Starting phenix.real_space_refine (version: dev) on Sat Dec 17 01:27:45 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5gag_8003/12_2022/5gag_8003_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5gag_8003/12_2022/5gag_8003.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5gag_8003/12_2022/5gag_8003.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5gag_8003/12_2022/5gag_8003.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5gag_8003/12_2022/5gag_8003_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5gag_8003/12_2022/5gag_8003_neut.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.016 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 ARG 133": "NH1" <-> "NH2" Residue "C GLU 145": "OE1" <-> "OE2" 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 GLU 28": "OE1" <-> "OE2" Residue "D GLU 30": "OE1" <-> "OE2" Residue "D ARG 33": "NH1" <-> "NH2" Residue "D ASP 43": "OD1" <-> "OD2" 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 PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 83": "NH1" <-> "NH2" Residue "D PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 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 191": "OD1" <-> "OD2" Residue "E GLU 197": "OE1" <-> "OE2" Residue "F TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 "F PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 3": "NH1" <-> "NH2" Residue "G ASP 16": "OD1" <-> "OD2" Residue "G PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 124": "OE1" <-> "OE2" Residue "G ARG 153": "NH1" <-> "NH2" 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 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 114": "OE1" <-> "OE2" Residue "H GLU 137": "OE1" <-> "OE2" Residue "I GLU 87": "OE1" <-> "OE2" Residue "I PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 114": "OE1" <-> "OE2" Residue "J PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 121": "OD1" <-> "OD2" Residue "K PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 13": "NH1" <-> "NH2" Residue "K GLU 31": "OE1" <-> "OE2" Residue "K ARG 37": "NH1" <-> "NH2" Residue "K GLU 43": "OE1" <-> "OE2" Residue "K TYR 75": "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 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 PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 75": "OE1" <-> "OE2" Residue "N TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 104": "OE1" <-> "OE2" Residue "N ARG 114": "NH1" <-> "NH2" 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 PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 82": "OE1" <-> "OE2" Residue "O ARG 96": "NH1" <-> "NH2" 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 GLU 55": "OE1" <-> "OE2" Residue "P ARG 81": "NH1" <-> "NH2" Residue "P ARG 94": "NH1" <-> "NH2" Residue "P ARG 102": "NH1" <-> "NH2" Residue "P ARG 111": "NH1" <-> "NH2" Residue "P PHE 117": "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 ARG 89": "NH1" <-> "NH2" 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 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 PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 111": "OE1" <-> "OE2" Residue "S TYR 2": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 78": "NH1" <-> "NH2" Residue "S ARG 79": "NH1" <-> "NH2" Residue "S ARG 84": "NH1" <-> "NH2" 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 89": "OE1" <-> "OE2" Residue "V ARG 6": "NH1" <-> "NH2" Residue "V ARG 7": "NH1" <-> "NH2" Residue "V GLU 37": "OE1" <-> "OE2" Residue "V ARG 82": "NH1" <-> "NH2" Residue "V ARG 86": "NH1" <-> "NH2" Residue "V PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 88": "OE1" <-> "OE2" Residue "V ARG 94": "NH1" <-> "NH2" Residue "W PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 11": "OE1" <-> "OE2" Residue "W GLU 41": "OE1" <-> "OE2" Residue "W ASP 43": "OD1" <-> "OD2" Residue "W GLU 55": "OE1" <-> "OE2" Residue "W PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 GLU 29": "OE1" <-> "OE2" Residue "X PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 60": "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 ARG 37": "NH1" <-> "NH2" Residue "Y PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 5": "OE1" <-> "OE2" 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 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 ARG 30": "NH1" <-> "NH2" Residue "e ARG 40": "NH1" <-> "NH2" Residue "e ARG 42": "NH1" <-> "NH2" Residue "f ARG 24": "NH1" <-> "NH2" Residue "i GLU 392": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 94030 Number of models: 1 Model: "" Number of chains: 46 Chain: "1" Number of atoms: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 926 Classifications: {'RNA': 43} Modifications used: {'rna3p_pur': 26, 'rna3p_pyr': 17} Link IDs: {'rna3p': 42} Chain: "2" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 62 Classifications: {'RNA': 3} Modifications used: {'rna2p_pur': 1, 'rna3p_pyr': 2} Link IDs: {'rna3p': 2} Chain: "A" Number of atoms: 61902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2883, 61902 Classifications: {'RNA': 2883} Modifications used: {'rna2p_pur': 280, 'rna2p_pyr': 148, 'rna3p_pur': 1386, 'rna3p_pyr': 1069} Link IDs: {'rna2p': 428, 'rna3p': 2454} 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: 2083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2083 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 17, 'TRANS': 254} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 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: 1411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1411 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 6, 'TRANS': 171} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 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: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 780 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 3, 'TRANS': 99} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "W" Number of atoms: 753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 753 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "X" Number of atoms: 580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 580 Classifications: {'peptide': 76} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 74} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "Y" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 625 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "Z" Number of atoms: 501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 501 Classifications: {'peptide': 62} Modifications used: {'COO': 1} Link IDs: {'TRANS': 61} Chain: "a" Number of atoms: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 449 Classifications: {'peptide': 58} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "b" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 444 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 54} Chain: "c" Number of atoms: 414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 414 Classifications: {'peptide': 51} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 48} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "d" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 377 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "e" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 504 Classifications: {'peptide': 64} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "f" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 302 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "i" Number of atoms: 916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 916 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 124} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'UNK:plan-1': 41} Unresolved non-hydrogen