Starting phenix.real_space_refine on Tue Mar 19 21:17:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5gaf_8002/03_2024/5gaf_8002_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5gaf_8002/03_2024/5gaf_8002.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5gaf_8002/03_2024/5gaf_8002.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5gaf_8002/03_2024/5gaf_8002.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5gaf_8002/03_2024/5gaf_8002_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5gaf_8002/03_2024/5gaf_8002_updated.pdb" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.023 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 3052 5.49 5 Mg 431 5.21 5 S 102 5.16 5 C 48201 2.51 5 N 17806 2.21 5 O 26589 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C GLU 23": "OE1" <-> "OE2" Residue "C GLU 35": "OE1" <-> "OE2" Residue "C ARG 52": "NH1" <-> "NH2" Residue "C ARG 63": "NH1" <-> "NH2" Residue "C ARG 80": "NH1" <-> "NH2" Residue "C TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 133": "NH1" <-> "NH2" Residue "C GLU 145": "OE1" <-> "OE2" Residue "C TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 167": "NH1" <-> "NH2" Residue "C TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 177": "NH1" <-> "NH2" Residue "C ARG 182": "NH1" <-> "NH2" Residue "C ARG 189": "NH1" <-> "NH2" Residue "C GLU 199": "OE1" <-> "OE2" Residue "C ARG 203": "NH1" <-> "NH2" Residue "C ARG 212": "NH1" <-> "NH2" Residue "D ARG 13": "NH1" <-> "NH2" Residue "D GLU 17": "OE1" <-> "OE2" Residue "D ASP 18": "OD1" <-> "OD2" Residue "D GLU 28": "OE1" <-> "OE2" Residue "D GLU 30": "OE1" <-> "OE2" Residue "D ARG 33": "NH1" <-> "NH2" Residue "D ASP 43": "OD1" <-> "OD2" Residue "D TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 59": "NH1" <-> "NH2" Residue "D GLU 64": "OE1" <-> "OE2" Residue "D ARG 77": "NH1" <-> "NH2" Residue "D GLU 81": "OE1" <-> "OE2" Residue "D ARG 83": "NH1" <-> "NH2" Residue "D GLU 168": "OE1" <-> "OE2" Residue "D ARG 169": "NH1" <-> "NH2" Residue "D GLU 183": "OE1" <-> "OE2" Residue "D ARG 184": "NH1" <-> "NH2" Residue "E ASP 7": "OD1" <-> "OD2" Residue "E ARG 21": "NH1" <-> "NH2" Residue "E GLU 25": "OE1" <-> "OE2" Residue "E ARG 44": "NH1" <-> "NH2" Residue "E ARG 49": "NH1" <-> "NH2" Residue "E ARG 61": "NH1" <-> "NH2" Residue "E PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 88": "NH1" <-> "NH2" Residue "E ARG 102": "NH1" <-> "NH2" Residue "E ASP 145": "OD1" <-> "OD2" Residue "E GLU 152": "OE1" <-> "OE2" Residue "E ARG 162": "NH1" <-> "NH2" Residue "E ARG 170": "NH1" <-> "NH2" Residue "E ASP 176": "OD1" <-> "OD2" Residue "E GLU 197": "OE1" <-> "OE2" Residue "F GLU 19": "OE1" <-> "OE2" Residue "F GLU 32": "OE1" <-> "OE2" Residue "F ARG 71": "NH1" <-> "NH2" Residue "F ARG 80": "NH1" <-> "NH2" Residue "F ARG 92": "NH1" <-> "NH2" Residue "F GLU 94": "OE1" <-> "OE2" Residue "F GLU 98": "OE1" <-> "OE2" Residue "F ARG 102": "NH1" <-> "NH2" Residue "F ARG 110": "NH1" <-> "NH2" Residue "F ARG 112": "NH1" <-> "NH2" Residue "F ARG 115": "NH1" <-> "NH2" Residue "F PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 133": "NH1" <-> "NH2" Residue "G ARG 3": "NH1" <-> "NH2" Residue "G PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 56": "OD1" <-> "OD2" Residue "G TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 124": "OE1" <-> "OE2" Residue "G ARG 153": "NH1" <-> "NH2" Residue "G TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 163": "NH1" <-> "NH2" Residue "G ASP 166": "OD1" <-> "OD2" Residue "G ARG 170": "NH1" <-> "NH2" Residue "H ARG 27": "NH1" <-> "NH2" Residue "H PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 60": "OE1" <-> "OE2" Residue "H ASP 86": "OD1" <-> "OD2" Residue "H GLU 87": "OE1" <-> "OE2" Residue "H GLU 114": "OE1" <-> "OE2" Residue "H GLU 137": "OE1" <-> "OE2" Residue "H PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 87": "OE1" <-> "OE2" Residue "I PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 114": "OE1" <-> "OE2" Residue "I ASP 124": "OD1" <-> "OD2" Residue "J PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 13": "NH1" <-> "NH2" Residue "K TYR 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 31": "OE1" <-> "OE2" Residue "K ARG 37": "NH1" <-> "NH2" Residue "K GLU 43": "OE1" <-> "OE2" Residue "K TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 90": "OE1" <-> "OE2" Residue "K GLU 91": "OE1" <-> "OE2" Residue "K ARG 96": "NH1" <-> "NH2" Residue "K ARG 120": "NH1" <-> "NH2" Residue "L GLU 45": "OE1" <-> "OE2" Residue "L GLU 110": "OE1" <-> "OE2" Residue "L GLU 121": "OE1" <-> "OE2" Residue "M ARG 21": "NH1" <-> "NH2" Residue "M ARG 33": "NH1" <-> "NH2" Residue "M ARG 41": "NH1" <-> "NH2" Residue "M ARG 47": "NH1" <-> "NH2" Residue "M GLU 51": "OE1" <-> "OE2" Residue "M ARG 60": "NH1" <-> "NH2" Residue "M PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 76": "OE1" <-> "OE2" Residue "M ARG 78": "NH1" <-> "NH2" Residue "M ASP 91": "OD1" <-> "OD2" Residue "M GLU 106": "OE1" <-> "OE2" Residue "M ARG 126": "NH1" <-> "NH2" Residue "M GLU 144": "OE1" <-> "OE2" Residue "N ARG 10": "NH1" <-> "NH2" Residue "N ARG 18": "NH1" <-> "NH2" Residue "N PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 40": "NH1" <-> "NH2" Residue "N ARG 44": "NH1" <-> "NH2" Residue "N GLU 47": "OE1" <-> "OE2" Residue "N ARG 50": "NH1" <-> "NH2" Residue "N ARG 55": "NH1" <-> "NH2" Residue "N ARG 59": "NH1" <-> "NH2" Residue "N GLU 75": "OE1" <-> "OE2" Residue "N TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 104": "OE1" <-> "OE2" Residue "N ARG 114": "NH1" <-> "NH2" Residue "N PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 8": "NH1" <-> "NH2" Residue "O ARG 12": "NH1" <-> "NH2" Residue "O ARG 17": "NH1" <-> "NH2" Residue "O ARG 22": "NH1" <-> "NH2" Residue "O GLU 43": "OE1" <-> "OE2" Residue "O ARG 46": "NH1" <-> "NH2" Residue "O ARG 63": "NH1" <-> "NH2" Residue "O ARG 64": "NH1" <-> "NH2" Residue "O ARG 69": "NH1" <-> "NH2" Residue "O ARG 71": "NH1" <-> "NH2" Residue "O GLU 82": "OE1" <-> "OE2" Residue "O ARG 96": "NH1" <-> "NH2" Residue "O TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 114": "OE1" <-> "OE2" Residue "P ARG 10": "NH1" <-> "NH2" Residue "P ARG 16": "NH1" <-> "NH2" Residue "P GLU 20": "OE1" <-> "OE2" Residue "P ARG 25": "NH1" <-> "NH2" Residue "P ARG 81": "NH1" <-> "NH2" Residue "P ARG 94": "NH1" <-> "NH2" Residue "P TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 102": "NH1" <-> "NH2" Residue "P ARG 111": "NH1" <-> "NH2" Residue "Q PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 21": "NH1" <-> "NH2" Residue "Q ARG 39": "NH1" <-> "NH2" Residue "Q GLU 44": "OE1" <-> "OE2" Residue "Q ARG 62": "NH1" <-> "NH2" Residue "Q GLU 71": "OE1" <-> "OE2" Residue "Q ASP 82": "OD1" <-> "OD2" Residue "Q ARG 89": "NH1" <-> "NH2" Residue "Q TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 101": "NH1" <-> "NH2" Residue "Q ARG 109": "NH1" <-> "NH2" Residue "R ARG 3": "NH1" <-> "NH2" Residue "R ARG 6": "NH1" <-> "NH2" Residue "R ARG 13": "NH1" <-> "NH2" Residue "R TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 33": "NH1" <-> "NH2" Residue "R TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 48": "NH1" <-> "NH2" Residue "R PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 70": "NH1" <-> "NH2" Residue "R TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 111": "OE1" <-> "OE2" Residue "S GLU 16": "OE1" <-> "OE2" Residue "S ARG 21": "NH1" <-> "NH2" Residue "S GLU 23": "OE1" <-> "OE2" Residue "S GLU 31": "OE1" <-> "OE2" Residue "S GLU 45": "OE1" <-> "OE2" Residue "S ARG 68": "NH1" <-> "NH2" Residue "S GLU 70": "OE1" <-> "OE2" Residue "S ARG 78": "NH1" <-> "NH2" Residue "S ARG 79": "NH1" <-> "NH2" Residue "S TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 84": "NH1" <-> "NH2" Residue "S PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 59": "OE1" <-> "OE2" Residue "T PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 78": "OE1" <-> "OE2" Residue "T ARG 84": "NH1" <-> "NH2" Residue "T ARG 88": "NH1" <-> "NH2" Residue "T ARG 95": "NH1" <-> "NH2" Residue "T ARG 110": "NH1" <-> "NH2" Residue "U GLU 4": "OE1" <-> "OE2" Residue "U GLU 5": "OE1" <-> "OE2" Residue "U GLU 52": "OE1" <-> "OE2" Residue "U GLU 54": "OE1" <-> "OE2" Residue "U GLU 56": "OE1" <-> "OE2" Residue "U GLU 89": "OE1" <-> "OE2" Residue "U PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 6": "NH1" <-> "NH2" Residue "V ARG 7": "NH1" <-> "NH2" Residue "V ARG 82": "NH1" <-> "NH2" Residue "V PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 86": "NH1" <-> "NH2" Residue "V GLU 88": "OE1" <-> "OE2" Residue "V ARG 94": "NH1" <-> "NH2" Residue "V PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 11": "OE1" <-> "OE2" Residue "W PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 41": "OE1" <-> "OE2" Residue "W GLU 55": "OE1" <-> "OE2" Residue "W GLU 69": "OE1" <-> "OE2" Residue "W PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 17": "OE1" <-> "OE2" Residue "X PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 85": "OE1" <-> "OE2" Residue "Y ARG 3": "NH1" <-> "NH2" Residue "Y ARG 11": "NH1" <-> "NH2" Residue "Y ARG 18": "NH1" <-> "NH2" Residue "Y PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 37": "NH1" <-> "NH2" Residue "Y GLU 41": "OE1" <-> "OE2" Residue "Y GLU 43": "OE1" <-> "OE2" Residue "Y ARG 50": "NH1" <-> "NH2" Residue "Y ARG 57": "NH1" <-> "NH2" Residue "Y ARG 74": "NH1" <-> "NH2" Residue "Z GLU 12": "OE1" <-> "OE2" Residue "Z ARG 47": "NH1" <-> "NH2" Residue "Z ARG 52": "NH1" <-> "NH2" Residue "a ARG 11": "NH1" <-> "NH2" Residue "a ARG 30": "NH1" <-> "NH2" Residue "a GLU 37": "OE1" <-> "OE2" Residue "a ARG 45": "NH1" <-> "NH2" Residue "a PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 10": "NH1" <-> "NH2" Residue "b ARG 16": "NH1" <-> "NH2" Residue "b ASP 31": "OD1" <-> "OD2" Residue "b ARG 52": "NH1" <-> "NH2" Residue "c GLU 32": "OE1" <-> "OE2" Residue "c GLU 35": "OE1" <-> "OE2" Residue "c ARG 44": "NH1" <-> "NH2" Residue "d ARG 3": "NH1" <-> "NH2" Residue "d ARG 14": "NH1" <-> "NH2" Residue "d PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 19": "NH1" <-> "NH2" Residue "d ARG 21": "NH1" <-> "NH2" Residue "d ARG 33": "NH1" <-> "NH2" Residue "e ARG 13": "NH1" <-> "NH2" Residue "e PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ARG 30": "NH1" <-> "NH2" Residue "e ARG 40": "NH1" <-> "NH2" Residue "e ARG 42": "NH1" <-> "NH2" Residue "f ARG 24": "NH1" <-> "NH2" Residue "i PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ASP 42": "OD1" <-> "OD2" Residue "i GLU 57": "OE1" <-> "OE2" Residue "i PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ASP 185": "OD1" <-> "OD2" Residue "i ASP 198": "OD1" <-> "OD2" Residue "i GLU 204": "OE1" <-> "OE2" Residue "i ASP 253": "OD1" <-> "OD2" Residue "i PHE 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i GLU 277": "OE1" <-> "OE2" Residue "i GLU 392": "OE1" <-> "OE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 96182 Number of models: 1 Model: "" Number of chains: 47 Chain: "1" Number of atoms: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 926 Classifications: {'RNA': 43} Modifications used: {'rna3p_pur': 26, 'rna3p_pyr': 17} Link IDs: {'rna3p': 42} Chain: "2" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 62 Classifications: {'RNA': 3} Modifications used: {'rna2p_pur': 1, 'rna3p_pyr': 2} Link IDs: {'rna3p': 2} Chain: "A" Number of atoms: 61902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2883, 61902 Classifications: {'RNA': 2883} Modifications used: {'rna2p_pur': 280, 'rna2p_pyr': 149, 'rna3p_pur': 1386, 'rna3p_pyr': 1068} Link IDs: {'rna2p': 429, 'rna3p': 2453} Chain breaks: 4 Chain: "B" Number of atoms: 2569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 2569 Classifications: {'RNA': 120} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 6, 'rna3p_pur': 57, 'rna3p_pyr': 50} Link IDs: {'rna2p': 13, 'rna3p': 106} Chain: "C" Number of atoms: 2083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2083 Classifications: {'peptide': 271} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 253} Chain: "D" Number of atoms: 1565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1565 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 202} Chain: "E" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1552 Classifications: {'peptide': 201} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 195} Chain: "F" Number of atoms: 1411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1411 Classifications: {'peptide': 177} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 170} Chain: "G" Number of atoms: 1323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1323 Classifications: {'peptide': 176} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "H" Number of atoms: 1110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1110 Classifications: {'peptide': 149} Link IDs: {'PTRANS': 3, 'TRANS': 145} Chain: "I" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 946 Classifications: {'peptide': 125} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 120} Chain: "J" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 979 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 9, 'TRANS': 124} Chain: "K" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1129 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 135} Chain: "L" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 946 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 5, 'TRANS': 117} Chain: "M" Number of atoms: 1053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1053 Classifications: {'peptide': 144} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 139} Chain: "N" Number of atoms: 1074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1074 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 128} Chain: "O" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 993 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 4, 'TRANS': 120} Chain: "P" Number of atoms: 900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 900 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 114} Chain: "Q" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 917 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "R" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 947 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'TRANS': 116} Chain: "S" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 816 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'TRANS': 101} Chain: "T" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 857 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 107} Chain: "U" Number of atoms: 756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 756 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 1, 'TRANS': 93} Chain: "V" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 780 Classifications: {'peptide': 102} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "W" Number of atoms: 753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 753 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "X" Number of atoms: 580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 580 Classifications: {'peptide': 76} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 74} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "Y" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 625 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "Z" Number of atoms: 501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 501 Classifications: {'peptide': 62} Modifications used: {'COO': 1} Link IDs: {'TRANS': 61} Chain: "a" Number of atoms: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 449 Classifications: {'peptide': 58} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "b" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 444 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 54} Chain: "c" Number of atoms: 414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 414 Classifications: {'peptide': 51} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 48} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "d" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 377 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "e" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 504 Classifications: {'peptide': 64} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "f" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 302 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "i" Number of atoms: 3036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3036 Classifications: {'peptide': 398} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 13, 'TRANS': 384} Chain breaks: 2 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'UNK:plan-1': 19} Unresolved non-hydrogen planarities: 19 Chain: "k" Number of atoms: 137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 137 Classifications: {'peptide': 18} Link IDs: {'PTRANS': 1, 'TRANS': 16} Chain: "2" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 412, 412 Unusual residues: {' MG': 412} Classifications: {'undetermined': 412} Link IDs: {None: 411} Chain: "B" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Unusual residues: {' MG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "b" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "f" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "i" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GNP': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 92328 SG CYS f 11 72.603 85.821 179.633 1.00 60.00 S ATOM 92353 SG CYS f 14 75.793 87.107 178.504 1.00 60.00 S ATOM 92456 SG CYS f 27 75.991 83.976 180.529 1.00 60.00 S Time building chain proxies: 39.77, per 1000 atoms: 0.41 Number of scatterers: 96182 At special positions: 0 Unit cell: (263.15, 199.44, 240.99, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 102 16.00 P 3052 15.00 Mg 431 11.99 O 26589 8.00 N 17806 7.00 C 48201 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 42.30 Conformation dependent library (CDL) restraints added in 5.