Starting phenix.real_space_refine (version: dev) on Sat Dec 17 13:17:05 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bl5_12218/12_2022/7bl5_12218_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bl5_12218/12_2022/7bl5_12218.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bl5_12218/12_2022/7bl5_12218.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bl5_12218/12_2022/7bl5_12218.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bl5_12218/12_2022/7bl5_12218_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bl5_12218/12_2022/7bl5_12218_updated.pdb" } resolution = 3.3 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= 0.034 sd= 0.789 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 "C ARG 13": "NH1" <-> "NH2" Residue "C ARG 51": "NH1" <-> "NH2" Residue "C ARG 62": "NH1" <-> "NH2" Residue "C PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 78": "OE1" <-> "OE2" Residue "C ARG 79": "NH1" <-> "NH2" Residue "C GLU 99": "OE1" <-> "OE2" Residue "C TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 113": "OD1" <-> "OD2" Residue "C ARG 132": "NH1" <-> "NH2" Residue "C ARG 166": "NH1" <-> "NH2" Residue "C ARG 176": "NH1" <-> "NH2" Residue "C GLU 179": "OE1" <-> "OE2" Residue "C ARG 181": "NH1" <-> "NH2" Residue "C ARG 188": "NH1" <-> "NH2" Residue "C GLU 193": "OE1" <-> "OE2" Residue "C GLU 198": "OE1" <-> "OE2" Residue "C ARG 211": "NH1" <-> "NH2" Residue "C PHE 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 13": "NH1" <-> "NH2" Residue "D GLU 17": "OE1" <-> "OE2" Residue "D GLU 28": "OE1" <-> "OE2" Residue "D ARG 33": "NH1" <-> "NH2" Residue "D ARG 59": "NH1" <-> "NH2" Residue "D GLU 64": "OE1" <-> "OE2" Residue "D ARG 77": "NH1" <-> "NH2" Residue "D ARG 83": "NH1" <-> "NH2" Residue "D PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 169": "NH1" <-> "NH2" Residue "D ASP 181": "OD1" <-> "OD2" Residue "D ARG 184": "NH1" <-> "NH2" Residue "E ARG 21": "NH1" <-> "NH2" Residue "E TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 44": "NH1" <-> "NH2" Residue "E ARG 49": "NH1" <-> "NH2" Residue "E ARG 61": "NH1" <-> "NH2" Residue "E ARG 88": "NH1" <-> "NH2" Residue "E ARG 102": "NH1" <-> "NH2" Residue "E ARG 162": "NH1" <-> "NH2" Residue "E ARG 170": "NH1" <-> "NH2" Residue "E GLU 197": "OE1" <-> "OE2" Residue "E GLU 198": "OE1" <-> "OE2" Residue "G ARG 2": "NH1" <-> "NH2" Residue "G GLU 41": "OE1" <-> "OE2" Residue "G ASP 46": "OD1" <-> "OD2" Residue "G TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 152": "NH1" <-> "NH2" Residue "G GLU 154": "OE1" <-> "OE2" Residue "G ARG 162": "NH1" <-> "NH2" Residue "G ARG 169": "NH1" <-> "NH2" Residue "J ARG 13": "NH1" <-> "NH2" Residue "J TYR 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 37": "NH1" <-> "NH2" Residue "J GLU 43": "OE1" <-> "OE2" Residue "J TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 60": "OD1" <-> "OD2" Residue "J TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 96": "NH1" <-> "NH2" Residue "J GLU 98": "OE1" <-> "OE2" Residue "J PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 120": "NH1" <-> "NH2" Residue "L ARG 21": "NH1" <-> "NH2" Residue "L ARG 33": "NH1" <-> "NH2" Residue "L ARG 41": "NH1" <-> "NH2" Residue "L ARG 47": "NH1" <-> "NH2" Residue "L TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 60": "NH1" <-> "NH2" Residue "L PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 78": "NH1" <-> "NH2" Residue "L ASP 91": "OD1" <-> "OD2" Residue "L ARG 126": "NH1" <-> "NH2" Residue "L GLU 136": "OE1" <-> "OE2" Residue "N ARG 8": "NH1" <-> "NH2" Residue "N ARG 12": "NH1" <-> "NH2" Residue "N ARG 17": "NH1" <-> "NH2" Residue "N ARG 22": "NH1" <-> "NH2" Residue "N ARG 46": "NH1" <-> "NH2" Residue "N ARG 63": "NH1" <-> "NH2" Residue "N ARG 64": "NH1" <-> "NH2" Residue "N ARG 69": "NH1" <-> "NH2" Residue "N ARG 71": "NH1" <-> "NH2" Residue "N GLU 74": "OE1" <-> "OE2" Residue "N PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 96": "NH1" <-> "NH2" Residue "N PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 120": "OE1" <-> "OE2" Residue "O ARG 10": "NH1" <-> "NH2" Residue "O ARG 16": "NH1" <-> "NH2" Residue "O GLU 20": "OE1" <-> "OE2" Residue "O ARG 25": "NH1" <-> "NH2" Residue "O ARG 81": "NH1" <-> "NH2" Residue "O ARG 94": "NH1" <-> "NH2" Residue "O ARG 102": "NH1" <-> "NH2" Residue "O ARG 111": "NH1" <-> "NH2" Residue "Q ARG 2": "NH1" <-> "NH2" Residue "Q ARG 5": "NH1" <-> "NH2" Residue "Q ARG 12": "NH1" <-> "NH2" Residue "Q TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 32": "NH1" <-> "NH2" Residue "Q PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 47": "NH1" <-> "NH2" Residue "Q ARG 69": "NH1" <-> "NH2" Residue "Q PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 21": "NH1" <-> "NH2" Residue "R ASP 26": "OD1" <-> "OD2" Residue "R GLU 31": "OE1" <-> "OE2" Residue "R PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 37": "OE1" <-> "OE2" Residue "R GLU 45": "OE1" <-> "OE2" Residue "R GLU 46": "OE1" <-> "OE2" Residue "R ASP 55": "OD1" <-> "OD2" Residue "R ARG 68": "NH1" <-> "NH2" Residue "R GLU 70": "OE1" <-> "OE2" Residue "R ARG 78": "NH1" <-> "NH2" Residue "R ARG 79": "NH1" <-> "NH2" Residue "R ARG 84": "NH1" <-> "NH2" Residue "S GLU 2": "OE1" <-> "OE2" Residue "S ASP 77": "OD1" <-> "OD2" Residue "S ARG 84": "NH1" <-> "NH2" Residue "S ARG 88": "NH1" <-> "NH2" Residue "S ARG 95": "NH1" <-> "NH2" Residue "S ARG 110": "NH1" <-> "NH2" Residue "T GLU 4": "OE1" <-> "OE2" Residue "T ARG 6": "NH1" <-> "NH2" Residue "T GLU 25": "OE1" <-> "OE2" Residue "T PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 54": "OE1" <-> "OE2" Residue "T ARG 73": "NH1" <-> "NH2" Residue "T ASP 79": "OD1" <-> "OD2" Residue "T TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 89": "OE1" <-> "OE2" Residue "U ARG 5": "NH1" <-> "NH2" Residue "U ARG 6": "NH1" <-> "NH2" Residue "U GLU 59": "OE1" <-> "OE2" Residue "U ARG 81": "NH1" <-> "NH2" Residue "U PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 85": "NH1" <-> "NH2" Residue "U GLU 87": "OE1" <-> "OE2" Residue "V PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 11": "OD1" <-> "OD2" Residue "W GLU 13": "OE1" <-> "OE2" Residue "W GLU 25": "OE1" <-> "OE2" Residue "W PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 66": "OE1" <-> "OE2" Residue "W PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 2": "NH1" <-> "NH2" Residue "X ARG 10": "NH1" <-> "NH2" Residue "X ARG 17": "NH1" <-> "NH2" Residue "X PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 36": "NH1" <-> "NH2" Residue "X GLU 40": "OE1" <-> "OE2" Residue "X ARG 49": "NH1" <-> "NH2" Residue "X ARG 56": "NH1" <-> "NH2" Residue "X ARG 73": "NH1" <-> "NH2" Residue "X TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 17": "OE1" <-> "OE2" Residue "Y GLU 24": "OE1" <-> "OE2" Residue "Y ARG 29": "NH1" <-> "NH2" Residue "Y ARG 47": "NH1" <-> "NH2" Residue "Y ARG 52": "NH1" <-> "NH2" Residue "Z ARG 10": "NH1" <-> "NH2" Residue "Z ARG 29": "NH1" <-> "NH2" Residue "Z GLU 36": "OE1" <-> "OE2" Residue "Z GLU 38": "OE1" <-> "OE2" Residue "Z ARG 44": "NH1" <-> "NH2" Residue "Z GLU 57": "OE1" <-> "OE2" Residue "0 ARG 9": "NH1" <-> "NH2" Residue "0 ARG 15": "NH1" <-> "NH2" Residue "0 TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 ARG 51": "NH1" <-> "NH2" Residue "1 ASP 39": "OD1" <-> "OD2" Residue "1 ARG 43": "NH1" <-> "NH2" Residue "1 TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ARG 3": "NH1" <-> "NH2" Residue "2 ARG 12": "NH1" <-> "NH2" Residue "2 ARG 14": "NH1" <-> "NH2" Residue "2 ARG 19": "NH1" <-> "NH2" Residue "2 ARG 21": "NH1" <-> "NH2" Residue "2 ARG 33": "NH1" <-> "NH2" Residue "2 ARG 41": "NH1" <-> "NH2" Residue "I PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 45": "OE1" <-> "OE2" Residue "K GLU 92": "OE1" <-> "OE2" Residue "P ARG 20": "NH1" <-> "NH2" Residue "P ARG 38": "NH1" <-> "NH2" Residue "P PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 61": "NH1" <-> "NH2" Residue "P ASP 81": "OD1" <-> "OD2" Residue "P ARG 88": "NH1" <-> "NH2" Residue "P TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 100": "NH1" <-> "NH2" Residue "P ARG 108": "NH1" <-> "NH2" Residue "6 ASP 35": "OD1" <-> "OD2" Residue "6 GLU 70": "OE1" <-> "OE2" Residue "6 ARG 96": "NH1" <-> "NH2" Residue "6 TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ARG 4": "NH1" <-> "NH2" Residue "7 ARG 19": "NH1" <-> "NH2" Residue "7 ARG 33": "NH1" <-> "NH2" Residue "7 GLU 57": "OE1" <-> "OE2" Residue "7 ARG 76": "NH1" <-> "NH2" Residue "7 GLU 78": "OE1" <-> "OE2" Residue "7 ASP 92": "OD1" <-> "OD2" Residue "7 ASP 101": "OD1" <-> "OD2" Residue "7 ARG 131": "NH1" <-> "NH2" Residue "7 ARG 157": "NH1" <-> "NH2" Residue "7 GLU 160": "OE1" <-> "OE2" Residue "7 GLU 166": "OE1" <-> "OE2" Residue "7 GLU 172": "OE1" <-> "OE2" Residue "7 ARG 196": "NH1" <-> "NH2" Residue "7 TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 TYR 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ARG 272": "NH1" <-> "NH2" Residue "7 ARG 276": "NH1" <-> "NH2" Residue "7 GLU 294": "OE1" <-> "OE2" Residue "7 GLU 307": "OE1" <-> "OE2" Residue "7 ASP 315": "OD1" <-> "OD2" Residue "8 ARG 90": "NH1" <-> "NH2" Residue "8 ASP 93": "OD1" <-> "OD2" Residue "8 PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 GLU 119": "OE1" <-> "OE2" Residue "8 ASP 144": "OD1" <-> "OD2" Residue "8 GLU 158": "OE1" <-> "OE2" Residue "8 ARG 169": "NH1" <-> "NH2" Residue "8 GLU 182": "OE1" <-> "OE2" Residue "9 GLU 6": "OE1" <-> "OE2" Residue "9 ARG 25": "NH1" <-> "NH2" Residue "9 GLU 48": "OE1" <-> "OE2" Residue "9 GLU 51": "OE1" <-> "OE2" Residue "9 PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 ARG 129": "NH1" <-> "NH2" Residue "9 ARG 136": "NH1" <-> "NH2" Residue "9 GLU 151": "OE1" <-> "OE2" Residue "9 ARG 177": "NH1" <-> "NH2" Residue "9 PHE 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 GLU 206": "OE1" <-> "OE2" Residue "9 PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 ARG 230": "NH1" <-> "NH2" Residue "9 ARG 239": "NH1" <-> "NH2" Residue "9 GLU 307": "OE1" <-> "OE2" Residue "9 TYR 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 10": "NH1" <-> "NH2" Residue "M ARG 18": "NH1" <-> "NH2" Residue "M ARG 40": "NH1" <-> "NH2" Residue "M ARG 44": "NH1" <-> "NH2" Residue "M ARG 50": "NH1" <-> "NH2" Residue "M ARG 55": "NH1" <-> "NH2" Residue "M ARG 59": "NH1" <-> "NH2" Residue "M ARG 114": "NH1" <-> "NH2" Residue "H ARG 27": "NH1" <-> "NH2" Residue "H PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 48": "OE1" <-> "OE2" Residue "H GLU 109": "OE1" <-> "OE2" Residue "H GLU 127": "OE1" <-> "OE2" Residue "H PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 31": "OE1" <-> "OE2" Residue "F ARG 70": "NH1" <-> "NH2" Residue "F ARG 79": "NH1" <-> "NH2" Residue "F ARG 91": "NH1" <-> "NH2" Residue "F GLU 97": "OE1" <-> "OE2" Residue "F PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 101": "NH1" <-> "NH2" Residue "F ARG 109": "NH1" <-> "NH2" Residue "F ARG 111": "NH1" <-> "NH2" Residue "F ARG 114": "NH1" <-> "NH2" Residue "F PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 122": "OD1" <-> "OD2" Residue "F ARG 132": "NH1" <-> "NH2" Residue "F PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 35": "OD1" <-> "OD2" Residue "b PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 98927 Number of models: 1 Model: "" Number of chains: 46 Chain: "C" Number of atoms: 2082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2082 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 17, 'TRANS': 253} Chain: "D" Number of atoms: 1565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1565 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 202} Chain: "E" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1552 Classifications: {'peptide': 201} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 195} Chain: "G" Number of atoms: 1281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1281 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 8, 'TRANS': 162} Chain: "J" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1129 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 135} Chain: "L" Number of atoms: 1045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1045 Classifications: {'peptide': 143} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 138} Chain: "N" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 960 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "O" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 892 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "Q" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 947 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'TRANS': 116} Chain: "R" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 816 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 101} Chain: "S" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 857 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 107} Chain: "T" Number of atoms: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 738 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 1, 'TRANS': 91} Chain: "U" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 779 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "V" Number of atoms: 753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 753 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "W" Number of atoms: 575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 575 Classifications: {'peptide': 76} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 74} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU%COO:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "X" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 625 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "Y" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 509 Classifications: {'peptide': 63} Modifications used: {'COO': 1} Link IDs: {'TRANS': 62} Chain: "Z" Number of atoms: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 449 Classifications: {'peptide': 58} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "0" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 444 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 54} Chain: "1" Number of atoms: 409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 409 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "2" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 377 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "B" Number of atoms: 2548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 2548 Classifications: {'RNA': 119} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 6, 'rna3p_pur': 57, 'rna3p_pyr': 49} Link IDs: {'rna2p': 13, 'rna3p': 105} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 1032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1032 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 131} Chain: "K" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 938 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "P" Number of atoms: 911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 911 Classifications: {'peptide': 113} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 109} Chain: "6" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 780 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 1, 'TRANS': 100} Chain: "7" Number of atoms: 2533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2533 Classifications: {'peptide': 317} Link IDs: {'PTRANS': 23, 'TRANS': 293} Chain breaks: 1 Chain: "8" Number of atoms: 1281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1281 Classifications: {'peptide': 157} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 151} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "9" Number of atoms: 2582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2582 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 14, 'TRANS': 323} Chain: "M" Number of atoms: 1074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1074 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 128} Chain: "A" Number of atoms: 62534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2913, 62534 Classifications: {'RNA': 2913} Modifications used: {'rna2p_pur': 274, 'rna2p_pyr': 156, 'rna3p_pur': 1406, 'rna3p_pyr': 1077} Link IDs: {'rna2p': 430, 'rna3p': 2482} Chain breaks: 1 Chain: "H" Number of atoms: 1110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1110 Classifications: {'peptide': 149} Link IDs: {'PTRANS': 3, 'TRANS': 145} Chain: "e" Number of atoms: 988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 988 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 5, 'TRANS': 125} Chain: "F" Number of atoms: 1410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1410 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 6, 'TRANS': 170} Chain: "b" Number of atoms: 364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 364 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 2, 'TRANS': 44} Chain: "9" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 29 Unusual residues: {' MG': 1, 'GDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "b" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "N" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "S" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "2" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "A" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 98635 SG CYS b 16 79.008 16.543 86.917 1.00241.22 S ATOM 98647 SG CYS b 18 81.272 13.966 87.816 1.00237.97 S ATOM 98789 SG CYS b 37 78.821 16.632 90.288 1.00237.10 S ATOM 98810 SG CYS b 40 79.991 14.096 90.093 1.00239.59 S Time building chain proxies: 41.26, per 1000 atoms: 0.42 Number of scatterers: 98927 At special positions: 0 Unit cell: (230.64, 225.68, 261.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 116 16.00 P 3033 15.00 Mg 2 11.99 O 27193 8.00 N 18357 7.00 C 50225 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 44.19 Conformation dependent library (CDL) restraints added in 4.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN b 100 " pdb="ZN ZN b 100 " - pdb=" SG CYS b 37 " pdb="ZN ZN b 100 " - pdb=" SG CYS b 40 " pdb="ZN ZN b 100 " - pdb=" SG CYS b 18 " pdb="ZN ZN b 100 " - pdb=" SG CYS b 16 " Number of angles added : 6 8560 Ramachandran restraints generated. 4280 Oldfield, 0 Emsley, 4280 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7948 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 126 helices and 51 sheets defined 25.9% alpha, 15.3% beta 978 base pairs and 1556 stacking pairs defined. Time for finding SS restraints: 39.79 Creating SS restraints... Processing helix chain 'C' and resid 11 through 13 No H-bonds generated for 'chain 'C' and resid 11 through 13' Processing helix chain 'C' and resid 30 through 32 No H-bonds generated for 'chain 'C' and resid 30 through 32' Processing helix chain 'C' and resid 207 through 213 removed outlier: 3.585A pdb=" N ARG C 213 " --> pdb=" O ALA C 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 71 removed outlier: 3.623A pdb=" N ALA D 71 " --> pdb=" O HIS D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 99 through 102 Processing helix chain 'D' and resid 121 through 124 No H-bonds generated for 'chain 'D' and resid 121 through 124' Processing helix chain 'E' and resid 25 through 39 Processing helix chain 'E' and resid 98 through 114 Processing helix chain 'E' and resid 131 through 141 Processing helix chain 'E' and resid 155 through 161 Processing helix chain 'E' and resid 179 through 182 No H-bonds generated for 'chain 'E' and resid 179 through 182' Processing helix chain 'E' and resid 190 through 200 Processing helix chain 'G' and resid 2 through 5 No H-bonds generated for 'chain 'G' and resid 2 through 5' Processing helix chain 'G' and resid 60 through 75 removed outlier: 3.523A pdb=" N GLN G 63 " --> pdb=" O GLY G 60 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLY G 65 " --> pdb=" O ALA G 62 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG G 68 " --> pdb=" O GLY G 65 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N VAL G 75 " --> pdb=" O ASN G 72 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 150 removed outlier: 3.714A pdb=" N GLN G 142 " --> pdb=" O GLN G 138 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N TYR G 150 " --> pdb=" O ASP G 146 " (cutoff:3.500A) Processing helix chain 'J' and resid 25 