: E 97 TRP cc_start: 0.9113 (m100) cc_final: 0.8884 (m100) REVERT: E 128 TYR cc_start: 0.8753 (t80) cc_final: 0.8464 (t80) REVERT: E 145 LYS cc_start: 0.7615 (mmtt) cc_final: 0.7150 (mtpt) REVERT: F 20 ASN cc_start: 0.7730 (t0) cc_final: 0.7445 (t0) REVERT: F 130 GLU cc_start: 0.8308 (mm-30) cc_final: 0.7930 (mm-30) REVERT: F 133 LEU cc_start: 0.8588 (OUTLIER) cc_final: 0.8014 (mt) REVERT: F 157 TYR cc_start: 0.8545 (m-80) cc_final: 0.8259 (m-80) REVERT: G 28 ASN cc_start: 0.9285 (m-40) cc_final: 0.8698 (m-40) REVERT: G 53 GLU cc_start: 0.6446 (mp0) cc_final: 0.5156 (mm-30) REVERT: J 17 VAL cc_start: 0.9047 (t) cc_final: 0.8710 (p) REVERT: J 98 GLU cc_start: 0.8117 (mp0) cc_final: 0.7869 (mp0) REVERT: K 12 ASP cc_start: 0.8620 (p0) cc_final: 0.8314 (p0) REVERT: K 121 GLU cc_start: 0.7027 (tt0) cc_final: 0.6678 (tt0) REVERT: M 17 ASN cc_start: 0.9109 (t0) cc_final: 0.8520 (t0) REVERT: M 76 LYS cc_start: 0.8666 (mtpp) cc_final: 0.8340 (mmmm) REVERT: M 106 ASP cc_start: 0.8131 (t0) cc_final: 0.7614 (t0) REVERT: M 124 LEU cc_start: 0.8878 (mp) cc_final: 0.8527 (mt) REVERT: N 2 ARG cc_start: 0.8302 (OUTLIER) cc_final: 0.8016 (ttp80) REVERT: P 7 GLN cc_start: 0.8173 (tm-30) cc_final: 0.7285 (tp40) REVERT: P 11 GLU cc_start: 0.7928 (pt0) cc_final: 0.6624 (mt-10) REVERT: Q 15 LYS cc_start: 0.8365 (ttpt) cc_final: 0.7774 (tttm) REVERT: Q 66 ASN cc_start: 0.8893 (t0) cc_final: 0.8550 (t0) REVERT: Q 71 GLN cc_start: 0.8199 (tp-100) cc_final: 0.7789 (tp40) REVERT: S 97 LEU cc_start: 0.9090 (mm) cc_final: 0.8705 (mm) REVERT: S 99 ARG cc_start: 0.9032 (mmt90) cc_final: 0.8459 (mtt-85) REVERT: T 28 ASN cc_start: 0.8788 (m-40) cc_final: 0.8307 (m-40) REVERT: T 86 THR cc_start: 0.8992 (m) cc_final: 0.8621 (p) REVERT: V 29 ILE cc_start: 0.9208 (tt) cc_final: 0.8813 (tt) REVERT: V 46 LYS cc_start: 0.8309 (mmmm) cc_final: 0.7810 (ttpp) REVERT: W 55 ARG cc_start: 0.8673 (ttp80) cc_final: 0.7053 (ttp80) REVERT: W 75 LYS cc_start: 0.9095 (mtpp) cc_final: 0.8876 (mtpp) REVERT: X 58 VAL cc_start: 0.9041 (t) cc_final: 0.8840 (t) REVERT: X 74 ARG cc_start: 0.8524 (ttm170) cc_final: 0.8138 (mtp180) REVERT: X 77 LYS cc_start: 0.8223 (mttt) cc_final: 0.7852 (mmmt) REVERT: Z 27 LEU cc_start: 0.8706 (tp) cc_final: 0.8356 (tp) REVERT: b 11 SER cc_start: 0.9089 (t) cc_final: 0.8727 (p) REVERT: b 40 ARG cc_start: 0.8759 (OUTLIER) cc_final: 0.7679 (ttt90) REVERT: c 44 ARG cc_start: 0.8181 (mtp85) cc_final: 0.7877 (mtp85) REVERT: d 14 ARG cc_start: 0.8398 (mtt180) cc_final: 0.8002 (mtt180) REVERT: f 1 MET cc_start: 0.8204 (tpp) cc_final: 0.7921 (tpp) REVERT: g 15 HIS cc_start: 0.8871 (p-80) cc_final: 0.8548 (p90) REVERT: g 27 MET cc_start: 0.8541 (mmm) cc_final: 0.6932 (mmm) REVERT: h 142 MET cc_start: 0.8591 (mmm) cc_final: 0.8272 (mmm) REVERT: h 177 THR cc_start: 0.8706 (m) cc_final: 0.8390 (p) REVERT: h 185 ASN cc_start: 0.8097 (t0) cc_final: 0.7884 (t0) REVERT: h 188 GLU cc_start: 0.7785 (mt-10) cc_final: 0.7396 (mt-10) REVERT: i 4 TYR cc_start: 0.8705 (t80) cc_final: 0.8471 (t80) REVERT: i 51 TYR cc_start: 0.8462 (t80) cc_final: 0.8218 (t80) REVERT: i 178 MET cc_start: 0.6527 (ptt) cc_final: 0.5895 (ptt) REVERT: i 187 GLU cc_start: 0.7152 (mp0) cc_final: 0.6748 (mp0) REVERT: j 86 LYS cc_start: 0.7870 (mtmt) cc_final: 0.7612 (mttt) REVERT: k 14 GLN cc_start: 0.7119 (mm-40) cc_final: 