Starting phenix.real_space_refine (version: 1.21rc1) on Fri Aug 25 07:32:17 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ool_3842/08_2023/5ool_3842_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ool_3842/08_2023/5ool_3842.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ool_3842/08_2023/5ool_3842_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ool_3842/08_2023/5ool_3842_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ool_3842/08_2023/5ool_3842_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ool_3842/08_2023/5ool_3842.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ool_3842/08_2023/5ool_3842.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ool_3842/08_2023/5ool_3842_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ool_3842/08_2023/5ool_3842_neut_updated.pdb" } resolution = 3.06 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- 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= 0.015 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 3 6.06 5 P 1498 5.49 5 Mg 92 5.21 5 S 285 5.16 5 C 57071 2.51 5 N 18009 2.21 5 O 22040 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 "D ARG 274": "NH1" <-> "NH2" Residue "D ARG 284": "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 104": "NH1" <-> "NH2" 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 "T ARG 157": "NH1" <-> "NH2" 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 PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 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 49": "NH1" <-> "NH2" Residue "2 GLU 52": "OE1" <-> "OE2" 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 162": "NH1" <-> "NH2" Residue "5 PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 "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 "9 PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 216": "NH1" <-> "NH2" Residue "d ARG 74": "NH1" <-> "NH2" Residue "d ARG 159": "NH1" <-> "NH2" 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 "m GLU 70": "OE1" <-> "OE2" Residue "o ARG 23": "NH1" <-> "NH2" 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 PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 98998 Number of models: 1 Model: "" Number of chains: 66 Chain: "A" Number of atoms: 30607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1441, 30607 Classifications: {'RNA': 1441} Modifications used: {'rna2p_pur': 153, 'rna2p_pyr': 114, 'rna3p_pur': 610, 'rna3p_pyr': 564} Link IDs: {'rna2p': 266, 'rna3p': 1174} Chain breaks: 16 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: 1842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1842 Classifications: {'peptide': 236} Link IDs: {'PTRANS': 12, 'TRANS': 223} Chain: "E" Number of atoms: 2396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2396 Classifications: {'peptide': 304} Link IDs: {'PTRANS': 24, 'TRANS': 279} 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: 1368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1368 Classifications: {'peptide': 166} Link IDs: {'PTRANS': 12, 'TRANS': 153} 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: 367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 367 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 2, 'TRANS': 42} 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: "4" Number of atoms: 333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 333 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 1, 'TRANS': 35} 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: 771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 771 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 5, 'TRANS': 85} 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: 87 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 87 Unusual residues: {' MG': 87} Classifications: {'undetermined': 87} Link IDs: {None: 86} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 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: "4" 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 39120 SG CYS I 64 75.322 81.449 81.778 1.00 26.56 S ATOM 92585 SG CYS r 70 72.874 78.765 84.288 1.00 61.90 S ATOM 92900 SG CYS r 108 75.638 78.401 84.271 1.00 54.31 S ATOM 63828 SG CYS 0 110 58.654 132.558 184.300 1.00 57.96 S ATOM 63850 SG CYS 0 113 59.249 135.786 183.969 1.00 59.12 S ATOM 63930 SG CYS 0 123 61.960 134.436 183.188 1.00 57.07 S ATOM 63953 SG CYS 0 126 60.618 134.287 186.876 1.00 60.80 S ATOM 66169 SG CYS 4 76 102.053 62.336 107.472 1.00 72.94 S ATOM 66192 SG CYS 4 79 99.427 65.256 107.060 1.00 70.78 S ATOM 66316 SG CYS 4 92 98.692 62.451 109.242 1.00 69.61 S Time building chain proxies: 36.49, per 1000 atoms: 0.37 Number of scatterers: 98998 At special positions: 0 Unit cell: (222.6, 245.92, 251.22, 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 3 29.99 S 285 16.00 P 1498 15.00 Mg 92 11.99 O 22040 8.00 N 18009 7.00 C 57071 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: 34.13 Conformation dependent library (CDL) restraints added in 7.1 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 4 200 " pdb="ZN ZN 4 200 " - pdb=" ND1 HIS 4 98 " pdb="ZN ZN 4 200 " - pdb=" SG CYS 4 79 " pdb="ZN ZN 4 200 " - pdb=" SG CYS 4 76 " pdb="ZN ZN 4 200 " - pdb=" SG CYS 4 92 " 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 : 9 16084 Ramachandran restraints generated. 8042 Oldfield, 0 Emsley, 8042 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15524 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 262 helices and 80 sheets defined 31.6% alpha, 11.6% beta 404 base pairs and 833 stacking pairs defined. Time for finding SS restraints: 30.61 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 264 Processing helix chain 'D' and resid 280 through 282 No H-bonds generated for 'chain 'D' and resid 280 through 282' Processing helix chain 'E' and resid 55 through 76 Proline residue: E 59 - end of helix removed outlier: 3.989A pdb=" N LYS E 76 " --> pdb=" O GLN E 72 " (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 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 '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 236 removed outlier: 4.366A pdb=" N ARG F 236 " --> pdb=" O GLU F 232 " (cutoff:3.500A) Processing helix chain 'F' and resid 245 through 247 No H-bonds generated for 'chain 'F' and resid 245 through 247' Processing helix chain 'F' and resid 251 through 255 Processing helix chain 'F' and resid 263 through 276 removed outlier: 3.810A pdb=" N GLN F 276 " --> pdb=" O LYS F 272 " (cutoff:3.500A) 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 134 through 146 removed outlier: 3.953A pdb=" N LYS H 138 " --> pdb=" O PRO H 134 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LEU H 139 " --> pdb=" O GLU H 135 " (cutoff:3.500A) removed outlier: 3.550A 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: 3.684A 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: 4.205A pdb=" N GLU I 136 " --> pdb=" O LYS I 132 " (cutoff:3.500A) Processing helix chain 'I' and resid 161 through 169 Processing helix chain 'I' and resid 188 through 196 Processing helix chain 'J' and resid 36 through 39 No H-bonds generated for 'chain 'J' and resid 36 through 39' Processing helix chain 'J' and resid 46 through 58 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 150 removed outlier: 4.106A pdb=" N SER J 143 " --> pdb=" O SER J 139 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N SER J 150 " --> pdb=" O GLY J 146 " (cutoff:3.500A) Processing helix chain 'K' and resid 6 through 14 Processing helix chain 'K' and resid 28 through 40 removed outlier: 3.875A pdb=" N MET K 34 " --> pdb=" O LYS K 30 " (cutoff:3.500A) Processing helix chain 'K' and resid 69 through 74 removed outlier: 4.552A pdb=" N TRP K 72 " --> pdb=" O GLY K 69 " (cutoff:3.500A) removed outlier: 3.875A 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 123 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 125 through 127 No H-bonds generated for 'chain 'L' and resid 125 through 127' Processing helix chain 'L' and resid 135 through 138 No H-bonds generated for 'chain 'L' and resid 135 through 138' Processing helix chain 'M' and resid 11 through 18 removed outlier: 4.464A pdb=" N GLY M 18 " --> pdb=" O ASP M 14 " (cutoff:3.500A) Processing helix chain 'M' and resid 98 through 107 Processing helix chain 'M' and resid 118 through 123 Processing helix chain 'M' and resid 161 through 170 removed outlier: 4.298A pdb=" N ASN M 170 " --> pdb=" O ALA M 166 " (cutoff:3.500A) 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 240 Processing helix chain 'M' and resid 253 through 257 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 109 Processing helix chain 'N' and resid 173 through 182 Processing helix chain 'N' and resid 193 through 208 Processing helix chain 'N' and resid 215 through 221 removed outlier: 3.747A 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 'O' and resid 22 through 39 Processing helix chain 'O' and resid 46 through 63 removed outlier: 3.806A 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 85 through 91 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 113 No H-bonds generated for 'chain 'P' and resid 110 through 113' Processing helix chain 'P' and resid 