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN f 101 " pdb="ZN ZN f 101 " - pdb=" SG CYS f 14 " pdb="ZN ZN f 101 " - pdb=" ND1 HIS f 33 " pdb="ZN ZN f 101 " - pdb=" SG CYS f 11 " pdb="ZN ZN f 101 " - pdb=" SG CYS f 27 " Number of angles added : 3 7642 Ramachandran restraints generated. 3821 Oldfield, 0 Emsley, 3821 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7152 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 126 helices and 49 sheets defined 31.3% alpha, 17.9% beta 1020 base pairs and 1575 stacking pairs defined. Time for finding SS restraints: 49.51 Creating SS restraints... Processing helix chain 'C' and resid 11 through 13 No H-bonds generated for 'chain 'C' and resid 11 through 13' Processing helix chain 'C' and resid 31 through 33 No H-bonds generated for 'chain 'C' and resid 31 through 33' Processing helix chain 'C' and resid 132 through 134 No H-bonds generated for 'chain 'C' and resid 132 through 134' Processing helix chain 'C' and resid 198 through 202 removed outlier: 4.213A pdb=" N MET C 201 " --> pdb=" O ALA C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 214 Processing helix chain 'C' and resid 222 through 224 No H-bonds generated for 'chain 'C' and resid 222 through 224' Processing helix chain 'C' and resid 263 through 266 Processing helix chain 'D' and resid 40 through 43 No H-bonds generated for 'chain 'D' and resid 40 through 43' Processing helix chain 'D' and resid 62 through 71 removed outlier: 3.713A pdb=" N ALA D 71 " --> pdb=" O HIS D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 101 Processing helix chain 'D' and resid 121 through 125 Processing helix chain 'E' and resid 16 through 19 No H-bonds generated for 'chain 'E' and resid 16 through 19' Processing helix chain 'E' and resid 25 through 38 Processing helix chain 'E' and resid 98 through 114 Processing helix chain 'E' and resid 131 through 141 Processing helix chain 'E' and resid 155 through 160 Processing helix chain 'E' and resid 172 through 174 No H-bonds generated for 'chain 'E' and resid 172 through 174' Processing helix chain 'E' and resid 177 through 182 Processing helix chain 'E' and resid 190 through 199 Processing helix chain 'F' and resid 3 through 10 Processing helix chain 'F' and resid 12 through 20 Processing helix chain 'F' and resid 25 through 27 No H-bonds generated for 'chain 'F' and resid 25 through 27' Processing helix chain 'F' and resid 48 through 61 removed outlier: 3.725A pdb=" N ASP F 56 " --> pdb=" O ASN F 52 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 105 Processing helix chain 'F' and resid 108 through 110 No H-bonds generated for 'chain 'F' and resid 108 through 110' Processing helix chain 'F' and resid 143 through 145 No H-bonds generated for 'chain 'F' and resid 143 through 145' Processing helix chain 'F' and resid 163 through 173 Processing helix chain 'G' and resid 61 through 80 Processing helix chain 'G' and resid 138 through 151 removed outlier: 3.661A pdb=" N TYR G 151 " --> pdb=" O ASP G 147 " (cutoff:3.500A) Processing helix chain 'H' and resid 23 through 28 Processing helix chain 'H' and resid 41 through 72 removed outlier: 5.674A pdb=" N ALA H 52 " --> pdb=" O GLU H 48 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N GLU H 53 " --> pdb=" O ALA H 49 " (cutoff:3.500A) Processing helix chain 'H' and resid 86 through 88 No H-bonds generated for 'chain 'H' and resid 86 through 88' Processing helix chain 'H' and resid 96 through 104 Processing helix chain 'H' and resid 112 through 114 No H-bonds generated for 'chain 'H' and resid 112 through 114' Processing helix chain 'I' and resid 5 through 21 Processing helix chain 'I' and resid 35 through 46 Processing helix chain 'I' and resid 57 through 66 removed outlier: 3.934A pdb=" N ARG I 62 " --> pdb=" O THR I 58 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N GLY I 66 " --> pdb=" O ARG I 62 " (cutoff:3.500A) Processing helix chain 'I' and resid 70 through 72 No H-bonds generated for 'chain 'I' and resid 70 through 72' Processing helix chain 'I' and resid 93 through 103 removed outlier: 3.859A pdb=" N LYS I 97 " --> pdb=" O ALA I 93 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLU I 98 " --> pdb=" O ARG I 94 " (cutoff:3.500A) Processing helix chain 'I' and resid 123 through 125 No H-bonds generated for 'chain 'I' and resid 123 through 125' Processing helix chain 'J' and resid 35 through 48 removed outlier: 5.607A pdb=" N SER J 48 " --> pdb=" O ALA J 44 " (cutoff:3.500A) Processing helix chain 'J' and resid 76 through 83 Processing helix chain 'J' and resid 103 through 116 Processing helix chain 'J' and resid 122 through 135 Processing helix chain 'K' and resid 25 through 37 removed outlier: 4.026A pdb=" N GLU K 31 " --> pdb=" O ARG K 27 " (cutoff:3.500A) Processing helix chain 'K' and resid 68 through 71 No H-bonds generated for 'chain 'K' and resid 68 through 71' Processing helix chain 'K' and resid 89 through 108 Proline residue: K 97 - end of helix removed outlier: 4.316A pdb=" N VAL K 100 " --> pdb=" O ARG K 96 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ILE K 101 " --> pdb=" O PRO K 97 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N MET K 108 " --> pdb=" O ALA K 104 " (cutoff:3.500A) Processing helix chain 'K' and resid 113 through 121 removed outlier: 4.047A pdb=" N LYS K 121 " --> pdb=" O ALA K 117 " (cutoff:3.500A) Processing helix chain 'K' and resid 132 through 135 Processing helix chain 'L' and resid 105 through 107 No H-bonds generated for 'chain 'L' and resid 105 through 107' Processing helix chain 'L' and resid 113 through 117 Processing helix chain 'M' and resid 23 through 25 No H-bonds generated for 'chain 'M' and resid 23 through 25' Processing helix chain 'M' and resid 37 through 40 No H-bonds generated for 'chain 'M' and resid 37 through 40' Processing helix chain 'M' and resid 57 through 60 No H-bonds generated for 'chain 'M' and resid 57 through 60' Processing helix chain 'M' and resid 69 through 72 No H-bonds generated for 'chain 'M' and resid 69 through 72' Processing helix chain 'M' and resid 79 through 84 removed outlier: 4.207A pdb=" N ALA M 83 " --> pdb=" O LEU M 79 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N LYS M 84 " --> pdb=" O SER M 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 79 through 84' Processing helix chain 'M' and resid 92 through 97 Processing helix chain 'M' and resid 129 through 136 Processing helix chain 'N' and resid 43 through 56 Processing helix chain 'N' and resid 110 through 123 removed outlier: 4.355A pdb=" N LYS N 123 " --> pdb=" O LEU N 119 " (cutoff:3.500A) Processing helix chain 'O' and resid 14 through 31 Processing helix chain 'O' and resid 38 through 55 removed outlier: 3.713A pdb=" N ARG O 45 " --> pdb=" O ALA O 41 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ARG O 46 " --> pdb=" O LYS O 42 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N VAL O 47 " --> pdb=" O GLU O 43 " (cutoff:3.500A) Proline residue: O 50 - end of helix Processing helix chain 'O' and resid 60 through 70 Processing helix chain 'O' and resid 73 through 81 Processing helix chain 'O' and resid 83 through 86 No H-bonds generated for 'chain 'O' and resid 83 through 86' Processing helix chain 'O' and resid 118 through 123 Processing helix chain 'P' and resid 3 through 20 removed outlier: 4.861A pdb=" N ARG P 13 " --> pdb=" O ARG P 9 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N ALA P 14 " --> pdb=" O ARG P 10 " (cutoff:3.500A) Processing helix chain 'P' and resid 56 through 61 removed outlier: 5.193A pdb=" N GLN P 61 " --> pdb=" O ALA P 57 " (cutoff:3.500A) Processing helix chain 'P' and resid 68 through 83 Processing helix chain 'P' and resid 101 through 112 Processing helix chain 'Q' and resid 3 through 10 Processing helix chain 'Q' and resid 54 through 56 No H-bonds generated for 'chain 'Q' and resid 54 through 56' Processing helix chain 'Q' and resid 98 through 101 Processing helix chain 'Q' and resid 105 through 107 No H-bonds generated for 'chain 'Q' and resid 105 through 107' Processing helix chain 'R' and resid 7 through 20 Processing helix chain 'R' and resid 26 through 30 Processing helix chain 'R' and resid 32 through 71 removed outlier: 3.639A pdb=" N GLN R 37 " --> pdb=" O ARG R 33 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ARG R 51 " --> pdb=" O TYR R 47 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LYS R 54 " --> pdb=" O ARG R 50 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ARG R 55 " --> pdb=" O ARG R 51 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ARG R 58 " --> pdb=" O LYS R 54 " (cutoff:3.500A) Processing helix chain 'R' and resid 76 through 85 Processing helix chain 'R' and resid 92 through 101 Processing helix chain 'R' and resid 103 through 117 Processing helix chain 'T' and resid 14 through 24 removed outlier: 3.554A pdb=" N LEU T 19 " --> pdb=" O GLN T 15 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N VAL T 20 " --> pdb=" O LYS T 16 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU T 23 " --> pdb=" O LEU T 19 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE T 24 " --> pdb=" O VAL T 20 " (cutoff:3.500A) Processing helix chain 'T' and resid 29 through 38 Processing helix chain 'T' and resid 43 through 62 Processing helix chain 'T' and resid 66 through 68 No H-bonds generated for 'chain 'T' and resid 66 through 68' Processing helix chain 'T' and resid 89 through 91 No H-bonds generated for 'chain 'T' and resid 89 through 91' Processing helix chain 'U' and resid 4 through 9 removed outlier: 3.926A pdb=" N LYS U 9 " --> pdb=" O GLU U 5 " (cutoff:3.500A) Processing helix chain 'U' and resid 18 through 26 Processing helix chain 'U' and resid 40 through 50 Processing helix chain 'V' and resid 67 through 69 No H-bonds generated for 'chain 'V' and resid 67 through 69' Processing helix chain 'W' and resid 13 through 22 Processing helix chain 'W' and resid 44 through 50 Processing helix chain 'W' and resid 55 through 58 No H-bonds generated for 'chain 'W' and resid 55 through 58' Processing helix chain 'Y' and resid 53 through 62 Processing helix chain 'Y' and resid 64 through 74 Processing helix chain 'Z' and resid 6 through 8 No H-bonds generated for 'chain 'Z' and resid 6 through 8' Processing helix chain 'Z' and resid 11 through 34 Processing helix chain 'Z' and resid 41 through 62 removed outlier: 3.689A pdb=" N GLN Z 45 " --> pdb=" O HIS Z 41 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ALA Z 51 " --> pdb=" O ARG Z 47 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLU Z 59 " --> pdb=" O THR Z 55 " (cutoff:3.500A) Processing helix chain 'a' and resid 18 through 27 Processing helix chain 'a' and resid 42 through 50 Processing helix chain 'b' and resid 10 through 19 removed outlier: 3.580A pdb=" N ARG b 17 " --> pdb=" O ARG b 13 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N HIS b 19 " --> pdb=" O MET b 15 " (cutoff:3.500A) Processing helix chain 'd' and resid 9 through 16 Processing helix chain 'd' and resid 18 through 22 Processing helix chain 'd' and resid 25 through 37 Processing helix chain 'e' and resid 8 through 13 removed outlier: 3.689A pdb=" N LYS e 12 " --> pdb=" O ARG e 8 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ARG e 13 " --> pdb=" O GLY e 9 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 8 through 13' Processing helix chain 'e' and resid 38 through 45 Processing helix chain 'e' and resid 55 through 61 Processing helix chain 'f' and resid 31 through 33 No H-bonds generated for 'chain 'f' and resid 31 through 33' Processing helix chain 'i' and resid 3 through 18 removed outlier: 3.789A pdb=" N THR i 12 " --> pdb=" O ARG i 8 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLY i 18 " --> pdb=" O ARG i 14 " (cutoff:3.500A) Processing helix chain 'i' and resid 24 through 41 Processing helix chain 'i' and resid 45 through 59 Processing helix chain 'i' and resid 70 through 85 Processing helix chain 'i' and resid 113 through 127 Processing helix chain 'i' and resid 142 through 154 removed outlier: 3.634A pdb=" N LEU i 148 " --> pdb=" O ALA i 144 " (cutoff:3.500A) Processing helix chain 'i' and resid 168 through 181 Processing helix chain 'i' and resid 199 through 212 Processing helix chain 'i' and resid 223 through 239 removed outlier: 6.634A pdb=" N GLN i 227 " --> pdb=" O MET i 224 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N THR i 232 " --> pdb=" O ALA i 229 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N PHE i 236 " --> pdb=" O ALA i 233 " (cutoff:3.500A) Processing helix chain 'i' and resid 257 through 266 removed outlier: 4.820A pdb=" N ARG i 263 " --> pdb=" O ALA i 259 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N HIS i 264 " --> pdb=" O LEU i 260 " (cutoff:3.500A) Processing helix chain 'i' and resid 287 through 294 Processing helix chain 'i' and resid 331 through 341 Processing helix chain 'i' and resid 370 through 382 Processing helix chain 'i' and resid 385 through 389 Processing helix chain 'i' and resid 391 through 393 No H-bonds generated for 'chain 'i' and resid 391 through 393' Processing helix chain 'i' and resid 396 through 405 Processing helix chain 'i' and resid 410 through 432 Processing helix chain 'i' and resid 435 through 440 Processing helix chain 'k' and resid 28 through 43 removed outlier: 3.508A pdb=" N LEU k 36 " --> pdb=" O LEU k 32 " (cutoff:3.500A) Proline residue: k 43 - end of helix Processing sheet with id= A, first strand: chain 'C' and resid 3 through 5 Processing sheet with id= B, first strand: chain 'C' and resid 101 through 105 removed outlier: 3.525A pdb=" N ARG C 80 " --> pdb=" O LEU C 93 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LEU C 95 " --> pdb=" O