Starting phenix.real_space_refine (version: dev) on Sat Dec 17 01:00:20 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5gah_8004/12_2022/5gah_8004.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5gah_8004/12_2022/5gah_8004.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5gah_8004/12_2022/5gah_8004.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5gah_8004/12_2022/5gah_8004.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5gah_8004/12_2022/5gah_8004.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5gah_8004/12_2022/5gah_8004.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.023 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "C GLU 23": "OE1" <-> "OE2" Residue "C GLU 35": "OE1" <-> "OE2" Residue "C ARG 52": "NH1" <-> "NH2" Residue "C ARG 63": "NH1" <-> "NH2" Residue "C ARG 80": "NH1" <-> "NH2" Residue "C TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 133": "NH1" <-> "NH2" Residue "C GLU 145": "OE1" <-> "OE2" Residue "C TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 167": "NH1" <-> "NH2" Residue "C TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 177": "NH1" <-> "NH2" Residue "C ARG 182": "NH1" <-> "NH2" Residue "C ARG 189": "NH1" <-> "NH2" Residue "C GLU 199": "OE1" <-> "OE2" Residue "C ARG 203": "NH1" <-> "NH2" Residue "C ARG 212": "NH1" <-> "NH2" Residue "D ARG 13": "NH1" <-> "NH2" Residue "D GLU 17": "OE1" <-> "OE2" Residue "D ASP 18": "OD1" <-> "OD2" Residue "D GLU 28": "OE1" <-> "OE2" Residue "D GLU 30": "OE1" <-> "OE2" Residue "D ARG 33": "NH1" <-> "NH2" Residue "D ASP 43": "OD1" <-> "OD2" Residue "D TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 59": "NH1" <-> "NH2" Residue "D GLU 64": "OE1" <-> "OE2" Residue "D ARG 77": "NH1" <-> "NH2" Residue "D GLU 81": "OE1" <-> "OE2" Residue "D ARG 83": "NH1" <-> "NH2" Residue "D GLU 168": "OE1" <-> "OE2" Residue "D ARG 169": "NH1" <-> "NH2" Residue "D GLU 183": "OE1" <-> "OE2" Residue "D ARG 184": "NH1" <-> "NH2" Residue "E ASP 7": "OD1" <-> "OD2" Residue "E ARG 21": "NH1" <-> "NH2" Residue "E GLU 25": "OE1" <-> "OE2" Residue "E ARG 44": "NH1" <-> "NH2" Residue "E ARG 49": "NH1" <-> "NH2" Residue "E ARG 61": "NH1" <-> "NH2" Residue "E PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 88": "NH1" <-> "NH2" Residue "E ARG 102": "NH1" <-> "NH2" Residue "E ASP 145": "OD1" <-> "OD2" Residue "E GLU 152": "OE1" <-> "OE2" Residue "E ARG 162": "NH1" <-> "NH2" Residue "E ARG 170": "NH1" <-> "NH2" Residue "E ASP 176": "OD1" <-> "OD2" Residue "E GLU 197": "OE1" <-> "OE2" Residue "F GLU 19": "OE1" <-> "OE2" Residue "F GLU 32": "OE1" <-> "OE2" Residue "F ARG 71": "NH1" <-> "NH2" Residue "F ARG 80": "NH1" <-> "NH2" Residue "F ARG 92": "NH1" <-> "NH2" Residue "F GLU 94": "OE1" <-> "OE2" Residue "F GLU 98": "OE1" <-> "OE2" Residue "F ARG 102": "NH1" <-> "NH2" Residue "F ARG 110": "NH1" <-> "NH2" Residue "F ARG 112": "NH1" <-> "NH2" Residue "F ARG 115": "NH1" <-> "NH2" Residue "F PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 133": "NH1" <-> "NH2" Residue "G ARG 3": "NH1" <-> "NH2" Residue "G PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 56": "OD1" <-> "OD2" Residue "G TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 124": "OE1" <-> "OE2" Residue "G ARG 153": "NH1" <-> "NH2" Residue "G TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 163": "NH1" <-> "NH2" Residue "G ASP 166": "OD1" <-> "OD2" Residue "G ARG 170": "NH1" <-> "NH2" Residue "H ARG 27": "NH1" <-> "NH2" Residue "H PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 60": "OE1" <-> "OE2" Residue "H ASP 86": "OD1" <-> "OD2" Residue "H GLU 87": "OE1" <-> "OE2" Residue "H GLU 114": "OE1" <-> "OE2" Residue "H GLU 137": "OE1" <-> "OE2" Residue "H PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 87": "OE1" <-> "OE2" Residue "I PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 114": "OE1" <-> "OE2" Residue "I ASP 124": "OD1" <-> "OD2" Residue "J PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 13": "NH1" <-> "NH2" Residue "K TYR 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 31": "OE1" <-> "OE2" Residue "K ARG 37": "NH1" <-> "NH2" Residue "K GLU 43": "OE1" <-> "OE2" Residue "K TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 90": "OE1" <-> "OE2" Residue "K GLU 91": "OE1" <-> "OE2" Residue "K ARG 96": "NH1" <-> "NH2" Residue "K ARG 120": "NH1" <-> "NH2" Residue "L GLU 45": "OE1" <-> "OE2" Residue "L GLU 110": "OE1" <-> "OE2" Residue "L GLU 121": "OE1" <-> "OE2" Residue "M ARG 21": "NH1" <-> "NH2" Residue "M ARG 33": "NH1" <-> "NH2" Residue "M ARG 41": "NH1" <-> "NH2" Residue "M ARG 47": "NH1" <-> "NH2" Residue "M GLU 51": "OE1" <-> "OE2" Residue "M ARG 60": "NH1" <-> "NH2" Residue "M PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 76": "OE1" <-> "OE2" Residue "M ARG 78": "NH1" <-> "NH2" Residue "M ASP 91": "OD1" <-> "OD2" Residue "M GLU 106": "OE1" <-> "OE2" Residue "M ARG 126": "NH1" <-> "NH2" Residue "M GLU 144": "OE1" <-> "OE2" Residue "N ARG 10": "NH1" <-> "NH2" Residue "N ARG 18": "NH1" <-> "NH2" Residue "N PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 40": "NH1" <-> "NH2" Residue "N ARG 44": "NH1" <-> "NH2" Residue "N GLU 47": "OE1" <-> "OE2" Residue "N ARG 50": "NH1" <-> "NH2" Residue "N ARG 55": "NH1" <-> "NH2" Residue "N ARG 59": "NH1" <-> "NH2" Residue "N GLU 75": "OE1" <-> "OE2" Residue "N TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 104": "OE1" <-> "OE2" Residue "N ARG 114": "NH1" <-> "NH2" Residue "N PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 8": "NH1" <-> "NH2" Residue "O ARG 12": "NH1" <-> "NH2" Residue "O ARG 17": "NH1" <-> "NH2" Residue "O ARG 22": "NH1" <-> "NH2" Residue "O GLU 43": "OE1" <-> "OE2" Residue "O ARG 46": "NH1" <-> "NH2" Residue "O ARG 63": "NH1" <-> "NH2" Residue "O ARG 64": "NH1" <-> "NH2" Residue "O ARG 69": "NH1" <-> "NH2" Residue "O ARG 71": "NH1" <-> "NH2" Residue "O GLU 82": "OE1" <-> "OE2" Residue "O ARG 96": "NH1" <-> "NH2" Residue "O TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 114": "OE1" <-> "OE2" Residue "P ARG 10": "NH1" <-> "NH2" Residue "P ARG 16": "NH1" <-> "NH2" Residue "P GLU 20": "OE1" <-> "OE2" Residue "P ARG 25": "NH1" <-> "NH2" Residue "P ARG 81": "NH1" <-> "NH2" Residue "P ARG 94": "NH1" <-> "NH2" Residue "P TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 102": "NH1" <-> "NH2" Residue "P ARG 111": "NH1" <-> "NH2" Residue "Q PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 21": "NH1" <-> "NH2" Residue "Q ARG 39": "NH1" <-> "NH2" Residue "Q GLU 44": "OE1" <-> "OE2" Residue "Q ARG 62": "NH1" <-> "NH2" Residue "Q GLU 71": "OE1" <-> "OE2" Residue "Q ASP 82": "OD1" <-> "OD2" Residue "Q ARG 89": "NH1" <-> "NH2" Residue "Q TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 101": "NH1" <-> "NH2" Residue "Q ARG 109": "NH1" <-> "NH2" Residue "R ARG 3": "NH1" <-> "NH2" Residue "R ARG 6": "NH1" <-> "NH2" Residue "R ARG 13": "NH1" <-> "NH2" Residue "R TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 33": "NH1" <-> "NH2" Residue "R TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 48": "NH1" <-> "NH2" Residue "R PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 70": "NH1" <-> "NH2" Residue "R TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 111": "OE1" <-> "OE2" Residue "S GLU 16": "OE1" <-> "OE2" Residue "S ARG 21": "NH1" <-> "NH2" Residue "S GLU 23": "OE1" <-> "OE2" Residue "S GLU 31": "OE1" <-> "OE2" Residue "S GLU 45": "OE1" <-> "OE2" Residue "S ARG 68": "NH1" <-> "NH2" Residue "S GLU 70": "OE1" <-> "OE2" Residue "S ARG 78": "NH1" <-> "NH2" Residue "S ARG 79": "NH1" <-> "NH2" Residue "S TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 84": "NH1" <-> "NH2" Residue "S PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 59": "OE1" <-> "OE2" Residue "T PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 78": "OE1" <-> "OE2" Residue "T ARG 84": "NH1" <-> "NH2" Residue "T ARG 88": "NH1" <-> "NH2" Residue "T ARG 95": "NH1" <-> "NH2" Residue "T ARG 110": "NH1" <-> "NH2" Residue "U GLU 4": "OE1" <-> "OE2" Residue "U GLU 5": "OE1" <-> "OE2" Residue "U GLU 52": "OE1" <-> "OE2" Residue "U GLU 54": "OE1" <-> "OE2" Residue "U GLU 56": "OE1" <-> "OE2" Residue "U GLU 89": "OE1" <-> "OE2" Residue "V ARG 6": "NH1" <-> "NH2" Residue "V ARG 7": "NH1" <-> "NH2" Residue "V ARG 82": "NH1" <-> "NH2" Residue "V PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 86": "NH1" <-> "NH2" Residue "V GLU 88": "OE1" <-> "OE2" Residue "V ARG 94": "NH1" <-> "NH2" Residue "V PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 11": "OE1" <-> "OE2" Residue "W PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 41": "OE1" <-> "OE2" Residue "W GLU 55": "OE1" <-> "OE2" Residue "W GLU 69": "OE1" <-> "OE2" Residue "W PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 17": "OE1" <-> "OE2" Residue "X PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 85": "OE1" <-> "OE2" Residue "Y ARG 3": "NH1" <-> "NH2" Residue "Y ARG 11": "NH1" <-> "NH2" Residue "Y ARG 