Starting phenix.real_space_refine (version: dev) on Sat Dec 17 11:01:37 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5gad_8000/12_2022/5gad_8000_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5gad_8000/12_2022/5gad_8000.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5gad_8000/12_2022/5gad_8000.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5gad_8000/12_2022/5gad_8000.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5gad_8000/12_2022/5gad_8000_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5gad_8000/12_2022/5gad_8000_neut_updated.pdb" } resolution = 3.7 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= 0.000 sd= 0.013 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 "U PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 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 57": "OE1" <-> "OE2" Residue "i ASP 163": "OD1" <-> "OD2" Residue "i TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ASP 185": "OD1" <-> "OD2" Residue "i GLU 204": "OE1" <-> "OE2" Residue "i GLU 277": "OE1" <-> "OE2" Residue "i GLU 392": "OE1" <-> "OE2" Residue "l PHE 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l PHE 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l GLU 436": "OE1" <-> "OE2" Residue "l PHE 458": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l TYR 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 98006 Number of models: 1 Model: "" Number of chains: 49 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 breaks: 1 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: 3337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3337 Classifications: {'peptide': 450} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 13, 'TRANS': 436} Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 150 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'UNK:plan-1': 71} Unresolved non-hydrogen planarities: 71 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: "l" Number of atoms: 1492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1492 Classifications: {'peptide': 198} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 192} 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} Chain: "i" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GNP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "l" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GNP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 92325 SG CYS f 11 74.500 81.470 178.879 1.00 60.00 S ATOM 92350 SG CYS f 14 77.644 82.923 177.829 1.00 60.00 S ATOM 92453 SG CYS f 27 77.955 79.762 179.788 1.00 60.00 S Time building chain proxies: 43.88, per 1000 atoms: 0.45 Number of scatterers: 98006 At special positions: 0 Unit cell: (268.69, 198.055, 239.605, 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 107 16.00 P 3055 15.00 Mg 433 11.99 O 26926 8.00 N 18130 7.00 C 49354 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: 44.56 Conformation dependent library (CDL) restraints added in 5.2 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 8026 Ramachandran restraints generated. 4013 Oldfield, 0 Emsley, 4013 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7610 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 136 helices and 50 sheets defined 32.5% alpha, 17.7% beta 1020 base pairs and 1574 stacking pairs defined. Time for finding SS restraints: 46.02 Creating SS restraints... Processing helix chain 'C' and resid 11 through 13 No H-bonds generated for 'chain 'C' and resid 11 through 13' Processing helix chain 'C' and resid 31 through 33 No H-bonds generated for 'chain 'C' and resid 31 through 33' Processing helix chain 'C' and resid 132 through 134 No H-bonds generated for 'chain 'C' and resid 132 through 134' Processing helix chain 'C' and resid 198 through 202 removed outlier: 4.212A pdb=" N MET C 201 " --> pdb=" O ALA C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 214 Processing helix chain 'C' and resid 222 through 224 No H-bonds generated for 'chain 'C' and resid 222 through 224' Processing helix chain 'C' and resid 263 through 266 Processing helix chain 'D' and resid 40 through 43 No H-bonds generated for 'chain 'D' and resid 40 through 43' Processing helix chain 'D' and resid 62 through 71 removed outlier: 3.714A pdb=" N ALA D 71 " --> pdb=" O HIS D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 101 Processing helix chain 'D' and resid 121 through 125 Processing helix chain 'E' and resid 16 through 19 No H-bonds generated for 'chain 'E' and resid 16 through 19' Processing helix chain 'E' and resid 25 through 38 Processing helix chain 'E' and resid 98 through 114 Processing helix chain 'E' and resid 131 through 141 Processing helix chain 'E' and resid 155 through 160 Processing helix chain 'E' and resid 172 through 174 No H-bonds generated for 'chain 'E' and resid 172 through 174' Processing helix chain 'E' and resid 177 through 182 Processing helix chain 'E' and resid 190 through 199 Processing helix chain 'F' and resid 3 through 10 Processing helix chain 'F' and resid 12 through 20 Processing helix chain 'F' and resid 25 through 27 No H-bonds generated for 'chain 'F' and resid 25 through 27' Processing helix chain 'F' and resid 48 through 61 removed outlier: 3.727A pdb=" N ASP F 56 " --> pdb=" O ASN F 52 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 105 Processing helix chain 'F' and resid 108 through 110 No H-bonds generated for 'chain 'F' and resid 108 through 110' Processing helix chain 'F' and resid 143 through 145 No H-bonds generated for 'chain 'F' and resid 143 through 145' Processing helix chain 'F' and resid 163 through 173 Processing helix chain 'G' and resid 61 through 80 Processing helix chain 'G' and resid 138 through 151 removed outlier: 3.661A pdb=" N TYR G 151 " --> pdb=" O ASP G 147 " (cutoff:3.500A) Processing helix chain 'H' and resid 23 through 28 Processing helix chain 'H' and resid 41 through 72 removed outlier: 5.673A 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 86 through 88 No H-bonds generated for 'chain 'H' and resid 86 through 88' Processing helix chain 'H' and resid 96 through 104 Processing helix chain 'H' and resid 112 through 114 No H-bonds generated for 'chain 'H' and resid 112 through 114' Processing helix chain 'I' and resid 5 through 21 Processing helix chain 'I' and resid 35 through 46 Processing helix chain 'I' and resid 57 through 66 removed outlier: 3.935A pdb=" N ARG I 62 " --> pdb=" O THR I 58 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N GLY I 66 " --> pdb=" O ARG I 62 " (cutoff:3.500A) Processing helix chain 'I' and resid 70 through 72 No H-bonds generated for 'chain 'I' and resid 70 through 72' Processing helix chain 'I' and resid 93 through 103 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 123 through 125 No H-bonds generated for 'chain 'I' and resid 123 through 125' Processing helix chain 'J' and resid 35 through 48 removed outlier: 5.607A pdb=" N SER J 48 " --> pdb=" O ALA J 44 " (cutoff:3.500A) Processing helix chain 'J' and resid 76 through 83 Processing helix chain 'J' and resid 103 through 116 Processing helix chain 'J' and resid 122 through 135 Processing helix chain 'K' and resid 25 through 37 removed outlier: 4.026A pdb=" N GLU K 31 " --> pdb=" O ARG K 27 " (cutoff:3.500A) Processing helix chain 'K' and resid 68 