Starting phenix.real_space_refine (version: dev) on Mon Apr 11 14:47:42 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ouo_20204/04_2022/6ouo_20204_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ouo_20204/04_2022/6ouo_20204.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ouo_20204/04_2022/6ouo_20204_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ouo_20204/04_2022/6ouo_20204_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ouo_20204/04_2022/6ouo_20204_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ouo_20204/04_2022/6ouo_20204.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ouo_20204/04_2022/6ouo_20204.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ouo_20204/04_2022/6ouo_20204_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ouo_20204/04_2022/6ouo_20204_updated.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "B ARG 52": "NH1" <-> "NH2" Residue "B ARG 63": "NH1" <-> "NH2" Residue "B ARG 80": "NH1" <-> "NH2" Residue "B ARG 167": "NH1" <-> "NH2" Residue "B ARG 177": "NH1" <-> "NH2" Residue "B ARG 182": "NH1" <-> "NH2" Residue "B ARG 212": "NH1" <-> "NH2" Residue "B ARG 269": "NH1" <-> "NH2" Residue "C ARG 13": "NH1" <-> "NH2" Residue "C ARG 33": "NH1" <-> "NH2" Residue "C ARG 59": "NH1" <-> "NH2" Residue "C ARG 77": "NH1" <-> "NH2" Residue "C ARG 83": "NH1" <-> "NH2" Residue "C ARG 169": "NH1" <-> "NH2" Residue "C ARG 184": "NH1" <-> "NH2" Residue "D ARG 21": "NH1" <-> "NH2" Residue "D ARG 44": "NH1" <-> "NH2" Residue "D ARG 49": "NH1" <-> "NH2" Residue "D ARG 102": "NH1" <-> "NH2" Residue "D ARG 162": "NH1" <-> "NH2" Residue "D ARG 170": "NH1" <-> "NH2" Residue "E ARG 30": "NH1" <-> "NH2" Residue "E ARG 71": "NH1" <-> "NH2" Residue "E ARG 92": "NH1" <-> "NH2" Residue "E ARG 102": "NH1" <-> "NH2" Residue "E ARG 110": "NH1" <-> "NH2" Residue "E ARG 112": "NH1" <-> "NH2" Residue "E ARG 115": "NH1" <-> "NH2" Residue "E ARG 148": "NH1" <-> "NH2" Residue "F ARG 3": "NH1" <-> "NH2" Residue "F ARG 152": "NH1" <-> "NH2" Residue "F ARG 153": "NH1" <-> "NH2" Residue "F ARG 163": "NH1" <-> "NH2" Residue "F ARG 170": "NH1" <-> "NH2" Residue "G ARG 50": "NH1" <-> "NH2" Residue "G ARG 51": "NH1" <-> "NH2" Residue "G ARG 68": "NH1" <-> "NH2" Residue "J ARG 13": "NH1" <-> "NH2" Residue "J ARG 34": "NH1" <-> "NH2" Residue "J ARG 37": "NH1" <-> "NH2" Residue "J ARG 95": "NH1" <-> "NH2" Residue "J ARG 96": "NH1" <-> "NH2" Residue "J ARG 120": "NH1" <-> "NH2" Residue "K ARG 17": "NH1" <-> "NH2" Residue "K ARG 18": "NH1" <-> "NH2" Residue "L ARG 21": "NH1" <-> "NH2" Residue "L ARG 33": "NH1" <-> "NH2" Residue "L ARG 41": "NH1" <-> "NH2" Residue "L ARG 47": "NH1" <-> "NH2" Residue "L ARG 60": "NH1" <-> "NH2" Residue "L ARG 78": "NH1" <-> "NH2" Residue "L ARG 123": "NH1" <-> "NH2" Residue "L ARG 126": "NH1" <-> "NH2" Residue "M ARG 10": "NH1" <-> "NH2" Residue "M ARG 18": "NH1" <-> "NH2" Residue "M ARG 40": "NH1" <-> "NH2" Residue "M ARG 50": "NH1" <-> "NH2" Residue "M ARG 55": "NH1" <-> "NH2" Residue "M ARG 114": "NH1" <-> "NH2" Residue "N ARG 8": "NH1" <-> "NH2" Residue "N ARG 12": "NH1" <-> "NH2" Residue "N ARG 17": "NH1" <-> "NH2" Residue "N ARG 22": "NH1" <-> "NH2" Residue "N ARG 46": "NH1" <-> "NH2" Residue "N ARG 63": "NH1" <-> "NH2" Residue "N ARG 64": "NH1" <-> "NH2" Residue "N ARG 69": "NH1" <-> "NH2" Residue "N ARG 96": "NH1" <-> "NH2" Residue "N ARG 118": "NH1" <-> "NH2" Residue "O ARG 10": "NH1" <-> "NH2" Residue "O ARG 13": "NH1" <-> "NH2" Residue "O ARG 16": "NH1" <-> "NH2" Residue "O ARG 25": "NH1" <-> "NH2" Residue "O ARG 81": "NH1" <-> "NH2" Residue "O ARG 94": "NH1" <-> "NH2" Residue "O ARG 102": "NH1" <-> "NH2" Residue "O ARG 111": "NH1" <-> "NH2" Residue "P ARG 21": "NH1" <-> "NH2" Residue "P ARG 62": "NH1" <-> "NH2" Residue "P ARG 89": "NH1" <-> "NH2" Residue "P TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 101": "NH1" <-> "NH2" Residue "P ARG 109": "NH1" <-> "NH2" Residue "Q ARG 3": "NH1" <-> "NH2" Residue "Q ARG 6": "NH1" <-> "NH2" Residue "Q ARG 13": "NH1" <-> "NH2" Residue "Q ARG 33": "NH1" <-> "NH2" Residue "Q ARG 48": "NH1" <-> "NH2" Residue "Q ARG 70": "NH1" <-> "NH2" Residue "R ARG 21": "NH1" <-> "NH2" Residue "R ARG 68": "NH1" <-> "NH2" Residue "R ARG 78": "NH1" <-> "NH2" Residue "R ARG 79": "NH1" <-> "NH2" Residue "R ARG 84": "NH1" <-> "NH2" Residue "R PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 84": "NH1" <-> "NH2" Residue "S ARG 88": "NH1" <-> "NH2" Residue "S ARG 92": "NH1" <-> "NH2" Residue "S ARG 110": "NH1" <-> "NH2" Residue "T ARG 3": "NH1" <-> "NH2" Residue "T ARG 6": "NH1" <-> "NH2" Residue "U ARG 6": "NH1" <-> "NH2" Residue "U ARG 82": "NH1" <-> "NH2" Residue "U ARG 86": "NH1" <-> "NH2" Residue "U ARG 94": "NH1" <-> "NH2" Residue "V ARG 19": "NH1" <-> "NH2" Residue "V TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 3": "NH1" <-> "NH2" Residue "X ARG 18": "NH1" <-> "NH2" Residue "X ARG 37": "NH1" <-> "NH2" Residue "X ARG 45": "NH1" <-> "NH2" Residue "X ARG 50": "NH1" <-> "NH2" Residue "X ARG 57": "NH1" <-> "NH2" Residue "X ARG 74": "NH1" <-> "NH2" Residue "Y ARG 29": "NH1" <-> "NH2" Residue "Y ARG 47": "NH1" <-> "NH2" Residue "Y ARG 52": "NH1" <-> "NH2" Residue "Z ARG 11": "NH1" <-> "NH2" Residue "Z ARG 30": "NH1" <-> "NH2" Residue "Z ARG 45": "NH1" <-> "NH2" Residue "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 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 PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k ARG 45": "NH1" <-> "NH2" Residue "k ARG 79": "NH1" <-> "NH2" Residue "l ARG 4": "NH1" <-> "NH2" Residue "l ARG 53": "NH1" <-> "NH2" Residue "l ARG 78": "NH1" <-> "NH2" Residue "l ARG 79": "NH1" <-> "NH2" Residue "l ARG 92": "NH1" <-> "NH2" Residue "n ARG 11": "NH1" <-> "NH2" Residue "n ARG 41": "NH1" <-> "NH2" Residue "n ARG 130": "NH1" <-> "NH2" Residue "o ARG 5": "NH1" <-> "NH2" Residue "o ARG 45": "NH1" <-> "NH2" Residue "o ARG 89": "NH1" <-> "NH2" Residue "p ARG 37": "NH1" <-> "NH2" Residue "p ARG 69": "NH1" <-> "NH2" Residue "p ARG 93": "NH1" <-> "NH2" Residue "p ARG 106": "NH1" <-> "NH2" Residue "q ARG 9": "NH1" <-> "NH2" Residue "q ARG 14": "NH1" <-> "NH2" Residue "q ARG 50": "NH1" <-> "NH2" Residue "q ARG 83": "NH1" <-> "NH2" Residue "r ARG 29": "NH1" <-> "NH2" Residue "r ARG 70": "NH1" <-> "NH2" Residue "r ARG 87": "NH1" <-> "NH2" Residue "r ARG 109": "NH1" <-> "NH2" Residue "s ARG 59": "NH1" <-> "NH2" Residue "s ARG 63": "NH1" <-> "NH2" Residue "s ARG 65": "NH1" <-> "NH2" Residue "s ARG 69": "NH1" <-> "NH2" Residue "s ARG 85": "NH1" <-> "NH2" Residue "t ARG 72": "NH1" <-> "NH2" Residue "t ARG 89": "NH1" <-> "NH2" Residue "u ARG 28": "NH1" <-> "NH2" Residue "u PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u ARG 51": "NH1" <-> "NH2" Residue "v ARG 11": "NH1" <-> "NH2" Residue "v ARG 27": "NH1" <-> "NH2" Residue "v ARG 65": "NH1" <-> "NH2" Residue "v ARG 77": "NH1" <-> "NH2" Residue "w ARG 61": "NH1" <-> "NH2" Residue "x ARG 32": "NH1" <-> "NH2" Residue "y ARG 60": "NH1" <-> "NH2" Residue "y ARG 74": "NH1" <-> "NH2" Residue "z ARG 33": "NH1" <-> "NH2" Residue "z ARG 45": "NH1" <-> "NH2" Residue "z ARG 55": "NH1" <-> "NH2" Residue "z ARG 62": "NH1" <-> "NH2" Residue "z ARG 67": "NH1" <-> "NH2" Residue "z ARG 69": "NH1" <-> "NH2" Residue "A ARG 262": "NH1" <-> "NH2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 146867 Number of models: 1 Model: "" Number of chains: 61 Chain: "1" Number of atoms: 62336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2903, 62336 Classifications: {'RNA': 2903} Modifications used: {'rna3p': 16, 'rna2p': 6, 'rna3p_pur': 1379, 'rna3p_pyr': 1049, 'rna2p_pur': 288, 'rna2p_pyr': 165} Link IDs: {'rna3p': 2444, 'rna2p': 458} 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: {'rna3p': 10, 'rna2p': 1, 'rna3p_pur': 750, 'rna3p_pyr': 564, 'rna2p_pur': 119, 'rna2p_pyr': 89} Link IDs: {'rna3p': 1325, 'rna2p': 208} 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: {'rna3p_pyr': 48, 'rna2p_pur': 7, 'rna3p_pur': 57, 'rna2p_pyr': 8} Link IDs: {'rna3p': 105, 'rna2p': 14} Chain: "4" Number of atoms: 184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 184 Classifications: {'RNA': 9} Modifications used: {'rna3p_pyr': 6, 'rna2p_pur': 1, 'rna3p_pur': 1, 'rna2p_pyr': 1} Link IDs: {'rna3p': 7, 'rna2p': 1} 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: 673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 673 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 5, 'TRANS': 81} Chain: "r" Number of atoms: 900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 900 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain: "s" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 805 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "t" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 714 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'TRANS': 87} Chain: "u" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 649 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "v" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 648 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain: "w" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 544 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "x" Number of atoms: 663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 663 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 5, 'TRANS': 77} Chain: "y" Number of atoms: 669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 669 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "z" Number of atoms: 589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 589 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "5" Number of atoms: 1627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1627 Classifications: {'RNA': 76} Modifications used: {'rna3p': 3, 'rna2p_pyr': 6, 'rna3p_pur': 34, 'rna2p': 2, 'rna3p_pyr': 25, 'rna2p_pur': 6} Link IDs: {'rna3p': 62, 'rna2p': 13} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 3 Chain: "A" Number of atoms: 2833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 2833 Classifications: {'peptide': 357} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'CIS': 1, 'TRANS': 349} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "1" 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: "2" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "3" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Unusual residues: {' MG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "a" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "f" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "i" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM A0GD2 SG CYS a 16 66.011 87.056 69.343 1.00247.56 S ATOM A0GDE SG CYS a 18 63.119 88.736 66.183 1.00253.50 S ATOM A0GHX SG CYS a 40 64.820 90.463 69.002 1.00237.13 S ATOM A0I2Y SG CYS f 11 140.264 171.403 68.067 1.00215.71 S ATOM A0I3N SG CYS f 14 142.860 168.971 68.240 1.00216.29 S ATOM A0I6I SG CYS f 27 142.904 173.535 69.264 1.00214.21 S Time building chain proxies: 60.86, per 1000 atoms: 0.41 Number of scatterers: 146867 At special positions: 0 Unit cell: (279.65, 266.49, 235.235, 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 12 11.99 O 40718 8.00 N 27340 7.00 C 73996 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: 63.47 Conformation dependent library (CDL) restraints added in 5.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination Zn2+ tetrahedral coordination pdb=" ZN a 101 " pdb="ZN ZN a 101 " - pdb=" SG CYS a 18 " pdb="ZN ZN a 101 " - pdb=" SG CYS a 16 " pdb="ZN ZN a 101 " - pdb=" SG CYS a 40 " pdb=" ZN f 101 " pdb="ZN ZN f 101 " - pdb=" ND1 HIS f 33 " pdb="ZN ZN f 101 " - pdb=" SG CYS f 14 " pdb="ZN ZN f 101 " - pdb=" SG CYS f 27 " pdb="ZN ZN f 101 " - pdb=" SG CYS f 11 " Number of angles added : 3 11856 Ramachandran restraints generated. 5928 Oldfield, 0 Emsley, 5928 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11086 Finding SS restraints... Warning!!! ksdssp method is not applicable forstructures with more than 99999 atoms! Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 184 helices and 77 sheets defined 39.9% alpha, 19.3% beta 1348 base pairs and 2513 stacking pairs defined. Time for finding SS restraints: 67.62 Creating SS restraints... Processing helix chain 'B' and resid 10 through 16 removed outlier: 3.546A pdb=" N ARG B 14 " --> pdb=" O SER B 10 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N HIS B 15 " --> pdb=" O PRO B 11 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N VAL B 16 " --> pdb=" O GLY B 12 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 10 through 16' Processing helix chain 'B' and resid 30 through 35 removed outlier: 4.034A pdb=" N LEU B 34 " --> pdb=" O PHE B 30 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N GLU B 35 " --> pdb=" O ALA B 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 30 through 35' Processing helix chain 'B' and resid 131 through 136 removed outlier: 3.713A pdb=" N ILE B 135 " --> pdb=" O PRO B 131 " (cutoff:3.500A) Proline residue: B 136 - end of helix No H-bonds generated for 'chain 'B' and resid 131 through 136' Processing helix chain 'B' and resid 207 through 215 removed outlier: 3.711A pdb=" N ALA B 211 " --> pdb=" O LYS B 207 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG B 214 " --> pdb=" O ALA B 210 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLY B 215 " --> pdb=" O ALA B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 268 removed outlier: 4.136A pdb=" N ASP B 264 " --> pdb=" O ASN B 260 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N LYS B 265 " --> pdb=" O LYS B 261 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N PHE B 266 " --> pdb=" O ARG B 262 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N VAL B 268 " --> pdb=" O ASP B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 202 removed outlier: 3.698A pdb=" N HIS B 200 " --> pdb=" O ASN B 197 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N MET B 201 " --> pdb=" O ALA B 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 72 removed outlier: 3.648A pdb=" N GLY C 66 " --> pdb=" O LYS C 62 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N HIS C 67 " --> pdb=" O PRO C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 103 removed outlier: 4.214A pdb=" N ALA C 102 " --> pdb=" O VAL C 98 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N ASP C 103 " --> pdb=" O GLU C 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 98 through 103' Processing helix chain 'C' and resid 120 through 125 Processing helix chain 'D' and resid 15 through 20 Processing helix chain 'D' and resid 24 through 41 removed outlier: 3.705A pdb=" N VAL D 33 " --> pdb=" O HIS D 29 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N GLN D 41 " --> pdb=" O ALA D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 116 removed outlier: 3.634A pdb=" N LEU D 105 " --> pdb=" O TYR D 101 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLU D 111 " --> pdb=" O SER D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 142 removed outlier: 3.551A pdb=" N LEU D 134 " --> pdb=" O LYS D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 154 through 163 removed outlier: 3.658A pdb=" N PHE D 158 " --> pdb=" O ASP D 154 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU D 159 " --> pdb=" O GLU D 155 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ASN D 163 " --> pdb=" O LEU D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 184 removed outlier: 4.106A pdb=" N LEU D 180 " --> pdb=" O ASP D 176 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ILE D 181 " --> pdb=" O PRO D 177 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N ASP D 184 " --> pdb=" O LEU D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 201 removed outlier: 3.578A pdb=" N LYS D 194 " --> pdb=" O ALA D 190 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 21 removed outlier: 3.754A pdb=" N GLU E 11 " --> pdb=" O TYR E 7 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N VAL E 13 " --> pdb=" O LYS E 9 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N LYS E 14 " --> pdb=" O ASP E 10 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N THR E 18 " --> pdb=" O LYS E 14 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 62 removed outlier: 4.320A pdb=" N LEU E 50 " --> pdb=" O ASP E 46 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA E 53 " --> pdb=" O LEU E 49 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLY E 62 " --> pdb=" O ALA E 58 " (cutoff:3.500A) Processing helix chain 'E' and resid 93 through 111 removed outlier: 3.605A pdb=" N THR E 105 " --> pdb=" O GLU E 101 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N VAL E 108 " --> pdb=" O ILE E 104 " (cutoff:3.500A) Proline residue: E 109 - end of helix Processing helix chain 'E' and resid 142 through 147 removed outlier: 3.513A pdb=" N VAL E 146 " --> pdb=" O ASP E 142 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N ASP E 147 " --> pdb=" O TYR E 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 142 through 147' Processing helix chain 'E' and resid 162 through 174 removed outlier: 3.869A pdb=" N GLY E 166 " --> pdb=" O SER E 162 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE E 173 " --> pdb=" O LEU E 169 " (cutoff:3.500A) Processing helix chain 'E' and resid 134 through 139 removed outlier: 4.600A pdb=" N ILE E 137 " --> pdb=" O GLU E 134 " (cutoff:3.500A) Proline residue: E 139 - end of helix Processing helix chain 'F' and resid 2 through 8 removed outlier: 3.832A 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: 3.509A pdb=" N ILE F 77 " --> pdb=" O ASN F 73 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N VAL F 79 " --> pdb=" O MET F 75 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N THR F 80 " --> pdb=" O VAL F 76 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 153 removed outlier: 4.556A pdb=" N ARG F 152 " --> pdb=" O LEU F 148 " (cutoff:3.500A) Processing helix chain 'G' and resid 22 through 27 removed outlier: 3.623A pdb=" N ALA G 26 " --> pdb=" O LYS G 22 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 34 Processing helix chain 'G' and resid 40 through 47 Processing helix chain 'G' and resid 50 through 74 removed outlier: 4.369A pdb=" N ALA G 56 " --> pdb=" O ALA G 52 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU G 60 " --> pdb=" O ALA G 56 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N VAL G 61 " --> pdb=" O LYS G 57 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N LEU G 62 " --> pdb=" O LEU G 58 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA G 63 " --> pdb=" O ALA G 59 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA G 67 " --> pdb=" O ALA G 63 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N GLU G 70 " --> pdb=" O ASN G 66 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ILE G 72 " --> pdb=" O ARG G 68 " (cutoff:3.500A) Processing helix chain 'G' and resid 95 through 107 removed outlier: 3.818A pdb=" N ILE G 99 " --> pdb=" O GLY G 95 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N VAL G 103 " --> pdb=" O ILE G 99 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N THR G 104 " --> pdb=" O ALA G 100 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 116 removed outlier: 6.271A pdb=" N ARG G 116 " --> pdb=" O LYS G 112 " (cutoff:3.500A) Processing helix chain 'J' and resid 24 through 38 removed outlier: 5.276A pdb=" N GLU J 31 " --> pdb=" O ARG J 27 " (cutoff:3.500A) Processing helix chain 'J' and resid 67 through 72 Processing helix chain 'J' and resid 88 through 96 removed outlier: 3.757A pdb=" N MET J 92 " --> pdb=" O THR J 88 " (cutoff:3.500A) Processing helix chain 'J' and resid 97 through 110 removed outlier: 5.017A pdb=" N ILE J 101 " --> pdb=" O PRO J 97 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N MET J 108 " --> pdb=" O ALA J 104 " (cutoff:3.500A) Proline residue: J 110 - end of helix Processing helix chain 'J' and resid 112 through 123 removed outlier: 3.837A pdb=" N PHE J 119 " --> pdb=" O GLY J 115 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ARG J 120 " --> pdb=" O ARG J 116 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LYS J 121 " --> pdb=" O ALA J 117 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LEU J 122 " --> pdb=" O MET J 118 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N LYS J 123 " --> pdb=" O PHE J 119 " (cutoff:3.500A) Processing helix chain 'K' and resid 112 through 119 removed outlier: 4.146A pdb=" N ILE K 116 " --> pdb=" O PHE K 112 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N SER K 117 " --> pdb=" O MET K 113 " (cutoff:3.500A) removed outlier: 3.539A 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: 4.372A pdb=" N ALA L 72 " --> pdb=" O SER L 68 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N ILE L 73 " --> pdb=" O ARG L 69 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N THR L 74 " --> pdb=" O LYS L 70 " (cutoff:3.500A) removed outlier: 5.629A 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: 3.771A pdb=" N LEU L 82 " --> pdb=" O ARG L 78 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ALA L 83 " --> pdb=" O LEU L 79 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N LYS L 84 " --> pdb=" O SER L 80 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N VAL L 85 " --> pdb=" O ASP L 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 78 through 85' Processing helix chain 'L' and resid 91 through 99 removed outlier: 3.508A pdb=" N ALA L 97 " --> pdb=" O ASN L 93 " (cutoff:3.500A) Processing helix chain 'L' and resid 128 through 139 removed outlier: 3.545A pdb=" N ALA L 133 " --> pdb=" O LYS L 129 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ALA L 134 " --> pdb=" O GLY L 130 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ALA L 138 " --> pdb=" O ALA L 134 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLY L 139 " --> pdb=" O ILE L 135 " (cutoff:3.500A) Processing helix chain 'M' and resid 42 through 58 Processing helix chain 'M' and resid 109 through 125 removed outlier: 3.870A pdb=" N LYS M 118 " --> pdb=" O ARG M 114 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ALA M 122 " --> pdb=" O LYS M 118 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N LYS M 123 " --> pdb=" O LEU M 119 " (cutoff:3.500A) removed outlier: 3.827A 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: 3.632A pdb=" N PHE N 21 " --> pdb=" O ARG N 17 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ARG N 22 " --> pdb=" O GLN N 18 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ASN N 23 " --> pdb=" O ALA N 19 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL N 29 " --> pdb=" O ALA N 25 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ARG N 30 " --> pdb=" O GLY N 26 " (cutoff:3.500A) Processing helix chain 'N' and resid 37 through 46 removed outlier: 4.565A pdb=" N LEU N 44 " --> pdb=" O LYS N 40 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ARG N 46 " --> pdb=" O LYS N 42 " (cutoff:3.500A) Processing helix chain 'N' and resid 47 through 56 removed outlier: 3.933A pdb=" N THR N 53 " --> pdb=" O GLU N 49 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ALA N 55 " --> pdb=" O LEU N 51 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LYS N 56 " --> pdb=" O ILE N 52 " (cutoff:3.500A) Processing helix chain 'N' and resid 63 through 70 removed outlier: 3.750A pdb=" N PHE N 67 " --> pdb=" O ARG N 63 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N THR N 70 " --> pdb=" O ALA N 66 " (cutoff:3.500A) Processing helix chain 'N' and resid 72 through 88 removed outlier: 4.813A pdb=" N VAL N 76 " --> pdb=" O ASP N 72 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N PHE N 80 " --> pdb=" O VAL N 76 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ASN N 81 " --> pdb=" O ALA N 77 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N GLY N 84 " --> pdb=" O PHE N 80 " (cutoff:3.500A) Proline residue: N 85 - end of helix removed outlier: 3.515A pdb=" N ALA N 88 " --> pdb=" O GLY N 84 " (cutoff:3.500A) Processing helix chain 'O' and resid 2 through 22 removed outlier: 4.761A pdb=" N ARG O 13 " --> pdb=" O ARG O 9 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N ALA O 14 " --> pdb=" O ARG O 10 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ARG O 16 " --> pdb=" O THR O 12 " (cutoff:3.500A) Processing helix chain 'O' and resid 55 through 63 removed outlier: 3.542A pdb=" N ALA O 59 " --> pdb=" O GLU O 55 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N GLN O 61 " --> pdb=" O ALA O 57 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU O 62 " --> pdb=" O ILE O 58 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N LYS O 63 " --> pdb=" O ALA O 59 " (cutoff:3.500A) Processing helix chain 'O' and resid 67 through 86 removed outlier: 3.575A pdb=" N ALA O 79 " --> pdb=" O GLY O 75 " (cutoff:3.500A) Processing helix chain 'O' and resid 101 through 114 removed outlier: 3.597A pdb=" N ALA O 107 " --> pdb=" O VAL O 103 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 13 removed outlier: 3.951A pdb=" N GLN P 7 " --> pdb=" O ASN P 3 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N GLU P 11 " --> pdb=" O GLN P 7 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLN P 12 " --> pdb=" O LEU P 8 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N MET P 13 " --> pdb=" O GLU P 9 " (cutoff:3.500A) Processing helix chain 'P' and resid 97 through 103 removed outlier: 4.332A pdb=" N ARG P 101 " --> pdb=" O LEU P 97 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N GLU P 102 " --> pdb=" O TYR P 98 " (cutoff:3.500A) Processing helix chain 'Q' and resid 6 through 22 removed outlier: 3.552A pdb=" N ALA Q 10 " --> pdb=" O ARG Q 6 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ALA Q 12 " --> pdb=" O VAL Q 8 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE Q 17 " --> pdb=" O ARG Q 13 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLN Q 20 " --> pdb=" O LYS Q 16 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS Q 22 " --> pdb=" O LEU Q 18 " (cutoff:3.500A) Processing helix chain 'Q' and resid 26 through 31 Processing helix chain 'Q' and resid 36 through 72 removed outlier: 3.596A pdb=" N ILE Q 40 " --> pdb=" O PHE Q 36 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N LYS Q 41 " --> pdb=" O GLN Q 37 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA Q 42 " --> pdb=" O ALA Q 38 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TYR Q 47 " --> pdb=" O GLY Q 43 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG Q 51 " --> pdb=" O TYR Q 47 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LYS Q 54 " --> pdb=" O ARG Q 50 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ARG Q 55 " --> pdb=" O ARG Q 51 " (cutoff:3.500A) Processing helix chain 'Q' and resid 75 through 87 Processing helix chain 'Q' and resid 91 through 102 removed outlier: 3.513A pdb=" N ALA Q 99 " --> pdb=" O LEU Q 95 " (cutoff:3.500A) Processing helix chain 'Q' and resid 103 through 118 removed outlier: 3.907A pdb=" N ALA Q 118 " --> pdb=" O LYS Q 114 " (cutoff:3.500A) Processing helix chain 'S' and resid 13 through 25 removed outlier: 3.994A pdb=" N LEU S 19 " --> pdb=" O GLN S 15 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N VAL S 20 " --> pdb=" O LYS S 16 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LEU S 23 " --> pdb=" O LEU S 19 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ILE S 24 " --> pdb=" O