Starting phenix.real_space_refine on Tue Mar 19 15:22:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5gag_8003/03_2024/5gag_8003_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5gag_8003/03_2024/5gag_8003.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5gag_8003/03_2024/5gag_8003.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5gag_8003/03_2024/5gag_8003.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5gag_8003/03_2024/5gag_8003_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5gag_8003/03_2024/5gag_8003_neut.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= 0.000 sd= 0.016 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 3049 5.49 5 Mg 431 5.21 5 S 95 5.16 5 C 46856 2.51 5 N 17424 2.21 5 O 26174 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C GLU 23": "OE1" <-> "OE2" Residue "C GLU 35": "OE1" <-> "OE2" Residue "C ARG 52": "NH1" <-> "NH2" Residue "C ARG 63": "NH1" <-> "NH2" Residue "C ARG 80": "NH1" <-> "NH2" Residue "C ARG 133": "NH1" <-> "NH2" Residue "C GLU 145": "OE1" <-> "OE2" Residue "C ARG 167": "NH1" <-> "NH2" Residue "C TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 177": "NH1" <-> "NH2" Residue "C ARG 182": "NH1" <-> "NH2" Residue "C ARG 189": "NH1" <-> "NH2" Residue "C GLU 199": "OE1" <-> "OE2" Residue "C ARG 203": "NH1" <-> "NH2" Residue "C ARG 212": "NH1" <-> "NH2" Residue "D ARG 13": "NH1" <-> "NH2" Residue "D GLU 17": "OE1" <-> "OE2" Residue "D GLU 28": "OE1" <-> "OE2" Residue "D GLU 30": "OE1" <-> "OE2" Residue "D ARG 33": "NH1" <-> "NH2" Residue "D ASP 43": "OD1" <-> "OD2" Residue "D ARG 59": "NH1" <-> "NH2" Residue "D GLU 64": "OE1" <-> "OE2" Residue "D ARG 77": "NH1" <-> "NH2" Residue "D GLU 81": "OE1" <-> "OE2" Residue "D PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 83": "NH1" <-> "NH2" Residue "D PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 168": "OE1" <-> "OE2" Residue "D ARG 169": "NH1" <-> "NH2" Residue "D GLU 183": "OE1" <-> "OE2" Residue "D ARG 184": "NH1" <-> "NH2" Residue "E ASP 7": "OD1" <-> "OD2" Residue "E ARG 21": "NH1" <-> "NH2" Residue "E GLU 25": "OE1" <-> "OE2" Residue "E ARG 44": "NH1" <-> "NH2" Residue "E ARG 49": "NH1" <-> "NH2" Residue "E ARG 61": "NH1" <-> "NH2" Residue "E ARG 88": "NH1" <-> "NH2" Residue "E ARG 102": "NH1" <-> "NH2" Residue "E ASP 145": "OD1" <-> "OD2" Residue "E GLU 152": "OE1" <-> "OE2" Residue "E ARG 162": "NH1" <-> "NH2" Residue "E ARG 170": "NH1" <-> "NH2" Residue "E ASP 191": "OD1" <-> "OD2" Residue "E GLU 197": "OE1" <-> "OE2" Residue "F TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 19": "OE1" <-> "OE2" Residue "F GLU 32": "OE1" <-> "OE2" Residue "F ARG 71": "NH1" <-> "NH2" Residue "F ARG 80": "NH1" <-> "NH2" Residue "F ARG 92": "NH1" <-> "NH2" Residue "F GLU 94": "OE1" <-> "OE2" Residue "F GLU 98": "OE1" <-> "OE2" Residue "F ARG 102": "NH1" <-> "NH2" Residue "F ARG 110": "NH1" <-> "NH2" Residue "F ARG 112": "NH1" <-> "NH2" Residue "F ARG 115": "NH1" <-> "NH2" Residue "F PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 133": "NH1" <-> "NH2" Residue "F PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 3": "NH1" <-> "NH2" Residue "G ASP 16": "OD1" <-> "OD2" Residue "G PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 124": "OE1" <-> "OE2" Residue "G ARG 153": "NH1" <-> "NH2" Residue "G ARG 163": "NH1" <-> "NH2" Residue "G ASP 166": "OD1" <-> "OD2" Residue "G ARG 170": "NH1" <-> "NH2" Residue "H ARG 27": "NH1" <-> "NH2" Residue "H PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 114": "OE1" <-> "OE2" Residue "H GLU 137": "OE1" <-> "OE2" Residue "I GLU 87": "OE1" <-> "OE2" Residue "I PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 114": "OE1" <-> "OE2" Residue "J PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 121": "OD1" <-> "OD2" Residue "K PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 13": "NH1" <-> "NH2" Residue "K GLU 31": "OE1" <-> "OE2" Residue "K ARG 37": "NH1" <-> "NH2" Residue "K GLU 43": "OE1" <-> "OE2" Residue "K TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 90": "OE1" <-> "OE2" Residue "K GLU 91": "OE1" <-> "OE2" Residue "K ARG 96": "NH1" <-> "NH2" Residue "K ARG 120": "NH1" <-> "NH2" Residue "L GLU 45": "OE1" <-> "OE2" Residue "L GLU 110": "OE1" <-> "OE2" Residue "L GLU 121": "OE1" <-> "OE2" Residue "M ARG 21": "NH1" <-> "NH2" Residue "M ARG 33": "NH1" <-> "NH2" Residue "M ARG 41": "NH1" <-> "NH2" Residue "M ARG 47": "NH1" <-> "NH2" Residue "M GLU 51": "OE1" <-> "OE2" Residue "M ARG 60": "NH1" <-> "NH2" Residue "M PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 76": "OE1" <-> "OE2" Residue "M ARG 78": "NH1" <-> "NH2" Residue "M GLU 106": "OE1" <-> "OE2" Residue "M ARG 126": "NH1" <-> "NH2" Residue "M GLU 144": "OE1" <-> "OE2" Residue "N ARG 10": "NH1" <-> "NH2" Residue "N ARG 18": "NH1" <-> "NH2" Residue "N PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 40": "NH1" <-> "NH2" Residue "N ARG 44": "NH1" <-> "NH2" Residue "N GLU 47": "OE1" <-> "OE2" Residue "N ARG 50": "NH1" <-> "NH2" Residue "N ARG 55": "NH1" <-> "NH2" Residue "N ARG 59": "NH1" <-> "NH2" Residue "N PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 75": "OE1" <-> "OE2" Residue "N TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 104": "OE1" <-> "OE2" Residue "N ARG 114": "NH1" <-> "NH2" Residue "O ARG 8": "NH1" <-> "NH2" Residue "O ARG 12": "NH1" <-> "NH2" Residue "O ARG 17": "NH1" <-> "NH2" Residue "O ARG 22": "NH1" <-> "NH2" Residue "O GLU 43": "OE1" <-> "OE2" Residue "O ARG 46": "NH1" <-> "NH2" Residue "O ARG 63": "NH1" <-> "NH2" Residue "O ARG 64": "NH1" <-> "NH2" Residue "O ARG 69": "NH1" <-> "NH2" Residue "O ARG 71": "NH1" <-> "NH2" Residue "O PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 82": "OE1" <-> "OE2" Residue "O ARG 96": "NH1" <-> "NH2" Residue "O GLU 114": "OE1" <-> "OE2" Residue "P ARG 10": "NH1" <-> "NH2" Residue "P ARG 16": "NH1" <-> "NH2" Residue "P GLU 20": "OE1" <-> "OE2" Residue "P ARG 25": "NH1" <-> "NH2" Residue "P GLU 55": "OE1" <-> "OE2" Residue "P ARG 81": "NH1" <-> "NH2" Residue "P ARG 94": "NH1" <-> "NH2" Residue "P ARG 102": "NH1" <-> "NH2" Residue "P ARG 111": "NH1" <-> "NH2" Residue "P PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 21": "NH1" <-> "NH2" Residue "Q ARG 39": "NH1" <-> "NH2" Residue "Q GLU 44": "OE1" <-> "OE2" Residue "Q ARG 62": "NH1" <-> "NH2" Residue "Q GLU 71": "OE1" <-> "OE2" Residue "Q ARG 89": "NH1" <-> "NH2" Residue "Q ARG 101": "NH1" <-> "NH2" Residue "Q ARG 109": "NH1" <-> "NH2" Residue "R ARG 3": "NH1" <-> "NH2" Residue "R ARG 6": "NH1" <-> "NH2" Residue "R ARG 13": "NH1" <-> "NH2" Residue "R ARG 33": "NH1" <-> "NH2" Residue "R TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 48": "NH1" <-> "NH2" Residue "R PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 70": "NH1" <-> "NH2" Residue "R PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 111": "OE1" <-> "OE2" Residue "S TYR 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 16": "OE1" <-> "OE2" Residue "S ARG 21": "NH1" <-> "NH2" Residue "S GLU 23": "OE1" <-> "OE2" Residue "S GLU 31": "OE1" <-> "OE2" Residue "S GLU 45": "OE1" <-> "OE2" Residue "S ARG 68": "NH1" <-> "NH2" Residue "S GLU 70": "OE1" <-> "OE2" Residue "S PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 78": "NH1" <-> "NH2" Residue "S ARG 79": "NH1" <-> "NH2" Residue "S ARG 84": "NH1" <-> "NH2" Residue "T GLU 59": "OE1" <-> "OE2" Residue "T PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 78": "OE1" <-> "OE2" Residue "T ARG 84": "NH1" <-> "NH2" Residue "T ARG 88": "NH1" <-> "NH2" Residue "T ARG 95": "NH1" <-> "NH2" Residue "T ARG 110": "NH1" <-> "NH2" Residue "U GLU 4": "OE1" <-> "OE2" Residue "U GLU 5": "OE1" <-> "OE2" Residue "U GLU 52": "OE1" <-> "OE2" Residue "U GLU 54": "OE1" <-> "OE2" Residue "U GLU 89": "OE1" <-> "OE2" Residue "V ARG 6": "NH1" <-> "NH2" Residue "V ARG 7": "NH1" <-> "NH2" Residue "V GLU 37": "OE1" <-> "OE2" Residue "V ARG 82": "NH1" <-> "NH2" Residue "V ARG 86": "NH1" <-> "NH2" Residue "V PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 88": "OE1" <-> "OE2" Residue "V ARG 94": "NH1" <-> "NH2" Residue "W PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 11": "OE1" <-> "OE2" Residue "W GLU 41": "OE1" <-> "OE2" Residue "W ASP 43": "OD1" <-> "OD2" Residue "W GLU 55": "OE1" <-> "OE2" Residue "W PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 69": "OE1" <-> "OE2" Residue "W PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 17": "OE1" <-> "OE2" Residue "X PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 29": "OE1" <-> "OE2" Residue "X PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 85": "OE1" <-> "OE2" Residue "Y ARG 3": "NH1" <-> "NH2" Residue "Y ARG 11": "NH1" <-> "NH2" Residue "Y ARG 18": "NH1" <-> "NH2" Residue "Y ARG 37": "NH1" <-> "NH2" Residue "Y PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 41": "OE1" <-> "OE2" Residue "Y GLU 43": "OE1" <-> "OE2" Residue "Y ARG 50": "NH1" <-> "NH2" Residue "Y ARG 57": "NH1" <-> "NH2" Residue "Y ARG 74": "NH1" <-> "NH2" Residue "Z GLU 5": "OE1" <-> "OE2" Residue "Z GLU 12": "OE1" <-> "OE2" Residue "Z ARG 47": "NH1" <-> "NH2" Residue "Z ARG 52": "NH1" <-> "NH2" Residue "a ARG 11": "NH1" <-> "NH2" Residue "a ARG 30": "NH1" <-> "NH2" Residue "a GLU 37": "OE1" <-> "OE2" Residue "a ARG 45": "NH1" <-> "NH2" Residue "a PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 10": "NH1" <-> "NH2" Residue "b ARG 16": "NH1" <-> "NH2" Residue "b ASP 31": "OD1" <-> "OD2" Residue "b ARG 52": "NH1" <-> "NH2" Residue "c GLU 32": "OE1" <-> "OE2" Residue "c ARG 44": "NH1" <-> "NH2" Residue "d ARG 3": "NH1" <-> "NH2" Residue "d ARG 14": "NH1" <-> "NH2" Residue "d PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 19": "NH1" <-> "NH2" Residue "d ARG 21": "NH1" <-> "NH2" Residue "d ARG 33": "NH1" <-> "NH2" Residue "e ARG 13": "NH1" <-> "NH2" Residue "e ARG 30": "NH1" <-> "NH2" Residue "e ARG 40": "NH1" <-> "NH2" Residue "e ARG 42": "NH1" <-> "NH2" Residue "f ARG 24": "NH1" <-> "NH2" Residue "i GLU 392": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 94030 Number of models: 1 Model: "" Number of chains: 46 Chain: "1" Number of atoms: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 926 Classifications: {'RNA': 43} Modifications used: {'rna3p_pur': 26, 'rna3p_pyr': 17} Link IDs: {'rna3p': 42} Chain: "2" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 62 Classifications: {'RNA': 3} Modifications used: {'rna2p_pur': 1, 'rna3p_pyr': 2} Link IDs: {'rna3p': 2} Chain: "A" Number of atoms: 61902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2883, 61902 Classifications: {'RNA': 2883} Modifications used: {'rna2p_pur': 280, 'rna2p_pyr': 148, 'rna3p_pur': 1386, 'rna3p_pyr': 1069} Link IDs: {'rna2p': 428, 'rna3p': 2454} Chain breaks: 4 Chain: "B" Number of atoms: 2569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 2569 Classifications: {'RNA': 120} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 6, 'rna3p_pur': 57, 'rna3p_pyr': 50} Link IDs: {'rna2p': 13, 'rna3p': 106} Chain: "C" Number of atoms: 2083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2083 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 17, 'TRANS': 254} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 1565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1565 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 202} Chain: "E" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1552 Classifications: {'peptide': 201} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 195} Chain: "F" Number of atoms: 1411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1411 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 6, 'TRANS': 171} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 1323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1323 Classifications: {'peptide': 176} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "H" Number of atoms: 1110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1110 Classifications: {'peptide': 149} Link IDs: {'PTRANS': 3, 'TRANS': 145} Chain: "I" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 946 Classifications: {'peptide': 125} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 120} Chain: "J" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 979 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 9, 'TRANS': 124} Chain: "K" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1129 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 135} Chain: "L" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 946 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 5, 'TRANS': 117} Chain: "M" Number of atoms: 1053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1053 Classifications: {'peptide': 144} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 139} Chain: "N" Number of atoms: 1074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1074 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 128} Chain: "O" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 993 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 4, 'TRANS': 120} Chain: "P" Number of atoms: 900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 900 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 114} Chain: "Q" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 917 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "R" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 947 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'TRANS': 116} Chain: "S" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 816 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'TRANS': 101} Chain: "T" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 857 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 107} Chain: "U" Number of atoms: 756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 756 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 1, 'TRANS': 93} Chain: "V" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 780 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 3, 'TRANS': 99} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "W" Number of atoms: 753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 753 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "X" Number of atoms: 580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 580 Classifications: {'peptide': 76} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 74} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "Y" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 625 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "Z" Number of atoms: 501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 501 Classifications: {'peptide': 62} Modifications used: {'COO': 1} Link IDs: {'TRANS': 61} Chain: "a" Number of atoms: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 449 Classifications: {'peptide': 58} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "b" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 444 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 54} Chain: "c" Number of atoms: 414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 414 Classifications: {'peptide': 51} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 48} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "d" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 377 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "e" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 504 Classifications: {'peptide': 64} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "f" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 302 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "i" Number of atoms: 916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 916 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 124} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'UNK:plan-1': 41} Unresolved non-hydrogen planarities: 41 Chain: "k" Number of atoms: 137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 137 Classifications: {'peptide': 18} Link IDs: {'PTRANS': 1, 'TRANS': 16} Chain: "2" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 411, 411 Unusual residues: {' MG': 411} Classifications: {'undetermined': 411} Link IDs: {None: 410} Chain: "B" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Unusual residues: {' MG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "Y" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "b" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "f" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 92328 SG CYS f 11 74.909 81.051 178.600 1.00 92.14 S ATOM 92353 SG CYS f 14 78.108 82.541 177.489 1.00 85.62 S ATOM 92456 SG CYS f 27 78.079 78.983 178.947 1.00 94.45 S Time building chain proxies: 37.05, per 1000 atoms: 0.39 Number of scatterers: 94030 At special positions: 0 Unit cell: (243.76, 198.055, 239.605, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 95 16.00 P 3049 15.00 Mg 431 11.99 O 26174 8.00 N 17424 7.00 C 46856 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 41.08 Conformation dependent library (CDL) restraints added in 4.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN f 101 " pdb="ZN ZN f 101 " - pdb=" ND1 HIS f 33 " pdb="ZN ZN f 101 " - pdb=" SG CYS f 27 " pdb="ZN ZN f 101 " - pdb=" SG CYS f 11 " pdb="ZN ZN f 101 " - pdb=" SG CYS f 14 " Number of angles added : 3 7058 Ramachandran restraints generated. 3529 Oldfield, 0 Emsley, 3529 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6648 Finding SS restraints... Secondary structure from input PDB file: 110 helices and 52 sheets defined 33.1% alpha, 21.2% beta 1017 base pairs and 1608 stacking pairs defined. Time for finding SS restraints: 33.91 Creating SS restraints... Processing helix chain 'C' and resid 12 through 15 removed outlier: 3.877A pdb=" N HIS C 15 " --> pdb=" O GLY C 12 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 12 through 15' Processing helix chain 'C' and resid 207 through 214 removed outlier: 3.792A pdb=" N ALA C 211 " --> pdb=" O LYS C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 225 Processing helix chain 'C' and resid 263 through 265 No H-bonds generated for 'chain 'C' and resid 263 through 265' Processing helix chain 'D' and resid 56 through 60 Processing helix chain 'D' and resid 61 through 72 removed outlier: 3.610A pdb=" N ALA D 71 " --> pdb=" O HIS D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 102 Processing helix chain 'D' and resid 120 through 125 Processing helix chain 'E' and resid 24 through 39 Processing helix chain 'E' and resid 97 through 115 Processing helix chain 'E' and resid 130 through 142 removed outlier: 3.705A pdb=" N LEU E 134 " --> pdb=" O LYS E 130 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N MET E 141 " --> pdb=" O LYS E 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 154 through 161 removed outlier: 3.722A pdb=" N ALA E 161 " --> pdb=" O LEU E 157 " (cutoff:3.500A) Processing helix chain 'E' and resid 162 through 164 No H-bonds generated for 'chain 'E' and resid 162 through 164' Processing helix chain 'E' and resid 173 through 175 No H-bonds generated for 'chain 'E' and resid 173 through 175' Processing helix chain 'E' and resid 176 through 182 Processing helix chain 'E' and resid 190 through 201 Processing helix chain 'F' and resid 3 through 11 Processing helix chain 'F' and resid 11 through 20 Processing helix chain 'F' and resid 24 through 28 Processing helix chain 'F' and resid 47 through 62 removed outlier: 3.610A pdb=" N ASP F 51 " --> pdb=" O LYS F 47 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASP F 56 " --> pdb=" O ASN F 52 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 106 Processing helix chain 'F' and resid 107 through 111 Processing helix chain 'F' and resid 142 through 146 Processing helix chain 'F' and resid 162 through 173 removed outlier: 3.508A pdb=" N PHE F 173 " --> pdb=" O LEU F 169 " (cutoff:3.500A) Processing helix chain 'G' and resid 60 through 79 Processing helix chain 'G' and resid 137 through 150 Processing helix chain 'H' and resid 22 through 29 removed outlier: 3.695A pdb=" N ALA H 26 " --> pdb=" O LYS H 22 " (cutoff:3.500A) Processing helix chain 'H' and resid 40 through 73 removed outlier: 6.094A pdb=" N ALA H 52 " --> pdb=" O GLU H 48 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N GLU H 53 " --> pdb=" O ALA H 49 " (cutoff:3.500A) Processing helix chain 'H' and resid 85 through 89 removed outlier: 3.829A pdb=" N GLY H 88 " --> pdb=" O GLY H 85 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS H 89 " --> pdb=" O ASP H 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 85 through 89' Processing helix chain 'H' and resid 95 through 104 removed outlier: 3.531A pdb=" N ILE H 99 " --> pdb=" O GLY H 95 " (cutoff:3.500A) Processing helix chain 'I' and resid 4 through 20 Processing helix chain 'I' and resid 34 through 47 Processing helix chain 'I' and resid 56 through 65 removed outlier: 3.656A pdb=" N ARG I 62 " --> pdb=" O THR I 58 " (cutoff:3.500A) Processing helix chain 'I' and resid 94 through 103 Processing helix chain 'J' and resid 24 through 30 Processing helix chain 'J' and resid 34 through 46 removed outlier: 3.898A pdb=" N PHE J 38 " --> pdb=" O ASN J 34 " (cutoff:3.500A) Processing helix chain 'J' and resid 47 through 49 No H-bonds generated for 'chain 'J' and resid 47 through 49' Processing helix chain 'J' and resid 75 through 84 Processing helix chain 'J' and resid 102 through 117 Processing helix chain 'J' and resid 121 through 136 removed outlier: 3.720A pdb=" N MET J 136 " --> pdb=" O THR J 132 " (cutoff:3.500A) Processing helix chain 'K' and resid 24 through 38 removed outlier: 4.063A pdb=" N GLU K 31 " --> pdb=" O ARG K 27 " (cutoff:3.500A) Processing helix chain 'K' and resid 58 through 62 Processing helix chain 'K' and resid 67 through 72 Processing helix chain 'K' and resid 89 through 96 Processing helix chain 'K' and resid 97 through 107 removed outlier: 3.973A pdb=" N ILE K 101 " --> pdb=" O PRO K 97 " (cutoff:3.500A) Processing helix chain 'K' and resid 112 through 120 Processing helix chain 'K' and resid 132 through 136 Processing helix chain 'L' and resid 104 through 108 Processing helix chain 'L' and resid 112 through 118 removed outlier: 3.721A pdb=" N ILE L 116 " --> pdb=" O PHE L 112 " (cutoff:3.500A) Processing helix chain 'M' and resid 56 through 61 Processing helix chain 'M' and resid 68 through 72 Processing helix chain 'M' and resid 80 through 84 removed outlier: 3.816A pdb=" N ALA M 83 " --> pdb=" O SER M 80 " (cutoff:3.500A) Processing helix chain 'M' and resid 91 through 98 Processing helix chain 'M' and resid 128 through 136 Processing helix chain 'N' and resid 43 through 57 Processing helix chain 'N' and resid 109 through 122 Processing helix chain 'O' and resid 13 through 31 Processing helix chain 'O' and resid 38 through 56 removed outlier: 4.182A pdb=" N ARG O 46 " --> pdb=" O LYS O 42 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N VAL O 47 " --> pdb=" O GLU O 43 " (cutoff:3.500A) Proline residue: O 50 - end of helix Processing helix chain 'O' and resid 59 through 71 Processing helix chain 'O' and resid 72 through 82 Processing helix chain 'O' and resid 82 through 87 Processing helix chain 'O' and resid 117 through 125 removed outlier: 3.773A pdb=" N ALA O 125 " --> pdb=" O LYS O 121 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 22 removed outlier: 3.892A pdb=" N ALA P 6 " --> pdb=" O ASP P 2 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ARG P 13 " --> pdb=" O ARG P 9 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N ALA P 14 " --> pdb=" O ARG P 10 " (cutoff:3.500A) Processing helix chain 'P' and resid 55 through 60 Processing helix chain 'P' and resid 67 through 84 Processing helix chain 'P' and resid 100 through 113 Processing helix chain 'Q' and resid 3 through 10 Processing helix chain 'Q' and resid 53 through 56 removed outlier: 3.937A pdb=" N HIS Q 56 " --> pdb=" O ARG Q 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 53 through 56' Processing helix chain 'Q' and resid 97 through 102 Processing helix chain 'Q' and resid 104 through 109 removed outlier: 3.954A pdb=" N ARG Q 109 " --> pdb=" O LYS Q 106 " (cutoff:3.500A) Processing helix chain 'R' and resid 6 through 21 removed outlier: 3.826A pdb=" N GLN R 20 " --> pdb=" O LYS R 16 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA R 21 " --> pdb=" O ILE R 17 " (cutoff:3.500A) Processing helix chain 'R' and resid 25 through 30 Processing helix chain 'R' and resid 31 through 72 removed outlier: 3.814A pdb=" N GLN R 37 " --> pdb=" O ARG R 33 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG R 51 " --> pdb=" O TYR R 47 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N LYS R 54 " --> pdb=" O ARG R 50 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ARG R 55 " --> pdb=" O ARG R 51 " (cutoff:3.500A) Processing helix chain 'R' and resid 75 through 86 Processing helix chain 'R' and resid 91 through 102 Processing helix chain 'R' and resid 102 through 117 removed outlier: 3.503A pdb=" N PHE R 106 " --> pdb=" O ASP R 102 " (cutoff:3.500A) Processing helix chain 'T' and resid 13 through 22 removed outlier: 3.533A pdb=" N VAL T 17 " --> pdb=" O SER T 13 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU T 19 " --> pdb=" O GLN T 15 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N VAL T 20 " --> pdb=" O LYS T 16 " (cutoff:3.500A) Processing helix chain 'T' and resid 28 through 39 Processing helix chain 'T' and resid 41 through 63 removed outlier: 3.988A pdb=" N VAL T 45 " --> pdb=" O LYS T 41 " (cutoff:3.500A) Processing helix chain 'T' and resid 65 through 69 Processing helix chain 'T' and resid 89 through 91 No H-bonds generated for 'chain 'T' and resid 89 through 91' Processing helix chain 'U' and resid 3 through 8 Processing helix chain 'U' and resid 17 through 28 Processing helix chain 'U' and resid 39 through 51 Processing helix chain 'W' and resid 