Starting phenix.real_space_refine (version: 1.21rc1) on Mon May 15 11:28:49 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5oom_3843/05_2023/5oom_3843_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5oom_3843/05_2023/5oom_3843.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5oom_3843/05_2023/5oom_3843_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5oom_3843/05_2023/5oom_3843_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5oom_3843/05_2023/5oom_3843_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5oom_3843/05_2023/5oom_3843.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5oom_3843/05_2023/5oom_3843.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5oom_3843/05_2023/5oom_3843_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5oom_3843/05_2023/5oom_3843_neut_updated.pdb" } resolution = 3.03 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= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 1149 5.49 5 Mg 49 5.21 5 S 282 5.16 5 C 53252 2.51 5 N 16497 2.21 5 O 19508 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D ARG 80": "NH1" <-> "NH2" Residue "D ARG 92": "NH1" <-> "NH2" Residue "D ARG 103": "NH1" <-> "NH2" Residue "D ARG 113": "NH1" <-> "NH2" Residue "D ARG 147": "NH1" <-> "NH2" Residue "D TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 232": "NH1" <-> "NH2" Residue "E ARG 154": "NH1" <-> "NH2" Residue "E ARG 156": "NH1" <-> "NH2" Residue "E ARG 166": "NH1" <-> "NH2" Residue "F ARG 49": "NH1" <-> "NH2" Residue "F ARG 59": "NH1" <-> "NH2" Residue "F ARG 70": "NH1" <-> "NH2" Residue "F ARG 76": "NH1" <-> "NH2" Residue "F ARG 108": "NH1" <-> "NH2" Residue "F ARG 121": "NH1" <-> "NH2" Residue "F ARG 156": "NH1" <-> "NH2" Residue "H ARG 76": "NH1" <-> "NH2" Residue "I ARG 83": "NH1" <-> "NH2" Residue "K ARG 16": "NH1" <-> "NH2" Residue "K ARG 118": "NH1" <-> "NH2" Residue "K ARG 177": "NH1" <-> "NH2" Residue "L ARG 37": "NH1" <-> "NH2" Residue "L ARG 95": "NH1" <-> "NH2" Residue "L ARG 99": "NH1" <-> "NH2" Residue "L ARG 118": "NH1" <-> "NH2" Residue "L ARG 128": "NH1" <-> "NH2" Residue "L ARG 130": "NH1" <-> "NH2" Residue "M ARG 38": "NH1" <-> "NH2" Residue "M ARG 44": "NH1" <-> "NH2" Residue "M ARG 51": "NH1" <-> "NH2" Residue "M ARG 57": "NH1" <-> "NH2" Residue "M ARG 62": "NH1" <-> "NH2" Residue "M ARG 134": "NH1" <-> "NH2" Residue "M ARG 182": "NH1" <-> "NH2" Residue "M TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 259": "NH1" <-> "NH2" Residue "N ARG 51": "NH1" <-> "NH2" Residue "N ARG 123": "NH1" <-> "NH2" Residue "O ARG 38": "NH1" <-> "NH2" Residue "O ARG 106": "NH1" <-> "NH2" Residue "O ARG 137": "NH1" <-> "NH2" Residue "O ARG 138": "NH1" <-> "NH2" Residue "O ARG 153": "NH1" <-> "NH2" Residue "P ARG 51": "NH1" <-> "NH2" Residue "P ARG 54": "NH1" <-> "NH2" Residue "P ARG 63": "NH1" <-> "NH2" Residue "P ARG 75": "NH1" <-> "NH2" Residue "P ARG 80": "NH1" <-> "NH2" Residue "P ARG 108": "NH1" <-> "NH2" Residue "P ARG 177": "NH1" <-> "NH2" Residue "Q ARG 74": "NH1" <-> "NH2" Residue "Q ARG 86": "NH1" <-> "NH2" Residue "Q ARG 143": "NH1" <-> "NH2" Residue "Q ARG 191": "NH1" <-> "NH2" Residue "Q ARG 244": "NH1" <-> "NH2" Residue "Q ARG 271": "NH1" <-> "NH2" Residue "R ARG 13": "NH1" <-> "NH2" Residue "R ARG 32": "NH1" <-> "NH2" Residue "R ARG 122": "NH1" <-> "NH2" Residue "R ARG 123": "NH1" <-> "NH2" Residue "S PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 155": "NH1" <-> "NH2" Residue "S ARG 184": "NH1" <-> "NH2" Residue "T ARG 49": "NH1" <-> "NH2" Residue "T ARG 130": "NH1" <-> "NH2" Residue "T ARG 149": "NH1" <-> "NH2" Residue "U PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 30": "NH1" <-> "NH2" Residue "U ARG 71": "NH1" <-> "NH2" Residue "U ARG 80": "NH1" <-> "NH2" Residue "U ARG 83": "NH1" <-> "NH2" Residue "U ARG 143": "NH1" <-> "NH2" Residue "V ARG 20": "NH1" <-> "NH2" Residue "V ARG 40": "NH1" <-> "NH2" Residue "V ARG 96": "NH1" <-> "NH2" Residue "V ARG 118": "NH1" <-> "NH2" Residue "V ARG 143": "NH1" <-> "NH2" Residue "V ARG 145": "NH1" <-> "NH2" Residue "V ARG 185": "NH1" <-> "NH2" Residue "W ARG 49": "NH1" <-> "NH2" Residue "W ARG 74": "NH1" <-> "NH2" Residue "W ARG 109": "NH1" <-> "NH2" Residue "X ARG 23": "NH1" <-> "NH2" Residue "X ARG 59": "NH1" <-> "NH2" Residue "X ARG 77": "NH1" <-> "NH2" Residue "X ARG 163": "NH1" <-> "NH2" Residue "X ARG 184": "NH1" <-> "NH2" Residue "X ARG 216": "NH1" <-> "NH2" Residue "Y ARG 91": "NH1" <-> "NH2" Residue "Y ARG 109": "NH1" <-> "NH2" Residue "Y ARG 162": "NH1" <-> "NH2" Residue "Y ARG 175": "NH1" <-> "NH2" Residue "Y ARG 196": "NH1" <-> "NH2" Residue "Y ARG 210": "NH1" <-> "NH2" Residue "1 ARG 19": "NH1" <-> "NH2" Residue "1 ARG 34": "NH1" <-> "NH2" Residue "2 ARG 69": "NH1" <-> "NH2" Residue "3 ARG 104": "NH1" <-> "NH2" Residue "3 ARG 116": "NH1" <-> "NH2" Residue "3 ARG 125": "NH1" <-> "NH2" Residue "3 ARG 168": "NH1" <-> "NH2" Residue "3 ARG 183": "NH1" <-> "NH2" Residue "5 ARG 80": "NH1" <-> "NH2" Residue "5 ARG 162": "NH1" <-> "NH2" Residue "5 ARG 223": "NH1" <-> "NH2" Residue "5 ARG 303": "NH1" <-> "NH2" Residue "5 ARG 350": "NH1" <-> "NH2" Residue "6 ARG 27": "NH1" <-> "NH2" Residue "6 ARG 56": "NH1" <-> "NH2" Residue "6 ARG 58": "NH1" <-> "NH2" Residue "6 ARG 60": "NH1" <-> "NH2" Residue "6 ARG 72": "NH1" <-> "NH2" Residue "6 ARG 124": "NH1" <-> "NH2" Residue "6 ARG 136": "NH1" <-> "NH2" Residue "6 ARG 159": "NH1" <-> "NH2" Residue "6 ARG 261": "NH1" <-> "NH2" Residue "6 ARG 296": "NH1" <-> "NH2" Residue "6 ARG 299": "NH1" <-> "NH2" Residue "6 ARG 322": "NH1" <-> "NH2" Residue "6 ARG 364": "NH1" <-> "NH2" Residue "6 TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ARG 168": "NH1" <-> "NH2" Residue "7 ARG 250": "NH1" <-> "NH2" Residue "7 ARG 271": "NH1" <-> "NH2" Residue "8 ARG 137": "NH1" <-> "NH2" Residue "9 ARG 25": "NH1" <-> "NH2" Residue "9 ARG 28": "NH1" <-> "NH2" Residue "9 ARG 49": "NH1" <-> "NH2" Residue "a ARG 122": "NH1" <-> "NH2" Residue "a ARG 128": "NH1" <-> "NH2" Residue "a ARG 131": "NH1" <-> "NH2" Residue "a ARG 133": "NH1" <-> "NH2" Residue "a ARG 142": "NH1" <-> "NH2" Residue "b ARG 28": "NH1" <-> "NH2" Residue "b ARG 41": "NH1" <-> "NH2" Residue "b ARG 49": "NH1" <-> "NH2" Residue "b ARG 114": "NH1" <-> "NH2" Residue "b ARG 144": "NH1" <-> "NH2" Residue "b ARG 146": "NH1" <-> "NH2" Residue "c ARG 52": "NH1" <-> "NH2" Residue "c ARG 216": "NH1" <-> "NH2" Residue "d ARG 74": "NH1" <-> "NH2" Residue "d ARG 159": "NH1" <-> "NH2" Residue "f TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ARG 90": "NH1" <-> "NH2" Residue "g ARG 105": "NH1" <-> "NH2" Residue "h ARG 69": "NH1" <-> "NH2" Residue "h ARG 116": "NH1" <-> "NH2" Residue "i ARG 46": "NH1" <-> "NH2" Residue "i ARG 75": "NH1" <-> "NH2" Residue "i ARG 93": "NH1" <-> "NH2" Residue "i ARG 123": "NH1" <-> "NH2" Residue "j ARG 28": "NH1" <-> "NH2" Residue "j ARG 55": "NH1" <-> "NH2" Residue "j ARG 65": "NH1" <-> "NH2" Residue "j ARG 66": "NH1" <-> "NH2" Residue "j ARG 76": "NH1" <-> "NH2" Residue "j ARG 94": "NH1" <-> "NH2" Residue "j ARG 103": "NH1" <-> "NH2" Residue "k ARG 31": "NH1" <-> "NH2" Residue "k ARG 77": "NH1" <-> "NH2" Residue "l ARG 115": "NH1" <-> "NH2" Residue "l ARG 120": "NH1" <-> "NH2" Residue "l ARG 128": "NH1" <-> "NH2" Residue "l ARG 131": "NH1" <-> "NH2" Residue "m TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o ARG 60": "NH1" <-> "NH2" Residue "o ARG 68": "NH1" <-> "NH2" Residue "q ARG 33": "NH1" <-> "NH2" Residue "q ARG 38": "NH1" <-> "NH2" Residue "q ARG 63": "NH1" <-> "NH2" Residue "q ARG 114": "NH1" <-> "NH2" Residue "r ARG 132": "NH1" <-> "NH2" Residue "r ARG 153": "NH1" <-> "NH2" Residue "r ARG 168": "NH1" <-> "NH2" Residue "r ARG 171": "NH1" <-> "NH2" Residue "s ARG 59": "NH1" <-> "NH2" Residue "s ARG 81": "NH1" <-> "NH2" Residue "s ARG 158": "NH1" <-> "NH2" Residue "s ARG 160": "NH1" <-> "NH2" Residue "s ARG 162": "NH1" <-> "NH2" Residue "s ARG 212": "NH1" <-> "NH2" Residue "s ARG 219": "NH1" <-> "NH2" Residue "s ARG 222": "NH1" <-> "NH2" Residue "s ARG 223": "NH1" <-> "NH2" Residue "s TYR 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s ARG 242": "NH1" <-> "NH2" Residue "s ARG 276": "NH1" <-> "NH2" Residue "s ARG 308": "NH1" <-> "NH2" Residue "s ARG 389": "NH1" <-> "NH2" Residue "v ARG 6": "NH1" <-> "NH2" Residue "v ARG 14": "NH1" <-> "NH2" Residue "v ARG 24": "NH1" <-> "NH2" Residue "v ARG 28": "NH1" <-> "NH2" Time to flip residues: 0.