through 37 Processing helix chain 'J' and resid 59 through 61 No H-bonds generated for 'chain 'J' and resid 59 through 61' Processing helix chain 'J' and resid 68 through 71 No H-bonds generated for 'chain 'J' and resid 68 through 71' Processing helix chain 'J' and resid 89 through 106 removed outlier: 3.531A pdb=" N ALA J 94 " --> pdb=" O GLU J 90 " (cutoff:3.500A) Proline residue: J 97 - end of helix removed outlier: 4.462A pdb=" N VAL J 100 " --> pdb=" O ARG J 96 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N ILE J 101 " --> pdb=" O PRO J 97 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N GLU J 102 " --> pdb=" O GLU J 98 " (cutoff:3.500A) Processing helix chain 'J' and resid 113 through 121 removed outlier: 3.946A pdb=" N LYS J 121 " --> pdb=" O ALA J 117 " (cutoff:3.500A) Processing helix chain 'J' and resid 133 through 135 No H-bonds generated for 'chain 'J' and resid 133 through 135' Processing helix chain 'L' and resid 3 through 5 No H-bonds generated for 'chain 'L' and resid 3 through 5' Processing helix chain 'L' and resid 57 through 60 No H-bonds generated for 'chain 'L' and resid 57 through 60' Processing helix chain 'L' and resid 129 through 138 removed outlier: 3.591A pdb=" N ALA L 133 " --> pdb=" O LYS L 129 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA L 137 " --> pdb=" O ALA L 133 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA L 138 " --> pdb=" O ALA L 134 " (cutoff:3.500A) Processing helix chain 'N' and resid 14 through 31 Processing helix chain 'N' and resid 38 through 46 removed outlier: 4.239A pdb=" N ARG N 46 " --> pdb=" O LYS N 42 " (cutoff:3.500A) Processing helix chain 'N' and resid 48 through 56 removed outlier: 3.759A pdb=" N ILE N 52 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR N 53 " --> pdb=" O GLU N 49 " (cutoff:3.500A) Processing helix chain 'N' and resid 60 through 68 Processing helix chain 'N' and resid 73 through 78 Processing helix chain 'N' and resid 83 through 86 No H-bonds generated for 'chain 'N' and resid 83 through 86' Processing helix chain 'O' and resid 3 through 21 removed outlier: 4.110A pdb=" N ARG O 7 " --> pdb=" O LYS O 3 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR O 12 " --> pdb=" O ILE O 8 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N ARG O 13 " --> pdb=" O ARG O 9 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N ALA O 14 " --> pdb=" O ARG O 10 " (cutoff:3.500A) Processing helix chain 'O' and resid 68 through 83 removed outlier: 4.172A pdb=" N ALA O 73 " --> pdb=" O ASP O 69 " (cutoff:3.500A) Processing helix chain 'O' and resid 102 through 113 removed outlier: 3.710A pdb=" N LEU O 106 " --> pdb=" O ARG O 102 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA O 110 " --> pdb=" O LEU O 106 " (cutoff:3.500A) Processing helix chain 'Q' and resid 8 through 19 Processing helix chain 'Q' and resid 25 through 28 Processing helix chain 'Q' and resid 31 through 71 removed outlier: 4.291A pdb=" N GLN Q 36 " --> pdb=" O ARG Q 32 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE Q 39 " --> pdb=" O PHE Q 35 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ARG Q 50 " --> pdb=" O TYR Q 46 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LYS Q 53 " --> pdb=" O ARG Q 49 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ARG Q 54 " --> pdb=" O ARG Q 50 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE Q 61 " --> pdb=" O ARG Q 57 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ALA Q 62 " --> pdb=" O GLN Q 58 " (cutoff:3.500A) Processing helix chain 'Q' and resid 75 through 84 Processing helix chain 'Q' and resid 91 through 100 Processing helix chain 'Q' and resid 102 through 116 removed outlier: 3.518A pdb=" N GLU Q 110 " --> pdb=" O THR Q 106 " (cutoff:3.500A) Processing helix chain 'S' and resid 14 through 23 removed outlier: 3.553A pdb=" N LEU S 19 " --> pdb=" O GLN S 15 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N VAL S 20 " --> pdb=" O LYS S 16 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASP S 22 " --> pdb=" O ARG S 18 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N LEU S 23 " --> pdb=" O LEU S 19 " (cutoff:3.500A) Processing helix chain 'S' and resid 29 through 37 Processing helix chain 'S' and resid 42 through 60 Processing helix chain 'S' and resid 89 through 91 No H-bonds generated for 'chain 'S' and resid 89 through 91' Processing helix chain 'T' and resid 4 through 9 removed outlier: 3.881A pdb=" N LYS T 9 " --> pdb=" O GLU T 5 " (cutoff:3.500A) Processing helix chain 'T' and resid 18 through 25 removed outlier: 4.418A pdb=" N GLU T 25 " --> pdb=" O SER T 21 " (cutoff:3.500A) Processing helix chain 'T' and resid 40 through 50 removed outlier: 3.843A pdb=" N VAL T 47 " --> pdb=" O ILE T 43 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLN T 48 " --> pdb=" O LYS T 44 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LYS T 49 " --> pdb=" O ALA T 45 " (cutoff:3.500A) Processing helix chain 'U' and resid 66 through 68 No H-bonds generated for 'chain 'U' and resid 66 through 68' Processing helix chain 'V' and resid 14 through 23 removed outlier: 3.791A pdb=" N ALA V 22 " --> pdb=" O ARG V 18 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ALA V 23 " --> pdb=" O ARG V 19 " (cutoff:3.500A) Processing helix chain 'V' and resid 45 through 52 removed outlier: 3.821A pdb=" N ASN V 49 " --> pdb=" O ASP V 45 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA V 52 " --> pdb=" O MET V 48 " (cutoff:3.500A) Processing helix chain 'V' and resid 54 through 57 removed outlier: 4.001A pdb=" N TYR V 57 " --> pdb=" O ALA V 54 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 54 through 57' Processing helix chain 'X' and resid 52 through 61 Processing helix chain 'X' and resid 63 through 73 Processing helix chain 'Y' and resid 5 through 7 No H-bonds generated for 'chain 'Y' and resid 5 through 7' Processing helix chain 'Y' and resid 10 through 23 removed outlier: 3.539A pdb=" N LEU Y 21 " --> pdb=" O GLU Y 17 " (cutoff:3.500A) Processing helix chain 'Y' and resid 27 through 33 removed outlier: 3.770A pdb=" N GLN Y 31 " --> pdb=" O ASN Y 27 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA Y 32 " --> pdb=" O LEU Y 28 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA Y 33 " --> pdb=" O ARG Y 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 27 through 33' Processing helix chain 'Y' and resid 41 through 54 removed outlier: 4.092A pdb=" N ARG Y 48 " --> pdb=" O LYS Y 44 " (cutoff:3.500A) Processing helix chain 'Z' and resid 17 through 26 Processing helix chain 'Z' and resid 41 through 50 removed outlier: 3.721A pdb=" N VAL Z 50 " --> pdb=" O MET Z 46 " (cutoff:3.500A) Processing helix chain '0' and resid 9 through 15 removed outlier: 3.564A pdb=" N ARG 0 15 " --> pdb=" O LYS 0 11 " (cutoff:3.500A) Processing helix chain '0' and resid 17 through 19 No H-bonds generated for 'chain '0' and resid 17 through 19' Processing helix chain '2' and resid 9 through 16 removed outlier: 3.532A pdb=" N SER 2 15 " --> pdb=" O LYS 2 11 " (cutoff:3.500A) Processing helix chain '2' and resid 18 through 21 No H-bonds generated for 'chain '2' and resid 18 through 21' Processing helix chain '2' and resid 25 through 37 Processing helix chain 'I' and resid 35 through 38 removed outlier: 4.074A pdb=" N CYS I 38 " --> pdb=" O MET I 35 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 35 through 38' Processing helix chain 'I' and resid 41 through 43 No H-bonds generated for 'chain 'I' and resid 41 through 43' Processing helix chain 'I' and resid 45 through 48 No H-bonds generated for 'chain 'I' and resid 45 through 48' Processing helix chain 'I' and resid 77 through 80 removed outlier: 3.887A pdb=" N LYS I 80 " --> pdb=" O VAL I 77 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 77 through 80' Processing helix chain 'I' and resid 108 through 111 Processing helix chain 'I' and resid 121 through 125 Processing helix chain 'I' and resid 129 through 131 No H-bonds generated for 'chain 'I' and resid 129 through 131' Processing helix chain 'K' and resid 105 through 107 No H-bonds generated for 'chain 'K' and resid 105 through 107' Processing helix chain 'K' and resid 113 through 117 Processing helix chain 'P' and resid 5 through 11 removed outlier: 4.054A pdb=" N GLN P 9 " --> pdb=" O LYS P 5 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLU P 10 " --> pdb=" O GLN P 6 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN P 11 " --> pdb=" O LEU P 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 5 through 11' Processing helix chain 'P' and resid 53 through 55 No H-bonds generated for 'chain 'P' and resid 53 through 55' Processing helix chain 'P' and resid 97 through 100 removed outlier: 3.600A pdb=" N ARG P 100 " --> pdb=" O TYR P 97 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 97 through 100' Processing helix chain '6' and resid 3 through 17 removed outlier: 3.850A pdb=" N ASP 6 12 " --> pdb=" O ASP 6 8 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N LYS 6 13 " --> pdb=" O PHE 6 9 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU 6 17 " --> pdb=" O LYS 6 13 " (cutoff:3.500A) Processing helix chain '6' and resid 45 through 61 removed outlier: 3.631A pdb=" N ALA 6 61 " --> pdb=" O GLN 6 57 " (cutoff:3.500A) Processing helix chain '6' and resid 92 through 97 removed outlier: 4.070A pdb=" N ARG 6 96 " --> pdb=" O GLU 6 92 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N LEU 6 97 " --> pdb=" O GLU 6 93 " (cutoff:3.500A) No H-bonds generated for 'chain '6' and resid 92 through 97' Processing helix chain '7' and resid 20 through 27 removed outlier: 3.594A pdb=" N LEU 7 24 " --> pdb=" O LEU 7 20 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA 7 25 " --> pdb=" O ASP 7 21 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU 7 26 " --> pdb=" O GLN 7 22 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N MET 7 27 " --> pdb=" O ALA 7 23 " (cutoff:3.500A) No H-bonds generated for 'chain '7' and resid 20 through 27' Processing helix chain '7' and resid 33 through 41 removed outlier: 3.915A pdb=" N TRP 7 39 " --> pdb=" O ARG 7 35 " (cutoff:3.500A) Processing helix