18": "NH1" <-> "NH2" Residue "Y PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 37": "NH1" <-> "NH2" Residue "Y GLU 41": "OE1" <-> "OE2" Residue "Y GLU 43": "OE1" <-> "OE2" Residue "Y ARG 50": "NH1" <-> "NH2" Residue "Y ARG 57": "NH1" <-> "NH2" Residue "Y ARG 74": "NH1" <-> "NH2" Residue "Z GLU 12": "OE1" <-> "OE2" Residue "Z PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 47": "NH1" <-> "NH2" Residue "Z ARG 52": "NH1" <-> "NH2" Residue "a ARG 11": "NH1" <-> "NH2" Residue "a ARG 30": "NH1" <-> "NH2" Residue "a GLU 37": "OE1" <-> "OE2" Residue "a ARG 45": "NH1" <-> "NH2" Residue "a PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 10": "NH1" <-> "NH2" Residue "b ARG 16": "NH1" <-> "NH2" Residue "b ASP 31": "OD1" <-> "OD2" Residue "b ARG 52": "NH1" <-> "NH2" Residue "c GLU 32": "OE1" <-> "OE2" Residue "c GLU 35": "OE1" <-> "OE2" Residue "c ARG 44": "NH1" <-> "NH2" Residue "d ARG 3": "NH1" <-> "NH2" Residue "d ARG 14": "NH1" <-> "NH2" Residue "d PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 19": "NH1" <-> "NH2" Residue "d ARG 21": "NH1" <-> "NH2" Residue "d ARG 33": "NH1" <-> "NH2" Residue "e ARG 13": "NH1" <-> "NH2" Residue "e PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ARG 30": "NH1" <-> "NH2" Residue "e ARG 40": "NH1" <-> "NH2" Residue "e ARG 42": "NH1" <-> "NH2" Residue "f ARG 24": "NH1" <-> "NH2" Residue "i GLU 392": "OE1" <-> "OE2" 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: 94027 Number of models: 1 Model: "" Number of chains: 46 Chain: "1" Number of atoms: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 926 Classifications: {'RNA': 43} Modifications used: {'rna3p_pur': 26, 'rna3p_pyr': 17} Link IDs: {'rna3p': 42} Chain: "2" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 62 Classifications: {'RNA': 3} Modifications used: {'rna2p_pur': 1, 'rna3p_pyr': 2} Link IDs: {'rna3p': 2} Chain: "A" Number of atoms: 61902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2883, 61902 Classifications: {'RNA': 2883} Modifications used: {'rna2p_pur': 280, 'rna2p_pyr': 149, 'rna3p_pur': 1386, 'rna3p_pyr': 1068} Link IDs: {'rna2p': 429, 'rna3p': 2453} Chain breaks: 4 Chain: "B" Number of atoms: 2569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 2569 Classifications: {'RNA': 120} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 6, 'rna3p_pur': 57, 'rna3p_pyr': 50} Link IDs: {'rna2p': 13, 'rna3p': 106} 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: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 202} Chain: "E" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1552 Classifications: {'peptide': 201} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 195} Chain: "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: "H" Number of atoms: 1110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1110 Classifications: {'peptide': 149} Link IDs: {'PTRANS': 3, 'TRANS': 145} Chain: "I" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 946 Classifications: {'peptide': 125} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 120} Chain: "J" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 979 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 9, 'TRANS': 124} Chain: "K" 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: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 946 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 5, 'TRANS': 117} Chain: "M" 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: 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: "O" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 993 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 4, 'TRANS': 120} Chain: "P" Number of atoms: 900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 900 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 114} Chain: "Q" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 917 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "R" 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: "S" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 816 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'TRANS': 101} Chain: "T" 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: "U" Number of atoms: 756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 756 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 1, 'TRANS': 93} Chain: "V" 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: "W" 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: "X" Number of atoms: 580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 580 Classifications: {'peptide': 76} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 74} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "Y" 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: "Z" Number of atoms: 501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 501 Classifications: {'peptide': 62} Modifications used: {'COO': 1} Link IDs: {'TRANS': 61} Chain: "a" 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: "b" 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: "c" Number of atoms: 414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 414 Classifications: {'peptide': 51} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 48} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "d" 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: "e" 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: "f" 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: "i" Number of atoms: 916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 916 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 124} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'UNK:plan-1': 41} Unresolved non-hydrogen planarities: 41 Chain: "k" Number of atoms: 137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 137 Classifications: {'peptide': 18} Link IDs: {'PTRANS': 1, 'TRANS': 16} Chain: "2" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 412, 412 Unusual residues: {' MG': 412} Classifications: {'undetermined': 412} Link IDs: {None: 411} Chain: "B" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Unusual residues: {' MG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "b" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "f" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 92325 SG CYS f 11 72.587 85.762 179.614 1.00 65.90 S ATOM 92350 SG CYS f 14 75.777 87.050 178.486 1.00 40.68 S ATOM 92453 SG CYS f 27 75.976 83.920 180.512 1.00 52.38 S Time building chain proxies: 38.71, per 1000 atoms: 0.41 Number of scatterers: 94027 At special positions: 0 Unit cell: (240.99, 199.44, 240.99, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 95 16.00 P 3049 15.00 Mg 431 11.99 O 26174 8.00 N 17421 7.00 C 46856 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: 40.76 Conformation dependent library (CDL) restraints added in 3.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN f 101 " pdb="ZN ZN f 101 " - pdb=" SG CYS f 14 " pdb="ZN ZN f 101 " - pdb=" ND1 HIS f 33 " pdb="ZN ZN f 101 " - pdb=" SG CYS f 11 " pdb="ZN ZN f 101 " - pdb=" SG CYS f 27 " Number of angles added : 3 7058 Ramachandran restraints generated. 3529 Oldfield, 0 Emsley, 3529 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6648 Finding SS restraints... Secondary structure from input PDB file: 119 helices and 50 sheets defined 35.2% alpha, 20.8% beta 1020 base pairs and 1574 stacking pairs defined. Time for finding SS restraints: 32.72 Creating SS restraints... Processing helix chain 'C' and resid 10 through 14 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 133 through 135 No H-bonds generated for 'chain 'C' and resid 133 through 135' Processing helix chain 'C' and resid 197 through 203 removed outlier: 4.213A pdb=" N MET C 201 " --> pdb=" O ALA C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 214 removed outlier: 3.823A pdb=" N ALA C 211 " --> pdb=" O LYS C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 225 Processing helix chain 'C' and resid 262 through 265 removed outlier: 4.254A pdb=" N LYS C 265 " --> pdb=" O ARG C 262 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 262 through 265' Processing helix chain 'D' and resid 39 through 44 Processing helix chain 'D' and resid 61 through 72 removed outlier: 3.714A pdb=" N ALA D 71 " --> pdb=" O HIS D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 102 Processing helix chain 'D' and resid 120 through 126 Processing helix chain 'E' and resid 15 through 20 Processing helix chain 'E' and resid 24 through 39 Processing helix chain 'E' and resid 97 through 115 Processing helix chain 'E' and resid 130 through 142 removed outlier: 3.615A pdb=" N LEU E 134 " --> pdb=" O LYS E 130 " (cutoff:3.500A) Processing helix chain 'E' and resid 154 through 161 removed outlier: 3.529A pdb=" N ALA E 161 " --> pdb=" O LEU E 157 " (cutoff:3.500A) Processing helix chain 'E' and resid 173 through 175 No H-bonds generated for 'chain 'E' and resid 173 through 175' Processing helix chain 'E' and resid 176 through 183 removed outlier: 4.207A