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/chem_data/mon_lib" Total number of atoms: 90739 Number of models: 1 Model: "" Number of chains: 61 Chain: "A" Number of atoms: 23184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1092, 23184 Classifications: {'RNA': 1092} Modifications used: {'rna2p_pur': 118, 'rna2p_pyr': 88, 'rna3p_pur': 463, 'rna3p_pyr': 423} Link IDs: {'rna2p': 205, 'rna3p': 886} Chain breaks: 22 Chain: "B" Number of atoms: 1191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 1191 Classifications: {'RNA': 56} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 29, 'rna3p_pyr': 26} Link IDs: {'rna2p': 1, 'rna3p': 54} Chain breaks: 4 Chain: "D" Number of atoms: 1706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1706 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 11, 'TRANS': 208} Chain breaks: 1 Chain: "E" Number of atoms: 2258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2258 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 22, 'TRANS': 262} Chain breaks: 1 Chain: "F" Number of atoms: 2013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 2013 Classifications: {'peptide': 250} Link IDs: {'PTRANS': 21, 'TRANS': 228} Chain: "H" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 784 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 5, 'TRANS': 89} Chain: "I" Number of atoms: 1283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1283 Classifications: {'peptide': 158} Link IDs: {'PTRANS': 11, 'TRANS': 146} Chain breaks: 1 Chain: "J" Number of atoms: 1061 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1061 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 9, 'TRANS': 130} Chain: "K" Number of atoms: 1451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1451 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 15, 'TRANS': 161} Chain: "L" Number of atoms: 889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 889 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 8, 'TRANS': 106} Chain: "M" Number of atoms: 2305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2305 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 26, 'TRANS': 260} Chain: "N" Number of atoms: 1654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1654 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 14, 'TRANS': 190} Chain: "O" Number of atoms: 1245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1245 Classifications: {'peptide': 152} Link IDs: {'PTRANS': 9, 'TRANS': 142} Chain: "P" Number of atoms: 1148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1148 Classifications: {'peptide': 141} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 134} Chain: "Q" Number of atoms: 1805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1805 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 14, 'TRANS': 202} Chain: "R" Number of atoms: 1153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1153 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 3, 'TRANS': 136} Chain: "S" Number of atoms: 1251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1251 Classifications: {'peptide': 156} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 145} Chain: "T" Number of atoms: 1305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1305 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 12, 'TRANS': 146} Chain breaks: 1 Chain: "U" Number of atoms: 1154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1154 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 11, 'TRANS': 127} Chain breaks: 1 Chain: "V" Number of atoms: 1575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1575 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 16, 'TRANS': 175} Chain breaks: 1 Chain: "W" Number of atoms: 859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 859 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "X" Number of atoms: 2035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 2035 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 18, 'TRANS': 224} Chain: "Y" Number of atoms: 1517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1517 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 7, 'TRANS': 168} Chain: "Z" Number of atoms: 978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 978 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 11, 'TRANS': 108} Chain: "0" Number of atoms: 880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 880 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 7, 'TRANS': 100} Chain: "1" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 433 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 1, 'TRANS': 50} Chain: "2" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 2, 'TRANS': 40} Chain: "3" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 831 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "5" Number of atoms: 3156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 3156 Classifications: {'peptide': 387} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 354} Chain breaks: 1 Chain: "6" Number of atoms: 2640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2640 Classifications: {'peptide': 324} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 28, 'TRANS': 295} Chain breaks: 3 Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 103 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 5, 'ARG:plan': 4, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 59 Chain: "7" Number of atoms: 2334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2334 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 17, 'TRANS': 269} Chain: "8" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 836 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 9, 'TRANS': 89} Chain: "9" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 947 Classifications: {'peptide': 117} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 107} Chain breaks: 1 Chain: "a" Number of atoms: 686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 686 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 10, 'TRANS': 71} Chain breaks: 1 Chain: "b" Number of atoms: 1178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1178 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 9, 'TRANS': 138} Chain: "c" Number of atoms: 2217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2217 Classifications: {'peptide': 275} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 258} Chain breaks: 1 Chain: "d" Number of atoms: 1741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1741 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 17, 'TRANS': 193} Chain breaks: 3 Chain: "e" Number of atoms: 1762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1762 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 9, 'TRANS': 207} Chain breaks: 2 Chain: "f" Number of atoms: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 915 Classifications: {'peptide': 116} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 112} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "g" Number of atoms: 1067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1067 Classifications: {'peptide': 129} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 113} Chain: "h" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 827 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 7, 'TRANS': 92} Chain breaks: 1 Chain: "i" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 827 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 5, 'TRANS': 91} Chain: "j" Number of atoms: 684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 684 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 6, 'TRANS': 78} Chain: "k" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 627 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain breaks: 1 Chain: "l" Number of atoms: 221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 221 Classifications: {'peptide': 23} Link IDs: {'TRANS': 22} Chain: "m" Number of atoms: 372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 372 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 3, 'TRANS': 41} Chain: "o" Number of atoms: 665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 665 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "p" Number of atoms: 1058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1058 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain breaks: 3 Chain: "q" Number of atoms: 1076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1076 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 14, 'TRANS': 113} Chain: "r" Number of atoms: 1203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1203 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 16, 'TRANS': 129} Chain breaks: 2 Chain: "s" Number of atoms: 3036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 3036 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 21, 'TRANS': 348} Chain breaks: 1 Chain: "t" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 140 Classifications: {'peptide': 28} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'TRANS': 27} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'UNK:plan-1': 28} Unresolved non-hydrogen planarities: 28 Chain: "u" Number of atoms: 927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 927 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 4, 'TRANS': 106} Chain: "v" Number of atoms: 588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 588 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain: "w" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 638 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "A" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 47 Unusual residues: {' MG': 47} Classifications: {'undetermined': 47} Link IDs: {None: 46} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "0" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "g" 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: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'PNS': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 31423 SG CYS I 64 77.154 81.078 81.896 1.00 19.37 S ATOM 84370 SG CYS r 70 74.444 78.669 84.190 1.00 69.84 S ATOM 84685 SG CYS r 108 77.025 78.404 84.328 1.00 58.65 S ATOM 56068 SG CYS 0 110 59.807 132.606 184.230 1.00 49.22 S ATOM 56090 SG CYS 0 113 60.400 135.838 184.261 1.00 51.45 S ATOM 56170 SG CYS 0 123 63.191 134.470 183.194 1.00 46.16 S ATOM 56193 SG CYS 0 126 61.697 134.578 186.750 1.00 49.53 S Time building chain proxies: 34.51, per 1000 atoms: 0.38 Number of scatterers: 90739 At special positions: 0 Unit cell: (223.66, 245.92, 252.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 282 16.00 P 1149 15.00 Mg 49 11.99 O 19508 8.00 N 16497 7.00 C 53252 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 32.70 Conformation dependent library (CDL) restraints added in 7.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 0 200 " pdb="ZN ZN 0 200 " - pdb=" SG CYS 0 113 " pdb="ZN ZN 0 200 " - pdb=" SG CYS 0 110 " pdb="ZN ZN 0 200 " - pdb=" SG CYS 0 123 " pdb="ZN ZN 0 200 " - pdb=" SG CYS 0 126 " pdb=" ZN I 301 " pdb="ZN ZN I 301 " - pdb=" SG CYS r 70 " pdb="ZN ZN I 301 " - pdb=" SG CYS I 64 " pdb="ZN ZN I 301 " - pdb=" SG CYS r 108 " Number of angles added : 6 15890 Ramachandran restraints generated. 