VAL C 78 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N VAL C 78 " --> pdb=" O LEU C 95 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 129 through 131 Processing sheet with id= D, first strand: chain 'C' and resid 181 through 185 removed outlier: 6.540A pdb=" N ARG C 175 " --> pdb=" O ILE C 164 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N ILE C 164 " --> pdb=" O ARG C 175 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'D' and resid 169 through 172 removed outlier: 4.533A pdb=" N THR D 112 " --> pdb=" O ASP D 200 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N ASP D 200 " --> pdb=" O THR D 112 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N VAL D 26 " --> pdb=" O VAL D 9 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N MET D 11 " --> pdb=" O VAL D 24 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N VAL D 24 " --> pdb=" O MET D 11 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N ARG D 13 " --> pdb=" O ILE D 22 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ILE D 22 " --> pdb=" O ARG D 13 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N LYS D 190 " --> pdb=" O VAL D 177 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N VAL D 177 " --> pdb=" O LYS D 190 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'D' and resid 80 through 83 removed outlier: 6.548A pdb=" N THR D 51 " --> pdb=" O VAL D 34 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N VAL D 34 " --> pdb=" O THR D 51 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'E' and resid 2 through 4 Processing sheet with id= H, first strand: chain 'E' and resid 118 through 121 removed outlier: 6.373A pdb=" N VAL E 186 " --> pdb=" O ILE E 119 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N VAL E 121 " --> pdb=" O VAL E 186 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N MET E 188 " --> pdb=" O VAL E 121 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'F' and resid 128 through 132 removed outlier: 6.844A pdb=" N THR F 68 " --> pdb=" O ILE F 85 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N CYS F 87 " --> pdb=" O LEU F 66 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N LEU F 66 " --> pdb=" O CYS F 87 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'G' and resid 16 through 20 Processing sheet with id= K, first strand: chain 'G' and resid 41 through 45 Processing sheet with id= L, first strand: chain 'G' and resid 161 through 164 Processing sheet with id= M, first strand: chain 'G' and resid 95 through 99 Processing sheet with id= N, first strand: chain 'H' and resid 18 through 20 Processing sheet with id= O, first strand: chain 'H' and resid 78 through 82 removed outlier: 3.720A pdb=" N VAL H 147 " --> pdb=" O ILE H 80 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'I' and resid 116 through 118 removed outlier: 3.625A pdb=" N ALA I 110 " --> pdb=" O VAL I 27 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA I 25 " --> pdb=" O ALA I 112 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N SER I 24 " --> pdb=" O VAL I 85 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'J' and resid 9 through 14 Processing sheet with id= R, first strand: chain 'K' and resid 15 through 19 removed outlier: 6.641A pdb=" N TYR K 53 " --> pdb=" O TYR K 16 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N VAL K 18 " --> pdb=" O TYR K 53 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N ILE K 55 " --> pdb=" O VAL K 18 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'K' and resid 73 through 77 Processing sheet with id= T, first strand: chain 'L' and resid 19 through 24 removed outlier: 6.689A pdb=" N LYS L 40 " --> pdb=" O ILE L 22 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N VAL L 24 " --> pdb=" O ILE L 38 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N ILE L 38 " --> pdb=" O VAL L 24 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ALA L 83 " --> pdb=" O VAL L 63 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'M' and resid 74 through 77 removed outlier: 6.282A pdb=" N PHE M 107 " --> pdb=" O ALA M 75 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N ILE M 77 " --> pdb=" O PHE M 107 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N LYS M 109 " --> pdb=" O ILE M 77 " (cutoff:3.500A) No H-bonds generated for sheet with id= U Processing sheet with id= V, first strand: chain 'M' and resid 121 through 123 removed outlier: 6.688A pdb=" N LYS M 141 " --> pdb=" O VAL M 122 " (cutoff:3.500A) No H-bonds generated for sheet with id= V Processing sheet with id= W, first strand: chain 'N' and resid 128 through 132 removed outlier: 3.720A pdb=" N TYR N 103 " --> pdb=" O LEU N 33 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ALA N 35 " --> pdb=" O VAL N 101 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N VAL N 101 " --> pdb=" O ALA N 35 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'N' and resid 39 through 42 removed outlier: 3.513A pdb=" N ASN N 88 " --> pdb=" O GLU N 75 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ILE N 73 " --> pdb=" O GLU N 90 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N TRP N 92 " --> pdb=" O LYS N 71 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N LYS N 71 " --> pdb=" O TRP N 92 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'O' and resid 33 through 37 removed outlier: 3.700A pdb=" N ALA O 108 " --> pdb=" O ARG O 103 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N GLY O 101 " --> pdb=" O MET O 110 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N TYR O 112 " --> pdb=" O LYS O 99 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N LYS O 99 " --> pdb=" O TYR O 112 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N GLU O 114 " --> pdb=" O ILE O 97 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N ILE O 97 " --> pdb=" O GLU O 114 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'P' and resid 91 through 93 removed outlier: 3.551A pdb=" N VAL P 49 " --> pdb=" O VAL P 39 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'Q' and resid 83 through 88 removed outlier: 6.881A pdb=" N THR Q 25 " --> pdb=" O LYS Q 87 " (cutoff:3.500A) removed outlier: 9.098A pdb=" N GLU Q 44 " --> pdb=" O ILE Q 64 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N ILE Q 64 " --> pdb=" O GLU Q 44 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N THR Q 60 " --> pdb=" O ILE Q 48 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N ILE Q 50 " --> pdb=" O ALA Q 58 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N ALA Q 58 " --> pdb=" O ILE Q 50 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'S' and resid 10 through 14 removed outlier: 6.964A pdb=" N GLN S 6 " --> pdb=" O VAL S 38 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N VAL S 38 " --> pdb=" O GLN S 6 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'S' and resid 19 through 23 Processing sheet with id= AD, first strand: chain 'S' and resid 32 through 35 removed outlier: 6.484A pdb=" N GLU S 62 " --> pdb=" O ILE S 98 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N ILE S 98 " --> pdb=" O GLU S 62 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'S' and resid 72 through 78 removed outlier: 4.209A pdb=" N TYR S 83 " --> pdb=" O ARG S 78 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'T' and resid 2 through 7 removed outlier: 6.839A pdb=" N SER T 108 " --> pdb=" O VAL T 71 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N VAL T 71 " --> pdb=" O SER T 108 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'T' and resid 82 through 87 Processing sheet with id= AH, first strand: chain 'U' and resid 11 through 14 removed outlier: 6.843A pdb=" N LYS U 33 " --> pdb=" O ARG U 12 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N VAL U 31 " --> pdb=" O PRO U 14 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LYS U 81 " --> pdb=" O VAL U 34 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL U 57 " --> pdb=" O THR U 86 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'U' and resid 67 through 70 Processing sheet with id= AJ, first strand: chain 'V' and resid 22 through 24 Processing sheet with id= AK, first strand: chain 'V' and resid 41 through 45 Processing sheet with id= AL, first strand: chain 'V' and resid 83 through 88 Processing sheet with id= AM, first strand: chain 'V' and resid 25 through 28 removed outlier: 7.135A pdb=" N ILE V 35 " --> pdb=" O LYS V 26 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'W' and resid 3 through 6 removed outlier: 6.567A pdb=" N THR W 62 " --> pdb=" O ILE W 4 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N ALA W 6 " --> pdb=" O THR W 62 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N VAL W 64 " --> pdb=" O ALA W 6 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ASP W 90 " --> pdb=" O GLN W 75 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N VAL W 77 " --> pdb=" O HIS W 88 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N HIS W 88 " --> pdb=" O VAL W 77 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ILE W 89 " --> pdb=" O PRO W 27 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'X' and resid 45 through 47 removed outlier: 7.252A pdb=" N LYS X 78 " --> pdb=" O HIS X 46 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'X' and resid 51 through 53 Processing sheet with id= AQ, first strand: chain 'Y' and resid 13 through 18 Processing sheet with id= AR, first strand: chain 'Y' and resid 33 through 40 Processing sheet with id= AS, first strand: chain 'a' and resid 35 through 38 Processing sheet with id= AT, first strand: chain 'c' and resid 20 through 25 Processing sheet with id= AU, first strand: chain 'f' and resid 2 through 4 Processing sheet with id= AV, first strand: chain 'f' and resid 14 through 19 Processing sheet with id= AW, first strand: chain 'i' and resid 282 through 284 removed outlier: 8.074A pdb=" N VAL i 245 " --> pdb=" O LYS i 271 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N LEU i 273 " --> pdb=" O VAL i 245 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N LEU i 247 " --> pdb=" O LEU i 273 " (cutoff:3.500A) 1103 hydrogen bonds defined for protein. 3105 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2566 hydrogen bonds 4034 hydrogen bond angles 0 basepair planarities 1020 basepair parallelities 1575 stacking parallelities Total time for adding SS restraints: 179.37 Time building geometry restraints manager: 45.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.34: 18939 1.34 - 1.47: 43891 1.47 - 1.60: 38193 1.60 - 1.74: 2783 1.74 - 1.87: 189 Bond restraints: 103995 Sorted by residual: bond pdb=" CA LYS U 88 " pdb=" C LYS U 88 " ideal model delta sigma weight residual 1.525 1.742 -0.218 1.32e-02 5.74e+03 2.72e+02 bond pdb=" C LYS U 88 " pdb=" N GLU U 89 " ideal model delta sigma weight residual 1.332 1.465 -0.133 1.40e-02 5.10e+03 8.98e+01 bond pdb=" N GLU U 89 " pdb=" CA GLU U 89 " ideal model delta sigma weight residual 1.457 1.539 -0.082 1.29e-02 6.01e+03 4.03e+01 bond pdb=" CA PRO J 22 " pdb=" C PRO J 22 " ideal model delta sigma weight residual 1.517 1.570 -0.053 9.30e-03 1.16e+04 3.29e+01 bond pdb=" CA VAL F 108 " pdb=" CB VAL F 108 " ideal model delta sigma weight residual 1.534 1.572 -0.037 6.80e-03 2.16e+04 2.96e+01 ... (remaining 103990 not shown) Histogram of bond angle deviations from ideal: 94.94 - 102.96: 6038 102.96 - 110.99: 55022 110.99 - 119.02: 44102 119.02 - 127.05: 42758 127.05 - 135.07: 7597 Bond angle restraints: 155517 Sorted by residual: angle pdb=" CA LYS U 88 " pdb=" C LYS U 88 " pdb=" N GLU U 89 " ideal model delta sigma weight residual 115.51 129.22 -13.71 1.27e+00 6.20e-01 1.17e+02 angle pdb=" C LEU i 240 " pdb=" N PRO i 241 " pdb=" CA PRO i 241 " ideal model delta sigma weight residual 119.84 133.17 -13.33 1.25e+00 6.40e-01 1.14e+02 angle pdb=" C LYS U 88 " pdb=" CA LYS U 88 " pdb=" CB LYS U 88 " ideal model delta sigma weight residual 109.54 128.07 -18.53 1.84e+00 2.95e-01 1.01e+02 angle pdb=" C GLU G 155 " pdb=" N PRO G 156 " pdb=" CA PRO G 156 " ideal model delta sigma weight residual 119.82 129.02 -9.20 9.80e-01 1.04e+00 8.81e+01 angle pdb=" N ASP J 116 " pdb=" CA ASP J 116 " pdb=" C ASP J 116 " ideal model delta sigma weight residual 113.17 123.21 -10.04 1.26e+00 6.30e-01 6.34e+01 ... (remaining 155512 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.38: 58059 35.38 - 70.77: 7632 70.77 - 106.15: 844 106.15 - 141.54: 16 141.54 - 176.92: 10 Dihedral angle restraints: 66561 sinusoidal: 55472 harmonic: 11089 Sorted by residual: dihedral pdb=" CA LEU i 240 " pdb=" C LEU i 240 " pdb=" N PRO i 241 " pdb=" CA PRO i 241 " ideal model delta harmonic sigma weight residual 180.00 125.46 54.54 0 5.00e+00 4.00e-02 1.19e+02 dihedral pdb=" C4' U A1344 " pdb=" C3' U A1344 " pdb=" C2' U A1344 " pdb=" C1' U A1344 " ideal model delta sinusoidal sigma weight residual -35.00 32.01 -67.01 1 8.00e+00 1.56e-02 9.14e+01 dihedral pdb=" C4' C A 645 " pdb=" C3' C A 645 " pdb=" C2' C A 645 " pdb=" C1' C A 645 " ideal model delta sinusoidal sigma weight residual -35.00 30.64 -65.64 1 8.00e+00 1.56e-02 8.81e+01 ... (remaining 66558 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 17875 0.074 - 0.149: 1879 0.149 - 0.223: 141 0.223 - 0.298: 11 0.298 - 0.372: 4 Chirality restraints: 19910 Sorted by residual: chirality pdb=" C3' C A 645 " pdb=" C4' C A 645 " pdb=" O3' C A 645 " pdb=" C2' C A 645 " both_signs ideal model delta sigma weight residual False -2.74 -2.37 -0.37 2.00e-01 2.50e+01 3.47e+00 chirality pdb=" C3' U A1344 " pdb=" C4' U A1344 " pdb=" O3' U A1344 " pdb=" C2' U A1344 " both_signs ideal model delta sigma weight residual False -2.74 -2.38 -0.36 2.00e-01 2.50e+01 3.31e+00 chirality pdb=" C1' U 1 37 " pdb=" O4' U 1 37 " pdb=" C2' U 1 37 " pdb=" N1 U 1 37 " both_signs ideal model delta sigma weight residual False 2.47 2.16 0.30 2.00e-01 2.50e+01 2.32e+00 ... (remaining 19907 not shown) Planarity restraints: 8357 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY J 25 " -0.059 5.00e-02 4.00e+02 9.01e-02 1.30e+01 pdb=" N PRO J 26 " 0.156 5.00e-02 4.00e+02 pdb=" CA PRO J 26 " -0.050 5.00e-02 4.00e+02 pdb=" CD PRO J 26 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU i 240 " -0.057 5.00e-02 4.00e+02 8.44e-02 1.14e+01 pdb=" N PRO i 241 " 0.146 5.00e-02 4.00e+02 pdb=" CA PRO i 241 " -0.050 5.00e-02 4.00e+02 pdb=" CD PRO i 241 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' A A 984 " -0.046 2.00e-02 2.50e+03 1.92e-02 1.02e+01 pdb=" N9 A A 984 " 0.035 2.00e-02 2.50e+03 pdb=" C8 A A 984 " 0.012 2.00e-02 2.50e+03 pdb=" N7 A A 984 " -0.001 2.00e-02 2.50e+03 pdb=" C5 A A 984 " -0.002 2.00e-02 2.50e+03 pdb=" C6 A A 984 " -0.011 2.00e-02 2.50e+03 pdb=" N6 A A 984 " -0.008 2.00e-02 2.50e+03 pdb=" N1 A A 984 " -0.008 2.00e-02 2.50e+03 pdb=" C2 A A 984 " 0.004 2.00e-02 2.50e+03 pdb=" N3 A A 984 " 0.015 2.00e-02 2.50e+03 pdb=" C4 A A 984 " 0.010 2.00e-02 2.50e+03 ... (remaining 8354 not shown) Histogram of nonbonded interaction distances: 1.27 - 1.99: 40 1.99 - 2.72: 9775 2.72 - 3.45: 124637 3.45 - 4.17: 322639 4.17 - 4.90: 432329 Nonbonded interactions: 889420 Sorted by model distance: nonbonded pdb=" O2' C A 96 " pdb=" CE1 HIS Z 41 " model vdw 1.266 3.260 nonbonded pdb=" O2' C A 96 " pdb=" NE2 HIS Z 41 " model vdw 1.478 2.520 nonbonded pdb=" OP1 A A 751 " pdb="MG MG A3020 " model vdw 1.738 2.170 nonbonded pdb=" OP1 U A 827 " pdb="MG MG A3027 " model vdw 1.759 2.170 nonbonded pdb=" OP2 U A 963 " pdb="MG MG A3030 " model vdw 1.771 2.170 ... (remaining 889415 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 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: 1.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.090 Extract box with map and model: 9.450 Check model and map are aligned: 1.140 Set scattering table: 0.680 Process input model: 391.650 Find NCS groups from input model: 1.790 Set up NCS constraints: 0.230 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 409.