Starting phenix.real_space_refine on Tue Mar 19 14:54:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5gah_8004/03_2024/5gah_8004.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5gah_8004/03_2024/5gah_8004.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5gah_8004/03_2024/5gah_8004.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5gah_8004/03_2024/5gah_8004.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5gah_8004/03_2024/5gah_8004.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5gah_8004/03_2024/5gah_8004.pdb" } resolution = 3.8 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 3049 5.49 5 Mg 431 5.21 5 S 95 5.16 5 C 46856 2.51 5 N 17421 2.21 5 O 26174 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C GLU 23": "OE1" <-> "OE2" Residue "C GLU 35": "OE1" <-> "OE2" Residue "C ARG 52": "NH1" <-> "NH2" Residue "C ARG 63": "NH1" <-> "NH2" Residue "C ARG 80": "NH1" <-> "NH2" Residue "C TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 133": "NH1" <-> "NH2" Residue "C GLU 145": "OE1" <-> "OE2" Residue "C TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 167": "NH1" <-> "NH2" Residue "C TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 177": "NH1" <-> "NH2" Residue "C ARG 182": "NH1" <-> "NH2" Residue "C ARG 189": "NH1" <-> "NH2" Residue "C GLU 199": "OE1" <-> "OE2" Residue "C ARG 203": "NH1" <-> "NH2" Residue "C ARG 212": "NH1" <-> "NH2" Residue "D ARG 13": "NH1" <-> "NH2" Residue "D GLU 17": "OE1" <-> "OE2" Residue "D ASP 18": "OD1" <-> "OD2" Residue "D GLU 28": "OE1" <-> "OE2" Residue "D GLU 30": "OE1" <-> "OE2" Residue "D ARG 33": "NH1" <-> "NH2" Residue "D ASP 43": "OD1" <-> "OD2" Residue "D TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 59": "NH1" <-> "NH2" Residue "D GLU 64": "OE1" <-> "OE2" Residue "D ARG 77": "NH1" <-> "NH2" Residue "D GLU 81": "OE1" <-> "OE2" Residue "D ARG 83": "NH1" <-> "NH2" Residue "D GLU 168": "OE1" <-> "OE2" Residue "D ARG 169": "NH1" <-> "NH2" Residue "D GLU 183": "OE1" <-> "OE2" Residue "D ARG 184": "NH1" <-> "NH2" Residue "E ASP 7": "OD1" <-> "OD2" Residue "E ARG 21": "NH1" <-> "NH2" Residue "E GLU 25": "OE1" <-> "OE2" Residue "E ARG 44": "NH1" <-> "NH2" Residue "E ARG 49": "NH1" <-> "NH2" Residue "E ARG 61": "NH1" <-> "NH2" Residue "E PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 88": "NH1" <-> "NH2" Residue "E ARG 102": "NH1" <-> "NH2" Residue "E ASP 145": "OD1" <-> "OD2" Residue "E GLU 152": "OE1" <-> "OE2" Residue "E ARG 162": "NH1" <-> "NH2" Residue "E ARG 170": "NH1" <-> "NH2" Residue "E ASP 176": "OD1" <-> "OD2" Residue "E GLU 197": "OE1" <-> "OE2" Residue "F GLU 19": "OE1" <-> "OE2" Residue "F GLU 32": "OE1" <-> "OE2" Residue "F ARG 71": "NH1" <-> "NH2" Residue "F ARG 80": "NH1" <-> "NH2" Residue "F ARG 92": "NH1" <-> "NH2" Residue "F GLU 94": "OE1" <-> "OE2" Residue "F GLU 98": "OE1" <-> "OE2" Residue "F ARG 102": "NH1" <-> "NH2" Residue "F ARG 110": "NH1" <-> "NH2" Residue "F ARG 112": "NH1" <-> "NH2" Residue "F ARG 115": "NH1" <-> "NH2" Residue "F PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 133": "NH1" <-> "NH2" Residue "G ARG 3": "NH1" <-> "NH2" Residue "G PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 56": "OD1" <-> "OD2" Residue "G TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 124": "OE1" <-> "OE2" Residue "G ARG 153": "NH1" <-> "NH2" Residue "G TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 163": "NH1" <-> "NH2" Residue "G ASP 166": "OD1" <-> "OD2" Residue "G ARG 170": "NH1" <-> "NH2" Residue "H ARG 27": "NH1" <-> "NH2" Residue "H PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 60": "OE1" <-> "OE2" Residue "H ASP 86": "OD1" <-> "OD2" Residue "H GLU 87": "OE1" <-> "OE2" Residue "H GLU 114": "OE1" <-> "OE2" Residue "H GLU 137": "OE1" <-> "OE2" Residue "H PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 87": "OE1" <-> "OE2" Residue "I PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 114": "OE1" <-> "OE2" Residue "I ASP 124": "OD1" <-> "OD2" Residue "J PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 13": "NH1" <-> "NH2" Residue "K TYR 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 31": "OE1" <-> "OE2" Residue "K ARG 37": "NH1" <-> "NH2" Residue "K GLU 43": "OE1" <-> "OE2" Residue "K TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 90": "OE1" <-> "OE2" Residue "K GLU 91": "OE1" <-> "OE2" Residue "K ARG 96": "NH1" <-> "NH2" Residue "K ARG 120": "NH1" <-> "NH2" Residue "L GLU 45": "OE1" <-> "OE2" Residue "L GLU 110": "OE1" <-> "OE2" Residue "L GLU 121": "OE1" <-> "OE2" Residue "M ARG 21": "NH1" <-> "NH2" Residue "M ARG 33": "NH1" <-> "NH2" Residue "M ARG 41": "NH1" <-> "NH2" Residue "M ARG 47": "NH1" <-> "NH2" Residue "M GLU 51": "OE1" <-> "OE2" Residue "M ARG 60": "NH1" <-> "NH2" Residue "M PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 76": "OE1" <-> "OE2" Residue "M ARG 78": "NH1" <-> "NH2" Residue "M ASP 91": "OD1" <-> "OD2" Residue "M GLU 106": "OE1" <-> "OE2" Residue "M ARG 126": "NH1" <-> "NH2" Residue "M GLU 144": "OE1" <-> "OE2" Residue "N ARG 10": "NH1" <-> "NH2" Residue "N ARG 18": "NH1" <-> "NH2" Residue "N PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 40": "NH1" <-> "NH2" Residue "N ARG 44": "NH1" <-> "NH2" Residue "N GLU 47": "OE1" <-> "OE2" Residue "N ARG 50": "NH1" <-> "NH2" Residue "N ARG 55": "NH1" <-> "NH2" Residue "N ARG 59": "NH1" <-> "NH2" Residue "N GLU 75": "OE1" <-> "OE2" Residue "N TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 104": "OE1" <-> "OE2" Residue "N ARG 114": "NH1" <-> "NH2" Residue "N PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 8": "NH1" <-> "NH2" Residue "O ARG 12": "NH1" <-> "NH2" Residue "O ARG 17": "NH1" <-> "NH2" Residue "O ARG 22": "NH1" <-> "NH2" Residue "O GLU 43": "OE1" <-> "OE2" Residue "O ARG 46": "NH1" <-> "NH2" Residue "O ARG 63": "NH1" <-> "NH2" Residue "O ARG 64": "NH1" <-> "NH2" Residue "O ARG 69": "NH1" <-> "NH2" Residue "O ARG 71": "NH1" <-> "NH2" Residue "O GLU 82": "OE1" <-> "OE2" Residue "O ARG 96": "NH1" <-> "NH2" Residue "O TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 114": "OE1" <-> "OE2" Residue "P ARG 10": "NH1" <-> "NH2" Residue "P ARG 16": "NH1" <-> "NH2" Residue "P GLU 20": "OE1" <-> "OE2" Residue "P ARG 25": "NH1" <-> "NH2" Residue "P ARG 81": "NH1" <-> "NH2" Residue "P ARG 94": "NH1" <-> "NH2" Residue "P TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 102": "NH1" <-> "NH2" Residue "P ARG 111": "NH1" <-> "NH2" Residue "Q PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 21": "NH1" <-> "NH2" Residue "Q ARG 39": "NH1" <-> "NH2" Residue "Q GLU 44": "OE1" <-> "OE2" Residue "Q ARG 62": "NH1" <-> "NH2" Residue "Q GLU 71": "OE1" <-> "OE2" Residue "Q ASP 82": "OD1" <-> "OD2" Residue "Q ARG 89": "NH1" <-> "NH2" Residue "Q TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 101": "NH1" <-> "NH2" Residue "Q ARG 109": "NH1" <-> "NH2" Residue "R ARG 3": "NH1" <-> "NH2" Residue "R ARG 6": "NH1" <-> "NH2" Residue "R ARG 13": "NH1" <-> "NH2" Residue "R TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 33": "NH1" <-> "NH2" Residue "R TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 48": "NH1" <-> "NH2" Residue "R PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 70": "NH1" <-> "NH2" Residue "R TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 111": "OE1" <-> "OE2" Residue "S GLU 16": "OE1" <-> "OE2" Residue "S ARG 21": "NH1" <-> "NH2" Residue "S GLU 23": "OE1" <-> "OE2" Residue "S GLU 31": "OE1" <-> "OE2" Residue "S GLU 45": "OE1" <-> "OE2" Residue "S ARG 68": "NH1" <-> "NH2" Residue "S GLU 70": "OE1" <-> "OE2" Residue "S ARG 78": "NH1" <-> "NH2" Residue "S ARG 79": "NH1" <-> "NH2" Residue "S TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 84": "NH1" <-> "NH2" Residue "S PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 59": "OE1" <-> "OE2" Residue "T PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 78": "OE1" <-> "OE2" Residue "T ARG 84": "NH1" <-> "NH2" Residue "T ARG 88": "NH1" <-> "NH2" Residue "T ARG 95": "NH1" <-> "NH2" Residue "T ARG 110": "NH1" <-> "NH2" Residue "U GLU 4": "OE1" <-> "OE2" Residue "U GLU 5": "OE1" <-> "OE2" Residue "U GLU 52": "OE1" <-> "OE2" Residue "U GLU 54": "OE1" <-> "OE2" Residue "U GLU 56": "OE1" <-> "OE2" Residue "U GLU 89": "OE1" <-> "OE2" Residue "V ARG 6": "NH1" <-> "NH2" Residue "V ARG 7": "NH1" <-> "NH2" Residue "V ARG 82": "NH1" <-> "NH2" Residue "V PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 86": "NH1" <-> "NH2" Residue "V GLU 88": "OE1" <-> "OE2" Residue "V ARG 94": "NH1" <-> "NH2" Residue "V PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 11": "OE1" <-> "OE2" Residue "W PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 41": "OE1" <-> "OE2" Residue "W GLU 55": "OE1" <-> "OE2" Residue "W GLU 69": "OE1" <-> "OE2" Residue "W PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 17": "OE1" <-> "OE2" Residue "X PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 85": "OE1" <-> "OE2" Residue "Y ARG 3": "NH1" <-> "NH2" Residue "Y ARG 11": "NH1" <-> "NH2" Residue "Y ARG 18": "NH1" <-> "NH2" Residue "Y PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 37": "NH1" <-> "NH2" Residue "Y GLU 41": "OE1" <-> "OE2" Residue "Y GLU 43": "OE1" <-> "OE2" Residue "Y ARG 50": "NH1" <-> "NH2" Residue "Y ARG 57": "NH1" <-> "NH2" Residue "Y ARG 74": "NH1" <-> "NH2" Residue "Z GLU 12": "OE1" <-> "OE2" Residue "Z PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 47": "NH1" <-> "NH2" Residue "Z ARG 52": "NH1" <-> "NH2" Residue "a ARG 11": "NH1" <-> "NH2" Residue "a ARG 30": "NH1" <-> "NH2" Residue "a GLU 37": "OE1" <-> "OE2" Residue "a ARG 45": "NH1" <-> "NH2" Residue "a PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 10": "NH1" <-> "NH2" Residue "b ARG 16": "NH1" <-> "NH2" Residue "b ASP 31": "OD1" <-> "OD2" Residue "b ARG 52": "NH1" <-> "NH2" Residue "c GLU 32": "OE1" <-> "OE2" Residue "c GLU 35": "OE1" <-> "OE2" Residue "c ARG 44": "NH1" <-> "NH2" Residue "d ARG 3": "NH1" <-> "NH2" Residue "d ARG 14": "NH1" <-> "NH2" Residue "d PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 19": "NH1" <-> "NH2" Residue "d ARG 21": "NH1" <-> "NH2" Residue "d ARG 33": "NH1" <-> "NH2" Residue "e ARG 13": "NH1" <-> "NH2" Residue "e PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ARG 30": "NH1" <-> "NH2" Residue "e ARG 40": "NH1" <-> "NH2" Residue "e ARG 42": "NH1" <-> "NH2" Residue "f ARG 24": "NH1" <-> "NH2" Residue "i GLU 392": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 94027 Number of models: 1 Model: "" Number of chains: 46 Chain: "1" Number of atoms: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 926 Classifications: {'RNA': 43} Modifications used: {'rna3p_pur': 26, 'rna3p_pyr': 17} Link IDs: {'rna3p': 42} Chain: "2" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 62 Classifications: {'RNA': 3} Modifications used: {'rna2p_pur': 1, 'rna3p_pyr': 2} Link IDs: {'rna3p': 2} Chain: "A" Number of atoms: 61902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2883, 61902 Classifications: {'RNA': 2883} Modifications used: {'rna2p_pur': 280, 'rna2p_pyr': 149, 'rna3p_pur': 1386, 'rna3p_pyr': 1068} Link IDs: {'rna2p': 429, 'rna3p': 2453} Chain breaks: 4 Chain: "B" Number of atoms: 2569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 2569 Classifications: {'RNA': 120} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 6, 'rna3p_pur': 57, 'rna3p_pyr': 50} Link IDs: {'rna2p': 13, 'rna3p': 106} Chain: "C" Number of atoms: 2082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2082 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 17, 'TRANS': 253} Chain: "D" Number of atoms: 1565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1565 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 202} Chain: "E" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1552 Classifications: {'peptide': 201} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 195} Chain: "F" Number of atoms: 1410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1410 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 6, 'TRANS': 170} Chain: "G" Number of atoms: 1323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1323 Classifications: {'peptide': 176} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "H" Number of atoms: 1110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1110 Classifications: {'peptide': 149} Link IDs: {'PTRANS': 3, 'TRANS': 145} Chain: "I" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 946 Classifications: {'peptide': 125} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 120} Chain: "J" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 979 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 9, 'TRANS': 124} Chain: "K" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1129 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 135} Chain: "L" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 946 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 5, 'TRANS': 117} Chain: "M" Number of atoms: 1053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1053 Classifications: {'peptide': 144} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 139} Chain: "N" Number of atoms: 1074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1074 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 128} Chain: "O" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 993 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 4, 'TRANS': 120} Chain: "P" Number of atoms: 900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 900 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 114} Chain: "Q" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 917 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "R" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 947 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'TRANS': 116} Chain: "S" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 816 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'TRANS': 101} Chain: "T" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 857 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 107} Chain: "U" Number of atoms: 756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 756 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 1, 'TRANS': 93} Chain: "V" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 779 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "W" Number of atoms: 753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 753 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "X" Number of atoms: 580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 580 Classifications: {'peptide': 76} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 74} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "Y" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 625 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "Z" Number of atoms: 501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 501 Classifications: {'peptide': 62} Modifications used: {'COO': 1} Link IDs: {'TRANS': 61} Chain: "a" Number of atoms: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 449 Classifications: {'peptide': 58} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "b" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 444 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 54} Chain: "c" Number of atoms: 414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 414 Classifications: {'peptide': 51} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 48} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "d" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 377 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "e" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 504 Classifications: {'peptide': 64} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "f" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 302 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "i" Number of atoms: 916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 916 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 124} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'UNK:plan-1': 41} Unresolved non-hydrogen planarities: 41 Chain: "k" Number of atoms: 137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 137 Classifications: {'peptide': 18} Link IDs: {'PTRANS': 1, 'TRANS': 16} Chain: "2" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 412, 412 Unusual residues: {' MG': 412} Classifications: {'undetermined': 412} Link IDs: {None: 411} Chain: "B" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Unusual residues: {' MG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "b" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "f" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 92325 SG CYS f 11 72.587 85.762 179.614 1.00 65.90 S ATOM 92350 SG CYS f 14 75.777 87.050 178.486 1.00 40.68 S ATOM 92453 SG CYS f 27 75.976 83.920 180.512 1.00 52.38 S Time building chain proxies: 37.54, per 1000 atoms: 0.40 Number of scatterers: 94027 At special positions: 0 Unit cell: (240.99, 199.44, 240.99, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 95 16.00 P 3049 15.00 Mg 431 11.99 O 26174 8.00 N 17421 7.00 C 46856 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 40.33 Conformation dependent library (CDL) restraints added in 5.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN f 101 " pdb="ZN ZN f 101 " - pdb=" SG CYS f 14 " pdb="ZN ZN f 101 " - pdb=" ND1 HIS f 33 " pdb="ZN ZN f 101 " - pdb=" SG CYS f 11 " pdb="ZN ZN f 101 " - pdb=" SG CYS f 27 " Number of angles added : 3 7058 Ramachandran restraints generated. 3529 Oldfield, 0 Emsley, 3529 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6648 Finding SS restraints... Secondary structure from input PDB file: 119 helices and 50 sheets defined 35.2% alpha, 20.8% beta 1020 base pairs and 1574 stacking pairs defined. Time for finding SS restraints: 34.41 Creating SS restraints... Processing helix chain 'C' and resid 10 through 14 Processing helix chain 'C' and resid 30 through 32 No H-bonds generated for 'chain 'C' and resid 30 through 32' Processing helix chain 'C' and resid 133 through 135 No H-bonds generated for 'chain 'C' and resid 133 through 135' Processing helix chain 'C' and resid 197 through 203 removed outlier: 4.213A pdb=" N MET C 201 " --> pdb=" O ALA C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 214 removed outlier: 3.823A pdb=" N ALA C 211 " --> pdb=" O LYS C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 225 Processing helix chain 'C' and resid 262 through 265 removed outlier: 4.254A pdb=" N LYS C 265 " --> pdb=" O ARG C 262 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 262 through 265' Processing helix chain 'D' and resid 39 through 44 Processing helix chain 'D' and resid 61 through 72 removed outlier: 3.714A pdb=" N ALA D 71 " --> pdb=" O HIS D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 102 Processing helix chain 'D' and resid 120 through 126 Processing helix chain 'E' and resid 15 through 20 Processing helix chain 'E' and resid 24 through 39 Processing helix chain 'E' and resid 97 through 115 Processing helix chain 'E' and resid 130 through 142 removed outlier: 3.615A pdb=" N LEU E 134 " --> pdb=" O LYS E 130 " (cutoff:3.500A) Processing helix chain 'E' and resid 154 through 161 removed outlier: 3.529A pdb=" N ALA E 161 " --> pdb=" O LEU E 157 " (cutoff:3.500A) Processing helix chain 'E' and resid 173 through 175 No H-bonds generated for 'chain 'E' and resid 173 through 175' Processing helix chain 'E' and resid 176 through 183 removed outlier: 4.207A pdb=" N PHE E 183 " --> pdb=" O SER E 179 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 200 Processing helix chain 'F' and resid 3 through 11 Processing helix chain 'F' and resid 11 through 21 Processing helix chain 'F' and resid 24 through 28 Processing helix chain 'F' and resid 47 through 62 removed outlier: 3.759A pdb=" N ASP F 51 " --> pdb=" O LYS F 47 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ASP F 56 " --> pdb=" O ASN F 52 " (cutoff:3.500A) Processing helix chain 'F' and resid 92 through 106 Processing helix chain 'F' and resid 107 through 111 Processing helix chain 'F' and resid 142 through 146 removed outlier: 3.680A pdb=" N VAL F 146 " --> pdb=" O TYR F 143 " (cutoff:3.500A) Processing helix chain 'F' and resid 162 through 173 Processing helix chain 'G' and resid 60 through 81 Processing helix chain 'G' and resid 137 through 152 removed outlier: 3.661A pdb=" N TYR G 151 " --> pdb=" O ASP G 147 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N ARG G 152 " --> pdb=" O LEU G 148 " (cutoff:3.500A) Processing helix chain 'H' and resid 22 through 29 removed outlier: 3.611A pdb=" N ALA H 26 " --> pdb=" O LYS H 22 " (cutoff:3.500A) Processing helix chain 'H' and resid 40 through 73 removed outlier: 5.675A pdb=" N ALA H 52 " --> pdb=" O GLU H 48 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N GLU H 53 " --> pdb=" O ALA H 49 " (cutoff:3.500A) Processing helix chain 'H' and resid 85 through 89 removed outlier: 3.769A pdb=" N GLY H 88 " --> pdb=" O GLY H 85 " (cutoff:3.500A) Processing helix chain 'H' and resid 95 through 105 removed outlier: 3.527A pdb=" N ILE H 99 " --> pdb=" O GLY H 95 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ALA H 105 " --> pdb=" O ASP H 101 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 113 No H-bonds generated for 'chain 'H' and resid 111 through 113' Processing helix chain 'I' and resid 4 through 22 Processing helix chain 'I' and resid 34 through 47 Processing helix chain 'I' and resid 56 through 65 removed outlier: 3.934A pdb=" N ARG I 62 " --> pdb=" O THR I 58 " (cutoff:3.500A) Processing helix chain 'I' and resid 69 through 73 removed outlier: 3.568A pdb=" N LYS I 73 " --> pdb=" O GLU I 70 " (cutoff:3.500A) Processing helix chain 'I' and resid 92 through 104 removed outlier: 3.859A pdb=" N LYS I 97 " --> pdb=" O ALA I 93 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLU I 98 " --> pdb=" O ARG I 94 " (cutoff:3.500A) Processing helix chain 