13 through 23 Processing helix chain 'W' and resid 44 through 51 Processing helix chain 'W' and resid 54 through 59 removed outlier: 3.599A pdb=" N SER W 58 " --> pdb=" O ALA W 54 " (cutoff:3.500A) Processing helix chain 'Y' and resid 53 through 63 Processing helix chain 'Y' and resid 63 through 75 removed outlier: 3.662A pdb=" N VAL Y 67 " --> pdb=" O GLY Y 63 " (cutoff:3.500A) Processing helix chain 'Z' and resid 10 through 35 Processing helix chain 'Z' and resid 40 through 63 removed outlier: 3.831A pdb=" N LYS Z 44 " --> pdb=" O SER Z 40 " (cutoff:3.500A) Processing helix chain 'a' and resid 17 through 28 Processing helix chain 'a' and resid 41 through 52 removed outlier: 3.543A pdb=" N VAL a 51 " --> pdb=" O MET a 47 " (cutoff:3.500A) Processing helix chain 'b' and resid 9 through 17 removed outlier: 3.591A pdb=" N ARG b 17 " --> pdb=" O ARG b 13 " (cutoff:3.500A) Processing helix chain 'b' and resid 18 through 21 removed outlier: 3.727A pdb=" N ALA b 21 " --> pdb=" O SER b 18 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 18 through 21' Processing helix chain 'd' and resid 8 through 17 Processing helix chain 'd' and resid 17 through 22 Processing helix chain 'd' and resid 24 through 37 Processing helix chain 'e' and resid 7 through 14 removed outlier: 3.795A pdb=" N LYS e 12 " --> pdb=" O ARG e 8 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ARG e 13 " --> pdb=" O GLY e 9 " (cutoff:3.500A) Processing helix chain 'e' and resid 37 through 45 Processing helix chain 'e' and resid 54 through 62 Processing helix chain 'f' and resid 30 through 33 Processing helix chain 'i' and resid 332 through 345 removed outlier: 4.177A pdb=" N ASN i 343 " --> pdb=" O ARG i 339 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N MET i 344 " --> pdb=" O GLN i 340 " (cutoff:3.500A) Processing helix chain 'i' and resid 346 through 351 Processing helix chain 'i' and resid 368 through 382 Processing helix chain 'i' and resid 384 through 389 Processing helix chain 'i' and resid 395 through 406 removed outlier: 3.554A pdb=" N CYS i 406 " --> pdb=" O ILE i 402 " (cutoff:3.500A) Processing helix chain 'i' and resid 409 through 433 removed outlier: 3.601A pdb=" N GLY i 433 " --> pdb=" O LYS i 429 " (cutoff:3.500A) Processing helix chain 'i' and resid 434 through 441 Processing helix chain 'k' and resid 28 through 42 removed outlier: 3.639A pdb=" N LEU k 36 " --> pdb=" O LEU k 32 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 3 through 5 Processing sheet with id=AA2, first strand: chain 'C' and resid 34 through 35 Processing sheet with id=AA3, first strand: chain 'C' and resid 101 through 105 removed outlier: 6.725A pdb=" N ILE C 91 " --> pdb=" O LEU C 81 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N LEU C 81 " --> pdb=" O ILE C 91 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N LEU C 93 " --> pdb=" O GLU C 79 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 129 through 131 removed outlier: 6.052A pdb=" N ILE C 164 " --> pdb=" O ARG C 175 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ARG C 175 " --> pdb=" O ILE C 164 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N MET C 181 " --> pdb=" O VAL C 268 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 144 through 145 removed outlier: 5.406A pdb=" N VAL C 144 " --> pdb=" O GLN C 153 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 4 through 15 removed outlier: 5.714A pdb=" N LYS D 8 " --> pdb=" O GLU D 28 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N GLU D 28 " --> pdb=" O LYS D 8 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLY D 10 " --> pdb=" O VAL D 26 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N LYS D 190 " --> pdb=" O VAL D 177 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N VAL D 177 " --> pdb=" O LYS D 190 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N SER D 174 " --> pdb=" O VAL D 107 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N VAL D 107 " --> pdb=" O SER D 174 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N THR D 112 " --> pdb=" O ASP D 200 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N ASP D 200 " --> pdb=" O THR D 112 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 80 through 83 removed outlier: 3.571A pdb=" N GLN D 36 " --> pdb=" O GLN D 49 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N THR D 51 " --> pdb=" O VAL D 34 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N VAL D 34 " --> pdb=" O THR D 51 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'E' and resid 2 through 4 Processing sheet with id=AB1, first strand: chain 'E' and resid 118 through 121 removed outlier: 6.650A pdb=" N VAL E 146 " --> pdb=" O ASP E 168 " (cutoff:3.500A) removed outlier: 8.089A pdb=" N ARG E 170 " --> pdb=" O VAL E 146 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N ILE E 148 " --> pdb=" O ARG E 170 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 66 through 69 removed outlier: 3.738A pdb=" N GLY F 86 " --> pdb=" O THR F 68 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 16 through 20 Processing sheet with id=AB4, first strand: chain 'G' and resid 41 through 45 Processing sheet with id=AB5, first strand: chain 'G' and resid 122 through 124 Processing sheet with id=AB6, first strand: chain 'G' and resid 95 through 99 Processing sheet with id=AB7, first strand: chain 'H' and resid 18 through 20 Processing sheet with id=AB8, first strand: chain 'H' and resid 77 through 82 removed outlier: 6.097A pdb=" N VAL H 78 " --> pdb=" O ASN H 145 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N VAL H 147 " --> pdb=" O VAL H 78 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ILE H 80 " --> pdb=" O VAL H 147 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER H 131 " --> pdb=" O ARG H 116 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 50 through 54 removed outlier: 3.752A pdb=" N SER I 24 " --> pdb=" O VAL I 85 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N VAL I 27 " --> pdb=" O ALA I 110 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ALA I 110 " --> pdb=" O VAL I 27 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'J' and resid 9 through 14 Processing sheet with id=AC2, first strand: chain 'J' and resid 100 through 101 Processing sheet with id=AC3, first strand: chain 'K' and resid 122 through 124 removed outlier: 6.213A pdb=" N ILE K 54 " --> pdb=" O LYS K 123 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N TRP K 15 " --> pdb=" O GLN K 138 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'K' and resid 73 through 77 Processing sheet with id=AC5, first strand: chain 'L' and resid 7 through 10 removed outlier: 6.554A pdb=" N LYS L 40 " --> pdb=" O ILE L 22 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N VAL L 24 " --> pdb=" O ILE L 38 " (cutoff:3.500A) removed outlier: 8.389A pdb=" N ILE L 38 " --> pdb=" O VAL L 24 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LYS L 59 " --> pdb=" O LEU L 87 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ALA L 83 " --> pdb=" O VAL L 63 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N CYS L 84 " --> pdb=" O MET L 7 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ASN L 9 " --> pdb=" O CYS L 84 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N LEU L 86 " --> pdb=" O ASN L 9 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 69 through 70 removed outlier: 6.848A pdb=" N ALA Q 58 " --> pdb=" O ILE Q 50 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N ILE Q 50 " --> pdb=" O ALA Q 58 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N THR Q 60 " --> pdb=" O ILE Q 48 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N ILE Q 64 " --> pdb=" O GLU Q 44 " (cutoff:3.500A) removed outlier: 9.201A pdb=" N GLU Q 44 " --> pdb=" O ILE Q 64 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N THR Q 25 " --> pdb=" O LYS Q 87 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N TRP Q 31 " --> pdb=" O VAL Q 81 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N VAL Q 81 " --> pdb=" O TRP Q 31 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'L' and resid 102 through 103 Processing sheet with id=AC8, first strand: chain 'M' and resid 74 through 78 Processing sheet with id=AC9, first strand: chain 'M' and resid 89 through 90 removed outlier: 5.823A pdb=" N VAL M 122 " --> pdb=" O GLU M 143 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'N' and resid 62 through 65 removed outlier: 6.437A pdb=" N VAL N 101 " --> pdb=" O ALA N 35 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ALA N 35 " --> pdb=" O VAL N 101 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N TYR N 103 " --> pdb=" O LEU N 33 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'N' and resid 39 through 42 removed outlier: 5.847A pdb=" N VAL N 89 " --> pdb=" O GLU N 75 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N GLU N 75 " --> pdb=" O VAL N 89 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N TYR N 91 " --> pdb=" O ILE N 73 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'O' and resid 33 through 37 removed outlier: 4.337A pdb=" N MET O 110 " --> pdb=" O CYS O 100 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'P' and resid 47 through 52 removed outlier: 3.690A pdb=" N VAL P 49 " --> pdb=" O VAL P 39 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N LEU P 26 " --> pdb=" O ASP P 93 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'S' and resid 10 through 14 removed outlier: 7.105A pdb=" N GLN S 6 " --> pdb=" O VAL S 38 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N VAL S 38 " --> pdb=" O GLN S 6 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'S' and resid 19 through 23 removed outlier: 6.779A pdb=" N TRP S 92 " --> pdb=" O ARG S 68 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ARG S 68 " --> pdb=" O TRP S 92 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N THR S 94 " --> pdb=" O HIS S 66 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N HIS S 66 " --> pdb=" O THR S 94 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N VAL S 96 " --> pdb=" O VAL S 64 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N VAL S 64 " --> pdb=" O VAL S 96 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N ILE S 98 " --> pdb=" O GLU S 62 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N GLU S 62 " --> pdb=" O ILE S 98 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'S' and resid 72 through 78 removed outlier: 3.996A pdb=" N TYR S 83 " --> pdb=" O ARG S 78 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'T' and resid 2 through 11 removed outlier: 3.522A pdb=" N HIS T 9 " --> pdb=" O SER T 101 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N SER T 101 " --> pdb=" O HIS T 9 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N SER T 108 " --> pdb=" O VAL T 71 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N VAL T 71 " --> pdb=" O SER T 108 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'T' and resid 82 through 87 Processing sheet with id=AE1, first strand: chain 'U' and resid 11 through 14 removed outlier: 4.136A pdb=" N LYS U 81 " --> pdb=" O VAL U 34 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N TRP U 80 " --> pdb=" O VAL U 62 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N VAL U 62 " --> pdb=" O TRP U 80 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N LYS U 82 " --> pdb=" O THR U 60 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N THR U 60 " --> pdb=" O LYS U 82 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N TYR U 84 " --> pdb=" O VAL U 58 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N VAL U 58 " --> pdb=" O TYR U 84 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N THR U 86 " --> pdb=" O GLU U 56 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'U' and resid 67 through 70 Processing sheet with id=AE3, first strand: chain 'V' and resid 65 through 66 removed outlier: 3.553A pdb=" N LYS V 33 " --> pdb=" O LEU V 29 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASN V 27 " --> pdb=" O ILE V 35 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N GLU V 10 " --> pdb=" O PHE V 73 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'V' and resid 41 through 46 Processing sheet with id=AE5, first strand: chain 'V' and resid 83 through 88 Processing sheet with id=AE6, first strand: chain 'W' and resid 3 through 8 removed outlier: 7.649A pdb=" N ASN W 5 " --> pdb=" O ASP W 43 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N ASP W 43 " --> pdb=" O ASN W 5 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLU W 7 " --> pdb=" O GLU W 41 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N GLN W 87 " --> pdb=" O LYS W 25 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ILE W 89 " --> pdb=" O PRO W 27 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N VAL W 92 " --> pdb=" O ALA W 74 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N ALA W 74 " --> pdb=" O VAL W 92 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ILE W 4 " --> pdb=" O VAL W 64 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'X' and resid 22 through 23 removed outlier: 3.968A pdb=" N ARG X 39 " --> pdb=" O GLY X 22 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N LEU X 59 " --> pdb=" O ILE X 37 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'X' and resid 30 through 31 removed outlier: 6.100A pdb=" N HIS X 46 " --> pdb=" O ILE X 80 " (cutoff:3.500A) removed outlier: 8.396A pdb=" N ILE X 82 " --> pdb=" O HIS X 46 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'Y' and resid 13 through 18 Processing sheet with id=AF1, first strand: chain 'Y' and resid 33 through 40 Processing sheet with id=AF2, first strand: chain 'a' and resid 35 through 39 Processing sheet with id=AF3, first strand: chain 'b' and resid 29 through 30 Processing sheet with id=AF4, first strand: chain 'b' and resid 48 through 49 Processing sheet with id=AF5, first strand: chain 'c' and resid 20 through 25 Processing sheet with id=AF6, first strand: chain 'e' and resid 15 through 16 Processing sheet with id=AF7, first strand: chain 'f' and resid 2 through 4 removed outlier: 6.154A pdb=" N LYS f 2 " --> pdb=" O ARG f 36 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N ILE f 23 " --> pdb=" O GLN f 37 " (cutoff:3.500A) 1164 hydrogen bonds defined for protein. 3204 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2560 hydrogen bonds 4030 hydrogen bond angles 0 basepair planarities 1017 basepair parallelities 1608 stacking parallelities Total time for adding SS restraints: 186.01 Time building geometry restraints manager: 44.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 16074 1.33 - 1.46: 44408 1.46 - 1.59: 36746 1.59 - 1.73: 4410 1.73 - 1.86: 174 Bond restraints: 101812 Sorted by residual: bond pdb=" CA UNK i 357 " pdb=" C UNK i 357 " ideal model delta sigma weight residual 1.525 1.690 -0.165 2.10e-02 2.27e+03 6.19e+01 bond pdb=" CA UNK i 449 " pdb=" C UNK i 449 " ideal model delta sigma weight residual 1.525 1.678 -0.153 2.10e-02 2.27e+03 5.30e+01 bond pdb=" N UNK i 451 " pdb=" CA UNK i 451 " ideal model delta sigma weight residual 1.458 1.592 -0.134 1.90e-02 2.77e+03 4.95e+01 bond pdb=" CA UNK i 446 " pdb=" C UNK i 446 " ideal model delta sigma weight residual 1.525 1.673 -0.148 2.10e-02 2.27e+03 4.94e+01 bond pdb=" CA UNK i 452 " pdb=" C UNK i 452 " ideal model delta sigma weight residual 1.525 1.670 -0.145 2.10e-02 2.27e+03 4.75e+01 ... (remaining 101807 not shown) Histogram of bond angle deviations from ideal: 93.90 - 102.80: 5517 102.80 - 111.69: 61193 111.69 - 120.59: 51421 120.59 - 129.49: 31815 129.49 - 138.39: 2612 Bond angle restraints: 152558 Sorted by residual: angle pdb=" C VAL D 142 " pdb=" N PRO D 143 " pdb=" CA PRO D 143 " ideal model delta sigma weight residual 119.82 129.90 -10.08 9.80e-01 1.04e+00 1.06e+02 angle pdb=" C LYS i 390 " pdb=" N PRO i 391 " pdb=" CA PRO i 391 " ideal model delta sigma weight residual 119.87 129.93 -10.06 1.04e+00 9.25e-01 9.35e+01 angle pdb=" N ASP J 116 " pdb=" CA ASP J 116 " pdb=" C ASP J 116 " ideal model delta sigma weight residual 113.17 124.65 -11.48 1.26e+00 6.30e-01 8.30e+01 angle pdb=" C LEU N 124 " pdb=" N PRO N 125 " pdb=" CA PRO N 125 " ideal model delta sigma weight residual 119.56 128.02 -8.46 1.01e+00 9.80e-01 7.01e+01 angle pdb=" N VAL D 142 " pdb=" CA VAL D 142 " pdb=" C VAL D 142 " ideal model delta sigma weight residual 109.02 116.29 -7.27 9.30e-01 1.16e+00 6.11e+01 ... (remaining 152553 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.95: 56998 35.95 - 71.91: 7373 71.91 - 107.86: 808 107.86 - 143.82: 13 143.82 - 179.77: 10 Dihedral angle restraints: 65202 sinusoidal: 54889 harmonic: 10313 Sorted by residual: dihedral pdb=" C4' C A 645 " pdb=" C3' C A 645 " pdb=" C2' C A 645 " pdb=" C1' C A 645 " ideal model delta sinusoidal sigma weight residual -35.00 30.64 -65.64 1 8.00e+00 1.56e-02 8.81e+01 dihedral pdb=" C4' U A1344 " pdb=" C3' U A1344 " pdb=" C2' U A1344 " pdb=" C1' U A1344 " ideal model delta sinusoidal sigma weight residual -35.00 30.20 -65.20 1 8.00e+00 1.56e-02 8.71e+01 dihedral pdb=" C5' C A 645 " pdb=" C4' C A 645 " pdb=" C3' C A 645 " pdb=" O3' C A 645 " ideal model delta sinusoidal sigma weight residual 147.00 83.98 63.02 1 8.00e+00 1.56e-02 8.20e+01 ... (remaining 65199 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 17879 0.078 - 0.155: 1559 0.155 - 0.233: 112 0.233 - 0.310: 7 0.310 - 0.388: 2 Chirality restraints: 19559 Sorted by residual: chirality pdb=" C3' C A 645 " pdb=" C4' C A 645 " pdb=" O3' C A 645 " pdb=" C2' C A 645 " both_signs ideal model delta sigma weight residual False -2.74 -2.36 -0.39 2.00e-01 2.50e+01 3.76e+00 chirality pdb=" C3' U A1344 " pdb=" C4' U A1344 " pdb=" O3' U A1344 " pdb=" C2' U A1344 " both_signs ideal model delta sigma weight residual False -2.74 -2.43 -0.32 2.00e-01 2.50e+01 2.53e+00 chirality pdb=" C1' G A 748 " pdb=" O4' G A 748 " pdb=" C2' G A 748 " pdb=" N9 G A 748 " both_signs ideal model delta sigma weight residual False 2.46 2.15 0.31 2.00e-01 2.50e+01 2.39e+00 ... (remaining 19556 not shown) Planarity restraints: 7978 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU U 93 " -0.023 2.00e-02 2.50e+03 4.49e-02 2.02e+01 pdb=" C LEU U 93 " 0.078 2.00e-02 2.50e+03 pdb=" O LEU U 93 " -0.030 2.00e-02 2.50e+03 pdb=" N ASP U 94 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY J 25 " -0.057 5.00e-02 4.00e+02 8.69e-02 1.21e+01 pdb=" N PRO J 26 " 0.150 5.00e-02 4.00e+02 pdb=" CA PRO J 26 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO J 26 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' C A2422 " 0.030 2.00e-02 2.50e+03 1.94e-02 8.46e+00 pdb=" N1 C A2422 " -0.049 2.00e-02 2.50e+03 pdb=" C2 C A2422 " 0.003 2.00e-02 2.50e+03 pdb=" O2 C A2422 " 0.000 2.00e-02 2.50e+03 pdb=" N3 C A2422 " 0.002 2.00e-02 2.50e+03 pdb=" C4 C A2422 " 0.003 2.00e-02 2.50e+03 pdb=" N4 C A2422 " 0.006 2.00e-02 2.50e+03 pdb=" C5 C A2422 " 0.003 2.00e-02 2.50e+03 pdb=" C6 C A2422 " 0.001 2.00e-02 2.50e+03 ... (remaining 7975 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.41: 337 2.41 - 3.03: 50118 3.03 - 3.66: 169249 3.66 - 4.28: 278285 4.28 - 4.90: 369902 Nonbonded interactions: 867891 Sorted by model distance: nonbonded pdb=" OP1 C A 787 " pdb="MG MG A3174 " model vdw 1.789 2.170 nonbonded pdb=" OP2 U A1023 " pdb="MG MG A3212 " model vdw 1.792 2.170 nonbonded pdb=" OP2 A A 422 " pdb="MG MG A3066 " model vdw 1.802 2.170 nonbonded pdb=" OP2 U A1379 " pdb="MG MG A3138 " model vdw 1.806 2.170 nonbonded pdb=" OP1 A A1614 " pdb="MG MG A3020 " model vdw 1.810 2.170 ... (remaining 867886 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators 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: 1.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.090 Extract box with map and model: 10.860 Check model and map are aligned: 1.050 Set scattering table: 0.690 Process input model: 378.960 Find NCS groups from input model: 1.820 Set up NCS constraints: 0.260 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:2.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 398.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8839 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.165 101812 Z= 0.456 Angle : 1.042 14.102 152558 Z= 0.597 Chirality : 0.045 0.388 19559 Planarity : 0.005 0.087 7978 Dihedral : 23.624 179.770 58554 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.00 % Favored : 96.94 % Rotamer: Outliers : 9.03 % Allowed : 11.89 % Favored : 79.08 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.35 (0.11), residues: 3529 helix: -3.59 (0.10), residues: 1074 sheet: -1.47 (0.17), residues: 666 loop : -1.50 (0.12), residues: 1789 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 248 HIS 0.010 0.002 HIS C 15 PHE 0.038 0.003 PHE I 106 TYR 0.025 0.003 TYR T 38 ARG 0.005 0.001 ARG K 95 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7058 Ramachandran restraints generated. 3529 Oldfield, 0 Emsley, 3529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7058 Ramachandran restraints generated. 3529 Oldfield, 0 Emsley, 3529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1494 residues out of total 2908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 262 poor density : 1232 time to evaluate : 4.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 24 LEU cc_start: 0.9025 (OUTLIER) cc_final: 0.8695 (mm) REVERT: C 66 ASP cc_start: 0.9021 (t0) cc_final: 0.8642 (t0) REVERT: C 72 ASP cc_start: 0.8589 (m-30) cc_final: 0.7978 (t0) REVERT: C 83 TYR cc_start: 0.8456 (t80) cc_final: 0.8128 (t80) REVERT: C 120 VAL cc_start: 0.9439 (OUTLIER) cc_final: 0.9143 (p) REVERT: C 182 ARG cc_start: 0.8940 (OUTLIER) cc_final: 0.8646 (ttm-80) REVERT: C 185 GLU cc_start: 0.8663 (OUTLIER) cc_final: 0.8227 (pm20) REVERT: C 207 LYS cc_start: 0.9616 (OUTLIER) cc_final: 0.8916 (pttm) REVERT: C 270 ARG cc_start: 0.8073 (mmm160) cc_final: 0.7807 (tpt170) REVERT: D 21 SER cc_start: 0.9601 (t) cc_final: 0.9253 (p) REVERT: D 39 ASP cc_start: 0.8657 (p0) cc_final: 0.8361 (p0) REVERT: D 45 TYR cc_start: 0.8164 (p90) cc_final: 0.7824 (p90) REVERT: D 103 ASP cc_start: 0.8736 (m-30) cc_final: 0.8002 (t0) REVERT: D 137 SER cc_start: 0.9717 (m) cc_final: 0.9336 (p) REVERT: D 165 MET cc_start: 0.9557 (ttt) cc_final: 0.9319 (ttt) REVERT: D 181 ASP cc_start: 0.7692 (t0) cc_final: 0.7491 (t0) REVERT: E 12 LEU cc_start: 0.8736 (tp) cc_final: 0.8392 (tp) REVERT: E 46 GLN cc_start: 0.9289 (mp10) cc_final: 0.8910 (mp10) REVERT: E 120 VAL cc_start: 0.9254 (OUTLIER) cc_final: 0.8786 (m) REVERT: E 145 ASP cc_start: 0.8274 (t70) cc_final: 0.7460 (p0) REVERT: E 162 ARG cc_start: 0.9140 (OUTLIER) cc_final: 0.8460 (mtm110) REVERT: E 198 GLU cc_start: 0.8381 (mt-10) cc_final: 0.8145 (mt-10) REVERT: F 7 TYR cc_start: 0.8343 (t80) cc_final: 0.8108 (t80) REVERT: F 35 THR cc_start: 0.9374 (m) cc_final: 0.9125 (p) REVERT: F 63 GLN cc_start: 0.6818 (pt0) cc_final: 0.6550 (tp40) REVERT: F 72 LYS cc_start: 0.8701 (tppt) cc_final: 0.8169 (ttpt) REVERT: F 90 THR cc_start: 0.9194 (m) cc_final: 0.8938 (p) REVERT: F 96 MET cc_start: 0.8789 (ttp) cc_final: 0.8112 (tmm) REVERT: F 153 ASP cc_start: 0.8606 (OUTLIER) cc_final: 0.7935 (m-30) REVERT: G 11 VAL cc_start: 0.9254 (OUTLIER) cc_final: 0.8623 (m) REVERT: G 24 ILE cc_start: 0.9286 (mm) cc_final: 0.9035 (tp) REVERT: G 69 ARG cc_start: 0.8936 (tmt170) cc_final: 0.8675 (tpt90) REVERT: G 115 HIS cc_start: 0.8873 (t70) cc_final: 0.8211 (t-90) REVERT: G 127 THR cc_start: 0.9138 (OUTLIER) cc_final: 0.8504 (p) REVERT: G 130 GLU cc_start: 0.8672 (tt0) cc_final: 0.8165 (tm-30) REVERT: G 131 ILE cc_start: 0.9467 (mt) cc_final: 0.9113 (mt) REVERT: G 137 ASP cc_start: 0.8639 (t0) cc_final: 0.8333 (t0) REVERT: H 14 SER cc_start: 0.8606 (m) cc_final: 0.7561 (p) REVERT: H 15 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.7980 (pp) REVERT: H 17 ASP cc_start: 0.8895 (m-30) cc_final: 0.8624 (m-30) REVERT: H 28 ASN cc_start: 0.8961 (m-40) cc_final: 0.8632 (p0) REVERT: H 35 LYS cc_start: 0.9062 (mtpp) cc_final: 0.8796 (mmtm) REVERT: H 90 LEU cc_start: 0.6908 (OUTLIER) cc_final: 0.6621 (mt) REVERT: H 122 LEU cc_start: 0.8613 (mt) cc_final: 0.8072 (mt) REVERT: I 5 LEU cc_start: 0.7319 (tp) cc_final: 0.6745 (mt) REVERT: I 38 MET cc_start: 0.8247 (mmm) cc_final: 0.7133 (ttp) REVERT: I 55 VAL cc_start: 0.8802 (t) cc_final: 0.8379 (t) REVERT: I 72 LEU cc_start: 0.6356 (mt) cc_final: 0.5798 (mt) REVERT: I 109 LYS cc_start: 0.6722 (OUTLIER) cc_final: 0.6414 (ptpt) REVERT: I 116 GLU cc_start: 0.5728 (mt-10) cc_final: 0.5409 (mm-30) REVERT: J 40 LYS cc_start: 0.7083 (OUTLIER) cc_final: 0.6609 (pttp) REVERT: J 55 ILE cc_start: 0.3234 (OUTLIER) cc_final: 0.2602 (mp) REVERT: J 102 SER cc_start: 0.8507 (p) cc_final: 0.7935 (m) REVERT: J 128 SER cc_start: 0.2398 (OUTLIER) cc_final: 0.1772 (p) REVERT: J 140 VAL cc_start: 0.5416 (m) cc_final: 0.5012 (t) REVERT: K 34 ARG cc_start: 0.8421 (OUTLIER) cc_final: 0.8027 (ttp80) REVERT: K 71 ASP cc_start: 0.8475 (m-30) cc_final: 0.8153 (t0) REVERT: K 108 MET cc_start: 0.9535 (mtt) cc_final: 0.9290 (mtt) REVERT: L 1 MET cc_start: 0.9440 (ttp) cc_final: 0.9092 (ttp) REVERT: L 41 ILE cc_start: 0.9582 (pt) cc_final: 0.9352 (pt) REVERT: L 44 LYS cc_start: 0.8826 (mmtt) cc_final: 0.8459 (mmmt) REVERT: L 59 LYS cc_start: 0.9347 (mttt) cc_final: 0.8902 (mtmm) REVERT: L 88 ASN cc_start: 0.8936 (t0) cc_final: 0.8582 (t0) REVERT: L 89 ASN cc_start: 0.8305 (t0) cc_final: 0.7994 (t0) REVERT: L 93 GLN cc_start: 0.8896 (mm110) cc_final: 0.8456 (mm-40) REVERT: L 104 THR cc_start: 0.9277 (p) cc_final: 0.9053 (p) REVERT: L 113 MET cc_start: 0.9102 (tpt) cc_final: 0.8894 (tpt) REVERT: M 1 MET cc_start: 0.8116 (ttp) cc_final: 0.7462 (ptm) REVERT: M 25 SER cc_start: 0.9433 (p) cc_final: 0.9227 (p) REVERT: M 51 GLU cc_start: 0.8392 (mt-10) cc_final: 0.8064 (mt-10) REVERT: M 80 SER cc_start: 0.9376 (p) cc_final: 0.8862 (t) REVERT: M 104 GLN cc_start: 0.8423 (OUTLIER) cc_final: 