122 through 138 removed outlier: 3.554A pdb=" N GLU P 138 " --> pdb=" O GLN P 134 " (cutoff:3.500A) Processing helix chain 'P' and resid 150 through 153 No H-bonds generated for 'chain 'P' and resid 150 through 153' Processing helix chain 'P' and resid 156 through 168 Processing helix chain 'Q' and resid 89 through 105 removed outlier: 4.180A pdb=" N VAL Q 105 " --> pdb=" O GLU Q 101 " (cutoff:3.500A) Processing helix chain 'Q' and resid 144 through 146 No H-bonds generated for 'chain 'Q' and resid 144 through 146' Processing helix chain 'Q' and resid 188 through 191 removed outlier: 3.580A pdb=" N ARG Q 191 " --> pdb=" O LEU Q 188 " (cutoff:3.500A) No H-bonds generated for '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: 3.960A pdb=" N LYS Q 259 " --> pdb=" O LYS Q 255 " (cutoff:3.500A) Processing helix chain 'Q' and resid 263 through 267 removed outlier: 3.664A pdb=" N GLU Q 266 " --> pdb=" O PRO Q 263 " (cutoff:3.500A) Processing helix chain 'Q' and resid 277 through 289 removed outlier: 3.522A pdb=" N SER Q 289 " --> pdb=" O GLU Q 285 " (cutoff:3.500A) Processing helix chain 'R' and resid 16 through 28 removed outlier: 3.593A pdb=" N ILE R 21 " --> pdb=" O TYR R 18 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLN R 22 " --> pdb=" O PHE R 19 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LEU R 25 " --> pdb=" O GLN R 22 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N LYS R 26 " --> pdb=" O GLU R 23 " (cutoff:3.500A) Processing helix chain 'R' and resid 39 through 77 removed outlier: 4.068A pdb=" N ARG R 44 " --> pdb=" O ARG R 40 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ARG R 57 " --> pdb=" O CYS R 53 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N TYR R 58 " --> pdb=" O THR R 54 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LEU R 59 " --> pdb=" O LYS R 55 " (cutoff:3.500A) Processing helix chain 'R' and resid 83 through 93 removed outlier: 3.803A pdb=" N CYS R 93 " --> pdb=" O ASN R 89 " (cutoff:3.500A) Processing helix chain 'R' and resid 99 through 108 Processing helix chain 'R' and resid 110 through 132 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: 3.826A 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 131 removed outlier: 3.969A pdb=" N ILE T 116 " --> pdb=" O LYS T 112 " (cutoff:3.500A) Processing helix chain 'T' and resid 192 through 205 Processing helix chain 'U' and resid 50 through 59 Processing helix chain 'U' and resid 127 through 134 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 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 181 through 183 No H-bonds generated for 'chain 'V' and resid 181 through 183' Processing helix chain 'V' and resid 194 through 202 Processing helix chain 'W' and resid 111 through 117 Processing helix chain 'X' and resid 8 through 16 removed outlier: 4.534A pdb=" N LYS X 12 " --> pdb=" O TRP X 9 " (cutoff:3.500A) Processing helix chain 'X' and resid 20 through 23 Processing helix chain 'X' and resid 26 through 33 removed outlier: 3.506A 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 170 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 219 Processing helix chain 'X' and resid 226 through 242 Processing helix chain 'Y' and resid 64 through 67 Processing helix chain 'Y' and resid 87 through 91 Processing helix chain 'Y' and resid 95 through 121 Processing helix chain 'Y' and resid 130 through 157 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 69 No H-bonds generated for 'chain '2' and resid 66 through 69' 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 '4' and resid 96 through 98 No H-bonds generated for 'chain '4' and resid 96 through 98' Processing helix chain '5' and resid 36 through 38 No H-bonds generated for 'chain '5' and resid 36 through 38' Processing helix chain '5' and resid 48 through 51 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 137 No H-bonds generated for 'chain '5' and resid 134 through 137' Processing helix chain '5' and resid 150 through 162 Processing helix chain '5' and resid 173 through 191 Proline residue: 5 178 - end of helix removed outlier: 4.477A pdb=" N GLN 5 191 " --> pdb=" O LEU 5 187 " (cutoff:3.500A) Processing helix chain '5' and resid 196 through 200 Processing helix chain '5' and resid 242 through 249 removed outlier: 4.377A pdb=" N LYS 5 249 " --> pdb=" O ILE 5 245 " (cutoff:3.500A) 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 77 No H-bonds generated for 'chain '6' and resid 74 through 77' 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 142 Processing helix chain '6' and resid 144 through 154 Processing helix chain '6' and resid 157 through 161 Processing helix chain '6' and resid 293 through 296 No H-bonds generated for 'chain '6' and resid 293 through 296' Processing helix chain '6' and resid 300 through 306 removed outlier: 3.514A 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: 3.696A 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 56 Processing helix chain '7' and resid 88 through 95 Processing helix chain '7' and resid 97 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: 4.478A 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 246 removed outlier: 3.729A pdb=" N SER 7 245 " --> pdb=" O GLU 7 241 " (cutoff:3.500A) Processing helix chain '7' and resid 310 through 318 Processing helix chain '8' and resid 108 through 153 Processing helix chain '9' and resid 28 through 33 removed outlier: 3.691A pdb=" N ARG 9 33 " --> pdb=" O SER 9 29 " (cutoff:3.500A) Processing helix chain '9' and resid 88 through 102 Proline residue: 9 98 - end of helix Processing helix chain '9' and resid 114 through 117 removed outlier: 3.598A pdb=" N TYR 9 117 " --> pdb=" O LEU 9 114 " (cutoff:3.500A) No H-bonds generated for 'chain '9' and resid 114 through 117' 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 120 through 122 No H-bonds generated for 'chain 'a' and resid 120 through 122' Processing helix chain 'a' and resid 128 through 131 No H-bonds generated for 'chain 'a' and resid 128 through 131' Processing helix chain 'b' and resid 38 through 49 removed outlier: 3.573A pdb=" N ARG b 41 " --> pdb=" O ALA b 38 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N GLY b 42 " --> pdb=" O SER b 39 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ALA b 43 " --> pdb=" O SER b 40 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLU b 45 " --> pdb=" O GLY b 42 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLU b 48 " --> pdb=" O GLU b 45 " (cutoff:3.500A) removed outlier: 3.719A 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 91 Processing helix chain 'c' and resid 96 through 105 Processing helix chain 'c' and resid 123 through 144 Processing helix chain 'c' and resid 150 through 160 Processing helix chain 'c' and resid 163 through 170 Processing helix chain 'c' and resid 175 through 178 No H-bonds generated for 'chain 'c' and resid 175 through 178' Processing helix chain 'c' and resid 188 through 218 Proline residue: c 208 - end of helix removed outlier: 3.832A 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 305 Processing helix chain 'd' and resid 53 through 62 Processing helix chain 'd' and resid 119 through 129 removed outlier: 4.574A pdb=" N TYR d 128 " --> pdb=" O ARG d 124 " (cutoff:3.500A) Processing helix chain 'd' and resid 134 through 154 Proline residue: d 138 - end of helix removed outlier: 3.808A pdb=" N ALA d 141 " --> pdb=" O PRO d 138 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE d 144 " --> pdb=" O ALA d 141 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ILE d 146 " --> pdb=" O ASP d 143 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N GLU d 147 " --> pdb=" O ILE d 144 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ASN d 154 " --> pdb=" O CYS d 151 " (cutoff:3.500A) Processing helix chain 'd' and resid 157 through 163 removed outlier: 4.110A 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 80 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 192 Processing helix chain 'e' and resid 258 through 263 removed outlier: 3.693A pdb=" N GLY e 261 " --> pdb=" O ASP e 258 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N TYR e 263 " --> pdb=" O LEU e 260 " (cutoff:3.500A) Processing helix chain 'e' and resid 272 through 274 No H-bonds generated for 'chain 'e' and resid 272 through 274' Processing helix chain 'f' and resid 60 through 62 No H-bonds generated for 'chain 'f' and resid 60 through 62' Processing helix chain 'f' and resid 100 through 116 Processing helix chain 'f' and resid 164 through 177 removed outlier: 4.245A pdb=" N GLU f 168 " --> pdb=" O ALA f 164 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ILE f 173 " --> pdb=" O ILE f 169 " (cutoff:3.500A) removed outlier: 3.809A 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 125 Processing helix chain 'g' and resid 129 through 132 No H-bonds generated for 'chain 'g' and resid 129 through 132' Processing helix chain 'g' and resid 154 through 163 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 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 70 through 72 No H-bonds generated for 'chain 'i' and resid 70 through 72' 