Starting phenix.real_space_refine on Wed Mar 20 22:20:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5nco_3617/03_2024/5nco_3617_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5nco_3617/03_2024/5nco_3617.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5nco_3617/03_2024/5nco_3617.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5nco_3617/03_2024/5nco_3617.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5nco_3617/03_2024/5nco_3617_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5nco_3617/03_2024/5nco_3617_neut_updated.pdb" } resolution = 4.8 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= 0.014 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: 9 Type Number sf(0) Gaussians Zn 1 6.06 5 Al 2 5.89 5 P 3114 5.49 5 Mg 2 5.21 5 S 108 5.16 5 C 51412 2.51 5 N 19002 2.21 5 O 28045 1.98 5 F 8 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C GLU 23": "OE1" <-> "OE2" Residue "C GLU 35": "OE1" <-> "OE2" Residue "C ARG 52": "NH1" <-> "NH2" Residue "C ARG 63": "NH1" <-> "NH2" Residue "C ARG 80": "NH1" <-> "NH2" Residue "C TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 133": "NH1" <-> "NH2" Residue "C GLU 145": "OE1" <-> "OE2" Residue "C TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 167": "NH1" <-> "NH2" Residue "C TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 177": "NH1" <-> "NH2" Residue "C ARG 182": "NH1" <-> "NH2" Residue "C ARG 189": "NH1" <-> "NH2" Residue "C GLU 199": "OE1" <-> "OE2" Residue "C ARG 203": "NH1" <-> "NH2" Residue "C ARG 212": "NH1" <-> "NH2" Residue "D ARG 13": "NH1" <-> "NH2" Residue "D GLU 17": "OE1" <-> "OE2" Residue "D ASP 18": "OD1" <-> "OD2" Residue "D GLU 28": "OE1" <-> "OE2" Residue "D GLU 30": "OE1" <-> "OE2" Residue "D ARG 33": "NH1" <-> "NH2" Residue "D ASP 43": "OD1" <-> "OD2" Residue "D TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 59": "NH1" <-> "NH2" Residue "D GLU 64": "OE1" <-> "OE2" Residue "D ARG 77": "NH1" <-> "NH2" Residue "D GLU 81": "OE1" <-> "OE2" Residue "D ARG 83": "NH1" <-> "NH2" Residue "D GLU 168": "OE1" <-> "OE2" Residue "D ARG 169": "NH1" <-> "NH2" Residue "D GLU 183": "OE1" <-> "OE2" Residue "D ARG 184": "NH1" <-> "NH2" Residue "E ASP 7": "OD1" <-> "OD2" Residue "E ARG 21": "NH1" <-> "NH2" Residue "E GLU 25": "OE1" <-> "OE2" Residue "E ARG 44": "NH1" <-> "NH2" Residue "E ARG 49": "NH1" <-> "NH2" Residue "E ARG 61": "NH1" <-> "NH2" Residue "E PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 88": "NH1" <-> "NH2" Residue "E ARG 102": "NH1" <-> "NH2" Residue "E ASP 145": "OD1" <-> "OD2" Residue "E GLU 152": "OE1" <-> "OE2" Residue "E ARG 162": "NH1" <-> "NH2" Residue "E ARG 170": "NH1" <-> "NH2" Residue "E ASP 176": "OD1" <-> "OD2" Residue "E GLU 197": "OE1" <-> "OE2" Residue "F GLU 19": "OE1" <-> "OE2" Residue "F GLU 32": "OE1" <-> "OE2" Residue "F ARG 71": "NH1" <-> "NH2" Residue "F ARG 80": "NH1" <-> "NH2" Residue "F ARG 92": "NH1" <-> "NH2" Residue "F GLU 94": "OE1" <-> "OE2" Residue "F GLU 98": "OE1" <-> "OE2" Residue "F ARG 102": "NH1" <-> "NH2" Residue "F ARG 110": "NH1" <-> "NH2" Residue "F ARG 112": "NH1" <-> "NH2" Residue "F ARG 115": "NH1" <-> "NH2" Residue "F PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 133": "NH1" <-> "NH2" Residue "G ARG 3": "NH1" <-> "NH2" Residue "G PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 56": "OD1" <-> "OD2" Residue "G TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 124": "OE1" <-> "OE2" Residue "G ARG 153": "NH1" <-> "NH2" Residue "G TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 163": "NH1" <-> "NH2" Residue "G ASP 166": "OD1" <-> "OD2" Residue "G ARG 170": "NH1" <-> "NH2" Residue "H ARG 27": "NH1" <-> "NH2" Residue "H PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 60": "OE1" <-> "OE2" Residue "H ASP 86": "OD1" <-> "OD2" Residue "H GLU 87": "OE1" <-> "OE2" Residue "H GLU 114": "OE1" <-> "OE2" Residue "H GLU 137": "OE1" <-> "OE2" Residue "H PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 87": "OE1" <-> "OE2" Residue "I PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 114": "OE1" <-> "OE2" Residue "I ASP 124": "OD1" <-> "OD2" Residue "J PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 13": "NH1" <-> "NH2" Residue "K TYR 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 31": "OE1" <-> "OE2" Residue "K ARG 37": "NH1" <-> "NH2" Residue "K GLU 43": "OE1" <-> "OE2" Residue "K TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 90": "OE1" <-> "OE2" Residue "K GLU 91": "OE1" <-> "OE2" Residue "K ARG 96": "NH1" <-> "NH2" Residue "K ARG 120": "NH1" <-> "NH2" Residue "L GLU 45": "OE1" <-> "OE2" Residue "L GLU 110": "OE1" <-> "OE2" Residue "L GLU 121": "OE1" <-> "OE2" Residue "M ARG 21": "NH1" <-> "NH2" Residue "M ARG 33": "NH1" <-> "NH2" Residue "M ARG 41": "NH1" <-> "NH2" Residue "M ARG 47": "NH1" <-> "NH2" Residue "M GLU 51": "OE1" <-> "OE2" Residue "M ARG 60": "NH1" <-> "NH2" Residue "M PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 76": "OE1" <-> "OE2" Residue "M ARG 78": "NH1" <-> "NH2" Residue "M ASP 91": "OD1" <-> "OD2" Residue "M GLU 106": "OE1" <-> "OE2" Residue "M ARG 126": "NH1" <-> "NH2" Residue "M GLU 144": "OE1" <-> "OE2" Residue "N ARG 10": "NH1" <-> "NH2" Residue "N ARG 18": "NH1" <-> "NH2" Residue "N PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 40": "NH1" <-> "NH2" Residue "N ARG 44": "NH1" <-> "NH2" Residue "N GLU 47": "OE1" <-> "OE2" Residue "N ARG 50": "NH1" <-> "NH2" Residue "N ARG 55": "NH1" <-> "NH2" Residue "N ARG 59": "NH1" <-> "NH2" Residue "N GLU 75": "OE1" <-> "OE2" Residue "N TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 104": "OE1" <-> "OE2" Residue "N ARG 114": "NH1" <-> "NH2" Residue "N PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 8": "NH1" <-> "NH2" Residue "O ARG 12": "NH1" <-> "NH2" Residue "O ARG 17": "NH1" <-> "NH2" Residue "O ARG 22": "NH1" <-> "NH2" Residue "O GLU 43": "OE1" <-> "OE2" Residue "O ARG 46": "NH1" <-> "NH2" Residue "O ARG 63": "NH1" <-> "NH2" Residue "O ARG 64": "NH1" <-> "NH2" Residue "O ARG 69": "NH1" <-> "NH2" Residue "O ARG 71": "NH1" <-> "NH2" Residue "O GLU 82": "OE1" <-> "OE2" Residue "O ARG 96": "NH1" <-> "NH2" Residue "O TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 114": "OE1" <-> "OE2" Residue "P ARG 10": "NH1" <-> "NH2" Residue "P ARG 16": "NH1" <-> "NH2" Residue "P GLU 20": "OE1" <-> "OE2" Residue "P ARG 25": "NH1" <-> "NH2" Residue "P ARG 81": "NH1" <-> "NH2" Residue "P ARG 94": "NH1" <-> "NH2" Residue "P TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 102": "NH1" <-> "NH2" Residue "P ARG 111": "NH1" <-> "NH2" Residue "Q PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 21": "NH1" <-> "NH2" Residue "Q ARG 39": "NH1" <-> "NH2" Residue "Q GLU 44": "OE1" <-> "OE2" Residue "Q ARG 62": "NH1" <-> "NH2" Residue "Q GLU 71": "OE1" <-> "OE2" Residue "Q ASP 82": "OD1" <-> "OD2" Residue "Q ARG 89": "NH1" <-> "NH2" Residue "Q TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 101": "NH1" <-> "NH2" Residue "Q ARG 109": "NH1" <-> "NH2" Residue "R ARG 3": "NH1" <-> "NH2" Residue "R ARG 6": "NH1" <-> "NH2" Residue "R ARG 13": "NH1" <-> "NH2" Residue "R TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 33": "NH1" <-> "NH2" Residue "R TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 48": "NH1" <-> "NH2" Residue "R PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 70": "NH1" <-> "NH2" Residue "R TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 111": "OE1" <-> "OE2" Residue "S GLU 16": "OE1" <-> "OE2" Residue "S ARG 21": "NH1" <-> "NH2" Residue "S GLU 23": "OE1" <-> "OE2" Residue "S GLU 31": "OE1" <-> "OE2" Residue "S GLU 45": "OE1" <-> "OE2" Residue "S ARG 68": "NH1" <-> "NH2" Residue "S GLU 70": "OE1" <-> "OE2" Residue "S ARG 78": "NH1" <-> "NH2" Residue "S ARG 79": "NH1" <-> "NH2" Residue "S TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 84": "NH1" <-> "NH2" Residue "S PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 59": "OE1" <-> "OE2" Residue "T PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 78": "OE1" <-> "OE2" Residue "T ARG 84": "NH1" <-> "NH2" Residue "T ARG 88": "NH1" <-> "NH2" Residue "T ARG 95": "NH1" <-> "NH2" Residue "T ARG 110": "NH1" <-> "NH2" Residue "U GLU 4": "OE1" <-> "OE2" Residue "U GLU 5": "OE1" <-> "OE2" Residue "U GLU 52": "OE1" <-> "OE2" Residue "U GLU 54": "OE1" <-> "OE2" Residue "U GLU 56": "OE1" <-> "OE2" Residue "U GLU 89": "OE1" <-> "OE2" Residue "V ARG 6": "NH1" <-> "NH2" Residue "V ARG 7": "NH1" <-> "NH2" Residue "V ARG 82": "NH1" <-> "NH2" Residue "V PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 86": "NH1" <-> "NH2" Residue "V GLU 88": "OE1" <-> "OE2" Residue "V ARG 94": "NH1" <-> "NH2" Residue "V PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 11": "OE1" <-> "OE2" Residue "W PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 41": "OE1" <-> "OE2" Residue "W GLU 55": "OE1" <-> "OE2" Residue "W GLU 69": "OE1" <-> "OE2" Residue "W PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 17": "OE1" <-> "OE2" Residue "X PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 85": "OE1" <-> "OE2" Residue "Y ARG 3": "NH1" <-> "NH2" Residue "Y ARG 11": "NH1" <-> "NH2" Residue "Y ARG 18": "NH1" <-> "NH2" Residue "Y PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 37": "NH1" <-> "NH2" Residue "Y GLU 41": "OE1" <-> "OE2" Residue "Y GLU 43": "OE1" <-> "OE2" Residue "Y ARG 50": "NH1" <-> "NH2" Residue "Y ARG 57": "NH1" <-> "NH2" Residue "Y ARG 74": "NH1" <-> "NH2" Residue "Z GLU 12": "OE1" <-> "OE2" Residue "Z PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 47": "NH1" <-> "NH2" Residue "Z ARG 52": "NH1" <-> "NH2" Residue "a ARG 11": "NH1" <-> "NH2" Residue "a ARG 30": "NH1" <-> "NH2" Residue "a GLU 37": "OE1" <-> "OE2" Residue "a ARG 45": "NH1" <-> "NH2" Residue "a PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 10": "NH1" <-> "NH2" Residue "b ARG 16": "NH1" <-> "NH2" Residue "b ASP 31": "OD1" <-> "OD2" Residue "b ARG 52": "NH1" <-> "NH2" Residue "c GLU 32": "OE1" <-> "OE2" Residue "c GLU 35": "OE1" <-> "OE2" Residue "c ARG 44": "NH1" <-> "NH2" Residue "d ARG 3": "NH1" <-> "NH2" Residue "d ARG 14": "NH1" <-> "NH2" Residue "d PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 19": "NH1" <-> "NH2" Residue "d ARG 21": "NH1" <-> "NH2" Residue "d ARG 33": "NH1" <-> "NH2" Residue "e ARG 13": "NH1" <-> "NH2" Residue "e PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ARG 30": "NH1" <-> "NH2" Residue "e ARG 40": "NH1" <-> "NH2" Residue "e ARG 42": "NH1" <-> "NH2" Residue "f ARG 24": "NH1" <-> "NH2" Residue "i PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i GLU 305": "OE1" <-> "OE2" Residue "i GLU 392": "OE1" <-> "OE2" Residue "l PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l PHE 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l PHE 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 101694 Number of models: 1 Model: "" Number of chains: 43 Chain: "1" Number of atoms: 2224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 2224 Classifications: {'RNA': 104} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 2, 'rna3p_pur': 54, 'rna3p_pyr': 46} Link IDs: {'rna2p': 2, 'rna3p': 101} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "2" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 62 Classifications: {'RNA': 3} Modifications used: {'rna2p_pur': 1, 'rna3p_pyr': 2} Link IDs: {'rna3p': 2} Chain: "A" Number of atoms: 61902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2883, 61902 Classifications: {'RNA': 2883} Modifications used: {'rna2p_pur': 280, 'rna2p_pyr': 149, 'rna3p_pur': 1386, 'rna3p_pyr': 1068} Link IDs: {'rna2p': 429, 'rna3p': 2453} Chain breaks: 4 Chain: "B" Number of atoms: 2569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 2569 Classifications: {'RNA': 120} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 6, 'rna3p_pur': 57, 'rna3p_pyr': 50} Link IDs: {'rna2p': 13, 'rna3p': 106} Chain: "C" Number of atoms: 2083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2083 Classifications: {'peptide': 271} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 253} Chain: "D" Number of atoms: 1565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1565 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 202} Chain: "E" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1552 Classifications: {'peptide': 201} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 195} Chain: "F" Number of atoms: 1411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1411 Classifications: {'peptide': 177} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 170} Chain: "G" Number of atoms: 1323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1323 Classifications: {'peptide': 176} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "H" Number of atoms: 1110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1110 Classifications: {'peptide': 149} Link IDs: {'PTRANS': 3, 'TRANS': 145} Chain: "I" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 946 Classifications: {'peptide': 125} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 120} Chain: "J" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 979 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 9, 'TRANS': 124} Chain: "K" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1129 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 135} Chain: "L" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 946 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 5, 'TRANS': 117} Chain: "M" Number of atoms: 1053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1053 Classifications: {'peptide': 144} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 139} Chain: "N" Number of atoms: 1074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1074 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 128} Chain: "O" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 993 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 4, 'TRANS': 120} Chain: "P" Number of atoms: 900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 900 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 114} Chain: "Q" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 917 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "R" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 947 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'TRANS': 116} Chain: "S" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 816 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'TRANS': 101} Chain: "T" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 857 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 107} Chain: "U" Number of atoms: 756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 756 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 1, 'TRANS': 93} Chain: "V" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 780 Classifications: {'peptide': 102} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "W" Number of atoms: 753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 753 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "X" Number of atoms: 580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 580 Classifications: {'peptide': 76} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 74} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "Y" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 625 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "Z" Number of atoms: 501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 501 Classifications: {'peptide': 62} Modifications used: {'COO': 1} Link IDs: {'TRANS': 61} Chain: "a" Number of atoms: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 449 Classifications: {'peptide': 58} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "b" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 444 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 54} Chain: "c" Number of atoms: 414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 414 Classifications: {'peptide': 51} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 48} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "d" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 377 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "e" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 504 Classifications: {'peptide': 64} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "f" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 302 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "g" Number of atoms: 1664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 1664 Classifications: {'peptide': 416} Incomplete info: {'backbone_only': 376} Link IDs: {'CIS': 5, 'PTRANS': 19, 'TRANS': 391} Unresolved chain link angles: 19 Unresolved non-hydrogen bonds: 1629 Unresolved non-hydrogen angles: 2373 Unresolved non-hydrogen dihedrals: 1044 Unresolved non-hydrogen chiralities: 526 Planarities with less than four sites: {'GLN:plan1': 19, 'HIS:plan': 4, 'TYR:plan': 14, 'ASN:plan1': 9, 'TRP:plan': 4, 'ASP:plan': 6, 'PHE:plan': 31, 'GLU:plan': 13, 'ARG:plan': 20} Unresolved non-hydrogen planarities: 681 Chain: "h" Number of atoms: 224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 224 Classifications: {'peptide': 56} Incomplete info: {'backbone_only': 54} Link IDs: {'PTRANS': 1, 'TRANS': 54} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 223 Unresolved non-hydrogen angles: 331 Unresolved non-hydrogen dihedrals: 136 Unresolved non-hydrogen chiralities: 81 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'TRP:plan': 2, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 3, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 85 Chain: "i" Number of atoms: 3384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3384 Classifications: {'peptide': 450} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 436} 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: "j" Number of atoms: 284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 284 Classifications: {'peptide': 71} Incomplete info: {'backbone_only': 60} Link IDs: {'TRANS': 70} Unresolved non-hydrogen bonds: 228 Unresolved non-hydrogen angles: 335 Unresolved non-hydrogen dihedrals: 136 Unresolved non-hydrogen chiralities: 86 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 6, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 75 Chain: "k" Number of atoms: 159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 159 Classifications: {'peptide': 23} Link IDs: {'PTRANS': 1, 'TRANS': 21} Chain: "l" Number of atoms: 2067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2067 Classifications: {'peptide': 271} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 264} Chain: "f" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "i" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 34 Unusual residues: {' MG': 1, 'ALF': 1, 'GDP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "l" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 34 Unusual residues: {' MG': 1, 'ALF': 1, 'GDP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 93626 SG CYS f 11 71.126 133.681 178.939 1.00231.86 S ATOM 93651 SG CYS f 14 74.341 134.970 177.886 1.00223.74 S ATOM 93754 SG CYS f 27 74.489 131.809 179.867 1.00222.45 S Time building chain proxies: 40.44, per 1000 atoms: 0.40 Number of scatterers: 101694 At special positions: 0 Unit cell: (241.86, 247.42, 240.47, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) Zn 1 29.99 S 108 16.00 P 3114 15.00 Al 2 13.00 Mg 2 11.99 F 8 9.00 O 28045 8.00 N 19002 7.00 C 51412 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 43.29 Conformation dependent library (CDL) restraints added in 5.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN f 101 " pdb="ZN ZN f 101 " - pdb=" SG CYS f 14 " pdb="ZN ZN f 101 " - pdb=" ND1 HIS f 33 " pdb="ZN ZN f 101 " - pdb=" SG CYS f 11 " pdb="ZN ZN f 101 " - pdb=" SG CYS f 27 " Number of angles added : 3 9328 Ramachandran restraints generated. 4664 Oldfield, 0 Emsley, 4664 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7754 Finding SS restraints... Warning!!! ksdssp method is not applicable for structures that cannot fit in PDB format. Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 147 helices and 51 sheets defined 44.2% alpha, 16.6% beta 1039 base pairs and 1618 stacking pairs defined. Time for finding SS restraints: 56.18 Creating SS restraints... Processing helix chain 'C' and resid 10 through 17 removed outlier: 4.724A pdb=" N HIS C 15 " --> pdb=" O PRO C 11 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N VAL C 16 " --> pdb=" O GLY C 12 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N VAL C 17 " --> pdb=" O ARG C 13 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 35 removed outlier: 3.941A pdb=" N LEU C 34 " --> pdb=" O PHE C 30 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N GLU C 35 " --> pdb=" O ALA C 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 30 through 35' Processing helix chain 'C' and resid 131 through 136 removed outlier: 4.146A pdb=" N ILE C 135 " --> pdb=" O PRO C 131 " (cutoff:3.500A) Proline residue: C 136 - end of helix No H-bonds generated for 'chain 'C' and resid 131 through 136' Processing helix chain 'C' and resid 207 through 215 removed outlier: 3.821A pdb=" N ALA C 211 " --> pdb=" O LYS C 207 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLY C 215 " --> pdb=" O ALA C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 226 removed outlier: 3.744A pdb=" N MET C 225 " --> pdb=" O ARG C 221 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N ASN C 226 " --> pdb=" O GLY C 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 221 through 226' Processing helix chain 'C' and resid 260 through 268 removed outlier: 4.764A pdb=" N ASP C 264 " --> pdb=" O ASN C 260 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N LYS C 265 " --> pdb=" O LYS C 261 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N PHE C 266 " --> pdb=" O ARG C 262 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE C 267 " --> pdb=" O THR C 263 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N VAL C 268 " --> pdb=" O ASP C 264 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 260 through 268' Processing helix chain 'D' and resid 61 through 72 removed outlier: 3.714A pdb=" N ALA D 71 " --> pdb=" O HIS D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 103 removed outlier: 4.182A pdb=" N ALA D 102 " --> pdb=" O VAL D 98 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N ASP D 103 " --> pdb=" O GLU D 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 98 through 103' Processing helix chain 'D' and resid 120 through 125 Processing helix chain 'D' and resid 39 through 44 Processing helix chain 'E' and resid 24 through 41 removed outlier: 3.846A pdb=" N ARG E 40 " --> pdb=" O ALA E 36 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N GLN E 41 " --> pdb=" O ALA E 37 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 116 removed outlier: 3.551A pdb=" N ASP E 116 " --> pdb=" O LEU E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 130 through 142 removed outlier: 3.615A pdb=" N LEU E 134 " --> pdb=" O LYS E 130 " (cutoff:3.500A) Processing helix chain 'E' and resid 154 through 165 removed outlier: 3.530A pdb=" N ALA E 161 " --> pdb=" O LEU E 157 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ARG E 162 " --> pdb=" O PHE E 158 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ASN E 163 " --> pdb=" O LEU E 159 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N LEU E 164 " --> pdb=" O ALA E 160 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N HIS E 165 " --> pdb=" O ALA E 161 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 183 removed outlier: 4.206A pdb=" N PHE E 183 " --> pdb=" O SER E 179 " (cutoff:3.500A) Processing helix chain 'E' and resid 189 through 201 Processing helix chain 'F' and resid 2 through 21 removed outlier: 4.362A pdb=" N VAL F 13 " --> pdb=" O LYS F 9 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N LYS F 14 " --> pdb=" O ASP F 10 " (cutoff:3.500A) Processing helix chain 'F' and resid 42 through 47 removed outlier: 3.711A pdb=" N LYS F 47 " --> pdb=" O ALA F 43 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 62 removed outlier: 3.727A pdb=" N ASP F 56 " --> pdb=" O ASN F 52 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 111 removed outlier: 3.565A pdb=" N ALA F 107 " --> pdb=" O LEU F 103 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N VAL F 108 " --> pdb=" O ILE F 104 " (cutoff:3.500A) Proline residue: F 109 - end of helix Processing helix chain 'F' and resid 162 through 174 removed outlier: 3.687A pdb=" N ASP F 174 " --> pdb=" O LEU F 170 " (cutoff:3.500A) Processing helix chain 'F' and resid 134 through 139 removed outlier: 4.187A pdb=" N ILE F 137 " --> pdb=" O GLU F 134 " (cutoff:3.500A) Proline residue: F 139 - end of helix Processing helix chain 'G' and resid 2 through 8 removed outlier: 4.217A pdb=" N ALA G 7 " --> pdb=" O ARG G 3 " (cutoff:3.500A) Proline residue: G 8 - end of helix Processing helix chain 'G' and resid 60 through 81 Processing helix chain 'G' and resid 137 through 153 removed outlier: 3.661A pdb=" N TYR G 151 " --> pdb=" O ASP G 147 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ARG G 152 " --> pdb=" O LEU G 148 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARG G 153 " --> pdb=" O ARG G 149 " (cutoff:3.500A) Processing helix chain 'H' and resid 22 through 29 removed outlier: 3.612A pdb=" N ALA H 26 " --> pdb=" O LYS H 22 " (cutoff:3.500A) Processing helix chain 'H' and resid 40 through 51 Processing helix chain 'H' and resid 52 through 73 Processing helix chain 'H' and resid 95 through 107 removed outlier: 3.527A pdb=" N ILE H 99 " --> pdb=" O GLY H 95 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ALA H 105 " --> pdb=" O ASP H 101 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ALA H 106 " --> pdb=" O ALA H 102 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY H 107 " --> pdb=" O VAL H 103 " (cutoff:3.500A) Processing helix chain 'I' and resid 4 through 22 Processing helix chain 'I' and resid 34 through 49 removed outlier: 3.572A pdb=" N ALA I 48 " --> pdb=" O ALA I 44 " (cutoff:3.500A) Processing helix chain 'I' and resid 56 through 68 removed outlier: 3.934A pdb=" N ARG I 62 " --> pdb=" O THR I 58 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N GLY I 66 " --> pdb=" O ARG I 62 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N THR I 67 " --> pdb=" O ALA I 63 " (cutoff:3.500A) Proline residue: I 68 - end of helix Processing helix chain 'I' and resid 72 through 77 removed outlier: 3.601A pdb=" N PHE I 76 " --> pdb=" O LEU I 72 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N VAL I 77 " --> pdb=" O LYS I 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 72 through 77' Processing helix chain 'I' and resid 90 through 104 removed outlier: 6.176A pdb=" N ARG I 94 " --> pdb=" O GLY I 90 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N LEU I 95 " --> pdb=" O ALA I 91 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LYS I 97 " --> pdb=" O ALA I 93 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLU I 98 " --> pdb=" O ARG I 94 " (cutoff:3.500A) Processing helix chain 'I' and resid 120 through 125 removed outlier: 3.881A pdb=" N ILE I 123 " --> pdb=" O ALA I 120 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ASP I 124 " --> pdb=" O SER I 121 " (cutoff:3.500A) Processing helix chain 'J' and resid 24 through 32 removed outlier: 4.765A pdb=" N GLN J 31 " --> pdb=" O ALA J 27 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N GLY J 32 " --> pdb=" O LEU J 28 " (cutoff:3.500A) Processing helix chain 'J' and resid 34 through 47 removed outlier: 3.899A pdb=" N PHE J 38 " --> pdb=" O ASN J 34 " (cutoff:3.500A) Processing helix chain 'J' and resid 75 through 85 removed outlier: 3.561A pdb=" N ALA J 84 " --> pdb=" O LEU J 80 " (cutoff:3.500A) Processing helix chain 'J' and resid 102 through 115 Processing helix chain 'J' and resid 121 through 137 removed outlier: 3.668A pdb=" N MET J 136 " --> pdb=" O THR J 132 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLY J 137 " --> pdb=" O ALA J 133 " (cutoff:3.500A) Processing helix chain 'K' and resid 24 through 38 removed outlier: 4.026A pdb=" N GLU K 31 " --> pdb=" O ARG K 27 " (cutoff:3.500A) Processing helix chain 'K' and resid 88 through 96 Processing helix chain 'K' and resid 97 through 110 removed outlier: 4.310A pdb=" N ILE K 101 " --> pdb=" O PRO K 97 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N MET K 108 " --> pdb=" O ALA K 104 " (cutoff:3.500A) Proline residue: K 110 - end of helix Processing helix chain 'K' and resid 112 through 123 removed outlier: 4.048A pdb=" N LYS K 121 " --> pdb=" O ALA K 117 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N LEU K 122 " --> pdb=" O MET K 118 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N LYS K 123 " --> pdb=" O PHE K 119 " (cutoff:3.500A) Processing helix chain 'K' and resid 130 through 135 removed outlier: 4.482A pdb=" N ALA K 133 " --> pdb=" O HIS K 130 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ALA K 134 " --> pdb=" O ASN K 131 " (cutoff:3.500A) Processing helix chain 'K' and resid 67 through 72 removed outlier: 4.791A pdb=" N LYS K 72 " --> pdb=" O ASN K 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 67 through 72' Processing helix chain 'L' and resid 104 through 109 removed outlier: 4.521A pdb=" N ARG L 108 " --> pdb=" O THR L 104 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N SER L 109 " --> pdb=" O ARG L 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 104 through 109' Processing helix chain 'L' and resid 112 through 119 removed outlier: 3.584A pdb=" N ILE L 116 " --> pdb=" O PHE L 112 " (cutoff:3.500A) Processing helix chain 'M' and resid 56 through 62 Proline residue: M 62 - end of helix Processing helix chain 'M' and resid 68 through 75 removed outlier: 3.786A pdb=" N ALA M 72 " --> pdb=" O SER M 68 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE M 73 " --> pdb=" O ARG M 69 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N THR M 74 " --> pdb=" O LYS M 70 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N ALA M 75 " --> pdb=" O ALA M 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 68 through 75' Processing helix chain 'M' and resid 78 through 85 removed outlier: 3.865A pdb=" N LEU M 82 " --> pdb=" O ARG M 78 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ALA M 83 " --> pdb=" O LEU M 79 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N LYS M 84 " --> pdb=" O SER M 80 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N VAL M 85 " --> pdb=" O ASP M 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 78 through 85' Processing helix chain 'M' and resid 91 through 99 Processing helix chain 'M' and resid 128 through 139 Processing helix chain 'N' and resid 42 through 58 removed outlier: 3.676A pdb=" N LYS N 58 " --> pdb=" O THR N 54 " (cutoff:3.500A) Processing helix chain 'N' and resid 109 through 125 removed outlier: 4.355A pdb=" N LYS N 123 " --> pdb=" O LEU N 119 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N LEU N 124 " --> pdb=" O ALA N 120 " (cutoff:3.500A) Proline residue: N 125 - end of helix Processing helix chain 'O' and resid 13 through 32 Processing helix chain 'O' and resid 37 through 58 removed outlier: 3.714A pdb=" N ARG O 45 " --> pdb=" O ALA O 41 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ARG O 46 " --> pdb=" O LYS O 42 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N VAL O 47 " --> pdb=" O GLU O 43 " (cutoff:3.500A) Proline residue: O 50 - end of helix removed outlier: 4.148A pdb=" N THR O 57 " --> pdb=" O THR O 53 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N ASP O 58 " --> pdb=" O LEU O 54 " (cutoff:3.500A) Processing helix chain 'O' and resid 59 through 71 Processing helix chain 'O' and resid 72 through 88 removed outlier: 4.524A pdb=" N GLY O 84 " --> pdb=" O PHE O 80 " (cutoff:3.500A) Proline residue: O 85 - end of helix Processing helix chain 'O' and resid 117 through 125 removed outlier: 3.692A pdb=" N ALA O 125 " --> pdb=" O LYS O 121 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 22 removed outlier: 3.507A pdb=" N ALA P 6 " --> pdb=" O ASP P 2 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N ARG P 13 " --> pdb=" O ARG P 9 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N ALA P 14 " --> pdb=" O ARG P 10 " (cutoff:3.500A) Processing helix chain 'P' and resid 55 through 63 removed outlier: 5.192A pdb=" N GLN P 61 " --> pdb=" O ALA P 57 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N LEU P 62 " --> pdb=" O ILE P 58 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N LYS P 63 " --> pdb=" O ALA P 59 " (cutoff:3.500A) Processing helix chain 'P' and resid 67 through 86 removed outlier: 3.597A pdb=" N LYS P 85 " --> pdb=" O ARG P 81 " (cutoff:3.500A) Processing helix chain 'P' and resid 101 through 114 Processing helix chain 'Q' and resid 2 through 14 removed outlier: 3.774A pdb=" N GLU Q 11 " --> pdb=" O GLN Q 7 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLN Q 12 " --> pdb=" O LEU Q 8 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N MET Q 13 " --> pdb=" O GLU Q 9 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N LYS Q 14 " --> pdb=" O GLN Q 10 " (cutoff:3.500A) Processing helix chain 'Q' and resid 97 through 104 removed outlier: 4.898A pdb=" N ARG Q 101 " --> pdb=" O LEU Q 97 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N GLU Q 102 " --> pdb=" O TYR Q 98 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG Q 103 " --> pdb=" O TYR Q 99 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N THR Q 104 " --> pdb=" O LEU Q 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 97 through 104' Processing helix chain 'R' and resid 6 through 22 removed outlier: 4.038A pdb=" N LYS R 22 " --> pdb=" O LEU R 18 " (cutoff:3.500A) Processing helix chain 'R' and resid 26 through 31 removed outlier: 3.860A pdb=" N ARG R 30 " --> pdb=" O GLY R 26 " (cutoff:3.500A) Processing helix chain 'R' and resid 32 through 37 removed outlier: 3.639A pdb=" N GLN R 37 " --> pdb=" O ARG R 33 " (cutoff:3.500A) Processing helix chain 'R' and resid 39 through 72 removed outlier: 3.744A pdb=" N ARG R 51 " --> pdb=" O TYR R 47 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LYS R 54 " --> pdb=" O ARG R 50 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ARG R 55 " --> pdb=" O ARG R 51 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ARG R 58 " --> pdb=" O LYS R 54 " (cutoff:3.500A) Processing helix chain 'R' and resid 75 through 87 Processing helix chain 'R' and resid 91 through 102 Processing helix chain 'R' and resid 103 through 118 Processing helix chain 'T' and resid 13 through 25 removed outlier: 3.554A pdb=" N LEU T 19 " --> pdb=" O GLN T 15 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N VAL T 20 " --> pdb=" O LYS T 16 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU T 23 " --> pdb=" O LEU T 19 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE T 24 " --> pdb=" O VAL T 20 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ARG T 25 " --> pdb=" O ALA T 21 " (cutoff:3.500A) Processing helix chain 'T' and resid 28 through 39 Processing helix chain 'T' and resid 41 through 61 removed outlier: 4.087A pdb=" N VAL T 45 " --> pdb=" O LYS T 41 " (cutoff:3.500A) Processing helix chain 'U' and resid 3 through 11 removed outlier: 3.741A pdb=" N LEU U 7 " --> pdb=" O ARG U 3 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LYS U 9 " --> pdb=" O GLU U 5 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL U 10 " --> pdb=" O ARG U 6 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N LEU U 11 " --> pdb=" O LEU U 7 " (cutoff:3.500A) Processing helix chain 'U' and resid 17 through 27 Processing helix chain 'U' and resid 39 through 51 Processing helix chain 'V' and resid 66 through 71 removed outlier: 3.851A pdb=" N VAL V 70 " --> pdb=" O GLN V 66 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N ALA V 71 " --> pdb=" O VAL V 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 66 through 71' Processing helix chain 'W' and resid 13 through 24 removed outlier: 3.545A pdb=" N ASN W 24 " --> pdb=" O LEU W 20 " (cutoff:3.500A) Processing helix chain 'W' and resid 43 through 53 removed outlier: 3.613A pdb=" N ALA W 52 " --> pdb=" O MET W 48 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N LYS W 53 " --> pdb=" O ASN W 49 " (cutoff:3.500A) Processing helix chain 'W' and resid 54 through 59 removed outlier: 3.861A pdb=" N SER W 58 " --> pdb=" O ALA W 54 " (cutoff:3.500A) Processing helix chain 'Y' and resid 52 through 63 Processing helix chain 'Y' and resid 64 through 75 Processing helix chain 'Z' and resid 2 through 10 removed outlier: 5.928A pdb=" N LEU Z 6 " --> pdb=" O LYS Z 2 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ARG Z 7 " --> pdb=" O ALA Z 3 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N LYS Z 9 " --> pdb=" O GLU Z 5 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N SER Z 10 " --> pdb=" O LEU Z 6 " (cutoff:3.500A) Processing helix chain 'Z' and resid 11 through 35 Processing helix chain 'Z' and resid 39 through 63 removed outlier: 5.024A pdb=" N LEU Z 43 " --> pdb=" O GLN Z 39 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N LYS Z 44 " --> pdb=" O SER Z 40 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ALA Z 51 " --> pdb=" O ARG Z 47 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLU Z 59 " --> pdb=" O THR Z 55 " (cutoff:3.500A) Processing helix chain 'a' and resid 17 through 28 Processing helix chain 'a' and resid 41 through 52 removed outlier: 3.681A pdb=" N VAL a 51 " --> pdb=" O MET a 47 " (cutoff:3.500A) Processing helix chain 'b' and resid 9 through 21 removed outlier: 3.582A pdb=" N ARG b 17 " --> pdb=" O ARG b 13 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N HIS b 19 " --> pdb=" O MET b 15 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N ASP b 20 " --> pdb=" O ARG b 16 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ALA b 21 " --> pdb=" O ARG b 17 " (cutoff:3.500A) Processing helix chain 'd' and resid 8 through 16 Processing helix chain 'd' and resid 17 through 24 removed outlier: 4.524A pdb=" N THR d 24 " --> pdb=" O ALA d 20 " (cutoff:3.500A) Processing helix chain 'd' and resid 25 through 38 Processing helix chain 'e' and resid 7 through 14 removed outlier: 3.689A pdb=" N LYS e 12 " --> pdb=" O ARG e 8 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ARG e 13 " --> pdb=" O GLY e 9 " (cutoff:3.500A) Processing helix chain 'e' and resid 32 through 37 removed outlier: 4.384A pdb=" N LYS e 36 " --> pdb=" O ILE e 32 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N ALA e 37 " --> pdb=" O LEU e 33 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 32 through 37' Processing helix chain 'e' and resid 38 through 46 Proline residue: e 46 - end of helix Processing helix chain 'e' and resid 51 through 63 removed outlier: 5.237A pdb=" N GLY e 56 " --> pdb=" O LYS e 52 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N LEU e 57 " --> pdb=" O GLY e 53 " (cutoff:3.500A) Proline residue: e 63 - end of helix Processing helix chain 'g' and resid 16 through 40 removed outlier: 3.590A pdb=" N ARG g 22 " --> pdb=" O GLU g 18 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE g 39 " --> pdb=" O ILE g 35 " (cutoff:3.500A) Proline residue: g 40 - end of helix Processing helix chain 'g' and resid 45 through 55 removed outlier: 3.906A pdb=" N LEU g 49 " --> pdb=" O ASP g 45 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLU g 54 " --> pdb=" O ALA g 50 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N GLN g 55 " --> pdb=" O LYS g 51 " (cutoff:3.500A) Processing helix chain 'g' and resid 56 through 66 removed outlier: 4.204A pdb=" N ILE g 60 " --> pdb=" O GLN g 56 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N ILE g 61 " --> pdb=" O ARG g 57 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU g 62 " --> pdb=" O GLY g 58 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N MET g 63 " --> pdb=" O THR g 59 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N PHE g 64 " --> pdb=" O ILE g 60 " (cutoff:3.500A) Processing helix chain 'g' and resid 70 through 75 removed outlier: 4.126A pdb=" N ARG g 74 " --> pdb=" O GLY g 70 " (cutoff:3.500A) Processing helix chain 'g' and resid 82 through 99 Processing helix chain 'g' and resid 100 through 109 removed outlier: 4.326A pdb=" N GLY g 109 " --> pdb=" O ILE g 105 " (cutoff:3.500A) Processing helix chain 'g' and resid 110 through 137 removed outlier: 3.810A pdb=" N LYS g 115 " --> pdb=" O SER g 111 " (cutoff:3.500A) Processing helix chain 'g' and resid 139 through 144 Proline residue: g 143 - end of helix No H-bonds generated for 'chain 'g' and resid 139 through 144' Processing helix chain 'g' and resid 153 through 181 removed outlier: 3.545A pdb=" N TYR g 157 " --> pdb=" O GLY g 153 " (cutoff:3.500A) Processing helix chain 'g' and resid 185 through 213 removed outlier: 4.221A pdb=" N GLY g 198 " --> pdb=" O GLY g 194 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LEU g 199 " --> pdb=" O ILE g 195 " (cutoff:3.500A) Proline residue: g 200 - end of helix removed outlier: 3.522A pdb=" N ARG g 211 " --> pdb=" O ILE g 207 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLN g 212 " --> pdb=" O GLU g 208 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLY g 213 " --> pdb=" O GLN g 209 " (cutoff:3.500A) Processing helix chain 'g' and resid 216 through 240 removed outlier: 3.504A pdb=" N LEU g 220 " --> pdb=" O HIS g 216 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY g 240 " --> pdb=" O PHE g 236 " (cutoff:3.500A) Processing helix chain 'g' and resid 274 through 289 Proline residue: g 287 - end of helix Processing helix chain 'g' and resid 297 through 311 removed outlier: 3.561A pdb=" N ASN g 301 " --> pdb=" O GLY g 297 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N THR g 304 " --> pdb=" O TRP g 300 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N THR g 305 " --> pdb=" O ASN g 301 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU g 310 " --> pdb=" O ILE g 306 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N GLN g 311 " --> pdb=" O SER g 307 " (cutoff:3.500A) Processing helix chain 'g' and resid 314 through 350 removed outlier: 5.365A pdb=" N ASN g 338 " --> pdb=" O ALA g 334 " (cutoff:3.500A) Proline residue: g 339 - end