planarities: 41 Chain: "k" Number of atoms: 137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 137 Classifications: {'peptide': 18} Link IDs: {'PTRANS': 1, 'TRANS': 16} Chain: "2" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 411, 411 Unusual residues: {' MG': 411} Classifications: {'undetermined': 411} Link IDs: {None: 410} Chain: "B" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Unusual residues: {' MG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} 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: "O" 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: "Y" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "b" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "f" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 92328 SG CYS f 11 74.909 81.051 178.600 1.00 92.14 S ATOM 92353 SG CYS f 14 78.108 82.541 177.489 1.00 85.62 S ATOM 92456 SG CYS f 27 78.079 78.983 178.947 1.00 94.45 S Time building chain proxies: 40.09, per 1000 atoms: 0.43 Number of scatterers: 94030 At special positions: 0 Unit cell: (243.76, 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 95 16.00 P 3049 15.00 Mg 431 11.99 O 26174 8.00 N 17424 7.00 C 46856 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 41.31 Conformation dependent library (CDL) restraints added in 4.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN f 101 " pdb="ZN ZN f 101 " - pdb=" ND1 HIS f 33 " pdb="ZN ZN f 101 " - pdb=" SG CYS f 27 " pdb="ZN ZN f 101 " - pdb=" SG CYS f 11 " pdb="ZN ZN f 101 " - pdb=" SG CYS f 14 " Number of angles added : 3 7058 Ramachandran restraints generated. 3529 Oldfield, 0 Emsley, 3529 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6648 Finding SS restraints... Secondary structure from input PDB file: 110 helices and 52 sheets defined 33.1% alpha, 21.2% beta 1017 base pairs and 1608 stacking pairs defined. Time for finding SS restraints: 32.36 Creating SS restraints... Processing helix chain 'C' and resid 12 through 15 removed outlier: 3.877A pdb=" N HIS C 15 " --> pdb=" O GLY C 12 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 12 through 15' Processing helix chain 'C' and resid 207 through 214 removed outlier: 3.792A pdb=" N ALA C 211 " --> pdb=" O LYS C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 225 Processing helix chain 'C' and resid 263 through 265 No H-bonds generated for 'chain 'C' and resid 263 through 265' Processing helix chain 'D' and resid 56 through 60 Processing helix chain 'D' and resid 61 through 72 removed outlier: 3.610A pdb=" N ALA D 71 " --> pdb=" O HIS D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 102 Processing helix chain 'D' and resid 120 through 125 Processing helix chain 'E' and resid 24 through 39 Processing helix chain 'E' and resid 97 through 115 Processing helix chain 'E' and resid 130 through 142 removed outlier: 3.705A pdb=" N LEU E 134 " --> pdb=" O LYS E 130 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N MET E 141 " --> pdb=" O LYS E 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 154 through 161 removed outlier: 3.722A pdb=" N ALA E 161 " --> pdb=" O LEU E 157 " (cutoff:3.500A) Processing helix chain 'E' and resid 162 through 164 No H-bonds generated for 'chain 'E' and resid 162 through 164' Processing helix chain 'E' and resid 173 through 175 No H-bonds generated for 'chain 'E' and resid 173 through 175' Processing helix chain 'E' and resid 176 through 182 Processing helix chain 'E' and resid 190 through 201 Processing helix chain 'F' and resid 3 through 11 Processing helix chain 'F' and resid 11 through 20 Processing helix chain 'F' and resid 24 through 28 Processing helix chain 'F' and resid 47 through 62 removed outlier: 3.610A pdb=" N ASP F 51 " --> pdb=" O LYS F 47 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASP F 56 " --> pdb=" O ASN F 52 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 106 Processing helix chain 'F' and resid 107 through 111 Processing helix chain 'F' and resid 142 through 146 Processing helix chain 'F' and resid 162 through 173 removed outlier: 3.508A pdb=" N PHE F 173 " --> pdb=" O LEU F 169 " (cutoff:3.500A) Processing helix chain 'G' and resid 60 through 79 Processing helix chain 'G' and resid 137 through 150 Processing helix chain 'H' and resid 22 through 29 removed outlier: 3.695A pdb=" N ALA H 26 " --> pdb=" O LYS H 22 " (cutoff:3.500A) Processing helix chain 'H' and resid 40 through 73 removed outlier: 6.094A pdb=" N ALA H 52 " --> pdb=" O GLU H 48 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N GLU H 53 " --> pdb=" O ALA H 49 " (cutoff:3.500A) Processing helix chain 'H' and resid 85 through 89 removed outlier: 3.829A pdb=" N GLY H 88 " --> pdb=" O GLY H 85 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS H 89 " --> pdb=" O ASP H 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 85 through 89' Processing helix chain 'H' and resid 95 through 104 removed outlier: 3.531A pdb=" N ILE H 99 " --> pdb=" O GLY H 95 " (cutoff:3.500A) Processing helix chain 'I' and resid 4 through 20 Processing helix chain 'I' and resid 34 through 47 Processing helix chain 'I' and resid 56 through 65 removed outlier: 3.656A pdb=" N ARG I 62 " --> pdb=" O THR I 58 " (cutoff:3.500A) Processing helix chain 'I' and resid 94 through 103 Processing helix chain 'J' and resid 24 through 30 Processing helix chain 'J' and resid 34 through 46 removed outlier: 3.898A pdb=" N PHE J 38 " --> pdb=" O ASN J 34 " (cutoff:3.500A) Processing helix chain 'J' and resid 47 through 49 No H-bonds generated for 'chain 'J' and resid 47 through 49' Processing helix chain 'J' and resid 75 through 84 Processing helix chain 'J' and resid 102 through 117 Processing helix chain 'J' and resid 121 through 136 removed outlier: 3.720A pdb=" N MET J 136 " --> pdb=" O THR J 132 " (cutoff:3.500A) Processing helix chain 'K' and resid 24 through 38 removed outlier: 4.063A pdb=" N GLU K 31 " --> pdb=" O ARG K 27 " (cutoff:3.500A) Processing helix chain 'K' and resid 58 through 62 Processing helix chain 'K' and resid 67 through 72 Processing helix chain 'K' and resid 89 through 96 Processing helix chain 'K' and resid 97 through 107 removed outlier: 3.973A pdb=" N ILE K 101 " --> pdb=" O PRO K 97 " (cutoff:3.500A) Processing helix chain 'K' and resid 112 through 120 Processing helix chain 'K' and resid 132 through 136 Processing helix chain 'L' and resid 104 through 108 Processing helix chain 'L' and resid 112 through 118 removed outlier: 3.721A pdb=" N ILE L 116 " --> pdb=" O PHE L 112 " (cutoff:3.500A) Processing helix chain 'M' and resid 56 through 61 Processing helix chain 'M' and resid 68 through 72 Processing helix chain 'M' and resid 80 through 84 removed outlier: 3.816A pdb=" N ALA M 83 " --> pdb=" O SER M 80 " (cutoff:3.500A) Processing helix chain 'M' and resid 91 through 98 Processing helix chain 'M' and resid 128 through 136 Processing helix chain 'N' and resid 43 through 57 Processing helix chain 'N' and resid 109 through 122 Processing helix chain 'O' and resid 13 through 31 Processing helix chain 'O' and resid 38 through 56 removed outlier: 4.182A pdb=" N ARG O 46 " --> pdb=" O LYS O 42 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N VAL O 47 " --> pdb=" O GLU O 43 " (cutoff:3.500A) Proline residue: O 50 - end of helix Processing helix chain 'O' and resid 59 through 71 Processing helix chain 'O' and resid 72 through 82 Processing helix chain 'O' and resid 82 through 87 Processing helix chain 'O' and resid 117 through 125 removed outlier: 3.773A pdb=" N ALA O 125 " --> pdb=" O LYS O 121 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 22 removed outlier: 3.892A pdb=" N ALA P 6 " --> pdb=" O ASP P 2 