0.8189 (mt0) REVERT: M 122 VAL cc_start: 0.9498 (t) cc_final: 0.9177 (p) REVERT: N 9 PHE cc_start: 0.9005 (m-80) cc_final: 0.8254 (m-10) REVERT: N 12 MET cc_start: 0.9089 (ttm) cc_final: 0.8600 (mtp) REVERT: N 20 LEU cc_start: 0.9212 (mt) cc_final: 0.8928 (mt) REVERT: N 30 SER cc_start: 0.9480 (m) cc_final: 0.9018 (p) REVERT: N 82 MET cc_start: 0.9415 (mmp) cc_final: 0.8775 (mmt) REVERT: N 104 GLU cc_start: 0.8637 (mt-10) cc_final: 0.8343 (mt-10) REVERT: O 9 GLN cc_start: 0.8476 (tt0) cc_final: 0.8247 (tt0) REVERT: O 17 ARG cc_start: 0.9186 (OUTLIER) cc_final: 0.8960 (ttp-110) REVERT: O 24 MET cc_start: 0.9298 (mtt) cc_final: 0.9096 (mtt) REVERT: O 72 ASP cc_start: 0.8554 (t0) cc_final: 0.7929 (m-30) REVERT: P 24 THR cc_start: 0.8799 (m) cc_final: 0.8469 (p) REVERT: P 26 LEU cc_start: 0.9027 (tp) cc_final: 0.8741 (tt) REVERT: P 27 VAL cc_start: 0.8861 (t) cc_final: 0.8447 (t) REVERT: P 68 LYS cc_start: 0.9359 (mtmt) cc_final: 0.9105 (mttm) REVERT: Q 5 ILE cc_start: 0.9339 (mt) cc_final: 0.9030 (mt) REVERT: Q 13 MET cc_start: 0.8014 (mtp) cc_final: 0.7635 (ttm) REVERT: Q 24 ASP cc_start: 0.9144 (m-30) cc_final: 0.8935 (m-30) REVERT: Q 25 THR cc_start: 0.9445 (m) cc_final: 0.9220 (p) REVERT: Q 27 GLU cc_start: 0.8598 (tt0) cc_final: 0.8386 (tp30) REVERT: Q 43 PHE cc_start: 0.8588 (t80) cc_final: 0.8325 (t80) REVERT: Q 63 LYS cc_start: 0.8872 (pttt) cc_final: 0.8655 (ptmm) REVERT: Q 89 ARG cc_start: 0.8671 (mtm-85) cc_final: 0.8360 (mtm110) REVERT: Q 94 LYS cc_start: 0.9124 (mttm) cc_final: 0.8836 (mtpp) REVERT: Q 98 TYR cc_start: 0.9285 (m-10) cc_final: 0.9059 (m-10) REVERT: Q 112 GLU cc_start: 0.8314 (tt0) cc_final: 0.7843 (pm20) REVERT: R 4 VAL cc_start: 0.9566 (t) cc_final: 0.9365 (p) REVERT: R 25 TYR cc_start: 0.9213 (t80) cc_final: 0.9004 (t80) REVERT: R 51 ARG cc_start: 0.9268 (OUTLIER) cc_final: 0.8485 (mtt90) REVERT: R 52 GLN cc_start: 0.8922 (OUTLIER) cc_final: 0.8711 (tt0) REVERT: R 87 SER cc_start: 0.9194 (m) cc_final: 0.8941 (p) REVERT: R 97 ASP cc_start: 0.8375 (t0) cc_final: 0.8071 (t70) REVERT: R 102 ASP cc_start: 0.7495 (t0) cc_final: 0.7142 (t0) REVERT: S 19 THR cc_start: 0.9163 (m) cc_final: 0.8500 (t) REVERT: S 41 ILE cc_start: 0.9277 (mt) cc_final: 0.8946 (mm) REVERT: S 51 VAL cc_start: 0.8527 (OUTLIER) cc_final: 0.8194 (t) REVERT: S 78 ARG cc_start: 0.9208 (tpp-160) cc_final: 0.8600 (tpp80) REVERT: S 95 ASP cc_start: 0.8382 (m-30) cc_final: 0.7849 (m-30) REVERT: T 12 SER cc_start: 0.9435 (OUTLIER) cc_final: 0.9168 (p) REVERT: T 25 ARG cc_start: 0.8775 (ttm110) cc_final: 0.8444 (ttm110) REVERT: T 42 LYS cc_start: 0.9140 (OUTLIER) cc_final: 0.8868 (ttpt) REVERT: T 68 ASP cc_start: 0.8828 (m-30) cc_final: 0.8522 (t0) REVERT: T 77 ASP cc_start: 0.9129 (m-30) cc_final: 0.8925 (m-30) REVERT: T 101 SER cc_start: 0.9473 (p) cc_final: 0.9273 (m) REVERT: U 22 THR cc_start: 0.9244 (m) cc_final: 0.8973 (t) REVERT: U 28 ASN cc_start: 0.9143 (t0) cc_final: 0.8615 (t0) REVERT: U 33 LYS cc_start: 0.9433 (mttt) cc_final: 0.9062 (mtmt) REVERT: U 39 THR cc_start: 0.9231 (p) cc_final: 0.8934 (t) REVERT: U 42 GLU cc_start: 0.8812 (mt-10) cc_final: 0.8459 (mt-10) REVERT: U 51 PHE cc_start: 0.8808 (m-80) cc_final: 0.8343 (m-80) REVERT: U 57 VAL cc_start: 0.9538 (OUTLIER) cc_final: 0.9114 (m) REVERT: U 61 LEU cc_start: 0.9451 (OUTLIER) cc_final: 0.9212 (pt) REVERT: U 79 ASP cc_start: 0.8988 (m-30) cc_final: 0.8625 (m-30) REVERT: U 86 THR cc_start: 0.9601 (m) cc_final: 0.9358 (p) REVERT: U 91 GLN cc_start: 0.8190 (mm-40) cc_final: 0.7930 (mm-40) REVERT: V 21 LYS cc_start: 0.9324 (mttt) cc_final: 0.8797 (mtpt) REVERT: V 22 ARG cc_start: 0.8660 (mtp180) cc_final: 0.8333 (ptm160) REVERT: V 52 LEU cc_start: 0.8274 (OUTLIER) cc_final: 0.7229 (tp) REVERT: W 2 PHE cc_start: 0.8372 (m-80) cc_final: 0.7952 (m-80) REVERT: W 12 GLN cc_start: 0.8565 (mt0) cc_final: 0.8182 (mp10) REVERT: W 25 LYS cc_start: 0.9063 (OUTLIER) cc_final: 0.8460 (mmmt) REVERT: W 29 ILE cc_start: 0.9269 (tp) cc_final: 0.9049 (tt) REVERT: W 42 LEU cc_start: 0.9221 (mt) cc_final: 0.9018 (mt) REVERT: W 48 MET cc_start: 0.9146 (tpt) cc_final: 0.8588 (tpp) REVERT: W 50 MET cc_start: 0.9284 (mtp) cc_final: 0.9028 (mtt) REVERT: W 55 GLU cc_start: 0.8843 (mp0) cc_final: 0.8457 (mp0) REVERT: W 61 LEU cc_start: 0.9120 (mt) cc_final: 0.8769 (mp) REVERT: W 63 ILE cc_start: 0.9493 (mt) cc_final: 0.9278 (mt) REVERT: W 64 VAL cc_start: 0.9111 (OUTLIER) cc_final: 0.8738 (m) REVERT: W 65 VAL cc_start: 0.8993 (OUTLIER) cc_final: 0.8774 (p) REVERT: W 70 ILE cc_start: 0.9356 (OUTLIER) cc_final: 0.8774 (mt) REVERT: W 87 GLN cc_start: 0.8659 (mm110) cc_final: 0.8269 (mt0) REVERT: X 20 ARG cc_start: 0.8860 (mpt180) cc_final: 0.8585 (mtt90) REVERT: X 25 ARG cc_start: 0.8870 (mmt-90) cc_final: 0.8399 (mmt90) REVERT: X 75 LYS cc_start: 0.8693 (mttt) cc_final: 0.8418 (mttm) REVERT: X 77 ARG cc_start: 0.8508 (OUTLIER) cc_final: 0.7913 (mtt-85) REVERT: X 81 SER cc_start: 0.9435 (p) cc_final: 0.9147 (t) REVERT: X 83 GLU cc_start: 0.7941 (mt-10) cc_final: 0.7585 (mt-10) REVERT: Y 28 ARG cc_start: 0.9398 (OUTLIER) cc_final: 0.9101 (ptm160) REVERT: Y 48 THR cc_start: 0.9555 (m) cc_final: 0.9222 (p) REVERT: Y 66 THR cc_start: 0.9334 (m) cc_final: 0.8970 (p) REVERT: Z 15 ASN cc_start: 0.9037 (m-40) cc_final: 0.8825 (t0) REVERT: Z 17 GLU cc_start: 0.8565 (tp30) cc_final: 0.8197 (tp30) REVERT: Z 30 MET cc_start: 0.9269 (mmm) cc_final: 0.9040 (tpp) REVERT: Z 34 SER cc_start: 0.8576 (OUTLIER) cc_final: 0.7405 (p) REVERT: Z 36 GLN cc_start: 0.7909 (tt0) cc_final: 0.7506 (mt0) REVERT: Z 58 ASN cc_start: 0.8591 (OUTLIER) cc_final: 0.8359 (m-40) REVERT: a 4 THR cc_start: 0.9176 (m) cc_final: 0.8135 (m) REVERT: a 30 ARG cc_start: 0.8798 (OUTLIER) cc_final: 0.8336 (mmm-85) REVERT: a 32 ILE cc_start: 0.9503 (mt) cc_final: 0.9150 (pt) REVERT: a 57 VAL cc_start: 0.9331 (t) cc_final: 0.8955 (p) REVERT: b 5 GLN cc_start: 0.9179 (OUTLIER) cc_final: 0.8950 (tt0) REVERT: c 5 ILE cc_start: 0.8991 (OUTLIER) cc_final: 0.8645 (pt) REVERT: c 6 ARG cc_start: 0.8787 (OUTLIER) cc_final: 0.8187 (mmt90) REVERT: c 7 GLU cc_start: 0.8721 (mt-10) cc_final: 0.8409 (mt-10) REVERT: c 26 ASN cc_start: 0.8022 (t0) cc_final: 0.7791 (t0) REVERT: c 29 THR cc_start: 0.8885 (p) cc_final: 0.8286 (p) REVERT: c 35 GLU cc_start: 0.8163 (tt0) cc_final: 0.7935 (mm-30) REVERT: c 50 LYS cc_start: 0.9256 (mttt) cc_final: 0.8848 (mttt) REVERT: d 1 MET cc_start: 0.8800 (OUTLIER) cc_final: 0.8403 (ptp) REVERT: d 3 ARG cc_start: 0.9060 (mmm160) cc_final: 0.8634 (mmt-90) REVERT: d 12 ARG cc_start: 0.8914 (OUTLIER) cc_final: 0.8669 (tpp80) REVERT: d 14 ARG cc_start: 0.9230 (mtt180) cc_final: 0.8683 (mtt90) REVERT: d 25 LYS cc_start: 0.9101 (OUTLIER) cc_final: 0.8868 (tttt) REVERT: e 6 THR cc_start: 0.9212 (OUTLIER) cc_final: 0.8957 (p) REVERT: f 1 MET cc_start: 0.9067 (tpp) cc_final: 0.8786 (ttm) REVERT: i 331 LEU cc_start: 0.7234 (OUTLIER) cc_final: 0.6796 (mt) REVERT: i 340 GLN cc_start: 0.5578 (tt0) cc_final: 0.5096 (mm110) REVERT: i 341 MET cc_start: 0.6755 (mtp) cc_final: 0.4941 (tpt) REVERT: i 377 GLU cc_start: 0.7599 (tp30) cc_final: 0.7178 (pp20) REVERT: i 383 MET cc_start: 0.8692 (mtt) cc_final: 0.8228 (mtp) REVERT: i 395 LYS cc_start: 0.8805 (mmtt) cc_final: 0.8593 (mmtt) REVERT: i 399 LYS cc_start: 0.9135 (mttt) cc_final: 0.8401 (mttp) REVERT: i 420 PHE cc_start: 0.8141 (t80) cc_final: 0.7474 (t80) REVERT: i 421 ASP cc_start: 0.7515 (OUTLIER) cc_final: 0.6661 (m-30) REVERT: i 423 MET cc_start: 0.7817 (mmp) cc_final: 0.7591 (mmt) REVERT: i 426 MET cc_start: 0.8413 (tpp) cc_final: 0.7647 (ttt) REVERT: i 430 MET cc_start: 0.6218 (OUTLIER) cc_final: 0.5426 (mtt) REVERT: k 36 LEU cc_start: 0.7101 (mt) cc_final: 0.6794 (mt) outliers start: 262 outliers final: 69 residues processed: 1387 average time/residue: 0.9586 time to fit residues: 2197.6402 Evaluate side-chains 1011 residues out of total 2908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 896 time to evaluate : 4.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 156 ARG Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 182 ARG Chi-restraints excluded: chain C residue 185 GLU Chi-restraints excluded: chain C residue 194 GLU Chi-restraints excluded: chain C residue 207 LYS Chi-restraints excluded: chain C residue 242 LYS Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 114 LYS Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 130 LYS Chi-restraints excluded: chain E residue 162 ARG Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 132 VAL Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain F residue 153 ASP Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 74 SER Chi-restraints excluded: chain G residue 127 THR Chi-restraints excluded: chain H residue 9 VAL Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 90 LEU Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain I residue 85 VAL Chi-restraints excluded: chain I residue 109 LYS Chi-restraints excluded: chain J residue 40 LYS Chi-restraints excluded: chain J residue 55 ILE Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 61 VAL Chi-restraints excluded: chain J residue 101 ILE Chi-restraints excluded: chain J residue 128 SER Chi-restraints excluded: chain K residue 34 ARG Chi-restraints excluded: chain K residue 91 GLU Chi-restraints excluded: chain K residue 131 ASN Chi-restraints excluded: chain L residue 21 CYS Chi-restraints excluded: chain L residue 61 VAL Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 67 THR Chi-restraints excluded: chain M residue 101 ILE Chi-restraints excluded: chain M residue 104 GLN Chi-restraints excluded: chain N residue 6 ARG Chi-restraints excluded: chain N residue 44 ARG Chi-restraints excluded: chain N residue 67 VAL Chi-restraints excluded: chain N residue 105 MET Chi-restraints excluded: chain O residue 17 ARG Chi-restraints excluded: chain O residue 37 THR Chi-restraints excluded: chain O residue 38 LEU Chi-restraints excluded: chain P residue 5 SER Chi-restraints excluded: chain P residue 53 THR Chi-restraints excluded: chain R residue 8 VAL Chi-restraints excluded: chain R residue 51 ARG Chi-restraints excluded: chain R residue 52 GLN Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain S residue 51 VAL Chi-restraints excluded: chain T residue 12 SER Chi-restraints excluded: chain T residue 39 THR Chi-restraints excluded: chain T residue 42 LYS Chi-restraints excluded: chain T residue 67 ASP Chi-restraints excluded: chain T residue 72 THR Chi-restraints excluded: chain U residue 17 SER Chi-restraints excluded: chain U residue 57 VAL Chi-restraints excluded: chain U residue 61 LEU Chi-restraints excluded: chain V residue 12 ILE Chi-restraints excluded: chain V residue 52 LEU Chi-restraints excluded: chain V residue 65 ILE Chi-restraints excluded: chain V residue 67 VAL Chi-restraints excluded: chain W residue 20 LEU Chi-restraints excluded: chain W residue 25 LYS Chi-restraints excluded: chain W residue 64 VAL Chi-restraints excluded: chain W residue 65 VAL Chi-restraints excluded: chain W residue 70 ILE Chi-restraints excluded: chain W residue 77 VAL Chi-restraints excluded: chain W residue 92 VAL Chi-restraints excluded: chain X residue 58 THR Chi-restraints excluded: chain X residue 76 ASN Chi-restraints excluded: chain X residue 77 ARG Chi-restraints excluded: chain Y residue 28 ARG Chi-restraints excluded: chain Y residue 68 LEU Chi-restraints excluded: chain Z residue 34 SER Chi-restraints excluded: chain Z residue 48 ARG Chi-restraints excluded: chain Z residue 58 ASN Chi-restraints excluded: chain a residue 24 LEU Chi-restraints excluded: chain a residue 30 ARG Chi-restraints excluded: chain b residue 5 GLN Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain b residue 25 VAL Chi-restraints excluded: chain b residue 43 ILE Chi-restraints excluded: chain b residue 57 LYS Chi-restraints excluded: chain c residue 5 ILE Chi-restraints excluded: chain c residue 6 ARG Chi-restraints excluded: chain c residue 46 HIS Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 12 ARG Chi-restraints excluded: chain d residue 24 THR Chi-restraints excluded: chain d residue 25 LYS Chi-restraints excluded: chain e residue 6 THR Chi-restraints excluded: chain i residue 331 LEU Chi-restraints excluded: chain i residue 421 ASP Chi-restraints excluded: chain i residue 430 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 640 random chunks: chunk 540 optimal weight: 0.9990 chunk 485 optimal weight: 9.9990 chunk 269 optimal weight: 10.0000 chunk 165 optimal weight: 10.0000 chunk 327 optimal weight: 10.0000 chunk 259 optimal weight: 10.0000 chunk 501 optimal weight: 5.9990 chunk 194 optimal weight: 10.0000 chunk 305 optimal weight: 9.9990 chunk 373 optimal weight: 1.9990 chunk 581 optimal weight: 4.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 32 ASN D 140 HIS E 9 GLN E 90 GLN E 92 HIS E 163 ASN E 165 HIS F 27 GLN F 52 ASN ** G 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 ASN G 111 HIS H 33 GLN ** I 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 12 GLN J 30 GLN J 31 GLN ** K 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 128 ASN K 136 GLN L 93 GLN ** N 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 9 GLN P 29 HIS Q 77 HIS R 37 GLN R 72 ASN T 7 HIS U 48 GLN ** V 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 20 HIS Y 23 ASN ** Z 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 5 GLN d 29 GLN f 35 GLN i 381 ASN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8778 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 101812 Z= 0.280 Angle : 0.664 13.110 152558 Z= 0.342 Chirality : 0.038 0.313 19559 Planarity : 0.005 0.062 7978 Dihedral : 23.515 179.303 51803 Min Nonbonded Distance : 1.775 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.87 % Favored : 98.07 % Rotamer: Outliers : 6.96 % Allowed : 19.72 % Favored : 73.32 % 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: -1.48 (0.12), residues: 3529 helix: -1.03 (0.14), residues: 1070 sheet: -0.91 (0.17), residues: 711 loop : -0.85 (0.13), residues: 1748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 248 HIS 0.034 0.002 HIS E 165 PHE 0.032 0.002 PHE H 46 TYR 0.031 0.002 TYR N 103 ARG 0.008 0.001 ARG G 170 *********************** 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 1173 residues out of total 2908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 202 poor density : 971 time to evaluate : 4.244 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: C 72 ASP cc_start: 0.8651 (m-30) cc_final: 0.8386 (t0) REVERT: C 120 VAL cc_start: 0.9402 (OUTLIER) cc_final: 0.8977 (p) REVERT: C 242 LYS cc_start: 0.8911 (OUTLIER) cc_final: 0.8599 (ptpp) REVERT: D 39 ASP cc_start: 0.8592 (p0) cc_final: 0.8303 (p0) REVERT: D 45 TYR cc_start: 0.8183 (p90) cc_final: 0.7979 (p90) REVERT: D 64 GLU cc_start: 0.9002 (mt-10) cc_final: 0.8731 (mt-10) REVERT: D 137 SER cc_start: 0.9707 (m) cc_final: 0.9366 (p) REVERT: E 12 LEU cc_start: 0.8450 (tp) cc_final: 0.7958 (tp) REVERT: E 25 GLU cc_start: 0.8399 (tp30) cc_final: 0.8114 (tp30) REVERT: E 46 GLN cc_start: 0.9256 (mp10) cc_final: 0.8820 (mp10) REVERT: E 115 GLN cc_start: 0.9371 (mm-40) cc_final: 0.9065 (mt0) REVERT: E 130 LYS cc_start: 0.9068 (OUTLIER) cc_final: 0.8682 (mmmm) REVERT: E 145 ASP cc_start: 0.8265 (t70) cc_final: 0.7159 (p0) REVERT: E 163 ASN cc_start: 0.9524 (OUTLIER) cc_final: 0.9274 (t0) REVERT: E 197 GLU cc_start: 0.8686 (tt0) cc_final: 0.8412 (tp30) REVERT: F 26 MET cc_start: 0.9368 (mmp) cc_final: 0.9027 (mmm) REVERT: F 32 GLU cc_start: 0.8595 (tp30) cc_final: 0.8221 (tp30) REVERT: F 35 THR cc_start: 0.9371 (m) cc_final: 0.9046 (p) REVERT: F 96 MET cc_start: 0.8712 (ttp) cc_final: 0.8126 (tmm) REVERT: F 138 PHE cc_start: 0.9117 (m-80) cc_final: 0.8812 (m-10) REVERT: F 140 GLU cc_start: 0.8106 (mp0) cc_final: 0.6776 (mm-30) REVERT: F 153 ASP cc_start: 0.7718 (OUTLIER) cc_final: 0.7374 (m-30) REVERT: G 11 VAL cc_start: 0.8915 (OUTLIER) cc_final: 0.8628 (m) REVERT: G 48 ASN cc_start: 0.6615 (t0) cc_final: 0.6393 (t0) REVERT: G 69 ARG cc_start: 0.8887 (tmt170) cc_final: 0.7772 (tpt90) REVERT: G 95 ARG cc_start: 0.8507 (mtm110) cc_final: 0.8089 (mtm110) REVERT: G 104 ASN cc_start: 0.9408 (t0) cc_final: 0.9154 (t0) REVERT: G 106 SER cc_start: 0.8606 (t) cc_final: 0.8074 (p) REVERT: G 115 HIS cc_start: 0.8377 (t70) cc_final: 0.7978 (t-90) REVERT: G 137 ASP cc_start: 0.8509 (t0) cc_final: 0.8221 (t70) REVERT: G 155 GLU cc_start: 0.7496 (pp20) cc_final: 0.6832 (pp20) REVERT: H 14 SER cc_start: 0.8519 (m) cc_final: 0.7679 (p) REVERT: H 35 LYS cc_start: 0.9040 (mtpp) cc_final: 0.8741 (mmtm) REVERT: H 42 LYS cc_start: 0.8702 (tmtt) cc_final: 0.8406 (tmtt) REVERT: H 43 ASN cc_start: 0.7792 (m-40) cc_final: 0.7568 (m-40) REVERT: H 46 PHE cc_start: 0.8002 (m-80) cc_final: 0.7761 (m-80) REVERT: H 78 VAL cc_start: 0.7883 (OUTLIER) cc_final: 0.7461 (t) REVERT: H 83 LYS cc_start: 0.6808 (mmtp) cc_final: 0.5491 (ttpt) REVERT: H 90 LEU cc_start: 0.6662 (tp) cc_final: 0.6261 (mt) REVERT: I 14 GLU cc_start: 0.8400 (tt0) cc_final: 0.8175 (tt0) REVERT: I 38 MET cc_start: 0.8044 (mmm) cc_final: 0.7381 (ttp) REVERT: I 55 VAL cc_start: 0.8715 (t) cc_final: 0.8376 (t) REVERT: I 116 GLU cc_start: 0.5622 (mt-10) cc_final: 0.5336 (mm-30) REVERT: J 40 LYS cc_start: 0.6853 (OUTLIER) cc_final: 0.6612 (pttp) REVERT: J 55 ILE cc_start: 0.2138 (OUTLIER) cc_final: 0.1632 (mp) REVERT: J 80 LEU cc_start: 0.2442 (OUTLIER) cc_final: 0.2169 (tp) REVERT: J 94 ASN cc_start: 0.6375 (OUTLIER) cc_final: 0.5866 (m110) REVERT: J 102 SER cc_start: 0.8182 (p) cc_final: 0.7819 (m) REVERT: J 128 SER cc_start: 0.1747 (OUTLIER) cc_final: 0.1501 (p) REVERT: K 19 ASP cc_start: 0.7645 (t0) cc_final: 0.7202 (t0) REVERT: K 34 ARG cc_start: 0.8403 (OUTLIER) cc_final: 0.8040 (ttp-110) REVERT: K 52 ASP cc_start: 0.9385 (m-30) cc_final: 0.9095 (m-30) REVERT: K 71 ASP cc_start: 0.8519 (m-30) cc_final: 0.8287 (t0) REVERT: K 91 GLU cc_start: 0.8584 (OUTLIER) cc_final: 0.8152 (tp30) REVERT: K 108 MET cc_start: 0.9333 (mtt) cc_final: 0.8920 (mtt) REVERT: L 1 MET cc_start: 0.9319 (ttp) cc_final: 0.9091 (ttp) REVERT: L 88 ASN cc_start: 0.9008 (t0) cc_final: 0.7947 (t0) REVERT: L 98 ARG cc_start: 0.8508 (ttm-80) cc_final: 0.8015 (mtt180) REVERT: L 100 PHE cc_start: 0.8191 (m-80) cc_final: 0.7879 (m-10) REVERT: M 1 MET cc_start: 0.7983 (ttp) cc_final: 0.7055 (ptm) REVERT: M 25 SER cc_start: 0.9517 (p) cc_final: 0.9315 (p) REVERT: M 58 TYR cc_start: 0.8996 (p90) cc_final: 0.8531 (p90) REVERT: M 67 THR cc_start: 0.8956 (m) cc_final: 0.8706 (p) REVERT: M 80 SER cc_start: 0.9252 (p) cc_final: 0.8654 (t) REVERT: M 104 GLN cc_start: 0.8492 (OUTLIER) cc_final: 0.8045 (mt0) REVERT: N 9 PHE cc_start: 0.9157 (m-80) cc_final: 0.8410 (m-80) REVERT: N 12 MET cc_start: 0.9000 (ttm) cc_final: 0.8784 (mtp) REVERT: N 30 SER cc_start: 0.9532 (m) cc_final: 0.9098 (p) REVERT: N 104 GLU cc_start: 0.8524 (mt-10) cc_final: 0.8190 (mt-10) REVERT: O 49 GLU cc_start: 0.8072 (mt-10) cc_final: 0.7647 (mt-10) REVERT: O 72 ASP cc_start: 0.8473 (t0) cc_final: 0.7977 (m-30) REVERT: O 110 MET cc_start: 0.9341 (mmm) cc_final: 0.9058 (mmt) REVERT: P 26 LEU cc_start: 0.8895 (tp) cc_final: 0.8663 (tt) REVERT: P 58 ILE cc_start: 0.9200 (mp) cc_final: 0.8735 (mp) REVERT: P 116 GLN cc_start: 0.7188 (tm-30) cc_final: 0.6775 (tm-30) REVERT: Q 5 ILE cc_start: 0.9268 (mt) cc_final: 0.8987 (mt) REVERT: Q 6 LYS cc_start: 0.8770 (OUTLIER) cc_final: 0.8349 (ptpt) REVERT: Q 24 ASP cc_start: 0.9083 (m-30) cc_final: 0.8813 (m-30) REVERT: Q 25 THR cc_start: 0.9337 (m) cc_final: 0.8968 (p) REVERT: Q 43 PHE cc_start: 0.8522 (t80) cc_final: 0.8151 (t80) REVERT: Q 98 TYR cc_start: 0.9091 (m-10) cc_final: 0.8854 (m-10) REVERT: Q 112 GLU cc_start: 0.8338 (tt0) cc_final: 0.7916 (pm20) REVERT: R 4 VAL cc_start: 0.9542 (t) cc_final: 0.9337 (p) REVERT: R 51 ARG cc_start: 0.9035 (OUTLIER) cc_final: 0.8667 (mtt90) REVERT: R 87 SER cc_start: 0.9140 (m) cc_final: 0.8529 (p) REVERT: S 95 ASP cc_start: 0.8199 (m-30) cc_final: 0.7798 (m-30) REVERT: T 25 ARG cc_start: 0.8861 (ttm110) cc_final: 0.8576 (ttm110) REVERT: T 59 GLU cc_start: 0.8982 (tm-30) cc_final: 0.8751 (tm-30) REVERT: U 5 GLU cc_start: 0.8889 (mp0) cc_final: 0.8266 (mp0) REVERT: U 7 LEU cc_start: 0.9262 (mt) cc_final: 0.9010 (mt) REVERT: U 28 ASN cc_start: 0.9210 (t0) cc_final: 0.8700 (t0) REVERT: U 33 LYS cc_start: 0.9382 (mttt) cc_final: 0.9082 (mtpt) REVERT: V 21 LYS cc_start: 0.9312 (mttt) cc_final: 0.8891 (mtpt) REVERT: V 33 LYS cc_start: 0.9333 (OUTLIER) cc_final: 0.8629 (mtpp) REVERT: V 52 LEU cc_start: 0.8173 (OUTLIER) cc_final: 0.7960 (tp) REVERT: W 2 PHE cc_start: 0.8114 (m-80) cc_final: 0.7818 (m-80) REVERT: W 17 SER cc_start: 0.9440 (m) cc_final: 0.9089 (p) REVERT: W 55 GLU cc_start: 0.8830 (mp0) cc_final: 0.8242 (mp0) REVERT: W 56 PHE cc_start: 0.8889 (t80) cc_final: 0.8657 (t80) REVERT: W 59 GLU cc_start: 0.8965 (mt-10) cc_final: 0.8325 (mp0) REVERT: W 65 VAL cc_start: 0.9245 (OUTLIER) cc_final: 0.8681 (p) REVERT: W 68 LYS cc_start: 0.8503 (mtmm) cc_final: 0.8058 (ptpp) REVERT: W 76 ASP cc_start: 0.9092 (t0) cc_final: 0.8798 (t0) REVERT: W 87 GLN cc_start: 0.8865 (mm110) cc_final: 0.8255 (mt0) REVERT: X 20 ARG cc_start: 0.8800 (mpt180) cc_final: 0.8582 (mtt90) REVERT: Y 19 SER cc_start: 0.9159 (OUTLIER) cc_final: 0.8675 (t) REVERT: Y 23 ASN cc_start: 0.9382 (OUTLIER) cc_final: 0.8737 (m110) REVERT: Y 28 ARG cc_start: 0.9526 (OUTLIER) cc_final: 0.9098 (ptm160) REVERT: Y 40 VAL cc_start: 0.9096 (t) cc_final: 0.8762 (p) REVERT: Y 48 THR cc_start: 0.9398 (m) cc_final: 0.9103 (p) REVERT: Y 62 LYS cc_start: 0.9338 (mttt) cc_final: 0.9096 (mttm) REVERT: Y 66 THR cc_start: 0.9403 (m) cc_final: 0.9193 (p) REVERT: Z 17 GLU cc_start: 0.8192 (tp30) cc_final: 0.7781 (tp30) REVERT: Z 31 GLN cc_start: 0.8528 (OUTLIER) cc_final: 0.8081 (mp10) REVERT: Z 58 ASN cc_start: 0.8754 (t0) cc_final: 0.8024 (t0) REVERT: a 6 LYS cc_start: 0.8434 (mtpt) cc_final: 0.8220 (mmmm) REVERT: a 44 ILE cc_start: 0.9477 (mm) cc_final: 0.9247 (tp) REVERT: b 13 ARG cc_start: 0.8970 (OUTLIER) cc_final: 0.8217 (ttm-80) REVERT: b 52 ARG cc_start: 0.8128 (mtp180) cc_final: 0.7918 (ttp80) REVERT: c 29 THR cc_start: 0.9004 (p) cc_final: 0.8616 (p) REVERT: c 33 LYS cc_start: 0.7529 (mmtp) cc_final: 0.6548 (mmtm) REVERT: c 51 GLU cc_start: 0.8714 (tt0) cc_final: 0.8023 (pt0) REVERT: d 3 ARG cc_start: 0.8986 (mmm160) cc_final: 0.8645 (mmt-90) REVERT: d 14 ARG cc_start: 0.9187 (mtt180) cc_final: 0.8712 (mtt90) REVERT: d 41 ARG cc_start: 0.8831 (mtm-85) cc_final: 0.8610 (mtm110) REVERT: e 7 VAL cc_start: 0.9118 (t) cc_final: 0.8895 (m) REVERT: e 49 MET cc_start: 0.8519 (mmp) cc_final: 0.8187 (tpt) REVERT: f 1 MET cc_start: 0.9114 (tpp) cc_final: 0.8868 (ttm) REVERT: f 26 ILE cc_start: 0.9264 (mm) cc_final: 0.8990 (tt) REVERT: i 338 LEU cc_start: 0.7448 (OUTLIER) cc_final: 0.6425 (tp) REVERT: i 341 MET cc_start: 0.6156 (mtp) cc_final: 0.4660 (tpt) REVERT: i 387 GLU cc_start: 0.7887 (mt-10) cc_final: 0.7640 (mt-10) REVERT: i 395 LYS cc_start: 0.8763 (mmtt) cc_final: 0.8453 (mmtt) REVERT: i 398 ARG cc_start: 0.8658 (OUTLIER) cc_final: 0.8223 (mmt90) REVERT: i 399 LYS cc_start: 0.8960 (mttt) cc_final: 0.8176 (mttp) REVERT: i 421 ASP cc_start: 0.6967 (OUTLIER) cc_final: 0.6760 (m-30) REVERT: i 424 GLN cc_start: 0.7805 (pp30) cc_final: 0.7592 (pp30) REVERT: i 425 ARG cc_start: 0.8641 (ttm-80) cc_final: 0.8066 (ttm-80) REVERT: i 426 MET cc_start: 0.8261 (tpp) cc_final: 0.7617 (ttt) REVERT: k 38 LEU cc_start: 0.3777 (OUTLIER) cc_final: 0.3454 (mt) outliers start: 202 outliers final: 101 residues processed: 1093 average time/residue: 0.9060 time to fit residues: 1678.1625 Evaluate side-chains 987 residues out of total 2908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 857 time to evaluate : 4.