Starting phenix.real_space_refine (version: 1.21rc1) on Sat Jul 22 03:56:09 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ot3_20193/07_2023/6ot3_20193_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ot3_20193/07_2023/6ot3_20193.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ot3_20193/07_2023/6ot3_20193_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ot3_20193/07_2023/6ot3_20193_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ot3_20193/07_2023/6ot3_20193_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ot3_20193/07_2023/6ot3_20193.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ot3_20193/07_2023/6ot3_20193.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ot3_20193/07_2023/6ot3_20193_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ot3_20193/07_2023/6ot3_20193_updated.pdb" } resolution = 3.9 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= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 4642 5.49 5 Mg 12 5.21 5 S 158 5.16 5 C 74020 2.51 5 N 27343 2.21 5 O 40722 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ARG 52": "NH1" <-> "NH2" Residue "B ARG 63": "NH1" <-> "NH2" Residue "B ARG 80": "NH1" <-> "NH2" Residue "B ARG 167": "NH1" <-> "NH2" Residue "B ARG 177": "NH1" <-> "NH2" Residue "B ARG 182": "NH1" <-> "NH2" Residue "B ARG 212": "NH1" <-> "NH2" Residue "B ARG 269": "NH1" <-> "NH2" Residue "C ARG 13": "NH1" <-> "NH2" Residue "C ARG 33": "NH1" <-> "NH2" Residue "C ARG 59": "NH1" <-> "NH2" Residue "C ARG 77": "NH1" <-> "NH2" Residue "C ARG 83": "NH1" <-> "NH2" Residue "C ARG 169": "NH1" <-> "NH2" Residue "C ARG 184": "NH1" <-> "NH2" Residue "D ARG 21": "NH1" <-> "NH2" Residue "D ARG 44": "NH1" <-> "NH2" Residue "D ARG 49": "NH1" <-> "NH2" Residue "D ARG 102": "NH1" <-> "NH2" Residue "D ARG 162": "NH1" <-> "NH2" Residue "D ARG 170": "NH1" <-> "NH2" Residue "E ARG 30": "NH1" <-> "NH2" Residue "E ARG 71": "NH1" <-> "NH2" Residue "E ARG 92": "NH1" <-> "NH2" Residue "E ARG 102": "NH1" <-> "NH2" Residue "E ARG 110": "NH1" <-> "NH2" Residue "E ARG 112": "NH1" <-> "NH2" Residue "E ARG 115": "NH1" <-> "NH2" Residue "E ARG 148": "NH1" <-> "NH2" Residue "F ARG 3": "NH1" <-> "NH2" Residue "F ARG 152": "NH1" <-> "NH2" Residue "F ARG 153": "NH1" <-> "NH2" Residue "F ARG 163": "NH1" <-> "NH2" Residue "F ARG 170": "NH1" <-> "NH2" Residue "G ARG 50": "NH1" <-> "NH2" Residue "G ARG 51": "NH1" <-> "NH2" Residue "G ARG 68": "NH1" <-> "NH2" Residue "J ARG 13": "NH1" <-> "NH2" Residue "J ARG 34": "NH1" <-> "NH2" Residue "J ARG 37": "NH1" <-> "NH2" Residue "J ARG 95": "NH1" <-> "NH2" Residue "J ARG 96": "NH1" <-> "NH2" Residue "J ARG 120": "NH1" <-> "NH2" Residue "K ARG 17": "NH1" <-> "NH2" Residue "K ARG 18": "NH1" <-> "NH2" Residue "L ARG 21": "NH1" <-> "NH2" Residue "L ARG 33": "NH1" <-> "NH2" Residue "L ARG 41": "NH1" <-> "NH2" Residue "L ARG 47": "NH1" <-> "NH2" Residue "L ARG 60": "NH1" <-> "NH2" Residue "L ARG 78": "NH1" <-> "NH2" Residue "L ARG 123": "NH1" <-> "NH2" Residue "L ARG 126": "NH1" <-> "NH2" Residue "M ARG 10": "NH1" <-> "NH2" Residue "M ARG 18": "NH1" <-> "NH2" Residue "M ARG 40": "NH1" <-> "NH2" Residue "M ARG 50": "NH1" <-> "NH2" Residue "M ARG 55": "NH1" <-> "NH2" Residue "M ARG 114": "NH1" <-> "NH2" Residue "N ARG 8": "NH1" <-> "NH2" Residue "N ARG 12": "NH1" <-> "NH2" Residue "N ARG 17": "NH1" <-> "NH2" Residue "N ARG 22": "NH1" <-> "NH2" Residue "N ARG 46": "NH1" <-> "NH2" Residue "N ARG 63": "NH1" <-> "NH2" Residue "N ARG 64": "NH1" <-> "NH2" Residue "N ARG 69": "NH1" <-> "NH2" Residue "N ARG 96": "NH1" <-> "NH2" Residue "N ARG 118": "NH1" <-> "NH2" Residue "O ARG 10": "NH1" <-> "NH2" Residue "O ARG 13": "NH1" <-> "NH2" Residue "O ARG 16": "NH1" <-> "NH2" Residue "O ARG 25": "NH1" <-> "NH2" Residue "O ARG 81": "NH1" <-> "NH2" Residue "O ARG 94": "NH1" <-> "NH2" Residue "O ARG 102": "NH1" <-> "NH2" Residue "O ARG 111": "NH1" <-> "NH2" Residue "P 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" Residue "6 PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 146899 Number of models: 1 Model: "" Number of chains: 62 Chain: "1" Number of atoms: 62336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2903, 62336 Classifications: {'RNA': 2903} Modifications used: {'rna2p': 6, 'rna2p_pur': 289, 'rna2p_pyr': 165, 'rna3p': 16, 'rna3p_pur': 1378, 'rna3p_pyr': 1049} Link IDs: {'rna2p': 459, 'rna3p': 2443} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 9 Chain: "2" Number of atoms: 32929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1534, 32929 Classifications: {'RNA': 1534} Modifications used: {'rna2p': 1, 'rna2p_pur': 119, 'rna2p_pyr': 89, 'rna3p': 10, 'rna3p_pur': 750, 'rna3p_pyr': 564} Link IDs: {'rna2p': 208, 'rna3p': 1325} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 2 Chain: "3" Number of atoms: 2569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 2569 Classifications: {'RNA': 120} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 8, 'rna3p_pur': 57, 'rna3p_pyr': 48} Link IDs: {'rna2p': 14, 'rna3p': 105} Chain: "4" Number of atoms: 184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 184 Classifications: {'RNA': 9} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 1, 'rna3p_pyr': 6} Link IDs: {'rna2p': 1, 'rna3p': 7} Chain: "B" Number of atoms: 2082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2082 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 17, 'TRANS': 253} Chain: "C" Number of atoms: 1565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1565 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 202} Chain: "D" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1552 Classifications: {'peptide': 201} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 195} Chain: "E" Number of atoms: 1410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1410 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 6, 'TRANS': 170} Chain: "F" Number of atoms: 1313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1313 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 8, 'TRANS': 166} Chain: "G" Number of atoms: 1111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1111 Classifications: {'peptide': 149} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 145} Chain: "J" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1129 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 135} Chain: "K" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 946 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 5, 'TRANS': 117} Chain: "L" Number of atoms: 1053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1053 Classifications: {'peptide': 144} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 139} Chain: "M" Number of atoms: 1074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1074 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 128} Chain: "N" Number of atoms: 951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 951 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain: "O" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 892 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "P" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 917 