Starting phenix.real_space_refine (version: dev) on Wed Apr 20 21:53:22 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r6p_4737/04_2022/6r6p_4737.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r6p_4737/04_2022/6r6p_4737.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r6p_4737/04_2022/6r6p_4737.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r6p_4737/04_2022/6r6p_4737.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r6p_4737/04_2022/6r6p_4737.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r6p_4737/04_2022/6r6p_4737.pdb" } resolution = 3.1 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= 0.002 sd= 0.024 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 ARG 242": "NH1" <-> "NH2" Residue "B ARG 10": "NH1" <-> "NH2" Residue "B ARG 97": "NH1" <-> "NH2" Residue "B ARG 268": "NH1" <-> "NH2" Residue "C ARG 49": "NH1" <-> "NH2" Residue "C ARG 204": "NH1" <-> "NH2" Residue "C ARG 306": "NH1" <-> "NH2" Residue "C ARG 323": "NH1" <-> "NH2" Residue "C ARG 337": "NH1" <-> "NH2" Residue "D ARG 15": "NH1" <-> "NH2" Residue "D ARG 23": "NH1" <-> "NH2" Residue "D ARG 24": "NH1" <-> "NH2" Residue "D ARG 33": "NH1" <-> "NH2" Residue "D ARG 50": "NH1" <-> "NH2" Residue "D ARG 108": "NH1" <-> "NH2" Residue "D ARG 179": "NH1" <-> "NH2" Residue "E ARG 101": "NH1" <-> "NH2" Residue "E ARG 157": "NH1" <-> "NH2" Residue "E ARG 184": "NH1" <-> "NH2" Residue "E PHE 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 48": "NH1" <-> "NH2" Residue "F ARG 96": "NH1" <-> "NH2" Residue "F ARG 159": "NH1" <-> "NH2" Residue "F ARG 238": "NH1" <-> "NH2" Residue "F ARG 247": "NH1" <-> "NH2" Residue "G ARG 89": "NH1" <-> "NH2" Residue "G ARG 113": "NH1" <-> "NH2" Residue "G ARG 189": "NH1" <-> "NH2" Residue "G ARG 234": "NH1" <-> "NH2" Residue "H ARG 23": "NH1" <-> "NH2" Residue "H ARG 89": "NH1" <-> "NH2" Residue "I ARG 4": "NH1" <-> "NH2" Residue "I ARG 69": "NH1" <-> "NH2" Residue "I ARG 98": "NH1" <-> "NH2" Residue "I ARG 116": "NH1" <-> "NH2" Residue "I ARG 153": "NH1" <-> "NH2" Residue "I ARG 162": "NH1" <-> "NH2" Residue "I ARG 203": "NH1" <-> "NH2" Residue "I ARG 210": "NH1" <-> "NH2" Residue "J ARG 64": "NH1" <-> "NH2" Residue "J ARG 146": "NH1" <-> "NH2" Residue "J ARG 164": "NH1" <-> "NH2" Residue "L ARG 31": "NH1" <-> "NH2" Residue "L ARG 102": "NH1" <-> "NH2" Residue "L ARG 116": "NH1" <-> "NH2" Residue "L ARG 158": "NH1" <-> "NH2" Residue "M ARG 11": "NH1" <-> "NH2" Residue "M ARG 98": "NH1" <-> "NH2" Residue "M ARG 109": "NH1" <-> "NH2" Residue "M ARG 119": "NH1" <-> "NH2" Residue "M ARG 121": "NH1" <-> "NH2" Residue "N ARG 24": "NH1" <-> "NH2" Residue "N ARG 50": "NH1" <-> "NH2" Residue "N ARG 65": "NH1" <-> "NH2" Residue "N ARG 96": "NH1" <-> "NH2" Residue "N ARG 169": "NH1" <-> "NH2" Residue "N ARG 189": "NH1" <-> "NH2" Residue "N ARG 194": "NH1" <-> "NH2" Residue "O ARG 78": "NH1" <-> "NH2" Residue "O ARG 128": "NH1" <-> "NH2" Residue "O ARG 140": "NH1" <-> "NH2" Residue "P ARG 62": "NH1" <-> "NH2" Residue "P TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 37": "NH1" <-> "NH2" Residue "Q ARG 55": "NH1" <-> "NH2" Residue "Q ARG 91": "NH1" <-> "NH2" Residue "Q ARG 180": "NH1" <-> "NH2" Residue "Q ARG 181": "NH1" <-> "NH2" Residue "R ARG 38": "NH1" <-> "NH2" Residue "R ARG 42": "NH1" <-> "NH2" Residue "R ARG 74": "NH1" <-> "NH2" Residue "R ARG 117": "NH1" <-> "NH2" Residue "R ARG 173": "NH1" <-> "NH2" Residue "R ARG 176": "NH1" <-> "NH2" Residue "S ARG 31": "NH1" <-> "NH2" Residue "S ARG 43": "NH1" <-> "NH2" Residue "S ARG 83": "NH1" <-> "NH2" Residue "S ARG 111": "NH1" <-> "NH2" Residue "S ARG 118": "NH1" <-> "NH2" Residue "S ARG 139": "NH1" <-> "NH2" Residue "T ARG 130": "NH1" <-> "NH2" Residue "T ARG 136": "NH1" <-> "NH2" Residue "V ARG 48": "NH1" <-> "NH2" Residue "V ARG 51": "NH1" <-> "NH2" Residue "V ARG 89": "NH1" <-> "NH2" Residue "V ARG 131": "NH1" <-> "NH2" Residue "W ARG 19": "NH1" <-> "NH2" Residue "X ARG 53": "NH1" <-> "NH2" Residue "X PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 129": "NH1" <-> "NH2" Residue "X ARG 139": "NH1" <-> "NH2" Residue "Y ARG 27": "NH1" <-> "NH2" Residue "Y ARG 87": "NH1" <-> "NH2" Residue "Z TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 65": "NH1" <-> "NH2" Residue "a ARG 9": "NH1" <-> "NH2" Residue "a ARG 21": "NH1" <-> "NH2" Residue "a ARG 65": "NH1" <-> "NH2" Residue "a ARG 105": "NH1" <-> "NH2" Residue "b ARG 14": "NH1" <-> "NH2" Residue "b ARG 18": "NH1" <-> "NH2" Residue "b ARG 28": "NH1" <-> "NH2" Residue "c ARG 39": "NH1" <-> "NH2" Residue "d ARG 90": "NH1" <-> "NH2" Residue "e ARG 36": "NH1" <-> "NH2" Residue "e ARG 39": "NH1" <-> "NH2" Residue "e ARG 128": "NH1" <-> "NH2" Residue "f ARG 89": "NH1" <-> "NH2" Residue "g ARG 29": "NH1" <-> "NH2" Residue "g ARG 60": "NH1" <-> "NH2" Residue "h ARG 7": "NH1" <-> "NH2" Residue "h ARG 94": "NH1" <-> "NH2" Residue "i ARG 45": "NH1" <-> "NH2" Residue "i ARG 68": "NH1" <-> "NH2" Residue "i ARG 76": "NH1" <-> "NH2" Residue "j ARG 20": "NH1" <-> "NH2" Residue "j ARG 45": "NH1" <-> "NH2" Residue "j ARG 55": "NH1" <-> "NH2" Residue "j ARG 56": "NH1" <-> "NH2" Residue "j ARG 72": "NH1" <-> "NH2" Residue "j ARG 79": "NH1" <-> "NH2" Residue "k ARG 3": "NH1" <-> "NH2" Residue "l ARG 28": "NH1" <-> "NH2" Residue "l ARG 46": "NH1" <-> "NH2" Residue "m ARG 97": "NH1" <-> "NH2" Residue "m ARG 111": "NH1" <-> "NH2" Residue "n ARG 2": "NH1" <-> "NH2" Residue "n ARG 23": "NH1" <-> "NH2" Residue "o ARG 40": "NH1" <-> "NH2" Residue "o ARG 43": "NH1" <-> "NH2" Residue "o ARG 78": "NH1" <-> "NH2" Residue "p ARG 17": "NH1" <-> "NH2" Residue "p ARG 49": "NH1" <-> "NH2" Residue "p ARG 84": "NH1" <-> "NH2" Residue "r ARG 35": "NH1" <-> "NH2" Residue "r ARG 112": "NH1" <-> "NH2" Residue "r ARG 113": "NH1" <-> "NH2" Residue "q ARG 128": "NH1" <-> "NH2" Residue "u ARG 51": "NH1" <-> "NH2" Residue "u PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u ARG 82": "NH1" <-> "NH2" Residue "u ARG 107": "NH1" <-> "NH2" Residue "u ARG 136": "NH1" <-> "NH2" Residue "u ARG 162": "NH1" <-> "NH2" Residue "u ARG 165": "NH1" <-> "NH2" Residue "u ARG 213": "NH1" <-> "NH2" Residue "v ARG 68": "NH1" <-> "NH2" Residue "v ARG 117": "NH1" <-> "NH2" Residue "v ARG 123": "NH1" <-> "NH2" Residue "v ARG 166": "NH1" <-> "NH2" Residue "v ARG 167": "NH1" <-> "NH2" Residue "v ARG 200": "NH1" <-> "NH2" Residue "v ARG 227": "NH1" <-> "NH2" Residue "x ARG 11": "NH1" <-> "NH2" Residue "x ARG 49": "NH1" <-> "NH2" Residue "x ARG 68": "NH1" <-> "NH2" Residue "x ARG 77": "NH1" <-> "NH2" Residue "x ARG 108": "NH1" <-> "NH2" Residue "x ARG 191": "NH1" <-> "NH2" Residue "x ARG 198": "NH1" <-> "NH2" Residue "x ARG 221": "NH1" <-> "NH2" Residue "x ARG 252": "NH1" <-> "NH2" Residue "z ARG 72": "NH1" <-> "NH2" Residue "z ARG 131": "NH1" <-> "NH2" Residue "z ARG 132": "NH1" <-> "NH2" Residue "z ARG 178": "NH1" <-> "NH2" Residue "z ARG 198": "NH1" <-> "NH2" Residue "z ARG 216": "NH1" <-> "NH2" Residue "z ARG 231": "NH1" <-> "NH2" Residue "z ARG 233": "NH1" <-> "NH2" Residue "y ARG 41": "NH1" <-> "NH2" Residue "y ARG 81": "NH1" <-> "NH2" Residue "y ARG 143": "NH1" <-> "NH2" Residue "CC ARG 25": "NH1" <-> "NH2" Residue "CC TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CC ARG 41": "NH1" <-> "NH2" Residue "CC ARG 47": "NH1" <-> "NH2" Residue "CC ARG 123": "NH1" <-> "NH2" Residue "CC ARG 141": "NH1" <-> "NH2" Residue "XX ARG 18": "NH1" <-> "NH2" Residue "XX ARG 38": "NH1" <-> "NH2" Residue "XX ARG 54": "NH1" <-> "NH2" Residue "XX ARG 69": "NH1" <-> "NH2" Residue "XX ARG 83": "NH1" <-> "NH2" Residue "XX ARG 138": "NH1" <-> "NH2" Residue "EE ARG 97": "NH1" <-> "NH2" Residue "QQ ARG 20": "NH1" <-> "NH2" Residue "QQ ARG 104": "NH1" <-> "NH2" Residue "QQ ARG 114": "NH1" <-> "NH2" Residue "QQ ARG 121": "NH1" <-> "NH2" Residue "MM ARG 104": "NH1" <-> "NH2" Residue "MM ARG 117": "NH1" <-> "NH2" Residue "MM ARG 128": "NH1" <-> "NH2" Residue "MM ARG 141": "NH1" <-> "NH2" Residue "MM ARG 150": "NH1" <-> "NH2" Residue "UU ARG 126": "NH1" <-> "NH2" Residue "UU ARG 140": "NH1" <-> "NH2" Residue "YY ARG 5": "NH1" <-> "NH2" Residue "YY ARG 63": "NH1" <-> "NH2" Residue "YY ARG 81": "NH1" <-> "NH2" Residue "TT ARG 36": "NH1" <-> "NH2" Residue "VV ARG 8": "NH1" <-> "NH2" Residue "VV ARG 17": "NH1" <-> "NH2" Residue "VV ARG 18": "NH1" <-> "NH2" Residue "VV ARG 67": "NH1" <-> "NH2" Residue "VV ARG 107": "NH1" <-> "NH2" Residue "NN ARG 20": "NH1" <-> "NH2" Residue "NN ARG 61": "NH1" <-> "NH2" Residue "NN ARG 110": "NH1" <-> "NH2" Residue "ZZ ARG 10": "NH1" <-> "NH2" Residue "ZZ ARG 85": "NH1" <-> "NH2" Residue "ZZ ARG 87": "NH1" <-> "NH2" Residue "ZZ ARG 89": "NH1" <-> "NH2" Residue "JJ ARG 72": "NH1" <-> "NH2" Residue "AA ARG 101": "NH1" <-> "NH2" Residue "AA ARG 104": "NH1" <-> "NH2" Residue "DD ARG 67": "NH1" <-> "NH2" Residue "DD ARG 143": "NH1" <-> "NH2" Residue "DD ARG 146": "NH1" <-> "NH2" Residue "BB ARG 55": "NH1" <-> "NH2" Residue "BB ARG 62": "NH1" <-> "NH2" Residue "BB ARG 71": "NH1" <-> "NH2" Residue "BB ARG 81": "NH1" <-> "NH2" Residue "BB ARG 127": "NH1" <-> "NH2" Residue "BB ARG 135": "NH1" <-> "NH2" Residue "BB ARG 164": "NH1" <-> "NH2" Residue "BB ARG 198": "NH1" <-> "NH2" Residue "SS ARG 65": "NH1" <-> "NH2" Residue "SS ARG 95": "NH1" <-> "NH2" Residue "SS ARG 96": "NH1" <-> "NH2" Residue "RR ARG 45": "NH1" <-> "NH2" Residue "9 ARG 42": "NH1" <-> "NH2" Residue "9 ARG 51": "NH1" <-> "NH2" Residue "9 ARG 59": "NH1" <-> "NH2" Residue "9 ARG 130": "NH1" <-> "NH2" Residue "II ARG 14": "NH1" <-> "NH2" Residue "II ARG 39": "NH1" <-> "NH2" Residue "II ARG 55": "NH1" <-> "NH2" Residue "II ARG 86": "NH1" <-> "NH2" Residue "II ARG 121": "NH1" <-> "NH2" Residue "II ARG 142": "NH1" <-> "NH2" Residue "PP ARG 16": "NH1" <-> "NH2" Residue "PP ARG 62": "NH1" <-> "NH2" Residue "PP ARG 84": "NH1" <-> "NH2" Residue "PP ARG 102": "NH1" <-> "NH2" Residue "PP ARG 121": "NH1" <-> "NH2" Residue "GG ARG 19": "NH1" <-> "NH2" Residue "GG ARG 87": "NH1" <-> "NH2" Residue "OO ARG 80": "NH1" <-> "NH2" Residue "OO ARG 85": "NH1" <-> "NH2" Residue "FF ARG 13": "NH1" <-> "NH2" Residue "FF ARG 40": "NH1" <-> "NH2" Residue "FF ARG 44": "NH1" <-> "NH2" Residue "FF ARG 66": "NH1" <-> "NH2" Residue "FF ARG 67": "NH1" <-> "NH2" Residue "0 ARG 138": "NH1" <-> "NH2" Residue "6 ARG 47": "NH1" <-> "NH2" Residue "6 ARG 60": "NH1" <-> "NH2" Residue "6 ARG 100": "NH1" <-> "NH2" Residue "6 TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.20s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 218067 Number of models: 1 Model: "" Number of chains: 98 Chain: "5" Number of atoms: 78486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3662, 78486 Classifications: {'RNA': 3661, 'DNA': 1} Modifications used: {'5*END': 1, 'rna2p_pur': 343, 'rna3p_pur': 1658, 'rna2p_pyr': 226, 'rna3p_pyr': 1433} Link IDs: {'rna3p': 3092, 'rna2p': 569} Chain breaks: 12 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {' U:plan': 1, ' C:plan': 1, ' C:plan2': 1} Unresolved non-hydrogen planarities: 20 Chain: "7" Number of atoms: 2558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 2558 Classifications: {'RNA': 120} Modifications used: {'5*END': 1, 'rna2p_pur': 6, 'rna3p_pur': 55, 'rna2p_pyr': 6, 'rna3p_pyr': 53} Link IDs: {'rna3p': 107, 'rna2p': 12} Chain: "8" Number of atoms: 3314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 3314 Classifications: {'RNA': 156} Modifications used: {'rna3p_pyr': 67, 'rna2p_pur': 14, 'rna3p_pur': 62, 'rna2p_pyr': 13, '5*END': 1} Link IDs: {'rna3p': 129, 'rna2p': 26} Chain: "A" Number of atoms: 1868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1868 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 14, 'TRANS': 229} Chain: "B" Number of atoms: 3148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3148 Classifications: {'peptide': 394} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 15, 'TRANS': 378} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 15 Chain: "C" Number of atoms: 2883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2883 Classifications: {'peptide': 362} Link IDs: {'PTRANS': 18, 'TRANS': 343} Chain: "D" Number of atoms: 2386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2386 Classifications: {'peptide': 292} Link IDs: {'PTRANS': 9, 'TRANS': 282} Chain: "E" Number of atoms: 1898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1898 Classifications: {'peptide': 236} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 220} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Chain: "F" Number of atoms: 1870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1870 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 7, 'TRANS': 217} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 1934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1934 Classifications: {'peptide': 241} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 226} Chain: "H" Number of atoms: 1516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1516 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 4, 'TRANS': 185} Chain: "I" Number of atoms: 1655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1655 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 192} Chain breaks: 1 Chain: "J" Number of atoms: 1353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1353 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 5, 'TRANS': 163} Chain: "L" Number of atoms: 1703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1703 Classifications: {'peptide': 210} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 195} Chain: "M" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1137 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 4, 'TRANS': 133} Chain: "N" Number of atoms: 1701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1701 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 193} Chain: "O" Number of atoms: 1638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1638 Classifications: {'peptide': 199} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 189} Chain: "P" Number of atoms: 1242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1242 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 7, 'TRANS': 145} Chain: "Q" Number of atoms: 1506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1506 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 176} Chain: "R" Number of atoms: 1508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1508 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 3, 'TRANS': 176} Chain: "S" Number of atoms: 1454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1454 Classifications: {'peptide': 175} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 163} Chain: "T" Number of atoms: 1298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1298 Classifications: {'peptide': 159} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 149} Chain: "U" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 808 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 2, 'TRANS': 96} Chain: "V" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 979 Classifications: {'peptide': 131} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 124} Chain: "W" Number of atoms: 528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 528 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 2, 'TRANS': 60} Chain: "X" Number of atoms: 976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 976 Classifications: {'peptide': 119} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 110} Chain: "Y" Number of atoms: 1115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1115 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 5, 'TRANS': 128} Chain: "Z" Number of atoms: 1107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1107 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 128} Chain: "a" Number of atoms: 1162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1162 Classifications: {'peptide': 147} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 140} Chain: "b" Number of atoms: 609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 609 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain: "c" Number of atoms: 732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 732 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "d" Number of atoms: 888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 888 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "e" Number of atoms: 1053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1053 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 6, 'TRANS': 121} Chain: "f" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 876 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 104} Chain: "g" Number of atoms: 906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 906 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 4, 'TRANS': 109} Chain: "h" Number of atoms: 1013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1013 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "i" Number of atoms: 830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 830 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "j" Number of atoms: 705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 705 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 3, 'TRANS': 82} Chain: "k" Number of atoms: 569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 569 Classifications: {'peptide': 69} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "l" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 444 Classifications: {'peptide': 50} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "m" Number of atoms: 429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 429 Classifications: {'peptide': 52} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 48} Chain: "n" Number of atoms: 222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 222 Classifications: {'peptide': 23} Link IDs: {'TRANS': 22} Chain: "o" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 851 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 4, 'TRANS': 99} Chain: "p" Number of atoms: 708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 708 Classifications: {'peptide': 91} Modifications used: {'COO': 1} Link IDs: {'TRANS': 90} Chain: "r" Number of atoms: 1001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1001 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 5, 'TRANS': 119} Chain: "s" Number of atoms: 1523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1523 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 9, 'TRANS': 188} Chain: "t" Number of atoms: 1238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1238 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 10, 'CIS': 2, 'TRANS': 149, 'PCIS': 1} Chain: "1" Number of atoms: 204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 204 Classifications: {'peptide': 24} Link IDs: {'PTRANS': 6, 'TRANS': 17} Chain: "2" Number of atoms: 1614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1614 Classifications: {'RNA': 76} Modifications used: {'5*END': 1, 'rna2p_pur': 7, 'rna3p_pur': 31, 'rna2p_pyr': 5, 'rna3p_pyr': 33} Link IDs: {'rna3p': 63, 'rna2p': 12} Chain breaks: 1 Chain: "3" Number of atoms: 1597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1597 Classifications: {'RNA': 75} Modifications used: {'5*END': 1, 'rna2p_pur': 6, 'rna3p_pur': 33, 'rna2p_pyr': 7, 'rna3p_pyr': 29} Link IDs: {'rna3p': 62, 'rna2p': 12} Chain breaks: 2 Chain: "K" Number of atoms: 36248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1698, 36248 Classifications: {'RNA': 1698} Modifications used: {'5*END': 1, 'rna2p_pur': 148, 'rna3p_pur': 750, 'rna2p_pyr': 107, 'rna3p_pyr': 693} Link IDs: {'rna3p': 1443, 'rna2p': 254} Chain breaks: 11 Chain: "q" Number of atoms: 1710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1710 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 204} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "u" Number of atoms: 1729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1729 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 5, 'TRANS': 207} Chain: "v" Number of atoms: 1716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1716 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 12, 'TRANS': 208} Chain: "x" Number of atoms: 2076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2076 Classifications: {'peptide': 262} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 247} Chain: "z" Number of atoms: 1923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1923 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 10, 'TRANS': 226} Chain: "y" Number of atoms: 1488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1488 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 9, 'TRANS': 175} Chain breaks: 1 Chain: "CC" Number of atoms: 1686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1686 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 7, 'TRANS': 198} Chain: "XX" Number of atoms: 1525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1525 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 6, 'TRANS': 178} Chain: "EE" Number of atoms: 1175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1175 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 6, 'TRANS': 136} Chain breaks: 1 Chain: "QQ" Number of atoms: 1202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1202 Classifications: {'peptide': 149} Link IDs: {'PTRANS': 8, 'TRANS': 140} Chain: "MM" Number of atoms: 1016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1016 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 129} Chain: "UU" Number of atoms: 1128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1128 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 135, 'PCIS': 1} Chain: "YY" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1068 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 6, 'TRANS': 125} Chain: "HH" Number of atoms: 636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 636 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "TT" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1034 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 125, 'PCIS': 1} Chain: "VV" Number of atoms: 1098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1098 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 5, 'TRANS': 135} Chain: "NN" Number of atoms: 1011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1011 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "ZZ" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 814 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 6, 'TRANS': 94} Chain: "JJ" Number of atoms: 651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 651 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 77} Chain: "AA" Number of atoms: 443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 443 Classifications: {'peptide': 55} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "DD" Number of atoms: 1768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1768 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 11, 'TRANS': 216} Chain: "BB" Number of atoms: 1471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1471 Classifications: {'peptide': 185} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 178} Chain breaks: 1 Chain: "SS" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 810 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 7, 'TRANS': 88} Chain: "RR" Number of atoms: 908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 908 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 2, 'TRANS': 114} Chain: "9" Number of atoms: 997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 997 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 7, 'TRANS': 112} Chain: "II" Number of atoms: 1190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1190 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 3, 'TRANS': 140} Chain: "PP" Number of atoms: 1097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1097 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 4, 'TRANS': 136} Chain: "GG" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 795 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 5, 'TRANS': 94} Chain: "OO" Number of atoms: 598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 598 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain: "FF" Number of atoms: 488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 488 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 2, 'TRANS': 59} Chain: "w" Number of atoms: 459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 459 Classifications: {'peptide': 55} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 53} Chain: "0" Number of atoms: 555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 555 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 2, 'TRANS': 65} Chain: "6" Number of atoms: 2436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2436 Classifications: {'peptide': 313} Link IDs: {'PTRANS': 10, 'TRANS': 302} Chain: "4" Number of atoms: 211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 211 Classifications: {'RNA': 10} Modifications used: {'rna3p_pyr': 4, 'rna2p_pur': 2, 'rna3p_pur': 3, 'rna2p_pyr': 1} Link IDs: {'rna3p': 6, 'rna2p': 3} Chain: "5" Number of atoms: 148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 148 Unusual residues: {' MG': 148} Classifications: {'undetermined': 148} Link IDs: {None: 147} Chain: "7" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "8" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "e" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "g" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 1, ' MG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "j" 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} Chain: "o" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "p" 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 A0MKN SG CYS g 46 175.106 174.288 206.354 1.00 33.26 S ATOM A0ML4 SG CYS g 49 175.309 178.257 205.021 1.00 30.61 S ATOM A0MSF SG CYS g 83 177.206 178.266 208.179 1.00 19.74 S ATOM A0MSZ SG CYS g 86 173.749 177.126 208.129 1.00 25.03 S ATOM A0OIQ SG CYS j 19 203.336 128.137 186.702 1.00 17.76 S ATOM A0OJI SG CYS j 22 204.901 125.491 183.798 1.00 18.52 S ATOM A0OM1 SG CYS j 34 201.404 126.846 183.358 1.00 15.48 S ATOM A0OMK SG CYS j 37 201.794 124.229 185.958 1.00 16.55 S ATOM A0PV2 SG CYS m 96 184.065 138.942 73.312 1.00 15.14 S ATOM A0PVS SG CYS m 99 187.710 140.492 74.762 1.00 16.69 S ATOM A0PYA SG CYS m 110 188.012 139.037 71.264 1.00 15.26 S ATOM A0PZI SG CYS m 115 187.873 136.808 74.132 1.00 17.23 S ATOM A0QB6 SG CYS o 12 137.669 71.301 148.062 1.00 18.94 S ATOM A0QBU SG CYS o 15 135.437 67.811 149.003 1.00 20.01 S ATOM A0QPW SG CYS o 77 136.394 70.359 151.436 1.00 31.82 S ATOM A0R4M SG CYS p 39 162.762 179.854 195.731 1.00 19.86 S ATOM A0R59 SG CYS p 42 164.578 182.854 196.830 1.00 19.65 S ATOM A0R8N SG CYS p 57 166.550 180.135 195.097 1.00 20.39 S Time building chain proxies: 78.84, per 1000 atoms: 0.36 Number of scatterers: 218067 At special positions: 0 Unit cell: (292.68, 303.52, 282.924, 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 427 16.00 P 5791 15.00 Mg 159 11.99 O 56426 8.00 N 40633 7.00 C 114626 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 66.36 Conformation dependent library (CDL) restraints added in 10.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination Zn2+ tetrahedral coordination pdb=" ZN g 201 " pdb="ZN ZN g 201 " - pdb=" SG CYS g 83 " pdb="ZN ZN g 201 " - pdb=" SG CYS g 46 " pdb="ZN ZN g 201 " - pdb=" SG CYS g 86 " pdb="ZN ZN g 201 " - pdb=" SG CYS g 49 " pdb=" ZN j 101 " pdb="ZN ZN j 101 " - pdb=" SG CYS j 19 " pdb="ZN ZN j 101 " - pdb=" SG CYS j 37 " pdb="ZN ZN j 101 " - pdb=" SG CYS j 34 " pdb="ZN ZN j 101 " - pdb=" SG CYS j 22 " pdb=" ZN m 201 " pdb="ZN ZN m 201 " - pdb=" SG CYS m 99 " pdb="ZN ZN m 201 " - pdb=" SG CYS m 96 " pdb="ZN ZN m 201 " - pdb=" SG CYS m 115 " pdb="ZN ZN m 201 " - pdb=" SG CYS m 110 " pdb=" ZN o 201 " pdb="ZN ZN o 201 " - pdb=" SG CYS o 77 " pdb="ZN ZN o 201 " - pdb=" SG CYS o 12 " pdb="ZN ZN o 201 " - pdb=" SG CYS o 15 " pdb=" ZN p 100 " pdb="ZN ZN p 100 " - pdb=" SG CYS p 42 " pdb="ZN ZN p 100 " - pdb=" SG CYS p 57 " pdb="ZN ZN p 100 " - pdb=" SG CYS p 39 " Number of angles added : 18 23014 Ramachandran restraints generated. 11507 Oldfield, 0 Emsley, 11507 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 21700 Finding SS restraints... Secondary structure from input PDB file: 361 helices and 130 sheets defined 35.5% alpha, 15.5% beta 1786 base pairs and 3152 stacking pairs defined. Time for finding SS restraints: 61.66 Creating SS restraints... Processing helix chain 'A' and resid 8 through 12 removed outlier: 3.847A pdb=" N GLY A 11 " --> pdb=" O GLN A 8 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA A 12 " --> pdb=" O ARG A 9 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 8 through 12' Processing helix chain 'A' and resid 33 through 38 Processing helix chain 'A' and resid 173 through 177 removed outlier: 3.843A pdb=" N LYS A 177 " --> pdb=" O ARG A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 191 removed outlier: 3.870A pdb=" N ALA A 191 " --> pdb=" O HIS A 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 116 Processing helix chain 'B' and resid 133 through 137 removed outlier: 3.863A pdb=" N TRP B 137 " --> pdb=" O CYS B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 157 Processing helix chain 'B' and resid 189 through 200 Processing helix chain 'B' and resid 230 through 236 Processing helix chain 'B' and resid 356 through 361 Processing helix chain 'B' and resid 381 through 390 Processing helix chain 'C' and resid 33 through 45 Processing helix chain 'C' and resid 46 through 49 removed outlier: 3.909A pdb=" N ARG C 49 " --> pdb=" O LYS C 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 46 through 49' Processing helix chain 'C' and resid 116 through 130 Processing helix chain 'C' and resid 133 through 139 Processing helix chain 'C' and resid 163 through 174 Processing helix chain 'C' and resid 176 through 186 removed outlier: 4.170A pdb=" N ILE C 180 " --> pdb=" O ALA C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 198 removed outlier: 3.953A pdb=" N LYS C 195 " --> pdb=" O GLY C 192 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N MET C 196 " --> pdb=" O LYS C 193 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ASN C 198 " --> pdb=" O LYS C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 221 Processing helix chain 'C' and resid 236 through 241 Processing helix chain 'C' and resid 242 through 245 removed outlier: 3.574A pdb=" N HIS C 245 " --> pdb=" O PRO C 242 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 242 through 245' Processing helix chain 'C' and resid 254 through 258 Processing helix chain 'C' and resid 259 through 264 Processing helix chain 'C' and resid 288 through 295 Processing helix chain 'C' and resid 295 through 300 removed outlier: 3.550A pdb=" N GLN C 299 " --> pdb=" O SER C 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 329 Processing helix chain 'C' and resid 331 through 338 Processing helix chain 'C' and resid 340 through 363 Processing helix chain 'D' and resid 9 through 16 Processing helix chain 'D' and resid 20 through 26 Processing helix chain 'D' and resid 29 through 37 removed outlier: 3.978A pdb=" N ARG D 35 " --> pdb=" O TYR D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 83 No H-bonds generated for 'chain 'D' and resid 81 through 83' Processing helix chain 'D' and resid 94 through 114 Processing helix chain 'D' and resid 157 through 170 Processing helix chain 'D' and resid 193 through 201 Processing helix chain 'D' and resid 201 through 215 removed outlier: 3.549A pdb=" N TYR D 207 " --> pdb=" O ASN D 203 " (cutoff:3.500A) Processing helix chain 'D' and resid 215 through 223 Processing helix chain 'D' and resid 223 through 228 Processing helix chain 'D' and resid 235 through 250 Processing helix chain 'D' and resid 272 through 292 Processing helix chain 'E' and resid 55 through 63 Processing helix chain 'E' and resid 128 through 132 removed outlier: 3.676A pdb=" N HIS E 132 " --> pdb=" O PHE E 129 " (cutoff:3.500A) Processing helix chain 'E' and resid 240 through 254 removed outlier: 4.132A pdb=" N GLN E 252 " --> pdb=" O ALA E 248 " (cutoff:3.500A) Processing helix chain 'E' and resid 255 through 257 No H-bonds generated for 'chain 'E' and resid 255 through 257' Processing helix chain 'E' and resid 262 through 269 Processing helix chain 'F' and resid 27 through 80 removed outlier: 3.884A pdb=" N ILE F 71 " --> pdb=" O TYR F 67 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ALA F 80 " --> pdb=" O MET F 76 " (cutoff:3.500A) Processing helix chain 'F' and resid 104 through 114 Processing helix chain 'F' and resid 128 through 138 Processing helix chain 'F' and resid 148 through 158 Processing helix chain 'F' and resid 173 through 181 removed outlier: 4.403A pdb=" N ILE F 177 " --> pdb=" O ASP F 173 " (cutoff:3.500A) Processing helix chain 'F' and resid 188 through 198 Processing helix chain 'F' and resid 202 through 210 Processing helix chain 'F' and resid 241 through 250 removed outlier: 4.062A pdb=" N LEU F 245 " --> pdb=" O GLN F 241 " (cutoff:3.500A) Processing helix chain 'G' and resid 51 through 55 removed outlier: 3.960A pdb=" N VAL G 55 " --> pdb=" O THR G 52 " (cutoff:3.500A) Processing helix chain 'G' and resid 58 through 74 removed outlier: 3.835A pdb=" N ALA G 68 " --> pdb=" O GLN G 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 82 Processing helix chain 'G' and resid 88 through 101 removed outlier: 3.818A pdb=" N LYS G 101 " --> pdb=" O LYS G 97 " (cutoff:3.500A) Processing helix chain 'G' and resid 108 through 122 removed outlier: 3.559A pdb=" N ARG G 117 " --> pdb=" O ARG G 113 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N ALA G 122 " --> pdb=" O ALA G 118 " (cutoff:3.500A) Processing helix chain 'G' and resid 139 through 149 Processing helix chain 'G' and resid 163 through 167 removed outlier: 3.707A pdb=" N LEU G 166 " --> pdb=" O PRO G 163 " (cutoff:3.500A) Processing helix chain 'G' and resid 168 through 178 removed outlier: 4.474A pdb=" N ALA G 172 " --> pdb=" O VAL G 168 " (cutoff:3.500A) Processing helix chain 'G' and resid 186 through 192 Processing helix chain 'G' and resid 211 through 224 Processing helix chain 'G' and resid 229 through 236 Processing helix chain 'G' and resid 243 through 261 removed outlier: 3.705A pdb=" N ARG G 249 " --> pdb=" O LYS G 245 " (cutoff:3.500A) Processing helix chain 'H' and resid 63 through 68 Processing helix chain 'H' and resid 69 through 86 Processing helix chain 'H' and resid 150 through 165 removed outlier: 3.531A pdb=" N ILE H 161 " --> pdb=" O SER H 157 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N THR H 165 " --> pdb=" O ILE H 161 " (cutoff:3.500A) Processing helix chain 'I' and resid 62 through 80 Processing helix chain 'I' and resid 141 through 143 No