Starting phenix.real_space_refine (version: dev) on Sat Apr 9 18:31:33 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6fyy_4328/04_2022/6fyy_4328_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6fyy_4328/04_2022/6fyy_4328.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6fyy_4328/04_2022/6fyy_4328_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6fyy_4328/04_2022/6fyy_4328_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6fyy_4328/04_2022/6fyy_4328_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6fyy_4328/04_2022/6fyy_4328.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6fyy_4328/04_2022/6fyy_4328.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6fyy_4328/04_2022/6fyy_4328_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6fyy_4328/04_2022/6fyy_4328_neut_updated.pdb" } resolution = 3.02 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= 0.037 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A GLU 12": "OE1" <-> "OE2" Residue "A GLU 34": "OE1" <-> "OE2" Residue "A ARG 41": "NH1" <-> "NH2" Residue "A GLU 55": "OE1" <-> "OE2" Residue "A GLU 71": "OE1" <-> "OE2" Residue "A GLU 117": "OE1" <-> "OE2" Residue "A GLU 135": "OE1" <-> "OE2" Residue "A GLU 208": "OE1" <-> "OE2" Residue "B GLU 28": "OE1" <-> "OE2" Residue "B GLU 39": "OE1" <-> "OE2" Residue "B GLU 77": "OE1" <-> "OE2" Residue "B GLU 90": "OE1" <-> "OE2" Residue "B GLU 170": "OE1" <-> "OE2" Residue "B GLU 175": "OE1" <-> "OE2" Residue "B GLU 191": "OE1" <-> "OE2" Residue "B GLU 196": "OE1" <-> "OE2" Residue "C GLU 60": "OE1" <-> "OE2" Residue "C GLU 70": "OE1" <-> "OE2" Residue "C GLU 125": "OE1" <-> "OE2" Residue "C ARG 131": "NH1" <-> "NH2" Residue "C GLU 199": "OE1" <-> "OE2" Residue "C GLU 213": "OE1" <-> "OE2" Residue "C GLU 236": "OE1" <-> "OE2" Residue "D GLU 23": "OE1" <-> "OE2" Residue "D ARG 27": "NH1" <-> "NH2" Residue "D GLU 28": "OE1" <-> "OE2" Residue "D GLU 38": "OE1" <-> "OE2" Residue "D ARG 40": "NH1" <-> "NH2" Residue "D GLU 61": "OE1" <-> "OE2" Residue "D GLU 68": "OE1" <-> "OE2" Residue "D ARG 81": "NH1" <-> "NH2" Residue "D GLU 89": "OE1" <-> "OE2" Residue "D GLU 103": "OE1" <-> "OE2" Residue "D ARG 124": "NH1" <-> "NH2" Residue "D GLU 128": "OE1" <-> "OE2" Residue "D ARG 143": "NH1" <-> "NH2" Residue "D GLU 169": "OE1" <-> "OE2" Residue "D GLU 210": "OE1" <-> "OE2" Residue "D GLU 213": "OE1" <-> "OE2" Residue "D GLU 215": "OE1" <-> "OE2" Residue "D GLU 219": "OE1" <-> "OE2" Residue "E GLU 40": "OE1" <-> "OE2" Residue "E ARG 59": "NH1" <-> "NH2" Residue "E GLU 60": "OE1" <-> "OE2" Residue "E GLU 93": "OE1" <-> "OE2" Residue "E GLU 117": "OE1" <-> "OE2" Residue "E GLU 118": "OE1" <-> "OE2" Residue "E GLU 202": "OE1" <-> "OE2" Residue "E GLU 230": "OE1" <-> "OE2" Residue "E GLU 251": "OE1" <-> "OE2" Residue "F GLU 26": "OE1" <-> "OE2" Residue "F GLU 34": "OE1" <-> "OE2" Residue "F GLU 41": "OE1" <-> "OE2" Residue "F GLU 51": "OE1" <-> "OE2" Residue "F GLU 54": "OE1" <-> "OE2" Residue "F ARG 114": "NH1" <-> "NH2" Residue "F ARG 158": "NH1" <-> "NH2" Residue "F GLU 183": "OE1" <-> "OE2" Residue "F GLU 194": "OE1" <-> "OE2" Residue "F GLU 199": "OE1" <-> "OE2" Residue "F GLU 218": "OE1" <-> "OE2" Residue "F ARG 221": "NH1" <-> "NH2" Residue "F ARG 227": "NH1" <-> "NH2" Residue "G GLU 17": "OE1" <-> "OE2" Residue "G GLU 21": "OE1" <-> "OE2" Residue "G GLU 35": "OE1" <-> "OE2" Residue "G GLU 44": "OE1" <-> "OE2" Residue "G GLU 91": "OE1" <-> "OE2" Residue "G GLU 118": "OE1" <-> "OE2" Residue "G GLU 120": "OE1" <-> "OE2" Residue "G GLU 150": "OE1" <-> "OE2" Residue "G GLU 161": "OE1" <-> "OE2" Residue "G GLU 203": "OE1" <-> "OE2" Residue "G GLU 207": "OE1" <-> "OE2" Residue "G GLU 222": "OE1" <-> "OE2" Residue "G GLU 225": "OE1" <-> "OE2" Residue "H GLU 15": "OE1" <-> "OE2" Residue "H GLU 28": "OE1" <-> "OE2" Residue "H GLU 33": "OE1" <-> "OE2" Residue "H GLU 48": "OE1" <-> "OE2" Residue "H GLU 50": "OE1" <-> "OE2" Residue "H GLU 82": "OE1" <-> "OE2" Residue "H ARG 107": "NH1" <-> "NH2" Residue "H GLU 134": "OE1" <-> "OE2" Residue "H GLU 184": "OE1" <-> "OE2" Residue "I ARG 74": "NH1" <-> "NH2" Residue "I ARG 92": "NH1" <-> "NH2" Residue "I GLU 141": "OE1" <-> "OE2" Residue "I GLU 150": "OE1" <-> "OE2" Residue "I GLU 186": "OE1" <-> "OE2" Residue "J ARG 6": "NH1" <-> "NH2" Residue "J GLU 20": "OE1" <-> "OE2" Residue "J GLU 64": "OE1" <-> "OE2" Residue "J ARG 69": "NH1" <-> "NH2" Residue "J ARG 82": "NH1" <-> "NH2" Residue "J GLU 88": "OE1" <-> "OE2" Residue "J PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 171": "NH1" <-> "NH2" Residue "J ARG 176": "NH1" <-> "NH2" Residue "J GLU 183": "OE1" <-> "OE2" Residue "K GLU 6": "OE1" <-> "OE2" Residue "K GLU 18": "OE1" <-> "OE2" Residue "K ARG 77": "NH1" <-> "NH2" Residue "K GLU 84": "OE1" <-> "OE2" Residue "L GLU 10": "OE1" <-> "OE2" Residue "L PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 50": "OE1" <-> "OE2" Residue "L GLU 101": "OE1" <-> "OE2" Residue "M GLU 18": "OE1" <-> "OE2" Residue "M GLU 40": "OE1" <-> "OE2" Residue "M GLU 49": "OE1" <-> "OE2" Residue "M GLU 57": "OE1" <-> "OE2" Residue "M GLU 61": "OE1" <-> "OE2" Residue "N GLU 83": "OE1" <-> "OE2" Residue "N GLU 86": "OE1" <-> "OE2" Residue "N GLU 142": "OE1" <-> "OE2" Residue "O GLU 37": "OE1" <-> "OE2" Residue "O GLU 116": "OE1" <-> "OE2" Residue "P GLU 51": "OE1" <-> "OE2" Residue "P GLU 69": "OE1" <-> "OE2" Residue "P GLU 71": "OE1" <-> "OE2" Residue "P GLU 106": "OE1" <-> "OE2" Residue "P ARG 108": "NH1" <-> "NH2" Residue "P GLU 110": "OE1" <-> "OE2" Residue "P GLU 118": "OE1" <-> "OE2" Residue "Q GLU 50": "OE1" <-> "OE2" Residue "R ARG 3": "NH1" <-> "NH2" Residue "R GLU 37": "OE1" <-> "OE2" Residue "R ARG 128": "NH1" <-> "NH2" Residue "S GLU 7": "OE1" <-> "OE2" Residue "S ARG 16": "NH1" <-> "NH2" Residue "S GLU 64": "OE1" <-> "OE2" Residue "S GLU 65": "OE1" <-> "OE2" Residue "S GLU 67": "OE1" <-> "OE2" Residue "S ARG 143": "NH1" <-> "NH2" Residue "S ARG 144": "NH1" <-> "NH2" Residue "T GLU 29": "OE1" <-> "OE2" Residue "T GLU 141": "OE1" <-> "OE2" Residue "T GLU 144": "OE1" <-> "OE2" Residue "U GLU 16": "OE1" <-> "OE2" Residue "U GLU 35": "OE1" <-> "OE2" Residue "U GLU 46": "OE1" <-> "OE2" Residue "U GLU 74": "OE1" <-> "OE2" Residue "U TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 109": "OE1" <-> "OE2" Residue "U GLU 115": "OE1" <-> "OE2" Residue "V GLU 2": "OE1" <-> "OE2" Residue "V GLU 41": "OE1" <-> "OE2" Residue "V GLU 42": "OE1" <-> "OE2" Residue "V ARG 62": "NH1" <-> "NH2" Residue "V GLU 64": "OE1" <-> "OE2" Residue "W ARG 23": "NH1" <-> "NH2" Residue "W GLU 51": "OE1" <-> "OE2" Residue "W GLU 87": "OE1" <-> "OE2" Residue "W ARG 97": "NH1" <-> "NH2" Residue "X GLU 26": "OE1" <-> "OE2" Residue "X GLU 98": "OE1" <-> "OE2" Residue "X GLU 138": "OE1" <-> "OE2" Residue "Y ARG 8": "NH1" <-> "NH2" Residue "Y GLU 39": "OE1" <-> "OE2" Residue "Y GLU 46": "OE1" <-> "OE2" Residue "Y GLU 86": "OE1" <-> "OE2" Residue "Y ARG 131": "NH1" <-> "NH2" Residue "Z ARG 68": "NH1" <-> "NH2" Residue "Z ARG 81": "NH1" <-> "NH2" Residue "a ARG 51": "NH1" <-> "NH2" Residue "a GLU 61": "OE1" <-> "OE2" Residue "a ARG 82": "NH1" <-> "NH2" Residue "a ARG 89": "NH1" <-> "NH2" Residue "b GLU 15": "OE1" <-> "OE2" Residue "b GLU 75": "OE1" <-> "OE2" Residue "c GLU 34": "OE1" <-> "OE2" Residue "c GLU 50": "OE1" <-> "OE2" Residue "c ARG 64": "NH1" <-> "NH2" Residue "c ARG 65": "NH1" <-> "NH2" Residue "d GLU 4": "OE1" <-> "OE2" Residue "d ARG 32": "NH1" <-> "NH2" Residue "e GLU 22": "OE1" <-> "OE2" Residue "e ARG 54": "NH1" <-> "NH2" Residue "f ARG 80": "NH1" <-> "NH2" Residue "f GLU 111": "OE1" <-> "OE2" Residue "g ARG 47": "NH1" <-> "NH2" Residue "g GLU 50": "OE1" <-> "OE2" Residue "g GLU 52": "OE1" <-> "OE2" Residue "g GLU 101": "OE1" <-> "OE2" Residue "g PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 280": "OE1" <-> "OE2" Residue "h ARG 15": "NH1" <-> "NH2" Residue "h ARG 17": "NH1" <-> "NH2" Residue "h ARG 18": "NH1" <-> "NH2" Residue "h ARG 21": "NH1" <-> "NH2" Residue "i ARG 13": "NH1" <-> "NH2" Residue "i ARG 14": "NH1" <-> "NH2" Residue "i GLU 31": "OE1" <-> "OE2" Residue "i GLU 34": "OE1" <-> "OE2" Residue "i ARG 62": "NH1" <-> "NH2" Residue "i GLU 99": "OE1" <-> "OE2" Residue "j GLU 10": "OE1" <-> "OE2" Residue "j GLU 15": "OE1" <-> "OE2" Residue "j GLU 29": "OE1" <-> "OE2" Residue "j GLU 43": "OE1" <-> "OE2" Residue "j ARG 53": "NH1" <-> "NH2" Residue "j ARG 64": "NH1" <-> "NH2" Residue "j ARG 88": "NH1" <-> "NH2" Residue "j GLU 93": "OE1" <-> "OE2" Residue "j GLU 100": "OE1" <-> "OE2" Residue "j GLU 117": "OE1" <-> "OE2" Residue "j GLU 125": "OE1" <-> "OE2" Residue "j GLU 152": "OE1" <-> "OE2" Residue "j GLU 159": "OE1" <-> "OE2" Residue "j GLU 168": "OE1" <-> "OE2" Residue "j GLU 209": "OE1" <-> "OE2" Residue "k GLU 222": "OE1" <-> "OE2" Residue "k GLU 231": "OE1" <-> "OE2" Residue "k GLU 383": "OE1" <-> "OE2" Residue "k GLU 494": "OE1" <-> "OE2" Residue "k GLU 506": "OE1" <-> "OE2" Residue "l GLU 189": "OE1" <-> "OE2" Residue "l GLU 249": "OE1" <-> "OE2" Residue "m ARG 7": "NH1" <-> "NH2" Residue "m ARG 28": "NH1" <-> "NH2" Residue "o GLU 9": "OE1" <-> "OE2" Residue "o GLU 61": "OE1" <-> "OE2" Residue "o GLU 176": "OE1" <-> "OE2" Residue "o TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o GLU 284": "OE1" <-> "OE2" Residue "o GLU 365": "OE1" <-> "OE2" Residue "o GLU 372": "OE1" <-> "OE2" Residue "o GLU 386": "OE1" <-> "OE2" Residue "o GLU 392": "OE1" <-> "OE2" Residue "p GLU 118": "OE1" <-> "OE2" Residue "p GLU 130": "OE1" <-> "OE2" Residue "p ARG 154": "NH1" <-> "NH2" Residue "p GLU 295": "OE1" <-> "OE2" Residue "p TYR 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p PHE 501": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q PHE 322": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q GLU 445": "OE1" <-> "OE2" Residue "q PHE 555": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q GLU 561": "OE1" <-> "OE2" Residue "q TYR 637": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q GLU 762": "OE1" <-> "OE2" Residue "r GLU 91": "OE1" <-> "OE2" Residue "s GLU 100": "OE1" <-> "OE2" Residue "s GLU 141": "OE1" <-> "OE2" Time to flip residues: 0.19s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 104316 Number of models: 1 Model: "" Number of chains: 54 Chain: "1" Number of atoms: 1639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1639 Unusual residues: {'RIA': 1} Classifications: {'undetermined': 1, 'RNA': 74} Modifications used: {'rna3p': 7, 'rna2p_pyr': 2, 'p5*END': 1, 'rna3p_pur': 27, 'rna2p': 3, 'rna3p_pyr': 28, 'rna2p_pur': 7} Link IDs: {'p': 1, None: 1, 'rna3p': 61, 'rna2p': 11} Not linked: pdbres=" G 1 63 " pdbres="RIA 1 64 " Chain breaks: 2 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 8 Chain: "2" Number of atoms: 37812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1780, 37812 Classifications: {'RNA': 1780} Modifications used: {'rna3p_pyr': 688, 'rna2p_pur': 145, 'rna3p_pur': 788, 'rna2p_pyr': 147, 'rna3p': 12} Link IDs: {'rna3p': 1487, 'rna2p': 292} Chain breaks: 2 Unresolved non-hydrogen bonds: 165 Unresolved non-hydrogen angles: 272 Unresolved non-hydrogen dihedrals: 116 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {' G%rna3p_pur:plan2': 5, ' C%rna3p_pyr:plan': 4, ' A%rna3p_pur:plan2': 4, ' U%rna3p_pyr:plan': 1, ' C%rna3p_pyr:plan2': 4, ' G%rna3p_pur:plan': 5, ' A%rna3p_pur:plan': 4} Unresolved non-hydrogen planarities: 161 Chain: "3" Number of atoms: 719 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 31, 639 Classifications: {'RNA': 31} Modifications used: {'rna3p_pyr': 19, 'rna2p_pur': 2, 'rna3p_pur': 7, 'rna2p_pyr': 3} Link IDs: {'rna3p': 25, 'rna2p': 5} Conformer: "B" Number of residues, atoms: 31, 639 Classifications: {'RNA': 31} Modifications used: {'rna3p_pyr': 19, 'rna2p_pur': 2, 'rna3p_pur': 7, 'rna2p_pyr': 3} Link IDs: {'rna3p': 25, 'rna2p': 5} bond proxies already assigned to first conformer: 621 Chain: "A" Number of atoms: 1702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1702 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 16, 'TRANS': 202} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 1797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1797 Classifications: {'peptide': 225} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 219} Chain breaks: 2 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'AYA:plan-2': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "C" Number of atoms: 1648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1648 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 12, 'TRANS': 207} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 1774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1774 Classifications: {'peptide': 227} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 217} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 2078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2078 Classifications: {'peptide': 260} Link IDs: {'PTRANS': 13, 'TRANS': 246} Chain: "F" Number of atoms: 1609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1609 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 7, 'TRANS': 198} Chain: "G" Number of atoms: 1832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1832 Classifications: {'peptide': 230} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 9, 'TRANS': 220} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'ARG:plan': 3} Unresolved non-hydrogen planarities: 15 Chain: "H" Number of atoms: 1483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1483 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 9, 'TRANS': 174} Chain: "I" Number of atoms: 1489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1489 Classifications: {'peptide': 188} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 183} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "J" Number of atoms: 1471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1471 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 7, 'TRANS': 174} Chain: "K" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 809 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 4, 'TRANS': 91} Chain: "L" Number of atoms: 1248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1248 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 8, 'TRANS': 146} Chain: "M" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 885 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 1, 'TRANS': 115} Chain breaks: 1 Chain: "N" Number of atoms: 1195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1195 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 7, 'TRANS': 143} Chain: "O" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 955 Classifications: {'peptide': 129} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 123} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "P" Number of atoms: 923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 923 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 108} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "Q" Number of atoms: 1105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1105 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 6, 'TRANS': 134} Chain: "R" Number of atoms: 1033 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1033 Classifications: {'peptide': 130} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 125} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "S" Number of atoms: 1189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1189 Classifications: {'peptide': 145} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 142} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "T" Number of atoms: 1110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1110 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 6, 'TRANS': 136} Chain: "U" Number of atoms: 845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 845 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "V" Number of atoms: 687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 