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6336 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 0.218 103995 Z= 0.446 Angle : 1.094 18.533 155517 Z= 0.625 Chirality : 0.047 0.372 19910 Planarity : 0.005 0.090 8357 Dihedral : 23.645 176.919 59409 Min Nonbonded Distance : 1.266 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.48 % Favored : 96.41 % Rotamer: Outliers : 11.04 % Allowed : 12.44 % Favored : 76.52 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 1.59 % Twisted General : 0.08 % 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: -3.28 (0.11), residues: 3821 helix: -3.18 (0.10), residues: 1229 sheet: -1.40 (0.16), residues: 734 loop : -1.65 (0.11), residues: 1858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP C 248 HIS 0.010 0.002 HIS K 130 PHE 0.026 0.002 PHE I 106 TYR 0.030 0.003 TYR T 38 ARG 0.005 0.001 ARG N 6 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7642 Ramachandran restraints generated. 3821 Oldfield, 0 Emsley, 3821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7642 Ramachandran restraints generated. 3821 Oldfield, 0 Emsley, 3821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1719 residues out of total 3147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 347 poor density : 1372 time to evaluate : 4.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 72 ASP cc_start: 0.5363 (OUTLIER) cc_final: 0.3833 (t70) REVERT: C 85 PRO cc_start: 0.6839 (Cg_endo) cc_final: 0.6589 (Cg_exo) REVERT: C 134 ASN cc_start: 0.4071 (OUTLIER) cc_final: 0.3442 (m-40) REVERT: C 146 MET cc_start: 0.5627 (mtm) cc_final: 0.5416 (mpp) REVERT: C 156 ARG cc_start: 0.5399 (OUTLIER) cc_final: 0.5099 (mtm180) REVERT: C 180 GLU cc_start: 0.5249 (OUTLIER) cc_final: 0.4697 (tm-30) REVERT: C 230 HIS cc_start: 0.8662 (t-90) cc_final: 0.7713 (t-90) REVERT: D 43 ASP cc_start: 0.6057 (m-30) cc_final: 0.5801 (m-30) REVERT: D 125 TRP cc_start: 0.8870 (m100) cc_final: 0.8336 (m100) REVERT: D 149 ASN cc_start: 0.9103 (t0) cc_final: 0.8508 (t0) REVERT: E 24 ASN cc_start: 0.3554 (t0) cc_final: 0.3341 (t0) REVERT: E 27 LEU cc_start: 0.7796 (tp) cc_final: 0.7279 (tp) REVERT: E 46 GLN cc_start: 0.9193 (mp10) cc_final: 0.8794 (mp10) REVERT: E 63 LYS cc_start: 0.8189 (mtpp) cc_final: 0.7466 (mttp) REVERT: E 84 THR cc_start: 0.8923 (OUTLIER) cc_final: 0.8571 (p) REVERT: E 167 VAL cc_start: 0.6608 (t) cc_final: 0.6372 (t) REVERT: E 179 SER cc_start: 0.8021 (OUTLIER) cc_final: 0.7586 (t) REVERT: E 197 GLU cc_start: 0.7951 (mt-10) cc_final: 0.7390 (tm-30) REVERT: F 96 MET cc_start: 0.3677 (ttp) cc_final: 0.2521 (ttp) REVERT: F 138 PHE cc_start: 0.4826 (m-80) cc_final: 0.4307 (m-80) REVERT: F 144 ASP cc_start: 0.3720 (OUTLIER) cc_final: 0.2950 (m-30) REVERT: G 43 VAL cc_start: 0.7179 (OUTLIER) cc_final: 0.6359 (p) REVERT: G 75 MET cc_start: 0.8151 (mtp) cc_final: 0.7718 (mtp) REVERT: G 103 ILE cc_start: 0.8968 (mt) cc_final: 0.8560 (tp) REVERT: G 151 TYR cc_start: 0.8380 (m-10) cc_final: 0.7863 (m-80) REVERT: G 164 TYR cc_start: 0.7673 (m-80) cc_final: 0.6663 (m-80) REVERT: I 69 PHE cc_start: 0.4735 (m-80) cc_final: 0.4453 (m-80) REVERT: K 77 HIS cc_start: 0.8870 (t-90) cc_final: 0.8104 (t-90) REVERT: L 7 MET cc_start: 0.6860 (mmt) cc_final: 0.6029 (tpp) REVERT: L 8 LEU cc_start: 0.6992 (mp) cc_final: 0.6757 (mp) REVERT: L 19 VAL cc_start: 0.5957 (m) cc_final: 0.5707 (t) REVERT: L 24 VAL cc_start: 0.8892 (t) cc_final: 0.8684 (p) REVERT: L 65 THR cc_start: 0.6674 (OUTLIER) cc_final: 0.6192 (p) REVERT: M 94 THR cc_start: 0.8019 (m) cc_final: 0.7182 (p) REVERT: N 70 ASP cc_start: 0.8061 (p0) cc_final: 0.7764 (p0) REVERT: N 92 TRP cc_start: 0.8033 (m100) cc_final: 0.7090 (m100) REVERT: N 101 VAL cc_start: 0.8673 (t) cc_final: 0.8233 (m) REVERT: N 117 PHE cc_start: 0.8523 (m-10) cc_final: 0.7313 (m-10) REVERT: N 133 LYS cc_start: 0.7077 (OUTLIER) cc_final: 0.6785 (tptm) REVERT: O 16 HIS cc_start: 0.6461 (t-170) cc_final: 0.5636 (t-170) REVERT: O 42 LYS cc_start: 0.7674 (mttt) cc_final: 0.7370 (mtmt) REVERT: O 78 LYS cc_start: 0.6475 (tttt) cc_final: 0.6263 (tttm) REVERT: P 55 GLU cc_start: 0.1347 (OUTLIER) cc_final: 0.0335 (tp30) REVERT: Q 55 LEU cc_start: 0.6922 (tp) cc_final: 0.6318 (mm) REVERT: Q 65 SER cc_start: 0.5504 (OUTLIER) cc_final: 0.4751 (m) REVERT: Q 76 THR cc_start: 0.7177 (m) cc_final: 0.6969 (p) REVERT: R 24 TYR cc_start: 0.6658 (OUTLIER) cc_final: 0.6381 (m-10) REVERT: R 72 ASN cc_start: 0.7966 (m-40) cc_final: 0.6913 (t0) REVERT: T 77 ASP cc_start: 0.7448 (m-30) cc_final: 0.7162 (m-30) REVERT: W 26 PHE cc_start: 0.7156 (p90) cc_final: 0.6768 (p90) REVERT: W 38 LEU cc_start: 0.6238 (tp) cc_final: 0.6034 (tp) REVERT: W 73 LYS cc_start: 0.7032 (mtpt) cc_final: 0.6727 (mtpt) REVERT: X 26 PHE cc_start: 0.5577 (m-80) cc_final: 0.4975 (m-10) REVERT: X 56 ASP cc_start: 0.6357 (OUTLIER) cc_final: 0.6071 (p0) REVERT: X 85 GLU cc_start: 0.5495 (OUTLIER) cc_final: 0.5293 (mt-10) REVERT: Y 23 ASN cc_start: 0.8589 (m110) cc_final: 0.8328 (m110) REVERT: Y 27 ARG cc_start: 0.8136 (ptm160) cc_final: 0.7749 (ptm160) REVERT: Y 30 LEU cc_start: 0.8988 (mt) cc_final: 0.8700 (mp) REVERT: Y 68 LEU cc_start: 0.9120 (mt) cc_final: 0.8762 (tp) REVERT: Y 77 LYS cc_start: 0.7050 (OUTLIER) cc_final: 0.6065 (mmtt) REVERT: Z 46 VAL cc_start: 0.6745 (t) cc_final: 0.6392 (p) REVERT: Z 48 ARG cc_start: 0.7421 (OUTLIER) cc_final: 0.6760 (tpp-160) REVERT: a 27 LEU cc_start: 0.5964 (mt) cc_final: 0.5580 (mp) REVERT: a 41 THR cc_start: 0.7172 (p) cc_final: 0.6546 (p) REVERT: b 20 ASP cc_start: 0.6788 (m-30) cc_final: 0.6564 (m-30) REVERT: d 26 ASN cc_start: 0.8799 (m110) cc_final: 0.8340 (m110) REVERT: e 5 LYS cc_start: 0.7866 (mttt) cc_final: 0.7638 (mttm) REVERT: e 6 THR cc_start: 0.7810 (m) cc_final: 0.7486 (p) REVERT: f 7 VAL cc_start: 0.9141 (m) cc_final: 0.8939 (p) REVERT: i 124 LEU cc_start: 0.0631 (OUTLIER) cc_final: 0.0256 (mp) REVERT: i 185 ASP cc_start: 0.3123 (OUTLIER) cc_final: 0.2199 (m-30) REVERT: i 240 LEU cc_start: -0.1999 (OUTLIER) cc_final: -0.2572 (mt) outliers start: 347 outliers final: 52 residues processed: 1579 average time/residue: 1.0583 time to fit residues: 2723.4503 Evaluate side-chains 822 residues out of total 3147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 750 time to evaluate : 4.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 679 random chunks: chunk 573 optimal weight: 6.9990 chunk 514 optimal weight: 10.0000 chunk 285 optimal weight: 10.0000 chunk 175 optimal weight: 30.0000 chunk 347 optimal weight: 5.9990 chunk 274 optimal weight: 9.9990 chunk 532 optimal weight: 5.9990 chunk 205 optimal weight: 9.9990 chunk 323 optimal weight: 5.9990 chunk 396 optimal weight: 6.9990 chunk 616 optimal weight: 4.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 58 HIS C 117 GLN C 153 GLN ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 140 HIS D 173 GLN E 195 GLN F 63 GLN G 20 ASN G 30 ASN ** G 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 11 ASN H 66 ASN H 73 ASN L 93 GLN M 35 HIS M 54 GLN N 3 GLN N 13 HIS O 9 GLN O 62 ASN P 100 HIS Q 10 GLN Q 52 ASN Q 56 HIS Q 66 ASN ** T 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 15 GLN T 31 GLN ** W 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 78 GLN ** Z 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 41 HIS ** Z 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 19 HIS ** d 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 24 HIS f 35 GLN i 26 ASN i 62 HIS ** i 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 147 GLN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7130 moved from start: 0.4584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.188 103995 Z= 0.312 Angle : 0.814 14.366 155517 Z= 0.412 Chirality : 0.043 0.323 19910 Planarity : 0.007 0.112 8357 Dihedral : 23.600 179.529 51869 Min Nonbonded Distance : 1.608 Molprobity Statistics. All-atom Clashscore : 19.20 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.41 % Favored : 97.44 % Rotamer: Outliers : 0.16 % Allowed : 6.27 % Favored : 93.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.79 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.12), residues: 3821 helix: -0.94 (0.13), residues: 1221 sheet: -0.71 (0.17), residues: 755 loop : -0.99 (0.13), residues: 1845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP G 62 HIS 0.014 0.002 HIS W 80 PHE 0.025 0.003 PHE i 51 TYR 0.026 0.003 TYR F 7 ARG 0.011 0.001 ARG T 95 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7642 Ramachandran restraints generated. 3821 Oldfield, 0 Emsley, 3821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7642 Ramachandran restraints generated. 3821 Oldfield, 0 Emsley, 3821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1036 residues out of total 3147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 1031 time to evaluate : 4.450 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: C 15 HIS cc_start: 0.7428 (m-70) cc_final: 0.7187 (m170) REVERT: C 202 LEU cc_start: 0.6745 (mt) cc_final: 0.6514 (mt) REVERT: C 230 HIS cc_start: 0.8621 (t-90) cc_final: 0.8141 (t-90) REVERT: D 11 MET cc_start: 0.6757 (ttm) cc_final: 0.5152 (tpp) REVERT: D 49 GLN cc_start: 0.5995 (tt0) cc_final: 0.4927 (tt0) REVERT: D 125 TRP cc_start: 0.9015 (m100) cc_final: 0.8447 (m100) REVERT: D 149 ASN cc_start: 0.8700 (t0) cc_final: 0.8460 (t0) REVERT: D 161 MET cc_start: 0.7381 (mtp) cc_final: 0.6448 (mtp) REVERT: D 199 SER cc_start: 0.9180 (p) cc_final: 0.8923 (m) REVERT: E 27 LEU cc_start: 0.8609 (tp) cc_final: 0.8104 (tp) REVERT: E 46 GLN cc_start: 0.9163 (mp10) cc_final: 0.8825 (mp10) REVERT: E 57 LYS cc_start: 0.8642 (tptt) cc_final: 0.8426 (tptt) REVERT: E 84 THR cc_start: 0.9388 (p) cc_final: 0.9100 (p) REVERT: E 165 HIS cc_start: 0.7205 (t-90) cc_final: 0.6599 (t-170) REVERT: E 197 GLU cc_start: 0.8485 (mt-10) cc_final: 0.8102 (tm-30) REVERT: F 138 PHE cc_start: 0.5802 (m-80) cc_final: 0.5484 (m-80) REVERT: F 141 ILE cc_start: 0.3162 (mp) cc_final: 0.2850 (mt) REVERT: G 75 MET cc_start: 0.8663 (mtp) cc_final: 0.8121 (mtm) REVERT: G 151 TYR cc_start: 0.8461 (m-10) cc_final: 0.7922 (m-80) REVERT: G 153 ARG cc_start: 0.8276 (ttp80) cc_final: 0.8036 (ttp80) REVERT: H 42 LYS cc_start: 0.7486 (tptm) cc_final: 0.7253 (tptp) REVERT: H 43 ASN cc_start: 0.6950 (m-40) cc_final: 0.6191 (m-40) REVERT: H 116 ARG cc_start: 0.7102 (mmt-90) cc_final: 0.6691 (tmt170) REVERT: I 69 PHE cc_start: 0.5608 (m-80) cc_final: 0.5229 (m-80) REVERT: K 1 MET cc_start: 0.8837 (tpp) cc_final: 0.8333 (tpt) REVERT: K 54 ILE cc_start: 0.9456 (mt) cc_final: 0.9125 (mm) REVERT: K 60 ASP cc_start: 0.8002 (p0) cc_final: 0.7693 (p0) REVERT: L 2 ILE cc_start: 0.8566 (mm) cc_final: 0.8292 (tp) REVERT: L 3 GLN cc_start: 0.8763 (pt0) cc_final: 0.8334 (pt0) REVERT: L 7 MET cc_start: 0.8225 (mmt) cc_final: 0.7882 (tpp) REVERT: L 8 LEU cc_start: 0.8293 (mp) cc_final: 0.7641 (mp) REVERT: L 87 LEU cc_start: 0.9161 (mt) cc_final: 0.8760 (mt) REVERT: M 5 THR cc_start: 0.8918 (m) cc_final: 0.8705 (p) REVERT: M 50 PHE cc_start: 0.8988 (t80) cc_final: 0.8612 (t80) REVERT: M 55 MET cc_start: 0.9084 (tpt) cc_final: 0.8748 (tpt) REVERT: M 79 LEU cc_start: 0.8169 (mt) cc_final: 0.7857 (mt) REVERT: M 103 ILE cc_start: 0.8939 (mm) cc_final: 0.8600 (mt) REVERT: N 70 ASP cc_start: 0.8297 (p0) cc_final: 0.8066 (p0) REVERT: N 92 TRP cc_start: 0.8247 (m100) cc_final: 0.7804 (m100) REVERT: O 24 MET cc_start: 0.6791 (mtt) cc_final: 0.6409 (mtt) REVERT: O 38 LEU cc_start: 0.9148 (tp) cc_final: 0.8863 (tp) REVERT: O 47 VAL cc_start: 0.8408 (t) cc_final: 0.8177 (p) REVERT: Q 76 THR cc_start: 0.8981 (m) cc_final: 0.8675 (p) REVERT: R 32 TYR cc_start: 0.8270 (t80) cc_final: 0.8020 (t80) REVERT: R 72 ASN cc_start: 0.7797 (m-40) cc_final: 0.7430 (t0) REVERT: S 43 ASN cc_start: 0.6743 (m-40) cc_final: 0.5809 (m-40) REVERT: S 81 LYS cc_start: 0.9312 (mmtm) cc_final: 0.8967 (mmmm) REVERT: T 1 MET cc_start: 0.3775 (ppp) cc_final: 0.3182 (ptm) REVERT: T 86 MET cc_start: 0.6401 (tpt) cc_final: 0.5822 (tpt) REVERT: T 88 ARG cc_start: 0.8650 (mmm-85) cc_final: 0.8333 (mtp85) REVERT: T 102 HIS cc_start: 0.8335 (m-70) cc_final: 0.6827 (m-70) REVERT: V 6 ARG cc_start: 0.7568 (mtm180) cc_final: 0.7292 (ttp-110) REVERT: W 1 MET cc_start: 0.6839 (tmm) cc_final: 0.6517 (tmm) REVERT: W 20 LEU cc_start: 0.7405 (mt) cc_final: 0.7123 (tp) REVERT: W 87 GLN cc_start: 0.8742 (mp10) cc_final: 0.8135 (mp10) REVERT: X 21 LEU cc_start: 0.9037 (mp) cc_final: 0.8732 (mt) REVERT: X 26 PHE cc_start: 0.7136 (m-80) cc_final: 0.6707 (m-10) REVERT: X 77 ARG cc_start: 0.7088 (mtt180) cc_final: 0.6670 (mtt180) REVERT: Y 23 ASN cc_start: 0.8866 (m110) cc_final: 0.7971 (p0) REVERT: Y 26 LYS cc_start: 0.8820 (mmtt) cc_final: 0.8369 (mmmt) REVERT: Y 30 LEU cc_start: 0.9349 (mt) cc_final: 0.9051 (mp) REVERT: Y 33 LEU cc_start: 0.8756 (mt) cc_final: 0.8467 (mp) REVERT: Y 68 LEU cc_start: 0.9224 (mt) cc_final: 0.8977 (mt) REVERT: Z 37 LEU cc_start: 0.7277 (tp) cc_final: 0.6703 (mt) REVERT: Z 49 ASP cc_start: 0.8062 (t0) cc_final: 0.7784 (t0) REVERT: b 9 THR cc_start: 0.9213 (t) cc_final: 0.9000 (m) REVERT: b 20 ASP cc_start: 0.8347 (m-30) cc_final: 0.8045 (m-30) REVERT: b 49 TYR cc_start: 0.4447 (t80) cc_final: 0.4133 (t80) REVERT: d 26 ASN cc_start: 0.9031 (m110) cc_final: 0.8446 (m110) REVERT: f 13 ASN cc_start: 0.8743 (m110) cc_final: 0.7918 (t0) REVERT: i 176 LEU cc_start: 0.4054 (pp) cc_final: 0.3664 (tp) REVERT: i 297 MET cc_start: 0.3293 (tpt) cc_final: 0.2724 (mmm) REVERT: k 27 MET cc_start: 0.4705 (ppp) cc_final: 0.1749 (mmt) outliers start: 5 outliers final: 2 residues processed: 1035 average time/residue: 0.9748 time to fit residues: 1691.2423 Evaluate side-chains 734 residues out of total 3147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 732 time to evaluate : 4.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 679 random chunks: chunk 342 optimal weight: 8.9990 chunk 191 optimal weight: 20.0000 chunk 513 optimal weight: 10.0000 chunk 419 optimal weight: 0.4980 chunk 170 optimal weight: 10.0000 chunk 617 optimal weight: 20.0000 chunk 667 optimal weight: 7.9990 chunk 550 optimal weight: 6.9990 chunk 612 optimal weight: 10.0000 chunk 210 optimal weight: 20.0000 chunk 495 optimal weight: 3.9990 overall best weight: 5.6988 ------------------------------------------------------------------------------- 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** D 32 ASN ** D 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 130 GLN E 115 GLN F 63 GLN F 135 GLN G 20 ASN ** K 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 3 GLN L 5 GLN O 16 HIS Q 77 HIS T 7 HIS ** T 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 78 GLN Y 6 GLN ** Z 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 58 ASN ** a 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 26 ASN i 72 GLN i 91 GLN i 147 GLN i 207 GLN i 381 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.7012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.191 103995 Z= 0.308 Angle : 0.714 17.825 155517 Z= 0.365 Chirality : 0.038 0.347 19910 Planarity : 0.007 0.128 8357 Dihedral : 23.539 174.255 51869 Min Nonbonded Distance : 1.614 Molprobity Statistics. All-atom Clashscore : 16.92 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.90 % Favored : 96.99 % Rotamer: Outliers : 0.35 % Allowed : 6.46 % Favored : 93.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.79 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.12), residues: 3821 helix: -0.48 (0.14), residues: 1208 sheet: -0.44 (0.18), residues: 733 loop : -0.88 (0.13), residues: 1880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.003 TRP F 97 HIS 0.011 0.002 HIS S 89 PHE 0.027 0.003 PHE d 18 TYR 0.046 0.003 TYR L 32 ARG 0.052 0.001 ARG C 167 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7642 Ramachandran restraints generated. 