through 71 No H-bonds generated for 'chain 'K' and resid 68 through 71' Processing helix chain 'K' and resid 89 through 108 Proline residue: K 97 - end of helix removed outlier: 4.317A pdb=" N VAL K 100 " --> pdb=" O ARG K 96 " (cutoff:3.500A) 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 113 through 121 removed outlier: 4.047A pdb=" N LYS K 121 " --> pdb=" O ALA K 117 " (cutoff:3.500A) Processing helix chain 'K' and resid 132 through 135 Processing helix chain 'L' and resid 105 through 107 No H-bonds generated for 'chain 'L' and resid 105 through 107' Processing helix chain 'L' and resid 113 through 117 Processing helix chain 'M' and resid 23 through 25 No H-bonds generated for 'chain 'M' and resid 23 through 25' Processing helix chain 'M' and resid 37 through 40 No H-bonds generated for 'chain 'M' and resid 37 through 40' Processing helix chain 'M' and resid 57 through 60 No H-bonds generated for 'chain 'M' and resid 57 through 60' Processing helix chain 'M' and resid 69 through 72 No H-bonds generated for 'chain 'M' and resid 69 through 72' Processing helix chain 'M' and resid 79 through 84 removed outlier: 4.206A pdb=" N ALA M 83 " --> pdb=" O LEU M 79 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N LYS M 84 " --> pdb=" O SER M 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 79 through 84' Processing helix chain 'M' and resid 92 through 97 Processing helix chain 'M' and resid 129 through 136 Processing helix chain 'N' and resid 43 through 56 Processing helix chain 'N' and resid 110 through 123 removed outlier: 4.354A pdb=" N LYS N 123 " --> pdb=" O LEU N 119 " (cutoff:3.500A) Processing helix chain 'O' and resid 14 through 31 Processing helix chain 'O' and resid 38 through 55 removed outlier: 3.715A 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 60 through 70 Processing helix chain 'O' and resid 73 through 81 Processing helix chain 'O' and resid 83 through 86 No H-bonds generated for 'chain 'O' and resid 83 through 86' Processing helix chain 'O' and resid 118 through 123 Processing helix chain 'P' and resid 3 through 20 removed outlier: 4.861A pdb=" N ARG P 13 " --> pdb=" O ARG P 9 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N ALA P 14 " --> pdb=" O ARG P 10 " (cutoff:3.500A) Processing helix chain 'P' and resid 56 through 61 removed outlier: 5.193A pdb=" N GLN P 61 " --> pdb=" O ALA P 57 " (cutoff:3.500A) Processing helix chain 'P' and resid 68 through 83 Processing helix chain 'P' and resid 101 through 112 Processing helix chain 'Q' and resid 3 through 10 Processing helix chain 'Q' and resid 54 through 56 No H-bonds generated for 'chain 'Q' and resid 54 through 56' Processing helix chain 'Q' and resid 98 through 101 Processing helix chain 'Q' and resid 105 through 107 No H-bonds generated for 'chain 'Q' and resid 105 through 107' Processing helix chain 'R' and resid 7 through 20 Processing helix chain 'R' and resid 26 through 30 Processing helix chain 'R' and resid 32 through 71 removed outlier: 3.639A 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: 3.769A pdb=" N LYS R 54 " --> pdb=" O ARG R 50 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ARG R 55 " --> pdb=" O ARG R 51 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ARG R 58 " --> pdb=" O LYS R 54 " (cutoff:3.500A) Processing helix chain 'R' and resid 76 through 85 Processing helix chain 'R' and resid 92 through 101 Processing helix chain 'R' and resid 103 through 117 Processing helix chain 'T' and resid 14 through 24 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) Processing helix chain 'T' and resid 29 through 38 Processing helix chain 'T' and resid 43 through 62 Processing helix chain 'T' and resid 66 through 68 No H-bonds generated for 'chain 'T' and resid 66 through 68' 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 4 through 9 removed outlier: 3.925A pdb=" N LYS U 9 " --> pdb=" O GLU U 5 " (cutoff:3.500A) Processing helix chain 'U' and resid 18 through 26 Processing helix chain 'U' and resid 40 through 50 Processing helix chain 'V' and resid 67 through 69 No H-bonds generated for 'chain 'V' and resid 67 through 69' Processing helix chain 'W' and resid 13 through 22 Processing helix chain 'W' and resid 44 through 50 Processing helix chain 'W' and resid 55 through 58 No H-bonds generated for 'chain 'W' and resid 55 through 58' Processing helix chain 'Y' and resid 53 through 62 Processing helix chain 'Y' and resid 64 through 74 Processing helix chain 'Z' and resid 6 through 8 No H-bonds generated for 'chain 'Z' and resid 6 through 8' Processing helix chain 'Z' and resid 11 through 34 removed outlier: 3.581A pdb=" N LEU Z 19 " --> pdb=" O ASN Z 15 " (cutoff:3.500A) Processing helix chain 'Z' and resid 41 through 62 removed outlier: 3.938A 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 18 through 27 Processing helix chain 'a' and resid 42 through 50 Processing helix chain 'b' and resid 10 through 19 removed outlier: 3.581A pdb=" N ARG b 17 " --> pdb=" O ARG b 13 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N HIS b 19 " --> pdb=" O MET b 15 " (cutoff:3.500A) Processing helix chain 'd' and resid 9 through 16 Processing helix chain 'd' and resid 18 through 22 Processing helix chain 'd' and resid 25 through 37 Processing helix chain 'e' and resid 8 through 13 removed outlier: 3.687A 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) No H-bonds generated for 'chain 'e' and resid 8 through 13' Processing helix chain 'e' and resid 38 through 45 Processing helix chain 'e' and resid 55 through 61 Processing helix chain 'f' and resid 31 through 33 No H-bonds generated for 'chain 'f' and resid 31 through 33' Processing helix chain 'i' and resid 5 through 18 Processing helix chain 'i' and resid 24 through 40 Processing helix chain 'i' and resid 45 through 58 Processing helix chain 'i' and resid 70 through 85 Processing helix chain 'i' and resid 113 through 128 Processing helix chain 'i' and resid 144 through 154 Processing helix chain 'i' and resid 168 through 182 Processing helix chain 'i' and resid 199 through 212 Processing helix chain 'i' and resid 227 through 238 removed outlier: 3.890A pdb=" N ALA i 230 " --> pdb=" O GLN i 227 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ALA i 233 " --> pdb=" O ALA i 230 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LYS i 234 " --> pdb=" O ASN i 231 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE i 236 " --> pdb=" O ALA i 233 " (cutoff:3.500A) Processing helix chain 'i' and resid 258 through 265 Processing helix chain 'i' and resid 279 through 281 No H-bonds generated for 'chain 'i' and resid 279 through 281' Processing helix chain 'i' and resid 287 through 295 Processing helix chain 'i' and resid 300 through 326 removed outlier: 5.357A pdb=" N UNK i 315 " --> pdb=" O UNK i 311 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N UNK i 316 " --> pdb=" O UNK i 312 " (cutoff:3.500A) Processing helix chain 'i' and resid 331 through 343 Processing helix chain 'i' and resid 348 through 353 removed outlier: 3.853A pdb=" N UNK i 353 " --> pdb=" O UNK i 349 " (cutoff:3.500A) Processing helix chain 'i' and resid 355 through 358 No H-bonds generated for 'chain 'i' and resid 355 through 358' Processing helix chain 'i' and resid 369 through 380 removed outlier: 3.775A pdb=" N VAL