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 178 SER Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 207 LYS Chi-restraints excluded: chain C residue 242 LYS Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain D residue 13 ARG Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 184 ARG Chi-restraints excluded: chain E residue 51 GLU Chi-restraints excluded: chain E residue 70 SER Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain E residue 73 ILE Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain E residue 130 LYS Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain E residue 163 ASN Chi-restraints excluded: chain E residue 168 ASP Chi-restraints excluded: chain F residue 23 ASN Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 127 ASN Chi-restraints excluded: chain F residue 132 VAL Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain F residue 153 ASP Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 51 THR Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 147 VAL Chi-restraints excluded: chain J residue 40 LYS Chi-restraints excluded: chain J residue 55 ILE Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 61 VAL Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain J residue 94 ASN Chi-restraints excluded: chain J residue 128 SER Chi-restraints excluded: chain K residue 34 ARG Chi-restraints excluded: chain K residue 36 LEU Chi-restraints excluded: chain K residue 91 GLU Chi-restraints excluded: chain K residue 131 ASN Chi-restraints excluded: chain L residue 9 ASN Chi-restraints excluded: chain L residue 38 ILE Chi-restraints excluded: chain L residue 109 SER Chi-restraints excluded: chain M residue 104 GLN Chi-restraints excluded: chain M residue 127 VAL Chi-restraints excluded: chain N residue 7 THR Chi-restraints excluded: chain N residue 63 ILE Chi-restraints excluded: chain N residue 105 MET Chi-restraints excluded: chain N residue 108 VAL Chi-restraints excluded: chain N residue 134 THR Chi-restraints excluded: chain O residue 13 ASN Chi-restraints excluded: chain O residue 14 SER Chi-restraints excluded: chain O residue 27 SER Chi-restraints excluded: chain O residue 37 THR Chi-restraints excluded: chain P residue 5 SER Chi-restraints excluded: chain P residue 43 ASN Chi-restraints excluded: chain Q residue 6 LYS Chi-restraints excluded: chain Q residue 12 GLN Chi-restraints excluded: chain Q residue 65 SER Chi-restraints excluded: chain R residue 8 VAL Chi-restraints excluded: chain R residue 39 VAL Chi-restraints excluded: chain R residue 40 ILE Chi-restraints excluded: chain R residue 51 ARG Chi-restraints excluded: chain R residue 75 SER Chi-restraints excluded: chain R residue 109 LEU Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain T residue 13 SER Chi-restraints excluded: chain T residue 67 ASP Chi-restraints excluded: chain T residue 72 THR Chi-restraints excluded: chain T residue 81 SER Chi-restraints excluded: chain T residue 82 MET Chi-restraints excluded: chain U residue 17 SER Chi-restraints excluded: chain U residue 29 THR Chi-restraints excluded: chain U residue 93 LEU Chi-restraints excluded: chain V residue 12 ILE Chi-restraints excluded: chain V residue 33 LYS Chi-restraints excluded: chain V residue 52 LEU Chi-restraints excluded: chain V residue 65 ILE Chi-restraints excluded: chain V residue 68 SER Chi-restraints excluded: chain V residue 77 THR Chi-restraints excluded: chain V residue 102 THR Chi-restraints excluded: chain W residue 20 LEU Chi-restraints excluded: chain W residue 45 ASP Chi-restraints excluded: chain W residue 65 VAL Chi-restraints excluded: chain W residue 77 VAL Chi-restraints excluded: chain W residue 92 VAL Chi-restraints excluded: chain X residue 12 ASN Chi-restraints excluded: chain X residue 50 ASN Chi-restraints excluded: chain X residue 76 ASN Chi-restraints excluded: chain Y residue 19 SER Chi-restraints excluded: chain Y residue 22 LEU Chi-restraints excluded: chain Y residue 23 ASN Chi-restraints excluded: chain Y residue 28 ARG Chi-restraints excluded: chain Y residue 35 SER Chi-restraints excluded: chain Y residue 42 SER Chi-restraints excluded: chain Y residue 56 MET Chi-restraints excluded: chain Z residue 31 GLN Chi-restraints excluded: chain Z residue 48 ARG Chi-restraints excluded: chain a residue 52 SER Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain b residue 13 ARG Chi-restraints excluded: chain b residue 25 VAL Chi-restraints excluded: chain b residue 43 ILE Chi-restraints excluded: chain c residue 24 THR 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 8 SER Chi-restraints excluded: chain d residue 24 THR Chi-restraints excluded: chain d residue 43 THR Chi-restraints excluded: chain e residue 6 THR Chi-restraints excluded: chain f residue 20 ASP Chi-restraints excluded: chain f residue 22 VAL Chi-restraints excluded: chain i residue 338 LEU Chi-restraints excluded: chain i residue 398 ARG Chi-restraints excluded: chain i residue 421 ASP Chi-restraints excluded: chain k residue 38 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 640 random chunks: chunk 322 optimal weight: 7.9990 chunk 180 optimal weight: 10.0000 chunk 483 optimal weight: 4.9990 chunk 395 optimal weight: 10.0000 chunk 160 optimal weight: 20.0000 chunk 582 optimal weight: 6.9990 chunk 628 optimal weight: 5.9990 chunk 518 optimal weight: 8.9990 chunk 577 optimal weight: 7.9990 chunk 198 optimal weight: 10.0000 chunk 467 optimal weight: 6.9990 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 153 GLN ** E 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 28 ASN H 43 ASN K 128 ASN L 93 GLN ** N 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 62 ASN ** O 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 37 GLN U 48 GLN ** V 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 46 HIS Z 38 GLN b 42 HIS i 343 ASN i 381 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8775 moved from start: 0.3206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 101812 Z= 0.349 Angle : 0.659 11.104 152558 Z= 0.340 Chirality : 0.038 0.266 19559 Planarity : 0.005 0.065 7978 Dihedral : 23.423 179.698 51673 Min Nonbonded Distance : 0.829 Molprobity Statistics. All-atom Clashscore : 14.95 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.89 % Favored : 97.02 % Rotamer: Outliers : 8.03 % Allowed : 21.82 % Favored : 70.15 % 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: -0.92 (0.13), residues: 3529 helix: -0.16 (0.15), residues: 1065 sheet: -0.74 (0.17), residues: 764 loop : -0.71 (0.14), residues: 1700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP S 92 HIS 0.009 0.002 HIS E 165 PHE 0.021 0.002 PHE H 132 TYR 0.018 0.002 TYR N 103 ARG 0.011 0.001 ARG d 12 *********************** 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 1127 residues out of total 2908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 233 poor density : 894 time to evaluate : 4.137 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 20 VAL cc_start: 0.9370 (OUTLIER) cc_final: 0.9039 (p) REVERT: C 21 ASN cc_start: 0.9131 (t0) cc_final: 0.8923 (t0) REVERT: C 72 ASP cc_start: 0.8757 (m-30) cc_final: 0.8218 (t0) REVERT: C 117 GLN cc_start: 0.8849 (OUTLIER) cc_final: 0.8635 (pp30) REVERT: C 120 VAL cc_start: 0.9449 (OUTLIER) cc_final: 0.9059 (p) REVERT: C 207 LYS cc_start: 0.9372 (OUTLIER) cc_final: 0.8971 (pttm) REVERT: C 225 MET cc_start: 0.9148 (mtt) cc_final: 0.8663 (mtt) REVERT: D 39 ASP cc_start: 0.8782 (p0) cc_final: 0.8445 (p0) REVERT: E 46 GLN cc_start: 0.9367 (mp10) cc_final: 0.9066 (mp10) REVERT: E 49 ARG cc_start: 0.9467 (OUTLIER) cc_final: 0.7670 (ptm160) REVERT: E 122 GLU cc_start: 0.8834 (pm20) cc_final: 0.8443 (pm20) REVERT: E 123 LYS cc_start: 0.9168 (mmmt) cc_final: 0.8700 (ptmt) REVERT: E 145 ASP cc_start: 0.8437 (t70) cc_final: 0.7268 (p0) REVERT: E 152 GLU cc_start: 0.8216 (pp20) cc_final: 0.7704 (pp20) REVERT: E 155 GLU cc_start: 0.8895 (tp30) cc_final: 0.8494 (tp30) REVERT: E 184 ASP cc_start: 0.8566 (t0) cc_final: 0.8366 (t0) REVERT: F 32 GLU cc_start: 0.8667 (tp30) cc_final: 0.8321 (tp30) REVERT: F 35 THR cc_start: 0.9412 (m) cc_final: 0.9103 (p) REVERT: F 90 THR cc_start: 0.8993 (OUTLIER) cc_final: 0.8423 (p) REVERT: F 96 MET cc_start: 0.8809 (ttp) cc_final: 0.8159 (tmm) REVERT: G 60 ASP cc_start: 0.8648 (p0) cc_final: 0.8390 (p0) REVERT: G 69 ARG cc_start: 0.8963 (tmt170) cc_final: 0.7644 (tpt90) REVERT: G 95 ARG cc_start: 0.8577 (mtm110) cc_final: 0.7995 (mtm110) REVERT: G 115 HIS cc_start: 0.8402 (t70) cc_final: 0.8124 (t-90) REVERT: G 137 ASP cc_start: 0.8575 (t70) cc_final: 0.8318 (t70) REVERT: G 155 GLU cc_start: 0.7751 (pp20) cc_final: 0.7035 (pp20) REVERT: H 4 ILE cc_start: 0.9040 (OUTLIER) cc_final: 0.8828 (tp) REVERT: H 7 ASP cc_start: 0.9058 (t0) cc_final: 0.8646 (t0) REVERT: H 35 LYS cc_start: 0.9153 (mtpp) cc_final: 0.8866 (mmtm) REVERT: H 42 LYS cc_start: 0.8717 (tmtt) cc_final: 0.8139 (tmtt) REVERT: H 47 PHE cc_start: 0.7346 (t80) cc_final: 0.7099 (t80) REVERT: H 83 LYS cc_start: 0.7223 (mmtp) cc_final: 0.5850 (pttt) REVERT: H 135 HIS cc_start: 0.8287 (t70) cc_final: 0.8047 (t-170) REVERT: H 144 VAL cc_start: 0.8662 (t) cc_final: 0.8406 (p) REVERT: I 38 MET cc_start: 0.8050 (mmm) cc_final: 0.7151 (ttp) REVERT: I 53 ARG cc_start: 0.7604 (mmm160) cc_final: 0.7067 (mmm160) REVERT: I 55 VAL cc_start: 0.8488 (OUTLIER) cc_final: 0.7981 (t) REVERT: I 116 GLU cc_start: 0.5834 (mt-10) cc_final: 0.5414 (mm-30) REVERT: I 123 ILE cc_start: 0.5873 (OUTLIER) cc_final: 0.5311 (mm) REVERT: J 40 LYS cc_start: 0.6878 (OUTLIER) cc_final: 0.6576 (pttp) REVERT: J 94 ASN cc_start: 0.7110 (OUTLIER) cc_final: 0.6637 (m-40) REVERT: J 117 MET cc_start: 0.1940 (OUTLIER) cc_final: 0.1061 (mtp) REVERT: J 136 MET cc_start: 0.2957 (OUTLIER) cc_final: 0.0847 (mtp) REVERT: K 19 ASP cc_start: 0.7887 (t0) cc_final: 0.7506 (t0) REVERT: K 34 ARG cc_start: 0.8474 (OUTLIER) cc_final: 0.8069 (ttm-80) REVERT: K 71 ASP cc_start: 0.8674 (m-30) cc_final: 0.8351 (t0) REVERT: K 108 MET cc_start: 0.9238 (mtt) cc_final: 0.8955 (mtt) REVERT: K 138 GLN cc_start: 0.8786 (mp10) cc_final: 0.8551 (mp10) REVERT: L 88 ASN cc_start: 0.8971 (t0) cc_final: 0.8164 (t0) REVERT: L 100 PHE cc_start: 0.8397 (m-80) cc_final: 0.7898 (m-80) REVERT: M 1 MET cc_start: 0.8195 (ttp) cc_final: 0.7397 (ptm) REVERT: M 67 THR cc_start: 0.9102 (OUTLIER) cc_final: 0.8896 (p) REVERT: M 80 SER cc_start: 0.9314 (p) cc_final: 0.8709 (t) REVERT: M 104 GLN cc_start: 0.8490 (OUTLIER) cc_final: 0.7956 (mt0) REVERT: M 142 ILE cc_start: 0.8939 (mt) cc_final: 0.8597 (tt) REVERT: N 9 PHE cc_start: 0.9273 (m-80) cc_final: 0.8754 (m-80) REVERT: N 30 SER cc_start: 0.9571 (m) cc_final: 0.9010 (p) REVERT: N 45 GLN cc_start: 0.8665 (mt0) cc_final: 0.8302 (mt0) REVERT: N 96 ILE cc_start: 0.9604 (mm) cc_final: 0.9144 (pt) REVERT: N 104 GLU cc_start: 0.8475 (mt-10) cc_final: 0.8235 (mt-10) REVERT: O 49 GLU cc_start: 0.8150 (mt-10) cc_final: 0.7876 (mt-10) REVERT: O 72 ASP cc_start: 0.8328 (t0) cc_final: 0.8038 (m-30) REVERT: O 86 ARG cc_start: 0.9056 (OUTLIER) cc_final: 0.7941 (mtm180) REVERT: P 2 ASP cc_start: 0.7698 (OUTLIER) cc_final: 0.7183 (m-30) REVERT: P 58 ILE cc_start: 0.8873 (mp) cc_final: 0.8642 (mp) REVERT: P 68 LYS cc_start: 0.9230 (mttm) cc_final: 0.8974 (mmtp) REVERT: P 116 GLN cc_start: 0.7378 (tm-30) cc_final: 0.6943 (tm-30) REVERT: Q 24 ASP cc_start: 0.8941 (m-30) cc_final: 0.8703 (m-30) REVERT: Q 25 THR cc_start: 0.9374 (m) cc_final: 0.8893 (p) REVERT: Q 112 GLU cc_start: 0.8367 (tt0) cc_final: 0.7880 (pm20) REVERT: Q 113 ARG cc_start: 0.8287 (ttp-170) cc_final: 0.7771 (ttm170) REVERT: T 25 ARG cc_start: 0.9034 (ttm110) cc_final: 0.8780 (ttm110) REVERT: T 34 ASP cc_start: 0.8287 (m-30) cc_final: 0.7685 (m-30) REVERT: T 84 ARG cc_start: 0.8917 (mmt-90) cc_final: 0.8517 (mmt180) REVERT: U 5 GLU cc_start: 0.8853 (mp0) cc_final: 0.8580 (mp0) REVERT: U 7 LEU cc_start: 0.9225 (mt) cc_final: 0.8908 (mt) REVERT: U 28 ASN cc_start: 0.9188 (t0) cc_final: 0.8668 (t0) REVERT: U 33 LYS cc_start: 0.9300 (mttt) cc_final: 0.9077 (mtmt) REVERT: U 72 GLN cc_start: 0.9040 (mp10) cc_final: 0.8729 (mp10) REVERT: U 73 ARG cc_start: 0.7773 (OUTLIER) cc_final: 0.7410 (mtt90) REVERT: U 91 GLN cc_start: 0.8634 (mm-40) cc_final: 0.8412 (mt0) REVERT: V 33 LYS cc_start: 0.9373 (OUTLIER) cc_final: 0.8588 (mtpp) REVERT: V 37 GLU cc_start: 0.9158 (tp30) cc_final: 0.8731 (tm-30) REVERT: V 52 LEU cc_start: 0.8294 (OUTLIER) cc_final: 0.8003 (tt) REVERT: V 66 GLN cc_start: 0.8850 (mm-40) cc_final: 0.8355 (mt0) REVERT: W 7 GLU cc_start: 0.8370 (pm20) cc_final: 0.7369 (pm20) REVERT: W 10 LYS cc_start: 0.8845 (mmmm) cc_final: 0.8346 (mmmm) REVERT: W 17 SER cc_start: 0.9361 (m) cc_final: 0.8780 (p) REVERT: W 24 ASN cc_start: 0.8937 (OUTLIER) cc_final: 0.8246 (t0) REVERT: W 41 GLU cc_start: 0.8448 (pp20) cc_final: 0.7657 (pp20) REVERT: W 55 GLU cc_start: 0.8839 (mp0) cc_final: 0.8358 (mp0) REVERT: W 59 GLU cc_start: 0.8813 (mt-10) cc_final: 0.8280 (mp0) REVERT: W 65 VAL cc_start: 0.9180 (OUTLIER) cc_final: 0.8739 (p) REVERT: W 76 ASP cc_start: 0.9100 (t0) cc_final: 0.8777 (t0) REVERT: W 83 LYS cc_start: 0.8930 (OUTLIER) cc_final: 0.8594 (mtmt) REVERT: W 87 GLN cc_start: 0.8925 (mm110) cc_final: 0.8248 (mt0) REVERT: X 68 LYS cc_start: 0.9362 (mmmt) cc_final: 0.9057 (mtpp) REVERT: X 77 ARG cc_start: 0.8476 (OUTLIER) cc_final: 0.7329 (mtp180) REVERT: X 83 GLU cc_start: 0.7818 (mt-10) cc_final: 0.7571 (mt-10) REVERT: Y 28 ARG cc_start: 0.9589 (OUTLIER) cc_final: 0.9168 (ptm160) REVERT: Y 40 VAL cc_start: 0.9065 (t) cc_final: 0.8812 (p) REVERT: Y 48 THR cc_start: 0.9400 (m) cc_final: 0.9112 (p) REVERT: Y 62 LYS cc_start: 0.9149 (mttt) cc_final: 0.8752 (mttt) REVERT: Z 17 GLU cc_start: 0.8393 (tp30) cc_final: 0.8103 (tp30) REVERT: Z 24 GLU cc_start: 0.7838 (tp30) cc_final: 0.7541 (tp30) REVERT: a 3 LYS cc_start: 0.8752 (ttpp) cc_final: 0.8542 (ttpp) REVERT: a 44 ILE cc_start: 0.9520 (mm) cc_final: 0.9071 (tp) REVERT: b 13 ARG cc_start: 0.8896 (OUTLIER) cc_final: 0.8007 (ttm-80) REVERT: b 37 LYS cc_start: 0.8574 (mtmt) cc_final: 0.8232 (mtpt) REVERT: c 33 LYS cc_start: 0.7649 (mmtp) cc_final: 0.6693 (mmtm) REVERT: c 51 GLU cc_start: 0.8603 (tt0) cc_final: 0.7582 (pt0) REVERT: d 14 ARG cc_start: 0.9146 (mtt180) cc_final: 0.8660 (mtt90) REVERT: i 335 LEU cc_start: 0.6856 (tp) cc_final: 0.6491 (tp) REVERT: i 341 MET cc_start: 0.6033 (mtp) cc_final: 0.4788 (tpt) REVERT: i 385 MET cc_start: 0.7829 (mmm) cc_final: 0.6500 (mtt) REVERT: i 387 GLU cc_start: 0.7848 (mt-10) cc_final: 0.7545 (mt-10) REVERT: i 395 LYS cc_start: 0.8735 (mmtt) cc_final: 0.8374 (mmtt) REVERT: i 398 ARG cc_start: 0.8845 (mmt90) cc_final: 0.8435 (mmt90) REVERT: i 399 LYS cc_start: 0.9074 (mttt) cc_final: 0.8292 (mttp) REVERT: i 425 ARG cc_start: 0.8589 (ttm-80) cc_final: 0.8038 (ttm-80) REVERT: i 426 MET cc_start: 0.8229 (tpp) cc_final: 0.7393 (ttp) REVERT: k 36 LEU cc_start: 0.7056 (OUTLIER) cc_final: 0.6735 (tp) REVERT: k 38 LEU cc_start: 0.3634 (OUTLIER) cc_final: 0.3231 (mt) outliers start: 233 outliers final: 137 residues processed: 1031 average time/residue: 0.8989 time to fit residues: 1574.2219 Evaluate side-chains 976 residues out of total 2908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 810 time to evaluate : 4.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 38 SER Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 117 GLN Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 178 SER Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 207 LYS Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain D residue 13 ARG Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 74 GLU Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain D residue 165 MET Chi-restraints excluded: chain D residue 184 ARG Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 49 ARG Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain E residue 130 LYS Chi-restraints excluded: chain E residue 168 ASP Chi-restraints excluded: chain F residue 23 ASN Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 127 ASN Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain F residue 157 THR Chi-restraints excluded: chain G residue 51 THR Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 89 LYS Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 147 VAL Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 123 ILE Chi-restraints excluded: chain J residue 40 LYS Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 61 VAL Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain J residue 94 ASN Chi-restraints excluded: chain J residue 117 MET Chi-restraints excluded: chain J residue 136 MET Chi-restraints excluded: chain K residue 34 ARG Chi-restraints excluded: chain K residue 36 LEU Chi-restraints excluded: chain K residue 86 GLN Chi-restraints excluded: chain K residue 128 ASN Chi-restraints excluded: chain K residue 131 ASN Chi-restraints excluded: chain L residue 9 ASN Chi-restraints excluded: chain L residue 21 CYS Chi-restraints excluded: chain L residue 38 ILE Chi-restraints excluded: chain L residue 61 VAL Chi-restraints excluded: chain L residue 65 THR Chi-restraints excluded: chain L residue 104 THR Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 67 THR Chi-restraints excluded: chain M residue 104 GLN Chi-restraints excluded: chain M residue 121 THR Chi-restraints excluded: chain N residue 7 THR Chi-restraints excluded: chain N residue 78 LEU Chi-restraints excluded: chain N residue 102 LEU Chi-restraints excluded: chain N residue 105 MET Chi-restraints excluded: chain N residue 112 LEU Chi-restraints excluded: chain N residue 134 THR Chi-restraints excluded: chain O residue 13 ASN Chi-restraints excluded: chain O residue 14 SER Chi-restraints excluded: chain O residue 27 SER Chi-restraints excluded: chain O residue 37 THR Chi-restraints excluded: chain O residue 86 ARG Chi-restraints excluded: chain P residue 2 ASP Chi-restraints excluded: chain P residue 40 ILE Chi-restraints excluded: chain P residue 43 ASN Chi-restraints excluded: chain P residue 53 THR Chi-restraints excluded: chain P residue 55 GLU Chi-restraints excluded: chain Q residue 46 VAL Chi-restraints excluded: chain Q residue 48 ILE Chi-restraints excluded: chain R residue 18 LEU Chi-restraints excluded: chain R residue 39 VAL Chi-restraints excluded: chain R residue 40 ILE Chi-restraints excluded: chain R residue 60 LEU Chi-restraints excluded: chain R residue 75 SER Chi-restraints excluded: chain R residue 109 LEU Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain S residue 19 THR Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain T residue 39 THR Chi-restraints excluded: chain T residue 45 VAL Chi-restraints excluded: chain T residue 67 ASP Chi-restraints excluded: chain T residue 72 THR Chi-restraints excluded: chain T residue 81 SER Chi-restraints excluded: chain U residue 10 VAL Chi-restraints excluded: chain U residue 17 SER Chi-restraints excluded: chain U residue 39 THR Chi-restraints excluded: chain U residue 73 ARG Chi-restraints excluded: chain U residue 93 LEU Chi-restraints excluded: chain V residue 12 ILE Chi-restraints excluded: chain V residue 33 LYS Chi-restraints excluded: chain V residue 52 LEU Chi-restraints excluded: chain V residue 67 VAL Chi-restraints excluded: chain V residue 68 SER Chi-restraints excluded: chain V residue 77 THR Chi-restraints excluded: chain V residue 102 THR Chi-restraints excluded: chain V residue 103 ILE Chi-restraints excluded: chain W residue 24 ASN Chi-restraints excluded: chain W residue 61 LEU Chi-restraints excluded: chain W residue 65 VAL Chi-restraints excluded: chain W residue 66 ASP Chi-restraints excluded: chain W residue 71 LYS Chi-restraints excluded: chain W residue 77 VAL Chi-restraints excluded: chain W residue 83 LYS Chi-restraints excluded: chain W residue 92 VAL Chi-restraints excluded: chain X residue 12 ASN Chi-restraints excluded: chain X residue 50 ASN Chi-restraints excluded: chain X residue 76 ASN Chi-restraints excluded: chain X residue 77 ARG Chi-restraints excluded: chain X residue 80 ILE Chi-restraints excluded: chain Y residue 14 THR Chi-restraints excluded: chain Y residue 19 SER Chi-restraints excluded: chain Y residue 28 ARG Chi-restraints excluded: chain Y residue 35 SER Chi-restraints excluded: chain Y residue 42 SER Chi-restraints excluded: chain Y residue 56 MET Chi-restraints excluded: chain Z residue 15 ASN Chi-restraints excluded: chain Z residue 19 LEU Chi-restraints excluded: chain Z residue 48 ARG Chi-restraints excluded: chain Z residue 50 VAL Chi-restraints excluded: chain a residue 32 ILE Chi-restraints excluded: chain a residue 52 SER Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain b residue 13 ARG Chi-restraints excluded: chain b residue 25 VAL Chi-restraints excluded: chain b residue 55 ILE 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 8 SER Chi-restraints excluded: chain d residue 24 THR Chi-restraints excluded: chain f residue 13 ASN Chi-restraints excluded: chain f residue 20 ASP Chi-restraints excluded: chain f residue 22 VAL Chi-restraints excluded: chain i residue 342 LYS Chi-restraints excluded: chain k residue 36 LEU Chi-restraints excluded: chain k residue 38 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 640 random chunks: chunk 575 optimal weight: 8.9990 chunk 437 optimal weight: 40.0000 chunk 302 optimal weight: 10.0000 chunk 64 optimal weight: 10.0000 chunk 277 optimal weight: 10.0000 chunk 390 optimal weight: 9.9990 chunk 584 optimal weight: 0.5980 chunk 618 optimal weight: 4.9990 chunk 305 optimal weight: 0.6980 chunk 553 optimal weight: 5.9990 chunk 166 optimal weight: 10.0000 overall best weight: 4.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 200 HIS E 195 GLN ** G 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 43 ASN K 128 ASN ** N 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 37 GLN ** V 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 78 GLN Z 58 ASN d 6 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8744 moved from start: 0.3521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 101812 Z= 0.238 Angle : 0.579 7.707 152558 Z= 0.302 Chirality : 0.035 0.254 19559 Planarity : 0.005 0.080 7978 Dihedral : 23.348 178.637 51642 Min Nonbonded Distance : 1.014 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.83 % Favored : 97.08 % Rotamer: Outliers : 6.58 % Allowed : 24.96 % Favored : 68.46 % 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: -0.53 (0.13), residues: 3529 helix: 0.37 (0.16), residues: 1074 sheet: -0.57 (0.18), residues: 748 loop : -0.60 (0.14), residues: 1707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 248 HIS 0.005 0.001 HIS I 88 PHE 0.019 0.002 PHE H 46 TYR 0.016 0.002 TYR N 103 ARG 0.010 0.001 ARG F 148 *********************** 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 1054 residues out of total 2908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 191 poor density : 863 time to evaluate : 4.157 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: C 20 VAL cc_start: 0.9299 (OUTLIER) cc_final: 0.8962 (p) REVERT: C 72 ASP cc_start: 0.8738 (m-30) cc_final: 0.8486 (t0) REVERT: C 120 VAL cc_start: 0.9354 (OUTLIER) cc_final: 0.8877 (p) REVERT: D 1 MET cc_start: 0.8126 (mpp) cc_final: 0.7915 (mpp) REVERT: D 39 ASP cc_start: 0.8764 (p0) cc_final: 0.8413 (p0) REVERT: D 155 VAL cc_start: 0.9338 (t) cc_final: 0.9127 (p) REVERT: E 46 GLN cc_start: 0.9335 (mp10) cc_final: 0.9030 (mp10) REVERT: E 123 LYS cc_start: 0.9111 (mmmt) cc_final: 0.8680 (ptmt) REVERT: E 130 LYS cc_start: 0.9139 (OUTLIER) cc_final: 0.8803 (mmmm) REVERT: F 32 GLU cc_start: 0.8547 (tp30) cc_final: 0.8131 (tp30) REVERT: F 35 THR cc_start: 0.9363 (m) cc_final: 0.9025 (p) REVERT: F 90 THR cc_start: 0.9137 (OUTLIER) cc_final: 0.8781 (p) REVERT: F 96 MET cc_start: 0.8802 (ttp) cc_final: 0.8387 (tmm) REVERT: G 69 ARG cc_start: 0.8983 (tmt170) cc_final: 0.8454 (tpt90) REVERT: G 88 GLN cc_start: 0.9248 (pm20) cc_final: 0.8500 (mp10) REVERT: G 95 ARG cc_start: 0.8234 (mtm110) cc_final: 0.8004 (mtm110) REVERT: G 137 ASP cc_start: 0.8546 (t70) cc_final: 0.8283 (t70) REVERT: G 155 GLU cc_start: 0.7739 (pp20) cc_final: 0.6914 (pp20) REVERT: H 4 ILE cc_start: 0.9107 (tp) cc_final: 0.8840 (tp) REVERT: H 7 ASP cc_start: 0.9073 (t0) cc_final: 0.8765 (t0) REVERT: H 35 LYS cc_start: 0.9150 (mtpp) cc_final: 0.8895 (mmtm) REVERT: H 46 PHE cc_start: 0.8361 (m-80) cc_final: 0.7962 (m-80) REVERT: H 47 PHE cc_start: 0.7539 (t80) cc_final: 0.7339 (t80) REVERT: H 83 LYS cc_start: 0.7279 (mmtp) cc_final: 0.5946 (tttt) REVERT: I 116 GLU cc_start: 0.5558 (mt-10) cc_final: 0.5227 (mm-30) REVERT: I 123 ILE cc_start: 0.5308 (OUTLIER) cc_final: 0.4937 (mm) REVERT: J 94 ASN cc_start: 0.6846 (OUTLIER) cc_final: 0.6166 (m110) REVERT: J 100 LYS cc_start: 0.2318 (OUTLIER) cc_final: 0.1707 (tmmt) REVERT: J 136 MET cc_start: 0.2687 (ttt) cc_final: 0.0956 (mtm) REVERT: K 19 ASP cc_start: 0.7872 (t0) cc_final: 0.7491 (t0) REVERT: K 34 ARG cc_start: 0.8482 (OUTLIER) cc_final: 0.8032 (ttm-80) REVERT: K 71 ASP cc_start: 0.8549 (m-30) cc_final: 0.8245 (t0) REVERT: K 91 GLU cc_start: 0.8149 (tp30) cc_final: 0.7758 (tp30) REVERT: K 108 MET cc_start: 0.9169 (mtt) cc_final: 0.8871 (mtt) REVERT: L 88 ASN cc_start: 0.8646 (t0) cc_final: 0.8065 (t0) REVERT: L 92 GLU cc_start: 0.7778 (mm-30) cc_final: 0.7531 (mm-30) REVERT: L 100 PHE cc_start: 0.8371 (m-80) cc_final: 0.7853 (m-80) REVERT: M 67 THR cc_start: 0.9068 (OUTLIER) cc_final: 0.8773 (t) REVERT: M 80 SER cc_start: 0.9252 (p) cc_final: 0.8685 (t) REVERT: M 104 GLN cc_start: 0.8437 (OUTLIER) cc_final: 0.7886 (mt0) REVERT: M 142 ILE cc_start: 0.8930 (mt) cc_final: 0.8697 (tt) REVERT: N 9 PHE cc_start: 0.9261 (m-80) cc_final: 0.8569 (m-80) REVERT: N 30 SER cc_start: 0.9560 (m) cc_final: 0.8999 (p) REVERT: O 27 SER cc_start: 0.9689 (OUTLIER) cc_final: 0.9335 (t) REVERT: O 72 ASP cc_start: 0.8278 (t0) cc_final: 0.7972 (m-30) REVERT: O 94 TYR cc_start: 0.8787 (m-80) cc_final: 0.8376 (m-80) REVERT: P 2 ASP cc_start: 0.7989 (OUTLIER) cc_final: 0.6521 (m-30) REVERT: P 26 LEU cc_start: 0.8896 (tp) cc_final: 0.8694 (tt) REVERT: P 58 ILE cc_start: 0.9080 (mp) cc_final: 0.8835 (mp) REVERT: P 116 GLN cc_start: 0.7478 (tm-30) cc_final: 0.7222 (tm-30) REVERT: Q 9 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.7662 (tt0) REVERT: Q 25 THR cc_start: 0.9310 (m) cc_final: 0.8831 (p) REVERT: Q 112 GLU cc_start: 0.8355 (tt0) cc_final: 0.7888 (pm20) REVERT: Q 113 ARG cc_start: 0.8197 (ttp-170) cc_final: 0.7904 (ttm170) REVERT: T 25 ARG cc_start: 0.8978 (ttm110) cc_final: 0.8761 (ttm110) REVERT: T 34 ASP cc_start: 0.8241 (m-30) cc_final: 0.7820 (m-30) REVERT: T 67 ASP cc_start: 0.8755 (OUTLIER) cc_final: 0.8400 (p0) REVERT: T 84 ARG cc_start: 0.8930 (mmt-90) cc_final: 0.8569 (mmt180) REVERT: U 4 GLU cc_start: 0.8396 (pm20) cc_final: 0.8079 (pm20) REVERT: U 5 GLU cc_start: 0.8814 (mp0) cc_final: 0.8165 (mp0) REVERT: U 7 LEU cc_start: 0.9170 (mt) cc_final: 0.8890 (mt) REVERT: U 28 ASN cc_start: 0.9134 (t0) cc_final: 0.8604 (t0) REVERT: U 33 LYS cc_start: 0.9337 (mttt) cc_final: 0.9098 (mtpt) REVERT: U 72 GLN cc_start: 0.8950 (mp10) cc_final: 0.8540 (mp10) REVERT: U 73 ARG cc_start: 0.7668 (OUTLIER) cc_final: 0.6936 (mtt-85) REVERT: U 91 GLN cc_start: 0.8605 (mm-40) cc_final: 0.7696 (mt0) REVERT: V 33 LYS cc_start: 0.9329 (OUTLIER) cc_final: 0.8595 (mtpp) REVERT: V 37 GLU cc_start: 0.9130 (tp30) cc_final: 0.8747 (tm-30) REVERT: V 52 LEU cc_start: 0.8313 (OUTLIER) cc_final: 0.7853 (tp) REVERT: V 54 GLN cc_start: 0.7622 (pm20) cc_final: 0.7365 (pm20) REVERT: V 66 GLN cc_start: 0.8846 (mm-40) cc_final: 0.8379 (mt0) REVERT: W 2 PHE cc_start: 0.8396 (m-80) cc_final: 0.7659 (m-80) REVERT: W 7 GLU cc_start: 0.8161 (pm20) cc_final: 0.7467 (pm20) REVERT: W 9 ARG cc_start: 0.8772 (OUTLIER) cc_final: 0.8365 (ttm170) REVERT: W 17 SER cc_start: 0.9332 (m) cc_final: 0.8973 (p) REVERT: W 34 LYS cc_start: 0.8764 (mmmt) cc_final: 0.8335 (mtmm) REVERT: W 41 GLU cc_start: 0.8384 (pp20) cc_final: 0.7548 (pp20) REVERT: W 53 LYS cc_start: 0.9083 (mtmt) cc_final: 0.8849 (ptmm) REVERT: W 55 GLU cc_start: 0.8803 (mp0) cc_final: 0.8573 (mp0) REVERT: W 59 GLU cc_start: 0.8837 (mt-10) cc_final: 0.8384 (mp0) REVERT: W 68 LYS cc_start: 0.8585 (mtmm) cc_final: 0.8077 (mtmm) REVERT: W 76 ASP cc_start: 0.8972 (t0) cc_final: 0.8588 (t0) REVERT: W 87 GLN cc_start: 0.8879 (mm110) cc_final: 0.8283 (mt0) REVERT: X 77 ARG cc_start: 0.8574 (OUTLIER) cc_final: 0.7425 (mtp180) REVERT: X 83 GLU cc_start: 0.8114 (mt-10) cc_final: 0.7799 (mt-10) REVERT: Y 28 ARG cc_start: 0.9585 (OUTLIER) cc_final: 0.9185 (ptm160) REVERT: Y 40 VAL cc_start: 0.9067 (t) cc_final: 0.8772 (p) REVERT: Y 48 THR cc_start: 0.9326 (m) cc_final: 0.9058 (p) REVERT: Y 70 GLU cc_start: 0.8448 (tm-30) cc_final: 0.8061 (tm-30) REVERT: Z 13 GLU cc_start: 0.8751 (mt-10) cc_final: 0.8458 (mp0) REVERT: Z 17 GLU cc_start: 0.8383 (tp30) cc_final: 0.8103 (tp30) REVERT: a 3 LYS cc_start: 0.8618 (ttpp) cc_final: 0.8309 (ttpp) REVERT: a 44 ILE cc_start: 0.9463 (mm) cc_final: 0.9083 (tp) REVERT: b 13 ARG cc_start: 0.8886 (OUTLIER) cc_final: 0.8118 (ttm-80) REVERT: b 37 LYS cc_start: 0.8832 (mtmt) cc_final: 0.8592 (mtmm) REVERT: c 32 GLU cc_start: 0.8452 (pm20) cc_final: 0.8226 (pm20) REVERT: c 33 LYS cc_start: 0.7647 (mmtp) cc_final: 0.6687 (mmtm) REVERT: c 51 GLU cc_start: 0.8628 (tt0) cc_final: 0.7654 (pt0) REVERT: e 49 MET cc_start: 0.8672 (mmm) cc_final: 0.8471 (tpt) REVERT: i 341 MET cc_start: 0.6067 (mtp) cc_final: 0.4839 (tpt) REVERT: i 383 MET cc_start: 0.8856 (mtt) cc_final: 0.8024 (ttm) REVERT: i 385 MET cc_start: 0.7860 (mmm) cc_final: 0.6673 (mtt) REVERT: i 395 LYS cc_start: 0.8622 (mmtt) cc_final: 0.8169 (mmtt) REVERT: i 398 ARG cc_start: 0.8912 (mmt90) cc_final: 0.8427 (mmt90) REVERT: i 399 LYS cc_start: 0.9001 (mttt) cc_final: 0.8164 (mttp) REVERT: i 424 GLN cc_start: 0.7364 (pp30) cc_final: 0.6819 (pp30) REVERT: i 425 ARG cc_start: 0.8661 (ttm-80) cc_final: 0.8232 (ttm-80) REVERT: i 426 MET cc_start: 0.8088 (tpp) cc_final: 0.7476 (ttp) REVERT: i 428 LYS cc_start: 0.7483 (mmtm) cc_final: 0.7089 (mmtm) REVERT: k 38 LEU cc_start: 0.4299 (OUTLIER) cc_final: 0.3957 (mt) outliers start: 191 outliers final: 136 residues processed: 969 average time/residue: 0.9967 time to fit residues: 1662.4226 Evaluate side-chains 973 residues out of total 2908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 815 time to evaluate : 4.