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "Q" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 947 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'TRANS': 116} Chain: "R" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 816 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 101} Chain: "S" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 857 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 107} Chain: "T" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 746 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 1, 'TRANS': 92} Chain: "U" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 788 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 3, 'TRANS': 99} Chain: "V" Number of atoms: 753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 753 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "W" Number of atoms: 582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 582 Classifications: {'peptide': 76} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 74} Chain: "X" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 625 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "Y" Number of atoms: 501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 501 Classifications: {'peptide': 62} Modifications used: {'COO': 1} Link IDs: {'TRANS': 61} Chain: "Z" Number of atoms: 448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 448 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "a" Number of atoms: 522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 522 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "b" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 444 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 54} Chain: "c" Number of atoms: 426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 426 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 2, 'TRANS': 49} Chain: "d" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 377 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "e" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 504 Classifications: {'peptide': 64} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "f" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 302 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "g" Number of atoms: 1760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1760 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 7, 'TRANS': 217} Chain: "h" Number of atoms: 1636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1636 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 7, 'TRANS': 200} Chain: "i" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1643 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 198} Chain: "j" Number of atoms: 1152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1152 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 5, 'TRANS': 150} Chain: "k" Number of atoms: 848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 848 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "l" Number of atoms: 1181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1181 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain: "m" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 979 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "n" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1022 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "o" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 790 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 5, 'TRANS': 93} Chain: "p" Number of atoms: 877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 877 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 109} Chain: "q" Number of atoms: 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: {'rna2p': 2, 'rna2p_pur': 6, 'rna2p_pyr': 6, 'rna3p': 3, 'rna3p_pur': 34, 'rna3p_pyr': 25} Link IDs: {'rna2p': 13, 'rna3p': 62} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 3 Chain: "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: {'CIS': 1, 'PTRANS': 6, 'TRANS': 349} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "6" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "1" Number of atoms: 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 73.004 74.170 68.048 1.00247.56 S ATOM A0GDE SG CYS a 18 70.061 75.211 64.668 1.00253.50 S ATOM A0GHX SG CYS a 40 71.511 77.389 67.309 1.00237.13 S ATOM A0I2Y SG CYS f 11 139.053 164.625 58.827 1.00215.71 S ATOM A0I3N SG CYS f 14 141.859 162.487 59.317 1.00216.29 S ATOM A0I6I SG CYS f 27 141.447 167.118 59.830 1.00214.21 S Time building chain proxies: 50.25, per 1000 atoms: 0.34 Number of scatterers: 146899 At special positions: 0 Unit cell: (287.18, 270.58, 230.74, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 158 16.00 P 4642 15.00 Mg 12 11.99 O 40722 8.00 N 27343 7.00 C 74020 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: 71.27 Conformation dependent library (CDL) restraints added in 5.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN a 101 " pdb="ZN ZN a 101 " - pdb=" SG CYS a 18 " pdb="ZN ZN a 101 " - pdb=" SG CYS a 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: 11092 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 1350 base pairs and 2513 stacking pairs defined. Time for finding SS restraints: 65.21 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: 5.222A 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: 3.714A 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: 3.712A 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: 4.135A 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: 5.613A pdb=" N VAL B 268 " --> pdb=" O ASP B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 202 removed outlier: 3.697A 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: 3.647A 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: 4.213A 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: 3.704A pdb=" N VAL D 33 " --> pdb=" O HIS D 29 " (cutoff:3.500A) removed outlier: 5.891A 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: 3.797A pdb=" N LEU D 159 " --> pdb=" O GLU D 155 " (cutoff:3.500A) removed outlier: 4.178A 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: 3.830A 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: 3.755A 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: 4.321A 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: 3.606A 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: 3.848A 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: 3.606A 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: 4.756A 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: 3.725A pdb=" N ALA G 67 " --> pdb=" O ALA G 63 " (cutoff:3.500A) removed outlier: 4.474A 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: 5.277A 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: 3.758A 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: 3.836A pdb=" N PHE J 119 " --> pdb=" O GLY J 115 " (cutoff:3.500A) removed outlier: 3.856A 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: 5.323A 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: 3.540A 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: 3.915A 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: 3.772A pdb=" N LEU L 