i 374 " --> pdb=" O ASP i 370 " (cutoff:3.500A) Processing helix chain 'i' and resid 385 through 389 Processing helix chain 'i' and resid 391 through 393 No H-bonds generated for 'chain 'i' and resid 391 through 393' Processing helix chain 'i' and resid 396 through 405 Processing helix chain 'i' and resid 410 through 432 Processing helix chain 'i' and resid 435 through 440 Processing helix chain 'k' and resid 28 through 43 removed outlier: 3.685A pdb=" N LEU k 36 " --> pdb=" O LEU k 32 " (cutoff:3.500A) Proline residue: k 43 - end of helix Processing helix chain 'l' and resid 306 through 319 Processing helix chain 'l' and resid 336 through 347 removed outlier: 4.152A pdb=" N LEU l 340 " --> pdb=" O ALA l 336 " (cutoff:3.500A) Processing helix chain 'l' and resid 360 through 373 Processing helix chain 'l' and resid 393 through 407 Processing helix chain 'l' and resid 425 through 438 removed outlier: 3.943A pdb=" N SER l 429 " --> pdb=" O GLN l 425 " (cutoff:3.500A) Processing helix chain 'l' and resid 455 through 464 removed outlier: 3.686A pdb=" N ALA l 461 " --> pdb=" O PHE l 458 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ASP l 462 " --> pdb=" O SER l 459 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N PHE l 464 " --> pdb=" O ALA l 461 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'C' and resid 3 through 5 Processing sheet with id= B, first strand: chain 'C' and resid 101 through 105 removed outlier: 3.525A 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: 5.781A pdb=" N VAL C 78 " --> pdb=" O LEU C 95 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 129 through 131 Processing sheet with id= D, first strand: chain 'C' and resid 181 through 185 removed outlier: 6.540A pdb=" N ARG C 175 " --> pdb=" O ILE C 164 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N ILE C 164 " --> pdb=" O ARG C 175 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'D' and resid 169 through 172 removed outlier: 4.534A pdb=" N THR D 112 " --> pdb=" O ASP D 200 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N ASP D 200 " --> pdb=" O THR D 112 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N VAL D 26 " --> pdb=" O VAL D 9 " (cutoff:3.500A) removed outlier: 4.459A 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: 6.434A pdb=" N ILE D 22 " --> pdb=" O ARG D 13 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N LYS D 190 " --> pdb=" O VAL D 177 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N VAL D 177 " --> pdb=" O LYS D 190 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'D' and resid 80 through 83 removed outlier: 6.549A pdb=" N THR D 51 " --> pdb=" O VAL D 34 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N VAL D 34 " --> pdb=" O THR D 51 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'E' and resid 2 through 4 Processing sheet with id= H, first strand: chain 'E' and resid 118 through 121 removed outlier: 6.374A pdb=" N VAL E 186 " --> pdb=" O ILE E 119 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N VAL E 121 " --> pdb=" O VAL E 186 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N MET E 188 " --> pdb=" O VAL E 121 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'F' and resid 128 through 132 removed outlier: 6.844A pdb=" N THR F 68 " --> pdb=" O ILE F 85 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N CYS F 87 " --> pdb=" O LEU F 66 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N LEU F 66 " --> pdb=" O CYS F 87 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'G' and resid 16 through 20 Processing sheet with id= K, first strand: chain 'G' and resid 41 through 45 Processing sheet with id= L, first strand: chain 'G' and resid 161 through 164 Processing sheet with id= M, first strand: chain 'G' and resid 95 through 99 Processing sheet with id= N, first strand: chain 'H' and resid 18 through 20 Processing sheet with id= O, 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) Processing sheet with id= P, first strand: chain 'I' and resid 116 through 118 removed outlier: 3.624A pdb=" N ALA I 110 " --> pdb=" O VAL I 27 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA I 25 " --> pdb=" O ALA I 112 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N SER I 24 " --> pdb=" O VAL I 85 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'J' and resid 9 through 14 Processing sheet with id= R, first strand: chain 'K' and resid 15 through 19 removed outlier: 6.640A pdb=" N TYR K 53 " --> pdb=" O TYR K 16 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N VAL K 18 " --> pdb=" O TYR K 53 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N ILE K 55 " --> pdb=" O VAL K 18 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'K' and resid 73 through 77 Processing sheet with id= T, first strand: chain 'L' and resid 19 through 24 removed outlier: 6.690A pdb=" N LYS L 40 " --> pdb=" O ILE L 22 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N VAL L 24 " --> pdb=" O ILE L 38 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N ILE L 38 " --> pdb=" O VAL L 24 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ALA L 83 " --> pdb=" O VAL L 63 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'M' and resid 74 through 77 removed outlier: 6.282A pdb=" N PHE M 107 " --> pdb=" O ALA M 75 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N ILE M 77 " --> pdb=" O PHE M 107 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N LYS M 109 " --> pdb=" O ILE M 77 " (cutoff:3.500A) No H-bonds generated for sheet with id= U Processing sheet with id= V, first strand: chain 'M' and resid 121 through 123 removed outlier: 6.686A pdb=" N LYS M 141 " --> pdb=" O VAL M 122 " (cutoff:3.500A) No H-bonds generated for sheet with id= V Processing sheet with id= W, first strand: chain 'N' and resid 128 through 132 removed outlier: 3.721A pdb=" N TYR N 103 " --> pdb=" O LEU N 33 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ALA N 35 " --> pdb=" O VAL N 101 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N VAL N 101 " --> pdb=" O ALA N 35 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'N' and resid 39 through 42 removed outlier: 3.514A pdb=" N ASN N 88 " --> pdb=" O GLU N 75 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ILE N 73 " --> pdb=" O GLU N 90 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N TRP N 92 " --> pdb=" O LYS N 71 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N LYS N 71 " --> pdb=" O TRP N 92 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'O' and resid 33 through 37 removed outlier: 3.698A pdb=" N ALA O 108 " --> pdb=" O ARG O 103 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N GLY O 101 " --> pdb=" O MET O 110 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N TYR O 112 " --> pdb=" O LYS O 99 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N LYS O 99 " --> pdb=" O TYR O 112 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N GLU O 114 " --> pdb=" O ILE O 97 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N ILE O 97 " --> pdb=" O GLU O 114 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'P' and resid 91 through 93 removed outlier: 3.552A pdb=" N VAL P 49 " --> pdb=" O VAL P 39 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'Q' and resid 83 through 88 removed outlier: 6.882A pdb=" N THR Q 25 " --> pdb=" O