Starting phenix.real_space_refine (version: dev) on Thu Apr 14 23:59:21 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j6b_2566/04_2022/3j6b_2566.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j6b_2566/04_2022/3j6b_2566.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j6b_2566/04_2022/3j6b_2566.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j6b_2566/04_2022/3j6b_2566.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j6b_2566/04_2022/3j6b_2566.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j6b_2566/04_2022/3j6b_2566.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.039 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "B ARG 95": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 107": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 118": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 149": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 161": "OE1" <-> "OE2" Residue "B GLU 190": "OE1" <-> "OE2" Residue "B GLU 207": "OE1" <-> "OE2" Residue "B ARG 211": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 293": "OE1" <-> "OE2" Residue "B ARG 373": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 23": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 47": "OE1" <-> "OE2" Residue "C GLU 78": "OE1" <-> "OE2" Residue "C GLU 91": "OE1" <-> "OE2" Residue "C GLU 145": "OE1" <-> "OE2" Residue "C GLU 242": "OE1" <-> "OE2" Residue "D GLU 97": "OE1" <-> "OE2" Residue "D ARG 129": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 133": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D GLU 142": "OE1" <-> "OE2" Residue "D GLU 171": "OE1" <-> "OE2" Residue "D GLU 204": "OE1" <-> "OE2" Residue "D GLU 252": "OE1" <-> "OE2" Residue "E ARG 43": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E GLU 46": "OE1" <-> "OE2" Residue "E GLU 138": "OE1" <-> "OE2" Residue "E GLU 148": "OE1" <-> "OE2" Residue "E GLU 196": "OE1" <-> "OE2" Residue "E GLU 211": "OE1" <-> "OE2" Residue "F GLU 92": "OE1" <-> "OE2" Residue "F GLU 116": "OE1" <-> "OE2" Residue "F GLU 192": "OE1" <-> "OE2" Residue "G ARG 15": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 46": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 83": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H GLU 103": "OE1" <-> "OE2" Residue "H GLU 133": "OE1" <-> "OE2" Residue "I GLU 20": "OE1" <-> "OE2" Residue "I ARG 26": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 83": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J GLU 107": "OE1" <-> "OE2" Residue "J GLU 132": "OE1" <-> "OE2" Residue "J GLU 191": "OE1" <-> "OE2" Residue "J GLU 204": "OE1" <-> "OE2" Residue "J GLU 255": "OE1" <-> "OE2" Residue "J GLU 263": "OE1" <-> "OE2" Residue "K GLU 40": "OE1" <-> "OE2" Residue "K ARG 44": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K GLU 92": "OE1" <-> "OE2" Residue "K GLU 223": "OE1" <-> "OE2" Residue "K ARG 230": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 232": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L GLU 48": "OE1" <-> "OE2" Residue "L GLU 112": "OE1" <-> "OE2" Residue "L GLU 134": "OE1" <-> "OE2" Residue "L GLU 179": "OE1" <-> "OE2" Residue "L GLU 196": "OE1" <-> "OE2" Residue "L GLU 208": "OE1" <-> "OE2" Residue "L GLU 216": "OE1" <-> "OE2" Residue "M GLU 50": "OE1" <-> "OE2" Residue "M ARG 155": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 64": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N GLU 84": "OE1" <-> "OE2" Residue "O GLU 145": "OE1" <-> "OE2" Residue "O GLU 160": "OE1" <-> "OE2" Residue "O GLU 209": "OE1" <-> "OE2" Residue "O ARG 276": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "P GLU 60": "OE1" <-> "OE2" Residue "P GLU 75": "OE1" <-> "OE2" Residue "P ARG 90": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "P PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P GLU 173": "OE1" <-> "OE2" Residue "P GLU 178": "OE1" <-> "OE2" Residue "P GLU 191": "OE1" <-> "OE2" Residue "P ARG 194": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "P GLU 196": "OE1" <-> "OE2" Residue "P GLU 220": "OE1" <-> "OE2" Residue "Q GLU 48": "OE1" <-> "OE2" Residue "Q PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Q ARG 204": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Q GLU 205": "OE1" <-> "OE2" Residue "Q ARG 215": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Q GLU 263": "OE1" <-> "OE2" Residue "Q ARG 270": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Q GLU 277": "OE1" <-> "OE2" Residue "R GLU 53": "OE1" <-> "OE2" Residue "R GLU 61": "OE1" <-> "OE2" Residue "R GLU 75": "OE1" <-> "OE2" Residue "R PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R GLU 133": "OE1" <-> "OE2" Residue "R GLU 143": "OE1" <-> "OE2" Residue "R GLU 171": "OE1" <-> "OE2" Residue "R GLU 192": "OE1" <-> "OE2" Residue "R GLU 212": "OE1" <-> "OE2" Residue "R ARG 231": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R GLU 242": "OE1" <-> "OE2" Residue "R GLU 358": "OE1" <-> "OE2" Residue "S ARG 25": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "S GLU 51": "OE1" <-> "OE2" Residue "S GLU 62": "OE1" <-> "OE2" Residue "S GLU 139": "OE1" <-> "OE2" Residue "S GLU 146": "OE1" <-> "OE2" Residue "S GLU 164": "OE1" <-> "OE2" Residue "S GLU 166": "OE1" <-> "OE2" Residue "T ARG 48": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "T ARG 91": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "T GLU 116": "OE1" <-> "OE2" Residue "T GLU 140": "OE1" <-> "OE2" Residue "T ARG 159": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "T ARG 176": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "U ARG 31": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "U TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "U GLU 57": "OE1" <-> "OE2" Residue "U GLU 70": "OE1" <-> "OE2" Residue "U GLU 81": "OE1" <-> "OE2" Residue "V ARG 21": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "V ARG 26": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "V ARG 27": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "V GLU 50": "OE1" <-> "OE2" Residue "V GLU 67": "OE1" <-> "OE2" Residue "V ARG 75": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "W GLU 136": "OE1" <-> "OE2" Residue "W GLU 142": "OE1" <-> "OE2" Residue "W GLU 147": "OE1" <-> "OE2" Residue "W ARG 151": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "W TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "X GLU 59": "OE1" <-> "OE2" Residue "Y ARG 62": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Z ARG 74": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Z ARG 79": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "1 ARG 28": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "1 TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "1 ARG 57": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "1 ARG 58": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "1 GLU 72": "OE1" <-> "OE2" Residue "1 ARG 84": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "1 GLU 148": "OE1" <-> "OE2" Residue "1 GLU 160": "OE1" <-> "OE2" Residue "1 GLU 177": "OE1" <-> "OE2" Residue "1 PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "1 GLU 193": "OE1" <-> "OE2" Residue "1 PHE 197": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "1 GLU 309": "OE1" <-> "OE2" Residue "1 ARG 317": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "1 GLU 342": "OE1" <-> "OE2" Residue "1 ARG 366": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "2 GLU 64": "OE1" <-> "OE2" Residue "3 GLU 124": "OE1" <-> "OE2" Residue "3 ARG 130": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "3 GLU 144": "OE1" <-> "OE2" Residue "4 GLU 38": "OE1" <-> "OE2" Residue "4 GLU 55": "OE1" <-> "OE2" Residue "4 GLU 62": "OE1" <-> "OE2" Residue "4 ARG 65": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "4 GLU 75": "OE1" <-> "OE2" Residue "4 GLU 81": "OE1" <-> "OE2" Residue "4 ARG 112": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "4 GLU 119": "OE1" <-> "OE2" Residue "5 GLU 89": "OE1" <-> "OE2" Residue "5 ARG 177": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "5 GLU 206": "OE1" <-> "OE2" Residue "5 GLU 220": "OE1" <-> "OE2" Residue "5 GLU 252": "OE1" <-> "OE2" Residue "5 GLU 317": "OE1" <-> "OE2" Residue "5 PHE 341": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "6 GLU 56": "OE1" <-> "OE2" Residue "6 ARG 160": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "6 GLU 252": "OE1" <-> "OE2" Residue "7 GLU 48": "OE1" <-> "OE2" Residue "7 GLU 69": "OE1" <-> "OE2" Residue "7 GLU 97": "OE1" <-> "OE2" Residue "7 ARG 104": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "7 GLU 109": "OE1" <-> "OE2" Residue "7 GLU 136": "OE1" <-> "OE2" Residue "8 GLU 89": "OE1" <-> "OE2" Residue "8 GLU 104": "OE1" <-> "OE2" Residue "8 PHE 162": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "8 GLU 206": "OE1" <-> "OE2" Residue "8 GLU 208": "OE1" <-> "OE2" Residue "8 GLU 234": "OE1" <-> "OE2" Residue "8 ARG 262": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "9 ARG 37": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "9 GLU 85": "OE1" <-> "OE2" Residue "9 ARG 177": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "9 GLU 210": "OE1" <-> "OE2" Residue "a GLU 59": "OE1" <-> "OE2" Residue "a ARG 82": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "a ARG 83": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "a GLU 157": "OE1" <-> "OE2" Residue "a GLU 169": "OE1" <-> "OE2" Residue "a ARG 179": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "a GLU 183": "OE1" <-> "OE2" Residue "b ARG 52": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "b PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b GLU 91": "OE1" <-> "OE2" Residue "b GLU 92": "OE1" <-> "OE2" Residue "b TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b GLU 117": "OE1" <-> "OE2" Residue "b ARG 122": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "b GLU 124": "OE1" <-> "OE2" Residue "b GLU 131": "OE1" <-> "OE2" Residue "b TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "c ARG 22": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "c ARG 30": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "c GLU 33": "OE1" <-> "OE2" Residue "c ARG 53": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "c TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "c ARG 74": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "d ARG 9": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "d GLU 17": "OE1" <-> "OE2" Residue "d ARG 56": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "d GLU 106": "OE1" <-> "OE2" Residue "d ARG 111": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "d ARG 138": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "d ARG 170": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "d GLU 189": "OE1" <-> "OE2" Residue "d GLU 202": "OE1" <-> "OE2" Residue "d GLU 214": "OE1" <-> "OE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 195137 Number of models: 1 Model: "" Number of chains: 46 Chain: "A" Number of atoms: 86569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2713, 86569 Inner-chain residues flagged as termini: ['pdbres=" A A 83 "', 'pdbres=" U A 766 "', 'pdbres=" U A1137 "', 'pdbres=" A A1481 "', 'pdbres=" A A2408 "', 'pdbres=" A A3005 "', 'pdbres=" U A3188 "'] Classifications: {'RNA': 2713} Modifications used: {'rna3p_pyr': 1025, 'rna2p_pur': 262, 'rna3p_pur': 1273, 'rna2p_pyr': 153, '5*END': 7} Link IDs: {'rna3p': 2297, 'rna2p': 415} Chain breaks: 24 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {' U%rna3p_pyr:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 4603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 4603 Classifications: {'peptide': 295} Link IDs: {'PTRANS': 17, 'TRANS': 277} Chain breaks: 1 Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 28 Chain: "C" Number of atoms: 3906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 3906 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 14, 'TRANS': 234} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 3780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 3780 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 17, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 22 Chain: "E" Number of atoms: 4294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 4294 Classifications: {'peptide': 274} Link IDs: {'PTRANS': 19, 'TRANS': 254} Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 50 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'PHE:plan': 1, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 50 Chain: "F" Number of atoms: 2747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 2747 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 11, 'TRANS': 173} Chain breaks: 4 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 99 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 3, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 43 Chain: "G" Number of atoms: 929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 929 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "H" Number of atoms: 2394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 2394 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 5, 'TRANS': 142} Chain: "I" Number of atoms: 1952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1952 Classifications: {'peptide': 125} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 120} Chain breaks: 1 Chain: "J" Number of atoms: 3555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 3555 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 12, 'TRANS': 207} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 13 Chain: "K" Number of atoms: 3208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 3208 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 9, 'TRANS': 185} Chain: "L" Number of atoms: 3698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 3698 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 10, 'TRANS': 218} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "M" Number of atoms: 2492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 2492 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 8, 'TRANS': 142} Chain: "N" Number of atoms: 1958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 1958 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "O" Number of atoms: 3684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 3684 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 8, 'TRANS': 214} Chain breaks: 1 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "P" Number of atoms: 3450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 3450 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 14, 'TRANS': 192} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "Q" Number of atoms: 4287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 4287 Classifications: {'peptide': 279} Link IDs: {'PTRANS': 22, 'TRANS': 256} Chain breaks: 4 Unresolved non-hydrogen bonds: 110 Unresolved non-hydrogen angles: 133 Unresolved non-hydrogen dihedrals: 87 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 2, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 56 Chain: "R" Number of atoms: 4981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 4981 Classifications: {'peptide': 318} Link IDs: {'PTRANS': 11, 'TRANS': 306} Chain breaks: 3 Unresolved non-hydrogen bonds: 157 Unresolved non-hydrogen angles: 187 Unresolved non-hydrogen dihedrals: 132 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 5, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 7, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 86 Chain: "S" Number of atoms: 2440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2440 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 8, 'TRANS': 137} Chain breaks: 1 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "T" Number of atoms: 3264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 3264 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 15, 'TRANS': 193} Chain breaks: 2 Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 116 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 4, 'ARG:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 55 Chain: "U" Number of atoms: 1341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 1341 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 4, 'TRANS': 77} Chain: "V" Number of atoms: 1083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 1083 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 6, 'TRANS': 57} Chain: "W" Number of atoms: 1922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 1922 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 5, 'TRANS': 106} Chain: "X" Number of atoms: 1077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 1077 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 3, 'TRANS': 60} Chain: "Y" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 788 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 1, 'TRANS': 43} Chain: "Z" Number of atoms: 1054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 1054 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 2, 'TRANS': 59} Chain: "0" Number of atoms: 673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 673 Classifications: {'peptide': 38} Link IDs: {'TRANS': 37} Chain: "1" Number of atoms: 5397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 5397 Classifications: {'peptide': 332} Link IDs: {'PTRANS': 23, 'TRANS': 308} Chain breaks: 3 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 38 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "2" Number of atoms: 1858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 1858 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 7, 'TRANS': 105} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "3" Number of atoms: 2025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 2025 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 8, 'TRANS': 117} Chain breaks: 1 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "4" Number of atoms: 2263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 2263 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 4, 'TRANS': 133} Chain: "5" Number of atoms: 5026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 5026 Classifications: {'peptide': 326} Link IDs: {'PTRANS': 17, 'TRANS': 308} Unresolved non-hydrogen bonds: 82 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 9, 'ASN:plan1': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 54 Chain: "6" Number of atoms: 3187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 3187 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 11, 'TRANS': 197} Chain breaks: 5 Unresolved non-hydrogen bonds: 138 Unresolved non-hydrogen angles: 164 Unresolved non-hydrogen dihedrals: 114 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 10, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 75 Chain: "7" Number of atoms: 1755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 1755 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 100} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "8" Number of atoms: 2829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 2829 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 9, 'TRANS': 172} Chain breaks: 1 Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 35 Chain: "9" Number of atoms: 2865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 2865 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 7, 'TRANS': 187} Chain breaks: 4 Unresolved non-hydrogen bonds: 105 Unresolved non-hydrogen angles: 124 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 5, 'HIS:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 5, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 51 Chain: "a" Number of atoms: 2882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 2882 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 11, 'TRANS': 164} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "b" Number of atoms: 2671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 2671 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 11, 'TRANS': 143} Chain: "c" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 2066 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 6, 'TRANS': 111} Chain: "d" Number of atoms: 3423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 3423 Classifications: {'peptide': 204} Link IDs: {'PTRANS': 9, 'TRANS': 194} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "e" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 648 Classifications: {'RNA': 20} Modifications used: {'5*END': 1, 'rna2p_pur': 1, '3*END': 1, 'rna3p_pur': 10, 'rna3p_pyr': 9} Link IDs: {'rna3p': 19} Chain breaks: 1 Chain: "A" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 109 Unusual residues: {' MG': 109} Classifications: {'undetermined': 109} Link IDs: {None: 108} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "N" 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: {' ZN': 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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM A13I1 SG CYS W 104 211.427 159.446 116.383 1.00 60.45 S ATOM A13J1 SG CYS W 107 213.471 156.557 118.656 1.00 79.08 S ATOM A13NH SG CYS W 117 208.956 157.646 118.597 1.00 68.08 S ATOM A13OU SG CYS W 120 211.277 159.806 119.881 1.00 73.39 S ATOM A16XT SG CYS 0 66 123.557 149.051 44.429 1.00109.37 S ATOM A16YR SG CYS 0 69 126.320 147.906 46.262 1.00102.54 S ATOM A175K SG CYS 0 82 126.510 150.984 45.199 1.00 83.94 S Time building chain proxies: 58.22, per 1000 atoms: 0.30 Number of scatterers: 195137 At special positions: 0 Unit cell: (263.98, 235.84, 239.86, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) Zn 2 29.99 S 167 16.00 P 2725 15.00 Mg 110 11.99 Na 1 11.00 O 28237 8.00 N 20077 7.00 C 60000 6.00 H 83818 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 112.11 Conformation dependent library (CDL) restraints added in 6.