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: 6.254A pdb=" N SER i 100 " --> pdb=" O LYS i 96 " (cutoff:3.500A) removed outlier: 6.399A 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 25 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 103 Processing helix chain 'k' and resid 28 through 36 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 50 removed outlier: 4.050A pdb=" N SER o 50 " --> pdb=" O HIS o 46 " (cutoff:3.500A) Processing helix chain 'o' and resid 64 through 78 Processing helix chain 'o' and resid 88 through 98 removed outlier: 4.159A pdb=" N LEU o 95 " --> pdb=" O GLN o 91 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ASN o 96 " --> pdb=" O LEU o 92 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N VAL o 97 " --> pdb=" O ASP o 93 " (cutoff:3.500A) removed outlier: 5.344A 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 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 54 through 68 removed outlier: 7.342A pdb=" N ALA q 66 " --> pdb=" O ALA q 62 " (cutoff:3.500A) removed outlier: 8.902A pdb=" N ALA q 67 " --> pdb=" O ARG q 63 " (cutoff:3.500A) removed outlier: 3.765A 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 151 Proline residue: q 129 - end of helix removed outlier: 4.138A pdb=" N GLU q 151 " --> pdb=" O GLN q 147 " (cutoff:3.500A) Processing helix chain 'r' and resid 71 through 75 removed outlier: 3.592A pdb=" N TRP r 75 " --> pdb=" O PRO r 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'r' and resid 71 through 75' Processing helix chain 'r' and resid 86 through 92 removed outlier: 4.299A pdb=" N GLN r 91 " --> pdb=" O LEU r 87 " (cutoff:3.500A) removed outlier: 4.313A 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 168 through 170 No H-bonds generated for 'chain 'r' and resid 168 through 170' Processing helix chain 's' and resid 56 through 71 Processing helix chain 's' and resid 76 through 83 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 187 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 320 through 342 removed outlier: 3.582A pdb=" N PHE s 324 " --> pdb=" O ILE s 320 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N SER s 331 " --> pdb=" O ASN s 327 " (cutoff:3.500A) Processing helix chain 's' and resid 416 through 425 Processing helix chain 't' and resid 3 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 6 through 21 removed outlier: 4.284A pdb=" N LEU v 10 " --> pdb=" O ARG v 6 " (cutoff:3.500A) Processing helix chain 'v' and resid 28 through 39 Processing helix chain 'v' and resid 50 through 63 Processing helix chain 'w' and resid 76 through 89 Processing helix chain 'w' and resid 112 through 123 Processing helix chain 'w' and resid 132 through 135 No H-bonds generated for 'chain 'w' and resid 132 through 135' 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: 6.757A pdb=" N LEU D 141 " --> pdb=" O ILE D 127 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N VAL D 129 " --> pdb=" O ILE D 139 " (cutoff:3.500A) removed outlier: 6.353A 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: 3.742A pdb=" N ARG D 218 " --> pdb=" O ILE D 225 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N GLN D 227 " --> pdb=" O LEU D 216 " (cutoff:3.500A) removed outlier: 5.996A 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: 5.239A pdb=" N LYS E 209 " --> pdb=" O LEU E 296 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N LEU E 296 " --> pdb=" O LYS E 209 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N LEU E 121 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N MET E 106 " --> pdb=" O VAL E 119 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N VAL E 119 " --> pdb=" O MET E 106 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N HIS E 117 " --> pdb=" O PRO E 108 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ARG E 275 " --> pdb=" O TYR E 284 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ASN E 286 " --> pdb=" O VAL E 273 " (cutoff:3.500A) removed outlier: 7.106A 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: 3.534A pdb=" N THR E 175 " --> pdb=" O GLY E 149 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N GLY E 148 " --> pdb=" O VAL E 129 " (cutoff:3.500A) removed outlier: 5.607A 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 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: 6.403A pdb=" N LEU F 259 " --> pdb=" O HIS F 188 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N MET F 190 " --> pdb=" O LEU F 259 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N LEU F 261 " --> pdb=" O MET F 190 " (cutoff:3.500A) removed outlier: 3.789A 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: 6.347A pdb=" N GLU H 57 " --> pdb=" O LEU H 82 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N LEU H 82 " --> pdb=" O GLU H 57 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'I' and resid 179 through 181 Processing sheet with id= M, first strand: chain 'J' and resid 110 through 113 Processing sheet with id= N, first strand: chain 'K' and resid 125 through 127 removed outlier: 6.450A pdb=" N VAL K 57 " --> pdb=" O HIS K 126 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N LEU K 20 " --> pdb=" O VAL K 142 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N GLU K 144 " --> pdb=" O LEU K 20 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N ASP K 22 " --> pdb=" O GLU K 144 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'K' and resid 76 through 80 Processing sheet with id= P, first strand: chain 'L' and resid 105 through 107 removed outlier: 3.968A pdb=" N HIS L 59 " --> pdb=" O LEU L 74 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N ALA L 76 " --> pdb=" O CYS L 57 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N CYS L 57 " --> pdb=" O ALA L 76 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'M' and resid 94 through 97 Processing sheet with id= R, first strand: chain 'M' and resid 153 through 155 removed outlier: 6.298A pdb=" N VAL M 173 " --> pdb=" O ILE M 154 " (cutoff:3.500A) No H-bonds generated for sheet with id= R Processing sheet with id= S, first strand: chain 'M' and resid 274 through 276 Processing sheet with id= T, first strand: chain 'N' and resid 88 through 91 Processing sheet with id= U, first strand: chain 'N' and resid 95 through 97 Processing sheet with id= V, first strand: chain 'N' and resid 118 through 122 Processing sheet with id= W, first strand: chain 'N' and resid 129 through 133 removed outlier: 6.284A pdb=" N ARG N 133 " --> pdb=" O ILE N 147 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N ILE N 147 " --> pdb=" O ARG N 133 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'O' and resid 41 through 45 Processing sheet with id= Y, first strand: chain 'P' and resid 80 through 85 Processing sheet with id= Z, first strand: chain 'Q' and resid 173 through 178 removed outlier: 3.690A pdb=" N GLU Q 173 " --> pdb=" O THR Q 120 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ILE Q 116 " --> pdb=" O VAL Q 177 " (cutoff:3.500A) removed outlier: 9.210A pdb=" N LEU Q 134 " --> pdb=" O VAL Q 154 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N VAL Q 154 " --> pdb=" O LEU Q 134 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ILE Q 150 " --> pdb=" O ILE Q 138 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'Q' and resid 180 through 182 No H-bonds generated for sheet with id= AA 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: 3.719A pdb=" N ASP S 112 " --> pdb=" O ILE S 195 " (cutoff:3.500A) removed outlier: 3.843A 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 130 removed outlier: 4.313A pdb=" N VAL S 156 " --> pdb=" O LEU S 130 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER S 197 " --> pdb=" O GLU S 157 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N THR S 159 " --> pdb=" O ILE S 195 " (cutoff:3.500A) removed outlier: 5.378A 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: 3.998A 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: 6.327A pdb=" N VAL T 179 " --> pdb=" O ILE T 142 " (cutoff:3.500A) removed outlier: 5.545A 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 158 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 73 through 75 Processing sheet with id= AJ, first strand: chain 'V' and resid 93 through 98 Processing sheet with id= AK, first strand: chain 'V' and resid 76 through 80 removed outlier: 6.908A pdb=" N VAL V 87 " --> pdb=" O VAL V 77 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N VAL V 79 " --> pdb=" O TRP V 85 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N TRP V 85 " --> pdb=" O VAL V 79 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'W' and resid 81 through 83 removed outlier: 6.279A pdb=" N ALA W 91 " --> pdb=" O ILE W 66 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ILE W 66 " --> pdb=" O ALA W 91 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'W' and resid 95 through 103 Processing sheet with id= AN, first strand: chain 'X' and resid 50 through 52 Processing sheet with id= AO, first strand: chain 'X' and resid 86 through 91 Processing sheet with id= AP, first strand: chain 'X' and resid 109 through 116 Processing sheet with id= AQ, first strand: chain 'Y' and resid 