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 178 SER Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 194 GLU Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain D residue 13 ARG Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 74 GLU Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 139 SER Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 130 LYS Chi-restraints excluded: chain E residue 168 ASP Chi-restraints excluded: chain F residue 20 PHE Chi-restraints excluded: chain F residue 21 ASN Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 87 CYS Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 127 ASN Chi-restraints excluded: chain F residue 132 VAL Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain G residue 51 THR Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 89 LYS Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 147 VAL Chi-restraints excluded: chain I residue 50 VAL Chi-restraints excluded: chain I residue 123 ILE Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 55 ILE Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 61 VAL Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain J residue 94 ASN Chi-restraints excluded: chain J residue 100 LYS Chi-restraints excluded: chain J residue 122 ILE Chi-restraints excluded: chain K residue 34 ARG Chi-restraints excluded: chain K residue 36 LEU Chi-restraints excluded: chain K residue 86 GLN Chi-restraints excluded: chain K residue 131 ASN Chi-restraints excluded: chain L residue 21 CYS Chi-restraints excluded: chain L residue 25 LEU Chi-restraints excluded: chain L residue 38 ILE Chi-restraints excluded: chain L residue 52 VAL Chi-restraints excluded: chain L residue 61 VAL Chi-restraints excluded: chain L residue 104 THR Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 25 SER Chi-restraints excluded: chain M residue 67 THR Chi-restraints excluded: chain M residue 104 GLN Chi-restraints excluded: chain M residue 122 VAL Chi-restraints excluded: chain N residue 7 THR Chi-restraints excluded: chain N residue 73 ILE Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain N residue 102 LEU Chi-restraints excluded: chain N residue 105 MET Chi-restraints excluded: chain N residue 108 VAL Chi-restraints excluded: chain N residue 134 THR Chi-restraints excluded: chain O residue 13 ASN Chi-restraints excluded: chain O residue 20 MET Chi-restraints excluded: chain O residue 27 SER Chi-restraints excluded: chain O residue 37 THR Chi-restraints excluded: chain P residue 2 ASP Chi-restraints excluded: chain P residue 40 ILE Chi-restraints excluded: chain P residue 43 ASN Chi-restraints excluded: chain P residue 53 THR Chi-restraints excluded: chain P residue 55 GLU Chi-restraints excluded: chain P residue 87 ILE Chi-restraints excluded: chain Q residue 9 GLU Chi-restraints excluded: chain Q residue 12 GLN Chi-restraints excluded: chain Q residue 48 ILE Chi-restraints excluded: chain Q residue 66 ASN Chi-restraints excluded: chain Q residue 76 THR Chi-restraints excluded: chain R residue 18 LEU Chi-restraints excluded: chain R residue 39 VAL Chi-restraints excluded: chain R residue 40 ILE Chi-restraints excluded: chain R residue 60 LEU Chi-restraints excluded: chain R residue 75 SER Chi-restraints excluded: chain R residue 87 SER Chi-restraints excluded: chain R residue 109 LEU Chi-restraints excluded: chain S residue 19 THR Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain T residue 39 THR Chi-restraints excluded: chain T residue 45 VAL Chi-restraints excluded: chain T residue 67 ASP Chi-restraints excluded: chain T residue 72 THR Chi-restraints excluded: chain T residue 81 SER Chi-restraints excluded: chain U residue 39 THR Chi-restraints excluded: chain U residue 73 ARG Chi-restraints excluded: chain U residue 93 LEU Chi-restraints excluded: chain V residue 12 ILE Chi-restraints excluded: chain V residue 33 LYS Chi-restraints excluded: chain V residue 52 LEU Chi-restraints excluded: chain V residue 67 VAL Chi-restraints excluded: chain V residue 68 SER Chi-restraints excluded: chain V residue 102 THR Chi-restraints excluded: chain V residue 103 ILE Chi-restraints excluded: chain W residue 9 ARG Chi-restraints excluded: chain W residue 65 VAL Chi-restraints excluded: chain W residue 66 ASP Chi-restraints excluded: chain W residue 71 LYS Chi-restraints excluded: chain W residue 72 VAL Chi-restraints excluded: chain W residue 77 VAL Chi-restraints excluded: chain W residue 92 VAL Chi-restraints excluded: chain X residue 12 ASN Chi-restraints excluded: chain X residue 50 ASN Chi-restraints excluded: chain X residue 76 ASN Chi-restraints excluded: chain X residue 77 ARG Chi-restraints excluded: chain X residue 80 ILE Chi-restraints excluded: chain X residue 81 SER Chi-restraints excluded: chain Y residue 4 VAL Chi-restraints excluded: chain Y residue 22 LEU Chi-restraints excluded: chain Y residue 28 ARG Chi-restraints excluded: chain Y residue 35 SER Chi-restraints excluded: chain Y residue 42 SER Chi-restraints excluded: chain Y residue 56 MET Chi-restraints excluded: chain Y residue 66 THR Chi-restraints excluded: chain Y residue 68 LEU Chi-restraints excluded: chain Z residue 19 LEU Chi-restraints excluded: chain Z residue 58 ASN Chi-restraints excluded: chain a residue 29 LEU Chi-restraints excluded: chain a residue 32 ILE Chi-restraints excluded: chain a residue 52 SER Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain b residue 13 ARG Chi-restraints excluded: chain b residue 25 VAL Chi-restraints excluded: chain b residue 28 LEU Chi-restraints excluded: chain b residue 55 ILE 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 8 SER Chi-restraints excluded: chain d residue 44 VAL Chi-restraints excluded: chain f residue 13 ASN Chi-restraints excluded: chain i residue 342 LYS Chi-restraints excluded: chain k residue 36 LEU Chi-restraints excluded: chain k residue 38 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 640 random chunks: chunk 515 optimal weight: 4.9990 chunk 351 optimal weight: 8.9990 chunk 8 optimal weight: 10.0000 chunk 460 optimal weight: 7.9990 chunk 255 optimal weight: 10.0000 chunk 527 optimal weight: 9.9990 chunk 427 optimal weight: 8.9990 chunk 0 optimal weight: 40.0000 chunk 315 optimal weight: 2.9990 chunk 555 optimal weight: 1.9990 chunk 156 optimal weight: 20.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 195 GLN ** G 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 135 HIS ** N 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 88 ASN ** O 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 66 ASN R 37 GLN T 15 GLN ** V 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 6 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8750 moved from start: 0.3654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 101812 Z= 0.286 Angle : 0.604 9.987 152558 Z= 0.313 Chirality : 0.036 0.254 19559 Planarity : 0.005 0.075 7978 Dihedral : 23.324 178.330 51621 Min Nonbonded Distance : 1.041 Molprobity Statistics. All-atom Clashscore : 13.86 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.43 % Favored : 96.51 % Rotamer: Outliers : 7.58 % Allowed : 24.68 % Favored : 67.74 % 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: -0.47 (0.14), residues: 3529 helix: 0.51 (0.16), residues: 1072 sheet: -0.61 (0.18), residues: 774 loop : -0.59 (0.14), residues: 1683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP N 64 HIS 0.006 0.001 HIS I 88 PHE 0.024 0.002 PHE Z 26 TYR 0.015 0.002 TYR F 22 ARG 0.011 0.001 ARG U 12 *********************** 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 1069 residues out of total 2908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 220 poor density : 849 time to evaluate : 4.098 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 7 LYS cc_start: 0.9335 (mtmm) cc_final: 0.9021 (mtmt) REVERT: C 20 VAL cc_start: 0.9320 (OUTLIER) cc_final: 0.8996 (p) REVERT: C 72 ASP cc_start: 0.8753 (m-30) cc_final: 0.8507 (t0) REVERT: C 120 VAL cc_start: 0.9329 (OUTLIER) cc_final: 0.8831 (p) REVERT: C 121 ASP cc_start: 0.8354 (p0) cc_final: 0.7980 (p0) REVERT: C 225 MET cc_start: 0.9156 (mtt) cc_final: 0.8816 (mtt) REVERT: D 39 ASP cc_start: 0.8772 (p0) cc_final: 0.8415 (p0) REVERT: D 112 THR cc_start: 0.9421 (OUTLIER) cc_final: 0.9001 (p) REVERT: D 116 LYS cc_start: 0.9396 (OUTLIER) cc_final: 0.9075 (mttm) REVERT: D 155 VAL cc_start: 0.9309 (t) cc_final: 0.9066 (p) REVERT: E 46 GLN cc_start: 0.9369 (mp10) cc_final: 0.9049 (mp10) REVERT: E 49 ARG cc_start: 0.9227 (OUTLIER) cc_final: 0.7104 (ptm160) REVERT: E 130 LYS cc_start: 0.8977 (OUTLIER) cc_final: 0.8539 (mmmm) REVERT: E 156 ASN cc_start: 0.8954 (m-40) cc_final: 0.8452 (m-40) REVERT: E 188 MET cc_start: 0.9577 (mmm) cc_final: 0.9361 (mmm) REVERT: F 19 GLU cc_start: 0.8355 (pp20) cc_final: 0.8059 (pp20) REVERT: F 32 GLU cc_start: 0.8570 (tp30) cc_final: 0.8142 (tp30) REVERT: F 35 THR cc_start: 0.9356 (m) cc_final: 0.9019 (p) REVERT: F 90 THR cc_start: 0.9049 (OUTLIER) cc_final: 0.8570 (p) REVERT: F 96 MET cc_start: 0.8864 (ttp) cc_final: 0.8428 (tmm) REVERT: G 69 ARG cc_start: 0.8997 (tmt170) cc_final: 0.8463 (tpt90) REVERT: G 88 GLN cc_start: 0.9241 (pm20) cc_final: 0.8485 (mp10) REVERT: G 121 ILE cc_start: 0.8803 (mm) cc_final: 0.8542 (mm) REVERT: G 137 ASP cc_start: 0.8565 (t70) cc_final: 0.8304 (t70) REVERT: G 155 GLU cc_start: 0.7733 (pp20) cc_final: 0.6800 (pp20) REVERT: H 4 ILE cc_start: 0.9126 (tp) cc_final: 0.8831 (tp) REVERT: H 9 VAL cc_start: 0.9103 (OUTLIER) cc_final: 0.8737 (m) REVERT: H 35 LYS cc_start: 0.9171 (mtpp) cc_final: 0.8948 (mmtm) REVERT: H 47 PHE cc_start: 0.7557 (t80) cc_final: 0.7183 (t80) REVERT: H 50 ARG cc_start: 0.7879 (mtt180) cc_final: 0.7657 (mtm180) REVERT: H 83 LYS cc_start: 0.7297 (mmtp) cc_final: 0.5929 (pttt) REVERT: I 9 GLN cc_start: 0.8429 (pt0) cc_final: 0.8129 (mt0) REVERT: I 82 ILE cc_start: 0.7140 (tp) cc_final: 0.6708 (tp) REVERT: I 116 GLU cc_start: 0.5604 (mt-10) cc_final: 0.5217 (mm-30) REVERT: I 123 ILE cc_start: 0.5395 (OUTLIER) cc_final: 0.4999 (mm) REVERT: J 94 ASN cc_start: 0.7045 (OUTLIER) cc_final: 0.6334 (m110) REVERT: J 136 MET cc_start: 0.2576 (ttt) cc_final: 0.0966 (mtm) REVERT: K 19 ASP cc_start: 0.7627 (t0) cc_final: 0.7223 (t0) REVERT: K 31 GLU cc_start: 0.8755 (mm-30) cc_final: 0.8406 (mp0) REVERT: K 34 ARG cc_start: 0.8557 (OUTLIER) cc_final: 0.8110 (ttm-80) REVERT: K 71 ASP cc_start: 0.8670 (m-30) cc_final: 0.8210 (t0) REVERT: K 91 GLU cc_start: 0.8142 (tp30) cc_final: 0.7841 (tp30) REVERT: K 108 MET cc_start: 0.9162 (mtt) cc_final: 0.8889 (mtt) REVERT: L 1 MET cc_start: 0.9111 (ttp) cc_final: 0.8785 (ttp) REVERT: L 88 ASN cc_start: 0.8724 (t0) cc_final: 0.8127 (t0) REVERT: L 92 GLU cc_start: 0.7695 (mm-30) cc_final: 0.7425 (mm-30) REVERT: L 100 PHE cc_start: 0.8502 (m-80) cc_final: 0.7917 (m-80) REVERT: M 54 GLN cc_start: 0.8589 (tt0) cc_final: 0.8251 (tt0) REVERT: M 67 THR cc_start: 0.9080 (OUTLIER) cc_final: 0.8874 (p) REVERT: M 80 SER cc_start: 0.9268 (p) cc_final: 0.8719 (t) REVERT: M 104 GLN cc_start: 0.8441 (OUTLIER) cc_final: 0.7892 (mt0) REVERT: M 142 ILE cc_start: 0.8945 (mt) cc_final: 0.8699 (tt) REVERT: N 9 PHE cc_start: 0.9210 (m-80) cc_final: 0.8420 (m-80) REVERT: N 30 SER cc_start: 0.9441 (m) cc_final: 0.9005 (p) REVERT: N 45 GLN cc_start: 0.8729 (mt0) cc_final: 0.8307 (mt0) REVERT: O 27 SER cc_start: 0.9678 (OUTLIER) cc_final: 0.9303 (t) REVERT: O 72 ASP cc_start: 0.8282 (t0) cc_final: 0.8036 (m-30) REVERT: O 94 TYR cc_start: 0.8929 (m-80) cc_final: 0.8469 (m-80) REVERT: P 17 LYS cc_start: 0.9195 (tppp) cc_final: 0.8963 (tppt) REVERT: P 116 GLN cc_start: 0.7578 (tm-30) cc_final: 0.7324 (tm-30) REVERT: Q 9 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7871 (tt0) REVERT: Q 25 THR cc_start: 0.9342 (m) cc_final: 0.8812 (p) REVERT: Q 112 GLU cc_start: 0.8381 (tt0) cc_final: 0.7872 (pm20) REVERT: S 52 PRO cc_start: 0.8586 (Cg_endo) cc_final: 0.8266 (Cg_exo) REVERT: T 25 ARG cc_start: 0.8995 (ttm110) cc_final: 0.8779 (ttm110) REVERT: T 67 ASP cc_start: 0.8772 (OUTLIER) cc_final: 0.8447 (p0) REVERT: T 84 ARG cc_start: 0.8946 (mmt-90) cc_final: 0.8597 (mmt180) REVERT: U 4 GLU cc_start: 0.8305 (pm20) cc_final: 0.8038 (pm20) REVERT: U 5 GLU cc_start: 0.8733 (mp0) cc_final: 0.8230 (mp0) REVERT: U 7 LEU cc_start: 0.9157 (mt) cc_final: 0.8858 (mt) REVERT: U 28 ASN cc_start: 0.9060 (t0) cc_final: 0.8621 (t0) REVERT: U 33 LYS cc_start: 0.9325 (mttt) cc_final: 0.9001 (mtmm) REVERT: U 72 GLN cc_start: 0.8939 (mp10) cc_final: 0.8565 (mp10) REVERT: U 73 ARG cc_start: 0.7627 (OUTLIER) cc_final: 0.7264 (mtt-85) REVERT: U 91 GLN cc_start: 0.8217 (mm-40) cc_final: 0.7881 (mt0) REVERT: V 33 LYS cc_start: 0.9331 (OUTLIER) cc_final: 0.8615 (mtpp) REVERT: V 37 GLU cc_start: 0.9076 (tp30) cc_final: 0.8784 (tm-30) REVERT: V 52 LEU cc_start: 0.8331 (mt) cc_final: 0.7859 (tp) REVERT: V 54 GLN cc_start: 0.7648 (pm20) cc_final: 0.7444 (pm20) REVERT: V 66 GLN cc_start: 0.8889 (mm-40) cc_final: 0.8452 (mt0) REVERT: W 7 GLU cc_start: 0.8126 (pm20) cc_final: 0.7573 (pm20) REVERT: W 9 ARG cc_start: 0.8775 (OUTLIER) cc_final: 0.8452 (ttm170) REVERT: W 17 SER cc_start: 0.9350 (m) cc_final: 0.8852 (p) REVERT: W 24 ASN cc_start: 0.8965 (OUTLIER) cc_final: 0.8239 (t0) REVERT: W 41 GLU cc_start: 0.8478 (pp20) cc_final: 0.7560 (pp20) REVERT: W 55 GLU cc_start: 0.8766 (mp0) cc_final: 0.8237 (mp0) REVERT: W 59 GLU cc_start: 0.8834 (mt-10) cc_final: 0.8366 (mp0) REVERT: W 76 ASP cc_start: 0.8946 (t0) cc_final: 0.8597 (t0) REVERT: W 87 GLN cc_start: 0.8856 (mm110) cc_final: 0.8275 (mt0) REVERT: X 68 LYS cc_start: 0.9359 (mtpp) cc_final: 0.9071 (mtpp) REVERT: X 77 ARG cc_start: 0.8487 (OUTLIER) cc_final: 0.7260 (mtp180) REVERT: Y 28 ARG cc_start: 0.9586 (OUTLIER) cc_final: 0.9186 (ptm160) REVERT: Y 40 VAL cc_start: 0.9055 (t) cc_final: 0.8754 (p) REVERT: Y 48 THR cc_start: 0.9316 (m) cc_final: 0.9049 (p) REVERT: Z 13 GLU cc_start: 0.8795 (mt-10) cc_final: 0.8488 (mp0) REVERT: Z 17 GLU cc_start: 0.8410 (tp30) cc_final: 0.8114 (tp30) REVERT: a 44 ILE cc_start: 0.9494 (mm) cc_final: 0.9065 (tp) REVERT: b 13 ARG cc_start: 0.8855 (OUTLIER) cc_final: 0.8073 (ttm-80) REVERT: b 52 ARG cc_start: 0.8341 (mtp180) cc_final: 0.8033 (ttt180) REVERT: c 32 GLU cc_start: 0.8457 (pm20) cc_final: 0.8215 (pm20) REVERT: c 33 LYS cc_start: 0.7604 (mmtp) cc_final: 0.6590 (mmtm) REVERT: c 48 ILE cc_start: 0.9113 (tt) cc_final: 0.8912 (tp) REVERT: c 51 GLU cc_start: 0.8612 (tt0) cc_final: 0.7679 (pt0) REVERT: e 49 MET cc_start: 0.8598 (mmm) cc_final: 0.8384 (tpt) REVERT: i 341 MET cc_start: 0.5989 (mtp) cc_final: 0.4749 (tpt) REVERT: i 383 MET cc_start: 0.8727 (mtt) cc_final: 0.7976 (ttm) REVERT: i 385 MET cc_start: 0.7932 (mmm) cc_final: 0.6842 (mtt) REVERT: i 395 LYS cc_start: 0.8632 (mmtt) cc_final: 0.8190 (mmtt) REVERT: i 398 ARG cc_start: 0.8820 (mmt90) cc_final: 0.8483 (mmt90) REVERT: i 399 LYS cc_start: 0.8991 (mttt) cc_final: 0.8489 (mttp) REVERT: i 424 GLN cc_start: 0.7393 (pp30) cc_final: 0.6737 (pp30) REVERT: i 425 ARG cc_start: 0.8621 (ttm-80) cc_final: 0.8247 (ttm-80) REVERT: i 428 LYS cc_start: 0.7465 (mmtm) cc_final: 0.6993 (mmtm) REVERT: k 38 LEU cc_start: 0.4328 (OUTLIER) cc_final: 0.4005 (mt) outliers start: 220 outliers final: 167 residues processed: 973 average time/residue: 0.9515 time to fit residues: 1595.2433 Evaluate side-chains 1005 residues out of total 2908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 191 poor density : 814 time to evaluate : 4.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 38 SER Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 178 SER Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 194 GLU Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 74 GLU Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain D residue 116 LYS Chi-restraints excluded: chain D residue 139 SER Chi-restraints excluded: chain E residue 49 ARG Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain E residue 130 LYS Chi-restraints excluded: chain E residue 168 ASP Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain F residue 20 PHE Chi-restraints excluded: chain F residue 21 ASN Chi-restraints excluded: chain F residue 23 ASN Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 87 CYS Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 127 ASN Chi-restraints excluded: chain F residue 132 VAL Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain G residue 51 THR Chi-restraints excluded: chain G residue 56 ASP Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain H residue 9 VAL Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 89 LYS Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 144 VAL Chi-restraints excluded: chain H residue 147 VAL Chi-restraints excluded: chain I residue 123 ILE Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 61 VAL Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain J residue 94 ASN Chi-restraints excluded: chain J residue 101 ILE Chi-restraints excluded: chain J residue 122 ILE Chi-restraints excluded: chain J residue 125 MET Chi-restraints excluded: chain K residue 34 ARG Chi-restraints excluded: chain K residue 36 LEU Chi-restraints excluded: chain K residue 86 GLN Chi-restraints excluded: chain K residue 106 LYS Chi-restraints excluded: chain K residue 131 ASN Chi-restraints excluded: chain L residue 21 CYS Chi-restraints excluded: chain L residue 25 LEU Chi-restraints excluded: chain L residue 38 ILE Chi-restraints excluded: chain L residue 52 VAL Chi-restraints excluded: chain L residue 61 VAL Chi-restraints excluded: chain L residue 62 VAL Chi-restraints excluded: chain L residue 65 THR Chi-restraints excluded: chain L residue 104 THR Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 25 SER Chi-restraints excluded: chain M residue 67 THR Chi-restraints excluded: chain M residue 104 GLN Chi-restraints excluded: chain M residue 121 THR Chi-restraints excluded: chain M residue 122 VAL Chi-restraints excluded: chain N residue 7 THR Chi-restraints excluded: chain N residue 73 ILE Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain N residue 78 LEU Chi-restraints excluded: chain N residue 102 LEU Chi-restraints excluded: chain N residue 105 MET Chi-restraints excluded: chain N residue 108 VAL Chi-restraints excluded: chain N residue 112 LEU Chi-restraints excluded: chain N residue 134 THR Chi-restraints excluded: chain O residue 13 ASN Chi-restraints excluded: chain O residue 14 SER Chi-restraints excluded: chain O residue 20 MET Chi-restraints excluded: chain O residue 27 SER Chi-restraints excluded: chain O residue 37 THR Chi-restraints excluded: chain P residue 40 ILE Chi-restraints excluded: chain P residue 43 ASN Chi-restraints excluded: chain P residue 53 THR Chi-restraints excluded: chain P residue 55 GLU Chi-restraints excluded: chain P residue 87 ILE Chi-restraints excluded: chain Q residue 9 GLU Chi-restraints excluded: chain Q residue 12 GLN Chi-restraints excluded: chain Q residue 46 VAL Chi-restraints excluded: chain Q residue 66 ASN Chi-restraints excluded: chain Q residue 115 ASN Chi-restraints excluded: chain R residue 18 LEU Chi-restraints excluded: chain R residue 39 VAL Chi-restraints excluded: chain R residue 40 ILE Chi-restraints excluded: chain R residue 60 LEU Chi-restraints excluded: chain R residue 75 SER Chi-restraints excluded: chain R residue 87 SER Chi-restraints excluded: chain R residue 91 ASP Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain R residue 109 LEU Chi-restraints excluded: chain S residue 19 THR Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain S residue 85 LYS Chi-restraints excluded: chain S residue 99 THR Chi-restraints excluded: chain T residue 39 THR Chi-restraints excluded: chain T residue 45 VAL Chi-restraints excluded: chain T residue 67 ASP Chi-restraints excluded: chain T residue 72 THR Chi-restraints excluded: chain T residue 81 SER Chi-restraints excluded: chain U residue 17 SER Chi-restraints excluded: chain U residue 39 THR Chi-restraints excluded: chain U residue 73 ARG Chi-restraints excluded: chain U residue 93 LEU Chi-restraints excluded: chain V residue 12 ILE Chi-restraints excluded: chain V residue 33 LYS Chi-restraints excluded: chain V residue 67 VAL Chi-restraints excluded: chain V residue 68 SER Chi-restraints excluded: chain V residue 77 THR Chi-restraints excluded: chain V residue 102 THR Chi-restraints excluded: chain V residue 103 ILE Chi-restraints excluded: chain W residue 9 ARG Chi-restraints excluded: chain W residue 20 LEU Chi-restraints excluded: chain W residue 24 ASN Chi-restraints excluded: chain W residue 45 ASP Chi-restraints excluded: chain W residue 58 SER Chi-restraints excluded: chain W residue 61 LEU Chi-restraints excluded: chain W residue 65 VAL Chi-restraints excluded: chain W residue 66 ASP Chi-restraints excluded: chain W residue 71 LYS Chi-restraints excluded: chain W residue 72 VAL Chi-restraints excluded: chain W residue 77 VAL Chi-restraints excluded: chain W residue 92 VAL Chi-restraints excluded: chain X residue 12 ASN Chi-restraints excluded: chain X residue 30 SER Chi-restraints excluded: chain X residue 50 ASN Chi-restraints excluded: chain X residue 76 ASN Chi-restraints excluded: chain X residue 77 ARG Chi-restraints excluded: chain X residue 80 ILE Chi-restraints excluded: chain X residue 81 SER Chi-restraints excluded: chain Y residue 4 VAL Chi-restraints excluded: chain Y residue 22 LEU Chi-restraints excluded: chain Y residue 28 ARG Chi-restraints excluded: chain Y residue 35 SER Chi-restraints excluded: chain Y residue 42 SER Chi-restraints excluded: chain Y residue 56 MET Chi-restraints excluded: chain Y residue 68 LEU Chi-restraints excluded: chain Z residue 19 LEU Chi-restraints excluded: chain a residue 29 LEU Chi-restraints excluded: chain a residue 32 ILE Chi-restraints excluded: chain a residue 52 SER Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain b residue 13 ARG Chi-restraints excluded: chain b residue 25 VAL Chi-restraints excluded: chain b residue 28 LEU Chi-restraints excluded: chain b residue 36 GLU Chi-restraints excluded: chain b residue 55 ILE 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 8 SER Chi-restraints excluded: chain d residue 24 THR Chi-restraints excluded: chain d residue 43 THR Chi-restraints excluded: chain d residue 44 VAL Chi-restraints excluded: chain f residue 13 ASN Chi-restraints excluded: chain i residue 342 LYS Chi-restraints excluded: chain k residue 38 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 640 random chunks: chunk 208 optimal weight: 10.0000 chunk 557 optimal weight: 0.9990 chunk 122 optimal weight: 10.0000 chunk 363 optimal weight: 8.9990 chunk 152 optimal weight: 10.0000 chunk 619 optimal weight: 10.0000 chunk 514 optimal weight: 5.9990 chunk 286 optimal weight: 10.0000 chunk 51 optimal weight: 10.0000 chunk 204 optimal weight: 10.0000 chunk 325 optimal weight: 6.9990 overall best weight: 6.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 115 GLN E 195 GLN ** G 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 128 GLN ** N 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 37 GLN ** V 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8759 moved from start: 0.3774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 101812 Z= 0.342 Angle : 0.638 10.301 152558 Z= 0.328 Chirality : 0.037 0.257 19559 Planarity : 0.005 0.068 7978 Dihedral : 23.319 178.574 51615 Min Nonbonded Distance : 1.023 Molprobity Statistics. All-atom Clashscore : 14.67 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.94 % Favored : 96.00 % Rotamer: Outliers : 7.79 % Allowed : 25.44 % Favored : 66.