pdb=" N PHE E 183 " --> pdb=" O SER E 179 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 200 Processing helix chain 'F' and resid 3 through 11 Processing helix chain 'F' and resid 11 through 21 Processing helix chain 'F' and resid 24 through 28 Processing helix chain 'F' and resid 47 through 62 removed outlier: 3.759A pdb=" N ASP F 51 " --> pdb=" O LYS F 47 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ASP F 56 " --> pdb=" O ASN F 52 " (cutoff:3.500A) Processing helix chain 'F' and resid 92 through 106 Processing helix chain 'F' and resid 107 through 111 Processing helix chain 'F' and resid 142 through 146 removed outlier: 3.680A pdb=" N VAL F 146 " --> pdb=" O TYR F 143 " (cutoff:3.500A) Processing helix chain 'F' and resid 162 through 173 Processing helix chain 'G' and resid 60 through 81 Processing helix chain 'G' and resid 137 through 152 removed outlier: 3.661A pdb=" N TYR G 151 " --> pdb=" O ASP G 147 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N ARG G 152 " --> pdb=" O LEU G 148 " (cutoff:3.500A) Processing helix chain 'H' and resid 22 through 29 removed outlier: 3.611A pdb=" N ALA H 26 " --> pdb=" O LYS H 22 " (cutoff:3.500A) Processing helix chain 'H' and resid 40 through 73 removed outlier: 5.675A pdb=" N ALA H 52 " --> pdb=" O GLU H 48 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N GLU H 53 " --> pdb=" O ALA H 49 " (cutoff:3.500A) Processing helix chain 'H' and resid 85 through 89 removed outlier: 3.769A pdb=" N GLY H 88 " --> pdb=" O GLY H 85 " (cutoff:3.500A) Processing helix chain 'H' and resid 95 through 105 removed outlier: 3.527A pdb=" N ILE H 99 " --> pdb=" O GLY H 95 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ALA H 105 " --> pdb=" O ASP H 101 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 113 No H-bonds generated for 'chain 'H' and resid 111 through 113' Processing helix chain 'I' and resid 4 through 22 Processing helix chain 'I' and resid 34 through 47 Processing helix chain 'I' and resid 56 through 65 removed outlier: 3.934A pdb=" N ARG I 62 " --> pdb=" O THR I 58 " (cutoff:3.500A) Processing helix chain 'I' and resid 69 through 73 removed outlier: 3.568A pdb=" N LYS I 73 " --> pdb=" O GLU I 70 " (cutoff:3.500A) Processing helix chain 'I' and resid 92 through 104 removed outlier: 3.859A pdb=" N LYS I 97 " --> pdb=" O ALA I 93 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLU I 98 " --> pdb=" O ARG I 94 " (cutoff:3.500A) Processing helix chain 'I' and resid 122 through 126 Processing helix chain 'J' and resid 34 through 46 removed outlier: 3.899A pdb=" N PHE J 38 " --> pdb=" O ASN J 34 " (cutoff:3.500A) Processing helix chain 'J' and resid 47 through 49 No H-bonds generated for 'chain 'J' and resid 47 through 49' Processing helix chain 'J' and resid 75 through 84 removed outlier: 3.561A pdb=" N ALA J 84 " --> pdb=" O LEU J 80 " (cutoff:3.500A) Processing helix chain 'J' and resid 102 through 117 Processing helix chain 'J' and resid 121 through 136 removed outlier: 3.668A pdb=" N MET J 136 " --> pdb=" O THR J 132 " (cutoff:3.500A) Processing helix chain 'K' and resid 24 through 38 removed outlier: 4.025A pdb=" N GLU K 31 " --> pdb=" O ARG K 27 " (cutoff:3.500A) Processing helix chain 'K' and resid 67 through 72 Processing helix chain 'K' and resid 89 through 96 Processing helix chain 'K' and resid 97 through 108 removed outlier: 4.310A pdb=" N ILE K 101 " --> pdb=" O PRO K 97 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N MET K 108 " --> pdb=" O ALA K 104 " (cutoff:3.500A) Processing helix chain 'K' and resid 112 through 120 Processing helix chain 'K' and resid 131 through 136 removed outlier: 4.258A pdb=" N ALA K 134 " --> pdb=" O ASN K 131 " (cutoff:3.500A) Processing helix chain 'L' and resid 104 through 108 Processing helix chain 'L' and resid 112 through 119 removed outlier: 3.585A pdb=" N ILE L 116 " --> pdb=" O PHE L 112 " (cutoff:3.500A) Processing helix chain 'M' and resid 22 through 26 Processing helix chain 'M' and resid 36 through 41 removed outlier: 3.653A pdb=" N SER M 40 " --> pdb=" O LYS M 36 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ARG M 41 " --> pdb=" O GLY M 37 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 36 through 41' Processing helix chain 'M' and resid 56 through 61 Processing helix chain 'M' and resid 68 through 73 removed outlier: 3.785A pdb=" N ALA M 72 " --> pdb=" O SER M 68 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE M 73 " --> pdb=" O ARG M 69 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 68 through 73' Processing helix chain 'M' and resid 78 through 83 removed outlier: 3.866A pdb=" N LEU M 82 " --> pdb=" O ARG M 78 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ALA M 83 " --> pdb=" O LEU M 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 78 through 83' Processing helix chain 'M' and resid 91 through 98 Processing helix chain 'M' and resid 128 through 137 Processing helix chain 'N' and resid 43 through 57 Processing helix chain 'N' and resid 109 through 122 Processing helix chain 'O' and resid 13 through 32 Processing helix chain 'O' and resid 38 through 56 removed outlier: 3.714A pdb=" N ARG O 45 " --> pdb=" O ALA O 41 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ARG O 46 " --> pdb=" O LYS O 42 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N VAL O 47 " --> pdb=" O GLU O 43 " (cutoff:3.500A) Proline residue: O 50 - end of helix Processing helix chain 'O' and resid 59 through 71 Processing helix chain 'O' and resid 72 through 82 Processing helix chain 'O' and resid 82 through 87 Processing helix chain 'O' and resid 117 through 124 Processing helix chain 'P' and resid 2 through 21 removed outlier: 3.508A pdb=" N ALA P 6 " --> pdb=" O ASP P 2 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N ARG P 13 " --> pdb=" O ARG P 9 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N ALA P 14 " --> pdb=" O ARG P 10 " (cutoff:3.500A) Processing helix chain 'P' and resid 55 through 60 Processing helix chain 'P' and resid 67 through 84 Processing helix chain 'P' and resid 100 through 113 Processing helix chain 'Q' and resid 3 through 11 removed outlier: 3.775A pdb=" N GLU Q 11 " --> pdb=" O GLN Q 7 " (cutoff:3.500A) Processing helix chain 'Q' and resid 53 through 56 removed outlier: 4.004A pdb=" N HIS Q 56 " --> pdb=" O ARG Q 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 53 through 56' Processing helix chain 'Q' and resid 97 through 102 Processing helix chain 'Q' and resid 104 through 108 Processing helix chain 'R' and resid 6 through 21 Processing helix chain 'R' and resid 26 through 31 removed outlier: 3.861A pdb=" N ARG R 30 " --> pdb=" O GLY R 26 " (cutoff:3.500A) Processing helix chain 'R' and resid 31 through 72 removed outlier: 3.638A pdb=" N GLN R 37 " --> pdb=" O ARG R 33 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ARG R 51 " --> pdb=" O TYR R 47 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LYS R 54 " --> pdb=" O ARG R 50 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ARG R 55 " --> pdb=" O ARG R 51 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ARG R 58 " --> pdb=" O LYS R 54 " (cutoff:3.500A) Processing helix chain 'R' and resid 75 through 85 Processing helix chain 'R' and resid 91 through 102 Processing helix chain 'R' and resid 102 through 118 removed outlier: 3.559A pdb=" N PHE R 106 " --> pdb=" O ASP R 102 " (cutoff:3.500A) Processing helix chain 'T' and resid 13 through 25 removed outlier: 3.554A pdb=" N LEU T 19 " --> pdb=" O GLN T 15 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N VAL T 20 " --> pdb=" O LYS T 16 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU T 23 " --> pdb=" O LEU T 19 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE T 24 " --> pdb=" O VAL T 20 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG T 25 " --> pdb=" O ALA T 21 " (cutoff:3.500A) Processing helix chain 'T' and resid 28 through 39 Processing helix chain 'T' and resid 41 through 63 removed outlier: 4.087A pdb=" N VAL T 45 " --> pdb=" O LYS T 41 " (cutoff:3.500A) Processing helix chain 'T' and resid 65 through 69 Processing helix chain 'T' and resid 89 through 91 No H-bonds generated for 'chain 'T' and resid 89 through 91' Processing helix chain 'U' and resid 3 through 8 removed outlier: 3.741A pdb=" N LEU U 7 " --> pdb=" O ARG U 3 " (cutoff:3.500A) Processing helix chain 'U' and resid 17 through 27 Processing helix chain 'U' and resid 39 through 51 Processing helix chain 'W' and resid 12 through 23 removed outlier: 4.165A pdb=" N ALA W 16 " --> pdb=" O GLN W 12 " (cutoff:3.500A) Processing helix chain 'W' and resid 44 through 51 Processing helix chain 'W' and resid 54 through 59 removed outlier: 3.861A pdb=" N SER W 58 " --> pdb=" O ALA W 54 " (cutoff:3.500A) Processing helix chain 'Y' and resid 53 through 63 Processing helix chain 'Y' and resid 63 through 75 removed outlier: 3.666A pdb=" N VAL Y 67 " --> pdb=" O GLY Y 63 " (cutoff:3.500A) Processing helix chain 'Z' and