166 through 170 Processing sheet with id= AR, first strand: chain 'Z' and resid 98 through 101 Processing sheet with id= AS, first strand: chain '0' and resid 156 through 159 removed outlier: 6.437A pdb=" N ARG 0 173 " --> pdb=" O VAL 0 157 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N LEU 0 159 " --> pdb=" O ARG 0 173 " (cutoff:3.500A) removed outlier: 5.781A 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: 5.726A pdb=" N ARG 1 19 " --> pdb=" O LYS 1 61 " (cutoff:3.500A) removed outlier: 5.898A 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 '4' and resid 80 through 84 Processing sheet with id= AX, first strand: chain '5' and resid 266 through 268 removed outlier: 6.768A pdb=" N LEU 5 219 " --> pdb=" O TYR 5 105 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N PHE 5 107 " --> pdb=" O LEU 5 219 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N GLN 5 221 " --> pdb=" O PHE 5 107 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain '5' and resid 126 through 130 removed outlier: 6.730A pdb=" N ASN 5 372 " --> pdb=" O LYS 5 127 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N ILE 5 129 " --> pdb=" O ASN 5 372 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ALA 5 374 " --> pdb=" O ILE 5 129 " (cutoff:3.500A) removed outlier: 10.007A pdb=" N VAL 5 341 " --> pdb=" O TYR 5 287 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N HIS 5 289 " --> pdb=" O VAL 5 341 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N LEU 5 230 " --> pdb=" O HIS 5 289 " (cutoff:3.500A) Processing sheet with id= AZ, first strand: chain '5' and resid 385 through 387 Processing sheet with id= BA, first strand: chain '6' and resid 203 through 205 removed outlier: 3.794A pdb=" N ASP 6 183 " --> pdb=" O VAL 6 179 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain '6' and resid 213 through 220 removed outlier: 5.272A pdb=" N LYS 6 274 " --> pdb=" O PRO 6 313 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain '6' and resid 236 through 238 removed outlier: 3.679A pdb=" N CYS 6 252 " --> pdb=" O LEU 6 236 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N THR 6 238 " --> pdb=" O VAL 6 250 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N VAL 6 250 " --> pdb=" O THR 6 238 " (cutoff:3.500A) Processing sheet with id= BD, first strand: chain '7' and resid 64 through 68 Processing sheet with id= BE, first strand: chain '7' and resid 112 through 114 Processing sheet with id= BF, first strand: chain '7' and resid 282 through 285 removed outlier: 3.684A pdb=" N ALA 7 282 " --> pdb=" O GLN 7 298 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG 7 168 " --> pdb=" O ASP 7 182 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N VAL 7 184 " --> pdb=" O LEU 7 166 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N LEU 7 166 " --> pdb=" O VAL 7 184 " (cutoff:3.500A) Processing sheet with id= BG, first strand: chain '7' and resid 217 through 222 Processing sheet with id= BH, first strand: chain '7' and resid 275 through 280 removed outlier: 6.533A pdb=" N LEU 7 302 " --> pdb=" O PHE 7 276 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N TYR 7 278 " --> pdb=" O VAL 7 300 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N VAL 7 300 " --> pdb=" O TYR 7 278 " (cutoff:3.500A) Processing sheet with id= BI, first strand: chain '9' and resid 42 through 45 Processing sheet with id= BJ, first strand: chain 'a' and resid 45 through 51 Processing sheet with id= BK, first strand: chain 'b' and resid 62 through 65 removed outlier: 6.636A pdb=" N GLU b 78 " --> pdb=" O GLN b 27 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N LEU b 29 " --> pdb=" O VAL b 76 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N VAL b 76 " --> pdb=" O LEU b 29 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N PHE b 31 " --> pdb=" O ARG b 74 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N ARG b 74 " --> pdb=" O PHE b 31 " (cutoff:3.500A) Processing sheet with id= BL, first strand: chain 'c' and resid 254 through 261 removed outlier: 6.758A pdb=" N PHE c 271 " --> pdb=" O THR c 258 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N GLN c 260 " --> pdb=" O LEU c 269 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N LEU c 269 " --> pdb=" O GLN c 260 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ALA c 282 " --> pdb=" O LEU c 274 " (cutoff:3.500A) Processing sheet with id= BM, first strand: chain 'd' and resid 184 through 186 removed outlier: 3.966A pdb=" N ARG d 219 " --> pdb=" O VAL d 186 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N TYR d 245 " --> pdb=" O ILE d 265 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N GLU d 249 " --> pdb=" O MET d 261 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N MET d 261 " --> pdb=" O GLU d 249 " (cutoff:3.500A) Processing sheet with id= BN, first strand: chain 'd' and resid 193 through 198 removed outlier: 6.805A pdb=" N THR d 213 " --> pdb=" O VAL d 195 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N VAL d 197 " --> pdb=" O GLN d 211 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N GLN d 211 " --> pdb=" O VAL d 197 " (cutoff:3.500A) Processing sheet with id= BO, first strand: chain 'e' and resid 175 through 177 removed outlier: 7.262A pdb=" N GLY e 228 " --> pdb=" O ARG e 46 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N LEU e 48 " --> pdb=" O GLY e 228 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N LYS e 230 " --> pdb=" O LEU e 48 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N ALA e 50 " --> pdb=" O LYS e 230 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N PHE e 232 " --> pdb=" O ALA e 50 " (cutoff:3.500A) Processing sheet with id= BP, first strand: chain 'e' and resid 161 through 163 Processing sheet with id= BQ, first strand: chain 'e' and resid 199 through 204 removed outlier: 6.068A pdb=" N LYS e 203 " --> pdb=" O LEU e 238 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N LEU e 238 " --> pdb=" O LYS e 203 " (cutoff:3.500A) Processing sheet with id= BR, first strand: chain 'f' and resid 93 through 97 Processing sheet with id= BS, first strand: chain 'g' and resid 84 through 86 Processing sheet with id= BT, first strand: chain 'g' and resid 96 through 101 Processing sheet with id= BU, first strand: chain 'k' and resid 51 through 55 removed outlier: 5.825A pdb=" N VAL k 16 " --> pdb=" O ILE k 52 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N ASP k 54 " --> pdb=" O VAL k 16 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N VAL k 18 " --> pdb=" O ASP k 54 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLN k 15 " --> pdb=" O LEU k 67 " (cutoff:3.500A) Processing sheet with id= BV, first strand: chain 'm' and resid 64 through 68 Processing sheet with id= BW, first strand: chain 'p' and resid 77 through 80 Processing sheet with id= BX, first strand: chain 'r' and resid 36 through 41 Processing sheet with id= BY, first strand: chain 's' and resid 91 through 94 removed outlier: 3.930A pdb=" N ASP s 234 " --> pdb=" O VAL s 93 " (cutoff:3.500A) Processing sheet with id= BZ, first strand: chain 's' and resid 112 through 116 removed outlier: 6.966A pdb=" N ASN s 391 " --> pdb=" O VAL s 113 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N LEU s 115 " --> pdb=" O ASN s 391 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N CYS s 393 " --> pdb=" O LEU s 115 " (cutoff:3.500A) Processing sheet with id= CA, first strand: chain 's' and resid 199 through 202 removed outlier: 5.707A pdb=" N ILE s 243 " --> pdb=" O GLY s 295 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N GLY s 295 " --> pdb=" O ILE s 243 " (cutoff:3.500A) Processing sheet with id= CB, first strand: chain 'u' and resid 108 through 110 removed outlier: 3.735A pdb=" N ASP u 108 " --> pdb=" O SER u 128 " (cutoff:3.500A) 2046 hydrogen bonds defined for protein. 5796 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 985 hydrogen bonds 1678 hydrogen bond angles 0 basepair planarities 404 basepair parallelities 833 stacking parallelities Total time for adding SS restraints: 63.38 Time building geometry restraints manager: 37.