3821 Oldfield, 0 Emsley, 3821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7642 Ramachandran restraints generated. 3821 Oldfield, 0 Emsley, 3821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 989 residues out of total 3147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 978 time to evaluate : 4.463 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: C 67 PHE cc_start: 0.7462 (m-80) cc_final: 0.7167 (m-80) REVERT: C 93 LEU cc_start: 0.8950 (tp) cc_final: 0.8697 (tp) REVERT: C 100 GLU cc_start: 0.7894 (pp20) cc_final: 0.7516 (pp20) REVERT: C 131 PRO cc_start: 0.7167 (Cg_exo) cc_final: 0.6956 (Cg_endo) REVERT: C 140 THR cc_start: 0.7408 (m) cc_final: 0.6926 (p) REVERT: C 180 GLU cc_start: 0.6513 (pt0) cc_final: 0.5965 (pt0) REVERT: C 225 MET cc_start: 0.9304 (mtt) cc_final: 0.8875 (mtt) REVERT: C 263 THR cc_start: 0.8815 (p) cc_final: 0.8381 (t) REVERT: D 11 MET cc_start: 0.7569 (ttm) cc_final: 0.7217 (tpp) REVERT: D 125 TRP cc_start: 0.9175 (m100) cc_final: 0.8949 (m100) REVERT: D 126 ASN cc_start: 0.7860 (t0) cc_final: 0.7391 (t0) REVERT: D 161 MET cc_start: 0.8077 (mtp) cc_final: 0.7400 (mmm) REVERT: D 164 GLN cc_start: 0.8429 (tp40) cc_final: 0.8090 (tp-100) REVERT: E 1 MET cc_start: 0.6122 (tmm) cc_final: 0.5846 (tmm) REVERT: E 57 LYS cc_start: 0.8538 (tptt) cc_final: 0.8326 (ptpp) REVERT: E 85 PHE cc_start: 0.9074 (m-80) cc_final: 0.8635 (m-80) REVERT: E 165 HIS cc_start: 0.7601 (t-90) cc_final: 0.6622 (t-170) REVERT: F 16 LEU cc_start: 0.6058 (mt) cc_final: 0.5396 (mt) REVERT: F 83 TYR cc_start: 0.6800 (t80) cc_final: 0.6219 (t80) REVERT: F 130 MET cc_start: 0.7677 (pmm) cc_final: 0.7303 (pmm) REVERT: G 75 MET cc_start: 0.8663 (mtp) cc_final: 0.8372 (mtm) REVERT: J 117 MET cc_start: 0.1600 (tpt) cc_final: 0.0780 (tpt) REVERT: K 50 THR cc_start: 0.7247 (p) cc_final: 0.6887 (p) REVERT: K 99 ARG cc_start: 0.8580 (mmm160) cc_final: 0.7839 (mmm160) REVERT: L 3 GLN cc_start: 0.9109 (pt0) cc_final: 0.8630 (pt0) REVERT: L 8 LEU cc_start: 0.8756 (mp) cc_final: 0.8300 (mp) REVERT: L 76 VAL cc_start: 0.9104 (t) cc_final: 0.8647 (p) REVERT: L 87 LEU cc_start: 0.9137 (mt) cc_final: 0.8803 (mt) REVERT: M 50 PHE cc_start: 0.8954 (t80) cc_final: 0.8599 (t80) REVERT: N 68 PHE cc_start: 0.8344 (t80) cc_final: 0.7935 (t80) REVERT: N 70 ASP cc_start: 0.8339 (p0) cc_final: 0.7930 (p0) REVERT: N 73 ILE cc_start: 0.8280 (mm) cc_final: 0.7871 (mp) REVERT: N 86 LYS cc_start: 0.8149 (tptp) cc_final: 0.7921 (tptt) REVERT: N 104 GLU cc_start: 0.7669 (tt0) cc_final: 0.7183 (tp30) REVERT: O 2 ARG cc_start: 0.8769 (ptm-80) cc_final: 0.8326 (ttp80) REVERT: O 16 HIS cc_start: 0.7588 (t-90) cc_final: 0.6969 (t70) REVERT: Q 40 LEU cc_start: 0.7601 (mt) cc_final: 0.6832 (mt) REVERT: R 72 ASN cc_start: 0.7716 (m-40) cc_final: 0.7147 (t0) REVERT: S 1 MET cc_start: 0.5721 (mmp) cc_final: 0.5360 (mmp) REVERT: S 43 ASN cc_start: 0.7072 (m-40) cc_final: 0.5772 (m-40) REVERT: S 48 LYS cc_start: 0.8123 (mtpt) cc_final: 0.7851 (mmtp) REVERT: S 58 VAL cc_start: 0.7563 (t) cc_final: 0.7307 (t) REVERT: S 73 LYS cc_start: 0.9043 (mtpp) cc_final: 0.8694 (mtpt) REVERT: S 76 LYS cc_start: 0.8822 (mmtp) cc_final: 0.8514 (mmtt) REVERT: S 81 LYS cc_start: 0.9525 (mmtm) cc_final: 0.9002 (mmtp) REVERT: T 82 MET cc_start: 0.7825 (mtm) cc_final: 0.7548 (mtp) REVERT: T 88 ARG cc_start: 0.8527 (mmm-85) cc_final: 0.8292 (mtp85) REVERT: T 99 ARG cc_start: 0.7417 (mmt180) cc_final: 0.7118 (mmt180) REVERT: T 104 THR cc_start: 0.8690 (m) cc_final: 0.8405 (p) REVERT: V 6 ARG cc_start: 0.7494 (mtm180) cc_final: 0.6828 (ttp-110) REVERT: V 74 ASN cc_start: 0.6621 (t0) cc_final: 0.6139 (m-40) REVERT: W 10 LYS cc_start: 0.6293 (pptt) cc_final: 0.5894 (pttp) REVERT: W 17 SER cc_start: 0.8573 (m) cc_final: 0.8037 (p) REVERT: W 48 MET cc_start: 0.7818 (tpp) cc_final: 0.7328 (tpp) REVERT: W 51 GLN cc_start: 0.6825 (pp30) cc_final: 0.6101 (pp30) REVERT: X 77 ARG cc_start: 0.7046 (mtt180) cc_final: 0.6456 (mtt180) REVERT: Y 23 ASN cc_start: 0.8730 (m110) cc_final: 0.8089 (p0) REVERT: Y 30 LEU cc_start: 0.9164 (mt) cc_final: 0.8946 (mp) REVERT: Y 33 LEU cc_start: 0.8835 (mt) cc_final: 0.8603 (mp) REVERT: Y 58 VAL cc_start: 0.8931 (t) cc_final: 0.8668 (p) REVERT: Y 77 LYS cc_start: 0.8043 (ttpp) cc_final: 0.7577 (mmtp) REVERT: Z 37 LEU cc_start: 0.7175 (tp) cc_final: 0.6965 (mt) REVERT: Z 42 LEU cc_start: 0.7168 (OUTLIER) cc_final: 0.6932 (pp) REVERT: b 9 THR cc_start: 0.9494 (t) cc_final: 0.9136 (m) REVERT: d 8 SER cc_start: 0.9321 (t) cc_final: 0.8716 (m) REVERT: d 14 ARG cc_start: 0.8914 (ttp-170) cc_final: 0.8669 (ttm110) REVERT: d 26 ASN cc_start: 0.9299 (m-40) cc_final: 0.8609 (m-40) REVERT: e 32 ILE cc_start: 0.9075 (mp) cc_final: 0.8714 (mp) REVERT: e 45 ARG cc_start: 0.7449 (mtm180) cc_final: 0.7039 (mtp85) REVERT: f 1 MET cc_start: 0.8681 (tpt) cc_final: 0.8479 (tpt) REVERT: f 13 ASN cc_start: 0.8600 (m110) cc_final: 0.8287 (m-40) REVERT: k 27 MET cc_start: 0.4319 (ppp) cc_final: 0.1984 (mpp) outliers start: 11 outliers final: 1 residues processed: 984 average time/residue: 0.9525 time to fit residues: 1590.3855 Evaluate side-chains 719 residues out of total 3147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 717 time to evaluate : 4.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 679 random chunks: chunk 610 optimal weight: 5.9990 chunk 464 optimal weight: 8.9990 chunk 320 optimal weight: 3.9990 chunk 68 optimal weight: 20.0000 chunk 294 optimal weight: 20.0000 chunk 414 optimal weight: 20.0000 chunk 619 optimal weight: 4.9990 chunk 656 optimal weight: 20.0000 chunk 323 optimal weight: 0.5980 chunk 587 optimal weight: 1.9990 chunk 176 optimal weight: 20.0000 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 117 GLN C 142 HIS ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 63 GLN G 20 ASN H 73 ASN ** H 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 30 GLN J 107 GLN L 13 ASN L 89 ASN M 35 HIS ** N 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 56 HIS ** R 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 7 HIS T 31 GLN ** T 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 6 GLN ** Z 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 58 ASN a 9 GLN i 147 GLN ** i 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.7840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 103995 Z= 0.186 Angle : 0.586 12.194 155517 Z= 0.303 Chirality : 0.034 0.295 19910 Planarity : 0.005 0.103 8357 Dihedral : 23.346 178.281 51869 Min Nonbonded Distance : 1.461 Molprobity Statistics. All-atom Clashscore : 15.90 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.85 % Favored : 97.04 % Rotamer: Outliers : 0.06 % Allowed : 3.37 % Favored : 96.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.79 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.13), residues: 3821 helix: 0.08 (0.14), residues: 1208 sheet: -0.19 (0.18), residues: 714 loop : -0.72 (0.13), residues: 1899 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP N 64 HIS 0.015 0.001 HIS O 16 PHE 0.025 0.002 PHE R 79 TYR 0.020 0.002 TYR e 64 ARG 0.010 0.001 ARG O 12 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7642 Ramachandran restraints generated. 3821 Oldfield, 0 Emsley, 3821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7642 Ramachandran restraints generated. 3821 Oldfield, 0 Emsley, 3821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 951 residues out of total 3147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 949 time to evaluate : 4.531 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: C 34 LEU cc_start: 0.8633 (mp) cc_final: 0.8328 (mp) REVERT: C 66 ASP cc_start: 0.8808 (t70) cc_final: 0.8522 (t0) REVERT: C 67 PHE cc_start: 0.7386 (m-80) cc_final: 0.7002 (m-80) REVERT: C 100 GLU cc_start: 0.7630 (pp20) cc_final: 0.7423 (pp20) REVERT: C 135 ILE cc_start: 0.8801 (pt) cc_final: 0.8241 (pt) REVERT: C 225 MET cc_start: 0.9127 (mtt) cc_final: 0.8468 (mtt) REVERT: C 263 THR cc_start: 0.8535 (p) cc_final: 0.8082 (t) REVERT: D 126 ASN cc_start: 0.7912 (t0) cc_final: 0.7539 (t0) REVERT: D 161 MET cc_start: 0.7720 (mtp) cc_final: 0.7248 (mmm) REVERT: E 27 LEU cc_start: 0.9131 (tp) cc_final: 0.8547 (tp) REVERT: E 46 GLN cc_start: 0.9244 (mp10) cc_final: 0.9035 (mp10) REVERT: E 57 LYS cc_start: 0.8518 (tptt) cc_final: 0.8301 (ptpt) REVERT: E 78 TRP cc_start: 0.8743 (m-10) cc_final: 0.8486 (m-10) REVERT: E 85 PHE cc_start: 0.8991 (m-80) cc_final: 0.8546 (m-80) REVERT: E 91 ASP cc_start: 0.8034 (t70) cc_final: 0.7564 (p0) REVERT: E 165 HIS cc_start: 0.7528 (t-90) cc_final: 0.6603 (t-170) REVERT: E 197 GLU cc_start: 0.7517 (tm-30) cc_final: 0.7289 (tm-30) REVERT: F 130 MET cc_start: 0.7576 (pmm) cc_final: 0.7034 (pmm) REVERT: G 106 SER cc_start: 0.8890 (t) cc_final: 0.8579 (p) REVERT: J 117 MET cc_start: 0.1188 (tpt) cc_final: 0.0522 (tpt) REVERT: K 14 ASP cc_start: 0.5266 (t0) cc_final: 0.5054 (t70) REVERT: K 91 GLU cc_start: 0.7589 (pt0) cc_final: 0.7107 (pt0) REVERT: K 98 GLU cc_start: 0.8530 (pm20) cc_final: 0.8050 (mp0) REVERT: L 3 GLN cc_start: 0.8632 (pt0) cc_final: 0.8171 (pt0) REVERT: L 8 LEU cc_start: 0.8750 (mp) cc_final: 0.8169 (mp) REVERT: L 113 MET cc_start: 0.6890 (ppp) cc_final: 0.6520 (ppp) REVERT: M 1 MET cc_start: 0.7989 (ppp) cc_final: 0.7361 (ppp) REVERT: M 50 PHE cc_start: 0.8880 (t80) cc_final: 0.8225 (t80) REVERT: M 112 LEU cc_start: 0.8496 (tp) cc_final: 0.8097 (tp) REVERT: N 68 PHE cc_start: 0.8258 (t80) cc_final: 0.7836 (t80) REVERT: N 70 ASP cc_start: 0.8086 (p0) cc_final: 0.7631 (p0) REVERT: N 73 ILE cc_start: 0.8255 (mm) cc_final: 0.8006 (mp) REVERT: N 104 GLU cc_start: 0.7430 (tt0) cc_final: 0.7021 (tt0) REVERT: N 105 MET cc_start: 0.8015 (ptt) cc_final: 0.7488 (ptt) REVERT: O 106 ASP cc_start: 0.8134 (p0) cc_final: 0.7882 (p0) REVERT: O 113 ILE cc_start: 0.8645 (tp) cc_final: 0.8402 (tp) REVERT: P 36 TYR cc_start: 0.7110 (m-10) cc_final: 0.6873 (m-10) REVERT: Q 83 SER cc_start: 0.8811 (p) cc_final: 0.8557 (p) REVERT: Q 100 LEU cc_start: 0.8404 (tt) cc_final: 0.8096 (tt) REVERT: R 72 ASN cc_start: 0.7870 (m-40) cc_final: 0.7429 (t0) REVERT: R 107 THR cc_start: 0.7990 (m) cc_final: 0.6775 (m) REVERT: S 40 MET cc_start: 0.7602 (tmm) cc_final: 0.7086 (tmm) REVERT: S 43 ASN cc_start: 0.6421 (m-40) cc_final: 0.5410 (m-40) REVERT: S 79 ARG cc_start: 0.9041 (ptt180) cc_final: 0.8698 (ptt180) REVERT: T 1 MET cc_start: 0.5516 (ppp) cc_final: 0.4400 (ptt) REVERT: T 69 LEU cc_start: 0.7271 (tp) cc_final: 0.6938 (tp) REVERT: T 86 MET cc_start: 0.6984 (tpt) cc_final: 0.6572 (tpt) REVERT: T 88 ARG cc_start: 0.8672 (mmm-85) cc_final: 0.8194 (mtp85) REVERT: T 99 ARG cc_start: 0.7434 (mmt180) cc_final: 0.7124 (mmt180) REVERT: U 56 GLU cc_start: 0.7142 (tp30) cc_final: 0.6796 (tm-30) REVERT: U 63 VAL cc_start: 0.8486 (t) cc_final: 0.8212 (t) REVERT: V 74 ASN cc_start: 0.7582 (t0) cc_final: 0.7064 (t0) REVERT: W 17 SER cc_start: 0.8687 (m) cc_final: 0.8415 (m) REVERT: W 90 ASP cc_start: 0.6331 (m-30) cc_final: 0.4793 (m-30) REVERT: X 75 LYS cc_start: 0.8083 (mttt) cc_final: 0.7573 (mmmm) REVERT: Z 20 ASN cc_start: 0.8318 (m-40) cc_final: 0.7552 (t0) REVERT: b 9 THR cc_start: 0.9450 (t) cc_final: 0.9115 (m) REVERT: b 52 ARG cc_start: 0.6924 (ttp80) cc_final: 0.6712 (ptm160) REVERT: b 53 LYS cc_start: 0.8034 (tttm) cc_final: 0.7813 (tptt) REVERT: d 8 SER cc_start: 0.9217 (t) cc_final: 0.8663 (m) REVERT: d 26 ASN cc_start: 0.9285 (m-40) cc_final: 0.8700 (m-40) REVERT: e 52 LYS cc_start: 0.9205 (tmmt) cc_final: 0.8869 (tmmt) REVERT: f 10 LEU cc_start: 0.8319 (mp) cc_final: 0.7828 (mt) REVERT: i 415 ARG cc_start: 0.6995 (mpt180) cc_final: 0.6149 (mtt180) REVERT: i 426 MET cc_start: 0.4281 (tmm) cc_final: 0.4048 (tmm) REVERT: k 27 MET cc_start: 0.5274 (ppp) cc_final: 0.1611 (mmt) outliers start: 2 outliers final: 1 residues processed: 950 average time/residue: 0.9572 time to fit residues: 1546.1685 Evaluate side-chains 749 residues out of total 3147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 748 time to evaluate : 4.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 679 random chunks: chunk 546 optimal weight: 6.9990 chunk 372 optimal weight: 7.9990 chunk 9 optimal weight: 20.0000 chunk 488 optimal weight: 7.9990 chunk 270 optimal weight: 20.0000 chunk 560 optimal weight: 6.9990 chunk 453 optimal weight: 7.9990 chunk 0 optimal weight: 50.0000 chunk 335 optimal weight: 6.9990 chunk 589 optimal weight: 10.0000 chunk 165 optimal weight: 20.0000 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 153 GLN ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 173 GLN E 115 GLN ** E 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 20 ASN H 145 ASN L 13 ASN L 89 ASN ** M 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 75 GLN ** R 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 15 GLN T 31 GLN ** T 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 49 ASN X 46 HIS X 76 ASN Y 6 GLN ** Z 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 41 HIS ** Z 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 58 ASN d 6 GLN i 4 ASN i 26 ASN i 147 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.9526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.119 103995 Z= 0.326 Angle : 0.742 12.165 155517 Z= 0.379 Chirality : 0.040 0.516 19910 Planarity : 0.006 0.105 8357 Dihedral : 23.570 171.821 51869 Min Nonbonded Distance : 1.009 Molprobity Statistics. All-atom Clashscore : 22.13 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.00 % Favored : 95.84 % Rotamer: Outliers : 0.16 % Allowed : 4.39 % Favored : 95.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.79 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.13), residues: 3821 helix: -0.49 (0.14), residues: 1214 sheet: -0.34 (0.18), residues: 728 loop : -0.98 (0.13), residues: 1879 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP Q 31 HIS 0.015 0.002 HIS Q 56 PHE 0.028 0.003 PHE d 18 TYR 0.033 0.003 TYR P 99 ARG 0.074 0.001 ARG Q 113 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7642 Ramachandran restraints generated. 3821 Oldfield, 0 Emsley, 3821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7642 Ramachandran restraints generated. 