82 " --> pdb=" O ARG L 78 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ALA L 83 " --> pdb=" O LEU L 79 " (cutoff:3.500A) removed outlier: 4.475A 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: 3.835A pdb=" N ALA L 134 " --> pdb=" O GLY L 130 " (cutoff:3.500A) removed outlier: 3.790A 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: 4.141A pdb=" N ALA M 122 " --> pdb=" O LYS M 118 " (cutoff:3.500A) removed outlier: 4.137A 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: 3.588A pdb=" N ARG N 22 " --> pdb=" O GLN N 18 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ASN N 23 " --> pdb=" O ALA N 19 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL N 29 " --> pdb=" O ALA N 25 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N ARG N 30 " --> pdb=" O GLY N 26 " (cutoff:3.500A) Processing helix chain 'N' and resid 37 through 46 removed outlier: 4.566A 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: 4.035A 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: 3.612A pdb=" N PHE N 80 " --> pdb=" O VAL N 76 " (cutoff:3.500A) removed outlier: 4.263A 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: 4.799A 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: 5.680A 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: 3.950A 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: 4.981A 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: 3.574A 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: 4.141A 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: 3.616A pdb=" N TYR Q 47 " --> pdb=" O GLY Q 43 " (cutoff:3.500A) removed outlier: 3.537A 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: 3.799A 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: 3.512A 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: 4.700A pdb=" N ILE S 24 " --> pdb=" O VAL S 20 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ARG S 25 " --> pdb=" O ALA S 21 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 39 removed outlier: 3.811A pdb=" N ASP S 34 " --> pdb=" O SER S 30 " (cutoff:3.500A) removed outlier: 3.557A 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: 3.583A 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: 4.648A 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: 3.940A pdb=" N VAL U 70 " --> pdb=" O GLN U 66 " (cutoff:3.500A) removed outlier: 4.990A 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: 3.911A 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: 3.913A pdb=" N TYR V 57 " --> pdb=" O LYS V 53 " (cutoff:3.500A) Processing helix chain 'X' and resid 52 through 63 removed outlier: 3.600A pdb=" N VAL X 58 " --> pdb=" O LYS X 54 " (cutoff:3.500A) Processing helix chain 'X' and resid 64 through 75 removed outlier: 3.674A 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: 3.854A 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: 3.597A pdb=" N ARG Y 23 " --> pdb=" O LEU Y 19 " (cutoff:3.500A) removed outlier: 3.502A 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: 4.652A 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: 3.519A 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: 4.629A pdb=" N PHE a 64 " --> pdb=" O PHE a 60 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N ASN a 65 " --> pdb=" O ASN a 61 " (cutoff:3.500A) Processing helix chain 'b' and resid 9 through 21 removed outlier: 4.753A 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: 3.547A 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: 4.449A 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: 3.697A 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: 3.750A 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: 3.538A 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: 4.030A pdb=" N LYS g 81 " --> pdb=" O SER g 77 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU g 85 " --> pdb=" O LYS g 81 " (cutoff:3.500A) Processing helix chain 'g' and resid 103 through 121 removed outlier: 3.548A pdb=" N GLN g 109 " --> pdb=" O LYS g 105 " (cutoff:3.500A) Processing helix chain 'g' and resid 130 through 148 removed outlier: 4.098A pdb=" N LEU g 135 " --> pdb=" O LYS g 131 " (cutoff:3.500A) removed outlier: 4.012A 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: 3.657A 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: 4.385A 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: 3.507A 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: 3.601A 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: 4.830A 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: 4.092A 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: 3.542A pdb=" N GLU i 160 " --> pdb=" O LYS i 156 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N GLU i 166 " --> pdb=" O ALA i 162 " (cutoff:3.500A) Processing helix chain 'i' and resid 187 through 192 removed outlier: 4.628A 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: 3.540A 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: 3.667A 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: 5.618A pdb=" N GLU k 16 " --> pdb=" O PRO k 12 " (cutoff:3.500A) removed outlier: 6.445A 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: 3.572A 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: 4.957A 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: 3.738A 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: 3.790A pdb=" N ASN l 68 " --> pdb=" O VAL l 64 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N VAL l 69 " --> pdb=" O ALA l 65 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG l 70 " --> pdb=" O LEU l 66 " (cutoff:3.500A) Processing helix chain 'l' and resid 92 through 111 removed outlier: 3.979A pdb=" N ASN l 97 " --> pdb=" O PRO l 93 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA l 98 " --> pdb=" O VAL l 94 " (cutoff:3.500A) removed outlier: 3.560A 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: 3.578A 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: 4.243A 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: 4.630A 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: 4.156A 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: 5.075A pdb=" N GLU p 76 " --> pdb=" O ASP p 72 " (cutoff:3.500A) Processing helix chain 'p' and resid 94 through 104 removed outlier: 3.571A 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: 3.872A 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: 3.558A 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: 3.557A 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: 3.684A 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: 3.688A pdb=" N ILE s 30 " --> pdb=" O GLU s 26 " (cutoff:3.500A) Processing helix chain 's' and resid 37 through 52 removed outlier: 3.557A 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: 5.518A 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 50 through 74 removed outlier: 3.541A pdb=" N ARG t 54 " --> pdb=" O HIS t 50 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG t 64 " --> pdb=" O VAL t 60 " (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: 4.556A pdb=" N LEU t 70 " --> pdb=" O LEU t 66 " (cutoff:3.500A) removed outlier: 3.781A 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: 