7945 Oldfield, 0 Emsley, 7945 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15362 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 264 helices and 78 sheets defined 32.1% alpha, 11.8% beta 301 base pairs and 661 stacking pairs defined. Time for finding SS restraints: 25.23 Creating SS restraints... Processing helix chain 'D' and resid 184 through 186 No H-bonds generated for 'chain 'D' and resid 184 through 186' Processing helix chain 'D' and resid 260 through 265 Processing helix chain 'E' and resid 55 through 77 Proline residue: E 59 - end of helix removed outlier: 3.864A pdb=" N LYS E 76 " --> pdb=" O GLN E 72 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N LEU E 77 " --> pdb=" O LEU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 135 through 138 No H-bonds generated for 'chain 'E' and resid 135 through 138' Processing helix chain 'E' and resid 154 through 156 No H-bonds generated for 'chain 'E' and resid 154 through 156' Processing helix chain 'E' and resid 159 through 168 Processing helix chain 'E' and resid 195 through 197 No H-bonds generated for 'chain 'E' and resid 195 through 197' Processing helix chain 'E' and resid 218 through 221 No H-bonds generated for 'chain 'E' and resid 218 through 221' Processing helix chain 'E' and resid 305 through 307 No H-bonds generated for 'chain 'E' and resid 305 through 307' Processing helix chain 'E' and resid 321 through 323 No H-bonds generated for 'chain 'E' and resid 321 through 323' Processing helix chain 'F' and resid 84 through 87 No H-bonds generated for 'chain 'F' and resid 84 through 87' Processing helix chain 'F' and resid 93 through 105 Processing helix chain 'F' and resid 167 through 183 Processing helix chain 'F' and resid 200 through 209 Processing helix chain 'F' and resid 228 through 234 Processing helix chain 'F' and resid 251 through 255 Processing helix chain 'F' and resid 263 through 273 Processing helix chain 'H' and resid 86 through 88 No H-bonds generated for 'chain 'H' and resid 86 through 88' Processing helix chain 'H' and resid 116 through 121 Processing helix chain 'H' and resid 136 through 146 removed outlier: 3.878A pdb=" N LEU H 146 " --> pdb=" O GLU H 142 " (cutoff:3.500A) Processing helix chain 'I' and resid 42 through 50 Processing helix chain 'I' and resid 62 through 64 No H-bonds generated for 'chain 'I' and resid 62 through 64' Processing helix chain 'I' and resid 78 through 92 removed outlier: 3.501A pdb=" N GLN I 91 " --> pdb=" O ALA I 87 " (cutoff:3.500A) Processing helix chain 'I' and resid 106 through 117 Processing helix chain 'I' and resid 128 through 137 Proline residue: I 133 - end of helix removed outlier: 3.894A pdb=" N GLU I 136 " --> pdb=" O LYS I 132 " (cutoff:3.500A) Processing helix chain 'I' and resid 161 through 170 removed outlier: 4.306A pdb=" N THR I 170 " --> pdb=" O ARG I 166 " (cutoff:3.500A) Processing helix chain 'I' and resid 188 through 196 Processing helix chain 'J' and resid 46 through 59 Processing helix chain 'J' and resid 88 through 94 Processing helix chain 'J' and resid 114 through 121 Processing helix chain 'J' and resid 138 through 149 removed outlier: 4.292A pdb=" N SER J 143 " --> pdb=" O SER J 139 " (cutoff:3.500A) Processing helix chain 'K' and resid 6 through 14 removed outlier: 3.520A pdb=" N PHE K 14 " --> pdb=" O GLN K 10 " (cutoff:3.500A) Processing helix chain 'K' and resid 28 through 40 removed outlier: 3.898A pdb=" N MET K 34 " --> pdb=" O LYS K 30 " (cutoff:3.500A) Processing helix chain 'K' and resid 69 through 74 removed outlier: 4.452A pdb=" N TRP K 72 " --> pdb=" O GLY K 69 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLN K 74 " --> pdb=" O LYS K 71 " (cutoff:3.500A) Processing helix chain 'K' and resid 92 through 98 Processing helix chain 'K' and resid 102 through 111 Processing helix chain 'K' and resid 117 through 122 Processing helix chain 'K' and resid 135 through 138 No H-bonds generated for 'chain 'K' and resid 135 through 138' Processing helix chain 'K' and resid 160 through 165 Processing helix chain 'L' and resid 45 through 48 No H-bonds generated for 'chain 'L' and resid 45 through 48' Processing helix chain 'L' and resid 125 through 127 No H-bonds generated for 'chain 'L' and resid 125 through 127' Processing helix chain 'M' and resid 11 through 18 removed outlier: 4.368A pdb=" N GLY M 18 " --> pdb=" O ASP M 14 " (cutoff:3.500A) Processing helix chain 'M' and resid 98 through 106 Processing helix chain 'M' and resid 118 through 123 Processing helix chain 'M' and resid 161 through 169 Processing helix chain 'M' and resid 181 through 188 Processing helix chain 'M' and resid 191 through 194 No H-bonds generated for 'chain 'M' and resid 191 through 194' Processing helix chain 'M' and resid 208 through 214 Proline residue: M 212 - end of helix No H-bonds generated for 'chain 'M' and resid 208 through 214' Processing helix chain 'M' and resid 229 through 239 Processing helix chain 'M' and resid 253 through 256 No H-bonds generated for 'chain 'M' and resid 253 through 256' Processing helix chain 'M' and resid 288 through 294 Processing helix chain 'N' and resid 69 through 71 No H-bonds generated for 'chain 'N' and resid 69 through 71' Processing helix chain 'N' and resid 99 through 111 Processing helix chain 'N' and resid 169 through 182 removed outlier: 4.775A pdb=" N GLY N 174 " --> pdb=" O GLU N 170 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N PHE N 175 " --> pdb=" O GLU N 171 " (cutoff:3.500A) Processing helix chain 'N' and resid 193 through 208 Processing helix chain 'N' and resid 215 through 221 removed outlier: 3.637A pdb=" N ALA N 221 " --> pdb=" O ARG N 217 " (cutoff:3.500A) Processing helix chain 'N' and resid 226 through 228 No H-bonds generated for 'chain 'N' and resid 226 through 228' Processing helix chain 'N' and resid 233 through 235 No H-bonds generated for 'chain 'N' and resid 233 through 235' Processing helix chain 'O' and resid 22 through 39 Processing helix chain 'O' and resid 46 through 63 removed outlier: 3.713A pdb=" N LYS O 58 " --> pdb=" O GLY O 54 " (cutoff:3.500A) Processing helix chain 'O' and resid 70 through 79 Processing helix chain 'O' and resid 83 through 91 Proline residue: O 87 - end of helix removed outlier: 3.661A pdb=" N PHE O 90 " --> pdb=" O PRO O 87 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLN O 91 " --> pdb=" O LYS O 88 " (cutoff:3.500A) Processing helix chain 'O' and resid 93 through 96 No H-bonds generated for 'chain 'O' and resid 93 through 96' Processing helix chain 'O' and resid 144 through 157 Processing helix chain 'P' and resid 55 through 58 No H-bonds generated for 'chain 'P' and resid 55 through 58' Processing helix chain 'P' and resid 110 through 115 removed outlier: 3.562A pdb=" N LYS P 114 " --> pdb=" O TRP P 110 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N HIS P 115 " --> pdb=" O ALA P 111 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 110 through 115' Processing helix chain 'P' and resid 122 through 139 removed outlier: 3.627A pdb=" N GLU P 138 " --> pdb=" O GLN P 134 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA P 139 " --> pdb=" O ARG P 135 " (cutoff:3.500A) Processing helix chain 'P' and resid 156 through 168 Processing helix chain 'Q' and resid 89 through 105 removed outlier: 4.093A pdb=" N VAL Q 105 " --> pdb=" O GLU Q 101 " (cutoff:3.500A) Processing helix chain 'Q' and resid 188 through 191 Processing helix chain 'Q' and resid 195 through 197 No H-bonds generated for 'chain 'Q' and resid 195 through 197' Processing helix chain 'Q' and resid 245 through 247 No H-bonds generated for 'chain 'Q' and resid 245 through 247' Processing helix chain 'Q' and resid 251 through 259 removed outlier: 3.943A pdb=" N LYS Q 259 " --> pdb=" O LYS Q 255 " (cutoff:3.500A) Processing helix chain 'Q' and resid 265 through 267 No H-bonds generated for 'chain 'Q' and resid 265 through 267' Processing helix chain 'Q' and resid 277 through 288 Processing helix chain 'R' and resid 18 through 25 Processing helix chain 'R' and resid 33 through 36 removed outlier: 3.787A pdb=" N ASN R 36 " --> pdb=" O GLY R 33 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 33 through 36' Processing helix chain 'R' and resid 39 through 79 removed outlier: 3.948A pdb=" N ARG R 44 " --> pdb=" O ARG R 40 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ARG R 57 " --> pdb=" O CYS R 53 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N TYR R 58 " --> pdb=" O THR R 54 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LEU R 59 " --> pdb=" O LYS R 55 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N HIS R 79 " --> pdb=" O ALA R 75 " (cutoff:3.500A) Processing helix chain 'R' and resid 83 through 91 Processing helix chain 'R' and resid 99 through 108 Processing helix chain 'R' and resid 110 through 130 Processing helix chain 'S' and resid 69 through 88 Processing helix chain 'T' and resid 53 through 56 Processing helix chain 'T' and resid 87 through 94 removed outlier: 3.992A pdb=" N ILE T 94 " --> pdb=" O LEU T 90 " (cutoff:3.500A) Processing helix chain 'T' and resid 99 through 106 Processing helix chain 'T' and resid 112 through 132 removed outlier: 4.023A pdb=" N ILE T 116 " --> pdb=" O LYS T 112 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N HIS T 132 " --> pdb=" O ALA T 128 " (cutoff:3.500A) Processing helix chain 'T' and resid 192 through 204 Processing helix chain 'U' and resid 50 through 61 Processing helix chain 'U' and resid 127 through 131 Processing helix chain 'U' and resid 142 through 144 No H-bonds generated for 'chain 'U' and resid 142 through 144' Processing helix chain 'V' and resid 29 through 34 Processing