0.6446 (tp40) REVERT: k 39 LEU cc_start: 0.8127 (tt) cc_final: 0.7887 (tt) REVERT: k 44 ARG cc_start: 0.7382 (mtt90) cc_final: 0.7078 (mtt90) REVERT: l 20 SER cc_start: 0.8031 (t) cc_final: 0.7683 (t) REVERT: l 22 LEU cc_start: 0.6890 (tp) cc_final: 0.6117 (mm) REVERT: l 50 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.8259 (tm) REVERT: l 68 ASN cc_start: 0.7863 (t0) cc_final: 0.7316 (t0) REVERT: l 92 ARG cc_start: 0.7664 (ttp-110) cc_final: 0.7388 (mtm-85) REVERT: m 79 SER cc_start: 0.8578 (t) cc_final: 0.8351 (t) REVERT: n 38 TYR cc_start: 0.8389 (t80) cc_final: 0.8026 (t80) REVERT: n 79 ILE cc_start: 0.9064 (mt) cc_final: 0.8778 (mt) REVERT: n 119 ARG cc_start: 0.8344 (ttm-80) cc_final: 0.7913 (ttm110) REVERT: n 124 ARG cc_start: 0.8540 (mtt-85) cc_final: 0.8258 (mmt180) REVERT: o 69 THR cc_start: 0.9004 (m) cc_final: 0.8499 (p) REVERT: o 100 ILE cc_start: 0.8710 (mp) cc_final: 0.8350 (mt) REVERT: p 87 LYS cc_start: 0.8321 (ttmm) cc_final: 0.7873 (ttpp) REVERT: p 101 ASN cc_start: 0.8616 (t0) cc_final: 0.8379 (t0) REVERT: q 56 ARG cc_start: 0.7715 (ttm-80) cc_final: 0.7286 (tpp-160) REVERT: q 58 THR cc_start: 0.8366 (OUTLIER) cc_final: 0.8088 (p) REVERT: q 67 ILE cc_start: 0.9234 (mp) cc_final: 0.8999 (mp) REVERT: q 75 GLN cc_start: 0.8434 (OUTLIER) cc_final: 0.7690 (mm110) REVERT: r 7 ILE cc_start: 0.7999 (pt) cc_final: 0.7650 (pt) REVERT: s 6 MET cc_start: 0.8282 (mmt) cc_final: 0.7937 (mmm) REVERT: t 10 LYS cc_start: 0.8597 (mmmm) cc_final: 0.8207 (mtpt) REVERT: t 14 GLU cc_start: 0.7625 (tm-30) cc_final: 0.6551 (tm-30) REVERT: t 74 ASP cc_start: 0.7207 (t70) cc_final: 0.6613 (p0) REVERT: t 77 ARG cc_start: 0.7706 (mtm180) cc_final: 0.7243 (ttm170) REVERT: u 56 ARG cc_start: 0.7657 (mmm-85) cc_final: 0.7445 (mmm-85) REVERT: v 19 LYS cc_start: 0.7714 (mttt) cc_final: 0.7338 (mmmt) REVERT: v 28 PHE cc_start: 0.8741 (OUTLIER) cc_final: 0.8215 (t80) REVERT: v 80 GLU cc_start: 0.7787 (tm-30) cc_final: 0.7124 (tm-30) REVERT: x 21 LYS cc_start: 0.8617 (mmtt) cc_final: 0.7910 (mtpt) REVERT: z 12 PHE cc_start: 0.7953 (t80) cc_final: 0.7589 (t80) REVERT: A 160 LYS cc_start: 0.8642 (ttpp) cc_final: 0.7935 (tppt) outliers start: 138 outliers final: 84 residues processed: 1438 average time/residue: 1.3326 time to fit residues: 3286.4023 Evaluate side-chains 1377 residues out of total 4878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 1286 time to evaluate : 6.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 28 GLU Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 7 ASP Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 39 ASP Chi-restraints excluded: chain F residue 49 THR Chi-restraints excluded: chain F residue 71 LEU Chi-restraints excluded: chain F residue 84 THR Chi-restraints excluded: chain F residue 127 THR Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain F residue 168 VAL Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain J residue 131 ASN Chi-restraints excluded: chain K residue 28 SER Chi-restraints excluded: chain K residue 61 VAL Chi-restraints excluded: chain K residue 123 LEU Chi-restraints excluded: chain L residue 4 ASN Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 67 THR Chi-restraints excluded: chain M residue 36 VAL Chi-restraints excluded: chain M residue 132 THR Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain N residue 2 ARG Chi-restraints excluded: chain N residue 45 ARG Chi-restraints excluded: chain O residue 28 VAL Chi-restraints excluded: chain O residue 63 LYS Chi-restraints excluded: chain P residue 34 GLU Chi-restraints excluded: chain P residue 40 LEU Chi-restraints excluded: chain P residue 110 ILE Chi-restraints excluded: chain P residue 114 LEU Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain T residue 21 SER Chi-restraints excluded: chain U residue 12 ILE Chi-restraints excluded: chain U residue 15 THR Chi-restraints excluded: chain W residue 21 LEU Chi-restraints excluded: chain W residue 30 SER Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain b residue 40 ARG Chi-restraints excluded: chain c residue 13 SER Chi-restraints excluded: chain c residue 47 VAL Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 42 LEU Chi-restraints excluded: chain e residue 58 VAL Chi-restraints excluded: chain g residue 199 VAL Chi-restraints excluded: chain h residue 58 GLU Chi-restraints excluded: chain h residue 128 VAL Chi-restraints excluded: chain h residue 200 VAL Chi-restraints excluded: chain j residue 103 THR Chi-restraints excluded: chain k residue 55 HIS Chi-restraints excluded: chain k residue 84 VAL Chi-restraints excluded: chain l residue 50 LEU Chi-restraints excluded: chain l residue 77 SER Chi-restraints excluded: chain l residue 120 LEU Chi-restraints excluded: chain l residue 133 THR Chi-restraints excluded: chain m residue 104 VAL Chi-restraints excluded: chain o residue 54 SER Chi-restraints excluded: chain p residue 35 THR Chi-restraints excluded: chain q residue 58 THR Chi-restraints excluded: chain q residue 75 GLN Chi-restraints excluded: chain q residue 82 ILE Chi-restraints excluded: chain q residue 111 LYS Chi-restraints excluded: chain r residue 65 VAL Chi-restraints excluded: chain s residue 45 VAL Chi-restraints excluded: chain t residue 75 VAL Chi-restraints excluded: chain u residue 24 SER Chi-restraints excluded: chain v residue 28 PHE Chi-restraints excluded: chain v residue 38 ILE Chi-restraints excluded: chain v residue 55 ILE Chi-restraints excluded: chain v residue 67 LEU Chi-restraints excluded: chain x residue 13 LEU Chi-restraints excluded: chain y residue 23 SER Chi-restraints excluded: chain y residue 57 ILE Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 134 MET Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 341 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1034 random chunks: chunk 609 optimal weight: 2.9990 chunk 982 optimal weight: 0.6980 chunk 599 optimal weight: 3.9990 chunk 465 optimal weight: 0.9990 chunk 682 optimal weight: 6.9990 chunk 1030 optimal weight: 6.9990 chunk 948 optimal weight: 5.9990 chunk 820 optimal weight: 5.9990 chunk 85 optimal weight: 10.0000 chunk 633 optimal weight: 2.9990 chunk 502 optimal weight: 0.2980 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 153 GLN ** C 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 22 GLN F 73 ASN K 3 GLN L 4 ASN N 62 ASN Q 37 GLN R 43 ASN U 46 GLN ** a 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 120 GLN ** h 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 131 ASN ** i 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 55 HIS n 5 GLN ** u 