687 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 2, 'TRANS': 84} Chain: "W" Number of atoms: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1021 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 3, 'TRANS': 125} Chain: "X" Number of atoms: 1119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1119 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 6, 'TRANS': 137} Chain: "Y" Number of atoms: 1061 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1061 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 3, 'TRANS': 130} Chain: "Z" Number of atoms: 594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 594 Classifications: {'peptide': 78} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 2, 'TRANS': 75} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "a" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 812 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 6, 'TRANS': 96} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 14 Chain: "b" Number of atoms: 609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 609 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 4, 'TRANS': 76} Chain: "c" Number of atoms: 499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 499 Classifications: {'peptide': 64} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 61} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "d" Number of atoms: 461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 461 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 1, 'TRANS': 53} Chain: "e" Number of atoms: 472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 472 Classifications: {'peptide': 60} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 54} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "f" Number of atoms: 584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 584 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 70} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "g" Number of atoms: 2469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2469 Classifications: {'peptide': 320} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 8, 'TRANS': 311} Chain breaks: 2 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "h" Number of atoms: 233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 233 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Chain: "i" Number of atoms: 958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 958 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 118} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "j" Number of atoms: 2006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 2006 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 6, 'TRANS': 242} Chain breaks: 2 Chain: "k" Number of atoms: 3034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 3034 Classifications: {'peptide': 396} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 375} Chain breaks: 3 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "l" Number of atoms: 1036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1036 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain breaks: 3 Chain: "m" Number of atoms: 1140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1140 Classifications: {'peptide': 147} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 10, 'TRANS': 136} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "o" Number of atoms: 4070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 4070 Classifications: {'peptide': 529} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PTRANS': 19, 'TRANS': 509} Chain breaks: 4 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 216 Unresolved non-hydrogen angles: 263 Unresolved non-hydrogen dihedrals: 177 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 12, 'ARG:plan': 11, 'ASN:plan1': 1, 'GLN:plan1': 3} Unresolved non-hydrogen planarities: 125 Chain: "p" Number of atoms: 5114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 647, 5114 Classifications: {'peptide': 647} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 34, 'TRANS': 612} Chain breaks: 4 Unresolved non-hydrogen bonds: 144 Unresolved non-hydrogen angles: 180 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 6, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 106 Chain: "q" Number of atoms: 4827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 621, 4827 Classifications: {'peptide': 621} Incomplete info: {'truncation_to_alanine': 77} Link IDs: {'PTRANS': 17, 'TRANS': 603} Chain breaks: 8 Unresolved non-hydrogen bonds: 154 Unresolved non-hydrogen angles: 231 Unresolved non-hydrogen dihedrals: 77 Planarities with less than four sites: {'UNK:plan-1': 77} Unresolved non-hydrogen planarities: 77 Chain: "r" Number of atoms: 392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 392 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} Chain: "s" Number of atoms: 2606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2606 Classifications: {'peptide': 330} Link IDs: {'PTRANS': 11, 'TRANS': 318} Chain breaks: 1 Chain: "2" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 116 Unusual residues: {' MG': 116} Classifications: {'undetermined': 116} Link IDs: {None: 115} Chain: "a" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "b" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' 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: "k" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 41 Unusual residues: {'GCP': 1, ' MG': 1} Classifications: {'undetermined': 2, 'peptide': 1} Link IDs: {None: 2} Chain: "l" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "m" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 73004 SG CYS a 23 156.089 97.522 146.141 1.00 54.13 S ATOM 73025 SG CYS a 26 158.613 97.892 143.309 1.00 55.37 S ATOM 73407 SG CYS a 74 155.431 99.470 143.078 1.00 45.56 S ATOM 73427 SG CYS a 77 155.768 95.810 142.673 1.00 48.38 S ATOM 74085 SG CYS b 59 140.147 136.192 203.611 1.00150.17 S ATOM 76059 SG CYS f 121 128.835 74.241 31.117 1.00174.10 S ATOM 76194 SG CYS f 139 130.722 75.787 33.653 1.00124.38 S ATOM 76213 SG CYS f 142 129.537 73.083 35.741 1.00133.92 S ATOM 85931 SG CYS l 259 215.927 94.494 88.203 1.00252.01 S Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" P A C 3 15 " occ=0.20 ... (38 atoms not shown) pdb=" C6 B C 3 15 " occ=0.80 residue: pdb=" P A U 3 16 " occ=0.20 ... (38 atoms not shown) pdb=" C6 B U 3 16 " occ=0.80 residue: pdb=" P A C 3 17 " occ=0.20 ... (38 atoms not shown) pdb=" C6 B C 3 17 " occ=0.80 residue: pdb=" P A U 3 18 " occ=0.20 ... (38 atoms not shown) pdb=" C6 B U 3 18 " occ=0.80 Time building chain proxies: 45.28, per 1000 atoms: 0.43 Number of scatterers: 104316 At special positions: 0 Unit cell: (269.34, 261.3, 266.66, 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 5 29.99 S 169 16.00 P 1894 15.00 Mg 117 11.99 O 24938 8.00 N 18685 7.00 C 58508 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 Atom "ATOM 39498 O4'A U 3 16 .*. O " rejected from bonding due to valence issues. Atom "ATOM 39498 O4'A U 3 16 .*. O " rejected from bonding due to valence issues. Atom "ATOM 39498 O4'A U 3 16 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 38.33 Conformation dependent library (CDL) restraints added in 8.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination Zn2+ tetrahedral coordination pdb=" ZN a 500 " pdb="ZN ZN a 500 " - pdb=" SG CYS a 26 " pdb="ZN ZN a 500 " - pdb=" SG CYS a 77 " pdb="ZN ZN a 500 " - pdb=" SG CYS a 23 " pdb="ZN ZN a 500 " - pdb=" SG CYS a 74 " pdb=" ZN b 101 " pdb="ZN ZN b 101 " - pdb=" SG CYS b 59 " pdb=" ZN f 501 " pdb="ZN ZN f 501 " - pdb=" SG CYS f 142 " pdb="ZN ZN f 501 " - pdb=" SG CYS f 121 " pdb="ZN ZN f 501 " - pdb=" SG CYS f 139 " pdb=" ZN l 301 " pdb="ZN ZN l 301 " - pdb=" SG CYS l 259 " Number of angles added : 6 15856 Ramachandran restraints generated. 7928 Oldfield, 0 Emsley, 7928 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15290 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: 243 helices and 96 sheets defined 40.2% alpha, 18.9% beta 526 base pairs and 940 stacking pairs defined. Time for finding SS restraints: 46.47 Creating SS restraints... Processing helix chain 'A' and resid 10 through 21 Processing helix chain 'A' and resid 49 through 68 Proline residue: A 68 - end of helix Processing helix chain 'A' and resid 79 through 93 removed outlier: 4.016A pdb=" N GLN A 83 " --> pdb=" O ARG A 79 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N ARG A 84 " --> pdb=" O THR A 80 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N ALA A 85 " --> pdb=" O TYR A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 130 Processing helix chain 'A' and resid 131 through 140 Processing helix chain 'A' and resid 166 through 186 removed outlier: 5.627A pdb=" N ILE A 170 " --> pdb=" O GLY A 166 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLY A 171 " --> pdb=" O LYS A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 204 removed outlier: 4.619A pdb=" N TYR A 202 " --> pdb=" O MET A 198 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N PHE A 203 " --> pdb=" O PRO A 199 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N TYR A 204 " --> pdb=" O ASP A 200 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 198 through 204' Processing helix chain 'A' and resid 206 through 220 removed outlier: 4.582A pdb=" N ILE A 210 " --> pdb=" O ASN A 206 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N VAL A 220 " --> pdb=" O GLU A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 74 removed outlier: 3.558A pdb=" N VAL A 73 " --> pdb=" O PRO A 70 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N VAL A 74 " --> pdb=" O GLU A 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 28 removed outlier: 4.114A pdb=" N ARG B 26 " --> pdb=" O ASP B 22 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N LYS B 27 " --> pdb=" O PRO B 23 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N GLU B 28 " --> pdb=" O PHE B 24 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 22 through 28' Processing helix chain 'B' and resid 56 through 63 removed outlier: 5.178A pdb=" N GLY B 63 " --> pdb=" O ASP B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 75 removed outlier: 3.709A pdb=" N LEU B 73 " --> pdb=" O CYS B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 81 removed outlier: 4.555A pdb=" N SER B 80 " --> pdb=" O SER B 76 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N PHE B 81 " --> pdb=" O GLU B 77 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 76 through 81' Processing helix chain 'B' and resid 106 through 115 removed outlier: 4.690A pdb=" N ARG B 115 " --> pdb=" O ARG B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 179 removed outlier: 3.624A pdb=" N ASN B 178 " --> pdb=" O ARG B 174 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N SER B 179 " --> pdb=" O GLU B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 191 Proline residue: B 190 - end of helix Processing helix chain 'B' and resid 192 through 203 removed outlier: 4.838A pdb=" N ASP B 203 " --> pdb=" O ASN B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 233 removed outlier: 4.779A pdb=" N GLY B 233 " --> pdb=" O LEU B 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 53 Processing helix chain 'C' and resid 57 through 65 removed outlier: 3.979A pdb=" N ILE C 61 " --> pdb=" O SER C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 79 removed outlier: 4.315A pdb=" N ILE C 74 " --> pdb=" O GLU C 70 " (cutoff:3.500A) Proline residue: C 79 - end of helix Processing helix chain 'C' and resid 125 through 141 Processing helix chain 'C' and resid 186 through 197 Processing helix chain 'C' and resid 211 through 229 removed outlier: 4.249A pdb=" N TYR C 227 " --> pdb=" O ILE C 223 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLY C 228 " --> pdb=" O GLY C 224 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N PHE C 229 " --> pdb=" O ASN C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 236 removed outlier: 3.751A pdb=" N TRP C 235 " --> pdb=" O THR C 231 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N GLU C 236 " --> pdb=" O PRO C 232 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 231 through 236' Processing helix chain 'C' and resid 243 through 249 removed outlier: 3.594A pdb=" N ALA C 249 " --> pdb=" O MET C 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 6 through 29 Processing helix chain 'D' and resid 54 through 60 Processing helix chain 'D' and resid 63 through 78 removed outlier: 3.945A pdb=" N ASN D 67 " --> pdb=" O GLY D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 98 removed outlier: 3.712A pdb=" N SER D 97 " --> pdb=" O ASP D 93 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N ALA D 98 " --> pdb=" O ARG D 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 93 through 98' Processing helix chain 'D' and resid 99 through 112 Processing helix chain 'D' and resid 114 through 130 Processing helix chain 'D' and resid 161 through 167 removed outlier: 4.516A pdb=" N ASN D 165 " --> pdb=" O GLY D 161 " (cutoff:3.500A) Processing helix chain 'E' and resid 10 through 15 Proline residue: E 15 - end of helix Processing helix chain 'E' and resid 43 through 50 Processing helix chain 'E' and resid 57 through 68 removed outlier: 3.813A pdb=" N ARG E 68 " --> pdb=" O ILE E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 115 through 122 removed outlier: 4.645A pdb=" N TYR E 121 " --> pdb=" O GLU E 117 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N LYS E 122 " --> pdb=" O GLU E 118 " (cutoff:3.500A) Processing helix chain 'E' and resid 221 through 226 removed outlier: 5.395A pdb=" N PHE E 226 " --> pdb=" O LEU E 222 " (cutoff:3.500A) Processing helix chain 'E' and resid 247 through 259 removed outlier: 4.119A pdb=" N HIS E 259 " --> pdb=" O ARG E 255 " (cutoff:3.500A) Processing helix chain 'F' and resid 32 through 37 Processing helix chain 'F' and resid 49 through 54 removed outlier: 4.869A pdb=" N VAL F 53 " --> pdb=" O SER F 49 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N GLU F 54 " --> pdb=" O PHE F 50 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 49 through 54' Processing helix chain 'F' and resid 84 through 90 removed outlier: 4.345A pdb=" N GLN F 88 " --> pdb=" O PHE F 84 " (cutoff:3.500A) Proline residue: F 90 - end of helix Processing helix chain 'F' and resid 91 through 101 removed outlier: 4.939A pdb=" N MET F 101 " --> pdb=" O ASN F 97 " (cutoff:3.500A) Processing helix chain 'F' and resid 108 through 127 removed outlier: 4.248A pdb=" N THR F 127 " --> pdb=" O ILE F 123 " (cutoff:3.500A) Processing helix chain 'F' and resid 130 through 143 removed outlier: 3.534A pdb=" N GLY F 143 " --> pdb=" O ILE F 139 " (cutoff:3.500A) Processing helix chain 'F' and resid 165 through 186 Processing helix chain 'F' and resid 191 through 206 removed outlier: 3.779A pdb=" N GLY F 206 " --> pdb=" O ASN F 202 " (cutoff:3.500A) Processing helix chain 'F' and resid 210 through 227 Processing helix chain 'G' and resid 20 through 29 removed outlier: 3.946A pdb=" N VAL G 24 " --> pdb=" O ASP G 20 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N VAL G 26 " --> pdb=" O HIS G 22 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N PHE G 27 " --> pdb=" O ARG G 23 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N TYR G 28 " --> pdb=" O VAL G 24 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N ASP G 29 " --> pdb=" O ARG G 25 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 146 Processing helix chain 'G' and resid 152 through 157 removed outlier: 5.150A pdb=" N TYR G 156 " --> pdb=" O ASP G 152 " (cutoff:3.500A) Processing helix chain 'G' and resid 180 through 230 Processing helix chain 'H' and resid 4 through 10 removed outlier: 4.052A pdb=" N ILE H 8 " --> pdb=" O PRO H 4 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU H 9 " --> pdb=" O GLN H 5 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N