helix chain 'V' and resid 51 through 53 No H-bonds generated for 'chain 'V' and resid 51 through 53' Processing helix chain 'V' and resid 81 through 83 No H-bonds generated for 'chain 'V' and resid 81 through 83' Processing helix chain 'V' and resid 117 through 119 No H-bonds generated for 'chain 'V' and resid 117 through 119' Processing helix chain 'V' and resid 179 through 182 No H-bonds generated for 'chain 'V' and resid 179 through 182' Processing helix chain 'V' and resid 194 through 201 Processing helix chain 'W' and resid 111 through 118 Processing helix chain 'X' and resid 8 through 18 removed outlier: 4.912A pdb=" N LYS X 12 " --> pdb=" O TRP X 9 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLU X 18 " --> pdb=" O GLN X 15 " (cutoff:3.500A) Processing helix chain 'X' and resid 20 through 23 removed outlier: 3.637A pdb=" N ARG X 23 " --> pdb=" O ILE X 20 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 20 through 23' Processing helix chain 'X' and resid 26 through 33 removed outlier: 3.678A pdb=" N SER X 31 " --> pdb=" O HIS X 27 " (cutoff:3.500A) Processing helix chain 'X' and resid 73 through 77 Processing helix chain 'X' and resid 129 through 138 Processing helix chain 'X' and resid 141 through 147 Processing helix chain 'X' and resid 150 through 153 No H-bonds generated for 'chain 'X' and resid 150 through 153' Processing helix chain 'X' and resid 156 through 171 Processing helix chain 'X' and resid 181 through 190 Processing helix chain 'X' and resid 192 through 194 No H-bonds generated for 'chain 'X' and resid 192 through 194' Processing helix chain 'X' and resid 198 through 201 No H-bonds generated for 'chain 'X' and resid 198 through 201' Processing helix chain 'X' and resid 208 through 218 Processing helix chain 'X' and resid 226 through 242 Processing helix chain 'Y' and resid 64 through 67 Processing helix chain 'Y' and resid 71 through 73 No H-bonds generated for 'chain 'Y' and resid 71 through 73' Processing helix chain 'Y' and resid 87 through 90 No H-bonds generated for 'chain 'Y' and resid 87 through 90' Processing helix chain 'Y' and resid 95 through 121 Processing helix chain 'Y' and resid 130 through 157 Processing helix chain 'Y' and resid 188 through 190 No H-bonds generated for 'chain 'Y' and resid 188 through 190' Processing helix chain 'Y' and resid 194 through 196 No H-bonds generated for 'chain 'Y' and resid 194 through 196' Processing helix chain 'Y' and resid 206 through 237 Processing helix chain 'Z' and resid 43 through 46 Processing helix chain 'Z' and resid 50 through 55 Processing helix chain 'Z' and resid 80 through 89 Processing helix chain 'Z' and resid 104 through 112 Processing helix chain '0' and resid 87 through 94 Processing helix chain '0' and resid 124 through 145 Processing helix chain '2' and resid 57 through 64 Processing helix chain '2' and resid 66 through 71 Processing helix chain '2' and resid 73 through 85 Processing helix chain '3' and resid 108 through 113 Processing helix chain '3' and resid 133 through 135 No H-bonds generated for 'chain '3' and resid 133 through 135' Processing helix chain '3' and resid 138 through 144 Processing helix chain '3' and resid 152 through 160 Processing helix chain '3' and resid 178 through 180 No H-bonds generated for 'chain '3' and resid 178 through 180' Processing helix chain '5' and resid 48 through 50 No H-bonds generated for 'chain '5' and resid 48 through 50' Processing helix chain '5' and resid 85 through 87 No H-bonds generated for 'chain '5' and resid 85 through 87' Processing helix chain '5' and resid 117 through 124 Processing helix chain '5' and resid 134 through 140 removed outlier: 4.520A pdb=" N LEU 5 139 " --> pdb=" O LYS 5 135 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N VAL 5 140 " --> pdb=" O VAL 5 136 " (cutoff:3.500A) Processing helix chain '5' and resid 150 through 162 Processing helix chain '5' and resid 173 through 192 Proline residue: 5 178 - end of helix removed outlier: 4.233A pdb=" N GLN 5 191 " --> pdb=" O LEU 5 187 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N ILE 5 192 " --> pdb=" O CYS 5 188 " (cutoff:3.500A) Processing helix chain '5' and resid 196 through 200 Processing helix chain '5' and resid 242 through 248 Processing helix chain '5' and resid 306 through 329 Processing helix chain '5' and resid 409 through 418 Processing helix chain '6' and resid 55 through 66 Processing helix chain '6' and resid 74 through 78 Processing helix chain '6' and resid 100 through 113 Processing helix chain '6' and resid 117 through 124 Processing helix chain '6' and resid 132 through 141 Processing helix chain '6' and resid 144 through 154 Processing helix chain '6' and resid 157 through 161 Processing helix chain '6' and resid 197 through 199 No H-bonds generated for 'chain '6' and resid 197 through 199' Processing helix chain '6' and resid 300 through 306 removed outlier: 3.755A pdb=" N LYS 6 306 " --> pdb=" O ASP 6 302 " (cutoff:3.500A) Processing helix chain '6' and resid 325 through 333 Processing helix chain '6' and resid 363 through 366 removed outlier: 3.658A pdb=" N LEU 6 366 " --> pdb=" O LEU 6 363 " (cutoff:3.500A) No H-bonds generated for 'chain '6' and resid 363 through 366' Processing helix chain '7' and resid 37 through 57 Processing helix chain '7' and resid 88 through 95 Processing helix chain '7' and resid 98 through 101 No H-bonds generated for 'chain '7' and resid 98 through 101' Processing helix chain '7' and resid 136 through 155 Processing helix chain '7' and resid 174 through 176 No H-bonds generated for 'chain '7' and resid 174 through 176' Processing helix chain '7' and resid 187 through 191 removed outlier: 4.508A pdb=" N GLU 7 191 " --> pdb=" O LYS 7 188 " (cutoff:3.500A) Processing helix chain '7' and resid 196 through 211 Processing helix chain '7' and resid 223 through 229 Processing helix chain '7' and resid 234 through 244 Processing helix chain '7' and resid 272 through 274 No H-bonds generated for 'chain '7' and resid 272 through 274' Processing helix chain '7' and resid 310 through 319 Processing helix chain '8' and resid 108 through 153 Processing helix chain '9' and resid 28 through 33 removed outlier: 3.752A pdb=" N ARG 9 33 " --> pdb=" O SER 9 29 " (cutoff:3.500A) Processing helix chain '9' and resid 88 through 104 Proline residue: 9 98 - end of helix Processing helix chain '9' and resid 114 through 116 No H-bonds generated for 'chain '9' and resid 114 through 116' Processing helix chain 'a' and resid 69 through 71 No H-bonds generated for 'chain 'a' and resid 69 through 71' Processing helix chain 'a' and resid 105 through 116 Processing helix chain 'a' and resid 128 through 132 Processing helix chain 'b' and resid 38 through 49 removed outlier: 3.903A pdb=" N ARG b 41 " --> pdb=" O ALA b 38 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N GLY b 42 " --> pdb=" O SER b 39 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA b 43 " --> pdb=" O SER b 40 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N GLU b 45 " --> pdb=" O GLY b 42 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLU b 48 " --> pdb=" O GLU b 45 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARG b 49 " --> pdb=" O PHE b 46 " (cutoff:3.500A) Processing helix chain 'b' and resid 51 through 57 Processing helix chain 'b' and resid 94 through 106 Processing helix chain 'b' and resid 140 through 142 No H-bonds generated for 'chain 'b' and resid 140 through 142' Processing helix chain 'c' and resid 36 through 52 Processing helix chain 'c' and resid 60 through 62 No H-bonds generated for 'chain 'c' and resid 60 through 62' Processing helix chain 'c' and resid 68 through 78 Processing helix chain 'c' and resid 85 through 92 Processing helix chain 'c' and resid 95 through 105 Processing helix chain 'c' and resid 123 through 143 Processing helix chain 'c' and resid 150 through 160 Processing helix chain 'c' and resid 163 through 170 Processing helix chain 'c' and resid 188 through 218 Proline residue: c 208 - end of helix removed outlier: 3.638A pdb=" N THR c 211 " --> pdb=" O GLY c 207 " (cutoff:3.500A) Processing helix chain 'c' and resid 220 through 223 Processing helix chain 'c' and resid 228 through 231 No H-bonds generated for 'chain 'c' and resid 228 through 231' Processing helix chain 'c' and resid 237 through 247 Processing helix chain 'c' and resid 289 through 304 Processing helix chain 'd' and resid 53 through 63 Processing helix chain 'd' and resid 119 through 126 Processing helix chain 'd' and resid 134 through 153 Proline residue: d 138 - end of helix removed outlier: 3.662A pdb=" N ALA d 141 " --> pdb=" O PRO d 138 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ILE d 144 " --> pdb=" O ALA d 141 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ILE d 146 " --> pdb=" O ASP d 143 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N GLU d 147 " --> pdb=" O ILE d 144 " (cutoff:3.500A) Processing helix chain 'd' and resid 157 through 163 removed outlier: 4.069A pdb=" N THR d 162 " --> pdb=" O ASP d 158 " (cutoff:3.500A) Processing helix chain 'd' and resid 166 through 173 Proline residue: d 170 - end of helix Processing helix chain 'e' and resid 65 through 81 removed outlier: 3.589A pdb=" N ARG e 81 " --> pdb=" O ILE e 77 " (cutoff:3.500A) Processing helix chain 'e' and resid 86 through 89 No H-bonds generated for 'chain 'e' and resid 86 through 89' Processing helix chain 'e' and resid 92 through 103 Processing helix chain 'e' and resid 117 through 130 Processing helix chain 'e' and resid 184 through 195 removed outlier: 4.019A pdb=" N ALA e 193 " --> pdb=" O GLU e 189 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N THR e 194 " --> pdb=" O ARG e 190 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N