of helix removed outlier: 3.516A pdb=" N THR g 342 " --> pdb=" O ASN g 338 " (cutoff:3.500A) Processing helix chain 'g' and resid 359 through 395 removed outlier: 3.874A pdb=" N ALA g 363 " --> pdb=" O GLY g 359 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG g 372 " --> pdb=" O LYS g 368 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU g 375 " --> pdb=" O THR g 371 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N VAL g 376 " --> pdb=" O ARG g 372 " (cutoff:3.500A) Proline residue: g 388 - end of helix Processing helix chain 'g' and resid 402 through 429 Processing helix chain 'h' and resid 71 through 83 removed outlier: 3.573A pdb=" N LYS h 81 " --> pdb=" O THR h 77 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N ILE h 83 " --> pdb=" O VAL h 79 " (cutoff:3.500A) Processing helix chain 'h' and resid 86 through 122 removed outlier: 3.738A pdb=" N THR h 90 " --> pdb=" O THR h 86 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N PHE h 121 " --> pdb=" O ARG h 117 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ILE h 122 " --> pdb=" O LEU h 118 " (cutoff:3.500A) Processing helix chain 'i' and resid 4 through 17 removed outlier: 3.720A pdb=" N SER i 17 " --> pdb=" O LEU i 13 " (cutoff:3.500A) Processing helix chain 'i' and resid 23 through 42 removed outlier: 3.745A pdb=" N VAL i 27 " --> pdb=" O THR i 23 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N LYS i 28 " --> pdb=" O GLU i 24 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N ASP i 29 " --> pdb=" O ASP i 25 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N THR i 30 " --> pdb=" O ASN i 26 " (cutoff:3.500A) Processing helix chain 'i' and resid 44 through 62 removed outlier: 3.640A pdb=" N ARG i 54 " --> pdb=" O GLU i 50 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N GLY i 61 " --> pdb=" O GLU i 57 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N HIS i 62 " --> pdb=" O LYS i 58 " (cutoff:3.500A) Processing helix chain 'i' and resid 69 through 87 Processing helix chain 'i' and resid 112 through 127 Processing helix chain 'i' and resid 143 through 156 Processing helix chain 'i' and resid 167 through 183 Processing helix chain 'i' and resid 198 through 213 Processing helix chain 'i' and resid 226 through 240 removed outlier: 4.720A pdb=" N ALA i 230 " --> pdb=" O GLY i 226 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N ASN i 231 " --> pdb=" O GLN i 227 " (cutoff:3.500A) Processing helix chain 'i' and resid 256 through 266 removed outlier: 4.498A pdb=" N LEU i 260 " --> pdb=" O GLY i 256 " (cutoff:3.500A) Processing helix chain 'i' and resid 286 through 294 removed outlier: 3.728A pdb=" N ARG i 293 " --> pdb=" O ARG i 289 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N ILE i 294 " --> pdb=" O ILE i 290 " (cutoff:3.500A) Processing helix chain 'i' and resid 299 through 327 removed outlier: 4.677A pdb=" N LEU i 303 " --> pdb=" O ASP i 299 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ILE i 304 " --> pdb=" O VAL i 300 " (cutoff:3.500A) Processing helix chain 'i' and resid 330 through 345 Processing helix chain 'i' and resid 370 through 384 removed outlier: 3.900A pdb=" N MET i 383 " --> pdb=" O ILE i 379 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N THR i 384 " --> pdb=" O ILE i 380 " (cutoff:3.500A) Processing helix chain 'i' and resid 385 through 391 Proline residue: i 391 - end of helix Processing helix chain 'i' and resid 395 through 407 Processing helix chain 'i' and resid 409 through 433 removed outlier: 3.549A pdb=" N VAL i 413 " --> pdb=" O GLN i 409 " (cutoff:3.500A) Processing helix chain 'j' and resid 1 through 24 removed outlier: 5.048A pdb=" N GLN j 24 " --> pdb=" O ILE j 20 " (cutoff:3.500A) Processing helix chain 'j' and resid 46 through 71 Processing helix chain 'k' and resid 28 through 39 removed outlier: 3.744A pdb=" N LEU k 38 " --> pdb=" O LEU k 34 " (cutoff:3.500A) Processing helix chain 'k' and resid 40 through 50 removed outlier: 4.850A pdb=" N VAL k 44 " --> pdb=" O LEU k 40 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ALA k 45 " --> pdb=" O LEU k 41 " (cutoff:3.500A) Processing helix chain 'l' and resid 30 through 45 removed outlier: 3.784A pdb=" N ALA l 44 " --> pdb=" O GLN l 40 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ASP l 45 " --> pdb=" O LEU l 41 " (cutoff:3.500A) Processing helix chain 'l' and resid 47 through 66 Processing helix chain 'l' and resid 69 through 90 removed outlier: 3.603A pdb=" N LEU l 73 " --> pdb=" O ASP l 69 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N LYS l 87 " --> pdb=" O GLU l 83 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N VAL l 88 " --> pdb=" O ILE l 84 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ASP l 89 " --> pdb=" O LEU l 85 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N GLU l 90 " --> pdb=" O ALA l 86 " (cutoff:3.500A) Processing helix chain 'l' and resid 111 through 127 removed outlier: 3.918A pdb=" N ARG l 121 " --> pdb=" O GLY l 117 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N GLN l 126 " --> pdb=" O GLN l 122 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N GLY l 127 " --> pdb=" O PHE l 123 " (cutoff:3.500A) Processing helix chain 'l' and resid 141 through 154 Processing helix chain 'l' and resid 165 through 181 Processing helix chain 'l' and resid 196 through 214 removed outlier: 3.567A pdb=" N MET l 200 " --> pdb=" O LYS l 196 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LYS l 212 " --> pdb=" O ARG l 208 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N LEU l 213 " --> pdb=" O VAL l 209 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASP l 214 " --> pdb=" O MET l 210 " (cutoff:3.500A) Processing helix chain 'l' and resid 230 through 244 removed outlier: 4.792A pdb=" N VAL l 234 " --> pdb=" O GLY l 230 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N SER l 235 " --> pdb=" O GLN l 231 " (cutoff:3.500A) Processing helix chain 'l' and resid 261 through 270 removed outlier: 4.111A pdb=" N SER l 265 " --> pdb=" O GLY l 261 " (cutoff:3.500A) Processing helix chain 'l' and resid 290 through 300 removed outlier: 3.522A pdb=" N ALA l 300 " --> pdb=" O GLU l 296 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'C' and resid 80 through 83 removed outlier: 3.526A pdb=" N ARG C 80 " --> pdb=" O LEU C 93 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N LEU C 93 " --> pdb=" O GLU C 79 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N ILE C 74 " --> pdb=" O SER C 118 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N SER C 118 " --> pdb=" O ILE C 74 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ASP C 114 " --> pdb=" O VAL C 78 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'C' and resid 138 through 142 removed outlier: 4.128A pdb=" N SER C 139 " --> pdb=" O ILE C 164 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N THR C 173 " --> pdb=" O VAL C 165 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLU C 180 " --> pdb=" O LEU C 176 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'D' and resid 3 through 6 Processing sheet with id= 4, first strand: chain 'D' and resid 10 through 16 removed outlier: 3.830A pdb=" N GLY D 10 " --> pdb=" O VAL D 26 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N VAL D 20 " --> pdb=" O THR D 16 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'D' and resid 79 through 84 removed outlier: 3.583A pdb=" N LEU D 84 " --> pdb=" O ARG D 46 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N ARG D 46 " --> pdb=" O LEU D 84 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N GLN D 49 " --> pdb=" O THR D 35 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N GLN D 94 " --> pdb=" O VAL D 34 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'D' and resid 105 through 108 removed outlier: 6.864A pdb=" N LYS D 105 " --> pdb=" O VAL D 177 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'E' and resid 1 through 5 removed outlier: 4.415A pdb=" N SER E 10 " --> pdb=" O LEU E 5 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'E' and resid 117 through 120 Processing sheet with id= 9, first strand: chain 'F' and resid 65 through 69 removed outlier: 3.899A pdb=" N GLY F 86 " --> pdb=" O THR F 68 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N GLY F 39 " --> pdb=" O GLY F 151 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N GLY F 151 " --> pdb=" O GLY F 39 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'G' and resid 16 through 19 Processing sheet with id= 11, first strand: chain 'G' and resid 41 through 45 Processing sheet with id= 12, first strand: chain 'G' and resid 82 through 89 removed outlier: 6.068A pdb=" N THR G 129 " --> pdb=" O LEU G 89 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'G' and resid 94 through 98 Processing sheet with id= 14, first strand: chain 'H' and resid 17 through 21 removed outlier: 4.928A pdb=" N ASP H 17 " --> pdb=" O LEU H 5 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N GLN H 2 " --> pdb=" O ALA H 39 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N LYS H 35 " --> pdb=" O LEU H 6 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'H' and resid 77 through 82 removed outlier: 3.718A pdb=" N VAL H 147 " --> pdb=" O ILE H 80 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N SER H 131 " --> pdb=" O ARG H 116 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N GLU H 114 " --> pdb=" O GLN H 133 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'I' and resid 23 through 29 removed outlier: 3.887A pdb=" N SER I 24 " --> pdb=" O SER I 85 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'J' and resid 8 through 14 Processing sheet with id= 18, first strand: chain 'K' and resid 52 through 57 removed outlier: 4.761A pdb=" N ASP K 19 " --> pdb=" O LEU K 140 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'K' and resid 74 through 78 removed outlier: 7.341A pdb=" N GLY K 83 " --> pdb=" O THR K 78 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'L' and resid 56 through 60 removed outlier: 4.584A pdb=" N ASP L 56 " --> pdb=" O ILE L 43 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N LYS L 40 " --> pdb=" O ILE L 22 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N THR L 6 " --> pdb=" O CYS L 21 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N ASN L 82 " --> pdb=" O MET L 7 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'L' and resid 68 through 71 removed outlier: 4.157A pdb=" N SER L 75 " --> pdb=" O ARG L 71 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'M' and resid 120 through 123 Processing sheet with id= 23, first strand: chain 'N' and resid 62 through 65 removed outlier: 3.722A pdb=" N TYR N 103 " --> pdb=" O LEU N 33 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N LEU N 33 " --> pdb=" O LEU N 102 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LYS N 100 " --> pdb=" O ALA N 35 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'N' and resid 71 through 74 removed outlier: 3.554A pdb=" N TYR N 91 " --> pdb=" O ILE N 73 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'N' and resid 30 through 36 removed outlier: 7.331A pdb=" N SER N 30 " --> pdb=" O LYS N 133 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LYS N 127 " --> pdb=" O VAL N 36 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'O' and resid 33 through 36 removed outlier: 4.034A pdb=" N MET O 110 " --> pdb=" O CYS O 100 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'P' and resid 49 through 52 removed outlier: 3.552A pdb=" N VAL P 49 " --> pdb=" O VAL P 39 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'Q' and resid 38 through 45 removed outlier: 6.881A pdb=" N THR Q 25 " --> pdb=" O LYS Q 87 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'Q' and resid 49 through 53 removed outlier: 3.621A pdb=" N ALA Q 49 " --> pdb=" O THR Q 60 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N ARG Q 53 " --> pdb=" O HIS Q 56 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N HIS Q 56 " --> pdb=" O ARG Q 53 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N SER Q 57 " --> pdb=" O THR Q 76 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'S' and resid 11 through 15 removed outlier: 7.247A pdb=" N LEU S 39 " --> pdb=" O GLY S 50 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'S' and resid 18 through 23 removed outlier: 4.320A pdb=" N GLN S 18 " --> pdb=" O ILE S 98 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ASP S 95 " --> pdb=" O VAL S 64 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N LYS S 60 " --> pdb=" O THR S 99 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLU S 31 " --> pdb=" O VAL S 63 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'S' and resid 57 through 60 Processing sheet with id= 33, first strand: chain 'S' and resid 65 through 68 Processing sheet with id= 34, first strand: chain 'S' and resid 71 through 78 removed outlier: 4.209A pdb=" N TYR S 83 " --> pdb=" O ARG S 78 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'T' and resid 2 through 8 removed outlier: 6.886A pdb=" N VAL T 106 " --> pdb=" O THR T 72 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'T' and resid 81 through 88 removed outlier: 3.954A pdb=" N ARG T 92 " --> pdb=" O ARG T 88 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'U' and resid 12 through 15 removed outlier: 5.237A pdb=" N VAL U 31 " --> pdb=" O HIS U 15 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LYS U 81 " --> pdb=" O VAL U 34 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N LYS U 66 " --> pdb=" O ARG U 77 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ASP U 79 " --> pdb=" O LYS U 64 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N LYS U 64 " --> pdb=" O ASP U 79 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N LYS U 81 " --> pdb=" O VAL U 62 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N VAL U 62 " --> pdb=" O LYS U 81 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ALA U 83 " --> pdb=" O THR U 60 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N THR U 60 " --> pdb=" O ALA U 83 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N VAL U 85 " --> pdb=" O VAL U 58 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N VAL U 58 " --> pdb=" O VAL U 85 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'V' and resid 40 through 45 removed outlier: 5.632A pdb=" N ASN V 40 " --> pdb=" O ALA V 63 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'V' and resid 82 through 87 removed outlier: 7.762A pdb=" N ARG V 82 " --> pdb=" O LYS V 97 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N ARG V 94 " --> pdb=" O ILE V 103 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLU V 101 " --> pdb=" O PHE V 96 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'W' and resid 69 through 72 removed outlier: 3.940A pdb=" N ILE W 89 " --> pdb=" O PRO W 27 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'X' and resid 51 through 54 removed outlier: 6.442A pdb=" N GLY X 52 " --> pdb=" O LEU X 59 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N LEU X 59 " --> pdb=" O GLY X 52 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N GLY X 54 " --> pdb=" O HIS X 57 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'X' and resid 65 through 71 Processing sheet with id= 43, first strand: chain 'Y' and resid 12 through 19 removed outlier: 3.520A pdb=" N SER Y 19 " --> pdb=" O ASN Y 23 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N ASN Y 23 " --> pdb=" O SER Y 19 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'a' and resid 33 through 39 removed outlier: 4.410A pdb=" N HIS a 34 " --> pdb=" O GLN a 9 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N MET a 54 " --> pdb=" O THR a 10 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'c' and resid 20 through 25 removed outlier: 6.964A pdb=" N ILE c 48 " --> pdb=" O SER c 14 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N LEU c 34 " --> pdb=" O GLU c 51 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'e' and resid 22 through 25 removed outlier: 5.541A pdb=" N PHE e 22 " --> pdb=" O VAL e 50 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'f' and resid 1 through 5 removed outlier: 5.893A pdb=" N ILE f 23 " --> pdb=" O GLN f 37 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'g' and resid 241 through 245 Processing sheet with id= 49, first strand: chain 'i' and resid 131 through 137 removed outlier: 4.559A pdb=" N THR i 191 " --> pdb=" O MET i 105 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N GLY i 107 " --> pdb=" O THR i 191 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'i' and resid 272 through 275 removed outlier: 4.346A pdb=" N VAL i 275 " --> pdb=" O ALA i 281 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N ALA i 281 " --> pdb=" O VAL i 275 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'l' and resid 156 through 159 removed outlier: 3.557A pdb=" N THR l 189 " --> pdb=" O MET l 104 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N GLY l 106 " --> pdb=" O THR l 189 " (cutoff:3.500A) 1710 hydrogen bonds defined for protein. 5052 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2617 hydrogen bonds 4116 hydrogen bond angles 0 basepair planarities 1039 basepair parallelities 1618 stacking parallelities Total time for adding SS restraints: 163.42 Time building geometry restraints manager: 46.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.34: 21542 1.34 - 1.47: 45318 1.47 - 1.60: 40270 1.60 - 1.74: 2771 1.74 - 1.87: 208 Bond restraints: 110109 Sorted by residual: bond pdb=" C GLY g 355 " pdb=" N ILE g 356 " ideal model delta sigma weight residual 1.332 1.419 -0.087 1.36e-02 5.41e+03 4.08e+01 bond pdb=" CA PRO J 22 " pdb=" C PRO J 22 " ideal model delta sigma weight residual 1.517 1.570 -0.053 9.30e-03 1.16e+04 3.20e+01 bond pdb=" CA VAL F 108 " pdb=" CB VAL F 108 " ideal model delta sigma weight residual 1.534 1.571 -0.037 6.80e-03 2.16e+04 2.94e+01 bond pdb=" N ASP U 94 " pdb=" CA ASP U 94 " ideal model delta sigma weight residual 1.456 1.520 -0.063 1.21e-02 6.83e+03 2.74e+01 bond pdb=" F1 ALF l1001 " pdb="AL ALF l1001 " ideal model delta sigma weight residual 1.684 1.785 -0.101 2.00e-02 2.50e+03 2.54e+01 ... (remaining 110104 not shown) Histogram of bond angle deviations from ideal: 89.90 - 107.88: 27812 107.88 - 125.86: 125573 125.86 - 143.84: 10463 143.84 - 161.82: 0 161.82 - 179.79: 4 Bond angle restraints: 163852 Sorted by residual: angle pdb=" F1 ALF l1001 " pdb="AL ALF l1001 " pdb=" F2 ALF l1001 " ideal model delta sigma weight residual 108.68 179.79 -71.11 3.00e+00 1.11e-01 5.62e+02 angle pdb=" F1 ALF i1001 " pdb="AL ALF i1001 " pdb=" F2 ALF i1001 " ideal model delta sigma weight residual 108.68 179.76 -71.08 3.00e+00 1.11e-01 5.61e+02 angle pdb=" F3 ALF l1001 " pdb="AL ALF l1001 " pdb=" F4 ALF l1001 " ideal model delta sigma weight residual 109.63 179.76 -70.13 3.00e+00 1.11e-01 5.46e+02 angle pdb=" F3 ALF i1001 " pdb="AL ALF i1001 " pdb=" F4 ALF i1001 " ideal model delta sigma weight residual 109.63 179.57 -69.94 3.00e+00 1.11e-01 5.44e+02 angle pdb=" C GLU G 155 " pdb=" N PRO G 156 " pdb=" CA PRO G 156 " ideal model delta sigma weight residual 119.82 128.98 -9.16 9.80e-01 1.04e+00 8.74e+01 ... (remaining 163847 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.39: 60974 35.39 - 70.78: 7741 70.78 - 106.17: 860 106.17 - 141.56: 13 141.56 - 176.96: 12 Dihedral angle restraints: 69600 sinusoidal: 57038 harmonic: 12562 Sorted by residual: dihedral pdb=" C4' U A1344 " pdb=" C3' U A1344 " pdb=" C2' U A1344 " pdb=" C1' U A1344 " ideal model delta sinusoidal sigma weight residual -35.00 32.13 -67.13 1 8.00e+00 1.56e-02 9.17e+01 dihedral pdb=" C4' C A 645 " pdb=" C3' C A 645 " pdb=" C2' C A 645 " pdb=" C1' C A 645 " ideal model delta sinusoidal sigma weight residual -35.00 30.60 -65.60 1 8.00e+00 1.56e-02 8.80e+01 dihedral pdb=" C5' U A1344 " pdb=" C4' U A1344 " pdb=" C3' U A1344 " pdb=" O3' U A1344 " ideal model delta sinusoidal sigma weight residual 147.00 83.19 63.81 1 8.00e+00 1.56e-02 8.38e+01 ... (remaining 69597 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 18563 0.074 - 0.148: 1907 0.148 - 0.223: 128 0.223 - 0.297: 11 0.297 - 0.371: 3 Chirality restraints: 20612 Sorted by residual: chirality pdb=" C3' C A 645 " pdb=" C4' C A 645 " pdb=" O3' C A 645 " pdb=" C2' C A 645 " both_signs ideal model delta sigma weight residual False -2.74 -2.37 -0.37 2.00e-01 2.50e+01 3.44e+00 chirality pdb=" C3' U A1344 " pdb=" C4' U A1344 " pdb=" O3' U A1344 " pdb=" C2' U A1344 " both_signs ideal model delta sigma weight residual False -2.74 -2.38 -0.37 2.00e-01 2.50e+01 3.33e+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 2.16 0.30 2.00e-01 2.50e+01 2.29e+00 ... (remaining 20609 not shown) Planarity restraints: 9393 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN i 94 " 0.023 2.00e-02 2.50e+03 4.76e-02 2.27e+01 pdb=" C ASN i 94 " -0.082 2.00e-02 2.50e+03 pdb=" O ASN i 94 " 0.032 2.00e-02 2.50e+03 pdb=" N LEU i 95 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA i 96 " 0.021 2.00e-02 2.50e+03 4.29e-02 1.84e+01 pdb=" C ALA i 96 " -0.074 2.00e-02 2.50e+03 pdb=" O ALA i 96 " 0.028 2.00e-02 2.50e+03 pdb=" N ALA i 97 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY i 433 " 0.020 2.00e-02 2.50e+03 4.15e-02 1.72e+01 pdb=" C GLY i 433 " -0.072 2.00e-02 2.50e+03 pdb=" O GLY i 433 " 0.028 2.00e-02 2.50e+03 pdb=" N GLY i 434 " 0.024 2.00e-02 2.50e+03 ... (remaining 9390 not shown) Histogram of nonbonded interaction distances: 1.17 - 1.91: 4 1.91 - 2.66: 4397 2.66 - 3.41: 127876 3.41 - 4.15: 334341 4.15 - 4.90: 461487 Nonbonded interactions: 928105 Sorted by model distance: nonbonded pdb=" O2 C A 490 " pdb=" NZ LYS i 418 " model vdw 1.168 2.520 nonbonded pdb=" C5 C A 490 " pdb=" NH2 ARG i 425 " model vdw 1.247 3.420 nonbonded pdb=" C2 C A 490 " pdb=" NZ LYS i 418 " model vdw 1.717 3.340 nonbonded pdb=" OP1 G A1283 " pdb=" NZ LYS i 428 " model vdw 1.790 2.520 nonbonded pdb=" OP1 U A1460 " pdb=" O GLY g 355 " model vdw 1.996 3.040 ... (remaining 928100 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: 2.