'I' and resid 122 through 126 Processing helix chain 'J' and resid 34 through 46 removed outlier: 3.899A pdb=" N PHE J 38 " --> pdb=" O ASN J 34 " (cutoff:3.500A) Processing helix chain 'J' and resid 47 through 49 No H-bonds generated for 'chain 'J' and resid 47 through 49' Processing helix chain 'J' and resid 75 through 84 removed outlier: 3.561A pdb=" N ALA J 84 " --> pdb=" O LEU J 80 " (cutoff:3.500A) Processing helix chain 'J' and resid 102 through 117 Processing helix chain 'J' and resid 121 through 136 removed outlier: 3.668A pdb=" N MET J 136 " --> pdb=" O THR J 132 " (cutoff:3.500A) Processing helix chain 'K' and resid 24 through 38 removed outlier: 4.025A pdb=" N GLU K 31 " --> pdb=" O ARG K 27 " (cutoff:3.500A) Processing helix chain 'K' and resid 67 through 72 Processing helix chain 'K' and resid 89 through 96 Processing helix chain 'K' and resid 97 through 108 removed outlier: 4.310A pdb=" N ILE K 101 " --> pdb=" O PRO K 97 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N MET K 108 " --> pdb=" O ALA K 104 " (cutoff:3.500A) Processing helix chain 'K' and resid 112 through 120 Processing helix chain 'K' and resid 131 through 136 removed outlier: 4.258A pdb=" N ALA K 134 " --> pdb=" O ASN K 131 " (cutoff:3.500A) Processing helix chain 'L' and resid 104 through 108 Processing helix chain 'L' and resid 112 through 119 removed outlier: 3.585A pdb=" N ILE L 116 " --> pdb=" O PHE L 112 " (cutoff:3.500A) Processing helix chain 'M' and resid 22 through 26 Processing helix chain 'M' and resid 36 through 41 removed outlier: 3.653A pdb=" N SER M 40 " --> pdb=" O LYS M 36 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ARG M 41 " --> pdb=" O GLY M 37 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 36 through 41' Processing helix chain 'M' and resid 56 through 61 Processing helix chain 'M' and resid 68 through 73 removed outlier: 3.785A pdb=" N ALA M 72 " --> pdb=" O SER M 68 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE M 73 " --> pdb=" O ARG M 69 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 68 through 73' Processing helix chain 'M' and resid 78 through 83 removed outlier: 3.866A pdb=" N LEU M 82 " --> pdb=" O ARG M 78 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ALA M 83 " --> pdb=" O LEU M 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 78 through 83' Processing helix chain 'M' and resid 91 through 98 Processing helix chain 'M' and resid 128 through 137 Processing helix chain 'N' and resid 43 through 57 Processing helix chain 'N' and resid 109 through 122 Processing helix chain 'O' and resid 13 through 32 Processing helix chain 'O' and resid 38 through 56 removed outlier: 3.714A pdb=" N ARG O 45 " --> pdb=" O ALA O 41 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ARG O 46 " --> pdb=" O LYS O 42 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N VAL O 47 " --> pdb=" O GLU O 43 " (cutoff:3.500A) Proline residue: O 50 - end of helix Processing helix chain 'O' and resid 59 through 71 Processing helix chain 'O' and resid 72 through 82 Processing helix chain 'O' and resid 82 through 87 Processing helix chain 'O' and resid 117 through 124 Processing helix chain 'P' and resid 2 through 21 removed outlier: 3.508A pdb=" N ALA P 6 " --> pdb=" O ASP P 2 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N ARG P 13 " --> pdb=" O ARG P 9 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N ALA P 14 " --> pdb=" O ARG P 10 " (cutoff:3.500A) Processing helix chain 'P' and resid 55 through 60 Processing helix chain 'P' and resid 67 through 84 Processing helix chain 'P' and resid 100 through 113 Processing helix chain 'Q' and resid 3 through 11 removed outlier: 3.775A pdb=" N GLU Q 11 " --> pdb=" O GLN Q 7 " (cutoff:3.500A) Processing helix chain 'Q' and resid 53 through 56 removed outlier: 4.004A pdb=" N HIS Q 56 " --> pdb=" O ARG Q 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 53 through 56' Processing helix chain 'Q' and resid 97 through 102 Processing helix chain 'Q' and resid 104 through 108 Processing helix chain 'R' and resid 6 through 21 Processing helix chain 'R' and resid 26 through 31 removed outlier: 3.861A pdb=" N ARG R 30 " --> pdb=" O GLY R 26 " (cutoff:3.500A) Processing helix chain 'R' and resid 31 through 72 removed outlier: 3.638A pdb=" N GLN R 37 " --> pdb=" O ARG R 33 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ARG R 51 " --> pdb=" O TYR R 47 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LYS R 54 " --> pdb=" O ARG R 50 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ARG R 55 " --> pdb=" O ARG R 51 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ARG R 58 " --> pdb=" O LYS R 54 " (cutoff:3.500A) Processing helix chain 'R' and resid 75 through 85 Processing helix chain 'R' and resid 91 through 102 Processing helix chain 'R' and resid 102 through 118 removed outlier: 3.559A pdb=" N PHE R 106 " --> pdb=" O ASP R 102 " (cutoff:3.500A) Processing helix chain 'T' and resid 13 through 25 removed outlier: 3.554A pdb=" N LEU T 19 " --> pdb=" O GLN T 15 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N VAL T 20 " --> pdb=" O LYS T 16 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU T 23 " --> pdb=" O LEU T 19 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE T 24 " --> pdb=" O VAL T 20 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG T 25 " --> pdb=" O ALA T 21 " (cutoff:3.500A) Processing helix chain 'T' and resid 28 through 39 Processing helix chain 'T' and resid 41 through 63 removed outlier: 4.087A pdb=" N VAL T 45 " --> pdb=" O LYS T 41 " (cutoff:3.500A) Processing helix chain 'T' and resid 65 through 69 Processing helix chain 'T' and resid 89 through 91 No H-bonds generated for 'chain 'T' and resid 89 through 91' Processing helix chain 'U' and resid 3 through 8 removed outlier: 3.741A pdb=" N LEU U 7 " --> pdb=" O ARG U 3 " (cutoff:3.500A) Processing helix chain 'U' and resid 17 through 27 Processing helix chain 'U' and resid 39 through 51 Processing helix chain 'W' and resid 12 through 23 removed outlier: 4.165A pdb=" N ALA W 16 " --> pdb=" O GLN W 12 " (cutoff:3.500A) Processing helix chain 'W' and resid 44 through 51 Processing helix chain 'W' and resid 54 through 59 removed outlier: 3.861A pdb=" N SER W 58 " --> pdb=" O ALA W 54 " (cutoff:3.500A) Processing helix chain 'Y' and resid 53 through 63 Processing helix chain 'Y' and resid 63 through 75 removed outlier: 3.666A pdb=" N VAL Y 67 " --> pdb=" O GLY Y 63 " (cutoff:3.500A) Processing helix chain 'Z' and resid 5 through 9 removed outlier: 3.661A pdb=" N GLU Z 8 " --> pdb=" O GLU Z 5 " (cutoff:3.500A) Processing helix chain 'Z' and resid 10 through 34 Processing helix chain 'Z' and resid 40 through 63 removed outlier: 4.192A pdb=" N LYS Z 44 " --> pdb=" O SER Z 40 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ALA Z 51 " --> pdb=" O ARG Z 47 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLU Z 59 " --> pdb=" O THR Z 55 " (cutoff:3.500A) Processing helix chain 'a' and resid 17 through 28 Processing helix chain 'a' and resid 41 through 52 removed outlier: 3.682A pdb=" N VAL a 51 " --> pdb=" O MET a 47 " (cutoff:3.500A) Processing helix chain 'b' and resid 9 through 18 removed outlier: 3.581A pdb=" N ARG b 17 " --> pdb=" O ARG b 13 " (cutoff:3.500A) Processing helix chain 'd' and resid 8 through 17 Processing helix chain 'd' and resid 17 through 23 Processing helix chain 'd' and resid 24 through 38 Processing helix chain 'e' and resid 7 through 14 removed outlier: 3.688A pdb=" N LYS e 12 " --> pdb=" O ARG e 8 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ARG e 13 " --> pdb=" O GLY e 9 " (cutoff:3.500A) Processing helix chain 'e' and resid 37 through 45 Processing helix chain 'e' and resid 54 through 62 Processing helix chain 'f' and resid 30 through 33 Processing helix chain 'i' and resid 330 through 345 removed outlier: 4.114A pdb=" N ASN i 343 " --> pdb=" O ARG i 339 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N MET i 344 " --> pdb=" O GLN i 340 " (cutoff:3.500A) Processing helix chain 'i' and resid 346 through 351 Processing helix chain 'i' and resid 356 through 361 removed outlier: 3.752A pdb=" N UNK i 360 " --> pdb=" O UNK i 356 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N UNK i 361 " --> pdb=" O UNK i 357 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 356 through 361' Processing helix chain 'i' and resid 362 through 366 removed outlier: 4.030A pdb=" N UNK i 366 " --> pdb=" O UNK i 363 " (cutoff:3.500A) Processing helix chain 'i' and resid 368 through 382 Processing helix chain 'i' and resid 384 through 389 Processing helix chain 'i' and resid 390 through 394 removed outlier: 3.639A pdb=" N ILE i 394 " --> pdb=" O PRO i 391 " (cutoff:3.500A) Processing helix chain 'i' and resid 395 through 406 Processing helix chain 'i' and resid 409 through 433 Processing helix chain 'i' and resid 434 through 441 removed outlier: 3.598A pdb=" N UNK i 441 " --> pdb=" O UNK i 437 " (cutoff:3.500A) Processing helix chain 'k' and resid 28 through 42 removed outlier: 3.999A pdb=" N LEU k 36 " --> pdb=" O LEU k 32 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 3 through 5 Processing sheet with id=AA2, first strand: chain 'C' and resid 34 through 35 Processing sheet with id=AA3, first strand: chain 'C' and resid 101 through 105 removed outlier: 3.526A pdb=" N ARG C 80 " --> pdb=" O LEU C 93 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LEU C 95 " --> pdb=" O VAL C 78 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N VAL C 78 " --> pdb=" O LEU C 95 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 129 through 131 removed outlier: 6.263A pdb=" N THR C 173 " --> pdb=" O VAL C 165 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N ARG C 167 " --> pdb=" O TYR C 171 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N TYR C 171 " --> pdb=" O ARG C 167 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N MET C 181 " --> pdb=" O VAL C 268 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 4 through 15 removed outlier: 6.824A pdb=" N VAL D 26 " --> pdb=" O VAL D 9 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N MET D 11 " --> pdb=" O VAL D 24 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N VAL D 24 " --> pdb=" O MET D 11 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N ARG D 13 " --> pdb=" O ILE D 22 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ILE D 22 " --> pdb=" O ARG D 13 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N LEU D 186 " --> pdb=" O VAL D 180 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N VAL D 180 " --> pdb=" O LEU D 186 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N LEU D 188 " --> pdb=" O VAL D 178 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ASP D 176 " --> pdb=" O LYS D 190 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N THR D 171 " --> pdb=" O GLY D 111 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N GLY D 111 " --> pdb=" O THR D 171 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N GLN D 173 " --> pdb=" O VAL D 109 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N VAL D 109 " --> pdb=" O GLN D 173 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N THR D 112 " --> pdb=" O ASP D 200 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N ASP D 200 " --> pdb=" O THR D 112 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 80 through 83 removed outlier: 6.708A pdb=" N ALA D 47 " --> pdb=" O VAL D 37 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N VAL D 37 " --> pdb=" O ALA D 47 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N GLN D 49 " --> pdb=" O THR D 35 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 118 through 119 Processing sheet with id=AA8, first strand: chain 'E' and resid 2 through 4 Processing sheet with id=AA9, first strand: chain 'E' and resid 118 through 121 Processing sheet with id=AB1, first strand: chain 'F' and resid 66 through 69 removed outlier: 3.898A pdb=" N GLY F 86 " --> pdb=" O THR F 68 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 16 through 20 Processing sheet with id=AB3, first strand: chain 'G' and resid 41 through 45 Processing sheet with id=AB4, first strand: chain 'G' and resid 121 through 124 Processing sheet with id=AB5, first strand: chain 'G' and resid 95 through 99 Processing sheet with id=AB6, first strand: chain 'H' and resid 18 through 20 Processing sheet with id=AB7, first strand: chain 'H' and resid 78 through 82 removed outlier: 3.719A pdb=" N VAL H 147 " --> pdb=" O ILE H 80 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N SER H 131 " --> pdb=" O ARG H 116 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 50 through 54 removed outlier: 3.887A pdb=" N SER I 24 " --> pdb=" O VAL I 85 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA I 25 " --> pdb=" O ALA I 112 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'J' and resid 9 through 14 Processing sheet with id=AC1, first strand: chain 'J' and resid 100 through 101 Processing sheet with id=AC2, first strand: chain 'K' and resid 122 through 124 removed outlier: 6.493A pdb=" N TRP K 15 " --> pdb=" O GLN K 138 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'K' and resid 73 through 77 Processing sheet with id=AC4, first strand: chain 'L' and resid 7 through 10 removed outlier: 3.788A pdb=" N VAL L 10 " --> pdb=" O ARG L 17 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N ARG L 17 " --> pdb=" O VAL L 10 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N GLU L 45 " --> pdb=" O ARG L 17 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N VAL L 19 " --> pdb=" O ILE L 43 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ILE L 43 " --> pdb=" O VAL L 19 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N CYS L 21 " --> pdb=" O ILE L 41 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ILE L 41 " --> pdb=" O CYS L 21 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N LYS L 23 " --> pdb=" O ILE L 39 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N ILE L 39 " --> pdb=" O LYS L 23 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ALA L 83 " --> pdb=" O VAL L 63 " (cutoff:3.500A) removed outlier: 8.303A pdb=" N CYS L 84 " --> pdb=" O MET L 7 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ASN L 9 " --> pdb=" O CYS L 84 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N LEU L 86 " --> pdb=" O ASN L 9 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 69 through 70 removed outlier: 3.801A pdb=" N VAL L 76 " --> pdb=" O VAL Q 73 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ALA Q 58 " --> pdb=" O ILE Q 50 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N ILE Q 50 " --> pdb=" O ALA Q 58 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N THR Q 60 " --> pdb=" O ILE Q 48 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N ILE Q 64 " --> pdb=" O GLU Q 44 " (cutoff:3.500A) removed outlier: 9.098A pdb=" N GLU Q 44 " --> pdb=" O ILE Q 64 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N THR Q 25 " --> pdb=" O LYS Q 87 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N TRP Q 31 " --> pdb=" O VAL Q 81 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N VAL Q 81 " --> pdb=" O TRP Q 31 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'M' and resid 74 through 77 Processing sheet with id=AC7, first strand: chain 'M' and resid 89 through 90 Processing sheet with id=AC8, first strand: chain 'N' and resid 62 through 65 removed outlier: 6.465A pdb=" N VAL N 101 " --> pdb=" O ALA N 35 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ALA N 35 " --> pdb=" O VAL N 101 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N TYR N 103 " --> pdb=" O LEU N 33 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'N' and resid 39 through 42 removed outlier: 5.570A pdb=" N VAL N 89 " --> pdb=" O GLU N 75 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N GLU N 75 " --> pdb=" O VAL N 89 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TYR N 91 " --> pdb=" O ILE N 73 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'O' and resid 33 through 37 removed outlier: 4.034A pdb=" N MET O 110 " --> pdb=" O CYS O 100 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'P' and resid 47 through 52 removed outlier: 6.699A pdb=" N VAL P 39 " --> pdb=" O LEU P 48 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N ALA P 50 " --> pdb=" O ALA P 37 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N ALA P 37 " --> pdb=" O ALA P 50 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N SER P 52 " --> pdb=" O ILE P 35 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ILE P 35 " --> pdb=" O SER P 52 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'S' and resid 10 through 14 removed outlier: 6.758A pdb=" N TYR S 2 " --> pdb=" O ILE S 41 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N ILE S 41 " --> pdb=" O TYR S 2 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N VAL S 4 " --> pdb=" O LEU S 39 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'S' and resid 19 through 23 removed outlier: 6.852A pdb=" N PHE S 93 " --> pdb=" O HIS S 66 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N HIS S 66 " --> pdb=" O PHE S 93 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ASP S 95 " --> pdb=" O VAL S 64 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N LYS S 60 " --> pdb=" O THR S 99 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N ILE S 101 " --> pdb=" O VAL S 58 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N VAL S 58 " --> pdb=" O ILE S 101 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'S' and resid 72 through 78 removed outlier: 4.209A pdb=" N TYR S 83 " --> pdb=" O ARG S 78 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'T' and resid 2 through 11 removed outlier: 5.628A pdb=" N SER T 101 " --> pdb=" O HIS T 9 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N SER T 108 " --> pdb=" O VAL T 71 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N VAL T 71 " --> pdb=" O SER T 108 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'T' and resid 82 through 87 Processing sheet with id=AD8, first strand: chain 'U' and resid 11 through 14 removed outlier: 3.861A pdb=" N LYS U 81 " --> pdb=" O VAL U 34 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N TRP U 80 " --> pdb=" O VAL U 62 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N VAL U 62 " --> pdb=" O TRP U 80 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N LYS U 82 " --> pdb=" O THR U 60 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N THR U 60 " --> pdb=" O LYS U 82 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N TYR U 84 " --> pdb=" O VAL U 58 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N VAL U 58 " --> pdb=" O TYR U 84 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N THR U 86 " --> pdb=" O GLU U 56 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'U' and resid 67 through 70 Processing sheet with id=AE1, first strand: chain 'V' and resid 65 through 66 removed outlier: 7.004A pdb=" N LYS V 33 " --> pdb=" O VAL V 28 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N VAL V 28 " --> pdb=" O LYS V 33 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N ILE V 35 " --> pdb=" O LYS V 26 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N GLU V 10 " --> pdb=" O PHE V 73 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ILE V 72 " --> pdb=" O ASP V 81 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'V' and resid 41 through 45 Processing sheet with id=AE3, first strand: chain 'V' and resid 83 through 88 Processing sheet with id=AE4, first strand: chain 'W' and resid 3 through 8 removed outlier: 7.906A pdb=" N ASN W 5 " --> pdb=" O ASP W 43 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N ASP W 43 " --> pdb=" O ASN W 5 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ILE W 89 " --> pdb=" O PRO W 27 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ASP W 76 " --> pdb=" O ASP W 90 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N VAL W 92 " --> pdb=" O ALA W 74 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N ALA W 74 " --> pdb=" O VAL W 92 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'X' and resid 22 through 23 removed outlier: 3.542A pdb=" N ARG X 39 " --> pdb=" O GLY X 22 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N LEU X 59 " --> pdb=" O ILE X 37 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'X' and resid 30 through 31 removed outlier: 6.458A pdb=" N HIS X 46 " --> pdb=" O ILE X 80 " (cutoff:3.500A) removed outlier: 8.651A pdb=" N ILE X 82 " --> pdb=" O HIS X 46 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'Y' and resid 13 through 18 Processing sheet with id=AE8, first strand: chain 'Y' and resid 33 through 40 Processing sheet with id=AE9, first strand: chain 'a' and resid 35 through 38 Processing sheet with id=AF1, first strand: chain 'b' and resid 29 through 30 Processing sheet with id=AF2, first strand: chain 'b' and resid 48 through 49 Processing sheet with id=AF3, first strand: chain 'c' and resid 20 through 25 Processing sheet with id=AF4, first strand: chain 'e' and resid 15 through 16 Processing sheet with id=AF5, first strand: chain 'f' and resid 2 through 4 removed outlier: 6.065A pdb=" N LYS f 2 " --> pdb=" O ARG f 36 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N ILE f 23 " --> pdb=" O GLN f 37 " (cutoff:3.500A) 1173 hydrogen bonds defined for protein. 3240 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2567 hydrogen bonds 4040 hydrogen bond angles 0 basepair planarities 1020 basepair parallelities 1574 stacking parallelities Total time for adding SS restraints: 175.15 Time building geometry restraints manager: 43.