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination Zn2+ tetrahedral coordination pdb=" ZN 0 100 " pdb="ZN ZN 0 100 " - pdb=" SG CYS 0 66 " pdb="ZN ZN 0 100 " - pdb=" SG CYS 0 69 " pdb="ZN ZN 0 100 " - pdb=" ND1 HIS 0 88 " pdb="ZN ZN 0 100 " - pdb=" SG CYS 0 82 " pdb=" ZN W 200 " pdb="ZN ZN W 200 " - pdb=" SG CYS W 107 " pdb="ZN ZN W 200 " - pdb=" SG CYS W 120 " pdb="ZN ZN W 200 " - pdb=" SG CYS W 104 " pdb="ZN ZN W 200 " - pdb=" SG CYS W 117 " Number of angles added : 9 13120 Ramachandran restraints generated. 6560 Oldfield, 0 Emsley, 6560 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 12642 Finding SS restraints... Secondary structure from input PDB file: 245 helices and 65 sheets defined 40.3% alpha, 12.9% beta 870 base pairs and 1331 stacking pairs defined. Time for finding SS restraints: 61.32 Creating SS restraints... Processing helix chain 'B' and resid 79 through 89 Processing helix chain 'B' and resid 120 through 122 No H-bonds generated for 'chain 'B' and resid 120 through 122' Processing helix chain 'B' and resid 244 through 246 No H-bonds generated for 'chain 'B' and resid 244 through 246' Processing helix chain 'B' and resid 310 through 316 removed outlier: 4.025A pdb=" N GLN B 314 " --> pdb=" O ILE B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 327 removed outlier: 3.913A pdb=" N SER B 324 " --> pdb=" O LYS B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 338 Processing helix chain 'B' and resid 378 through 382 removed outlier: 4.486A pdb=" N VAL B 382 " --> pdb=" O ARG B 379 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 33 Processing helix chain 'C' and resid 45 through 53 Processing helix chain 'C' and resid 97 through 102 Processing helix chain 'C' and resid 114 through 118 Processing helix chain 'C' and resid 119 through 129 Processing helix chain 'C' and resid 144 through 148 removed outlier: 3.656A pdb=" N GLY C 147 " --> pdb=" O ASP C 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 160 Processing helix chain 'C' and resid 179 through 184 Processing helix chain 'D' and resid 62 through 66 Processing helix chain 'D' and resid 70 through 86 Processing helix chain 'D' and resid 144 through 163 Processing helix chain 'D' and resid 202 through 215 Processing helix chain 'D' and resid 229 through 237 Processing helix chain 'D' and resid 238 through 241 removed outlier: 5.312A pdb=" N GLN D 241 " --> pdb=" O PRO D 238 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 238 through 241' Processing helix chain 'D' and resid 249 through 251 No H-bonds generated for 'chain 'D' and resid 249 through 251' Processing helix chain 'D' and resid 252 through 259 Processing helix chain 'D' and resid 266 through 276 Processing helix chain 'E' and resid 36 through 40 Processing helix chain 'E' and resid 67 through 76 Processing helix chain 'E' and resid 76 through 86 removed outlier: 3.722A pdb=" N ASP E 80 " --> pdb=" O THR E 76 " (cutoff:3.500A) Processing helix chain 'E' and resid 105 through 109 Processing helix chain 'E' and resid 146 through 151 Processing helix chain 'E' and resid 153 through 168 removed outlier: 3.656A pdb=" N ILE E 157 " --> pdb=" O GLN E 153 " (cutoff:3.500A) Processing helix chain 'E' and resid 198 through 212 Processing helix chain 'E' and resid 212 through 217 Processing helix chain 'E' and resid 241 through 245 Processing helix chain 'E' and resid 246 through 251 Processing helix chain 'E' and resid 272 through 283 removed outlier: 3.512A pdb=" N PHE E 283 " --> pdb=" O LEU E 279 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 115 removed outlier: 3.505A pdb=" N GLY F 101 " --> pdb=" O ARG F 97 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N THR F 102 " --> pdb=" O SER F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 174 through 188 removed outlier: 3.808A pdb=" N PHE F 188 " --> pdb=" O LYS F 184 " (cutoff:3.500A) Processing helix chain 'G' and resid 11 through 17 Processing helix chain 'G' and resid 41 through 48 Processing helix chain 'G' and resid 50 through 53 Processing helix chain 'H' and resid 27 through 41 Processing helix chain 'H' and resid 61 through 65 Processing helix chain 'H' and resid 70 through 75 Processing helix chain 'H' and resid 92 through 99 Processing helix chain 'H' and resid 100 through 113 removed outlier: 3.661A pdb=" N ILE H 104 " --> pdb=" O GLY H 100 " (cutoff:3.500A) Processing helix chain 'H' and resid 118 through 126 removed outlier: 3.506A pdb=" N LEU H 126 " --> pdb=" O ARG H 122 " (cutoff:3.500A) Processing helix chain 'H' and resid 136 through 140 removed outlier: 3.819A pdb=" N ILE H 140 " --> pdb=" O LYS H 137 " (cutoff:3.500A) Processing helix chain 'H' and resid 145 through 149 removed outlier: 4.167A pdb=" N SER H 148 " --> pdb=" O HIS H 145 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N SER H 149 " --> pdb=" O GLU H 146 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 145 through 149' Processing helix chain 'I' and resid 120 through 126 Processing helix chain 'I' and resid 127 through 134 Processing helix chain 'J' and resid 59 through 64 removed outlier: 3.960A pdb=" N GLY J 62 " --> pdb=" O SER J 59 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N LEU J 64 " --> pdb=" O LEU J 61 " (cutoff:3.500A) Processing helix chain 'J' and resid 112 through 117 removed outlier: 3.979A pdb=" N PHE J 117 " --> pdb=" O ILE J 113 " (cutoff:3.500A) Processing helix chain 'J' and resid 135 through 145 Processing helix chain 'J' and resid 156 through 164 Processing helix chain 'J' and resid 196 through 206 Processing helix chain 'J' and resid 216 through 225 Processing helix chain 'J' and resid 225 through 234 removed outlier: 4.063A pdb=" N PHE J 229 " --> pdb=" O ASN J 225 " (cutoff:3.500A) Processing helix chain 'J' and resid 244 through 253 Processing helix chain 'J' and resid 258 through 263 removed outlier: 3.606A pdb=" N GLU J 263 " --> pdb=" O TYR J 259 " (cutoff:3.500A) Processing helix chain 'J' and resid 265 through 277 removed outlier: 3.790A pdb=" N GLN J 269 " --> pdb=" O ASP J 265 " (cutoff:3.500A) Processing helix chain 'K' and resid 87 through 102 removed outlier: 4.035A pdb=" N TYR K 100 " --> pdb=" O ALA K 96 " (cutoff:3.500A) Processing helix chain 'K' and resid 157 through 171 removed outlier: 3.891A pdb=" N LYS K 171 " --> pdb=" O LYS K 167 " (cutoff:3.500A) Processing helix chain 'K' and resid 202 through 210 Processing helix chain 'K' and resid 212 through 223 Processing helix chain 'K' and resid 223 through 230 Processing helix chain 'L' and resid 12 through 31 Processing helix chain 'L' and resid 37 through 60 removed outlier: 3.537A pdb=" N ARG L 45 " --> pdb=" O LYS L 41 " (cutoff:3.500A) Processing helix chain 'L' and resid 62 through 76 Processing helix chain 'L' and resid 85 through 93 Processing helix chain 'L' and resid 94 through 99 Processing helix chain 'L' and resid 142 through 159 removed outlier: 3.509A pdb=" N TRP L 146 " --> pdb=" O ASN L 142 " (cutoff:3.500A) Processing helix chain 'L' and resid 163 through 176 removed outlier: 4.519A pdb=" N PHE L 176 " --> pdb=" O LYS L 172 " (cutoff:3.500A) Processing helix chain 'L' and resid 178 through 197 removed outlier: 3.665A pdb=" N VAL L 192 " --> pdb=" O LEU L 188 " (cutoff:3.500A) Processing helix chain 'L' and resid 202 through 219 Processing helix chain 'M' and resid 39 through 53 Processing helix chain 'M' and resid 56 through 61 removed outlier: 3.939A pdb=" N LEU M 61 " --> pdb=" O VAL M 57 " (cutoff:3.500A) Processing helix chain 'M' and resid 148 through 152 Processing helix chain 'M' and resid 160 through 166 Processing helix chain 'N' and resid 46 through 52 removed outlier: 3.598A pdb=" N SER N 52 " --> pdb=" O PRO N 48 " (cutoff:3.500A) Processing helix chain 'O' and resid 92 through 102 Processing helix chain 'O' and resid 107 through 113 removed outlier: 3.874A pdb=" N LEU O 113 " --> pdb=" O SER O 109 " (cutoff:3.500A) Processing helix chain 'O' and resid 114 through 128 Processing helix chain 'O' and resid 152 through 160 Processing helix chain 'O' and resid 173 through 182 removed outlier: 3.657A pdb=" N LEU O 180 " --> pdb=" O LYS O 176 " (cutoff:3.500A) Processing helix chain 'O' and resid 183 through 185 No H-bonds generated for 'chain 'O' and resid 183 through 185' Processing helix chain 'O' and resid 188 through 199 Processing helix chain 'O' and resid 201 through 222 removed outlier: 4.055A pdb=" N ARG O 205 " --> pdb=" O LYS O 201 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N GLU O 206 " --> pdb=" O LYS O 202 " (cutoff:3.500A) Processing helix chain 'O' and resid 224 through 226 No H-bonds generated for 'chain 'O' and resid 224 through 226' Processing helix chain 'O' and resid 272 through 288 Processing helix chain 'P' and resid 57 through 73 Processing helix chain 'P' and resid 114 through 127 Processing helix chain 'P' and resid 184 through 199 removed outlier: 4.046A pdb=" N ASP P 188 " --> pdb=" O SER P 184 " (cutoff:3.500A) Processing helix chain 'P' and resid 210 through 215 removed outlier: 3.535A pdb=" N ASP P 213 " --> pdb=" O THR P 210 " (cutoff:3.500A) Processing helix chain 'P' and resid 228 through 259 removed outlier: 3.840A pdb=" N GLU P 234 " --> pdb=" O PHE P 230 " (cutoff:3.500A) Processing helix chain 'Q' and resid 5 through 9 Processing helix chain 'Q' and resid 12 through 21 Processing helix chain 'Q' and resid 23 through 25 No H-bonds generated for 'chain 'Q' and resid 23 through 25' Processing helix chain 'Q' and resid 26 through 37 removed outlier: 3.749A pdb=" N SER Q 30 " --> pdb=" O PHE Q 26 " (cutoff:3.500A) Processing helix chain 'Q' and resid 199 through 205 Processing helix chain 'Q' and resid 219 through 221 No H-bonds generated for 'chain 'Q' and resid 219 through 221' Processing helix chain 'Q' and resid 222 through 227 Processing helix chain 'Q' and resid 239 through 247 Processing helix chain 'Q' and resid 254 through 270 removed outlier: 3.648A pdb=" N ARG Q 270 " --> pdb=" O GLU Q 266 " (cutoff:3.500A) Processing helix chain 'Q' and resid 276 through 297 Processing helix chain 'R' and resid 136 through 146 Processing helix chain 'R' and resid 148 through 154 Processing helix chain 'R' and resid 154 through 184 Processing helix chain 'R' and resid 191 through 207 Processing helix chain 'R' and resid 210 through 234 Processing helix chain 'R' and resid 236 through 257 Processing helix chain 'R' and resid 271 through 289 Processing helix chain 'R' and resid 294 through 306 Processing helix chain 'R' and resid 307 through 312 removed outlier: 3.655A pdb=" N ASN R 310 " --> pdb=" O ASP R 307 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU R 312 " --> pdb=" O CYS R 309 " (cutoff:3.500A) Processing helix chain 'R' and resid 313 through 325 Processing helix chain 'S' and resid 24 through 29 Processing helix chain 'S' and resid 66 through 72 removed outlier: 3.617A pdb=" N LYS S 71 " --> pdb=" O GLN S 68 " (cutoff:3.500A) Processing helix chain 'S' and resid 120 through 130 Processing helix chain 'S' and resid 131 through 137 Processing helix chain 'S' and resid 140 through 146 Processing helix chain 'S' and resid 148 through 167 Processing helix chain 'T' and resid 30 through 34 removed outlier: 3.515A pdb=" N ILE T 34 " --> pdb=" O LYS T 31 " (cutoff:3.500A) Processing helix chain 'T' and resid 56 through 60 Processing helix chain 'T' and resid 66 through 72 Processing helix chain 'T' and resid 94 through 100 removed outlier: 3.967A pdb=" N HIS T 100 " --> pdb=" O PRO T 96 " (cutoff:3.500A) Processing helix chain 'T' and resid 102 through 130 Processing helix chain 'T' and resid 136 through 172 Processing helix chain 'T' and resid 172 through 188 removed outlier: 3.547A pdb=" N LYS T 178 " --> pdb=" O SER T 174 " (cutoff:3.500A) Processing helix chain 'T' and resid 196 through 211 Processing helix chain 'T' and resid 223 through 239 Processing helix chain 'U' and resid 16 through 26 Processing helix chain 'U' and resid 40 through 50 removed outlier: 3.698A pdb=" N VAL U 50 " --> pdb=" O SER U 46 " (cutoff:3.500A) Processing helix chain 'U' and resid 64 through 73 Processing helix chain 'W' and resid 79 through 89 Processing helix chain 'W' and resid 117 through 132 Processing helix chain 'W' and resid 141 through 145 removed outlier: 3.655A pdb=" N LEU W 145 " --> pdb=" O GLU W 142 " (cutoff:3.500A) Processing helix chain 'W' and resid 146 through 154 Processing helix chain 'W' and resid 160 through 168 Processing helix chain 'W' and resid 168 through 173 removed outlier: 4.181A pdb=" N TYR W 172 " --> pdb=" O ASP W 168 " (cutoff:3.500A) Processing helix chain 'Y' and resid 69 through 78 Processing helix chain 'Y' and resid 78 through 85 removed outlier: 3.749A pdb=" N SER Y 85 " --> pdb=" O ALA Y 81 " (cutoff:3.500A) Processing helix chain 'Y' and resid 85 through 99 Processing helix chain 'Z' and resid 58 through 65 Processing helix chain 'Z' and resid 87 through 92 Processing helix chain 'Z' and resid 101 through 103 No H-bonds generated for 'chain 'Z' and resid 101 through 103' Processing helix chain 'Z' and resid 104 through 112 Processing helix chain '1' and resid 29 through 33 removed outlier: 3.649A pdb=" N LEU 1 32 " --> pdb=" O PRO 1 29 " (cutoff:3.500A) Processing helix chain '1' and resid 36 through 45 removed outlier: 3.598A pdb=" N LYS 1 40 " --> pdb=" O SER 1 36 " (cutoff:3.500A) Processing helix chain '1' and resid 57 through 64 Processing helix chain '1' and resid 69 through 89 removed outlier: 3.773A pdb=" N ILE 1 73 " --> pdb=" O HIS 1 69 " (cutoff:3.500A) Processing helix chain '1' and resid 98 through 110 Processing helix chain '1' and resid 112 through 121 Processing helix chain '1' and resid 136 through 150 Processing helix chain '1' and resid 150 through 162 Processing helix chain '1' and resid 164 through 169 Processing helix chain '1' and resid 262 through 267 removed outlier: 3.711A pdb=" N PHE 1 266 " --> pdb=" O ASP 1 262 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N HIS 1 267 " --> pdb=" O PRO 1 263 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 262 through 267' Processing helix chain '1' and resid 321 through 330 Processing helix chain '1' and resid 346 through 355 Processing helix chain '2' and resid 36 through 50 removed outlier: 3.529A pdb=" N MET 2 49 " --> pdb=" O GLN 2 45 " (cutoff:3.500A) Processing helix chain '2' and resid 62 through 109 Processing helix chain '2' and resid 109 through 118 Processing helix chain '3' and resid 73 through 76 Processing helix chain '3' and resid 114 through 128 Processing helix chain '4' and resid 34 through 36 No H-bonds generated for 'chain '4' and resid 34 through 36' Processing helix chain '4' and resid 37 through 46 Processing helix chain '4' and resid 47 through 56 Processing helix chain '4' and resid 90 through 104 Processing helix chain '5' and resid 68 through 87 Processing helix chain '5' and resid 88 through 95 Processing helix chain '5' and resid 95 through 105 removed outlier: 3.719A pdb=" N ARG 5 99 " --> pdb=" O SER 5 95 " (cutoff:3.500A) Processing helix chain '5' and resid 112 through 120 Processing helix chain '5' and resid 152 through 175 removed outlier: 3.561A pdb=" N ILE 5 157 " --> pdb=" O HIS 5 153 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THR 5 168 " --> pdb=" O SER 5 164 " (cutoff:3.500A) Processing helix chain '5' and resid 179 through 192 Processing helix chain '5' and resid 192 through 204 Processing helix chain '5' and resid 211 through 219 Processing helix chain '5' and resid 221 through 228 removed outlier: 4.155A pdb=" N THR 5 225 " --> pdb=" O PRO 5 221 " (cutoff:3.500A) Processing helix chain '5' and resid 238 through 240 No H-bonds generated for 'chain '5' and resid 238 through 240' Processing helix chain '5' and resid 247 through 250 removed outlier: 3.530A pdb=" N PHE 5 250 " --> pdb=" O GLY 5 247 " (cutoff:3.500A) No H-bonds generated for 'chain '5' and resid 247 through 250' Processing helix chain '5' and resid 251 through 271 Processing helix chain '5' and resid 277 through 287 Processing helix chain '5' and resid 293 through 296 Processing helix chain '5' and resid 302 through 314 removed outlier: 3.805A pdb=" N GLU 5 306 " --> pdb=" O GLN 5 302 " (cutoff:3.500A) Processing helix chain '5' and resid 354 through 372 Processing helix chain '6' and resid 42 through 60 Processing helix chain '6' and resid 64 through 69 removed outlier: 3.806A pdb=" N TYR 6 68 " --> pdb=" O PRO 6 64 " (cutoff:3.500A) Processing helix chain '6' and resid 73 through 83 Processing helix chain '6' and resid 147 through 152 Processing helix chain '6' and resid 190 through 204 removed outlier: 4.001A pdb=" N LEU 6 202 " --> pdb=" O GLU 6 198 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N SER 6 203 " --> pdb=" O LEU 6 199 " (cutoff:3.500A) Processing helix chain '6' and resid 258 through 265 removed outlier: 4.117A pdb=" N SER 6 263 " --> pdb=" O LYS 6 259 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLU 6 264 " --> pdb=" O GLY 6 260 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N TYR 6 265 " --> pdb=" O GLU 6 261 " (cutoff:3.500A) Processing helix chain '6' and resid 267 through 274 Processing helix chain '7' and resid 51 through 55 removed outlier: 3.539A pdb=" N GLU 7 54 " --> pdb=" O LYS 7 51 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU 7 55 " --> pdb=" O MET 7 52 " (cutoff:3.500A) No H-bonds generated for 'chain '7' and resid 51 through 55' Processing helix chain '7' and resid 83 through 87 Processing helix chain '7' and resid 99 through 111 Processing helix chain '7' and resid 115 through 117 No H-bonds generated for 'chain '7' and resid 115 through 117' Processing helix chain '7' and resid 134 through 144 removed outlier: 3.940A pdb=" N VAL 7 138 " --> pdb=" O ALA 7 134 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N LYS 7 144 " --> pdb=" O ARG 7 140 " (cutoff:3.500A) Processing helix chain '8' and resid 96 through 111 removed outlier: 3.601A pdb=" N GLN 8 102 " --> pdb=" O ARG 8 98 " (cutoff:3.500A) Processing helix chain '8' and resid 126 through 141 removed outlier: 4.153A pdb=" N LEU 8 134 " --> pdb=" O ASP 8 130 " (cutoff:3.500A) Processing helix chain '8' and resid 152 through 168 Processing helix chain '8' and resid 172 through 179 Processing helix chain '8' and resid 181 through 199 removed outlier: 4.237A pdb=" N LEU 8 194 " --> pdb=" O LYS 8 190 " (cutoff:3.500A) Proline residue: 8 195 - end of helix Processing helix chain '8' and resid 215 through 220 removed outlier: 3.662A pdb=" N TYR 8 219 " --> pdb=" O SER 8 216 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA 8 220 " --> pdb=" O ASP 8 217 " (cutoff:3.500A) Processing helix chain '8' and resid 231 through 264 removed outlier: 3.753A pdb=" N LYS 8 236 " --> pdb=" O SER 8 232 " (cutoff:3.500A) Processing helix chain '9' and resid 44 through 49 removed outlier: 4.285A pdb=" N TYR 9 48 " --> pdb=" O ASP 9 44 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU 9 49 " --> pdb=" O PRO 9 45 " (cutoff:3.500A) No H-bonds generated for 'chain '9' and resid 44 through 49' Processing helix chain '9' and resid 64 through 74 Processing helix chain '9' and resid 83 through 92 Processing helix chain '9' and resid 95 through 100 removed outlier: 3.626A pdb=" N HIS 9 98 " --> pdb=" O SER 9 95 " (cutoff:3.500A) Processing helix chain '9' and resid 104 through 126 Processing helix chain '9' and resid 147 through 155 Processing helix chain '9' and resid 155 through 167 Processing helix chain '9' and resid 168 through 172 Processing helix chain '9' and resid 183 through 186 removed outlier: 3.818A pdb=" N ASN 9 186 " --> pdb=" O GLY 9 183 " (cutoff:3.500A) No H-bonds generated for 'chain '9' and resid 183 through 186' Processing helix chain '9' and resid 187 through 207 removed outlier: 3.611A pdb=" N ILE 9 191 " --> pdb=" O GLY 9 187 " (cutoff:3.500A) Processing helix chain '9' and resid 209 through 220 Processing helix chain '9' and resid 228 through 241 Processing helix chain 'a' and resid 40 through 47 removed outlier: 4.271A pdb=" N TYR a 44 " --> pdb=" O ASN a 40 " (cutoff:3.500A) Processing helix chain 'a' and resid 72 through 76 Processing helix chain 'a' and resid 80 through 84 Processing helix chain 'a' and resid 103 through 108 removed outlier: 3.681A pdb=" N VAL a 107 " --> pdb=" O GLY a 103 " (cutoff:3.500A) Processing helix chain 'a' and resid 115 through 129 removed outlier: 3.555A pdb=" N ILE a 119 " --> pdb=" O GLY a 115 " (cutoff:3.500A) Processing helix chain 'a' and resid 134 through 143 Processing helix chain 'a' and resid 145 through 153 Processing helix chain 'a' and resid 156 through 174 Processing helix chain 'a' and resid 175 through 192 removed outlier: 3.618A pdb=" N ARG a 179 " --> pdb=" O LYS a 175 " (cutoff:3.500A) Processing helix chain 'b' and resid 4 through 10 Processing helix chain 'b' and resid 11 through 21 Processing helix chain 'b' and resid 59 through 73 Processing helix chain 'b' and resid 89 through 97 removed outlier: 3.852A pdb=" N LYS b 93 " --> pdb=" O PHE b 89 " (cutoff:3.500A) Processing helix chain 'b' and resid 100 through 105 Processing helix chain 'b' and resid 109 through 114 Processing helix chain 'b' and resid 114 through 128 removed outlier: 3.639A pdb=" N LYS b 118 " --> pdb=" O LYS b 114 " (cutoff:3.500A) Processing helix chain 'b' and resid 129 through 138 Processing helix chain 'b' and resid 138 through 151 removed outlier: 3.608A pdb=" N ALA b 142 " --> pdb=" O GLY b 138 " (cutoff:3.500A) Processing helix chain 'c' and resid 24 through 58 Processing helix chain 'c' and resid 60 through 67 Processing helix chain 'c' and resid 75 through 83 Processing helix chain 'c' and resid 94 through 99 Processing helix chain 'c' and resid 106 through 108 No H-bonds generated for 'chain 'c' and resid 106 through 108' Processing helix chain 'c' and resid 114 through 116 No H-bonds generated for 'chain 'c' and resid 114 through 116' Processing helix chain 'd' and resid 12 through 20 Processing helix chain 'd' and resid 46 through 54 removed outlier: 3.778A pdb=" N VAL d 50 " --> pdb=" O SER d 46 " (cutoff:3.500A) Processing helix chain 'd' and resid 67 through 71 removed outlier: 3.537A pdb=" N TRP d 71 " --> pdb=" O ARG d 68 " (cutoff:3.500A) Processing helix chain 'd' and resid 81 through 101 Processing helix chain 'd' and resid 103 through 109 Processing helix chain 'd' and resid 127 through 148 removed outlier: 3.531A pdb=" N GLN d 131 " --> pdb=" O PRO d 127 " (cutoff:3.500A) Processing helix chain 'd' and resid 180 through 186 Processing helix chain 'd' and resid 202 through 214 Processing sheet with id= A, first strand: chain 'B' and resid 93 through 94 Processing sheet with id= B, first strand: chain 'B' and resid 124 through 126 Processing sheet with id= C, first strand: chain 'B' and resid 191 through 195 removed outlier: 3.692A pdb=" N ARG B 169 " --> pdb=" O LEU B 182 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N LYS B 184 " --> pdb=" O VAL B 167 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N VAL B 167 " --> pdb=" O LYS B 184 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 240 through 242 removed outlier: 6.709A pdb=" N VAL B 302 " --> pdb=" O VAL B 255 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N VAL B 255 " --> pdb=" O VAL B 302 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N THR B 304 " --> pdb=" O HIS B 253 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 240 through 242 removed outlier: 6.709A pdb=" N VAL B 302 " --> pdb=" O VAL B 255 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N VAL B 255 " --> pdb=" O VAL B 302 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N THR B 304 " --> pdb=" O HIS B 253 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ILE B 286 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N LYS B 278 " --> pdb=" O LYS B 284 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N LYS B 284 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 60 through 72 removed outlier: 5.766A pdb=" N LYS C 65 " --> pdb=" O GLU C 86 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N GLU C 86 " --> pdb=" O LYS C 65 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLY C 67 " --> pdb=" O ILE C 84 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N LYS C 249 " --> pdb=" O VAL C 236 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N VAL C 236 " --> pdb=" O LYS C 249 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N THR C 230 " --> pdb=" O SER C 170 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N SER C 170 " --> pdb=" O THR C 230 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N GLN C 232 " --> pdb=" O VAL C 168 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N VAL C 168 " --> pdb=" O GLN C 232 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N VAL C 171 " --> pdb=" O PHE C 259 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N PHE C 259 " --> pdb=" O VAL C 171 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 134 through 142 removed outlier: 6.313A pdb=" N LYS C 134 " --> pdb=" O SER C 112 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N SER C 112 " --> pdb=" O LYS C 134 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N PHE C 104 " --> pdb=" O VAL C 142 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N MET C 94 " --> pdb=" O GLN C 107 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N GLY C 109 " --> pdb=" O VAL C 92 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N VAL C 92 " --> pdb=" O GLY C 109 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N GLY C 111 " --> pdb=" O VAL C 90 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N VAL C 90 " --> pdb=" O GLY C 111 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N VAL C 90 " --> pdb=" O LEU C 155 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 176 through 178 removed outlier: 3.672A pdb=" N GLY C 176 " --> pdb=" O MET C 224 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'D' and resid 56 through 61 removed outlier: 3.728A pdb=" N THR D 56 " --> pdb=" O VAL D 46 " (cutoff:3.500A) removed outlier: 10.091A pdb=" N LEU D 165 " --> pdb=" O LEU D 43 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N THR D 45 " --> pdb=" O LEU D 165 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N VAL D 167 " --> pdb=" O THR D 45 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N LEU D 222 " --> pdb=" O PHE D 263 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N GLU D 265 " --> pdb=" O LEU D 222 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N ILE D 224 " --> pdb=" O GLU D 265 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 172 through 175 removed outlier: 6.162A pdb=" N HIS E 172 " --> pdb=" O ALA E 193 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N ALA E 193 " --> pdb=" O HIS E 172 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ILE E 174 " --> pdb=" O MET E 191 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'F' and resid 31 through 43 removed outlier: 11.525A pdb=" N ASN F 35 " --> pdb=" O VAL F 58 " (cutoff:3.500A) removed outlier: 10.714A pdb=" N VAL F 58 " --> pdb=" O ASN F 35 " (cutoff:3.500A) removed outlier: 10.526A pdb=" N LEU F 37 " --> pdb=" O ILE F 56 " (cutoff:3.500A) removed outlier: 10.700A pdb=" N ILE F 56 " --> pdb=" O LEU F 37 " (cutoff:3.500A) removed outlier: 9.433A pdb=" N MET F 39 " --> pdb=" O GLN F 54 " (cutoff:3.500A) removed outlier: 8.652A pdb=" N GLN F 54 " --> pdb=" O MET F 39 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'F' and resid 73 through 77 Processing sheet with id= M, first strand: chain 'F' and resid 158 through 161 Processing sheet with id= N, first strand: chain 'F' and resid 130 through 134 removed outlier: 4.123A pdb=" N GLN F 150 " --> pdb=" O VAL F 142 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'G' and resid 37 through 40 Processing sheet with id= P, first strand: chain 'H' and resid 16 through 20 removed outlier: 6.305A pdb=" N HIS H 17 " --> pdb=" O VAL H 58 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N THR H 60 " --> pdb=" O HIS H 17 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N VAL H 19 " --> pdb=" O THR H 60 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N VAL H 57 " --> pdb=" O LYS H 127 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'H' and resid 76 through 80 Processing sheet with id= R, first strand: chain 'H' and resid 142 through 143 removed outlier: 5.368A pdb=" N SER 5 321 " --> pdb=" O PHE 5 341 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N PHE 5 341 " --> pdb=" O SER 5 321 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N LEU 5 323 " --> pdb=" O HIS 5 339 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N HIS 5 339 " --> pdb=" O LEU 5 323 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLY 5 348 " --> pdb=" O VAL 5 340 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N SER 5 342 " --> pdb=" O THR 5 346 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N THR 5 346 " --> pdb=" O SER 5 342 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'I' and resid 7 through 10 removed outlier: 5.273A pdb=" N GLN I 17 " --> pdb=" O VAL I 10 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ALA I 16 " --> pdb=" O ALA I 47 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ALA I 47 " --> pdb=" O ALA I 16 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N LEU I 18 " --> pdb=" O GLN I 45 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N VAL I 41 " --> pdb=" O ILE I 22 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N VAL I 24 " --> pdb=" O ARG I 39 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N ARG I 39 " --> pdb=" O VAL I 24 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N HIS I 70 " --> pdb=" O ILE I 99 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ALA I 95 " --> pdb=" O VAL I 74 " (cutoff:3.500A) removed outlier: 8.533A pdb=" N CYS I 96 " --> pdb=" O VAL I 7 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N LYS I 9 " --> pdb=" O CYS I 96 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N LEU I 98 " --> pdb=" O LYS I 9 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'I' and resid 88 through 91 removed outlier: 6.622A pdb=" N SER M 107 " --> pdb=" O ILE M 97 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N ILE M 97 " --> pdb=" O SER M 107 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N LEU M 109 " --> pdb=" O LEU M 95 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N GLN M 113 " --> pdb=" O VAL M 91 " (cutoff:3.500A) removed outlier: 9.730A pdb=" N VAL M 91 " --> pdb=" O GLN M 113 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ARG M 77 " --> pdb=" O LEU M 135 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N LEU M 135 " --> pdb=" O ARG M 77 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N VAL M 79 " --> pdb=" O ILE M 133 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N ILE M 133 " --> pdb=" O VAL M 79 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'I' and resid 117 through 119 removed outlier: 6.425A pdb=" N VAL I 118 " --> pdb=" O ILE I 138 " (cutoff:3.500A) No H-bonds generated for sheet with id= U Processing sheet with id= V, first strand: chain 'J' and resid 131 through 134 removed outlier: 6.162A pdb=" N LYS J 131 " --> pdb=" O LYS J 175 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N LEU J 177 " --> pdb=" O LYS J 131 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N LEU J 133 " --> pdb=" O LEU J 177 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG J 194 " --> pdb=" O VAL J 174 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'J' and resid 154 through 155 removed outlier: 3.680A pdb=" N ALA J 192 " --> pdb=" O THR J 211 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'K' and resid 108 through 111 removed outlier: 6.741A pdb=" N LEU K 76 " --> pdb=" O LEU K 148 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N GLU K 150 " --> pdb=" O TYR K 74 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N TYR K 74 " --> pdb=" O GLU K 150 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'K' and resid 83 through 86 removed outlier: 5.625A pdb=" N PHE K 135 " --> pdb=" O ILE K 121 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N ILE K 121 " --> pdb=" O PHE K 135 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'K' and resid 185 through 186 Processing sheet with id= AA, first strand: chain 'L' and resid 32 through 36 Processing sheet with id= AB, first strand: chain 'L' and resid 232 through 234 removed outlier: 6.231A pdb=" N VAL L 233 " --> pdb=" O VAL M 28 " (cutoff:3.500A) No H-bonds generated for sheet with id= AB Processing sheet with id= AC, first strand: chain 'N' and resid 64 through 68 removed outlier: 3.774A pdb=" N THR N 96 " --> pdb=" O ILE N 58 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N LYS N 60 " --> pdb=" O VAL N 94 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N VAL N 94 " --> pdb=" O LYS N 60 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'U' and resid 79 through 81 removed outlier: 6.149A pdb=" N TYR N 114 " --> pdb=" O MET N 160 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N MET N 160 " --> pdb=" O TYR N 114 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N LEU N 116 " --> pdb=" O LEU N 158 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N LEU N 158 " --> pdb=" O LEU N 116 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N ALA N 118 " --> pdb=" O SER N 156 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N SER N 156 " --> pdb=" O ALA N 118 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N VAL N 120 " --> pdb=" O ARG N 154 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ARG N 154 " --> pdb=" O VAL N 120 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'N' and resid 129 through 133 Processing sheet with id= AF, first strand: chain 'O' and resid 138 through 139 removed outlier: 4.710A pdb=" N ARG O 146 " --> pdb=" O ILE 5 245 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'O' and resid 163 through 166 removed outlier: 6.275A pdb=" N ARG O 268 " --> pdb=" O ILE O 230 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N ILE O 230 " --> pdb=" O ARG O 268 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'O' and resid 242 through 247 removed outlier: 4.115A pdb=" N ARG O 242 " --> pdb=" O HIS O 258 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'P' and resid 82 through 84 Processing sheet with id= AJ, first strand: chain 'P' and resid 92 through 94 removed outlier: 4.661A pdb=" N LYS P 106 " --> pdb=" O LEU P 94 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N LYS P 158 " --> pdb=" O VAL P 109 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE P 157 " --> pdb=" O LEU P 138 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ASN P 132 " --> pdb=" O GLU P 163 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'P' and resid 142 through 143 removed outlier: 3.545A pdb=" N PHE P 152 " --> pdb=" O ASN P 143 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'Q' and resid 126 through 127 Processing sheet with id= AM, first strand: chain 'Q' and resid 101 through 105 Processing sheet with id= AN, first strand: chain 'Q' and resid 159 through 161 Processing sheet with id= AO, first strand: chain 'Q' and resid 172 through 173 removed outlier: 4.002A pdb=" N ARG Q 172 " --> pdb=" O ILE Q 182 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'Q' and resid 197 through 198 Processing sheet with id= AQ, first strand: chain 'R' and resid 48 through 49 removed outlier: 6.627A pdb=" N ILE R 85 " --> pdb=" O ILE R 63 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'R' and resid 56 through 57 Processing sheet with id= AS, first strand: chain 'R' and resid 258 through 260 Processing sheet with id= AT, first strand: chain 'R' and resid 347 through 349 Processing sheet with id= AU, first strand: chain 'S' and resid 80 through 84 Processing sheet with id= AV, first strand: chain 'S' and resid 100 through 107 removed outlier: 3.542A pdb=" N ARG S 112 " --> pdb=" O SER S 107 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'U' and resid 34 through 38 Processing sheet with id= AX, first strand: chain 'V' and resid 56 through 61 Processing sheet with id= AY, first strand: chain 'W' and resid 101 through 103 Processing sheet with id= AZ, first