resid 5 through 9 removed outlier: 3.661A pdb=" N GLU Z 8 " --> pdb=" O GLU Z 5 " (cutoff:3.500A) Processing helix chain 'Z' and resid 10 through 34 Processing helix chain 'Z' and resid 40 through 63 removed outlier: 4.192A pdb=" N LYS Z 44 " --> pdb=" O SER Z 40 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ALA Z 51 " --> pdb=" O ARG Z 47 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLU Z 59 " --> pdb=" O THR Z 55 " (cutoff:3.500A) Processing helix chain 'a' and resid 17 through 28 Processing helix chain 'a' and resid 41 through 52 removed outlier: 3.682A pdb=" N VAL a 51 " --> pdb=" O MET a 47 " (cutoff:3.500A) Processing helix chain 'b' and resid 9 through 18 removed outlier: 3.581A pdb=" N ARG b 17 " --> pdb=" O ARG b 13 " (cutoff:3.500A) Processing helix chain 'd' and resid 8 through 17 Processing helix chain 'd' and resid 17 through 23 Processing helix chain 'd' and resid 24 through 38 Processing helix chain 'e' and resid 7 through 14 removed outlier: 3.688A pdb=" N LYS e 12 " --> pdb=" O ARG e 8 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ARG e 13 " --> pdb=" O GLY e 9 " (cutoff:3.500A) Processing helix chain 'e' and resid 37 through 45 Processing helix chain 'e' and resid 54 through 62 Processing helix chain 'f' and resid 30 through 33 Processing helix chain 'i' and resid 330 through 345 removed outlier: 4.114A pdb=" N ASN i 343 " --> pdb=" O ARG i 339 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N MET i 344 " --> pdb=" O GLN i 340 " (cutoff:3.500A) Processing helix chain 'i' and resid 346 through 351 Processing helix chain 'i' and resid 356 through 361 removed outlier: 3.752A pdb=" N UNK i 360 " --> pdb=" O UNK i 356 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N UNK i 361 " --> pdb=" O UNK i 357 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 356 through 361' Processing helix chain 'i' and resid 362 through 366 removed outlier: 4.030A pdb=" N UNK i 366 " --> pdb=" O UNK i 363 " (cutoff:3.500A) Processing helix chain 'i' and resid 368 through 382 Processing helix chain 'i' and resid 384 through 389 Processing helix chain 'i' and resid 390 through 394 removed outlier: 3.639A pdb=" N ILE i 394 " --> pdb=" O PRO i 391 " (cutoff:3.500A) Processing helix chain 'i' and resid 395 through 406 Processing helix chain 'i' and resid 409 through 433 Processing helix chain 'i' and resid 434 through 441 removed outlier: 3.598A pdb=" N UNK i 441 " --> pdb=" O UNK i 437 " (cutoff:3.500A) Processing helix chain 'k' and resid 28 through 42 removed outlier: 3.999A pdb=" N LEU k 36 " --> pdb=" O LEU k 32 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 3 through 5 Processing sheet with id=AA2, first strand: chain 'C' and resid 34 through 35 Processing sheet with id=AA3, first strand: chain 'C' and resid 101 through 105 removed outlier: 3.526A pdb=" N ARG C 80 " --> pdb=" O LEU C 93 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LEU C 95 " --> pdb=" O VAL C 78 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N VAL C 78 " --> pdb=" O LEU C 95 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 129 through 131 removed outlier: 6.263A pdb=" N THR C 173 " --> pdb=" O VAL C 165 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N ARG C 167 " --> pdb=" O TYR C 171 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N TYR C 171 " --> pdb=" O ARG C 167 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N MET C 181 " --> pdb=" O VAL C 268 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 4 through 15 removed outlier: 6.824A pdb=" N VAL D 26 " --> pdb=" O VAL D 9 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N MET D 11 " --> pdb=" O VAL D 24 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N VAL D 24 " --> pdb=" O MET D 11 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N ARG D 13 " --> pdb=" O ILE D 22 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ILE D 22 " --> pdb=" O ARG D 13 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N LEU D 186 " --> pdb=" O VAL D 180 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N VAL D 180 " --> pdb=" O LEU D 186 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N LEU D 188 " --> pdb=" O VAL D 178 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ASP D 176 " --> pdb=" O LYS D 190 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N THR D 171 " --> pdb=" O GLY D 111 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N GLY D 111 " --> pdb=" O THR D 171 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N GLN D 173 " --> pdb=" O VAL D 109 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N VAL D 109 " --> pdb=" O GLN D 173 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N THR D 112 " --> pdb=" O ASP D 200 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N ASP D 200 " --> pdb=" O THR D 112 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 80 through 83 removed outlier: 6.708A pdb=" N ALA D 47 " --> pdb=" O VAL D 37 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N VAL D 37 " --> pdb=" O ALA D 47 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N GLN D 49 " --> pdb=" O THR D 35 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 118 through 119 Processing sheet with id=AA8, first strand: chain 'E' and resid 2 through 4 Processing sheet with id=AA9, first strand: chain 'E' and resid 118 through 121 Processing sheet with id=AB1, first strand: chain 'F' and resid 66 through 69 removed outlier: 3.898A pdb=" N GLY F 86 " --> pdb=" O THR F 68 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 16 through 20 Processing sheet with id=AB3, first strand: chain 'G' and resid 41 through 45 Processing sheet with id=AB4, first strand: chain 'G' and resid 121 through 124 Processing sheet with id=AB5, first strand: chain 'G' and resid 95 through 99 Processing sheet with id=AB6, first strand: chain 'H' and resid 18 through 20 Processing sheet with id=AB7, first strand: chain 'H' and resid 78 through 82 removed outlier: 3.719A pdb=" N VAL H 147 " --> pdb=" O ILE H 80 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N SER H 131 " --> pdb=" O ARG H 116 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 50 through 54 removed outlier: 3.887A pdb=" N SER I 24 " --> pdb=" O VAL I 85 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA I 25 " --> pdb=" O ALA I 112 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'J' and resid 9 through 14 Processing sheet with id=AC1, first strand: chain 'J' and resid 100 through 101 Processing sheet with id=AC2, first strand: chain 'K' and resid 122 through 124 removed outlier: 6.493A pdb=" N TRP K 15 " --> pdb=" O GLN K 138 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'K' and resid 73 through 77 Processing sheet with id=AC4, first strand: chain 'L' and resid 7 through 10 removed outlier: 3.788A pdb=" N VAL L 10 " --> pdb=" O ARG L 17 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N ARG L 17 " --> pdb=" O VAL L 10 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N GLU L 45 " --> pdb=" O ARG L 17 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N VAL L 19 " --> pdb=" O ILE L 43 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ILE L 43 " --> pdb=" O VAL L 19 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N CYS L 21 " --> pdb=" O ILE L 41 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ILE L 41 " --> pdb=" O CYS L 21 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N LYS L 23 " --> pdb=" O ILE L 39 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N ILE L 39 " --> pdb=" O LYS L 23 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ALA L 83 " --> pdb=" O VAL L 63 " (cutoff:3.500A) removed outlier: 8.303A pdb=" N CYS L 84 " --> pdb=" O MET L 7 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ASN L 9 " --> pdb=" O CYS L 84 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N LEU L 86 " --> pdb=" O ASN L 9 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 69 through 70 removed outlier: 3.801A pdb=" N VAL L 76 " --> pdb=" O VAL Q 73 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ALA Q 58 " --> pdb=" O ILE Q 50 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N ILE Q 50 " --> pdb=" O ALA Q 58 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N THR Q 60 " --> pdb=" O ILE Q 48 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N ILE Q 64 " --> pdb=" O GLU Q 44 " (cutoff:3.500A) removed outlier: 9.098A pdb=" N GLU Q 44 " --> pdb=" O ILE Q 64 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N THR Q 25 " --> pdb=" O LYS Q 87 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N TRP Q 31 " --> pdb=" O VAL Q 81 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N VAL Q 81 " --> pdb=" O TRP Q 31 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'M' and resid 74 through 77 Processing sheet with id=AC7, first strand: chain 'M' and resid 89 through 90 Processing sheet with id=AC8, first strand: chain 'N' and resid 62 through 65 removed outlier: 6.465A pdb=" N VAL