LEU e 195 " --> pdb=" O THR e 191 " (cutoff:3.500A) Processing helix chain 'e' and resid 258 through 263 removed outlier: 4.057A pdb=" N TYR e 263 " --> pdb=" O LEU e 260 " (cutoff:3.500A) Processing helix chain 'f' and resid 100 through 115 Processing helix chain 'f' and resid 164 through 177 removed outlier: 3.736A pdb=" N GLU f 168 " --> pdb=" O ALA f 164 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ILE f 173 " --> pdb=" O ILE f 169 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ILE f 174 " --> pdb=" O PHE f 170 " (cutoff:3.500A) Processing helix chain 'g' and resid 45 through 49 Processing helix chain 'g' and resid 117 through 128 Processing helix chain 'g' and resid 154 through 164 Processing helix chain 'h' and resid 66 through 77 Processing helix chain 'h' and resid 86 through 88 No H-bonds generated for 'chain 'h' and resid 86 through 88' Processing helix chain 'h' and resid 94 through 108 Processing helix chain 'h' and resid 114 through 116 No H-bonds generated for 'chain 'h' and resid 114 through 116' Processing helix chain 'h' and resid 123 through 129 Processing helix chain 'h' and resid 139 through 143 Processing helix chain 'i' and resid 49 through 52 No H-bonds generated for 'chain 'i' and resid 49 through 52' Processing helix chain 'i' and resid 60 through 63 No H-bonds generated for 'chain 'i' and resid 60 through 63' Processing helix chain 'i' and resid 70 through 73 Processing helix chain 'i' and resid 78 through 80 No H-bonds generated for 'chain 'i' and resid 78 through 80' Processing helix chain 'i' and resid 87 through 101 removed outlier: 6.148A pdb=" N SER i 100 " --> pdb=" O LYS i 96 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ARG i 101 " --> pdb=" O MET i 97 " (cutoff:3.500A) Processing helix chain 'i' and resid 104 through 121 Processing helix chain 'j' and resid 26 through 30 Processing helix chain 'j' and resid 42 through 45 No H-bonds generated for 'chain 'j' and resid 42 through 45' Processing helix chain 'j' and resid 61 through 105 removed outlier: 3.814A pdb=" N GLN j 105 " --> pdb=" O GLU j 101 " (cutoff:3.500A) Processing helix chain 'k' and resid 28 through 36 Processing helix chain 'k' and resid 40 through 43 No H-bonds generated for 'chain 'k' and resid 40 through 43' Processing helix chain 'k' and resid 83 through 95 Processing helix chain 'l' and resid 115 through 132 Processing helix chain 'o' and resid 29 through 48 Processing helix chain 'o' and resid 64 through 78 Processing helix chain 'o' and resid 88 through 98 removed outlier: 4.300A pdb=" N LEU o 95 " --> pdb=" O GLN o 91 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ASN o 96 " --> pdb=" O LEU o 92 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N VAL o 97 " --> pdb=" O ASP o 93 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N THR o 98 " --> pdb=" O HIS o 94 " (cutoff:3.500A) Processing helix chain 'p' and resid 45 through 48 No H-bonds generated for 'chain 'p' and resid 45 through 48' Processing helix chain 'p' and resid 55 through 58 removed outlier: 3.778A pdb=" N ALA p 58 " --> pdb=" O SER p 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'p' and resid 55 through 58' Processing helix chain 'p' and resid 113 through 122 Processing helix chain 'p' and resid 143 through 162 Processing helix chain 'p' and resid 175 through 188 Processing helix chain 'q' and resid 49 through 51 No H-bonds generated for 'chain 'q' and resid 49 through 51' Processing helix chain 'q' and resid 55 through 68 removed outlier: 7.421A pdb=" N ALA q 66 " --> pdb=" O ALA q 62 " (cutoff:3.500A) removed outlier: 8.879A pdb=" N ALA q 67 " --> pdb=" O ARG q 63 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER q 68 " --> pdb=" O TYR q 64 " (cutoff:3.500A) Processing helix chain 'q' and resid 72 through 74 No H-bonds generated for 'chain 'q' and resid 72 through 74' Processing helix chain 'q' and resid 79 through 92 Processing helix chain 'q' and resid 96 through 150 Proline residue: q 129 - end of helix Processing helix chain 'r' and resid 73 through 75 No H-bonds generated for 'chain 'r' and resid 73 through 75' Processing helix chain 'r' and resid 86 through 92 removed outlier: 4.257A pdb=" N GLN r 91 " --> pdb=" O LEU r 87 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N PHE r 92 " --> pdb=" O LEU r 88 " (cutoff:3.500A) Processing helix chain 'r' and resid 102 through 105 No H-bonds generated for 'chain 'r' and resid 102 through 105' Processing helix chain 'r' and resid 109 through 123 Processing helix chain 'r' and resid 156 through 158 No H-bonds generated for 'chain 'r' and resid 156 through 158' Processing helix chain 'r' and resid 179 through 181 No H-bonds generated for 'chain 'r' and resid 179 through 181' Processing helix chain 's' and resid 57 through 71 Processing helix chain 's' and resid 76 through 82 Processing helix chain 's' and resid 102 through 110 Processing helix chain 's' and resid 141 through 154 Processing helix chain 's' and resid 168 through 171 No H-bonds generated for 'chain 's' and resid 168 through 171' Processing helix chain 's' and resid 173 through 189 removed outlier: 3.566A pdb=" N SER s 189 " --> pdb=" O VAL s 185 " (cutoff:3.500A) Processing helix chain 's' and resid 193 through 197 removed outlier: 3.529A pdb=" N ALA s 197 " --> pdb=" O ALA s 194 " (cutoff:3.500A) Processing helix chain 's' and resid 304 through 306 No H-bonds generated for 'chain 's' and resid 304 through 306' Processing helix chain 's' and resid 308 through 313 Processing helix chain 's' and resid 319 through 342 removed outlier: 3.654A pdb=" N PHE s 324 " --> pdb=" O ILE s 320 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER s 331 " --> pdb=" O ASN s 327 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA s 338 " --> pdb=" O ALA s 334 " (cutoff:3.500A) Processing helix chain 's' and resid 416 through 425 Processing helix chain 't' and resid 2 through 26 Processing helix chain 'u' and resid 94 through 104 Processing helix chain 'u' and resid 132 through 149 Processing helix chain 'u' and resid 182 through 188 Processing helix chain 'u' and resid 190 through 193 No H-bonds generated for 'chain 'u' and resid 190 through 193' Processing helix chain 'v' and resid 7 through 22 removed outlier: 3.520A pdb=" N GLN v 22 " --> pdb=" O ARG v 18 " (cutoff:3.500A) Processing helix chain 'v' and resid 28 through 39 Processing helix chain 'v' and resid 48 through 63 removed outlier: 3.922A pdb=" N GLU v 52 " --> pdb=" O ALA v 48 " (cutoff:3.500A) Processing helix chain 'w' and resid 76 through 89 Processing helix chain 'w' and resid 112 through 123 Processing helix chain 'w' and resid 141 through 151 Processing sheet with id= A, first strand: chain 'D' and resid 76 through 78 Processing sheet with id= B, first strand: chain 'D' and resid 162 through 165 removed outlier: 6.759A pdb=" N LEU D 141 " --> pdb=" O ILE D 127 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N VAL D 129 " --> pdb=" O ILE D 139 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N ILE D 139 " --> pdb=" O VAL D 129 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'D' and resid 181 through 183 Processing sheet with id= D, first strand: chain 'D' and resid 233 through 237 removed outlier: 3.657A pdb=" N ARG D 218 " --> pdb=" O ILE D 225 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N GLN D 227 " --> pdb=" O LEU D 216 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N LEU D 216 " --> pdb=" O GLN D 227 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'E' and resid 265 through 268 removed outlier: 5.167A pdb=" N LYS E 209 " --> pdb=" O LEU E 296 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N LEU E 296 " --> pdb=" O LYS E 209 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N LEU E 121 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N MET E 106 " --> pdb=" O VAL E 119 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N VAL E 119 " --> pdb=" O MET E 106 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N HIS E 117 " --> pdb=" O PRO E 108 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG E 275 " --> pdb=" O TYR E 284 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ASN E 286 " --> pdb=" O VAL E 273 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N VAL E 273 " --> pdb=" O ASN E 286 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'E' and resid 175 through 181 removed outlier: 3.581A pdb=" N THR E 175 " --> pdb=" O GLY E 149 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N GLY E 148 " --> pdb=" O VAL E 129 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N VAL E 129 " --> pdb=" O GLY E 148 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'E' and resid 214 through 216 removed outlier: 3.525A pdb=" N GLY E 214 " --> pdb=" O MET E 261 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'F' and resid 62 through 65 Processing sheet with id= I, first strand: chain 'F' and resid 187 through 190 removed outlier: 6.349A pdb=" N LEU F 259 " --> pdb=" O HIS F 188 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N MET F 190 " --> pdb=" O LEU F 259 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N LEU F 261 " --> pdb=" O MET F 190 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N THR F 262 " --> pdb=" O VAL F 219 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'H' and resid 111 through 114 Processing sheet with id= K, first strand: chain 'H' and resid 54 through 58 removed outlier: 6.471A pdb=" N GLU H 57 " --> pdb=" O LEU H 82 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N LEU H 82 " --> pdb=" O GLU H 57 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'I' and resid 122 through 125 Processing sheet with id= M, first strand: chain 'I' and resid 179 through 181 