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 17675 1.33 - 1.47: 43808 1.47 - 1.60: 37260 1.60 - 1.74: 2892 1.74 - 1.87: 174 Bond restraints: 101809 Sorted by residual: bond pdb=" CA UNK i 453 " pdb=" C UNK i 453 " ideal model delta sigma weight residual 1.525 1.678 -0.153 2.10e-02 2.27e+03 5.34e+01 bond pdb=" N UNK i 447 " pdb=" CA UNK i 447 " ideal model delta sigma weight residual 1.458 1.592 -0.134 1.90e-02 2.77e+03 4.98e+01 bond pdb=" CA UNK i 350 " pdb=" C UNK i 350 " ideal model delta sigma weight residual 1.525 1.673 -0.148 2.10e-02 2.27e+03 4.98e+01 bond pdb=" CA UNK i 449 " pdb=" C UNK i 449 " ideal model delta sigma weight residual 1.525 1.659 -0.134 2.10e-02 2.27e+03 4.04e+01 bond pdb=" CA UNK i 436 " pdb=" C UNK i 436 " ideal model delta sigma weight residual 1.525 1.656 -0.131 2.10e-02 2.27e+03 3.92e+01 ... (remaining 101804 not shown) Histogram of bond angle deviations from ideal: 97.09 - 105.08: 14467 105.08 - 113.07: 61717 113.07 - 121.06: 46903 121.06 - 129.05: 26060 129.05 - 137.05: 3405 Bond angle restraints: 152552 Sorted by residual: angle pdb=" C GLU G 155 " pdb=" N PRO G 156 " pdb=" CA PRO G 156 " ideal model delta sigma weight residual 119.82 129.01 -9.19 9.80e-01 1.04e+00 8.80e+01 angle pdb=" N ASP J 116 " pdb=" CA ASP J 116 " pdb=" C ASP J 116 " ideal model delta sigma weight residual 113.17 123.25 -10.08 1.26e+00 6.30e-01 6.41e+01 angle pdb=" N VAL J 98 " pdb=" CA VAL J 98 " pdb=" C VAL J 98 " ideal model delta sigma weight residual 112.83 120.32 -7.49 9.90e-01 1.02e+00 5.73e+01 angle pdb=" N PRO J 22 " pdb=" CA PRO J 22 " pdb=" C PRO J 22 " ideal model delta sigma weight residual 110.70 118.69 -7.99 1.22e+00 6.72e-01 4.29e+01 angle pdb=" C LYS N 71 " pdb=" N PRO N 72 " pdb=" CA PRO N 72 " ideal model delta sigma weight residual 119.90 126.67 -6.77 1.05e+00 9.07e-01 4.16e+01 ... (remaining 152547 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.37: 56727 35.37 - 70.75: 7607 70.75 - 106.12: 844 106.12 - 141.49: 14 141.49 - 176.87: 10 Dihedral angle restraints: 65202 sinusoidal: 54889 harmonic: 10313 Sorted by residual: dihedral pdb=" C4' U A1344 " pdb=" C3' U A1344 " pdb=" C2' U A1344 " pdb=" C1' U A1344 " ideal model delta sinusoidal sigma weight residual -35.00 32.08 -67.08 1 8.00e+00 1.56e-02 9.16e+01 dihedral pdb=" C4' C A 645 " pdb=" C3' C A 645 " pdb=" C2' C A 645 " pdb=" C1' C A 645 " ideal model delta sinusoidal sigma weight residual -35.00 30.58 -65.58 1 8.00e+00 1.56e-02 8.80e+01 dihedral pdb=" C5' U A1344 " pdb=" C4' U A1344 " pdb=" C3' U A1344 " pdb=" O3' U A1344 " ideal model delta sinusoidal sigma weight residual 147.00 83.15 63.85 1 8.00e+00 1.56e-02 8.39e+01 ... (remaining 65199 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 17544 0.074 - 0.149: 1865 0.149 - 0.223: 135 0.223 - 0.297: 11 0.297 - 0.372: 4 Chirality restraints: 19559 Sorted by residual: chirality pdb=" C3' C A 645 " pdb=" C4' C A 645 " pdb=" O3' C A 645 " pdb=" C2' C A 645 " both_signs ideal model delta sigma weight residual False -2.74 -2.37 -0.37 2.00e-01 2.50e+01 3.46e+00 chirality pdb=" C3' U A1344 " pdb=" C4' U A1344 " pdb=" O3' U A1344 " pdb=" C2' U A1344 " both_signs ideal model delta sigma weight residual False -2.74 -2.38 -0.37 2.00e-01 2.50e+01 3.34e+00 chirality pdb=" CA UNK i 453 " pdb=" N UNK i 453 " pdb=" C UNK i 453 " pdb=" CB UNK i 453 " both_signs ideal model delta sigma weight residual False 2.52 2.84 -0.32 2.00e-01 2.50e+01 2.63e+00 ... (remaining 19556 not shown) Planarity restraints: 7975 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU U 93 " 0.019 2.00e-02 2.50e+03 3.64e-02 1.33e+01 pdb=" C LEU U 93 " -0.063 2.00e-02 2.50e+03 pdb=" O LEU U 93 " 0.024 2.00e-02 2.50e+03 pdb=" N ASP U 94 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY J 25 " -0.059 5.00e-02 4.00e+02 9.02e-02 1.30e+01 pdb=" N PRO J 26 " 0.156 5.00e-02 4.00e+02 pdb=" CA PRO J 26 " -0.050 5.00e-02 4.00e+02 pdb=" CD PRO J 26 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' A A 984 " -0.046 2.00e-02 2.50e+03 1.91e-02 1.00e+01 pdb=" N9 A A 984 " 0.034 2.00e-02 2.50e+03 pdb=" C8 A A 984 " 0.012 2.00e-02 2.50e+03 pdb=" N7 A A 984 " -0.001 2.00e-02 2.50e+03 pdb=" C5 A A 984 " -0.002 2.00e-02 2.50e+03 pdb=" C6 A A 984 " -0.010 2.00e-02 2.50e+03 pdb=" N6 A A 984 " -0.008 2.00e-02 2.50e+03 pdb=" N1 A A 984 " -0.008 2.00e-02 2.50e+03 pdb=" C2 A A 984 " 0.004 2.00e-02 2.50e+03 pdb=" N3 A A 984 " 0.016 2.00e-02 2.50e+03 pdb=" C4 A A 984 " 0.010 2.00e-02 2.50e+03 ... (remaining 7972 not shown) Histogram of nonbonded interaction distances: 1.74 - 2.37: 291 2.37 - 3.00: 46197 3.00 - 3.63: 162875 3.63 - 4.27: 284591 4.27 - 4.90: 375963 Nonbonded interactions: 869917 Sorted by model distance: nonbonded pdb=" OP1 A A 751 " pdb="MG MG A3020 " model vdw 1.737 2.170 nonbonded pdb=" OP1 U A 827 " pdb="MG MG A3027 " model vdw 1.758 2.170 nonbonded pdb=" OP2 U A 963 " pdb="MG MG A3030 " model vdw 1.771 2.170 nonbonded pdb=" OP1 A A1780 " pdb="MG MG A3086 " model vdw 1.819 2.170 nonbonded pdb=" O4 U A1263 " pdb="MG MG A3180 " model vdw 1.822 2.170 ... (remaining 869912 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators 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: 1.690 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: 0.050 Extract box with map and model: 8.900 Check model and map are aligned: 1.060 Set scattering table: 0.640 Process input model: 372.250 Find NCS groups from input model: 1.900 Set up NCS constraints: 0.220 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 389.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.153 101809 Z= 0.474 Angle : 1.096 14.098 152552 Z= 0.619 Chirality : 0.047 0.372 19559 Planarity : 0.005 0.090 7975 Dihedral : 23.753 176.868 58554 Min Nonbonded Distance : 1.737 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.26 % Favored : 96.68 % Rotamer: Outliers : 11.31 % Allowed : 13.17 % Favored : 75.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.88 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.33 (0.11), residues: 3529 helix: -3.48 (0.10), residues: 1067 sheet: -1.39 (0.16), residues: 705 loop : -1.60 (0.12), residues: 1757 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 0.025 0.003 PHE I 106 TYR 0.029 0.003 TYR T 38 ARG 0.006 0.001 ARG N 6 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7058 Ramachandran restraints generated. 3529 Oldfield, 0 Emsley, 3529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7058 Ramachandran restraints generated. 3529 Oldfield, 0 Emsley, 3529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1521 residues out of total 2905 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 328 poor density : 1193 time to evaluate : 4.147 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: C 5 LYS cc_start: 0.8732 (mttt) cc_final: 0.8371 (mtpp) REVERT: C 25 HIS cc_start: 0.8775 (t70) cc_final: 0.7976 (t-170) REVERT: C 70 ASN cc_start: 0.8375 (p0) cc_final: 0.8006 (t0) REVERT: C 134 ASN cc_start: 0.8699 (OUTLIER) cc_final: 0.8330 (m-40) REVERT: C 140 THR cc_start: 0.8842 (m) cc_final: 0.8482 (p) REVERT: C 178 SER cc_start: 0.9177 (p) cc_final: 0.8933 (m) REVERT: C 189 ARG cc_start: 0.8917 (OUTLIER) cc_final: 0.8378 (mtp-110) REVERT: D 1 MET cc_start: 0.7963 (ttt) cc_final: 0.7634 (mpp) REVERT: D 28 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.8083 (tm-30) REVERT: D 29 VAL cc_start: 0.9030 (OUTLIER) cc_final: 0.8738 (t) REVERT: D 40 LEU cc_start: 0.8722 (mt) cc_final: 0.8054 (mp) REVERT: D 43 ASP cc_start: 0.8802 (m-30) cc_final: 0.8332 (m-30) REVERT: D 60 VAL cc_start: 0.8454 (OUTLIER) cc_final: 0.8183 (m) REVERT: D 84 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8009 (mt) REVERT: D 104 VAL cc_start: 0.9000 (t) cc_final: 0.8682 (m) REVERT: D 128 ARG cc_start: 0.8702 (OUTLIER) cc_final: 0.8203 (ttp-110) REVERT: D 129 THR cc_start: 0.8957 (p) cc_final: 0.8718 (p) REVERT: D 146 ILE cc_start: 0.8908 (pt) cc_final: 0.8675 (pt) REVERT: D 176 ASP cc_start: 0.8142 (m-30) cc_final: 0.7938 (m-30) REVERT: E 116 ASP cc_start: 0.8210 (m-30) cc_final: 0.7915 (t0) REVERT: E 143 LEU cc_start: 0.7688 (mt) cc_final: 0.7456 (mp) REVERT: E 153 LEU cc_start: 0.7978 (tp) cc_final: 0.7680 (tt) REVERT: E 168 ASP cc_start: 0.6848 (t0) cc_final: 0.6555 (t0) REVERT: E 169 VAL cc_start: 0.9114 (OUTLIER) cc_final: 0.8648 (m) REVERT: E 171 ASP cc_start: 0.8466 (p0) cc_final: 0.8236 (p0) REVERT: E 181 ILE cc_start: 0.9082 (mt) cc_final: 0.8871 (mm) REVERT: F 35 THR cc_start: 0.8434 (m) cc_final: 0.8213 (p) REVERT: F 44 ILE cc_start: 0.7553 (pt) cc_final: 0.6725 (tt) REVERT: F 56 ASP cc_start: 0.8329 (m-30) cc_final: 0.7603 (m-30) REVERT: F 99 PHE cc_start: 0.8863 (t80) cc_final: 0.8606 (t80) REVERT: F 120 LYS cc_start: 0.7951 (pttt) cc_final: 0.7541 (tptt) REVERT: F 153 ASP cc_start: 0.7149 (OUTLIER) cc_final: 0.6922 (m-30) REVERT: F 178 ARG cc_start: 0.6994 (OUTLIER) cc_final: 0.6594 (mmm160) REVERT: G 25 THR cc_start: 0.8081 (m) cc_final: 0.7844 (p) REVERT: G 34 THR cc_start: 0.7798 (m) cc_final: 0.7495 (t) REVERT: G 75 MET cc_start: 0.8815 (mtp) cc_final: 0.8606 (mtt) REVERT: G 114 ASP cc_start: 0.7979 (OUTLIER) cc_final: 0.7380 (m-30) REVERT: G 116 GLN cc_start: 0.8051 (tp-100) cc_final: 0.7575 (tp40) REVERT: G 155 GLU cc_start: 0.8776 (pp20) cc_final: 0.8339 (pp20) REVERT: G 175 LYS cc_start: 0.5471 (tttt) cc_final: 0.4943 (tmtt) REVERT: H 15 LEU cc_start: 0.8112 (OUTLIER) cc_final: 0.7472 (tp) REVERT: H 30 LEU cc_start: 0.8980 (mt) cc_final: 0.8491 (mt) REVERT: H 47 PHE cc_start: 0.7471 (t80) cc_final: 0.6307 (t80) REVERT: H 110 VAL cc_start: 0.7953 (OUTLIER) cc_final: 0.6823 (m) REVERT: H 112 LYS cc_start: 0.6038 (OUTLIER) cc_final: 0.5830 (tmtt) REVERT: I 18 VAL cc_start: 0.5662 (t) cc_final: 0.5363 (p) REVERT: I 55 VAL cc_start: 0.8044 (OUTLIER) cc_final: 0.7665 (t) REVERT: J 17 MET cc_start: 0.6788 (mtp) cc_final: 0.6312 (tpt) REVERT: J 31 GLN cc_start: 0.2038 (OUTLIER) cc_final: 0.1772 (tp40) REVERT: J 35 ILE cc_start: 0.4146 (OUTLIER) cc_final: 0.3876 (pt) REVERT: J 125 MET cc_start: 0.3916 (mtt) cc_final: 0.3501 (mtt) REVERT: K 10 THR cc_start: 0.8645 (p) cc_final: 0.8138 (t) REVERT: K 16 TYR cc_start: 0.8579 (m-80) cc_final: 0.8196 (m-10) REVERT: K 80 HIS cc_start: 0.7963 (m90) cc_final: 0.7590 (m170) REVERT: L 1 MET cc_start: 0.8669 (tpt) cc_final: 0.8415 (tpp) REVERT: L 7 MET cc_start: 0.7811 (mmt) cc_final: 0.7396 (mmm) REVERT: L 9 ASN cc_start: 0.7881 (m-40) cc_final: 0.7613 (m-40) REVERT: L 17 ARG cc_start: 0.8363 (mmt90) cc_final: 0.8138 (mtp85) REVERT: L 58 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.7922 (pp) REVERT: L 71 ARG cc_start: 0.8182 (mmt90) cc_final: 0.7825 (mmm-85) REVERT: L 78 ARG cc_start: 0.8334 (mtm-85) cc_final: 0.7927 (mtm180) REVERT: M 25 SER cc_start: 0.9475 (p) cc_final: 0.9193 (t) REVERT: M 76 GLU cc_start: 0.7880 (pt0) cc_final: 0.7578 (pt0) REVERT: M 121 THR cc_start: 0.7268 (m) cc_final: 0.6570 (p) REVERT: N 6 ARG cc_start: 0.8250 (OUTLIER) cc_final: 0.7080 (ptm-80) REVERT: N 106 ASP cc_start: 0.8811 (p0) cc_final: 0.8566 (p0) REVERT: P 1 MET cc_start: 0.6380 (mtt) cc_final: 0.6164 (mtp) REVERT: P 31 THR cc_start: 0.8977 (OUTLIER) cc_final: 0.8487 (p) REVERT: P 69 ASP cc_start: 0.7861 (OUTLIER) cc_final: 0.7461 (m-30) REVERT: P 87 ILE cc_start: 0.7983 (mp) cc_final: 0.7777 (mp) REVERT: Q 106 LYS cc_start: 0.4516 (mmtt) cc_final: 0.3538 (mptt) REVERT: R 15 LYS cc_start: 0.8349 (ttpt) cc_final: 0.8078 (ttpp) REVERT: R 30 ARG cc_start: 0.8074 (mtt90) cc_final: 0.7832 (mtm-85) REVERT: R 51 ARG cc_start: 0.8445 (OUTLIER) cc_final: 0.6383 (mtm-85) REVERT: R 61 TRP cc_start: 0.8502 (m-10) cc_final: 0.8228 (m-10) REVERT: R 87 SER cc_start: 0.7792 (m) cc_final: 0.7243 (p) REVERT: S 1 MET cc_start: 0.7898 (ttp) cc_final: 0.7575 (ttm) REVERT: S 59 ILE cc_start: 0.8923 (mt) cc_final: 0.8677 (mm) REVERT: T 12 SER cc_start: 0.8718 (OUTLIER) cc_final: 0.8368 (p) REVERT: T 38 TYR cc_start: 0.8311 (m-80) cc_final: 0.8109 (m-10) REVERT: T 100 THR cc_start: 0.8502 (p) cc_final: 0.8258 (t) REVERT: T 104 THR cc_start: 0.8915 (m) cc_final: 0.8710 (m) REVERT: U 82 LYS cc_start: 0.8596 (ttmt) cc_final: 0.8326 (ttpp) REVERT: V 24 LYS cc_start: 0.8381 (tttt) cc_final: 0.8109 (tttp) REVERT: W 1 MET cc_start: 0.6141 (tpp) cc_final: 0.5910 (mpp) REVERT: W 4 ILE cc_start: 0.9067 (mt) cc_final: 0.8849 (mt) REVERT: W 76 ASP cc_start: 0.7642 (t0) cc_final: 0.7086 (p0) REVERT: W 80 HIS cc_start: 0.8709 (t-90) cc_final: 0.8390 (t-90) REVERT: W 83 LYS cc_start: 0.9007 (mttt) cc_final: 0.8790 (mttt) REVERT: X 25 ARG cc_start: 0.8153 (mmt-90) cc_final: 0.7885 (mmt90) REVERT: X 64 ASP cc_start: 0.8407 (m-30) cc_final: 0.8098 (m-30) REVERT: X 68 LYS cc_start: 0.9155 (tptp) cc_final: 0.8698 (tppt) REVERT: X 75 LYS cc_start: 0.8200 (mttp) cc_final: 0.7968 (mttp) REVERT: Y 4 VAL cc_start: 0.9268 (OUTLIER) cc_final: 0.8855 (p) REVERT: Y 26 LYS cc_start: 0.8971 (mmtt) cc_final: 0.8377 (mmmm) REVERT: Y 74 ARG cc_start: 0.6851 (OUTLIER) cc_final: 0.6443 (ttp-110) REVERT: Z 48 ARG cc_start: 0.8652 (OUTLIER) cc_final: 0.8216 (mmt90) REVERT: c 5 ILE cc_start: 0.8012 (OUTLIER) cc_final: 0.7329 (pt) REVERT: c 6 ARG cc_start: 0.8157 (OUTLIER) cc_final: 0.7809 (mmm160) REVERT: c 49 TYR cc_start: 0.8444 (m-80) cc_final: 0.7620 (m-80) REVERT: d 11 LYS cc_start: 0.8870 (mttt) cc_final: 0.8532 (tttt) REVERT: d 25 LYS cc_start: 0.8511 (OUTLIER) cc_final: 0.8183 (ttpp) REVERT: e 8 ARG cc_start: 0.8349 (OUTLIER) cc_final: 0.7498 (tpp80) REVERT: e 16 LYS cc_start: 0.9003 (tptt) cc_final: 0.8589 (tttm) REVERT: e 58 VAL cc_start: 0.8775 (t) cc_final: 0.8487 (t) REVERT: f 19 ARG cc_start: 0.8498 (mtt180) cc_final: 0.8290 (mtt180) REVERT: i 375 ARG cc_start: 0.7999 (mtm180) cc_final: 0.7491 (mtt180) REVERT: i 379 ILE cc_start: 0.8173 (OUTLIER) cc_final: 0.7840 (mp) REVERT: i 381 ASN cc_start: 0.5650 (m-40) cc_final: 0.5415 (m-40) REVERT: i 382 SER cc_start: 0.6553 (m) cc_final: 0.6019 (t) REVERT: i 420 PHE cc_start: 0.8506 (t80) cc_final: 0.8136 (t80) REVERT: i 423 MET cc_start: 0.8328 (mmp) cc_final: 0.7304 (mmm) REVERT: i 424 GLN cc_start: 0.7700 (tt0) cc_final: 0.7160 (tm-30) REVERT: i 426 MET cc_start: 0.7799 (tpp) cc_final: 0.7339 (mmm) outliers start: 328 outliers final: 83 residues processed: 1388 average time/residue: 0.9768 time to fit residues: 2232.2490 Evaluate side-chains 926 residues out of total 2905 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 812 time to evaluate : 4.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 134 ASN Chi-restraints excluded: chain C residue 156 ARG Chi-restraints excluded: chain C residue 189 ARG Chi-restraints excluded: chain C residue 242 LYS Chi-restraints excluded: chain C residue 251 GLN Chi-restraints excluded: chain D residue 28 GLU Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 128 ARG Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain E residue 184 ASP Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain F residue 14 LYS Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain F residue 153 ASP Chi-restraints excluded: chain F residue 162 SER Chi-restraints excluded: chain F residue 178 ARG Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 114 ASP Chi-restraints excluded: chain G residue 125 CYS Chi-restraints excluded: chain G residue 133 LEU Chi-restraints excluded: chain G residue 141 ILE Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain H residue 110 VAL Chi-restraints excluded: chain H residue 112 LYS Chi-restraints excluded: chain I residue 54 VAL Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain J residue 31 GLN Chi-restraints excluded: chain J residue 35 ILE Chi-restraints excluded: chain J residue 78 VAL Chi-restraints excluded: chain J residue 111 GLN Chi-restraints excluded: chain J residue 128 SER Chi-restraints excluded: chain K residue 7 LYS Chi-restraints excluded: chain K residue 17 VAL Chi-restraints excluded: chain K residue 28 LEU Chi-restraints excluded: chain K residue 40 HIS Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 88 THR Chi-restraints excluded: chain K residue 131 ASN Chi-restraints excluded: chain K residue 142 ILE Chi-restraints excluded: chain L residue 49 ARG Chi-restraints excluded: chain L residue 58 LEU Chi-restraints excluded: chain L residue 116 ILE Chi-restraints excluded: chain M residue 46 VAL Chi-restraints excluded: chain M residue 141 LYS Chi-restraints excluded: chain N residue 6 ARG Chi-restraints excluded: chain N residue 7 THR Chi-restraints excluded: chain O residue 33 ILE Chi-restraints excluded: chain O residue 36 THR Chi-restraints excluded: chain O residue 100 CYS Chi-restraints excluded: chain P residue 2 ASP Chi-restraints excluded: chain P residue 31 THR Chi-restraints excluded: chain P residue 36 TYR Chi-restraints excluded: chain P residue 49 VAL Chi-restraints excluded: chain P residue 55 GLU Chi-restraints excluded: chain P residue 69 ASP Chi-restraints excluded: chain Q residue 26 VAL Chi-restraints excluded: chain Q residue 92 VAL Chi-restraints excluded: chain R residue 17 ILE Chi-restraints excluded: chain R residue 40 ILE Chi-restraints excluded: chain R residue 51 ARG Chi-restraints excluded: chain R residue 74 ILE Chi-restraints excluded: chain R residue 80 ILE Chi-restraints excluded: chain R residue 109 LEU Chi-restraints excluded: chain S residue 4 VAL Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain S residue 72 VAL Chi-restraints excluded: chain S residue 83 TYR Chi-restraints excluded: chain T residue 12 SER Chi-restraints excluded: chain T residue 68 ASP Chi-restraints excluded: chain T residue 74 ILE Chi-restraints excluded: chain T residue 98 LYS Chi-restraints excluded: chain U residue 7 LEU Chi-restraints excluded: chain V residue 7 ARG Chi-restraints excluded: chain V residue 42 VAL Chi-restraints excluded: chain V residue 68 SER Chi-restraints excluded: chain V residue 83 VAL Chi-restraints excluded: chain W residue 61 LEU Chi-restraints excluded: chain X residue 38 VAL Chi-restraints excluded: chain Y residue 4 VAL Chi-restraints excluded: chain Y residue 13 VAL Chi-restraints excluded: chain Y residue 42 SER Chi-restraints excluded: chain Y residue 74 ARG Chi-restraints excluded: chain Z residue 16 THR Chi-restraints excluded: chain Z residue 28 LEU Chi-restraints excluded: chain Z residue 48 ARG Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain b residue 15 MET Chi-restraints excluded: chain b residue 52 ARG Chi-restraints excluded: chain c residue 5 ILE Chi-restraints excluded: chain c residue 6 ARG Chi-restraints excluded: chain c residue 22 THR Chi-restraints excluded: chain c residue 42 VAL Chi-restraints excluded: chain c residue 47 VAL Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 24 THR Chi-restraints excluded: chain d residue 25 LYS Chi-restraints excluded: chain e residue 8 ARG Chi-restraints excluded: chain e residue 51 SER Chi-restraints excluded: chain i residue 333 ASP Chi-restraints excluded: chain i residue 374 VAL Chi-restraints excluded: chain i residue 379 ILE Chi-restraints excluded: chain k residue 40 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 640 random chunks: chunk 540 optimal weight: 5.9990 chunk 485 optimal weight: 4.9990 chunk 269 optimal weight: 10.0000 chunk 165 optimal weight: 10.0000 chunk 327 optimal weight: 0.4980 chunk 259 optimal weight: 9.9990 chunk 501 optimal weight: 2.9990 chunk 194 optimal weight: 10.0000 chunk 305 optimal weight: 0.0010 chunk 373 optimal weight: 7.9990 chunk 581 optimal weight: 9.9990 overall best weight: 2.8992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 90 ASN C 200 HIS C 251 GLN D 136 ASN D 140 HIS D 173 GLN E 163 ASN E 165 HIS G 101 ASN H 18 GLN H 20 ASN H 43 ASN H 135 HIS J 31 GLN K 80 HIS K 138 GLN L 3 GLN M 35 HIS ** N 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 52 ASN ** R 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 81 ASN S 18 GLN ** S 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 91 GLN T 7 HIS T 57 ASN ** U 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 70 HIS W 44 HIS Y 20 HIS Z 58 ASN i 381 ASN ** i 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.2619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 101809 Z= 0.203 Angle : 0.638 8.753 152552 Z= 0.332 Chirality : 0.037 0.319 19559 Planarity : 0.005 0.073 7975 Dihedral : 23.485 179.565 51791 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.18 % Favored : 97.76 % Rotamer: Outliers : 7.00 % Allowed : 20.58 % Favored : 72.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.13), residues: 3529 helix: -0.76 (0.15), residues: 1067 sheet: -0.82 (0.17), residues: 746 loop : -0.85 (0.13), residues: 1716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 213 HIS 0.008 0.001 HIS F 5 PHE 0.025 0.002 PHE V 73 TYR 0.020 0.002 TYR F 7 ARG 0.030 0.001 ARG Q 39 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7058 Ramachandran restraints generated. 3529 Oldfield, 0 Emsley, 3529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7058 Ramachandran restraints generated. 