3.986A 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: 3.517A 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: 3.695A pdb=" N ARG w 61 " --> pdb=" O ARG w 57 " (cutoff:3.500A) removed outlier: 3.522A 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: 4.736A 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: 4.025A 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: 3.573A pdb=" N THR y 30 " --> pdb=" O SER y 26 " (cutoff:3.500A) removed outlier: 3.604A 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: 3.870A 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: 3.570A 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: 4.304A 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: 3.692A 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: 4.006A 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: 4.320A 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: 4.375A 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: 3.853A 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: 3.529A pdb=" N GLN A 72 " --> pdb=" O ASP A 68 " (cutoff:3.500A) removed outlier: 3.573A 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: 3.705A pdb=" N GLU A 107 " --> pdb=" O LEU A 103 " (cutoff:3.500A) removed outlier: 4.144A 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: 4.869A 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: 4.785A 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: 3.542A 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: 3.608A pdb=" N LEU A 239 " --> pdb=" O ASN A 235 " (cutoff:3.500A) removed outlier: 5.653A 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: 3.770A 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: 3.626A pdb=" N LYS A 302 " --> pdb=" O LEU A 298 " (cutoff:3.500A) removed outlier: 4.588A 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: 3.610A 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: 4.038A 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: 4.025A 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: 4.878A 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: 3.773A 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: 4.389A 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: 5.489A pdb=" N ASP C 200 " --> pdb=" O THR C 112 " (cutoff:3.500A) removed outlier: 4.170A 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: 6.479A 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: 5.473A 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: 5.543A 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: 3.663A 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: 5.796A 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: 3.827A 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: 6.533A 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: 4.031A 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: 8.544A 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: 3.697A 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: 4.524A 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: 3.833A 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: 4.383A 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: 5.360A 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: 4.342A 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: 6.624A 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: 3.636A pdb=" N SER X 19 " --> pdb=" O ASN X 23 " (cutoff:3.500A) removed outlier: 4.706A 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: 6.492A pdb=" N LEU c 34 " --> pdb=" O GLU c 51 " (cutoff:3.500A) removed outlier: 3.565A 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: 5.397A 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: 4.030A 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: 6.731A 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: 4.204A pdb=" N HIS k 3 " --> pdb=" O THR k 92 " (cutoff:3.500A) removed outlier: 3.522A 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: 4.685A pdb=" N ARG k 38 " --> pdb=" O ASN k 63 " (cutoff:3.500A) removed outlier: 4.968A 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: 7.346A 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: 5.604A 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: 4.173A pdb=" N TYR m 128 " --> pdb=" O GLN m 76 " (cutoff:3.500A) removed outlier: 6.823A 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: 3.795A 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: 4.221A pdb=" N ASN p 29 " --> pdb=" O SER p 26 " (cutoff:3.500A) removed outlier: 3.527A 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: 6.878A 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: 4.950A 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: 8.028A pdb=" N LYS A 177 " --> pdb=" O ALA A 134 " (cutoff:3.500A) removed outlier: 3.616A 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: 3.593A pdb=" N GLU A 225 " --> pdb=" O ASP A 127 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N PHE A 217 " --> pdb=" O GLY A 135 " (cutoff:3.500A) removed outlier: 4.137A 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: 3.743A 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 1817 hydrogen bonds defined for protein. 5361 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3194 hydrogen bonds 4354 hydrogen bond angles 0 basepair planarities 1350 basepair parallelities 2513 stacking parallelities Total time for adding SS restraints: 248.80 Time building geometry restraints manager: 76.35 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: 12187 1.29 - 1.42: 70673 1.42 - 1.55: 67045 1.55 - 1.69: 9290 1.69 - 1.82: 281 Bond restraints: 159476 Sorted by residual: bond pdb=" C5 5MU 11939 " pdb=" C6 5MU 11939 " ideal model delta sigma weight residual 1.155 1.438 -0.283 2.00e-02 2.50e+03 2.00e+02 bond pdb=" C5 5MU 1 747 " pdb=" C6 5MU 1 747 " ideal model delta sigma weight residual 1.155 1.434 -0.279 2.00e-02 2.50e+03 1.94e+02 bond pdb=" C5 5MU 5 54 " pdb=" C6 5MU 5 54 " ideal model delta sigma weight residual 1.155 1.433 -0.278 2.00e-02 2.50e+03 1.94e+02 bond pdb=" C4 5MU 5 54 " pdb=" C5 5MU 5 54 " ideal model delta sigma weight residual 1.802 1.602 0.200 2.00e-02 2.50e+03 9.97e+01 bond pdb=" C4 5MU 11939 " pdb=" C5 5MU 11939 " ideal model delta sigma weight residual 1.802 1.603 0.199 2.00e-02 2.50e+03 9.94e+01 ... (remaining 159471 not shown) Histogram of bond angle deviations from ideal: 98.59 - 106.76: 28716 106.76 - 114.94: 104288 114.94 - 123.12: 79567 123.12 - 131.30: 24397 131.30 - 139.48: 1318 Bond angle restraints: 238286 Sorted by residual: angle pdb=" C1' G7M 12069 " pdb=" N9 G7M 12069 " pdb=" C8 G7M 12069 " ideal model delta sigma weight residual 94.96 135.84 -40.88 3.00e+00 1.11e-01 1.86e+02 angle pdb=" C1' G7M 2 527 " pdb=" N9 G7M 2 527 " pdb=" C8 G7M 2 527 " ideal model delta sigma weight residual 94.96 127.57 -32.61 3.00e+00 1.11e-01 1.18e+02 angle pdb=" C1' G7M 12069 " pdb=" N9 G7M 12069 " pdb=" C4 G7M 12069 " ideal model delta sigma weight residual 142.80 115.89 26.91 3.00e+00 1.11e-01 8.04e+01 angle pdb=" N SER t 52 " pdb=" CA SER t 52 " pdb=" C SER t 52 " ideal model delta sigma