Processing sheet with id= N, first strand: chain 'J' and resid 110 through 113 Processing sheet with id= O, first strand: chain 'K' and resid 125 through 127 removed outlier: 6.259A pdb=" N VAL K 57 " --> pdb=" O HIS K 126 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N LEU K 20 " --> pdb=" O VAL K 142 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N GLU K 144 " --> pdb=" O LEU K 20 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N ASP K 22 " --> pdb=" O GLU K 144 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'K' and resid 76 through 80 Processing sheet with id= Q, first strand: chain 'L' and resid 72 through 77 Processing sheet with id= R, first strand: chain 'M' and resid 94 through 97 Processing sheet with id= S, first strand: chain 'M' and resid 153 through 155 removed outlier: 6.363A pdb=" N VAL M 173 " --> pdb=" O ILE M 154 " (cutoff:3.500A) No H-bonds generated for sheet with id= S Processing sheet with id= T, first strand: chain 'M' and resid 274 through 276 Processing sheet with id= U, first strand: chain 'N' and resid 87 through 91 Processing sheet with id= V, first strand: chain 'N' and resid 95 through 97 Processing sheet with id= W, first strand: chain 'N' and resid 118 through 122 Processing sheet with id= X, first strand: chain 'N' and resid 129 through 132 Processing sheet with id= Y, first strand: chain 'O' and resid 41 through 45 removed outlier: 4.526A pdb=" N MET O 120 " --> pdb=" O ILE O 110 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'P' and resid 80 through 85 Processing sheet with id= AA, first strand: chain 'Q' and resid 173 through 178 removed outlier: 3.756A pdb=" N GLU Q 173 " --> pdb=" O THR Q 120 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ILE Q 116 " --> pdb=" O VAL Q 177 " (cutoff:3.500A) removed outlier: 9.165A pdb=" N LEU Q 134 " --> pdb=" O VAL Q 154 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N VAL Q 154 " --> pdb=" O LEU Q 134 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ILE Q 150 " --> pdb=" O ILE Q 138 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'S' and resid 106 through 109 Processing sheet with id= AC, first strand: chain 'S' and resid 112 through 116 removed outlier: 3.561A pdb=" N ASP S 112 " --> pdb=" O ILE S 195 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLU S 162 " --> pdb=" O VAL S 192 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'S' and resid 127 through 129 removed outlier: 3.631A pdb=" N SER S 197 " --> pdb=" O GLU S 157 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N THR S 159 " --> pdb=" O ILE S 195 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N ILE S 195 " --> pdb=" O THR S 159 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'S' and resid 169 through 175 removed outlier: 3.833A pdb=" N PHE S 180 " --> pdb=" O ARG S 175 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'T' and resid 72 through 77 removed outlier: 6.301A pdb=" N VAL T 179 " --> pdb=" O ILE T 142 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N ILE T 142 " --> pdb=" O VAL T 179 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'T' and resid 153 through 155 Processing sheet with id= AH, first strand: chain 'U' and resid 39 through 42 Processing sheet with id= AI, first strand: chain 'V' and resid 120 through 122 removed outlier: 4.462A pdb=" N LYS V 75 " --> pdb=" O GLY V 89 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N VAL V 87 " --> pdb=" O VAL V 77 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N VAL V 79 " --> pdb=" O TRP V 85 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N TRP V 85 " --> pdb=" O VAL V 79 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'V' and resid 93 through 98 Processing sheet with id= AK, first strand: chain 'W' and resid 81 through 83 removed outlier: 6.439A pdb=" N ALA W 91 " --> pdb=" O ILE W 66 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ILE W 66 " --> pdb=" O ALA W 91 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'W' and resid 95 through 103 Processing sheet with id= AM, first strand: chain 'X' and resid 50 through 52 Processing sheet with id= AN, first strand: chain 'X' and resid 86 through 91 Processing sheet with id= AO, first strand: chain 'X' and resid 109 through 116 Processing sheet with id= AP, first strand: chain 'Y' and resid 166 through 170 Processing sheet with id= AQ, first strand: chain 'Z' and resid 97 through 101 Processing sheet with id= AR, first strand: chain '0' and resid 107 through 109 Processing sheet with id= AS, first strand: chain '0' and resid 156 through 159 removed outlier: 6.236A pdb=" N ARG 0 173 " --> pdb=" O VAL 0 157 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N LEU 0 159 " --> pdb=" O ARG 0 173 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N ILE 0 175 " --> pdb=" O LEU 0 159 " (cutoff:3.500A) No H-bonds generated for sheet with id= AS Processing sheet with id= AT, first strand: chain '1' and resid 29 through 35 Processing sheet with id= AU, first strand: chain '1' and resid 17 through 19 removed outlier: 6.112A pdb=" N ARG 1 19 " --> pdb=" O LYS 1 61 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N LYS 1 61 " --> pdb=" O ARG 1 19 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain '3' and resid 123 through 125 Processing sheet with id= AW, first strand: chain '5' and resid 266 through 268 removed outlier: 3.583A pdb=" N LEU 5 218 " --> pdb=" O ARG 5 215 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ARG 5 215 " --> pdb=" O LEU 5 218 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N GLY 5 226 " --> pdb=" O SER 5 207 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N SER 5 207 " --> pdb=" O GLY 5 226 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain '5' and resid 126 through 130 removed outlier: 6.427A pdb=" N ASN 5 372 " --> pdb=" O LYS 5 127 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N ILE 5 129 " --> pdb=" O ASN 5 372 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N ALA 5 374 " --> pdb=" O ILE 5 129 " (cutoff:3.500A) removed outlier: 9.637A pdb=" N VAL 5 341 " --> pdb=" O TYR 5 287 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N HIS 5 289 " --> pdb=" O VAL 5 341 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N LEU 5 230 " --> pdb=" O HIS 5 289 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain '5' and resid 385 through 387 Processing sheet with id= AZ, first strand: chain '6' and resid 203 through 205 removed outlier: 4.472A pdb=" N VAL 6 175 " --> pdb=" O VAL 6 187 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASP 6 183 " --> pdb=" O VAL 6 179 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain '6' and resid 249 through 252 removed outlier: 6.584A pdb=" N LEU 6 236 " --> pdb=" O THR 6 251 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N TYR 6 232 " --> pdb=" O SER 6 220 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N LEU 6 218 " --> pdb=" O HIS 6 234 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N LEU 6 236 " --> pdb=" O LEU 6 216 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N LEU 6 216 " --> pdb=" O LEU 6 236 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N THR 6 238 " --> pdb=" O TRP 6 214 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N TRP 6 214 " --> pdb=" O THR 6 238 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N LYS 6 274 " --> pdb=" O PRO 6 313 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain '7' and resid 64 through 69 removed outlier: 4.231A pdb=" N THR 7 77 " --> pdb=" O HIS 7 69 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain '7' and resid 111 through 113 removed outlier: 6.425A pdb=" N LEU 7 128 " --> pdb=" O ILE 7 104 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ALA 7 106 " --> pdb=" O LYS 7 126 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N LYS 7 126 " --> pdb=" O ALA 7 106 " (cutoff:3.500A) Processing sheet with id= BD, first strand: chain '7' and resid 282 through 285 removed outlier: 3.511A pdb=" N ARG 7 168 " --> pdb=" O ASP 7 182 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N VAL 7 184 " --> pdb=" O LEU 7 166 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N LEU 7 166 " --> pdb=" O VAL 7 184 " (cutoff:3.500A) Processing sheet with id= BE, first strand: chain '7' and resid 217 through 221 Processing sheet with id= BF, first strand: chain '7' and resid 275 through 280 removed outlier: 6.551A pdb=" N LEU 7 302 " --> pdb=" O PHE 7 276 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N TYR 7 278 " --> pdb=" O VAL 7 300 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N VAL 7 300 " --> pdb=" O TYR 7 278 " (cutoff:3.500A) Processing sheet with id= BG, first strand: chain '9' and resid 42 through 45 Processing sheet with id= BH, first strand: chain 'a' and resid 45 through 51 Processing sheet with id= BI, first strand: chain 'b' and resid 62 through 65 removed outlier: 6.499A pdb=" N GLU b 78 " --> pdb=" O GLN b 27 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N LEU b 29 " --> pdb=" O VAL b 76 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N VAL b 76 " --> pdb=" O LEU b 29 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N PHE b 31 " --> pdb=" O ARG b 74 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ARG b 74 " --> pdb=" O PHE b 31 " (cutoff:3.500A) Processing sheet with id= BJ, first strand: chain 'c' and resid 254 through 261 removed outlier: 6.742A pdb=" N PHE c 271 " --> pdb=" O THR c 258 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N GLN c 260 " --> pdb=" O LEU c 269 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N LEU c 269 " --> pdb=" O GLN c 260 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ALA c 282 " --> pdb=" O LEU c 274 " (cutoff:3.500A) Processing sheet with id= BK, first