strand: chain 'X' and resid 22 through 28 Processing sheet with id= BA, first strand: chain 'Z' and resid 66 through 68 Processing sheet with id= BB, first strand: chain '0' and resid 57 through 59 removed outlier: 4.435A pdb=" N VAL 0 78 " --> pdb=" O GLN 0 92 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain '1' and resid 177 through 181 removed outlier: 4.061A pdb=" N PHE 1 209 " --> pdb=" O ILE 1 261 " (cutoff:3.500A) Processing sheet with id= BD, first strand: chain '1' and resid 271 through 273 removed outlier: 6.440A pdb=" N GLY 1 248 " --> pdb=" O ILE 1 272 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N PHE 1 241 " --> pdb=" O PRO 1 234 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N THR 1 243 " --> pdb=" O ASP 1 232 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N ASP 1 232 " --> pdb=" O THR 1 243 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N LEU 1 245 " --> pdb=" O ASN 1 230 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ASN 1 230 " --> pdb=" O LEU 1 245 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N TYR 1 224 " --> pdb=" O ASN 1 251 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N ARG 1 288 " --> pdb=" O PRO 1 231 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ARG 1 295 " --> pdb=" O ALA 1 333 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N ALA 1 333 " --> pdb=" O ARG 1 295 " (cutoff:3.500A) Processing sheet with id= BE, first strand: chain '3' and resid 63 through 64 Processing sheet with id= BF, first strand: chain '3' and resid 102 through 103 removed outlier: 6.600A pdb=" N LYS 3 102 " --> pdb=" O LYS 3 143 " (cutoff:3.500A) No H-bonds generated for sheet with id= BF Processing sheet with id= BG, first strand: chain '4' and resid 3 through 5 Processing sheet with id= BH, first strand: chain '4' and resid 81 through 85 removed outlier: 6.210A pdb=" N PHE 4 61 " --> pdb=" O TYR 8 225 " (cutoff:3.500A) Processing sheet with id= BI, first strand: chain '6' and resid 209 through 211 removed outlier: 6.576A pdb=" N GLY 6 28 " --> pdb=" O VAL 6 232 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N SER 6 234 " --> pdb=" O GLY 6 28 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N LEU 6 30 " --> pdb=" O SER 6 234 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N ILE 6 236 " --> pdb=" O LEU 6 30 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N SER 6 32 " --> pdb=" O ILE 6 236 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N LEU 6 31 " --> pdb=" O LEU 6 168 " (cutoff:3.500A) Processing sheet with id= BJ, first strand: chain '7' and resid 66 through 68 Processing sheet with id= BK, first strand: chain '7' and resid 78 through 82 Processing sheet with id= BL, first strand: chain 'c' and resid 100 through 102 Processing sheet with id= BM, first strand: chain 'd' and resid 37 through 40 removed outlier: 6.378A pdb=" N VAL d 26 " --> pdb=" O VAL d 76 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N VAL d 76 " --> pdb=" O VAL d 26 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ILE d 28 " --> pdb=" O MET d 74 " (cutoff:3.500A) 2172 hydrogen bonds defined for protein. 6159 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1920 hydrogen bonds 3282 hydrogen bond angles 0 basepair planarities 870 basepair parallelities 1331 stacking parallelities Total time for adding SS restraints: 152.31 Time building geometry restraints manager: 118.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.65 - 1.11: 83751 1.11 - 1.58: 113654 1.58 - 2.04: 5697 2.04 - 2.51: 0 2.51 - 2.97: 3 Bond restraints: 203105 Sorted by residual: bond pdb=" C ASP 3 138 " pdb=" N SER 3 140 " ideal model delta sigma weight residual 1.332 2.970 -1.637 1.40e-02 5.10e+03 1.37e+04 bond pdb=" C GLU F 134 " pdb=" N GLY F 137 " ideal model delta sigma weight residual 1.331 2.852 -1.521 1.46e-02 4.69e+03 1.09e+04 bond pdb=" C VAL 6 219 " pdb=" N PHE 6 230 " ideal model delta sigma weight residual 1.331 2.947 -1.616 1.65e-02 3.67e+03 9.59e+03 bond pdb=" O2' A A 909 " pdb="HO2' A A 909 " ideal model delta sigma weight residual 0.840 1.220 -0.380 2.00e-02 2.50e+03 3.62e+02 bond pdb=" CB GLU F 79 " pdb=" HB3 GLU F 79 " ideal model delta sigma weight residual 0.970 0.647 0.323 2.00e-02 2.50e+03 2.61e+02 ... (remaining 203100 not shown) Histogram of bond angle deviations from ideal: 18.46 - 48.31: 2 48.31 - 78.17: 7 78.17 - 108.02: 50252 108.02 - 137.87: 315455 137.87 - 167.72: 3 Bond angle restraints: 365719 Sorted by residual: angle pdb=" O ASP 3 138 " pdb=" C ASP 3 138 " pdb=" N SER 3 140 " ideal model delta sigma weight residual 122.46 70.02 52.44 1.19e+00 7.06e-01 1.94e+03 angle pdb=" O VAL 6 219 " pdb=" C VAL 6 219 " pdb=" N PHE 6 230 " ideal model delta sigma weight residual 122.57 71.11 51.46 1.25e+00 6.40e-01 1.70e+03 angle pdb=" O GLU F 134 " pdb=" C GLU F 134 " pdb=" N GLY F 137 " ideal model delta sigma weight residual 123.27 75.02 48.25 1.18e+00 7.18e-01 1.67e+03 angle pdb=" CA GLU F 134 " pdb=" C GLU F 134 " pdb=" N GLY F 137 " ideal model delta sigma weight residual 116.37 163.11 -46.74 1.19e+00 7.06e-01 1.54e+03 angle pdb=" CA VAL 6 219 " pdb=" C VAL 6 219 " pdb=" N PHE 6 230 " ideal model delta sigma weight residual 116.60 167.72 -51.12 1.45e+00 4.76e-01 1.24e+03 ... (remaining 365714 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.95: 74189 35.95 - 71.91: 6042 71.91 - 107.86: 249 107.86 - 143.82: 57 143.82 - 179.77: 84 Dihedral angle restraints: 80621 sinusoidal: 57770 harmonic: 22851 Sorted by residual: dihedral pdb=" CA GLU F 134 " pdb=" C GLU F 134 " pdb=" N GLY F 137 " pdb=" CA GLY F 137 " ideal model delta harmonic sigma weight residual 180.00 -90.39 -89.61 0 5.00e+00 4.00e-02 3.21e+02 dihedral pdb=" CA VAL 6 219 " pdb=" C VAL 6 219 " pdb=" N PHE 6 230 " pdb=" CA PHE 6 230 " ideal model delta harmonic sigma weight residual 180.00 99.01 80.99 0 5.00e+00 4.00e-02 2.62e+02 dihedral pdb=" C5' A A 746 " pdb=" C4' A A 746 " pdb=" C3' A A 746 " pdb=" O3' A A 746 " ideal model delta sinusoidal sigma weight residual 147.00 69.54 77.46 1 8.00e+00 1.56e-02 1.17e+02 ... (remaining 80618 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.868: 21692 0.868 - 1.736: 1 1.736 - 2.604: 0 2.604 - 3.472: 0 3.472 - 4.340: 1 Chirality restraints: 21694 Sorted by residual: chirality pdb=" C1' G A1665 " pdb=" O4' G A1665 " pdb=" C2' G A1665 " pdb=" N9 G A1665 " both_signs ideal model delta sigma weight residual False 2.46 -1.88 4.34 2.00e-01 2.50e+01 4.71e+02 chirality pdb=" C4' G e 1 " pdb=" C5' G e 1 " pdb=" O4' G e 1 " pdb=" C3' G e 1 " both_signs ideal model delta sigma weight residual False -2.50 -1.47 -1.03 2.00e-01 2.50e+01 2.64e+01 chirality pdb=" C3' G A1892 " pdb=" C4' G A1892 " pdb=" O3' G A1892 " pdb=" C2' G A1892 " both_signs ideal model delta sigma weight residual False -2.74 -2.07 -0.67 2.00e-01 2.50e+01 1.13e+01 ... (remaining 21691 not shown) Planarity restraints: 20103 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN R 261 " -0.302 2.00e-02 2.50e+03 4.28e-01 2.74e+03 pdb=" CG ASN R 261 " 0.028 2.00e-02 2.50e+03 pdb=" OD1 ASN R 261 " 0.292 2.00e-02 2.50e+03 pdb=" ND2 ASN R 261 " 0.001 2.00e-02 2.50e+03 pdb="HD21 ASN R 261 " -0.687 2.00e-02 2.50e+03 pdb="HD22 ASN R 261 " 0.669 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN 0 85 " 0.315 2.00e-02 2.50e+03 4.07e-01 2.49e+03 pdb=" CG ASN 0 85 " -0.018 2.00e-02 2.50e+03 pdb=" OD1 ASN 0 85 " -0.310 2.00e-02 2.50e+03 pdb=" ND2 ASN 0 85 " 0.000 2.00e-02 2.50e+03 pdb="HD21 ASN 0 85 " 0.639 2.00e-02 2.50e+03 pdb="HD22 ASN 0 85 " -0.627 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN L 116 " 0.318 2.00e-02 2.50e+03 4.04e-01 2.45e+03 pdb=" CG ASN L 116 " -0.024 2.00e-02 2.50e+03 pdb=" OD1 ASN L 116 " -0.305 2.00e-02 2.50e+03 pdb=" ND2 ASN L 116 " 0.000 2.00e-02 2.50e+03 pdb="HD21 ASN L 116 " 0.632 2.00e-02 2.50e+03 pdb="HD22 ASN L 116 " -0.622 2.00e-02 2.50e+03 ... (remaining 20100 not shown) Histogram of nonbonded interaction distances: 0.65 - 1.44: 142 1.44 - 2.23: 16353 2.23 - 3.02: 482689 3.02 - 3.81: 849091 3.81 - 4.60: 1336029 Warning: very small nonbonded interaction distances. Nonbonded interactions: 2684304 Sorted by model distance: nonbonded pdb="HO2' A A 504 " pdb="HO2' U A 566 " model vdw 0.645 2.100 nonbonded pdb="HO2' C A2959 " pdb="HO2' U A3167 " model vdw 0.669 2.100 nonbonded pdb="HO2' C A1899 " pdb="HO2' U A2954 " model vdw 0.716 2.100 nonbonded pdb="HO2' C A 351 " pdb="HO2' U A1773 " model vdw 0.726 2.100 nonbonded pdb="HO2' U A2441 " pdb="HO2' C A2641 " model vdw 0.793 2.100 ... (remaining 2684299 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 9 Type Number sf(0) Gaussians Zn 2 6.06 5 P 2725 5.49 5 Mg 110 5.21 5 S 167 5.16 5 Na 1 4.78 5 C 60000 2.51 5 N 20077 2.21 5 O 28237 1.98 5 H 83818 0.53 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.98 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: 1.610 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: 1.520 Extract box with map and model: 19.780 Check model and map are aligned: 1.880 Convert atoms to be neutral: 1.090 Process input model: 583.550 Find NCS groups from input model: 2.730 Set up NCS constraints: 0.340 Set refine NCS operators: 0.000 Set scattering table: 0.040 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:2.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 614.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 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 : 0.010 1.637 119287 Z= 0.600 Angle : 1.185 52.435 174283 Z= 0.837 Chirality : 0.096 4.340 21694 Planarity : 0.006 0.248 12032 Dihedral : 18.545 179.770 53326 Min Nonbonded Distance : 0.862 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 1.55 % Allowed : 6.42 % Favored : 92.03 % Rotamer Outliers : 10.99 % Cbeta Deviations : 0.21 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.84 % 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: -1.19 (0.09), residues: 6560 helix: 1.12 (0.08), residues: 2365 sheet: -1.80 (0.16), residues: 765 loop : -2.01 (0.09), residues: 3430 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13120 Ramachandran restraints generated. 6560 Oldfield, 0 Emsley, 6560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13120 Ramachandran restraints generated. 6560 Oldfield, 0 Emsley, 6560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 79 is missing expected H atoms. Skipping. Residue ILE 80 is missing expected H atoms. Skipping. Residue LYS 81 is missing expected H atoms. Skipping. Residue LYS 85 is missing expected H atoms. Skipping. Residue LEU 86 is missing expected H atoms. Skipping. Residue LYS 88 is missing expected H atoms. Skipping. Residue LEU 230 is missing expected H atoms. Skipping. Residue LYS 233 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 244 is missing expected H atoms. Skipping. Residue MET 39 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue THR 48 is missing expected H atoms. Skipping. Residue LYS 62 is missing expected H atoms. Skipping. Residue LYS 77 is missing expected H atoms. Skipping. Residue LEU 133 is missing expected H atoms. Skipping. Residue LYS 197 is missing expected H atoms. Skipping. Residue LYS 207 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue LYS 211 is missing expected H atoms. Skipping. Residue VAL 58 is missing expected H atoms. Skipping. Residue THR 137 is missing expected H atoms. Skipping. Residue ILE 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue ILE 88 is missing expected H atoms. Skipping. Residue LYS 139 is missing expected H atoms. Skipping. Residue VAL 49 is missing expected H atoms. Skipping. Residue LYS 52 is missing expected H atoms. Skipping. Residue THR 53 is missing expected H atoms. Skipping. Residue LYS 56 is missing expected H atoms. Skipping. Residue LYS 59 is missing expected H atoms. Skipping. Residue THR 116 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue THR 148 is missing expected H atoms. Skipping. Residue SER 155 is missing expected H atoms. Skipping. Residue LYS 167 is missing expected H atoms. Skipping. Residue LYS 234 is missing expected H atoms. Skipping. Residue THR 237 is missing expected H atoms. Skipping. Residue LEU 238 is missing expected H atoms. Skipping. Residue THR 239 is missing expected H atoms. Skipping. Residue LYS 241 is missing expected H atoms. Skipping. Residue ILE 243 is missing expected H atoms. Skipping. Residue LYS 245 is missing expected H atoms. Skipping. Residue LYS 274 is missing expected H atoms. Skipping. Residue LYS 185 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue LYS 281 is missing expected H atoms. Skipping. Residue LEU 283 is missing expected H atoms. Skipping. Residue LYS 288 is missing expected H atoms. Skipping. Residue LEU 292 is missing expected H atoms. Skipping. Residue THR 294 is missing expected H atoms. Skipping. Residue LYS 295 is missing expected H atoms. Skipping. Residue LYS 296 is missing expected H atoms. Skipping. Residue LYS 298 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue LYS 306 is missing expected H atoms. Skipping. Residue LYS 326 is missing expected H atoms. Skipping. Residue TYR 352 is missing expected H atoms. Skipping. Residue THR 353 is missing expected H atoms. Skipping. Residue LYS 354 is missing expected H atoms. Skipping. Residue SER 363 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue MET 48 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 18 is missing expected H atoms. Skipping. Residue THR 20 is missing expected H atoms. Skipping. Residue LYS 21 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue LEU 183 is missing expected H atoms. Skipping. Residue VAL 198 is missing expected H atoms. Skipping. Residue SER 200 is missing expected H atoms. Skipping. Residue MET 201 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue ILE 209 is missing expected H atoms. Skipping. Residue LEU 232 is missing expected H atoms. Skipping. Residue LYS 87 is missing expected H atoms. Skipping. Residue LYS 129 is missing expected H atoms. Skipping. Residue LYS 221 is missing expected H atoms. Skipping. Residue LYS 313 is missing expected H atoms. Skipping. Residue LEU 112 is missing expected H atoms. Skipping. Residue LYS 123 is missing expected H atoms. Skipping. Residue THR 139 is missing expected H atoms. Skipping. Residue THR 137 is missing expected H atoms. Skipping. Residue SER 140 is missing expected H atoms. Skipping. Residue LEU 65 is missing expected H atoms. Skipping. Residue SER 68 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 126 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Residue LYS 218 is missing expected H atoms. Skipping. Residue LYS 274 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue LYS 38 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Residue THR 73 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 90 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 171 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue LYS 200 is missing expected H atoms. Skipping. Residue LEU 201 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue THR 258 is missing expected H atoms. Skipping. Residue LYS 259 is missing expected H atoms. Skipping. Residue LYS 268 is missing expected H atoms. Skipping. Residue LEU 278 is missing expected H atoms. Skipping. Residue LYS 63 is missing expected H atoms. Skipping. Residue LEU 86 is missing expected H atoms. Skipping. Residue LYS 100 is missing expected H atoms. Skipping. Residue LYS 106 is missing expected H atoms. Skipping. Residue LYS 122 is missing expected H atoms. Skipping. Residue LYS 139 is missing expected H atoms. Skipping. Residue LYS 143 is missing expected H atoms. Skipping. Residue VAL 29 is missing expected H atoms. Skipping. Residue LYS 63 is missing expected H atoms. Skipping. Residue LYS 68 is missing expected H atoms. Skipping. Residue SER 71 is missing expected H atoms. Skipping. Residue LYS 77 is missing expected H atoms. Skipping. Residue LYS 94 is missing expected H atoms. Skipping. Residue LYS 148 is missing expected H atoms. Skipping. Residue LYS 151 is missing expected H atoms. Skipping. Residue LYS 181 is missing expected H atoms. Skipping. Residue LYS 214 is missing expected H atoms. Skipping. Residue LEU 221 is missing expected H atoms. Skipping. Residue LYS 223 is missing expected H atoms. Skipping. Residue LEU 229 is missing expected H atoms. Skipping. Residue VAL 237 is missing expected H atoms. Skipping. Residue SER 239 is missing expected H atoms. Skipping. Residue LYS 154 is missing expected H atoms. Skipping. Residue LYS 18 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Evaluate side-chains 2393 residues out of total 5967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 621 poor density : 1772 time to evaluate : 8.314 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 outliers start: 621 outliers final: 180 residues processed: 2141 average time/residue: 2.3373 time to fit residues: 8081.9104 Evaluate side-chains 1366 residues out of total 5967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 180 poor density : 1186 time to evaluate : 7.454 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: 180 outliers final: 29 residues processed: 180 average time/residue: 2.1080 time to fit residues: 647.6007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 923 random chunks: chunk 779 optimal weight: 0.8980 chunk 699 optimal weight: 0.9990 chunk 388 optimal weight: 1.9990 chunk 238 optimal weight: 0.8980 chunk 471 optimal weight: 0.7980 chunk 373 optimal weight: 1.9990 chunk 723 optimal weight: 0.9990 chunk 279 optimal weight: 0.8980 chunk 439 optimal weight: 0.7980 chunk 538 optimal weight: 0.8980 chunk 838 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 378 ASN D 137 ASN E 164 GLN E 165 GLN E 204 GLN F 54 GLN H 74 GLN H 121 GLN ** I 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 100 ASN J 185 ASN K 95 ASN L 116 ASN L 154 ASN L 163 ASN M 43 GLN N 138 ASN P 156 GLN Q 21 ASN R 145 ASN R 255 ASN ** R 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 268 GLN S 23 GLN S 84 ASN T 45 ASN ** V 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 81 ASN 0 90 GLN 1 122 ASN 1 238 ASN ** 1 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 94 GLN 4 29 GLN 5 106 GLN 8 135 GLN 8 235 GLN 9 74 GLN 9 118 GLN b 84 ASN d 36 GLN d 179 ASN Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.2578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.133 119287 Z= 0.177 Angle : 0.646 14.517 174283 Z= 0.341 Chirality : 0.048 4.141 21694 Planarity : 0.005 0.109 12032 Dihedral : 16.825 179.734 40024 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.41 % Allowed : 4.65 % Favored : 94.94 % Rotamer Outliers : 3.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.84 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.10), residues: 6566 helix: 2.88 (0.11), residues: 2384 sheet: -1.41 (0.17), residues: 777 loop : -1.57 (0.10), residues: 3405 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13132 Ramachandran restraints generated. 6566 Oldfield, 0 Emsley, 6566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13132 Ramachandran restraints generated. 