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ARG P 13 " --> pdb=" O ARG P 9 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N ALA P 14 " --> pdb=" O ARG P 10 " (cutoff:3.500A) Processing helix chain 'P' and resid 55 through 60 Processing helix chain 'P' and resid 67 through 84 Processing helix chain 'P' and resid 100 through 113 Processing helix chain 'Q' and resid 3 through 10 Processing helix chain 'Q' and resid 53 through 56 removed outlier: 3.937A pdb=" N HIS Q 56 " --> pdb=" O ARG Q 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 53 through 56' Processing helix chain 'Q' and resid 97 through 102 Processing helix chain 'Q' and resid 104 through 109 removed outlier: 3.954A pdb=" N ARG Q 109 " --> pdb=" O LYS Q 106 " (cutoff:3.500A) Processing helix chain 'R' and resid 6 through 21 removed outlier: 3.826A pdb=" N GLN R 20 " --> pdb=" O LYS R 16 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA R 21 " --> pdb=" O ILE R 17 " (cutoff:3.500A) Processing helix chain 'R' and resid 25 through 30 Processing helix chain 'R' and resid 31 through 72 removed outlier: 3.814A pdb=" N GLN R 37 " --> pdb=" O ARG R 33 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG R 51 " --> pdb=" O TYR R 47 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N LYS R 54 " --> pdb=" O ARG R 50 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ARG R 55 " --> pdb=" O ARG R 51 " (cutoff:3.500A) Processing helix chain 'R' and resid 75 through 86 Processing helix chain 'R' and resid 91 through 102 Processing helix chain 'R' and resid 102 through 117 removed outlier: 3.503A pdb=" N PHE R 106 " --> pdb=" O ASP R 102 " (cutoff:3.500A) Processing helix chain 'T' and resid 13 through 22 removed outlier: 3.533A pdb=" N VAL T 17 " --> pdb=" O SER T 13 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU T 19 " --> pdb=" O GLN T 15 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N VAL T 20 " --> pdb=" O LYS T 16 " (cutoff:3.500A) Processing helix chain 'T' and resid 28 through 39 Processing helix chain 'T' and resid 41 through 63 removed outlier: 3.988A pdb=" N VAL T 45 " --> pdb=" O LYS T 41 " (cutoff:3.500A) Processing helix chain 'T' and resid 65 through 69 Processing helix chain 'T' and resid 89 through 91 No H-bonds generated for 'chain 'T' and resid 89 through 91' Processing helix chain 'U' and resid 3 through 8 Processing helix chain 'U' and resid 17 through 28 Processing helix chain 'U' and resid 39 through 51 Processing helix chain 'W' and resid 13 through 23 Processing helix chain 'W' and resid 44 through 51 Processing helix chain 'W' and resid 54 through 59 removed outlier: 3.599A pdb=" N SER W 58 " --> pdb=" O ALA W 54 " (cutoff:3.500A) Processing helix chain 'Y' and resid 53 through 63 Processing helix chain 'Y' and resid 63 through 75 removed outlier: 3.662A pdb=" N VAL Y 67 " --> pdb=" O GLY Y 63 " (cutoff:3.500A) Processing helix chain 'Z' and resid 10 through 35 Processing helix chain 'Z' and resid 40 through 63 removed outlier: 3.831A pdb=" N LYS Z 44 " --> pdb=" O SER Z 40 " (cutoff:3.500A) Processing helix chain 'a' and resid 17 through 28 Processing helix chain 'a' and resid 41 through 52 removed outlier: 3.543A pdb=" N VAL a 51 " --> pdb=" O MET a 47 " (cutoff:3.500A) Processing helix chain 'b' and resid 9 through 17 removed outlier: 3.591A pdb=" N ARG b 17 " --> pdb=" O ARG b 13 " (cutoff:3.500A) Processing helix chain 'b' and resid 18 through 21 removed outlier: 3.727A pdb=" N ALA b 21 " --> pdb=" O SER b 18 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 18 through 21' Processing helix chain 'd' and resid 8 through 17 Processing helix chain 'd' and resid 17 through 22 Processing helix chain 'd' and resid 24 through 37 Processing helix chain 'e' and resid 7 through 14 removed outlier: 3.795A pdb=" N LYS e 12 " --> pdb=" O ARG e 8 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ARG e 13 " --> pdb=" O GLY e 9 " (cutoff:3.500A) Processing helix chain 'e' and resid 37 through 45 Processing helix chain 'e' and resid 54 through 62 Processing helix chain 'f' and resid 30 through 33 Processing helix chain 'i' and resid 332 through 345 removed outlier: 4.177A pdb=" N ASN i 343 " --> pdb=" O ARG i 339 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N MET i 344 " --> pdb=" O GLN i 340 " (cutoff:3.500A) Processing helix chain 'i' and resid 346 through 351 Processing helix chain 'i' and resid 368 through 382 Processing helix chain 'i' and resid 384 through 389 Processing helix chain 'i' and resid 395 through 406 removed outlier: 3.554A pdb=" N CYS i 406 " --> pdb=" O ILE i 402 " (cutoff:3.500A) Processing helix chain 'i' and resid 409 through 433 removed outlier: 3.601A pdb=" N GLY i 433 " --> pdb=" O LYS i 429 " (cutoff:3.500A) Processing helix chain 'i' and resid 434 through 441 Processing helix chain 'k' and resid 28 through 42 removed outlier: 3.639A pdb=" N LEU k 36 " --> pdb=" O LEU k 32 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 3 through 5 Processing sheet with id=AA2, first strand: chain 'C' and resid 34 through 35 Processing sheet with id=AA3, first strand: chain 'C' and resid 101 through 105 removed outlier: 6.725A pdb=" N ILE C 91 " --> pdb=" O LEU C 81 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N LEU C 81 " --> pdb=" O ILE C 91 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N LEU C 93 " --> pdb=" O GLU C 79 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 129 through 131 removed outlier: 6.052A pdb=" N ILE C 164 " --> pdb=" O ARG C 175 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ARG C 175 " --> pdb=" O ILE C 164 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N MET C 181 " --> pdb=" O VAL C 268 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 144 through 145 removed outlier: 5.406A pdb=" N VAL C 144 " --> pdb=" O GLN C 153 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 4 through 15 removed outlier: 5.714A pdb=" N LYS D 8 " --> pdb=" O GLU D 28 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N GLU D 28 " --> pdb=" O LYS D 8 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLY D 10 " --> pdb=" O VAL D 26 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N LYS D 190 " --> pdb=" O VAL D 177 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N VAL D 177 " --> pdb=" O LYS D 190 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N SER D 174 " --> pdb=" O VAL D 107 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N VAL D 107 " --> pdb=" O SER D 174 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N THR D 112 " --> pdb=" O ASP D 200 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N ASP D 200 " --> pdb=" O THR D 112 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 80 through 83 removed outlier: 3.571A pdb=" N GLN D 36 " --> pdb=" O GLN D 49 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N THR D 51 " --> pdb=" O VAL D 34 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N VAL D 34 " --> pdb=" O THR D 51 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'E' and resid 2 through 4 Processing sheet with id=AB1, first strand: chain 'E' and resid 118 through 121 removed outlier: 6.650A pdb=" N VAL E 146 " --> pdb=" O ASP E 168 " (cutoff:3.500A) removed outlier: 8.089A pdb=" N ARG E 170 " --> pdb=" O VAL E 146 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N ILE E 148 " --> pdb=" O ARG E 170 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 66 through 69 removed outlier: 3.738A pdb=" N GLY F 86 " --> pdb=" O THR F 68 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 16 through 20 Processing sheet with id=AB4, first strand: chain 'G' and resid 41 through 45 Processing sheet with id=AB5, first strand: chain 'G' and resid 122 through 124 Processing sheet with id=AB6, first strand: chain 'G' and resid 95 through 99 Processing sheet with id=AB7, first strand: chain 'H' and resid 18 through 20 Processing sheet with id=AB8, first strand: chain 'H' and resid 77 through 82 removed outlier: 6.097A pdb=" N VAL H 78 " --> pdb=" O ASN H 145 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N VAL H 147 " --> pdb=" O VAL H 78 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ILE H 80 " --> pdb=" O VAL H 147 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER H 131 " --> pdb=" O ARG H 116 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 50 through 54 removed outlier: 3.752A pdb=" N SER I 24 " --> pdb=" O VAL I 85 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N VAL I 27 " --> pdb=" O ALA I 110 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ALA I 110 " --> pdb=" O VAL I 27 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'J' and resid 9 through 14 Processing sheet with id=AC2, first strand: chain 'J' and resid 100 through 101 Processing sheet with id=AC3, first strand: chain 'K' and resid 122 through 124 removed outlier: 6.213A pdb=" N ILE K 54 " --> pdb=" O LYS K 123 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N TRP K 15 " --> pdb=" O GLN K 138 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'K' and resid 73 through 77 Processing sheet with id=AC5, first strand: chain 'L' and resid 7 through 10 removed outlier: 6.554A pdb=" N LYS L 40 " --> pdb=" O ILE L 22 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N VAL L 24 " --> pdb=" O ILE L 38 " (cutoff:3.500A) removed outlier: 8.389A pdb=" N ILE L 38 " --> pdb=" O VAL L 24 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LYS L 59 " --> pdb=" O LEU L 87 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ALA L 83 " --> pdb=" O VAL L 63 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N CYS L 84 " --> pdb=" O MET L 7 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ASN L 9 " --> pdb=" O CYS L 84 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N LEU L 86 " --> pdb=" O ASN L 9 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 69 through 70 removed outlier: 6.848A pdb=" N ALA Q 58 " --> pdb=" O ILE Q 50 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N ILE Q 50 " --> pdb=" O ALA Q 58 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N THR Q 60 " --> pdb=" O ILE Q 48 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N ILE Q 64 " --> pdb=" O GLU Q 44 " (cutoff:3.500A) removed outlier: 9.201A pdb=" N GLU Q 44 " --> pdb=" O ILE Q 64 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N THR Q 25 " --> pdb=" O LYS Q 87 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N TRP Q 31 " --> pdb=" O VAL Q 81 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N VAL Q 81 " --> pdb=" O TRP Q 31 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'L' and resid 102 through 103 Processing sheet with id=AC8, first strand: chain 'M' and resid 74 through 78 Processing sheet with id=AC9, first strand: chain 'M' and resid 89 through 90 removed outlier: 5.823A pdb=" N VAL M 122 " --> pdb=" O GLU M 143 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'N' and resid 62 through 65 removed outlier: 6.437A pdb=" N VAL N 101 " --> pdb=" O ALA N 35 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ALA N 35 " --> pdb=" O VAL N 101 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N TYR N 103 " --> pdb=" O LEU N 33 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'N' and resid 39 through 42 removed outlier: 5.847A pdb=" N VAL N 89 " --> pdb=" O GLU N 75 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N GLU N 75 " --> pdb=" O VAL N 89 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N TYR N 91 " --> pdb=" O ILE N 73 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'O' and resid 33 through 37 removed outlier: 4.337A pdb=" N MET O 110 " --> pdb=" O CYS O 100 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'P' and resid 47 through 52 removed outlier: 3.690A pdb=" N VAL P 49 " --> pdb=" O VAL P 39 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N LEU P 26 " --> pdb=" O ASP P 93 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'S' and resid 10 through 14 removed outlier: 7.105A pdb=" N GLN S 6 " --> pdb=" O VAL S 38 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N VAL S 38 " --> pdb=" O GLN S 6 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'S' and resid 19 through 23 removed outlier: 6.779A pdb=" N TRP S 92 " --> pdb=" O ARG S 68 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ARG S 68 " --> pdb=" O TRP S 92 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N THR S 94 " --> pdb=" O HIS S 66 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N HIS S 66 " --> pdb=" O THR S 94 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N VAL S 96 " --> pdb=" O VAL S 64 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N VAL S 64 " --> pdb=" O VAL S 96 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N ILE S 98 " --> pdb=" O GLU S 62 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N GLU S 62 " --> pdb=" O ILE S 98 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'S' and resid 72 through 78 removed outlier: 3.996A pdb=" N TYR S 83 " --> pdb=" O ARG S 78 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'T' and resid 2 through 11 removed outlier: 3.522A pdb=" N HIS T 9 " --> pdb=" O SER T 101 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N SER T 101 " --> pdb=" O HIS T 9 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N SER T 108 " --> pdb=" O VAL T 71 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N VAL T 71 " --> pdb=" O SER T 108 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'T' and resid 82 through 87 Processing sheet with id=AE1, first strand: chain 'U' and resid 11 through 14 removed outlier: 4.136A pdb=" N LYS U 81 " --> pdb=" O VAL U 34 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N TRP U 80 " --> pdb=" O VAL U 62 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N VAL U 62 " --> pdb=" O TRP U 80 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N LYS U 82 " --> pdb=" O THR U 60 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N THR U 60 " --> pdb=" O LYS U 82 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N TYR U 84 " --> pdb=" O VAL U 58 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N VAL U 58 " --> pdb=" O TYR U 84 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N THR U 86 " --> pdb=" O GLU U 56 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'U' and resid 67 through 70 Processing sheet with id=AE3, first strand: chain 'V' and resid 65 through 66 removed outlier: 3.553A pdb=" N LYS V 33 " --> pdb=" O LEU V 29 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASN V 27 " --> pdb=" O ILE V 35 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N GLU V 10 " --> pdb=" O PHE V 73 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'V' and resid 41 through 46 Processing sheet with id=AE5, first strand: chain 'V' and resid 83 through 88 Processing sheet with id=AE6, first strand: chain 'W' and resid 3 through 8 removed outlier: 7.649A pdb=" N ASN W 5 " --> pdb=" O ASP W 43 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N ASP W 43 " --> pdb=" O ASN W 5 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLU W 7 " --> pdb=" O GLU W 41 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N GLN W 87 " --> pdb=" O LYS W 25 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ILE W 89 " --> pdb=" O PRO W 27 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N VAL W 92 " --> pdb=" O ALA W 74 