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.3954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 158905 Z= 0.157 Angle : 0.556 13.624 237521 Z= 0.300 Chirality : 0.030 0.230 30217 Planarity : 0.005 0.124 12870 Dihedral : 23.188 179.236 78933 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.40 % Allowed : 23.33 % Favored : 74.27 % 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: -1.09 (0.11), residues: 5863 helix: 0.14 (0.12), residues: 1923 sheet: -1.17 (0.16), residues: 1041 loop : -1.08 (0.11), residues: 2899 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP s 42 HIS 0.010 0.001 HIS k 55 PHE 0.025 0.001 PHE N 80 TYR 0.015 0.001 TYR V 31 ARG 0.012 0.000 ARG v 27 ********************** 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 1431 residues out of total 4878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 1314 time to evaluate : 5.922 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: B 88 SER cc_start: 0.9414 (p) cc_final: 0.9063 (p) REVERT: B 96 TYR cc_start: 0.8491 (m-80) cc_final: 0.7736 (m-80) REVERT: C 91 THR cc_start: 0.7939 (p) cc_final: 0.7626 (t) REVERT: D 116 ASP cc_start: 0.7964 (t0) cc_final: 0.7695 (t0) REVERT: E 97 TRP cc_start: 0.9160 (m100) cc_final: 0.8946 (m100) REVERT: E 117 LEU cc_start: 0.8065 (OUTLIER) cc_final: 0.7543 (mt) REVERT: E 128 TYR cc_start: 0.8808 (t80) cc_final: 0.8585 (t80) REVERT: E 134 GLU cc_start: 0.7941 (mp0) cc_final: 0.7456 (mp0) REVERT: E 145 LYS cc_start: 0.7536 (mmtt) cc_final: 0.7010 (mtpt) REVERT: F 20 ASN cc_start: 0.7728 (t0) cc_final: 0.7448 (t0) REVERT: F 117 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.8219 (mm) REVERT: F 133 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8216 (mt) REVERT: F 157 TYR cc_start: 0.8523 (m-80) cc_final: 0.8217 (m-80) REVERT: G 53 GLU cc_start: 0.6464 (mp0) cc_final: 0.5185 (mm-30) REVERT: G 72 ILE cc_start: 0.3291 (OUTLIER) cc_final: 0.2678 (tp) REVERT: J 17 VAL cc_start: 0.9203 (t) cc_final: 0.8878 (p) REVERT: J 98 GLU cc_start: 0.8187 (mp0) cc_final: 0.7950 (mp0) REVERT: K 12 ASP cc_start: 0.8549 (p0) cc_final: 0.8219 (p0) REVERT: K 59 LYS cc_start: 0.8901 (OUTLIER) cc_final: 0.8666 (ttmm) REVERT: K 121 GLU cc_start: 0.7106 (tt0) cc_final: 0.6695 (tt0) REVERT: M 17 ASN cc_start: 0.9114 (t0) cc_final: 0.8365 (t0) REVERT: M 76 LYS cc_start: 0.8667 (mtpp) cc_final: 0.8372 (mmmm) REVERT: M 106 ASP cc_start: 0.8226 (t0) cc_final: 0.7686 (t0) REVERT: N 2 ARG cc_start: 0.8430 (OUTLIER) cc_final: 0.8052 (ttp80) REVERT: P 7 GLN cc_start: 0.8313 (tm-30) cc_final: 0.7784 (tp40) REVERT: Q 15 LYS cc_start: 0.8348 (ttpt) cc_final: 0.7766 (tttm) REVERT: Q 66 ASN cc_start: 0.8752 (t0) cc_final: 0.8430 (t0) REVERT: Q 71 GLN cc_start: 0.7983 (tp-100) cc_final: 0.7465 (tp40) REVERT: T 1 MET cc_start: 0.6448 (tpt) cc_final: 0.6226 (mmm) REVERT: T 28 ASN cc_start: 0.8775 (m-40) cc_final: 0.8339 (m-40) REVERT: T 86 THR cc_start: 0.9073 (m) cc_final: 0.8685 (p) REVERT: U 60 GLU cc_start: 0.7672 (tt0) cc_final: 0.7296 (tt0) REVERT: V 29 ILE cc_start: 0.9237 (tt) cc_final: 0.8846 (tt) REVERT: V 46 LYS cc_start: 0.8390 (mmmm) cc_final: 0.7865 (ttpp) REVERT: W 25 ARG cc_start: 0.8678 (mmm160) cc_final: 0.8472 (mmm160) REVERT: X 77 LYS cc_start: 0.8238 (mttt) cc_final: 0.7899 (mmmt) REVERT: b 11 SER cc_start: 0.9111 (t) cc_final: 0.8785 (p) REVERT: d 14 ARG cc_start: 