chain '7' and resid 115 through 122 Processing helix chain '7' and resid 124 through 128 removed outlier: 3.959A pdb=" N ALA 7 127 " --> pdb=" O PRO 7 124 " (cutoff:3.500A) Processing helix chain '7' and resid 130 through 133 Processing helix chain '7' and resid 152 through 164 Processing helix chain '7' and resid 235 through 241 Processing helix chain '7' and resid 265 through 273 Processing helix chain '7' and resid 303 through 319 Processing helix chain '8' and resid 29 through 47 Processing helix chain '8' and resid 51 through 56 removed outlier: 3.832A pdb=" N ASP 8 55 " --> pdb=" O LYS 8 51 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N LYS 8 56 " --> pdb=" O ASN 8 52 " (cutoff:3.500A) No H-bonds generated for 'chain '8' and resid 51 through 56' Processing helix chain '8' and resid 61 through 72 removed outlier: 3.688A pdb=" N LEU 8 69 " --> pdb=" O ALA 8 65 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLN 8 71 " --> pdb=" O ILE 8 67 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ARG 8 72 " --> pdb=" O GLU 8 68 " (cutoff:3.500A) Processing helix chain '8' and resid 75 through 90 removed outlier: 3.502A pdb=" N MET 8 88 " --> pdb=" O LEU 8 84 " (cutoff:3.500A) Processing helix chain '8' and resid 95 through 104 Processing helix chain '8' and resid 109 through 126 removed outlier: 3.720A pdb=" N ARG 8 122 " --> pdb=" O LEU 8 118 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ASP 8 123 " --> pdb=" O GLU 8 119 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ARG 8 124 " --> pdb=" O ASN 8 120 " (cutoff:3.500A) Processing helix chain '8' and resid 133 through 139 Processing helix chain '8' and resid 145 through 160 removed outlier: 4.031A pdb=" N THR 8 150 " --> pdb=" O GLN 8 146 " (cutoff:3.500A) Processing helix chain '8' and resid 168 through 180 removed outlier: 3.662A pdb=" N PHE 8 172 " --> pdb=" O ALA 8 168 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLU 8 180 " --> pdb=" O ARG 8 176 " (cutoff:3.500A) Processing helix chain '9' and resid 57 through 61 Processing helix chain '9' and resid 128 through 130 No H-bonds generated for 'chain '9' and resid 128 through 130' Processing helix chain '9' and resid 172 through 176 Processing helix chain '9' and resid 229 through 234 removed outlier: 5.018A pdb=" N HIS 9 234 " --> pdb=" O ARG 9 230 " (cutoff:3.500A) Processing helix chain '9' and resid 258 through 267 removed outlier: 4.273A pdb=" N ILE 9 263 " --> pdb=" O ALA 9 259 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU 9 266 " --> pdb=" O ILE 9 262 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLU 9 267 " --> pdb=" O ILE 9 263 " (cutoff:3.500A) Processing helix chain '9' and resid 272 through 275 Processing helix chain '9' and resid 292 through 303 removed outlier: 4.013A pdb=" N LYS 9 296 " --> pdb=" O GLU 9 292 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA 9 297 " --> pdb=" O ALA 9 293 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA 9 301 " --> pdb=" O ALA 9 297 " (cutoff:3.500A) Processing helix chain '9' and resid 321 through 334 Processing helix chain 'M' and resid 43 through 56 removed outlier: 4.086A pdb=" N ALA M 56 " --> pdb=" O ALA M 52 " (cutoff:3.500A) Processing helix chain 'M' and resid 110 through 123 removed outlier: 3.688A pdb=" N ALA M 122 " --> pdb=" O LYS M 118 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N LYS M 123 " --> pdb=" O LEU M 119 " (cutoff:3.500A) Processing helix chain 'H' and resid 23 through 26 No H-bonds generated for 'chain 'H' and resid 23 through 26' Processing helix chain 'H' and resid 43 through 58 removed outlier: 3.593A pdb=" N ALA H 49 " --> pdb=" O GLU H 45 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG H 50 " --> pdb=" O PHE H 46 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA H 52 " --> pdb=" O GLU H 48 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLU H 53 " --> pdb=" O ALA H 49 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU H 55 " --> pdb=" O ARG H 51 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N ALA H 56 " --> pdb=" O ALA H 52 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 74 removed outlier: 3.520A pdb=" N ALA H 65 " --> pdb=" O VAL H 61 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASN H 66 " --> pdb=" O LEU H 62 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ALA H 67 " --> pdb=" O ALA H 63 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ARG H 68 " --> pdb=" O ALA H 64 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ILE H 72 " --> pdb=" O ARG H 68 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ASN H 73 " --> pdb=" O ALA H 69 " (cutoff:3.500A) Processing helix chain 'H' and resid 86 through 88 No H-bonds generated for 'chain 'H' and resid 86 through 88' Processing helix chain 'H' and resid 96 through 106 Processing helix chain 'H' and resid 112 through 114 No H-bonds generated for 'chain 'H' and resid 112 through 114' Processing helix chain 'e' and resid 5 through 20 removed outlier: 3.725A pdb=" N ALA e 19 " --> pdb=" O VAL e 15 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LYS e 20 " --> pdb=" O SER e 16 " (cutoff:3.500A) Processing helix chain 'e' and resid 34 through 40 removed outlier: 3.569A pdb=" N THR e 39 " --> pdb=" O VAL e 35 " (cutoff:3.500A) Processing helix chain 'e' and resid 42 through 47 Processing helix chain 'e' and resid 64 through 66 No H-bonds generated for 'chain 'e' and resid 64 through 66' Processing helix chain 'e' and resid 72 through 78 removed outlier: 4.222A pdb=" N PHE e 76 " --> pdb=" O LYS e 73 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL e 77 " --> pdb=" O ASP e 74 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLY e 78 " --> pdb=" O ALA e 75 " (cutoff:3.500A) Processing helix chain 'e' and resid 94 through 101 removed outlier: 4.034A pdb=" N PHE e 99 " --> pdb=" O PHE e 96 " (cutoff:3.500A) Processing helix chain 'e' and resid 111 through 113 No H-bonds generated for 'chain 'e' and resid 111 through 113' Processing helix chain 'F' and resid 2 through 9 Processing helix chain 'F' and resid 11 through 19 removed outlier: 3.577A pdb=" N MET F 16 " --> pdb=" O VAL F 12 " (cutoff:3.500A) Processing helix chain 'F' and resid 46 through 59 Processing helix chain 'F' and resid 94 through 104 removed outlier: 3.719A pdb=" N ARG F 101 " --> pdb=" O GLU F 97 " (cutoff:3.500A) Processing helix chain 'F' and resid 107 through 109 No H-bonds generated for 'chain 'F' and resid 107 through 109' Processing helix chain 'F' and resid 134 through 136 No H-bonds generated for 'chain 'F' and resid 134 through 136' Processing helix chain 'F' and resid 162 through 172 removed outlier: 3.629A pdb=" N ARG F 166 " --> pdb=" O ASP F 162 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA F 167 " --> pdb=" O GLU F 163 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'C' and resid 2 through 4 Processing sheet with id= B, first strand: chain 'C' and resid 100 through 104 removed outlier: 5.762A pdb=" N LEU C 94 " --> pdb=" O VAL C 77 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N VAL C 77 " --> pdb=" O LEU C 94 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 128 through 130 Processing sheet with id= D, first strand: chain 'C' and resid 180 through 184 removed outlier: 4.089A pdb=" N ALA C 165 " --> pdb=" O THR C 172 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ARG C 174 " --> pdb=" O ILE C 163 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ILE C 163 " --> pdb=" O ARG C 174 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'D' and resid 169 through 172 removed outlier: 4.563A pdb=" N THR D 112 " --> pdb=" O ASP D 200 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ASP D 200 " --> pdb=" O THR D 112 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N VAL D 26 " --> pdb=" O VAL D 9 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N MET D 11 " --> pdb=" O VAL D 24 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N VAL D 24 " --> pdb=" O MET D 11 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N ARG D 13 " --> pdb=" O ILE D 22 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ILE D 22 " --> pdb=" O ARG D 13 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'D' and resid 78 through 83 removed outlier: 3.929A pdb=" N GLY D 78 " --> pdb=" O THR D 52 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N THR D 52 " --> pdb=" O GLY D 78 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N THR D 51 " --> pdb=" O VAL D 34 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N VAL D 34 " --> pdb=" O THR D 51 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'E' and resid 167 through 171 removed outlier: 7.166A pdb=" N VAL E 146 " --> pdb=" O ASP E 168 " (cutoff:3.500A) removed outlier: 8.373A pdb=" N ARG E 170 " --> pdb=" O VAL E 146 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ILE E 148 " --> pdb=" O ARG E 170 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N LYS E 185 " --> pdb=" O LEU E 147 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N ILE E 149 " --> pdb=" O LYS E 185 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N VAL E 187 " --> pdb=" O ILE E 149 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'G' and resid 17 through 19 removed outlier: 4.373A pdb=" N VAL G 22 " --> pdb=" O ASN G 19 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'G' and resid 160 through 163 removed outlier: 3.643A pdb=" N PHE G 82 " --> pdb=" O GLY G 134 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU G 86 " --> pdb=" O ILE G 130 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ILE G 130 " --> pdb=" O LEU G 86 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'G' and resid 94 through 98 Processing sheet with id= K, first strand: chain 'J' and resid 138 through 140 removed outlier: 4.616A pdb=" N ASP J 19 " --> pdb=" O LEU J 140 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'J' and resid 73 through 77 Processing sheet with id= M, first strand: chain 'L' and resid 121 through 123 removed outlier: 6.493A pdb=" N LYS L 141 " --> pdb=" O VAL L 122 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'N' and resid 33 through 37 Processing