H-bonds generated for 'chain 'I' and resid 141 through 143' Processing helix chain 'I' and resid 144 through 157 removed outlier: 3.871A pdb=" N PHE I 157 " --> pdb=" O ARG I 153 " (cutoff:3.500A) Processing helix chain 'I' and resid 177 through 187 removed outlier: 4.480A pdb=" N GLU I 182 " --> pdb=" O ALA I 178 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N ASP I 183 " --> pdb=" O ASP I 179 " (cutoff:3.500A) Processing helix chain 'I' and resid 205 through 212 removed outlier: 3.733A pdb=" N TRP I 209 " --> pdb=" O PRO I 205 " (cutoff:3.500A) Processing helix chain 'J' and resid 29 through 45 removed outlier: 3.826A pdb=" N LEU J 33 " --> pdb=" O SER J 29 " (cutoff:3.500A) Processing helix chain 'J' and resid 76 through 90 Processing helix chain 'J' and resid 111 through 116 removed outlier: 3.581A pdb=" N ASP J 114 " --> pdb=" O GLU J 111 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLY J 116 " --> pdb=" O ILE J 113 " (cutoff:3.500A) Processing helix chain 'J' and resid 158 through 170 Processing helix chain 'L' and resid 27 through 46 Processing helix chain 'L' and resid 77 through 85 Processing helix chain 'L' and resid 90 through 95 Processing helix chain 'L' and resid 107 through 124 Processing helix chain 'L' and resid 140 through 145 Processing helix chain 'L' and resid 170 through 176 Processing helix chain 'L' and resid 177 through 191 removed outlier: 3.659A pdb=" N SER L 181 " --> pdb=" O LYS L 177 " (cutoff:3.500A) Processing helix chain 'L' and resid 191 through 211 Processing helix chain 'M' and resid 70 through 81 Processing helix chain 'M' and resid 81 through 89 Processing helix chain 'M' and resid 89 through 103 Processing helix chain 'M' and resid 105 through 139 Processing helix chain 'N' and resid 3 through 13 Processing helix chain 'N' and resid 16 through 32 Processing helix chain 'N' and resid 44 through 52 Processing helix chain 'N' and resid 97 through 110 Processing helix chain 'N' and resid 139 through 144 Processing helix chain 'N' and resid 153 through 157 removed outlier: 3.756A pdb=" N LYS N 157 " --> pdb=" O PRO N 154 " (cutoff:3.500A) Processing helix chain 'N' and resid 158 through 163 Processing helix chain 'N' and resid 165 through 170 removed outlier: 3.680A pdb=" N LYS N 170 " --> pdb=" O SER N 166 " (cutoff:3.500A) Processing helix chain 'N' and resid 171 through 173 No H-bonds generated for 'chain 'N' and resid 171 through 173' Processing helix chain 'N' and resid 187 through 197 Processing helix chain 'O' and resid 15 through 29 removed outlier: 3.853A pdb=" N ILE O 22 " --> pdb=" O ARG O 18 " (cutoff:3.500A) Processing helix chain 'O' and resid 37 through 40 Processing helix chain 'O' and resid 46 through 60 Processing helix chain 'O' and resid 75 through 86 Processing helix chain 'O' and resid 92 through 102 Processing helix chain 'O' and resid 120 through 123 Processing helix chain 'O' and resid 124 through 129 Processing helix chain 'O' and resid 138 through 146 Processing helix chain 'O' and resid 149 through 186 Processing helix chain 'O' and resid 189 through 198 removed outlier: 4.151A pdb=" N VAL O 195 " --> pdb=" O ARG O 191 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LEU O 196 " --> pdb=" O PHE O 192 " (cutoff:3.500A) Processing helix chain 'P' and resid 10 through 12 No H-bonds generated for 'chain 'P' and resid 10 through 12' Processing helix chain 'P' and resid 25 through 37 Processing helix chain 'P' and resid 40 through 53 Processing helix chain 'P' and resid 71 through 75 removed outlier: 3.502A pdb=" N LYS P 74 " --> pdb=" O ALA P 71 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLN P 75 " --> pdb=" O GLN P 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 71 through 75' Processing helix chain 'P' and resid 84 through 106 removed outlier: 3.800A pdb=" N LEU P 95 " --> pdb=" O LEU P 91 " (cutoff:3.500A) Processing helix chain 'P' and resid 108 through 110 No H-bonds generated for 'chain 'P' and resid 108 through 110' Processing helix chain 'Q' and resid 22 through 39 Processing helix chain 'Q' and resid 42 through 53 removed outlier: 3.706A pdb=" N MET Q 53 " --> pdb=" O LYS Q 49 " (cutoff:3.500A) Processing helix chain 'Q' and resid 63 through 71 Processing helix chain 'Q' and resid 106 through 117 Processing helix chain 'Q' and resid 122 through 130 Processing helix chain 'Q' and resid 142 through 152 removed outlier: 3.503A pdb=" N GLY Q 145 " --> pdb=" O PRO Q 142 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N ARG Q 146 " --> pdb=" O ARG Q 143 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N GLU Q 147 " --> pdb=" O LYS Q 144 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N VAL Q 148 " --> pdb=" O GLY Q 145 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N PHE Q 152 " --> pdb=" O TYR Q 149 " (cutoff:3.500A) Processing helix chain 'R' and resid 4 through 16 Processing helix chain 'R' and resid 29 through 34 Processing helix chain 'R' and resid 40 through 48 Processing helix chain 'R' and resid 60 through 73 Processing helix chain 'R' and resid 77 through 81 removed outlier: 3.710A pdb=" N LYS R 80 " --> pdb=" O GLY R 77 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ARG R 81 " --> pdb=" O ILE R 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 77 through 81' Processing helix chain 'R' and resid 84 through 89 Processing helix chain 'R' and resid 90 through 112 removed outlier: 3.914A pdb=" N ARG R 104 " --> pdb=" O ARG R 100 " (cutoff:3.500A) Processing helix chain 'R' and resid 116 through 129 Processing helix chain 'R' and resid 135 through 181 Processing helix chain 'S' and resid 36 through 52 Processing helix chain 'S' and resid 101 through 117 Processing helix chain 'S' and resid 139 through 144 Processing helix chain 'T' and resid 26 through 31 removed outlier: 3.735A pdb=" N TYR T 30 " --> pdb=" O PRO T 26 " (cutoff:3.500A) Processing helix chain 'T' and resid 54 through 58 removed outlier: 3.599A pdb=" N HIS T 58 " --> pdb=" O LYS T 55 " (cutoff:3.500A) Processing helix chain 'T' and resid 94 through 96 No H-bonds generated for 'chain 'T' and resid 94 through 96' Processing helix chain 'T' and resid 102 through 118 Processing helix chain 'U' and resid 35 through 47 Processing helix chain 'U' and resid 53 through 58 removed outlier: 4.008A pdb=" N LEU U 56 " --> pdb=" O ALA U 53 " (cutoff:3.500A) Processing helix chain 'U' and resid 80 through 94 removed outlier: 3.716A pdb=" N LYS U 84 " --> pdb=" O LYS U 80 " (cutoff:3.500A) Processing helix chain 'V' and resid 122 through 127 Processing helix chain 'V' and resid 129 through 136 removed outlier: 3.646A pdb=" N ASN V 135 " --> pdb=" O ARG V 131 " (cutoff:3.500A) Processing helix chain 'W' and resid 33 through 42 Processing helix chain 'W' and resid 52 through 60 Processing helix chain 'X' and resid 72 through 76 Processing helix chain 'X' and resid 83 through 94 removed outlier: 3.619A pdb=" N ASN X 94 " --> pdb=" O ILE X 90 " (cutoff:3.500A) Processing helix chain 'X' and resid 105 through 118 Processing helix chain 'X' and resid 145 through 154 removed outlier: 3.701A pdb=" N VAL X 149 " --> pdb=" O ASP X 145 " (cutoff:3.500A) Processing helix chain 'Y' and resid 10 through 20 Processing helix chain 'Y' and resid 22 through 30 removed outlier: 3.921A pdb=" N LYS Y 28 " --> pdb=" O HIS Y 24 " (cutoff:3.500A) Processing helix chain 'Y' and resid 35 through 43 Processing helix chain 'Y' and resid 100 through 102 No H-bonds generated for 'chain 'Y' and resid 100 through 102' Processing helix chain 'Y' and resid 112 through 134 Processing helix chain 'Z' and resid 59 through 66 Processing helix chain 'Z' and resid 103 through 123 removed outlier: 3.662A pdb=" N ARG Z 108 " --> pdb=" O PRO Z 104 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LYS Z 109 " --> pdb=" O ALA Z 105 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N VAL Z 116 " --> pdb=" O ARG Z 112 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LYS Z 117 " --> pdb=" O GLU Z 113 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE Z 118 " --> pdb=" O ALA Z 114 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ARG Z 121 " --> pdb=" O LYS Z 117 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LYS Z 123 " --> pdb=" O GLU Z 119 " (cutoff:3.500A) Processing helix chain 'Z' and resid 124 through 126 No H-bonds generated for 'chain 'Z' and resid 124 through 126' Processing helix chain 'a' and resid 6 through 10 removed outlier: 3.663A pdb=" N ARG a 9 " --> pdb=" O ARG a 6 " (cutoff:3.500A) Processing helix chain 'a' and resid 41 through 48 Processing helix chain 'a' and resid 83 through 89 removed outlier: 4.116A pdb=" N ARG a 87 " --> pdb=" O SER a 83 " (cutoff:3.500A) Processing helix chain 'a' and resid 103 through 107 Processing helix chain 'a' and resid 130 through 141 Processing helix chain 'b' and resid 11 through 19 removed outlier: 4.170A pdb=" N ASN b 19 " --> pdb=" O LYS b 15 " (cutoff:3.500A) Processing helix chain 'b' and resid 36 through 50 Processing helix chain 'b' and resid 53 through 76 Processing helix chain 'c' and resid 14 through 24 Processing helix chain 'c' and resid 30 through 41 removed outlier: 3.625A pdb=" N LYS c 36 " --> pdb=" O LYS c 32 " (cutoff:3.500A) Processing helix chain 'c' and resid 53 through 68 Processing helix chain 'c' and resid 77 through 86 Processing helix chain 'd' and resid 29 through 34 Processing helix chain 'd' and resid 40 through 57 Processing helix chain 'd' and resid 65 through 73 Processing helix chain 'e' and resid 57 through 61 removed outlier: 3.738A pdb=" N TYR e 60 " --> pdb=" O ASN e 57 " (cutoff:3.500A) Processing helix chain 'e' and resid 85 through 91 removed outlier: 4.449A pdb=" N MET e 90 " --> pdb=" O VAL e 87 " (cutoff:3.500A) Processing helix chain 'e' and resid 104 through 118 removed outlier: 4.035A pdb=" N LYS e 109 " --> pdb=" O SER e 105 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ALA e 110 " --> pdb=" O LYS e 106 " (cutoff:3.500A) Processing helix chain 'f' and resid 37 through 41 removed outlier: 3.976A pdb=" N GLU f 40 " --> pdb=" O ASP f 37 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N PHE f 41 " --> pdb=" O GLU f 38 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 37 through 41' Processing helix chain 'g' and resid 83 through 115 Processing helix chain 'h' and resid 13 through 37 Processing helix chain 'h' and resid 40 through 45 Processing helix chain 'h' and resid 45 through 74 removed outlier: 4.405A pdb=" N VAL h 49 " --> pdb=" O SER h 45 " (cutoff:3.500A) Processing helix chain 'h' and resid 88 through 93 Processing helix chain 'h' and resid 104 through 114 Processing helix chain 'i' and resid 34 through 48 removed outlier: 3.890A pdb=" N GLU i 46 " --> pdb=" O ASP i 42 " (cutoff:3.500A) Processing helix chain 'i' and resid 51 through 64 removed outlier: 3.552A pdb=" N VAL i 63 " --> pdb=" O GLU i 59 " (cutoff:3.500A) Processing helix chain 'i' and resid 65 through 78 Processing helix chain 'i' and resid 79 through 102 Processing helix chain 'j' and resid 4 through 10 removed outlier: 3.990A pdb=" N LYS j 10 " --> pdb=" O SER j 6 " (cutoff:3.500A) Processing helix chain 'j' and resid 50 through 57 removed outlier: 3.830A pdb=" N ASN j 57 " --> pdb=" O ALA j 53 " (cutoff:3.500A) Processing helix chain 'j' and resid 66 through 77 Processing helix chain 'k' and resid 7 through 16 Processing helix chain 'k' and resid 49 through 58 removed outlier: 3.682A pdb=" N GLN k 58 " --> pdb=" O GLU k 54 " (cutoff:3.500A) Processing helix chain 'l' and resid 6 through 20 Processing helix chain 'm' and resid 79 through 91 removed outlier: 3.770A pdb=" N TYR m 89 " --> pdb=" O LEU m 85 " (cutoff:3.500A) Processing helix chain 'n' and resid 3 through 23 Processing helix chain 'o' and resid 35 through 46 Processing helix chain 'p' and resid 8 through 15 removed outlier: 3.819A pdb=" N LYS p 13 " --> pdb=" O ILE p 10 " (cutoff:3.500A) Processing helix chain 'p' and resid 19 through 35 removed outlier: 4.390A pdb=" N LYS p 28 " --> pdb=" O LYS p 24 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ILE p 29 " --> pdb=" O MET p 25 " (cutoff:3.500A) Processing helix chain 'p' and resid 73 through 92 Processing helix chain 'r' and resid 3 through 11 Processing helix chain 'r' and resid 86 through 100 removed outlier: 3.878A pdb=" N ASN r 100 " --> pdb=" O MET r 96 " (cutoff:3.500A) Processing helix chain 'r' and resid 103 through 105 No H-bonds generated for 'chain 'r' and resid 103 through 105' Processing helix chain 'r' and resid 106 through 121 Processing helix chain 's' and resid 7 through 24 Processing helix chain 's' and resid 36 through 47 Processing helix chain 's' and resid 57 through 61 removed outlier: 3.769A pdb=" N MET s 61 " --> pdb=" O ASN s 58 " (cutoff:3.500A) Processing helix chain 's' and resid 62 through 69 Processing helix chain 's' and resid 95 through 105 Processing helix chain 's' and resid 135 through 140 Processing helix chain 's' and resid 168 through 179 Processing helix chain 't' and resid 40 through 51 Processing helix chain 't' and resid 77 through 86 Processing helix chain 't' and resid 109 through 116 Processing helix chain 't' and resid 126 through 137 removed outlier: 3.838A pdb=" N GLU t 131 " --> pdb=" O GLY t 127 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N THR t 135 " --> pdb=" O GLU t 131 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N GLN t 137 " --> pdb=" O LEU t 133 " (cutoff:3.500A) Processing helix chain 'q' and resid 11 through 22 Processing helix chain 'q' and resid 33 through 36 removed outlier: 4.530A pdb=" N GLN q 36 " --> pdb=" O GLN q 33 " (cutoff:3.500A) No H-bonds generated for 'chain 'q' and resid 33 through 36' Processing helix chain 'q' and resid 43 through 45 No H-bonds generated for 'chain 'q' and resid 43 through 45' Processing helix chain 'q' and resid 50 through 67 Processing helix chain 'q' and resid 83 through 95 Processing helix chain 'q' and resid 130 through 138 removed outlier: 3.775A pdb=" N LEU q 134 " --> pdb=" O ASP q 130 " (cutoff:3.500A) Processing helix chain 'q' and resid 167 through 186 Processing helix chain 'q' and resid 198 through 202 removed outlier: 3.605A pdb=" N TYR q 202 " --> pdb=" O PRO q 199 " (cutoff:3.500A) Processing helix chain 'q' and resid 206 through 218 removed outlier: 3.729A pdb=" N ALA q 218 " --> pdb=" O GLU q 214 " (cutoff:3.500A) Processing helix chain 'u' and resid 23 through 26 Processing helix chain 'u' and resid 57 through 64 removed outlier: 4.208A pdb=" N GLY u 64 " --> pdb=" O ASP u 60 " (cutoff:3.500A) Processing helix chain 'u' and resid 72 through 74 No H-bonds generated for 'chain 'u' and resid 72 through 74' Processing helix chain 'u' and resid 106 through 114 Processing helix chain 'u' and resid 157 through 177 Processing helix chain 'u' and resid 180 through 189 Processing helix chain 'u' and resid 191 through 201 Processing helix chain 'u' and resid 224 through 232 Processing helix chain 'v' and resid 64 through 73 Processing helix chain 'v' and resid 78 through 85 Processing helix chain 'v' and resid 91 through 98 removed outlier: 4.113A pdb=" N ASP v 95 " --> pdb=" O SER v 91 " (cutoff:3.500A) Processing helix chain 'v' and resid 146 through 161 Processing helix chain 'v' and resid 207 through 218 Processing helix chain 'v' and resid 232 through 247 Processing helix chain 'v' and resid 252 through 256 removed outlier: 3.705A pdb=" N TRP v 256 " --> pdb=" O PRO v 253 " (cutoff:3.500A) Processing helix chain 'v' and resid 264 through 269 Processing helix chain 'v' and resid 271 through 276 Processing helix chain 'x' and resid 15 through 19 removed outlier: 3.647A pdb=" N TRP x 18 " --> pdb=" O PRO x 15 " (cutoff:3.500A) Processing helix chain 'x' and resid 44 through 50 Processing helix chain 'x' and resid 57 through 67 Processing helix chain 'x' and resid 115 through 120 Processing helix chain 'x' and resid 247 through 263 removed outlier: 3.504A pdb=" N ALA x 258 " --> pdb=" O LYS x 254 " (cutoff:3.500A) Processing helix chain 'z' and resid 20 through 25 Processing helix chain 'z' and resid 39 through 42 removed outlier: 4.013A pdb=" N GLY z 42 " --> pdb=" O ASP z 39 " (cutoff:3.500A) No H-bonds generated for 'chain 'z' and resid 39 through 42' Processing helix chain 'z' and resid 137 through 146 Processing helix chain 'z' and resid 181 through 237 removed outlier: 3.617A pdb=" N ILE z 192 " --> pdb=" O LYS z 188 " (cutoff:3.500A) Processing helix chain 'y' and resid 17 through 34 Processing helix chain 'y' and resid 36 through 41 Processing helix chain 'y' and resid 68 through 75 Processing helix chain 'y' and resid 75 through 87 removed outlier: 4.227A pdb=" N LYS y 85 " --> pdb=" O ARG y 81 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS y 86 " --> pdb=" O GLU y 82 " (cutoff:3.500A) Processing helix chain 'y' and resid 117 through 120 Processing helix chain 'y' and resid 121 through 134 removed outlier: 3.730A pdb=" N HIS y 126 " --> pdb=" O LEU y 122 " (cutoff:3.500A) Processing helix chain 'y' and resid 166 through 168 No H-bonds generated for 'chain 'y' and resid 166 through 168' Processing helix chain 'y' and resid 169 through 181 Processing helix chain 'CC' and resid 88 through 93 Processing helix chain 'CC' and resid 106 through 117 Processing helix chain 'CC' and resid 132 through 139 Processing helix chain 'CC' and resid 144 through 155 removed outlier: 4.126A pdb=" N LYSCC 148 " --> pdb=" O LYSCC 144 