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 13253 1.32 - 1.45: 38966 1.45 - 1.58: 49081 1.58 - 1.72: 2525 1.72 - 1.85: 452 Bond restraints: 104277 Sorted by residual: bond pdb=" N LEU S 130 " pdb=" CA LEU S 130 " ideal model delta sigma weight residual 1.459 1.403 0.057 1.24e-02 6.50e+03 2.09e+01 bond pdb=" C LEU Z 151 " pdb=" N LYS Z 152 " ideal model delta sigma weight residual 1.333 1.237 0.095 2.74e-02 1.33e+03 1.21e+01 bond pdb=" CG1 ILE M 78 " pdb=" CD1 ILE M 78 " ideal model delta sigma weight residual 1.513 1.396 0.117 3.90e-02 6.57e+02 8.98e+00 bond pdb=" CB VAL W 83 " pdb=" CG2 VAL W 83 " ideal model delta sigma weight residual 1.521 1.423 0.098 3.30e-02 9.18e+02 8.83e+00 bond pdb=" C ARG b 116 " pdb=" N LYS b 117 " ideal model delta sigma weight residual 1.331 1.272 0.059 2.07e-02 2.33e+03 8.07e+00 ... (remaining 104272 not shown) Histogram of bond angle deviations from ideal: 95.30 - 104.73: 8152 104.73 - 114.16: 64317 114.16 - 123.59: 66150 123.59 - 133.01: 9281 133.01 - 142.44: 221 Bond angle restraints: 148121 Sorted by residual: angle pdb=" C GLU m 70 " pdb=" N PRO m 71 " pdb=" CA PRO m 71 " ideal model delta sigma weight residual 119.84 130.26 -10.42 1.25e+00 6.40e-01 6.95e+01 angle pdb=" N SER S 103 " pdb=" CA SER S 103 " pdb=" C SER S 103 " ideal model delta sigma weight residual 111.28 119.17 -7.89 1.09e+00 8.42e-01 5.24e+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 95.94 15.36 2.30e+00 1.89e-01 4.46e+01 angle pdb=" O3' A A2243 " pdb=" C3' A A2243 " pdb=" C2' A A2243 " ideal model delta sigma weight residual 109.50 118.59 -9.09 1.50e+00 4.44e-01 3.68e+01 angle pdb=" C3' A A2243 " pdb=" O3' A A2243 " pdb=" P U A2244 " ideal model delta sigma weight residual 120.20 128.99 -8.79 1.50e+00 4.44e-01 3.44e+01 ... (remaining 148116 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.91: 58407 35.91 - 71.82: 1363 71.82 - 107.72: 115 107.72 - 143.63: 14 143.63 - 179.54: 35 Dihedral angle restraints: 59934 sinusoidal: 35969 harmonic: 23965 Sorted by residual: 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 14.54 -174.54 1 1.50e+01 4.44e-03 8.51e+01 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 27.95 172.05 1 1.50e+01 4.44e-03 8.49e+01 dihedral pdb=" O4' C A2493 " pdb=" C1' C A2493 " pdb=" N1 C A2493 " pdb=" C2 C A2493 " ideal model delta sinusoidal sigma weight residual -160.00 11.56 -171.56 1 1.50e+01 4.44e-03 8.49e+01 ... (remaining 59931 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.109: 16339 0.109 - 0.218: 982 0.218 - 0.326: 60 0.326 - 0.435: 16 0.435 - 0.544: 1 Chirality restraints: 17398 Sorted by residual: chirality pdb=" CA ARG m 73 " pdb=" N ARG m 73 " pdb=" C ARG m 73 " pdb=" CB ARG m 73 " both_signs ideal model delta sigma weight residual False 2.51 1.97 0.54 2.00e-01 2.50e+01 7.40e+00 chirality pdb=" C3' A A2457 " pdb=" C4' A A2457 " pdb=" O3' A A2457 " pdb=" C2' A A2457 " both_signs ideal model delta sigma weight residual False -2.74 -2.32 -0.43 2.00e-01 2.50e+01 4.59e+00 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 -2.33 -0.42 2.00e-01 2.50e+01 4.39e+00 ... (remaining 17395 not shown) Planarity restraints: 13464 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A A1811 " -0.052 2.00e-02 2.50e+03 2.38e-02 1.55e+01 pdb=" N9 A A1811 " 0.056 2.00e-02 2.50e+03 pdb=" C8 A A1811 " 0.005 2.00e-02 2.50e+03 pdb=" N7 A A1811 " -0.002 2.00e-02 2.50e+03 pdb=" C5 A A1811 " 0.000 2.00e-02 2.50e+03 pdb=" C6 A A1811 " -0.006 2.00e-02 2.50e+03 pdb=" N6 A A1811 " -0.013 2.00e-02 2.50e+03 pdb=" N1 A A1811 " -0.005 2.00e-02 2.50e+03 pdb=" C2 A A1811 " 0.003 2.00e-02 2.50e+03 pdb=" N3 A A1811 " 0.010 2.00e-02 2.50e+03 pdb=" C4 A A1811 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G A1671 " 0.044 2.00e-02 2.50e+03 1.95e-02 1.13e+01 pdb=" N9 G A1671 " -0.046 2.00e-02 2.50e+03 pdb=" C8 G A1671 " -0.001 2.00e-02 2.50e+03 pdb=" N7 G A1671 " 0.002 2.00e-02 2.50e+03 pdb=" C5 G A1671 " 0.000 2.00e-02 2.50e+03 pdb=" C6 G A1671 " 0.014 2.00e-02 2.50e+03 pdb=" O6 G A1671 " 0.007 2.00e-02 2.50e+03 pdb=" N1 G A1671 " 0.002 2.00e-02 2.50e+03 pdb=" C2 G A1671 " -0.002 2.00e-02 2.50e+03 pdb=" N2 G A1671 " -0.000 2.00e-02 2.50e+03 pdb=" N3 G A1671 " -0.005 2.00e-02 2.50e+03 pdb=" C4 G A1671 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 284 " 0.021 2.00e-02 2.50e+03 2.34e-02 1.10e+01 pdb=" CG TYR E 284 " -0.053 2.00e-02 2.50e+03 pdb=" CD1 TYR E 284 " 0.027 2.00e-02 2.50e+03 pdb=" CD2 TYR E 284 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR E 284 " -0.015 2.00e-02 2.50e+03 pdb=" CE2 TYR E 284 " 0.009 2.00e-02 2.50e+03 pdb=" CZ TYR E 284 " 0.009 2.00e-02 2.50e+03 pdb=" OH TYR E 284 " -0.000 2.00e-02 2.50e+03 ... (remaining 13461 not shown) Histogram of nonbonded interaction distances: 0.04 - 1.01: 1 1.01 - 1.98: 59 1.98 - 2.95: 41899 2.95 - 3.93: 283422 3.93 - 4.90: 532672 Warning: very small nonbonded interaction distances. Nonbonded interactions: 858053 Sorted by model distance: nonbonded pdb=" P A A1907 " pdb="MG MG A3345 " model vdw 0.037 2.530 nonbonded pdb=" OP1 C A2217 " pdb=" N ASN I 128 " model vdw 1.303 2.520 nonbonded pdb=" O6 G A2724 " pdb=" O6 G A2934 " model vdw 1.370 3.040 nonbonded pdb=" OP1 U A1857 " pdb="MG MG A3348 " model vdw 1.426 2.170 nonbonded pdb=" OP1 A A1907 " pdb="MG MG A3345 " model vdw 1.445 2.170 ... (remaining 858048 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: 2.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.060 Extract box with map and model: 15.670 Check model and map are aligned: 1.090 Set scattering table: 0.640 Process input model: 248.490 Find NCS groups from input model: 2.650 Set up NCS constraints: 0.260 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: 0.020 Load rotamer database and sin/cos tables:2.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 273.510 ------------------------------------------------------------------------------- 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 : 0.009 0.118 104277 Z= 0.565 Angle : 1.048 20.493 148121 Z= 0.542 Chirality : 0.058 0.544 17398 Planarity : 0.007 0.075 13464 Dihedral : 14.175 179.541 44410 Min Nonbonded Distance : 0.037 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.99 % Favored : 94.94 % Rotamer Outliers : 0.54 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 1.29 % 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: -3.52 (0.08), residues: 8042 helix: -3.07 (0.07), residues: 2638 sheet: -1.92 (0.15), residues: 1006 loop : -1.91 (0.08), residues: 4398 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16084 Ramachandran restraints generated. 8042 Oldfield, 0 Emsley, 8042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16084 Ramachandran restraints generated. 8042 Oldfield, 0 Emsley, 8042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 4431 residues out of total 7245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 4392 time to evaluate : 6.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: 39 outliers final: 9 residues processed: 4402 average time/residue: 1.0654 time to fit residues: 7825.1946 Evaluate side-chains 2643 residues out of total 7245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 2634 time to evaluate : 6.819 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 1.0327 time to fit residues: 24.3691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 945 random chunks: chunk 797 optimal weight: 4.9990 chunk 716 optimal weight: 4.9990 chunk 397 optimal weight: 5.9990 chunk 244 optimal weight: 6.9990 chunk 483 optimal weight: 6.9990 chunk 382 optimal weight: 4.9990 chunk 740 optimal weight: 8.9990 chunk 286 optimal weight: 5.9990 chunk 450 optimal weight: 8.9990 chunk 551 optimal weight: 3.9990 chunk 858 optimal weight: 3.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 57 ASN ** E 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 188 HIS ** F 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 48 GLN ** J 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 133 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 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 147 GLN ** L 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 26 ASN ** M 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 181 HIS N 202 GLN ** N 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 147 GLN ** P 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 97 GLN Q 175 GLN Q 262 GLN R 12 ASN R 70 ASN ** R 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 41 GLN U 62 ASN U 82 HIS V 117 HIS W 80 HIS ** W 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 4 HIS Z 47 GLN ** Z 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 154 GLN ** 5 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 63 GLN ** 7 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 69 HIS ** 7 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 143 GLN ** 9 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 113 ASN ** a 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 25 GLN c 77 HIS ** d 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 179 GLN f 153 HIS ** f 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 104 ASN ** h 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 65 ASN ** i 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 135 ASN ** m 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 79 HIS r 91 GLN r 112 HIS s 152 GLN ** s 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 343 GLN ** s 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 136 HIS u 178 HIS ** v 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6524 moved from start: 0.4344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.102 104277 Z= 0.344 Angle : 0.833 14.185 148121 Z= 0.424 Chirality : 0.046 0.481 17398 Planarity : 0.007 0.141 13464 Dihedral : 15.431 179.641 27089 Min Nonbonded Distance : 1.690 Molprobity Statistics. All-atom Clashscore : 25.20 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.23 % Favored : 95.73 % Rotamer Outliers : 6.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.29 % 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: -1.90 (0.09), residues: 8042 helix: -1.08 (0.09), residues: 2694 sheet: -1.33 (0.16), residues: 959 loop : -1.30 (0.09), residues: 4389 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16084 Ramachandran restraints generated. 