SER H 10 " --> pdb=" O ALA H 6 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 4 through 10' Processing helix chain 'H' and resid 14 through 31 removed outlier: 3.569A pdb=" N ASN H 30 " --> pdb=" O ASP H 26 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N SER H 31 " --> pdb=" O LEU H 27 " (cutoff:3.500A) Processing helix chain 'H' and resid 35 through 41 removed outlier: 5.841A pdb=" N ARG H 39 " --> pdb=" O LYS H 35 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N ALA H 40 " --> pdb=" O ALA H 36 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N LEU H 41 " --> pdb=" O ASP H 37 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 35 through 41' Processing helix chain 'H' and resid 63 through 74 removed outlier: 6.867A pdb=" N LEU H 67 " --> pdb=" O PRO H 63 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N ALA H 68 " --> pdb=" O VAL H 64 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N ALA H 69 " --> pdb=" O PRO H 65 " (cutoff:3.500A) Processing helix chain 'H' and resid 75 through 86 removed outlier: 3.678A pdb=" N GLN H 86 " --> pdb=" O GLU H 82 " (cutoff:3.500A) Processing helix chain 'H' and resid 113 through 118 removed outlier: 3.675A pdb=" N THR H 117 " --> pdb=" O PRO H 113 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N LEU H 118 " --> pdb=" O ARG H 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 113 through 118' Processing helix chain 'H' and resid 119 through 131 removed outlier: 3.841A pdb=" N PHE H 131 " --> pdb=" O GLU H 127 " (cutoff:3.500A) Processing helix chain 'H' and resid 164 through 177 removed outlier: 4.660A pdb=" N SER H 168 " --> pdb=" O ASN H 164 " (cutoff:3.500A) Processing helix chain 'I' and resid 6 through 11 removed outlier: 4.953A pdb=" N LYS I 10 " --> pdb=" O ASP I 6 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N ARG I 11 " --> pdb=" O SER I 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 6 through 11' Processing helix chain 'I' and resid 87 through 94 removed outlier: 3.680A pdb=" N VAL I 91 " --> pdb=" O ASN I 87 " (cutoff:3.500A) Processing helix chain 'I' and resid 106 through 117 Processing helix chain 'I' and resid 137 through 148 removed outlier: 3.711A pdb=" N GLU I 141 " --> pdb=" O SER I 137 " (cutoff:3.500A) Processing helix chain 'I' and resid 154 through 164 removed outlier: 3.526A pdb=" N ASP I 158 " --> pdb=" O GLU I 154 " (cutoff:3.500A) Processing helix chain 'I' and resid 187 through 201 removed outlier: 3.603A pdb=" N ALA I 191 " --> pdb=" O GLY I 187 " (cutoff:3.500A) Processing helix chain 'J' and resid 20 through 35 Processing helix chain 'J' and resid 38 through 63 removed outlier: 4.147A pdb=" N ILE J 42 " --> pdb=" O ASN J 38 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N ASP J 63 " --> pdb=" O LEU J 59 " (cutoff:3.500A) Processing helix chain 'J' and resid 66 through 84 removed outlier: 3.627A pdb=" N ASN J 74 " --> pdb=" O LEU J 70 " (cutoff:3.500A) Processing helix chain 'J' and resid 92 through 99 removed outlier: 6.459A pdb=" N VAL J 96 " --> pdb=" O LYS J 92 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LEU J 97 " --> pdb=" O LEU J 93 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ALA J 98 " --> pdb=" O ASP J 94 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N LEU J 99 " --> pdb=" O TYR J 95 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 92 through 99' Processing helix chain 'J' and resid 100 through 109 removed outlier: 4.171A pdb=" N PHE J 104 " --> pdb=" O LYS J 100 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N LEU J 109 " --> pdb=" O LEU J 105 " (cutoff:3.500A) Processing helix chain 'J' and resid 110 through 117 removed outlier: 3.695A pdb=" N GLY J 117 " --> pdb=" O VAL J 113 " (cutoff:3.500A) Processing helix chain 'J' and resid 121 through 132 Processing helix chain 'J' and resid 149 through 154 removed outlier: 4.769A pdb=" N LYS J 154 " --> pdb=" O LEU J 150 " (cutoff:3.500A) Processing helix chain 'J' and resid 170 through 183 removed outlier: 4.644A pdb=" N ARG J 174 " --> pdb=" O GLY J 170 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU J 183 " --> pdb=" O ALA J 179 " (cutoff:3.500A) Processing helix chain 'K' and resid 4 through 19 Processing helix chain 'K' and resid 38 through 53 Processing helix chain 'K' and resid 69 through 81 Processing helix chain 'K' and resid 88 through 93 removed outlier: 3.759A pdb=" N LEU K 92 " --> pdb=" O PRO K 88 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N ALA K 93 " --> pdb=" O ALA K 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 88 through 93' Processing helix chain 'L' and resid 45 through 51 Processing helix chain 'M' and resid 18 through 32 removed outlier: 4.512A pdb=" N LYS M 22 " --> pdb=" O GLU M 18 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N VAL M 23 " --> pdb=" O ASP M 19 " (cutoff:3.500A) Processing helix chain 'M' and resid 37 through 48 removed outlier: 5.819A pdb=" N SER M 41 " --> pdb=" O GLY M 37 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N GLY M 48 " --> pdb=" O ALA M 44 " (cutoff:3.500A) Processing helix chain 'M' and resid 62 through 74 Processing helix chain 'M' and resid 84 through 93 Processing helix chain 'M' and resid 123 through 132 removed outlier: 4.242A pdb=" N LEU M 127 " --> pdb=" O GLU M 123 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LEU M 128 " --> pdb=" O ARG M 124 " (cutoff:3.500A) Processing helix chain 'N' and resid 29 through 44 Processing helix chain 'N' and resid 46 through 57 Processing helix chain 'N' and resid 62 through 67 Processing helix chain 'N' and resid 70 through 79 Processing helix chain 'N' and resid 85 through 106 Processing helix chain 'N' and resid 108 through 133 Processing helix chain 'N' and resid 143 through 151 Processing helix chain 'O' and resid 43 through 49 removed outlier: 4.228A pdb=" N LYS O 47 " --> pdb=" O THR O 43 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N VAL O 48 " --> pdb=" O GLY O 44 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N LYS O 49 " --> pdb=" O GLY O 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 43 through 49' Processing helix chain 'O' and resid 50 through 55 removed outlier: 6.925A pdb=" N GLU O 54 " --> pdb=" O ALA O 50 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N SER O 55 " --> pdb=" O ASP O 51 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 50 through 55' Processing helix chain 'O' and resid 56 through 75 Processing helix chain 'O' and resid 95 through 109 removed outlier: 4.564A pdb=" N GLN O 99 " --> pdb=" O GLY O 95 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ALA O 100 " --> pdb=" O PRO O 96 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N GLY O 109 " --> pdb=" O LEU O 105 " (cutoff:3.500A) Processing helix chain 'P' and resid 21 through 28 removed outlier: 3.951A pdb=" N GLU P 27 " --> pdb=" O GLU P 23 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N MET P 28 " --> pdb=" O LYS P 24 " (cutoff:3.500A) Processing helix chain 'P' and resid 29 through 37 Processing helix chain 'P' and resid 38 through 48 removed outlier: 3.928A pdb=" N GLY P 48 " --> pdb=" O LYS P 44 " (cutoff:3.500A) Processing helix chain 'P' and resid 50 through 67 removed outlier: 4.129A pdb=" N ALA P 54 " --> pdb=" O SER P 50 " (cutoff:3.500A) Processing helix chain 'P' and resid 115 through 121 removed outlier: 4.426A pdb=" N PHE P 119 " --> pdb=" O TYR P 115 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N SER P 120 " --> pdb=" O LEU P 116 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N ILE P 121 " --> pdb=" O GLY P 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 115 through 121' Processing helix chain 'Q' and resid 41 through 56 removed outlier: 5.613A pdb=" N ARG Q 45 " --> pdb=" O PRO Q 41 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N PHE Q 46 " --> pdb=" O GLU Q 42 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N LYS Q 47 " --> pdb=" O ILE Q 43 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL Q 48 " --> pdb=" O LEU Q 44 " (cutoff:3.500A) Proline residue: Q 51 - end of helix Processing helix chain 'Q' and resid 74 through 96 Processing helix chain 'Q' and resid 98 through 113 removed outlier: 3.733A pdb=" N TYR Q 112 " --> pdb=" O ALA Q 108 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ASP Q 113 " --> pdb=" O PHE Q 109 " (cutoff:3.500A) Processing helix chain 'R' and resid 6 through 20 Processing helix chain 'R' and resid 27 through 38 removed outlier: 3.597A pdb=" N ASN R 31 " --> pdb=" O ASP R 27 " (cutoff:3.500A) Processing helix chain 'R' and resid 43 through 64 Processing helix chain 'R' and resid 71 through 85 removed outlier: 5.687A pdb=" N VAL R 85 " --> pdb=" O LYS R 81 " (cutoff:3.500A) Processing helix chain 'R' and resid 103 through 114 Processing helix chain 'S' and resid 27 through 36 removed outlier: 3.589A pdb=" N THR S 34 " --> pdb=" O TYR S 30 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ILE S 35 " --> pdb=" O ALA S 31 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N ARG S 36 " --> pdb=" O LEU S 32 " (cutoff:3.500A) Processing helix chain 'S' and resid 39 through 51 Processing helix chain 'S' and resid 62 through 76 Proline residue: S 76 - end of helix Processing helix chain 'S' and resid 102 through 120 removed outlier: 3.874A pdb=" N GLU S 106 " --> pdb=" O ALA S 102 " (cutoff:3.500A) Processing helix chain 'S' and resid 121 through 130 Processing helix chain 'T' and resid 5 through 10 removed outlier: 4.040A pdb=" N VAL T 9 " --> pdb=" O SER T 5 " (cutoff:3.500A) Proline residue: T 10 - end of helix No H-bonds generated for 'chain 'T' and resid 5 through 10' Processing helix chain 'T' and resid 11 through 26 removed outlier: 4.848A pdb=" N GLY T 26 " --> pdb=" O LEU T 22 " (cutoff:3.500A) Processing helix chain 'T' and resid 52 through 69 removed outlier: 4.702A pdb=" N LYS T 69 " --> pdb=" O ILE T 65 " (cutoff:3.500A) Processing helix chain 'T' and resid 72 through 81 removed outlier: 4.518A pdb=" N GLY T 81 " --> pdb=" O ASN T 77 " (cutoff:3.500A) Processing helix chain 'T' and resid 97 through 112 removed outlier: 3.643A pdb=" N ASN T 101 " --> pdb=" O SER T 97 " (cutoff:3.500A) Processing helix chain 'T' and resid 125 through 144 Processing helix chain 'U' and resid 30 through 49 removed outlier: 3.948A pdb=" N LEU U 34 " --> pdb=" O LYS U 30 " (cutoff:3.500A) Processing helix chain 'U' and resid 96 through 107 removed outlier: 5.828A pdb=" N VAL U 100 " --> pdb=" O PRO U 96 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N THR U 107 " --> pdb=" O ILE U 103 " (cutoff:3.500A) Processing helix chain 'V' and resid 56 through 63 removed outlier: 3.552A pdb=" N ARG V 60 " --> pdb=" O SER V 56 " (cutoff:3.500A) Processing helix chain 'V' and resid 64 through 77 Processing helix chain 'W' and resid 5 through 21 Processing helix chain 'W' and resid 31 through 45 Processing helix chain 'W' and resid 83 through 94 removed outlier: 4.459A pdb=" N GLU W 87 " --> pdb=" O ILE W 83 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N LYS W 88 " --> pdb=" O ALA W 84 " (cutoff:3.500A) Processing helix chain 'W' and resid 112 through 120 Processing helix chain 'X' and resid 11 through 27 removed outlier: 3.774A pdb=" N TRP X 24 " --> pdb=" O ARG X 20 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N ALA X 25 " --> pdb=" O ASN X 21 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLU X 26 " --> pdb=" O ASN X 22 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N THR X 27 " --> pdb=" O ARG X 23 " (cutoff:3.500A) Processing helix chain 'X' and resid 28 through 35 Processing helix chain 'X' and resid 91 through 97 removed outlier: 3.917A pdb=" N PHE X 95 " --> pdb=" O GLY X 91 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL X 96 " --> pdb=" O CYS X 92 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ASP X 97 " --> pdb=" O LEU X 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 91 through 97' Processing helix chain 'X' and resid 131 through 138 Processing helix chain 'X' and resid 36 through 41 removed outlier: 3.847A pdb=" N SER X 41 " --> pdb=" O THR X 36 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 36 through 41' Processing helix chain 'Y' and resid 36 through 49 Processing helix chain 'Y' and resid 51 through 56 removed outlier: 5.273A pdb=" N SER Y 56 " --> pdb=" O LYS Y 52 " (cutoff:3.500A) Processing helix chain 'Y' and resid 78 through 86 Processing helix chain 'Y' and resid 87 through 95 Processing helix chain 'Y' and resid 104 through 119 removed outlier: 4.818A pdb=" N PHE Y 119 " --> pdb=" O GLY Y 115 " (cutoff:3.500A) Processing helix chain 'Y' and resid 122 through 135 removed outlier: 3.506A pdb=" N ALA Y 126 " --> pdb=" O GLY Y 122 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N LYS Y 127 " --> pdb=" O LYS Y 123 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N LYS Y 128 " --> pdb=" O SER Y 124 " (cutoff:3.500A) Processing helix chain 'Z' and resid 43 through 54 Processing helix chain 'Z' and resid 61 through 69 removed outlier: 3.507A pdb=" N ARG Z 68 " --> pdb=" O VAL Z 64 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N PHE Z 69 " --> pdb=" O LEU Z 65 " (cutoff:3.500A) Processing helix chain 'Z' and resid 72 through 85 removed outlier: 5.909A pdb=" N ALA Z 76 " --> pdb=" O GLY Z 72 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N VAL Z 78 " --> pdb=" O SER Z 74 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N ASN Z 85 " --> pdb=" O ARG Z 81 " (cutoff:3.500A) Processing helix chain 'a' and resid 47 through 57 removed outlier: 4.986A pdb=" N ARG a 51 " --> pdb=" O ALA a 47 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N ASP a 52 " --> pdb=" O ALA a 48 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU a 55 " --> pdb=" O ARG a 51 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ALA a 56 " --> pdb=" O ASP a 52 " (cutoff:3.500A) Processing helix chain 'a' and resid 74 through 82 removed outlier: 3.629A pdb=" N ARG a 82 " --> pdb=" O ALA a 78 " (cutoff:3.500A) Processing helix chain 'a' and resid 88 through 94 removed outlier: 4.690A pdb=" N ARG a 93 " --> pdb=" O ARG a 89 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N ILE a 94 " --> pdb=" O THR a 90 " (cutoff:3.500A) Processing helix chain 'b' and resid 11 through 19 removed outlier: 5.115A pdb=" N HIS b 19 " --> pdb=" O GLU b 15 " (cutoff:3.500A) Processing helix chain 'd' and resid 15 through 20 removed outlier: 4.239A pdb=" N ARG d 19 " --> pdb=" O GLY d 15 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N GLN d 20 " --> pdb=" O LYS d 16 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 15 through 20' Processing helix chain 'd' and resid 39 through 47 Processing helix chain 'e' and resid 12 through 18 removed outlier: 3.898A pdb=" N SER e 16 " --> pdb=" O GLY e 12 " (cutoff:3.500A) Processing helix chain 'e' and resid 32 through 44 Processing helix chain 'f' and resid 100 through 107 removed outlier: 4.807A pdb=" N ASN f 104 " --> pdb=" O LEU f 100 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N TYR f 105 " --> pdb=" O ALA f 101 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N TYR f 106 " --> pdb=" O VAL f 102 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N LYS f 107 " --> pdb=" O LEU f 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 100 through 107' Processing helix chain 'h' and resid 2 through 25 Processing helix chain 'i' and resid 9 through 15 removed outlier: 4.828A pdb=" N ARG i 13 " --> pdb=" O GLY i 9 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N ARG i 14 " --> pdb=" O LYS i 10 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N GLY i 15 " --> pdb=" O LYS i 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 9 through 15' Processing helix chain 'i' and resid 96 through 107 removed outlier: 5.342A pdb=" N ALA i 100 " --> pdb=" O ASN i 96 " (cutoff:3.500A) Processing helix chain 'j' and resid 47 through 52 