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.080 Extract box with map and model: 11.550 Check model and map are aligned: 1.140 Set scattering table: 0.710 Process input model: 394.820 Find NCS groups from input model: 2.070 Set up NCS constraints: 0.240 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:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 415.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 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 0.105 110109 Z= 0.458 Angle : 1.142 71.115 163852 Z= 0.636 Chirality : 0.046 0.371 20612 Planarity : 0.005 0.090 9393 Dihedral : 23.354 176.956 61846 Min Nonbonded Distance : 1.168 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.07 % Favored : 96.85 % Rotamer: Outliers : 9.43 % Allowed : 11.41 % Favored : 79.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.95 % Cis-general : 0.11 % Twisted Proline : 0.66 % Twisted General : 0.09 % 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: -2.95 (0.10), residues: 4664 helix: -2.46 (0.09), residues: 1785 sheet: -1.32 (0.15), residues: 794 loop : -1.56 (0.11), residues: 2085 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP C 248 HIS 0.010 0.002 HIS K 130 PHE 0.025 0.002 PHE I 106 TYR 0.029 0.003 TYR T 38 ARG 0.006 0.001 ARG N 6 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9328 Ramachandran restraints generated. 4664 Oldfield, 0 Emsley, 4664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9328 Ramachandran restraints generated. 4664 Oldfield, 0 Emsley, 4664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1722 residues out of total 3823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 319 poor density : 1403 time to evaluate : 4.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 0.9184 (OUTLIER) cc_final: 0.8795 (pp) REVERT: C 74 ILE cc_start: 0.4934 (OUTLIER) cc_final: 0.3049 (pt) REVERT: C 94 VAL cc_start: 0.9328 (m) cc_final: 0.9060 (t) REVERT: C 95 LEU cc_start: 0.8437 (tp) cc_final: 0.8016 (tp) REVERT: C 96 TYR cc_start: 0.9019 (m-80) cc_final: 0.8779 (m-80) REVERT: C 132 MET cc_start: 0.9081 (mtm) cc_final: 0.8719 (mtm) REVERT: C 156 ARG cc_start: 0.8241 (OUTLIER) cc_final: 0.7099 (mtm180) REVERT: C 180 GLU cc_start: 0.7163 (OUTLIER) cc_final: 0.6841 (pt0) REVERT: C 187 ASP cc_start: 0.8942 (m-30) cc_final: 0.8703 (m-30) REVERT: C 200 HIS cc_start: 0.9242 (t70) cc_final: 0.8904 (t70) REVERT: C 201 MET cc_start: 0.7579 (ptt) cc_final: 0.7194 (ttp) REVERT: C 225 MET cc_start: 0.8917 (mtt) cc_final: 0.8384 (mpp) REVERT: D 11 MET cc_start: 0.8438 (mtp) cc_final: 0.7838 (tpp) REVERT: D 14 ILE cc_start: 0.9098 (mm) cc_final: 0.8867 (tp) REVERT: D 43 ASP cc_start: 0.6130 (m-30) cc_final: 0.5909 (m-30) REVERT: D 74 GLU cc_start: 0.9576 (mt-10) cc_final: 0.9132 (tm-30) REVERT: D 84 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8106 (mp) REVERT: D 125 TRP cc_start: 0.6992 (m100) cc_final: 0.6783 (m100) REVERT: D 160 LYS cc_start: 0.5569 (OUTLIER) cc_final: 0.5275 (mtmm) REVERT: D 201 LEU cc_start: 0.7710 (mt) cc_final: 0.7169 (mt) REVERT: E 3 LEU cc_start: 0.9007 (mt) cc_final: 0.8401 (pp) REVERT: E 25 GLU cc_start: 0.8692 (tt0) cc_final: 0.8381 (tp30) REVERT: E 48 THR cc_start: 0.7055 (p) cc_final: 0.5952 (p) REVERT: E 51 GLU cc_start: 0.7925 (mt-10) cc_final: 0.7644 (tt0) REVERT: E 115 GLN cc_start: 0.8534 (mm-40) cc_final: 0.7998 (tt0) REVERT: E 119 ILE cc_start: 0.9539 (OUTLIER) cc_final: 0.9186 (tp) REVERT: E 139 LYS cc_start: 0.9060 (tttt) cc_final: 0.8679 (ptpp) REVERT: E 157 LEU cc_start: 0.9388 (tp) cc_final: 0.9156 (mp) REVERT: E 179 SER cc_start: 0.8543 (OUTLIER) cc_final: 0.8324 (p) REVERT: E 185 LYS cc_start: 0.8858 (mmtt) cc_final: 0.8556 (mmmt) REVERT: E 195 GLN cc_start: 0.8560 (mt0) cc_final: 0.8312 (tp-100) REVERT: F 22 TYR cc_start: 0.7309 (m-80) cc_final: 0.7108 (m-10) REVERT: F 51 ASP cc_start: 0.6666 (OUTLIER) cc_final: 0.6307 (m-30) REVERT: F 72 LYS cc_start: 0.8868 (tppt) cc_final: 0.8436 (mmtp) REVERT: F 73 SER cc_start: 0.4052 (m) cc_final: 0.3255 (t) REVERT: F 149 VAL cc_start: 0.8291 (OUTLIER) cc_final: 0.7818 (p) REVERT: F 162 SER cc_start: 0.8770 (OUTLIER) cc_final: 0.8469 (p) REVERT: G 42 GLU cc_start: 0.8965 (tm-30) cc_final: 0.8732 (pp20) REVERT: G 48 ASN cc_start: 0.7842 (m-40) cc_final: 0.7493 (m-40) REVERT: G 52 PHE cc_start: 0.6447 (m-80) cc_final: 0.5927 (m-80) REVERT: G 107 LEU cc_start: 0.8710 (mt) cc_final: 0.8091 (tp) REVERT: G 130 GLU cc_start: 0.8907 (tt0) cc_final: 0.8605 (tm-30) REVERT: G 131 ILE cc_start: 0.9085 (mt) cc_final: 0.8879 (tp) REVERT: G 164 TYR cc_start: 0.8036 (m-80) cc_final: 0.7742 (m-80) REVERT: H 4 ILE cc_start: 0.7256 (OUTLIER) cc_final: 0.6571 (mp) REVERT: H 46 PHE cc_start: 0.9198 (m-80) cc_final: 0.8761 (m-80) REVERT: H 76 GLU cc_start: 0.2713 (OUTLIER) cc_final: 0.1690 (tm-30) REVERT: H 77 THR cc_start: 0.7862 (OUTLIER) cc_final: 0.6896 (m) REVERT: H 142 VAL cc_start: 0.7481 (OUTLIER) cc_final: 0.6401 (t) REVERT: I 4 ASN cc_start: 0.8722 (t0) cc_final: 0.8460 (t0) REVERT: I 34 THR cc_start: 0.7774 (p) cc_final: 0.7399 (t) REVERT: I 96 PHE cc_start: 0.0963 (OUTLIER) cc_final: 0.0755 (m-10) REVERT: J 130 GLU cc_start: 0.5135 (mt-10) cc_final: 0.4808 (mm-30) REVERT: K 13 ARG cc_start: 0.7846 (mtt90) cc_final: 0.7260 (ttm-80) REVERT: K 31 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.7736 (mm-30) REVERT: K 35 ARG cc_start: 0.9088 (mtt-85) cc_final: 0.8627 (mmt-90) REVERT: K 57 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8249 (mt) REVERT: K 69 ARG cc_start: 0.8855 (OUTLIER) cc_final: 0.8233 (tpp80) REVERT: K 89 PHE cc_start: 0.9453 (t80) cc_final: 0.9059 (t80) REVERT: K 91 GLU cc_start: 0.8861 (mt-10) cc_final: 0.8622 (pt0) REVERT: K 92 MET cc_start: 0.8628 (mmm) cc_final: 0.8196 (mmm) REVERT: K 103 ILE cc_start: 0.8717 (OUTLIER) cc_final: 0.8180 (mp) REVERT: K 108 MET cc_start: 0.8990 (mtt) cc_final: 0.8327 (mtm) REVERT: K 114 LEU cc_start: 0.9516 (tp) cc_final: 0.9245 (mt) REVERT: L 2 ILE cc_start: 0.8806 (mm) cc_final: 0.8501 (tp) REVERT: L 7 MET cc_start: 0.9016 (mmt) cc_final: 0.8797 (mmm) REVERT: L 14 SER cc_start: 0.8816 (p) cc_final: 0.8165 (m) REVERT: L 24 VAL cc_start: 0.7519 (t) cc_final: 0.7023 (m) REVERT: L 35 VAL cc_start: 0.8221 (t) cc_final: 0.8016 (t) REVERT: L 67 LYS cc_start: 0.9130 (tptp) cc_final: 0.8725 (tptm) REVERT: L 75 SER cc_start: 0.9125 (m) cc_final: 0.8868 (m) REVERT: L 84 CYS cc_start: 0.9016 (OUTLIER) cc_final: 0.8424 (m) REVERT: L 112 PHE cc_start: 0.7206 (m-80) cc_final: 0.6922 (m-80) REVERT: L 118 LEU cc_start: 0.8242 (mt) cc_final: 0.8011 (mt) REVERT: M 81 ASP cc_start: 0.8276 (m-30) cc_final: 0.7866 (m-30) REVERT: M 92 LEU cc_start: 0.8403 (mp) cc_final: 0.7844 (tt) REVERT: M 143 GLU cc_start: 0.4963 (OUTLIER) cc_final: 0.4559 (pm20) REVERT: N 6 ARG cc_start: 0.6848 (OUTLIER) cc_final: 0.6520 (tmm160) REVERT: N 88 ASN cc_start: 0.7264 (m-40) cc_final: 0.6529 (t0) REVERT: N 108 VAL cc_start: 0.8638 (m) cc_final: 0.8363 (m) REVERT: O 6 SER cc_start: 0.7756 (m) cc_final: 0.7379 (p) REVERT: O 79 LEU cc_start: 0.9527 (mt) cc_final: 0.9288 (mt) REVERT: O 99 LYS cc_start: 0.7587 (mtmm) cc_final: 0.7289 (mtmt) REVERT: O 102 PHE cc_start: 0.8368 (m-80) cc_final: 0.7917 (m-80) REVERT: O 106 ASP cc_start: 0.8470 (p0) cc_final: 0.8243 (p0) REVERT: P 12 THR cc_start: 0.8707 (m) cc_final: 0.8468 (p) REVERT: P 20 GLU cc_start: 0.7703 (OUTLIER) cc_final: 0.6578 (tp30) REVERT: P 43 ASN cc_start: 0.7406 (OUTLIER) cc_final: 0.7200 (p0) REVERT: Q 13 MET cc_start: 0.8670 (mtp) cc_final: 0.8356 (tmm) REVERT: Q 52 ASN cc_start: 0.8911 (m-40) cc_final: 0.8707 (m-40) REVERT: Q 96 LYS cc_start: 0.8857 (mmtp) cc_final: 0.8257 (mttp) REVERT: Q 98 TYR cc_start: 0.8553 (m-80) cc_final: 0.8044 (m-80) REVERT: R 20 GLN cc_start: 0.9597 (mt0) cc_final: 0.9338 (mt0) REVERT: R 52 GLN cc_start: 0.8288 (mt0) cc_final: 0.7729 (tp40) REVERT: R 74 ILE cc_start: 0.9127 (OUTLIER) cc_final: 0.8775 (tp) REVERT: R 95 LEU cc_start: 0.9564 (mt) cc_final: 0.9060 (tp) REVERT: R 106 PHE cc_start: 0.8698 (t80) cc_final: 0.8413 (t80) REVERT: S 10 LYS cc_start: 0.8551 (OUTLIER) cc_final: 0.8310 (ptmt) REVERT: S 23 GLU cc_start: 0.7900 (mm-30) cc_final: 0.7524 (tp30) REVERT: S 31 GLU cc_start: 0.9543 (mm-30) cc_final: 0.9241 (mp0) REVERT: S 37 GLU cc_start: 0.9025 (mt-10) cc_final: 0.8674 (pm20) REVERT: S 41 ILE cc_start: 0.8669 (mt) cc_final: 0.8025 (mm) REVERT: S 76 LYS cc_start: 0.8584 (mttt) cc_final: 0.8276 (mtmt) REVERT: S 81 LYS cc_start: 0.8588 (mmtm) cc_final: 0.8151 (tppt) REVERT: T 24 ILE cc_start: 0.8598 (pt) cc_final: 0.8287 (pt) REVERT: T 86 MET cc_start: 0.5008 (tpt) cc_final: 0.4681 (ttm) REVERT: U 52 GLU cc_start: 0.8720 (mt-10) cc_final: 0.8429 (tp30) REVERT: U 61 LEU cc_start: 0.6141 (pp) cc_final: 0.4619 (pt) REVERT: V 35 ILE cc_start: 0.8904 (mt) cc_final: 0.8406 (tp) REVERT: V 37 GLU cc_start: 0.8485 (tt0) cc_final: 0.8223 (tm-30) REVERT: V 61 LYS cc_start: 0.8860 (tttt) cc_final: 0.8601 (mtpt) REVERT: V 89 ASP cc_start: 0.7508 (t0) cc_final: 0.7279 (t70) REVERT: W 19 ARG cc_start: 0.8563 (mtm-85) cc_final: 0.8058 (mtt180) REVERT: W 56 PHE cc_start: 0.8941 (t80) cc_final: 0.8718 (t80) REVERT: W 71 LYS cc_start: 0.9026 (mtpt) cc_final: 0.8793 (mmtt) REVERT: W 83 LYS cc_start: 0.8297 (mttt) cc_final: 0.7952 (mtpp) REVERT: W 91 PHE cc_start: 0.9183 (m-80) cc_final: 0.8946 (m-10) REVERT: X 14 ARG cc_start: 0.6161 (mtm-85) cc_final: 0.5897 (mtt180) REVERT: X 17 GLU cc_start: 0.8928 (mm-30) cc_final: 0.8610 (tp30) REVERT: X 25 ARG cc_start: 0.8686 (mmt-90) cc_final: 0.7868 (mmm-85) REVERT: X 29 GLU cc_start: 0.8323 (tt0) cc_final: 0.8000 (tp30) REVERT: X 32 LEU cc_start: 0.9073 (mt) cc_final: 0.8831 (tt) REVERT: X 35 SER cc_start: 0.8092 (OUTLIER) cc_final: 0.7837 (m) REVERT: X 58 THR cc_start: 0.8474 (OUTLIER) cc_final: 0.8226 (m) REVERT: X 82 ILE cc_start: 0.7790 (mm) cc_final: 0.7544 (mt) REVERT: Y 6 GLN cc_start: 0.8078 (mt0) cc_final: 0.7819 (tt0) REVERT: Y 50 ARG cc_start: 0.7530 (ttt180) cc_final: 0.6918 (mtp85) REVERT: Z 24 GLU cc_start: 0.9272 (mt-10) cc_final: 0.9038 (tm-30) REVERT: Z 27 ASN cc_start: 0.9105 (t0) cc_final: 0.8852 (t0) REVERT: Z 28 LEU cc_start: 0.9302 (OUTLIER) cc_final: 0.9056 (mt) REVERT: Z 30 MET cc_start: 0.8116 (mmm) cc_final: 0.7753 (mmm) REVERT: Z 48 ARG cc_start: 0.8586 (OUTLIER) cc_final: 0.8323 (ttm110) REVERT: Z 49 ASP cc_start: 0.9068 (m-30) cc_final: 0.8823 (t0) REVERT: Z 50 VAL cc_start: 0.8729 (t) cc_final: 0.8501 (t) REVERT: a 47 MET cc_start: 0.8806 (mtm) cc_final: 0.8303 (tpp) REVERT: b 4 GLN cc_start: 0.7899 (OUTLIER) cc_final: 0.7568 (pm20) REVERT: b 20 ASP cc_start: 0.8076 (m-30) cc_final: 0.7858 (m-30) REVERT: b 46 ASP cc_start: 0.9408 (OUTLIER) cc_final: 0.9040 (t0) REVERT: b 48 TYR cc_start: 0.9026 (m-80) cc_final: 0.8392 (m-80) REVERT: c 7 GLU cc_start: 0.8570 (mt-10) cc_final: 0.8180 (tm-30) REVERT: c 10 LYS cc_start: 0.6910 (pttp) cc_final: 0.6544 (pttt) REVERT: c 19 HIS cc_start: 0.8595 (t-90) cc_final: 0.8160 (t-90) REVERT: c 20 PHE cc_start: 0.8983 (p90) cc_final: 0.8513 (p90) REVERT: c 21 TYR cc_start: 0.8234 (m-80) cc_final: 0.6465 (m-80) REVERT: c 30 LYS cc_start: 0.7014 (mmtp) cc_final: 0.6657 (mtpp) REVERT: c 33 LYS cc_start: 0.8683 (mmtp) cc_final: 0.8321 (ttpp) REVERT: d 13 ASN cc_start: 0.8689 (m-40) cc_final: 0.8143 (t0) REVERT: d 26 ASN cc_start: 0.8647 (m110) cc_final: 0.8277 (m-40) REVERT: d 30 VAL cc_start: 0.8818 (t) cc_final: 0.8509 (t) REVERT: d 31 LEU cc_start: 0.8618 (mt) cc_final: 0.8350 (mt) REVERT: e 22 PHE cc_start: 0.7867 (m-80) cc_final: 0.7223 (m-10) REVERT: e 33 LEU cc_start: 0.8452 (mt) cc_final: 0.8227 (mt) REVERT: e 50 VAL cc_start: 0.8248 (OUTLIER) cc_final: 0.8035 (m) REVERT: f 15 LYS cc_start: 0.8492 (mtpt) cc_final: 0.8126 (ptmt) REVERT: f 34 LYS cc_start: 0.8854 (ttpt) cc_final: 0.8612 (ttmt) REVERT: i 23 THR cc_start: 0.3286 (OUTLIER) cc_final: 0.3064 (t) REVERT: i 375 ARG cc_start: 0.9072 (mtt180) cc_final: 0.8314 (mmp80) REVERT: i 423 MET cc_start: 0.8203 (tpp) cc_final: 0.7963 (tpt) REVERT: l 246 LEU cc_start: -0.0543 (mt) cc_final: -0.0773 (mt) outliers start: 319 outliers final: 57 residues processed: 1595 average time/residue: 1.0772 time to fit residues: 2798.4283 Evaluate side-chains 866 residues out of total 3823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 774 time to evaluate : 4.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 772 random chunks: chunk 651 optimal weight: 10.0000 chunk 585 optimal weight: 2.9990 chunk 324 optimal weight: 0.7980 chunk 199 optimal weight: 20.0000 chunk 394 optimal weight: 9.9990 chunk 312 optimal weight: 9.9990 chunk 605 optimal weight: 20.0000 chunk 234 optimal weight: 20.0000 chunk 367 optimal weight: 5.9990 chunk 450 optimal weight: 7.9990 chunk 701 optimal weight: 8.9990 overall best weight: 5.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 15 HIS C 86 ASN C 90 ASN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 163 GLN C 197 ASN C 200 HIS C 251 GLN D 49 GLN D 140 HIS D 150 GLN D 173 GLN E 41 GLN ** E 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN ** F 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN ** H 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 86 GLN M 104 GLN ** N 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 19 GLN Q 75 GLN R 72 ASN ** R 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 59 ASN ** U 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 49 ASN Z 58 ASN b 6 ASN d 26 ASN i 26 ASN ** i 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.3102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.114 110109 Z= 0.254 Angle : 0.716 28.615 163852 Z= 0.357 Chirality : 0.038 0.316 20612 Planarity : 0.006 0.068 9393 Dihedral : 23.420 178.408 53755 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 17.01 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.06 % Favored : 97.90 % Rotamer: Outliers : 0.09 % Allowed : 3.64 % Favored : 96.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.95 % Cis-general : 0.11 % 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: -0.70 (0.11), residues: 4664 helix: 0.12 (0.12), residues: 1817 sheet: -0.68 (0.16), residues: 839 loop : -0.77 (0.12), residues: 2008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 248 HIS 0.010 0.002 HIS C 53 PHE 0.025 0.002 PHE H 47 TYR 0.024 0.002 TYR H 25 ARG 0.023 0.001 ARG G 163 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9328 Ramachandran restraints generated. 4664 Oldfield, 0 Emsley, 4664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9328 Ramachandran restraints generated. 4664 Oldfield, 0 Emsley, 4664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 972 residues out of total 3823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 969 time to evaluate : 4.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 6 CYS cc_start: 0.7667 (t) cc_final: 0.7428 (t) REVERT: C 96 TYR cc_start: 0.9201 (m-80) cc_final: 0.8615 (m-80) REVERT: C 114 ASP cc_start: 0.7622 (m-30) cc_final: 0.7405 (m-30) REVERT: C 132 MET cc_start: 0.9182 (mtm) cc_final: 0.8707 (mtm) REVERT: C 176 LEU cc_start: 0.9310 (mt) cc_final: 0.9080 (mp) REVERT: C 180 GLU cc_start: 0.7316 (pt0) cc_final: 0.6931 (pt0) REVERT: C 181 MET cc_start: 0.7658 (tpt) cc_final: 0.7181 (tpp) REVERT: C 201 MET cc_start: 0.7709 (ptt) cc_final: 0.7229 (ttp) REVERT: C 225 MET cc_start: 0.8826 (mtt) cc_final: 0.8544 (mmp) REVERT: D 11 MET cc_start: 0.8460 (mtp) cc_final: 0.8140 (mpp) REVERT: D 100 LEU cc_start: 0.9038 (mm) cc_final: 0.8687 (mm) REVERT: D 125 TRP cc_start: 0.7061 (m100) cc_final: 0.6616 (m100) REVERT: E 25 GLU cc_start: 0.8674 (tt0) cc_final: 0.8341 (tp30) REVERT: E 157 LEU cc_start: 0.9427 (tp) cc_final: 0.9207 (mt) REVERT: F 17 MET cc_start: 0.9063 (tmm) cc_final: 0.8819 (tmm) REVERT: F 20 PHE cc_start: 0.7701 (m-10) cc_final: 0.7339 (m-10) REVERT: F 21 ASN cc_start: 0.9434 (t0) cc_final: 0.9163 (p0) REVERT: F 169 LEU cc_start: 0.9329 (tp) cc_final: 0.9047 (pp) REVERT: F 175 PHE cc_start: 0.9099 (t80) cc_final: 0.8808 (t80) REVERT: G 37 LEU cc_start: 0.7954 (tp) cc_final: 0.7364 (tp) REVERT: G 130 GLU cc_start: 0.9142 (tt0) cc_final: 0.8797 (tm-30) REVERT: G 147 ASP cc_start: 0.8571 (m-30) cc_final: 0.8349 (m-30) REVERT: G 148 LEU cc_start: 0.9736 (mm) cc_final: 0.9532 (mm) REVERT: H 9 VAL cc_start: 0.7121 (m) cc_final: 0.6332 (p) REVERT: H 132 PHE cc_start: 0.6784 (m-80) cc_final: 0.6555 (m-80) REVERT: H 142 VAL cc_start: 0.6592 (t) cc_final: 0.5935 (t) REVERT: I 4 ASN cc_start: 0.8388 (t0) cc_final: 0.8167 (t0) REVERT: I 52 MET cc_start: 0.3723 (ptp) cc_final: 0.3520 (ptp) REVERT: J 117 MET cc_start: 0.6240 (tpt) cc_final: 0.5994 (tpt) REVERT: K 16 TYR cc_start: 0.7967 (m-80) cc_final: 0.7481 (m-80) REVERT: K 32 LEU cc_start: 0.9698 (mt) cc_final: 0.9385 (mt) REVERT: K 89 PHE cc_start: 0.9617 (t80) cc_final: 0.9263 (t80) REVERT: K 92 MET cc_start: 0.8841 (mmm) cc_final: 0.8369 (mmp) REVERT: K 108 MET cc_start: 0.9192 (mtt) cc_final: 0.8467 (mtm) REVERT: K 109 LEU cc_start: 0.9474 (mt) cc_final: 0.9023 (mt) REVERT: K 120 ARG cc_start: 0.9075 (mmm-85) cc_final: 0.8796 (mmm-85) REVERT: L 1 MET cc_start: 0.9218 (mmp) cc_final: 0.8972 (mmp) REVERT: L 2 ILE cc_start: 0.8740 (mm) cc_final: 0.8448 (tp) REVERT: L 35 VAL cc_start: 0.7674 (t) cc_final: 0.7409 (t) REVERT: L 37 ASP cc_start: 0.8196 (t0) cc_final: 0.7699 (t0) REVERT: L 66 LYS cc_start: 0.9109 (mtpt) cc_final: 0.8743 (mtmp) REVERT: L 67 LYS cc_start: 0.9042 (tptp) cc_final: 0.8771 (tptm) REVERT: L 73 ASP cc_start: 0.9235 (p0) cc_final: 0.8661 (p0) REVERT: L 84 CYS cc_start: 0.9204 (p) cc_final: 0.8920 (p) REVERT: L 106 GLU cc_start: 0.8035 (mt-10) cc_final: 0.7730 (pp20) REVERT: L 112 PHE cc_start: 0.7888 (m-80) cc_final: 0.6833 (m-80) REVERT: L 113 MET cc_start: 0.8959 (tmm) cc_final: 0.8742 (tpp) REVERT: M 51 GLU cc_start: 0.7237 (mt-10) cc_final: 0.6921 (tp30) REVERT: M 81 ASP cc_start: 0.8553 (m-30) cc_final: 0.8223 (m-30) REVERT: N 2 LEU cc_start: 0.9145 (mt) cc_final: 0.8628 (mp) REVERT: N 6 ARG cc_start: 0.7674 (ptm-80) cc_final: 0.7409 (ptt90) REVERT: N 65 ILE cc_start: 0.9104 (pt) cc_final: 0.8821 (pt) REVERT: N 82 MET cc_start: 0.8895 (tpp) cc_final: 0.8003 (tpp) REVERT: N 88 ASN cc_start: 0.7589 (m-40) cc_final: 0.6800 (t0) REVERT: N 96 ILE cc_start: 0.9197 (mm) cc_final: 0.8228 (mm) REVERT: N 97 GLN cc_start: 0.8928 (mp10) cc_final: 0.7855 (mt0) REVERT: N 103 TYR cc_start: 0.7668 (m-10) cc_final: 0.7356 (m-10) REVERT: O 6 SER cc_start: 0.8378 (m) cc_final: 0.8072 (p) REVERT: O 80 PHE cc_start: 0.8958 (m-80) cc_final: 0.8644 (m-80) REVERT: O 106 ASP cc_start: 0.8557 (p0) cc_final: 0.8333 (p0) REVERT: P 93 ASP cc_start: 0.8077 (t70) cc_final: 0.7753 (t0) REVERT: Q 25 THR cc_start: 0.7977 (m) cc_final: 0.7512 (p) REVERT: Q 52 ASN cc_start: 0.8916 (m-40) cc_final: 0.8702 (m-40) REVERT: Q 56 HIS cc_start: 0.8651 (m-70) cc_final: 0.8194 (m-70) REVERT: Q 96 LYS cc_start: 0.8729 (mmtp) cc_final: 0.8142 (mmtm) REVERT: R 52 GLN cc_start: 0.8237 (mt0) cc_final: 0.7826 (mt0) REVERT: R 90 ILE cc_start: 0.9224 (pt) cc_final: 0.8928 (pt) REVERT: R 106 PHE cc_start: 0.9257 (t80) cc_final: 0.9050 (t80) REVERT: S 23 GLU cc_start: 0.8400 (mm-30) cc_final: 0.7881 (pp20) REVERT: S 37 GLU cc_start: 0.8745 (mt-10) cc_final: 0.8532 (pm20) REVERT: S 43 ASN cc_start: 0.9552 (p0) cc_final: 0.9329 (p0) REVERT: S 46 GLU cc_start: 0.9186 (tm-30) cc_final: 0.8709 (tm-30) REVERT: S 86 GLN cc_start: 0.8417 (pt0) cc_final: 0.8116 (pm20) REVERT: S 95 ASP cc_start: 0.8811 (m-30) cc_final: 0.8529 (m-30) REVERT: T 65 ASP cc_start: 0.8883 (p0) cc_final: 0.8641 (p0) REVERT: U 52 GLU cc_start: 0.8950 (mt-10) cc_final: 0.8537 (tp30) REVERT: U 87 LEU cc_start: 0.8753 (mp) cc_final: 0.8475 (mp) REVERT: V 37 GLU cc_start: 0.8432 (tt0) cc_final: 0.7940 (tm-30) REVERT: V 41 LEU cc_start: 0.9446 (mm) cc_final: 0.8715 (mm) REVERT: W 1 MET cc_start: 0.8172 (tpt) cc_final: 0.7888 (tmm) REVERT: W 7 GLU cc_start: 0.9366 (tt0) cc_final: 0.9152 (pm20) REVERT: W 40 ILE cc_start: 0.9240 (pt) cc_final: 0.8812 (pt) REVERT: W 41 GLU cc_start: 0.9318 (mt-10) cc_final: 0.8656 (mp0) REVERT: W 56 PHE cc_start: 0.9112 (t80) cc_final: 0.8716 (t80) REVERT: W 57 TYR cc_start: 0.7814 (m-80) cc_final: 0.7001 (m-80) REVERT: W 84 PRO cc_start: 0.8344 (Cg_exo) cc_final: 0.7886 (Cg_endo) REVERT: X 14 ARG cc_start: 0.6372 (mtm-85) cc_final: 0.5704 (mtm180) REVERT: X 25 ARG cc_start: 0.8767 (mmt-90) cc_final: 0.7982 (mmm-85) REVERT: X 29 GLU cc_start: 0.8163 (tt0) cc_final: 0.7548 (tp30) REVERT: X 32 LEU cc_start: 0.9050 (mt) cc_final: 0.8840 (tt) REVERT: X 51 VAL cc_start: 0.6114 (t) cc_final: 0.5660 (t) REVERT: X 82 ILE cc_start: 0.8176 (mm) cc_final: 0.7690 (mt) REVERT: Y 6 GLN cc_start: 0.8954 (mt0) cc_final: 0.8644 (tt0) REVERT: Y 23 ASN cc_start: 0.7944 (m110) cc_final: 0.6582 (p0) REVERT: Y 27 ARG cc_start: 0.7108 (ptm160) cc_final: 0.6795 (ptm160) REVERT: Y 46 PHE cc_start: 0.8307 (m-10) cc_final: 0.7951 (m-80) REVERT: Y 50 ARG cc_start: 0.7422 (ttt180) cc_final: 0.6978 (mtp85) REVERT: Y 68 LEU cc_start: 0.8119 (mt) cc_final: 0.7691 (mt) REVERT: Y 72 ARG cc_start: 0.8116 (mpp80) cc_final: 0.7372 (mmm160) REVERT: Z 30 MET cc_start: 0.8139 (mmm) cc_final: 0.7832 (mmm) REVERT: Z 49 ASP cc_start: 0.9263 (m-30) cc_final: 0.8690 (t0) REVERT: Z 53 VAL cc_start: 0.9041 (t) cc_final: 0.8607 (p) REVERT: a 37 GLU cc_start: 0.9069 (mm-30) cc_final: 0.8630 (mm-30) REVERT: a 54 MET cc_start: 0.8471 (ppp) cc_final: 0.7726 (tmm) REVERT: b 15 MET cc_start: 0.7597 (mtm) cc_final: 0.7354 (mtm) REVERT: b 20 ASP cc_start: 0.8501 (m-30) cc_final: 0.8101 (m-30) REVERT: b 46 ASP cc_start: 0.9609 (m-30) cc_final: 0.9221 (t0) REVERT: b 48 TYR cc_start: 0.9241 (m-80) cc_final: 0.8746 (m-80) REVERT: c 11 LEU cc_start: 0.8577 (mm) cc_final: 0.8299 (mm) REVERT: c 20 PHE cc_start: 0.8923 (p90) cc_final: 0.8233 (p90) REVERT: c 21 TYR cc_start: 0.8194 (m-80) cc_final: 0.6977 (m-80) REVERT: c 35 GLU cc_start: 0.8555 (tt0) cc_final: 0.8016 (mm-30) REVERT: c 36 LEU cc_start: 0.6612 (mt) cc_final: 0.6057 (tp) REVERT: d 13 ASN cc_start: 0.8910 (m-40) cc_final: 0.8369 (t0) REVERT: d 16 HIS cc_start: 0.7516 (m-70) cc_final: 0.7035 (m-70) REVERT: d 22 MET cc_start: 0.9079 (mmt) cc_final: 0.8770 (ptm) REVERT: d 26 ASN cc_start: 0.8710 (m-40) cc_final: 0.8288 (m110) REVERT: d 31 LEU cc_start: 0.8998 (mt) cc_final: 0.8725 (mt) REVERT: d 41 ARG cc_start: 0.7803 (mtp180) cc_final: 0.7596 (mtp180) REVERT: e 64 TYR cc_start: 0.5903 (m-80) cc_final: 0.5368 (m-80) REVERT: f 1 MET cc_start: 0.8203 (ptm) cc_final: 0.7501 (ptm) REVERT: f 15 LYS cc_start: 0.8883 (mtpt) cc_final: 0.8564 (ptmt) REVERT: f 28 SER cc_start: 0.8697 (p) cc_final: 0.8192 (p) REVERT: f 34 LYS cc_start: 0.8809 (ttpt) cc_final: 0.8285 (ttmt) REVERT: f 37 GLN cc_start: 0.8484 (mt0) cc_final: 0.8177 (tt0) REVERT: i 344 MET cc_start: 0.5647 (tmm) cc_final: 0.5355 (ppp) REVERT: i 375 ARG cc_start: 0.9101 (mtt180) cc_final: 0.8362 (mmp80) REVERT: l 210 MET cc_start: -0.2695 (mmt) cc_final: -0.3960 (mmt) outliers start: 3 outliers final: 0 residues processed: 971 average time/residue: 1.0245 time to fit residues: 1652.6909 Evaluate side-chains 675 residues out of total 3823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 675 time to evaluate : 4.