0.8333 (mtt180) cc_final: 0.7884 (mtt180) REVERT: f 1 MET cc_start: 0.8045 (tpp) cc_final: 0.7721 (tpp) REVERT: g 15 HIS cc_start: 0.8781 (p-80) cc_final: 0.8459 (p90) REVERT: g 27 MET cc_start: 0.8593 (mmm) cc_final: 0.6957 (mmm) REVERT: g 94 HIS cc_start: 0.7091 (m-70) cc_final: 0.6839 (m170) REVERT: h 100 GLN cc_start: 0.8286 (tm-30) cc_final: 0.8030 (tm-30) REVERT: h 132 ARG cc_start: 0.7722 (ttm-80) cc_final: 0.7309 (mtt90) REVERT: h 142 MET cc_start: 0.8584 (mmm) cc_final: 0.8157 (mmm) REVERT: h 144 LEU cc_start: 0.8974 (mm) cc_final: 0.8687 (mm) REVERT: h 177 THR cc_start: 0.8762 (m) cc_final: 0.8453 (p) REVERT: h 185 ASN cc_start: 0.8164 (t0) cc_final: 0.7937 (t0) REVERT: h 188 GLU cc_start: 0.7818 (mt-10) cc_final: 0.7465 (mt-10) REVERT: i 4 TYR cc_start: 0.8711 (t80) cc_final: 0.8498 (t80) REVERT: i 51 TYR cc_start: 0.8535 (t80) cc_final: 0.8297 (t80) REVERT: i 187 GLU cc_start: 0.7156 (mp0) cc_final: 0.6755 (mp0) REVERT: i 196 ASN cc_start: 0.7691 (m-40) cc_final: 0.7405 (m110) REVERT: j 68 ARG cc_start: 0.8249 (tpp-160) cc_final: 0.8026 (tpp-160) REVERT: j 86 LYS cc_start: 0.7855 (mtmt) cc_final: 0.7616 (mttt) REVERT: j 156 LYS cc_start: 0.8795 (ttpt) cc_final: 0.8517 (ttmm) REVERT: k 39 LEU cc_start: 0.8175 (tt) cc_final: 0.7898 (tt) REVERT: k 44 ARG cc_start: 0.7411 (mtt90) cc_final: 0.7100 (mtt90) REVERT: k 88 MET cc_start: 0.6921 (OUTLIER) cc_final: 0.6535 (ttt) REVERT: l 20 SER cc_start: 0.8164 (t) cc_final: 0.7844 (t) REVERT: l 22 LEU cc_start: 0.7122 (tp) cc_final: 0.6398 (mm) REVERT: l 68 ASN cc_start: 0.7905 (t0) cc_final: 0.7387 (t0) REVERT: m 56 LYS cc_start: 0.8811 (pttt) cc_final: 0.8358 (ptpp) REVERT: m 79 SER cc_start: 0.8630 (t) cc_final: 0.8401 (t) REVERT: m 94 LYS cc_start: 0.8192 (mttm) cc_final: 0.7763 (mtpp) REVERT: n 38 TYR cc_start: 0.8464 (t80) cc_final: 0.8139 (t80) REVERT: n 79 ILE cc_start: 0.8948 (mt) cc_final: 0.8741 (mt) REVERT: n 124 ARG cc_start: 0.8593 (mtt-85) cc_final: 0.8297 (mmt180) REVERT: o 69 THR cc_start: 0.8984 (m) cc_final: 0.8504 (p) REVERT: o 100 ILE cc_start: 0.8509 (mp) cc_final: 0.8237 (mt) REVERT: p 37 ARG cc_start: 0.7527 (mmm-85) cc_final: 0.7142 (mtp85) REVERT: p 87 LYS cc_start: 0.8451 (ttmm) cc_final: 0.8071 (ttpp) REVERT: p 101 ASN cc_start: 0.8711 (t0) cc_final: 0.8456 (t0) REVERT: q 56 ARG cc_start: 0.7697 (ttm-80) cc_final: 0.7225 (tpp-160) REVERT: q 67 ILE cc_start: 0.9209 (mp) cc_final: 0.8972 (mp) REVERT: q 75 GLN cc_start: 0.8551 (OUTLIER) cc_final: 0.8125 (mm110) REVERT: r 7 ILE cc_start: 0.8354 (pt) cc_final: 0.8032 (pt) REVERT: r 76 SER cc_start: 0.8895 (m) cc_final: 0.8601 (m) REVERT: s 6 MET cc_start: 0.8425 (mmt) cc_final: 0.8143 (mmt) REVERT: t 10 LYS cc_start: 0.8697 (mmmm) cc_final: 0.8342 (mtpt) REVERT: t 14 GLU cc_start: 0.7623 (tm-30) cc_final: 0.6510 (tm-30) REVERT: t 74 ASP cc_start: 0.7298 (t70) cc_final: 0.6531 (p0) REVERT: u 56 ARG cc_start: 0.7723 (mmm-85) cc_final: 0.7506 (mmm-85) REVERT: v 19 LYS cc_start: 0.7733 (mttt) cc_final: 0.7341 (mmmt) REVERT: v 28 PHE cc_start: 0.8793 (OUTLIER) cc_final: 0.8255 (t80) REVERT: v 80 GLU cc_start: 0.7584 (tm-30) cc_final: 0.6866 (tm-30) REVERT: x 21 LYS cc_start: 0.8754 (mmtt) cc_final: 0.7982 (mtpt) REVERT: z 12 PHE cc_start: 0.8001 (t80) cc_final: 0.7632 (t80) REVERT: A 110 ASN cc_start: 0.7858 (m-40) cc_final: 0.7327 (m110) REVERT: A 160 LYS cc_start: 0.8668 (ttpp) cc_final: 0.7925 (tppt) REVERT: A 323 ASN cc_start: 0.6070 (p0) cc_final: 0.5724 (p0) outliers start: 117 outliers final: 96 residues processed: 1379 average time/residue: 1.3106 time to fit residues: 3107.6221 Evaluate side-chains 1391 residues out of total 4878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 1286 time to evaluate : 5.