removed outlier: 4.383A pdb=" N SER j 52 " --> pdb=" O LEU j 48 " (cutoff:3.500A) Processing helix chain 'j' and resid 58 through 63 removed outlier: 4.174A pdb=" N LEU j 62 " --> pdb=" O SER j 58 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ILE j 63 " --> pdb=" O ILE j 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'j' and resid 58 through 63' Processing helix chain 'j' and resid 92 through 120 removed outlier: 4.659A pdb=" N ILE j 96 " --> pdb=" O SER j 92 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LYS j 97 " --> pdb=" O GLU j 93 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG j 113 " --> pdb=" O HIS j 109 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N TYR j 114 " --> pdb=" O SER j 110 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N CYS j 115 " --> pdb=" O ILE j 111 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N ALA j 116 " --> pdb=" O LEU j 112 " (cutoff:3.500A) Processing helix chain 'j' and resid 122 through 134 removed outlier: 3.680A pdb=" N LEU j 126 " --> pdb=" O PRO j 122 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N TRP j 132 " --> pdb=" O LYS j 128 " (cutoff:3.500A) Proline residue: j 133 - end of helix Processing helix chain 'j' and resid 140 through 151 removed outlier: 4.194A pdb=" N ALA j 144 " --> pdb=" O HIS j 140 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE j 150 " --> pdb=" O LYS j 146 " (cutoff:3.500A) Processing helix chain 'j' and resid 152 through 159 removed outlier: 6.009A pdb=" N GLU j 156 " --> pdb=" O GLU j 152 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N GLY j 157 " --> pdb=" O THR j 153 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N ILE j 158 " --> pdb=" O VAL j 154 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N GLU j 159 " --> pdb=" O TRP j 155 " (cutoff:3.500A) No H-bonds generated for 'chain 'j' and resid 152 through 159' Processing helix chain 'j' and resid 162 through 174 removed outlier: 3.714A pdb=" N LEU j 166 " --> pdb=" O SER j 162 " (cutoff:3.500A) Processing helix chain 'j' and resid 196 through 209 removed outlier: 5.716A pdb=" N ALA j 200 " --> pdb=" O GLU j 196 " (cutoff:3.500A) Processing helix chain 'j' and resid 236 through 259 removed outlier: 6.939A pdb=" N GLY j 240 " --> pdb=" O ASP j 236 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N ILE j 241 " --> pdb=" O LYS j 237 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N GLU j 242 " --> pdb=" O GLN j 238 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N LYS j 257 " --> pdb=" O GLU j 253 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N TYR j 258 " --> pdb=" O VAL j 254 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLY j 259 " --> pdb=" O ILE j 255 " (cutoff:3.500A) Processing helix chain 'k' and resid 112 through 121 Processing helix chain 'k' and resid 129 through 135 removed outlier: 5.460A pdb=" N GLU k 133 " --> pdb=" O LYS k 129 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N ARG k 134 " --> pdb=" O ASP k 130 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ASN k 135 " --> pdb=" O GLU k 131 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 129 through 135' Processing helix chain 'k' and resid 200 through 211 removed outlier: 4.719A pdb=" N MET k 204 " --> pdb=" O LEU k 200 " (cutoff:3.500A) Processing helix chain 'k' and resid 226 through 240 removed outlier: 3.791A pdb=" N LYS k 240 " --> pdb=" O ILE k 236 " (cutoff:3.500A) Processing helix chain 'k' and resid 250 through 255 removed outlier: 4.785A pdb=" N MET k 254 " --> pdb=" O LYS k 250 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N ARG k 255 " --> pdb=" O VAL k 251 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 250 through 255' Processing helix chain 'k' and resid 256 through 271 removed outlier: 3.531A pdb=" N LEU k 260 " --> pdb=" O GLU k 256 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ARG k 271 " --> pdb=" O LEU k 267 " (cutoff:3.500A) Processing helix chain 'k' and resid 290 through 302 removed outlier: 3.934A pdb=" N VAL k 294 " --> pdb=" O ASN k 290 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE k 302 " --> pdb=" O ILE k 298 " (cutoff:3.500A) Processing helix chain 'k' and resid 403 through 408 removed outlier: 3.589A pdb=" N CYS k 407 " --> pdb=" O ASP k 403 " (cutoff:3.500A) Processing helix chain 'l' and resid 128 through 142 removed outlier: 4.454A pdb=" N SER l 132 " --> pdb=" O GLY l 128 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLU l 133 " --> pdb=" O LEU l 129 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N LEU l 134 " --> pdb=" O PRO l 130 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N LEU l 142 " --> pdb=" O PHE l 138 " (cutoff:3.500A) Processing helix chain 'l' and resid 176 through 185 Processing helix chain 'l' and resid 187 through 199 Processing helix chain 'l' and resid 218 through 233 removed outlier: 3.659A pdb=" N MET l 222 " --> pdb=" O GLN l 218 " (cutoff:3.500A) Processing helix chain 'm' and resid 38 through 47 Processing helix chain 'm' and resid 49 through 62 Processing helix chain 'm' and resid 81 through 96 Processing helix chain 'm' and resid 134 through 144 removed outlier: 3.727A pdb=" N SER m 138 " --> pdb=" O HIS m 134 " (cutoff:3.500A) Proline residue: m 144 - end of helix Processing helix chain 'o' and resid 7 through 22 Processing helix chain 'o' and resid 23 through 37 removed outlier: 3.824A pdb=" N ALA o 27 " --> pdb=" O GLU o 23 " (cutoff:3.500A) Processing helix chain 'o' and resid 38 through 44 removed outlier: 4.465A pdb=" N TRP o 42 " --> pdb=" O ARG o 38 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N THR o 44 " --> pdb=" O ILE o 40 " (cutoff:3.500A) Processing helix chain 'o' and resid 45 through 63 removed outlier: 3.767A pdb=" N GLU o 49 " --> pdb=" O PRO o 45 " (cutoff:3.500A) Proline residue: o 50 - end of helix removed outlier: 4.273A pdb=" N LYS o 63 " --> pdb=" O GLY o 59 " (cutoff:3.500A) Processing helix chain 'o' and resid 64 through 80 removed outlier: 3.566A pdb=" N GLN o 80 " --> pdb=" O LYS o 76 " (cutoff:3.500A) Processing helix chain 'o' and resid 82 through 120 Processing helix chain 'o' and resid 150 through 170 removed outlier: 3.636A pdb=" N TRP o 154 " --> pdb=" O ALA o 150 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ARG o 170 " --> pdb=" O LEU o 166 " (cutoff:3.500A) Processing helix chain 'o' and resid 175 through 194 removed outlier: 5.393A pdb=" N TYR o 179 " --> pdb=" O LEU o 175 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N GLN o 194 " --> pdb=" O CYS o 190 " (cutoff:3.500A) Processing helix chain 'o' and resid 195 through 217 removed outlier: 4.604A pdb=" N PHE o 199 " --> pdb=" O ARG o 195 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLN o 217 " --> pdb=" O ALA o 213 " (cutoff:3.500A) Processing helix chain 'o' and resid 230 through 251 removed outlier: 4.305A pdb=" N GLN o 234 " --> pdb=" O ALA o 230 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N GLU o 251 " --> pdb=" O SER o 247 " (cutoff:3.500A) Processing helix chain 'o' and resid 252 through 270 removed outlier: 4.448A pdb=" N ALA o 256 " --> pdb=" O LEU o 252 " (cutoff:3.500A) Processing helix chain 'o' and resid 275 through 291 removed outlier: 4.856A pdb=" N ALA o 280 " --> pdb=" O PRO o 276 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N PHE o 291 " --> pdb=" O VAL o 287 " (cutoff:3.500A) Processing helix chain 'o' and resid 295 through 313 removed outlier: 4.232A pdb=" N HIS o 299 " --> pdb=" O ASP o 295 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N THR o 312 " --> pdb=" O LYS o 308 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ASN o 313 " --> pdb=" O LEU o 309 " (cutoff:3.500A) Processing helix chain 'o' and resid 317 through 335 Processing helix chain 'o' and resid 348 through 356 removed outlier: 4.611A pdb=" N TYR o 352 " --> pdb=" O HIS o 348 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N ARG o 353 " --> pdb=" O LEU o 349 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N LEU o 354 " --> pdb=" O ARG o 350 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N LEU o 355 " --> pdb=" O MET o 351 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASN o 356 " --> pdb=" O TYR o 352 " (cutoff:3.500A) No H-bonds generated for 'chain 'o' and resid 348 through 356' Processing helix chain 'o' and resid 362 through 374 removed outlier: 5.234A pdb=" N GLU o 374 " --> pdb=" O ILE o 370 " (cutoff:3.500A) Processing helix chain 'o' and resid 375 through 380 removed outlier: 4.172A pdb=" N LYS o 379 " --> pdb=" O SER o 375 " (cutoff:3.500A) Processing helix chain 'o' and resid 381 through 393 Processing helix chain 'o' and resid 396 through 414 removed outlier: 5.059A pdb=" N VAL o 409 " --> pdb=" O GLU o 405 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N LYS o 410 " --> pdb=" O ASN o 406 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N LYS o 414 " --> pdb=" O LYS o 410 " (cutoff:3.500A) Processing helix chain 'o' and resid 415 through 421 removed outlier: 6.425A pdb=" N GLN o 419 " --> pdb=" O THR o 415 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N TYR o 420 " --> pdb=" O TYR o 416 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ILE o 421 " --> pdb=" O PHE o 417 " (cutoff:3.500A) No H-bonds generated for 'chain 'o' and resid 415 through 421' Processing helix chain 'o' and resid 422 through 440 Processing helix chain 'o' and resid 444 through 454 removed outlier: 5.669A pdb=" N LEU o 454 " --> pdb=" O LYS o 450 " (cutoff:3.500A) Processing helix chain 'o' and resid 461 through 476 Processing helix chain 'o' and resid 813 through 857 removed outlier: 4.701A pdb=" N GLU o 829 " --> pdb=" O ARG o 825 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA o 830 " --> pdb=" O ARG o 826 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU o 842 " --> pdb=" O ILE o 838 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ALA o 847 " --> pdb=" O ARG o 843 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N GLN o 848 " --> pdb=" O GLN o 844 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N THR o 854 " --> pdb=" O LEU o 850 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N ARG o 855 " --> pdb=" O ALA o 851 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS o 856 " --> pdb=" O GLU o 852 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLN o 857 " --> pdb=" O ALA o 853 " (cutoff:3.500A) Processing helix chain 'o' and resid 919 through 939 removed outlier: 3.625A pdb=" N GLY o 924 " --> pdb=" O ARG o 920 " (cutoff:3.500A) Proline residue: o 927 - end of helix Proline residue: o 930 - end of helix Proline residue: o 933 - end of helix Proline residue: o 936 - end of helix Proline residue: o 939 - end of helix Processing helix chain 'p' and resid 88 through 107 removed outlier: 3.586A pdb=" N VAL p 92 " --> pdb=" O PRO p 88 " (cutoff:3.500A) Proline residue: p 93 - end of helix removed outlier: 3.514A pdb=" N LYS p 97 " --> pdb=" O PRO p 93 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N LYS p 105 " --> pdb=" O SER p 101 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ALA p 106 " --> pdb=" O LEU p 102 " (cutoff:3.500A) Processing helix chain 'p' and resid 133 through 144 removed outlier: 3.817A pdb=" N ILE p 141 " --> pdb=" O ALA p 137 " (cutoff:3.500A) Processing helix chain 'p' and resid 160 through 167 removed outlier: 3.966A pdb=" N ASN p 167 " --> pdb=" O VAL p 163 " (cutoff:3.500A) Processing helix chain 'p' and resid 185 through 195 removed outlier: 5.615A pdb=" N TRP p 192 " --> pdb=" O SER p 188 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N LEU p 193 " --> pdb=" O LEU p 189 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N MET p 194 " --> pdb=" O LYS p 190 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ASP p 195 " --> pdb=" O SER p 191 " (cutoff:3.500A) Processing helix chain 'p' and resid 304 through 309 removed outlier: 3.636A pdb=" N GLU p 308 " --> pdb=" O THR p 304 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N GLY p 309 " --> pdb=" O LYS p 305 " (cutoff:3.500A) No H-bonds generated for 'chain 'p' and resid 304 through 309' Processing helix chain 'p' and resid 370 through 375 Proline residue: p 375 - end of helix Processing helix chain 'p' and resid 669 through 679 removed outlier: 5.168A pdb=" N ASN p 679 " --> pdb=" O LYS p 675 " (cutoff:3.500A) Processing helix chain 'p' and resid 687 through 701 removed outlier: 3.636A pdb=" N ASP p 691 " --> pdb=" O PHE p 687 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA p 692 " --> pdb=" O GLU p 688 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ARG p 700 " --> pdb=" O ASP p 696 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N ASP p 701 " --> pdb=" O THR p 697 " (cutoff:3.500A) Processing helix chain 'p' and resid 705 through 728 Processing helix chain 'q' and resid 251 through 268 removed outlier: 5.088A pdb=" N LYS q 268 " --> pdb=" O SER q 264 " (cutoff:3.500A) Processing helix chain 'q' and resid 271 through 287 removed outlier: 5.158A pdb=" N GLU q 287 " --> pdb=" O LEU q 283 " (cutoff:3.500A) Processing helix chain 'q' and resid 288 through 308 Proline residue: q 301 - end of helix Processing helix chain 'q' and resid 314 through 336 Processing helix chain 'q' and resid 351 through 356 Proline residue: q 355 - end of helix No H-bonds generated for 'chain 'q' and resid 351 through 356' Processing helix chain 'q' and resid 367 through 388 removed outlier: 5.173A pdb=" N SER q 371 " --> pdb=" O GLY q 367 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N ASP q 388 " --> pdb=" O LEU q 384 " (cutoff:3.500A) Processing helix chain 'q' and resid 391 through 419 removed outlier: 3.549A pdb=" N LEU q 395 " --> pdb=" O SER q 391 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N GLN q 402 " --> pdb=" O LEU q 398 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N SER q 403 " --> pdb=" O ARG q 399 " (cutoff:3.500A) Processing helix chain 'q' and resid 421 through 441 removed outlier: 5.283A pdb=" N ARG q 431 " --> pdb=" O ARG q 427 " (cutoff:3.500A) Proline residue: q 432 - end of helix Processing helix chain 'q' and resid 444 through 460 Proline residue: q 460 - end of helix Processing helix chain 'q' and resid 477 through 493 removed outlier: 5.443A pdb=" N ASN q 481 " --> pdb=" O ASP q 477 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N LYS q 492 " --> pdb=" O THR q 488 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N GLN q 493 " --> pdb=" O ILE q 489 " (cutoff:3.500A) Processing helix chain 'q' and resid 495 through 513 removed outlier: 3.933A pdb=" N GLN q 499 " --> pdb=" O ASN q 495 " (cutoff:3.500A) Processing helix chain 'q' and resid 515 through 527 removed outlier: 4.648A pdb=" N ALA q 519 " --> pdb=" O ASP q 515 " (cutoff:3.500A) Processing helix chain 'q' and resid 528 through 536 removed outlier: 6.525A pdb=" N ILE q 532 " --> pdb=" O VAL q 528 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ASN q 533 " --> pdb=" O GLN q 529 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLN q 534 " --> pdb=" O THR q 530 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N PHE q 535 " --> pdb=" O ASN q 531 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N ASP q 536 " --> pdb=" O ILE q 532 " (cutoff:3.500A) No H-bonds generated for 'chain 'q' and resid 528 through 536' Processing helix chain 'q' and resid 537 through 558 Processing helix chain 'q' and resid 559 through 572 removed outlier: 5.037A pdb=" N ASP q 569 " --> pdb=" O GLN q 565 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N LEU q 570 " --> pdb=" O ILE q 566 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU q 571 " --> pdb=" O LEU q 567 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N SER q 572 " --> pdb=" O ASN q 568 " (cutoff:3.500A) Processing helix chain 'q' and resid 575 through 580 removed outlier: 4.166A pdb=" N ILE q 579 " --> pdb=" O HIS q 575 " (cutoff:3.500A) Processing helix chain 