VAL S 20 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ARG S 25 " --> pdb=" O ALA S 21 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 39 removed outlier: 3.810A pdb=" N ASP S 34 " --> pdb=" O SER S 30 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TYR S 38 " --> pdb=" O ASP S 34 " (cutoff:3.500A) Processing helix chain 'S' and resid 41 through 61 removed outlier: 4.031A pdb=" N VAL S 45 " --> pdb=" O LYS S 41 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU S 46 " --> pdb=" O LYS S 42 " (cutoff:3.500A) Processing helix chain 'T' and resid 3 through 11 removed outlier: 3.728A pdb=" N LYS T 9 " --> pdb=" O GLU T 5 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N VAL T 10 " --> pdb=" O ARG T 6 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N LEU T 11 " --> pdb=" O LEU T 7 " (cutoff:3.500A) Processing helix chain 'T' and resid 17 through 27 removed outlier: 3.853A pdb=" N LYS T 26 " --> pdb=" O THR T 22 " (cutoff:3.500A) Processing helix chain 'T' and resid 39 through 51 removed outlier: 3.698A pdb=" N LEU T 50 " --> pdb=" O ALA T 46 " (cutoff:3.500A) Processing helix chain 'U' and resid 66 through 71 removed outlier: 3.939A pdb=" N VAL U 70 " --> pdb=" O GLN U 66 " (cutoff:3.500A) removed outlier: 4.989A 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: 3.783A pdb=" N SER V 17 " --> pdb=" O GLY V 13 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ASN V 24 " --> pdb=" O LEU V 20 " (cutoff:3.500A) Processing helix chain 'V' and resid 43 through 52 removed outlier: 4.052A pdb=" N VAL V 47 " --> pdb=" O ASP V 43 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ALA V 52 " --> pdb=" O MET V 48 " (cutoff:3.500A) Processing helix chain 'V' and resid 53 through 59 removed outlier: 3.914A pdb=" N TYR V 57 " --> pdb=" O LYS V 53 " (cutoff:3.500A) Processing helix chain 'X' and resid 52 through 63 removed outlier: 3.601A pdb=" N VAL X 58 " --> pdb=" O LYS X 54 " (cutoff:3.500A) Processing helix chain 'X' and resid 64 through 75 removed outlier: 3.673A pdb=" N ALA X 69 " --> pdb=" O ASP X 65 " (cutoff:3.500A) Processing helix chain 'Y' and resid 2 through 10 removed outlier: 3.533A pdb=" N ARG Y 7 " --> pdb=" O ALA Y 3 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LYS Y 9 " --> pdb=" O GLU Y 5 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N SER Y 10 " --> pdb=" O LEU Y 6 " (cutoff:3.500A) Processing helix chain 'Y' and resid 11 through 35 removed outlier: 3.596A pdb=" N ARG Y 23 " --> pdb=" O LEU Y 19 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLN Y 31 " --> pdb=" O ASN Y 27 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N GLY Y 35 " --> pdb=" O GLN Y 31 " (cutoff:3.500A) Processing helix chain 'Y' and resid 39 through 62 removed outlier: 4.653A pdb=" N LEU Y 43 " --> pdb=" O GLN Y 39 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LYS Y 44 " --> pdb=" O SER Y 40 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA Y 51 " --> pdb=" O ARG Y 47 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL Y 53 " --> pdb=" O ASP Y 49 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N GLY Y 62 " --> pdb=" O ASN Y 58 " (cutoff:3.500A) Processing helix chain 'Z' and resid 17 through 28 Processing helix chain 'Z' and resid 41 through 52 removed outlier: 3.622A pdb=" N MET Z 47 " --> pdb=" O ALA Z 43 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL Z 51 " --> pdb=" O MET Z 47 " (cutoff:3.500A) Processing helix chain 'a' and resid 44 through 51 removed outlier: 5.050A pdb=" N GLN a 48 " --> pdb=" O PHE a 44 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N VAL a 51 " --> pdb=" O LYS a 47 " (cutoff:3.500A) Processing helix chain 'a' and resid 55 through 65 removed outlier: 3.975A pdb=" N LYS a 62 " --> pdb=" O ASP a 58 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ARG a 63 " --> pdb=" O ARG a 59 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N PHE a 64 " --> pdb=" O PHE a 60 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N ASN a 65 " --> pdb=" O ASN a 61 " (cutoff:3.500A) Processing helix chain 'b' and resid 9 through 21 removed outlier: 4.754A pdb=" N HIS b 19 " --> pdb=" O MET b 15 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N ASP b 20 " --> pdb=" O ARG b 16 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ALA b 21 " --> pdb=" O ARG b 17 " (cutoff:3.500A) Processing helix chain 'c' and resid 26 through 31 removed outlier: 3.548A pdb=" N LYS c 30 " --> pdb=" O ASN c 26 " (cutoff:3.500A) 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: 3.818A pdb=" N ALA d 23 " --> pdb=" O ARG d 19 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N THR d 24 " --> pdb=" O ALA d 20 " (cutoff:3.500A) Processing helix chain 'd' and resid 25 through 38 removed outlier: 4.475A pdb=" N VAL d 30 " --> pdb=" O ASN d 26 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA d 36 " --> pdb=" O ALA d 32 " (cutoff:3.500A) Processing helix chain 'e' and resid 7 through 14 removed outlier: 3.698A pdb=" N LYS e 12 " --> pdb=" O ARG e 8 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARG e 13 " --> pdb=" O GLY e 9 " (cutoff:3.500A) Processing helix chain 'e' and resid 37 through 46 removed outlier: 3.751A pdb=" N LEU e 44 " --> pdb=" O ARG e 40 " (cutoff:3.500A) Proline residue: e 46 - end of helix Processing helix chain 'e' and resid 51 through 63 removed outlier: 4.361A pdb=" N GLY e 56 " --> pdb=" O LYS e 52 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N LEU e 57 " --> pdb=" O GLY e 53 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL e 58 " --> pdb=" O ASP e 54 " (cutoff:3.500A) removed outlier: 3.603A 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 Processing helix chain 'g' and resid 43 through 64 Proline residue: g 48 - end of helix removed outlier: 3.539A pdb=" N ALA g 55 " --> pdb=" O ASN g 51 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLU g 56 " --> pdb=" O GLU g 52 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG g 63 " --> pdb=" O LYS g 59 " (cutoff:3.500A) Processing helix chain 'g' and resid 76 through 88 removed outlier: 3.614A pdb=" N VAL g 80 " --> pdb=" O ALA g 76 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LYS g 81 " --> pdb=" O SER g 77 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU g 85 " --> pdb=" O LYS g 81 " (cutoff:3.500A) Processing helix chain 'g' and resid 103 through 121 removed outlier: 3.549A pdb=" N GLN g 109 " --> pdb=" O LYS g 105 " (cutoff:3.500A) Processing helix chain 'g' and resid 130 through 148 removed outlier: 4.097A pdb=" N LEU g 135 " --> pdb=" O LYS g 131 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N SER g 147 " --> pdb=" O LYS g 143 " (cutoff:3.500A) Processing helix chain 'g' and resid 165 through 170 Processing helix chain 'g' and resid 171 through 180 removed outlier: 3.656A pdb=" N GLU g 175 " --> pdb=" O ILE g 171 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU g 179 " --> pdb=" O GLU g 175 " (cutoff:3.500A) Processing helix chain 'g' and resid 206 through 227 removed outlier: 3.508A pdb=" N ALA g 219 " --> pdb=" O GLY g 215 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N THR g 220 " --> pdb=" O ALA g 216 " (cutoff:3.500A) Processing helix chain 'h' and resid 6 through 13 removed outlier: 3.528A pdb=" N ARG h 11 " --> pdb=" O PRO h 7 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N GLY h 13 " --> pdb=" O GLY h 9 " (cutoff:3.500A) Processing helix chain 'h' and resid 28 through 48 removed outlier: 4.052A pdb=" N LEU h 43 " --> pdb=" O VAL h 39 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N LEU h 47 " --> pdb=" O LEU h 43 " (cutoff:3.500A) Processing helix chain 'h' and resid 72 through 78 removed outlier: 4.386A pdb=" N VAL h 76 " --> pdb=" O ARG h 72 " (cutoff:3.500A) Processing helix chain 'h' and resid 81 through 96 removed outlier: 3.763A pdb=" N VAL h 90 " --> pdb=" O LYS h 86 " (cutoff:3.500A) Processing helix chain 'h' and resid 108 through 113 removed outlier: 4.130A pdb=" N ASP h 112 " --> pdb=" O LYS h 108 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N ALA h 113 " --> pdb=" O PRO h 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 108 through 113' Processing helix chain 'h' and resid 114 through 127 Processing helix chain 'h' and resid 129 through 145 removed outlier: 3.508A pdb=" N ALA h 141 " --> pdb=" O ALA h 137 " (cutoff:3.500A) Processing helix chain 'i' and resid 7 through 16 removed outlier: 3.696A pdb=" N LEU i 11 " --> pdb=" O PRO i 7 " (cutoff:3.500A) Processing helix chain 'i' and resid 27 through 32 removed outlier: 3.600A pdb=" N LYS i 31 " --> pdb=" O ALA i 27 " (cutoff:3.500A) Processing helix chain 'i' and resid 49 through 66 Processing helix chain 'i' and resid 68 through 83 removed outlier: 4.831A pdb=" N LYS i 83 " --> pdb=" O ALA i 79 " (cutoff:3.500A) Processing helix chain 'i' and resid 85 through 97 Processing helix chain 'i' and resid 98 through 106 removed outlier: 3.605A pdb=" N TYR i 103 " --> pdb=" O ASP i 99 " (cutoff:3.500A) Processing helix chain 'i' and resid 110 through 121 removed outlier: 4.091A pdb=" N LEU i 117 " --> pdb=" O GLU i 113 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL i 118 " --> pdb=" O ALA i 114 " (cutoff:3.500A) Processing helix chain 'i' and resid 146 through 151 removed outlier: 5.503A pdb=" N LYS i 151 " --> pdb=" O GLU i 147 " (cutoff:3.500A) Processing helix chain 'i' and resid 152 through 166 removed outlier: 3.867A pdb=" N LYS i 156 " --> pdb=" O GLN i 152 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ALA i 158 " --> pdb=" O ARG i 154 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU i 160 " --> pdb=" O LYS i 156 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N GLU i 166 " --> pdb=" O ALA i 162 " (cutoff:3.500A) Processing helix chain 'i' and resid 187 through 192 removed outlier: 4.629A pdb=" N SER i 192 " --> pdb=" O ARG i 188 " (cutoff:3.500A) Processing helix chain 'i' and resid 196 through 206 removed outlier: 3.865A pdb=" N ILE i 200 " --> pdb=" O ASN i 196 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N VAL i 201 " --> pdb=" O GLU i 197 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N GLU i 202 " --> pdb=" O HIS i 198 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N TYR i 204 " --> pdb=" O ILE i 200 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LYS i 206 " --> pdb=" O GLU i 202 " (cutoff:3.500A) Processing helix chain 'j' and resid 55 through 71 removed outlier: 3.746A pdb=" N ILE j 60 " --> pdb=" O VAL j 56 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N GLN j 61 " --> pdb=" O PRO j 57 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LYS j 62 " --> pdb=" O ALA j 58 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG j 69 " --> pdb=" O GLU j 65 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ASN j 70 " --> pdb=" O LYS j 66 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N MET j 71 " --> pdb=" O ALA j 67 " (cutoff:3.500A) Processing helix chain 'j' and resid 109 through 119 removed outlier: 4.179A pdb=" N ALA j 113 " --> pdb=" O GLY j 109 " (cutoff:3.500A) Processing helix chain 'j' and resid 132 through 147 removed outlier: 3.589A pdb=" N VAL j 137 " --> pdb=" O PRO j 133 " (cutoff:3.500A) Processing helix chain 'j' and resid 149 through 158 Processing helix chain 'j' and resid 160 through 165 Processing helix chain 'k' and resid 11 through 17 removed outlier: 3.843A pdb=" N SER k 15 " --> pdb=" O HIS k 11 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N GLU k 16 " --> pdb=" O PRO k 12 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N GLN k 17 " --> pdb=" O ASP k 13 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 11 through 17' Processing helix chain 'k' and resid 18 through 33 removed outlier: 3.700A pdb=" N ILE k 29 " --> pdb=" O TYR k 25 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA k 32 " --> pdb=" O ALA k 28 " (cutoff:3.500A) Processing helix chain 'k' and resid 67 through 82 removed outlier: 3.932A pdb=" N ILE k 71 " --> pdb=" O PRO k 67 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N THR k 76 " --> pdb=" O ASP k 72 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N ASP k 82 " --> pdb=" O PHE k 78 " (cutoff:3.500A) Processing helix chain 'l' and resid 20 through 32 removed outlier: 5.670A pdb=" N VAL l 32 " --> pdb=" O ASN l 28 " (cutoff:3.500A) Processing helix chain 'l' and resid 35 through 55 removed outlier: 3.507A pdb=" N ILE l 42 " --> pdb=" O THR l 38 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N THR l 49 " --> pdb=" O SER l 45 " (cutoff:3.500A) Processing helix chain 'l' and resid 57 through 70 removed outlier: 3.541A pdb=" N GLU l 63 " --> pdb=" O LEU l 59 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ASN l 68 " --> pdb=" O VAL l 64 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N VAL l 69 " --> pdb=" O ALA l 65 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ARG l 70 " --> pdb=" O LEU l 66 " (cutoff:3.500A) Processing helix chain 'l' and resid 92 through 111 removed outlier: 3.978A pdb=" N ASN l 97 " --> pdb=" O PRO l 93 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA l 98 " --> pdb=" O VAL l 94 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS l 110 " --> pdb=" O GLU l 106 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ARG l 111 " --> pdb=" O ALA l 107 " (cutoff:3.500A) Processing helix chain 'l' and resid 115 through 130 removed outlier: 3.552A pdb=" N ASN l 122 " --> pdb=" O LEU l 118 " (cutoff:3.500A) Processing helix chain 'l' and resid 132 through 149 removed outlier: 3.577A pdb=" N ARG l 138 " --> pdb=" O ALA l 134 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N GLU l 146 " --> pdb=" O HIS l 142 " (cutoff:3.500A) Processing helix chain 'm' and resid 5 through 21 removed outlier: 3.730A pdb=" N ASP m 9 " --> pdb=" O ASP m 5 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALA m 19 " --> pdb=" O ARG m 15 " (cutoff:3.500A) Processing helix chain 'm' and resid 30 through 44 removed outlier: 4.315A pdb=" N VAL m 39 " --> pdb=" O ALA m 35 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LYS m 41 " --> pdb=" O ALA m 37 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLU m 42 " --> pdb=" O ASN m 38 " (cutoff:3.500A) Processing helix chain 'm' and resid 112 through 120 Processing helix chain 'n' and resid 34 through 39 Processing helix chain 'n' and resid 41 through 56 removed outlier: 3.659A pdb=" N VAL n 48 " --> pdb=" O ALA n 44 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ARG n 49 " --> pdb=" O ARG n 45 " (cutoff:3.500A) Proline residue: n 51 - end of helix removed outlier: 4.629A pdb=" N ASP n 56 " --> pdb=" O LEU n 52 " (cutoff:3.500A) Processing helix chain 'n' and resid 71 through 91 removed outlier: 3.854A pdb=" N ARG n 80 " --> pdb=" O ALA n 76 " (cutoff:3.500A) Processing helix chain 'n' and resid 94 through 102 removed outlier: 4.155A pdb=" N LYS n 100 " --> pdb=" O SER n 96 " (cutoff:3.500A) Processing helix chain 'o' and resid 14 through 33 removed outlier: 3.668A pdb=" N ALA o 23 " --> pdb=" O ASP o 19 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N GLU o 24 " --> pdb=" O GLN o 20 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ILE o 25 " --> pdb=" O ALA o 21 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU o 27 " --> pdb=" O ALA o 23 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ALA o 29 " --> pdb=" O ILE o 25 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ARG o 31 " --> pdb=" O GLU o 27 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N THR o 32 " --> pdb=" O THR o 28 " (cutoff:3.500A) Processing helix chain 'o' and resid 80 through 91 removed outlier: 3.658A pdb=" N VAL o 84 " --> pdb=" O THR o 80 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASP o 85 " --> pdb=" O GLU o 81 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LEU o 87 " --> pdb=" O THR o 83 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N MET o 88 " --> pdb=" O VAL o 84 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU o 90 " --> pdb=" O ALA o 86 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N ASP o 91 " --> pdb=" O LEU o 87 " (cutoff:3.500A) Processing helix chain 'p' and resid 46 through 51 removed outlier: 3.770A pdb=" N SER p 50 " --> pdb=" O THR p 46 " (cutoff:3.500A) removed outlier: 4.597A 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: 3.749A pdb=" N SER p 58 " --> pdb=" O GLY p 54 " (cutoff:3.500A) removed outlier: 4.723A 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 76 removed outlier: 3.513A pdb=" N ASP p 72 " --> pdb=" O GLU p 68 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N GLU p 76 " --> pdb=" O ASP p 72 " (cutoff:3.500A) Processing helix chain 'p' and resid 94 through 104 removed outlier: 3.570A pdb=" N GLY p 104 " --> pdb=" O LEU p 100 " (cutoff:3.500A) Processing helix chain 'q' and resid 3 through 10 Processing helix chain 'r' and resid 14 through 22 removed outlier: 3.871A pdb=" N SER r 21 " --> pdb=" O ILE r 17 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N ILE r 22 " --> pdb=" O ALA r 18 " (cutoff:3.500A) Processing helix chain 'r' and resid 26 through 38 removed outlier: 3.769A pdb=" N LEU r 34 " --> pdb=" O SER r 30 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA r 35 " --> pdb=" O LYS r 31 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA r 36 " --> pdb=" O ALA r 32 " (cutoff:3.500A) Processing helix chain 'r' and resid 49 through 64 removed outlier: 3.816A pdb=" N LYS r 62 " --> pdb=" O ASP r 58 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N PHE r 63 " --> pdb=" O GLU r 59 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N VAL r 64 " --> pdb=" O VAL r 60 " (cutoff:3.500A) Processing helix chain 'r' and resid 66 through 84 removed outlier: 3.509A pdb=" N GLY r 84 " --> pdb=" O LEU r 80 " (cutoff:3.500A) Processing helix chain 'r' and resid 85 through 94 removed outlier: 3.558A 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: 3.613A pdb=" N ALA s 15 " --> pdb=" O VAL s 11 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N TYR s 20 " --> pdb=" O LEU s 16 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N PHE s 21 " --> pdb=" O ALA s 17 " (cutoff:3.500A) Processing helix chain 's' and resid 22 through 32 removed outlier: 3.689A pdb=" N ILE s 30 " --> pdb=" O GLU s 26 " (cutoff:3.500A) Processing helix chain 's' and resid 37 through 52 removed outlier: 3.558A pdb=" N THR s 50 " --> pdb=" O LEU s 46 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU s 51 " --> pdb=" O LYS s 47 " (cutoff:3.500A) Proline residue: s 52 - end of helix Processing helix chain 's' and resid 56 through 61 removed outlier: 3.997A pdb=" N GLN s 60 " --> pdb=" O SER s 56 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N ARG s 61 " --> pdb=" O PRO s 57 " (cutoff:3.500A) No H-bonds generated for 'chain 's' and resid 56 through 61' Processing helix chain 's' and resid 80 through 91 Processing helix chain 't' and resid 4 through 16 Processing helix chain 't' and resid 24 through 42 removed outlier: 4.315A pdb=" N GLY t 41 " --> pdb=" O ASN t 37 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N HIS t 42 " --> pdb=" O HIS t 38 " (cutoff:3.500A) Processing helix chain 't' and resid 51 through 74 removed outlier: 4.927A pdb=" N ARG t 58 " --> pdb=" O ARG t 54 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N MET t 59 " --> pdb=" O GLY t 55 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU t 66 " --> pdb=" O GLN t 62 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N TYR t 69 " --> pdb=" O LYS t 65 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N LEU t 70 " --> pdb=" O LEU t 66 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ARG t 72 " --> pdb=" O ASP t 68 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N ASP t 74 " --> pdb=" O LEU t 70 " (cutoff:3.500A) Processing helix chain 't' and resid 75 through 86 removed outlier: 3.987A pdb=" N GLN t 80 " --> pdb=" O ALA t 76 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLU t 83 " --> pdb=" O THR t 79 " (cutoff:3.500A) Processing helix chain 'u' and resid 53 through 64 removed outlier: 3.515A pdb=" N ILE u 57 " --> pdb=" O ASP u 53 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ALA u 58 " --> pdb=" O LEU u 54 " (cutoff:3.500A) Processing helix chain 'u' and resid 68 through 82 removed outlier: 3.518A pdb=" N LYS u 76 " --> pdb=" O ALA u 72 " (cutoff:3.500A) Processing helix chain 'w' and resid 11 through 17 removed outlier: 5.731A pdb=" N ALA w 15 " --> pdb=" O CYS w 11 " (cutoff:3.500A) Processing helix chain 'w' and resid 25 through 34 removed outlier: 3.628A pdb=" N ASN w 31 " --> pdb=" O ALA w 27 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N TYR w 32 " --> pdb=" O THR w 28 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE w 33 " --> pdb=" O LEU w 29 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N THR w 34 " --> pdb=" O LYS w 30 " (cutoff:3.500A) Processing helix chain 'w' and resid 41 through 46 removed outlier: 3.607A pdb=" N THR w 45 " --> pdb=" O PRO w 41 " (cutoff:3.500A) Processing helix chain 'w' and resid 49 through 66 removed outlier: 3.503A pdb=" N GLN w 54 " --> pdb=" O LYS w 50 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS w 60 " --> pdb=" O ALA w 56 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ARG w 61 " --> pdb=" O ARG w 57 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER w 66 " --> pdb=" O ALA w 62 " (cutoff:3.500A) Processing helix chain 'x' and resid 12 through 26 Processing helix chain 'x' and resid 70 through 76 removed outlier: 4.735A pdb=" N PHE x 74 " --> pdb=" O LYS x 70 " (cutoff:3.500A) removed outlier: 3.842A 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 'x' and resid 64 through 69 removed outlier: 4.746A pdb=" N GLY x 68 " --> pdb=" O GLU x 65 " (cutoff:3.500A) Processing helix chain 'y' and resid 4 through 42 removed outlier: 3.569A pdb=" N LYS y 8 " --> pdb=" O ILE y 4 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N GLN y 13 " --> pdb=" O LYS y 9 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER y 14 " --> pdb=" O ARG y 10 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLU y 15 " --> pdb=" O ALA y 11 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LYS y 16 " --> pdb=" O ILE y 12 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR y 30 " --> pdb=" O SER y 26 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE y 31 " --> pdb=" O MET y 27 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL y 35 " --> pdb=" O PHE y 31 " (cutoff:3.500A) Processing helix chain 'y' and resid 43 through 65 Proline residue: y 56 - end of helix Processing helix chain 'y' and resid 68 through 87 removed outlier: 4.050A pdb=" N LEU y 79 " --> pdb=" O HIS y 75 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLN y 82 " --> pdb=" O ASN y 78 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LYS y 85 " --> pdb=" O ALA y 81 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ALA y 87 " --> pdb=" O ILE y 83 " (cutoff:3.500A) Processing helix chain 'z' and resid 11 through 27 removed outlier: 3.717A pdb=" N ALA z 15 " --> pdb=" O PRO z 11 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU z 24 " --> pdb=" O LYS z 20 " (cutoff:3.500A) Processing helix chain 'z' and resid 28 through 36 Processing helix chain 'z' and resid 40 through 66 removed outlier: 3.620A pdb=" N ALA z 48 " --> pdb=" O GLU z 44 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VAL z 53 " --> pdb=" O LYS z 49 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS z 54 " --> pdb=" O ALA z 50 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N LYS z 58 " --> pdb=" O LYS z 54 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N LYS z 59 " --> pdb=" O ARG z 55 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA z 65 " --> pdb=" O ALA z 61 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N ARG z 66 " --> pdb=" O ARG z 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 6 through 26 removed outlier: 5.696A pdb=" N ARG A 10 " --> pdb=" O PRO A 6 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ILE A 11 " --> pdb=" O VAL A 7 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ARG A 17 " --> pdb=" O ASP A 13 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASP A 19 " --> pdb=" O THR A 15 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ARG A 22 " --> pdb=" O SER A 18 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLY A 23 " --> pdb=" O ASP A 19 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N TYR A 24 " --> pdb=" O VAL A 20 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N LEU A 25 " --> pdb=" O LEU A 21 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ASP A 26 " --> pdb=" O ARG A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 27 through 41 removed outlier: 4.321A pdb=" N GLU A 36 " --> pdb=" O GLU A 32 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL A 37 " --> pdb=" O ARG A 33 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ALA A 39 " --> pdb=" O GLU A 35 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N GLU A 40 " --> pdb=" O GLU A 36 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU A 41 " --> pdb=" O VAL A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 88 removed outlier: 3.653A pdb=" N ALA A 53 " --> pdb=" O GLU A 49 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA A 55 " --> pdb=" O GLU A 51 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU A 56 " --> pdb=" O ARG A 52 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N SER A 61 " --> pdb=" O GLY A 57 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N VAL A 66 " --> pdb=" O SER A 62 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N THR A 69 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ASP A 71 " --> pdb=" O VAL A 67 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLN A 72 " --> pdb=" O ASP A 68 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU A 86 " --> pdb=" O GLY A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 121 removed outlier: 4.025A pdb=" N VAL A 100 " --> pdb=" O PHE A 96 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ALA A 101 " --> pdb=" O ASN A 97 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLU A 107 " --> pdb=" O LEU A 103 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N GLN A 112 " --> pdb=" O GLU A 108 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU A 113 " --> pdb=" O LYS A 109 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N ARG A 116 " --> pdb=" O GLN A 112 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ARG A 117 " --> pdb=" O LEU A 113 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N MET A 118 " --> pdb=" O GLU A 114 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N GLY A 121 " --> pdb=" O ARG A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 160 removed outlier: 3.738A pdb=" N GLU A 149 " --> pdb=" O ALA A 145 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N ARG A 150 " --> pdb=" O SER A 146 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N MET A 151 " --> pdb=" O MET A 147 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N TYR A 152 " --> pdb=" O LEU A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 193 removed outlier: 3.541A pdb=" N LEU A 192 " --> pdb=" O ALA A 188 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG A 193 " --> pdb=" O TYR A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 