3529 Oldfield, 0 Emsley, 3529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1138 residues out of total 2905 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 203 poor density : 935 time to evaluate : 4.223 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: C 5 LYS cc_start: 0.8691 (mttt) cc_final: 0.8294 (mtpp) REVERT: C 25 HIS cc_start: 0.8777 (t70) cc_final: 0.8181 (t70) REVERT: C 178 SER cc_start: 0.9278 (p) cc_final: 0.8962 (m) REVERT: C 213 TRP cc_start: 0.8341 (m-10) cc_final: 0.7614 (m-10) REVERT: C 225 MET cc_start: 0.8606 (mtm) cc_final: 0.8401 (mtm) REVERT: C 251 GLN cc_start: 0.8182 (OUTLIER) cc_final: 0.7811 (tt0) REVERT: D 28 GLU cc_start: 0.8471 (OUTLIER) cc_final: 0.7961 (tm-30) REVERT: D 40 LEU cc_start: 0.8460 (mt) cc_final: 0.8103 (mp) REVERT: D 42 ASN cc_start: 0.8311 (t0) cc_final: 0.8001 (t0) REVERT: D 43 ASP cc_start: 0.8553 (m-30) cc_final: 0.8353 (m-30) REVERT: D 84 LEU cc_start: 0.8624 (mt) cc_final: 0.8380 (mm) REVERT: D 104 VAL cc_start: 0.9057 (t) cc_final: 0.8625 (m) REVERT: D 128 ARG cc_start: 0.8952 (OUTLIER) cc_final: 0.8429 (ttp-110) REVERT: E 153 LEU cc_start: 0.7845 (tp) cc_final: 0.7226 (tp) REVERT: E 168 ASP cc_start: 0.7343 (t0) cc_final: 0.7095 (t0) REVERT: E 169 VAL cc_start: 0.8983 (OUTLIER) cc_final: 0.8483 (m) REVERT: F 4 LEU cc_start: 0.8421 (mt) cc_final: 0.8087 (mt) REVERT: F 27 GLN cc_start: 0.8480 (mt0) cc_final: 0.7776 (tt0) REVERT: F 35 THR cc_start: 0.8227 (m) cc_final: 0.8023 (p) REVERT: F 42 GLU cc_start: 0.7721 (pm20) cc_final: 0.6904 (pm20) REVERT: F 44 ILE cc_start: 0.7043 (pt) cc_final: 0.6385 (tt) REVERT: F 71 ARG cc_start: 0.8459 (ttp80) cc_final: 0.8239 (ttt-90) REVERT: F 99 PHE cc_start: 0.8900 (t80) cc_final: 0.8654 (t80) REVERT: F 120 LYS cc_start: 0.8004 (pttt) cc_final: 0.7555 (tptt) REVERT: F 134 GLU cc_start: 0.8456 (pm20) cc_final: 0.8233 (pm20) REVERT: F 138 PHE cc_start: 0.8910 (m-80) cc_final: 0.8633 (m-80) REVERT: F 161 LYS cc_start: 0.7322 (mmmt) cc_final: 0.6817 (ptpt) REVERT: F 165 GLU cc_start: 0.7931 (mp0) cc_final: 0.6753 (mp0) REVERT: F 178 ARG cc_start: 0.6875 (OUTLIER) cc_final: 0.6463 (mmm160) REVERT: G 48 ASN cc_start: 0.7673 (OUTLIER) cc_final: 0.7426 (t0) REVERT: G 58 TYR cc_start: 0.8140 (m-80) cc_final: 0.7879 (m-80) REVERT: G 130 GLU cc_start: 0.8401 (tm-30) cc_final: 0.7615 (mm-30) REVERT: G 151 TYR cc_start: 0.8794 (m-10) cc_final: 0.8537 (m-10) REVERT: G 175 LYS cc_start: 0.5447 (tttt) cc_final: 0.5073 (tmtt) REVERT: H 40 THR cc_start: 0.6473 (m) cc_final: 0.6232 (m) REVERT: H 109 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.7469 (pm20) REVERT: H 112 LYS cc_start: 0.6652 (OUTLIER) cc_final: 0.6191 (tmtt) REVERT: J 35 ILE cc_start: 0.4059 (tp) cc_final: 0.3168 (pt) REVERT: J 40 LYS cc_start: 0.6162 (mptt) cc_final: 0.5748 (mmtm) REVERT: K 10 THR cc_start: 0.8633 (p) cc_final: 0.8150 (t) REVERT: K 91 GLU cc_start: 0.8215 (mt-10) cc_final: 0.7984 (mt-10) REVERT: K 96 ARG cc_start: 0.8685 (tpt170) cc_final: 0.8467 (tpt170) REVERT: L 58 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.7938 (pp) REVERT: L 93 GLN cc_start: 0.8002 (mm110) cc_final: 0.7342 (mm110) REVERT: M 25 SER cc_start: 0.9541 (p) cc_final: 0.9262 (t) REVERT: M 121 THR cc_start: 0.7271 (m) cc_final: 0.6797 (p) REVERT: N 9 PHE cc_start: 0.8607 (m-80) cc_final: 0.8031 (m-10) REVERT: N 38 ARG cc_start: 0.9026 (OUTLIER) cc_final: 0.8503 (ttm-80) REVERT: N 47 GLU cc_start: 0.7948 (mm-30) cc_final: 0.7100 (tp30) REVERT: O 75 ILE cc_start: 0.8289 (tt) cc_final: 0.7971 (tt) REVERT: O 110 MET cc_start: 0.8205 (mmm) cc_final: 0.7976 (mmm) REVERT: P 31 THR cc_start: 0.8839 (OUTLIER) cc_final: 0.8509 (p) REVERT: P 69 ASP cc_start: 0.7722 (OUTLIER) cc_final: 0.7324 (m-30) REVERT: P 78 VAL cc_start: 0.9384 (m) cc_final: 0.9163 (t) REVERT: P 85 LYS cc_start: 0.8561 (mtpt) cc_final: 0.8241 (mptt) REVERT: P 87 ILE cc_start: 0.7752 (mp) cc_final: 0.7495 (mp) REVERT: Q 86 VAL cc_start: 0.9290 (t) cc_final: 0.9032 (m) REVERT: Q 106 LYS cc_start: 0.5424 (mmtt) cc_final: 0.4498 (mptt) REVERT: R 55 ARG cc_start: 0.8717 (mtm-85) cc_final: 0.8300 (ttm170) REVERT: R 61 TRP cc_start: 0.8421 (m-10) cc_final: 0.8133 (m-10) REVERT: T 104 THR cc_start: 0.9185 (m) cc_final: 0.8877 (m) REVERT: U 91 GLN cc_start: 0.7780 (mp10) cc_final: 0.7420 (mp10) REVERT: V 18 ASP cc_start: 0.7149 (m-30) cc_final: 0.6877 (m-30) REVERT: W 1 MET cc_start: 0.6113 (tpp) cc_final: 0.5664 (mpp) REVERT: W 40 ILE cc_start: 0.8625 (OUTLIER) cc_final: 0.8345 (pt) REVERT: W 59 GLU cc_start: 0.7937 (tt0) cc_final: 0.7560 (tt0) REVERT: W 76 ASP cc_start: 0.8222 (t0) cc_final: 0.7998 (p0) REVERT: W 83 LYS cc_start: 0.8975 (mttt) cc_final: 0.8740 (mttt) REVERT: W 90 ASP cc_start: 0.7738 (m-30) cc_final: 0.6927 (m-30) REVERT: X 25 ARG cc_start: 0.8274 (mmt-90) cc_final: 0.8022 (mmt180) REVERT: Y 4 VAL cc_start: 0.9541 (OUTLIER) cc_final: 0.8976 (p) REVERT: Y 26 LYS cc_start: 0.8965 (mmtt) cc_final: 0.8696 (mmtt) REVERT: b 4 GLN cc_start: 0.9053 (OUTLIER) cc_final: 0.8408 (pm20) REVERT: b 36 GLU cc_start: 0.7868 (pm20) cc_final: 0.7606 (pm20) REVERT: c 10 LYS cc_start: 0.7220 (OUTLIER) cc_final: 0.6917 (ptmm) REVERT: c 21 TYR cc_start: 0.8535 (m-10) cc_final: 0.8287 (m-10) REVERT: c 49 TYR cc_start: 0.8499 (m-80) cc_final: 0.7620 (m-80) REVERT: e 16 LYS cc_start: 0.8905 (tptt) cc_final: 0.8244 (tttm) REVERT: i 382 SER cc_start: 0.7243 (m) cc_final: 0.6569 (t) REVERT: i 412 ASP cc_start: 0.7412 (m-30) cc_final: 0.6989 (t0) REVERT: i 423 MET cc_start: 0.8068 (mmp) cc_final: 0.7826 (mmm) REVERT: i 424 GLN cc_start: 0.7531 (tt0) cc_final: 0.7168 (tm-30) REVERT: k 40 LEU cc_start: 0.2869 (OUTLIER) cc_final: 0.2399 (tt) outliers start: 203 outliers final: 108 residues processed: 1062 average time/residue: 0.9135 time to fit residues: 1634.8006 Evaluate side-chains 921 residues out of total 2905 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 796 time to evaluate : 3.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 115 GLN Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 156 ARG Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 242 LYS Chi-restraints excluded: chain C residue 251 GLN Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 28 GLU Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 128 ARG Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 139 LYS Chi-restraints excluded: chain E residue 163 ASN Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain F residue 159 THR Chi-restraints excluded: chain F residue 178 ARG Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 48 ASN Chi-restraints excluded: chain G residue 84 THR Chi-restraints excluded: chain G residue 125 CYS Chi-restraints excluded: chain G residue 131 ILE Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain H residue 109 GLU Chi-restraints excluded: chain H residue 112 LYS Chi-restraints excluded: chain H residue 116 ARG Chi-restraints excluded: chain I residue 17 GLU Chi-restraints excluded: chain I residue 24 SER Chi-restraints excluded: chain I residue 34 THR Chi-restraints excluded: chain I residue 36 ASP Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain K residue 17 VAL Chi-restraints excluded: chain K residue 40 HIS Chi-restraints excluded: chain K residue 88 THR Chi-restraints excluded: chain K residue 93 ILE Chi-restraints excluded: chain K residue 131 ASN Chi-restraints excluded: chain L residue 20 MET Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 49 ARG Chi-restraints excluded: chain L residue 58 LEU Chi-restraints excluded: chain L residue 61 VAL Chi-restraints excluded: chain L residue 107 LEU Chi-restraints excluded: chain L residue 115 ILE Chi-restraints excluded: chain L residue 116 ILE Chi-restraints excluded: chain L residue 117 SER Chi-restraints excluded: chain M residue 46 VAL Chi-restraints excluded: chain M residue 110 VAL Chi-restraints excluded: chain M residue 116 VAL Chi-restraints excluded: chain M residue 118 THR Chi-restraints excluded: chain N residue 7 THR Chi-restraints excluded: chain N residue 36 VAL Chi-restraints excluded: chain N residue 38 ARG Chi-restraints excluded: chain N residue 54 THR Chi-restraints excluded: chain N residue 102 LEU Chi-restraints excluded: chain N residue 133 LYS Chi-restraints excluded: chain O residue 36 THR Chi-restraints excluded: chain O residue 57 THR Chi-restraints excluded: chain O residue 113 ILE Chi-restraints excluded: chain P residue 2 ASP Chi-restraints excluded: chain P residue 31 THR Chi-restraints excluded: chain P residue 36 TYR Chi-restraints excluded: chain P residue 49 VAL Chi-restraints excluded: chain P residue 69 ASP Chi-restraints excluded: chain Q residue 2 SER Chi-restraints excluded: chain Q residue 16 ASP Chi-restraints excluded: chain Q residue 26 VAL Chi-restraints excluded: chain Q residue 30 VAL Chi-restraints excluded: chain Q residue 63 LYS Chi-restraints excluded: chain Q residue 76 THR Chi-restraints excluded: chain Q residue 92 VAL Chi-restraints excluded: chain R residue 31 VAL Chi-restraints excluded: chain R residue 39 VAL Chi-restraints excluded: chain S residue 20 VAL Chi-restraints excluded: chain S residue 32 THR Chi-restraints excluded: chain S residue 45 GLU Chi-restraints excluded: chain S residue 49 ILE Chi-restraints excluded: chain S residue 72 VAL Chi-restraints excluded: chain T residue 74 ILE Chi-restraints excluded: chain T residue 81 SER Chi-restraints excluded: chain U residue 16 VAL Chi-restraints excluded: chain U residue 60 THR Chi-restraints excluded: chain U residue 79 ASP Chi-restraints excluded: chain V residue 12 ILE Chi-restraints excluded: chain V residue 59 VAL Chi-restraints excluded: chain V residue 91 LYS Chi-restraints excluded: chain W residue 20 LEU Chi-restraints excluded: chain W residue 40 ILE Chi-restraints excluded: chain W residue 61 LEU Chi-restraints excluded: chain W residue 77 VAL Chi-restraints excluded: chain X residue 38 VAL Chi-restraints excluded: chain Y residue 4 VAL Chi-restraints excluded: chain Y residue 14 THR Chi-restraints excluded: chain Z residue 48 ARG Chi-restraints excluded: chain a residue 41 THR Chi-restraints excluded: chain b residue 4 GLN Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain b residue 26 THR Chi-restraints excluded: chain c residue 10 LYS Chi-restraints excluded: chain c residue 22 THR Chi-restraints excluded: chain c residue 47 VAL Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 24 THR Chi-restraints excluded: chain e residue 51 SER Chi-restraints excluded: chain e residue 57 LEU Chi-restraints excluded: chain f residue 7 VAL Chi-restraints excluded: chain i residue 333 ASP Chi-restraints excluded: chain i residue 374 VAL Chi-restraints excluded: chain i residue 410 VAL Chi-restraints excluded: chain k residue 40 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 640 random chunks: chunk 322 optimal weight: 6.9990 chunk 180 optimal weight: 10.0000 chunk 483 optimal weight: 10.0000 chunk 395 optimal weight: 5.9990 chunk 160 optimal weight: 20.0000 chunk 582 optimal weight: 2.9990 chunk 628 optimal weight: 10.0000 chunk 518 optimal weight: 8.9990 chunk 577 optimal weight: 5.9990 chunk 198 optimal weight: 10.0000 chunk 467 optimal weight: 3.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 70 ASN C 134 ASN C 239 ASN E 163 ASN ** F 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 43 ASN J 12 GLN K 138 GLN L 9 ASN L 29 HIS M 35 HIS M 104 GLN O 62 ASN O 107 ASN P 29 HIS ** Q 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 44 GLN S 18 GLN T 7 HIS T 31 GLN T 40 ASN ** V 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 87 GLN X 46 HIS Y 32 ASN ** Z 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 25 GLN d 26 ASN i 381 ASN i 411 GLN i 419 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.4545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 101809 Z= 0.282 Angle : 0.647 15.091 152552 Z= 0.333 Chirality : 0.037 0.299 19559 Planarity : 0.006 0.106 7975 Dihedral : 23.307 179.443 51658 Min Nonbonded Distance : 1.774 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.52 % Favored : 97.42 % Rotamer: Outliers : 7.41 % Allowed : 22.30 % Favored : 70.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.13), residues: 3529 helix: 0.04 (0.16), residues: 1084 sheet: -0.64 (0.18), residues: 701 loop : -0.75 (0.14), residues: 1744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP N 64 HIS 0.008 0.001 HIS Z 41 PHE 0.031 0.002 PHE X 69 TYR 0.021 0.002 TYR O 112 ARG 0.011 0.001 ARG a 11 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7058 Ramachandran restraints generated. 3529 Oldfield, 0 Emsley, 3529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7058 Ramachandran restraints generated. 3529 Oldfield, 0 Emsley, 3529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1093 residues out of total 2905 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 215 poor density : 878 time to evaluate : 4.045 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: C 5 LYS cc_start: 0.8930 (mttt) cc_final: 0.8497 (mtpp) REVERT: C 25 HIS cc_start: 0.8961 (t70) cc_final: 0.8079 (t70) REVERT: C 84 ASP cc_start: 0.8572 (t0) cc_final: 0.8370 (t0) REVERT: C 98 ASP cc_start: 0.9175 (p0) cc_final: 0.8809 (p0) REVERT: C 178 SER cc_start: 0.9455 (p) cc_final: 0.9065 (t) REVERT: C 251 GLN cc_start: 0.8390 (OUTLIER) cc_final: 0.8076 (tt0) REVERT: D 28 GLU cc_start: 0.8575 (OUTLIER) cc_final: 0.8289 (tm-30) REVERT: D 139 SER cc_start: 0.8535 (p) cc_final: 0.8270 (p) REVERT: E 24 ASN cc_start: 0.9195 (t0) cc_final: 0.8904 (t0) REVERT: E 35 TYR cc_start: 0.8194 (t80) cc_final: 0.7970 (t80) REVERT: E 153 LEU cc_start: 0.8022 (tp) cc_final: 0.7473 (tp) REVERT: E 156 ASN cc_start: 0.8546 (m-40) cc_final: 0.8195 (m-40) REVERT: E 168 ASP cc_start: 0.7282 (t0) cc_final: 0.7050 (t70) REVERT: E 178 VAL cc_start: 0.9056 (m) cc_final: 0.8776 (t) REVERT: F 17 MET cc_start: 0.8685 (tpp) cc_final: 0.8268 (tpt) REVERT: F 22 TYR cc_start: 0.7274 (m-80) cc_final: 0.6905 (m-80) REVERT: F 27 GLN cc_start: 0.8921 (mt0) cc_final: 0.8258 (tt0) REVERT: F 35 THR cc_start: 0.8514 (m) cc_final: 0.8219 (p) REVERT: F 42 GLU cc_start: 0.7691 (pm20) cc_final: 0.7461 (pm20) REVERT: F 81 GLN cc_start: 0.8545 (tm-30) cc_final: 0.8123 (tm-30) REVERT: F 96 MET cc_start: 0.8820 (ttp) cc_final: 0.8211 (ttt) REVERT: F 99 PHE cc_start: 0.9124 (t80) cc_final: 0.8825 (t80) REVERT: F 120 LYS cc_start: 0.8334 (pttt) cc_final: 0.8124 (mtpp) REVERT: G 48 ASN cc_start: 0.7662 (OUTLIER) cc_final: 0.7197 (t0) REVERT: G 60 ASP cc_start: 0.8462 (p0) cc_final: 0.8146 (p0) REVERT: G 130 GLU cc_start: 0.8586 (tm-30) cc_final: 0.7950 (mp0) REVERT: G 155 GLU cc_start: 0.8303 (pp20) cc_final: 0.8100 (pp20) REVERT: G 175 LYS cc_start: 0.6715 (tttt) cc_final: 0.6141 (tmtt) REVERT: H 17 ASP cc_start: 0.7713 (m-30) cc_final: 0.7032 (t0) REVERT: H 57 LYS cc_start: 0.7806 (mmpt) cc_final: 0.7256 (ttmt) REVERT: I 125 ARG cc_start: 0.2631 (ttm170) cc_final: 0.2364 (mmm-85) REVERT: J 127 ARG cc_start: 0.7599 (mtp85) cc_final: 0.7109 (tpm170) REVERT: L 89 ASN cc_start: 0.8955 (t0) cc_final: 0.8735 (m110) REVERT: M 25 SER cc_start: 0.9497 (p) cc_final: 0.9297 (t) REVERT: M 54 GLN cc_start: 0.8256 (tt0) cc_final: 0.7964 (tt0) REVERT: M 58 TYR cc_start: 0.8704 (p90) cc_final: 0.8377 (p90) REVERT: M 104 GLN cc_start: 0.8835 (mm110) cc_final: 0.8531 (mm-40) REVERT: N 30 SER cc_start: 0.8906 (m) cc_final: 0.8586 (t) REVERT: O 58 ASP cc_start: 0.7600 (t0) cc_final: 0.7217 (t0) REVERT: O 110 MET cc_start: 0.8700 (mmm) cc_final: 0.8289 (mmt) REVERT: P 17 LYS cc_start: 0.8873 (tttm) cc_final: 0.8654 (ttmm) REVERT: P 69 ASP cc_start: 0.7974 (OUTLIER) cc_final: 0.7680 (m-30) REVERT: P 85 LYS cc_start: 0.8822 (mtpt) cc_final: 0.8548 (mttm) REVERT: P 87 ILE cc_start: 0.8135 (mp) cc_final: 0.7883 (mp) REVERT: Q 106 LYS cc_start: 0.4533 (mmtt) cc_final: 0.3868 (mptt) REVERT: R 11 ARG cc_start: 0.9007 (tpm-80) cc_final: 0.8801 (mmm160) REVERT: R 55 ARG cc_start: 0.9047 (mtm-85) cc_final: 0.8582 (ttm110) REVERT: R 61 TRP cc_start: 0.8989 (m-10) cc_final: 0.8779 (m-10) REVERT: S 55 ASP cc_start: 0.8841 (OUTLIER) cc_final: 0.8545 (t0) REVERT: T 7 HIS cc_start: 0.8838 (OUTLIER) cc_final: 0.8574 (t70) REVERT: U 3 ARG cc_start: 0.8448 (tpp80) cc_final: 0.7884 (mtm110) REVERT: U 18 GLU cc_start: 0.8825 (mm-30) cc_final: 0.8611 (mm-30) REVERT: U 91 GLN cc_start: 0.7619 (mp10) cc_final: 0.7321 (mp10) REVERT: W 1 MET cc_start: 0.5703 (tpp) cc_final: 0.5358 (mpp) REVERT: W 17 SER cc_start: 0.8939 (m) cc_final: 0.8642 (p) REVERT: W 59 GLU cc_start: 0.8037 (tt0) cc_final: 0.7491 (tt0) REVERT: X 56 ASP cc_start: 0.8007 (t0) cc_final: 0.7806 (t0) REVERT: Z 4 LYS cc_start: 0.8562 (pttt) cc_final: 0.8146 (mmmt) REVERT: a 7 ILE cc_start: 0.9354 (mt) cc_final: 0.9123 (mt) REVERT: a 24 LEU cc_start: 0.9239 (mt) cc_final: 0.9007 (mt) REVERT: b 3 VAL cc_start: 0.9051 (OUTLIER) cc_final: 0.8790 (m) REVERT: b 4 GLN cc_start: 0.9008 (OUTLIER) cc_final: 0.8368 (pm20) REVERT: b 17 ARG cc_start: 0.8386 (mtt180) cc_final: 0.8036 (mtt180) REVERT: b 29 SER cc_start: 0.8766 (m) cc_final: 0.8301 (t) REVERT: b 50 ARG cc_start: 0.7990 (mtp180) cc_final: 0.7598 (tpp80) REVERT: c 10 LYS cc_start: 0.8735 (OUTLIER) cc_final: 0.8526 (ptmm) REVERT: c 40 ASP cc_start: 0.8414 (t0) cc_final: 0.7631 (t0) REVERT: e 28 ASN cc_start: 0.8654 (t0) cc_final: 0.8446 (t0) REVERT: i 398 ARG cc_start: 0.8637 (mtt180) cc_final: 0.8267 (mmm-85) REVERT: i 412 ASP cc_start: 0.7311 (OUTLIER) cc_final: 0.6852 (t0) REVERT: i 423 MET cc_start: 0.8213 (mmp) cc_final: 0.7465 (tpp) REVERT: i 424 GLN cc_start: 0.7867 (tt0) cc_final: 0.7373 (tm-30) REVERT: i 429 LYS cc_start: 0.6834 (mttt) cc_final: 0.6366 (tttm) outliers start: 215 outliers final: 123 residues processed: 1003 average time/residue: 0.8970 time to fit residues: 1536.7424 Evaluate side-chains 918 residues out of total 2905 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 785 time to evaluate : 4.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 115 GLN Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 145 GLU Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 242 LYS Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 251 GLN Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 28 GLU Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 144 GLU Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 37 ASN Chi-restraints excluded: chain F residue 118 SER Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 48 ASN Chi-restraints excluded: chain G residue 56 ASP Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain G residue 84 THR Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain H residue 135 HIS Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain I residue 14 GLU Chi-restraints excluded: chain I residue 17 GLU Chi-restraints excluded: chain I residue 24 SER Chi-restraints excluded: chain I residue 34 THR Chi-restraints excluded: chain I residue 36 ASP Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain K residue 17 VAL Chi-restraints excluded: chain K residue 40 HIS Chi-restraints excluded: chain K residue 88 THR Chi-restraints excluded: chain K residue 93 ILE Chi-restraints excluded: chain K residue 118 MET Chi-restraints excluded: chain K residue 131 ASN Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 29 HIS Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 58 LEU Chi-restraints excluded: chain L residue 116 ILE Chi-restraints excluded: chain M residue 46 VAL Chi-restraints excluded: chain M residue 93 ASN Chi-restraints excluded: chain M residue 118 THR Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 54 THR Chi-restraints excluded: chain N residue 102 LEU Chi-restraints excluded: chain N residue 132 THR Chi-restraints excluded: chain N residue 133 LYS Chi-restraints excluded: chain N residue 134 THR Chi-restraints excluded: chain O residue 53 THR Chi-restraints excluded: chain O residue 57 THR Chi-restraints excluded: chain O residue 113 ILE Chi-restraints excluded: chain P residue 2 ASP Chi-restraints excluded: chain P residue 27 VAL Chi-restraints excluded: chain P residue 36 TYR Chi-restraints excluded: chain P residue 49 VAL Chi-restraints excluded: chain P residue 53 THR Chi-restraints excluded: chain P residue 62 LEU Chi-restraints excluded: chain P residue 69 ASP Chi-restraints excluded: chain Q residue 2 SER Chi-restraints excluded: chain Q residue 16 ASP Chi-restraints excluded: chain Q residue 32 VAL Chi-restraints excluded: chain Q residue 63 LYS Chi-restraints excluded: chain Q residue 76 THR Chi-restraints excluded: chain Q residue 82 ASP Chi-restraints excluded: chain Q residue 92 VAL Chi-restraints excluded: chain R residue 31 VAL Chi-restraints excluded: chain R residue 39 VAL Chi-restraints excluded: chain R residue 59 GLN Chi-restraints excluded: chain S residue 16 GLU Chi-restraints excluded: chain S residue 18 GLN Chi-restraints excluded: chain S residue 49 ILE Chi-restraints excluded: chain S residue 55 ASP Chi-restraints excluded: chain S residue 86 GLN Chi-restraints excluded: chain T residue 4 ILE Chi-restraints excluded: chain T residue 7 HIS Chi-restraints excluded: chain T residue 66 ILE Chi-restraints excluded: chain T residue 74 ILE Chi-restraints excluded: chain T residue 81 SER Chi-restraints excluded: chain U residue 16 VAL Chi-restraints excluded: chain U residue 17 SER Chi-restraints excluded: chain U residue 60 THR Chi-restraints excluded: chain U residue 79 ASP Chi-restraints excluded: chain V residue 12 ILE Chi-restraints excluded: chain V residue 59 VAL Chi-restraints excluded: chain W residue 20 LEU Chi-restraints excluded: chain W residue 61 LEU Chi-restraints excluded: chain W residue 90 ASP Chi-restraints excluded: chain X residue 38 VAL Chi-restraints excluded: chain Y residue 4 VAL Chi-restraints excluded: chain Y residue 8 THR Chi-restraints excluded: chain Z residue 16 THR Chi-restraints excluded: chain Z residue 34 SER Chi-restraints excluded: chain Z residue 48 ARG Chi-restraints excluded: chain Z residue 53 VAL Chi-restraints excluded: chain Z residue 54 LYS Chi-restraints excluded: chain a residue 41 THR Chi-restraints excluded: chain b residue 3 VAL Chi-restraints excluded: chain b residue 4 GLN Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain b residue 26 THR Chi-restraints excluded: chain c residue 10 LYS Chi-restraints excluded: chain c residue 12 VAL Chi-restraints excluded: chain c residue 29 THR Chi-restraints excluded: chain c residue 47 VAL Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 4 THR Chi-restraints excluded: chain f residue 7 VAL Chi-restraints excluded: chain i residue 333 ASP Chi-restraints excluded: chain i residue 374 VAL Chi-restraints excluded: chain i residue 412 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 640 random chunks: chunk 575 optimal weight: 6.9990 chunk 437 optimal weight: 5.9990 chunk 302 optimal weight: 10.0000 chunk 64 optimal weight: 10.0000 chunk 277 optimal weight: 20.0000 chunk 390 optimal weight: 6.9990 chunk 584 optimal weight: 8.9990 chunk 618 optimal weight: 9.9990 chunk 305 optimal weight: 10.0000 chunk 553 optimal weight: 3.9990 chunk 166 optimal weight: 10.