sheet with id= O, first strand: chain 'O' and resid 25 through 27 Processing sheet with id= P, first strand: chain 'R' and resid 11 through 14 removed outlier: 3.531A pdb=" N PHE R 5 " --> pdb=" O HIS R 12 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N MET R 40 " --> pdb=" O VAL R 4 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N GLN R 6 " --> pdb=" O VAL R 38 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N VAL R 38 " --> pdb=" O GLN R 6 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'R' and resid 19 through 22 removed outlier: 6.132A pdb=" N LYS R 97 " --> pdb=" O VAL R 63 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N VAL R 63 " --> pdb=" O LYS R 97 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'R' and resid 72 through 78 removed outlier: 4.303A pdb=" N TYR R 83 " --> pdb=" O ARG R 78 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'S' and resid 3 through 7 removed outlier: 6.141A pdb=" N SER S 108 " --> pdb=" O VAL S 71 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N VAL S 71 " --> pdb=" O SER S 108 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'S' and resid 81 through 87 removed outlier: 3.992A pdb=" N MET S 82 " --> pdb=" O LYS S 98 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LYS S 98 " --> pdb=" O MET S 82 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'T' and resid 11 through 14 removed outlier: 6.398A pdb=" N LYS T 33 " --> pdb=" O ARG T 12 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N VAL T 31 " --> pdb=" O PRO T 14 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LYS T 81 " --> pdb=" O VAL T 34 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU T 61 " --> pdb=" O LYS T 82 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL T 57 " --> pdb=" O THR T 86 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'U' and resid 21 through 23 Processing sheet with id= W, first strand: chain 'U' and resid 40 through 45 removed outlier: 3.774A pdb=" N LYS U 60 " --> pdb=" O VAL U 41 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLY U 56 " --> pdb=" O GLN U 45 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'U' and resid 82 through 86 Processing sheet with id= Y, first strand: chain 'U' and resid 24 through 27 removed outlier: 7.001A pdb=" N ILE U 34 " --> pdb=" O LYS U 25 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'V' and resid 3 through 5 removed outlier: 6.973A pdb=" N THR V 62 " --> pdb=" O ILE V 4 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N ASP V 90 " --> pdb=" O GLN V 75 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ILE V 89 " --> pdb=" O PRO V 27 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ILE V 29 " --> pdb=" O ILE V 89 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N PHE V 91 " --> pdb=" O ILE V 29 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N TYR V 31 " --> pdb=" O PHE V 91 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU V 41 " --> pdb=" O GLU V 7 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N GLU V 7 " --> pdb=" O GLU V 41 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'W' and resid 47 through 49 Processing sheet with id= AB, first strand: chain 'W' and resid 62 through 68 Processing sheet with id= AC, first strand: chain 'X' and resid 12 through 15 Processing sheet with id= AD, first strand: chain 'X' and resid 32 through 39 removed outlier: 3.718A pdb=" N VAL X 39 " --> pdb=" O ARG X 44 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ARG X 44 " --> pdb=" O VAL X 39 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'Z' and resid 34 through 38 Processing sheet with id= AF, first strand: chain '1' and resid 6 through 11 Processing sheet with id= AG, first strand: chain '1' and resid 35 through 39 removed outlier: 3.528A pdb=" N GLN 1 44 " --> pdb=" O ASP 1 39 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'I' and resid 98 through 101 Processing sheet with id= AI, first strand: chain 'K' and resid 6 through 9 removed outlier: 6.739A pdb=" N LYS K 40 " --> pdb=" O ILE K 22 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LYS K 59 " --> pdb=" O LEU K 87 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ALA K 83 " --> pdb=" O VAL K 63 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'P' and resid 82 through 87 removed outlier: 3.781A pdb=" N SER P 82 " --> pdb=" O LYS P 28 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N THR P 24 " --> pdb=" O LYS P 86 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLY P 44 " --> pdb=" O VAL P 25 " (cutoff:3.500A) removed outlier: 8.789A pdb=" N GLU P 43 " --> pdb=" O ILE P 63 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N ILE P 63 " --> pdb=" O GLU P 43 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N THR P 59 " --> pdb=" O ILE P 47 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N ILE P 49 " --> pdb=" O ALA P 57 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ALA P 57 " --> pdb=" O ILE P 49 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain '6' and resid 23 through 26 removed outlier: 3.656A pdb=" N ILE 6 23 " --> pdb=" O ILE 6 39 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL 6 89 " --> pdb=" O ILE 6 78 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ILE 6 78 " --> pdb=" O VAL 6 89 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain '7' and resid 4 through 10 removed outlier: 4.401A pdb=" N ALA 7 69 " --> pdb=" O VAL 7 5 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain '7' and resid 144 through 149 removed outlier: 6.250A pdb=" N ASN 7 97 " --> pdb=" O ILE 7 86 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N ILE 7 86 " --> pdb=" O ASN 7 97 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain '7' and resid 169 through 176 removed outlier: 4.292A pdb=" N ARG 7 169 " --> pdb=" O LEU 7 228 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain '7' and resid 283 through 287 removed outlier: 3.568A pdb=" N TRP 7 297 " --> pdb=" O LEU 7 284 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU 7 286 " --> pdb=" O MET 7 295 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain '9' and resid 64 through 66 removed outlier: 8.773A pdb=" N PHE 9 65 " --> pdb=" O SER 9 8 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N LEU 9 10 " --> pdb=" O PHE 9 65 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ALA 9 7 " --> pdb=" O LEU 9 154 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG 9 150 " --> pdb=" O VAL 9 11 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain '9' and resid 86 through 91 removed outlier: 3.639A pdb=" N ALA 9 118 " --> pdb=" O VAL 9 45 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N MET 9 47 " --> pdb=" O LEU 9 116 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N LEU 9 116 " --> pdb=" O MET 9 47 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N ALA 9 49 " --> pdb=" O ARG 9 114 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N ARG 9 114 " --> pdb=" O ALA 9 49 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain '9' and resid 162 through 166 removed outlier: 5.855A pdb=" N VAL 9 240 " --> pdb=" O GLY 9 163 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N LEU 9 165 " --> pdb=" O VAL 9 240 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N LEU 9 242 " --> pdb=" O LEU 9 165 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain '9' and resid 199 through 201 Processing sheet with id= AT, first strand: chain 'M' and resid 128 through 132 removed outlier: 3.606A pdb=" N TYR M 103 " --> pdb=" O LEU M 33 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N ALA M 35 " --> pdb=" O VAL M 101 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N VAL M 101 " --> pdb=" O ALA M 35 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'M' and resid 39 through 42 removed outlier: 3.621A pdb=" N GLY M 39 " --> pdb=" O ILE M 96 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N GLU M 90 " --> pdb=" O ILE M 73 " (cutoff:3.500A) removed outlier: 8.410A pdb=" N ILE M 73 " --> pdb=" O GLU M 90 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N TRP M 92 " --> pdb=" O LYS M 71 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N LYS M 71 " --> pdb=" O TRP M 92 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'H' and resid 3 through 5 removed outlier: 3.544A pdb=" N ILE H 4 " --> pdb=" O VAL H 37 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'H' and resid 78 through 82 removed outlier: 4.049A pdb=" N ILE H 80 " --> pdb=" O ASN H 145 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL H 147 " --> pdb=" O ILE H 80 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ALA H 140 " --> pdb=" O PHE H 132 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'F' and resid 152 through 155 removed outlier: 7.103A pdb=" N THR F 67 " --> pdb=" O ILE F 84 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N CYS F 86 " --> pdb=" O LEU F 65 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LEU F 65 " --> pdb=" O CYS F 86 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'b' and resid 21 through 24 removed outlier: 3.756A pdb=" N ILE b 24 " --> pdb=" O ILE b 12 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N ILE b 12 " --> pdb=" O ILE b 24 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N LEU b 32 " --> pdb=" O SER b 15 " (cutoff:3.500A) 892 hydrogen bonds defined for protein. 2493 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2474 hydrogen bonds 3866 hydrogen bond angles 0 basepair planarities 978 basepair parallelities 1556 stacking parallelities Total time for adding SS restraints: 153.89 Time building geometry restraints manager: 47.