6566 Oldfield, 0 Emsley, 6566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 79 is missing expected H atoms. Skipping. Residue ILE 80 is missing expected H atoms. Skipping. Residue LYS 81 is missing expected H atoms. Skipping. Residue LYS 85 is missing expected H atoms. Skipping. Residue LEU 86 is missing expected H atoms. Skipping. Residue LYS 88 is missing expected H atoms. Skipping. Residue LEU 230 is missing expected H atoms. Skipping. Residue LYS 233 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 244 is missing expected H atoms. Skipping. Residue MET 39 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue THR 48 is missing expected H atoms. Skipping. Residue LYS 62 is missing expected H atoms. Skipping. Residue LYS 77 is missing expected H atoms. Skipping. Residue LEU 133 is missing expected H atoms. Skipping. Residue LYS 197 is missing expected H atoms. Skipping. Residue LYS 207 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue LYS 211 is missing expected H atoms. Skipping. Residue VAL 58 is missing expected H atoms. Skipping. Residue THR 137 is missing expected H atoms. Skipping. Residue ILE 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue ILE 88 is missing expected H atoms. Skipping. Residue LYS 139 is missing expected H atoms. Skipping. Residue VAL 49 is missing expected H atoms. Skipping. Residue LYS 52 is missing expected H atoms. Skipping. Residue THR 53 is missing expected H atoms. Skipping. Residue LYS 56 is missing expected H atoms. Skipping. Residue LYS 59 is missing expected H atoms. Skipping. Residue THR 116 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue THR 148 is missing expected H atoms. Skipping. Residue SER 155 is missing expected H atoms. Skipping. Residue LYS 167 is missing expected H atoms. Skipping. Residue LYS 234 is missing expected H atoms. Skipping. Residue THR 237 is missing expected H atoms. Skipping. Residue LEU 238 is missing expected H atoms. Skipping. Residue THR 239 is missing expected H atoms. Skipping. Residue LYS 241 is missing expected H atoms. Skipping. Residue ILE 243 is missing expected H atoms. Skipping. Residue LYS 245 is missing expected H atoms. Skipping. Residue LYS 274 is missing expected H atoms. Skipping. Residue LYS 185 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue LYS 281 is missing expected H atoms. Skipping. Residue LEU 283 is missing expected H atoms. Skipping. Residue LYS 288 is missing expected H atoms. Skipping. Residue LEU 292 is missing expected H atoms. Skipping. Residue THR 294 is missing expected H atoms. Skipping. Residue LYS 295 is missing expected H atoms. Skipping. Residue LYS 296 is missing expected H atoms. Skipping. Residue LYS 298 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue LYS 306 is missing expected H atoms. Skipping. Residue LYS 326 is missing expected H atoms. Skipping. Residue TYR 352 is missing expected H atoms. Skipping. Residue THR 353 is missing expected H atoms. Skipping. Residue LYS 354 is missing expected H atoms. Skipping. Residue SER 363 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue MET 48 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 18 is missing expected H atoms. Skipping. Residue THR 20 is missing expected H atoms. Skipping. Residue LYS 21 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue LEU 183 is missing expected H atoms. Skipping. Residue VAL 198 is missing expected H atoms. Skipping. Residue SER 200 is missing expected H atoms. Skipping. Residue MET 201 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue ILE 209 is missing expected H atoms. Skipping. Residue LEU 232 is missing expected H atoms. Skipping. Residue LYS 87 is missing expected H atoms. Skipping. Residue LYS 129 is missing expected H atoms. Skipping. Residue LYS 221 is missing expected H atoms. Skipping. Residue LYS 313 is missing expected H atoms. Skipping. Residue LEU 112 is missing expected H atoms. Skipping. Residue LYS 123 is missing expected H atoms. Skipping. Residue THR 139 is missing expected H atoms. Skipping. Residue THR 137 is missing expected H atoms. Skipping. Residue SER 140 is missing expected H atoms. Skipping. Residue LEU 65 is missing expected H atoms. Skipping. Residue SER 68 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 126 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Residue LYS 218 is missing expected H atoms. Skipping. Residue LYS 274 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue LYS 38 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Residue THR 73 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 90 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 171 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue LYS 200 is missing expected H atoms. Skipping. Residue LEU 201 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue THR 258 is missing expected H atoms. Skipping. Residue LYS 259 is missing expected H atoms. Skipping. Residue LYS 268 is missing expected H atoms. Skipping. Residue LEU 278 is missing expected H atoms. Skipping. Residue LYS 63 is missing expected H atoms. Skipping. Residue LEU 86 is missing expected H atoms. Skipping. Residue LYS 100 is missing expected H atoms. Skipping. Residue LYS 106 is missing expected H atoms. Skipping. Residue LYS 122 is missing expected H atoms. Skipping. Residue LYS 139 is missing expected H atoms. Skipping. Residue LYS 143 is missing expected H atoms. Skipping. Residue VAL 29 is missing expected H atoms. Skipping. Residue LYS 63 is missing expected H atoms. Skipping. Residue LYS 68 is missing expected H atoms. Skipping. Residue SER 71 is missing expected H atoms. Skipping. Residue LYS 77 is missing expected H atoms. Skipping. Residue LYS 94 is missing expected H atoms. Skipping. Residue LYS 148 is missing expected H atoms. Skipping. Residue LYS 151 is missing expected H atoms. Skipping. Residue LYS 181 is missing expected H atoms. Skipping. Residue LYS 214 is missing expected H atoms. Skipping. Residue LEU 221 is missing expected H atoms. Skipping. Residue LYS 223 is missing expected H atoms. Skipping. Residue LEU 229 is missing expected H atoms. Skipping. Residue VAL 237 is missing expected H atoms. Skipping. Residue SER 239 is missing expected H atoms. Skipping. Residue LYS 154 is missing expected H atoms. Skipping. Residue LYS 18 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Evaluate side-chains 1513 residues out of total 5967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 189 poor density : 1324 time to evaluate : 8.372 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 outliers start: 189 outliers final: 102 residues processed: 1447 average time/residue: 2.1434 time to fit residues: 5088.8594 Evaluate side-chains 1260 residues out of total 5967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 1158 time to evaluate : 8.646 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 102 outliers final: 19 residues processed: 102 average time/residue: 1.9280 time to fit residues: 353.5977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 923 random chunks: chunk 465 optimal weight: 3.9990 chunk 260 optimal weight: 4.9990 chunk 697 optimal weight: 6.9990 chunk 570 optimal weight: 1.9990 chunk 231 optimal weight: 5.9990 chunk 839 optimal weight: 5.9990 chunk 907 optimal weight: 3.9990 chunk 747 optimal weight: 0.3980 chunk 832 optimal weight: 6.9990 chunk 286 optimal weight: 2.9990 chunk 673 optimal weight: 0.0980 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 376 ASN ** D 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 55 ASN G 51 ASN H 74 GLN ** I 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 158 ASN ** K 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 68 GLN 1 122 ASN 3 38 ASN ** 7 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 128 GLN ** c 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 179 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.3264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.140 119287 Z= 0.254 Angle : 0.616 15.757 174283 Z= 0.322 Chirality : 0.048 4.114 21694 Planarity : 0.005 0.155 12032 Dihedral : 16.362 179.858 40024 Min Nonbonded Distance : 1.768 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.35 % Allowed : 5.27 % Favored : 94.38 % Rotamer Outliers : 2.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.84 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.11), residues: 6566 helix: 2.83 (0.11), residues: 2386 sheet: -1.25 (0.17), residues: 783 loop : -1.26 (0.10), residues: 3397 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13132 Ramachandran restraints generated. 6566 Oldfield, 0 Emsley, 6566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13132 Ramachandran restraints generated. 6566 Oldfield, 0 Emsley, 6566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 79 is missing expected H atoms. Skipping. Residue ILE 80 is missing expected H atoms. Skipping. Residue LYS 81 is missing expected H atoms. Skipping. Residue LYS 85 is missing expected H atoms. Skipping. Residue LEU 86 is missing expected H atoms. Skipping. Residue LYS 88 is missing expected H atoms. Skipping. Residue LEU 230 is missing expected H atoms. Skipping. Residue LYS 233 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 244 is missing expected H atoms. Skipping. Residue MET 39 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue THR 48 is missing expected H atoms. Skipping. Residue LYS 62 is missing expected H atoms. Skipping. Residue LYS 77 is missing expected H atoms. Skipping. Residue LEU 133 is missing expected H atoms. Skipping. Residue LYS 197 is missing expected H atoms. Skipping. Residue LYS 207 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue LYS 211 is missing expected H atoms. Skipping. Residue VAL 58 is missing expected H atoms. Skipping. Residue THR 137 is missing expected H atoms. Skipping. Residue ILE 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue ILE 88 is missing expected H atoms. Skipping. Residue LYS 139 is missing expected H atoms. Skipping. Residue VAL 49 is missing expected H atoms. Skipping. Residue LYS 52 is missing expected H atoms. Skipping. Residue THR 53 is missing expected H atoms. Skipping. Residue LYS 56 is missing expected H atoms. Skipping. Residue LYS 59 is missing expected H atoms. Skipping. Residue THR 116 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue THR 148 is missing expected H atoms. Skipping. Residue SER 155 is missing expected H atoms. Skipping. Residue LYS 167 is missing expected H atoms. Skipping. Residue LYS 234 is missing expected H atoms. Skipping. Residue THR 237 is missing expected H atoms. Skipping. Residue LEU 238 is missing expected H atoms. Skipping. Residue THR 239 is missing expected H atoms. Skipping. Residue LYS 241 is missing expected H atoms. Skipping. Residue ILE 243 is missing expected H atoms. Skipping. Residue LYS 245 is missing expected H atoms. Skipping. Residue LYS 274 is missing expected H atoms. Skipping. Residue LYS 185 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue LYS 281 is missing expected H atoms. Skipping. Residue LEU 283 is missing expected H atoms. Skipping. Residue LYS 288 is missing expected H atoms. Skipping. Residue LEU 292 is missing expected H atoms. Skipping. Residue THR 294 is missing expected H atoms. Skipping. Residue LYS 295 is missing expected H atoms. Skipping. Residue LYS 296 is missing expected H atoms. Skipping. Residue LYS 298 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue LYS 306 is missing expected H atoms. Skipping. Residue LYS 326 is missing expected H atoms. Skipping. Residue TYR 352 is missing expected H atoms. Skipping. Residue THR 353 is missing expected H atoms. Skipping. Residue LYS 354 is missing expected H atoms. Skipping. Residue SER 363 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue MET 48 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 18 is missing expected H atoms. Skipping. Residue THR 20 is missing expected H atoms. Skipping. Residue LYS 21 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue LEU 183 is missing expected H atoms. Skipping. Residue VAL 198 is missing expected H atoms. Skipping. Residue SER 200 is missing expected H atoms. Skipping. Residue MET 201 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue ILE 209 is missing expected H atoms. Skipping. Residue LEU 232 is missing expected H atoms. Skipping. Residue LYS 87 is missing expected H atoms. Skipping. Residue LYS 129 is missing expected H atoms. Skipping. Residue LYS 221 is missing expected H atoms. Skipping. Residue LYS 313 is missing expected H atoms. Skipping. Residue LEU 112 is missing expected H atoms. Skipping. Residue LYS 123 is missing expected H atoms. Skipping. Residue THR 139 is missing expected H atoms. Skipping. Residue THR 137 is missing expected H atoms. Skipping. Residue SER 140 is missing expected H atoms. Skipping. Residue LEU 65 is missing expected H atoms. Skipping. Residue SER 68 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 126 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Residue LYS 218 is missing expected H atoms. Skipping. Residue LYS 274 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue LYS 38 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Residue THR 73 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 90 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 171 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue LYS 200 is missing expected H atoms. Skipping. Residue LEU 201 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue THR 258 is missing expected H atoms. Skipping. Residue LYS 259 is missing expected H atoms. Skipping. Residue LYS 268 is missing expected H atoms. Skipping. Residue LEU 278 is missing expected H atoms. Skipping. Residue LYS 63 is missing expected H atoms. Skipping. Residue LEU 86 is missing expected H atoms. Skipping. Residue LYS 100 is missing expected H atoms. Skipping. Residue LYS 106 is missing expected H atoms. Skipping. Residue LYS 122 is missing expected H atoms. Skipping. Residue LYS 139 is missing expected H atoms. Skipping. Residue LYS 143 is missing expected H atoms. Skipping. Residue VAL 29 is missing expected H atoms. Skipping. Residue LYS 63 is missing expected H atoms. Skipping. Residue LYS 68 is missing expected H atoms. Skipping. Residue SER 71 is missing expected H atoms. Skipping. Residue LYS 77 is missing expected H atoms. Skipping. Residue LYS 94 is missing expected H atoms. Skipping. Residue LYS 148 is missing expected H atoms. Skipping. Residue LYS 151 is missing expected H atoms. Skipping. Residue LYS 181 is missing expected H atoms. Skipping. Residue LYS 214 is missing expected H atoms. Skipping. Residue LEU 221 is missing expected H atoms. Skipping. Residue LYS 223 is missing expected H atoms. Skipping. Residue LEU 229 is missing expected H atoms. Skipping. Residue VAL 237 is missing expected H atoms. Skipping. Residue SER 239 is missing expected H atoms. Skipping. Residue LYS 154 is missing expected H atoms. Skipping. Residue LYS 18 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Evaluate side-chains 1362 residues out of total 5967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 1233 time to evaluate : 7.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: 129 outliers final: 75 residues processed: 1314 average time/residue: 2.0456 time to fit residues: 4456.8295 Evaluate side-chains 1225 residues out of total 5967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 1150 time to evaluate : 7.529 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: 75 outliers final: 15 residues processed: 75 average time/residue: 1.7014 time to fit residues: 236.6083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 923 random chunks: chunk 829 optimal weight: 7.9990 chunk 631 optimal weight: 1.9990 chunk 435 optimal weight: 0.8980 chunk 92 optimal weight: 10.0000 chunk 400 optimal weight: 2.9990 chunk 563 optimal weight: 7.9990 chunk 842 optimal weight: 8.9990 chunk 892 optimal weight: 2.9990 chunk 440 optimal weight: 3.9990 chunk 798 optimal weight: 3.9990 chunk 240 optimal weight: 5.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 355 ASN ** C 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 74 GLN ** I 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 185 ASN ** K 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 116 ASN R 173 GLN ** R 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 123 ASN 3 97 ASN 4 29 GLN 5 106 GLN 8 128 GLN d 124 GLN d 179 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.3690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.096 119287 Z= 0.306 Angle : 0.638 15.681 174283 Z= 0.329 Chirality : 0.049 4.169 21694 Planarity : 0.006 0.125 12032 Dihedral : 16.354 179.668 40024 Min Nonbonded Distance : 1.731 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.34 % Allowed : 4.93 % Favored : 94.73 % Rotamer Outliers : 2.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.84 % 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: 0.31 (0.10), residues: 6566 helix: 2.46 (0.11), residues: 2390 sheet: -1.10 (0.18), residues: 791 loop : -1.18 (0.10), residues: 3385 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13132 Ramachandran restraints generated. 6566 Oldfield, 0 Emsley, 6566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13132 Ramachandran restraints generated. 