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASNCC 155 " --> pdb=" O GLUCC 151 " (cutoff:3.500A) Processing helix chain 'CC' and resid 159 through 169 Processing helix chain 'CC' and resid 178 through 183 removed outlier: 3.772A pdb=" N CYSCC 182 " --> pdb=" O ARGCC 178 " (cutoff:3.500A) Processing helix chain 'CC' and resid 192 through 207 Processing helix chain 'XX' and resid 21 through 36 Processing helix chain 'XX' and resid 40 through 62 removed outlier: 4.052A pdb=" N VALXX 46 " --> pdb=" O GLUXX 42 " (cutoff:3.500A) Processing helix chain 'XX' and resid 67 through 85 Processing helix chain 'XX' and resid 101 through 107 Processing helix chain 'XX' and resid 109 through 118 Processing helix chain 'XX' and resid 122 through 133 Processing helix chain 'XX' and resid 171 through 186 Processing helix chain 'EE' and resid 47 through 53 removed outlier: 4.047A pdb=" N ILEEE 51 " --> pdb=" O PROEE 47 " (cutoff:3.500A) Processing helix chain 'QQ' and resid 29 through 44 Processing helix chain 'QQ' and resid 46 through 57 Processing helix chain 'QQ' and resid 62 through 67 Processing helix chain 'QQ' and resid 70 through 79 Processing helix chain 'QQ' and resid 85 through 105 Processing helix chain 'QQ' and resid 108 through 132 Processing helix chain 'MM' and resid 58 through 62 Processing helix chain 'MM' and resid 64 through 68 removed outlier: 3.678A pdb=" N ASPMM 67 " --> pdb=" O ALAMM 64 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLUMM 68 " --> pdb=" O ASPMM 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'MM' and resid 64 through 68' Processing helix chain 'MM' and resid 70 through 87 Processing helix chain 'MM' and resid 110 through 123 removed outlier: 4.020A pdb=" N SERMM 114 " --> pdb=" O PROMM 110 " (cutoff:3.500A) Processing helix chain 'UU' and resid 44 through 49 removed outlier: 3.627A pdb=" N LEUUU 47 " --> pdb=" O PROUU 44 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLNUU 48 " --> pdb=" O ARGUU 45 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N TYRUU 49 " --> pdb=" O THRUU 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'UU' and resid 44 through 49' Processing helix chain 'UU' and resid 52 through 59 Processing helix chain 'UU' and resid 76 through 99 removed outlier: 3.826A pdb=" N SERUU 89 " --> pdb=" O ARGUU 85 " (cutoff:3.500A) Processing helix chain 'UU' and resid 101 through 116 removed outlier: 3.854A pdb=" N LYSUU 105 " --> pdb=" O ASPUU 101 " (cutoff:3.500A) Processing helix chain 'UU' and resid 117 through 120 Processing helix chain 'YY' and resid 6 through 20 removed outlier: 4.044A pdb=" N ALAYY 12 " --> pdb=" O THRYY 8 " (cutoff:3.500A) Processing helix chain 'YY' and resid 27 through 38 removed outlier: 4.283A pdb=" N ARGYY 33 " --> pdb=" O HISYY 29 " (cutoff:3.500A) Processing helix chain 'YY' and resid 43 through 64 Processing helix chain 'YY' and resid 71 through 83 Processing helix chain 'YY' and resid 99 through 109 Processing helix chain 'HH' and resid 56 through 63 removed outlier: 3.615A pdb=" N ARGHH 60 " --> pdb=" O CYSHH 56 " (cutoff:3.500A) Processing helix chain 'HH' and resid 64 through 77 Processing helix chain 'TT' and resid 5 through 21 Processing helix chain 'TT' and resid 31 through 44 Processing helix chain 'TT' and resid 85 through 94 Processing helix chain 'TT' and resid 113 through 120 Processing helix chain 'VV' and resid 9 through 21 Processing helix chain 'VV' and resid 24 through 32 Processing helix chain 'VV' and resid 32 through 39 removed outlier: 4.130A pdb=" N LEUVV 36 " --> pdb=" O LEUVV 32 " (cutoff:3.500A) Processing helix chain 'VV' and resid 130 through 136 Processing helix chain 'NN' and resid 36 through 49 Processing helix chain 'NN' and resid 51 through 53 No H-bonds generated for 'chain 'NN' and resid 51 through 53' Processing helix chain 'NN' and resid 78 through 85 Processing helix chain 'NN' and resid 87 through 95 removed outlier: 3.702A pdb=" N HISNN 94 " --> pdb=" O ARGNN 90 " (cutoff:3.500A) Processing helix chain 'NN' and resid 103 through 117 removed outlier: 3.527A pdb=" N VALNN 117 " --> pdb=" O ARGNN 113 " (cutoff:3.500A) Processing helix chain 'NN' and resid 121 through 126 Processing helix chain 'ZZ' and resid 49 through 57 removed outlier: 3.807A pdb=" N GLUZZ 55 " --> pdb=" O ARGZZ 51 " (cutoff:3.500A) Processing helix chain 'ZZ' and resid 74 through 81 Processing helix chain 'JJ' and resid 11 through 16 Processing helix chain 'AA' and resid 83 through 89 Processing helix chain 'AA' and resid 103 through 115 Processing helix chain 'DD' and resid 6 through 29 removed outlier: 3.600A pdb=" N VALDD 12 " --> pdb=" O LYSDD 8 " (cutoff:3.500A) Processing helix chain 'DD' and resid 54 through 60 Processing helix chain 'DD' and resid 63 through 77 Processing helix chain 'DD' and resid 93 through 96 Processing helix chain 'DD' and resid 97 through 112 Processing helix chain 'DD' and resid 114 through 130 Processing helix chain 'DD' and resid 162 through 167 removed outlier: 4.238A pdb=" N TYRDD 166 " --> pdb=" O ASPDD 162 " (cutoff:3.500A) Processing helix chain 'BB' and resid 32 through 36 removed outlier: 3.524A pdb=" N LEUBB 35 " --> pdb=" O ASPBB 32 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLNBB 36 " --> pdb=" O ILEBB 33 " (cutoff:3.500A) No H-bonds generated for 'chain 'BB' and resid 32 through 36' Processing helix chain 'BB' and resid 62 through 66 Processing helix chain 'BB' and resid 67 through 77 removed outlier: 4.038A pdb=" N METBB 77 " --> pdb=" O THRBB 73 " (cutoff:3.500A) Processing helix chain 'BB' and resid 85 through 104 Processing helix chain 'BB' and resid 107 through 120 Processing helix chain 'BB' and resid 142 through 163 Processing helix chain 'BB' and resid 168 through 183 Processing helix chain 'BB' and resid 187 through 203 Processing helix chain 'SS' and resid 4 through 18 Processing helix chain 'SS' and resid 41 through 55 removed outlier: 3.988A pdb=" N ARGSS 55 " --> pdb=" O SERSS 51 " (cutoff:3.500A) Processing helix chain 'SS' and resid 72 through 84 Processing helix chain 'SS' and resid 91 through 95 Processing helix chain 'RR' and resid 15 through 29 Processing helix chain 'RR' and resid 34 through 44 Processing helix chain 'RR' and resid 58 through 70 Processing helix chain 'RR' and resid 81 through 90 Processing helix chain 'RR' and resid 118 through 130 Processing helix chain '9' and resid 21 through 27 Processing helix chain '9' and resid 29 through 37 Processing helix chain '9' and resid 38 through 48 Processing helix chain '9' and resid 50 through 67 removed outlier: 3.642A pdb=" N LEU 9 56 " --> pdb=" O LYS 9 52 " (cutoff:3.500A) Processing helix chain '9' and resid 108 through 112 removed outlier: 3.919A pdb=" N ILE 9 112 " --> pdb=" O PRO 9 109 " (cutoff:3.500A) Processing helix chain 'II' and resid 25 through 30 Processing helix chain 'II' and resid 31 through 33 No H-bonds generated for 'chain 'II' and resid 31 through 33' Processing helix chain 'II' and resid 37 through 48 Processing helix chain 'II' and resid 60 through 73 Processing helix chain 'II' and resid 101 through 118 Processing helix chain 'II' and resid 119 through 128 Processing helix chain 'PP' and resid 10 through 26 removed outlier: 3.994A pdb=" N ARGPP 16 " --> pdb=" O GLNPP 12 " (cutoff:3.500A) Processing helix chain 'PP' and resid 31 through 37 removed outlier: 3.826A pdb=" N VALPP 34 " --> pdb=" O PROPP 31 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ASPPP 35 " --> pdb=" O GLUPP 32 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N THRPP 36 " --> pdb=" O TRPPP 33 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VALPP 37 " --> pdb=" O VALPP 34 " (cutoff:3.500A) No H-bonds generated for 'chain 'PP' and resid 31 through 37' Processing helix chain 'PP' and resid 51 through 67 removed outlier: 3.739A pdb=" N THRPP 55 " --> pdb=" O ASNPP 51 " (cutoff:3.500A) Processing helix chain 'PP' and resid 71 through 79 Processing helix chain 'PP' and resid 96 through 110 removed outlier: 4.103A pdb=" N ALAPP 100 " --> pdb=" O SERPP 96 " (cutoff:3.500A) Processing helix chain 'PP' and resid 124 through 143 Processing helix chain 'GG' and resid 29 through 47 Processing helix chain 'GG' and resid 94 through 103 removed outlier: 3.523A pdb=" N VALGG 98 " --> pdb=" O PROGG 94 " (cutoff:3.500A) Processing helix chain 'OO' and resid 51 through 61 Processing helix chain 'OO' and resid 62 through 65 Processing helix chain 'OO' and resid 69 through 78 Processing helix chain 'OO' and resid 80 through 95 Processing helix chain 'w' and resid 3 through 7 Processing helix chain 'w' and resid 32 through 36 Processing helix chain 'w' and resid 40 through 51 removed outlier: 5.396A pdb=" N LYS w 48 " --> pdb=" O ARG w 44 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N ASP w 49 " --> pdb=" O GLN w 45 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 71 through 77 removed outlier: 6.484A pdb=" N LEU A 58 " --> pdb=" O ILE A 48 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ILE A 48 " --> pdb=" O LEU A 58 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N LYS A 60 " --> pdb=" O LYS A 46 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ARG A 64 " --> pdb=" O LYS A 42 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N LYS A 42 " --> pdb=" O ARG A 64 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 82 through 83 removed outlier: 3.776A pdb=" N ILE A 82 " --> pdb=" O ALA p 65 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N ILE p 54 " --> pdb=" O ARG p 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 102 through 103 removed outlier: 3.656A pdb=" N ALA A 164 " --> pdb=" O LEU A 102 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N VAL A 136 " --> pdb=" O LYS A 149 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N LYS A 149 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N SER A 138 " --> pdb=" O ARG A 147 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LYS A 145 " --> pdb=" O ASN A 140 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 224 through 225 Processing sheet with id=AA5, first strand: chain 'B' and resid 42 through 43 removed outlier: 5.060A pdb=" N ILE B 160 " --> pdb=" O VAL B 185 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N HIS B 165 " --> pdb=" O VAL B 86 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N VAL B 86 " --> pdb=" O HIS B 165 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N VAL B 87 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N PHE B 106 " --> pdb=" O VAL B 87 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ILE B 89 " --> pdb=" O THR B 104 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N THR B 104 " --> pdb=" O ILE B 89 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N GLY B 91 " --> pdb=" O PHE B 102 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 42 through 43 removed outlier: 5.060A pdb=" N ILE B 160 " --> pdb=" O VAL B 185 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N HIS B 165 " --> pdb=" O VAL B 86 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N VAL B 86 " --> pdb=" O HIS B 165 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 365 through 368 removed outlier: 6.923A pdb=" N LEU B 365 " --> pdb=" O GLU B 59 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N GLU B 59 " --> pdb=" O LEU B 365 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N VAL B 344 " --> pdb=" O VAL B 222 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N VAL B 222 " --> pdb=" O VAL B 344 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N VAL B 219 " --> pdb=" O ILE B 280 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N ILE B 280 " --> pdb=" O VAL B 219 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N GLY B 221 " --> pdb=" O THR B 278 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N THR B 278 " --> pdb=" O GLY B 221 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N LYS B 283 " --> pdb=" O LYS B 334 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N MET B 332 " --> pdb=" O TYR B 285 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N ILE B 287 " --> pdb=" O PHE B 330 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N PHE B 330 " --> pdb=" O ILE B 287 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N VAL B 72 " --> pdb=" O VAL B 57 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N VAL B 57 " --> pdb=" O VAL B 72 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N GLU B 74 " --> pdb=" O HIS B 55 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N HIS B 55 " --> pdb=" O GLU B 74 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N VAL B 76 " --> pdb=" O MET B 53 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N MET B 53 " --> pdb=" O VAL B 76 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ILE B 78 " --> pdb=" O ALA B 51 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 227 through 229 Processing sheet with id=AA9, first strand: chain 'C' and resid 7 through 9 Processing sheet with id=AB1, first strand: chain 'C' and resid 152 through 154 removed outlier: 6.180A pdb=" N LEU C 152 " --> pdb=" O TRP C 252 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N THR C 253 " --> pdb=" O ILE C 210 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N VAL C 209 " --> pdb=" O LEU C 230 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 188 through 189 Processing sheet with id=AB3, first strand: chain 'D' and resid 73 through 79 removed outlier: 5.525A pdb=" N ILE D 74 " --> pdb=" O TYR D 66 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N TYR D 66 " --> pdb=" O ILE D 74 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 182 through 185 removed outlier: 4.415A pdb=" N LYS E 162 " --> pdb=" O LEU E 170 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N THR E 172 " --> pdb=" O PHE E 160 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N PHE E 160 " --> pdb=" O THR E 172 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS E 156 " --> pdb=" O ILE E 148 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE E 145 " --> pdb=" O THR E 193 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 82 through 84 Processing sheet with id=AB6, first strand: chain 'F' and resid 213 through 214 removed outlier: 3.903A pdb=" N ASN F 121 " --> pdb=" O ARG F 96 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 161 through 163 Processing sheet with id=AB8, first strand: chain 'G' and resid 181 through 184 removed outlier: 6.162A pdb=" N VAL G 155 " --> pdb=" O CYS G 182 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N LEU G 184 " --> pdb=" O VAL G 155 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ILE G 157 " --> pdb=" O LEU G 184 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LEU G 154 " --> pdb=" O PHE G 204 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 6 through 11 Processing sheet with id=AC1, first strand: chain 'H' and resid 17 through 21 Processing sheet with id=AC2, first strand: chain 'H' and resid 133 through 136 removed outlier: 6.196A pdb=" N ARG H 93 " --> pdb=" O VAL H 181 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N VAL H 181 " --> pdb=" O ARG H 93 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N VAL H 95 " --> pdb=" O ILE H 179 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N ILE H 179 " --> pdb=" O VAL H 95 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 102 through 105 Processing sheet with id=AC4, first strand: chain 'I' and resid 35 through 37 removed outlier: 6.518A pdb=" N MET I 52 " --> pdb=" O ILE I 135 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N SER I 137 " --> pdb=" O GLY I 50 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N GLY I 50 " --> pdb=" O SER I 137 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 58 through 61 removed outlier: 6.785A pdb=" N ILE I 97 " --> pdb=" O GLN I 123 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N THR I 125 " --> pdb=" O HIS I 95 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N HIS I 95 " --> pdb=" O THR I 125 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 190 through 193 Processing sheet with id=AC7, first strand: chain 'J' and resid 49 through 52 removed outlier: 6.816A pdb=" N VAL J 133 " --> pdb=" O ARG J 18 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N LEU J 20 " --> pdb=" O TYR J 131 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N TYR J 131 " --> pdb=" O LEU J 20 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N LEU J 22 " --> pdb=" O ASP J 129 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ASP J 129 " --> pdb=" O LEU J 22 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'L' and resid 22 through 24 removed outlier: 3.646A pdb=" N LEU N 200 " --> pdb=" O ALA L 23 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'L' and resid 58 through 60 Processing sheet with id=AD1, first strand: chain 'L' and resid 125 through 127 removed outlier: 4.620A pdb=" N LYS h 118 " --> pdb=" O PHE L 127 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'M' and resid 45 through 50 removed outlier: 5.476A pdb=" N ARG M 46 " --> pdb=" O GLY M 40 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N GLY M 40 " --> pdb=" O ARG M 46 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ARG M 35 " --> pdb=" O ILE M 31 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASP M 29 " --> pdb=" O LEU M 37 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ASP M 39 " --> pdb=" O ILE M 27 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N