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 17762 1.33 - 1.46: 42727 1.46 - 1.58: 40420 1.58 - 1.70: 6063 1.70 - 1.82: 210 Bond restraints: 107182 Sorted by residual: bond pdb=" C2 C A 106 " pdb=" O2 C A 106 " ideal model delta sigma weight residual 1.240 1.216 0.024 2.00e-02 2.50e+03 1.44e+00 bond pdb=" CA VAL 6 27 " pdb=" C VAL 6 27 " ideal model delta sigma weight residual 1.520 1.534 -0.014 1.23e-02 6.61e+03 1.33e+00 bond pdb=" C3' G A 271 " pdb=" O3' G A 271 " ideal model delta sigma weight residual 1.427 1.444 -0.017 1.50e-02 4.44e+03 1.25e+00 bond pdb=" C PRO I 21 " pdb=" N PRO I 22 " ideal model delta sigma weight residual 1.334 1.359 -0.025 2.34e-02 1.83e+03 1.16e+00 bond pdb=" C3' U A2249 " pdb=" O3' U A2249 " ideal model delta sigma weight residual 1.427 1.443 -0.016 1.50e-02 4.44e+03 1.16e+00 ... (remaining 107177 not shown) Histogram of bond angle deviations from ideal: 98.87 - 106.34: 18100 106.34 - 113.81: 66496 113.81 - 121.28: 47690 121.28 - 128.75: 24383 128.75 - 136.23: 3109 Bond angle restraints: 159778 Sorted by residual: angle pdb=" C PRO V 81 " pdb=" N TYR V 82 " pdb=" CA TYR V 82 " ideal model delta sigma weight residual 121.54 114.09 7.45 1.91e+00 2.74e-01 1.52e+01 angle pdb=" C SER L 68 " pdb=" N ARG L 69 " pdb=" CA ARG L 69 " ideal model delta sigma weight residual 121.54 128.79 -7.25 1.91e+00 2.74e-01 1.44e+01 angle pdb=" C3' U A2249 " pdb=" O3' U A2249 " pdb=" P G A2250 " ideal model delta sigma weight residual 120.20 125.08 -4.88 1.50e+00 4.44e-01 1.06e+01 angle pdb=" C3' G A 271 " pdb=" O3' G A 271 " pdb=" P A A 272 " ideal model delta sigma weight residual 120.20 125.07 -4.87 1.50e+00 4.44e-01 1.05e+01 angle pdb=" CB MET 6 49 " pdb=" CG MET 6 49 " pdb=" SD MET 6 49 " ideal model delta sigma weight residual 112.70 121.77 -9.07 3.00e+00 1.11e-01 9.14e+00 ... (remaining 159773 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.68: 55576 35.68 - 71.36: 1778 71.36 - 107.03: 177 107.03 - 142.71: 13 142.71 - 178.39: 9 Dihedral angle restraints: 57553 sinusoidal: 45214 harmonic: 12339 Sorted by residual: dihedral pdb=" O4' U A 545 " pdb=" C1' U A 545 " pdb=" N1 U A 545 " pdb=" C2 U A 545 " ideal model delta sinusoidal sigma weight residual 200.00 62.30 137.70 1 1.50e+01 4.44e-03 7.42e+01 dihedral pdb=" O4' C A1914 " pdb=" C1' C A1914 " pdb=" N1 C A1914 " pdb=" C2 C A1914 " ideal model delta sinusoidal sigma weight residual -128.00 50.39 -178.39 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U A1915 " pdb=" C1' U A1915 " pdb=" N1 U A1915 " pdb=" C2 U A1915 " ideal model delta sinusoidal sigma weight residual -128.00 50.32 -178.32 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 57550 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 18121 0.039 - 0.078: 1616 0.078 - 0.117: 555 0.117 - 0.155: 50 0.155 - 0.194: 6 Chirality restraints: 20348 Sorted by residual: chirality pdb=" C3' G A 271 " pdb=" C4' G A 271 " pdb=" O3' G A 271 " pdb=" C2' G A 271 " both_signs ideal model delta sigma weight residual False -2.74 -2.55 -0.19 2.00e-01 2.50e+01 9.43e-01 chirality pdb=" C3' U A2249 " pdb=" C4' U A2249 " pdb=" O3' U A2249 " pdb=" C2' U A2249 " both_signs ideal model delta sigma weight residual False -2.74 -2.55 -0.19 2.00e-01 2.50e+01 9.16e-01 chirality pdb=" C1' U A1313 " pdb=" O4' U A1313 " pdb=" C2' U A1313 " pdb=" N1 U A1313 " both_signs ideal model delta sigma weight residual False 2.47 2.28 0.19 2.00e-01 2.50e+01 8.63e-01 ... (remaining 20345 not shown) Planarity restraints: 9003 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C A 106 " 0.005 2.00e-02 2.50e+03 2.75e-02 1.70e+01 pdb=" N1 C A 106 " -0.001 2.00e-02 2.50e+03 pdb=" C2 C A 106 " -0.068 2.00e-02 2.50e+03 pdb=" O2 C A 106 " 0.043 2.00e-02 2.50e+03 pdb=" N3 C A 106 " 0.002 2.00e-02 2.50e+03 pdb=" C4 C A 106 " -0.008 2.00e-02 2.50e+03 pdb=" N4 C A 106 " 0.010 2.00e-02 2.50e+03 pdb=" C5 C A 106 " 0.012 2.00e-02 2.50e+03 pdb=" C6 C A 106 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY e 78 " 0.044 5.00e-02 4.00e+02 6.66e-02 7.10e+00 pdb=" N PRO e 79 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO e 79 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO e 79 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' G A 81 " -0.005 2.00e-02 2.50e+03 1.30e-02 5.08e+00 pdb=" N9 G A 81 " 0.001 2.00e-02 2.50e+03 pdb=" C8 G A 81 " 0.002 2.00e-02 2.50e+03 pdb=" N7 G A 81 " -0.005 2.00e-02 2.50e+03 pdb=" C5 G A 81 " -0.002 2.00e-02 2.50e+03 pdb=" C6 G A 81 " 0.004 2.00e-02 2.50e+03 pdb=" O6 G A 81 " -0.007 2.00e-02 2.50e+03 pdb=" N1 G A 81 " 0.003 2.00e-02 2.50e+03 pdb=" C2 G A 81 " 0.035 2.00e-02 2.50e+03 pdb=" N2 G A 81 " -0.026 2.00e-02 2.50e+03 pdb=" N3 G A 81 " 0.001 2.00e-02 2.50e+03 pdb=" C4 G A 81 " -0.001 2.00e-02 2.50e+03 ... (remaining 9000 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 2101 2.60 - 3.18: 78741 3.18 - 3.75: 197015 3.75 - 4.33: 256457 4.33 - 4.90: 349208 Nonbonded interactions: 883522 Sorted by model distance: nonbonded pdb=" O SER F 117 " pdb=" OH TYR F 127 " model vdw 2.029 2.440 nonbonded pdb=" N2 G A2294 " pdb=" O2 C A2338 " model vdw 2.076 2.496 nonbonded pdb=" O2B GDP 91001 " pdb="MG MG 91002 " model vdw 2.099 2.170 nonbonded pdb=" OG SER 7 34 " pdb=" OP2 U A1923 " model vdw 2.107 2.440 nonbonded pdb=" N2 G A1948 " pdb=" O6 G A1959 " model vdw 2.125 2.520 ... (remaining 883517 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 3033 5.49 5 Mg 2 5.21 5 S 116 5.16 5 C 50225 2.51 5 N 18357 2.21 5 O 27193 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.070 Extract box with map and model: 11.730 Check model and map are aligned: 1.080 Convert atoms to be neutral: 0.680 Process input model: 359.220 Find NCS groups from input model: 1.800 Set up NCS constraints: 0.240 Set refine NCS operators: 0.000 Set scattering table: 0.030 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 378.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 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 : 0.002 0.031 107182 Z= 0.109 Angle : 0.451 9.806 159778 Z= 0.242 Chirality : 0.027 0.194 20348 Planarity : 0.003 0.067 9003 Dihedral : 14.152 178.388 49605 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer Outliers : 0.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.13), residues: 4280 helix: -0.33 (0.16), residues: 1057 sheet: 0.26 (0.20), residues: 744 loop : -1.17 (0.12), residues: 2479 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8560 Ramachandran restraints generated. 4280 Oldfield, 0 Emsley, 4280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8560 Ramachandran restraints generated. 4280 Oldfield, 0 Emsley, 4280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 995 residues out of total 3542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 991 time to evaluate : 4.975 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 outliers start: 4 outliers final: 1 residues processed: 992 average time/residue: 0.8772 time to fit residues: 1513.5054 Evaluate side-chains 823 residues out of total 3542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 822 time to evaluate : 4.567 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.6737 time to fit residues: 6.3197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 723 random chunks: chunk 610 optimal weight: 20.0000 chunk 548 optimal weight: 10.0000 chunk 304 optimal weight: 10.0000 chunk 187 optimal weight: 8.9990 chunk 369 optimal weight: 30.0000 chunk 292 optimal weight: 30.0000 chunk 566 optimal weight: 10.0000 chunk 219 optimal weight: 0.6980 chunk 344 optimal weight: 20.0000 chunk 421 optimal weight: 20.0000 chunk 656 optimal weight: 10.0000 overall best weight: 7.9394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 225 ASN ** D 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 110 HIS ** G 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 86 GLN ** J 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 73 ASN O 104 GLN Q 51 GLN Q 55 GLN Q 70 GLN ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 43 ASN ** U 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 78 GLN Y 20 ASN ** Y 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 48 ASN ** 0 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 16 HIS P 11 GLN 6 20 GLN 6 47 HIS ** 7 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 91 GLN 8 154 ASN ** 9 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 13 HIS H 43 ASN b 41 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.2103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.112 107182 Z= 0.361 Angle : 0.665 9.335 159778 Z= 0.336 Chirality : 0.037 0.276 20348 Planarity : 0.005 0.073 9003 Dihedral : 14.107 179.357 41166 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 17.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer Outliers : 3.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.12), residues: 4280 helix: -0.48 (0.15), residues: 1132 sheet: -0.24 (0.19), residues: 773 loop : -1.32 (0.12), residues: 2375 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8560 Ramachandran restraints generated. 4280 Oldfield, 0 Emsley, 4280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8560 Ramachandran restraints generated. 4280 Oldfield, 0 Emsley, 4280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1034 residues out of total 3542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 915 time to evaluate : 4.706 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 119 outliers final: 93 residues processed: 970 average time/residue: 0.8958 time to fit residues: 1499.0950 Evaluate side-chains 901 residues out of total 3542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 808 time to evaluate : 4.608 Switching outliers to nearest non-outliers outliers start: 93 outliers final: 0 residues processed: 93 average time/residue: 0.7010 time to fit residues: 129.2665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 723 random chunks: chunk 364 optimal weight: 8.9990 chunk 203 optimal weight: 10.0000 chunk 546 optimal weight: 10.0000 chunk 447 optimal weight: 10.0000 chunk 181 optimal weight: 20.0000 chunk 657 optimal weight: 10.0000 chunk 710 optimal weight: 6.9990 chunk 585 optimal weight: 10.0000 chunk 652 optimal weight: 10.0000 chunk 224 optimal weight: 0.8980 chunk 527 optimal weight: 10.0000 overall best weight: 7.3792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 GLN ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 72 ASN ** G 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN ** N 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 38 GLN O 100 HIS ** Q 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 91 GLN X 22 ASN Z 48 ASN 0 18 HIS ** 2 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 3 GLN K 88 ASN 6 47 HIS ** 7 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 155 GLN 7 217 HIS ** 7 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 245 HIS 8 108 HIS ** 8 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 20 ASN F 20 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.3092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.090 107182 Z= 0.316 Angle : 0.632 10.888 159778 Z= 0.322 Chirality : 0.036 0.253 20348 Planarity : 0.005 0.074 9003 Dihedral : 14.454 179.612 41166 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 18.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer Outliers : 3.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.65 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.12), residues: 4280 helix: -0.48 (0.15), residues: 1139 sheet: -0.50 (0.18), residues: 776 loop : -1.52 (0.12), residues: 2365 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8560 Ramachandran restraints generated. 4280 Oldfield, 0 Emsley, 4280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8560 Ramachandran restraints generated. 4280 Oldfield, 0 Emsley, 4280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1008 residues out of total 3542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 898 time to evaluate : 4.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 110 outliers final: 63 residues processed: 947 average time/residue: 0.9048 time to fit residues: 1481.7361 Evaluate side-chains 870 residues out of total 3542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 807 time to evaluate : 4.590 Switching outliers to nearest non-outliers outliers start: 63 outliers final: 0 residues processed: 63 average time/residue: 0.7160 time to fit residues: 90.6749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 723 random chunks: chunk 649 optimal weight: 20.0000 chunk 494 optimal weight: 30.0000 chunk 341 optimal weight: 30.0000 chunk 72 optimal weight: 7.9990 chunk 313 optimal weight: 0.0570 chunk 441 optimal weight: 10.0000 chunk 660 optimal weight: 10.0000 chunk 698 optimal weight: 6.9990 chunk 344 optimal weight: 0.0020 chunk 625 optimal weight: 20.0000 chunk 188 optimal weight: 5.9990 overall best weight: 4.2112 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 126 ASN D 148 GLN ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 142 GLN ** J 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 13 HIS ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 91 GLN ** Y 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 48 ASN K 88 ASN 6 47 HIS ** 7 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 154 ASN ** 9 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 20 ASN H 133 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.3180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.056 107182 Z= 0.205 Angle : 0.554 10.623 159778 Z= 0.284 Chirality : 0.033 0.294 20348 Planarity : 0.004 0.074 9003 Dihedral : 14.363 177.948 41166 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 16.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer Outliers : 2.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.65 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.12), residues: 4280 helix: -0.30 (0.15), residues: 1138 sheet: -0.41 (0.18), residues: 746 loop : -1.45 (0.12), residues: 2396 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8560 Ramachandran restraints generated. 4280 Oldfield, 0 Emsley, 4280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8560 Ramachandran restraints generated. 4280 Oldfield, 0 Emsley, 4280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 978 residues out of total 3542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 875 time to evaluate : 4.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 103 outliers final: 61 residues processed: 922 average time/residue: 0.8793 time to fit residues: 1410.3172 Evaluate side-chains 876 residues out of total 3542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 815 time to evaluate : 4.559 Switching outliers to nearest non-outliers outliers start: 61 outliers final: 0 residues processed: 61 average time/residue: 0.7250 time to fit residues: 88.2287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 723 random chunks: chunk 582 optimal weight: 10.0000 chunk 396 optimal weight: 10.0000 chunk 10 optimal weight: 3.9990 chunk 520 optimal weight: 10.0000 chunk 288 optimal weight: 0.8980 chunk 596 optimal weight: 50.0000 chunk 483 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 356 optimal weight: 8.9990 chunk 627 optimal weight: 10.0000 chunk 176 optimal weight: 9.9990 overall best weight: 6.7790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 90 GLN G 72 ASN ** J 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 36 GLN Q 70 GLN ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 9 HIS T 91 GLN ** U 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 22 ASN ** Y 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 48 ASN K 3 GLN ** K 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 47 HIS ** 7 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 117 ASN ** 8 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 113 GLN ** 9 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 20 ASN ** e 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.3797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.094 107182 Z= 0.303 Angle : 0.639 12.266 159778 Z= 0.326 Chirality : 0.037 0.346 20348 Planarity : 0.005 0.072 9003 Dihedral : 14.662 178.397 41166 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 19.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.92 % Favored : 92.08 % Rotamer Outliers : 3.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.12), residues: 4280 helix: -0.47 (0.15), residues: 1145 sheet: -0.71 (0.18), residues: 750 loop : -1.53 (0.12), residues: 2385 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8560 Ramachandran restraints generated. 4280 Oldfield, 0 Emsley, 4280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8560 Ramachandran restraints generated. 4280 Oldfield, 0 Emsley, 4280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 984 residues out of total 3542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 852 time to evaluate : 5.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 132 outliers final: 79 residues processed: 917 average time/residue: 0.9059 time to fit residues: 1448.5939 Evaluate side-chains 876 residues out of total 3542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 797 time to evaluate : 4.641 Switching outliers to nearest non-outliers outliers start: 79 outliers final: 0 residues processed: 79 average time/residue: 0.7176 time to fit residues: 113.8009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 723 random chunks: chunk 235 optimal weight: 20.0000 chunk 629 optimal weight: 20.0000 chunk 138 optimal weight: 5.9990 chunk 410 optimal weight: 20.0000 chunk 172 optimal weight: 0.6980 chunk 699 optimal weight: 40.0000 chunk 580 optimal weight: 20.0000 chunk 323 optimal weight: 10.0000 chunk 58 optimal weight: 8.9990 chunk 231 optimal weight: 9.9990 chunk 367 optimal weight: 6.9990 overall best weight: 6.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 127 GLN ** J 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 36 GLN Q 55 GLN ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 70 HIS T 91 GLN ** U 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 48 ASN ** K 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 47 HIS 7 288 HIS ** 8 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 20 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.4013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.067 107182 Z= 0.287 Angle : 0.619 11.426 159778 Z= 0.316 Chirality : 0.036 0.335 20348 Planarity : 0.004 0.067 9003 Dihedral : 14.665 178.036 41166 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 18.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.01 % Favored : 91.99 % Rotamer Outliers : 3.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.12), residues: 4280 helix: -0.46 (0.15), residues: 1137 sheet: -0.90 (0.18), residues: 758 loop : -1.52 (0.12), residues: 2385 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8560 Ramachandran restraints generated. 4280 Oldfield, 0 Emsley, 4280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8560 Ramachandran restraints generated. 4280 Oldfield, 0 Emsley, 4280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 983 residues out of total 3542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 868 time to evaluate : 4.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 115 outliers final: 59 residues processed: 923 average time/residue: 0.8912 time to fit residues: 1423.1800 Evaluate side-chains 881 residues out of total 3542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 822 time to evaluate : 4.657 Switching outliers to nearest non-outliers outliers start: 59 outliers final: 0 residues processed: 59 average time/residue: 0.7549 time to fit residues: 87.6834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 723 random chunks: chunk 674 optimal weight: 40.0000 chunk 78 optimal weight: 0.0030 chunk 398 optimal weight: 20.0000 chunk 510 optimal weight: 10.0000 chunk 395 optimal weight: 10.0000 chunk 588 optimal weight: 10.0000 chunk 390 optimal weight: 10.0000 chunk 696 optimal weight: 0.0470 chunk 436 optimal weight: 10.0000 chunk 424 optimal weight: 10.0000 chunk 321 optimal weight: 5.9990 overall best weight: 5.2098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 9 GLN ** N 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 38 GLN O 104 GLN Q 36 GLN Q 55 GLN Q 70 GLN ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 91 GLN ** U 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 22 ASN ** Y 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 48 ASN ** 1 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 120 ASN ** 8 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 154 ASN H 20 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.4109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.057 107182 Z= 0.241 Angle : 0.596 11.484 159778 Z= 0.304 Chirality : 0.035 0.339 20348 Planarity : 0.004 0.067 9003 Dihedral : 14.641 178.961 41166 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 17.