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 153 GLN Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 28 GLU Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain D residue 80 SER Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 39 ASP Chi-restraints excluded: chain F residue 49 THR Chi-restraints excluded: chain F residue 71 LEU Chi-restraints excluded: chain F residue 84 THR Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 127 THR Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain F residue 168 VAL Chi-restraints excluded: chain G residue 72 ILE Chi-restraints excluded: chain J residue 52 ASP Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain J residue 131 ASN Chi-restraints excluded: chain K residue 28 SER Chi-restraints excluded: chain K residue 59 LYS Chi-restraints excluded: chain K residue 123 LEU Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain M residue 36 VAL Chi-restraints excluded: chain M residue 132 THR Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain N residue 2 ARG Chi-restraints excluded: chain N residue 45 ARG Chi-restraints excluded: chain O residue 28 VAL Chi-restraints excluded: chain P residue 34 GLU Chi-restraints excluded: chain P residue 40 LEU Chi-restraints excluded: chain P residue 110 ILE Chi-restraints excluded: chain P residue 114 LEU Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain T residue 21 SER Chi-restraints excluded: chain T residue 27 SER Chi-restraints excluded: chain T residue 74 ILE Chi-restraints excluded: chain U residue 12 ILE Chi-restraints excluded: chain U residue 15 THR Chi-restraints excluded: chain U residue 72 ILE Chi-restraints excluded: chain W residue 21 LEU Chi-restraints excluded: chain W residue 30 SER Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain b residue 40 ARG Chi-restraints excluded: chain c residue 13 SER Chi-restraints excluded: chain c residue 47 VAL Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 42 LEU Chi-restraints excluded: chain e residue 58 VAL Chi-restraints excluded: chain g residue 142 GLU Chi-restraints excluded: chain g residue 199 VAL Chi-restraints excluded: chain h residue 200 VAL Chi-restraints excluded: chain j residue 103 THR Chi-restraints excluded: chain k residue 51 ILE Chi-restraints excluded: chain k residue 84 VAL Chi-restraints excluded: chain k residue 88 MET Chi-restraints excluded: chain l residue 6 VAL Chi-restraints excluded: chain l residue 30 LEU Chi-restraints excluded: chain l residue 77 SER Chi-restraints excluded: chain l residue 120 LEU Chi-restraints excluded: chain l residue 133 THR Chi-restraints excluded: chain m residue 104 VAL Chi-restraints excluded: chain n residue 111 VAL Chi-restraints excluded: chain o residue 54 SER Chi-restraints excluded: chain p residue 35 THR Chi-restraints excluded: chain q residue 58 THR Chi-restraints excluded: chain q residue 75 GLN Chi-restraints excluded: chain q residue 82 ILE Chi-restraints excluded: chain q residue 111 LYS Chi-restraints excluded: chain r residue 65 VAL Chi-restraints excluded: chain s residue 45 VAL Chi-restraints excluded: chain s residue 62 ASN Chi-restraints excluded: chain t residue 75 VAL Chi-restraints excluded: chain u residue 3 THR Chi-restraints excluded: chain u residue 24 SER Chi-restraints excluded: chain v residue 28 PHE Chi-restraints excluded: chain v residue 38 ILE Chi-restraints excluded: chain v residue 55 ILE Chi-restraints excluded: chain v residue 67 LEU Chi-restraints excluded: chain v residue 70 THR Chi-restraints excluded: chain x residue 13 LEU Chi-restraints excluded: chain y residue 57 ILE Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 134 MET Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 256 GLU Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 341 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1034 random chunks: chunk 651 optimal weight: 4.9990 chunk 873 optimal weight: 6.9990 chunk 251 optimal weight: 8.9990 chunk 756 optimal weight: 4.9990 chunk 121 optimal weight: 10.0000 chunk 227 optimal weight: 10.0000 chunk 821 optimal weight: 0.4980 chunk 343 optimal weight: 9.9990 chunk 843 optimal weight: 6.9990 chunk 104 optimal weight: 20.0000 chunk 151 optimal weight: 10.0000 overall best weight: 4.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 260 ASN ** C 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 115 GLN F 22 GLN F 73 ASN G 28 ASN G 119 ASN K 3 GLN L 4 ASN L 54 GLN N 62 ASN P 10 GLN R 43 ASN U 46 GLN V 24 ASN ** V 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 120 GLN g 146 ASN ** h 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 52 GLN r 105 ASN ** u 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** x 69 HIS ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.117910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.092897 restraints weight = 237562.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.095546 restraints weight = 139547.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.095287 restraints weight = 68295.512| |-----------------------------------------------------------------------------| r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2950 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2950 r_free = 0.2950 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2950 r_free = 0.2950 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2950 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.3752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 158905 Z= 0.376 Angle : 0.694 13.653 237521 Z= 0.361 Chirality : 0.037 0.286 30217 Planarity : 0.006 0.133 12870 Dihedral : 23.304 179.602 78933 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 3.05 % Allowed : 23.06 % Favored : 73.88 % 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: -1.35 (0.11), residues: 5863 helix: -0.18 (0.12), residues: 1919 sheet: -1.26 (0.15), residues: 1078 loop : -1.17 (0.11), residues: 2866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP s 42 HIS 0.009 0.002 HIS S 7 PHE 0.031 0.002 PHE N 80 TYR 0.024 0.003 TYR D 35 ARG 0.015 0.001 ARG o 62 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 44285.40 seconds wall clock time: 773 minutes 36.73 seconds (46416.73 seconds total)