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N ALA W 74 " --> pdb=" O VAL W 92 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ILE W 4 " --> pdb=" O VAL W 64 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'X' and resid 22 through 23 removed outlier: 3.968A pdb=" N ARG X 39 " --> pdb=" O GLY X 22 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N LEU X 59 " --> pdb=" O ILE X 37 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'X' and resid 30 through 31 removed outlier: 6.100A pdb=" N HIS X 46 " --> pdb=" O ILE X 80 " (cutoff:3.500A) removed outlier: 8.396A pdb=" N ILE X 82 " --> pdb=" O HIS X 46 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'Y' and resid 13 through 18 Processing sheet with id=AF1, first strand: chain 'Y' and resid 33 through 40 Processing sheet with id=AF2, first strand: chain 'a' and resid 35 through 39 Processing sheet with id=AF3, first strand: chain 'b' and resid 29 through 30 Processing sheet with id=AF4, first strand: chain 'b' and resid 48 through 49 Processing sheet with id=AF5, first strand: chain 'c' and resid 20 through 25 Processing sheet with id=AF6, first strand: chain 'e' and resid 15 through 16 Processing sheet with id=AF7, first strand: chain 'f' and resid 2 through 4 removed outlier: 6.154A pdb=" N LYS f 2 " --> pdb=" O ARG f 36 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N ILE f 23 " --> pdb=" O GLN f 37 " (cutoff:3.500A) 1164 hydrogen bonds defined for protein. 3204 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2560 hydrogen bonds 4030 hydrogen bond angles 0 basepair planarities 1017 basepair parallelities 1608 stacking parallelities Total time for adding SS restraints: 181.90 Time building geometry restraints manager: 44.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 16074 1.33 - 1.46: 44408 1.46 - 1.59: 36746 1.59 - 1.73: 4410 1.73 - 1.86: 174 Bond restraints: 101812 Sorted by residual: bond pdb=" CA UNK i 357 " pdb=" C UNK i 357 " ideal model delta sigma weight residual 1.525 1.690 -0.165 2.10e-02 2.27e+03 6.19e+01 bond pdb=" CA UNK i 449 " pdb=" C UNK i 449 " ideal model delta sigma weight residual 1.525 1.678 -0.153 2.10e-02 2.27e+03 5.30e+01 bond pdb=" N UNK i 451 " pdb=" CA UNK i 451 " ideal model delta sigma weight residual 1.458 1.592 -0.134 1.90e-02 2.77e+03 4.95e+01 bond pdb=" CA UNK i 446 " pdb=" C UNK i 446 " ideal model delta sigma weight residual 1.525 1.673 -0.148 2.10e-02 2.27e+03 4.94e+01 bond pdb=" CA UNK i 452 " pdb=" C UNK i 452 " ideal model delta sigma weight residual 1.525 1.670 -0.145 2.10e-02 2.27e+03 4.75e+01 ... (remaining 101807 not shown) Histogram of bond angle deviations from ideal: 93.90 - 102.80: 5517 102.80 - 111.69: 61193 111.69 - 120.59: 51421 120.59 - 129.49: 31815 129.49 - 138.39: 2612 Bond angle restraints: 152558 Sorted by residual: angle pdb=" C VAL D 142 " pdb=" N PRO D 143 " pdb=" CA PRO D 143 " ideal model delta sigma weight residual 119.82 129.90 -10.08 9.80e-01 1.04e+00 1.06e+02 angle pdb=" C LYS i 390 " pdb=" N PRO i 391 " pdb=" CA PRO i 391 " ideal model delta sigma weight residual 119.87 129.93 -10.06 1.04e+00 9.25e-01 9.35e+01 angle pdb=" N ASP J 116 " pdb=" CA ASP J 116 " pdb=" C ASP J 116 " ideal model delta sigma weight residual 113.17 124.65 -11.48 1.26e+00 6.30e-01 8.30e+01 angle pdb=" C LEU N 124 " pdb=" N PRO N 125 " pdb=" CA PRO N 125 " ideal model delta sigma weight residual 119.56 128.02 -8.46 1.01e+00 9.80e-01 7.01e+01 angle pdb=" N VAL D 142 " pdb=" CA VAL D 142 " pdb=" C VAL D 142 " ideal model delta sigma weight residual 109.02 116.29 -7.27 9.30e-01 1.16e+00 6.11e+01 ... (remaining 152553 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.95: 51899 35.95 - 71.91: 2176 71.91 - 107.86: 146 107.86 - 143.82: 13 143.82 - 179.77: 10 Dihedral angle restraints: 54244 sinusoidal: 43931 harmonic: 10313 Sorted by residual: 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 30.64 -65.64 1 8.00e+00 1.56e-02 8.81e+01 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 30.20 -65.20 1 8.00e+00 1.56e-02 8.71e+01 dihedral pdb=" C5' C A 645 " pdb=" C4' C A 645 " pdb=" C3' C A 645 " pdb=" O3' C A 645 " ideal model delta sinusoidal sigma weight residual 147.00 83.98 63.02 1 8.00e+00 1.56e-02 8.20e+01 ... (remaining 54241 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 17879 0.078 - 0.155: 1559 0.155 - 0.233: 112 0.233 - 0.310: 7 0.310 - 0.388: 2 Chirality restraints: 19559 Sorted by residual: chirality pdb=" C3' C A 645 " pdb=" C4' C A 645 " pdb=" O3' C A 645 " pdb=" C2' C A 645 " both_signs ideal model delta sigma weight residual False -2.74 -2.36 -0.39 2.00e-01 2.50e+01 3.76e+00 chirality pdb=" C3' U A1344 " pdb=" C4' U A1344 " pdb=" O3' U A1344 " pdb=" C2' U A1344 " both_signs ideal model delta sigma weight residual False -2.74 -2.43 -0.32 2.00e-01 2.50e+01 2.53e+00 chirality pdb=" C1' G A 748 " pdb=" O4' G A 748 " pdb=" C2' G A 748 " pdb=" N9 G A 748 " both_signs ideal model delta sigma weight residual False 2.46 2.15 0.31 2.00e-01 2.50e+01 2.39e+00 ... (remaining 19556 not shown) Planarity restraints: 7978 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU U 93 " -0.023 2.00e-02 2.50e+03 4.49e-02 2.02e+01 pdb=" C LEU U 93 " 0.078 2.00e-02 2.50e+03 pdb=" O LEU U 93 " -0.030 2.00e-02 2.50e+03 pdb=" N ASP U 94 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY J 25 " -0.057 5.00e-02 4.00e+02 8.69e-02 1.21e+01 pdb=" N PRO J 26 " 0.150 5.00e-02 4.00e+02 pdb=" CA PRO J 26 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO J 26 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' C A2422 " 0.030 2.00e-02 2.50e+03 1.94e-02 8.46e+00 pdb=" N1 C A2422 " -0.049 2.00e-02 2.50e+03 pdb=" C2 C A2422 " 0.003 2.00e-02 2.50e+03 pdb=" O2 C A2422 " 0.000 2.00e-02 2.50e+03 pdb=" N3 C A2422 " 0.002 2.00e-02 2.50e+03 pdb=" C4 C A2422 " 0.003 2.00e-02 2.50e+03 pdb=" N4 C A2422 " 0.006 2.00e-02 2.50e+03 pdb=" C5 C A2422 " 0.003 2.00e-02 2.50e+03 pdb=" C6 C A2422 " 0.001 2.00e-02 2.50e+03 ... (remaining 7975 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.41: 337 2.41 - 3.03: 50118 3.03 - 3.66: 169249 3.66 - 4.28: 278285 4.28 - 4.90: 369902 Nonbonded interactions: 867891 Sorted by model distance: nonbonded pdb=" OP1 C A 787 " pdb="MG MG A3174 " model vdw 1.789 2.170 nonbonded pdb=" OP2 U A1023 " pdb="MG MG A3212 " model vdw 1.792 2.170 nonbonded pdb=" OP2 A A 422 " pdb="MG MG A3066 " model vdw 1.802 2.170 nonbonded pdb=" OP2 U A1379 " pdb="MG MG A3138 " model vdw 1.806 2.170 nonbonded pdb=" OP1 A A1614 " pdb="MG MG A3020 " model vdw 1.810 2.170 ... (remaining 867886 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 3049 5.49 5 Mg 431 5.21 5 S 95 5.16 5 C 46856 2.51 5 N 17424 2.21 5 O 26174 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 13.570 Check model and map are aligned: 1.060 Convert atoms to be neutral: 0.630 Process input model: 379.580 Find NCS groups from input model: 1.740 Set up NCS constraints: 0.230 Set refine NCS operators: 0.000 Set scattering table: 0.020 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 400.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8993 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 : 0.007 0.165 101812 Z= 0.456 Angle : 1.042 14.102 152558 Z= 0.597 Chirality : 0.045 0.388 19559 Planarity : 0.005 0.087 7978 Dihedral : 15.709 179.770 47596 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.00 % Favored : 96.94 % Rotamer Outliers : 9.03 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.35 (0.11), residues: 3529 helix: -3.59 (0.10), residues: 1074 sheet: -1.47 (0.17), residues: 666 loop : -1.50 (0.12), residues: 1789 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7058 Ramachandran restraints generated. 