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 772 random chunks: chunk 389 optimal weight: 6.9990 chunk 217 optimal weight: 30.0000 chunk 583 optimal weight: 4.9990 chunk 477 optimal weight: 30.0000 chunk 193 optimal weight: 20.0000 chunk 702 optimal weight: 50.0000 chunk 758 optimal weight: 10.0000 chunk 625 optimal weight: 20.0000 chunk 696 optimal weight: 8.9990 chunk 239 optimal weight: 30.0000 chunk 563 optimal weight: 6.9990 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 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 117 GLN ** C 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 41 GLN ** E 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 5 HIS F 52 ASN J 30 GLN K 58 ASN ** K 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 90 ASN M 104 GLN ** N 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 16 HIS O 23 ASN ** O 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 19 GLN ** R 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 91 GLN ** V 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 87 GLN X 46 HIS ** Z 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 19 HIS ** d 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 13 ASN ** i 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 160 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.5463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.125 110109 Z= 0.302 Angle : 0.767 32.138 163852 Z= 0.384 Chirality : 0.039 0.620 20612 Planarity : 0.007 0.103 9393 Dihedral : 23.628 179.756 53755 Min Nonbonded Distance : 1.775 Molprobity Statistics. All-atom Clashscore : 24.47 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.19 % Favored : 96.76 % Rotamer: Outliers : 0.12 % Allowed : 5.12 % Favored : 94.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.95 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.27 (0.12), residues: 4664 helix: 0.72 (0.12), residues: 1787 sheet: -0.51 (0.16), residues: 831 loop : -0.75 (0.13), residues: 2046 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.005 TRP N 64 HIS 0.010 0.002 HIS a 34 PHE 0.088 0.003 PHE N 28 TYR 0.029 0.003 TYR F 83 ARG 0.057 0.001 ARG K 99 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9328 Ramachandran restraints generated. 4664 Oldfield, 0 Emsley, 4664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9328 Ramachandran restraints generated. 4664 Oldfield, 0 Emsley, 4664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 874 residues out of total 3823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 870 time to evaluate : 4.876 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 6 CYS cc_start: 0.8436 (t) cc_final: 0.8139 (t) REVERT: C 96 TYR cc_start: 0.9016 (m-80) cc_final: 0.8456 (m-80) REVERT: C 132 MET cc_start: 0.9331 (mtm) cc_final: 0.8804 (mtm) REVERT: C 181 MET cc_start: 0.7465 (tpt) cc_final: 0.6940 (tpp) REVERT: C 200 HIS cc_start: 0.9198 (t70) cc_final: 0.8809 (t70) REVERT: C 205 LEU cc_start: 0.9008 (mm) cc_final: 0.8622 (mm) REVERT: D 49 GLN cc_start: 0.9203 (tt0) cc_final: 0.8953 (tm-30) REVERT: D 100 LEU cc_start: 0.9386 (mm) cc_final: 0.9032 (mm) REVERT: D 125 TRP cc_start: 0.8091 (m100) cc_final: 0.7052 (m100) REVERT: D 161 MET cc_start: 0.7556 (pmm) cc_final: 0.6741 (pmm) REVERT: D 201 LEU cc_start: 0.8010 (mt) cc_final: 0.7712 (mt) REVERT: E 1 MET cc_start: 0.8546 (ptp) cc_final: 0.7831 (pmm) REVERT: E 157 LEU cc_start: 0.9594 (tp) cc_final: 0.9268 (mt) REVERT: F 21 ASN cc_start: 0.9393 (t0) cc_final: 0.9084 (p0) REVERT: G 101 ASN cc_start: 0.9228 (p0) cc_final: 0.8596 (t0) REVERT: G 130 GLU cc_start: 0.9208 (tt0) cc_final: 0.8837 (tm-30) REVERT: G 147 ASP cc_start: 0.8335 (m-30) cc_final: 0.8128 (m-30) REVERT: H 116 ARG cc_start: 0.8017 (mmt-90) cc_final: 0.7666 (mmt180) REVERT: H 132 PHE cc_start: 0.6547 (m-80) cc_final: 0.6245 (m-80) REVERT: H 142 VAL cc_start: 0.7050 (t) cc_final: 0.6173 (t) REVERT: I 57 ASN cc_start: 0.4893 (p0) cc_final: 0.4222 (p0) REVERT: K 25 LEU cc_start: 0.9696 (tt) cc_final: 0.9454 (tt) REVERT: K 89 PHE cc_start: 0.9582 (t80) cc_final: 0.9214 (t80) REVERT: K 99 ARG cc_start: 0.8991 (mmm160) cc_final: 0.8550 (mmm160) REVERT: K 108 MET cc_start: 0.9349 (mtt) cc_final: 0.8440 (mpp) REVERT: K 109 LEU cc_start: 0.9324 (mt) cc_final: 0.9054 (mt) REVERT: L 1 MET cc_start: 0.9406 (mmp) cc_final: 0.8870 (mmp) REVERT: L 20 MET cc_start: 0.8295 (tmm) cc_final: 0.7935 (tmm) REVERT: L 37 ASP cc_start: 0.8593 (t0) cc_final: 0.8057 (t0) REVERT: L 53 LYS cc_start: 0.7338 (mmmm) cc_final: 0.7098 (mmmt) REVERT: L 63 VAL cc_start: 0.9314 (m) cc_final: 0.9046 (p) REVERT: L 67 LYS cc_start: 0.9274 (tptp) cc_final: 0.8878 (mtpt) REVERT: L 73 ASP cc_start: 0.9159 (p0) cc_final: 0.8561 (p0) REVERT: L 106 GLU cc_start: 0.8707 (mt-10) cc_final: 0.8084 (pp20) REVERT: L 107 LEU cc_start: 0.9530 (tp) cc_final: 0.9283 (tp) REVERT: L 112 PHE cc_start: 0.8251 (m-80) cc_final: 0.7762 (m-80) REVERT: M 77 ILE cc_start: 0.8122 (tt) cc_final: 0.7900 (tp) REVERT: M 81 ASP cc_start: 0.8851 (m-30) cc_final: 0.8250 (t0) REVERT: N 2 LEU cc_start: 0.9134 (mt) cc_final: 0.8639 (mp) REVERT: N 68 PHE cc_start: 0.6241 (t80) cc_final: 0.5655 (t80) REVERT: N 82 MET cc_start: 0.8548 (tpp) cc_final: 0.8008 (tpp) REVERT: N 88 ASN cc_start: 0.7477 (m-40) cc_final: 0.6627 (t0) REVERT: N 96 ILE cc_start: 0.9478 (mm) cc_final: 0.8762 (mm) REVERT: N 97 GLN cc_start: 0.9099 (mp10) cc_final: 0.8345 (mt0) REVERT: N 103 TYR cc_start: 0.7721 (m-10) cc_final: 0.7451 (m-10) REVERT: O 6 SER cc_start: 0.8591 (m) cc_final: 0.8148 (p) REVERT: O 44 LEU cc_start: 0.9511 (mt) cc_final: 0.9302 (mt) REVERT: O 46 ARG cc_start: 0.8657 (mtm110) cc_final: 0.8407 (ttp80) REVERT: O 80 PHE cc_start: 0.8962 (m-80) cc_final: 0.8516 (m-10) REVERT: P 93 ASP cc_start: 0.8025 (t70) cc_final: 0.7709 (t0) REVERT: Q 52 ASN cc_start: 0.8951 (m-40) cc_final: 0.8640 (m-40) REVERT: Q 56 HIS cc_start: 0.9066 (m-70) cc_final: 0.8532 (m-70) REVERT: R 95 LEU cc_start: 0.9370 (mm) cc_final: 0.9108 (mm) REVERT: R 106 PHE cc_start: 0.9488 (t80) cc_final: 0.8976 (t80) REVERT: S 10 LYS cc_start: 0.8493 (mtmm) cc_final: 0.7734 (mttm) REVERT: S 18 GLN cc_start: 0.6998 (tt0) cc_final: 0.6708 (tt0) REVERT: S 23 GLU cc_start: 0.8707 (mm-30) cc_final: 0.8212 (tp30) REVERT: S 43 ASN cc_start: 0.9285 (p0) cc_final: 0.8826 (p0) REVERT: S 46 GLU cc_start: 0.9079 (tm-30) cc_final: 0.8873 (tm-30) REVERT: S 82 HIS cc_start: 0.8376 (t-90) cc_final: 0.8137 (t-90) REVERT: T 31 GLN cc_start: 0.8940 (tp-100) cc_final: 0.8504 (tp-100) REVERT: T 78 GLU cc_start: 0.9467 (pt0) cc_final: 0.8927 (pp20) REVERT: U 52 GLU cc_start: 0.8983 (mt-10) cc_final: 0.8667 (tp30) REVERT: U 69 ARG cc_start: 0.8699 (mpp-170) cc_final: 0.8316 (ptp-170) REVERT: U 84 TYR cc_start: 0.9208 (m-80) cc_final: 0.8423 (m-80) REVERT: V 10 GLU cc_start: 0.7291 (tp30) cc_final: 0.6562 (tp30) REVERT: V 22 ARG cc_start: 0.8653 (mtp180) cc_final: 0.8275 (mtp-110) REVERT: V 37 GLU cc_start: 0.8092 (tt0) cc_final: 0.7817 (tm-30) REVERT: V 73 PHE cc_start: 0.8173 (t80) cc_final: 0.6626 (t80) REVERT: V 94 ARG cc_start: 0.7798 (mpp80) cc_final: 0.7519 (mpp80) REVERT: W 1 MET cc_start: 0.8322 (tpt) cc_final: 0.7346 (tmm) REVERT: W 7 GLU cc_start: 0.9432 (tt0) cc_final: 0.8929 (pm20) REVERT: W 40 ILE cc_start: 0.9133 (pt) cc_final: 0.8657 (pt) REVERT: W 41 GLU cc_start: 0.9375 (mt-10) cc_final: 0.8633 (mp0) REVERT: W 46 LYS cc_start: 0.9609 (mmtm) cc_final: 0.9350 (mmmt) REVERT: X 12 ASN cc_start: 0.6810 (m110) cc_final: 0.6175 (m110) REVERT: X 20 ARG cc_start: 0.8592 (mpt-90) cc_final: 0.8274 (mpp80) REVERT: X 32 LEU cc_start: 0.8857 (mt) cc_final: 0.8615 (tt) REVERT: Y 6 GLN cc_start: 0.9074 (mt0) cc_final: 0.8190 (mt0) REVERT: Y 23 ASN cc_start: 0.9109 (m110) cc_final: 0.7877 (p0) REVERT: Y 46 PHE cc_start: 0.8376 (m-10) cc_final: 0.8051 (m-80) REVERT: Y 54 LYS cc_start: 0.8693 (mppt) cc_final: 0.8431 (tptt) REVERT: Z 17 GLU cc_start: 0.9007 (pp20) cc_final: 0.8741 (pp20) REVERT: Z 24 GLU cc_start: 0.9626 (mt-10) cc_final: 0.9425 (tm-30) REVERT: Z 30 MET cc_start: 0.8245 (mmm) cc_final: 0.7851 (mmm) REVERT: Z 49 ASP cc_start: 0.9353 (m-30) cc_final: 0.8847 (t0) REVERT: a 32 ILE cc_start: 0.9353 (mm) cc_final: 0.9138 (mm) REVERT: a 45 ARG cc_start: 0.9332 (mmm-85) cc_final: 0.9113 (mmm160) REVERT: a 47 MET cc_start: 0.8987 (ttt) cc_final: 0.8382 (tpt) REVERT: a 54 MET cc_start: 0.8555 (ppp) cc_final: 0.8035 (tmm) REVERT: b 5 GLN cc_start: 0.7496 (tp40) cc_final: 0.7247 (tp40) REVERT: b 7 LYS cc_start: 0.9274 (ttpt) cc_final: 0.9061 (ttpp) REVERT: b 46 ASP cc_start: 0.9467 (m-30) cc_final: 0.9112 (t0) REVERT: b 48 TYR cc_start: 0.9350 (m-80) cc_final: 0.8789 (m-80) REVERT: c 11 LEU cc_start: 0.8819 (mm) cc_final: 0.8461 (mm) REVERT: c 20 PHE cc_start: 0.8865 (p90) cc_final: 0.8084 (p90) REVERT: c 35 GLU cc_start: 0.8844 (tt0) cc_final: 0.8295 (mp0) REVERT: c 36 LEU cc_start: 0.7274 (mt) cc_final: 0.6641 (tp) REVERT: d 10 LEU cc_start: 0.9238 (tp) cc_final: 0.8987 (tp) REVERT: d 13 ASN cc_start: 0.8879 (m-40) cc_final: 0.8466 (t0) REVERT: d 16 HIS cc_start: 0.8105 (m-70) cc_final: 0.7658 (m90) REVERT: d 26 ASN cc_start: 0.8702 (m-40) cc_final: 0.8212 (m110) REVERT: d 31 LEU cc_start: 0.9179 (mt) cc_final: 0.8836 (mp) REVERT: e 49 MET cc_start: 0.6940 (mmp) cc_final: 0.6508 (mmm) REVERT: f 1 MET cc_start: 0.8522 (ptm) cc_final: 0.7611 (ptm) REVERT: f 15 LYS cc_start: 0.9234 (mtpt) cc_final: 0.8794 (mtmm) REVERT: f 36 ARG cc_start: 0.8449 (tmm-80) cc_final: 0.7659 (ttp-170) REVERT: f 37 GLN cc_start: 0.8947 (mt0) cc_final: 0.8303 (tt0) REVERT: i 86 MET cc_start: 0.5105 (mtp) cc_final: 0.4808 (ptp) REVERT: i 339 ARG cc_start: 0.6829 (ttp80) cc_final: 0.6624 (ttp80) REVERT: i 375 ARG cc_start: 0.9101 (mtt180) cc_final: 0.8301 (mmp80) REVERT: i 423 MET cc_start: 0.8044 (tpt) cc_final: 0.7696 (tpt) outliers start: 4 outliers final: 1 residues processed: 873 average time/residue: 1.0134 time to fit residues: 1480.5419 Evaluate side-chains 624 residues out of total 3823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 623 time to evaluate : 4.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 772 random chunks: chunk 693 optimal weight: 30.0000 chunk 528 optimal weight: 7.9990 chunk 364 optimal weight: 8.9990 chunk 77 optimal weight: 20.0000 chunk 335 optimal weight: 1.9990 chunk 471 optimal weight: 0.9990 chunk 704 optimal weight: 8.9990 chunk 746 optimal weight: 2.9990 chunk 368 optimal weight: 6.9990 chunk 668 optimal weight: 9.9990 chunk 201 optimal weight: 20.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 117 GLN C 200 HIS ** C 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 36 GLN D 130 GLN ** D 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 115 GLN ** E 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 139 GLN ** K 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 104 GLN ** O 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 19 GLN Q 15 GLN ** R 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 16 ASN Y 20 HIS Z 20 ASN Z 58 ASN f 13 ASN ** i 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.5867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 110109 Z= 0.173 Angle : 0.606 29.967 163852 Z= 0.300 Chirality : 0.033 0.306 20612 Planarity : 0.005 0.066 9393 Dihedral : 23.500 179.202 53755 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 17.38 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.68 % Favored : 97.26 % Rotamer: Outliers : 0.03 % Allowed : 3.19 % Favored : 96.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.95 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.12), residues: 4664 helix: 1.30 (0.12), residues: 1792 sheet: -0.22 (0.17), residues: 842 loop : -0.58 (0.13), residues: 2030 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP N 64 HIS 0.013 0.001 HIS i 62 PHE 0.022 0.002 PHE d 18 TYR 0.018 0.002 TYR W 57 ARG 0.013 0.001 ARG K 99 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9328 Ramachandran restraints generated. 4664 Oldfield, 0 Emsley, 4664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9328 Ramachandran restraints generated. 4664 Oldfield, 0 Emsley, 4664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 848 residues out of total 3823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 847 time to evaluate : 5.045 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 6 CYS cc_start: 0.8501 (t) cc_final: 0.8108 (t) REVERT: C 91 ILE cc_start: 0.9451 (mm) cc_final: 0.8874 (tp) REVERT: C 96 TYR cc_start: 0.8987 (m-80) cc_final: 0.8433 (m-80) REVERT: C 132 MET cc_start: 0.9166 (mtm) cc_final: 0.8658 (mtm) REVERT: C 163 GLN cc_start: 0.8534 (tp-100) cc_final: 0.8273 (tm-30) REVERT: C 181 MET cc_start: 0.7796 (tpt) cc_final: 0.7127 (tpp) REVERT: C 200 HIS cc_start: 0.9123 (t-90) cc_final: 0.8597 (t70) REVERT: D 32 ASN cc_start: 0.8049 (t0) cc_final: 0.7790 (t0) REVERT: D 33 ARG cc_start: 0.7936 (ptt180) cc_final: 0.7091 (ptt180) REVERT: D 35 THR cc_start: 0.9313 (p) cc_final: 0.8260 (t) REVERT: D 125 TRP cc_start: 0.8170 (m100) cc_final: 0.7152 (m100) REVERT: D 161 MET cc_start: 0.7639 (pmm) cc_final: 0.7230 (pmm) REVERT: D 165 MET cc_start: 0.8055 (tpp) cc_final: 0.7703 (tpt) REVERT: E 1 MET cc_start: 0.8708 (ptp) cc_final: 0.7911 (pmm) REVERT: E 157 LEU cc_start: 0.9566 (tp) cc_final: 0.9290 (mt) REVERT: E 188 MET cc_start: 0.8928 (mtp) cc_final: 0.7999 (ttm) REVERT: F 21 ASN cc_start: 0.9383 (t0) cc_final: 0.9126 (p0) REVERT: F 22 TYR cc_start: 0.7333 (m-10) cc_final: 0.6785 (m-80) REVERT: F 175 PHE cc_start: 0.8992 (m-80) cc_final: 0.8729 (m-80) REVERT: G 33 LEU cc_start: 0.7971 (mt) cc_final: 0.7164 (mt) REVERT: G 37 LEU cc_start: 0.7891 (tp) cc_final: 0.7630 (tp) REVERT: G 52 PHE cc_start: 0.7430 (m-80) cc_final: 0.7227 (m-10) REVERT: G 69 ARG cc_start: 0.8354 (tmt170) cc_final: 0.7981 (tmt-80) REVERT: G 101 ASN cc_start: 0.9250 (p0) cc_final: 0.8637 (t0) REVERT: G 130 GLU cc_start: 0.9111 (tt0) cc_final: 0.8778 (tp30) REVERT: G 147 ASP cc_start: 0.8474 (m-30) cc_final: 0.8255 (m-30) REVERT: H 47 PHE cc_start: 0.8065 (t80) cc_final: 0.7777 (t80) REVERT: H 132 PHE cc_start: 0.6887 (m-80) cc_final: 0.6580 (m-80) REVERT: H 142 VAL cc_start: 0.7138 (t) cc_final: 0.6256 (t) REVERT: I 52 MET cc_start: 0.5164 (pmm) cc_final: 0.4814 (pmm) REVERT: I 57 ASN cc_start: 0.4705 (p0) cc_final: 0.4054 (p0) REVERT: K 13 ARG cc_start: 0.7882 (mtt180) cc_final: 0.7002 (ttm-80) REVERT: K 14 ASP cc_start: 0.9410 (m-30) cc_final: 0.9144 (m-30) REVERT: K 31 GLU cc_start: 0.9044 (tp30) cc_final: 0.8514 (mp0) REVERT: K 44 TYR cc_start: 0.8496 (t80) cc_final: 0.7665 (t80) REVERT: K 69 ARG cc_start: 0.8888 (tpp80) cc_final: 0.8209 (tmm160) REVERT: K 93 ILE cc_start: 0.9158 (mm) cc_final: 0.8915 (mm) REVERT: K 97 PRO cc_start: 0.8535 (Cg_exo) cc_final: 0.8316 (Cg_endo) REVERT: K 108 MET cc_start: 0.9407 (mtt) cc_final: 0.8471 (mpp) REVERT: K 120 ARG cc_start: 0.8975 (mmm-85) cc_final: 0.8762 (ttt180) REVERT: L 37 ASP cc_start: 0.8648 (t0) cc_final: 0.8267 (t0) REVERT: L 54 LYS cc_start: 0.8088 (tttt) cc_final: 0.7654 (tptt) REVERT: L 63 VAL cc_start: 0.9292 (m) cc_final: 0.9048 (p) REVERT: L 67 LYS cc_start: 0.9217 (tptp) cc_final: 0.8900 (mmtt) REVERT: L 73 ASP cc_start: 0.9185 (p0) cc_final: 0.8541 (p0) REVERT: L 106 GLU cc_start: 0.8843 (mt-10) cc_final: 0.8204 (pp20) REVERT: L 112 PHE cc_start: 0.8046 (m-80) cc_final: 0.7292 (m-80) REVERT: M 23 ILE cc_start: 0.9321 (pt) cc_final: 0.8871 (mt) REVERT: N 65 ILE cc_start: 0.9417 (pt) cc_final: 0.9030 (pt) REVERT: N 68 PHE cc_start: 0.6221 (t80) cc_final: 0.5907 (t80) REVERT: N 73 ILE cc_start: 0.8718 (mt) cc_final: 0.8430 (mt) REVERT: N 88 ASN cc_start: 0.7901 (m-40) cc_final: 0.6751 (t0) REVERT: N 90 GLU cc_start: 0.8900 (mm-30) cc_final: 0.7869 (mp0) REVERT: N 96 ILE cc_start: 0.9434 (mm) cc_final: 0.8784 (mm) REVERT: N 97 GLN cc_start: 0.8992 (mp10) cc_final: 0.8357 (mt0) REVERT: N 103 TYR cc_start: 0.7733 (m-10) cc_final: 0.7234 (m-10) REVERT: N 124 LEU cc_start: 0.8859 (mm) cc_final: 0.8560 (mm) REVERT: N 135 VAL cc_start: 0.6091 (m) cc_final: 0.5622 (m) REVERT: O 6 SER cc_start: 0.8644 (m) cc_final: 0.8217 (p) REVERT: O 23 ASN cc_start: 0.9030 (m110) cc_final: 0.8767 (m110) REVERT: O 43 GLU cc_start: 0.9109 (tp30) cc_final: 0.8863 (tp30) REVERT: O 44 LEU cc_start: 0.9554 (mt) cc_final: 0.9244 (mt) REVERT: O 72 ASP cc_start: 0.7032 (t0) cc_final: 0.6116 (t0) REVERT: O 86 ARG cc_start: 0.8800 (ttm110) cc_final: 0.8329 (ttm-80) REVERT: P 55 GLU cc_start: 0.8315 (mt-10) cc_final: 0.7734 (mm-30) REVERT: P 93 ASP cc_start: 0.8012 (t70) cc_final: 0.7710 (t0) REVERT: Q 52 ASN cc_start: 0.8843 (m-40) cc_final: 0.8491 (m-40) REVERT: R 44 GLN cc_start: 0.9304 (tp40) cc_final: 0.9074 (tp-100) REVERT: R 52 GLN cc_start: 0.8395 (mt0) cc_final: 0.8100 (mt0) REVERT: R 83 LEU cc_start: 0.9106 (mm) cc_final: 0.8880 (mm) REVERT: R 90 ILE cc_start: 0.8903 (pt) cc_final: 0.8695 (pt) REVERT: R 97 ASP cc_start: 0.9141 (m-30) cc_final: 0.8906 (m-30) REVERT: S 10 LYS cc_start: 0.8544 (mtmm) cc_final: 0.7597 (mttm) REVERT: S 23 GLU cc_start: 0.8730 (mm-30) cc_final: 0.7942 (tp30) REVERT: S 43 ASN cc_start: 0.9421 (p0) cc_final: 0.9006 (p0) REVERT: S 46 GLU cc_start: 0.8917 (tm-30) cc_final: 0.8654 (tm-30) REVERT: S 82 HIS cc_start: 0.8554 (t-90) cc_final: 0.8279 (t-90) REVERT: S 99 THR cc_start: 0.8681 (p) cc_final: 0.8458 (p) REVERT: T 78 GLU cc_start: 0.9380 (pt0) cc_final: 0.8728 (pp20) REVERT: U 52 GLU cc_start: 0.9086 (mt-10) cc_final: 0.8566 (tp30) REVERT: U 53 VAL cc_start: 0.8650 (m) cc_final: 0.8301 (t) REVERT: U 69 ARG cc_start: 0.8827 (mtm-85) cc_final: 0.8374 (ptp-170) REVERT: U 84 TYR cc_start: 0.9174 (m-80) cc_final: 0.8879 (m-80) REVERT: U 92 ASN cc_start: 0.8069 (p0) cc_final: 0.7796 (p0) REVERT: V 39 ILE cc_start: 0.9563 (mm) cc_final: 0.9012 (mm) REVERT: V 73 PHE cc_start: 0.8395 (t80) cc_final: 0.7442 (t80) REVERT: V 94 ARG cc_start: 0.7870 (mpp80) cc_final: 0.7430 (mpp80) REVERT: W 41 GLU cc_start: 0.9386 (mt-10) cc_final: 0.8759 (mt-10) REVERT: W 59 GLU cc_start: 0.8141 (tp30) cc_final: 0.7855 (tp30) REVERT: X 25 ARG cc_start: 0.9053 (mmt-90) cc_final: 0.8724 (mmm-85) REVERT: X 32 LEU cc_start: 0.8851 (mt) cc_final: 0.8610 (tt) REVERT: X 39 ARG cc_start: 0.8554 (mtp-110) cc_final: 0.8338 (mtp-110) REVERT: Y 6 GLN cc_start: 0.8963 (mt0) cc_final: 0.8453 (tt0) REVERT: Y 23 ASN cc_start: 0.9080 (m110) cc_final: 0.7813 (p0) REVERT: Y 45 ARG cc_start: 0.8290 (mtt-85) cc_final: 0.8002 (mmt180) REVERT: Y 46 PHE cc_start: 0.8613 (m-10) cc_final: 0.8127 (m-80) REVERT: Z 30 MET cc_start: 0.8251 (mmm) cc_final: 0.7895 (mmm) REVERT: Z 49 ASP cc_start: 0.9342 (m-30) cc_final: 0.8838 (t0) REVERT: a 21 LYS cc_start: 0.8735 (mptt) cc_final: 0.8528 (mmtp) REVERT: a 32 ILE cc_start: 0.9381 (mm) cc_final: 0.9149 (mm) REVERT: a 45 ARG cc_start: 0.9501 (mmm-85) cc_final: 0.9295 (mmm160) REVERT: a 54 MET cc_start: 0.8575 (ppp) cc_final: 0.8048 (tmm) REVERT: b 5 GLN cc_start: 0.7182 (tp40) cc_final: 0.6880 (tp40) REVERT: b 36 GLU cc_start: 0.8931 (tp30) cc_final: 0.8696 (tp30) REVERT: b 48 TYR cc_start: 0.9087 (m-80) cc_final: 0.8704 (m-80) REVERT: c 20 PHE cc_start: 0.8782 (p90) cc_final: 0.7924 (p90) REVERT: c 33 LYS cc_start: 0.8636 (mmtp) cc_final: 0.8148 (ttpt) REVERT: d 10 LEU cc_start: 0.9216 (tp) cc_final: 0.8989 (tp) REVERT: d 13 ASN cc_start: 0.8858 (m-40) cc_final: 0.8357 (t0) REVERT: d 16 HIS cc_start: 0.7953 (m-70) cc_final: 0.7363 (m-70) REVERT: d 25 LYS cc_start: 0.9280 (ptmt) cc_final: 0.8855 (mmmt) REVERT: d 26 ASN cc_start: 0.8860 (m-40) cc_final: 0.8120 (m110) REVERT: e 49 MET cc_start: 0.6530 (mmp) cc_final: 0.6243 (mmm) REVERT: f 1 MET cc_start: 0.8542 (ptm) cc_final: 0.8115 (ptm) REVERT: f 8 LYS cc_start: 0.7738 (tppt) cc_final: 0.7226 (mmtt) REVERT: f 15 LYS cc_start: 0.9199 (mtpt) cc_final: 0.8860 (mtmm) REVERT: f 36 ARG cc_start: 0.8466 (tmm-80) cc_final: 0.7994 (tmm-80) REVERT: i 86 MET cc_start: 0.6005 (mtp) cc_final: 0.5643 (ptm) REVERT: i 181 LEU cc_start: 0.8674 (mt) cc_final: 0.8406 (pp) REVERT: i 202 MET cc_start: 0.5565 (tpp) cc_final: 0.4439 (mmp) REVERT: i 375 ARG cc_start: 0.9083 (mtt180) cc_final: 0.8270 (mmp80) REVERT: i 423 MET cc_start: 0.8024 (tpt) cc_final: 0.7743 (tpt) REVERT: l 210 MET cc_start: -0.3246 (mmp) cc_final: -0.3805 (mmt) outliers start: 1 outliers final: 0 residues processed: 847 average time/residue: 0.9877 time to fit residues: 1409.8394 Evaluate side-chains 637 residues out of total 3823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 637 time to evaluate : 4.