'q' and resid 584 through 593 removed outlier: 4.321A pdb=" N ILE q 588 " --> pdb=" O SER q 584 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LEU q 590 " --> pdb=" O HIS q 586 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N ASN q 591 " --> pdb=" O ARG q 587 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N SER q 592 " --> pdb=" O ILE q 588 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N SER q 593 " --> pdb=" O SER q 589 " (cutoff:3.500A) Processing helix chain 'q' and resid 594 through 605 removed outlier: 4.165A pdb=" N ALA q 598 " --> pdb=" O ASN q 594 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N ASP q 599 " --> pdb=" O ASN q 595 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N GLU q 600 " --> pdb=" O ALA q 596 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ALA q 602 " --> pdb=" O ALA q 598 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ARG q 603 " --> pdb=" O ASP q 599 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N GLN q 604 " --> pdb=" O GLU q 600 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N CYS q 605 " --> pdb=" O ARG q 601 " (cutoff:3.500A) Processing helix chain 'q' and resid 613 through 639 removed outlier: 4.042A pdb=" N ILE q 630 " --> pdb=" O LEU q 626 " (cutoff:3.500A) Proline residue: q 631 - end of helix Processing helix chain 'q' and resid 651 through 663 removed outlier: 4.004A pdb=" N SER q 655 " --> pdb=" O SER q 651 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N SER q 663 " --> pdb=" O TYR q 659 " (cutoff:3.500A) Processing helix chain 'q' and resid 670 through 685 Processing helix chain 'q' and resid 686 through 698 removed outlier: 5.854A pdb=" N SER q 690 " --> pdb=" O ASN q 686 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N LYS q 698 " --> pdb=" O LEU q 694 " (cutoff:3.500A) Processing helix chain 'q' and resid 706 through 729 Processing helix chain 'q' and resid 737 through 746 removed outlier: 3.979A pdb=" N LEU q 741 " --> pdb=" O SER q 737 " (cutoff:3.500A) Processing helix chain 'q' and resid 748 through 764 Processing helix chain 'q' and resid 782 through 794 removed outlier: 4.997A pdb=" N LYS q 786 " --> pdb=" O ASP q 782 " (cutoff:3.500A) Processing helix chain 'r' and resid 48 through 56 removed outlier: 5.950A pdb=" N HIS r 56 " --> pdb=" O ARG r 52 " (cutoff:3.500A) Processing helix chain 'r' and resid 86 through 96 Processing helix chain 's' and resid 323 through 329 removed outlier: 3.606A pdb=" N PHE s 327 " --> pdb=" O GLU s 323 " (cutoff:3.500A) Processing helix chain 's' and resid 331 through 342 removed outlier: 4.714A pdb=" N HIS s 342 " --> pdb=" O GLU s 338 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'A' and resid 120 through 124 removed outlier: 4.202A pdb=" N VAL A 158 " --> pdb=" O VAL A 143 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'B' and resid 43 through 47 removed outlier: 3.522A pdb=" N GLY B 44 " --> pdb=" O ILE B 32 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'B' and resid 64 through 68 removed outlier: 3.970A pdb=" N ARG B 64 " --> pdb=" O VAL B 88 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'B' and resid 119 through 128 removed outlier: 4.913A pdb=" N THR B 119 " --> pdb=" O THR B 143 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N PHE B 138 " --> pdb=" O ARG B 213 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'B' and resid 134 through 138 removed outlier: 6.675A pdb=" N VAL B 134 " --> pdb=" O LEU B 218 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N LYS B 214 " --> pdb=" O PHE B 138 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'C' and resid 81 through 86 removed outlier: 6.734A pdb=" N VAL C 106 " --> pdb=" O MET C 86 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'C' and resid 162 through 166 removed outlier: 3.888A pdb=" N ALA C 177 " --> pdb=" O ASP C 200 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N ASP C 200 " --> pdb=" O ALA C 177 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'C' and resid 102 through 111 removed outlier: 6.652A pdb=" N HIS C 115 " --> pdb=" O ASP C 111 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'D' and resid 45 through 53 removed outlier: 3.580A pdb=" N VAL D 91 " --> pdb=" O ALA D 52 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'D' and resid 148 through 153 removed outlier: 3.687A pdb=" N GLY D 133 " --> pdb=" O MET D 189 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLY D 180 " --> pdb=" O LEU D 177 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'E' and resid 88 through 93 removed outlier: 4.326A pdb=" N ASP E 88 " --> pdb=" O LEU E 101 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU E 97 " --> pdb=" O LEU E 92 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'E' and resid 123 through 126 removed outlier: 4.524A pdb=" N ASP E 158 " --> pdb=" O VAL E 126 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ASP E 171 " --> pdb=" O LYS E 161 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'E' and resid 128 through 131 removed outlier: 4.001A pdb=" N ARG E 145 " --> pdb=" O THR E 141 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'E' and resid 197 through 200 Processing sheet with id= 15, first strand: chain 'F' and resid 145 through 153 No H-bonds generated for sheet with id= 15 Processing sheet with id= 16, first strand: chain 'G' and resid 11 through 18 removed outlier: 4.645A pdb=" N ALA G 110 " --> pdb=" O ALA G 53 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N VAL G 49 " --> pdb=" O THR G 114 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N GLN G 34 " --> pdb=" O ILE G 52 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'G' and resid 71 through 76 removed outlier: 6.332A pdb=" N THR G 71 " --> pdb=" O GLY G 99 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'G' and resid 159 through 164 removed outlier: 6.271A pdb=" N LYS G 167 " --> pdb=" O LYS G 164 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'G' and resid 54 through 57 removed outlier: 3.930A pdb=" N GLY G 54 " --> pdb=" O ALA G 110 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'H' and resid 44 through 51 removed outlier: 4.292A pdb=" N SER H 45 " --> pdb=" O PHE H 61 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS H 55 " --> pdb=" O VAL H 51 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'H' and resid 137 through 143 removed outlier: 3.921A pdb=" N ASN H 147 " --> pdb=" O LEU H 143 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N GLN H 180 " --> pdb=" O LYS H 148 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'I' and resid 42 through 48 removed outlier: 4.173A pdb=" N ARG I 42 " --> pdb=" O LEU I 58 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU I 58 " --> pdb=" O ARG I 42 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N ASN I 52 " --> pdb=" O THR I 48 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'I' and resid 72 through 75 removed outlier: 3.750A pdb=" N ASN I 64 " --> pdb=" O CYS I 180 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ASP I 181 " --> pdb=" O SER I 171 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N TYR I 167 " --> pdb=" O LEU I 185 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ALA I 100 " --> pdb=" O ILE I 170 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'K' and resid 20 through 24 removed outlier: 4.675A pdb=" N ALA K 23 " --> pdb=" O TYR K 64 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N TYR K 64 " --> pdb=" O ALA K 23 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'L' and resid 69 through 74 removed outlier: 5.634A pdb=" N LYS L 69 " --> pdb=" O GLN L 127 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N THR L 124 " --> pdb=" O LEU L 140 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'L' and resid 82 through 95 removed outlier: 6.381A pdb=" N THR L 83 " --> pdb=" O HIS L 110 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N HIS L 110 " --> pdb=" O THR L 83 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N VAL L 85 " --> pdb=" O PRO L 108 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ARG L 87 " --> pdb=" O ASN L 106 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ASN L 106 " --> pdb=" O ARG L 87 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ASP L 89 " --> pdb=" O HIS L 104 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N HIS L 104 " --> pdb=" O ASP L 89 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N LEU L 91 " --> pdb=" O LYS L 102 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N LYS L 102 " --> pdb=" O LEU L 91 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N TYR L 93 " --> pdb=" O TYR L 100 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N TYR L 100 " --> pdb=" O TYR L 93 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'M' and resid 51 through 55 removed outlier: 3.637A pdb=" N LEU M 52 " --> pdb=" O VAL M 114 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'O' and resid 26 through 32 removed outlier: 3.688A pdb=" N HIS O 29 " --> pdb=" O ARG O 18 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ARG O 18 " --> pdb=" O HIS O 29 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N LYS O 82 " --> pdb=" O ALA O 17 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ILE O 81 " --> pdb=" O GLY O 113 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'P' and resid 75 through 79 removed outlier: 4.354A pdb=" N SER P 92 " --> pdb=" O ILE P 107 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'Q' and resid 5 through 12 removed outlier: 4.591A pdb=" N ASN Q 62 " --> pdb=" O GLY Q 25 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'R' and resid 99 through 102 Processing sheet with id= 32, first strand: chain 'T' and resid 114 through 117 removed outlier: 3.566A pdb=" N SER T 117 " --> pdb=" O GLY T 121 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N GLY T 121 " --> pdb=" O SER T 117 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'U' and resid 55 through 58 removed outlier: 6.191A pdb=" N LEU U 58 " --> pdb=" O LYS U 88 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N LYS U 88 " --> pdb=" O LEU U 58 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ARG U 89 " --> pdb=" O LEU U 26 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ALA U 95 " --> pdb=" O HIS U 20 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N LYS U 21 " --> pdb=" O ALA U 119 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N ALA U 119 " --> pdb=" O LYS U 21 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'U' and resid 60 through 68 Processing sheet with id= 35, first strand: chain 'V' and resid 15 through 18 removed outlier: 4.396A pdb=" N ARG V 15 " --> pdb=" O ILE V 24 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ARG V 22 " --> pdb=" O CYS V 17 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'W' and resid 23 through 28 removed outlier: 5.615A pdb=" N ARG W 23 " --> pdb=" O LEU W 65 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N GLN W 64 " --> pdb=" O GLU W 49 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N GLU W 49 " --> pdb=" O GLN W 64 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'W' and resid 71 through 74 removed outlier: 4.407A pdb=" N LYS W 71 " --> pdb=" O TYR W 130 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLY W 73 " --> pdb=" O PHE W 128 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'W' and resid 78 through 81 removed outlier: 4.076A pdb=" N PHE W 79 " --> pdb=" O ILE W 125 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLY W 123 " --> pdb=" O VAL W 81 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'X' and resid 48 through 52 removed outlier: 6.542A pdb=" N LEU X 103 " --> pdb=" O VAL X 125 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'X' and resid 55 through 61 removed outlier: 5.384A pdb=" N ALA X 67 " --> pdb=" O SER X 61 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N LYS X 81 " --> pdb=" O LEU X 76 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'Y' and resid 5 through 10 removed outlier: 4.331A pdb=" N VAL Y 24 " --> pdb=" O LYS Y 11 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N LYS Y 11 " --> pdb=" O VAL Y 24 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'Y' and resid 59 through 63 removed outlier: 5.125A pdb=" N GLY Y 59 " --> pdb=" O PHE Y 72 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N PHE Y 72 " --> pdb=" O GLY Y 59 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N LYS Y 68 " --> pdb=" O GLN Y 63 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'Y' and resid 20 through 29 removed outlier: 4.187A pdb=" N GLY Y 67 " --> pdb=" O HIS Y 29 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'Z' and resid 89 through 92 removed outlier: 6.815A pdb=" N ILE Z 100 " --> pdb=" O VAL Z 92 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'b' and resid 43 through 47 removed outlier: 6.799A pdb=" N PHE b 32 " --> pdb=" O LYS b 82 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'c' and resid 17 through 20 removed outlier: 3.889A pdb=" N GLY c 17 " --> pdb=" O GLN c 27 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL c 25 " --> pdb=" O THR c 19 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ARG c 29 " --> pdb=" O ILE c 13 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ASP c 52 " --> pdb=" O VAL c 12 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'c' and resid 25 through 31 Processing sheet with id= 48, first strand: chain 'f' and resid 136 through 139 removed outlier: 4.053A pdb=" N SER f 144 " --> pdb=" O CYS f 139 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'g' and resid 6 through 11 removed outlier: 4.012A pdb=" N MET g 7 " --> pdb=" O MET g 323 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N VAL g 319 " --> pdb=" O ARG g 11 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'g' and resid 22 through 26 removed outlier: 5.314A pdb=" N ASN g 32 " --> pdb=" O LEU g 48 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N SER g 45 " --> pdb=" O VAL g 59 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N PHE g 55 " --> pdb=" O THR g 49 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'g' and resid 70 through 75 removed outlier: 5.558A pdb=" N TYR g 80 " --> pdb=" O SER g 75 " (cutoff:3.500A) removed outlier: 8.190A pdb=" N ASN g 79 " --> pdb=" O LEU g 95 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N THR g 89 " --> pdb=" O SER g 85 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N LEU g 92 " --> pdb=" O GLU g 101 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ASN g 99 " --> pdb=" O ASN g 94 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'g' and resid 112 through 117 removed outlier: 6.069A pdb=" N LYS g 122 " --> pdb=" O ASP g 117 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER g 127 " --> pdb=" O THR g 131 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N THR g 131 " --> pdb=" O SER g 127 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'g' and resid 154 through 158 removed outlier: 4.462A pdb=" N THR g 173 " --> pdb=" O ALA g 158 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'g' and resid 207 through 212 removed outlier: 5.882A pdb=" N LEU g 217 " --> pdb=" O SER g 212 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N GLY g 222 " --> pdb=" O GLN g 226 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N GLN g 226 " --> pdb=" O GLY g 222 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N GLY g 225 " --> pdb=" O ALA g 243 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'g' and resid 249 through 253 removed outlier: 3.995A pdb=" N ALA g 249 " --> pdb=" O ALA g 262 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER g 253 " --> pdb=" O TRP g 258 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N TRP g 258 " --> pdb=" O SER g 253 " (cutoff:3.500A) removed outlier: 8.766A pdb=" N PHE g 257 " --> pdb=" O LEU g 272 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLY g 266 " --> pdb=" O THR g 263 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ILE g 269 " --> pdb=" O ILE g 278 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'g' and resid 298 through 302 removed outlier: 3.513A pdb=" N SER g 298 " --> pdb=" O GLY g 311 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N THR g 307 " --> pdb=" O SER g 302 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'g' and resid 42 through 45 removed outlier: 3.567A pdb=" N LEU g 43 " --> pdb=" O TYR g 62 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG g 60 " --> pdb=" O SER g 45 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'g' and resid 89 through 92 removed outlier: 3.649A pdb=" N ALA g 102 " --> pdb=" O LEU g 92 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'g' and resid 266 through 269 removed outlier: 3.625A pdb=" N ASP g 279 " --> pdb=" O ILE g 269 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'g' and resid 306 through 313 removed outlier: 7.334A pdb=" N GLN g 306 " --> pdb=" O VAL g 322 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N VAL g 316 " --> pdb=" O TYR g 312 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'i' and resid 33 through 37 removed outlier: 6.725A pdb=" N LEU i 78 " --> pdb=" O VAL i 92 " (cutoff:3.500A) removed outlier: 8.419A pdb=" N ASP i 87 " --> pdb=" O LYS i 56 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N MET i 58 " --> pdb=" O ASP i 87 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'j' and resid 20 through 23 Processing sheet with id= 63, first strand: chain 'j' and resid 32 through 35 Processing sheet with id= 64, first strand: chain 'j' and resid 74 through 77 removed outlier: 4.102A pdb=" N TYR j 82 " --> pdb=" O ASP j 77 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'j' and resid 219 through 222 removed outlier: 4.666A pdb=" N LYS j 219 " --> pdb=" O THR j 231 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL j 188 " --> pdb=" O TYR j 228 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N VAL j 261 " --> pdb=" O SER j 191 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'k' and resid 140 through 150 removed outlier: 4.212A pdb=" N ILE k 101 " --> pdb=" O HIS k 188 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N THR k 105 " --> pdb=" O VAL k 192 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N HIS k 243 " --> pdb=" O ASP k 212 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'k' and resid 315 through 318 removed outlier: 6.808A pdb=" N GLY k 339 " --> pdb=" O ILE k 318 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLY k 335 " --> pdb=" O VAL k 323 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'k' and resid 358 through 361 removed outlier: 6.103A pdb=" N GLN k 369 " --> pdb=" O THR k 361 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ASP k 351 " --> pdb=" O ILE k 377 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N VAL k 416 " --> pdb=" O ARG k 356 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'k' and resid 424 through 428 Processing sheet with id= 70, first strand: chain 'k' and resid 470 through 475 removed outlier: 3.870A pdb=" N VAL k 475 " --> pdb=" O GLU k 460 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N GLU k 460 " --> pdb=" O VAL k 475 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N VAL k 461 " --> pdb=" O ARG k 504 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N ARG k 504 " --> pdb=" O VAL k 461 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'k' and resid 336 through 341 removed outlier: 3.657A pdb=" N GLY k 336 " --> pdb=" O THR k 400 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'l' and resid 171 through 175 Processing sheet with id= 73, first strand: chain 'l' and resid 244 through 248 removed outlier: 3.654A pdb=" N LYS l 247 " --> pdb=" O PHE l 256 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain 'm' and resid 22 through 26 removed outlier: 7.028A pdb=" N GLN m 22 " --> pdb=" O LEU m 37 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ILE m 32 " --> pdb=" O GLY m 78 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N TYR m 74 " --> pdb=" O VAL m 36 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N ARG m 73 " --> pdb=" O SER m 68 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N GLN m 64 " --> pdb=" O ASN m 77 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain 'm' and resid 107 through 111 removed outlier: 3.513A pdb=" N VAL m 118 " --> pdb=" O ILE m 110 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N LEU m 117 " --> pdb=" O MET m 130 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N LYS m 126 " --> pdb=" O CYS m 121 " (cutoff:3.500A) Processing sheet with id= 76, first strand: chain 'o' and resid 479 through 484 removed outlier: 5.107A pdb=" N SER o 479 " --> pdb=" O ALA o 492 " (cutoff:3.500A) Processing sheet with id= 77, first strand: chain 'p' and resid 110 through 114 removed outlier: 3.856A pdb=" N CYS p 131 " --> pdb=" O GLN p 77 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N GLN p 77 " --> pdb=" O CYS p 131 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N HIS p 153 " --> pdb=" O LEU p 149 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LYS p 147 " --> pdb=" O LEU p 155 " (cutoff:3.500A) Processing sheet with id= 78, first strand: chain 'p' and resid 225 through 229 removed outlier: 3.514A pdb=" N GLU p 226 " --> pdb=" O VAL p 212 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N GLN p 201 " --> pdb=" O ARG p 661 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASN p 657 " --> pdb=" O GLN p 205 " (cutoff:3.500A) Processing sheet with id= 79, first strand: chain 'p' and resid 236 through 239 removed outlier: 5.874A pdb=" N TYR p 244 " --> pdb=" O SER p 239 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ARG p 265 " --> pdb=" O ALA p 255 " (cutoff:3.500A) Processing sheet with id= 80, first strand: chain 'p' and resid 273 through 278 removed outlier: 5.717A pdb=" N TYR p 283 " --> pdb=" O SER p 278 " (cutoff:3.500A) removed outlier: 8.096A pdb=" N LYS p 282 " --> pdb=" O ILE p 317 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N GLN p 311 " --> pdb=" O SER p 288 " (cutoff:3.500A) Processing sheet with id= 81, first strand: chain 'p' and resid 339 through 342 removed outlier: 6.215A pdb=" N TYR p 347 " --> pdb=" O SER p 342 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N LYS p 346 " --> pdb=" O ALA p 361 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N CYS p 348 " --> pdb=" O HIS p 359 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER p 355 " --> pdb=" O VAL p 352 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N VAL p 358 " --> pdb=" O LEU p 368 " (cutoff:3.500A) Processing sheet with id= 82, first strand: chain 'p' and resid 381 through 384 removed outlier: 6.062A pdb=" N LEU p 402 " --> pdb=" O ALA p 384 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N GLU p 409 " --> pdb=" O ALA p 414 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ALA p 414 " --> pdb=" O GLU p 409 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N CYS p 415 " --> pdb=" O LEU p 433 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS p 429 " --> pdb=" O ILE p 419 " (cutoff:3.500A) Processing sheet with id= 83, first strand: chain 'p' and resid 437 through 444 removed outlier: 3.581A pdb=" N ASN p 438 " --> pdb=" O GLU p 455 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N PHE p 449 " --> pdb=" O GLN p 444 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N GLU p 448 " --> pdb=" O LEU p 473 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N THR p 463 " --> pdb=" O THR p 458 " (cutoff:3.500A) Processing sheet with id= 84, first strand: chain 'p' and resid 491 through 495 removed outlier: 5.593A pdb=" N ARG p 500 " --> pdb=" O GLU p 495 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N PHE p 523 " --> pdb=" O VAL p 541 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N ARG p 537 " --> pdb=" O GLU p 527 " (cutoff:3.500A) Processing sheet with id= 85, first strand: chain 'p' and resid 550 through 555 removed outlier: 5.990A pdb=" N PHE p 560 " --> pdb=" O SER p 555 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N ARG p 559 " --> pdb=" O MET p 581 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N VAL p 567 " --> pdb=" O ARG p 573 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N ARG p 573 " --> pdb=" O VAL p 567 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N PHE p 578 " --> pdb=" O VAL p 602 " (cutoff:3.500A) Processing sheet with id= 86, first strand: chain 'p' and resid 612 through 616 removed outlier: 5.309A pdb=" N TYR p 621 " --> pdb=" O ASP p 616 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N HIS p 635 " --> pdb=" O ILE p 652 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYS p 648 " --> pdb=" O ILE p 639 " (cutoff:3.500A) Processing sheet with id= 87, first strand: chain 'p' and resid 520 through 523 removed outlier: 3.825A pdb=" N LYS p 542 " --> pdb=" O PHE p 523 " (cutoff:3.500A) Processing sheet with id= 88, first strand: chain 's' and resid 1 through 7 removed outlier: 4.840A pdb=" N LYS s 2 " --> pdb=" O HIS s 321 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N HIS s 321 " --> pdb=" O LYS s 2 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N PHE s 316 " --> pdb=" O GLY s 312 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N THR s 306 " --> pdb=" O PHE s 322 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N SER s 307 " --> pdb=" O SER s 302 " (cutoff:3.500A) Processing sheet with id= 89, first strand: chain 's' and resid 15 through 19 removed outlier: 6.112A pdb=" N LEU s 24 " --> pdb=" O ASN s 19 " (cutoff:3.500A) Processing sheet with id= 90, first strand: chain 's' and resid 57 through 60 removed outlier: 3.611A pdb=" N ALA s 88 " --> pdb=" O LEU s 78 " (cutoff:3.500A) Processing sheet with id= 91, first strand: chain 's' and resid 98 through 102 removed outlier: 4.213A pdb=" N ARG s 98 " --> pdb=" O ILE s 111 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU s 100 " --> pdb=" O LEU s 109 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N TYR s 107 " --> pdb=" O SER s 102 " (cutoff:3.500A) Processing sheet with id= 92, first strand: chain 's' and resid 121 through 125 removed outlier: 3.583A pdb=" N HIS s 145 " --> pdb=" O ILE s 124 " (cutoff:3.500A) Processing sheet with id= 93, first strand: chain 's' and resid 158 through 162 removed outlier: 5.775A pdb=" N TYR s 167 " --> pdb=" O SER s 162 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N LYS s 166 " --> pdb=" O VAL s 182 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N LYS s 176 " --> pdb=" O HIS s 172 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N GLY s 175 " --> pdb=" O LEU s 194 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ASP s 190 " --> pdb=" O LYS s 179 " (cutoff:3.500A) Processing sheet with id= 94, first strand: chain 's' and resid 201 through 205 removed outlier: 3.634A pdb=" N ASP s 201 " --> pdb=" O SER s 214 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N TYR s 210 " --> pdb=" O SER s 205 " (cutoff:3.500A) removed outlier: 9.101A pdb=" N THR s 209 " --> pdb=" O VAL s 225 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N LEU s 222 " --> pdb=" O LEU s 231 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLN s 229 " --> pdb=" O ASP s 224 " (cutoff:3.500A) Processing sheet with id= 95, first strand: chain 's' and resid 242 through 246 removed outlier: 4.680A pdb=" N PHE s 251 " --> pdb=" O THR s 246 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N ALA s 275 " --> pdb=" O ARG s 288 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ARG s 288 " --> pdb=" O ALA s 275 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N PHE s 277 " --> pdb=" O ILE s 286 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N GLU s 284 " --> pdb=" O HIS s 279 " (cutoff:3.500A) Processing sheet with id= 96, first strand: chain 's' and resid 219 through 222 2736 hydrogen bonds defined for protein. 8130 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1286 hydrogen bonds 2058 hydrogen bond angles 0 basepair planarities 526 basepair parallelities 941 stacking parallelities Total time for adding SS restraints: 73.88 Time building geometry restraints manager: 41.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 14633 1.33 - 1.45: 38777 1.45 - 1.57: 52600 1.57 - 1.70: 3776 1.70 - 1.82: 265 Bond restraints: 110051 Sorted by residual: bond pdb=" C2A RIA 1 64 " pdb=" C3A RIA 1 64 " ideal model delta sigma weight residual 1.235 1.533 -0.298 2.00e-02 2.50e+03 2.21e+02 bond pdb=" C3' RIA 1 64 " pdb=" C2' RIA 1 64 " ideal model delta sigma weight residual 1.240 1.528 -0.288 2.00e-02 2.50e+03 2.08e+02 bond pdb=" C1' GCP k 603 " pdb=" C2' GCP k 603 " ideal model delta sigma weight residual 1.276 1.528 -0.252 2.00e-02 2.50e+03 1.58e+02 bond pdb=" C3' GCP k 603 " pdb=" C4' GCP k 603 " ideal model delta sigma weight residual 1.276 1.527 -0.251 2.00e-02 2.50e+03 1.57e+02 bond pdb=" N3 2MG 21426 " pdb=" C4 2MG 21426 " ideal model delta sigma weight residual 1.500 1.341 0.159 2.00e-02 2.50e+03 6.29e+01 ... (remaining 110046 not shown) Histogram of bond angle deviations from ideal: 96.24 - 104.73: 8731 104.73 - 113.23: 61747 113.23 - 121.72: 57456 121.72 - 130.21: 28542 130.21 - 138.71: 1295 Bond angle restraints: 157771 Sorted by residual: angle pdb=" C1' 1MA 1 58 " pdb=" N9 1MA 1 58 " pdb=" C8 1MA 1 58 " ideal model delta sigma weight residual 93.44 123.86 -30.42 3.00e+00 1.11e-01 1.03e+02 angle pdb=" C1' 1MA 1 58 " pdb=" N9 1MA 1 58 " pdb=" C4 1MA 1 58 " ideal model delta sigma weight residual 158.43 128.76 29.67 3.00e+00 1.11e-01 9.78e+01 angle pdb=" O3' C 21470 " pdb=" C3' C 21470 " pdb=" C2' C 21470 " ideal model delta sigma weight residual 109.50 123.33 -13.83 1.50e+00 4.44e-01 8.51e+01 angle pdb=" O3' C 21206 " pdb=" C3' C 21206 " pdb=" C2' C 21206 " ideal model delta sigma weight residual 109.50 122.98 -13.48 1.50e+00 4.44e-01 8.08e+01 angle pdb=" C4' A 21080 " pdb=" C3' A 21080 " pdb=" O3' A 21080 " ideal model delta sigma weight residual 109.40 122.57 -13.17 1.50e+00 4.44e-01 7.71e+01 ... (remaining 157766 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 36.00: 58467 36.00 - 72.00: 3600 72.00 - 107.99: 336 107.99 - 143.99: 33 143.99 - 179.99: 73 Dihedral angle restraints: 62509 sinusoidal: 38900 harmonic: 23609 Sorted by residual: dihedral pdb=" C5' C 2 130 " pdb=" C4' C 2 130 " pdb=" C3' C 2 130 " pdb=" O3' C 2 130 " ideal model delta sinusoidal sigma weight residual 147.00 72.74 74.26 1 8.00e+00 1.56e-02 1.09e+02 dihedral pdb=" C5' U 2 279 " pdb=" C4' U 2 279 " pdb=" C3' U 2 279 " pdb=" O3' U 2 279 " ideal model delta sinusoidal sigma weight residual 147.00 74.58 72.42 1 8.00e+00 1.56e-02 1.05e+02 dihedral pdb=" N PHE K 41 " pdb=" C PHE K 41 " pdb=" CA PHE K 41 " pdb=" CB PHE K 41 " ideal model delta harmonic sigma weight residual 122.80 147.03 -24.23 0 2.50e+00 1.60e-01 9.39e+01 ... (remaining 62506 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.997: 19272 0.997 - 1.994: 1 1.994 - 2.991: 0 2.991 - 3.988: 0 3.988 - 4.985: 1 Chirality restraints: 19274 Sorted by residual: chirality pdb=" C4' C4J 21190 " pdb=" C5' C4J 21190 " pdb=" O4' C4J 21190 " pdb=" C3' C4J 21190 " both_signs ideal model delta sigma weight residual False 2.50 -2.49 4.98 2.00e-01 2.50e+01 6.21e+02 chirality pdb=" CA PHE K 41 " pdb=" N PHE K 41 " pdb=" C PHE K 41 " pdb=" CB PHE K 41 " both_signs ideal model delta sigma weight residual False 2.51 1.49 1.02 2.00e-01 2.50e+01 2.62e+01 chirality pdb=" C3' G 21765 " pdb=" C4' G 21765 " pdb=" O3' G 21765 " pdb=" C2' G 21765 " both_signs ideal model delta sigma weight residual False -2.74 -1.84 -0.90 2.00e-01 2.50e+01 2.03e+01 ... (remaining 19271 not shown) Planarity restraints: 13117 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 5MC 21006 " 0.011 2.00e-02 2.50e+03 5.86e-01 7.72e+03 pdb=" C4' 5MC 21006 " -0.475 2.00e-02 2.50e+03 pdb=" O4' 5MC 21006 " -0.668 2.00e-02 2.50e+03 pdb=" C3' 5MC 21006 " 0.535 2.00e-02 2.50e+03 pdb=" O3' 5MC 21006 " 0.585 2.00e-02 2.50e+03 pdb=" C2' 5MC 21006 " 0.190 2.00e-02 2.50e+03 pdb=" O2' 5MC 21006 " -0.895 2.00e-02 2.50e+03 pdb=" C1' 5MC 21006 " -0.231 2.00e-02 2.50e+03 pdb=" N1 5MC 21006 " 0.947 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG 1 10 " 0.061 2.00e-02 2.50e+03 5.79e-01 7.55e+03 pdb=" C4' 2MG 1 10 " -0.476 2.00e-02 2.50e+03 pdb=" O4' 2MG 1 10 " -0.815 2.00e-02 2.50e+03 pdb=" C3' 2MG 1 10 " 0.552 2.00e-02 2.50e+03 pdb=" O3' 2MG 1 10 " 0.496 2.00e-02 2.50e+03 pdb=" C2' 2MG 1 10 " 0.251 2.00e-02 2.50e+03 pdb=" O2' 2MG 1 10 " -0.765 2.00e-02 2.50e+03 pdb=" C1' 2MG 1 10 " -0.236 2.00e-02 2.50e+03 pdb=" N9 2MG 1 10 " 0.933 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 5MC 21637 " 0.032 2.00e-02 2.50e+03 5.66e-01 7.22e+03 pdb=" C4' 5MC 21637 " -0.458 2.00e-02 2.50e+03 pdb=" O4' 5MC 21637 " -0.640 2.00e-02 2.50e+03 pdb=" C3' 5MC 21637 " 0.550 2.00e-02 2.50e+03 pdb=" O3' 5MC 21637 " 0.555 2.00e-02 2.50e+03 pdb=" C2' 5MC 21637 " 0.190 2.00e-02 2.50e+03 pdb=" O2' 5MC 21637 " -0.881 2.00e-02 2.50e+03 pdb=" C1' 5MC 21637 " -0.237 2.00e-02 2.50e+03 pdb=" N1 5MC 21637 " 0.888 2.00e-02 2.50e+03 ... (remaining 13114 not shown) Histogram of nonbonded interaction distances: 0.82 - 1.63: 7 1.63 - 2.45: 214 2.45 - 3.27: 100946 3.27 - 4.08: 326513 4.08 - 4.90: 498266 Warning: very small nonbonded interaction distances. Nonbonded interactions: 925946 Sorted by model distance: nonbonded pdb=" C4'A U 3 16 " pdb=" CZ ARG o 38 " model vdw 0.817 3.700 nonbonded pdb=" C4'A U 3 16 " pdb=" NH2 ARG o 38 " model vdw 0.941 3.550 nonbonded pdb=" C5'A U 3 16 " pdb=" NH2 ARG o 38 " model vdw 0.992 3.520 nonbonded pdb=" O4 A U 3 16 " pdb=" CG ARG o 41 " model vdw 1.121 3.440 nonbonded pdb=" O4'A U 3 16 " pdb=" NE ARG o 38 " model vdw 1.228 2.520 ... (remaining 925941 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 5 6.06 5 P 1894 5.49 5 Mg 117 5.21 5 S 169 5.16 5 C 58508 2.51 5 N 18685 2.21 5 O 24938 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 2.