3529 Oldfield, 0 Emsley, 3529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7058 Ramachandran restraints generated. 3529 Oldfield, 0 Emsley, 3529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1494 residues out of total 2908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 262 poor density : 1232 time to evaluate : 4.227 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 outliers start: 262 outliers final: 69 residues processed: 1387 average time/residue: 0.9598 time to fit residues: 2202.9725 Evaluate side-chains 928 residues out of total 2908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 859 time to evaluate : 4.186 Switching outliers to nearest non-outliers outliers start: 69 outliers final: 0 residues processed: 69 average time/residue: 0.9104 time to fit residues: 115.6829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 640 random chunks: chunk 540 optimal weight: 4.9990 chunk 485 optimal weight: 8.9990 chunk 269 optimal weight: 10.0000 chunk 165 optimal weight: 10.0000 chunk 327 optimal weight: 10.0000 chunk 259 optimal weight: 10.0000 chunk 501 optimal weight: 7.9990 chunk 194 optimal weight: 10.0000 chunk 305 optimal weight: 5.9990 chunk 373 optimal weight: 1.9990 chunk 581 optimal weight: 4.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 32 ASN D 140 HIS E 9 GLN E 90 GLN E 92 HIS ** E 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN F 52 ASN ** G 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 ASN G 111 HIS H 33 GLN ** I 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 12 GLN J 31 GLN ** K 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 128 ASN K 136 GLN M 104 GLN ** N 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 29 HIS Q 77 HIS R 37 GLN R 72 ASN T 7 HIS U 48 GLN ** V 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 20 HIS Y 23 ASN ** Z 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 29 GLN f 35 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8936 moved from start: 0.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.059 101812 Z= 0.291 Angle : 0.657 8.329 152558 Z= 0.341 Chirality : 0.038 0.299 19559 Planarity : 0.005 0.064 7978 Dihedral : 14.280 179.398 40609 Min Nonbonded Distance : 1.762 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.13 % Favored : 97.85 % Rotamer Outliers : 5.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.12), residues: 3529 helix: -1.14 (0.14), residues: 1063 sheet: -0.90 (0.17), residues: 706 loop : -0.88 (0.13), residues: 1760 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7058 Ramachandran restraints generated. 3529 Oldfield, 0 Emsley, 3529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7058 Ramachandran restraints generated. 3529 Oldfield, 0 Emsley, 3529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1096 residues out of total 2908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 948 time to evaluate : 4.312 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: 148 outliers final: 75 residues processed: 1026 average time/residue: 0.8753 time to fit residues: 1518.9434 Evaluate side-chains 909 residues out of total 2908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 834 time to evaluate : 4.237 Switching outliers to nearest non-outliers outliers start: 75 outliers final: 0 residues processed: 75 average time/residue: 0.6750 time to fit residues: 99.7859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 640 random chunks: chunk 322 optimal weight: 10.0000 chunk 180 optimal weight: 10.0000 chunk 483 optimal weight: 4.9990 chunk 395 optimal weight: 8.9990 chunk 160 optimal weight: 20.0000 chunk 582 optimal weight: 8.9990 chunk 628 optimal weight: 0.9990 chunk 518 optimal weight: 6.9990 chunk 577 optimal weight: 6.9990 chunk 198 optimal weight: 10.0000 chunk 467 optimal weight: 9.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 153 GLN ** G 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 128 HIS ** I 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 128 ASN ** M 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 62 ASN ** O 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 75 GLN R 37 GLN U 48 GLN ** V 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 38 GLN Z 58 ASN i 343 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8930 moved from start: 0.3155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.068 101812 Z= 0.311 Angle : 0.627 12.193 152558 Z= 0.326 Chirality : 0.037 0.272 19559 Planarity : 0.005 0.070 7978 Dihedral : 14.189 178.738 40609 Min Nonbonded Distance : 0.877 Molprobity Statistics. All-atom Clashscore : 13.86 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.06 % Favored : 96.85 % Rotamer Outliers : 4.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.13), residues: 3529 helix: -0.20 (0.15), residues: 1075 sheet: -0.64 (0.18), residues: 718 loop : -0.70 (0.14), residues: 1736 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7058 Ramachandran restraints generated. 3529 Oldfield, 0 Emsley, 3529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7058 Ramachandran restraints generated. 3529 Oldfield, 0 Emsley, 3529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1017 residues out of total 2908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 890 time to evaluate : 4.479 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: 127 outliers final: 66 residues processed: 957 average time/residue: 0.9103 time to fit residues: 1482.1926 Evaluate side-chains 857 residues out of total 2908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 791 time to evaluate : 5.364 Switching outliers to nearest non-outliers outliers start: 66 outliers final: 0 residues processed: 66 average time/residue: 0.7546 time to fit residues: 98.3417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 640 random chunks: chunk 575 optimal weight: 8.9990 chunk 437 optimal weight: 0.1980 chunk 302 optimal weight: 10.0000 chunk 64 optimal weight: 10.0000 chunk 277 optimal weight: 10.0000 chunk 390 optimal weight: 10.0000 chunk 584 optimal weight: 1.9990 chunk 618 optimal weight: 6.9990 chunk 305 optimal weight: 0.3980 chunk 553 optimal weight: 10.0000 chunk 166 optimal weight: 10.0000 overall best weight: 3.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 200 HIS E 115 GLN E 195 GLN F 37 ASN ** G 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 111 GLN ** M 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 66 ASN R 37 GLN ** V 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 78 GLN Y 23 ASN d 6 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8893 moved from start: 0.3619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.065 101812 Z= 0.215 Angle : 0.557 8.516 152558 Z= 0.292 Chirality : 0.034 0.250 19559 Planarity : 0.004 0.059 7978 Dihedral : 13.987 178.970 40609 Min Nonbonded Distance : 1.057 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.98 % Favored : 96.94 % Rotamer Outliers : 3.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.13), residues: 3529 helix: 0.27 (0.16), residues: 1079 sheet: -0.60 (0.18), residues: 729 loop : -0.58 (0.14), residues: 1721 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7058 Ramachandran restraints generated. 3529 Oldfield, 0 Emsley, 3529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7058 Ramachandran restraints generated. 3529 Oldfield, 0 Emsley, 3529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 962 residues out of total 2908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 864 time to evaluate : 4.