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 772 random chunks: chunk 621 optimal weight: 7.9990 chunk 423 optimal weight: 30.0000 chunk 10 optimal weight: 20.0000 chunk 555 optimal weight: 6.9990 chunk 307 optimal weight: 30.0000 chunk 636 optimal weight: 8.9990 chunk 515 optimal weight: 30.0000 chunk 0 optimal weight: 40.0000 chunk 381 optimal weight: 2.9990 chunk 669 optimal weight: 50.0000 chunk 188 optimal weight: 20.0000 overall best weight: 9.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 115 GLN ** E 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 93 ASN M 104 GLN ** N 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 98 GLN R 37 GLN R 81 ASN S 12 HIS T 7 HIS ** V 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 20 HIS ** Z 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 45 GLN f 13 ASN f 35 GLN ** i 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 91 GLN ** i 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 381 ASN l 154 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.7697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.108 110109 Z= 0.330 Angle : 0.806 31.935 163852 Z= 0.398 Chirality : 0.041 0.321 20612 Planarity : 0.006 0.115 9393 Dihedral : 23.792 179.395 53755 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 32.20 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.63 % Favored : 95.30 % Rotamer: Outliers : 0.06 % Allowed : 4.55 % Favored : 95.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.95 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.24 (0.12), residues: 4664 helix: 0.83 (0.12), residues: 1800 sheet: -0.46 (0.17), residues: 846 loop : -0.85 (0.13), residues: 2018 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP C 248 HIS 0.011 0.002 HIS S 12 PHE 0.055 0.003 PHE F 175 TYR 0.033 0.003 TYR e 64 ARG 0.075 0.001 ARG L 17 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9328 Ramachandran restraints generated. 4664 Oldfield, 0 Emsley, 4664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9328 Ramachandran restraints generated. 4664 Oldfield, 0 Emsley, 4664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 753 residues out of total 3823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 751 time to evaluate : 6.612 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: C 6 CYS cc_start: 0.8823 (t) cc_final: 0.8517 (t) REVERT: C 91 ILE cc_start: 0.9649 (mm) cc_final: 0.9121 (tp) REVERT: C 173 THR cc_start: 0.7890 (m) cc_final: 0.7228 (m) REVERT: C 176 LEU cc_start: 0.9289 (mt) cc_final: 0.9068 (mp) REVERT: C 181 MET cc_start: 0.8241 (tpt) cc_final: 0.7503 (tpp) REVERT: C 200 HIS cc_start: 0.9072 (t-90) cc_final: 0.8709 (t70) REVERT: C 240 PHE cc_start: 0.7488 (t80) cc_final: 0.7176 (t80) REVERT: D 11 MET cc_start: 0.8199 (tpt) cc_final: 0.7919 (tpp) REVERT: D 35 THR cc_start: 0.9352 (p) cc_final: 0.8222 (p) REVERT: D 39 ASP cc_start: 0.8342 (p0) cc_final: 0.7971 (p0) REVERT: D 49 GLN cc_start: 0.9130 (tt0) cc_final: 0.8803 (tt0) REVERT: E 1 MET cc_start: 0.8754 (ptp) cc_final: 0.8144 (pmm) REVERT: E 88 ARG cc_start: 0.8556 (tmm-80) cc_final: 0.7969 (tmm-80) REVERT: E 157 LEU cc_start: 0.9558 (tp) cc_final: 0.9231 (mt) REVERT: E 195 GLN cc_start: 0.9071 (tp-100) cc_final: 0.8451 (tp-100) REVERT: E 199 MET cc_start: 0.9315 (mmp) cc_final: 0.9059 (mmp) REVERT: F 22 TYR cc_start: 0.8138 (m-10) cc_final: 0.7779 (m-10) REVERT: F 150 ARG cc_start: 0.8130 (tpm170) cc_final: 0.7705 (ttp80) REVERT: G 37 LEU cc_start: 0.7762 (tp) cc_final: 0.7479 (tp) REVERT: G 164 TYR cc_start: 0.8382 (m-80) cc_final: 0.8115 (m-80) REVERT: H 41 LYS cc_start: 0.8807 (mttt) cc_final: 0.8463 (tmtt) REVERT: H 101 ASP cc_start: 0.9058 (m-30) cc_final: 0.8526 (p0) REVERT: H 116 ARG cc_start: 0.8158 (mmt-90) cc_final: 0.7929 (mmt180) REVERT: H 132 PHE cc_start: 0.7264 (m-80) cc_final: 0.6731 (m-80) REVERT: I 51 TYR cc_start: 0.6227 (t80) cc_final: 0.5931 (t80) REVERT: I 57 ASN cc_start: 0.4658 (p0) cc_final: 0.4140 (p0) REVERT: I 86 MET cc_start: 0.3479 (mmt) cc_final: 0.3023 (mtm) REVERT: J 117 MET cc_start: 0.6611 (tpt) cc_final: 0.6290 (tpt) REVERT: K 28 LEU cc_start: 0.9367 (pp) cc_final: 0.9149 (pp) REVERT: K 31 GLU cc_start: 0.9206 (tp30) cc_final: 0.8783 (mp0) REVERT: K 44 TYR cc_start: 0.8923 (t80) cc_final: 0.8143 (t80) REVERT: K 89 PHE cc_start: 0.9513 (t80) cc_final: 0.9134 (t80) REVERT: K 91 GLU cc_start: 0.9539 (mt-10) cc_final: 0.9225 (mt-10) REVERT: K 108 MET cc_start: 0.9345 (mtt) cc_final: 0.8682 (mpp) REVERT: K 109 LEU cc_start: 0.9484 (mt) cc_final: 0.9223 (mt) REVERT: L 22 ILE cc_start: 0.9020 (pt) cc_final: 0.8625 (mt) REVERT: L 37 ASP cc_start: 0.8661 (t0) cc_final: 0.8367 (t0) REVERT: L 40 LYS cc_start: 0.8921 (ttmt) cc_final: 0.8538 (ttpt) REVERT: L 66 LYS cc_start: 0.9249 (mtpt) cc_final: 0.8964 (mtpt) REVERT: L 67 LYS cc_start: 0.9420 (tptp) cc_final: 0.9155 (mmmt) REVERT: L 106 GLU cc_start: 0.9014 (mt-10) cc_final: 0.8403 (pp20) REVERT: M 51 GLU cc_start: 0.8090 (tt0) cc_final: 0.7869 (tt0) REVERT: N 68 PHE cc_start: 0.6765 (t80) cc_final: 0.6563 (t80) REVERT: N 75 GLU cc_start: 0.8937 (pp20) cc_final: 0.8702 (pp20) REVERT: N 88 ASN cc_start: 0.7868 (m-40) cc_final: 0.7043 (t0) REVERT: N 96 ILE cc_start: 0.9400 (mm) cc_final: 0.8818 (mm) REVERT: N 97 GLN cc_start: 0.9005 (mp10) cc_final: 0.8298 (mt0) REVERT: N 103 TYR cc_start: 0.7537 (m-10) cc_final: 0.7258 (m-10) REVERT: N 124 LEU cc_start: 0.8946 (mm) cc_final: 0.8553 (mm) REVERT: O 1 MET cc_start: 0.7914 (mpp) cc_final: 0.7304 (tmm) REVERT: O 43 GLU cc_start: 0.9272 (tp30) cc_final: 0.8980 (tp30) REVERT: O 44 LEU cc_start: 0.9555 (mt) cc_final: 0.9208 (mt) REVERT: O 49 GLU cc_start: 0.8726 (tt0) cc_final: 0.7560 (tm-30) REVERT: O 72 ASP cc_start: 0.7277 (t0) cc_final: 0.6371 (t70) REVERT: O 74 GLU cc_start: 0.9407 (tm-30) cc_final: 0.9200 (tm-30) REVERT: O 80 PHE cc_start: 0.9174 (m-80) cc_final: 0.8958 (m-10) REVERT: O 106 ASP cc_start: 0.8966 (p0) cc_final: 0.8685 (p0) REVERT: P 55 GLU cc_start: 0.8476 (mt-10) cc_final: 0.8124 (mp0) REVERT: Q 27 GLU cc_start: 0.8511 (tp30) cc_final: 0.8219 (pm20) REVERT: Q 52 ASN cc_start: 0.8649 (m-40) cc_final: 0.8249 (m-40) REVERT: R 24 TYR cc_start: 0.8744 (m-80) cc_final: 0.7537 (m-80) REVERT: R 83 LEU cc_start: 0.9089 (OUTLIER) cc_final: 0.8766 (mm) REVERT: R 106 PHE cc_start: 0.9571 (t80) cc_final: 0.9121 (t80) REVERT: S 10 LYS cc_start: 0.8602 (mtmm) cc_final: 0.7773 (mttm) REVERT: S 23 GLU cc_start: 0.8879 (mm-30) cc_final: 0.8195 (mm-30) REVERT: S 43 ASN cc_start: 0.9367 (p0) cc_final: 0.8818 (p0) REVERT: S 46 GLU cc_start: 0.8774 (tm-30) cc_final: 0.8246 (tm-30) REVERT: S 73 LYS cc_start: 0.8793 (mmpt) cc_final: 0.8569 (mmpt) REVERT: S 83 TYR cc_start: 0.8517 (t80) cc_final: 0.8207 (t80) REVERT: S 84 ARG cc_start: 0.8145 (pmt-80) cc_final: 0.7719 (ppt170) REVERT: T 8 ARG cc_start: 0.8865 (mtp-110) cc_final: 0.8572 (ptp-170) REVERT: T 23 LEU cc_start: 0.9250 (mm) cc_final: 0.8980 (mp) REVERT: T 41 LYS cc_start: 0.8399 (mmtt) cc_final: 0.8196 (mmtm) REVERT: T 78 GLU cc_start: 0.9234 (pt0) cc_final: 0.8607 (pm20) REVERT: U 52 GLU cc_start: 0.8956 (mt-10) cc_final: 0.8690 (tm-30) REVERT: U 69 ARG cc_start: 0.8677 (mtm-85) cc_final: 0.8207 (ptp-170) REVERT: U 87 LEU cc_start: 0.9130 (mp) cc_final: 0.8797 (tp) REVERT: U 92 ASN cc_start: 0.8091 (p0) cc_final: 0.7783 (p0) REVERT: V 89 ASP cc_start: 0.8808 (m-30) cc_final: 0.8564 (t0) REVERT: V 94 ARG cc_start: 0.7660 (mpp80) cc_final: 0.7366 (mpp80) REVERT: W 1 MET cc_start: 0.8552 (tpt) cc_final: 0.7346 (tmm) REVERT: W 7 GLU cc_start: 0.9249 (pm20) cc_final: 0.9016 (pm20) REVERT: W 41 GLU cc_start: 0.9202 (mt-10) cc_final: 0.8882 (mp0) REVERT: W 59 GLU cc_start: 0.8393 (tp30) cc_final: 0.7850 (tp30) REVERT: X 17 GLU cc_start: 0.8907 (tm-30) cc_final: 0.8403 (tm-30) REVERT: X 29 GLU cc_start: 0.7820 (tt0) cc_final: 0.7399 (tp30) REVERT: X 32 LEU cc_start: 0.8912 (mt) cc_final: 0.8607 (tt) REVERT: X 39 ARG cc_start: 0.8700 (mtp-110) cc_final: 0.8363 (ttp-110) REVERT: Y 23 ASN cc_start: 0.9191 (m110) cc_final: 0.8384 (p0) REVERT: Y 45 ARG cc_start: 0.8568 (mtt-85) cc_final: 0.8176 (mmt90) REVERT: Y 46 PHE cc_start: 0.8509 (m-10) cc_final: 0.8154 (m-80) REVERT: Z 26 PHE cc_start: 0.8874 (t80) cc_final: 0.8577 (t80) REVERT: Z 30 MET cc_start: 0.8448 (mmm) cc_final: 0.8113 (mmm) REVERT: a 54 MET cc_start: 0.8818 (ppp) cc_final: 0.8175 (tmm) REVERT: b 5 GLN cc_start: 0.7346 (tp40) cc_final: 0.6901 (tp40) REVERT: b 7 LYS cc_start: 0.8909 (ttpp) cc_final: 0.8599 (mtpp) REVERT: b 46 ASP cc_start: 0.9234 (t0) cc_final: 0.8602 (t0) REVERT: c 11 LEU cc_start: 0.8843 (mm) cc_final: 0.8612 (mm) REVERT: c 20 PHE cc_start: 0.8812 (p90) cc_final: 0.7879 (p90) REVERT: c 35 GLU cc_start: 0.8815 (tt0) cc_final: 0.8232 (mm-30) REVERT: d 22 MET cc_start: 0.9422 (tpp) cc_final: 0.9056 (tpp) REVERT: d 26 ASN cc_start: 0.9020 (m-40) cc_final: 0.8569 (m110) REVERT: e 45 ARG cc_start: 0.8572 (ptp-170) cc_final: 0.8134 (ptp-170) REVERT: e 49 MET cc_start: 0.6562 (mmp) cc_final: 0.6335 (mmm) REVERT: f 1 MET cc_start: 0.8557 (ptm) cc_final: 0.8196 (ptm) REVERT: f 8 LYS cc_start: 0.7744 (tppt) cc_final: 0.7151 (mmtt) REVERT: f 26 ILE cc_start: 0.9399 (mt) cc_final: 0.9184 (mp) REVERT: f 36 ARG cc_start: 0.8440 (tmm-80) cc_final: 0.8025 (tmm-80) REVERT: i 95 LEU cc_start: 0.6607 (mt) cc_final: 0.6326 (tp) REVERT: i 181 LEU cc_start: 0.8711 (mt) cc_final: 0.8367 (pp) REVERT: i 202 MET cc_start: 0.5646 (tpp) cc_final: 0.4428 (mmp) REVERT: i 341 MET cc_start: 0.5499 (mtt) cc_final: 0.5014 (mtp) REVERT: i 344 MET cc_start: 0.6377 (ppp) cc_final: 0.5429 (tpp) outliers start: 2 outliers final: 0 residues processed: 752 average time/residue: 0.9626 time to fit residues: 1233.5685 Evaluate side-chains 571 residues out of total 3823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 570 time to evaluate : 4.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 772 random chunks: chunk 251 optimal weight: 20.0000 chunk 672 optimal weight: 5.9990 chunk 147 optimal weight: 20.0000 chunk 438 optimal weight: 5.9990 chunk 184 optimal weight: 20.0000 chunk 746 optimal weight: 20.0000 chunk 620 optimal weight: 7.9990 chunk 345 optimal weight: 0.0030 chunk 62 optimal weight: 20.0000 chunk 247 optimal weight: 20.0000 chunk 392 optimal weight: 50.0000 overall best weight: 8.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 243 HIS ** C 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 5 HIS ** H 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 88 HIS ** K 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 35 HIS M 104 GLN O 23 ASN ** O 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 20 GLN R 37 GLN R 59 GLN T 7 HIS ** V 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 57 HIS Y 20 HIS ** Z 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 58 ASN ** a 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 13 ASN ** f 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 343 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.8214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 110109 Z= 0.254 Angle : 0.678 30.613 163852 Z= 0.337 Chirality : 0.037 0.314 20612 Planarity : 0.005 0.057 9393 Dihedral : 23.745 178.149 53755 Min Nonbonded Distance : 1.814 Molprobity Statistics. All-atom Clashscore : 24.92 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.03 % Favored : 95.93 % Rotamer: Outliers : 0.06 % Allowed : 2.54 % Favored : 97.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.95 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.09 (0.12), residues: 4664 helix: 1.02 (0.12), residues: 1790 sheet: -0.43 (0.18), residues: 820 loop : -0.80 (0.13), residues: 2054 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP E 60 HIS 0.013 0.002 HIS i 128 PHE 0.031 0.002 PHE F 175 TYR 0.024 0.002 TYR b 48 ARG 0.011 0.001 ARG E 67 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9328 Ramachandran restraints generated. 4664 Oldfield, 0 Emsley, 4664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9328 Ramachandran restraints generated. 4664 Oldfield, 0 Emsley, 4664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 725 residues out of total 3823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 723 time to evaluate : 4.848 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: C 6 CYS cc_start: 0.9014 (t) cc_final: 0.8758 (t) REVERT: C 91 ILE cc_start: 0.9613 (mm) cc_final: 0.9081 (tp) REVERT: C 114 ASP cc_start: 0.8800 (m-30) cc_final: 0.8511 (m-30) REVERT: C 132 MET cc_start: 0.9299 (mtt) cc_final: 0.9053 (tmm) REVERT: C 173 THR cc_start: 0.7842 (m) cc_final: 0.7053 (m) REVERT: C 181 MET cc_start: 0.8358 (tpt) cc_final: 0.7498 (tpp) REVERT: C 200 HIS cc_start: 0.9003 (t-90) cc_final: 0.8694 (t70) REVERT: C 205 LEU cc_start: 0.8868 (mm) cc_final: 0.8287 (mp) REVERT: D 32 ASN cc_start: 0.8268 (t0) cc_final: 0.8032 (t0) REVERT: D 35 THR cc_start: 0.9353 (p) cc_final: 0.8597 (p) REVERT: D 39 ASP cc_start: 0.8552 (p0) cc_final: 0.8018 (p0) REVERT: D 49 GLN cc_start: 0.9160 (tt0) cc_final: 0.8822 (tt0) REVERT: D 137 SER cc_start: 0.9199 (m) cc_final: 0.8716 (p) REVERT: D 174 SER cc_start: 0.8973 (m) cc_final: 0.8716 (t) REVERT: E 88 ARG cc_start: 0.8739 (tmm-80) cc_final: 0.8306 (tmm-80) REVERT: E 157 LEU cc_start: 0.9561 (tp) cc_final: 0.9316 (mt) REVERT: E 188 MET cc_start: 0.7674 (mmp) cc_final: 0.6910 (mmt) REVERT: E 195 GLN cc_start: 0.9125 (tp-100) cc_final: 0.8587 (tp-100) REVERT: E 199 MET cc_start: 0.9269 (mmp) cc_final: 0.8983 (mmp) REVERT: F 11 GLU cc_start: 0.9151 (mp0) cc_final: 0.8932 (mp0) REVERT: F 22 TYR cc_start: 0.7891 (m-10) cc_final: 0.7571 (m-10) REVERT: F 32 GLU cc_start: 0.7987 (tt0) cc_final: 0.7776 (mt-10) REVERT: F 133 ARG cc_start: 0.7709 (mpt180) cc_final: 0.7397 (mmt-90) REVERT: F 175 PHE cc_start: 0.9363 (m-80) cc_final: 0.9102 (m-80) REVERT: G 27 LYS cc_start: 0.9078 (mmpt) cc_final: 0.8637 (tmtt) REVERT: G 37 LEU cc_start: 0.7675 (tp) cc_final: 0.7382 (tp) REVERT: G 101 ASN cc_start: 0.9233 (p0) cc_final: 0.8500 (t0) REVERT: H 93 SER cc_start: 0.6143 (p) cc_final: 0.5724 (t) REVERT: H 101 ASP cc_start: 0.9012 (m-30) cc_final: 0.8562 (p0) REVERT: H 132 PHE cc_start: 0.7270 (m-80) cc_final: 0.6849 (m-80) REVERT: I 57 ASN cc_start: 0.4638 (p0) cc_final: 0.3922 (p0) REVERT: K 28 LEU cc_start: 0.9377 (pp) cc_final: 0.9117 (pp) REVERT: K 31 GLU cc_start: 0.9034 (tp30) cc_final: 0.8702 (mp0) REVERT: K 44 TYR cc_start: 0.8902 (t80) cc_final: 0.8136 (t80) REVERT: K 84 ILE cc_start: 0.9507 (pt) cc_final: 0.9266 (mp) REVERT: K 89 PHE cc_start: 0.9585 (t80) cc_final: 0.9138 (t80) REVERT: K 108 MET cc_start: 0.9401 (mtt) cc_final: 0.8679 (mpp) REVERT: K 109 LEU cc_start: 0.9557 (mt) cc_final: 0.9307 (mt) REVERT: L 22 ILE cc_start: 0.9138 (pt) cc_final: 0.8818 (mt) REVERT: L 37 ASP cc_start: 0.8678 (t0) cc_final: 0.8347 (t0) REVERT: L 40 LYS cc_start: 0.8955 (ttmt) cc_final: 0.8154 (pttt) REVERT: L 44 LYS cc_start: 0.8846 (mmtm) cc_final: 0.8599 (mmmt) REVERT: L 67 LYS cc_start: 0.9396 (tptp) cc_final: 0.9078 (mmmt) REVERT: L 106 GLU cc_start: 0.9072 (mt-10) cc_final: 0.8458 (pp20) REVERT: M 23 ILE cc_start: 0.9151 (pt) cc_final: 0.8663 (mt) REVERT: N 2 LEU cc_start: 0.8825 (mp) cc_final: 0.8223 (mp) REVERT: N 68 PHE cc_start: 0.6697 (t80) cc_final: 0.6013 (t80) REVERT: N 75 GLU cc_start: 0.8971 (pp20) cc_final: 0.8690 (pp20) REVERT: N 88 ASN cc_start: 0.7984 (m-40) cc_final: 0.7103 (t0) REVERT: N 95 LEU cc_start: 0.9520 (mt) cc_final: 0.9290 (mm) REVERT: N 96 ILE cc_start: 0.9364 (mm) cc_final: 0.8825 (mm) REVERT: N 97 GLN cc_start: 0.8849 (mp10) cc_final: 0.8251 (mt0) REVERT: N 103 TYR cc_start: 0.7330 (m-10) cc_final: 0.7109 (m-10) REVERT: O 23 ASN cc_start: 0.9353 (m-40) cc_final: 0.9109 (m110) REVERT: O 43 GLU cc_start: 0.9224 (tp30) cc_final: 0.8960 (tp30) REVERT: O 44 LEU cc_start: 0.9616 (mt) cc_final: 0.9272 (mt) REVERT: O 72 ASP cc_start: 0.7467 (t0) cc_final: 0.6501 (t0) REVERT: O 106 ASP cc_start: 0.8947 (p0) cc_final: 0.8641 (p0) REVERT: O 110 MET cc_start: 0.8263 (mmp) cc_final: 0.7975 (mmm) REVERT: P 55 GLU cc_start: 0.8441 (mt-10) cc_final: 0.8164 (pm20) REVERT: Q 9 GLU cc_start: 0.8603 (OUTLIER) cc_final: 0.8221 (pp20) REVERT: Q 24 ASP cc_start: 0.9009 (m-30) cc_final: 0.8579 (m-30) REVERT: Q 25 THR cc_start: 0.9358 (m) cc_final: 0.8893 (p) REVERT: Q 52 ASN cc_start: 0.8578 (m-40) cc_final: 0.8153 (m110) REVERT: Q 56 HIS cc_start: 0.9375 (m-70) cc_final: 0.8779 (m-70) REVERT: R 24 TYR cc_start: 0.8768 (m-80) cc_final: 0.7475 (m-80) REVERT: R 106 PHE cc_start: 0.9631 (t80) cc_final: 0.9218 (t80) REVERT: S 10 LYS cc_start: 0.8695 (mtmm) cc_final: 0.8014 (mmtt) REVERT: S 43 ASN cc_start: 0.9484 (p0) cc_final: 0.9055 (p0) REVERT: S 46 GLU cc_start: 0.9067 (tm-30) cc_final: 0.8537 (tm-30) REVERT: S 73 LYS cc_start: 0.8750 (mmpt) cc_final: 0.8459 (mmpt) REVERT: S 82 HIS cc_start: 0.8636 (t-90) cc_final: 0.8351 (t-90) REVERT: S 83 TYR cc_start: 0.8695 (t80) cc_final: 0.8451 (t80) REVERT: S 97 LYS cc_start: 0.9475 (tmmt) cc_final: 0.9262 (tmtt) REVERT: T 8 ARG cc_start: 0.8969 (mtp-110) cc_final: 0.8426 (mtp180) REVERT: T 78 GLU cc_start: 0.9223 (pt0) cc_final: 0.8548 (pm20) REVERT: U 52 GLU cc_start: 0.9010 (mt-10) cc_final: 0.8709 (tm-30) REVERT: U 69 ARG cc_start: 0.8605 (mtm-85) cc_final: 0.7953 (ptp-170) REVERT: U 87 LEU cc_start: 0.9120 (mp) cc_final: 0.8757 (tp) REVERT: U 92 ASN cc_start: 0.8013 (p0) cc_final: 0.7676 (p0) REVERT: V 7 ARG cc_start: 0.7997 (ttp-110) cc_final: 0.7706 (ttp-110) REVERT: V 8 ASP cc_start: 0.9142 (m-30) cc_final: 0.8599 (t0) REVERT: V 89 ASP cc_start: 0.8784 (m-30) cc_final: 0.8520 (t0) REVERT: V 94 ARG cc_start: 0.7727 (mpp80) cc_final: 0.7441 (mpp80) REVERT: W 41 GLU cc_start: 0.9185 (mt-10) cc_final: 0.8941 (mp0) REVERT: W 59 GLU cc_start: 0.8618 (tp30) cc_final: 0.7974 (tp30) REVERT: W 69 GLU cc_start: 0.8483 (tm-30) cc_final: 0.8234 (tm-30) REVERT: X 29 GLU cc_start: 0.7745 (tt0) cc_final: 0.7475 (tp30) REVERT: X 32 LEU cc_start: 0.8869 (mt) cc_final: 0.8551 (tt) REVERT: X 39 ARG cc_start: 0.8643 (mtp-110) cc_final: 0.8436 (mtp-110) REVERT: X 68 LYS cc_start: 0.7834 (ttmm) cc_final: 0.7607 (tttm) REVERT: X 69 PHE cc_start: 0.8030 (m-10) cc_final: 0.7830 (m-10) REVERT: Y 23 ASN cc_start: 0.9272 (m110) cc_final: 0.8157 (p0) REVERT: Y 45 ARG cc_start: 0.8692 (mtt-85) cc_final: 0.8348 (mmt180) REVERT: Y 46 PHE cc_start: 0.8707 (m-10) cc_final: 0.8357 (m-80) REVERT: Y 56 MET cc_start: 0.9381 (mmt) cc_final: 0.9157 (mmm) REVERT: Y 60 ASP cc_start: 0.9184 (m-30) cc_final: 0.8926 (m-30) REVERT: Y 70 GLU cc_start: 0.7917 (tm-30) cc_final: 0.7640 (tm-30) REVERT: Z 30 MET cc_start: 0.8444 (mmm) cc_final: 0.8006 (mmm) REVERT: a 54 MET cc_start: 0.8827 (ppp) cc_final: 0.8355 (tmm) REVERT: a 58 GLU cc_start: 0.8974 (mp0) cc_final: 0.8558 (mp0) REVERT: c 11 LEU cc_start: 0.8756 (mm) cc_final: 0.8479 (mm) REVERT: c 20 PHE cc_start: 0.8817 (p90) cc_final: 0.7906 (p90) REVERT: c 35 GLU cc_start: 0.8941 (tt0) cc_final: 0.8331 (mm-30) REVERT: d 1 MET cc_start: 0.5057 (mpp) cc_final: 0.4745 (mpp) REVERT: d 22 MET cc_start: 0.9328 (tpp) cc_final: 0.9005 (tpp) REVERT: d 26 ASN cc_start: 0.9039 (m-40) cc_final: 0.8538 (m110) REVERT: e 33 LEU cc_start: 0.8700 (mt) cc_final: 0.8487 (mt) REVERT: e 54 ASP cc_start: 0.8536 (p0) cc_final: 0.7944 (t0) REVERT: f 1 MET cc_start: 0.8454 (ptm) cc_final: 0.7813 (ptm) REVERT: f 8 LYS cc_start: 0.7969 (tppt) cc_final: 0.7377 (mmtt) REVERT: f 34 LYS cc_start: 0.8708 (ttpt) cc_final: 0.8505 (ttmm) REVERT: i 95 LEU cc_start: 0.6642 (mt) cc_final: 0.6436 (tp) REVERT: i 202 MET cc_start: 0.5775 (tpp) cc_final: 0.4466 (mmp) REVERT: i 341 MET cc_start: 0.6039 (mtt) cc_final: 0.5773 (mtp) REVERT: i 344 MET cc_start: 0.6575 (ppp) cc_final: 0.5928 (tpp) REVERT: i 375 ARG cc_start: 0.9222 (mtt180) cc_final: 0.8517 (mmp-170) REVERT: i 423 MET cc_start: 0.7725 (tpt) cc_final: 0.7373 (tpt) outliers start: 2 outliers final: 0 residues processed: 723 average time/residue: 0.9629 time to fit residues: 1187.6766 Evaluate side-chains 573 residues out of total 3823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 572 time to evaluate : 4.