weight residual 112.45 101.31 11.14 1.39e+00 5.18e-01 6.43e+01 angle pdb=" N VAL t 60 " pdb=" CA VAL t 60 " pdb=" C VAL t 60 " ideal model delta sigma weight residual 110.82 103.27 7.55 9.70e-01 1.06e+00 6.05e+01 ... (remaining 238281 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.95: 81104 35.95 - 71.90: 3777 71.90 - 107.85: 299 107.85 - 143.80: 12 143.80 - 179.75: 32 Dihedral angle restraints: 85224 sinusoidal: 68033 harmonic: 17191 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 31.57 168.43 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 39.54 160.46 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 43.90 156.10 1 1.50e+01 4.44e-03 8.17e+01 ... (remaining 85221 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.113: 29675 0.113 - 0.227: 597 0.227 - 0.340: 22 0.340 - 0.454: 2 0.454 - 0.567: 2 Chirality restraints: 30298 Sorted by residual: chirality pdb=" C3' A 1 404 " pdb=" C4' A 1 404 " pdb=" O3' A 1 404 " pdb=" C2' A 1 404 " both_signs ideal model delta sigma weight residual False -2.74 -2.18 -0.57 2.00e-01 2.50e+01 8.04e+00 chirality pdb=" CA HIS t 51 " pdb=" N HIS t 51 " pdb=" C HIS t 51 " pdb=" CB HIS t 51 " both_signs ideal model delta sigma weight residual False 2.51 1.97 0.54 2.00e-01 2.50e+01 7.26e+00 chirality pdb=" C3' U 1 894 " pdb=" C4' U 1 894 " pdb=" O3' U 1 894 " pdb=" C2' U 1 894 " both_signs ideal model delta sigma weight residual False -2.74 -2.37 -0.38 2.00e-01 2.50e+01 3.56e+00 ... (remaining 30295 not shown) Planarity restraints: 12969 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 " 0.176 2.00e-02 2.50e+03 pdb=" O2' 5MC 21407 " -0.980 2.00e-02 2.50e+03 pdb=" C1' 5MC 21407 " -0.225 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 " -0.224 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 " 0.519 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 12966 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 2353 2.53 - 3.12: 104340 3.12 - 3.72: 322561 3.72 - 4.31: 425212 4.31 - 4.90: 564262 Nonbonded interactions: 1418728 Sorted by model distance: 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 2.002 3.040 nonbonded pdb=" O4 U 3 65 " pdb="MG MG 3 204 " model vdw 2.032 2.170 nonbonded pdb=" O6 G 3 18 " pdb="MG MG 3 204 " model vdw 2.040 2.170 ... (remaining 1418723 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.760 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: 0.080 Extract box with map and model: 13.790 Check model and map are aligned: 1.600 Set scattering table: 0.980 Process input model: 562.920 Find NCS groups from input model: 2.980 Set up NCS constraints: 0.410 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.040 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 586.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8811 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 0.283 159476 Z= 0.407 Angle : 0.845 40.885 238286 Z= 0.440 Chirality : 0.043 0.567 30298 Planarity : 0.019 0.598 12969 Dihedral : 15.896 179.747 74132 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.98 % Favored : 94.91 % Rotamer Outliers : 0.28 % Cbeta Deviations : 0.04 % 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: -3.85 (0.09), residues: 5928 helix: -2.95 (0.08), residues: 1860 sheet: -2.42 (0.14), residues: 1128 loop : -2.24 (0.10), residues: 2940 *********************** 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 1913 residues out of total 4947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 1899 time to evaluate : 6.385 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 4 residues processed: 1911 average time/residue: 1.4225 time to fit residues: 4597.3035 Evaluate side-chains 1108 residues out of total 4947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1104 time to evaluate : 6.370 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 1.7268 time to fit residues: 17.3989 ------------------------------------------------------------------------------- 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: 6.9990 chunk 788 optimal weight: 7.9990 chunk 437 optimal weight: 20.0000 chunk 269 optimal weight: 20.0000 chunk 531 optimal weight: 7.9990 chunk 421 optimal weight: 30.0000 chunk 815 optimal weight: 10.0000 chunk 315 optimal weight: 20.0000 chunk 495 optimal weight: 6.9990 chunk 606 optimal weight: 30.0000 chunk 944 optimal weight: 0.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 37 ASN B 60 GLN B 86 ASN ** B 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 260 ASN C 130 GLN C 136 ASN ** C 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 30 GLN ** D 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 163 ASN ** F 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 116 GLN G 2 GLN ** G 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 33 GLN ** G 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 80 HIS ** J 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 104 GLN ** N 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 29 HIS O 38 GLN O 61 GLN O 100 HIS P 66 ASN ** P 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 56 GLN Q 72 ASN ** R 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 86 GLN S 7 HIS S 61 ASN T 70 HIS W 50 ASN X 34 HIS Y 15 ASN ** Y 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 5 GLN c 26 ASN e 26 HIS g 39 HIS g 177 ASN h 8 ASN h 139 GLN i 59 GLN ** i 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 164 GLN ** j 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 14 GLN k 17 GLN k 46 GLN ** k 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 28 ASN l 97 ASN m 67 GLN n 31 ASN o 35 GLN ** p 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 14 HIS s 43 ASN t 37 ASN t 50 HIS ** t 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 26 ASN ** x 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** y 3 ASN ** y 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 78 ASN A 43 GLN A 308 GLN A 313 ASN Total number of N/Q/H flips: 54 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8774 moved from start: 0.2290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.067 159476 Z= 0.238 Angle : 0.710 17.059 238286 Z= 0.370 Chirality : 0.036 0.290 30298 Planarity : 0.007 0.132 12969 Dihedral : 16.471 179.559 62248 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 25.38 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.72 % Favored : 95.23 % Rotamer Outliers : 3.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -2.55 (0.10), residues: 5928 helix: -1.13 (0.10), residues: 1995 sheet: -2.03 (0.14), residues: 1118 loop : -1.88 (0.11), residues: 2815 *********************** 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 1495 residues out of total 4947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 1333 time to evaluate : 6.438 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: 162 outliers final: 90 residues processed: 1423 average time/residue: 1.3838 time to fit residues: 3369.8919 Evaluate side-chains 1157 residues out of total 4947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 1067 time to evaluate : 6.273 Switching outliers to nearest non-outliers outliers start: 90 outliers final: 0 residues processed: 90 average time/residue: 1.1491 time to fit residues: 198.1192 ------------------------------------------------------------------------------- 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: 20.0000 chunk 293 optimal weight: 30.0000 chunk 786 optimal weight: 4.9990 chunk 643 optimal weight: 30.0000 chunk 260 optimal weight: 20.0000 chunk 946 optimal weight: 8.9990 chunk 1022 optimal weight: 8.9990 chunk 842 optimal weight: 5.9990 chunk 938 optimal weight: 20.0000 chunk 322 optimal weight: 20.0000 chunk 759 optimal weight: 7.