LYS Q 87 " (cutoff:3.500A) removed outlier: 9.098A pdb=" N GLU Q 44 " --> pdb=" O ILE Q 64 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N ILE Q 64 " --> pdb=" O GLU Q 44 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N THR Q 60 " --> pdb=" O ILE Q 48 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N ILE Q 50 " --> pdb=" O ALA Q 58 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N ALA Q 58 " --> pdb=" O ILE Q 50 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'S' and resid 10 through 14 removed outlier: 6.963A pdb=" N GLN S 6 " --> pdb=" O VAL S 38 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N VAL S 38 " --> pdb=" O GLN S 6 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'S' and resid 19 through 23 Processing sheet with id= AD, first strand: chain 'S' and resid 32 through 35 removed outlier: 6.483A pdb=" N GLU S 62 " --> pdb=" O ILE S 98 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N ILE S 98 " --> pdb=" O GLU S 62 " (cutoff:3.500A) Processing sheet with id= AE, 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= AF, first strand: chain 'T' and resid 2 through 7 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= AG, first strand: chain 'T' and resid 82 through 87 Processing sheet with id= AH, first strand: chain 'U' and resid 11 through 14 removed outlier: 6.843A pdb=" N LYS U 33 " --> pdb=" O ARG U 12 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N VAL U 31 " --> pdb=" O PRO U 14 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LYS U 81 " --> pdb=" O VAL U 34 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL U 57 " --> pdb=" O THR U 86 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'U' and resid 67 through 70 Processing sheet with id= AJ, first strand: chain 'V' and resid 22 through 24 Processing sheet with id= AK, first strand: chain 'V' and resid 41 through 45 Processing sheet with id= AL, first strand: chain 'V' and resid 83 through 88 Processing sheet with id= AM, first strand: chain 'V' and resid 25 through 28 removed outlier: 7.135A pdb=" N ILE V 35 " --> pdb=" O LYS V 26 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'W' and resid 3 through 6 removed outlier: 6.567A pdb=" N THR W 62 " --> pdb=" O ILE W 4 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N ALA W 6 " --> pdb=" O THR W 62 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N VAL W 64 " --> pdb=" O ALA W 6 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ASP W 90 " --> pdb=" O GLN W 75 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N VAL W 77 " --> pdb=" O HIS W 88 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N HIS W 88 " --> pdb=" O VAL W 77 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ILE W 89 " --> pdb=" O PRO W 27 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'X' and resid 45 through 47 removed outlier: 7.252A pdb=" N LYS X 78 " --> pdb=" O HIS X 46 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'X' and resid 51 through 53 Processing sheet with id= AQ, first strand: chain 'Y' and resid 13 through 18 Processing sheet with id= AR, first strand: chain 'Y' and resid 33 through 40 Processing sheet with id= AS, first strand: chain 'a' and resid 35 through 38 Processing sheet with id= AT, first strand: chain 'c' and resid 20 through 25 Processing sheet with id= AU, first strand: chain 'f' and resid 2 through 4 Processing sheet with id= AV, first strand: chain 'f' and resid 14 through 19 Processing sheet with id= AW, first strand: chain 'i' and resid 282 through 284 removed outlier: 7.865A pdb=" N VAL i 245 " --> pdb=" O LYS i 271 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N LEU i 273 " --> pdb=" O VAL i 245 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N LEU i 247 " --> pdb=" O LEU i 273 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N ASP i 158 " --> pdb=" O VAL i 134 " (cutoff:3.500A) removed outlier: 8.943A pdb=" N SER i 136 " --> pdb=" O ASP i 158 " (cutoff:3.500A) removed outlier: 8.657A pdb=" N PHE i 160 " --> pdb=" O SER i 136 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'l' and resid 480 through 482 removed outlier: 7.488A pdb=" N ILE l 443 " --> pdb=" O ARG l 469 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ILE l 471 " --> pdb=" O ILE l 443 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N LEU l 445 " --> pdb=" O ILE l 471 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLU l 414 " --> pdb=" O VAL l 295 " (cutoff:3.500A) 1186 hydrogen bonds defined for protein. 3357 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2566 hydrogen bonds 4034 hydrogen bond angles 0 basepair planarities 1020 basepair parallelities 1574 stacking parallelities Total time for adding SS restraints: 196.52 Time building geometry restraints manager: 48.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.54: 98607 1.54 - 1.88: 7230 1.88 - 2.22: 0 2.22 - 2.56: 0 2.56 - 2.90: 1 Bond restraints: 105838 Sorted by residual: bond pdb=" C SER Z 40 " pdb=" N HIS Z 41 " ideal model delta sigma weight residual 1.335 2.898 -1.563 1.33e-02 5.65e+03 1.38e+04 bond pdb=" N GLU U 89 " pdb=" CA GLU U 89 " ideal model delta sigma weight residual 1.457 1.596 -0.138 1.29e-02 6.01e+03 1.15e+02 bond pdb=" CA LYS U 88 " pdb=" C LYS U 88 " ideal model delta sigma weight residual 1.524 1.657 -0.134 1.33e-02 5.65e+03 1.01e+02 bond pdb=" C LYS U 88 " pdb=" N GLU U 89 " ideal model delta sigma weight residual 1.332 1.471 -0.139 1.40e-02 5.10e+03 9.81e+01 bond pdb=" N3B GNP i1400 " pdb=" PG GNP i1400 " ideal model delta sigma weight residual 1.801 1.680 0.121 2.00e-02 2.50e+03 3.64e+01 ... (remaining 105833 not shown) Histogram of bond angle deviations from ideal: 93.15 - 103.42: 7596 103.42 - 113.69: 74450 113.69 - 123.96: 61653 123.96 - 134.23: 14297 134.23 - 144.50: 11 Bond angle restraints: 158007 Sorted by residual: angle pdb=" O SER Z 40 " pdb=" C SER Z 40 " pdb=" N HIS Z 41 " ideal model delta sigma weight residual 122.33 93.15 29.18 1.34e+00 5.57e-01 4.74e+02 angle pdb=" NH1 ARG l 476 " pdb=" CZ ARG l 476 " pdb=" NH2 ARG l 476 " ideal model delta sigma weight residual 119.30 144.50 -25.20 1.30e+00 5.92e-01 3.76e+02 angle pdb=" CA SER Z 40 " pdb=" C SER Z 40 " pdb=" N HIS Z 41 " ideal model delta sigma weight residual 117.82 95.19 22.63 1.42e+00 4.96e-01 2.54e+02 angle pdb=" NE ARG l 476 " pdb=" CZ ARG l 476 " pdb=" NH1 ARG l 476 " ideal model delta sigma weight residual 121.50 107.78 13.72 1.00e+00 1.00e+00 1.88e+02 angle pdb=" NE ARG l 476 " pdb=" CZ ARG l 476 " pdb=" NH2 ARG l 476 " ideal model delta sigma weight residual 119.20 107.72 11.48 9.00e-01 1.23e+00 1.63e+02 ... (remaining 158002 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.39: 54096 35.39 - 70.77: 2404 70.77 - 106.16: 165 106.16 - 141.55: 16 141.55 - 176.93: 10 Dihedral angle restraints: 56691 sinusoidal: 44893 harmonic: 11798 Sorted by residual: dihedral pdb=" CA LEU i 240 " pdb=" C LEU i 240 " pdb=" N PRO i 241 " pdb=" CA PRO i 241 " ideal model delta harmonic sigma weight residual -180.00 -119.87 -60.13 0 5.00e+00 4.00e-02 1.45e+02 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 31.98 -66.98 1 8.00e+00 1.56e-02 9.13e+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 30.67 -65.67 1 8.00e+00 1.56e-02 8.82e+01 ... (remaining 56688 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.118: 