N 101 " --> pdb=" O ALA N 35 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ALA N 35 " --> pdb=" O VAL N 101 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N TYR N 103 " --> pdb=" O LEU N 33 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'N' and resid 39 through 42 removed outlier: 5.570A pdb=" N VAL N 89 " --> pdb=" O GLU N 75 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N GLU N 75 " --> pdb=" O VAL N 89 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TYR N 91 " --> pdb=" O ILE N 73 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'O' and resid 33 through 37 removed outlier: 4.034A pdb=" N MET O 110 " --> pdb=" O CYS O 100 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'P' and resid 47 through 52 removed outlier: 6.699A pdb=" N VAL P 39 " --> pdb=" O LEU P 48 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N ALA P 50 " --> pdb=" O ALA P 37 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N ALA P 37 " --> pdb=" O ALA P 50 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N SER P 52 " --> pdb=" O ILE P 35 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ILE P 35 " --> pdb=" O SER P 52 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'S' and resid 10 through 14 removed outlier: 6.758A pdb=" N TYR S 2 " --> pdb=" O ILE S 41 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N ILE S 41 " --> pdb=" O TYR S 2 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N VAL S 4 " --> pdb=" O LEU S 39 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'S' and resid 19 through 23 removed outlier: 6.852A pdb=" N PHE S 93 " --> pdb=" O HIS S 66 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N HIS S 66 " --> pdb=" O PHE S 93 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ASP S 95 " --> pdb=" O VAL S 64 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N LYS S 60 " --> pdb=" O THR S 99 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N ILE S 101 " --> pdb=" O VAL S 58 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N VAL S 58 " --> pdb=" O ILE S 101 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'S' and resid 72 through 78 removed outlier: 4.209A pdb=" N TYR S 83 " --> pdb=" O ARG S 78 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'T' and resid 2 through 11 removed outlier: 5.628A pdb=" N SER T 101 " --> pdb=" O HIS T 9 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N SER T 108 " --> pdb=" O VAL T 71 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N VAL T 71 " --> pdb=" O SER T 108 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'T' and resid 82 through 87 Processing sheet with id=AD8, first strand: chain 'U' and resid 11 through 14 removed outlier: 3.861A pdb=" N LYS U 81 " --> pdb=" O VAL U 34 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N TRP U 80 " --> pdb=" O VAL U 62 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N VAL U 62 " --> pdb=" O TRP U 80 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N LYS U 82 " --> pdb=" O THR U 60 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N THR U 60 " --> pdb=" O LYS U 82 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N TYR U 84 " --> pdb=" O VAL U 58 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N VAL U 58 " --> pdb=" O TYR U 84 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N THR U 86 " --> pdb=" O GLU U 56 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'U' and resid 67 through 70 Processing sheet with id=AE1, first strand: chain 'V' and resid 65 through 66 removed outlier: 7.004A pdb=" N LYS V 33 " --> pdb=" O VAL V 28 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N VAL V 28 " --> pdb=" O LYS V 33 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N ILE V 35 " --> pdb=" O LYS V 26 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N GLU V 10 " --> pdb=" O PHE V 73 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ILE V 72 " --> pdb=" O ASP V 81 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'V' and resid 41 through 45 Processing sheet with id=AE3, first strand: chain 'V' and resid 83 through 88 Processing sheet with id=AE4, first strand: chain 'W' and resid 3 through 8 removed outlier: 7.906A pdb=" N ASN W 5 " --> pdb=" O ASP W 43 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N ASP W 43 " --> pdb=" O ASN W 5 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ILE W 89 " --> pdb=" O PRO W 27 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ASP W 76 " --> pdb=" O ASP W 90 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N VAL W 92 " --> pdb=" O ALA W 74 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N ALA W 74 " --> pdb=" O VAL W 92 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'X' and resid 22 through 23 removed outlier: 3.542A pdb=" N ARG X 39 " --> pdb=" O GLY X 22 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N LEU X 59 " --> pdb=" O ILE X 37 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'X' and resid 30 through 31 removed outlier: 6.458A pdb=" N HIS X 46 " --> pdb=" O ILE X 80 " (cutoff:3.500A) removed outlier: 8.651A pdb=" N ILE X 82 " --> pdb=" O HIS X 46 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'Y' and resid 13 through 18 Processing sheet with id=AE8, first strand: chain 'Y' and resid 33 through 40 Processing sheet with id=AE9, first strand: chain 'a' and resid 35 through 38 Processing sheet with id=AF1, first strand: chain 'b' and resid 29 through 30 Processing sheet with id=AF2, first strand: chain 'b' and resid 48 through 49 Processing sheet with id=AF3, first strand: chain 'c' and resid 20 through 25 Processing sheet with id=AF4, first strand: chain 'e' and resid 15 through 16 Processing sheet with id=AF5, first strand: chain 'f' and resid 2 through 4 removed outlier: 6.065A pdb=" N LYS f 2 " --> pdb=" O ARG f 36 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N ILE f 23 " --> pdb=" O GLN f 37 " (cutoff:3.500A) 1173 hydrogen bonds defined for protein. 3240 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2567 hydrogen bonds 4040 hydrogen bond angles 0 basepair planarities 1020 basepair parallelities 1574 stacking parallelities Total time for adding SS restraints: 184.97 Time building geometry restraints manager: 44.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 17675 1.33 - 1.47: 43808 1.47 - 1.60: 37260 1.60 - 1.74: 2892 1.74 - 1.87: 174 Bond restraints: 101809 Sorted by residual: bond pdb=" CA UNK i 453 " pdb=" C UNK i 453 " ideal model delta sigma weight residual 1.525 1.678 -0.153 2.10e-02 2.27e+03 5.34e+01 bond pdb=" N UNK i 447 " pdb=" CA UNK i 447 " ideal model delta sigma weight residual 1.458 1.592 -0.134 1.90e-02 2.77e+03 4.98e+01 bond pdb=" CA UNK i 350 " pdb=" C UNK i 350 " ideal model delta sigma weight residual 1.525 1.673 -0.148 2.10e-02 2.27e+03 4.98e+01 bond pdb=" CA UNK i 449 " pdb=" C UNK i 449 " ideal model delta sigma weight residual 1.525 1.659 -0.134 2.10e-02 2.27e+03 4.04e+01 bond pdb=" CA UNK i 436 " pdb=" C UNK i 436 " ideal model delta sigma weight residual 1.525 1.656 -0.131 2.10e-02 2.27e+03 3.92e+01 ... (remaining 101804 not shown) Histogram of bond angle deviations from ideal: 97.09 - 105.08: 14467 105.08 - 113.07: 61717 113.07 - 121.06: 46903 121.06 - 129.05: 26060 129.05 - 137.05: 3405 Bond angle restraints: 152552 Sorted by residual: angle pdb=" C GLU G 155 " pdb=" N PRO G 156 " pdb=" CA PRO G 156 " ideal model delta sigma weight residual 119.82 129.01 -9.19 9.80e-01 1.04e+00 8.80e+01 angle pdb=" N ASP J 116 " pdb=" CA ASP J 116 " pdb=" C ASP J 116 " ideal model delta sigma weight residual 113.17 123.25 -10.08 1.26e+00 6.30e-01 6.41e+01 angle pdb=" N VAL J 98 " pdb=" CA VAL J 98 " pdb=" C VAL J 98 " ideal model delta sigma weight residual 112.83 120.32 -7.49 9.90e-01 1.02e+00 5.73e+01 angle pdb=" N PRO J 22 " pdb=" CA PRO J 22 " pdb=" C PRO J 22 " ideal model delta sigma weight residual 110.70 118.69 -7.99 1.22e+00 6.72e-01 4.29e+01 angle pdb=" C LYS N 71 " pdb=" N PRO N 72 " pdb=" CA PRO N 72 " ideal model delta sigma weight residual 119.90 126.67 -6.77 1.05e+00 9.07e-01 4.16e+01 ... (remaining 152547 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.37: 51710 35.37 - 70.75: 2347 70.75 - 106.12: 163 106.12 - 141.49: 14 141.49 - 176.87: 10 Dihedral angle restraints: 54244 sinusoidal: 43931 harmonic: 10313 Sorted by residual: dihedral pdb=" C4' U A1344 " pdb=" C3' U A1344 " pdb=" C2' U A1344 " pdb=" C1' U A1344 " ideal model delta sinusoidal sigma weight residual -35.00 32.08 -67.08 1 8.00e+00 1.56e-02 9.16e+01 dihedral pdb=" C4' C A 645 " pdb=" C3' C A 645 " pdb=" C2' C A 645 " pdb=" C1' C A 645 " ideal model delta sinusoidal sigma weight residual -35.00 30.58 -65.58 1 8.00e+00 1.56e-02 8.80e+01 dihedral pdb=" C5' U A1344 " pdb=" C4' U A1344 " pdb=" C3' U A1344 " pdb=" O3' U A1344 " ideal model delta sinusoidal sigma weight residual 147.00 83.15 63.85 1 8.00e+00 1.56e-02 8.39e+01 ... (remaining 54241 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 17544 0.074 - 0.149: 1865 0.149 - 0.223: 135 0.223 - 0.297: 11 0.297 - 0.372: 4 Chirality restraints: 19559 Sorted by residual: chirality pdb=" C3' C A 645 " pdb=" C4' C A 645 " pdb=" O3' C A 645 " pdb=" C2' C A 645 " both_signs ideal model delta sigma weight residual False -2.74 -2.37 -0.37 2.00e-01 2.50e+01 3.46e+00 chirality pdb=" C3' U A1344 " pdb=" C4' U A1344 " pdb=" O3' U A1344 " pdb=" C2' U A1344 " both_signs ideal model delta sigma weight residual False -2.74 -2.38 -0.37 2.00e-01 2.50e+01 3.34e+00 chirality pdb=" CA UNK i 453 " pdb=" N UNK i 453 " pdb=" C UNK i 453 " pdb=" CB UNK i 453 " both_signs ideal model delta sigma weight residual False 2.52 2.84 -0.32 2.00e-01 2.50e+01 2.63e+00 ... (remaining 19556 not shown) Planarity restraints: 7975 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU U 93 " 0.019 2.00e-02 2.50e+03 3.64e-02 1.33e+01 pdb=" C LEU U 93 " -0.063 2.00e-02 2.50e+03 pdb=" O LEU U 93 " 0.024 2.00e-02 2.50e+03 pdb=" N ASP U 94 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY J 25 " -0.059 5.00e-02 4.00e+02 9.02e-02 1.30e+01 pdb=" N PRO J 26 " 0.156 5.00e-02 4.00e+02 pdb=" CA PRO J 26 " -0.050 5.00e-02 4.00e+02 pdb=" CD PRO J 26 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' A A 984 " -0.046 2.00e-02 2.50e+03 1.91e-02 1.00e+01 pdb=" N9 A A 984 " 0.034 2.00e-02 2.50e+03 pdb=" C8 A A 984 " 0.012 2.00e-02 2.50e+03 pdb=" N7 A A 984 " -0.001 2.00e-02 2.50e+03 pdb=" C5 A A 984 " -0.002 2.00e-02 2.50e+03 pdb=" C6 A A 984 " -0.010 2.00e-02 2.50e+03 pdb=" N6 A A 984 " -0.008 2.00e-02 2.50e+03 pdb=" N1 A A 984 " -0.008 2.00e-02 2.50e+03 pdb=" C2 A A 984 " 0.004 2.00e-02 2.50e+03 pdb=" N3 A A 984 " 0.016 2.00e-02 2.50e+03 pdb=" C4 A A 984 " 0.010 2.00e-02 2.50e+03 ... (remaining 7972 not shown) Histogram of nonbonded interaction distances: 1.74 - 2.37: 291 2.37 - 3.00: 46197 3.00 - 3.63: 162875 3.63 - 4.27: 284591 4.27 - 4.90: 375963 Nonbonded interactions: 869917 Sorted by model distance: nonbonded pdb=" OP1 A A 751 " pdb="MG MG A3020 " model vdw 1.737 2.170 nonbonded pdb=" OP1 U A 827 " pdb="MG MG A3027 " model vdw 1.758 2.170 nonbonded pdb=" OP2 U A 963 " pdb="MG MG A3030 " model vdw 1.771 2.170 nonbonded pdb=" OP1 A A1780 " pdb="MG MG A3086 " model vdw 1.819 2.170 nonbonded pdb=" O4 U A1263 " pdb="MG MG A3180 " model vdw 1.822 2.170 ... (remaining 869912 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 3049 5.49 5 Mg 431 5.21 5 S 95 5.16 5 C 46856 2.51 5 N 17421 2.21 5 O 26174 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=1.00 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: 1.950 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: 0.100 Extract box with map and model: 11.660 Check model and map are aligned: 1.020 Convert atoms to be neutral: 0.590 Process input model: 377.640 Find NCS groups from input model: 1.770 Set up NCS constraints: 0.250 Set refine NCS operators: 0.000 Set scattering table: 0.040 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 397.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 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 : 0.008 0.153 101809 Z= 0.474 Angle : 1.096 14.098 152552 Z= 0.619 Chirality : 0.047 0.372 19559 Planarity : 0.005 0.090 7975 Dihedral : 15.969 176.868 47596 Min Nonbonded Distance : 1.737 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.26 % Favored : 96.68 % Rotamer Outliers : 11.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.88 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.33 (0.11), residues: 3529 helix: -3.48 (0.10), residues: 1067 sheet: -1.39 (0.16), residues: 705 loop : -1.60 (0.12), residues: 1757 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7058 Ramachandran restraints generated. 3529 Oldfield, 0 Emsley, 3529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7058 Ramachandran restraints generated. 3529 Oldfield, 0 Emsley, 3529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1521 residues out of total 2905 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 328 poor density : 1193 time to evaluate : 4.039 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 328 outliers final: 83 residues processed: 1388 average time/residue: 0.9491 time to fit residues: 2175.6917 Evaluate side-chains 853 residues out of total 2905 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 770 time to evaluate : 4.055 Switching outliers to nearest non-outliers outliers start: 83 outliers final: 0 residues processed: 83 average time/residue: 0.7507 time to fit residues: 117.0363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 640 random chunks: chunk 540 optimal weight: 8.9990 chunk 485 optimal weight: 4.9990 chunk 269 optimal weight: 10.0000 chunk 165 optimal weight: 10.0000 chunk 327 optimal weight: 3.9990 chunk 259 optimal weight: 10.0000 chunk 501 optimal weight: 2.9990 chunk 194 optimal weight: 10.0000 chunk 305 optimal weight: 5.9990 chunk 373 optimal weight: 7.9990 chunk 581 optimal weight: 6.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 90 ASN C 134 ASN C 200 HIS C 251 GLN D 136 ASN D 140 HIS D 173 GLN E 41 GLN E 163 ASN ** E 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 18 GLN H 43 ASN H 135 HIS I 6 GLN K 138 GLN L 3 GLN M 35 HIS ** N 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 62 ASN R 81 ASN S 18 GLN ** S 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 91 GLN T 7 HIS T 57 ASN ** U 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 70 HIS W 44 HIS X 12 ASN X 46 HIS Y 20 HIS Y 32 ASN Z 58 ASN d 26 ASN i 381 ASN ** i 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.3074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.146 101809 Z= 0.288 Angle : 0.691 8.739 152552 Z= 0.357 Chirality : 0.039 0.321 19559 Planarity : 0.006 0.077 7975 Dihedral : 14.311 178.352 40609 Min Nonbonded Distance : 1.762 Molprobity Statistics. All-atom Clashscore : 15.05 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.35 % Favored : 97.59 % Rotamer Outliers : 5.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.12), residues: 3529 helix: -0.93 (0.14), residues: 1068 sheet: -0.90 (0.17), residues: 691 loop : -0.95 (0.13), residues: 1770 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7058 Ramachandran restraints generated. 3529 Oldfield, 0 Emsley, 3529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7058 Ramachandran restraints generated. 3529 Oldfield, 0 Emsley, 3529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1051 residues out of total 2905 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 892 time to evaluate : 4.141 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 159 outliers final: 91 residues processed: 992 average time/residue: 0.8726 time to fit residues: 1469.0292 Evaluate side-chains 835 residues out of total 2905 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 744 time to evaluate : 4.117 Switching outliers to nearest non-outliers outliers start: 91 outliers final: 0 residues processed: 91 average time/residue: 0.6993 time to fit residues: 123.0696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 640 random chunks: chunk 322 optimal weight: 10.0000 chunk 180 optimal weight: 10.0000 chunk 483 optimal weight: 7.9990 chunk 395 optimal weight: 3.9990 chunk 160 optimal weight: 20.0000 chunk 582 optimal weight: 6.9990 chunk 628 optimal weight: 8.9990 chunk 518 optimal weight: 3.9990 chunk 577 optimal weight: 7.9990 chunk 198 optimal weight: 10.0000 chunk 467 optimal weight: 6.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 70 ASN ** C 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 163 ASN ** E 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 43 ASN J 12 GLN K 138 GLN M 35 HIS M 104 GLN ** N 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 18 GLN O 107 ASN ** Q 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 44 GLN R 52 GLN R 71 GLN S 18 GLN ** T 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 31 GLN U 28 ASN U 48 GLN W 87 GLN Z 25 GLN i 411 GLN i 419 GLN ** i 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8810 moved from start: 0.4730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.083 101809 Z= 0.300 Angle : 0.653 14.140 152552 Z= 0.338 Chirality : 0.037 0.303 19559 Planarity : 0.005 0.064 7975 Dihedral : 14.168 179.727 40609 Min Nonbonded Distance : 1.771 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.81 % Favored : 97.14 % Rotamer Outliers : 4.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.13), residues: 3529 helix: -0.03 (0.15), residues: 1085 sheet: -0.73 (0.18), residues: 707 loop : -0.81 (0.14), residues: 1737 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7058 Ramachandran restraints generated. 3529 Oldfield, 0 Emsley, 3529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7058 Ramachandran restraints generated. 