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 98 outliers final: 61 residues processed: 909 average time/residue: 0.9543 time to fit residues: 1480.1745 Evaluate side-chains 864 residues out of total 2908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 803 time to evaluate : 4.188 Switching outliers to nearest non-outliers outliers start: 61 outliers final: 0 residues processed: 61 average time/residue: 0.6947 time to fit residues: 84.5469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 640 random chunks: chunk 515 optimal weight: 0.9990 chunk 351 optimal weight: 5.9990 chunk 8 optimal weight: 10.0000 chunk 460 optimal weight: 8.9990 chunk 255 optimal weight: 10.0000 chunk 527 optimal weight: 10.0000 chunk 427 optimal weight: 0.0670 chunk 0 optimal weight: 50.0000 chunk 315 optimal weight: 0.0370 chunk 555 optimal weight: 1.9990 chunk 156 optimal weight: 20.0000 overall best weight: 1.8202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 ASN ** D 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 115 GLN ** E 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 195 GLN ** G 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 9 ASN M 54 GLN ** N 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 88 ASN ** O 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 37 GLN R 72 ASN ** V 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 58 ASN d 6 GLN f 35 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8844 moved from start: 0.4017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.065 101812 Z= 0.144 Angle : 0.517 11.788 152558 Z= 0.269 Chirality : 0.031 0.243 19559 Planarity : 0.004 0.080 7978 Dihedral : 13.773 178.824 40609 Min Nonbonded Distance : 1.152 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.72 % Favored : 97.19 % Rotamer Outliers : 2.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.14), residues: 3529 helix: 0.66 (0.16), residues: 1083 sheet: -0.52 (0.18), residues: 748 loop : -0.41 (0.14), residues: 1698 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7058 Ramachandran restraints generated. 3529 Oldfield, 0 Emsley, 3529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7058 Ramachandran restraints generated. 3529 Oldfield, 0 Emsley, 3529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 935 residues out of total 2908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 876 time to evaluate : 4.344 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: 59 outliers final: 26 residues processed: 893 average time/residue: 0.8923 time to fit residues: 1351.5933 Evaluate side-chains 816 residues out of total 2908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 790 time to evaluate : 4.251 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.7511 time to fit residues: 40.0312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 640 random chunks: chunk 208 optimal weight: 10.0000 chunk 557 optimal weight: 6.9990 chunk 122 optimal weight: 10.0000 chunk 363 optimal weight: 6.9990 chunk 152 optimal weight: 20.0000 chunk 619 optimal weight: 8.9990 chunk 514 optimal weight: 10.0000 chunk 286 optimal weight: 10.0000 chunk 51 optimal weight: 10.0000 chunk 204 optimal weight: 10.0000 chunk 325 optimal weight: 2.9990 overall best weight: 7.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 134 ASN E 115 GLN ** E 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 195 GLN ** G 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 135 HIS J 107 GLN ** N 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 107 ASN Q 12 GLN R 37 GLN R 52 GLN ** V 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 23 ASN d 6 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8915 moved from start: 0.4092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.058 101812 Z= 0.373 Angle : 0.661 10.820 152558 Z= 0.339 Chirality : 0.038 0.312 19559 Planarity : 0.005 0.072 7978 Dihedral : 14.140 177.886 40609 Min Nonbonded Distance : 0.978 Molprobity Statistics. All-atom Clashscore : 15.98 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.63 % Favored : 96.29 % Rotamer Outliers : 3.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.14), residues: 3529 helix: 0.39 (0.16), residues: 1089 sheet: -0.65 (0.18), residues: 764 loop : -0.60 (0.14), residues: 1676 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7058 Ramachandran restraints generated. 3529 Oldfield, 0 Emsley, 3529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7058 Ramachandran restraints generated. 3529 Oldfield, 0 Emsley, 3529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 916 residues out of total 2908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 810 time to evaluate : 4.610 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 outliers start: 106 outliers final: 70 residues processed: 858 average time/residue: 0.9137 time to fit residues: 1339.0059 Evaluate side-chains 846 residues out of total 2908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 776 time to evaluate : 4.315 Switching outliers to nearest non-outliers outliers start: 70 outliers final: 0 residues processed: 70 average time/residue: 0.7113 time to fit residues: 99.0162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 640 random chunks: chunk 597 optimal weight: 0.5980 chunk 69 optimal weight: 10.0000 chunk 352 optimal weight: 7.9990 chunk 452 optimal weight: 3.9990 chunk 350 optimal weight: 0.0970 chunk 521 optimal weight: 8.9990 chunk 345 optimal weight: 5.9990 chunk 616 optimal weight: 4.9990 chunk 386 optimal weight: 20.0000 chunk 376 optimal weight: 6.9990 chunk 284 optimal weight: 10.0000 overall best weight: 3.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 134 ASN E 115 GLN E 195 GLN ** G 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 128 GLN I 4 ASN ** N 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 66 ASN R 52 GLN ** V 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8873 moved from start: 0.4282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.059 101812 Z= 0.193 Angle : 0.553 11.850 152558 Z= 0.287 Chirality : 0.033 0.257 19559 Planarity : 0.004 0.076 7978 Dihedral : 13.895 178.963 40609 Min Nonbonded Distance : 1.076 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.09 % Favored : 96.83 % Rotamer Outliers : 1.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.14), residues: 3529 helix: 0.54 (0.16), residues: 1090 sheet: -0.64 (0.18), residues: 769 loop : -0.48 (0.15), residues: 1670 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7058 Ramachandran restraints generated. 3529 Oldfield, 0 Emsley, 3529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7058 Ramachandran restraints generated. 3529 Oldfield, 0 Emsley, 3529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 854 residues out of total 2908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 815 time to evaluate : 4.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 26 residues processed: 831 average time/residue: 0.8945 time to fit residues: 1267.7464 Evaluate side-chains 797 residues out of total 2908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 771 time to evaluate : 4.255 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.6682 time to fit residues: 37.8771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 640 random chunks: chunk 381 optimal weight: 6.9990 chunk 246 optimal weight: 10.0000 chunk 368 optimal weight: 6.9990 chunk 185 optimal weight: 10.0000 chunk 121 optimal weight: 10.0000 chunk 119 optimal weight: 10.0000 chunk 392 optimal weight: 5.9990 chunk 420 optimal weight: 4.9990 chunk 304 optimal weight: 0.9980 chunk 57 optimal weight: 10.0000 chunk 484 optimal weight: 8.9990 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 134 ASN E 115 GLN E 195 GLN ** G 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 136 GLN ** N 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 37 GLN R 52 GLN R 56 GLN ** T 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 23 ASN ** i 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8886 moved from start: 0.4321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.063 101812 Z= 0.284 Angle : 0.591 12.786 152558 Z= 0.305 Chirality : 0.035 0.261 19559 Planarity : 0.005 0.074 7978 Dihedral : 13.925 178.687 40609 Min Nonbonded Distance : 1.030 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.54 % Favored : 96.37 % Rotamer Outliers : 1.