6566 Oldfield, 0 Emsley, 6566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 79 is missing expected H atoms. Skipping. Residue ILE 80 is missing expected H atoms. Skipping. Residue LYS 81 is missing expected H atoms. Skipping. Residue LYS 85 is missing expected H atoms. Skipping. Residue LEU 86 is missing expected H atoms. Skipping. Residue LYS 88 is missing expected H atoms. Skipping. Residue LEU 230 is missing expected H atoms. Skipping. Residue LYS 233 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 244 is missing expected H atoms. Skipping. Residue MET 39 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue THR 48 is missing expected H atoms. Skipping. Residue LYS 62 is missing expected H atoms. Skipping. Residue LYS 77 is missing expected H atoms. Skipping. Residue LEU 133 is missing expected H atoms. Skipping. Residue LYS 197 is missing expected H atoms. Skipping. Residue LYS 207 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue LYS 211 is missing expected H atoms. Skipping. Residue VAL 58 is missing expected H atoms. Skipping. Residue THR 137 is missing expected H atoms. Skipping. Residue ILE 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue ILE 88 is missing expected H atoms. Skipping. Residue LYS 139 is missing expected H atoms. Skipping. Residue VAL 49 is missing expected H atoms. Skipping. Residue LYS 52 is missing expected H atoms. Skipping. Residue THR 53 is missing expected H atoms. Skipping. Residue LYS 56 is missing expected H atoms. Skipping. Residue LYS 59 is missing expected H atoms. Skipping. Residue THR 116 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue THR 148 is missing expected H atoms. Skipping. Residue SER 155 is missing expected H atoms. Skipping. Residue LYS 167 is missing expected H atoms. Skipping. Residue LYS 234 is missing expected H atoms. Skipping. Residue THR 237 is missing expected H atoms. Skipping. Residue LEU 238 is missing expected H atoms. Skipping. Residue THR 239 is missing expected H atoms. Skipping. Residue LYS 241 is missing expected H atoms. Skipping. Residue ILE 243 is missing expected H atoms. Skipping. Residue LYS 245 is missing expected H atoms. Skipping. Residue LYS 274 is missing expected H atoms. Skipping. Residue LYS 185 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue LYS 281 is missing expected H atoms. Skipping. Residue LEU 283 is missing expected H atoms. Skipping. Residue LYS 288 is missing expected H atoms. Skipping. Residue LEU 292 is missing expected H atoms. Skipping. Residue THR 294 is missing expected H atoms. Skipping. Residue LYS 295 is missing expected H atoms. Skipping. Residue LYS 296 is missing expected H atoms. Skipping. Residue LYS 298 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue LYS 306 is missing expected H atoms. Skipping. Residue LYS 326 is missing expected H atoms. Skipping. Residue TYR 352 is missing expected H atoms. Skipping. Residue THR 353 is missing expected H atoms. Skipping. Residue LYS 354 is missing expected H atoms. Skipping. Residue SER 363 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue MET 48 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 18 is missing expected H atoms. Skipping. Residue THR 20 is missing expected H atoms. Skipping. Residue LYS 21 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue LEU 183 is missing expected H atoms. Skipping. Residue VAL 198 is missing expected H atoms. Skipping. Residue SER 200 is missing expected H atoms. Skipping. Residue MET 201 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue ILE 209 is missing expected H atoms. Skipping. Residue LEU 232 is missing expected H atoms. Skipping. Residue LYS 87 is missing expected H atoms. Skipping. Residue LYS 129 is missing expected H atoms. Skipping. Residue LYS 221 is missing expected H atoms. Skipping. Residue LYS 313 is missing expected H atoms. Skipping. Residue LEU 112 is missing expected H atoms. Skipping. Residue LYS 123 is missing expected H atoms. Skipping. Residue THR 139 is missing expected H atoms. Skipping. Residue THR 137 is missing expected H atoms. Skipping. Residue SER 140 is missing expected H atoms. Skipping. Residue LEU 65 is missing expected H atoms. Skipping. Residue SER 68 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 126 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Residue LYS 218 is missing expected H atoms. Skipping. Residue LYS 274 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue LYS 38 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Residue THR 73 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 90 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 171 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue LYS 200 is missing expected H atoms. Skipping. Residue LEU 201 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue THR 258 is missing expected H atoms. Skipping. Residue LYS 259 is missing expected H atoms. Skipping. Residue LYS 268 is missing expected H atoms. Skipping. Residue LEU 278 is missing expected H atoms. Skipping. Residue LYS 63 is missing expected H atoms. Skipping. Residue LEU 86 is missing expected H atoms. Skipping. Residue LYS 100 is missing expected H atoms. Skipping. Residue LYS 106 is missing expected H atoms. Skipping. Residue LYS 122 is missing expected H atoms. Skipping. Residue LYS 139 is missing expected H atoms. Skipping. Residue LYS 143 is missing expected H atoms. Skipping. Residue VAL 29 is missing expected H atoms. Skipping. Residue LYS 63 is missing expected H atoms. Skipping. Residue LYS 68 is missing expected H atoms. Skipping. Residue SER 71 is missing expected H atoms. Skipping. Residue LYS 77 is missing expected H atoms. Skipping. Residue LYS 94 is missing expected H atoms. Skipping. Residue LYS 148 is missing expected H atoms. Skipping. Residue LYS 151 is missing expected H atoms. Skipping. Residue LYS 181 is missing expected H atoms. Skipping. Residue LYS 214 is missing expected H atoms. Skipping. Residue LEU 221 is missing expected H atoms. Skipping. Residue LYS 223 is missing expected H atoms. Skipping. Residue LEU 229 is missing expected H atoms. Skipping. Residue VAL 237 is missing expected H atoms. Skipping. Residue SER 239 is missing expected H atoms. Skipping. Residue LYS 154 is missing expected H atoms. Skipping. Residue LYS 18 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Evaluate side-chains 1346 residues out of total 5967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 1206 time to evaluate : 8.440 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 outliers start: 140 outliers final: 97 residues processed: 1295 average time/residue: 1.9989 time to fit residues: 4291.3313 Evaluate side-chains 1237 residues out of total 5967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 1140 time to evaluate : 7.486 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: 97 outliers final: 15 residues processed: 97 average time/residue: 1.7158 time to fit residues: 303.7927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 923 random chunks: chunk 743 optimal weight: 4.9990 chunk 506 optimal weight: 4.9990 chunk 12 optimal weight: 8.9990 chunk 664 optimal weight: 4.9990 chunk 368 optimal weight: 4.9990 chunk 761 optimal weight: 0.0070 chunk 616 optimal weight: 3.9990 chunk 1 optimal weight: 9.9990 chunk 455 optimal weight: 2.9990 chunk 800 optimal weight: 0.0770 chunk 225 optimal weight: 5.9990 overall best weight: 2.4162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 92 GLN ** D 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 116 ASN ** R 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 23 GLN 1 116 GLN 1 122 ASN 2 70 GLN 4 29 GLN 5 106 GLN ** 7 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 235 GLN d 179 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.3935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.209 119287 Z= 0.288 Angle : 0.616 15.769 174283 Z= 0.318 Chirality : 0.048 4.164 21694 Planarity : 0.005 0.110 12032 Dihedral : 16.296 179.392 40024 Min Nonbonded Distance : 1.752 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.29 % Allowed : 5.47 % Favored : 94.24 % Rotamer Outliers : 1.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.84 % 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: 0.31 (0.11), residues: 6566 helix: 2.34 (0.11), residues: 2390 sheet: -1.08 (0.18), residues: 777 loop : -1.10 (0.10), residues: 3399 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13132 Ramachandran restraints generated. 6566 Oldfield, 0 Emsley, 6566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13132 Ramachandran restraints generated. 6566 Oldfield, 0 Emsley, 6566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 79 is missing expected H atoms. Skipping. Residue ILE 80 is missing expected H atoms. Skipping. Residue LYS 81 is missing expected H atoms. Skipping. Residue LYS 85 is missing expected H atoms. Skipping. Residue LEU 86 is missing expected H atoms. Skipping. Residue LYS 88 is missing expected H atoms. Skipping. Residue LEU 230 is missing expected H atoms. Skipping. Residue LYS 233 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 244 is missing expected H atoms. Skipping. Residue MET 39 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue THR 48 is missing expected H atoms. Skipping. Residue LYS 62 is missing expected H atoms. Skipping. Residue LYS 77 is missing expected H atoms. Skipping. Residue LEU 133 is missing expected H atoms. Skipping. Residue LYS 197 is missing expected H atoms. Skipping. Residue LYS 207 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue LYS 211 is missing expected H atoms. Skipping. Residue VAL 58 is missing expected H atoms. Skipping. Residue THR 137 is missing expected H atoms. Skipping. Residue ILE 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue ILE 88 is missing expected H atoms. Skipping. Residue LYS 139 is missing expected H atoms. Skipping. Residue VAL 49 is missing expected H atoms. Skipping. Residue LYS 52 is missing expected H atoms. Skipping. Residue THR 53 is missing expected H atoms. Skipping. Residue LYS 56 is missing expected H atoms. Skipping. Residue LYS 59 is missing expected H atoms. Skipping. Residue THR 116 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue THR 148 is missing expected H atoms. Skipping. Residue SER 155 is missing expected H atoms. Skipping. Residue LYS 167 is missing expected H atoms. Skipping. Residue LYS 234 is missing expected H atoms. Skipping. Residue THR 237 is missing expected H atoms. Skipping. Residue LEU 238 is missing expected H atoms. Skipping. Residue THR 239 is missing expected H atoms. Skipping. Residue LYS 241 is missing expected H atoms. Skipping. Residue ILE 243 is missing expected H atoms. Skipping. Residue LYS 245 is missing expected H atoms. Skipping. Residue LYS 274 is missing expected H atoms. Skipping. Residue LYS 185 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue LYS 281 is missing expected H atoms. Skipping. Residue LEU 283 is missing expected H atoms. Skipping. Residue LYS 288 is missing expected H atoms. Skipping. Residue LEU 292 is missing expected H atoms. Skipping. Residue THR 294 is missing expected H atoms. Skipping. Residue LYS 295 is missing expected H atoms. Skipping. Residue LYS 296 is missing expected H atoms. Skipping. Residue LYS 298 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue LYS 306 is missing expected H atoms. Skipping. Residue LYS 326 is missing expected H atoms. Skipping. Residue TYR 352 is missing expected H atoms. Skipping. Residue THR 353 is missing expected H atoms. Skipping. Residue LYS 354 is missing expected H atoms. Skipping. Residue SER 363 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue MET 48 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 18 is missing expected H atoms. Skipping. Residue THR 20 is missing expected H atoms. Skipping. Residue LYS 21 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue LEU 183 is missing expected H atoms. Skipping. Residue VAL 198 is missing expected H atoms. Skipping. Residue SER 200 is missing expected H atoms. Skipping. Residue MET 201 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue ILE 209 is missing expected H atoms. Skipping. Residue LEU 232 is missing expected H atoms. Skipping. Residue LYS 87 is missing expected H atoms. Skipping. Residue LYS 129 is missing expected H atoms. Skipping. Residue LYS 221 is missing expected H atoms. Skipping. Residue LYS 313 is missing expected H atoms. Skipping. Residue LEU 112 is missing expected H atoms. Skipping. Residue LYS 123 is missing expected H atoms. Skipping. Residue THR 139 is missing expected H atoms. Skipping. Residue THR 137 is missing expected H atoms. Skipping. Residue SER 140 is missing expected H atoms. Skipping. Residue LEU 65 is missing expected H atoms. Skipping. Residue SER 68 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 126 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Residue LYS 218 is missing expected H atoms. Skipping. Residue LYS 274 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue LYS 38 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Residue THR 73 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 90 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 171 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue LYS 200 is missing expected H atoms. Skipping. Residue LEU 201 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue THR 258 is missing expected H atoms. Skipping. Residue LYS 259 is missing expected H atoms. Skipping. Residue LYS 268 is missing expected H atoms. Skipping. Residue LEU 278 is missing expected H atoms. Skipping. Residue LYS 63 is missing expected H atoms. Skipping. Residue LEU 86 is missing expected H atoms. Skipping. Residue LYS 100 is missing expected H atoms. Skipping. Residue LYS 106 is missing expected H atoms. Skipping. Residue LYS 122 is missing expected H atoms. Skipping. Residue LYS 139 is missing expected H atoms. Skipping. Residue LYS 143 is missing expected H atoms. Skipping. Residue VAL 29 is missing expected H atoms. Skipping. Residue LYS 63 is missing expected H atoms. Skipping. Residue LYS 68 is missing expected H atoms. Skipping. Residue SER 71 is missing expected H atoms. Skipping. Residue LYS 77 is missing expected H atoms. Skipping. Residue LYS 94 is missing expected H atoms. Skipping. Residue LYS 148 is missing expected H atoms. Skipping. Residue LYS 151 is missing expected H atoms. Skipping. Residue LYS 181 is missing expected H atoms. Skipping. Residue LYS 214 is missing expected H atoms. Skipping. Residue LEU 221 is missing expected H atoms. Skipping. Residue LYS 223 is missing expected H atoms. Skipping. Residue LEU 229 is missing expected H atoms. Skipping. Residue VAL 237 is missing expected H atoms. Skipping. Residue SER 239 is missing expected H atoms. Skipping. Residue LYS 154 is missing expected H atoms. Skipping. Residue LYS 18 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Evaluate side-chains 1298 residues out of total 5967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 1188 time to evaluate : 7.527 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 outliers start: 110 outliers final: 71 residues processed: 1264 average time/residue: 1.9953 time to fit residues: 4164.0739 Evaluate side-chains 1206 residues out of total 5967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 1135 time to evaluate : 7.530 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: 71 outliers final: 15 residues processed: 71 average time/residue: 1.6871 time to fit residues: 219.2701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 923 random chunks: chunk 300 optimal weight: 1.9990 chunk 803 optimal weight: 4.9990 chunk 176 optimal weight: 4.9990 chunk 523 optimal weight: 2.9990 chunk 220 optimal weight: 4.9990 chunk 893 optimal weight: 2.9990 chunk 741 optimal weight: 5.9990 chunk 413 optimal weight: 0.9990 chunk 74 optimal weight: 7.9990 chunk 295 optimal weight: 0.1980 chunk 468 optimal weight: 3.9990 overall best weight: 1.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 185 ASN O 103 GLN P 148 GLN P 156 GLN S 23 GLN 1 123 ASN 4 29 GLN 5 106 GLN ** 7 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 149 GLN 8 235 GLN ** c 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 179 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.4118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.091 119287 Z= 0.232 Angle : 0.584 15.779 174283 Z= 0.302 Chirality : 0.047 4.142 21694 Planarity : 0.005 0.100 12032 Dihedral : 16.199 179.809 40024 Min Nonbonded Distance : 1.766 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.01 % Favored : 94.72 % Rotamer Outliers : 1.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.84 % 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: 0.43 (0.11), residues: 6566 helix: 2.41 (0.11), residues: 2390 sheet: -1.02 (0.18), residues: 771 loop : -0.99 (0.10), residues: 3405 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13132 Ramachandran restraints generated. 6566 Oldfield, 0 Emsley, 6566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13132 Ramachandran restraints generated. 6566 Oldfield, 0 Emsley, 6566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 79 is missing expected H atoms. Skipping. Residue ILE 80 is missing expected H atoms. Skipping. Residue LYS 81 is missing expected H atoms. Skipping. Residue LYS 85 is missing expected H atoms. Skipping. Residue LEU 86 is missing expected H atoms. Skipping. Residue LYS 88 is missing expected H atoms. Skipping. Residue LEU 230 is missing expected H atoms. Skipping. Residue LYS 233 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 244 is missing expected H atoms. Skipping. Residue MET 39 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue THR 48 is missing expected H atoms. Skipping. Residue LYS 62 is missing expected H atoms. Skipping. Residue LYS 77 is missing expected H atoms. Skipping. Residue LEU 133 is missing expected H atoms. Skipping. Residue LYS 197 is missing expected H atoms. Skipping. Residue LYS 207 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue LYS 211 is missing expected H atoms. Skipping. Residue VAL 58 is missing expected H atoms. Skipping. Residue THR 137 is missing expected H atoms. Skipping. Residue ILE 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue ILE 88 is missing expected H atoms. Skipping. Residue LYS 139 is missing expected H atoms. Skipping. Residue VAL 49 is missing expected H atoms. Skipping. Residue LYS 52 is missing expected H atoms. Skipping. Residue THR 53 is missing expected H atoms. Skipping. Residue LYS 56 is missing expected H atoms. Skipping. Residue LYS 59 is missing expected H atoms. Skipping. Residue THR 116 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue THR 148 is missing expected H atoms. Skipping. Residue SER 155 is missing expected H atoms. Skipping. Residue LYS 167 is missing expected H atoms. Skipping. Residue LYS 234 is missing expected H atoms. Skipping. Residue THR 237 is missing expected H atoms. Skipping. Residue LEU 238 is missing expected H atoms. Skipping. Residue THR 239 is missing expected H atoms. Skipping. Residue LYS 241 is missing expected H atoms. Skipping. Residue ILE 243 is missing expected H atoms. Skipping. Residue LYS 245 is missing expected H atoms. Skipping. Residue LYS 274 is missing expected H atoms. Skipping. Residue LYS 185 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue LYS 281 is missing expected H atoms. Skipping. Residue LEU 283 is missing expected H atoms. Skipping. Residue LYS 288 is missing expected H atoms. Skipping. Residue LEU 292 is missing expected H atoms. Skipping. Residue THR 294 is missing expected H atoms. Skipping. Residue LYS 295 is missing expected H atoms. Skipping. Residue LYS 296 is missing expected H atoms. Skipping. Residue LYS 298 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue LYS 306 is missing expected H atoms. Skipping. Residue LYS 326 is missing expected H atoms. Skipping. Residue TYR 352 is missing expected H atoms. Skipping. Residue THR 353 is missing expected H atoms. Skipping. Residue LYS 354 is missing expected H atoms. Skipping. Residue SER 363 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue MET 48 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 18 is missing expected H atoms. Skipping. Residue THR 20 is missing expected H atoms. Skipping. Residue LYS 21 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue LEU 183 is missing expected H atoms. Skipping. Residue VAL 198 is missing expected H atoms. Skipping. Residue SER 200 is missing expected H atoms. Skipping. Residue MET 201 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue ILE 209 is missing expected H atoms. Skipping. Residue LEU 232 is missing expected H atoms. Skipping. Residue LYS 87 is missing expected H atoms. Skipping. Residue LYS 129 is missing expected H atoms. Skipping. Residue LYS 221 is missing expected H atoms. Skipping. Residue LYS 313 is missing expected H atoms. Skipping. Residue LEU 112 is missing expected H atoms. Skipping. Residue LYS 123 is missing expected H atoms. Skipping. Residue THR 139 is missing expected H atoms. Skipping. Residue THR 137 is missing expected H atoms. Skipping. Residue SER 140 is missing expected H atoms. Skipping. Residue LEU 65 is missing expected H atoms. Skipping. Residue SER 68 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 126 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Residue LYS 218 is missing expected H atoms. Skipping. Residue LYS 274 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue LYS 38 