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 239 ASN ** D 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 90 GLN ** E 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 37 ASN F 63 GLN G 128 GLN H 43 ASN K 138 GLN M 35 HIS ** Q 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 71 GLN T 31 GLN U 28 ASN U 48 GLN U 70 HIS W 87 GLN X 12 ASN ** Z 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 25 GLN ** i 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 419 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.5301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 101809 Z= 0.314 Angle : 0.644 11.022 152552 Z= 0.331 Chirality : 0.038 0.292 19559 Planarity : 0.005 0.069 7975 Dihedral : 23.265 179.947 51624 Min Nonbonded Distance : 1.644 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.89 % Favored : 97.05 % Rotamer: Outliers : 6.83 % Allowed : 25.27 % Favored : 67.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.13), residues: 3529 helix: 0.15 (0.16), residues: 1088 sheet: -0.65 (0.18), residues: 737 loop : -0.73 (0.14), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP U 80 HIS 0.054 0.002 HIS L 29 PHE 0.026 0.002 PHE X 69 TYR 0.018 0.002 TYR F 7 ARG 0.013 0.001 ARG L 49 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7058 Ramachandran restraints generated. 3529 Oldfield, 0 Emsley, 3529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7058 Ramachandran restraints generated. 3529 Oldfield, 0 Emsley, 3529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1017 residues out of total 2905 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 198 poor density : 819 time to evaluate : 4.128 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: C 5 LYS cc_start: 0.8961 (mttt) cc_final: 0.8535 (mtpp) REVERT: C 97 LYS cc_start: 0.8928 (mmtm) cc_final: 0.8499 (pttm) REVERT: C 98 ASP cc_start: 0.9208 (p0) cc_final: 0.8938 (p0) REVERT: C 178 SER cc_start: 0.9374 (p) cc_final: 0.9125 (m) REVERT: D 28 GLU cc_start: 0.8687 (OUTLIER) cc_final: 0.8366 (tm-30) REVERT: D 40 LEU cc_start: 0.8865 (mt) cc_final: 0.8621 (mp) REVERT: D 84 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.8165 (mt) REVERT: D 185 ASN cc_start: 0.8860 (m-40) cc_final: 0.8617 (m110) REVERT: E 24 ASN cc_start: 0.9105 (t0) cc_final: 0.8867 (t0) REVERT: E 153 LEU cc_start: 0.8143 (tp) cc_final: 0.7625 (tp) REVERT: E 156 ASN cc_start: 0.8696 (m-40) cc_final: 0.8314 (m-40) REVERT: E 178 VAL cc_start: 0.9077 (m) cc_final: 0.8840 (t) REVERT: F 17 MET cc_start: 0.8817 (tpp) cc_final: 0.8365 (tpt) REVERT: F 27 GLN cc_start: 0.8955 (mt0) cc_final: 0.8298 (tt0) REVERT: F 35 THR cc_start: 0.8813 (m) cc_final: 0.8453 (p) REVERT: F 81 GLN cc_start: 0.8704 (tm-30) cc_final: 0.8445 (tm-30) REVERT: F 96 MET cc_start: 0.8790 (ttp) cc_final: 0.8352 (ttp) REVERT: F 99 PHE cc_start: 0.9107 (t80) cc_final: 0.8845 (t80) REVERT: F 120 LYS cc_start: 0.8476 (pttt) cc_final: 0.7915 (tptt) REVERT: G 48 ASN cc_start: 0.6973 (OUTLIER) cc_final: 0.6680 (t0) REVERT: G 60 ASP cc_start: 0.8504 (p0) cc_final: 0.8133 (p0) REVERT: G 77 ILE cc_start: 0.9468 (mm) cc_final: 0.9263 (tt) REVERT: G 175 LYS cc_start: 0.6349 (tttt) cc_final: 0.5951 (tmtt) REVERT: H 1 MET cc_start: 0.7574 (ttm) cc_final: 0.7354 (tmm) REVERT: H 3 VAL cc_start: 0.7980 (OUTLIER) cc_final: 0.7720 (t) REVERT: H 57 LYS cc_start: 0.7993 (mmpt) cc_final: 0.7308 (ttmt) REVERT: H 112 LYS cc_start: 0.5867 (pttm) cc_final: 0.5552 (tmtt) REVERT: J 117 MET cc_start: 0.0889 (mtp) cc_final: 0.0552 (mtp) REVERT: K 12 LYS cc_start: 0.8893 (pttp) cc_final: 0.8577 (tppt) REVERT: L 51 LYS cc_start: 0.8847 (mttm) cc_final: 0.8583 (mttm) REVERT: L 88 ASN cc_start: 0.8982 (t0) cc_final: 0.8680 (t0) REVERT: L 89 ASN cc_start: 0.9049 (t0) cc_final: 0.8691 (m110) REVERT: M 54 GLN cc_start: 0.8515 (tt0) cc_final: 0.8192 (tt0) REVERT: M 58 TYR cc_start: 0.8555 (p90) cc_final: 0.8196 (p90) REVERT: M 77 ILE cc_start: 0.9334 (mp) cc_final: 0.9063 (tt) REVERT: M 116 VAL cc_start: 0.9379 (OUTLIER) cc_final: 0.8827 (t) REVERT: N 30 SER cc_start: 0.8669 (m) cc_final: 0.8444 (t) REVERT: N 110 GLU cc_start: 0.8589 (tp30) cc_final: 0.8300 (tp30) REVERT: O 58 ASP cc_start: 0.7546 (t0) cc_final: 0.7118 (t0) REVERT: O 106 ASP cc_start: 0.8404 (p0) cc_final: 0.8189 (p0) REVERT: O 110 MET cc_start: 0.8741 (mmm) cc_final: 0.8487 (mmm) REVERT: P 17 LYS cc_start: 0.8818 (tttm) cc_final: 0.8584 (ttmm) REVERT: P 69 ASP cc_start: 0.8343 (OUTLIER) cc_final: 0.8032 (m-30) REVERT: P 85 LYS cc_start: 0.9232 (mtpt) cc_final: 0.8663 (mttp) REVERT: P 87 ILE cc_start: 0.8284 (mp) cc_final: 0.7990 (mp) REVERT: Q 106 LYS cc_start: 0.3904 (mmtt) cc_final: 0.2856 (mptt) REVERT: R 11 ARG cc_start: 0.9035 (tpm-80) cc_final: 0.8736 (mmm160) REVERT: R 55 ARG cc_start: 0.9053 (mtm-85) cc_final: 0.8580 (ttm110) REVERT: R 57 PHE cc_start: 0.9227 (m-80) cc_final: 0.9003 (m-80) REVERT: R 87 SER cc_start: 0.8957 (m) cc_final: 0.8705 (p) REVERT: S 55 ASP cc_start: 0.8783 (OUTLIER) cc_final: 0.8439 (t0) REVERT: T 15 GLN cc_start: 0.8675 (pt0) cc_final: 0.8446 (pt0) REVERT: T 45 VAL cc_start: 0.9263 (t) cc_final: 0.9061 (p) REVERT: T 104 THR cc_start: 0.9435 (m) cc_final: 0.8863 (p) REVERT: U 3 ARG cc_start: 0.8231 (tpp80) cc_final: 0.7630 (mtm110) REVERT: U 42 GLU cc_start: 0.8093 (mp0) cc_final: 0.7768 (mp0) REVERT: V 46 GLN cc_start: 0.8567 (mm-40) cc_final: 0.8314 (tm-30) REVERT: W 1 MET cc_start: 0.5736 (tpp) cc_final: 0.5368 (mpp) REVERT: W 17 SER cc_start: 0.9067 (m) cc_final: 0.8803 (p) REVERT: W 59 GLU cc_start: 0.7994 (tt0) cc_final: 0.7700 (tt0) REVERT: Z 24 GLU cc_start: 0.8463 (tp30) cc_final: 0.8253 (tp30) REVERT: Z 30 MET cc_start: 0.8955 (mmm) cc_final: 0.8627 (mmm) REVERT: a 7 ILE cc_start: 0.9401 (mt) cc_final: 0.9158 (mt) REVERT: b 3 VAL cc_start: 0.9075 (OUTLIER) cc_final: 0.8780 (m) REVERT: b 4 GLN cc_start: 0.8973 (OUTLIER) cc_final: 0.8301 (pm20) REVERT: b 29 SER cc_start: 0.8674 (m) cc_final: 0.8177 (p) REVERT: c 7 GLU cc_start: 0.7997 (mp0) cc_final: 0.7621 (mp0) REVERT: c 10 LYS cc_start: 0.8905 (OUTLIER) cc_final: 0.8697 (ptmm) REVERT: c 40 ASP cc_start: 0.8477 (t0) cc_final: 0.7593 (t0) REVERT: i 375 ARG cc_start: 0.7810 (mtm180) cc_final: 0.7478 (mtt180) REVERT: i 412 ASP cc_start: 0.7271 (m-30) cc_final: 0.7035 (t0) REVERT: i 423 MET cc_start: 0.8239 (mmp) cc_final: 0.7526 (tpp) REVERT: i 424 GLN cc_start: 0.7861 (tt0) cc_final: 0.7357 (tm-30) REVERT: i 429 LYS cc_start: 0.6548 (mttt) cc_final: 0.6064 (tttm) outliers start: 198 outliers final: 145 residues processed: 939 average time/residue: 0.9477 time to fit residues: 1518.8445 Evaluate side-chains 929 residues out of total 2905 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 774 time to evaluate : 4.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 115 GLN Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 242 LYS Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 28 GLU Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 99 GLU Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 144 GLU Chi-restraints excluded: chain E residue 148 ILE Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain F residue 118 SER Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 48 ASN Chi-restraints excluded: chain G residue 51 THR Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 84 THR Chi-restraints excluded: chain G residue 125 CYS Chi-restraints excluded: chain G residue 127 THR Chi-restraints excluded: chain G residue 131 ILE Chi-restraints excluded: chain G residue 141 ILE Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 135 HIS Chi-restraints excluded: chain I residue 5 LEU Chi-restraints excluded: chain I residue 14 GLU Chi-restraints excluded: chain I residue 17 GLU Chi-restraints excluded: chain I residue 24 SER Chi-restraints excluded: chain I residue 34 THR Chi-restraints excluded: chain I residue 36 ASP Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain K residue 17 VAL Chi-restraints excluded: chain K residue 40 HIS Chi-restraints excluded: chain K residue 93 ILE Chi-restraints excluded: chain K residue 122 LEU Chi-restraints excluded: chain K residue 131 ASN Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 58 LEU Chi-restraints excluded: chain L residue 116 ILE Chi-restraints excluded: chain L residue 117 SER Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 35 HIS Chi-restraints excluded: chain M residue 42 SER Chi-restraints excluded: chain M residue 46 VAL Chi-restraints excluded: chain M residue 93 ASN Chi-restraints excluded: chain M residue 100 ILE Chi-restraints excluded: chain M residue 101 ILE Chi-restraints excluded: chain M residue 111 ILE Chi-restraints excluded: chain M residue 116 VAL Chi-restraints excluded: chain M residue 118 THR Chi-restraints excluded: chain N residue 7 THR Chi-restraints excluded: chain N residue 54 THR Chi-restraints excluded: chain N residue 102 LEU Chi-restraints excluded: chain N residue 132 THR Chi-restraints excluded: chain N residue 133 LYS Chi-restraints excluded: chain N residue 134 THR Chi-restraints excluded: chain O residue 33 ILE Chi-restraints excluded: chain O residue 57 THR Chi-restraints excluded: chain O residue 59 SER Chi-restraints excluded: chain O residue 113 ILE Chi-restraints excluded: chain P residue 2 ASP Chi-restraints excluded: chain P residue 27 VAL Chi-restraints excluded: chain P residue 49 VAL Chi-restraints excluded: chain P residue 62 LEU Chi-restraints excluded: chain P residue 69 ASP Chi-restraints excluded: chain Q residue 2 SER Chi-restraints excluded: chain Q residue 16 ASP Chi-restraints excluded: chain Q residue 26 VAL Chi-restraints excluded: chain Q residue 30 VAL Chi-restraints excluded: chain Q residue 32 VAL Chi-restraints excluded: chain Q residue 63 LYS Chi-restraints excluded: chain Q residue 76 THR Chi-restraints excluded: chain Q residue 92 VAL Chi-restraints excluded: chain R residue 39 VAL Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain S residue 16 GLU Chi-restraints excluded: chain S residue 29 THR Chi-restraints excluded: chain S residue 45 GLU Chi-restraints excluded: chain S residue 49 ILE Chi-restraints excluded: chain S residue 55 ASP Chi-restraints excluded: chain T residue 4 ILE Chi-restraints excluded: chain T residue 7 HIS Chi-restraints excluded: chain T residue 29 VAL Chi-restraints excluded: chain T residue 66 ILE Chi-restraints excluded: chain T residue 74 ILE Chi-restraints excluded: chain T residue 77 ASP Chi-restraints excluded: chain T residue 81 SER Chi-restraints excluded: chain U residue 16 VAL Chi-restraints excluded: chain U residue 34 VAL Chi-restraints excluded: chain U residue 60 THR Chi-restraints excluded: chain U residue 79 ASP Chi-restraints excluded: chain V residue 28 VAL Chi-restraints excluded: chain V residue 59 VAL Chi-restraints excluded: chain V residue 102 THR Chi-restraints excluded: chain W residue 20 LEU Chi-restraints excluded: chain W residue 58 SER Chi-restraints excluded: chain W residue 61 LEU Chi-restraints excluded: chain W residue 77 VAL Chi-restraints excluded: chain X residue 31 VAL Chi-restraints excluded: chain X residue 38 VAL Chi-restraints excluded: chain X residue 64 ASP Chi-restraints excluded: chain X residue 67 VAL Chi-restraints excluded: chain Y residue 4 VAL Chi-restraints excluded: chain Y residue 5 CYS Chi-restraints excluded: chain Y residue 8 THR Chi-restraints excluded: chain Y residue 59 ILE Chi-restraints excluded: chain Z residue 16 THR Chi-restraints excluded: chain Z residue 54 LYS Chi-restraints excluded: chain Z residue 55 THR Chi-restraints excluded: chain a residue 10 THR Chi-restraints excluded: chain a residue 41 THR Chi-restraints excluded: chain b residue 3 VAL Chi-restraints excluded: chain b residue 4 GLN Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain b residue 26 THR Chi-restraints excluded: chain b residue 28 LEU Chi-restraints excluded: chain c residue 5 ILE Chi-restraints excluded: chain c residue 10 LYS Chi-restraints excluded: chain c residue 12 VAL Chi-restraints excluded: chain c residue 46 HIS Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 4 THR Chi-restraints excluded: chain d residue 24 THR Chi-restraints excluded: chain e residue 6 THR Chi-restraints excluded: chain e residue 50 VAL Chi-restraints excluded: chain f residue 7 VAL Chi-restraints excluded: chain f residue 17 VAL Chi-restraints excluded: chain i residue 333 ASP Chi-restraints excluded: chain i residue 374 VAL Chi-restraints excluded: chain i residue 406 CYS Chi-restraints excluded: chain i residue 410 VAL Chi-restraints excluded: chain i residue 421 ASP Chi-restraints excluded: chain i residue 427 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 640 random chunks: chunk 515 optimal weight: 2.9990 chunk 351 optimal weight: 6.9990 chunk 8 optimal weight: 10.0000 chunk 460 optimal weight: 0.4980 chunk 255 optimal weight: 10.0000 chunk 527 optimal weight: 8.9990 chunk 427 optimal weight: 20.0000 chunk 0 optimal weight: 50.0000 chunk 315 optimal weight: 7.9990 chunk 555 optimal weight: 4.9990 chunk 156 optimal weight: 30.0000 overall best weight: 4.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 239 ASN ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 ASN E 115 GLN ** E 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 37 ASN G 22 GLN G 45 HIS H 128 HIS K 138 GLN M 104 GLN ** Q 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 37 GLN S 18 GLN T 7 HIS U 48 GLN U 92 ASN W 87 GLN ** Z 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 25 GLN a 9 GLN i 381 ASN ** i 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 419 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.5671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 101809 Z= 0.238 Angle : 0.580 12.308 152552 Z= 0.300 Chirality : 0.035 0.279 19559 Planarity : 0.005 0.061 7975 Dihedral : 23.195 179.126 51612 Min Nonbonded Distance : 1.518 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.03 % Favored : 96.88 % Rotamer: Outliers : 6.10 % Allowed : 26.47 % Favored : 67.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.14), residues: 3529 helix: 0.40 (0.16), residues: 1094 sheet: -0.54 (0.18), residues: 720 loop : -0.71 (0.14), residues: 1715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP R 61 HIS 0.026 0.001 HIS M 35 PHE 0.021 0.002 PHE V 73 TYR 0.015 0.002 TYR W 82 ARG 0.011 0.001 ARG i 425 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7058 Ramachandran restraints generated. 3529 Oldfield, 0 Emsley, 3529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7058 Ramachandran restraints generated. 3529 Oldfield, 0 Emsley, 3529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1009 residues out of total 2905 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 177 poor density : 832 time to evaluate : 4.164 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 5 LYS cc_start: 0.8963 (mttt) cc_final: 0.8548 (mtpp) REVERT: C 84 ASP cc_start: 0.8557 (t0) cc_final: 0.7492 (t0) REVERT: C 97 LYS cc_start: 0.8910 (mmtm) cc_final: 0.8501 (pttm) REVERT: C 98 ASP cc_start: 0.9209 (p0) cc_final: 0.8947 (p0) REVERT: C 178 SER cc_start: 0.9370 (p) cc_final: 0.9026 (m) REVERT: D 40 LEU cc_start: 0.8824 (mt) cc_final: 0.8612 (mp) REVERT: D 185 ASN cc_start: 0.8873 (m-40) cc_final: 0.8664 (m110) REVERT: E 24 ASN cc_start: 0.8987 (t0) cc_final: 0.8705 (t0) REVERT: E 153 LEU cc_start: 0.8034 (tp) cc_final: 0.7427 (tp) REVERT: E 156 ASN cc_start: 0.8727 (m-40) cc_final: 0.8401 (m-40) REVERT: F 17 MET cc_start: 0.8842 (tpp) cc_final: 0.8416 (tpt) REVERT: F 27 GLN cc_start: 0.8923 (mt0) cc_final: 0.8682 (tt0) REVERT: F 32 GLU cc_start: 0.8338 (mm-30) cc_final: 0.8078 (mm-30) REVERT: F 35 THR cc_start: 0.8796 (m) cc_final: 0.8438 (p) REVERT: F 96 MET cc_start: 0.8881 (ttp) cc_final: 0.8432 (ttp) REVERT: F 99 PHE cc_start: 0.9131 (t80) cc_final: 0.8818 (t80) REVERT: F 120 LYS cc_start: 0.8630 (pttt) cc_final: 0.8090 (ttmm) REVERT: G 60 ASP cc_start: 0.8503 (p0) cc_final: 0.8053 (p0) REVERT: G 95 ARG cc_start: 0.8392 (mtm110) cc_final: 0.7988 (mtm110) REVERT: G 124 GLU cc_start: 0.8808 (pm20) cc_final: 0.8578 (pm20) REVERT: G 130 GLU cc_start: 0.8515 (tm-30) cc_final: 0.8110 (mp0) REVERT: G 175 LYS cc_start: 0.6779 (tttt) cc_final: 0.6360 (tmtt) REVERT: H 15 LEU cc_start: 0.8285 (OUTLIER) cc_final: 0.7407 (pp) REVERT: H 17 ASP cc_start: 0.7290 (m-30) cc_final: 0.6897 (t0) REVERT: H 57 LYS cc_start: 0.7849 (mmpt) cc_final: 0.7149 (ttmt) REVERT: H 112 LYS cc_start: 0.5824 (pttm) cc_final: 0.5504 (tmtt) REVERT: J 96 ASP cc_start: 0.7368 (t70) cc_final: 0.6931 (t70) REVERT: J 127 ARG cc_start: 0.7623 (mtp85) cc_final: 0.6743 (tpm170) REVERT: K 12 LYS cc_start: 0.8871 (pttp) cc_final: 0.8532 (tppt) REVERT: L 1 MET cc_start: 0.8187 (mmm) cc_final: 0.7978 (mmm) REVERT: L 51 LYS cc_start: 0.8768 (mttm) cc_final: 0.8511 (mttm) REVERT: L 86 LEU cc_start: 0.9221 (mp) cc_final: 0.8846 (mp) REVERT: L 89 ASN cc_start: 0.9034 (t0) cc_final: 0.8696 (m110) REVERT: M 54 GLN cc_start: 0.8465 (tt0) cc_final: 0.8240 (tt0) REVERT: M 58 TYR cc_start: 0.8726 (p90) cc_final: 0.8477 (p90) REVERT: N 30 SER cc_start: 0.8736 (m) cc_final: 0.8477 (t) REVERT: N 45 GLN cc_start: 0.8902 (mt0) cc_final: 0.8679 (mt0) REVERT: O 58 ASP cc_start: 0.7705 (t0) cc_final: 0.7299 (t0) REVERT: O 110 MET cc_start: 0.8770 (mmm) cc_final: 0.8188 (mtp) REVERT: P 85 LYS cc_start: 0.9141 (mtpt) cc_final: 0.8516 (mttp) REVERT: P 87 ILE cc_start: 0.8130 (mp) cc_final: 0.7885 (mp) REVERT: Q 106 LYS cc_start: 0.4231 (mmtt) cc_final: 0.3497 (mptt) REVERT: R 11 ARG cc_start: 0.8935 (tpm-80) cc_final: 0.8627 (mmm160) REVERT: R 55 ARG cc_start: 0.9016 (mtm-85) cc_final: 0.8572 (ttm110) REVERT: R 87 SER cc_start: 0.8974 (m) cc_final: 0.8687 (p) REVERT: T 7 HIS cc_start: 0.8896 (OUTLIER) cc_final: 0.8665 (t70) REVERT: T 15 GLN cc_start: 0.8664 (pt0) cc_final: 0.8419 (pt0) REVERT: T 51 LEU cc_start: 0.9585 (tp) cc_final: 0.9257 (tp) REVERT: T 104 THR cc_start: 0.9489 (m) cc_final: 0.8972 (p) REVERT: U 3 ARG cc_start: 0.8299 (tpp80) cc_final: 0.7764 (mtm110) REVERT: U 18 GLU cc_start: 0.9129 (mm-30) cc_final: 0.8929 (mm-30) REVERT: U 42 GLU cc_start: 0.8147 (mp0) cc_final: 0.7812 (mp0) REVERT: V 18 ASP cc_start: 0.7493 (t0) cc_final: 0.6574 (t0) REVERT: V 46 GLN cc_start: 0.8552 (mm-40) cc_final: 0.8329 (tm-30) REVERT: W 1 MET cc_start: 0.5812 (tpp) cc_final: 0.5482 (mpp) REVERT: W 17 SER cc_start: 0.9028 (m) cc_final: 0.8812 (p) REVERT: W 59 GLU cc_start: 0.7951 (tt0) cc_final: 0.7567 (tt0) REVERT: a 7 ILE cc_start: 0.9420 (mt) cc_final: 0.9161 (mt) REVERT: a 47 MET cc_start: 0.8873 (mtp) cc_final: 0.8647 (mtm) REVERT: b 3 VAL cc_start: 0.9042 (OUTLIER) cc_final: 0.8765 (m) REVERT: b 4 GLN cc_start: 0.8944 (OUTLIER) cc_final: 0.8303 (pm20) REVERT: b 29 SER cc_start: 0.8695 (m) cc_final: 0.8165 (p) REVERT: c 7 GLU cc_start: 0.8158 (mp0) cc_final: 0.7730 (mp0) REVERT: c 8 LYS cc_start: 0.8475 (tmtt) cc_final: 0.8229 (tmtt) REVERT: c 10 LYS cc_start: 0.9053 (OUTLIER) cc_final: 0.8787 (ptmm) REVERT: c 40 ASP cc_start: 0.8457 (t0) cc_final: 0.7914 (t0) REVERT: i 375 ARG cc_start: 0.7811 (mtm180) cc_final: 0.7477 (mtt180) REVERT: i 397 SER cc_start: 0.8377 (m) cc_final: 0.8039 (t) REVERT: i 398 ARG cc_start: 0.8770 (mmt90) cc_final: 0.8293 (mmm-85) REVERT: i 412 ASP cc_start: 0.7204 (m-30) cc_final: 0.6960 (t0) REVERT: i 423 MET cc_start: 0.8162 (mmp) cc_final: 0.7498 (tpp) REVERT: i 424 GLN cc_start: 0.7843 (tt0) cc_final: 0.7235 (tm-30) REVERT: i 429 LYS cc_start: 0.6748 (mttt) cc_final: 0.6177 (tttm) outliers start: 177 outliers final: 135 residues processed: 944 average time/residue: 0.8721 time to fit residues: 1417.8928 Evaluate side-chains 907 residues out of total 2905 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 767 time to evaluate : 4.