19747 0.118 - 0.236: 441 0.236 - 0.354: 13 0.354 - 0.473: 2 0.473 - 0.591: 4 Chirality restraints: 20207 Sorted by residual: chirality pdb=" C2' GNP i1400 " pdb=" C1' GNP i1400 " pdb=" C3' GNP i1400 " pdb=" O2' GNP i1400 " both_signs ideal model delta sigma weight residual False -2.55 -1.96 -0.59 2.00e-01 2.50e+01 8.72e+00 chirality pdb=" C1' GNP l1400 " pdb=" C2' GNP l1400 " pdb=" N9 GNP l1400 " pdb=" O4' GNP l1400 " both_signs ideal model delta sigma weight residual False 2.36 1.79 0.57 2.00e-01 2.50e+01 8.20e+00 chirality pdb=" C2' GNP l1400 " pdb=" C1' GNP l1400 " pdb=" C3' GNP l1400 " pdb=" O2' GNP l1400 " both_signs ideal model delta sigma weight residual False -2.55 -2.06 -0.49 2.00e-01 2.50e+01 6.08e+00 ... (remaining 20204 not shown) Planarity restraints: 8670 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER Z 40 " 0.173 2.00e-02 2.50e+03 2.63e-01 6.91e+02 pdb=" C SER Z 40 " -0.437 2.00e-02 2.50e+03 pdb=" O SER Z 40 " 0.234 2.00e-02 2.50e+03 pdb=" N HIS Z 41 " 0.029 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 9.00e-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' GNP i1400 " -0.037 2.00e-02 2.50e+03 1.83e-02 1.01e+01 pdb=" C2 GNP i1400 " 0.014 2.00e-02 2.50e+03 pdb=" C4 GNP i1400 " 0.001 2.00e-02 2.50e+03 pdb=" C5 GNP i1400 " 0.009 2.00e-02 2.50e+03 pdb=" C6 GNP i1400 " -0.016 2.00e-02 2.50e+03 pdb=" C8 GNP i1400 " -0.005 2.00e-02 2.50e+03 pdb=" N1 GNP i1400 " 0.011 2.00e-02 2.50e+03 pdb=" N2 GNP i1400 " -0.013 2.00e-02 2.50e+03 pdb=" N3 GNP i1400 " 0.018 2.00e-02 2.50e+03 pdb=" N7 GNP i1400 " 0.020 2.00e-02 2.50e+03 pdb=" N9 GNP i1400 " 0.022 2.00e-02 2.50e+03 pdb=" O6 GNP i1400 " -0.024 2.00e-02 2.50e+03 ... (remaining 8667 not shown) Histogram of nonbonded interaction distances: 1.74 - 2.37: 311 2.37 - 3.00: 48645 3.00 - 3.63: 169910 3.63 - 4.27: 295003 4.27 - 4.90: 392067 Nonbonded interactions: 905936 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 1.770 2.170 nonbonded pdb=" OP1 A A1780 " pdb="MG MG A3086 " model vdw 1.817 2.170 nonbonded pdb=" O4 U A1263 " pdb="MG MG A3180 " model vdw 1.821 2.170 ... (remaining 905931 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 3055 5.49 5 Mg 433 5.21 5 S 107 5.16 5 C 49354 2.51 5 N 18130 2.21 5 O 26926 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: 1.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.090 Extract box with map and model: 13.980 Check model and map are aligned: 1.130 Convert atoms to be neutral: 0.650 Process input model: 412.700 Find NCS groups from input model: 1.830 Set up NCS constraints: 0.230 Set refine NCS operators: 0.000 Set scattering table: 0.030 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:3.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 435.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 1.563 105838 Z= 0.592 Angle : 1.109 29.179 158007 Z= 0.635 Chirality : 0.048 0.591 20207 Planarity : 0.006 0.263 8670 Dihedral : 15.934 176.933 49081 Min Nonbonded Distance : 1.737 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.46 % Favored : 96.46 % Rotamer Outliers : 10.34 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 3.82 % Cis-general : 0.00 % Twisted Proline : 1.53 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.19 (0.10), residues: 4013 helix: -3.25 (0.10), residues: 1309 sheet: -1.30 (0.16), residues: 770 loop : -1.47 (0.11), residues: 1934 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8026 Ramachandran restraints generated. 4013 Oldfield, 0 Emsley, 4013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8026 Ramachandran restraints generated. 4013 Oldfield, 0 Emsley, 4013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1704 residues out of total 3301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 341 poor density : 1363 time to evaluate : 4.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 341 outliers final: 54 residues processed: 1561 average time/residue: 1.0238 time to fit residues: 2641.3343 Evaluate side-chains 915 residues out of total 3301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 861 time to evaluate : 4.657 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 54 outliers final: 1 residues processed: 54 average time/residue: 0.8078 time to fit residues: 85.7273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 704 random chunks: chunk 594 optimal weight: 5.9990 chunk 533 optimal weight: 2.9990 chunk 296 optimal weight: 10.0000 chunk 182 optimal weight: 10.0000 chunk 359 optimal weight: 4.9990 chunk 285 optimal weight: 10.0000 chunk 551 optimal weight: 3.9990 chunk 213 optimal weight: 40.0000 chunk 335 optimal weight: 9.9990 chunk 410 optimal weight: 20.0000 chunk 639 optimal weight: 8.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- 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 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 153 GLN D 140 HIS D 167 ASN D 185 ASN E 41 GLN E 94 GLN ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 52 ASN G 115 HIS H 11 ASN H 33 GLN J 105 GLN K 136 GLN L 3 GLN L 82 ASN M 35 HIS ** M 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 9 GLN O 23 ASN Q 41 GLN Q 66 ASN ** R 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 44 GLN R 72 ASN U 48 GLN ** W 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 46 HIS Y 23 ASN Z 15 ASN Z 31 GLN ** Z 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 58 ASN c 19 HIS i 26 ASN i 62 HIS i 196 HIS ** i 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 409 GLN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.2817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.071 105838 Z= 0.286 Angle : 0.660 12.339 158007 Z= 0.344 Chirality : 0.038 0.314 20207 Planarity : 0.005 0.096 8670 Dihedral : 14.189 179.934 41196 Min Nonbonded Distance : 1.771 Molprobity Statistics. All-atom Clashscore : 15.97 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.44 % Favored : 97.48 % Rotamer Outliers : 5.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.82 % Cis-general : 0.00 % Twisted Proline : 0.76 % 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: -1.32 (0.12), residues: 4015 helix: -0.89 (0.13), residues: 1294 sheet: -0.79 (0.16), residues: 812 loop : -0.75 (0.13), residues: 1909 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8030 Ramachandran restraints generated. 4015 Oldfield, 0 Emsley, 4015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8030 Ramachandran restraints generated. 4015 Oldfield, 0 Emsley, 4015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1122 residues out of total 3301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 954 time to evaluate : 4.