ILE M 27 " --> pdb=" O ASP M 39 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ARG M 11 " --> pdb=" O ILE M 27 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N VAL M 12 " --> pdb=" O THR M 58 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'N' and resid 36 through 39 removed outlier: 4.297A pdb=" N ILE N 61 " --> pdb=" O ALA N 39 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N TYR N 127 " --> pdb=" O GLY N 122 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N GLY N 122 " --> pdb=" O TYR N 127 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N PHE N 129 " --> pdb=" O TRP N 120 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N TRP N 120 " --> pdb=" O PHE N 129 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N GLU N 131 " --> pdb=" O SER N 118 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N SER N 118 " --> pdb=" O GLU N 131 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ILE N 133 " --> pdb=" O LEU N 116 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'O' and resid 6 through 10 removed outlier: 6.519A pdb=" N LEU O 7 " --> pdb=" O VAL O 34 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N VAL O 36 " --> pdb=" O LEU O 7 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N LEU O 9 " --> pdb=" O VAL O 36 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N VAL O 33 " --> pdb=" O LYS O 103 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'O' and resid 42 through 44 Processing sheet with id=AD6, first strand: chain 'P' and resid 14 through 22 removed outlier: 3.932A pdb=" N ASN P 21 " --> pdb=" O CYS P 144 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N CYS P 144 " --> pdb=" O ASN P 21 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N THR P 151 " --> pdb=" O ILE P 114 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N ILE P 114 " --> pdb=" O THR P 151 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'P' and resid 125 through 131 removed outlier: 3.673A pdb=" N ARG P 135 " --> pdb=" O ARG P 131 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'Q' and resid 60 through 62 Processing sheet with id=AD9, first strand: chain 'Q' and resid 119 through 121 Processing sheet with id=AE1, first strand: chain 'R' and resid 22 through 23 removed outlier: 3.556A pdb=" N ILE R 51 " --> pdb=" O TRP R 23 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'S' and resid 60 through 66 removed outlier: 6.779A pdb=" N VAL S 13 " --> pdb=" O VAL S 62 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N CYS S 64 " --> pdb=" O LYS S 11 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N LYS S 11 " --> pdb=" O CYS S 64 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N GLN S 66 " --> pdb=" O GLU S 9 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N GLU S 9 " --> pdb=" O GLN S 66 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'S' and resid 90 through 99 removed outlier: 3.877A pdb=" N ASN S 77 " --> pdb=" O ILE S 132 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LYS S 128 " --> pdb=" O TRP S 81 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ARG S 83 " --> pdb=" O ILE S 126 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N ILE S 126 " --> pdb=" O ARG S 83 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'T' and resid 39 through 41 removed outlier: 6.527A pdb=" N THR T 61 " --> pdb=" O ASN T 77 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N ASN T 77 " --> pdb=" O THR T 61 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N GLY T 73 " --> pdb=" O TYR T 65 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N VAL T 67 " --> pdb=" O ALA T 71 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ALA T 71 " --> pdb=" O VAL T 67 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'U' and resid 62 through 65 removed outlier: 3.768A pdb=" N THR U 71 " --> pdb=" O GLU U 64 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ILE U 70 " --> pdb=" O LEU U 23 " (cutoff:3.500A) removed outlier: 8.553A pdb=" N TYR U 110 " --> pdb=" O LYS U 20 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N THR U 22 " --> pdb=" O TYR U 110 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N LEU U 112 " --> pdb=" O THR U 22 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N ASP U 24 " --> pdb=" O LEU U 112 " (cutoff:3.500A) removed outlier: 9.395A pdb=" N TYR U 114 " --> pdb=" O ASP U 24 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'V' and resid 25 through 28 removed outlier: 5.609A pdb=" N ILE V 39 " --> pdb=" O THR V 64 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N THR V 64 " --> pdb=" O ILE V 39 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER V 41 " --> pdb=" O MET V 62 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ALA V 102 " --> pdb=" O ILE V 82 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N GLY V 103 " --> pdb=" O VAL V 25 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N ASN V 27 " --> pdb=" O GLY V 103 " (cutoff:3.500A) removed outlier: 8.191A pdb=" N ILE V 105 " --> pdb=" O ASN V 27 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'V' and resid 88 through 89 removed outlier: 3.560A pdb=" N TYR V 88 " --> pdb=" O LEU V 96 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU V 96 " --> pdb=" O TYR V 88 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'V' and resid 120 through 121 Processing sheet with id=AE9, first strand: chain 'W' and resid 4 through 5 Processing sheet with id=AF1, first strand: chain 'W' and resid 19 through 22 Processing sheet with id=AF2, first strand: chain 'X' and resid 77 through 80 removed outlier: 3.542A pdb=" N PHE X 79 " --> pdb=" O ILE X 99 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'Y' and resid 31 through 33 Processing sheet with id=AF4, first strand: chain 'Y' and resid 79 through 82 removed outlier: 6.935A pdb=" N VAL Y 79 " --> pdb=" O VAL Y 73 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N VAL Y 73 " --> pdb=" O VAL Y 79 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N TYR Y 81 " --> pdb=" O VAL Y 71 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N GLU Y 54 " --> pdb=" O THR Y 107 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'Y' and resid 86 through 88 Processing sheet with id=AF6, first strand: chain 'Z' and resid 69 through 75 removed outlier: 6.289A pdb=" N LYS Z 69 " --> pdb=" O ASP Z 47 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N LEU Z 42 " --> pdb=" O VAL Z 26 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N LYS Z 22 " --> pdb=" O ILE Z 46 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N LYS Z 9 " --> pdb=" O ILE Z 25 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N VAL Z 10 " --> pdb=" O THR Z 83 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'a' and resid 72 through 74 removed outlier: 6.464A pdb=" N VAL a 73 " --> pdb=" O LEU a 112 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'a' and resid 100 through 102 removed outlier: 5.982A pdb=" N VAL a 124 " --> pdb=" O VAL a 145 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'c' and resid 26 through 29 removed outlier: 6.547A pdb=" N LYS c 26 " --> pdb=" O ILE c 97 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'd' and resid 22 through 28 Processing sheet with id=AG2, first strand: chain 'e' and resid 75 through 79 Processing sheet with id=AG3, first strand: chain 'f' and resid 47 through 48 removed outlier: 3.672A pdb=" N ALA f 9 " --> pdb=" O ILE f 101 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL f 103 " --> pdb=" O CYS f 7 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N PHE f 11 " --> pdb=" O LYS f 29 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N LYS f 29 " --> pdb=" O PHE f 11 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLY f 13 " --> pdb=" O LEU f 27 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N THR f 25 " --> pdb=" O LYS f 15 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ARG f 76 " --> pdb=" O ARG f 85 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'f' and resid 51 through 57 removed outlier: 5.838A pdb=" N LYS f 66 " --> pdb=" O ALA f 53 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'g' and resid 20 through 24 Processing sheet with id=AG6, first strand: chain 'j' and resid 16 through 18 Processing sheet with id=AG7, first strand: chain 'k' and resid 3 through 4 removed outlier: 6.504A pdb=" N ARG k 3 " --> pdb=" O THR k 44 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N VAL k 46 " --> pdb=" O ARG k 3 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'm' and resid 102 through 103 Processing sheet with id=AG9, first strand: chain 'o' and resid 3 through 4 Processing sheet with id=AH1, first strand: chain 'o' and resid 7 through 11 removed outlier: 6.904A pdb=" N LYS o 64 " --> pdb=" O ARG o 87 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N ARG o 87 " --> pdb=" O LYS o 64 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ILE o 66 " --> pdb=" O ILE o 85 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'r' and resid 17 through 18 Processing sheet with id=AH3, first strand: chain 'r' and resid 49 through 53 Processing sheet with id=AH4, first strand: chain 's' and resid 52 through 55 removed outlier: 3.604A pdb=" N LYS s 26 " --> pdb=" O THR s 91 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N CYS s 27 " --> pdb=" O PHE s 193 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLN s 191 " --> pdb=" O ILE s 29 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N VAL s 192 " --> pdb=" O TYR s 199 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 's' and resid 121 through 122 removed outlier: 3.956A pdb=" N ILE s 161 " --> pdb=" O VAL s 121 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 's' and resid 145 through 147 Processing sheet with id=AH7, first strand: chain 't' and resid 62 through 65 Processing sheet with id=AH8, first strand: chain 'q' and resid 38 through 41 removed outlier: 7.091A pdb=" N ILE q 48 " --> pdb=" O TYR q 39 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'q' and resid 97 through 100 removed outlier: 6.210A pdb=" N VAL q 74 " --> pdb=" O THR q 97 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N ILE q 99 " --> pdb=" O VAL q 74 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N VAL q 76 " --> pdb=" O ILE q 99 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N THR q 144 " --> pdb=" O ILE q 159 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N ILE q 161 " --> pdb=" O THR q 144 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ALA q 146 " --> pdb=" O ILE q 161 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'u' and resid 43 through 50 removed outlier: 4.716A pdb=" N GLY u 45 " --> pdb=" O VAL u 33 " (cutoff:3.500A) removed outlier: 8.749A pdb=" N CYS u 96 " --> pdb=" O TRP u 30 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N ASP u 32 " --> pdb=" O CYS u 96 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N THR u 98 " --> pdb=" O ASP u 32 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N LYS u 34 " --> pdb=" O THR u 98 " (cutoff:3.500A) removed outlier: 8.714A pdb=" N PHE u 100 " --> pdb=" O LYS u 34 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N CYS u 96 " --> pdb=" O VAL u 91 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N VAL u 91 " --> pdb=" O CYS u 96 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N THR u 98 " --> pdb=" O GLU u 89 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N GLU u 89 " --> pdb=" O THR u 98 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N PHE u 100 " --> pdb=" O ILE u 87 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N ILE u 87 " --> pdb=" O PHE u 100 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'u' and resid 43 through 50 removed outlier: 4.716A pdb=" N GLY u 45 " --> pdb=" O VAL u 33 " (cutoff:3.500A) removed outlier: 8.749A pdb=" N CYS u 96 " --> pdb=" O TRP u 30 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N ASP u 32 " --> pdb=" O CYS u 96 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N THR u 98 " --> pdb=" O ASP u 32 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N LYS u 34 " --> pdb=" O THR u 98 " (cutoff:3.500A) removed outlier: 8.714A pdb=" N PHE u 100 " --> pdb=" O LYS u 34 " (cutoff:3.500A) removed outlier: 13.524A pdb=" N ASN u 99 " --> pdb=" O LYS u 219 " (cutoff:3.500A) removed outlier: 12.602A pdb=" N LYS u 219 " --> pdb=" O ASN u 99 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N HIS u 101 " --> pdb=" O MET u 217 " (cutoff:3.500A) removed outlier: 8.712A pdb=" N ARG u 213 " --> pdb=" O LEU u 105 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N VAL u 210 " --> pdb=" O PHE u 142 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N PHE u 142 " --> pdb=" O VAL u 210 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N VAL u 212 " --> pdb=" O VAL u 140 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N VAL u 140 " --> pdb=" O VAL u 212 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N LEU u 134 " --> pdb=" O LEU u 218 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'v' and resid 104 through 115 removed outlier: 5.864A pdb=" N ASP v 104 " --> pdb=" O GLY v 131 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N GLY v 131 " --> pdb=" O ASP v 104 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N VAL v 106 " --> pdb=" O ALA v 129 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N ALA v 129 " --> pdb=" O VAL v 106 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LYS v 108 " --> pdb=" O PHE v 127 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL v 112 " --> pdb=" O ARG v 123 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYS v 114 " --> pdb=" O ARG v 121 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'v' and resid 184 through 188 removed outlier: 3.593A pdb=" N CYS v 188 " --> pdb=" O VAL v 191 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL v 191 " --> pdb=" O CYS v 188 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'x' and resid 42 through 43 removed outlier: 3.511A pdb=" N ALA x 84 " --> pdb=" O LEU x 42 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'x' and resid 70 through 72 removed outlier: 3.693A pdb=" N GLU x 97 " --> pdb=" O ILE x 92 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ASN x 98 " --> pdb=" O ILE x 114 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'x' and resid 102 through 103 removed outlier: 4.594A pdb=" N ILE x 102 " --> pdb=" O ALA x 110 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'x' and resid 146 through 148 removed outlier: 6.207A pdb=" N HIS x 138 " --> pdb=" O ILE x 129 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ILE x 129 " --> pdb=" O HIS x 138 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N VAL x 140 " --> pdb=" O ARG x 127 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ASP x 171 " --> pdb=" O GLN x 161 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N ASP x 163 " --> pdb=" O ILE x 169 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ILE x 169 " --> pdb=" O ASP x 163 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'x' and resid 217 through 221 removed outlier: 6.996A pdb=" N VAL x 207 " --> pdb=" O ARG x 198 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N ARG x 198 " --> pdb=" O VAL x 207 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N HIS x 209 " --> pdb=" O THR x 196 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'x' and resid 229 through 230 removed outlier: 3.596A pdb=" N LYS x 230 " --> pdb=" O LYS x 233 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'z' and resid 12 through 17 removed outlier: 6.751A pdb=" N LYS z 2 " --> pdb=" O LEU z 109 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N LEU z 111 " --> pdb=" O LYS z 2 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N ASN z 4 " --> pdb=" O LEU z 111 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N ILE z 113 " --> pdb=" O ASN z 4 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N SER z 6 " --> pdb=" O ILE z 113 " (cutoff:3.500A) removed outlier: 8.304A pdb=" N LYS z 115 " --> pdb=" O SER z 6 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N VAL z 49 " --> pdb=" O VAL z 114 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'z' and resid 30 through 31 removed outlier: 3.861A pdb=" N LYS z 30 " --> pdb=" O VAL z 102 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'z' and resid 73 through 77 Processing sheet with id=AJ5, first strand: chain 'z' and resid 160 through 162 Processing sheet with id=AJ6, first strand: chain 'y' and resid 47 through 53 removed outlier: 3.945A pdb=" N ALA y 47 " --> pdb=" O PHE y 63 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ARG y 57 " --> pdb=" O VAL y 53 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N HIS y 91 " --> pdb=" O LYS y 58 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N VAL y 93 " --> pdb=" O ILE y 60 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE y 62 " --> pdb=" O VAL y 93 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE y 95 " --> pdb=" O ILE y 62 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'y' and resid 184 through 188 removed outlier: 7.003A pdb=" N ARG y 152 " --> pdb=" O ASP y 184 " (cutoff:3.500A) removed outlier: 8.335A pdb=" N ASN y 186 " --> pdb=" O ARG y 152 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N ILE y 154 " --> pdb=" O ASN y 186 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N GLU y 188 " --> pdb=" O ILE y 154 