3821 Oldfield, 0 Emsley, 3821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 924 residues out of total 3147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 919 time to evaluate : 4.521 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: C 67 PHE cc_start: 0.8136 (m-80) cc_final: 0.7719 (m-80) REVERT: C 86 ASN cc_start: 0.9265 (p0) cc_final: 0.8908 (p0) REVERT: C 100 GLU cc_start: 0.7192 (pp20) cc_final: 0.6989 (pp20) REVERT: C 180 GLU cc_start: 0.6127 (pt0) cc_final: 0.5897 (pt0) REVERT: C 205 LEU cc_start: 0.8648 (mp) cc_final: 0.8139 (mt) REVERT: C 225 MET cc_start: 0.9161 (mtt) cc_final: 0.8697 (mtt) REVERT: C 263 THR cc_start: 0.8559 (p) cc_final: 0.8091 (t) REVERT: D 126 ASN cc_start: 0.8230 (t0) cc_final: 0.7714 (t0) REVERT: D 161 MET cc_start: 0.8088 (mtp) cc_final: 0.7622 (mmm) REVERT: D 185 ASN cc_start: 0.8257 (m110) cc_final: 0.7948 (m-40) REVERT: E 1 MET cc_start: 0.7310 (tmm) cc_final: 0.6948 (tmm) REVERT: E 57 LYS cc_start: 0.8623 (tptt) cc_final: 0.8362 (ptpt) REVERT: E 61 ARG cc_start: 0.8265 (ptt90) cc_final: 0.7726 (ptm-80) REVERT: E 65 THR cc_start: 0.9101 (p) cc_final: 0.8753 (p) REVERT: E 85 PHE cc_start: 0.9270 (m-80) cc_final: 0.8724 (m-80) REVERT: E 165 HIS cc_start: 0.7666 (t-90) cc_final: 0.6864 (t-170) REVERT: F 47 LYS cc_start: 0.7961 (tppt) cc_final: 0.7703 (mmmt) REVERT: G 80 THR cc_start: 0.7463 (t) cc_final: 0.5698 (t) REVERT: J 117 MET cc_start: 0.2190 (tpt) cc_final: 0.1015 (tpt) REVERT: K 49 ASP cc_start: 0.8376 (p0) cc_final: 0.7983 (p0) REVERT: K 98 GLU cc_start: 0.8603 (pm20) cc_final: 0.8167 (mp0) REVERT: K 129 GLU cc_start: 0.7572 (mp0) cc_final: 0.7295 (mp0) REVERT: L 1 MET cc_start: 0.8679 (tpp) cc_final: 0.8257 (tpp) REVERT: L 3 GLN cc_start: 0.8799 (pt0) cc_final: 0.8503 (pt0) REVERT: L 8 LEU cc_start: 0.8837 (mp) cc_final: 0.8192 (mp) REVERT: L 9 ASN cc_start: 0.8759 (m110) cc_final: 0.8332 (p0) REVERT: L 53 LYS cc_start: 0.8011 (mptt) cc_final: 0.7789 (tmtt) REVERT: L 56 ASP cc_start: 0.8655 (OUTLIER) cc_final: 0.8426 (m-30) REVERT: L 73 ASP cc_start: 0.8292 (p0) cc_final: 0.8004 (p0) REVERT: L 88 ASN cc_start: 0.8718 (t0) cc_final: 0.8462 (t0) REVERT: L 90 ASN cc_start: 0.8730 (m110) cc_final: 0.8520 (m110) REVERT: L 92 GLU cc_start: 0.8913 (mt-10) cc_final: 0.8053 (mp0) REVERT: L 93 GLN cc_start: 0.8583 (mm-40) cc_final: 0.8037 (mm-40) REVERT: M 112 LEU cc_start: 0.8504 (tp) cc_final: 0.8017 (tp) REVERT: N 30 SER cc_start: 0.8637 (m) cc_final: 0.8270 (p) REVERT: N 68 PHE cc_start: 0.8361 (t80) cc_final: 0.8066 (t80) REVERT: N 70 ASP cc_start: 0.8119 (p0) cc_final: 0.7679 (p0) REVERT: N 105 MET cc_start: 0.8144 (ptt) cc_final: 0.7751 (ptt) REVERT: N 117 PHE cc_start: 0.9417 (m-10) cc_final: 0.9070 (m-10) REVERT: O 24 MET cc_start: 0.8684 (mtp) cc_final: 0.7825 (mmt) REVERT: O 72 ASP cc_start: 0.7709 (t0) cc_final: 0.7307 (t70) REVERT: O 79 LEU cc_start: 0.8384 (mp) cc_final: 0.8096 (mp) REVERT: O 115 LEU cc_start: 0.8653 (mt) cc_final: 0.8421 (mp) REVERT: Q 97 LEU cc_start: 0.8818 (tp) cc_final: 0.8599 (tp) REVERT: R 98 ILE cc_start: 0.8812 (mm) cc_final: 0.8535 (mt) REVERT: R 107 THR cc_start: 0.8967 (m) cc_final: 0.7909 (m) REVERT: S 40 MET cc_start: 0.8038 (tmm) cc_final: 0.7595 (tmm) REVERT: S 48 LYS cc_start: 0.8348 (mtpt) cc_final: 0.8042 (mmtm) REVERT: S 73 LYS cc_start: 0.9050 (mtpp) cc_final: 0.8842 (mtpt) REVERT: T 1 MET cc_start: 0.4967 (ppp) cc_final: 0.4600 (ptt) REVERT: T 69 LEU cc_start: 0.8307 (tp) cc_final: 0.7999 (tp) REVERT: T 86 MET cc_start: 0.7245 (tpt) cc_final: 0.6906 (tpt) REVERT: T 99 ARG cc_start: 0.7536 (mmt180) cc_final: 0.7264 (mmt180) REVERT: T 104 THR cc_start: 0.8954 (m) cc_final: 0.8508 (p) REVERT: U 29 THR cc_start: 0.9101 (m) cc_final: 0.8839 (p) REVERT: W 40 ILE cc_start: 0.7593 (mp) cc_final: 0.7391 (mp) REVERT: W 51 GLN cc_start: 0.7801 (pp30) cc_final: 0.7479 (pp30) REVERT: X 21 LEU cc_start: 0.9022 (mt) cc_final: 0.8754 (mp) REVERT: Y 23 ASN cc_start: 0.8419 (m110) cc_final: 0.8185 (p0) REVERT: Y 26 LYS cc_start: 0.8391 (mmmt) cc_final: 0.8030 (mmmt) REVERT: Y 33 LEU cc_start: 0.8482 (mp) cc_final: 0.8133 (mp) REVERT: Y 48 THR cc_start: 0.9277 (m) cc_final: 0.8952 (p) REVERT: Y 56 MET cc_start: 0.8526 (tpp) cc_final: 0.8231 (tmm) REVERT: Z 16 THR cc_start: 0.9124 (p) cc_final: 0.8741 (p) REVERT: Z 20 ASN cc_start: 0.8274 (m-40) cc_final: 0.7444 (t0) REVERT: a 31 ARG cc_start: 0.8624 (ptp90) cc_final: 0.8356 (ptt90) REVERT: a 39 GLU cc_start: 0.7642 (pp20) cc_final: 0.7220 (pp20) REVERT: a 41 THR cc_start: 0.8809 (p) cc_final: 0.8423 (p) REVERT: b 15 MET cc_start: 0.8468 (ttm) cc_final: 0.8215 (ttp) REVERT: b 53 LYS cc_start: 0.8627 (tttm) cc_final: 0.7991 (tmtt) REVERT: c 9 ILE cc_start: 0.9350 (pt) cc_final: 0.8787 (pt) REVERT: c 38 LYS cc_start: 0.8342 (tptt) cc_final: 0.7610 (tptp) REVERT: c 51 GLU cc_start: 0.7236 (tt0) cc_final: 0.6846 (tt0) REVERT: d 13 ASN cc_start: 0.8450 (m-40) cc_final: 0.8148 (t0) REVERT: d 26 ASN cc_start: 0.9191 (m-40) cc_final: 0.8908 (m110) REVERT: i 415 ARG cc_start: 0.7646 (mpt180) cc_final: 0.6705 (mtt180) REVERT: k 27 MET cc_start: 0.5577 (ppp) cc_final: 0.1311 (mpp) outliers start: 5 outliers final: 2 residues processed: 923 average time/residue: 1.0369 time to fit residues: 1644.1601 Evaluate side-chains 700 residues out of total 3147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 697 time to evaluate : 4.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 679 random chunks: chunk 220 optimal weight: 30.0000 chunk 591 optimal weight: 30.0000 chunk 129 optimal weight: 10.0000 chunk 385 optimal weight: 0.3980 chunk 162 optimal weight: 20.0000 chunk 656 optimal weight: 20.0000 chunk 545 optimal weight: 0.6980 chunk 304 optimal weight: 8.9990 chunk 54 optimal weight: 20.0000 chunk 217 optimal weight: 50.0000 chunk 344 optimal weight: 9.9990 overall best weight: 6.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 173 GLN ** E 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 63 GLN L 13 ASN L 89 ASN ** N 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 104 GLN ** Q 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 7 HIS T 31 GLN ** X 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 6 GLN ** Z 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 58 ASN a 20 HIS ** d 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 147 GLN i 207 GLN i 424 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 1.0074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 103995 Z= 0.251 Angle : 0.632 10.725 155517 Z= 0.326 Chirality : 0.036 0.290 19910 Planarity : 0.005 0.093 8357 Dihedral : 23.481 179.870 51869 Min Nonbonded Distance : 1.163 Molprobity Statistics. All-atom Clashscore : 18.33 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.69 % Favored : 96.15 % Rotamer: Outliers : 0.06 % Allowed : 3.09 % Favored : 96.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.79 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.13), residues: 3821 helix: -0.23 (0.14), residues: 1207 sheet: -0.37 (0.18), residues: 757 loop : -0.93 (0.14), residues: 1857 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP U 80 HIS 0.009 0.001 HIS S 89 PHE 0.036 0.002 PHE F 122 TYR 0.022 0.002 TYR L 32 ARG 0.024 0.001 ARG D 124 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7642 Ramachandran restraints generated. 3821 Oldfield, 0 Emsley, 3821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7642 Ramachandran restraints generated. 3821 Oldfield, 0 Emsley, 3821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 878 residues out of total 3147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 876 time to evaluate : 4.482 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: C 28 LYS cc_start: 0.8918 (mptt) cc_final: 0.8494 (mmmm) REVERT: C 54 ILE cc_start: 0.9345 (mm) cc_final: 0.9069 (mm) REVERT: C 86 ASN cc_start: 0.9180 (p0) cc_final: 0.8767 (p0) REVERT: C 91 ILE cc_start: 0.9459 (pt) cc_final: 0.9222 (pt) REVERT: C 100 GLU cc_start: 0.6803 (pp20) cc_final: 0.6433 (pt0) REVERT: C 205 LEU cc_start: 0.8473 (mp) cc_final: 0.7998 (mp) REVERT: C 225 MET cc_start: 0.9086 (mtt) cc_final: 0.8507 (mtt) REVERT: C 236 GLU cc_start: 0.7508 (tp30) cc_final: 0.7280 (tp30) REVERT: C 238 ARG cc_start: 0.8070 (mtm-85) cc_final: 0.7414 (mtm-85) REVERT: C 263 THR cc_start: 0.8401 (p) cc_final: 0.7881 (t) REVERT: D 126 ASN cc_start: 0.8213 (t0) cc_final: 0.7641 (t0) REVERT: D 185 ASN cc_start: 0.8431 (m110) cc_final: 0.8208 (m-40) REVERT: E 57 LYS cc_start: 0.8599 (tptt) cc_final: 0.8330 (ptpt) REVERT: E 61 ARG cc_start: 0.8206 (ptt90) cc_final: 0.7756 (ptm-80) REVERT: E 65 THR cc_start: 0.9053 (p) cc_final: 0.8655 (p) REVERT: E 85 PHE cc_start: 0.9189 (m-80) cc_final: 0.8652 (m-80) REVERT: E 136 GLN cc_start: 0.7949 (mp-120) cc_final: 0.7726 (mp10) REVERT: E 165 HIS cc_start: 0.7655 (t-90) cc_final: 0.6903 (t-170) REVERT: F 12 VAL cc_start: 0.8475 (t) cc_final: 0.8223 (t) REVERT: F 94 GLU cc_start: 0.6896 (pm20) cc_final: 0.6626 (pm20) REVERT: G 106 SER cc_start: 0.9161 (t) cc_final: 0.8847 (p) REVERT: J 117 MET cc_start: 0.2025 (tpt) cc_final: 0.1042 (tpt) REVERT: L 1 MET cc_start: 0.8392 (tpp) cc_final: 0.7984 (tpp) REVERT: L 3 GLN cc_start: 0.8983 (pt0) cc_final: 0.8564 (pt0) REVERT: L 8 LEU cc_start: 0.8860 (mp) cc_final: 0.8150 (mp) REVERT: L 9 ASN cc_start: 0.8772 (m110) cc_final: 0.8368 (p0) REVERT: L 73 ASP cc_start: 0.8313 (p0) cc_final: 0.7977 (p0) REVERT: L 90 ASN cc_start: 0.8794 (m110) cc_final: 0.8307 (m110) REVERT: L 92 GLU cc_start: 0.8831 (mt-10) cc_final: 0.8045 (mp0) REVERT: L 93 GLN cc_start: 0.8441 (mm-40) cc_final: 0.7834 (mm-40) REVERT: L 111 LYS cc_start: 0.7402 (ttpp) cc_final: 0.7111 (ttpp) REVERT: M 50 PHE cc_start: 0.8862 (t80) cc_final: 0.7976 (t80) REVERT: M 58 TYR cc_start: 0.8444 (p90) cc_final: 0.8225 (p90) REVERT: N 25 ASP cc_start: 0.8109 (t70) cc_final: 0.7840 (t70) REVERT: N 30 SER cc_start: 0.8483 (m) cc_final: 0.8142 (p) REVERT: N 70 ASP cc_start: 0.7974 (p0) cc_final: 0.7521 (p0) REVERT: N 97 GLN cc_start: 0.9247 (mm-40) cc_final: 0.8824 (mm-40) REVERT: N 105 MET cc_start: 0.8280 (ptt) cc_final: 0.7704 (ptt) REVERT: N 117 PHE cc_start: 0.9464 (m-10) cc_final: 0.9012 (m-10) REVERT: O 24 MET cc_start: 0.8990 (mtp) cc_final: 0.8053 (mmt) REVERT: O 38 LEU cc_start: 0.9558 (tt) cc_final: 0.8785 (mp) REVERT: O 56 LYS cc_start: 0.8224 (mtmt) cc_final: 0.7528 (pttt) REVERT: O 79 LEU cc_start: 0.8415 (mp) cc_final: 0.7950 (mt) REVERT: O 94 TYR cc_start: 0.8067 (m-80) cc_final: 0.7564 (m-80) REVERT: O 106 ASP cc_start: 0.8289 (p0) cc_final: 0.7955 (p0) REVERT: O 107 ASN cc_start: 0.9156 (t0) cc_final: 0.8929 (t0) REVERT: P 3 LYS cc_start: 0.6518 (mttt) cc_final: 0.5480 (tttt) REVERT: P 19 GLN cc_start: 0.8335 (tp40) cc_final: 0.7922 (tm-30) REVERT: P 24 THR cc_start: 0.7463 (m) cc_final: 0.7189 (p) REVERT: R 66 ASN cc_start: 0.8846 (t0) cc_final: 0.8538 (m-40) REVERT: R 72 ASN cc_start: 0.7900 (m110) cc_final: 0.6912 (t0) REVERT: S 48 LYS cc_start: 0.8402 (mtpt) cc_final: 0.8180 (mmtp) REVERT: S 79 ARG cc_start: 0.9022 (ptt180) cc_final: 0.8598 (ptt180) REVERT: T 1 MET cc_start: 0.5613 (ppp) cc_final: 0.5159 (ptt) REVERT: T 69 LEU cc_start: 0.8231 (tp) cc_final: 0.7859 (tp) REVERT: T 88 ARG cc_start: 0.8686 (mmm-85) cc_final: 0.8351 (mtp85) REVERT: T 97 LEU cc_start: 0.9078 (mt) cc_final: 0.8878 (mt) REVERT: T 99 ARG cc_start: 0.7453 (mmt180) cc_final: 0.7172 (mmt180) REVERT: U 29 THR cc_start: 0.9140 (m) cc_final: 0.8821 (p) REVERT: U 80 TRP cc_start: 0.8352 (p-90) cc_final: 0.8114 (p-90) REVERT: W 12 GLN cc_start: 0.7969 (mt0) cc_final: 0.7235 (mt0) REVERT: W 51 GLN cc_start: 0.7825 (pp30) cc_final: 0.7544 (pp30) REVERT: Y 23 ASN cc_start: 0.8297 (m110) cc_final: 0.8086 (p0) REVERT: Y 26 LYS cc_start: 0.8208 (mmmt) cc_final: 0.7687 (mmtp) REVERT: Y 33 LEU cc_start: 0.8584 (mp) cc_final: 0.8233 (mp) REVERT: Y 48 THR cc_start: 0.9193 (m) cc_final: 0.8873 (p) REVERT: Y 59 ILE cc_start: 0.8916 (pt) cc_final: 0.8698 (pt) REVERT: Y 67 VAL cc_start: 0.8672 (t) cc_final: 0.8414 (t) REVERT: Y 71 LEU cc_start: 0.8396 (mm) cc_final: 0.7969 (mm) REVERT: Z 6 LEU cc_start: 0.8749 (mt) cc_final: 0.8490 (mt) REVERT: Z 16 THR cc_start: 0.8818 (p) cc_final: 0.8451 (p) REVERT: Z 20 ASN cc_start: 0.8279 (m-40) cc_final: 0.7999 (t0) REVERT: Z 36 GLN cc_start: 0.6287 (pp30) cc_final: 0.5935 (tm-30) REVERT: a 31 ARG cc_start: 0.8825 (ptp90) cc_final: 0.8513 (ptt90) REVERT: a 39 GLU cc_start: 0.8073 (pp20) cc_final: 0.7784 (pp20) REVERT: a 41 THR cc_start: 0.8603 (p) cc_final: 0.8169 (p) REVERT: b 53 LYS cc_start: 0.8205 (tttm) cc_final: 0.7876 (tptt) REVERT: c 9 ILE cc_start: 0.9319 (pt) cc_final: 0.8634 (pt) REVERT: c 38 LYS cc_start: 0.8457 (tptt) cc_final: 0.7727 (tptp) REVERT: c 51 GLU cc_start: 0.7310 (tt0) cc_final: 0.6999 (tt0) REVERT: d 26 ASN cc_start: 0.9240 (m-40) cc_final: 0.8861 (m110) REVERT: f 1 MET cc_start: 0.8785 (tpt) cc_final: 0.8295 (tpt) REVERT: f 10 LEU cc_start: 0.8001 (mp) cc_final: 0.7749 (mp) REVERT: i 36 MET cc_start: 0.5943 (mtm) cc_final: 0.5698 (mtm) REVERT: i 415 ARG cc_start: 0.7606 (mpt180) cc_final: 0.6799 (mtt180) REVERT: k 27 MET cc_start: 0.5552 (ppp) cc_final: 0.1401 (mpp) outliers start: 2 outliers final: 0 residues processed: 877 average time/residue: 0.9211 time to fit residues: 1388.0077 Evaluate side-chains 721 residues out of total 3147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 721 time to evaluate : 4.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 679 random chunks: chunk 633 optimal weight: 20.0000 chunk 74 optimal weight: 20.0000 chunk 374 optimal weight: 7.9990 chunk 479 optimal weight: 5.9990 chunk 371 optimal weight: 20.0000 chunk 553 optimal weight: 6.9990 chunk 366 optimal weight: 3.9990 chunk 654 optimal weight: 1.9990 chunk 409 optimal weight: 6.9990 chunk 398 optimal weight: 7.9990 chunk 302 optimal weight: 20.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 58 HIS C 153 GLN ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 150 GLN D 173 GLN ** E 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 115 HIS L 13 ASN M 35 HIS N 97 GLN ** Q 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 75 GLN ** Q 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 43 ASN T 31 GLN ** W 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 41 HIS ** Z 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 58 ASN d 6 GLN i 147 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 1.0526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.108 103995 Z= 0.235 Angle : 0.615 10.107 155517 Z= 0.317 Chirality : 0.035 0.319 19910 Planarity : 0.005 0.085 8357 Dihedral : 23.426 176.515 51869 Min Nonbonded Distance : 1.103 Molprobity Statistics. All-atom Clashscore : 18.18 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.06 % Favored : 95.81 % Rotamer: Outliers : 0.13 % Allowed : 1.72 % Favored : 98.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.79 % 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: -0.84 (0.13), residues: 3821 helix: -0.10 (0.14), residues: 1208 sheet: -0.35 (0.18), residues: 744 loop : -0.86 (0.14), residues: 1869 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP R 61 HIS 0.019 0.002 HIS N 13 PHE 0.049 0.002 PHE d 18 TYR 0.018 0.002 TYR R 32 ARG 0.028 0.001 ARG i 388 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7642 Ramachandran restraints generated. 3821 Oldfield, 0 Emsley, 3821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7642 Ramachandran restraints generated. 