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.14), residues: 3529 helix: 0.52 (0.16), residues: 1071 sheet: -0.67 (0.18), residues: 766 loop : -0.69 (0.14), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP N 64 HIS 0.006 0.001 HIS D 140 PHE 0.030 0.002 PHE N 68 TYR 0.021 0.002 TYR W 82 ARG 0.008 0.001 ARG b 17 *********************** 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 1055 residues out of total 2908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 226 poor density : 829 time to evaluate : 4.040 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: C 20 VAL cc_start: 0.9346 (OUTLIER) cc_final: 0.9014 (p) REVERT: C 72 ASP cc_start: 0.8772 (m-30) cc_final: 0.8519 (t0) REVERT: C 120 VAL cc_start: 0.9337 (OUTLIER) cc_final: 0.8833 (p) REVERT: C 121 ASP cc_start: 0.8278 (p0) cc_final: 0.7881 (p0) REVERT: C 225 MET cc_start: 0.9183 (mtt) cc_final: 0.8792 (mtt) REVERT: D 39 ASP cc_start: 0.8781 (p0) cc_final: 0.8425 (p0) REVERT: D 112 THR cc_start: 0.9421 (OUTLIER) cc_final: 0.8999 (p) REVERT: D 116 LYS cc_start: 0.9397 (OUTLIER) cc_final: 0.9154 (mttm) REVERT: E 46 GLN cc_start: 0.9377 (mp10) cc_final: 0.9099 (mp10) REVERT: E 123 LYS cc_start: 0.9100 (mmmt) cc_final: 0.8692 (ptmm) REVERT: E 156 ASN cc_start: 0.8919 (m-40) cc_final: 0.8409 (m-40) REVERT: E 188 MET cc_start: 0.9586 (mmm) cc_final: 0.9262 (mmt) REVERT: F 26 MET cc_start: 0.9391 (mmp) cc_final: 0.8864 (mmm) REVERT: F 32 GLU cc_start: 0.8585 (tp30) cc_final: 0.8169 (tp30) REVERT: F 35 THR cc_start: 0.9349 (m) cc_final: 0.9017 (p) REVERT: F 90 THR cc_start: 0.9050 (OUTLIER) cc_final: 0.8575 (p) REVERT: F 96 MET cc_start: 0.8890 (ttp) cc_final: 0.8449 (tmm) REVERT: G 69 ARG cc_start: 0.9001 (tmt170) cc_final: 0.8481 (tpt90) REVERT: G 88 GLN cc_start: 0.9227 (pm20) cc_final: 0.8473 (mp10) REVERT: G 121 ILE cc_start: 0.8813 (mm) cc_final: 0.8561 (mm) REVERT: G 137 ASP cc_start: 0.8614 (t70) cc_final: 0.8338 (t0) REVERT: G 155 GLU cc_start: 0.7820 (pp20) cc_final: 0.6860 (pp20) REVERT: H 4 ILE cc_start: 0.9178 (tp) cc_final: 0.8893 (tp) REVERT: H 9 VAL cc_start: 0.9136 (OUTLIER) cc_final: 0.8754 (m) REVERT: H 35 LYS cc_start: 0.9180 (mtpp) cc_final: 0.8952 (mmtm) REVERT: H 47 PHE cc_start: 0.7729 (t80) cc_final: 0.7415 (t80) REVERT: H 50 ARG cc_start: 0.7985 (mtt180) cc_final: 0.7662 (mtm180) REVERT: H 68 ARG cc_start: 0.6354 (mtp85) cc_final: 0.6069 (mtp-110) REVERT: H 83 LYS cc_start: 0.7258 (mmtp) cc_final: 0.6067 (tttt) REVERT: I 116 GLU cc_start: 0.5655 (mt-10) cc_final: 0.5226 (mm-30) REVERT: I 123 ILE cc_start: 0.5387 (OUTLIER) cc_final: 0.4999 (mm) REVERT: J 94 ASN cc_start: 0.7067 (OUTLIER) cc_final: 0.6328 (m110) REVERT: J 136 MET cc_start: 0.2580 (ttt) cc_final: 0.0874 (mtm) REVERT: K 31 GLU cc_start: 0.8762 (mm-30) cc_final: 0.8405 (mp0) REVERT: K 34 ARG cc_start: 0.8614 (OUTLIER) cc_final: 0.8154 (ttm-80) REVERT: K 71 ASP cc_start: 0.8749 (m-30) cc_final: 0.8285 (t0) REVERT: K 91 GLU cc_start: 0.8166 (tp30) cc_final: 0.7836 (tp30) REVERT: K 108 MET cc_start: 0.9168 (mtt) cc_final: 0.8906 (mtt) REVERT: L 1 MET cc_start: 0.9134 (ttp) cc_final: 0.8882 (ttp) REVERT: L 88 ASN cc_start: 0.8764 (t0) cc_final: 0.8161 (t0) REVERT: L 92 GLU cc_start: 0.7745 (mm-30) cc_final: 0.7482 (mm-30) REVERT: L 100 PHE cc_start: 0.8562 (m-80) cc_final: 0.7947 (m-80) REVERT: M 54 GLN cc_start: 0.8559 (tt0) cc_final: 0.8169 (tt0) REVERT: M 67 THR cc_start: 0.9118 (OUTLIER) cc_final: 0.8913 (p) REVERT: M 80 SER cc_start: 0.9343 (p) cc_final: 0.8858 (t) REVERT: M 104 GLN cc_start: 0.8441 (OUTLIER) cc_final: 0.7911 (mt0) REVERT: M 142 ILE cc_start: 0.8951 (mt) cc_final: 0.8717 (tt) REVERT: N 9 PHE cc_start: 0.9240 (m-80) cc_final: 0.8576 (m-80) REVERT: N 30 SER cc_start: 0.9472 (m) cc_final: 0.8963 (p) REVERT: O 27 SER cc_start: 0.9682 (OUTLIER) cc_final: 0.9295 (t) REVERT: Q 9 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7935 (tt0) REVERT: Q 25 THR cc_start: 0.9300 (m) cc_final: 0.8737 (p) REVERT: Q 112 GLU cc_start: 0.8356 (tt0) cc_final: 0.7880 (pm20) REVERT: T 25 ARG cc_start: 0.8999 (ttm110) cc_final: 0.8760 (ttm110) REVERT: T 84 ARG cc_start: 0.8953 (mmt-90) cc_final: 0.8621 (mmt180) REVERT: U 4 GLU cc_start: 0.8335 (pm20) cc_final: 0.8059 (pm20) REVERT: U 5 GLU cc_start: 0.8715 (mp0) cc_final: 0.8208 (mp0) REVERT: U 7 LEU cc_start: 0.9153 (mt) cc_final: 0.8877 (mt) REVERT: U 28 ASN cc_start: 0.9032 (t0) cc_final: 0.8583 (t0) REVERT: U 72 GLN cc_start: 0.8960 (mp10) cc_final: 0.8563 (mp10) REVERT: U 73 ARG cc_start: 0.7638 (OUTLIER) cc_final: 0.7252 (mtt-85) REVERT: V 10 GLU cc_start: 0.8537 (tp30) cc_final: 0.7898 (tp30) REVERT: V 22 ARG cc_start: 0.8685 (ptm160) cc_final: 0.8129 (ttm-80) REVERT: V 33 LYS cc_start: 0.9338 (OUTLIER) cc_final: 0.8775 (mtmm) REVERT: V 37 GLU cc_start: 0.9078 (tp30) cc_final: 0.8831 (tm-30) REVERT: V 52 LEU cc_start: 0.8354 (OUTLIER) cc_final: 0.7876 (tp) REVERT: V 54 GLN cc_start: 0.7671 (pm20) cc_final: 0.7437 (pm20) REVERT: V 66 GLN cc_start: 0.8895 (mm-40) cc_final: 0.8507 (mt0) REVERT: W 7 GLU cc_start: 0.8039 (pm20) cc_final: 0.7480 (pm20) REVERT: W 9 ARG cc_start: 0.8829 (OUTLIER) cc_final: 0.8489 (ttm170) REVERT: W 17 SER cc_start: 0.9357 (m) cc_final: 0.8838 (p) REVERT: W 24 ASN cc_start: 0.8915 (OUTLIER) cc_final: 0.8205 (t0) REVERT: W 41 GLU cc_start: 0.8479 (pp20) cc_final: 0.7595 (pp20) REVERT: W 55 GLU cc_start: 0.8764 (mp0) cc_final: 0.8221 (mp0) REVERT: W 59 GLU cc_start: 0.8805 (mt-10) cc_final: 0.8418 (mp0) REVERT: W 76 ASP cc_start: 0.8968 (t0) cc_final: 0.8619 (t0) REVERT: W 87 GLN cc_start: 0.8872 (mm110) cc_final: 0.8308 (mt0) REVERT: X 58 THR cc_start: 0.9469 (OUTLIER) cc_final: 0.9227 (m) REVERT: X 77 ARG cc_start: 0.8372 (OUTLIER) cc_final: 0.7090 (mtp180) REVERT: X 83 GLU cc_start: 0.7930 (mt-10) cc_final: 0.7603 (pp20) REVERT: Y 28 ARG cc_start: 0.9532 (OUTLIER) cc_final: 0.9137 (ptm160) REVERT: Y 40 VAL cc_start: 0.9087 (t) cc_final: 0.8809 (p) REVERT: Y 48 THR cc_start: 0.9327 (m) cc_final: 0.9061 (p) REVERT: Z 13 GLU cc_start: 0.8799 (mt-10) cc_final: 0.8481 (mp0) REVERT: Z 17 GLU cc_start: 0.8382 (tp30) cc_final: 0.8061 (tp30) REVERT: Z 36 GLN cc_start: 0.8757 (mm-40) cc_final: 0.8112 (mp10) REVERT: a 30 ARG cc_start: 0.9094 (OUTLIER) cc_final: 0.8887 (mmm-85) REVERT: b 13 ARG cc_start: 0.8925 (OUTLIER) cc_final: 0.8092 (ttm-80) REVERT: b 52 ARG cc_start: 0.8371 (mtp180) cc_final: 0.8021 (ttt180) REVERT: c 32 GLU cc_start: 0.8490 (pm20) cc_final: 0.8223 (pm20) REVERT: c 33 LYS cc_start: 0.7738 (mmtp) cc_final: 0.6769 (mmtm) REVERT: c 51 GLU cc_start: 0.8683 (tt0) cc_final: 0.7803 (pt0) REVERT: i 341 MET cc_start: 0.6144 (mtp) cc_final: 0.4753 (tpt) REVERT: i 383 MET cc_start: 0.8716 (mtt) cc_final: 0.7986 (ttm) REVERT: i 385 MET cc_start: 0.7874 (mmm) cc_final: 0.6768 (mtt) REVERT: i 395 LYS cc_start: 0.8632 (mmtt) cc_final: 0.8172 (mmtt) REVERT: i 398 ARG cc_start: 0.8817 (mmt90) cc_final: 0.8509 (mmt90) REVERT: i 399 LYS cc_start: 0.9029 (mttt) cc_final: 0.8542 (mttp) REVERT: i 424 GLN cc_start: 0.7482 (pp30) cc_final: 0.7226 (pp30) REVERT: i 425 ARG cc_start: 0.8570 (ttm-80) cc_final: 0.8185 (ttm-80) REVERT: k 36 LEU cc_start: 0.8091 (tp) cc_final: 0.7840 (pp) REVERT: k 38 LEU cc_start: 0.4130 (OUTLIER) cc_final: 0.3914 (mt) outliers start: 226 outliers final: 180 residues processed: 959 average time/residue: 0.9027 time to fit residues: 1489.5241 Evaluate side-chains 1011 residues out of total 2908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 204 poor density : 807 time to evaluate : 4.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 38 SER Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 178 SER Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 194 GLU Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 74 GLU Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain D residue 116 LYS Chi-restraints excluded: chain D residue 139 SER Chi-restraints excluded: chain D residue 156 PHE Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain E residue 130 LYS Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain E residue 168 ASP Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain F residue 6 ASP Chi-restraints excluded: chain F residue 20 PHE Chi-restraints excluded: chain F residue 21 ASN Chi-restraints excluded: chain F residue 23 ASN Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 87 CYS Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 127 ASN Chi-restraints excluded: chain F residue 132 VAL Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain F residue 157 THR Chi-restraints excluded: chain G residue 51 THR Chi-restraints excluded: chain G residue 56 ASP Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain G residue 140 VAL Chi-restraints excluded: chain H residue 9 VAL Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 89 LYS Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 144 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 147 VAL Chi-restraints excluded: chain I residue 123 ILE Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 55 ILE Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 61 VAL Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain J residue 94 ASN Chi-restraints excluded: chain J residue 101 ILE Chi-restraints excluded: chain J residue 122 ILE Chi-restraints excluded: chain K residue 34 ARG Chi-restraints excluded: chain K residue 36 LEU Chi-restraints excluded: chain K residue 86 GLN Chi-restraints excluded: chain K residue 106 LYS Chi-restraints excluded: chain K residue 131 ASN Chi-restraints excluded: chain L residue 21 CYS Chi-restraints excluded: chain L residue 25 LEU Chi-restraints excluded: chain L residue 38 ILE Chi-restraints excluded: chain L residue 52 VAL Chi-restraints excluded: chain L residue 61 VAL Chi-restraints excluded: chain L residue 62 VAL Chi-restraints excluded: chain L residue 65 THR Chi-restraints excluded: chain L residue 104 THR Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 25 SER Chi-restraints excluded: chain M residue 67 THR Chi-restraints excluded: chain M residue 104 GLN Chi-restraints excluded: chain M residue 121 THR Chi-restraints excluded: chain M residue 122 VAL Chi-restraints excluded: chain N residue 7 THR Chi-restraints excluded: chain N residue 24 THR Chi-restraints excluded: chain N residue 73 ILE Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain N residue 78 LEU Chi-restraints excluded: chain N residue 102 LEU Chi-restraints excluded: chain N residue 105 MET Chi-restraints excluded: chain N residue 108 VAL Chi-restraints excluded: chain N residue 112 LEU Chi-restraints excluded: chain N residue 132 THR Chi-restraints excluded: chain N residue 134 THR Chi-restraints excluded: chain N residue 136 MET Chi-restraints excluded: chain O residue 13 ASN Chi-restraints excluded: chain O residue 14 SER Chi-restraints excluded: chain O residue 20 MET Chi-restraints excluded: chain O residue 27 SER Chi-restraints excluded: chain O residue 37 THR Chi-restraints excluded: chain O residue 48 VAL Chi-restraints excluded: chain P residue 40 ILE Chi-restraints excluded: chain P residue 43 ASN Chi-restraints excluded: chain P residue 53 THR Chi-restraints excluded: chain P residue 55 GLU Chi-restraints excluded: chain P residue 69 ASP Chi-restraints excluded: chain P residue 87 ILE Chi-restraints excluded: chain Q residue 9 GLU Chi-restraints excluded: chain Q residue 12 GLN Chi-restraints excluded: chain Q residue 46 VAL Chi-restraints excluded: chain Q residue 48 ILE Chi-restraints excluded: chain Q residue 66 ASN Chi-restraints excluded: chain Q residue 76 THR Chi-restraints excluded: chain Q residue 115 ASN Chi-restraints excluded: chain R residue 18 LEU Chi-restraints excluded: chain R residue 39 VAL Chi-restraints excluded: chain R residue 40 ILE Chi-restraints excluded: chain R residue 60 LEU Chi-restraints excluded: chain R residue 75 SER Chi-restraints excluded: chain R residue 87 SER Chi-restraints excluded: chain R residue 91 ASP Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain R residue 109 LEU Chi-restraints excluded: chain S residue 19 THR Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain S residue 85 LYS Chi-restraints excluded: chain S residue 99 THR Chi-restraints excluded: chain T residue 36 LEU Chi-restraints excluded: chain T residue 39 THR Chi-restraints excluded: chain T residue 45 VAL Chi-restraints excluded: chain T residue 50 VAL Chi-restraints excluded: chain T residue 72 THR Chi-restraints excluded: chain T residue 81 SER Chi-restraints excluded: chain U residue 17 SER Chi-restraints excluded: chain U residue 39 THR Chi-restraints excluded: chain U residue 73 ARG Chi-restraints excluded: chain V residue 12 ILE Chi-restraints excluded: chain V residue 33 LYS Chi-restraints excluded: chain V residue 52 LEU Chi-restraints excluded: chain V residue 67 VAL Chi-restraints excluded: chain V residue 68 SER Chi-restraints excluded: chain V residue 77 THR Chi-restraints excluded: chain V residue 102 THR Chi-restraints excluded: chain V residue 103 ILE Chi-restraints excluded: chain W residue 9 ARG Chi-restraints excluded: chain W residue 20 LEU Chi-restraints excluded: chain W residue 24 ASN Chi-restraints excluded: chain W residue 58 SER Chi-restraints excluded: chain W residue 61 LEU Chi-restraints excluded: chain W residue 65 VAL Chi-restraints excluded: chain W residue 66 ASP Chi-restraints excluded: chain W residue 71 LYS Chi-restraints excluded: chain W residue 92 VAL Chi-restraints excluded: chain X residue 12 ASN Chi-restraints excluded: chain X residue 50 ASN Chi-restraints excluded: chain X residue 58 THR Chi-restraints excluded: chain X residue 76 ASN Chi-restraints excluded: chain X residue 77 ARG Chi-restraints excluded: chain X residue 80 ILE Chi-restraints excluded: chain X residue 81 SER Chi-restraints excluded: chain Y residue 5 CYS Chi-restraints excluded: chain Y residue 22 LEU Chi-restraints excluded: chain Y residue 28 ARG Chi-restraints excluded: chain Y residue 35 SER Chi-restraints excluded: chain Y residue 42 SER Chi-restraints excluded: chain Y residue 56 MET Chi-restraints excluded: chain Y residue 68 LEU Chi-restraints excluded: chain Z residue 15 ASN Chi-restraints excluded: chain Z residue 19 LEU Chi-restraints excluded: chain a residue 30 ARG Chi-restraints excluded: chain a residue 32 ILE Chi-restraints excluded: chain a residue 52 SER Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain b residue 13 ARG Chi-restraints excluded: chain b residue 25 VAL Chi-restraints excluded: chain b residue 28 LEU Chi-restraints excluded: chain b residue 36 GLU Chi-restraints excluded: chain b residue 46 ASP Chi-restraints excluded: chain b residue 55 ILE 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 8 SER Chi-restraints excluded: chain d residue 24 THR Chi-restraints excluded: chain d residue 43 THR Chi-restraints excluded: chain d residue 44 VAL Chi-restraints excluded: chain i residue 331 LEU Chi-restraints excluded: chain i residue 342 LYS Chi-restraints excluded: chain k residue 38 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 640 random chunks: chunk 597 optimal weight: 10.0000 chunk 69 optimal weight: 10.0000 chunk 352 optimal weight: 20.0000 chunk 452 optimal weight: 9.9990 chunk 350 optimal weight: 6.9990 chunk 521 optimal weight: 6.9990 chunk 345 optimal weight: 9.9990 chunk 616 optimal weight: 3.9990 chunk 386 optimal weight: 7.9990 chunk 376 optimal weight: 7.9990 chunk 284 optimal weight: 10.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 115 GLN E 195 GLN F 37 ASN ** G 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 66 ASN R 37 GLN ** V 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 12 ASN Z 58 ASN ** b 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8762 moved from start: 0.3954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.091 101812 Z= 0.355 Angle : 0.652 10.844 152558 Z= 0.335 Chirality : 0.037 0.266 19559 Planarity : 0.005 0.067 7978 Dihedral : 23.345 178.419 51612 Min Nonbonded Distance : 0.988 Molprobity Statistics. All-atom Clashscore : 15.39 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.25 % Favored : 95.69 % Rotamer: Outliers : 8.20 % Allowed : 25.92 % Favored : 65.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.14), residues: 3529 helix: 0.46 (0.16), residues: 1079 sheet: -0.78 (0.18), residues: 765 loop : -0.72 (0.14), residues: 1685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP N 64 HIS 0.006 0.001 HIS D 140 PHE 0.026 0.002 PHE H 46 TYR 0.019 0.002 TYR W 82 ARG 0.009 0.001 ARG Z 48 *********************** 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 1059 residues out of total 2908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 238 poor density : 821 time to evaluate : 4.094 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: C 20 VAL cc_start: 0.9353 (OUTLIER) cc_final: 0.9039 (p) REVERT: C 72 ASP cc_start: 0.8787 (m-30) cc_final: 0.8528 (t0) REVERT: C 121 ASP cc_start: 0.8309 (p0) cc_final: 0.7985 (p0) REVERT: C 225 MET cc_start: 0.9170 (mtt) cc_final: 0.8749 (mtt) REVERT: D 39 ASP cc_start: 0.8713 (p0) cc_final: 0.8326 (p0) REVERT: D 116 LYS cc_start: 0.9388 (OUTLIER) cc_final: 0.9136 (mttm) REVERT: E 46 GLN cc_start: 0.9377 (mp10) cc_final: 0.9092 (mp10) REVERT: E 49 ARG cc_start: 0.9215 (OUTLIER) cc_final: 0.7035 (ptm160) REVERT: E 149 ILE cc_start: 0.9474 (mp) cc_final: 0.8893 (mp) REVERT: E 156 ASN cc_start: 0.8899 (m-40) cc_final: 0.8427 (m-40) REVERT: E 188 MET cc_start: 0.9510 (mmm) cc_final: 0.9266 (mmm) REVERT: F 26 MET cc_start: 0.9404 (mmp) cc_final: 0.9046 (mmm) REVERT: F 32 GLU cc_start: 0.8605 (tp30) cc_final: 0.8188 (tp30) REVERT: F 35 THR cc_start: 0.9335 (m) cc_final: 0.9003 (p) REVERT: F 90 THR cc_start: 0.9042 (OUTLIER) cc_final: 0.8557 (p) REVERT: F 96 MET cc_start: 0.8901 (ttp) cc_final: 0.8462 (tmm) REVERT: G 69 ARG cc_start: 0.8974 (tmt170) cc_final: 0.8435 (tpt90) REVERT: G 121 ILE cc_start: 0.8719 (mm) cc_final: 0.8471 (mm) REVERT: G 137 ASP cc_start: 0.8629 (t70) cc_final: 0.8388 (t70) REVERT: G 155 GLU cc_start: 0.7962 (pp20) cc_final: 0.7013 (pp20) REVERT: H 4 ILE cc_start: 0.9179 (tp) cc_final: 0.8906 (tp) REVERT: H 9 VAL cc_start: 0.9145 (OUTLIER) cc_final: 0.8768 (m) REVERT: H 35 LYS cc_start: 0.9151 (mtpp) cc_final: 0.8930 (mmtm) REVERT: H 47 PHE cc_start: 0.7658 (t80) cc_final: 0.7409 (t80) REVERT: H 50 ARG cc_start: 0.7808 (mtt180) cc_final: 0.7522 (mtt-85) REVERT: H 68 ARG cc_start: 0.6386 (mtp85) cc_final: 0.5869 (mtp-110) REVERT: H 83 LYS cc_start: 0.7397 (mmtp) cc_final: 0.6181 (tttt) REVERT: I 116 GLU cc_start: 0.5797 (mt-10) cc_final: 0.5257 (mm-30) REVERT: I 123 ILE cc_start: 0.5725 (OUTLIER) cc_final: 0.5252 (mm) REVERT: J 59 ILE cc_start: 0.4242 (mp) cc_final: 0.4033 (mm) REVERT: K 19 ASP cc_start: 0.7770 (t0) cc_final: 0.7431 (t0) REVERT: K 34 ARG cc_start: 0.8603 (OUTLIER) cc_final: 0.8226 (ttp-110) REVERT: K 71 ASP cc_start: 0.8777 (m-30) cc_final: 0.8263 (t0) REVERT: K 78 THR cc_start: 0.9184 (p) cc_final: 0.8840 (t) REVERT: K 91 GLU cc_start: 0.8193 (tp30) cc_final: 0.7799 (tp30) REVERT: K 108 MET cc_start: 0.9170 (mtt) cc_final: 0.8867 (mtt) REVERT: L 88 ASN cc_start: 0.8810 (t0) cc_final: 0.8199 (t0) REVERT: L 92 GLU cc_start: 0.7837 (mm-30) cc_final: 0.7562 (mm-30) REVERT: L 100 PHE cc_start: 0.8668 (m-80) cc_final: 0.7957 (m-80) REVERT: M 54 GLN cc_start: 0.8468 (tt0) cc_final: 0.8027 (tt0) REVERT: M 67 THR cc_start: 0.9117 (OUTLIER) cc_final: 0.8904 (p) REVERT: M 80 SER cc_start: 0.9373 (p) cc_final: 0.8911 (t) REVERT: M 104 GLN cc_start: 0.8463 (OUTLIER) cc_final: 0.7828 (mt0) REVERT: M 142 ILE cc_start: 0.8961 (mt) cc_final: 0.8736 (tt) REVERT: N 9 PHE cc_start: 0.9236 (m-80) cc_final: 0.8713 (m-80) REVERT: N 30 SER cc_start: 0.9547 (m) cc_final: 0.8916 (p) REVERT: N 45 GLN cc_start: 0.8566 (OUTLIER) cc_final: 0.7777 (mp10) REVERT: O 27 SER cc_start: 0.9691 (OUTLIER) cc_final: 0.9283 (t) REVERT: O 94 TYR cc_start: 0.8887 (m-80) cc_final: 0.8479 (m-80) REVERT: P 2 ASP cc_start: 0.7760 (OUTLIER) cc_final: 0.7452 (m-30) REVERT: Q 21 ARG cc_start: 0.8639 (OUTLIER) cc_final: 0.8203 (ptm160) REVERT: Q 25 THR cc_start: 0.9308 (m) cc_final: 0.8731 (p) REVERT: Q 112 GLU cc_start: 0.8379 (tt0) cc_final: 0.7902 (pm20) REVERT: U 7 LEU cc_start: 0.9160 (mt) cc_final: 0.8886 (mt) REVERT: U 28 ASN cc_start: 0.9040 (t0) cc_final: 0.8589 (t0) REVERT: U 72 GLN cc_start: 0.8946 (mp10) cc_final: 0.8511 (mp10) REVERT: U 73 ARG cc_start: 0.7646 (OUTLIER) cc_final: 0.7221 (mtt-85) REVERT: V 33 LYS cc_start: 0.9349 (OUTLIER) cc_final: 0.8820 (mtmm) REVERT: V 52 LEU cc_start: 0.8415 (OUTLIER) cc_final: 0.7916 (tp) REVERT: V 54 GLN cc_start: 0.7680 (pm20) cc_final: 0.7426 (pm20) REVERT: V 66 GLN cc_start: 0.8942 (mm-40) cc_final: 0.8539 (mt0) REVERT: W 7 GLU cc_start: 0.8160 (pm20) cc_final: 0.7500 (pm20) REVERT: W 9 ARG cc_start: 0.8829 (OUTLIER) cc_final: 0.8443 (ttm170) REVERT: W 17 SER cc_start: 0.9352 (m) cc_final: 0.8819 (p) REVERT: W 24 ASN cc_start: 0.8902 (OUTLIER) cc_final: 0.8211 (t0) REVERT: W 41 GLU cc_start: 0.8470 (pp20) cc_final: 0.7614 (pp20) REVERT: W 55 GLU cc_start: 0.8760 (mp0) cc_final: 0.8253 (mp0) REVERT: W 59 GLU cc_start: 0.8835 (mt-10) cc_final: 0.8447 (mp0) REVERT: W 76 ASP cc_start: 0.9022 (t0) cc_final: 0.8718 (t0) REVERT: W 87 GLN cc_start: 0.8898 (mm110) cc_final: 0.8318 (mt0) REVERT: X 29 GLU cc_start: 0.8284 (pt0) cc_final: 0.8043 (pp20) REVERT: X 58 THR cc_start: 0.9471 (OUTLIER) cc_final: 0.9236 (m) REVERT: X 77 ARG cc_start: 0.8403 (OUTLIER) cc_final: 0.7136 (mtp180) REVERT: Y 28 ARG cc_start: 0.9529 (OUTLIER) cc_final: 0.9083 (ptm160) REVERT: Y 40 VAL cc_start: 0.9116 (t) cc_final: 0.8868 (p) REVERT: Y 48 THR cc_start: 0.9352 (m) cc_final: 0.9089 (p) REVERT: Z 13 GLU cc_start: 0.8829 (mt-10) cc_final: 0.8502 (mp0) REVERT: Z 17 GLU cc_start: 0.8399 (tp30) cc_final: 0.8081 (tp30) REVERT: Z 36 GLN cc_start: 0.8830 (mm-40) cc_final: 0.8141 (mp10) REVERT: a 58 GLU cc_start: 0.8578 (mp0) cc_final: 0.8132 (mp0) REVERT: b 13 ARG cc_start: 0.8912 (OUTLIER) cc_final: 0.8026 (ttm-80) REVERT: b 52 ARG cc_start: 0.8333 (mtp180) cc_final: 0.8010 (ttt180) REVERT: c 32 GLU cc_start: 0.8513 (pm20) cc_final: 0.8178 (pm20) REVERT: c 33 LYS cc_start: 0.7793 (mmtp) cc_final: 0.6940 (mmtm) REVERT: c 51 GLU cc_start: 0.8699 (tt0) cc_final: 0.7874 (pt0) REVERT: i 341 MET cc_start: 0.6175 (mtp) cc_final: 0.4695 (tpt) REVERT: i 383 MET cc_start: 0.8672 (mtt) cc_final: 0.7904 (ttm) REVERT: i 385 MET cc_start: 0.7981 (mmm) cc_final: 0.7041 (mtt) REVERT: i 395 LYS cc_start: 0.8626 (mmtt) cc_final: 0.8151 (mmtt) REVERT: i 398 ARG cc_start: 0.8808 (mmt90) cc_final: 0.8569 (mmt90) REVERT: i 399 LYS cc_start: 0.9008 (mttt) cc_final: 0.8526 (mttp) REVERT: i 424 GLN cc_start: 0.7498 (pp30) cc_final: 0.7282 (pp30) REVERT: i 425 ARG cc_start: 0.8584 (ttm-80) cc_final: 0.8215 (ttm-80) outliers start: 238 outliers final: 184 residues processed: 953 average time/residue: 0.9045 time to fit residues: 1478.6945 Evaluate side-chains 1001 residues out of total 2908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 206 poor density : 795 time to evaluate : 4.