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N VAL y 156 " --> pdb=" O GLU y 188 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLY y 141 " --> pdb=" O HIS y 157 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N PHETT 50 " --> pdb=" O VAL y 146 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'CC' and resid 42 through 47 removed outlier: 6.659A pdb=" N ARGCC 42 " --> pdb=" O LEUCC 58 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'CC' and resid 62 through 67 removed outlier: 8.763A pdb=" N ILECC 79 " --> pdb=" O ASPCC 105 " (cutoff:3.500A) removed outlier: 8.967A pdb=" N ASPCC 105 " --> pdb=" O ILECC 79 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N VALCC 81 " --> pdb=" O LEUCC 103 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N LEUCC 103 " --> pdb=" O VALCC 81 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N CYSCC 100 " --> pdb=" O ILECC 175 " (cutoff:3.500A) removed outlier: 8.436A pdb=" N GLYCC 187 " --> pdb=" O VALCC 62 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ASNCC 64 " --> pdb=" O GLYCC 187 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N VALCC 189 " --> pdb=" O ASNCC 64 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N SERCC 66 " --> pdb=" O VALCC 189 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'XX' and resid 135 through 137 Processing sheet with id=AK2, first strand: chain 'EE' and resid 72 through 79 removed outlier: 6.976A pdb=" N VALEE 87 " --> pdb=" O THREE 78 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N SEREE 110 " --> pdb=" O VALEE 138 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N PHEEE 140 " --> pdb=" O SEREE 110 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N THREE 127 " --> pdb=" O LEUEE 143 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N VALEE 145 " --> pdb=" O ILEEE 125 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N ILEEE 125 " --> pdb=" O VALEE 145 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'EE' and resid 91 through 93 Processing sheet with id=AK4, first strand: chain 'MM' and resid 52 through 57 removed outlier: 6.805A pdb=" N VALMM 44 " --> pdb=" O ILEMM 53 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ARGMM 55 " --> pdb=" O VALMM 42 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N VALMM 42 " --> pdb=" O ARGMM 55 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N THRMM 57 " --> pdb=" O THRMM 40 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N THRMM 40 " --> pdb=" O THRMM 57 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N HISMM 43 " --> pdb=" O HISMM 32 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N GLYMM 29 " --> pdb=" O HISMM 94 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N LYSMM 96 " --> pdb=" O GLYMM 29 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N CYSMM 31 " --> pdb=" O LYSMM 96 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N ARGMM 98 " --> pdb=" O CYSMM 31 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N ILEMM 33 " --> pdb=" O ARGMM 98 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N LEUMM 93 " --> pdb=" O ILEMM 126 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N ARGMM 128 " --> pdb=" O LEUMM 93 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain 'UU' and resid 10 through 15 removed outlier: 3.720A pdb=" N LYSUU 73 " --> pdb=" O THRUU 20 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASPUU 67 " --> pdb=" O LYSUU 26 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'YY' and resid 39 through 40 Processing sheet with id=AK7, first strand: chain 'YY' and resid 96 through 98 removed outlier: 5.621A pdb=" N ILEYY 96 " --> pdb=" O GLNYY 118 " (cutoff:3.500A) No H-bonds generated for sheet with id=AK7 Processing sheet with id=AK8, first strand: chain 'HH' and resid 32 through 36 Processing sheet with id=AK9, first strand: chain 'TT' and resid 71 through 72 Processing sheet with id=AL1, first strand: chain 'TT' and resid 71 through 72 removed outlier: 5.289A pdb=" N ILETT 125 " --> pdb=" O THRTT 105 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N THRTT 105 " --> pdb=" O ILETT 125 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLYTT 127 " --> pdb=" O VALTT 103 " (cutoff:3.500A) Processing sheet with id=AL2, first strand: chain 'VV' and resid 128 through 129 removed outlier: 5.274A pdb=" N VALVV 122 " --> pdb=" O ALAVV 103 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ALAVV 103 " --> pdb=" O VALVV 122 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LYSVV 124 " --> pdb=" O LEUVV 101 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ARGVV 71 " --> pdb=" O LEUVV 52 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N LYSVV 54 " --> pdb=" O CYSVV 69 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N CYSVV 69 " --> pdb=" O LYSVV 54 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N GLYVV 56 " --> pdb=" O ARGVV 67 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N ARGVV 67 " --> pdb=" O GLYVV 56 " (cutoff:3.500A) removed outlier: 9.447A pdb=" N PHEVV 120 " --> pdb=" O LYSVV 80 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N THRVV 82 " --> pdb=" O PHEVV 120 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N VALVV 122 " --> pdb=" O THRVV 82 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N PHEVV 84 " --> pdb=" O VALVV 122 " (cutoff:3.500A) removed outlier: 8.590A pdb=" N LYSVV 124 " --> pdb=" O PHEVV 84 " (cutoff:3.500A) Processing sheet with id=AL3, first strand: chain 'NN' and resid 6 through 15 removed outlier: 4.339A pdb=" N PHENN 12 " --> pdb=" O GLNNN 22 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N GLNNN 22 " --> pdb=" O PHENN 12 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N THRNN 14 " --> pdb=" O ARGNN 20 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ARGNN 20 " --> pdb=" O THRNN 14 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N PHENN 72 " --> pdb=" O GLYNN 59 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N GLYNN 59 " --> pdb=" O PHENN 72 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N METNN 74 " --> pdb=" O VALNN 57 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N VALNN 57 " --> pdb=" O METNN 74 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N TYRNN 76 " --> pdb=" O ILENN 55 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N ILENN 55 " --> pdb=" O TYRNN 76 " (cutoff:3.500A) Processing sheet with id=AL4, first strand: chain 'ZZ' and resid 20 through 22 Processing sheet with id=AL5, first strand: chain 'ZZ' and resid 36 through 40 Processing sheet with id=AL6, first strand: chain 'JJ' and resid 44 through 47 Processing sheet with id=AL7, first strand: chain 'JJ' and resid 64 through 65 removed outlier: 3.594A pdb=" N ARGJJ 72 " --> pdb=" O GLNJJ 65 " (cutoff:3.500A) Processing sheet with id=AL8, first strand: chain 'DD' and resid 34 through 41 removed outlier: 6.432A pdb=" N THRDD 46 " --> pdb=" O GLUDD 85 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N TYRDD 87 " --> pdb=" O THRDD 46 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ILEDD 48 " --> pdb=" O TYRDD 87 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N GLUDD 89 " --> pdb=" O ILEDD 48 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ILEDD 50 " --> pdb=" O GLUDD 89 " (cutoff:3.500A) Processing sheet with id=AL9, first strand: chain 'DD' and resid 150 through 152 removed outlier: 3.793A pdb=" N GLYDD 133 " --> pdb=" O METDD 189 " (cutoff:3.500A) Processing sheet with id=AM1, first strand: chain 'DD' and resid 223 through 224 removed outlier: 6.790A pdb=" N VAL 6 176 " --> pdb=" O LYS 6 185 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ASN 6 187 " --> pdb=" O VAL 6 174 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N VAL 6 174 " --> pdb=" O ASN 6 187 " (cutoff:3.500A) Processing sheet with id=AM2, first strand: chain 'BB' and resid 19 through 20 Processing sheet with id=AM3, first strand: chain 'BB' and resid 123 through 126 removed outlier: 8.395A pdb=" N ALABB 138 " --> pdb=" O ASNFF 45 " (cutoff:3.500A) removed outlier: 8.909A pdb=" N LYSFF 47 " --> pdb=" O ALABB 138 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N ASPBB 140 " --> pdb=" O LYSFF 47 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N CYSFF 27 " --> pdb=" O ARGFF 20 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N ARGFF 20 " --> pdb=" O CYSFF 27 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N GLNFF 29 " --> pdb=" O LEUFF 18 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N GLUFF 33 " --> pdb=" O VALFF 14 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N VALFF 14 " --> pdb=" O GLUFF 33 " (cutoff:3.500A) Processing sheet with id=AM4, first strand: chain 'SS' and resid 21 through 24 Processing sheet with id=AM5, first strand: chain 'RR' and resid 76 through 78 removed outlier: 3.670A pdb=" N LEURR 49 " --> pdb=" O VALRR 111 " (cutoff:3.500A) Processing sheet with id=AM6, first strand: chain '9' and resid 75 through 78 Processing sheet with id=AM7, first strand: chain 'II' and resid 12 through 14 Processing sheet with id=AM8, first strand: chain 'PP' and resid 81 through 83 Processing sheet with id=AM9, first strand: chain 'PP' and resid 113 through 115 Processing sheet with id=AN1, first strand: chain 'GG' and resid 49 through 50 removed outlier: 4.428A pdb=" N LYSGG 49 " --> pdb=" O HISGG 92 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N LYSGG 86 " --> pdb=" O PROGG 57 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N LEUGG 88 " --> pdb=" O ARGGG 55 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N ARGGG 55 " --> pdb=" O LEUGG 88 " (cutoff:3.500A) Processing sheet with id=AN2, first strand: chain 'GG' and resid 49 through 50 removed outlier: 4.428A pdb=" N LYSGG 49 " --> pdb=" O HISGG 92 " (cutoff:3.500A) Processing sheet with id=AN3, first strand: chain 'OO' and resid 98 through 101 removed outlier: 7.165A pdb=" N ILEOO 108 " --> pdb=" O VALOO 100 " (cutoff:3.500A) Processing sheet with id=AN4, first strand: chain 'w' and resid 30 through 31 removed outlier: 3.525A pdb=" N MET w 38 " --> pdb=" O ILE w 31 " (cutoff:3.500A) Processing sheet with id=AN5, first strand: chain '0' and resid 106 through 108 Processing sheet with id=AN6, first strand: chain '0' and resid 133 through 134 removed outlier: 3.652A pdb=" N TYR 0 140 " --> pdb=" O ALA 0 133 " (cutoff:3.500A) Processing sheet with id=AN7, first strand: chain '6' and resid 5 through 6 Processing sheet with id=AN8, first strand: chain '6' and resid 5 through 6 Processing sheet with id=AN9, first strand: chain '6' and resid 18 through 22 removed outlier: 3.728A pdb=" N GLN 6 20 " --> pdb=" O ALA 6 34 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE 6 31 " --> pdb=" O TRP 6 43 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N MET 6 42 " --> pdb=" O GLN 6 56 " (cutoff:3.500A) Processing sheet with id=AO1, first strand: chain '6' and resid 66 through 71 removed outlier: 3.939A pdb=" N SER 6 82 " --> pdb=" O THR 6 86 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N THR 6 86 " --> pdb=" O SER 6 82 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ARG 6 99 " --> pdb=" O LEU 6 89 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ASP 6 91 " --> pdb=" O THR 6 97 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N THR 6 97 " --> pdb=" O ASP 6 91 " (cutoff:3.500A) Processing sheet with id=AO2, first strand: chain '6' and resid 108 through 113 removed outlier: 3.829A pdb=" N ILE 6 129 " --> pdb=" O VAL 6 142 " (cutoff:3.500A) Processing sheet with id=AO3, first strand: chain '6' and resid 195 through 200 removed outlier: 5.014A pdb=" N GLY 6 211 " --> pdb=" O GLN 6 215 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N GLN 6 215 " --> pdb=" O GLY 6 211 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N TYR 6 228 " --> pdb=" O LEU 6 218 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ASP 6 220 " --> pdb=" O HIS 6 226 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N HIS 6 226 " --> pdb=" O ASP 6 220 " (cutoff:3.500A) Processing sheet with id=AO4, first strand: chain '6' and resid 236 through 241 removed outlier: 4.435A pdb=" N ALA 6 238 " --> pdb=" O ALA 6 251 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER 6 255 " --> pdb=" O THR 6 252 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ASP 6 268 " --> pdb=" O ILE 6 258 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ASP 6 260 " --> pdb=" O ILE 6 266 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N ILE 6 266 " --> pdb=" O ASP 6 260 " (cutoff:3.500A) 3573 hydrogen bonds defined for protein. 10287 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 4629 hydrogen bonds 7852 hydrogen bond angles 0 basepair planarities 1786 basepair parallelities 3152 stacking parallelities Total time for adding SS restraints: 467.85 Time building geometry restraints manager: 73.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 23391 1.32 - 1.44: 96379 1.44 - 1.57: 102257 1.57 - 1.69: 11558 1.69 - 1.82: 667 Bond restraints: 234252 Sorted by residual: bond pdb=" C PRO t 2 " pdb=" N PRO t 3 " ideal model delta sigma weight residual 1.334 1.417 -0.083 2.34e-02 1.83e+03 1.27e+01 bond pdb=" C ALA L 47 " pdb=" N PRO L 48 " ideal model delta sigma weight residual 1.336 1.370 -0.034 9.80e-03 1.04e+04 1.20e+01 bond pdb=" C THR P 129 " pdb=" O THR P 129 " ideal model delta sigma weight residual 1.234 1.201 0.034 1.11e-02 8.12e+03 9.12e+00 bond pdb=" C ILE P 136 " pdb=" O ILE P 136 " ideal model delta sigma weight residual 1.238 1.206 0.032 1.10e-02 8.26e+03 8.23e+00 bond pdb=" C ASN A 205 " pdb=" N PRO A 206 " ideal model delta sigma weight residual 1.334 1.358 -0.024 8.40e-03 1.42e+04 8.11e+00 ... (remaining 234247 not shown) Histogram of bond angle deviations from ideal: 96.97 - 104.97: 27326 104.97 - 112.97: 136487 112.97 - 120.97: 114259 120.97 - 128.98: 61516 128.98 - 136.98: 4659 Bond angle restraints: 344247 Sorted by residual: angle pdb=" O3' U 52015 " pdb=" C3' U 52015 " pdb=" C2' U 52015 " ideal model delta sigma weight residual 113.70 125.91 -12.21 1.50e+00 4.44e-01 6.63e+01 angle pdb=" N VAL G 27 " pdb=" CA VAL G 27 " pdb=" C VAL G 27 " ideal model delta sigma weight residual 113.43 106.61 6.82 1.09e+00 8.42e-01 3.91e+01 angle pdb=" O3' A 52017 " pdb=" C3' A 52017 " pdb=" C2' A 52017 " ideal model delta sigma weight residual 113.70 104.54 9.16 1.50e+00 4.44e-01 3.73e+01 angle pdb=" O3' G K 798 " pdb=" C3' G K 798 " pdb=" C2' G K 798 " ideal model delta sigma weight residual 109.50 117.98 -8.48 1.50e+00 4.44e-01 3.20e+01 angle pdb=" C LYS t 93 " pdb=" N LYS t 94 " pdb=" CA LYS t 94 " ideal model delta sigma weight residual 122.36 130.46 -8.10 1.47e+00 4.63e-01 3.04e+01 ... (remaining 344242 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 36.00: 124407 36.00 - 71.99: 3941 71.99 - 107.99: 338 107.99 - 143.98: 48 143.98 - 179.98: 150 Dihedral angle restraints: 128884 sinusoidal: 95229 harmonic: 33655 Sorted by residual: dihedral pdb=" CA LYS S 164 " pdb=" C LYS S 164 " pdb=" N PRO S 165 " pdb=" CA PRO S 165 " ideal model delta harmonic sigma weight residual -180.00 -115.70 -64.30 0 5.00e+00 4.00e-02 1.65e+02 dihedral pdb=" CA HIS B 258 " pdb=" C HIS B 258 " pdb=" N PRO B 259 " pdb=" CA PRO B 259 " ideal model delta harmonic sigma weight residual 180.00 -126.68 -53.32 0 5.00e+00 4.00e-02 1.14e+02 dihedral pdb=" CA LEU B 17 " pdb=" C LEU B 17 " pdb=" N PRO B 18 " pdb=" CA PRO B 18 " ideal model delta harmonic sigma weight residual 180.00 130.11 49.89 0 5.00e+00 4.00e-02 9.96e+01 ... (remaining 128881 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.122: 42065 0.122 - 0.243: 749 0.243 - 0.365: 65 0.365 - 0.487: 5 0.487 - 0.608: 2 Chirality restraints: 42886 Sorted by residual: chirality pdb=" C3' G K 798 " pdb=" C4' G K 798 " pdb=" O3' G K 798 " pdb=" C2' G K 798 " both_signs ideal model delta sigma weight residual False -2.74 -2.14 -0.61 2.00e-01 2.50e+01 9.25e+00 chirality pdb=" C3' U 52015 " pdb=" C4' U 52015 " pdb=" O3' U 52015 " pdb=" C2' U 52015 " both_signs ideal model delta sigma weight residual False -2.48 -1.94 -0.54 2.00e-01 2.50e+01 7.19e+00 chirality pdb=" CA GLNVV 61 " pdb=" N GLNVV 61 " pdb=" C GLNVV 61 " pdb=" CB GLNVV 61 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.46e+00 ... (remaining 42883 not shown) Planarity restraints: 22047 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLNVV 61 " 0.041 2.00e-02 2.50e+03 8.50e-02 7.22e+01 pdb=" C GLNVV 61 " -0.147 2.00e-02 2.50e+03 pdb=" O GLNVV 61 " 0.055 2.00e-02 2.50e+03 pdb=" N PROVV 62 " 0.051 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLNVV 61 " 0.082 5.00e-02 4.00e+02 1.25e-01 2.51e+01 pdb=" N PROVV 62 " -0.217 5.00e-02 4.00e+02 pdb=" CA PROVV 62 " 0.065 5.00e-02 4.00e+02 pdb=" CD PROVV 62 " 0.069 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR f 106 " 0.078 5.00e-02 4.00e+02 1.18e-01 2.24e+01 pdb=" N PRO f 107 " -0.205 5.00e-02 4.00e+02 pdb=" CA PRO f 107 " 0.063 5.00e-02 4.00e+02 pdb=" CD PRO f 107 " 0.064 5.00e-02 4.00e+02 ... (remaining 22044 not shown) Histogram of nonbonded interaction distances: 1.32 - 2.04: 7 2.04 - 2.75: 27818 2.75 - 3.47: 276088 3.47 - 4.18: 665320 4.18 - 4.90: 941766 Nonbonded interactions: 1910999 Sorted by model distance: nonbonded pdb="MG MG 55104 " pdb="MG MG 55120 " model vdw 1.319 1.300 nonbonded pdb="MG MG 55210 " pdb="MG MG 55213 " model vdw 1.321 1.300 nonbonded pdb="MG MG 55212 " pdb="MG MG 55226 " model vdw 1.383 1.300 nonbonded pdb=" C MET 1 260 " pdb=" O3' A 2 76 " model vdw 1.411 3.270 nonbonded pdb=" O2' C 53909 " pdb=" O2' A 2 76 " model vdw 1.847 2.440 ... (remaining 1910994 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 5791 5.49 5 Mg 159 5.21 5 S 427 5.16 5 C 114626 2.51 5 N 40633 2.21 5 O 56426 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 3.520 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: 0.200 Extract box with map and model: 24.430 Check model and map are aligned: 2.260 Convert atoms to be neutral: 1.200 Process input model: 836.420 Find NCS groups from input model: 5.680 Set up NCS constraints: 0.490 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:2.