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.090 Extract box with map and model: 13.270 Check model and map are aligned: 1.220 Convert atoms to be neutral: 0.650 Process input model: 302.710 Find NCS groups from input model: 2.730 Set up NCS constraints: 0.330 Set refine NCS operators: 0.000 Set scattering table: 0.050 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.030 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 326.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.298 110051 Z= 0.517 Angle : 1.344 30.418 157771 Z= 0.873 Chirality : 0.108 4.985 19274 Planarity : 0.017 0.586 13117 Dihedral : 20.667 179.991 47219 Min Nonbonded Distance : 0.817 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 2.69 % Allowed : 8.20 % Favored : 89.11 % Rotamer Outliers : 10.74 % Cbeta Deviations : 0.75 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.95 % 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: -1.95 (0.08), residues: 7928 helix: 0.48 (0.09), residues: 2725 sheet: -1.67 (0.12), residues: 1425 loop : -2.55 (0.09), residues: 3778 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15856 Ramachandran restraints generated. 7928 Oldfield, 0 Emsley, 7928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15856 Ramachandran restraints generated. 7928 Oldfield, 0 Emsley, 7928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2722 residues out of total 6963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 733 poor density : 1989 time to evaluate : 6.575 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 outliers start: 733 outliers final: 202 residues processed: 2418 average time/residue: 1.0266 time to fit residues: 4119.7018 Evaluate side-chains 1638 residues out of total 6963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 202 poor density : 1436 time to evaluate : 6.483 Switching outliers to nearest non-outliers outliers start: 202 outliers final: 0 residues processed: 202 average time/residue: 0.8622 time to fit residues: 317.0516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 982 random chunks: chunk 829 optimal weight: 20.0000 chunk 744 optimal weight: 20.0000 chunk 413 optimal weight: 6.9990 chunk 254 optimal weight: 0.9990 chunk 502 optimal weight: 0.7980 chunk 397 optimal weight: 0.8980 chunk 769 optimal weight: 8.9990 chunk 297 optimal weight: 0.6980 chunk 468 optimal weight: 0.8980 chunk 572 optimal weight: 3.9990 chunk 891 optimal weight: 7.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 ASN A 83 GLN A 109 ASN A 131 GLN A 213 GLN B 40 ASN B 74 GLN B 124 ASN B 177 GLN ** B 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 64 HIS C 92 GLN C 157 HIS C 233 ASN C 238 GLN D 159 HIS E 112 HIS ** E 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 142 HIS ** E 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 65 GLN F 102 ASN F 133 GLN F 188 ASN G 22 HIS ** G 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 139 ASN G 182 GLN H 71 HIS H 74 GLN H 108 GLN H 110 GLN H 150 GLN H 170 GLN I 32 GLN I 64 ASN I 88 ASN I 94 ASN ** I 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 110 GLN J 112 GLN J 142 ASN J 155 HIS K 39 ASN K 85 HIS L 14 GLN L 18 HIS M 69 GLN M 87 GLN N 62 GLN N 69 ASN N 151 ASN O 24 ASN P 82 ASN Q 40 GLN ** R 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 75 ASN S 78 HIS S 87 ASN S 99 HIS T 17 ASN ** T 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 20 HIS V 33 GLN W 12 ASN ** W 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 39 GLN W 42 GLN W 80 ASN Y 29 HIS Z 82 HIS a 17 HIS a 43 ASN a 80 HIS ** b 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 31 HIS b 42 ASN c 43 ASN d 37 ASN e 46 ASN f 95 HIS g 51 ASN ** g 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 203 ASN g 234 HIS i 85 GLN j 11 ASN j 60 GLN j 103 GLN j 109 HIS k 98 GLN ** k 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 197 HIS ** k 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 286 GLN ** k 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 415 GLN l 224 ASN ** m 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 94 ASN m 134 HIS o 194 GLN ** o 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 394 ASN o 403 GLN o 445 GLN p 135 ASN ** p 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 467 ASN p 592 ASN p 705 HIS p 712 GLN q 323 ASN q 495 ASN ** q 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 582 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 610 GLN s 106 ASN s 145 HIS Total number of N/Q/H flips: 101 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.2319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.100 110051 Z= 0.205 Angle : 0.804 17.752 157771 Z= 0.425 Chirality : 0.043 0.377 19274 Planarity : 0.007 0.142 13117 Dihedral : 18.618 179.461 31505 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 14.22 Ramachandran Plot: Outliers : 0.93 % Allowed : 6.74 % Favored : 92.33 % Rotamer Outliers : 3.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.89 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.09), residues: 7928 helix: 2.22 (0.10), residues: 2754 sheet: -1.35 (0.12), residues: 1500 loop : -2.24 (0.09), residues: 3674 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15856 Ramachandran restraints generated. 7928 Oldfield, 0 Emsley, 7928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15856 Ramachandran restraints generated. 7928 Oldfield, 0 Emsley, 7928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1877 residues out of total 6963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 269 poor density : 1608 time to evaluate : 6.529 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 outliers start: 269 outliers final: 112 residues processed: 1767 average time/residue: 0.9881 time to fit residues: 2932.3798 Evaluate side-chains 1484 residues out of total 6963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 1372 time to evaluate : 8.032 Switching outliers to nearest non-outliers outliers start: 112 outliers final: 0 residues processed: 112 average time/residue: 0.7740 time to fit residues: 168.7471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 982 random chunks: chunk 495 optimal weight: 4.9990 chunk 276 optimal weight: 0.5980 chunk 742 optimal weight: 20.0000 chunk 607 optimal weight: 9.9990 chunk 245 optimal weight: 0.5980 chunk 893 optimal weight: 20.0000 chunk 965 optimal weight: 30.0000 chunk 795 optimal weight: 30.0000 chunk 885 optimal weight: 50.0000 chunk 304 optimal weight: 0.9980 chunk 716 optimal weight: 40.0000 overall best weight: 3.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 163 GLN B 177 GLN ** C 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 87 ASN ** E 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 142 HIS E 209 HIS ** G 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 197 ASN H 11 GLN H 42 GLN H 74 GLN H 108 GLN H 122 HIS I 32 GLN I 116 HIS ** I 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 58 GLN ** K 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 14 GLN M 76 ASN N 62 GLN N 69 ASN O 12 GLN ** O 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 87 ASN U 20 HIS ** V 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 21 ASN X 99 ASN Y 31 ASN Z 44 GLN Z 82 HIS b 42 ASN ** b 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 43 ASN f 143 HIS ** g 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 108 HIS k 249 ASN ** k 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 295 ASN ** k 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 465 ASN l 176 ASN l 252 ASN ** m 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 254 HIS p 513 ASN ** q 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.2821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.102 110051 Z= 0.342 Angle : 0.779 16.945 157771 Z= 0.414 Chirality : 0.044 0.338 19274 Planarity : 0.007 0.140 13117 Dihedral : 18.310 178.607 31505 Min Nonbonded Distance : 0.957 Molprobity Statistics. All-atom Clashscore : 13.99 Ramachandran Plot: Outliers : 0.85 % Allowed : 7.68 % Favored : 91.47 % Rotamer Outliers : 4.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.58 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.09), residues: 7928 helix: 2.15 (0.10), residues: 2762 sheet: -1.19 (0.12), residues: 1481 loop : -2.11 (0.09), residues: 3685 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15856 Ramachandran restraints generated. 7928 Oldfield, 0 Emsley, 7928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15856 Ramachandran restraints generated. 7928 Oldfield, 0 Emsley, 7928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1680 residues out of total 6963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 273 poor density : 1407 time to evaluate : 7.237 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 outliers start: 273 outliers final: 133 residues processed: 1572 average time/residue: 0.9798 time to fit residues: 2609.5900 Evaluate side-chains 1451 residues out of total 6963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 1318 time to evaluate : 6.495 Switching outliers to nearest non-outliers outliers start: 133 outliers final: 0 residues processed: 133 average time/residue: 0.7664 time to fit residues: 198.5296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 982 random chunks: chunk 882 optimal weight: 0.5980 chunk 671 optimal weight: 10.0000 chunk 463 optimal weight: 1.9990 chunk 98 optimal weight: 5.9990 chunk 426 optimal weight: 0.2980 chunk 599 optimal weight: 0.1980 chunk 896 optimal weight: 4.9990 chunk 949 optimal weight: 20.0000 chunk 468 optimal weight: 1.9990 chunk 849 optimal weight: 6.9990 chunk 255 optimal weight: 9.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN A 69 ASN B 79 HIS B 101 HIS ** C 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 113 ASN D 67 ASN E 142 HIS F 124 ASN ** G 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 139 ASN G 197 ASN ** H 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 108 GLN I 32 GLN K 39 ASN L 14 GLN N 69 ASN R 95 HIS ** R 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 75 ASN S 78 HIS ** V 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 33 GLN W 56 HIS X 21 ASN X 99 ASN Z 85 ASN e 46 ASN g 94 ASN ** k 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.3250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.132 110051 Z= 0.178 Angle : 0.706 16.232 157771 Z= 0.376 Chirality : 0.039 0.309 19274 Planarity : 0.006 0.136 13117 Dihedral : 18.203 179.418 31505 Min Nonbonded Distance : 1.153 Molprobity Statistics. All-atom Clashscore : 14.16 Ramachandran Plot: Outliers : 0.79 % Allowed : 6.74 % Favored : 92.47 % Rotamer Outliers : 2.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.26 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.09), residues: 7928 helix: 2.23 (0.10), residues: 2761 sheet: -0.99 (0.13), residues: 1462 loop : -2.00 (0.09), residues: 3705 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15856 Ramachandran restraints generated. 7928 Oldfield, 0 Emsley, 7928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15856 Ramachandran restraints generated. 7928 Oldfield, 0 Emsley, 7928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1572 residues out of total 6963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 1410 time to evaluate : 6.693 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 outliers start: 162 outliers final: 61 residues processed: 1512 average time/residue: 0.9684 time to fit residues: 2467.6160 Evaluate side-chains 1369 residues out of total 6963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 1308 time to evaluate : 6.609 Switching outliers to nearest non-outliers outliers start: 61 outliers final: 0 residues processed: 61 average time/residue: 0.8111 time to fit residues: 98.2846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 982 random chunks: chunk 790 optimal weight: 5.9990 chunk 538 optimal weight: 0.9990 chunk 13 optimal weight: 10.0000 chunk 706 optimal weight: 0.0020 chunk 391 optimal weight: 0.9990 chunk 809 optimal weight: 30.0000 chunk 656 optimal weight: 1.9990 chunk 1 optimal weight: 30.0000 chunk 484 optimal weight: 5.9990 chunk 851 optimal weight: 7.9990 chunk 239 optimal weight: 7.9990 overall best weight: 1.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN A 131 GLN B 163 GLN C 113 ASN D 67 ASN E 130 GLN E 142 HIS E 157 ASN ** G 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 108 GLN I 32 GLN N 69 ASN O 29 HIS ** O 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 95 HIS ** R 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 93 ASN ** V 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 33 GLN X 21 ASN X 99 ASN Y 31 ASN ** Z 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 24 GLN ** k 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 513 ASN p 612 ASN ** q 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 544 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.3447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.110 110051 Z= 0.236 Angle : 0.709 16.131 157771 Z= 0.377 Chirality : 0.040 0.269 19274 Planarity : 0.006 0.131 13117 Dihedral : 18.009 179.929 31505 Min Nonbonded Distance : 1.034 Molprobity Statistics. All-atom Clashscore : 14.22 Ramachandran Plot: Outliers : 0.73 % Allowed : 7.34 % Favored : 91.93 % Rotamer Outliers : 2.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.26 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.09), residues: 7928 helix: 2.14 (0.10), residues: 2762 sheet: -0.93 (0.13), residues: 1506 loop : -1.94 (0.09), residues: 3660 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15856 Ramachandran restraints generated. 7928 Oldfield, 0 Emsley, 7928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15856 Ramachandran restraints generated. 