240 removed outlier: 3.609A pdb=" N LEU A 239 " --> pdb=" O ASN A 235 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N ARG A 240 " --> pdb=" O PRO A 236 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 235 through 240' Processing helix chain 'A' and resid 279 through 312 removed outlier: 3.703A pdb=" N ASP A 285 " --> pdb=" O HIS A 281 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N GLN A 286 " --> pdb=" O LYS A 282 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLU A 297 " --> pdb=" O ALA A 293 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLU A 299 " --> pdb=" O LEU A 295 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LYS A 302 " --> pdb=" O LEU A 298 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ALA A 305 " --> pdb=" O GLN A 301 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N GLU A 306 " --> pdb=" O LYS A 302 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LYS A 307 " --> pdb=" O LYS A 303 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA A 309 " --> pdb=" O ALA A 305 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N MET A 310 " --> pdb=" O GLU A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 351 removed outlier: 3.813A pdb=" N VAL A 348 " --> pdb=" O ASN A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 362 removed outlier: 3.723A pdb=" N GLU A 358 " --> pdb=" O ASP A 354 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ALA A 359 " --> pdb=" O GLN A 355 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N LYS A 362 " --> pdb=" O GLU A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 48 removed outlier: 4.270A pdb=" N VAL A 46 " --> pdb=" O GLN A 43 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N TRP A 47 " --> pdb=" O PRO A 44 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N ASN A 48 " --> pdb=" O ASP A 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 43 through 48' Processing helix chain 'A' and resid 250 through 256 removed outlier: 6.194A pdb=" N ASN A 255 " --> pdb=" O GLY A 250 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ARG A 256 " --> pdb=" O GLY A 251 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 250 through 256' Processing sheet with id= 1, first strand: chain 'B' and resid 2 through 5 Processing sheet with id= 2, first strand: chain 'B' and resid 80 through 83 removed outlier: 6.822A pdb=" N LEU B 93 " --> pdb=" O GLU B 79 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ILE B 74 " --> pdb=" O SER B 118 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N SER B 118 " --> pdb=" O ILE B 74 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ASP B 114 " --> pdb=" O VAL B 78 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'B' and resid 138 through 142 removed outlier: 4.393A pdb=" N SER B 139 " --> pdb=" O ILE B 164 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLN B 163 " --> pdb=" O ARG B 175 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N THR B 173 " --> pdb=" O VAL B 165 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLU B 180 " --> pdb=" O LEU B 176 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'B' and resid 91 through 96 removed outlier: 4.024A pdb=" N GLU B 100 " --> pdb=" O TYR B 96 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'C' and resid 11 through 16 removed outlier: 4.877A pdb=" N VAL C 20 " --> pdb=" O THR C 16 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N VAL C 26 " --> pdb=" O VAL C 9 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLU C 28 " --> pdb=" O LYS C 7 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LYS C 7 " --> pdb=" O GLU C 28 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N SER C 199 " --> pdb=" O LYS C 8 " (cutoff:3.500A) removed outlier: 12.875A pdb=" N GLY C 198 " --> pdb=" O LYS C 114 " (cutoff:3.500A) removed outlier: 11.053A pdb=" N LYS C 114 " --> pdb=" O GLY C 198 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N ASP C 200 " --> pdb=" O THR C 112 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N THR C 112 " --> pdb=" O ASP C 200 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N GLU C 168 " --> pdb=" O SER C 113 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'C' and resid 36 through 39 removed outlier: 6.478A pdb=" N GLN C 49 " --> pdb=" O THR C 35 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N GLN C 94 " --> pdb=" O VAL C 34 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'C' and resid 179 through 182 Processing sheet with id= 8, first strand: chain 'C' and resid 24 through 29 removed outlier: 3.648A pdb=" N THR C 25 " --> pdb=" O VAL C 189 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL C 189 " --> pdb=" O THR C 25 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N ASN C 185 " --> pdb=" O VAL C 29 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'C' and resid 46 through 51 removed outlier: 5.453A pdb=" N ARG C 46 " --> pdb=" O LEU C 84 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'C' and resid 105 through 108 removed outlier: 6.999A pdb=" N LYS C 105 " --> pdb=" O VAL C 177 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'D' and resid 1 through 5 removed outlier: 5.214A pdb=" N SER D 10 " --> pdb=" O LEU D 5 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'D' and resid 117 through 120 Processing sheet with id= 13, first strand: chain 'E' and resid 65 through 69 removed outlier: 5.544A pdb=" N ILE E 85 " --> pdb=" O VAL E 40 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N CYS E 87 " --> pdb=" O MET E 38 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL E 89 " --> pdb=" O LEU E 36 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASN E 37 " --> pdb=" O ASP E 153 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'F' and resid 16 through 19 Processing sheet with id= 15, first strand: chain 'F' and resid 41 through 45 removed outlier: 4.181A pdb=" N LYS F 44 " --> pdb=" O THR F 51 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'F' and resid 94 through 98 removed outlier: 3.664A pdb=" N ARG F 95 " --> pdb=" O SER F 106 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N VAL F 113 " --> pdb=" O LEU F 105 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'F' and resid 129 through 136 removed outlier: 5.797A pdb=" N THR F 129 " --> pdb=" O LEU F 89 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'G' and resid 7 through 10 removed outlier: 6.410A pdb=" N ASP G 7 " --> pdb=" O LEU G 15 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'G' and resid 17 through 21 removed outlier: 4.399A pdb=" N ASP G 17 " --> pdb=" O LEU G 5 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N MET G 1 " --> pdb=" O VAL G 21 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N LYS G 35 " --> pdb=" O LEU G 6 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'G' and resid 76 through 83 removed outlier: 6.534A pdb=" N GLU G 76 " --> pdb=" O LYS G 141 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE G 143 " --> pdb=" O GLU G 76 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N VAL G 78 " --> pdb=" O ILE G 143 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALA G 140 " --> pdb=" O PHE G 132 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'J' and resid 14 through 19 Processing sheet with id= 22, first strand: chain 'J' and resid 74 through 78 removed outlier: 7.306A pdb=" N GLY J 83 " --> pdb=" O THR J 78 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'K' and resid 18 through 21 removed outlier: 4.200A pdb=" N THR K 6 " --> pdb=" O CYS K 21 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N ASN K 82 " --> pdb=" O MET K 7 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N GLY K 81 " --> pdb=" O LYS K 66 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LYS K 66 " --> pdb=" O GLY K 81 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'K' and resid 68 through 71 removed outlier: 3.788A pdb=" N SER K 75 " --> pdb=" O ARG K 71 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'L' and resid 120 through 123 Processing sheet with id= 26, first strand: chain 'M' and resid 37 through 40 No H-bonds generated for sheet with id= 26 Processing sheet with id= 27, first strand: chain 'M' and resid 62 through 65 removed outlier: 3.768A pdb=" N TYR M 103 " --> pdb=" O LEU M 33 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N LEU M 33 " --> pdb=" O LEU M 102 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LYS M 100 " --> pdb=" O ALA M 35 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'M' and resid 73 through 76 No H-bonds generated for sheet with id= 28 Processing sheet with id= 29, first strand: chain 'M' and resid 30 through 36 removed outlier: 6.993A pdb=" N SER M 30 " --> pdb=" O LYS M 133 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N LYS M 127 " --> pdb=" O VAL M 36 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'N' and resid 33 through 36 removed outlier: 6.008A pdb=" N MET N 110 " --> pdb=" O CYS N 100 " (cutoff:3.500A) removed outlier: 8.545A pdb=" N TYR N 94 " --> pdb=" O VAL N 116 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'O' and resid 49 through 52 removed outlier: 3.696A pdb=" N VAL O 49 " --> pdb=" O VAL O 39 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL O 39 " --> pdb=" O VAL O 49 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG O 25 " --> pdb=" O ILE O 40 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N VAL O 28 " --> pdb=" O ASP O 93 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'P' and resid 37 through 46 Processing sheet with id= 33, first strand: chain 'P' and resid 49 through 53 removed outlier: 4.525A pdb=" N ALA P 49 " --> pdb=" O THR P 60 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ARG P 53 " --> pdb=" O HIS P 56 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N SER P 57 " --> pdb=" O THR P 76 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL P 61 " --> pdb=" O ARG P 72 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LYS P 63 " --> pdb=" O VAL P 70 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'R' and resid 11 through 15 removed outlier: 6.199A pdb=" N LEU R 39 " --> pdb=" O GLY R 50 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLU R 46 " --> pdb=" O ASN R 43 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'R' and resid 18 through 23 removed outlier: 4.034A pdb=" N GLN R 18 " --> pdb=" O ILE R 98 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N GLN R 87 " --> pdb=" O LYS R 73 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N LYS R 73 " --> pdb=" O GLN R 87 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N HIS R 89 " --> pdb=" O LYS R 71 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N LYS R 71 " --> pdb=" O HIS R 89 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N GLN R 91 " --> pdb=" O GLY R 69 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'S' and resid 2 through 8 Processing sheet with id= 37, first strand: chain 'T' and resid 12 through 15 removed outlier: 4.674A pdb=" N VAL T 31 " --> pdb=" O HIS T 15 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N ASN T 28 " --> pdb=" O LEU T 87 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N LYS T 81 " --> pdb=" O VAL T 34 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N LYS T 66 " --> pdb=" O ARG T 77 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N ASP T 79 " --> pdb=" O LYS T 64 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N LYS T 64 " --> pdb=" O ASP T 79 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N LYS T 81 " --> pdb=" O VAL T 62 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N VAL T 62 " --> pdb=" O LYS T 81 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ALA T 83 " --> pdb=" O THR T 60 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N THR T 60 " --> pdb=" O ALA T 83 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N VAL T 85 " --> pdb=" O VAL T 58 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N VAL T 58 " --> pdb=" O VAL T 85 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'U' and resid 40 through 44 removed outlier: 5.198A pdb=" N ASN U 40 " --> pdb=" O ALA U 63 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'U' and resid 83 through 86 Processing sheet with id= 40, first strand: chain 'V' and resid 2 through 5 Processing sheet with id= 41, first strand: chain 'V' and resid 37 through 42 removed outlier: 3.968A pdb=" N PHE V 26 " --> pdb=" O LEU V 42 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ILE V 89 " --> pdb=" O PRO V 27 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'W' and resid 34 through 37 removed outlier: 3.992A pdb=" N SER W 35 " --> pdb=" O ALA W 61 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N LEU W 59 " --> pdb=" O ILE W 37 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N THR W 58 " --> pdb=" O GLY W 54 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N ASN W 50 " --> pdb=" O LYS W 62 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'W' and resid 45 through 48 Processing sheet with id= 44, first strand: chain 'X' and resid 12 through 19 removed outlier: 4.168A pdb=" N THR X 25 " --> pdb=" O ASN X 17 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER X 19 " --> pdb=" O ASN X 23 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N ASN X 23 " --> pdb=" O SER X 19 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'Z' and resid 35 through 39 removed outlier: 7.813A pdb=" N MET Z 54 " --> pdb=" O THR Z 10 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'a' and resid 20 through 25 removed outlier: 4.832A pdb=" N ASN a 20 " --> pdb=" O CYS a 16 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N