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Residue THR 73 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 90 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 171 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue LYS 200 is missing expected H atoms. Skipping. Residue LEU 201 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue THR 258 is missing expected H atoms. Skipping. Residue LYS 259 is missing expected H atoms. Skipping. Residue LYS 268 is missing expected H atoms. Skipping. Residue LEU 278 is missing expected H atoms. Skipping. Residue LYS 63 is missing expected H atoms. Skipping. Residue LEU 86 is missing expected H atoms. Skipping. Residue LYS 100 is missing expected H atoms. Skipping. Residue LYS 106 is missing expected H atoms. Skipping. Residue LYS 122 is missing expected H atoms. Skipping. Residue LYS 139 is missing expected H atoms. Skipping. Residue LYS 143 is missing expected H atoms. Skipping. Residue VAL 29 is missing expected H atoms. Skipping. Residue LYS 63 is missing expected H atoms. Skipping. Residue LYS 68 is missing expected H atoms. Skipping. Residue SER 71 is missing expected H atoms. Skipping. Residue LYS 77 is missing expected H atoms. Skipping. Residue LYS 94 is missing expected H atoms. Skipping. Residue LYS 148 is missing expected H atoms. Skipping. Residue LYS 151 is missing expected H atoms. Skipping. Residue LYS 181 is missing expected H atoms. Skipping. Residue LYS 214 is missing expected H atoms. Skipping. Residue LEU 221 is missing expected H atoms. Skipping. Residue LYS 223 is missing expected H atoms. Skipping. Residue LEU 229 is missing expected H atoms. Skipping. Residue VAL 237 is missing expected H atoms. Skipping. Residue SER 239 is missing expected H atoms. Skipping. Residue LYS 154 is missing expected H atoms. Skipping. Residue LYS 18 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Evaluate side-chains 1270 residues out of total 5967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 1176 time to evaluate : 7.491 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 outliers start: 94 outliers final: 67 residues processed: 1234 average time/residue: 1.9554 time to fit residues: 3968.8982 Evaluate side-chains 1196 residues out of total 5967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 1129 time to evaluate : 7.477 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 67 outliers final: 14 residues processed: 67 average time/residue: 1.6875 time to fit residues: 211.6612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 923 random chunks: chunk 861 optimal weight: 2.9990 chunk 100 optimal weight: 9.9990 chunk 508 optimal weight: 2.9990 chunk 652 optimal weight: 0.6980 chunk 505 optimal weight: 2.9990 chunk 751 optimal weight: 1.9990 chunk 498 optimal weight: 0.6980 chunk 889 optimal weight: 2.9990 chunk 556 optimal weight: 3.9990 chunk 542 optimal weight: 2.9990 chunk 410 optimal weight: 3.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 376 ASN ** D 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 148 GLN P 156 GLN S 23 GLN ** 1 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 29 GLN 5 106 GLN 5 379 GLN ** 7 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 149 GLN 8 164 GLN 8 235 GLN a 108 ASN ** c 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 179 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.4286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.246 119287 Z= 0.240 Angle : 0.585 15.915 174283 Z= 0.302 Chirality : 0.046 4.091 21694 Planarity : 0.005 0.115 12032 Dihedral : 16.132 179.734 40024 Min Nonbonded Distance : 1.757 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.29 % Allowed : 5.38 % Favored : 94.33 % Rotamer Outliers : 1.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.56 % 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: 0.43 (0.11), residues: 6566 helix: 2.38 (0.11), residues: 2390 sheet: -1.06 (0.18), residues: 808 loop : -0.94 (0.11), residues: 3368 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13132 Ramachandran restraints generated. 6566 Oldfield, 0 Emsley, 6566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13132 Ramachandran restraints generated. 6566 Oldfield, 0 Emsley, 6566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 79 is missing expected H atoms. Skipping. Residue ILE 80 is missing expected H atoms. Skipping. Residue LYS 81 is missing expected H atoms. Skipping. Residue LYS 85 is missing expected H atoms. Skipping. Residue LEU 86 is missing expected H atoms. Skipping. Residue LYS 88 is missing expected H atoms. Skipping. Residue LEU 230 is missing expected H atoms. Skipping. Residue LYS 233 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 244 is missing expected H atoms. Skipping. Residue MET 39 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue THR 48 is missing expected H atoms. Skipping. Residue LYS 62 is missing expected H atoms. Skipping. Residue LYS 77 is missing expected H atoms. Skipping. Residue LEU 133 is missing expected H atoms. Skipping. Residue LYS 197 is missing expected H atoms. Skipping. Residue LYS 207 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue LYS 211 is missing expected H atoms. Skipping. Residue VAL 58 is missing expected H atoms. Skipping. Residue THR 137 is missing expected H atoms. Skipping. Residue ILE 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue ILE 88 is missing expected H atoms. Skipping. Residue LYS 139 is missing expected H atoms. Skipping. Residue VAL 49 is missing expected H atoms. Skipping. Residue LYS 52 is missing expected H atoms. Skipping. Residue THR 53 is missing expected H atoms. Skipping. Residue LYS 56 is missing expected H atoms. Skipping. Residue LYS 59 is missing expected H atoms. Skipping. Residue THR 116 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue THR 148 is missing expected H atoms. Skipping. Residue SER 155 is missing expected H atoms. Skipping. Residue LYS 167 is missing expected H atoms. Skipping. Residue LYS 234 is missing expected H atoms. Skipping. Residue THR 237 is missing expected H atoms. Skipping. Residue LEU 238 is missing expected H atoms. Skipping. Residue THR 239 is missing expected H atoms. Skipping. Residue LYS 241 is missing expected H atoms. Skipping. Residue ILE 243 is missing expected H atoms. Skipping. Residue LYS 245 is missing expected H atoms. Skipping. Residue LYS 274 is missing expected H atoms. Skipping. Residue LYS 185 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue LYS 281 is missing expected H atoms. Skipping. Residue LEU 283 is missing expected H atoms. Skipping. Residue LYS 288 is missing expected H atoms. Skipping. Residue LEU 292 is missing expected H atoms. Skipping. Residue THR 294 is missing expected H atoms. Skipping. Residue LYS 295 is missing expected H atoms. Skipping. Residue LYS 296 is missing expected H atoms. Skipping. Residue LYS 298 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue LYS 306 is missing expected H atoms. Skipping. Residue LYS 326 is missing expected H atoms. Skipping. Residue TYR 352 is missing expected H atoms. Skipping. Residue THR 353 is missing expected H atoms. Skipping. Residue LYS 354 is missing expected H atoms. Skipping. Residue SER 363 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue MET 48 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 18 is missing expected H atoms. Skipping. Residue THR 20 is missing expected H atoms. Skipping. Residue LYS 21 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue LEU 183 is missing expected H atoms. Skipping. Residue VAL 198 is missing expected H atoms. Skipping. Residue SER 200 is missing expected H atoms. Skipping. Residue MET 201 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue ILE 209 is missing expected H atoms. Skipping. Residue LEU 232 is missing expected H atoms. Skipping. Residue LYS 87 is missing expected H atoms. Skipping. Residue LYS 129 is missing expected H atoms. Skipping. Residue LYS 221 is missing expected H atoms. Skipping. Residue LYS 313 is missing expected H atoms. Skipping. Residue LEU 112 is missing expected H atoms. Skipping. Residue LYS 123 is missing expected H atoms. Skipping. Residue THR 139 is missing expected H atoms. Skipping. Residue THR 137 is missing expected H atoms. Skipping. Residue SER 140 is missing expected H atoms. Skipping. Residue LEU 65 is missing expected H atoms. Skipping. Residue SER 68 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 126 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Residue LYS 218 is missing expected H atoms. Skipping. Residue LYS 274 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue LYS 38 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Residue THR 73 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 90 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 171 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue LYS 200 is missing expected H atoms. Skipping. Residue LEU 201 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue THR 258 is missing expected H atoms. Skipping. Residue LYS 259 is missing expected H atoms. Skipping. Residue LYS 268 is missing expected H atoms. Skipping. Residue LEU 278 is missing expected H atoms. Skipping. Residue LYS 63 is missing expected H atoms. Skipping. Residue LEU 86 is missing expected H atoms. Skipping. Residue LYS 100 is missing expected H atoms. Skipping. Residue LYS 106 is missing expected H atoms. Skipping. Residue LYS 122 is missing expected H atoms. Skipping. Residue LYS 139 is missing expected H atoms. Skipping. Residue LYS 143 is missing expected H atoms. Skipping. Residue VAL 29 is missing expected H atoms. Skipping. Residue LYS 63 is missing expected H atoms. Skipping. Residue LYS 68 is missing expected H atoms. Skipping. Residue SER 71 is missing expected H atoms. Skipping. Residue LYS 77 is missing expected H atoms. Skipping. Residue LYS 94 is missing expected H atoms. Skipping. Residue LYS 148 is missing expected H atoms. Skipping. Residue LYS 151 is missing expected H atoms. Skipping. Residue LYS 181 is missing expected H atoms. Skipping. Residue LYS 214 is missing expected H atoms. Skipping. Residue LEU 221 is missing expected H atoms. Skipping. Residue LYS 223 is missing expected H atoms. Skipping. Residue LEU 229 is missing expected H atoms. Skipping. Residue VAL 237 is missing expected H atoms. Skipping. Residue SER 239 is missing expected H atoms. Skipping. Residue LYS 154 is missing expected H atoms. Skipping. Residue LYS 18 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Evaluate side-chains 1251 residues out of total 5967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 1160 time to evaluate : 7.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 91 outliers final: 51 residues processed: 1216 average time/residue: 2.0116 time to fit residues: 4036.9865 Evaluate side-chains 1173 residues out of total 5967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 1122 time to evaluate : 7.433 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: 51 outliers final: 14 residues processed: 51 average time/residue: 1.7178 time to fit residues: 161.8945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 923 random chunks: chunk 550 optimal weight: 4.9990 chunk 355 optimal weight: 2.9990 chunk 531 optimal weight: 3.9990 chunk 267 optimal weight: 6.9990 chunk 174 optimal weight: 5.9990 chunk 172 optimal weight: 3.9990 chunk 565 optimal weight: 8.9990 chunk 606 optimal weight: 20.0000 chunk 439 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 699 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 260 GLN E 110 ASN F 109 ASN ** I 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 185 ASN M 43 GLN P 148 GLN W 150 GLN 4 29 GLN 5 106 GLN ** 7 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 149 GLN 9 207 ASN d 179 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.4384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.161 119287 Z= 0.388 Angle : 0.672 15.989 174283 Z= 0.344 Chirality : 0.050 4.051 21694 Planarity : 0.006 0.095 12032 Dihedral : 16.267 178.541 40024 Min Nonbonded Distance : 1.686 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.29 % Allowed : 6.02 % Favored : 93.69 % Rotamer Outliers : 1.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.84 % 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: 0.11 (0.10), residues: 6566 helix: 2.00 (0.11), residues: 2390 sheet: -1.11 (0.18), residues: 796 loop : -1.07 (0.10), residues: 3380 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13132 Ramachandran restraints generated. 6566 Oldfield, 0 Emsley, 6566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13132 Ramachandran restraints generated. 6566 Oldfield, 0 Emsley, 6566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 79 is missing expected H atoms. Skipping. Residue ILE 80 is missing expected H atoms. Skipping. Residue LYS 81 is missing expected H atoms. Skipping. Residue LYS 85 is missing expected H atoms. Skipping. Residue LEU 86 is missing expected H atoms. Skipping. Residue LYS 88 is missing expected H atoms. Skipping. Residue LEU 230 is missing expected H atoms. Skipping. Residue LYS 233 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 244 is missing expected H atoms. Skipping. Residue MET 39 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue THR 48 is missing expected H atoms. Skipping. Residue LYS 62 is missing expected H atoms. Skipping. Residue LYS 77 is missing expected H atoms. Skipping. Residue LEU 133 is missing expected H atoms. Skipping. Residue LYS 197 is missing expected H atoms. Skipping. Residue LYS 207 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue LYS 211 is missing expected H atoms. Skipping. Residue VAL 58 is missing expected H atoms. Skipping. Residue THR 137 is missing expected H atoms. Skipping. Residue ILE 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue ILE 88 is missing expected H atoms. Skipping. Residue LYS 139 is missing expected H atoms. Skipping. Residue VAL 49 is missing expected H atoms. Skipping. Residue LYS 52 is missing expected H atoms. Skipping. Residue THR 53 is missing expected H atoms. Skipping. Residue LYS 56 is missing expected H atoms. Skipping. Residue LYS 59 is missing expected H atoms. Skipping. Residue THR 116 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue THR 148 is missing expected H atoms. Skipping. Residue SER 155 is missing expected H atoms. Skipping. Residue LYS 167 is missing expected H atoms. Skipping. Residue LYS 234 is missing expected H atoms. Skipping. Residue THR 237 is missing expected H atoms. Skipping. Residue LEU 238 is missing expected H atoms. Skipping. Residue THR 239 is missing expected H atoms. Skipping. Residue LYS 241 is missing expected H atoms. Skipping. Residue ILE 243 is missing expected H atoms. Skipping. Residue LYS 245 is missing expected H atoms. Skipping. Residue LYS 274 is missing expected H atoms. Skipping. Residue LYS 185 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue LYS 281 is missing expected H atoms. Skipping. Residue LEU 283 is missing expected H atoms. Skipping. Residue LYS 288 is missing expected H atoms. Skipping. Residue LEU 292 is missing expected H atoms. Skipping. Residue THR 294 is missing expected H atoms. Skipping. Residue LYS 295 is missing expected H atoms. Skipping. Residue LYS 296 is missing expected H atoms. Skipping. Residue LYS 298 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue LYS 306 is missing expected H atoms. Skipping. Residue LYS 326 is missing expected H atoms. Skipping. Residue TYR 352 is missing expected H atoms. Skipping. Residue THR 353 is missing expected H atoms. Skipping. Residue LYS 354 is missing expected H atoms. Skipping. Residue SER 363 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue MET 48 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 18 is missing expected H atoms. Skipping. Residue THR 20 is missing expected H atoms. Skipping. Residue LYS 21 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue LEU 183 is missing expected H atoms. Skipping. Residue VAL 198 is missing expected H atoms. Skipping. Residue SER 200 is missing expected H atoms. Skipping. Residue MET 201 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue ILE 209 is missing expected H atoms. Skipping. Residue LEU 232 is missing expected H atoms. Skipping. Residue LYS 87 is missing expected H atoms. Skipping. Residue LYS 129 is missing expected H atoms. Skipping. Residue LYS 221 is missing expected H atoms. Skipping. Residue LYS 313 is missing expected H atoms. Skipping. Residue LEU 112 is missing expected H atoms. Skipping. Residue LYS 123 is missing expected H atoms. Skipping. Residue THR 139 is missing expected H atoms. Skipping. Residue THR 137 is missing expected H atoms. Skipping. Residue SER 140 is missing expected H atoms. Skipping. Residue LEU 65 is missing expected H atoms. Skipping. Residue SER 68 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 126 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Residue LYS 218 is missing expected H atoms. Skipping. Residue LYS 274 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue LYS 38 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Residue THR 73 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 90 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 171 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue LYS 200 is missing expected H atoms. Skipping. Residue LEU 201 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue THR 258 is missing expected H atoms. Skipping. Residue LYS 259 is missing expected H atoms. Skipping. Residue LYS 268 is missing expected H atoms. Skipping. Residue LEU 278 is missing expected H atoms. Skipping. Residue LYS 63 is missing expected H atoms. Skipping. Residue LEU 86 is missing expected H atoms. Skipping. Residue LYS 100 is missing expected H atoms. Skipping. Residue LYS 106 is missing expected H atoms. Skipping. Residue LYS 122 is missing expected H atoms. Skipping. Residue LYS 139 is missing expected H atoms. Skipping. Residue LYS 143 is missing expected H atoms. Skipping. Residue VAL 29 is missing expected H atoms. Skipping. Residue LYS 63 is missing expected H atoms. Skipping. Residue LYS 68 is missing expected H atoms. Skipping. Residue SER 71 is missing expected H atoms. Skipping. Residue LYS 77 is missing expected H atoms. Skipping. Residue LYS 94 is missing expected H atoms. Skipping. Residue LYS 148 is missing expected H atoms. Skipping. Residue LYS 151 is missing expected H atoms. Skipping. Residue LYS 181 is missing expected H atoms. Skipping. Residue LYS 214 is missing expected H atoms. Skipping. Residue LEU 221 is missing expected H atoms. Skipping. Residue LYS 223 is missing expected H atoms. Skipping. Residue LEU 229 is missing expected H atoms. Skipping. Residue VAL 237 is missing expected H atoms. Skipping. Residue SER 239 is missing expected H atoms. Skipping. Residue LYS 154 is missing expected H atoms. Skipping. Residue LYS 18 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Evaluate side-chains 1231 residues out of total 5967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 1149 time to evaluate : 7.489 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 outliers start: 82 outliers final: 65 residues processed: 1193 average time/residue: 2.0309 time to fit residues: 3999.0067 Evaluate side-chains 1195 residues out of total 5967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 1130 time to evaluate : 7.494 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: 65 outliers final: 13 residues processed: 65 average time/residue: 1.6606 time to fit residues: 200.4431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 923 random chunks: chunk 809 optimal weight: 10.0000 chunk 852 optimal weight: 6.9990 chunk 777 optimal weight: 1.9990 chunk 829 optimal weight: 5.9990 chunk 498 optimal weight: 3.9990 chunk 361 optimal weight: 4.9990 chunk 650 optimal weight: 0.9990 chunk 254 optimal weight: 5.9990 chunk 749 optimal weight: 1.9990 chunk 784 optimal weight: 2.9990 chunk 826 optimal weight: 4.