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 115 GLN Chi-restraints excluded: chain C residue 134 ASN Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 242 LYS Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 144 GLU Chi-restraints excluded: chain E residue 148 ILE Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain F residue 159 THR Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 51 THR Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 84 THR Chi-restraints excluded: chain G residue 127 THR Chi-restraints excluded: chain G residue 141 ILE Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 135 HIS Chi-restraints excluded: chain I residue 5 LEU Chi-restraints excluded: chain I residue 7 ASP Chi-restraints excluded: chain I residue 14 GLU Chi-restraints excluded: chain I residue 17 GLU Chi-restraints excluded: chain I residue 24 SER Chi-restraints excluded: chain I residue 34 THR Chi-restraints excluded: chain I residue 36 ASP Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain K residue 17 VAL Chi-restraints excluded: chain K residue 40 HIS Chi-restraints excluded: chain K residue 93 ILE Chi-restraints excluded: chain K residue 122 LEU Chi-restraints excluded: chain K residue 131 ASN Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 58 LEU Chi-restraints excluded: chain L residue 116 ILE Chi-restraints excluded: chain L residue 117 SER Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 25 SER Chi-restraints excluded: chain M residue 35 HIS Chi-restraints excluded: chain M residue 42 SER Chi-restraints excluded: chain M residue 46 VAL Chi-restraints excluded: chain M residue 93 ASN Chi-restraints excluded: chain M residue 101 ILE Chi-restraints excluded: chain M residue 111 ILE Chi-restraints excluded: chain M residue 118 THR Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 7 THR Chi-restraints excluded: chain N residue 25 ASP Chi-restraints excluded: chain N residue 54 THR Chi-restraints excluded: chain N residue 102 LEU Chi-restraints excluded: chain N residue 132 THR Chi-restraints excluded: chain N residue 133 LYS Chi-restraints excluded: chain O residue 33 ILE Chi-restraints excluded: chain O residue 34 ILE Chi-restraints excluded: chain O residue 57 THR Chi-restraints excluded: chain O residue 113 ILE Chi-restraints excluded: chain P residue 2 ASP Chi-restraints excluded: chain P residue 27 VAL Chi-restraints excluded: chain P residue 36 TYR Chi-restraints excluded: chain P residue 43 ASN Chi-restraints excluded: chain P residue 49 VAL Chi-restraints excluded: chain P residue 62 LEU Chi-restraints excluded: chain Q residue 2 SER Chi-restraints excluded: chain Q residue 16 ASP Chi-restraints excluded: chain Q residue 26 VAL Chi-restraints excluded: chain Q residue 30 VAL Chi-restraints excluded: chain Q residue 76 THR Chi-restraints excluded: chain Q residue 92 VAL Chi-restraints excluded: chain R residue 39 VAL Chi-restraints excluded: chain S residue 29 THR Chi-restraints excluded: chain T residue 4 ILE Chi-restraints excluded: chain T residue 7 HIS Chi-restraints excluded: chain T residue 29 VAL Chi-restraints excluded: chain T residue 66 ILE Chi-restraints excluded: chain T residue 74 ILE Chi-restraints excluded: chain T residue 76 VAL Chi-restraints excluded: chain T residue 81 SER Chi-restraints excluded: chain U residue 16 VAL Chi-restraints excluded: chain U residue 34 VAL Chi-restraints excluded: chain U residue 60 THR Chi-restraints excluded: chain U residue 61 LEU Chi-restraints excluded: chain U residue 79 ASP Chi-restraints excluded: chain V residue 28 VAL Chi-restraints excluded: chain V residue 34 VAL Chi-restraints excluded: chain V residue 59 VAL Chi-restraints excluded: chain W residue 20 LEU Chi-restraints excluded: chain W residue 61 LEU Chi-restraints excluded: chain X residue 38 VAL Chi-restraints excluded: chain X residue 64 ASP Chi-restraints excluded: chain Y residue 4 VAL Chi-restraints excluded: chain Y residue 5 CYS Chi-restraints excluded: chain Y residue 8 THR Chi-restraints excluded: chain Z residue 5 GLU Chi-restraints excluded: chain Z residue 16 THR Chi-restraints excluded: chain Z residue 54 LYS Chi-restraints excluded: chain a residue 41 THR Chi-restraints excluded: chain b residue 3 VAL Chi-restraints excluded: chain b residue 4 GLN Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain b residue 26 THR Chi-restraints excluded: chain c residue 10 LYS Chi-restraints excluded: chain c residue 12 VAL Chi-restraints excluded: chain c residue 22 THR Chi-restraints excluded: chain c residue 46 HIS Chi-restraints excluded: chain c residue 47 VAL Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 4 THR Chi-restraints excluded: chain d residue 24 THR Chi-restraints excluded: chain e residue 6 THR Chi-restraints excluded: chain e residue 59 ILE Chi-restraints excluded: chain f residue 7 VAL Chi-restraints excluded: chain i residue 333 ASP Chi-restraints excluded: chain i residue 374 VAL Chi-restraints excluded: chain i residue 392 GLU Chi-restraints excluded: chain i residue 421 ASP Chi-restraints excluded: chain i residue 427 MET Chi-restraints excluded: chain k residue 27 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 640 random chunks: chunk 208 optimal weight: 10.0000 chunk 557 optimal weight: 9.9990 chunk 122 optimal weight: 10.0000 chunk 363 optimal weight: 8.9990 chunk 152 optimal weight: 20.0000 chunk 619 optimal weight: 10.0000 chunk 514 optimal weight: 6.9990 chunk 286 optimal weight: 10.0000 chunk 51 optimal weight: 10.0000 chunk 204 optimal weight: 10.0000 chunk 325 optimal weight: 0.9980 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 239 ASN E 115 GLN ** J 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 138 GLN L 88 ASN N 17 ASN O 107 ASN ** Q 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 7 HIS ** T 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 48 GLN W 87 GLN ** Z 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 9 GLN f 35 GLN ** i 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 419 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.5980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.108 101809 Z= 0.350 Angle : 0.667 10.957 152552 Z= 0.339 Chirality : 0.038 0.282 19559 Planarity : 0.005 0.126 7975 Dihedral : 23.218 178.349 51606 Min Nonbonded Distance : 1.366 Molprobity Statistics. All-atom Clashscore : 14.99 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.83 % Favored : 96.09 % Rotamer: Outliers : 6.89 % Allowed : 27.27 % Favored : 65.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.14), residues: 3529 helix: 0.31 (0.16), residues: 1084 sheet: -0.56 (0.18), residues: 732 loop : -0.82 (0.14), residues: 1713 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP R 61 HIS 0.013 0.001 HIS T 7 PHE 0.023 0.002 PHE V 73 TYR 0.016 0.002 TYR Q 99 ARG 0.027 0.001 ARG i 425 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7058 Ramachandran restraints generated. 3529 Oldfield, 0 Emsley, 3529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7058 Ramachandran restraints generated. 3529 Oldfield, 0 Emsley, 3529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 970 residues out of total 2905 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 200 poor density : 770 time to evaluate : 4.212 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: C 5 LYS cc_start: 0.9011 (mttt) cc_final: 0.8603 (mtpp) REVERT: C 97 LYS cc_start: 0.8963 (mmtm) cc_final: 0.8532 (pttm) REVERT: C 98 ASP cc_start: 0.9229 (p0) cc_final: 0.8957 (p0) REVERT: C 146 MET cc_start: 0.9020 (mmm) cc_final: 0.8815 (mmm) REVERT: C 178 SER cc_start: 0.9440 (p) cc_final: 0.9164 (m) REVERT: E 24 ASN cc_start: 0.8959 (t0) cc_final: 0.8741 (t0) REVERT: E 46 GLN cc_start: 0.8650 (mp10) cc_final: 0.8416 (mp10) REVERT: E 153 LEU cc_start: 0.8100 (tp) cc_final: 0.7531 (tt) REVERT: F 35 THR cc_start: 0.8782 (m) cc_final: 0.8404 (p) REVERT: F 99 PHE cc_start: 0.9131 (t80) cc_final: 0.8849 (t80) REVERT: F 120 LYS cc_start: 0.8777 (pttt) cc_final: 0.8093 (tptt) REVERT: G 60 ASP cc_start: 0.8584 (p0) cc_final: 0.8149 (p0) REVERT: G 130 GLU cc_start: 0.8589 (tm-30) cc_final: 0.8169 (mp0) REVERT: G 175 LYS cc_start: 0.6403 (tttt) cc_final: 0.6087 (tmtt) REVERT: H 14 SER cc_start: 0.8538 (t) cc_final: 0.8218 (p) REVERT: H 57 LYS cc_start: 0.8023 (mmpt) cc_final: 0.7342 (ttmt) REVERT: H 112 LYS cc_start: 0.6261 (pttm) cc_final: 0.5661 (tmtt) REVERT: H 133 GLN cc_start: 0.8153 (mm110) cc_final: 0.7119 (mm-40) REVERT: I 57 ASN cc_start: 0.8236 (m-40) cc_final: 0.7850 (m-40) REVERT: K 12 LYS cc_start: 0.8918 (pttp) cc_final: 0.8548 (tppt) REVERT: L 1 MET cc_start: 0.8333 (mmm) cc_final: 0.8097 (mmm) REVERT: L 58 LEU cc_start: 0.9006 (OUTLIER) cc_final: 0.8491 (pp) REVERT: L 89 ASN cc_start: 0.9028 (t0) cc_final: 0.8713 (m110) REVERT: M 116 VAL cc_start: 0.9088 (m) cc_final: 0.8871 (t) REVERT: N 30 SER cc_start: 0.8775 (m) cc_final: 0.8511 (t) REVERT: N 45 GLN cc_start: 0.8964 (mt0) cc_final: 0.8660 (mt0) REVERT: N 103 TYR cc_start: 0.8849 (m-80) cc_final: 0.8617 (m-80) REVERT: O 1 MET cc_start: 0.8178 (mmt) cc_final: 0.7878 (mmt) REVERT: O 21 PHE cc_start: 0.8907 (m-80) cc_final: 0.8643 (m-80) REVERT: O 58 ASP cc_start: 0.7759 (t0) cc_final: 0.7343 (t0) REVERT: O 75 ILE cc_start: 0.9174 (mm) cc_final: 0.8959 (mt) REVERT: O 110 MET cc_start: 0.8798 (mmm) cc_final: 0.8337 (mtp) REVERT: O 117 ASP cc_start: 0.8742 (m-30) cc_final: 0.8497 (m-30) REVERT: P 85 LYS cc_start: 0.9157 (mtpt) cc_final: 0.8839 (tttm) REVERT: P 87 ILE cc_start: 0.8179 (mp) cc_final: 0.7908 (mp) REVERT: Q 24 ASP cc_start: 0.7384 (m-30) cc_final: 0.7123 (m-30) REVERT: Q 106 LYS cc_start: 0.4181 (mmtt) cc_final: 0.3235 (mptt) REVERT: R 11 ARG cc_start: 0.8970 (tpm-80) cc_final: 0.8644 (mmm160) REVERT: R 55 ARG cc_start: 0.8993 (mtm-85) cc_final: 0.8676 (ttm110) REVERT: R 87 SER cc_start: 0.8925 (m) cc_final: 0.8682 (p) REVERT: S 55 ASP cc_start: 0.8770 (OUTLIER) cc_final: 0.8356 (t0) REVERT: T 104 THR cc_start: 0.9506 (m) cc_final: 0.8982 (p) REVERT: U 3 ARG cc_start: 0.8319 (tpp80) cc_final: 0.7619 (mtm110) REVERT: U 42 GLU cc_start: 0.8209 (mp0) cc_final: 0.7889 (mp0) REVERT: V 46 GLN cc_start: 0.8549 (mm-40) cc_final: 0.8332 (tm-30) REVERT: W 1 MET cc_start: 0.5936 (tpp) cc_final: 0.5348 (mpp) REVERT: W 59 GLU cc_start: 0.7972 (tt0) cc_final: 0.7729 (tt0) REVERT: X 44 LYS cc_start: 0.9025 (mtpt) cc_final: 0.8770 (mtpt) REVERT: Z 17 GLU cc_start: 0.8809 (tp30) cc_final: 0.8592 (tp30) REVERT: a 7 ILE cc_start: 0.9438 (mt) cc_final: 0.9167 (mt) REVERT: b 4 GLN cc_start: 0.8963 (OUTLIER) cc_final: 0.8378 (pm20) REVERT: b 10 ARG cc_start: 0.9044 (ptp90) cc_final: 0.8540 (ptp-170) REVERT: b 29 SER cc_start: 0.8750 (m) cc_final: 0.8235 (p) REVERT: c 7 GLU cc_start: 0.8199 (mp0) cc_final: 0.7802 (mp0) REVERT: c 10 LYS cc_start: 0.9096 (OUTLIER) cc_final: 0.8798 (ptmm) REVERT: c 40 ASP cc_start: 0.8644 (t0) cc_final: 0.8015 (t0) REVERT: i 375 ARG cc_start: 0.7795 (mtm180) cc_final: 0.7450 (mtt180) REVERT: i 397 SER cc_start: 0.8426 (m) cc_final: 0.8056 (t) REVERT: i 398 ARG cc_start: 0.8787 (mmt90) cc_final: 0.8504 (mmm-85) REVERT: i 412 ASP cc_start: 0.7221 (OUTLIER) cc_final: 0.6954 (t0) REVERT: i 423 MET cc_start: 0.8454 (mmp) cc_final: 0.8101 (tpp) REVERT: i 424 GLN cc_start: 0.7774 (tt0) cc_final: 0.7140 (tm-30) REVERT: i 429 LYS cc_start: 0.6253 (mttt) cc_final: 0.5763 (tttm) REVERT: k 40 LEU cc_start: 0.2981 (OUTLIER) cc_final: 0.2644 (tt) outliers start: 200 outliers final: 169 residues processed: 889 average time/residue: 0.8780 time to fit residues: 1348.8308 Evaluate side-chains 915 residues out of total 2905 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 175 poor density : 740 time to evaluate : 4.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 115 GLN Chi-restraints excluded: chain C residue 134 ASN Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 201 MET Chi-restraints excluded: chain C residue 242 LYS Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 144 GLU Chi-restraints excluded: chain E residue 148 ILE Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain F residue 118 SER Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 26 ILE Chi-restraints excluded: chain G residue 51 THR Chi-restraints excluded: chain G residue 56 ASP Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 84 THR Chi-restraints excluded: chain G residue 125 CYS Chi-restraints excluded: chain G residue 127 THR Chi-restraints excluded: chain G residue 131 ILE Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 135 HIS Chi-restraints excluded: chain I residue 5 LEU Chi-restraints excluded: chain I residue 7 ASP Chi-restraints excluded: chain I residue 14 GLU Chi-restraints excluded: chain I residue 17 GLU Chi-restraints excluded: chain I residue 24 SER Chi-restraints excluded: chain I residue 34 THR Chi-restraints excluded: chain I residue 36 ASP Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain K residue 17 VAL Chi-restraints excluded: chain K residue 40 HIS Chi-restraints excluded: chain K residue 93 ILE Chi-restraints excluded: chain K residue 122 LEU Chi-restraints excluded: chain K residue 131 ASN Chi-restraints excluded: chain L residue 22 ILE Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 29 HIS Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 58 LEU Chi-restraints excluded: chain L residue 116 ILE Chi-restraints excluded: chain L residue 117 SER Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 25 SER Chi-restraints excluded: chain M residue 40 SER Chi-restraints excluded: chain M residue 42 SER Chi-restraints excluded: chain M residue 46 VAL Chi-restraints excluded: chain M residue 93 ASN Chi-restraints excluded: chain M residue 101 ILE Chi-restraints excluded: chain M residue 111 ILE Chi-restraints excluded: chain M residue 118 THR Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 7 THR Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 25 ASP Chi-restraints excluded: chain N residue 53 MET Chi-restraints excluded: chain N residue 54 THR Chi-restraints excluded: chain N residue 102 LEU Chi-restraints excluded: chain N residue 119 LEU Chi-restraints excluded: chain N residue 132 THR Chi-restraints excluded: chain N residue 133 LYS Chi-restraints excluded: chain N residue 136 MET Chi-restraints excluded: chain O residue 27 SER Chi-restraints excluded: chain O residue 34 ILE Chi-restraints excluded: chain O residue 57 THR Chi-restraints excluded: chain O residue 59 SER Chi-restraints excluded: chain O residue 113 ILE Chi-restraints excluded: chain P residue 2 ASP Chi-restraints excluded: chain P residue 27 VAL Chi-restraints excluded: chain P residue 36 TYR Chi-restraints excluded: chain P residue 43 ASN Chi-restraints excluded: chain P residue 49 VAL Chi-restraints excluded: chain P residue 53 THR Chi-restraints excluded: chain P residue 62 LEU Chi-restraints excluded: chain Q residue 2 SER Chi-restraints excluded: chain Q residue 16 ASP Chi-restraints excluded: chain Q residue 26 VAL Chi-restraints excluded: chain Q residue 30 VAL Chi-restraints excluded: chain Q residue 63 LYS Chi-restraints excluded: chain Q residue 66 ASN Chi-restraints excluded: chain Q residue 76 THR Chi-restraints excluded: chain Q residue 92 VAL Chi-restraints excluded: chain R residue 39 VAL Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain S residue 29 THR Chi-restraints excluded: chain S residue 45 GLU Chi-restraints excluded: chain S residue 55 ASP Chi-restraints excluded: chain T residue 4 ILE Chi-restraints excluded: chain T residue 29 VAL Chi-restraints excluded: chain T residue 66 ILE Chi-restraints excluded: chain T residue 74 ILE Chi-restraints excluded: chain T residue 76 VAL Chi-restraints excluded: chain T residue 77 ASP Chi-restraints excluded: chain T residue 81 SER Chi-restraints excluded: chain T residue 85 ILE Chi-restraints excluded: chain U residue 16 VAL Chi-restraints excluded: chain U residue 34 VAL Chi-restraints excluded: chain U residue 60 THR Chi-restraints excluded: chain U residue 61 LEU Chi-restraints excluded: chain V residue 28 VAL Chi-restraints excluded: chain V residue 59 VAL Chi-restraints excluded: chain V residue 102 THR Chi-restraints excluded: chain W residue 3 THR Chi-restraints excluded: chain W residue 20 LEU Chi-restraints excluded: chain W residue 58 SER Chi-restraints excluded: chain W residue 61 LEU Chi-restraints excluded: chain X residue 31 VAL Chi-restraints excluded: chain X residue 38 VAL Chi-restraints excluded: chain X residue 64 ASP Chi-restraints excluded: chain Y residue 4 VAL Chi-restraints excluded: chain Y residue 5 CYS Chi-restraints excluded: chain Y residue 8 THR Chi-restraints excluded: chain Z residue 16 THR Chi-restraints excluded: chain Z residue 54 LYS Chi-restraints excluded: chain Z residue 55 THR Chi-restraints excluded: chain a residue 41 THR Chi-restraints excluded: chain b residue 3 VAL Chi-restraints excluded: chain b residue 4 GLN Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain b residue 26 THR Chi-restraints excluded: chain b residue 28 LEU Chi-restraints excluded: chain b residue 44 THR Chi-restraints excluded: chain c residue 10 LYS Chi-restraints excluded: chain c residue 12 VAL Chi-restraints excluded: chain c residue 17 THR Chi-restraints excluded: chain c residue 22 THR Chi-restraints excluded: chain c residue 23 THR Chi-restraints excluded: chain c residue 24 THR Chi-restraints excluded: chain c residue 46 HIS Chi-restraints excluded: chain c residue 47 VAL Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 4 THR Chi-restraints excluded: chain d residue 24 THR Chi-restraints excluded: chain e residue 6 THR Chi-restraints excluded: chain e residue 50 VAL Chi-restraints excluded: chain e residue 59 ILE Chi-restraints excluded: chain f residue 7 VAL Chi-restraints excluded: chain f residue 16 ILE Chi-restraints excluded: chain f residue 17 VAL Chi-restraints excluded: chain i residue 333 ASP Chi-restraints excluded: chain i residue 374 VAL Chi-restraints excluded: chain i residue 392 GLU Chi-restraints excluded: chain i residue 410 VAL Chi-restraints excluded: chain i residue 412 ASP Chi-restraints excluded: chain i residue 421 ASP Chi-restraints excluded: chain i residue 427 MET Chi-restraints excluded: chain k residue 27 MET Chi-restraints excluded: chain k residue 40 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 640 random chunks: chunk 597 optimal weight: 0.9980 chunk 69 optimal weight: 10.0000 chunk 352 optimal weight: 6.9990 chunk 452 optimal weight: 8.9990 chunk 350 optimal weight: 4.9990 chunk 521 optimal weight: 10.0000 chunk 345 optimal weight: 0.9990 chunk 616 optimal weight: 5.9990 chunk 386 optimal weight: 20.0000 chunk 376 optimal weight: 10.0000 chunk 284 optimal weight: 10.0000 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 185 ASN ** J 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 138 GLN M 35 HIS M 104 GLN ** Q 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 48 GLN ** Z 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 25 GLN ** d 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 411 GLN i 419 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.6184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 101809 Z= 0.206 Angle : 0.565 12.510 152552 Z= 0.292 Chirality : 0.034 0.272 19559 Planarity : 0.005 0.068 7975 Dihedral : 23.166 177.585 51606 Min Nonbonded Distance : 1.294 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.23 % Favored : 96.66 % Rotamer: Outliers : 5.83 % Allowed : 29.02 % Favored : 65.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.14), residues: 3529 helix: 0.61 (0.16), residues: 1070 sheet: -0.61 (0.18), residues: 722 loop : -0.75 (0.14), residues: 1737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP R 61 HIS 0.006 0.001 HIS N 13 PHE 0.022 0.002 PHE V 73 TYR 0.014 0.001 TYR Q 99 ARG 0.012 0.000 ARG i 425 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7058 Ramachandran restraints generated. 3529 Oldfield, 0 Emsley, 3529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7058 Ramachandran restraints generated. 3529 Oldfield, 0 Emsley, 3529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 970 residues out of total 2905 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 801 time to evaluate : 4.226 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: C 5 LYS cc_start: 0.8965 (mttt) cc_final: 0.8567 (mtpp) REVERT: C 97 LYS cc_start: 0.8888 (mmtm) cc_final: 0.8504 (pttm) REVERT: C 98 ASP cc_start: 0.9182 (p0) cc_final: 0.8946 (p0) REVERT: C 178 SER cc_start: 0.9409 (p) cc_final: 0.8969 (m) REVERT: E 24 ASN cc_start: 0.8889 (t0) cc_final: 0.8646 (t0) REVERT: E 46 GLN cc_start: 0.8584 (mp10) cc_final: 0.8365 (mp10) REVERT: E 156 ASN cc_start: 0.8864 (m-40) cc_final: 0.8529 (m-40) REVERT: F 17 MET cc_start: 0.8552 (tpt) cc_final: 0.8249 (tpt) REVERT: F 35 THR cc_start: 0.8817 (m) cc_final: 0.8459 (p) REVERT: F 96 MET cc_start: 0.8731 (ttp) cc_final: 0.8496 (ttp) REVERT: F 103 LEU cc_start: 0.8291 (tt) cc_final: 0.7858 (tp) REVERT: F 120 LYS cc_start: 0.8718 (pttt) cc_final: 0.8068 (tptt) REVERT: G 60 ASP cc_start: 0.8484 (p0) cc_final: 0.8009 (p0) REVERT: G 130 GLU cc_start: 0.8594 (tm-30) cc_final: 0.8230 (mp0) REVERT: G 175 LYS cc_start: 0.6421 (tttt) cc_final: 0.6097 (tmtt) REVERT: H 17 ASP cc_start: 0.7396 (m-30) cc_final: 0.6833 (t0) REVERT: H 57 LYS cc_start: 0.8074 (mmpt) cc_final: 0.7382 (ttmt) REVERT: I 57 ASN cc_start: 0.8163 (m-40) cc_final: 0.7750 (m-40) REVERT: K 12 LYS cc_start: 0.8872 (pttp) cc_final: 0.8521 (tppt) REVERT: L 1 MET cc_start: 0.8343 (mmm) cc_final: 0.8125 (mmm) REVERT: L 8 LEU cc_start: 0.9241 (OUTLIER) cc_final: 0.9027 (mt) REVERT: L 51 LYS cc_start: 0.8691 (mttm) cc_final: 0.8403 (mttm) REVERT: L 58 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8509 (pp) REVERT: L 86 LEU cc_start: 0.9218 (mp) cc_final: 0.8851 (mp) REVERT: L 89 ASN cc_start: 0.8993 (t0) cc_final: 0.8667 (m-40) REVERT: M 58 TYR cc_start: 0.8687 (p90) cc_final: 0.8332 (p90) REVERT: N 30 SER cc_start: 0.8844 (m) cc_final: 0.8560 (t) REVERT: N 31 PHE cc_start: 0.8741 (m-80) cc_final: 0.8518 (m-80) REVERT: O 1 MET cc_start: 0.8268 (mmt) cc_final: 0.8061 (mmt) REVERT: O 21 PHE cc_start: 0.8863 (m-80) cc_final: 0.8651 (m-80) REVERT: O 75 ILE cc_start: 0.9114 (mm) cc_final: 0.8890 (mt) REVERT: O 110 MET cc_start: 0.8742 (mmm) cc_final: 0.8247 (mtp) REVERT: P 85 LYS cc_start: 0.9132 (mtpt) cc_final: 0.8802 (tttm) REVERT: Q 37 LYS cc_start: 0.6872 (OUTLIER) cc_final: 0.6512 (mmmm) REVERT: Q 99 TYR cc_start: 0.9030 (p90) cc_final: 0.8770 (p90) REVERT: Q 106 LYS cc_start: 0.3841 (mmtt) cc_final: 0.2907 (mptt) REVERT: R 11 ARG cc_start: 0.8890 (tpm-80) cc_final: 0.8579 (mmm160) REVERT: R 55 ARG cc_start: 0.8971 (mtm-85) cc_final: 0.8616 (ttm110) REVERT: R 87 SER cc_start: 0.8963 (m) cc_final: 0.8652 (p) REVERT: S 55 ASP cc_start: 0.8674 (OUTLIER) cc_final: 0.8241 (t0) REVERT: T 51 LEU cc_start: 0.9537 (tp) cc_final: 0.9320 (tp) REVERT: T 104 THR cc_start: 0.9478 (m) cc_final: 0.8923 (p) REVERT: U 3 ARG cc_start: 0.8332 (tpp80) cc_final: 0.7967 (mtm110) REVERT: U 42 GLU cc_start: 0.8228 (mp0) cc_final: 0.7874 (mp0) REVERT: W 12 GLN cc_start: 0.7305 (OUTLIER) cc_final: 0.6998 (mp10) REVERT: W 41 GLU cc_start: 0.8901 (pt0) cc_final: 0.8090 (mt-10) REVERT: W 59 GLU cc_start: 0.7999 (tt0) cc_final: 0.7732 (tt0) REVERT: Z 17 GLU cc_start: 0.8778 (tp30) cc_final: 0.8538 (tp30) REVERT: a 7 ILE cc_start: 0.9463 (mt) cc_final: 0.9231 (mt) REVERT: b 3 VAL cc_start: 0.9002 (OUTLIER) cc_final: 0.8724 (m) REVERT: b 4 GLN cc_start: 0.8893 (OUTLIER) cc_final: 0.8289 (pm20) REVERT: b 29 SER cc_start: 0.8688 (m) cc_final: 0.8140 (p) REVERT: c 7 GLU cc_start: 0.8209 (mp0) cc_final: 0.7776 (mp0) REVERT: c 23 THR cc_start: 0.8203 (OUTLIER) cc_final: 0.7775 (p) REVERT: c 40 ASP cc_start: 0.8509 (t0) cc_final: 0.7961 (t0) REVERT: d 22 MET cc_start: 0.8871 (tpp) cc_final: 0.8632 (mmt) REVERT: d 29 GLN cc_start: 0.7924 (pt0) cc_final: 0.7678 (pt0) REVERT: i 375 ARG cc_start: 0.7830 (mtm180) cc_final: 0.7531 (mtt180) REVERT: i 397 SER cc_start: 0.8471 (m) cc_final: 0.8268 (t) REVERT: i 398 ARG cc_start: 0.8832 (mmt90) cc_final: 0.8279 (mmm-85) REVERT: i 408 MET cc_start: 0.8022 (mmm) cc_final: 0.7417 (mmm) REVERT: i 423 MET cc_start: 0.8295 (mmp) cc_final: 0.7904 (tpp) REVERT: i 424 GLN cc_start: 0.7769 (tt0) cc_final: 0.7126 (tm-30) REVERT: i 429 LYS cc_start: 0.6536 (mttt) cc_final: 0.5959 (tttm) outliers start: 169 outliers final: 138 residues processed: 903 average time/residue: 0.8882 time to fit residues: 1381.0475 Evaluate side-chains 907 residues out of total 2905 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 761 time to evaluate : 4.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 115 GLN Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 134 ASN Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 242 LYS Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 148 ILE Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 51 THR Chi-restraints excluded: chain G residue 56 ASP Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 84 THR Chi-restraints excluded: chain G residue 125 CYS Chi-restraints excluded: chain G residue 127 THR Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 135 HIS Chi-restraints excluded: chain I residue 5 LEU Chi-restraints excluded: chain I residue 7 ASP Chi-restraints excluded: chain I residue 14 GLU Chi-restraints excluded: chain I residue 17 GLU Chi-restraints excluded: chain I residue 24 SER Chi-restraints excluded: chain I residue 34 THR Chi-restraints excluded: chain I residue 36 ASP Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain K residue 17 VAL Chi-restraints excluded: chain K residue 40 HIS Chi-restraints excluded: chain K residue 122 LEU Chi-restraints excluded: chain K residue 131 ASN Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain L residue 22 ILE Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 29 HIS Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 58 LEU Chi-restraints excluded: chain L residue 62 VAL Chi-restraints excluded: chain L residue 117 SER Chi-restraints excluded: chain M residue 25 SER Chi-restraints excluded: chain M residue 40 SER Chi-restraints excluded: chain M residue 42 SER Chi-restraints excluded: chain M residue 46 VAL Chi-restraints excluded: chain M residue 54 GLN Chi-restraints excluded: chain M residue 93 ASN Chi-restraints excluded: chain M residue 100 ILE Chi-restraints excluded: chain M residue 101 ILE Chi-restraints excluded: chain M residue 111 ILE Chi-restraints excluded: chain M residue 118 THR Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 25 ASP Chi-restraints excluded: chain N residue 53 MET Chi-restraints excluded: chain N residue 102 LEU Chi-restraints excluded: chain N residue 132 THR Chi-restraints excluded: chain N residue 133 LYS Chi-restraints excluded: chain O residue 27 SER Chi-restraints excluded: chain O residue 34 ILE Chi-restraints excluded: chain O residue 57 THR Chi-restraints excluded: chain O residue 59 SER Chi-restraints excluded: chain O residue 113 ILE Chi-restraints excluded: chain P residue 2 ASP Chi-restraints excluded: chain P residue 27 VAL Chi-restraints excluded: chain P residue 31 THR Chi-restraints excluded: chain P residue 43 ASN Chi-restraints excluded: chain P residue 49 VAL Chi-restraints excluded: chain P residue 62 LEU Chi-restraints excluded: chain Q residue 16 ASP Chi-restraints excluded: chain Q residue 26 VAL Chi-restraints excluded: chain Q residue 30 VAL Chi-restraints excluded: chain Q residue 32 VAL Chi-restraints excluded: chain Q residue 37 LYS Chi-restraints excluded: chain Q residue 92 VAL Chi-restraints excluded: chain R residue 39 VAL Chi-restraints excluded: chain S residue 29 THR Chi-restraints excluded: chain S residue 55 ASP Chi-restraints excluded: chain T residue 4 ILE Chi-restraints excluded: chain T residue 29 VAL Chi-restraints excluded: chain T residue 66 ILE Chi-restraints excluded: chain T residue 74 ILE Chi-restraints excluded: chain T residue 77 ASP Chi-restraints excluded: chain T residue 81 SER Chi-restraints excluded: chain T residue 85 ILE Chi-restraints excluded: chain U residue 16 VAL Chi-restraints excluded: chain U residue 60 THR Chi-restraints excluded: chain U residue 61 LEU Chi-restraints excluded: chain V residue 28 VAL Chi-restraints excluded: chain V residue 59 VAL Chi-restraints excluded: chain V residue 102 THR Chi-restraints excluded: chain W residue 12 GLN Chi-restraints excluded: chain W residue 20 LEU Chi-restraints excluded: chain W residue 58 SER Chi-restraints excluded: chain W residue 61 LEU Chi-restraints excluded: chain X residue 12 ASN Chi-restraints excluded: chain X residue 38 VAL Chi-restraints excluded: chain X residue 64 ASP Chi-restraints excluded: chain Y residue 5 CYS Chi-restraints excluded: chain Y residue 8 THR Chi-restraints excluded: chain Y residue 19 SER Chi-restraints excluded: chain Z residue 40 SER Chi-restraints excluded: chain Z residue 54 LYS Chi-restraints excluded: chain a residue 41 THR Chi-restraints excluded: chain b residue 3 VAL Chi-restraints excluded: chain b residue 4 GLN Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain b residue 15 MET Chi-restraints excluded: chain b residue 26 THR Chi-restraints excluded: chain b residue 44 THR Chi-restraints excluded: chain c residue 17 THR Chi-restraints excluded: chain c residue 23 THR Chi-restraints excluded: chain c residue 24 THR Chi-restraints excluded: chain c residue 47 VAL Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 4 THR Chi-restraints excluded: chain e residue 6 THR Chi-restraints excluded: chain f residue 7 VAL Chi-restraints excluded: chain f residue 16 ILE Chi-restraints excluded: chain i residue 333 ASP Chi-restraints excluded: chain i residue 374 VAL Chi-restraints excluded: chain i residue 392 GLU Chi-restraints excluded: chain i residue 421 ASP Chi-restraints excluded: chain i residue 427 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 640 random chunks: chunk 381 optimal weight: 4.9990 chunk 246 optimal weight: 10.0000 chunk 368 optimal weight: 10.0000 chunk 185 optimal weight: 10.0000 chunk 121 optimal weight: 10.0000 chunk 119 optimal weight: 20.0000 chunk 392 optimal weight: 0.0270 chunk 420 optimal weight: 10.0000 chunk 304 optimal weight: 0.3980 chunk 57 optimal weight: 10.0000 chunk 484 optimal weight: 9.9990 overall best weight: 5.0846 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 ASN D 136 ASN ** E 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 138 GLN M 104 GLN N 17 ASN ** Q 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 48 GLN ** Z 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 25 GLN d 29 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.6226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 101809 Z= 0.255 Angle : 0.596 12.041 152552 Z= 0.306 Chirality : 0.035 0.275 19559 Planarity : 0.005 0.066 7975 Dihedral : 23.147 177.387 51603 Min Nonbonded Distance : 1.275 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.51 % Favored : 96.37 % Rotamer: Outliers : 6.45 % Allowed : 29.02 % Favored : 64.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.14), residues: 3529 helix: 0.57 (0.16), residues: 1079 sheet: -0.56 (0.18), residues: 727 loop : -0.75 (0.15), residues: 1723 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP R 61 HIS 0.010 0.001 HIS W 80 PHE 0.031 0.002 PHE i 420 TYR 0.027 0.002 TYR Q 99 ARG 0.010 0.001 ARG E 88 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7058 Ramachandran restraints generated. 3529 Oldfield, 0 Emsley, 3529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7058 Ramachandran restraints generated. 3529 Oldfield, 0 Emsley, 3529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 947 residues out of total 2905 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 187 poor density : 760 time to evaluate : 4.050 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: C 5 LYS cc_start: 0.8975 (mttt) cc_final: 0.8583 (mtpp) REVERT: C 97 LYS cc_start: 0.8900 (mmtm) cc_final: 0.8506 (pttm) REVERT: C 98 ASP cc_start: 0.9187 (p0) cc_final: 0.8942 (p0) REVERT: C 178 SER cc_start: 0.9410 (p) cc_final: 0.9008 (m) REVERT: C 213 TRP cc_start: 0.8573 (m-10) cc_final: 0.7509 (m-10) REVERT: D 11 MET cc_start: 0.8162 (ttp) cc_final: 0.7961 (ttp) REVERT: E 46 GLN cc_start: 0.8628 (mp10) cc_final: 0.8409 (mp10) REVERT: E 136 GLN cc_start: 0.7901 (pp30) cc_final: 0.7688 (pp30) REVERT: E 156 ASN cc_start: 0.8868 (m-40) cc_final: 0.8550 (m-40) REVERT: F 26 MET cc_start: 0.8135 (ptm) cc_final: 0.7674 (ppp) REVERT: F 35 THR cc_start: 0.8853 (m) cc_final: 0.8485 (p) REVERT: F 96 MET cc_start: 0.8938 (ttp) cc_final: 0.8666 (ttp) REVERT: F 103 LEU cc_start: 0.8262 (tt) cc_final: 0.7795 (tp) REVERT: F 120 LYS cc_start: 0.8716 (pttt) cc_final: 0.8090 (tptt) REVERT: F 130 MET cc_start: 0.8768 (ppp) cc_final: 0.8469 (ppp) REVERT: G 60 ASP cc_start: 0.8539 (p0) cc_final: 0.8078 (p0) REVERT: G 130 GLU cc_start: 0.8632 (tm-30) cc_final: 0.8228 (mp0) REVERT: H 17 ASP cc_start: 0.7556 (m-30) cc_final: 0.6928 (t0) REVERT: H 57 LYS cc_start: 0.8131 (mmpt) cc_final: 0.7438 (ttmt) REVERT: H 133 GLN cc_start: 0.8254 (mm110) cc_final: 0.7305 (mm-40) REVERT: I 57 ASN cc_start: 0.8154 (m-40) cc_final: 0.7764 (m-40) REVERT: K 12 LYS cc_start: 0.8878 (pttp) cc_final: 0.8524 (tppt) REVERT: L 1 MET cc_start: 0.8368 (mmm) cc_final: 0.8133 (mmm) REVERT: L 51 LYS cc_start: 0.8703 (mttm) cc_final: 0.8424 (mttm) REVERT: L 58 LEU cc_start: 0.8977 (OUTLIER) cc_final: 0.8541 (pp) REVERT: L 86 LEU cc_start: 0.9264 (mp) cc_final: 0.8867 (mp) REVERT: L 89 ASN cc_start: 0.9012 (t0) cc_final: 0.8703 (m-40) REVERT: M 1 MET cc_start: 0.7856 (ttp) cc_final: 0.7623 (ptp) REVERT: M 58 TYR cc_start: 0.8701 (p90) cc_final: 0.8355 (p90) REVERT: N 30 SER cc_start: 0.8783 (m) cc_final: 0.8535 (t) REVERT: N 31 PHE cc_start: 0.8772 (m-80) cc_final: 0.8497 (m-10) REVERT: N 110 GLU cc_start: 0.8564 (tp30) cc_final: 0.8352 (tp30) REVERT: O 1 MET cc_start: 0.8249 (mmt) cc_final: 0.8012 (mmt) REVERT: O 21 PHE cc_start: 0.8923 (m-80) cc_final: 0.8662 (m-80) REVERT: O 110 MET cc_start: 0.8756 (mmm) cc_final: 0.8281 (mtp) REVERT: P 85 LYS cc_start: 0.9129 (mtpt) cc_final: 0.8802 (tttm) REVERT: Q 101 ARG cc_start: 0.8101 (mtt90) cc_final: 0.7688 (mtt90) REVERT: Q 106 LYS cc_start: 0.3876 (mmtt) cc_final: 0.2892 (mptt) REVERT: R 11 ARG cc_start: 0.8909 (tpm-80) cc_final: 0.8611 (mmm160) REVERT: R 55 ARG cc_start: 0.8976 (mtm-85) cc_final: 0.8626 (ttm110) REVERT: R 87 SER cc_start: 0.8943 (m) cc_final: 0.8646 (p) REVERT: S 55 ASP cc_start: 0.8678 (OUTLIER) cc_final: 0.8247 (t0) REVERT: T 51 LEU cc_start: 0.9542 (tp) cc_final: 0.9293 (tp) REVERT: T 104 THR cc_start: 0.9488 (m) cc_final: 0.8931 (p) REVERT: U 3 ARG cc_start: 0.8203 (tpp80) cc_final: 0.7958 (mtm110) REVERT: U 42 GLU cc_start: 0.8167 (mp0) cc_final: 0.7879 (mp0) REVERT: W 1 MET cc_start: 0.6629 (tmm) cc_final: 0.4714 (mtm) REVERT: W 41 GLU cc_start: 0.8905 (pt0) cc_final: 0.8074 (mt-10) REVERT: W 59 GLU cc_start: 0.7991 (tt0) cc_final: 0.7733 (tt0) REVERT: Y 71 LEU cc_start: 0.8860 (mt) cc_final: 0.8592 (mt) REVERT: Z 17 GLU cc_start: 0.8832 (tp30) cc_final: 0.8534 (tp30) REVERT: a 7 ILE cc_start: 0.9520 (mt) cc_final: 0.9268 (mt) REVERT: b 3 VAL cc_start: 0.9022 (OUTLIER) cc_final: 0.8743 (m) REVERT: b 4 GLN cc_start: 0.8906 (OUTLIER) cc_final: 0.8261 (pm20) REVERT: b 29 SER cc_start: 0.8716 (m) cc_final: 0.8181 (p) REVERT: c 7 GLU cc_start: 0.8115 (mp0) cc_final: 0.7698 (mp0) REVERT: c 23 THR cc_start: 0.8201 (OUTLIER) cc_final: 0.7847 (p) REVERT: c 40 ASP cc_start: 0.8565 (t0) cc_final: 0.7952 (t0) REVERT: d 29 GLN cc_start: 0.7909 (pt0) cc_final: 0.7690 (pt0) REVERT: f 30 GLU cc_start: 0.8602 (mp0) cc_final: 0.8242 (mp0) REVERT: i 375 ARG cc_start: 0.7856 (mtm180) cc_final: 0.7597 (mtt180) REVERT: i 398 ARG cc_start: 0.8843 (mmt90) cc_final: 0.8283 (mmm-85) REVERT: i 408 MET cc_start: 0.7943 (mmm) cc_final: 0.7466 (mmm) REVERT: i 423 MET cc_start: 0.8282 (mmp) cc_final: 0.7466 (tpp) REVERT: i 424 GLN cc_start: 0.7756 (tt0) cc_final: 0.7127 (tm-30) REVERT: i 429 LYS cc_start: 0.6544 (mttt) cc_final: 0.5965 (tttm) REVERT: k 40 LEU cc_start: 0.3308 (OUTLIER) cc_final: 0.2821 (tt) outliers start: 187 outliers final: 161 residues processed: 874 average time/residue: 0.8798 time to fit residues: 1326.3388 Evaluate side-chains 913 residues out of total 2905 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 746 time to evaluate : 4.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 115 GLN Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 134 ASN Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 242 LYS Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 148 ILE Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 118 SER Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 51 THR Chi-restraints excluded: chain G residue 56 ASP Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 84 THR Chi-restraints excluded: chain G residue 127 THR Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 135 HIS Chi-restraints excluded: chain I residue 5 LEU Chi-restraints excluded: chain I residue 7 ASP Chi-restraints excluded: chain I residue 14 GLU Chi-restraints excluded: chain I residue 17 GLU Chi-restraints excluded: chain I residue 24 SER Chi-restraints excluded: chain I residue 34 THR Chi-restraints excluded: chain I residue 36 ASP Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain K residue 17 VAL Chi-restraints excluded: chain K residue 40 HIS Chi-restraints excluded: chain K residue 93 ILE Chi-restraints excluded: chain K residue 122 LEU Chi-restraints excluded: chain K residue 131 ASN Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 29 HIS Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 58 LEU Chi-restraints excluded: chain L residue 62 VAL Chi-restraints excluded: chain M residue 25 SER Chi-restraints excluded: chain M residue 40 SER Chi-restraints excluded: chain M residue 42 SER Chi-restraints excluded: chain M residue 46 VAL Chi-restraints excluded: chain M residue 93 ASN Chi-restraints excluded: chain M residue 100 ILE Chi-restraints excluded: chain M residue 101 ILE Chi-restraints excluded: chain M residue 111 ILE Chi-restraints excluded: chain M residue 118 THR Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 7 THR Chi-restraints excluded: chain N residue 17 ASN Chi-restraints excluded: chain N residue 25 ASP Chi-restraints excluded: chain N residue 53 MET Chi-restraints excluded: chain N residue 102 LEU Chi-restraints excluded: chain N residue 132 THR Chi-restraints excluded: chain N residue 133 LYS Chi-restraints excluded: chain N residue 134 THR Chi-restraints excluded: chain N residue 136 MET Chi-restraints excluded: chain O residue 27 SER Chi-restraints excluded: chain O residue 34 ILE Chi-restraints excluded: chain O residue 57 THR Chi-restraints excluded: chain O residue 59 SER Chi-restraints excluded: chain O residue 113 ILE Chi-restraints excluded: chain P residue 2 ASP Chi-restraints excluded: chain P residue 27 VAL Chi-restraints excluded: chain P residue 31 THR Chi-restraints excluded: chain P residue 36 TYR Chi-restraints excluded: chain P residue 43 ASN Chi-restraints excluded: chain P residue 49 VAL Chi-restraints excluded: chain P residue 53 THR Chi-restraints excluded: chain P residue 62 LEU Chi-restraints excluded: chain Q residue 2 SER Chi-restraints excluded: chain Q residue 16 ASP Chi-restraints excluded: chain Q residue 26 VAL Chi-restraints excluded: chain Q residue 30 VAL Chi-restraints excluded: chain Q residue 32 VAL Chi-restraints excluded: chain Q residue 63 LYS Chi-restraints excluded: chain Q residue 76 THR Chi-restraints excluded: chain Q residue 92 VAL Chi-restraints excluded: chain R residue 39 VAL Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain S residue 55 ASP Chi-restraints excluded: chain S residue 99 THR Chi-restraints excluded: chain T residue 4 ILE Chi-restraints excluded: chain T residue 29 VAL Chi-restraints excluded: chain T residue 66 ILE Chi-restraints excluded: chain T residue 74 ILE Chi-restraints excluded: chain T residue 76 VAL Chi-restraints excluded: chain T residue 77 ASP Chi-restraints excluded: chain T residue 81 SER Chi-restraints excluded: chain T residue 85 ILE Chi-restraints excluded: chain U residue 16 VAL Chi-restraints excluded: chain U residue 34 VAL Chi-restraints excluded: chain U residue 60 THR Chi-restraints excluded: chain U residue 61 LEU Chi-restraints excluded: chain V residue 12 ILE Chi-restraints excluded: chain V residue 28 VAL Chi-restraints excluded: chain V residue 59 VAL Chi-restraints excluded: chain V residue 102 THR Chi-restraints excluded: chain W residue 20 LEU Chi-restraints excluded: chain W residue 58 SER Chi-restraints excluded: chain W residue 61 LEU Chi-restraints excluded: chain X residue 12 ASN Chi-restraints excluded: chain X residue 38 VAL Chi-restraints excluded: chain X residue 64 ASP Chi-restraints excluded: chain Y residue 4 VAL Chi-restraints excluded: chain Y residue 5 CYS Chi-restraints excluded: chain Y residue 8 THR Chi-restraints excluded: chain Y residue 19 SER Chi-restraints excluded: chain Y residue 59 ILE Chi-restraints excluded: chain Z residue 16 THR Chi-restraints excluded: chain Z residue 40 SER Chi-restraints excluded: chain Z residue 54 LYS Chi-restraints excluded: chain Z residue 55 THR Chi-restraints excluded: chain a residue 10 THR Chi-restraints excluded: chain a residue 41 THR Chi-restraints excluded: chain b residue 3 VAL Chi-restraints excluded: chain b residue 4 GLN Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain b residue 15 MET Chi-restraints excluded: chain b residue 26 THR Chi-restraints excluded: chain b residue 44 THR Chi-restraints excluded: chain c residue 12 VAL Chi-restraints excluded: chain c residue 17 THR Chi-restraints excluded: chain c residue 23 THR Chi-restraints excluded: chain c residue 24 THR Chi-restraints excluded: chain c residue 46 HIS Chi-restraints excluded: chain c residue 47 VAL Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 4 THR Chi-restraints excluded: chain d residue 24 THR Chi-restraints excluded: chain e residue 6 THR Chi-restraints excluded: chain e residue 50 VAL Chi-restraints excluded: chain f residue 7 VAL Chi-restraints excluded: chain f residue 16 ILE Chi-restraints excluded: chain i residue 333 ASP Chi-restraints excluded: chain i residue 374 VAL Chi-restraints excluded: chain i residue 421 ASP Chi-restraints excluded: chain i residue 427 MET Chi-restraints excluded: chain k residue 27 MET Chi-restraints excluded: chain k residue 40 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 640 random chunks: chunk 561 optimal weight: 9.9990 chunk 590 optimal weight: 20.0000 chunk 539 optimal weight: 8.9990 chunk 574 optimal weight: 6.9990 chunk 345 optimal weight: 8.9990 chunk 250 optimal weight: 10.0000 chunk 451 optimal weight: 5.9990 chunk 176 optimal weight: 20.0000 chunk 519 optimal weight: 10.0000 chunk 543 optimal weight: 5.9990 chunk 572 optimal weight: 9.9990 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 239 ASN ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 138 GLN M 104 GLN ** Q 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 48 GLN ** Z 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 25 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.6269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 101809 Z= 0.346 Angle : 0.655 11.853 152552 Z= 0.332 Chirality : 0.037 0.367 19559 Planarity : 0.005 0.098 7975 Dihedral : 23.124 177.043 51603 Min Nonbonded Distance : 1.242 Molprobity Statistics. All-atom Clashscore : 14.55 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.02 % Favored : 95.86 % Rotamer: Outliers : 6.48 % Allowed : 29.09 % Favored : 64.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.14), residues: 3529 helix: 0.42 (0.16), residues: 1075 sheet: -0.54 (0.18), residues: 730 loop : -0.84 (0.14), residues: 1724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP R 61 HIS 0.005 0.001 HIS W 80 PHE 0.050 0.002 PHE F 99 TYR 0.016 0.002 TYR K 75 ARG 0.009 0.001 ARG E 88 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7058 Ramachandran restraints generated. 3529 Oldfield, 0 Emsley, 3529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7058 Ramachandran restraints generated. 3529 Oldfield, 0 Emsley, 3529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 937 residues out of total 2905 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 188 poor density : 749 time to evaluate : 4.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 5 LYS cc_start: 0.8996 (mttt) cc_final: 0.8603 (mtpp) REVERT: C 97 LYS cc_start: 0.8923 (mmtm) cc_final: 0.8515 (pttm) REVERT: C 98 ASP cc_start: 0.9265 (p0) cc_final: 0.9022 (p0) REVERT: C 178 SER cc_start: 0.9504 (p) cc_final: 0.9146 (m) REVERT: C 181 MET cc_start: 0.8919 (mmp) cc_final: 0.8690 (mmt) REVERT: C 213 TRP cc_start: 0.8650 (m-10) cc_final: 0.7534 (m-10) REVERT: D 11 MET cc_start: 0.8142 (ttp) cc_final: 0.7847 (ttp) REVERT: E 46 GLN cc_start: 0.8687 (mp10) cc_final: 0.8453 (mp10) REVERT: E 156 ASN cc_start: 0.8914 (m-40) cc_final: 0.8590 (m-40) REVERT: F 35 THR cc_start: 0.8829 (m) cc_final: 0.8460 (p) REVERT: F 96 MET cc_start: 0.8964 (ttp) cc_final: 0.8685 (ttp) REVERT: F 103 LEU cc_start: 0.8392 (tt) cc_final: 0.7779 (tp) REVERT: F 120 LYS cc_start: 0.8765 (pttt) cc_final: 0.8107 (tptt) REVERT: G 60 ASP cc_start: 0.8579 (p0) cc_final: 0.8121 (p0) REVERT: G 130 GLU cc_start: 0.8708 (tm-30) cc_final: 0.8298 (mp0) REVERT: H 57 LYS cc_start: 0.8144 (mmpt) cc_final: 0.7423 (ttmt) REVERT: I 57 ASN cc_start: 0.8044 (m-40) cc_final: 0.7640 (m-40) REVERT: K 12 LYS cc_start: 0.8812 (pttp) cc_final: 0.8529 (tppt) REVERT: L 1 MET cc_start: 0.8381 (mmm) cc_final: 0.7968 (mmm) REVERT: L 51 LYS cc_start: 0.8711 (mttm) cc_final: 0.8416 (mttm) REVERT: L 58 LEU cc_start: 0.9015 (OUTLIER) cc_final: 0.8544 (pp) REVERT: L 89 ASN cc_start: 0.9042 (t0) cc_final: 0.8796 (m110) REVERT: N 30 SER cc_start: 0.8817 (m) cc_final: 0.8572 (t) REVERT: O 1 MET cc_start: 0.8196 (mmt) cc_final: 0.7887 (mmt) REVERT: O 21 PHE cc_start: 0.8927 (m-80) cc_final: 0.8670 (m-80) REVERT: O 106 ASP cc_start: 0.8640 (p0) cc_final: 0.8198 (p0) REVERT: O 110 MET cc_start: 0.8779 (mmm) cc_final: 0.8323 (mtp) REVERT: P 85 LYS cc_start: 0.9126 (mtpt) cc_final: 0.8800 (tttm) REVERT: Q 101 ARG cc_start: 0.8120 (mtt90) cc_final: 0.7681 (mtt90) REVERT: R 11 ARG cc_start: 0.8949 (tpm-80) cc_final: 0.8641 (mmm160) REVERT: R 55 ARG cc_start: 0.9006 (mtm-85) cc_final: 0.8661 (ttm110) REVERT: R 87 SER cc_start: 0.8938 (m) cc_final: 0.8655 (p) REVERT: S 6 GLN cc_start: 0.8611 (OUTLIER) cc_final: 0.8238 (tt0) REVERT: S 55 ASP cc_start: 0.8688 (OUTLIER) cc_final: 0.8235 (t0) REVERT: T 51 LEU cc_start: 0.9562 (tp) cc_final: 0.9299 (tp) REVERT: T 104 THR cc_start: 0.9509 (m) cc_final: 0.8949 (p) REVERT: U 3 ARG cc_start: 0.8239 (tpp80) cc_final: 0.7943 (mtm110) REVERT: U 42 GLU cc_start: 0.8156 (mp0) cc_final: 0.7866 (mp0) REVERT: W 1 MET cc_start: 0.6649 (tmm) cc_final: 0.4707 (mtm) REVERT: W 12 GLN cc_start: 0.7377 (OUTLIER) cc_final: 0.7083 (mp10) REVERT: W 59 GLU cc_start: 0.8212 (tt0) cc_final: 0.7808 (tt0) REVERT: Z 17 GLU cc_start: 0.8820 (tp30) cc_final: 0.8587 (tp30) REVERT: a 7 ILE cc_start: 0.9522 (mt) cc_final: 0.9275 (mt) REVERT: b 3 VAL cc_start: 0.9046 (OUTLIER) cc_final: 0.8767 (m) REVERT: b 4 GLN cc_start: 0.8930 (OUTLIER) cc_final: 0.8228 (pm20) REVERT: b 29 SER cc_start: 0.8768 (m) cc_final: 0.8228 (p) REVERT: c 7 GLU cc_start: 0.8338 (mp0) cc_final: 0.7832 (mp0) REVERT: c 40 ASP cc_start: 0.8615 (t0) cc_final: 0.7985 (t0) REVERT: f 30 GLU cc_start: 0.8591 (mp0) cc_final: 0.8281 (mp0) REVERT: i 375 ARG cc_start: 0.7856 (mtm180) cc_final: 0.7596 (mtt180) REVERT: i 398 ARG cc_start: 0.8843 (mmt90) cc_final: 0.8287 (mmm-85) REVERT: i 408 MET cc_start: 0.8023 (mmm) cc_final: 0.7474 (mmm) REVERT: i 423 MET cc_start: 0.8302 (mmp) cc_final: 0.7616 (tpp) REVERT: i 429 LYS cc_start: 0.6101 (mttt) cc_final: 0.5633 (tttm) REVERT: k 40 LEU cc_start: 0.3294 (OUTLIER) cc_final: 0.2763 (tt) outliers start: 188 outliers final: 164 residues processed: 873 average time/residue: 0.8725 time to fit residues: 1316.6356 Evaluate side-chains 915 residues out of total 2905 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 171 poor density : 744 time to evaluate : 4.