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 876.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 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 : 0.003 0.083 234252 Z= 0.201 Angle : 0.799 14.553 344247 Z= 0.402 Chirality : 0.042 0.608 42886 Planarity : 0.006 0.125 22047 Dihedral : 15.363 179.978 107184 Min Nonbonded Distance : 1.319 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.79 % Favored : 94.13 % Rotamer Outliers : 0.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % Cis-general : 0.02 % Twisted Proline : 1.22 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.27 (0.06), residues: 11507 helix: -2.12 (0.06), residues: 3845 sheet: -1.44 (0.12), residues: 1760 loop : -2.43 (0.07), residues: 5902 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23014 Ramachandran restraints generated. 11507 Oldfield, 0 Emsley, 11507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23014 Ramachandran restraints generated. 11507 Oldfield, 0 Emsley, 11507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3646 residues out of total 10038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 3629 time to evaluate : 10.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 3 residues processed: 3639 average time/residue: 2.0821 time to fit residues: 12430.8262 Evaluate side-chains 2290 residues out of total 10038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 2287 time to evaluate : 10.021 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 1.5184 time to fit residues: 22.3240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1710 random chunks: chunk 1443 optimal weight: 8.9990 chunk 1296 optimal weight: 9.9990 chunk 719 optimal weight: 7.9990 chunk 442 optimal weight: 5.9990 chunk 874 optimal weight: 8.9990 chunk 692 optimal weight: 2.9990 chunk 1340 optimal weight: 1.9990 chunk 518 optimal weight: 1.9990 chunk 814 optimal weight: 0.9990 chunk 997 optimal weight: 10.0000 chunk 1552 optimal weight: 0.9980 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN A 194 ASN B 167 GLN B 204 GLN B 245 HIS B 289 GLN ** B 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 ASN C 43 ASN C 50 GLN C 112 HIS C 212 ASN C 286 ASN ** D 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 198 HIS E 178 ASN E 187 GLN E 207 HIS E 280 HIS F 41 GLN ** F 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 85 GLN ** G 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 149 ASN ** G 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 240 ASN H 8 GLN H 39 ASN ** I 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 130 HIS I 213 HIS J 98 ASN L 19 GLN L 67 HIS L 87 HIS ** L 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 32 GLN N 201 HIS O 50 ASN O 65 ASN O 173 GLN O 199 HIS P 25 HIS P 75 GLN ** P 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 130 ASN R 141 HIS S 50 GLN S 66 GLN S 125 GLN S 163 HIS T 3 ASN T 70 HIS T 95 HIS U 44 GLN U 94 ASN V 77 HIS V 135 ASN W 45 ASN X 94 ASN X 105 ASN X 107 HIS X 125 ASN X 151 ASN Y 14 ASN Y 96 HIS Z 97 ASN a 14 HIS a 34 ASN b 6 ASN ** b 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 19 ASN b 42 ASN ** b 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 15 ASN ** c 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 18 ASN ** e 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 52 GLN ** f 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 99 HIS g 112 GLN ** h 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 108 GLN i 15 HIS j 48 ASN l 19 GLN m 119 ASN r 30 ASN r 31 ASN ** r 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 83 ASN s 191 GLN t 111 ASN q 50 ASN q 111 GLN q 131 HIS q 141 ASN u 101 HIS u 124 HIS u 147 ASN u 158 HIS u 179 ASN u 232 HIS ** x 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 112 HIS x 179 ASN x 232 ASN z 13 GLN z 81 HIS CC 84 ASN CC 87 ASN CC 88 ASN CC 138 ASN CC 165 GLN ** XX 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** XX 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** EE 83 GLN MM 94 HIS ** UU 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** UU 80 GLN UU 97 GLN UU 142 GLN YY 62 GLN HH 47 ASN HH 82 ASN TT 113 HIS VV 20 GLN ** NN 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** NN 63 HIS ZZ 17 HIS JJ 26 GLN JJ 29 ASN AA 88 GLN DD 101 GLN BB 65 GLN BB 82 ASN BB 114 ASN BB 118 ASN BB 149 GLN SS 28 HIS ** SS 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SS 61 GLN RR 19 GLN RR 48 HIS RR 82 ASN 9 41 GLN 9 104 GLN 9 128 HIS PP 85 ASN GG 47 ASN FF 29 GLN w 28 HIS 0 135 HIS 6 178 ASN Total number of N/Q/H flips: 134 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.136 234252 Z= 0.193 Angle : 0.578 13.848 344247 Z= 0.292 Chirality : 0.034 0.329 42886 Planarity : 0.005 0.119 22047 Dihedral : 16.103 179.794 82600 Min Nonbonded Distance : 0.981 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.75 % Favored : 95.19 % Rotamer Outliers : 2.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % Cis-general : 0.02 % Twisted Proline : 1.22 % 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: -1.67 (0.07), residues: 11507 helix: -0.01 (0.08), residues: 3822 sheet: -1.01 (0.12), residues: 1817 loop : -1.92 (0.07), residues: 5868 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23014 Ramachandran restraints generated. 11507 Oldfield, 0 Emsley, 11507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23014 Ramachandran restraints generated. 11507 Oldfield, 0 Emsley, 11507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2763 residues out of total 10038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 294 poor density : 2469 time to evaluate : 9.992 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 outliers start: 294 outliers final: 152 residues processed: 2606 average time/residue: 1.8233 time to fit residues: 8006.4144 Evaluate side-chains 2275 residues out of total 10038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 2123 time to evaluate : 9.946 Switching outliers to nearest non-outliers outliers start: 152 outliers final: 0 residues processed: 152 average time/residue: 1.3570 time to fit residues: 404.5804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1710 random chunks: chunk 863 optimal weight: 1.9990 chunk 481 optimal weight: 0.9990 chunk 1292 optimal weight: 9.9990 chunk 1057 optimal weight: 30.0000 chunk 428 optimal weight: 7.9990 chunk 1555 optimal weight: 6.9990 chunk 1680 optimal weight: 9.9990 chunk 1385 optimal weight: 10.0000 chunk 1542 optimal weight: 5.9990 chunk 530 optimal weight: 2.9990 chunk 1248 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN B 42 HIS B 55 HIS ** B 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 223 ASN D 17 GLN D 122 GLN G 46 GLN G 112 GLN ** G 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 98 ASN L 87 HIS L 104 ASN L 159 ASN O 42 ASN P 137 ASN R 130 ASN ** S 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 92 ASN U 44 GLN V 31 ASN W 50 ASN X 93 ASN X 105 ASN Y 96 HIS ** Z 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 28 HIS ** a 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 30 HIS ** e 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 19 GLN l 33 ASN m 87 GLN o 3 ASN r 30 ASN ** r 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 71 ASN 1 252 HIS u 157 GLN u 160 GLN ** v 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 13 GLN ** z 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 202 ASN y 91 HIS y 126 HIS CC 87 ASN XX 75 ASN ** XX 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** EE 5 GLN ** UU 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** TT 56 HIS TT 64 ASN VV 20 GLN JJ 29 ASN BB 101 HIS BB 114 ASN ** BB 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SS 28 HIS FF 29 GLN 6 117 ASN ** 6 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 191 HIS Total number of N/Q/H flips: 50 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.3274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.214 234252 Z= 0.282 Angle : 0.651 16.017 344247 Z= 0.330 Chirality : 0.038 0.321 42886 Planarity : 0.006 0.095 22047 Dihedral : 16.233 179.802 82600 Min Nonbonded Distance : 1.005 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.41 % Favored : 94.53 % Rotamer Outliers : 2.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % Cis-general : 0.02 % Twisted Proline : 1.22 % 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: -1.15 (0.07), residues: 11507 helix: 0.55 (0.08), residues: 3875 sheet: -0.91 (0.12), residues: 1843 loop : -1.64 (0.08), residues: 5789 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23014 Ramachandran restraints generated. 11507 Oldfield, 0 Emsley, 11507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23014 Ramachandran restraints generated. 11507 Oldfield, 0 Emsley, 11507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2642 residues out of total 10038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 272 poor density : 2370 time to evaluate : 14.043 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 outliers start: 272 outliers final: 143 residues processed: 2512 average time/residue: 1.9302 time to fit residues: 8258.7894 Evaluate side-chains 2249 residues out of total 10038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 2106 time to evaluate : 9.967 Switching outliers to nearest non-outliers outliers start: 143 outliers final: 0 residues processed: 143 average time/residue: 1.4083 time to fit residues: 399.1756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1710 random chunks: chunk 1537 optimal weight: 9.9990 chunk 1169 optimal weight: 10.0000 chunk 807 optimal weight: 3.9990 chunk 172 optimal weight: 9.9990 chunk 742 optimal weight: 4.9990 chunk 1044 optimal weight: 3.9990 chunk 1561 optimal weight: 8.9990 chunk 1652 optimal weight: 0.0070 chunk 815 optimal weight: 0.9990 chunk 1479 optimal weight: 3.9990 chunk 445 optimal weight: 3.9990 overall best weight: 2.6006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN A 218 HIS B 167 GLN ** B 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 204 GLN D 230 ASN E 131 GLN ** G 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 82 GLN G 195 HIS H 8 GLN I 95 HIS L 104 ASN ** M 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 130 ASN ** S 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 125 GLN T 79 GLN U 44 GLN X 93 ASN X 105 ASN Y 14 ASN Z 97 ASN ** b 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 52 GLN ** h 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 3 ASN r 30 ASN ** r 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 24 HIS u 160 GLN v 272 HIS ** x 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 70 HIS z 202 ASN y 73 GLN XX 124 HIS XX 156 HIS ** XX 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** EE 11 GLN QQ 36 GLN ** UU 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** UU 142 GLN TT 15 ASN TT 64 ASN VV 20 GLN NN 19 GLN NN 29 HIS NN 63 HIS JJ 29 ASN JJ 84 HIS BB 114 ASN BB 118 ASN ** BB 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** II 87 GLN ** II 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 10 HIS ** 6 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 45 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.3590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.141 234252 Z= 0.230 Angle : 0.586 17.070 344247 Z= 0.298 Chirality : 0.036 0.295 42886 Planarity : 0.005 0.112 22047 Dihedral : 16.177 179.857 82600 Min Nonbonded Distance : 1.028 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.88 % Favored : 95.05 % Rotamer Outliers : 2.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % Cis-general : 0.02 % Twisted Proline : 1.22 % 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: -0.77 (0.08), residues: 11507 helix: 0.96 (0.08), residues: 3871 sheet: -0.82 (0.12), residues: 1847 loop : -1.45 (0.08), residues: 5789 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23014 Ramachandran restraints generated. 11507 Oldfield, 0 Emsley, 11507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23014 Ramachandran restraints generated. 11507 Oldfield, 0 Emsley, 11507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2421 residues out of total 10038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 240 poor density : 2181 time to evaluate : 11.221 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 outliers start: 240 outliers final: 128 residues processed: 2304 average time/residue: 1.8252 time to fit residues: 7112.3332 Evaluate side-chains 2192 residues out of total 10038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 2064 time to evaluate : 11.211 Switching outliers to nearest non-outliers outliers start: 128 outliers final: 0 residues processed: 128 average time/residue: 1.5007 time to fit residues: 378.9703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1710 random chunks: chunk 1376 optimal weight: 5.9990 chunk 938 optimal weight: 6.9990 chunk 24 optimal weight: 10.0000 chunk 1230 optimal weight: 30.0000 chunk 681 optimal weight: 0.9980 chunk 1410 optimal weight: 0.6980 chunk 1142 optimal weight: 40.0000 chunk 1 optimal weight: 8.9990 chunk 844 optimal weight: 8.9990 chunk 1483 optimal weight: 6.9990 chunk 417 optimal weight: 0.4980 overall best weight: 3.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 354 GLN D 230 ASN E 186 HIS ** G 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 236 HIS ** I 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 20 HIS M 70 GLN O 173 GLN Q 8 ASN Q 57 ASN R 34 ASN ** S 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 79 GLN U 44 GLN V 135 ASN X 93 ASN ** Z 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 97 ASN ** b 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 118 GLN ** e 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 73 HIS ** r 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 124 HIS u 160 GLN u 179 ASN ** v 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 67 GLN x 142 HIS ** z 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 202 ASN CC 138 ASN ** XX 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** XX 156 HIS ** XX 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** EE 5 GLN ** UU 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** TT 64 ASN TT 82 GLN VV 20 GLN NN 19 GLN JJ 29 ASN BB 114 ASN ** BB 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** II 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 10 HIS 0 139 HIS Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.4059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.176 234252 Z= 0.265 Angle : 0.618 19.852 344247 Z= 0.313 Chirality : 0.038 0.318 42886 Planarity : 0.005 0.097 22047 Dihedral : 16.230 179.894 82600 Min Nonbonded Distance : 1.026 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.74 % Favored : 94.19 % Rotamer Outliers : 2.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % Cis-general : 0.02 % Twisted Proline : 1.22 % Twisted General : 0.05 % 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: -0.68 (0.08), residues: 11507 helix: 1.05 (0.08), residues: 3882 sheet: -0.77 (0.12), residues: 1836 loop : -1.41 (0.08), residues: 5789 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23014 Ramachandran restraints generated. 11507 Oldfield, 0 Emsley, 11507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23014 Ramachandran restraints generated. 11507 Oldfield, 0 Emsley, 11507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2410 residues out of total 10038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 227 poor density : 2183 time to evaluate : 9.952 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 outliers start: 227 outliers final: 119 residues processed: 2298 average time/residue: 1.8154 time to fit residues: 7054.9873 Evaluate side-chains 2182 residues out of total 10038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 2063 time to evaluate : 10.239 Switching outliers to nearest non-outliers outliers start: 119 outliers final: 0 residues processed: 119 average time/residue: 1.3986 time to fit residues: 326.1211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1710 random chunks: chunk 556 optimal weight: 2.9990 chunk 1488 optimal weight: 6.9990 chunk 326 optimal weight: 7.9990 chunk 970 optimal weight: 7.9990 chunk 408 optimal weight: 10.0000 chunk 1654 optimal weight: 0.0050 chunk 1373 optimal weight: 10.0000 chunk 766 optimal weight: 0.8980 chunk 137 optimal weight: 7.9990 chunk 547 optimal weight: 4.9990 chunk 868 optimal weight: 3.9990 overall best weight: 2.5800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN ** B 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 82 GLN I 100 ASN J 71 HIS J 167 GLN N 29 GLN Q 8 ASN Q 57 ASN ** S 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 135 ASN X 93 ASN Z 97 ASN ** a 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 118 GLN ** e 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 126 ASN ** r 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 71 ASN t 118 HIS 1 248 GLN u 124 HIS u 160 GLN u 179 ASN x 138 HIS z 202 ASN y 25 GLN CC 116 HIS XX 111 GLN ** XX 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** XX 156 HIS ** XX 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** EE 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** HH 21 ASN TT 64 ASN VV 20 GLN NN 19 GLN NN 63 HIS NN 106 GLN ** ZZ 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** JJ 29 ASN BB 82 ASN BB 114 ASN BB 118 ASN II 11 HIS ** II 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** GG 92 HIS w 45 GLN Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.4233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.176 234252 Z= 0.232 Angle : 0.593 19.837 344247 Z= 0.301 Chirality : 0.036 0.308 42886 Planarity : 0.005 0.102 22047 Dihedral : 16.198 179.901 82600 Min Nonbonded Distance : 1.036 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.08 % Favored : 94.85 % Rotamer Outliers : 1.