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 33 GLN ** G 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 86 GLN J 131 ASN ** J 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 60 GLN ** N 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 115 ASN ** R 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 39 GLN ** Y 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 5 GLN f 35 GLN g 178 ASN ** i 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 148 ASN ** n 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 38 GLN ** p 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 119 ASN q 73 ASN r 8 ASN ** t 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 31 ASN ** x 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** y 48 GLN ** y 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 70 ASN A 38 ASN ** A 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 281 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8782 moved from start: 0.2942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.054 159476 Z= 0.251 Angle : 0.678 13.925 238286 Z= 0.359 Chirality : 0.035 0.323 30298 Planarity : 0.007 0.145 12969 Dihedral : 16.409 179.719 62248 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 26.97 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.15 % Favored : 94.84 % Rotamer Outliers : 3.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.53 % Twisted General : 0.02 % 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: -2.01 (0.10), residues: 5928 helix: -0.57 (0.11), residues: 2006 sheet: -1.68 (0.14), residues: 1147 loop : -1.68 (0.11), residues: 2775 *********************** 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 1383 residues out of total 4947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 1210 time to evaluate : 6.352 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 outliers start: 173 outliers final: 84 residues processed: 1286 average time/residue: 1.3859 time to fit residues: 3067.8848 Evaluate side-chains 1102 residues out of total 4947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 1018 time to evaluate : 6.368 Switching outliers to nearest non-outliers outliers start: 84 outliers final: 0 residues processed: 84 average time/residue: 1.2399 time to fit residues: 197.7838 ------------------------------------------------------------------------------- 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: 30.0000 chunk 711 optimal weight: 10.0000 chunk 491 optimal weight: 8.9990 chunk 104 optimal weight: 30.0000 chunk 451 optimal weight: 20.0000 chunk 635 optimal weight: 8.9990 chunk 949 optimal weight: 5.9990 chunk 1005 optimal weight: 5.9990 chunk 496 optimal weight: 6.9990 chunk 899 optimal weight: 20.0000 chunk 270 optimal weight: 20.0000 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 49 GLN ** C 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 81 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** L 54 GLN ** N 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 56 GLN T 48 GLN ** U 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 49 ASN V 75 GLN Y 27 ASN ** Y 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 20 ASN b 5 GLN ** g 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 32 ASN i 89 ASN ** i 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 97 ASN n 31 ASN ** n 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 75 GLN s 49 GLN ** t 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 70 ASN ** A 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 265 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8778 moved from start: 0.3258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.063 159476 Z= 0.245 Angle : 0.669 13.795 238286 Z= 0.354 Chirality : 0.034 0.321 30298 Planarity : 0.006 0.157 12969 Dihedral : 16.351 179.689 62248 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 27.82 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.99 % Favored : 94.97 % Rotamer Outliers : 2.81 % 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: -1.74 (0.10), residues: 5928 helix: -0.30 (0.11), residues: 2004 sheet: -1.52 (0.14), residues: 1133 loop : -1.57 (0.11), residues: 2791 *********************** 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 1266 residues out of total 4947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 1127 time to evaluate : 6.511 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 outliers start: 139 outliers final: 81 residues processed: 1189 average time/residue: 1.3387 time to fit residues: 2751.3371 Evaluate side-chains 1078 residues out of total 4947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 997 time to evaluate : 6.206 Switching outliers to nearest non-outliers outliers start: 81 outliers final: 0 residues processed: 81 average time/residue: 1.1180 time to fit residues: 178.3263 ------------------------------------------------------------------------------- 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: 20.0000 chunk 570 optimal weight: 7.9990 chunk 14 optimal weight: 30.0000 chunk 748 optimal weight: 20.0000 chunk 414 optimal weight: 20.0000 chunk 857 optimal weight: 0.5980 chunk 694 optimal weight: 30.0000 chunk 1 optimal weight: 20.0000 chunk 513 optimal weight: 8.9990 chunk 902 optimal weight: 20.0000 chunk 253 optimal weight: 20.0000 overall best weight: 11.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 22 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** ** P 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 48 GLN ** U 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 31 HIS h 3 GLN h 32 ASN ** h 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 35 GLN p 24 HIS ** p 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 75 GLN ** t 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 9 ASN ** A 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8804 moved from start: 0.3622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.091 159476 Z= 0.344 Angle : 0.731 14.325 238286 Z= 0.385 Chirality : 0.037 0.322 30298 Planarity : 0.007 0.164 12969 Dihedral : 16.578 179.573 62248 Min Nonbonded Distance : 1.782 Molprobity Statistics. All-atom Clashscore : 35.