strand: chain 'd' and resid 184 through 186 removed outlier: 3.972A pdb=" N ARG d 219 " --> pdb=" O VAL d 186 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N TYR d 245 " --> pdb=" O ILE d 265 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N GLU d 249 " --> pdb=" O MET d 261 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N MET d 261 " --> pdb=" O GLU d 249 " (cutoff:3.500A) Processing sheet with id= BL, first strand: chain 'd' and resid 193 through 198 removed outlier: 6.736A pdb=" N THR d 213 " --> pdb=" O VAL d 195 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N VAL d 197 " --> pdb=" O GLN d 211 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N GLN d 211 " --> pdb=" O VAL d 197 " (cutoff:3.500A) Processing sheet with id= BM, first strand: chain 'e' and resid 175 through 177 removed outlier: 7.094A pdb=" N GLY e 228 " --> pdb=" O ARG e 46 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N LEU e 48 " --> pdb=" O GLY e 228 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N LYS e 230 " --> pdb=" O LEU e 48 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N ALA e 50 " --> pdb=" O LYS e 230 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N PHE e 232 " --> pdb=" O ALA e 50 " (cutoff:3.500A) Processing sheet with id= BN, first strand: chain 'e' and resid 161 through 164 Processing sheet with id= BO, first strand: chain 'e' and resid 199 through 203 removed outlier: 5.939A pdb=" N LYS e 203 " --> pdb=" O LEU e 238 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N LEU e 238 " --> pdb=" O LYS e 203 " (cutoff:3.500A) Processing sheet with id= BP, first strand: chain 'f' and resid 94 through 97 Processing sheet with id= BQ, first strand: chain 'g' and resid 84 through 86 Processing sheet with id= BR, first strand: chain 'g' and resid 96 through 101 Processing sheet with id= BS, first strand: chain 'k' and resid 50 through 55 removed outlier: 3.987A pdb=" N PHE k 20 " --> pdb=" O ASP k 54 " (cutoff:3.500A) Processing sheet with id= BT, first strand: chain 'm' and resid 52 through 56 Processing sheet with id= BU, first strand: chain 'p' and resid 77 through 80 Processing sheet with id= BV, first strand: chain 'r' and resid 36 through 41 Processing sheet with id= BW, first strand: chain 's' and resid 90 through 92 removed outlier: 4.640A pdb=" N PHE s 274 " --> pdb=" O MET s 92 " (cutoff:3.500A) Processing sheet with id= BX, first strand: chain 's' and resid 112 through 116 removed outlier: 6.762A pdb=" N ASN s 391 " --> pdb=" O VAL s 113 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N LEU s 115 " --> pdb=" O ASN s 391 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N CYS s 393 " --> pdb=" O LEU s 115 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N GLN s 298 " --> pdb=" O VAL s 360 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N THR s 362 " --> pdb=" O GLN s 298 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N HIS s 300 " --> pdb=" O THR s 362 " (cutoff:3.500A) Processing sheet with id= BY, first strand: chain 's' and resid 205 through 211 Processing sheet with id= BZ, first strand: chain 'u' and resid 108 through 113 removed outlier: 3.632A pdb=" N ASP u 108 " --> pdb=" O SER u 128 " (cutoff:3.500A) 2059 hydrogen bonds defined for protein. 5838 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 732 hydrogen bonds 1268 hydrogen bond angles 0 basepair planarities 301 basepair parallelities 661 stacking parallelities Total time for adding SS restraints: 55.75 Time building geometry restraints manager: 35.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 11902 1.29 - 1.43: 32641 1.43 - 1.57: 47918 1.57 - 1.70: 2238 1.70 - 1.84: 449 Bond restraints: 95148 Sorted by residual: bond pdb=" C MET Q 204 " pdb=" N LYS Q 205 " ideal model delta sigma weight residual 1.331 1.212 0.119 2.07e-02 2.33e+03 3.32e+01 bond pdb=" C VAL T 58 " pdb=" N TYR T 59 " ideal model delta sigma weight residual 1.331 1.225 0.106 2.07e-02 2.33e+03 2.63e+01 bond pdb=" CB ARG R 11 " pdb=" CG ARG R 11 " ideal model delta sigma weight residual 1.520 1.384 0.136 3.00e-02 1.11e+03 2.07e+01 bond pdb=" CG1 ILE M 78 " pdb=" CD1 ILE M 78 " ideal model delta sigma weight residual 1.513 1.338 0.175 3.90e-02 6.57e+02 2.02e+01 bond pdb=" CG ARG 2 87 " pdb=" CD ARG 2 87 " ideal model delta sigma weight residual 1.520 1.386 0.134 3.00e-02 1.11e+03 1.99e+01 ... (remaining 95143 not shown) Histogram of bond angle deviations from ideal: 91.91 - 102.87: 3040 102.87 - 113.83: 60522 113.83 - 124.79: 64594 124.79 - 135.75: 5905 135.75 - 146.71: 4 Bond angle restraints: 134065 Sorted by residual: angle pdb=" N GLN D 205 " pdb=" CA GLN D 205 " pdb=" C GLN D 205 " ideal model delta sigma weight residual 111.36 121.37 -10.01 1.09e+00 8.42e-01 8.43e+01 angle pdb=" C TYR m 52 " pdb=" N PRO m 53 " pdb=" CA PRO m 53 " ideal model delta sigma weight residual 119.84 130.52 -10.68 1.25e+00 6.40e-01 7.29e+01 angle pdb=" CB ARG R 34 " pdb=" CG ARG R 34 " pdb=" CD ARG R 34 " ideal model delta sigma weight residual 111.30 91.91 19.39 2.30e+00 1.89e-01 7.11e+01 angle pdb=" C GLU m 70 " pdb=" N PRO m 71 " pdb=" CA PRO m 71 " ideal model delta sigma weight residual 119.84 130.25 -10.41 1.25e+00 6.40e-01 6.93e+01 angle pdb=" O3' A A1823 " pdb=" C3' A A1823 " pdb=" C2' A A1823 " ideal model delta sigma weight residual 109.50 120.78 -11.28 1.50e+00 4.44e-01 5.66e+01 ... (remaining 134060 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.97: 53940 35.97 - 71.93: 1178 71.93 - 107.90: 78 107.90 - 143.87: 10 143.87 - 179.83: 33 Dihedral angle restraints: 55239 sinusoidal: 31535 harmonic: 23704 Sorted by residual: dihedral pdb=" O4' C A2379 " pdb=" C1' C A2379 " pdb=" N1 C A2379 " pdb=" C2 C A2379 " ideal model delta sinusoidal sigma weight residual 200.00 20.33 179.67 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U A2898 " pdb=" C1' U A2898 " pdb=" N1 U A2898 " pdb=" C2 U A2898 " ideal model delta sinusoidal sigma weight residual -160.00 18.88 -178.88 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' C A2066 " pdb=" C1' C A2066 " pdb=" N1 C A2066 " pdb=" C2 C A2066 " ideal model delta sinusoidal sigma weight residual -160.00 14.11 -174.11 1 1.50e+01 4.44e-03 8.51e+01 ... (remaining 55236 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.134: 14621 0.134 - 0.267: 875 0.267 - 0.401: 53 0.401 - 0.534: 7 0.534 - 0.668: 2 Chirality restraints: 15558 Sorted by residual: chirality pdb=" C3' A A1823 " pdb=" C4' A A1823 " pdb=" O3' A A1823 " pdb=" C2' A A1823 " both_signs ideal model delta sigma weight residual False -2.74 -2.08 -0.67 2.00e-01 2.50e+01 1.11e+01 chirality pdb=" C3' U A1780 " pdb=" C4' U A1780 " pdb=" O3' U A1780 " pdb=" C2' U A1780 " both_signs ideal model delta sigma weight residual False -2.74 -2.20 -0.55 2.00e-01 2.50e+01 7.43e+00 chirality pdb=" CB ILE O 123 " pdb=" CA ILE O 123 " pdb=" CG1 ILE O 123 " pdb=" CG2 ILE O 123 " both_signs ideal model delta sigma weight residual False 2.64 2.15 0.49 2.00e-01 2.50e+01 6.06e+00 ... (remaining 15555 not shown) Planarity restraints: 12972 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO m 53 " 0.028 2.00e-02 2.50e+03 5.20e-02 2.70e+01 pdb=" C PRO m 53 " -0.090 2.00e-02 2.50e+03 pdb=" O PRO m 53 " 0.032 2.00e-02 2.50e+03 pdb=" N VAL m 54 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G A2289 " -0.067 2.00e-02 2.50e+03 2.79e-02 2.33e+01 pdb=" N9 G A2289 " 0.044 2.00e-02 2.50e+03 pdb=" C8 G A2289 " 0.034 2.00e-02 2.50e+03 pdb=" N7 G A2289 " 0.010 2.00e-02 2.50e+03 pdb=" C5 G A2289 " -0.007 2.00e-02 2.50e+03 pdb=" C6 G A2289 " -0.011 2.00e-02 2.50e+03 pdb=" O6 G A2289 " -0.023 2.00e-02 2.50e+03 pdb=" N1 G A2289 " -0.005 2.00e-02 2.50e+03 pdb=" C2 G A2289 " -0.008 2.00e-02 2.50e+03 pdb=" N2 G A2289 " 0.023 2.00e-02 2.50e+03 pdb=" N3 G A2289 " 0.017 2.00e-02 2.50e+03 pdb=" C4 G A2289 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A A2682 " -0.068 2.00e-02 2.50e+03 2.90e-02 2.31e+01 pdb=" N9 A A2682 " 0.057 2.00e-02 2.50e+03 pdb=" C8 A A2682 " 0.013 2.00e-02 2.50e+03 pdb=" N7 A A2682 " 0.005 2.00e-02 2.50e+03 pdb=" C5 A A2682 " -0.003 2.00e-02 2.50e+03 pdb=" C6 A A2682 " -0.004 2.00e-02 2.50e+03 pdb=" N6 A A2682 " -0.026 2.00e-02 2.50e+03 pdb=" N1 A A2682 " -0.008 2.00e-02 2.50e+03 pdb=" C2 A A2682 " 0.014 2.00e-02 2.50e+03 pdb=" N3 A A2682 " 0.007 2.00e-02 2.50e+03 pdb=" C4 A A2682 " 0.013 2.00e-02 2.50e+03 ... (remaining 12969 not shown) Histogram of nonbonded interaction distances: 1.30 - 2.02: 27 2.02 - 2.74: 13349 2.74 - 3.46: 115668 3.46 - 4.18: 254777 4.18 - 4.90: 399629 Nonbonded interactions: 783450 Sorted by model distance: nonbonded pdb=" OP1 C A2511 " pdb=" ND2 ASN D 263 " model vdw 1.296 2.520 nonbonded pdb=" OP1 C A2036 " pdb="MG MG A3327 " model vdw 1.639 2.170 nonbonded pdb=" OP1 C A2252 " pdb="MG MG A3310 " model vdw 1.675 2.170 nonbonded pdb=" OP2 A A2451 " pdb="MG MG A3312 " model vdw 1.695 2.170 nonbonded pdb=" CE2 TYR 8 178 " pdb=" CE1 HIS m 65 " model vdw 1.708 3.560 ... (remaining 783445 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 3.200 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: 0.050 Extract box with map and model: 15.420 Check model and map are aligned: 1.080 Set scattering table: 0.630 Process input model: 230.720 Find NCS groups from input model: 2.690 Set up NCS constraints: 0.250 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 256.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6040 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 : 0.016 0.183 95148 Z= 1.007 Angle : 1.290 26.003 134065 Z= 0.661 Chirality : 0.071 0.668 15558 Planarity : 0.009 0.095 12972 Dihedral : 14.235 179.835 39877 Min Nonbonded Distance : 1.296 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.45 % Favored : 94.49 % Rotamer Outliers : 0.94 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -3.55 (0.08), residues: 7945 helix: -3.13 (0.07), residues: 2672 sheet: -2.02 (0.14), residues: 977 loop : -1.86 (0.08), residues: 4296 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15890 Ramachandran restraints generated. 