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % Cis-general : 0.02 % Twisted Proline : 1.22 % Twisted General : 0.05 % 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 (0.08), residues: 11507 helix: 1.18 (0.08), residues: 3881 sheet: -0.73 (0.12), residues: 1836 loop : -1.34 (0.08), residues: 5790 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23014 Ramachandran restraints generated. 11507 Oldfield, 0 Emsley, 11507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23014 Ramachandran restraints generated. 11507 Oldfield, 0 Emsley, 11507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2323 residues out of total 10038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 181 poor density : 2142 time to evaluate : 9.963 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 outliers start: 181 outliers final: 95 residues processed: 2229 average time/residue: 1.9333 time to fit residues: 7316.1570 Evaluate side-chains 2122 residues out of total 10038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 2027 time to evaluate : 10.255 Switching outliers to nearest non-outliers outliers start: 95 outliers final: 0 residues processed: 95 average time/residue: 1.4318 time to fit residues: 272.9387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1710 random chunks: chunk 1595 optimal weight: 9.9990 chunk 186 optimal weight: 7.9990 chunk 942 optimal weight: 7.9990 chunk 1208 optimal weight: 20.0000 chunk 936 optimal weight: 0.6980 chunk 1392 optimal weight: 7.9990 chunk 923 optimal weight: 2.9990 chunk 1648 optimal weight: 6.9990 chunk 1031 optimal weight: 9.9990 chunk 1004 optimal weight: 3.9990 chunk 760 optimal weight: 0.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 29 GLN Q 8 ASN ** S 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 79 GLN V 135 ASN ** Z 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 100 ASN d 118 GLN ** e 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 191 GLN 1 248 GLN u 124 HIS u 160 GLN u 179 ASN z 202 ASN y 25 GLN ** XX 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** XX 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** XX 156 HIS ** XX 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** EE 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** MM 83 GLN UU 80 GLN TT 64 ASN VV 20 GLN NN 63 HIS NN 106 GLN ** ZZ 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BB 114 ASN BB 179 ASN II 11 HIS ** II 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** GG 28 ASN w 10 HIS 0 135 HIS Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.4496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.240 234252 Z= 0.272 Angle : 0.621 21.278 344247 Z= 0.315 Chirality : 0.038 0.325 42886 Planarity : 0.005 0.123 22047 Dihedral : 16.243 179.957 82600 Min Nonbonded Distance : 1.023 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.74 % Favored : 94.20 % Rotamer Outliers : 1.48 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 0.61 % Cis-general : 0.02 % Twisted Proline : 1.22 % Twisted General : 0.05 % 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 (0.08), residues: 11507 helix: 1.13 (0.08), residues: 3889 sheet: -0.69 (0.12), residues: 1866 loop : -1.34 (0.08), residues: 5752 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23014 Ramachandran restraints generated. 11507 Oldfield, 0 Emsley, 11507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23014 Ramachandran restraints generated. 11507 Oldfield, 0 Emsley, 11507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2292 residues out of total 10038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 2144 time to evaluate : 11.275 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 outliers start: 148 outliers final: 83 residues processed: 2215 average time/residue: 2.0116 time to fit residues: 7583.0099 Evaluate side-chains 2134 residues out of total 10038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 2051 time to evaluate : 10.239 Switching outliers to nearest non-outliers outliers start: 83 outliers final: 0 residues processed: 83 average time/residue: 1.4655 time to fit residues: 241.8165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1710 random chunks: chunk 1019 optimal weight: 7.9990 chunk 658 optimal weight: 0.9980 chunk 984 optimal weight: 7.9990 chunk 496 optimal weight: 0.8980 chunk 323 optimal weight: 6.9990 chunk 319 optimal weight: 6.9990 chunk 1047 optimal weight: 8.9990 chunk 1122 optimal weight: 10.0000 chunk 814 optimal weight: 4.9990 chunk 153 optimal weight: 20.0000 chunk 1295 optimal weight: 0.9980 overall best weight: 2.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN ** B 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 191 ASN G 81 ASN G 82 GLN H 163 GLN N 29 GLN R 34 ASN ** S 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 135 ASN a 120 GLN ** b 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 100 ASN d 118 GLN ** e 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 33 GLN ** r 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 124 HIS u 179 ASN x 161 GLN x 224 ASN z 202 ASN ** CC 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** XX 111 GLN ** XX 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** XX 156 HIS ** XX 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** EE 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** EE 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** UU 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** TT 15 ASN TT 64 ASN VV 20 GLN NN 63 HIS ** ZZ 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BB 74 ASN BB 114 ASN SS 61 GLN II 11 HIS ** II 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 10 HIS Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.4643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.156 234252 Z= 0.258 Angle : 0.610 20.350 344247 Z= 0.309 Chirality : 0.037 0.320 42886 Planarity : 0.005 0.108 22047 Dihedral : 16.248 179.938 82600 Min Nonbonded Distance : 1.023 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.41 % Favored : 94.51 % Rotamer Outliers : 1.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % Cis-general : 0.02 % Twisted Proline : 1.22 % Twisted General : 0.05 % 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: -0.53 (0.08), residues: 11507 helix: 1.15 (0.08), residues: 3893 sheet: -0.66 (0.12), residues: 1851 loop : -1.31 (0.08), residues: 5763 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23014 Ramachandran restraints generated. 11507 Oldfield, 0 Emsley, 11507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23014 Ramachandran restraints generated. 11507 Oldfield, 0 Emsley, 11507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2217 residues out of total 10038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 2103 time to evaluate : 10.131 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: 114 outliers final: 79 residues processed: 2144 average time/residue: 1.8854 time to fit residues: 6834.1629 Evaluate side-chains 2116 residues out of total 10038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 2037 time to evaluate : 10.095 Switching outliers to nearest non-outliers outliers start: 79 outliers final: 0 residues processed: 79 average time/residue: 1.3345 time to fit residues: 214.5831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1710 random chunks: chunk 1499 optimal weight: 9.9990 chunk 1578 optimal weight: 6.9990 chunk 1440 optimal weight: 4.9990 chunk 1535 optimal weight: 9.9990 chunk 924 optimal weight: 0.8980 chunk 669 optimal weight: 8.9990 chunk 1206 optimal weight: 10.0000 chunk 471 optimal weight: 0.8980 chunk 1387 optimal weight: 6.9990 chunk 1452 optimal weight: 8.9990 chunk 1530 optimal weight: 0.0670 overall best weight: 2.7722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN ** B 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 29 GLN O 173 GLN V 135 ASN a 120 GLN ** b 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 100 ASN d 118 GLN ** e 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 124 HIS u 160 GLN u 179 ASN u 232 HIS z 202 ASN ** XX 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** XX 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** XX 156 HIS ** XX 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** EE 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** EE 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** MM 83 GLN TT 64 ASN VV 20 GLN ** NN 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** NN 63 HIS NN 106 GLN ** ZZ 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BB 74 ASN BB 114 ASN ** SS 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** II 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** FF 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 10 HIS w 45 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.4759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.127 234252 Z= 0.245 Angle : 0.607 20.484 344247 Z= 0.308 Chirality : 0.037 0.319 42886 Planarity : 0.005 0.123 22047 Dihedral : 16.240 179.903 82600 Min Nonbonded Distance : 1.028 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.61 % Favored : 94.32 % Rotamer Outliers : 0.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % Cis-general : 0.02 % Twisted Proline : 1.22 % Twisted General : 0.05 % 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: -0.46 (0.08), residues: 11507 helix: 1.19 (0.08), residues: 3877 sheet: -0.61 (0.12), residues: 1851 loop : -1.26 (0.08), residues: 5779 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23014 Ramachandran restraints generated. 11507 Oldfield, 0 Emsley, 11507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23014 Ramachandran restraints generated. 11507 Oldfield, 0 Emsley, 11507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2163 residues out of total 10038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 2095 time to evaluate : 11.569 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 outliers start: 68 outliers final: 46 residues processed: 2116 average time/residue: 1.8991 time to fit residues: 6781.9776 Evaluate side-chains 2086 residues out of total 10038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 2040 time to evaluate : 10.016 Switching outliers to nearest non-outliers outliers start: 46 outliers final: 0 residues processed: 46 average time/residue: 1.4288 time to fit residues: 134.3041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1710 random chunks: chunk 1008 optimal weight: 2.9990 chunk 1624 optimal weight: 1.9990 chunk 991 optimal weight: 2.9990 chunk 770 optimal weight: 6.9990 chunk 1129 optimal weight: 10.0000 chunk 1703 optimal weight: 6.9990 chunk 1567 optimal weight: 7.9990 chunk 1356 optimal weight: 10.0000 chunk 140 optimal weight: 10.0000 chunk 1047 optimal weight: 0.1980 chunk 831 optimal weight: 0.0010 overall best weight: 1.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 29 GLN ** S 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 135 ASN X 73 HIS a 120 GLN ** b 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 100 ASN ** e 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 124 HIS u 160 GLN u 179 ASN ** u 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** x 17 HIS z 202 ASN XX 111 GLN ** XX 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** XX 156 HIS ** XX 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** EE 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** EE 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** VV 20 GLN ** NN 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** NN 63 HIS ** ZZ 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** DD 159 HIS ** BB 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BB 114 ASN ** SS 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** II 101 ASN ** FF 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 10 HIS w 45 GLN 6 188 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.4749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.412 234252 Z= 0.199 Angle : 0.590 20.417 344247 Z= 0.300 Chirality : 0.035 0.299 42886 Planarity : 0.005 0.135 22047 Dihedral : 16.219 179.999 82600 Min Nonbonded Distance : 1.077 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.43 % Favored : 94.50 % Rotamer Outliers : 0.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % Cis-general : 0.02 % Twisted Proline : 1.22 % Twisted General : 0.05 % 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: -0.41 (0.08), residues: 11507 helix: 1.24 (0.08), residues: 3897 sheet: -0.61 (0.12), residues: 1869 loop : -1.23 (0.08), residues: 5741 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23014 Ramachandran restraints generated. 11507 Oldfield, 0 Emsley, 11507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23014 Ramachandran restraints generated. 11507 Oldfield, 0 Emsley, 11507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2144 residues out of total 10038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 2104 time to evaluate : 9.992 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: 40 outliers final: 22 residues processed: 2119 average time/residue: 1.9129 time to fit residues: 6834.0777 Evaluate side-chains 2063 residues out of total 10038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 2041 time to evaluate : 9.973 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 1.3642 time to fit residues: 69.6283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1710 random chunks: chunk 1077 optimal weight: 20.0000 chunk 1445 optimal weight: 20.0000 chunk 415 optimal weight: 2.9990 chunk 1250 optimal weight: 10.0000 chunk 200 optimal weight: 10.0000 chunk 376 optimal weight: 10.0000 chunk 1358 optimal weight: 7.9990 chunk 568 optimal weight: 0.9990 chunk 1395 optimal weight: 0.0370 chunk 172 optimal weight: 10.0000 chunk 250 optimal weight: 10.0000 overall best weight: 4.4068 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 55 HIS ** B 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 HIS F 153 ASN G 64 GLN N 29 GLN R 34 ASN V 36 ASN V 135 ASN X 73 HIS Z 132 GLN a 17 HIS ** a 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 100 ASN ** e 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 124 HIS u 160 GLN u 179 ASN ** u 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 202 ASN ** CC 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** XX 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** XX 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** XX 156 HIS ** XX 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** EE 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** EE 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** VV 20 GLN ** NN 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** NN 63 HIS NN 106 GLN ** ZZ 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BB 74 ASN BB 82 ASN BB 114 ASN SS 28 HIS ** SS 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** PP 85 ASN PP 91 HIS w 45 GLN 6 237 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.171773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.131926 restraints weight = 274992.610| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 2.25 r_work: 0.3326 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3285 rms_B_bonded: 2.34 restraints_weight: 0.2500 r_work: 0.3241 rms_B_bonded: 2.85 restraints_weight: 0.1250 r_work: 0.3190 rms_B_bonded: 3.61 restraints_weight: 0.0625 r_work: 0.3124 rms_B_bonded: 4.69 restraints_weight: 0.0312 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.5073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.478 234252 Z= 0.372 Angle : 0.684 26.357 344247 Z= 0.347 Chirality : 0.041 0.357 42886 Planarity : 0.006 0.141 22047 Dihedral : 16.362 179.664 82600 Min Nonbonded Distance : 1.013 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.40 % Favored : 93.53 % Rotamer Outliers : 0.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % Cis-general : 0.02 % Twisted Proline : 1.22 % Twisted General : 0.07 % 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: -0.61 (0.08), residues: 11507 helix: 1.04 (0.08), residues: 3884 sheet: -0.67 (0.12), residues: 1836 loop : -1.33 (0.08), residues: 5787 =============================================================================== Job complete usr+sys time: 91423.94 seconds wall clock time: 1572 minutes 24.38 seconds (94344.38 seconds total)