8042 Oldfield, 0 Emsley, 8042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16084 Ramachandran restraints generated. 8042 Oldfield, 0 Emsley, 8042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3368 residues out of total 7245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 474 poor density : 2894 time to evaluate : 6.850 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 outliers start: 474 outliers final: 265 residues processed: 3104 average time/residue: 0.9254 time to fit residues: 4895.2047 Evaluate side-chains 2691 residues out of total 7245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 265 poor density : 2426 time to evaluate : 6.707 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 265 outliers final: 1 residues processed: 265 average time/residue: 0.7677 time to fit residues: 385.4763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 945 random chunks: chunk 476 optimal weight: 0.9990 chunk 266 optimal weight: 0.9980 chunk 714 optimal weight: 7.9990 chunk 584 optimal weight: 4.9990 chunk 236 optimal weight: 5.9990 chunk 859 optimal weight: 10.0000 chunk 928 optimal weight: 10.0000 chunk 765 optimal weight: 9.9990 chunk 852 optimal weight: 5.9990 chunk 293 optimal weight: 4.9990 chunk 689 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 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 184 GLN F 223 HIS ** I 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 100 GLN ** I 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 141 GLN ** J 126 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 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 43 ASN ** L 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 104 ASN L 113 ASN ** L 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 84 ASN ** M 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 115 HIS ** Q 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 70 ASN ** R 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 94 GLN S 118 ASN ** T 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 138 GLN ** V 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 4 HIS ** Z 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 54 GLN 2 77 GLN 3 154 GLN ** 5 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 324 GLN 6 320 GLN 7 45 ASN 7 255 HIS 8 144 GLN 9 113 ASN ** a 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 77 HIS ** c 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 63 HIS ** g 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 124 HIS ** k 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 80 HIS p 143 GLN ** p 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 60 GLN ** q 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 19 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6555 moved from start: 0.5019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.081 104277 Z= 0.266 Angle : 0.760 14.079 148121 Z= 0.382 Chirality : 0.044 0.452 17398 Planarity : 0.006 0.115 13464 Dihedral : 15.310 178.591 27089 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 23.93 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.04 % Favored : 95.93 % Rotamer Outliers : 3.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.29 % 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: -1.37 (0.09), residues: 8042 helix: -0.45 (0.10), residues: 2666 sheet: -1.16 (0.15), residues: 1012 loop : -1.09 (0.09), residues: 4364 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16084 Ramachandran restraints generated. 8042 Oldfield, 0 Emsley, 8042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16084 Ramachandran restraints generated. 8042 Oldfield, 0 Emsley, 8042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2912 residues out of total 7245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 243 poor density : 2669 time to evaluate : 7.059 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 outliers start: 243 outliers final: 114 residues processed: 2780 average time/residue: 0.9597 time to fit residues: 4601.5083 Evaluate side-chains 2462 residues out of total 7245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 2348 time to evaluate : 6.737 Switching outliers to nearest non-outliers outliers start: 114 outliers final: 0 residues processed: 114 average time/residue: 0.7491 time to fit residues: 169.3799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 945 random chunks: chunk 849 optimal weight: 40.0000 chunk 646 optimal weight: 20.0000 chunk 446 optimal weight: 5.9990 chunk 95 optimal weight: 10.0000 chunk 410 optimal weight: 20.0000 chunk 577 optimal weight: 4.9990 chunk 862 optimal weight: 5.9990 chunk 913 optimal weight: 10.0000 chunk 450 optimal weight: 7.9990 chunk 817 optimal weight: 10.0000 chunk 246 optimal weight: 10.0000 overall best weight: 6.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 93 ASN ** H 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 141 GLN ** I 150 HIS ** 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 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 72 GLN L 142 GLN L 143 ASN ** M 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 173 GLN ** N 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 147 GLN ** O 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0 170 GLN ** 1 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 154 GLN ** 5 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 221 GLN 6 37 ASN 8 177 HIS 9 113 ASN ** a 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 120 HIS c 77 HIS ** c 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 63 HIS g 121 GLN ** h 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 382 GLN v 19 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6780 moved from start: 0.6048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.131 104277 Z= 0.427 Angle : 0.843 14.609 148121 Z= 0.431 Chirality : 0.047 0.423 17398 Planarity : 0.007 0.076 13464 Dihedral : 15.583 179.647 27089 Min Nonbonded Distance : 1.337 Molprobity Statistics. All-atom Clashscore : 30.65 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.40 % Favored : 94.58 % Rotamer Outliers : 5.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.09), residues: 8042 helix: -0.32 (0.10), residues: 2661 sheet: -1.10 (0.15), residues: 995 loop : -1.09 (0.09), residues: 4386 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16084 Ramachandran restraints generated. 8042 Oldfield, 0 Emsley, 8042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16084 Ramachandran restraints generated. 8042 Oldfield, 0 Emsley, 8042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2840 residues out of total 7245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 404 poor density : 2436 time to evaluate : 6.847 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 outliers start: 404 outliers final: 252 residues processed: 2602 average time/residue: 0.9047 time to fit residues: 4062.9069 Evaluate side-chains 2434 residues out of total 7245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 252 poor density : 2182 time to evaluate : 6.717 Switching outliers to nearest non-outliers outliers start: 252 outliers final: 0 residues processed: 252 average time/residue: 0.7566 time to fit residues: 365.6724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 945 random chunks: chunk 760 optimal weight: 20.0000 chunk 518 optimal weight: 7.9990 chunk 13 optimal weight: 10.0000 chunk 680 optimal weight: 10.0000 chunk 376 optimal weight: 4.9990 chunk 779 optimal weight: 50.0000 chunk 631 optimal weight: 2.9990 chunk 1 optimal weight: 10.0000 chunk 466 optimal weight: 5.9990 chunk 819 optimal weight: 5.9990 chunk 230 optimal weight: 8.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 237 HIS ** H 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 141 GLN ** I 150 HIS ** 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 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 147 GLN ** L 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 80 GLN ** M 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 173 GLN ** N 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 213 GLN ** R 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 84 ASN ** S 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 4 HIS X 46 HIS ** X 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 57 ASN 3 154 GLN ** 5 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 305 HIS ** 8 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 113 ASN ** a 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 77 HIS ** d 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 59 ASN ** i 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 80 HIS m 44 HIS ** p 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 382 GLN ** u 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6790 moved from start: 0.6610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.114 104277 Z= 0.347 Angle : 0.796 14.253 148121 Z= 0.403 Chirality : 0.045 0.396 17398 Planarity : 0.006 0.097 13464 Dihedral : 15.621 179.899 27089 Min Nonbonded Distance : 1.059 Molprobity Statistics. All-atom Clashscore : 28.07 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.47 % Favored : 94.50 % Rotamer Outliers : 3.