3529 Oldfield, 0 Emsley, 3529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 988 residues out of total 2905 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 850 time to evaluate : 4.005 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 138 outliers final: 67 residues processed: 930 average time/residue: 0.8560 time to fit residues: 1364.9354 Evaluate side-chains 824 residues out of total 2905 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 757 time to evaluate : 4.064 Switching outliers to nearest non-outliers outliers start: 67 outliers final: 0 residues processed: 67 average time/residue: 0.7087 time to fit residues: 92.2920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 640 random chunks: chunk 575 optimal weight: 6.9990 chunk 437 optimal weight: 10.0000 chunk 302 optimal weight: 10.0000 chunk 64 optimal weight: 10.0000 chunk 277 optimal weight: 10.0000 chunk 390 optimal weight: 10.0000 chunk 584 optimal weight: 6.9990 chunk 618 optimal weight: 9.9990 chunk 305 optimal weight: 9.9990 chunk 553 optimal weight: 9.9990 chunk 166 optimal weight: 10.0000 overall best weight: 8.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 70 ASN ** C 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 90 GLN E 163 ASN ** E 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 88 GLN H 43 ASN H 133 GLN H 135 HIS K 138 GLN M 35 HIS M 54 GLN M 104 GLN ** Q 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 71 GLN ** T 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 31 GLN U 28 ASN U 48 GLN U 70 HIS U 92 ASN W 87 GLN Z 25 GLN i 419 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8857 moved from start: 0.5717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.057 101809 Z= 0.407 Angle : 0.736 9.237 152552 Z= 0.375 Chirality : 0.041 0.295 19559 Planarity : 0.006 0.102 7975 Dihedral : 14.451 179.822 40609 Min Nonbonded Distance : 1.477 Molprobity Statistics. All-atom Clashscore : 16.81 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.08 % Favored : 95.86 % Rotamer Outliers : 4.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.13), residues: 3529 helix: -0.06 (0.15), residues: 1080 sheet: -0.72 (0.18), residues: 738 loop : -0.97 (0.14), residues: 1711 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7058 Ramachandran restraints generated. 3529 Oldfield, 0 Emsley, 3529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7058 Ramachandran restraints generated. 3529 Oldfield, 0 Emsley, 3529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 929 residues out of total 2905 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 789 time to evaluate : 4.071 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: 140 outliers final: 90 residues processed: 865 average time/residue: 0.8764 time to fit residues: 1309.1882 Evaluate side-chains 813 residues out of total 2905 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 723 time to evaluate : 3.977 Switching outliers to nearest non-outliers outliers start: 90 outliers final: 0 residues processed: 90 average time/residue: 0.6875 time to fit residues: 122.5788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 640 random chunks: chunk 515 optimal weight: 9.9990 chunk 351 optimal weight: 9.9990 chunk 8 optimal weight: 10.0000 chunk 460 optimal weight: 5.9990 chunk 255 optimal weight: 10.0000 chunk 527 optimal weight: 3.9990 chunk 427 optimal weight: 20.0000 chunk 0 optimal weight: 50.0000 chunk 315 optimal weight: 20.0000 chunk 555 optimal weight: 6.9990 chunk 156 optimal weight: 20.0000 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 70 ASN ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 115 GLN E 163 ASN ** E 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 128 HIS K 138 GLN L 88 ASN L 90 ASN M 104 GLN O 107 ASN ** Q 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 48 GLN W 87 GLN Z 25 GLN ** a 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 42 HIS f 35 GLN i 419 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8839 moved from start: 0.6072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.059 101809 Z= 0.345 Angle : 0.667 12.473 152552 Z= 0.342 Chirality : 0.038 0.285 19559 Planarity : 0.005 0.077 7975 Dihedral : 14.291 177.348 40609 Min Nonbonded Distance : 1.352 Molprobity Statistics. All-atom Clashscore : 15.03 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.94 % Favored : 95.98 % Rotamer Outliers : 3.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.14), residues: 3529 helix: 0.16 (0.16), residues: 1077 sheet: -0.73 (0.18), residues: 732 loop : -0.92 (0.14), residues: 1720 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7058 Ramachandran restraints generated. 3529 Oldfield, 0 Emsley, 3529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7058 Ramachandran restraints generated. 3529 Oldfield, 0 Emsley, 3529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 874 residues out of total 2905 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 781 time to evaluate : 4.059 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 93 outliers final: 61 residues processed: 833 average time/residue: 0.8547 time to fit residues: 1221.9885 Evaluate side-chains 784 residues out of total 2905 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 723 time to evaluate : 4.007 Switching outliers to nearest non-outliers outliers start: 61 outliers final: 0 residues processed: 61 average time/residue: 0.6927 time to fit residues: 83.1310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 640 random chunks: chunk 208 optimal weight: 10.0000 chunk 557 optimal weight: 0.9990 chunk 122 optimal weight: 10.0000 chunk 363 optimal weight: 0.9980 chunk 152 optimal weight: 20.0000 chunk 619 optimal weight: 10.0000 chunk 514 optimal weight: 8.9990 chunk 286 optimal weight: 10.0000 chunk 51 optimal weight: 10.0000 chunk 204 optimal weight: 10.0000 chunk 325 optimal weight: 2.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 70 ASN ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 185 ASN E 115 GLN F 23 ASN K 138 GLN L 90 ASN M 104 GLN N 17 ASN ** Q 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 28 ASN U 48 GLN ** W 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 419 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8811 moved from start: 0.6240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.054 101809 Z= 0.246 Angle : 0.598 12.610 152552 Z= 0.310 Chirality : 0.035 0.275 19559 Planarity : 0.005 0.068 7975 Dihedral : 14.110 178.397 40609 Min Nonbonded Distance : 1.298 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.66 % Favored : 96.23 % Rotamer Outliers : 2.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.14), residues: 3529 helix: 0.44 (0.16), residues: 1073 sheet: -0.61 (0.18), residues: 722 loop : -0.86 (0.15), residues: 1734 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7058 Ramachandran restraints generated. 3529 Oldfield, 0 Emsley, 3529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7058 Ramachandran restraints generated. 3529 Oldfield, 0 Emsley, 3529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 831 residues out of total 2905 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 767 time to evaluate : 4.145 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: 64 outliers final: 41 residues processed: 797 average time/residue: 0.9294 time to fit residues: 1283.3804 Evaluate side-chains 772 residues out of total 2905 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 731 time to evaluate : 4.071 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 0 residues processed: 41 average time/residue: 0.6819 time to fit residues: 57.4523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 640 random chunks: chunk 597 optimal weight: 5.9990 chunk 69 optimal weight: 10.0000 chunk 352 optimal weight: 6.9990 chunk 452 optimal weight: 0.9980 chunk 350 optimal weight: 5.9990 chunk 521 optimal weight: 7.9990 chunk 345 optimal weight: 0.7980 chunk 616 optimal weight: 6.9990 chunk 386 optimal weight: 20.0000 chunk 376 optimal weight: 10.0000 chunk 284 optimal weight: 10.0000 overall best weight: 4.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 70 ASN F 23 ASN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 138 GLN L 90 ASN ** Q 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 37 GLN ** T 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 15 GLN U 48 GLN W 49 ASN W 87 GLN d 29 GLN i 419 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8787 moved from start: 0.6444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.063 101809 Z= 0.217 Angle : 0.573 13.801 152552 Z= 0.297 Chirality : 0.034 0.267 19559 Planarity : 0.005 0.069 7975 Dihedral : 13.949 177.496 40609 Min Nonbonded Distance : 1.222 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.43 % Favored : 96.46 % Rotamer Outliers : 2.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.14), residues: 3529 helix: 0.54 (0.16), residues: 1072 sheet: -0.56 (0.18), residues: 729 loop : -0.82 (0.14), residues: 1728 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7058 Ramachandran restraints generated. 