3821 Oldfield, 0 Emsley, 3821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 885 residues out of total 3147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 881 time to evaluate : 4.414 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: C 28 LYS cc_start: 0.8941 (mptt) cc_final: 0.8472 (mmmm) REVERT: C 54 ILE cc_start: 0.9370 (mm) cc_final: 0.9108 (mm) REVERT: C 86 ASN cc_start: 0.9177 (p0) cc_final: 0.8733 (p0) REVERT: C 100 GLU cc_start: 0.7020 (pp20) cc_final: 0.6758 (pt0) REVERT: C 174 LEU cc_start: 0.8534 (mm) cc_final: 0.8156 (mt) REVERT: C 205 LEU cc_start: 0.8646 (mp) cc_final: 0.8224 (mp) REVERT: C 225 MET cc_start: 0.9062 (mtt) cc_final: 0.8489 (mtt) REVERT: C 236 GLU cc_start: 0.7548 (tp30) cc_final: 0.7326 (tp30) REVERT: C 263 THR cc_start: 0.8531 (p) cc_final: 0.8006 (t) REVERT: D 126 ASN cc_start: 0.8057 (t0) cc_final: 0.7636 (t0) REVERT: D 130 GLN cc_start: 0.8648 (mt0) cc_final: 0.8398 (mt0) REVERT: E 35 TYR cc_start: 0.9093 (t80) cc_final: 0.8706 (t80) REVERT: E 57 LYS cc_start: 0.8537 (tptt) cc_final: 0.8333 (ptpt) REVERT: E 61 ARG cc_start: 0.8234 (ptt90) cc_final: 0.7903 (ptm-80) REVERT: E 65 THR cc_start: 0.8990 (p) cc_final: 0.8601 (p) REVERT: E 85 PHE cc_start: 0.9175 (m-80) cc_final: 0.8584 (m-80) REVERT: E 165 HIS cc_start: 0.7670 (t-90) cc_final: 0.6863 (t-170) REVERT: F 16 LEU cc_start: 0.8254 (mt) cc_final: 0.7943 (mt) REVERT: F 94 GLU cc_start: 0.6922 (pm20) cc_final: 0.6652 (pm20) REVERT: G 75 MET cc_start: 0.8797 (ttm) cc_final: 0.8550 (ttm) REVERT: G 80 THR cc_start: 0.7575 (p) cc_final: 0.6982 (p) REVERT: G 106 SER cc_start: 0.9175 (t) cc_final: 0.8914 (p) REVERT: G 131 ILE cc_start: 0.8962 (mt) cc_final: 0.8760 (mt) REVERT: H 73 ASN cc_start: 0.5053 (m110) cc_final: 0.4557 (t0) REVERT: J 125 MET cc_start: 0.5533 (mmt) cc_final: 0.5290 (mmt) REVERT: K 98 GLU cc_start: 0.8836 (mp0) cc_final: 0.8439 (mp0) REVERT: K 108 MET cc_start: 0.7568 (mpp) cc_final: 0.6724 (mpp) REVERT: L 1 MET cc_start: 0.8473 (tpp) cc_final: 0.8104 (tpp) REVERT: L 3 GLN cc_start: 0.8851 (pt0) cc_final: 0.8402 (pt0) REVERT: L 8 LEU cc_start: 0.8851 (mp) cc_final: 0.8221 (mp) REVERT: L 9 ASN cc_start: 0.8772 (m110) cc_final: 0.8483 (p0) REVERT: L 18 ARG cc_start: 0.8681 (mtp-110) cc_final: 0.7839 (ttm-80) REVERT: L 73 ASP cc_start: 0.8247 (p0) cc_final: 0.7912 (p0) REVERT: L 87 LEU cc_start: 0.9010 (mp) cc_final: 0.8271 (mt) REVERT: L 88 ASN cc_start: 0.8662 (t0) cc_final: 0.8332 (t0) REVERT: L 92 GLU cc_start: 0.8763 (mt-10) cc_final: 0.7885 (mp0) REVERT: L 93 GLN cc_start: 0.8177 (mm-40) cc_final: 0.7649 (mm-40) REVERT: M 50 PHE cc_start: 0.8865 (t80) cc_final: 0.8128 (t80) REVERT: N 30 SER cc_start: 0.8557 (m) cc_final: 0.8224 (p) REVERT: N 70 ASP cc_start: 0.7872 (p0) cc_final: 0.7650 (p0) REVERT: N 82 MET cc_start: 0.8799 (tpp) cc_final: 0.8528 (tpp) REVERT: N 97 GLN cc_start: 0.9135 (mm110) cc_final: 0.8921 (mm-40) REVERT: N 105 MET cc_start: 0.8173 (ptt) cc_final: 0.7513 (ptt) REVERT: N 117 PHE cc_start: 0.9456 (m-10) cc_final: 0.8966 (m-10) REVERT: O 24 MET cc_start: 0.9106 (mtp) cc_final: 0.8182 (mmt) REVERT: O 56 LYS cc_start: 0.8492 (mtpt) cc_final: 0.7985 (pttt) REVERT: O 72 ASP cc_start: 0.7467 (t70) cc_final: 0.7044 (t70) REVERT: O 79 LEU cc_start: 0.8545 (mp) cc_final: 0.8145 (mt) REVERT: O 83 LEU cc_start: 0.8909 (mt) cc_final: 0.8674 (mt) REVERT: O 94 TYR cc_start: 0.8395 (m-80) cc_final: 0.7989 (m-80) REVERT: P 3 LYS cc_start: 0.6127 (mttt) cc_final: 0.5924 (tttt) REVERT: P 19 GLN cc_start: 0.8339 (tp40) cc_final: 0.7891 (tm-30) REVERT: P 24 THR cc_start: 0.7480 (m) cc_final: 0.7076 (p) REVERT: P 26 LEU cc_start: 0.8634 (mp) cc_final: 0.8399 (mp) REVERT: P 43 ASN cc_start: 0.7382 (p0) cc_final: 0.7022 (t0) REVERT: P 45 SER cc_start: 0.9041 (m) cc_final: 0.8462 (p) REVERT: P 88 LYS cc_start: 0.9063 (tptm) cc_final: 0.8792 (tptm) REVERT: R 72 ASN cc_start: 0.7927 (m110) cc_final: 0.7118 (t0) REVERT: S 1 MET cc_start: 0.4239 (mmp) cc_final: 0.3995 (mmp) REVERT: S 40 MET cc_start: 0.7847 (tmm) cc_final: 0.7248 (tmm) REVERT: S 48 LYS cc_start: 0.8495 (mtpt) cc_final: 0.8190 (mmtm) REVERT: S 79 ARG cc_start: 0.8954 (ptt180) cc_final: 0.8556 (ptt180) REVERT: T 69 LEU cc_start: 0.8279 (tp) cc_final: 0.8049 (tp) REVERT: T 88 ARG cc_start: 0.8610 (mmm-85) cc_final: 0.8381 (mtp85) REVERT: U 22 THR cc_start: 0.9246 (m) cc_final: 0.8895 (m) REVERT: U 29 THR cc_start: 0.9189 (m) cc_final: 0.8859 (p) REVERT: W 12 GLN cc_start: 0.7945 (mt0) cc_final: 0.7394 (mt0) REVERT: W 46 LYS cc_start: 0.8427 (mptt) cc_final: 0.8019 (mmtp) REVERT: W 87 GLN cc_start: 0.8253 (mp10) cc_final: 0.8034 (mp10) REVERT: Y 33 LEU cc_start: 0.8600 (mp) cc_final: 0.8260 (mp) REVERT: Y 48 THR cc_start: 0.9095 (m) cc_final: 0.8820 (p) REVERT: Y 71 LEU cc_start: 0.8414 (mm) cc_final: 0.8124 (mm) REVERT: Z 6 LEU cc_start: 0.8770 (mt) cc_final: 0.8550 (mt) REVERT: Z 16 THR cc_start: 0.8895 (p) cc_final: 0.8369 (p) REVERT: Z 20 ASN cc_start: 0.8351 (m-40) cc_final: 0.8069 (t0) REVERT: a 31 ARG cc_start: 0.8833 (ptp90) cc_final: 0.8469 (ptt90) REVERT: a 39 GLU cc_start: 0.8256 (pp20) cc_final: 0.7930 (pp20) REVERT: a 41 THR cc_start: 0.8595 (p) cc_final: 0.8101 (p) REVERT: c 9 ILE cc_start: 0.9396 (pt) cc_final: 0.8819 (pt) REVERT: c 38 LYS cc_start: 0.8296 (tptt) cc_final: 0.7289 (tptp) REVERT: c 51 GLU cc_start: 0.7238 (tt0) cc_final: 0.6872 (tt0) REVERT: d 26 ASN cc_start: 0.9168 (m-40) cc_final: 0.8782 (m110) REVERT: e 57 LEU cc_start: 0.9008 (mt) cc_final: 0.8718 (mt) REVERT: f 10 LEU cc_start: 0.8044 (mp) cc_final: 0.7730 (mp) REVERT: k 27 MET cc_start: 0.5586 (ppp) cc_final: 0.1280 (mpp) outliers start: 4 outliers final: 0 residues processed: 882 average time/residue: 0.9311 time to fit residues: 1404.4165 Evaluate side-chains 723 residues out of total 3147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 723 time to evaluate : 4.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 679 random chunks: chunk 404 optimal weight: 4.9990 chunk 261 optimal weight: 10.0000 chunk 390 optimal weight: 6.9990 chunk 197 optimal weight: 10.0000 chunk 128 optimal weight: 10.0000 chunk 126 optimal weight: 20.0000 chunk 416 optimal weight: 5.9990 chunk 445 optimal weight: 6.9990 chunk 323 optimal weight: 5.9990 chunk 60 optimal weight: 10.0000 chunk 514 optimal weight: 4.9990 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 58 HIS C 153 GLN ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 20 ASN G 115 HIS H 33 GLN ** J 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 13 ASN L 89 ASN L 90 ASN ** P 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 31 GLN ** T 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 15 HIS ** X 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 38 GLN Z 58 ASN ** d 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 26 ASN i 72 GLN i 147 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 1.1150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 103995 Z= 0.249 Angle : 0.639 11.330 155517 Z= 0.328 Chirality : 0.036 0.290 19910 Planarity : 0.005 0.085 8357 Dihedral : 23.441 175.883 51869 Min Nonbonded Distance : 0.997 Molprobity Statistics. All-atom Clashscore : 18.94 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.27 % Favored : 95.60 % Rotamer: Outliers : 0.03 % Allowed : 1.81 % Favored : 98.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.79 % 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: -0.95 (0.13), residues: 3821 helix: -0.12 (0.14), residues: 1193 sheet: -0.51 (0.18), residues: 719 loop : -0.93 (0.14), residues: 1909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.004 TRP Q 31 HIS 0.021 0.002 HIS N 13 PHE 0.035 0.002 PHE d 5 TYR 0.019 0.002 TYR R 32 ARG 0.010 0.001 ARG I 53 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7642 Ramachandran restraints generated. 3821 Oldfield, 0 Emsley, 3821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7642 Ramachandran restraints generated. 3821 Oldfield, 0 Emsley, 3821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 871 residues out of total 3147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 870 time to evaluate : 4.480 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: C 21 ASN cc_start: 0.8120 (t0) cc_final: 0.7100 (t0) REVERT: C 28 LYS cc_start: 0.8842 (mptt) cc_final: 0.8360 (mmmm) REVERT: C 86 ASN cc_start: 0.9199 (p0) cc_final: 0.8563 (p0) REVERT: C 205 LEU cc_start: 0.8681 (mp) cc_final: 0.8101 (mp) REVERT: C 225 MET cc_start: 0.9083 (mtt) cc_final: 0.8463 (mtt) REVERT: C 236 GLU cc_start: 0.7564 (tp30) cc_final: 0.7362 (tp30) REVERT: C 238 ARG cc_start: 0.8189 (mtm-85) cc_final: 0.7143 (mtm-85) REVERT: C 263 THR cc_start: 0.8732 (p) cc_final: 0.8409 (t) REVERT: C 266 PHE cc_start: 0.8425 (m-10) cc_final: 0.8162 (m-10) REVERT: D 126 ASN cc_start: 0.8276 (t0) cc_final: 0.8001 (t0) REVERT: D 127 PHE cc_start: 0.8850 (m-10) cc_final: 0.8481 (m-10) REVERT: D 164 GLN cc_start: 0.8196 (tp-100) cc_final: 0.7959 (tp-100) REVERT: D 185 ASN cc_start: 0.8512 (m110) cc_final: 0.8264 (m-40) REVERT: E 1 MET cc_start: 0.7411 (tmm) cc_final: 0.7048 (ptt) REVERT: E 35 TYR cc_start: 0.9069 (t80) cc_final: 0.8770 (t80) REVERT: E 57 LYS cc_start: 0.8578 (tptt) cc_final: 0.8370 (ptpt) REVERT: E 61 ARG cc_start: 0.8281 (ptt90) cc_final: 0.7994 (ptm-80) REVERT: E 65 THR cc_start: 0.8896 (p) cc_final: 0.8350 (p) REVERT: E 85 PHE cc_start: 0.9178 (m-80) cc_final: 0.8537 (m-80) REVERT: E 165 HIS cc_start: 0.7644 (t-90) cc_final: 0.6803 (t-170) REVERT: F 12 VAL cc_start: 0.8879 (t) cc_final: 0.8605 (t) REVERT: F 96 MET cc_start: 0.6922 (ptt) cc_final: 0.6555 (ptt) REVERT: F 128 TYR cc_start: 0.7286 (t80) cc_final: 0.6997 (t80) REVERT: F 164 GLU cc_start: 0.6271 (pp20) cc_final: 0.6054 (tm-30) REVERT: G 80 THR cc_start: 0.7615 (p) cc_final: 0.6520 (p) REVERT: G 106 SER cc_start: 0.9203 (t) cc_final: 0.8912 (p) REVERT: H 22 LYS cc_start: 0.8313 (mttp) cc_final: 0.7966 (mttm) REVERT: H 73 ASN cc_start: 0.5039 (m110) cc_final: 0.4594 (t0) REVERT: J 36 MET cc_start: 0.4262 (mmp) cc_final: 0.3682 (ptp) REVERT: K 92 MET cc_start: 0.8281 (mtm) cc_final: 0.8069 (mtm) REVERT: K 108 MET cc_start: 0.7670 (mpp) cc_final: 0.6957 (mpp) REVERT: K 128 ASN cc_start: 0.8893 (t0) cc_final: 0.8657 (t0) REVERT: L 3 GLN cc_start: 0.8766 (pt0) cc_final: 0.8559 (pt0) REVERT: L 8 LEU cc_start: 0.8921 (mp) cc_final: 0.8290 (mp) REVERT: L 9 ASN cc_start: 0.8825 (m110) cc_final: 0.8446 (p0) REVERT: L 17 ARG cc_start: 0.8695 (mmt180) cc_final: 0.8256 (mmt180) REVERT: L 73 ASP cc_start: 0.8320 (p0) cc_final: 0.8016 (p0) REVERT: L 88 ASN cc_start: 0.8704 (t0) cc_final: 0.8467 (t0) REVERT: L 92 GLU cc_start: 0.8723 (mt-10) cc_final: 0.7743 (mp0) REVERT: L 93 GLN cc_start: 0.8187 (mm-40) cc_final: 0.7665 (mm-40) REVERT: M 50 PHE cc_start: 0.8762 (t80) cc_final: 0.8058 (t80) REVERT: M 90 VAL cc_start: 0.8891 (t) cc_final: 0.8650 (t) REVERT: M 104 GLN cc_start: 0.7922 (mm-40) cc_final: 0.7353 (tp-100) REVERT: M 121 THR cc_start: 0.7720 (m) cc_final: 0.7514 (p) REVERT: N 25 ASP cc_start: 0.7541 (t70) cc_final: 0.7254 (t70) REVERT: N 30 SER cc_start: 0.8768 (m) cc_final: 0.8412 (p) REVERT: N 70 ASP cc_start: 0.7676 (p0) cc_final: 0.7327 (p0) REVERT: N 82 MET cc_start: 0.8864 (tpp) cc_final: 0.8605 (tpt) REVERT: N 105 MET cc_start: 0.8180 (ptt) cc_final: 0.7535 (ptt) REVERT: N 117 PHE cc_start: 0.9440 (m-10) cc_final: 0.8852 (m-10) REVERT: O 24 MET cc_start: 0.9217 (mtp) cc_final: 0.8873 (mmm) REVERT: O 72 ASP cc_start: 0.8079 (t70) cc_final: 0.6574 (t70) REVERT: O 79 LEU cc_start: 0.8712 (mp) cc_final: 0.8345 (mp) REVERT: O 94 TYR cc_start: 0.8334 (m-80) cc_final: 0.7734 (m-80) REVERT: P 17 LYS cc_start: 0.8603 (tptt) cc_final: 0.8129 (tmtt) REVERT: P 26 LEU cc_start: 0.8574 (mp) cc_final: 0.8231 (mp) REVERT: P 40 ILE cc_start: 0.9306 (mt) cc_final: 0.9096 (mt) REVERT: P 43 ASN cc_start: 0.7832 (p0) cc_final: 0.7291 (t0) REVERT: Q 24 ASP cc_start: 0.8086 (m-30) cc_final: 0.7689 (m-30) REVERT: Q 31 TRP cc_start: 0.6860 (m100) cc_final: 0.6348 (m100) REVERT: Q 75 GLN cc_start: 0.9279 (mm-40) cc_final: 0.8918 (mp10) REVERT: R 72 ASN cc_start: 0.7817 (m110) cc_final: 0.7372 (t0) REVERT: S 6 GLN cc_start: 0.8555 (mm-40) cc_final: 0.8277 (mm-40) REVERT: S 40 MET cc_start: 0.7740 (tmm) cc_final: 0.7450 (tmm) REVERT: S 79 ARG cc_start: 0.8893 (ptt180) cc_final: 0.8532 (ptt180) REVERT: T 1 MET cc_start: 0.5544 (ppp) cc_final: 0.4640 (ptt) REVERT: T 19 LEU cc_start: 0.9136 (mt) cc_final: 0.8902 (mp) REVERT: T 69 LEU cc_start: 0.8367 (tp) cc_final: 0.7808 (tp) REVERT: T 94 ASP cc_start: 0.8248 (t70) cc_final: 0.7887 (t0) REVERT: T 104 THR cc_start: 0.9023 (m) cc_final: 0.8571 (p) REVERT: T 110 ARG cc_start: 0.8428 (ttp80) cc_final: 0.6419 (mtm180) REVERT: U 11 LEU cc_start: 0.8180 (mp) cc_final: 0.7916 (mp) REVERT: U 29 THR cc_start: 0.9092 (m) cc_final: 0.8721 (p) REVERT: U 80 TRP cc_start: 0.8359 (p-90) cc_final: 0.8081 (p-90) REVERT: V 47 LYS cc_start: 0.8893 (tptp) cc_final: 0.8474 (ttpt) REVERT: W 12 GLN cc_start: 0.8206 (mt0) cc_final: 0.7998 (mt0) REVERT: W 40 ILE cc_start: 0.7578 (mp) cc_final: 0.7293 (mp) REVERT: W 41 GLU cc_start: 0.6652 (pm20) cc_final: 0.6286 (pp20) REVERT: W 42 LEU cc_start: 0.8680 (mt) cc_final: 0.8194 (mt) REVERT: W 51 GLN cc_start: 0.8169 (pp30) cc_final: 0.7398 (pp30) REVERT: Y 33 LEU cc_start: 0.8559 (mp) cc_final: 0.8248 (mp) REVERT: Y 48 THR cc_start: 0.9234 (m) cc_final: 0.8972 (p) REVERT: Z 16 THR cc_start: 0.8768 (p) cc_final: 0.8331 (p) REVERT: Z 31 GLN cc_start: 0.7389 (mt0) cc_final: 0.7054 (mt0) REVERT: a 19 LYS cc_start: 0.8814 (ptpt) cc_final: 0.8481 (ptpt) REVERT: a 31 ARG cc_start: 0.8820 (ptp90) cc_final: 0.8507 (ptt90) REVERT: a 39 GLU cc_start: 0.8215 (pp20) cc_final: 0.7689 (pp20) REVERT: a 41 THR cc_start: 0.8772 (p) cc_final: 0.8332 (p) REVERT: a 45 ARG cc_start: 0.8882 (mmm160) cc_final: 0.8611 (mmm160) REVERT: c 9 ILE cc_start: 0.9283 (pt) cc_final: 0.8692 (pt) REVERT: c 38 LYS cc_start: 0.8346 (tptt) cc_final: 0.8083 (mttt) REVERT: c 51 GLU cc_start: 0.7312 (tt0) cc_final: 0.7044 (tt0) REVERT: d 13 ASN cc_start: 0.8471 (m-40) cc_final: 0.8198 (t0) REVERT: d 26 ASN cc_start: 0.9254 (m-40) cc_final: 0.8889 (m110) REVERT: e 49 MET cc_start: 0.8565 (mmp) cc_final: 0.8322 (mmp) REVERT: e 57 LEU cc_start: 0.8970 (mt) cc_final: 0.8264 (mt) REVERT: f 1 MET cc_start: 0.8880 (tpt) cc_final: 0.8280 (tpt) REVERT: f 10 LEU cc_start: 0.7939 (mp) cc_final: 0.7630 (mp) REVERT: k 27 MET cc_start: 0.5462 (ppp) cc_final: 0.1365 (mmt) outliers start: 1 outliers final: 0 residues processed: 870 average time/residue: 0.9298 time to fit residues: 1397.5297 Evaluate side-chains 698 residues out of total 3147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 698 time to evaluate : 4.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 679 random chunks: chunk 595 optimal weight: 0.2980 chunk 626 optimal weight: 0.9990 chunk 572 optimal weight: 20.0000 chunk 609 optimal weight: 6.9990 chunk 367 optimal weight: 20.0000 chunk 265 optimal weight: 20.0000 chunk 478 optimal weight: 30.0000 chunk 187 optimal weight: 20.0000 chunk 551 optimal weight: 5.9990 chunk 576 optimal weight: 3.9990 chunk 607 optimal weight: 6.9990 overall best weight: 3.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 153 GLN ** C 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 115 HIS ** I 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 19 ASN ** K 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 13 ASN L 89 ASN M 35 HIS ** Q 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 31 GLN ** T 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 23 ASN ** Z 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 38 GLN Z 58 ASN d 6 GLN i 147 GLN ** i 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 1.1328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 103995 Z= 0.178 Angle : 0.574 13.700 155517 Z= 0.296 Chirality : 0.033 0.289 19910 Planarity : 0.005 0.107 8357 Dihedral : 23.377 177.794 51869 Min Nonbonded Distance : 1.137 Molprobity Statistics. All-atom Clashscore : 16.45 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.61 % Favored : 96.23 % Rotamer: Outliers : 0.10 % Allowed : 0.80 % Favored : 99.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.79 % 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: -0.75 (0.13), residues: 3821 helix: 0.04 (0.15), residues: 1195 sheet: -0.34 (0.19), residues: 721 loop : -0.83 (0.14), residues: 1905 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP Q 31 HIS 0.014 0.001 HIS N 13 PHE 0.026 0.002 PHE d 5 TYR 0.017 0.002 TYR F 22 ARG 0.016 0.001 ARG Y 72 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7642 Ramachandran restraints generated. 3821 Oldfield, 0 Emsley, 3821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7642 Ramachandran restraints generated. 