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 109 ASN ** I 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 161 ASN P 148 GLN Q 177 GLN 3 132 GLN 4 29 GLN 5 106 GLN ** 7 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 149 GLN d 25 GLN ** d 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 179 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.4466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.220 119287 Z= 0.292 Angle : 0.620 18.982 174283 Z= 0.319 Chirality : 0.047 4.028 21694 Planarity : 0.005 0.114 12032 Dihedral : 16.196 179.107 40024 Min Nonbonded Distance : 1.736 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.73 % Favored : 94.01 % Rotamer Outliers : 0.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.56 % 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: 0.18 (0.10), residues: 6566 helix: 2.07 (0.11), residues: 2389 sheet: -1.12 (0.17), residues: 806 loop : -1.03 (0.10), residues: 3371 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13132 Ramachandran restraints generated. 6566 Oldfield, 0 Emsley, 6566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13132 Ramachandran restraints generated. 6566 Oldfield, 0 Emsley, 6566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 79 is missing expected H atoms. Skipping. Residue ILE 80 is missing expected H atoms. Skipping. Residue LYS 81 is missing expected H atoms. Skipping. Residue LYS 85 is missing expected H atoms. Skipping. Residue LEU 86 is missing expected H atoms. Skipping. Residue LYS 88 is missing expected H atoms. Skipping. Residue LEU 230 is missing expected H atoms. Skipping. Residue LYS 233 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 244 is missing expected H atoms. Skipping. Residue MET 39 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue THR 48 is missing expected H atoms. Skipping. Residue LYS 62 is missing expected H atoms. Skipping. Residue LYS 77 is missing expected H atoms. Skipping. Residue LEU 133 is missing expected H atoms. Skipping. Residue LYS 197 is missing expected H atoms. Skipping. Residue LYS 207 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue LYS 211 is missing expected H atoms. Skipping. Residue VAL 58 is missing expected H atoms. Skipping. Residue THR 137 is missing expected H atoms. Skipping. Residue ILE 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue ILE 88 is missing expected H atoms. Skipping. Residue LYS 139 is missing expected H atoms. Skipping. Residue VAL 49 is missing expected H atoms. Skipping. Residue LYS 52 is missing expected H atoms. Skipping. Residue THR 53 is missing expected H atoms. Skipping. Residue LYS 56 is missing expected H atoms. Skipping. Residue LYS 59 is missing expected H atoms. Skipping. Residue THR 116 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue THR 148 is missing expected H atoms. Skipping. Residue SER 155 is missing expected H atoms. Skipping. Residue LYS 167 is missing expected H atoms. Skipping. Residue LYS 234 is missing expected H atoms. Skipping. Residue THR 237 is missing expected H atoms. Skipping. Residue LEU 238 is missing expected H atoms. Skipping. Residue THR 239 is missing expected H atoms. Skipping. Residue LYS 241 is missing expected H atoms. Skipping. Residue ILE 243 is missing expected H atoms. Skipping. Residue LYS 245 is missing expected H atoms. Skipping. Residue LYS 274 is missing expected H atoms. Skipping. Residue LYS 185 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue LYS 281 is missing expected H atoms. Skipping. Residue LEU 283 is missing expected H atoms. Skipping. Residue LYS 288 is missing expected H atoms. Skipping. Residue LEU 292 is missing expected H atoms. Skipping. Residue THR 294 is missing expected H atoms. Skipping. Residue LYS 295 is missing expected H atoms. Skipping. Residue LYS 296 is missing expected H atoms. Skipping. Residue LYS 298 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue LYS 306 is missing expected H atoms. Skipping. Residue LYS 326 is missing expected H atoms. Skipping. Residue TYR 352 is missing expected H atoms. Skipping. Residue THR 353 is missing expected H atoms. Skipping. Residue LYS 354 is missing expected H atoms. Skipping. Residue SER 363 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue MET 48 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 18 is missing expected H atoms. Skipping. Residue THR 20 is missing expected H atoms. Skipping. Residue LYS 21 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue LEU 183 is missing expected H atoms. Skipping. Residue VAL 198 is missing expected H atoms. Skipping. Residue SER 200 is missing expected H atoms. Skipping. Residue MET 201 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue ILE 209 is missing expected H atoms. Skipping. Residue LEU 232 is missing expected H atoms. Skipping. Residue LYS 87 is missing expected H atoms. Skipping. Residue LYS 129 is missing expected H atoms. Skipping. Residue LYS 221 is missing expected H atoms. Skipping. Residue LYS 313 is missing expected H atoms. Skipping. Residue LEU 112 is missing expected H atoms. Skipping. Residue LYS 123 is missing expected H atoms. Skipping. Residue THR 139 is missing expected H atoms. Skipping. Residue THR 137 is missing expected H atoms. Skipping. Residue SER 140 is missing expected H atoms. Skipping. Residue LEU 65 is missing expected H atoms. Skipping. Residue SER 68 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 126 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Residue LYS 218 is missing expected H atoms. Skipping. Residue LYS 274 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue LYS 38 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Residue THR 73 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 90 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 171 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue LYS 200 is missing expected H atoms. Skipping. Residue LEU 201 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue THR 258 is missing expected H atoms. Skipping. Residue LYS 259 is missing expected H atoms. Skipping. Residue LYS 268 is missing expected H atoms. Skipping. Residue LEU 278 is missing expected H atoms. Skipping. Residue LYS 63 is missing expected H atoms. Skipping. Residue LEU 86 is missing expected H atoms. Skipping. Residue LYS 100 is missing expected H atoms. Skipping. Residue LYS 106 is missing expected H atoms. Skipping. Residue LYS 122 is missing expected H atoms. Skipping. Residue LYS 139 is missing expected H atoms. Skipping. Residue LYS 143 is missing expected H atoms. Skipping. Residue VAL 29 is missing expected H atoms. Skipping. Residue LYS 63 is missing expected H atoms. Skipping. Residue LYS 68 is missing expected H atoms. Skipping. Residue SER 71 is missing expected H atoms. Skipping. Residue LYS 77 is missing expected H atoms. Skipping. Residue LYS 94 is missing expected H atoms. Skipping. Residue LYS 148 is missing expected H atoms. Skipping. Residue LYS 151 is missing expected H atoms. Skipping. Residue LYS 181 is missing expected H atoms. Skipping. Residue LYS 214 is missing expected H atoms. Skipping. Residue LEU 221 is missing expected H atoms. Skipping. Residue LYS 223 is missing expected H atoms. Skipping. Residue LEU 229 is missing expected H atoms. Skipping. Residue VAL 237 is missing expected H atoms. Skipping. Residue SER 239 is missing expected H atoms. Skipping. Residue LYS 154 is missing expected H atoms. Skipping. Residue LYS 18 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Evaluate side-chains 1200 residues out of total 5967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 1146 time to evaluate : 7.420 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 outliers start: 54 outliers final: 36 residues processed: 1181 average time/residue: 2.0191 time to fit residues: 3952.3864 Evaluate side-chains 1153 residues out of total 5967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 1117 time to evaluate : 7.439 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: 36 outliers final: 13 residues processed: 36 average time/residue: 1.9114 time to fit residues: 125.6611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 923 random chunks: chunk 544 optimal weight: 1.9990 chunk 876 optimal weight: 3.9990 chunk 535 optimal weight: 2.9990 chunk 415 optimal weight: 2.9990 chunk 609 optimal weight: 0.9990 chunk 919 optimal weight: 3.9990 chunk 846 optimal weight: 4.9990 chunk 732 optimal weight: 4.9990 chunk 76 optimal weight: 9.9990 chunk 565 optimal weight: 9.9990 chunk 448 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 185 ASN ** K 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 148 GLN 3 132 GLN 4 29 GLN 5 106 GLN ** 7 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 149 GLN ** d 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 61 ASN d 179 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.4579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.086 119287 Z= 0.312 Angle : 0.630 15.956 174283 Z= 0.324 Chirality : 0.048 3.957 21694 Planarity : 0.005 0.092 12032 Dihedral : 16.176 179.381 40024 Min Nonbonded Distance : 1.720 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.09 % Favored : 93.65 % Rotamer Outliers : 0.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.56 % 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: 0.14 (0.10), residues: 6566 helix: 2.01 (0.11), residues: 2380 sheet: -1.13 (0.18), residues: 783 loop : -1.03 (0.10), residues: 3403 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13132 Ramachandran restraints generated. 6566 Oldfield, 0 Emsley, 6566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13132 Ramachandran restraints generated. 6566 Oldfield, 0 Emsley, 6566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 79 is missing expected H atoms. Skipping. Residue ILE 80 is missing expected H atoms. Skipping. Residue LYS 81 is missing expected H atoms. Skipping. Residue LYS 85 is missing expected H atoms. Skipping. Residue LEU 86 is missing expected H atoms. Skipping. Residue LYS 88 is missing expected H atoms. Skipping. Residue LEU 230 is missing expected H atoms. Skipping. Residue LYS 233 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 244 is missing expected H atoms. Skipping. Residue MET 39 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue THR 48 is missing expected H atoms. Skipping. Residue LYS 62 is missing expected H atoms. Skipping. Residue LYS 77 is missing expected H atoms. Skipping. Residue LEU 133 is missing expected H atoms. Skipping. Residue LYS 197 is missing expected H atoms. Skipping. Residue LYS 207 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue LYS 211 is missing expected H atoms. Skipping. Residue VAL 58 is missing expected H atoms. Skipping. Residue THR 137 is missing expected H atoms. Skipping. Residue ILE 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue ILE 88 is missing expected H atoms. Skipping. Residue LYS 139 is missing expected H atoms. Skipping. Residue VAL 49 is missing expected H atoms. Skipping. Residue LYS 52 is missing expected H atoms. Skipping. Residue THR 53 is missing expected H atoms. Skipping. Residue LYS 56 is missing expected H atoms. Skipping. Residue LYS 59 is missing expected H atoms. Skipping. Residue THR 116 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue THR 148 is missing expected H atoms. Skipping. Residue SER 155 is missing expected H atoms. Skipping. Residue LYS 167 is missing expected H atoms. Skipping. Residue LYS 234 is missing expected H atoms. Skipping. Residue THR 237 is missing expected H atoms. Skipping. Residue LEU 238 is missing expected H atoms. Skipping. Residue THR 239 is missing expected H atoms. Skipping. Residue LYS 241 is missing expected H atoms. Skipping. Residue ILE 243 is missing expected H atoms. Skipping. Residue LYS 245 is missing expected H atoms. Skipping. Residue LYS 274 is missing expected H atoms. Skipping. Residue LYS 185 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue LYS 281 is missing expected H atoms. Skipping. Residue LEU 283 is missing expected H atoms. Skipping. Residue LYS 288 is missing expected H atoms. Skipping. Residue LEU 292 is missing expected H atoms. Skipping. Residue THR 294 is missing expected H atoms. Skipping. Residue LYS 295 is missing expected H atoms. Skipping. Residue LYS 296 is missing expected H atoms. Skipping. Residue LYS 298 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue LYS 306 is missing expected H atoms. Skipping. Residue LYS 326 is missing expected H atoms. Skipping. Residue TYR 352 is missing expected H atoms. Skipping. Residue THR 353 is missing expected H atoms. Skipping. Residue LYS 354 is missing expected H atoms. Skipping. Residue SER 363 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue MET 48 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 18 is missing expected H atoms. Skipping. Residue THR 20 is missing expected H atoms. Skipping. Residue LYS 21 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue LEU 183 is missing expected H atoms. Skipping. Residue VAL 198 is missing expected H atoms. Skipping. Residue SER 200 is missing expected H atoms. Skipping. Residue MET 201 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue ILE 209 is missing expected H atoms. Skipping. Residue LEU 232 is missing expected H atoms. Skipping. Residue LYS 87 is missing expected H atoms. Skipping. Residue LYS 129 is missing expected H atoms. Skipping. Residue LYS 221 is missing expected H atoms. Skipping. Residue LYS 313 is missing expected H atoms. Skipping. Residue LEU 112 is missing expected H atoms. Skipping. Residue LYS 123 is missing expected H atoms. Skipping. Residue THR 139 is missing expected H atoms. Skipping. Residue THR 137 is missing expected H atoms. Skipping. Residue SER 140 is missing expected H atoms. Skipping. Residue LEU 65 is missing expected H atoms. Skipping. Residue SER 68 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 126 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Residue LYS 218 is missing expected H atoms. Skipping. Residue LYS 274 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue LYS 38 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Residue THR 73 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 90 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 171 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue LYS 200 is missing expected H atoms. Skipping. Residue LEU 201 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue THR 258 is missing expected H atoms. Skipping. Residue LYS 259 is missing expected H atoms. Skipping. Residue LYS 268 is missing expected H atoms. Skipping. Residue LEU 278 is missing expected H atoms. Skipping. Residue LYS 63 is missing expected H atoms. Skipping. Residue LEU 86 is missing expected H atoms. Skipping. Residue LYS 100 is missing expected H atoms. Skipping. Residue LYS 106 is missing expected H atoms. Skipping. Residue LYS 122 is missing expected H atoms. Skipping. Residue LYS 139 is missing expected H atoms. Skipping. Residue LYS 143 is missing expected H atoms. Skipping. Residue VAL 29 is missing expected H atoms. Skipping. Residue LYS 63 is missing expected H atoms. Skipping. Residue LYS 68 is missing expected H atoms. Skipping. Residue SER 71 is missing expected H atoms. Skipping. Residue LYS 77 is missing expected H atoms. Skipping. Residue LYS 94 is missing expected H atoms. Skipping. Residue LYS 148 is missing expected H atoms. Skipping. Residue LYS 151 is missing expected H atoms. Skipping. Residue LYS 181 is missing expected H atoms. Skipping. Residue LYS 214 is missing expected H atoms. Skipping. Residue LEU 221 is missing expected H atoms. Skipping. Residue LYS 223 is missing expected H atoms. Skipping. Residue LEU 229 is missing expected H atoms. Skipping. Residue VAL 237 is missing expected H atoms. Skipping. Residue SER 239 is missing expected H atoms. Skipping. Residue LYS 154 is missing expected H atoms. Skipping. Residue LYS 18 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Evaluate side-chains 1182 residues out of total 5967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 1143 time to evaluate : 7.472 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 outliers start: 39 outliers final: 30 residues processed: 1164 average time/residue: 2.0160 time to fit residues: 3865.7921 Evaluate side-chains 1150 residues out of total 5967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 1120 time to evaluate : 7.489 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: 30 outliers final: 12 residues processed: 30 average time/residue: 1.7526 time to fit residues: 99.5995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 923 random chunks: chunk 581 optimal weight: 4.9990 chunk 780 optimal weight: 3.9990 chunk 224 optimal weight: 5.9990 chunk 675 optimal weight: 3.9990 chunk 108 optimal weight: 4.9990 chunk 203 optimal weight: 3.9990 chunk 733 optimal weight: 5.9990 chunk 306 optimal weight: 0.7980 chunk 753 optimal weight: 0.9990 chunk 92 optimal weight: 10.0000 chunk 135 optimal weight: 4.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 109 ASN ** I 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 29 GLN 5 106 GLN ** 7 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 149 GLN ** d 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 179 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.139125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.108139 restraints weight = 347436.020| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 0.85 r_work: 0.3050 rms_B_bonded: 1.01 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 1.40 restraints_weight: 0.2500 r_work: 0.2984 rms_B_bonded: 2.02 restraints_weight: 0.1250 r_work: 0.2921 rms_B_bonded: 3.19 restraints_weight: 0.0625 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.4660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.133 119287 Z= 0.323 Angle : 0.635 15.976 174283 Z= 0.326 Chirality : 0.047 3.823 21694 Planarity : 0.005 0.091 12032 Dihedral : 16.185 178.937 40024 Min Nonbonded Distance : 1.676 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.92 % Favored : 93.82 % Rotamer Outliers : 0.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.56 % 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: 0.07 (0.10), residues: 6566 helix: 1.95 (0.11), residues: 2383 sheet: -1.12 (0.18), residues: 778 loop : -1.08 (0.10), residues: 3405 =============================================================================== Job complete usr+sys time: 70989.12 seconds wall clock time: 1212 minutes 13.49 seconds (72733.49 seconds total)