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.29 % 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: -1.23 (0.09), residues: 8042 helix: -0.22 (0.10), residues: 2666 sheet: -1.12 (0.15), residues: 1020 loop : -1.07 (0.09), residues: 4356 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16084 Ramachandran restraints generated. 8042 Oldfield, 0 Emsley, 8042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16084 Ramachandran restraints generated. 8042 Oldfield, 0 Emsley, 8042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2651 residues out of total 7245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 253 poor density : 2398 time to evaluate : 6.906 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 outliers start: 253 outliers final: 134 residues processed: 2500 average time/residue: 0.9123 time to fit residues: 3924.1377 Evaluate side-chains 2345 residues out of total 7245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 2211 time to evaluate : 6.787 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 134 outliers final: 1 residues processed: 134 average time/residue: 0.7339 time to fit residues: 192.9902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 945 random chunks: chunk 307 optimal weight: 2.9990 chunk 822 optimal weight: 8.9990 chunk 180 optimal weight: 9.9990 chunk 536 optimal weight: 0.7980 chunk 225 optimal weight: 4.9990 chunk 914 optimal weight: 5.9990 chunk 759 optimal weight: 6.9990 chunk 423 optimal weight: 0.6980 chunk 76 optimal weight: 10.0000 chunk 302 optimal weight: 4.9990 chunk 480 optimal weight: 5.9990 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 221 ASN ** D 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 223 HIS ** I 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 141 GLN I 150 HIS ** K 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 89 GLN K 147 GLN L 33 GLN ** L 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 173 GLN ** N 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 31 ASN ** O 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 79 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 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 138 GLN ** V 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 154 GLN 3 178 GLN ** 5 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 113 ASN ** a 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 77 HIS ** d 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 59 ASN ** i 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 80 HIS k 93 HIS p 143 GLN ** p 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 382 GLN s 397 GLN ** v 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6730 moved from start: 0.6860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.070 104277 Z= 0.245 Angle : 0.762 14.650 148121 Z= 0.381 Chirality : 0.044 0.411 17398 Planarity : 0.005 0.075 13464 Dihedral : 15.513 179.729 27089 Min Nonbonded Distance : 1.137 Molprobity Statistics. All-atom Clashscore : 24.69 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.26 % Favored : 94.70 % Rotamer Outliers : 2.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.09), residues: 8042 helix: -0.02 (0.10), residues: 2644 sheet: -1.07 (0.15), residues: 1003 loop : -0.95 (0.09), residues: 4395 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16084 Ramachandran restraints generated. 8042 Oldfield, 0 Emsley, 8042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16084 Ramachandran restraints generated. 8042 Oldfield, 0 Emsley, 8042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2637 residues out of total 7245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 208 poor density : 2429 time to evaluate : 6.999 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 outliers start: 208 outliers final: 122 residues processed: 2492 average time/residue: 0.9188 time to fit residues: 3952.6845 Evaluate side-chains 2334 residues out of total 7245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 2212 time to evaluate : 6.773 Switching outliers to nearest non-outliers outliers start: 122 outliers final: 0 residues processed: 122 average time/residue: 0.7766 time to fit residues: 185.7486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 945 random chunks: chunk 881 optimal weight: 5.9990 chunk 103 optimal weight: 10.0000 chunk 520 optimal weight: 0.5980 chunk 667 optimal weight: 4.9990 chunk 517 optimal weight: 2.9990 chunk 769 optimal weight: 20.0000 chunk 510 optimal weight: 5.9990 chunk 910 optimal weight: 5.9990 chunk 570 optimal weight: 10.0000 chunk 555 optimal weight: 10.0000 chunk 420 optimal weight: 7.9990 overall best weight: 4.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 221 ASN ** D 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 339 GLN ** I 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 141 GLN ** K 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 147 GLN ** L 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 114 GLN ** M 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 173 GLN ** O 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 4 HIS ** 0 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 154 GLN ** 5 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 324 GLN ** 5 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 113 ASN ** a 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 77 HIS ** d 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 80 HIS m 44 HIS ** p 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 382 GLN ** v 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 103 HIS w 115 GLN ** w 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6781 moved from start: 0.7210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.088 104277 Z= 0.293 Angle : 0.790 15.504 148121 Z= 0.396 Chirality : 0.044 0.291 17398 Planarity : 0.006 0.091 13464 Dihedral : 15.531 179.631 27089 Min Nonbonded Distance : 1.071 Molprobity Statistics. All-atom Clashscore : 27.45 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.70 % Favored : 94.28 % Rotamer Outliers : 2.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.29 % 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: -1.08 (0.09), residues: 8042 helix: -0.11 (0.10), residues: 2668 sheet: -0.92 (0.16), residues: 953 loop : -1.02 (0.09), residues: 4421 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16084 Ramachandran restraints generated. 8042 Oldfield, 0 Emsley, 8042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16084 Ramachandran restraints generated. 8042 Oldfield, 0 Emsley, 8042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2520 residues out of total 7245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 196 poor density : 2324 time to evaluate : 6.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 196 outliers final: 123 residues processed: 2389 average time/residue: 0.9178 time to fit residues: 3789.6044 Evaluate side-chains 2294 residues out of total 7245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 2171 time to evaluate : 6.758 Switching outliers to nearest non-outliers outliers start: 123 outliers final: 0 residues processed: 123 average time/residue: 0.7578 time to fit residues: 182.9350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 945 random chunks: chunk 563 optimal weight: 0.3980 chunk 363 optimal weight: 8.9990 chunk 543 optimal weight: 20.0000 chunk 274 optimal weight: 0.0670 chunk 178 optimal weight: 0.9990 chunk 176 optimal weight: 5.9990 chunk 579 optimal weight: 9.9990 chunk 620 optimal weight: 0.0970 chunk 450 optimal weight: 3.9990 chunk 84 optimal weight: 40.0000 chunk 715 optimal weight: 7.9990 overall best weight: 1.1120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 102 GLN ** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 100 GLN ** K 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 173 GLN O 31 ASN ** O 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 41 GLN U 98 GLN ** V 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 82 GLN ** V 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 80 HIS ** W 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 4 HIS ** Z 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 154 GLN ** 5 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 144 GLN ** 8 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 113 ASN 9 134 ASN ** a 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 48 GLN c 77 HIS ** d 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 251 HIS f 158 GLN ** f 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 59 ASN ** i 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 72 HIS k 80 HIS ** p 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 382 GLN ** v 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6684 moved from start: 0.7322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.077 104277 Z= 0.214 Angle : 0.792 17.467 148121 Z= 0.390 Chirality : 0.043 0.591 17398 Planarity : 0.006 0.100 13464 Dihedral : 15.389 178.778 27089 Min Nonbonded Distance : 1.183 Molprobity Statistics. All-atom Clashscore : 23.41 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.33 % Favored : 94.64 % Rotamer Outliers : 1.