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 772 random chunks: chunk 720 optimal weight: 0.3980 chunk 84 optimal weight: 20.0000 chunk 425 optimal weight: 9.9990 chunk 545 optimal weight: 5.9990 chunk 422 optimal weight: 20.0000 chunk 628 optimal weight: 30.0000 chunk 417 optimal weight: 10.0000 chunk 744 optimal weight: 10.0000 chunk 465 optimal weight: 20.0000 chunk 453 optimal weight: 6.9990 chunk 343 optimal weight: 20.0000 overall best weight: 6.6790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 115 GLN ** E 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 135 HIS ** K 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 104 GLN ** N 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 7 HIS ** V 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 20 HIS ** Z 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 13 ASN ** f 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 128 HIS i 343 ASN i 381 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.8709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 110109 Z= 0.229 Angle : 0.663 30.301 163852 Z= 0.327 Chirality : 0.035 0.294 20612 Planarity : 0.005 0.101 9393 Dihedral : 23.694 178.054 53755 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 25.01 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.50 % Favored : 95.45 % Rotamer: Outliers : 0.03 % Allowed : 1.48 % Favored : 98.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.95 % Cis-general : 0.11 % 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: -0.01 (0.12), residues: 4664 helix: 1.17 (0.12), residues: 1793 sheet: -0.45 (0.17), residues: 830 loop : -0.83 (0.13), residues: 2041 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP E 60 HIS 0.009 0.002 HIS l 219 PHE 0.030 0.002 PHE R 79 TYR 0.015 0.002 TYR K 75 ARG 0.012 0.001 ARG Q 113 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9328 Ramachandran restraints generated. 4664 Oldfield, 0 Emsley, 4664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9328 Ramachandran restraints generated. 4664 Oldfield, 0 Emsley, 4664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 735 residues out of total 3823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 734 time to evaluate : 4.890 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: C 6 CYS cc_start: 0.9121 (t) cc_final: 0.8874 (t) REVERT: C 91 ILE cc_start: 0.9616 (mm) cc_final: 0.9090 (tp) REVERT: C 200 HIS cc_start: 0.8927 (t-90) cc_final: 0.8652 (t70) REVERT: D 32 ASN cc_start: 0.8324 (t0) cc_final: 0.8117 (t0) REVERT: D 35 THR cc_start: 0.9373 (p) cc_final: 0.8640 (p) REVERT: D 39 ASP cc_start: 0.8703 (p0) cc_final: 0.8125 (p0) REVERT: D 49 GLN cc_start: 0.9210 (tt0) cc_final: 0.8890 (tt0) REVERT: D 103 ASP cc_start: 0.9328 (m-30) cc_final: 0.8650 (p0) REVERT: D 137 SER cc_start: 0.9123 (m) cc_final: 0.8620 (p) REVERT: D 174 SER cc_start: 0.9066 (m) cc_final: 0.8778 (t) REVERT: D 187 LEU cc_start: 0.9533 (mt) cc_final: 0.9264 (tp) REVERT: D 201 LEU cc_start: 0.8725 (mt) cc_final: 0.8422 (mt) REVERT: E 88 ARG cc_start: 0.8780 (tmm-80) cc_final: 0.8505 (tmm-80) REVERT: E 157 LEU cc_start: 0.9569 (tp) cc_final: 0.9292 (mt) REVERT: E 188 MET cc_start: 0.8355 (mmp) cc_final: 0.8123 (mmp) REVERT: E 195 GLN cc_start: 0.9184 (tp-100) cc_final: 0.8636 (tp-100) REVERT: F 11 GLU cc_start: 0.9151 (mp0) cc_final: 0.8932 (mp0) REVERT: F 22 TYR cc_start: 0.7690 (m-10) cc_final: 0.7385 (m-10) REVERT: F 26 MET cc_start: 0.7177 (mmp) cc_final: 0.6684 (mmm) REVERT: F 32 GLU cc_start: 0.8185 (tt0) cc_final: 0.7923 (mt-10) REVERT: F 35 THR cc_start: 0.7476 (m) cc_final: 0.7113 (t) REVERT: F 175 PHE cc_start: 0.9306 (m-80) cc_final: 0.8986 (m-80) REVERT: G 27 LYS cc_start: 0.8972 (mmpt) cc_final: 0.8613 (tmtt) REVERT: G 37 LEU cc_start: 0.7640 (tp) cc_final: 0.7341 (tp) REVERT: G 101 ASN cc_start: 0.9302 (p0) cc_final: 0.8683 (t0) REVERT: G 164 TYR cc_start: 0.8264 (m-10) cc_final: 0.7937 (m-80) REVERT: H 41 LYS cc_start: 0.8784 (mttt) cc_final: 0.8448 (tmtt) REVERT: H 101 ASP cc_start: 0.8917 (m-30) cc_final: 0.8400 (p0) REVERT: H 132 PHE cc_start: 0.7462 (m-80) cc_final: 0.7023 (m-80) REVERT: I 52 MET cc_start: 0.4446 (pmm) cc_final: 0.4101 (pmm) REVERT: I 57 ASN cc_start: 0.4772 (p0) cc_final: 0.4102 (p0) REVERT: J 65 ARG cc_start: 0.5083 (mmp80) cc_final: 0.4882 (mmm160) REVERT: J 117 MET cc_start: 0.6632 (tpt) cc_final: 0.6352 (tpt) REVERT: K 44 TYR cc_start: 0.8914 (t80) cc_final: 0.8051 (t80) REVERT: K 84 ILE cc_start: 0.9457 (pt) cc_final: 0.9174 (mp) REVERT: K 89 PHE cc_start: 0.9613 (t80) cc_final: 0.9066 (t80) REVERT: K 91 GLU cc_start: 0.9307 (tt0) cc_final: 0.9103 (pt0) REVERT: K 108 MET cc_start: 0.9505 (mtt) cc_final: 0.8677 (mpp) REVERT: K 109 LEU cc_start: 0.9538 (mt) cc_final: 0.9271 (mt) REVERT: L 22 ILE cc_start: 0.9253 (pt) cc_final: 0.8730 (mt) REVERT: L 37 ASP cc_start: 0.8667 (t0) cc_final: 0.8326 (t0) REVERT: L 44 LYS cc_start: 0.8965 (mmtm) cc_final: 0.8630 (mmmt) REVERT: L 45 GLU cc_start: 0.8914 (pp20) cc_final: 0.8704 (pp20) REVERT: L 106 GLU cc_start: 0.9068 (mt-10) cc_final: 0.8458 (pp20) REVERT: L 107 LEU cc_start: 0.9431 (tp) cc_final: 0.9153 (tp) REVERT: M 23 ILE cc_start: 0.9211 (pt) cc_final: 0.8678 (mt) REVERT: N 2 LEU cc_start: 0.8796 (mp) cc_final: 0.8205 (mp) REVERT: N 68 PHE cc_start: 0.6765 (t80) cc_final: 0.6027 (t80) REVERT: N 75 GLU cc_start: 0.8939 (pp20) cc_final: 0.8610 (pp20) REVERT: N 82 MET cc_start: 0.7860 (tpp) cc_final: 0.7121 (mmm) REVERT: N 88 ASN cc_start: 0.8095 (m-40) cc_final: 0.7233 (t0) REVERT: N 95 LEU cc_start: 0.9536 (mt) cc_final: 0.9298 (mm) REVERT: N 96 ILE cc_start: 0.9316 (mm) cc_final: 0.9052 (tp) REVERT: N 97 GLN cc_start: 0.8839 (mp10) cc_final: 0.8425 (mt0) REVERT: N 103 TYR cc_start: 0.7530 (m-10) cc_final: 0.7080 (m-10) REVERT: O 23 ASN cc_start: 0.9328 (m-40) cc_final: 0.9078 (m-40) REVERT: O 43 GLU cc_start: 0.9194 (tp30) cc_final: 0.8861 (tp30) REVERT: O 44 LEU cc_start: 0.9622 (mt) cc_final: 0.9231 (mt) REVERT: O 72 ASP cc_start: 0.7446 (t0) cc_final: 0.6131 (t70) REVERT: O 74 GLU cc_start: 0.9422 (tm-30) cc_final: 0.9208 (tm-30) REVERT: O 75 ILE cc_start: 0.9425 (mm) cc_final: 0.8540 (mm) REVERT: O 106 ASP cc_start: 0.8841 (p0) cc_final: 0.8522 (p0) REVERT: O 110 MET cc_start: 0.8128 (mmp) cc_final: 0.7894 (mmm) REVERT: Q 25 THR cc_start: 0.9223 (m) cc_final: 0.8910 (p) REVERT: Q 52 ASN cc_start: 0.8587 (m-40) cc_final: 0.8294 (m-40) REVERT: Q 56 HIS cc_start: 0.9367 (m-70) cc_final: 0.8729 (m-70) REVERT: Q 63 LYS cc_start: 0.8604 (ptmt) cc_final: 0.7244 (ptpt) REVERT: Q 64 ILE cc_start: 0.8122 (tp) cc_final: 0.7774 (tp) REVERT: Q 70 VAL cc_start: 0.9474 (t) cc_final: 0.8960 (t) REVERT: Q 87 LYS cc_start: 0.9268 (tmtt) cc_final: 0.9056 (tmtt) REVERT: R 24 TYR cc_start: 0.8820 (m-80) cc_final: 0.7524 (m-80) REVERT: R 97 ASP cc_start: 0.9119 (m-30) cc_final: 0.8808 (m-30) REVERT: R 106 PHE cc_start: 0.9538 (t80) cc_final: 0.9071 (t80) REVERT: S 10 LYS cc_start: 0.8765 (mtmm) cc_final: 0.7930 (mmtt) REVERT: S 23 GLU cc_start: 0.9174 (mm-30) cc_final: 0.8734 (pm20) REVERT: S 35 PHE cc_start: 0.7930 (m-10) cc_final: 0.7633 (m-10) REVERT: S 43 ASN cc_start: 0.9525 (p0) cc_final: 0.9087 (p0) REVERT: S 46 GLU cc_start: 0.9041 (tm-30) cc_final: 0.8518 (tm-30) REVERT: S 73 LYS cc_start: 0.8658 (mmpt) cc_final: 0.8283 (mmpt) REVERT: S 82 HIS cc_start: 0.8504 (t-90) cc_final: 0.8087 (t70) REVERT: S 83 TYR cc_start: 0.8677 (t80) cc_final: 0.8309 (t80) REVERT: S 86 GLN cc_start: 0.9248 (pt0) cc_final: 0.8431 (pp30) REVERT: T 78 GLU cc_start: 0.9174 (pt0) cc_final: 0.8489 (pm20) REVERT: U 52 GLU cc_start: 0.9021 (mt-10) cc_final: 0.8573 (tm-30) REVERT: U 69 ARG cc_start: 0.8549 (mtm-85) cc_final: 0.8008 (ptp-170) REVERT: U 87 LEU cc_start: 0.9141 (mp) cc_final: 0.8907 (tp) REVERT: U 92 ASN cc_start: 0.7840 (p0) cc_final: 0.7381 (p0) REVERT: V 7 ARG cc_start: 0.8089 (ttp-110) cc_final: 0.7673 (ttp-110) REVERT: V 8 ASP cc_start: 0.9178 (m-30) cc_final: 0.8629 (t0) REVERT: V 39 ILE cc_start: 0.9634 (mm) cc_final: 0.9373 (mm) REVERT: W 7 GLU cc_start: 0.9253 (mp0) cc_final: 0.9027 (pm20) REVERT: W 41 GLU cc_start: 0.9402 (mt-10) cc_final: 0.8466 (mp0) REVERT: W 59 GLU cc_start: 0.8554 (tp30) cc_final: 0.7575 (tp30) REVERT: W 69 GLU cc_start: 0.8500 (tm-30) cc_final: 0.8223 (tm-30) REVERT: X 12 ASN cc_start: 0.6708 (m-40) cc_final: 0.6469 (p0) REVERT: X 17 GLU cc_start: 0.9010 (tm-30) cc_final: 0.8446 (tm-30) REVERT: X 20 ARG cc_start: 0.9029 (mpt-90) cc_final: 0.8778 (mmt90) REVERT: X 29 GLU cc_start: 0.7979 (tt0) cc_final: 0.7722 (tp30) REVERT: X 32 LEU cc_start: 0.8854 (mt) cc_final: 0.8521 (tt) REVERT: X 39 ARG cc_start: 0.8664 (mtp-110) cc_final: 0.8459 (mtp-110) REVERT: X 69 PHE cc_start: 0.8014 (m-10) cc_final: 0.7648 (m-10) REVERT: Y 23 ASN cc_start: 0.9175 (m110) cc_final: 0.8147 (p0) REVERT: Y 45 ARG cc_start: 0.8801 (mtt-85) cc_final: 0.8359 (mmt90) REVERT: Y 46 PHE cc_start: 0.8681 (m-10) cc_final: 0.8427 (m-80) REVERT: Y 70 GLU cc_start: 0.7836 (tm-30) cc_final: 0.7565 (tm-30) REVERT: Z 30 MET cc_start: 0.8536 (mmm) cc_final: 0.7980 (mmm) REVERT: a 54 MET cc_start: 0.8994 (ppp) cc_final: 0.8410 (tmm) REVERT: c 33 LYS cc_start: 0.8888 (mmtm) cc_final: 0.8482 (mmtm) REVERT: c 35 GLU cc_start: 0.8971 (tt0) cc_final: 0.8309 (mm-30) REVERT: d 13 ASN cc_start: 0.8903 (m-40) cc_final: 0.8688 (t0) REVERT: d 22 MET cc_start: 0.9347 (tpp) cc_final: 0.8968 (tpp) REVERT: d 26 ASN cc_start: 0.9124 (m-40) cc_final: 0.8639 (m110) REVERT: e 4 ILE cc_start: 0.9682 (pt) cc_final: 0.9378 (pt) REVERT: e 33 LEU cc_start: 0.8675 (mt) cc_final: 0.8452 (mt) REVERT: e 54 ASP cc_start: 0.8585 (p0) cc_final: 0.7988 (t0) REVERT: f 1 MET cc_start: 0.8521 (ptm) cc_final: 0.7883 (ptm) REVERT: f 8 LYS cc_start: 0.8150 (tppt) cc_final: 0.7583 (mmtt) REVERT: i 95 LEU cc_start: 0.6924 (mt) cc_final: 0.6588 (tp) REVERT: i 153 GLU cc_start: 0.7835 (mm-30) cc_final: 0.7505 (mm-30) REVERT: i 181 LEU cc_start: 0.8611 (mt) cc_final: 0.8226 (pp) REVERT: i 341 MET cc_start: 0.5981 (mtt) cc_final: 0.5702 (mtp) REVERT: i 344 MET cc_start: 0.6516 (ppp) cc_final: 0.5717 (tpt) REVERT: i 375 ARG cc_start: 0.9134 (mtt180) cc_final: 0.8500 (mmp80) REVERT: i 390 LYS cc_start: 0.8385 (ttmt) cc_final: 0.8184 (tppt) REVERT: i 423 MET cc_start: 0.7629 (tpt) cc_final: 0.7089 (tpt) outliers start: 1 outliers final: 0 residues processed: 734 average time/residue: 0.9817 time to fit residues: 1225.4494 Evaluate side-chains 578 residues out of total 3823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 578 time to evaluate : 4.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 772 random chunks: chunk 460 optimal weight: 9.9990 chunk 297 optimal weight: 30.0000 chunk 444 optimal weight: 0.9980 chunk 224 optimal weight: 40.0000 chunk 146 optimal weight: 20.0000 chunk 144 optimal weight: 20.0000 chunk 473 optimal weight: 6.9990 chunk 506 optimal weight: 5.9990 chunk 367 optimal weight: 4.9990 chunk 69 optimal weight: 20.0000 chunk 584 optimal weight: 20.0000 overall best weight: 5.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 167 ASN ** E 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 133 GLN ** K 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 104 GLN ** N 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 15 GLN R 20 GLN S 18 GLN ** V 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 20 HIS Z 58 ASN f 13 ASN ** f 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 128 HIS i 343 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.9021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 110109 Z= 0.204 Angle : 0.635 29.946 163852 Z= 0.313 Chirality : 0.034 0.284 20612 Planarity : 0.005 0.060 9393 Dihedral : 23.659 177.026 53755 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 22.91 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.03 % Favored : 95.93 % Rotamer: Outliers : 0.06 % Allowed : 1.18 % Favored : 98.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.95 % Cis-general : 0.11 % 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: 0.02 (0.12), residues: 4664 helix: 1.22 (0.12), residues: 1798 sheet: -0.47 (0.17), residues: 841 loop : -0.83 (0.14), residues: 2025 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP Q 31 HIS 0.012 0.001 HIS Q 77 PHE 0.029 0.002 PHE d 18 TYR 0.027 0.002 TYR O 112 ARG 0.009 0.001 ARG S 13 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9328 Ramachandran restraints generated. 4664 Oldfield, 0 Emsley, 4664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9328 Ramachandran restraints generated. 4664 Oldfield, 0 Emsley, 4664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 726 residues out of total 3823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 724 time to evaluate : 4.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 6 CYS cc_start: 0.9278 (t) cc_final: 0.8997 (t) REVERT: C 91 ILE cc_start: 0.9607 (mm) cc_final: 0.9089 (tp) REVERT: C 200 HIS cc_start: 0.8967 (t-90) cc_final: 0.8693 (t70) REVERT: D 32 ASN cc_start: 0.8256 (t0) cc_final: 0.8015 (t0) REVERT: D 35 THR cc_start: 0.9413 (p) cc_final: 0.8738 (p) REVERT: D 39 ASP cc_start: 0.8759 (p0) cc_final: 0.8359 (p0) REVERT: D 49 GLN cc_start: 0.9213 (tt0) cc_final: 0.8910 (tt0) REVERT: D 103 ASP cc_start: 0.9359 (m-30) cc_final: 0.8682 (p0) REVERT: D 137 SER cc_start: 0.9163 (m) cc_final: 0.8584 (p) REVERT: D 174 SER cc_start: 0.9063 (m) cc_final: 0.8776 (t) REVERT: D 201 LEU cc_start: 0.8761 (mt) cc_final: 0.8439 (mt) REVERT: E 88 ARG cc_start: 0.8916 (tmm-80) cc_final: 0.8514 (tmm-80) REVERT: E 100 MET cc_start: 0.8015 (ptp) cc_final: 0.7645 (mpp) REVERT: E 115 GLN cc_start: 0.8235 (tt0) cc_final: 0.7724 (pt0) REVERT: E 157 LEU cc_start: 0.9571 (tp) cc_final: 0.9303 (mt) REVERT: E 188 MET cc_start: 0.8218 (mmp) cc_final: 0.8006 (mmp) REVERT: E 195 GLN cc_start: 0.9189 (tp-100) cc_final: 0.8604 (tp-100) REVERT: E 199 MET cc_start: 0.9276 (mmp) cc_final: 0.9035 (mmp) REVERT: F 11 GLU cc_start: 0.9146 (mp0) cc_final: 0.8924 (mp0) REVERT: F 26 MET cc_start: 0.7158 (mmp) cc_final: 0.6607 (mmm) REVERT: F 32 GLU cc_start: 0.8206 (tt0) cc_final: 0.7894 (mt-10) REVERT: F 35 THR cc_start: 0.7500 (m) cc_final: 0.7131 (t) REVERT: F 175 PHE cc_start: 0.9240 (m-80) cc_final: 0.8825 (m-80) REVERT: G 27 LYS cc_start: 0.9020 (mmpt) cc_final: 0.8595 (tmtt) REVERT: G 37 LEU cc_start: 0.7721 (tp) cc_final: 0.7406 (tp) REVERT: G 101 ASN cc_start: 0.9299 (p0) cc_final: 0.8690 (t0) REVERT: G 164 TYR cc_start: 0.8096 (m-10) cc_final: 0.7883 (m-80) REVERT: H 11 ASN cc_start: 0.8671 (t0) cc_final: 0.8379 (t0) REVERT: H 12 LEU cc_start: 0.9100 (mt) cc_final: 0.8867 (tp) REVERT: H 41 LYS cc_start: 0.8815 (mttt) cc_final: 0.8498 (tmtt) REVERT: H 101 ASP cc_start: 0.8939 (m-30) cc_final: 0.8417 (p0) REVERT: H 116 ARG cc_start: 0.8210 (mmt-90) cc_final: 0.7969 (mmt180) REVERT: H 132 PHE cc_start: 0.7454 (m-80) cc_final: 0.7030 (m-80) REVERT: I 57 ASN cc_start: 0.4692 (p0) cc_final: 0.4097 (p0) REVERT: I 86 MET cc_start: 0.3887 (mpp) cc_final: 0.3287 (mtm) REVERT: J 117 MET cc_start: 0.6685 (tpt) cc_final: 0.6390 (tpt) REVERT: K 44 TYR cc_start: 0.8907 (t80) cc_final: 0.8122 (t80) REVERT: K 75 TYR cc_start: 0.9234 (m-80) cc_final: 0.8865 (m-10) REVERT: K 84 ILE cc_start: 0.9522 (pt) cc_final: 0.9245 (mp) REVERT: K 89 PHE cc_start: 0.9607 (t80) cc_final: 0.9177 (t80) REVERT: K 91 GLU cc_start: 0.9291 (tt0) cc_final: 0.9086 (pt0) REVERT: K 108 MET cc_start: 0.9482 (mtt) cc_final: 0.8689 (mpp) REVERT: K 109 LEU cc_start: 0.9453 (mt) cc_final: 0.9209 (mt) REVERT: L 22 ILE cc_start: 0.9188 (pt) cc_final: 0.8546 (mt) REVERT: L 37 ASP cc_start: 0.8738 (t0) cc_final: 0.8395 (t0) REVERT: L 40 LYS cc_start: 0.8807 (ttmt) cc_final: 0.8473 (ttmt) REVERT: L 44 LYS cc_start: 0.8893 (mmtm) cc_final: 0.8585 (mmmt) REVERT: L 45 GLU cc_start: 0.8695 (pp20) cc_final: 0.8470 (pp20) REVERT: L 67 LYS cc_start: 0.9398 (tptp) cc_final: 0.9080 (ttmm) REVERT: L 106 GLU cc_start: 0.9076 (mt-10) cc_final: 0.8505 (pp20) REVERT: M 23 ILE cc_start: 0.9185 (pt) cc_final: 0.8531 (mt) REVERT: N 2 LEU cc_start: 0.8819 (mp) cc_final: 0.8216 (mp) REVERT: N 68 PHE cc_start: 0.6737 (t80) cc_final: 0.6018 (t80) REVERT: N 75 GLU cc_start: 0.8911 (pp20) cc_final: 0.8578 (pp20) REVERT: N 82 MET cc_start: 0.7740 (tpp) cc_final: 0.7010 (mmm) REVERT: N 88 ASN cc_start: 0.8082 (m-40) cc_final: 0.7218 (t0) REVERT: N 95 LEU cc_start: 0.9550 (mt) cc_final: 0.9326 (mm) REVERT: N 96 ILE cc_start: 0.9376 (mm) cc_final: 0.8928 (mm) REVERT: N 97 GLN cc_start: 0.8656 (mp10) cc_final: 0.8206 (mt0) REVERT: N 103 TYR cc_start: 0.7605 (m-10) cc_final: 0.7304 (m-10) REVERT: O 23 ASN cc_start: 0.9312 (m-40) cc_final: 0.8990 (m-40) REVERT: O 27 SER cc_start: 0.9470 (m) cc_final: 0.9199 (p) REVERT: O 44 LEU cc_start: 0.9591 (mt) cc_final: 0.9257 (mt) REVERT: O 72 ASP cc_start: 0.7499 (t0) cc_final: 0.6136 (t70) REVERT: O 74 GLU cc_start: 0.9418 (tm-30) cc_final: 0.9204 (tm-30) REVERT: O 75 ILE cc_start: 0.9419 (mm) cc_final: 0.8514 (mm) REVERT: O 106 ASP cc_start: 0.8880 (p0) cc_final: 0.8572 (p0) REVERT: O 115 LEU cc_start: 0.8788 (mm) cc_final: 0.8314 (tp) REVERT: Q 13 MET cc_start: 0.8172 (tmm) cc_final: 0.7945 (tmm) REVERT: Q 24 ASP cc_start: 0.8841 (m-30) cc_final: 0.8489 (m-30) REVERT: Q 25 THR cc_start: 0.9307 (m) cc_final: 0.8946 (p) REVERT: Q 52 ASN cc_start: 0.8584 (m-40) cc_final: 0.8279 (m-40) REVERT: Q 56 HIS cc_start: 0.9336 (m-70) cc_final: 0.8621 (m-70) REVERT: R 24 TYR cc_start: 0.8828 (m-80) cc_final: 0.7503 (m-80) REVERT: R 95 LEU cc_start: 0.9494 (mm) cc_final: 0.9272 (mm) REVERT: R 106 PHE cc_start: 0.9505 (t80) cc_final: 0.9001 (t80) REVERT: S 10 LYS cc_start: 0.8833 (mtmm) cc_final: 0.8079 (mmtt) REVERT: S 43 ASN cc_start: 0.9555 (p0) cc_final: 0.9129 (p0) REVERT: S 46 GLU cc_start: 0.9023 (tm-30) cc_final: 0.8538 (tm-30) REVERT: S 73 LYS cc_start: 0.8628 (mmpt) cc_final: 0.8292 (mmpt) REVERT: S 82 HIS cc_start: 0.8537 (t-90) cc_final: 0.8088 (t-90) REVERT: S 83 TYR cc_start: 0.8781 (t80) cc_final: 0.8315 (t80) REVERT: S 86 GLN cc_start: 0.9181 (pt0) cc_final: 0.8308 (pp30) REVERT: T 78 GLU cc_start: 0.9068 (pt0) cc_final: 0.8482 (pm20) REVERT: U 52 GLU cc_start: 0.9025 (mt-10) cc_final: 0.8567 (tm-30) REVERT: U 69 ARG cc_start: 0.8533 (mtm-85) cc_final: 0.8000 (ptp-170) REVERT: U 87 LEU cc_start: 0.9351 (mp) cc_final: 0.8869 (tp) REVERT: U 92 ASN cc_start: 0.7903 (p0) cc_final: 0.7408 (p0) REVERT: V 7 ARG cc_start: 0.8229 (ttp-110) cc_final: 0.7686 (ttp-110) REVERT: V 8 ASP cc_start: 0.9157 (m-30) cc_final: 0.8630 (t0) REVERT: V 39 ILE cc_start: 0.9596 (mm) cc_final: 0.9351 (mm) REVERT: W 41 GLU cc_start: 0.9408 (mt-10) cc_final: 0.8836 (mp0) REVERT: W 57 TYR cc_start: 0.8461 (m-80) cc_final: 0.7523 (m-80) REVERT: W 59 GLU cc_start: 0.8457 (tp30) cc_final: 0.7568 (tp30) REVERT: W 69 GLU cc_start: 0.8358 (tm-30) cc_final: 0.8096 (tm-30) REVERT: X 25 ARG cc_start: 0.9341 (mmt-90) cc_final: 0.9008 (mmm-85) REVERT: Y 6 GLN cc_start: 0.8704 (tt0) cc_final: 0.8489 (tt0) REVERT: Y 23 ASN cc_start: 0.9193 (m110) cc_final: 0.8045 (p0) REVERT: Y 45 ARG cc_start: 0.8788 (mtt-85) cc_final: 0.8388 (mtt-85) REVERT: Y 46 PHE cc_start: 0.8625 (m-10) cc_final: 0.8416 (m-80) REVERT: Y 60 ASP cc_start: 0.9142 (m-30) cc_final: 0.8937 (m-30) REVERT: Y 62 LYS cc_start: 0.9500 (tptp) cc_final: 0.9234 (tptt) REVERT: Y 70 GLU cc_start: 0.7992 (tm-30) cc_final: 0.7699 (tm-30) REVERT: Z 20 ASN cc_start: 0.9040 (m110) cc_final: 0.8789 (m110) REVERT: Z 24 GLU cc_start: 0.8963 (pp20) cc_final: 0.8745 (pp20) REVERT: Z 30 MET cc_start: 0.8605 (mmm) cc_final: 0.8145 (mmm) REVERT: Z 49 ASP cc_start: 0.9328 (m-30) cc_final: 0.8779 (t0) REVERT: a 54 MET cc_start: 0.9018 (ppp) cc_final: 0.8470 (tmm) REVERT: c 11 LEU cc_start: 0.8750 (mm) cc_final: 0.8488 (mm) REVERT: c 33 LYS cc_start: 0.8874 (mmtm) cc_final: 0.8488 (mmtm) REVERT: c 35 GLU cc_start: 0.9044 (tt0) cc_final: 0.8367 (mm-30) REVERT: d 13 ASN cc_start: 0.8911 (m-40) cc_final: 0.8701 (t0) REVERT: d 22 MET cc_start: 0.9329 (tpp) cc_final: 0.8968 (tpp) REVERT: d 26 ASN cc_start: 0.9160 (m-40) cc_final: 0.8714 (m110) REVERT: e 54 ASP cc_start: 0.8630 (p0) cc_final: 0.8348 (t0) REVERT: f 1 MET cc_start: 0.8526 (ptm) cc_final: 0.7753 (ptm) REVERT: f 34 LYS cc_start: 0.8685 (ttmt) cc_final: 0.8483 (ttmm) REVERT: f 35 GLN cc_start: 0.9068 (mt0) cc_final: 0.8751 (tp-100) REVERT: f 36 ARG cc_start: 0.8513 (tmm-80) cc_final: 0.8051 (tmm-80) REVERT: i 95 LEU cc_start: 0.7045 (mt) cc_final: 0.6608 (tp) REVERT: i 149 GLU cc_start: 0.8342 (tp30) cc_final: 0.7932 (mt-10) REVERT: i 341 MET cc_start: 0.6056 (mtt) cc_final: 0.5765 (mtp) REVERT: i 344 MET cc_start: 0.6263 (ppp) cc_final: 0.5499 (tpt) REVERT: i 375 ARG cc_start: 0.9163 (mtt180) cc_final: 0.8535 (mmp-170) outliers start: 2 outliers final: 0 residues processed: 725 average time/residue: 1.0219 time to fit residues: 1265.5855 Evaluate side-chains 572 residues out of total 3823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 572 time to evaluate : 4.