7945 Oldfield, 0 Emsley, 7945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15890 Ramachandran restraints generated. 7945 Oldfield, 0 Emsley, 7945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 4156 residues out of total 7169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 4089 time to evaluate : 7.243 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: 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clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: 67 outliers final: 13 residues processed: 4111 average time/residue: 1.0181 time to fit residues: 6978.4934 Evaluate side-chains 2359 residues out of total 7169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 2346 time to evaluate : 7.176 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 1.1704 time to fit residues: 32.5995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 901 random chunks: chunk 760 optimal weight: 7.9990 chunk 682 optimal weight: 0.9980 chunk 378 optimal weight: 5.9990 chunk 233 optimal weight: 5.9990 chunk 460 optimal weight: 6.9990 chunk 364 optimal weight: 5.9990 chunk 706 optimal weight: 5.9990 chunk 273 optimal weight: 4.9990 chunk 429 optimal weight: 4.9990 chunk 525 optimal weight: 4.9990 chunk 818 optimal weight: 5.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 102 GLN ** D 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 184 ASN F 184 GLN ** F 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 113 ASN ** M 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 130 GLN ** M 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 86 ASN N 222 ASN ** O 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 87 GLN P 115 HIS ** P 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 36 ASN R 94 GLN ** S 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 140 ASN ** S 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 125 GLN U 73 GLN ** U 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 80 HIS ** W 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 4 HIS X 46 HIS ** X 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 241 GLN Y 110 ASN Y 160 GLN Y 191 ASN ** Z 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 98 GLN ** Z 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 168 GLN ** 1 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 305 GLN 6 277 GLN 6 320 GLN ** 8 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 9 113 ASN ** 9 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 135 ASN c 168 HIS ** c 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 59 HIS ** d 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 92 ASN ** f 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 106 GLN h 67 GLN h 85 ASN ** h 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 65 ASN ** i 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 108 HIS j 107 ASN ** k 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 26 ASN ** o 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 148 ASN ** s 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 296 HIS s 343 GLN ** s 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 63 ASN w 115 GLN Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6503 moved from start: 0.4475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.077 95148 Z= 0.341 Angle : 0.851 16.008 134065 Z= 0.433 Chirality : 0.047 0.316 15558 Planarity : 0.007 0.096 12972 Dihedral : 15.269 179.506 22766 Min Nonbonded Distance : 1.652 Molprobity Statistics. All-atom Clashscore : 25.27 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.07 % Favored : 95.91 % Rotamer Outliers : 6.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.84 (0.09), residues: 7945 helix: -1.10 (0.09), residues: 2680 sheet: -1.29 (0.15), residues: 971 loop : -1.21 (0.09), residues: 4294 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15890 Ramachandran restraints generated. 7945 Oldfield, 0 Emsley, 7945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15890 Ramachandran restraints generated. 7945 Oldfield, 0 Emsley, 7945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3100 residues out of total 7169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 444 poor density : 2656 time to evaluate : 7.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 444 outliers final: 254 residues processed: 2877 average time/residue: 0.9222 time to fit residues: 4531.0629 Evaluate side-chains 2424 residues out of total 7169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 254 poor density : 2170 time to evaluate : 7.108 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 254 outliers final: 1 residues processed: 254 average time/residue: 0.6938 time to fit residues: 340.6786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 901 random chunks: chunk 454 optimal weight: 5.9990 chunk 253 optimal weight: 1.9990 chunk 680 optimal weight: 7.9990 chunk 557 optimal weight: 0.9980 chunk 225 optimal weight: 6.9990 chunk 819 optimal weight: 6.9990 chunk 885 optimal weight: 10.0000 chunk 730 optimal weight: 0.0070 chunk 812 optimal weight: 4.9990 chunk 279 optimal weight: 0.5980 chunk 657 optimal weight: 20.0000 overall best weight: 1.7202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 102 GLN ** D 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 339 GLN F 153 HIS F 228 GLN H 100 GLN ** I 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 114 HIS ** K 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 84 ASN ** M 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 98 HIS O 109 GLN ** P 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 94 GLN ** S 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 4 ASN ** W 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 76 HIS X 4 HIS ** Z 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 136 ASN 1 15 ASN 2 57 ASN ** 2 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 353 HIS ** 6 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 25 GLN ** b 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 59 HIS ** d 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 92 ASN f 108 GLN ** g 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 109 ASN ** k 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 184 ASN r 91 GLN r 112 HIS s 96 GLN ** s 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 343 GLN ** s 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 19 GLN ** v 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6484 moved from start: 0.5145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.116 95148 Z= 0.237 Angle : 0.764 16.164 134065 Z= 0.383 Chirality : 0.044 0.298 15558 Planarity : 0.006 0.126 12972 Dihedral : 15.024 179.503 22766 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 21.89 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.20 % Favored : 95.78 % Rotamer Outliers : 3.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.09), residues: 7945 helix: -0.54 (0.09), residues: 2686 sheet: -1.13 (0.15), residues: 1041 loop : -0.98 (0.10), residues: 4218 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15890 Ramachandran restraints generated. 7945 Oldfield, 0 Emsley, 7945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15890 Ramachandran restraints generated. 7945 Oldfield, 0 Emsley, 7945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2664 residues out of total 7169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 230 poor density : 2434 time to evaluate : 7.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 230 outliers final: 95 residues processed: 2526 average time/residue: 0.8487 time to fit residues: 3663.3694 Evaluate side-chains 2211 residues out of total 7169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 2116 time to evaluate : 7.168 Switching outliers to nearest non-outliers outliers start: 95 outliers final: 0 residues processed: 95 average time/residue: 0.6868 time to fit residues: 132.2260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 901 random chunks: chunk 809 optimal weight: 9.9990 chunk 616 optimal weight: 8.9990 chunk 425 optimal weight: 9.9990 chunk 90 optimal weight: 10.0000 chunk 391 optimal weight: 0.9980 chunk 550 optimal weight: 2.9990 chunk 822 optimal weight: 4.9990 chunk 870 optimal weight: 2.9990 chunk 429 optimal weight: 9.9990 chunk 779 optimal weight: 9.9990 chunk 234 optimal weight: 2.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 336 ASN F 103 GLN F 153 HIS ** F 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 40 GLN K 64 HIS ** K 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 96 HIS ** L 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 170 ASN ** N 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 94 GLN S 118 ASN ** T 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 117 HIS ** W 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 80 HIS ** W 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 207 HIS ** Z 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 354 GLN ** 8 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 59 HIS ** d 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 92 ASN f 108 GLN ** g 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 184 ASN ** s 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 314 GLN s 343 GLN ** s 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 80 GLN w 103 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6588 moved from start: 0.5799 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: