Starting phenix.real_space_refine (version: dev) on Fri Dec 16 20:31:43 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bl6_12219/12_2022/7bl6_12219_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bl6_12219/12_2022/7bl6_12219.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bl6_12219/12_2022/7bl6_12219.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bl6_12219/12_2022/7bl6_12219.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bl6_12219/12_2022/7bl6_12219_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bl6_12219/12_2022/7bl6_12219_updated.pdb" } resolution = 4.0 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= 0.170 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 "g ARG 24": "NH1" <-> "NH2" Residue "C ARG 51": "NH1" <-> "NH2" Residue "C ARG 62": "NH1" <-> "NH2" Residue "C ASP 65": "OD1" <-> "OD2" Residue "C ARG 79": "NH1" <-> "NH2" Residue "C ASP 83": "OD1" <-> "OD2" Residue "C TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 99": "OE1" <-> "OE2" Residue "C ARG 132": "NH1" <-> "NH2" Residue "C TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 166": "NH1" <-> "NH2" Residue "C ARG 176": "NH1" <-> "NH2" Residue "C ARG 181": "NH1" <-> "NH2" Residue "C ARG 188": "NH1" <-> "NH2" Residue "C ARG 202": "NH1" <-> "NH2" Residue "C ARG 211": "NH1" <-> "NH2" Residue "C ASP 228": "OD1" <-> "OD2" Residue "C GLU 235": "OE1" <-> "OE2" Residue "C ASP 263": "OD1" <-> "OD2" Residue "D ARG 13": "NH1" <-> "NH2" Residue "D ASP 18": "OD1" <-> "OD2" Residue "D ARG 33": "NH1" <-> "NH2" Residue "D ASP 43": "OD1" <-> "OD2" Residue "D ARG 59": "NH1" <-> "NH2" Residue "D PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 77": "NH1" <-> "NH2" Residue "D PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 83": "NH1" <-> "NH2" Residue "D ASP 108": "OD1" <-> "OD2" Residue "D ARG 169": "NH1" <-> "NH2" Residue "D ASP 176": "OD1" <-> "OD2" Residue "D ARG 184": "NH1" <-> "NH2" Residue "E ASP 7": "OD1" <-> "OD2" Residue "E ARG 21": "NH1" <-> "NH2" Residue "E PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 44": "NH1" <-> "NH2" Residue "E ARG 49": "NH1" <-> "NH2" Residue "E ARG 88": "NH1" <-> "NH2" Residue "E ARG 102": "NH1" <-> "NH2" Residue "E ASP 145": "OD1" <-> "OD2" Residue "E ARG 162": "NH1" <-> "NH2" Residue "E ARG 170": "NH1" <-> "NH2" Residue "E ASP 171": "OD1" <-> "OD2" Residue "E PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 9": "OD1" <-> "OD2" Residue "F ARG 70": "NH1" <-> "NH2" Residue "F ARG 79": "NH1" <-> "NH2" Residue "F PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 101": "NH1" <-> "NH2" Residue "F ARG 109": "NH1" <-> "NH2" Residue "F ARG 111": "NH1" <-> "NH2" Residue "F ASP 112": "OD1" <-> "OD2" Residue "F ARG 114": "NH1" <-> "NH2" Residue "F ASP 122": "OD1" <-> "OD2" Residue "F ARG 132": "NH1" <-> "NH2" Residue "F PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 2": "NH1" <-> "NH2" Residue "G PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 113": "OD1" <-> "OD2" Residue "G ARG 152": "NH1" <-> "NH2" Residue "G ARG 162": "NH1" <-> "NH2" Residue "G ARG 169": "NH1" <-> "NH2" Residue "J ARG 13": "NH1" <-> "NH2" Residue "J ARG 37": "NH1" <-> "NH2" Residue "J ASP 52": "OD1" <-> "OD2" Residue "J TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 60": "OD1" <-> "OD2" Residue "J TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 96": "NH1" <-> "NH2" 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 ARG 60": "NH1" <-> "NH2" Residue "L ARG 78": "NH1" <-> "NH2" Residue "L GLU 115": "OE1" <-> "OE2" Residue "L ARG 126": "NH1" <-> "NH2" 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 GLU 43": "OE1" <-> "OE2" Residue "N ARG 46": "NH1" <-> "NH2" Residue "N ASP 58": "OD1" <-> "OD2" 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 PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 82": "OE1" <-> "OE2" Residue "N PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 96": "NH1" <-> "NH2" Residue "N PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 106": "OD1" <-> "OD2" Residue "N TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 114": "OE1" <-> "OE2" Residue "N ARG 118": "NH1" <-> "NH2" Residue "O ARG 10": "NH1" <-> "NH2" Residue "O ARG 16": "NH1" <-> "NH2" Residue "O ARG 25": "NH1" <-> "NH2" Residue "O ARG 81": "NH1" <-> "NH2" Residue "O PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 ARG 32": "NH1" <-> "NH2" Residue "Q ARG 47": "NH1" <-> "NH2" Residue "Q ARG 69": "NH1" <-> "NH2" Residue "Q TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 21": "NH1" <-> "NH2" Residue "R ARG 68": "NH1" <-> "NH2" Residue "R ARG 78": "NH1" <-> "NH2" Residue "R ARG 79": "NH1" <-> "NH2" Residue "R ARG 84": "NH1" <-> "NH2" Residue "S TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 67": "OD1" <-> "OD2" Residue "S PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 84": "NH1" <-> "NH2" Residue "S ARG 88": "NH1" <-> "NH2" Residue "S ARG 95": "NH1" <-> "NH2" Residue "S ASP 109": "OD1" <-> "OD2" Residue "S ARG 110": "NH1" <-> "NH2" Residue "T GLU 56": "OE1" <-> "OE2" Residue "T ASP 79": "OD1" <-> "OD2" Residue "U ARG 5": "NH1" <-> "NH2" Residue "U ARG 6": "NH1" <-> "NH2" Residue "U ARG 81": "NH1" <-> "NH2" Residue "U PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 85": "NH1" <-> "NH2" Residue "U ARG 93": "NH1" <-> "NH2" Residue "V TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 7": "NH1" <-> "NH2" Residue "W ASP 52": "OD1" <-> "OD2" Residue "W PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 2": "NH1" <-> "NH2" Residue "X ARG 10": "NH1" <-> "NH2" Residue "X ARG 17": "NH1" <-> "NH2" Residue "X ARG 36": "NH1" <-> "NH2" Residue "X ARG 49": "NH1" <-> "NH2" Residue "X ARG 56": "NH1" <-> "NH2" Residue "X ARG 73": "NH1" <-> "NH2" Residue "Y GLU 5": "OE1" <-> "OE2" Residue "Y GLU 12": "OE1" <-> "OE2" Residue "Y PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 29": "NH1" <-> "NH2" Residue "Y ARG 47": "NH1" <-> "NH2" Residue "Y ASP 49": "OD1" <-> "OD2" Residue "Y ARG 52": "NH1" <-> "NH2" Residue "Z ARG 10": "NH1" <-> "NH2" Residue "Z ARG 29": "NH1" <-> "NH2" Residue "Z ASP 39": "OD1" <-> "OD2" Residue "Z ARG 44": "NH1" <-> "NH2" Residue "Z PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 ARG 9": "NH1" <-> "NH2" Residue "0 ARG 15": "NH1" <-> "NH2" Residue "0 ASP 19": "OD1" <-> "OD2" Residue "0 GLU 35": "OE1" <-> "OE2" Residue "0 TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ARG 5": "NH1" <-> "NH2" Residue "1 PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 "K ASP 56": "OD1" <-> "OD2" Residue "P ARG 20": "NH1" <-> "NH2" Residue "P GLU 26": "OE1" <-> "OE2" Residue "P ARG 38": "NH1" <-> "NH2" Residue "P ARG 61": "NH1" <-> "NH2" Residue "P GLU 70": "OE1" <-> "OE2" Residue "P ARG 88": "NH1" <-> "NH2" Residue "P ARG 100": "NH1" <-> "NH2" Residue "P ARG 108": "NH1" <-> "NH2" Residue "M ARG 10": "NH1" <-> "NH2" Residue "M ARG 18": "NH1" <-> "NH2" Residue "M PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 38": "NH1" <-> "NH2" Residue "M ARG 40": "NH1" <-> "NH2" Residue "M ARG 50": "NH1" <-> "NH2" Residue "M ARG 51": "NH1" <-> "NH2" Residue "M ARG 55": "NH1" <-> "NH2" Residue "M PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 114": "NH1" <-> "NH2" Residue "M PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 27": "NH1" <-> "NH2" Residue "H PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 ARG 60": "NH1" <-> "NH2" Residue "9 PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 ARG 66": "NH1" <-> "NH2" Residue "9 ARG 114": "NH1" <-> "NH2" Residue "9 ARG 139": "NH1" <-> "NH2" Residue "9 ARG 150": "NH1" <-> "NH2" Residue "9 GLU 155": "OE1" <-> "OE2" Residue "9 ASP 161": "OD1" <-> "OD2" Residue "9 PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 ARG 177": "NH1" <-> "NH2" Residue "9 TYR 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 ARG 230": "NH1" <-> "NH2" Residue "9 PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 ARG 239": "NH1" <-> "NH2" Residue "9 ARG 278": "NH1" <-> "NH2" Residue "9 TYR 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 12": "NH1" <-> "NH2" Residue "3 ARG 29": "NH1" <-> "NH2" Residue "3 ARG 39": "NH1" <-> "NH2" Residue "3 ARG 41": "NH1" <-> "NH2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 92769 Number of models: 1 Model: "" Number of chains: 42 Chain: "g" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 302 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 36} 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: 1483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1483 Classifications: {'peptide': 193} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 187} Chain breaks: 1 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: "G" Number of atoms: 1323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1323 Classifications: {'peptide': 176} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 167} 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: 1053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1053 Classifications: {'peptide': 144} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 139} Chain: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 961 Classifications: {'peptide': 120} Modifications used: {'COO': 1} 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: {'CIS': 1, 'PTRANS': 1, 'TRANS': 90} 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: 577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 577 Classifications: {'peptide': 76} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 74} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU%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: "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: "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: "H" Number of atoms: 1110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1110 Classifications: {'peptide': 149} Link IDs: {'CIS': 1, 'PTRANS': 3, 'TRANS': 144} Chain: "d" 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: "A" Number of atoms: 62195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2897, 62195 Classifications: {'RNA': 2897} Modifications used: {'rna2p_pur': 273, 'rna2p_pyr': 144, 'rna3p_pur': 1399, 'rna3p_pyr': 1081} Link IDs: {'rna2p': 417, 'rna3p': 2479} Chain breaks: 1 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: "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: "3" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 504 Classifications: {'peptide': 64} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "g" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "d" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 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: "9" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GNP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "N" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "S" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "A" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Chain: "B" 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 85 SG CYS g 11 67.792 178.993 66.710 1.00277.97 S ATOM 110 SG CYS g 14 70.774 177.662 68.668 1.00281.13 S ATOM 213 SG CYS g 27 69.296 181.145 69.478 1.00293.05 S ATOM 24643 SG CYS d 16 21.903 84.234 28.463 1.00436.92 S ATOM 24797 SG CYS d 37 23.738 87.221 26.891 1.00411.36 S Time building chain proxies: 38.66, per 1000 atoms: 0.42 Number of scatterers: 92769 At special positions: 0 Unit cell: (180.96, 233.16, 234.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 94 16.00 P 3018 15.00 Mg 2 11.99 O 25977 8.00 N 17251 7.00 C 46425 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 42.02 Conformation dependent library (CDL) restraints added in 3.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN d 100 " pdb="ZN ZN d 100 " - pdb=" SG CYS d 37 " pdb="ZN ZN d 100 " - pdb=" SG CYS d 16 " pdb=" ZN g 101 " pdb="ZN ZN g 101 " - pdb=" ND1 HIS g 33 " pdb="ZN ZN g 101 " - pdb=" SG CYS g 11 " pdb="ZN ZN g 101 " - pdb=" SG CYS g 27 " pdb="ZN ZN g 101 " - pdb=" SG CYS g 14 " Number of angles added : 3 7076 Ramachandran restraints generated. 3538 Oldfield, 0 Emsley, 3538 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6548 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 101 helices and 48 sheets defined 24.2% alpha, 17.6% beta 979 base pairs and 1519 stacking pairs defined. Time for finding SS restraints: 43.26 Creating SS restraints... Processing helix chain 'g' and resid 31 through 33 No H-bonds generated for 'chain 'g' and resid 31 through 33' 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 131 through 133 No H-bonds generated for 'chain 'C' and resid 131 through 133' Processing helix chain 'C' and resid 207 through 211 Processing helix chain 'C' and resid 263 through 265 No H-bonds generated for 'chain 'C' and resid 263 through 265' Processing helix chain 'D' and resid 62 through 71 removed outlier: 3.603A pdb=" N ALA D 71 " --> pdb=" O HIS D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 99 through 101 No H-bonds generated for 'chain 'D' and resid 99 through 101' Processing helix chain 'D' and resid 121 through 125 Processing helix chain 'E' and resid 16 through 20 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 140 Processing helix chain 'E' and resid 155 through 162 Processing helix chain 'E' and resid 177 through 182 Processing helix chain 'E' and resid 190 through 200 Processing helix chain 'F' and resid 2 through 9 removed outlier: 3.980A pdb=" N LYS F 8 " --> pdb=" O HIS F 4 " (cutoff:3.500A) Processing helix chain 'F' and resid 11 through 17 Processing helix chain 'F' and resid 24 through 26 No H-bonds generated for 'chain 'F' and resid 24 through 26' Processing helix chain 'F' and resid 41 through 43 No H-bonds generated for 'chain 'F' and resid 41 through 43' Processing helix chain 'F' and resid 47 through 59 Processing helix chain 'F' and resid 93 through 104 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 171 Processing helix chain 'G' and resid 3 through 5 No H-bonds generated for 'chain 'G' and resid 3 through 5' Processing helix chain 'G' and resid 60 through 79 removed outlier: 3.960A pdb=" N GLY G 65 " --> pdb=" O ALA G 62 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL G 75 " --> pdb=" O ASN G 72 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N THR G 79 " --> pdb=" O ILE G 76 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 151 removed outlier: 3.877A pdb=" N TYR G 150 " --> pdb=" O ASP G 146 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ARG G 151 " --> pdb=" O LEU G 147 " (cutoff:3.500A) Processing helix chain 'J' and resid 25 through 37 removed outlier: 3.837A pdb=" N GLU J 31 " --> pdb=" O ARG J 27 " (cutoff:3.500A) 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 95 Processing helix chain 'J' and resid 99 through 108 removed outlier: 3.688A pdb=" N ALA J 104 " --> pdb=" O VAL J 100 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLY J 107 " --> pdb=" O ILE J 103 " (cutoff:3.500A) Processing helix chain 'J' and resid 113 through 121 removed outlier: 3.799A 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 57 through 60 No H-bonds generated for 'chain 'L' and resid 57 through 60' Processing helix chain 'L' and resid 70 through 73 Processing helix chain 'L' and resid 79 through 82 Processing helix chain 'L' and resid 129 through 137 Processing helix chain 'N' and resid 14 through 31 Processing helix chain 'N' and resid 38 through 56 removed outlier: 3.925A pdb=" N ARG N 46 " --> pdb=" O LYS N 42 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL N 47 " --> pdb=" O GLU N 43 " (cutoff:3.500A) Proline residue: N 50 - end of helix 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 88 Processing helix chain 'O' and resid 4 through 20 removed outlier: 4.494A pdb=" N ARG O 13 " --> pdb=" O ARG O 9 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N ALA O 14 " --> pdb=" O ARG O 10 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLU O 20 " --> pdb=" O ARG O 16 " (cutoff:3.500A) Processing helix chain 'O' and resid 68 through 85 Processing helix chain 'O' and resid 102 through 113 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 70 removed outlier: 4.440A pdb=" N GLN Q 36 " --> pdb=" O ARG Q 32 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ARG Q 50 " --> pdb=" O TYR Q 46 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N LYS Q 53 " --> pdb=" O ARG Q 49 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG Q 54 " --> pdb=" O ARG Q 50 " (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 Processing helix chain 'S' and resid 14 through 23 removed outlier: 3.623A pdb=" N VAL S 20 " --> pdb=" O LYS S 16 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N LEU S 23 " --> pdb=" O LEU S 19 " (cutoff:3.500A) Processing helix chain 'S' and resid 29 through 37 removed outlier: 3.761A pdb=" N ASP S 34 " --> pdb=" O SER S 30 " (cutoff:3.500A) 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 10 Processing helix chain 'T' and resid 18 through 25 Processing helix chain 'T' and resid 40 through 50 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 22 Processing helix chain 'V' and resid 44 through 51 Processing helix chain 'V' and resid 54 through 57 removed outlier: 3.963A 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 72 Processing helix chain 'Y' and resid 10 through 21 Processing helix chain 'Y' and resid 25 through 33 Processing helix chain 'Y' and resid 40 through 55 removed outlier: 3.525A pdb=" N LYS Y 44 " --> pdb=" O HIS Y 41 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL Y 46 " --> pdb=" O LEU Y 43 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARG Y 47 " --> pdb=" O LYS Y 44 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ARG Y 48 " --> pdb=" O GLN Y 45 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THR Y 55 " --> pdb=" O ARG Y 52 " (cutoff:3.500A) Processing helix chain 'Z' and resid 17 through 26 Processing helix chain 'Z' and resid 41 through 49 Processing helix chain '0' and resid 9 through 19 removed outlier: 3.713A pdb=" N SER 0 17 " --> pdb=" O GLY 0 13 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N HIS 0 18 " --> pdb=" O MET 0 14 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N ASP 0 19 " --> pdb=" O ARG 0 15 " (cutoff:3.500A) Processing helix chain '2' and resid 9 through 16 Processing helix chain '2' and resid 18 through 22 Processing helix chain '2' and resid 25 through 37 Processing helix chain 'K' and resid 105 through 109 Processing helix chain 'K' and resid 113 through 117 Processing helix chain 'P' and resid 3 through 11 removed outlier: 4.352A pdb=" N GLU P 10 " --> pdb=" O GLN P 6 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLN P 11 " --> pdb=" O LEU P 7 " (cutoff:3.500A) 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: 3.539A 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 'M' and resid 43 through 56 Processing helix chain 'M' and resid 110 through 123 removed outlier: 3.896A pdb=" N ALA M 122 " --> pdb=" O LYS M 118 " (cutoff:3.500A) removed outlier: 4.086A 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 46 No H-bonds generated for 'chain 'H' and resid 43 through 46' Processing helix chain 'H' and resid 48 through 51 removed outlier: 3.588A pdb=" N ARG H 51 " --> pdb=" O GLU H 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 48 through 51' Processing helix chain 'H' and resid 54 through 74 removed outlier: 4.096A pdb=" N GLU H 60 " --> pdb=" O ALA H 56 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N VAL H 61 " --> pdb=" O LYS H 57 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LEU H 62 " --> pdb=" O LEU H 58 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ALA H 63 " --> pdb=" O ALA H 59 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA H 74 " --> pdb=" O GLU H 70 " (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 '9' and resid 57 through 59 No H-bonds generated for 'chain '9' and resid 57 through 59' Processing helix chain '9' and resid 127 through 130 Processing helix chain '9' and resid 172 through 179 removed outlier: 3.691A pdb=" N ILE 9 176 " --> pdb=" O LYS 9 172 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ARG 9 177 " --> pdb=" O SER 9 173 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA 9 178 " --> pdb=" O THR 9 174 " (cutoff:3.500A) Processing helix chain '9' and resid 230 through 233 Processing helix chain '9' and resid 255 through 268 removed outlier: 3.989A pdb=" N ARG 9 260 " --> pdb=" O VAL 9 256 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ILE 9 262 " --> pdb=" O ASN 9 258 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N ILE 9 263 " --> pdb=" O ALA 9 259 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N SER 9 264 " --> pdb=" O ARG 9 260 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLU 9 265 " --> pdb=" O ILE 9 261 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LYS 9 268 " --> pdb=" O SER 9 264 " (cutoff:3.500A) Processing helix chain '9' and resid 272 through 275 Processing helix chain '9' and resid 285 through 287 No H-bonds generated for 'chain '9' and resid 285 through 287' Processing helix chain '9' and resid 291 through 304 removed outlier: 3.503A pdb=" N GLU 9 294 " --> pdb=" O VAL 9 291 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N GLU 9 295 " --> pdb=" O GLU 9 292 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LYS 9 296 " --> pdb=" O ALA 9 293 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE 9 300 " --> pdb=" O ALA 9 297 " (cutoff:3.500A) Processing helix chain '9' and resid 321 through 334 removed outlier: 3.859A pdb=" N TRP 9 326 " --> pdb=" O LYS 9 322 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLU 9 334 " --> pdb=" O THR 9 330 " (cutoff:3.500A) Processing helix chain '3' and resid 7 through 12 removed outlier: 3.612A pdb=" N ARG 3 12 " --> pdb=" O GLY 3 8 " (cutoff:3.500A) Processing helix chain '3' and resid 32 through 34 No H-bonds generated for 'chain '3' and resid 32 through 34' Processing helix chain '3' and resid 37 through 44 removed outlier: 3.635A pdb=" N ARG 3 44 " --> pdb=" O LYS 3 40 " (cutoff:3.500A) Processing helix chain '3' and resid 54 through 60 Processing sheet with id= A, first strand: chain 'g' and resid 14 through 19 Processing sheet with id= B, first strand: chain 'C' and resid 2 through 4 Processing sheet with id= C, first strand: chain 'C' and resid 114 through 117 removed outlier: 4.340A pdb=" N SER C 117 " --> pdb=" O ILE C 73 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE C 73 " --> pdb=" O SER C 117 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N LEU C 92 " --> pdb=" O GLU C 78 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N LEU C 80 " --> pdb=" O ILE C 90 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N ILE C 90 " --> pdb=" O LEU C 80 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 128 through 130 Processing sheet with id= E, first strand: chain 'C' and resid 180 through 184 removed outlier: 3.966A pdb=" N ALA C 165 " --> pdb=" O THR C 172 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ARG C 174 " --> pdb=" O ILE C 163 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N ILE C 163 " --> pdb=" O ARG C 174 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'D' and resid 169 through 172 removed outlier: 4.582A pdb=" N THR D 112 " --> pdb=" O ASP D 200 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ASP D 200 " --> pdb=" O THR D 112 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N VAL D 26 " --> pdb=" O VAL D 9 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N MET D 11 " --> pdb=" O VAL D 24 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N VAL D 24 " --> pdb=" O MET D 11 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N ARG D 13 " --> pdb=" O ILE D 22 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N ILE D 22 " --> pdb=" O ARG D 13 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG D 179 " --> pdb=" O LEU D 188 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N LYS D 190 " --> pdb=" O VAL D 177 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N VAL D 177 " --> pdb=" O LYS D 190 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 78 through 83 removed outlier: 4.072A pdb=" N GLY D 78 " --> pdb=" O THR D 52 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N THR D 52 " --> pdb=" O GLY D 78 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N THR D 51 " --> pdb=" O VAL D 34 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N VAL D 34 " --> pdb=" O THR D 51 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 117 through 119 Processing sheet with id= I, first strand: chain 'E' and resid 118 through 121 removed outlier: 6.939A pdb=" N VAL E 186 " --> pdb=" O ILE E 119 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N VAL E 121 " --> pdb=" O VAL E 186 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N MET E 188 " --> pdb=" O VAL E 121 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASP E 168 " --> pdb=" O VAL E 146 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'F' and resid 126 through 130 removed outlier: 6.812A pdb=" N THR F 67 " --> pdb=" O ILE F 84 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N CYS F 86 " --> pdb=" O LEU F 65 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N LEU F 65 " --> pdb=" O CYS F 86 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'G' and resid 22 through 24 Processing sheet with id= L, first strand: chain 'G' and resid 40 through 43 removed outlier: 3.792A pdb=" N LYS G 43 " --> pdb=" O THR G 50 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N THR G 50 " --> pdb=" O LYS G 43 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'G' and resid 160 through 163 Processing sheet with id= N, first strand: chain 'G' and resid 93 through 98 removed outlier: 3.510A pdb=" N ALA G 96 " --> pdb=" O ASN G 103 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE G 102 " --> pdb=" O HIS G 114 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'J' and resid 138 through 140 removed outlier: 4.957A pdb=" N ASP J 19 " --> pdb=" O LEU J 140 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N TYR J 53 " --> pdb=" O TYR J 16 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N VAL J 18 " --> pdb=" O TYR J 53 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N ILE J 55 " --> pdb=" O VAL J 18 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'J' and resid 73 through 77 Processing sheet with id= Q, first strand: chain 'L' and resid 74 through 76 removed outlier: 6.667A pdb=" N PHE L 107 " --> pdb=" O ALA L 75 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'L' and resid 121 through 123 removed outlier: 6.855A pdb=" N LYS L 141 " --> pdb=" O VAL L 122 " (cutoff:3.500A) No H-bonds generated for sheet with id= R Processing sheet with id= S, first strand: chain 'N' and resid 33 through 37 removed outlier: 3.649A pdb=" N GLY N 101 " --> pdb=" O MET N 110 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N TYR N 112 " --> pdb=" O LYS N 99 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N LYS N 99 " --> pdb=" O TYR N 112 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N GLU N 114 " --> pdb=" O ILE N 97 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N ILE N 97 " --> pdb=" O GLU N 114 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'O' and resid 25 through 30 Processing sheet with id= U, first strand: chain 'R' and resid 40 through 42 removed outlier: 3.733A pdb=" N MET R 40 " --> pdb=" O VAL R 4 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'R' and resid 20 through 23 removed outlier: 4.157A pdb=" N VAL R 20 " --> pdb=" O VAL R 96 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N VAL R 96 " --> pdb=" O VAL R 20 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA R 65 " --> pdb=" O ASP R 95 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'R' and resid 32 through 35 removed outlier: 3.929A pdb=" N VAL R 58 " --> pdb=" O SER R 102 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N SER R 102 " --> pdb=" O VAL R 58 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LYS R 60 " --> pdb=" O GLY R 100 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N GLY R 100 " --> pdb=" O LYS R 60 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N GLU R 62 " --> pdb=" O ILE R 98 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N ILE R 98 " --> pdb=" O GLU R 62 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'R' and resid 72 through 78 removed outlier: 4.143A pdb=" N TYR R 83 " --> pdb=" O ARG R 78 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'S' and resid 3 through 7 removed outlier: 6.271A pdb=" N SER S 108 " --> pdb=" O VAL S 71 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N VAL S 71 " --> pdb=" O SER S 108 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'S' and resid 81 through 87 Processing sheet with id= AA, first strand: chain 'T' and resid 11 through 14 removed outlier: 6.673A pdb=" N LYS T 33 " --> pdb=" O ARG T 12 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N VAL T 31 " --> pdb=" O PRO T 14 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N LYS T 81 " --> pdb=" O VAL T 34 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N VAL T 57 " --> pdb=" O THR T 86 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'T' and resid 67 through 69 Processing sheet with id= AC, first strand: chain 'U' and resid 69 through 71 removed outlier: 4.176A pdb=" N ASP U 8 " --> pdb=" O VAL U 24 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL U 24 " --> pdb=" O ASP U 8 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N ILE U 34 " --> pdb=" O LYS U 25 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N VAL U 27 " --> pdb=" O LYS U 32 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N LYS U 32 " --> pdb=" O VAL U 27 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'U' and resid 40 through 44 Processing sheet with id= AE, first strand: chain 'U' and resid 82 through 84 Processing sheet with id= AF, first strand: chain 'V' and resid 3 through 6 removed outlier: 6.879A pdb=" N THR V 62 " --> pdb=" O ILE V 4 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N ALA V 6 " --> pdb=" O THR V 62 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N VAL V 64 " --> pdb=" O ALA V 6 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ASP V 90 " --> pdb=" O GLN V 75 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N VAL V 77 " --> pdb=" O HIS V 88 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N HIS V 88 " --> pdb=" O VAL V 77 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ILE V 89 " --> pdb=" O PRO V 27 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'W' and resid 47 through 49 Processing sheet with id= AH, first strand: chain 'W' and resid 62 through 68 Processing sheet with id= AI, first strand: chain 'X' and resid 12 through 15 Processing sheet with id= AJ, first strand: chain 'X' and resid 32 through 39 removed outlier: 3.559A pdb=" N VAL X 39 " --> pdb=" O ARG X 44 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG X 44 " --> pdb=" O VAL X 39 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'Z' and resid 34 through 38 removed outlier: 3.516A pdb=" N ILE Z 6 " --> pdb=" O VAL Z 35 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LYS Z 5 " --> pdb=" O GLU Z 57 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLU Z 57 " --> pdb=" O LYS Z 5 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain '1' and resid 19 through 24 removed outlier: 3.634A pdb=" N GLN 1 44 " --> pdb=" O ASP 1 39 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LEU 1 35 " --> pdb=" O TYR 1 48 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'K' and resid 6 through 9 removed outlier: 6.964A pdb=" N LYS K 40 " --> pdb=" O ILE K 22 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N VAL K 24 " --> pdb=" O ILE K 38 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N ILE K 38 " --> pdb=" O VAL K 24 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS K 59 " --> pdb=" O LEU K 87 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'P' and resid 80 through 85 removed outlier: 6.601A pdb=" N LYS P 28 " --> pdb=" O ASP P 81 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N ILE P 83 " --> pdb=" O GLU P 26 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N GLU P 26 " --> pdb=" O ILE P 83 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N VAL P 85 " --> pdb=" O THR P 24 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N THR P 24 " --> pdb=" O VAL P 85 " (cutoff:3.500A) removed outlier: 8.763A pdb=" N GLU P 43 " --> pdb=" O ILE P 63 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N ILE P 63 " --> pdb=" O GLU P 43 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N THR P 59 " --> pdb=" O ILE P 47 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N ILE P 49 " --> pdb=" O ALA P 57 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ALA P 57 " --> pdb=" O ILE P 49 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N PHE P 58 " --> pdb=" O PHE P 73 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'M' and resid 128 through 132 removed outlier: 6.316A pdb=" N ALA M 35 " --> pdb=" O VAL M 101 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N VAL M 101 " --> pdb=" O ALA M 35 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLU M 104 " --> pdb=" O TRP M 64 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TRP M 64 " --> pdb=" O GLU M 104 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ASP M 106 " --> pdb=" O LYS M 62 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS M 62 " --> pdb=" O ASP M 106 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'M' and resid 39 through 42 removed outlier: 4.183A pdb=" N GLY M 39 " --> pdb=" O ILE M 96 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ILE M 96 " --> pdb=" O GLY M 39 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'M' and resid 72 through 74 removed outlier: 3.874A pdb=" N TYR M 91 " --> pdb=" O ILE M 73 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'H' and resid 78 through 83 Processing sheet with id= AS, first strand: chain 'd' and resid 11 through 15 removed outlier: 3.912A pdb=" N ILE d 24 " --> pdb=" O ILE d 12 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA d 14 " --> pdb=" O MET d 22 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain '9' and resid 64 through 66 removed outlier: 8.737A pdb=" N PHE 9 65 " --> pdb=" O SER 9 8 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N LEU 9 10 " --> pdb=" O PHE 9 65 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain '9' and resid 45 through 50 removed outlier: 5.875A pdb=" N VAL 9 86 " --> pdb=" O TRP 9 46 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N GLU 9 48 " --> pdb=" O VAL 9 86 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ILE 9 88 " --> pdb=" O GLU 9 48 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N ASP 9 50 " --> pdb=" O ILE 9 88 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N VAL 9 90 " --> pdb=" O ASP 9 50 " (cutoff:3.500A) No H-bonds generated for sheet with id= AU Processing sheet with id= AV, first strand: chain '9' and resid 162 through 166 removed outlier: 6.482A pdb=" N VAL 9 240 " --> pdb=" O GLY 9 163 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N LEU 9 165 " --> pdb=" O VAL 9 240 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N LEU 9 242 " --> pdb=" O LEU 9 165 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N VAL 9 281 " --> pdb=" O ILE 9 245 " (cutoff:3.500A) No H-bonds generated for sheet with id= AV 760 hydrogen bonds defined for protein. 2079 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2492 hydrogen bonds 3934 hydrogen bond angles 0 basepair planarities 979 basepair parallelities 1519 stacking parallelities Total time for adding SS restraints: 152.95 Time building geometry restraints manager: 45.37 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: 15888 1.33 - 1.46: 41822 1.46 - 1.58: 36978 1.58 - 1.70: 6032 1.70 - 1.82: 168 Bond restraints: 100888 Sorted by residual: bond pdb=" N3B GNP 9 402 " pdb=" PG GNP 9 402 " ideal model delta sigma weight residual 1.801 1.709 0.092 2.00e-02 2.50e+03 2.14e+01 bond pdb=" O5' GNP 9 402 " pdb=" PA GNP 9 402 " ideal model delta sigma weight residual 1.660 1.574 0.086 2.00e-02 2.50e+03 1.85e+01 bond pdb=" CA LYS 9 31 " pdb=" CB LYS 9 31 " ideal model delta sigma weight residual 1.528 1.587 -0.059 2.61e-02 1.47e+03 5.07e+00 bond pdb=" O3A GNP 9 402 " pdb=" PB GNP 9 402 " ideal model delta sigma weight residual 1.687 1.643 0.044 2.00e-02 2.50e+03 4.77e+00 bond pdb=" N3B GNP 9 402 " pdb=" PB GNP 9 402 " ideal model delta sigma weight residual 1.681 1.639 0.042 2.00e-02 2.50e+03 4.49e+00 ... (remaining 100883 not shown) Histogram of bond angle deviations from ideal: 98.08 - 105.25: 14040 105.25 - 112.43: 58162 112.43 - 119.61: 32275 119.61 - 126.79: 38356 126.79 - 133.97: 8345 Bond angle restraints: 151178 Sorted by residual: angle pdb=" N GLU Q 110 " pdb=" CA GLU Q 110 " pdb=" CB GLU Q 110 " ideal model delta sigma weight residual 110.28 118.17 -7.89 1.55e+00 4.16e-01 2.59e+01 angle pdb=" CB ARG Y 23 " pdb=" CG ARG Y 23 " pdb=" CD ARG Y 23 " ideal model delta sigma weight residual 111.30 122.83 -11.53 2.30e+00 1.89e-01 2.51e+01 angle pdb=" C VAL Q 109 " pdb=" N GLU Q 110 " pdb=" CA GLU Q 110 " ideal model delta sigma weight residual 120.31 112.96 7.35 1.52e+00 4.33e-01 2.34e+01 angle pdb=" CA GLU Q 110 " pdb=" CB GLU Q 110 " pdb=" CG GLU Q 110 " ideal model delta sigma weight residual 114.10 122.06 -7.96 2.00e+00 2.50e-01 1.59e+01 angle pdb=" CB MET 0 14 " pdb=" CG MET 0 14 " pdb=" SD MET 0 14 " ideal model delta sigma weight residual 112.70 101.69 11.01 3.00e+00 1.11e-01 1.35e+01 ... (remaining 151173 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.66: 52130 35.66 - 71.33: 1424 71.33 - 106.99: 124 106.99 - 142.66: 5 142.66 - 178.32: 10 Dihedral angle restraints: 53693 sinusoidal: 43512 harmonic: 10181 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 53.66 146.34 1 1.50e+01 4.44e-03 7.82e+01 dihedral pdb=" O4' U A1061 " pdb=" C1' U A1061 " pdb=" N1 U A1061 " pdb=" C2 U A1061 " ideal model delta sinusoidal sigma weight residual -128.00 50.32 -178.32 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U A1340 " pdb=" C1' U A1340 " pdb=" N1 U A1340 " pdb=" C2 U A1340 " ideal model delta sinusoidal sigma weight residual -128.00 50.31 -178.31 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 53690 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 18341 0.054 - 0.109: 888 0.109 - 0.163: 114 0.163 - 0.218: 7 0.218 - 0.272: 1 Chirality restraints: 19351 Sorted by residual: chirality pdb=" C1' U A1736 " pdb=" O4' U A1736 " pdb=" C2' U A1736 " pdb=" N1 U A1736 " both_signs ideal model delta sigma weight residual False 2.47 2.19 0.27 2.00e-01 2.50e+01 1.85e+00 chirality pdb=" C3' G A2505 " pdb=" C4' G A2505 " pdb=" O3' G A2505 " pdb=" C2' G A2505 " both_signs ideal model delta sigma weight residual False -2.74 -2.53 -0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" CA ARG Y 23 " pdb=" N ARG Y 23 " pdb=" C ARG Y 23 " pdb=" CB ARG Y 23 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.85e-01 ... (remaining 19348 not shown) Planarity restraints: 7924 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' U A1736 " -0.031 2.00e-02 2.50e+03 1.69e-02 6.41e+00 pdb=" N1 U A1736 " 0.038 2.00e-02 2.50e+03 pdb=" C2 U A1736 " 0.000 2.00e-02 2.50e+03 pdb=" O2 U A1736 " 0.004 2.00e-02 2.50e+03 pdb=" N3 U A1736 " -0.003 2.00e-02 2.50e+03 pdb=" C4 U A1736 " -0.005 2.00e-02 2.50e+03 pdb=" O4 U A1736 " -0.009 2.00e-02 2.50e+03 pdb=" C5 U A1736 " 0.003 2.00e-02 2.50e+03 pdb=" C6 U A1736 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A A 643 " -0.029 2.00e-02 2.50e+03 1.33e-02 4.90e+00 pdb=" N9 A A 643 " 0.031 2.00e-02 2.50e+03 pdb=" C8 A A 643 " 0.002 2.00e-02 2.50e+03 pdb=" N7 A A 643 " -0.002 2.00e-02 2.50e+03 pdb=" C5 A A 643 " -0.002 2.00e-02 2.50e+03 pdb=" C6 A A 643 " -0.000 2.00e-02 2.50e+03 pdb=" N6 A A 643 " -0.008 2.00e-02 2.50e+03 pdb=" N1 A A 643 " -0.002 2.00e-02 2.50e+03 pdb=" C2 A A 643 " 0.002 2.00e-02 2.50e+03 pdb=" N3 A A 643 " 0.004 2.00e-02 2.50e+03 pdb=" C4 A A 643 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN G 100 " 0.011 2.00e-02 2.50e+03 2.17e-02 4.70e+00 pdb=" C ASN G 100 " -0.038 2.00e-02 2.50e+03 pdb=" O ASN G 100 " 0.014 2.00e-02 2.50e+03 pdb=" N VAL G 101 " 0.012 2.00e-02 2.50e+03 ... (remaining 7921 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 5251 2.67 - 3.23: 81646 3.23 - 3.79: 191011 3.79 - 4.34: 245200 4.34 - 4.90: 323028 Nonbonded interactions: 846136 Sorted by model distance: nonbonded pdb="MG MG 9 401 " pdb=" O2G GNP 9 402 " model vdw 2.117 2.170 nonbonded pdb=" O2' C A1351 " pdb=" O2' A A1571 " model vdw 2.126 2.440 nonbonded pdb=" O2' C A2258 " pdb=" OP2 C A2427 " model vdw 2.130 2.440 nonbonded pdb=" OG1 THR O 31 " pdb=" O HIS O 34 " model vdw 2.154 2.440 nonbonded pdb=" N2 G A1171 " pdb=" O2 C A1178 " model vdw 2.157 2.496 ... (remaining 846131 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 2 6.06 5 P 3018 5.49 5 Mg 2 5.21 5 S 94 5.16 5 C 46425 2.51 5 N 17251 2.21 5 O 25977 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 group one per residue 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: 0.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 9.490 Check model and map are aligned: 1.180 Convert atoms to be neutral: 0.740 Process input model: 344.840 Find NCS groups from input model: 1.570 Set up NCS constraints: 0.250 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: 0.020 Load rotamer database and sin/cos tables:2.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 361.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 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 0.092 100888 Z= 0.098 Angle : 0.423 11.526 151178 Z= 0.226 Chirality : 0.025 0.272 19351 Planarity : 0.003 0.052 7924 Dihedral : 13.165 178.319 47145 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.69 % Favored : 95.25 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % 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: -0.28 (0.14), residues: 3538 helix: 0.52 (0.18), residues: 858 sheet: 0.89 (0.21), residues: 672 loop : -0.89 (0.13), residues: 2008 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7076 Ramachandran restraints generated. 3538 Oldfield, 0 Emsley, 3538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7076 Ramachandran restraints generated. 3538 Oldfield, 0 Emsley, 3538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 2919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 155 time to evaluate : 4.136 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 157 average time/residue: 0.8500 time to fit residues: 234.8618 Evaluate side-chains 129 residues out of total 2919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 128 time to evaluate : 4.049 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.7383 time to fit residues: 5.5879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 646 random chunks: chunk 545 optimal weight: 40.0000 chunk 489 optimal weight: 40.0000 chunk 271 optimal weight: 1.9990 chunk 167 optimal weight: 4.9990 chunk 330 optimal weight: 30.0000 chunk 261 optimal weight: 40.0000 chunk 506 optimal weight: 30.0000 chunk 195 optimal weight: 50.0000 chunk 307 optimal weight: 30.0000 chunk 376 optimal weight: 40.0000 chunk 586 optimal weight: 40.0000 overall best weight: 19.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** g 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 57 HIS C 152 GLN ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 36 GLN D 67 HIS ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 134 HIS ** E 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 62 GLN F 126 ASN ** G 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 128 ASN J 135 GLN N 11 ASN N 107 ASN R 43 ASN S 7 HIS S 31 GLN T 59 ASN U 68 ASN ** V 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 87 GLN 0 3 GLN 2 6 GLN K 3 GLN ** P 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.3082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.131 100888 Z= 0.447 Angle : 0.795 11.856 151178 Z= 0.393 Chirality : 0.038 0.332 19351 Planarity : 0.006 0.068 7924 Dihedral : 14.012 179.841 40157 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 34.38 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.85 % Favored : 94.06 % Rotamer Outliers : 0.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % 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: -0.67 (0.14), residues: 3538 helix: 0.06 (0.17), residues: 889 sheet: 0.18 (0.19), residues: 738 loop : -0.91 (0.14), residues: 1911 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7076 Ramachandran restraints generated. 3538 Oldfield, 0 Emsley, 3538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7076 Ramachandran restraints generated. 3538 Oldfield, 0 Emsley, 3538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 2919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 146 time to evaluate : 5.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 11 residues processed: 157 average time/residue: 0.8381 time to fit residues: 233.7248 Evaluate side-chains 135 residues out of total 2919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 124 time to evaluate : 4.035 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.7295 time to fit residues: 18.9752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 646 random chunks: chunk 326 optimal weight: 30.0000 chunk 182 optimal weight: 20.0000 chunk 488 optimal weight: 30.0000 chunk 399 optimal weight: 30.0000 chunk 161 optimal weight: 30.0000 chunk 587 optimal weight: 30.0000 chunk 634 optimal weight: 20.0000 chunk 523 optimal weight: 50.0000 chunk 582 optimal weight: 30.0000 chunk 200 optimal weight: 50.0000 chunk 471 optimal weight: 30.0000 overall best weight: 26.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 185 ASN E 41 GLN E 195 GLN F 20 ASN ** F 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 29 ASN G 44 HIS G 63 GLN G 72 ASN ** G 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 128 ASN L 104 GLN ** O 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 36 GLN ** Q 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 89 HIS ** S 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 75 GLN ** W 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 25 GLN ** 0 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 18 HIS 2 29 GLN K 3 GLN H 18 GLN ** H 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 145 ASN 9 71 GLN ** 9 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.5777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.140 100888 Z= 0.538 Angle : 0.893 15.970 151178 Z= 0.446 Chirality : 0.045 0.365 19351 Planarity : 0.007 0.080 7924 Dihedral : 16.205 175.994 40157 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 52.61 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.29 % Favored : 92.57 % Rotamer Outliers : 2.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.13), residues: 3538 helix: -0.84 (0.16), residues: 893 sheet: -0.56 (0.18), residues: 757 loop : -1.38 (0.13), residues: 1888 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7076 Ramachandran restraints generated. 3538 Oldfield, 0 Emsley, 3538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7076 Ramachandran restraints generated. 3538 Oldfield, 0 Emsley, 3538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 2919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 129 time to evaluate : 4.001 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: 77 outliers final: 32 residues processed: 194 average time/residue: 0.8186 time to fit residues: 283.5401 Evaluate side-chains 143 residues out of total 2919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 111 time to evaluate : 4.142 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 0 residues processed: 32 average time/residue: 0.7501 time to fit residues: 47.4118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 646 random chunks: chunk 580 optimal weight: 20.0000 chunk 441 optimal weight: 20.0000 chunk 305 optimal weight: 50.0000 chunk 65 optimal weight: 40.0000 chunk 280 optimal weight: 9.9990 chunk 394 optimal weight: 30.0000 chunk 589 optimal weight: 20.0000 chunk 624 optimal weight: 20.0000 chunk 308 optimal weight: 20.0000 chunk 558 optimal weight: 20.0000 chunk 168 optimal weight: 8.9990 overall best weight: 15.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 133 ASN ** C 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 19 ASN ** G 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 25 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.5706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.077 100888 Z= 0.333 Angle : 0.657 11.763 151178 Z= 0.334 Chirality : 0.036 0.334 19351 Planarity : 0.005 0.047 7924 Dihedral : 15.971 176.989 40157 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 35.75 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.36 % Favored : 93.58 % Rotamer Outliers : 1.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % 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: -1.27 (0.14), residues: 3538 helix: -0.31 (0.17), residues: 888 sheet: -0.45 (0.19), residues: 730 loop : -1.24 (0.14), residues: 1920 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7076 Ramachandran restraints generated. 3538 Oldfield, 0 Emsley, 3538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7076 Ramachandran restraints generated. 3538 Oldfield, 0 Emsley, 3538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 2919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 125 time to evaluate : 4.035 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 outliers start: 58 outliers final: 15 residues processed: 175 average time/residue: 0.8565 time to fit residues: 271.6826 Evaluate side-chains 133 residues out of total 2919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 118 time to evaluate : 4.010 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.7047 time to fit residues: 23.9700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 646 random chunks: chunk 520 optimal weight: 50.0000 chunk 354 optimal weight: 30.0000 chunk 9 optimal weight: 8.9990 chunk 464 optimal weight: 30.0000 chunk 257 optimal weight: 3.9990 chunk 532 optimal weight: 40.0000 chunk 431 optimal weight: 30.0000 chunk 0 optimal weight: 50.0000 chunk 318 optimal weight: 30.0000 chunk 560 optimal weight: 30.0000 chunk 157 optimal weight: 20.0000 overall best weight: 18.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** g 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 142 ASN ** C 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 110 HIS J 136 GLN N 31 HIS ** S 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 33 GLN ** H 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.6403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.098 100888 Z= 0.403 Angle : 0.723 12.590 151178 Z= 0.365 Chirality : 0.038 0.337 19351 Planarity : 0.005 0.067 7924 Dihedral : 16.369 177.038 40157 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 44.43 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.03 % Favored : 91.92 % Rotamer Outliers : 2.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.14), residues: 3538 helix: -0.54 (0.17), residues: 897 sheet: -0.74 (0.19), residues: 743 loop : -1.29 (0.14), residues: 1898 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7076 Ramachandran restraints generated. 3538 Oldfield, 0 Emsley, 3538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7076 Ramachandran restraints generated. 3538 Oldfield, 0 Emsley, 3538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 2919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 121 time to evaluate : 4.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 63 outliers final: 24 residues processed: 181 average time/residue: 0.8215 time to fit residues: 268.0452 Evaluate side-chains 141 residues out of total 2919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 117 time to evaluate : 4.105 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.7696 time to fit residues: 37.5436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 646 random chunks: chunk 210 optimal weight: 5.9990 chunk 562 optimal weight: 30.0000 chunk 123 optimal weight: 20.0000 chunk 366 optimal weight: 30.0000 chunk 154 optimal weight: 40.0000 chunk 625 optimal weight: 20.0000 chunk 518 optimal weight: 50.0000 chunk 289 optimal weight: 3.9990 chunk 51 optimal weight: 20.0000 chunk 206 optimal weight: 10.0000 chunk 328 optimal weight: 30.0000 overall best weight: 11.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 133 ASN ** D 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.6313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.073 100888 Z= 0.272 Angle : 0.615 11.857 151178 Z= 0.313 Chirality : 0.035 0.359 19351 Planarity : 0.004 0.048 7924 Dihedral : 16.185 176.525 40157 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 34.27 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.78 % Favored : 93.16 % Rotamer Outliers : 1.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.14), residues: 3538 helix: -0.20 (0.18), residues: 902 sheet: -0.64 (0.19), residues: 718 loop : -1.22 (0.14), residues: 1918 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7076 Ramachandran restraints generated. 3538 Oldfield, 0 Emsley, 3538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7076 Ramachandran restraints generated. 3538 Oldfield, 0 Emsley, 3538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 2919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 126 time to evaluate : 4.164 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: 34 outliers final: 17 residues processed: 157 average time/residue: 0.8279 time to fit residues: 233.1251 Evaluate side-chains 138 residues out of total 2919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 121 time to evaluate : 4.258 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.7197 time to fit residues: 27.2939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 646 random chunks: chunk 602 optimal weight: 30.0000 chunk 70 optimal weight: 6.9990 chunk 356 optimal weight: 30.0000 chunk 456 optimal weight: 30.0000 chunk 353 optimal weight: 20.0000 chunk 526 optimal weight: 40.0000 chunk 349 optimal weight: 30.0000 chunk 622 optimal weight: 7.9990 chunk 389 optimal weight: 30.0000 chunk 379 optimal weight: 30.0000 chunk 287 optimal weight: 8.9990 overall best weight: 14.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: g 13 ASN ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 114 HIS N 23 ASN ** S 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 5 GLN ** P 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.6509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.071 100888 Z= 0.324 Angle : 0.649 11.347 151178 Z= 0.329 Chirality : 0.036 0.371 19351 Planarity : 0.005 0.047 7924 Dihedral : 16.219 176.959 40157 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 38.57 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.22 % Favored : 91.69 % Rotamer Outliers : 1.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.14), residues: 3538 helix: -0.33 (0.18), residues: 898 sheet: -0.81 (0.19), residues: 728 loop : -1.21 (0.14), residues: 1912 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7076 Ramachandran restraints generated. 3538 Oldfield, 0 Emsley, 3538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7076 Ramachandran restraints generated. 3538 Oldfield, 0 Emsley, 3538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 2919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 124 time to evaluate : 4.098 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 10 residues processed: 152 average time/residue: 0.8812 time to fit residues: 242.9585 Evaluate side-chains 133 residues out of total 2919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 123 time to evaluate : 4.002 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.7999 time to fit residues: 18.4528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 646 random chunks: chunk 385 optimal weight: 30.0000 chunk 248 optimal weight: 9.9990 chunk 371 optimal weight: 30.0000 chunk 187 optimal weight: 30.0000 chunk 122 optimal weight: 50.0000 chunk 120 optimal weight: 1.9990 chunk 395 optimal weight: 40.0000 chunk 424 optimal weight: 30.0000 chunk 307 optimal weight: 30.0000 chunk 58 optimal weight: 8.9990 chunk 489 optimal weight: 30.0000 overall best weight: 16.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 133 ASN ** C 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 36 ASN ** F 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 23 ASN R 12 HIS ** S 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.6846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.081 100888 Z= 0.346 Angle : 0.677 13.588 151178 Z= 0.341 Chirality : 0.037 0.368 19351 Planarity : 0.005 0.048 7924 Dihedral : 16.426 177.077 40157 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 40.61 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.25 % Favored : 91.66 % Rotamer Outliers : 0.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.14), residues: 3538 helix: -0.33 (0.17), residues: 895 sheet: -0.89 (0.18), residues: 766 loop : -1.26 (0.14), residues: 1877 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7076 Ramachandran restraints generated. 3538 Oldfield, 0 Emsley, 3538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7076 Ramachandran restraints generated. 3538 Oldfield, 0 Emsley, 3538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 2919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 127 time to evaluate : 4.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 9 residues processed: 143 average time/residue: 0.8524 time to fit residues: 218.2442 Evaluate side-chains 135 residues out of total 2919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 126 time to evaluate : 4.024 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.8603 time to fit residues: 17.6165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 646 random chunks: chunk 566 optimal weight: 30.0000 chunk 596 optimal weight: 30.0000 chunk 544 optimal weight: 30.0000 chunk 580 optimal weight: 30.0000 chunk 349 optimal weight: 30.0000 chunk 252 optimal weight: 8.9990 chunk 455 optimal weight: 40.0000 chunk 178 optimal weight: 10.0000 chunk 524 optimal weight: 70.0000 chunk 548 optimal weight: 30.0000 chunk 578 optimal weight: 30.0000 overall best weight: 21.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** g 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 23 ASN ** U 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 29 HIS ** P 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 73 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.7481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.104 100888 Z= 0.459 Angle : 0.793 13.549 151178 Z= 0.395 Chirality : 0.041 0.351 19351 Planarity : 0.006 0.064 7924 Dihedral : 16.943 178.240 40157 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 51.50 Ramachandran Plot: Outliers : 0.11 % Allowed : 10.23 % Favored : 89.66 % Rotamer Outliers : 0.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.14), residues: 3538 helix: -0.66 (0.17), residues: 891 sheet: -1.19 (0.18), residues: 751 loop : -1.42 (0.14), residues: 1896 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7076 Ramachandran restraints generated. 3538 Oldfield, 0 Emsley, 3538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7076 Ramachandran restraints generated. 3538 Oldfield, 0 Emsley, 3538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 2919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 128 time to evaluate : 4.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 9 residues processed: 148 average time/residue: 0.8367 time to fit residues: 220.8733 Evaluate side-chains 134 residues out of total 2919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 125 time to evaluate : 4.168 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.7514 time to fit residues: 16.6306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 646 random chunks: chunk 381 optimal weight: 30.0000 chunk 613 optimal weight: 50.0000 chunk 374 optimal weight: 30.0000 chunk 291 optimal weight: 20.0000 chunk 426 optimal weight: 30.0000 chunk 643 optimal weight: 40.0000 chunk 592 optimal weight: 30.0000 chunk 512 optimal weight: 40.0000 chunk 53 optimal weight: 6.9990 chunk 395 optimal weight: 40.0000 chunk 314 optimal weight: 30.0000 overall best weight: 23.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** g 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 11 ASN N 23 ASN N 62 ASN ** Q 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 19 HIS ** P 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 73 ASN ** H 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 9 99 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.7989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.096 100888 Z= 0.472 Angle : 0.814 12.144 151178 Z= 0.407 Chirality : 0.042 0.352 19351 Planarity : 0.006 0.073 7924 Dihedral : 17.350 179.325 40157 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 53.22 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.21 % Favored : 90.67 % Rotamer Outliers : 0.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.05 (0.13), residues: 3538 helix: -0.89 (0.17), residues: 879 sheet: -1.38 (0.18), residues: 722 loop : -1.55 (0.14), residues: 1937 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7076 Ramachandran restraints generated. 3538 Oldfield, 0 Emsley, 3538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7076 Ramachandran restraints generated. 3538 Oldfield, 0 Emsley, 3538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 2919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 119 time to evaluate : 4.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 8 residues processed: 128 average time/residue: 0.8625 time to fit residues: 199.3323 Evaluate side-chains 126 residues out of total 2919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 118 time to evaluate : 5.575 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 1.0579 time to fit residues: 19.1841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 646 random chunks: chunk 407 optimal weight: 20.0000 chunk 545 optimal weight: 30.0000 chunk 157 optimal weight: 7.9990 chunk 472 optimal weight: 20.0000 chunk 75 optimal weight: 8.9990 chunk 142 optimal weight: 3.9990 chunk 513 optimal weight: 30.0000 chunk 214 optimal weight: 30.0000 chunk 527 optimal weight: 30.0000 chunk 64 optimal weight: 20.0000 chunk 94 optimal weight: 50.0000 overall best weight: 12.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** g 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 36 GLN ** D 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 22 GLN ** H 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 73 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.023319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.018834 restraints weight = 2019633.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.019240 restraints weight = 742895.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.019454 restraints weight = 416816.176| |-----------------------------------------------------------------------------| r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.7667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.052 100888 Z= 0.275 Angle : 0.652 14.564 151178 Z= 0.329 Chirality : 0.036 0.345 19351 Planarity : 0.005 0.053 7924 Dihedral : 16.877 179.404 40157 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 37.80 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.48 % Favored : 91.41 % Rotamer Outliers : 0.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.14), residues: 3538 helix: -0.45 (0.17), residues: 886 sheet: -1.20 (0.18), residues: 723 loop : -1.34 (0.14), residues: 1929 =============================================================================== Job complete usr+sys time: 8670.54 seconds wall clock time: 164 minutes 53.01 seconds (9893.01 seconds total)