SER a 17 " --> pdb=" O LEU a 34 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'c' and resid 7 through 12 No H-bonds generated for sheet with id= 47 Processing sheet with id= 48, first strand: chain 'c' and resid 34 through 39 removed outlier: 6.491A pdb=" N LEU c 34 " --> pdb=" O GLU c 51 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU c 51 " --> pdb=" O LEU c 34 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU c 36 " --> pdb=" O TYR c 49 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'e' and resid 22 through 25 No H-bonds generated for sheet with id= 49 Processing sheet with id= 50, first strand: chain 'f' and resid 1 through 5 removed outlier: 6.732A pdb=" N HIS f 33 " --> pdb=" O CYS f 27 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N CYS f 27 " --> pdb=" O HIS f 33 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N ILE f 23 " --> pdb=" O GLN f 37 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'g' and resid 15 through 18 removed outlier: 5.398A pdb=" N HIS g 15 " --> pdb=" O ILE g 41 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N HIS g 39 " --> pdb=" O GLY g 17 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'g' and resid 89 through 93 removed outlier: 3.526A pdb=" N LEU g 68 " --> pdb=" O ALA g 160 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'h' and resid 19 through 22 removed outlier: 5.889A pdb=" N ASN h 19 " --> pdb=" O ILE h 55 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ARG h 59 " --> pdb=" O THR h 21 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG h 54 " --> pdb=" O HIS h 69 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'h' and resid 164 through 169 removed outlier: 5.876A pdb=" N ARG h 164 " --> pdb=" O GLY h 155 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'i' and resid 140 through 145 removed outlier: 4.031A pdb=" N ASP i 141 " --> pdb=" O PHE i 182 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL i 143 " --> pdb=" O GLY i 180 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N MET i 178 " --> pdb=" O ILE i 145 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N GLU i 179 " --> pdb=" O ASP i 174 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'j' and resid 11 through 16 removed outlier: 6.289A pdb=" N LEU j 36 " --> pdb=" O ILE j 16 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'j' and resid 84 through 88 removed outlier: 6.346A pdb=" N ASN j 122 " --> pdb=" O ALA j 99 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'j' and resid 33 through 41 removed outlier: 6.912A pdb=" N ARG j 45 " --> pdb=" O ASP j 41 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'k' and resid 34 through 37 removed outlier: 6.417A pdb=" N ASN k 63 " --> pdb=" O HIS k 37 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N HIS k 3 " --> pdb=" O THR k 92 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N MET k 90 " --> pdb=" O GLU k 5 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'k' and resid 38 through 43 removed outlier: 4.686A pdb=" N ARG k 38 " --> pdb=" O ASN k 63 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N TYR k 59 " --> pdb=" O TRP k 42 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'k' and resid 44 through 47 removed outlier: 7.345A pdb=" N HIS k 55 " --> pdb=" O LEU k 47 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'l' and resid 73 through 79 removed outlier: 5.603A pdb=" N TYR l 85 " --> pdb=" O ARG l 78 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'm' and resid 23 through 29 removed outlier: 6.252A pdb=" N ALA m 23 " --> pdb=" O LEU m 63 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL m 25 " --> pdb=" O LEU m 61 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ASP m 48 " --> pdb=" O THR m 62 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'm' and resid 74 through 77 removed outlier: 4.172A pdb=" N TYR m 128 " --> pdb=" O GLN m 76 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N VAL m 103 " --> pdb=" O ILE m 126 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N ILE m 85 " --> pdb=" O ILE m 125 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'n' and resid 5 through 11 removed outlier: 3.796A pdb=" N LYS n 22 " --> pdb=" O ASP n 62 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'o' and resid 35 through 39 removed outlier: 7.566A pdb=" N GLN o 35 " --> pdb=" O VAL o 77 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ASP o 75 " --> pdb=" O ARG o 37 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N LEU o 73 " --> pdb=" O PRO o 39 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N ARG o 5 " --> pdb=" O GLY o 103 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'o' and resid 44 through 52 Processing sheet with id= 68, first strand: chain 'p' and resid 42 through 45 removed outlier: 4.222A pdb=" N ASN p 29 " --> pdb=" O SER p 26 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLU p 83 " --> pdb=" O GLY p 19 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ASN p 109 " --> pdb=" O LEU p 82 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'q' and resid 29 through 34 removed outlier: 3.589A pdb=" N LYS q 30 " --> pdb=" O ILE q 82 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N SER q 78 " --> pdb=" O CYS q 34 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'q' and resid 35 through 41 removed outlier: 5.203A pdb=" N LYS q 51 " --> pdb=" O ILE q 67 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'u' and resid 16 through 20 Processing sheet with id= 72, first strand: chain 'v' and resid 7 through 11 removed outlier: 6.879A pdb=" N GLU v 60 " --> pdb=" O VAL v 76 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'v' and resid 19 through 30 No H-bonds generated for sheet with id= 73 Processing sheet with id= 74, first strand: chain 'x' and resid 30 through 34 removed outlier: 4.006A pdb=" N LEU x 31 " --> pdb=" O THR x 48 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N LEU x 47 " --> pdb=" O VAL x 62 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain 'A' and resid 161 through 166 removed outlier: 6.055A pdb=" N THR A 180 " --> pdb=" O ILE A 166 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N LYS A 177 " --> pdb=" O ALA A 134 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N CYS A 128 " --> pdb=" O ILE A 183 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N ASP A 127 " --> pdb=" O GLU A 225 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLU A 225 " --> pdb=" O ASP A 127 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N PHE A 217 " --> pdb=" O GLY A 135 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ARG A 324 " --> pdb=" O VAL A 198 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG A 200 " --> pdb=" O ARG A 324 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL A 202 " --> pdb=" O TYR A 326 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL A 327 " --> pdb=" O ARG A 332 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N VAL A 340 " --> pdb=" O ASP A 335 " (cutoff:3.500A) Processing sheet with id= 76, first strand: chain 'A' and resid 241 through 245 removed outlier: 4.061A pdb=" N ILE A 270 " --> pdb=" O HIS A 265 " (cutoff:3.500A) Processing sheet with id= 77, first strand: chain 'A' and resid 167 through 170 1816 hydrogen bonds defined for protein. 5358 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3189 hydrogen bonds 4348 hydrogen bond angles 0 basepair planarities 1348 basepair parallelities 2513 stacking parallelities Total time for adding SS restraints: 256.16 Time building geometry restraints manager: 69.48 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: 12184 1.29 - 1.42: 70620 1.42 - 1.55: 67070 1.55 - 1.69: 9290 1.69 - 1.82: 279 Bond restraints: 159443 Sorted by residual: bond pdb=" C5 5MU 11939 " pdb=" C6 5MU 11939 " ideal model delta sigma weight residual 1.150 1.438 -0.288 2.00e-02 2.50e+03 2.08e+02 bond pdb=" C5 5MU 1 747 " pdb=" C6 5MU 1 747 " ideal model delta sigma weight residual 1.150 1.434 -0.284 2.00e-02 2.50e+03 2.02e+02 bond pdb=" C5 5MU 5 54 " pdb=" C6 5MU 5 54 " ideal model delta sigma weight residual 1.150 1.434 -0.284 2.00e-02 2.50e+03 2.01e+02 bond pdb=" C4 5MU 5 54 " pdb=" C5 5MU 5 54 " ideal model delta sigma weight residual 1.805 1.602 0.203 2.00e-02 2.50e+03 1.03e+02 bond pdb=" C4 5MU 11939 " pdb=" C5 5MU 11939 " ideal model delta sigma weight residual 1.805 1.602 0.203 2.00e-02 2.50e+03 1.03e+02 ... (remaining 159438 not shown) Histogram of bond angle deviations from ideal: 98.56 - 106.75: 28672 106.75 - 114.94: 104298 114.94 - 123.13: 79642 123.13 - 131.32: 24324 131.32 - 139.51: 1309 Bond angle restraints: 238245 Sorted by residual: angle pdb=" C1' 2MA 12503 " pdb=" N9 2MA 12503 " pdb=" C4 2MA 12503 " ideal model delta sigma weight residual 103.49 125.83 -22.34 3.00e+00 1.11e-01 5.54e+01 angle pdb=" C1' 2MA 12503 " pdb=" N9 2MA 12503 " pdb=" C8 2MA 12503 " ideal model delta sigma weight residual 144.94 124.06 20.88 3.00e+00 1.11e-01 4.84e+01 angle pdb=" C4' G 1 784 " pdb=" C3' G 1 784 " pdb=" O3' G 1 784 " ideal model delta sigma weight residual 113.00 122.97 -9.97 1.50e+00 4.44e-01 4.42e+01 angle pdb=" O HIS e 31 " pdb=" C HIS e 31 " pdb=" N ILE e 32 " ideal model delta sigma weight residual 123.25 130.62 -7.37 1.14e+00 7.69e-01 4.18e+01 angle pdb=" C THR g 46 " pdb=" N VAL g 47 " pdb=" CA VAL g 47 " ideal model delta sigma weight residual 120.43 126.04 -5.61 9.60e-01 1.09e+00 3.41e+01 ... (remaining 238240 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.95: 81065 35.95 - 71.91: 3798 71.91 - 107.86: 305 107.86 - 143.82: 12 143.82 - 179.77: 31 Dihedral angle restraints: 85211 sinusoidal: 68028 harmonic: 17183 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 31.60 168.40 1 1.50e+01 4.44e-03 8.45e+01 dihedral pdb=" O4' U 2 4 " pdb=" C1' U 2 4 " pdb=" N1 U 2 4 " pdb=" C2 U 2 4 " ideal model delta sinusoidal sigma weight residual 200.00 39.60 160.40 1 1.50e+01 4.44e-03 8.29e+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 43.91 156.09 1 1.50e+01 4.44e-03 8.17e+01 ... (remaining 85208 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 28029 0.075 - 0.150: 2065 0.150 - 0.225: 178 0.225 - 0.301: 17 0.301 - 0.376: 6 Chirality restraints: 30295 Sorted by residual: chirality pdb=" C3' U 1 894 " pdb=" C4' U 1 894 " pdb=" O3' U 1 894 " pdb=" C2' U 1 894 " both_signs ideal model delta sigma weight residual False -2.74 -2.37 -0.38 2.00e-01 2.50e+01 3.53e+00 chirality pdb=" C3' A 1 947 " pdb=" C4' A 1 947 " pdb=" O3' A 1 947 " pdb=" C2' A 1 947 " both_signs ideal model delta sigma weight residual False -2.48 -2.11 -0.37 2.00e-01 2.50e+01 3.34e+00 chirality pdb=" C2' A 1 404 " pdb=" C3' A 1 404 " pdb=" O2' A 1 404 " pdb=" C1' A 1 404 " both_signs ideal model delta sigma weight residual False -2.75 -2.41 -0.34 2.00e-01 2.50e+01 2.97e+00 ... (remaining 30292 not shown) Planarity restraints: 12964 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 5MC 21407 " -0.061 2.00e-02 2.50e+03 5.98e-01 8.04e+03 pdb=" C4' 5MC 21407 " -0.447 2.00e-02 2.50e+03 pdb=" O4' 5MC 21407 " -0.614 2.00e-02 2.50e+03 pdb=" C3' 5MC 21407 " 0.594 2.00e-02 2.50e+03 pdb=" O3' 5MC 21407 " 0.655 2.00e-02 2.50e+03 pdb=" C2' 5MC 21407 " 0.177 2.00e-02 2.50e+03 pdb=" O2' 5MC 21407 " -0.980 2.00e-02 2.50e+03 pdb=" C1' 5MC 21407 " -0.224 2.00e-02 2.50e+03 pdb=" N1 5MC 21407 " 0.902 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMC 12498 " -0.052 2.00e-02 2.50e+03 5.94e-01 7.93e+03 pdb=" C4' OMC 12498 " -0.443 2.00e-02 2.50e+03 pdb=" O4' OMC 12498 " -0.616 2.00e-02 2.50e+03 pdb=" C3' OMC 12498 " 0.587 2.00e-02 2.50e+03 pdb=" O3' OMC 12498 " 0.629 2.00e-02 2.50e+03 pdb=" C2' OMC 12498 " 0.178 2.00e-02 2.50e+03 pdb=" O2' OMC 12498 " -0.969 2.00e-02 2.50e+03 pdb=" C1' OMC 12498 " -0.225 2.00e-02 2.50e+03 pdb=" N1 OMC 12498 " 0.911 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG 12445 " 0.000 2.00e-02 2.50e+03 5.88e-01 7.79e+03 pdb=" C4' 2MG 12445 " -0.458 2.00e-02 2.50e+03 pdb=" O4' 2MG 12445 " -0.808 2.00e-02 2.50e+03 pdb=" C3' 2MG 12445 " 0.587 2.00e-02 2.50e+03 pdb=" O3' 2MG 12445 " 0.520 2.00e-02 2.50e+03 pdb=" C2' 2MG 12445 " 0.267 2.00e-02 2.50e+03 pdb=" O2' 2MG 12445 " -0.830 2.00e-02 2.50e+03 pdb=" C1' 2MG 12445 " -0.195 2.00e-02 2.50e+03 pdb=" N9 2MG 12445 " 0.918 2.00e-02 2.50e+03 ... (remaining 12961 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.25: 51 2.25 - 2.91: 58180 2.91 - 3.57: 258156 3.57 - 4.24: 478439 4.24 - 4.90: 623335 Nonbonded interactions: 1418161 Sorted by model distance: nonbonded pdb=" O SER t 52 " pdb=" CB LEU t 56 " model vdw 1.584 2.752 nonbonded pdb=" O2' U 11065 " pdb=" O4' U 11066 " model vdw 1.940 2.440 nonbonded pdb=" OP1 G 11266 " pdb="MG MG 13001 " model vdw 1.966 2.170 nonbonded pdb=" O PHE E 122 " pdb=" OD1 ASP E 123 " model vdw 2.003 3.040 nonbonded pdb=" O4 U 3 65 " pdb="MG MG 3 204 " model vdw 2.032 2.170 ... (remaining 1418156 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 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 12 5.21 5 S 157 5.16 5 C 73996 2.51 5 N 27340 2.21 5 O 40718 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.900 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: 0.130 Extract box with map and model: 17.770 Check model and map are aligned: 1.670 Convert atoms to be neutral: 0.970 Process input model: 580.940 Find NCS groups from input model: 3.070 Set up NCS constraints: 0.420 Set refine NCS operators: 0.000 Set scattering table: 0.040 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 609.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 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 : 0.007 0.288 159443 Z= 0.409 Angle : 0.828 22.336 238245 Z= 0.436 Chirality : 0.043 0.376 30295 Planarity : 0.019 0.598 12964 Dihedral : 15.930 179.770 74125 Min Nonbonded Distance : 1.584 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.09 % Favored : 94.79 % Rotamer Outliers : 0.36 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % 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: -3.86 (0.09), residues: 5928 helix: -2.97 (0.08), residues: 1861 sheet: -2.42 (0.14), residues: 1128 loop : -2.25 (0.10), residues: 2939 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11856 Ramachandran restraints generated. 5928 Oldfield, 0 Emsley, 5928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11856 Ramachandran restraints generated. 5928 Oldfield, 0 Emsley, 5928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2043 residues out of total 4945 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 2025 time to evaluate : 6.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 4 residues processed: 2034 average time/residue: 1.5463 time to fit residues: 5302.3831 Evaluate side-chains 1141 residues out of total 4945 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1137 time to evaluate : 6.735 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 1.8546 time to fit residues: 18.7471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1040 random chunks: chunk 878 optimal weight: 8.9990 chunk 788 optimal weight: 9.9990 chunk 437 optimal weight: 10.0000 chunk 269 optimal weight: 10.0000 chunk 531 optimal weight: 4.9990 chunk 421 optimal weight: 10.0000 chunk 815 optimal weight: 20.0000 chunk 315 optimal weight: 9.9990 chunk 495 optimal weight: 5.9990 chunk 606 optimal weight: 1.9990 chunk 944 optimal weight: 7.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 90 ASN ** B 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 260 ASN C 150 GLN ** C 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 5 HIS ** F 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 67 ASN ** J 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 107 ASN ** O 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 38 GLN ** P 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 66 ASN Q 72 ASN R 12 HIS R 66 HIS S 7 HIS ** S 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 48 GLN ** T 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 46 HIS ** X 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 23 ASN Y 15 ASN Y 39 GLN ** Z 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 20 ASN ** b 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 26 ASN ** d 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 13 ASN ** f 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 15 HIS g 168 HIS ** g 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 3 GLN h 8 ASN h 32 ASN i 54 GLN ** i 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 46 GLN k 52 ASN ** k 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 130 ASN ** m 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 31 ASN ** o 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 5 ASN q 46 ASN r 8 ASN s 43 ASN t 20 ASN ** t 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 50 ASN x 52 HIS ** x 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** y 20 HIS ** y 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 38 ASN A 43 GLN ** A 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 97 ASN ** A 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 281 HIS ** A 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 313 ASN Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.4162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.169 159443 Z= 0.347 Angle : 0.868 17.205 238245 Z= 0.444 Chirality : 0.042 0.410 30295 Planarity : 0.009 0.175 12964 Dihedral : 16.914 178.869 62245 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 38.19 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.09 % Favored : 94.84 % Rotamer Outliers : 5.26 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 1.06 % 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: -2.64 (0.10), residues: 5928 helix: -1.28 (0.10), residues: 2002 sheet: -2.10 (0.14), residues: 1119 loop : -1.86 (0.11), residues: 2807 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11856 Ramachandran restraints generated. 5928 Oldfield, 0 Emsley, 5928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11856 Ramachandran restraints generated. 5928 Oldfield, 0 Emsley, 5928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1664 residues out of total 4945 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 260 poor density : 1404 time to evaluate : 6.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 260 outliers final: 148 residues processed: 1532 average time/residue: 1.5717 time to fit residues: 4138.5670 Evaluate side-chains 1254 residues out of total 4945 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 1106 time to evaluate : 6.795 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 148 outliers final: 1 residues processed: 148 average time/residue: 1.3140 time to fit residues: 370.3343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1040 random chunks: chunk 524 optimal weight: 7.9990 chunk 293 optimal weight: 10.0000 chunk 786 optimal weight: 5.9990 chunk 643 optimal weight: 20.0000 chunk 260 optimal weight: 10.0000 chunk 946 optimal weight: 5.9990 chunk 1022 optimal weight: 6.9990 chunk 842 optimal weight: 0.7980 chunk 938 optimal weight: 5.9990 chunk 322 optimal weight: 10.0000 chunk 759 optimal weight: 6.9990 overall best weight: 5.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 163 ASN ** F 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 29 HIS M 60 GLN N 81 ASN ** O 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 60 HIS S 61 ASN T 70 HIS ** Y 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 42 HIS e 28 ASN ** e 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 178 ASN ** g 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 3 GLN i 71 GLN i 126 ASN i 136 GLN i 164 GLN j 97 GLN ** j 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 37 HIS ** k 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 86 GLN l 148 ASN ** m 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 26 ASN ** v 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 31 ASN x 57 HIS A 9 ASN A 54 GLN ** A 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 346 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.5836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.198 159443 Z= 0.304 Angle : 0.767 15.945 238245 Z= 0.398 Chirality : 0.038 0.339 30295 Planarity : 0.008 0.170 12964 Dihedral : 16.892 179.553 62245 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 29.92 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.26 % Favored : 94.69 % Rotamer Outliers : 4.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.53 % 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: -2.14 (0.10), residues: 5928 helix: -0.73 (0.11), residues: 2007 sheet: -1.73 (0.14), residues: 1082 loop : -1.73 (0.11), residues: 2839 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11856 Ramachandran restraints generated. 5928 Oldfield, 0 Emsley, 5928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11856 Ramachandran restraints generated. 5928 Oldfield, 0 Emsley, 5928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1549 residues out of total 4945 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 216 poor density : 1333 time to evaluate : 6.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 216 outliers final: 96 residues processed: 1457 average time/residue: 1.4025 time to fit residues: 3487.2370 Evaluate side-chains 1185 residues out of total 4945 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 1089 time to evaluate : 6.702 Switching outliers to nearest non-outliers outliers start: 96 outliers final: 0 residues processed: 96 average time/residue: 1.1824 time to fit residues: 212.7697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1040 random chunks: chunk 934 optimal weight: 20.0000 chunk 711 optimal weight: 8.9990 chunk 491 optimal weight: 0.0670 chunk 104 optimal weight: 20.0000 chunk 451 optimal weight: 20.0000 chunk 635 optimal weight: 0.9990 chunk 949 optimal weight: 7.9990 chunk 1005 optimal weight: 9.9990 chunk 496 optimal weight: 6.9990 chunk 899 optimal weight: 8.9990 chunk 270 optimal weight: 10.0000 overall best weight: 5.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 15 HIS ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 117 GLN B 163 GLN ** B 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 15 HIS ** g 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 170 HIS ** g 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 3 GLN ** i 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 46 GLN k 52 ASN ** m 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 75 GLN t 28 GLN ** t 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** y 48 GLN ** y 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 54 GLN ** A 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 346 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.7150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.137 159443 Z= 0.275 Angle : 0.740 14.611 238245 Z= 0.388 Chirality : 0.037 0.318 30295 Planarity : 0.007 0.146 12964 Dihedral : 16.841 179.770 62245 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 35.28 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.38 % Favored : 94.57 % Rotamer Outliers : 4.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.53 % 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: -1.86 (0.10), residues: 5928 helix: -0.52 (0.11), residues: 2011 sheet: -1.57 (0.15), residues: 1108 loop : -1.56 (0.11), residues: 2809 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11856 Ramachandran restraints generated. 5928 Oldfield, 0 Emsley, 5928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11856 Ramachandran restraints generated. 5928 Oldfield, 0 Emsley, 5928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1483 residues out of total 4945 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 198 poor density : 1285 time to evaluate : 6.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 198 outliers final: 102 residues processed: 1393 average time/residue: 1.4501 time to fit residues: 3462.3687 Evaluate side-chains 1169 residues out of total 4945 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 1067 time to evaluate : 6.778 Switching outliers to nearest non-outliers outliers start: 102 outliers final: 0 residues processed: 102 average time/residue: 1.2884 time to fit residues: 247.8878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1040 random chunks: chunk 837 optimal weight: 8.9990 chunk 570 optimal weight: 2.9990 chunk 14 optimal weight: 20.0000 chunk 748 optimal weight: 7.9990 chunk 414 optimal weight: 10.0000 chunk 857 optimal weight: 20.0000 chunk 694 optimal weight: 10.0000 chunk 1 optimal weight: 9.9990 chunk 513 optimal weight: 5.9990 chunk 902 optimal weight: 6.9990 chunk 253 optimal weight: 10.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 30 ASN ** F 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 128 ASN ** J 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 71 GLN ** U 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 24 ASN ** V 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 31 GLN Y 38 GLN ** Y 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 15 HIS ** g 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 5 GLN ** n 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 20 ASN t 37 ASN ** t 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 54 GLN A 253 HIS ** A 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.8436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.147 159443 Z= 0.332 Angle : 0.786 14.297 238245 Z= 0.409 Chirality : 0.040 0.369 30295 Planarity : 0.008 0.133 12964 Dihedral : 17.072 179.867 62245 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 39.60 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.21 % Favored : 93.76 % Rotamer Outliers : 4.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.53 % 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: -1.96 (0.10), residues: 5928 helix: -0.64 (0.11), residues: 1995 sheet: -1.62 (0.15), residues: 1076 loop : -1.58 (0.11), residues: 2857 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11856 Ramachandran restraints generated. 5928 Oldfield, 0 Emsley, 5928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11856 Ramachandran restraints generated. 5928 Oldfield, 0 Emsley, 5928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1410 residues out of total 4945 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 200 poor density : 1210 time to evaluate : 6.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 200 outliers final: 104 residues processed: 1323 average time/residue: 1.3900 time to fit residues: 3180.6692 Evaluate side-chains 1148 residues out of total 4945 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 1044 time to evaluate : 6.904 Switching outliers to nearest non-outliers outliers start: 104 outliers final: 0 residues processed: 104 average time/residue: 1.1812 time to fit residues: 236.4967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1040 random chunks: chunk 338 optimal weight: 20.0000 chunk 905 optimal weight: 3.9990 chunk 198 optimal weight: 10.0000 chunk 590 optimal weight: 6.9990 chunk 248 optimal weight: 10.0000 chunk 1006 optimal weight: 5.9990 chunk 835 optimal weight: 0.6980 chunk 465 optimal weight: 6.9990 chunk 83 optimal weight: 10.0000 chunk 332 optimal weight: 20.0000 chunk 528 optimal weight: 6.9990 overall best weight: 4.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 22 GLN ** F 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 71 GLN ** U 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 5 ASN ** V 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 31 GLN ** Y 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 168 HIS ** i 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 52 ASN ** k 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 14 HIS ** x 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 54 GLN ** A 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.8951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.162 159443 Z= 0.263 Angle : 0.718 15.985 238245 Z= 0.377 Chirality : 0.036 0.310 30295 Planarity : 0.007 0.128 12964 Dihedral : 16.917 179.786 62245 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 35.10 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.82 % Favored : 94.16 % Rotamer Outliers : 2.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.53 % 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: -1.70 (0.11), residues: 5928 helix: -0.38 (0.11), residues: 1987 sheet: -1.56 (0.15), residues: 1071 loop : -1.42 (0.11), residues: 2870 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11856 Ramachandran restraints generated. 5928 Oldfield, 0 Emsley, 5928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11856 Ramachandran restraints generated. 5928 Oldfield, 0 Emsley, 5928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1325 residues out of total 4945 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 1178 time to evaluate : 6.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 147 outliers final: 80 residues processed: 1263 average time/residue: 1.3923 time to fit residues: 3038.9212 Evaluate side-chains 1134 residues out of total 4945 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 1054 time to evaluate : 6.733 Switching outliers to nearest non-outliers outliers start: 80 outliers final: 0 residues processed: 80 average time/residue: 1.1407 time to fit residues: 177.8217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1040 random chunks: chunk 970 optimal weight: 5.9990 chunk 113 optimal weight: 10.0000 chunk 573 optimal weight: 7.9990 chunk 734 optimal weight: 2.9990 chunk 569 optimal weight: 9.9990 chunk 847 optimal weight: 6.9990 chunk 561 optimal weight: 7.9990 chunk 1002 optimal weight: 20.0000 chunk 627 optimal weight: 8.9990 chunk 611 optimal weight: 20.0000 chunk 462 optimal weight: 10.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 22 GLN F 30 ASN ** F 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 66 ASN R 89 HIS ** U 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 24 ASN ** V 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 75 GLN ** X 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 15 HIS h 8 ASN ** h 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 3 HIS ** k 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 54 GLN A 214 HIS ** A 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.9833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.143 159443 Z= 0.323 Angle : 0.788 22.651 238245 Z= 0.410 Chirality : 0.040 0.511 30295 Planarity : 0.008 0.189 12964 Dihedral : 17.093 179.868 62245 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 42.21 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.10 % Favored : 92.88 % Rotamer Outliers : 2.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.53 % 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: -1.91 (0.10), residues: 5928 helix: -0.69 (0.11), residues: 2004 sheet: -1.60 (0.15), residues: 1071 loop : -1.46 (0.11), residues: 2853 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11856 Ramachandran restraints generated. 5928 Oldfield, 0 Emsley, 5928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11856 Ramachandran restraints generated. 5928 Oldfield, 0 Emsley, 5928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1260 residues out of total 4945 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 1112 time to evaluate : 6.796 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 148 outliers final: 91 residues processed: 1189 average time/residue: 1.3689 time to fit residues: 2824.4291 Evaluate side-chains 1077 residues out of total 4945 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 986 time to evaluate : 6.876 Switching outliers to nearest non-outliers outliers start: 91 outliers final: 0 residues processed: 91 average time/residue: 1.2590 time to fit residues: 218.5050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1040 random chunks: chunk 620 optimal weight: 6.9990 chunk 400 optimal weight: 10.0000 chunk 598 optimal weight: 10.0000 chunk 301 optimal weight: 10.0000 chunk 196 optimal weight: 10.0000 chunk 194 optimal weight: 10.0000 chunk 637 optimal weight: 40.0000 chunk 682 optimal weight: 10.0000 chunk 495 optimal weight: 0.9990 chunk 93 optimal weight: 10.0000 chunk 787 optimal weight: 8.9990 overall best weight: 7.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 243 HIS ** C 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 64 GLN ** F 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 28 GLN t 37 ASN ** x 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 54 GLN ** A 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 1.0597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.206 159443 Z= 0.352 Angle : 0.811 16.933 238245 Z= 0.423 Chirality : 0.041 0.433 30295 Planarity : 0.008 0.140 12964 Dihedral : 17.260 179.664 62245 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 43.61 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.87 % Favored : 93.12 % Rotamer Outliers : 2.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.53 % 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: -1.96 (0.10), residues: 5928 helix: -0.77 (0.11), residues: 2011 sheet: -1.51 (0.15), residues: 1046 loop : -1.52 (0.11), residues: 2871 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11856 Ramachandran restraints generated. 5928 Oldfield, 0 Emsley, 5928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11856 Ramachandran restraints generated. 5928 Oldfield, 0 Emsley, 5928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1198 residues out of total 4945 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 1093 time to evaluate : 6.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 105 outliers final: 54 residues processed: 1149 average time/residue: 1.3863 time to fit residues: 2764.8763 Evaluate side-chains 1053 residues out of total 4945 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 999 time to evaluate : 6.808 Switching outliers to nearest non-outliers outliers start: 54 outliers final: 0 residues processed: 54 average time/residue: 1.1624 time to fit residues: 125.9398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1040 random chunks: chunk 911 optimal weight: 0.9990 chunk 960 optimal weight: 6.9990 chunk 876 optimal weight: 5.9990 chunk 934 optimal weight: 3.9990 chunk 562 optimal weight: 9.9990 chunk 406 optimal weight: 10.0000 chunk 733 optimal weight: 8.9990 chunk 286 optimal weight: 10.0000 chunk 844 optimal weight: 0.9990 chunk 883 optimal weight: 0.0170 chunk 930 optimal weight: 10.0000 overall best weight: 2.4026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 86 GLN ** J 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 66 ASN ** U 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 20 ASN ** f 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 168 HIS ** j 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 20 ASN t 37 ASN ** x 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 70 ASN z 56 HIS ** A 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 1.0697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.178 159443 Z= 0.202 Angle : 0.726 16.633 238245 Z= 0.379 Chirality : 0.036 0.386 30295 Planarity : 0.007 0.125 12964 Dihedral : 16.838 179.864 62245 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 31.15 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.68 % Favored : 94.30 % Rotamer Outliers : 1.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.53 % 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: -1.78 (0.10), residues: 5928 helix: -0.57 (0.11), residues: 2006 sheet: -1.52 (0.15), residues: 1066 loop : -1.40 (0.11), residues: 2856 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11856 Ramachandran restraints generated. 5928 Oldfield, 0 Emsley, 5928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11856 Ramachandran restraints generated. 5928 Oldfield, 0 Emsley, 5928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1185 residues out of total 4945 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 1132 time to evaluate : 6.841 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 53 outliers final: 31 residues processed: 1151 average time/residue: 1.3822 time to fit residues: 2756.5828 Evaluate side-chains 1057 residues out of total 4945 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 1026 time to evaluate : 6.813 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 0 residues processed: 31 average time/residue: 1.1829 time to fit residues: 73.8407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1040 random chunks: chunk 613 optimal weight: 6.9990 chunk 987 optimal weight: 10.0000 chunk 602 optimal weight: 10.0000 chunk 468 optimal weight: 10.0000 chunk 686 optimal weight: 4.9990 chunk 1036 optimal weight: 3.9990 chunk 953 optimal weight: 40.0000 chunk 825 optimal weight: 5.9990 chunk 85 optimal weight: 20.0000 chunk 637 optimal weight: 0.8980 chunk 505 optimal weight: 8.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 243 HIS ** C 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 168 HIS h 139 GLN ** i 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 136 GLN ** k 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 70 ASN ** A 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 1.0762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.532 159443 Z= 0.292 Angle : 0.780 73.900 238245 Z= 0.402 Chirality : 0.037 0.352 30295 Planarity : 0.007 0.138 12964 Dihedral : 16.813 179.810 62245 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 34.20 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.02 % Favored : 93.94 % Rotamer Outliers : 0.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.53 % 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: -1.76 (0.10), residues: 5928 helix: -0.58 (0.11), residues: 2005 sheet: -1.47 (0.15), residues: 1062 loop : -1.39 (0.11), residues: 2861 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11856 Ramachandran restraints generated. 5928 Oldfield, 0 Emsley, 5928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11856 Ramachandran restraints generated. 5928 Oldfield, 0 Emsley, 5928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1103 residues out of total 4945 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 1068 time to evaluate : 6.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 24 residues processed: 1085 average time/residue: 1.3637 time to fit residues: 2574.4005 Evaluate side-chains 1053 residues out of total 4945 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 1029 time to evaluate : 9.134 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 1.2950 time to fit residues: 63.0616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1040 random chunks: chunk 655 optimal weight: 10.0000 chunk 878 optimal weight: 7.9990 chunk 252 optimal weight: 10.0000 chunk 760 optimal weight: 9.9990 chunk 121 optimal weight: 10.0000 chunk 229 optimal weight: 20.0000 chunk 826 optimal weight: 0.0670 chunk 345 optimal weight: 10.0000 chunk 848 optimal weight: 2.9990 chunk 104 optimal weight: 20.0000 chunk 152 optimal weight: 10.0000 overall best weight: 6.2128 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 243 HIS ** C 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN ** L 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 168 HIS h 139 GLN ** i 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 37 ASN ** x 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 70 ASN z 56 HIS ** A 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 235 ASN ** A 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.042951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.035258 restraints weight = 1244653.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.036462 restraints weight = 467685.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 69)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.037099 restraints weight = 251119.097| |-----------------------------------------------------------------------------| r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 1.1099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.444 159443 Z= 0.325 Angle : 0.793 27.643 238245 Z= 0.413 Chirality : 0.039 0.445 30295 Planarity : 0.007 0.132 12964 Dihedral : 16.972 179.618 62245 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 40.64 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.87 % Favored : 93.12 % Rotamer Outliers : 0.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.53 % 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: -1.93 (0.10), residues: 5928 helix: -0.73 (0.11), residues: 2004 sheet: -1.57 (0.15), residues: 1027 loop : -1.49 (0.11), residues: 2897 =============================================================================== Job complete usr+sys time: 44544.46 seconds wall clock time: 769 minutes 12.07 seconds (46152.07 seconds total)