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 168 outliers final: 86 residues processed: 1044 average time/residue: 0.9199 time to fit residues: 1634.7168 Evaluate side-chains 875 residues out of total 3301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 789 time to evaluate : 4.759 Switching outliers to nearest non-outliers outliers start: 86 outliers final: 0 residues processed: 86 average time/residue: 0.7516 time to fit residues: 126.8132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 704 random chunks: chunk 355 optimal weight: 9.9990 chunk 198 optimal weight: 10.0000 chunk 532 optimal weight: 2.9990 chunk 435 optimal weight: 5.9990 chunk 176 optimal weight: 10.0000 chunk 640 optimal weight: 6.9990 chunk 691 optimal weight: 0.4980 chunk 570 optimal weight: 6.9990 chunk 635 optimal weight: 6.9990 chunk 218 optimal weight: 30.0000 chunk 513 optimal weight: 0.9980 overall best weight: 3.4986 ------------------------------------------------------------------------------- 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 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 142 HIS D 173 GLN ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 52 ASN ** I 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 136 GLN M 35 HIS M 104 GLN O 16 HIS O 23 ASN ** P 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 20 GLN ** R 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 82 HIS U 59 ASN ** V 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 76 ASN Z 15 ASN Z 38 GLN c 45 GLN f 35 GLN i 209 HIS l 413 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.3574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.061 105838 Z= 0.201 Angle : 0.568 12.852 158007 Z= 0.297 Chirality : 0.034 0.325 20207 Planarity : 0.005 0.084 8670 Dihedral : 13.841 179.846 41196 Min Nonbonded Distance : 1.675 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.47 % Favored : 97.43 % Rotamer Outliers : 3.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.82 % Cis-general : 0.00 % Twisted Proline : 0.76 % 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: -0.51 (0.12), residues: 4015 helix: -0.01 (0.14), residues: 1299 sheet: -0.39 (0.17), residues: 799 loop : -0.39 (0.13), residues: 1917 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8030 Ramachandran restraints generated. 4015 Oldfield, 0 Emsley, 4015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8030 Ramachandran restraints generated. 4015 Oldfield, 0 Emsley, 4015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1005 residues out of total 3301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 891 time to evaluate : 4.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 114 outliers final: 50 residues processed: 939 average time/residue: 0.9165 time to fit residues: 1466.2284 Evaluate side-chains 810 residues out of total 3301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 760 time to evaluate : 4.671 Switching outliers to nearest non-outliers outliers start: 50 outliers final: 0 residues processed: 50 average time/residue: 0.7077 time to fit residues: 71.7332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 704 random chunks: chunk 632 optimal weight: 0.8980 chunk 481 optimal weight: 8.9990 chunk 332 optimal weight: 10.0000 chunk 70 optimal weight: 10.0000 chunk 305 optimal weight: 8.9990 chunk 430 optimal weight: 50.0000 chunk 642 optimal weight: 10.0000 chunk 680 optimal weight: 8.9990 chunk 335 optimal weight: 5.9990 chunk 609 optimal weight: 2.9990 chunk 183 optimal weight: 10.0000 overall best weight: 5.5788 ------------------------------------------------------------------------------- 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 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN ** F 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 145 ASN ** I 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 105 GLN P 43 ASN ** P 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 20 GLN ** R 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 72 ASN ** W 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 76 ASN Y 23 ASN Z 15 ASN c 45 GLN ** d 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 43 HIS i 154 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.4072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.105 105838 Z= 0.280 Angle : 0.592 12.370 158007 Z= 0.308 Chirality : 0.035 0.325 20207 Planarity : 0.005 0.084 8670 Dihedral : 13.818 178.358 41196 Min Nonbonded Distance : 0.967 Molprobity Statistics. All-atom Clashscore : 16.39 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.96 % Favored : 96.91 % Rotamer Outliers : 3.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.82 % Cis-general : 0.00 % Twisted Proline : 0.76 % 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: -0.29 (0.13), residues: 4015 helix: 0.23 (0.14), residues: 1298 sheet: -0.24 (0.17), residues: 826 loop : -0.33 (0.14), residues: 1891 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8030 Ramachandran restraints generated. 4015 Oldfield, 0 Emsley, 4015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8030 Ramachandran restraints generated. 4015 Oldfield, 0 Emsley, 4015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 925 residues out of total 3301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 801 time to evaluate : 4.742 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 outliers start: 124 outliers final: 80 residues processed: 865 average time/residue: 0.9002 time to fit residues: 1336.0622 Evaluate side-chains 830 residues out of total 3301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 750 time to evaluate : 4.690 Switching outliers to nearest non-outliers outliers start: 80 outliers final: 0 residues processed: 80 average time/residue: 0.7462 time to fit residues: 115.0630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 704 random chunks: chunk 566 optimal weight: 5.9990 chunk 386 optimal weight: 9.9990 chunk 9 optimal weight: 10.0000 chunk 506 optimal weight: 7.9990 chunk 280 optimal weight: 10.0000 chunk 580 optimal weight: 6.9990 chunk 470 optimal weight: 4.9990 chunk 0 optimal weight: 50.0000 chunk 347 optimal weight: 9.9990 chunk 610 optimal weight: 7.9990 chunk 171 optimal weight: 10.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- 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 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 111 HIS ** G 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 145 ASN ** I 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 43 ASN ** P 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 20 GLN ** R 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 56 GLN R 72 ASN ** U 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 49 ASN X 76 ASN ** d 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 26 ASN i 381 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.4590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.074 105838 Z= 0.325 Angle : 0.626 12.760 158007 Z= 0.324 Chirality : 0.036 0.324 20207 Planarity : 0.005 0.081 8670 Dihedral : 13.950 177.440 41196 Min Nonbonded Distance : 1.016 Molprobity Statistics. All-atom Clashscore : 18.14 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.09 % Favored : 96.81 % Rotamer Outliers : 2.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.82 % Cis-general : 0.00 % Twisted Proline : 0.76 % 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: -0.25 (0.13), residues: 4015 helix: 0.25 (0.14), residues: 1299 sheet: -0.20 (0.18), residues: 835 loop : -0.30 (0.14), residues: 1881 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8030 Ramachandran restraints generated. 4015 Oldfield, 0 Emsley, 4015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8030 Ramachandran restraints generated. 