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 38 SER Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 178 SER Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 194 GLU Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 74 GLU Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain D residue 116 LYS Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 139 SER Chi-restraints excluded: chain E residue 49 ARG Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain E residue 73 ILE Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain E residue 130 LYS Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain E residue 168 ASP Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain F residue 6 ASP Chi-restraints excluded: chain F residue 20 PHE Chi-restraints excluded: chain F residue 21 ASN Chi-restraints excluded: chain F residue 23 ASN Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 87 CYS Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 127 ASN Chi-restraints excluded: chain F residue 132 VAL Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain F residue 157 THR Chi-restraints excluded: chain G residue 19 ILE Chi-restraints excluded: chain G residue 51 THR Chi-restraints excluded: chain G residue 56 ASP Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain H residue 9 VAL Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 89 LYS Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 144 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 147 VAL Chi-restraints excluded: chain I residue 123 ILE Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 55 ILE Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 61 VAL Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain J residue 94 ASN Chi-restraints excluded: chain J residue 101 ILE Chi-restraints excluded: chain J residue 123 GLU Chi-restraints excluded: chain J residue 125 MET Chi-restraints excluded: chain K residue 34 ARG Chi-restraints excluded: chain K residue 36 LEU Chi-restraints excluded: chain K residue 86 GLN Chi-restraints excluded: chain K residue 106 LYS Chi-restraints excluded: chain K residue 131 ASN Chi-restraints excluded: chain L residue 21 CYS Chi-restraints excluded: chain L residue 25 LEU Chi-restraints excluded: chain L residue 38 ILE Chi-restraints excluded: chain L residue 52 VAL Chi-restraints excluded: chain L residue 61 VAL Chi-restraints excluded: chain L residue 62 VAL Chi-restraints excluded: chain L residue 65 THR Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain L residue 104 THR Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 25 SER Chi-restraints excluded: chain M residue 67 THR Chi-restraints excluded: chain M residue 104 GLN Chi-restraints excluded: chain M residue 121 THR Chi-restraints excluded: chain M residue 122 VAL Chi-restraints excluded: chain N residue 7 THR Chi-restraints excluded: chain N residue 24 THR Chi-restraints excluded: chain N residue 42 THR Chi-restraints excluded: chain N residue 45 GLN Chi-restraints excluded: chain N residue 73 ILE Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain N residue 78 LEU Chi-restraints excluded: chain N residue 102 LEU Chi-restraints excluded: chain N residue 105 MET Chi-restraints excluded: chain N residue 108 VAL Chi-restraints excluded: chain N residue 112 LEU Chi-restraints excluded: chain N residue 132 THR Chi-restraints excluded: chain N residue 134 THR Chi-restraints excluded: chain N residue 136 MET Chi-restraints excluded: chain O residue 13 ASN Chi-restraints excluded: chain O residue 14 SER Chi-restraints excluded: chain O residue 27 SER Chi-restraints excluded: chain O residue 29 VAL Chi-restraints excluded: chain O residue 37 THR Chi-restraints excluded: chain P residue 2 ASP Chi-restraints excluded: chain P residue 40 ILE Chi-restraints excluded: chain P residue 43 ASN Chi-restraints excluded: chain P residue 53 THR Chi-restraints excluded: chain P residue 55 GLU Chi-restraints excluded: chain P residue 69 ASP Chi-restraints excluded: chain P residue 87 ILE Chi-restraints excluded: chain Q residue 12 GLN Chi-restraints excluded: chain Q residue 21 ARG Chi-restraints excluded: chain Q residue 46 VAL Chi-restraints excluded: chain Q residue 48 ILE Chi-restraints excluded: chain Q residue 66 ASN Chi-restraints excluded: chain Q residue 76 THR Chi-restraints excluded: chain Q residue 115 ASN Chi-restraints excluded: chain R residue 18 LEU Chi-restraints excluded: chain R residue 39 VAL Chi-restraints excluded: chain R residue 40 ILE Chi-restraints excluded: chain R residue 60 LEU Chi-restraints excluded: chain R residue 75 SER Chi-restraints excluded: chain R residue 87 SER Chi-restraints excluded: chain R residue 90 ILE Chi-restraints excluded: chain R residue 91 ASP Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain R residue 109 LEU Chi-restraints excluded: chain R residue 110 VAL Chi-restraints excluded: chain S residue 19 THR Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain S residue 85 LYS Chi-restraints excluded: chain T residue 36 LEU Chi-restraints excluded: chain T residue 39 THR Chi-restraints excluded: chain T residue 45 VAL Chi-restraints excluded: chain T residue 50 VAL Chi-restraints excluded: chain T residue 72 THR Chi-restraints excluded: chain T residue 81 SER Chi-restraints excluded: chain U residue 17 SER Chi-restraints excluded: chain U residue 39 THR Chi-restraints excluded: chain U residue 73 ARG Chi-restraints excluded: chain V residue 12 ILE Chi-restraints excluded: chain V residue 33 LYS Chi-restraints excluded: chain V residue 52 LEU Chi-restraints excluded: chain V residue 67 VAL Chi-restraints excluded: chain V residue 68 SER Chi-restraints excluded: chain V residue 77 THR Chi-restraints excluded: chain V residue 102 THR Chi-restraints excluded: chain V residue 103 ILE Chi-restraints excluded: chain W residue 9 ARG Chi-restraints excluded: chain W residue 24 ASN Chi-restraints excluded: chain W residue 61 LEU Chi-restraints excluded: chain W residue 65 VAL Chi-restraints excluded: chain W residue 66 ASP Chi-restraints excluded: chain W residue 71 LYS Chi-restraints excluded: chain W residue 92 VAL Chi-restraints excluded: chain X residue 12 ASN Chi-restraints excluded: chain X residue 50 ASN Chi-restraints excluded: chain X residue 58 THR Chi-restraints excluded: chain X residue 76 ASN Chi-restraints excluded: chain X residue 77 ARG Chi-restraints excluded: chain X residue 80 ILE Chi-restraints excluded: chain X residue 81 SER Chi-restraints excluded: chain Y residue 5 CYS Chi-restraints excluded: chain Y residue 22 LEU Chi-restraints excluded: chain Y residue 28 ARG Chi-restraints excluded: chain Y residue 35 SER Chi-restraints excluded: chain Y residue 42 SER Chi-restraints excluded: chain Y residue 56 MET Chi-restraints excluded: chain Y residue 68 LEU Chi-restraints excluded: chain Y residue 77 LYS Chi-restraints excluded: chain Z residue 15 ASN Chi-restraints excluded: chain Z residue 19 LEU Chi-restraints excluded: chain Z residue 58 ASN Chi-restraints excluded: chain a residue 17 LEU Chi-restraints excluded: chain a residue 32 ILE Chi-restraints excluded: chain a residue 52 SER Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain b residue 13 ARG Chi-restraints excluded: chain b residue 25 VAL Chi-restraints excluded: chain b residue 28 LEU Chi-restraints excluded: chain b residue 36 GLU Chi-restraints excluded: chain b residue 46 ASP Chi-restraints excluded: chain b residue 55 ILE Chi-restraints excluded: chain c residue 24 THR Chi-restraints excluded: chain c residue 46 HIS Chi-restraints excluded: chain c residue 48 ILE Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 4 THR Chi-restraints excluded: chain d residue 8 SER Chi-restraints excluded: chain d residue 24 THR Chi-restraints excluded: chain d residue 43 THR Chi-restraints excluded: chain d residue 44 VAL Chi-restraints excluded: chain i residue 331 LEU Chi-restraints excluded: chain i residue 342 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 640 random chunks: chunk 381 optimal weight: 10.0000 chunk 246 optimal weight: 10.0000 chunk 368 optimal weight: 8.9990 chunk 185 optimal weight: 10.0000 chunk 121 optimal weight: 10.0000 chunk 119 optimal weight: 10.0000 chunk 392 optimal weight: 7.9990 chunk 420 optimal weight: 1.9990 chunk 304 optimal weight: 8.9990 chunk 57 optimal weight: 10.0000 chunk 484 optimal weight: 10.0000 overall best weight: 7.5992 ------------------------------------------------------------------------------- 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 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 115 GLN ** G 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 128 GLN ** N 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 107 ASN R 37 GLN ** V 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8768 moved from start: 0.4095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 101812 Z= 0.393 Angle : 0.685 13.605 152558 Z= 0.350 Chirality : 0.039 0.277 19559 Planarity : 0.005 0.082 7978 Dihedral : 23.368 178.595 51611 Min Nonbonded Distance : 0.970 Molprobity Statistics. All-atom Clashscore : 16.62 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.53 % Favored : 95.35 % Rotamer: Outliers : 8.20 % Allowed : 26.58 % Favored : 65.22 % 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: -0.77 (0.14), residues: 3529 helix: 0.41 (0.16), residues: 1071 sheet: -0.88 (0.18), residues: 793 loop : -0.84 (0.14), residues: 1665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP N 64 HIS 0.006 0.001 HIS Q 77 PHE 0.024 0.002 PHE E 158 TYR 0.021 0.002 TYR W 82 ARG 0.008 0.001 ARG X 11 *********************** 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 1045 residues out of total 2908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 238 poor density : 807 time to evaluate : 4.272 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 20 VAL cc_start: 0.9371 (OUTLIER) cc_final: 0.9064 (p) REVERT: C 72 ASP cc_start: 0.8813 (m-30) cc_final: 0.8532 (t0) REVERT: C 121 ASP cc_start: 0.8400 (p0) cc_final: 0.8082 (p0) REVERT: C 225 MET cc_start: 0.9167 (mtt) cc_final: 0.8770 (mtt) REVERT: D 39 ASP cc_start: 0.8716 (p0) cc_final: 0.8340 (p0) REVERT: D 116 LYS cc_start: 0.9399 (OUTLIER) cc_final: 0.9144 (mttm) REVERT: E 49 ARG cc_start: 0.9233 (OUTLIER) cc_final: 0.7083 (ptm160) REVERT: E 80 SER cc_start: 0.9393 (OUTLIER) cc_final: 0.9183 (p) REVERT: E 123 LYS cc_start: 0.9013 (mmmm) cc_final: 0.8512 (ptmm) REVERT: E 149 ILE cc_start: 0.9490 (mp) cc_final: 0.8906 (mp) REVERT: E 156 ASN cc_start: 0.8907 (m-40) cc_final: 0.8445 (m-40) REVERT: E 188 MET cc_start: 0.9518 (mmm) cc_final: 0.9285 (mmm) REVERT: F 32 GLU cc_start: 0.8565 (tp30) cc_final: 0.8189 (tp30) REVERT: F 35 THR cc_start: 0.9290 (m) cc_final: 0.8945 (p) REVERT: F 44 ILE cc_start: 0.8678 (OUTLIER) cc_final: 0.7963 (tt) REVERT: F 90 THR cc_start: 0.9033 (OUTLIER) cc_final: 0.8547 (p) REVERT: F 96 MET cc_start: 0.8901 (ttp) cc_final: 0.8438 (tmm) REVERT: G 69 ARG cc_start: 0.8982 (tmt170) cc_final: 0.8733 (tpt90) REVERT: G 121 ILE cc_start: 0.8699 (mm) cc_final: 0.8450 (mm) REVERT: G 137 ASP cc_start: 0.8651 (t70) cc_final: 0.8410 (t70) REVERT: G 155 GLU cc_start: 0.7882 (pp20) cc_final: 0.6910 (pp20) REVERT: H 4 ILE cc_start: 0.9159 (tp) cc_final: 0.8921 (tp) REVERT: H 9 VAL cc_start: 0.9141 (OUTLIER) cc_final: 0.8766 (m) REVERT: H 35 LYS cc_start: 0.9146 (mtpp) cc_final: 0.8936 (mmtm) REVERT: H 47 PHE cc_start: 0.7810 (t80) cc_final: 0.7434 (t80) REVERT: H 83 LYS cc_start: 0.7554 (mmtp) cc_final: 0.6132 (pttt) REVERT: I 116 GLU cc_start: 0.5940 (mt-10) cc_final: 0.5340 (mm-30) REVERT: I 123 ILE cc_start: 0.5924 (OUTLIER) cc_final: 0.5448 (mm) REVERT: J 59 ILE cc_start: 0.4241 (mp) cc_final: 0.4029 (mm) REVERT: J 107 GLN cc_start: 0.7900 (mt0) cc_final: 0.6856 (tm-30) REVERT: J 125 MET cc_start: 0.6311 (OUTLIER) cc_final: 0.6010 (mtt) REVERT: K 19 ASP cc_start: 0.7729 (t0) cc_final: 0.7443 (t0) REVERT: K 27 ARG cc_start: 0.9089 (OUTLIER) cc_final: 0.8606 (mmm-85) REVERT: K 34 ARG cc_start: 0.8610 (OUTLIER) cc_final: 0.8253 (ttp-110) REVERT: K 71 ASP cc_start: 0.8803 (m-30) cc_final: 0.8238 (t0) REVERT: K 78 THR cc_start: 0.9259 (p) cc_final: 0.8957 (t) REVERT: K 91 GLU cc_start: 0.8211 (tp30) cc_final: 0.7774 (tp30) REVERT: K 108 MET cc_start: 0.9161 (mtt) cc_final: 0.8858 (mtt) REVERT: L 88 ASN cc_start: 0.8823 (t0) cc_final: 0.8266 (t0) REVERT: L 93 GLN cc_start: 0.9112 (mm110) cc_final: 0.8864 (mm110) REVERT: L 100 PHE cc_start: 0.8929 (m-80) cc_final: 0.8213 (m-80) REVERT: M 54 GLN cc_start: 0.8566 (tt0) cc_final: 0.8228 (tt0) REVERT: M 67 THR cc_start: 0.9121 (OUTLIER) cc_final: 0.8906 (p) REVERT: M 80 SER cc_start: 0.9384 (p) cc_final: 0.8936 (t) REVERT: M 104 GLN cc_start: 0.8395 (OUTLIER) cc_final: 0.7735 (mt0) REVERT: N 9 PHE cc_start: 0.9255 (m-80) cc_final: 0.8737 (m-80) REVERT: N 30 SER cc_start: 0.9566 (m) cc_final: 0.8866 (p) REVERT: N 45 GLN cc_start: 0.8759 (OUTLIER) cc_final: 0.8541 (mt0) REVERT: O 27 SER cc_start: 0.9691 (OUTLIER) cc_final: 0.9274 (t) REVERT: O 94 TYR cc_start: 0.8897 (m-80) cc_final: 0.8528 (m-80) REVERT: Q 21 ARG cc_start: 0.8687 (OUTLIER) cc_final: 0.8261 (ptm160) REVERT: Q 25 THR cc_start: 0.9308 (m) cc_final: 0.8726 (p) REVERT: Q 112 GLU cc_start: 0.8388 (tt0) cc_final: 0.7910 (pm20) REVERT: T 109 ASP cc_start: 0.8750 (p0) cc_final: 0.8538 (p0) REVERT: U 7 LEU cc_start: 0.9190 (mt) cc_final: 0.8903 (mt) REVERT: U 28 ASN cc_start: 0.9034 (t0) cc_final: 0.8575 (t0) REVERT: U 72 GLN cc_start: 0.8861 (mp10) cc_final: 0.8349 (mp10) REVERT: U 73 ARG cc_start: 0.7509 (OUTLIER) cc_final: 0.7079 (mtt-85) REVERT: U 91 GLN cc_start: 0.8338 (mm-40) cc_final: 0.7897 (tp40) REVERT: V 10 GLU cc_start: 0.8415 (tp30) cc_final: 0.7573 (tp30) REVERT: V 22 ARG cc_start: 0.8443 (ptm160) cc_final: 0.7832 (ttm-80) REVERT: V 33 LYS cc_start: 0.9345 (OUTLIER) cc_final: 0.8830 (mtmm) REVERT: V 52 LEU cc_start: 0.8361 (OUTLIER) cc_final: 0.7847 (tp) REVERT: V 54 GLN cc_start: 0.7703 (pm20) cc_final: 0.7421 (pm20) REVERT: V 66 GLN cc_start: 0.8958 (mm-40) cc_final: 0.8561 (mt0) REVERT: W 7 GLU cc_start: 0.8159 (pm20) cc_final: 0.7509 (pm20) REVERT: W 9 ARG cc_start: 0.8854 (OUTLIER) cc_final: 0.8373 (ttm110) REVERT: W 17 SER cc_start: 0.9366 (m) cc_final: 0.8813 (p) REVERT: W 24 ASN cc_start: 0.8868 (OUTLIER) cc_final: 0.8197 (t0) REVERT: W 41 GLU cc_start: 0.8474 (pp20) cc_final: 0.7639 (pp20) REVERT: W 55 GLU cc_start: 0.8777 (mp0) cc_final: 0.8225 (mp0) REVERT: W 59 GLU cc_start: 0.8861 (mt-10) cc_final: 0.8436 (mp0) REVERT: W 76 ASP cc_start: 0.9054 (t0) cc_final: 0.8731 (t0) REVERT: W 87 GLN cc_start: 0.8972 (mm110) cc_final: 0.8373 (mt0) REVERT: X 58 THR cc_start: 0.9484 (OUTLIER) cc_final: 0.9251 (m) REVERT: X 77 ARG cc_start: 0.8499 (OUTLIER) cc_final: 0.7275 (mtp180) REVERT: Y 28 ARG cc_start: 0.9537 (OUTLIER) cc_final: 0.9106 (ptm160) REVERT: Y 40 VAL cc_start: 0.9130 (t) cc_final: 0.8899 (p) REVERT: Y 48 THR cc_start: 0.9369 (m) cc_final: 0.9106 (p) REVERT: Z 13 GLU cc_start: 0.8795 (mt-10) cc_final: 0.8438 (mp0) REVERT: Z 17 GLU cc_start: 0.8412 (tp30) cc_final: 0.8079 (tp30) REVERT: Z 36 GLN cc_start: 0.8804 (mm-40) cc_final: 0.8164 (mp10) REVERT: Z 58 ASN cc_start: 0.8851 (OUTLIER) cc_final: 0.8612 (t0) REVERT: a 58 GLU cc_start: 0.8576 (mp0) cc_final: 0.8128 (mp0) REVERT: b 13 ARG cc_start: 0.8906 (OUTLIER) cc_final: 0.7966 (ttm-80) REVERT: b 52 ARG cc_start: 0.8319 (mtp180) cc_final: 0.8019 (ttt180) REVERT: c 32 GLU cc_start: 0.8542 (pm20) cc_final: 0.8092 (pm20) REVERT: c 33 LYS cc_start: 0.7737 (mmtp) cc_final: 0.6932 (mmtm) REVERT: c 51 GLU cc_start: 0.8591 (tt0) cc_final: 0.7707 (pt0) REVERT: i 341 MET cc_start: 0.6426 (mtp) cc_final: 0.5029 (tpt) REVERT: i 383 MET cc_start: 0.8635 (mtt) cc_final: 0.7854 (ttm) REVERT: i 385 MET cc_start: 0.7965 (mmm) cc_final: 0.7146 (mtt) REVERT: i 395 LYS cc_start: 0.8616 (mmtt) cc_final: 0.8122 (mmtt) REVERT: i 418 LYS cc_start: 0.7997 (tptp) cc_final: 0.7429 (mptt) REVERT: i 424 GLN cc_start: 0.7607 (pp30) cc_final: 0.7296 (pp30) REVERT: i 425 ARG cc_start: 0.8690 (ttm-80) cc_final: 0.8186 (ttm-80) REVERT: i 426 MET cc_start: 0.8323 (tpp) cc_final: 0.7844 (ttt) outliers start: 238 outliers final: 194 residues processed: 948 average time/residue: 0.9110 time to fit residues: 1489.3837 Evaluate side-chains 1014 residues out of total 2908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 220 poor density : 794 time to evaluate : 4.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 38 SER Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 178 SER Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 194 GLU Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 226 ASN Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 74 GLU Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain D residue 116 LYS Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 161 MET Chi-restraints excluded: chain E residue 49 ARG Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain E residue 73 ILE Chi-restraints excluded: chain E residue 80 SER Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain E residue 130 LYS Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain E residue 168 ASP Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain F residue 6 ASP Chi-restraints excluded: chain F residue 20 PHE Chi-restraints excluded: chain F residue 21 ASN Chi-restraints excluded: chain F residue 23 ASN Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 127 ASN Chi-restraints excluded: chain F residue 132 VAL Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain F residue 157 THR Chi-restraints excluded: chain G residue 19 ILE Chi-restraints excluded: chain G residue 51 THR Chi-restraints excluded: chain G residue 56 ASP Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain G residue 140 VAL Chi-restraints excluded: chain H residue 9 VAL Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 89 LYS Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 147 VAL Chi-restraints excluded: chain I residue 123 ILE Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 55 ILE Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 61 VAL Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain J residue 94 ASN Chi-restraints excluded: chain J residue 101 ILE Chi-restraints excluded: chain J residue 123 GLU Chi-restraints excluded: chain J residue 125 MET Chi-restraints excluded: chain J residue 126 THR Chi-restraints excluded: chain K residue 27 ARG Chi-restraints excluded: chain K residue 34 ARG Chi-restraints excluded: chain K residue 36 LEU Chi-restraints excluded: chain K residue 86 GLN Chi-restraints excluded: chain K residue 106 LYS Chi-restraints excluded: chain K residue 131 ASN Chi-restraints excluded: chain L residue 21 CYS Chi-restraints excluded: chain L residue 25 LEU Chi-restraints excluded: chain L residue 38 ILE Chi-restraints excluded: chain L residue 52 VAL Chi-restraints excluded: chain L residue 61 VAL Chi-restraints excluded: chain L residue 62 VAL Chi-restraints excluded: chain L residue 65 THR Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain L residue 73 ASP Chi-restraints excluded: chain L residue 104 THR Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 25 SER Chi-restraints excluded: chain M residue 67 THR Chi-restraints excluded: chain M residue 104 GLN Chi-restraints excluded: chain M residue 121 THR Chi-restraints excluded: chain M residue 122 VAL Chi-restraints excluded: chain N residue 7 THR Chi-restraints excluded: chain N residue 24 THR Chi-restraints excluded: chain N residue 42 THR Chi-restraints excluded: chain N residue 45 GLN Chi-restraints excluded: chain N residue 73 ILE Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain N residue 78 LEU Chi-restraints excluded: chain N residue 102 LEU Chi-restraints excluded: chain N residue 105 MET Chi-restraints excluded: chain N residue 108 VAL Chi-restraints excluded: chain N residue 112 LEU Chi-restraints excluded: chain N residue 132 THR Chi-restraints excluded: chain N residue 134 THR Chi-restraints excluded: chain O residue 13 ASN Chi-restraints excluded: chain O residue 14 SER Chi-restraints excluded: chain O residue 27 SER Chi-restraints excluded: chain O residue 29 VAL Chi-restraints excluded: chain O residue 37 THR Chi-restraints excluded: chain O residue 48 VAL Chi-restraints excluded: chain O residue 57 THR Chi-restraints excluded: chain P residue 40 ILE Chi-restraints excluded: chain P residue 43 ASN Chi-restraints excluded: chain P residue 53 THR Chi-restraints excluded: chain P residue 55 GLU Chi-restraints excluded: chain P residue 69 ASP Chi-restraints excluded: chain P residue 74 VAL Chi-restraints excluded: chain P residue 87 ILE Chi-restraints excluded: chain Q residue 12 GLN Chi-restraints excluded: chain Q residue 21 ARG Chi-restraints excluded: chain Q residue 46 VAL Chi-restraints excluded: chain Q residue 48 ILE Chi-restraints excluded: chain Q residue 76 THR Chi-restraints excluded: chain Q residue 115 ASN Chi-restraints excluded: chain R residue 18 LEU Chi-restraints excluded: chain R residue 39 VAL Chi-restraints excluded: chain R residue 40 ILE Chi-restraints excluded: chain R residue 60 LEU Chi-restraints excluded: chain R residue 75 SER Chi-restraints excluded: chain R residue 87 SER Chi-restraints excluded: chain R residue 90 ILE Chi-restraints excluded: chain R residue 91 ASP Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain R residue 109 LEU Chi-restraints excluded: chain R residue 110 VAL Chi-restraints excluded: chain S residue 19 THR Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain S residue 85 LYS Chi-restraints excluded: chain T residue 36 LEU Chi-restraints excluded: chain T residue 39 THR Chi-restraints excluded: chain T residue 45 VAL Chi-restraints excluded: chain T residue 50 VAL Chi-restraints excluded: chain T residue 72 THR Chi-restraints excluded: chain T residue 81 SER Chi-restraints excluded: chain U residue 10 VAL Chi-restraints excluded: chain U residue 17 SER Chi-restraints excluded: chain U residue 39 THR Chi-restraints excluded: chain U residue 73 ARG Chi-restraints excluded: chain U residue 87 LEU Chi-restraints excluded: chain V residue 12 ILE Chi-restraints excluded: chain V residue 33 LYS Chi-restraints excluded: chain V residue 52 LEU Chi-restraints excluded: chain V residue 67 VAL Chi-restraints excluded: chain V residue 68 SER Chi-restraints excluded: chain V residue 72 ILE Chi-restraints excluded: chain V residue 77 THR Chi-restraints excluded: chain V residue 102 THR Chi-restraints excluded: chain V residue 103 ILE Chi-restraints excluded: chain W residue 3 THR Chi-restraints excluded: chain W residue 9 ARG Chi-restraints excluded: chain W residue 20 LEU Chi-restraints excluded: chain W residue 24 ASN Chi-restraints excluded: chain W residue 61 LEU Chi-restraints excluded: chain W residue 65 VAL Chi-restraints excluded: chain W residue 66 ASP Chi-restraints excluded: chain W residue 71 LYS Chi-restraints excluded: chain W residue 72 VAL Chi-restraints excluded: chain W residue 92 VAL Chi-restraints excluded: chain X residue 12 ASN Chi-restraints excluded: chain X residue 50 ASN Chi-restraints excluded: chain X residue 58 THR Chi-restraints excluded: chain X residue 76 ASN Chi-restraints excluded: chain X residue 77 ARG Chi-restraints excluded: chain X residue 80 ILE Chi-restraints excluded: chain X residue 81 SER Chi-restraints excluded: chain Y residue 5 CYS Chi-restraints excluded: chain Y residue 19 SER Chi-restraints excluded: chain Y residue 22 LEU Chi-restraints excluded: chain Y residue 28 ARG Chi-restraints excluded: chain Y residue 35 SER Chi-restraints excluded: chain Y residue 42 SER Chi-restraints excluded: chain Y residue 56 MET Chi-restraints excluded: chain Y residue 68 LEU Chi-restraints excluded: chain Z residue 15 ASN Chi-restraints excluded: chain Z residue 19 LEU Chi-restraints excluded: chain Z residue 58 ASN Chi-restraints excluded: chain a residue 17 LEU Chi-restraints excluded: chain a residue 32 ILE Chi-restraints excluded: chain a residue 52 SER Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain b residue 13 ARG Chi-restraints excluded: chain b residue 25 VAL Chi-restraints excluded: chain b residue 28 LEU Chi-restraints excluded: chain b residue 36 GLU Chi-restraints excluded: chain b residue 55 ILE Chi-restraints excluded: chain c residue 24 THR Chi-restraints excluded: chain c residue 46 HIS Chi-restraints excluded: chain c residue 48 ILE Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 4 THR Chi-restraints excluded: chain d residue 8 SER Chi-restraints excluded: chain d residue 24 THR Chi-restraints excluded: chain d residue 43 THR Chi-restraints excluded: chain d residue 44 VAL Chi-restraints excluded: chain i residue 331 LEU Chi-restraints excluded: chain i residue 342 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 640 random chunks: chunk 561 optimal weight: 2.9990 chunk 590 optimal weight: 1.9990 chunk 539 optimal weight: 4.9990 chunk 574 optimal weight: 7.9990 chunk 345 optimal weight: 5.9990 chunk 250 optimal weight: 10.0000 chunk 451 optimal weight: 10.0000 chunk 176 optimal weight: 10.0000 chunk 519 optimal weight: 6.9990 chunk 543 optimal weight: 1.9990 chunk 572 optimal weight: 6.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 115 GLN ** G 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 128 GLN ** N 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 66 ASN R 37 GLN ** V 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 58 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.4289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 101812 Z= 0.210 Angle : 0.570 13.971 152558 Z= 0.296 Chirality : 0.034 0.283 19559 Planarity : 0.004 0.078 7978 Dihedral : 23.326 179.722 51611 Min Nonbonded Distance : 1.079 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.37 % Favored : 96.54 % Rotamer: Outliers : 5.93 % Allowed : 28.85 % Favored : 65.22 % 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: 0.69 (0.16), residues: 1084 sheet: -0.84 (0.18), residues: 792 loop : -0.68 (0.15), residues: 1653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 213 HIS 0.005 0.001 HIS N 13 PHE 0.028 0.002 PHE H 46 TYR 0.017 0.001 TYR F 83 ARG 0.012 0.001 ARG J 127 *********************** 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 1004 residues out of total 2908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 832 time to evaluate : 4.