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer Outliers : 3.05 % Cbeta Deviations : 0.00 % 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: -1.84 (0.10), residues: 5928 helix: -0.43 (0.11), residues: 2024 sheet: -1.55 (0.14), residues: 1150 loop : -1.60 (0.11), residues: 2754 *********************** 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 1189 residues out of total 4947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 1038 time to evaluate : 6.508 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 outliers start: 151 outliers final: 97 residues processed: 1124 average time/residue: 1.3488 time to fit residues: 2624.6032 Evaluate side-chains 1036 residues out of total 4947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 939 time to evaluate : 6.309 Switching outliers to nearest non-outliers outliers start: 97 outliers final: 0 residues processed: 97 average time/residue: 1.1366 time to fit residues: 212.2299 ------------------------------------------------------------------------------- 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: 30.0000 chunk 905 optimal weight: 50.0000 chunk 198 optimal weight: 20.0000 chunk 590 optimal weight: 5.9990 chunk 248 optimal weight: 20.0000 chunk 1006 optimal weight: 2.9990 chunk 835 optimal weight: 20.0000 chunk 465 optimal weight: 5.9990 chunk 83 optimal weight: 20.0000 chunk 332 optimal weight: 30.0000 chunk 528 optimal weight: 8.9990 overall best weight: 8.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 167 ASN D 136 GLN ** E 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 22 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** ** K 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 48 GLN ** U 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 53 ASN ** X 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 5 GLN ** f 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 198 HIS ** j 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 46 GLN ** k 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 68 GLN l 97 ASN ** n 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 9 ASN A 54 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8791 moved from start: 0.3815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.073 159476 Z= 0.274 Angle : 0.686 13.764 238286 Z= 0.364 Chirality : 0.035 0.339 30298 Planarity : 0.006 0.149 12969 Dihedral : 16.505 178.771 62248 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 31.27 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.33 % Favored : 94.65 % Rotamer Outliers : 2.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.71 (0.10), residues: 5928 helix: -0.32 (0.11), residues: 2031 sheet: -1.43 (0.15), residues: 1117 loop : -1.55 (0.11), residues: 2780 *********************** 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 1155 residues out of total 4947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 1053 time to evaluate : 6.483 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 outliers start: 102 outliers final: 51 residues processed: 1101 average time/residue: 1.3311 time to fit residues: 2537.4743 Evaluate side-chains 1005 residues out of total 4947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 954 time to evaluate : 6.333 Switching outliers to nearest non-outliers outliers start: 51 outliers final: 0 residues processed: 51 average time/residue: 1.1905 time to fit residues: 116.3199 ------------------------------------------------------------------------------- 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: 10.0000 chunk 113 optimal weight: 20.0000 chunk 573 optimal weight: 10.0000 chunk 734 optimal weight: 0.8980 chunk 569 optimal weight: 10.0000 chunk 847 optimal weight: 20.0000 chunk 561 optimal weight: 9.9990 chunk 1002 optimal weight: 30.0000 chunk 627 optimal weight: 5.9990 chunk 611 optimal weight: 2.9990 chunk 462 optimal weight: 30.0000 overall best weight: 5.9790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 167 ASN ** C 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 22 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** L 104 GLN ** M 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 12 GLN ** Q 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 15 GLN S 40 ASN ** S 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 53 ASN ** U 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 8 ASN h 139 GLN ** i 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8774 moved from start: 0.3987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.074 159476 Z= 0.215 Angle : 0.661 14.886 238286 Z= 0.351 Chirality : 0.034 0.344 30298 Planarity : 0.006 0.127 12969 Dihedral : 16.354 179.054 62248 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 28.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer Outliers : 1.48 % Cbeta Deviations : 0.00 % 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: -1.53 (0.11), residues: 5928 helix: -0.19 (0.11), residues: 2035 sheet: -1.29 (0.15), residues: 1113 loop : -1.45 (0.11), residues: 2780 *********************** 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 1136 residues out of total 4947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 1063 time to evaluate : 6.476 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 outliers start: 73 outliers final: 46 residues processed: 1099 average time/residue: 1.3552 time to fit residues: 2575.9962 Evaluate side-chains 1009 residues out of total 4947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 963 time to evaluate : 6.339 Switching outliers to nearest non-outliers outliers start: 46 outliers final: 0 residues processed: 46 average time/residue: 1.0788 time to fit residues: 100.4574 ------------------------------------------------------------------------------- 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: 9.9990 chunk 400 optimal weight: 30.0000 chunk 598 optimal weight: 20.0000 chunk 301 optimal weight: 20.0000 chunk 196 optimal weight: 20.0000 chunk 194 optimal weight: 20.0000 chunk 637 optimal weight: 10.0000 chunk 682 optimal weight: 20.0000 chunk 495 optimal weight: 20.0000 chunk 93 optimal weight: 20.0000 chunk 787 optimal weight: 7.9990 overall best weight: 13.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 167 ASN ** C 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 52 ASN ** F 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 116 GLN ** G 43 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** ** K 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 19 GLN ** S 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 53 ASN V 5 ASN ** W 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 12 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** l 97 ASN ** m 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8812 moved from start: 0.4222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.091 159476 Z= 0.404 Angle : 0.787 13.788 238286 Z= 0.411 Chirality : 0.040 0.402 30298 Planarity : 0.007 0.130 12969 Dihedral : 16.703 178.378 62248 Min Nonbonded Distance : 1.767 Molprobity Statistics. All-atom Clashscore : 40.27 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.97 % Favored : 93.02 % Rotamer Outliers : 2.