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 772 random chunks: chunk 676 optimal weight: 6.9990 chunk 712 optimal weight: 6.9990 chunk 650 optimal weight: 3.9990 chunk 693 optimal weight: 10.0000 chunk 417 optimal weight: 8.9990 chunk 302 optimal weight: 40.0000 chunk 544 optimal weight: 4.9990 chunk 212 optimal weight: 20.0000 chunk 626 optimal weight: 0.4980 chunk 655 optimal weight: 50.0000 chunk 690 optimal weight: 7.9990 overall best weight: 4.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 164 GLN ** E 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 104 GLN ** N 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 20 HIS ** Z 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 13 ASN ** i 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 128 HIS i 343 ASN ** i 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.9283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 110109 Z= 0.182 Angle : 0.613 29.736 163852 Z= 0.301 Chirality : 0.033 0.289 20612 Planarity : 0.004 0.060 9393 Dihedral : 23.585 176.659 53755 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 21.70 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.03 % Favored : 95.90 % Rotamer: Outliers : 0.03 % Allowed : 1.09 % Favored : 98.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.95 % Cis-general : 0.11 % 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: 0.15 (0.12), residues: 4664 helix: 1.38 (0.12), residues: 1798 sheet: -0.46 (0.17), residues: 844 loop : -0.76 (0.14), residues: 2022 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 60 HIS 0.007 0.001 HIS Y 20 PHE 0.033 0.002 PHE Z 26 TYR 0.029 0.002 TYR c 49 ARG 0.009 0.001 ARG L 108 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9328 Ramachandran restraints generated. 4664 Oldfield, 0 Emsley, 4664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9328 Ramachandran restraints generated. 4664 Oldfield, 0 Emsley, 4664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 712 residues out of total 3823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 711 time to evaluate : 4.876 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: C 6 CYS cc_start: 0.9306 (t) cc_final: 0.9036 (t) REVERT: C 91 ILE cc_start: 0.9578 (mm) cc_final: 0.9049 (tp) REVERT: C 200 HIS cc_start: 0.8915 (t-90) cc_final: 0.8597 (t70) REVERT: D 32 ASN cc_start: 0.8264 (t0) cc_final: 0.7989 (t0) REVERT: D 35 THR cc_start: 0.9404 (p) cc_final: 0.8641 (p) REVERT: D 39 ASP cc_start: 0.8868 (p0) cc_final: 0.8353 (p0) REVERT: D 49 GLN cc_start: 0.9219 (tt0) cc_final: 0.8912 (tt0) REVERT: D 103 ASP cc_start: 0.9355 (m-30) cc_final: 0.8652 (p0) REVERT: D 174 SER cc_start: 0.9063 (m) cc_final: 0.8775 (t) REVERT: E 88 ARG cc_start: 0.8932 (tmm-80) cc_final: 0.8404 (tmm-80) REVERT: E 157 LEU cc_start: 0.9553 (tp) cc_final: 0.9300 (mt) REVERT: E 188 MET cc_start: 0.8228 (mmp) cc_final: 0.8005 (mmp) REVERT: E 195 GLN cc_start: 0.9221 (tp-100) cc_final: 0.8626 (tp-100) REVERT: F 11 GLU cc_start: 0.9132 (mp0) cc_final: 0.8913 (mp0) REVERT: F 22 TYR cc_start: 0.7679 (m-10) cc_final: 0.7349 (m-10) REVERT: F 26 MET cc_start: 0.7258 (mmp) cc_final: 0.6642 (mtp) REVERT: F 35 THR cc_start: 0.7482 (m) cc_final: 0.7139 (t) REVERT: F 175 PHE cc_start: 0.9224 (m-80) cc_final: 0.8784 (m-80) REVERT: G 27 LYS cc_start: 0.8990 (mmpt) cc_final: 0.8598 (tmtt) REVERT: G 37 LEU cc_start: 0.7692 (tp) cc_final: 0.7377 (tp) REVERT: G 101 ASN cc_start: 0.9305 (p0) cc_final: 0.8709 (t0) REVERT: G 153 ARG cc_start: 0.8477 (ttm170) cc_final: 0.8185 (ttm-80) REVERT: G 164 TYR cc_start: 0.8222 (m-10) cc_final: 0.7999 (m-80) REVERT: H 11 ASN cc_start: 0.8622 (t0) cc_final: 0.8365 (t0) REVERT: H 12 LEU cc_start: 0.9064 (mt) cc_final: 0.8852 (tp) REVERT: H 41 LYS cc_start: 0.8777 (mttt) cc_final: 0.8426 (tmtt) REVERT: H 101 ASP cc_start: 0.8884 (m-30) cc_final: 0.8343 (p0) REVERT: H 116 ARG cc_start: 0.8187 (mmt-90) cc_final: 0.7967 (mmt180) REVERT: H 132 PHE cc_start: 0.7466 (m-80) cc_final: 0.6993 (m-80) REVERT: I 57 ASN cc_start: 0.5034 (p0) cc_final: 0.4472 (p0) REVERT: I 86 MET cc_start: 0.3934 (mpp) cc_final: 0.3350 (mtm) REVERT: K 44 TYR cc_start: 0.8908 (t80) cc_final: 0.8056 (t80) REVERT: K 84 ILE cc_start: 0.9508 (pt) cc_final: 0.9231 (mp) REVERT: K 89 PHE cc_start: 0.9529 (t80) cc_final: 0.9173 (t80) REVERT: K 91 GLU cc_start: 0.9308 (tt0) cc_final: 0.9043 (pt0) REVERT: K 108 MET cc_start: 0.9473 (mtt) cc_final: 0.8769 (mpp) REVERT: K 109 LEU cc_start: 0.9494 (mt) cc_final: 0.9222 (mt) REVERT: K 129 GLU cc_start: 0.9031 (mp0) cc_final: 0.8815 (mp0) REVERT: L 37 ASP cc_start: 0.8755 (t0) cc_final: 0.8420 (t0) REVERT: L 40 LYS cc_start: 0.8900 (ttmt) cc_final: 0.8688 (ttmt) REVERT: L 44 LYS cc_start: 0.8841 (mmtm) cc_final: 0.8550 (mmmt) REVERT: L 106 GLU cc_start: 0.9021 (mt-10) cc_final: 0.8498 (pp20) REVERT: M 23 ILE cc_start: 0.9204 (pt) cc_final: 0.8507 (mt) REVERT: N 2 LEU cc_start: 0.8825 (mp) cc_final: 0.8228 (mp) REVERT: N 68 PHE cc_start: 0.6723 (t80) cc_final: 0.5987 (t80) REVERT: N 75 GLU cc_start: 0.8892 (pp20) cc_final: 0.8562 (pp20) REVERT: N 82 MET cc_start: 0.7720 (tpp) cc_final: 0.6976 (mmm) REVERT: N 88 ASN cc_start: 0.8094 (m-40) cc_final: 0.7310 (t0) REVERT: N 95 LEU cc_start: 0.9573 (mt) cc_final: 0.9333 (mm) REVERT: N 96 ILE cc_start: 0.9404 (mm) cc_final: 0.8951 (mm) REVERT: N 97 GLN cc_start: 0.8354 (mp10) cc_final: 0.7952 (mt0) REVERT: N 103 TYR cc_start: 0.7458 (m-10) cc_final: 0.7122 (m-10) REVERT: O 23 ASN cc_start: 0.9259 (m-40) cc_final: 0.8843 (m-40) REVERT: O 24 MET cc_start: 0.8806 (mmm) cc_final: 0.8192 (mmt) REVERT: O 27 SER cc_start: 0.9495 (m) cc_final: 0.9121 (p) REVERT: O 36 THR cc_start: 0.7995 (t) cc_final: 0.7530 (t) REVERT: O 44 LEU cc_start: 0.9495 (mt) cc_final: 0.9089 (mt) REVERT: O 72 ASP cc_start: 0.7543 (t0) cc_final: 0.6499 (t70) REVERT: O 106 ASP cc_start: 0.8840 (p0) cc_final: 0.8541 (p0) REVERT: O 110 MET cc_start: 0.8156 (mmp) cc_final: 0.7911 (mmm) REVERT: Q 25 THR cc_start: 0.9317 (m) cc_final: 0.8982 (p) REVERT: Q 56 HIS cc_start: 0.9223 (m-70) cc_final: 0.8564 (m-70) REVERT: R 24 TYR cc_start: 0.8764 (m-80) cc_final: 0.7317 (m-80) REVERT: R 95 LEU cc_start: 0.9552 (mm) cc_final: 0.9348 (mm) REVERT: S 10 LYS cc_start: 0.8623 (mtmm) cc_final: 0.7761 (mmtt) REVERT: S 43 ASN cc_start: 0.9473 (p0) cc_final: 0.9060 (p0) REVERT: S 46 GLU cc_start: 0.8921 (tm-30) cc_final: 0.8415 (tm-30) REVERT: S 73 LYS cc_start: 0.8613 (mmpt) cc_final: 0.8259 (mmpt) REVERT: S 82 HIS cc_start: 0.8463 (t-90) cc_final: 0.8217 (t-90) REVERT: S 83 TYR cc_start: 0.8599 (t80) cc_final: 0.8172 (t80) REVERT: S 86 GLN cc_start: 0.9025 (pt0) cc_final: 0.8567 (pm20) REVERT: T 19 LEU cc_start: 0.8913 (mm) cc_final: 0.8678 (mm) REVERT: T 68 ASP cc_start: 0.8786 (m-30) cc_final: 0.8566 (m-30) REVERT: T 78 GLU cc_start: 0.9017 (pt0) cc_final: 0.8438 (pm20) REVERT: U 52 GLU cc_start: 0.9025 (mt-10) cc_final: 0.8568 (tm-30) REVERT: U 69 ARG cc_start: 0.8528 (mtm-85) cc_final: 0.7961 (ptp-170) REVERT: U 84 TYR cc_start: 0.9409 (m-80) cc_final: 0.9198 (m-80) REVERT: U 87 LEU cc_start: 0.9335 (mp) cc_final: 0.8862 (tp) REVERT: U 92 ASN cc_start: 0.7906 (p0) cc_final: 0.7393 (p0) REVERT: V 8 ASP cc_start: 0.9122 (m-30) cc_final: 0.8608 (t0) REVERT: V 18 ASP cc_start: 0.8703 (m-30) cc_final: 0.8476 (m-30) REVERT: V 39 ILE cc_start: 0.9574 (mm) cc_final: 0.9284 (mm) REVERT: W 7 GLU cc_start: 0.8606 (pm20) cc_final: 0.8196 (pm20) REVERT: W 41 GLU cc_start: 0.9118 (mt-10) cc_final: 0.8845 (mp0) REVERT: W 57 TYR cc_start: 0.8503 (m-80) cc_final: 0.7646 (m-80) REVERT: W 59 GLU cc_start: 0.8555 (tp30) cc_final: 0.7787 (tp30) REVERT: W 69 GLU cc_start: 0.8368 (tm-30) cc_final: 0.8095 (tm-30) REVERT: Y 23 ASN cc_start: 0.9170 (m110) cc_final: 0.7863 (p0) REVERT: Y 45 ARG cc_start: 0.8849 (mtt-85) cc_final: 0.8399 (mtt-85) REVERT: Y 70 GLU cc_start: 0.8131 (tm-30) cc_final: 0.7827 (tm-30) REVERT: Z 20 ASN cc_start: 0.8990 (m110) cc_final: 0.8744 (m110) REVERT: Z 30 MET cc_start: 0.8669 (mmm) cc_final: 0.8204 (mmm) REVERT: a 5 ILE cc_start: 0.8199 (pt) cc_final: 0.7623 (mp) REVERT: a 54 MET cc_start: 0.8933 (ppp) cc_final: 0.8320 (tmm) REVERT: b 37 LYS cc_start: 0.9445 (pttm) cc_final: 0.9071 (ptmm) REVERT: d 22 MET cc_start: 0.9327 (tpp) cc_final: 0.8982 (tpp) REVERT: d 26 ASN cc_start: 0.9165 (m-40) cc_final: 0.8781 (m110) REVERT: e 4 ILE cc_start: 0.9699 (pt) cc_final: 0.9348 (pt) REVERT: e 33 LEU cc_start: 0.8726 (mt) cc_final: 0.8482 (mt) REVERT: f 1 MET cc_start: 0.8448 (ptm) cc_final: 0.7696 (ptm) REVERT: i 95 LEU cc_start: 0.6922 (mt) cc_final: 0.6586 (tt) REVERT: i 341 MET cc_start: 0.6281 (mtt) cc_final: 0.6028 (mtp) REVERT: i 344 MET cc_start: 0.6234 (ppp) cc_final: 0.5535 (tpt) REVERT: i 375 ARG cc_start: 0.9111 (mtt180) cc_final: 0.8501 (mmp-170) REVERT: i 423 MET cc_start: 0.7840 (tpt) cc_final: 0.7508 (tpp) outliers start: 1 outliers final: 0 residues processed: 711 average time/residue: 0.9554 time to fit residues: 1167.5942 Evaluate side-chains 567 residues out of total 3823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 567 time to evaluate : 4.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 772 random chunks: chunk 455 optimal weight: 20.0000 chunk 733 optimal weight: 20.0000 chunk 447 optimal weight: 6.9990 chunk 347 optimal weight: 6.9990 chunk 509 optimal weight: 5.9990 chunk 769 optimal weight: 10.0000 chunk 707 optimal weight: 10.0000 chunk 612 optimal weight: 7.9990 chunk 63 optimal weight: 20.0000 chunk 473 optimal weight: 3.9990 chunk 375 optimal weight: 5.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 115 GLN F 5 HIS ** K 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 104 GLN ** N 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 20 GLN S 18 GLN ** V 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 20 HIS ** Z 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 31 GLN ** Z 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 13 ASN ** i 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 128 HIS i 343 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.9582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 110109 Z= 0.211 Angle : 0.638 29.752 163852 Z= 0.315 Chirality : 0.034 0.282 20612 Planarity : 0.005 0.061 9393 Dihedral : 23.600 177.283 53755 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 24.13 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.35 % Favored : 95.56 % Rotamer: Outliers : 0.06 % Allowed : 0.44 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.95 % Cis-general : 0.11 % 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: 0.09 (0.12), residues: 4664 helix: 1.36 (0.12), residues: 1778 sheet: -0.54 (0.17), residues: 842 loop : -0.79 (0.14), residues: 2044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP Q 31 HIS 0.009 0.001 HIS O 16 PHE 0.039 0.002 PHE Q 43 TYR 0.020 0.002 TYR c 49 ARG 0.017 0.001 ARG Z 23 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9328 Ramachandran restraints generated. 4664 Oldfield, 0 Emsley, 4664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9328 Ramachandran restraints generated. 4664 Oldfield, 0 Emsley, 4664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 703 residues out of total 3823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 701 time to evaluate : 4.864 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: C 6 CYS cc_start: 0.9340 (t) cc_final: 0.9061 (t) REVERT: C 25 HIS cc_start: 0.9110 (t70) cc_final: 0.8889 (t-170) REVERT: C 91 ILE cc_start: 0.9593 (mm) cc_final: 0.9056 (tp) REVERT: C 132 MET cc_start: 0.9401 (mtt) cc_final: 0.9182 (tmm) REVERT: C 181 MET cc_start: 0.8450 (mmt) cc_final: 0.7616 (mmm) REVERT: C 200 HIS cc_start: 0.8929 (t-90) cc_final: 0.8589 (t70) REVERT: C 257 THR cc_start: 0.8808 (p) cc_final: 0.8522 (p) REVERT: D 32 ASN cc_start: 0.8242 (t0) cc_final: 0.8017 (t0) REVERT: D 35 THR cc_start: 0.9395 (p) cc_final: 0.8731 (p) REVERT: D 39 ASP cc_start: 0.8921 (p0) cc_final: 0.8375 (p0) REVERT: D 49 GLN cc_start: 0.9262 (tt0) cc_final: 0.8940 (tt0) REVERT: D 89 GLU cc_start: 0.8933 (tm-30) cc_final: 0.8401 (mp0) REVERT: D 103 ASP cc_start: 0.9260 (m-30) cc_final: 0.8584 (p0) REVERT: D 174 SER cc_start: 0.9108 (m) cc_final: 0.8809 (t) REVERT: D 201 LEU cc_start: 0.8740 (mt) cc_final: 0.8423 (mt) REVERT: E 88 ARG cc_start: 0.8925 (tmm-80) cc_final: 0.8434 (tmm-80) REVERT: E 149 ILE cc_start: 0.8865 (mm) cc_final: 0.8511 (mm) REVERT: E 157 LEU cc_start: 0.9557 (tp) cc_final: 0.9294 (mt) REVERT: E 188 MET cc_start: 0.8216 (mmp) cc_final: 0.7613 (tpp) REVERT: F 11 GLU cc_start: 0.9106 (mp0) cc_final: 0.8878 (mp0) REVERT: F 22 TYR cc_start: 0.7541 (m-10) cc_final: 0.7232 (m-10) REVERT: F 26 MET cc_start: 0.7267 (mmp) cc_final: 0.6618 (mtp) REVERT: F 35 THR cc_start: 0.7633 (m) cc_final: 0.7355 (t) REVERT: F 175 PHE cc_start: 0.9153 (m-80) cc_final: 0.8718 (m-80) REVERT: G 27 LYS cc_start: 0.8770 (mmpt) cc_final: 0.8501 (tmtt) REVERT: G 37 LEU cc_start: 0.7833 (tp) cc_final: 0.7499 (tp) REVERT: G 101 ASN cc_start: 0.9310 (p0) cc_final: 0.8703 (t0) REVERT: G 153 ARG cc_start: 0.8460 (ttm170) cc_final: 0.8194 (ttm-80) REVERT: H 11 ASN cc_start: 0.8717 (t0) cc_final: 0.8393 (t0) REVERT: H 41 LYS cc_start: 0.8784 (mttt) cc_final: 0.8413 (tmtt) REVERT: H 101 ASP cc_start: 0.8819 (m-30) cc_final: 0.8258 (p0) REVERT: H 116 ARG cc_start: 0.8171 (mmt-90) cc_final: 0.7959 (mmt180) REVERT: H 132 PHE cc_start: 0.7459 (m-80) cc_final: 0.6992 (m-80) REVERT: I 57 ASN cc_start: 0.5007 (p0) cc_final: 0.4471 (p0) REVERT: I 86 MET cc_start: 0.4090 (mpp) cc_final: 0.3413 (mtm) REVERT: I 116 GLU cc_start: 0.5601 (tp30) cc_final: 0.5394 (tp30) REVERT: K 14 ASP cc_start: 0.9215 (t0) cc_final: 0.8935 (m-30) REVERT: K 36 LEU cc_start: 0.9662 (pp) cc_final: 0.9461 (pp) REVERT: K 44 TYR cc_start: 0.8873 (t80) cc_final: 0.8078 (t80) REVERT: K 84 ILE cc_start: 0.9526 (pt) cc_final: 0.9241 (mp) REVERT: K 89 PHE cc_start: 0.9511 (t80) cc_final: 0.9162 (t80) REVERT: K 91 GLU cc_start: 0.9353 (tt0) cc_final: 0.8990 (pt0) REVERT: K 108 MET cc_start: 0.9452 (mtt) cc_final: 0.8775 (mpp) REVERT: K 109 LEU cc_start: 0.9527 (mt) cc_final: 0.9248 (mt) REVERT: L 37 ASP cc_start: 0.8873 (t0) cc_final: 0.8551 (t0) REVERT: L 44 LYS cc_start: 0.8770 (mmtm) cc_final: 0.8450 (mmmt) REVERT: L 67 LYS cc_start: 0.9367 (tptp) cc_final: 0.9143 (ttmm) REVERT: L 106 GLU cc_start: 0.9035 (mt-10) cc_final: 0.8472 (pp20) REVERT: M 23 ILE cc_start: 0.9048 (pt) cc_final: 0.8363 (mt) REVERT: M 105 ILE cc_start: 0.8711 (mp) cc_final: 0.8402 (mm) REVERT: N 75 GLU cc_start: 0.8891 (pp20) cc_final: 0.8561 (pp20) REVERT: N 82 MET cc_start: 0.7742 (tpp) cc_final: 0.7016 (mmm) REVERT: N 88 ASN cc_start: 0.8159 (m-40) cc_final: 0.7398 (t0) REVERT: N 95 LEU cc_start: 0.9578 (mt) cc_final: 0.9236 (mm) REVERT: N 96 ILE cc_start: 0.9452 (mm) cc_final: 0.9212 (tp) REVERT: N 103 TYR cc_start: 0.7644 (m-10) cc_final: 0.7174 (m-10) REVERT: O 23 ASN cc_start: 0.9255 (m-40) cc_final: 0.8798 (m-40) REVERT: O 27 SER cc_start: 0.9494 (m) cc_final: 0.9206 (p) REVERT: O 44 LEU cc_start: 0.9561 (mt) cc_final: 0.9306 (mt) REVERT: O 72 ASP cc_start: 0.7589 (t0) cc_final: 0.6524 (t70) REVERT: O 106 ASP cc_start: 0.8859 (p0) cc_final: 0.8568 (p0) REVERT: Q 13 MET cc_start: 0.8236 (tmm) cc_final: 0.8012 (tmm) REVERT: Q 24 ASP cc_start: 0.8797 (m-30) cc_final: 0.8562 (m-30) REVERT: Q 25 THR cc_start: 0.9304 (m) cc_final: 0.8974 (p) REVERT: R 24 TYR cc_start: 0.8773 (m-80) cc_final: 0.7344 (m-80) REVERT: R 91 ASP cc_start: 0.8061 (p0) cc_final: 0.7801 (p0) REVERT: R 106 PHE cc_start: 0.9522 (t80) cc_final: 0.9159 (t80) REVERT: S 10 LYS cc_start: 0.8697 (mtmm) cc_final: 0.7842 (mmtp) REVERT: S 43 ASN cc_start: 0.9468 (p0) cc_final: 0.9068 (p0) REVERT: S 46 GLU cc_start: 0.8846 (tm-30) cc_final: 0.8326 (tm-30) REVERT: S 82 HIS cc_start: 0.8489 (t-90) cc_final: 0.8121 (t-90) REVERT: S 83 TYR cc_start: 0.8590 (t80) cc_final: 0.8303 (t80) REVERT: S 86 GLN cc_start: 0.9074 (pt0) cc_final: 0.8551 (pm20) REVERT: T 1 MET cc_start: 0.5910 (tmm) cc_final: 0.5609 (tmm) REVERT: T 23 LEU cc_start: 0.9299 (mt) cc_final: 0.9020 (mt) REVERT: T 68 ASP cc_start: 0.8822 (m-30) cc_final: 0.8611 (m-30) REVERT: T 78 GLU cc_start: 0.9060 (pt0) cc_final: 0.8445 (pm20) REVERT: U 12 ARG cc_start: 0.8212 (mmp80) cc_final: 0.7981 (mmp-170) REVERT: U 52 GLU cc_start: 0.9056 (mt-10) cc_final: 0.8594 (tm-30) REVERT: U 69 ARG cc_start: 0.8527 (mtm-85) cc_final: 0.7955 (ptp-170) REVERT: U 87 LEU cc_start: 0.9347 (mp) cc_final: 0.8896 (tp) REVERT: U 92 ASN cc_start: 0.7454 (p0) cc_final: 0.6890 (p0) REVERT: U 95 PHE cc_start: 0.7454 (t80) cc_final: 0.7203 (t80) REVERT: V 8 ASP cc_start: 0.9152 (m-30) cc_final: 0.8613 (t0) REVERT: W 45 ASP cc_start: 0.9261 (t70) cc_final: 0.9056 (t70) REVERT: W 57 TYR cc_start: 0.8515 (m-80) cc_final: 0.7748 (m-80) REVERT: W 69 GLU cc_start: 0.8389 (tm-30) cc_final: 0.8140 (tm-30) REVERT: X 69 PHE cc_start: 0.7920 (m-10) cc_final: 0.7698 (m-10) REVERT: Y 23 ASN cc_start: 0.9225 (m110) cc_final: 0.7978 (p0) REVERT: Y 70 GLU cc_start: 0.8126 (tm-30) cc_final: 0.7794 (tm-30) REVERT: Z 30 MET cc_start: 0.8697 (mmm) cc_final: 0.8270 (mmm) REVERT: a 11 ARG cc_start: 0.9081 (mtt90) cc_final: 0.8789 (mtt-85) REVERT: a 47 MET cc_start: 0.8935 (ttt) cc_final: 0.8248 (ttt) REVERT: b 32 LYS cc_start: 0.9022 (pttt) cc_final: 0.8451 (ptpp) REVERT: d 22 MET cc_start: 0.9398 (tpp) cc_final: 0.9053 (tpp) REVERT: d 26 ASN cc_start: 0.9197 (m-40) cc_final: 0.8798 (m110) REVERT: e 4 ILE cc_start: 0.9651 (pt) cc_final: 0.9274 (mp) REVERT: e 33 LEU cc_start: 0.8774 (mt) cc_final: 0.8519 (mt) REVERT: e 45 ARG cc_start: 0.8889 (mtm180) cc_final: 0.8668 (ptp-170) REVERT: f 1 MET cc_start: 0.8462 (ptm) cc_final: 0.7801 (ptm) REVERT: f 8 LYS cc_start: 0.8250 (tppt) cc_final: 0.8029 (mmtt) REVERT: f 34 LYS cc_start: 0.8733 (ttmt) cc_final: 0.8529 (ttmm) REVERT: f 35 GLN cc_start: 0.9056 (mt0) cc_final: 0.8816 (tp40) REVERT: f 36 ARG cc_start: 0.8686 (tmm-80) cc_final: 0.6961 (tmm-80) REVERT: i 95 LEU cc_start: 0.6937 (mt) cc_final: 0.6647 (tt) REVERT: i 341 MET cc_start: 0.6294 (mtt) cc_final: 0.6052 (mtp) REVERT: i 344 MET cc_start: 0.6462 (ppp) cc_final: 0.5953 (tpt) REVERT: i 375 ARG cc_start: 0.9115 (mtt180) cc_final: 0.8477 (mmp-170) REVERT: i 383 MET cc_start: 0.8629 (mmp) cc_final: 0.8414 (mmp) REVERT: i 423 MET cc_start: 0.7954 (tpt) cc_final: 0.7582 (tpp) outliers start: 2 outliers final: 0 residues processed: 702 average time/residue: 1.0242 time to fit residues: 1239.6061 Evaluate side-chains 558 residues out of total 3823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 558 time to evaluate : 4.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 772 random chunks: chunk 486 optimal weight: 8.9990 chunk 652 optimal weight: 9.9990 chunk 187 optimal weight: 20.0000 chunk 564 optimal weight: 0.9990 chunk 90 optimal weight: 20.0000 chunk 170 optimal weight: 20.0000 chunk 613 optimal weight: 5.9990 chunk 256 optimal weight: 20.0000 chunk 629 optimal weight: 20.0000 chunk 77 optimal weight: 10.0000 chunk 112 optimal weight: 30.0000 overall best weight: 7.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 104 GLN ** N 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 50 ASN Y 20 HIS ** Z 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 13 ASN i 128 HIS i 343 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.048966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.038840 restraints weight = 892121.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.040026 restraints weight = 357869.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.040715 restraints weight = 190867.303| |-----------------------------------------------------------------------------| r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.9971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 110109 Z= 0.237 Angle : 0.668 30.053 163852 Z= 0.330 Chirality : 0.035 0.277 20612 Planarity : 0.005 0.060 9393 Dihedral : 23.667 178.415 53755 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 26.45 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.19 % Favored : 94.73 % Rotamer: Outliers : 0.03 % Allowed : 0.38 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.95 % Cis-general : 0.11 % 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: -0.07 (0.12), residues: 4664 helix: 1.23 (0.12), residues: 1785 sheet: -0.62 (0.17), residues: 837 loop : -0.89 (0.14), residues: 2042 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP E 78 HIS 0.012 0.002 HIS O 16 PHE 0.032 0.002 PHE Z 26 TYR 0.021 0.002 TYR c 49 ARG 0.030 0.001 ARG C 269 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 21427.08 seconds wall clock time: 381 minutes 28.75 seconds (22888.75 seconds total)