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 20 VAL cc_start: 0.9366 (OUTLIER) cc_final: 0.9077 (p) REVERT: C 72 ASP cc_start: 0.8791 (m-30) cc_final: 0.8503 (t0) REVERT: C 121 ASP cc_start: 0.8438 (p0) cc_final: 0.8148 (p0) REVERT: C 225 MET cc_start: 0.9140 (mtt) cc_final: 0.8928 (mtt) REVERT: C 251 GLN cc_start: 0.9428 (OUTLIER) cc_final: 0.8845 (tp40) REVERT: D 39 ASP cc_start: 0.8747 (p0) cc_final: 0.8387 (p0) REVERT: D 155 VAL cc_start: 0.9270 (t) cc_final: 0.9068 (p) REVERT: E 46 GLN cc_start: 0.9339 (mp10) cc_final: 0.9123 (mp10) REVERT: E 49 ARG cc_start: 0.9110 (OUTLIER) cc_final: 0.6948 (ptm160) REVERT: E 57 LYS cc_start: 0.9019 (tppt) cc_final: 0.8760 (ttpp) REVERT: E 123 LYS cc_start: 0.9062 (mmmm) cc_final: 0.8508 (ptmm) REVERT: E 149 ILE cc_start: 0.9431 (mp) cc_final: 0.8800 (mp) REVERT: F 26 MET cc_start: 0.9357 (mmp) cc_final: 0.9079 (mmm) REVERT: F 32 GLU cc_start: 0.8548 (tp30) cc_final: 0.8227 (tp30) REVERT: F 35 THR cc_start: 0.9305 (m) cc_final: 0.8944 (p) REVERT: F 96 MET cc_start: 0.8858 (ttp) cc_final: 0.8247 (tmm) REVERT: G 60 ASP cc_start: 0.8582 (p0) cc_final: 0.8276 (p0) REVERT: G 69 ARG cc_start: 0.8991 (tmt170) cc_final: 0.8489 (tpt90) REVERT: G 121 ILE cc_start: 0.8652 (mm) cc_final: 0.8401 (mm) REVERT: G 137 ASP cc_start: 0.8613 (t70) cc_final: 0.8372 (t70) REVERT: G 155 GLU cc_start: 0.7913 (pp20) cc_final: 0.6971 (pp20) REVERT: H 4 ILE cc_start: 0.8908 (tp) cc_final: 0.8606 (tp) REVERT: H 9 VAL cc_start: 0.9088 (OUTLIER) cc_final: 0.8725 (m) REVERT: H 35 LYS cc_start: 0.9153 (mtpp) cc_final: 0.8944 (mmtm) REVERT: H 42 LYS cc_start: 0.8722 (mppt) cc_final: 0.8418 (tmtt) REVERT: H 47 PHE cc_start: 0.7558 (t80) cc_final: 0.7292 (t80) REVERT: H 83 LYS cc_start: 0.7556 (mmtp) cc_final: 0.6132 (pttt) REVERT: I 70 GLU cc_start: 0.4825 (mp0) cc_final: 0.4076 (mp0) REVERT: I 123 ILE cc_start: 0.5569 (OUTLIER) cc_final: 0.5132 (mm) REVERT: J 107 GLN cc_start: 0.7899 (mt0) cc_final: 0.6873 (tm-30) REVERT: J 123 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.7678 (tm-30) REVERT: J 136 MET cc_start: 0.2327 (ttt) cc_final: 0.0650 (mtm) REVERT: K 19 ASP cc_start: 0.7787 (t0) cc_final: 0.7517 (t0) REVERT: K 34 ARG cc_start: 0.8486 (OUTLIER) cc_final: 0.7940 (ttm-80) REVERT: K 71 ASP cc_start: 0.8757 (m-30) cc_final: 0.8224 (t0) REVERT: K 78 THR cc_start: 0.9134 (p) cc_final: 0.8780 (t) REVERT: K 96 ARG cc_start: 0.8536 (mpp80) cc_final: 0.8263 (mpp80) REVERT: K 108 MET cc_start: 0.9060 (mtt) cc_final: 0.8804 (mtt) REVERT: L 88 ASN cc_start: 0.8788 (t0) cc_final: 0.8250 (t0) REVERT: L 93 GLN cc_start: 0.9099 (mm110) cc_final: 0.8867 (mm110) REVERT: L 100 PHE cc_start: 0.8935 (m-80) cc_final: 0.8193 (m-80) REVERT: M 67 THR cc_start: 0.9083 (m) cc_final: 0.8880 (p) REVERT: M 80 SER cc_start: 0.9234 (p) cc_final: 0.8741 (t) REVERT: M 104 GLN cc_start: 0.8470 (OUTLIER) cc_final: 0.7830 (mt0) REVERT: M 115 GLU cc_start: 0.8742 (mt-10) cc_final: 0.8337 (mp0) REVERT: N 9 PHE cc_start: 0.9200 (m-80) cc_final: 0.8522 (m-80) REVERT: N 30 SER cc_start: 0.9550 (m) cc_final: 0.8873 (p) REVERT: N 45 GLN cc_start: 0.8589 (OUTLIER) cc_final: 0.7833 (mp10) REVERT: O 27 SER cc_start: 0.9607 (OUTLIER) cc_final: 0.9291 (t) REVERT: O 94 TYR cc_start: 0.8858 (m-80) cc_final: 0.8656 (m-80) REVERT: O 97 ILE cc_start: 0.9461 (mt) cc_final: 0.9216 (mm) REVERT: P 20 GLU cc_start: 0.8324 (tt0) cc_final: 0.8052 (pt0) REVERT: Q 21 ARG cc_start: 0.8673 (OUTLIER) cc_final: 0.8198 (ptm160) REVERT: Q 25 THR cc_start: 0.9306 (m) cc_final: 0.8731 (p) REVERT: Q 112 GLU cc_start: 0.8381 (tt0) cc_final: 0.7859 (pm20) REVERT: R 102 ASP cc_start: 0.7951 (m-30) cc_final: 0.7741 (t0) REVERT: S 85 LYS cc_start: 0.9360 (OUTLIER) cc_final: 0.8900 (ptmt) REVERT: T 84 ARG cc_start: 0.8911 (mmt-90) cc_final: 0.8628 (mmt180) REVERT: U 7 LEU cc_start: 0.9169 (mt) cc_final: 0.8882 (mt) REVERT: U 28 ASN cc_start: 0.9012 (t0) cc_final: 0.8561 (t0) REVERT: V 33 LYS cc_start: 0.9307 (OUTLIER) cc_final: 0.8500 (mtpp) REVERT: V 66 GLN cc_start: 0.8926 (mm-40) cc_final: 0.8485 (mt0) REVERT: W 1 MET cc_start: 0.7356 (tpp) cc_final: 0.7041 (tpp) REVERT: W 7 GLU cc_start: 0.8141 (pm20) cc_final: 0.7600 (pm20) REVERT: W 17 SER cc_start: 0.9326 (m) cc_final: 0.8887 (p) REVERT: W 24 ASN cc_start: 0.8873 (OUTLIER) cc_final: 0.8253 (t0) REVERT: W 41 GLU cc_start: 0.8439 (pp20) cc_final: 0.7640 (pp20) REVERT: W 55 GLU cc_start: 0.8736 (mp0) cc_final: 0.8230 (mp0) REVERT: W 59 GLU cc_start: 0.8852 (mt-10) cc_final: 0.8462 (mp0) REVERT: W 63 ILE cc_start: 0.9185 (mp) cc_final: 0.8984 (mm) REVERT: W 76 ASP cc_start: 0.9024 (t0) cc_final: 0.8778 (t0) REVERT: W 87 GLN cc_start: 0.8874 (mm110) cc_final: 0.8324 (mt0) REVERT: X 56 ASP cc_start: 0.9268 (p0) cc_final: 0.9034 (p0) REVERT: X 58 THR cc_start: 0.9447 (OUTLIER) cc_final: 0.9198 (m) REVERT: X 77 ARG cc_start: 0.8579 (OUTLIER) cc_final: 0.7411 (mtp180) REVERT: Y 28 ARG cc_start: 0.9513 (OUTLIER) cc_final: 0.9047 (ptm160) REVERT: Y 40 VAL cc_start: 0.9049 (t) cc_final: 0.8794 (p) REVERT: Y 48 THR cc_start: 0.9303 (m) cc_final: 0.9049 (p) REVERT: Z 13 GLU cc_start: 0.8818 (mt-10) cc_final: 0.8486 (mp0) REVERT: Z 17 GLU cc_start: 0.8344 (tp30) cc_final: 0.8010 (tp30) REVERT: Z 36 GLN cc_start: 0.8776 (mm-40) cc_final: 0.8193 (mp10) REVERT: a 58 GLU cc_start: 0.8615 (mp0) cc_final: 0.8136 (mp0) REVERT: b 52 ARG cc_start: 0.8241 (mtp180) cc_final: 0.7985 (ttt180) REVERT: c 33 LYS cc_start: 0.7647 (mmtp) cc_final: 0.6824 (mmtm) REVERT: c 34 LEU cc_start: 0.8545 (tt) cc_final: 0.8145 (tt) REVERT: c 51 GLU cc_start: 0.8646 (tt0) cc_final: 0.7926 (pt0) REVERT: d 11 LYS cc_start: 0.9107 (mttt) cc_final: 0.8573 (tttt) REVERT: i 341 MET cc_start: 0.6486 (mtp) cc_final: 0.5126 (tpt) REVERT: i 383 MET cc_start: 0.8639 (mtt) cc_final: 0.7825 (ttm) REVERT: i 385 MET cc_start: 0.7918 (mmm) cc_final: 0.7128 (mtt) REVERT: i 395 LYS cc_start: 0.8590 (mmtt) cc_final: 0.8113 (mmtt) REVERT: i 398 ARG cc_start: 0.8456 (mmt90) cc_final: 0.7504 (mmm-85) REVERT: i 399 LYS cc_start: 0.8777 (mttt) cc_final: 0.8196 (mttp) REVERT: i 424 GLN cc_start: 0.7540 (pp30) cc_final: 0.7048 (pp30) REVERT: i 425 ARG cc_start: 0.8586 (ttm-80) cc_final: 0.8052 (ttm-80) REVERT: i 426 MET cc_start: 0.8098 (tpp) cc_final: 0.7684 (ttt) outliers start: 172 outliers final: 135 residues processed: 932 average time/residue: 0.8934 time to fit residues: 1426.8375 Evaluate side-chains 952 residues out of total 2908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 800 time to evaluate : 3.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 38 SER Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 178 SER Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 194 GLU Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 251 GLN Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 74 GLU Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain E residue 49 ARG Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain E residue 130 LYS Chi-restraints excluded: chain E residue 168 ASP Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain F residue 20 PHE Chi-restraints excluded: chain F residue 87 CYS Chi-restraints excluded: chain F residue 127 ASN Chi-restraints excluded: chain F residue 132 VAL Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain G residue 19 ILE Chi-restraints excluded: chain G residue 56 ASP Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain G residue 140 VAL Chi-restraints excluded: chain H residue 9 VAL Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 147 VAL Chi-restraints excluded: chain I residue 123 ILE Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 55 ILE Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 61 VAL Chi-restraints excluded: chain J residue 94 ASN Chi-restraints excluded: chain J residue 123 GLU Chi-restraints excluded: chain J residue 129 ILE Chi-restraints excluded: chain K residue 34 ARG Chi-restraints excluded: chain K residue 36 LEU Chi-restraints excluded: chain K residue 86 GLN Chi-restraints excluded: chain K residue 131 ASN Chi-restraints excluded: chain L residue 21 CYS Chi-restraints excluded: chain L residue 38 ILE Chi-restraints excluded: chain L residue 52 VAL Chi-restraints excluded: chain L residue 62 VAL Chi-restraints excluded: chain L residue 65 THR Chi-restraints excluded: chain L residue 73 ASP Chi-restraints excluded: chain M residue 25 SER Chi-restraints excluded: chain M residue 104 GLN Chi-restraints excluded: chain M residue 121 THR Chi-restraints excluded: chain M residue 122 VAL Chi-restraints excluded: chain N residue 7 THR Chi-restraints excluded: chain N residue 45 GLN Chi-restraints excluded: chain N residue 73 ILE Chi-restraints excluded: chain N residue 102 LEU Chi-restraints excluded: chain N residue 105 MET Chi-restraints excluded: chain N residue 108 VAL Chi-restraints excluded: chain N residue 112 LEU Chi-restraints excluded: chain N residue 134 THR Chi-restraints excluded: chain N residue 136 MET Chi-restraints excluded: chain O residue 13 ASN Chi-restraints excluded: chain O residue 27 SER Chi-restraints excluded: chain O residue 37 THR Chi-restraints excluded: chain P residue 40 ILE Chi-restraints excluded: chain P residue 43 ASN Chi-restraints excluded: chain P residue 53 THR Chi-restraints excluded: chain P residue 55 GLU Chi-restraints excluded: chain P residue 87 ILE Chi-restraints excluded: chain Q residue 12 GLN Chi-restraints excluded: chain Q residue 21 ARG Chi-restraints excluded: chain Q residue 76 THR Chi-restraints excluded: chain R residue 18 LEU Chi-restraints excluded: chain R residue 40 ILE Chi-restraints excluded: chain R residue 60 LEU Chi-restraints excluded: chain R residue 75 SER Chi-restraints excluded: chain R residue 87 SER Chi-restraints excluded: chain R residue 90 ILE Chi-restraints excluded: chain R residue 91 ASP Chi-restraints excluded: chain R residue 109 LEU Chi-restraints excluded: chain R residue 110 VAL Chi-restraints excluded: chain S residue 19 THR Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain S residue 85 LYS Chi-restraints excluded: chain T residue 45 VAL Chi-restraints excluded: chain T residue 72 THR Chi-restraints excluded: chain T residue 81 SER Chi-restraints excluded: chain U residue 39 THR Chi-restraints excluded: chain U residue 43 ILE Chi-restraints excluded: chain U residue 73 ARG Chi-restraints excluded: chain V residue 12 ILE Chi-restraints excluded: chain V residue 33 LYS Chi-restraints excluded: chain V residue 68 SER Chi-restraints excluded: chain V residue 77 THR Chi-restraints excluded: chain V residue 102 THR Chi-restraints excluded: chain V residue 103 ILE Chi-restraints excluded: chain W residue 3 THR Chi-restraints excluded: chain W residue 20 LEU Chi-restraints excluded: chain W residue 24 ASN Chi-restraints excluded: chain W residue 45 ASP Chi-restraints excluded: chain W residue 61 LEU Chi-restraints excluded: chain W residue 71 LYS Chi-restraints excluded: chain W residue 72 VAL Chi-restraints excluded: chain W residue 92 VAL Chi-restraints excluded: chain X residue 30 SER Chi-restraints excluded: chain X residue 50 ASN Chi-restraints excluded: chain X residue 58 THR Chi-restraints excluded: chain X residue 76 ASN Chi-restraints excluded: chain X residue 77 ARG Chi-restraints excluded: chain X residue 80 ILE Chi-restraints excluded: chain X residue 81 SER Chi-restraints excluded: chain Y residue 22 LEU Chi-restraints excluded: chain Y residue 28 ARG Chi-restraints excluded: chain Y residue 35 SER Chi-restraints excluded: chain Y residue 42 SER Chi-restraints excluded: chain Y residue 56 MET Chi-restraints excluded: chain Y residue 77 LYS Chi-restraints excluded: chain Z residue 19 LEU Chi-restraints excluded: chain Z residue 58 ASN Chi-restraints excluded: chain a residue 17 LEU Chi-restraints excluded: chain a residue 32 ILE Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain b residue 13 ARG Chi-restraints excluded: chain b residue 25 VAL Chi-restraints excluded: chain b residue 28 LEU Chi-restraints excluded: chain b residue 36 GLU Chi-restraints excluded: chain b residue 55 ILE Chi-restraints excluded: chain c residue 24 THR Chi-restraints excluded: chain c residue 46 HIS Chi-restraints excluded: chain c residue 48 ILE 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 d residue 44 VAL Chi-restraints excluded: chain i residue 331 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 640 random chunks: chunk 377 optimal weight: 10.0000 chunk 607 optimal weight: 1.9990 chunk 371 optimal weight: 8.9990 chunk 288 optimal weight: 10.0000 chunk 422 optimal weight: 30.0000 chunk 637 optimal weight: 10.0000 chunk 586 optimal weight: 9.9990 chunk 507 optimal weight: 9.9990 chunk 52 optimal weight: 10.0000 chunk 392 optimal weight: 4.9990 chunk 311 optimal weight: 7.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 156 ASN E 195 GLN ** G 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 128 GLN ** I 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 88 ASN ** O 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 20 GLN R 37 GLN ** V 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 12 ASN ** b 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8741 moved from start: 0.4316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 101812 Z= 0.347 Angle : 0.650 16.443 152558 Z= 0.331 Chirality : 0.037 0.284 19559 Planarity : 0.005 0.086 7978 Dihedral : 23.281 179.828 51610 Min Nonbonded Distance : 0.984 Molprobity Statistics. All-atom Clashscore : 15.42 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.19 % Favored : 95.72 % Rotamer: Outliers : 5.69 % Allowed : 29.33 % Favored : 64.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.14), residues: 3529 helix: 0.58 (0.16), residues: 1086 sheet: -0.83 (0.18), residues: 784 loop : -0.79 (0.15), residues: 1659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP N 64 HIS 0.006 0.001 HIS Q 77 PHE 0.027 0.002 PHE H 46 TYR 0.022 0.002 TYR C 83 ARG 0.008 0.001 ARG c 44 ********************** 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 965 residues out of total 2908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 800 time to evaluate : 4.156 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 20 VAL cc_start: 0.9372 (OUTLIER) cc_final: 0.9074 (p) REVERT: C 72 ASP cc_start: 0.8826 (m-30) cc_final: 0.8552 (t0) REVERT: C 121 ASP cc_start: 0.8474 (p0) cc_final: 0.8204 (p0) REVERT: C 225 MET cc_start: 0.9173 (mtt) cc_final: 0.8860 (mtt) REVERT: C 251 GLN cc_start: 0.9449 (OUTLIER) cc_final: 0.8874 (tp40) REVERT: D 39 ASP cc_start: 0.8677 (p0) cc_final: 0.8308 (p0) REVERT: E 49 ARG cc_start: 0.9163 (OUTLIER) cc_final: 0.6984 (ptm160) REVERT: E 57 LYS cc_start: 0.8959 (tppt) cc_final: 0.8720 (ttpp) REVERT: E 123 LYS cc_start: 0.9088 (mmmm) cc_final: 0.8515 (ptmm) REVERT: E 156 ASN cc_start: 0.8960 (m-40) cc_final: 0.8745 (m-40) REVERT: E 188 MET cc_start: 0.9655 (mmm) cc_final: 0.9430 (mmm) REVERT: F 26 MET cc_start: 0.9356 (mmp) cc_final: 0.8954 (mmm) REVERT: F 32 GLU cc_start: 0.8590 (tp30) cc_final: 0.8288 (tp30) REVERT: F 35 THR cc_start: 0.9309 (m) cc_final: 0.8944 (p) REVERT: F 96 MET cc_start: 0.8880 (ttp) cc_final: 0.8263 (tmm) REVERT: G 60 ASP cc_start: 0.8620 (p0) cc_final: 0.8312 (p0) REVERT: G 69 ARG cc_start: 0.9022 (tmt170) cc_final: 0.8790 (tpt90) REVERT: G 121 ILE cc_start: 0.8665 (mm) cc_final: 0.8422 (mm) REVERT: G 137 ASP cc_start: 0.8626 (t70) cc_final: 0.8366 (t0) REVERT: G 155 GLU cc_start: 0.7866 (pp20) cc_final: 0.6894 (pp20) REVERT: H 4 ILE cc_start: 0.9088 (tp) cc_final: 0.8788 (tp) REVERT: H 9 VAL cc_start: 0.9110 (OUTLIER) cc_final: 0.8736 (m) REVERT: H 35 LYS cc_start: 0.9160 (mtpp) cc_final: 0.8954 (mmtm) REVERT: H 42 LYS cc_start: 0.8762 (mppt) cc_final: 0.8430 (tmtt) REVERT: H 47 PHE cc_start: 0.7626 (t80) cc_final: 0.7338 (t80) REVERT: H 83 LYS cc_start: 0.7563 (mmtp) cc_final: 0.6132 (pttt) REVERT: I 123 ILE cc_start: 0.5721 (OUTLIER) cc_final: 0.5277 (mm) REVERT: J 36 MET cc_start: 0.4606 (mmp) cc_final: 0.4346 (mmp) REVERT: J 107 GLN cc_start: 0.7976 (mt0) cc_final: 0.6970 (tm-30) REVERT: J 136 MET cc_start: 0.2617 (ttt) cc_final: 0.1901 (tpp) REVERT: K 19 ASP cc_start: 0.7721 (t0) cc_final: 0.7436 (t0) REVERT: K 34 ARG cc_start: 0.8538 (OUTLIER) cc_final: 0.8014 (ttm-80) REVERT: K 71 ASP cc_start: 0.8794 (m-30) cc_final: 0.8211 (t0) REVERT: K 78 THR cc_start: 0.9191 (p) cc_final: 0.8861 (t) REVERT: K 96 ARG cc_start: 0.8590 (mpp80) cc_final: 0.8279 (mpp80) REVERT: K 108 MET cc_start: 0.9123 (mtt) cc_final: 0.8856 (mtt) REVERT: L 88 ASN cc_start: 0.8809 (t0) cc_final: 0.8477 (t0) REVERT: L 93 GLN cc_start: 0.9109 (mm110) cc_final: 0.8875 (mm110) REVERT: L 100 PHE cc_start: 0.8953 (m-80) cc_final: 0.8311 (m-80) REVERT: M 67 THR cc_start: 0.9115 (m) cc_final: 0.8900 (p) REVERT: M 80 SER cc_start: 0.9348 (p) cc_final: 0.8879 (t) REVERT: M 104 GLN cc_start: 0.8477 (OUTLIER) cc_final: 0.7858 (mt0) REVERT: M 115 GLU cc_start: 0.8773 (mt-10) cc_final: 0.8363 (mp0) REVERT: N 9 PHE cc_start: 0.9257 (m-80) cc_final: 0.8614 (m-80) REVERT: N 30 SER cc_start: 0.9551 (m) cc_final: 0.9019 (p) REVERT: N 45 GLN cc_start: 0.8698 (OUTLIER) cc_final: 0.7961 (mt0) REVERT: O 27 SER cc_start: 0.9709 (OUTLIER) cc_final: 0.9342 (t) REVERT: O 94 TYR cc_start: 0.8894 (m-80) cc_final: 0.8690 (m-80) REVERT: O 97 ILE cc_start: 0.9497 (mt) cc_final: 0.9253 (mm) REVERT: P 20 GLU cc_start: 0.8353 (tt0) cc_final: 0.8055 (pt0) REVERT: Q 21 ARG cc_start: 0.8645 (OUTLIER) cc_final: 0.8195 (ptm160) REVERT: Q 25 THR cc_start: 0.9296 (m) cc_final: 0.8703 (p) REVERT: Q 112 GLU cc_start: 0.8410 (tt0) cc_final: 0.7918 (pm20) REVERT: S 85 LYS cc_start: 0.9371 (OUTLIER) cc_final: 0.8916 (ptmt) REVERT: T 84 ARG cc_start: 0.8938 (mmt-90) cc_final: 0.8620 (mmt180) REVERT: U 7 LEU cc_start: 0.9195 (mt) cc_final: 0.8918 (mt) REVERT: U 28 ASN cc_start: 0.8998 (t0) cc_final: 0.8545 (t0) REVERT: V 33 LYS cc_start: 0.9373 (OUTLIER) cc_final: 0.8853 (mtmm) REVERT: V 52 LEU cc_start: 0.8276 (OUTLIER) cc_final: 0.7796 (tp) REVERT: V 54 GLN cc_start: 0.7702 (pm20) cc_final: 0.6977 (pm20) REVERT: V 66 GLN cc_start: 0.8942 (mm-40) cc_final: 0.8547 (mt0) REVERT: V 73 PHE cc_start: 0.8995 (t80) cc_final: 0.8443 (t80) REVERT: W 7 GLU cc_start: 0.8134 (pm20) cc_final: 0.7544 (pm20) REVERT: W 17 SER cc_start: 0.9380 (m) cc_final: 0.8825 (p) REVERT: W 24 ASN cc_start: 0.8885 (OUTLIER) cc_final: 0.8252 (t0) REVERT: W 41 GLU cc_start: 0.8462 (pp20) cc_final: 0.7684 (pp20) REVERT: W 55 GLU cc_start: 0.8761 (mp0) cc_final: 0.8209 (mp0) REVERT: W 59 GLU cc_start: 0.8846 (mt-10) cc_final: 0.8425 (mp0) REVERT: W 76 ASP cc_start: 0.9058 (t0) cc_final: 0.8794 (t0) REVERT: W 87 GLN cc_start: 0.8885 (mm110) cc_final: 0.8285 (mt0) REVERT: X 77 ARG cc_start: 0.8684 (OUTLIER) cc_final: 0.7662 (mtp180) REVERT: Y 28 ARG cc_start: 0.9537 (OUTLIER) cc_final: 0.9087 (ptm160) REVERT: Y 40 VAL cc_start: 0.9089 (t) cc_final: 0.8840 (p) REVERT: Y 48 THR cc_start: 0.9321 (m) cc_final: 0.9061 (p) REVERT: Z 13 GLU cc_start: 0.8833 (mt-10) cc_final: 0.8495 (mp0) REVERT: Z 17 GLU cc_start: 0.8424 (tp30) cc_final: 0.8075 (tp30) REVERT: Z 36 GLN cc_start: 0.8741 (mm-40) cc_final: 0.8145 (mp10) REVERT: Z 58 ASN cc_start: 0.8867 (OUTLIER) cc_final: 0.8604 (t0) REVERT: a 58 GLU cc_start: 0.8621 (mp0) cc_final: 0.8148 (mp0) REVERT: b 13 ARG cc_start: 0.8905 (OUTLIER) cc_final: 0.8117 (ttm-80) REVERT: b 52 ARG cc_start: 0.8306 (mtp180) cc_final: 0.8045 (ttt180) REVERT: c 33 LYS cc_start: 0.7651 (mmtp) cc_final: 0.6823 (mmtm) REVERT: c 37 LYS cc_start: 0.8962 (mtpt) cc_final: 0.8494 (ttmt) REVERT: c 51 GLU cc_start: 0.8697 (tt0) cc_final: 0.7923 (pt0) REVERT: i 341 MET cc_start: 0.6513 (mtp) cc_final: 0.5147 (tpt) REVERT: i 383 MET cc_start: 0.8640 (mtt) cc_final: 0.7852 (ttm) REVERT: i 385 MET cc_start: 0.7991 (mmm) cc_final: 0.7207 (mtt) REVERT: i 395 LYS cc_start: 0.8594 (mmtt) cc_final: 0.8011 (mmtt) REVERT: i 398 ARG cc_start: 0.8514 (mmt90) cc_final: 0.7477 (mmm-85) REVERT: i 399 LYS cc_start: 0.8857 (mttt) cc_final: 0.8270 (mttp) REVERT: i 425 ARG cc_start: 0.8627 (ttm-80) cc_final: 0.8099 (ttm-80) REVERT: i 426 MET cc_start: 0.8142 (tpp) cc_final: 0.7785 (ttt) outliers start: 165 outliers final: 136 residues processed: 898 average time/residue: 0.8941 time to fit residues: 1377.4081 Evaluate side-chains 945 residues out of total 2908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 791 time to evaluate : 4.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 38 SER Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 178 SER Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 251 GLN Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 74 GLU Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain E residue 49 ARG Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain E residue 73 ILE Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain E residue 130 LYS Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain E residue 168 ASP Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain F residue 20 PHE Chi-restraints excluded: chain F residue 127 ASN Chi-restraints excluded: chain F residue 132 VAL Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain G residue 19 ILE Chi-restraints excluded: chain G residue 51 THR Chi-restraints excluded: chain G residue 56 ASP Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain G residue 128 GLN Chi-restraints excluded: chain G residue 140 VAL Chi-restraints excluded: chain H residue 9 VAL Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 144 VAL Chi-restraints excluded: chain H residue 147 VAL Chi-restraints excluded: chain I residue 123 ILE Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 55 ILE Chi-restraints excluded: chain J residue 61 VAL Chi-restraints excluded: chain J residue 94 ASN Chi-restraints excluded: chain J residue 125 MET Chi-restraints excluded: chain K residue 34 ARG Chi-restraints excluded: chain K residue 36 LEU Chi-restraints excluded: chain K residue 86 GLN Chi-restraints excluded: chain K residue 131 ASN Chi-restraints excluded: chain L residue 21 CYS Chi-restraints excluded: chain L residue 38 ILE Chi-restraints excluded: chain L residue 52 VAL Chi-restraints excluded: chain L residue 62 VAL Chi-restraints excluded: chain L residue 65 THR Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain L residue 73 ASP Chi-restraints excluded: chain M residue 25 SER Chi-restraints excluded: chain M residue 104 GLN Chi-restraints excluded: chain M residue 121 THR Chi-restraints excluded: chain M residue 122 VAL Chi-restraints excluded: chain N residue 7 THR Chi-restraints excluded: chain N residue 45 GLN Chi-restraints excluded: chain N residue 73 ILE Chi-restraints excluded: chain N residue 102 LEU Chi-restraints excluded: chain N residue 108 VAL Chi-restraints excluded: chain N residue 112 LEU Chi-restraints excluded: chain N residue 134 THR Chi-restraints excluded: chain N residue 136 MET Chi-restraints excluded: chain O residue 13 ASN Chi-restraints excluded: chain O residue 27 SER Chi-restraints excluded: chain O residue 37 THR Chi-restraints excluded: chain P residue 40 ILE Chi-restraints excluded: chain P residue 43 ASN Chi-restraints excluded: chain P residue 53 THR Chi-restraints excluded: chain P residue 55 GLU Chi-restraints excluded: chain P residue 69 ASP Chi-restraints excluded: chain P residue 87 ILE Chi-restraints excluded: chain Q residue 12 GLN Chi-restraints excluded: chain Q residue 21 ARG Chi-restraints excluded: chain Q residue 76 THR Chi-restraints excluded: chain R residue 18 LEU Chi-restraints excluded: chain R residue 40 ILE Chi-restraints excluded: chain R residue 60 LEU Chi-restraints excluded: chain R residue 75 SER Chi-restraints excluded: chain R residue 87 SER Chi-restraints excluded: chain R residue 90 ILE Chi-restraints excluded: chain R residue 109 LEU Chi-restraints excluded: chain R residue 110 VAL Chi-restraints excluded: chain S residue 19 THR Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain S residue 85 LYS Chi-restraints excluded: chain T residue 45 VAL Chi-restraints excluded: chain T residue 72 THR Chi-restraints excluded: chain T residue 81 SER Chi-restraints excluded: chain U residue 39 THR Chi-restraints excluded: chain U residue 87 LEU Chi-restraints excluded: chain V residue 12 ILE Chi-restraints excluded: chain V residue 14 LEU Chi-restraints excluded: chain V residue 33 LYS Chi-restraints excluded: chain V residue 52 LEU Chi-restraints excluded: chain V residue 68 SER Chi-restraints excluded: chain V residue 77 THR Chi-restraints excluded: chain V residue 102 THR Chi-restraints excluded: chain V residue 103 ILE Chi-restraints excluded: chain W residue 3 THR Chi-restraints excluded: chain W residue 20 LEU Chi-restraints excluded: chain W residue 24 ASN Chi-restraints excluded: chain W residue 61 LEU Chi-restraints excluded: chain W residue 71 LYS Chi-restraints excluded: chain W residue 72 VAL Chi-restraints excluded: chain W residue 92 VAL Chi-restraints excluded: chain X residue 12 ASN Chi-restraints excluded: chain X residue 30 SER Chi-restraints excluded: chain X residue 50 ASN Chi-restraints excluded: chain X residue 76 ASN Chi-restraints excluded: chain X residue 77 ARG Chi-restraints excluded: chain X residue 80 ILE Chi-restraints excluded: chain X residue 81 SER Chi-restraints excluded: chain Y residue 22 LEU Chi-restraints excluded: chain Y residue 28 ARG Chi-restraints excluded: chain Y residue 35 SER Chi-restraints excluded: chain Y residue 42 SER Chi-restraints excluded: chain Y residue 56 MET Chi-restraints excluded: chain Y residue 77 LYS Chi-restraints excluded: chain Z residue 19 LEU Chi-restraints excluded: chain Z residue 58 ASN Chi-restraints excluded: chain a residue 17 LEU Chi-restraints excluded: chain a residue 27 LEU Chi-restraints excluded: chain a residue 32 ILE Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain b residue 13 ARG Chi-restraints excluded: chain b residue 25 VAL Chi-restraints excluded: chain b residue 28 LEU Chi-restraints excluded: chain b residue 36 GLU Chi-restraints excluded: chain b residue 55 ILE Chi-restraints excluded: chain c residue 24 THR 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 d residue 44 VAL Chi-restraints excluded: chain i residue 331 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 640 random chunks: chunk 403 optimal weight: 8.9990 chunk 540 optimal weight: 4.9990 chunk 155 optimal weight: 20.0000 chunk 468 optimal weight: 1.9990 chunk 74 optimal weight: 10.0000 chunk 141 optimal weight: 10.0000 chunk 508 optimal weight: 1.9990 chunk 212 optimal weight: 30.0000 chunk 522 optimal weight: 6.9990 chunk 64 optimal weight: 10.0000 chunk 93 optimal weight: 10.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 128 GLN I 4 ASN ** N 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 20 GLN R 37 GLN ** V 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.069531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.054708 restraints weight = 348944.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.056052 restraints weight = 132012.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.056811 restraints weight = 74270.283| |-----------------------------------------------------------------------------| r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.4379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 101812 Z= 0.273 Angle : 0.612 16.236 152558 Z= 0.315 Chirality : 0.035 0.316 19559 Planarity : 0.005 0.083 7978 Dihedral : 23.317 179.770 51606 Min Nonbonded Distance : 1.005 Molprobity Statistics. All-atom Clashscore : 15.17 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.14 % Favored : 95.78 % Rotamer: Outliers : 5.55 % Allowed : 29.33 % Favored : 65.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.14), residues: 3529 helix: 0.60 (0.16), residues: 1086 sheet: -0.83 (0.18), residues: 783 loop : -0.78 (0.15), residues: 1660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP N 64 HIS 0.005 0.001 HIS N 13 PHE 0.027 0.002 PHE E 158 TYR 0.020 0.002 TYR C 83 ARG 0.012 0.001 ARG U 73 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 22161.73 seconds wall clock time: 391 minutes 50.76 seconds (23510.76 seconds total)