4015 Oldfield, 0 Emsley, 4015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 879 residues out of total 3301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 795 time to evaluate : 5.160 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 outliers start: 84 outliers final: 44 residues processed: 835 average time/residue: 0.8963 time to fit residues: 1286.9771 Evaluate side-chains 772 residues out of total 3301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 728 time to evaluate : 4.662 Switching outliers to nearest non-outliers outliers start: 44 outliers final: 0 residues processed: 44 average time/residue: 0.7195 time to fit residues: 64.4113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 704 random chunks: chunk 228 optimal weight: 10.0000 chunk 612 optimal weight: 6.9990 chunk 134 optimal weight: 10.0000 chunk 399 optimal weight: 1.9990 chunk 167 optimal weight: 10.0000 chunk 681 optimal weight: 6.9990 chunk 565 optimal weight: 9.9990 chunk 315 optimal weight: 8.9990 chunk 56 optimal weight: 10.0000 chunk 225 optimal weight: 10.0000 chunk 357 optimal weight: 4.9990 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 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 134 HIS E 41 GLN ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN ** G 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 145 ASN ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 20 GLN ** R 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 7 HIS T 31 GLN ** U 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 59 ASN ** W 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 23 ASN ** Z 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.4907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.059 105838 Z= 0.290 Angle : 0.603 10.745 158007 Z= 0.314 Chirality : 0.035 0.333 20207 Planarity : 0.005 0.079 8670 Dihedral : 13.956 177.524 41196 Min Nonbonded Distance : 1.032 Molprobity Statistics. All-atom Clashscore : 18.11 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.49 % Favored : 96.41 % Rotamer Outliers : 2.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.82 % Cis-general : 0.00 % Twisted Proline : 0.76 % 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: -0.20 (0.13), residues: 4015 helix: 0.32 (0.14), residues: 1297 sheet: -0.13 (0.18), residues: 817 loop : -0.32 (0.14), residues: 1901 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8030 Ramachandran restraints generated. 4015 Oldfield, 0 Emsley, 4015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8030 Ramachandran restraints generated. 4015 Oldfield, 0 Emsley, 4015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 863 residues out of total 3301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 779 time to evaluate : 4.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 84 outliers final: 47 residues processed: 812 average time/residue: 0.9166 time to fit residues: 1277.6935 Evaluate side-chains 772 residues out of total 3301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 725 time to evaluate : 4.713 Switching outliers to nearest non-outliers outliers start: 47 outliers final: 0 residues processed: 47 average time/residue: 0.7162 time to fit residues: 68.2447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 704 random chunks: chunk 656 optimal weight: 10.0000 chunk 76 optimal weight: 10.0000 chunk 388 optimal weight: 0.8980 chunk 497 optimal weight: 1.9990 chunk 385 optimal weight: 3.9990 chunk 573 optimal weight: 1.9990 chunk 380 optimal weight: 0.8980 chunk 678 optimal weight: 7.9990 chunk 424 optimal weight: 7.9990 chunk 413 optimal weight: 6.9990 chunk 313 optimal weight: 8.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 86 ASN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 167 ASN E 41 GLN ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 111 GLN ** P 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 20 GLN ** R 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 56 GLN S 12 HIS T 7 HIS T 31 GLN U 28 ASN V 46 GLN ** W 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 4 GLN d 6 GLN d 26 ASN ** i 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.5066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.043 105838 Z= 0.151 Angle : 0.548 15.850 158007 Z= 0.283 Chirality : 0.032 0.330 20207 Planarity : 0.004 0.079 8670 Dihedral : 13.757 179.196 41196 Min Nonbonded Distance : 1.154 Molprobity Statistics. All-atom Clashscore : 14.84 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.79 % Favored : 97.11 % Rotamer Outliers : 1.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.82 % Cis-general : 0.00 % Twisted Proline : 0.76 % 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: 0.04 (0.13), residues: 4015 helix: 0.59 (0.15), residues: 1286 sheet: -0.01 (0.18), residues: 811 loop : -0.22 (0.14), residues: 1918 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8030 Ramachandran restraints generated. 4015 Oldfield, 0 Emsley, 4015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8030 Ramachandran restraints generated. 4015 Oldfield, 0 Emsley, 4015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 850 residues out of total 3301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 801 time to evaluate : 4.879 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 outliers start: 49 outliers final: 17 residues processed: 822 average time/residue: 0.9299 time to fit residues: 1314.3227 Evaluate side-chains 753 residues out of total 3301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 736 time to evaluate : 4.782 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.7380 time to fit residues: 28.9440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 704 random chunks: chunk 419 optimal weight: 30.0000 chunk 270 optimal weight: 10.0000 chunk 405 optimal weight: 0.2980 chunk 204 optimal weight: 10.0000 chunk 133 optimal weight: 10.0000 chunk 131 optimal weight: 10.0000 chunk 431 optimal weight: 0.2980 chunk 462 optimal weight: 4.9990 chunk 335 optimal weight: 0.9980 chunk 63 optimal weight: 10.0000 chunk 533 optimal weight: 5.9990 overall best weight: 2.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 64 GLN ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 20 GLN R 37 GLN R 56 GLN S 82 HIS ** T 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 27 ASN ** V 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 23 ASN ** Y 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 45 GLN ** d 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.5192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 105838 Z= 0.164 Angle : 0.546 13.767 158007 Z= 0.282 Chirality : 0.032 0.331 20207 Planarity : 0.004 0.078 8670 Dihedral : 13.693 179.789 41196 Min Nonbonded Distance : 1.083 Molprobity Statistics. All-atom Clashscore : 15.29 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.44 % Favored : 96.46 % Rotamer Outliers : 1.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.82 % Cis-general : 0.00 % Twisted Proline : 0.76 % 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: 0.08 (0.13), residues: 4015 helix: 0.66 (0.15), residues: 1286 sheet: -0.01 (0.18), residues: 803 loop : -0.21 (0.14), residues: 1926 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8030 Ramachandran restraints generated. 4015 Oldfield, 0 Emsley, 4015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8030 Ramachandran restraints generated. 