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 115 GLN Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 134 ASN Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 242 LYS Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 148 ILE Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 197 GLU Chi-restraints excluded: chain F residue 42 GLU Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain F residue 118 SER Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 51 THR Chi-restraints excluded: chain G residue 56 ASP Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 84 THR Chi-restraints excluded: chain G residue 127 THR Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 135 HIS Chi-restraints excluded: chain I residue 5 LEU Chi-restraints excluded: chain I residue 7 ASP Chi-restraints excluded: chain I residue 14 GLU Chi-restraints excluded: chain I residue 17 GLU Chi-restraints excluded: chain I residue 34 THR Chi-restraints excluded: chain I residue 36 ASP Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain K residue 17 VAL Chi-restraints excluded: chain K residue 40 HIS Chi-restraints excluded: chain K residue 122 LEU Chi-restraints excluded: chain K residue 131 ASN Chi-restraints excluded: chain L residue 22 ILE Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 29 HIS Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 58 LEU Chi-restraints excluded: chain L residue 62 VAL Chi-restraints excluded: chain M residue 25 SER Chi-restraints excluded: chain M residue 40 SER Chi-restraints excluded: chain M residue 42 SER Chi-restraints excluded: chain M residue 46 VAL Chi-restraints excluded: chain M residue 93 ASN Chi-restraints excluded: chain M residue 100 ILE Chi-restraints excluded: chain M residue 101 ILE Chi-restraints excluded: chain M residue 111 ILE Chi-restraints excluded: chain M residue 118 THR Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 7 THR Chi-restraints excluded: chain N residue 17 ASN Chi-restraints excluded: chain N residue 25 ASP Chi-restraints excluded: chain N residue 53 MET Chi-restraints excluded: chain N residue 54 THR Chi-restraints excluded: chain N residue 102 LEU Chi-restraints excluded: chain N residue 132 THR Chi-restraints excluded: chain N residue 133 LYS Chi-restraints excluded: chain N residue 134 THR Chi-restraints excluded: chain O residue 27 SER Chi-restraints excluded: chain O residue 34 ILE Chi-restraints excluded: chain O residue 57 THR Chi-restraints excluded: chain O residue 59 SER Chi-restraints excluded: chain O residue 113 ILE Chi-restraints excluded: chain P residue 2 ASP Chi-restraints excluded: chain P residue 27 VAL Chi-restraints excluded: chain P residue 36 TYR Chi-restraints excluded: chain P residue 43 ASN Chi-restraints excluded: chain P residue 49 VAL Chi-restraints excluded: chain P residue 53 THR Chi-restraints excluded: chain P residue 62 LEU Chi-restraints excluded: chain Q residue 2 SER Chi-restraints excluded: chain Q residue 16 ASP Chi-restraints excluded: chain Q residue 26 VAL Chi-restraints excluded: chain Q residue 30 VAL Chi-restraints excluded: chain Q residue 32 VAL Chi-restraints excluded: chain Q residue 76 THR Chi-restraints excluded: chain Q residue 92 VAL Chi-restraints excluded: chain R residue 39 VAL Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain S residue 6 GLN Chi-restraints excluded: chain S residue 54 VAL Chi-restraints excluded: chain S residue 55 ASP Chi-restraints excluded: chain S residue 99 THR Chi-restraints excluded: chain T residue 4 ILE Chi-restraints excluded: chain T residue 29 VAL Chi-restraints excluded: chain T residue 66 ILE Chi-restraints excluded: chain T residue 74 ILE Chi-restraints excluded: chain T residue 77 ASP Chi-restraints excluded: chain T residue 81 SER Chi-restraints excluded: chain T residue 85 ILE Chi-restraints excluded: chain U residue 16 VAL Chi-restraints excluded: chain U residue 34 VAL Chi-restraints excluded: chain U residue 60 THR Chi-restraints excluded: chain U residue 61 LEU Chi-restraints excluded: chain U residue 78 SER Chi-restraints excluded: chain V residue 28 VAL Chi-restraints excluded: chain V residue 59 VAL Chi-restraints excluded: chain V residue 102 THR Chi-restraints excluded: chain W residue 12 GLN Chi-restraints excluded: chain W residue 17 SER Chi-restraints excluded: chain W residue 20 LEU Chi-restraints excluded: chain W residue 58 SER Chi-restraints excluded: chain X residue 12 ASN Chi-restraints excluded: chain X residue 31 VAL Chi-restraints excluded: chain X residue 38 VAL Chi-restraints excluded: chain X residue 64 ASP Chi-restraints excluded: chain Y residue 4 VAL Chi-restraints excluded: chain Y residue 5 CYS Chi-restraints excluded: chain Y residue 8 THR Chi-restraints excluded: chain Y residue 19 SER Chi-restraints excluded: chain Y residue 59 ILE Chi-restraints excluded: chain Z residue 16 THR Chi-restraints excluded: chain Z residue 40 SER Chi-restraints excluded: chain Z residue 54 LYS Chi-restraints excluded: chain Z residue 55 THR Chi-restraints excluded: chain a residue 10 THR Chi-restraints excluded: chain a residue 41 THR Chi-restraints excluded: chain b residue 3 VAL Chi-restraints excluded: chain b residue 4 GLN Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain b residue 15 MET Chi-restraints excluded: chain b residue 26 THR Chi-restraints excluded: chain b residue 44 THR Chi-restraints excluded: chain c residue 12 VAL Chi-restraints excluded: chain c residue 17 THR Chi-restraints excluded: chain c residue 23 THR Chi-restraints excluded: chain c residue 24 THR Chi-restraints excluded: chain c residue 46 HIS Chi-restraints excluded: chain c residue 47 VAL Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 4 THR Chi-restraints excluded: chain d residue 24 THR Chi-restraints excluded: chain e residue 6 THR Chi-restraints excluded: chain e residue 50 VAL Chi-restraints excluded: chain f residue 7 VAL Chi-restraints excluded: chain f residue 16 ILE Chi-restraints excluded: chain i residue 333 ASP Chi-restraints excluded: chain i residue 374 VAL Chi-restraints excluded: chain i residue 392 GLU Chi-restraints excluded: chain i residue 421 ASP Chi-restraints excluded: chain i residue 427 MET Chi-restraints excluded: chain k residue 27 MET Chi-restraints excluded: chain k residue 40 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 640 random chunks: chunk 377 optimal weight: 9.9990 chunk 607 optimal weight: 6.9990 chunk 371 optimal weight: 6.9990 chunk 288 optimal weight: 10.0000 chunk 422 optimal weight: 10.0000 chunk 637 optimal weight: 5.9990 chunk 586 optimal weight: 0.7980 chunk 507 optimal weight: 1.9990 chunk 52 optimal weight: 10.0000 chunk 392 optimal weight: 8.9990 chunk 311 optimal weight: 9.9990 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 239 ASN ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 138 GLN M 104 GLN ** Q 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 48 GLN ** Z 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 25 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.6448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 101809 Z= 0.233 Angle : 0.589 11.586 152552 Z= 0.303 Chirality : 0.034 0.270 19559 Planarity : 0.005 0.065 7975 Dihedral : 23.138 177.144 51601 Min Nonbonded Distance : 1.172 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.66 % Favored : 96.23 % Rotamer: Outliers : 5.79 % Allowed : 29.92 % Favored : 64.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.14), residues: 3529 helix: 0.54 (0.16), residues: 1063 sheet: -0.56 (0.19), residues: 730 loop : -0.80 (0.15), residues: 1736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP R 61 HIS 0.007 0.001 HIS W 80 PHE 0.052 0.002 PHE F 99 TYR 0.014 0.001 TYR K 75 ARG 0.010 0.000 ARG E 88 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7058 Ramachandran restraints generated. 3529 Oldfield, 0 Emsley, 3529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7058 Ramachandran restraints generated. 3529 Oldfield, 0 Emsley, 3529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 929 residues out of total 2905 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 761 time to evaluate : 4.093 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: C 5 LYS cc_start: 0.8970 (mttt) cc_final: 0.8586 (mtpp) REVERT: C 97 LYS cc_start: 0.8910 (mmtm) cc_final: 0.8516 (pttm) REVERT: C 98 ASP cc_start: 0.9241 (p0) cc_final: 0.9008 (p0) REVERT: C 178 SER cc_start: 0.9462 (p) cc_final: 0.9066 (m) REVERT: C 181 MET cc_start: 0.8893 (mmp) cc_final: 0.8644 (mmt) REVERT: C 213 TRP cc_start: 0.8552 (m-10) cc_final: 0.7514 (m-10) REVERT: E 156 ASN cc_start: 0.8907 (m-40) cc_final: 0.8587 (m-40) REVERT: F 26 MET cc_start: 0.8091 (ptm) cc_final: 0.7678 (ppp) REVERT: F 35 THR cc_start: 0.8821 (m) cc_final: 0.8429 (p) REVERT: F 96 MET cc_start: 0.8774 (ttp) cc_final: 0.8484 (ttp) REVERT: F 103 LEU cc_start: 0.8400 (tt) cc_final: 0.7815 (tp) REVERT: F 120 LYS cc_start: 0.8745 (pttt) cc_final: 0.8053 (tptt) REVERT: G 60 ASP cc_start: 0.8512 (p0) cc_final: 0.8018 (p0) REVERT: G 130 GLU cc_start: 0.8685 (tm-30) cc_final: 0.8338 (mp0) REVERT: H 17 ASP cc_start: 0.7616 (m-30) cc_final: 0.6987 (t0) REVERT: H 57 LYS cc_start: 0.8002 (mmpt) cc_final: 0.7291 (ttmt) REVERT: H 133 GLN cc_start: 0.8096 (mm110) cc_final: 0.7204 (mm-40) REVERT: I 57 ASN cc_start: 0.7989 (m-40) cc_final: 0.7585 (m-40) REVERT: J 117 MET cc_start: 0.1693 (mtp) cc_final: 0.0859 (mtm) REVERT: K 12 LYS cc_start: 0.8796 (pttp) cc_final: 0.8520 (tppt) REVERT: L 1 MET cc_start: 0.8359 (mmm) cc_final: 0.8123 (mmm) REVERT: L 51 LYS cc_start: 0.8697 (mttm) cc_final: 0.8419 (mttm) REVERT: L 58 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8479 (pp) REVERT: L 86 LEU cc_start: 0.9241 (mp) cc_final: 0.8809 (mp) REVERT: L 89 ASN cc_start: 0.9008 (t0) cc_final: 0.8667 (m-40) REVERT: M 58 TYR cc_start: 0.8707 (p90) cc_final: 0.8383 (p90) REVERT: N 30 SER cc_start: 0.8848 (m) cc_final: 0.8574 (t) REVERT: N 31 PHE cc_start: 0.8776 (m-80) cc_final: 0.8546 (m-10) REVERT: O 21 PHE cc_start: 0.8832 (m-80) cc_final: 0.8612 (m-80) REVERT: O 106 ASP cc_start: 0.8334 (p0) cc_final: 0.7863 (p0) REVERT: O 110 MET cc_start: 0.8764 (mmm) cc_final: 0.8243 (mtp) REVERT: P 85 LYS cc_start: 0.9168 (mtpt) cc_final: 0.8878 (tttm) REVERT: Q 25 THR cc_start: 0.8057 (m) cc_final: 0.7192 (p) REVERT: R 11 ARG cc_start: 0.8987 (tpm-80) cc_final: 0.8622 (mmm160) REVERT: R 55 ARG cc_start: 0.8928 (mtm-85) cc_final: 0.8660 (ttm110) REVERT: R 87 SER cc_start: 0.8866 (m) cc_final: 0.8600 (p) REVERT: S 6 GLN cc_start: 0.8643 (OUTLIER) cc_final: 0.8285 (tt0) REVERT: S 55 ASP cc_start: 0.8706 (OUTLIER) cc_final: 0.8335 (t0) REVERT: T 51 LEU cc_start: 0.9528 (tp) cc_final: 0.9311 (tp) REVERT: T 104 THR cc_start: 0.9497 (m) cc_final: 0.8966 (p) REVERT: U 42 GLU cc_start: 0.8168 (mp0) cc_final: 0.7882 (mp0) REVERT: W 1 MET cc_start: 0.6761 (tmm) cc_final: 0.4828 (mtm) REVERT: W 12 GLN cc_start: 0.7422 (OUTLIER) cc_final: 0.6939 (mp10) REVERT: W 41 GLU cc_start: 0.8920 (pt0) cc_final: 0.8085 (mt-10) REVERT: W 59 GLU cc_start: 0.8132 (tt0) cc_final: 0.7779 (tt0) REVERT: X 70 GLU cc_start: 0.8339 (pm20) cc_final: 0.8138 (pm20) REVERT: Y 5 CYS cc_start: 0.8751 (OUTLIER) cc_final: 0.8202 (t) REVERT: Z 17 GLU cc_start: 0.8795 (tp30) cc_final: 0.8575 (tp30) REVERT: a 7 ILE cc_start: 0.9505 (mt) cc_final: 0.9255 (mt) REVERT: b 3 VAL cc_start: 0.8987 (OUTLIER) cc_final: 0.8721 (m) REVERT: b 4 GLN cc_start: 0.8895 (OUTLIER) cc_final: 0.8225 (pm20) REVERT: b 29 SER cc_start: 0.8719 (m) cc_final: 0.8176 (p) REVERT: c 7 GLU cc_start: 0.8291 (mp0) cc_final: 0.7866 (mp0) REVERT: c 23 THR cc_start: 0.8227 (OUTLIER) cc_final: 0.7842 (p) REVERT: c 40 ASP cc_start: 0.8530 (t0) cc_final: 0.7929 (t0) REVERT: f 30 GLU cc_start: 0.8573 (mp0) cc_final: 0.8251 (mp0) REVERT: i 375 ARG cc_start: 0.7826 (mtm180) cc_final: 0.7523 (mtt180) REVERT: i 398 ARG cc_start: 0.8838 (mmt90) cc_final: 0.8287 (mmm-85) REVERT: i 408 MET cc_start: 0.7800 (mmm) cc_final: 0.7334 (mmm) REVERT: i 423 MET cc_start: 0.8302 (mmp) cc_final: 0.7621 (tpp) REVERT: i 429 LYS cc_start: 0.6454 (mttt) cc_final: 0.5916 (tttm) REVERT: k 40 LEU cc_start: 0.4284 (OUTLIER) cc_final: 0.3831 (tt) outliers start: 168 outliers final: 147 residues processed: 874 average time/residue: 0.8832 time to fit residues: 1329.2154 Evaluate side-chains 896 residues out of total 2905 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 740 time to evaluate : 4.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 115 GLN Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 134 ASN Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 242 LYS Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 148 ILE Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 51 THR Chi-restraints excluded: chain G residue 56 ASP Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 84 THR Chi-restraints excluded: chain G residue 127 THR Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 135 HIS Chi-restraints excluded: chain I residue 5 LEU Chi-restraints excluded: chain I residue 7 ASP Chi-restraints excluded: chain I residue 14 GLU Chi-restraints excluded: chain I residue 34 THR Chi-restraints excluded: chain I residue 36 ASP Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 118 THR Chi-restraints excluded: chain K residue 17 VAL Chi-restraints excluded: chain K residue 40 HIS Chi-restraints excluded: chain K residue 122 LEU Chi-restraints excluded: chain K residue 131 ASN Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 29 HIS Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 58 LEU Chi-restraints excluded: chain L residue 62 VAL Chi-restraints excluded: chain M residue 25 SER Chi-restraints excluded: chain M residue 40 SER Chi-restraints excluded: chain M residue 42 SER Chi-restraints excluded: chain M residue 46 VAL Chi-restraints excluded: chain M residue 93 ASN Chi-restraints excluded: chain M residue 100 ILE Chi-restraints excluded: chain M residue 101 ILE Chi-restraints excluded: chain M residue 111 ILE Chi-restraints excluded: chain M residue 118 THR Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 7 THR Chi-restraints excluded: chain N residue 17 ASN Chi-restraints excluded: chain N residue 25 ASP Chi-restraints excluded: chain N residue 53 MET Chi-restraints excluded: chain N residue 54 THR Chi-restraints excluded: chain N residue 102 LEU Chi-restraints excluded: chain N residue 132 THR Chi-restraints excluded: chain N residue 133 LYS Chi-restraints excluded: chain N residue 134 THR Chi-restraints excluded: chain O residue 27 SER Chi-restraints excluded: chain O residue 34 ILE Chi-restraints excluded: chain O residue 57 THR Chi-restraints excluded: chain O residue 59 SER Chi-restraints excluded: chain O residue 113 ILE Chi-restraints excluded: chain P residue 2 ASP Chi-restraints excluded: chain P residue 27 VAL Chi-restraints excluded: chain P residue 36 TYR Chi-restraints excluded: chain P residue 43 ASN Chi-restraints excluded: chain P residue 49 VAL Chi-restraints excluded: chain P residue 53 THR Chi-restraints excluded: chain P residue 62 LEU Chi-restraints excluded: chain Q residue 2 SER Chi-restraints excluded: chain Q residue 16 ASP Chi-restraints excluded: chain Q residue 26 VAL Chi-restraints excluded: chain Q residue 30 VAL Chi-restraints excluded: chain Q residue 32 VAL Chi-restraints excluded: chain Q residue 76 THR Chi-restraints excluded: chain R residue 39 VAL Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain S residue 6 GLN Chi-restraints excluded: chain S residue 55 ASP Chi-restraints excluded: chain T residue 4 ILE Chi-restraints excluded: chain T residue 29 VAL Chi-restraints excluded: chain T residue 66 ILE Chi-restraints excluded: chain T residue 74 ILE Chi-restraints excluded: chain T residue 76 VAL Chi-restraints excluded: chain T residue 77 ASP Chi-restraints excluded: chain T residue 81 SER Chi-restraints excluded: chain T residue 85 ILE Chi-restraints excluded: chain U residue 16 VAL Chi-restraints excluded: chain U residue 34 VAL Chi-restraints excluded: chain U residue 60 THR Chi-restraints excluded: chain U residue 61 LEU Chi-restraints excluded: chain V residue 28 VAL Chi-restraints excluded: chain V residue 59 VAL Chi-restraints excluded: chain V residue 102 THR Chi-restraints excluded: chain W residue 12 GLN Chi-restraints excluded: chain W residue 20 LEU Chi-restraints excluded: chain W residue 58 SER Chi-restraints excluded: chain X residue 12 ASN Chi-restraints excluded: chain X residue 38 VAL Chi-restraints excluded: chain X residue 64 ASP Chi-restraints excluded: chain Y residue 4 VAL Chi-restraints excluded: chain Y residue 5 CYS Chi-restraints excluded: chain Y residue 19 SER Chi-restraints excluded: chain Y residue 59 ILE Chi-restraints excluded: chain Z residue 16 THR Chi-restraints excluded: chain Z residue 40 SER Chi-restraints excluded: chain Z residue 54 LYS Chi-restraints excluded: chain Z residue 55 THR Chi-restraints excluded: chain a residue 10 THR Chi-restraints excluded: chain a residue 41 THR Chi-restraints excluded: chain b residue 3 VAL Chi-restraints excluded: chain b residue 4 GLN Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain b residue 15 MET Chi-restraints excluded: chain b residue 26 THR Chi-restraints excluded: chain b residue 44 THR Chi-restraints excluded: chain c residue 12 VAL Chi-restraints excluded: chain c residue 17 THR Chi-restraints excluded: chain c residue 23 THR Chi-restraints excluded: chain c residue 24 THR Chi-restraints excluded: chain c residue 46 HIS Chi-restraints excluded: chain c residue 47 VAL Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 4 THR Chi-restraints excluded: chain e residue 6 THR Chi-restraints excluded: chain e residue 50 VAL Chi-restraints excluded: chain f residue 7 VAL Chi-restraints excluded: chain f residue 16 ILE Chi-restraints excluded: chain i residue 333 ASP Chi-restraints excluded: chain i residue 374 VAL Chi-restraints excluded: chain i residue 392 GLU Chi-restraints excluded: chain i residue 421 ASP Chi-restraints excluded: chain k residue 40 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 640 random chunks: chunk 403 optimal weight: 7.9990 chunk 540 optimal weight: 6.9990 chunk 155 optimal weight: 20.0000 chunk 468 optimal weight: 8.9990 chunk 74 optimal weight: 10.0000 chunk 141 optimal weight: 10.0000 chunk 508 optimal weight: 4.9990 chunk 212 optimal weight: 40.0000 chunk 522 optimal weight: 5.9990 chunk 64 optimal weight: 10.0000 chunk 93 optimal weight: 10.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 23 ASN ** G 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 90 ASN M 104 GLN ** N 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 11 ASN ** Q 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 28 ASN U 48 GLN ** Z 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 25 GLN d 29 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.084206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.066770 restraints weight = 279284.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.068408 restraints weight = 105817.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.069217 restraints weight = 57772.025| |-----------------------------------------------------------------------------| r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.6468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 101809 Z= 0.335 Angle : 0.647 12.877 152552 Z= 0.328 Chirality : 0.037 0.327 19559 Planarity : 0.005 0.102 7975 Dihedral : 23.116 176.609 51600 Min Nonbonded Distance : 1.161 Molprobity Statistics. All-atom Clashscore : 14.34 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.25 % Favored : 95.64 % Rotamer: Outliers : 6.48 % Allowed : 29.37 % Favored : 64.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.14), residues: 3529 helix: 0.43 (0.16), residues: 1071 sheet: -0.64 (0.19), residues: 725 loop : -0.86 (0.14), residues: 1733 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP R 61 HIS 0.008 0.001 HIS E 165 PHE 0.051 0.002 PHE F 99 TYR 0.014 0.002 TYR T 38 ARG 0.011 0.001 ARG E 88 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20936.09 seconds wall clock time: 371 minutes 2.96 seconds (22262.96 seconds total)