3821 Oldfield, 0 Emsley, 3821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 888 residues out of total 3147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 885 time to evaluate : 4.524 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: C 28 LYS cc_start: 0.8876 (mptt) cc_final: 0.8331 (mmmm) REVERT: C 86 ASN cc_start: 0.9190 (p0) cc_final: 0.8652 (p0) REVERT: C 205 LEU cc_start: 0.8623 (mp) cc_final: 0.7958 (tp) REVERT: C 225 MET cc_start: 0.9043 (mtt) cc_final: 0.8465 (mtt) REVERT: C 236 GLU cc_start: 0.7597 (tp30) cc_final: 0.7393 (tp30) REVERT: C 238 ARG cc_start: 0.8099 (mtm-85) cc_final: 0.7111 (mtm-85) REVERT: C 263 THR cc_start: 0.8676 (p) cc_final: 0.8461 (t) REVERT: C 266 PHE cc_start: 0.8465 (m-10) cc_final: 0.8160 (m-10) REVERT: D 11 MET cc_start: 0.8939 (tpp) cc_final: 0.8593 (tpp) REVERT: D 45 TYR cc_start: 0.8009 (p90) cc_final: 0.7801 (p90) REVERT: D 126 ASN cc_start: 0.8177 (t0) cc_final: 0.7941 (t0) REVERT: D 127 PHE cc_start: 0.8797 (m-10) cc_final: 0.8457 (m-10) REVERT: D 168 GLU cc_start: 0.8418 (pm20) cc_final: 0.8205 (pm20) REVERT: E 35 TYR cc_start: 0.9024 (t80) cc_final: 0.8677 (t80) REVERT: E 46 GLN cc_start: 0.9232 (mp10) cc_final: 0.9004 (mp10) REVERT: E 61 ARG cc_start: 0.8264 (ptt90) cc_final: 0.7942 (ptm-80) REVERT: E 65 THR cc_start: 0.8835 (p) cc_final: 0.8224 (p) REVERT: E 85 PHE cc_start: 0.9090 (m-80) cc_final: 0.8391 (m-80) REVERT: E 136 GLN cc_start: 0.8236 (mp10) cc_final: 0.7928 (mp10) REVERT: E 165 HIS cc_start: 0.7745 (t-90) cc_final: 0.6855 (t-170) REVERT: F 94 GLU cc_start: 0.7185 (pm20) cc_final: 0.6861 (pm20) REVERT: F 96 MET cc_start: 0.6735 (ptt) cc_final: 0.6013 (ptt) REVERT: F 128 TYR cc_start: 0.7286 (t80) cc_final: 0.6858 (t80) REVERT: F 164 GLU cc_start: 0.5873 (pp20) cc_final: 0.5627 (tm-30) REVERT: F 175 PHE cc_start: 0.6178 (t80) cc_final: 0.5904 (t80) REVERT: G 80 THR cc_start: 0.7876 (p) cc_final: 0.6929 (p) REVERT: G 106 SER cc_start: 0.9188 (t) cc_final: 0.8896 (p) REVERT: G 170 ARG cc_start: 0.6498 (ptm-80) cc_final: 0.5969 (ppt170) REVERT: H 22 LYS cc_start: 0.8254 (mttp) cc_final: 0.7964 (mttm) REVERT: H 57 LYS cc_start: 0.6493 (mmmt) cc_final: 0.6250 (mmmt) REVERT: H 73 ASN cc_start: 0.5079 (m110) cc_final: 0.4711 (t0) REVERT: H 112 LYS cc_start: 0.6629 (ptmm) cc_final: 0.6399 (pttm) REVERT: J 36 MET cc_start: 0.4175 (mmp) cc_final: 0.3653 (ptp) REVERT: J 117 MET cc_start: 0.0912 (tpt) cc_final: 0.0606 (tpt) REVERT: J 125 MET cc_start: 0.6272 (mmt) cc_final: 0.5836 (mmt) REVERT: K 91 GLU cc_start: 0.7672 (pt0) cc_final: 0.7400 (pt0) REVERT: K 92 MET cc_start: 0.7954 (mtm) cc_final: 0.7671 (mtm) REVERT: K 98 GLU cc_start: 0.8771 (mp0) cc_final: 0.7957 (mm-30) REVERT: K 108 MET cc_start: 0.7469 (mpp) cc_final: 0.6716 (mpp) REVERT: K 128 ASN cc_start: 0.9041 (t0) cc_final: 0.8831 (t0) REVERT: L 3 GLN cc_start: 0.8909 (pt0) cc_final: 0.8637 (pt0) REVERT: L 9 ASN cc_start: 0.8788 (m110) cc_final: 0.8376 (p0) REVERT: L 17 ARG cc_start: 0.8779 (mmt180) cc_final: 0.8079 (mmt180) REVERT: L 73 ASP cc_start: 0.8390 (p0) cc_final: 0.8029 (p0) REVERT: L 87 LEU cc_start: 0.9047 (mp) cc_final: 0.8684 (mt) REVERT: L 88 ASN cc_start: 0.8832 (t0) cc_final: 0.8568 (t0) REVERT: L 92 GLU cc_start: 0.8645 (mt-10) cc_final: 0.7811 (mp0) REVERT: L 93 GLN cc_start: 0.8084 (mm-40) cc_final: 0.7631 (mm-40) REVERT: L 117 SER cc_start: 0.9254 (p) cc_final: 0.8576 (p) REVERT: M 50 PHE cc_start: 0.8802 (t80) cc_final: 0.8173 (t80) REVERT: M 58 TYR cc_start: 0.8450 (p90) cc_final: 0.8232 (p90) REVERT: M 90 VAL cc_start: 0.8863 (t) cc_final: 0.8651 (t) REVERT: N 25 ASP cc_start: 0.7532 (t70) cc_final: 0.7305 (t70) REVERT: N 30 SER cc_start: 0.8720 (m) cc_final: 0.8395 (p) REVERT: N 64 TRP cc_start: 0.8363 (m-90) cc_final: 0.7670 (m-90) REVERT: N 97 GLN cc_start: 0.8514 (mp10) cc_final: 0.8292 (mm-40) REVERT: N 105 MET cc_start: 0.8337 (ptt) cc_final: 0.7879 (ptt) REVERT: O 24 MET cc_start: 0.9179 (mtp) cc_final: 0.8799 (mmm) REVERT: O 94 TYR cc_start: 0.7901 (m-80) cc_final: 0.7690 (m-80) REVERT: P 17 LYS cc_start: 0.8539 (tptt) cc_final: 0.8049 (tmtt) REVERT: P 19 GLN cc_start: 0.8401 (tp40) cc_final: 0.8147 (tm-30) REVERT: P 26 LEU cc_start: 0.8666 (mp) cc_final: 0.8384 (mp) REVERT: P 40 ILE cc_start: 0.9294 (mt) cc_final: 0.9076 (mt) REVERT: P 43 ASN cc_start: 0.7902 (p0) cc_final: 0.7521 (t0) REVERT: P 45 SER cc_start: 0.8599 (p) cc_final: 0.8107 (p) REVERT: Q 24 ASP cc_start: 0.8149 (m-30) cc_final: 0.7755 (m-30) REVERT: Q 31 TRP cc_start: 0.6981 (m100) cc_final: 0.6236 (m100) REVERT: Q 82 ASP cc_start: 0.7623 (t0) cc_final: 0.7324 (t0) REVERT: R 32 TYR cc_start: 0.9178 (t80) cc_final: 0.8787 (t80) REVERT: R 72 ASN cc_start: 0.7826 (m110) cc_final: 0.7348 (t0) REVERT: S 40 MET cc_start: 0.7665 (tmm) cc_final: 0.7176 (tmm) REVERT: S 79 ARG cc_start: 0.8927 (ptt180) cc_final: 0.8464 (ptt180) REVERT: T 1 MET cc_start: 0.5623 (ppp) cc_final: 0.4795 (ptt) REVERT: T 69 LEU cc_start: 0.8518 (tp) cc_final: 0.8063 (tp) REVERT: T 110 ARG cc_start: 0.8537 (ttp80) cc_final: 0.6493 (mtm180) REVERT: U 11 LEU cc_start: 0.8069 (mp) cc_final: 0.7824 (mp) REVERT: U 29 THR cc_start: 0.9194 (m) cc_final: 0.8801 (p) REVERT: V 47 LYS cc_start: 0.8813 (tptp) cc_final: 0.8488 (ttpt) REVERT: W 51 GLN cc_start: 0.8160 (pp30) cc_final: 0.7188 (pp30) REVERT: Y 33 LEU cc_start: 0.8579 (mp) cc_final: 0.8193 (mp) REVERT: Y 48 THR cc_start: 0.9125 (m) cc_final: 0.8848 (p) REVERT: Y 71 LEU cc_start: 0.8266 (mm) cc_final: 0.7746 (mm) REVERT: a 19 LYS cc_start: 0.8817 (ptpt) cc_final: 0.8497 (ptpt) REVERT: a 31 ARG cc_start: 0.8856 (ptp90) cc_final: 0.8417 (ptt90) REVERT: a 39 GLU cc_start: 0.8151 (pp20) cc_final: 0.7869 (pp20) REVERT: a 41 THR cc_start: 0.8828 (p) cc_final: 0.8331 (p) REVERT: a 45 ARG cc_start: 0.8792 (mmm160) cc_final: 0.8578 (mmm160) REVERT: c 9 ILE cc_start: 0.9243 (pt) cc_final: 0.8695 (pt) REVERT: c 38 LYS cc_start: 0.8327 (tptt) cc_final: 0.7996 (mttt) REVERT: c 51 GLU cc_start: 0.7302 (tt0) cc_final: 0.7040 (tt0) REVERT: d 13 ASN cc_start: 0.8367 (m-40) cc_final: 0.7979 (t0) REVERT: d 22 MET cc_start: 0.8282 (mmm) cc_final: 0.8074 (tpp) REVERT: d 26 ASN cc_start: 0.9226 (m-40) cc_final: 0.8861 (m110) REVERT: e 57 LEU cc_start: 0.9005 (mt) cc_final: 0.8769 (mt) REVERT: e 61 CYS cc_start: 0.8185 (m) cc_final: 0.7818 (t) REVERT: i 68 LEU cc_start: 0.4103 (mp) cc_final: 0.3726 (mp) REVERT: k 27 MET cc_start: 0.5489 (ppp) cc_final: 0.1357 (mmt) outliers start: 3 outliers final: 0 residues processed: 886 average time/residue: 0.9729 time to fit residues: 1484.0848 Evaluate side-chains 701 residues out of total 3147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 701 time to evaluate : 4.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 679 random chunks: chunk 400 optimal weight: 10.0000 chunk 644 optimal weight: 3.9990 chunk 393 optimal weight: 2.9990 chunk 305 optimal weight: 5.9990 chunk 448 optimal weight: 10.0000 chunk 676 optimal weight: 30.0000 chunk 622 optimal weight: 7.9990 chunk 538 optimal weight: 7.9990 chunk 55 optimal weight: 20.0000 chunk 416 optimal weight: 5.9990 chunk 330 optimal weight: 0.8980 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 58 HIS C 153 GLN ** C 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 20 ASN J 19 ASN ** K 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 136 GLN L 13 ASN L 89 ASN M 35 HIS ** O 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 31 GLN ** T 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 31 GLN Z 38 GLN Z 58 ASN ** d 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 147 GLN ** i 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 1.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 103995 Z= 0.188 Angle : 0.584 9.405 155517 Z= 0.300 Chirality : 0.033 0.301 19910 Planarity : 0.005 0.084 8357 Dihedral : 23.335 176.264 51869 Min Nonbonded Distance : 1.087 Molprobity Statistics. All-atom Clashscore : 16.96 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.21 % Favored : 95.66 % Rotamer: Outliers : 0.03 % Allowed : 0.48 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.79 % 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: -0.80 (0.13), residues: 3821 helix: 0.02 (0.15), residues: 1211 sheet: -0.33 (0.19), residues: 690 loop : -0.89 (0.14), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP U 80 HIS 0.014 0.001 HIS N 13 PHE 0.029 0.002 PHE E 158 TYR 0.015 0.002 TYR e 64 ARG 0.016 0.001 ARG Y 3 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7642 Ramachandran restraints generated. 3821 Oldfield, 0 Emsley, 3821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7642 Ramachandran restraints generated. 3821 Oldfield, 0 Emsley, 3821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 831 residues out of total 3147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 830 time to evaluate : 4.475 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: C 28 LYS cc_start: 0.8864 (mptt) cc_final: 0.8332 (mmmm) REVERT: C 66 ASP cc_start: 0.8622 (t70) cc_final: 0.8389 (t0) REVERT: C 67 PHE cc_start: 0.8186 (m-10) cc_final: 0.7901 (m-10) REVERT: C 86 ASN cc_start: 0.9172 (p0) cc_final: 0.8529 (p0) REVERT: C 225 MET cc_start: 0.9055 (mtt) cc_final: 0.8468 (mtt) REVERT: C 236 GLU cc_start: 0.7798 (tp30) cc_final: 0.7569 (tp30) REVERT: C 238 ARG cc_start: 0.8179 (mtm-85) cc_final: 0.7089 (mtm-85) REVERT: C 263 THR cc_start: 0.8689 (p) cc_final: 0.8444 (t) REVERT: C 266 PHE cc_start: 0.8505 (m-10) cc_final: 0.8232 (m-10) REVERT: D 1 MET cc_start: 0.6902 (ptt) cc_final: 0.6507 (ptt) REVERT: D 11 MET cc_start: 0.8850 (tpp) cc_final: 0.8482 (tpp) REVERT: D 126 ASN cc_start: 0.8066 (t0) cc_final: 0.7862 (t0) REVERT: D 127 PHE cc_start: 0.8709 (m-10) cc_final: 0.8403 (m-10) REVERT: D 161 MET cc_start: 0.7245 (mmm) cc_final: 0.7002 (mmm) REVERT: D 164 GLN cc_start: 0.8152 (tp-100) cc_final: 0.7949 (tp-100) REVERT: E 35 TYR cc_start: 0.9039 (t80) cc_final: 0.8702 (t80) REVERT: E 61 ARG cc_start: 0.8245 (ptt90) cc_final: 0.7939 (ptm-80) REVERT: E 65 THR cc_start: 0.8760 (p) cc_final: 0.8185 (p) REVERT: E 67 ARG cc_start: 0.8593 (mtm180) cc_final: 0.8387 (mtp-110) REVERT: E 85 PHE cc_start: 0.9123 (m-80) cc_final: 0.8387 (m-80) REVERT: E 136 GLN cc_start: 0.8400 (mp10) cc_final: 0.7946 (mp10) REVERT: E 165 HIS cc_start: 0.7596 (t-90) cc_final: 0.6671 (t-170) REVERT: F 19 GLU cc_start: 0.7967 (tm-30) cc_final: 0.7710 (tm-30) REVERT: F 96 MET cc_start: 0.7091 (ptt) cc_final: 0.6580 (ptt) REVERT: F 128 TYR cc_start: 0.7079 (t80) cc_final: 0.6499 (t80) REVERT: F 165 GLU cc_start: 0.4527 (pt0) cc_final: 0.4192 (pt0) REVERT: G 106 SER cc_start: 0.9222 (t) cc_final: 0.8919 (p) REVERT: G 170 ARG cc_start: 0.6464 (ptm-80) cc_final: 0.5780 (ppt170) REVERT: G 172 LYS cc_start: 0.8241 (ptpt) cc_final: 0.7825 (ptpt) REVERT: H 22 LYS cc_start: 0.8208 (mttp) cc_final: 0.7946 (mttm) REVERT: H 57 LYS cc_start: 0.6390 (mmmt) cc_final: 0.6174 (mmmt) REVERT: H 73 ASN cc_start: 0.5086 (m110) cc_final: 0.4743 (t0) REVERT: J 36 MET cc_start: 0.4167 (mmp) cc_final: 0.3355 (ptp) REVERT: K 98 GLU cc_start: 0.8886 (mp0) cc_final: 0.8286 (mm-30) REVERT: K 108 MET cc_start: 0.7479 (mpp) cc_final: 0.6719 (mpp) REVERT: K 128 ASN cc_start: 0.9050 (t0) cc_final: 0.8802 (t0) REVERT: L 1 MET cc_start: 0.8638 (mmm) cc_final: 0.8042 (mmm) REVERT: L 3 GLN cc_start: 0.9007 (pt0) cc_final: 0.8798 (pt0) REVERT: L 8 LEU cc_start: 0.8800 (mp) cc_final: 0.8277 (mp) REVERT: L 9 ASN cc_start: 0.8785 (m110) cc_final: 0.8422 (p0) REVERT: L 17 ARG cc_start: 0.8805 (mmt180) cc_final: 0.8112 (mmt180) REVERT: L 32 TYR cc_start: 0.8670 (m-10) cc_final: 0.8278 (m-10) REVERT: L 44 LYS cc_start: 0.7978 (mtmm) cc_final: 0.7578 (mmtt) REVERT: L 73 ASP cc_start: 0.8558 (p0) cc_final: 0.8037 (p0) REVERT: L 79 PHE cc_start: 0.8296 (m-80) cc_final: 0.7508 (m-80) REVERT: L 92 GLU cc_start: 0.8706 (mt-10) cc_final: 0.8309 (mp0) REVERT: L 117 SER cc_start: 0.9248 (p) cc_final: 0.8829 (p) REVERT: M 50 PHE cc_start: 0.8800 (t80) cc_final: 0.8193 (t80) REVERT: N 25 ASP cc_start: 0.7924 (t70) cc_final: 0.7693 (t70) REVERT: N 30 SER cc_start: 0.8629 (m) cc_final: 0.8402 (p) REVERT: N 70 ASP cc_start: 0.7662 (p0) cc_final: 0.7317 (p0) REVERT: O 94 TYR cc_start: 0.7862 (m-80) cc_final: 0.7573 (m-80) REVERT: P 17 LYS cc_start: 0.8554 (tptt) cc_final: 0.8032 (tmtt) REVERT: P 19 GLN cc_start: 0.8288 (tp40) cc_final: 0.8008 (tm-30) REVERT: P 26 LEU cc_start: 0.8629 (mp) cc_final: 0.8353 (mp) REVERT: P 45 SER cc_start: 0.8623 (p) cc_final: 0.8310 (p) REVERT: Q 24 ASP cc_start: 0.8137 (m-30) cc_final: 0.7769 (m-30) REVERT: R 32 TYR cc_start: 0.9310 (t80) cc_final: 0.9023 (t80) REVERT: R 72 ASN cc_start: 0.7779 (m110) cc_final: 0.7365 (t0) REVERT: R 98 ILE cc_start: 0.8850 (mt) cc_final: 0.8612 (mt) REVERT: S 32 THR cc_start: 0.8870 (m) cc_final: 0.8624 (p) REVERT: S 40 MET cc_start: 0.7669 (tmm) cc_final: 0.7315 (tmm) REVERT: S 46 GLU cc_start: 0.7815 (mp0) cc_final: 0.7313 (mp0) REVERT: S 79 ARG cc_start: 0.8954 (ptt180) cc_final: 0.8511 (ptt180) REVERT: T 69 LEU cc_start: 0.8388 (tp) cc_final: 0.7981 (tp) REVERT: T 104 THR cc_start: 0.9021 (m) cc_final: 0.8591 (p) REVERT: U 11 LEU cc_start: 0.8154 (mp) cc_final: 0.7879 (mp) REVERT: U 12 ARG cc_start: 0.8887 (tpp-160) cc_final: 0.8487 (mmp80) REVERT: U 29 THR cc_start: 0.9036 (m) cc_final: 0.8614 (p) REVERT: V 47 LYS cc_start: 0.8807 (tptp) cc_final: 0.8432 (ttpt) REVERT: W 41 GLU cc_start: 0.6561 (pm20) cc_final: 0.6326 (pp20) REVERT: W 42 LEU cc_start: 0.8507 (mt) cc_final: 0.8182 (mt) REVERT: W 75 GLN cc_start: 0.8761 (tp40) cc_final: 0.8515 (tp40) REVERT: Y 33 LEU cc_start: 0.8550 (mp) cc_final: 0.8265 (mp) REVERT: Y 48 THR cc_start: 0.9158 (m) cc_final: 0.8892 (p) REVERT: Y 71 LEU cc_start: 0.8131 (mm) cc_final: 0.7916 (mm) REVERT: a 19 LYS cc_start: 0.8779 (ptpt) cc_final: 0.8446 (ptpt) REVERT: a 31 ARG cc_start: 0.8875 (ptp90) cc_final: 0.8422 (ptt90) REVERT: a 39 GLU cc_start: 0.8133 (pp20) cc_final: 0.7685 (pp20) REVERT: a 41 THR cc_start: 0.8803 (p) cc_final: 0.8234 (p) REVERT: a 45 ARG cc_start: 0.8872 (mmm160) cc_final: 0.8640 (mmm160) REVERT: c 9 ILE cc_start: 0.9339 (pt) cc_final: 0.8916 (pt) REVERT: c 38 LYS cc_start: 0.8184 (tptt) cc_final: 0.7928 (mttt) REVERT: c 51 GLU cc_start: 0.7333 (tt0) cc_final: 0.7086 (tt0) REVERT: d 8 SER cc_start: 0.9441 (t) cc_final: 0.8916 (m) REVERT: d 13 ASN cc_start: 0.8382 (m-40) cc_final: 0.8025 (t0) REVERT: d 26 ASN cc_start: 0.9223 (m-40) cc_final: 0.8858 (m110) REVERT: e 57 LEU cc_start: 0.8995 (mt) cc_final: 0.8739 (mt) REVERT: e 61 CYS cc_start: 0.8142 (m) cc_final: 0.7870 (t) REVERT: f 10 LEU cc_start: 0.7981 (mp) cc_final: 0.7615 (mp) REVERT: k 27 MET cc_start: 0.5515 (ppp) cc_final: 0.1333 (mmt) outliers start: 1 outliers final: 1 residues processed: 830 average time/residue: 0.9153 time to fit residues: 1311.3205 Evaluate side-chains 682 residues out of total 3147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 681 time to evaluate : 4.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 679 random chunks: chunk 427 optimal weight: 6.9990 chunk 573 optimal weight: 20.0000 chunk 165 optimal weight: 20.0000 chunk 496 optimal weight: 0.9990 chunk 79 optimal weight: 10.0000 chunk 149 optimal weight: 20.0000 chunk 539 optimal weight: 2.9990 chunk 225 optimal weight: 20.0000 chunk 554 optimal weight: 6.9990 chunk 68 optimal weight: 20.0000 chunk 99 optimal weight: 10.0000 overall best weight: 5.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 58 HIS C 153 GLN ** C 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 19 ASN ** K 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 136 GLN L 9 ASN L 89 ASN ** M 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 17 ASN ** Q 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 38 GLN Z 58 ASN a 9 GLN ** d 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 147 GLN ** i 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.082384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.068294 restraints weight = 360700.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.069596 restraints weight = 154466.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.070208 restraints weight = 90299.437| |-----------------------------------------------------------------------------| r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 1.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 103995 Z= 0.237 Angle : 0.624 9.524 155517 Z= 0.319 Chirality : 0.035 0.324 19910 Planarity : 0.005 0.084 8357 Dihedral : 23.386 175.699 51869 Min Nonbonded Distance : 1.057 Molprobity Statistics. All-atom Clashscore : 18.83 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.32 % Favored : 95.52 % Rotamer: Outliers : 0.03 % Allowed : 0.76 % Favored : 99.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.79 % 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: -0.84 (0.13), residues: 3821 helix: -0.02 (0.15), residues: 1201 sheet: -0.37 (0.19), residues: 697 loop : -0.90 (0.14), residues: 1923 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP E 78 HIS 0.014 0.001 HIS N 13 PHE 0.033 0.002 PHE d 5 TYR 0.016 0.002 TYR e 64 ARG 0.015 0.001 ARG Y 72 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 22317.93 seconds wall clock time: 395 minutes 26.31 seconds (23726.31 seconds total)