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.09), residues: 8042 helix: -0.01 (0.10), residues: 2633 sheet: -0.95 (0.15), residues: 985 loop : -0.96 (0.09), residues: 4424 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16084 Ramachandran restraints generated. 8042 Oldfield, 0 Emsley, 8042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16084 Ramachandran restraints generated. 8042 Oldfield, 0 Emsley, 8042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2501 residues out of total 7245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 2402 time to evaluate : 6.846 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 outliers start: 99 outliers final: 61 residues processed: 2438 average time/residue: 0.9214 time to fit residues: 3874.1974 Evaluate side-chains 2270 residues out of total 7245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 2209 time to evaluate : 6.741 Switching outliers to nearest non-outliers outliers start: 61 outliers final: 0 residues processed: 61 average time/residue: 0.7525 time to fit residues: 94.5658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 945 random chunks: chunk 828 optimal weight: 20.0000 chunk 872 optimal weight: 6.9990 chunk 796 optimal weight: 6.9990 chunk 848 optimal weight: 20.0000 chunk 510 optimal weight: 3.9990 chunk 369 optimal weight: 20.0000 chunk 666 optimal weight: 5.9990 chunk 260 optimal weight: 7.9990 chunk 766 optimal weight: 8.9990 chunk 802 optimal weight: 8.9990 chunk 845 optimal weight: 10.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 103 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 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 72 GLN ** L 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 173 GLN ** N 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 31 ASN ** O 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 22 GLN ** R 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 140 ASN ** T 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 83 ASN ** 0 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 154 GLN ** 5 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 113 ASN ** 9 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 44 HIS ** o 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 123 HIS ** q 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 71 HIS ** s 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6854 moved from start: 0.7739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.103 104277 Z= 0.402 Angle : 0.870 13.504 148121 Z= 0.440 Chirality : 0.047 0.464 17398 Planarity : 0.006 0.088 13464 Dihedral : 15.615 179.375 27089 Min Nonbonded Distance : 1.022 Molprobity Statistics. All-atom Clashscore : 33.01 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.64 % Favored : 93.32 % Rotamer Outliers : 2.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.09), residues: 8042 helix: -0.23 (0.10), residues: 2639 sheet: -1.03 (0.15), residues: 986 loop : -1.06 (0.09), residues: 4417 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16084 Ramachandran restraints generated. 8042 Oldfield, 0 Emsley, 8042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16084 Ramachandran restraints generated. 8042 Oldfield, 0 Emsley, 8042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2365 residues out of total 7245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 2207 time to evaluate : 6.784 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 outliers start: 158 outliers final: 113 residues processed: 2256 average time/residue: 0.9065 time to fit residues: 3546.3666 Evaluate side-chains 2227 residues out of total 7245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 2114 time to evaluate : 6.687 Switching outliers to nearest non-outliers outliers start: 113 outliers final: 0 residues processed: 113 average time/residue: 0.7497 time to fit residues: 168.9418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 945 random chunks: chunk 557 optimal weight: 0.7980 chunk 897 optimal weight: 6.9990 chunk 547 optimal weight: 4.9990 chunk 425 optimal weight: 0.9990 chunk 623 optimal weight: 0.4980 chunk 941 optimal weight: 10.0000 chunk 866 optimal weight: 3.9990 chunk 749 optimal weight: 4.9990 chunk 77 optimal weight: 10.0000 chunk 579 optimal weight: 9.9990 chunk 459 optimal weight: 5.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 168 HIS ** D 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 103 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 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 72 GLN ** L 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 31 ASN ** O 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 22 GLN ** R 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 215 GLN ** Y 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 98 GLN ** Z 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 102 GLN ** 5 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 113 ASN ** 9 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 77 HIS ** d 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 196 HIS s 71 HIS ** s 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 382 GLN ** u 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6740 moved from start: 0.7827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.097 104277 Z= 0.246 Angle : 0.847 15.339 148121 Z= 0.419 Chirality : 0.045 0.393 17398 Planarity : 0.006 0.097 13464 Dihedral : 15.497 179.039 27089 Min Nonbonded Distance : 1.143 Molprobity Statistics. All-atom Clashscore : 25.82 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.47 % Favored : 94.49 % Rotamer Outliers : 0.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.09), residues: 8042 helix: -0.12 (0.10), residues: 2617 sheet: -0.96 (0.16), residues: 960 loop : -0.99 (0.09), residues: 4465 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16084 Ramachandran restraints generated. 8042 Oldfield, 0 Emsley, 8042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16084 Ramachandran restraints generated. 8042 Oldfield, 0 Emsley, 8042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2337 residues out of total 7245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 2281 time to evaluate : 6.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 56 outliers final: 33 residues processed: 2300 average time/residue: 0.9421 time to fit residues: 3749.5191 Evaluate side-chains 2175 residues out of total 7245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 2142 time to evaluate : 6.686 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 0 residues processed: 33 average time/residue: 0.7885 time to fit residues: 56.4802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 945 random chunks: chunk 595 optimal weight: 6.9990 chunk 798 optimal weight: 0.9980 chunk 229 optimal weight: 0.9980 chunk 691 optimal weight: 8.9990 chunk 110 optimal weight: 10.0000 chunk 208 optimal weight: 5.9990 chunk 750 optimal weight: 30.0000 chunk 314 optimal weight: 3.9990 chunk 771 optimal weight: 0.8980 chunk 95 optimal weight: 10.0000 chunk 138 optimal weight: 10.0000 overall best weight: 2.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 9 GLN ** K 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 64 HIS ** L 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 102 GLN ** M 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 31 ASN ** O 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 162 GLN ** Q 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 22 GLN ** R 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 18 HIS ** V 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 4 HIS ** Y 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 51 ASN ** 5 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 113 ASN ** a 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 129 GLN ** d 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 71 HIS ** s 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 382 GLN ** u 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.080815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.064120 restraints weight = 343964.890| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 4.78 r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7076 moved from start: 0.7972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.084 104277 Z= 0.256 Angle : 0.842 16.990 148121 Z= 0.417 Chirality : 0.044 0.476 17398 Planarity : 0.006 0.075 13464 Dihedral : 15.451 179.627 27089 Min Nonbonded Distance : 1.106 Molprobity Statistics. All-atom Clashscore : 26.24 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.04 % Favored : 93.91 % Rotamer Outliers : 0.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.09), residues: 8042 helix: -0.14 (0.10), residues: 2613 sheet: -1.00 (0.16), residues: 996 loop : -1.02 (0.09), residues: 4433 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 54419.01 seconds wall clock time: 940 minutes 0.21 seconds (56400.21 seconds total)