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.53 % Twisted General : 0.02 % 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: -0.57 (0.11), residues: 2054 sheet: -1.42 (0.15), residues: 1141 loop : -1.58 (0.11), residues: 2733 *********************** 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 1082 residues out of total 4947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 972 time to evaluate : 6.394 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: 110 outliers final: 71 residues processed: 1028 average time/residue: 1.4260 time to fit residues: 2551.6152 Evaluate side-chains 983 residues out of total 4947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 912 time to evaluate : 6.448 Switching outliers to nearest non-outliers outliers start: 71 outliers final: 0 residues processed: 71 average time/residue: 1.1658 time to fit residues: 162.4147 ------------------------------------------------------------------------------- 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: 6.9990 chunk 960 optimal weight: 7.9990 chunk 876 optimal weight: 8.9990 chunk 934 optimal weight: 30.0000 chunk 562 optimal weight: 40.0000 chunk 406 optimal weight: 20.0000 chunk 733 optimal weight: 5.9990 chunk 286 optimal weight: 20.0000 chunk 844 optimal weight: 0.9990 chunk 883 optimal weight: 10.0000 chunk 930 optimal weight: 9.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 32 ASN ** C 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 62 GLN ** D 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 22 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** ** K 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 60 HIS ** 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 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 42 HIS ** g 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 61 GLN ** j 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 63 ASN m 67 GLN ** p 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 70 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8780 moved from start: 0.4293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.061 159476 Z= 0.226 Angle : 0.691 14.353 238286 Z= 0.365 Chirality : 0.035 0.388 30298 Planarity : 0.006 0.127 12969 Dihedral : 16.479 179.546 62248 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 29.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer Outliers : 0.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.53 % Twisted General : 0.02 % 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 (0.10), residues: 5928 helix: -0.43 (0.11), residues: 2048 sheet: -1.31 (0.15), residues: 1137 loop : -1.50 (0.11), residues: 2743 *********************** 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 1069 residues out of total 4947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 1021 time to evaluate : 6.406 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 outliers start: 48 outliers final: 29 residues processed: 1040 average time/residue: 1.3540 time to fit residues: 2436.8540 Evaluate side-chains 969 residues out of total 4947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 940 time to evaluate : 6.293 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 0 residues processed: 29 average time/residue: 1.0352 time to fit residues: 64.5807 ------------------------------------------------------------------------------- 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: 5.9990 chunk 602 optimal weight: 50.0000 chunk 468 optimal weight: 7.9990 chunk 686 optimal weight: 6.9990 chunk 1036 optimal weight: 30.0000 chunk 953 optimal weight: 10.0000 chunk 825 optimal weight: 4.9990 chunk 85 optimal weight: 20.0000 chunk 637 optimal weight: 7.9990 chunk 505 optimal weight: 9.9990 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 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 243 HIS ** C 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 53 ASN ** W 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 52 ASN ** k 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 97 ASN ** p 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 38 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8775 moved from start: 0.4431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.063 159476 Z= 0.233 Angle : 0.696 17.088 238286 Z= 0.367 Chirality : 0.035 0.461 30298 Planarity : 0.006 0.126 12969 Dihedral : 16.389 179.798 62248 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 29.96 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.95 % Favored : 94.03 % Rotamer Outliers : 0.57 % Cbeta Deviations : 0.00 % 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: -1.66 (0.11), residues: 5928 helix: -0.45 (0.11), residues: 2056 sheet: -1.28 (0.15), residues: 1134 loop : -1.44 (0.12), residues: 2738 ********************** 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 1025 residues out of total 4947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 997 time to evaluate : 6.436 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: 28 outliers final: 16 residues processed: 1008 average time/residue: 1.3623 time to fit residues: 2381.8533 Evaluate side-chains 956 residues out of total 4947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 940 time to evaluate : 6.346 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 1.0678 time to fit residues: 39.3841 ------------------------------------------------------------------------------- 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: 7.9990 chunk 878 optimal weight: 0.7980 chunk 252 optimal weight: 20.0000 chunk 760 optimal weight: 20.0000 chunk 121 optimal weight: 20.0000 chunk 229 optimal weight: 30.0000 chunk 826 optimal weight: 6.9990 chunk 345 optimal weight: 20.0000 chunk 848 optimal weight: 7.9990 chunk 104 optimal weight: 30.0000 chunk 152 optimal weight: 20.0000 overall best weight: 8.7590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 243 HIS ** C 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 12 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** ** l 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 62 ASN ** u 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.029950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2660 r_free = 0.2660 target = 0.025099 restraints weight = 1659763.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2693 r_free = 0.2693 target = 0.025942 restraints weight = 622477.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2715 r_free = 0.2715 target = 0.026439 restraints weight = 336086.430| |-----------------------------------------------------------------------------| r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8803 moved from start: 0.4545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.074 159476 Z= 0.278 Angle : 0.718 15.771 238286 Z= 0.378 Chirality : 0.036 0.446 30298 Planarity : 0.006 0.127 12969 Dihedral : 16.445 179.973 62248 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 32.91 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.51 % Favored : 93.47 % Rotamer Outliers : 0.83 % Cbeta Deviations : 0.00 % 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: -1.71 (0.10), residues: 5928 helix: -0.51 (0.11), residues: 2053 sheet: -1.27 (0.15), residues: 1111 loop : -1.47 (0.11), residues: 2764 =============================================================================== Job complete usr+sys time: 38212.85 seconds wall clock time: 672 minutes 56.37 seconds (40376.37 seconds total)