7928 Oldfield, 0 Emsley, 7928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1556 residues out of total 6963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 196 poor density : 1360 time to evaluate : 6.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 196 outliers final: 92 residues processed: 1475 average time/residue: 1.0224 time to fit residues: 2568.2530 Evaluate side-chains 1362 residues out of total 6963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 1270 time to evaluate : 6.476 Switching outliers to nearest non-outliers outliers start: 92 outliers final: 0 residues processed: 92 average time/residue: 0.7908 time to fit residues: 144.7729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 982 random chunks: chunk 319 optimal weight: 8.9990 chunk 854 optimal weight: 8.9990 chunk 187 optimal weight: 30.0000 chunk 557 optimal weight: 0.9990 chunk 234 optimal weight: 1.9990 chunk 950 optimal weight: 30.0000 chunk 788 optimal weight: 7.9990 chunk 439 optimal weight: 0.8980 chunk 78 optimal weight: 50.0000 chunk 314 optimal weight: 10.0000 chunk 498 optimal weight: 10.0000 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 113 ASN ** D 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 65 GLN F 226 ASN ** G 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 139 ASN ** H 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 108 GLN I 32 GLN ** I 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 62 GLN N 69 ASN ** O 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 83 GLN ** S 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 91 HIS ** V 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 21 ASN X 99 ASN Y 106 GLN b 49 HIS e 24 GLN k 221 ASN k 263 GLN ** k 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 415 GLN m 64 GLN p 307 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.3677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.156 110051 Z= 0.381 Angle : 0.779 16.197 157771 Z= 0.411 Chirality : 0.044 0.307 19274 Planarity : 0.007 0.133 13117 Dihedral : 17.955 179.898 31505 Min Nonbonded Distance : 1.002 Molprobity Statistics. All-atom Clashscore : 14.92 Ramachandran Plot: Outliers : 0.78 % Allowed : 7.72 % Favored : 91.50 % Rotamer Outliers : 2.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.26 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.09), residues: 7928 helix: 1.87 (0.10), residues: 2764 sheet: -1.00 (0.13), residues: 1509 loop : -1.93 (0.09), residues: 3655 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15856 Ramachandran restraints generated. 7928 Oldfield, 0 Emsley, 7928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15856 Ramachandran restraints generated. 7928 Oldfield, 0 Emsley, 7928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1510 residues out of total 6963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 1338 time to evaluate : 6.493 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 outliers start: 172 outliers final: 98 residues processed: 1429 average time/residue: 0.9816 time to fit residues: 2370.9676 Evaluate side-chains 1386 residues out of total 6963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 1288 time to evaluate : 6.419 Switching outliers to nearest non-outliers outliers start: 98 outliers final: 0 residues processed: 98 average time/residue: 0.7505 time to fit residues: 147.1166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 982 random chunks: chunk 916 optimal weight: 50.0000 chunk 107 optimal weight: 6.9990 chunk 541 optimal weight: 4.9990 chunk 693 optimal weight: 20.0000 chunk 537 optimal weight: 2.9990 chunk 799 optimal weight: 5.9990 chunk 530 optimal weight: 2.9990 chunk 946 optimal weight: 30.0000 chunk 592 optimal weight: 3.9990 chunk 577 optimal weight: 4.9990 chunk 436 optimal weight: 0.8980 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 GLN C 113 ASN C 194 GLN C 238 GLN D 22 ASN ** D 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 65 GLN F 226 ASN ** G 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 32 GLN I 88 ASN ** I 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 14 HIS K 62 GLN L 14 GLN N 69 ASN O 80 HIS S 78 HIS ** S 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 21 ASN X 22 ASN X 99 ASN Y 106 GLN ** Z 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 24 GLN g 240 ASN g 295 HIS ** i 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 64 GLN ** o 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.3882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.196 110051 Z= 0.306 Angle : 0.740 16.184 157771 Z= 0.393 Chirality : 0.041 0.281 19274 Planarity : 0.006 0.130 13117 Dihedral : 17.915 179.264 31505 Min Nonbonded Distance : 1.017 Molprobity Statistics. All-atom Clashscore : 15.02 Ramachandran Plot: Outliers : 0.73 % Allowed : 7.24 % Favored : 92.03 % Rotamer Outliers : 1.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.26 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.09), residues: 7928 helix: 1.80 (0.10), residues: 2765 sheet: -0.86 (0.13), residues: 1443 loop : -1.92 (0.09), residues: 3720 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15856 Ramachandran restraints generated. 7928 Oldfield, 0 Emsley, 7928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15856 Ramachandran restraints generated. 7928 Oldfield, 0 Emsley, 7928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1440 residues out of total 6963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 1319 time to evaluate : 6.533 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 outliers start: 121 outliers final: 73 residues processed: 1382 average time/residue: 0.9646 time to fit residues: 2251.5146 Evaluate side-chains 1347 residues out of total 6963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 1274 time to evaluate : 6.400 Switching outliers to nearest non-outliers outliers start: 73 outliers final: 0 residues processed: 73 average time/residue: 0.7266 time to fit residues: 105.5577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 982 random chunks: chunk 585 optimal weight: 5.9990 chunk 377 optimal weight: 0.8980 chunk 565 optimal weight: 0.9980 chunk 285 optimal weight: 0.5980 chunk 185 optimal weight: 50.0000 chunk 183 optimal weight: 6.9990 chunk 601 optimal weight: 0.9990 chunk 644 optimal weight: 8.9990 chunk 467 optimal weight: 0.0370 chunk 88 optimal weight: 40.0000 chunk 743 optimal weight: 0.7980 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 163 GLN C 113 ASN ** D 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 195 ASN ** E 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 153 ASN F 226 ASN ** G 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 19 GLN H 74 GLN I 32 GLN ** I 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 18 HIS N 69 ASN ** O 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 33 GLN X 21 ASN X 99 ASN Y 106 GLN g 295 HIS ** k 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.4144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.251 110051 Z= 0.191 Angle : 0.697 17.355 157771 Z= 0.372 Chirality : 0.038 0.291 19274 Planarity : 0.006 0.123 13117 Dihedral : 17.802 179.769 31505 Min Nonbonded Distance : 1.193 Molprobity Statistics. All-atom Clashscore : 15.30 Ramachandran Plot: Outliers : 0.71 % Allowed : 6.79 % Favored : 92.51 % Rotamer Outliers : 1.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.26 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.09), residues: 7928 helix: 2.02 (0.10), residues: 2745 sheet: -0.79 (0.13), residues: 1453 loop : -1.80 (0.10), residues: 3730 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15856 Ramachandran restraints generated. 7928 Oldfield, 0 Emsley, 7928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15856 Ramachandran restraints generated. 7928 Oldfield, 0 Emsley, 7928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1456 residues out of total 6963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 1369 time to evaluate : 6.425 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 outliers start: 87 outliers final: 31 residues processed: 1408 average time/residue: 0.9598 time to fit residues: 2268.4458 Evaluate side-chains 1308 residues out of total 6963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 1277 time to evaluate : 5.711 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 0 residues processed: 31 average time/residue: 0.7037 time to fit residues: 47.5462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 982 random chunks: chunk 860 optimal weight: 40.0000 chunk 906 optimal weight: 5.9990 chunk 827 optimal weight: 20.0000 chunk 882 optimal weight: 0.9990 chunk 530 optimal weight: 0.0270 chunk 384 optimal weight: 0.8980 chunk 692 optimal weight: 6.9990 chunk 270 optimal weight: 1.9990 chunk 797 optimal weight: 20.0000 chunk 834 optimal weight: 20.0000 chunk 878 optimal weight: 8.9990 overall best weight: 1.9844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 113 ASN D 67 ASN ** E 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 19 GLN ** H 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 32 GLN ** I 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 39 ASN K 62 GLN L 18 HIS N 69 ASN O 24 ASN ** O 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 21 ASN X 99 ASN e 24 GLN g 295 HIS ** i 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 465 ASN ** o 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.4165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.601 110051 Z= 0.281 Angle : 0.745 73.898 157771 Z= 0.387 Chirality : 0.040 0.277 19274 Planarity : 0.007 0.157 13117 Dihedral : 17.708 179.870 31505 Min Nonbonded Distance : 1.075 Molprobity Statistics. All-atom Clashscore : 14.99 Ramachandran Plot: Outliers : 0.69 % Allowed : 6.87 % Favored : 92.43 % Rotamer Outliers : 0.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.26 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.09), residues: 7928 helix: 1.94 (0.10), residues: 2761 sheet: -0.74 (0.13), residues: 1460 loop : -1.77 (0.10), residues: 3707 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15856 Ramachandran restraints generated. 7928 Oldfield, 0 Emsley, 7928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15856 Ramachandran restraints generated. 7928 Oldfield, 0 Emsley, 7928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1379 residues out of total 6963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 1319 time to evaluate : 5.831 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 outliers start: 60 outliers final: 33 residues processed: 1337 average time/residue: 0.9676 time to fit residues: 2180.7352 Evaluate side-chains 1312 residues out of total 6963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 1279 time to evaluate : 6.382 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 0 residues processed: 33 average time/residue: 0.7599 time to fit residues: 54.9980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 982 random chunks: chunk 579 optimal weight: 0.9980 chunk 932 optimal weight: 20.0000 chunk 569 optimal weight: 1.9990 chunk 442 optimal weight: 0.7980 chunk 648 optimal weight: 0.7980 chunk 978 optimal weight: 7.9990 chunk 900 optimal weight: 0.3980 chunk 779 optimal weight: 6.9990 chunk 80 optimal weight: 7.9990 chunk 601 optimal weight: 0.8980 chunk 477 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 113 ASN ** E 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 226 ASN ** G 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 32 GLN ** I 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 69 ASN O 24 ASN ** O 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 21 ASN ** X 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 24 GLN ** i 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.4179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 1.756 110051 Z= 0.479 Angle : 0.775 73.898 157771 Z= 0.413 Chirality : 0.040 0.277 19274 Planarity : 0.007 0.253 13117 Dihedral : 17.708 179.870 31505 Min Nonbonded Distance : 1.075 Molprobity Statistics. All-atom Clashscore : 16.49 Ramachandran Plot: Outliers : 0.69 % Allowed : 6.87 % Favored : 92.43 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.26 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.09), residues: 7928 helix: 1.94 (0.10), residues: 2761 sheet: -0.74 (0.13), residues: 1460 loop : -1.77 (0.10), residues: 3707 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15856 Ramachandran restraints generated. 7928 Oldfield, 0 Emsley, 7928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15856 Ramachandran restraints generated. 7928 Oldfield, 0 Emsley, 7928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1280 residues out of total 6963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1278 time to evaluate : 5.762 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 outliers start: 2 outliers final: 0 residues processed: 1278 average time/residue: 0.9063 time to fit residues: 1950.5637 Evaluate side-chains 1276 residues out of total 6963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1276 time to evaluate : 5.825 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.4185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 982 random chunks: chunk 618 optimal weight: 0.9990 chunk 829 optimal weight: 40.0000 chunk 238 optimal weight: 5.9990 chunk 718 optimal weight: 0.5980 chunk 115 optimal weight: 5.9990 chunk 216 optimal weight: 1.9990 chunk 780 optimal weight: 6.9990 chunk 326 optimal weight: 8.9990 chunk 801 optimal weight: 0.7980 chunk 98 optimal weight: 6.9990 chunk 143 optimal weight: 10.0000 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 113 ASN ** E 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 226 ASN ** G 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 32 GLN ** I 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 69 ASN O 24 ASN ** O 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 24 GLN ** i 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.201768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.149738 restraints weight = 160150.716| |-----------------------------------------------------------------------------| r_work (start): 0.3688 rms_B_bonded: 1.71 r_work: 0.3656 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.3634 rms_B_bonded: 1.65 restraints_weight: 0.2500 r_work: 0.3611 rms_B_bonded: 1.85 restraints_weight: 0.1250 r_work: 0.3585 rms_B_bonded: 2.15 restraints_weight: 0.0625 r_work: 0.3555 rms_B_bonded: 2.56 restraints_weight: 0.0312 r_work: 0.3518 rms_B_bonded: 3.12 restraints_weight: 0.0156 r_work: 0.3473 rms_B_bonded: 3.87 restraints_weight: 0.0078 r_work: 0.3414 rms_B_bonded: 4.90 restraints_weight: 0.0039 r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4339 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4339 r_free = 0.4339 target_work(ls_wunit_k1) = 0.202 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4339 r_free = 0.4339 target_work(ls_wunit_k1) = 0.202 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.4339 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.4178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 1.183 110051 Z= 0.389 Angle : 0.766 73.898 157771 Z= 0.405 Chirality : 0.040 0.277 19274 Planarity : 0.007 0.259 13117 Dihedral : 17.708 179.870 31505 Min Nonbonded Distance : 1.075 Molprobity Statistics. All-atom Clashscore : 16.51 Ramachandran Plot: Outliers : 0.69 % Allowed : 6.87 % Favored : 92.43 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.26 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.09), residues: 7928 helix: 1.94 (0.10), residues: 2761 sheet: -0.74 (0.13), residues: 1460 loop : -1.77 (0.10), residues: 3707 =============================================================================== Job complete usr+sys time: 34035.16 seconds wall clock time: 593 minutes 4.83 seconds (35584.83 seconds total)