4015 Oldfield, 0 Emsley, 4015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 799 residues out of total 3301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 763 time to evaluate : 4.963 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 outliers start: 36 outliers final: 21 residues processed: 773 average time/residue: 0.9143 time to fit residues: 1213.5505 Evaluate side-chains 744 residues out of total 3301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 723 time to evaluate : 4.792 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.7300 time to fit residues: 33.8021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 704 random chunks: chunk 617 optimal weight: 9.9990 chunk 650 optimal weight: 8.9990 chunk 593 optimal weight: 9.9990 chunk 632 optimal weight: 9.9990 chunk 649 optimal weight: 40.0000 chunk 380 optimal weight: 10.0000 chunk 275 optimal weight: 10.0000 chunk 496 optimal weight: 5.9990 chunk 194 optimal weight: 10.0000 chunk 571 optimal weight: 5.9990 chunk 598 optimal weight: 0.0000 overall best weight: 6.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 185 ASN F 21 ASN ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 20 GLN R 44 GLN ** T 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 50 ASN Y 16 ASN Z 15 ASN c 45 GLN ** d 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.5280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.050 105838 Z= 0.299 Angle : 0.620 14.594 158007 Z= 0.319 Chirality : 0.035 0.355 20207 Planarity : 0.005 0.078 8670 Dihedral : 13.795 178.384 41196 Min Nonbonded Distance : 1.052 Molprobity Statistics. All-atom Clashscore : 18.53 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.94 % Favored : 95.97 % Rotamer Outliers : 1.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.82 % Cis-general : 0.00 % Twisted Proline : 0.76 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.13), residues: 4015 helix: 0.55 (0.15), residues: 1288 sheet: -0.14 (0.18), residues: 833 loop : -0.26 (0.14), residues: 1894 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8030 Ramachandran restraints generated. 4015 Oldfield, 0 Emsley, 4015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8030 Ramachandran restraints generated. 4015 Oldfield, 0 Emsley, 4015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 779 residues out of total 3301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 745 time to evaluate : 4.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 20 residues processed: 757 average time/residue: 0.9393 time to fit residues: 1226.5821 Evaluate side-chains 734 residues out of total 3301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 714 time to evaluate : 4.796 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.7596 time to fit residues: 33.2834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 704 random chunks: chunk 630 optimal weight: 10.0000 chunk 415 optimal weight: 7.9990 chunk 668 optimal weight: 50.0000 chunk 408 optimal weight: 9.9990 chunk 317 optimal weight: 7.9990 chunk 464 optimal weight: 9.9990 chunk 701 optimal weight: 40.0000 chunk 645 optimal weight: 5.9990 chunk 558 optimal weight: 3.9990 chunk 57 optimal weight: 10.0000 chunk 431 optimal weight: 40.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 20 GLN R 44 GLN ** T 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 53 ASN Y 23 ASN Z 36 GLN c 45 GLN ** d 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 26 ASN ** l 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.5460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.056 105838 Z= 0.343 Angle : 0.665 19.550 158007 Z= 0.342 Chirality : 0.037 0.338 20207 Planarity : 0.005 0.078 8670 Dihedral : 14.053 177.262 41196 Min Nonbonded Distance : 1.031 Molprobity Statistics. All-atom Clashscore : 20.28 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.13 % Favored : 95.77 % Rotamer Outliers : 0.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.82 % Cis-general : 0.00 % Twisted Proline : 0.76 % 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: -0.26 (0.13), residues: 4015 helix: 0.40 (0.14), residues: 1280 sheet: -0.23 (0.18), residues: 777 loop : -0.42 (0.14), residues: 1958 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8030 Ramachandran restraints generated. 4015 Oldfield, 0 Emsley, 4015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8030 Ramachandran restraints generated. 4015 Oldfield, 0 Emsley, 4015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 766 residues out of total 3301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 745 time to evaluate : 4.792 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 outliers start: 21 outliers final: 16 residues processed: 753 average time/residue: 0.9254 time to fit residues: 1195.9411 Evaluate side-chains 731 residues out of total 3301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 715 time to evaluate : 4.734 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.7094 time to fit residues: 26.6381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 704 random chunks: chunk 342 optimal weight: 10.0000 chunk 443 optimal weight: 6.9990 chunk 594 optimal weight: 9.9990 chunk 171 optimal weight: 10.0000 chunk 514 optimal weight: 6.9990 chunk 82 optimal weight: 10.0000 chunk 155 optimal weight: 20.0000 chunk 559 optimal weight: 5.9990 chunk 234 optimal weight: 10.0000 chunk 574 optimal weight: 7.9990 chunk 70 optimal weight: 10.0000 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 94 GLN D 167 ASN ** E 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 21 ASN ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 31 GLN ** M 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 11 ASN ** P 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 20 GLN ** R 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 72 ASN ** T 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 44 HIS Z 36 GLN c 45 GLN ** d 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 409 GLN k 29 GLN ** l 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.055149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.040493 restraints weight = 541206.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.041609 restraints weight = 186673.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.042216 restraints weight = 102240.757| |-----------------------------------------------------------------------------| r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8838 moved from start: 0.5589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.067 105838 Z= 0.357 Angle : 0.679 17.571 158007 Z= 0.348 Chirality : 0.037 0.330 20207 Planarity : 0.005 0.081 8670 Dihedral : 14.162 178.791 41196 Min Nonbonded Distance : 1.013 Molprobity Statistics. All-atom Clashscore : 21.05 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.33 % Favored : 95.59 % Rotamer Outliers : 0.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.82 % Cis-general : 0.00 % Twisted Proline : 0.76 % 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: -0.41 (0.13), residues: 4015 helix: 0.29 (0.14), residues: 1279 sheet: -0.29 (0.18), residues: 775 loop : -0.53 (0.14), residues: 1961 =============================================================================== Job complete usr+sys time: 21305.49 seconds wall clock time: 377 minutes 29.57 seconds (22649.57 seconds total)