3529 Oldfield, 0 Emsley, 3529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7058 Ramachandran restraints generated. 3529 Oldfield, 0 Emsley, 3529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 846 residues out of total 2905 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 784 time to evaluate : 4.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 62 outliers final: 35 residues processed: 809 average time/residue: 0.9024 time to fit residues: 1261.0663 Evaluate side-chains 753 residues out of total 2905 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 718 time to evaluate : 4.030 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 0 residues processed: 35 average time/residue: 0.6744 time to fit residues: 49.1638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 640 random chunks: chunk 381 optimal weight: 9.9990 chunk 246 optimal weight: 10.0000 chunk 368 optimal weight: 6.9990 chunk 185 optimal weight: 10.0000 chunk 121 optimal weight: 10.0000 chunk 119 optimal weight: 20.0000 chunk 392 optimal weight: 8.9990 chunk 420 optimal weight: 8.9990 chunk 304 optimal weight: 2.9990 chunk 57 optimal weight: 10.0000 chunk 484 optimal weight: 0.1980 overall best weight: 5.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 138 GLN L 90 ASN ** N 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 18 GLN ** Q 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 48 GLN ** W 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 419 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8800 moved from start: 0.6498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.077 101809 Z= 0.276 Angle : 0.605 15.573 152552 Z= 0.312 Chirality : 0.035 0.272 19559 Planarity : 0.005 0.062 7975 Dihedral : 13.977 177.187 40609 Min Nonbonded Distance : 1.201 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.88 % Favored : 96.00 % Rotamer Outliers : 1.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.14), residues: 3529 helix: 0.50 (0.16), residues: 1076 sheet: -0.59 (0.19), residues: 728 loop : -0.86 (0.14), residues: 1725 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7058 Ramachandran restraints generated. 3529 Oldfield, 0 Emsley, 3529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7058 Ramachandran restraints generated. 3529 Oldfield, 0 Emsley, 3529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 780 residues out of total 2905 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 728 time to evaluate : 4.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 52 outliers final: 36 residues processed: 751 average time/residue: 0.8593 time to fit residues: 1119.0963 Evaluate side-chains 748 residues out of total 2905 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 712 time to evaluate : 3.986 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 0 residues processed: 36 average time/residue: 0.6858 time to fit residues: 51.5424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 640 random chunks: chunk 561 optimal weight: 5.9990 chunk 590 optimal weight: 1.9990 chunk 539 optimal weight: 10.0000 chunk 574 optimal weight: 9.9990 chunk 345 optimal weight: 10.0000 chunk 250 optimal weight: 10.0000 chunk 451 optimal weight: 9.9990 chunk 176 optimal weight: 20.0000 chunk 519 optimal weight: 5.9990 chunk 543 optimal weight: 0.4980 chunk 572 optimal weight: 7.9990 overall best weight: 4.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 63 GLN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 138 GLN L 90 ASN ** N 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 18 GLN ** Q 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 48 GLN ** W 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 419 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8785 moved from start: 0.6624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.058 101809 Z= 0.231 Angle : 0.583 10.802 152552 Z= 0.302 Chirality : 0.034 0.266 19559 Planarity : 0.005 0.058 7975 Dihedral : 13.939 177.357 40609 Min Nonbonded Distance : 1.078 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.43 % Favored : 96.46 % Rotamer Outliers : 0.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.14), residues: 3529 helix: 0.51 (0.16), residues: 1063 sheet: -0.57 (0.18), residues: 740 loop : -0.83 (0.15), residues: 1726 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7058 Ramachandran restraints generated. 3529 Oldfield, 0 Emsley, 3529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7058 Ramachandran restraints generated. 3529 Oldfield, 0 Emsley, 3529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 771 residues out of total 2905 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 744 time to evaluate : 4.055 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: 27 outliers final: 19 residues processed: 754 average time/residue: 0.8673 time to fit residues: 1122.8567 Evaluate side-chains 732 residues out of total 2905 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 713 time to evaluate : 4.024 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.6743 time to fit residues: 28.5464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 640 random chunks: chunk 377 optimal weight: 0.0570 chunk 607 optimal weight: 3.9990 chunk 371 optimal weight: 6.9990 chunk 288 optimal weight: 10.0000 chunk 422 optimal weight: 8.9990 chunk 637 optimal weight: 2.9990 chunk 586 optimal weight: 5.9990 chunk 507 optimal weight: 9.9990 chunk 52 optimal weight: 10.0000 chunk 392 optimal weight: 10.0000 chunk 311 optimal weight: 1.9990 overall best weight: 3.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 73 ASN K 138 GLN L 90 ASN O 18 GLN ** Q 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 48 GLN ** W 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 419 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8756 moved from start: 0.6731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.091 101809 Z= 0.183 Angle : 0.557 12.274 152552 Z= 0.288 Chirality : 0.032 0.261 19559 Planarity : 0.004 0.062 7975 Dihedral : 13.825 177.783 40609 Min Nonbonded Distance : 1.156 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.49 % Favored : 96.40 % Rotamer Outliers : 0.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.14), residues: 3529 helix: 0.55 (0.16), residues: 1074 sheet: -0.58 (0.18), residues: 763 loop : -0.80 (0.15), residues: 1692 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7058 Ramachandran restraints generated. 3529 Oldfield, 0 Emsley, 3529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7058 Ramachandran restraints generated. 3529 Oldfield, 0 Emsley, 3529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 783 residues out of total 2905 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 766 time to evaluate : 4.198 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: 17 outliers final: 12 residues processed: 774 average time/residue: 0.8815 time to fit residues: 1170.1117 Evaluate side-chains 737 residues out of total 2905 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 725 time to evaluate : 4.088 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.6971 time to fit residues: 20.0228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 640 random chunks: chunk 403 optimal weight: 0.9990 chunk 540 optimal weight: 0.9980 chunk 155 optimal weight: 20.0000 chunk 468 optimal weight: 9.9990 chunk 74 optimal weight: 10.0000 chunk 141 optimal weight: 10.0000 chunk 508 optimal weight: 0.3980 chunk 212 optimal weight: 40.0000 chunk 522 optimal weight: 8.9990 chunk 64 optimal weight: 20.0000 chunk 93 optimal weight: 10.0000 overall best weight: 4.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 138 GLN L 90 ASN O 18 GLN P 98 GLN ** Q 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 48 GLN ** W 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 419 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.086001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.068720 restraints weight = 278724.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.070331 restraints weight = 105365.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.071243 restraints weight = 57968.961| |-----------------------------------------------------------------------------| r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.6753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.055 101809 Z= 0.223 Angle : 0.579 13.808 152552 Z= 0.298 Chirality : 0.033 0.264 19559 Planarity : 0.005 0.084 7975 Dihedral : 13.829 177.399 40609 Min Nonbonded Distance : 1.128 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.60 % Favored : 96.29 % Rotamer Outliers : 0.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.14), residues: 3529 helix: 0.58 (0.16), residues: 1067 sheet: -0.62 (0.18), residues: 763 loop : -0.82 (0.15), residues: 1699 =============================================================================== Job complete usr+sys time: 19217.97 seconds wall clock time: 341 minutes 0.75 seconds (20460.75 seconds total)