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.14), residues: 3529 helix: 0.53 (0.16), residues: 1084 sheet: -0.66 (0.18), residues: 767 loop : -0.55 (0.15), residues: 1678 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7058 Ramachandran restraints generated. 3529 Oldfield, 0 Emsley, 3529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7058 Ramachandran restraints generated. 3529 Oldfield, 0 Emsley, 3529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 827 residues out of total 2908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 781 time to evaluate : 4.473 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 outliers start: 46 outliers final: 31 residues processed: 797 average time/residue: 0.8826 time to fit residues: 1201.8554 Evaluate side-chains 798 residues out of total 2908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 767 time to evaluate : 4.302 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 0 residues processed: 31 average time/residue: 0.7074 time to fit residues: 45.3701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 640 random chunks: chunk 561 optimal weight: 10.0000 chunk 590 optimal weight: 2.9990 chunk 539 optimal weight: 0.9980 chunk 574 optimal weight: 8.9990 chunk 345 optimal weight: 0.0570 chunk 250 optimal weight: 10.0000 chunk 451 optimal weight: 6.9990 chunk 176 optimal weight: 10.0000 chunk 519 optimal weight: 6.9990 chunk 543 optimal weight: 8.9990 chunk 572 optimal weight: 20.0000 overall best weight: 3.6104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 115 GLN E 195 GLN ** G 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 136 GLN ** N 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 66 ASN T 15 GLN ** V 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8866 moved from start: 0.4493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.057 101812 Z= 0.212 Angle : 0.564 13.556 152558 Z= 0.292 Chirality : 0.033 0.272 19559 Planarity : 0.004 0.069 7978 Dihedral : 13.869 179.382 40609 Min Nonbonded Distance : 1.045 Molprobity Statistics. All-atom Clashscore : 13.86 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.63 % Favored : 96.29 % Rotamer Outliers : 0.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.14), residues: 3529 helix: 0.60 (0.16), residues: 1078 sheet: -0.64 (0.18), residues: 769 loop : -0.50 (0.15), residues: 1682 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7058 Ramachandran restraints generated. 3529 Oldfield, 0 Emsley, 3529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7058 Ramachandran restraints generated. 3529 Oldfield, 0 Emsley, 3529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 817 residues out of total 2908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 794 time to evaluate : 4.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 10 residues processed: 800 average time/residue: 0.9110 time to fit residues: 1246.3685 Evaluate side-chains 776 residues out of total 2908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 766 time to evaluate : 4.289 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.6953 time to fit residues: 17.5868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 640 random chunks: chunk 377 optimal weight: 0.8980 chunk 607 optimal weight: 0.9990 chunk 371 optimal weight: 8.9990 chunk 288 optimal weight: 10.0000 chunk 422 optimal weight: 9.9990 chunk 637 optimal weight: 7.9990 chunk 586 optimal weight: 2.9990 chunk 507 optimal weight: 0.0030 chunk 52 optimal weight: 10.0000 chunk 392 optimal weight: 7.9990 chunk 311 optimal weight: 7.9990 overall best weight: 2.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 115 GLN E 195 GLN ** F 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 37 ASN ** G 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 23 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8835 moved from start: 0.4714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 101812 Z= 0.172 Angle : 0.541 15.814 152558 Z= 0.279 Chirality : 0.031 0.282 19559 Planarity : 0.004 0.065 7978 Dihedral : 13.747 179.713 40609 Min Nonbonded Distance : 1.084 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.23 % Favored : 96.68 % Rotamer Outliers : 0.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.14), residues: 3529 helix: 0.72 (0.16), residues: 1084 sheet: -0.64 (0.18), residues: 760 loop : -0.45 (0.15), residues: 1685 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7058 Ramachandran restraints generated. 3529 Oldfield, 0 Emsley, 3529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7058 Ramachandran restraints generated. 3529 Oldfield, 0 Emsley, 3529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 819 residues out of total 2908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 805 time to evaluate : 4.342 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 outliers start: 14 outliers final: 8 residues processed: 805 average time/residue: 0.9031 time to fit residues: 1233.3422 Evaluate side-chains 776 residues out of total 2908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 768 time to evaluate : 4.259 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.6901 time to fit residues: 14.7128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 640 random chunks: chunk 403 optimal weight: 3.9990 chunk 540 optimal weight: 3.9990 chunk 155 optimal weight: 20.0000 chunk 468 optimal weight: 7.9990 chunk 74 optimal weight: 10.0000 chunk 141 optimal weight: 10.0000 chunk 508 optimal weight: 0.7980 chunk 212 optimal weight: 40.0000 chunk 522 optimal weight: 5.9990 chunk 64 optimal weight: 10.0000 chunk 93 optimal weight: 10.0000 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 115 GLN E 195 GLN ** F 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 136 GLN ** N 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 15 GLN U 91 GLN ** V 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 46 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.071110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.056237 restraints weight = 347283.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.057711 restraints weight = 131123.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.058420 restraints weight = 70616.841| |-----------------------------------------------------------------------------| r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8731 moved from start: 0.4727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.055 101812 Z= 0.252 Angle : 0.580 12.558 152558 Z= 0.299 Chirality : 0.033 0.316 19559 Planarity : 0.005 0.069 7978 Dihedral : 13.801 179.068 40609 Min Nonbonded Distance : 1.013 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.57 % Favored : 96.34 % Rotamer Outliers : 0.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.14), residues: 3529 helix: 0.67 (0.16), residues: 1084 sheet: -0.68 (0.18), residues: 781 loop : -0.50 (0.15), residues: 1664 =============================================================================== Job complete usr+sys time: 20179.17 seconds wall clock time: 357 minutes 28.53 seconds (21448.53 seconds total)