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.80 % Favored : 92.20 % Rotamer Outliers : 2.37 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.65 % 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: -1.66 (0.12), residues: 4280 helix: -0.40 (0.15), residues: 1134 sheet: -0.92 (0.18), residues: 742 loop : -1.52 (0.12), residues: 2404 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8560 Ramachandran restraints generated. 4280 Oldfield, 0 Emsley, 4280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8560 Ramachandran restraints generated. 4280 Oldfield, 0 Emsley, 4280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 947 residues out of total 3542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 863 time to evaluate : 4.679 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 outliers start: 84 outliers final: 48 residues processed: 901 average time/residue: 0.9304 time to fit residues: 1456.4391 Evaluate side-chains 866 residues out of total 3542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 818 time to evaluate : 4.689 Switching outliers to nearest non-outliers outliers start: 48 outliers final: 0 residues processed: 48 average time/residue: 0.7198 time to fit residues: 70.4365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 723 random chunks: chunk 431 optimal weight: 10.0000 chunk 278 optimal weight: 3.9990 chunk 416 optimal weight: 20.0000 chunk 209 optimal weight: 20.0000 chunk 136 optimal weight: 6.9990 chunk 135 optimal weight: 0.0170 chunk 443 optimal weight: 9.9990 chunk 474 optimal weight: 40.0000 chunk 344 optimal weight: 20.0000 chunk 64 optimal weight: 0.3980 chunk 547 optimal weight: 10.0000 overall best weight: 4.2824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 142 GLN ** J 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 55 GLN ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 91 GLN ** U 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 51 GLN ** Y 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 99 GLN ** 8 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 111 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.4156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 107182 Z= 0.211 Angle : 0.575 13.740 159778 Z= 0.293 Chirality : 0.034 0.321 20348 Planarity : 0.004 0.082 9003 Dihedral : 14.576 179.674 41166 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 17.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer Outliers : 1.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.61 (0.12), residues: 4280 helix: -0.32 (0.15), residues: 1133 sheet: -0.98 (0.18), residues: 743 loop : -1.47 (0.12), residues: 2404 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8560 Ramachandran restraints generated. 4280 Oldfield, 0 Emsley, 4280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8560 Ramachandran restraints generated. 4280 Oldfield, 0 Emsley, 4280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 904 residues out of total 3542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 850 time to evaluate : 4.645 Fit side-chains 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: 32 residues processed: 867 average time/residue: 0.9552 time to fit residues: 1438.3908 Evaluate side-chains 851 residues out of total 3542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 819 time to evaluate : 4.588 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 0 residues processed: 32 average time/residue: 0.7713 time to fit residues: 51.0645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 723 random chunks: chunk 633 optimal weight: 20.0000 chunk 667 optimal weight: 10.0000 chunk 609 optimal weight: 20.0000 chunk 649 optimal weight: 20.0000 chunk 390 optimal weight: 10.0000 chunk 282 optimal weight: 7.9990 chunk 509 optimal weight: 10.0000 chunk 199 optimal weight: 20.0000 chunk 586 optimal weight: 10.0000 chunk 614 optimal weight: 30.0000 chunk 647 optimal weight: 10.0000 overall best weight: 9.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 41 GLN ** G 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 11 ASN ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 22 ASN ** K 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 2 GLN 7 234 HIS 8 99 GLN ** 8 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 154 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.4762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.084 107182 Z= 0.421 Angle : 0.752 11.545 159778 Z= 0.379 Chirality : 0.042 0.325 20348 Planarity : 0.005 0.067 9003 Dihedral : 15.064 179.600 41166 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 22.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.70 % Favored : 90.30 % Rotamer Outliers : 2.01 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.65 % 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: -1.95 (0.12), residues: 4280 helix: -0.67 (0.15), residues: 1123 sheet: -1.07 (0.18), residues: 757 loop : -1.69 (0.12), residues: 2400 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8560 Ramachandran restraints generated. 4280 Oldfield, 0 Emsley, 4280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8560 Ramachandran restraints generated. 4280 Oldfield, 0 Emsley, 4280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 907 residues out of total 3542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 836 time to evaluate : 4.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 71 outliers final: 48 residues processed: 860 average time/residue: 0.9032 time to fit residues: 1345.5610 Evaluate side-chains 856 residues out of total 3542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 808 time to evaluate : 4.610 Switching outliers to nearest non-outliers outliers start: 48 outliers final: 0 residues processed: 48 average time/residue: 0.7169 time to fit residues: 70.6156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 723 random chunks: chunk 426 optimal weight: 10.0000 chunk 686 optimal weight: 5.9990 chunk 419 optimal weight: 20.0000 chunk 325 optimal weight: 10.0000 chunk 477 optimal weight: 10.0000 chunk 720 optimal weight: 20.0000 chunk 662 optimal weight: 10.0000 chunk 573 optimal weight: 10.0000 chunk 59 optimal weight: 20.0000 chunk 443 optimal weight: 10.0000 chunk 351 optimal weight: 5.9990 overall best weight: 8.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 55 GLN ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 91 GLN ** U 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 88 ASN ** 8 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 99 GLN 8 108 HIS ** 8 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.4900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.091 107182 Z= 0.357 Angle : 0.696 13.348 159778 Z= 0.354 Chirality : 0.040 0.346 20348 Planarity : 0.005 0.062 9003 Dihedral : 15.058 179.463 41166 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 21.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.90 % Favored : 91.10 % Rotamer Outliers : 0.65 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -2.02 (0.12), residues: 4280 helix: -0.72 (0.15), residues: 1120 sheet: -1.29 (0.18), residues: 784 loop : -1.67 (0.12), residues: 2376 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8560 Ramachandran restraints generated. 4280 Oldfield, 0 Emsley, 4280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8560 Ramachandran restraints generated. 4280 Oldfield, 0 Emsley, 4280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 853 residues out of total 3542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 830 time to evaluate : 4.706 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 14 residues processed: 836 average time/residue: 0.9228 time to fit residues: 1335.4120 Evaluate side-chains 826 residues out of total 3542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 812 time to evaluate : 4.626 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.7163 time to fit residues: 24.1711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 723 random chunks: chunk 455 optimal weight: 20.0000 chunk 610 optimal weight: 10.0000 chunk 175 optimal weight: 0.9990 chunk 528 optimal weight: 10.0000 chunk 84 optimal weight: 0.3980 chunk 159 optimal weight: 3.9990 chunk 574 optimal weight: 20.0000 chunk 240 optimal weight: 30.0000 chunk 589 optimal weight: 10.0000 chunk 72 optimal weight: 4.9990 chunk 105 optimal weight: 20.0000 overall best weight: 4.0790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 148 GLN G 127 GLN ** G 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 55 GLN Q 70 GLN ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 91 GLN ** U 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 22 ASN ** Y 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 3 GLN ** K 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 88 ASN ** 8 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 154 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.109304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.087847 restraints weight = 302669.780| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 2.04 r_work: 0.3386 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.4754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.067 107182 Z= 0.208 Angle : 0.596 12.259 159778 Z= 0.305 Chirality : 0.035 0.304 20348 Planarity : 0.004 0.064 9003 Dihedral : 14.810 179.798 41166 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 17.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.22 % Favored : 91.78 % Rotamer Outliers : 0.76 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.81 (0.12), residues: 4280 helix: -0.52 (0.15), residues: 1119 sheet: -1.21 (0.18), residues: 758 loop : -1.52 (0.12), residues: 2403 =============================================================================== Job complete usr+sys time: 22448.57 seconds wall clock time: 397 minutes 21.07 seconds (23841.07 seconds total)